From d020c739c0bacf4add0c05bc80428116e3508f7b Mon Sep 17 00:00:00 2001 From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com> Date: Thu, 2 Oct 2025 13:38:03 -0700 Subject: [PATCH] Attempt to refactor workflow using copier --- .config/dotnet-tools.json | 2 +- .copier-answers.yml | 5 + .editorconfig | 27 + .flake8 | 7 + .../aind-behavior-device-water-tuner-cicd.yml | 207 ++ .github/workflows/ci.yml | 25 - .github/workflows/docs.yml | 24 - .github/workflows/tag_and_publish.yml | 10 - .gitignore | 15 +- .python-version | 4 +- bonsai/NuGet.config | 7 +- bonsai/setup.ps1 | 1 - docs/conf.py | 35 +- docs/index.rst | 9 +- docs/json-schemas.rig.rst | 10 - docs/json-schemas.rst | 22 +- docs/json-schemas.session.rst | 8 - docs/json-schemas.task_logic.rst | 9 - examples/clabe.yml | 19 + examples/example.py | 83 - examples/rig.py | 49 + examples/session.py | 29 + examples/task_logic.py | 31 + pyproject.toml | 61 +- ...{regenerate_environment.cmd => deploy.cmd} | 0 scripts/deploy.ps1 | 31 + scripts/launcher.cmd | 6 + scripts/launcher.ps1 | 3 + scripts/regenerate_environment.ps1 | 15 - src/.gitignore | 5 + .../aind_behavior_device_water_tuner.json | 956 ++++++ src/Extensions.csproj | 18 +- .../AindBehaviorDeviceWaterTuner.Generated.cs | 2817 +++++++++++++++++ src/Extensions/AindBehaviorSessionModel.cs | 379 --- src/Extensions/AindBehaviorWaterTunerRig.cs | 1539 --------- .../AindBehaviorWaterTunerTaskLogic.cs | 364 --- src/Extensions/ExtensionDataTypes.cs | 667 ---- src/Extensions/Logging.bonsai | 25 +- src/Extensions/WaterCalibrationModel.cs | 2 +- .../__init__.py | 31 +- src/aind_behavior_device_water_tuner/cli.py | 44 + .../data_types.py | 2 - .../launcher.py | 84 +- .../regenerate.py | 41 +- src/aind_behavior_device_water_tuner/rig.py | 7 +- .../task_logic.py | 25 +- src/main.bonsai | 81 +- tests/__init__.py | 3 +- uv.lock | 1600 ++++------ 49 files changed, 5123 insertions(+), 4321 deletions(-) create mode 100644 .copier-answers.yml create mode 100644 .editorconfig create mode 100644 .flake8 create mode 100644 .github/workflows/aind-behavior-device-water-tuner-cicd.yml delete mode 100644 .github/workflows/ci.yml delete mode 100644 .github/workflows/docs.yml delete mode 100644 .github/workflows/tag_and_publish.yml delete mode 100644 docs/json-schemas.rig.rst delete mode 100644 docs/json-schemas.session.rst delete mode 100644 docs/json-schemas.task_logic.rst create mode 100644 examples/clabe.yml delete mode 100644 examples/example.py create mode 100644 examples/rig.py create mode 100644 examples/session.py create mode 100644 examples/task_logic.py rename scripts/{regenerate_environment.cmd => deploy.cmd} (100%) create mode 100644 scripts/deploy.ps1 create mode 100644 scripts/launcher.cmd create mode 100644 scripts/launcher.ps1 delete mode 100644 scripts/regenerate_environment.ps1 create mode 100644 src/.gitignore create mode 100644 src/DataSchemas/aind_behavior_device_water_tuner.json create mode 100644 src/Extensions/AindBehaviorDeviceWaterTuner.Generated.cs delete mode 100644 src/Extensions/AindBehaviorSessionModel.cs delete mode 100644 src/Extensions/AindBehaviorWaterTunerRig.cs delete mode 100644 src/Extensions/AindBehaviorWaterTunerTaskLogic.cs delete mode 100644 src/Extensions/ExtensionDataTypes.cs create mode 100644 src/aind_behavior_device_water_tuner/cli.py diff --git a/.config/dotnet-tools.json b/.config/dotnet-tools.json index a1a9bfe..44b1c27 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": "0.6.1", "commands": [ "bonsai.sgen" ] diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 0000000..50327d1 --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,5 @@ +_src_path: ..\Aind.Behavior.CopierTemplate\aind-behavior-template\ +author_email: bruno.cruz@alleninstitute.org +author_name: Bruno F. Cruz +prefix: aind-behavior-device +project_name: water-tuner diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..eaec598 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,27 @@ +# To learn more about .editorconfig see https://aka.ms/editorconfigdocs +############################### +# Core EditorConfig Options # +############################### +# All files +[*] +indent_style = space + +# XML project files +[*.{csproj,vcxproj,vcxproj.filters,proj,projitems,shproj,bonsai}] +indent_size = 2 + +# XML config files +[*.{props,targets,ruleset,config,nuspec,resx,vsixmanifest,vsct}] +indent_size = 2 + +# Code files +[*.{cs,csx}] +indent_size = 4 +insert_final_newline = true +charset = utf-8-bom +############################### +# .NET Coding Conventions # +############################### +[*.{cs}] +# Organize usings +dotnet_sort_system_directives_first = true diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..07bd2e2 --- /dev/null +++ b/.flake8 @@ -0,0 +1,7 @@ +[flake8] +exclude = + .git, + __pycache__, + build +max-complexity = 10 +max-line-length = 120 \ No newline at end of file diff --git a/.github/workflows/aind-behavior-device-water-tuner-cicd.yml b/.github/workflows/aind-behavior-device-water-tuner-cicd.yml new file mode 100644 index 0000000..32450ea --- /dev/null +++ b/.github/workflows/aind-behavior-device-water-tuner-cicd.yml @@ -0,0 +1,207 @@ +name: water-tuner test suite + +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + - dev* + - release* + release: + types: [published] + +jobs: + # ╔──────────────────────────╗ + # │ _____ _ │ + # │ |_ _|__ ___| |_ ___ │ + # │ | |/ _ \/ __| __/ __| │ + # │ | | __/\__ \ |_\__ \ │ + # │ |_|\___||___/\__|___/ │ + # │ │ + # ╚──────────────────────────╝ + tests: + runs-on: windows-latest + name: water-tuner unit tests + steps: + - uses: actions/checkout@v5 + + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + + - name: Install python dependencies + run: uv sync + + - name: Run ruff format + run: uv run ruff format + + - name: Run ruff check + run: uv run ruff check + + - name: Run codespell + run: uv run codespell + + - name: Setup .NET Core SDK + uses: actions/setup-dotnet@v4 + with: + dotnet-version: 8.x + + - name: Restore dotnet tools + run: dotnet tool restore + + - name: Setup Bonsai environment + working-directory: ./bonsai + run: ./setup.ps1 + + - name: Run python unit tests + run: uv run python -m unittest + + - name: Regenerate schemas + run: uv run water-tuner 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@v5 + with: + fetch-depth: 0 + ref: main + + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + + - name: Bump pre-release by default + run: uv version --bump rc + + - name: Regenerate schemas + run: uv run water-tuner 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: github.event_name == 'release' && + github.event.action == 'published' && + !github.event.release.prerelease + steps: + - uses: actions/checkout@v5 + with: + fetch-depth: 0 + ref: main + + - uses: astral-sh/setup-uv@v6 + 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 water-tuner 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@v5 + + - name: Install uv + uses: astral-sh/setup-uv@v3 + + - name: Setup Graphviz + uses: ts-graphviz/setup-graphviz@v2 + + - name: Install docs group of dependencies + run: uv sync --group docs + + - name: Build Sphinx documentation + run: uv run sphinx-build -b html docs/ _build/html + + - name: Deploy to GitHub Pages + uses: peaceiris/actions-gh-pages@v4 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: _build/html + force_orphan: true diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 1f9538a..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: windows-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 - runs-on: windows-latest \ No newline at end of file diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml deleted file mode 100644 index 68c570b..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-latest - 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 59231ef..4053511 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ bin obj Packages Bonsai.exe.WebView2 +Bonsai/Settings/ *.bin *.avi *.dll @@ -12,7 +13,8 @@ Bonsai.exe.WebView2 *.exe.settings *.bonsai.layout local -*.snl +.venv + # Byte-compiled / optimized / DLL files __pycache__/ @@ -80,13 +82,4 @@ ipython_config.py # pyenv # For a library or package, you might want to ignore these files since the code is # intended to run in multiple environments; otherwise, check them in: -# .python-version - -# mypy -.mypy_cache/ - -# ruff -.ruff_cache/ - -# venv files -.venv +# .python-version \ No newline at end of file diff --git a/.python-version b/.python-version index 06c7113..31a10be 100644 --- a/.python-version +++ b/.python-version @@ -1,3 +1,3 @@ -3.11 +3.13 3.12 -3.13 \ No newline at end of file +3.11 \ No newline at end of file diff --git a/bonsai/NuGet.config b/bonsai/NuGet.config index a0adc59..35696f8 100644 --- a/bonsai/NuGet.config +++ b/bonsai/NuGet.config @@ -1,9 +1,6 @@  - - - - - + + 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 5db92dc..a9e589f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,24 +1,21 @@ -import os -import sys - -import erdantic as erd -from pydantic import BaseModel +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html import aind_behavior_device_water_tuner import aind_behavior_device_water_tuner.rig import aind_behavior_device_water_tuner.task_logic -sys.path.insert(0, os.path.abspath("../src/DataSchemas")) - -SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Behavior.WaterTuner/tree/main/src/DataSchemas/" +SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.WaterTuner/tree/main/src/" # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -project = "Aind Behavior WaterTuner project" +project = " water-tuner " copyright = "2025, Allen Institute for Neural Dynamics" -author = "Bruno Cruz" -release = aind_behavior_device_water_tuner.__version__ +author = " Bruno F. Cruz " +release = aind_behavior_device_water_tuner.__semver__ # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration @@ -32,7 +29,7 @@ "sphinx.ext.intersphinx", "sphinx.ext.githubpages", "sphinx.ext.linkcode", - "sphinx_mdinclude", + "myst_parser", "sphinxcontrib.autodoc_pydantic", ] @@ -49,7 +46,7 @@ html_theme = "furo" html_static_path = ["_static"] -html_title = "Aind Behavior WaterTuner" +html_title = "water-tuner" html_favicon = "_static/favicon.ico" html_theme_options = { "light_logo": "light-logo.svg", @@ -64,6 +61,8 @@ # -- Options for linkcode extension --------------------------------------- + + def linkcode_resolve(domain, info): if domain != "py": return None @@ -71,13 +70,3 @@ def linkcode_resolve(domain, info): return None filename = info["module"].replace(".", "/") return f"{SOURCE_ROOT}/{filename}.py" - - -# -- Class diagram generation (Optional) --------------------------------------- -def export_model_diagram(model: BaseModel, root: str = "_static") -> None: - diagram = erd.create(model) - diagram.draw(f"{root}/{model.__name__}.svg") - - -_diagram_root = "_static" -# export_model_diagram(MyPydanticBaseModel, _diagram_root) diff --git a/docs/index.rst b/docs/index.rst index 2e2e8ee..b2213ba 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,14 +1,17 @@ -Welcome to the Aind Behavior WaterTuner project documentation! -======================================================================== +Welcome to the water-tuner project documentation! +========================================================= -.. mdinclude:: ../README.md +.. include:: ../README.md + :parser: myst_parser.sphinx_ .. toctree:: :maxdepth: 2 :caption: Contents: + self api json-schemas + GitHub Source Code Indices and tables ================== diff --git a/docs/json-schemas.rig.rst b/docs/json-schemas.rig.rst deleted file mode 100644 index beb79f0..0000000 --- a/docs/json-schemas.rig.rst +++ /dev/null @@ -1,10 +0,0 @@ - -json-schemas.rig ------------------- - -`Download Schema `_ - -.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.WaterTuner/main/src/DataSchemas/aind_behavior_water_tuner_rig.json - :lift_definitions: - :auto_reference: - diff --git a/docs/json-schemas.rst b/docs/json-schemas.rst index 1fdf2c9..fd6da12 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_water_tuner`, and are also used to generate `src/Extensions/AindBehaviorDeviceWaterTuner.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.WaterTuner/main/src/DataSchemas/aind_behavior_device_water_tuner.json#/$defs/AindBehaviorDeviceWaterTunerTaskLogic + :lift_definitions: + :auto_reference: + + +Rig Schema +~~~~~~~~~~~~~~ +.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.WaterTuner/main/src/DataSchemas/aind_behavior_device_water_tuner.json#/$defs/AindBehaviorDeviceWaterTunerRig + :lift_definitions: + :auto_reference: diff --git a/docs/json-schemas.session.rst b/docs/json-schemas.session.rst deleted file mode 100644 index 2c1f2cf..0000000 --- a/docs/json-schemas.session.rst +++ /dev/null @@ -1,8 +0,0 @@ -json-schemas.session ---------------------- - -`Download Schema `_ - -.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.WaterTuner/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 9221e19..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.WaterTuner/main/src/DataSchemas/aind_behavior_water_tuner_task_logic.json - :lift_definitions: - :auto_reference: diff --git a/examples/clabe.yml b/examples/clabe.yml new file mode 100644 index 0000000..0ea914b --- /dev/null +++ b/examples/clabe.yml @@ -0,0 +1,19 @@ +# In order to get picked up, move this file to the root of the project or ./local + +data_dir: C:/Data +allow_dirty: true + +watchdog: + project_name: "ADD PROJECT NAME HERE" + destination: '\\allen\\aind\\scratch\\water-tuner\\data' + delete_modalities_source_after_success: true + job_type: "ADD JOB TYPE HERE" + transfer_endpoint: "http://aind-data-transfer-service-dev/api/v2/submit_jobs" + s3_bucket: "default" + +default_behavior_picker: + config_library_dir: '\\allen\aind\scratch\AindBehavior.db\AindBehaviorDeviceWaterTuner' + +curriculum: + script: "curriculum run" + project_directory: "./src/aind_behavior_device_water_tuner/curricula/Aind.Behavior.Device.WaterTuner.Curricula" diff --git a/examples/example.py b/examples/example.py deleted file mode 100644 index da171c2..0000000 --- a/examples/example.py +++ /dev/null @@ -1,83 +0,0 @@ -import datetime -import os - -from aind_behavior_services import rig -from aind_behavior_services.calibration import aind_manipulator -from aind_behavior_services.calibration.aind_manipulator import ( - AindManipulatorCalibration, - AindManipulatorCalibrationInput, - AindManipulatorCalibrationOutput, - Axis, - AxisConfiguration, - ManipulatorPosition, -) -from aind_behavior_services.session import AindBehaviorSessionModel - -from aind_behavior_device_water_tuner.rig import AindBehaviorWaterTunerRig, SerialScale -from aind_behavior_device_water_tuner.task_logic import ( - AindBehaviorWaterTunerParameters, - AindBehaviorWaterTunerTaskLogic, -) - - -def mock_session() -> AindBehaviorSessionModel: - """Generates a mock AindBehaviorSessionModel model""" - return AindBehaviorSessionModel( - date=datetime.datetime.now(tz=datetime.timezone.utc), - experiment="AindBehaviorWaterTuner", - root_path="c://Data", - subject="test", - notes="test session", - experiment_version="0.0.0", - allow_dirty_repo=True, - skip_hardware_validation=False, - experimenter=["Foo", "Bar"], - ) - - -def mock_rig() -> AindBehaviorWaterTunerRig: - manipulator_calibration = AindManipulatorCalibration( - output=AindManipulatorCalibrationOutput(), - input=AindManipulatorCalibrationInput( - full_step_to_mm=(ManipulatorPosition(x=0.010, y1=0.010, y2=0.010, z=0.010)), - axis_configuration=[ - AxisConfiguration(axis=Axis.Y1, min_limit=-1, max_limit=15000), - AxisConfiguration(axis=Axis.Y2, min_limit=-1, max_limit=15000), - AxisConfiguration(axis=Axis.X, min_limit=-1, max_limit=15000), - AxisConfiguration(axis=Axis.Z, min_limit=-1, max_limit=15000), - ], - homing_order=[Axis.Y1, Axis.Y2, Axis.X, Axis.Z], - initial_position=ManipulatorPosition(y1=0, y2=0, x=0, z=0), - ), - ) - - return AindBehaviorWaterTunerRig( - rig_name="testrig", - harp_behavior=rig.harp.HarpBehavior(port_name="COM3"), - manipulator=aind_manipulator.AindManipulatorDevice(port_name="COM10", calibration=manipulator_calibration), - scale=SerialScale(port_name="COM12"), - ) - - -def mock_task_logic() -> AindBehaviorWaterTunerTaskLogic: - return AindBehaviorWaterTunerTaskLogic( - task_parameters=AindBehaviorWaterTunerParameters( - repeat_count=200, valve_open_interval=0.2, valve_open_time=[0.02, 0.05, 0.1] - ) - ) - - -def main(path_seed: str = "./local/{schema}.json"): - example_session = mock_session() - example_rig = mock_rig() - example_task_logic = mock_task_logic() - - os.makedirs(os.path.dirname(path_seed), exist_ok=True) - - for model in [example_task_logic, example_session, example_rig]: - with open(path_seed.format(schema=model.__class__.