diff --git a/.config/dotnet-tools.json b/.config/dotnet-tools.json index 44b1c27..134d7ab 100644 --- a/.config/dotnet-tools.json +++ b/.config/dotnet-tools.json @@ -3,7 +3,7 @@ "isRoot": true, "tools": { "bonsai.sgen": { - "version": "0.6.1", + "version": "0.9.0", "commands": [ "bonsai.sgen" ] diff --git a/.github/workflows/aind-behavior-device-olfactometer-cicd.yml b/.github/workflows/aind-behavior-device-olfactometer-cicd.yml new file mode 100644 index 0000000..136a7c9 --- /dev/null +++ b/.github/workflows/aind-behavior-device-olfactometer-cicd.yml @@ -0,0 +1,208 @@ +name: device-olfactometer test suite + +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + - dev* + - release* + release: + types: [published] + +jobs: + # ╔──────────────────────────╗ + # │ _____ _ │ + # │ |_ _|__ ___| |_ ___ │ + # │ | |/ _ \/ __| __/ __| │ + # │ | | __/\__ \ |_\__ \ │ + # │ |_|\___||___/\__|___/ │ + # │ │ + # ╚──────────────────────────╝ + tests: + runs-on: windows-latest + name: device-olfactometer unit tests + steps: + - uses: actions/checkout@v6 + + - uses: astral-sh/setup-uv@v7 + 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 device-olfactometer 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: ubuntu-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@v6 + with: + fetch-depth: 0 + ref: main + + - uses: astral-sh/setup-uv@v7 + with: + enable-cache: true + + - name: Bump pre-release by default + run: uv version --bump rc + + - name: Regenerate schemas + run: uv run device-olfactometer 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 + run: | + version=$(uv version --output-format json | jq -r '.version') + echo "version=$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 }} + + # ╔─────────────────────────────────────────────────────────────────╗ + # │ ____ _ _ _ ____ _ │ + # │ | _ \ _ _| |__ | (_) ___ | _ \ ___| | ___ __ _ ___ ___ │ + # │ | |_) | | | | '_ \| | |/ __| | |_) / _ \ |/ _ \/ _` / __|/ _ \ │ + # │ | __/| |_| | |_) | | | (__ | _ < __/ | __/ (_| \__ \ __/ │ + # │ |_| \__,_|_.__/|_|_|\___| |_| \_\___|_|\___|\__,_|___/\___| │ + # │ │ + # ╚─────────────────────────────────────────────────────────────────╝ + + github-public-release: + runs-on: ubuntu-latest + name: Create GitHub public release + needs: tests + if: false + # if: github.event_name == 'release' && + # github.event.action == 'published' && + # !github.event.release.prerelease + steps: + - uses: actions/checkout@v6 + with: + fetch-depth: 0 + ref: main + + - uses: astral-sh/setup-uv@v7 + with: + enable-cache: true + + - name: Get release version from tag + id: get_version + run: echo "version=${{ github.event.release.tag_name }}" >> $GITHUB_OUTPUT + + - name: Validate version tag 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 device-olfactometer 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 "Set version and regenerate schemas" || echo "No changes to commit" + git push origin main + + # ╔─────────────────────────╗ + # │ ____ │ + # │ | _ \ ___ ___ ___ │ + # │ | | | |/ _ \ / __/ __| │ + # │ | |_| | (_) | (__\__ \ │ + # │ |____/ \___/ \___|___/ │ + # │ │ + # ╚─────────────────────────╝ + 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@v6 + + - name: Install uv + uses: astral-sh/setup-uv@v7 + + - 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 \ No newline at end of file diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index f50a5d0..0000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,25 +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 - diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml deleted file mode 100644 index beeb07d..0000000 --- a/.github/workflows/docs.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: Deploy Sphinx documentation to Pages - -on: - workflow_dispatch: - push: - branches: main - -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/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/README.md b/README.md index a12d7b9..8980537 100644 --- a/README.md +++ b/README.md @@ -1,38 +1,106 @@ -# Aind.Behavior.Device.Olfactometer -![CI](https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/actions/workflows/ci.yml/badge.svg) - +# aind-behavior-device-olfactometer + +![CI](https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/actions/workflows/aind-behavior-device-olfactometer-cicd.yml/badge.svg) [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE) [![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv) -A repository for calibration and configuration of the harp olfactometer device +A library with a SDK for the Olfactometer behavior task +--- -## Getting started +## 📋 General instructions -- Acquire data with `src/main.bonsai` -- Run `olfactometer-qc --path ` from the command line for a quality control check +This repository follows the project structure laid out in the [Aind.Behavior.Services repository](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services). --- -## General instructions +## 🔧 Prerequisites -This repository follows the project structure laid out in the [Aind.Behavior.Services repository](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services). +[Pre-requisites for running the project can be found here](https://allenneuraldynamics.github.io/Aind.Behavior.Services/articles/requirements.html). --- -## Deployment +## 🚀 Deployment -Deployment instructions can be found [here](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?tab=readme-ov-file#deployment). +For convenience, once third-party dependencies are installed, `Bonsai` and `python` virtual environments can be bootstrapped by running: ---- +```powershell +./scripts/deploy.ps1 +``` -## Prerequisites +from the root of the repository. -Pre-requisites for running the project can be found [here](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?tab=readme-ov-file#prerequisites). +## ⚙️ Generating settings files ---- +The task is instantiated by a set of three settings files that strictly follow a DSL schema. These files are: + +- `task_logic.json` +- `rig.json` +- `session.json` + +Examples on how to generate these files can be found in the `./examples` directory of the repository. Once generated, these are the only required inputs to run the Bonsai workflow in `./src/main.bonsai`. + +The workflow can thus be executed using the [Bonsai CLI](https://bonsai-rx.org/docs/articles/cli.html): + +```powershell +"./bonsai/bonsai.exe" "./src/main.bonsai" -p SessionPath= -p RigPath= -p TaskLogicPath= +``` + +However, for a better experiment management user experience, it is recommended to use the provided experiment launcher below. + +## [> ] CLI tools + +### Task CLI + +The platform exposes a few CLI tools to facilitate various tasks. Tools are available via: + +```powershell +uv run device-olfactometer +``` + +for a list of all sub commands available: + +```powershell +uv run device-olfactometer -h +``` + +You may need to install optional dependencies depending on the sub-commands you run. + + + +## 🎮 Experiment launcher (CLABE) + +To manage experiments and input files, this repository contains a launcher script that can be used to run the Olfactometer task. A default script is located at `./scripts/aind-launcher.py`. It can be run from the command line as follows: + +```powershell +uv run clabe run ./scripts/aind-launcher.py +# or uv run ./scripts/aind-launcher.py.py +``` + +Additional arguments can be passed to the script as needed. For instance to allow the script to run with uncommitted changes in the repository, the `--allow-dirty` flag can be used: + +```powershell +uv run clabe run ./scripts/aind-launcher.py --allow-dirty +``` + +or via a `./local/clabe.yml` file. Additional custom launcher scripts can be created and used as needed. See documentation in the [`clabe` repository](https://allenneuraldynamics.github.io/clabe/) for more details. + + +## 🔍 Primary data quality-control + +Once an experiment is collected, the primary data quality-control script can be run to check the data for issues. This script can be launcher using: + +```powershell +uv run device-olfactometer data-qc +``` + +## 🔄 Regenerating schemas + +DSL schemas can be modified in `./src/aind_behavior_device_olfactometer/rig.py` (or `(...)/task_logic.py`). -## Regenerating schemas +Once modified, changes to the DSL must be propagated to `json-schema` and `csharp` API. This can be done by running: -Instructions for regenerating schemas can be found [here](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?tab=readme-ov-file#regenerating-schemas). \ No newline at end of file +```powershell +uv run device-olfactometer regenerate +``` \ No newline at end of file diff --git a/bonsai/Bonsai.config b/bonsai/Bonsai.config index 0ceba29..a99cc3a 100644 --- a/bonsai/Bonsai.config +++ b/bonsai/Bonsai.config @@ -1,11 +1,12 @@  - - + + + - + @@ -18,7 +19,7 @@ - + @@ -36,9 +37,13 @@ - + - + + + + + @@ -66,6 +71,7 @@ + @@ -106,11 +112,12 @@ - - + + + - + @@ -127,7 +134,7 @@ - + @@ -143,9 +150,13 @@ - + - + + + + + @@ -181,6 +192,15 @@ + + + + + + + + + diff --git a/examples/olfactometer.py b/examples/olfactometer.py index d4e8527..b65968b 100644 --- a/examples/olfactometer.py +++ b/examples/olfactometer.py @@ -1,35 +1,35 @@ import os -from aind_behavior_services.base import get_commit_hash -from aind_behavior_services.calibration import aind_manipulator as man -from aind_behavior_services.calibration import olfactometer as olf +from aind_behavior_services.rig import aind_manipulator as man +from aind_behavior_services.rig import olfactometer as olf from aind_behavior_services.rig.harp import HarpAnalogInput, HarpWhiteRabbit -from aind_behavior_services.session import AindBehaviorSessionModel +from aind_behavior_services.session import Session from aind_behavior_services.utils import utcnow from aind_behavior_device_olfactometer import rig, task_logic from aind_behavior_device_olfactometer.rig import AlicatFlowmeter -channels_config = { - olf.OlfactometerChannel.Channel0: olf.OlfactometerChannelConfig( - channel_index=olf.OlfactometerChannel.Channel0, - channel_type=olf.OlfactometerChannelType.ODOR, - flow_rate=100, - odorant="Banana", - odorant_dilution=0.1, - ), - olf.OlfactometerChannel.Channel3: olf.OlfactometerChannelConfig( - channel_index=olf.OlfactometerChannel.Channel3, channel_type=olf.OlfactometerChannelType.CARRIER, odorant="Air" - ), -} - -calibration = olf.OlfactometerCalibration( - input=olf.OlfactometerCalibrationInput(), output=olf.OlfactometerCalibrationOutput() +olf_calibration = olf.OlfactometerCalibration( + channel_config={ + olf.OlfactometerChannel.Channel0: olf.OlfactometerChannelConfig( + channel_index=olf.OlfactometerChannel.Channel0, + channel_type=olf.OlfactometerChannelType.ODOR, + flow_rate=100, + odorant="Banana", + odorant_dilution=0.1, + ), + olf.OlfactometerChannel.Channel3: olf.OlfactometerChannelConfig( + channel_index=olf.OlfactometerChannel.Channel3, + channel_type=olf.OlfactometerChannelType.CARRIER, + odorant="Air", + ), + } ) + calibration_logic = task_logic.OlfactometerCalibrationLogic( task_parameters=task_logic.OlfactometerCalibrationParameters( - channel_config=channels_config, + channel_config=olf_calibration.channel_config, full_flow_rate=1000, n_repeats_per_stimulus=10, time_on=2, @@ -37,37 +37,34 @@ ) ) -calibration_session = AindBehaviorSessionModel( - root_path="C:\\Data", +calibration_session = Session( date=utcnow(), allow_dirty_repo=False, experiment="OlfactometerCalibration", - experiment_version="0.0.0", subject="Olfactometer", - commit_hash=get_commit_hash(), + experimenter=["A. Scientist"], ) manipulator_calibration = man.AindManipulatorCalibration( - output=man.AindManipulatorCalibrationOutput(), - input=man.AindManipulatorCalibrationInput( - full_step_to_mm=(man.ManipulatorPosition(x=0.010, y1=0.010, y2=0.010, z=0.010)), - axis_configuration=[ - man.AxisConfiguration(axis=man.Axis.Y1, min_limit=-0.01, max_limit=25), - man.AxisConfiguration(axis=man.Axis.Y2, min_limit=-0.01, max_limit=25), - man.AxisConfiguration(axis=man.Axis.X, min_limit=-0.01, max_limit=25), - man.AxisConfiguration(axis=man.Axis.Z, min_limit=-0.01, max_limit=25), - ], - homing_order=[man.Axis.Y1, man.Axis.Y2, man.Axis.X, man.Axis.Z], - initial_position=man.ManipulatorPosition(y1=0, y2=0, x=0, z=0), - ), + full_step_to_mm=(man.ManipulatorPosition(x=0.010, y1=0.010, y2=0.010, z=0.010)), + axis_configuration=[ + man.AxisConfiguration(axis=man.Axis.Y1, min_limit=-0.01, max_limit=25), + man.AxisConfiguration(axis=man.Axis.Y2, min_limit=-0.01, max_limit=25), + man.AxisConfiguration(axis=man.Axis.X, min_limit=-0.01, max_limit=25), + man.AxisConfiguration(axis=man.Axis.Z, min_limit=-0.01, max_limit=25), + ], + homing_order=[man.Axis.Y1, man.Axis.Y2, man.Axis.X, man.Axis.Z], + initial_position=man.ManipulatorPosition(y1=0, y2=0, x=0, z=0), ) _rig = rig.OlfactometerCalibrationRig( + computer_name="TestPC", + data_directory="c:/data", rig_name="OlfactometerRig", - harp_olfactometer=olf.Olfactometer(port_name="COM10", calibration=calibration), + harp_olfactometer=olf.Olfactometer(port_name="COM10", calibration=olf_calibration), harp_analog_input=HarpAnalogInput(port_name="COM8"), harp_clock_generator=HarpWhiteRabbit(port_name="COM9"), - harp_manipulator=man.AindManipulatorDevice(port_name="COM7", calibration=manipulator_calibration), + harp_manipulator=man.AindManipulator(port_name="COM7", calibration=manipulator_calibration), flowmeter=AlicatFlowmeter(port_name="COM6", device_id="A", pooling_period=0.2), ) diff --git a/pyproject.toml b/pyproject.toml index 5ec9911..e589680 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,25 +1,21 @@ [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-device-olfactometer" description = "A library that can be used to generate models and configuration files for the harp olfactometer device." -authors = [ - { name = "Bruno Cruz", email = "bruno.cruz@alleninstitute.org" }, -] -license = {text = "MIT"} +authors = [{ name = "Bruno Cruz", email = "bruno.cruz@alleninstitute.org" }] +license = { text = "MIT" } requires-python = ">=3.11" -dynamic = ["version", "readme"] +version = "0.2.0rc0" +readme = { file = "README.md", content-type = "text/markdown" } classifiers = [ "Programming Language :: Python :: 3.11", - "License :: OSI Approved :: MIT License", "Operating System :: Microsoft :: Windows", ] -dependencies = [ - "aind_behavior_services<0.13", -] +dependencies = ["aind_behavior_services>=0.13.5, <0.14", "pydantic-settings"] [project.urls] Documentation = "https://allenneuraldynamics.github.io/Aind.Behavior.Device.Olfactometer/" @@ -29,11 +25,23 @@ Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfacto [project.optional-dependencies] -launcher = ["aind_clabe[aind-services]"] +launcher = ["aind-clabe[aind-services]>=0.10.0"] + +data = [ + "contraqctor>= 0.5.3, < 0.6", + "numpy", + "pandas", + "matplotlib", + "jupyter", +] + +[dependency-groups] -dev = ["aind_behavior_device_olfactometer[launcher]", +dev = [ + "aind_behavior_device_olfactometer[launcher]", + "aind_behavior_device_olfactometer[data]", "ruff", - "codespell" + "codespell", ] docs = [ @@ -46,28 +54,9 @@ docs = [ "sphinx_mdinclude", ] -analysis = [ - "contraqctor", - "numpy", - "pandas", - "matplotlib", - "jupyter", -] [project.scripts] -clabe = "aind_behavior_device_olfactometer.launcher:main" -regenerate = "aind_behavior_device_olfactometer.regenerate:main" -olfactometer-qc = "aind_behavior_device_olfactometer.analysis:main" - -[tool.setuptools.packages.find] -where = ["src"] - -[tool.setuptools.package-data] -aind_behavior_device_olfactometer = ["py.typed"] - -[tool.setuptools.dynamic] -version = {attr = "aind_behavior_device_olfactometer.