From 88669ad2860c35478c3398d0ddbf5dd2c57cf5fb Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 7 Nov 2025 11:03:31 -0800
Subject: [PATCH 01/19] Update launcher dependency
---
pyproject.toml | 2 +-
.../data_mappers/__init__.py | 6 ++--
.../data_mappers/_session.py | 6 ++--
src/aind_behavior_vr_foraging/launcher.py | 32 ++++++++++---------
tests/test_aind_data_mapper.py | 4 +--
uv.lock | 9 +++---
6 files changed, 31 insertions(+), 28 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 367c12f4..346ad3b8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,7 +31,7 @@ Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.VrForaging/rel
data = ["contraqctor<0.6.0"]
launcher = [
- "aind-clabe[aind-services] >= 0.8.2 ,<0.9.0",
+ "aind-clabe[aind-services] >0.8 ,<0.10.0",
"aind-data-schema>=2",
"aind_behavior_vr_foraging[data]",
]
diff --git a/src/aind_behavior_vr_foraging/data_mappers/__init__.py b/src/aind_behavior_vr_foraging/data_mappers/__init__.py
index 70fe42e8..d92f371b 100644
--- a/src/aind_behavior_vr_foraging/data_mappers/__init__.py
+++ b/src/aind_behavior_vr_foraging/data_mappers/__init__.py
@@ -7,7 +7,7 @@
import pydantic_settings
from aind_behavior_services.session import AindBehaviorSessionModel
from aind_behavior_services.utils import model_from_json_file
-from clabe.apps import BonsaiAppSettings, CurriculumSuggestion
+from clabe.apps import BonsaiApp, CurriculumSuggestion
from git import Repo
from aind_behavior_vr_foraging.rig import AindVrForagingRig
@@ -41,7 +41,7 @@ def cli_cmd(self):
curriculum_suggestion = None
repo = Repo(self.repo_path)
- settings = BonsaiAppSettings(
+ settings = BonsaiApp(
workflow=Path(repo.working_dir) / "src" / "main.bonsai",
executable=Path(repo.working_dir) / "bonsai/bonsai.exe",
)
@@ -51,7 +51,7 @@ def cli_cmd(self):
rig=rig,
task_logic=task_logic,
repository=repo,
- bonsai_app_settings=settings,
+ bonsai_app=settings,
curriculum_suggestion=curriculum_suggestion,
).map()
rig_mapped = AindRigDataMapper(rig=rig).map()
diff --git a/src/aind_behavior_vr_foraging/data_mappers/_session.py b/src/aind_behavior_vr_foraging/data_mappers/_session.py
index acb9a0a5..d003b0bc 100644
--- a/src/aind_behavior_vr_foraging/data_mappers/_session.py
+++ b/src/aind_behavior_vr_foraging/data_mappers/_session.py
@@ -14,7 +14,7 @@
from aind_data_schema.core import acquisition
from aind_data_schema_models import units
from aind_data_schema_models.modalities import Modality
-from clabe.apps import BonsaiAppSettings, CurriculumSuggestion
+from clabe.apps import BonsaiApp, CurriculumSuggestion
from clabe.data_mapper import aind_data_schema as ads
from clabe.data_mapper import helpers as data_mapper_helpers
@@ -32,7 +32,7 @@ def __init__(
session: AindBehaviorSessionModel,
rig: AindVrForagingRig,
task_logic: AindVrForagingTaskLogic,
- bonsai_app_settings: BonsaiAppSettings = BonsaiAppSettings(workflow=Path("./src/main.bonsai")),
+ bonsai_app: BonsaiApp = BonsaiApp(workflow=Path("./src/main.bonsai")),
repository: Union[os.PathLike, git.Repo] = Path("."),
session_end_time: Optional[datetime.datetime] = None,
curriculum_suggestion: Optional[CurriculumSuggestion] = None,
@@ -43,7 +43,7 @@ def __init__(
self.repository = repository
if isinstance(self.repository, os.PathLike | str):
self.repository = git.Repo(Path(self.repository))
- self.bonsai_app = bonsai_app_settings
+ self.bonsai_app = bonsai_app
self._session_end_time = session_end_time
self._mapped: Optional[acquisition.Acquisition] = None
self.curriculum = curriculum_suggestion
diff --git a/src/aind_behavior_vr_foraging/launcher.py b/src/aind_behavior_vr_foraging/launcher.py
index 0727a53d..aa286784 100644
--- a/src/aind_behavior_vr_foraging/launcher.py
+++ b/src/aind_behavior_vr_foraging/launcher.py
@@ -7,7 +7,6 @@
from clabe import resource_monitor
from clabe.apps import (
AindBehaviorServicesBonsaiApp,
- BonsaiAppSettings,
CurriculumApp,
CurriculumSettings,
CurriculumSuggestion,
@@ -27,7 +26,7 @@
logger = logging.getLogger(__name__)
-def experiment(launcher: Launcher) -> None:
+async def experiment(launcher: Launcher) -> None:
monitor = resource_monitor.ResourceMonitor(
constrains=[
resource_monitor.available_storage_constraint_factory(launcher.settings.data_dir, 2e11),
@@ -56,9 +55,14 @@ def experiment(launcher: Launcher) -> None:
manipulator_modifier.inject(rig)
# Run the task via Bonsai
- bonsai_app = AindBehaviorServicesBonsaiApp(BonsaiAppSettings(workflow=Path(r"./src/main.bonsai")))
- bonsai_app.add_app_settings(launcher, rig=rig, session=session, task_logic=task_logic)
- bonsai_app.run().get_result(allow_stderr=True)
+ bonsai_app = AindBehaviorServicesBonsaiApp(
+ workflow=Path(r"./src/main.bonsai"),
+ temp_directory=launcher.temp_dir,
+ rig=rig,
+ session=session,
+ task_logic=task_logic,
+ )
+ await bonsai_app.run_async()
# Update manipulator initial position for next session
manipulator_modifier.dump()
@@ -76,9 +80,10 @@ def experiment(launcher: Launcher) -> None:
)
)
# Run the curriculum
- suggestion = trainer.run().get_result(allow_stderr=True)
+ await trainer.run_async()
+ suggestion = trainer.process_suggestion()
# Dump suggestion for debugging (for now, but we will prob remove this later)
- _dump_suggestion(launcher, suggestion)
+ _dump_suggestion(suggestion, launcher.session_directory)
# Push updated trainer state back to the database
picker.push_new_suggestion(suggestion.trainer_state)
@@ -88,7 +93,7 @@ def experiment(launcher: Launcher) -> None:
session=session,
task_logic=task_logic,
curriculum_suggestion=suggestion,
- bonsai_app_settings=bonsai_app.settings,
+ bonsai_app=bonsai_app,
).map()
ads_session.write_standard_file(launcher.session_directory)
ads_rig = AindRigDataMapper(rig=rig).map()
@@ -107,18 +112,15 @@ def experiment(launcher: Launcher) -> None:
WatchdogDataTransferService(
source=launcher.session_directory,
settings=watchdog_settings,
- aind_data_schema_session=ads_session,
- session_name=session.session_name,
+ session=session,
).transfer()
return
-def _dump_suggestion(launcher: Launcher, suggestion: CurriculumSuggestion) -> None:
- launcher.logger.info(
- f"Dumping curriculum suggestion to: {launcher.session_directory / 'Behavior' / 'Logs' / 'suggestion.json'}"
- )
- with open(launcher.session_directory / "Behavior" / "Logs" / "suggestion.json", "w", encoding="utf-8") as f:
+def _dump_suggestion(suggestion: CurriculumSuggestion, session_directory: Path) -> None:
+ logger.info(f"Dumping curriculum suggestion to: {session_directory / 'Behavior' / 'Logs' / 'suggestion.json'}")
+ with open(session_directory / "Behavior" / "Logs" / "suggestion.json", "w", encoding="utf-8") as f:
f.write(suggestion.model_dump_json(indent=2))
diff --git a/tests/test_aind_data_mapper.py b/tests/test_aind_data_mapper.py
index 7e11667d..d31a0485 100644
--- a/tests/test_aind_data_mapper.py
+++ b/tests/test_aind_data_mapper.py
@@ -32,7 +32,7 @@ def setUp(self):
rig=self.rig,
task_logic=self.task_logic,
repository=self.repository,
- bonsai_app_settings=self.bonsai_app_settings,
+ bonsai_app=self.bonsai_app_settings,
session_end_time=self.session_end_time,
)
@@ -92,7 +92,7 @@ def setUp(self):
rig=self.rig,
task_logic=self.task_logic,
repository=Repo(Path("./")),
- bonsai_app_settings=self.bonsai_app_settings,
+ bonsai_app=self.bonsai_app_settings,
session_end_time=datetime.now(),
)
diff --git a/uv.lock b/uv.lock
index af33bd8f..3d963691 100644
--- a/uv.lock
+++ b/uv.lock
@@ -94,7 +94,7 @@ docs = [
requires-dist = [
{ name = "aind-behavior-services", specifier = ">=0.12,<0.13" },
{ name = "aind-behavior-vr-foraging", extras = ["data"], marker = "extra == 'launcher'" },
- { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = ">=0.8.2,<0.9.0" },
+ { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = ">0.8,<0.10.0" },
{ name = "aind-data-schema", marker = "extra == 'launcher'", specifier = ">=2" },
{ name = "contraqctor", marker = "extra == 'data'", specifier = "<0.6.0" },
{ name = "pydantic-settings" },
@@ -120,19 +120,20 @@ docs = [
[[package]]
name = "aind-clabe"
-version = "0.8.2"
+version = "0.9.0rc5"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "aind-behavior-services" },
{ name = "gitpython" },
{ name = "pydantic" },
{ name = "pydantic-settings" },
+ { name = "requests" },
{ name = "rich" },
{ name = "semver" },
]
-sdist = { url = "https://files.pythonhosted.org/packages/8e/37/dff7f633606ce87600a4114bd1dd506f2109d5d891f66030b5769426ac1c/aind_clabe-0.8.2.tar.gz", hash = "sha256:f384d51a541b900f5783a9523eba4f885cfa69850a2ac33881db07ca7a7f1d3a", size = 48635, upload-time = "2025-10-21T02:29:17.795Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/c6/10/19c53e3d9468d7cd7477cb0667b2c8f19529eed7a0c765d6420dcea9a9c8/aind_clabe-0.9.0rc5.tar.gz", hash = "sha256:4aa25fd8e991ec3cefe1b3b4a03789bd9410f1d1c38cadfb48a7c688148da4a4", size = 62483, upload-time = "2025-11-05T22:53:27.74Z" }
wheels = [
- { url = "https://files.pythonhosted.org/packages/6d/14/0ac35972d01f3a82bc1a720b42589929dd8beabc6066dc26ef16597e4e96/aind_clabe-0.8.2-py3-none-any.whl", hash = "sha256:d366a0495763d64d8bfb2fbc195951269b7e0fb3152bd967f944b48155384698", size = 66180, upload-time = "2025-10-21T02:29:16.829Z" },
+ { url = "https://files.pythonhosted.org/packages/d7/eb/b9e61427eea514f5bbe199908c7275a44762446358b468e4f257b3b4cad5/aind_clabe-0.9.0rc5-py3-none-any.whl", hash = "sha256:0b0c468eeac6189b88456bba7b4c94ec76a3589a698c9f1341aa5ccbfb79a0ac", size = 83225, upload-time = "2025-11-05T22:53:26.289Z" },
]
[package.optional-dependencies]
From c3f9f7074a654f9aaab6b64675ee438f58adcb6a Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 7 Nov 2025 11:10:44 -0800
Subject: [PATCH 02/19] Fix unittest
---
tests/test_aind_data_mapper.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/tests/test_aind_data_mapper.py b/tests/test_aind_data_mapper.py
index d31a0485..d7e715d6 100644
--- a/tests/test_aind_data_mapper.py
+++ b/tests/test_aind_data_mapper.py
@@ -6,7 +6,7 @@
from aind_data_schema.core import acquisition, instrument
from aind_data_schema.utils import compatibility_check
-from clabe.apps import BonsaiAppSettings
+from clabe.apps import BonsaiApp
from git import Repo
from aind_behavior_vr_foraging.data_mappers import AindRigDataMapper, AindSessionDataMapper
@@ -23,7 +23,7 @@ def setUp(self):
self.rig = rig
self.task_logic = task_logic
self.repository = Repo(Path("./"))
- self.bonsai_app_settings = BonsaiAppSettings(workflow=Path("./src/main.bonsai"))
+ self.bonsai_app = BonsaiApp(workflow=Path("./src/main.bonsai"))
self.session_end_time = datetime.now()
self.session_directory = None
@@ -32,7 +32,7 @@ def setUp(self):
rig=self.rig,
task_logic=self.task_logic,
repository=self.repository,
- bonsai_app=self.bonsai_app_settings,
+ bonsai_app=self.bonsai_app,
session_end_time=self.session_end_time,
)
@@ -85,7 +85,7 @@ def setUp(self):
self.rig_mapper = AindRigDataMapper(
rig=self.rig,
)
- self.bonsai_app_settings = BonsaiAppSettings(workflow=Path("./src/main.bonsai"))
+ self.bonsai_app_settings = BonsaiApp(workflow=Path("./src/main.bonsai"))
self.session_mapper = AindSessionDataMapper(
session=self.session,
From b0c9ef13a075e868e56d20cf4012cba952b0edb2 Mon Sep 17 00:00:00 2001
From: Bruno Cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 10:43:44 -0800
Subject: [PATCH 03/19] Update contraqctor to render to optionally render to
html (#452)
---
pyproject.toml | 2 +-
src/aind_behavior_vr_foraging/data_qc.py | 10 +++++++++-
uv.lock | 9 +++++----
3 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 346ad3b8..23686791 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,7 @@ Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.VrForaging/rel
[project.optional-dependencies]
-data = ["contraqctor<0.6.0"]
+data = ["contraqctor>=0.5.3, <0.6.0"]
launcher = [
"aind-clabe[aind-services] >0.8 ,<0.10.0",
diff --git a/src/aind_behavior_vr_foraging/data_qc.py b/src/aind_behavior_vr_foraging/data_qc.py
index fa36593d..81294ad8 100644
--- a/src/aind_behavior_vr_foraging/data_qc.py
+++ b/src/aind_behavior_vr_foraging/data_qc.py
@@ -285,11 +285,19 @@ class DataQcCli(pydantic_settings.BaseSettings, cli_kebab_case=True):
description="Path to the session data directory."
)
version: str = pydantic.Field(default=__semver__, description="Version of the dataset.")
+ report_path: Path | None = pydantic.Field(
+ default=None, description="Path to save the Html QC report. If not provided, report is not saved."
+ )
def cli_cmd(self):
vr_dataset = dataset(Path(self.data_path), self.version)
runner = make_qc_runner(vr_dataset)
- runner.run_all_with_progress()
+ results = runner.run_all_with_progress()
+ if report_path := self.report_path:
+ from contraqctor.qc.reporters import HtmlReporter
+
+ reporter = HtmlReporter(output_path=report_path)
+ reporter.report_results(results, serialize_context_exportable_obj=True)
if __name__ == "__main__":
diff --git a/uv.lock b/uv.lock
index 3d963691..4e101b10 100644
--- a/uv.lock
+++ b/uv.lock
@@ -96,7 +96,7 @@ requires-dist = [
{ name = "aind-behavior-vr-foraging", extras = ["data"], marker = "extra == 'launcher'" },
{ name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = ">0.8,<0.10.0" },
{ name = "aind-data-schema", marker = "extra == 'launcher'", specifier = ">=2" },
- { name = "contraqctor", marker = "extra == 'data'", specifier = "<0.6.0" },
+ { name = "contraqctor", marker = "extra == 'data'", specifier = ">=0.5.3,<0.6.0" },
{ name = "pydantic-settings" },
]
provides-extras = ["data", "launcher"]
@@ -569,11 +569,12 @@ wheels = [
[[package]]
name = "contraqctor"
-version = "0.5.0"
+version = "0.5.3"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "aind-behavior-services" },
{ name = "harp-python" },
+ { name = "jinja2" },
{ name = "matplotlib" },
{ name = "numpy" },
{ name = "opencv-python" },
@@ -585,9 +586,9 @@ dependencies = [
{ name = "scipy" },
{ name = "semver" },
]
-sdist = { url = "https://files.pythonhosted.org/packages/cd/0d/cfe3c022bc3cb9591340f3e73bf6e99bfacf65d08476bffca3e315afb153/contraqctor-0.5.0.tar.gz", hash = "sha256:f585b0543392572f92586bbad0c0c7f3646dc4aa65e5f137ea937d3f5f9310cc", size = 45208, upload-time = "2025-10-14T23:59:14.807Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/95/33/e0dfd99fc23ab1ac6162b496727edef844e9279e13a969b05a1b4b05d426/contraqctor-0.5.3.tar.gz", hash = "sha256:0d11e4cf50acf01288b5ed66053211105c3a716fe8a31d63bcc2bf423037ac20", size = 54226, upload-time = "2025-11-10T17:31:19.497Z" }
wheels = [
- { url = "https://files.pythonhosted.org/packages/f9/52/41dcff4dd54ef55e2334c023e029ca9de5a1500af7e3a62cac13b83a479c/contraqctor-0.5.0-py3-none-any.whl", hash = "sha256:f0d0692a14707f294e4c18021bb288b7eb0097875f7ae6471de13ce85ae90fd8", size = 57442, upload-time = "2025-10-14T23:59:13.653Z" },
+ { url = "https://files.pythonhosted.org/packages/b4/9a/94fa67d2aecf7703a68be18b97b8d1af09ec9c26c73b2c21d5e881e46353/contraqctor-0.5.3-py3-none-any.whl", hash = "sha256:9306521efd6165007409319be39d4a8d9e286028693237584dbfc9f87e974292", size = 67638, upload-time = "2025-11-10T17:31:18.482Z" },
]
[[package]]
From 9006ef198023a7ffe901f412b337464a8b8e1791 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 10:51:15 -0800
Subject: [PATCH 04/19] Add qc to launcher
---
pyproject.toml | 3 +-
src/aind_behavior_vr_foraging/launcher.py | 18 +
uv.lock | 520 +---------------------
3 files changed, 24 insertions(+), 517 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 23686791..12541728 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,7 +31,8 @@ Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.VrForaging/rel
data = ["contraqctor>=0.5.3, <0.6.0"]
launcher = [
- "aind-clabe[aind-services] >0.8 ,<0.10.0",
+ #"aind-clabe[aind-services] >0.8 ,<0.10.0",
+ "aind-clabe @git+https://github.com/AllenNeuralDynamics/clabe.git@v0.9.0rc6",
"aind-data-schema>=2",
"aind_behavior_vr_foraging[data]",
]
diff --git a/src/aind_behavior_vr_foraging/launcher.py b/src/aind_behavior_vr_foraging/launcher.py
index aa286784..174070b4 100644
--- a/src/aind_behavior_vr_foraging/launcher.py
+++ b/src/aind_behavior_vr_foraging/launcher.py
@@ -99,6 +99,24 @@ async def experiment(launcher: Launcher) -> None:
ads_rig = AindRigDataMapper(rig=rig).map()
ads_rig.write_standard_file(launcher.session_directory)
+ if picker.ui_helper.prompt_yes_no_question("Would you like to run data transfer?"):
+ try:
+ import webbrowser
+
+ from contraqctor.qc.reporters import HtmlReporter
+
+ from .data_qc import make_qc_runner
+
+ vr_dataset = data_contract.dataset(launcher.session_directory)
+ runner = make_qc_runner(vr_dataset)
+ qc_path = launcher.session_directory / "Behavior" / "Logs" / "qc_report.json"
+ reporter = HtmlReporter(output_path=qc_path)
+ runner.run_all_with_progress(reporter=reporter)
+ webbrowser.open(qc_path.as_uri(), new=2)
+ except Exception as e:
+ logger.error(f"Failed to run data QC: {e}")
+
+
# Watchdog
is_transfer = picker.ui_helper.prompt_yes_no_question("Would you like to transfer data?")
