From 7fc7b536e1fe7f219b984723fd020744d884bd54 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Mon, 24 Mar 2025 12:28:18 -0700 Subject: [PATCH 01/32] Upgrade launcher script to the latest launcher version --- clabe_default.yml | 2 + .../launcher.py | 69 +-- uv.lock | 396 +++++------------- 3 files changed, 130 insertions(+), 337 deletions(-) create mode 100644 clabe_default.yml diff --git a/clabe_default.yml b/clabe_default.yml new file mode 100644 index 0000000..c04e48d --- /dev/null +++ b/clabe_default.yml @@ -0,0 +1,2 @@ +data_dir: C:/Data +subject: "123456" \ No newline at end of file diff --git a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/launcher.py b/src/DataSchemas/aind_behavior_video_encoding_benchmarks/launcher.py index 6dcebda..ab1bcbc 100644 --- a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/launcher.py +++ b/src/DataSchemas/aind_behavior_video_encoding_benchmarks/launcher.py @@ -1,16 +1,19 @@ +import logging from pathlib import Path -from typing import Optional +from typing import final import aind_behavior_experiment_launcher.launcher.behavior_launcher as behavior_launcher -from aind_behavior_experiment_launcher.apps import BonsaiApp +from aind_behavior_experiment_launcher.apps import AindBehaviorServicesBonsaiApp +from aind_behavior_experiment_launcher.launcher.behavior_launcher import DefaultBehaviorPicker from aind_behavior_experiment_launcher.resource_monitor import ( ResourceMonitor, available_storage_constraint_factory, remote_dir_exists_constraint_factory, ) -from aind_behavior_experiment_launcher.ui_helper import prompt_field_from_input +from aind_behavior_experiment_launcher.ui import prompt_field_from_input from aind_behavior_services.session import AindBehaviorSessionModel from pydantic import ValidationError +from pydantic_settings import CliApp from typing_extensions import override from aind_behavior_video_encoding_benchmarks.rig import AindVideoEncodingBenchmarksRig @@ -19,36 +22,13 @@ AindVideoEncodingBenchmarksTaskParameters, ) +logger = logging.getLogger(__name__) -class AindVideoEncodingBenchmarksLauncher( - behavior_launcher.BehaviorLauncher[ - AindVideoEncodingBenchmarksRig, AindBehaviorSessionModel, AindVideoEncodingBenchmarksTaskLogic - ] -): - @override - def _prompt_session_input(self, directory: Optional[str] = None) -> AindBehaviorSessionModel: - experimenter = self._ui_helper.prompt_experimenter(strict=True) - subject = input("Enter subject name: [defaults to 00000]") - if subject == "": - subject = "00000" - notes = self._ui_helper.prompt_get_notes() - - return self.session_schema_model( - experiment="", # Will be set later - root_path=str(self.data_dir.resolve()) - if not self.group_by_subject_log - else str(self.data_dir.resolve() / subject), - subject=subject, - notes=notes, - experimenter=experimenter if experimenter is not None else [], - commit_hash=self.repository.head.commit.hexsha, - allow_dirty_repo=self._debug_mode or self.allow_dirty, - skip_hardware_validation=self.skip_hardware_validation, - experiment_version="", # Will be set later - ) +@final +class _CustomPicker(DefaultBehaviorPicker): @override - def _prompt_task_logic_input(self, *args, **kwargs) -> AindVideoEncodingBenchmarksTaskLogic: + def pick_task_logic(self) -> AindVideoEncodingBenchmarksTaskLogic: save_raw = None while save_raw is None: try: @@ -56,47 +36,44 @@ def _prompt_task_logic_input(self, *args, **kwargs) -> AindVideoEncodingBenchmar AindVideoEncodingBenchmarksTaskParameters, "save_raw_video", default=False ) except ValidationError as e: - self._logger.error("Failed to parse input: %s", e) + self.launcher._logger.error("Failed to parse input: %s", e) else: - self._logger.info("save_raw_video set to: %s", save_raw) + self.launcher._logger.info("save_raw_video set to: %s", save_raw) return AindVideoEncodingBenchmarksTaskLogic( task_parameters=AindVideoEncodingBenchmarksTaskParameters(save_raw_video=save_raw) ) -def make_launcher() -> AindVideoEncodingBenchmarksLauncher: - data_dir = r"C:/Data" +def make_launcher(settings: behavior_launcher.BehaviorCliArgs) -> behavior_launcher.BehaviorLauncher: + data_dir = settings.data_dir remote_dir = Path(r"\\allen\aind\scratch\video-encoding-benchmarks\data") srv = behavior_launcher.BehaviorServicesFactoryManager() - srv.attach_bonsai_app(BonsaiApp(r"./src/main.bonsai")) + srv.attach_app(AindBehaviorServicesBonsaiApp(Path(r"./src/main.bonsai"))) srv.attach_data_transfer(behavior_launcher.robocopy_data_transfer_factory(Path(remote_dir))) srv.attach_resource_monitor( ResourceMonitor( constrains=[ - available_storage_constraint_factory(data_dir, 2e11), + available_storage_constraint_factory(Path(data_dir), 2e11), remote_dir_exists_constraint_factory(Path(remote_dir)), ] ) ) - return AindVideoEncodingBenchmarksLauncher( + return behavior_launcher.BehaviorLauncher( rig_schema_model=AindVideoEncodingBenchmarksRig, session_schema_model=AindBehaviorSessionModel, task_logic_schema_model=AindVideoEncodingBenchmarksTaskLogic, - data_dir=data_dir, - config_library_dir=r"\\allen\aind\scratch\AindBehavior.db\AindVideoEncodingBenchmarks", - temp_dir=r"./local/.temp", - allow_dirty=False, - skip_hardware_validation=False, - debug_mode=False, - group_by_subject_log=True, + picker=_CustomPicker( + config_library_dir=Path(r"\\allen\aind\scratch\AindBehavior.db\AindVideoEncodingBenchmarks") + ), + settings=settings, services=srv, - validate_init=True, ) def main(): - launcher = make_launcher() + args = CliApp().run(behavior_launcher.BehaviorCliArgs) + launcher = make_launcher(args) launcher.main() return None diff --git a/uv.lock b/uv.lock index 649f48b..2332c35 100644 --- a/uv.lock +++ b/uv.lock @@ -1,5 +1,4 @@ version = 1 -revision = 1 requires-python = ">=3.11" resolution-markers = [ "python_full_version >= '3.12'", @@ -22,19 +21,20 @@ wheels = [ [[package]] name = "aind-behavior-experiment-launcher" -version = "0.3.3" +version = "0.4.1" source = { 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examples/examples.py | 7 +- pyproject.toml | 43 +- ...ig.json => aind_behavior_just_frames.json} | 438 +++- .../aind_behavior_session_model.json | 110 - .../__init__.py | 1 - .../launcher.py | 82 - .../regenerate.py | 42 - .../task_logic.py | 25 - ..._video_encoding_benchmarks_task_logic.json | 79 - ...cs => AindBehaviorJustFrames.Generated.cs} | 1364 +++++++++--- src/Extensions/AindBehaviorSessionModel.cs | 379 ---- .../AindVideoEncodingBenchmarksTaskLogic.cs | 325 --- src/Extensions/TriggeredCamerasLogger.bonsai | 2 +- src/aind_behavior_just_frames/__init__.py | 30 + src/aind_behavior_just_frames/cli.py | 44 + src/aind_behavior_just_frames/launcher.py | 25 + src/aind_behavior_just_frames/regenerate.py | 34 + .../rig.py | 19 +- src/main.bonsai | 6 +- src/test_deserialization.bonsai | 6 +- tests/test_bonsai.py | 9 +- uv.lock | 1924 ++++++++++------- 25 files changed, 2734 insertions(+), 2273 deletions(-) delete mode 100644 clabe_default.yml rename src/DataSchemas/{aind_video_encoding_benchmarks_rig.json => aind_behavior_just_frames.json} (59%) delete mode 100644 src/DataSchemas/aind_behavior_session_model.json delete mode 100644 src/DataSchemas/aind_behavior_video_encoding_benchmarks/__init__.py delete mode 100644 src/DataSchemas/aind_behavior_video_encoding_benchmarks/launcher.py delete mode 100644 src/DataSchemas/aind_behavior_video_encoding_benchmarks/regenerate.py delete mode 100644 src/DataSchemas/aind_behavior_video_encoding_benchmarks/task_logic.py delete mode 100644 src/DataSchemas/aind_video_encoding_benchmarks_task_logic.json rename src/Extensions/{AindVideoEncodingBenchmarksRig.cs => AindBehaviorJustFrames.Generated.cs} (65%) delete mode 100644 src/Extensions/AindBehaviorSessionModel.cs delete mode 100644 src/Extensions/AindVideoEncodingBenchmarksTaskLogic.cs create mode 100644 src/aind_behavior_just_frames/__init__.py create mode 100644 src/aind_behavior_just_frames/cli.py create mode 100644 src/aind_behavior_just_frames/launcher.py create mode 100644 src/aind_behavior_just_frames/regenerate.py rename src/{DataSchemas/aind_behavior_video_encoding_benchmarks => aind_behavior_just_frames}/rig.py (50%) diff --git a/.config/dotnet-tools.json b/.config/dotnet-tools.json index d5d9d94..44b1c27 100644 --- a/.config/dotnet-tools.json +++ b/.config/dotnet-tools.json @@ -3,7 +3,7 @@ "isRoot": true, "tools": { "bonsai.sgen": { - "version": "0.3.0", + "version": "0.6.1", "commands": [ "bonsai.sgen" ] diff --git a/clabe_default.yml b/clabe_default.yml deleted file mode 100644 index c04e48d..0000000 --- a/clabe_default.yml +++ /dev/null @@ -1,2 +0,0 @@ -data_dir: C:/Data -subject: "123456" \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index d09e9a9..bfc27f7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -6,13 +6,14 @@ import os import sys -import aind_behavior_video_encoding_benchmarks.rig -import aind_behavior_video_encoding_benchmarks.task_logic +import aind_behavior_just_frames.task_logic import erdantic as erd from pydantic import BaseModel +import aind_behavior_just_frames.rig + sys.path.insert(0, os.path.abspath("../src/DataSchemas")) -import aind_behavior_video_encoding_benchmarks +import aind_behavior_just_frames SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Behavior.VideoEncodingBenchmarks/tree/main/src/DataSchemas/" @@ -22,7 +23,7 @@ project = "AIND Video Encoding Benchmarks project" copyright = "2024, Allen Institute for Neural Dynamics" author = "Bruno Cruz" -release = aind_behavior_video_encoding_benchmarks.__version__ +release = aind_behavior_just_frames.__semver__ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration diff --git a/examples/examples.py b/examples/examples.py index 1435a94..f083223 100644 --- a/examples/examples.py +++ b/examples/examples.py @@ -2,12 +2,13 @@ import os import aind_behavior_services.rig as rig -from aind_behavior_services.session import AindBehaviorSessionModel -from aind_behavior_video_encoding_benchmarks.rig import AindVideoEncodingBenchmarksRig -from aind_behavior_video_encoding_benchmarks.task_logic import ( +from aind_behavior_just_frames.task_logic import ( AindVideoEncodingBenchmarksTaskLogic, AindVideoEncodingBenchmarksTaskParameters, ) +from aind_behavior_services.session import AindBehaviorSessionModel + +from aind_behavior_just_frames.rig import AindVideoEncodingBenchmarksRig def main(path_seed: str = "./local/{schema}.json"): diff --git a/pyproject.toml b/pyproject.toml index 4d826e2..08a6eb9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,51 +1,48 @@ [build-system] -requires = ["setuptools", "setuptools-scm"] -build-backend = "setuptools.build_meta" +requires = ["uv_build>=0.8.22"] +build-backend = "uv_build" [project] -name = "aind-behavior-video-encoding-benchmarks" +name = "aind-behavior-just_frames" description = "A library for benchmarking online video acquisition/encoding pipelines" +authors = [ {name = "Bruno Cruz", email = "bruno.cruz@alleninstitute.org"}] license = {text = "MIT"} requires-python = ">=3.11" classifiers = [ - "Programming Language :: Python :: 3" + "Programming Language :: Python :: 3.11", + "Operating System :: Microsoft :: Windows", ] -readme = "README.md" -dynamic = ["version"] +version = "0.5.0rc0" +readme = {file = "README.md", content-type = "text/markdown"} dependencies = [ - "aind_behavior_services>=0.10, <0.11", + "aind_behavior_services>=0.12, <0.13", + "pydantic-settings" ] [project.optional-dependencies] -launcher = ["aind_behavior_experiment_launcher[aind-services]"] +launcher = ["aind-clabe[aind-services] >= 0.8.2 ,<0.9.0"] -dev = ["aind_behavior_video_encoding_benchmarks[launcher]", + +[dependency-groups] + +dev = ["aind_behavior_just_frames[launcher]", "ruff", "codespell" ] - docs = [ - 'Sphinx<7.3', + 'Sphinx', 'furo', 'sphinx-jinja', 'autodoc_pydantic[erdantic]', 'myst_parser', - 'sphinx-jsonschema' + 'sphinx-jsonschema', ] [project.scripts] -clabe = "aind_behavior_video_encoding_benchmarks.launcher:main" -regenerate = "aind_behavior_video_encoding_benchmarks.regenerate:main" - -[tool.setuptools.packages.find] -where = ["src/DataSchemas"] - -[tool.setuptools.dynamic] -version = {attr = "aind_behavior_video_encoding_benchmarks.__version__"} -readme = {file = ["README.md"]} +just-frames = "aind_behavior_just_frames.cli:main" [tool.ruff] line-length = 120 @@ -60,3 +57,7 @@ pydocstyle = { convention = 'google' } [tool.codespell] skip = '.git,*.pdf,*.svg' ignore-words-list = 'nd' + +[tool.uv] +default-groups = ['dev'] +required-version = '>=0.8.4' \ No newline at end of file diff --git a/src/DataSchemas/aind_video_encoding_benchmarks_rig.json b/src/DataSchemas/aind_behavior_just_frames.json similarity index 59% rename from src/DataSchemas/aind_video_encoding_benchmarks_rig.json rename to src/DataSchemas/aind_behavior_just_frames.json index 94df6d7..785f362 100644 --- a/src/DataSchemas/aind_video_encoding_benchmarks_rig.json +++ b/src/DataSchemas/aind_behavior_just_frames.json @@ -1,5 +1,195 @@ { - "definitions": { + "$defs": { + "AindBehaviorSessionModel": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.12.3", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.12.3", + "default": "0.12.3", + "title": "Version", + "type": "string" + }, + "experiment": { + "default": null, + "description": "Name of the experiment", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Experiment" + }, + "experimenter": { + "default": [], + "description": "Name of the experimenter", + "items": { + "type": "string" + }, + "title": "Experimenter", + "type": "array" + }, + "date": { + "description": "Date of the experiment", + "format": "date-time", + "title": "Date", + "type": "string" + }, + "root_path": { + "description": "Root path where data will be logged", + "title": "Root Path", + "type": "string" + }, + "session_name": { + "default": null, + "description": "Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date.", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Session Name" + }, + "subject": { + "description": "Name of the subject", + "title": "Subject", + "type": "string" + }, + "experiment_version": { + "default": "", + "deprecated": true, + "description": "Version of the experiment", + "title": "Experiment Version", + "type": "string" + }, + "notes": { + "default": null, + "description": "Notes about the experiment", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Notes" + }, + "commit_hash": { + "default": null, + "description": "Commit hash of the repository", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Commit Hash" + }, + "allow_dirty_repo": { + "default": false, + "description": "Allow running from a dirty repository", + "title": "Allow Dirty Repo", + "type": "boolean" + }, + "skip_hardware_validation": { + "default": false, + "description": "Skip hardware validation", + "title": "Skip Hardware Validation", + "type": "boolean" + } + }, + "required": [ + "root_path", + "subject" + ], + "title": "AindBehaviorSessionModel", + "type": "object" + }, + "AindJustFramesRig": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.12.3", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.5.0-rc0", + "default": "0.5.0-rc0", + "title": "Version", + "type": "string" + }, + "computer_name": { + "description": "Computer name", + "title": "Computer Name", + "type": "string" + }, + "rig_name": { + "description": "Rig name", + "title": "Rig Name", + "type": "string" + }, + "triggered_camera_controller_0": { + "default": null, + "description": "Camera controller to triggered cameras. Will use Camera0 register as a trigger.", + "oneOf": [ + { + "$ref": "#/$defs/CameraController_SpinnakerCamera_" + }, + { + "type": "null" + } + ] + }, + "triggered_camera_controller_1": { + "default": null, + "description": "Camera controller to triggered cameras. Will use Camera1 register as a trigger.", + "oneOf": [ + { + "$ref": "#/$defs/CameraController_SpinnakerCamera_" + }, + { + "type": "null" + } + ] + }, + "harp_behavior": { + "$ref": "#/$defs/HarpBehavior", + "description": "Harp behavior board. Will be the source of triggers for the two camera controllers." + }, + "harp_white_rabbit": { + "default": null, + "description": "Harp White Rabbit for time synchronization.", + "oneOf": [ + { + "$ref": "#/$defs/HarpWhiteRabbit" + }, + { + "type": "null" + } + ] + } + }, + "required": [ + "rig_name", + "harp_behavior" + ], + "title": "AindJustFramesRig", + "type": "object" + }, "BaseModel": { "properties": {}, "title": "BaseModel", @@ -13,12 +203,25 @@ "title": "Device Type", "type": "string" }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, "additional_settings": { "default": null, "description": "Additional settings", "oneOf": [ { - "$ref": "#/definitions/BaseModel" + "$ref": "#/$defs/BaseModel" }, { "type": "null" @@ -30,7 +233,7 @@ "description": "Calibration", "oneOf": [ { - "$ref": "#/definitions/BaseModel" + "$ref": "#/$defs/BaseModel" }, { "type": "null" @@ -39,7 +242,7 @@ }, "cameras": { "additionalProperties": { - "$ref": "#/definitions/SpinnakerCamera" + "$ref": "#/$defs/SpinnakerCamera" }, "description": "Cameras to be instantiated", "title": "Cameras", @@ -66,6 +269,34 @@ "title": "CameraController[SpinnakerCamera]", "type": "object" }, + "ConnectedClockOutput": { + "properties": { + "target_device": { + "default": null, + "description": "Optional device name to provide user additional information", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Target Device" + }, + "output_channel": { + "description": "Output channel", + "minimum": 0, + "title": "Output Channel", + "type": "integer" + } + }, + "required": [ + "output_channel" + ], + "title": "ConnectedClockOutput", + "type": "object" + }, "HarpBehavior": { "properties": { "device_type": { @@ -74,12 +305,25 @@ "title": "Device Type", "type": "string" }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, "additional_settings": { "default": null, "description": "Additional settings", "oneOf": [ { - "$ref": "#/definitions/BaseModel" + "$ref": "#/$defs/BaseModel" }, { "type": "null" @@ -91,7 +335,7 @@ "description": "Calibration", "oneOf": [ { - "$ref": "#/definitions/BaseModel" + "$ref": "#/$defs/BaseModel" }, { "type": "null" @@ -129,6 +373,91 @@ "title": "HarpBehavior", "type": "object" }, + "HarpWhiteRabbit": { + "properties": { + "device_type": { + "const": "WhiteRabbit", + "default": "WhiteRabbit", + "title": "Device Type", + "type": "string" + }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, + "additional_settings": { + "default": null, + "description": "Additional settings", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "calibration": { + "default": null, + "description": "Calibration", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "who_am_i": { + "const": 1404, + "default": 1404, + "title": "Who Am I", + "type": "integer" + }, + "serial_number": { + "default": null, + "description": "Device serial number", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Serial Number" + }, + "port_name": { + "description": "Device port name", + "title": "Port Name", + "type": "string" + }, + "connected_clock_outputs": { + "default": [], + "description": "Connected clock outputs", + "items": { + "$ref": "#/$defs/ConnectedClockOutput" + }, + "title": "Connected Clock Outputs", + "type": "array" + } + }, + "required": [ + "port_name" + ], + "title": "HarpWhiteRabbit", + "type": "object" + }, "Rect": { "properties": { "x": { @@ -172,12 +501,25 @@ "title": "Device Type", "type": "string" }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, "additional_settings": { "default": null, "description": "Additional settings", "oneOf": [ { - "$ref": "#/definitions/BaseModel" + "$ref": "#/$defs/BaseModel" }, { "type": "null" @@ -189,7 +531,7 @@ "description": "Calibration", "oneOf": [ { - "$ref": "#/definitions/BaseModel" + "$ref": "#/$defs/BaseModel" }, { "type": "null" @@ -228,7 +570,7 @@ "gain": { "default": 0, "description": "Gain", - "minimum": 0.0, + "minimum": 0, "title": "Gain", "type": "number" }, @@ -237,7 +579,7 @@ "description": "Gamma. If None, will disable gamma correction.", "oneOf": [ { - "minimum": 0.0, + "minimum": 0, "type": "number" }, { @@ -251,7 +593,7 @@ "description": "ADC bit depth. If None will be left as default.", "oneOf": [ { - "$ref": "#/definitions/SpinnakerCameraAdcBitDepth" + "$ref": "#/$defs/SpinnakerCameraAdcBitDepth" }, { "type": "null" @@ -263,7 +605,7 @@ "description": "Pixel format. If None will be left as default.", "oneOf": [ { - "$ref": "#/definitions/SpinnakerCameraPixelFormat" + "$ref": "#/$defs/SpinnakerCameraPixelFormat" }, { "type": "null" @@ -271,7 +613,7 @@ ] }, "region_of_interest": { - "$ref": "#/definitions/Rect", + "$ref": "#/$defs/Rect", "default": { "x": 0, "y": 0, @@ -285,7 +627,7 @@ "description": "Video writer. If not provided, no video will be saved.", "oneOf": [ { - "$ref": "#/definitions/VideoWriter" + "$ref": "#/$defs/VideoWriter" }, { "type": "null" @@ -612,17 +954,17 @@ "VideoWriter": { "discriminator": { "mapping": { - "FFMPEG": "#/definitions/VideoWriterFfmpeg", - "OPENCV": "#/definitions/VideoWriterOpenCv" + "FFMPEG": "#/$defs/VideoWriterFfmpeg", + "OPENCV": "#/$defs/VideoWriterOpenCv" }, "propertyName": "video_writer_type" }, "oneOf": [ { - "$ref": "#/definitions/VideoWriterFfmpeg" + "$ref": "#/$defs/VideoWriterFfmpeg" }, { - "$ref": "#/definitions/VideoWriterOpenCv" + "$ref": "#/$defs/VideoWriterOpenCv" } ] }, @@ -694,63 +1036,5 @@ "title": "VideoWriterOpenCv", "type": "object" } - }, - "properties": { - "aind_behavior_services_pkg_version": { - "default": "0.10.2", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "version": { - "const": "0.2.1", - "default": "0.2.1", - "title": "Version", - "type": "string" - }, - "computer_name": { - "description": "Computer name", - "title": "Computer Name", - "type": "string" - }, - "rig_name": { - "description": "Rig name", - "title": "Rig Name", - "type": "string" - }, - "triggered_camera_controller_0": { - "default": null, - "description": "Camera controller to triggered cameras. Will use Camera0 register as a trigger.", - "oneOf": [ - { - "$ref": "#/definitions/CameraController_SpinnakerCamera_" - }, - { - "type": "null" - } - ] - }, - "triggered_camera_controller_1": { - "default": null, - "description": "Camera controller to triggered cameras. Will use Camera1 register as a trigger.", - "oneOf": [ - { - "$ref": "#/definitions/CameraController_SpinnakerCamera_" - }, - { - "type": "null" - } - ] - }, - "harp_behavior": { - "$ref": "#/definitions/HarpBehavior", - "description": "Harp behavior board. Will be the source of triggers for the two camera controllers." - } - }, - "required": [ - "rig_name", - "harp_behavior" - ], - "title": "AindVideoEncodingBenchmarksRig", - "type": "object" + } } \ No newline at end of file diff --git a/src/DataSchemas/aind_behavior_session_model.json b/src/DataSchemas/aind_behavior_session_model.json deleted file mode 100644 index 09966ba..0000000 --- a/src/DataSchemas/aind_behavior_session_model.json +++ /dev/null @@ -1,110 +0,0 @@ -{ - "properties": { - "aind_behavior_services_pkg_version": { - "default": "0.10.2", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "version": { - "const": "0.3.1", - "default": "0.3.1", - "title": "Version", - "type": "string" - }, - "experiment": { - "description": "Name of the experiment", - "title": "Experiment", - "type": "string" - }, - "experimenter": { - "default": [], - "description": "Name of the experimenter", - "items": { - "type": "string" - }, - "title": "Experimenter", - "type": "array" - }, - "date": { - "description": "Date of the experiment", - "format": "date-time", - "title": "Date", - "type": "string" - }, - "root_path": { - "description": "Root path where data will be logged", - "title": "Root Path", - "type": "string" - }, - "session_name": { - "default": null, - "description": "Name of the session. This will be used to create a folder in the root path.", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Session Name" - }, - "subject": { - "description": "Name of the subject", - "title": "Subject", - "type": "string" - }, - "experiment_version": { - "description": "Version of the experiment", - "title": "Experiment Version", - "type": "string" - }, - "notes": { - "default": null, - "description": "Notes about the experiment", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Notes" - }, - "commit_hash": { - "default": null, - "description": "Commit hash of the repository", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Commit Hash" - }, - "allow_dirty_repo": { - "default": false, - "description": "Allow running from a dirty repository", - "title": "Allow Dirty Repo", - "type": "boolean" - }, - "skip_hardware_validation": { - "default": false, - "description": "Skip hardware validation", - "title": "Skip Hardware Validation", - "type": "boolean" - } - }, - "required": [ - "experiment", - "root_path", - "subject", - "experiment_version" - ], - "title": "AindBehaviorSessionModel", - "type": "object" -} \ No newline at end of file diff --git a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/__init__.py b/src/DataSchemas/aind_behavior_video_encoding_benchmarks/__init__.py deleted file mode 100644 index 6a9beea..0000000 --- a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/__init__.py +++ /dev/null @@ -1 +0,0 @@ -__version__ = "0.4.0" diff --git a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/launcher.py b/src/DataSchemas/aind_behavior_video_encoding_benchmarks/launcher.py deleted file mode 100644 index ab1bcbc..0000000 --- a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/launcher.py +++ /dev/null @@ -1,82 +0,0 @@ -import logging -from pathlib import Path -from typing import final - -import aind_behavior_experiment_launcher.launcher.behavior_launcher as behavior_launcher -from aind_behavior_experiment_launcher.apps import AindBehaviorServicesBonsaiApp -from aind_behavior_experiment_launcher.launcher.behavior_launcher import DefaultBehaviorPicker -from aind_behavior_experiment_launcher.resource_monitor import ( - ResourceMonitor, - available_storage_constraint_factory, - remote_dir_exists_constraint_factory, -) -from aind_behavior_experiment_launcher.ui import prompt_field_from_input -from aind_behavior_services.session import AindBehaviorSessionModel -from pydantic import ValidationError -from pydantic_settings import CliApp -from typing_extensions import override - -from aind_behavior_video_encoding_benchmarks.rig import AindVideoEncodingBenchmarksRig -from aind_behavior_video_encoding_benchmarks.task_logic import ( - AindVideoEncodingBenchmarksTaskLogic, - AindVideoEncodingBenchmarksTaskParameters, -) - -logger = logging.getLogger(__name__) - - -@final -class _CustomPicker(DefaultBehaviorPicker): - @override - def pick_task_logic(self) -> AindVideoEncodingBenchmarksTaskLogic: - save_raw = None - while save_raw is None: - try: - save_raw = prompt_field_from_input( - AindVideoEncodingBenchmarksTaskParameters, "save_raw_video", default=False - ) - except ValidationError as e: - self.launcher._logger.error("Failed to parse input: %s", e) - else: - self.launcher._logger.info("save_raw_video set to: %s", save_raw) - return AindVideoEncodingBenchmarksTaskLogic( - task_parameters=AindVideoEncodingBenchmarksTaskParameters(save_raw_video=save_raw) - ) - - -def make_launcher(settings: behavior_launcher.BehaviorCliArgs) -> behavior_launcher.BehaviorLauncher: - data_dir = settings.data_dir - remote_dir = Path(r"\\allen\aind\scratch\video-encoding-benchmarks\data") - srv = behavior_launcher.BehaviorServicesFactoryManager() - srv.attach_app(AindBehaviorServicesBonsaiApp(Path(r"./src/main.bonsai"))) - srv.attach_data_transfer(behavior_launcher.robocopy_data_transfer_factory(Path(remote_dir))) - srv.attach_resource_monitor( - ResourceMonitor( - constrains=[ - available_storage_constraint_factory(Path(data_dir), 2e11), - remote_dir_exists_constraint_factory(Path(remote_dir)), - ] - ) - ) - - return behavior_launcher.BehaviorLauncher( - rig_schema_model=AindVideoEncodingBenchmarksRig, - session_schema_model=AindBehaviorSessionModel, - task_logic_schema_model=AindVideoEncodingBenchmarksTaskLogic, - picker=_CustomPicker( - config_library_dir=Path(r"\\allen\aind\scratch\AindBehavior.db\AindVideoEncodingBenchmarks") - ), - settings=settings, - services=srv, - ) - - -def main(): - args = CliApp().run(behavior_launcher.BehaviorCliArgs) - launcher = make_launcher(args) - launcher.main() - return None - - -if __name__ == "__main__": - main() diff --git a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/regenerate.py b/src/DataSchemas/aind_behavior_video_encoding_benchmarks/regenerate.py deleted file mode 100644 index 87e0ddc..0000000 --- a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/regenerate.py +++ /dev/null @@ -1,42 +0,0 @@ -import inspect -from pathlib import Path - -from aind_behavior_services.session import AindBehaviorSessionModel -from aind_behavior_services.utils import ( - convert_pydantic_to_bonsai, - pascal_to_snake_case, - snake_to_pascal_case, -) - -import aind_behavior_video_encoding_benchmarks.rig -import aind_behavior_video_encoding_benchmarks.task_logic - -SCHEMA_ROOT = Path("./src/DataSchemas/") -EXTENSIONS_ROOT = Path("./src/Extensions/") -NAMESPACE_PREFIX = "AindVideoEncodingBenchmarksSchemas" - - -def main(): - models = [ - aind_behavior_video_encoding_benchmarks.task_logic.AindVideoEncodingBenchmarksTaskLogic, - aind_behavior_video_encoding_benchmarks.rig.AindVideoEncodingBenchmarksRig, - AindBehaviorSessionModel, - ] - - for model in models: - module_name = inspect.getmodule(model).__name__ - module_name = module_name.split(".")[-1] - schema_name = f"{pascal_to_snake_case(model.__name__)}" - namespace = f"{NAMESPACE_PREFIX}.{snake_to_pascal_case(module_name)}" - - print((schema_name, namespace)) - convert_pydantic_to_bonsai( - {schema_name: model}, - schema_path=SCHEMA_ROOT, - output_path=EXTENSIONS_ROOT, - namespace=namespace, - ) - - -if __name__ == "__main__": - main() diff --git a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/task_logic.py b/src/DataSchemas/aind_behavior_video_encoding_benchmarks/task_logic.py deleted file mode 100644 index 97f5abe..0000000 --- a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/task_logic.py +++ /dev/null @@ -1,25 +0,0 @@ -from __future__ import annotations - -from typing import Literal - -from aind_behavior_services.task_logic import AindBehaviorTaskLogicModel, TaskParameters -from pydantic import Field - -__version__ = "0.1.1" - - -class AindVideoEncodingBenchmarksTaskParameters(TaskParameters): - save_raw_video: bool = Field( - default=False, - description="For each video-writer object, will also save the RAW encoded video to disk. Use at your own risk.", - ) - - -class AindVideoEncodingBenchmarksTaskLogic(AindBehaviorTaskLogicModel): - version: Literal[__version__] = __version__ - name: str = Field( - default="AindVideoEncodingBenchmarks", - description="Name of the task logic", - frozen=True, - ) - task_parameters: AindVideoEncodingBenchmarksTaskParameters = Field(..., description="Parameters of the task logic") diff --git a/src/DataSchemas/aind_video_encoding_benchmarks_task_logic.json b/src/DataSchemas/aind_video_encoding_benchmarks_task_logic.json deleted file mode 100644 index 288b4c5..0000000 --- a/src/DataSchemas/aind_video_encoding_benchmarks_task_logic.json +++ /dev/null @@ -1,79 +0,0 @@ -{ - "definitions": { - "AindVideoEncodingBenchmarksTaskParameters": { - "additionalProperties": true, - "properties": { - "rng_seed": { - "default": null, - "description": "Seed of the random number generator", - "oneOf": [ - { - "type": "number" - }, - { - "type": "null" - } - ], - "title": "Rng Seed" - }, - "aind_behavior_services_pkg_version": { - "default": "0.10.2", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "save_raw_video": { - "default": false, - "description": "For each video-writer object, will also save the RAW encoded video to disk. Use at your own risk.", - "title": "Save Raw Video", - "type": "boolean" - } - }, - "title": "AindVideoEncodingBenchmarksTaskParameters", - "type": "object" - } - }, - "additionalProperties": false, - "properties": { - "name": { - "default": "AindVideoEncodingBenchmarks", - "description": "Name of the task logic", - "title": "Name", - "type": "string" - }, - "description": { - "default": "", - "description": "Description of the task.", - "title": "Description", - "type": "string" - }, - "task_parameters": { - "$ref": "#/definitions/AindVideoEncodingBenchmarksTaskParameters", - "description": "Parameters of the task logic" - }, - "version": { - "const": "0.1.1", - "default": "0.1.1", - "title": "Version", - "type": "string" - }, - "stage_name": { - "default": null, - "description": "Optional stage name the `Task` object instance represents.", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Stage Name" - } - }, - "required": [ - "task_parameters" - ], - "title": "AindVideoEncodingBenchmarksTaskLogic", - "type": "object" -} \ No newline at end of file diff --git a/src/Extensions/AindVideoEncodingBenchmarksRig.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs similarity index 65% rename from src/Extensions/AindVideoEncodingBenchmarksRig.cs rename to src/Extensions/AindBehaviorJustFrames.Generated.cs index 27012ba..38d9208 100644 --- a/src/Extensions/AindVideoEncodingBenchmarksRig.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -5,13 +5,543 @@ //---------------------- -namespace AindVideoEncodingBenchmarksSchemas.Rig +namespace AindJustFramesSchemas { #pragma warning disable // Disable all warnings - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindBehaviorSessionModel + { + + private string _aindBehaviorServicesPkgVersion; + + private string _version; + + private string _experiment; + + private System.Collections.Generic.List _experimenter; + + private System.DateTimeOffset _date; + + private string _rootPath; + + private string _sessionName; + + private string _subject; + + private string _experimentVersion; + + private string _notes; + + private string _commitHash; + + private bool _allowDirtyRepo; + + private bool _skipHardwareValidation; + + public AindBehaviorSessionModel() + { + _aindBehaviorServicesPkgVersion = "0.12.3"; + _version = "0.12.3"; + _experimenter = new System.Collections.Generic.List(); + _experimentVersion = ""; + _allowDirtyRepo = false; + _skipHardwareValidation = false; + } + + protected AindBehaviorSessionModel(AindBehaviorSessionModel other) + { + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _experiment = other._experiment; + _experimenter = other._experimenter; + _date = other._date; + _rootPath = other._rootPath; + _sessionName = other._sessionName; + _subject = other._subject; + _experimentVersion = other._experimentVersion; + _notes = other._notes; + _commitHash = other._commitHash; + _allowDirtyRepo = other._allowDirtyRepo; + _skipHardwareValidation = other._skipHardwareValidation; + } + + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version + { + get + { + return _version; + } + set + { + _version = value; + } + } + + /// + /// Name of the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("experiment")] + [System.ComponentModel.DescriptionAttribute("Name of the experiment")] + public string Experiment + { + get + { + return _experiment; + } + set + { + _experiment = value; + } + } + + /// + /// Name of the experimenter + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] + [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] + public System.Collections.Generic.List Experimenter + { + get + { + return _experimenter; + } + set + { + _experimenter = value; + } + } + + /// + /// Date of the experiment + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("date")] + [System.ComponentModel.DescriptionAttribute("Date of the experiment")] + public System.DateTimeOffset Date + { + get + { + return _date; + } + set + { + _date = value; + } + } + + /// + /// Root path where data will be logged + /// + [Newtonsoft.Json.JsonPropertyAttribute("root_path", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Root path where data will be logged")] + public string RootPath + { + get + { + return _rootPath; + } + set + { + _rootPath = value; + } + } + + /// + /// Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date. + /// + [Newtonsoft.Json.JsonPropertyAttribute("session_name")] + [System.ComponentModel.DescriptionAttribute("Name of the session. This will be used to create a folder in the root path. If no" + + "t provided, it will be generated using subject and date.")] + public string SessionName + { + get + { + return _sessionName; + } + set + { + _sessionName = value; + } + } + + /// + /// Name of the subject + /// + [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Name of the subject")] + public string Subject + { + get + { + return _subject; + } + set + { + _subject = value; + } + } + + /// + /// Version of the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("experiment_version")] + [System.ComponentModel.DescriptionAttribute("Version of the experiment")] + public string ExperimentVersion + { + get + { + return _experimentVersion; + } + set + { + _experimentVersion = value; + } + } + + /// + /// Notes about the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("notes")] + [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] + public string Notes + { + get + { + return _notes; + } + set + { + _notes = value; + } + } + + /// + /// Commit hash of the repository + /// + [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")] + [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")] + public string CommitHash + { + get + { + return _commitHash; + } + set + { + _commitHash = value; + } + } + + /// + /// Allow running from a dirty repository + /// + [Newtonsoft.Json.JsonPropertyAttribute("allow_dirty_repo")] + [System.ComponentModel.DescriptionAttribute("Allow running from a dirty repository")] + public bool AllowDirtyRepo + { + get + { + return _allowDirtyRepo; + } + set + { + _allowDirtyRepo = value; + } + } + + /// + /// Skip hardware validation + /// + [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")] + [System.ComponentModel.DescriptionAttribute("Skip hardware validation")] + public bool SkipHardwareValidation + { + get + { + return _skipHardwareValidation; + } + set + { + _skipHardwareValidation = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorSessionModel(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorSessionModel(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("Experiment = " + _experiment + ", "); + stringBuilder.Append("Experimenter = " + _experimenter + ", "); + stringBuilder.Append("Date = " + _date + ", "); + stringBuilder.Append("RootPath = " + _rootPath + ", "); + stringBuilder.Append("SessionName = " + _sessionName + ", "); + stringBuilder.Append("Subject = " + _subject + ", "); + stringBuilder.Append("ExperimentVersion = " + _experimentVersion + ", "); + stringBuilder.Append("Notes = " + _notes + ", "); + stringBuilder.Append("CommitHash = " + _commitHash + ", "); + stringBuilder.Append("AllowDirtyRepo = " + _allowDirtyRepo + ", "); + stringBuilder.Append("SkipHardwareValidation = " + _skipHardwareValidation); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindJustFramesRig + { + + private string _aindBehaviorServicesPkgVersion; + + private string _version; + + private string _computerName; + + private string _rigName; + + private CameraControllerSpinnakerCamera _triggeredCameraController0; + + private CameraControllerSpinnakerCamera _triggeredCameraController1; + + private HarpBehavior _harpBehavior; + + private HarpWhiteRabbit _harpWhiteRabbit; + + public AindJustFramesRig() + { + _aindBehaviorServicesPkgVersion = "0.12.3"; + _version = "0.5.0-rc0"; + _harpBehavior = new HarpBehavior(); + } + + protected AindJustFramesRig(AindJustFramesRig other) + { + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _computerName = other._computerName; + _rigName = other._rigName; + _triggeredCameraController0 = other._triggeredCameraController0; + _triggeredCameraController1 = other._triggeredCameraController1; + _harpBehavior = other._harpBehavior; + _harpWhiteRabbit = other._harpWhiteRabbit; + } + + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version + { + get + { + return _version; + } + set + { + _version = value; + } + } + + /// + /// Computer name + /// + [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] + [System.ComponentModel.DescriptionAttribute("Computer name")] + public string ComputerName + { + get + { + return _computerName; + } + set + { + _computerName = value; + } + } + + /// + /// Rig name + /// + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Rig name")] + public string RigName + { + get + { + return _rigName; + } + set + { + _rigName = value; + } + } + + /// + /// Camera controller to triggered cameras. Will use Camera0 register as a trigger. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_0")] + [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera0 register as a trigger.")] + public CameraControllerSpinnakerCamera TriggeredCameraController0 + { + get + { + return _triggeredCameraController0; + } + set + { + _triggeredCameraController0 = value; + } + } + + /// + /// Camera controller to triggered cameras. Will use Camera1 register as a trigger. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_1")] + [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera1 register as a trigger.")] + public CameraControllerSpinnakerCamera TriggeredCameraController1 + { + get + { + return _triggeredCameraController1; + } + set + { + _triggeredCameraController1 = value; + } + } + + /// + /// Harp behavior board. Will be the source of triggers for the two camera controllers. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("harp_behavior", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Harp behavior board. Will be the source of triggers for the two camera controller" + + "s.")] + public HarpBehavior HarpBehavior + { + get + { + return _harpBehavior; + } + set + { + _harpBehavior = value; + } + } + + /// + /// Harp White Rabbit for time synchronization. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("harp_white_rabbit")] + [System.ComponentModel.DescriptionAttribute("Harp White Rabbit for time synchronization.")] + public HarpWhiteRabbit HarpWhiteRabbit + { + get + { + return _harpWhiteRabbit; + } + set + { + _harpWhiteRabbit = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindJustFramesRig(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindJustFramesRig(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("ComputerName = " + _computerName + ", "); + stringBuilder.Append("RigName = " + _rigName + ", "); + stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); + stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); + stringBuilder.Append("HarpBehavior = " + _harpBehavior + ", "); + stringBuilder.Append("HarpWhiteRabbit = " + _harpWhiteRabbit); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class BaseModel { @@ -23,12 +553,12 @@ protected BaseModel(BaseModel other) { } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new BaseModel(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new BaseModel(this)); } @@ -53,29 +583,34 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class CameraControllerSpinnakerCamera { - private string _deviceType = "CameraController"; + private string _deviceType; + + private string _deviceName; private BaseModel _additionalSettings; private BaseModel _calibration; - private System.Collections.Generic.IDictionary _cameras = new System.Collections.Generic.Dictionary(); + private System.Collections.Generic.Dictionary _cameras; private int? _frameRate; public CameraControllerSpinnakerCamera() { + _deviceType = "CameraController"; + _cameras = new System.Collections.Generic.Dictionary(); } protected CameraControllerSpinnakerCamera(CameraControllerSpinnakerCamera other) { _deviceType = other._deviceType; + _deviceName = other._deviceName; _additionalSettings = other._additionalSettings; _calibration = other._calibration; _cameras = other._cameras; @@ -95,6 +630,23 @@ public string DeviceType } } + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + /// /// Additional settings /// @@ -137,53 +689,327 @@ public BaseModel Calibration [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("cameras", Required=Newtonsoft.Json.Required.Always)] [System.ComponentModel.DescriptionAttribute("Cameras to be instantiated")] - public System.Collections.Generic.IDictionary Cameras + public System.Collections.Generic.Dictionary Cameras + { + get + { + return _cameras; + } + set + { + _cameras = value; + } + } + + /// + /// Frame rate of the trigger to all cameras + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("frame_rate")] + [System.ComponentModel.DescriptionAttribute("Frame rate of the trigger to all cameras")] + public int? FrameRate + { + get + { + return _frameRate; + } + set + { + _frameRate = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new CameraControllerSpinnakerCamera(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new CameraControllerSpinnakerCamera(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("Cameras = " + _cameras + ", "); + stringBuilder.Append("FrameRate = " + _frameRate); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class ConnectedClockOutput + { + + private string _targetDevice; + + private int _outputChannel; + + public ConnectedClockOutput() + { + } + + protected ConnectedClockOutput(ConnectedClockOutput other) + { + _targetDevice = other._targetDevice; + _outputChannel = other._outputChannel; + } + + /// + /// Optional device name to provide user additional information + /// + [Newtonsoft.Json.JsonPropertyAttribute("target_device")] + [System.ComponentModel.DescriptionAttribute("Optional device name to provide user additional information")] + public string TargetDevice + { + get + { + return _targetDevice; + } + set + { + _targetDevice = value; + } + } + + /// + /// Output channel + /// + [Newtonsoft.Json.JsonPropertyAttribute("output_channel", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Output channel")] + public int OutputChannel + { + get + { + return _outputChannel; + } + set + { + _outputChannel = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ConnectedClockOutput(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new ConnectedClockOutput(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("TargetDevice = " + _targetDevice + ", "); + stringBuilder.Append("OutputChannel = " + _outputChannel); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class HarpBehavior + { + + private string _deviceType; + + private string _deviceName; + + private BaseModel _additionalSettings; + + private BaseModel _calibration; + + private int _whoAmI; + + private string _serialNumber; + + private string _portName; + + public HarpBehavior() + { + _deviceType = "Behavior"; + _whoAmI = 1216; + } + + protected HarpBehavior(HarpBehavior other) + { + _deviceType = other._deviceType; + _deviceName = other._deviceName; + _additionalSettings = other._additionalSettings; + _calibration = other._calibration; + _whoAmI = other._whoAmI; + _serialNumber = other._serialNumber; + _portName = other._portName; + } + + [Newtonsoft.Json.JsonPropertyAttribute("device_type")] + public string DeviceType + { + get + { + return _deviceType; + } + set + { + _deviceType = value; + } + } + + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + + /// + /// Additional settings + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] + [System.ComponentModel.DescriptionAttribute("Additional settings")] + public BaseModel AdditionalSettings + { + get + { + return _additionalSettings; + } + set + { + _additionalSettings = value; + } + } + + /// + /// Calibration + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration")] + public BaseModel Calibration + { + get + { + return _calibration; + } + set + { + _calibration = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("who_am_i")] + public int WhoAmI + { + get + { + return _whoAmI; + } + set + { + _whoAmI = value; + } + } + + /// + /// Device serial number + /// + [Newtonsoft.Json.JsonPropertyAttribute("serial_number")] + [System.ComponentModel.DescriptionAttribute("Device serial number")] + public string SerialNumber { get { - return _cameras; + return _serialNumber; } set { - _cameras = value; + _serialNumber = value; } } /// - /// Frame rate of the trigger to all cameras + /// Device port name /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("frame_rate")] - [System.ComponentModel.DescriptionAttribute("Frame rate of the trigger to all cameras")] - public int? FrameRate + [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Device port name")] + public string PortName { get { - return _frameRate; + return _portName; } set { - _frameRate = value; + _portName = value; } } - public System.IObservable Process() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new CameraControllerSpinnakerCamera(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpBehavior(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new CameraControllerSpinnakerCamera(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new HarpBehavior(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("additional_settings = " + _additionalSettings + ", "); - stringBuilder.Append("calibration = " + _calibration + ", "); - stringBuilder.Append("cameras = " + _cameras + ", "); - stringBuilder.Append("frame_rate = " + _frameRate); + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("PortName = " + _portName); return true; } @@ -202,36 +1028,45 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class HarpBehavior + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class HarpWhiteRabbit { - private string _deviceType = "Behavior"; + private string _deviceType; + + private string _deviceName; private BaseModel _additionalSettings; private BaseModel _calibration; - private int _whoAmI = 1216; + private int _whoAmI; private string _serialNumber; private string _portName; - public HarpBehavior() + private System.Collections.Generic.List _connectedClockOutputs; + + public HarpWhiteRabbit() { + _deviceType = "WhiteRabbit"; + _whoAmI = 1404; + _connectedClockOutputs = new System.Collections.Generic.List(); } - protected HarpBehavior(HarpBehavior other) + protected HarpWhiteRabbit(HarpWhiteRabbit other) { _deviceType = other._deviceType; + _deviceName = other._deviceName; _additionalSettings = other._additionalSettings; _calibration = other._calibration; _whoAmI = other._whoAmI; _serialNumber = other._serialNumber; _portName = other._portName; + _connectedClockOutputs = other._connectedClockOutputs; } [Newtonsoft.Json.JsonPropertyAttribute("device_type")] @@ -247,6 +1082,23 @@ public string DeviceType } } + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + /// /// Additional settings /// @@ -330,24 +1182,44 @@ public string PortName } } - public System.IObservable Process() + /// + /// Connected clock outputs + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("connected_clock_outputs")] + [System.ComponentModel.DescriptionAttribute("Connected clock outputs")] + public System.Collections.Generic.List ConnectedClockOutputs { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpBehavior(this))); + get + { + return _connectedClockOutputs; + } + set + { + _connectedClockOutputs = value; + } } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Select(source, _ => new HarpBehavior(this)); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpWhiteRabbit(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new HarpWhiteRabbit(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("additional_settings = " + _additionalSettings + ", "); - stringBuilder.Append("calibration = " + _calibration + ", "); - stringBuilder.Append("who_am_i = " + _whoAmI + ", "); - stringBuilder.Append("serial_number = " + _serialNumber + ", "); - stringBuilder.Append("port_name = " + _portName); + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("PortName = " + _portName + ", "); + stringBuilder.Append("ConnectedClockOutputs = " + _connectedClockOutputs); return true; } @@ -366,22 +1238,26 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class Rect { - private int _x = 0; + private int _x; - private int _y = 0; + private int _y; - private int _width = 0; + private int _width; - private int _height = 0; + private int _height; public Rect() { + _x = 0; + _y = 0; + _width = 0; + _height = 0; } protected Rect(Rect other) @@ -460,22 +1336,22 @@ public int Height } } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Rect(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new Rect(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("x = " + _x + ", "); - stringBuilder.Append("y = " + _y + ", "); - stringBuilder.Append("width = " + _width + ", "); - stringBuilder.Append("height = " + _height); + stringBuilder.Append("X = " + _x + ", "); + stringBuilder.Append("Y = " + _y + ", "); + stringBuilder.Append("Width = " + _width + ", "); + stringBuilder.Append("Height = " + _height); return true; } @@ -494,13 +1370,15 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class SpinnakerCamera { - private string _deviceType = "SpinnakerCamera"; + private string _deviceType; + + private string _deviceName; private BaseModel _additionalSettings; @@ -508,19 +1386,19 @@ public partial class SpinnakerCamera private string _serialNumber; - private int _binning = 1; + private int _binning; - private SpinnakerCameraColorProcessing _colorProcessing = AindVideoEncodingBenchmarksSchemas.Rig.SpinnakerCameraColorProcessing.Default; + private SpinnakerCameraColorProcessing _colorProcessing; - private int _exposure = 1000; + private int _exposure; - private double _gain = 0D; + private double _gain; private double? _gamma; - private SpinnakerCameraAdcBitDepth? _adcBitDepth = AindVideoEncodingBenchmarksSchemas.Rig.SpinnakerCameraAdcBitDepth.Adc8bit; + private SpinnakerCameraAdcBitDepth? _adcBitDepth; - private SpinnakerCameraPixelFormat? _pixelFormat = AindVideoEncodingBenchmarksSchemas.Rig.SpinnakerCameraPixelFormat.Mono8; + private SpinnakerCameraPixelFormat? _pixelFormat; private Rect _regionOfInterest; @@ -528,11 +1406,20 @@ public partial class SpinnakerCamera public SpinnakerCamera() { + _deviceType = "SpinnakerCamera"; + _binning = 1; + _colorProcessing = AindJustFramesSchemas.SpinnakerCameraColorProcessing.Default; + _exposure = 1000; + _gain = 0D; + _adcBitDepth = AindJustFramesSchemas.SpinnakerCameraAdcBitDepth.Adc8bit; + _pixelFormat = AindJustFramesSchemas.SpinnakerCameraPixelFormat.Mono8; + _regionOfInterest = new Rect(); } protected SpinnakerCamera(SpinnakerCamera other) { _deviceType = other._deviceType; + _deviceName = other._deviceName; _additionalSettings = other._additionalSettings; _calibration = other._calibration; _serialNumber = other._serialNumber; @@ -564,6 +1451,23 @@ public string DeviceType } } + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + /// /// Additional settings /// @@ -776,31 +1680,32 @@ public VideoWriter VideoWriter } } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SpinnakerCamera(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new SpinnakerCamera(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("additional_settings = " + _additionalSettings + ", "); - stringBuilder.Append("calibration = " + _calibration + ", "); - stringBuilder.Append("serial_number = " + _serialNumber + ", "); - stringBuilder.Append("binning = " + _binning + ", "); - stringBuilder.Append("color_processing = " + _colorProcessing + ", "); - stringBuilder.Append("exposure = " + _exposure + ", "); - stringBuilder.Append("gain = " + _gain + ", "); - stringBuilder.Append("gamma = " + _gamma + ", "); - stringBuilder.Append("adc_bit_depth = " + _adcBitDepth + ", "); - stringBuilder.Append("pixel_format = " + _pixelFormat + ", "); - stringBuilder.Append("region_of_interest = " + _regionOfInterest + ", "); - stringBuilder.Append("video_writer = " + _videoWriter); + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("Binning = " + _binning + ", "); + stringBuilder.Append("ColorProcessing = " + _colorProcessing + ", "); + stringBuilder.Append("Exposure = " + _exposure + ", "); + stringBuilder.Append("Gain = " + _gain + ", "); + stringBuilder.Append("Gamma = " + _gamma + ", "); + stringBuilder.Append("AdcBitDepth = " + _adcBitDepth + ", "); + stringBuilder.Append("PixelFormat = " + _pixelFormat + ", "); + stringBuilder.Append("RegionOfInterest = " + _regionOfInterest + ", "); + stringBuilder.Append("VideoWriter = " + _videoWriter); return true; } @@ -819,7 +1724,7 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] public enum SpinnakerCameraAdcBitDepth { @@ -834,7 +1739,7 @@ public enum SpinnakerCameraAdcBitDepth } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] public enum SpinnakerCameraPixelFormat { @@ -1272,12 +2177,12 @@ public enum SpinnakerCameraPixelFormat } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "video_writer_type")] [JsonInheritanceAttribute("FFMPEG", typeof(VideoWriterFfmpeg))] [JsonInheritanceAttribute("OPENCV", typeof(VideoWriterOpenCv))] - [Bonsai.CombinatorAttribute()] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class VideoWriter { @@ -1289,12 +2194,12 @@ protected VideoWriter(VideoWriter other) { } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriter(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriter(this)); } @@ -1319,22 +2224,26 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class VideoWriterFfmpeg : VideoWriter { - private int _frameRate = 30; + private int _frameRate; - private string _containerExtension = "mp4"; + private string _containerExtension; - private string _outputArguments = "-vf \"scale=out_color_matrix=bt709:out_range=full,format=bgr24,scale=out_range=full\" -c:v h264_nvenc -pix_fmt yuv420p -color_range full -colorspace bt709 -color_trc linear -tune hq -preset p4 -rc vbr -cq 12 -b:v 0M -metadata author=\"Allen Institute for Neural Dynamics\" -maxrate 700M -bufsize 350M"; + private string _outputArguments; - private string _inputArguments = "-colorspace bt709 -color_primaries bt709 -color_range full -color_trc linear"; + private string _inputArguments; public VideoWriterFfmpeg() { + _frameRate = 30; + _containerExtension = "mp4"; + _outputArguments = "-vf \"scale=out_color_matrix=bt709:out_range=full,format=bgr24,scale=out_range=full\" -c:v h264_nvenc -pix_fmt yuv420p -color_range full -colorspace bt709 -color_trc linear -tune hq -preset p4 -rc vbr -cq 12 -b:v 0M -metadata author=\"Allen Institute for Neural Dynamics\" -maxrate 700M -bufsize 350M"; + _inputArguments = "-colorspace bt709 -color_primaries bt709 -color_range full -color_trc linear"; } protected VideoWriterFfmpeg(VideoWriterFfmpeg other) : @@ -1414,12 +2323,12 @@ public string InputArguments } } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriterFfmpeg(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriterFfmpeg(this)); } @@ -1430,29 +2339,32 @@ protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append(", "); } - stringBuilder.Append("frame_rate = " + _frameRate + ", "); - stringBuilder.Append("container_extension = " + _containerExtension + ", "); - stringBuilder.Append("output_arguments = " + _outputArguments + ", "); - stringBuilder.Append("input_arguments = " + _inputArguments); + stringBuilder.Append("FrameRate = " + _frameRate + ", "); + stringBuilder.Append("ContainerExtension = " + _containerExtension + ", "); + stringBuilder.Append("OutputArguments = " + _outputArguments + ", "); + stringBuilder.Append("InputArguments = " + _inputArguments); return true; } } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class VideoWriterOpenCv : VideoWriter { - private int _frameRate = 30; + private int _frameRate; - private string _containerExtension = "avi"; + private string _containerExtension; - private string _fourCc = "FMP4"; + private string _fourCc; public VideoWriterOpenCv() { + _frameRate = 30; + _containerExtension = "avi"; + _fourCc = "FMP4"; } protected VideoWriterOpenCv(VideoWriterOpenCv other) : @@ -1514,12 +2426,12 @@ public string FourCc } } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriterOpenCv(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriterOpenCv(this)); } @@ -1530,202 +2442,15 @@ protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append(", "); } - stringBuilder.Append("frame_rate = " + _frameRate + ", "); - stringBuilder.Append("container_extension = " + _containerExtension + ", "); - stringBuilder.Append("four_cc = " + _fourCc); - return true; - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindVideoEncodingBenchmarksRig - { - - private string _aindBehaviorServicesPkgVersion = "0.10.2"; - - private string _version = "0.2.1"; - - private string _computerName; - - private string _rigName; - - private CameraControllerSpinnakerCamera _triggeredCameraController0; - - private CameraControllerSpinnakerCamera _triggeredCameraController1; - - private HarpBehavior _harpBehavior = new HarpBehavior(); - - public AindVideoEncodingBenchmarksRig() - { - } - - protected AindVideoEncodingBenchmarksRig(AindVideoEncodingBenchmarksRig other) - { - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _version = other._version; - _computerName = other._computerName; - _rigName = other._rigName; - _triggeredCameraController0 = other._triggeredCameraController0; - _triggeredCameraController1 = other._triggeredCameraController1; - _harpBehavior = other._harpBehavior; - } - - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion - { - get - { - return _aindBehaviorServicesPkgVersion; - } - set - { - _aindBehaviorServicesPkgVersion = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version - { - get - { - return _version; - } - set - { - _version = value; - } - } - - /// - /// Computer name - /// - [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] - [System.ComponentModel.DescriptionAttribute("Computer name")] - public string ComputerName - { - get - { - return _computerName; - } - set - { - _computerName = value; - } - } - - /// - /// Rig name - /// - [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Rig name")] - public string RigName - { - get - { - return _rigName; - } - set - { - _rigName = value; - } - } - - /// - /// Camera controller to triggered cameras. Will use Camera0 register as a trigger. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_0")] - [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera0 register as a trigger.")] - public CameraControllerSpinnakerCamera TriggeredCameraController0 - { - get - { - return _triggeredCameraController0; - } - set - { - _triggeredCameraController0 = value; - } - } - - /// - /// Camera controller to triggered cameras. Will use Camera1 register as a trigger. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_1")] - [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera1 register as a trigger.")] - public CameraControllerSpinnakerCamera TriggeredCameraController1 - { - get - { - return _triggeredCameraController1; - } - set - { - _triggeredCameraController1 = value; - } - } - - /// - /// Harp behavior board. Will be the source of triggers for the two camera controllers. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_behavior", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Harp behavior board. Will be the source of triggers for the two camera controller" + - "s.")] - public HarpBehavior HarpBehavior - { - get - { - return _harpBehavior; - } - set - { - _harpBehavior = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindVideoEncodingBenchmarksRig(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindVideoEncodingBenchmarksRig(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("aind_behavior_services_pkg_version = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("version = " + _version + ", "); - stringBuilder.Append("computer_name = " + _computerName + ", "); - stringBuilder.Append("rig_name = " + _rigName + ", "); - stringBuilder.Append("triggered_camera_controller_0 = " + _triggeredCameraController0 + ", "); - stringBuilder.Append("triggered_camera_controller_1 = " + _triggeredCameraController1 + ", "); - stringBuilder.Append("harp_behavior = " + _harpBehavior); + stringBuilder.Append("FrameRate = " + _frameRate + ", "); + stringBuilder.Append("ContainerExtension = " + _containerExtension + ", "); + stringBuilder.Append("FourCc = " + _fourCc); return true; } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] public enum SpinnakerCameraColorProcessing { @@ -1875,7 +2600,7 @@ private string GetSubtypeDiscriminator(System.Type objectType) } } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [System.ComponentModel.DefaultPropertyAttribute("Type")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Combinator)] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] @@ -1919,16 +2644,29 @@ private static System.IObservable Process(System.IObservable /// Serializes a sequence of data model objects into JSON strings. /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into JSON strings.")] - [Bonsai.CombinatorAttribute()] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] + [Bonsai.CombinatorAttribute()] public partial class SerializeToJson { + public Newtonsoft.Json.Formatting Formatting { get; set; } + private System.IObservable Process(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value)); + var formatting = Formatting; + return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value, formatting)); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); } public System.IObservable Process(System.IObservable source) @@ -1941,11 +2679,21 @@ public System.IObservable Process(System.IObservable(source); } + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + public System.IObservable Process(System.IObservable source) { return Process(source); } + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + public System.IObservable Process(System.IObservable source) { return Process(source); @@ -1970,36 +2718,34 @@ public System.IObservable Process(System.IObservable { return Process(source); } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } } /// /// Deserializes a sequence of JSON strings into data model objects. /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of JSON strings into data model objects.")] [System.ComponentModel.DefaultPropertyAttribute("Type")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder { public DeserializeFromJson() { - Type = new Bonsai.Expressions.TypeMapping(); + Type = new Bonsai.Expressions.TypeMapping(); } public Bonsai.Expressions.TypeMapping Type { get; set; } diff --git a/src/Extensions/AindBehaviorSessionModel.cs b/src/Extensions/AindBehaviorSessionModel.cs deleted file mode 100644 index 2b1cf32..0000000 --- a/src/Extensions/AindBehaviorSessionModel.cs +++ /dev/null @@ -1,379 +0,0 @@ -//---------------------- -// -// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) -// -//---------------------- - - -namespace AindVideoEncodingBenchmarksSchemas.Session -{ - #pragma warning disable // Disable all warnings - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindBehaviorSessionModel - { - - private string _aindBehaviorServicesPkgVersion = "0.10.2"; - - private string _version = "0.3.1"; - - private string _experiment; - - private System.Collections.Generic.List _experimenter = new System.Collections.Generic.List(); - - private System.DateTimeOffset _date; - - private string _rootPath; - - private string _sessionName; - - private string _subject; - - private string _experimentVersion; - - private string _notes; - - private string _commitHash; - - private bool _allowDirtyRepo = false; - - private bool _skipHardwareValidation = false; - - public AindBehaviorSessionModel() - { - } - - protected AindBehaviorSessionModel(AindBehaviorSessionModel other) - { - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _version = other._version; - _experiment = other._experiment; - _experimenter = other._experimenter; - _date = other._date; - _rootPath = other._rootPath; - _sessionName = other._sessionName; - _subject = other._subject; - _experimentVersion = other._experimentVersion; - _notes = other._notes; - _commitHash = other._commitHash; - _allowDirtyRepo = other._allowDirtyRepo; - _skipHardwareValidation = other._skipHardwareValidation; - } - - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion - { - get - { - return _aindBehaviorServicesPkgVersion; - } - set - { - _aindBehaviorServicesPkgVersion = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version - { - get - { - return _version; - } - set - { - _version = value; - } - } - - /// - /// Name of the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("experiment", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Name of the experiment")] - public string Experiment - { - get - { - return _experiment; - } - set - { - _experiment = value; - } - } - - /// - /// Name of the experimenter - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] - [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] - public System.Collections.Generic.List Experimenter - { - get - { - return _experimenter; - } - set - { - _experimenter = value; - } - } - - /// - /// Date of the experiment - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("date")] - [System.ComponentModel.DescriptionAttribute("Date of the experiment")] - public System.DateTimeOffset Date - { - get - { - return _date; - } - set - { - _date = value; - } - } - - /// - /// Root path where data will be logged - /// - [Newtonsoft.Json.JsonPropertyAttribute("root_path", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Root path where data will be logged")] - public string RootPath - { - get - { - return _rootPath; - } - set - { - _rootPath = value; - } - } - - /// - /// Name of the session. This will be used to create a folder in the root path. - /// - [Newtonsoft.Json.JsonPropertyAttribute("session_name")] - [System.ComponentModel.DescriptionAttribute("Name of the session. This will be used to create a folder in the root path.")] - public string SessionName - { - get - { - return _sessionName; - } - set - { - _sessionName = value; - } - } - - /// - /// Name of the subject - /// - [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Name of the subject")] - public string Subject - { - get - { - return _subject; - } - set - { - _subject = value; - } - } - - /// - /// Version of the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("experiment_version", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Version of the experiment")] - public string ExperimentVersion - { - get - { - return _experimentVersion; - } - set - { - _experimentVersion = value; - } - } - - /// - /// Notes about the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("notes")] - [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] - public string Notes - { - get - { - return _notes; - } - set - { - _notes = value; - } - } - - /// - /// Commit hash of the repository - /// - [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")] - [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")] - public string CommitHash - { - get - { - return _commitHash; - } - set - { - _commitHash = value; - } - } - - /// - /// Allow running from a dirty repository - /// - [Newtonsoft.Json.JsonPropertyAttribute("allow_dirty_repo")] - [System.ComponentModel.DescriptionAttribute("Allow running from a dirty repository")] - public bool AllowDirtyRepo - { - get - { - return _allowDirtyRepo; - } - set - { - _allowDirtyRepo = value; - } - } - - /// - /// Skip hardware validation - /// - [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")] - [System.ComponentModel.DescriptionAttribute("Skip hardware validation")] - public bool SkipHardwareValidation - { - get - { - return _skipHardwareValidation; - } - set - { - _skipHardwareValidation = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorSessionModel(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorSessionModel(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("aind_behavior_services_pkg_version = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("version = " + _version + ", "); - stringBuilder.Append("experiment = " + _experiment + ", "); - stringBuilder.Append("experimenter = " + _experimenter + ", "); - stringBuilder.Append("date = " + _date + ", "); - stringBuilder.Append("root_path = " + _rootPath + ", "); - stringBuilder.Append("session_name = " + _sessionName + ", "); - stringBuilder.Append("subject = " + _subject + ", "); - stringBuilder.Append("experiment_version = " + _experimentVersion + ", "); - stringBuilder.Append("notes = " + _notes + ", "); - stringBuilder.Append("commit_hash = " + _commitHash + ", "); - stringBuilder.Append("allow_dirty_repo = " + _allowDirtyRepo + ", "); - stringBuilder.Append("skip_hardware_validation = " + _skipHardwareValidation); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - /// - /// Serializes a sequence of data model objects into JSON strings. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into JSON strings.")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] - public partial class SerializeToJson - { - - private System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value)); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - } - - - /// - /// Deserializes a sequence of JSON strings into data model objects. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of JSON strings into data model objects.")] - [System.ComponentModel.DefaultPropertyAttribute("Type")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder - { - - public DeserializeFromJson() - { - Type = new Bonsai.Expressions.TypeMapping(); - } - - public Bonsai.Expressions.TypeMapping Type { get; set; } - - public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) - { - var typeMapping = (Bonsai.Expressions.TypeMapping)Type; - var returnType = typeMapping.GetType().GetGenericArguments()[0]; - return System.Linq.Expressions.Expression.Call( - typeof(DeserializeFromJson), - "Process", - new System.Type[] { returnType }, - System.Linq.Enumerable.Single(arguments)); - } - - private static System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.DeserializeObject(value)); - } - } -} \ No newline at end of file diff --git a/src/Extensions/AindVideoEncodingBenchmarksTaskLogic.cs b/src/Extensions/AindVideoEncodingBenchmarksTaskLogic.cs deleted file mode 100644 index 1855d0d..0000000 --- a/src/Extensions/AindVideoEncodingBenchmarksTaskLogic.cs +++ /dev/null @@ -1,325 +0,0 @@ -//---------------------- -// -// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) -// -//---------------------- - - -namespace AindVideoEncodingBenchmarksSchemas.TaskLogic -{ - #pragma warning disable // Disable all warnings - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindVideoEncodingBenchmarksTaskParameters - { - - private double? _rngSeed; - - private string _aindBehaviorServicesPkgVersion = "0.10.2"; - - private bool _saveRawVideo = false; - - public AindVideoEncodingBenchmarksTaskParameters() - { - } - - protected AindVideoEncodingBenchmarksTaskParameters(AindVideoEncodingBenchmarksTaskParameters other) - { - _rngSeed = other._rngSeed; - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _saveRawVideo = other._saveRawVideo; - } - - /// - /// Seed of the random number generator - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("rng_seed")] - [System.ComponentModel.DescriptionAttribute("Seed of the random number generator")] - public double? RngSeed - { - get - { - return _rngSeed; - } - set - { - _rngSeed = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion - { - get - { - return _aindBehaviorServicesPkgVersion; - } - set - { - _aindBehaviorServicesPkgVersion = value; - } - } - - /// - /// For each video-writer object, will also save the RAW encoded video to disk. Use at your own risk. - /// - [Newtonsoft.Json.JsonPropertyAttribute("save_raw_video")] - [System.ComponentModel.DescriptionAttribute("For each video-writer object, will also save the RAW encoded video to disk. Use a" + - "t your own risk.")] - public bool SaveRawVideo - { - get - { - return _saveRawVideo; - } - set - { - _saveRawVideo = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindVideoEncodingBenchmarksTaskParameters(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindVideoEncodingBenchmarksTaskParameters(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("rng_seed = " + _rngSeed + ", "); - stringBuilder.Append("aind_behavior_services_pkg_version = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("save_raw_video = " + _saveRawVideo); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindVideoEncodingBenchmarksTaskLogic - { - - private string _name = "AindVideoEncodingBenchmarks"; - - private string _description = ""; - - private AindVideoEncodingBenchmarksTaskParameters _taskParameters = new AindVideoEncodingBenchmarksTaskParameters(); - - private string _version = "0.1.1"; - - private string _stageName; - - public AindVideoEncodingBenchmarksTaskLogic() - { - } - - protected AindVideoEncodingBenchmarksTaskLogic(AindVideoEncodingBenchmarksTaskLogic other) - { - _name = other._name; - _description = other._description; - _taskParameters = other._taskParameters; - _version = other._version; - _stageName = other._stageName; - } - - /// - /// Name of the task logic - /// - [Newtonsoft.Json.JsonPropertyAttribute("name")] - [System.ComponentModel.DescriptionAttribute("Name of the task logic")] - public string Name - { - get - { - return _name; - } - set - { - _name = value; - } - } - - /// - /// Description of the task. - /// - [Newtonsoft.Json.JsonPropertyAttribute("description")] - [System.ComponentModel.DescriptionAttribute("Description of the task.")] - public string Description - { - get - { - return _description; - } - set - { - _description = value; - } - } - - /// - /// Parameters of the task logic - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("task_parameters", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Parameters of the task logic")] - public AindVideoEncodingBenchmarksTaskParameters TaskParameters - { - get - { - return _taskParameters; - } - set - { - _taskParameters = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version - { - get - { - return _version; - } - set - { - _version = value; - } - } - - /// - /// Optional stage name the `Task` object instance represents. - /// - [Newtonsoft.Json.JsonPropertyAttribute("stage_name")] - [System.ComponentModel.DescriptionAttribute("Optional stage name the `Task` object instance represents.")] - public string StageName - { - get - { - return _stageName; - } - set - { - _stageName = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindVideoEncodingBenchmarksTaskLogic(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindVideoEncodingBenchmarksTaskLogic(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("name = " + _name + ", "); - stringBuilder.Append("description = " + _description + ", "); - stringBuilder.Append("task_parameters = " + _taskParameters + ", "); - stringBuilder.Append("version = " + _version + ", "); - stringBuilder.Append("stage_name = " + _stageName); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - /// - /// Serializes a sequence of data model objects into JSON strings. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into JSON strings.")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] - public partial class SerializeToJson - { - - private System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value)); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - } - - - /// - /// Deserializes a sequence of JSON strings into data model objects. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.3.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of JSON strings into data model objects.")] - [System.ComponentModel.DefaultPropertyAttribute("Type")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder - { - - public DeserializeFromJson() - { - Type = new Bonsai.Expressions.TypeMapping(); - } - - public Bonsai.Expressions.TypeMapping Type { get; set; } - - public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) - { - var typeMapping = (Bonsai.Expressions.TypeMapping)Type; - var returnType = typeMapping.GetType().GetGenericArguments()[0]; - return System.Linq.Expressions.Expression.Call( - typeof(DeserializeFromJson), - "Process", - new System.Type[] { returnType }, - System.Linq.Enumerable.Single(arguments)); - } - - private static System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.DeserializeObject(value)); - } - } -} \ No newline at end of file diff --git a/src/Extensions/TriggeredCamerasLogger.bonsai b/src/Extensions/TriggeredCamerasLogger.bonsai index ac2c41a..dc1fcca 100644 --- a/src/Extensions/TriggeredCamerasLogger.bonsai +++ b/src/Extensions/TriggeredCamerasLogger.bonsai @@ -2,7 +2,7 @@ diff --git a/src/aind_behavior_just_frames/__init__.py b/src/aind_behavior_just_frames/__init__.py new file mode 100644 index 0000000..98cffdf --- /dev/null +++ b/src/aind_behavior_just_frames/__init__.py @@ -0,0 +1,30 @@ +import re +from importlib.metadata import PackageNotFoundError, version + + +def pep440_to_semver(ver: str) -> str: + """ + Convert a PEP 440 version to a SemVer-compatible string. + + Examples: + 1.2.3rc2 -> 1.2.3-rc2 + 1.2.3a1 -> 1.2.3-a1 + 1.2.3b1 -> 1.2.3-b1 + 1.2.3.dev4 -> 1.2.3-dev4 + 1.2.3.post1 -> 1.2.3+post1 + """ + # pre-release: a, b, rc -> -aN, -bN, -rcN + ver = re.sub(r"(?<=\d)(a|b|rc)(\d+)", r"-\1\2", ver) + # dev release: .devN -> -devN + ver = re.sub(r"\.dev(\d+)", r"-dev\1", ver) + # post release: .postN -> +postN + ver = re.sub(r"\.post(\d+)", r"+post\1", ver) + return ver + + +try: + __version__ = version(__name__) +except PackageNotFoundError: + __version__ = "0.0.0" + +__semver__ = pep440_to_semver(__version__) diff --git a/src/aind_behavior_just_frames/cli.py b/src/aind_behavior_just_frames/cli.py new file mode 100644 index 0000000..89231fb --- /dev/null +++ b/src/aind_behavior_just_frames/cli.py @@ -0,0 +1,44 @@ +import typing as t + +from pydantic import Field, RootModel +from pydantic_settings import BaseSettings, CliApp, CliSubCommand + +from aind_behavior_just_frames import __semver__, regenerate +from aind_behavior_just_frames.launcher import ClabeCli + + +class VersionCli(RootModel): + root: t.Any + + def cli_cmd(self) -> None: + print(__semver__) + + +class DslRegenerateCli(RootModel): + root: t.Any + + def cli_cmd(self) -> None: + regenerate.main() + + +class VrForagingCli(BaseSettings, cli_prog_name="vr-foraging", cli_kebab_case=True): + version: CliSubCommand[VersionCli] = Field( + description="Print the version of the vr-foraging package.", + ) + regenerate: CliSubCommand[DslRegenerateCli] = Field( + description="Regenerate the vr-foraging dsl dependencies.", + ) + clabe: CliSubCommand[ClabeCli] = Field( + description="Run the Clabe CLI.", + ) + + def cli_cmd(self): + return CliApp().run_subcommand(self) + + +def main(): + CliApp().run(VrForagingCli) + + +if __name__ == "__main__": + main() diff --git a/src/aind_behavior_just_frames/launcher.py b/src/aind_behavior_just_frames/launcher.py new file mode 100644 index 0000000..40a3449 --- /dev/null +++ b/src/aind_behavior_just_frames/launcher.py @@ -0,0 +1,25 @@ +import logging + +from clabe.launcher import Launcher, LauncherCliArgs +from pydantic_settings import CliApp + +logger = logging.getLogger(__name__) + + +def experiment(launcher: Launcher) -> None: + return + + +class ClabeCli(LauncherCliArgs): + def cli_cmd(self): + launcher = Launcher(settings=self) + launcher.run_experiment(experiment) + return None + + +def main() -> None: + CliApp().run(ClabeCli) + + +if __name__ == "__main__": + main() diff --git a/src/aind_behavior_just_frames/regenerate.py b/src/aind_behavior_just_frames/regenerate.py new file mode 100644 index 0000000..d9cdd7c --- /dev/null +++ b/src/aind_behavior_just_frames/regenerate.py @@ -0,0 +1,34 @@ +from pathlib import Path +from typing import Union + +import pydantic +from aind_behavior_services.session import AindBehaviorSessionModel +from aind_behavior_services.utils import BonsaiSgenSerializers, convert_pydantic_to_bonsai + +from aind_behavior_just_frames.rig import AindJustFramesRig + +SCHEMA_ROOT = Path("./src/DataSchemas/") +EXTENSIONS_ROOT = Path("./src/Extensions/") +NAMESPACE_PREFIX = "AindJustFramesSchemas" + + +def main(): + models = [ + AindJustFramesRig, + AindBehaviorSessionModel, + ] + model = pydantic.RootModel[Union[tuple(models)]] + + convert_pydantic_to_bonsai( + model, + model_name="aind_behavior_just_frames", + root_element="Root", + cs_namespace=NAMESPACE_PREFIX, + json_schema_output_dir=SCHEMA_ROOT, + cs_output_dir=EXTENSIONS_ROOT, + cs_serializer=[BonsaiSgenSerializers.JSON], + ) + + +if __name__ == "__main__": + main() diff --git a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/rig.py b/src/aind_behavior_just_frames/rig.py similarity index 50% rename from src/DataSchemas/aind_behavior_video_encoding_benchmarks/rig.py rename to src/aind_behavior_just_frames/rig.py index 7ae23cd..c34fb2f 100644 --- a/src/DataSchemas/aind_behavior_video_encoding_benchmarks/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -1,27 +1,26 @@ -# Import core types -from __future__ import annotations - -# Import core types from typing import Literal, Optional import aind_behavior_services.rig as rig from aind_behavior_services.rig import AindBehaviorRigModel from pydantic import Field -__version__ = "0.2.1" +from . import __semver__ -class AindVideoEncodingBenchmarksRig(AindBehaviorRigModel): - version: Literal[__version__] = __version__ - triggered_camera_controller_0: Optional[rig.CameraController[rig.SpinnakerCamera]] = Field( +class AindJustFramesRig(AindBehaviorRigModel): + version: Literal[__semver__] = __semver__ + triggered_camera_controller_0: Optional[rig.cameras.CameraController[rig.cameras.SpinnakerCamera]] = Field( default=None, description="Camera controller to triggered cameras. Will use Camera0 register as a trigger.", ) - triggered_camera_controller_1: Optional[rig.CameraController[rig.SpinnakerCamera]] = Field( + triggered_camera_controller_1: Optional[rig.cameras.CameraController[rig.cameras.SpinnakerCamera]] = Field( default=None, description="Camera controller to triggered cameras. Will use Camera1 register as a trigger.", ) - harp_behavior: rig.HarpBehavior = Field( + harp_behavior: rig.harp.HarpBehavior = Field( ..., description="Harp behavior board. Will be the source of triggers for the two camera controllers.", ) + harp_white_rabbit: Optional[rig.harp.HarpWhiteRabbit] = Field( + default=None, description="Harp White Rabbit for time synchronization." + ) diff --git a/src/main.bonsai b/src/main.bonsai index cf44557..6b1f6f3 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -1,10 +1,10 @@  diff --git a/tests/test_bonsai.py b/tests/test_bonsai.py index 4cf6029..a060d4b 100644 --- a/tests/test_bonsai.py +++ b/tests/test_bonsai.py @@ -4,14 +4,15 @@ from pathlib import Path from typing import Generic, List, Optional, TypeVar, Union -from aind_behavior_services.session import AindBehaviorSessionModel -from aind_behavior_services.utils import run_bonsai_process -from aind_behavior_video_encoding_benchmarks.rig import AindVideoEncodingBenchmarksRig -from aind_behavior_video_encoding_benchmarks.task_logic import ( +from aind_behavior_just_frames.task_logic import ( AindVideoEncodingBenchmarksTaskLogic, ) +from aind_behavior_services.session import AindBehaviorSessionModel +from aind_behavior_services.utils import run_bonsai_process from pydantic import ValidationError +from aind_behavior_just_frames.rig import AindVideoEncodingBenchmarksRig + sys.path.append(".") from examples import examples # isort:skip # pylint: disable=wrong-import-position from tests import JSON_ROOT # isort:skip # pylint: disable=wrong-import-position diff --git a/uv.lock b/uv.lock index 2332c35..daf53c9 100644 --- a/uv.lock +++ b/uv.lock @@ -1,75 +1,55 @@ version = 1 +revision = 3 requires-python = ">=3.11" resolution-markers = [ - "python_full_version >= '3.12'", + "python_full_version >= '3.14'", + "python_full_version >= '3.12' and python_full_version < '3.14'", "python_full_version < '3.12'", ] [[package]] -name = "aind-behavior-curriculum" -version = "0.0.32" -source = { registry = "https://pypi.org/simple" } -dependencies = [ - { name = "jinja2" }, - { name = "pydantic" }, - { name = "semver" }, -] -sdist = { 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src/main.bonsai | 283 ++++++++++--------- 6 files changed, 257 insertions(+), 210 deletions(-) diff --git a/.gitignore b/.gitignore index a2ce5ef..c490561 100644 --- a/.gitignore +++ b/.gitignore @@ -14,6 +14,7 @@ Bonsai.exe.WebView2 local .venv *.sln +Bonsai/Settings/ # Byte-compiled / optimized / DLL files diff --git a/LICENSE b/LICENSE index 41f6723..df0d99b 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2024 Allen Institute for Neural Dynamics +Copyright (c) 2025 Allen Institute for Neural Dynamics Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/bonsai/Bonsai.config b/bonsai/Bonsai.config index ecabce8..42020c3 100644 --- a/bonsai/Bonsai.config +++ b/bonsai/Bonsai.config @@ -4,30 +4,30 @@ - - - + + + - + - + - - - - - - - + + + + + + + - + - + @@ -35,27 +35,32 @@ - + - + - - - - + + + + + + - + + + + - + - + @@ -65,15 +70,15 @@ - - + + - - + + - - + + @@ -120,63 +125,65 @@ - - - - + + + - + - + - - - - - - - + + + + + + + - + - + - + - + - - - - + + + + - + + + + - + - - - + + + @@ -184,19 +191,21 @@ - - + + - - + + - - + + + + @@ -204,15 +213,24 @@ + + + + + + + + + - - - - - - + + + + + + diff --git a/bonsai/setup.ps1 b/bonsai/setup.ps1 index 7f43d41..890eeda 100644 --- a/bonsai/setup.ps1 +++ b/bonsai/setup.ps1 @@ -1,9 +1,20 @@ +Push-Location $PSScriptRoot if (!(Test-Path "./Bonsai.exe")) { - Invoke-WebRequest "https://github.com/bonsai-rx/bonsai/releases/download/2.8.5/Bonsai.zip" -OutFile "temp.zip" - Move-Item -Path "NuGet.config" "temp.config" + $release = "https://github.com/bonsai-rx/bonsai/releases/latest/download/Bonsai.zip" + $configPath = "./Bonsai.config" + if (Test-Path $configPath) { + [xml]$config = Get-Content $configPath + $bootstrapper = $config.PackageConfiguration.Packages.Package.where{$_.id -eq 'Bonsai'} + if ($bootstrapper) { + $version = $bootstrapper.version + $release = "https://github.com/bonsai-rx/bonsai/releases/download/$version/Bonsai.zip" + } + } + Invoke-WebRequest $release -OutFile "temp.zip" + Move-Item -Path "NuGet.config" "temp.config" -ErrorAction SilentlyContinue Expand-Archive "temp.zip" -DestinationPath "." -Force - Move-Item -Path "temp.config" "NuGet.config" -Force + Move-Item -Path "temp.config" "NuGet.config" -Force -ErrorAction SilentlyContinue Remove-Item -Path "temp.zip" - Remove-Item -Path "Bonsai32.exe" } -& .\Bonsai.exe --no-editor \ No newline at end of file +& .\Bonsai.exe --no-editor +Pop-Location \ No newline at end of file diff --git a/src/Extensions/TriggeredCamerasLogger.bonsai b/src/Extensions/TriggeredCamerasLogger.bonsai index dc1fcca..f924fbb 100644 --- a/src/Extensions/TriggeredCamerasLogger.bonsai +++ b/src/Extensions/TriggeredCamerasLogger.bonsai @@ -1,5 +1,5 @@  - - TaskLogicParameters - - - SaveRawVideo + SaveRawVideo - diff --git a/src/main.bonsai b/src/main.bonsai index 6b1f6f3..d82c534 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -1,18 +1,16 @@  - @@ -48,8 +46,8 @@ RawRigSchema - - + + @@ -59,26 +57,6 @@ RigSchema - - RawTaskLogicSchema - - - - - - - 1 - - - - TaskLogicSchema - - - TaskParameters - - - TaskLogicParameters - @@ -87,11 +65,6 @@ - - - - - @@ -100,8 +73,8 @@ - - ../. + + ../. @@ -129,7 +102,7 @@ CompoundRootPath - + SoftwareEvent @@ -150,7 +123,68 @@ HarpDevices - + + HarpBehavior + + + + RigSchema + + + HarpBehavior.PortName + + + + + + + + COM5 + TriggerHarpReadDump + + + HarpBehaviorEvents + + + + + + Seconds + + + HarpTimestampSource + + + HarpBehaviorEvents + + + + 1 + + + + Write + + PortDI PortDIO AnalogData Camera0 Camera1 + + + + HarpBehaviorCommands + + + + + + + + + + + + + + + StartExperiment @@ -378,6 +412,19 @@ + + + false + + + + + 1 + + + + SaveRawVideo + QualityControl @@ -430,8 +477,8 @@ Repository - - false + + false @@ -462,8 +509,8 @@ - - Repository is not clean! Please discard all local changes. + + Repository is not clean! Please discard all local changes. @@ -503,7 +550,7 @@ - + @@ -550,7 +597,7 @@ - + Modality Behavior @@ -582,11 +629,11 @@ - + LoggingRootPath Behavior - Behavior - Behavior + + @@ -622,9 +669,9 @@ - - - + + + @@ -635,11 +682,11 @@ - + LoggingRootPath Behavior - HarpCommands/Behavior - Behavior + + @@ -681,7 +728,7 @@ - + Modality @@ -708,8 +755,8 @@ Head - - RepositoryStatus + + RepositoryStatus @@ -719,13 +766,13 @@ Repository - - false + + false - - IsRepositoryClean + + IsRepositoryClean @@ -782,7 +829,9 @@ SubjectSchema - + + None + Modality @@ -806,39 +855,13 @@ Config session_output - - TaskLogicSchema - - - - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - Config - tasklogic_output - RigSchema - + + None + Modality @@ -941,30 +964,24 @@ - + - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -981,8 +998,8 @@ - - SoftwareEvent + + SoftwareEvent @@ -995,10 +1012,12 @@ - + - + + None + Modality @@ -1062,7 +1081,7 @@ - + Modality BehaviorVideos @@ -1431,21 +1450,23 @@ - - - - - - - - - - - + + + + + + + + + + + - - + + + + \ No newline at end of file From 5a0fcfd109258b06858e5975cd6425c52f809292 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:14:22 -0700 Subject: [PATCH 04/32] Fix examples --- examples/examples.py | 31 +++++++------------ src/test_deserialization.bonsai | 53 +++++++-------------------------- tests/test_bonsai.py | 15 ++-------- 3 files changed, 25 insertions(+), 74 deletions(-) diff --git a/examples/examples.py b/examples/examples.py index f083223..bedd038 100644 --- a/examples/examples.py +++ b/examples/examples.py @@ -2,13 +2,10 @@ import os import aind_behavior_services.rig as rig -from aind_behavior_just_frames.task_logic import ( - AindVideoEncodingBenchmarksTaskLogic, - AindVideoEncodingBenchmarksTaskParameters, -) + from aind_behavior_services.session import AindBehaviorSessionModel -from aind_behavior_just_frames.rig import AindVideoEncodingBenchmarksRig +from aind_behavior_just_frames.rig import AindJustFramesRig def main(path_seed: str = "./local/{schema}.json"): @@ -24,48 +21,42 @@ def main(path_seed: str = "./local/{schema}.json"): experimenter=["Foo", "Bar"], ) - this_task = AindVideoEncodingBenchmarksTaskLogic( - task_parameters=AindVideoEncodingBenchmarksTaskParameters( - save_raw_video=False, - ) - ) - - video_writer = rig.VideoWriterFfmpeg( + video_writer = rig.cameras.VideoWriterFfmpeg( frame_rate=120, container_extension="mp4", # input and output arguments can be overridden by the user ) - this_rig = AindVideoEncodingBenchmarksRig( + this_rig = AindJustFramesRig( rig_name="this_rig", - triggered_camera_controller_0=rig.CameraController[rig.SpinnakerCamera]( + triggered_camera_controller_0=rig.cameras.CameraController[rig.cameras.SpinnakerCamera]( frame_rate=120, cameras={ - "FaceCamera": rig.SpinnakerCamera( + "FaceCamera": rig.cameras.SpinnakerCamera( serial_number="SerialNumber", binning=1, exposure=5000, gain=0, video_writer=video_writer, - adc_bit_depth=rig.SpinnakerCameraAdcBitDepth.ADC10BIT, + adc_bit_depth=rig.cameras.SpinnakerCameraAdcBitDepth.ADC10BIT, ), - "SideCamera": rig.SpinnakerCamera( + "SideCamera": rig.cameras.SpinnakerCamera( serial_number="SerialNumber", binning=1, exposure=5000, gain=0, video_writer=video_writer, - adc_bit_depth=rig.SpinnakerCameraAdcBitDepth.ADC10BIT, + adc_bit_depth=rig.cameras.SpinnakerCameraAdcBitDepth.ADC10BIT, ), }, ), triggered_camera_controller_1=None, - harp_behavior=rig.HarpBehavior(port_name="COM3"), + harp_behavior=rig.harp.HarpBehavior(port_name="COM3"), ) os.makedirs(os.path.dirname(path_seed), exist_ok=True) - models = [this_session, this_rig, this_task] + models = [this_session, this_rig] for model in models: with open(path_seed.format(schema=model.__class__.__name__), "w", encoding="utf-8") as f: diff --git a/src/test_deserialization.bonsai b/src/test_deserialization.bonsai index ea0d5c9..73caef8 100644 --- a/src/test_deserialization.bonsai +++ b/src/test_deserialization.bonsai @@ -1,10 +1,8 @@  - @@ -40,8 +38,8 @@ RawRigSchema - - + + @@ -51,26 +49,6 @@ RigSchema - - RawTaskLogicSchema - - - - - - - 1 - - - - TaskLogicSchema - - - TaskParameters - - - TaskLogicParameters - @@ -79,11 +57,6 @@ - - - - - @@ -91,19 +64,17 @@ SubjectSchema - - - - TaskLogicSchema - - - + + None + RigSchema - + + None + @@ -115,12 +86,10 @@ - + - + - - \ No newline at end of file diff --git a/tests/test_bonsai.py b/tests/test_bonsai.py index a060d4b..d36ff41 100644 --- a/tests/test_bonsai.py +++ b/tests/test_bonsai.py @@ -4,14 +4,11 @@ from pathlib import Path from typing import Generic, List, Optional, TypeVar, Union -from aind_behavior_just_frames.task_logic import ( - AindVideoEncodingBenchmarksTaskLogic, -) from aind_behavior_services.session import AindBehaviorSessionModel from aind_behavior_services.utils import run_bonsai_process from pydantic import ValidationError -from aind_behavior_just_frames.rig import AindVideoEncodingBenchmarksRig +from aind_behavior_just_frames.rig import AindBehaviorRigModel sys.path.append(".") from examples import examples # isort:skip # pylint: disable=wrong-import-position @@ -20,8 +17,7 @@ TModel = TypeVar( "TModel", bound=Union[ - AindVideoEncodingBenchmarksRig, - AindVideoEncodingBenchmarksTaskLogic, + AindBehaviorRigModel, AindBehaviorSessionModel, ], ) @@ -40,12 +36,7 @@ def test_deserialization(self): TestModel( bonsai_property="RigPath", json_root=JSON_ROOT, - model=AindVideoEncodingBenchmarksRig, - ), - TestModel( - bonsai_property="TaskLogicPath", - json_root=JSON_ROOT, - model=AindVideoEncodingBenchmarksTaskLogic, + model=AindBehaviorRigModel, ), ] From 1827787cb18f7bf63c39fa533efb05cdb55bb2fb Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:15:21 -0700 Subject: [PATCH 05/32] Fix tests --- tests/test_bonsai.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_bonsai.py b/tests/test_bonsai.py index d36ff41..9666a9a 100644 --- a/tests/test_bonsai.py +++ b/tests/test_bonsai.py @@ -8,7 +8,7 @@ from aind_behavior_services.utils import run_bonsai_process from pydantic import ValidationError -from aind_behavior_just_frames.rig import AindBehaviorRigModel +from aind_behavior_just_frames.rig import AindJustFramesRig sys.path.append(".") from examples import examples # isort:skip # pylint: disable=wrong-import-position @@ -17,7 +17,7 @@ TModel = TypeVar( "TModel", bound=Union[ - AindBehaviorRigModel, + AindJustFramesRig, AindBehaviorSessionModel, ], ) @@ -36,7 +36,7 @@ def test_deserialization(self): TestModel( bonsai_property="RigPath", json_root=JSON_ROOT, - model=AindBehaviorRigModel, + model=AindJustFramesRig, ), ] From 9aa229512bf896a5fa5b77faef330fffa620692e Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:20:02 -0700 Subject: [PATCH 06/32] Refactor CICD and docs --- .github/workflows/ci.yml | 24 -- .github/workflows/docs.yml | 24 -- .github/workflows/just-frames-cicd.yml | 325 +++++++++++++++++++++++++ .github/workflows/tag_and_publish.yml | 10 - docs/conf.py | 14 +- docs/json-schemas.rig.rst | 9 - docs/json-schemas.rst | 15 +- docs/json-schemas.session.rst | 9 - docs/json-schemas.task_logic.rst | 9 - scripts/deploy.ps1 | 28 ++- 10 files changed, 358 insertions(+), 109 deletions(-) delete mode 100644 .github/workflows/ci.yml delete mode 100644 .github/workflows/docs.yml create mode 100644 .github/workflows/just-frames-cicd.yml delete mode 100644 .github/workflows/tag_and_publish.yml delete mode 100644 docs/json-schemas.rig.rst delete mode 100644 docs/json-schemas.session.rst delete mode 100644 docs/json-schemas.task_logic.rst diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 5cf85bb..0000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: ci/cd - -on: - workflow_dispatch: - pull_request: - branches: - - main - push: - branches: - - main - -jobs: - - python-linting: - uses: AllenNeuralDynamics/Aind.Behavior.GitHubActions/.github/workflows/python-linting.yml@main - with: - runs-on: ubuntu-latest - - aind-behavior-framework-testing: - uses: AllenNeuralDynamics/Aind.Behavior.GitHubActions/.github/workflows/test-aind-behavior-framework.yml@main - with: - python-version-path: .python-version - run-coverage: false - run-schema: true \ No newline at end of file diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml deleted file mode 100644 index 2439d16..0000000 --- a/.github/workflows/docs.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: Deploy Sphinx documentation to Pages - -on: - workflow_dispatch: - push: - branches: [main] # branch to trigger deployment - -jobs: - pages: - runs-on: ubuntu-20.04 - steps: - - name: Setup Graphviz - uses: ts-graphviz/setup-graphviz@v2.0.2 - - id: deployment - uses: sphinx-notes/pages@v3 - with: - publish: false - python_version: 3.11 - checkout: true - - uses: peaceiris/actions-gh-pages@v3 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ${{ steps.deployment.outputs.artifact }} - force_orphan: true \ No newline at end of file diff --git a/.github/workflows/just-frames-cicd.yml b/.github/workflows/just-frames-cicd.yml new file mode 100644 index 0000000..2597e20 --- /dev/null +++ b/.github/workflows/just-frames-cicd.yml @@ -0,0 +1,325 @@ +name: JustFrames test suite + +on: + workflow_dispatch: + inputs: + bump_type: + description: "Version bump type" + required: false + default: "rc" + type: choice + options: + - rc + - patch + - minor + - major + - stable + pull_request: + push: + branches: + - main + - dev* + - release* + release: + types: [published] + +jobs: + # ╔──────────────────────────╗ + # │ _____ _ │ + # │ |_ _|__ ___| |_ ___ │ + # │ | |/ _ \/ __| __/ __| │ + # │ | | __/\__ \ |_\__ \ │ + # │ |_|\___||___/\__|___/ │ + # │ │ + # ╚──────────────────────────╝ + tests: + runs-on: windows-latest + name: JustFrames unit tests + steps: + - uses: actions/checkout@v5 + + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + + - name: Install python dependencies + run: uv sync + + - name: Run ruff format + run: uv run ruff format + + - name: Run ruff check + run: uv run ruff check + + - name: Run codespell + run: uv run codespell + + - name: Setup .NET Core SDK + uses: actions/setup-dotnet@v4 + with: + dotnet-version: 8.x + + - name: Restore dotnet tools + run: dotnet tool restore + + - name: Setup Bonsai environment + working-directory: ./bonsai + run: ./setup.ps1 + + - name: Run python unit tests + run: uv run python -m unittest + + - name: Regenerate schemas + run: uv run just-frames regenerate + + - name: Check for uncommitted changes + run: | + git config --global core.safecrlf false + git diff --exit-code || (echo "Untracked changes found" && exit 1) + + # ╔───────────────────────────────────────────────────────────╗ + # │ ____ ___ ____ ____ ____ _ │ + # │ / ___|_ _/ ___| _ \ | _ \ ___| | ___ __ _ ___ ___ │ + # │ | | | | | | | | | | |_) / _ \ |/ _ \/ _` / __|/ _ \ │ + # │ | |___ | | |___| |_| | | _ < __/ | __/ (_| \__ \ __/ │ + # │ \____|___\____|____/ |_| \_\___|_|\___|\__,_|___/\___| │ + # │ │ + # ╚───────────────────────────────────────────────────────────╝ + github-rc-release: + needs: tests + runs-on: windows-latest + if: > + github.ref == 'refs/heads/main' && + github.event_name == 'push' && + github.event.head_commit.author.email != 'github-actions[bot]@users.noreply.github.com' + name: Create GitHub pre-release + steps: + - uses: actions/checkout@v5 + with: + fetch-depth: 0 + ref: main + + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + + - name: Bump pre-release by default + # Note: Bumping the rc will fail if the version is not currently an rc + # To solve it, we bump the patch and rc atomically + shell: bash # interop with win/linux for if statement + run: | + if uv version --bump rc --dry-run; then + uv version --bump rc + else + uv version --bump rc --bump patch + fi + + - name: Regenerate schemas + run: uv run just-frames regenerate + + - name: Commit version and schema changes + run: | + git config --global user.name "github-actions[bot]" + git config --global user.email "github-actions[bot]@users.noreply.github.com" + git add . + git commit -m "Bump version and regenerate schemas [skip ci]" || echo "No changes to commit" + git push origin main + + - name: Get version + id: get_version + shell: bash + run: | + version=$(uv version --short) + echo "version=$version" >> $GITHUB_OUTPUT + + - name: Create GitHub Release + uses: softprops/action-gh-release@v2 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + tag_name: v${{ steps.get_version.outputs.version }} + name: v${{ steps.get_version.outputs.version }} + generate_release_notes: true + prerelease: true + body: | + Automated pre-release v${{ steps.get_version.outputs.version }} + + # ╔─────────────────────────────────────────────────────────────────╗ + # │ ____ _ _ _ ____ _ │ + # │ | _ \ _ _| |__ | (_) ___ | _ \ ___| | ___ __ _ ___ ___ │ + # │ | |_) | | | | '_ \| | |/ __| | |_) / _ \ |/ _ \/ _` / __|/ _ \ │ + # │ | __/| |_| | |_) | | | (__ | _ < __/ | __/ (_| \__ \ __/ │ + # │ |_| \__,_|_.__/|_|_|\___| |_| \_\___|_|\___|\__,_|___/\___| │ + # │ │ + # ╚─────────────────────────────────────────────────────────────────╝ + + prepare-public-release: + runs-on: windows-latest + name: Prepare files for public release + needs: tests + if: false + # if: github.event_name == 'workflow_dispatch' + outputs: + version: ${{ steps.get_version.outputs.version }} + is_prerelease: ${{ steps.check_prerelease.outputs.prerelease }} + steps: + - uses: actions/checkout@v5 + with: + fetch-depth: 0 + ref: main + + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + + - name: Get target version + id: get_version + shell: bash + run: | + # Use bump type from input (defaults to rc) + bump_type="${{ github.event.inputs.bump_type || 'rc' }}" + echo "Bumping version with type: $bump_type" + + # Handle version bumping based on type + if [[ "$bump_type" == "rc" ]]; then + # Handle rc bumping logic (same as in github-rc-release) + if uv version --bump rc --dry-run; then + uv version --bump rc + else + uv version --bump rc --bump patch + fi + else + # Handle patch, minor, major, stable + uv version --bump $bump_type + fi + + release_version=$(uv run uv version --short) + echo "version=$release_version" >> $GITHUB_OUTPUT + echo "Release version will be: $release_version" + + - name: Validate version format + run: uv version ${{ steps.get_version.outputs.version }} --dry-run + + - name: Update package version + run: uv version ${{ steps.get_version.outputs.version }} + + - name: Regenerate schemas + run: uv run just-frames regenerate + + - name: Commit version, schema changes and create tag + run: | + git config --global user.name "github-actions[bot]" + git config --global user.email "github-actions[bot]@users.noreply.github.com" + git add . + git commit -m "Release v${{ steps.get_version.outputs.version }} [skip ci]" + git tag -a "v${{ steps.get_version.outputs.version }}" -m "v${{ steps.get_version.outputs.version }}" + git push origin main + git push origin "v${{ steps.get_version.outputs.version }}" + + - name: Determine if prerelease + id: check_prerelease + shell: bash + run: | + version="${{ steps.get_version.outputs.version }}" + if [[ "$version" == *"rc"* ]]; then + echo "prerelease=true" >> $GITHUB_OUTPUT + else + echo "prerelease=false" >> $GITHUB_OUTPUT + fi + + - name: Create GitHub Release + uses: softprops/action-gh-release@v2 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + tag_name: v${{ steps.get_version.outputs.version }} + name: Release v${{ steps.get_version.outputs.version }} + generate_release_notes: true + prerelease: ${{ steps.check_prerelease.outputs.prerelease }} + body: | + Release v${{ steps.get_version.outputs.version }} + + This release was manually triggered. + + publish-to-pypi: + runs-on: windows-latest + name: Publish to PyPI + needs: [tests, prepare-public-release] + if: | + (github.event_name == 'workflow_dispatch') || + (github.event_name == 'release' && + github.event.action == 'published' && + !github.event.release.prerelease && + startsWith(github.ref, 'refs/tags/v')) + steps: + - uses: actions/checkout@v5 + with: + fetch-depth: 0 + ref: ${{ github.event_name == 'workflow_dispatch' && 'main' || github.ref_name }} + + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + + - name: Verify version consistency (for automatic releases) + if: github.event_name == 'release' + shell: bash + run: | + tag_version=$(echo "${{ github.ref_name }}" | sed 's/^v//') + package_version=$(uv run uv version --short) + if [[ "$tag_version" != "$package_version" ]]; then + echo "ERROR: Tag version ($tag_version) doesn't match package version ($package_version)" + exit 1 + fi + echo "✅ Version consistency verified: $tag_version" + + - name: Get current version (for manual releases) + if: github.event_name == 'workflow_dispatch' + shell: bash + run: | + package_version=$(uv run uv version --short) + echo "📦 Publishing version: $package_version" + + - name: Build + run: uv build + + - name: Publish to PyPI + run: uv publish --token ${{ secrets.AIND_PYPI_TOKEN }} + + # ╔─────────────────────────╗ + # │ ____ │ + # │ | _ \ ___ ___ ___ │ + # │ | | | |/ _ \ / __/ __| │ + # │ | |_| | (_) | (__\__ \ │ + # │ |____/ \___/ \___|___/ │ + # │ │ + # ╚─────────────────────────╝ + build-docs: + name: Build and deploy documentation to GitHub Pages + runs-on: ubuntu-latest + needs: github-rc-release + if: github.ref == 'refs/heads/main' && github.event_name == 'push' + steps: + - name: Checkout repository + uses: actions/checkout@v5 + + - name: Install uv + uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + + - name: Setup Graphviz + uses: ts-graphviz/setup-graphviz@v2 + + - name: Install docs group of dependencies + run: uv sync --group docs + + - name: Build Sphinx documentation + run: uv run sphinx-build -b html docs/ _build/html + + - name: Deploy to GitHub Pages + uses: peaceiris/actions-gh-pages@v4 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: _build/html + force_orphan: true diff --git a/.github/workflows/tag_and_publish.yml b/.github/workflows/tag_and_publish.yml deleted file mode 100644 index 1f566ac..0000000 --- a/.github/workflows/tag_and_publish.yml +++ /dev/null @@ -1,10 +0,0 @@ -name: Tag and Publish - -on: - workflow_dispatch: {} - -jobs: - tag-and-publish: - uses : AllenNeuralDynamics/Aind.Behavior.GitHubActions/.github/workflows/python-package-tag-and-publish.yml@main - with: - publish: false \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index bfc27f7..89e17cc 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -15,13 +15,13 @@ sys.path.insert(0, os.path.abspath("../src/DataSchemas")) import aind_behavior_just_frames -SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Behavior.VideoEncodingBenchmarks/tree/main/src/DataSchemas/" +SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Behavior.JustFrames/tree/main/src/DataSchemas/" # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = "AIND Video Encoding Benchmarks project" -copyright = "2024, Allen Institute for Neural Dynamics" +copyright = "2025, Allen Institute for Neural Dynamics" author = "Bruno Cruz" release = aind_behavior_just_frames.__semver__ @@ -79,13 +79,3 @@ def linkcode_resolve(domain, info): filename = info["module"].replace(".", "/") return f"{SOURCE_ROOT}/{filename}.py" - -# -- Class diagram generation - - -def export_model_diagram(model: BaseModel, root: str = "_static") -> None: - diagram = erd.create(model) - diagram.draw(f"{root}/{model.__name__}.svg") - - -_diagram_root = "_static" diff --git a/docs/json-schemas.rig.rst b/docs/json-schemas.rig.rst deleted file mode 100644 index 1c30d42..0000000 --- a/docs/json-schemas.rig.rst +++ /dev/null @@ -1,9 +0,0 @@ -json-schemas.rig ------------------- - -`Download Schema `_ - -.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.VideoEncodingBenchmarks/main/src/DataSchemas/aind_video_encoding_benchmarks_rig.json - :lift_definitions: - :auto_reference: - diff --git a/docs/json-schemas.rst b/docs/json-schemas.rst index 1fdf2c9..836672e 100644 --- a/docs/json-schemas.rst +++ b/docs/json-schemas.rst @@ -1,8 +1,11 @@ -json-schemas +json-schema ------------- -.. toctree:: - :maxdepth: 4 +The following json-schemas are used as the format definition of the input for this task. They are the result of the `Pydantic`` models defined in `src/aind_behavior_just_frames`, and are also used to generate `src/Extensions/AindBehaviorVrForaging.cs` via `Bonsai.Sgen`. - json-schemas.session - json-schemas.rig - json-schemas.task_logic \ No newline at end of file +`Download Schema `_ + +Rig Schema +~~~~~~~~~~~~~~ +.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.VrForaging/main/src/DataSchemas/aind_behavior_just_frames.json#/$defs/AindJustFramesRig + :lift_definitions: + :auto_reference: diff --git a/docs/json-schemas.session.rst b/docs/json-schemas.session.rst deleted file mode 100644 index 9929f86..0000000 --- a/docs/json-schemas.session.rst +++ /dev/null @@ -1,9 +0,0 @@ -json-schemas.session ---------------------- - -`Download Schema `_ - -.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.VideoEncodingBenchmarks/main/src/DataSchemas/aind_behavior_session_model.json - :lift_definitions: - :auto_reference: - diff --git a/docs/json-schemas.task_logic.rst b/docs/json-schemas.task_logic.rst deleted file mode 100644 index 5f03a9d..0000000 --- a/docs/json-schemas.task_logic.rst +++ /dev/null @@ -1,9 +0,0 @@ -json-schemas.task_logic -------------------------- - -`Download Schema `_ - -.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.VideoEncodingBenchmarks/main/src/DataSchemas/aind_video_encoding_benchmarks_task_logic.json - :lift_definitions: - :auto_reference: - diff --git a/scripts/deploy.ps1 b/scripts/deploy.ps1 index 5de218e..9c937f1 100644 --- a/scripts/deploy.ps1 +++ b/scripts/deploy.ps1 @@ -1,15 +1,31 @@ $scriptPath = $MyInvocation.MyCommand.Path $scriptDirectory = Split-Path -Parent $scriptPath Set-Location (Split-Path -Parent $scriptDirectory) -Write-Output "Creating a Python environment..." + +Write-Output "Initializing and updating submodules..." +&git submodule update --init --recursive + +Write-Output "Creating a Python environment..." + +if (-not (Get-Command uv -ErrorAction SilentlyContinue)) { + throw "The 'uv' command was not found. See https://docs.astral.sh/uv/getting-started/installation/ for instructions." +} + if (Test-Path -Path ./.venv) { Remove-Item ./.venv -Recurse -Force } -&python -m venv ./.venv +&uv venv .\.venv\Scripts\Activate.ps1 -Write-Output "Installing python packages..." -&pip install .[launcher] +Write-Output "Synchronizing environment..." +&uv sync --extra launcher Write-Output "Creating a Bonsai environment and installing packages..." -Set-Location "bonsai" -.\setup.ps1 +if (Test-Path -Path "bonsai") { + Set-Location "bonsai" + .\setup.ps1 +} elseif (Test-Path -Path ".bonsai") { + Set-Location ".bonsai" + .\setup.ps1 +} else { + throw "Neither 'bonsai' nor '.bonsai' directory found." +} Set-Location .. \ No newline at end of file From 387e1058689765180c5f3d0b690301721f87d9e6 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:20:20 -0700 Subject: [PATCH 07/32] Linting --- docs/conf.py | 3 --- examples/examples.py | 1 - 2 files changed, 4 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 89e17cc..dd6481c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -7,8 +7,6 @@ import sys import aind_behavior_just_frames.task_logic -import erdantic as erd -from pydantic import BaseModel import aind_behavior_just_frames.rig @@ -78,4 +76,3 @@ def linkcode_resolve(domain, info): return None filename = info["module"].replace(".", "/") return f"{SOURCE_ROOT}/{filename}.py" - diff --git a/examples/examples.py b/examples/examples.py index bedd038..9d10ef8 100644 --- a/examples/examples.py +++ b/examples/examples.py @@ -2,7 +2,6 @@ import os import aind_behavior_services.rig as rig - from aind_behavior_services.session import AindBehaviorSessionModel from aind_behavior_just_frames.rig import AindJustFramesRig From 42e26ee903c76921a4427396199d2abd7dd08d21 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:25:45 -0700 Subject: [PATCH 08/32] Add instructions --- README.md | 12 ++++----- examples/clabe.yml | 10 +++++++ src/aind_behavior_just_frames/launcher.py | 32 ++++++++++++++++++++++- 3 files changed, 47 insertions(+), 7 deletions(-) create mode 100644 examples/clabe.yml diff --git a/README.md b/README.md index cd35173..7f0f8df 100644 --- a/README.md +++ b/README.md @@ -7,22 +7,22 @@ A repository with code for benchmarking online video acquisition/encoding pipeli The easiest way to get started is to clone this repository and run the `deploy.cmd` script. This script will install the necessary dependencies. If you use any python-dependent scripts (e.g. create settings json instances, `regenerate` or `clabe` commands), make sure to run them from an activated environment (`./.venv` directory in the root of the repo). -To run the benchmark workflow you will need a valid set of schemas. Examples of how to generate these can be found in the `./examples/examples.py` file. For the most part, you will only need to generate the rig schema, as the others can be automatically generated using the `clabe` script. In summary: +To run the workflow you will need a valid set of schemas. Examples of how to generate these can be found in the `./examples/examples.py` file. For the most part, you will only need to generate the rig schema, as the others can be automatically generated using the `clabe` script. In summary: -1. Generate the rig and task logic schemas by adapting the script in `./examples/examples.py`. You should make a copy of the example and modify it outside the repository directory, otherwise, any untracked changes / new files in the local repository will flag it as "dirty" and the benchmarks will not be allowed to run. +1. Generate the rig configuration by adapting the script in `./examples/examples.py`. You should make a copy of the example and modify it outside the repository directory, otherwise, any untracked changes / new files in the local repository will flag it as "dirty" and the benchmarks will not be allowed to run. 2. Once the schema is defined in the `.py` file, run the script to generate a valid `.json` file that will be the input to the benchmark workflow. -3. Copy and Paste the generated rig schema (i.e. the `.json` file) to the target config folder (by default `\\allen\aind\scratch\AindBehavior.db\AindVideoEncodingBenchmarks\Rig\\.json`) and the task logic schema to `(...)\AindVideoEncodingBenchmarks\TaskLogic\.json` -4. Run the `clabe`, from the root of the repository, and follow the prompt. +3. Copy and Paste the generated rig schema (i.e. the `.json` file) to the target config folder (by default `\\allen\aind\scratch\AindBehavior.db\AindBehaviorJustFrames\Rig\\.json`)/ +4. Run the `uv run just-frames clabe`, from the root of the repository, and follow the prompt. 