__version__"} -readme = {file = "README.md", content-type = "text/markdown"} +device-olfactometer = "aind_behavior_device_olfactometer.cli:main" [tool.ruff] line-length = 120 @@ -80,5 +69,10 @@ mccabe = { max-complexity = 14 } pydocstyle = { convention = 'google' } [tool.codespell] -skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build,uv.lock' +skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build,uv.lock,*Generated.cs' ignore-words-list = 'nd' + + +[tool.uv] +default-groups = ['dev'] +required-version = '>=0.8.4' diff --git a/src/DataSchemas/aind_behavior_device_olfactometer.json b/schema/aind_behavior_device_olfactometer.json similarity index 75% rename from src/DataSchemas/aind_behavior_device_olfactometer.json rename to schema/aind_behavior_device_olfactometer.json index a7b6e3c..4451b84 100644 --- a/src/DataSchemas/aind_behavior_device_olfactometer.json +++ b/schema/aind_behavior_device_olfactometer.json @@ -1,47 +1,90 @@ { "$defs": { - "AindBehaviorSessionModel": { + "AindManipulator": { + "description": "AindManipulator device definition", "properties": { - "aind_behavior_services_pkg_version": { - "default": "0.12.0", - "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-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "version": { - "const": "0.3.1", - "default": "0.3.1", - "title": "Version", - "type": "string" - }, - "experiment": { - "description": "Name of the experiment", - "title": "Experiment", + "device_type": { + "const": "StepperDriver", + "default": "StepperDriver", + "title": "Device Type", "type": "string" }, - "experimenter": { - "default": [], - "description": "Name of the experimenter", - "items": { - "type": "string" + "calibration": { + "$ref": "#/$defs/AindManipulatorCalibration", + "default": { + "description": "AindManipulator calibration and settings", + "full_step_to_mm": { + "x": 0.01, + "y1": 0.01, + "y2": 0.01, + "z": 0.01 + }, + "axis_configuration": [ + { + "axis": 2, + "max_limit": 25.0, + "maximum_step_interval": 2000, + "microstep_resolution": 0, + "min_limit": -0.01, + "motor_operation_mode": 0, + "step_acceleration_interval": 100, + "step_interval": 100 + }, + { + "axis": 3, + "max_limit": 25.0, + "maximum_step_interval": 2000, + "microstep_resolution": 0, + "min_limit": -0.01, + "motor_operation_mode": 0, + "step_acceleration_interval": 100, + "step_interval": 100 + }, + { + "axis": 1, + "max_limit": 25.0, + "maximum_step_interval": 2000, + "microstep_resolution": 0, + "min_limit": -0.01, + "motor_operation_mode": 0, + "step_acceleration_interval": 100, + "step_interval": 100 + }, + { + "axis": 4, + "max_limit": 25.0, + "maximum_step_interval": 2000, + "microstep_resolution": 0, + "min_limit": -0.01, + "motor_operation_mode": 0, + "step_acceleration_interval": 100, + "step_interval": 100 + } + ], + "homing_order": [ + 2, + 3, + 1, + 4 + ], + "initial_position": { + "x": 0.0, + "y1": 0.0, + "y2": 0.0, + "z": 0.0 + } }, - "title": "Experimenter", - "type": "array" - }, - "date": { - "description": "Date of the experiment", - "format": "date-time", - "title": "Date", - "type": "string" + "description": "Calibration for the device." }, - "root_path": { - "description": "Root path where data will be logged", - "title": "Root Path", - "type": "string" + "who_am_i": { + "const": 1130, + "default": 1130, + "title": "Who Am I", + "type": "integer" }, - "session_name": { + "serial_number": { "default": null, - "description": "Name of the session. This will be used to create a folder in the root path.", + "description": "Device serial number", "oneOf": [ { "type": "string" @@ -50,124 +93,30 @@ "type": "null" } ], - "title": "Session Name" - }, - "subject": { - "description": "Name of the subject", - "title": "Subject", - "type": "string" + "title": "Serial Number" }, - "experiment_version": { - "description": "Version of the experiment", - "title": "Experiment Version", + "port_name": { + "description": "Device port name", + "title": "Port Name", "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" + "port_name" ], - "title": "AindBehaviorSessionModel", - "type": "object" + "title": "AindManipulator", + "type": "object", + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.AindManipulator" }, "AindManipulatorCalibration": { - "description": "Aind manipulator calibration class", + "description": "AindManipulator calibration class", "properties": { - "device_name": { - "default": "AindManipulator", - "description": "Must match a device name in rig/instrument", - "title": "Device name", - "type": "string" - }, - "input": { - "$ref": "#/$defs/AindManipulatorCalibrationInput", - "title": "Input of the calibration" - }, - "output": { - "$ref": "#/$defs/AindManipulatorCalibrationOutput", - "title": "Output of the calibration." - }, - "date": { - "default": null, - "oneOf": [ - { - "format": "date-time", - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Date" - }, "description": { - "const": "Calibration of the load cells system", - "default": "Calibration of the load cells system", + "const": "AindManipulator calibration and settings", + "default": "AindManipulator calibration and settings", "title": "Description", "type": "string" }, - "notes": { - "default": null, - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Notes" - } - }, - "required": [ - "input", - "output" - ], - "title": "AindManipulatorCalibration", - "type": "object" - }, - "AindManipulatorCalibrationInput": { - "properties": { "full_step_to_mm": { "$ref": "#/$defs/ManipulatorPosition", "default": { @@ -250,89 +199,9 @@ } } }, - "title": "AindManipulatorCalibrationInput", - "type": "object" - }, - "AindManipulatorCalibrationOutput": { - "properties": {}, - "title": "AindManipulatorCalibrationOutput", - "type": "object" - }, - "AindManipulatorDevice": { - "properties": { - "device_type": { - "const": "StepperDriver", - "default": "StepperDriver", - "title": "Device Type", - "type": "string" - }, - "device_name": { - "default": null, - "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, - "calibration": { - "default": null, - "oneOf": [ - { - "$ref": "#/$defs/AindManipulatorCalibration" - }, - { - "type": "null" - } - ], - "title": "Calibration of the manipulator" - }, - "who_am_i": { - "const": 1130, - "default": 1130, - "title": "Who Am I", - "type": "integer" - }, - "serial_number": { - "default": null, - "description": "Device serial number", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Serial Number" - }, - "port_name": { - "description": "Device port name", - "title": "Port Name", - "type": "string" - } - }, - "required": [ - "port_name" - ], - "title": "AindManipulatorDevice", - "type": "object" + "title": "AindManipulatorCalibration", + "type": "object", + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.AindManipulatorCalibration" }, "AlicatFlowmeter": { "properties": { @@ -342,34 +211,9 @@ "title": "Device Type", "type": "string" }, - "device_name": { - "default": null, - "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, "calibration": { "default": null, - "description": "Calibration", + "description": "Calibration for the device.", "oneOf": [ { "$ref": "#/$defs/BaseModel" @@ -421,7 +265,8 @@ "Y1", "Y2", "Z" - ] + ], + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.Axis" }, "AxisConfiguration": { "description": "Axis configuration", @@ -478,7 +323,8 @@ "axis" ], "title": "AxisConfiguration", - "type": "object" + "type": "object", + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.AxisConfiguration" }, "BaseModel": { "properties": {}, @@ -521,34 +367,9 @@ "title": "Device Type", "type": "string" }, - "device_name": { - "default": null, - "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, "calibration": { "default": null, - "description": "Calibration", + "description": "Calibration for the device.", "oneOf": [ { "$ref": "#/$defs/BaseModel" @@ -597,34 +418,9 @@ "title": "Device Type", "type": "string" }, - "device_name": { - "default": null, - "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, "calibration": { "default": null, - "description": "Calibration", + "description": "Calibration for the device.", "oneOf": [ { "$ref": "#/$defs/BaseModel" @@ -675,6 +471,7 @@ "type": "object" }, "ManipulatorPosition": { + "description": "Represents a position in the manipulator coordinate system", "properties": { "x": { "title": "X coordinate", @@ -700,9 +497,11 @@ "z" ], "title": "ManipulatorPosition", - "type": "object" + "type": "object", + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.ManipulatorPosition" }, "MicrostepResolution": { + "description": "Microstep resolution available", "enum": [ 0, 1, @@ -716,9 +515,11 @@ "Microstep16", "Microstep32", "Microstep64" - ] + ], + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.MicrostepResolution" }, "MotorOperationMode": { + "description": "Motor operation mode", "enum": [ 0, 1 @@ -728,9 +529,11 @@ "x-enumNames": [ "Quiet", "Dynamic" - ] + ], + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.MotorOperationMode" }, "Olfactometer": { + "description": "A calibrated olfactometer device", "properties": { "device_type": { "const": "Olfactometer", @@ -738,41 +541,12 @@ "title": "Device Type", "type": "string" }, - "device_name": { - "default": null, - "description": "Device name", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Device Name" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/$defs/BaseModel" - }, - { - "type": "null" - } - ] - }, "calibration": { - "default": null, - "oneOf": [ - { - "$ref": "#/$defs/OlfactometerCalibration" - }, - { - "type": "null" - } - ], + "$ref": "#/$defs/OlfactometerCalibration", + "default": { + "date": null, + "channel_config": {} + }, "title": "Calibration of the olfactometer" }, "who_am_i": { @@ -807,24 +581,11 @@ "type": "object" }, "OlfactometerCalibration": { - "description": "Olfactometer calibration class", + "description": "Olfactometer device configuration model", "properties": { - "device_name": { - "default": "Olfactometer", - "description": "Name of the device being calibrated", - "title": "Device name", - "type": "string" - }, - "input": { - "$ref": "#/$defs/OlfactometerCalibrationInput", - "title": "Input of the calibration" - }, - "output": { - "$ref": "#/$defs/OlfactometerCalibrationOutput", - "title": "Output of the calibration" - }, "date": { "default": null, + "description": "Date of the calibration", "oneOf": [ { "format": "date-time", @@ -836,34 +597,6 @@ ], "title": "Date" }, - "description": { - "const": "Calibration of the harp olfactometer device", - "default": "Calibration of the harp olfactometer device", - "title": "Description", - "type": "string" - }, - "notes": { - "default": null, - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Notes" - } - }, - "required": [ - "input", - "output" - ], - "title": "OlfactometerCalibration", - "type": "object" - }, - "OlfactometerCalibrationInput": { - "properties": { "channel_config": { "additionalProperties": { "$ref": "#/$defs/OlfactometerChannelConfig" @@ -877,7 +610,7 @@ "type": "object" } }, - "title": "OlfactometerCalibrationInput", + "title": "OlfactometerCalibration", "type": "object" }, "OlfactometerCalibrationLogic": { @@ -900,8 +633,8 @@ "title": "Task parameters" }, "version": { - "const": "0.3.0", - "default": "0.3.0", + "const": "0.2.0-rc0", + "default": "0.2.0-rc0", "title": "Version", "type": "string" }, @@ -925,11 +658,6 @@ "title": "OlfactometerCalibrationLogic", "type": "object" }, - "OlfactometerCalibrationOutput": { - "properties": {}, - "title": "OlfactometerCalibrationOutput", - "type": "object" - }, "OlfactometerCalibrationParameters": { "additionalProperties": true, "properties": { @@ -947,7 +675,7 @@ "title": "Rng Seed" }, "aind_behavior_services_pkg_version": { - "default": "0.12.0", + "default": "0.13.6", "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", "title": "aind_behavior_services package version", "type": "string" @@ -956,7 +684,6 @@ "additionalProperties": { "$ref": "#/$defs/OlfactometerChannelConfig" }, - "default": {}, "description": "Configuration of olfactometer channels", "propertyNames": { "$ref": "#/$defs/OlfactometerChannel" @@ -1000,14 +727,14 @@ "OlfactometerCalibrationRig": { "properties": { "aind_behavior_services_pkg_version": { - "default": "0.12.0", + "default": "0.13.6", "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-]+)*))?$", "title": "aind_behavior_services package version", "type": "string" }, "version": { - "const": "0.3.0", - "default": "0.3.0", + "const": "0.2.0-rc0", + "default": "0.2.0-rc0", "title": "Version", "type": "string" }, @@ -1021,6 +748,12 @@ "title": "Rig Name", "type": "string" }, + "data_directory": { + "description": "Directory where data will be saved to", + "format": "path", + "title": "Data Directory", + "type": "string" + }, "harp_olfactometer": { "$ref": "#/$defs/Olfactometer", "title": "Olfactometer device" @@ -1034,7 +767,7 @@ "title": "Clock generator device" }, "harp_manipulator": { - "$ref": "#/$defs/AindManipulatorDevice", + "$ref": "#/$defs/AindManipulator", "description": "Manipulator" }, "flowmeter": { @@ -1051,7 +784,9 @@ } }, "required": [ + "computer_name", "rig_name", + "data_directory", "harp_olfactometer", "harp_analog_input", "harp_clock_generator", @@ -1078,15 +813,16 @@ ] }, "OlfactometerChannelConfig": { + "description": "Configuration for a single olfactometer channel", "properties": { "channel_index": { - "title": "Channel index", + "title": "Odor channel index", "type": "integer" }, "channel_type": { "$ref": "#/$defs/OlfactometerChannelType", "default": "Odor", - "title": "Channel type" + "title": "Olfactometer channel type" }, "flow_rate_capacity": { "default": 100, @@ -1135,13 +871,118 @@ "type": "object" }, "OlfactometerChannelType": { - "description": "Channel type", + "description": "Olfactometer channel type", "enum": [ "Odor", "Carrier" ], "title": "OlfactometerChannelType", "type": "string" + }, + "Session": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.13.6", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.13.6", + "default": "0.13.6", + "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" } } } \ No newline at end of file diff --git a/schema/aind_behavior_telekinesis.json b/schema/aind_behavior_telekinesis.json new file mode 100644 index 0000000..7118590 --- /dev/null +++ b/schema/aind_behavior_telekinesis.json @@ -0,0 +1,988 @@ +{ + "$defs": { + "AindManipulator": { + "description": "AindManipulator device definition", + "properties": { + "device_type": { + "const": "StepperDriver", + "default": "StepperDriver", + "title": "Device Type", + "type": "string" + }, + "calibration": { + "$ref": "#/$defs/AindManipulatorCalibration", + "default": { + "description": "AindManipulator calibration and settings", + "full_step_to_mm": { + "x": 0.01, + "y1": 0.01, + "y2": 0.01, + "z": 0.01 + }, + "axis_configuration": [ + { + "axis": 2, + "max_limit": 25.0, + "maximum_step_interval": 2000, + "microstep_resolution": 0, + "min_limit": -0.01, + "motor_operation_mode": 0, + "step_acceleration_interval": 100, + "step_interval": 100 + }, + { + "axis": 3, + "max_limit": 25.0, + "maximum_step_interval": 2000, + "microstep_resolution": 0, + "min_limit": -0.01, + "motor_operation_mode": 0, + "step_acceleration_interval": 100, + "step_interval": 100 + }, + { + "axis": 1, + "max_limit": 25.0, + "maximum_step_interval": 2000, + "microstep_resolution": 0, + "min_limit": -0.01, + "motor_operation_mode": 0, + "step_acceleration_interval": 100, + "step_interval": 100 + }, + { + "axis": 4, + "max_limit": 25.0, + "maximum_step_interval": 2000, + "microstep_resolution": 0, + "min_limit": -0.01, + "motor_operation_mode": 0, + "step_acceleration_interval": 100, + "step_interval": 100 + } + ], + "homing_order": [ + 2, + 3, + 1, + 4 + ], + "initial_position": { + "x": 0.0, + "y1": 0.0, + "y2": 0.0, + "z": 0.0 + } + }, + "description": "Calibration for the device." + }, + "who_am_i": { + "const": 1130, + "default": 1130, + "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" + } + }, + "required": [ + "port_name" + ], + "title": "AindManipulator", + "type": "object", + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.AindManipulator" + }, + "AindManipulatorCalibration": { + "description": "AindManipulator calibration class", + "properties": { + "description": { + "const": "AindManipulator calibration and settings", + "default": "AindManipulator calibration and settings", + "title": "Description", + "type": "string" + }, + "full_step_to_mm": { + "$ref": "#/$defs/ManipulatorPosition", + "default": { + "x": 0.01, + "y1": 0.01, + "y2": 0.01, + "z": 0.01 + }, + "title": "Full step to mm. Used to convert steps to SI Units" + }, + "axis_configuration": { + "default": [ + { + "axis": 2, + "step_acceleration_interval": 100, + "step_interval": 100, + "microstep_resolution": 0, + "maximum_step_interval": 2000, + "motor_operation_mode": 0, + "max_limit": 25.0, + "min_limit": -0.01 + }, + { + "axis": 3, + "step_acceleration_interval": 100, + "step_interval": 