__name__), "w", encoding="utf-8") as f: - f.write(model.model_dump_json(indent=2)) - - -if __name__ == "__main__": - main() diff --git a/examples/rig.py b/examples/rig.py new file mode 100644 index 0000000..f55fdb4 --- /dev/null +++ b/examples/rig.py @@ -0,0 +1,49 @@ +import os + +import aind_behavior_services.rig +from aind_behavior_services.calibration import aind_manipulator +from aind_behavior_services.calibration.aind_manipulator import ( + AindManipulatorCalibration, + AindManipulatorCalibrationInput, + AindManipulatorCalibrationOutput, + Axis, + AxisConfiguration, + ManipulatorPosition, +) + +from aind_behavior_device_water_tuner.rig import AindBehaviorDeviceWaterTunerRig, SerialScale + +manipulator_calibration = AindManipulatorCalibration( + output=AindManipulatorCalibrationOutput(), + input=AindManipulatorCalibrationInput( + full_step_to_mm=(ManipulatorPosition(x=0.010, y1=0.010, y2=0.010, z=0.010)), + axis_configuration=[ + AxisConfiguration(axis=Axis.Y1, min_limit=-1, max_limit=15000), + AxisConfiguration(axis=Axis.Y2, min_limit=-1, max_limit=15000), + AxisConfiguration(axis=Axis.X, min_limit=-1, max_limit=15000), + AxisConfiguration(axis=Axis.Z, min_limit=-1, max_limit=15000), + ], + homing_order=[Axis.Y1, Axis.Y2, Axis.X, Axis.Z], + initial_position=ManipulatorPosition(y1=0, y2=0, x=0, z=0), + ), +) + +rig = AindBehaviorDeviceWaterTunerRig( + rig_name="testrig", + harp_behavior=aind_behavior_services.rig.harp.HarpBehavior(port_name="COM3"), + manipulator=aind_manipulator.AindManipulatorDevice(port_name="COM10", calibration=manipulator_calibration), + scale=SerialScale(port_name="COM12"), +) + + +def main(path_seed: str = "./local/{schema}.json"): + os.makedirs(os.path.dirname(path_seed), exist_ok=True) + models = [rig] + + for model in models: + with open(path_seed.format(schema=model.__class__.__name__), "w", encoding="utf-8") as f: + f.write(model.model_dump_json(indent=2)) + + +if __name__ == "__main__": + main() diff --git a/examples/session.py b/examples/session.py new file mode 100644 index 0000000..dbc87c1 --- /dev/null +++ b/examples/session.py @@ -0,0 +1,29 @@ +import datetime +import os + +from aind_behavior_services.session import AindBehaviorSessionModel + +session = AindBehaviorSessionModel( + date=datetime.datetime.now(tz=datetime.timezone.utc), + experiment="AindBehaviorDeviceWaterTuner", + root_path="c://", + subject="test", + notes="test session", + experiment_version="0.1.0", + allow_dirty_repo=True, + skip_hardware_validation=False, + experimenter=["Foo", "Bar"], +) + + +def main(path_seed: str = "./local/{schema}.json"): + os.makedirs(os.path.dirname(path_seed), exist_ok=True) + models = [session] + + for model in models: + with open(path_seed.format(schema=model.__class__.__name__), "w", encoding="utf-8") as f: + f.write(model.model_dump_json(indent=2)) + + +if __name__ == "__main__": + main() diff --git a/examples/task_logic.py b/examples/task_logic.py new file mode 100644 index 0000000..65137ea --- /dev/null +++ b/examples/task_logic.py @@ -0,0 +1,31 @@ +import os + +from aind_behavior_curriculum import Stage, TrainerState + +from aind_behavior_device_water_tuner.task_logic import ( + AindBehaviorDeviceWaterTunerTaskLogic, + AindBehaviorDeviceWaterTunerTaskParameters, +) + +task_logic = AindBehaviorDeviceWaterTunerTaskLogic( + task_parameters=AindBehaviorDeviceWaterTunerTaskParameters( + repeat_count=200, valve_open_interval=0.2, valve_open_time=[0.02, 0.05, 0.1] + ) +) + + +def main(path_seed: str = "./local/example_{schema}.json"): + example_task_logic = task_logic + example_trainer_state = TrainerState( + stage=Stage(name="example_stage", task=example_task_logic), curriculum=None, is_on_curriculum=False + ) + os.makedirs(os.path.dirname(path_seed), exist_ok=True) + models = [example_task_logic, example_trainer_state] + + for model in models: + with open(path_seed.format(schema=model.__class__.__name__), "w", encoding="utf-8") as f: + f.write(model.model_dump_json(indent=2)) + + +if __name__ == "__main__": + main() diff --git a/pyproject.toml b/pyproject.toml index 19f69d5..9cb9b15 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,65 +1,52 @@ [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-water-tuner" -description = "A repository with a pipeline for automatic water calibration for animal experiments." -authors = [ - { name = "Bruno Cruz", email = "bruno.cruz@alleninstitute.org" }, -] -license = {text = "MIT"} +description = "A library that defines AIND data schema for the water-tuner experiment." +authors = [ {name = "Bruno F. Cruz", email = "bruno.cruz@alleninstitute.org"}] +license = "MIT" requires-python = ">=3.11" -dynamic = ["version", "readme"] classifiers = [ "Programming Language :: Python :: 3.11", - "License :: OSI Approved :: MIT License", "Operating System :: Microsoft :: Windows", ] +version = "0.4.0" +readme = {file = "README.md", content-type = "text/markdown"} dependencies = [ - "aind_behavior_services < 0.12", + "aind_behavior_services>=0.12, <0.13", + "pydantic-settings" ] [project.urls] -Documentation = "https://allenneuraldynamics.github.io/Aind.Behavior.WaterTuner/" -Repository = "https://github.com/AllenNeuralDynamics/Aind.Behavior.WaterTuner/" -Issues = "https://github.com/AllenNeuralDynamics/Aind.Behavior.WaterTuner/issues" -Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.WaterTuner/releases" +Documentation = "https://allenneuraldynamics.github.io/Aind.Behavior.Device.WaterTuner/" +Repository = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.WaterTuner/" +Issues = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.WaterTuner/issues" +Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.WaterTuner/releases" [project.optional-dependencies] -launcher = ["aind_behavior_experiment_launcher[aind-services]==0.5.0rc1"] +launcher = ["aind-clabe[aind-services]"] + +[dependency-groups] dev = [ - "aind_behavior_device_water_tuner[launcher]", + "aind-behavior-device-water-tuner[launcher]", "ruff", "codespell" ] docs = [ - 'Sphinx<7.3', + 'Sphinx', 'furo', 'sphinx-jinja', - 'autodoc_pydantic[erdantic]', - 'sphinx-jsonschema', - 'sphinx-copybutton', - "sphinx_mdinclude", -] + 'myst_parser', + 'sphinx-jsonschema'] [project.scripts] -clabe = "aind_behavior_device_water_tuner.launcher:main" -regenerate = "aind_behavior_device_water_tuner.regenerate:main" - -[tool.setuptools.packages.find] -where = ["src"] - -[tool.setuptools.package-data] -aind_behavior_device_water_tuner = ["py.typed"] - -[tool.setuptools.dynamic] -version = {attr = "aind_behavior_device_water_tuner.__version__"} -readme = {file = "README.md", content-type = "text/markdown"} +water-tuner = "aind_behavior_device_water_tuner.cli:main" [tool.ruff] line-length = 120 @@ -72,5 +59,9 @@ 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/scripts/regenerate_environment.cmd b/scripts/deploy.cmd similarity index 100% rename from scripts/regenerate_environment.cmd rename to scripts/deploy.cmd diff --git a/scripts/deploy.ps1 b/scripts/deploy.ps1 new file mode 100644 index 0000000..9c937f1 --- /dev/null +++ b/scripts/deploy.ps1 @@ -0,0 +1,31 @@ +$scriptPath = $MyInvocation.MyCommand.Path +$scriptDirectory = Split-Path -Parent $scriptPath +Set-Location (Split-Path -Parent $scriptDirectory) + +Write-Output "Initializing and updating submodules..." +&git submodule update --init --recursive + +Write-Output "Creating a Python environment..." + +if (-not (Get-Command uv -ErrorAction SilentlyContinue)) { + throw "The 'uv' command was not found. See https://docs.astral.sh/uv/getting-started/installation/ for instructions." +} + +if (Test-Path -Path ./.venv) { + Remove-Item ./.venv -Recurse -Force +} +&uv venv +.\.venv\Scripts\Activate.ps1 +Write-Output "Synchronizing environment..." +&uv sync --extra launcher +Write-Output "Creating a Bonsai environment and installing packages..." +if (Test-Path -Path "bonsai") { + Set-Location "bonsai" + .\setup.ps1 +} elseif (Test-Path -Path ".bonsai") { + Set-Location ".bonsai" + .\setup.ps1 +} else { + throw "Neither 'bonsai' nor '.bonsai' directory found." +} +Set-Location .. \ No newline at end of file diff --git a/scripts/launcher.cmd b/scripts/launcher.cmd new file mode 100644 index 0000000..4ded834 --- /dev/null +++ b/scripts/launcher.cmd @@ -0,0 +1,6 @@ +@echo off +setlocal +set "scriptPath=%~dp0" +set "launcherPath=%scriptPath%launcher.ps1" +powershell -ExecutionPolicy Bypass -File "%launcherPath%" +endlocal diff --git a/scripts/launcher.ps1 b/scripts/launcher.ps1 new file mode 100644 index 0000000..16a4eb1 --- /dev/null +++ b/scripts/launcher.ps1 @@ -0,0 +1,3 @@ +$scriptPath = Split-Path -Parent $MyInvocation.MyCommand.Path +Set-Location -Path (Split-Path -Parent $scriptPath) +&uv run water-tuner clabe diff --git a/scripts/regenerate_environment.ps1 b/scripts/regenerate_environment.ps1 deleted file mode 100644 index 5de218e..0000000 --- a/scripts/regenerate_environment.ps1 +++ /dev/null @@ -1,15 +0,0 @@ -$scriptPath = $MyInvocation.MyCommand.Path -$scriptDirectory = Split-Path -Parent $scriptPath -Set-Location (Split-Path -Parent $scriptDirectory) -Write-Output "Creating a Python environment..." -if (Test-Path -Path ./.venv) { - Remove-Item ./.venv -Recurse -Force -} -&python -m venv ./.venv -.\.venv\Scripts\Activate.ps1 -Write-Output "Installing python packages..." -&pip install .[launcher] -Write-Output "Creating a Bonsai environment and installing packages..." -Set-Location "bonsai" -.\setup.ps1 -Set-Location .. \ No newline at end of file diff --git a/src/.gitignore b/src/.gitignore new file mode 100644 index 0000000..f2d70a3 --- /dev/null +++ b/src/.gitignore @@ -0,0 +1,5 @@ +# Bonsai scripting files +.vs +.vscode +src.sln +.bonsai \ No newline at end of file diff --git a/src/DataSchemas/aind_behavior_device_water_tuner.json b/src/DataSchemas/aind_behavior_device_water_tuner.json new file mode 100644 index 0000000..f7b3a14 --- /dev/null +++ b/src/DataSchemas/aind_behavior_device_water_tuner.json @@ -0,0 +1,956 @@ +{ + "$defs": { + "AindBehaviorDeviceWaterTunerRig": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.12.1", + "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-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "version": { + "const": "0.4.0", + "default": "0.4.0", + "title": "Version", + "type": "string" + }, + "computer_name": { + "description": "Computer name", + "title": "Computer Name", + "type": "string" + }, + "rig_name": { + "description": "Rig name", + "title": "Rig Name", + "type": "string" + }, + "scale": { + "$ref": "#/$defs/SerialScale", + "title": "Serial scale device" + }, + "harp_behavior": { + "$ref": "#/$defs/HarpBehavior", + "description": "Harp behavior" + }, + "manipulator": { + "default": null, + "description": "Manipulator", + "oneOf": [ + { + "$ref": "#/$defs/AindManipulatorDevice" + }, + { + "type": "null" + } + ] + } + }, + "required": [ + "rig_name", + "scale", + "harp_behavior" + ], + "title": "AindBehaviorDeviceWaterTunerRig", + "type": "object" + }, + "AindBehaviorDeviceWaterTunerTaskLogic": { + "additionalProperties": false, + "description": "Main task logic model for the water-tuner task.", + "properties": { + "name": { + "const": "AindBehaviorDeviceWaterTuner", + "default": "AindBehaviorDeviceWaterTuner", + "description": "Name of the task logic", + "title": "Name", + "type": "string" + }, + "description": { + "default": "", + "description": "Description of the task.", + "title": "Description", + "type": "string" + }, + "task_parameters": { + "$ref": "#/$defs/AindBehaviorDeviceWaterTunerTaskParameters", + "description": "Parameters of the task logic" + }, + "version": { + "const": "0.4.0", + "default": "0.4.0", + "title": "Version", + "type": "string" + }, + "stage_name": { + "default": null, + "description": "Optional stage name the `Task` object instance represents.", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Stage Name" + } + }, + "required": [ + "task_parameters" + ], + "title": "AindBehaviorDeviceWaterTunerTaskLogic", + "type": "object" + }, + "AindBehaviorDeviceWaterTunerTaskParameters": { + "additionalProperties": true, + "properties": { + "rng_seed": { + "default": null, + "description": "Seed of the random number generator", + "oneOf": [ + { + "type": "number" + }, + { + "type": "null" + } + ], + "title": "Rng Seed" + }, + "aind_behavior_services_pkg_version": { + "default": "0.12.1", + "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$", + "title": "aind_behavior_services package version", + "type": "string" + }, + "valve_open_time": { + "description": "An array with the times (s) the valve is open during calibration", + "items": { + "exclusiveMinimum": 0, + "type": "number" + }, + "minItems": 1, + "title": "Valve Open Time", + "type": "array" + }, + "valve_open_interval": { + "default": 0.2, + "description": "Time between two consecutive valve openings (s)", + "exclusiveMinimum": 0, + "title": "Valve open interval", + "type": "number" + }, + "repeat_count": { + "default": 200, + "description": "Number of times the valve opened per measure valve_open_time entry", + "minimum": 1, + "title": "Repeat count", + "type": "integer" + } + }, + "required": [ + "valve_open_time" + ], + "title": "AindBehaviorDeviceWaterTunerTaskParameters", + "type": "object" + }, + "AindBehaviorSessionModel": { + "properties": { + "aind_behavior_services_pkg_version": { + "default": "0.12.1", + "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" + }, + "AindManipulatorCalibration": { + "description": "Aind manipulator calibration class", + "properties": { + "device_name": { + "default": "AindManipulator", + "description": "Must match a device name in rig/instrument", + "title": "Device name", + "type": "string" + }, + "input": { + "$ref": "#/$defs/AindManipulatorCalibrationInput", + "title": "Input of the calibration" + }, + "output": { + "$ref": "#/$defs/AindManipulatorCalibrationOutput", + "title": "Output of the calibration." + }, + "date": { + "default": null, + "oneOf": [ + { + "format": "date-time", + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Date" + }, + "description": { + "const": "Calibration of the load cells system", + "default": "Calibration of the load cells system", + "title": "Description", + "type": "string" + }, + "notes": { + "default": null, + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Notes" + } + }, + "required": [ + "input", + "output" + ], + "title": "AindManipulatorCalibration", + "type": "object" + }, + "AindManipulatorCalibrationInput": { + "properties": { + "full_step_to_mm": { + "$ref": "#/$defs/ManipulatorPosition", + "default": { + "x": 0.01, + "y1": 0.01, + "y2": 0.01, + "z": 0.01 + }, + "title": "Full step to mm. Used to convert steps to SI Units" + }, + "axis_configuration": { + "default": [ + { + "axis": 2, + "step_acceleration_interval": 100, + "step_interval": 100, + "microstep_resolution": 0, + "maximum_step_interval": 2000, + "motor_operation_mode": 0, + "max_limit": 25.0, + "min_limit": -0.01 + }, + { + "axis": 3, + "step_acceleration_interval": 100, + "step_interval": 100, + "microstep_resolution": 0, + "maximum_step_interval": 2000, + "motor_operation_mode": 0, + "max_limit": 25.0, + "min_limit": -0.01 + }, + { + "axis": 1, + "step_acceleration_interval": 100, + "step_interval": 100, + "microstep_resolution": 0, + "maximum_step_interval": 2000, + "motor_operation_mode": 0, + "max_limit": 25.0, + "min_limit": -0.01 + }, + { + "axis": 4, + "step_acceleration_interval": 100, + "step_interval": 100, + "microstep_resolution": 0, + "maximum_step_interval": 2000, + "motor_operation_mode": 0, + "max_limit": 25.0, + "min_limit": -0.01 + } + ], + "items": { + "$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": "#/$defs/ManipulatorPosition", + "default": { + "x": 0.0, + "y1": 0.0, + "y2": 0.0, + "z": 0.0 + } + } + }, + "title": "AindManipulatorCalibrationInput", + "type": "object" + }, + "AindManipulatorCalibrationOutput": { + "properties": {}, + "title": "AindManipulatorCalibrationOutput", + "type": "object" + }, + "AindManipulatorDevice": { + "properties": { + "device_type": { + "const": "StepperDriver", + "default": "StepperDriver", + "title": "Device Type", + "type": "string" + }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, + "additional_settings": { + "default": null, + "description": "Additional settings", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "calibration": { + "default": null, + "oneOf": [ + { + "$ref": "#/$defs/AindManipulatorCalibration" + }, + { + "type": "null" + } + ], + "title": "Calibration of the manipulator" + }, + "who_am_i": { + "const": 1130, + "default": 1130, + "title": "Who Am I", + "type": "integer" + }, + "serial_number": { + "default": null, + "description": "Device serial number", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Serial Number" + }, + "port_name": { + "description": "Device port name", + "title": "Port Name", + "type": "string" + } + }, + "required": [ + "port_name" + ], + "title": "AindManipulatorDevice", + "type": "object" + }, + "Axis": { + "description": "Motor axis available", + "enum": [ + 0, + 1, + 2, + 3, + 4 + ], + "title": "Axis", + "type": "integer", + "x-enumNames": [ + "None", + "X", + "Y1", + "Y2", + "Z" + ] + }, + "AxisConfiguration": { + "description": "Axis configuration", + "properties": { + "axis": { + "$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": "#/$defs/MotorOperationMode", + "default": 0, + "title": "Motor operation mode" + }, + "max_limit": { + "default": 25, + "title": "Maximum limit in SI units. A value of 0 disables this limit.", + "type": "number" + }, + "min_limit": { + "default": -0.01, + "title": "Minimum