if not is_transfer:
diff --git a/uv.lock b/uv.lock
index 4e101b10..f80966a5 100644
--- a/uv.lock
+++ b/uv.lock
@@ -69,7 +69,7 @@ data = [
{ name = "contraqctor" },
]
launcher = [
- { name = "aind-clabe", extra = ["aind-services"] },
+ { name = "aind-clabe" },
{ name = "aind-data-schema" },
{ name = "contraqctor" },
]
@@ -94,7 +94,7 @@ docs = [
requires-dist = [
{ name = "aind-behavior-services", specifier = ">=0.12,<0.13" },
{ name = "aind-behavior-vr-foraging", extras = ["data"], marker = "extra == 'launcher'" },
- { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = ">0.8,<0.10.0" },
+ { name = "aind-clabe", marker = "extra == 'launcher'", git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=v0.9.0rc6" },
{ name = "aind-data-schema", marker = "extra == 'launcher'", specifier = ">=2" },
{ name = "contraqctor", marker = "extra == 'data'", specifier = ">=0.5.3,<0.6.0" },
{ name = "pydantic-settings" },
@@ -120,8 +120,8 @@ docs = [
[[package]]
name = "aind-clabe"
-version = "0.9.0rc5"
-source = { registry = "https://pypi.org/simple" }
+version = "0.9.0rc6"
+source = { git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=v0.9.0rc6#f1adc66e262977d5c5d43401dcb61d9b633eb1ad" }
dependencies = [
{ name = "aind-behavior-services" },
{ name = "gitpython" },
@@ -131,24 +131,6 @@ dependencies = [
{ name = "rich" },
{ name = "semver" },
]
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- { url = "https://files.pythonhosted.org/packages/4f/01/26c5b1435654596c07b314653183ffe42b64ea07041c328f0fd4c68fe9f9/winkerberos-0.12.2-cp312-cp312-win32.whl", hash = "sha256:46dac1300e20738cbaf6c17c2e4832062ed7faee346c7a96f0e57f8bbe279c25", size = 25396, upload-time = "2025-04-02T14:41:41.6Z" },
- { url = "https://files.pythonhosted.org/packages/64/b1/6c4a1e4e50553798eb44dbb0d71ba6af48e2a62a0eb01bd0d4e2b41914e3/winkerberos-0.12.2-cp312-cp312-win_amd64.whl", hash = "sha256:2c5c7a70c0d4a43546b20d5654e7e7e5e5e96f42084a7f293864f7ad0fb1e953", size = 27710, upload-time = "2025-04-02T14:41:42.656Z" },
- { url = "https://files.pythonhosted.org/packages/5f/91/cff6750c7c3b2a9f35e12cd7c4df901251fc3be985edef707a3458c43e9a/winkerberos-0.12.2-cp313-cp313-win32.whl", hash = "sha256:482a72500b7822cc8f941d0c6eed668a24c030ac145c97732e175b51441bebbf", size = 25391, upload-time = "2025-04-02T14:41:43.938Z" },
- { url = "https://files.pythonhosted.org/packages/2a/98/defb037ad127c4006c4e992dd55ce0df92059626d3df5f5f4c5fc8502c26/winkerberos-0.12.2-cp313-cp313-win_amd64.whl", hash = "sha256:efd65ba54534512070916cb9c91ef9798a0f9fb0b04e12732c9631e71553fd69", size = 27704, upload-time = "2025-04-02T14:41:45.203Z" },
-]
From d35b90930810973622ae4e97812cbdac7c2ab9c2 Mon Sep 17 00:00:00 2001
From: Bruno Cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 10:52:08 -0800
Subject: [PATCH 05/19] Implement stop delay as a distribution instead of
scalar value (#450)
---
.../aind_behavior_vr_foraging.json | 16 ++-
src/Extensions/AddRewardSite.bonsai | 79 ++-------------
.../AindBehaviorVrForaging.Generated.cs | 97 ++++++++++++++++++-
src/Extensions/InstantiateSite.bonsai | 37 +++++--
src/aind_behavior_vr_foraging/task_logic.py | 6 +-
5 files changed, 145 insertions(+), 90 deletions(-)
diff --git a/src/DataSchemas/aind_behavior_vr_foraging.json b/src/DataSchemas/aind_behavior_vr_foraging.json
index bf09d030..c934ff18 100644
--- a/src/DataSchemas/aind_behavior_vr_foraging.json
+++ b/src/DataSchemas/aind_behavior_vr_foraging.json
@@ -3013,11 +3013,17 @@
"type": "boolean"
},
"stop_duration": {
- "default": 0,
- "description": "Duration (s) the animal must stop for to lock its choice",
- "minimum": 0,
- "title": "Stop Duration",
- "type": "number"
+ "$ref": "#/$defs/Distribution",
+ "default": {
+ "family": "Scalar",
+ "distribution_parameters": {
+ "family": "Scalar",
+ "value": 0.0
+ },
+ "truncation_parameters": null,
+ "scaling_parameters": null
+ },
+ "description": "Duration (s) the animal must stop for to lock its choice"
},
"time_to_collect_reward": {
"default": 100000,
diff --git a/src/Extensions/AddRewardSite.bonsai b/src/Extensions/AddRewardSite.bonsai
index 31a4345d..68529ff8 100644
--- a/src/Extensions/AddRewardSite.bonsai
+++ b/src/Extensions/AddRewardSite.bonsai
@@ -121,64 +121,11 @@
ActivePatch
-
- RewardSpecification
-
-
-
-
-
-
-
- ActivePatch
-
-
- RewardSpecification
-
-
- OperantLogic
-
-
-
-
-
-
-
-
-
- ActivePatch
-
-
- RewardSpecification.OperantLogic.StopDuration
-
-
- StopDurationOffset
-
-
-
-
-
-
- 1
-
-
-
-
-
-
-
-
-
-
- true
- 0
- 100000
- 10
-
-
-
+
+
+
@@ -198,24 +145,10 @@
-
-
-
+
+
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/src/Extensions/AindBehaviorVrForaging.Generated.cs b/src/Extensions/AindBehaviorVrForaging.Generated.cs
index 617a6be2..34f127f6 100644
--- a/src/Extensions/AindBehaviorVrForaging.Generated.cs
+++ b/src/Extensions/AindBehaviorVrForaging.Generated.cs
@@ -8336,7 +8336,7 @@ public partial class OperantLogic
private bool _isOperant;
- private double _stopDuration;
+ private Distribution _stopDuration;
private double _timeToCollectReward;
@@ -8345,7 +8345,7 @@ public partial class OperantLogic
public OperantLogic()
{
_isOperant = true;
- _stopDuration = 0D;
+ _stopDuration = new Distribution();
_timeToCollectReward = 100000D;
_graceDistanceThreshold = 10D;
}
@@ -8378,9 +8378,10 @@ public bool IsOperant
///
/// Duration (s) the animal must stop for to lock its choice
///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
[Newtonsoft.Json.JsonPropertyAttribute("stop_duration")]
[System.ComponentModel.DescriptionAttribute("Duration (s) the animal must stop for to lock its choice")]
- public double StopDuration
+ public Distribution StopDuration
{
get
{
@@ -15277,6 +15278,51 @@ public override string ToString()
}
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "family")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class Delay
+ {
+
+ public Delay()
+ {
+ }
+
+ protected Delay(Delay other)
+ {
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Delay(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new Delay(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)")]
[Newtonsoft.Json.JsonConverter(typeof(JsonInheritanceConverter), "family")]
[Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
@@ -16217,6 +16263,45 @@ private static System.IObservable Process(System.IObservable arguments)
+ {
+ var typeMapping = Type;
+ var returnType = typeMapping != null ? typeMapping.GetType().GetGenericArguments()[0] : typeof(Delay);
+ return System.Linq.Expressions.Expression.Call(
+ typeof(MatchDelay),
+ "Process",
+ new System.Type[] { returnType },
+ System.Linq.Enumerable.Single(arguments));
+ }
+
+
+ private static System.IObservable Process(System.IObservable source)
+ where TResult : Delay
+ {
+ return System.Reactive.Linq.Observable.Create(observer =>
+ {
+ var sourceObserver = System.Reactive.Observer.Create(
+ value =>
+ {
+ var match = value as TResult;
+ if (match != null) observer.OnNext(match);
+ },
+ observer.OnError,
+ observer.OnCompleted);
+ return System.ObservableExtensions.SubscribeSafe(source, sourceObserver);
+ });
+ }
+ }
+
+
[System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
[System.ComponentModel.DefaultPropertyAttribute("Type")]
[Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Combinator)]
@@ -17093,6 +17178,11 @@ public System.IObservable Process(System.IObservable(source);
}
+ public System.IObservable Process(System.IObservable source)
+ {
+ return Process(source);
+ }
+
public System.IObservable Process(System.IObservable source)
{
return Process(source);
@@ -17264,6 +17354,7 @@ public System.IObservable Process(System.IObservable
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))]
+ [System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))]
[System.Xml.Serialization.XmlIncludeAttribute(typeof(Bonsai.Expressions.TypeMapping))]
diff --git a/src/Extensions/InstantiateSite.bonsai b/src/Extensions/InstantiateSite.bonsai
index 6b82502b..e76d82d1 100644
--- a/src/Extensions/InstantiateSite.bonsai
+++ b/src/Extensions/InstantiateSite.bonsai
@@ -3,11 +3,11 @@
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:scr="clr-namespace:Bonsai.Scripting.Expressions;assembly=Bonsai.Scripting.Expressions"
- xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders"
xmlns:p1="clr-namespace:AindVrForagingDataSchema;assembly=Extensions"
+ xmlns:p2="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core"
+ xmlns:gl="clr-namespace:Bonsai.Shaders;assembly=Bonsai.Shaders"
xmlns:dsp="clr-namespace:Bonsai.Dsp;assembly=Bonsai.Dsp"
xmlns:harp="clr-namespace:Bonsai.Harp;assembly=Bonsai.Harp"
- xmlns:p2="clr-namespace:AllenNeuralDynamics.Core;assembly=AllenNeuralDynamics.Core"
xmlns:p3="clr-namespace:Bonsai.Numerics.Distributions;assembly=Bonsai.Numerics"
xmlns:bv="clr-namespace:BonVision;assembly=BonVision"
xmlns="https://bonsai-rx.org/2018/workflow">
@@ -151,8 +151,25 @@
OperantLogic.StopDuration
+
+
+
+
+ StopDurationOffset
+
+
+
+
+
+
+
+
- TimeSpan.FromSeconds(it)
+ Math.Max(0, it)
+ Math.Max(0, it)
+
+
+
@@ -161,7 +178,7 @@
- PT0.0000001S
+ PT0S
@@ -178,12 +195,18 @@
-
+
-
-
+
+
+
+
+
+
+
+
diff --git a/src/aind_behavior_vr_foraging/task_logic.py b/src/aind_behavior_vr_foraging/task_logic.py
index b09276c6..25b90bf2 100644
--- a/src/aind_behavior_vr_foraging/task_logic.py
+++ b/src/aind_behavior_vr_foraging/task_logic.py
@@ -228,8 +228,10 @@ class OperantLogic(BaseModel):
"""
is_operant: bool = Field(default=True, description="Will the trial implement operant logic")
- stop_duration: float = Field(
- default=0, ge=0, description="Duration (s) the animal must stop for to lock its choice"
+ stop_duration: distributions.Distribution = Field(
+ default=scalar_value(0),
+ validate_default=True,
+ description="Duration (s) the animal must stop for to lock its choice",
)
time_to_collect_reward: float = Field(
default=100000, ge=0, description="Time(s) the animal has to collect the reward"
From d9c3876231f8abc25208c68bbdd283f692b9588c Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 10:54:27 -0800
Subject: [PATCH 06/19] Upgrade dependencies
---
uv.lock | 221 ++++++++++++++++++++++++++++----------------------------
1 file changed, 109 insertions(+), 112 deletions(-)
diff --git a/uv.lock b/uv.lock
index f80966a5..066ac12e 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2,12 +2,9 @@ version = 1
revision = 3
requires-python = ">=3.11"
resolution-markers = [
- "python_full_version >= '3.14' and sys_platform == 'darwin'",
- "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'darwin'",
- "python_full_version >= '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'",
- "python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'",
- "(python_full_version >= '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.14' and sys_platform != 'darwin' and sys_platform != 'linux')",
- "(python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform != 'darwin' and sys_platform != 'linux')",
+ "python_full_version >= '3.12' and sys_platform == 'darwin'",
+ "python_full_version >= '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'",
+ "(python_full_version >= '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux')",
"python_full_version < '3.12' and sys_platform == 'darwin'",
"python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'",
"(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux')",
@@ -27,21 +24,21 @@ wheels = [
[[package]]
name = "aind-behavior-curriculum"
-version = "0.0.35"
+version = "0.0.36"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "jinja2" },
{ name = "pydantic" },
{ name = "semver" },
]
-sdist = { url = "https://files.pythonhosted.org/packages/c5/c7/bb935282362302860d3ae7bc6765be7fc3b2f74af0ca200ad8ed91f03dac/aind_behavior_curriculum-0.0.35.tar.gz", hash = "sha256:594b735a254f6ab9112504efd9eb78b5e2bbd5d93d2c88608889c8a38cfcd234", size = 122480, upload-time = "2025-10-02T23:41:57.49Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/12/e3/3d565a7d29c22734ebb5ccf785b994d0c32beb963e087a60afa3c93bf648/aind_behavior_curriculum-0.0.36.tar.gz", hash = "sha256:d996aa1bd82b83bb48e381ee02c590c2ba17f54f7d863cf337d6fa63840a82df", size = 122460, upload-time = "2025-10-24T17:43:34.681Z" }
wheels = [
- { url = "https://files.pythonhosted.org/packages/a9/7d/d90a57207aebc7fa06c575d30248984821199450de78e932211da0becf76/aind_behavior_curriculum-0.0.35-py3-none-any.whl", hash = "sha256:bf4c64b61195fa15e73d381fe53aac438ede9ca09f8f57968220a48d335c0656", size = 47389, upload-time = "2025-10-02T23:41:56.296Z" },
+ { url = "https://files.pythonhosted.org/packages/18/a1/4f3116cf9539481f7c1dc62e86fc7bb0d7b3061a0c61cf17aae4f0b2f36c/aind_behavior_curriculum-0.0.36-py3-none-any.whl", hash = "sha256:11164ddf56d28b0a23330200582b20743d74bc2059ed07a4b3d2a660efc3c8d8", size = 47393, upload-time = "2025-10-24T17:43:33.3Z" },
]
[[package]]
name = "aind-behavior-services"
-version = "0.12.3"
+version = "0.12.5"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "aind-behavior-curriculum" },
@@ -50,9 +47,9 @@ dependencies = [
{ name = "pydantic" },
{ name = "semver" },
]
-sdist = { url = "https://files.pythonhosted.org/packages/46/62/68a09654bf253bc1e653040c68d456ca928e385bbbb1bbf038da25134a84/aind_behavior_services-0.12.3.tar.gz", hash = "sha256:20bae171993017ebfd5d5ce09b610110947902b05c583f517c2efb732ab336f8", size = 27418, upload-time = "2025-10-15T22:16:00.895Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/c6/01/6c71f219f5078d7ec3b0507724c2b63ec0af3c8571024053daa469d32e77/aind_behavior_services-0.12.5.tar.gz", hash = "sha256:ebcb1f56852265b988a777b22eeb1a9e4952c4cc7328b0e8c749844593372ccd", size = 27423, upload-time = "2025-11-06T19:06:26.875Z" }
wheels = [
- { url = "https://files.pythonhosted.org/packages/67/c9/5b1b1da5a8dccabf4b6b9b42235eceaa4ee1f2c816a402e322f192f77a8a/aind_behavior_services-0.12.3-py3-none-any.whl", hash = "sha256:0a00588c1e29bac1295534e0c17169de862f914cd83b29248ff508fb782bdb3e", size = 38254, upload-time = "2025-10-15T22:15:59.672Z" },
+ { url = "https://files.pythonhosted.org/packages/89/3c/3d28d25645df3502f1a708483623e3a225c1f195adf2cef5e1727a7cf8b9/aind_behavior_services-0.12.5-py3-none-any.whl", hash = "sha256:fd6d3b60d07fd5bc31ecade227c68f97122e9591e78919098e06fe72b6e1d679", size = 38243, upload-time = "2025-11-06T19:06:25.67Z" },
]
[[package]]
@@ -148,16 +145,16 @@ wheels = [
[[package]]
name = "aind-data-schema-models"
-version = "4.3.0"
+version = "4.5.0"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "importlib-resources" },
{ name = "pydantic" },
{ name = "requests" },
]
-sdist = { url = "https://files.pythonhosted.org/packages/2d/ea/a6b5bacf52de8e904ca9bb88dc1a5f8596dfa0b12fa5812e44041835d535/aind_data_schema_models-4.3.0.tar.gz", hash = "sha256:3608c89d91192d54dee40823e385e4f6dbdac658987af7fadefd68c02d3490fb", size = 324212, upload-time = "2025-09-22T21:54:25.374Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/ec/b7/098e5014506fc3b5c0d28d55ba61f79df1d15c71ae70f28cb0c4fb2e7015/aind_data_schema_models-4.5.0.tar.gz", hash = "sha256:f0fd24012ea9f95f73422301acebcb81da74fa6e728b4222c2016cd4a83fddfd", size = 327537, upload-time = "2025-11-07T18:44:24.004Z" }
wheels = [
- { url = "https://files.pythonhosted.org/packages/11/e6/136ff5288b154c022c4cb7a047faf946755aca597a75490767a479936921/aind_data_schema_models-4.3.0-py3-none-any.whl", hash = "sha256:62703b4425009c930511de366a85fb57e5dc52f7493fd0a49871a90429e5832f", size = 297854, upload-time = "2025-09-22T21:54:24.216Z" },
+ { url = "https://files.pythonhosted.org/packages/23/d0/8010321dc8c8d1c945f8a31a0872a73514e4c7550bf54db40ad5069ec1f3/aind_data_schema_models-4.5.0-py3-none-any.whl", hash = "sha256:a7ab4686f78a3911e3c868f10d277d861a2ef43095b8547f538c5750fb4c4a17", size = 299109, upload-time = "2025-11-07T18:44:22.605Z" },
]
[[package]]
@@ -220,11 +217,11 @@ wheels = [
[[package]]
name = "certifi"
-version = "2025.10.5"
+version = "2025.11.12"
source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/4c/5b/b6ce21586237c77ce67d01dc5507039d444b630dd76611bbca2d8e5dcd91/certifi-2025.10.5.tar.gz", hash = "sha256:47c09d31ccf2acf0be3f701ea53595ee7e0b8fa08801c6624be771df09ae7b43", size = 164519, upload-time = "2025-10-05T04:12:15.808Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/a2/8c/58f469717fa48465e4a50c014a0400602d3c437d7c0c468e17ada824da3a/certifi-2025.11.12.tar.gz", hash = "sha256:d8ab5478f2ecd78af242878415affce761ca6bc54a22a27e026d7c25357c3316", size = 160538, upload-time = "2025-11-12T02:54:51.517Z" }
wheels = [
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+ { url = "https://files.pythonhosted.org/packages/70/7d/9bc192684cea499815ff478dfcdc13835ddf401365057044fb721ec6bddb/certifi-2025.11.12-py3-none-any.whl", hash = "sha256:97de8790030bbd5c2d96b7ec782fc2f7820ef8dba6db909ccf95449f2d062d4b", size = 159438, upload-time = "2025-11-12T02:54:49.735Z" },
]
[[package]]
@@ -1230,16 +1227,16 @@ wheels = [
[[package]]
name = "pydantic-settings"
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[[package]]
From 8e979068944ed830aebe76efdda4a1c60e21966e Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 11:06:32 -0800
Subject: [PATCH 07/19] Pin to pypi rc
---
pyproject.toml | 2 +-
uv.lock | 529 ++++++++++++++++++++++++++++++++++++++++++++++++-
2 files changed, 523 insertions(+), 8 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 12541728..b7adec54 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,7 +32,7 @@ data = ["contraqctor>=0.5.3, <0.6.0"]
launcher = [
#"aind-clabe[aind-services] >0.8 ,<0.10.0",
- "aind-clabe @git+https://github.com/AllenNeuralDynamics/clabe.git@v0.9.0rc6",
+ "aind-clabe[aind-services]==0.9.0rc7",
"aind-data-schema>=2",
"aind_behavior_vr_foraging[data]",
]
diff --git a/uv.lock b/uv.lock
index 066ac12e..70c80d73 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2,9 +2,12 @@ version = 1
revision = 3
requires-python = ">=3.11"
resolution-markers = [
- "python_full_version >= '3.12' and sys_platform == 'darwin'",
- "python_full_version >= '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'",
- "(python_full_version >= '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.12' and sys_platform != 'darwin' and sys_platform != 'linux')",
+ "python_full_version >= '3.14' and sys_platform == 'darwin'",
+ "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'darwin'",
+ "python_full_version >= '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'",
+ "python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine == 'aarch64' and sys_platform == 'linux'",
+ "(python_full_version >= '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.14' and sys_platform != 'darwin' and sys_platform != 'linux')",
+ "(python_full_version >= '3.12' and python_full_version < '3.14' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform != 'darwin' and sys_platform != 'linux')",
"python_full_version < '3.12' and sys_platform == 'darwin'",
"python_full_version < '3.12' and platform_machine == 'aarch64' and sys_platform == 'linux'",
"(python_full_version < '3.12' and platform_machine != 'aarch64' and sys_platform == 'linux') or (python_full_version < '3.12' and sys_platform != 'darwin' and sys_platform != 'linux')",
@@ -66,7 +69,7 @@ data = [
{ name = "contraqctor" },
]
launcher = [
- { name = "aind-clabe" },
+ { name = "aind-clabe", extra = ["aind-services"] },
{ name = "aind-data-schema" },
{ name = "contraqctor" },
]
@@ -91,7 +94,7 @@ docs = [
requires-dist = [
{ name = "aind-behavior-services", specifier = ">=0.12,<0.13" },
{ name = "aind-behavior-vr-foraging", extras = ["data"], marker = "extra == 'launcher'" },
- { name = "aind-clabe", marker = "extra == 'launcher'", git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=v0.9.0rc6" },
+ { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = "==0.9.0rc7" },
{ name = "aind-data-schema", marker = "extra == 'launcher'", specifier = ">=2" },
{ name = "contraqctor", marker = "extra == 'data'", specifier = ">=0.5.3,<0.6.0" },
{ name = "pydantic-settings" },
@@ -117,8 +120,8 @@ docs = [
[[package]]
name = "aind-clabe"
-version = "0.9.0rc6"
-source = { git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=v0.9.0rc6#f1adc66e262977d5c5d43401dcb61d9b633eb1ad" }
+version = "0.9.0rc7"
+source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "aind-behavior-services" },
{ name = "gitpython" },
@@ -128,6 +131,24 @@ dependencies = [
{ name = "rich" },
{ name = "semver" },
]
+sdist = { url = "https://files.pythonhosted.org/packages/45/ac/3ac72a8fd10d23c5d5afcdd4d5240400f1ae4460db352a43c2794bd295ca/aind_clabe-0.9.0rc7.tar.gz", hash = "sha256:a5b605c223c51e7ca0e823f9064113b535b37b35dc77838a227df96d63d440fa", size = 67079, upload-time = "2025-11-14T16:48:02.816Z" }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/a9/4b/f9f12e5b7808270a3108fbbaf402c881637e59bd9db727e5b9d0fe4a8828/aind_clabe-0.9.0rc7-py3-none-any.whl", hash = "sha256:e79ca303bc8426329a430fd22f993b9d851e935cf95787c0ac436d576b10c1a1", size = 89703, upload-time = "2025-11-14T16:48:01.544Z" },
+]
+
+[package.optional-dependencies]
+aind-services = [
+ { name = "aind-data-schema" },
+ { name = "aind-data-transfer-service" },
+ { name = "cryptography" },
+ { name = "ldap3", marker = "sys_platform == 'win32'" },
+ { name = "ms-active-directory" },
+ { name = "msal", marker = "sys_platform == 'win32'" },
+ { name = "pykeepass" },
+ { name = "pyyaml" },
+ { name = "requests" },
+ { name = "winkerberos", marker = "sys_platform == 'win32'" },
+]
[[package]]
name = "aind-data-schema"
@@ -157,6 +178,21 @@ wheels = [
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]
+[[package]]
+name = "aind-data-transfer-service"
+version = "1.21.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "aind-data-schema-models" },
+ { name = "email-validator" },
+ { name = "pydantic" },
+ { name = "pydantic-settings" },
+]
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From d1659570cc0489cb6cc33fa5c60298c709124a44 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 11:54:42 -0800
Subject: [PATCH 08/19] Add modifier
---
src/Platforms/FIP_DAQ_Control | 1 +
src/aind_behavior_vr_foraging/launcher.py | 60 ++++++++++-------------
2 files changed, 26 insertions(+), 35 deletions(-)
create mode 160000 src/Platforms/FIP_DAQ_Control
diff --git a/src/Platforms/FIP_DAQ_Control b/src/Platforms/FIP_DAQ_Control
new file mode 160000
index 00000000..7791f296
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control
@@ -0,0 +1 @@
+Subproject commit 7791f296469cdafbf38e2d329f90a96ae5f1bc4a
diff --git a/src/aind_behavior_vr_foraging/launcher.py b/src/aind_behavior_vr_foraging/launcher.py
index 174070b4..7dddb902 100644
--- a/src/aind_behavior_vr_foraging/launcher.py
+++ b/src/aind_behavior_vr_foraging/launcher.py
@@ -15,6 +15,7 @@
from clabe.launcher import Launcher, LauncherCliArgs
from clabe.pickers import DefaultBehaviorPickerSettings
from clabe.pickers.dataverse import DataversePicker
+from clabe.pickers import ByAnimalModifier
from contraqctor.contract.json import SoftwareEvents
from pydantic_settings import CliApp
@@ -38,7 +39,12 @@ async def experiment(launcher: Launcher) -> None:
# Start experiment setup
picker = DataversePicker(launcher=launcher, settings=DefaultBehaviorPickerSettings())
- manipulator_modifier = ByAnimalManipulatorModifier(picker, launcher)
+ manipulator_modifier = ByAnimalManipulatorModifier(
+ subject_db_path=picker.subject_dir / picker.session.subject,
+ model_path="manipulator.calibration.input.initial_position",
+ model_name="manipulator_init.json",
+ launcher=launcher,
+ )
# Pick and register session
session = picker.pick_session(AindBehaviorSessionModel)
@@ -65,7 +71,10 @@ async def experiment(launcher: Launcher) -> None:
await bonsai_app.run_async()
# Update manipulator initial position for next session
- manipulator_modifier.dump()
+ try:
+ manipulator_modifier.dump()
+ except Exception as e:
+ logger.error(f"Failed to update manipulator initial position: {e}")
# Curriculum
suggestion: CurriculumSuggestion | None = None
@@ -116,7 +125,6 @@ async def experiment(launcher: Launcher) -> None:
except Exception as e:
logger.error(f"Failed to run data QC: {e}")
-
# Watchdog
is_transfer = picker.ui_helper.prompt_yes_no_question("Would you like to transfer data?")