100, + "microstep_resolution": 0, + "maximum_step_interval": 2000, + "motor_operation_mode": 0, + "max_limit": 25.0, + "min_limit": -0.01 + }, + { + "axis": 1, + "step_acceleration_interval": 100, + "step_interval": 100, + "microstep_resolution": 0, + "maximum_step_interval": 2000, + "motor_operation_mode": 0, + "max_limit": 25.0, + "min_limit": -0.01 + }, + { + "axis": 4, + "step_acceleration_interval": 100, + "step_interval": 100, + "microstep_resolution": 0, + "maximum_step_interval": 2000, + "motor_operation_mode": 0, + "max_limit": 25.0, + "min_limit": -0.01 + } + ], + "items": { + "$ref": "#/$defs/AxisConfiguration" + }, + "title": "Axes configuration. Only the axes that are configured will be enabled.", + "type": "array" + }, + "homing_order": { + "default": [ + 2, + 3, + 1, + 4 + ], + "items": { + "$ref": "#/$defs/Axis" + }, + "title": "Homing order", + "type": "array" + }, + "initial_position": { + "$ref": "#/$defs/ManipulatorPosition", + "default": { + "x": 0.0, + "y1": 0.0, + "y2": 0.0, + "z": 0.0 + } + } + }, + "title": "AindManipulatorCalibration", + "type": "object", + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.AindManipulatorCalibration" + }, + "AlicatFlowmeter": { + "properties": { + "device_type": { + "const": "AlicatFlowmeter", + "default": "AlicatFlowmeter", + "title": "Device Type", + "type": "string" + }, + "calibration": { + "default": null, + "description": "Calibration for the device.", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "port_name": { + "description": "Device port name", + "title": "Port Name", + "type": "string" + }, + "device_id": { + "default": "A", + "description": "Alicat device ID", + "title": "Device Id", + "type": "string" + }, + "pooling_period": { + "default": 0.2, + "description": "Device pooling interval in seconds", + "exclusiveMinimum": 0, + "title": "Pooling Period", + "type": "number" + } + }, + "required": [ + "port_name" + ], + "title": "AlicatFlowmeter", + "type": "object" + }, + "Axis": { + "description": "Motor axis available", + "enum": [ + 0, + 1, + 2, + 3, + 4 + ], + "title": "Axis", + "type": "integer", + "x-enumNames": [ + "None", + "X", + "Y1", + "Y2", + "Z" + ], + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.Axis" + }, + "AxisConfiguration": { + "description": "Axis configuration", + "properties": { + "axis": { + "$ref": "#/$defs/Axis", + "title": "Axis to be configured" + }, + "step_acceleration_interval": { + "default": 100, + "description": "Acceleration of the step interval in microseconds", + "maximum": 2000, + "minimum": 2, + "title": "Acceleration", + "type": "integer" + }, + "step_interval": { + "default": 100, + "description": "Step interval in microseconds.", + "maximum": 20000, + "minimum": 100, + "title": "Step interval", + "type": "integer" + }, + "microstep_resolution": { + "$ref": "#/$defs/MicrostepResolution", + "default": 0, + "title": "Microstep resolution" + }, + "maximum_step_interval": { + "default": 2000, + "maximum": 20000, + "minimum": 100, + "title": "Configures the time between step motor pulses (us) used when starting or stopping a movement", + "type": "integer" + }, + "motor_operation_mode": { + "$ref": "#/$defs/MotorOperationMode", + "default": 0, + "title": "Motor operation mode" + }, + "max_limit": { + "default": 25, + "title": "Maximum limit in SI units. A value of 0 disables this limit.", + "type": "number" + }, + "min_limit": { + "default": -0.01, + "title": "Minimum limit in SI units. A value of 0 disables this limit.", + "type": "number" + } + }, + "required": [ + "axis" + ], + "title": "AxisConfiguration", + "type": "object", + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.AxisConfiguration" + }, + "BaseModel": { + "properties": {}, + "title": "BaseModel", + "type": "object" + }, + "ConnectedClockOutput": { + "properties": { + "target_device": { + "default": null, + "description": "Optional device name to provide user additional information", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Target Device" + }, + "output_channel": { + "description": "Output channel", + "minimum": 0, + "title": "Output Channel", + "type": "integer" + } + }, + "required": [ + "output_channel" + ], + "title": "ConnectedClockOutput", + "type": "object" + }, + "HarpAnalogInput": { + "properties": { + "device_type": { + "const": "AnalogInput", + "default": "AnalogInput", + "title": "Device Type", + "type": "string" + }, + "calibration": { + "default": null, + "description": "Calibration for the device.", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "who_am_i": { + "const": 1236, + "default": 1236, + "title": "Who Am I", + "type": "integer" + }, + "serial_number": { + "default": null, + "description": "Device serial number", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Serial Number" + }, + "port_name": { + "description": "Device port name", + "title": "Port Name", + "type": "string" + } + }, + "required": [ + "port_name" + ], + "title": "HarpAnalogInput", + "type": "object" + }, + "HarpWhiteRabbit": { + "properties": { + "device_type": { + "const": "WhiteRabbit", + "default": "WhiteRabbit", + "title": "Device Type", + "type": "string" + }, + "calibration": { + "default": null, + "description": "Calibration for the device.", + "oneOf": [ + { + "$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": "#/$defs/ConnectedClockOutput" + }, + "title": "Connected Clock Outputs", + "type": "array" + } + }, + "required": [ + "port_name" + ], + "title": "HarpWhiteRabbit", + "type": "object" + }, + "ManipulatorPosition": { + "description": "Represents a position in the manipulator coordinate system", + "properties": { + "x": { + "title": "X coordinate", + "type": "number" + }, + "y1": { + "title": "Y1 coordinate", + "type": "number" + }, + "y2": { + "title": "Y2 coordinate", + "type": "number" + }, + "z": { + "title": "Z coordinate", + "type": "number" + } + }, + "required": [ + "x", + "y1", + "y2", + "z" + ], + "title": "ManipulatorPosition", + "type": "object", + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.ManipulatorPosition" + }, + "MicrostepResolution": { + "description": "Microstep resolution available", + "enum": [ + 0, + 1, + 2, + 3 + ], + "title": "MicrostepResolution", + "type": "integer", + "x-enumNames": [ + "Microstep8", + "Microstep16", + "Microstep32", + "Microstep64" + ], + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.MicrostepResolution" + }, + "MotorOperationMode": { + "description": "Motor operation mode", + "enum": [ + 0, + 1 + ], + "title": "MotorOperationMode", + "type": "integer", + "x-enumNames": [ + "Quiet", + "Dynamic" + ], + "x-sgen-typename": "AllenNeuralDynamics.AindManipulator.MotorOperationMode" + }, + "Olfactometer": { + "description": "A calibrated olfactometer device", + "properties": { + "device_type": { + "const": "Olfactometer", + "default": "Olfactometer", + "title": "Device Type", + "type": "string" + }, + "calibration": { + "$ref": "#/$defs/OlfactometerCalibration", + "default": { + "date": null, + "channel_config": {} + }, + "title": "Calibration of the olfactometer" + }, + "who_am_i": { + "const": 1140, + "default": 1140, + "title": "Who Am I", + "type": "integer" + }, + "serial_number": { + "default": null, + "description": "Device serial number", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Serial Number" + }, + "port_name": { + "description": "Device port name", + "title": "Port Name", + "type": "string" + } + }, + "required": [ + "port_name" + ], + "title": "Olfactometer", + "type": "object" + }, + "OlfactometerCalibration": { + "description": "Olfactometer device configuration model", + "properties": { + "date": { + "default": null, + "description": "Date of the calibration", + "oneOf": [ + { + "format": "date-time", + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Date" + }, + "channel_config": { + "additionalProperties": { + "$ref": "#/$defs/OlfactometerChannelConfig" + }, + "default": {}, + "description": "Configuration of olfactometer channels", + "propertyNames": { + "$ref": "#/$defs/OlfactometerChannel" + }, + "title": "Channel Config", + "type": "object" + } + }, + "title": "OlfactometerCalibration", + "type": "object" + }, + "OlfactometerCalibrationLogic": { + "additionalProperties": false, + "description": "Olfactometer operation control model that is used to run a calibration data acquisition workflow", + "properties": { + "name": { + "default": "OlfactometerCalibration", + "title": "Name of the task logic", + "type": "string" + }, + "description": { + "default": "", + "description": "Description of the task.", + "title": "Description", + "type": "string" + }, + "task_parameters": { + "$ref": "#/$defs/OlfactometerCalibrationParameters", + "title": "Task parameters" + }, + "version": { + "const": "0.2.0rc0", + "default": "0.2.0rc0", + "title": "Version", + "type": "string" + }, + "stage_name": { + "default": null, + "description": "Optional stage name the `Task` object instance represents.", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Stage Name" + } + }, + "required": [ + "task_parameters" + ], + "title": "OlfactometerCalibrationLogic", + "type": "object" + }, + "OlfactometerCalibrationParameters": { + "additionalProperties": true, + "properties": { + "rng_seed": { + "default": null, + "description": "Seed of the random number generator", + "oneOf": [ + { + "type": "number" + }, + { + "type": "null" + } + ], + "title": "Rng Seed" + }, + "aind_behavior_services_pkg_version": { + "default": "0.13.6", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "channel_config": { + "additionalProperties": { + "$ref": "#/$defs/OlfactometerChannelConfig" + }, + "description": "Configuration of olfactometer channels", + "propertyNames": { + "$ref": "#/$defs/OlfactometerChannel" + }, + "title": "Channel Config", + "type": "object" + }, + "full_flow_rate": { + "default": 1000, + "description": "Full flow rate of the olfactometer", + "maximum": 1000, + "minimum": 0, + "title": "Full Flow Rate", + "type": "number" + }, + "n_repeats_per_stimulus": { + "default": 1, + "description": "Number of repeats per stimulus", + "minimum": 1, + "title": "N Repeats Per Stimulus", + "type": "integer" + }, + "time_on": { + "default": 1, + "description": "Time (s) the valve is open during calibration", + "minimum": 0, + "title": "Time On", + "type": "number" + }, + "time_off": { + "default": 1, + "description": "Time (s) the valve is close during calibration", + "minimum": 0, + "title": "Time Off", + "type": "number" + } + }, + "title": "OlfactometerCalibrationParameters", + "type": "object" + }, + "OlfactometerCalibrationRig": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.13.6", + "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-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.2.0rc0", + "default": "0.2.0rc0", + "title": "Version", + "type": "string" + }, + "computer_name": { + "description": "Computer name", + "title": "Computer Name", + "type": "string" + }, + "rig_name": { + "description": "Rig name", + "title": "Rig Name", + "type": "string" + }, + "data_directory": { + "description": "Directory where data will be saved to", + "format": "path", + "title": "Data Directory", + "type": "string" + }, + "harp_olfactometer": { + "$ref": "#/$defs/Olfactometer", + "title": "Olfactometer device" + }, + "harp_analog_input": { + "$ref": "#/$defs/HarpAnalogInput", + "title": "Analog input device" + }, + "harp_clock_generator": { + "$ref": "#/$defs/HarpWhiteRabbit", + "title": "Clock generator device" + }, + "harp_manipulator": { + "$ref": "#/$defs/AindManipulator", + "description": "Manipulator" + }, + "flowmeter": { + "default": null, + "description": "Alicat flowmeter device", + "oneOf": [ + { + "$ref": "#/$defs/AlicatFlowmeter" + }, + { + "type": "null" + } + ] + } + }, + "required": [ + "computer_name", + "rig_name", + "data_directory", + "harp_olfactometer", + "harp_analog_input", + "harp_clock_generator", + "harp_manipulator" + ], + "title": "OlfactometerCalibrationRig", + "type": "object" + }, + "OlfactometerChannel": { + "description": "Harp Olfactometer available channel", + "enum": [ + 0, + 1, + 2, + 3 + ], + "title": "OlfactometerChannel", + "type": "integer", + "x-enumNames": [ + "Channel0", + "Channel1", + "Channel2", + "Channel3" + ] + }, + "OlfactometerChannelConfig": { + "description": "Configuration for a single olfactometer channel", + "properties": { + "channel_index": { + "title": "Odor channel index", + "type": "integer" + }, + "channel_type": { + "$ref": "#/$defs/OlfactometerChannelType", + "default": "Odor", + "title": "Olfactometer channel type" + }, + "flow_rate_capacity": { + "default": 100, + "enum": [ + 100, + 1000 + ], + "title": "Flow capacity. mL/min", + "type": "integer" + }, + "flow_rate": { + "default": 100, + "maximum": 100, + "title": "Target flow rate. mL/min. If channel_type == CARRIER, this value is ignored.", + "type": "number" + }, + "odorant": { + "default": null, + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Odorant name" + }, + "odorant_dilution": { + "default": null, + "oneOf": [ + { + "type": "number" + }, + { + "type": "null" + } + ], + "title": "Odorant dilution (%v/v)" + } + }, + "required": [ + "channel_index" + ], + "title": "OlfactometerChannelConfig", + "type": "object" + }, + "OlfactometerChannelType": { + "description": "Olfactometer channel type", + "enum": [ + "Odor", + "Carrier" + ], + "title": "OlfactometerChannelType", + "type": "string" + }, + "Session": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.13.6", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.13.6", + "default": "0.13.6", + "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" + } + } +} \ No newline at end of file diff --git a/scripts/aind_launcher.py b/scripts/aind_launcher.py new file mode 100644 index 0000000..ae41fe8 --- /dev/null +++ b/scripts/aind_launcher.py @@ -0,0 +1,126 @@ +import logging +from pathlib import Path + +import clabe.resource_monitor +from aind_behavior_services.session import Session +from clabe.apps import ( + AindBehaviorServicesBonsaiApp, +) +from clabe.data_transfer.robocopy import RobocopyService, RobocopySettings +from clabe.launcher import Launcher, LauncherCliArgs, experiment +from clabe.pickers import DefaultBehaviorPicker, DefaultBehaviorPickerSettings +from pydantic_settings import CliApp + +from aind_behavior_device_olfactometer.rig import OlfactometerCalibrationRig +from aind_behavior_device_olfactometer.task_logic import OlfactometerCalibrationLogic + +logger = logging.getLogger(__name__) + + +@experiment() +async def calibration_experiment(launcher: Launcher) -> None: + # Start experiment setup + picker = DefaultBehaviorPicker( + launcher=launcher, + settings=DefaultBehaviorPickerSettings( + config_library_dir=r"\\allen\aind\scratch\AindBehavior.db\AindBehaviorDeviceOlfactometer", + ), + experimenter_validator=None, + ) + + session = picker.pick_session(Session) + task_logic = picker.pick_task(OlfactometerCalibrationLogic) + rig = picker.pick_rig(OlfactometerCalibrationRig) + ensure_rig_and_computer_name(rig) + + launcher.register_session(session, rig.data_directory) + + clabe.resource_monitor.ResourceMonitor( + constrains=[ + clabe.resource_monitor.available_storage_constraint_factory(rig.data_directory, 2e10), + ] + ).run() + + bonsai_app = AindBehaviorServicesBonsaiApp( + workflow=Path(r"./src/main.bonsai"), + temp_directory=launcher.temp_dir, + rig=rig, + session=session, + task=task_logic, + ) + await bonsai_app.run_async() + + # 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 aind_behavior_device_olfactometer import data_contract + from aind_behavior_device_olfactometer.data_qc.data_qc import make_qc_runner + + vr_dataset = data_contract.dataset(launcher.session_directory) + runner = make_qc_runner(vr_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(f"Failed to run data QC: {e}") + + # Transfer data + is_transfer = picker.ui_helper.prompt_yes_no_question("Would you like to transfer data?") + if not is_transfer: + logger.info("Data transfer skipped by user.") + return + + launcher.copy_logs() + RobocopyService(source=launcher.session_directory, settings=RobocopySettings()).transfer() + return + + +def ensure_rig_and_computer_name(rig: OlfactometerCalibrationRig) -> None: + """Ensures rig and computer name are set from environment variables if