limit in SI units. A value of 0 disables this limit.", + "type": "number" + } + }, + "required": [ + "axis" + ], + "title": "AxisConfiguration", + "type": "object" + }, + "BaseModel": { + "properties": {}, + "title": "BaseModel", + "type": "object" + }, + "ExtensionDataTypes": { + "properties": { + "calibration": { + "$ref": "#/$defs/WaterValveCalibration" + } + }, + "required": [ + "calibration" + ], + "title": "ExtensionDataTypes", + "type": "object" + }, + "HarpBehavior": { + "properties": { + "device_type": { + "const": "Behavior", + "default": "Behavior", + "title": "Device Type", + "type": "string" + }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, + "additional_settings": { + "default": null, + "description": "Additional settings", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "calibration": { + "default": null, + "description": "Calibration", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "who_am_i": { + "const": 1216, + "default": 1216, + "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": "HarpBehavior", + "type": "object" + }, + "ManipulatorPosition": { + "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" + }, + "Measurement": { + "description": "Input for water valve calibration class", + "properties": { + "valve_open_interval": { + "description": "Time between two consecutive valve openings (s)", + "exclusiveMinimum": 0, + "title": "Valve open interval", + "type": "number" + }, + "valve_open_time": { + "description": "Valve open interval (s)", + "exclusiveMinimum": 0, + "title": "Valve open time", + "type": "number" + }, + "water_weight": { + "description": "Weight of water delivered (g)", + "items": { + "exclusiveMinimum": 0, + "type": "number" + }, + "minItems": 1, + "title": "Water weight", + "type": "array" + }, + "repeat_count": { + "description": "Number of times the valve opened.", + "minimum": 0, + "title": "Repeat count", + "type": "integer" + } + }, + "required": [ + "valve_open_interval", + "valve_open_time", + "water_weight", + "repeat_count" + ], + "title": "Measurement", + "type": "object" + }, + "MicrostepResolution": { + "enum": [ + 0, + 1, + 2, + 3 + ], + "title": "MicrostepResolution", + "type": "integer", + "x-enumNames": [ + "Microstep8", + "Microstep16", + "Microstep32", + "Microstep64" + ] + }, + "MotorOperationMode": { + "enum": [ + 0, + 1 + ], + "title": "MotorOperationMode", + "type": "integer", + "x-enumNames": [ + "Quiet", + "Dynamic" + ] + }, + "SerialScale": { + "properties": { + "device_type": { + "const": "SerialScale", + "default": "SerialScale", + "title": "Device Type", + "type": "string" + }, + "device_name": { + "default": null, + "description": "Device name", + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Device Name" + }, + "additional_settings": { + "default": null, + "description": "Additional settings", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "calibration": { + "default": null, + "description": "Calibration", + "oneOf": [ + { + "$ref": "#/$defs/BaseModel" + }, + { + "type": "null" + } + ] + }, + "port_name": { + "description": "COM port to which the scale is connected", + "title": "Port Name", + "type": "string" + } + }, + "required": [ + "port_name" + ], + "title": "SerialScale", + "type": "object" + }, + "WaterValveCalibration": { + "description": "Water valve calibration class", + "properties": { + "device_name": { + "default": "WaterValve", + "description": "Name of the device being calibrated", + "title": "Device name", + "type": "string" + }, + "input": { + "$ref": "#/$defs/WaterValveCalibrationInput", + "title": "Input of the calibration" + }, + "output": { + "$ref": "#/$defs/WaterValveCalibrationOutput", + "title": "Output of the calibration." + }, + "date": { + "default": null, + "oneOf": [ + { + "format": "date-time", + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Date" + }, + "description": { + "const": "Calibration of the water valve delivery system", + "default": "Calibration of the water valve delivery system", + "title": "Description", + "type": "string" + }, + "notes": { + "default": null, + "oneOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Notes" + } + }, + "required": [ + "input", + "output" + ], + "title": "WaterValveCalibration", + "type": "object" + }, + "WaterValveCalibrationInput": { + "properties": { + "measurements": { + "default": [], + "description": "List of measurements", + "items": { + "$ref": "#/$defs/Measurement" + }, + "title": "Measurements", + "type": "array" + } + }, + "title": "WaterValveCalibrationInput", + "type": "object" + }, + "WaterValveCalibrationOutput": { + "description": "Output for water valve calibration class", + "properties": { + "interval_average": { + "default": null, + "description": "Dictionary keyed by measured valve interval and corresponding average single event volume.", + "oneOf": [ + { + "additionalProperties": { + "exclusiveMinimum": 0, + "type": "number" + }, + "type": "object" + }, + { + "type": "null" + } + ], + "title": "Interval average" + }, + "slope": { + "description": "Slope of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)", + "title": "Regression slope", + "type": "number" + }, + "offset": { + "description": "Offset of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)", + "title": "Regression offset", + "type": "number" + }, + "r2": { + "default": null, + "description": "R2 metric from the linear model.", + "oneOf": [ + { + "maximum": 1, + "minimum": 0, + "type": "number" + }, + { + "type": "null" + } + ], + "title": "R2" + }, + "valid_domain": { + "default": null, + "description": "The optional time-intervals the calibration curve was calculated on.", + "oneOf": [ + { + "items": { + "exclusiveMinimum": 0, + "type": "number" + }, + "minItems": 2, + "type": "array" + }, + { + "type": "null" + } + ], + "title": "Valid domain" + } + }, + "required": [ + "slope", + "offset" + ], + "title": "WaterValveCalibrationOutput", + "type": "object" + } + } +} \ No newline at end of file diff --git a/src/Extensions.csproj b/src/Extensions.csproj index c36bbb2..cc5da87 100644 --- a/src/Extensions.csproj +++ b/src/Extensions.csproj @@ -1,10 +1,12 @@ - - net472 - - - - - - + + net48 + true + true + + + + + + \ No newline at end of file diff --git a/src/Extensions/AindBehaviorDeviceWaterTuner.Generated.cs b/src/Extensions/AindBehaviorDeviceWaterTuner.Generated.cs new file mode 100644 index 0000000..0e5160d --- /dev/null +++ b/src/Extensions/AindBehaviorDeviceWaterTuner.Generated.cs @@ -0,0 +1,2817 @@ +//---------------------- +// +// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) +// +//---------------------- + + +namespace AindBehaviorDeviceWaterTunerDataSchema +{ + #pragma warning disable // Disable all warnings + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindBehaviorDeviceWaterTunerRig + { + + private string _aindBehaviorServicesPkgVersion; + + private string _version; + + private string _computerName; + + private string _rigName; + + private SerialScale _scale; + + private HarpBehavior _harpBehavior; + + private AindManipulatorDevice _manipulator; + + public AindBehaviorDeviceWaterTunerRig() + { + _aindBehaviorServicesPkgVersion = "0.12.1"; + _version = "0.4.0"; + _scale = new SerialScale(); + _harpBehavior = new HarpBehavior(); + } + + protected AindBehaviorDeviceWaterTunerRig(AindBehaviorDeviceWaterTunerRig other) + { + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _computerName = other._computerName; + _rigName = other._rigName; + _scale = other._scale; + _harpBehavior = other._harpBehavior; + _manipulator = other._manipulator; + } + + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version + { + get + { + return _version; + } + set + { + _version = value; + } + } + + /// + /// Computer name + /// + [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] + [System.ComponentModel.DescriptionAttribute("Computer name")] + public string ComputerName + { + get + { + return _computerName; + } + set + { + _computerName = value; + } + } + + /// + /// Rig name + /// + [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Rig name")] + public string RigName + { + get + { + return _rigName; + } + set + { + _rigName = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("scale", Required=Newtonsoft.Json.Required.Always)] + public SerialScale Scale + { + get + { + return _scale; + } + set + { + _scale = value; + } + } + + /// + /// Harp behavior + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("harp_behavior", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Harp behavior")] + public HarpBehavior HarpBehavior + { + get + { + return _harpBehavior; + } + set + { + _harpBehavior = value; + } + } + + /// + /// Manipulator + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("manipulator")] + [System.ComponentModel.DescriptionAttribute("Manipulator")] + public AindManipulatorDevice Manipulator + { + get + { + return _manipulator; + } + set + { + _manipulator = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorDeviceWaterTunerRig(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorDeviceWaterTunerRig(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("ComputerName = " + _computerName + ", "); + stringBuilder.Append("RigName = " + _rigName + ", "); + stringBuilder.Append("Scale = " + _scale + ", "); + stringBuilder.Append("HarpBehavior = " + _harpBehavior + ", "); + stringBuilder.Append("Manipulator = " + _manipulator); + 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(); + } + } + + + /// + /// Main task logic model for the water-tuner task. + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Main task logic model for the water-tuner task.")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindBehaviorDeviceWaterTunerTaskLogic + { + + private string _name; + + private string _description; + + private AindBehaviorDeviceWaterTunerTaskParameters _taskParameters; + + private string _version; + + private string _stageName; + + public AindBehaviorDeviceWaterTunerTaskLogic() + { + _name = "AindBehaviorDeviceWaterTuner"; + _description = ""; + _taskParameters = new AindBehaviorDeviceWaterTunerTaskParameters(); + _version = "0.4.0"; + } + + protected AindBehaviorDeviceWaterTunerTaskLogic(AindBehaviorDeviceWaterTunerTaskLogic other) + { + _name = other._name; + _description = other._description; + _taskParameters = other._taskParameters; + _version = other._version; + _stageName = other._stageName; + } + + /// + /// Name of the task logic + /// + [Newtonsoft.Json.JsonPropertyAttribute("name")] + [System.ComponentModel.DescriptionAttribute("Name of the task logic")] + public string Name + { + get + { + return _name; + } + set + { + _name = value; + } + } + + /// + /// Description of the task. + /// + [Newtonsoft.Json.JsonPropertyAttribute("description")] + [System.ComponentModel.DescriptionAttribute("Description of the task.")] + public string Description + { + get + { + return _description; + } + set + { + _description = value; + } + } + + /// + /// Parameters of the task logic + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("task_parameters", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Parameters of the task logic")] + public AindBehaviorDeviceWaterTunerTaskParameters 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 Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorDeviceWaterTunerTaskLogic(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorDeviceWaterTunerTaskLogic(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Name = " + _name + ", "); + stringBuilder.Append("Description = " + _description + ", "); + stringBuilder.Append("TaskParameters = " + _taskParameters + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("StageName = " + _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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindBehaviorDeviceWaterTunerTaskParameters + { + + private double? _rngSeed; + + private string _aindBehaviorServicesPkgVersion; + + private System.Collections.Generic.List _valveOpenTime; + + private double _valveOpenInterval; + + private int _repeatCount; + + public AindBehaviorDeviceWaterTunerTaskParameters() + { + _aindBehaviorServicesPkgVersion = "0.12.1"; + _valveOpenTime = new System.Collections.Generic.List(); + _valveOpenInterval = 0.2D; + _repeatCount = 200; + } + + protected AindBehaviorDeviceWaterTunerTaskParameters(AindBehaviorDeviceWaterTunerTaskParameters other) + { + _rngSeed = other._rngSeed; + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _valveOpenTime = other._valveOpenTime; + _valveOpenInterval = other._valveOpenInterval; + _repeatCount = other._repeatCount; + } + + /// + /// 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; + } + } + + /// + /// An array with the times (s) the valve is open during calibration + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("valve_open_time", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("An array with the times (s) the valve is open during calibration")] + public System.Collections.Generic.List ValveOpenTime + { + get + { + return _valveOpenTime; + } + set + { + _valveOpenTime = value; + } + } + + /// + /// Time between two consecutive valve openings (s) + /// + [Newtonsoft.Json.JsonPropertyAttribute("valve_open_interval")] + [System.ComponentModel.DescriptionAttribute("Time between two consecutive valve openings (s)")] + public double ValveOpenInterval + { + get + { + return _valveOpenInterval; + } + set + { + _valveOpenInterval = value; + } + } + + /// + /// Number of times the valve opened per measure valve_open_time entry + /// + [Newtonsoft.Json.JsonPropertyAttribute("repeat_count")] + [System.ComponentModel.DescriptionAttribute("Number of times the valve opened per measure valve_open_time entry")] + public int RepeatCount + { + get + { + return _repeatCount; + } + set + { + _repeatCount = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorDeviceWaterTunerTaskParameters(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorDeviceWaterTunerTaskParameters(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("RngSeed = " + _rngSeed + ", "); + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("ValveOpenTime = " + _valveOpenTime + ", "); + stringBuilder.Append("ValveOpenInterval = " + _valveOpenInterval + ", "); + stringBuilder.Append("RepeatCount = " + _repeatCount); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindBehaviorSessionModel + { + + private string _aindBehaviorServicesPkgVersion; + + private string _version; + + private string _experiment; + + private System.Collections.Generic.List _experimenter; + + private System.DateTimeOffset _date; + + private string _rootPath; + + private string _sessionName; + + private string _subject; + + private string _experimentVersion; + + private string _notes; + + private string _commitHash; + + private bool _allowDirtyRepo; + + private bool _skipHardwareValidation; + + public AindBehaviorSessionModel() + { + _aindBehaviorServicesPkgVersion = "0.12.1"; + _version = "0.3.1"; + _experimenter = new System.Collections.Generic.List(); + _allowDirtyRepo = false; + _skipHardwareValidation = false; + } + + protected AindBehaviorSessionModel(AindBehaviorSessionModel other) + { + _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; + _version = other._version; + _experiment = other._experiment; + _experimenter = other._experimenter; + _date = other._date; + _rootPath = other._rootPath; + _sessionName = other._sessionName; + _subject = other._subject; + _experimentVersion = other._experimentVersion; + _notes = other._notes; + _commitHash = other._commitHash; + _allowDirtyRepo = other._allowDirtyRepo; + _skipHardwareValidation = other._skipHardwareValidation; + } + + [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] + public string AindBehaviorServicesPkgVersion + { + get + { + return _aindBehaviorServicesPkgVersion; + } + set + { + _aindBehaviorServicesPkgVersion = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("version")] + public string Version + { + get + { + return _version; + } + set + { + _version = value; + } + } + + /// + /// Name of the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("experiment", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Name of the experiment")] + public string Experiment + { + get + { + return _experiment; + } + set + { + _experiment = value; + } + } + + /// + /// Name of the experimenter + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("experimenter")] + [System.ComponentModel.DescriptionAttribute("Name of the experimenter")] + public System.Collections.Generic.List Experimenter + { + get + { + return _experimenter; + } + set + { + _experimenter = value; + } + } + + /// + /// Date of the experiment + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("date")] + [System.ComponentModel.DescriptionAttribute("Date of the experiment")] + public System.DateTimeOffset Date + { + get + { + return _date; + } + set + { + _date = value; + } + } + + /// + /// Root path where data will be logged + /// + [Newtonsoft.Json.JsonPropertyAttribute("root_path", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Root path where data will be logged")] + public string RootPath + { + get + { + return _rootPath; + } + set + { + _rootPath = value; + } + } + + /// + /// Name of the session. This will be used to create a folder in the root path. + /// + [Newtonsoft.Json.JsonPropertyAttribute("session_name")] + [System.ComponentModel.DescriptionAttribute("Name of the session. This will be used to create a folder in the root path.")] + public string SessionName + { + get + { + return _sessionName; + } + set + { + _sessionName = value; + } + } + + /// + /// Name of the subject + /// + [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Name of the subject")] + public string Subject + { + get + { + return _subject; + } + set + { + _subject = value; + } + } + + /// + /// Version of the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("experiment_version", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Version of the experiment")] + public string ExperimentVersion + { + get + { + return _experimentVersion; + } + set + { + _experimentVersion = value; + } + } + + /// + /// Notes about the experiment + /// + [Newtonsoft.Json.JsonPropertyAttribute("notes")] + [System.ComponentModel.DescriptionAttribute("Notes about the experiment")] + public string Notes + { + get + { + return _notes; + } + set + { + _notes = value; + } + } + + /// + /// Commit hash of the repository + /// + [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")] + [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")] + public string CommitHash + { + get + { + return _commitHash; + } + set + { + _commitHash = value; + } + } + + /// + /// Allow running from a dirty repository + /// + [Newtonsoft.Json.JsonPropertyAttribute("allow_dirty_repo")] + [System.ComponentModel.DescriptionAttribute("Allow running from a dirty repository")] + public bool AllowDirtyRepo + { + get + { + return _allowDirtyRepo; + } + set + { + _allowDirtyRepo = value; + } + } + + /// + /// Skip hardware validation + /// + [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")] + [System.ComponentModel.DescriptionAttribute("Skip hardware validation")] + public bool SkipHardwareValidation + { + get + { + return _skipHardwareValidation; + } + set + { + _skipHardwareValidation = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorSessionModel(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorSessionModel(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", "); + stringBuilder.Append("Version = " + _version + ", "); + stringBuilder.Append("Experiment = " + _experiment + ", "); + stringBuilder.Append("Experimenter = " + _experimenter + ", "); + stringBuilder.Append("Date = " + _date + ", "); + stringBuilder.Append("RootPath = " + _rootPath + ", "); + stringBuilder.Append("SessionName = " + _sessionName + ", "); + stringBuilder.Append("Subject = " + _subject + ", "); + stringBuilder.Append("ExperimentVersion = " + _experimentVersion + ", "); + stringBuilder.Append("Notes = " + _notes + ", "); + stringBuilder.Append("CommitHash = " + _commitHash + ", "); + stringBuilder.Append("AllowDirtyRepo = " + _allowDirtyRepo + ", "); + stringBuilder.Append("SkipHardwareValidation = " + _skipHardwareValidation); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + /// + /// Aind manipulator calibration class + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Aind manipulator calibration class")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindManipulatorCalibration + { + + private string _deviceName; + + private AindManipulatorCalibrationInput _input; + + private AindManipulatorCalibrationOutput _output; + + private System.DateTimeOffset? _date; + + private string _description; + + private string _notes; + + public AindManipulatorCalibration() + { + _deviceName = "AindManipulator"; + _input = new AindManipulatorCalibrationInput(); + _output = new AindManipulatorCalibrationOutput(); + _description = "Calibration of the load cells system"; + } + + protected AindManipulatorCalibration(AindManipulatorCalibration other) + { + _deviceName = other._deviceName; + _input = other._input; + _output = other._output; + _date = other._date; + _description = other._description; + _notes = other._notes; + } + + /// + /// Must match a device name in rig/instrument + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Must match a device name in rig/instrument")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("input", Required=Newtonsoft.Json.Required.Always)] + public AindManipulatorCalibrationInput Input + { + get + { + return _input; + } + set + { + _input = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("output", Required=Newtonsoft.Json.Required.Always)] + public AindManipulatorCalibrationOutput Output + { + get + { + return _output; + } + set + { + _output = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("date")] + public System.DateTimeOffset? Date + { + get + { + return _date; + } + set + { + _date = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("description")] + public string Description + { + get + { + return _description; + } + set + { + _description = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("notes")] + public string Notes + { + get + { + return _notes; + } + set + { + _notes = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibration(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibration(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("Input = " + _input + ", "); + stringBuilder.Append("Output = " + _output + ", "); + stringBuilder.Append("Date = " + _date + ", "); + stringBuilder.Append("Description = " + _description + ", "); + stringBuilder.Append("Notes = " + _notes); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindManipulatorCalibrationInput + { + + private ManipulatorPosition _fullStepToMm; + + private System.Collections.Generic.List _axisConfiguration; + + private System.Collections.Generic.List _homingOrder; + + private ManipulatorPosition _initialPosition; + + public AindManipulatorCalibrationInput() + { + _fullStepToMm = new ManipulatorPosition(); + _axisConfiguration = new System.Collections.Generic.List(); + _homingOrder = new System.Collections.Generic.List(); + _initialPosition = new ManipulatorPosition(); + } + + protected AindManipulatorCalibrationInput(AindManipulatorCalibrationInput other) + { + _fullStepToMm = other._fullStepToMm; + _axisConfiguration = other._axisConfiguration; + _homingOrder = other._homingOrder; + _initialPosition = other._initialPosition; + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("full_step_to_mm")] + public ManipulatorPosition FullStepToMm + { + get + { + return _fullStepToMm; + } + set + { + _fullStepToMm = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("axis_configuration")] + public System.Collections.Generic.List AxisConfiguration + { + get + { + return _axisConfiguration; + } + set + { + _axisConfiguration = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("homing_order")] + public System.Collections.Generic.List HomingOrder + { + get + { + return _homingOrder; + } + set + { + _homingOrder = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("initial_position")] + public ManipulatorPosition InitialPosition + { + get + { + return _initialPosition; + } + set + { + _initialPosition = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibrationInput(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibrationInput(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("FullStepToMm = " + _fullStepToMm + ", "); + stringBuilder.Append("AxisConfiguration = " + _axisConfiguration + ", "); + stringBuilder.Append("HomingOrder = " + _homingOrder + ", "); + stringBuilder.Append("InitialPosition = " + _initialPosition); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindManipulatorCalibrationOutput + { + + public AindManipulatorCalibrationOutput() + { + } + + protected AindManipulatorCalibrationOutput(AindManipulatorCalibrationOutput other) + { + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibrationOutput(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibrationOutput(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + return false; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AindManipulatorDevice + { + + private string _deviceType; + + private string _deviceName; + + private BaseModel _additionalSettings; + + private AindManipulatorCalibration _calibration; + + private int _whoAmI; + + private string _serialNumber; + + private string _portName; + + public AindManipulatorDevice() + { + _deviceType = "StepperDriver"; + _whoAmI = 1130; + } + + protected AindManipulatorDevice(AindManipulatorDevice other) + { + _deviceType = other._deviceType; + _deviceName = other._deviceName; + _additionalSettings = other._additionalSettings; + _calibration = other._calibration; + _whoAmI = other._whoAmI; + _serialNumber = other._serialNumber; + _portName = other._portName; + } + + [Newtonsoft.Json.JsonPropertyAttribute("device_type")] + public string DeviceType + { + get + { + return _deviceType; + } + set + { + _deviceType = value; + } + } + + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + + /// + /// Additional settings + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] + [System.ComponentModel.DescriptionAttribute("Additional settings")] + public BaseModel AdditionalSettings + { + get + { + return _additionalSettings; + } + set + { + _additionalSettings = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + public AindManipulatorCalibration Calibration + { + get + { + return _calibration; + } + set + { + _calibration = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("who_am_i")] + public int WhoAmI + { + get + { + return _whoAmI; + } + set + { + _whoAmI = value; + } + } + + /// + /// Device serial number + /// + [Newtonsoft.Json.JsonPropertyAttribute("serial_number")] + [System.ComponentModel.DescriptionAttribute("Device serial number")] + public string SerialNumber + { + get + { + return _serialNumber; + } + set + { + _serialNumber = value; + } + } + + /// + /// Device port name + /// + [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Device port name")] + public string PortName + { + get + { + return _portName; + } + set + { + _portName = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorDevice(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorDevice(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("PortName = " + _portName); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + /// + /// Motor axis available + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + public enum Axis + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + None = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] + X = 1, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] + Y1 = 2, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] + Y2 = 3, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="4")] + Z = 4, + } + + + /// + /// Axis configuration + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Axis configuration")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class AxisConfiguration + { + + private Axis _axis; + + private int _stepAccelerationInterval; + + private int _stepInterval; + + private MicrostepResolution _microstepResolution; + + private int _maximumStepInterval; + + private MotorOperationMode _motorOperationMode; + + private double _maxLimit; + + private double _minLimit; + + public AxisConfiguration() + { + _stepAccelerationInterval = 100; + _stepInterval = 100; + _microstepResolution = AindBehaviorDeviceWaterTunerDataSchema.MicrostepResolution.Microstep8; + _maximumStepInterval = 2000; + _motorOperationMode = AindBehaviorDeviceWaterTunerDataSchema.MotorOperationMode.Quiet; + _maxLimit = 25D; + _minLimit = -0.01D; + } + + protected AxisConfiguration(AxisConfiguration other) + { + _axis = other._axis; + _stepAccelerationInterval = other._stepAccelerationInterval; + _stepInterval = other._stepInterval; + _microstepResolution = other._microstepResolution; + _maximumStepInterval = other._maximumStepInterval; + _motorOperationMode = other._motorOperationMode; + _maxLimit = other._maxLimit; + _minLimit = other._minLimit; + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("axis", Required=Newtonsoft.Json.Required.Always)] + public Axis Axis + { + get + { + return _axis; + } + set + { + _axis = value; + } + } + + /// + /// Acceleration of the step interval in microseconds + /// + [Newtonsoft.Json.JsonPropertyAttribute("step_acceleration_interval")] + [System.ComponentModel.DescriptionAttribute("Acceleration of the step interval in microseconds")] + public int StepAccelerationInterval + { + get + { + return _stepAccelerationInterval; + } + set + { + _stepAccelerationInterval = value; + } + } + + /// + /// Step interval in microseconds. + /// + [Newtonsoft.Json.JsonPropertyAttribute("step_interval")] + [System.ComponentModel.DescriptionAttribute("Step interval in microseconds.")] + public int StepInterval + { + get + { + return _stepInterval; + } + set + { + _stepInterval = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("microstep_resolution")] + public MicrostepResolution MicrostepResolution + { + get + { + return _microstepResolution; + } + set + { + _microstepResolution = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("maximum_step_interval")] + public int MaximumStepInterval + { + get + { + return _maximumStepInterval; + } + set + { + _maximumStepInterval = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("motor_operation_mode")] + public MotorOperationMode MotorOperationMode + { + get + { + return _motorOperationMode; + } + set + { + _motorOperationMode = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("max_limit")] + public double MaxLimit + { + get + { + return _maxLimit; + } + set + { + _maxLimit = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("min_limit")] + public double MinLimit + { + get + { + return _minLimit; + } + set + { + _minLimit = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AxisConfiguration(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new AxisConfiguration(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Axis = " + _axis + ", "); + stringBuilder.Append("StepAccelerationInterval = " + _stepAccelerationInterval + ", "); + stringBuilder.Append("StepInterval = " + _stepInterval + ", "); + stringBuilder.Append("MicrostepResolution = " + _microstepResolution + ", "); + stringBuilder.Append("MaximumStepInterval = " + _maximumStepInterval + ", "); + stringBuilder.Append("MotorOperationMode = " + _motorOperationMode + ", "); + stringBuilder.Append("MaxLimit = " + _maxLimit + ", "); + stringBuilder.Append("MinLimit = " + _minLimit); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class BaseModel + { + + public BaseModel() + { + } + + protected BaseModel(BaseModel other) + { + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new BaseModel(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new BaseModel(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + return false; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class ExtensionDataTypes + { + + private WaterValveCalibration _calibration; + + public ExtensionDataTypes() + { + _calibration = new WaterValveCalibration(); + } + + protected ExtensionDataTypes(ExtensionDataTypes other) + { + _calibration = other._calibration; + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration", Required=Newtonsoft.Json.Required.Always)] + public WaterValveCalibration Calibration + { + get + { + return _calibration; + } + set + { + _calibration = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ExtensionDataTypes(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new ExtensionDataTypes(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Calibration = " + _calibration); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class HarpBehavior + { + + private string _deviceType; + + private string _deviceName; + + private BaseModel _additionalSettings; + + private BaseModel _calibration; + + private int _whoAmI; + + private string _serialNumber; + + private string _portName; + + public HarpBehavior() + { + _deviceType = "Behavior"; + _whoAmI = 1216; + } + + protected HarpBehavior(HarpBehavior other) + { + _deviceType = other._deviceType; + _deviceName = other._deviceName; + _additionalSettings = other._additionalSettings; + _calibration = other._calibration; + _whoAmI = other._whoAmI; + _serialNumber = other._serialNumber; + _portName = other._portName; + } + + [Newtonsoft.Json.JsonPropertyAttribute("device_type")] + public string DeviceType + { + get + { + return _deviceType; + } + set + { + _deviceType = value; + } + } + + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + + /// + /// Additional settings + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] + [System.ComponentModel.DescriptionAttribute("Additional settings")] + public BaseModel AdditionalSettings + { + get + { + return _additionalSettings; + } + set + { + _additionalSettings = value; + } + } + + /// + /// Calibration + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration")] + public BaseModel Calibration + { + get + { + return _calibration; + } + set + { + _calibration = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("who_am_i")] + public int WhoAmI + { + get + { + return _whoAmI; + } + set + { + _whoAmI = value; + } + } + + /// + /// Device serial number + /// + [Newtonsoft.Json.JsonPropertyAttribute("serial_number")] + [System.ComponentModel.DescriptionAttribute("Device serial number")] + public string SerialNumber + { + get + { + return _serialNumber; + } + set + { + _serialNumber = value; + } + } + + /// + /// Device port name + /// + [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Device port name")] + public string PortName + { + get + { + return _portName; + } + set + { + _portName = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpBehavior(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new HarpBehavior(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("WhoAmI = " + _whoAmI + ", "); + stringBuilder.Append("SerialNumber = " + _serialNumber + ", "); + stringBuilder.Append("PortName = " + _portName); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class ManipulatorPosition + { + + private double _x; + + private double _y1; + + private double _y2; + + private double _z; + + public ManipulatorPosition() + { + } + + protected ManipulatorPosition(ManipulatorPosition other) + { + _x = other._x; + _y1 = other._y1; + _y2 = other._y2; + _z = other._z; + } + + [Newtonsoft.Json.JsonPropertyAttribute("x", Required=Newtonsoft.Json.Required.Always)] + public double X + { + get + { + return _x; + } + set + { + _x = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("y1", Required=Newtonsoft.Json.Required.Always)] + public double Y1 + { + get + { + return _y1; + } + set + { + _y1 = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("y2", Required=Newtonsoft.Json.Required.Always)] + public double Y2 + { + get + { + return _y2; + } + set + { + _y2 = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("z", Required=Newtonsoft.Json.Required.Always)] + public double Z + { + get + { + return _z; + } + set + { + _z = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ManipulatorPosition(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new ManipulatorPosition(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("X = " + _x + ", "); + stringBuilder.Append("Y1 = " + _y1 + ", "); + stringBuilder.Append("Y2 = " + _y2 + ", "); + stringBuilder.Append("Z = " + _z); + 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(); + } + } + + + /// + /// Input for water valve calibration class + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Input for water valve calibration class")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class Measurement + { + + private double _valveOpenInterval; + + private double _valveOpenTime; + + private System.Collections.Generic.List _waterWeight; + + private int _repeatCount; + + public Measurement() + { + _waterWeight = new System.Collections.Generic.List(); + } + + protected Measurement(Measurement other) + { + _valveOpenInterval = other._valveOpenInterval; + _valveOpenTime = other._valveOpenTime; + _waterWeight = other._waterWeight; + _repeatCount = other._repeatCount; + } + + /// + /// Time between two consecutive valve openings (s) + /// + [Newtonsoft.Json.JsonPropertyAttribute("valve_open_interval", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Time between two consecutive valve openings (s)")] + public double ValveOpenInterval + { + get + { + return _valveOpenInterval; + } + set + { + _valveOpenInterval = value; + } + } + + /// + /// Valve open interval (s) + /// + [Newtonsoft.Json.JsonPropertyAttribute("valve_open_time", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Valve open interval (s)")] + public double ValveOpenTime + { + get + { + return _valveOpenTime; + } + set + { + _valveOpenTime = value; + } + } + + /// + /// Weight of water delivered (g) + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("water_weight", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Weight of water delivered (g)")] + public System.Collections.Generic.List WaterWeight + { + get + { + return _waterWeight; + } + set + { + _waterWeight = value; + } + } + + /// + /// Number of times the valve opened. + /// + [Newtonsoft.Json.JsonPropertyAttribute("repeat_count", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Number of times the valve opened.")] + public int RepeatCount + { + get + { + return _repeatCount; + } + set + { + _repeatCount = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Measurement(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new Measurement(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("ValveOpenInterval = " + _valveOpenInterval + ", "); + stringBuilder.Append("ValveOpenTime = " + _valveOpenTime + ", "); + stringBuilder.Append("WaterWeight = " + _waterWeight + ", "); + stringBuilder.Append("RepeatCount = " + _repeatCount); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + public enum MicrostepResolution + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Microstep8 = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] + Microstep16 = 1, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] + Microstep32 = 2, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] + Microstep64 = 3, + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + public enum MotorOperationMode + { + + [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] + Quiet = 0, + + [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] + Dynamic = 1, + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class SerialScale + { + + private string _deviceType; + + private string _deviceName; + + private BaseModel _additionalSettings; + + private BaseModel _calibration; + + private string _portName; + + public SerialScale() + { + _deviceType = "SerialScale"; + } + + protected SerialScale(SerialScale other) + { + _deviceType = other._deviceType; + _deviceName = other._deviceName; + _additionalSettings = other._additionalSettings; + _calibration = other._calibration; + _portName = other._portName; + } + + [Newtonsoft.Json.JsonPropertyAttribute("device_type")] + public string DeviceType + { + get + { + return _deviceType; + } + set + { + _deviceType = value; + } + } + + /// + /// Device name + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Device name")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + + /// + /// Additional settings + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] + [System.ComponentModel.DescriptionAttribute("Additional settings")] + public BaseModel AdditionalSettings + { + get + { + return _additionalSettings; + } + set + { + _additionalSettings = value; + } + } + + /// + /// Calibration + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("calibration")] + [System.ComponentModel.DescriptionAttribute("Calibration")] + public BaseModel Calibration + { + get + { + return _calibration; + } + set + { + _calibration = value; + } + } + + /// + /// COM port to which the scale is connected + /// + [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("COM port to which the scale is connected")] + public string PortName + { + get + { + return _portName; + } + set + { + _portName = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SerialScale(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new SerialScale(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceType = " + _deviceType + ", "); + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", "); + stringBuilder.Append("Calibration = " + _calibration + ", "); + stringBuilder.Append("PortName = " + _portName); + 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(); + } + } + + + /// + /// Water valve calibration class + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Water valve calibration class")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class WaterValveCalibration + { + + private string _deviceName; + + private WaterValveCalibrationInput _input; + + private WaterValveCalibrationOutput _output; + + private System.DateTimeOffset? _date; + + private string _description; + + private string _notes; + + public WaterValveCalibration() + { + _deviceName = "WaterValve"; + _input = new WaterValveCalibrationInput(); + _output = new WaterValveCalibrationOutput(); + _description = "Calibration of the water valve delivery system"; + } + + protected WaterValveCalibration(WaterValveCalibration other) + { + _deviceName = other._deviceName; + _input = other._input; + _output = other._output; + _date = other._date; + _description = other._description; + _notes = other._notes; + } + + /// + /// Name of the device being calibrated + /// + [Newtonsoft.Json.JsonPropertyAttribute("device_name")] + [System.ComponentModel.DescriptionAttribute("Name of the device being calibrated")] + public string DeviceName + { + get + { + return _deviceName; + } + set + { + _deviceName = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("input", Required=Newtonsoft.Json.Required.Always)] + public WaterValveCalibrationInput Input + { + get + { + return _input; + } + set + { + _input = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("output", Required=Newtonsoft.Json.Required.Always)] + public WaterValveCalibrationOutput Output + { + get + { + return _output; + } + set + { + _output = value; + } + } + + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("date")] + public System.DateTimeOffset? Date + { + get + { + return _date; + } + set + { + _date = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("description")] + public string Description + { + get + { + return _description; + } + set + { + _description = value; + } + } + + [Newtonsoft.Json.JsonPropertyAttribute("notes")] + public string Notes + { + get + { + return _notes; + } + set + { + _notes = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new WaterValveCalibration(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new WaterValveCalibration(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("DeviceName = " + _deviceName + ", "); + stringBuilder.Append("Input = " + _input + ", "); + stringBuilder.Append("Output = " + _output + ", "); + stringBuilder.Append("Date = " + _date + ", "); + stringBuilder.Append("Description = " + _description + ", "); + stringBuilder.Append("Notes = " + _notes); + return true; + } + + public override string ToString() + { + System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); + stringBuilder.Append(GetType().Name); + stringBuilder.Append(" { "); + if (PrintMembers(stringBuilder)) + { + stringBuilder.Append(" "); + } + stringBuilder.Append("}"); + return stringBuilder.ToString(); + } + } + + + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class WaterValveCalibrationInput + { + + private System.Collections.Generic.List _measurements; + + public WaterValveCalibrationInput() + { + _measurements = new System.Collections.Generic.List(); + } + + protected WaterValveCalibrationInput(WaterValveCalibrationInput other) + { + _measurements = other._measurements; + } + + /// + /// List of measurements + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("measurements")] + [System.ComponentModel.DescriptionAttribute("List of measurements")] + public System.Collections.Generic.List Measurements + { + get + { + return _measurements; + } + set + { + _measurements = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new WaterValveCalibrationInput(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new WaterValveCalibrationInput(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("Measurements = " + _measurements); + 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(); + } + } + + + /// + /// Output for water valve calibration class + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Output for water valve calibration class")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] + [Bonsai.CombinatorAttribute(MethodName="Generate")] + public partial class WaterValveCalibrationOutput + { + + private System.Collections.Generic.Dictionary _intervalAverage; + + private double _slope; + + private double _offset; + + private double? _r2; + + private System.Collections.Generic.List _validDomain; + + public WaterValveCalibrationOutput() + { + } + + protected WaterValveCalibrationOutput(WaterValveCalibrationOutput other) + { + _intervalAverage = other._intervalAverage; + _slope = other._slope; + _offset = other._offset; + _r2 = other._r2; + _validDomain = other._validDomain; + } + + /// + /// Dictionary keyed by measured valve interval and corresponding average single event volume. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("interval_average")] + [System.ComponentModel.DescriptionAttribute("Dictionary keyed by measured valve interval and corresponding average single even" + + "t volume.")] + public System.Collections.Generic.Dictionary IntervalAverage + { + get + { + return _intervalAverage; + } + set + { + _intervalAverage = value; + } + } + + /// + /// Slope of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g) + /// + [Newtonsoft.Json.JsonPropertyAttribute("slope", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Slope of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)")] + public double Slope + { + get + { + return _slope; + } + set + { + _slope = value; + } + } + + /// + /// Offset of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g) + /// + [Newtonsoft.Json.JsonPropertyAttribute("offset", Required=Newtonsoft.Json.Required.Always)] + [System.ComponentModel.DescriptionAttribute("Offset of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)")] + public double Offset + { + get + { + return _offset; + } + set + { + _offset = value; + } + } + + /// + /// R2 metric from the linear model. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("r2")] + [System.ComponentModel.DescriptionAttribute("R2 metric from the linear model.")] + public double? R2 + { + get + { + return _r2; + } + set + { + _r2 = value; + } + } + + /// + /// The optional time-intervals the calibration curve was calculated on. + /// + [System.Xml.Serialization.XmlIgnoreAttribute()] + [Newtonsoft.Json.JsonPropertyAttribute("valid_domain")] + [System.ComponentModel.DescriptionAttribute("The optional time-intervals the calibration curve was calculated on.")] + public System.Collections.Generic.List ValidDomain + { + get + { + return _validDomain; + } + set + { + _validDomain = value; + } + } + + public System.IObservable Generate() + { + return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new WaterValveCalibrationOutput(this))); + } + + public System.IObservable Generate(System.IObservable source) + { + return System.Reactive.Linq.Observable.Select(source, _ => new WaterValveCalibrationOutput(this)); + } + + protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) + { + stringBuilder.Append("IntervalAverage = " + _intervalAverage + ", "); + stringBuilder.Append("Slope = " + _slope + ", "); + stringBuilder.Append("Offset = " + _offset + ", "); + stringBuilder.Append("R2 = " + _r2 + ", "); + stringBuilder.Append("ValidDomain = " + _validDomain); + 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", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Serializes a sequence of data model objects into JSON strings.")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] + [Bonsai.CombinatorAttribute()] + public partial class SerializeToJson + { + + public Newtonsoft.Json.Formatting Formatting { get; set; } + + private System.IObservable Process(System.IObservable source) + { + var formatting = Formatting; + return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.SerializeObject(value, formatting)); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + + public System.IObservable Process(System.IObservable source) + { + return Process(source); + } + } + + + /// + /// Deserializes a sequence of JSON strings into data model objects. + /// + [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")] + [System.ComponentModel.DescriptionAttribute("Deserializes a sequence of JSON strings into data model objects.")] + [System.ComponentModel.DefaultPropertyAttribute("Type")] + [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Transform)] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] + 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/AindBehaviorSessionModel.cs b/src/Extensions/AindBehaviorSessionModel.cs deleted file mode 100644 index 3fc0ea4..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 AindBehaviorWaterTuner.