if not is_transfer:
@@ -142,41 +150,23 @@ def _dump_suggestion(suggestion: CurriculumSuggestion, session_directory: Path)
f.write(suggestion.model_dump_json(indent=2))
-class ByAnimalManipulatorModifier:
- def __init__(self, picker: DataversePicker, launcher: Launcher) -> None:
- self._picker = picker
+class ByAnimalManipulatorModifier(ByAnimalModifier[AindVrForagingRig]):
+ """Modifier to set and update manipulator initial position based on animal-specific data."""
+
+ def __init__(
+ self, subject_db_path: Path, model_path: str, model_name: str, *, launcher: Launcher, **kwargs
+ ) -> None:
+ super().__init__(subject_db_path, model_path, model_name, **kwargs)
self._launcher = launcher
- def inject(self, rig: AindVrForagingRig) -> AindVrForagingRig:
- subject = self._launcher.session.subject
- target_folder = self._picker.subject_dir / subject
- target_file = target_folder / "manipulator_init.json"
- if not target_file.exists():
- logger.warning(f"Manipulator initial position file not found: {target_file}. Using default.")
- else:
- cached = ManipulatorPosition.model_validate_json(target_file.read_text(encoding="utf-8"))
- logger.info(f"Loading manipulator initial position from: {target_file}. Deserialized: {cached}")
- assert rig.manipulator.calibration is not None
- rig.manipulator.calibration.input.initial_position = cached
- return rig
-
- def dump(self) -> None:
- target_folder = self._picker.subject_dir / self._launcher.session.subject
- target_file = target_folder / "manipulator_init.json"
+ def _process_before_dump(self) -> ManipulatorPosition:
_dataset = data_contract.dataset(self._launcher.session_directory)
- try:
- manipulator_parking_position: SoftwareEvents = cast(
- SoftwareEvents, _dataset["Behavior"]["SoftwareEvents"]["SpoutParkingPositions"].load()
- )
- data: dict[str, Any] = manipulator_parking_position.data.iloc[0]["data"]["ResetPosition"]
- position = ManipulatorPosition.model_validate(data)
- except Exception as e:
- logger.error(f"Failed to load manipulator parking position: {e}")
- return
- else:
- logger.info(f"Saving manipulator initial position to: {target_file}. Serialized: {position}")
- target_folder.mkdir(parents=True, exist_ok=True)
- target_file.write_text(position.model_dump_json(indent=2), encoding="utf-8")
+ manipulator_parking_position: SoftwareEvents = cast(
+ SoftwareEvents, _dataset["Behavior"]["SoftwareEvents"]["SpoutParkingPositions"].load()
+ )
+ data: dict[str, Any] = manipulator_parking_position.data.iloc[0]["data"]["ResetPosition"]
+ position = ManipulatorPosition.model_validate(data)
+ return position
class ClabeCli(LauncherCliArgs):
From 15c7da8af1ea13513001945e20e67b28d40f2d35 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 12:01:45 -0800
Subject: [PATCH 09/19] Update dependencies for tests
---
pyproject.toml | 2 +-
uv.lock | 8 ++------
2 files changed, 3 insertions(+), 7 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index b7adec54..9c465e7c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,7 +32,7 @@ data = ["contraqctor>=0.5.3, <0.6.0"]
launcher = [
#"aind-clabe[aind-services] >0.8 ,<0.10.0",
- "aind-clabe[aind-services]==0.9.0rc7",
+ "aind-clabe[aind-services] @git+https://github.com/AllenNeuralDynamics/clabe.git@fix-small-issues",
"aind-data-schema>=2",
"aind_behavior_vr_foraging[data]",
]
diff --git a/uv.lock b/uv.lock
index 70c80d73..70f7584b 100644
--- a/uv.lock
+++ b/uv.lock
@@ -94,7 +94,7 @@ docs = [
requires-dist = [
{ name = "aind-behavior-services", specifier = ">=0.12,<0.13" },
{ name = "aind-behavior-vr-foraging", extras = ["data"], marker = "extra == 'launcher'" },
- { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", specifier = "==0.9.0rc7" },
+ { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=fix-small-issues" },
{ name = "aind-data-schema", marker = "extra == 'launcher'", specifier = ">=2" },
{ name = "contraqctor", marker = "extra == 'data'", specifier = ">=0.5.3,<0.6.0" },
{ name = "pydantic-settings" },
@@ -121,7 +121,7 @@ docs = [
[[package]]
name = "aind-clabe"
version = "0.9.0rc7"
-source = { registry = "https://pypi.org/simple" }
+source = { git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=fix-small-issues#310bd9ae21f9505bea8e05a13393dc06fcea682c" }
dependencies = [
{ name = "aind-behavior-services" },
{ name = "gitpython" },
@@ -131,10 +131,6 @@ dependencies = [
{ name = "rich" },
{ name = "semver" },
]
-sdist = { url = "https://files.pythonhosted.org/packages/45/ac/3ac72a8fd10d23c5d5afcdd4d5240400f1ae4460db352a43c2794bd295ca/aind_clabe-0.9.0rc7.tar.gz", hash = "sha256:a5b605c223c51e7ca0e823f9064113b535b37b35dc77838a227df96d63d440fa", size = 67079, upload-time = "2025-11-14T16:48:02.816Z" }
-wheels = [
- { url = "https://files.pythonhosted.org/packages/a9/4b/f9f12e5b7808270a3108fbbaf402c881637e59bd9db727e5b9d0fe4a8828/aind_clabe-0.9.0rc7-py3-none-any.whl", hash = "sha256:e79ca303bc8426329a430fd22f993b9d851e935cf95787c0ac436d576b10c1a1", size = 89703, upload-time = "2025-11-14T16:48:01.544Z" },
-]
[package.optional-dependencies]
aind-services = [
From 2bda26d7959c656a48a93f73942233491950db2f Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 12:02:55 -0800
Subject: [PATCH 10/19] Update prompt for data transfer to generate QC report
---
src/aind_behavior_vr_foraging/launcher.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/aind_behavior_vr_foraging/launcher.py b/src/aind_behavior_vr_foraging/launcher.py
index 7dddb902..d9075beb 100644
--- a/src/aind_behavior_vr_foraging/launcher.py
+++ b/src/aind_behavior_vr_foraging/launcher.py
@@ -108,7 +108,8 @@ async def experiment(launcher: Launcher) -> None:
ads_rig = AindRigDataMapper(rig=rig).map()
ads_rig.write_standard_file(launcher.session_directory)
- if picker.ui_helper.prompt_yes_no_question("Would you like to run data transfer?"):
+ # Run data qc
+ if picker.ui_helper.prompt_yes_no_question("Would you like to generate a qc report?"):
try:
import webbrowser
From 7c4a90aa3c0339cf168f8721c940a00181855ea2 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 13:15:20 -0800
Subject: [PATCH 11/19] Ensure launcher is registered
---
src/aind_behavior_vr_foraging/launcher.py | 12 ++++++------
uv.lock | 2 +-
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/src/aind_behavior_vr_foraging/launcher.py b/src/aind_behavior_vr_foraging/launcher.py
index d9075beb..89af7e97 100644
--- a/src/aind_behavior_vr_foraging/launcher.py
+++ b/src/aind_behavior_vr_foraging/launcher.py
@@ -39,12 +39,6 @@ async def experiment(launcher: Launcher) -> None:
# Start experiment setup
picker = DataversePicker(launcher=launcher, settings=DefaultBehaviorPickerSettings())
- manipulator_modifier = ByAnimalManipulatorModifier(
- subject_db_path=picker.subject_dir / picker.session.subject,
- model_path="manipulator.calibration.input.initial_position",
- model_name="manipulator_init.json",
- launcher=launcher,
- )
# Pick and register session
session = picker.pick_session(AindBehaviorSessionModel)
@@ -58,6 +52,12 @@ async def experiment(launcher: Launcher) -> None:
rig = picker.pick_rig(AindVrForagingRig)
# Post-fetching modifications
+ manipulator_modifier = ByAnimalManipulatorModifier(
+ subject_db_path=picker.subject_dir / picker.session.subject,
+ model_path="manipulator.calibration.input.initial_position",
+ model_name="manipulator_init.json",
+ launcher=launcher,
+ )
manipulator_modifier.inject(rig)
# Run the task via Bonsai
diff --git a/uv.lock b/uv.lock
index 70f7584b..0437fef0 100644
--- a/uv.lock
+++ b/uv.lock
@@ -121,7 +121,7 @@ docs = [
[[package]]
name = "aind-clabe"
version = "0.9.0rc7"
-source = { git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=fix-small-issues#310bd9ae21f9505bea8e05a13393dc06fcea682c" }
+source = { git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=fix-small-issues#51e48ee12943f1b68baf9e5b58fa76fb46f04a7d" }
dependencies = [
{ name = "aind-behavior-services" },
{ name = "gitpython" },
From 9517155cb83524a6ebe0f40c142c9a51cd2497c0 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 13:17:07 -0800
Subject: [PATCH 12/19] Linting
---
src/aind_behavior_vr_foraging/launcher.py | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/src/aind_behavior_vr_foraging/launcher.py b/src/aind_behavior_vr_foraging/launcher.py
index 89af7e97..c93b1cf6 100644
--- a/src/aind_behavior_vr_foraging/launcher.py
+++ b/src/aind_behavior_vr_foraging/launcher.py
@@ -13,9 +13,8 @@
)
from clabe.data_transfer.aind_watchdog import WatchdogDataTransferService, WatchdogSettings
from clabe.launcher import Launcher, LauncherCliArgs
-from clabe.pickers import DefaultBehaviorPickerSettings
+from clabe.pickers import ByAnimalModifier, DefaultBehaviorPickerSettings
from clabe.pickers.dataverse import DataversePicker
-from clabe.pickers import ByAnimalModifier
from contraqctor.contract.json import SoftwareEvents
from pydantic_settings import CliApp
From 78c1fca45f8671725a070f70d127e243bbcbbdb6 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 13:18:43 -0800
Subject: [PATCH 13/19] Fix file extension
---
src/aind_behavior_vr_foraging/launcher.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/aind_behavior_vr_foraging/launcher.py b/src/aind_behavior_vr_foraging/launcher.py
index c93b1cf6..1f8a3223 100644
--- a/src/aind_behavior_vr_foraging/launcher.py
+++ b/src/aind_behavior_vr_foraging/launcher.py
@@ -118,7 +118,7 @@ async def experiment(launcher: Launcher) -> None:
vr_dataset = data_contract.dataset(launcher.session_directory)
runner = make_qc_runner(vr_dataset)
- qc_path = launcher.session_directory / "Behavior" / "Logs" / "qc_report.json"
+ qc_path = launcher.session_directory / "Behavior" / "Logs" / "qc_report.html"
reporter = HtmlReporter(output_path=qc_path)
runner.run_all_with_progress(reporter=reporter)
webbrowser.open(qc_path.as_uri(), new=2)
From 62e33291b403bfa46c8ff5b52af69677500798e4 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Fri, 14 Nov 2025 13:44:51 -0800
Subject: [PATCH 14/19] Regenerate
---
src/DataSchemas/aind_behavior_vr_foraging.json | 10 +++++-----
src/Extensions/AindBehaviorVrForaging.Generated.cs | 8 ++++----
src/aind_behavior_vr_foraging/data_mappers/_session.py | 4 ++--
3 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/src/DataSchemas/aind_behavior_vr_foraging.json b/src/DataSchemas/aind_behavior_vr_foraging.json
index c934ff18..fa690c4e 100644
--- a/src/DataSchemas/aind_behavior_vr_foraging.json
+++ b/src/DataSchemas/aind_behavior_vr_foraging.json
@@ -3,14 +3,14 @@
"AindBehaviorSessionModel": {
"properties": {
"aind_behavior_services_pkg_version": {
- "default": "0.12.3",
+ "default": "0.12.5",
"pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
"title": "aind_behavior_services package version",
"type": "string"
},
"version": {
- "const": "0.12.3",
- "default": "0.12.3",
+ "const": "0.12.5",
+ "default": "0.12.5",
"title": "Version",
"type": "string"
},
@@ -353,7 +353,7 @@
"AindVrForagingRig": {
"properties": {
"aind_behavior_services_pkg_version": {
- "default": "0.12.3",
+ "default": "0.12.5",
"pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
"title": "aind_behavior_services package version",
"type": "string"
@@ -611,7 +611,7 @@
"title": "Rng Seed"
},
"aind_behavior_services_pkg_version": {
- "default": "0.12.3",
+ "default": "0.12.5",
"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"
diff --git a/src/Extensions/AindBehaviorVrForaging.Generated.cs b/src/Extensions/AindBehaviorVrForaging.Generated.cs
index 34f127f6..88cf5f01 100644
--- a/src/Extensions/AindBehaviorVrForaging.Generated.cs
+++ b/src/Extensions/AindBehaviorVrForaging.Generated.cs
@@ -43,8 +43,8 @@ public partial class AindBehaviorSessionModel
public AindBehaviorSessionModel()
{
- _aindBehaviorServicesPkgVersion = "0.12.3";
- _version = "0.12.3";
+ _aindBehaviorServicesPkgVersion = "0.12.5";
+ _version = "0.12.5";
_experimenter = new System.Collections.Generic.List();
_experimentVersion = "";
_allowDirtyRepo = false;
@@ -954,7 +954,7 @@ public partial class AindVrForagingRig
public AindVrForagingRig()
{
- _aindBehaviorServicesPkgVersion = "0.12.3";
+ _aindBehaviorServicesPkgVersion = "0.12.5";
_version = "0.6.2-rc1";
_triggeredCameraController = new CameraControllerSpinnakerCamera();
_harpBehavior = new HarpBehavior();
@@ -1521,7 +1521,7 @@ public partial class AindVrForagingTaskParameters
public AindVrForagingTaskParameters()
{
- _aindBehaviorServicesPkgVersion = "0.12.3";
+ _aindBehaviorServicesPkgVersion = "0.12.5";
_environment = new BlockStructure();
_operationControl = new OperationControl();
}
diff --git a/src/aind_behavior_vr_foraging/data_mappers/_session.py b/src/aind_behavior_vr_foraging/data_mappers/_session.py
index d003b0bc..826755c5 100644
--- a/src/aind_behavior_vr_foraging/data_mappers/_session.py
+++ b/src/aind_behavior_vr_foraging/data_mappers/_session.py
@@ -32,7 +32,7 @@ def __init__(
session: AindBehaviorSessionModel,
rig: AindVrForagingRig,
task_logic: AindVrForagingTaskLogic,
- bonsai_app: BonsaiApp = BonsaiApp(workflow=Path("./src/main.bonsai")),
+ bonsai_app: Optional[BonsaiApp] = None,
repository: Union[os.PathLike, git.Repo] = Path("."),
session_end_time: Optional[datetime.datetime] = None,
curriculum_suggestion: Optional[CurriculumSuggestion] = None,
@@ -43,7 +43,7 @@ def __init__(
self.repository = repository
if isinstance(self.repository, os.PathLike | str):
self.repository = git.Repo(Path(self.repository))
- self.bonsai_app = bonsai_app
+ self.bonsai_app = bonsai_app if bonsai_app is not None else BonsaiApp(workflow=Path("./src/main.bonsai"))
self._session_end_time = session_end_time
self._mapped: Optional[acquisition.Acquisition] = None
self.curriculum = curriculum_suggestion
From 25a105eeaf338850808c251c9e753a1de270a804 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Sat, 15 Nov 2025 11:30:50 -0800
Subject: [PATCH 15/19] Remove enclosure
---
src/aind_behavior_vr_foraging/data_mappers/_rig.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/aind_behavior_vr_foraging/data_mappers/_rig.py b/src/aind_behavior_vr_foraging/data_mappers/_rig.py
index bf6413e0..c9650688 100644
--- a/src/aind_behavior_vr_foraging/data_mappers/_rig.py
+++ b/src/aind_behavior_vr_foraging/data_mappers/_rig.py
@@ -351,7 +351,7 @@ def _get_all_components_and_connections(
_components.append(cls._get_computer(rig))
- _components.append(cls._get_enclosure())
+ # _components.append(cls._get_enclosure()) # Enclosure is removed since we do not have a good way to ensure consistency across rigs
harp_behavior_node = cls._get_harp_behavior_node(rig)
_components.append(harp_behavior_node.device)
From 84d7e606c6e641c640cecad5fdbab0d516bc0967 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Sat, 15 Nov 2025 18:03:14 -0800
Subject: [PATCH 16/19] Only run bonsai tests on windows
---
tests/test_bonsai.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/tests/test_bonsai.py b/tests/test_bonsai.py
index 10bd2b7b..7c743d35 100644
--- a/tests/test_bonsai.py
+++ b/tests/test_bonsai.py
@@ -1,4 +1,5 @@
import os
+import platform
import sys
import unittest
import warnings
@@ -19,6 +20,7 @@
TModel = TypeVar("TModel", bound=Union[AindVrForagingRig, AindVrForagingTaskLogic, AindBehaviorSessionModel])
+@unittest.skipUnless(platform.system() == "Windows", "Bonsai tests only run on Windows")
class BonsaiTests(unittest.TestCase):
def test_deserialization(self):
rig.main("./local/{schema}.json")
From f221de491f7943d4718b1154d6f82a2f08458af4 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Sat, 15 Nov 2025 19:02:16 -0800
Subject: [PATCH 17/19] Upgrade dependencies
---
pyproject.toml | 2 +-
uv.lock | 40 ++++++++++++++++++++++++++++++++++++++--
2 files changed, 39 insertions(+), 3 deletions(-)
diff --git a/pyproject.toml b/pyproject.toml
index 9c465e7c..f35e85b7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,7 +32,7 @@ data = ["contraqctor>=0.5.3, <0.6.0"]
launcher = [
#"aind-clabe[aind-services] >0.8 ,<0.10.0",
- "aind-clabe[aind-services] @git+https://github.com/AllenNeuralDynamics/clabe.git@fix-small-issues",
+ "aind-clabe[aind-services] @git+https://github.com/AllenNeuralDynamics/clabe.git@development",
"aind-data-schema>=2",
"aind_behavior_vr_foraging[data]",
]
diff --git a/uv.lock b/uv.lock
index 0437fef0..d84cdb00 100644
--- a/uv.lock
+++ b/uv.lock
@@ -94,7 +94,7 @@ docs = [
requires-dist = [
{ name = "aind-behavior-services", specifier = ">=0.12,<0.13" },
{ name = "aind-behavior-vr-foraging", extras = ["data"], marker = "extra == 'launcher'" },
- { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=fix-small-issues" },
+ { name = "aind-clabe", extras = ["aind-services"], marker = "extra == 'launcher'", git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=development" },
{ name = "aind-data-schema", marker = "extra == 'launcher'", specifier = ">=2" },
{ name = "contraqctor", marker = "extra == 'data'", specifier = ">=0.5.3,<0.6.0" },
{ name = "pydantic-settings" },
@@ -121,12 +121,13 @@ docs = [
[[package]]
name = "aind-clabe"
version = "0.9.0rc7"
-source = { git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=fix-small-issues#51e48ee12943f1b68baf9e5b58fa76fb46f04a7d" }
+source = { git = "https://github.com/AllenNeuralDynamics/clabe.git?rev=development#e6a33f2b8b6d868e8cd724ed0e5172405b47c007" }
dependencies = [
{ name = "aind-behavior-services" },
{ name = "gitpython" },
