diff --git a/README.md b/README.md index 047bd7c..efb9166 100644 --- a/README.md +++ b/README.md @@ -4,4 +4,24 @@ 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 +![ZeroMQ Architecture](assets/zmq_architecture.svg) + +## Notes on workflow startup + +Button -> EnableExperiment +EnableExperiment(unit) -> StartLogging(unit) -> StartExperiment (unit) + -> StartLogging -> IsExperimentRunning(bool) + +In main: +zmqRequest (master) -> EnableExperiment + +In satellite: +zmqRequest (satellite) -> EnableExperiment + +## Refactored + +In master: + +Button | zmqRequest -> TryStart ( _ = >{ +zmqRequest (satellite) -> EnableExperiment(satellite) -> HasStarted .zip(). timeout} +) -> EnableExperiment -> StartLogging -> StartExperiment -> Trigger \ No newline at end of file diff --git a/docs/api.session.rst b/docs/api.session.rst index 88b54f5..5181118 100644 --- a/docs/api.session.rst +++ b/docs/api.session.rst @@ -1,7 +1,7 @@ api.session ------------- -.. autopydantic_model:: aind_behavior_services.session.AindBehaviorSessionModel +.. autopydantic_model:: aind_behavior_services.session.Session :members: :undoc-members: :show-inheritance: diff --git a/examples/clabe.yml b/examples/clabe.yml index 8a73949..400fb23 100644 --- a/examples/clabe.yml +++ b/examples/clabe.yml @@ -5,4 +5,7 @@ default_behavior_picker: config_library_dir: '\\allen\aind\scratch\AindBehavior.db\AindBehaviorJustFrames' robocopy: - destination: '\\allen\aind\scratch\data' \ No newline at end of file + destination: '\\allen\aind\scratch\data' + +xml_rpc_client: + token: '42' \ No newline at end of file diff --git a/examples/examples.py b/examples/examples.py index b2d5124..d0e7ba4 100644 --- a/examples/examples.py +++ b/examples/examples.py @@ -2,14 +2,14 @@ import os from pathlib import Path -import aind_behavior_services.rig as rig -from aind_behavior_services.session import AindBehaviorSessionModel +from aind_behavior_services.rig import cameras, harp +from aind_behavior_services.session import Session from aind_behavior_just_frames.rig import AindJustFramesRig def main(path_seed: str = "./local/{schema}.json"): - this_session = AindBehaviorSessionModel( + this_session = Session( date=datetime.datetime.now(tz=datetime.timezone.utc), experiment="AindVideoEncodingBenchmarks", subject="Test", @@ -19,7 +19,7 @@ def main(path_seed: str = "./local/{schema}.json"): experimenter=["Foo", "Bar"], ) - video_writer = rig.cameras.VideoWriterFfmpeg( + video_writer = cameras.VideoWriterFfmpeg( frame_rate=120, container_extension="mp4", # input and output arguments can be overridden by the user @@ -27,30 +27,31 @@ def main(path_seed: str = "./local/{schema}.json"): this_rig = AindJustFramesRig( data_directory=Path("C:/Data"), + computer_name="this_computer", rig_name="this_rig", - triggered_camera_controller_0=rig.cameras.CameraController[rig.cameras.SpinnakerCamera]( + triggered_camera_controller_0=cameras.CameraController[cameras.SpinnakerCamera]( frame_rate=120, cameras={ - "FaceCamera": rig.cameras.SpinnakerCamera( + "FaceCamera": cameras.SpinnakerCamera( serial_number="SerialNumber", binning=1, exposure=5000, gain=0, video_writer=video_writer, - adc_bit_depth=rig.cameras.SpinnakerCameraAdcBitDepth.ADC10BIT, + adc_bit_depth=cameras.SpinnakerCameraAdcBitDepth.ADC10BIT, ), - "SideCamera": rig.cameras.SpinnakerCamera( + "SideCamera": cameras.SpinnakerCamera( serial_number="SerialNumber", binning=1, exposure=5000, gain=0, video_writer=video_writer, - adc_bit_depth=rig.cameras.SpinnakerCameraAdcBitDepth.ADC10BIT, + adc_bit_depth=cameras.SpinnakerCameraAdcBitDepth.ADC10BIT, ), }, ), triggered_camera_controller_1=None, - harp_behavior=rig.harp.HarpBehavior(port_name="COM3"), + harp_behavior=harp.HarpBehavior(port_name="COM3"), ) os.makedirs(os.path.dirname(path_seed), exist_ok=True) diff --git a/examples/experiment.py b/examples/experiment.py new file mode 100644 index 0000000..91ac3ef --- /dev/null +++ b/examples/experiment.py @@ -0,0 +1,131 @@ +import asyncio +import dataclasses +import logging +from pathlib import Path + +import clabe.xml_rpc +from aind_behavior_services.session import Session +from clabe import resource_monitor +from clabe.apps import AindBehaviorServicesBonsaiApp, BonsaiApp +from clabe.data_transfer import robocopy +from clabe.launcher import Launcher, experiment +from clabe.pickers import DefaultBehaviorPicker, DefaultBehaviorPickerSettings + +from aind_behavior_just_frames.rig import AindJustFramesRig, SatelliteRig + +logger = logging.getLogger(__name__) + + +@experiment(name="just_frames_with_satellites") +async def my_experiment(launcher: Launcher) -> None: + picker = DefaultBehaviorPicker(launcher=launcher, settings=DefaultBehaviorPickerSettings()) + session = picker.pick_session(Session) + rig = picker.pick_rig(AindJustFramesRig) + launcher.register_session(session, rig.data_directory) + + monitor = resource_monitor.ResourceMonitor( + constrains=[ + resource_monitor.available_storage_constraint_factory(launcher.data_directory, 2e11), + ] + ) + + # Validate resources + monitor.run() + has_satellites = len(rig.satellite_rigs) > 0 + satellites: dict[str, SatelliteRigConnection] = {} + if has_satellites: + SATELLITE_UPLOAD_ROOT = "." + for s in rig.satellite_rigs: + xml_client = clabe.xml_rpc.XmlRpcClient( + settings=clabe.xml_rpc.XmlRpcClientSettings( + token="just-frames", server_url=f"{s.zmq_protocol_config.address}:8000" + ) + ) + this_session = xml_client.upload_model( + session, SATELLITE_UPLOAD_ROOT / f"{session.session_name}_session.json" + ) + this_rig = xml_client.upload_model(s, SATELLITE_UPLOAD_ROOT / f"{session.session_name}_rig.json") + + assert this_session.filename is not None, "Failed to upload session to satellite rig." + assert this_rig.filename is not None, "Failed to upload rig to satellite rig." + additional_externalized_properties = { + "RigPath": this_rig.filename, + "SessionPath": this_session.filename, + } + satellite_bonsai_app = BonsaiApp( + workflow=Path(r"./src/main.bonsai"), + additional_externalized_properties=additional_externalized_properties, + ) + satellites[s.rig_name] = SatelliteRigConnection( + rig=s, + xml_rpc_client=xml_client, + bonsai_app=satellite_bonsai_app, + xml_rpc_executor=clabe.xml_rpc.XmlRpcExecutor(client=xml_client), + ) + + bonsai_app = AindBehaviorServicesBonsaiApp( + workflow=Path(r"./src/main.bonsai"), + rig=rig, + session=session, + ) + + tasks = { + satellite.rig.rig_name: satellite.xml_rpc_executor.run_async(satellite.bonsai_app.command) + for satellite in satellites.values() + } + tasks[rig.rig_name] = bonsai_app.run_async() + results = await asyncio.gather(*tasks.values()) + + for rig_id, result in dict(zip(tasks.keys(), results)).items(): + if result.exit_code != 0: + logger.error( + "RigId %s 's, App exited with error code %d. With stdout %s and stderr %s", + rig_id, + result.exit_code, + result.stdout, + result.stderr, + ) + else: + logger.info("RigId %s 's, App completed successfully with stdout %s", rig_id, result.stdout) + logger.debug("RigId %s 's, App completed successfully with stderr %s", rig_id, result.stderr) + + launcher.copy_logs() + + settings = robocopy.RobocopySettings() + assert launcher.session.session_name is not None, "Session name is None" + settings.destination = Path(settings.destination) / launcher.session.subject / launcher.session.session_name + robocopy_tasks = { + satellite.rig.rig_name: satellite.xml_rpc_executor.run_async( + _make_robocopy_from_rig(settings, satellite.rig, launcher.session.session_name).command + ) + for satellite in satellites.values() + } + robocopy_tasks[rig.rig_name] = robocopy.RobocopyService( + source=rig.data_directory / launcher.session.session_name, settings=settings + ).run_async() + await asyncio.gather(*robocopy_tasks.values()) + return + + +@dataclasses.dataclass +class SatelliteRigConnection: + rig: SatelliteRig + xml_rpc_client: clabe.xml_rpc.XmlRpcClient + xml_rpc_executor: clabe.xml_rpc.XmlRpcExecutor + bonsai_app: BonsaiApp + + +def _make_robocopy_from_rig( + robocopy_settings: robocopy.RobocopySettings, rig: AindJustFramesRig | SatelliteRig, session_name: str +) -> robocopy.RobocopyService: + # For videos, we flatten everything in the behavior-videos directory + # Everything else gets dumped in the behavior directory under .satellites/rig_name/ + source = { + rig.data_directory / session_name / "behavior-videos": Path(robocopy_settings.destination) / "behavior-videos", + rig.data_directory / session_name / "behavior": Path(robocopy_settings.destination) + / "behavior" + / "satellites" + / rig.rig_name, + } + settings = robocopy_settings.model_copy(update={"destination": None}) # we will set destination per-path + return robocopy.RobocopyService(source=source, settings=settings) diff --git a/pyproject.toml b/pyproject.toml index 541404c..9d6a050 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,16 +16,18 @@ version = "0.5.0rc2" readme = {file = "README.md", content-type = "text/markdown"} dependencies = [ - "aind_behavior_services @git+https://github.com/AllenNeuralDynamics/Aind.Behavior.Services@90c77e682922288bc7779c4f8cde5d6f15115899", + "aind_behavior_services>=0.13", "pydantic-settings" ] [project.optional-dependencies] -data = ["contraqctor >= 0.5.3 ,<0.6.0"] +data = ["contraqctor >=0.5.3, <0.6.0"] + launcher = [ - "aind-clabe[aind-services] @ git+https://github.com/AllenNeuralDynamics/clabe@test-services-13", - "aind_behavior_just_frames[data]",] + "aind-clabe[aind-services]>=0.10.0", + "aind_behavior_just_frames[data]" + ] [dependency-groups] diff --git a/src/DataSchemas/aind_behavior_just_frames.json b/src/DataSchemas/aind_behavior_just_frames.json index fccfe62..d2526f3 100644 --- a/src/DataSchemas/aind_behavior_just_frames.json +++ b/src/DataSchemas/aind_behavior_just_frames.json @@ -1,114 +1,9 @@ { "$defs": { - "AindBehaviorSessionModel": { - "properties": { - "aind_behavior_services_pkg_version": { - "default": "0.13.0-rc0", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "version": { - "const": "0.13.0-rc0", - "default": "0.13.0-rc0", - "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" - }, - "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" - }, - "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": [ - "subject" - ], - "title": "AindBehaviorSessionModel", - "type": "object" - }, "AindJustFramesRig": { "properties": { "aind_behavior_services_pkg_version": { - "default": "0.13.0-rc0", + "default": "0.13.0", "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-]+)*))?