available, otherwise defaults to rig configuration values.""" + + import os + + rig_name = os.environ.get("aibs_comp_id", None) + computer_name = os.environ.get("hostname", None) + + if rig_name is None: + logger.warning( + "'aibs_comp_id' environment variable not set. Defaulting to rig name from configuration. %s", rig.rig_name + ) + rig_name = rig.rig_name + if computer_name is None: + computer_name = rig.computer_name + logger.warning( + "'hostname' environment variable not set. Defaulting to computer name from configuration. %s", + rig.computer_name, + ) + + if rig_name != rig.rig_name or computer_name != rig.computer_name: + logger.warning( + "Rig name or computer name from environment variables do not match the rig configuration. " + "Forcing rig name: %s and computer name: %s from environment variables.", + rig_name, + computer_name, + ) + rig.rig_name = rig_name + rig.computer_name = computer_name + + +class ClabeCli(LauncherCliArgs): + def cli_cmd(self): + launcher = Launcher(settings=self) + launcher.run_experiment(calibration_experiment) + return None + + +def main() -> None: + CliApp().run(ClabeCli) + + +if __name__ == "__main__": + main() diff --git a/src/Extensions.csproj b/src/Extensions.csproj index 9219f12..19ffa04 100644 --- a/src/Extensions.csproj +++ b/src/Extensions.csproj @@ -7,6 +7,10 @@ + + + + \ No newline at end of file diff --git a/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs b/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs index c694092..6780cbd 100644 --- a/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs +++ b/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs @@ -5,835 +5,11 @@ //---------------------- -namespace AindBehaviorDeviceOlfactometer +namespace AindBehaviorDeviceOlfactometerDataSchema { #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 = "0.12.0"; - _version = "0.3.1"; - _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; - _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 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(); - } - } - - - /// - /// Aind manipulator calibration class - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Aind manipulator calibration class")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class AindManipulatorCalibration - { - - private string _deviceName; - - private AindManipulatorCalibrationInput _input; - - private AindManipulatorCalibrationOutput _output; - - private System.DateTimeOffset? _date; - - private string _description; - - private string _notes; - - public AindManipulatorCalibration() - { - _deviceName = "AindManipulator"; - _input = new AindManipulatorCalibrationInput(); - _output = new AindManipulatorCalibrationOutput(); - _description = "Calibration of the load cells system"; - } - - protected AindManipulatorCalibration(AindManipulatorCalibration other) - { - _deviceName = other._deviceName; - _input = other._input; - _output = other._output; - _date = other._date; - _description = other._description; - _notes = other._notes; - } - - /// - /// Must match a device name in rig/instrument - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Must match a device name in rig/instrument")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("input", Required=Newtonsoft.Json.Required.Always)] - public AindManipulatorCalibrationInput Input - { - get - { - return _input; - } - set - { - _input = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("output", Required=Newtonsoft.Json.Required.Always)] - public AindManipulatorCalibrationOutput Output - { - get - { - return _output; - } - set - { - _output = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("date")] - public System.DateTimeOffset? Date - { - get - { - return _date; - } - set - { - _date = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("description")] - public string Description - { - get - { - return _description; - } - set - { - _description = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("notes")] - public string Notes - { - get - { - return _notes; - } - set - { - _notes = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibration(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibration(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("DeviceName = " + _deviceName + ", "); - stringBuilder.Append("Input = " + _input + ", "); - stringBuilder.Append("Output = " + _output + ", "); - stringBuilder.Append("Date = " + _date + ", "); - stringBuilder.Append("Description = " + _description + ", "); - stringBuilder.Append("Notes = " + _notes); - 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 AindManipulatorCalibrationInput - { - - private ManipulatorPosition _fullStepToMm; - - private System.Collections.Generic.List _axisConfiguration; - - private System.Collections.Generic.List _homingOrder; - - private ManipulatorPosition _initialPosition; - - public AindManipulatorCalibrationInput() - { - _fullStepToMm = new ManipulatorPosition(); - _axisConfiguration = new System.Collections.Generic.List(); - _homingOrder = new System.Collections.Generic.List(); - _initialPosition = new ManipulatorPosition(); - } - - protected AindManipulatorCalibrationInput(AindManipulatorCalibrationInput other) - { - _fullStepToMm = other._fullStepToMm; - _axisConfiguration = other._axisConfiguration; - _homingOrder = other._homingOrder; - _initialPosition = other._initialPosition; - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("full_step_to_mm")] - public ManipulatorPosition FullStepToMm - { - get - { - return _fullStepToMm; - } - set - { - _fullStepToMm = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("axis_configuration")] - public System.Collections.Generic.List AxisConfiguration - { - get - { - return _axisConfiguration; - } - set - { - _axisConfiguration = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("homing_order")] - public System.Collections.Generic.List HomingOrder - { - get - { - return _homingOrder; - } - set - { - _homingOrder = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("initial_position")] - public ManipulatorPosition InitialPosition - { - get - { - return _initialPosition; - } - set - { - _initialPosition = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibrationInput(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibrationInput(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("FullStepToMm = " + _fullStepToMm + ", "); - stringBuilder.Append("AxisConfiguration = " + _axisConfiguration + ", "); - stringBuilder.Append("HomingOrder = " + _homingOrder + ", "); - stringBuilder.Append("InitialPosition = " + _initialPosition); - 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 AindManipulatorCalibrationOutput - { - - public AindManipulatorCalibrationOutput() - { - } - - protected AindManipulatorCalibrationOutput(AindManipulatorCalibrationOutput other) - { - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibrationOutput(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibrationOutput(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 AindManipulatorDevice - { - - private string _deviceType; - - private string _deviceName; - - private BaseModel _additionalSettings; - - private AindManipulatorCalibration _calibration; - - private int _whoAmI; - - private string _serialNumber; - - private string _portName; - - public AindManipulatorDevice() - { - _deviceType = "StepperDriver"; - _whoAmI = 1130; - } - - protected AindManipulatorDevice(AindManipulatorDevice 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; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - public AindManipulatorCalibration 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 _serialNumber; - } - set - { - _serialNumber = value; - } - } - - /// - /// Device port name - /// - [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device port name")] - public string PortName - { - get - { - return _portName; - } - set - { - _portName = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorDevice(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorDevice(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); - 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)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class AlicatFlowmeter @@ -841,10 +17,6 @@ public partial class AlicatFlowmeter private string _deviceType; - private string _deviceName; - - private BaseModel _additionalSettings; - private BaseModel _calibration; private string _portName; @@ -859,380 +31,115 @@ public AlicatFlowmeter() _deviceId = "A"; _poolingPeriod = 0.2D; } - - protected AlicatFlowmeter(AlicatFlowmeter other) - { - _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; - _calibration = other._calibration; - _portName = other._portName; - _deviceId = other._deviceId; - _poolingPeriod = other._poolingPeriod; - } - - [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; - } - } - - /// - /// Device port name - /// - [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device port name")] - public string PortName - { - get - { - return _portName; - } - set - { - _portName = value; - } - } - - /// - /// Alicat device ID - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_id")] - [System.ComponentModel.DescriptionAttribute("Alicat device ID")] - public string DeviceId - { - get - { - return _deviceId; - } - set - { - _deviceId = value; - } - } - - /// - /// Device pooling interval in seconds - /// - [Newtonsoft.Json.JsonPropertyAttribute("pooling_period")] - [System.ComponentModel.DescriptionAttribute("Device pooling interval in seconds")] - public double PoolingPeriod - { - get - { - return _poolingPeriod; - } - set - { - _poolingPeriod = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AlicatFlowmeter(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AlicatFlowmeter(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("PortName = " + _portName + ", "); - stringBuilder.Append("DeviceId = " + _deviceId + ", "); - stringBuilder.Append("PoolingPeriod = " + _poolingPeriod); - 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(); - } - } - - - /// - /// Motor axis available - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - public enum Axis - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - None = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - X = 1, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] - Y1 = 2, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] - Y2 = 3, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="4")] - Z = 4, - } - - - /// - /// Axis configuration - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Axis configuration")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class AxisConfiguration - { - - private Axis _axis; - - private int _stepAccelerationInterval; - - private int _stepInterval; - - private MicrostepResolution _microstepResolution; - - private int _maximumStepInterval; - - private MotorOperationMode _motorOperationMode; - - private double _maxLimit; - - private double _minLimit; - - public AxisConfiguration() - { - _stepAccelerationInterval = 100; - _stepInterval = 100; - _microstepResolution = AindBehaviorDeviceOlfactometer.MicrostepResolution.Microstep8; - _maximumStepInterval = 2000; - _motorOperationMode = AindBehaviorDeviceOlfactometer.MotorOperationMode.Quiet; - _maxLimit = 25D; - _minLimit = -0.01D; - } - - protected AxisConfiguration(AxisConfiguration other) - { - _axis = other._axis; - _stepAccelerationInterval = other._stepAccelerationInterval; - _stepInterval = other._stepInterval; - _microstepResolution = other._microstepResolution; - _maximumStepInterval = other._maximumStepInterval; - _motorOperationMode = other._motorOperationMode; - _maxLimit = other._maxLimit; - _minLimit = other._minLimit; - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("axis", Required=Newtonsoft.Json.Required.Always)] - public Axis Axis - { - get - { - return _axis; - } - set - { - _axis = value; - } - } - - /// - /// Acceleration of the step interval in microseconds - /// - [Newtonsoft.Json.JsonPropertyAttribute("step_acceleration_interval")] - [System.ComponentModel.DescriptionAttribute("Acceleration of the step interval in microseconds")] - public int StepAccelerationInterval - { - get - { - return _stepAccelerationInterval; - } - set - { - _stepAccelerationInterval = value; - } - } - - /// - /// Step interval in microseconds. - /// - [Newtonsoft.Json.JsonPropertyAttribute("step_interval")] - [System.ComponentModel.DescriptionAttribute("Step interval in microseconds.")] - public int StepInterval - { - get - { - return _stepInterval; - } - set - { - _stepInterval = value; - } + + protected AlicatFlowmeter(AlicatFlowmeter other) + { + _deviceType = other._deviceType; + _calibration = other._calibration; + _portName = other._portName; + _deviceId = other._deviceId; + _poolingPeriod = other._poolingPeriod; } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("microstep_resolution")] - public MicrostepResolution MicrostepResolution + [Newtonsoft.Json.JsonPropertyAttribute("device_type")] + public string DeviceType { get { - return _microstepResolution; + return _deviceType; } set { - _microstepResolution = value; + _deviceType = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("maximum_step_interval")] - public int MaximumStepInterval + /// + /// Calibration for the device. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration for the device.")] + public BaseModel Calibration { get { - return _maximumStepInterval; + return _calibration; } set { - _maximumStepInterval = value; + _calibration = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("motor_operation_mode")] - public MotorOperationMode MotorOperationMode + /// + /// Device port name + /// + [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Device port name")] + public string PortName { get { - return _motorOperationMode; + return _portName; } set { - _motorOperationMode = value; + _portName = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("max_limit")] - public double MaxLimit + /// + /// Alicat device ID + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_id")] + [System.ComponentModel.DescriptionAttribute("Alicat device ID")] + public string DeviceId { get { - return _maxLimit; + return _deviceId; } set { - _maxLimit = value; + _deviceId = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("min_limit")] - public double MinLimit + /// + /// Device pooling interval in seconds + /// + [Newtonsoft.Json.JsonPropertyAttribute("pooling_period")] + [System.ComponentModel.DescriptionAttribute("Device pooling interval in seconds")] + public double PoolingPeriod { get { - return _minLimit; + return _poolingPeriod; } set { - _minLimit = value; + _poolingPeriod = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AxisConfiguration(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AlicatFlowmeter(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new AxisConfiguration(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new AlicatFlowmeter(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("Axis = " + _axis + ", "); - stringBuilder.Append("StepAccelerationInterval = " + _stepAccelerationInterval + ", "); - stringBuilder.Append("StepInterval = " + _stepInterval + ", "); - stringBuilder.Append("MicrostepResolution = " + _microstepResolution + ", "); - stringBuilder.Append("MaximumStepInterval = " + _maximumStepInterval + ", "); - stringBuilder.Append("MotorOperationMode = " + _motorOperationMode + ", "); - stringBuilder.Append("MaxLimit = " + _maxLimit + ", "); - stringBuilder.Append("MinLimit = " + _minLimit); + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("PortName = " + _portName + ", "); + stringBuilder.Append("DeviceId = " + _deviceId + ", "); + stringBuilder.Append("PoolingPeriod = " + _poolingPeriod); return true; } @@ -1251,7 +158,7 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class BaseModel @@ -1295,7 +202,7 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class ConnectedClockOutput @@ -1381,7 +288,7 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class HarpAnalogInput @@ -1389,10 +296,6 @@ public partial class HarpAnalogInput private string _deviceType; - private string _deviceName; - - private BaseModel _additionalSettings; - private BaseModel _calibration; private int _whoAmI; @@ -1410,8 +313,6 @@ public HarpAnalogInput() protected