diff --git a/.config/dotnet-tools.json b/.config/dotnet-tools.json index a1a9bfe..134d7ab 100644 --- a/.config/dotnet-tools.json +++ b/.config/dotnet-tools.json @@ -3,7 +3,7 @@ "isRoot": true, "tools": { "bonsai.sgen": { - "version": "0.4.0", + "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/.gitignore b/.gitignore index a66aeab..c5a31fc 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ bin obj Packages Bonsai.exe.WebView2 +Bonsai/Settings/ *.bin *.avi *.dll 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 46671e4..a99cc3a 100644 --- a/bonsai/Bonsai.config +++ b/bonsai/Bonsai.config @@ -1,26 +1,25 @@  - - - - - - - - + + + + + + + - - - + + + - + - + @@ -35,18 +34,22 @@ + + - - - - - + + + + + + + - + - + @@ -55,19 +58,22 @@ - - + + - - + + - - + + + + + @@ -102,32 +108,33 @@ - - - - - + + + + + + - + - - - + + + - + - + @@ -143,17 +150,19 @@ - - - - - + + + + + + + - + - - - + + + @@ -161,19 +170,21 @@ - - + + - - + + - - + + + + @@ -181,15 +192,24 @@ + + + + + + + + + - - - - - - + + + + + + diff --git a/bonsai/setup.ps1 b/bonsai/setup.ps1 index 01cfba6..890eeda 100644 --- a/bonsai/setup.ps1 +++ b/bonsai/setup.ps1 @@ -15,7 +15,6 @@ if (!(Test-Path "./Bonsai.exe")) { Expand-Archive "temp.zip" -DestinationPath "." -Force Move-Item -Path "temp.config" "NuGet.config" -Force -ErrorAction SilentlyContinue Remove-Item -Path "temp.zip" - Remove-Item -Path "Bonsai32.exe" } & .\Bonsai.exe --no-editor Pop-Location \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index c2256f2..4a17efc 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -6,24 +6,22 @@ import os import sys -import erdantic as erd -from pydantic import BaseModel - +import aind_behavior_device_olfactometer.data_contract as contract import aind_behavior_device_olfactometer.rig import aind_behavior_device_olfactometer.task_logic sys.path.insert(0, os.path.abspath("../src/DataSchemas")) import aind_behavior_device_olfactometer -SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/tree/main/src/DataSchemas/" +SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/tree/main/src/" # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = "AIND Behavior Device Olfactometer project" -copyright = "2024, Allen Institute for Neural Dynamics" +copyright = "2026, Allen Institute for Neural Dynamics" author = "Bruno Cruz" -release = aind_behavior_device_olfactometer.__version__ +release = aind_behavior_device_olfactometer.__semver__ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration @@ -80,12 +78,7 @@ def linkcode_resolve(domain, info): return f"{SOURCE_ROOT}/{filename}.py" -# -- Class diagram generation - - -def export_model_diagram(model: BaseModel, root: str = "_static") -> None: - diagram = erd.create(model) - diagram.draw(f"{root}/{model.__name__}.svg") - +# -- Dataset rendering -_diagram_root = "_static" +with open("_static/dataset.html", "w", encoding="utf-8") as f: + f.write(contract.render_dataset(version=aind_behavior_device_olfactometer.__semver__)) diff --git a/docs/dataset.rst b/docs/dataset.rst new file mode 100644 index 0000000..e526c5a --- /dev/null +++ b/docs/dataset.rst @@ -0,0 +1,10 @@ +Data Contract +------------- + +.. raw:: html + + \ No newline at end of file diff --git a/docs/json-schemas.rig.rst b/docs/json-schemas.rig.rst deleted file mode 100644 index 3b94a9b..0000000 --- a/docs/json-schemas.rig.rst +++ /dev/null @@ -1,9 +0,0 @@ -json-schemas.rig ------------------- - -`Download Schema `_ - -.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/main/src/DataSchemas/olfactometer_calibration_rig.json - :lift_definitions: - :auto_reference: - diff --git a/docs/json-schemas.rst b/docs/json-schemas.rst index 1fdf2c9..3b5d849 100644 --- a/docs/json-schemas.rst +++ b/docs/json-schemas.rst @@ -1,8 +1,18 @@ -json-schemas +json-schema ------------- -.. toctree:: - :maxdepth: 4 +The following json-schemas are used as the format definition of the input for this task. They are the result of the `Pydantic`` models defined in `src/aind_behavior_device_olfactometer`, and are also used to generate `src/Extensions/AindBehaviorDeviceOlfactometer.cs` via `Bonsai.Sgen`. - json-schemas.session - json-schemas.rig - json-schemas.task_logic \ No newline at end of file +`Download Schema `_ + +Task Logic Schema +~~~~~~~~~~~~~~~~~ +.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/main/schema/aind_behavior_device_olfactometer.json#/$defs/OlfactometerCalibrationLogic + :lift_definitions: + :auto_reference: + + +Rig Schema +~~~~~~~~~~~~~~ +.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/main/schema/aind_behavior_device_olfactometer.json#/$defs/OlfactometerCalibrationRig + :lift_definitions: + :auto_reference: diff --git a/docs/json-schemas.session.rst b/docs/json-schemas.session.rst deleted file mode 100644 index 657de12..0000000 --- a/docs/json-schemas.session.rst +++ /dev/null @@ -1,9 +0,0 @@ -json-schemas.session ---------------------- - -`Download Schema `_ - -.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/main/src/DataSchemas/aind_behavior_session_model.json - :lift_definitions: - :auto_reference: - diff --git a/docs/json-schemas.task_logic.rst b/docs/json-schemas.task_logic.rst deleted file mode 100644 index 14012eb..0000000 --- a/docs/json-schemas.task_logic.rst +++ /dev/null @@ -1,9 +0,0 @@ -json-schemas.task_logic -------------------------- - -`Download Schema `_ - -.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/main/src/DataSchemas/olfactometer_calibration_logic.json - :lift_definitions: - :auto_reference: - diff --git a/examples/clabe.yml b/examples/clabe.yml new file mode 100644 index 0000000..dcf0b5e --- /dev/null +++ b/examples/clabe.yml @@ -0,0 +1,6 @@ +# In order to get picked up, move this file to the root of the project or ./local + +data_dir: C:/Data + +default_behavior_picker: + config_library_dir: '\\allen\aind\scratch\AindBehavior.db\AindBehaviorDeviceOlfactometer' diff --git a/examples/olfactometer.py b/examples/olfactometer.py index 1adfed9..b65968b 100644 --- a/examples/olfactometer.py +++ b/examples/olfactometer.py @@ -1,33 +1,35 @@ import os -from aind_behavior_services.base import get_commit_hash -from aind_behavior_services.calibration import olfactometer as olf -from aind_behavior_services.rig import HarpAnalogInput, HarpWhiteRabbit -from aind_behavior_services.session import AindBehaviorSessionModel +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 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, @@ -35,21 +37,35 @@ ) ) -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( + 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=rig.HarpOlfactometer(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.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 c6ddc22..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>=0.10, <0.11", -] +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_behavior_experiment_launcher[aind-services]>=0.3.0"] +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 = [ - "aind-behavior-core-analysis@git+https://github.com/AllenNeuralDynamics/Aind.Behavior.CoreAnalysis@051bc0c", - "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/schema/aind_behavior_device_olfactometer.json b/schema/aind_behavior_device_olfactometer.json new file mode 100644 index 0000000..4451b84 --- /dev/null +++ b/schema/aind_behavior_device_olfactometer.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": "0.2.0-rc0", + "default": "0.2.0-rc0", + "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": "0.2.0-rc0", + "default": "0.2.0-rc0", + "title": "Version", + "type": "string" + }, + "computer_name": { + "description": "Computer name", + "title": "Computer Name", + "type": "string" + }, + "rig_name": { + "description": "Rig name", + "title": "Rig Name", + "type": "string" + }, + "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/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/scripts/deploy.cmd b/scripts/deploy.cmd new file mode 100644 index 0000000..98b4bba --- /dev/null +++ b/scripts/deploy.cmd @@ -0,0 +1 @@ +powershell -ExecutionPolicy Bypass -File .\scripts\deploy.ps1 \ No newline at end of file diff --git a/scripts/deploy.ps1 b/scripts/deploy.ps1 new file mode 100644 index 0000000..8758568 --- /dev/null +++ b/scripts/deploy.ps1 @@ -0,0 +1,27 @@ +$scriptPath = $MyInvocation.MyCommand.Path +$scriptDirectory = Split-Path -Parent $scriptPath +Set-Location (Split-Path -Parent $scriptDirectory) +Write-Output "Creating a Python environment..." + +if (-not (Get-Command uv -ErrorAction SilentlyContinue)) { + throw "The 'uv' command was not found. See https://docs.astral.sh/uv/getting-started/installation/ for instructions." +} + +if (Test-Path -Path ./.venv) { + Remove-Item ./.venv -Recurse -Force +} +&uv venv +.\.venv\Scripts\Activate.ps1 +Write-Output "Synchronizing environment..." +&uv sync --extra launcher +Write-Output "Creating a Bonsai environment and installing packages..." +if (Test-Path -Path "bonsai") { + Set-Location "bonsai" + .\setup.ps1 +} elseif (Test-Path -Path ".bonsai") { + Set-Location ".bonsai" + .\setup.ps1 +} else { + throw "Neither 'bonsai' nor '.bonsai' directory found." +} +Set-Location .. \ No newline at end of file diff --git a/src/DataSchemas/aind_behavior_session_model.json b/src/DataSchemas/aind_behavior_session_model.json deleted file mode 100644 index 09966ba..0000000 --- a/src/DataSchemas/aind_behavior_session_model.json +++ /dev/null @@ -1,110 +0,0 @@ -{ - "properties": { - "aind_behavior_services_pkg_version": { - "default": "0.10.2", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "version": { - "const": "0.3.1", - "default": "0.3.1", - "title": "Version", - "type": "string" - }, - "experiment": { - "description": "Name of the experiment", - "title": "Experiment", - "type": "string" - }, - "experimenter": { - "default": [], - "description": "Name of the experimenter", - "items": { - "type": "string" - }, - "title": "Experimenter", - "type": "array" - }, - "date": { - "description": "Date of the experiment", - "format": "date-time", - "title": "Date", - "type": "string" - }, - "root_path": { - "description": "Root path where data will be logged", - "title": "Root Path", - "type": "string" - }, - "session_name": { - "default": null, - "description": "Name of the session. This will be used to create a folder in the root path.", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Session Name" - }, - "subject": { - "description": "Name of the subject", - "title": "Subject", - "type": "string" - }, - "experiment_version": { - "description": "Version of the experiment", - "title": "Experiment Version", - "type": "string" - }, - "notes": { - "default": null, - "description": "Notes about the experiment", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Notes" - }, - "commit_hash": { - "default": null, - "description": "Commit hash of the repository", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Commit Hash" - }, - "allow_dirty_repo": { - "default": false, - "description": "Allow running from a dirty repository", - "title": "Allow Dirty Repo", - "type": "boolean" - }, - "skip_hardware_validation": { - "default": false, - "description": "Skip hardware validation", - "title": "Skip Hardware Validation", - "type": "boolean" - } - }, - "required": [ - "experiment", - "root_path", - "subject", - "experiment_version" - ], - "title": "AindBehaviorSessionModel", - "type": "object" -} \ No newline at end of file diff --git a/src/DataSchemas/olfactometer_calibration_logic.json b/src/DataSchemas/olfactometer_calibration_logic.json deleted file mode 100644 index 84641f4..0000000 --- a/src/DataSchemas/olfactometer_calibration_logic.json +++ /dev/null @@ -1,197 +0,0 @@ -{ - "definitions": { - "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": "0.10.2", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "channel_config": { - "additionalProperties": { - "$ref": "#/definitions/OlfactometerChannelConfig" - }, - "default": {}, - "description": "Configuration of olfactometer channels", - "propertyNames": { - "$ref": "#/definitions/OlfactometerChannel" - }, - "title": "Channel Config", - "type": "object" - }, - "full_flow_rate": { - "default": 1000, - "description": "Full flow rate of the olfactometer", - "maximum": 1000.0, - "minimum": 0.0, - "title": "Full Flow Rate", - "type": "number" - }, - "n_repeats_per_stimulus": { - "default": 1, - "description": "Number of repeats per stimulus", - "minimum": 1, - "title": "N Repeats Per Stimulus", - "type": "integer" - }, - "time_on": { - "default": 1, - "description": "Time (s) the valve is open during calibration", - "minimum": 0.0, - "title": "Time On", - "type": "number" - }, - "time_off": { - "default": 1, - "description": "Time (s) the valve is close during calibration", - "minimum": 0.0, - "title": "Time Off", - "type": "number" - } - }, - "title": "OlfactometerCalibrationParameters", - "type": "object" - }, - "OlfactometerChannel": { - "description": "Harp Olfactometer available channel", - "enum": [ - 0, - 1, - 2, - 3 - ], - "title": "OlfactometerChannel", - "type": "integer", - "x-enumNames": [ - "Channel0", - "Channel1", - "Channel2", - "Channel3" - ] - }, - "OlfactometerChannelConfig": { - "properties": { - "channel_index": { - "title": "Channel index", - "type": "integer" - }, - "channel_type": { - "$ref": "#/definitions/OlfactometerChannelType", - "default": "Odor", - "title": "Channel type" - }, - "flow_rate_capacity": { - "default": 100, - "enum": [ - 100, - 1000 - ], - "title": "Flow capacity. mL/min", - "type": "integer" - }, - "flow_rate": { - "default": 100, - "maximum": 100.0, - "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": "Channel type", - "enum": [ - "Odor", - "Carrier" - ], - "title": "OlfactometerChannelType", - "type": "string" - } - }, - "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": { - "$ref": "#/definitions/OlfactometerCalibrationParameters", - "title": "Task parameters" - }, - "version": { - "const": "0.1.0", - "default": "0.1.0", - "title": "Version", - "type": "string" - }, - "stage_name": { - "default": null, - "description": "Optional stage name the `Task` object instance represents.", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Stage Name" - } - }, - "required": [ - "task_parameters" - ], - "title": "OlfactometerCalibrationLogic", - "type": "object" -} \ No newline at end of file diff --git a/src/DataSchemas/olfactometer_calibration_rig.json b/src/DataSchemas/olfactometer_calibration_rig.json deleted file mode 100644 index a3a0b72..0000000 --- a/src/DataSchemas/olfactometer_calibration_rig.json +++ /dev/null @@ -1,435 +0,0 @@ -{ - "definitions": { - "BaseModel": { - "properties": {}, - "title": "BaseModel", - "type": "object" - }, - "ConnectedClockOutput": { - "properties": { - "target_device": { - "default": null, - "description": "Optional device name to provide user additional information", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Target Device" - }, - "output_channel": { - "description": "Output channel", - "minimum": 0, - "title": "Output Channel", - "type": "integer" - } - }, - "required": [ - "output_channel" - ], - "title": "ConnectedClockOutput", - "type": "object" - }, - "HarpAnalogInput": { - "properties": { - "device_type": { - "const": "AnalogInput", - "default": "AnalogInput", - "title": "Device