5. Once Bonsai is running, double-click the `UserInterface` operator to open the GUI 6. Click Start (Stop) to start (stop) the benchmark workflow. Alternatively, you can run the `main.bonsai` script directly using the following command from the root of the repository: ```cmd -"./bonsai/bonsai.exe" "./src/main.bonsai" -p TaskLogicPath="" -p RigPath="" -p SessionPath="" +"./bonsai/bonsai.exe" "./src/main.bonsai" -p RigPath="" -p SessionPath="" ``` -where ``, ``, and `` are the paths to the task logic, rig, and session schemas, respectively. +where `` and `` are the paths to the rig and session schemas, respectively. diff --git a/examples/clabe.yml b/examples/clabe.yml new file mode 100644 index 0000000..ba39807 --- /dev/null +++ b/examples/clabe.yml @@ -0,0 +1,10 @@ +# In order to get picked up, move this file to the root of the project or ./local + +data_dir: C:/Data +allow_dirty: true + +default_behavior_picker: + config_library_dir: '\\allen\aind\scratch\AindBehavior.db\AindBehaviorJustFrames' + +robocopy: + destination: '\\allen\aind\scratch\data' \ No newline at end of file diff --git a/src/aind_behavior_just_frames/launcher.py b/src/aind_behavior_just_frames/launcher.py index 40a3449..3ede67d 100644 --- a/src/aind_behavior_just_frames/launcher.py +++ b/src/aind_behavior_just_frames/launcher.py @@ -1,12 +1,42 @@ import logging - +from pathlib import Path + +from aind_behavior_services.session import AindBehaviorSessionModel +from clabe import resource_monitor +from clabe.apps import ( + AindBehaviorServicesBonsaiApp, + BonsaiAppSettings, +) +from clabe.data_transfer import robocopy from clabe.launcher import Launcher, LauncherCliArgs +from clabe.pickers import DefaultBehaviorPicker, DefaultBehaviorPickerSettings from pydantic_settings import CliApp +from aind_behavior_just_frames.rig import AindJustFramesRig + logger = logging.getLogger(__name__) def experiment(launcher: Launcher) -> None: + monitor = resource_monitor.ResourceMonitor( + constrains=[ + resource_monitor.available_storage_constraint_factory(launcher.settings.data_dir, 2e11), + ] + ) + + # Validate resources + monitor.run() + + picker = DefaultBehaviorPicker(launcher=launcher, settings=DefaultBehaviorPickerSettings()) + session = picker.pick_session(AindBehaviorSessionModel) + launcher.register_session(session) + rig = picker.pick_rig(AindJustFramesRig) + bonsai_app = AindBehaviorServicesBonsaiApp(BonsaiAppSettings(workflow=Path(r"./src/main.bonsai"))) + bonsai_app.add_app_settings(launcher, rig=rig, session=session) + bonsai_app.get_result(allow_stderr=True) + + launcher.copy_logs() + robocopy.RobocopyService(source=launcher.session_directory, settings=robocopy.RobocopySettings()) return From dbfe7cb0b206872bd9ec5fcdcbc482e9c6cf992b Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:28:40 -0700 Subject: [PATCH 09/32] Refactor readme --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 7f0f8df..11ff035 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# Aind.Behavior.VideoEncodingBenchmarks +# Aind.Behavior.JustFrames -A repository with code for benchmarking online video acquisition/encoding pipelines +A repository with code for a online video acquisition/encoding pipeline ## Getting started From 63f7c7b1d1aab6ac884db7431202c8d1a87002fd Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:43:36 -0700 Subject: [PATCH 10/32] Log WhiteRabbit --- src/Extensions/HarpBehavior.bonsai | 7 +- src/Extensions/HarpBehaviorGetMetadata.bonsai | 540 ++++++++++++++++++ src/main.bonsai | 279 +++++---- 3 files changed, 724 insertions(+), 102 deletions(-) create mode 100644 src/Extensions/HarpBehaviorGetMetadata.bonsai diff --git a/src/Extensions/HarpBehavior.bonsai b/src/Extensions/HarpBehavior.bonsai index 31da56a..a3c3a2e 100644 --- a/src/Extensions/HarpBehavior.bonsai +++ b/src/Extensions/HarpBehavior.bonsai @@ -1,5 +1,5 @@  -COM5 TriggerHarpReadDump + + HarpBehaviorEvents + @@ -31,7 +34,6 @@ HarpTimestampSource - HarpBehaviorEvents @@ -54,7 +56,6 @@ - diff --git a/src/Extensions/HarpBehaviorGetMetadata.bonsai b/src/Extensions/HarpBehaviorGetMetadata.bonsai new file mode 100644 index 0000000..108ca1f --- /dev/null +++ b/src/Extensions/HarpBehaviorGetMetadata.bonsai @@ -0,0 +1,540 @@ + + + + + + + %YAML 1.1 +--- +# yaml-language-server: $schema=https://harp-tech.org/draft-02/schema/device.json +device: Behavior +whoAmI: 1216 +firmwareVersion: "3.2" +hardwareTargets: "1.1" +registers: + DigitalInputState: + address: 32 + access: Event + type: U8 + maskType: DigitalInputs + description: Reflects the state of DI digital lines of each Port + Reserved0: &reserved + address: 33 + type: U8 + access: Read + description: Reserved for future use + visibility: private + OutputSet: &output + address: 34 + type: U16 + access: Write + maskType: DigitalOutputs + description: Set the specified digital output lines. + OutputClear: + <<: *output + address: 35 + description: Clear the specified digital output lines + OutputToggle: + <<: *output + address: 36 + description: Toggle the specified digital output lines + OutputState: + <<: *output + address: 37 + description: Write the state of all digital output lines + PortDIOSet: &portDIO + address: 38 + type: U8 + access: Write + maskType: PortDigitalIOS + description: Set the specified port DIO lines + PortDIOClear: + <<: *portDIO + address: 39 + description: Clear the specified port DIO lines + PortDIOToggle: + <<: *portDIO + address: 40 + description: Toggle the specified port DIO lines + PortDIOState: + <<: *portDIO + address: 41 + description: Write the state of all port DIO lines + PortDIODirection: + <<: *portDIO + address: 42 + description: Specifies which of the port DIO lines are outputs + PortDIOStateEvent: + <<: *portDIO + address: 43 + access: Event + description: Specifies the state of the port DIO lines on a line change + AnalogData: + address: 44 + type: S16 + length: 3 + access: Event + description: Voltage at the ADC input and encoder value on Port 2 + payloadSpec: + AnalogInput0: + offset: 0 + description: The voltage at the output of the ADC channel 0. + Encoder: + offset: 1 + description: The quadrature counter value on Port 2 + AnalogInput1: + offset: 2 + description: The voltage at the output of the ADC channel 1. + OutputPulseEnable: + <<: *output + address: 45 + description: Enables the pulse function for the specified output lines + PulseDOPort0: &pulseDO + address: 46 + type: U16 + access: Write + minValue: 1 + description: Specifies the duration of the output pulse in milliseconds. + PulseDOPort1: + <<: *pulseDO + address: 47 + PulseDOPort2: + <<: *pulseDO + address: 48 + PulseSupplyPort0: + <<: *pulseDO + address: 49 + PulseSupplyPort1: + <<: *pulseDO + address: 50 + PulseSupplyPort2: + <<: *pulseDO + address: 51 + PulseLed0: + <<: *pulseDO + address: 52 + PulseLed1: + <<: *pulseDO + address: 53 + PulseRgb0: + <<: *pulseDO + address: 54 + PulseRgb1: + <<: *pulseDO + address: 55 + PulseDO0: + <<: *pulseDO + address: 56 + PulseDO1: + <<: *pulseDO + address: 57 + PulseDO2: + <<: *pulseDO + address: 58 + PulseDO3: + <<: *pulseDO + address: 59 + PwmFrequencyDO0: &pwmFreq + address: 60 + type: U16 + access: Write + minValue: 1 + description: Specifies the frequency of the PWM at DO0. + PwmFrequencyDO1: + <<: *pwmFreq + address: 61 + description: Specifies the frequency of the PWM at DO1. + PwmFrequencyDO2: + <<: *pwmFreq + address: 62 + description: Specifies the frequency of the PWM at DO2. + PwmFrequencyDO3: + <<: *pwmFreq + address: 63 + description: Specifies the frequency of the PWM at DO3. + PwmDutyCycleDO0: &pwmDutyCycle + address: 64 + type: U8 + access: Write + minValue: 1 + maxValue: 99 + description: Specifies the duty cycle of the PWM at DO0. + PwmDutyCycleDO1: + <<: *pwmDutyCycle + address: 65 + description: Specifies the duty cycle of the PWM at DO1. + PwmDutyCycleDO2: + <<: *pwmDutyCycle + address: 66 + description: Specifies the duty cycle of the PWM at DO2. + PwmDutyCycleDO3: + <<: *pwmDutyCycle + address: 67 + description: Specifies the duty cycle of the PWM at DO3. + PwmStart: &pwmStartStop + address: 68 + type: U8 + access: Write + maskType: PwmOutputs + description: Starts the PWM on the selected output lines. + PwmStop: + <<: *pwmStartStop + address: 69 + description: Stops the PWM on the selected output lines. + RgbAll: + address: 70 + type: &rgbType U8 + length: 6 + access: &rgbAccess Write + description: Specifies the state of all RGB LED channels. + payloadSpec: + Green0: + offset: 0 + description: The intensity of the green channel in the RGB0 LED. + Red0: + offset: 1 + description: The intensity of the red channel in the RGB0 LED. + Blue0: + offset: 2 + description: The intensity of the blue channel in the RGB0 LED. + Green1: + offset: 3 + description: The intensity of the green channel in the RGB1 LED. + Red1: + offset: 4 + description: The intensity of the red channel in the RGB1 LED. + Blue1: + offset: 5 + description: The intensity of the blue channel in the RGB1 LED. + Rgb0: &rgbRegister + address: 71 + type: *rgbType + length: 3 + access: *rgbAccess + description: Specifies the state of the RGB0 LED channels. + interfaceType: RgbPayload + payloadSpec: + Green: + offset: 0 + description: The intensity of the green channel in the RGB LED. + Red: + offset: 1 + description: The intensity of the red channel in the RGB LED. + Blue: + offset: 2 + description: The intensity of the blue channel in the RGB LED. + Rgb1: + <<: *rgbRegister + address: 72 + description: Specifies the state of the RGB1 LED channels. + Led0Current: &ledCurrent + address: 73 + type: U8 + access: Write + minValue: 2 + maxValue: 100 + description: Specifies the configuration of current to drive LED 0. + Led1Current: + <<: *ledCurrent + address: 74 + description: Specifies the configuration of current to drive LED 1. + Led0MaxCurrent: &ledMaxCurrent + address: 75 + type: U8 + access: Write + minValue: 5 + maxValue: 100 + description: Specifies the configuration of current to drive LED 0. + Led1MaxCurrent: + <<: *ledMaxCurrent + address: 76 + description: Specifies the configuration of current to drive LED 1. + EventEnable: + address: 77 + type: U8 + access: Write + maskType: Events + description: Specifies the active events in the device. + StartCameras: &cameraControl + address: 78 + type: U8 + access: Write + maskType: CameraOutputs + description: Specifies the camera outputs to enable in the device. + StopCameras: + <<: *cameraControl + access: [Write, Event] + address: 79 + description: Specifies the camera outputs to disable in the device. An event will be issued when the trigger signal is actually stopped being generated. + EnableServos: &servoControl + address: 80 + type: U8 + access: Write + maskType: ServoOutputs + description: Specifies the servo outputs to enable in the device. + DisableServos: + <<: *servoControl + address: 81 + description: Specifies the servo outputs to disable in the device. + EnableEncoders: + address: 82 + type: U8 + access: Write + maskType: EncoderInputs + description: Specifies the port quadrature counters to enable in the device. + EncoderMode: + address: 83 + type: U8 + access: Write + maskType: EncoderModeConfig + description: Configures the operation mode of the quadrature encoders. + Reserved2: + <<: *reserved + address: 84 + Reserved3: + <<: *reserved + address: 85 + Reserved4: + <<: *reserved + address: 86 + Reserved5: + <<: *reserved + address: 87 + Reserved6: + <<: *reserved + address: 88 + Reserved7: + <<: *reserved + address: 89 + Reserved8: + <<: *reserved + address: 90 + Reserved9: + <<: *reserved + address: 91 + Camera0Frame: &frameAcquired + address: 92 + type: U8 + access: Event + maskType: FrameAcquired + description: Specifies that a frame was acquired on camera 0. + Camera0Frequency: &cameraFreq + address: 93 + type: U16 + access: Write + minValue: 1 + maxValue: 600 + description: Specifies the trigger frequency for camera 0. + Camera1Frame: + <<: *frameAcquired + address: 94 + description: Specifies that a frame was acquired on camera 1. + Camera1Frequency: + <<: *cameraFreq + address: 95 + description: Specifies the trigger frequency for camera 1. + Reserved10: + <<: *reserved + address: 96 + Reserved11: + <<: *reserved + address: 97 + Reserved12: + <<: *reserved + address: 98 + Reserved13: + <<: *reserved + address: 99 + ServoMotor2Period: &servoPeriod + address: 100 + type: U16 + access: Write + minValue: 2 + maxValue: 65534 + description: Specifies the period of the servo motor in DO2, in microseconds. + ServoMotor2Pulse: &servoPulse + address: 101 + type: U16 + access: Write + minValue: 6 + maxValue: 65530 + description: Specifies the pulse of the servo motor in DO2, in microseconds. + ServoMotor3Period: + <<: *servoPeriod + address: 102 + description: Specifies the period of the servo motor in DO3, in microseconds. + ServoMotor3Pulse: + <<: *servoPulse + address: 103 + description: Specifies the pulse of the servo motor in DO3, in microseconds. + Reserved14: + <<: *reserved + address: 104 + Reserved15: + <<: *reserved + address: 105 + Reserved16: + <<: *reserved + address: 106 + Reserved17: + <<: *reserved + address: 107 + EncoderReset: + address: 108 + type: U8 + access: Write + maskType: EncoderInputs + description: Reset the counter of the specified encoders to zero. + Reserved18: + <<: *reserved + address: 109 + EnableSerialTimestamp: + address: 110 + type: U8 + access: Write + description: Enables the timestamp for serial TX. + MimicPort0IR: &mimic + address: 111 + type: U8 + access: Write + maskType: MimicOutput + description: Specifies the digital output to mimic the Port 0 IR state. + MimicPort1IR: + <<: *mimic + address: 112 + description: Specifies the digital output to mimic the Port 1 IR state. + MimicPort2IR: + <<: *mimic + address: 113 + description: Specifies the digital output to mimic the Port 2 IR state. + Reserved20: + <<: *reserved + address: 114 + Reserved21: + <<: *reserved + address: 115 + Reserved22: + <<: *reserved + address: 116 + MimicPort0Valve: + <<: *mimic + address: 117 + description: Specifies the digital output to mimic the Port 0 valve state. + MimicPort1Valve: + <<: *mimic + address: 118 + description: Specifies the digital output to mimic the Port 1 valve state. + MimicPort2Valve: + <<: *mimic + address: 119 + description: Specifies the digital output to mimic the Port 2 valve state. + Reserved23: + <<: *reserved + address: 120 + Reserved24: + <<: *reserved + address: 121 + PokeInputFilter: + address: 122 + type: U8 + access: Write + description: Specifies the low pass filter time value for poke inputs, in ms. +bitMasks: + DigitalInputs: + description: Specifies the state of port digital input lines. + bits: + DIPort0: 0x1 + DIPort1: 0x2 + DIPort2: 0x4 + DI3: 0x8 + DigitalOutputs: + description: Specifies the state of port digital output lines. + bits: + DOPort0: 0x1 + DOPort1: 0x2 + DOPort2: 0x4 + SupplyPort0: 0x8 + SupplyPort1: 0x10 + SupplyPort2: 0x20 + Led0: 0x40 + Led1: 0x80 + Rgb0: 0x100 + Rgb1: 0x200 + DO0: 0x400 + DO1: 0x800 + DO2: 0x1000 + DO3: 0x2000 + PortDigitalIOS: + description: Specifies the state of the port DIO lines. + bits: + DIO0: 0x1 + DIO1: 0x2 + DIO2: 0x4 + PwmOutputs: + description: Specifies the state of PWM output lines. + bits: + PwmDO0: 0x1 + PwmDO1: 0x2 + PwmDO2: 0x4 + PwmDO3: 0x8 + Events: + description: Specifies the active events in the device. + bits: + PortDI: 0x1 + PortDIO: 0x2 + AnalogData: 0x4 + Camera0: 0x8 + Camera1: 0x10 + CameraOutputs: + description: Specifies camera output enable bits. + bits: + CameraOutput0: 0x1 + CameraOutput1: 0x2 + ServoOutputs: + description: Specifies servo output enable bits. + bits: + ServoOutput2: 0x4 + ServoOutput3: 0x8 + EncoderInputs: + description: Specifies quadrature counter enable bits. + bits: + EncoderPort2: 0x4 + FrameAcquired: + description: Specifies that camera frame was acquired. + bits: + FrameAcquired: 0x1 +groupMasks: + MimicOutput: + description: Specifies the target IO on which to mimic the specified register. + values: + None: 0 + DIO0: 1 + DIO1: 2 + DIO2: 3 + DO0: 4 + DO1: 5 + DO2: 6 + DO3: 7 + EncoderModeConfig: + description: Specifies the type of reading made from the quadrature encoder. + values: + Position: 0 + Displacement: 1 + + + + + 1 + + + + + + + + + + \ No newline at end of file diff --git a/src/main.bonsai b/src/main.bonsai index d82c534..9fbabdc 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -10,8 +10,10 @@ xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:p4="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" xmlns:sys="clr-namespace:System;assembly=mscorlib" - xmlns:p5="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" + xmlns:p5="clr-namespace:AllenNeuralDynamics.WhiteRabbit;assembly=AllenNeuralDynamics.WhiteRabbit" + xmlns:p6="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui" + xmlns:ui="clr-namespace:Bonsai.Design;assembly=Bonsai.Design" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -123,77 +125,52 @@ HarpDevices - - HarpBehavior - - - - RigSchema - - - HarpBehavior.PortName - - - - - - - - COM5 - TriggerHarpReadDump - - - HarpBehaviorEvents - - - - - - Seconds - - - HarpTimestampSource - - - HarpBehaviorEvents - - - - 1 - - - - Write - - PortDI PortDIO AnalogData Camera0 Camera1 - - - - HarpBehaviorCommands - - - - - - - - - - - - - - - + StartExperiment TriggerHarpReadDump + + RigSchema + + + HarpWhiteRabbit + + + PortName + + + + + + + + COMx + TriggerHarpReadDump + + + RigSchema + + + HarpWhiteRabbit + + + + + + + + + + + + + @@ -629,17 +606,67 @@ - - LoggingRootPath + + + + + + + + + Behavior + Behavior + + + HarpWhiteRabbitEvents + + + + + + + + + + + Modality + + + + + + + + Behavior - - + ClockGenerator + + + RigSchema + + + HarpWhiteRabbit + + + + - + - + + + + + + + + + + + + @@ -669,9 +696,9 @@ - - - + + + @@ -682,11 +709,62 @@ - - LoggingRootPath + + + + + + + + + Behavior + HarpCommands/Behavior + + + HarpWhiteRabbitCommands + + + HarpTimestampSource + + + + + + + + + + + + Modality + + + + + + + + + + + + + + + + Behavior - - + HarpCommands/ClockGenerator + + + RigSchema + + + HarpWhiteRabbit + + + + @@ -695,9 +773,23 @@ - + - + + + + + + + + + + + + + + + @@ -762,30 +854,11 @@ SoftwareEvent - - Repository - - - - false - - - - - IsRepositoryClean - - - - SoftwareEvent - - - - @@ -1039,7 +1112,7 @@ LoggingRootPath - endsession + EndSession @@ -1413,6 +1486,13 @@ true Microsoft Sans Serif, 16pt + + JustFrames + true + + + + EndExperiment @@ -1463,10 +1543,11 @@ - + + \ No newline at end of file From 4ad9d99082fab9795d6f84696a6592f38d6f326a Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 22 Oct 2025 14:52:35 -0700 Subject: [PATCH 11/32] Use saturation visualizer --- .../InstantitateTriggeredCameras.bonsai | 34 ++- ...ameraControllerSaturationVisualizer.bonsai | 220 ++++++++++++++++++ src/main.bonsai | 151 +++++++----- 3 files changed, 340 insertions(+), 65 deletions(-) create mode 100644 src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai diff --git a/src/Extensions/InstantitateTriggeredCameras.bonsai b/src/Extensions/InstantitateTriggeredCameras.bonsai index 466c0d9..775e9b8 100644 --- a/src/Extensions/InstantitateTriggeredCameras.bonsai +++ b/src/Extensions/InstantitateTriggeredCameras.bonsai @@ -1,5 +1,5 @@  - + + + 0 + + + + + 1 + + TriggeredCamerasInitialized @@ -393,6 +403,9 @@ 1 + + + TriggeredCameraController @@ -498,19 +511,22 @@ - - - + + + - - + + - + - - + + + + + diff --git a/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai b/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai new file mode 100644 index 0000000..66e3118 --- /dev/null +++ b/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai @@ -0,0 +1,220 @@ + + + + + + Source1 + + + + + + Source1 + + + CamerasStream + + + + CamerasStream + + + Key + + + + + + true + true + + + + SelectedControllerCamera + + + + + + SelectedControllerCamera + + + + + + GetStream + + + + Source1 + + + + 1 + + + + Camera + + + + + + CamerasStream + + + Camera + + + + + + + + + + + Source1 + + + Key + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Value.Image + + + 5 + 250 + 1 + + + + + + + false + + + + + 1 + + + + CamerasStream + + + + true + + + + + + + + + + + + + ControllerVisualization + true + true + 1 + 2 + + + + Percent + 0.1 + + + Percent + 0.9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/main.bonsai b/src/main.bonsai index 9fbabdc..ad42986 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -402,8 +402,8 @@ SaveRawVideo - - QualityControl + + RigQA @@ -450,46 +450,65 @@ - - Repository - - - - false - - - - - SubjectSchema - - - AllowDirtyRepo - - - - - - AllowDirty? - Item2 ? False : Item1 - - + + IsRepoClean - - Source1 + + Repository + + + + false + + + + + SubjectSchema + + + AllowDirtyRepo + + + + + + AllowDirty? + Item2 ? False : Item1 + + + + + + Source1 + + + + + + + + + + + Repository is not clean! Please discard all local changes. + + + + + + + + + - - - Repository is not clean! Please discard all local changes. - - ControllersInitialized @@ -543,26 +562,41 @@ - - + + - - - - - - - - + + SubjectSchema + + + SkipHardwareValidation + + + + + + + Source1 + + + + + + + + + + + Logging @@ -1413,7 +1447,7 @@ - + @@ -1463,7 +1497,7 @@ - + @@ -1532,22 +1566,27 @@ - + + - - - + + + - - - - - - - + + + + + + + - + + + + + \ No newline at end of file From 7f70b804f4dc5ba1970d392a1b5fb6cb8e15aa63 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Fri, 7 Nov 2025 09:47:08 -0800 Subject: [PATCH 12/32] Split into include workflows --- src/Extensions/Cameras.bonsai | 216 +++++++++++ src/Extensions/HarpDevices.bonsai | 56 +++ src/Extensions/Visualizers.bonsai | 275 ++++++++++++++ src/main.bonsai | 605 ++++-------------------------- 4 files changed, 615 insertions(+), 537 deletions(-) create mode 100644 src/Extensions/Cameras.bonsai create mode 100644 src/Extensions/HarpDevices.bonsai create mode 100644 src/Extensions/Visualizers.bonsai diff --git a/src/Extensions/Cameras.bonsai b/src/Extensions/Cameras.bonsai new file mode 100644 index 0000000..032f8b1 --- /dev/null +++ b/src/Extensions/Cameras.bonsai @@ -0,0 +1,216 @@ + + + + + + ControllersInitialized + + + + CameraController0 + + + + RigSchema + + + TriggeredCameraController0 + + + CameraOutput0 + + + Item2 + Item1 + + + TriggeredCamerasStream0 + + + + RigSchema + + + TriggeredCameraController0 + + + + + + + + + + + + + + + + + + + + + + CameraController1 + + + + RigSchema + + + TriggeredCameraController1 + + + CameraOutput1 + + + Item2 + Item1 + + + TriggeredCamerasStream1 + + + + RigSchema + + + TriggeredCameraController1 + + + + + + + + + + + + + + + + + + + + + + ControllersInitialized + + + StartCameras + None + + + + 1 + + + + + + + Source1 + + + Accumulation,Value + + + + + + + it + + + StartCameras + CameraOutput0 CameraOutput1 + + + + + + + + + + + + + + + + + CameraControllersActive + + + CameraControllersActive + + + Write + + + + HarpBehaviorCommands + + + StartExperiment + + + + PT1S + + + + + + + CameraControllersActive + + + Write + + + + HarpBehaviorCommands + + + EndExperiment + + + + PT1S + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/HarpDevices.bonsai b/src/Extensions/HarpDevices.bonsai new file mode 100644 index 0000000..8f6199e --- /dev/null +++ b/src/Extensions/HarpDevices.bonsai @@ -0,0 +1,56 @@ + + + + + + + StartExperiment + + + TriggerHarpReadDump + + + RigSchema + + + HarpWhiteRabbit + + + PortName + + + + + + + + COMx + TriggerHarpReadDump + + + RigSchema + + + HarpWhiteRabbit + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/Visualizers.bonsai b/src/Extensions/Visualizers.bonsai new file mode 100644 index 0000000..59a3e86 --- /dev/null +++ b/src/Extensions/Visualizers.bonsai @@ -0,0 +1,275 @@ + + + + + + + 0 + + + + ExperimentControlUI + + + + IsExperimentRunning + + + + + + + + + StartButton + true + true + Start! + + + + + + Source1 + + + + 1 + + + + + StartLogging + + + + true + + + + IsExperimentRunning + + + + + + + + + + + + + + + + IsExperimentRunning + + + + + + + + EndButton + true + true + End Session + + + + + + Source1 + + + + EndExperiment + + + + false + + + + IsExperimentRunning + + + + + + + + + + + + + + + true + true + 1 + 2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + + Controller0Visualization + + + + TriggeredCamerasStream0 + + + RigSchema + + + TriggeredCameraController0 + + + !IsNullOrEmpty + it != null ? (it.Cameras.Count > 0) : false + + + + + + Source1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + + Controller1Visualization + + + + TriggeredCamerasStream1 + + + RigSchema + + + TriggeredCameraController1 + + + !IsNullOrEmpty + it != null ? (it.Cameras.Count > 0) : false + + + + + + Source1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + UserInterface + true + true + Microsoft Sans Serif, 16pt + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/main.bonsai b/src/main.bonsai index ad42986..33af66b 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -5,14 +5,13 @@ xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" xmlns:p2="clr-namespace:AllenNeuralDynamics.VersionControl;assembly=AllenNeuralDynamics.VersionControl" xmlns:p3="clr-namespace:AllenNeuralDynamics.AindBehaviorServices.DataTypes;assembly=AllenNeuralDynamics.AindBehaviorServices" - xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior" - xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" + xmlns:p4="clr-namespace:System.Reactive;assembly=System.Reactive.Core" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" - xmlns:p4="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" + xmlns:p5="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" xmlns:sys="clr-namespace:System;assembly=mscorlib" - xmlns:p5="clr-namespace:AllenNeuralDynamics.WhiteRabbit;assembly=AllenNeuralDynamics.WhiteRabbit" - xmlns:p6="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" - xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui" + xmlns:p6="clr-namespace:AllenNeuralDynamics.WhiteRabbit;assembly=AllenNeuralDynamics.WhiteRabbit" + xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" + xmlns:p7="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" xmlns:ui="clr-namespace:Bonsai.Design;assembly=Bonsai.Design" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -107,6 +106,36 @@ SoftwareEvent + + EndExperiment + + + StartLogging + + + StartLogging + + + + PT1S + + + + StartExperiment + + + + false + + + + + 1 + + + + IsExperimentRunning + @@ -114,6 +143,10 @@ + + + + @@ -121,270 +154,8 @@ Hardware - - HarpDevices - - - - - StartExperiment - - - TriggerHarpReadDump - - - RigSchema - - - HarpWhiteRabbit - - - PortName - - - - - - - - COMx - TriggerHarpReadDump - - - RigSchema - - - HarpWhiteRabbit - - - - - - - - - - - - - - - - - - - - - Cameras - - - - ControllersInitialized - - - - CameraController0 - - - - RigSchema - - - TriggeredCameraController0 - - - CameraOutput0 - - - Item2 - Item1 - - - TriggeredCamerasStream0 - - - - RigSchema - - - TriggeredCameraController0 - - - - - - - - - - - - - - - - - - - - - - CameraController1 - - - - RigSchema - - - TriggeredCameraController1 - - - CameraOutput1 - - - Item2 - Item1 - - - TriggeredCamerasStream1 - - - - RigSchema - - - TriggeredCameraController1 - - - - - - - - - - - - - - - - - - - - - - ControllersInitialized - - - StartCameras - None - - - - 1 - - - - - - - Source1 - - - Accumulation,Value - - - - - - - it - - - StartCameras - CameraOutput0 CameraOutput1 - - - - - - - - - - - - - - - - - CameraControllersActive - - - CameraControllersActive - - - Write - - - - HarpBehaviorCommands - - - StartExperiment - - - - PT1S - - - - - - - CameraControllersActive - - - Write - - - - HarpBehaviorCommands - - - EndExperiment - - - - PT1S - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -490,8 +261,8 @@ - - Repository is not clean! Please discard all local changes. + + Repository is not clean! Please discard all local changes. @@ -546,7 +317,7 @@ - + @@ -608,7 +379,7 @@ - + Modality Behavior @@ -655,7 +426,7 @@ HarpWhiteRabbitEvents - + @@ -730,9 +501,9 @@ - - - + + + @@ -764,9 +535,9 @@ - - - + + + @@ -778,7 +549,7 @@ - + @@ -854,7 +625,7 @@ - + Modality @@ -881,8 +652,8 @@ Head - - RepositoryStatus + + RepositoryStatus @@ -1105,8 +876,8 @@ - - SoftwareEvent + + SoftwareEvent @@ -1119,7 +890,7 @@ - + @@ -1188,7 +959,7 @@ - + Modality BehaviorVideos @@ -1285,241 +1056,7 @@ - - ExperimentControlUI - - - - - false - - - - - 1 - - - - IsExperimentRunning - - - IsExperimentRunning - - - - - - - - - StartButton - true - true - Start! - - - - 1 - - - - - StartLogging - - - - true - - - - IsExperimentRunning - - - - IsExperimentRunning - - - - - - - - EndButton - true - true - End Session - - - - true - true - 1 - 2 - - - - - - - - EndExperiment - - - - false - - - - IsExperimentRunning - - - StartLogging - - - - PT1S - - - - StartExperiment - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Controller0Visualization - - - - TriggeredCamerasStream0 - - - RigSchema - - - TriggeredCameraController0 - - - !IsNullOrEmpty - it != null ? (it.Cameras.Count > 0) : false - - - - - - Source1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Controller1Visualization - - - - TriggeredCamerasStream1 - - - RigSchema - - - TriggeredCameraController1 - - - !IsNullOrEmpty - it != null ? (it.Cameras.Count > 0) : false - - - - - - Source1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - UserInterface - true - true - Microsoft Sans Serif, 16pt - + JustFrames true @@ -1535,11 +1072,6 @@ 1 - - - PT2S - - EndRoutine @@ -1560,6 +1092,11 @@ + + + PT2S + + @@ -1577,16 +1114,10 @@ - - + - - - - - - + \ No newline at end of file From b52bbc37c361a60ea26b584a083f97e373527c52 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Fri, 7 Nov 2025 15:27:09 -0800 Subject: [PATCH 13/32] Temp --- bonsai/Bonsai.config | 13 +++ src/main.bonsai | 249 ++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 260 insertions(+), 2 deletions(-) diff --git a/bonsai/Bonsai.config b/bonsai/Bonsai.config index 42020c3..85b7b88 100644 --- a/bonsai/Bonsai.config +++ b/bonsai/Bonsai.config @@ -15,6 +15,7 @@ + @@ -43,6 +44,7 @@ + @@ -61,6 +63,8 @@ + + @@ -78,6 +82,8 @@ + + @@ -119,6 +125,7 @@ + @@ -141,6 +148,7 @@ + @@ -168,6 +176,7 @@ + @@ -184,6 +193,8 @@ + + @@ -203,6 +214,8 @@ + + diff --git a/src/main.bonsai b/src/main.bonsai index 33af66b..d15412a 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -6,11 +6,13 @@ xmlns:p2="clr-namespace:AllenNeuralDynamics.VersionControl;assembly=AllenNeuralDynamics.VersionControl" xmlns:p3="clr-namespace:AllenNeuralDynamics.AindBehaviorServices.DataTypes;assembly=AllenNeuralDynamics.AindBehaviorServices" xmlns:p4="clr-namespace:System.Reactive;assembly=System.Reactive.Core" + xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" + xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior" + xmlns:zmq="clr-namespace:Bonsai.ZeroMQ;assembly=Bonsai.ZeroMQ" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:p5="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" xmlns:sys="clr-namespace:System;assembly=mscorlib" xmlns:p6="clr-namespace:AllenNeuralDynamics.WhiteRabbit;assembly=AllenNeuralDynamics.WhiteRabbit" - xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" xmlns:p7="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" xmlns:ui="clr-namespace:Bonsai.Design;assembly=Bonsai.Design" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -154,7 +156,250 @@ Hardware - + + HarpDevices + + + + HarpBehaviorCommands + + + todo + + + + + 0 + + + + BehaviorBoard + + + + HarpBehaviorCommands + + + internalPub + + + RigSchema + + + HarpBehavior.PortName + + + + + + + + + Active + On + false + On + Enabled + false + COM5 + + + + + internalPub + + + MessageBytes + + + + tcp://localhost:5557 + + + + + + + + + + + + + + + + + todo + + + + + 0 + + + + ZeroMQBehaviorBoard + + + + + tcp://localhost:5557 + + + + Last.Buffer + + + + + + + + + + + + + + + + + + + 1 + + + + + + + HarpBehaviorEvents + + + HarpBehaviorEvents + + + + + + Seconds + + + HarpTimestampSource + + + BehaviorBoard + + + + + + + TriggerHarpReadDump + + + Write + + Active + true + false + On + On + Enabled + + + + HarpBehaviorCommands + + + HarpBehaviorEvents + + + Write + + PortDI PortDIO AnalogData Camera0 Camera1 + + + + + 1 + + + + HarpBehaviorCommands + + + + + + + + + + + + + + StartExperiment + + + TriggerHarpReadDump + + + RigSchema + + + HarpWhiteRabbit + + + PortName + + + + + + + + COMx + TriggerHarpReadDump + + + RigSchema + + + HarpWhiteRabbit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 010dbbe3859eb19bafd1aa0873dc8dec184a906c Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Fri, 7 Nov 2025 15:59:24 -0800 Subject: [PATCH 14/32] Streamline camera observables --- src/Extensions/CameraQc.bonsai | 776 ++++++++++++++++-------------- src/Extensions/Cameras.bonsai | 135 +++--- src/Extensions/HarpDevices.bonsai | 204 ++++++-- src/main.bonsai | 651 +++++++++++++------------ 4 files changed, 1008 insertions(+), 758 deletions(-) diff --git a/src/Extensions/CameraQc.bonsai b/src/Extensions/CameraQc.bonsai index 31ffc99..b577de8 100644 --- a/src/Extensions/CameraQc.bonsai +++ b/src/Extensions/CameraQc.bonsai @@ -1,5 +1,5 @@  - - - Source1 - - - - - - - - CameraQC + CameraQc - - Source1 - - - - 1 - - - - TriggeredCameraController - - - - - TriggeredCamerasStream0 - - - ThisTriggeredCamerasStream - - - - ThisTriggeredCamerasStream + + + + - - CheckDroppedFrames + + CameraQC - - Source1 - - - - 1 - - - - InputSequence + + - InputSequence + TriggeredCamerasStreams - - + + ThisTriggeredCamerasStream + - - Value.ChunkData + + ThisTriggeredCamerasStream - FrameID - - - - 1 - + Item1 - - - 1 - - - - - 0 - - - + + CheckDroppedFrames Source1 + + + 1 + + + + InputSequence + + + InputSequence + + + + + + Value.ChunkData + + + FrameID + + + + 1 + + + + + 1 + + + + + 0 + + + + + + + Source1 + + + + + + + + + + InputSequence + + + Key + + + + + + Item2 + + + + + + + + + + + + + + - - InputSequence - - - Key - - + - - Item2 + + Camera {0} dropped frame detected during pre-session! + it - - - - - - - - - - - - - - - - - - - - - - - - - Camera {0} dropped frame detected during pre-session! - it - - - - - - it - - - - Dropped frame detected during pre-session! - - - - StartExperiment - - - - - - TriggeredCameraController - - - Cameras - - - - - - - - - CheckCameraSettings - - - - Source1 + + + + + it - - 1 + + Dropped frame detected during pre-session! - - ThisCamera - - ThisCamera + StartExperiment - - Value.Exposure + + - TriggeredCameraController - - - FrameRate - - - Value + TriggeredCamerasStreams - - - - - 0.0007 - + - - ToMilliseconds - int32(it*1000) - - - - - - ((1.0 / Item2) * 1000000) < double(Item1) + Item3 - - + + CheckCameraSettings Source1 + + stream + + + stream + + + Item2 + + + cameraController + + + stream + + + Item2 + + + Cameras + + + stream + + + Item1.Key + + + + + + + + + + + thisCamera + + + thisCamera + + + Exposure + + + cameraController + + + FrameRate + + + Value + + + + + + + 0.0007 + + + + ToMilliseconds + int32(it*1000) + + + + + + ((1.0 / Item2) * 1000000) < double(Item1) + Item3 + + + + + + Source1 + + + + + + + + + + + 1 + + + + stream + + + Item1.Key + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - 1 - + - - ThisCamera + + Camera {0} exposure setting not compatible with requested frame rate! + it - - Key + + + + + it - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Camera {0} exposure setting not compatible with requested frame rate! - it - - - - - - it - - - - Dropped frame detected during pre-session! - - - - TriggeredCameraController - - - FrameRate.HasValue - - - - - - - Source1 - - - - - - - - - - - TriggeredCameraControl must specify a valid FrameRate property! - - - - ThisTriggeredCamerasStream - - - - - - - OnlineQC - - - - Source1 - - - - 1 + + Dropped frame detected during pre-session! - - InputSequence - - InputSequence - - - + TriggeredCamerasStreams - Value.ChunkData - - - Timestamp - - - - 1 - - - - - 1E-09 - + Item2 - Seconds - - - - 1 - - - - - - - - - - - - - - - 0.0005 - + FrameRate.HasValue + @@ -392,123 +335,216 @@ - - TaskPoolScheduler + + TriggeredCameraControl must specify a valid FrameRate property! - - + + ThisTriggeredCamerasStream - - - PT0S - PT10S - + + Item1 - - + + + - - MakeUI + + OnlineQC + + Source1 + + + + 1 + + + + InputSequence + InputSequence + + + - Key + Value.ChunkData - - Camera {0} out-of-alignment qc was triggered. - it + + Timestamp - - - - + + + 1 + + + + + 1E-09 + + + + Seconds + + + + 1 + + + + + + + + + + + + + + + 0.0005 + + + + + + + Source1 + + + + + + + - - - Warning - Exclamation + + TaskPoolScheduler + + + + + + PT0S + PT10S + + + + + + + MakeUI + + + + InputSequence + + + Key + + + Camera {0} out-of-alignment qc was triggered. + it + + + + + + + + + + Warning + Exclamation + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + - - - + + - - - - + + + - - - + + + + + + + + + - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - + \ No newline at end of file diff --git a/src/Extensions/Cameras.bonsai b/src/Extensions/Cameras.bonsai index 032f8b1..06e0f94 100644 --- a/src/Extensions/Cameras.bonsai +++ b/src/Extensions/Cameras.bonsai @@ -3,6 +3,7 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior" + xmlns:p1="clr-namespace:AindJustFramesSchemas;assembly=Extensions" xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -11,15 +12,28 @@ ControllersInitialized - - CameraController0 + + RigSchema + + + TriggeredCameraController0 + + + + CameraOutput0 + + Source1 + + + thisCameraController + - RigSchema + thisCameraController - - TriggeredCameraController0 + + CameraOutput0 @@ -28,44 +42,47 @@ Item2 Item1 - - TriggeredCamerasStream0 - - - RigSchema + thisCameraController - - TriggeredCameraController0 - - - + - - - - - - - - + + + + + + - - CameraController1 + + RigSchema + + + TriggeredCameraController1 + + + + CameraOutput1 + + Source1 + + + thisCameraController + - RigSchema + thisCameraController - - TriggeredCameraController1 + + CameraOutput1 @@ -74,35 +91,35 @@ Item2 Item1 - - TriggeredCamerasStream1 - - - RigSchema + thisCameraController - - TriggeredCameraController1 - - - + - - - - - - - - + + + + + + + + + + + + + + TriggeredCamerasStreams + + ControllersInitialized @@ -196,21 +213,31 @@ - - - + + + + + + - - - + + + - - + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/HarpDevices.bonsai b/src/Extensions/HarpDevices.bonsai index 8f6199e..0b25592 100644 --- a/src/Extensions/HarpDevices.bonsai +++ b/src/Extensions/HarpDevices.bonsai @@ -2,55 +2,203 @@ - - - StartExperiment + + HarpBehaviorCommands - - TriggerHarpReadDump + + todo + - - RigSchema + + + 0 + - - HarpWhiteRabbit + + BehaviorBoard + + + + HarpBehaviorCommands + + + internalPub + + + RigSchema + + + HarpBehavior.PortName + + + + + + + + + Active + On + false + On + Enabled + false + COM5 + + + + + internalPub + + + MessageBytes + + + + tcp://localhost:5557 + + + + + + + + + + + + + + - - PortName + + todo + - - - - + + + 0 + - - COMx - TriggerHarpReadDump + + ZeroMQBehaviorBoard + + + + + tcp://localhost:5557 + + + + Last.Buffer + + + + + + + + + + + + - - RigSchema + + - - HarpWhiteRabbit + + + 1 + - - + + + + HarpBehaviorEvents + + + todo + + + + BehaviorBoardInitialization + + + + + + + TriggerHarpReadDump + + + Write + + Active + true + false + On + On + Enabled + + + + HarpBehaviorCommands + + + HarpBehaviorEvents + + + Write + + PortDI PortDIO AnalogData Camera0 Camera1 + + + + + 1 + + + + HarpBehaviorCommands + + + + + + + + + + + + + + StartExperiment + + + TriggerHarpReadDump - + + - - + + - + + \ No newline at end of file diff --git a/src/main.bonsai b/src/main.bonsai index d15412a..dddf0f7 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -6,14 +6,13 @@ xmlns:p2="clr-namespace:AllenNeuralDynamics.VersionControl;assembly=AllenNeuralDynamics.VersionControl" xmlns:p3="clr-namespace:AllenNeuralDynamics.AindBehaviorServices.DataTypes;assembly=AllenNeuralDynamics.AindBehaviorServices" xmlns:p4="clr-namespace:System.Reactive;assembly=System.Reactive.Core" + xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" + xmlns:p5="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior" xmlns:zmq="clr-namespace:Bonsai.ZeroMQ;assembly=Bonsai.ZeroMQ" - xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" - xmlns:p5="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" xmlns:sys="clr-namespace:System;assembly=mscorlib" - xmlns:p6="clr-namespace:AllenNeuralDynamics.WhiteRabbit;assembly=AllenNeuralDynamics.WhiteRabbit" - xmlns:p7="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" + xmlns:p6="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" xmlns:ui="clr-namespace:Bonsai.Design;assembly=Bonsai.Design" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -138,6 +137,65 @@ IsExperimentRunning + + IsRepoClean + + + + Repository + + + + false + + + + + SubjectSchema + + + AllowDirtyRepo + + + + + + AllowDirty? + Item2 ? False : Item1 + + + + + + Source1 + + + + + + + + + + + Repository is not clean! Please discard all local changes. + + + + + + + + + + + + + + + + + @@ -276,20 +334,12 @@ HarpBehaviorEvents - - HarpBehaviorEvents - - - - - - Seconds - - - HarpTimestampSource + + todo + - BehaviorBoard + BehaviorBoardInitialization @@ -346,34 +396,6 @@ TriggerHarpReadDump - - RigSchema - - - HarpWhiteRabbit - - - PortName - - - - - - - - COMx - TriggerHarpReadDump - - - RigSchema - - - HarpWhiteRabbit - - - - - @@ -386,210 +408,320 @@ - - - - - - - - - - - - - - - - - - false - - - - - 1 - - - - SaveRawVideo - - - RigQA - - - - RigSchema - - - TriggeredCameraController0 - - - TriggeredCamerasStream0 - 0.0007 - 0.0005 - PT10S - - - RigSchema - - - TriggeredCameraController0 - - - - - - - RigSchema - - - TriggeredCameraController1 - - - TriggeredCamerasStream1 - 0.0007 - 0.0005 - PT10S - - - RigSchema - - - TriggeredCameraController1 - - - - - - IsRepoClean + Cameras + + ControllersInitialized + + - Repository + RigSchema - - - false - + + TriggeredCameraController0 + + + + CameraOutput0 + + + + Source1 + + + thisCameraController + + + thisCameraController + + + + + + CameraOutput0 + + + Item2 + Item1 + + + thisCameraController + + + + + + + + + + + + + + + + - - SubjectSchema + RigSchema - AllowDirtyRepo + TriggeredCameraController1 + + + + CameraOutput1 + + + + Source1 + + + thisCameraController + + + thisCameraController + + + + + + CameraOutput1 + + + Item2 + Item1 + + + thisCameraController + + + + + + + + + + + + + + + + - + - - AllowDirty? - Item2 ? False : Item1 + + - + + TriggeredCamerasStreams + + + + ControllersInitialized + + + StartCameras + None + + + + 1 + + + Source1 + + Accumulation,Value + + + + + + + it + + + StartCameras + CameraOutput0 CameraOutput1 + + + + + - - Repository is not clean! Please discard all local changes. + + + + CameraControllersActive + + + CameraControllersActive + + + Write + + + + HarpBehaviorCommands + + + StartExperiment + + + + PT1S - + + + + + CameraControllersActive + + + Write + + + + HarpBehaviorCommands + + + EndExperiment + + + + PT1S + + + + + - - + - + - + + + + + + + + + + + + + + + + + + - ControllersInitialized + HarpBehaviorEvents - - + + - - RigSchema - - - ExpectedControllers - (it.TriggeredCameraController0==null ? 0 : 1)+(it.TriggeredCameraController1==null ? 0 : 1) - - - - - - - - - - Source1 - - - - - - - - - - StartExperiment - - - + + Seconds - - + + HarpTimestampSource - - - + - - - - - - - - - - - - - - - - + + + + + + false + + + + + 1 + + + + SaveRawVideo + + + + ControllersInitialized + + + + + + RigSchema + + + ExpectedControllers + (it.TriggeredCameraController0==null ? 0 : 1)+(it.TriggeredCameraController1==null ? 0 : 1) + + + + + + + + + + Source1 + + + + + + + StartExperiment + + + + + + + SubjectSchema @@ -667,40 +799,6 @@ Behavior Behavior - - HarpWhiteRabbitEvents - - - - - - - - - - - Modality - - - - - - - - - Behavior - ClockGenerator - - - RigSchema - - - HarpWhiteRabbit - - - - - @@ -708,15 +806,6 @@ - - - - - - - - - @@ -746,9 +835,9 @@ - - - + + + @@ -770,52 +859,6 @@ Behavior HarpCommands/Behavior - - HarpWhiteRabbitCommands - - - HarpTimestampSource - - - - - - - - - - - - Modality - - - - - - - - - - - - - - - - - Behavior - HarpCommands/ClockGenerator - - - RigSchema - - - HarpWhiteRabbit - - - - - @@ -828,18 +871,6 @@ - - - - - - - - - - - - @@ -1348,21 +1379,29 @@ - - + - - + + + - - + + + - - + + + + + + + + + \ No newline at end of file From 8a7af95b0832ebba59c46e9b1e5562d770f1f83b Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Fri, 7 Nov 2025 16:20:14 -0800 Subject: [PATCH 15/32] Cleanup code for N camera acquisition --- ...ameraControllerSaturationVisualizer.bonsai | 288 ++++---- src/Extensions/TriggeredCamerasLogger.bonsai | 317 +++------ src/Extensions/Visualizers.bonsai | 342 ++++------ src/main.bonsai | 640 +++--------------- 4 files changed, 441 insertions(+), 1146 deletions(-) diff --git a/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai b/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai index 66e3118..c952fcf 100644 --- a/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai +++ b/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai @@ -16,205 +16,183 @@ Source1 - + + CamerasStream + + + + CamerasStream + + + Key + + + + + + true + true + + + + SelectedControllerCamera + + + + + + SelectedControllerCamera + + + GetStream - + Source1 - - CamerasStream - - - - CamerasStream - - - Key - - - - - true - true - + + 1 + - - SelectedControllerCamera + + Camera - - + + CamerasStream - SelectedControllerCamera + Camera - - + + + + - - GetStream + Source1 - - - 1 - - - - Camera + + Key - + - - CamerasStream - - - Camera - - - - - - - - - - - Source1 - - - Key - - - - - - - - - - - - - - - - - - - + + - + + - - - - - - - - - - Value.Image - - - 5 - 250 - 1 - - - - - - - false - - - - - 1 - - - - CamerasStream - - - - true - - - - - - - - - - ControllerVisualization - true - true - 1 - 2 - - - - Percent - 0.1 - - - Percent - 0.9 - - - - - - + + - + - - - - - - - - - - - - - - - + + + + + + Value.Image + + + 5 + 250 + 1 + + + + + + + false + + + + + 1 + + + + CamerasStream + + + + true + + + + + + + + + + + + + ControllerVisualization + true + true + 1 + 2 + + + + Percent + 0.1 + + + Percent + 0.9 + + + + - + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/TriggeredCamerasLogger.bonsai b/src/Extensions/TriggeredCamerasLogger.bonsai index f924fbb..532cb0e 100644 --- a/src/Extensions/TriggeredCamerasLogger.bonsai +++ b/src/Extensions/TriggeredCamerasLogger.bonsai @@ -10,56 +10,64 @@ Source1 - - - - + TriggeredCamerasLogger Source1 - - - 1 - - - TriggeredCameraController + thisStream + + + thisStream - - + + Item2 + + + thisCameraController - TriggeredCamerasStream0 + thisStream + + + Item1.Key - - TriggeredCamerasStream - + + thisCameraName - TriggeredCameraController + thisCameraController Cameras - - + + thisCameraName + + + + + + + + + + + thisCamera + + + thisCamera - Value.VideoWriter + VideoWriter - - Key - - - - FfmpegWriter @@ -67,72 +75,20 @@ Source1 - - - 1 - - - - This - - - This - - - Item2 - - ThisCameraName + ThisWriter - This + thisStream Item1 - - ThisWriter - - - TriggeredCamerasStream - - - - - - Source1 - - - Key - - - ThisCameraName - - - - - - - - - - - - - - - - - - - 1 - - - ThisCameraName + thisCameraName @@ -191,7 +147,7 @@ - ThisCameraName + thisCameraName @@ -244,63 +200,35 @@ - + - - + + + - + + - - - - - + + + + + - + - + - + - + - - - - - - - - - - - - - TriggeredCameraController - - - Cameras - - - - - - Value.VideoWriter - - - - Key - - - - OpenCvWriter @@ -308,72 +236,20 @@ Source1 - - - 1 - - - This - - - This - - - Item2 - - - ThisCameraName + ThisWriter - This + thisStream Item1 - - ThisWriter - - - TriggeredCamerasStream - - - - - - Source1 - - - Key - - - ThisCameraName - - - - - - - - - - - - - - - - - - - 1 - - - ThisCameraName + thisCameraName @@ -416,7 +292,7 @@ FMP4 - ThisCameraName + thisCameraName @@ -469,75 +345,72 @@ - + - - + + + - + + - - - - + + + + - - - - - - - + + + + + + + - - - - - - - - + + + 1 + + + + + - + - + - - - + - - - + + + + - - + - - - - - + + + - - - + + \ No newline at end of file diff --git a/src/Extensions/Visualizers.bonsai b/src/Extensions/Visualizers.bonsai index 59a3e86..691ba39 100644 --- a/src/Extensions/Visualizers.bonsai +++ b/src/Extensions/Visualizers.bonsai @@ -3,101 +3,128 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui" - xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns="https://bonsai-rx.org/2018/workflow"> - - - 0 - + + Source1 - - ExperimentControlUI + + Visualizers - - IsExperimentRunning - - - - - - - - - StartButton - true - true - Start! + + + 0 + - + + ExperimentControlUI - - Source1 + + IsExperimentRunning - - - 1 - + + + + + - - - StartLogging + + StartButton + true + true + Start! - - - true - + + + + + Source1 + + + + 1 + + + + + StartLogging + + + + true + + + + IsExperimentRunning + + + + + + + + + + + + - + + IsExperimentRunning - - - - - - - - - - - - - - - IsExperimentRunning - - - - - - - - EndButton - true - true - End Session - - - - - - Source1 + + + + - - - EndExperiment + + EndButton + true + true + End Session - - - false - + + + + + Source1 + + + + EndExperiment + + + + false + + + + IsExperimentRunning + + + + + + + + + + + - - IsExperimentRunning + + + true + true + 1 + 2 + + + @@ -107,169 +134,54 @@ + + + + + + + - - - true - true - 1 - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0 - - - - Controller0Visualization - - - - TriggeredCamerasStream0 + + - RigSchema + TriggeredCamerasStreams - TriggeredCameraController0 - - - !IsNullOrEmpty - it != null ? (it.Cameras.Count > 0) : false - - - - - - Source1 - - - - - - - - - - + Item1 - - - - - - - - - - - - - - - - - - - 0 - - - - Controller1Visualization - - - - TriggeredCamerasStream1 + + - - RigSchema - - - TriggeredCameraController1 - - - !IsNullOrEmpty - it != null ? (it.Cameras.Count > 0) : false - - - - - - Source1 - - - - - - - - - - + + UserInterface + true + true + Microsoft Sans Serif, 16pt - - + - + - + - + + - - - - - UserInterface - true - true - Microsoft Sans Serif, 16pt - - - - - - - - - \ No newline at end of file diff --git a/src/main.bonsai b/src/main.bonsai index dddf0f7..f822b28 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -8,9 +8,8 @@ xmlns:p4="clr-namespace:System.Reactive;assembly=System.Reactive.Core" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:p5="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" - xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior" - xmlns:zmq="clr-namespace:Bonsai.ZeroMQ;assembly=Bonsai.ZeroMQ" + xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" xmlns:sys="clr-namespace:System;assembly=mscorlib" xmlns:p6="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" xmlns:ui="clr-namespace:Bonsai.Design;assembly=Bonsai.Design" @@ -104,6 +103,19 @@ CompoundRootPath + + + false + + + + + 1 + + + + SaveRawVideo + SoftwareEvent @@ -203,10 +215,12 @@ - - + + + + @@ -214,514 +228,77 @@ Hardware - - HarpDevices - - - - HarpBehaviorCommands - - - todo - - - - - 0 - - - - BehaviorBoard - - - - HarpBehaviorCommands - - - internalPub - - - RigSchema - - - HarpBehavior.PortName - - - - - - - - - Active - On - false - On - Enabled - false - COM5 - - - - - internalPub - - - MessageBytes - - - - tcp://localhost:5557 - - - - - - - - - - - - - - - - - todo - - - - - 0 - - - - ZeroMQBehaviorBoard - - - - - tcp://localhost:5557 - - - - Last.Buffer - - - - - - - - - - - - - - - - - - - 1 - - - - - - - HarpBehaviorEvents - - - todo - - - - BehaviorBoardInitialization - - - - - - - TriggerHarpReadDump - - - Write - - Active - true - false - On - On - Enabled - - - - HarpBehaviorCommands - - - HarpBehaviorEvents - - - Write - - PortDI PortDIO AnalogData Camera0 Camera1 - - - - - 1 - - - - HarpBehaviorCommands - - - - - - - - - - - - - - StartExperiment - - - TriggerHarpReadDump - - - - - - - - - - - - - - - - + + + + HarpBehaviorEvents - - Cameras + + + + + Seconds + + + HarpTimestampSource + + + ControllersInitialized + + + + + + RigSchema + + + ExpectedControllers + (it.TriggeredCameraController0==null ? 0 : 1)+(it.TriggeredCameraController1==null ? 0 : 1) + + + + + + - - ControllersInitialized - - - - RigSchema - - - TriggeredCameraController0 - - - - CameraOutput0 - - - - Source1 - - - thisCameraController - - - thisCameraController - - - - - - CameraOutput0 - - - Item2 - Item1 - - - thisCameraController - - - - - - - - - - - - - - - - - - - RigSchema - - - TriggeredCameraController1 - - - - CameraOutput1 - - - - Source1 - - - thisCameraController - - - thisCameraController - - - - - - CameraOutput1 - - - Item2 - Item1 - - - thisCameraController - - - - - - - - - - - - - - - - - - - - - - - - - TriggeredCamerasStreams - - - - ControllersInitialized - - - StartCameras - None - - - - 1 - - - - - - - Source1 - - - Accumulation,Value - - - - - - - it - - - StartCameras - CameraOutput0 CameraOutput1 - - - - - - - - - - - - - - - - - CameraControllersActive - - - CameraControllersActive - - - Write - - - - HarpBehaviorCommands - - - StartExperiment - - - - PT1S - - - - - - - CameraControllersActive - - - Write - - - - HarpBehaviorCommands - - - EndExperiment - - - - PT1S - - - - + + Source1 + - - - - - - - - - - - - - - - - - - - - - - - - - + - HarpBehaviorEvents - - - + StartExperiment - - Seconds + + - - HarpTimestampSource + + + + + + + + + + + - - - false - - - - - 1 - - - - SaveRawVideo - - - ControllersInitialized - - - - - - RigSchema - - - ExpectedControllers - (it.TriggeredCameraController0==null ? 0 : 1)+(it.TriggeredCameraController1==null ? 0 : 1) - - - - - - - - - - Source1 - - - - - - - - - - StartExperiment - - - - - - - SubjectSchema @@ -1253,42 +830,11 @@ Modality - RigSchema - - - TriggeredCameraController0 - - - TriggeredCamerasStream0 - - - RigSchema - - - TriggeredCameraController0 - - - - - - - RigSchema - - - TriggeredCameraController1 - - - TriggeredCamerasStream1 - - - RigSchema - - - TriggeredCameraController1 + TriggeredCamerasStreams - + - + @@ -1298,16 +844,6 @@ - - - - - - - - - - @@ -1332,6 +868,11 @@ + + + 0 + + JustFrames @@ -1377,31 +918,22 @@ - + - - - - - - - - + + + + + + + + - + - - - - - - - - - - + \ No newline at end of file From 1d31a089990ef9db774382c047cdc5014f1d45fd Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 12 Nov 2025 10:01:52 -0800 Subject: [PATCH 16/32] Working in progress --- .../aind_behavior_just_frames.json | 245 +- .../aind_physiology_fip_message_protocol.json | 1263 ++++++ src/Extensions.csproj | 3 +- .../AindBehaviorJustFrames.Generated.cs | 689 ++-- ...dPhysiologyFipMessageProtocol.Generated.cs | 3532 +++++++++++++++++ src/Extensions/BuildRegisteredMessage.cs | 51 + src/Extensions/CameraQc.bonsai | 120 +- src/Extensions/HarpDevices.bonsai | 474 ++- src/Extensions/Logging.bonsai | 635 +++ src/Extensions/Main.bonsai | 1217 ++++++ src/Extensions/TryParseRegisteredMessage.cs | 32 + src/Extensions/Visualizers.bonsai | 22 +- .../message_protocol.py | 45 + src/aind_behavior_just_frames/regenerate.py | 12 + src/aind_behavior_just_frames/rig.py | 34 +- src/main.bonsai | 906 +---- src/satellite.bonsai | 85 + 17 files changed, 8020 insertions(+), 1345 deletions(-) create mode 100644 src/DataSchemas/aind_physiology_fip_message_protocol.json create mode 100644 src/Extensions/AindPhysiologyFipMessageProtocol.Generated.cs create mode 100644 src/Extensions/BuildRegisteredMessage.cs create mode 100644 src/Extensions/Logging.bonsai create mode 100644 src/Extensions/Main.bonsai create mode 100644 src/Extensions/TryParseRegisteredMessage.cs create mode 100644 src/aind_behavior_just_frames/message_protocol.py create mode 100644 src/satellite.bonsai diff --git a/src/DataSchemas/aind_behavior_just_frames.json b/src/DataSchemas/aind_behavior_just_frames.json index 785f362..e783611 100644 --- a/src/DataSchemas/aind_behavior_just_frames.json +++ b/src/DataSchemas/aind_behavior_just_frames.json @@ -170,22 +170,29 @@ "$ref": "#/$defs/HarpBehavior", "description": "Harp behavior board. Will be the source of triggers for the two camera controllers." }, - "harp_white_rabbit": { - "default": null, - "description": "Harp White Rabbit for time synchronization.", - "oneOf": [ - { - "$ref": "#/$defs/HarpWhiteRabbit" - }, - { - "type": "null" - } - ] + "satellite_rigs": { + "description": "List of satellite rigs.", + "items": { + "$ref": "#/$defs/SatelliteRig" + }, + "minItems": 1, + "title": "Satellite Rigs", + "type": "array" + }, + "is_satellite": { + "default": false, + "title": "Is Satellite", + "type": "boolean" + }, + "zmq_connection": { + "$ref": "#/$defs/ZmqPubSub", + "description": "ZMQ connection for communication." } }, "required": [ "rig_name", - "harp_behavior" + "harp_behavior", + "zmq_connection" ], "title": "AindJustFramesRig", "type": "object" @@ -269,34 +276,6 @@ "title": "CameraController[SpinnakerCamera]", "type": "object" }, - "ConnectedClockOutput": { - "properties": { - "target_device": { - "default": null, - "description": "Optional device name to provide user additional information", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Target Device" - }, - "output_channel": { - "description": "Output channel", - "minimum": 0, - "title": "Output Channel", - "type": "integer" - } - }, - "required": [ - "output_channel" - ], - "title": "ConnectedClockOutput", - "type": "object" - }, "HarpBehavior": { "properties": { "device_type": { @@ -373,91 +352,6 @@ "title": "HarpBehavior", "type": "object" }, - "HarpWhiteRabbit": { - "properties": { - "device_type": { - "const": "WhiteRabbit", - "default": "WhiteRabbit", - "title": "Device Type", - "type": "string" - }, - "device_name": { - "default": null, - "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, - "calibration": { - "default": null, - "description": "Calibration", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, - "who_am_i": { - "const": 1404, - "default": 1404, - "title": "Who Am I", - "type": "integer" - }, - "serial_number": { - "default": null, - "description": "Device serial number", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Serial Number" - }, - "port_name": { - "description": "Device port name", - "title": "Port Name", - "type": "string" - }, - "connected_clock_outputs": { - "default": [], - "description": "Connected clock outputs", - "items": { - "$ref": "#/$defs/ConnectedClockOutput" - }, - "title": "Connected Clock Outputs", - "type": "array" - } - }, - "required": [ - "port_name" - ], - "title": "HarpWhiteRabbit", - "type": "object" - }, "Rect": { "properties": { "x": { @@ -492,6 +386,72 @@ "title": "Rect", "type": "object" }, + "SatelliteRig": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.12.3", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.5.0-rc0", + "default": "0.5.0-rc0", + "title": "Version", + "type": "string" + }, + "computer_name": { + "description": "Remote Computer name", + "title": "Computer Name", + "type": "string" + }, + "rig_name": { + "description": "Rig name", + "title": "Rig Name", + "type": "string" + }, + "zmq_connection": { + "$ref": "#/$defs/ZmqPubSub", + "description": "ZMQ connection for communication." + }, + "triggered_camera_controller_0": { + "default": null, + "description": "Camera controller to triggered cameras. Will use Camera0 register as a trigger.", + "oneOf": [ + { + "$ref": "#/$defs/CameraController_SpinnakerCamera_" + }, + { + "type": "null" + } + ] + }, + "triggered_camera_controller_1": { + "default": null, + "description": "Camera controller to triggered cameras. Will use Camera1 register as a trigger.", + "oneOf": [ + { + "$ref": "#/$defs/CameraController_SpinnakerCamera_" + }, + { + "type": "null" + } + ] + }, + "is_satellite": { + "default": true, + "title": "Is Satellite", + "type": "boolean" + } + }, + "required": [ + "computer_name", + "rig_name", + "zmq_connection" + ], + "title": "SatelliteRig", + "type": "object" + }, "SpinnakerCamera": { "properties": { "device_type": { @@ -1035,6 +995,41 @@ }, "title": "VideoWriterOpenCv", "type": "object" + }, + "ZmqConnection": { + "properties": { + "connection_string": { + "default": "@tcp://localhost:5556", + "description": "The connection string for the ZMQ socket.", + "title": "Connection String", + "type": "string" + }, + "topic": { + "default": "", + "title": "Topic", + "type": "string" + } + }, + "title": "ZmqConnection", + "type": "object" + }, + "ZmqPubSub": { + "properties": { + "pub": { + "$ref": "#/$defs/ZmqConnection", + "description": "ZMQ Publisher" + }, + "sub": { + "$ref": "#/$defs/ZmqConnection", + "description": "ZMQ Subscriber" + } + }, + "required": [ + "pub", + "sub" + ], + "title": "ZmqPubSub", + "type": "object" } } } \ No newline at end of file diff --git a/src/DataSchemas/aind_physiology_fip_message_protocol.json b/src/DataSchemas/aind_physiology_fip_message_protocol.json new file mode 100644 index 0000000..c2009cf --- /dev/null +++ b/src/DataSchemas/aind_physiology_fip_message_protocol.json @@ -0,0 +1,1263 @@ +{ + "$defs": { + "AindBehaviorSessionModel": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.12.3", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.12.3", + "default": "0.12.3", + "title": "Version", + "type": "string" + }, + "experiment": { + "default": null, + "description": "Name of the experiment", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Experiment" + }, + "experimenter": { + "default": [], + "description": "Name of the experimenter", + "items": { + "type": "string" + }, + "title": "Experimenter", + "type": "array" + }, + "date": { + "description": "Date of the experiment", + "format": "date-time", + "title": "Date", + "type": "string" + }, + "root_path": { + "description": "Root path where data will be logged", + "title": "Root Path", + "type": "string" + }, + "session_name": { + "default": null, + "description": "Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date.", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Session Name" + }, + "subject": { + "description": "Name of the subject", + "title": "Subject", + "type": "string" + }, + "experiment_version": { + "default": "", + "deprecated": true, + "description": "Version of the experiment", + "title": "Experiment Version", + "type": "string" + }, + "notes": { + "default": null, + "description": "Notes about the experiment", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Notes" + }, + "commit_hash": { + "default": null, + "description": "Commit hash of the repository", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Commit Hash" + }, + "allow_dirty_repo": { + "default": false, + "description": "Allow running from a dirty repository", + "title": "Allow Dirty Repo", + "type": "boolean" + }, + "skip_hardware_validation": { + "default": false, + "description": "Skip hardware validation", + "title": "Skip Hardware Validation", + "type": "boolean" + } + }, + "required": [ + "root_path", + "subject" + ], + "title": "AindBehaviorSessionModel", + "type": "object" + }, + "BaseModel": { + "properties": {}, + "title": "BaseModel", + "type": "object" + }, + "CameraController_SpinnakerCamera_": { + "properties": { + "device_type": { + "const": "CameraController", + "default": "CameraController", + "title": "Device Type", + "type": "string" + }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, + "additional_settings": { + "default": null, + "description": "Additional settings", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "calibration": { + "default": null, + "description": "Calibration", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "cameras": { + "additionalProperties": { + "$ref": "#/$defs/SpinnakerCamera" + }, + "description": "Cameras to be instantiated", + "title": "Cameras", + "type": "object" + }, + "frame_rate": { + "default": 30, + "description": "Frame rate of the trigger to all cameras", + "oneOf": [ + { + "minimum": 0, + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Frame Rate" + } + }, + "required": [ + "cameras" + ], + "title": "CameraController[SpinnakerCamera]", + "type": "object" + }, + "HeartbeatPayload": { + "description": "Payload for heartbeat messages indicating system health status.\n\nHeartbeat messages are used to monitor the health and availability\nof system components. They include a status indicator and optional\ncontext information.\n\nAttributes:\n context: Optional additional data about the system state\n status: Current health status of the component\n\nExamples:\n ```python\n heartbeat = HeartbeatPayload(\n status=HeartbeatStatus.OK,\n context={\"cpu_usage\": 0.25, \"memory_usage\": 0.60}\n )\n print(heartbeat.status) # HeartbeatStatus.OK\n\n warning_heartbeat = HeartbeatPayload(\n status=HeartbeatStatus.WARNING,\n context={\"disk_space_low\": True}\n )\n ```", + "properties": { + "payload_type": { + "const": "HeartbeatPayload", + "default": "HeartbeatPayload", + "title": "Payload Type", + "type": "string" + }, + "context": { + "default": null, + "description": "Additional context for the heartbeat message.", + "oneOf": [ + {}, + { + "type": "null" + } + ], + "title": "Context" + }, + "status": { + "$ref": "#/$defs/HeartbeatStatus", + "description": "The status of the heartbeat message" + } + }, + "required": [ + "status" + ], + "title": "HeartbeatPayload", + "type": "object" + }, + "HeartbeatStatus": { + "description": "Enumeration of possible heartbeat status values.\n\nRepresents the health status of a system component,\nwith higher values indicating more severe issues.\n\nExamples:\n ```python\n HeartbeatStatus.OK # \n HeartbeatStatus.CRITICAL > HeartbeatStatus.WARNING # True\n int(HeartbeatStatus.ERROR) # 2\n ```", + "enum": [ + 0, + 1, + 2, + 3 + ], + "title": "HeartbeatStatus", + "type": "integer", + "x-enumNames": [ + "Ok", + "Warning", + "Error", + "Critical" + ] + }, + "LogLevel": { + "description": "Enumeration of log levels for the logging system.\n\nFollows standard Python logging levels with integer values\nthat allow for easy comparison and filtering.\n\nExamples:\n ```python\n LogLevel.ERROR > LogLevel.WARNING # True\n LogLevel.DEBUG.value # 10\n str(LogLevel.INFO) # 'LogLevel.INFO'\n ```", + "enum": [ + 50, + 40, + 30, + 20, + 10, + 0 + ], + "title": "LogLevel", + "type": "integer", + "x-enumNames": [ + "Critical", + "Error", + "Warning", + "Info", + "Debug", + "Notset" + ] + }, + "LogPayload": { + "description": "Payload for log messages containing logging information.\n\nThis payload carries log data including the message content,\nseverity level, optional context, and application version.\n\nAttributes:\n message: The actual log message text\n level: Severity level of the log entry\n context: Optional additional data related to the log\n application_version: Version of the application generating the log\n\nExamples:\n ```python\n log_payload = LogPayload(\n message=\"System startup complete\",\n level=LogLevel.INFO,\n context={\"operator\": \"John Doe\"},\n application_version=\"1.0.0\"\n )\n print(log_payload.level) # LogLevel.INFO\n ```", + "properties": { + "payload_type": { + "const": "LogPayload", + "default": "LogPayload", + "title": "Payload Type", + "type": "string" + }, + "message": { + "description": "The message of the log", + "title": "Message", + "type": "string" + }, + "level": { + "$ref": "#/$defs/LogLevel", + "default": 10, + "description": "The level of the log message" + }, + "context": { + "default": null, + "description": "Additional context for the log message", + "oneOf": [ + {}, + { + "type": "null" + } + ], + "title": "Context" + }, + "application_version": { + "default": null, + "description": "The version of the application", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Application Version" + } + }, + "required": [ + "message" + ], + "title": "LogPayload", + "type": "object" + }, + "Message": { + "$ref": "#/$defs/_Message_Any_", + "title": "Message" + }, + "MessageType": { + "description": "Enumeration of possible message types in the protocol.