{ name = "pydantic" },
{ name = "pydantic-settings" },
+ { name = "questionary" },
{ name = "requests" },
{ name = "rich" },
{ name = "semver" },
@@ -1525,6 +1526,18 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/95/7e/f896623c3c635a90537ac093c6a618ebe1a90d87206e42309cb5d98a1b9e/pillow-12.0.0-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:b290fd8aa38422444d4b50d579de197557f182ef1068b75f5aa8558638b8d0a5", size = 6997850, upload-time = "2025-10-15T18:24:11.495Z" },
]
+[[package]]
+name = "prompt-toolkit"
+version = "3.0.52"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "wcwidth" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/a1/96/06e01a7b38dce6fe1db213e061a4602dd6032a8a97ef6c1a862537732421/prompt_toolkit-3.0.52.tar.gz", hash = "sha256:28cde192929c8e7321de85de1ddbe736f1375148b02f2e17edd840042b1be855", size = 434198, upload-time = "2025-08-27T15:24:02.057Z" }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/84/03/0d3ce49e2505ae70cf43bc5bb3033955d2fc9f932163e84dc0779cc47f48/prompt_toolkit-3.0.52-py3-none-any.whl", hash = "sha256:9aac639a3bbd33284347de5ad8d68ecc044b91a762dc39b7c21095fcd6a19955", size = 391431, upload-time = "2025-08-27T15:23:59.498Z" },
+]
+
[[package]]
name = "pyasn1"
version = "0.6.1"
@@ -1859,6 +1872,18 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/f1/12/de94a39c2ef588c7e6455cfbe7343d3b2dc9d6b6b2f40c4c6565744c873d/pyyaml-6.0.3-cp314-cp314t-win_arm64.whl", hash = "sha256:ebc55a14a21cb14062aa4162f906cd962b28e2e9ea38f9b4391244cd8de4ae0b", size = 149341, upload-time = "2025-09-25T21:32:56.828Z" },
]
+[[package]]
+name = "questionary"
+version = "2.1.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "prompt-toolkit" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/f6/45/eafb0bba0f9988f6a2520f9ca2df2c82ddfa8d67c95d6625452e97b204a5/questionary-2.1.1.tar.gz", hash = "sha256:3d7e980292bb0107abaa79c68dd3eee3c561b83a0f89ae482860b181c8bd412d", size = 25845, upload-time = "2025-08-28T19:00:20.851Z" }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/3c/26/1062c7ec1b053db9e499b4d2d5bc231743201b74051c973dadeac80a8f43/questionary-2.1.1-py3-none-any.whl", hash = "sha256:a51af13f345f1cdea62347589fbb6df3b290306ab8930713bfae4d475a7d4a59", size = 36753, upload-time = "2025-08-28T19:00:19.56Z" },
+]
+
[[package]]
name = "requests"
version = "2.32.5"
@@ -1948,6 +1973,8 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/6b/fa/3234f913fe9a6525a7b97c6dad1f51e72b917e6872e051a5e2ffd8b16fbb/ruamel.yaml.clib-0.2.14-cp314-cp314-macosx_15_0_arm64.whl", hash = "sha256:70eda7703b8126f5e52fcf276e6c0f40b0d314674f896fc58c47b0aef2b9ae83", size = 137970, upload-time = "2025-09-22T19:51:09.472Z" },
{ url = "https://files.pythonhosted.org/packages/ef/ec/4edbf17ac2c87fa0845dd366ef8d5852b96eb58fcd65fc1ecf5fe27b4641/ruamel.yaml.clib-0.2.14-cp314-cp314-musllinux_1_2_i686.whl", hash = "sha256:a0cb71ccc6ef9ce36eecb6272c81afdc2f565950cdcec33ae8e6cd8f7fc86f27", size = 739639, upload-time = "2025-09-22T19:51:10.566Z" },
{ url = "https://files.pythonhosted.org/packages/15/18/b0e1fafe59051de9e79cdd431863b03593ecfa8341c110affad7c8121efc/ruamel.yaml.clib-0.2.14-cp314-cp314-musllinux_1_2_x86_64.whl", hash = "sha256:e7cb9ad1d525d40f7d87b6df7c0ff916a66bc52cb61b66ac1b2a16d0c1b07640", size = 764456, upload-time = "2025-09-22T19:51:11.736Z" },
+ { url = "https://files.pythonhosted.org/packages/e7/cd/150fdb96b8fab27fe08d8a59fe67554568727981806e6bc2677a16081ec7/ruamel_yaml_clib-0.2.14-cp314-cp314-win32.whl", hash = "sha256:9b4104bf43ca0cd4e6f738cb86326a3b2f6eef00f417bd1e7efb7bdffe74c539", size = 102394, upload-time = "2025-11-14T21:57:36.703Z" },
+ { url = "https://files.pythonhosted.org/packages/bd/e6/a3fa40084558c7e1dc9546385f22a93949c890a8b2e445b2ba43935f51da/ruamel_yaml_clib-0.2.14-cp314-cp314-win_amd64.whl", hash = "sha256:13997d7d354a9890ea1ec5937a219817464e5cc344805b37671562a401ca3008", size = 122673, upload-time = "2025-11-14T21:57:38.177Z" },
]
[[package]]
@@ -2307,6 +2334,15 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/a7/c2/fe1e52489ae3122415c51f387e221dd0773709bad6c6cdaa599e8a2c5185/urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc", size = 129795, upload-time = "2025-06-18T14:07:40.39Z" },
]
+[[package]]
+name = "wcwidth"
+version = "0.2.14"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/24/30/6b0809f4510673dc723187aeaf24c7f5459922d01e2f794277a3dfb90345/wcwidth-0.2.14.tar.gz", hash = "sha256:4d478375d31bc5395a3c55c40ccdf3354688364cd61c4f6adacaa9215d0b3605", size = 102293, upload-time = "2025-09-22T16:29:53.023Z" }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/af/b5/123f13c975e9f27ab9c0770f514345bd406d0e8d3b7a0723af9d43f710af/wcwidth-0.2.14-py2.py3-none-any.whl", hash = "sha256:a7bb560c8aee30f9957e5f9895805edd20602f2d7f720186dfd906e82b4982e1", size = 37286, upload-time = "2025-09-22T16:29:51.641Z" },
+]
+
[[package]]
name = "winkerberos"
version = "0.12.2"
From c1a5b7cb3ff6e1533a0eb93ec4c15736f6dc9528 Mon Sep 17 00:00:00 2001
From: bruno-f-cruz <7049351+bruno-f-cruz@users.noreply.github.com>
Date: Mon, 17 Nov 2025 14:49:25 -0800
Subject: [PATCH 18/19] Remove broken submodule FIP_DAQ_Control
---
src/Platforms/FIP_DAQ_Control | 1 -
.../FIP_DAQ_Control/.config/dotnet-tools.json | 12 +
src/Platforms/FIP_DAQ_Control/.gitattributes | 4 +
.../.github/workflows/aind-physio-fip.yml | 327 +++
src/Platforms/FIP_DAQ_Control/.gitignore | 93 +
src/Platforms/FIP_DAQ_Control/.python-version | 3 +
src/Platforms/FIP_DAQ_Control/LICENSE | 21 +
src/Platforms/FIP_DAQ_Control/README.md | 179 ++
.../assets/images/fip_light_path.png | Bin 0 -> 9247 bytes
.../FIP_DAQ_Control/bonsai/Bonsai.config | 235 ++
.../FIP_DAQ_Control/bonsai/NuGet.config | 6 +
.../FIP_DAQ_Control/bonsai/setup.cmd | 1 +
.../FIP_DAQ_Control/bonsai/setup.ps1 | 20 +
src/Platforms/FIP_DAQ_Control/docs/Makefile | 20 +
.../docs/_static/dark-logo.svg | 129 +
.../FIP_DAQ_Control/docs/_static/favicon.ico | Bin 0 -> 259838 bytes
.../docs/_static/light-logo.svg | 128 +
.../FIP_DAQ_Control/docs/api.rig.rst | 7 +
src/Platforms/FIP_DAQ_Control/docs/api.rst | 7 +
.../FIP_DAQ_Control/docs/api.session.rst | 7 +
src/Platforms/FIP_DAQ_Control/docs/conf.py | 82 +
src/Platforms/FIP_DAQ_Control/docs/index.rst | 21 +
.../FIP_DAQ_Control/docs/json-schemas.rst | 12 +
src/Platforms/FIP_DAQ_Control/docs/make.bat | 35 +
.../examples/AindBehaviorSessionModel.json | 18 +
.../examples/AindPhysioFipRig.json | 205 ++
.../FIP_DAQ_Control/examples/example.py | 98 +
src/Platforms/FIP_DAQ_Control/pyproject.toml | 67 +
.../FIP_DAQ_Control/scripts/deploy.cmd | 1 +
.../FIP_DAQ_Control/scripts/deploy.ps1 | 27 +
.../src/DataSchemas/aind_physiology_fip.json | 804 ++++++
.../FIP_DAQ_Control/src/Extensions.csproj | 22 +
.../Extensions/AindPhysiologyFip.Generated.cs | 2380 +++++++++++++++++
.../src/Extensions/AindPhysiologyFip.cs | 11 +
.../src/Extensions/CircleActivity.cs | 49 +
.../Extensions/CircleActivityCalculator.cs | 164 ++
.../Extensions/CircleActivityCollection.cs | 21 +
.../CircleArrayDistinctUntilChanged.cs | 34 +
.../src/Extensions/CircleRoiConverter.cs | 111 +
.../Extensions/CreateTaskFromLightSource.cs | 70 +
.../src/Extensions/FipFrame.cs | 35 +
.../src/Extensions/FipLogger.bonsai | 93 +
.../src/Extensions/FipSignalVisualizer.cs | 282 ++
.../src/Extensions/FipSpinnakerCapture.cs | 91 +
.../src/Extensions/FipWriter.cs | 168 ++
.../src/Extensions/FlipFipFrame.cs | 63 +
.../src/Extensions/ImageEllipsePicker.cs | 391 +++
.../src/Extensions/Licenses.md | 25 +
.../src/Extensions/LoadRoiDefault.cs | 74 +
.../src/Extensions/Logging.bonsai | 540 ++++
.../src/Extensions/ModifyFipCameraSource.cs | 36 +
.../src/Extensions/PascalToSnake.cs | 28 +
.../src/Extensions/ReadSchemas.bonsai | 46 +
.../src/Extensions/SelectCircles.cs | 82 +
.../src/Extensions/SelectCirclesVisualizer.cs | 145 +
.../src/Extensions/ToFipFrame.cs | 22 +
.../src/Extensions/Visualization.bonsai | 2158 +++++++++++++++
.../src/aind_physiology_fip/__init__.py | 30 +
.../src/aind_physiology_fip/cli.py | 42 +
.../src/aind_physiology_fip/data_contract.py | 165 ++
.../src/aind_physiology_fip/data_qc.py | 360 +++
.../aind_physiology_fip/data_qc_helpers.py | 37 +
.../src/aind_physiology_fip/regenerate.py | 34 +
.../src/aind_physiology_fip/rig.py | 143 +
src/Platforms/FIP_DAQ_Control/src/main.bonsai | 2326 ++++++++++++++++
.../src/test_deserialization.bonsai | 52 +
.../FIP_DAQ_Control/tests/__init__.py | 29 +
.../FIP_DAQ_Control/tests/test_bonsai.py | 108 +
.../FIP_DAQ_Control/tests/test_examples.py | 24 +
src/Platforms/FIP_DAQ_Control/uv.lock | 1722 ++++++++++++
70 files changed, 14782 insertions(+), 1 deletion(-)
delete mode 160000 src/Platforms/FIP_DAQ_Control
create mode 100644 src/Platforms/FIP_DAQ_Control/.config/dotnet-tools.json
create mode 100644 src/Platforms/FIP_DAQ_Control/.gitattributes
create mode 100644 src/Platforms/FIP_DAQ_Control/.github/workflows/aind-physio-fip.yml
create mode 100644 src/Platforms/FIP_DAQ_Control/.gitignore
create mode 100644 src/Platforms/FIP_DAQ_Control/.python-version
create mode 100644 src/Platforms/FIP_DAQ_Control/LICENSE
create mode 100644 src/Platforms/FIP_DAQ_Control/README.md
create mode 100644 src/Platforms/FIP_DAQ_Control/assets/images/fip_light_path.png
create mode 100644 src/Platforms/FIP_DAQ_Control/bonsai/Bonsai.config
create mode 100644 src/Platforms/FIP_DAQ_Control/bonsai/NuGet.config
create mode 100644 src/Platforms/FIP_DAQ_Control/bonsai/setup.cmd
create mode 100644 src/Platforms/FIP_DAQ_Control/bonsai/setup.ps1
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/Makefile
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/_static/dark-logo.svg
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/_static/favicon.ico
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/_static/light-logo.svg
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/api.rig.rst
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/api.rst
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/api.session.rst
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/conf.py
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/index.rst
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/json-schemas.rst
create mode 100644 src/Platforms/FIP_DAQ_Control/docs/make.bat
create mode 100644 src/Platforms/FIP_DAQ_Control/examples/AindBehaviorSessionModel.json
create mode 100644 src/Platforms/FIP_DAQ_Control/examples/AindPhysioFipRig.json
create mode 100644 src/Platforms/FIP_DAQ_Control/examples/example.py
create mode 100644 src/Platforms/FIP_DAQ_Control/pyproject.toml
create mode 100644 src/Platforms/FIP_DAQ_Control/scripts/deploy.cmd
create mode 100644 src/Platforms/FIP_DAQ_Control/scripts/deploy.ps1
create mode 100644 src/Platforms/FIP_DAQ_Control/src/DataSchemas/aind_physiology_fip.json
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions.csproj
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/AindPhysiologyFip.Generated.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/AindPhysiologyFip.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/CircleActivity.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/CircleActivityCalculator.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/CircleActivityCollection.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/CircleArrayDistinctUntilChanged.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/CircleRoiConverter.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/CreateTaskFromLightSource.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/FipFrame.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/FipLogger.bonsai
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/FipSignalVisualizer.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/FipSpinnakerCapture.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/FipWriter.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/FlipFipFrame.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/ImageEllipsePicker.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/Licenses.md
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/LoadRoiDefault.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/Logging.bonsai
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/ModifyFipCameraSource.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/PascalToSnake.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/ReadSchemas.bonsai
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/SelectCircles.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/SelectCirclesVisualizer.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/ToFipFrame.cs
create mode 100644 src/Platforms/FIP_DAQ_Control/src/Extensions/Visualization.bonsai
create mode 100644 src/Platforms/FIP_DAQ_Control/src/aind_physiology_fip/__init__.py
create mode 100644 src/Platforms/FIP_DAQ_Control/src/aind_physiology_fip/cli.py
create mode 100644 src/Platforms/FIP_DAQ_Control/src/aind_physiology_fip/data_contract.py
create mode 100644 src/Platforms/FIP_DAQ_Control/src/aind_physiology_fip/data_qc.py
create mode 100644 src/Platforms/FIP_DAQ_Control/src/aind_physiology_fip/data_qc_helpers.py
create mode 100644 src/Platforms/FIP_DAQ_Control/src/aind_physiology_fip/regenerate.py
create mode 100644 src/Platforms/FIP_DAQ_Control/src/aind_physiology_fip/rig.py
create mode 100644 src/Platforms/FIP_DAQ_Control/src/main.bonsai
create mode 100644 src/Platforms/FIP_DAQ_Control/src/test_deserialization.bonsai
create mode 100644 src/Platforms/FIP_DAQ_Control/tests/__init__.py
create mode 100644 src/Platforms/FIP_DAQ_Control/tests/test_bonsai.py
create mode 100644 src/Platforms/FIP_DAQ_Control/tests/test_examples.py
create mode 100644 src/Platforms/FIP_DAQ_Control/uv.lock
diff --git a/src/Platforms/FIP_DAQ_Control b/src/Platforms/FIP_DAQ_Control
deleted file mode 160000
index 7791f296..00000000
--- a/src/Platforms/FIP_DAQ_Control
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 7791f296469cdafbf38e2d329f90a96ae5f1bc4a
diff --git a/src/Platforms/FIP_DAQ_Control/.config/dotnet-tools.json b/src/Platforms/FIP_DAQ_Control/.config/dotnet-tools.json
new file mode 100644
index 00000000..44b1c27d
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/.config/dotnet-tools.json
@@ -0,0 +1,12 @@
+{
+ "version": 1,
+ "isRoot": true,
+ "tools": {
+ "bonsai.sgen": {
+ "version": "0.6.1",
+ "commands": [
+ "bonsai.sgen"
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/.gitattributes b/src/Platforms/FIP_DAQ_Control/.gitattributes
new file mode 100644
index 00000000..d2d3c413
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/.gitattributes
@@ -0,0 +1,4 @@
+* text=auto
+*.cmd text eol=crlf
+*.bat text eol=crlf
+*.bonsai text
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/.github/workflows/aind-physio-fip.yml b/src/Platforms/FIP_DAQ_Control/.github/workflows/aind-physio-fip.yml
new file mode 100644
index 00000000..9d08e51f
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/.github/workflows/aind-physio-fip.yml
@@ -0,0 +1,327 @@
+name: FIP test suite
+
+on:
+ workflow_dispatch:
+ inputs:
+ bump_type:
+ description: "Version bump type"
+ required: false
+ default: "rc"
+ type: choice
+ options:
+ - rc
+ - patch
+ - minor
+ - major
+ - stable
+ pull_request:
+ push:
+ branches:
+ - main
+ - dev*
+ - release*
+ release:
+ types: [published]
+
+jobs:
+ # ╔──────────────────────────╗
+ # │ _____ _ │
+ # │ |_ _|__ ___| |_ ___ │
+ # │ | |/ _ \/ __| __/ __| │
+ # │ | | __/\__ \ |_\__ \ │
+ # │ |_|\___||___/\__|___/ │
+ # │ │
+ # ╚──────────────────────────╝
+ tests:
+ runs-on: windows-latest
+ name: FIP 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 fip regenerate
+
+ - name: Check for uncommitted changes
+ run: |
+ git config --global core.safecrlf false
+ git diff --exit-code || (echo "Untracked changes found" && exit 1)
+
+ # ╔───────────────────────────────────────────────────────────╗
+ # │ ____ ___ ____ ____ ____ _ │
+ # │ / ___|_ _/ ___| _ \ | _ \ ___| | ___ __ _ ___ ___ │
+ # │ | | | | | | | | | | |_) / _ \ |/ _ \/ _` / __|/ _ \ │
+ # │ | |___ | | |___| |_| | | _ < __/ | __/ (_| \__ \ __/ │
+ # │ \____|___\____|____/ |_| \_\___|_|\___|\__,_|___/\___| │
+ # │ │
+ # ╚───────────────────────────────────────────────────────────╝
+ github-rc-release:
+ needs: tests
+ runs-on: windows-latest
+ if: >
+ github.ref == 'refs/heads/main' &&
+ github.event_name == 'push' &&
+ github.event.head_commit.author.email != 'github-actions[bot]@users.noreply.github.com'
+ name: Create GitHub pre-release
+ steps:
+ - uses: actions/checkout@v5
+ with:
+ fetch-depth: 0
+ ref: main
+
+ - uses: astral-sh/setup-uv@v6
+ with:
+ enable-cache: true
+
+ - name: Bump pre-release by default
+ # Note: Bumping the rc will fail if the version is not currently an rc
+ # To solve it, we bump the patch and rc atomically
+ shell: bash # interop with win/linux for if statement
+ run: |
+ if uv version --bump rc --dry-run; then
+ uv version --bump rc
+ else
+ uv version --bump rc --bump patch
+ fi
+
+ - name: Regenerate schemas
+ run: uv run fip regenerate
+
+ - name: Regenerate examples
+ run: uv run ./examples/example.py --path-seed "./examples/{schema}.json"
+
+ - name: Commit version and schema changes
+ run: |
+ git config --global user.name "github-actions[bot]"
+ git config --global user.email "github-actions[bot]@users.noreply.github.com"
+ git add .