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 = "0.11.0"; - - 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/AindBehaviorWaterTunerRig.cs b/src/Extensions/AindBehaviorWaterTunerRig.cs deleted file mode 100644 index a1c779a..0000000 --- a/src/Extensions/AindBehaviorWaterTunerRig.cs +++ /dev/null @@ -1,1539 +0,0 @@ -//---------------------- -// -// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) -// -//---------------------- - - -namespace AindBehaviorWaterTuner.Rig -{ - #pragma warning disable // Disable all warnings - - /// - /// Aind manipulator calibration class - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Aind manipulator calibration class")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindManipulatorCalibration - { - - private string _deviceName = "AindManipulator"; - - private AindManipulatorCalibrationInput _input = new AindManipulatorCalibrationInput(); - - private AindManipulatorCalibrationOutput _output = new AindManipulatorCalibrationOutput(); - - private System.DateTimeOffset? _date; - - private string _description = "Calibration of the load cells system"; - - private string _notes; - - public AindManipulatorCalibration() - { - } - - protected AindManipulatorCalibration(AindManipulatorCalibration other) - { - _deviceName = other._deviceName; - _input = other._input; - _output = other._output; - _date = other._date; - _description = other._description; - _notes = other._notes; - } - - /// - /// Must match a device name in rig/instrument - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Must match a device name in rig/instrument")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("input", Required=Newtonsoft.Json.Required.Always)] - public AindManipulatorCalibrationInput Input - { - get - { - return _input; - } - set - { - _input = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("output", Required=Newtonsoft.Json.Required.Always)] - public AindManipulatorCalibrationOutput Output - { - get - { - return _output; - } - set - { - _output = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("date")] - public System.DateTimeOffset? Date - { - get - { - return _date; - } - set - { - _date = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("description")] - public string Description - { - get - { - return _description; - } - set - { - _description = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("notes")] - public string Notes - { - get - { - return _notes; - } - set - { - _notes = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibration(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibration(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); - 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)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindManipulatorCalibrationInput - { - - private ManipulatorPosition _fullStepToMm; - - private System.Collections.Generic.List _axisConfiguration = new System.Collections.Generic.List(); - - private System.Collections.Generic.List _homingOrder = new System.Collections.Generic.List(); - - private ManipulatorPosition _initialPosition; - - public AindManipulatorCalibrationInput() - { - } - - protected AindManipulatorCalibrationInput(AindManipulatorCalibrationInput other) - { - _fullStepToMm = other._fullStepToMm; - _axisConfiguration = other._axisConfiguration; - _homingOrder = other._homingOrder; - _initialPosition = other._initialPosition; - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("full_step_to_mm")] - public ManipulatorPosition FullStepToMm - { - get - { - return _fullStepToMm; - } - set - { - _fullStepToMm = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("axis_configuration")] - public System.Collections.Generic.List AxisConfiguration - { - get - { - return _axisConfiguration; - } - set - { - _axisConfiguration = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("homing_order")] - public System.Collections.Generic.List HomingOrder - { - get - { - return _homingOrder; - } - set - { - _homingOrder = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("initial_position")] - public ManipulatorPosition InitialPosition - { - get - { - return _initialPosition; - } - set - { - _initialPosition = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibrationInput(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibrationInput(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("full_step_to_mm = " + _fullStepToMm + ", "); - stringBuilder.Append("axis_configuration = " + _axisConfiguration + ", "); - stringBuilder.Append("homing_order = " + _homingOrder + ", "); - stringBuilder.Append("initial_position = " + _initialPosition); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindManipulatorCalibrationOutput - { - - public AindManipulatorCalibrationOutput() - { - } - - protected AindManipulatorCalibrationOutput(AindManipulatorCalibrationOutput other) - { - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorCalibrationOutput(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorCalibrationOutput(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - return false; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindManipulatorDevice - { - - private string _deviceType = "StepperDriver"; - - private string _deviceName; - - private BaseModel _additionalSettings; - - private AindManipulatorCalibration _calibration; - - private int _whoAmI = 1130; - - private string _serialNumber; - - private string _portName; - - public AindManipulatorDevice() - { - } - - protected AindManipulatorDevice(AindManipulatorDevice other) - { - _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; - _calibration = other._calibration; - _whoAmI = other._whoAmI; - _serialNumber = other._serialNumber; - _portName = other._portName; - } - - [Newtonsoft.Json.JsonPropertyAttribute("device_type")] - public string DeviceType - { - get - { - return _deviceType; - } - set - { - _deviceType = value; - } - } - - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings - { - get - { - return _additionalSettings; - } - set - { - _additionalSettings = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - public AindManipulatorCalibration Calibration - { - get - { - return _calibration; - } - set - { - _calibration = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("who_am_i")] - public int WhoAmI - { - get - { - return _whoAmI; - } - set - { - _whoAmI = value; - } - } - - /// - /// Device serial number - /// - [Newtonsoft.Json.JsonPropertyAttribute("serial_number")] - [System.ComponentModel.DescriptionAttribute("Device serial number")] - public string SerialNumber - { - get - { - return _serialNumber; - } - set - { - _serialNumber = value; - } - } - - /// - /// Device port name - /// - [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device port name")] - public string PortName - { - get - { - return _portName; - } - set - { - _portName = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindManipulatorDevice(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindManipulatorDevice(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("device_name = " + _deviceName + ", "); - 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); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - /// - /// Motor axis available - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - public enum Axis - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - None = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - X = 1, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] - Y1 = 2, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] - Y2 = 3, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="4")] - Z = 4, - } - - - /// - /// Axis configuration - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Axis configuration")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AxisConfiguration - { - - private Axis _axis; - - private int _stepAccelerationInterval = 100; - - private int _stepInterval = 100; - - private MicrostepResolution _microstepResolution = AindBehaviorWaterTuner.Rig.MicrostepResolution.Microstep8; - - private int _maximumStepInterval = 2000; - - private MotorOperationMode _motorOperationMode = AindBehaviorWaterTuner.Rig.MotorOperationMode.Quiet; - - private double _maxLimit = 25D; - - private double _minLimit = -0.01D; - - public AxisConfiguration() - { - } - - protected AxisConfiguration(AxisConfiguration other) - { - _axis = other._axis; - _stepAccelerationInterval = other._stepAccelerationInterval; - _stepInterval = other._stepInterval; - _microstepResolution = other._microstepResolution; - _maximumStepInterval = other._maximumStepInterval; - _motorOperationMode = other._motorOperationMode; - _maxLimit = other._maxLimit; - _minLimit = other._minLimit; - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("axis", Required=Newtonsoft.Json.Required.Always)] - public Axis Axis - { - get - { - return _axis; - } - set - { - _axis = value; - } - } - - /// - /// Acceleration of the step interval in microseconds - /// - [Newtonsoft.Json.JsonPropertyAttribute("step_acceleration_interval")] - [System.ComponentModel.DescriptionAttribute("Acceleration of the step interval in microseconds")] - public int StepAccelerationInterval - { - get - { - return _stepAccelerationInterval; - } - set - { - _stepAccelerationInterval = value; - } - } - - /// - /// Step interval in microseconds. - /// - [Newtonsoft.Json.JsonPropertyAttribute("step_interval")] - [System.ComponentModel.DescriptionAttribute("Step interval in microseconds.")] - public int StepInterval - { - get - { - return _stepInterval; - } - set - { - _stepInterval = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("microstep_resolution")] - public MicrostepResolution MicrostepResolution - { - get - { - return _microstepResolution; - } - set - { - _microstepResolution = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("maximum_step_interval")] - public int MaximumStepInterval - { - get - { - return _maximumStepInterval; - } - set - { - _maximumStepInterval = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("motor_operation_mode")] - public MotorOperationMode MotorOperationMode - { - get - { - return _motorOperationMode; - } - set - { - _motorOperationMode = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("max_limit")] - public double MaxLimit - { - get - { - return _maxLimit; - } - set - { - _maxLimit = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("min_limit")] - public double MinLimit - { - get - { - return _minLimit; - } - set - { - _minLimit = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AxisConfiguration(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AxisConfiguration(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("axis = " + _axis + ", "); - stringBuilder.Append("step_acceleration_interval = " + _stepAccelerationInterval + ", "); - stringBuilder.Append("step_interval = " + _stepInterval + ", "); - stringBuilder.Append("microstep_resolution = " + _microstepResolution + ", "); - stringBuilder.Append("maximum_step_interval = " + _maximumStepInterval + ", "); - stringBuilder.Append("motor_operation_mode = " + _motorOperationMode + ", "); - stringBuilder.Append("max_limit = " + _maxLimit + ", "); - stringBuilder.Append("min_limit = " + _minLimit); - 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)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class BaseModel - { - - public BaseModel() - { - } - - protected BaseModel(BaseModel other) - { - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new BaseModel(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new BaseModel(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - return false; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class HarpBehavior - { - - private string _deviceType = "Behavior"; - - private string _deviceName; - - private BaseModel _additionalSettings; - - private BaseModel _calibration; - - private int _whoAmI = 1216; - - private string _serialNumber; - - private string _portName; - - public HarpBehavior() - { - } - - protected HarpBehavior(HarpBehavior other) - { - _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; - _calibration = other._calibration; - _whoAmI = other._whoAmI; - _serialNumber = other._serialNumber; - _portName = other._portName; - } - - [Newtonsoft.Json.JsonPropertyAttribute("device_type")] - public string DeviceType - { - get - { - return _deviceType; - } - set - { - _deviceType = value; - } - } - - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings - { - get - { - return _additionalSettings; - } - set - { - _additionalSettings = value; - } - } - - /// - /// Calibration - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration")] - public BaseModel Calibration - { - get - { - return _calibration; - } - set - { - _calibration = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("who_am_i")] - public int WhoAmI - { - get - { - return _whoAmI; - } - set - { - _whoAmI = value; - } - } - - /// - /// Device serial number - /// - [Newtonsoft.Json.JsonPropertyAttribute("serial_number")] - [System.ComponentModel.DescriptionAttribute("Device serial number")] - public string SerialNumber - { - get - { - return _serialNumber; - } - set - { - _serialNumber = value; - } - } - - /// - /// Device port name - /// - [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Device port name")] - public string PortName - { - get - { - return _portName; - } - set - { - _portName = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new HarpBehavior(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new HarpBehavior(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("device_name = " + _deviceName + ", "); - 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); - 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)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class ManipulatorPosition - { - - private double _x; - - private double _y1; - - private double _y2; - - private double _z; - - public ManipulatorPosition() - { - } - - protected ManipulatorPosition(ManipulatorPosition other) - { - _x = other._x; - _y1 = other._y1; - _y2 = other._y2; - _z = other._z; - } - - [Newtonsoft.Json.JsonPropertyAttribute("x", Required=Newtonsoft.Json.Required.Always)] - public double X - { - get - { - return _x; - } - set - { - _x = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("y1", Required=Newtonsoft.Json.Required.Always)] - public double Y1 - { - get - { - return _y1; - } - set - { - _y1 = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("y2", Required=Newtonsoft.Json.Required.Always)] - public double Y2 - { - get - { - return _y2; - } - set - { - _y2 = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("z", Required=Newtonsoft.Json.Required.Always)] - public double Z - { - get - { - return _z; - } - set - { - _z = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ManipulatorPosition(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new ManipulatorPosition(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("x = " + _x + ", "); - stringBuilder.Append("y1 = " + _y1 + ", "); - stringBuilder.Append("y2 = " + _y2 + ", "); - stringBuilder.Append("z = " + _z); - 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 MicrostepResolution - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Microstep8 = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - Microstep16 = 1, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="2")] - Microstep32 = 2, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="3")] - Microstep64 = 3, - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - public enum MotorOperationMode - { - - [System.Runtime.Serialization.EnumMemberAttribute(Value="0")] - Quiet = 0, - - [System.Runtime.Serialization.EnumMemberAttribute(Value="1")] - Dynamic = 1, - } - - - [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 SerialScale - { - - private string _deviceType = "SerialScale"; - - private string _deviceName; - - private BaseModel _additionalSettings; - - private BaseModel _calibration; - - private string _portName; - - public SerialScale() - { - } - - protected SerialScale(SerialScale other) - { - _deviceType = other._deviceType; - _deviceName = other._deviceName; - _additionalSettings = other._additionalSettings; - _calibration = other._calibration; - _portName = other._portName; - } - - [Newtonsoft.Json.JsonPropertyAttribute("device_type")] - public string DeviceType - { - get - { - return _deviceType; - } - set - { - _deviceType = value; - } - } - - /// - /// Device name - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Device name")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - /// - /// Additional settings - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("additional_settings")] - [System.ComponentModel.DescriptionAttribute("Additional settings")] - public BaseModel AdditionalSettings - { - get - { - return _additionalSettings; - } - set - { - _additionalSettings = value; - } - } - - /// - /// Calibration - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration")] - [System.ComponentModel.DescriptionAttribute("Calibration")] - public BaseModel Calibration - { - get - { - return _calibration; - } - set - { - _calibration = value; - } - } - - /// - /// COM port to which the scale is connected - /// - [Newtonsoft.Json.JsonPropertyAttribute("port_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("COM port to which the scale is connected")] - public string PortName - { - get - { - return _portName; - } - set - { - _portName = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new SerialScale(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new SerialScale(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("device_type = " + _deviceType + ", "); - stringBuilder.Append("device_name = " + _deviceName + ", "); - stringBuilder.Append("additional_settings = " + _additionalSettings + ", "); - stringBuilder.Append("calibration = " + _calibration + ", "); - stringBuilder.Append("port_name = " + _portName); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindBehaviorWaterTunerRig - { - - private string _aindBehaviorServicesPkgVersion = "0.11.0"; - - private