\n\nExamples:\n ```python\n MessageType.REQUEST # 'request'\n MessageType.REPLY # 'reply'\n MessageType.EVENT # 'event'\n ```", + "enum": [ + "request", + "reply", + "event" + ], + "title": "MessageType", + "type": "string" + }, + "Rect": { + "properties": { + "x": { + "default": 0, + "description": "X coordinate of the top-left corner", + "minimum": 0, + "title": "X", + "type": "integer" + }, + "y": { + "default": 0, + "description": "Y coordinate of the top-left corner", + "minimum": 0, + "title": "Y", + "type": "integer" + }, + "width": { + "default": 0, + "description": "Width of the rectangle", + "minimum": 0, + "title": "Width", + "type": "integer" + }, + "height": { + "default": 0, + "description": "Height of the rectangle", + "minimum": 0, + "title": "Height", + "type": "integer" + } + }, + "title": "Rect", + "type": "object" + }, + "RegisteredMessages": { + "properties": { + "message_type": { + "$ref": "#/$defs/MessageType" + }, + "protocol_version": { + "const": 0, + "default": 0, + "title": "Protocol Version", + "type": "integer" + }, + "timestamp": { + "description": "The timestamp of the message", + "oneOf": [ + { + "format": "date-time", + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Timestamp" + }, + "payload": { + "$ref": "#/$defs/RegisteredPayload", + "description": "The payload of the message" + }, + "process_id": { + "description": "Process that created the message", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Process Id" + }, + "hostname": { + "description": "Hostname that created the message", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Hostname" + }, + "rig_name": { + "description": "Rig name that created the message", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Rig Name" + } + }, + "required": [ + "message_type", + "timestamp", + "payload", + "process_id", + "hostname", + "rig_name" + ], + "title": "RegisteredMessages", + "type": "object" + }, + "RegisteredPayload": { + "discriminator": { + "mapping": { + "HeartbeatPayload": "#/$defs/HeartbeatPayload", + "LogPayload": "#/$defs/LogPayload", + "SatelliteRig": "#/$defs/SatelliteRigPayload", + "SatelliteSession": "#/$defs/SatelliteSessionPayload", + "Start": "#/$defs/StartPayload", + "Stop": "#/$defs/StopPayload" + }, + "propertyName": "payload_type" + }, + "oneOf": [ + { + "$ref": "#/$defs/StartPayload" + }, + { + "$ref": "#/$defs/StopPayload" + }, + { + "$ref": "#/$defs/SatelliteRigPayload" + }, + { + "$ref": "#/$defs/SatelliteSessionPayload" + }, + { + "$ref": "#/$defs/LogPayload" + }, + { + "$ref": "#/$defs/HeartbeatPayload" + } + ], + "title": "RegisteredPayload", + "x-abstract": true + }, + "SatelliteRig": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.12.3", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.5.0-rc0", + "default": "0.5.0-rc0", + "title": "Version", + "type": "string" + }, + "computer_name": { + "description": "Remote Computer name", + "title": "Computer Name", + "type": "string" + }, + "rig_name": { + "description": "Rig name", + "title": "Rig Name", + "type": "string" + }, + "zmq_connection": { + "$ref": "#/$defs/ZmqPubSub", + "description": "ZMQ connection for communication." + }, + "triggered_camera_controller_0": { + "default": null, + "description": "Camera controller to triggered cameras. Will use Camera0 register as a trigger.", + "oneOf": [ + { + "$ref": "#/$defs/CameraController_SpinnakerCamera_" + }, + { + "type": "null" + } + ] + }, + "triggered_camera_controller_1": { + "default": null, + "description": "Camera controller to triggered cameras. Will use Camera1 register as a trigger.", + "oneOf": [ + { + "$ref": "#/$defs/CameraController_SpinnakerCamera_" + }, + { + "type": "null" + } + ] + }, + "is_satellite": { + "default": true, + "title": "Is Satellite", + "type": "boolean" + } + }, + "required": [ + "computer_name", + "rig_name", + "zmq_connection" + ], + "title": "SatelliteRig", + "type": "object" + }, + "SatelliteRigPayload": { + "properties": { + "payload_type": { + "const": "SatelliteRig", + "default": "SatelliteRig", + "title": "Payload Type", + "type": "string" + }, + "rig": { + "$ref": "#/$defs/SatelliteRig", + "description": "Satellite Rig configuration." + } + }, + "required": [ + "rig" + ], + "title": "SatelliteRigPayload", + "type": "object" + }, + "SatelliteSessionPayload": { + "properties": { + "payload_type": { + "const": "SatelliteSession", + "default": "SatelliteSession", + "title": "Payload Type", + "type": "string" + }, + "session": { + "$ref": "#/$defs/AindBehaviorSessionModel", + "description": "Satellite session configuration." + } + }, + "required": [ + "session" + ], + "title": "SatelliteSessionPayload", + "type": "object" + }, + "SpinnakerCamera": { + "properties": { + "device_type": { + "const": "SpinnakerCamera", + "default": "SpinnakerCamera", + "description": "Device type", + "title": "Device Type", + "type": "string" + }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, + "additional_settings": { + "default": null, + "description": "Additional settings", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "calibration": { + "default": null, + "description": "Calibration", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "serial_number": { + "description": "Camera serial number", + "title": "Serial Number", + "type": "string" + }, + "binning": { + "default": 1, + "description": "Binning", + "minimum": 1, + "title": "Binning", + "type": "integer" + }, + "color_processing": { + "default": "Default", + "description": "Color processing", + "enum": [ + "Default", + "NoColorProcessing" + ], + "title": "Color Processing", + "type": "string" + }, + "exposure": { + "default": 1000, + "description": "Exposure time", + "minimum": 100, + "title": "Exposure", + "type": "integer" + }, + "gain": { + "default": 0, + "description": "Gain", + "minimum": 0, + "title": "Gain", + "type": "number" + }, + "gamma": { + "default": null, + "description": "Gamma. If None, will disable gamma correction.", + "oneOf": [ + { + "minimum": 0, + "type": "number" + }, + { + "type": "null" + } + ], + "title": "Gamma" + }, + "adc_bit_depth": { + "default": 0, + "description": "ADC bit depth. If None will be left as default.", + "oneOf": [ + { + "$ref": "#/$defs/SpinnakerCameraAdcBitDepth" + }, + { + "type": "null" + } + ] + }, + "pixel_format": { + "default": 0, + "description": "Pixel format. If None will be left as default.", + "oneOf": [ + { + "$ref": "#/$defs/SpinnakerCameraPixelFormat" + }, + { + "type": "null" + } + ] + }, + "region_of_interest": { + "$ref": "#/$defs/Rect", + "default": { + "x": 0, + "y": 0, + "width": 0, + "height": 0 + }, + "description": "Region of interest" + }, + "video_writer": { + "default": null, + "description": "Video writer. If not provided, no video will be saved.", + "oneOf": [ + { + "$ref": "#/$defs/VideoWriter" + }, + { + "type": "null" + } + ] + } + }, + "required": [ + "serial_number" + ], + "title": "SpinnakerCamera", + "type": "object" + }, + "SpinnakerCameraAdcBitDepth": { + "enum": [ + 0, + 1, + 2 + ], + "title": "SpinnakerCameraAdcBitDepth", + "type": "integer", + "x-enumNames": [ + "Adc8bit", + "Adc10bit", + "Adc12bit" + ] + }, + "SpinnakerCameraPixelFormat": { + "enum": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23, + 24, + 25, + 26, + 27, + 28, + 29, + 30, + 31, + 32, + 33, + 34, + 35, + 36, + 37, + 38, + 39, + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47, + 48, + 49, + 50, + 51, + 52, + 53, + 54, + 55, + 56, + 57, + 58, + 59, + 60, + 61, + 62, + 63, + 64, + 65, + 66, + 67, + 68, + 69, + 70, + 71, + 72, + 73, + 74, + 75, + 76, + 77, + 78, + 79, + 80, + 81, + 82, + 83, + 84, + 85, + 86, + 87, + 88, + 89, + 90, + 91, + 92, + 93, + 94, + 95, + 96, + 97, + 98, + 99, + 100, + 101, + 102, + 103, + 104, + 105, + 106, + 107, + 108, + 109, + 110, + 111, + 112, + 113, + 114, + 115, + 116, + 117, + 118, + 119, + 120, + 121, + 122, + 123, + 124, + 125, + 126, + 127, + 128, + 129, + 130, + 131, + 132, + 133, + 134, + 135, + 136, + 137, + 138, + 139, + 140, + 141, + 142, + 143 + ], + "title": "SpinnakerCameraPixelFormat", + "type": "integer", + "x-enumNames": [ + "Mono8", + "Mono16", + "Rgb8packed", + "Bayergr8", + "Bayerrg8", + "Bayergb8", + "Bayerbg8", + "Bayergr16", + "Bayerrg16", + "Bayergb16", + "Bayerbg16", + "Mono12packed", + "Bayergr12packed", + "Bayerrg12packed", + "Bayergb12packed", + "Bayerbg12packed", + "Yuv411packed", + "Yuv422packed", + "Yuv444packed", + "Mono12p", + "Bayergr12p", + "Bayerrg12p", + "Bayergb12p", + "Bayerbg12p", + "Ycbcr8", + "Ycbcr4228", + "Ycbcr4118", + "Bgr8", + "Bgra8", + "Mono10packed", + "Bayergr10packed", + "Bayerrg10packed", + "Bayergb10packed", + "Bayerbg10packed", + "Mono10p", + "Bayergr10p", + "Bayerrg10p", + "Bayergb10p", + "Bayerbg10p", + "Mono1p", + "Mono2p", + "Mono4p", + "Mono8s", + "Mono10", + "Mono12", + "Mono14", + "Mono16s", + "Mono32f", + "Bayerbg10", + "Bayerbg12", + "Bayergb10", + "Bayergb12", + "Bayergr10", + "Bayergr12", + "Bayerrg10", + "Bayerrg12", + "Rgba8", + "Rgba10", + "Rgba10p", + "Rgba12", + "Rgba12p", + "Rgba14", + "Rgba16", + "Rgb8", + "Rgb8Planar", + "Rgb10", + "Rgb10Planar", + "Rgb10p", + "Rgb10p32", + "Rgb12", + "Rgb12Planar", + "Rgb12p", + "Rgb14", + "Rgb16", + "Rgb16s", + "Rgb32f", + "Rgb16Planar", + "Rgb565p", + "Bgra10", + "Bgra10p", + "Bgra12", + "Bgra12p", + "Bgra14", + "Bgra16", + "Rgba32f", + "Bgr10", + "Bgr10p", + "Bgr12", + "Bgr12p", + "Bgr14", + "Bgr16", + "Bgr565p", + "R8", + "R10", + "R12", + "R16", + "G8", + "G10", + "G12", + "G16", + "B8", + "B10", + "B12", + "B16", + "Coord3dAbc8", + "Coord3dAbc8Planar", + "Coord3dAbc10p", + "Coord3dAbc10pPlanar", + "Coord3dAbc12p", + "Coord3dAbc12pPlanar", + "Coord3dAbc16", + "Coord3dAbc16Planar", + "Coord3dAbc32f", + "Coord3dAbc32fPlanar", + "Coord3dAc8", + "Coord3dAc8Planar", + "Coord3dAc10p", + "Coord3dAc10pPlanar", + "Coord3dAc12p", + "Coord3dAc12pPlanar", + "Coord3dAc16", + "Coord3dAc16Planar", + "Coord3dAc32f", + "Coord3dAc32fPlanar", + "Coord3dA8", + "Coord3dA10p", + "Coord3dA12p", + "Coord3dA16", + "Coord3dA32f", + "Coord3dB8", + "Coord3dB10p", + "Coord3dB12p", + "Coord3dB16", + "Coord3dB32f", + "Coord3dC8", + "Coord3dC10p", + "Coord3dC12p", + "Coord3dC16", + "Coord3dC32f", + "Confidence1", + "Confidence1p", + "Confidence8", + "Confidence16", + "Confidence32f" + ] + }, + "StartPayload": { + "properties": { + "payload_type": { + "const": "Start", + "default": "Start", + "title": "Payload Type", + "type": "string" + } + }, + "title": "StartPayload", + "type": "object" + }, + "StopPayload": { + "properties": { + "payload_type": { + "const": "Stop", + "default": "Stop", + "title": "Payload Type", + "type": "string" + } + }, + "title": "StopPayload", + "type": "object" + }, + "VideoWriter": { + "discriminator": { + "mapping": { + "FFMPEG": "#/$defs/VideoWriterFfmpeg", + "OPENCV": "#/$defs/VideoWriterOpenCv" + }, + "propertyName": "video_writer_type" + }, + "oneOf": [ + { + "$ref": "#/$defs/VideoWriterFfmpeg" + }, + { + "$ref": "#/$defs/VideoWriterOpenCv" + } + ] + }, + "VideoWriterFfmpeg": { + "properties": { + "video_writer_type": { + "const": "FFMPEG", + "default": "FFMPEG", + "title": "Video Writer Type", + "type": "string" + }, + "frame_rate": { + "default": 30, + "description": "Encoding frame rate", + "minimum": 0, + "title": "Frame Rate", + "type": "integer" + }, + "container_extension": { + "default": "mp4", + "description": "Container extension", + "title": "Container Extension", + "type": "string" + }, + "output_arguments": { + "default": "-vf \"scale=out_color_matrix=bt709:out_range=full,format=bgr24,scale=out_range=full\" -c:v h264_nvenc -pix_fmt yuv420p -color_range full -colorspace bt709 -color_trc linear -tune hq -preset p4 -rc vbr -cq 12 -b:v 0M -metadata author=\"Allen Institute for Neural Dynamics\" -maxrate 700M -bufsize 350M", + "description": "Output arguments", + "title": "Output Arguments", + "type": "string" + }, + "input_arguments": { + "default": "-colorspace bt709 -color_primaries bt709 -color_range full -color_trc linear", + "description": "Input arguments", + "title": "Input Arguments", + "type": "string" + } + }, + "title": "VideoWriterFfmpeg", + "type": "object" + }, + "VideoWriterOpenCv": { + "properties": { + "video_writer_type": { + "const": "OPENCV", + "default": "OPENCV", + "title": "Video Writer Type", + "type": "string" + }, + "frame_rate": { + "default": 30, + "description": "Encoding frame rate", + "minimum": 0, + "title": "Frame Rate", + "type": "integer" + }, + "container_extension": { + "default": "avi", + "description": "Container extension", + "title": "Container Extension", + "type": "string" + }, + "four_cc": { + "default": "FMP4", + "description": "Four character code", + "title": "Four Cc", + "type": "string" + } + }, + "title": "VideoWriterOpenCv", + "type": "object" + }, + "ZmqConnection": { + "properties": { + "connection_string": { + "default": "@tcp://localhost:5556", + "description": "The connection string for the ZMQ socket.", + "title": "Connection String", + "type": "string" + }, + "topic": { + "default": "", + "title": "Topic", + "type": "string" + } + }, + "title": "ZmqConnection", + "type": "object" + }, + "ZmqPubSub": { + "properties": { + "pub": { + "$ref": "#/$defs/ZmqConnection", + "description": "ZMQ Publisher" + }, + "sub": { + "$ref": "#/$defs/ZmqConnection", + "description": "ZMQ Subscriber" + } + }, + "required": [ + "pub", + "sub" + ], + "title": "ZmqPubSub", + "type": "object" + }, + "_Message_Any_": { + "properties": { + "message_type": { + "$ref": "#/$defs/MessageType" + }, + "protocol_version": { + "const": 0, + "default": 0, + "title": "Protocol Version", + "type": "integer" + }, + "timestamp": { + "description": "The timestamp of the message", + "oneOf": [ + { + "format": "date-time", + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Timestamp" + }, + "payload": { + "description": "The payload of the message", + "title": "Payload" + }, + "process_id": { + "description": "Process that created the message", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Process Id" + }, + "hostname": { + "description": "Hostname that created the message", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Hostname" + }, + "rig_name": { + "description": "Rig name that created the message", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Rig Name" + } + }, + "required": [ + "message_type", + "timestamp", + "payload", + "process_id", + "hostname", + "rig_name" + ], + "title": "_Message[Any]", + "type": "object" + } + }, + "x-abstract": true +} \ No newline at end of file diff --git a/src/Extensions.csproj b/src/Extensions.csproj index 113a14b..4a83169 100644 --- a/src/Extensions.csproj +++ b/src/Extensions.csproj @@ -6,10 +6,11 @@ - + + \ No newline at end of file diff --git a/src/Extensions/AindBehaviorJustFrames.Generated.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs index 38d9208..22bb3b9 100644 --- a/src/Extensions/AindBehaviorJustFrames.Generated.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -347,13 +347,20 @@ public partial class AindJustFramesRig private HarpBehavior _harpBehavior; - private HarpWhiteRabbit _harpWhiteRabbit; + private System.Collections.Generic.List _satelliteRigs; + + private bool _isSatellite; + + private ZmqPubSub _zmqConnection; public AindJustFramesRig() { _aindBehaviorServicesPkgVersion = "0.12.3"; _version = "0.5.0-rc0"; _harpBehavior = new HarpBehavior(); + _satelliteRigs = new System.Collections.Generic.List(); + _isSatellite = false; + _zmqConnection = new ZmqPubSub(); } protected AindJustFramesRig(AindJustFramesRig other) @@ -365,7 +372,9 @@ protected AindJustFramesRig(AindJustFramesRig other) _triggeredCameraController0 = other._triggeredCameraController0; _triggeredCameraController1 = other._triggeredCameraController1; _harpBehavior = other._harpBehavior; - _harpWhiteRabbit = other._harpWhiteRabbit; + _satelliteRigs = other._satelliteRigs; + _isSatellite = other._isSatellite; + _zmqConnection = other._zmqConnection; } [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] @@ -484,20 +493,51 @@ public HarpBehavior HarpBehavior } /// - /// Harp White Rabbit for time synchronization. + /// List of satellite rigs. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("satellite_rigs")] + [System.ComponentModel.DescriptionAttribute("List of satellite rigs.")] + public System.Collections.Generic.List SatelliteRigs + { + get + { + return _satelliteRigs; + } + set + { + _satelliteRigs = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("is_satellite")] + public bool IsSatellite + { + get + { + return _isSatellite; + } + set + { + _isSatellite = value; + } + } + + /// + /// ZMQ connection for communication. /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_white_rabbit")] - [System.ComponentModel.DescriptionAttribute("Harp White Rabbit for time synchronization.")] - public HarpWhiteRabbit HarpWhiteRabbit + [Newtonsoft.Json.JsonPropertyAttribute("zmq_connection", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] + public ZmqPubSub ZmqConnection { get { - return _harpWhiteRabbit; + return _zmqConnection; } set { - _harpWhiteRabbit = value; + _zmqConnection = value; } } @@ -520,7 +560,9 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); stringBuilder.Append("HarpBehavior = " + _harpBehavior + ", "); - stringBuilder.Append("HarpWhiteRabbit = " + _harpWhiteRabbit); + stringBuilder.Append("SatelliteRigs = " + _satelliteRigs + ", "); + stringBuilder.Append("IsSatellite = " + _isSatellite + ", "); + stringBuilder.Append("ZmqConnection = " + _zmqConnection); return true; } @@ -755,92 +797,6 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class ConnectedClockOutput - { - - private string _targetDevice; - - private int _outputChannel; - - public ConnectedClockOutput() - { - } - - protected ConnectedClockOutput(ConnectedClockOutput other) - { - _targetDevice = other._targetDevice; - _outputChannel = other._outputChannel; - } - - /// - /// Optional device name to provide user additional information - /// - [Newtonsoft.Json.JsonPropertyAttribute("target_device")] - [System.ComponentModel.DescriptionAttribute("Optional device name to provide user additional information")] - public string TargetDevice - { - get - { - return _targetDevice; - } - set - { - _targetDevice = value; - } - } - - /// - /// Output channel - /// - [Newtonsoft.Json.JsonPropertyAttribute("output_channel", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Output channel")] - public int OutputChannel - { - get - { - return _outputChannel; - } - set - { - _outputChannel = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ConnectedClockOutput(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new ConnectedClockOutput(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("TargetDevice = " + _targetDevice + ", "); - stringBuilder.Append("OutputChannel = " + _outputChannel); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] @@ -1031,195 +987,117 @@ public override string ToString() [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class HarpWhiteRabbit + public partial class Rect { - private string _deviceType; - - private string _deviceName; - - private BaseModel _additionalSettings; - - private BaseModel _calibration; - - private int _whoAmI; - - private string _serialNumber; - - private string _portName; - - private System.Collections.Generic.List _connectedClockOutputs; + private int _x; - public HarpWhiteRabbit() - { - _deviceType = "WhiteRabbit"; - _whoAmI = 1404; - _connectedClockOutputs = new System.Collections.Generic.List(); - } + private int _y; - protected HarpWhiteRabbit(HarpWhiteRabbit other) - { - _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; - _calibration = other._calibration; - _whoAmI = other._whoAmI; - _serialNumber = other._serialNumber; - _portName = other._portName; - _connectedClockOutputs = other._connectedClockOutputs; - } + private int _width; - [Newtonsoft.Json.JsonPropertyAttribute("device_type")] - public string DeviceType - { - get - { - return _deviceType; - } - set - { - _deviceType = value; - } - } + private int _height; - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName + public Rect() { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } + _x = 0; + _y = 0; + _width = 0; + _height = 0; } - /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings + protected Rect(Rect other) { - get - { - return _additionalSettings; - } - set - { - _additionalSettings = value; - } + _x = other._x; + _y = other._y; + _width = other._width; + _height = other._height; } /// - /// Calibration + /// X coordinate of the top-left corner /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration")] - public BaseModel Calibration - { - get - { - return _calibration; - } - set - { - _calibration = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("who_am_i")] - public int WhoAmI + [Newtonsoft.Json.JsonPropertyAttribute("x")] + [System.ComponentModel.DescriptionAttribute("X coordinate of the top-left corner")] + public int X { get { - return _whoAmI; + return _x; } set { - _whoAmI = value; + _x = value; } } /// - /// Device serial number + /// Y coordinate of the top-left corner /// - [Newtonsoft.Json.JsonPropertyAttribute("serial_number")] - [System.ComponentModel.DescriptionAttribute("Device serial number")] - public string SerialNumber + [Newtonsoft.Json.JsonPropertyAttribute("y")] + [System.ComponentModel.DescriptionAttribute("Y coordinate of the top-left corner")] + public int Y { get { - return _serialNumber; + return _y; } set { - _serialNumber = value; + _y = value; } } /// - /// Device port name + /// Width of the rectangle /// - [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device port name")] - public string PortName + [Newtonsoft.Json.JsonPropertyAttribute("width")] + [System.ComponentModel.DescriptionAttribute("Width of the rectangle")] + public int Width { get { - return _portName; + return _width; } set { - _portName = value; + _width = value; } } /// - /// Connected clock outputs + /// Height of the rectangle /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("connected_clock_outputs")] - [System.ComponentModel.DescriptionAttribute("Connected clock outputs")] - public System.Collections.Generic.List ConnectedClockOutputs + [Newtonsoft.Json.JsonPropertyAttribute("height")] + [System.ComponentModel.DescriptionAttribute("Height of the rectangle")] + public int Height { get { - return _connectedClockOutputs; + return _height; } set { - _connectedClockOutputs = value; + _height = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpWhiteRabbit(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Rect(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new HarpWhiteRabbit(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new Rect(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("DeviceName = " + _deviceName + ", "); - stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); - stringBuilder.Append("Calibration = " + _calibration + ", "); - stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); - stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); - stringBuilder.Append("PortName = " + _portName + ", "); - stringBuilder.Append("ConnectedClockOutputs = " + _connectedClockOutputs); + stringBuilder.Append("X = " + _x + ", "); + stringBuilder.Append("Y = " + _y + ", "); + stringBuilder.Append("Width = " + _width + ", "); + stringBuilder.Append("Height = " + _height); return true; } @@ -1241,117 +1119,192 @@ public override string ToString() [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class Rect + public partial class SatelliteRig { - private int _x; + private string _aindBehaviorServicesPkgVersion; - private int _y; + private string _version; - private int _width; + private string _computerName; - private int _height; + private string _rigName; - public Rect() + private ZmqPubSub _zmqConnection; + + private CameraControllerSpinnakerCamera _triggeredCameraController0; + + private CameraControllerSpinnakerCamera _triggeredCameraController1; + + private bool _isSatellite; + + public SatelliteRig() { - _x = 0; - _y = 0; - _width = 0; - _height = 0; + _aindBehaviorServicesPkgVersion = "0.12.3"; + _version = "0.5.0-rc0"; + _zmqConnection = new ZmqPubSub(); + _isSatellite = true; } - protected Rect(Rect other) + protected SatelliteRig(SatelliteRig other) { - _x = other._x; - _y = other._y; - _width = other._width; - _height = other._height; + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _computerName = other._computerName; + _rigName = other._rigName; + _zmqConnection = other._zmqConnection; + _triggeredCameraController0 = other._triggeredCameraController0; + _triggeredCameraController1 = other._triggeredCameraController1; + _isSatellite = other._isSatellite; + } + + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version + { + get + { + return _version; + } + set + { + _version = value; + } } /// - /// X coordinate of the top-left corner + /// Remote Computer name /// - [Newtonsoft.Json.JsonPropertyAttribute("x")] - [System.ComponentModel.DescriptionAttribute("X coordinate of the top-left corner")] - public int X + [Newtonsoft.Json.JsonPropertyAttribute("computer_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Remote Computer name")] + public string ComputerName { get { - return _x; + return _computerName; } set { - _x = value; + _computerName = value; } } /// - /// Y coordinate of the top-left corner + /// Rig name /// - [Newtonsoft.Json.JsonPropertyAttribute("y")] - [System.ComponentModel.DescriptionAttribute("Y coordinate of the top-left corner")] - public int Y + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Rig name")] + public string RigName { get { - return _y; + return _rigName; } set { - _y = value; + _rigName = value; } } /// - /// Width of the rectangle + /// ZMQ connection for communication. /// - [Newtonsoft.Json.JsonPropertyAttribute("width")] - [System.ComponentModel.DescriptionAttribute("Width of the rectangle")] - public int Width + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("zmq_connection", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] + public ZmqPubSub ZmqConnection { get { - return _width; + return _zmqConnection; } set { - _width = value; + _zmqConnection = value; } } /// - /// Height of the rectangle + /// Camera controller to triggered cameras. Will use Camera0 register as a trigger. /// - [Newtonsoft.Json.JsonPropertyAttribute("height")] - [System.ComponentModel.DescriptionAttribute("Height of the rectangle")] - public int Height + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_0")] + [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera0 register as a trigger.")] + public CameraControllerSpinnakerCamera TriggeredCameraController0 { get { - return _height; + return _triggeredCameraController0; } set { - _height = value; + _triggeredCameraController0 = value; } } - public System.IObservable Generate() + /// + /// Camera controller to triggered cameras. Will use Camera1 register as a trigger. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_1")] + [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera1 register as a trigger.")] + public CameraControllerSpinnakerCamera TriggeredCameraController1 { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Rect(this))); + get + { + return _triggeredCameraController1; + } + set + { + _triggeredCameraController1 = value; + } } - public System.IObservable Generate(System.IObservable source) + [Newtonsoft.Json.JsonPropertyAttribute("is_satellite")] + public bool IsSatellite { - return System.Reactive.Linq.Observable.Select(source, _ => new Rect(this)); + get + { + return _isSatellite; + } + set + { + _isSatellite = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteRig(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new SatelliteRig(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("X = " + _x + ", "); - stringBuilder.Append("Y = " + _y + ", "); - stringBuilder.Append("Width = " + _width + ", "); - stringBuilder.Append("Height = " + _height); + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("ComputerName = " + _computerName + ", "); + stringBuilder.Append("RigName = " + _rigName + ", "); + stringBuilder.Append("ZmqConnection = " + _zmqConnection + ", "); + stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); + stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); + stringBuilder.Append("IsSatellite = " + _isSatellite); return true; } @@ -2450,6 +2403,180 @@ protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) } + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class ZmqConnection + { + + private string _connectionString; + + private string _topic; + + public ZmqConnection() + { + _connectionString = "@tcp://localhost:5556"; + _topic = ""; + } + + protected ZmqConnection(ZmqConnection other) + { + _connectionString = other._connectionString; + _topic = other._topic; + } + + /// + /// The connection string for the ZMQ socket. + /// + [Newtonsoft.Json.JsonPropertyAttribute("connection_string")] + [System.ComponentModel.DescriptionAttribute("The connection string for the ZMQ socket.")] + public string ConnectionString + { + get + { + return _connectionString; + } + set + { + _connectionString = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("topic")] + public string Topic + { + get + { + return _topic; + } + set + { + _topic = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqConnection(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new ZmqConnection(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("ConnectionString = " + _connectionString + ", "); + stringBuilder.Append("Topic = " + _topic); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class ZmqPubSub + { + + private ZmqConnection _pub; + + private ZmqConnection _sub; + + public ZmqPubSub() + { + _pub = new ZmqConnection(); + _sub = new ZmqConnection(); + } + + protected ZmqPubSub(ZmqPubSub other) + { + _pub = other._pub; + _sub = other._sub; + } + + /// + /// ZMQ Publisher + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("pub", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ Publisher")] + public ZmqConnection Pub + { + get + { + return _pub; + } + set + { + _pub = value; + } + } + + /// + /// ZMQ Subscriber + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("sub", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ Subscriber")] + public ZmqConnection Sub + { + get + { + return _sub; + } + set + { + _sub = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqPubSub(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new ZmqPubSub(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Pub = " + _pub + ", "); + stringBuilder.Append("Sub = " + _sub); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] public enum SpinnakerCameraColorProcessing @@ -2679,24 +2806,19 @@ public System.IObservable Process(System.IObservable(source); } - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - public System.IObservable Process(System.IObservable source) { return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); } public System.IObservable Process(System.IObservable source) @@ -2718,6 +2840,16 @@ public System.IObservable Process(System.IObservable { return Process(source); } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } } @@ -2732,14 +2864,15 @@ public System.IObservable Process(System.IObservable [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder { diff --git a/src/Extensions/AindPhysiologyFipMessageProtocol.Generated.cs b/src/Extensions/AindPhysiologyFipMessageProtocol.Generated.cs new file mode 100644 index 0000000..fae3503 --- /dev/null +++ b/src/Extensions/AindPhysiologyFipMessageProtocol.Generated.cs @@ -0,0 +1,3532 @@ +//---------------------- +// +// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) +// +//---------------------- + + +namespace AindJustFramesSchemas.MessageProtocol +{ + #pragma warning disable // Disable all warnings + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindBehaviorSessionModel + { + + private string _aindBehaviorServicesPkgVersion; + + private string _version; + + private string _experiment; + + private System.Collections.Generic.List _experimenter; + + private System.DateTimeOffset _date; + + private string _rootPath; + + private string _sessionName; + + private string _subject; + + private string _experimentVersion; + + private string _notes; + + private string _commitHash; + + private bool _allowDirtyRepo; + + private bool _skipHardwareValidation; + + public AindBehaviorSessionModel() + { + _aindBehaviorServicesPkgVersion = "0.12.3"; + _version = "0.12.3"; + _experimenter = new System.Collections.Generic.List(); + _experimentVersion = ""; + _allowDirtyRepo = false; + _skipHardwareValidation = false; + } + + protected AindBehaviorSessionModel(AindBehaviorSessionModel other) + { + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _experiment = other._experiment; + _experimenter = other._experimenter; + _date = other._date; + _rootPath = other._rootPath; + _sessionName = other._sessionName; + _subject = other._subject; + _experimentVersion = other._experimentVersion; + _notes = other._notes; + _commitHash = other._commitHash; + _allowDirtyRepo = other._allowDirtyRepo; + _skipHardwareValidation = other._skipHardwareValidation; + } + + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version + { + get + { + return _version; + } + set + { + _version = value; + } + } + + /// + /// Name of the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("experiment")] + [System.ComponentModel.DescriptionAttribute("Name of the experiment")] + public string Experiment + { + get + { + return _experiment; + } + set + { + _experiment = value; + } + } + + /// + /// Name of the experimenter + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] + [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] + public System.Collections.Generic.List Experimenter + { + get + { + return _experimenter; + } + set + { + _experimenter = value; + } + } + + /// + /// Date of the experiment + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("date")] + [System.ComponentModel.DescriptionAttribute("Date of the experiment")] + public System.DateTimeOffset Date + { + get + { + return _date; + } + set + { + _date = value; + } + } + + /// + /// Root path where data will be logged + /// + [Newtonsoft.Json.JsonPropertyAttribute("root_path", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Root path where data will be logged")] + public string RootPath + { + get + { + return _rootPath; + } + set + { + _rootPath = value; + } + } + + /// + /// Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date. + /// + [Newtonsoft.Json.JsonPropertyAttribute("session_name")] + [System.ComponentModel.DescriptionAttribute("Name of the session. This will be used to create a folder in the root path. If no" + + "t provided, it will be generated using subject and date.")] + public string SessionName + { + get + { + return _sessionName; + } + set + { + _sessionName = value; + } + } + + /// + /// Name of the subject + /// + [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Name of the subject")] + public string Subject + { + get + { + return _subject; + } + set + { + _subject = value; + } + } + + /// + /// Version of the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("experiment_version")] + [System.ComponentModel.DescriptionAttribute("Version of the experiment")] + public string ExperimentVersion + { + get + { + return _experimentVersion; + } + set + { + _experimentVersion = value; + } + } + + /// + /// Notes about the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("notes")] + [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] + public string Notes + { + get + { + return _notes; + } + set + { + _notes = value; + } + } + + /// + /// Commit hash of the repository + /// + [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")] + [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")] + public string CommitHash + { + get + { + return _commitHash; + } + set + { + _commitHash = value; + } + } + + /// + /// Allow running from a dirty repository + /// + [Newtonsoft.Json.JsonPropertyAttribute("allow_dirty_repo")] + [System.ComponentModel.DescriptionAttribute("Allow running from a dirty repository")] + public bool AllowDirtyRepo + { + get + { + return _allowDirtyRepo; + } + set + { + _allowDirtyRepo = value; + } + } + + /// + /// Skip hardware validation + /// + [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")] + [System.ComponentModel.DescriptionAttribute("Skip hardware validation")] + public bool SkipHardwareValidation + { + get + { + return _skipHardwareValidation; + } + set + { + _skipHardwareValidation = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorSessionModel(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorSessionModel(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("Experiment = " + _experiment + ", "); + stringBuilder.Append("Experimenter = " + _experimenter + ", "); + stringBuilder.Append("Date = " + _date + ", "); + stringBuilder.Append("RootPath = " + _rootPath + ", "); + stringBuilder.Append("SessionName = " + _sessionName + ", "); + stringBuilder.Append("Subject = " + _subject + ", "); + stringBuilder.Append("ExperimentVersion = " + _experimentVersion + ", "); + stringBuilder.Append("Notes = " + _notes + ", "); + stringBuilder.Append("CommitHash = " + _commitHash + ", "); + stringBuilder.Append("AllowDirtyRepo = " + _allowDirtyRepo + ", "); + stringBuilder.Append("SkipHardwareValidation = " + _skipHardwareValidation); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class BaseModel + { + + public BaseModel() + { + } + + protected BaseModel(BaseModel other) + { + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new BaseModel(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new BaseModel(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + return false; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class CameraControllerSpinnakerCamera + { + + private string _deviceType; + + private string _deviceName; + + private BaseModel _additionalSettings; + + private BaseModel _calibration; + + private System.Collections.Generic.Dictionary _cameras; + + private int? _frameRate; + + public CameraControllerSpinnakerCamera() + { + _deviceType = "CameraController"; + _cameras = new System.Collections.Generic.Dictionary(); + } + + protected CameraControllerSpinnakerCamera(CameraControllerSpinnakerCamera other) + { + _deviceType = other._deviceType; + _deviceName = other._deviceName; + _additionalSettings = other._additionalSettings; + _calibration = other._calibration; + _cameras = other._cameras; + _frameRate = other._frameRate; + } + + [Newtonsoft.Json.JsonPropertyAttribute("device_type")] + public string DeviceType + { + get + { + return _deviceType; + } + set + { + _deviceType = value; + } + } + + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + + /// + /// Additional settings + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] + [System.ComponentModel.DescriptionAttribute("Additional settings")] + public BaseModel AdditionalSettings + { + get + { + return _additionalSettings; + } + set + { + _additionalSettings = value; + } + } + + /// + /// Calibration + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration")] + public BaseModel Calibration + { + get + { + return _calibration; + } + set + { + _calibration = value; + } + } + + /// + /// Cameras to be instantiated + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("cameras", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Cameras to be instantiated")] + public System.Collections.Generic.Dictionary Cameras + { + get + { + return _cameras; + } + set + { + _cameras = value; + } + } + + /// + /// Frame rate of the trigger to all cameras + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("frame_rate")] + [System.ComponentModel.DescriptionAttribute("Frame rate of the trigger to all cameras")] + public int? FrameRate + { + get + { + return _frameRate; + } + set + { + _frameRate = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new CameraControllerSpinnakerCamera(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new CameraControllerSpinnakerCamera(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("Cameras = " + _cameras + ", "); + stringBuilder.Append("FrameRate = " + _frameRate); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + /// + /// Payload for heartbeat messages indicating system health status. + /// + ///Heartbeat messages are used to monitor the health and availability + ///of system components. They include a status indicator and optional + ///context information. + /// + ///Attributes: + /// context: Optional additional data about the system state + /// status: Current health status of the component + /// + ///Examples: + /// ```python + /// heartbeat = HeartbeatPayload( + /// status=HeartbeatStatus.OK, + /// context={"cpu_usage": 0.25, "memory_usage": 0.60} + /// ) + /// print(heartbeat.status) # HeartbeatStatus.OK + /// + /// warning_heartbeat = HeartbeatPayload( + /// status=HeartbeatStatus.WARNING, + /// context={"disk_space_low": True} + /// ) + /// ``` + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute(@"Payload for heartbeat messages indicating system health status. + + Heartbeat messages are used to monitor the health and availability + of system components. They include a status indicator and optional + context information. + + Attributes: + context: Optional additional data about the system state + status: Current health status of the component + + Examples: + ```python + heartbeat = HeartbeatPayload( + status=HeartbeatStatus.OK, + context={""cpu_usage"": 0.25, ""memory_usage"": 0.60} + ) + print(heartbeat.status) # HeartbeatStatus.OK + + warning_heartbeat = HeartbeatPayload( + status=HeartbeatStatus.WARNING, + context={""disk_space_low"": True} + ) + ```")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class HeartbeatPayload : RegisteredPayload + { + + private object _context; + + private HeartbeatStatus _status; + + public HeartbeatPayload() + { + } + + protected HeartbeatPayload(HeartbeatPayload other) : + base(other) + { + _context = other._context; + _status = other._status; + } + + /// + /// Additional context for the heartbeat message. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("context")] + [System.ComponentModel.DescriptionAttribute("Additional context for the heartbeat message.")] + public object Context + { + get + { + return _context; + } + set + { + _context = value; + } + } + + /// + /// The status of the heartbeat message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("status", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The status of the heartbeat message")] + public HeartbeatStatus Status + { + get + { + return _status; + } + set + { + _status = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HeartbeatPayload(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new HeartbeatPayload(this)); + } + + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + if (base.PrintMembers(stringBuilder)) + { + stringBuilder.Append(", "); + } + stringBuilder.Append("Context = " + _context + ", "); + stringBuilder.Append("Status = " + _status); + return true; + } + } + + + /// + /// Enumeration of possible heartbeat status values. + /// + ///Represents the health status of a system component, + ///with higher values indicating more severe issues. + /// + ///Examples: + /// ```python + /// HeartbeatStatus.OK # + /// HeartbeatStatus.CRITICAL > HeartbeatStatus.WARNING # True + /// int(HeartbeatStatus.ERROR) # 2 + /// ``` + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + public enum HeartbeatStatus + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Ok = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] + Warning = 1, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] + Error = 2, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] + Critical = 3, + } + + + /// + /// Enumeration of log levels for the logging system. + /// + ///Follows standard Python logging levels with integer values + ///that allow for easy comparison and filtering. + /// + ///Examples: + /// ```python + /// LogLevel.ERROR > LogLevel.WARNING # True + /// LogLevel.DEBUG.value # 10 + /// str(LogLevel.INFO) # 'LogLevel.INFO' + /// ``` + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + public enum LogLevel + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="50")] + Critical = 50, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="40")] + Error = 40, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="30")] + Warning = 30, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="20")] + Info = 20, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="10")] + Debug = 10, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Notset = 0, + } + + + /// + /// Payload for log messages containing logging information. + /// + ///This payload carries log data including the message content, + ///severity level, optional context, and application version. + /// + ///Attributes: + /// message: The actual log message text + /// level: Severity level of the log entry + /// context: Optional additional data related to the log + /// application_version: Version of the application generating the log + /// + ///Examples: + /// ```python + /// log_payload = LogPayload( + /// message="System startup complete", + /// level=LogLevel.INFO, + /// context={"operator": "John Doe"}, + /// application_version="1.0.0" + /// ) + /// print(log_payload.level) # LogLevel.INFO + /// ``` + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute(@"Payload for log messages containing logging information. + + This payload carries log data including the message content, + severity level, optional context, and application version. + + Attributes: + message: The actual log message text + level: Severity level of the log entry + context: Optional additional data related to the log + application_version: Version of the application generating the log + + Examples: + ```python + log_payload = LogPayload( + message=""System startup complete"", + level=LogLevel.INFO, + context={""operator"": ""John Doe""}, + application_version=""1.0.0"" + ) + print(log_payload.level) # LogLevel.INFO + ```")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class LogPayload : RegisteredPayload + { + + private string _message; + + private LogLevel _level; + + private object _context; + + private string _applicationVersion; + + public LogPayload() + { + _level = AindJustFramesSchemas.MessageProtocol.LogLevel.Debug; + } + + protected LogPayload(LogPayload other) : + base(other) + { + _message = other._message; + _level = other._level; + _context = other._context; + _applicationVersion = other._applicationVersion; + } + + /// + /// The message of the log + /// + [Newtonsoft.Json.JsonPropertyAttribute("message", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The message of the log")] + public string Message + { + get + { + return _message; + } + set + { + _message = value; + } + } + + /// + /// The level of the log message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("level")] + [System.ComponentModel.DescriptionAttribute("The level of the log message")] + public LogLevel Level + { + get + { + return _level; + } + set + { + _level = value; + } + } + + /// + /// Additional context for the log message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("context")] + [System.ComponentModel.DescriptionAttribute("Additional context for the log message")] + public object Context + { + get + { + return _context; + } + set + { + _context = value; + } + } + + /// + /// The version of the application + /// + [Newtonsoft.Json.JsonPropertyAttribute("application_version")] + [System.ComponentModel.DescriptionAttribute("The version of the application")] + public string ApplicationVersion + { + get + { + return _applicationVersion; + } + set + { + _applicationVersion = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new LogPayload(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new LogPayload(this)); + } + + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + if (base.PrintMembers(stringBuilder)) + { + stringBuilder.Append(", "); + } + stringBuilder.Append("Message = " + _message + ", "); + stringBuilder.Append("Level = " + _level + ", "); + stringBuilder.Append("Context = " + _context + ", "); + stringBuilder.Append("ApplicationVersion = " + _applicationVersion); + return true; + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class Message + { + + private MessageType _messageType; + + private int _protocolVersion; + + private System.DateTimeOffset? _timestamp; + + private object _payload; + + private string _processId; + + private string _hostname; + + private string _rigName; + + public Message() + { + _protocolVersion = 0; + } + + protected Message(Message other) + { + _messageType = other._messageType; + _protocolVersion = other._protocolVersion; + _timestamp = other._timestamp; + _payload = other._payload; + _processId = other._processId; + _hostname = other._hostname; + _rigName = other._rigName; + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("message_type", Required=Newtonsoft.Json.Required.Always)] + public MessageType MessageType + { + get + { + return _messageType; + } + set + { + _messageType = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("protocol_version")] + public int ProtocolVersion + { + get + { + return _protocolVersion; + } + set + { + _protocolVersion = value; + } + } + + /// + /// The timestamp of the message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("timestamp", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("The timestamp of the message")] + public System.DateTimeOffset? Timestamp + { + get + { + return _timestamp; + } + set + { + _timestamp = value; + } + } + + /// + /// The payload of the message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("payload", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The payload of the message")] + public object Payload + { + get + { + return _payload; + } + set + { + _payload = value; + } + } + + /// + /// Process that created the message + /// + [Newtonsoft.Json.JsonPropertyAttribute("process_id", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Process that created the message")] + public string ProcessId + { + get + { + return _processId; + } + set + { + _processId = value; + } + } + + /// + /// Hostname that created the message + /// + [Newtonsoft.Json.JsonPropertyAttribute("hostname", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Hostname that created the message")] + public string Hostname + { + get + { + return _hostname; + } + set + { + _hostname = value; + } + } + + /// + /// Rig name that created the message + /// + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Rig name that created the message")] + public string RigName + { + get + { + return _rigName; + } + set + { + _rigName = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Message(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new Message(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("MessageType = " + _messageType + ", "); + stringBuilder.Append("ProtocolVersion = " + _protocolVersion + ", "); + stringBuilder.Append("Timestamp = " + _timestamp + ", "); + stringBuilder.Append("Payload = " + _payload + ", "); + stringBuilder.Append("ProcessId = " + _processId + ", "); + stringBuilder.Append("Hostname = " + _hostname + ", "); + stringBuilder.Append("RigName = " + _rigName); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + /// + /// Enumeration of possible message types in the protocol. + /// + ///Examples: + /// ```python + /// MessageType.REQUEST # 'request' + /// MessageType.REPLY # 'reply' + /// MessageType.EVENT # 'event' + /// ``` + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] + public enum MessageType + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="request")] + Request = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="reply")] + Reply = 1, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="event")] + Event = 2, + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class Rect + { + + private int _x; + + private int _y; + + private int _width; + + private int _height; + + public Rect() + { + _x = 0; + _y = 0; + _width = 0; + _height = 0; + } + + protected Rect(Rect other) + { + _x = other._x; + _y = other._y; + _width = other._width; + _height = other._height; + } + + /// + /// X coordinate of the top-left corner + /// + [Newtonsoft.Json.JsonPropertyAttribute("x")] + [System.ComponentModel.DescriptionAttribute("X coordinate of the top-left corner")] + public int X + { + get + { + return _x; + } + set + { + _x = value; + } + } + + /// + /// Y coordinate of the top-left corner + /// + [Newtonsoft.Json.JsonPropertyAttribute("y")] + [System.ComponentModel.DescriptionAttribute("Y coordinate of the top-left corner")] + public int Y + { + get + { + return _y; + } + set + { + _y = value; + } + } + + /// + /// Width of the rectangle + /// + [Newtonsoft.Json.JsonPropertyAttribute("width")] + [System.ComponentModel.DescriptionAttribute("Width of the rectangle")] + public int Width + { + get + { + return _width; + } + set + { + _width = value; + } + } + + /// + /// Height of the rectangle + /// + [Newtonsoft.Json.JsonPropertyAttribute("height")] + [System.ComponentModel.DescriptionAttribute("Height of the rectangle")] + public int Height + { + get + { + return _height; + } + set + { + _height = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Rect(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new Rect(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("X = " + _x + ", "); + stringBuilder.Append("Y = " + _y + ", "); + stringBuilder.Append("Width = " + _width + ", "); + stringBuilder.Append("Height = " + _height); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class RegisteredMessages + { + + private MessageType _messageType; + + private int _protocolVersion; + + private System.DateTimeOffset? _timestamp; + + private RegisteredPayload _payload; + + private string _processId; + + private string _hostname; + + private string _rigName; + + public RegisteredMessages() + { + _protocolVersion = 0; + } + + protected RegisteredMessages(RegisteredMessages other) + { + _messageType = other._messageType; + _protocolVersion = other._protocolVersion; + _timestamp = other._timestamp; + _payload = other._payload; + _processId = other._processId; + _hostname = other._hostname; + _rigName = other._rigName; + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("message_type", Required=Newtonsoft.Json.Required.Always)] + public MessageType MessageType + { + get + { + return _messageType; + } + set + { + _messageType = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("protocol_version")] + public int ProtocolVersion + { + get + { + return _protocolVersion; + } + set + { + _protocolVersion = value; + } + } + + /// + /// The timestamp of the message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("timestamp", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("The timestamp of the message")] + public System.DateTimeOffset? Timestamp + { + get + { + return _timestamp; + } + set + { + _timestamp = value; + } + } + + /// + /// The payload of the message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("payload", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The payload of the message")] + public RegisteredPayload Payload + { + get + { + return _payload; + } + set + { + _payload = value; + } + } + + /// + /// Process that created the message + /// + [Newtonsoft.Json.JsonPropertyAttribute("process_id", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Process that created the message")] + public string ProcessId + { + get + { + return _processId; + } + set + { + _processId = value; + } + } + + /// + /// Hostname that created the message + /// + [Newtonsoft.Json.JsonPropertyAttribute("hostname", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Hostname that created the message")] + public string Hostname + { + get + { + return _hostname; + } + set + { + _hostname = value; + } + } + + /// + /// Rig name that created the message + /// + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Rig name that created the message")] + public string RigName + { + get + { + return _rigName; + } + set + { + _rigName = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new RegisteredMessages(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new RegisteredMessages(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("MessageType = " + _messageType + ", "); + stringBuilder.Append("ProtocolVersion = " + _protocolVersion + ", "); + stringBuilder.Append("Timestamp = " + _timestamp + ", "); + stringBuilder.Append("Payload = " + _payload + ", "); + stringBuilder.Append("ProcessId = " + _processId + ", "); + stringBuilder.Append("Hostname = " + _hostname + ", "); + stringBuilder.Append("RigName = " + _rigName); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "payload_type")] + [JsonInheritanceAttribute("HeartbeatPayload", typeof(HeartbeatPayload))] + [JsonInheritanceAttribute("LogPayload", typeof(LogPayload))] + [JsonInheritanceAttribute("Start", typeof(StartPayload))] + [JsonInheritanceAttribute("Stop", typeof(StopPayload))] + [JsonInheritanceAttribute("SatelliteRig", typeof(SatelliteRigPayload))] + [JsonInheritanceAttribute("SatelliteSession", typeof(SatelliteSessionPayload))] + public abstract partial class RegisteredPayload + { + + protected RegisteredPayload() + { + } + + protected RegisteredPayload(RegisteredPayload other) + { + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + return false; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class SatelliteRig + { + + private string _aindBehaviorServicesPkgVersion; + + private string _version; + + private string _computerName; + + private string _rigName; + + private ZmqPubSub _zmqConnection; + + private CameraControllerSpinnakerCamera _triggeredCameraController0; + + private CameraControllerSpinnakerCamera _triggeredCameraController1; + + private bool _isSatellite; + + public SatelliteRig() + { + _aindBehaviorServicesPkgVersion = "0.12.3"; + _version = "0.5.0-rc0"; + _zmqConnection = new ZmqPubSub(); + _isSatellite = true; + } + + protected SatelliteRig(SatelliteRig other) + { + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _computerName = other._computerName; + _rigName = other._rigName; + _zmqConnection = other._zmqConnection; + _triggeredCameraController0 = other._triggeredCameraController0; + _triggeredCameraController1 = other._triggeredCameraController1; + _isSatellite = other._isSatellite; + } + + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version + { + get + { + return _version; + } + set + { + _version = value; + } + } + + /// + /// Remote Computer name + /// + [Newtonsoft.Json.JsonPropertyAttribute("computer_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Remote Computer name")] + public string ComputerName + { + get + { + return _computerName; + } + set + { + _computerName = value; + } + } + + /// + /// Rig name + /// + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Rig name")] + public string RigName + { + get + { + return _rigName; + } + set + { + _rigName = value; + } + } + + /// + /// ZMQ connection for communication. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("zmq_connection", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] + public ZmqPubSub ZmqConnection + { + get + { + return _zmqConnection; + } + set + { + _zmqConnection = value; + } + } + + /// + /// Camera controller to triggered cameras. Will use Camera0 register as a trigger. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_0")] + [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera0 register as a trigger.")] + public CameraControllerSpinnakerCamera TriggeredCameraController0 + { + get + { + return _triggeredCameraController0; + } + set + { + _triggeredCameraController0 = value; + } + } + + /// + /// Camera controller to triggered cameras. Will use Camera1 register as a trigger. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_1")] + [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera1 register as a trigger.")] + public CameraControllerSpinnakerCamera TriggeredCameraController1 + { + get + { + return _triggeredCameraController1; + } + set + { + _triggeredCameraController1 = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("is_satellite")] + public bool IsSatellite + { + get + { + return _isSatellite; + } + set + { + _isSatellite = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteRig(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new SatelliteRig(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("ComputerName = " + _computerName + ", "); + stringBuilder.Append("RigName = " + _rigName + ", "); + stringBuilder.Append("ZmqConnection = " + _zmqConnection + ", "); + stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); + stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); + stringBuilder.Append("IsSatellite = " + _isSatellite); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class SatelliteRigPayload : RegisteredPayload + { + + private SatelliteRig _rig; + + public SatelliteRigPayload() + { + _rig = new SatelliteRig(); + } + + protected SatelliteRigPayload(SatelliteRigPayload other) : + base(other) + { + _rig = other._rig; + } + + /// + /// Satellite Rig configuration. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("rig", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Satellite Rig configuration.")] + public SatelliteRig Rig + { + get + { + return _rig; + } + set + { + _rig = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteRigPayload(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new SatelliteRigPayload(this)); + } + + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + if (base.PrintMembers(stringBuilder)) + { + stringBuilder.Append(", "); + } + stringBuilder.Append("Rig = " + _rig); + return true; + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class SatelliteSessionPayload : RegisteredPayload + { + + private AindBehaviorSessionModel _session; + + public SatelliteSessionPayload() + { + _session = new AindBehaviorSessionModel(); + } + + protected SatelliteSessionPayload(SatelliteSessionPayload other) : + base(other) + { + _session = other._session; + } + + /// + /// Satellite session configuration. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("session", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Satellite session configuration.")] + public AindBehaviorSessionModel Session + { + get + { + return _session; + } + set + { + _session = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteSessionPayload(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new SatelliteSessionPayload(this)); + } + + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + if (base.PrintMembers(stringBuilder)) + { + stringBuilder.Append(", "); + } + stringBuilder.Append("Session = " + _session); + return true; + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class SpinnakerCamera + { + + private string _deviceType; + + private string _deviceName; + + private BaseModel _additionalSettings; + + private BaseModel _calibration; + + private string _serialNumber; + + private int _binning; + + private SpinnakerCameraColorProcessing _colorProcessing; + + private int _exposure; + + private double _gain; + + private double? _gamma; + + private SpinnakerCameraAdcBitDepth? _adcBitDepth; + + private SpinnakerCameraPixelFormat? _pixelFormat; + + private Rect _regionOfInterest; + + private VideoWriter _videoWriter; + + public SpinnakerCamera() + { + _deviceType = "SpinnakerCamera"; + _binning = 1; + _colorProcessing = AindJustFramesSchemas.MessageProtocol.SpinnakerCameraColorProcessing.Default; + _exposure = 1000; + _gain = 0D; + _adcBitDepth = AindJustFramesSchemas.MessageProtocol.SpinnakerCameraAdcBitDepth.Adc8bit; + _pixelFormat = AindJustFramesSchemas.MessageProtocol.SpinnakerCameraPixelFormat.Mono8; + _regionOfInterest = new Rect(); + } + + protected SpinnakerCamera(SpinnakerCamera other) + { + _deviceType = other._deviceType; + _deviceName = other._deviceName; + _additionalSettings = other._additionalSettings; + _calibration = other._calibration; + _serialNumber = other._serialNumber; + _binning = other._binning; + _colorProcessing = other._colorProcessing; + _exposure = other._exposure; + _gain = other._gain; + _gamma = other._gamma; + _adcBitDepth = other._adcBitDepth; + _pixelFormat = other._pixelFormat; + _regionOfInterest = other._regionOfInterest; + _videoWriter = other._videoWriter; + } + + /// + /// Device type + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_type")] + [System.ComponentModel.DescriptionAttribute("Device type")] + public string DeviceType + { + get + { + return _deviceType; + } + set + { + _deviceType = value; + } + } + + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + + /// + /// Additional settings + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] + [System.ComponentModel.DescriptionAttribute("Additional settings")] + public BaseModel AdditionalSettings + { + get + { + return _additionalSettings; + } + set + { + _additionalSettings = value; + } + } + + /// + /// Calibration + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration")] + public BaseModel Calibration + { + get + { + return _calibration; + } + set + { + _calibration = value; + } + } + + /// + /// Camera serial number + /// + [Newtonsoft.Json.JsonPropertyAttribute("serial_number", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Camera serial number")] + public string SerialNumber + { + get + { + return _serialNumber; + } + set + { + _serialNumber = value; + } + } + + /// + /// Binning + /// + [Newtonsoft.Json.JsonPropertyAttribute("binning")] + [System.ComponentModel.DescriptionAttribute("Binning")] + public int Binning + { + get + { + return _binning; + } + set + { + _binning = value; + } + } + + /// + /// Color processing + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("color_processing")] + [System.ComponentModel.DescriptionAttribute("Color processing")] + public SpinnakerCameraColorProcessing ColorProcessing + { + get + { + return _colorProcessing; + } + set + { + _colorProcessing = value; + } + } + + /// + /// Exposure time + /// + [Newtonsoft.Json.JsonPropertyAttribute("exposure")] + [System.ComponentModel.DescriptionAttribute("Exposure time")] + public int Exposure + { + get + { + return _exposure; + } + set + { + _exposure = value; + } + } + + /// + /// Gain + /// + [Newtonsoft.Json.JsonPropertyAttribute("gain")] + [System.ComponentModel.DescriptionAttribute("Gain")] + public double Gain + { + get + { + return _gain; + } + set + { + _gain = value; + } + } + + /// + /// Gamma. If None, will disable gamma correction. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("gamma")] + [System.ComponentModel.DescriptionAttribute("Gamma. If None, will disable gamma correction.")] + public double? Gamma + { + get + { + return _gamma; + } + set + { + _gamma = value; + } + } + + /// + /// ADC bit depth. If None will be left as default. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("adc_bit_depth")] + [System.ComponentModel.DescriptionAttribute("ADC bit depth. If None will be left as default.")] + public SpinnakerCameraAdcBitDepth? AdcBitDepth + { + get + { + return _adcBitDepth; + } + set + { + _adcBitDepth = value; + } + } + + /// + /// Pixel format. If None will be left as default. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("pixel_format")] + [System.ComponentModel.DescriptionAttribute("Pixel format. If None will be left as default.")] + public SpinnakerCameraPixelFormat? PixelFormat + { + get + { + return _pixelFormat; + } + set + { + _pixelFormat = value; + } + } + + /// + /// Region of interest + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("region_of_interest")] + [System.ComponentModel.DescriptionAttribute("Region of interest")] + public Rect RegionOfInterest + { + get + { + return _regionOfInterest; + } + set + { + _regionOfInterest = value; + } + } + + /// + /// Video writer. If not provided, no video will be saved. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("video_writer")] + [System.ComponentModel.DescriptionAttribute("Video writer. If not provided, no video will be saved.")] + public VideoWriter VideoWriter + { + get + { + return _videoWriter; + } + set + { + _videoWriter = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SpinnakerCamera(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new SpinnakerCamera(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("Binning = " + _binning + ", "); + stringBuilder.Append("ColorProcessing = " + _colorProcessing + ", "); + stringBuilder.Append("Exposure = " + _exposure + ", "); + stringBuilder.Append("Gain = " + _gain + ", "); + stringBuilder.Append("Gamma = " + _gamma + ", "); + stringBuilder.Append("AdcBitDepth = " + _adcBitDepth + ", "); + stringBuilder.Append("PixelFormat = " + _pixelFormat + ", "); + stringBuilder.Append("RegionOfInterest = " + _regionOfInterest + ", "); + stringBuilder.Append("VideoWriter = " + _videoWriter); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + public enum SpinnakerCameraAdcBitDepth + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Adc8bit = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] + Adc10bit = 1, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] + Adc12bit = 2, + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + public enum SpinnakerCameraPixelFormat + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Mono8 = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] + Mono16 = 1, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] + Rgb8packed = 2, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] + Bayergr8 = 3, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="4")] + Bayerrg8 = 4, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="5")] + Bayergb8 = 5, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="6")] + Bayerbg8 = 6, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="7")] + Bayergr16 = 7, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="8")] + Bayerrg16 = 8, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="9")] + Bayergb16 = 9, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="10")] + Bayerbg16 = 10, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="11")] + Mono12packed = 11, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="12")] + Bayergr12packed = 12, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="13")] + Bayerrg12packed = 13, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="14")] + Bayergb12packed = 14, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="15")] + Bayerbg12packed = 15, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="16")] + Yuv411packed = 16, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="17")] + Yuv422packed = 17, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="18")] + Yuv444packed = 18, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="19")] + Mono12p = 19, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="20")] + Bayergr12p = 20, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="21")] + Bayerrg12p = 21, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="22")] + Bayergb12p = 22, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="23")] + Bayerbg12p = 23, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="24")] + Ycbcr8 = 24, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="25")] + Ycbcr4228 = 25, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="26")] + Ycbcr4118 = 26, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="27")] + Bgr8 = 27, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="28")] + Bgra8 = 28, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="29")] + Mono10packed = 29, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="30")] + Bayergr10packed = 30, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="31")] + Bayerrg10packed = 31, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="32")] + Bayergb10packed = 32, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="33")] + Bayerbg10packed = 33, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="34")] + Mono10p = 34, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="35")] + Bayergr10p = 35, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="36")] + Bayerrg10p = 36, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="37")] + Bayergb10p = 37, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="38")] + Bayerbg10p = 38, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="39")] + Mono1p = 39, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="40")] + Mono2p = 40, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="41")] + Mono4p = 41, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="42")] + Mono8s = 42, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="43")] + Mono10 = 43, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="44")] + Mono12 = 44, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="45")] + Mono14 = 45, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="46")] + Mono16s = 46, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="47")] + Mono32f = 47, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="48")] + Bayerbg10 = 48, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="49")] + Bayerbg12 = 49, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="50")] + Bayergb10 = 50, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="51")] + Bayergb12 = 51, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="52")] + Bayergr10 = 52, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="53")] + Bayergr12 = 53, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="54")] + Bayerrg10 = 54, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="55")] + Bayerrg12 = 55, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="56")] + Rgba8 = 56, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="57")] + Rgba10 = 57, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="58")] + Rgba10p = 58, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="59")] + Rgba12 = 59, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="60")] + Rgba12p = 60, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="61")] + Rgba14 = 61, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="62")] + Rgba16 = 62, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="63")] + Rgb8 = 63, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="64")] + Rgb8Planar = 64, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="65")] + Rgb10 = 65, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="66")] + Rgb10Planar = 66, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="67")] + Rgb10p = 67, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="68")] + Rgb10p32 = 68, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="69")] + Rgb12 = 69, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="70")] + Rgb12Planar = 70, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="71")] + Rgb12p = 71, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="72")] + Rgb14 = 72, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="73")] + Rgb16 = 73, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="74")] + Rgb16s = 74, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="75")] + Rgb32f = 75, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="76")] + Rgb16Planar = 76, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="77")] + Rgb565p = 77, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="78")] + Bgra10 = 78, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="79")] + Bgra10p = 79, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="80")] + Bgra12 = 80, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="81")] + Bgra12p = 81, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="82")] + Bgra14 = 82, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="83")] + Bgra16 = 83, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="84")] + Rgba32f = 84, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="85")] + Bgr10 = 85, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="86")] + Bgr10p = 86, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="87")] + Bgr12 = 87, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="88")] + Bgr12p = 88, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="89")] + Bgr14 = 89, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="90")] + Bgr16 = 90, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="91")] + Bgr565p = 91, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="92")] + R8 = 92, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="93")] + R10 = 93, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="94")] + R12 = 94, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="95")] + R16 = 95, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="96")] + G8 = 96, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="97")] + G10 = 97, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="98")] + G12 = 98, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="99")] + G16 = 99, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="100")] + B8 = 100, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="101")] + B10 = 101, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="102")] + B12 = 102, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="103")] + B16 = 103, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="104")] + Coord3dAbc8 = 104, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="105")] + Coord3dAbc8Planar = 105, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="106")] + Coord3dAbc10p = 106, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="107")] + Coord3dAbc10pPlanar = 107, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="108")] + Coord3dAbc12p = 108, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="109")] + Coord3dAbc12pPlanar = 109, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="110")] + Coord3dAbc16 = 110, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="111")] + Coord3dAbc16Planar = 111, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="112")] + Coord3dAbc32f = 112, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="113")] + Coord3dAbc32fPlanar = 113, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="114")] + Coord3dAc8 = 114, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="115")] + Coord3dAc8Planar = 115, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="116")] + Coord3dAc10p = 116, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="117")] + Coord3dAc10pPlanar = 117, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="118")] + Coord3dAc12p = 118, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="119")] + Coord3dAc12pPlanar = 119, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="120")] + Coord3dAc16 = 120, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="121")] + Coord3dAc16Planar = 121, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="122")] + Coord3dAc32f = 122, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="123")] + Coord3dAc32fPlanar = 123, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="124")] + Coord3dA8 = 124, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="125")] + Coord3dA10p = 125, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="126")] + Coord3dA12p = 126, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="127")] + Coord3dA16 = 127, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="128")] + Coord3dA32f = 128, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="129")] + Coord3dB8 = 129, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="130")] + Coord3dB10p = 130, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="131")] + Coord3dB12p = 131, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="132")] + Coord3dB16 = 132, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="133")] + Coord3dB32f = 133, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="134")] + Coord3dC8 = 134, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="135")] + Coord3dC10p = 135, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="136")] + Coord3dC12p = 136, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="137")] + Coord3dC16 = 137, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="138")] + Coord3dC32f = 138, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="139")] + Confidence1 = 139, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="140")] + Confidence1p = 140, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="141")] + Confidence8 = 141, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="142")] + Confidence16 = 142, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="143")] + Confidence32f = 143, + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class StartPayload : RegisteredPayload + { + + public StartPayload() + { + } + + protected StartPayload(StartPayload other) : + base(other) + { + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new StartPayload(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new StartPayload(this)); + } + + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + return base.PrintMembers(stringBuilder); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class StopPayload : RegisteredPayload + { + + public StopPayload() + { + } + + protected StopPayload(StopPayload other) : + base(other) + { + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new StopPayload(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new StopPayload(this)); + } + + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + return base.PrintMembers(stringBuilder); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "video_writer_type")] + [JsonInheritanceAttribute("FFMPEG", typeof(VideoWriterFfmpeg))] + [JsonInheritanceAttribute("OPENCV", typeof(VideoWriterOpenCv))] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class VideoWriter + { + + public VideoWriter() + { + } + + protected VideoWriter(VideoWriter other) + { + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriter(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriter(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + return false; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class VideoWriterFfmpeg : VideoWriter + { + + private int _frameRate; + + private string _containerExtension; + + private string _outputArguments; + + private string _inputArguments; + + public VideoWriterFfmpeg() + { + _frameRate = 30; + _containerExtension = "mp4"; + _outputArguments = "-vf \"scale=out_color_matrix=bt709:out_range=full,format=bgr24,scale=out_range=full\" -c:v h264_nvenc -pix_fmt yuv420p -color_range full -colorspace bt709 -color_trc linear -tune hq -preset p4 -rc vbr -cq 12 -b:v 0M -metadata author=\"Allen Institute for Neural Dynamics\" -maxrate 700M -bufsize 350M"; + _inputArguments = "-colorspace bt709 -color_primaries bt709 -color_range full -color_trc linear"; + } + + protected VideoWriterFfmpeg(VideoWriterFfmpeg other) : + base(other) + { + _frameRate = other._frameRate; + _containerExtension = other._containerExtension; + _outputArguments = other._outputArguments; + _inputArguments = other._inputArguments; + } + + /// + /// Encoding frame rate + /// + [Newtonsoft.Json.JsonPropertyAttribute("frame_rate")] + [System.ComponentModel.DescriptionAttribute("Encoding frame rate")] + public int FrameRate + { + get + { + return _frameRate; + } + set + { + _frameRate = value; + } + } + + /// + /// Container extension + /// + [Newtonsoft.Json.JsonPropertyAttribute("container_extension")] + [System.ComponentModel.DescriptionAttribute("Container extension")] + public string ContainerExtension + { + get + { + return _containerExtension; + } + set + { + _containerExtension = value; + } + } + + /// + /// Output arguments + /// + [Newtonsoft.Json.JsonPropertyAttribute("output_arguments")] + [System.ComponentModel.DescriptionAttribute("Output arguments")] + public string OutputArguments + { + get + { + return _outputArguments; + } + set + { + _outputArguments = value; + } + } + + /// + /// Input arguments + /// + [Newtonsoft.Json.JsonPropertyAttribute("input_arguments")] + [System.ComponentModel.DescriptionAttribute("Input arguments")] + public string InputArguments + { + get + { + return _inputArguments; + } + set + { + _inputArguments = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriterFfmpeg(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriterFfmpeg(this)); + } + + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + if (base.PrintMembers(stringBuilder)) + { + stringBuilder.Append(", "); + } + stringBuilder.Append("FrameRate = " + _frameRate + ", "); + stringBuilder.Append("ContainerExtension = " + _containerExtension + ", "); + stringBuilder.Append("OutputArguments = " + _outputArguments + ", "); + stringBuilder.Append("InputArguments = " + _inputArguments); + return true; + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class VideoWriterOpenCv : VideoWriter + { + + private int _frameRate; + + private string _containerExtension; + + private string _fourCc; + + public VideoWriterOpenCv() + { + _frameRate = 30; + _containerExtension = "avi"; + _fourCc = "FMP4"; + } + + protected VideoWriterOpenCv(VideoWriterOpenCv other) : + base(other) + { + _frameRate = other._frameRate; + _containerExtension = other._containerExtension; + _fourCc = other._fourCc; + } + + /// + /// Encoding frame rate + /// + [Newtonsoft.Json.JsonPropertyAttribute("frame_rate")] + [System.ComponentModel.DescriptionAttribute("Encoding frame rate")] + public int FrameRate + { + get + { + return _frameRate; + } + set + { + _frameRate = value; + } + } + + /// + /// Container extension + /// + [Newtonsoft.Json.JsonPropertyAttribute("container_extension")] + [System.ComponentModel.DescriptionAttribute("Container extension")] + public string ContainerExtension + { + get + { + return _containerExtension; + } + set + { + _containerExtension = value; + } + } + + /// + /// Four character code + /// + [Newtonsoft.Json.JsonPropertyAttribute("four_cc")] + [System.ComponentModel.DescriptionAttribute("Four character code")] + public string FourCc + { + get + { + return _fourCc; + } + set + { + _fourCc = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriterOpenCv(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriterOpenCv(this)); + } + + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + if (base.PrintMembers(stringBuilder)) + { + stringBuilder.Append(", "); + } + stringBuilder.Append("FrameRate = " + _frameRate + ", "); + stringBuilder.Append("ContainerExtension = " + _containerExtension + ", "); + stringBuilder.Append("FourCc = " + _fourCc); + return true; + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class ZmqConnection + { + + private string _connectionString; + + private string _topic; + + public ZmqConnection() + { + _connectionString = "@tcp://localhost:5556"; + _topic = ""; + } + + protected ZmqConnection(ZmqConnection other) + { + _connectionString = other._connectionString; + _topic = other._topic; + } + + /// + /// The connection string for the ZMQ socket. + /// + [Newtonsoft.Json.JsonPropertyAttribute("connection_string")] + [System.ComponentModel.DescriptionAttribute("The connection string for the ZMQ socket.")] + public string ConnectionString + { + get + { + return _connectionString; + } + set + { + _connectionString = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("topic")] + public string Topic + { + get + { + return _topic; + } + set + { + _topic = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqConnection(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new ZmqConnection(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("ConnectionString = " + _connectionString + ", "); + stringBuilder.Append("Topic = " + _topic); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class ZmqPubSub + { + + private ZmqConnection _pub; + + private ZmqConnection _sub; + + public ZmqPubSub() + { + _pub = new ZmqConnection(); + _sub = new ZmqConnection(); + } + + protected ZmqPubSub(ZmqPubSub other) + { + _pub = other._pub; + _sub = other._sub; + } + + /// + /// ZMQ Publisher + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("pub", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ Publisher")] + public ZmqConnection Pub + { + get + { + return _pub; + } + set + { + _pub = value; + } + } + + /// + /// ZMQ Subscriber + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("sub", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ Subscriber")] + public ZmqConnection Sub + { + get + { + return _sub; + } + set + { + _sub = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqPubSub(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new ZmqPubSub(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Pub = " + _pub + ", "); + stringBuilder.Append("Sub = " + _sub); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] + public enum SpinnakerCameraColorProcessing + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="Default")] + Default = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="NoColorProcessing")] + NoColorProcessing = 1, + } + + + [System.CodeDom.Compiler.GeneratedCode("NJsonSchema", "10.9.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.AttributeUsage(System.AttributeTargets.Class | System.AttributeTargets.Interface, AllowMultiple = true)] + internal class JsonInheritanceAttribute : System.Attribute + { + public JsonInheritanceAttribute(string key, System.Type type) + { + Key = key; + Type = type; + } + + public string Key { get; private set; } + + public System.Type Type { get; private set; } + } + + [System.CodeDom.Compiler.GeneratedCode("NJsonSchema", "10.9.0.0 (Newtonsoft.Json v13.0.0.0)")] + public class JsonInheritanceConverter : Newtonsoft.Json.JsonConverter + { + internal static readonly string DefaultDiscriminatorName = "discriminator"; + + private readonly string _discriminatorName; + + [System.ThreadStatic] + private static bool _isReading; + + [System.ThreadStatic] + private static bool _isWriting; + + public JsonInheritanceConverter() + { + _discriminatorName = DefaultDiscriminatorName; + } + + public JsonInheritanceConverter(string discriminatorName) + { + _discriminatorName = discriminatorName; + } + + public string DiscriminatorName { get { return _discriminatorName; } } + + public override void WriteJson(Newtonsoft.Json.JsonWriter writer, object value, Newtonsoft.Json.JsonSerializer serializer) + { + try + { + _isWriting = true; + + var jObject = Newtonsoft.Json.Linq.JObject.FromObject(value, serializer); + jObject.AddFirst(new Newtonsoft.Json.Linq.JProperty(_discriminatorName, GetSubtypeDiscriminator(value.GetType()))); + writer.WriteToken(jObject.CreateReader()); + } + finally + { + _isWriting = false; + } + } + + public override bool CanWrite + { + get + { + if (_isWriting) + { + _isWriting = false; + return false; + } + return true; + } + } + + public override bool CanRead + { + get + { + if (_isReading) + { + _isReading = false; + return false; + } + return true; + } + } + + public override bool CanConvert(System.Type objectType) + { + return true; + } + + public override object ReadJson(Newtonsoft.Json.JsonReader reader, System.Type objectType, object existingValue, Newtonsoft.Json.JsonSerializer serializer) + { + var jObject = serializer.Deserialize(reader); + if (jObject == null) + return null; + + var discriminatorValue = jObject.GetValue(_discriminatorName); + var discriminator = discriminatorValue != null ? Newtonsoft.Json.Linq.Extensions.Value(discriminatorValue) : null; + var subtype = GetObjectSubtype(objectType, discriminator); + + var objectContract = serializer.ContractResolver.ResolveContract(subtype) as Newtonsoft.Json.Serialization.JsonObjectContract; + if (objectContract == null || System.Linq.Enumerable.All(objectContract.Properties, p => p.PropertyName != _discriminatorName)) + { + jObject.Remove(_discriminatorName); + } + + try + { + _isReading = true; + return serializer.Deserialize(jObject.CreateReader(), subtype); + } + finally + { + _isReading = false; + } + } + + private System.Type GetObjectSubtype(System.Type objectType, string discriminator) + { + foreach (var attribute in System.Reflection.CustomAttributeExtensions.GetCustomAttributes(System.Reflection.IntrospectionExtensions.GetTypeInfo(objectType), true)) + { + if (attribute.Key == discriminator) + return attribute.Type; + } + + return objectType; + } + + private string GetSubtypeDiscriminator(System.Type objectType) + { + foreach (var attribute in System.Reflection.CustomAttributeExtensions.GetCustomAttributes(System.Reflection.IntrospectionExtensions.GetTypeInfo(objectType), true)) + { + if (attribute.Type == objectType) + return attribute.Key; + } + + return objectType.Name; + } + } + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DefaultPropertyAttribute("Type")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Combinator)] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + public partial class MatchRegisteredPayload : Bonsai.Expressions.SingleArgumentExpressionBuilder + { + + public Bonsai.Expressions.TypeMapping Type { get; set; } + + public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) + { + var typeMapping = Type; + var returnType = typeMapping != null ? typeMapping.GetType().GetGenericArguments()[0] : typeof(RegisteredPayload); + return System.Linq.Expressions.Expression.Call( + typeof(MatchRegisteredPayload), + "Process", + new System.Type[] { returnType }, + System.Linq.Enumerable.Single(arguments)); + } + + + private static System.IObservable Process(System.IObservable source) + where TResult : RegisteredPayload + { + return System.Reactive.Linq.Observable.Create(observer => + { + var sourceObserver = System.Reactive.Observer.Create( + value => + { + var match = value as TResult; + if (match != null) observer.OnNext(match); + }, + observer.OnError, + observer.OnCompleted); + return System.ObservableExtensions.SubscribeSafe(source, sourceObserver); + }); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DefaultPropertyAttribute("Type")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Combinator)] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + public partial class MatchVideoWriter : Bonsai.Expressions.SingleArgumentExpressionBuilder + { + + public Bonsai.Expressions.TypeMapping Type { get; set; } + + public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) + { + var typeMapping = Type; + var returnType = typeMapping != null ? typeMapping.GetType().GetGenericArguments()[0] : typeof(VideoWriter); + return System.Linq.Expressions.Expression.Call( + typeof(MatchVideoWriter), + "Process", + new System.Type[] { returnType }, + System.Linq.Enumerable.Single(arguments)); + } + + + private static System.IObservable Process(System.IObservable source) + where TResult : VideoWriter + { + return System.Reactive.Linq.Observable.Create(observer => + { + var sourceObserver = System.Reactive.Observer.Create( + value => + { + var match = value as TResult; + if (match != null) observer.OnNext(match); + }, + observer.OnError, + observer.OnCompleted); + return System.ObservableExtensions.SubscribeSafe(source, sourceObserver); + }); + } + } + + + /// + /// Serializes a sequence of data model objects into JSON strings. + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into JSON strings.")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] + [Bonsai.CombinatorAttribute()] + public partial class SerializeToJson + { + + public Newtonsoft.Json.Formatting Formatting { get; set; } + + private System.IObservable Process(System.IObservable source) + { + var formatting = Formatting; + return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value, formatting)); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + } + + + /// + /// Deserializes a sequence of JSON strings into data model objects. + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of JSON strings into data model objects.")] + [System.ComponentModel.DefaultPropertyAttribute("Type")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder + { + + public DeserializeFromJson() + { + Type = new Bonsai.Expressions.TypeMapping(); + } + + public Bonsai.Expressions.TypeMapping Type { get; set; } + + public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) + { + var typeMapping = (Bonsai.Expressions.TypeMapping)Type; + var returnType = typeMapping.GetType().GetGenericArguments()[0]; + return System.Linq.Expressions.Expression.Call( + typeof(DeserializeFromJson), + "Process", + new System.Type[] { returnType }, + System.Linq.Enumerable.Single(arguments)); + } + + private static System.IObservable Process(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.DeserializeObject(value)); + } + } +} \ No newline at end of file diff --git a/src/Extensions/BuildRegisteredMessage.cs b/src/Extensions/BuildRegisteredMessage.cs new file mode 100644 index 0000000..90b46ec --- /dev/null +++ b/src/Extensions/BuildRegisteredMessage.cs @@ -0,0 +1,51 @@ +using Bonsai; +using System; +using System.ComponentModel; +using System.Collections.Generic; +using System.Linq; +using System.Reactive.Linq; +using AindJustFramesSchemas.MessageProtocol; +using System.Reactive; + +[Combinator] +[Description("")] +[WorkflowElementCategory(ElementCategory.Transform)] +public class BuildRegisteredMessage +{ + private MessageType messageType = MessageType.Event; + public MessageType MessageType + { + get { return messageType; } + set { messageType = value; } + } + + private const int protocolVersion = 0; + + private string rigName; + public string RigName + { + get { return rigName; } + set { rigName = value; } + } + + public IObservable Process(IObservable source) + { + return Process(source.Select(value => new Timestamped(value, DateTimeOffset.UtcNow))); + } + + public IObservable Process(IObservable> source) + { + string hostname = Environment.MachineName; + string processId = System.Diagnostics.Process.GetCurrentProcess().Id.ToString(); + return source.Select(value => new RegisteredMessages() + { + MessageType = MessageType, + ProtocolVersion = protocolVersion, + Timestamp = value.Timestamp, + ProcessId = processId, + Hostname = hostname, + RigName = RigName, + Payload = value.Value + }); + } +} diff --git a/src/Extensions/CameraQc.bonsai b/src/Extensions/CameraQc.bonsai index b577de8..eb19dde 100644 --- a/src/Extensions/CameraQc.bonsai +++ b/src/Extensions/CameraQc.bonsai @@ -7,6 +7,8 @@ xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders" xmlns:p2="clr-namespace:AllenNeuralDynamics.Core.Design;assembly=AllenNeuralDynamics.Core.Design" + xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" + xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -541,10 +543,120 @@ - + + Check Trigger Order + + + + HarpBehaviorEvents + + + + Include + Write + + + + + + + + + + Source1 + + + Value + + + + None + + + + + + + + + + + + + Seconds + + + HarpBehaviorEvents + + + + Include + Event + + + + + + + + + + + + + Seconds + + + + + + + 1 + + + + + + + + Source1 + + + + + + + + + + + Received a frame event before start trigger. This likely means this workflow started after the master workflow. + + + + + + + + + + + + + + + + + + + + + + + + + - - - + \ No newline at end of file diff --git a/src/Extensions/HarpDevices.bonsai b/src/Extensions/HarpDevices.bonsai index 0b25592..bd63533 100644 --- a/src/Extensions/HarpDevices.bonsai +++ b/src/Extensions/HarpDevices.bonsai @@ -3,33 +3,66 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core" xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" + xmlns:p1="clr-namespace:AindJustFramesSchemas;assembly=Extensions" xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior" xmlns:zmq="clr-namespace:Bonsai.ZeroMQ;assembly=Bonsai.ZeroMQ" + xmlns:p2="clr-namespace:AindJustFramesSchemas.MessageProtocol;assembly=Extensions" + xmlns:p3="clr-namespace:;assembly=Extensions" xmlns="https://bonsai-rx.org/2018/workflow"> HarpBehaviorCommands - - todo - + + RigSchema + + + NotSatellite + + + + Source1 + + + IsSatellite + + + + + + + + + + - - 0 + + None BehaviorBoard + + Source1 + + + + 1 + + + + + + + RigSchema + HarpBehaviorCommands - - internalPub - RigSchema @@ -52,6 +85,9 @@ COM5 + + internalPub + internalPub @@ -59,6 +95,25 @@ MessageBytes + + HarpZmqTopic + + + + + + + + RigSchema + + + ZmqConnection.Pub.ConnectionString + + + + + + tcp://localhost:5557 @@ -67,29 +122,86 @@ - + - - + - + + + + + + + + + + - - todo - + + RigSchema + + + + + + Source1 + + + IsSatellite + + + + + + + + - - 0 + + None ZeroMQBehaviorBoard + + Source1 + + + + 1 + + + + + + + RigSchema + + + RigSchema + + + ZmqConnection.Sub.ConnectionString + + + + + + + + HarpZmqTopic + + + + + + tcp://localhost:5557 @@ -107,6 +219,14 @@ + + + + + + + + @@ -124,19 +244,35 @@ HarpBehaviorEvents - - todo - + + RigSchema - - BehaviorBoardInitialization + + NotSatellite - - + + Source1 + + IsSatellite + + + + + + + + + + + + + BehaviorBoardInitialization + + - TriggerHarpReadDump + StartExperiment Write @@ -158,7 +294,7 @@ Write - PortDI PortDIO AnalogData Camera0 Camera1 + PortDI PortDIO Camera0 Camera1 @@ -170,6 +306,169 @@ HarpBehaviorCommands + + + + + + + + + + + + + + RigSchema + + + NotSatellite + + + + Source1 + + + IsSatellite + + + + + + + + + + + + + + None + + + + MainZmqLogic + + + + Source1 + + + + 1 + + + + + + + RigSchema + + + RigSchema + + + SatelliteRigs + + + + + + + + + Source1 + + + satelliteRig + + + EnableExperiment + + + + + + satelliteRig + + + RigName + + + + + + + + + Request + + + + satelliteRig + + + ZmqConnection.Pub + + + ConnectionString + + + + + + + + MessageProtocolZmqTopic + + + + + + + + + tcp://localhost:5557 + + + + Last + + + + + + Payload + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -177,28 +476,137 @@ + + + + - StartExperiment + RigSchema - - TriggerHarpReadDump + + + + + Source1 + + + IsSatellite + + + + + + + + + + + + None + + + + SatelliteZmqLogic + + + + Source1 + + + + 1 + + + + + + + RigSchema + + + InboundMessages + + + Payload + + + + + + + 1 + + + + + EnableExperiment + + + InboundMessages + + + Payload + + + + + + + 1 + + + + + EndExperiment + + + + + + + + + + + + + + + + + + + + + - - + + - + - + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/Logging.bonsai b/src/Extensions/Logging.bonsai new file mode 100644 index 0000000..41074d4 --- /dev/null +++ b/src/Extensions/Logging.bonsai @@ -0,0 +1,635 @@ + + + + + + Logging + + + + Behavior + + + + + + + Modality + Behavior + + + + 1 + + + + + 1 + + + + Modality + + + HarpLogging + + + + HarpBehaviorEvents + + + Modality + + + + + + + + + + + + + + RigSchema + + + IsSatellite + + + + Source1 + + + IsSatellite + + + + + + + + + + + ComputerName + + + ZmqSatellite_{0} + it + + + + Behavior + + + + + + + + 1 + + + + + + + + + + Behavior + + + + + + + + + + + + + + + + + + + + + + HarpCommandsLogging + + + + HarpBehaviorEvents + + + + Timestamp + false + + + + HarpSeconds + + + HarpBehaviorCommands + + + HarpSeconds + + + + + + + + + + + + Modality + + + + + + + + + + + + + + + Behavior + HarpCommands/Behavior + + + + + + + + + + + + + + + + + + RigSchema + + + it.IsSatellite + it.IsSatellite + + + + + + SoftwareEvents + + + + SoftwareEvent + + + + TaskPoolScheduler + + + + HarpTimestampSource + + + + TaskPoolScheduler + + + + + + + + + + + + + Modality + + + + + + + + SoftwareEvents + LoggingRootPath + + + + + Metadata + + + + Repository + + + Head + + + + RepositoryStatus + + + + SoftwareEvent + + + + + + + + + + + + + + + + + + + + + + + + + + RigSchema + + + it.IsSatellite + it.IsSatellite + + + + + + Other + + + + RigSchema + + + IsSatellite + + + + Source1 + + + IsSatellite + + + + + + + + + + + ComputerName + + + Logs_{0} + it + + + + Logs + + + + + + + + 1 + + + + DeviceName + + + ConfigSchemaLogging + + + + SubjectSchema + + + + None + + + + Modality + + + + + + + + DeviceName + + + + + + + + LoggingRootPath + + Config + session_output + + + RigSchema + + + + None + + + + Modality + + + + + + + + LoggingRootPath + + Config + rig_output + + + RawRigSchema + + + Modality + + + + + + + + DeviceName + + + + + + + + LoggingRootPath + + Config + rig_input + json + + + RawSessionSchema + + + Modality + + + + + + + + DeviceName + + + + + + + + LoggingRootPath + + Config + session_input + json + + + + + + + + + + + + + + + + + + + + + + + + + + + + Logs + + + + EndExperiment + + + + ExperimentCompleted + + + + + SoftwareEvent + + + + HarpTimestampSource + + + + + + + + + + + + + None + + + + Modality + + + + + + + + DeviceName + + + + + + + + LoggingRootPath + + + EndSession + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BehaviorVideos + + + + + + + Modality + BehaviorVideos + + + + 1 + + + + + 1 + + + + Modality + + + TriggeredCamerasStreams + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/Main.bonsai b/src/Extensions/Main.bonsai new file mode 100644 index 0000000..2bc0990 --- /dev/null +++ b/src/Extensions/Main.bonsai @@ -0,0 +1,1217 @@ + + + + + + Source1 + + + Main + + + + Init + + + + + ../. + + + + Repository + + + SubjectSchema + + + + + + + + + + + LoggingRootPath + + + + 1 + + + + CompoundRootPath + + + + message_protocol + + + + + 1 + + + + MessageProtocolZmqTopic + + + + harp + + + + + 1 + + + + HarpZmqTopic + + + + false + + + + + 1 + + + + SaveRawVideo + + + SoftwareEvent + + + EndExperiment + + + + false + + + + IsExperimentRunning + + + EnableExperiment + + + StartLogging + + + + true + + + + IsExperimentRunning + + + StartLogging + + + StartLogging + + + + PT1S + + + + StartExperiment + + + + false + + + + + 1 + + + + IsExperimentRunning + + + IsRepoClean + + + + Repository + + + + false + + + + + SubjectSchema + + + AllowDirtyRepo + + + + + + AllowDirty? + Item2 ? False : Item1 + + + + + + Source1 + + + + + + + + + + + Repository is not clean! Please discard all local changes. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Hardware + + + + + + HarpBehaviorEvents + + + + Timestamp + false + + + + HarpTimestampSource + + + ControllersInitialized + + + + + + RigSchema + + + ExpectedControllers + (it.TriggeredCameraController0==null ? 0 : 1)+(it.TriggeredCameraController1==null ? 0 : 1) + + + + + + + + + + Source1 + + + + + + + + + + StartExperiment + + + + + + + + + OutboundMessages + + + NetworkCommunication + + + + RigSchema + + + ZmqConnection + + + ZmqConnection + + + + PT0S + PT1S + + + + + + + RigSchema + + + RigName + + + + + + + + + Event + + + + OutboundMessages + + + Source1 + + + + None + + + + ZmqConnection + + + + + + + + MessageProtocolZmqTopic + + + + + + + + + tcp://localhost:5557 + message_protocol + + + + InboundMessages + + + IsRequest + + + + Source1 + + + MessageType + + + + Request + + + + + + + + + + + + + Payload + + + + + + + 1 + + + + + EnableExperiment + + + + + + RigSchema + + + RigName + + + + + + + + + Reply + + + + OutboundMessages + + + ZmqConnection + + + + + + + + MessageProtocolZmqTopic + + + + + + + + + tcp://localhost:5557 + message_protocol + + + + Last + + + + + + InboundMessages + + + + InboundMessages + + + IsRequest + + + + Source1 + + + MessageType + + + + Request + + + + + + + + + + + + + Payload + + + + + + + 1 + + + + + EndExperiment + + + + + + RigSchema + + + RigName + + + + + + + + + Reply + + + + OutboundMessages + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + InboundMessages + + + + + + + + + + + + + + + + + + + + + + SubjectSchema + + + SkipHardwareValidation + + + + + + + Source1 + + + + + + + + + + + + + Logging + + + + Behavior + + + + + + + Modality + Behavior + + + + 1 + + + + + 1 + + + + Modality + + + HarpLogging + + + + HarpBehaviorEvents + + + Modality + + + + + + + + + + + + + + + Behavior + Behavior + + + + + + + + + + + + + HarpCommandsLogging + + + + HarpBehaviorEvents + + + + Timestamp + false + + + + HarpSeconds + + + HarpBehaviorCommands + + + HarpSeconds + + + + + + + + + + + + Modality + + + + + + + + + + + + + + + Behavior + HarpCommands/Behavior + + + + + + + + + + + + + + + + + + SoftwareEvents + + + + SoftwareEvent + + + + TaskPoolScheduler + + + + HarpTimestampSource + + + + TaskPoolScheduler + + + + + + + + + + + + + Modality + + + + + + + + SoftwareEvents + LoggingRootPath + + + + + Metadata + + + + Repository + + + Head + + + + RepositoryStatus + + + + SoftwareEvent + + + + + + + + + + + + + + + + + + + + + + + + + + Other + + + + + Logs + + + + + 1 + + + + DeviceName + + + ConfigSchemaLogging + + + + SubjectSchema + + + + None + + + + Modality + + + + + + + + DeviceName + + + + + + + + LoggingRootPath + + Config + session_output + + + RigSchema + + + + None + + + + Modality + + + + + + + + LoggingRootPath + + Config + rig_output + + + RawRigSchema + + + Modality + + + + + + + + DeviceName + + + + + + + + LoggingRootPath + + Config + rig_input + json + + + RawSessionSchema + + + Modality + + + + + + + + DeviceName + + + + + + + + LoggingRootPath + + Config + session_input + json + + + + + + + + + + + + + + + + + + + + + + + + + + + + Logs + + + + EndExperiment + + + + ExperimentCompleted + + + + + SoftwareEvent + + + + HarpTimestampSource + + + + + + + + + + + + + None + + + + Modality + + + + + + + + DeviceName + + + + + + + + LoggingRootPath + + + EndSession + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BehaviorVideos + + + + + + + Modality + BehaviorVideos + + + + 1 + + + + + 1 + + + + Modality + + + TriggeredCamerasStreams + + + + + + + + + + + + + + + + + + + + + + EndExperiment + + + + PT2S + + + + + + + StartLogging + + + + + + + 0 + + + + + JustFrames + true + + + + + + EndExperiment + + + + 1 + + + + EndRoutine + + + + Source1 + + + + 1 + + + + + + + + + + + + + PT2S + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/TryParseRegisteredMessage.cs b/src/Extensions/TryParseRegisteredMessage.cs new file mode 100644 index 0000000..36ea778 --- /dev/null +++ b/src/Extensions/TryParseRegisteredMessage.cs @@ -0,0 +1,32 @@ +using Bonsai; +using System; +using System.ComponentModel; +using System.Linq; +using System.Reactive.Linq; +using NetMQ; +using AindJustFramesSchemas.MessageProtocol; + +[Combinator] +[Description("Tries to parse NetMQFrame as RegisteredMessages and filters out invalid messages")] +[WorkflowElementCategory(ElementCategory.Combinator)] +public class TryParseRegisteredMessages +{ + public IObservable Process(IObservable source) + { + return source + .Select(frame => frame.ConvertToString()) + .Select(messageString => + { + try + { + return Newtonsoft.Json.JsonConvert.DeserializeObject(messageString); + } + catch + { + Console.WriteLine("Failed to parse message: " + messageString); + return null; + } + }) + .Where(msg => msg != null); + } +} diff --git a/src/Extensions/Visualizers.bonsai b/src/Extensions/Visualizers.bonsai index 691ba39..058b03d 100644 --- a/src/Extensions/Visualizers.bonsai +++ b/src/Extensions/Visualizers.bonsai @@ -50,15 +50,7 @@ - StartLogging - - - - true - - - - IsExperimentRunning + EnableExperiment @@ -67,8 +59,6 @@ - - @@ -97,22 +87,12 @@ EndExperiment - - - false - - - - IsExperimentRunning - - - diff --git a/src/aind_behavior_just_frames/message_protocol.py b/src/aind_behavior_just_frames/message_protocol.py new file mode 100644 index 0000000..55f4ffe --- /dev/null +++ b/src/aind_behavior_just_frames/message_protocol.py @@ -0,0 +1,45 @@ +from typing import Annotated, Any, Literal, Union + +from aind_behavior_services.message_protocol import HeartbeatPayload, LogPayload, _Message +from aind_behavior_just_frames.rig import SatelliteRig +from aind_behavior_services.session import AindBehaviorSessionModel +from pydantic import BaseModel, ConfigDict, Field, RootModel, create_model + +## This api is experimental and subject to change! + +# ================================================================================ +# Create custom messages for this platform +class StartPayload(BaseModel): + payload_type: Literal["Start"] = "Start" + +class StopPayload(BaseModel): + payload_type: Literal["Stop"] = "Stop" + +# ================================================================================ +# Register payloads into a protocol +class RegisteredPayload(RootModel): + root: Annotated[ + Union[StartPayload, StopPayload, LogPayload, HeartbeatPayload], + Field(discriminator="payload_type", json_schema_extra={"x-abstract": True}), + ] + + +RegisteredMessages = create_model( + "RegisteredMessages", + __base__=_Message[RegisteredPayload], +) + + +class Message(RootModel): + root: _Message[Any] + + +class MessageProtocol(BaseModel): + """ + Container for the complete message protocol including all registered message types. + + """ + + model_config = ConfigDict(json_schema_extra={"x-abstract": True}) + registered_message: RegisteredMessages + message: Message \ No newline at end of file diff --git a/src/aind_behavior_just_frames/regenerate.py b/src/aind_behavior_just_frames/regenerate.py index d9cdd7c..dba241d 100644 --- a/src/aind_behavior_just_frames/regenerate.py +++ b/src/aind_behavior_just_frames/regenerate.py @@ -6,6 +6,7 @@ from aind_behavior_services.utils import BonsaiSgenSerializers, convert_pydantic_to_bonsai from aind_behavior_just_frames.rig import AindJustFramesRig +from aind_behavior_just_frames.message_protocol import MessageProtocol SCHEMA_ROOT = Path("./src/DataSchemas/") EXTENSIONS_ROOT = Path("./src/Extensions/") @@ -29,6 +30,17 @@ def main(): cs_serializer=[BonsaiSgenSerializers.JSON], ) + convert_pydantic_to_bonsai( + MessageProtocol, + model_name="aind_physiology_fip_message_protocol", + root_element="Root", + cs_namespace=NAMESPACE_PREFIX + ".MessageProtocol", + json_schema_output_dir=SCHEMA_ROOT, + cs_output_dir=EXTENSIONS_ROOT, + cs_serializer=[BonsaiSgenSerializers.JSON], + ) + + if __name__ == "__main__": main() diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index c34fb2f..4014e8d 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -2,11 +2,37 @@ import aind_behavior_services.rig as rig from aind_behavior_services.rig import AindBehaviorRigModel -from pydantic import Field +from pydantic import BaseModel, Field, field_validator from . import __semver__ +class ZmqPubSub(BaseModel): + pub: rig.network.ZmqConnection = Field(description="ZMQ Publisher") + sub: rig.network.ZmqConnection = Field(description="ZMQ Subscriber") + +class SatelliteRig(AindBehaviorRigModel): + version: Literal[__semver__] = __semver__ + computer_name: str = Field(description="Remote Computer name") + zmq_connection: ZmqPubSub = Field(description="ZMQ connection for communication.") + triggered_camera_controller_0: Optional[rig.cameras.CameraController[rig.cameras.SpinnakerCamera]] = Field( + default=None, + description="Camera controller to triggered cameras. Will use Camera0 register as a trigger.", + ) + triggered_camera_controller_1: Optional[rig.cameras.CameraController[rig.cameras.SpinnakerCamera]] = Field( + default=None, + description="Camera controller to triggered cameras. Will use Camera1 register as a trigger.", + ) + is_satellite: bool = Field(default=True) + + @field_validator("zmq_connection", mode="after") + @classmethod + def validate_zmq_connection(cls, value: rig.network.ZmqConnection): + if isinstance(value, rig.network.ZmqConnection): + value.topic = "" + return value + + class AindJustFramesRig(AindBehaviorRigModel): version: Literal[__semver__] = __semver__ triggered_camera_controller_0: Optional[rig.cameras.CameraController[rig.cameras.SpinnakerCamera]] = Field( @@ -21,6 +47,8 @@ class AindJustFramesRig(AindBehaviorRigModel): ..., description="Harp behavior board. Will be the source of triggers for the two camera controllers.", ) - harp_white_rabbit: Optional[rig.harp.HarpWhiteRabbit] = Field( - default=None, description="Harp White Rabbit for time synchronization." + satellite_rigs: list[SatelliteRig] = Field( + default_factory=list, min_length=1, description="List of satellite rigs." ) + is_satellite: bool = Field(default=False) + zmq_connection: ZmqPubSub = Field(description="ZMQ connection for communication.") diff --git a/src/main.bonsai b/src/main.bonsai index f822b28..5131c58 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -1,939 +1,85 @@  - - - - - - - LoadSchemas + ReadSchemas - - RawSessionSchema - - - + + - - 1 + + - SubjectSchema - - RawRigSchema - - - 1 - - RigSchema - - - - - - - - - - - - - Init - - - - - ../. - - - - Repository - - - SubjectSchema - - - - - - - - - - - LoggingRootPath + + - - 1 + + - CompoundRootPath - - - - false - - - - - 1 - - - - SaveRawVideo - - - SoftwareEvent - - - EndExperiment - - - StartLogging - - - StartLogging - - - - PT1S - + RawSessionSchema - - StartExperiment + + - - - false - + + SubjectSchema - - 1 - - - - IsExperimentRunning - - - IsRepoClean - - - - Repository - - - - false - - - - - SubjectSchema - - - AllowDirtyRepo - - - - - - AllowDirty? - Item2 ? False : Item1 - - - - - - Source1 - - - - - - - - - - - Repository is not clean! Please discard all local changes. - - - - - - - - - - - - - - - - + + + - + - - - - - - - - - - - Hardware - - - - - - HarpBehaviorEvents - - - - - - Seconds - - - HarpTimestampSource - - - ControllersInitialized - - - - - - RigSchema - - - ExpectedControllers - (it.TriggeredCameraController0==null ? 0 : 1)+(it.TriggeredCameraController1==null ? 0 : 1) - - - - - - - - - - Source1 - - - - - - - - - - StartExperiment - - - - - - - - - - - - - + - - - - - - - - - - SubjectSchema - - - SkipHardwareValidation - - - - - - - Source1 - - - - - - - - - - - - - Logging - - - - Behavior - - - - - - - Modality - Behavior - - - - 1 - - - - - 1 - - - - Modality - - - HarpLogging - - - - HarpBehaviorEvents - - - Modality - - - - - - - - - - - - - - - Behavior - Behavior - - - - - - - - - - - - - HarpCommandsLogging - - - - HarpBehaviorEvents - - - - Timestamp - false - - - - HarpSeconds - - - HarpBehaviorCommands - - - HarpSeconds - - - - - - - - - - - - Modality - - - - - - - - - - - - - - - Behavior - HarpCommands/Behavior - - - - - - - - - - - - - - - - - - SoftwareEvents - - - - SoftwareEvent - - - - TaskPoolScheduler - - - - HarpTimestampSource - - - - TaskPoolScheduler - - - - - - - - - - - - - Modality - - - - - - - - SoftwareEvents - LoggingRootPath - - - - - Metadata - - - - Repository - - - Head - - - - RepositoryStatus - - - - SoftwareEvent - - - - - - - - - - - - - - - - - - - - - - - - - - Other - - - - - Logs - - - - - 1 - - - - DeviceName - - - ConfigSchemaLogging - - - - SubjectSchema - - - - None - - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - Config - session_output - - - RigSchema - - - - None - - - - Modality - - - - - - - - LoggingRootPath - - Config - rig_output - - - RawRigSchema - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - Config - rig_input - json - - - RawSessionSchema - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - Config - session_input - json - - - RawTaskLogicSchema - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - Config - tasklogic_input - json - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Logs - - - - EndExperiment - - - - ExperimentCompleted - - - - - SoftwareEvent - - - - HarpTimestampSource - - - - - - - - - - - - - None - - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - - EndSession - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BehaviorVideos - - - - - - - Modality - BehaviorVideos - - - - 1 - - - - - 1 - - - - Modality - - - TriggeredCamerasStreams - - - - - - - - - - - - - - - - - - - - - - EndExperiment - - - - PT2S - - - - - - - StartLogging - - - - - - - 0 - - - - - JustFrames - true - - - - - - EndExperiment - - - - 1 - - - - EndRoutine - - - - Source1 - - - - 1 - - - - - - - + - - PT2S - + - - - - - - - - - - - - - - - - + + + \ No newline at end of file diff --git a/src/satellite.bonsai b/src/satellite.bonsai new file mode 100644 index 0000000..15cf421 --- /dev/null +++ b/src/satellite.bonsai @@ -0,0 +1,85 @@ + + + + + + + + + + ReadSchemas + + + + + + + + + + + + RawRigSchema + + + + + + RigSchema + + + + + + + + + + + RawSessionSchema + + + + + + SubjectSchema + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From bf0b5328be36491515612fd8d3364918c675657c Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Mon, 24 Nov 2025 16:29:11 -0800 Subject: [PATCH 17/32] Target dev from Aind.Behavior.Services --- pyproject.toml | 2 +- .../aind_behavior_just_frames.json | 131 +- .../aind_physiology_fip_message_protocol.json | 922 ----- .../AindBehaviorJustFrames.Generated.cs | 243 +- ...dPhysiologyFipMessageProtocol.Generated.cs | 3375 +++-------------- src/aind_behavior_just_frames/rig.py | 1 - uv.lock | 518 +-- 7 files changed, 899 insertions(+), 4293 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 08a6eb9..5add741 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ version = "0.5.0rc0" readme = {file = "README.md", content-type = "text/markdown"} dependencies = [ - "aind_behavior_services>=0.12, <0.13", + "aind_behavior_services @git+https://github.com/AllenNeuralDynamics/Aind.Behavior.Services@feat-update-session", "pydantic-settings" ] diff --git a/src/DataSchemas/aind_behavior_just_frames.json b/src/DataSchemas/aind_behavior_just_frames.json index e783611..8d25f0e 100644 --- a/src/DataSchemas/aind_behavior_just_frames.json +++ b/src/DataSchemas/aind_behavior_just_frames.json @@ -3,14 +3,14 @@ "AindBehaviorSessionModel": { "properties": { "aind_behavior_services_pkg_version": { - "default": "0.12.3", + "default": "0.13.0-rc0", "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", "title": "aind_behavior_services package version", "type": "string" }, "version": { - "const": "0.12.3", - "default": "0.12.3", + "const": "0.13.0-rc0", + "default": "0.13.0-rc0", "title": "Version", "type": "string" }, @@ -42,11 +42,6 @@ "title": "Date", "type": "string" }, - "root_path": { - "description": "Root path where data will be logged", - "title": "Root Path", - "type": "string" - }, "session_name": { "default": null, "description": "Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date.", @@ -65,13 +60,6 @@ "title": "Subject", "type": "string" }, - "experiment_version": { - "default": "", - "deprecated": true, - "description": "Version of the experiment", - "title": "Experiment Version", - "type": "string" - }, "notes": { "default": null, "description": "Notes about the experiment", @@ -112,7 +100,6 @@ } }, "required": [ - "root_path", "subject" ], "title": "AindBehaviorSessionModel", @@ -121,7 +108,7 @@ "AindJustFramesRig": { "properties": { "aind_behavior_services_pkg_version": { - "default": "0.12.3", + "default": "0.13.0-rc0", "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", "title": "aind_behavior_services package version", "type": "string" @@ -142,6 +129,12 @@ "title": "Rig Name", "type": "string" }, + "data_directory": { + "description": "Directory where data will be saved to", + "format": "path", + "title": "Data Directory", + "type": "string" + }, "triggered_camera_controller_0": { "default": null, "description": "Camera controller to triggered cameras. Will use Camera0 register as a trigger.", @@ -191,6 +184,7 @@ }, "required": [ "rig_name", + "data_directory", "harp_behavior", "zmq_connection" ], @@ -210,34 +204,14 @@ "title": "Device Type", "type": "string" }, - "device_name": { - "default": null, + "name": { "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] + "title": "Name", + "type": "string" }, "calibration": { "default": null, - "description": "Calibration", + "description": "Calibration for the device.", "oneOf": [ { "$ref": "#/$defs/BaseModel" @@ -271,6 +245,7 @@ } }, "required": [ + "name", "cameras" ], "title": "CameraController[SpinnakerCamera]", @@ -284,34 +259,14 @@ "title": "Device Type", "type": "string" }, - "device_name": { - "default": null, + "name": { "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] + "title": "Name", + "type": "string" }, "calibration": { "default": null, - "description": "Calibration", + "description": "Calibration for the device.", "oneOf": [ { "$ref": "#/$defs/BaseModel" @@ -347,12 +302,14 @@ } }, "required": [ + "name", "port_name" ], "title": "HarpBehavior", "type": "object" }, "Rect": { + "description": "Represents a rectangle defined by its top-left corner, width, and height.", "properties": { "x": { "default": 0, @@ -389,7 +346,7 @@ "SatelliteRig": { "properties": { "aind_behavior_services_pkg_version": { - "default": "0.12.3", + "default": "0.13.0-rc0", "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", "title": "aind_behavior_services package version", "type": "string" @@ -410,6 +367,12 @@ "title": "Rig Name", "type": "string" }, + "data_directory": { + "description": "Directory where data will be saved to", + "format": "path", + "title": "Data Directory", + "type": "string" + }, "zmq_connection": { "$ref": "#/$defs/ZmqPubSub", "description": "ZMQ connection for communication." @@ -447,48 +410,29 @@ "required": [ "computer_name", "rig_name", + "data_directory", "zmq_connection" ], "title": "SatelliteRig", "type": "object" }, "SpinnakerCamera": { + "description": "Spinnaker camera device configuration.", "properties": { "device_type": { "const": "SpinnakerCamera", "default": "SpinnakerCamera", - "description": "Device type", "title": "Device Type", "type": "string" }, - "device_name": { - "default": null, + "name": { "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] + "title": "Name", + "type": "string" }, "calibration": { "default": null, - "description": "Calibration", + "description": "Calibration for the device.", "oneOf": [ { "$ref": "#/$defs/BaseModel" @@ -596,12 +540,14 @@ } }, "required": [ + "name", "serial_number" ], "title": "SpinnakerCamera", "type": "object" }, "SpinnakerCameraAdcBitDepth": { + "description": "ADC bit depth options for Spinnaker cameras.", "enum": [ 0, 1, @@ -616,6 +562,7 @@ ] }, "SpinnakerCameraPixelFormat": { + "description": "Pixel format options for Spinnaker cameras.", "enum": [ 0, 1, @@ -929,6 +876,7 @@ ] }, "VideoWriterFfmpeg": { + "description": "FFMPEG video writer configuration.", "properties": { "video_writer_type": { "const": "FFMPEG", @@ -966,6 +914,7 @@ "type": "object" }, "VideoWriterOpenCv": { + "description": "OpenCV video writer configuration.", "properties": { "video_writer_type": { "const": "OPENCV", diff --git a/src/DataSchemas/aind_physiology_fip_message_protocol.json b/src/DataSchemas/aind_physiology_fip_message_protocol.json index c2009cf..b1b45bf 100644 --- a/src/DataSchemas/aind_physiology_fip_message_protocol.json +++ b/src/DataSchemas/aind_physiology_fip_message_protocol.json @@ -1,202 +1,5 @@ { "$defs": { - "AindBehaviorSessionModel": { - "properties": { - "aind_behavior_services_pkg_version": { - "default": "0.12.3", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "version": { - "const": "0.12.3", - "default": "0.12.3", - "title": "Version", - "type": "string" - }, - "experiment": { - "default": null, - "description": "Name of the experiment", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Experiment" - }, - "experimenter": { - "default": [], - "description": "Name of the experimenter", - "items": { - "type": "string" - }, - "title": "Experimenter", - "type": "array" - }, - "date": { - "description": "Date of the experiment", - "format": "date-time", - "title": "Date", - "type": "string" - }, - "root_path": { - "description": "Root path where data will be logged", - "title": "Root Path", - "type": "string" - }, - "session_name": { - "default": null, - "description": "Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date.", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Session Name" - }, - "subject": { - "description": "Name of the subject", - "title": "Subject", - "type": "string" - }, - "experiment_version": { - "default": "", - "deprecated": true, - "description": "Version of the experiment", - "title": "Experiment Version", - "type": "string" - }, - "notes": { - "default": null, - "description": "Notes about the experiment", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Notes" - }, - "commit_hash": { - "default": null, - "description": "Commit hash of the repository", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Commit Hash" - }, - "allow_dirty_repo": { - "default": false, - "description": "Allow running from a dirty repository", - "title": "Allow Dirty Repo", - "type": "boolean" - }, - "skip_hardware_validation": { - "default": false, - "description": "Skip hardware validation", - "title": "Skip Hardware Validation", - "type": "boolean" - } - }, - "required": [ - "root_path", - "subject" - ], - "title": "AindBehaviorSessionModel", - "type": "object" - }, - "BaseModel": { - "properties": {}, - "title": "BaseModel", - "type": "object" - }, - "CameraController_SpinnakerCamera_": { - "properties": { - "device_type": { - "const": "CameraController", - "default": "CameraController", - "title": "Device Type", - "type": "string" - }, - "device_name": { - "default": null, - "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, - "calibration": { - "default": null, - "description": "Calibration", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, - "cameras": { - "additionalProperties": { - "$ref": "#/$defs/SpinnakerCamera" - }, - "description": "Cameras to be instantiated", - "title": "Cameras", - "type": "object" - }, - "frame_rate": { - "default": 30, - "description": "Frame rate of the trigger to all cameras", - "oneOf": [ - { - "minimum": 0, - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Frame Rate" - } - }, - "required": [ - "cameras" - ], - "title": "CameraController[SpinnakerCamera]", - "type": "object" - }, "HeartbeatPayload": { "description": "Payload for heartbeat messages indicating system health status.