HarpAnalogInput(HarpAnalogInput other) { _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; _calibration = other._calibration; _whoAmI = other._whoAmI; _serialNumber = other._serialNumber; @@ -1432,46 +333,11 @@ 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 - /// - [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 @@ -1544,8 +410,6 @@ 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("Calibration = " + _calibration + ", "); stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); @@ -1568,7 +432,7 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] public partial class HarpWhiteRabbit @@ -1576,10 +440,6 @@ public partial class HarpWhiteRabbit private string _deviceType; - private string _deviceName; - - private BaseModel _additionalSettings; - private BaseModel _calibration; private int _whoAmI; @@ -1600,8 +460,6 @@ public HarpWhiteRabbit() protected HarpWhiteRabbit(HarpWhiteRabbit other) { _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; _calibration = other._calibration; _whoAmI = other._whoAmI; _serialNumber = other._serialNumber; @@ -1623,46 +481,11 @@ 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 - /// - [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 @@ -1753,8 +576,6 @@ 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("Calibration = " + _calibration + ", "); stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); @@ -1778,100 +599,133 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + /// + /// A calibrated olfactometer device + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("A calibrated olfactometer device")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class ManipulatorPosition + public partial class Olfactometer { - private double _x; + private string _deviceType; + + private OlfactometerCalibration _calibration; + + private int _whoAmI; - private double _y1; + private string _serialNumber; - private double _y2; + private string _portName; - private double _z; + public Olfactometer() + { + _deviceType = "Olfactometer"; + _calibration = new OlfactometerCalibration(); + _whoAmI = 1140; + } - public ManipulatorPosition() + protected Olfactometer(Olfactometer other) { + _deviceType = other._deviceType; + _calibration = other._calibration; + _whoAmI = other._whoAmI; + _serialNumber = other._serialNumber; + _portName = other._portName; } - protected ManipulatorPosition(ManipulatorPosition other) + [Newtonsoft.Json.JsonPropertyAttribute("device_type")] + public string DeviceType { - _x = other._x; - _y1 = other._y1; - _y2 = other._y2; - _z = other._z; + get + { + return _deviceType; + } + set + { + _deviceType = value; + } } - [Newtonsoft.Json.JsonPropertyAttribute("x", Required=Newtonsoft.Json.Required.Always)] - public double X + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + public OlfactometerCalibration Calibration { get { - return _x; + return _calibration; } set { - _x = value; + _calibration = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("y1", Required=Newtonsoft.Json.Required.Always)] - public double Y1 + [Newtonsoft.Json.JsonPropertyAttribute("who_am_i")] + public int WhoAmI { get { - return _y1; + return _whoAmI; } set { - _y1 = value; + _whoAmI = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("y2", Required=Newtonsoft.Json.Required.Always)] - public double Y2 + /// + /// Device serial number + /// + [Newtonsoft.Json.JsonPropertyAttribute("serial_number")] + [System.ComponentModel.DescriptionAttribute("Device serial number")] + public string SerialNumber { get { - return _y2; + return _serialNumber; } set { - _y2 = value; + _serialNumber = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("z", Required=Newtonsoft.Json.Required.Always)] - public double Z + /// + /// Device port name + /// + [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Device port name")] + public string PortName { get { - return _z; + return _portName; } set { - _z = value; + _portName = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ManipulatorPosition(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Olfactometer(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new ManipulatorPosition(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new Olfactometer(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("X = " + _x + ", "); - stringBuilder.Append("Y1 = " + _y1 + ", "); - stringBuilder.Append("Y2 = " + _y2 + ", "); - stringBuilder.Append("Z = " + _z); + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("PortName = " + _portName); return true; } @@ -1890,201 +744,228 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - public enum MicrostepResolution + /// + /// Olfactometer device configuration model + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Olfactometer device configuration model")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class OlfactometerCalibration { - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Microstep8 = 0, + private System.DateTimeOffset? _date; - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - Microstep16 = 1, + private System.Collections.Generic.Dictionary _channelConfig; - [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] - Microstep32 = 2, + public OlfactometerCalibration() + { + _channelConfig = new System.Collections.Generic.Dictionary(); + } - [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] - Microstep64 = 3, - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - public enum MotorOperationMode - { + protected OlfactometerCalibration(OlfactometerCalibration other) + { + _date = other._date; + _channelConfig = other._channelConfig; + } - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Quiet = 0, + /// + /// Date of the calibration + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("date")] + [System.ComponentModel.DescriptionAttribute("Date of the calibration")] + public System.DateTimeOffset? Date + { + get + { + return _date; + } + set + { + _date = value; + } + } - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - Dynamic = 1, + /// + /// Configuration of olfactometer channels + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("channel_config")] + [System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")] + public System.Collections.Generic.Dictionary ChannelConfig + { + get + { + return _channelConfig; + } + set + { + _channelConfig = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibration(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibration(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Date = " + _date + ", "); + stringBuilder.Append("ChannelConfig = " + _channelConfig); + 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)")] + /// + /// Olfactometer operation control model that is used to run a calibration data acquisition workflow + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Olfactometer operation control model that is used to run a calibration data acqui" + + "sition workflow")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class Olfactometer + public partial class OlfactometerCalibrationLogic { - private string _deviceType; - - private string _deviceName; - - private BaseModel _additionalSettings; - - private OlfactometerCalibration _calibration; + private string _name; - private int _whoAmI; + private string _description; - private string _serialNumber; + private OlfactometerCalibrationParameters _taskParameters; - private string _portName; + private string _version; - public Olfactometer() - { - _deviceType = "Olfactometer"; - _whoAmI = 1140; - } + private string _stageName; - protected Olfactometer(Olfactometer other) + public OlfactometerCalibrationLogic() { - _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; - _calibration = other._calibration; - _whoAmI = other._whoAmI; - _serialNumber = other._serialNumber; - _portName = other._portName; + _name = "OlfactometerCalibration"; + _description = ""; + _taskParameters = new OlfactometerCalibrationParameters(); + _version = "0.2.0-rc0"; } - [Newtonsoft.Json.JsonPropertyAttribute("device_type")] - public string DeviceType + protected OlfactometerCalibrationLogic(OlfactometerCalibrationLogic other) { - get - { - return _deviceType; - } - set - { - _deviceType = value; - } + _name = other._name; + _description = other._description; + _taskParameters = other._taskParameters; + _version = other._version; + _stageName = other._stageName; } - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName + [Newtonsoft.Json.JsonPropertyAttribute("name")] + public string Name { get { - return _deviceName; + return _name; } set { - _deviceName = value; + _name = value; } } /// - /// Additional settings + /// Description of the task. /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings + [Newtonsoft.Json.JsonPropertyAttribute("description")] + [System.ComponentModel.DescriptionAttribute("Description of the task.")] + public string Description { get { - return _additionalSettings; + return _description; } set { - _additionalSettings = value; + _description = value; } } [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - public OlfactometerCalibration Calibration - { - get - { - return _calibration; - } - set - { - _calibration = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("who_am_i")] - public int WhoAmI + [Newtonsoft.Json.JsonPropertyAttribute("task_parameters", Required=Newtonsoft.Json.Required.Always)] + public OlfactometerCalibrationParameters TaskParameters { get { - return _whoAmI; + return _taskParameters; } set { - _whoAmI = value; + _taskParameters = value; } } - /// - /// Device serial number - /// - [Newtonsoft.Json.JsonPropertyAttribute("serial_number")] - [System.ComponentModel.DescriptionAttribute("Device serial number")] - public string SerialNumber + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version { get { - return _serialNumber; + return _version; } set { - _serialNumber = value; + _version = value; } } /// - /// Device port name + /// Optional stage name the `Task` object instance represents. /// - [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device port name")] - public string PortName + [Newtonsoft.Json.JsonPropertyAttribute("stage_name")] + [System.ComponentModel.DescriptionAttribute("Optional stage name the `Task` object instance represents.")] + public string StageName { get { - return _portName; + return _stageName; } set { - _portName = value; + _stageName = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Olfactometer(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationLogic(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new Olfactometer(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationLogic(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("Name = " + _name + ", "); + stringBuilder.Append("Description = " + _description + ", "); + stringBuilder.Append("TaskParameters = " + _taskParameters + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("StageName = " + _stageName); return true; } @@ -2103,216 +984,181 @@ public override string ToString() } - /// - /// Olfactometer calibration class - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Olfactometer calibration class")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class OlfactometerCalibration + public partial class OlfactometerCalibrationParameters { - private string _deviceName; + private double? _rngSeed; - private OlfactometerCalibrationInput _input; + private string _aindBehaviorServicesPkgVersion; - private OlfactometerCalibrationOutput _output; + private System.Collections.Generic.Dictionary _channelConfig; - private System.DateTimeOffset? _date; + private double _fullFlowRate; - private string _description; + private int _nRepeatsPerStimulus; - private string _notes; + private double _timeOn; - public OlfactometerCalibration() + private double _timeOff; + + public OlfactometerCalibrationParameters() { - _deviceName = "Olfactometer"; - _input = new OlfactometerCalibrationInput(); - _output = new OlfactometerCalibrationOutput(); - _description = "Calibration of the harp olfactometer device"; + _aindBehaviorServicesPkgVersion = "0.13.6"; + _fullFlowRate = 1000D; + _nRepeatsPerStimulus = 1; + _timeOn = 1D; + _timeOff = 1D; } - protected OlfactometerCalibration(OlfactometerCalibration other) + protected OlfactometerCalibrationParameters(OlfactometerCalibrationParameters other) { - _deviceName = other._deviceName; - _input = other._input; - _output = other._output; - _date = other._date; - _description = other._description; - _notes = other._notes; + _rngSeed = other._rngSeed; + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _channelConfig = other._channelConfig; + _fullFlowRate = other._fullFlowRate; + _nRepeatsPerStimulus = other._nRepeatsPerStimulus; + _timeOn = other._timeOn; + _timeOff = other._timeOff; } /// - /// Name of the device being calibrated + /// Seed of the random number generator /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Name of the device being calibrated")] - public string DeviceName + [Newtonsoft.Json.JsonPropertyAttribute("rng_seed")] + [System.ComponentModel.DescriptionAttribute("Seed of the random number generator")] + public double? RngSeed { get { - return _deviceName; + return _rngSeed; } set { - _deviceName = value; + _rngSeed = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("input", Required=Newtonsoft.Json.Required.Always)] - public OlfactometerCalibrationInput Input + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion { get { - return _input; + return _aindBehaviorServicesPkgVersion; } set { - _input = value; + _aindBehaviorServicesPkgVersion = value; } } + /// + /// Configuration of olfactometer channels + /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("output", Required=Newtonsoft.Json.Required.Always)] - public OlfactometerCalibrationOutput Output + [Newtonsoft.Json.JsonPropertyAttribute("channel_config")] + [System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")] + public System.Collections.Generic.Dictionary ChannelConfig { get { - return _output; + return _channelConfig; } set { - _output = value; + _channelConfig = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("date")] - public System.DateTimeOffset? Date + /// + /// Full flow rate of the olfactometer + /// + [Newtonsoft.Json.JsonPropertyAttribute("full_flow_rate")] + [System.ComponentModel.DescriptionAttribute("Full flow rate of the olfactometer")] + public double FullFlowRate { get { - return _date; + return _fullFlowRate; } set { - _date = value; + _fullFlowRate = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("description")] - public string Description + /// + /// Number of repeats per stimulus + /// + [Newtonsoft.Json.JsonPropertyAttribute("n_repeats_per_stimulus")] + [System.ComponentModel.DescriptionAttribute("Number of repeats per stimulus")] + public int NRepeatsPerStimulus { get { - return _description; + return _nRepeatsPerStimulus; } set { - _description = value; + _nRepeatsPerStimulus = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("notes")] - public string Notes + /// + /// Time (s) the valve is open during calibration + /// + [Newtonsoft.Json.JsonPropertyAttribute("time_on")] + [System.ComponentModel.DescriptionAttribute("Time (s) the valve is open during calibration")] + public double TimeOn { get { - return _notes; + return _timeOn; } set { - _notes = value; - } - } - - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibration(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibration(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("DeviceName = " + _deviceName + ", "); - stringBuilder.Append("Input = " + _input + ", "); - stringBuilder.Append("Output = " + _output + ", "); - stringBuilder.Append("Date = " + _date + ", "); - stringBuilder.Append("Description = " + _description + ", "); - stringBuilder.Append("Notes = " + _notes); - 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 OlfactometerCalibrationInput - { - - private System.Collections.Generic.Dictionary _channelConfig; - - public OlfactometerCalibrationInput() - { - _channelConfig = new System.Collections.Generic.Dictionary(); - } - - protected OlfactometerCalibrationInput(OlfactometerCalibrationInput other) - { - _channelConfig = other._channelConfig; + _timeOn = value; + } } /// - /// Configuration of olfactometer channels + /// Time (s) the valve is