Type", - "type": "string" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/definitions/BaseModel" - }, - { - "type": "null" - } - ] - }, - "calibration": { - "default": null, - "description": "Calibration", - "oneOf": [ - { - "$ref": "#/definitions/BaseModel" - }, - { - "type": "null" - } - ] - }, - "who_am_i": { - "const": 1236, - "default": 1236, - "title": "Who Am I", - "type": "integer" - }, - "serial_number": { - "default": null, - "description": "Device serial number", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Serial Number" - }, - "port_name": { - "description": "Device port name", - "title": "Port Name", - "type": "string" - } - }, - "required": [ - "port_name" - ], - "title": "HarpAnalogInput", - "type": "object" - }, - "HarpOlfactometer": { - "description": "Overrides the default settings for the olfactometer calibration", - "properties": { - "device_type": { - "const": "Olfactometer", - "default": "Olfactometer", - "title": "Device Type", - "type": "string" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/definitions/BaseModel" - }, - { - "type": "null" - } - ] - }, - "calibration": { - "$ref": "#/definitions/OlfactometerCalibration", - "description": "Olfactometer calibration" - }, - "who_am_i": { - "const": 1140, - "default": 1140, - "title": "Who Am I", - "type": "integer" - }, - "serial_number": { - "default": null, - "description": "Device serial number", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Serial Number" - }, - "port_name": { - "description": "Device port name", - "title": "Port Name", - "type": "string" - } - }, - "required": [ - "calibration", - "port_name" - ], - "title": "HarpOlfactometer", - "type": "object" - }, - "HarpWhiteRabbit": { - "properties": { - "device_type": { - "const": "WhiteRabbit", - "default": "WhiteRabbit", - "title": "Device Type", - "type": "string" - }, - "additional_settings": { - "default": null, - "description": "Additional settings", - "oneOf": [ - { - "$ref": "#/definitions/BaseModel" - }, - { - "type": "null" - } - ] - }, - "calibration": { - "default": null, - "description": "Calibration", - "oneOf": [ - { - "$ref": "#/definitions/BaseModel" - }, - { - "type": "null" - } - ] - }, - "who_am_i": { - "const": 1404, - "default": 1404, - "title": "Who Am I", - "type": "integer" - }, - "serial_number": { - "default": null, - "description": "Device serial number", - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Serial Number" - }, - "port_name": { - "description": "Device port name", - "title": "Port Name", - "type": "string" - }, - "connected_clock_outputs": { - "default": [], - "description": "Connected clock outputs", - "items": { - "$ref": "#/definitions/ConnectedClockOutput" - }, - "title": "Connected Clock Outputs", - "type": "array" - } - }, - "required": [ - "port_name" - ], - "title": "HarpWhiteRabbit", - "type": "object" - }, - "OlfactometerCalibration": { - "description": "Olfactometer calibration class", - "properties": { - "device_name": { - "default": "Olfactometer", - "description": "Name of the device being calibrated", - "title": "Device name", - "type": "string" - }, - "input": { - "$ref": "#/definitions/OlfactometerCalibrationInput", - "title": "Input of the calibration" - }, - "output": { - "$ref": "#/definitions/OlfactometerCalibrationOutput", - "title": "Output of the calibration" - }, - "date": { - "default": null, - "oneOf": [ - { - "format": "date-time", - "type": "string" - }, - { - "type": "null" - } - ], - "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": { - "$ref": "#/definitions/OlfactometerChannelConfig" - }, - "default": {}, - "description": "Configuration of olfactometer channels", - "propertyNames": { - "$ref": "#/definitions/OlfactometerChannel" - }, - "title": "Channel Config", - "type": "object" - } - }, - "title": "OlfactometerCalibrationInput", - "type": "object" - }, - "OlfactometerCalibrationOutput": { - "properties": {}, - "title": "OlfactometerCalibrationOutput", - "type": "object" - }, - "OlfactometerChannel": { - "description": "Harp Olfactometer available channel", - "enum": [ - 0, - 1, - 2, - 3 - ], - "title": "OlfactometerChannel", - "type": "integer", - "x-enumNames": [ - "Channel0", - "Channel1", - "Channel2", - "Channel3" - ] - }, - "OlfactometerChannelConfig": { - "properties": { - "channel_index": { - "title": "Channel index", - "type": "integer" - }, - "channel_type": { - "$ref": "#/definitions/OlfactometerChannelType", - "default": "Odor", - "title": "Channel type" - }, - "flow_rate_capacity": { - "default": 100, - "enum": [ - 100, - 1000 - ], - "title": "Flow capacity. mL/min", - "type": "integer" - }, - "flow_rate": { - "default": 100, - "maximum": 100.0, - "title": "Target flow rate. mL/min. If channel_type == CARRIER, this value is ignored.", - "type": "number" - }, - "odorant": { - "default": null, - "oneOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Odorant name" - }, - "odorant_dilution": { - "default": null, - "oneOf": [ - { - "type": "number" - }, - { - "type": "null" - } - ], - "title": "Odorant dilution (%v/v)" - } - }, - "required": [ - "channel_index" - ], - "title": "OlfactometerChannelConfig", - "type": "object" - }, - "OlfactometerChannelType": { - "description": "Channel type", - "enum": [ - "Odor", - "Carrier" - ], - "title": "OlfactometerChannelType", - "type": "string" - } - }, - "properties": { - "aind_behavior_services_pkg_version": { - "default": "0.10.2", - "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", - "title": "aind_behavior_services package version", - "type": "string" - }, - "version": { - "const": "0.2.0", - "default": "0.2.0", - "title": "Version", - "type": "string" - }, - "computer_name": { - "description": "Computer name", - "title": "Computer Name", - "type": "string" - }, - "rig_name": { - "description": "Rig name", - "title": "Rig Name", - "type": "string" - }, - "harp_olfactometer": { - "$ref": "#/definitions/HarpOlfactometer", - "title": "Olfactometer device" - }, - "harp_analog_input": { - "$ref": "#/definitions/HarpAnalogInput", - "title": "Analog input device" - }, - "harp_clock_generator": { - "$ref": "#/definitions/HarpWhiteRabbit", - "title": "Clock generator device" - } - }, - "required": [ - "rig_name", - "harp_olfactometer", - "harp_analog_input", - "harp_clock_generator" - ], - "title": "OlfactometerCalibrationRig", - "type": "object" -} \ No newline at end of file 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/OlfactometerCalibrationRig.cs b/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs similarity index 52% rename from src/Extensions/OlfactometerCalibrationRig.cs rename to src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs index e0bbbc0..6780cbd 100644 --- a/src/Extensions/OlfactometerCalibrationRig.cs +++ b/src/Extensions/AindBehaviorDeviceOlfactometer.Generated.cs @@ -5,13 +5,162 @@ //---------------------- -namespace AindBehaviorDeviceOlfactometer.Rig +namespace AindBehaviorDeviceOlfactometerDataSchema { #pragma warning disable // Disable all warnings - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [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 + { + + private string _deviceType; + + private BaseModel _calibration; + + private string _portName; + + private string _deviceId; + + private double _poolingPeriod; + + public AlicatFlowmeter() + { + _deviceType = "AlicatFlowmeter"; + _deviceId = "A"; + _poolingPeriod = 0.2D; + } + + protected AlicatFlowmeter(AlicatFlowmeter other) + { + _deviceType = other._deviceType; + _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; + } + } + + /// + /// Calibration for the device. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration for the device.")] + 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("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(); + } + } + + + [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 { @@ -23,12 +172,12 @@ protected BaseModel(BaseModel other) { } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new BaseModel(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new BaseModel(this)); } @@ -53,9 +202,9 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [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 { @@ -107,20 +256,20 @@ public int OutputChannel } } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ConnectedClockOutput(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new ConnectedClockOutput(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("target_device = " + _targetDevice + ", "); - stringBuilder.Append("output_channel = " + _outputChannel); + stringBuilder.Append("TargetDevice = " + _targetDevice + ", "); + stringBuilder.Append("OutputChannel = " + _outputChannel); return true; } @@ -139,19 +288,17 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [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 { - private string _deviceType = "AnalogInput"; - - private BaseModel _additionalSettings; + private string _deviceType; private BaseModel _calibration; - private int _whoAmI = 1236; + private int _whoAmI; private string _serialNumber; @@ -159,12 +306,13 @@ public partial class HarpAnalogInput public HarpAnalogInput() { + _deviceType = "AnalogInput"; + _whoAmI = 1236; } protected HarpAnalogInput(HarpAnalogInput other) { _deviceType = other._deviceType; - _additionalSettings = other._additionalSettings; _calibration = other._calibration; _whoAmI = other._whoAmI; _serialNumber = other._serialNumber; @@ -185,29 +333,11 @@ public string DeviceType } /// - /// 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 @@ -267,24 +397,23 @@ public string PortName } } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpAnalogInput(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new HarpAnalogInput(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("additional_settings = " + _additionalSettings + ", "); - stringBuilder.Append("calibration = " + _calibration + ", "); - stringBuilder.Append("who_am_i = " + _whoAmI + ", "); - stringBuilder.Append("serial_number = " + _serialNumber + ", "); - stringBuilder.Append("port_name = " + _portName); + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("PortName = " + _portName); return true; } @@ -303,40 +432,39 @@ public override string ToString() } - /// - /// Overrides the default settings for the olfactometer calibration - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Overrides the default settings for the olfactometer calibration")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class HarpOlfactometer + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class HarpWhiteRabbit { - private string _deviceType = "Olfactometer"; - - private BaseModel _additionalSettings; + private string _deviceType; - private OlfactometerCalibration _calibration = new OlfactometerCalibration(); + private BaseModel _calibration; - private int _whoAmI = 1140; + private int _whoAmI; private string _serialNumber; private string _portName; - public HarpOlfactometer() + private System.Collections.Generic.List _connectedClockOutputs; + + public HarpWhiteRabbit() { + _deviceType = "WhiteRabbit"; + _whoAmI = 1404; + _connectedClockOutputs = new System.Collections.Generic.List(); } - protected HarpOlfactometer(HarpOlfactometer other) + protected HarpWhiteRabbit(HarpWhiteRabbit other) { _deviceType = other._deviceType; - _additionalSettings = other._additionalSettings; _calibration = other._calibration; _whoAmI = other._whoAmI; _serialNumber = other._serialNumber; _portName = other._portName; + _connectedClockOutputs = other._connectedClockOutputs; } [Newtonsoft.Json.JsonPropertyAttribute("device_type")] @@ -353,30 +481,12 @@ public string DeviceType } /// - /// 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; - } - } - - /// - /// Olfactometer calibration + /// Calibration for the device. /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Olfactometer calibration")] - public OlfactometerCalibration Calibration + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration for the device.")] + public BaseModel Calibration { get { @@ -435,24 +545,42 @@ public string PortName } } - public System.IObservable Process() + /// + /// Connected clock outputs + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("connected_clock_outputs")] + [System.ComponentModel.DescriptionAttribute("Connected clock outputs")] + public System.Collections.Generic.List ConnectedClockOutputs + { + get + { + return _connectedClockOutputs; + } + set + { + _connectedClockOutputs = value; + } + } + + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpOlfactometer(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpWhiteRabbit(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new HarpOlfactometer(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new HarpWhiteRabbit(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("additional_settings = " + _additionalSettings + ", "); - stringBuilder.Append("calibration = " + _calibration + ", "); - stringBuilder.Append("who_am_i = " + _whoAmI + ", "); - stringBuilder.Append("serial_number = " + _serialNumber + ", "); - stringBuilder.Append("port_name = " + _portName); + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("PortName = " + _portName + ", "); + stringBuilder.Append("ConnectedClockOutputs = " + _connectedClockOutputs); return true; } @@ -471,39 +599,40 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + /// + /// 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)] - public partial class HarpWhiteRabbit + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class Olfactometer { - private string _deviceType = "WhiteRabbit"; + private string _deviceType; - private BaseModel _additionalSettings; - - private BaseModel _calibration; + private OlfactometerCalibration _calibration; - private int _whoAmI = 1404; + private int _whoAmI; private string _serialNumber; private string _portName; - private System.Collections.Generic.List _connectedClockOutputs = new System.Collections.Generic.List(); - - public HarpWhiteRabbit() + public Olfactometer() { + _deviceType = "Olfactometer"; + _calibration = new OlfactometerCalibration(); + _whoAmI = 1140; } - protected HarpWhiteRabbit(HarpWhiteRabbit other) + protected Olfactometer(Olfactometer other) { _deviceType = other._deviceType; - _additionalSettings = other._additionalSettings; _calibration = other._calibration; _whoAmI = other._whoAmI; _serialNumber = other._serialNumber; _portName = other._portName; - _connectedClockOutputs = other._connectedClockOutputs; } [Newtonsoft.Json.JsonPropertyAttribute("device_type")] @@ -519,31 +648,9 @@ public string DeviceType } } - /// - /// 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 + public OlfactometerCalibration Calibration { get { @@ -602,43 +709,23 @@ public string PortName } } - /// - /// Connected clock outputs - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("connected_clock_outputs")] - [System.ComponentModel.DescriptionAttribute("Connected clock outputs")] - public System.Collections.Generic.List ConnectedClockOutputs - { - get - { - return _connectedClockOutputs; - } - set - { - _connectedClockOutputs = value; - } - } - - public System.IObservable Process() + public System.IObservable