+ git commit -m "Bump version and regenerate schemas [skip ci]" || echo "No changes to commit"
+ git push origin main
+
+ - name: Get version
+ id: get_version
+ shell: bash
+ run: |
+ version=$(uv version --short)
+ echo "version=$version" >> $GITHUB_OUTPUT
+
+ - name: Create GitHub Release
+ uses: softprops/action-gh-release@v2
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ with:
+ tag_name: v${{ steps.get_version.outputs.version }}
+ name: v${{ steps.get_version.outputs.version }}
+ generate_release_notes: true
+ prerelease: true
+ body: |
+ Automated pre-release v${{ steps.get_version.outputs.version }}
+
+ # ╔─────────────────────────────────────────────────────────────────╗
+ # │ ____ _ _ _ ____ _ │
+ # │ | _ \ _ _| |__ | (_) ___ | _ \ ___| | ___ __ _ ___ ___ │
+ # │ | |_) | | | | '_ \| | |/ __| | |_) / _ \ |/ _ \/ _` / __|/ _ \ │
+ # │ | __/| |_| | |_) | | | (__ | _ < __/ | __/ (_| \__ \ __/ │
+ # │ |_| \__,_|_.__/|_|_|\___| |_| \_\___|_|\___|\__,_|___/\___| │
+ # │ │
+ # ╚─────────────────────────────────────────────────────────────────╝
+
+ prepare-public-release:
+ runs-on: windows-latest
+ name: Prepare files for public release
+ needs: tests
+ if: github.event_name == 'workflow_dispatch'
+ outputs:
+ version: ${{ steps.get_version.outputs.version }}
+ is_prerelease: ${{ steps.check_prerelease.outputs.prerelease }}
+ steps:
+ - uses: actions/checkout@v5
+ with:
+ fetch-depth: 0
+ ref: main
+
+ - uses: astral-sh/setup-uv@v6
+ with:
+ enable-cache: true
+
+ - name: Get target version
+ id: get_version
+ shell: bash
+ run: |
+ # Use bump type from input (defaults to rc)
+ bump_type="${{ github.event.inputs.bump_type || 'rc' }}"
+ echo "Bumping version with type: $bump_type"
+
+ # Handle version bumping based on type
+ if [[ "$bump_type" == "rc" ]]; then
+ # Handle rc bumping logic (same as in github-rc-release)
+ if uv version --bump rc --dry-run; then
+ uv version --bump rc
+ else
+ uv version --bump rc --bump patch
+ fi
+ else
+ # Handle patch, minor, major, stable
+ uv version --bump $bump_type
+ fi
+
+ release_version=$(uv run uv version --short)
+ echo "version=$release_version" >> $GITHUB_OUTPUT
+ echo "Release version will be: $release_version"
+
+ - name: Validate version format
+ run: uv version ${{ steps.get_version.outputs.version }} --dry-run
+
+ - name: Update package version
+ run: uv version ${{ steps.get_version.outputs.version }}
+
+ - name: Regenerate schemas
+ run: uv run fip regenerate
+
+ - name: Regenerate examples
+ run: uv run ./examples/example.py --path-seed "./examples/{schema}.json"
+
+ - name: Commit version, schema changes and create tag
+ run: |
+ git config --global user.name "github-actions[bot]"
+ git config --global user.email "github-actions[bot]@users.noreply.github.com"
+ git add .
+ git commit -m "v${{ steps.get_version.outputs.version }} [skip ci]"
+ git tag -a "v${{ steps.get_version.outputs.version }}" -m "Release v${{ steps.get_version.outputs.version }}"
+ git push origin main
+ git push origin "v${{ steps.get_version.outputs.version }}"
+
+ - name: Determine if prerelease
+ id: check_prerelease
+ shell: bash
+ run: |
+ version="${{ steps.get_version.outputs.version }}"
+ if [[ "$version" == *"rc"* ]]; then
+ echo "prerelease=true" >> $GITHUB_OUTPUT
+ else
+ echo "prerelease=false" >> $GITHUB_OUTPUT
+ fi
+
+ - name: Create GitHub Release
+ uses: softprops/action-gh-release@v2
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ with:
+ tag_name: v${{ steps.get_version.outputs.version }}
+ name: Release v${{ steps.get_version.outputs.version }}
+ generate_release_notes: true
+ prerelease: ${{ steps.check_prerelease.outputs.prerelease }}
+ body: |
+ Release v${{ steps.get_version.outputs.version }}
+
+ This release was manually triggered.
+
+ publish-to-pypi:
+ runs-on: windows-latest
+ name: Publish to PyPI
+ needs: [tests, prepare-public-release]
+ if: |
+ (github.event_name == 'workflow_dispatch') ||
+ (github.event_name == 'release' &&
+ github.event.action == 'published' &&
+ !github.event.release.prerelease &&
+ startsWith(github.ref, 'refs/tags/v'))
+ steps:
+ - uses: actions/checkout@v5
+ with:
+ fetch-depth: 0
+ ref: ${{ github.event_name == 'workflow_dispatch' && 'main' || github.ref_name }}
+
+ - uses: astral-sh/setup-uv@v6
+ with:
+ enable-cache: true
+
+ - name: Verify version consistency (for automatic releases)
+ if: github.event_name == 'release'
+ shell: bash
+ run: |
+ tag_version=$(echo "${{ github.ref_name }}" | sed 's/^v//')
+ package_version=$(uv run uv version --short)
+ if [[ "$tag_version" != "$package_version" ]]; then
+ echo "ERROR: Tag version ($tag_version) doesn't match package version ($package_version)"
+ exit 1
+ fi
+ echo "✅ Version consistency verified: $tag_version"
+
+ - name: Get current version (for manual releases)
+ if: github.event_name == 'workflow_dispatch'
+ shell: bash
+ run: |
+ package_version=$(uv run uv version --short)
+ echo "📦 Publishing version: $package_version"
+
+ - name: Build
+ run: uv build
+
+ - name: Publish to PyPI
+ run: uv publish --token ${{ secrets.AIND_PYPI_TOKEN }}
+
+ # ╔─────────────────────────╗
+ # │ ____ │
+ # │ | _ \ ___ ___ ___ │
+ # │ | | | |/ _ \ / __/ __| │
+ # │ | |_| | (_) | (__\__ \ │
+ # │ |____/ \___/ \___|___/ │
+ # │ │
+ # ╚─────────────────────────╝
+ build-docs:
+ name: Build and deploy documentation to GitHub Pages
+ runs-on: ubuntu-latest
+ needs: publish-to-pypi
+ 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: ${{ secrets.GITHUB_TOKEN }}
+ publish_dir: _build/html
+ force_orphan: true
diff --git a/src/Platforms/FIP_DAQ_Control/.gitignore b/src/Platforms/FIP_DAQ_Control/.gitignore
new file mode 100644
index 00000000..80053829
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/.gitignore
@@ -0,0 +1,93 @@
+# Bonsai scripting files
+.vs
+.vscode
+bin
+obj
+Packages
+Bonsai.exe.WebView2
+*.bin
+*.avi
+*.dll
+*.exe
+*.exe.settings
+*.bonsai.layout
+local
+*.snl
+bonsai/settings/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Sphinx documentation
+docs/_build/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+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
diff --git a/src/Platforms/FIP_DAQ_Control/.python-version b/src/Platforms/FIP_DAQ_Control/.python-version
new file mode 100644
index 00000000..06c7113d
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/.python-version
@@ -0,0 +1,3 @@
+3.11
+3.12
+3.13
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/LICENSE b/src/Platforms/FIP_DAQ_Control/LICENSE
new file mode 100644
index 00000000..df0d99bd
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Allen Institute for Neural Dynamics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/src/Platforms/FIP_DAQ_Control/README.md b/src/Platforms/FIP_DAQ_Control/README.md
new file mode 100644
index 00000000..6429384a
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/README.md
@@ -0,0 +1,179 @@
+# Fiber Photometry System Configuration
+
+
+
+[](LICENSE)
+[](https://github.com/astral-sh/ruff)
+[](https://github.com/astral-sh/uv)
+
+For FIP photometry data acquisition and hardware control.
+
+## Overview
+
+The FIP (Frame-projected Independent Photometry) system is a low-cost, scalable photometry setup designed for chronic recording of optical signals from behaving mice during daily training. The system is based on a modified design of Frame-projected Independent Photometry (Kim et al., 2016), using inexpensive, commercially available, off-the-shelf components.
+
+
+
+For more information, see the [AIND Fiber Photometry Platform Page](https://www.allenneuraldynamics.org/platforms/fiber-photometry) and the following protocols:
+
+* Protocol for system assembly:
+* Protocol for system triggering setup:
+
+## Wavelength Information
+
+The table below summarizes the photometry system's optical configuration, showing the relationship between emission channels and their corresponding excitation sources.
+
+| Excitation | | | | Emission | | |
+|------------------|---------------------|--------------|---|------------------|----------------------|-------------------|
+| **Name** | **Wavelength (nm)** | **Led Name** | | **name** | **Wavelength (nm)** | **Detector Name** |
+| Yellow | 565 | 565 nm LED | | Red | ~590 (peak) | Red CMOS |
+| Blue | 470 | 470 nm LED | | Green | ~510 (peak) | Green CMOS |
+| UV | 415 | 415 nm LED | | Isosbestic | 490-540 (passband) | Green CMOS |
+
+## Signal Detection
+
+* **Green Channel**: Primarily used for green GFP based indicators
+* **Red Channel**: Primarily used for RFP-based indicators (e.g., RdLight)
+* **Isosbestic Channel**: Used as a control measurement; shares same emission path as green but with different excitation
+
+The system uses dedicated CMOS cameras for the red and green emissions, with the isosbestic signal being captured by the green camera under different excitation conditions.
+
+## Temporal Multiplexing
+
+The system employs temporal multiplexing to acquire signals from multiple fluorescent indicators through the same optical fiber. This is achieved by rapidly cycling through different excitation wavelengths while synchronizing camera acquisitions:
+
+```
+ --->| |<--- period = 16.67 ms
+Blue LED(470) ████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░
+
+UV LED (415) ░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░
+
+Yellow LED (560)░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░
+
+Green CMOS ████░████░░░░░░████░████░░░░░░████░████░░░░░░████░████░░░░░░████░████░░░░░░ (captures 470/415)
+Red CMOS ░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░░░░░░░░░░░████░ (captures 560)
+ ───────────────────────────────────────────────────────────────────────────►
+ Time
+```
+
+The temporal multiplexing sequence:
+
+1. Blue LED (470nm) excitation -> Green CMOS camera captures signal from GFP-based sensors
+2. UV LED (415nm) excitation -> Green CMOS camera captures isosbestic signal
+3. Yellow LED (560nm) excitation -> Red CMOS camera captures signal from RFP-based sensors
+
+This cycling occurs at 60 Hz, allowing near-simultaneous measurement of multiple signals while preventing crosstalk between channels. Each LED is activated in sequence and cameras are synchronized to capture data only during their respective LED's ON period.
+
+## Using the acquisition system
+
+See [wiki](https://github.com/AllenNeuralDynamics/FIP_DAQ_Control/wiki) for AIND internal installation instructions.
+
+### Pre-requisites (some of these are optional, but recommended for a smoother experience)
+
+* [Visual Studio Code](https://code.visualstudio.com/) (highly recommended for editing code scripts and git commits)
+* [Git for Windows](https://gitforwindows.org/) (highly recommended for cloning and manipulating this repository)
+* [.NET Framework 4.7.2 Developer Pack](https://dotnet.microsoft.com/download/dotnet-framework/thank-you/net472-developer-pack-offline-installer) (required for intellisense when editing code scripts)
+* [Visual C++ Redistributable for Visual Studio 2012](https://www.microsoft.com/en-us/download/details.aspx?id=30679) (native dependency for OpenCV)
+* [Spinnaker SDK 1.29.0.5](https://www.teledynevisionsolutions.com/support/support-center/software-firmware-downloads/iis/spinnaker-sdk-download/spinnaker-sdk--download-files/#anchor6) (device drivers for FLIR cameras)
+ * On FLIR website: `Download > archive > 1.29.0.5 > SpinnakerSDK_FULL_1.29.0.5_x64.exe`
+* [Optional] [UV Python environment manager](https://docs.astral.sh/uv/getting-started/installation/) (highly recommended for managing the Python environment for this project. All examples will assume usage of `uv`. Alternatively, you can use other environment managers such as `venv` or `conda` to create a Python environment and install the required dependencies listed in the package metadata: `pyproject.toml`)
+
+### Installation Steps
+
+1. Clone this repository
+2. Create the environments for Bonsai, run `./bonsai/setup.cmd` (can be by double-clickin it too). This is required to run experiments using the Bonsai script in an experimental PC.
+3. [Optional] Create the environments for Python, run `uv venv` if using uv, or create a virtual environment using your preferred method. This is only used to run the Python script generating configuration files. (rig PCs can inherit those files from somewhere else)
+ * Alternatively, if you are using uv, run `./scripts/deploy.ps1` to bootstrap a Python and Bonsai environment at the same time for the project automatically.
+
+### Generating input configurations [Optional]
+
+The current pipeline relies on two input configuration files. These configure the rig/instruments and session parameters, respectively. These files are formalized as pydantic models as shown in `./examples/examples.py`. Template configuration files are included in the `./examples/` folder, and running the `examples.py` will create configuration files into `./local/`
+
+Briefly:
+
+```python
+from aind_behavior_services.session import AindBehaviorSessionModel
+from aind_physiology_fip.rig import AindPhysioFipRig
+
+this_rig = AindPhysioFipRig(...)
+this_session = AindBehaviorSessionModel(...)
+
+for model in [this_session, this_rig]:
+ with open(model.__class__.__name__ + ".json", "w", encoding="utf-8") as f:
+ f.write(model.model_dump_json(indent=2))
+```
+
+### Running the acquisition
+
+#### Running manually
+
+Acquisition is done through Bonsai via a single entry-point workflow. As any Bonsai workflow, one can run the acquisition workflow via the editor:
+
+* Open Bonsai from the bootstrapped environment in `./bonsai/bonsai.exe`
+* Open the workflow file `./src/main.bonsai`
+* Manually set the two highest level properties `RigPath` and `SessionPath` to the paths of the configuration files generated in the [previous step](#generating-input-configurations).
+* Launch the workflow by clicking the "Run" button in the Bonsai editor.
+* Settings in FipRig.json such as `camera_green_iso` `serial_number` and `cuttlefish_fip` `port_name` needs to be modified per PC for Bonsai to detect those hardware.
+
+> [!Important]
+> `AindBehaviorSessionModel.allow_dirty` property will be checked at the start of the workflow. If set to `False` the workflow will immediately throw an error and stop execution if the repository has uncommitted changes. If the user intends to run the workflow with a dirty repository, they should set this property to `True` in the session configuration file.
+
+#### Running via CLI
+
+The workflow can be launched via the Bonsai Command Line Interface (CLI). Additional documentation on the CLI can be found [here](https://bonsai-rx.org/docs/articles/cli.html).
+To run the acquisition workflow using the CLI, use the following command:
+
+```bash
+"./bonsai/bonsai.exe" "./src/main.bonsai" -p RigPath="../path/to/rig.json" -p SessionPath="../path/to/session.json"
+```
+
+> [!Note]
+> The paths to the configuration file are relative to the workflow working directory (i.e. `./src/`)
+
+Additional flags can be passed to automatically start the workflow (`--start`) or run in headless mode (`--no-editor`) as stated in the Bonsai CLI documentation.
+
+#### Acquiring data
+
+Once the workflow is running, a UI will pop up and users can start acquisition by clicking `Start`. The system will then begin to acquire data from the cameras and store it in the specified session directory. Once the session is ready to stop, users can click `Stop` in the UI. The system will then save the session data and stop/close the workflow.
+
+## Contributors
+
+Contributions to this repository are welcome! However, please ensure that your code adheres to the recommended DevOps practices below:
+
+### Linting
+
+We use [ruff](https://docs.astral.sh/ruff/) as our primary linting tool:.
+
+```bash
+ uv run ruff format .
+ uv run ruff check .
+```
+
+### Testing
+
+Attempt to add tests when new features are added.
+To run the currently available tests, run `uv run python -m unittest` from the root of the repository.
+
+### Lock files
+
+We use [uv](https://docs.astral.sh/uv/) to manage our lock files and therefore encourage everyone to use uv as a package manager as well.
+
+## CLI
+
+The package provides a command line interface (CLI) to facilitate common tasks. The CLI can be accessed by running the following command from the root of the repository:
+
+```bash
+ uv run fip [options]
+```
+
+For a list of available subcommands and options, run:
+
+```bash
+ uv run fip --help
+```
+
+(If you are not using `uv`, activate your python environment and run the `fip` tool directly.)
+
+## Regenerating schemas
+
+Instructions for regenerating schemas can be found [here](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services?tab=readme-ov-file#regenerating-schemas).
diff --git a/src/Platforms/FIP_DAQ_Control/assets/images/fip_light_path.png b/src/Platforms/FIP_DAQ_Control/assets/images/fip_light_path.png
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\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/bonsai/NuGet.config b/src/Platforms/FIP_DAQ_Control/bonsai/NuGet.config
new file mode 100644
index 00000000..bf53ec14
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/bonsai/NuGet.config
@@ -0,0 +1,6 @@
+
+
+
+
+
+
diff --git a/src/Platforms/FIP_DAQ_Control/bonsai/setup.cmd b/src/Platforms/FIP_DAQ_Control/bonsai/setup.cmd
new file mode 100644
index 00000000..3c53f3a9
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/bonsai/setup.cmd
@@ -0,0 +1 @@
+powershell -ExecutionPolicy Bypass -File .\setup.ps1
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/bonsai/setup.ps1 b/src/Platforms/FIP_DAQ_Control/bonsai/setup.ps1
new file mode 100644
index 00000000..217c7197
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/bonsai/setup.ps1
@@ -0,0 +1,20 @@
+Push-Location $PSScriptRoot
+if (!(Test-Path "./Bonsai.exe")) {
+ $release = "https://github.com/bonsai-rx/bonsai/releases/latest/download/Bonsai.zip"
+ $configPath = "./Bonsai.config"
+ if (Test-Path $configPath) {
+ [xml]$config = Get-Content $configPath
+ $bootstrapper = $config.PackageConfiguration.Packages.Package.where{$_.id -eq 'Bonsai'}
+ if ($bootstrapper) {
+ $version = $bootstrapper.version
+ $release = "https://github.com/bonsai-rx/bonsai/releases/download/$version/Bonsai.zip"
+ }
+ }
+ Invoke-WebRequest $release -OutFile "temp.zip"
+ Move-Item -Path "NuGet.config" "temp.config" -ErrorAction SilentlyContinue
+ Expand-Archive "temp.zip" -DestinationPath "." -Force
+ Move-Item -Path "temp.config" "NuGet.config" -Force -ErrorAction SilentlyContinue
+ Remove-Item -Path "temp.zip"
+}
+& .\Bonsai.exe --no-editor
+Pop-Location
diff --git a/src/Platforms/FIP_DAQ_Control/docs/Makefile b/src/Platforms/FIP_DAQ_Control/docs/Makefile
new file mode 100644
index 00000000..d4bb2cbb
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/src/Platforms/FIP_DAQ_Control/docs/_static/dark-logo.svg b/src/Platforms/FIP_DAQ_Control/docs/_static/dark-logo.svg
new file mode 100644
index 00000000..dcc68fb1
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/_static/dark-logo.svg
@@ -0,0 +1,129 @@
+
+
+
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+
+
diff --git a/src/Platforms/FIP_DAQ_Control/docs/api.rig.rst b/src/Platforms/FIP_DAQ_Control/docs/api.rig.rst
new file mode 100644
index 00000000..583f4265
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/api.rig.rst
@@ -0,0 +1,7 @@
+api.rig
+-------------
+
+.. automodule:: aind_physiology_fip.rig
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/src/Platforms/FIP_DAQ_Control/docs/api.rst b/src/Platforms/FIP_DAQ_Control/docs/api.rst
new file mode 100644
index 00000000..b0b82857
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/api.rst
@@ -0,0 +1,7 @@
+api
+-------------
+.. toctree::
+ :maxdepth: 2
+
+ api.session
+ api.rig
diff --git a/src/Platforms/FIP_DAQ_Control/docs/api.session.rst b/src/Platforms/FIP_DAQ_Control/docs/api.session.rst
new file mode 100644
index 00000000..88b54f51
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/api.session.rst
@@ -0,0 +1,7 @@
+api.session
+-------------
+
+.. autopydantic_model:: aind_behavior_services.session.AindBehaviorSessionModel
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/src/Platforms/FIP_DAQ_Control/docs/conf.py b/src/Platforms/FIP_DAQ_Control/docs/conf.py
new file mode 100644
index 00000000..ff0cc425
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/conf.py
@@ -0,0 +1,82 @@
+import os
+import sys
+
+import erdantic as erd
+from pydantic import BaseModel
+
+import aind_physiology_fip
+import aind_physiology_fip.rig
+
+sys.path.insert(0, os.path.abspath("../src/DataSchemas"))
+
+SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Physiology.Fip/tree/main/src/DataSchemas/"
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "Aind Physiology Fip project"
+copyright = "2025, Allen Institute for Neural Dynamics"
+author = "Bruno Cruz"
+release = aind_physiology_fip.__semver__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+ "sphinx-jsonschema",
+ "sphinx_jinja",
+ "sphinx.ext.napoleon",
+ "sphinx.ext.autodoc",
+ "sphinx.ext.autosummary",
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.githubpages",
+ "sphinx.ext.linkcode",
+ "sphinx_mdinclude",
+ "sphinxcontrib.autodoc_pydantic",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+autosummary_generate = True
+
+autodoc_pydantic_model_show_json = False
+autodoc_pydantic_settings_show_json = False
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "furo"
+html_static_path = ["_static"]
+html_title = "Aind Physiology Fip"
+html_favicon = "_static/favicon.ico"
+html_theme_options = {
+ "light_logo": "light-logo.svg",
+ "dark_logo": "dark-logo.svg",
+}
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = False
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = False
+
+
+# -- Options for linkcode extension ---------------------------------------
+def linkcode_resolve(domain, info):
+ if domain != "py":
+ return None
+ if not info["module"]:
+ 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/src/Platforms/FIP_DAQ_Control/docs/index.rst b/src/Platforms/FIP_DAQ_Control/docs/index.rst
new file mode 100644
index 00000000..2ab96a76
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/index.rst
@@ -0,0 +1,21 @@
+Welcome to the Aind Physiology Fip project documentation!
