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"aind-data-schema==0.33.3", "pydantic>=2.6.4", "npc-lims>=0.1.176", "npc-sync>=0.1.18", @@ -33,6 +32,7 @@ dependencies = [ "npc-session>=0.1.39", "npc-mvr>=0.1.7", "npc-io>=0.1.30", + "aind-data-schema @ git+https://github.com/AllenNeuralDynamics/aind-data-schema.git@1072-qc-automate-state-properties-in-qualitycontrol-and-evaluation-based-on-metric-states", ] requires-python = ">=3.9" readme = "README.md" diff --git a/src/npc_sessions/sessions.py b/src/npc_sessions/sessions.py index 044e11c..8c12daa 100644 --- a/src/npc_sessions/sessions.py +++ b/src/npc_sessions/sessions.py @@ -15,10 +15,10 @@ from typing import Any, Literal import aind_data_schema.core.session -import aind_data_schema.models.coordinates -import aind_data_schema.models.devices -import aind_data_schema.models.modalities -import aind_data_schema.models.stimulus +import aind_data_schema.components.coordinates +import aind_data_schema.components.devices +import aind_data_schema_models.modalities +import aind_data_schema.components.stimulus import cv2 import h5py import hdmf @@ -3156,23 +3156,23 @@ def _aind_reward_delivery( reward_spouts=[ aind_data_schema.core.session.RewardSpoutConfig( side="Center", - starting_position=aind_data_schema.models.coordinates.RelativePosition( + starting_position=aind_data_schema.components.coordinates.RelativePosition( device_position_transformations=[ - aind_data_schema.models.coordinates.Translation3dTransform( + aind_data_schema.components.coordinates.Translation3dTransform( translation=[0.0, 0.0, 0.0], ) ], device_origin="Located on the tip of the spout (which is also the lick sensor), centered in front of the subject's mouth", device_axes=[ - aind_data_schema.models.coordinates.Axis( + aind_data_schema.components.coordinates.Axis( name="X", direction="Positive is from the centerline of the subject's mouth towards its right", ), - aind_data_schema.models.coordinates.Axis( + aind_data_schema.components.coordinates.Axis( name="Y", direction="Positive is from the centerline of the subject's mouth towards the sky", ), - aind_data_schema.models.coordinates.Axis( + aind_data_schema.components.coordinates.Axis( name="Z", direction="Positive is from the anterior-most part of the subject's mouth towards its tail", ), @@ -3187,7 +3187,7 @@ def _aind_reward_delivery( def _aind_data_streams(self) -> tuple[aind_data_schema.core.session.Stream, ...]: data_streams = [] # sync, mvr cameras, ephys probes - modality = aind_data_schema.models.modalities.Modality + modality = aind_data_schema_models.modalities.Modality if self.is_sync: data_streams.append( aind_data_schema.core.session.Stream( @@ -3244,7 +3244,7 @@ def _aind_data_streams(self) -> tuple[aind_data_schema.core.session.Stream, ...] primary_targeted_structure="none", manipulator_coordinates=( ( - aind_data_schema.models.coordinates.Coordinates3d( + aind_data_schema.components.coordinates.Coordinates3d( x=( row := self._manipulator_positions.to_dataframe().query( f"electrode_group == '{probe.name}'" @@ -3256,7 +3256,7 @@ def _aind_data_streams(self) -> tuple[aind_data_schema.core.session.Stream, ...] ) ) # some old sessions didn't have newscale logging enabled: no way to get their coords if hasattr(self, "_manipulator_info") - else aind_data_schema.models.coordinates.Coordinates3d( + else aind_data_schema.components.coordinates.Coordinates3d( x=0.0, y=0.0, z=0.0, @@ -3351,7 +3351,7 @@ def get_parameters( epoch_name: str, ) -> list[Any] | None: # no baseclass for stim param classes stim = aind_data_schema.core.session.StimulusModality - stimulus = aind_data_schema.models.stimulus + stimulus = aind_data_schema.components.stimulus modalities = get_modalities(epoch_name) if modalities == [stim.NONE]: return None @@ -3560,13 +3560,13 @@ def get_task_metrics() -> dict[str, dict]: + self.session_start_time, stimulus_name=epoch_name, software=[ - aind_data_schema.models.devices.Software( + aind_data_schema.components.devices.Software( name="PsychoPy", version="2022.1.2", url="https://www.psychopy.org/", ), ], - script=aind_data_schema.models.devices.Software( + script=aind_data_schema.components.devices.Software( name=get_taskcontrol_file(epoch_name), version=get_version() or "unknown", url=get_url(epoch_name),