Generate() { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpWhiteRabbit(this))); + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Olfactometer(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, _ => new HarpWhiteRabbit(this)); + return System.Reactive.Linq.Observable.Select(source, _ => new Olfactometer(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("additional_settings = " + _additionalSettings + ", "); - stringBuilder.Append("calibration = " + _calibration + ", "); - stringBuilder.Append("who_am_i = " + _whoAmI + ", "); - stringBuilder.Append("serial_number = " + _serialNumber + ", "); - stringBuilder.Append("port_name = " + _portName + ", "); - stringBuilder.Append("connected_clock_outputs = " + _connectedClockOutputs); + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("PortName = " + _portName); return true; } @@ -658,101 +745,154 @@ public override string ToString() /// - /// Olfactometer calibration class + /// Olfactometer device configuration model /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Olfactometer calibration class")] - [Bonsai.CombinatorAttribute()] + [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 { - private string _deviceName = "Olfactometer"; - - private OlfactometerCalibrationInput _input = new OlfactometerCalibrationInput(); - - private OlfactometerCalibrationOutput _output = new OlfactometerCalibrationOutput(); - private System.DateTimeOffset? _date; - private string _description = "Calibration of the harp olfactometer device"; - - private string _notes; + private System.Collections.Generic.Dictionary _channelConfig; public OlfactometerCalibration() { + _channelConfig = new System.Collections.Generic.Dictionary(); } protected OlfactometerCalibration(OlfactometerCalibration other) { - _deviceName = other._deviceName; - _input = other._input; - _output = other._output; _date = other._date; - _description = other._description; - _notes = other._notes; + _channelConfig = other._channelConfig; } /// - /// Name of the device being calibrated + /// Date of the calibration /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Name of the device being calibrated")] - public string DeviceName + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("date")] + [System.ComponentModel.DescriptionAttribute("Date of the calibration")] + public System.DateTimeOffset? Date { get { - return _deviceName; + return _date; } set { - _deviceName = value; + _date = value; } } + /// + /// Configuration of olfactometer channels + /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("input", Required=Newtonsoft.Json.Required.Always)] - public OlfactometerCalibrationInput Input + [Newtonsoft.Json.JsonPropertyAttribute("channel_config")] + [System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")] + public System.Collections.Generic.Dictionary ChannelConfig { get { - return _input; + return _channelConfig; } set { - _input = value; + _channelConfig = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("output", Required=Newtonsoft.Json.Required.Always)] - public OlfactometerCalibrationOutput Output + public System.IObservable Generate() { - get - { - return _output; - } - set - { - _output = value; - } + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibration(this))); } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("date")] - public System.DateTimeOffset? Date + public System.IObservable Generate(System.IObservable source) { - get - { - return _date; - } + 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(); + } + } + + + /// + /// 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 OlfactometerCalibrationLogic + { + + private string _name; + + private string _description; + + private OlfactometerCalibrationParameters _taskParameters; + + private string _version; + + private string _stageName; + + public OlfactometerCalibrationLogic() + { + _name = "OlfactometerCalibration"; + _description = ""; + _taskParameters = new OlfactometerCalibrationParameters(); + _version = "0.2.0-rc0"; + } + + protected OlfactometerCalibrationLogic(OlfactometerCalibrationLogic other) + { + _name = other._name; + _description = other._description; + _taskParameters = other._taskParameters; + _version = other._version; + _stageName = other._stageName; + } + + [Newtonsoft.Json.JsonPropertyAttribute("name")] + public string Name + { + get + { + return _name; + } set { - _date = value; + _name = value; } } + /// + /// Description of the task. + /// [Newtonsoft.Json.JsonPropertyAttribute("description")] + [System.ComponentModel.DescriptionAttribute("Description of the task.")] public string Description { get @@ -765,37 +905,67 @@ public string Description } } - [Newtonsoft.Json.JsonPropertyAttribute("notes")] - public string Notes + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("task_parameters", Required=Newtonsoft.Json.Required.Always)] + public OlfactometerCalibrationParameters TaskParameters { get { - return _notes; + return _taskParameters; } set { - _notes = value; + _taskParameters = value; } } - public System.IObservable Process() + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibration(this))); + get + { + return _version; + } + set + { + _version = value; + } } - public System.IObservable Process(System.IObservable source) + /// + /// Optional stage name the `Task` object instance represents. + /// + [Newtonsoft.Json.JsonPropertyAttribute("stage_name")] + [System.ComponentModel.DescriptionAttribute("Optional stage name the `Task` object instance represents.")] + public string StageName { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibration(this)); + get + { + return _stageName; + } + set + { + _stageName = 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) + { + return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationLogic(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("device_name = " + _deviceName + ", "); - stringBuilder.Append("input = " + _input + ", "); - stringBuilder.Append("output = " + _output + ", "); - stringBuilder.Append("date = " + _date + ", "); - stringBuilder.Append("description = " + _description + ", "); - stringBuilder.Append("notes = " + _notes); + stringBuilder.Append("Name = " + _name + ", "); + stringBuilder.Append("Description = " + _description + ", "); + stringBuilder.Append("TaskParameters = " + _taskParameters + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("StageName = " + _stageName); return true; } @@ -814,21 +984,74 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class OlfactometerCalibrationInput + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class OlfactometerCalibrationParameters { - private System.Collections.Generic.IDictionary _channelConfig; + private double? _rngSeed; + + private string _aindBehaviorServicesPkgVersion; + + private System.Collections.Generic.Dictionary _channelConfig; + + private double _fullFlowRate; + + private int _nRepeatsPerStimulus; + + private double _timeOn; + + private double _timeOff; - public OlfactometerCalibrationInput() + public OlfactometerCalibrationParameters() { + _aindBehaviorServicesPkgVersion = "0.13.6"; + _fullFlowRate = 1000D; + _nRepeatsPerStimulus = 1; + _timeOn = 1D; + _timeOff = 1D; } - protected OlfactometerCalibrationInput(OlfactometerCalibrationInput other) + protected OlfactometerCalibrationParameters(OlfactometerCalibrationParameters other) { + _rngSeed = other._rngSeed; + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; _channelConfig = other._channelConfig; + _fullFlowRate = other._fullFlowRate; + _nRepeatsPerStimulus = other._nRepeatsPerStimulus; + _timeOn = other._timeOn; + _timeOff = other._timeOff; + } + + /// + /// Seed of the random number generator + /// + [Newtonsoft.Json.JsonPropertyAttribute("rng_seed")] + [System.ComponentModel.DescriptionAttribute("Seed of the random number generator")] + public double? RngSeed + { + get + { + return _rngSeed; + } + set + { + _rngSeed = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } } /// @@ -837,7 +1060,7 @@ protected OlfactometerCalibrationInput(OlfactometerCalibrationInput other) [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("channel_config")] [System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")] - public System.Collections.Generic.IDictionary ChannelConfig + public System.Collections.Generic.Dictionary ChannelConfig { get { @@ -849,19 +1072,93 @@ public System.Collections.Generic.IDictionary } } - public System.IObservable Process() + /// + /// Full flow rate of the olfactometer + /// + [Newtonsoft.Json.JsonPropertyAttribute("full_flow_rate")] + [System.ComponentModel.DescriptionAttribute("Full flow rate of the olfactometer")] + public double FullFlowRate { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationInput(this))); + get + { + return _fullFlowRate; + } + set + { + _fullFlowRate = value; + } } - public System.IObservable Process(System.IObservable source) + /// + /// Number of repeats per stimulus + /// + [Newtonsoft.Json.JsonPropertyAttribute("n_repeats_per_stimulus")] + [System.ComponentModel.DescriptionAttribute("Number of repeats per stimulus")] + public int NRepeatsPerStimulus { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationInput(this)); + get + { + return _nRepeatsPerStimulus; + } + set + { + _nRepeatsPerStimulus = 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 + { + get + { + return _timeOn; + } + set + { + _timeOn = 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 + { + get + { + return _timeOff; + } + set + { + _timeOff = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationParameters(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationParameters(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("channel_config = " + _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; } @@ -880,33 +1177,234 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class OlfactometerCalibrationOutput + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class OlfactometerCalibrationRig { - public OlfactometerCalibrationOutput() + private string _aindBehaviorServicesPkgVersion; + + private string _version; + + private string _computerName; + + private string _rigName; + + private string _dataDirectory; + + private Olfactometer _harpOlfactometer; + + private HarpAnalogInput _harpAnalogInput; + + private HarpWhiteRabbit _harpClockGenerator; + + private AllenNeuralDynamics.AindManipulator.AindManipulator _harpManipulator; + + private AlicatFlowmeter _flowmeter; + + public OlfactometerCalibrationRig() { + _aindBehaviorServicesPkgVersion = "0.13.6"; + _version = "0.2.0-rc0"; + _harpOlfactometer = new Olfactometer(); + _harpAnalogInput = new HarpAnalogInput(); + _harpClockGenerator = new HarpWhiteRabbit(); + _harpManipulator = new AllenNeuralDynamics.AindManipulator.AindManipulator(); } - protected OlfactometerCalibrationOutput(OlfactometerCalibrationOutput other) + protected OlfactometerCalibrationRig(OlfactometerCalibrationRig other) { + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _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("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } } - public System.IObservable Process() + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationOutput(this))); + get + { + return _version; + } + set + { + _version = value; + } } - public System.IObservable Process(System.IObservable source) + /// + /// Computer name + /// + [Newtonsoft.Json.JsonPropertyAttribute("computer_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Computer name")] + public string ComputerName { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationOutput(this)); + get + { + return _computerName; + } + set + { + _computerName = value; + } + } + + /// + /// Rig name + /// + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Rig name")] + public string RigName + { + get + { + return _rigName; + } + set + { + _rigName = value; + } + } + + /// + /// Directory where data will be saved to + /// + [Newtonsoft.Json.JsonPropertyAttribute("data_directory", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Directory where data will be saved to")] + public string DataDirectory + { + get + { + return _dataDirectory; + } + set + { + _dataDirectory = value; + } + } + + [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 + { + get + { + return _harpClockGenerator; + } + set + { + _harpClockGenerator = value; + } + } + + /// + /// 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; + } + } + + /// + /// 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() + { + 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) { - 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() @@ -927,7 +1425,7 @@ public override string ToString() /// /// Harp Olfactometer available channel /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] public enum OlfactometerChannel { @@ -945,19 +1443,23 @@ public enum OlfactometerChannel } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + /// + /// 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 int _channelIndex; - private OlfactometerChannelType _channelType = AindBehaviorDeviceOlfactometer.Rig.OlfactometerChannelType.Odor; + private OlfactometerChannelType _channelType; - private OlfactometerChannelConfigFlowRateCapacity _flowRateCapacity = AindBehaviorDeviceOlfactometer.Rig.OlfactometerChannelConfigFlowRateCapacity._100; + private OlfactometerChannelConfigFlowRateCapacity _flowRateCapacity; - private double _flowRate = 100D; + private double _flowRate; private string _odorant; @@ -965,6 +1467,9 @@ public partial class OlfactometerChannelConfig public OlfactometerChannelConfig() { + _channelType = OlfactometerChannelType.Odor; + _flowRateCapacity = OlfactometerChannelConfigFlowRateCapacity._100; + _flowRate = 100D; } protected OlfactometerChannelConfig(OlfactometerChannelConfig other) @@ -990,7 +1495,6 @@ public int ChannelIndex } } - [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("channel_type")] public OlfactometerChannelType ChannelType { @@ -1004,7 +1508,6 @@ public OlfactometerChannelType ChannelType } } - [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("flow_rate_capacity")] public OlfactometerChannelConfigFlowRateCapacity FlowRateCapacity { @@ -1044,7 +1547,6 @@ public string Odorant } } - [System.Xml.Serialization.XmlIgnoreAttribute()] [Newtonsoft.Json.JsonPropertyAttribute("odorant_dilution")] public double? OdorantDilution { @@ -1058,24 +1560,24 @@ public double? OdorantDilution } } - public System.IObservable Process() + public System.IObservable Generate() { return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerChannelConfig(this))); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Generate(System.IObservable source) { return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerChannelConfig(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("channel_index = " + _channelIndex + ", "); - stringBuilder.Append("channel_type = " + _channelType + ", "); - stringBuilder.Append("flow_rate_capacity = " + _flowRateCapacity + ", "); - stringBuilder.Append("flow_rate = " + _flowRate + ", "); - stringBuilder.Append("odorant = " + _odorant + ", "); - stringBuilder.Append("odorant_dilution = " + _odorantDilution); + 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; } @@ -1095,9 +1597,9 @@ public override string ToString() /// - /// Channel type + /// Olfactometer channel type /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] + [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 { @@ -1110,39 +1612,56 @@ public enum OlfactometerChannelType } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.9.0.0 (Newtonsoft.Json v13.0.0.0)")] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class OlfactometerCalibrationRig + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class Session { - private string _aindBehaviorServicesPkgVersion = "0.10.2"; + private string _aindBehaviorServicesPkgVersion; - private string _version = "0.2.0"; + private string _version; - private string _computerName; + private string _experiment; - private string _rigName; + private System.Collections.Generic.List _experimenter; - private HarpOlfactometer _harpOlfactometer = new HarpOlfactometer(); + private System.DateTimeOffset _date; - private HarpAnalogInput _harpAnalogInput = new HarpAnalogInput(); + private string _sessionName; - private HarpWhiteRabbit _harpClockGenerator = new HarpWhiteRabbit(); + private string _subject; - public OlfactometerCalibrationRig() + private string _notes; + + private string _commitHash; + + private bool _allowDirtyRepo; + + private bool _skipHardwareValidation; + + public Session() { + _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; + _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")] @@ -1172,100 +1691,200 @@ public string Version } /// - /// Computer name + /// Name of the experiment /// - [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] - [System.ComponentModel.DescriptionAttribute("Computer name")] - public string ComputerName + [Newtonsoft.Json.JsonPropertyAttribute("experiment")] + [System.ComponentModel.DescriptionAttribute("Name of the experiment")] + public string Experiment { get { - return _computerName; + return _experiment; } set { - _computerName = value; + _experiment = value; } } /// - /// Rig name + /// Name of the experimenter /// - [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Rig name")] - public string RigName + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] + [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] + public System.Collections.Generic.List Experimenter { get { - return _rigName; + return _experimenter; } set { - _rigName = value; + _experimenter = value; } } + /// + /// Date of the experiment + /// [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_olfactometer", Required=Newtonsoft.Json.Required.Always)] - public HarpOlfactometer HarpOlfactometer + [Newtonsoft.Json.JsonPropertyAttribute("date")] + [System.ComponentModel.DescriptionAttribute("Date of the experiment")] + public System.DateTimeOffset Date { get { - return _harpOlfactometer; + return _date; } set { - _harpOlfactometer = value; + _date = value; } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_analog_input", Required=Newtonsoft.Json.Required.Always)] - public HarpAnalogInput HarpAnalogInput + [Newtonsoft.Json.JsonIgnoreAttribute()] + [System.ComponentModel.BrowsableAttribute(false)] + [System.ComponentModel.EditorBrowsableAttribute(System.ComponentModel.EditorBrowsableState.Never)] + [System.Xml.Serialization.XmlElementAttribute("Date")] + public string DateXml { get { - return _harpAnalogInput; + return _date.ToString("o"); } set { - _harpAnalogInput = value; + _date = System.DateTimeOffset.Parse(value); } } - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_clock_generator", Required=Newtonsoft.Json.Required.Always)] - public HarpWhiteRabbit HarpClockGenerator + /// + /// 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 _harpClockGenerator; + return _sessionName; } set { - _harpClockGenerator = value; + _sessionName = value; } } - public System.IObservable Process() + /// + /// Name of the subject + /// + [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Name of the subject")] + public string Subject { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationRig(this))); + get + { + return _subject; + } + set + { + _subject = value; + } } - public System.IObservable Process(System.IObservable source) + /// + /// Notes about the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("notes")] + [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] + public string Notes { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationRig(this)); + 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 Session(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new Session(this)); } protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) { - stringBuilder.Append("aind_behavior_services_pkg_version = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("version = " + _version + ", "); - stringBuilder.Append("computer_name = " + _computerName + ", "); - stringBuilder.Append("rig_name = " + _rigName + ", "); - stringBuilder.Append("harp_olfactometer = " + _harpOlfactometer + ", "); - stringBuilder.Append("harp_analog_input = " + _harpAnalogInput + ", "); - stringBuilder.Append("harp_clock_generator = " + _harpClockGenerator); + 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; } @@ -1284,7 +1903,7 @@ public override string ToString() } - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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 { @@ -1299,16 +1918,24 @@ public enum OlfactometerChannelConfigFlowRateCapacity /// /// Serializes a sequence of data model objects into JSON strings. /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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.CombinatorAttribute()] [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] + [Bonsai.CombinatorAttribute()] public partial class SerializeToJson { + public Newtonsoft.Json.Formatting Formatting { get; set; } + private System.IObservable Process(System.IObservable source) { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value)); + var formatting = Formatting; + return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value, formatting)); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); } public System.IObservable Process(System.IObservable source) @@ -1326,14 +1953,14 @@ public System.IObservable Process(System.IObservable so return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); } public System.IObservable Process(System.IObservable source) @@ -1341,14 +1968,19 @@ public System.IObservable Process(System.IObservable(source); } - 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); + return Process(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); } public System.IObservable Process(System.IObservable source) @@ -1356,9 +1988,9 @@ public System.IObservable Process(System.IObservable(source); } - public System.IObservable Process(System.IObservable source) + public System.IObservable Process(System.IObservable source) { - return Process(source); + return Process(source); } } @@ -1366,26 +1998,28 @@ public System.IObservable Process(System.IObservable /// Deserializes a sequence of JSON strings into data model objects. /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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))] public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder { public DeserializeFromJson() { - Type = new Bonsai.Expressions.TypeMapping(); + Type = new Bonsai.Expressions.TypeMapping(); } public Bonsai.Expressions.TypeMapping Type { get; set; } diff --git a/src/Extensions/AindBehaviorSessionModel.cs b/src/Extensions/AindBehaviorSessionModel.cs deleted file mode 100644 index 4f7e8a0..0000000 --- a/src/Extensions/AindBehaviorSessionModel.cs +++ /dev/null @@ -1,379 +0,0 @@ -//---------------------- -// -// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) -// -//---------------------- - - -namespace AindBehaviorDeviceOlfactometer.Session -{ - #pragma warning disable // Disable all warnings - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindBehaviorSessionModel - { - - private string _aindBehaviorServicesPkgVersion = "0.10.2"; - - private string _version = "0.3.1"; - - private string _experiment; - - private System.Collections.Generic.List _experimenter = new System.Collections.Generic.List(); - - private System.DateTimeOffset _date; - - private string _rootPath; - - private string _sessionName; - - private string _subject; - - private string _experimentVersion; - - private string _notes; - - private string _commitHash; - - private bool _allowDirtyRepo = false; - - private bool _skipHardwareValidation = false; - - public AindBehaviorSessionModel() - { - } - - protected AindBehaviorSessionModel(AindBehaviorSessionModel other) - { - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _version = other._version; - _experiment = other._experiment; - _experimenter = other._experimenter; - _date = other._date; - _rootPath = other._rootPath; - _sessionName = other._sessionName; - _subject = other._subject; - _experimentVersion = other._experimentVersion; - _notes = other._notes; - _commitHash = other._commitHash; - _allowDirtyRepo = other._allowDirtyRepo; - _skipHardwareValidation = other._skipHardwareValidation; - } - - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion - { - get - { - return _aindBehaviorServicesPkgVersion; - } - set - { - _aindBehaviorServicesPkgVersion = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version - { - get - { - return _version; - } - set - { - _version = value; - } - } - - /// - /// Name of the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("experiment", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Name of the experiment")] - public string Experiment - { - get - { - return _experiment; - } - set - { - _experiment = value; - } - } - - /// - /// Name of the experimenter - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] - [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] - public System.Collections.Generic.List Experimenter - { - get - { - return _experimenter; - } - set - { - _experimenter = value; - } - } - - /// - /// Date of the experiment - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("date")] - [System.ComponentModel.DescriptionAttribute("Date of the experiment")] - public System.DateTimeOffset Date - { - get - { - return _date; - } - set - { - _date = value; - } - } - - /// - /// Root path where data will be logged - /// - [Newtonsoft.Json.JsonPropertyAttribute("root_path", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Root path where data will be logged")] - public string RootPath - { - get - { - return _rootPath; - } - set - { - _rootPath = value; - } - } - - /// - /// Name of the session. This will be used to create a folder in the root path. - /// - [Newtonsoft.Json.JsonPropertyAttribute("session_name")] - [System.ComponentModel.DescriptionAttribute("Name of the session. This will be used to create a folder in the root path.")] - public string SessionName - { - get - { - return _sessionName; - } - set - { - _sessionName = value; - } - } - - /// - /// Name of the subject - /// - [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Name of the subject")] - public string Subject - { - get - { - return _subject; - } - set - { - _subject = value; - } - } - - /// - /// Version of the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("experiment_version", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Version of the experiment")] - public string ExperimentVersion - { - get - { - return _experimentVersion; - } - set - { - _experimentVersion = value; - } - } - - /// - /// Notes about the experiment - /// - [Newtonsoft.Json.JsonPropertyAttribute("notes")] - [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] - public string Notes - { - get - { - return _notes; - } - set - { - _notes = value; - } - } - - /// - /// Commit hash of the repository - /// - [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")] - [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")] - public string CommitHash - { - get - { - return _commitHash; - } - set - { - _commitHash = value; - } - } - - /// - /// Allow running from a dirty repository - /// - [Newtonsoft.Json.JsonPropertyAttribute("allow_dirty_repo")] - [System.ComponentModel.DescriptionAttribute("Allow running from a dirty repository")] - public bool AllowDirtyRepo - { - get - { - return _allowDirtyRepo; - } - set - { - _allowDirtyRepo = value; - } - } - - /// - /// Skip hardware validation - /// - [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")] - [System.ComponentModel.DescriptionAttribute("Skip hardware validation")] - public bool SkipHardwareValidation - { - get - { - return _skipHardwareValidation; - } - set - { - _skipHardwareValidation = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorSessionModel(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorSessionModel(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("aind_behavior_services_pkg_version = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("version = " + _version + ", "); - stringBuilder.Append("experiment = " + _experiment + ", "); - stringBuilder.Append("experimenter = " + _experimenter + ", "); - stringBuilder.Append("date = " + _date + ", "); - stringBuilder.Append("root_path = " + _rootPath + ", "); - stringBuilder.Append("session_name = " + _sessionName + ", "); - stringBuilder.Append("subject = " + _subject + ", "); - stringBuilder.Append("experiment_version = " + _experimentVersion + ", "); - stringBuilder.Append("notes = " + _notes + ", "); - stringBuilder.Append("commit_hash = " + _commitHash + ", "); - stringBuilder.Append("allow_dirty_repo = " + _allowDirtyRepo + ", "); - stringBuilder.Append("skip_hardware_validation = " + _skipHardwareValidation); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - /// - /// Serializes a sequence of data model objects into JSON strings. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into JSON strings.")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] - public partial class SerializeToJson - { - - private System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value)); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - } - - - /// - /// Deserializes a sequence of JSON strings into data model objects. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of JSON strings into data model objects.")] - [System.ComponentModel.DefaultPropertyAttribute("Type")] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder - { - - public DeserializeFromJson() - { - Type = new Bonsai.Expressions.TypeMapping(); - } - - public Bonsai.Expressions.TypeMapping Type { get; set; } - - public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) - { - var typeMapping = (Bonsai.Expressions.TypeMapping)Type; - var returnType = typeMapping.GetType().GetGenericArguments()[0]; - return System.Linq.Expressions.Expression.Call( - typeof(DeserializeFromJson), - "Process", - new System.Type[] { returnType }, - System.Linq.Enumerable.Single(arguments)); - } - - private static System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.DeserializeObject(value)); - } - } -} \ No newline at end of file diff --git a/src/Extensions/AindManipulator.bonsai b/src/Extensions/AindManipulator.bonsai new file mode 100644 index 0000000..c1fcbc2 --- /dev/null +++ b/src/Extensions/AindManipulator.bonsai @@ -0,0 +1,50 @@ + + + + + + Source1 + + + + + + Active + On + false + On + Enabled + false + COMx + + + + TriggerHarpReadDump + + + Write + + Active + true + false + On + Off + Enabled + + + + StepperDriverCommands + + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/CalibrationLogic.bonsai b/src/Extensions/CalibrationLogic.bonsai index 4877ba8..