close during calibration /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("channel_config")] - [System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")] - public System.Collections.Generic.Dictionary ChannelConfig + [Newtonsoft.Json.JsonPropertyAttribute("time_off")] + [System.ComponentModel.DescriptionAttribute("Time (s) the valve is close during calibration")] + public double TimeOff { get { - return _channelConfig; + return _timeOff; } set { - _channelConfig = value; + _timeOff = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationInput(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationParameters(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationInput(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationParameters(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("ChannelConfig = " + _channelConfig); + stringBuilder.Append("RngSeed = " + _rngSeed + ", "); + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("ChannelConfig = " + _channelConfig + ", "); + stringBuilder.Append("FullFlowRate = " + _fullFlowRate + ", "); + stringBuilder.Append("NRepeatsPerStimulus = " + _nRepeatsPerStimulus + ", "); + stringBuilder.Append("TimeOn = " + _timeOn + ", "); + stringBuilder.Append("TimeOff = " + _timeOff); return true; } @@ -2331,180 +1177,234 @@ public override string ToString() } - /// - /// Olfactometer operation control model that is used to run a calibration data acquisition workflow - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Olfactometer operation control model that is used to run a calibration data acqui" + - "sition workflow")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class OlfactometerCalibrationLogic + public partial class OlfactometerCalibrationRig { - private string _name; + private string _aindBehaviorServicesPkgVersion; - private string _description; + private string _version; - private OlfactometerCalibrationParameters _taskParameters; + private string _computerName; - private string _version; + private string _rigName; - private string _stageName; + private string _dataDirectory; - public OlfactometerCalibrationLogic() + private Olfactometer _harpOlfactometer; + + private HarpAnalogInput _harpAnalogInput; + + private HarpWhiteRabbit _harpClockGenerator; + + private AllenNeuralDynamics.AindManipulator.AindManipulator _harpManipulator; + + private AlicatFlowmeter _flowmeter; + + public OlfactometerCalibrationRig() { - _name = "OlfactometerCalibration"; - _description = ""; - _taskParameters = new OlfactometerCalibrationParameters(); - _version = "0.3.0"; + _aindBehaviorServicesPkgVersion = "0.13.6"; + _version = "0.2.0-rc0"; + _harpOlfactometer = new Olfactometer(); + _harpAnalogInput = new HarpAnalogInput(); + _harpClockGenerator = new HarpWhiteRabbit(); + _harpManipulator = new AllenNeuralDynamics.AindManipulator.AindManipulator(); } - protected OlfactometerCalibrationLogic(OlfactometerCalibrationLogic other) + protected OlfactometerCalibrationRig(OlfactometerCalibrationRig other) { - _name = other._name; - _description = other._description; - _taskParameters = other._taskParameters; + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; _version = other._version; - _stageName = other._stageName; + _computerName = other._computerName; + _rigName = other._rigName; + _dataDirectory = other._dataDirectory; + _harpOlfactometer = other._harpOlfactometer; + _harpAnalogInput = other._harpAnalogInput; + _harpClockGenerator = other._harpClockGenerator; + _harpManipulator = other._harpManipulator; + _flowmeter = other._flowmeter; } - [Newtonsoft.Json.JsonPropertyAttribute("name")] - public string Name + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion { get { - return _name; + return _aindBehaviorServicesPkgVersion; } set { - _name = value; + _aindBehaviorServicesPkgVersion = value; } } - /// - /// Description of the task. - /// - [Newtonsoft.Json.JsonPropertyAttribute("description")] - [System.ComponentModel.DescriptionAttribute("Description of the task.")] - public string Description + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version { get { - return _description; + return _version; } set { - _description = value; + _version = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("task_parameters", Required=Newtonsoft.Json.Required.Always)] - public OlfactometerCalibrationParameters TaskParameters + /// + /// Computer name + /// + [Newtonsoft.Json.JsonPropertyAttribute("computer_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Computer name")] + public string ComputerName { get { - return _taskParameters; + return _computerName; } set { - _taskParameters = value; + _computerName = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version + /// + /// Rig name + /// + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Rig name")] + public string RigName { get { - return _version; + return _rigName; } set { - _version = value; + _rigName = value; } } /// - /// Optional stage name the `Task` object instance represents. + /// Directory where data will be saved to /// - [Newtonsoft.Json.JsonPropertyAttribute("stage_name")] - [System.ComponentModel.DescriptionAttribute("Optional stage name the `Task` object instance represents.")] - public string StageName + [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 _stageName; + return _dataDirectory; } set { - _stageName = value; + _dataDirectory = value; } } - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationLogic(this))); - } - - public System.IObservable Generate(System.IObservable source) + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("harp_olfactometer", Required=Newtonsoft.Json.Required.Always)] + public Olfactometer HarpOlfactometer { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationLogic(this)); + get + { + return _harpOlfactometer; + } + set + { + _harpOlfactometer = value; + } } - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("harp_analog_input", Required=Newtonsoft.Json.Required.Always)] + public HarpAnalogInput HarpAnalogInput { - stringBuilder.Append("Name = " + _name + ", "); - stringBuilder.Append("Description = " + _description + ", "); - stringBuilder.Append("TaskParameters = " + _taskParameters + ", "); - stringBuilder.Append("Version = " + _version + ", "); - stringBuilder.Append("StageName = " + _stageName); - return true; + get + { + return _harpAnalogInput; + } + set + { + _harpAnalogInput = value; + } } - public override string ToString() + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("harp_clock_generator", Required=Newtonsoft.Json.Required.Always)] + public HarpWhiteRabbit HarpClockGenerator { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) + get { - stringBuilder.Append(" "); + return _harpClockGenerator; + } + set + { + _harpClockGenerator = 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 OlfactometerCalibrationOutput - { - public OlfactometerCalibrationOutput() + /// + /// Manipulator + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("harp_manipulator", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Manipulator")] + public AllenNeuralDynamics.AindManipulator.AindManipulator HarpManipulator { + get + { + return _harpManipulator; + } + set + { + _harpManipulator = value; + } } - protected OlfactometerCalibrationOutput(OlfactometerCalibrationOutput other) + /// + /// Alicat flowmeter device + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("flowmeter")] + [System.ComponentModel.DescriptionAttribute("Alicat flowmeter device")] + public AlicatFlowmeter Flowmeter { + get + { + return _flowmeter; + } + set + { + _flowmeter = value; + } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationOutput(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationRig(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationOutput(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationRig(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - return false; + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("ComputerName = " + _computerName + ", "); + stringBuilder.Append("RigName = " + _rigName + ", "); + stringBuilder.Append("DataDirectory = " + _dataDirectory + ", "); + stringBuilder.Append("HarpOlfactometer = " + _harpOlfactometer + ", "); + stringBuilder.Append("HarpAnalogInput = " + _harpAnalogInput + ", "); + stringBuilder.Append("HarpClockGenerator = " + _harpClockGenerator + ", "); + stringBuilder.Append("HarpManipulator = " + _harpManipulator + ", "); + stringBuilder.Append("Flowmeter = " + _flowmeter); + return true; } public override string ToString() @@ -2522,183 +1422,162 @@ 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 OlfactometerCalibrationParameters + /// + /// Harp Olfactometer available channel + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] + public enum OlfactometerChannel { - private double? _rngSeed; + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Channel0 = 0, - private string _aindBehaviorServicesPkgVersion; + [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] + Channel1 = 1, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] + Channel2 = 2, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] + Channel3 = 3, + } + + + /// + /// Configuration for a single olfactometer channel + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Configuration for a single olfactometer channel")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class OlfactometerChannelConfig + { - private System.Collections.Generic.Dictionary _channelConfig; + private int _channelIndex; - private double _fullFlowRate; + private OlfactometerChannelType _channelType; - private int _nRepeatsPerStimulus; + private OlfactometerChannelConfigFlowRateCapacity _flowRateCapacity; - private double _timeOn; + private double _flowRate; - private double _timeOff; + private string _odorant; - public OlfactometerCalibrationParameters() - { - _aindBehaviorServicesPkgVersion = "0.12.0"; - _channelConfig = new System.Collections.Generic.Dictionary(); - _fullFlowRate = 1000D; - _nRepeatsPerStimulus = 1; - _timeOn = 1D; - _timeOff = 1D; - } + private double? _odorantDilution; - protected OlfactometerCalibrationParameters(OlfactometerCalibrationParameters other) + public OlfactometerChannelConfig() { - _rngSeed = other._rngSeed; - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _channelConfig = other._channelConfig; - _fullFlowRate = other._fullFlowRate; - _nRepeatsPerStimulus = other._nRepeatsPerStimulus; - _timeOn = other._timeOn; - _timeOff = other._timeOff; + _channelType = OlfactometerChannelType.Odor; + _flowRateCapacity = OlfactometerChannelConfigFlowRateCapacity._100; + _flowRate = 100D; } - /// - /// 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 + protected OlfactometerChannelConfig(OlfactometerChannelConfig other) { - get - { - return _rngSeed; - } - set - { - _rngSeed = value; - } + _channelIndex = other._channelIndex; + _channelType = other._channelType; + _flowRateCapacity = other._flowRateCapacity; + _flowRate = other._flowRate; + _odorant = other._odorant; + _odorantDilution = other._odorantDilution; } - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion + [Newtonsoft.Json.JsonPropertyAttribute("channel_index", Required=Newtonsoft.Json.Required.Always)] + public int ChannelIndex { get { - return _aindBehaviorServicesPkgVersion; + return _channelIndex; } set { - _aindBehaviorServicesPkgVersion = value; + _channelIndex = value; } } - /// - /// Configuration of olfactometer channels - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("channel_config")] - [System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")] - public System.Collections.Generic.Dictionary ChannelConfig + [Newtonsoft.Json.JsonPropertyAttribute("channel_type")] + public OlfactometerChannelType ChannelType { get { - return _channelConfig; + return _channelType; } set { - _channelConfig = value; + _channelType = value; } } - /// - /// Full flow rate of the olfactometer - /// - [Newtonsoft.Json.JsonPropertyAttribute("full_flow_rate")] - [System.ComponentModel.DescriptionAttribute("Full flow rate of the olfactometer")] - public double FullFlowRate + [Newtonsoft.Json.JsonPropertyAttribute("flow_rate_capacity")] + public OlfactometerChannelConfigFlowRateCapacity FlowRateCapacity { get { - return _fullFlowRate; + return _flowRateCapacity; } set { - _fullFlowRate = value; + _flowRateCapacity = value; } } - /// - /// Number of repeats per stimulus - /// - [Newtonsoft.Json.JsonPropertyAttribute("n_repeats_per_stimulus")] - [System.ComponentModel.DescriptionAttribute("Number of repeats per stimulus")] - public int NRepeatsPerStimulus + [Newtonsoft.Json.JsonPropertyAttribute("flow_rate")] + public double FlowRate { get { - return _nRepeatsPerStimulus; + return _flowRate; } set { - _nRepeatsPerStimulus = value; + _flowRate = value; } } - /// - /// Time (s) the valve is open during calibration - /// - [Newtonsoft.Json.JsonPropertyAttribute("time_on")] - [System.ComponentModel.DescriptionAttribute("Time (s) the valve is open during calibration")] - public double TimeOn + [Newtonsoft.Json.JsonPropertyAttribute("odorant")] + public string Odorant { get { - return _timeOn; + return _odorant; } set { - _timeOn = value; + _odorant = value; } } - /// - /// Time (s) the valve is close during calibration - /// - [Newtonsoft.Json.JsonPropertyAttribute("time_off")] - [System.ComponentModel.DescriptionAttribute("Time (s) the valve is close during calibration")] - public double TimeOff + [Newtonsoft.Json.JsonPropertyAttribute("odorant_dilution")] + public double? OdorantDilution { get { - return _timeOff; + return _odorantDilution; } set { - _timeOff = value; + _odorantDilution = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationParameters(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerChannelConfig(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationParameters(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerChannelConfig(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("RngSeed = " + _rngSeed + ", "); - stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("ChannelConfig = " + _channelConfig + ", "); - stringBuilder.Append("FullFlowRate = " + _fullFlowRate + ", "); - stringBuilder.Append("NRepeatsPerStimulus = " + _nRepeatsPerStimulus + ", "); - stringBuilder.Append("TimeOn = " + _timeOn + ", "); - stringBuilder.Append("TimeOff = " + _timeOff); + stringBuilder.Append("ChannelIndex = " + _channelIndex + ", "); + stringBuilder.Append("ChannelType = " + _channelType + ", "); + stringBuilder.Append("FlowRateCapacity = " + _flowRateCapacity + ", "); + stringBuilder.Append("FlowRate = " + _flowRate + ", "); + stringBuilder.Append("Odorant = " + _odorant + ", "); + stringBuilder.Append("OdorantDilution = " + _odorantDilution); return true; } @@ -2717,51 +1596,72 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + /// + /// Olfactometer channel type + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] + [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))] + public enum OlfactometerChannelType + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="Odor")] + Odor = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="Carrier")] + Carrier = 1, + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] [Bonsai.CombinatorAttribute(MethodName="Generate")] - public partial class OlfactometerCalibrationRig + 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 Olfactometer _harpOlfactometer; + private System.DateTimeOffset _date; - private HarpAnalogInput _harpAnalogInput; + private string _sessionName; - private HarpWhiteRabbit _harpClockGenerator; + private string _subject; - private AindManipulatorDevice _harpManipulator; + private string _notes; - private AlicatFlowmeter _flowmeter; + private string _commitHash; - public OlfactometerCalibrationRig() + private bool _allowDirtyRepo; + + private bool _skipHardwareValidation; + + public Session() { - _aindBehaviorServicesPkgVersion = "0.12.0"; - _version = "0.3.0"; - _harpOlfactometer = new Olfactometer(); - _harpAnalogInput = new HarpAnalogInput(); - _harpClockGenerator = new HarpWhiteRabbit(); - _harpManipulator = new AindManipulatorDevice(); + _aindBehaviorServicesPkgVersion = "0.13.6"; + _version = "0.13.6"; + _experimenter = new System.Collections.Generic.List(); + _allowDirtyRepo = false; + _skipHardwareValidation = false; } - protected