$", "title": "aind_behavior_services package version", "type": "string" @@ -198,6 +93,7 @@ } }, "required": [ + "computer_name", "rig_name", "data_directory", "harp_behavior" @@ -370,7 +266,7 @@ "SatelliteRig": { "properties": { "aind_behavior_services_pkg_version": { - "default": "0.13.0-rc0", + "default": "0.13.0", "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", "title": "aind_behavior_services package version", "type": "string" @@ -436,6 +332,7 @@ } }, "required": [ + "computer_name", "rig_name", "data_directory", "zmq_protocol_config", @@ -444,6 +341,111 @@ "title": "SatelliteRig", "type": "object" }, + "Session": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.13.0", + "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": "0.13.0", + "default": "0.13.0", + "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" + }, + "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" + }, + "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": [ + "subject" + ], + "title": "Session", + "type": "object" + }, "SpinnakerCamera": { "description": "Spinnaker camera device configuration.", "properties": { diff --git a/src/Extensions/AindBehaviorJustFrames.Generated.cs b/src/Extensions/AindBehaviorJustFrames.Generated.cs index d20eadb..08681d8 100644 --- a/src/Extensions/AindBehaviorJustFrames.Generated.cs +++ b/src/Extensions/AindBehaviorJustFrames.Generated.cs @@ -9,281 +9,6 @@ namespace AindJustFramesSchemas { #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 _sessionName; - - private string _subject; - - private string _notes; - - private string _commitHash; - - private bool _allowDirtyRepo; - - private bool _skipHardwareValidation; - - public AindBehaviorSessionModel() - { - _aindBehaviorServicesPkgVersion = "0.13.0-rc0"; - _version = "0.13.0-rc0"; - _experimenter = new System.Collections.Generic.List(); - _allowDirtyRepo = false; - _skipHardwareValidation = false; - } - - protected AindBehaviorSessionModel(AindBehaviorSessionModel other) - { - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _version = other._version; - _experiment = other._experiment; - _experimenter = other._experimenter; - _date = other._date; - _sessionName = other._sessionName; - _subject = other._subject; - _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; - } - } - - /// - /// 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; - } - } - - /// - /// 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("SessionName = " + _sessionName + ", "); - stringBuilder.Append("Subject = " + _subject + ", "); - 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")] @@ -316,7 +41,7 @@ public partial class AindJustFramesRig public AindJustFramesRig() { - _aindBehaviorServicesPkgVersion = "0.13.0-rc0"; + _aindBehaviorServicesPkgVersion = "0.13.0"; _version = "0.5.0-rc2"; _harpBehavior = new HarpBehavior(); _satelliteRigs = new System.Collections.Generic.List(); @@ -369,7 +94,7 @@ public string Version /// /// Computer name /// - [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] + [Newtonsoft.Json.JsonPropertyAttribute("computer_name", Required=Newtonsoft.Json.Required.Always)] [System.ComponentModel.DescriptionAttribute("Computer name")] public string ComputerName { @@ -1027,81 +752,332 @@ public int X { get { - return _x; + 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 SatelliteRig + { + + private string _aindBehaviorServicesPkgVersion; + + private string _version; + + private string _computerName; + + private string _rigName; + + private string _dataDirectory; + + private NetworkConfig _zmqProtocolConfig; + + private NetworkConfig _zmqTriggerConfig; + + private CameraControllerSpinnakerCamera _triggeredCameraController0; + + private CameraControllerSpinnakerCamera _triggeredCameraController1; + + private bool _isSatellite; + + public SatelliteRig() + { + _aindBehaviorServicesPkgVersion = "0.13.0"; + _version = "0.5.0-rc2"; + _zmqProtocolConfig = new NetworkConfig(); + _zmqTriggerConfig = new NetworkConfig(); + _isSatellite = true; + } + + protected SatelliteRig(SatelliteRig other) + { + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _computerName = other._computerName; + _rigName = other._rigName; + _dataDirectory = other._dataDirectory; + _zmqProtocolConfig = other._zmqProtocolConfig; + _zmqTriggerConfig = other._zmqTriggerConfig; + _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; + } + } + + /// + /// Computer name + /// + [Newtonsoft.Json.JsonPropertyAttribute("computer_name", Required=Newtonsoft.Json.Required.Always)] + [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; + } + } + + /// + /// 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. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("zmq_protocol_config", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] + public NetworkConfig ZmqProtocolConfig + { + get + { + return _zmqProtocolConfig; + } + set + { + _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 { - _x = value; + _zmqTriggerConfig = value; } } /// - /// Y coordinate of the top-left corner + /// Camera controller to triggered cameras. Will use Camera0 register as a trigger. /// - [Newtonsoft.Json.JsonPropertyAttribute("y")] - [System.ComponentModel.DescriptionAttribute("Y coordinate of the top-left corner")] - public int Y + [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 _y; + return _triggeredCameraController0; } set { - _y = value; + _triggeredCameraController0 = value; } } /// - /// Width of the rectangle + /// Camera controller to triggered cameras. Will use Camera1 register as a trigger. /// - [Newtonsoft.Json.JsonPropertyAttribute("width")] - [System.ComponentModel.DescriptionAttribute("Width of the rectangle")] - public int Width + [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 _width; + return _triggeredCameraController1; } set { - _width = value; + _triggeredCameraController1 = value; } } - /// - /// Height of the rectangle - /// - [Newtonsoft.Json.JsonPropertyAttribute("height")] - [System.ComponentModel.DescriptionAttribute("Height of the rectangle")] - public int Height + [Newtonsoft.Json.JsonPropertyAttribute("is_satellite")] + public bool IsSatellite { get { - return _height; + return _isSatellite; } set { - _height = value; + _isSatellite = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Rect(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteRig(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new Rect(this)); + 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("DataDirectory = " + _dataDirectory + ", "); + stringBuilder.Append("ZmqProtocolConfig = " + _zmqProtocolConfig + ", "); + stringBuilder.Append("ZmqTriggerConfig = " + _zmqTriggerConfig + ", "); + stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); + stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); + stringBuilder.Append("IsSatellite = " + _isSatellite); return true; } @@ -1123,50 +1099,53 @@ 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 SatelliteRig + public partial class Session { private string _aindBehaviorServicesPkgVersion; private string _version; - private string _computerName; + private string _experiment; - private string _rigName; + private System.Collections.Generic.List _experimenter; - private string _dataDirectory; + private System.DateTimeOffset _date; - private NetworkConfig _zmqProtocolConfig; + private string _sessionName; - private NetworkConfig _zmqTriggerConfig; + private string _subject; - private CameraControllerSpinnakerCamera _triggeredCameraController0; + private string _notes; - private CameraControllerSpinnakerCamera _triggeredCameraController1; + private string _commitHash; - private bool _isSatellite; + private bool _allowDirtyRepo; - public SatelliteRig() + private bool _skipHardwareValidation; + + public Session() { - _aindBehaviorServicesPkgVersion = "0.13.0-rc0"; - _version = "0.5.0-rc2"; - _zmqProtocolConfig = new NetworkConfig(); - _zmqTriggerConfig = new NetworkConfig(); - _isSatellite = true; + _aindBehaviorServicesPkgVersion = "0.13.0"; + _version = "0.13.0"; + _experimenter = new System.Collections.Generic.List(); + _allowDirtyRepo = false; + _skipHardwareValidation = false; } - protected SatelliteRig(SatelliteRig other) + protected Session(Session other) { _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; _version = other._version; - _computerName = other._computerName; - _rigName = other._rigName; - _dataDirectory = other._dataDirectory; - _zmqProtocolConfig = other._zmqProtocolConfig; - _zmqTriggerConfig = other._zmqTriggerConfig; - _triggeredCameraController0 = other._triggeredCameraController0; - _triggeredCameraController1 = other._triggeredCameraController1; - _isSatellite = other._isSatellite; + _experiment = other._experiment; + _experimenter = other._experimenter; + _date = other._date; + _sessionName = other._sessionName; + _subject = other._subject; + _notes = other._notes; + _commitHash = other._commitHash; + _allowDirtyRepo = other._allowDirtyRepo; + _skipHardwareValidation = other._skipHardwareValidation; } [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] @@ -1196,163 +1175,184 @@ public string Version } /// - /// Computer name + /// Name of the experiment /// - [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] - [System.ComponentModel.DescriptionAttribute("Computer name")] - public string ComputerName + [Newtonsoft.Json.JsonPropertyAttribute("experiment")] + [System.ComponentModel.DescriptionAttribute("Name of the experiment")] + public string Experiment { get { - return _computerName; + return _experiment; } set { - _computerName = value; + _experiment = value; } } /// - /// Rig name + /// Name of the experimenter /// - [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Rig name")] - public string RigName + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] + [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] + public System.Collections.Generic.List Experimenter { get { - return _rigName; + return _experimenter; } set { - _rigName = value; + _experimenter = value; } } /// - /// Directory where data will be saved to + /// Date of the experiment /// - [Newtonsoft.Json.JsonPropertyAttribute("data_directory", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Directory where data will be saved to")] - public string DataDirectory + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("date")] + [System.ComponentModel.DescriptionAttribute("Date of the experiment")] + public System.DateTimeOffset Date { get { - return _dataDirectory; + return _date; } set { - _dataDirectory = value; + _date = value; } } /// - /// ZMQ connection for communication. + /// 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. /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("zmq_protocol_config", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("ZMQ connection for communication.")] - public NetworkConfig ZmqProtocolConfig + [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 _zmqProtocolConfig; + return _sessionName; } set { - _zmqProtocolConfig = value; + _sessionName = value; } } /// - /// ZMQ connection for trigger communication. + /// Name of the subject /// - [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 + [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Name of the subject")] + public string Subject { get { - return _zmqTriggerConfig; + return _subject; } set { - _zmqTriggerConfig = value; + _subject = value; } } /// - /// Camera controller to triggered cameras. Will use Camera0 register as a trigger. + /// Notes about the experiment /// - [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 + [Newtonsoft.Json.JsonPropertyAttribute("notes")] + [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] + public string Notes { get { - return _triggeredCameraController0; + return _notes; } set { - _triggeredCameraController0 = value; + _notes = value; } } /// - /// Camera controller to triggered cameras. Will use Camera1 register as a trigger. + /// Commit hash of the repository /// - [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 + [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")] + [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")] + public string CommitHash { get { - return _triggeredCameraController1; + return _commitHash; } set { - _triggeredCameraController1 = value; + _commitHash = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("is_satellite")] - public bool IsSatellite + /// + /// 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 _isSatellite; + return _allowDirtyRepo; } set { - _isSatellite = value; + _allowDirtyRepo = value; } } - public System.IObservable Generate() + /// + /// Skip hardware validation + /// + [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")] + [System.ComponentModel.DescriptionAttribute("Skip hardware validation")] + public bool SkipHardwareValidation { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SatelliteRig(this))); + get + { + return _skipHardwareValidation; + } + set + { + _skipHardwareValidation = value; + } } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Select(source, _ => new SatelliteRig(this)); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Session(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new Session(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("DataDirectory = " + _dataDirectory + ", "); - stringBuilder.Append("ZmqProtocolConfig = " + _zmqProtocolConfig + ", "); - stringBuilder.Append("ZmqTriggerConfig = " + _zmqTriggerConfig + ", "); - stringBuilder.Append("TriggeredCameraController0 = " + _triggeredCameraController0 + ", "); - stringBuilder.Append("TriggeredCameraController1 = " + _triggeredCameraController1 + ", "); - stringBuilder.Append("IsSatellite = " + _isSatellite); + stringBuilder.Append("Experiment = " + _experiment + ", "); + stringBuilder.Append("Experimenter = " + _experimenter + ", "); + stringBuilder.Append("Date = " + _date + ", "); + stringBuilder.Append("SessionName = " + _sessionName + ", "); + stringBuilder.Append("Subject = " + _subject + ", "); + stringBuilder.Append("Notes = " + _notes + ", "); + stringBuilder.Append("CommitHash = " + _commitHash + ", "); + stringBuilder.Append("AllowDirtyRepo = " + _allowDirtyRepo + ", "); + stringBuilder.Append("SkipHardwareValidation = " + _skipHardwareValidation); return true; } @@ -2635,11 +2635,6 @@ 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); @@ -2675,6 +2670,11 @@ 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); @@ -2704,7 +2704,6 @@ public System.IObservable Process(System.IObservable [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))] @@ -2712,6 +2711,7 @@ 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))] @@ -2721,7 +2721,7 @@ public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpr public DeserializeFromJson() { - Type = new Bonsai.Expressions.TypeMapping(); + Type = new Bonsai.Expressions.TypeMapping(); } public Bonsai.Expressions.TypeMapping Type { get; set; } diff --git a/src/Extensions/Main.bonsai b/src/Extensions/Main.bonsai index d6a5c2d..34f5d6d 100644 --- a/src/Extensions/Main.bonsai +++ b/src/Extensions/Main.bonsai @@ -111,58 +111,42 @@ SoftwareEvent - - EndExperiment - false - - IsExperimentRunning - - - EnableExperiment - - - StartLogging - - - true + + 1 - - IsExperimentRunning + + IsAllSatellitesStarted - - StartLogging + + IsAllControllersInitialized - - StartLogging + + IsExperimentRunning - - - PT1S - + + IsHardwareReady - - StartExperiment + + EndExperiment false - - - 1 - - - + IsExperimentRunning + + StartLogging + IsRepoClean @@ -240,13 +224,11 @@ + - - - - - + + @@ -278,6 +260,11 @@ Index + + + 1 + + RigSchema @@ -288,8 +275,8 @@ - - + + IsAllControllersInitialized @@ -300,6 +287,7 @@ 1 + @@ -319,27 +307,60 @@ - StartExperiment + EnableExperiment + + RigSchema + + + IsSatellite + + + IsAllSatellitesStarted + + + + + + + IsAllControllersInitialized + + + + + + + IsHardwareReady + - - - - + + + + - + - - + + + + + + + + + + + + @@ -889,6 +910,61 @@ + + EnableExperiment + + + + PT0.5S + + + + CheckIfReady + + + + IsHardwareReady + + + + + + + + + + + + + Source1 + + + + + + + + + + + StartLogging + + + + true + + + + IsExperimentRunning + + + + PT1S + + + + StartExperiment + EndExperiment @@ -942,6 +1018,15 @@ + + + + + + + + + diff --git a/src/Extensions/VerifyBroadcastResponse.cs b/src/Extensions/VerifyBroadcastResponse.cs new file mode 100644 index 0000000..396d8fd --- /dev/null +++ b/src/Extensions/VerifyBroadcastResponse.cs @@ -0,0 +1,50 @@ +using Bonsai; +using System; +using System.ComponentModel; +using System.Collections.Generic; +using System.Linq; +using System.Reactive.Linq; +using AindJustFramesSchemas.MessageProtocol; + +[Combinator] +[Description("Ensures that all responses correspond to the payload type specified in the original broadcast request.")] +[WorkflowElementCategory(ElementCategory.Transform)] +public class VerifyBroadcastResponse +{ + private bool throwOnMismatch = true; + public bool ThrowOnMismatch + { + get { return throwOnMismatch; } + set { throwOnMismatch = value; } + } + + public IObservable Process(IObservable, RegisteredPayload>> source) + { + return Process(source.Select(tuple => Tuple.Create(tuple.Item2, tuple.Item1))); + } + + public IObservable Process(IObservable>> source) + { + return source.Select(value => + { + var request = value.Item1; + var responses = value.Item2; + var expectedPayloadType = request.GetType().Name; + foreach(var response in responses) + { + var responsePayloadType = response.Payload.GetType().Name; + if (responsePayloadType != expectedPayloadType) + { + if (ThrowOnMismatch){ + throw new InvalidOperationException(string.Format("Response payload type '{0}' does not match the expected payload type '{1}'. Response={2}", responsePayloadType, expectedPayloadType, response)); + } + else + { + return false; + } + } + } + return true; + }); + } +} diff --git a/src/Extensions/Visualizers.bonsai b/src/Extensions/Visualizers.bonsai index b495d04..8774626 100644 --- a/src/Extensions/Visualizers.bonsai +++ b/src/Extensions/Visualizers.bonsai @@ -3,7 +3,6 @@ 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"> @@ -100,22 +99,79 @@ + + IsExperimentRunning + + + + + + + + ExperimentRunning + false + true + ExperimentRunning + false + + IsAllControllersInitialized - - it ? "Cameras ready" : "Initializing cameras..." + + + + + + + IsAllControllersInitialized + false + true + IsAllControllersInitialized + false + + + + IsAllSatellitesStarted - + - - EndButton + + IsAllSatellitesStarted + false + true + IsAllSatellitesStarted + false + + + + IsHardwareReady + + + + + + + + IsHardwareReady false true - CameraStatus + IsHardwareReady + false + + + + Status + true + true + 1 + 4 + + + @@ -135,18 +191,31 @@ - + - + - - + + + + + + + + + + + + + + + diff --git a/src/Extensions/ZeroMQ.bonsai b/src/Extensions/ZeroMQ.bonsai index f3a1ea1..12409bd 100644 --- a/src/Extensions/ZeroMQ.bonsai +++ b/src/Extensions/ZeroMQ.bonsai @@ -56,106 +56,268 @@ RigSchema - RigSchema - - - SatelliteRigs + EnableExperiment - + - - CreateRequestToSatalite + + + GetResponse + + BroadcastResponses + Source1 - - satelliteRig - - - EnableExperiment + + BroadcastRequest - + + + Item1 + + + + + + + + + + + + + + + true + + + + + + + Source1 + + + + + + + + + + + 1 + + + + IsAllSatellitesStarted + + + EndExperiment + + + + + + + GetResponse + + - satelliteRig + BroadcastResponses - - RigName + + Source1 - - - - + + BroadcastRequest - - Request - + + + + Item1 + + + + + + + + + + + + + + BroadcastRequest + + + + BroadcastRequestToAll + + + + Source1 - - None + + 1 + + RequestPayload + - satelliteRig + RigSchema - ZmqProtocolConfig + SatelliteRigs - - tcp - Connect - + - - - - + + CreateRequestToSatellite + + + + Source1 + + + satelliteRig + + + RequestPayload + + + satelliteRig + + + RigName + + + + + + + + + Request + + + + + None + + + + satelliteRig + + + ZmqProtocolConfig + + + + tcp + Connect + + + + + + + + + + >tcp://localhost:5557 + + + + Last + + + + + + + + + + + + + + + + + + + + + + + + + + + + + RequestPayload + + + - - >tcp://localhost:5557 + + true + + + - Last + Item1 - + + 1 + - - Payload + + + PT2S + - - + + - - - + + + - + + - + - - - - + + BroadcastResponses RigSchema @@ -175,8 +337,8 @@ - - @tcp://*:5557 + + tcp://localhost:5557 @@ -206,7 +368,7 @@ Payload - + @@ -215,7 +377,7 @@ - EnableExperiment + EndExperiment MakeResponse @@ -224,6 +386,7 @@ IsExperimentRunning + @@ -238,12 +401,7 @@ - - 1 - - - - + RigSchema @@ -275,6 +433,9 @@ + + Out + Request @@ -282,7 +443,7 @@ Payload - + @@ -291,7 +452,7 @@ - EndExperiment + EnableExperiment MakeResponse @@ -300,7 +461,6 @@ IsExperimentRunning - @@ -315,7 +475,12 @@ - + + 1 + + + + RigSchema @@ -347,6 +512,9 @@ + + Out + Out @@ -360,9 +528,6 @@ None - - - @@ -376,16 +541,17 @@ - + + - + @@ -398,11 +564,20 @@ + - + + + + + + + + + @@ -470,8 +645,8 @@ - - @tcp://localhost:5557 + + tcp://localhost:5557 @@ -570,6 +745,9 @@ + + Out + Request @@ -642,6 +820,9 @@ + + Out + Out @@ -655,9 +836,6 @@ None - - - @@ -671,16 +849,17 @@ - + + - + diff --git a/src/aind_behavior_just_frames/cli.py b/src/aind_behavior_just_frames/cli.py index b95f4cb..d994aaf 100644 --- a/src/aind_behavior_just_frames/cli.py +++ b/src/aind_behavior_just_frames/cli.py @@ -5,7 +5,6 @@ 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 class VersionCli(RootModel): @@ -30,9 +29,6 @@ class JustFramesCli(BaseSettings, cli_prog_name="just-frames", cli_kebab_case=Tr regenerate: CliSubCommand[DslRegenerateCli] = Field( description="Regenerate the just-frames dsl dependencies.", ) - clabe: CliSubCommand[ClabeCli] = Field( - description="Run the Clabe CLI.", - ) def cli_cmd(self): return CliApp().run_subcommand(self) 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 index a556bf5..d74aca7 100644 --- a/src/aind_behavior_just_frames/data_contract/v0_5_0.py +++ b/src/aind_behavior_just_frames/data_contract/v0_5_0.py @@ -1,6 +1,6 @@ from pathlib import Path -from aind_behavior_services.session import AindBehaviorSessionModel +from aind_behavior_services.session import Session from contraqctor.contract import Dataset, DataStreamCollection from contraqctor.contract.camera import Camera from contraqctor.contract.harp import ( @@ -113,7 +113,7 @@ def dataset( PydanticModel( name="Session", reader_params=PydanticModel.make_params( - model=AindBehaviorSessionModel, + model=Session, path=root_path / "behavior/Logs/session_input.json", ), ), diff --git a/src/aind_behavior_just_frames/launcher.py b/src/aind_behavior_just_frames/launcher.py deleted file mode 100644 index 24ed666..0000000 --- a/src/aind_behavior_just_frames/launcher.py +++ /dev/null @@ -1,79 +0,0 @@ -import logging -from pathlib import Path - -from aind_behavior_services.session import AindBehaviorSessionModel -from clabe import resource_monitor -from clabe.apps import ( - AindBehaviorServicesBonsaiApp, -) -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 import data_contract -from aind_behavior_just_frames.rig import AindJustFramesRig - -logger = logging.getLogger(__name__) - - -def experiment(launcher: Launcher) -> None: - picker = DefaultBehaviorPicker(launcher=launcher, settings=DefaultBehaviorPickerSettings()) - session = picker.pick_session(AindBehaviorSessionModel) - rig = picker.pick_rig(AindJustFramesRig) - launcher.register_session(session, rig.data_directory) - - monitor = resource_monitor.ResourceMonitor( - constrains=[ - resource_monitor.available_storage_constraint_factory(launcher.data_directory, 2e11), - ] - ) - - # Validate resources - monitor.run() - - bonsai_app = AindBehaviorServicesBonsaiApp( - workflow=Path(r"./src/main.bonsai"), - rig=rig, - session=session, - ) - bonsai_app.run() - - # Run data qc - if picker.ui_helper.prompt_yes_no_question("Would you like to generate a qc 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() - settings = robocopy.RobocopySettings() - settings.destination = Path(settings.destination) / launcher.session.subject / launcher.session.session_name - robocopy.RobocopyService(source=launcher.session_directory, settings=settings).transfer() - 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 index 5fed95d..f243d66 100644 --- a/src/aind_behavior_just_frames/regenerate.py +++ b/src/aind_behavior_just_frames/regenerate.py @@ -2,8 +2,8 @@ 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_services.schema import BonsaiSgenSerializers, convert_pydantic_to_bonsai +from aind_behavior_services.session import Session from aind_behavior_just_frames.message_protocol import MessageProtocol from aind_behavior_just_frames.rig import AindJustFramesRig @@ -16,7 +16,7 @@ def main(): models = [ AindJustFramesRig, - AindBehaviorSessionModel, + Session, ] model = pydantic.RootModel[Union[tuple(models)]] diff --git a/src/aind_behavior_just_frames/rig.py b/src/aind_behavior_just_frames/rig.py index 2796eb8..48d1e8f 100644 --- a/src/aind_behavior_just_frames/rig.py +++ b/src/aind_behavior_just_frames/rig.py @@ -1,7 +1,7 @@ +from pathlib import Path from typing import Literal, Optional -import aind_behavior_services.rig as rig -from aind_behavior_services.rig import AindBehaviorRigModel +from aind_behavior_services.rig import Rig, cameras, harp from pydantic import BaseModel, Field, model_validator from . import __semver__ @@ -12,32 +12,34 @@ class NetworkConfig(BaseModel): port: int = Field(description="Port for ZMQ connection.", ge=1, le=65535) -class SatelliteRig(AindBehaviorRigModel): +class SatelliteRig(Rig): version: Literal[__semver__] = __semver__ + data_directory: Path = Field(description="Directory where data will be saved to") 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( + triggered_camera_controller_0: Optional[cameras.CameraController[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( + triggered_camera_controller_1: Optional[cameras.CameraController[cameras.SpinnakerCamera]] = Field( default=None, description="Camera controller to triggered cameras. Will use Camera1 register as a trigger.", ) is_satellite: bool = Field(default=True) -class AindJustFramesRig(AindBehaviorRigModel): +class AindJustFramesRig(Rig): version: Literal[__semver__] = __semver__ - triggered_camera_controller_0: Optional[rig.cameras.CameraController[rig.cameras.SpinnakerCamera]] = Field( + data_directory: Path = Field(description="Directory where data will be saved to") + triggered_camera_controller_0: Optional[cameras.CameraController[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( + triggered_camera_controller_1: Optional[cameras.CameraController[cameras.SpinnakerCamera]] = Field( default=None, description="Camera controller to triggered cameras. Will use Camera1 register as a trigger.", ) - harp_behavior: rig.harp.HarpBehavior = Field( + harp_behavior: 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.") diff --git a/src/main.bonsai b/src/main.bonsai index 05af53e..6cb3b93 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -41,7 +41,7 @@ RawSessionSchema - + diff --git a/src/satellite.bonsai b/src/satellite.bonsai index 83f8db2..2508f93 100644 --- a/src/satellite.bonsai +++ b/src/satellite.bonsai @@ -41,7 +41,7 @@ RawSessionSchema - + diff --git a/src/test_deserialization.bonsai b/src/test_deserialization.bonsai index 73caef8..d6f9725 100644 --- a/src/test_deserialization.bonsai +++ b/src/test_deserialization.bonsai @@ -15,7 +15,7 @@ C:\git\AllenNeuralDynamics\aind-vr-foraging\local\AindVrForagingTaskLogic.json C:\git\AllenNeuralDynamics\aind-vr-foraging\local\AindVrForagingRig.json - C:\git\AllenNeuralDynamics\aind-vr-foraging\local\AindBehaviorSessionModel.json + C:\git\AllenNeuralDynamics\aind-vr-foraging\local\Session.json LoadSchemas @@ -25,7 +25,7 @@ RawSessionSchema - + diff --git a/tests/test_bonsai.py b/tests/test_bonsai.py index 9666a9a..c0656f3 100644 --- a/tests/test_bonsai.py +++ b/tests/test_bonsai.py @@ -4,7 +4,7 @@ from pathlib import Path from typing import Generic, List, Optional, TypeVar, Union -from aind_behavior_services.session import AindBehaviorSessionModel +from aind_behavior_services.session import Session from aind_behavior_services.utils import run_bonsai_process from pydantic import ValidationError @@ -18,7 +18,7 @@ "TModel", bound=Union[ AindJustFramesRig, - AindBehaviorSessionModel, + Session, ], ) @@ -31,7 +31,7 @@ def test_deserialization(self): TestModel( bonsai_property="SessionPath", json_root=JSON_ROOT, - model=AindBehaviorSessionModel, + model=Session, ), TestModel( bonsai_property="RigPath", diff --git a/uv.lock b/uv.lock index 6f506be..0aa3d09 100644 --- a/uv.lock +++ b/uv.lock @@ -2,15 +2,15 @@ version = 1 revision = 3 requires-python = ">=3.11" resolution-markers = [ - "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')", + "python_full_version >= '3.14' and sys_platform == 'win32'", + "python_full_version >= '3.14' and sys_platform == 'emscripten'", + "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'win32'", + "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'emscripten'", + "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version < '3.12' and sys_platform == 'win32'", + "python_full_version < '3.12' and sys_platform == 'emscripten'", + "python_full_version < '3.12' and sys_platform != 'emscripten' and sys_platform != 'win32'", ] [[package]] @@ -67,7 +67,8 @@ docs = [ { name = "autodoc-pydantic", extra = ["erdantic"] }, { name = "furo" }, { name = "myst-parser" }, - { name = "sphinx" }, + { name = "sphinx", version = "9.0.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.12'" }, + { name = "sphinx", version = "9.1.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.12'" }, { name = "sphinx-jinja" }, { name = "sphinx-jsonschema" }, ] @@ -75,8 +76,8 @@ 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=90c77e682922288bc7779c4f8cde5d6f15115899" }, - { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", git = "https://github.com/AllenNeuralDynamics/clabe?rev=test-services-13" }, + { name = "aind-behavior-services", specifier = ">=0.13" }, + { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = ">=0.10.0" }, { name = "contraqctor", marker = "extra == 'data'", specifier = ">=0.5.3,<0.6.0" }, { name = "pydantic-settings" }, ] @@ -99,8 +100,8 @@ docs = [ [[package]] name = "aind-behavior-services" -version = "0.13.0rc0" -source = { git = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?rev=feat-update-session#90c77e682922288bc7779c4f8cde5d6f15115899" } +version = "0.13.0" +source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "aind-behavior-curriculum" }, { name = "gitpython" }, @@ -108,11 +109,15 @@ dependencies = [ { name = "pydantic" }, { name = "semver" }, ] +sdist = { url = "https://files.pythonhosted.org/packages/e8/52/169fe25fb69cb249ac86408cad77bcce0950e60cc6491e0117c26f206e91/aind_behavior_services-0.13.0.tar.gz", hash = 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