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.TaskLogic;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 96cf18c..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/HarpStepperDriverGetMetadata.bonsai b/src/Extensions/HarpStepperDriverGetMetadata.bonsai new file mode 100644 index 0000000..98a17bf --- /dev/null +++ b/src/Extensions/HarpStepperDriverGetMetadata.bonsai @@ -0,0 +1,812 @@ + + + + + + + %YAML 1.1 +--- +# yaml-language-server: $schema=https://harp-tech.org/draft-02/schema/device.json +device: StepperDriver +whoAmI: 1130 +firmwareVersion: "0.7" +hardwareTargets: "1.0" +registers: + ################################## + # Enable and disable + ################################## + EnableDriver: + address: 32 + type: U8 + access: Write + maskType: StepperMotors + description: Enables the driver for a specific motor. If the driver is already enabled, the driver remains enabled. + DisableDriver: + address: 33 + type: U8 + access: Write + maskType: StepperMotors + description: Disables the driver for a specific stepper motor, which prevents current from being sent to the motor or load. If the driver is already disabled, the driver remains disabled. + EnableEncoders: + address: 34 + type: U8 + access: Write + maskType: QuadratureEncoders + description: Specifies a set of port quadrature counters to enable in the device. + DisableEncoders: + address: 35 + type: U8 + access: Write + maskType: QuadratureEncoders + description: Specifies a set of port quadrature counters to disable in the device. + EnableDigitalInputs: + address: 36 + type: U8 + access: Write + maskType: DigitalInputs + description: Specifies a set of digital inputs to enable in the device. + DisableDigitalInputs: + address: 37 + type: U8 + access: Write + maskType: DigitalInputs + description: Specifies a set of digital inputs to disable in the device. + + ################################## + # Configuration + ################################## + Motor0OperationMode: &opmode + address: 38 + type: U8 + access: Write + maskType: MotorOperationMode + description: Configures the operation mode for motor 0. + Motor1OperationMode: + <<: *opmode + address: 39 + description: Configures the operation mode for motor 1. + Motor2OperationMode: + <<: *opmode + address: 40 + description: Configures the operation mode for motor 2. + Motor3OperationMode: + <<: *opmode + address: 41 + description: Configures the operation mode for motor 3. + Motor0MicrostepResolution: &microstep_resolution + address: 42 + type: U8 + access: Write + maskType: MicrostepResolution + description: Configures the microstep resolution for motor 0. + Motor1MicrostepResolution: + <<: *microstep_resolution + address: 43 + description: Configures the microstep resolution for motor 1. + Motor2MicrostepResolution: + <<: *microstep_resolution + address: 44 + description: Configures the microstep resolution for motor 2. + Motor3MicrostepResolution: + <<: *microstep_resolution + address: 45 + description: Configures the microstep resolution for motor 3. + + Motor0MaximumRunCurrent: &maxcurrent + address: 46 + minValue: 0.139 + maxValue: 2.1 + defaultValue: 0.2 + type: Float + access: Write + description: Configures the maximum run RMS current per phase for motor 0. + Motor1MaximumRunCurrent: + <<: *maxcurrent + address: 47 + description: Configures the maximum run RMS current per phase for motor 1. + Motor2MaximumRunCurrent: + <<: *maxcurrent + address: 48 + description: Configures the maximum run RMS current per phase for motor 2. + Motor3MaximumRunCurrent: + <<: *maxcurrent + address: 49 + description: Configures the maximum run RMS current per phase for motor 3. + + Motor0HoldCurrentReduction: &currentreduction + address: 50 + type: U8 + access: Write + maskType: HoldCurrentReduction + description: Configures the hold current reduction for motor 0. + Motor1HoldCurrentReduction: + <<: *currentreduction + address: 51 + description: Configures the hold current reduction for motor 1. + Motor2HoldCurrentReduction: + <<: *currentreduction + address: 52 + description: Configures the hold current reduction for motor 2. + Motor3HoldCurrentReduction: + <<: *currentreduction + address: 53 + description: Configures the hold current reduction for motor 3. + + Motor0StepInterval: &nominalinterval + address: 54 + minValue: 100 + maxValue: 20000 + defaultValue: 250 + type: U16 + access: Write + description: Configures the time between step motor pulses (us) when running at nominal speed for motor 0. + Motor1StepInterval: + <<: *nominalinterval + address: 55 + description: Configures the time between step motor pulses (us) when running at nominal speed for motor 1. + Motor2StepInterval: + <<: *nominalinterval + address: 56 + description: Configures the time between step motor pulses (us) when running at nominal speed for motor 2. + Motor3StepInterval: + <<: *nominalinterval + address: 57 + description: Configures the time between step motor pulses (us) when running at nominal speed for motor 3. + + Motor0MaximumStepInterval: &maxinterval + address: 58 + minValue: 100 + maxValue: 20000 + defaultValue: 2000 + type: U16 + access: Write + description: Configures the time between step motor pulses (us) used when starting or stopping a movement for motor 0. + Motor1MaximumStepInterval: + <<: *maxinterval + address: 59 + description: Configures the time between step motor pulses (us) used when starting or stopping a movement for motor 1. + Motor2MaximumStepInterval: + <<: *maxinterval + address: 60 + description: Configures the time between step motor pulses (us) used when starting or stopping a movement for motor 2. + Motor3MaximumStepInterval: + <<: *maxinterval + address: 61 + description: Configures the time between step motor pulses (us) used when starting or stopping a movement for motor 3. + + Motor0StepAccelerationInterval: &accperiod + address: 62 + minValue: 2 + maxValue: 2000 + defaultValue: 10 + type: U16 + access: Write + description: Configures the acceleration for motor 0. The time between step pulses is decreased by this value when accelerating and increased when decelerating. + Motor1StepAccelerationInterval: + <<: *accperiod + address: 63 + description: Configures the acceleration for motor 1. The time between step pulses is decreased by this value when accelerating and increased when decelerating. + Motor2StepAccelerationInterval: + <<: *accperiod + address: 64 + description: Configures the acceleration for motor 2. The time between step pulses is decreased by this value when accelerating and increased when decelerating. + Motor3StepAccelerationInterval: + <<: *accperiod + address: 65 + description: Configures the acceleration for motor 3. The time between step pulses is decreased by this value when accelerating and increased when decelerating. + + EncoderMode: + address: 66 + type: U8 + access: Write + maskType: EncoderModeConfig + description: Configures the operation mode of the quadrature encoder. + EncoderSamplingRate: + address: 67 + type: U8 + access: Write + maskType: EncoderSamplingRateConfig + description: Configures the sampling rate of the quadrature encoder event. + + Input0OpMode: &input_mode + address: 68 + type: U8 + access: Write + maskType: InputOpModeConfig + description: Configures the operation mode for digital input 0. + Input1OpMode: + <<: *input_mode + address: 69 + description: Configures the operation mode for digital input 1. + Input2OpMode: + <<: *input_mode + address: 70 + description: Configures the operation mode for digital input 2. + Input3OpMode: + <<: *input_mode + address: 71 + description: Configures the operation mode for digital input 3. + + InterlockEnabled: + address: 72 + type: U8 + access: Write + maskType: InterlockEnabledConfig + description: Configures the external interlock connector state required for the device to be enabled. + + AccumulatedStepsSamplingRate: + address: 73 + type: U8 + access: Write + maskType: AccumulatedStepsSamplingRateConfig + description: Configures the dispatch rate of the accumulated steps event. + + ################################## + # Events + ################################## + MotorStopped: + address: 74 + type: U8 + access: Event + description: Emitted when any of the motors stops. + payloadSpec: + State: + description: Specifies which motors are currently stopped. + maskType: StepperMotors + mask: 0x0F + Changed: + description: Specifies which motor just stopped. + maskType: StepperMotors + mask: 0xF0 + MotorOverVoltageDetection: + address: 75 + type: U8 + access: Event + maskType: StepperMotors + description: Contains a bit mask specifying the motor where the over voltage detection and protection mechanism occurred, which can happen when the there's a quick deceleration from a high velocity or when the motor stalls (not implemented). + MotorRaisedError: + address: 76 + type: U8 + access: Event + maskType: StepperMotors + description: Contains a bit mask specifying the motor that triggered the error which can be happen in case of short-circuit or driver temperature above 165 degrees celsius. + + Encoders: + address: 77 + type: S16 + length: 3 + access: [Event, Write] + description: Contains the quadrature encoder readings. + payloadSpec: + Encoder0: + offset: 0 + description: The quadrature counter on port ENC 0. + Encoder1: + offset: 1 + description: The quadrature counter on port ENC 1. + Encoder2: + offset: 2 + description: The quadrature counter on port ENC 2. + + DigitalInputState: + address: 78 + access: Event + type: U8 + maskType: DigitalInputStates + description: Reflects the state of the digital input lines. + + DeviceState: + address: 79 + type: U8 + access: Event + maskType: DeviceStateMode + description: Contains the state of the device. + + ################################## + # Movement control + ################################## + + MoveRelative: + address: 80 + type: S32 + length: 4 + access: Write + description: Moves all motors by the number of steps written in this array register and set the direction according to the value's signal. If a motor is disable, the user should set the value to 0. + payloadSpec: + Motor0: + offset: 0 + description: Contains the number of steps used to move motor 0. + Motor1: + offset: 1 + description: Contains the number of steps used to move motor 1. + Motor2: + offset: 2 + description: Contains the number of steps used to move motor 2. + Motor3: + offset: 3 + description: Contains the number of steps used to move motor 3. + + Motor0MoveRelative: &motorsteps + address: 81 + type: S32 + access: Write + description: Moves motor 0 by the number of steps written in this register and set the direction according to the value's signal. + Motor1MoveRelative: + <<: *motorsteps + address: 82 + description: Moves motor 1 by the number of steps written in this register and set the direction according to the value's signal. + Motor2MoveRelative: + <<: *motorsteps + address: 83 + description: Moves motor 2 by the number of steps written in this register and set the direction according to the value's signal. + Motor3MoveRelative: + <<: *motorsteps + address: 84 + description: Moves motor 3 by the number of steps written in this register and set the direction according to the value's signal. + + MoveAbsolute: + address: 85 + type: S32 + length: 4 + access: Write + description: Moves all motors to the absolute position written in this array register. If a motor is disable, the user should set the value to 0. + payloadSpec: + Motor0: + offset: 0 + description: Contains the absolute position to move motor 0. + Motor1: + offset: 1 + description: Contains the absolute position to move motor 1. + Motor2: + offset: 2 + description: Contains the absolute position to move motor 2. + Motor3: + offset: 3 + description: Contains the absolute position to move motor 3. + + Motor0MoveAbsolute: &motorabsolutesteps + address: 86 + type: S32 + access: Write + description: Moves motor 0 to the absolute position written in this register. + Motor1MoveAbsolute: + <<: *motorabsolutesteps + address: 87 + description: Moves motor 1 to the absolute position written in this register. + Motor2MoveAbsolute: + <<: *motorabsolutesteps + address: 88 + description: Moves motor 2 to the absolute position written in this register. + Motor3MoveAbsolute: + <<: *motorabsolutesteps + address: 89 + description: Moves motor 3 to the absolute position written in this register. + + AccumulatedSteps: + address: 90 + type: S32 + length: 4 + access: [Event, Write] + description: Contains the accumulated steps of all motors. Write a value to set the accumulated steps. An event will be emitted with a dispatch rate defined in AccumulatedStepsSamplingRate. + payloadSpec: + Motor0: + offset: 0 + description: Contains the accumulated steps of motor 0. + Motor1: + offset: 1 + description: Contains the accumulated steps of motor 1. + Motor2: + offset: 2 + description: Contains the accumulated steps of motor 2. + Motor3: + offset: 3 + description: Contains the accumulated steps of motor 3. + + Mortor0AccumulatedSteps: &motorsaccumulatedsteps + address: 91 + type: S32 + access: Write + description: Contains the accumulated number of steps of motor 0. Write a value to set the current number of accumulated steps. + Mortor1AccumulatedSteps: + <<: *motorsaccumulatedsteps + address: 92 + description: Contains the accumulated number of steps of motor 1. Write a value to set the current number of accumulated steps. + Mortor2AccumulatedSteps: + <<: *motorsaccumulatedsteps + address: 93 + description: Contains the accumulated number of steps of motor 2. Write a value to set the current number of accumulated steps. + Mortor3AccumulatedSteps: + <<: *motorsaccumulatedsteps + address: 94 + description: Contains the accumulated number of steps of motor 3. Write a value to set the current number of accumulated steps. + + MaxPosition: + address: 95 + type: S32 + length: 4 + access: Write + description: Defines the limit of the accumulated steps for the positive movement of all motors. The device will not let the motors move further than this value. A value equal to 0 will disable the limits. + payloadSpec: + Motor0: + offset: 0 + description: Defines the limit of the accumulated steps for the positive movement of motor 0. The device will not let the motor move further than this value. + Motor1: + offset: 1 + description: Defines the limit of the accumulated steps for the positive movement of motor 1. The device will not let the motor move further than this value. + Motor2: + offset: 2 + description: Defines the limit of the accumulated steps for the positive movement of motor 2. The device will not let the motor move further than this value. + Motor3: + offset: 3 + description: Defines the limit of the accumulated steps for the positive movement of motor 3. The device will not let the motor move further than this value. + + Motor0MaxPosition: &motorsmaxsteps + address: 96 + type: S32 + access: Write + description: Specifies the limit of the accumulated steps for the positive movement of motor 0. The