+========================================================================
+
+.. mdinclude:: ../README.md
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+ :glob:
+
+ self
+ api
+ json-schemas
+ articles/*
+ GitHub Source Code
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`
diff --git a/src/Platforms/FIP_DAQ_Control/docs/json-schemas.rst b/src/Platforms/FIP_DAQ_Control/docs/json-schemas.rst
new file mode 100644
index 00000000..1e5a1ab3
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/json-schemas.rst
@@ -0,0 +1,12 @@
+json-schema
+-------------
+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_physiology_fip`.
+
+`Download Schema `_
+
+
+Rig Schema
+~~~~~~~~~~~~~~
+.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Physiology.Fip/main/src/DataSchemas/aind_physio_fip_rig.json#/$defs/AindPhysioFipRig
+ :lift_definitions:
+ :auto_reference:
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/docs/make.bat b/src/Platforms/FIP_DAQ_Control/docs/make.bat
new file mode 100644
index 00000000..954237b9
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.https://www.sphinx-doc.org/
+ exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/src/Platforms/FIP_DAQ_Control/examples/AindBehaviorSessionModel.json b/src/Platforms/FIP_DAQ_Control/examples/AindBehaviorSessionModel.json
new file mode 100644
index 00000000..d751e339
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/examples/AindBehaviorSessionModel.json
@@ -0,0 +1,18 @@
+{
+ "aind_behavior_services_pkg_version": "0.12.3",
+ "version": "0.12.3",
+ "experiment": "AindPhysioFip",
+ "experimenter": [
+ "Foo",
+ "Bar"
+ ],
+ "date": "2025-10-20T00:46:40.173309Z",
+ "root_path": "c://",
+ "session_name": "test_2025-10-20T004640Z",
+ "subject": "test",
+ "experiment_version": "0.0.0",
+ "notes": "test session",
+ "commit_hash": null,
+ "allow_dirty_repo": true,
+ "skip_hardware_validation": false
+}
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/examples/AindPhysioFipRig.json b/src/Platforms/FIP_DAQ_Control/examples/AindPhysioFipRig.json
new file mode 100644
index 00000000..d11490ee
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/examples/AindPhysioFipRig.json
@@ -0,0 +1,205 @@
+{
+ "aind_behavior_services_pkg_version": "0.12.3",
+ "version": "0.1.2-rc2",
+ "computer_name": "test_computer",
+ "rig_name": "test_rig",
+ "camera_green_iso": {
+ "device_type": "FipCamera",
+ "name": "FipCamera",
+ "additional_settings": null,
+ "calibration": null,
+ "serial_number": "000000",
+ "gain": 0.0,
+ "offset": {
+ "x": 0.0,
+ "y": 0.0
+ }
+ },
+ "camera_red": {
+ "device_type": "FipCamera",
+ "name": "FipCamera",
+ "additional_settings": null,
+ "calibration": null,
+ "serial_number": "000001",
+ "gain": 0.0,
+ "offset": {
+ "x": 0.0,
+ "y": 0.0
+ }
+ },
+ "light_source_uv": {
+ "device_type": "LightSource",
+ "name": "LightSource",
+ "additional_settings": null,
+ "calibration": null,
+ "power": 0.1,
+ "task": {
+ "delta_1": 15650,
+ "delta_2": 666,
+ "delta_3": 300,
+ "delta_4": 50,
+ "light_source_port": 8,
+ "camera_port": 1,
+ "events_enabled": true,
+ "mute_output": false,
+ "pwm_frequency": 10000.0
+ }
+ },
+ "light_source_blue": {
+ "device_type": "LightSource",
+ "name": "mock_device",
+ "additional_settings": null,
+ "calibration": {
+ "device_name": "mock_device",
+ "input": null,
+ "output": {
+ "power_lut": {
+ "0.0": 0.0,
+ "0.1": 10.0,
+ "0.2": 20.0
+ }
+ },
+ "date": null,
+ "description": null,
+ "notes": null
+ },
+ "power": 10.0,
+ "task": {
+ "delta_1": 15650,
+ "delta_2": 666,
+ "delta_3": 300,
+ "delta_4": 50,
+ "light_source_port": 4,
+ "camera_port": 1,
+ "events_enabled": true,
+ "mute_output": false,
+ "pwm_frequency": 10000.0
+ }
+ },
+ "light_source_lime": {
+ "device_type": "LightSource",
+ "name": "mock_device",
+ "additional_settings": null,
+ "calibration": {
+ "device_name": "mock_device",
+ "input": null,
+ "output": {
+ "power_lut": {
+ "0.0": 0.0,
+ "0.1": 10.0,
+ "0.2": 20.0
+ }
+ },
+ "date": null,
+ "description": null,
+ "notes": null
+ },
+ "power": 20.0,
+ "task": {
+ "delta_1": 15650,
+ "delta_2": 666,
+ "delta_3": 300,
+ "delta_4": 50,
+ "light_source_port": 16,
+ "camera_port": 2,
+ "events_enabled": true,
+ "mute_output": false,
+ "pwm_frequency": 10000.0
+ }
+ },
+ "roi_settings": {
+ "camera_green_iso_background": {
+ "center": {
+ "x": 10.0,
+ "y": 10.0
+ },
+ "radius": 10.0
+ },
+ "camera_red_background": {
+ "center": {
+ "x": 10.0,
+ "y": 10.0
+ },
+ "radius": 10.0
+ },
+ "camera_green_iso_roi": [
+ {
+ "center": {
+ "x": 50.0,
+ "y": 50.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 50.0,
+ "y": 150.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 150.0,
+ "y": 50.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 150.0,
+ "y": 150.0
+ },
+ "radius": 20.0
+ }
+ ],
+ "camera_red_roi": [
+ {
+ "center": {
+ "x": 50.0,
+ "y": 50.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 50.0,
+ "y": 150.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 150.0,
+ "y": 50.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 150.0,
+ "y": 150.0
+ },
+ "radius": 20.0
+ }
+ ]
+ },
+ "cuttlefish_fip": {
+ "device_type": "cuTTLefishFip",
+ "name": "cuTTLefishFip",
+ "additional_settings": null,
+ "calibration": null,
+ "who_am_i": 1407,
+ "serial_number": null,
+ "port_name": "COM1"
+ },
+ "networking": {
+ "zmq_publisher": {
+ "connection_string": "@tcp://localhost:5556",
+ "topic": "fip"
+ },
+ "zmq_subscriber": {
+ "connection_string": "@tcp://localhost:5557",
+ "topic": "fip"
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/examples/example.py b/src/Platforms/FIP_DAQ_Control/examples/example.py
new file mode 100644
index 00000000..3b5aae45
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/examples/example.py
@@ -0,0 +1,98 @@
+import argparse
+import datetime
+import os
+
+from aind_behavior_services.rig.harp import HarpCuttlefishfip
+from aind_behavior_services.session import AindBehaviorSessionModel
+
+from aind_physiology_fip.rig import (
+ AindPhysioFipRig,
+ FipCamera,
+ FipTask,
+ LightSource,
+ LightSourceCalibration,
+ LightSourceCalibrationOutput,
+ Networking,
+ Ports,
+ RoiSettings,
+)
+
+
+def mock_session() -> AindBehaviorSessionModel:
+ """Generates a mock AindBehaviorSessionModel model"""
+ return AindBehaviorSessionModel(
+ date=datetime.datetime.now(tz=datetime.timezone.utc),
+ experiment="AindPhysioFip",
+ root_path="c://",
+ subject="test",
+ notes="test session",
+ experiment_version="0.0.0",
+ allow_dirty_repo=True,
+ skip_hardware_validation=False,
+ experimenter=["Foo", "Bar"],
+ )
+
+
+def mock_rig() -> AindPhysioFipRig:
+ mock_calibration = LightSourceCalibration(
+ device_name="mock_device", output=LightSourceCalibrationOutput(power_lut={0: 0, 0.1: 10, 0.2: 20})
+ )
+
+ return AindPhysioFipRig(
+ rig_name="test_rig",
+ computer_name="test_computer",
+ camera_green_iso=FipCamera(serial_number="000000"),
+ camera_red=FipCamera(serial_number="000001"),
+ light_source_blue=LightSource(
+ power=10,
+ calibration=mock_calibration,
+ task=FipTask(
+ camera_port=Ports.IO0, # GreenCamera + 470nm
+ light_source_port=Ports.IO2,
+ ),
+ ),
+ light_source_lime=LightSource(
+ power=20,
+ calibration=mock_calibration,
+ task=FipTask(
+ camera_port=Ports.IO1, # RedCamera + 560nm
+ light_source_port=Ports.IO4,
+ ),
+ ),
+ light_source_uv=LightSource(
+ power=0.1,
+ calibration=None,
+ task=FipTask(
+ camera_port=Ports.IO0, # GreenCamera + 410nm
+ light_source_port=Ports.IO3,
+ ),
+ ),
+ roi_settings=RoiSettings(),
+ networking=Networking(),
+ cuttlefish_fip=HarpCuttlefishfip(
+ port_name="COM1",
+ ),
+ )
+
+
+def main():
+ parser = argparse.ArgumentParser(description="Generate mock session and rig JSON files")
+ parser.add_argument(
+ "--path-seed",
+ default="./local/{schema}.json",
+ help="Path template for output files (default: ./local/{schema}.json)",
+ )
+ args = parser.parse_args()
+
+ example_session = mock_session()
+ example_rig = mock_rig()
+
+ os.makedirs(os.path.dirname(args.path_seed), exist_ok=True)
+
+ for model in [example_session, example_rig]:
+ with open(args.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/src/Platforms/FIP_DAQ_Control/pyproject.toml b/src/Platforms/FIP_DAQ_Control/pyproject.toml
new file mode 100644
index 00000000..9ffbe503
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/pyproject.toml
@@ -0,0 +1,67 @@
+[build-system]
+requires = ["uv_build>=0.8.22"]
+build-backend = "uv_build"
+
+[project]
+name = "aind-physiology-fip"
+description = "A repository for Fiber Photometry data acquisition"
+authors = [
+ { name = "Bruno Cruz", email = "bruno.cruz@alleninstitute.org" },
+ { name = "Kenta Hagihara", email = "kenta.hagihara@alleninstitute.org" },
+]
+license = { text = "MIT" }
+requires-python = ">=3.11"
+version = "0.1.2rc2"
+readme = { file = "README.md", content-type = "text/markdown" }
+classifiers = [
+ "Programming Language :: Python :: 3.11",
+ "License :: OSI Approved :: MIT License",
+ "Operating System :: Microsoft :: Windows",
+]
+
+dependencies = ["aind_behavior_services<0.13"]
+
+[project.urls]
+Documentation = "https://allenneuraldynamics.github.io/Aind.Physiology.Fip/"
+Repository = "https://github.com/AllenNeuralDynamics/Aind.Physiology.Fip/"
+Issues = "https://github.com/AllenNeuralDynamics/Aind.Physiology.Fip/issues"
+Changelog = "https://github.com/AllenNeuralDynamics/Aind.Physiology.Fip/releases"
+
+[project.optional-dependencies]
+
+data = ["contraqctor < 0.6", "pydantic_settings", "opencv-python"]
+
+[dependency-groups]
+
+dev = ["ruff", "codespell", "aind-physiology-fip[data]"]
+
+docs = [
+ 'Sphinx',
+ 'furo',
+ 'sphinx-jinja',
+ 'autodoc_pydantic[erdantic]',
+ 'sphinx-jsonschema',
+ 'sphinx-copybutton',
+ "sphinx_mdinclude",
+]
+
+[project.scripts]
+fip = "aind_physiology_fip.cli:main"
+
+[tool.ruff]
+line-length = 120
+target-version = 'py311'
+
+[tool.ruff.lint]
+extend-select = ['Q', 'RUF100', 'C90', 'I']
+extend-ignore = []
+mccabe = { max-complexity = 14 }
+pydocstyle = { convention = 'google' }
+
+[tool.codespell]
+skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build,uv.lock'
+ignore-words-list = 'nd'
+
+[tool.uv]
+default-groups = ['dev']
+required-version = '>=0.8.4'
diff --git a/src/Platforms/FIP_DAQ_Control/scripts/deploy.cmd b/src/Platforms/FIP_DAQ_Control/scripts/deploy.cmd
new file mode 100644
index 00000000..98b4bba3
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/scripts/deploy.cmd
@@ -0,0 +1 @@
+powershell -ExecutionPolicy Bypass -File .\scripts\deploy.ps1
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/scripts/deploy.ps1 b/src/Platforms/FIP_DAQ_Control/scripts/deploy.ps1
new file mode 100644
index 00000000..2bd416e6
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/scripts/deploy.ps1
@@ -0,0 +1,27 @@
+$scriptPath = $MyInvocation.MyCommand.Path
+$scriptDirectory = Split-Path -Parent $scriptPath
+Set-Location (Split-Path -Parent $scriptDirectory)
+Write-Output "Creating a Python environment..."
+
+if (-not (Get-Command uv -ErrorAction SilentlyContinue)) {
+ throw "The 'uv' command was not found. See https://docs.astral.sh/uv/getting-started/installation/ for instructions."
+}
+
+if (Test-Path -Path ./.venv) {
+ Remove-Item ./.venv -Recurse -Force
+}
+&uv venv
+.\.venv\Scripts\Activate.ps1
+Write-Output "Synchronizing environment..."
+&uv sync
+Write-Output "Creating a Bonsai environment and installing packages..."
+if (Test-Path -Path "bonsai") {
+ Set-Location "bonsai"
+ .\setup.ps1
+} elseif (Test-Path -Path ".bonsai") {
+ Set-Location ".bonsai"
+ .\setup.ps1
+} else {
+ throw "Neither 'bonsai' nor '.bonsai' directory found."
+}
+Set-Location ..
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/src/DataSchemas/aind_physiology_fip.json b/src/Platforms/FIP_DAQ_Control/src/DataSchemas/aind_physiology_fip.json
new file mode 100644
index 00000000..363a2562
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/src/DataSchemas/aind_physiology_fip.json
@@ -0,0 +1,804 @@
+{
+ "$defs": {
+ "AindBehaviorSessionModel": {
+ "properties": {
+ "aind_behavior_services_pkg_version": {
+ "default": "0.12.3",
+ "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
+ "title": "aind_behavior_services package version",
+ "type": "string"
+ },
+ "version": {
+ "const": "0.12.3",
+ "default": "0.12.3",
+ "title": "Version",
+ "type": "string"
+ },
+ "experiment": {
+ "default": null,
+ "description": "Name of the experiment",
+ "oneOf": [
+ {
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Experiment"
+ },
+ "experimenter": {
+ "default": [],
+ "description": "Name of the experimenter",
+ "items": {
+ "type": "string"
+ },
+ "title": "Experimenter",
+ "type": "array"
+ },
+ "date": {
+ "description": "Date of the experiment",
+ "format": "date-time",
+ "title": "Date",
+ "type": "string"
+ },
+ "root_path": {
+ "description": "Root path where data will be logged",
+ "title": "Root Path",
+ "type": "string"
+ },
+ "session_name": {
+ "default": null,
+ "description": "Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date.",
+ "oneOf": [
+ {
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Session Name"
+ },
+ "subject": {
+ "description": "Name of the subject",
+ "title": "Subject",
+ "type": "string"
+ },
+ "experiment_version": {
+ "default": "",
+ "deprecated": true,
+ "description": "Version of the experiment",
+ "title": "Experiment Version",
+ "type": "string"
+ },
+ "notes": {
+ "default": null,
+ "description": "Notes about the experiment",
+ "oneOf": [
+ {
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Notes"
+ },
+ "commit_hash": {
+ "default": null,
+ "description": "Commit hash of the repository",
+ "oneOf": [
+ {
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Commit Hash"
+ },
+ "allow_dirty_repo": {
+ "default": false,
+ "description": "Allow running from a dirty repository",
+ "title": "Allow Dirty Repo",
+ "type": "boolean"
+ },
+ "skip_hardware_validation": {
+ "default": false,
+ "description": "Skip hardware validation",
+ "title": "Skip Hardware Validation",
+ "type": "boolean"
+ }
+ },
+ "required": [
+ "root_path",
+ "subject"
+ ],
+ "title": "AindBehaviorSessionModel",
+ "type": "object"
+ },
+ "AindPhysioFipRig": {
+ "description": "Complete rig configuration model for AIND FIP photometry system.",
+ "properties": {
+ "aind_behavior_services_pkg_version": {
+ "default": "0.12.3",
+ "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
+ "title": "aind_behavior_services package version",
+ "type": "string"
+ },
+ "version": {
+ "const": "0.1.2-rc2",
+ "default": "0.1.2-rc2",
+ "title": "Version",
+ "type": "string"
+ },
+ "computer_name": {
+ "description": "Computer name",
+ "title": "Computer Name",
+ "type": "string"
+ },
+ "rig_name": {
+ "description": "Rig name",
+ "title": "Rig Name",
+ "type": "string"
+ },
+ "camera_green_iso": {
+ "$ref": "#/$defs/FipCamera",
+ "description": "Camera for the green and iso channels",
+ "title": "G/Iso Camera"
+ },
+ "camera_red": {
+ "$ref": "#/$defs/FipCamera",
+ "description": "Red camera",
+ "title": "Red Camera"
+ },
+ "light_source_uv": {
+ "$ref": "#/$defs/LightSource",
+ "description": "UV (415nm) light source",
+ "title": "UV light source"
+ },
+ "light_source_blue": {
+ "$ref": "#/$defs/LightSource",
+ "description": "Blue (470nm) light source",
+ "title": "Blue light source"
+ },
+ "light_source_lime": {
+ "$ref": "#/$defs/LightSource",
+ "description": "Lime (560nm) light source",
+ "title": "Lime light source"
+ },
+ "roi_settings": {
+ "default": null,
+ "description": "Region of interest settings. Leave empty to attempt to load from local file or manually define it in the program.",
+ "oneOf": [
+ {
+ "$ref": "#/$defs/RoiSettings"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Region of interest settings"
+ },
+ "cuttlefish_fip": {
+ "$ref": "#/$defs/HarpCuttlefishfip",
+ "description": "CuttlefishFip board for controlling the trigger of cameras and light-sources",
+ "title": "CuttlefishFip"
+ },
+ "networking": {
+ "$ref": "#/$defs/Networking",
+ "default": {
+ "zmq_publisher": {
+ "connection_string": "@tcp://localhost:5556",
+ "topic": "fip"
+ },
+ "zmq_subscriber": {
+ "connection_string": "@tcp://localhost:5557",
+ "topic": "fip"
+ }
+ },
+ "description": "Networking settings"
+ }
+ },
+ "required": [
+ "rig_name",
+ "camera_green_iso",
+ "camera_red",
+ "light_source_uv",
+ "light_source_blue",
+ "light_source_lime",
+ "cuttlefish_fip"
+ ],
+ "title": "AindPhysioFipRig",
+ "type": "object"
+ },
+ "BaseModel": {
+ "properties": {},
+ "title": "BaseModel",
+ "type": "object"
+ },
+ "Circle": {
+ "properties": {
+ "center": {
+ "$ref": "#/$defs/Point2f",
+ "default": {
+ "x": 0.0,
+ "y": 0.0
+ },
+ "description": "Center of the circle (px)"
+ },
+ "radius": {
+ "default": 1,
+ "description": "Radius of the circle (px)",
+ "minimum": 0,
+ "title": "Radius",
+ "type": "number"
+ }
+ },
+ "title": "Circle",
+ "type": "object"
+ },
+ "FipCamera": {
+ "description": "Camera device configuration for FIP photometry system.",
+ "properties": {
+ "device_type": {
+ "const": "FipCamera",
+ "default": "FipCamera",
+ "title": "Device Type",
+ "type": "string"
+ },
+ "device_name": {
+ "default": null,
+ "description": "Device name",
+ "oneOf": [
+ {
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Device Name"
+ },
+ "additional_settings": {
+ "default": null,
+ "description": "Additional settings",
+ "oneOf": [
+ {
+ "$ref": "#/$defs/BaseModel"
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "calibration": {
+ "default": null,
+ "description": "Calibration",
+ "oneOf": [
+ {
+ "$ref": "#/$defs/BaseModel"
+ },
+ {
+ "type": "null"
+ }
+ ]
+ },
+ "serial_number": {
+ "description": "Camera serial number",
+ "title": "Serial Number",
+ "type": "string"
+ },
+ "gain": {
+ "default": 0,
+ "description": "Gain",
+ "minimum": 0,
+ "title": "Gain",
+ "type": "number"
+ },
+ "offset": {
+ "$ref": "#/$defs/Point2f",
+ "default": {
+ "x": 0.0,
+ "y": 0.0
+ },
+ "description": "Offset (px)"
+ }
+ },
+ "required": [
+ "serial_number"
+ ],
+ "title": "FipCamera",
+ "type": "object"
+ },
+ "FipTask": {
+ "description": "Task configuration for FIP timing and triggering parameters.",
+ "properties": {
+ "delta_1": {
+ "default": 15650,
+ "description": "Delta 1 (us)",
+ "minimum": 0,
+ "title": "Delta 1",
+ "type": "integer"
+ },
+ "delta_2": {
+ "default": 666,
+ "description": "Delta 2 (us)",
+ "minimum": 0,
+ "title": "Delta 2",
+ "type": "integer"
+ },
+ "delta_3": {
+ "default": 300,
+ "description": "Delta 3 (us)",
+ "minimum": 0,
+ "title": "Delta 3",
+ "type": "integer"
+ },
+ "delta_4": {
+ "default": 50,
+ "description": "Delta 4 (us)",
+ "minimum": 0,
+ "title": "Delta 4",
+ "type": "integer"
+ },
+ "light_source_port": {
+ "$ref": "#/$defs/Ports",
+ "description": "Port that triggers the light source."