OlfactometerCalibrationRig(OlfactometerCalibrationRig other) + protected Session(Session other) { _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; _version = other._version; - _computerName = other._computerName; - _rigName = other._rigName; - _harpOlfactometer = other._harpOlfactometer; - _harpAnalogInput = other._harpAnalogInput; - _harpClockGenerator = other._harpClockGenerator; - _harpManipulator = other._harpManipulator; - _flowmeter = other._flowmeter; + _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")] @@ -2791,311 +1691,200 @@ public string Version } /// - /// Computer name - /// - [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] - [System.ComponentModel.DescriptionAttribute("Computer name")] - public string ComputerName - { - get - { - return _computerName; - } - set - { - _computerName = value; - } - } - - /// - /// Rig name + /// Name of the experiment /// - [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Rig name")] - public string RigName - { - get - { - return _rigName; - } - set - { - _rigName = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_olfactometer", Required=Newtonsoft.Json.Required.Always)] - public Olfactometer HarpOlfactometer - { - get - { - return _harpOlfactometer; - } - set - { - _harpOlfactometer = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_analog_input", Required=Newtonsoft.Json.Required.Always)] - public HarpAnalogInput HarpAnalogInput - { - get - { - return _harpAnalogInput; - } - set - { - _harpAnalogInput = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_clock_generator", Required=Newtonsoft.Json.Required.Always)] - public HarpWhiteRabbit HarpClockGenerator + [Newtonsoft.Json.JsonPropertyAttribute("experiment")] + [System.ComponentModel.DescriptionAttribute("Name of the experiment")] + public string Experiment { get { - return _harpClockGenerator; + return _experiment; } set { - _harpClockGenerator = value; + _experiment = value; } } /// - /// Manipulator + /// Name of the experimenter /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_manipulator", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Manipulator")] - public AindManipulatorDevice HarpManipulator + [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] + [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] + public System.Collections.Generic.List Experimenter { get { - return _harpManipulator; + return _experimenter; } set { - _harpManipulator = value; + _experimenter = value; } } /// - /// Alicat flowmeter device + /// Date of the experiment /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("flowmeter")] - [System.ComponentModel.DescriptionAttribute("Alicat flowmeter device")] - public AlicatFlowmeter Flowmeter + [Newtonsoft.Json.JsonPropertyAttribute("date")] + [System.ComponentModel.DescriptionAttribute("Date of the experiment")] + public System.DateTimeOffset Date { get { - return _flowmeter; + return _date; } set { - _flowmeter = value; + _date = value; } } - public System.IObservable Generate() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationRig(this))); - } - - public System.IObservable Generate(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationRig(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("HarpOlfactometer = " + _harpOlfactometer + ", "); - stringBuilder.Append("HarpAnalogInput = " + _harpAnalogInput + ", "); - stringBuilder.Append("HarpClockGenerator = " + _harpClockGenerator + ", "); - stringBuilder.Append("HarpManipulator = " + _harpManipulator + ", "); - stringBuilder.Append("Flowmeter = " + _flowmeter); - return true; - } - - public override string ToString() + [Newtonsoft.Json.JsonIgnoreAttribute()] + [System.ComponentModel.BrowsableAttribute(false)] + [System.ComponentModel.EditorBrowsableAttribute(System.ComponentModel.EditorBrowsableState.Never)] + [System.Xml.Serialization.XmlElementAttribute("Date")] + public string DateXml { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) + get { - stringBuilder.Append(" "); + return _date.ToString("o"); + } + set + { + _date = System.DateTimeOffset.Parse(value); } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - /// - /// Harp Olfactometer available channel - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] - public enum OlfactometerChannel - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Channel0 = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - Channel1 = 1, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] - Channel2 = 2, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] - Channel3 = 3, - } - - - [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 OlfactometerChannelConfig - { - - private int _channelIndex; - - private OlfactometerChannelType _channelType; - - private OlfactometerChannelConfigFlowRateCapacity _flowRateCapacity; - - private double _flowRate; - - private string _odorant; - - private double? _odorantDilution; - - public OlfactometerChannelConfig() - { - _channelType = AindBehaviorDeviceOlfactometer.OlfactometerChannelType.Odor; - _flowRateCapacity = AindBehaviorDeviceOlfactometer.OlfactometerChannelConfigFlowRateCapacity._100; - _flowRate = 100D; - } - - protected OlfactometerChannelConfig(OlfactometerChannelConfig other) - { - _channelIndex = other._channelIndex; - _channelType = other._channelType; - _flowRateCapacity = other._flowRateCapacity; - _flowRate = other._flowRate; - _odorant = other._odorant; - _odorantDilution = other._odorantDilution; } - [Newtonsoft.Json.JsonPropertyAttribute("channel_index", Required=Newtonsoft.Json.Required.Always)] - public int ChannelIndex + /// + /// 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 _channelIndex; + return _sessionName; } set { - _channelIndex = value; + _sessionName = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("channel_type")] - public OlfactometerChannelType ChannelType + /// + /// 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 _channelType; + return _subject; } set { - _channelType = value; + _subject = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("flow_rate_capacity")] - public OlfactometerChannelConfigFlowRateCapacity FlowRateCapacity + /// + /// Notes about the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("notes")] + [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] + public string Notes { get { - return _flowRateCapacity; + return _notes; } set { - _flowRateCapacity = value; + _notes = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("flow_rate")] - public double FlowRate + /// + /// Commit hash of the repository + /// + [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")] + [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")] + public string CommitHash { get { - return _flowRate; + return _commitHash; } set { - _flowRate = value; + _commitHash = value; } } - [Newtonsoft.Json.JsonPropertyAttribute("odorant")] - public string Odorant + /// + /// 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 _odorant; + return _allowDirtyRepo; } set { - _odorant = value; + _allowDirtyRepo = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("odorant_dilution")] - public double? OdorantDilution + /// + /// Skip hardware validation + /// + [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")] + [System.ComponentModel.DescriptionAttribute("Skip hardware validation")] + public bool SkipHardwareValidation { get { - return _odorantDilution; + return _skipHardwareValidation; } set { - _odorantDilution = value; + _skipHardwareValidation = value; } } - public System.IObservable Generate() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerChannelConfig(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Session(this))); } - public System.IObservable Generate(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerChannelConfig(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new Session(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("ChannelIndex = " + _channelIndex + ", "); - stringBuilder.Append("ChannelType = " + _channelType + ", "); - stringBuilder.Append("FlowRateCapacity = " + _flowRateCapacity + ", "); - stringBuilder.Append("FlowRate = " + _flowRate + ", "); - stringBuilder.Append("Odorant = " + _odorant + ", "); - stringBuilder.Append("OdorantDilution = " + _odorantDilution); + 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; } @@ -3114,23 +1903,7 @@ public override string ToString() } - /// - /// Channel type - /// - [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 OlfactometerChannelType - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="Odor")] - Odor = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="Carrier")] - Carrier = 1, - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] public enum OlfactometerChannelConfigFlowRateCapacity { @@ -3145,7 +1918,7 @@ public enum OlfactometerChannelConfigFlowRateCapacity /// /// 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.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (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()] @@ -3160,41 +1933,11 @@ 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); - } - - 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); @@ -3215,11 +1958,6 @@ public System.IObservable Process(System.IObservable so return Process(source); } - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - public System.IObservable Process(System.IObservable source) { return Process(source); @@ -3230,21 +1968,11 @@ 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); @@ -3259,42 +1987,39 @@ public System.IObservable Process(System.IObservable(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.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (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))] - [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/Extensions/CalibrationLogic.bonsai b/src/Extensions/CalibrationLogic.bonsai index 83a2580..a3741d4 100644 --- a/src/Extensions/CalibrationLogic.bonsai +++ b/src/Extensions/CalibrationLogic.bonsai @@ -5,7 +5,7 @@ xmlns:p1="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core" xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions" xmlns:p2="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" - xmlns:p3="clr-namespace:AindBehaviorDeviceOlfactometer;assembly=Extensions" + xmlns:p3="clr-namespace:AindBehaviorDeviceOlfactometerDataSchema;assembly=Extensions" xmlns="https://bonsai-rx.org/2018/workflow"> diff --git a/src/Extensions/DeserializeSchemas.bonsai b/src/Extensions/DeserializeSchemas.bonsai index 1dd2c50..6be2c15 100644 --- a/src/Extensions/DeserializeSchemas.bonsai +++ b/src/Extensions/DeserializeSchemas.bonsai @@ -1,10 +1,8 @@  - @@ -26,8 +24,8 @@ RawRigSchema - - + + @@ -40,8 +38,8 @@ RawSessionSchema - - + + diff --git a/src/Extensions/Hardware.bonsai b/src/Extensions/Hardware.bonsai new file mode 100644 index 0000000..fc4f0b3 --- /dev/null +++ b/src/Extensions/Hardware.bonsai @@ -0,0 +1,271 @@ + + + + + + HarpDevices + + + + TaskLogicParameters + + + ChannelConfig + + + + 3 + + + + ChannelType + + + + Carrier + + + + Channel3AsCarrier + + + Channel3AsCarrier + + + + + + + + RigSchema + + + HarpOlfactometer + + + PortName + + + + + + + + COM10 + TriggerHarpReadDump + true + + + RigSchema + + + HarpAnalogInput + + + PortName + + + + + + + + COM8 + TriggerHarpReadDump + + + RigSchema + + + HarpClockGenerator + + + PortName + + + + + + + + COMx + TriggerHarpReadDump + + + HarpWhiteRabbitEvents + + + + Include + Event + + + + + + + Seconds + + + HarpTimestampSource + + + RigSchema + + + HarpManipulator + + + Calibration + + + RigSchema + + + HarpManipulator + + + PortName + + + + + + + + COMx + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Flowmeter + + + + RigSchema + + + Flowmeter + + + + + + + + + RigSchema + + + Flowmeter + + + PoolingPeriod + + + + + + + + + + + A + 19200 + COMX + PT0.2S + + + + + + HarpTimestampSource + + + + + + + + + AlicatFlowmeterEvents + + + + + + + + + + + + + + + + + + + + + RigSchema + + + Flowmeter + + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/Logging.bonsai b/src/Extensions/Logging.bonsai index d312d0b..bb2b5c2 100644 --- a/src/Extensions/Logging.bonsai +++ b/src/Extensions/Logging.bonsai @@ -7,11 +7,11 @@ xmlns:p2="clr-namespace:Harp.Olfactometer;assembly=Harp.Olfactometer" xmlns:p3="clr-namespace:AllenNeuralDynamics.WhiteRabbit;assembly=AllenNeuralDynamics.WhiteRabbit" xmlns:p4="clr-namespace:Harp.AnalogInput;assembly=Harp.AnalogInput" - xmlns:p5="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" + xmlns:p5="clr-namespace:Harp.StepperDriver;assembly=Harp.StepperDriver" + xmlns:p6="clr-namespace:AllenNeuralDynamics.HarpUtils;assembly=AllenNeuralDynamics.HarpUtils" + xmlns:p7="clr-namespace:AllenNeuralDynamics.VersionControl;assembly=AllenNeuralDynamics.VersionControl" xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" - xmlns:p6="clr-namespace:AllenNeuralDynamics.VersionControl;assembly=AllenNeuralDynamics.VersionControl" - xmlns:p7="clr-namespace:AindBehaviorDeviceOlfactometer;assembly=Extensions" - xmlns:p8="clr-namespace:AllenNeuralDynamics.AindBehaviorServices.DataTypes;assembly=AllenNeuralDynamics.AindBehaviorServices" + xmlns:p8="clr-namespace:AindBehaviorDeviceOlfactometerDataSchema;assembly=Extensions" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -54,7 +54,7 @@ - + @@ -125,7 +125,9 @@ - + + + @@ -181,9 +183,9 @@ - - - + + + @@ -195,7 +197,7 @@ - + @@ -217,9 +219,9 @@ - - - + + + @@ -253,9 +255,9 @@ - - - + + + @@ -289,9 +291,9 @@ - - - + + + @@ -302,7 +304,9 @@ - + + + @@ -355,21 +359,64 @@ SoftwareEvents - - SoftwareEvent + + Metadata + + + + Repository + + + + false + + + + + RepositoryStatus + + + + EndExperiment + + + + ExperimentCompleted + + + + + EndSession + + + + + + + SoftwareEvent + + + + + + + + + + + + - - TaskPoolScheduler + + PT1S - HarpTimestampSource + SoftwareEvent - - - TaskPoolScheduler - + + HarpTimestampSource @@ -394,39 +441,10 @@ - - Metadata - - - - Repository - - - - false - - - - - RepositoryStatus - - - - SoftwareEvent - - - - - - - - - - - + @@ -462,8 +480,8 @@ SessionSchema - - None + + None @@ -492,8 +510,8 @@ TaskLogicSchema - - None + + None @@ -522,8 +540,8 @@ RigSchema - - None + + None @@ -664,79 +682,6 @@ - - Logs - - - - EndExperiment - - - - ExperimentCompleted - - - - - EndSession - - - - HarpTimestampSource - - - - - - - - - - - - - None - - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - - endsession - - - - - - - - - - - - - - - - - - diff --git a/src/aind_behavior_device_olfactometer/__init__.py b/src/aind_behavior_device_olfactometer/__init__.py index 493f741..98cffdf 100644 --- a/src/aind_behavior_device_olfactometer/__init__.py +++ b/src/aind_behavior_device_olfactometer/__init__.py @@ -1 +1,30 @@ -__version__ = "0.3.0" +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_device_olfactometer/cli.py b/src/aind_behavior_device_olfactometer/cli.py new file mode 100644 index 0000000..082a1c8 --- /dev/null +++ b/src/aind_behavior_device_olfactometer/cli.py @@ -0,0 +1,42 @@ +import typing as t + +from pydantic import Field, RootModel +from pydantic_settings import BaseSettings, CliApp, CliSubCommand + +from aind_behavior_device_olfactometer import __semver__, regenerate +from aind_behavior_device_olfactometer.data_qc import DataQcCli + + +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 DeviceOlfactometer(BaseSettings, cli_prog_name="telekinesis", cli_kebab_case=True): + data_qc: CliSubCommand[DataQcCli] = Field(description="Run data quality checks.") + version: CliSubCommand[VersionCli] = Field( + description="Print the version of the telekinesis package.", + ) + regenerate: CliSubCommand[DslRegenerateCli] = Field( + description="Regenerate the telekinesis dsl dependencies.", + ) + + def cli_cmd(self): + return CliApp().run_subcommand(self) + + +def main(): + CliApp().run(DeviceOlfactometer) + + +if __name__ == "__main__": + main() diff --git a/src/aind_behavior_device_olfactometer/data_qc/__init__.py b/src/aind_behavior_device_olfactometer/data_qc/__init__.py new file mode 100644 index 0000000..c1408d9 --- /dev/null +++ b/src/aind_behavior_device_olfactometer/data_qc/__init__.py @@ -0,0 +1,35 @@ +import logging +import os +from pathlib import Path + +from pydantic import Field +from pydantic_settings import BaseSettings, CliPositionalArg + +from aind_behavior_device_olfactometer import __semver__ + +logger = logging.getLogger(__name__) + + +class DataQcCli(BaseSettings, cli_kebab_case=True): + """CLI for running data quality checks on collected session data.""" + + 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 + + my_dataset = dataset(Path(self.data_path), self.version) + runner = make_qc_runner(my_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_device_olfactometer/analysis.py b/src/aind_behavior_device_olfactometer/data_qc/_utils.py similarity index 68% rename from src/aind_behavior_device_olfactometer/analysis.py rename to src/aind_behavior_device_olfactometer/data_qc/_utils.py index e65d59a..84dcbe6 100644 --- a/src/aind_behavior_device_olfactometer/analysis.py +++ b/src/aind_behavior_device_olfactometer/data_qc/_utils.py @@ -1,4 +1,6 @@ import argparse +import typing +import typing as t from dataclasses import dataclass, field from pathlib import Path from typing import List, Literal, cast @@ -6,12 +8,18 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd -from aind_behavior_services.calibration import olfactometer as olf +from aind_behavior_services.rig import olfactometer as olf +from contraqctor import contract, qc from contraqctor.contract import Dataset, DataStream +from contraqctor.contract.harp import HarpDevice +from contraqctor.qc._context_extensions import ContextExportableObj from matplotlib.colors import LinearSegmentedColormap -from .data_contract import dataset -from .task_logic import OlfactometerCalibrationLogic +from ..data_contract import dataset +from ..task_logic import OlfactometerCalibrationLogic + +if typing.TYPE_CHECKING: + pass plt.style.use("dark_background") @@ -170,6 +178,84 @@ def plot_channel( return fig, ax +class DeviceOlfactometerQcSuite(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"]["SoftwareEvents"]["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 test_plot_channels(self): + """Generate calibration plots for each odor channel and export as assets.""" + processed = ProcessedData.from_dataset(self.dataset) + channel_groups = list(processed.odor_channel_config.groupby(["channel_index"])) + + if not channel_groups: + return self.fail_test(None, "No odor channel configurations found in the dataset.") + + figs = [] + for _, channel_df in channel_groups: + fig, _ = plot_channel(channel_df, self.dataset) + fig.set_size_inches(10, 6) + figs.append(fig) + + return self.pass_test( + None, + f"Generated calibration plots for {len(figs)} channel(s).", + context=ContextExportableObj.as_context(figs), + ) + + +def make_qc_runner(dataset: contract.Dataset) -> qc.Runner: + _runner = qc.Runner() + dataset.load_all(strict=False) + exclude: list[contract.DataStream] = [] + + # 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 Harp Hub tests + _runner.add_suite( + qc.harp.HarpHubTestSuite( + dataset["Behavior"]["HarpClockGenerator"], + [harp_device for harp_device in dataset["Behavior"] if isinstance(harp_device, HarpDevice)], + ), + "HarpHub", + ) + # 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 DeviceOlfactometer specific tests + _runner.add_suite(DeviceOlfactometerQcSuite(dataset), "DeviceOlfactometer") + return _runner + + def main(): parser = argparse.ArgumentParser(description="Process olfactometer data.") parser.add_argument("--path", type=str, help="Path to the dataset root directory", required=True) diff --git a/src/aind_behavior_device_olfactometer/data_qc/data_qc.py b/src/aind_behavior_device_olfactometer/data_qc/data_qc.py new file mode 100644 index 0000000..8935868 --- /dev/null +++ b/src/aind_behavior_device_olfactometer/data_qc/data_qc.py @@ -0,0 +1,89 @@ +import typing as t + +import pandas as pd +from contraqctor import contract, qc +from contraqctor.contract.harp import HarpDevice +from contraqctor.qc._context_extensions import ContextExportableObj + + +class DeviceOlfactometerQcSuite(qc.Suite): + def __init__(self, dataset: contract.Dataset): + from ._utils import ProcessedData + + self._processed_data = ProcessedData.from_dataset(dataset) + self.dataset = dataset + + def test_end_session_exists(self): + """Check that the session has an end event.""" + end_session = self.dataset["Behavior"]["SoftwareEvents"]["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 test_plot_channels(self): + """Generate calibration plots for each odor channel and export as assets.""" + from ._utils import plot_channel + + processed = self._processed_data + channel_groups = list(processed.odor_channel_config.groupby(["channel_index"])) + + if not channel_groups: + return self.fail_test(None, "No odor channel configurations found in the dataset.") + + figs = [] + for _, channel_df in channel_groups: + fig, _ = plot_channel(channel_df, self.dataset) + fig.set_size_inches(10, 6) + figs.append(fig) + + return self.pass_test( + None, + f"Generated calibration plots for {len(figs)} channel(s).", + context=ContextExportableObj.as_context(figs), + ) + + +def make_qc_runner(dataset: contract.Dataset) -> qc.Runner: + _runner = qc.Runner() + dataset.load_all(strict=False) + exclude: list[contract.DataStream] = [] + + # 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 Harp Hub tests + _runner.add_suite( + qc.harp.HarpHubTestSuite( + dataset["Behavior"]["HarpClockGenerator"], + [harp_device for harp_device in dataset["Behavior"] if isinstance(harp_device, HarpDevice)], + ), + "HarpHub", + ) + # 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 DeviceOlfactometer specific tests + _runner.add_suite(DeviceOlfactometerQcSuite(dataset), "DeviceOlfactometer") + return _runner diff --git a/src/aind_behavior_device_olfactometer/launcher.py b/src/aind_behavior_device_olfactometer/launcher.py deleted file mode 100644 index 3e16fbd..0000000 --- a/src/aind_behavior_device_olfactometer/launcher.py +++ /dev/null @@ -1,51 +0,0 @@ -from pathlib import Path - -from aind_behavior_services.session import AindBehaviorSessionModel -from clabe import resource_monitor -from clabe.apps import AindBehaviorServicesBonsaiApp, BonsaiAppSettings -from clabe.launcher import DefaultBehaviorPicker, DefaultBehaviorPickerSettings, Launcher, LauncherCliArgs -from pydantic_settings import CliApp - -from .rig import OlfactometerCalibrationRig -from .task_logic import OlfactometerCalibrationLogic - - -def make_launcher(settings: LauncherCliArgs) -> Launcher: - monitor = resource_monitor.ResourceMonitor( - constrains=[ - resource_monitor.available_storage_constraint_factory(settings.data_dir, 2e11), - ] - ) - app = AindBehaviorServicesBonsaiApp(settings=BonsaiAppSettings(workflow=Path(r"./src/main.bonsai"))) - picker = DefaultBehaviorPicker[OlfactometerCalibrationRig, AindBehaviorSessionModel, OlfactometerCalibrationLogic]( - settings=DefaultBehaviorPickerSettings() # type: ignore[call-arg] - ) - launcher = Launcher( - rig=OlfactometerCalibrationRig, - session=AindBehaviorSessionModel, - task_logic=OlfactometerCalibrationLogic, - settings=settings, - ) - - launcher.register_callable( - [ - picker.initialize, - picker.pick_session, - picker.pick_task_logic, - picker.pick_rig, - ] - ) - launcher.register_callable(monitor.build_runner()) - launcher.register_callable(app.build_runner(allow_std_error=True)) - return launcher - - -def main(): - args = CliApp().run(LauncherCliArgs) - launcher = make_launcher(args) - launcher.main() - return None - - -if __name__ == "__main__": - main() diff --git a/src/aind_behavior_device_olfactometer/regenerate.py b/src/aind_behavior_device_olfactometer/regenerate.py index 38031a7..c0f1238 100644 --- a/src/aind_behavior_device_olfactometer/regenerate.py +++ b/src/aind_behavior_device_olfactometer/regenerate.py @@ -2,24 +2,21 @@ 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_device_olfactometer import rig, task_logic +from . import rig, task_logic -SCHEMA_ROOT = Path("./src/DataSchemas/") +SCHEMA_ROOT = Path("./schema/") EXTENSIONS_ROOT = Path("./src/Extensions/") -NAMESPACE_PREFIX = "AindBehaviorDeviceOlfactometer" +NAMESPACE_PREFIX = "AindBehaviorDeviceOlfactometerDataSchema" def main(): models = [ task_logic.OlfactometerCalibrationLogic, rig.OlfactometerCalibrationRig, - AindBehaviorSessionModel, + Session, ] model = pydantic.RootModel[Union[tuple(models)]] diff --git a/src/aind_behavior_device_olfactometer/rig.py b/src/aind_behavior_device_olfactometer/rig.py index e5be84e..b8e1542 100644 --- a/src/aind_behavior_device_olfactometer/rig.py +++ b/src/aind_behavior_device_olfactometer/rig.py @@ -1,24 +1,25 @@ from typing import Literal, Optional -import aind_behavior_services.calibration.aind_manipulator as man +import aind_behavior_services.rig.aind_manipulator as man from aind_behavior_services import rig -from aind_behavior_services.calibration import olfactometer as olf +from aind_behavior_services.rig import harp +from aind_behavior_services.rig import olfactometer as olf from pydantic import Field -from . import __version__ +from . import __semver__ class AlicatFlowmeter(rig.Device): device_type: Literal["AlicatFlowmeter"] = "AlicatFlowmeter" - port_name: str = Field(..., description="Device port name") - device_id: str = Field("A", description="Alicat device ID") + port_name: str = Field(description="Device port name") + device_id: str = Field(default="A", description="Alicat device ID") pooling_period: float = Field(default=0.2, gt=0, description="Device pooling interval in seconds") -class OlfactometerCalibrationRig(rig.AindBehaviorRigModel): - version: Literal[__version__] = __version__ - harp_olfactometer: olf.Olfactometer = Field(..., title="Olfactometer device") - harp_analog_input: rig.harp.HarpAnalogInput = Field(..., title="Analog input device") - harp_clock_generator: rig.harp.HarpWhiteRabbit = Field(..., title="Clock generator device") - harp_manipulator: man.AindManipulatorDevice = Field(..., description="Manipulator") +class OlfactometerCalibrationRig(rig.Rig): + version: Literal[__semver__] = __semver__ + harp_olfactometer: olf.Olfactometer = Field(title="Olfactometer device") + harp_analog_input: harp.HarpAnalogInput = Field(title="Analog input device") + harp_clock_generator: harp.HarpWhiteRabbit = Field(title="Clock generator device") + harp_manipulator: man.AindManipulator = Field(description="Manipulator") flowmeter: Optional[AlicatFlowmeter] = Field(default=None, description="Alicat flowmeter device") diff --git a/src/aind_behavior_device_olfactometer/task_logic.py b/src/aind_behavior_device_olfactometer/task_logic.py index 4dc2092..2b81577 100644 --- a/src/aind_behavior_device_olfactometer/task_logic.py +++ b/src/aind_behavior_device_olfactometer/task_logic.py @@ -1,15 +1,15 @@ from typing import Dict, Literal -from aind_behavior_services.calibration import olfactometer as olf -from aind_behavior_services.task_logic import AindBehaviorTaskLogicModel, TaskParameters +from aind_behavior_services.rig import olfactometer as olf +from aind_behavior_services.task import Task, TaskParameters from pydantic import Field -from . import __version__ +from . import __semver__ class OlfactometerCalibrationParameters(TaskParameters): channel_config: Dict[olf.OlfactometerChannel, olf.OlfactometerChannelConfig] = Field( - default={}, description="Configuration of olfactometer channels" + default_factory=dict, description="Configuration of olfactometer channels" ) full_flow_rate: float = Field(default=1000, ge=0, le=1000, description="Full flow rate of the olfactometer") n_repeats_per_stimulus: int = Field(default=1, ge=1, description="Number of repeats per stimulus") @@ -17,9 +17,9 @@ class OlfactometerCalibrationParameters(TaskParameters): time_off: float = Field(default=1, ge=0, description="Time (s) the valve is close during calibration") -class OlfactometerCalibrationLogic(AindBehaviorTaskLogicModel): +class OlfactometerCalibrationLogic(Task): """Olfactometer operation control model that is used to run a calibration data acquisition workflow""" name: str = Field(default="OlfactometerCalibration", title="Name of the task logic", frozen=True) - version: Literal[__version__] = __version__ - task_parameters: OlfactometerCalibrationParameters = Field(..., title="Task parameters", validate_default=True) + version: Literal[__semver__] = __semver__ + task_parameters: OlfactometerCalibrationParameters = Field(title="Task parameters", validate_default=True) diff --git a/src/main.bonsai b/src/main.bonsai index a3cc593..e324140 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -1,20 +1,13 @@  @@ -32,283 +25,7 @@ 10 - - Hardware - - - - HarpDevices - - - - TaskLogicParameters - - - ChannelConfig - - - - 3 - - - - ChannelType - - - - Carrier - - - - Channel3AsCarrier - - - Channel3AsCarrier - - - - - - - - RigSchema - - - HarpOlfactometer - - - PortName - - - - - - - - COM10 - TriggerHarpReadDump - true - - - RigSchema - - - HarpAnalogInput - - - PortName - - - - - - - - COM8 - TriggerHarpReadDump - - - RigSchema - - - HarpClockGenerator - - - PortName - - - - - - - - COMx - TriggerHarpReadDump - - - HarpWhiteRabbitEvents - - - - Include - Event - - - - - - - Seconds - - - HarpTimestampSource - - - RigSchema - - - HarpManipulator - - - Calibration - - - Input - - - - None - - - - - - - RigSchema - - - HarpManipulator - - - PortName - - - - - - - - COMx - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Flowmeter - - - - RigSchema - - - Flowmeter - - - - - - - - - RigSchema - - - Flowmeter - - - PoolingPeriod - - - - - - - - - - - A - 19200 - COMX - PT0.2S - - - - - - HarpTimestampSource - - - - - - - - - AlicatFlowmeterEvents - - - - - - - - - - - - - - - - - - - - - RigSchema - - - Flowmeter - - - - - - - - - - - - - - + SessionSchema @@ -374,7 +91,7 @@ - + EndValvesState EndValve0 @@ -393,16 +110,16 @@ - + EndValvesState None - + Write - + HarpOlfactometerCommands @@ -448,15 +165,15 @@ - - true - 0 - 0 - 0 - NaN - true - 100 - 1000 + + true + 0 + 0 + 0 + NaN + true + 100 + 1000 @@ -507,31 +224,44 @@ - + + RigSchema + + + DataDirectory + + + + + + LoggingRootPath - - ../. + + ../. Repository - + SoftwareEvent - + + + + @@ -555,782 +285,7 @@ - - Logging - - - - Logging - - - - Behavior - - - - - - - Modality - Behavior - - - - 1 - - - - Modality - - - HarpLogging - - - - HarpOlfactometerEvents - - - Modality - - - - - - - - - - - - - - - - - Behavior - Olfactometer - - - HarpWhiteRabbitEvents - - - Modality - - - - - - - - - - - - - - - - - Behavior - WhiteRabbit - - - HarpAnalogInputEvents - - - Modality - - - - - - - - - - - - - - - - - Behavior - AnalogInput - - - StepperDriverEvents - - - Modality - - - - - - - - - - - - - - - Behavior - StepperDriver - - - - - - - - - - - - - - - - - - - - - - - - - - - - HarpCommandsLogging - - - - HarpTimestampSource - - - HarpSeconds - - - HarpOlfactometerCommands - - - HarpSeconds - - - - - - - - - - - - Modality - - - - - - - - - - - - - - - - - Behavior - HarpCommands/Olfactometer - - - HarpAnalogInputCommands - - - HarpSeconds - - - - - - - - - - - - Modality - - - - - - - - - - - - - - - - - Behavior - HarpCommands/AnalogInput - - - HarpWhiteRabbitCommands - - - HarpSeconds - - - - - - - - - - - - Modality - - - - - - - - - - - - - - - - - Behavior - HarpCommands/WhiteRabbit - - - StepperDriverEvents - - - HarpSeconds - - - - - - - - - - - - Modality - - - - - - - - - - - - - - - Behavior - HarpCommands/StepperDriver - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SoftwareEvents - - - - SoftwareEvent - - - - TaskPoolScheduler - - - - HarpTimestampSource - - - - TaskPoolScheduler - - - - - - - - - - - - - Modality - - - - - - - - SoftwareEvents - LoggingRootPath - - - - - Metadata - - - - Repository - - - - false - - - - - RepositoryStatus - - - - SoftwareEvent - - - - - - - - - - - - - - - - - - - - - - - - - - Logs - - - - - Logs - - - - - 1 - - - - DeviceName - - - ConfigSchemaLogging - - - - SessionSchema - - - - None - - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - Config - session_output - - - TaskLogicSchema - - - - None - - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - Config - tasklogic_output - - - RigSchema - - - - None - - - - Modality - - - - - - - - DeviceName - - - - - - - - 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 - - - - - EndSession - - - - HarpTimestampSource - - - - - - - - - - - - - None - - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - - endsession - - - - - - - - - - - - - - - - - - - - - - - - - - - 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