device will not let the motor move further than this value. A value equal to 0 disables the feature. + Motor1MaxPosition: + <<: *motorsmaxsteps + address: 97 + description: Specifies the limit of the accumulated steps for the positive movement of motor 1. The device will not let the motor move further than this value. A value equal to 0 disables the feature. + Motor2MaxPosition: + <<: *motorsmaxsteps + address: 98 + description: Specifies the limit of the accumulated steps for the positive movement of motor 2. The device will not let the motor move further than this value. A value equal to 0 disables the feature. + Motor3MaxPosition: + <<: *motorsmaxsteps + address: 99 + description: Specifies the limit of the accumulated steps for the positive movement of motor 3. The device will not let the motor move further than this value. A value equal to 0 disables the feature. + + MinPosition: + address: 100 + type: S32 + length: 4 + access: Write + description: Defines the limit of the accumulated steps for the negative movement of all motors. The device will not let the motors move further than this value. A value equal to 0 will disable the limits. + payloadSpec: + Motor0: + offset: 0 + description: Defines the limit of the accumulated steps for the negative movement of motor 0. The device will not let the motor move further than this value. + Motor1: + offset: 1 + description: Defines the limit of the accumulated steps for the negative movement of motor 1. The device will not let the motor move further than this value. + Motor2: + offset: 2 + description: Defines the limit of the accumulated steps for the negative movement of motor 2. The device will not let the motor move further than this value. + Motor3: + offset: 3 + description: Defines the limit of the accumulated steps for the negative movement of motor 3. The device will not let the motor move further than this value. + + Motor0MinPosition: &motorsminsteps + address: 101 + type: S32 + access: Write + description: Specifies the limit of the accumulated steps for the negative movement of motor 0. The device will not let the motor move further than this value. A value equal to 0 disables the feature. + Motor1MinPosition: + <<: *motorsminsteps + address: 102 + description: Specifies the limit of the accumulated steps for the negative movement of motor 1. The device will not let the motor move further than this value. A value equal to 0 disables the feature. + Motor2MinPosition: + <<: *motorsminsteps + address: 103 + description: Specifies the limit of the accumulated steps for the negative movement of motor 2. The device will not let the motor move further than this value. A value equal to 0 disables the feature. + Motor3MinPosition: + <<: *motorsminsteps + address: 104 + description: Specifies the limit of the accumulated steps for the negative movement of motor 3. The device will not let the motor move further than this value. A value equal to 0 disables the feature. + + StepRelative: + address: 105 + type: S32 + length: 4 + access: Write + description: Starts the movement of all motors with the step interval defined by this array. The value's signal defines the direction. + payloadSpec: + Motor0: + offset: 0 + description: Starts the movement of motor 0 with the step interval defined by this register. The value's signal defines the direction. + Motor1: + offset: 1 + description: Starts the movement of motor 1 with the step interval defined by this register. The value's signal defines the direction. + Motor2: + offset: 2 + description: Starts the movement of motor 2 with the step interval defined by this register. The value's signal defines the direction. + Motor3: + offset: 3 + description: Starts the movement of motor 3 with the step interval defined by this register. The value's signal defines the direction. + + Motor0StepRelative: &immediatesteps + address: 106 + type: S32 + access: Write + description: Starts the movement of motor 0 with the step interval defined by this register, disregarding the acceleration protocol. The sign of the value specifies the direction. + Motor1StepRelative: + <<: *immediatesteps + address: 107 + description: Starts the movement of motor 1 with the step interval defined by this register, disregarding the acceleration protocol. The sign of the value specifies the direction. + Motor2StepRelative: + <<: *immediatesteps + address: 108 + description: Starts the movement of motor 2 with the step interval defined by this register, disregarding the acceleration protocol. The sign of the value specifies the direction. + Motor3StepRelative: + <<: *immediatesteps + address: 109 + description: Starts the movement of motor 3 with the step interval defined by this register, disregarding the acceleration protocol. The sign of the value specifies the direction. + + ################################## + # Actions + ################################## + StopMotors: + address: 110 + type: U8 + access: Write + maskType: StepperMotors + description: Stops the motors selected in the bit-mask immediately. + ResetMotors: + address: 111 + type: U8 + access: Write + visibility: private + maskType: StepperMotors + description: Resets the internal motor driver which also clears any eventual error (not implemented). + ResetEncoders: + address: 112 + type: U8 + access: Write + maskType: QuadratureEncoders + description: Resets the encoder. + + ################################## + # Reserved + ################################## + Reserved0: &reserved + address: 113 + type: U8 + access: Write + visibility: private + description: Contains the CFG configuration pins of the TMC2210 driver that controls motor 0. + Reserved1: + <<: *reserved + address: 114 + description: Contains the CFG configuration pins of the TMC2210 driver that controls motor 1. + Reserved2: + <<: *reserved + address: 115 + description: Contains the CFG configuration pins of the TMC2210 driver that controls motor 2. + Reserved3: + <<: *reserved + address: 116 + description: Contains the CFG configuration pins of the TMC2210 driver that controls motor 3. + Reserved4: + <<: *reserved + address: 117 + visibility: private + description: Contains the raw data of the digital potentiometer that controls current limit of motor 0. + Reserved5: + <<: *reserved + address: 118 + visibility: private + description: Contains the raw data of the digital potentiometer that controls current limit of motor 1. + Reserved6: + <<: *reserved + address: 119 + visibility: private + description: Contains the raw data of the digital potentiometer that controls current limit of motor 2. + Reserved7: + <<: *reserved + address: 120 + visibility: private + description: Contains the raw data of the digital potentiometer that controls current limit of motor 3. + + ################################## + # Reserved block + ################################## + Reserved8: &reserved_unused + address: 121 + visibility: private + type: U8 + access: Read + description: Reserved register. + Reserved9: + <<: *reserved_unused + address: 122 + Reserved10: + <<: *reserved_unused + address: 123 + Reserved11: + <<: *reserved_unused + address: 124 + Reserved12: + <<: *reserved_unused + address: 125 + Reserved13: + <<: *reserved_unused + address: 126 + Reserved14: + <<: *reserved_unused + address: 127 + Reserved15: + <<: *reserved_unused + address: 128 + Reserved16: + <<: *reserved_unused + address: 129 + + ################################## + # Quick movement + ################################## + TriggerQuickMovement: + address: 130 + type: U8 + access: Write + maskType: StepperMotors + description: Triggers the quick movement in the correspondent motor with the currently configured settings. + Motor1QuickMovementPulseDistance: &quickmovement_pulsedistance + address: 131 + type: Float + access: Write + description: Sets the single pulse distance for a quick movement, in millimeters, for the Motor 1. + Motor2QuickMovementPulseDistance: + <<: *quickmovement_pulsedistance + address: 132 + description: Sets the single pulse distance for a quick movement, in millimeters, for the Motor 2. + Motor1QuickMovementNominalSpeed: &quickmovement_nominalspeed + address: 133 + type: Float + access: Write + description: Sets the target speed for a quick movement, in millimeters per second, for the Motor 1. + Motor2QuickMovementNominalSpeed: + <<: *quickmovement_nominalspeed + address: 134 + description: Sets the target speed for a quick movement, in millimeters per second, for the Motor 2. + Motor1QuickMovementInitialSpeed: &quickmovement_initialspeed + address: 135 + type: Float + access: Write + description: Sets the initial speed for a quick movement, in millimeters per second, for the Motor 1. + Motor2QuickMovementInitialSpeed: + <<: *quickmovement_initialspeed + address: 136 + description: Sets the initial speed for a quick movement, in millimeters per second, for the Motor 2. + Motor1QuickMovementAcceleration: &quickmovement_acceleration + address: 137 + type: Float + access: Write + description: Sets the acceleration for a quick movement, in millimeters per second^2, for the Motor 1. + Motor2QuickMovementAcceleration: + <<: *quickmovement_acceleration + address: 138 + description: Sets the acceleration for a quick movement, in millimeters per second^2, for the Motor 2. + Motor1QuickMovementDistance: &quickmovement_distance + address: 139 + type: Float + access: Write + description: Sets the travel distance of a quick movement, in millimeters, for the Motor 1. + Motor2QuickMovementDistance: + <<: *quickmovement_distance + address: 140 + description: Sets the travel distance of a quick movement, in millimeters, for the Motor 1. + +################################## +# Bit masks +################################## +bitMasks: + StepperMotors: + description: Specifies the index of each motor. + bits: + Motor0: 0x01 + Motor1: 0x02 + Motor2: 0x04 + Motor3: 0x08 + QuadratureEncoders: + description: Specifies the index of each motor. + bits: + Encoder0: 0x01 + Encoder1: 0x02 + Encoder2: 0x04 + DigitalInputs: + description: Specifies the available digital input lines. + bits: + Input0: 0x1 + Input1: 0x2 + Input2: 0x4 + Input3: 0x8 + DigitalInputStates: + description: Specifies the state of the port and digital input line that changed. + bits: + Input0: 0x1 + Input1: 0x2 + Input2: 0x4 + Input3: 0x8 + Input0Changed: 0x10 + Input1Changed: 0x20 + Input2Changed: 0x40 + Input3Changed: 0x80 +################################## +# Group masks +################################## +groupMasks: + EncoderModeConfig: + description: Specifies the type of reading made from the quadrature QuadratureEncoders. + values: + Position: 0 + Displacement: 1 + EncoderSamplingRateConfig: + description: Specifies the rate of the events from the quadrature QuadratureEncoders. + values: + Rate100Hz: 0 + Rate200Hz: 1 + Rate250Hz: 2 + Rate500Hz: 3 + MotorOperationMode: + description: Specifies the motor operation mode. + values: + QuietMode: 0 + DynamicMovements: 1 + MicrostepResolution: + description: Specifies the microstep resolution for each step pulse. + values: + Microstep8: 0 + Microstep16: 1 + Microstep32: 2 + Microstep64: 3 + HoldCurrentReduction: + description: Specifies the hold current reduction. + values: + ReductionTo50Percent: 0 + ReductionTo25Percent: 1 + ReductionTo12Percent: 2 + NoReduction: 3 + InputOpModeConfig: + description: Specifies the inputs operation mode. + values: + EventOnly: 0x0 + StopMotor0OnRising: 0x10 + StopMotor1OnRising: 0x11 + StopMotor2OnRising: 0x12 + StopMotor3OnRising: 0x13 + StopMotor0OnFalling: 0x20 + StopMotor1OnFalling: 0x21 + StopMotor2OnFalling: 0x22 + StopMotor3OnFalling: 0x23 + TriggerConfig: + description: Specifies the input trigger configuration. + values: + FallingEdge: 0 + RisingEdge: 1 + InterlockEnabledConfig: + description: Specifies the external connector state that enables the device. + values: + Closed: 0 + Open: 1 + AccumulatedStepsSamplingRateConfig: + description: Specifies the rate of the accumulated steps events. + values: + Disabled: 0 + Rate10Hz: 1 + Rate50Hz: 2 + Rate100Hz: 3 + DeviceStateMode: + description: Specifies the current state of the device. + values: + Disabled: 0 + Enabled: 1 + + + + + 1 + + + + + + + + + + \ No newline at end of file diff --git a/src/Extensions/Logging.bonsai b/src/Extensions/Logging.bonsai index c3d4b14..bb2b5c2 100644 --- a/src/Extensions/Logging.bonsai +++ b/src/Extensions/Logging.bonsai @@ -1,16 +1,17 @@  - @@ -52,11 +53,18 @@ - - LoggingRootPath + + + + + + + + + + Behavior Olfactometer - Olfactometer HarpWhiteRabbitEvents @@ -69,11 +77,18 @@ - - LoggingRootPath + + + + + + + + + + Behavior WhiteRabbit - WhiteRabbit HarpAnalogInputEvents @@ -86,23 +101,65 @@ - - LoggingRootPath + + + + + + + + + + Behavior AnalogInput - AnalogInput + + + StepperDriverEvents + + + Modality + + + + + + + + + + + + + + + + + Behavior + StepperDriver - + - - - - - + + + + + + - + + + + + + + + + + + @@ -126,9 +183,9 @@ - - - + + + @@ -139,11 +196,18 @@ - - LoggingRootPath + + + + + + + + + + Behavior HarpCommands/Olfactometer - Olfactometer HarpAnalogInputCommands @@ -155,9 +219,9 @@ - - - + + + @@ -168,11 +232,18 @@ - - LoggingRootPath + + + + + + + + + + Behavior HarpCommands/AnalogInput - AnalogInput HarpWhiteRabbitCommands @@ -184,9 +255,9 @@ - - - + + + @@ -197,11 +268,54 @@ - - LoggingRootPath + + + + + + + + + + Behavior HarpCommands/WhiteRabbit - WhiteRabbit + + + StepperDriverEvents + + + HarpSeconds + + + + + + + + + + + + Modality + + + + + + + + + + + + + + + + + Behavior + HarpCommands/StepperDriver @@ -209,21 +323,35 @@ - + - - - - - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + @@ -231,21 +359,64 @@ SoftwareEvents - - SoftwareEvent + + Metadata + + + + Repository + + + + false + + + + + RepositoryStatus + + + + EndExperiment + + + + ExperimentCompleted + + + + + EndSession + + + + + + + SoftwareEvent + + + + + + + + + + + + - - TaskPoolScheduler + + PT1S - HarpTimestampSource + SoftwareEvent - - - TaskPoolScheduler - + + HarpTimestampSource @@ -270,39 +441,10 @@ - - Metadata - - - - Repository - - - - false - - - - - RepositoryStatus - - - - SoftwareEvent - - - - - - - - - - - + @@ -338,7 +480,9 @@ SessionSchema - + + None + Modality @@ -366,7 +510,9 @@ TaskLogicSchema - + + None + Modality @@ -394,7 +540,9 @@ RigSchema - + + None + Modality @@ -534,77 +682,6 @@ - - Logs - - - - EndExperiment - - - - ExperimentCompleted - - - - - SoftwareEvent - - - - HarpTimestampSource - - - - - - - - - - - - - - - Modality - - - - - - - - DeviceName - - - - - - - - LoggingRootPath - - - endsession - - - - - - - - - - - - - - - - - - @@ -612,11 +689,35 @@ + + AlicatFlowmeterEvents + + + LoggingRootPath + Behavior + AlicatFlowmeter + OperationControl + + + RigSchema + + + Flowmeter + + + + + + + + + + diff --git a/src/Extensions/OlfactometerCalibrationLogic.cs b/src/Extensions/OlfactometerCalibrationLogic.cs deleted file mode 100644 index 3acd83f..0000000 --- a/src/Extensions/OlfactometerCalibrationLogic.cs +++ /dev/null @@ -1,610 +0,0 @@ -//---------------------- -// -// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) -// -//---------------------- - - -namespace AindBehaviorDeviceOlfactometer.TaskLogic -{ - #pragma warning disable // Disable all warnings - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class