\n\nHeartbeat messages are used to monitor the health and availability\nof system components. They include a status indicator and optional\ncontext information.\n\nAttributes:\n context: Optional additional data about the system state\n status: Current health status of the component\n\nExamples:\n ```python\n heartbeat = HeartbeatPayload(\n status=HeartbeatStatus.OK,\n context={\"cpu_usage\": 0.25, \"memory_usage\": 0.60}\n )\n print(heartbeat.status) # HeartbeatStatus.OK\n\n warning_heartbeat = HeartbeatPayload(\n status=HeartbeatStatus.WARNING,\n context={\"disk_space_low\": True}\n )\n ```", "properties": { @@ -330,40 +133,6 @@ "title": "MessageType", "type": "string" }, - "Rect": { - "properties": { - "x": { - "default": 0, - "description": "X coordinate of the top-left corner", - "minimum": 0, - "title": "X", - "type": "integer" - }, - "y": { - "default": 0, - "description": "Y coordinate of the top-left corner", - "minimum": 0, - "title": "Y", - "type": "integer" - }, - "width": { - "default": 0, - "description": "Width of the rectangle", - "minimum": 0, - "title": "Width", - "type": "integer" - }, - "height": { - "default": 0, - "description": "Height of the rectangle", - "minimum": 0, - "title": "Height", - "type": "integer" - } - }, - "title": "Rect", - "type": "object" - }, "RegisteredMessages": { "properties": { "message_type": { @@ -445,8 +214,6 @@ "mapping": { "HeartbeatPayload": "#/$defs/HeartbeatPayload", "LogPayload": "#/$defs/LogPayload", - "SatelliteRig": "#/$defs/SatelliteRigPayload", - "SatelliteSession": "#/$defs/SatelliteSessionPayload", "Start": "#/$defs/StartPayload", "Stop": "#/$defs/StopPayload" }, @@ -459,12 +226,6 @@ { "$ref": "#/$defs/StopPayload" }, - { - "$ref": "#/$defs/SatelliteRigPayload" - }, - { - "$ref": "#/$defs/SatelliteSessionPayload" - }, { "$ref": "#/$defs/LogPayload" }, @@ -475,569 +236,6 @@ "title": "RegisteredPayload", "x-abstract": true }, - "SatelliteRig": { - "properties": { - "aind_behavior_services_pkg_version": { - "default": "0.12.3", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "version": { - "const": "0.5.0-rc0", - "default": "0.5.0-rc0", - "title": "Version", - "type": "string" - }, - "computer_name": { - "description": "Remote Computer name", - "title": "Computer Name", - "type": "string" - }, - "rig_name": { - "description": "Rig name", - "title": "Rig Name", - "type": "string" - }, - "zmq_connection": { - "$ref": "#/$defs/ZmqPubSub", - "description": "ZMQ connection for communication." - }, - "triggered_camera_controller_0": { - "default": null, - "description": "Camera controller to triggered cameras. Will use Camera0 register as a trigger.", - "oneOf": [ - { - "$ref": "#/$defs/CameraController_SpinnakerCamera_" - }, - { - "type": "null" - } - ] - }, - "triggered_camera_controller_1": { - "default": null, - "description": "Camera controller to triggered cameras. Will use Camera1 register as a trigger.", - "oneOf": [ - { - "$ref": "#/$defs/CameraController_SpinnakerCamera_" - }, - { - "type": "null" - } - ] - }, - "is_satellite": { - "default": true, - "title": "Is Satellite", - "type": "boolean" - } - }, - "required": [ - "computer_name", - "rig_name", - "zmq_connection" - ], - "title": "SatelliteRig", - "type": "object" - }, - "SatelliteRigPayload": { - "properties": { - "payload_type": { - "const": "SatelliteRig", - "default": "SatelliteRig", - "title": "Payload Type", - "type": "string" - }, - "rig": { - "$ref": "#/$defs/SatelliteRig", - "description": "Satellite Rig configuration." - } - }, - "required": [ - "rig" - ], - "title": "SatelliteRigPayload", - "type": "object" - }, - "SatelliteSessionPayload": { - "properties": { - "payload_type": { - "const": "SatelliteSession", - "default": "SatelliteSession", - "title": "Payload Type", - "type": "string" - }, - "session": { - "$ref": "#/$defs/AindBehaviorSessionModel", - "description": "Satellite session configuration." - } - }, - "required": [ - "session" - ], - "title": "SatelliteSessionPayload", - "type": "object" - }, - "SpinnakerCamera": { - "properties": { - "device_type": { - "const": "SpinnakerCamera", - "default": "SpinnakerCamera", - "description": "Device type", - "title": "Device Type", - "type": "string" - }, - "device_name": { - "default": null, - "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, - "calibration": { - "default": null, - "description": "Calibration", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, - "serial_number": { - "description": "Camera serial number", - "title": "Serial Number", - "type": "string" - }, - "binning": { - "default": 1, - "description": "Binning", - "minimum": 1, - "title": "Binning", - "type": "integer" - }, - "color_processing": { - "default": "Default", - "description": "Color processing", - "enum": [ - "Default", - "NoColorProcessing" - ], - "title": "Color Processing", - "type": "string" - }, - "exposure": { - "default": 1000, - "description": "Exposure time", - "minimum": 100, - "title": "Exposure", - "type": "integer" - }, - "gain": { - "default": 0, - "description": "Gain", - "minimum": 0, - "title": "Gain", - "type": "number" - }, - "gamma": { - "default": null, - "description": "Gamma. If None, will disable gamma correction.", - "oneOf": [ - { - "minimum": 0, - "type": "number" - }, - { - "type": "null" - } - ], - "title": "Gamma" - }, - "adc_bit_depth": { - "default": 0, - "description": "ADC bit depth. If None will be left as default.", - "oneOf": [ - { - "$ref": "#/$defs/SpinnakerCameraAdcBitDepth" - }, - { - "type": "null" - } - ] - }, - "pixel_format": { - "default": 0, - "description": "Pixel format. If None will be left as default.", - "oneOf": [ - { - "$ref": "#/$defs/SpinnakerCameraPixelFormat" - }, - { - "type": "null" - } - ] - }, - "region_of_interest": { - "$ref": "#/$defs/Rect", - "default": { - "x": 0, - "y": 0, - "width": 0, - "height": 0 - }, - "description": "Region of interest" - }, - "video_writer": { - "default": null, - "description": "Video writer. If not provided, no video will be saved.", - "oneOf": [ - { - "$ref": "#/$defs/VideoWriter" - }, - { - "type": "null" - } - ] - } - }, - "required": [ - "serial_number" - ], - "title": "SpinnakerCamera", - "type": "object" - }, - "SpinnakerCameraAdcBitDepth": { - "enum": [ - 0, - 1, - 2 - ], - "title": "SpinnakerCameraAdcBitDepth", - "type": "integer", - "x-enumNames": [ - "Adc8bit", - "Adc10bit", - "Adc12bit" - ] - }, - "SpinnakerCameraPixelFormat": { - "enum": [ - 0, - 1, - 2, - 3, - 4, - 5, - 6, - 7, - 8, - 9, - 10, - 11, - 12, - 13, - 14, - 15, - 16, - 17, - 18, - 19, - 20, - 21, - 22, - 23, - 24, - 25, - 26, - 27, - 28, - 29, - 30, - 31, - 32, - 33, - 34, - 35, - 36, - 37, - 38, - 39, - 40, - 41, - 42, - 43, - 44, - 45, - 46, - 47, - 48, - 49, - 50, - 51, - 52, - 53, - 54, - 55, - 56, - 57, - 58, - 59, - 60, - 61, - 62, - 63, - 64, - 65, - 66, - 67, - 68, - 69, - 70, - 71, - 72, - 73, - 74, - 75, - 76, - 77, - 78, - 79, - 80, - 81, - 82, - 83, - 84, - 85, - 86, - 87, - 88, - 89, - 90, - 91, - 92, - 93, - 94, - 95, - 96, - 97, - 98, - 99, - 100, - 101, - 102, - 103, - 104, - 105, - 106, - 107, - 108, - 109, - 110, - 111, - 112, - 113, - 114, - 115, - 116, - 117, - 118, - 119, - 120, - 121, - 122, - 123, - 124, - 125, - 126, - 127, - 128, - 129, - 130, - 131, - 132, - 133, - 134, - 135, - 136, - 137, - 138, - 139, - 140, - 141, - 142, - 143 - ], - "title": "SpinnakerCameraPixelFormat", - "type": "integer", - "x-enumNames": [ - "Mono8", - "Mono16", - "Rgb8packed", - "Bayergr8", - "Bayerrg8", - "Bayergb8", - "Bayerbg8", - "Bayergr16", - "Bayerrg16", - "Bayergb16", - "Bayerbg16", - "Mono12packed", - "Bayergr12packed", - "Bayerrg12packed", - "Bayergb12packed", - "Bayerbg12packed", - "Yuv411packed", - "Yuv422packed", - "Yuv444packed", - "Mono12p", - "Bayergr12p", - "Bayerrg12p", - "Bayergb12p", - "Bayerbg12p", - "Ycbcr8", - "Ycbcr4228", - "Ycbcr4118", - "Bgr8", - "Bgra8", - "Mono10packed", - "Bayergr10packed", - "Bayerrg10packed", - "Bayergb10packed", - "Bayerbg10packed", - "Mono10p", - "Bayergr10p", - "Bayerrg10p", - "Bayergb10p", - "Bayerbg10p", - "Mono1p", - "Mono2p", - "Mono4p", - "Mono8s", - "Mono10", - "Mono12", - "Mono14", - "Mono16s", - "Mono32f", - "Bayerbg10", - "Bayerbg12", - "Bayergb10", - "Bayergb12", - "Bayergr10", - "Bayergr12", - "Bayerrg10", - "Bayerrg12", - "Rgba8", - "Rgba10", - "Rgba10p", - "Rgba12", - "Rgba12p", - "Rgba14", - "Rgba16", - "Rgb8", - "Rgb8Planar", - "Rgb10", - "Rgb10Planar", - "Rgb10p", - "Rgb10p32", - "Rgb12", - "Rgb12Planar", - "Rgb12p", - "Rgb14", - "Rgb16", - "Rgb16s", - "Rgb32f", - "Rgb16Planar", - "Rgb565p", - "Bgra10", - "Bgra10p", - "Bgra12", - "Bgra12p", - "Bgra14", - "Bgra16", - "Rgba32f", - "Bgr10", - "Bgr10p", - "Bgr12", - "Bgr12p", - "Bgr14", - "Bgr16", - "Bgr565p", - "R8", - "R10", - "R12", - "R16", - "G8", - "G10", - "G12", - "G16", - "B8", - "B10", - "B12", - "B16", - "Coord3dAbc8", - "Coord3dAbc8Planar", - "Coord3dAbc10p", - "Coord3dAbc10pPlanar", - "Coord3dAbc12p", - "Coord3dAbc12pPlanar", - "Coord3dAbc16", - "Coord3dAbc16Planar", - "Coord3dAbc32f", - "Coord3dAbc32fPlanar", - "Coord3dAc8", - "Coord3dAc8Planar", - "Coord3dAc10p", - "Coord3dAc10pPlanar", - "Coord3dAc12p", - "Coord3dAc12pPlanar", - "Coord3dAc16", - "Coord3dAc16Planar", - "Coord3dAc32f", - "Coord3dAc32fPlanar", - "Coord3dA8", - "Coord3dA10p", - "Coord3dA12p", - "Coord3dA16", - "Coord3dA32f", - "Coord3dB8", - "Coord3dB10p", - "Coord3dB12p", - "Coord3dB16", - "Coord3dB32f", - "Coord3dC8", - "Coord3dC10p", - "Coord3dC12p", - "Coord3dC16", - "Coord3dC32f", - "Confidence1", - "Confidence1p", - "Confidence8", - "Confidence16", - "Confidence32f" - ] - }, "StartPayload": { "properties": { "payload_type": { @@ -1062,126 +260,6 @@ "title": "StopPayload", "type": "object" }, - "VideoWriter": { - "discriminator": { - "mapping": { - "FFMPEG": "#/$defs/VideoWriterFfmpeg", - "OPENCV": "#/$defs/VideoWriterOpenCv" - }, - "propertyName": "video_writer_type" - }, - "oneOf": [ - { - "$ref": "#/$defs/VideoWriterFfmpeg" - }, - { - "$ref": "#/$defs/VideoWriterOpenCv" - } - ] - }, - "VideoWriterFfmpeg": { - "properties": { - "video_writer_type": { - "const": "FFMPEG", - "default": "FFMPEG", - "title": "Video Writer Type", - "type": "string" - }, - "frame_rate": { - "default": 30, - "description": "Encoding frame rate", - "minimum": 0, - "title": "Frame Rate", - "type": "integer" - }, - "container_extension": { - "default": "mp4", - "description": "Container extension", - "title": "Container Extension", - "type": "string" - }, - "output_arguments": { - "default": "-vf \"scale=out_color_matrix=bt709:out_range=full,format=bgr24,scale=out_range=full\" -c:v h264_nvenc -pix_fmt yuv420p -color_range full -colorspace bt709 -color_trc linear -tune hq -preset p4 -rc vbr -cq 12 -b:v 0M -metadata author=\"Allen Institute for Neural Dynamics\" -maxrate 700M -bufsize 350M", - "description": "Output arguments", - "title": "Output Arguments", - "type": "string" - }, - "input_arguments": { - "default": "-colorspace bt709 -color_primaries bt709 -color_range full -color_trc linear", - "description": "Input arguments", - "title": "Input Arguments", - "type": "string" - } - }, - "title": "VideoWriterFfmpeg", - "type": "object" - }, - "VideoWriterOpenCv": { - "properties": { - "video_writer_type": { - "const": "OPENCV", - "default": "OPENCV", - "title": "Video Writer Type", - "type": "string" - }, - "frame_rate": { - "default": 30, - "description": "Encoding frame rate", - "minimum": 0, - "title": "Frame Rate", - "type": "integer" - }, - "container_extension": { - "default": "avi", - "description": "Container extension", - "title": "Container Extension", - "type": "string" - }, - "four_cc": { - "default": "FMP4", - "description": "Four character code", - "title": "Four Cc", - "type": "string" - } - }, - "title": "VideoWriterOpenCv", - "type": "object" - }, - "ZmqConnection": { - "properties": { - "connection_string": { - "default": "@tcp://localhost:5556", - "description": "The connection string for the ZMQ socket.", - "title": "Connection String", - "type": "string" - }, - "topic": { - "default": "", - "title": "Topic", - "type": "string" - } - }, - "title": "ZmqConnection", - "type": "object" - }, - "ZmqPubSub": { - "properties": { - "pub": { - "$ref": "#/$defs/ZmqConnection", - "description": "ZMQ Publisher" - }, - "sub": { - "$ref": "#/$defs/ZmqConnection", - "description": "ZMQ Subscriber" - } - }, - "required": [ - "pub", - "sub" - ], - "title": "ZmqPubSub", - "type": "object" - }, "_Message_Any_": { "properties": { "message_type": { diff --git a/src/Extensions/AindBehaviorJustFrames.Generated.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs index 22bb3b9..c803a5e 100644 --- a/src/Extensions/AindBehaviorJustFrames.Generated.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -25,14 +25,10 @@ public partial class AindBehaviorSessionModel private System.DateTimeOffset _date; - private string _rootPath; - private string _sessionName; private string _subject; - private string _experimentVersion; - private string _notes; private string _commitHash; @@ -43,10 +39,9 @@ public partial class AindBehaviorSessionModel public AindBehaviorSessionModel() { - _aindBehaviorServicesPkgVersion = "0.12.3"; - _version = "0.12.3"; + _aindBehaviorServicesPkgVersion = "0.13.0-rc0"; + _version = "0.13.0-rc0"; _experimenter = new System.Collections.Generic.List(); - _experimentVersion = ""; _allowDirtyRepo = false; _skipHardwareValidation = false; } @@ -58,10 +53,8 @@ protected AindBehaviorSessionModel(AindBehaviorSessionModel other) _experiment = other._experiment; _experimenter = other._experimenter; _date = other._date; - _rootPath = other._rootPath; _sessionName = other._sessionName; _subject = other._subject; - _experimentVersion = other._experimentVersion; _notes = other._notes; _commitHash = other._commitHash; _allowDirtyRepo = other._allowDirtyRepo; @@ -147,23 +140,6 @@ public System.DateTimeOffset Date } } - /// - /// Root path where data will be logged - /// - [Newtonsoft.Json.JsonPropertyAttribute("root_path", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Root path where data will be logged")] - public string RootPath - { - get - { - return _rootPath; - } - set - { - _rootPath = value; - } - } - /// /// Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date. /// @@ -199,23 +175,6 @@ public string Subject } } - /// - /// Version of the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("experiment_version")] - [System.ComponentModel.DescriptionAttribute("Version of the experiment")] - public string ExperimentVersion - { - get - { - return _experimentVersion; - } - set - { - _experimentVersion = value; - } - } - /// /// Notes about the experiment /// @@ -301,10 +260,8 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("Experiment = " + _experiment + ", "); stringBuilder.Append("Experimenter = " + _experimenter + ", "); stringBuilder.Append("Date = " + _date + ", "); - stringBuilder.Append("RootPath = " + _rootPath + ", "); stringBuilder.Append("SessionName = " + _sessionName + ", "); stringBuilder.Append("Subject = " + _subject + ", "); - stringBuilder.Append("ExperimentVersion = " + _experimentVersion + ", "); stringBuilder.Append("Notes = " + _notes + ", "); stringBuilder.Append("CommitHash = " + _commitHash + ", "); stringBuilder.Append("AllowDirtyRepo = " + _allowDirtyRepo + ", "); @@ -341,6 +298,8 @@ public partial class AindJustFramesRig private string _rigName; + private string _dataDirectory; + private CameraControllerSpinnakerCamera _triggeredCameraController0; private CameraControllerSpinnakerCamera _triggeredCameraController1; @@ -355,7 +314,7 @@ public partial class AindJustFramesRig public AindJustFramesRig() { - _aindBehaviorServicesPkgVersion = "0.12.3"; + _aindBehaviorServicesPkgVersion = "0.13.0-rc0"; _version = "0.5.0-rc0"; _harpBehavior = new HarpBehavior(); _satelliteRigs = new System.Collections.Generic.List(); @@ -369,6 +328,7 @@ protected AindJustFramesRig(AindJustFramesRig other) _version = other._version; _computerName = other._computerName; _rigName = other._rigName; + _dataDirectory = other._dataDirectory; _triggeredCameraController0 = other._triggeredCameraController0; _triggeredCameraController1 = other._triggeredCameraController1; _harpBehavior = other._harpBehavior; @@ -437,6 +397,23 @@ public string RigName } } + /// + /// Directory where data will be saved to + /// + [Newtonsoft.Json.JsonPropertyAttribute("data_directory", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Directory where data will be saved to")] + public string DataDirectory + { + get + { + return _dataDirectory; + } + set + { + _dataDirectory = value; + } + } + /// /// Camera controller to triggered cameras. Will use Camera0 register as a trigger. /// @@ -557,6 +534,7 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("Version = " + _version + ", "); stringBuilder.Append("ComputerName = " + _computerName + ", "); stringBuilder.Append("RigName = " + _rigName + ", "); + stringBuilder.Append("DataDirectory = " + _dataDirectory + ", "); stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); stringBuilder.Append("HarpBehavior = " + _harpBehavior + ", "); @@ -633,9 +611,7 @@ public partial class CameraControllerSpinnakerCamera private string _deviceType; - private string _deviceName; - - private BaseModel _additionalSettings; + private string _name; private BaseModel _calibration; @@ -652,8 +628,7 @@ public CameraControllerSpinnakerCamera() protected CameraControllerSpinnakerCamera(CameraControllerSpinnakerCamera other) { _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; + _name = other._name; _calibration = other._calibration; _cameras = other._cameras; _frameRate = other._frameRate; @@ -675,44 +650,26 @@ public string DeviceType /// /// Device name /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [Newtonsoft.Json.JsonPropertyAttribute("name", Required=Newtonsoft.Json.Required.Always)] [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings + public string Name { get { - return _additionalSettings; + return _name; } set { - _additionalSettings = value; + _name = value; } } /// - /// Calibration + /// Calibration for the device. /// [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration for the device.")] public BaseModel Calibration { get @@ -774,8 +731,7 @@ public System.IObservable Generate(Sys protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("DeviceName = " + _deviceName + ", "); - stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Name = " + _name + ", "); stringBuilder.Append("Calibration = " + _calibration + ", "); stringBuilder.Append("Cameras = " + _cameras + ", "); stringBuilder.Append("FrameRate = " + _frameRate); @@ -805,9 +761,7 @@ public partial class HarpBehavior private string _deviceType; - private string _deviceName; - - private BaseModel _additionalSettings; + private string _name; private BaseModel _calibration; @@ -826,8 +780,7 @@ public HarpBehavior() protected HarpBehavior(HarpBehavior other) { _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; + _name = other._name; _calibration = other._calibration; _whoAmI = other._whoAmI; _serialNumber = other._serialNumber; @@ -850,44 +803,26 @@ public string DeviceType /// /// Device name /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [Newtonsoft.Json.JsonPropertyAttribute("name", Required=Newtonsoft.Json.Required.Always)] [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName + public string Name { get { - return _deviceName; + return _name; } set { - _deviceName = value; + _name = value; } } /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings - { - get - { - return _additionalSettings; - } - set - { - _additionalSettings = value; - } - } - - /// - /// Calibration + /// Calibration for the device. /// [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration for the device.")] public BaseModel Calibration { get @@ -960,8 +895,7 @@ public System.IObservable Generate(System.IObservable + /// Represents a rectangle defined by its top-left corner, width, and height. + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Represents a rectangle defined by its top-left corner, width, and height.")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class Rect @@ -1130,6 +1068,8 @@ public partial class SatelliteRig private string _rigName; + private string _dataDirectory; + private ZmqPubSub _zmqConnection; private CameraControllerSpinnakerCamera _triggeredCameraController0; @@ -1140,7 +1080,7 @@ public partial class SatelliteRig public SatelliteRig() { - _aindBehaviorServicesPkgVersion = "0.12.3"; + _aindBehaviorServicesPkgVersion = "0.13.0-rc0"; _version = "0.5.0-rc0"; _zmqConnection = new ZmqPubSub(); _isSatellite = true; @@ -1152,6 +1092,7 @@ protected SatelliteRig(SatelliteRig other) _version = other._version; _computerName = other._computerName; _rigName = other._rigName; + _dataDirectory = other._dataDirectory; _zmqConnection = other._zmqConnection; _triggeredCameraController0 = other._triggeredCameraController0; _triggeredCameraController1 = other._triggeredCameraController1; @@ -1218,6 +1159,23 @@ public string RigName } } + /// + /// Directory where data will be saved to + /// + [Newtonsoft.Json.JsonPropertyAttribute("data_directory", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Directory where data will be saved to")] + public string DataDirectory + { + get + { + return _dataDirectory; + } + set + { + _dataDirectory = value; + } + } + /// /// ZMQ connection for communication. /// @@ -1301,6 +1259,7 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("Version = " + _version + ", "); stringBuilder.Append("ComputerName = " + _computerName + ", "); stringBuilder.Append("RigName = " + _rigName + ", "); + stringBuilder.Append("DataDirectory = " + _dataDirectory + ", "); stringBuilder.Append("ZmqConnection = " + _zmqConnection + ", "); stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); @@ -1323,7 +1282,11 @@ public override string ToString() } + /// + /// Spinnaker camera device configuration. + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Spinnaker camera device configuration.")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class SpinnakerCamera @@ -1331,9 +1294,7 @@ public partial class SpinnakerCamera private string _deviceType; - private string _deviceName; - - private BaseModel _additionalSettings; + private string _name; private BaseModel _calibration; @@ -1372,8 +1333,7 @@ public SpinnakerCamera() protected SpinnakerCamera(SpinnakerCamera other) { _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; + _name = other._name; _calibration = other._calibration; _serialNumber = other._serialNumber; _binning = other._binning; @@ -1387,11 +1347,7 @@ protected SpinnakerCamera(SpinnakerCamera other) _videoWriter = other._videoWriter; } - /// - /// Device type - /// [Newtonsoft.Json.JsonPropertyAttribute("device_type")] - [System.ComponentModel.DescriptionAttribute("Device type")] public string DeviceType { get @@ -1407,44 +1363,26 @@ public string DeviceType /// /// Device name /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [Newtonsoft.Json.JsonPropertyAttribute("name", Required=Newtonsoft.Json.Required.Always)] [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName + public string Name { get { - return _deviceName; + return _name; } set { - _deviceName = value; + _name = value; } } /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings - { - get - { - return _additionalSettings; - } - set - { - _additionalSettings = value; - } - } - - /// - /// Calibration + /// Calibration for the device. /// [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration for the device.")] public BaseModel Calibration { get @@ -1646,8 +1584,7 @@ public System.IObservable Generate(System.IObservable< protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("DeviceName = " + _deviceName + ", "); - stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Name = " + _name + ", "); stringBuilder.Append("Calibration = " + _calibration + ", "); stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); stringBuilder.Append("Binning = " + _binning + ", "); @@ -1677,6 +1614,9 @@ public override string ToString() } + /// + /// ADC bit depth options for Spinnaker cameras. + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] public enum SpinnakerCameraAdcBitDepth { @@ -1692,6 +1632,9 @@ public enum SpinnakerCameraAdcBitDepth } + /// + /// Pixel format options for Spinnaker cameras. + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] public enum SpinnakerCameraPixelFormat { @@ -2130,10 +2073,14 @@ public enum SpinnakerCameraPixelFormat } + /// + /// FFMPEG video writer configuration. + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "video_writer_type")] [JsonInheritanceAttribute("FFMPEG", typeof(VideoWriterFfmpeg))] [JsonInheritanceAttribute("OPENCV", typeof(VideoWriterOpenCv))] + [System.ComponentModel.DescriptionAttribute("FFMPEG video writer configuration.")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class VideoWriter @@ -2177,7 +2124,11 @@ public override string ToString() } + /// + /// FFMPEG video writer configuration. + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("FFMPEG video writer configuration.")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class VideoWriterFfmpeg : VideoWriter @@ -2301,7 +2252,11 @@ protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) } + /// + /// OpenCV video writer configuration. + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("OpenCV video writer configuration.")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class VideoWriterOpenCv : VideoWriter diff --git a/src/Extensions/AindPhysiologyFipMessageProtocol.Generated.cs b/src/Extensions/AindPhysiologyFipMessageProtocol.Generated.cs index fae3503..74253e5 100644 --- a/src/Extensions/AindPhysiologyFipMessageProtocol.Generated.cs +++ b/src/Extensions/AindPhysiologyFipMessageProtocol.Generated.cs @@ -9,2634 +9,365 @@ namespace AindJustFramesSchemas.MessageProtocol { #pragma warning disable // Disable all warnings + /// + /// Payload for heartbeat messages indicating system health status. + /// + ///Heartbeat messages are used to monitor the health and availability + ///of system components. They include a status indicator and optional + ///context information. + /// + ///Attributes: + /// context: Optional additional data about the system state + /// status: Current health status of the component + /// + ///Examples: + /// ```python + /// heartbeat = HeartbeatPayload( + /// status=HeartbeatStatus.OK, + /// context={"cpu_usage": 0.25, "memory_usage": 0.60} + /// ) + /// print(heartbeat.status) # HeartbeatStatus.OK + /// + /// warning_heartbeat = HeartbeatPayload( + /// status=HeartbeatStatus.WARNING, + /// context={"disk_space_low": True} + /// ) + /// ``` + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute(@"Payload for heartbeat messages indicating system health status. + + Heartbeat messages are used to monitor the health and availability + of system components. They include a status indicator and optional + context information. + + Attributes: + context: Optional additional data about the system state + status: Current health status of the component + + Examples: + ```python + heartbeat = HeartbeatPayload( + status=HeartbeatStatus.OK, + context={""cpu_usage"": 0.25, ""memory_usage"": 0.60} + ) + print(heartbeat.status) # HeartbeatStatus.OK + + warning_heartbeat = HeartbeatPayload( + status=HeartbeatStatus.WARNING, + context={""disk_space_low"": True} + ) + ```")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class AindBehaviorSessionModel + public partial class HeartbeatPayload : RegisteredPayload { - private string _aindBehaviorServicesPkgVersion; - - private string _version; - - private string _experiment; - - private System.Collections.Generic.List _experimenter; - - private System.DateTimeOffset _date; - - private string _rootPath; - - private string _sessionName; - - private string _subject; - - private string _experimentVersion; - - private string _notes; - - private string _commitHash; - - private bool _allowDirtyRepo; - - private bool _skipHardwareValidation; - - public AindBehaviorSessionModel() - { - _aindBehaviorServicesPkgVersion = "0.12.3"; - _version = "0.12.3"; - _experimenter = new System.Collections.Generic.List(); - _experimentVersion = ""; - _allowDirtyRepo = false; - _skipHardwareValidation = false; - } - - protected AindBehaviorSessionModel(AindBehaviorSessionModel other) - { - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _version = other._version; - _experiment = other._experiment; - _experimenter = other._experimenter; - _date = other._date; - _rootPath = other._rootPath; - _sessionName = other._sessionName; - _subject = other._subject; - _experimentVersion = other._experimentVersion; - _notes = other._notes; - _commitHash = other._commitHash; - _allowDirtyRepo = other._allowDirtyRepo; - _skipHardwareValidation = other._skipHardwareValidation; - } + private object _context; - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion - { - get - { - return _aindBehaviorServicesPkgVersion; - } - set - { - _aindBehaviorServicesPkgVersion = value; - } - } + private HeartbeatStatus _status; - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version + public HeartbeatPayload() { - get - { - return _version; - } - set - { - _version = value; - } } - /// - /// Name of the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("experiment")] - [System.ComponentModel.DescriptionAttribute("Name of the experiment")] - public string Experiment + protected HeartbeatPayload(HeartbeatPayload other) : + base(other) { - get - { - return _experiment; - } - set - { - _experiment = value; - } + _context = other._context; + _status = other._status; } /// - /// Name of the experimenter + /// Additional context for the heartbeat message. /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] - [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] - public System.Collections.Generic.List Experimenter + [Newtonsoft.Json.JsonPropertyAttribute("context")] + [System.ComponentModel.DescriptionAttribute("Additional context for the heartbeat message.")] + public object Context { get { - return _experimenter; + return _context; } set { - _experimenter = value; + _context = value; } } /// - /// Date of the experiment + /// The status of the heartbeat message /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("date")] - [System.ComponentModel.DescriptionAttribute("Date of the experiment")] - public System.DateTimeOffset Date - { - get - { - return _date; - } - set - { - _date = value; - } - } - - /// - /// Root path where data will be logged - /// - [Newtonsoft.Json.JsonPropertyAttribute("root_path", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Root path where data will be logged")] - public string RootPath - { - get - { - return _rootPath; - } - set - { - _rootPath = value; - } - } - - /// - /// Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date. - /// - [Newtonsoft.Json.JsonPropertyAttribute("session_name")] - [System.ComponentModel.DescriptionAttribute("Name of the session. This will be used to create a folder in the root path. If no" + - "t provided, it will be generated using subject and date.")] - public string SessionName - { - get - { - return _sessionName; - } - set - { - _sessionName = value; - } - } - - /// - /// Name of the subject - /// - [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Name of the subject")] - public string Subject - { - get - { - return _subject; - } - set - { - _subject = value; - } - } - - /// - /// Version of the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("experiment_version")] - [System.ComponentModel.DescriptionAttribute("Version of the experiment")] - public string ExperimentVersion - { - get - { - return _experimentVersion; - } - set - { - _experimentVersion = value; - } - } - - /// - /// Notes about the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("notes")] - [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] - public string Notes + [Newtonsoft.Json.JsonPropertyAttribute("status", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The status of the heartbeat message")] + public HeartbeatStatus Status { get { - return _notes; + return _status; } set { - _notes = value; + _status = value; } } - /// - /// Commit hash of the repository - /// - [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")] - [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")] - public string CommitHash + public System.IObservable Generate() { - get - { - return _commitHash; - } - set - { - _commitHash = value; - } + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HeartbeatPayload(this))); } - /// - /// Allow running from a dirty repository - /// - [Newtonsoft.Json.JsonPropertyAttribute("allow_dirty_repo")] - [System.ComponentModel.DescriptionAttribute("Allow running from a dirty repository")] - public bool AllowDirtyRepo + public System.IObservable Generate(System.IObservable source) { - get - { - return _allowDirtyRepo; - } - set - { - _allowDirtyRepo = value; - } + return System.Reactive.Linq.Observable.Select(source, _ => new HeartbeatPayload(this)); } - /// - /// Skip hardware validation - /// - [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")] - [System.ComponentModel.DescriptionAttribute("Skip hardware validation")] - public bool SkipHardwareValidation + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) { - get - { - return _skipHardwareValidation; - } - set + if (base.PrintMembers(stringBuilder)) { - _skipHardwareValidation = value; + stringBuilder.Append(", "); } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorSessionModel(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorSessionModel(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("Version = " + _version + ", "); - stringBuilder.Append("Experiment = " + _experiment + ", "); - stringBuilder.Append("Experimenter = " + _experimenter + ", "); - stringBuilder.Append("Date = " + _date + ", "); - stringBuilder.Append("RootPath = " + _rootPath + ", "); - stringBuilder.Append("SessionName = " + _sessionName + ", "); - stringBuilder.Append("Subject = " + _subject + ", "); - stringBuilder.Append("ExperimentVersion = " + _experimentVersion + ", "); - stringBuilder.Append("Notes = " + _notes + ", "); - stringBuilder.Append("CommitHash = " + _commitHash + ", "); - stringBuilder.Append("AllowDirtyRepo = " + _allowDirtyRepo + ", "); - stringBuilder.Append("SkipHardwareValidation = " + _skipHardwareValidation); + stringBuilder.Append("Context = " + _context + ", "); + stringBuilder.Append("Status = " + _status); return true; } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } } + /// + /// Enumeration of possible heartbeat status values. + /// + ///Represents the health status of a system component, + ///with higher values indicating more severe issues. + /// + ///Examples: + /// ```python + /// HeartbeatStatus.OK # + /// HeartbeatStatus.CRITICAL > HeartbeatStatus.WARNING # True + /// int(HeartbeatStatus.ERROR) # 2 + /// ``` + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class BaseModel + public enum HeartbeatStatus { - public BaseModel() - { - } - - protected BaseModel(BaseModel other) - { - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new BaseModel(this))); - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Ok = 0, - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new BaseModel(this)); - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] + Warning = 1, - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - return false; - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] + Error = 2, - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] + Critical = 3, } + /// + /// Enumeration of log levels for the logging system. + /// + ///Follows standard Python logging levels with integer values + ///that allow for easy comparison and filtering. + /// + ///Examples: + /// ```python + /// LogLevel.ERROR > LogLevel.WARNING # True + /// LogLevel.DEBUG.value # 10 + /// str(LogLevel.INFO) # 'LogLevel.INFO' + /// ``` + /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class CameraControllerSpinnakerCamera + public enum LogLevel { - private string _deviceType; - - private string _deviceName; - - private BaseModel _additionalSettings; - - private BaseModel _calibration; - - private System.Collections.Generic.Dictionary _cameras; - - private int? _frameRate; - - public CameraControllerSpinnakerCamera() - { - _deviceType = "CameraController"; - _cameras = new System.Collections.Generic.Dictionary(); - } - - protected CameraControllerSpinnakerCamera(CameraControllerSpinnakerCamera other) - { - _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; - _calibration = other._calibration; - _cameras = other._cameras; - _frameRate = other._frameRate; - } - - [Newtonsoft.Json.JsonPropertyAttribute("device_type")] - public string DeviceType - { - get - { - return _deviceType; - } - set - { - _deviceType = value; - } - } - - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings - { - get - { - return _additionalSettings; - } - set - { - _additionalSettings = value; - } - } - - /// - /// Calibration - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration")] - public BaseModel Calibration - { - get - { - return _calibration; - } - set - { - _calibration = value; - } - } - - /// - /// Cameras to be instantiated - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("cameras", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Cameras to be instantiated")] - public System.Collections.Generic.Dictionary Cameras - { - get - { - return _cameras; - } - set - { - _cameras = value; - } - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="50")] + Critical = 50, - /// - /// Frame rate of the trigger to all cameras - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("frame_rate")] - [System.ComponentModel.DescriptionAttribute("Frame rate of the trigger to all cameras")] - public int? FrameRate - { - get - { - return _frameRate; - } - set - { - _frameRate = value; - } - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="40")] + Error = 40, - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new CameraControllerSpinnakerCamera(this))); - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="30")] + Warning = 30, - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new CameraControllerSpinnakerCamera(this)); - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="20")] + Info = 20, - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("DeviceName = " + _deviceName + ", "); - stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); - stringBuilder.Append("Calibration = " + _calibration + ", "); - stringBuilder.Append("Cameras = " + _cameras + ", "); - stringBuilder.Append("FrameRate = " + _frameRate); - return true; - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="10")] + Debug = 10, - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Notset = 0, } /// - /// Payload for heartbeat messages indicating system health status. + /// Payload for log messages containing logging information. /// - ///Heartbeat messages are used to monitor the health and availability - ///of system components. They include a status indicator and optional - ///context information. + ///This payload carries log data including the message content, + ///severity level, optional context, and application version. /// ///Attributes: - /// context: Optional additional data about the system state - /// status: Current health status of the component + /// message: The actual log message text + /// level: Severity level of the log entry + /// context: Optional additional data related to the log + /// application_version: Version of the application generating the log /// ///Examples: /// ```python - /// heartbeat = HeartbeatPayload( - /// status=HeartbeatStatus.OK, - /// context={"cpu_usage": 0.25, "memory_usage": 0.60} - /// ) - /// print(heartbeat.status) # HeartbeatStatus.OK - /// - /// warning_heartbeat = HeartbeatPayload( - /// status=HeartbeatStatus.WARNING, - /// context={"disk_space_low": True} + /// log_payload = LogPayload( + /// message="System startup complete", + /// level=LogLevel.INFO, + /// context={"operator": "John Doe"}, + /// application_version="1.0.0" /// ) + /// print(log_payload.level) # LogLevel.INFO /// ``` /// [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute(@"Payload for heartbeat messages indicating system health status. + [System.ComponentModel.DescriptionAttribute(@"Payload for log messages containing logging information. - Heartbeat messages are used to monitor the health and availability - of system components. They include a status indicator and optional - context information. + This payload carries log data including the message content, + severity level, optional context, and application version. Attributes: - context: Optional additional data about the system state - status: Current health status of the component + message: The actual log message text + level: Severity level of the log entry + context: Optional additional data related to the log + application_version: Version of the application generating the log Examples: ```python - heartbeat = HeartbeatPayload( - status=HeartbeatStatus.OK, - context={""cpu_usage"": 0.25, ""memory_usage"": 0.60} - ) - print(heartbeat.status) # HeartbeatStatus.OK - - warning_heartbeat = HeartbeatPayload( - status=HeartbeatStatus.WARNING, - context={""disk_space_low"": True} + log_payload = LogPayload( + message=""System startup complete"", + level=LogLevel.INFO, + context={""operator"": ""John Doe""}, + application_version=""1.0.0"" ) + print(log_payload.level) # LogLevel.INFO ```")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class HeartbeatPayload : RegisteredPayload + public partial class LogPayload : RegisteredPayload { + private string _message; + + private LogLevel _level; + private object _context; - private HeartbeatStatus _status; + private string _applicationVersion; - public HeartbeatPayload() + public LogPayload() { + _level = AindJustFramesSchemas.MessageProtocol.LogLevel.Debug; } - protected HeartbeatPayload(HeartbeatPayload other) : + protected LogPayload(LogPayload other) : base(other) { + _message = other._message; + _level = other._level; _context = other._context; - _status = other._status; + _applicationVersion = other._applicationVersion; } /// - /// Additional context for the heartbeat message. + /// The message of the log /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("context")] - [System.ComponentModel.DescriptionAttribute("Additional context for the heartbeat message.")] - public object Context + [Newtonsoft.Json.JsonPropertyAttribute("message", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The message of the log")] + public string Message { get { - return _context; + return _message; } set { - _context = value; + _message = value; } } /// - /// The status of the heartbeat message + /// The level of the log message /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("status", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("The status of the heartbeat message")] - public HeartbeatStatus Status + [Newtonsoft.Json.JsonPropertyAttribute("level")] + [System.ComponentModel.DescriptionAttribute("The level of the log message")] + public LogLevel Level { get { - return _status; + return _level; } set { - _status = value; + _level = value; } } - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HeartbeatPayload(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new HeartbeatPayload(this)); - } - - protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + /// + /// Additional context for the log message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("context")] + [System.ComponentModel.DescriptionAttribute("Additional context for the log message")] + public object Context { - if (base.PrintMembers(stringBuilder)) + get { - stringBuilder.Append(", "); - } - stringBuilder.Append("Context = " + _context + ", "); - stringBuilder.Append("Status = " + _status); - return true; - } - } - - - /// - /// Enumeration of possible heartbeat status values. - /// - ///Represents the health status of a system component, - ///with higher values indicating more severe issues. - /// - ///Examples: - /// ```python - /// HeartbeatStatus.OK # - /// HeartbeatStatus.CRITICAL > HeartbeatStatus.WARNING # True - /// int(HeartbeatStatus.ERROR) # 2 - /// ``` - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - public enum HeartbeatStatus - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Ok = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - Warning = 1, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] - Error = 2, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] - Critical = 3, - } - - - /// - /// Enumeration of log levels for the logging system. - /// - ///Follows standard Python logging levels with integer values - ///that allow for easy comparison and filtering. - /// - ///Examples: - /// ```python - /// LogLevel.ERROR > LogLevel.WARNING # True - /// LogLevel.DEBUG.value # 10 - /// str(LogLevel.INFO) # 'LogLevel.INFO' - /// ``` - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - public enum LogLevel - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="50")] - Critical = 50, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="40")] - Error = 40, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="30")] - Warning = 30, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="20")] - Info = 20, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="10")] - Debug = 10, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Notset = 0, - } - - - /// - /// Payload for log messages containing logging information. - /// - ///This payload carries log data including the message content, - ///severity level, optional context, and application version. - /// - ///Attributes: - /// message: The actual log message text - /// level: Severity level of the log entry - /// context: Optional additional data related to the log - /// application_version: Version of the application generating the log - /// - ///Examples: - /// ```python - /// log_payload = LogPayload( - /// message="System startup complete", - /// level=LogLevel.INFO, - /// context={"operator": "John Doe"}, - /// application_version="1.0.0" - /// ) - /// print(log_payload.level) # LogLevel.INFO - /// ``` - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute(@"Payload for log messages containing logging information. - - This payload carries log data including the message content, - severity level, optional context, and application version. - - Attributes: - message: The actual log message text - level: Severity level of the log entry - context: Optional additional data related to the log - application_version: Version of the application generating the log - - Examples: - ```python - log_payload = LogPayload( - message=""System startup complete"", - level=LogLevel.INFO, - context={""operator"": ""John Doe""}, - application_version=""1.0.0"" - ) - print(log_payload.level) # LogLevel.INFO - ```")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class LogPayload : RegisteredPayload - { - - private string _message; - - private LogLevel _level; - - private object _context; - - private string _applicationVersion; - - public LogPayload() - { - _level = AindJustFramesSchemas.MessageProtocol.LogLevel.Debug; - } - - protected LogPayload(LogPayload other) : - base(other) - { - _message = other._message; - _level = other._level; - _context = other._context; - _applicationVersion = other._applicationVersion; - } - - /// - /// The message of the log - /// - [Newtonsoft.Json.JsonPropertyAttribute("message", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("The message of the log")] - public string Message - { - get - { - return _message; - } - set - { - _message = value; - } - } - - /// - /// The level of the log message - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("level")] - [System.ComponentModel.DescriptionAttribute("The level of the log message")] - public LogLevel Level - { - get - { - return _level; - } - set - { - _level = value; - } - } - - /// - /// Additional context for the log message - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("context")] - [System.ComponentModel.DescriptionAttribute("Additional context for the log message")] - public object Context - { - get - { - return _context; - } - set - { - _context = value; - } - } - - /// - /// The version of the application - /// - [Newtonsoft.Json.JsonPropertyAttribute("application_version")] - [System.ComponentModel.DescriptionAttribute("The version of the application")] - public string ApplicationVersion - { - get - { - return _applicationVersion; - } - set - { - _applicationVersion = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new LogPayload(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new LogPayload(this)); - } - - protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - if (base.PrintMembers(stringBuilder)) - { - stringBuilder.Append(", "); - } - stringBuilder.Append("Message = " + _message + ", "); - stringBuilder.Append("Level = " + _level + ", "); - stringBuilder.Append("Context = " + _context + ", "); - stringBuilder.Append("ApplicationVersion = " + _applicationVersion); - return true; - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class Message - { - - private MessageType _messageType; - - private int _protocolVersion; - - private System.DateTimeOffset? _timestamp; - - private object _payload; - - private string _processId; - - private string _hostname; - - private string _rigName; - - public Message() - { - _protocolVersion = 0; - } - - protected Message(Message other) - { - _messageType = other._messageType; - _protocolVersion = other._protocolVersion; - _timestamp = other._timestamp; - _payload = other._payload; - _processId = other._processId; - _hostname = other._hostname; - _rigName = other._rigName; - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("message_type", Required=Newtonsoft.Json.Required.Always)] - public MessageType MessageType - { - get - { - return _messageType; - } - set - { - _messageType = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("protocol_version")] - public int ProtocolVersion - { - get - { - return _protocolVersion; - } - set - { - _protocolVersion = value; - } - } - - /// - /// The timestamp of the message - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("timestamp", Required=Newtonsoft.Json.Required.AllowNull)] - [System.ComponentModel.DescriptionAttribute("The timestamp of the message")] - public System.DateTimeOffset? Timestamp - { - get - { - return _timestamp; - } - set - { - _timestamp = value; - } - } - - /// - /// The payload of the message - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("payload", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("The payload of the message")] - public object Payload - { - get - { - return _payload; - } - set - { - _payload = value; - } - } - - /// - /// Process that created the message - /// - [Newtonsoft.Json.JsonPropertyAttribute("process_id", Required=Newtonsoft.Json.Required.AllowNull)] - [System.ComponentModel.DescriptionAttribute("Process that created the message")] - public string ProcessId - { - get - { - return _processId; - } - set - { - _processId = value; - } - } - - /// - /// Hostname that created the message - /// - [Newtonsoft.Json.JsonPropertyAttribute("hostname", Required=Newtonsoft.Json.Required.AllowNull)] - [System.ComponentModel.DescriptionAttribute("Hostname that created the message")] - public string Hostname - { - get - { - return _hostname; - } - set - { - _hostname = value; - } - } - - /// - /// Rig name that created the message - /// - [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.AllowNull)] - [System.ComponentModel.DescriptionAttribute("Rig name that created the message")] - public string RigName - { - get - { - return _rigName; - } - set - { - _rigName = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Message(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new Message(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("MessageType = " + _messageType + ", "); - stringBuilder.Append("ProtocolVersion = " + _protocolVersion + ", "); - stringBuilder.Append("Timestamp = " + _timestamp + ", "); - stringBuilder.Append("Payload = " + _payload + ", "); - stringBuilder.Append("ProcessId = " + _processId + ", "); - stringBuilder.Append("Hostname = " + _hostname + ", "); - stringBuilder.Append("RigName = " + _rigName); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - /// - /// Enumeration of possible message types in the protocol. - /// - ///Examples: - /// ```python - /// MessageType.REQUEST # 'request' - /// MessageType.REPLY # 'reply' - /// MessageType.EVENT # 'event' - /// ``` - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] - public enum MessageType - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="request")] - Request = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="reply")] - Reply = 1, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="event")] - Event = 2, - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class Rect - { - - private int _x; - - private int _y; - - private int _width; - - private int _height; - - public Rect() - { - _x = 0; - _y = 0; - _width = 0; - _height = 0; - } - - protected Rect(Rect other) - { - _x = other._x; - _y = other._y; - _width = other._width; - _height = other._height; - } - - /// - /// X coordinate of the top-left corner - /// - [Newtonsoft.Json.JsonPropertyAttribute("x")] - [System.ComponentModel.DescriptionAttribute("X coordinate of the top-left corner")] - public int X - { - get - { - return _x; - } - set - { - _x = value; - } - } - - /// - /// Y coordinate of the top-left corner - /// - [Newtonsoft.Json.JsonPropertyAttribute("y")] - [System.ComponentModel.DescriptionAttribute("Y coordinate of the top-left corner")] - public int Y - { - get - { - return _y; - } - set - { - _y = value; - } - } - - /// - /// Width of the rectangle - /// - [Newtonsoft.Json.JsonPropertyAttribute("width")] - [System.ComponentModel.DescriptionAttribute("Width of the rectangle")] - public int Width - { - get - { - return _width; - } - set - { - _width = value; - } - } - - /// - /// Height of the rectangle - /// - [Newtonsoft.Json.JsonPropertyAttribute("height")] - [System.ComponentModel.DescriptionAttribute("Height of the rectangle")] - public int Height - { - get - { - return _height; - } - set - { - _height = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Rect(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new Rect(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("X = " + _x + ", "); - stringBuilder.Append("Y = " + _y + ", "); - stringBuilder.Append("Width = " + _width + ", "); - stringBuilder.Append("Height = " + _height); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class RegisteredMessages - { - - private MessageType _messageType; - - private int _protocolVersion; - - private System.DateTimeOffset? _timestamp; - - private RegisteredPayload _payload; - - private string _processId; - - private string _hostname; - - private string _rigName; - - public RegisteredMessages() - { - _protocolVersion = 0; - } - - protected RegisteredMessages(RegisteredMessages other) - { - _messageType = other._messageType; - _protocolVersion = other._protocolVersion; - _timestamp = other._timestamp; - _payload = other._payload; - _processId = other._processId; - _hostname = other._hostname; - _rigName = other._rigName; - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("message_type", Required=Newtonsoft.Json.Required.Always)] - public MessageType MessageType - { - get - { - return _messageType; - } - set - { - _messageType = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("protocol_version")] - public int ProtocolVersion - { - get - { - return _protocolVersion; - } - set - { - _protocolVersion = value; - } - } - - /// - /// The timestamp of the message - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("timestamp", Required=Newtonsoft.Json.Required.AllowNull)] - [System.ComponentModel.DescriptionAttribute("The timestamp of the message")] - public System.DateTimeOffset? Timestamp - { - get - { - return _timestamp; - } - set - { - _timestamp = value; - } - } - - /// - /// The payload of the message - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("payload", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("The payload of the message")] - public RegisteredPayload Payload - { - get - { - return _payload; - } - set - { - _payload = value; - } - } - - /// - /// Process that created the message - /// - [Newtonsoft.Json.JsonPropertyAttribute("process_id", Required=Newtonsoft.Json.Required.AllowNull)] - [System.ComponentModel.DescriptionAttribute("Process that created the message")] - public string ProcessId - { - get - { - return _processId; - } - set - { - _processId = value; - } - } - - /// - /// Hostname that created the message - /// - [Newtonsoft.Json.JsonPropertyAttribute("hostname", Required=Newtonsoft.Json.Required.AllowNull)] - [System.ComponentModel.DescriptionAttribute("Hostname that created the message")] - public string Hostname - { - get - { - return _hostname; - } - set - { - _hostname = value; - } - } - - /// - /// Rig name that created the message - /// - [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.AllowNull)] - [System.ComponentModel.DescriptionAttribute("Rig name that created the message")] - public string RigName - { - get - { - return _rigName; - } - set - { - _rigName = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new RegisteredMessages(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new RegisteredMessages(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("MessageType = " + _messageType + ", "); - stringBuilder.Append("ProtocolVersion = " + _protocolVersion + ", "); - stringBuilder.Append("Timestamp = " + _timestamp + ", "); - stringBuilder.Append("Payload = " + _payload + ", "); - stringBuilder.Append("ProcessId = " + _processId + ", "); - stringBuilder.Append("Hostname = " + _hostname + ", "); - stringBuilder.Append("RigName = " + _rigName); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "payload_type")] - [JsonInheritanceAttribute("HeartbeatPayload", typeof(HeartbeatPayload))] - [JsonInheritanceAttribute("LogPayload", typeof(LogPayload))] - [JsonInheritanceAttribute("Start", typeof(StartPayload))] - [JsonInheritanceAttribute("Stop", typeof(StopPayload))] - [JsonInheritanceAttribute("SatelliteRig", typeof(SatelliteRigPayload))] - [JsonInheritanceAttribute("SatelliteSession", typeof(SatelliteSessionPayload))] - public abstract partial class RegisteredPayload - { - - protected RegisteredPayload() - { - } - - protected RegisteredPayload(RegisteredPayload other) - { - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - return false; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class SatelliteRig - { - - private string _aindBehaviorServicesPkgVersion; - - private string _version; - - private string _computerName; - - private string _rigName; - - private ZmqPubSub _zmqConnection; - - private CameraControllerSpinnakerCamera _triggeredCameraController0; - - private CameraControllerSpinnakerCamera _triggeredCameraController1; - - private bool _isSatellite; - - public SatelliteRig() - { - _aindBehaviorServicesPkgVersion = "0.12.3"; - _version = "0.5.0-rc0"; - _zmqConnection = new ZmqPubSub(); - _isSatellite = true; - } - - protected SatelliteRig(SatelliteRig other) - { - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _version = other._version; - _computerName = other._computerName; - _rigName = other._rigName; - _zmqConnection = other._zmqConnection; - _triggeredCameraController0 = other._triggeredCameraController0; - _triggeredCameraController1 = other._triggeredCameraController1; - _isSatellite = other._isSatellite; - } - - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion - { - get - { - return _aindBehaviorServicesPkgVersion; - } - set - { - _aindBehaviorServicesPkgVersion = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version - { - get - { - return _version; - } - set - { - _version = value; - } - } - - /// - /// Remote Computer name - /// - [Newtonsoft.Json.JsonPropertyAttribute("computer_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Remote Computer name")] - public string ComputerName - { - get - { - return _computerName; - } - set - { - _computerName = value; - } - } - - /// - /// Rig name - /// - [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Rig name")] - public string RigName - { - get - { - return _rigName; - } - set - { - _rigName = value; - } - } - - /// - /// ZMQ connection for communication. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("zmq_connection", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] - public ZmqPubSub ZmqConnection - { - get - { - return _zmqConnection; - } - set - { - _zmqConnection = value; - } - } - - /// - /// Camera controller to triggered cameras. Will use Camera0 register as a trigger. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_0")] - [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera0 register as a trigger.")] - public CameraControllerSpinnakerCamera TriggeredCameraController0 - { - get - { - return _triggeredCameraController0; - } - set - { - _triggeredCameraController0 = value; - } - } - - /// - /// Camera controller to triggered cameras. Will use Camera1 register as a trigger. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("triggered_camera_controller_1")] - [System.ComponentModel.DescriptionAttribute("Camera controller to triggered cameras. Will use Camera1 register as a trigger.")] - public CameraControllerSpinnakerCamera TriggeredCameraController1 - { - get - { - return _triggeredCameraController1; - } - set - { - _triggeredCameraController1 = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("is_satellite")] - public bool IsSatellite - { - get - { - return _isSatellite; - } - set - { - _isSatellite = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteRig(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new SatelliteRig(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("Version = " + _version + ", "); - stringBuilder.Append("ComputerName = " + _computerName + ", "); - stringBuilder.Append("RigName = " + _rigName + ", "); - stringBuilder.Append("ZmqConnection = " + _zmqConnection + ", "); - stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); - stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); - stringBuilder.Append("IsSatellite = " + _isSatellite); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class SatelliteRigPayload : RegisteredPayload - { - - private SatelliteRig _rig; - - public SatelliteRigPayload() - { - _rig = new SatelliteRig(); - } - - protected SatelliteRigPayload(SatelliteRigPayload other) : - base(other) - { - _rig = other._rig; - } - - /// - /// Satellite Rig configuration. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("rig", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Satellite Rig configuration.")] - public SatelliteRig Rig - { - get - { - return _rig; - } - set - { - _rig = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteRigPayload(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new SatelliteRigPayload(this)); - } - - protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - if (base.PrintMembers(stringBuilder)) - { - stringBuilder.Append(", "); - } - stringBuilder.Append("Rig = " + _rig); - return true; - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class SatelliteSessionPayload : RegisteredPayload - { - - private AindBehaviorSessionModel _session; - - public SatelliteSessionPayload() - { - _session = new AindBehaviorSessionModel(); - } - - protected SatelliteSessionPayload(SatelliteSessionPayload other) : - base(other) - { - _session = other._session; - } - - /// - /// Satellite session configuration. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("session", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Satellite session configuration.")] - public AindBehaviorSessionModel Session - { - get - { - return _session; - } - set - { - _session = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteSessionPayload(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new SatelliteSessionPayload(this)); - } - - protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - if (base.PrintMembers(stringBuilder)) - { - stringBuilder.Append(", "); - } - stringBuilder.Append("Session = " + _session); - return true; - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class SpinnakerCamera - { - - private string _deviceType; - - private string _deviceName; - - private BaseModel _additionalSettings; - - private BaseModel _calibration; - - private string _serialNumber; - - private int _binning; - - private SpinnakerCameraColorProcessing _colorProcessing; - - private int _exposure; - - private double _gain; - - private double? _gamma; - - private SpinnakerCameraAdcBitDepth? _adcBitDepth; - - private SpinnakerCameraPixelFormat? _pixelFormat; - - private Rect _regionOfInterest; - - private VideoWriter _videoWriter; - - public SpinnakerCamera() - { - _deviceType = "SpinnakerCamera"; - _binning = 1; - _colorProcessing = AindJustFramesSchemas.MessageProtocol.SpinnakerCameraColorProcessing.Default; - _exposure = 1000; - _gain = 0D; - _adcBitDepth = AindJustFramesSchemas.MessageProtocol.SpinnakerCameraAdcBitDepth.Adc8bit; - _pixelFormat = AindJustFramesSchemas.MessageProtocol.SpinnakerCameraPixelFormat.Mono8; - _regionOfInterest = new Rect(); - } - - protected SpinnakerCamera(SpinnakerCamera other) - { - _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; - _calibration = other._calibration; - _serialNumber = other._serialNumber; - _binning = other._binning; - _colorProcessing = other._colorProcessing; - _exposure = other._exposure; - _gain = other._gain; - _gamma = other._gamma; - _adcBitDepth = other._adcBitDepth; - _pixelFormat = other._pixelFormat; - _regionOfInterest = other._regionOfInterest; - _videoWriter = other._videoWriter; - } - - /// - /// Device type - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_type")] - [System.ComponentModel.DescriptionAttribute("Device type")] - public string DeviceType - { - get - { - return _deviceType; - } - set - { - _deviceType = value; - } - } - - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings - { - get - { - return _additionalSettings; - } - set - { - _additionalSettings = value; - } - } - - /// - /// Calibration - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration")] - public BaseModel Calibration - { - get - { - return _calibration; - } - set - { - _calibration = value; - } - } - - /// - /// Camera serial number - /// - [Newtonsoft.Json.JsonPropertyAttribute("serial_number", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Camera serial number")] - public string SerialNumber - { - get - { - return _serialNumber; - } - set - { - _serialNumber = value; - } - } - - /// - /// Binning - /// - [Newtonsoft.Json.JsonPropertyAttribute("binning")] - [System.ComponentModel.DescriptionAttribute("Binning")] - public int Binning - { - get - { - return _binning; - } - set - { - _binning = value; - } - } - - /// - /// Color processing - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("color_processing")] - [System.ComponentModel.DescriptionAttribute("Color processing")] - public SpinnakerCameraColorProcessing ColorProcessing - { - get - { - return _colorProcessing; - } - set - { - _colorProcessing = value; - } - } - - /// - /// Exposure time - /// - [Newtonsoft.Json.JsonPropertyAttribute("exposure")] - [System.ComponentModel.DescriptionAttribute("Exposure time")] - public int Exposure - { - get - { - return _exposure; - } - set - { - _exposure = value; - } - } - - /// - /// Gain - /// - [Newtonsoft.Json.JsonPropertyAttribute("gain")] - [System.ComponentModel.DescriptionAttribute("Gain")] - public double Gain - { - get - { - return _gain; - } - set - { - _gain = value; - } - } - - /// - /// Gamma. If None, will disable gamma correction. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("gamma")] - [System.ComponentModel.DescriptionAttribute("Gamma. If None, will disable gamma correction.")] - public double? Gamma - { - get - { - return _gamma; - } - set - { - _gamma = value; - } - } - - /// - /// ADC bit depth. If None will be left as default. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("adc_bit_depth")] - [System.ComponentModel.DescriptionAttribute("ADC bit depth. If None will be left as default.")] - public SpinnakerCameraAdcBitDepth? AdcBitDepth - { - get - { - return _adcBitDepth; - } - set - { - _adcBitDepth = value; - } - } - - /// - /// Pixel format. If None will be left as default. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("pixel_format")] - [System.ComponentModel.DescriptionAttribute("Pixel format. If None will be left as default.")] - public SpinnakerCameraPixelFormat? PixelFormat - { - get - { - return _pixelFormat; - } - set - { - _pixelFormat = value; - } - } - - /// - /// Region of interest - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("region_of_interest")] - [System.ComponentModel.DescriptionAttribute("Region of interest")] - public Rect RegionOfInterest - { - get - { - return _regionOfInterest; - } - set - { - _regionOfInterest = value; - } - } - - /// - /// Video writer. If not provided, no video will be saved. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("video_writer")] - [System.ComponentModel.DescriptionAttribute("Video writer. If not provided, no video will be saved.")] - public VideoWriter VideoWriter - { - get - { - return _videoWriter; - } - set - { - _videoWriter = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SpinnakerCamera(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new SpinnakerCamera(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("DeviceName = " + _deviceName + ", "); - stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); - stringBuilder.Append("Calibration = " + _calibration + ", "); - stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); - stringBuilder.Append("Binning = " + _binning + ", "); - stringBuilder.Append("ColorProcessing = " + _colorProcessing + ", "); - stringBuilder.Append("Exposure = " + _exposure + ", "); - stringBuilder.Append("Gain = " + _gain + ", "); - stringBuilder.Append("Gamma = " + _gamma + ", "); - stringBuilder.Append("AdcBitDepth = " + _adcBitDepth + ", "); - stringBuilder.Append("PixelFormat = " + _pixelFormat + ", "); - stringBuilder.Append("RegionOfInterest = " + _regionOfInterest + ", "); - stringBuilder.Append("VideoWriter = " + _videoWriter); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - public enum SpinnakerCameraAdcBitDepth - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Adc8bit = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - Adc10bit = 1, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] - Adc12bit = 2, - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - public enum SpinnakerCameraPixelFormat - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Mono8 = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - Mono16 = 1, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] - Rgb8packed = 2, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] - Bayergr8 = 3, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="4")] - Bayerrg8 = 4, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="5")] - Bayergb8 = 5, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="6")] - Bayerbg8 = 6, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="7")] - Bayergr16 = 7, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="8")] - Bayerrg16 = 8, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="9")] - Bayergb16 = 9, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="10")] - Bayerbg16 = 10, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="11")] - Mono12packed = 11, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="12")] - Bayergr12packed = 12, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="13")] - Bayerrg12packed = 13, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="14")] - Bayergb12packed = 14, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="15")] - Bayerbg12packed = 15, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="16")] - Yuv411packed = 16, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="17")] - Yuv422packed = 17, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="18")] - Yuv444packed = 18, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="19")] - Mono12p = 19, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="20")] - Bayergr12p = 20, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="21")] - Bayerrg12p = 21, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="22")] - Bayergb12p = 22, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="23")] - Bayerbg12p = 23, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="24")] - Ycbcr8 = 24, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="25")] - Ycbcr4228 = 25, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="26")] - Ycbcr4118 = 26, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="27")] - Bgr8 = 27, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="28")] - Bgra8 = 28, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="29")] - Mono10packed = 29, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="30")] - Bayergr10packed = 30, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="31")] - Bayerrg10packed = 31, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="32")] - Bayergb10packed = 32, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="33")] - Bayerbg10packed = 33, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="34")] - Mono10p = 34, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="35")] - Bayergr10p = 35, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="36")] - Bayerrg10p = 36, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="37")] - Bayergb10p = 37, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="38")] - Bayerbg10p = 38, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="39")] - Mono1p = 39, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="40")] - Mono2p = 40, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="41")] - Mono4p = 41, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="42")] - Mono8s = 42, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="43")] - Mono10 = 43, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="44")] - Mono12 = 44, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="45")] - Mono14 = 45, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="46")] - Mono16s = 46, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="47")] - Mono32f = 47, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="48")] - Bayerbg10 = 48, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="49")] - Bayerbg12 = 49, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="50")] - Bayergb10 = 50, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="51")] - Bayergb12 = 51, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="52")] - Bayergr10 = 52, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="53")] - Bayergr12 = 53, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="54")] - Bayerrg10 = 54, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="55")] - Bayerrg12 = 55, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="56")] - Rgba8 = 56, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="57")] - Rgba10 = 57, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="58")] - Rgba10p = 58, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="59")] - Rgba12 = 59, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="60")] - Rgba12p = 60, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="61")] - Rgba14 = 61, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="62")] - Rgba16 = 62, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="63")] - Rgb8 = 63, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="64")] - Rgb8Planar = 64, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="65")] - Rgb10 = 65, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="66")] - Rgb10Planar = 66, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="67")] - Rgb10p = 67, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="68")] - Rgb10p32 = 68, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="69")] - Rgb12 = 69, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="70")] - Rgb12Planar = 70, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="71")] - Rgb12p = 71, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="72")] - Rgb14 = 72, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="73")] - Rgb16 = 73, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="74")] - Rgb16s = 74, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="75")] - Rgb32f = 75, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="76")] - Rgb16Planar = 76, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="77")] - Rgb565p = 77, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="78")] - Bgra10 = 78, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="79")] - Bgra10p = 79, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="80")] - Bgra12 = 80, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="81")] - Bgra12p = 81, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="82")] - Bgra14 = 82, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="83")] - Bgra16 = 83, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="84")] - Rgba32f = 84, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="85")] - Bgr10 = 85, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="86")] - Bgr10p = 86, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="87")] - Bgr12 = 87, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="88")] - Bgr12p = 88, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="89")] - Bgr14 = 89, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="90")] - Bgr16 = 90, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="91")] - Bgr565p = 91, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="92")] - R8 = 92, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="93")] - R10 = 93, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="94")] - R12 = 94, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="95")] - R16 = 95, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="96")] - G8 = 96, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="97")] - G10 = 97, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="98")] - G12 = 98, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="99")] - G16 = 99, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="100")] - B8 = 100, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="101")] - B10 = 101, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="102")] - B12 = 102, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="103")] - B16 = 103, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="104")] - Coord3dAbc8 = 104, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="105")] - Coord3dAbc8Planar = 105, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="106")] - Coord3dAbc10p = 106, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="107")] - Coord3dAbc10pPlanar = 107, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="108")] - Coord3dAbc12p = 108, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="109")] - Coord3dAbc12pPlanar = 109, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="110")] - Coord3dAbc16 = 110, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="111")] - Coord3dAbc16Planar = 111, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="112")] - Coord3dAbc32f = 112, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="113")] - Coord3dAbc32fPlanar = 113, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="114")] - Coord3dAc8 = 114, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="115")] - Coord3dAc8Planar = 115, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="116")] - Coord3dAc10p = 116, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="117")] - Coord3dAc10pPlanar = 117, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="118")] - Coord3dAc12p = 118, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="119")] - Coord3dAc12pPlanar = 119, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="120")] - Coord3dAc16 = 120, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="121")] - Coord3dAc16Planar = 121, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="122")] - Coord3dAc32f = 122, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="123")] - Coord3dAc32fPlanar = 123, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="124")] - Coord3dA8 = 124, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="125")] - Coord3dA10p = 125, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="126")] - Coord3dA12p = 126, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="127")] - Coord3dA16 = 127, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="128")] - Coord3dA32f = 128, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="129")] - Coord3dB8 = 129, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="130")] - Coord3dB10p = 130, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="131")] - Coord3dB12p = 131, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="132")] - Coord3dB16 = 132, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="133")] - Coord3dB32f = 133, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="134")] - Coord3dC8 = 134, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="135")] - Coord3dC10p = 135, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="136")] - Coord3dC12p = 136, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="137")] - Coord3dC16 = 137, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="138")] - Coord3dC32f = 138, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="139")] - Confidence1 = 139, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="140")] - Confidence1p = 140, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="141")] - Confidence8 = 141, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="142")] - Confidence16 = 142, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="143")] - Confidence32f = 143, - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class StartPayload : RegisteredPayload - { - - public StartPayload() - { + return _context; + } + set + { + _context = value; + } } - protected StartPayload(StartPayload other) : - base(other) + /// + /// The version of the application + /// + [Newtonsoft.Json.JsonPropertyAttribute("application_version")] + [System.ComponentModel.DescriptionAttribute("The version of the application")] + public string ApplicationVersion { + get + { + return _applicationVersion; + } + set + { + _applicationVersion = value; + } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new StartPayload(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new LogPayload(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new StartPayload(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new LogPayload(this)); } protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) { - return base.PrintMembers(stringBuilder); + if (base.PrintMembers(stringBuilder)) + { + stringBuilder.Append(", "); + } + stringBuilder.Append("Message = " + _message + ", "); + stringBuilder.Append("Level = " + _level + ", "); + stringBuilder.Append("Context = " + _context + ", "); + stringBuilder.Append("ApplicationVersion = " + _applicationVersion); + return true; } } @@ -2644,374 +375,385 @@ protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class StopPayload : RegisteredPayload + public partial class Message { - public StopPayload() - { - } - - protected StopPayload(StopPayload other) : - base(other) - { - } + private MessageType _messageType; - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new StopPayload(this))); - } + private int _protocolVersion; - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new StopPayload(this)); - } + private System.DateTimeOffset? _timestamp; - protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - return base.PrintMembers(stringBuilder); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "video_writer_type")] - [JsonInheritanceAttribute("FFMPEG", typeof(VideoWriterFfmpeg))] - [JsonInheritanceAttribute("OPENCV", typeof(VideoWriterOpenCv))] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class VideoWriter - { + private object _payload; - public VideoWriter() - { - } + private string _processId; - protected VideoWriter(VideoWriter other) - { - } + private string _hostname; - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriter(this))); - } + private string _rigName; - public System.IObservable Generate(System.IObservable source) + public Message() { - return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriter(this)); + _protocolVersion = 0; } - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + protected Message(Message other) { - return false; + _messageType = other._messageType; + _protocolVersion = other._protocolVersion; + _timestamp = other._timestamp; + _payload = other._payload; + _processId = other._processId; + _hostname = other._hostname; + _rigName = other._rigName; } - public override string ToString() + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("message_type", Required=Newtonsoft.Json.Required.Always)] + public MessageType MessageType { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) + get { - stringBuilder.Append(" "); + return _messageType; + } + set + { + _messageType = value; } - stringBuilder.Append("}"); - return stringBuilder.ToString(); } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class VideoWriterFfmpeg : VideoWriter - { - - private int _frameRate; - - private string _containerExtension; - private string _outputArguments; - - private string _inputArguments; - - public VideoWriterFfmpeg() + [Newtonsoft.Json.JsonPropertyAttribute("protocol_version")] + public int ProtocolVersion { - _frameRate = 30; - _containerExtension = "mp4"; - _outputArguments = "-vf \"scale=out_color_matrix=bt709:out_range=full,format=bgr24,scale=out_range=full\" -c:v h264_nvenc -pix_fmt yuv420p -color_range full -colorspace bt709 -color_trc linear -tune hq -preset p4 -rc vbr -cq 12 -b:v 0M -metadata author=\"Allen Institute for Neural Dynamics\" -maxrate 700M -bufsize 350M"; - _inputArguments = "-colorspace bt709 -color_primaries bt709 -color_range full -color_trc linear"; + get + { + return _protocolVersion; + } + set + { + _protocolVersion = value; + } } - protected VideoWriterFfmpeg(VideoWriterFfmpeg other) : - base(other) + /// + /// The timestamp of the message + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("timestamp", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("The timestamp of the message")] + public System.DateTimeOffset? Timestamp { - _frameRate = other._frameRate; - _containerExtension = other._containerExtension; - _outputArguments = other._outputArguments; - _inputArguments = other._inputArguments; + get + { + return _timestamp; + } + set + { + _timestamp = value; + } } /// - /// Encoding frame rate + /// The payload of the message /// - [Newtonsoft.Json.JsonPropertyAttribute("frame_rate")] - [System.ComponentModel.DescriptionAttribute("Encoding frame rate")] - public int FrameRate + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("payload", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The payload of the message")] + public object Payload { get { - return _frameRate; + return _payload; } set { - _frameRate = value; + _payload = value; } } /// - /// Container extension + /// Process that created the message /// - [Newtonsoft.Json.JsonPropertyAttribute("container_extension")] - [System.ComponentModel.DescriptionAttribute("Container extension")] - public string ContainerExtension + [Newtonsoft.Json.JsonPropertyAttribute("process_id", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Process that created the message")] + public string ProcessId { get { - return _containerExtension; + return _processId; } set { - _containerExtension = value; + _processId = value; } } /// - /// Output arguments + /// Hostname that created the message /// - [Newtonsoft.Json.JsonPropertyAttribute("output_arguments")] - [System.ComponentModel.DescriptionAttribute("Output arguments")] - public string OutputArguments + [Newtonsoft.Json.JsonPropertyAttribute("hostname", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Hostname that created the message")] + public string Hostname { get { - return _outputArguments; + return _hostname; } set { - _outputArguments = value; + _hostname = value; } } /// - /// Input arguments + /// Rig name that created the message /// - [Newtonsoft.Json.JsonPropertyAttribute("input_arguments")] - [System.ComponentModel.DescriptionAttribute("Input arguments")] - public string InputArguments + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Rig name that created the message")] + public string RigName { get { - return _inputArguments; + return _rigName; } set { - _inputArguments = value; + _rigName = value; } } - public System.IObservable Generate() + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Message(this))); + } + + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriterFfmpeg(this))); + return System.Reactive.Linq.Observable.Select(source, _ => new Message(this)); } - public System.IObservable Generate(System.IObservable source) + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriterFfmpeg(this)); + stringBuilder.Append("MessageType = " + _messageType + ", "); + stringBuilder.Append("ProtocolVersion = " + _protocolVersion + ", "); + stringBuilder.Append("Timestamp = " + _timestamp + ", "); + stringBuilder.Append("Payload = " + _payload + ", "); + stringBuilder.Append("ProcessId = " + _processId + ", "); + stringBuilder.Append("Hostname = " + _hostname + ", "); + stringBuilder.Append("RigName = " + _rigName); + return true; } - protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + public override string ToString() { - if (base.PrintMembers(stringBuilder)) + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) { - stringBuilder.Append(", "); + stringBuilder.Append(" "); } - stringBuilder.Append("FrameRate = " + _frameRate + ", "); - stringBuilder.Append("ContainerExtension = " + _containerExtension + ", "); - stringBuilder.Append("OutputArguments = " + _outputArguments + ", "); - stringBuilder.Append("InputArguments = " + _inputArguments); - return true; + stringBuilder.Append("}"); + return stringBuilder.ToString(); } } + /// + /// Enumeration of possible message types in the protocol. + /// + ///Examples: + /// ```python + /// MessageType.REQUEST # 'request' + /// MessageType.REPLY # 'reply' + /// MessageType.EVENT # 'event' + /// ``` + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] + public enum MessageType + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="request")] + Request = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="reply")] + Reply = 1, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="event")] + Event = 2, + } + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class VideoWriterOpenCv : VideoWriter + public partial class RegisteredMessages { - private int _frameRate; + private MessageType _messageType; + + private int _protocolVersion; + + private System.DateTimeOffset? _timestamp; + + private RegisteredPayload _payload; + + private string _processId; + + private string _hostname; - private string _containerExtension; + private string _rigName; - private string _fourCc; + public RegisteredMessages() + { + _protocolVersion = 0; + } - public VideoWriterOpenCv() + protected RegisteredMessages(RegisteredMessages other) { - _frameRate = 30; - _containerExtension = "avi"; - _fourCc = "FMP4"; + _messageType = other._messageType; + _protocolVersion = other._protocolVersion; + _timestamp = other._timestamp; + _payload = other._payload; + _processId = other._processId; + _hostname = other._hostname; + _rigName = other._rigName; } - protected VideoWriterOpenCv(VideoWriterOpenCv other) : - base(other) + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("message_type", Required=Newtonsoft.Json.Required.Always)] + public MessageType MessageType { - _frameRate = other._frameRate; - _containerExtension = other._containerExtension; - _fourCc = other._fourCc; + get + { + return _messageType; + } + set + { + _messageType = value; + } } - /// - /// Encoding frame rate - /// - [Newtonsoft.Json.JsonPropertyAttribute("frame_rate")] - [System.ComponentModel.DescriptionAttribute("Encoding frame rate")] - public int FrameRate + [Newtonsoft.Json.JsonPropertyAttribute("protocol_version")] + public int ProtocolVersion { get { - return _frameRate; + return _protocolVersion; } set { - _frameRate = value; + _protocolVersion = value; } } /// - /// Container extension + /// The timestamp of the message /// - [Newtonsoft.Json.JsonPropertyAttribute("container_extension")] - [System.ComponentModel.DescriptionAttribute("Container extension")] - public string ContainerExtension + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("timestamp", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("The timestamp of the message")] + public System.DateTimeOffset? Timestamp { get { - return _containerExtension; + return _timestamp; } set { - _containerExtension = value; + _timestamp = value; } } /// - /// Four character code + /// The payload of the message /// - [Newtonsoft.Json.JsonPropertyAttribute("four_cc")] - [System.ComponentModel.DescriptionAttribute("Four character code")] - public string FourCc + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("payload", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("The payload of the message")] + public RegisteredPayload Payload { get { - return _fourCc; + return _payload; } set { - _fourCc = value; + _payload = value; } } - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new VideoWriterOpenCv(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new VideoWriterOpenCv(this)); - } - - protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + /// + /// Process that created the message + /// + [Newtonsoft.Json.JsonPropertyAttribute("process_id", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Process that created the message")] + public string ProcessId { - if (base.PrintMembers(stringBuilder)) + get { - stringBuilder.Append(", "); + return _processId; + } + set + { + _processId = value; } - stringBuilder.Append("FrameRate = " + _frameRate + ", "); - stringBuilder.Append("ContainerExtension = " + _containerExtension + ", "); - stringBuilder.Append("FourCc = " + _fourCc); - return true; - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class ZmqConnection - { - - private string _connectionString; - - private string _topic; - - public ZmqConnection() - { - _connectionString = "@tcp://localhost:5556"; - _topic = ""; - } - - protected ZmqConnection(ZmqConnection other) - { - _connectionString = other._connectionString; - _topic = other._topic; } /// - /// The connection string for the ZMQ socket. + /// Hostname that created the message /// - [Newtonsoft.Json.JsonPropertyAttribute("connection_string")] - [System.ComponentModel.DescriptionAttribute("The connection string for the ZMQ socket.")] - public string ConnectionString + [Newtonsoft.Json.JsonPropertyAttribute("hostname", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Hostname that created the message")] + public string Hostname { get { - return _connectionString; + return _hostname; } set { - _connectionString = value; + _hostname = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("topic")] - public string Topic + /// + /// Rig name that created the message + /// + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.AllowNull)] + [System.ComponentModel.DescriptionAttribute("Rig name that created the message")] + public string RigName { get { - return _topic; + return _rigName; } set { - _topic = value; + _rigName = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqConnection(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new RegisteredMessages(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new ZmqConnection(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new RegisteredMessages(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("ConnectionString = " + _connectionString + ", "); - stringBuilder.Append("Topic = " + _topic); + stringBuilder.Append("MessageType = " + _messageType + ", "); + stringBuilder.Append("ProtocolVersion = " + _protocolVersion + ", "); + stringBuilder.Append("Timestamp = " + _timestamp + ", "); + stringBuilder.Append("Payload = " + _payload + ", "); + stringBuilder.Append("ProcessId = " + _processId + ", "); + stringBuilder.Append("Hostname = " + _hostname + ", "); + stringBuilder.Append("RigName = " + _rigName); return true; } @@ -3031,105 +773,103 @@ public override string ToString() [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class ZmqPubSub + [Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "payload_type")] + [JsonInheritanceAttribute("HeartbeatPayload", typeof(HeartbeatPayload))] + [JsonInheritanceAttribute("LogPayload", typeof(LogPayload))] + [JsonInheritanceAttribute("Start", typeof(StartPayload))] + [JsonInheritanceAttribute("Stop", typeof(StopPayload))] + public abstract partial class RegisteredPayload { - private ZmqConnection _pub; - - private ZmqConnection _sub; + protected RegisteredPayload() + { + } - public ZmqPubSub() + protected RegisteredPayload(RegisteredPayload other) { - _pub = new ZmqConnection(); - _sub = new ZmqConnection(); } - protected ZmqPubSub(ZmqPubSub other) + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - _pub = other._pub; - _sub = other._sub; + return false; } - /// - /// ZMQ Publisher - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("pub", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("ZMQ Publisher")] - public ZmqConnection Pub + public override string ToString() { - get - { - return _pub; - } - set + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) { - _pub = value; + stringBuilder.Append(" "); } + stringBuilder.Append("}"); + return stringBuilder.ToString(); } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class StartPayload : RegisteredPayload + { - /// - /// ZMQ Subscriber - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("sub", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("ZMQ Subscriber")] - public ZmqConnection Sub + public StartPayload() { - get - { - return _sub; - } - set - { - _sub = value; - } } - public System.IObservable Generate() + protected StartPayload(StartPayload other) : + base(other) { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqPubSub(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Select(source, _ => new ZmqPubSub(this)); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new StartPayload(this))); } - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + public System.IObservable Generate(System.IObservable source) { - stringBuilder.Append("Pub = " + _pub + ", "); - stringBuilder.Append("Sub = " + _sub); - return true; + return System.Reactive.Linq.Observable.Select(source, _ => new StartPayload(this)); } - public override string ToString() + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); + return base.PrintMembers(stringBuilder); } } [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] - public enum SpinnakerCameraColorProcessing + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class StopPayload : RegisteredPayload { - [System.Runtime.Serialization.EnumMemberAttribute(Value="Default")] - Default = 0, + public StopPayload() + { + } + + protected StopPayload(StopPayload other) : + base(other) + { + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new StopPayload(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new StopPayload(this)); + } - [System.Runtime.Serialization.EnumMemberAttribute(Value="NoColorProcessing")] - NoColorProcessing = 1, + protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + return base.PrintMembers(stringBuilder); + } } @@ -3277,8 +1017,6 @@ private string GetSubtypeDiscriminator(System.Type objectType) [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] public partial class MatchRegisteredPayload : Bonsai.Expressions.SingleArgumentExpressionBuilder { @@ -3315,47 +1053,6 @@ private static System.IObservable Process(System.IObservable))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - public partial class MatchVideoWriter : Bonsai.Expressions.SingleArgumentExpressionBuilder - { - - public Bonsai.Expressions.TypeMapping Type { get; set; } - - public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) - { - var typeMapping = Type; - var returnType = typeMapping != null ? typeMapping.GetType().GetGenericArguments()[0] : typeof(VideoWriter); - return System.Linq.Expressions.Expression.Call( - typeof(MatchVideoWriter), - "Process", - new System.Type[] { returnType }, - System.Linq.Enumerable.Single(arguments)); - } - - - private static System.IObservable Process(System.IObservable source) - where TResult : VideoWriter - { - return System.Reactive.Linq.Observable.Create(observer => - { - var sourceObserver = System.Reactive.Observer.Create( - value => - { - var match = value as TResult; - if (match != null) observer.OnNext(match); - }, - observer.OnError, - observer.OnCompleted); - return System.ObservableExtensions.SubscribeSafe(source, sourceObserver); - }); - } - } - - /// /// Serializes a sequence of data model objects into JSON strings. /// @@ -3374,21 +1071,6 @@ private System.IObservable Process(System.IObservable source) return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value, formatting)); } - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - public System.IObservable Process(System.IObservable source) { return Process(source); @@ -3404,11 +1086,6 @@ public System.IObservable Process(System.IObservable source) return Process(source); } - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - public System.IObservable Process(System.IObservable source) { return Process(source); @@ -3419,26 +1096,6 @@ public System.IObservable Process(System.IObservable return Process(source); } - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - public System.IObservable Process(System.IObservable source) { return Process(source); @@ -3448,31 +1105,6 @@ public System.IObservable Process(System.IObservable source { return Process(source); } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } } @@ -3483,32 +1115,19 @@ public System.IObservable Process(System.IObservable source) [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of JSON strings into data model objects.")] [System.ComponentModel.DefaultPropertyAttribute("Type")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder { public DeserializeFromJson() { - Type = new Bonsai.Expressions.TypeMapping(); + Type = new Bonsai.Expressions.TypeMapping(); } public Bonsai.Expressions.TypeMapping Type { get; set; } diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index 4014e8d..30aa75e 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -44,7 +44,6 @@ class AindJustFramesRig(AindBehaviorRigModel): description="Camera controller to triggered cameras. Will use Camera1 register as a trigger.", ) harp_behavior: rig.harp.HarpBehavior = Field( - ..., description="Harp behavior board. Will be the source of triggers for the two camera controllers.", ) satellite_rigs: list[SatelliteRig] = Field( diff --git a/uv.lock b/uv.lock index daf53c9..57bce32 100644 --- a/uv.lock +++ b/uv.lock @@ -21,16 +21,16 @@ wheels = [ [[package]] name = "aind-behavior-curriculum" -version = "0.0.35" +version = "0.0.36" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "jinja2" }, { name = "pydantic" }, { name = "semver" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/c5/c7/bb935282362302860d3ae7bc6765be7fc3b2f74af0ca200ad8ed91f03dac/aind_behavior_curriculum-0.0.35.tar.gz", hash = "sha256:594b735a254f6ab9112504efd9eb78b5e2bbd5d93d2c88608889c8a38cfcd234", size = 122480, upload-time = "2025-10-02T23:41:57.49Z" } +sdist = { url = "https://files.pythonhosted.org/packages/12/e3/3d565a7d29c22734ebb5ccf785b994d0c32beb963e087a60afa3c93bf648/aind_behavior_curriculum-0.0.36.tar.gz", hash = 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2bc0990..ed58ea0 100644 --- a/src/Extensions/Main.bonsai +++ b/src/Extensions/Main.bonsai @@ -42,10 +42,20 @@ - + + RigSchema + + + DataDirectory + + + + + + @@ -216,24 +226,27 @@ - + + + - - + + - + + @@ -401,69 +414,76 @@ - - - 1 - - EnableExperiment - - - - - RigSchema - - - RigName - - - - - - - - - Reply - + + Response + + + + IsExperimentRunning + + + + + + Source1 + + + + + + + + + + + 1 + + + + + + + RigSchema + + + RigName + + + + + + + + + Reply + + + + + + + + + + + + + + + OutboundMessages - - ZmqConnection - - - - - - - - MessageProtocolZmqTopic - - - - - - - - tcp://localhost:5557 - message_protocol + + 1 - - Last - - - - - - InboundMessages - - InboundMessages @@ -497,37 +517,104 @@ - - - 1 - - EndExperiment + + Response + + + + IsExperimentRunning + + + + + + + Source1 + + + + + + + + + + + + + RigSchema + + + RigName + + + + + + + + + Reply + + + + + + + + + + + + + + + + + + OutboundMessages + - + + 1 + - RigSchema + ZmqConnection - - RigName + + + + + + + MessageProtocolZmqTopic - + - - Reply + + tcp://localhost:5557 + message_protocol - - OutboundMessages + + Last + + + + + InboundMessages + + @@ -551,31 +638,23 @@ - - + - + + - + - - + - + + - - - - - - - - From c12b545439fab0137a25259fcadac6891095bd17 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Tue, 2 Dec 2025 15:41:13 -0800 Subject: [PATCH 19/32] Simplify rig schema --- examples/examples.py | 4 +- pyproject.toml | 2 +- .../aind_behavior_just_frames.json | 33 ++++------ .../AindBehaviorJustFrames.Generated.cs | 66 +------------------ .../message_protocol.py | 9 +-- src/aind_behavior_just_frames/regenerate.py | 3 +- src/aind_behavior_just_frames/rig.py | 14 +++- uv.lock | 4 +- 8 files changed, 35 insertions(+), 100 deletions(-) diff --git a/examples/examples.py b/examples/examples.py index 9d10ef8..b2d5124 100644 --- a/examples/examples.py +++ b/examples/examples.py @@ -1,5 +1,6 @@ import datetime import os +from pathlib import Path import aind_behavior_services.rig as rig from aind_behavior_services.session import AindBehaviorSessionModel @@ -11,10 +12,8 @@ def main(path_seed: str = "./local/{schema}.json"): this_session = AindBehaviorSessionModel( date=datetime.datetime.now(tz=datetime.timezone.utc), experiment="AindVideoEncodingBenchmarks", - root_path="c://", subject="Test", notes="test session", - experiment_version="0.0.0", allow_dirty_repo=False, skip_hardware_validation=False, experimenter=["Foo", "Bar"], @@ -27,6 +26,7 @@ def main(path_seed: str = "./local/{schema}.json"): ) this_rig = AindJustFramesRig( + data_directory=Path("C:/Data"), rig_name="this_rig", triggered_camera_controller_0=rig.cameras.CameraController[rig.cameras.SpinnakerCamera]( frame_rate=120, diff --git a/pyproject.toml b/pyproject.toml index 5add741..66d12de 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ version = "0.5.0rc0" readme = {file = "README.md", content-type = "text/markdown"} dependencies = [ - "aind_behavior_services @git+https://github.com/AllenNeuralDynamics/Aind.Behavior.Services@feat-update-session", + "aind_behavior_services @git+https://github.com/AllenNeuralDynamics/Aind.Behavior.Services@0bb8b68c83a4d97b5d972a8595cbef05c7ba4f39", "pydantic-settings" ] diff --git a/src/DataSchemas/aind_behavior_just_frames.json b/src/DataSchemas/aind_behavior_just_frames.json index 8d25f0e..e26d504 100644 --- a/src/DataSchemas/aind_behavior_just_frames.json +++ b/src/DataSchemas/aind_behavior_just_frames.json @@ -178,15 +178,22 @@ "type": "boolean" }, "zmq_connection": { - "$ref": "#/$defs/ZmqPubSub", - "description": "ZMQ connection for communication." + "default": null, + "description": "ZMQ connection for communication.", + "oneOf": [ + { + "$ref": "#/$defs/ZmqPubSub" + }, + { + "type": "null" + } + ] } }, "required": [ "rig_name", "data_directory", - "harp_behavior", - "zmq_connection" + "harp_behavior" ], "title": "AindJustFramesRig", "type": "object" @@ -204,11 +211,6 @@ "title": "Device Type", "type": "string" }, - "name": { - "description": "Device name", - "title": "Name", - "type": "string" - }, "calibration": { "default": null, "description": "Calibration for the device.", @@ -245,7 +247,6 @@ } }, "required": [ - "name", "cameras" ], "title": "CameraController[SpinnakerCamera]", @@ -259,11 +260,6 @@ "title": "Device Type", "type": "string" }, - "name": { - "description": "Device name", - "title": "Name", - "type": "string" - }, "calibration": { "default": null, "description": "Calibration for the device.", @@ -302,7 +298,6 @@ } }, "required": [ - "name", "port_name" ], "title": "HarpBehavior", @@ -425,11 +420,6 @@ "title": "Device Type", "type": "string" }, - "name": { - "description": "Device name", - "title": "Name", - "type": "string" - }, "calibration": { "default": null, "description": "Calibration for the device.", @@ -540,7 +530,6 @@ } }, "required": [ - "name", "serial_number" ], "title": "SpinnakerCamera", diff --git a/src/Extensions/AindBehaviorJustFrames.Generated.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs index c803a5e..0213122 100644 --- a/src/Extensions/AindBehaviorJustFrames.Generated.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -319,7 +319,6 @@ public AindJustFramesRig() _harpBehavior = new HarpBehavior(); _satelliteRigs = new System.Collections.Generic.List(); _isSatellite = false; - _zmqConnection = new ZmqPubSub(); } protected AindJustFramesRig(AindJustFramesRig other) @@ -504,7 +503,7 @@ public bool IsSatellite /// ZMQ connection for communication. /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("zmq_connection", Required=Newtonsoft.Json.Required.Always)] + [Newtonsoft.Json.JsonPropertyAttribute("zmq_connection")] [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] public ZmqPubSub ZmqConnection { @@ -611,8 +610,6 @@ public partial class CameraControllerSpinnakerCamera private string _deviceType; - private string _name; - private BaseModel _calibration; private System.Collections.Generic.Dictionary _cameras; @@ -628,7 +625,6 @@ public CameraControllerSpinnakerCamera() protected CameraControllerSpinnakerCamera(CameraControllerSpinnakerCamera other) { _deviceType = other._deviceType; - _name = other._name; _calibration = other._calibration; _cameras = other._cameras; _frameRate = other._frameRate; @@ -647,23 +643,6 @@ public string DeviceType } } - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string Name - { - get - { - return _name; - } - set - { - _name = value; - } - } - /// /// Calibration for the device. /// @@ -731,7 +710,6 @@ public System.IObservable Generate(Sys protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("Name = " + _name + ", "); stringBuilder.Append("Calibration = " + _calibration + ", "); stringBuilder.Append("Cameras = " + _cameras + ", "); stringBuilder.Append("FrameRate = " + _frameRate); @@ -761,8 +739,6 @@ public partial class HarpBehavior private string _deviceType; - private string _name; - private BaseModel _calibration; private int _whoAmI; @@ -780,7 +756,6 @@ public HarpBehavior() protected HarpBehavior(HarpBehavior other) { _deviceType = other._deviceType; - _name = other._name; _calibration = other._calibration; _whoAmI = other._whoAmI; _serialNumber = other._serialNumber; @@ -800,23 +775,6 @@ public string DeviceType } } - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string Name - { - get - { - return _name; - } - set - { - _name = value; - } - } - /// /// Calibration for the device. /// @@ -895,7 +853,6 @@ public System.IObservable Generate(System.IObservable - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string Name - { - get - { - return _name; - } - set - { - _name = value; - } - } - /// /// Calibration for the device. /// @@ -1584,7 +1521,6 @@ public System.IObservable Generate(System.IObservable< protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { stringBuilder.Append("DeviceType = " + _deviceType + ", "); - stringBuilder.Append("Name = " + _name + ", "); stringBuilder.Append("Calibration = " + _calibration + ", "); stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); stringBuilder.Append("Binning = " + _binning + ", "); diff --git a/src/aind_behavior_just_frames/message_protocol.py b/src/aind_behavior_just_frames/message_protocol.py index 55f4ffe..0a2cf60 100644 --- a/src/aind_behavior_just_frames/message_protocol.py +++ b/src/aind_behavior_just_frames/message_protocol.py @@ -1,25 +1,26 @@ from typing import Annotated, Any, Literal, Union from aind_behavior_services.message_protocol import HeartbeatPayload, LogPayload, _Message -from aind_behavior_just_frames.rig import SatelliteRig -from aind_behavior_services.session import AindBehaviorSessionModel from pydantic import BaseModel, ConfigDict, Field, RootModel, create_model ## This api is experimental and subject to change! + # ================================================================================ # Create custom messages for this platform class StartPayload(BaseModel): payload_type: Literal["Start"] = "Start" + class StopPayload(BaseModel): payload_type: Literal["Stop"] = "Stop" + # ================================================================================ # Register payloads into a protocol class RegisteredPayload(RootModel): root: Annotated[ - Union[StartPayload, StopPayload, LogPayload, HeartbeatPayload], + Union[StartPayload, StopPayload, LogPayload, HeartbeatPayload], Field(discriminator="payload_type", json_schema_extra={"x-abstract": True}), ] @@ -42,4 +43,4 @@ class MessageProtocol(BaseModel): model_config = ConfigDict(json_schema_extra={"x-abstract": True}) registered_message: RegisteredMessages - message: Message \ No newline at end of file + message: Message diff --git a/src/aind_behavior_just_frames/regenerate.py b/src/aind_behavior_just_frames/regenerate.py index dba241d..5fed95d 100644 --- a/src/aind_behavior_just_frames/regenerate.py +++ b/src/aind_behavior_just_frames/regenerate.py @@ -5,8 +5,8 @@ from aind_behavior_services.session import AindBehaviorSessionModel from aind_behavior_services.utils import BonsaiSgenSerializers, convert_pydantic_to_bonsai -from aind_behavior_just_frames.rig import AindJustFramesRig from aind_behavior_just_frames.message_protocol import MessageProtocol +from aind_behavior_just_frames.rig import AindJustFramesRig SCHEMA_ROOT = Path("./src/DataSchemas/") EXTENSIONS_ROOT = Path("./src/Extensions/") @@ -41,6 +41,5 @@ def main(): ) - if __name__ == "__main__": main() diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index 30aa75e..24e91fd 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -2,7 +2,7 @@ import aind_behavior_services.rig as rig from aind_behavior_services.rig import AindBehaviorRigModel -from pydantic import BaseModel, Field, field_validator +from pydantic import BaseModel, Field, field_validator, model_validator from . import __semver__ @@ -11,6 +11,7 @@ class ZmqPubSub(BaseModel): pub: rig.network.ZmqConnection = Field(description="ZMQ Publisher") sub: rig.network.ZmqConnection = Field(description="ZMQ Subscriber") + class SatelliteRig(AindBehaviorRigModel): version: Literal[__semver__] = __semver__ computer_name: str = Field(description="Remote Computer name") @@ -50,4 +51,13 @@ class AindJustFramesRig(AindBehaviorRigModel): default_factory=list, min_length=1, description="List of satellite rigs." ) is_satellite: bool = Field(default=False) - zmq_connection: ZmqPubSub = Field(description="ZMQ connection for communication.") + zmq_connection: Optional[ZmqPubSub] = Field(default=None, description="ZMQ connection for communication.") + + @model_validator(mode="after") + def verify_zmq_nullability(self): + if self.zmq_connection is None: + if self.is_satellite: + raise ValueError("Satellite rigs must define a ZMQ connection.") + if len(self.satellite_rigs) > 0: + raise ValueError("Master rigs with satellite rigs must define a ZMQ connection.") + return self diff --git a/uv.lock b/uv.lock index 57bce32..0a833bd 100644 --- a/uv.lock +++ b/uv.lock @@ -64,7 +64,7 @@ docs = [ [package.metadata] requires-dist = [ - { name = "aind-behavior-services", git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=feat-update-session" }, + { name = "aind-behavior-services", git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=0bb8b68c83a4d97b5d972a8595cbef05c7ba4f39" }, { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = ">=0.8.2,<0.9.0" }, { name = "pydantic-settings" }, ] @@ -88,7 +88,7 @@ docs = [ [[package]] name = "aind-behavior-services" version = "0.13.0rc0" -source = { git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=feat-update-session#e874dab47d70af621ad4dd01ebc3d41010f1d3cd" } +source = { git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=0bb8b68c83a4d97b5d972a8595cbef05c7ba4f39#0bb8b68c83a4d97b5d972a8595cbef05c7ba4f39" } dependencies = [ { name = "aind-behavior-curriculum" }, { name = "gitpython" }, From bddd7e51e9bdf994d5621fb664b794ee7267fce4 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Tue, 2 Dec 2025 16:05:39 -0800 Subject: [PATCH 20/32] Fix visualizer edge case --- src/Extensions/Main.bonsai | 9 +-------- .../SpinnakerCameraControllerSaturationVisualizer.bonsai | 7 +++---- src/Extensions/Visualizers.bonsai | 8 +++++--- 3 files changed, 9 insertions(+), 15 deletions(-) diff --git a/src/Extensions/Main.bonsai b/src/Extensions/Main.bonsai index ed58ea0..7ff9b60 100644 --- a/src/Extensions/Main.bonsai +++ b/src/Extensions/Main.bonsai @@ -1218,14 +1218,8 @@ - - - 0 - - - JustFrames true @@ -1278,11 +1272,10 @@ - + - diff --git a/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai b/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai index c952fcf..41a522b 100644 --- a/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai +++ b/src/Extensions/SpinnakerCameraControllerSaturationVisualizer.bonsai @@ -9,7 +9,6 @@ xmlns:p2="clr-namespace:AllenNeuralDynamics.Core.Design;assembly=AllenNeuralDynamics.Core.Design" xmlns:gui="clr-namespace:Bonsai.Gui;assembly=Bonsai.Gui" xmlns:p3="clr-namespace:AllenNeuralDynamics.VrForaging;assembly=AllenNeuralDynamics.Core.Design" - xmlns:p4="clr-namespace:Bonsai.Vision.Design;assembly=Bonsai.Vision.Design" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -117,12 +116,12 @@ Value.Image - 5 - 250 + 1 + 254 1 - + diff --git a/src/Extensions/Visualizers.bonsai b/src/Extensions/Visualizers.bonsai index 058b03d..afb4d37 100644 --- a/src/Extensions/Visualizers.bonsai +++ b/src/Extensions/Visualizers.bonsai @@ -6,10 +6,12 @@ xmlns="https://bonsai-rx.org/2018/workflow"> - - Source1 + + + 0 + - + Visualizers From 8bf3d83093e540da0f20a17ce0a12f97699130bf Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Tue, 2 Dec 2025 20:26:24 -0800 Subject: [PATCH 21/32] Solve race condition for configuration --- src/Extensions/Main.bonsai | 81 +++++++++++++++++++++++++++----------- src/main.bonsai | 14 ++----- src/satellite.bonsai | 14 ++----- 3 files changed, 64 insertions(+), 45 deletions(-) diff --git a/src/Extensions/Main.bonsai b/src/Extensions/Main.bonsai index 7ff9b60..4955b63 100644 --- a/src/Extensions/Main.bonsai +++ b/src/Extensions/Main.bonsai @@ -25,10 +25,39 @@ Main + + Source1 + + + + 1 + + + + ConfigurationInput + Init + + ConfigurationInput + + + Item1 + + + RigSchema + + + ConfigurationInput + + + Item2 + + + SubjectSchema + ../. @@ -225,28 +254,32 @@ - - + + - - - + + + + - + - - - + + + - + + + + @@ -1261,21 +1294,23 @@ - - - - - - - - - - - - + + + + + + + + + + + + - + + + diff --git a/src/main.bonsai b/src/main.bonsai index 5131c58..05af53e 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -29,9 +29,6 @@ - - RigSchema - @@ -46,9 +43,6 @@ - - SubjectSchema - @@ -58,14 +52,12 @@ - - + + - + - - diff --git a/src/satellite.bonsai b/src/satellite.bonsai index 15cf421..83f8db2 100644 --- a/src/satellite.bonsai +++ b/src/satellite.bonsai @@ -29,9 +29,6 @@ - - RigSchema - @@ -46,9 +43,6 @@ - - SubjectSchema - @@ -58,14 +52,12 @@ - - + + - + - - From 068dbe81e78220edded13d9fdd35e6aeb49fdc13 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Tue, 2 Dec 2025 20:27:52 -0800 Subject: [PATCH 22/32] Remove outdate readme information --- README.md | 50 -------------------------------------------------- 1 file changed, 50 deletions(-) diff --git a/README.md b/README.md index 11ff035..c35ca34 100644 --- a/README.md +++ b/README.md @@ -1,53 +1,3 @@ # Aind.Behavior.JustFrames A repository with code for a online video acquisition/encoding pipeline - - -## Getting started - -The easiest way to get started is to clone this repository and run the `deploy.cmd` script. This script will install the necessary dependencies. If you use any python-dependent scripts (e.g. create settings json instances, `regenerate` or `clabe` commands), make sure to run them from an activated environment (`./.venv` directory in the root of the repo). - -To run the workflow you will need a valid set of schemas. Examples of how to generate these can be found in the `./examples/examples.py` file. For the most part, you will only need to generate the rig schema, as the others can be automatically generated using the `clabe` script. In summary: - -1. Generate the rig configuration by adapting the script in `./examples/examples.py`. You should make a copy of the example and modify it outside the repository directory, otherwise, any untracked changes / new files in the local repository will flag it as "dirty" and the benchmarks will not be allowed to run. -2. Once the schema is defined in the `.py` file, run the script to generate a valid `.json` file that will be the input to the benchmark workflow. -3. Copy and Paste the generated rig schema (i.e. the `.json` file) to the target config folder (by default `\\allen\aind\scratch\AindBehavior.db\AindBehaviorJustFrames\Rig\\.json`)/ -4. Run the `uv run just-frames clabe`, from the root of the repository, and follow the prompt. -5. Once Bonsai is running, double-click the `UserInterface` operator to open the GUI -6. Click Start (Stop) to start (stop) the benchmark workflow. - -Alternatively, you can run the `main.bonsai` script directly using the following command from the root of the repository: - -```cmd -"./bonsai/bonsai.exe" "./src/main.bonsai" -p RigPath="" -p SessionPath="" -``` - -where `` and `` are the paths to the rig and session schemas, respectively. - - - ---- - -## General instructions - -This repository follows the project structure laid out in the [Aind.Behavior.Services repository](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services). - ---- - -## Deployment - -Deployment instructions can be found [here](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?tab=readme-ov-file#deployment). - -Specifically, Ffmpeg and CUDA support must be installed on the computer. - ---- - -## Prerequisites - -Pre-requisites for running the project can be found [here](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?tab=readme-ov-file#prerequisites). - ---- - -## Regenerating schemas - -Instructions for regenerating schemas can be found [here](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?tab=readme-ov-file#regenerating-schemas). From 31b20d00645b07221c86b9b590f798fa12e5c3f6 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Tue, 2 Dec 2025 20:31:14 -0800 Subject: [PATCH 23/32] Update launcher dependencies --- pyproject.toml | 3 +- src/aind_behavior_just_frames/launcher.py | 12 +-- uv.lock | 103 +++++++++++++++------- 3 files changed, 77 insertions(+), 41 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 66d12de..26c9c6c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,8 +22,7 @@ dependencies = [ [project.optional-dependencies] -launcher = ["aind-clabe[aind-services] >= 0.8.2 ,<0.9.0"] - +launcher = ["aind-clabe[aind-services] >= 0.9 ,<0.10.0"] [dependency-groups] diff --git a/src/aind_behavior_just_frames/launcher.py b/src/aind_behavior_just_frames/launcher.py index 3ede67d..b592f54 100644 --- a/src/aind_behavior_just_frames/launcher.py +++ b/src/aind_behavior_just_frames/launcher.py @@ -5,7 +5,6 @@ from clabe import resource_monitor from 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.../data_contract/__init__.py | 45 ++ .../data_contract/v0_5_0.py | 137 +++++ .../data_qc/__init__.py | 32 ++ .../data_qc/data_qc.py | 77 +++ uv.lock | 526 +++++++++++++++++- 7 files changed, 822 insertions(+), 12 deletions(-) create mode 100644 src/aind_behavior_just_frames/data_contract/__init__.py create mode 100644 src/aind_behavior_just_frames/data_contract/v0_5_0.py create mode 100644 src/aind_behavior_just_frames/data_qc/__init__.py create mode 100644 src/aind_behavior_just_frames/data_qc/data_qc.py diff --git a/pyproject.toml b/pyproject.toml index 26c9c6c..be1e78c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,11 +22,14 @@ dependencies = [ [project.optional-dependencies] -launcher = ["aind-clabe[aind-services] >= 0.9 ,<0.10.0"] +data = ["contraqctor >= 0.5.3 ,<0.6.0"] +launcher = [ + "aind-clabe[aind-services] >= 0.9 ,<0.10.0", + "aind_behavior_just_frames[data]",] [dependency-groups] -dev = ["aind_behavior_just_frames[launcher]", +dev = ["aind_behavior_just_frames[launcher, data]", "ruff", "codespell" ] diff --git a/src/aind_behavior_just_frames/cli.py b/src/aind_behavior_just_frames/cli.py index 89231fb..b95f4cb 100644 --- a/src/aind_behavior_just_frames/cli.py +++ b/src/aind_behavior_just_frames/cli.py @@ -4,6 +4,7 @@ from pydantic_settings import BaseSettings, CliApp, CliSubCommand from aind_behavior_just_frames import __semver__, regenerate +from aind_behavior_just_frames.data_qc import DataQcCli from aind_behavior_just_frames.launcher import ClabeCli @@ -21,12 +22,13 @@ def cli_cmd(self) -> None: regenerate.main() -class VrForagingCli(BaseSettings, cli_prog_name="vr-foraging", cli_kebab_case=True): +class JustFramesCli(BaseSettings, cli_prog_name="just-frames", cli_kebab_case=True): version: CliSubCommand[VersionCli] = Field( - description="Print the version of the vr-foraging package.", + description="Print the version of the just-frames package.", ) + data_qc: CliSubCommand[DataQcCli] = Field(description="Run data quality checks.") regenerate: CliSubCommand[DslRegenerateCli] = Field( - description="Regenerate the vr-foraging dsl dependencies.", + description="Regenerate the just-frames dsl dependencies.", ) clabe: CliSubCommand[ClabeCli] = Field( description="Run the Clabe CLI.", @@ -37,7 +39,7 @@ def cli_cmd(self): def main(): - CliApp().run(VrForagingCli) + CliApp().run(JustFramesCli) if __name__ == "__main__": diff --git a/src/aind_behavior_just_frames/data_contract/__init__.py b/src/aind_behavior_just_frames/data_contract/__init__.py new file mode 100644 index 0000000..8e668d4 --- /dev/null +++ b/src/aind_behavior_just_frames/data_contract/__init__.py @@ -0,0 +1,45 @@ +import os +import typing as t +from functools import partial +from pathlib import Path + +import contraqctor +import semver + +from aind_behavior_just_frames import __semver__ + + +def _dataset_lookup_helper(version: str) -> t.Callable[[Path], contraqctor.contract.Dataset]: + parsed_version = semver.Version.parse(version) + # Ignore release candidate suffix for version comparison + parsed_version = semver.Version(parsed_version.major, parsed_version.minor, parsed_version.patch) + if parsed_version >= semver.Version.parse("0.5.0"): + from .v0_5_0 import dataset as _dataset + else: + raise ValueError(f"Unsupported version: {version}") + return partial(_dataset, version=version) + + +def dataset(path: os.PathLike, version: str = __semver__) -> contraqctor.contract.Dataset: + """ + Loads the dataset for the Aind Just Frames project from a specified version. + + Args: + path (os.PathLike): The path to the dataset root directory. + version (str): The version of the dataset to load. By default, it uses the package version. + + Returns: + contraqctor.contract.Dataset: The loaded dataset. + """ + dataset_constructor = _dataset_lookup_helper(version) + return dataset_constructor(Path(path)) + + +def render_dataset(version: str = __semver__) -> str: + """Renders the dataset as a tree-like structure for visualization.""" + from contraqctor.contract.utils import print_data_stream_tree_html + + dataset_constructor = _dataset_lookup_helper(version) + return print_data_stream_tree_html( + dataset_constructor(Path("")), show_missing_indicator=False, show_type=True + ) diff --git a/src/aind_behavior_just_frames/data_contract/v0_5_0.py b/src/aind_behavior_just_frames/data_contract/v0_5_0.py new file mode 100644 index 0000000..a556bf5 --- /dev/null +++ b/src/aind_behavior_just_frames/data_contract/v0_5_0.py @@ -0,0 +1,137 @@ +from pathlib import Path + +from aind_behavior_services.session import AindBehaviorSessionModel +from contraqctor.contract import Dataset, DataStreamCollection +from contraqctor.contract.camera import Camera +from contraqctor.contract.harp import ( + DeviceYmlByFile, + HarpDevice, +) +from contraqctor.contract.json import PydanticModel, SoftwareEvents +from contraqctor.contract.mux import MapFromPaths +from contraqctor.contract.text import Text + +from aind_behavior_just_frames.rig import AindJustFramesRig + + +def dataset( + root_path: Path, + name: str = "JustFramesDataset", + description: str = "A JustFrames dataset", + version: str = "0.5.0", +) -> Dataset: + """ + Creates a Dataset object for the JustFrames experiment. + This function constructs a hierarchical representation of the data streams collected + during a JustFrames experiment, including hardware device data, software events, + and configuration files. + Parameters + ---------- + root_path : Path + Path to the root directory containing the dataset + name : str, optional + Name of the dataset, defaults to "JustFramesDataset" + description : str, optional + Description of the dataset, defaults to "A JustFrames dataset" + version : str, optional + Version of the dataset, defaults to the package version (This is also the version of the experiment) + Returns + ------- + Dataset + A Dataset object containing a hierarchical representation of all data streams + from the JustFrames experiment, including: + - Camera/Video (meta)data + - Log files + - Configuration schemas (rig, session) + """ + + root_path = Path(root_path) + return Dataset( + name=name, + version=version, + description=description, + data_streams=[ + DataStreamCollection( + name="Behavior", + description="Data from the Behavior modality", + data_streams=[ + HarpDevice( + name="HarpBehavior", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/Behavior.