+ },
+ "camera_port": {
+ "$ref": "#/$defs/Ports",
+ "description": "Port that triggers the camera."
+ },
+ "events_enabled": {
+ "default": true,
+ "description": "Whether to enable events for the task. If False, the task will not trigger any events.",
+ "title": "Events Enabled",
+ "type": "boolean"
+ },
+ "mute_output": {
+ "default": false,
+ "description": "Whether to mute the output of the task. If True, the task will not trigger any outputs but timing will be preserved.",
+ "title": "Mute Output",
+ "type": "boolean"
+ },
+ "pwm_frequency": {
+ "default": 10000,
+ "description": "PWM frequency (Hz) of the light source output.",
+ "minimum": 10000,
+ "title": "Pwm Frequency",
+ "type": "number"
+ }
+ },
+ "required": [
+ "light_source_port",
+ "camera_port"
+ ],
+ "title": "FipTask",
+ "type": "object"
+ },
+ "HarpCuttlefishfip": {
+ "properties": {
+ "device_type": {
+ "const": "cuTTLefishFip",
+ "default": "cuTTLefishFip",
+ "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": 1407,
+ "default": 1407,
+ "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": "HarpCuttlefishfip",
+ "type": "object"
+ },
+ "LightSource": {
+ "description": "Light source device configuration with power control and timing tasks.",
+ "properties": {
+ "device_type": {
+ "const": "LightSource",
+ "default": "LightSource",
+ "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 for the LightSource. If left empty, 'power' will be used as duty-cycle (0-100).",
+ "oneOf": [
+ {
+ "$ref": "#/$defs/LightSourceCalibration"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Calibration"
+ },
+ "power": {
+ "default": 0,
+ "description": "Power (mW)",
+ "minimum": 0,
+ "title": "Power",
+ "type": "number"
+ },
+ "task": {
+ "$ref": "#/$defs/FipTask",
+ "description": "Task for the light source",
+ "title": "Task"
+ }
+ },
+ "required": [
+ "task"
+ ],
+ "title": "LightSource",
+ "type": "object"
+ },
+ "LightSourceCalibration": {
+ "description": "Calibration model for converting light source duty cycle to power output.",
+ "properties": {
+ "device_name": {
+ "description": "Name of the device being calibrated",
+ "title": "Device name",
+ "type": "string"
+ },
+ "input": {
+ "default": null,
+ "oneOf": [
+ {
+ "$ref": "#/$defs/BaseModel"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Input data"
+ },
+ "output": {
+ "$ref": "#/$defs/LightSourceCalibrationOutput",
+ "title": "Lookup table to convert duty cycle to power (mW)"
+ },
+ "date": {
+ "default": null,
+ "oneOf": [
+ {
+ "format": "date-time",
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Date"
+ },
+ "description": {
+ "default": null,
+ "oneOf": [
+ {
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Brief description of what is being calibrated"
+ },
+ "notes": {
+ "default": null,
+ "oneOf": [
+ {
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "title": "Notes"
+ }
+ },
+ "required": [
+ "device_name",
+ "output"
+ ],
+ "title": "LightSourceCalibration",
+ "type": "object"
+ },
+ "LightSourceCalibrationOutput": {
+ "description": "Output of the light source calibration process.",
+ "properties": {
+ "power_lut": {
+ "additionalProperties": {
+ "default": 0,
+ "description": "Power (mW)",
+ "minimum": 0,
+ "type": "number"
+ },
+ "description": "Look-up table for LightSource power vs. duty cycle",
+ "title": "Power Lut",
+ "type": "object"
+ }
+ },
+ "required": [
+ "power_lut"
+ ],
+ "title": "LightSourceCalibrationOutput",
+ "type": "object"
+ },
+ "Networking": {
+ "description": "Network configuration settings for ZeroMQ communication.",
+ "properties": {
+ "zmq_publisher": {
+ "$ref": "#/$defs/ZmqConnection",
+ "default": {
+ "connection_string": "@tcp://localhost:5556",
+ "topic": "fip"
+ }
+ },
+ "zmq_subscriber": {
+ "$ref": "#/$defs/ZmqConnection",
+ "default": {
+ "connection_string": "@tcp://localhost:5557",
+ "topic": "fip"
+ }
+ }
+ },
+ "title": "Networking",
+ "type": "object"
+ },
+ "Point2f": {
+ "properties": {
+ "x": {
+ "description": "X coordinate of the point (px)",
+ "title": "X",
+ "type": "number"
+ },
+ "y": {
+ "description": "Y coordinate of the point (px)",
+ "title": "Y",
+ "type": "number"
+ }
+ },
+ "required": [
+ "x",
+ "y"
+ ],
+ "title": "Point2f",
+ "type": "object"
+ },
+ "Ports": {
+ "description": "Available hardware ports in the FIP cuttlefish board.",
+ "enum": [
+ 0,
+ 1,
+ 2,
+ 4,
+ 8,
+ 16,
+ 32,
+ 64,
+ 128
+ ],
+ "title": "Ports",
+ "type": "integer",
+ "x-enumNames": [
+ "None",
+ "Io0",
+ "Io1",
+ "Io2",
+ "Io3",
+ "Io4",
+ "Io5",
+ "Io6",
+ "Io7"
+ ]
+ },
+ "RoiSettings": {
+ "description": "Region of Interest (ROI) settings for camera channels in the FIP system.",
+ "properties": {
+ "camera_green_iso_background": {
+ "$ref": "#/$defs/Circle",
+ "default": {
+ "center": {
+ "x": 10.0,
+ "y": 10.0
+ },
+ "radius": 10.0
+ },
+ "description": "ROI to compute the background for the green/iso camera channel"
+ },
+ "camera_red_background": {
+ "$ref": "#/$defs/Circle",
+ "default": {
+ "center": {
+ "x": 10.0,
+ "y": 10.0
+ },
+ "radius": 10.0
+ },
+ "description": "ROI to compute the background for the red camera channel"
+ },
+ "camera_green_iso_roi": {
+ "default": [
+ {
+ "center": {
+ "x": 50.0,
+ "y": 50.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 50.0,
+ "y": 150.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 150.0,
+ "y": 50.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 150.0,
+ "y": 150.0
+ },
+ "radius": 20.0
+ }
+ ],
+ "description": "ROI for the green/iso camera channel",
+ "items": {
+ "$ref": "#/$defs/Circle"
+ },
+ "title": "Camera Green Iso Roi",
+ "type": "array"
+ },
+ "camera_red_roi": {
+ "default": [
+ {
+ "center": {
+ "x": 50.0,
+ "y": 50.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 50.0,
+ "y": 150.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 150.0,
+ "y": 50.0
+ },
+ "radius": 20.0
+ },
+ {
+ "center": {
+ "x": 150.0,
+ "y": 150.0
+ },
+ "radius": 20.0
+ }
+ ],
+ "description": "ROI for the red camera channel",
+ "items": {
+ "$ref": "#/$defs/Circle"
+ },
+ "title": "Camera Red Roi",
+ "type": "array"
+ }
+ },
+ "title": "RoiSettings",
+ "type": "object"
+ },
+ "ZmqConnection": {
+ "properties": {
+ "connection_string": {
+ "default": "@tcp://localhost:5556",
+ "description": "The connection string for the ZMQ socket.",
+ "title": "Connection String",
+ "type": "string"
+ },
+ "topic": {
+ "default": "",
+ "title": "Topic",
+ "type": "string"
+ }
+ },
+ "title": "ZmqConnection",
+ "type": "object"
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/src/Extensions.csproj b/src/Platforms/FIP_DAQ_Control/src/Extensions.csproj
new file mode 100644
index 00000000..ee04ad08
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/src/Extensions.csproj
@@ -0,0 +1,22 @@
+
+
+ net472
+ true
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/src/Platforms/FIP_DAQ_Control/src/Extensions/AindPhysiologyFip.Generated.cs b/src/Platforms/FIP_DAQ_Control/src/Extensions/AindPhysiologyFip.Generated.cs
new file mode 100644
index 00000000..25a67fd9
--- /dev/null
+++ b/src/Platforms/FIP_DAQ_Control/src/Extensions/AindPhysiologyFip.Generated.cs
@@ -0,0 +1,2380 @@
+//----------------------
+//
+// Generated using the NJsonSchema v10.9.0.0 (Newtonsoft.Json v13.0.0.0) (http://NJsonSchema.org)
+//
+//----------------------
+
+
+namespace AindPhysiologyFip
+{
+ #pragma warning disable // Disable all warnings
+
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class AindBehaviorSessionModel
+ {
+
+ private string _aindBehaviorServicesPkgVersion;
+
+ private string _version;
+
+ private string _experiment;
+
+ private System.Collections.Generic.List _experimenter;
+
+ private System.DateTimeOffset _date;
+
+ private string _rootPath;
+
+ private string _sessionName;
+
+ private string _subject;
+
+ private string _experimentVersion;
+
+ private string _notes;
+
+ private string _commitHash;
+
+ private bool _allowDirtyRepo;
+
+ private bool _skipHardwareValidation;
+
+ public AindBehaviorSessionModel()
+ {
+ _aindBehaviorServicesPkgVersion = "0.12.3";
+ _version = "0.12.3";
+ _experimenter = new System.Collections.Generic.List();
+ _experimentVersion = "";
+ _allowDirtyRepo = false;
+ _skipHardwareValidation = false;
+ }
+
+ protected AindBehaviorSessionModel(AindBehaviorSessionModel other)
+ {
+ _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion;
+ _version = other._version;
+ _experiment = other._experiment;
+ _experimenter = other._experimenter;
+ _date = other._date;
+ _rootPath = other._rootPath;
+ _sessionName = other._sessionName;
+ _subject = other._subject;
+ _experimentVersion = other._experimentVersion;
+ _notes = other._notes;
+ _commitHash = other._commitHash;
+ _allowDirtyRepo = other._allowDirtyRepo;
+ _skipHardwareValidation = other._skipHardwareValidation;
+ }
+
+ [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")]
+ public string AindBehaviorServicesPkgVersion
+ {
+ get
+ {
+ return _aindBehaviorServicesPkgVersion;
+ }
+ set
+ {
+ _aindBehaviorServicesPkgVersion = value;
+ }
+ }
+
+ [Newtonsoft.Json.JsonPropertyAttribute("version")]
+ public string Version
+ {
+ get
+ {
+ return _version;
+ }
+ set
+ {
+ _version = value;
+ }
+ }
+
+ ///
+ /// Name of the experiment
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("experiment")]
+ [System.ComponentModel.DescriptionAttribute("Name of the experiment")]
+ public string Experiment
+ {
+ get
+ {
+ return _experiment;
+ }
+ set
+ {
+ _experiment = value;
+ }
+ }
+
+ ///
+ /// Name of the experimenter
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("experimenter")]
+ [System.ComponentModel.DescriptionAttribute("Name of the experimenter")]
+ public System.Collections.Generic.List Experimenter
+ {
+ get
+ {
+ return _experimenter;
+ }
+ set
+ {
+ _experimenter = value;
+ }
+ }
+
+ ///
+ /// Date of the experiment
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("date")]
+ [System.ComponentModel.DescriptionAttribute("Date of the experiment")]
+ public System.DateTimeOffset Date
+ {
+ get
+ {
+ return _date;
+ }
+ set
+ {
+ _date = value;
+ }
+ }
+
+ ///
+ /// Root path where data will be logged
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("root_path", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Root path where data will be logged")]
+ public string RootPath
+ {
+ get
+ {
+ return _rootPath;
+ }
+ set
+ {
+ _rootPath = value;
+ }
+ }
+
+ ///
+ /// Name of the session. This will be used to create a folder in the root path. If not provided, it will be generated using subject and date.
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("session_name")]
+ [System.ComponentModel.DescriptionAttribute("Name of the session. This will be used to create a folder in the root path. If no" +
+ "t provided, it will be generated using subject and date.")]
+ public string SessionName
+ {
+ get
+ {
+ return _sessionName;
+ }
+ set
+ {
+ _sessionName = value;
+ }
+ }
+
+ ///
+ /// Name of the subject
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("subject", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Name of the subject")]
+ public string Subject
+ {
+ get
+ {
+ return _subject;
+ }
+ set
+ {
+ _subject = value;
+ }
+ }
+
+ ///
+ /// Version of the experiment
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("experiment_version")]
+ [System.ComponentModel.DescriptionAttribute("Version of the experiment")]
+ public string ExperimentVersion
+ {
+ get
+ {
+ return _experimentVersion;
+ }
+ set
+ {
+ _experimentVersion = value;
+ }
+ }
+
+ ///
+ /// Notes about the experiment
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("notes")]
+ [System.ComponentModel.DescriptionAttribute("Notes about the experiment")]
+ public string Notes
+ {
+ get
+ {
+ return _notes;
+ }
+ set
+ {
+ _notes = value;
+ }
+ }
+
+ ///
+ /// Commit hash of the repository
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("commit_hash")]
+ [System.ComponentModel.DescriptionAttribute("Commit hash of the repository")]
+ public string CommitHash
+ {
+ get
+ {
+ return _commitHash;
+ }
+ set
+ {
+ _commitHash = value;
+ }
+ }
+
+ ///
+ /// Allow running from a dirty repository
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("allow_dirty_repo")]
+ [System.ComponentModel.DescriptionAttribute("Allow running from a dirty repository")]
+ public bool AllowDirtyRepo
+ {
+ get
+ {
+ return _allowDirtyRepo;
+ }
+ set
+ {
+ _allowDirtyRepo = value;
+ }
+ }
+
+ ///
+ /// Skip hardware validation
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("skip_hardware_validation")]
+ [System.ComponentModel.DescriptionAttribute("Skip hardware validation")]
+ public bool SkipHardwareValidation
+ {
+ get
+ {
+ return _skipHardwareValidation;
+ }
+ set
+ {
+ _skipHardwareValidation = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindBehaviorSessionModel(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new AindBehaviorSessionModel(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("AindBehaviorServicesPkgVersion = " + _aindBehaviorServicesPkgVersion + ", ");
+ stringBuilder.Append("Version = " + _version + ", ");
+ stringBuilder.Append("Experiment = " + _experiment + ", ");
+ stringBuilder.Append("Experimenter = " + _experimenter + ", ");
+ stringBuilder.Append("Date = " + _date + ", ");
+ stringBuilder.Append("RootPath = " + _rootPath + ", ");
+ stringBuilder.Append("SessionName = " + _sessionName + ", ");
+ stringBuilder.Append("Subject = " + _subject + ", ");
+ stringBuilder.Append("ExperimentVersion = " + _experimentVersion + ", ");
+ stringBuilder.Append("Notes = " + _notes + ", ");
+ stringBuilder.Append("CommitHash = " + _commitHash + ", ");
+ stringBuilder.Append("AllowDirtyRepo = " + _allowDirtyRepo + ", ");
+ stringBuilder.Append("SkipHardwareValidation = " + _skipHardwareValidation);
+ return true;
+ }
+
+ public override string ToString()
+ {
+ System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder();
+ stringBuilder.Append(GetType().Name);
+ stringBuilder.Append(" { ");
+ if (PrintMembers(stringBuilder))
+ {
+ stringBuilder.Append(" ");
+ }
+ stringBuilder.Append("}");
+ return stringBuilder.ToString();
+ }
+ }
+
+
+ ///
+ /// Complete rig configuration model for AIND FIP photometry system.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [System.ComponentModel.DescriptionAttribute("Complete rig configuration model for AIND FIP photometry system.")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class AindPhysioFipRig
+ {
+
+ private string _aindBehaviorServicesPkgVersion;
+
+ private string _version;
+
+ private string _computerName;
+
+ private string _rigName;
+
+ private FipCamera _cameraGreenIso;
+
+ private FipCamera _cameraRed;
+
+ private LightSource _lightSourceUv;
+
+ private LightSource _lightSourceBlue;
+
+ private LightSource _lightSourceLime;
+
+ private RoiSettings _roiSettings;
+
+ private HarpCuttlefishfip _cuttlefishFip;
+
+ private Networking _networking;
+
+ public AindPhysioFipRig()
+ {
+ _aindBehaviorServicesPkgVersion = "0.12.3";
+ _version = "0.1.2-rc2";
+ _cameraGreenIso = new FipCamera();
+ _cameraRed = new FipCamera();
+ _lightSourceUv = new LightSource();
+ _lightSourceBlue = new LightSource();
+ _lightSourceLime = new LightSource();
+ _cuttlefishFip = new HarpCuttlefishfip();
+ _networking = new Networking();
+ }
+
+ protected AindPhysioFipRig(AindPhysioFipRig other)
+ {
+ _aindBehaviorServicesPkgVersion = other._aindBehaviorServicesPkgVersion;
+ _version = other._version;
+ _computerName = other._computerName;
+ _rigName = other._rigName;
+ _cameraGreenIso = other._cameraGreenIso;
+ _cameraRed = other._cameraRed;
+ _lightSourceUv = other._lightSourceUv;
+ _lightSourceBlue = other._lightSourceBlue;
+ _lightSourceLime = other._lightSourceLime;
+ _roiSettings = other._roiSettings;
+ _cuttlefishFip = other._cuttlefishFip;
+ _networking = other._networking;
+ }
+
+ [Newtonsoft.Json.JsonPropertyAttribute("aind_behavior_services_pkg_version")]
+ public string AindBehaviorServicesPkgVersion
+ {
+ get
+ {
+ return _aindBehaviorServicesPkgVersion;
+ }
+ set
+ {
+ _aindBehaviorServicesPkgVersion = value;
+ }
+ }
+
+ [Newtonsoft.Json.JsonPropertyAttribute("version")]
+ public string Version
+ {
+ get
+ {
+ return _version;
+ }
+ set
+ {
+ _version = value;
+ }
+ }
+
+ ///
+ /// Computer name
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("computer_name")]
+ [System.ComponentModel.DescriptionAttribute("Computer name")]
+ public string ComputerName
+ {
+ get
+ {
+ return _computerName;
+ }
+ set
+ {
+ _computerName = value;
+ }
+ }
+
+ ///
+ /// Rig name
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("rig_name", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Rig name")]
+ public string RigName
+ {
+ get
+ {
+ return _rigName;
+ }
+ set
+ {
+ _rigName = value;
+ }
+ }
+
+ ///
+ /// Camera for the green and iso channels
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("camera_green_iso", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Camera for the green and iso channels")]
+ public FipCamera CameraGreenIso
+ {
+ get
+ {
+ return _cameraGreenIso;
+ }
+ set
+ {
+ _cameraGreenIso = value;
+ }
+ }
+
+ ///
+ /// Red camera
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("camera_red", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Red camera")]
+ public FipCamera CameraRed
+ {
+ get
+ {
+ return _cameraRed;
+ }
+ set
+ {
+ _cameraRed = value;
+ }
+ }
+
+ ///
+ /// UV (415nm) light source
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("light_source_uv", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("UV (415nm) light source")]
+ public LightSource LightSourceUv
+ {
+ get
+ {
+ return _lightSourceUv;
+ }
+ set
+ {
+ _lightSourceUv = value;
+ }
+ }
+
+ ///
+ /// Blue (470nm) light source
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("light_source_blue", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Blue (470nm) light source")]
+ public LightSource LightSourceBlue
+ {
+ get
+ {
+ return _lightSourceBlue;
+ }
+ set
+ {
+ _lightSourceBlue = value;
+ }
+ }
+
+ ///
+ /// Lime (560nm) light source
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("light_source_lime", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Lime (560nm) light source")]
+ public LightSource LightSourceLime
+ {
+ get
+ {
+ return _lightSourceLime;
+ }
+ set
+ {
+ _lightSourceLime = value;
+ }
+ }
+
+ ///
+ /// Region of interest settings. Leave empty to attempt to load from local file or manually define it in the program.
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("roi_settings")]
+ [System.ComponentModel.DescriptionAttribute("Region of interest settings. Leave empty to attempt to load from local file or ma" +
+ "nually define it in the program.")]