OlfactometerCalibrationParameters - { - - private double? _rngSeed; - - private string _aindBehaviorServicesPkgVersion = "0.10.2"; - - private System.Collections.Generic.IDictionary _channelConfig; - - private double _fullFlowRate = 1000D; - - private int _nRepeatsPerStimulus = 1; - - private double _timeOn = 1D; - - private double _timeOff = 1D; - - public OlfactometerCalibrationParameters() - { - } - - protected OlfactometerCalibrationParameters(OlfactometerCalibrationParameters other) - { - _rngSeed = other._rngSeed; - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _channelConfig = other._channelConfig; - _fullFlowRate = other._fullFlowRate; - _nRepeatsPerStimulus = other._nRepeatsPerStimulus; - _timeOn = other._timeOn; - _timeOff = other._timeOff; - } - - /// - /// Seed of the random number generator - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("rng_seed")] - [System.ComponentModel.DescriptionAttribute("Seed of the random number generator")] - public double? RngSeed - { - get - { - return _rngSeed; - } - set - { - _rngSeed = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion - { - get - { - return _aindBehaviorServicesPkgVersion; - } - set - { - _aindBehaviorServicesPkgVersion = value; - } - } - - /// - /// Configuration of olfactometer channels - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("channel_config")] - [System.ComponentModel.DescriptionAttribute("Configuration of olfactometer channels")] - public System.Collections.Generic.IDictionary ChannelConfig - { - get - { - return _channelConfig; - } - set - { - _channelConfig = 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 - { - get - { - return _fullFlowRate; - } - set - { - _fullFlowRate = value; - } - } - - /// - /// 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 _nRepeatsPerStimulus; - } - set - { - _nRepeatsPerStimulus = 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 - { - get - { - return _timeOn; - } - set - { - _timeOn = 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 - { - get - { - return _timeOff; - } - set - { - _timeOff = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationParameters(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationParameters(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("rng_seed = " + _rngSeed + ", "); - stringBuilder.Append("aind_behavior_services_pkg_version = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("channel_config = " + _channelConfig + ", "); - stringBuilder.Append("full_flow_rate = " + _fullFlowRate + ", "); - stringBuilder.Append("n_repeats_per_stimulus = " + _nRepeatsPerStimulus + ", "); - stringBuilder.Append("time_on = " + _timeOn + ", "); - stringBuilder.Append("time_off = " + _timeOff); - 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(); - } - } - - - /// - /// Harp Olfactometer available channel - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class OlfactometerChannelConfig - { - - private int _channelIndex; - - private OlfactometerChannelType _channelType = AindBehaviorDeviceOlfactometer.TaskLogic.OlfactometerChannelType.Odor; - - private OlfactometerChannelConfigFlowRateCapacity _flowRateCapacity = AindBehaviorDeviceOlfactometer.TaskLogic.OlfactometerChannelConfigFlowRateCapacity._100; - - private double _flowRate = 100D; - - private string _odorant; - - private double? _odorantDilution; - - public OlfactometerChannelConfig() - { - } - - 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 - { - get - { - return _channelIndex; - } - set - { - _channelIndex = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("channel_type")] - public OlfactometerChannelType ChannelType - { - get - { - return _channelType; - } - set - { - _channelType = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("flow_rate_capacity")] - public OlfactometerChannelConfigFlowRateCapacity FlowRateCapacity - { - get - { - return _flowRateCapacity; - } - set - { - _flowRateCapacity = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("flow_rate")] - public double FlowRate - { - get - { - return _flowRate; - } - set - { - _flowRate = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("odorant")] - public string Odorant - { - get - { - return _odorant; - } - set - { - _odorant = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("odorant_dilution")] - public double? OdorantDilution - { - get - { - return _odorantDilution; - } - set - { - _odorantDilution = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerChannelConfig(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerChannelConfig(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("channel_index = " + _channelIndex + ", "); - stringBuilder.Append("channel_type = " + _channelType + ", "); - stringBuilder.Append("flow_rate_capacity = " + _flowRateCapacity + ", "); - stringBuilder.Append("flow_rate = " + _flowRate + ", "); - stringBuilder.Append("odorant = " + _odorant + ", "); - stringBuilder.Append("odorant_dilution = " + _odorantDilution); - 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(); - } - } - - - /// - /// Channel type - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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, - } - - - /// - /// Olfactometer operation control model that is used to run a calibration data acquisition workflow - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class OlfactometerCalibrationLogic - { - - private string _name = "OlfactometerCalibration"; - - private string _description = ""; - - private OlfactometerCalibrationParameters _taskParameters = new OlfactometerCalibrationParameters(); - - private string _version = "0.1.0"; - - private string _stageName; - - public OlfactometerCalibrationLogic() - { - } - - protected OlfactometerCalibrationLogic(OlfactometerCalibrationLogic other) - { - _name = other._name; - _description = other._description; - _taskParameters = other._taskParameters; - _version = other._version; - _stageName = other._stageName; - } - - [Newtonsoft.Json.JsonPropertyAttribute("name")] - public string Name - { - get - { - return _name; - } - set - { - _name = value; - } - } - - /// - /// Description of the task. - /// - [Newtonsoft.Json.JsonPropertyAttribute("description")] - [System.ComponentModel.DescriptionAttribute("Description of the task.")] - public string Description - { - get - { - return _description; - } - set - { - _description = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("task_parameters", Required=Newtonsoft.Json.Required.Always)] - public OlfactometerCalibrationParameters TaskParameters - { - get - { - return _taskParameters; - } - set - { - _taskParameters = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version - { - get - { - return _version; - } - set - { - _version = value; - } - } - - /// - /// Optional stage name the `Task` object instance represents. - /// - [Newtonsoft.Json.JsonPropertyAttribute("stage_name")] - [System.ComponentModel.DescriptionAttribute("Optional stage name the `Task` object instance represents.")] - public string StageName - { - get - { - return _stageName; - } - set - { - _stageName = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new OlfactometerCalibrationLogic(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new OlfactometerCalibrationLogic(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("name = " + _name + ", "); - stringBuilder.Append("description = " + _description + ", "); - stringBuilder.Append("task_parameters = " + _taskParameters + ", "); - stringBuilder.Append("version = " + _version + ", "); - stringBuilder.Append("stage_name = " + _stageName); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - public enum OlfactometerChannelConfigFlowRateCapacity - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="100")] - _100 = 100, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1000")] - _1000 = 1000, - } - - - /// - /// Serializes a sequence of data model objects into JSON strings. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into JSON strings.")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] - public partial class SerializeToJson - { - - private System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value)); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - 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", "0.4.0.0 (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))] - public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder - { - - public DeserializeFromJson() - { - Type = new Bonsai.Expressions.TypeMapping(); - } - - public Bonsai.Expressions.TypeMapping Type { get; set; } - - public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) - { - var typeMapping = (Bonsai.Expressions.TypeMapping)Type; - var returnType = typeMapping.GetType().GetGenericArguments()[0]; - return System.Linq.Expressions.Expression.Call( - typeof(DeserializeFromJson), - "Process", - new System.Type[] { returnType }, - System.Linq.Enumerable.Single(arguments)); - } - - private static System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.DeserializeObject(value)); - } - } -} \ No newline at end of file diff --git a/src/Extensions/UserInterface.bonsai b/src/Extensions/UserInterface.bonsai index 7d30d1f..62f4032 100644 --- a/src/Extensions/UserInterface.bonsai +++ b/src/Extensions/UserInterface.bonsai @@ -1,5 +1,5 @@  - @@ -286,6 +287,7 @@ + OlfactometerCalibration true true 2 @@ -321,6 +323,77 @@ + + + + + + + + + AlicatFlowmeterEvents + + + Seconds + Value.VolumetricFlowRate,Value.MassFlowRate,Value.MassFlowTotal + None + 2 + + + EndValveState + Orange + + + 200 + + + + + + + + Seconds + Value.AbsolutePressure,Value.Temperature + None + 2 + + + EndValveState + Orange + + + 200 + + + + + + + + AlicatFlowmeter + true + true + 1 + 2 + + + + + + + + + UserInterface + true + true + + + OlfactometerCalibration + true + + + Minimized + StartButton @@ -383,9 +456,22 @@ + - + + + + + + + + + + + + + \ No newline at end of file diff --git a/src/aind_behavior_device_olfactometer/__init__.py b/src/aind_behavior_device_olfactometer/__init__.py index 3dc1f76..98cffdf 100644 --- a/src/aind_behavior_device_olfactometer/__init__.py +++ b/src/aind_behavior_device_olfactometer/__init__.py @@ -1 +1,30 @@ -__version__ = "0.1.0" +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_contract/__init__.py b/src/aind_behavior_device_olfactometer/data_contract/__init__.py new file mode 100644 index 0000000..af54785 --- /dev/null +++ b/src/aind_behavior_device_olfactometer/data_contract/__init__.py @@ -0,0 +1,43 @@ +import os +import typing as t +from functools import partial +from pathlib import Path + +import contraqctor +import semver + +from .. import __version__ + + +def _dataset_lookup_helper(version: str) -> t.Callable[[Path], contraqctor.contract.Dataset]: + parsed_version = semver.Version.parse(version) + if semver.Version.parse("0.3.0") <= parsed_version < semver.Version.parse("0.4.0"): + from .v0_3_0 import dataset as _dataset + else: + raise ValueError(f"Unsupported version: {version}") + return partial(_dataset, version=version) + + +def dataset(path: os.PathLike, version: str = __version__) -> contraqctor.contract.Dataset: + """ + Loads the dataset for the Aind VR Foraging project from a specified version. + + Args: + path (os.PathLike): The path to the dataset root directory. + version (str): The version of the dataset to load. By default, it uses the package version. + + Returns: + contraqctor.contract.Dataset: The loaded dataset. + """ + dataset_constructor = _dataset_lookup_helper(version) + return dataset_constructor(Path(path)) + + +def render_dataset(version: str = __version__) -> str: + """Renders the dataset as a tree-like structure for visualization.""" + from contraqctor.contract.utils import print_data_stream_tree_html + + dataset_constructor = _dataset_lookup_helper(version) + return print_data_stream_tree_html( + dataset_constructor(Path("")), show_missing_indicator=False, show_type=True + ) diff --git a/src/aind_behavior_device_olfactometer/data_contract/v0_3_0.py b/src/aind_behavior_device_olfactometer/data_contract/v0_3_0.py new file mode 100644 index 0000000..2dd8328 --- /dev/null +++ b/src/aind_behavior_device_olfactometer/data_contract/v0_3_0.py @@ -0,0 +1,167 @@ +from pathlib import Path + +from aind_behavior_services.session import AindBehaviorSessionModel +from contraqctor.contract import Dataset, DataStreamCollection +from contraqctor.contract.harp import ( + DeviceYmlByFile, + HarpDevice, +) +from contraqctor.contract.json import PydanticModel, SoftwareEvents +from contraqctor.contract.text import Text + +from ..rig import OlfactometerCalibrationRig +from ..task_logic import OlfactometerCalibrationLogic + + +def dataset( + root_path: Path, + name: str = "OlfactometerCalibrationDataset", + description: str = "A Olfactometer Calibration dataset", + version: str = "0.3.0", +) -> Dataset: + """ + Creates a Dataset object for the Olfactometer calibration procedure. + """ + + root_path = Path(root_path) + return Dataset( + name=name, + version=version, + description=description, + data_streams=[ + DataStreamCollection( + name="Behavior", + description="Data from the Behavior modality", + data_streams=[ + HarpDevice( + name="HarpOlfactometer", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/Olfactometer.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpClockGenerator", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/WhiteRabbit.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpAnalogInput", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/AnalogInput.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpManipulator", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/StepperDriver.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + DataStreamCollection( + name="HarpCommands", + description="Commands sent to Harp devices", + data_streams=[ + HarpDevice( + name="HarpOlfactometer", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/Olfactometer.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpManipulator", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/StepperDriver.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpClockGenerator", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/WhiteRabbit.