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + DataStreamCollection( + name="HarpCommands", + description="Commands sent to Harp devices", + data_streams=[ + HarpDevice( + name="HarpBehavior", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/Behavior.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ) + ], + ), + DataStreamCollection( + name="SoftwareEvents", + description="Software events generated by the workflow. The timestamps of these events are low precision and should not be used to align to physiology data.", + data_streams=[], + ), + DataStreamCollection( + name="Logs", + data_streams=[ + Text( + name="Launcher", + description="Contains the console log of the launcher process.", + reader_params=Text.make_params( + path=root_path / "behavior/Logs/.launcher/launcher.log", + ), + ), + SoftwareEvents( + name="EndSession", + description="A file that determines the end of the session. If the file is empty, the session is still running or it was not closed properly.", + reader_params=SoftwareEvents.make_params( + path=root_path / "behavior/Logs/EndSession.json", + ), + ), + ], + ), + DataStreamCollection( + name="InputSchemas", + description="Configuration files for the behavior rig, task_logic and session.", + data_streams=[ + PydanticModel( + name="Rig", + reader_params=PydanticModel.make_params( + model=AindJustFramesRig, + path=root_path / "behavior/Logs/rig_input.json", + ), + ), + PydanticModel( + name="Session", + reader_params=PydanticModel.make_params( + model=AindBehaviorSessionModel, + path=root_path / "behavior/Logs/session_input.json", + ), + ), + ], + ), + ], + ), + MapFromPaths( + name="BehaviorVideos", + description="Data from BehaviorVideos modality", + reader_params=MapFromPaths.make_params( + paths=root_path / "behavior-videos", + include_glob_pattern=["*"], + inner_data_stream=Camera, + inner_param_factory=lambda camera_name: Camera.make_params( + path=root_path / "behavior-videos" / camera_name + ), + ), + ), + ], + ) diff --git a/src/aind_behavior_just_frames/data_qc/__init__.py b/src/aind_behavior_just_frames/data_qc/__init__.py new file mode 100644 index 0000000..c0bdbdb --- /dev/null +++ b/src/aind_behavior_just_frames/data_qc/__init__.py @@ -0,0 +1,32 @@ +import logging +import os +from pathlib import Path + +from pydantic import Field +from pydantic_settings import BaseSettings, CliPositionalArg + +from aind_behavior_just_frames import __semver__ + +logger = logging.getLogger(__name__) + + +class DataQcCli(BaseSettings, cli_kebab_case=True): + data_path: CliPositionalArg[os.PathLike] = Field(description="Path to the session data directory.") + version: str = Field(default=__semver__, description="Version of the dataset.") + report_path: Path | None = Field( + default=None, description="Path to save the Html QC report. If not provided, report is not saved." + ) + + def cli_cmd(self): + """Run data quality checks on the dataset located at the specified path.""" + from ..data_contract import dataset + from .data_qc import make_qc_runner + + _dataset = dataset(Path(self.data_path), self.version) + runner = make_qc_runner(_dataset) + results = runner.run_all_with_progress() + if report_path := self.report_path: + from contraqctor.qc.reporters import HtmlReporter + + reporter = HtmlReporter(output_path=report_path) + reporter.report_results(results, serialize_context_exportable_obj=True) diff --git a/src/aind_behavior_just_frames/data_qc/data_qc.py b/src/aind_behavior_just_frames/data_qc/data_qc.py new file mode 100644 index 0000000..f42111f --- /dev/null +++ b/src/aind_behavior_just_frames/data_qc/data_qc.py @@ -0,0 +1,77 @@ +import logging +import typing as t + +import pandas as pd +from contraqctor import contract, qc +from contraqctor.contract.harp import HarpDevice + +from aind_behavior_just_frames.rig import AindJustFramesRig + +logger = logging.getLogger(__name__) + + +class JustFramesQcSuite(qc.Suite): + def __init__(self, dataset: contract.Dataset): + self.dataset = dataset + + def test_end_session_exists(self): + """Check that the session has an end event.""" + end_session = self.dataset["Behavior"]["Logs"]["EndSession"] + + if not end_session.has_data: + return self.fail_test( + None, "EndSession event does not exist. Session may be corrupted or not ended properly." + ) + + assert isinstance(end_session.data, pd.DataFrame) + if end_session.data.empty: + return self.fail_test(None, "No data in EndSession. Session may be corrupted or not ended properly.") + else: + return self.pass_test(None, "EndSession event exists with data.") + + +def make_qc_runner(dataset: contract.Dataset) -> qc.Runner: + _runner = qc.Runner() + dataset.load_all(strict=False) + exclude: list[contract.DataStream] = [] + rig: AindJustFramesRig = dataset["Behavior"]["InputSchemas"]["Rig"].data + + # Exclude commands to Harp boards as these are tested separately + for cmd in dataset["Behavior"]["HarpCommands"]: + for stream in cmd: + if isinstance(stream, contract.harp.HarpRegister): + exclude.append(stream) + + # Add the outcome of the dataset loading step to the automatic qc + _runner.add_suite(qc.contract.ContractTestSuite(dataset.collect_errors(), exclude=exclude), group="Data contract") + + # Add Harp tests for ALL Harp devices in the dataset + for stream in (_r := dataset["Behavior"]): + if isinstance(stream, HarpDevice): + commands = t.cast(HarpDevice, _r["HarpCommands"][stream.name]) + _runner.add_suite(qc.harp.HarpDeviceTestSuite(stream, commands), stream.name) + + # Add camera qc + for camera in dataset["BehaviorVideos"]: + if rig.triggered_camera_controller_0 is not None and camera.name in rig.triggered_camera_controller_0.cameras: + controller = rig.triggered_camera_controller_0 + elif rig.triggered_camera_controller_1 is not None and camera.name in rig.triggered_camera_controller_1.cameras: + controller = rig.triggered_camera_controller_1 + else: + logger.warning("Camera %s not found in any triggered camera controller.", camera.name) + continue + + _runner.add_suite( + qc.camera.CameraTestSuite(camera, expected_fps=controller.frame_rate, saturation_bounds=(1, 254)), + camera.name, + ) + + # Add Csv tests + csv_streams = [stream for stream in dataset.iter_all() if isinstance(stream, contract.csv.Csv)] + for stream in csv_streams: + _runner.add_suite(qc.csv.CsvTestSuite(stream), stream.name) + + # Add the Just Frames specific tests + _runner.add_suite(JustFramesQcSuite(dataset), "JustFrames") + + return _runner diff --git a/uv.lock b/uv.lock index fb8cfdf..9a94719 100644 --- a/uv.lock +++ b/uv.lock @@ -2,9 +2,15 @@ version = 1 revision = 3 requires-python = ">=3.11" resolution-markers = [ - "python_full_version >= '3.14'", - "python_full_version >= '3.12' and python_full_version < '3.14'", - "python_full_version < '3.12'", + "python_full_version >= '3.14' and sys_platform == 'darwin'", + "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'darwin'", + "python_full_version >= '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version >= '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.14' and sys_platform != 'darwin' and sys_platform != 'linux')", + "(python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform != 'darwin' and sys_platform != 'linux')", + "python_full_version < '3.12' and sys_platform == 'darwin'", + "python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'", + "(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux')", ] [[package]] @@ -43,13 +49,17 @@ dependencies = [ ] [package.optional-dependencies] +data = [ + { name = "contraqctor" }, +] launcher = [ { name = "aind-clabe", extra = ["aind-services"] }, + { name = "contraqctor" }, ] [package.dev-dependencies] dev = [ - { name = "aind-behavior-just-frames", extra = ["launcher"] }, + { name = "aind-behavior-just-frames", extra = ["data", "launcher"] }, { name = "codespell" }, { name = "ruff" }, ] @@ -64,15 +74,17 @@ docs = [ [package.metadata] requires-dist = [ + { name = "aind-behavior-just-frames", extras = ["data"], marker = "extra == 'launcher'" }, { name = "aind-behavior-services", git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=0bb8b68c83a4d97b5d972a8595cbef05c7ba4f39" }, { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = ">=0.9,<0.10.0" }, + { name = "contraqctor", marker = "extra == 'data'", specifier = ">=0.5.3,<0.6.0" }, { name = "pydantic-settings" }, ] -provides-extras = ["launcher"] +provides-extras = ["data", "launcher"] [package.metadata.requires-dev] dev = [ - { name = "aind-behavior-just-frames", extras = ["launcher"] }, + { name = "aind-behavior-just-frames", extras = ["launcher", "data"] }, { name = "codespell" }, { name = "ruff" }, ] @@ -465,6 +477,112 @@ wheels = [ { url = 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report?"): + try: + import webbrowser + + from contraqctor.qc.reporters import HtmlReporter + + from .data_qc.data_qc import make_qc_runner + + _dataset = data_contract.dataset(launcher.session_directory) + runner = make_qc_runner(_dataset) + qc_path = launcher.session_directory / "Behavior" / "Logs" / "qc_report.html" + reporter = HtmlReporter(output_path=qc_path) + runner.run_all_with_progress(reporter=reporter) + webbrowser.open(qc_path.as_uri(), new=2) + except Exception as e: + logger.error("Failed to run data QC: %s", e) + launcher.copy_logs() robocopy.RobocopyService(source=launcher.session_directory, settings=robocopy.RobocopySettings()).transfer() return From a6459bbf2d22734587151bb8902e14288da2b10a Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 3 Dec 2025 10:44:54 -0800 Subject: [PATCH 26/32] Add temporary launcher dependencies --- pyproject.toml | 2 +- uv.lock | 50 ++++++++++++++++++++++++++++++++------------------ 2 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-168,7 +168,6 @@ "items": { "$ref": "#/$defs/SatelliteRig" }, - "minItems": 1, "title": "Satellite Rigs", "type": "array" }, @@ -353,7 +352,7 @@ "type": "string" }, "computer_name": { - "description": "Remote Computer name", + "description": "Computer name", "title": "Computer Name", "type": "string" }, @@ -403,7 +402,6 @@ } }, "required": [ - "computer_name", "rig_name", "data_directory", "zmq_connection" diff --git a/src/Extensions/AindBehaviorJustFrames.Generated.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs index 0213122..a4ece91 100644 --- a/src/Extensions/AindBehaviorJustFrames.Generated.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -1083,10 +1083,10 @@ public string Version } /// - /// Remote Computer name + /// Computer name /// - [Newtonsoft.Json.JsonPropertyAttribute("computer_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Remote Computer name")] + [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] + [System.ComponentModel.DescriptionAttribute("Computer name")] public string ComputerName { get diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index 24e91fd..535e619 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -14,7 +14,6 @@ class ZmqPubSub(BaseModel): class SatelliteRig(AindBehaviorRigModel): version: Literal[__semver__] = __semver__ - computer_name: str = Field(description="Remote Computer name") zmq_connection: ZmqPubSub = Field(description="ZMQ connection for communication.") triggered_camera_controller_0: Optional[rig.cameras.CameraController[rig.cameras.SpinnakerCamera]] = Field( default=None, @@ -48,7 +47,7 @@ class AindJustFramesRig(AindBehaviorRigModel): description="Harp behavior board. Will be the source of triggers for the two camera controllers.", ) satellite_rigs: list[SatelliteRig] = Field( - default_factory=list, min_length=1, description="List of satellite rigs." + default_factory=list, description="List of satellite rigs." ) is_satellite: bool = Field(default=False) zmq_connection: Optional[ZmqPubSub] = Field(default=None, description="ZMQ connection for communication.") @@ -61,3 +60,10 @@ def verify_zmq_nullability(self): if len(self.satellite_rigs) > 0: raise ValueError("Master rigs with satellite rigs must define a ZMQ connection.") return self + + @model_validator(mode="after") + def verify_satellite_rigs(self): + for _r in self.satellite_rigs: + if not _r.is_satellite: + raise ValueError("All rigs in satellite_rigs must have is_satellite=True.") + return self diff --git a/uv.lock b/uv.lock index 863e154..403c6e5 100644 --- a/uv.lock +++ b/uv.lock @@ -112,7 +112,7 @@ dependencies = [ [[package]] name = "aind-clabe" version = "0.9.1rc1" -source = { git = "https://github.com/AllenNeuralDynamics/clabe?rev=test-services-13#1e05a67bfa706e948f0fbd960a037b2a1e16d318" } +source = { git = "https://github.com/AllenNeuralDynamics/clabe?rev=test-services-13#dfa2668ef278a57bc11f0ac9c643a54c9e9bda27" } dependencies = [ { name = "aind-behavior-services" }, { name = "gitpython" }, From b403f39b278441bd85d755462f60b266c33ef62a Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 3 Dec 2025 11:13:50 -0800 Subject: [PATCH 28/32] Regenerate against latest zmq definition --- pyproject.toml | 2 +- .../aind_behavior_just_frames.json | 38 ++++++- .../AindBehaviorJustFrames.Generated.cs | 103 +++++++++++++++++- src/aind_behavior_just_frames/launcher.py | 2 +- src/aind_behavior_just_frames/rig.py | 5 +- uv.lock | 4 +- 6 files changed, 144 insertions(+), 10 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index c7008d6..db0bc68 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ version = "0.5.0rc0" readme = {file = "README.md", content-type = "text/markdown"} dependencies = [ - "aind_behavior_services @git+https://github.com/AllenNeuralDynamics/Aind.Behavior.Services@0bb8b68c83a4d97b5d972a8595cbef05c7ba4f39", + "aind_behavior_services @git+https://github.com/AllenNeuralDynamics/Aind.Behavior.Services@90c77e682922288bc7779c4f8cde5d6f15115899", "pydantic-settings" ] diff --git a/src/DataSchemas/aind_behavior_just_frames.json b/src/DataSchemas/aind_behavior_just_frames.json index aeaef5c..aacf94d 100644 --- a/src/DataSchemas/aind_behavior_just_frames.json +++ b/src/DataSchemas/aind_behavior_just_frames.json @@ -934,8 +934,44 @@ }, "ZmqConnection": { "properties": { + "protocol": { + "const": "Tcp", + "default": "Tcp", + "description": "The protocol to use for the ZMQ connection.", + "title": "Protocol", + "type": "string" + }, + "address": { + "default": "localhost", + "description": "The address of the ZMQ socket.", + "title": "Address", + "type": "string" + }, + "port": { + "default": 5556, + "description": "The port of the ZMQ socket.", + "title": "Port", + "type": "integer" + }, + "action": { + "default": null, + "description": "Whether to bind or connect the socket.", + "oneOf": [ + { + "enum": [ + "bind", + "connect" + ], + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Action" + }, "connection_string": { - "default": "@tcp://localhost:5556", + "default": "", "description": "The connection string for the ZMQ socket.", "title": "Connection String", "type": "string" diff --git a/src/Extensions/AindBehaviorJustFrames.Generated.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs index a4ece91..4c46b58 100644 --- a/src/Extensions/AindBehaviorJustFrames.Generated.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -2300,22 +2300,106 @@ protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) public partial class ZmqConnection { + private string _protocol; + + private string _address; + + private int _port; + + private Action? _action; + private string _connectionString; private string _topic; public ZmqConnection() { - _connectionString = "@tcp://localhost:5556"; + _protocol = "Tcp"; + _address = "localhost"; + _port = 5556; + _connectionString = ""; _topic = ""; } protected ZmqConnection(ZmqConnection other) { + _protocol = other._protocol; + _address = other._address; + _port = other._port; + _action = other._action; _connectionString = other._connectionString; _topic = other._topic; } + /// + /// The protocol to use for the ZMQ connection. + /// + [Newtonsoft.Json.JsonPropertyAttribute("protocol")] + [System.ComponentModel.DescriptionAttribute("The protocol to use for the ZMQ connection.")] + public string Protocol + { + get + { + return _protocol; + } + set + { + _protocol = value; + } + } + + /// + /// The address of the ZMQ socket. + /// + [Newtonsoft.Json.JsonPropertyAttribute("address")] + [System.ComponentModel.DescriptionAttribute("The address of the ZMQ socket.")] + public string Address + { + get + { + return _address; + } + set + { + _address = value; + } + } + + /// + /// The port of the ZMQ socket. + /// + [Newtonsoft.Json.JsonPropertyAttribute("port")] + [System.ComponentModel.DescriptionAttribute("The port of the ZMQ socket.")] + public int Port + { + get + { + return _port; + } + set + { + _port = value; + } + } + + /// + /// Whether to bind or connect the socket. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("action")] + [System.ComponentModel.DescriptionAttribute("Whether to bind or connect the socket.")] + public Action? Action + { + get + { + return _action; + } + set + { + _action = value; + } + } + /// /// The connection string for the ZMQ socket. /// @@ -2358,6 +2442,10 @@ public System.IObservable Generate(System.IObservable None: picker = DefaultBehaviorPicker(launcher=launcher, settings=DefaultBehaviorPickerSettings()) session = picker.pick_session(AindBehaviorSessionModel) - launcher.register_session(session) rig = picker.pick_rig(AindJustFramesRig) + launcher.register_session(session, rig.data_directory) bonsai_app = AindBehaviorServicesBonsaiApp( workflow=Path(r"./src/main.bonsai"), rig=rig, diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index 535e619..0cbb45c 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -11,7 +11,6 @@ class ZmqPubSub(BaseModel): pub: rig.network.ZmqConnection = Field(description="ZMQ Publisher") sub: rig.network.ZmqConnection = Field(description="ZMQ Subscriber") - class SatelliteRig(AindBehaviorRigModel): version: Literal[__semver__] = __semver__ zmq_connection: ZmqPubSub = Field(description="ZMQ connection for communication.") @@ -46,9 +45,7 @@ class AindJustFramesRig(AindBehaviorRigModel): harp_behavior: rig.harp.HarpBehavior = Field( description="Harp behavior board. Will be the source of triggers for the two camera controllers.", ) - satellite_rigs: list[SatelliteRig] = Field( - default_factory=list, description="List of satellite rigs." - ) + satellite_rigs: list[SatelliteRig] = Field(default_factory=list, description="List of satellite rigs.") is_satellite: bool = Field(default=False) zmq_connection: Optional[ZmqPubSub] = Field(default=None, description="ZMQ connection for communication.") diff --git a/uv.lock b/uv.lock index 403c6e5..4ce5d5d 100644 --- a/uv.lock +++ b/uv.lock @@ -75,7 +75,7 @@ docs = [ [package.metadata] requires-dist = [ { name = "aind-behavior-just-frames", extras = ["data"], marker = "extra == 'launcher'" }, - { name = "aind-behavior-services", git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=0bb8b68c83a4d97b5d972a8595cbef05c7ba4f39" }, + { name = "aind-behavior-services", git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=90c77e682922288bc7779c4f8cde5d6f15115899" }, { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", git = "https://github.com/AllenNeuralDynamics/clabe?rev=test-services-13" }, { name = "contraqctor", marker = "extra == 'data'", specifier = ">=0.5.3,<0.6.0" }, { name = "pydantic-settings" }, @@ -100,7 +100,7 @@ docs = [ [[package]] name = "aind-behavior-services" version = "0.13.0rc0" -source = { git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=feat-update-session#0bb8b68c83a4d97b5d972a8595cbef05c7ba4f39" } +source = { git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=feat-update-session#90c77e682922288bc7779c4f8cde5d6f15115899" } dependencies = [ { name = "aind-behavior-curriculum" }, { name = "gitpython" }, From 63efe124a6135ff9769becd247adea0c4b72b2f0 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 3 Dec 2025 14:17:20 -0800 Subject: [PATCH 29/32] Add draft of zmq architecture --- README.md | 4 ++ assets/zmq_architecture.drawio | 78 ++++++++++++++++++++++++++++++++++ assets/zmq_architecture.svg | 4 ++ 3 files changed, 86 insertions(+) create mode 100644 assets/zmq_architecture.drawio create mode 100644 assets/zmq_architecture.svg diff --git a/README.md b/README.md index c35ca34..047bd7c 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,7 @@ # Aind.Behavior.JustFrames A repository with code for a online video acquisition/encoding pipeline + +## ZeroMQ Architecture + +![ZeroMQ Architecture](assets/zmq_architecture.svg) \ No newline at end of file diff --git a/assets/zmq_architecture.drawio b/assets/zmq_architecture.drawio new file mode 100644 index 0000000..69216cb --- /dev/null +++ b/assets/zmq_architecture.drawio @@ -0,0 +1,78 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/assets/zmq_architecture.svg b/assets/zmq_architecture.svg new file mode 100644 index 0000000..561edc1 --- /dev/null +++ b/assets/zmq_architecture.svg @@ -0,0 +1,4 @@ + + + +
@ binds
> connects
@ binds...
Master
Master
Trigger
PubSocker -> @tcp://<*>:trigger_port
Trigger...
Trigger
SubSocket -> >tcp://master_ip:trigger_port
Trigger...
Slave
Slave
Protocol
Req/Resp-> >/@tcp://<slave_ip>:slave_specific_port
Protocol...
Slave
Slave
Protocol
Req/Resp-> >/@tcp://<slave_ip>:slave_specific_port
Protocol...
Protocol
Req/Resp-> >/@tcp://<master_ip>:pc_port
Protocol...Text is not SVG - cannot display \ No newline at end of file From db253f745820b6a025cf8e024fd63732c6a50d08 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 3 Dec 2025 15:48:45 -0800 Subject: [PATCH 30/32] Add zeromq protocol --- .../aind_behavior_just_frames.json | 121 ++- src/Extensions.csproj | 1 + .../AindBehaviorJustFrames.Generated.cs | 454 ++++------- src/Extensions/HarpDevices.bonsai | 324 +------- src/Extensions/Main.bonsai | 436 +---------- .../NetworkConfigToConnectionString.cs | 63 ++ src/Extensions/ZeroMQ.bonsai | 715 ++++++++++++++++++ src/aind_behavior_just_frames/rig.py | 22 +- 8 files changed, 1035 insertions(+), 1101 deletions(-) create mode 100644 src/Extensions/NetworkConfigToConnectionString.cs create mode 100644 src/Extensions/ZeroMQ.bonsai diff --git a/src/DataSchemas/aind_behavior_just_frames.json b/src/DataSchemas/aind_behavior_just_frames.json index aacf94d..edfc7da 100644 --- a/src/DataSchemas/aind_behavior_just_frames.json +++ b/src/DataSchemas/aind_behavior_just_frames.json @@ -176,12 +176,24 @@ "title": "Is Satellite", "type": "boolean" }, - "zmq_connection": { + "zmq_protocol_config": { "default": null, "description": "ZMQ connection for communication.", "oneOf": [ { - "$ref": "#/$defs/ZmqPubSub" + "$ref": "#/$defs/NetworkConfig" + }, + { + "type": "null" + } + ] + }, + "zmq_trigger_config": { + "default": null, + "description": "ZMQ connection for trigger communication.", + "oneOf": [ + { + "$ref": "#/$defs/NetworkConfig" }, { "type": "null" @@ -302,6 +314,29 @@ "title": "HarpBehavior", "type": "object" }, + "NetworkConfig": { + "properties": { + "address": { + "description": "Address for ZMQ connection.", + "format": "ipv4", + "title": "Address", + "type": "string" + }, + "port": { + "description": "Port for ZMQ connection.", + "maximum": 65535, + "minimum": 1, + "title": "Port", + "type": "integer" + } + }, + "required": [ + "address", + "port" + ], + "title": "NetworkConfig", + "type": "object" + }, "Rect": { "description": "Represents a rectangle defined by its top-left corner, width, and height.", "properties": { @@ -367,10 +402,14 @@ "title": "Data Directory", "type": "string" }, - "zmq_connection": { - "$ref": "#/$defs/ZmqPubSub", + "zmq_protocol_config": { + "$ref": "#/$defs/NetworkConfig", "description": "ZMQ connection for communication." }, + "zmq_trigger_config": { + "$ref": "#/$defs/NetworkConfig", + "description": "ZMQ connection for trigger communication." + }, "triggered_camera_controller_0": { "default": null, "description": "Camera controller to triggered cameras. Will use Camera0 register as a trigger.", @@ -404,7 +443,8 @@ "required": [ "rig_name", "data_directory", - "zmq_connection" + "zmq_protocol_config", + "zmq_trigger_config" ], "title": "SatelliteRig", "type": "object" @@ -931,77 +971,6 @@ }, "title": "VideoWriterOpenCv", "type": "object" - }, - "ZmqConnection": { - "properties": { - "protocol": { - "const": "Tcp", - "default": "Tcp", - "description": "The protocol to use for the ZMQ connection.", - "title": "Protocol", - "type": "string" - }, - "address": { - "default": "localhost", - "description": "The address of the ZMQ socket.", - "title": "Address", - "type": "string" - }, - "port": { - "default": 5556, - "description": "The port of the ZMQ socket.", - "title": "Port", - "type": "integer" - }, - "action": { - "default": null, - "description": "Whether to bind or connect the socket.", - "oneOf": [ - { - "enum": [ - "bind", - "connect" - ], - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Action" - }, - "connection_string": { - "default": "", - "description": "The connection string for the ZMQ socket.", - "title": "Connection String", - "type": "string" - }, - "topic": { - "default": "", - "title": "Topic", - "type": "string" - } - }, - "title": "ZmqConnection", - "type": "object" - }, - "ZmqPubSub": { - "properties": { - "pub": { - "$ref": "#/$defs/ZmqConnection", - "description": "ZMQ Publisher" - }, - "sub": { - "$ref": "#/$defs/ZmqConnection", - "description": "ZMQ Subscriber" - } - }, - "required": [ - "pub", - "sub" - ], - "title": "ZmqPubSub", - "type": "object" } } } \ No newline at end of file diff --git a/src/Extensions.csproj b/src/Extensions.csproj index 4a83169..47de4a4 100644 --- a/src/Extensions.csproj +++ b/src/Extensions.csproj @@ -11,6 +11,7 @@ + \ No newline at end of file diff --git a/src/Extensions/AindBehaviorJustFrames.Generated.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs index 4c46b58..2c3aa93 100644 --- a/src/Extensions/AindBehaviorJustFrames.Generated.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -310,7 +310,9 @@ public partial class AindJustFramesRig private bool _isSatellite; - private ZmqPubSub _zmqConnection; + private NetworkConfig _zmqProtocolConfig; + + private NetworkConfig _zmqTriggerConfig; public AindJustFramesRig() { @@ -333,7 +335,8 @@ protected AindJustFramesRig(AindJustFramesRig other) _harpBehavior = other._harpBehavior; _satelliteRigs = other._satelliteRigs; _isSatellite = other._isSatellite; - _zmqConnection = other._zmqConnection; + _zmqProtocolConfig = other._zmqProtocolConfig; + _zmqTriggerConfig = other._zmqTriggerConfig; } [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] @@ -503,17 +506,35 @@ public bool IsSatellite /// ZMQ connection for communication. /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("zmq_connection")] + [Newtonsoft.Json.JsonPropertyAttribute("zmq_protocol_config")] [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] - public ZmqPubSub ZmqConnection + public NetworkConfig ZmqProtocolConfig { get { - return _zmqConnection; + return _zmqProtocolConfig; } set { - _zmqConnection = value; + _zmqProtocolConfig = value; + } + } + + /// + /// ZMQ connection for trigger communication. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("zmq_trigger_config")] + [System.ComponentModel.DescriptionAttribute("ZMQ connection for trigger communication.")] + public NetworkConfig ZmqTriggerConfig + { + get + { + return _zmqTriggerConfig; + } + set + { + _zmqTriggerConfig = value; } } @@ -539,7 +560,8 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("HarpBehavior = " + _harpBehavior + ", "); stringBuilder.Append("SatelliteRigs = " + _satelliteRigs + ", "); stringBuilder.Append("IsSatellite = " + _isSatellite + ", "); - stringBuilder.Append("ZmqConnection = " + _zmqConnection); + stringBuilder.Append("ZmqProtocolConfig = " + _zmqProtocolConfig + ", "); + stringBuilder.Append("ZmqTriggerConfig = " + _zmqTriggerConfig); return true; } @@ -875,6 +897,92 @@ public override string ToString() } + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class NetworkConfig + { + + private string _address; + + private int _port; + + public NetworkConfig() + { + } + + protected NetworkConfig(NetworkConfig other) + { + _address = other._address; + _port = other._port; + } + + /// + /// Address for ZMQ connection. + /// + [Newtonsoft.Json.JsonPropertyAttribute("address", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Address for ZMQ connection.")] + public string Address + { + get + { + return _address; + } + set + { + _address = value; + } + } + + /// + /// Port for ZMQ connection. + /// + [Newtonsoft.Json.JsonPropertyAttribute("port", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Port for ZMQ connection.")] + public int Port + { + get + { + return _port; + } + set + { + _port = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new NetworkConfig(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new NetworkConfig(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Address = " + _address + ", "); + stringBuilder.Append("Port = " + _port); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + /// /// Represents a rectangle defined by its top-left corner, width, and height. /// @@ -1027,7 +1135,9 @@ public partial class SatelliteRig private string _dataDirectory; - private ZmqPubSub _zmqConnection; + private NetworkConfig _zmqProtocolConfig; + + private NetworkConfig _zmqTriggerConfig; private CameraControllerSpinnakerCamera _triggeredCameraController0; @@ -1039,7 +1149,8 @@ public SatelliteRig() { _aindBehaviorServicesPkgVersion = "0.13.0-rc0"; _version = "0.5.0-rc0"; - _zmqConnection = new ZmqPubSub(); + _zmqProtocolConfig = new NetworkConfig(); + _zmqTriggerConfig = new NetworkConfig(); _isSatellite = true; } @@ -1050,7 +1161,8 @@ protected SatelliteRig(SatelliteRig other) _computerName = other._computerName; _rigName = other._rigName; _dataDirectory = other._dataDirectory; - _zmqConnection = other._zmqConnection; + _zmqProtocolConfig = other._zmqProtocolConfig; + _zmqTriggerConfig = other._zmqTriggerConfig; _triggeredCameraController0 = other._triggeredCameraController0; _triggeredCameraController1 = other._triggeredCameraController1; _isSatellite = other._isSatellite; @@ -1137,17 +1249,35 @@ public string DataDirectory /// ZMQ connection for communication. /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("zmq_connection", Required=Newtonsoft.Json.Required.Always)] + [Newtonsoft.Json.JsonPropertyAttribute("zmq_protocol_config", Required=Newtonsoft.Json.Required.Always)] [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] - public ZmqPubSub ZmqConnection + public NetworkConfig ZmqProtocolConfig { get { - return _zmqConnection; + return _zmqProtocolConfig; } set { - _zmqConnection = value; + _zmqProtocolConfig = value; + } + } + + /// + /// ZMQ connection for trigger communication. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("zmq_trigger_config", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ connection for trigger communication.")] + public NetworkConfig ZmqTriggerConfig + { + get + { + return _zmqTriggerConfig; + } + set + { + _zmqTriggerConfig = value; } } @@ -1217,7 +1347,8 @@ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) stringBuilder.Append("ComputerName = " + _computerName + ", "); stringBuilder.Append("RigName = " + _rigName + ", "); stringBuilder.Append("DataDirectory = " + _dataDirectory + ", "); - stringBuilder.Append("ZmqConnection = " + _zmqConnection + ", "); + stringBuilder.Append("ZmqProtocolConfig = " + _zmqProtocolConfig + ", "); + stringBuilder.Append("ZmqTriggerConfig = " + _zmqTriggerConfig + ", "); stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); stringBuilder.Append("IsSatellite = " + _isSatellite); @@ -2294,268 +2425,6 @@ protected override bool PrintMembers(System.Text.StringBuilder stringBuilder) } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class ZmqConnection - { - - private string _protocol; - - private string _address; - - private int _port; - - private Action? _action; - - private string _connectionString; - - private string _topic; - - public ZmqConnection() - { - _protocol = "Tcp"; - _address = "localhost"; - _port = 5556; - _connectionString = ""; - _topic = ""; - } - - protected ZmqConnection(ZmqConnection other) - { - _protocol = other._protocol; - _address = other._address; - _port = other._port; - _action = other._action; - _connectionString = other._connectionString; - _topic = other._topic; - } - - /// - /// The protocol to use for the ZMQ connection. - /// - [Newtonsoft.Json.JsonPropertyAttribute("protocol")] - [System.ComponentModel.DescriptionAttribute("The protocol to use for the ZMQ connection.")] - public string Protocol - { - get - { - return _protocol; - } - set - { - _protocol = value; - } - } - - /// - /// The address of the ZMQ socket. - /// - [Newtonsoft.Json.JsonPropertyAttribute("address")] - [System.ComponentModel.DescriptionAttribute("The address of the ZMQ socket.")] - public string Address - { - get - { - return _address; - } - set - { - _address = value; - } - } - - /// - /// The port of the ZMQ socket. - /// - [Newtonsoft.Json.JsonPropertyAttribute("port")] - [System.ComponentModel.DescriptionAttribute("The port of the ZMQ socket.")] - public int Port - { - get - { - return _port; - } - set - { - _port = value; - } - } - - /// - /// Whether to bind or connect the socket. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("action")] - [System.ComponentModel.DescriptionAttribute("Whether to bind or connect the socket.")] - public Action? Action - { - get - { - return _action; - } - set - { - _action = value; - } - } - - /// - /// The connection string for the ZMQ socket. - /// - [Newtonsoft.Json.JsonPropertyAttribute("connection_string")] - [System.ComponentModel.DescriptionAttribute("The connection string for the ZMQ socket.")] - public string ConnectionString - { - get - { - return _connectionString; - } - set - { - _connectionString = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("topic")] - public string Topic - { - get - { - return _topic; - } - set - { - _topic = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqConnection(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new ZmqConnection(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("Protocol = " + _protocol + ", "); - stringBuilder.Append("Address = " + _address + ", "); - stringBuilder.Append("Port = " + _port + ", "); - stringBuilder.Append("Action = " + _action + ", "); - stringBuilder.Append("ConnectionString = " + _connectionString + ", "); - stringBuilder.Append("Topic = " + _topic); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class ZmqPubSub - { - - private ZmqConnection _pub; - - private ZmqConnection _sub; - - public ZmqPubSub() - { - _pub = new ZmqConnection(); - _sub = new ZmqConnection(); - } - - protected ZmqPubSub(ZmqPubSub other) - { - _pub = other._pub; - _sub = other._sub; - } - - /// - /// ZMQ Publisher - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("pub", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("ZMQ Publisher")] - public ZmqConnection Pub - { - get - { - return _pub; - } - set - { - _pub = value; - } - } - - /// - /// ZMQ Subscriber - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("sub", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("ZMQ Subscriber")] - public ZmqConnection Sub - { - get - { - return _sub; - } - set - { - _sub = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqPubSub(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new ZmqPubSub(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("Pub = " + _pub + ", "); - stringBuilder.Append("Sub = " + _sub); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] public enum SpinnakerCameraColorProcessing @@ -2569,19 +2438,6 @@ public enum SpinnakerCameraColorProcessing } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] - public enum Action - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="bind")] - Bind = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="connect")] - Connect = 1, - } - - [System.CodeDom.Compiler.GeneratedCode("NJsonSchema", "10.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [System.AttributeUsage(System.AttributeTargets.Class | System.AttributeTargets.Interface, AllowMultiple = true)] internal class JsonInheritanceAttribute : System.Attribute @@ -2803,6 +2659,11 @@ public System.IObservable Process(System.IObservable sourc return Process(source); } + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + public System.IObservable Process(System.IObservable source) { return Process(source); @@ -2832,16 +2693,6 @@ public System.IObservable Process(System.IObservable { return Process(source); } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } } @@ -2857,14 +2708,13 @@ public System.IObservable Process(System.IObservable source) [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder { diff --git a/src/Extensions/HarpDevices.bonsai b/src/Extensions/HarpDevices.bonsai index bd63533..36929c6 100644 --- a/src/Extensions/HarpDevices.bonsai +++ b/src/Extensions/HarpDevices.bonsai @@ -5,9 +5,8 @@ xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" xmlns:p1="clr-namespace:AindJustFramesSchemas;assembly=Extensions" xmlns:beh="clr-namespace:Harp.Behavior;assembly=Harp.Behavior" + xmlns:p2="clr-namespace:;assembly=Extensions" xmlns:zmq="clr-namespace:Bonsai.ZeroMQ;assembly=Bonsai.ZeroMQ" - xmlns:p2="clr-namespace:AindJustFramesSchemas.MessageProtocol;assembly=Extensions" - xmlns:p3="clr-namespace:;assembly=Extensions" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -95,19 +94,17 @@ MessageBytes - - HarpZmqTopic - - - - - - RigSchema - ZmqConnection.Pub.ConnectionString + ZmqTriggerConfig + + + + tcp + Bind + @@ -116,7 +113,7 @@ - tcp://localhost:5557 + @tcp://localhost:5557 @@ -131,12 +128,11 @@ - + - + - - + @@ -187,24 +183,22 @@ RigSchema - ZmqConnection.Sub.ConnectionString + ZmqTriggerConfig - - - - - - - HarpZmqTopic + + + tcp + Connect + - + - tcp://localhost:5557 + >tcp://localhost:5557 @@ -221,12 +215,11 @@ - + - + - @@ -318,271 +311,6 @@ - - RigSchema - - - NotSatellite - - - - Source1 - - - IsSatellite - - - - - - - - - - - - - - None - - - - MainZmqLogic - - - - Source1 - - - - 1 - - - - - - - RigSchema - - - RigSchema - - - SatelliteRigs - - - - - - - - - Source1 - - - satelliteRig - - - EnableExperiment - - - - - - satelliteRig - - - RigName - - - - - - - - - Request - - - - satelliteRig - - - ZmqConnection.Pub - - - ConnectionString - - - - - - - - MessageProtocolZmqTopic - - - - - - - - - tcp://localhost:5557 - - - - Last - - - - - - Payload - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - RigSchema - - - - - - Source1 - - - IsSatellite - - - - - - - - - - - - None - - - - SatelliteZmqLogic - - - - Source1 - - - - 1 - - - - - - - RigSchema - - - InboundMessages - - - Payload - - - - - - - 1 - - - - - EnableExperiment - - - InboundMessages - - - Payload - - - - - - - 1 - - - - - EndExperiment - - - - - - - - - - - - - - - - - - - - - - @@ -599,14 +327,6 @@ - - - - - - - - \ No newline at end of file diff --git a/src/Extensions/Main.bonsai b/src/Extensions/Main.bonsai index 4955b63..39bab7a 100644 --- a/src/Extensions/Main.bonsai +++ b/src/Extensions/Main.bonsai @@ -8,12 +8,9 @@ xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:p4="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" - xmlns:p5="clr-namespace:AindJustFramesSchemas.MessageProtocol;assembly=Extensions" - xmlns:p6="clr-namespace:;assembly=Extensions" - xmlns:zmq="clr-namespace:Bonsai.ZeroMQ;assembly=Bonsai.ZeroMQ" xmlns:sys="clr-namespace:System;assembly=mscorlib" - xmlns:p7="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" - xmlns:p8="clr-namespace:AindJustFramesSchemas;assembly=Extensions" + xmlns:p5="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" + xmlns:p6="clr-namespace:AindJustFramesSchemas;assembly=Extensions" xmlns:ui="clr-namespace:Bonsai.Design;assembly=Bonsai.Design" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -98,32 +95,6 @@ CompoundRootPath - - - message_protocol - - - - - 1 - - - - MessageProtocolZmqTopic - - - - harp - - - - - 1 - - - - HarpZmqTopic - false @@ -267,19 +238,15 @@ - - + - - + + + - - - - - + @@ -288,6 +255,7 @@ + HarpBehaviorEvents @@ -340,375 +308,19 @@ - - OutboundMessages - - - NetworkCommunication - - - - RigSchema - - - ZmqConnection - - - ZmqConnection - - - - PT0S - PT1S - - - - - - - RigSchema - - - RigName - - - - - - - - - Event - - - - OutboundMessages - - - Source1 - - - - None - - - - ZmqConnection - - - - - - - - MessageProtocolZmqTopic - - - - - - - - - tcp://localhost:5557 - message_protocol - - - - InboundMessages - - - IsRequest - - - - Source1 - - - MessageType - - - - Request - - - - - - - - - - - - - Payload - - - - - - - EnableExperiment - - - Response - - - - IsExperimentRunning - - - - - - Source1 - - - - - - - - - - - 1 - - - - - - - RigSchema - - - RigName - - - - - - - - - Reply - - - - - - - - - - - - - - - - - - OutboundMessages - - - - 1 - - - - InboundMessages - - - IsRequest - - - - Source1 - - - MessageType - - - - Request - - - - - - - - - - - - - Payload - - - - - - - EndExperiment - - - Response - - - - IsExperimentRunning - - - - - - - Source1 - - - - - - - - - - - - - RigSchema - - - RigName - - - - - - - - - Reply - - - - - - - - - - - - - - - - - - OutboundMessages - - - - 1 - - - - ZmqConnection - - - - - - - - MessageProtocolZmqTopic - - - - - - - - - tcp://localhost:5557 - message_protocol - - - - Last - - - - - - InboundMessages - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - InboundMessages - - - - - - - + + + + + - - - - - + + + + @@ -826,9 +438,9 @@ - - - + + + @@ -974,8 +586,8 @@ SubjectSchema - - None + + None @@ -1004,8 +616,8 @@ RigSchema - - None + + None diff --git a/src/Extensions/NetworkConfigToConnectionString.cs b/src/Extensions/NetworkConfigToConnectionString.cs new file mode 100644 index 0000000..8af6f2b --- /dev/null +++ b/src/Extensions/NetworkConfigToConnectionString.cs @@ -0,0 +1,63 @@ +using Bonsai; +using System; +using System.ComponentModel; +using System.Linq; +using System.Reactive.Linq; +using AindJustFramesSchemas; +using System.Collections.Generic; + +[Combinator] +[Description("Returns a formatted ZeroMQ connection string based on the provided NetworkConfig object.")] +[WorkflowElementCategory(ElementCategory.Transform)] +public class NetworkConfigToConnectionString +{ + private string protocol = "tcp"; + public string Protocol + { + get { return protocol; } + set { protocol = value; } + } + + private ActionType action = ActionType.Connect; + public ActionType Action + { + get { return action; } + set { action = value; } + } + + + public IObservable Process(IObservable source) + { + return source.Select(value => + { + string address = value.Address; + System.Net.IPAddress ip; + if (!(System.Net.IPAddress.TryParse(address, out ip) && ip.AddressFamily == System.Net.Sockets.AddressFamily.InterNetwork) + && !string.Equals(address, "localhost", StringComparison.OrdinalIgnoreCase)) + { + throw new FormatException(string.Format("Invalid address format: {0}. Must be IPv4 or 'localhost'.", address)); + } + + return string.Format("{0}{1}://{2}:{3}", + actionPrefixCharacter[Action], + Protocol, + address, + value.Port); + }); + } + + + public enum ActionType + { + Connect, + Bind, + None + } + + private readonly Dictionary actionPrefixCharacter = new Dictionary + { + { ActionType.Connect, ">" }, + { ActionType.Bind, "@" }, + { ActionType.None, "" } + }; +} diff --git a/src/Extensions/ZeroMQ.bonsai b/src/Extensions/ZeroMQ.bonsai new file mode 100644 index 0000000..f3a1ea1 --- /dev/null +++ b/src/Extensions/ZeroMQ.bonsai @@ -0,0 +1,715 @@ + + + + + + RigSchema + + + NotSatellite + + + + Source1 + + + IsSatellite + + + + + + + + + + + + + + None + + + + MainZmqLogic + + + + Source1 + + + + 1 + + + + + + + RigSchema + + + RigSchema + + + SatelliteRigs + + + + + + CreateRequestToSatalite + + + + Source1 + + + satelliteRig + + + EnableExperiment + + + + + + satelliteRig + + + RigName + + + + + + + + + Request + + + + + None + + + + satelliteRig + + + ZmqProtocolConfig + + + + tcp + Connect + + + + + + + + + + >tcp://localhost:5557 + + + + Last + + + + + + Payload + + + + + + + + + + + + + + + + + + + + + + + + + + + + RigSchema + + + ZmqProtocolConfig + + + + tcp + Bind + + + + + + + + + + @tcp://*:5557 + + + + + + + Source1 + + + + 1 + + + + Last + + + + + + Request + + + Request + + + Payload + + + + + + + 1 + + + + + EnableExperiment + + + MakeResponse + + + + IsExperimentRunning + + + + + + Source1 + + + + + + + + + + + 1 + + + + + + + RigSchema + + + RigName + + + + + + + + + Reply + + + + + + + + + + + + + + + + + + Request + + + Payload + + + + + + + 1 + + + + + EndExperiment + + + MakeResponse + + + + IsExperimentRunning + + + + + + + Source1 + + + + + + + + + + + + + RigSchema + + + RigName + + + + + + + + + Reply + + + + + + + + + + + + + + + + + + Out + + + + 1 + + + + + None + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + RigSchema + + + + + + Source1 + + + IsSatellite + + + + + + + + + + + + None + + + + SatelliteZmqLogic + + + + Source1 + + + + 1 + + + + + + + SatelliteRigSchema + + + SatelliteRigSchema + + + ZmqProtocolConfig + + + + tcp + Bind + + + + + + + + + + @tcp://localhost:5557 + + + + + + + Source1 + + + + 1 + + + + Last + + + + + + Request + + + Request + + + Payload + + + + + + + 1 + + + + + EnableExperiment + + + MakeResponse + + + + IsExperimentRunning + + + + + + Source1 + + + + + + + + + + + 1 + + + + + + + RigSchema + + + RigName + + + + + + + + + Reply + + + + + + + + + + + + + + + + + + Request + + + Payload + + + + + + + 1 + + + + + EndExperiment + + + MakeResponse + + + + IsExperimentRunning + + + + + + + Source1 + + + + + + + + + + + + + RigSchema + + + RigName + + + + + + + + + Reply + + + + + + + + + + + + + + + + + + Out + + + + 1 + + + + + None + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index 0cbb45c..877722d 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -3,17 +3,18 @@ import aind_behavior_services.rig as rig from aind_behavior_services.rig import AindBehaviorRigModel from pydantic import BaseModel, Field, field_validator, model_validator +from ipaddress import IPv4Address from . import __semver__ - -class ZmqPubSub(BaseModel): - pub: rig.network.ZmqConnection = Field(description="ZMQ Publisher") - sub: rig.network.ZmqConnection = Field(description="ZMQ Subscriber") +class NetworkConfig(BaseModel): + address: IPv4Address = Field(description="Address for ZMQ connection.") + port: int = Field(description="Port for ZMQ connection.", ge=1, le=65535) class SatelliteRig(AindBehaviorRigModel): version: Literal[__semver__] = __semver__ - zmq_connection: ZmqPubSub = Field(description="ZMQ connection for communication.") + zmq_protocol_config: NetworkConfig = Field(description="ZMQ connection for communication.") + zmq_trigger_config: NetworkConfig = Field(description="ZMQ connection for trigger communication.") triggered_camera_controller_0: Optional[rig.cameras.CameraController[rig.cameras.SpinnakerCamera]] = Field( default=None, description="Camera controller to triggered cameras. Will use Camera0 register as a trigger.", @@ -24,9 +25,9 @@ class SatelliteRig(AindBehaviorRigModel): ) is_satellite: bool = Field(default=True) - @field_validator("zmq_connection", mode="after") + @field_validator("zmq_protocol_config", mode="after") @classmethod - def validate_zmq_connection(cls, value: rig.network.ZmqConnection): + def validate_zmq_protocol_config(cls, value: rig.network.ZmqConnection): if isinstance(value, rig.network.ZmqConnection): value.topic = "" return value @@ -47,11 +48,14 @@ class AindJustFramesRig(AindBehaviorRigModel): ) satellite_rigs: list[SatelliteRig] = Field(default_factory=list, description="List of satellite rigs.") is_satellite: bool = Field(default=False) - zmq_connection: Optional[ZmqPubSub] = Field(default=None, description="ZMQ connection for communication.") + zmq_protocol_config: Optional[NetworkConfig] = Field(default=None, description="ZMQ connection for communication.") + zmq_trigger_config: Optional[NetworkConfig] = Field( + default=None, description="ZMQ connection for trigger communication." + ) @model_validator(mode="after") def verify_zmq_nullability(self): - if self.zmq_connection is None: + if self.zmq_protocol_config is None: if self.is_satellite: raise ValueError("Satellite rigs must define a ZMQ connection.") if len(self.satellite_rigs) > 0: From 61ddd3ba0f04b9953c5933d721fdedf798bc0028 Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 3 Dec 2025 15:56:15 -0800 Subject: [PATCH 31/32] Cleanup models --- .../aind_behavior_just_frames.json | 17 +++---- .../AindBehaviorJustFrames.Generated.cs | 1 + src/Extensions/HarpDevices.bonsai | 50 ++++++++++++------- src/aind_behavior_just_frames/rig.py | 20 +++++--- 4 files changed, 51 insertions(+), 37 deletions(-) diff --git a/src/DataSchemas/aind_behavior_just_frames.json b/src/DataSchemas/aind_behavior_just_frames.json index edfc7da..cbddcc1 100644 --- a/src/DataSchemas/aind_behavior_just_frames.json +++ b/src/DataSchemas/aind_behavior_just_frames.json @@ -177,16 +177,12 @@ "type": "boolean" }, "zmq_protocol_config": { - "default": null, - "description": "ZMQ connection for communication.", - "oneOf": [ - { - "$ref": "#/$defs/NetworkConfig" - }, - { - "type": "null" - } - ] + "$ref": "#/$defs/NetworkConfig", + "default": { + "address": "localhost", + "port": 5555 + }, + "description": "ZMQ connection for communication." }, "zmq_trigger_config": { "default": null, @@ -318,7 +314,6 @@ "properties": { "address": { "description": "Address for ZMQ connection.", - "format": "ipv4", "title": "Address", "type": "string" }, diff --git a/src/Extensions/AindBehaviorJustFrames.Generated.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs index 2c3aa93..cc90a7e 100644 --- a/src/Extensions/AindBehaviorJustFrames.Generated.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -321,6 +321,7 @@ public AindJustFramesRig() _harpBehavior = new HarpBehavior(); _satelliteRigs = new System.Collections.Generic.List(); _isSatellite = false; + _zmqProtocolConfig = new NetworkConfig(); } protected AindJustFramesRig(AindJustFramesRig other) diff --git a/src/Extensions/HarpDevices.bonsai b/src/Extensions/HarpDevices.bonsai index 36929c6..a8664a3 100644 --- a/src/Extensions/HarpDevices.bonsai +++ b/src/Extensions/HarpDevices.bonsai @@ -45,20 +45,6 @@ BehaviorBoard - - Source1 - - - - 1 - - - - - - - RigSchema - HarpBehaviorCommands @@ -88,6 +74,20 @@ internalPub + + Source1 + + + + 1 + + + + + + + RigSchema + internalPub @@ -116,15 +116,25 @@ @tcp://localhost:5557 + + RigSchema + + + ZmqTriggerConfig + + + + + - + - + + - - + @@ -133,6 +143,10 @@ + + + + diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index 877722d..0a28b5e 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -3,12 +3,11 @@ import aind_behavior_services.rig as rig from aind_behavior_services.rig import AindBehaviorRigModel from pydantic import BaseModel, Field, field_validator, model_validator -from ipaddress import IPv4Address from . import __semver__ class NetworkConfig(BaseModel): - address: IPv4Address = Field(description="Address for ZMQ connection.") + address: str = Field(description="Address for ZMQ connection.") port: int = Field(description="Port for ZMQ connection.", ge=1, le=65535) class SatelliteRig(AindBehaviorRigModel): @@ -48,23 +47,28 @@ class AindJustFramesRig(AindBehaviorRigModel): ) satellite_rigs: list[SatelliteRig] = Field(default_factory=list, description="List of satellite rigs.") is_satellite: bool = Field(default=False) - zmq_protocol_config: Optional[NetworkConfig] = Field(default=None, description="ZMQ connection for communication.") + zmq_protocol_config: NetworkConfig = Field(default=NetworkConfig(address="localhost", port=5555), description="ZMQ connection for communication.", validate_default=True) zmq_trigger_config: Optional[NetworkConfig] = Field( default=None, description="ZMQ connection for trigger communication." ) @model_validator(mode="after") def verify_zmq_nullability(self): - if self.zmq_protocol_config is None: - if self.is_satellite: - raise ValueError("Satellite rigs must define a ZMQ connection.") - if len(self.satellite_rigs) > 0: - raise ValueError("Master rigs with satellite rigs must define a ZMQ connection.") + if len(self.satellite_rigs) > 0: + if self.zmq_trigger_config is None: + raise ValueError("zmq_trigger_config cannot be None when satellite_rigs are defined.") + for _r in self.satellite_rigs: + _r.zmq_trigger_config = self.zmq_trigger_config return self @model_validator(mode="after") def verify_satellite_rigs(self): + seen = set() for _r in self.satellite_rigs: if not _r.is_satellite: raise ValueError("All rigs in satellite_rigs must have is_satellite=True.") + addr_port = (_r.zmq_protocol_config.address, _r.zmq_protocol_config.port) + if addr_port in seen: + raise ValueError(f"Duplicate address:port found in satellite_rigs: {addr_port}") + seen.add(addr_port) return self From 05693e102f0db062fe991f55c141811e7f06287b Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Wed, 3 Dec 2025 15:57:18 -0800 Subject: [PATCH 32/32] Linting --- src/aind_behavior_just_frames/rig.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index 0a28b5e..1dea51b 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -6,10 +6,12 @@ from . import __semver__ + class NetworkConfig(BaseModel): address: str = Field(description="Address for ZMQ connection.") port: int = Field(description="Port for ZMQ connection.", ge=1, le=65535) + class SatelliteRig(AindBehaviorRigModel): version: Literal[__semver__] = __semver__ zmq_protocol_config: NetworkConfig = Field(description="ZMQ connection for communication.") @@ -47,7 +49,11 @@ class AindJustFramesRig(AindBehaviorRigModel): ) satellite_rigs: list[SatelliteRig] = Field(default_factory=list, description="List of satellite rigs.") is_satellite: bool = Field(default=False) - zmq_protocol_config: NetworkConfig = Field(default=NetworkConfig(address="localhost", port=5555), description="ZMQ connection for communication.", validate_default=True) + zmq_protocol_config: NetworkConfig = Field( + default=NetworkConfig(address="localhost", port=5555), + description="ZMQ connection for communication.", + validate_default=True, + ) zmq_trigger_config: Optional[NetworkConfig] = Field( default=None, description="ZMQ connection for trigger communication." )