+ public RoiSettings RoiSettings
+ {
+ get
+ {
+ return _roiSettings;
+ }
+ set
+ {
+ _roiSettings = value;
+ }
+ }
+
+ ///
+ /// CuttlefishFip board for controlling the trigger of cameras and light-sources
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("cuttlefish_fip", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("CuttlefishFip board for controlling the trigger of cameras and light-sources")]
+ public HarpCuttlefishfip CuttlefishFip
+ {
+ get
+ {
+ return _cuttlefishFip;
+ }
+ set
+ {
+ _cuttlefishFip = value;
+ }
+ }
+
+ ///
+ /// Networking settings
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("networking")]
+ [System.ComponentModel.DescriptionAttribute("Networking settings")]
+ public Networking Networking
+ {
+ get
+ {
+ return _networking;
+ }
+ set
+ {
+ _networking = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new AindPhysioFipRig(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new AindPhysioFipRig(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("CameraGreenIso = " + _cameraGreenIso + ", ");
+ stringBuilder.Append("CameraRed = " + _cameraRed + ", ");
+ stringBuilder.Append("LightSourceUv = " + _lightSourceUv + ", ");
+ stringBuilder.Append("LightSourceBlue = " + _lightSourceBlue + ", ");
+ stringBuilder.Append("LightSourceLime = " + _lightSourceLime + ", ");
+ stringBuilder.Append("RoiSettings = " + _roiSettings + ", ");
+ stringBuilder.Append("CuttlefishFip = " + _cuttlefishFip + ", ");
+ stringBuilder.Append("Networking = " + _networking);
+ 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 Circle
+ {
+
+ private Point2f _center;
+
+ private double _radius;
+
+ public Circle()
+ {
+ _center = new Point2f();
+ _radius = 1D;
+ }
+
+ protected Circle(Circle other)
+ {
+ _center = other._center;
+ _radius = other._radius;
+ }
+
+ ///
+ /// Center of the circle (px)
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("center")]
+ [System.ComponentModel.DescriptionAttribute("Center of the circle (px)")]
+ public Point2f Center
+ {
+ get
+ {
+ return _center;
+ }
+ set
+ {
+ _center = value;
+ }
+ }
+
+ ///
+ /// Radius of the circle (px)
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("radius")]
+ [System.ComponentModel.DescriptionAttribute("Radius of the circle (px)")]
+ public double Radius
+ {
+ get
+ {
+ return _radius;
+ }
+ set
+ {
+ _radius = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Circle(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new Circle(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("Center = " + _center + ", ");
+ stringBuilder.Append("Radius = " + _radius);
+ 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();
+ }
+ }
+
+
+ ///
+ /// Camera device configuration for FIP photometry system.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [System.ComponentModel.DescriptionAttribute("Camera device configuration for FIP photometry system.")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class FipCamera
+ {
+
+ private string _deviceType;
+
+ private string _deviceName;
+
+ private BaseModel _additionalSettings;
+
+ private BaseModel _calibration;
+
+ private string _serialNumber;
+
+ private double _gain;
+
+ private Point2f _offset;
+
+ public FipCamera()
+ {
+ _deviceType = "FipCamera";
+ _gain = 0D;
+ _offset = new Point2f();
+ }
+
+ protected FipCamera(FipCamera other)
+ {
+ _deviceType = other._deviceType;
+ _deviceName = other._deviceName;
+ _additionalSettings = other._additionalSettings;
+ _calibration = other._calibration;
+ _serialNumber = other._serialNumber;
+ _gain = other._gain;
+ _offset = other._offset;
+ }
+
+ [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;
+ }
+ }
+
+ ///
+ /// Camera serial number
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("serial_number", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Camera serial number")]
+ public string SerialNumber
+ {
+ get
+ {
+ return _serialNumber;
+ }
+ set
+ {
+ _serialNumber = value;
+ }
+ }
+
+ ///
+ /// Gain
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("gain")]
+ [System.ComponentModel.DescriptionAttribute("Gain")]
+ public double Gain
+ {
+ get
+ {
+ return _gain;
+ }
+ set
+ {
+ _gain = value;
+ }
+ }
+
+ ///
+ /// Offset (px)
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("offset")]
+ [System.ComponentModel.DescriptionAttribute("Offset (px)")]
+ public Point2f Offset
+ {
+ get
+ {
+ return _offset;
+ }
+ set
+ {
+ _offset = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new FipCamera(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new FipCamera(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("DeviceType = " + _deviceType + ", ");
+ stringBuilder.Append("DeviceName = " + _deviceName + ", ");
+ stringBuilder.Append("AdditionalSettings = " + _additionalSettings + ", ");
+ stringBuilder.Append("Calibration = " + _calibration + ", ");
+ stringBuilder.Append("SerialNumber = " + _serialNumber + ", ");
+ stringBuilder.Append("Gain = " + _gain + ", ");
+ stringBuilder.Append("Offset = " + _offset);
+ 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();
+ }
+ }
+
+
+ ///
+ /// Task configuration for FIP timing and triggering parameters.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [System.ComponentModel.DescriptionAttribute("Task configuration for FIP timing and triggering parameters.")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class FipTask
+ {
+
+ private int _delta1;
+
+ private int _delta2;
+
+ private int _delta3;
+
+ private int _delta4;
+
+ private Ports _lightSourcePort;
+
+ private Ports _cameraPort;
+
+ private bool _eventsEnabled;
+
+ private bool _muteOutput;
+
+ private double _pwmFrequency;
+
+ public FipTask()
+ {
+ _delta1 = 15650;
+ _delta2 = 666;
+ _delta3 = 300;
+ _delta4 = 50;
+ _eventsEnabled = true;
+ _muteOutput = false;
+ _pwmFrequency = 10000D;
+ }
+
+ protected FipTask(FipTask other)
+ {
+ _delta1 = other._delta1;
+ _delta2 = other._delta2;
+ _delta3 = other._delta3;
+ _delta4 = other._delta4;
+ _lightSourcePort = other._lightSourcePort;
+ _cameraPort = other._cameraPort;
+ _eventsEnabled = other._eventsEnabled;
+ _muteOutput = other._muteOutput;
+ _pwmFrequency = other._pwmFrequency;
+ }
+
+ ///
+ /// Delta 1 (us)
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("delta_1")]
+ [System.ComponentModel.DescriptionAttribute("Delta 1 (us)")]
+ public int Delta1
+ {
+ get
+ {
+ return _delta1;
+ }
+ set
+ {
+ _delta1 = value;
+ }
+ }
+
+ ///
+ /// Delta 2 (us)
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("delta_2")]
+ [System.ComponentModel.DescriptionAttribute("Delta 2 (us)")]
+ public int Delta2
+ {
+ get
+ {
+ return _delta2;
+ }
+ set
+ {
+ _delta2 = value;
+ }
+ }
+
+ ///
+ /// Delta 3 (us)
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("delta_3")]
+ [System.ComponentModel.DescriptionAttribute("Delta 3 (us)")]
+ public int Delta3
+ {
+ get
+ {
+ return _delta3;
+ }
+ set
+ {
+ _delta3 = value;
+ }
+ }
+
+ ///
+ /// Delta 4 (us)
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("delta_4")]
+ [System.ComponentModel.DescriptionAttribute("Delta 4 (us)")]
+ public int Delta4
+ {
+ get
+ {
+ return _delta4;
+ }
+ set
+ {
+ _delta4 = value;
+ }
+ }
+
+ ///
+ /// Port that triggers the light source.
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("light_source_port", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Port that triggers the light source.")]
+ public Ports LightSourcePort
+ {
+ get
+ {
+ return _lightSourcePort;
+ }
+ set
+ {
+ _lightSourcePort = value;
+ }
+ }
+
+ ///
+ /// Port that triggers the camera.
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("camera_port", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Port that triggers the camera.")]
+ public Ports CameraPort
+ {
+ get
+ {
+ return _cameraPort;
+ }
+ set
+ {
+ _cameraPort = value;
+ }
+ }
+
+ ///
+ /// Whether to enable events for the task. If False, the task will not trigger any events.
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("events_enabled")]
+ [System.ComponentModel.DescriptionAttribute("Whether to enable events for the task. If False, the task will not trigger any ev" +
+ "ents.")]
+ public bool EventsEnabled
+ {
+ get
+ {
+ return _eventsEnabled;
+ }
+ set
+ {
+ _eventsEnabled = value;
+ }
+ }
+
+ ///
+ /// Whether to mute the output of the task. If True, the task will not trigger any outputs but timing will be preserved.
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("mute_output")]
+ [System.ComponentModel.DescriptionAttribute("Whether to mute the output of the task. If True, the task will not trigger any ou" +
+ "tputs but timing will be preserved.")]
+ public bool MuteOutput
+ {
+ get
+ {
+ return _muteOutput;
+ }
+ set
+ {
+ _muteOutput = value;
+ }
+ }
+
+ ///
+ /// PWM frequency (Hz) of the light source output.
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("pwm_frequency")]
+ [System.ComponentModel.DescriptionAttribute("PWM frequency (Hz) of the light source output.")]
+ public double PwmFrequency
+ {
+ get
+ {
+ return _pwmFrequency;
+ }
+ set
+ {
+ _pwmFrequency = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new FipTask(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new FipTask(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("Delta1 = " + _delta1 + ", ");
+ stringBuilder.Append("Delta2 = " + _delta2 + ", ");
+ stringBuilder.Append("Delta3 = " + _delta3 + ", ");
+ stringBuilder.Append("Delta4 = " + _delta4 + ", ");
+ stringBuilder.Append("LightSourcePort = " + _lightSourcePort + ", ");
+ stringBuilder.Append("CameraPort = " + _cameraPort + ", ");
+ stringBuilder.Append("EventsEnabled = " + _eventsEnabled + ", ");
+ stringBuilder.Append("MuteOutput = " + _muteOutput + ", ");
+ stringBuilder.Append("PwmFrequency = " + _pwmFrequency);
+ 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 HarpCuttlefishfip
+ {
+
+ private string _deviceType;
+
+ private string _deviceName;
+
+ private BaseModel _additionalSettings;
+
+ private BaseModel _calibration;
+
+ private int _whoAmI;
+
+ private string _serialNumber;
+
+ private string _portName;
+
+ public HarpCuttlefishfip()
+ {
+ _deviceType = "cuTTLefishFip";
+ _whoAmI = 1407;
+ }
+
+ protected HarpCuttlefishfip(HarpCuttlefishfip 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 HarpCuttlefishfip(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new HarpCuttlefishfip(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();
+ }
+ }
+
+
+ ///
+ /// Light source device configuration with power control and timing tasks.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [System.ComponentModel.DescriptionAttribute("Light source device configuration with power control and timing tasks.")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class LightSource
+ {
+
+ private string _deviceType;
+
+ private string _deviceName;
+
+ private BaseModel _additionalSettings;
+
+ private LightSourceCalibration _calibration;
+
+ private double _power;
+
+ private FipTask _task;
+
+ public LightSource()
+ {
+ _deviceType = "LightSource";
+ _power = 0D;
+ _task = new FipTask();
+ }
+
+ protected LightSource(LightSource other)
+ {
+ _deviceType = other._deviceType;
+ _deviceName = other._deviceName;
+ _additionalSettings = other._additionalSettings;
+ _calibration = other._calibration;
+ _power = other._power;
+ _task = other._task;
+ }
+
+ [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 for the LightSource. If left empty, 'power' will be used as duty-cycle (0-100).
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("calibration")]
+ [System.ComponentModel.DescriptionAttribute("Calibration for the LightSource. If left empty, \'power\' will be used as duty-cycl" +
+ "e (0-100).")]
+ public LightSourceCalibration Calibration
+ {
+ get
+ {
+ return _calibration;
+ }
+ set
+ {
+ _calibration = value;
+ }
+ }
+
+ ///
+ /// Power (mW)
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("power")]
+ [System.ComponentModel.DescriptionAttribute("Power (mW)")]
+ public double Power
+ {
+ get
+ {
+ return _power;
+ }
+ set
+ {
+ _power = value;
+ }
+ }
+
+ ///
+ /// Task for the light source
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("task", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Task for the light source")]
+ public FipTask Task
+ {
+ get
+ {
+ return _task;
+ }
+ set
+ {
+ _task = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new LightSource(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new LightSource(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("Power = " + _power + ", ");
+ stringBuilder.Append("Task = " + _task);
+ 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();
+ }
+ }
+
+
+ ///
+ /// Calibration model for converting light source duty cycle to power output.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [System.ComponentModel.DescriptionAttribute("Calibration model for converting light source duty cycle to power output.")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class LightSourceCalibration
+ {
+
+ private string _deviceName;
+
+ private BaseModel _input;
+
+ private LightSourceCalibrationOutput _output;
+
+ private System.DateTimeOffset? _date;
+
+ private string _description;
+
+ private string _notes;
+
+ public LightSourceCalibration()
+ {
+ _output = new LightSourceCalibrationOutput();
+ }
+
+ protected LightSourceCalibration(LightSourceCalibration 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", Required=Newtonsoft.Json.Required.Always)]
+ [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")]
+ public BaseModel Input
+ {
+ get
+ {
+ return _input;
+ }
+ set
+ {
+ _input = value;
+ }
+ }
+
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("output", Required=Newtonsoft.Json.Required.Always)]
+ public LightSourceCalibrationOutput 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 LightSourceCalibration(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new LightSourceCalibration(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();
+ }
+ }
+
+
+ ///
+ /// Output of the light source calibration process.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [System.ComponentModel.DescriptionAttribute("Output of the light source calibration process.")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class LightSourceCalibrationOutput
+ {
+
+ private System.Collections.Generic.Dictionary _powerLut;
+
+ public LightSourceCalibrationOutput()
+ {
+ _powerLut = new System.Collections.Generic.Dictionary();
+ }
+
+ protected LightSourceCalibrationOutput(LightSourceCalibrationOutput other)
+ {
+ _powerLut = other._powerLut;
+ }
+
+ ///
+ /// Look-up table for LightSource power vs. duty cycle
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("power_lut", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Look-up table for LightSource power vs. duty cycle")]
+ public System.Collections.Generic.Dictionary PowerLut
+ {
+ get
+ {
+ return _powerLut;
+ }
+ set
+ {
+ _powerLut = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new LightSourceCalibrationOutput(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new LightSourceCalibrationOutput(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("PowerLut = " + _powerLut);
+ 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();
+ }
+ }
+
+
+ ///
+ /// Network configuration settings for ZeroMQ communication.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [System.ComponentModel.DescriptionAttribute("Network configuration settings for ZeroMQ communication.")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class Networking
+ {
+
+ private ZmqConnection _zmqPublisher;
+
+ private ZmqConnection _zmqSubscriber;
+
+ public Networking()
+ {
+ _zmqPublisher = new ZmqConnection();
+ _zmqSubscriber = new ZmqConnection();
+ }
+
+ protected Networking(Networking other)
+ {
+ _zmqPublisher = other._zmqPublisher;
+ _zmqSubscriber = other._zmqSubscriber;
+ }
+
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("zmq_publisher")]
+ public ZmqConnection ZmqPublisher
+ {
+ get
+ {
+ return _zmqPublisher;
+ }
+ set
+ {
+ _zmqPublisher = value;
+ }
+ }
+
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("zmq_subscriber")]
+ public ZmqConnection ZmqSubscriber
+ {
+ get
+ {
+ return _zmqSubscriber;
+ }
+ set
+ {
+ _zmqSubscriber = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Networking(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new Networking(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("ZmqPublisher = " + _zmqPublisher + ", ");
+ stringBuilder.Append("ZmqSubscriber = " + _zmqSubscriber);
+ 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 Point2f
+ {
+
+ private double _x;
+
+ private double _y;
+
+ public Point2f()
+ {
+ }
+
+ protected Point2f(Point2f other)
+ {
+ _x = other._x;
+ _y = other._y;
+ }
+
+ ///
+ /// X coordinate of the point (px)
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("x", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("X coordinate of the point (px)")]
+ public double X
+ {
+ get
+ {
+ return _x;
+ }
+ set
+ {
+ _x = value;
+ }
+ }
+
+ ///
+ /// Y coordinate of the point (px)
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("y", Required=Newtonsoft.Json.Required.Always)]
+ [System.ComponentModel.DescriptionAttribute("Y coordinate of the point (px)")]
+ public double Y
+ {
+ get
+ {
+ return _y;
+ }
+ set
+ {
+ _y = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new Point2f(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new Point2f(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("X = " + _x + ", ");
+ stringBuilder.Append("Y = " + _y);
+ 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();
+ }
+ }
+
+
+ ///
+ /// Available hardware ports in the FIP cuttlefish board.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ public enum Ports
+ {
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="0")]
+ None = 0,
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="1")]
+ Io0 = 1,
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="2")]
+ Io1 = 2,
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="4")]
+ Io2 = 4,
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="8")]
+ Io3 = 8,
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="16")]
+ Io4 = 16,
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="32")]
+ Io5 = 32,
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="64")]
+ Io6 = 64,
+
+ [System.Runtime.Serialization.EnumMemberAttribute(Value="128")]
+ Io7 = 128,
+ }
+
+
+ ///
+ /// Region of Interest (ROI) settings for camera channels in the FIP system.
+ ///
+ [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+ [System.ComponentModel.DescriptionAttribute("Region of Interest (ROI) settings for camera channels in the FIP system.")]
+ [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
+ [Bonsai.CombinatorAttribute(MethodName="Generate")]
+ public partial class RoiSettings
+ {
+
+ private Circle _cameraGreenIsoBackground;
+
+ private Circle _cameraRedBackground;
+
+ private System.Collections.Generic.List _cameraGreenIsoRoi;
+
+ private System.Collections.Generic.List _cameraRedRoi;
+
+ public RoiSettings()
+ {
+ _cameraGreenIsoBackground = new Circle();
+ _cameraRedBackground = new Circle();
+ _cameraGreenIsoRoi = new System.Collections.Generic.List();
+ _cameraRedRoi = new System.Collections.Generic.List();
+ }
+
+ protected RoiSettings(RoiSettings other)
+ {
+ _cameraGreenIsoBackground = other._cameraGreenIsoBackground;
+ _cameraRedBackground = other._cameraRedBackground;
+ _cameraGreenIsoRoi = other._cameraGreenIsoRoi;
+ _cameraRedRoi = other._cameraRedRoi;
+ }
+
+ ///
+ /// ROI to compute the background for the green/iso camera channel
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("camera_green_iso_background")]
+ [System.ComponentModel.DescriptionAttribute("ROI to compute the background for the green/iso camera channel")]
+ public Circle CameraGreenIsoBackground
+ {
+ get
+ {
+ return _cameraGreenIsoBackground;
+ }
+ set
+ {
+ _cameraGreenIsoBackground = value;
+ }
+ }
+
+ ///
+ /// ROI to compute the background for the red camera channel
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("camera_red_background")]
+ [System.ComponentModel.DescriptionAttribute("ROI to compute the background for the red camera channel")]
+ public Circle CameraRedBackground
+ {
+ get
+ {
+ return _cameraRedBackground;
+ }
+ set
+ {
+ _cameraRedBackground = value;
+ }
+ }
+
+ ///
+ /// ROI for the green/iso camera channel
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("camera_green_iso_roi")]
+ [System.ComponentModel.DescriptionAttribute("ROI for the green/iso camera channel")]
+ public System.Collections.Generic.List CameraGreenIsoRoi
+ {
+ get
+ {
+ return _cameraGreenIsoRoi;
+ }
+ set
+ {
+ _cameraGreenIsoRoi = value;
+ }
+ }
+
+ ///
+ /// ROI for the red camera channel
+ ///
+ [System.Xml.Serialization.XmlIgnoreAttribute()]
+ [Newtonsoft.Json.JsonPropertyAttribute("camera_red_roi")]
+ [System.ComponentModel.DescriptionAttribute("ROI for the red camera channel")]
+ public System.Collections.Generic.List CameraRedRoi
+ {
+ get
+ {
+ return _cameraRedRoi;
+ }
+ set
+ {
+ _cameraRedRoi = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new RoiSettings(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new RoiSettings(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("CameraGreenIsoBackground = " + _cameraGreenIsoBackground + ", ");
+ stringBuilder.Append("CameraRedBackground = " + _cameraRedBackground + ", ");
+ stringBuilder.Append("CameraGreenIsoRoi = " + _cameraGreenIsoRoi + ", ");
+ stringBuilder.Append("CameraRedRoi = " + _cameraRedRoi);
+ 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 ZmqConnection
+ {
+
+ private string _connectionString;
+
+ private string _topic;
+
+ public ZmqConnection()
+ {
+ _connectionString = "@tcp://localhost:5556";
+ _topic = "";
+ }
+
+ protected ZmqConnection(ZmqConnection other)
+ {
+ _connectionString = other._connectionString;
+ _topic = other._topic;
+ }
+
+ ///
+ /// The connection string for the ZMQ socket.
+ ///
+ [Newtonsoft.Json.JsonPropertyAttribute("connection_string")]
+ [System.ComponentModel.DescriptionAttribute("The connection string for the ZMQ socket.")]
+ public string ConnectionString
+ {
+ get
+ {
+ return _connectionString;
+ }
+ set
+ {
+ _connectionString = value;
+ }
+ }
+
+ [Newtonsoft.Json.JsonPropertyAttribute("topic")]
+ public string Topic
+ {
+ get
+ {
+ return _topic;
+ }
+ set
+ {
+ _topic = value;
+ }
+ }
+
+ public System.IObservable Generate()
+ {
+ return System.Reactive.Linq.Observable.Defer(() => System.Reactive.Linq.Observable.Return(new ZmqConnection(this)));
+ }
+
+ public System.IObservable Generate(System.IObservable source)
+ {
+ return System.Reactive.Linq.Observable.Select(source, _ => new ZmqConnection(this));
+ }
+
+ protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
+ {
+ stringBuilder.Append("ConnectionString = " + _connectionString + ", ");
+ stringBuilder.Append("Topic = " + _topic);
+ return true;
+ }
+
+ public override string ToString()
+ {
+ System.Text.StringBuilder stringBuilder = new System.Text.StringBuilder();
+ stringBuilder.Append(GetType().Name);
+ stringBuilder.Append(" { ");
+ if (PrintMembers(stringBuilder))
+ {
+ stringBuilder.Append(" ");
+ }
+ stringBuilder.Append("}");
+ return stringBuilder.ToString();
+ }
+ }
+
+
+ ///