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + HarpDevice( + name="HarpAnalogInput", + reader_params=HarpDevice.make_params( + path=root_path / "behavior/HarpCommands/AnalogInput.harp", + device_yml_hint=DeviceYmlByFile(), + ), + ), + ], + ), + DataStreamCollection( + name="SoftwareEvents", + description="Software events generated by the workflow. The timestamps of these events are low precision and should not be used to align to physiology data.", + data_streams=[ + SoftwareEvents( + name="OdorChannel", + description="The OdorChannel currently being used.", + reader_params=SoftwareEvents.make_params( + root_path / "behavior/SoftwareEvents/OdorChannel.json" + ), + ), + SoftwareEvents( + name="IsEndValveCalibration", + description="Whether the calibration is running in end-valve mode or not.", + reader_params=SoftwareEvents.make_params( + root_path / "behavior/SoftwareEvents/IsEndValveCalibration.json" + ), + ), + ], + ), + DataStreamCollection( + name="Logs", + data_streams=[ + Text( + name="Launcher", + description="Contains the console log of the launcher process.", + reader_params=Text.make_params( + path=root_path / "behavior/Logs/.launcher/launcher.log", + ), + ), + SoftwareEvents( + name="EndSession", + description="A file that determines the end of the session. If the file is empty, the session is still running or it was not closed properly.", + reader_params=SoftwareEvents.make_params( + path=root_path / "behavior/Logs/EndSession.json", + ), + ), + ], + ), + DataStreamCollection( + name="InputSchemas", + description="Configuration files for the behavior rig, task_logic and session.", + data_streams=[ + PydanticModel( + name="Rig", + reader_params=PydanticModel.make_params( + model=OlfactometerCalibrationRig, + path=root_path / "behavior/Logs/rig_input.json", + ), + ), + PydanticModel( + name="TaskLogic", + reader_params=PydanticModel.make_params( + model=OlfactometerCalibrationLogic, + path=root_path / "behavior/Logs/tasklogic_input.json", + ), + ), + PydanticModel( + name="Session", + reader_params=PydanticModel.make_params( + model=AindBehaviorSessionModel, + path=root_path / "behavior/Logs/session_input.json", + ), + ), + ], + ), + ], + ), + ], + ) 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 50% rename from src/aind_behavior_device_olfactometer/analysis.py rename to src/aind_behavior_device_olfactometer/data_qc/_utils.py index 7635a38..84dcbe6 100644 --- a/src/aind_behavior_device_olfactometer/analysis.py +++ b/src/aind_behavior_device_olfactometer/data_qc/_utils.py @@ -1,30 +1,32 @@ import argparse +import typing +import typing as t from dataclasses import dataclass, field from pathlib import Path -from typing import List, Literal +from typing import List, Literal, cast import matplotlib.pyplot as plt import numpy as np import pandas as pd -from aind_behavior_core_analysis.io._core import DataStreamCollection -from aind_behavior_core_analysis.io.data_stream import ( - DataStreamCollectionFromFilePattern, - HarpDataStreamCollectionFactory, - SoftwareEventStream, -) -from aind_behavior_services.calibration import olfactometer as olf -from aind_behavior_services.utils import model_from_json_file +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 aind_behavior_device_olfactometer.rig import OlfactometerCalibrationRig -from aind_behavior_device_olfactometer.task_logic import OlfactometerCalibrationLogic +from ..data_contract import dataset +from ..task_logic import OlfactometerCalibrationLogic + +if typing.TYPE_CHECKING: + pass plt.style.use("dark_background") @dataclass class ProcessedData: - _parent_dataset_ref: "Dataset" = field(repr=False) + _parent_dataset_ref: Dataset = field(repr=False) pid: pd.Series = field(init=False) end_valve_state: pd.Series = field(init=False) odor_mixture: pd.Series = field(init=False) @@ -42,51 +44,36 @@ def from_dataset(cls, parent_dataset: "Dataset") -> "ProcessedData": return _p -@dataclass -class Dataset: - root_path: Path - analog_input: DataStreamCollection = field(init=False) - olfactometer: DataStreamCollection = field(init=False) - software_events: DataStreamCollection = field(init=False) - metadata_task_logic: OlfactometerCalibrationLogic = field(init=False) - metadata_rig: OlfactometerCalibrationRig = field(init=False) - processed_data: ProcessedData = field(init=False) - - def __post_init__(self): - self.analog_input = HarpDataStreamCollectionFactory( - path=self.root_path / "behavior" / "AnalogInput.harp", default_inference_mode="register_0" - ).build() - self.olfactometer = HarpDataStreamCollectionFactory( - path=self.root_path / "behavior" / "Olfactometer.harp", default_inference_mode="register_0" - ).build() - self.software_events = DataStreamCollectionFromFilePattern( - path=self.root_path / "behavior" / "SoftwareEvents", pattern="*.json", stream_type=SoftwareEventStream - ).build() - self.metadata_task_logic = model_from_json_file( - self.root_path / "behavior" / "Logs" / "tasklogic_input.json", OlfactometerCalibrationLogic - ) - self.metadata_rig = model_from_json_file( - self.root_path / "behavior" / "Logs" / "rig_input.json", OlfactometerCalibrationRig - ) +class ProcessedDataStream(DataStream[ProcessedData, Dataset]): + @staticmethod + def _reader(params: Dataset) -> ProcessedData: + return ProcessedData.from_dataset(params) + - def make_processed_data(self): - self.processed_data = ProcessedData.from_dataset(self) +def append_processed_data(dataset: Dataset): + dataset.add_stream( + ProcessedDataStream( + name="Processed", + description="Processed data from the Olfactometer calibration procedure", + reader_params=dataset, + ) + ) def load_pid( dataset: Dataset, channel: Literal["Channel0", "Channel1", "Channel2", "Channel3"] = "Channel0" ) -> pd.Series: - _data = dataset.analog_input["AnalogData"].load() + _data = dataset["Behavior"]["HarpAnalogInput"]["AnalogData"].data return _data[_data["MessageType"] == "EVENT"][channel] def load_end_valve_state(dataset: Dataset, channel: Literal["EndValve0", "EndValve1"] = "EndValve0") -> pd.Series: - _data = dataset.olfactometer["EndValveState"].load()[channel] + _data = dataset["Behavior"]["HarpOlfactometer"]["EndValveState"].data return _data[_data.shift() != _data] def load_odor_mixture(dataset: Dataset) -> pd.Series: - target_flow = dataset.olfactometer["ChannelsTargetFlow"].reload() + target_flow = dataset["Behavior"]["HarpOlfactometer"]["ChannelsTargetFlow"].data target_flow = target_flow[target_flow["MessageType"] == "WRITE"] return target_flow @@ -95,15 +82,15 @@ def load_flowmeter(dataset: Dataset) -> List[pd.Series]: channel_data: List[pd.Series] = [] for i in range(5): _channel_reg = f"Channel{i}ActualFlow" - _data = dataset.olfactometer[_channel_reg].load() + _data = dataset["Behavior"]["HarpOlfactometer"][_channel_reg].data channel_data.append(_data[_data["MessageType"] == "EVENT"][_channel_reg]) return channel_data def load_odor_channel_configuration(dataset: Dataset, tolerance_seconds: float = 0.01) -> pd.DataFrame: - _is_end_valve = dataset.software_events["IsEndValveCalibration"].reload()["data"] + _is_end_valve: pd.DataFrame = dataset["Behavior"]["IsEndValveCalibration"].data - _odor_config = dataset.software_events["OdorChannel"].reload() + _odor_config: pd.DataFrame = dataset["Behavior"]["SoftwareEvents"]["OdorChannel"].data _odor_config["data_parsed"] = _odor_config["data"].apply(lambda x: olf.OlfactometerChannelConfig.model_validate(x)) _odor_config = _odor_config["data_parsed"] @@ -136,11 +123,13 @@ def stream_slice(event: tuple[float, float], stream: pd.Series, window: tuple[fl def plot_channel( df: pd.DataFrame, dataset: Dataset, window: tuple[float, float] = (-0.2, 0.5) ) -> tuple[plt.Figure, plt.Axes]: - expected_repeats = dataset.metadata_task_logic.task_parameters.n_repeats_per_stimulus + task_logic: OlfactometerCalibrationLogic = dataset["Behavior"]["InputSchemas"]["TaskLogic"].data + expected_repeats = task_logic.task_parameters.n_repeats_per_stimulus cmap = LinearSegmentedColormap.from_list("blue_to_yellow", ["blue", "yellow"], expected_repeats) channel_config: olf.OlfactometerChannelConfig = df.iloc[0].odor_channel_config fig, ax = plt.subplots(2, 2, sharex=True) + processed = cast(ProcessedData, dataset["Processed"].data) for env_valve_mode, mode_df in df.groupby(["is_end_valve_calibration"]): t = mode_df.index[0] @@ -148,28 +137,25 @@ def plot_channel( if env_valve_mode[0] == 1: # if end_valve_calibration we use the valve state to find the start and end of each trial _plt_col = 0 - _start = dataset.processed_data.end_valve_state[ - (dataset.processed_data.end_valve_state.index >= t) & (dataset.processed_data.end_valve_state == 1) + _start = processed.end_valve_state[ + (processed.end_valve_state.index >= t) & (processed.end_valve_state == 1) ].head(expected_repeats) - _end = dataset.processed_data.end_valve_state[ - (dataset.processed_data.end_valve_state.index >= _start.index[0]) - & (dataset.processed_data.end_valve_state == 0) + _end = processed.end_valve_state[ + (processed.end_valve_state.index >= _start.index[0]) & (processed.end_valve_state == 0) ].head(expected_repeats) else: _plt_col = 1 _channel = olf.OlfactometerChannel(channel_config.channel_index).name - _odor_mix = dataset.processed_data.odor_mixture[_channel] + _odor_mix = processed.odor_mixture[_channel] _start = _odor_mix[(_odor_mix.index >= t) & (_odor_mix > 0)].head(expected_repeats) _end = _odor_mix[(_odor_mix.index >= _start.index[0]) & (_odor_mix == 0)].head(expected_repeats) color_iter = iter(cmap(np.linspace(0, 1, expected_repeats))) for t_on, t_off in zip(_start.index, _end.index): - pid_slice = stream_slice((t_on, t_off), dataset.processed_data.pid, window) - flowmeter_slice = stream_slice( - (t_on, t_off), dataset.processed_data.flowmeter[channel_config.channel_index], window - ) + pid_slice = stream_slice((t_on, t_off), processed.pid, window) + flowmeter_slice = stream_slice((t_on, t_off), processed.flowmeter[channel_config.channel_index], window) _color = next(color_iter) ax[0, _plt_col].plot(pid_slice.index - t_on, pid_slice, color=_color) @@ -192,14 +178,95 @@ 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) args = parser.parse_args() - data = Dataset(Path(args.path)) - data.make_processed_data() + data = dataset(Path(args.path)) + append_processed_data(data) + data.load_all() - for _, valve_calibration_df in data.processed_data.odor_channel_config.groupby(["channel_index"]): + for _, valve_calibration_df in cast(ProcessedDataStream, data["Processed"]).data.odor_channel_config.groupby( + ["channel_index"] + ): fig = plot_channel(valve_calibration_df, data)[0] fig.set_size_inches(10, 6) plt.show() 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 ddbf5ab..0000000 --- a/src/aind_behavior_device_olfactometer/launcher.py +++ /dev/null @@ -1,50 +0,0 @@ -from pathlib import Path - -import aind_behavior_experiment_launcher.launcher.behavior_launcher as behavior_launcher -from aind_behavior_experiment_launcher.apps import BonsaiApp -from aind_behavior_experiment_launcher.resource_monitor import ( - ResourceMonitor, - available_storage_constraint_factory, -) -from aind_behavior_services.session import AindBehaviorSessionModel - -from aind_behavior_device_olfactometer.rig import OlfactometerCalibrationRig -from aind_behavior_device_olfactometer.task_logic import OlfactometerCalibrationLogic - - -def make_launcher() -> behavior_launcher.BehaviorLauncher: - data_dir = r"C:/Data" - srv = behavior_launcher.BehaviorServicesFactoryManager() - srv.attach_bonsai_app(BonsaiApp(Path(r"./src/main.bonsai"))) - srv.attach_resource_monitor( - ResourceMonitor( - constrains=[ - available_storage_constraint_factory(data_dir, 2e11), - ] - ) - ) - - return behavior_launcher.BehaviorLauncher( - rig_schema_model=OlfactometerCalibrationRig, - session_schema_model=AindBehaviorSessionModel, - task_logic_schema_model=OlfactometerCalibrationLogic, - data_dir=data_dir, - config_library_dir=r"\\allen\aind\scratch\AindBehavior.db\AindBehaviorDeviceOlfactometer", - temp_dir=r"./local/.temp", - allow_dirty=False, - skip_hardware_validation=False, - debug_mode=False, - group_by_subject_log=True, - services=srv, - validate_init=True, - ) - - -def main(): - launcher = make_launcher() - 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 0edfc07..c0f1238 100644 --- a/src/aind_behavior_device_olfactometer/regenerate.py +++ b/src/aind_behavior_device_olfactometer/regenerate.py @@ -1,37 +1,34 @@ -import inspect from pathlib import Path +from typing import Union -from aind_behavior_services.session import AindBehaviorSessionModel -from aind_behavior_services.utils import ( - convert_pydantic_to_bonsai, - pascal_to_snake_case, - snake_to_pascal_case, -) +import pydantic +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, ] - - for model in models: - module_name = inspect.getmodule(model).__name__ - module_name = module_name.split(".")[-1] - schema_name = f"{pascal_to_snake_case(model.__name__)}" - namespace = f"{NAMESPACE_PREFIX}.{snake_to_pascal_case(module_name)}" - - print((schema_name, namespace)) - convert_pydantic_to_bonsai( - {schema_name: model}, schema_path=SCHEMA_ROOT, output_path=EXTENSIONS_ROOT, namespace=namespace - ) + model = pydantic.RootModel[Union[tuple(models)]] + + convert_pydantic_to_bonsai( + model, + model_name="aind_behavior_device_olfactometer", + root_element="Root", + cs_namespace=NAMESPACE_PREFIX, + json_schema_output_dir=SCHEMA_ROOT, + cs_output_dir=EXTENSIONS_ROOT, + cs_serializer=[BonsaiSgenSerializers.JSON], + ) if __name__ == "__main__": diff --git a/src/aind_behavior_device_olfactometer/rig.py b/src/aind_behavior_device_olfactometer/rig.py index 77b615c..b8e1542 100644 --- a/src/aind_behavior_device_olfactometer/rig.py +++ b/src/aind_behavior_device_olfactometer/rig.py @@ -1,20 +1,25 @@ -from typing import Literal +from typing import Literal, Optional +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 -__version__ = "0.2.0" +from . import __semver__ -class HarpOlfactometer(rig.HarpOlfactometer): - """Overrides the default settings for the olfactometer calibration""" +class AlicatFlowmeter(rig.Device): + device_type: Literal["AlicatFlowmeter"] = "AlicatFlowmeter" + 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") - calibration: olf.OlfactometerCalibration = Field(description="Olfactometer calibration") - -class OlfactometerCalibrationRig(rig.AindBehaviorRigModel): - version: Literal[__version__] = __version__ - harp_olfactometer: HarpOlfactometer = Field(..., title="Olfactometer device") - harp_analog_input: rig.HarpAnalogInput = Field(..., title="Analog input device") - harp_clock_generator: rig.HarpWhiteRabbit = Field(..., title="Clock generator device") +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 e4b4bd9..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 -__version__ = "0.1.0" +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 7330ea7..e324140 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -1,15 +1,13 @@  - @@ -27,141 +25,7 @@ 10 - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + SessionSchema @@ -227,7 +91,7 @@ - + EndValvesState EndValve0 @@ -246,16 +110,16 @@ - + EndValvesState None - + Write - + HarpOlfactometerCommands @@ -301,15 +165,15 @@ - - true - 0 - 0 - 0 - NaN - true - 100 - 1000 + + true + 0 + 0 + 0 + NaN + true + 100 + 1000 @@ -360,31 +224,44 @@ - + + RigSchema + + + DataDirectory + + + + + + LoggingRootPath - - ../. + + ../. Repository - + SoftwareEvent - + + + + @@ -426,7 +303,7 @@ - + StartExperimentTrigger @@ -456,15 +333,15 @@ - - true - 0 - 0 - 0 - NaN - true - 100 - 1000 + + true + 0 + 0 + 0 + NaN + true + 100 + 1000 diff --git a/uv.lock b/uv.lock index cdf5b16..3af7702 100644 --- a/uv.lock +++ b/uv.lock @@ -1,52 +1,68 @@ version = 1 +revision = 3 requires-python = ">=3.11" resolution-markers = [ - "python_full_version >= '3.12'", - "python_full_version < '3.12'", + "python_full_version >= '3.14' and sys_platform == 'win32'", + "python_full_version >= '3.14' and sys_platform == 'emscripten'", + "python_full_version >= '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'win32'", + "python_full_version < '3.12' and sys_platform == 'win32'", + "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'emscripten'", + "python_full_version < '3.12' and sys_platform == 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