string _version = "0.2.0"; - - private string _computerName; - - private string _rigName; - - private SerialScale _scale = new SerialScale(); - - private HarpBehavior _harpBehavior = new HarpBehavior(); - - private AindManipulatorDevice _manipulator; - - public AindBehaviorWaterTunerRig() - { - } - - protected AindBehaviorWaterTunerRig(AindBehaviorWaterTunerRig other) - { - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _version = other._version; - _computerName = other._computerName; - _rigName = other._rigName; - _scale = other._scale; - _harpBehavior = other._harpBehavior; - _manipulator = other._manipulator; - } - - [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")] - public string AindBehaviorServicesPkgVersion - { - get - { - return _aindBehaviorServicesPkgVersion; - } - set - { - _aindBehaviorServicesPkgVersion = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("version")] - public string Version - { - get - { - return _version; - } - set - { - _version = value; - } - } - - /// - /// Computer name - /// - [Newtonsoft.Json.JsonPropertyAttribute("computer_name")] - [System.ComponentModel.DescriptionAttribute("Computer name")] - public string ComputerName - { - get - { - return _computerName; - } - set - { - _computerName = value; - } - } - - /// - /// Rig name - /// - [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Rig name")] - public string RigName - { - get - { - return _rigName; - } - set - { - _rigName = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("scale", Required=Newtonsoft.Json.Required.Always)] - public SerialScale Scale - { - get - { - return _scale; - } - set - { - _scale = value; - } - } - - /// - /// Harp behavior - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("harp_behavior", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Harp behavior")] - public HarpBehavior HarpBehavior - { - get - { - return _harpBehavior; - } - set - { - _harpBehavior = value; - } - } - - /// - /// Manipulator - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("manipulator")] - [System.ComponentModel.DescriptionAttribute("Manipulator")] - public AindManipulatorDevice Manipulator - { - get - { - return _manipulator; - } - set - { - _manipulator = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorWaterTunerRig(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorWaterTunerRig(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("scale = " + _scale + ", "); - stringBuilder.Append("harp_behavior = " + _harpBehavior + ", "); - stringBuilder.Append("manipulator = " + _manipulator); - 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); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - } - - - /// - /// Deserializes a sequence of JSON strings into data model objects. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))] - public partial class DeserializeFromJson : Bonsai.Expressions.SingleArgumentExpressionBuilder - { - - public DeserializeFromJson() - { - Type = new Bonsai.Expressions.TypeMapping(); - } - - public Bonsai.Expressions.TypeMapping Type { get; set; } - - public override System.Linq.Expressions.Expression Build(System.Collections.Generic.IEnumerable arguments) - { - var typeMapping = (Bonsai.Expressions.TypeMapping)Type; - var returnType = typeMapping.GetType().GetGenericArguments()[0]; - return System.Linq.Expressions.Expression.Call( - typeof(DeserializeFromJson), - "Process", - new System.Type[] { returnType }, - System.Linq.Enumerable.Single(arguments)); - } - - private static System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, value => Newtonsoft.Json.JsonConvert.DeserializeObject(value)); - } - } -} \ No newline at end of file diff --git a/src/Extensions/AindBehaviorWaterTunerTaskLogic.cs b/src/Extensions/AindBehaviorWaterTunerTaskLogic.cs deleted file mode 100644 index 9da6311..0000000 --- a/src/Extensions/AindBehaviorWaterTunerTaskLogic.cs +++ /dev/null @@ -1,364 +0,0 @@ -//---------------------- -// -// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) -// -//---------------------- - - -namespace AindBehaviorWaterTuner.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 AindBehaviorWaterTunerParameters - { - - private double? _rngSeed; - - private string _aindBehaviorServicesPkgVersion = "0.11.0"; - - private System.Collections.Generic.List _valveOpenTime = new System.Collections.Generic.List(); - - private double _valveOpenInterval = 0.2D; - - private int _repeatCount = 200; - - public AindBehaviorWaterTunerParameters() - { - } - - protected AindBehaviorWaterTunerParameters(AindBehaviorWaterTunerParameters other) - { - _rngSeed = other._rngSeed; - _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion; - _valveOpenTime = other._valveOpenTime; - _valveOpenInterval = other._valveOpenInterval; - _repeatCount = other._repeatCount; - } - - /// - /// 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; - } - } - - /// - /// An array with the times (s) the valve is open during calibration - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("valve_open_time", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("An array with the times (s) the valve is open during calibration")] - public System.Collections.Generic.List ValveOpenTime - { - get - { - return _valveOpenTime; - } - set - { - _valveOpenTime = value; - } - } - - /// - /// Time between two consecutive valve openings (s) - /// - [Newtonsoft.Json.JsonPropertyAttribute("valve_open_interval")] - [System.ComponentModel.DescriptionAttribute("Time between two consecutive valve openings (s)")] - public double ValveOpenInterval - { - get - { - return _valveOpenInterval; - } - set - { - _valveOpenInterval = value; - } - } - - /// - /// Number of times the valve opened per measure valve_open_time entry - /// - [Newtonsoft.Json.JsonPropertyAttribute("repeat_count")] - [System.ComponentModel.DescriptionAttribute("Number of times the valve opened per measure valve_open_time entry")] - public int RepeatCount - { - get - { - return _repeatCount; - } - set - { - _repeatCount = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorWaterTunerParameters(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorWaterTunerParameters(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("rng_seed = " + _rngSeed + ", "); - stringBuilder.Append("aind_behavior_services_pkg_version = " + _aindBehaviorServicesPkgVersion + ", "); - stringBuilder.Append("valve_open_time = " + _valveOpenTime + ", "); - stringBuilder.Append("valve_open_interval = " + _valveOpenInterval + ", "); - stringBuilder.Append("repeat_count = " + _repeatCount); - 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(); - } - } - - - /// - /// WaterTuner 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("WaterTuner operation control model that is used to run a calibration data acquisi" + - "tion workflow")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class AindBehaviorWaterTunerTaskLogic - { - - private string _name = "WaterValveCalibrationLogic"; - - private string _description = ""; - - private AindBehaviorWaterTunerParameters _taskParameters = new AindBehaviorWaterTunerParameters(); - - private string _version = "0.2.0"; - - private string _stageName; - - public AindBehaviorWaterTunerTaskLogic() - { - } - - protected AindBehaviorWaterTunerTaskLogic(AindBehaviorWaterTunerTaskLogic 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 AindBehaviorWaterTunerParameters 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 AindBehaviorWaterTunerTaskLogic(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorWaterTunerTaskLogic(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("name = " + _name + ", "); - stringBuilder.Append("description = " + _description + ", "); - stringBuilder.Append("task_parameters = " + _taskParameters + ", "); - stringBuilder.Append("version = " + _version + ", "); - stringBuilder.Append("stage_name = " + _stageName); - return true; - } - - public override string ToString() - { - System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder(); - stringBuilder.Append(GetType().Name); - stringBuilder.Append(" { "); - if (PrintMembers(stringBuilder)) - { - stringBuilder.Append(" "); - } - stringBuilder.Append("}"); - return stringBuilder.ToString(); - } - } - - - /// - /// Serializes a sequence of data model objects into JSON strings. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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); - } - } - - - /// - /// 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))] - 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/ExtensionDataTypes.cs b/src/Extensions/ExtensionDataTypes.cs deleted file mode 100644 index e2aa30d..0000000 --- a/src/Extensions/ExtensionDataTypes.cs +++ /dev/null @@ -1,667 +0,0 @@ -//---------------------- -// -// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org) -// -//---------------------- - - -namespace AindBehaviorWaterTuner.DataTypes -{ - #pragma warning disable // Disable all warnings - - /// - /// Input for water valve calibration class - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Input for water valve calibration class")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class Measurement - { - - private double _valveOpenInterval; - - private double _valveOpenTime; - - private System.Collections.Generic.List _waterWeight = new System.Collections.Generic.List(); - - private int _repeatCount; - - public Measurement() - { - } - - protected Measurement(Measurement other) - { - _valveOpenInterval = other._valveOpenInterval; - _valveOpenTime = other._valveOpenTime; - _waterWeight = other._waterWeight; - _repeatCount = other._repeatCount; - } - - /// - /// Time between two consecutive valve openings (s) - /// - [Newtonsoft.Json.JsonPropertyAttribute("valve_open_interval", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Time between two consecutive valve openings (s)")] - public double ValveOpenInterval - { - get - { - return _valveOpenInterval; - } - set - { - _valveOpenInterval = value; - } - } - - /// - /// Valve open interval (s) - /// - [Newtonsoft.Json.JsonPropertyAttribute("valve_open_time", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Valve open interval (s)")] - public double ValveOpenTime - { - get - { - return _valveOpenTime; - } - set - { - _valveOpenTime = value; - } - } - - /// - /// Weight of water delivered (g) - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("water_weight", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Weight of water delivered (g)")] - public System.Collections.Generic.List WaterWeight - { - get - { - return _waterWeight; - } - set - { - _waterWeight = value; - } - } - - /// - /// Number of times the valve opened. - /// - [Newtonsoft.Json.JsonPropertyAttribute("repeat_count", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Number of times the valve opened.")] - public int RepeatCount - { - get - { - return _repeatCount; - } - set - { - _repeatCount = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Measurement(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new Measurement(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("valve_open_interval = " + _valveOpenInterval + ", "); - stringBuilder.Append("valve_open_time = " + _valveOpenTime + ", "); - stringBuilder.Append("water_weight = " + _waterWeight + ", "); - stringBuilder.Append("repeat_count = " + _repeatCount); - 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(); - } - } - - - /// - /// Water valve calibration class - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Water valve calibration class")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class WaterValveCalibration - { - - private string _deviceName = "WaterValve"; - - private WaterValveCalibrationInput _input = new WaterValveCalibrationInput(); - - private WaterValveCalibrationOutput _output = new WaterValveCalibrationOutput(); - - private System.DateTimeOffset? _date; - - private string _description = "Calibration of the water valve delivery system"; - - private string _notes; - - public WaterValveCalibration() - { - } - - protected WaterValveCalibration(WaterValveCalibration other) - { - _deviceName = other._deviceName; - _input = other._input; - _output = other._output; - _date = other._date; - _description = other._description; - _notes = other._notes; - } - - /// - /// Name of the device being calibrated - /// - [Newtonsoft.Json.JsonPropertyAttribute("device_name")] - [System.ComponentModel.DescriptionAttribute("Name of the device being calibrated")] - public string DeviceName - { - get - { - return _deviceName; - } - set - { - _deviceName = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("input", Required=Newtonsoft.Json.Required.Always)] - public WaterValveCalibrationInput Input - { - get - { - return _input; - } - set - { - _input = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("output", Required=Newtonsoft.Json.Required.Always)] - public WaterValveCalibrationOutput Output - { - get - { - return _output; - } - set - { - _output = value; - } - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("date")] - public System.DateTimeOffset? Date - { - get - { - return _date; - } - set - { - _date = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("description")] - public string Description - { - get - { - return _description; - } - set - { - _description = value; - } - } - - [Newtonsoft.Json.JsonPropertyAttribute("notes")] - public string Notes - { - get - { - return _notes; - } - set - { - _notes = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new WaterValveCalibration(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new WaterValveCalibration(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); - 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)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class WaterValveCalibrationInput - { - - private System.Collections.Generic.List _measurements = new System.Collections.Generic.List(); - - public WaterValveCalibrationInput() - { - } - - protected WaterValveCalibrationInput(WaterValveCalibrationInput other) - { - _measurements = other._measurements; - } - - /// - /// List of measurements - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("measurements")] - [System.ComponentModel.DescriptionAttribute("List of measurements")] - public System.Collections.Generic.List Measurements - { - get - { - return _measurements; - } - set - { - _measurements = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new WaterValveCalibrationInput(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new WaterValveCalibrationInput(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("measurements = " + _measurements); - 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(); - } - } - - - /// - /// Output for water valve calibration class - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (Newtonsoft.Json v13.0.0.0)")] - [System.ComponentModel.DescriptionAttribute("Output for water valve calibration class")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class WaterValveCalibrationOutput - { - - private System.Collections.Generic.IDictionary _intervalAverage; - - private double _slope; - - private double _offset; - - private double? _r2; - - private System.Collections.Generic.List _validDomain; - - public WaterValveCalibrationOutput() - { - } - - protected WaterValveCalibrationOutput(WaterValveCalibrationOutput other) - { - _intervalAverage = other._intervalAverage; - _slope = other._slope; - _offset = other._offset; - _r2 = other._r2; - _validDomain = other._validDomain; - } - - /// - /// Dictionary keyed by measured valve interval and corresponding average single event volume. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("interval_average")] - [System.ComponentModel.DescriptionAttribute("Dictionary keyed by measured valve interval and corresponding average single even" + - "t volume.")] - public System.Collections.Generic.IDictionary IntervalAverage - { - get - { - return _intervalAverage; - } - set - { - _intervalAverage = value; - } - } - - /// - /// Slope of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g) - /// - [Newtonsoft.Json.JsonPropertyAttribute("slope", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Slope of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)")] - public double Slope - { - get - { - return _slope; - } - set - { - _slope = value; - } - } - - /// - /// Offset of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g) - /// - [Newtonsoft.Json.JsonPropertyAttribute("offset", Required=Newtonsoft.Json.Required.Always)] - [System.ComponentModel.DescriptionAttribute("Offset of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)")] - public double Offset - { - get - { - return _offset; - } - set - { - _offset = value; - } - } - - /// - /// R2 metric from the linear model. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("r2")] - [System.ComponentModel.DescriptionAttribute("R2 metric from the linear model.")] - public double? R2 - { - get - { - return _r2; - } - set - { - _r2 = value; - } - } - - /// - /// The optional time-intervals the calibration curve was calculated on. - /// - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("valid_domain")] - [System.ComponentModel.DescriptionAttribute("The optional time-intervals the calibration curve was calculated on.")] - public System.Collections.Generic.List ValidDomain - { - get - { - return _validDomain; - } - set - { - _validDomain = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new WaterValveCalibrationOutput(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new WaterValveCalibrationOutput(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("interval_average = " + _intervalAverage + ", "); - stringBuilder.Append("slope = " + _slope + ", "); - stringBuilder.Append("offset = " + _offset + ", "); - stringBuilder.Append("r2 = " + _r2 + ", "); - stringBuilder.Append("valid_domain = " + _validDomain); - 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)")] - [Bonsai.CombinatorAttribute()] - [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)] - public partial class ExtensionDataTypes - { - - private WaterValveCalibration _calibration = new WaterValveCalibration(); - - public ExtensionDataTypes() - { - } - - protected ExtensionDataTypes(ExtensionDataTypes other) - { - _calibration = other._calibration; - } - - [System.Xml.Serialization.XmlIgnoreAttribute()] - [Newtonsoft.Json.JsonPropertyAttribute("calibration", Required=Newtonsoft.Json.Required.Always)] - public WaterValveCalibration Calibration - { - get - { - return _calibration; - } - set - { - _calibration = value; - } - } - - public System.IObservable Process() - { - return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ExtensionDataTypes(this))); - } - - public System.IObservable Process(System.IObservable source) - { - return System.Reactive.Linq.Observable.Select(source, _ => new ExtensionDataTypes(this)); - } - - protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder) - { - stringBuilder.Append("calibration = " + _calibration); - 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); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - - public System.IObservable Process(System.IObservable source) - { - return Process(source); - } - } - - - /// - /// Deserializes a sequence of JSON strings into data model objects. - /// - [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.4.0.0 (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))] - [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/Logging.bonsai b/src/Extensions/Logging.bonsai index ab9a80f..b6d7a08 100644 --- a/src/Extensions/Logging.bonsai +++ b/src/Extensions/Logging.bonsai @@ -6,11 +6,8 @@ xmlns:sys="clr-namespace:System;assembly=mscorlib" xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp" xmlns:p2="clr-namespace:AllenNeuralDynamics.VersionControl;assembly=AllenNeuralDynamics.VersionControl" - xmlns:p3="clr-namespace:AindBehaviorWaterTuner.Session;assembly=Extensions" - xmlns:p4="clr-namespace:AindBehaviorWaterTuner.TaskLogic;assembly=Extensions" - xmlns:p5="clr-namespace:AindBehaviorWaterTuner.Rig;assembly=Extensions" - xmlns:p6="clr-namespace:AllenNeuralDynamics.AindBehaviorServices.DataTypes;assembly=AllenNeuralDynamics.AindBehaviorServices" - xmlns:p7="clr-namespace:AindBehaviorWaterTuner.DataTypes;assembly=Extensions" + xmlns:p3="clr-namespace:AindBehaviorDeviceWaterTunerDataSchema;assembly=Extensions" + xmlns:p4="clr-namespace:AllenNeuralDynamics.AindBehaviorServices.DataTypes;assembly=AllenNeuralDynamics.AindBehaviorServices" xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System" xmlns="https://bonsai-rx.org/2018/workflow"> @@ -215,7 +212,9 @@ SubjectSchema - + + None + Modality @@ -243,7 +242,9 @@ TaskLogicSchema - + + None + Modality @@ -271,7 +272,9 @@ RigSchema - + + None + Modality @@ -441,7 +444,7 @@ - + Modality @@ -493,7 +496,9 @@ CalibrationModel - + + None + diff --git a/src/Extensions/WaterCalibrationModel.cs b/src/Extensions/WaterCalibrationModel.cs index a805d5a..72e5aca 100644 --- a/src/Extensions/WaterCalibrationModel.cs +++ b/src/Extensions/WaterCalibrationModel.cs @@ -4,7 +4,7 @@ using System.Linq; using System.Reactive.Linq; using MathNet.Numerics; -using AindBehaviorWaterTuner.DataTypes; +using AindBehaviorDeviceWaterTunerDataSchema; using System.Collections.Generic; [Combinator] diff --git a/src/aind_behavior_device_water_tuner/__init__.py b/src/aind_behavior_device_water_tuner/__init__.py index d3ec452..98cffdf 100644 --- a/src/aind_behavior_device_water_tuner/__init__.py +++ b/src/aind_behavior_device_water_tuner/__init__.py @@ -1 +1,30 @@ -__version__ = "0.2.0" +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_water_tuner/cli.py b/src/aind_behavior_device_water_tuner/cli.py new file mode 100644 index 0000000..40675c6 --- /dev/null +++ b/src/aind_behavior_device_water_tuner/cli.py @@ -0,0 +1,44 @@ +import typing as t + +from pydantic import Field, RootModel +from pydantic_settings import BaseSettings, CliApp, CliSubCommand + +from aind_behavior_device_water_tuner import __semver__, regenerate +from aind_behavior_device_water_tuner.launcher import ClabeCli + + +class VersionCli(RootModel): + root: t.Any + + def cli_cmd(self) -> None: + print(__semver__) + + +class DslRegenerateCli(RootModel): + root: t.Any + + def cli_cmd(self) -> None: + regenerate.main() + + +class WaterTuner(BaseSettings, cli_prog_name="water-tuner", cli_kebab_case=True): + version: CliSubCommand[VersionCli] = Field( + description="Print the version of the water-tuner package.", + ) + regenerate: CliSubCommand[DslRegenerateCli] = Field( + description="Regenerate the water-tuner dsl dependencies.", + ) + clabe: CliSubCommand[ClabeCli] = Field( + description="Run the Clabe CLI.", + ) + + def cli_cmd(self): + return CliApp().run_subcommand(self) + + +def main(): + CliApp().run(WaterTuner) + + +if __name__ == "__main__": + main() diff --git a/src/aind_behavior_device_water_tuner/data_types.py b/src/aind_behavior_device_water_tuner/data_types.py index 94f5b3f..4ba7d19 100644 --- a/src/aind_behavior_device_water_tuner/data_types.py +++ b/src/aind_behavior_device_water_tuner/data_types.py @@ -1,8 +1,6 @@ from aind_behavior_services.calibration import water_valve as wv from pydantic import BaseModel -__version__ = "0.1.0" - class ExtensionDataTypes(BaseModel): calibration: wv.WaterValveCalibration diff --git a/src/aind_behavior_device_water_tuner/launcher.py b/src/aind_behavior_device_water_tuner/launcher.py index b03f725..f7561cb 100644 --- a/src/aind_behavior_device_water_tuner/launcher.py +++ b/src/aind_behavior_device_water_tuner/launcher.py @@ -1,44 +1,70 @@ from pathlib import Path -import aind_behavior_experiment_launcher.behavior_launcher as behavior_launcher -from aind_behavior_experiment_launcher import resource_monitor -from aind_behavior_experiment_launcher.apps import AindBehaviorServicesBonsaiApp from aind_behavior_services.session import AindBehaviorSessionModel +from clabe import resource_monitor +from clabe.apps import ( + AindBehaviorServicesBonsaiApp, + BonsaiAppSettings, +) +from clabe.launcher import ( + DefaultBehaviorPicker, + DefaultBehaviorPickerSettings, + Launcher, + LauncherCliArgs, +) from pydantic_settings import CliApp -from aind_behavior_device_water_tuner.rig import AindBehaviorWaterTunerRig -from aind_behavior_device_water_tuner.task_logic import AindBehaviorWaterTunerTaskLogic +from .rig import AindBehaviorDeviceWaterTunerRig +from .task_logic import AindBehaviorDeviceWaterTunerTaskLogic -def make_launcher(settings: behavior_launcher.BehaviorCliArgs) -> behavior_launcher.BehaviorLauncher: - data_dir = r"C:/Data" - srv = behavior_launcher.BehaviorServicesFactoryManager() - srv.attach_app(AindBehaviorServicesBonsaiApp(Path(r"./src/main.bonsai"))) - srv.attach_resource_monitor( - resource_monitor.ResourceMonitor( - constrains=[ - resource_monitor.available_storage_constraint_factory(data_dir, 2e11), - ] - ) +def make_launcher(settings: LauncherCliArgs) -> Launcher: + monitor = resource_monitor.ResourceMonitor( + constrains=[ + resource_monitor.available_storage_constraint_factory(settings.data_dir, 2e11), + ] ) - - return behavior_launcher.BehaviorLauncher( - rig_schema_model=AindBehaviorWaterTunerRig, - session_schema_model=AindBehaviorSessionModel, - task_logic_schema_model=AindBehaviorWaterTunerTaskLogic, + bonsai_app = AindBehaviorServicesBonsaiApp(BonsaiAppSettings(workflow=Path(r"./src/main.bonsai"))) + picker = DefaultBehaviorPicker[ + AindBehaviorDeviceWaterTunerRig, AindBehaviorSessionModel, AindBehaviorDeviceWaterTunerTaskLogic + ]( + settings=DefaultBehaviorPickerSettings() # type: ignore[call-arg] + ) + launcher = Launcher( + rig=AindBehaviorDeviceWaterTunerRig, + session=AindBehaviorSessionModel, + task_logic=AindBehaviorDeviceWaterTunerTaskLogic, settings=settings, - picker=behavior_launcher.DefaultBehaviorPicker( - config_library_dir=Path(r"\\allen\aind\scratch\AindBehavior.db\AindBehaviorWaterTuner") - ), - services=srv, ) + # Get user input + launcher.register_callable( + [ + picker.initialize, + picker.pick_session, + picker.pick_trainer_state, + picker.pick_rig, + ] + ) + + # Check resources + launcher.register_callable(monitor.build_runner()) + + # Run the task via Bonsai + launcher.register_callable(bonsai_app.build_runner(allow_std_error=True)) + + return launcher + + +class ClabeCli(LauncherCliArgs): + def cli_cmd(self): + launcher = make_launcher(self) + launcher.main() + return None + -def main(): - args = CliApp().run(behavior_launcher.BehaviorCliArgs) - launcher = make_launcher(args) - launcher.main() - return None +def main() -> None: + CliApp().run(ClabeCli) if __name__ == "__main__": diff --git a/src/aind_behavior_device_water_tuner/regenerate.py b/src/aind_behavior_device_water_tuner/regenerate.py index 028cceb..48b1c60 100644 --- a/src/aind_behavior_device_water_tuner/regenerate.py +++ b/src/aind_behavior_device_water_tuner/regenerate.py @@ -1,38 +1,37 @@ -import inspect from pathlib import Path +from typing import Union +import pydantic 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, -) +from aind_behavior_services.utils import BonsaiSgenSerializers, convert_pydantic_to_bonsai -from aind_behavior_device_water_tuner import data_types, rig, task_logic +import aind_behavior_device_water_tuner.rig +import aind_behavior_device_water_tuner.task_logic +from aind_behavior_device_water_tuner import data_types SCHEMA_ROOT = Path("./src/DataSchemas/") EXTENSIONS_ROOT = Path("./src/Extensions/") -NAMESPACE_PREFIX = "AindBehaviorWaterTuner" +NAMESPACE_PREFIX = "AindBehaviorDeviceWaterTunerDataSchema" def main(): models = [ - task_logic.AindBehaviorWaterTunerTaskLogic, - rig.AindBehaviorWaterTunerRig, + aind_behavior_device_water_tuner.task_logic.AindBehaviorDeviceWaterTunerTaskLogic, + aind_behavior_device_water_tuner.rig.AindBehaviorDeviceWaterTunerRig, AindBehaviorSessionModel, data_types.ExtensionDataTypes, ] - - 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_water_tuner", + 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_water_tuner/rig.py b/src/aind_behavior_device_water_tuner/rig.py index 264fe0d..21648a9 100644 --- a/src/aind_behavior_device_water_tuner/rig.py +++ b/src/aind_behavior_device_water_tuner/rig.py @@ -2,10 +2,9 @@ import aind_behavior_services.rig as rig from aind_behavior_services.calibration import aind_manipulator -from aind_behavior_services.rig import AindBehaviorRigModel from pydantic import Field -__version__ = "0.2.0" +from . import __semver__ class SerialScale(rig.Device): @@ -13,8 +12,8 @@ class SerialScale(rig.Device): port_name: str = Field(..., description="COM port to which the scale is connected") -class AindBehaviorWaterTunerRig(AindBehaviorRigModel): - version: Literal[__version__] = __version__ +class AindBehaviorDeviceWaterTunerRig(rig.AindBehaviorRigModel): + version: Literal[__semver__] = __semver__ scale: SerialScale = Field(..., title="Serial scale device") harp_behavior: rig.harp.HarpBehavior = Field(..., description="Harp behavior") manipulator: Optional[aind_manipulator.AindManipulatorDevice] = Field(default=None, description="Manipulator") diff --git a/src/aind_behavior_device_water_tuner/task_logic.py b/src/aind_behavior_device_water_tuner/task_logic.py index 0b0858a..d5c007f 100644 --- a/src/aind_behavior_device_water_tuner/task_logic.py +++ b/src/aind_behavior_device_water_tuner/task_logic.py @@ -1,12 +1,19 @@ +import logging from typing import Literal from aind_behavior_services.task_logic import AindBehaviorTaskLogicModel, TaskParameters from pydantic import Field, PositiveFloat -from . import __version__ +from aind_behavior_device_water_tuner import ( + __semver__, +) +logger = logging.getLogger(__name__) -class AindBehaviorWaterTunerParameters(TaskParameters): +# ==================== MAIN TASK LOGIC CLASSES ==================== + + +class AindBehaviorDeviceWaterTunerTaskParameters(TaskParameters): valve_open_time: list[PositiveFloat] = Field( ..., min_length=1, @@ -26,9 +33,13 @@ class AindBehaviorWaterTunerParameters(TaskParameters): ) -class AindBehaviorWaterTunerTaskLogic(AindBehaviorTaskLogicModel): - """WaterTuner operation control model that is used to run a calibration data acquisition workflow""" +class AindBehaviorDeviceWaterTunerTaskLogic(AindBehaviorTaskLogicModel): + """ + Main task logic model for the water-tuner task. + """ - name: str = Field(default="WaterValveCalibrationLogic", title="Task name") - version: Literal[__version__] = __version__ - task_parameters: AindBehaviorWaterTunerParameters = Field(..., title="Task parameters", validate_default=True) + version: Literal[__semver__] = __semver__ + name: Literal["AindBehaviorDeviceWaterTuner"] = Field( + default="AindBehaviorDeviceWaterTuner", description="Name of the task logic", frozen=True + ) + task_parameters: AindBehaviorDeviceWaterTunerTaskParameters = Field(description="Parameters of the task logic") diff --git a/src/main.bonsai b/src/main.bonsai index 7e6b9f5..7921ac2 100644 --- a/src/main.bonsai +++ b/src/main.bonsai @@ -1,23 +1,20 @@  @@ -54,8 +51,8 @@ RawRigSchema - - + + @@ -68,8 +65,8 @@ RawTaskLogicSchema - - + + @@ -106,8 +103,8 @@ - - ../. + + ../. @@ -139,13 +136,13 @@ - - 0 - 10 + + 0 + 10 - + @@ -180,19 +177,19 @@ RngSeed - + StartExperiment Annotations - + StartLogging - + SoftwareEvent - + EndExperiment @@ -329,8 +326,8 @@ Repository - - false + + false @@ -361,8 +358,8 @@ - - Repository is not clean! Please discard all local changes. + + Repository is not clean! Please discard all local changes. @@ -433,7 +430,7 @@ HarpBehaviorCommands - + TriggerValve @@ -561,10 +558,12 @@ Input - + + None + - - + + RigSchema @@ -710,7 +709,7 @@ ValveOpenInterval - + @@ -831,10 +830,10 @@ - - 0 - 0 - 0 + + 0 + 0 + 0 @@ -885,7 +884,7 @@ - + CalibrationModel @@ -894,8 +893,8 @@ CalibrationModel - - CalibrationModel + + CalibrationModel diff --git a/tests/__init__.py b/tests/__init__.py index 97cf86f..f7760d5 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -5,6 +5,7 @@ from types import ModuleType EXAMPLES_DIR = Path(__file__).parents[1] / "examples" +JSON_ROOT = Path("./local").resolve() logger = logging.getLogger(__name__) logger.addHandler(logging.NullHandler()) @@ -17,8 +18,6 @@ def build_example(script_path: str) -> ModuleType: if spec is None: raise ImportError(f"Can't find {script_path}") module = importlib.util.module_from_spec(spec) - if spec.loader is None: - raise ImportError(f"Can't load {script_path}") spec.loader.exec_module(module) return module diff --git a/uv.lock b/uv.lock index 48f3a5b..e920400 100644 --- a/uv.lock +++ b/uv.lock @@ -1,4 +1,5 @@ version = 1 +revision = 3 requires-python = ">=3.11" resolution-markers = [ "python_full_version >= '3.12'", @@ -14,83 +15,64 @@ dependencies = [ { name = "pydantic" }, { name = "semver" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/9e/10/00e82fd42dc971458d4a377f4cf288beea15f119c0810e34a9310f71c38f/aind_behavior_curriculum-0.0.33.tar.gz", hash = "sha256:c01bea389e35f2450952d9120e6cc2c70f61add9512c38a7b101c77387b99bf8", size = 121893 } +sdist = { url = "https://files.pythonhosted.org/packages/9e/10/00e82fd42dc971458d4a377f4cf288beea15f119c0810e34a9310f71c38f/aind_behavior_curriculum-0.0.33.tar.gz", hash = "sha256:c01bea389e35f2450952d9120e6cc2c70f61add9512c38a7b101c77387b99bf8", size = 121893, upload-time = "2025-03-27T17:15:39.727Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/2c/ce/cd3fe2f9b05a47515f9bf4af067da0f8d639cda023a3c5059cb102c06335/aind_behavior_curriculum-0.0.33-py3-none-any.whl", hash = "sha256:234d45b4d2edab5aa1088aed91751d797b3af0c8710bc06131adca7bdb3c495a", size = 46804 }, + { url = "https://files.pythonhosted.org/packages/2c/ce/cd3fe2f9b05a47515f9bf4af067da0f8d639cda023a3c5059cb102c06335/aind_behavior_curriculum-0.0.33-py3-none-any.whl", hash = "sha256:234d45b4d2edab5aa1088aed91751d797b3af0c8710bc06131adca7bdb3c495a", size = 46804, upload-time = "2025-03-27T17:15:38.102Z" }, ] [[package]] name = "aind-behavior-device-water-tuner" +version = "0.4.0" source = { editable = "." } dependencies = [ { name = "aind-behavior-services" }, + { name = "pydantic-settings" }, ] [package.optional-dependencies] +launcher = [ + { name = "aind-clabe", extra = ["aind-services"] }, +] + +[package.dev-dependencies] dev = [ - { name = "aind-behavior-experiment-launcher", extra = ["aind-services"] }, + { name = 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