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57 changes: 33 additions & 24 deletions
57
...ervatory/behavior/data_objects/metadata/ophys_experiment_metadata/target_imaging_depth.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,54 @@ | ||
| from pynwb import NWBFile | ||
|
|
||
| from allensdk.core import DataObject | ||
| from allensdk.core import \ | ||
| JsonReadableInterface, LimsReadableInterface, NwbReadableInterface | ||
| from allensdk.core import DataObject, JsonReadableInterface, LimsReadableInterface, NwbReadableInterface # NOQA | ||
| from allensdk.internal.api import PostgresQueryMixin | ||
|
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||
|
|
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| class TargetImagingDepth(DataObject, LimsReadableInterface, NwbReadableInterface, | ||
| JsonReadableInterface): | ||
| class TargetImagingDepth( | ||
| DataObject, | ||
| LimsReadableInterface, | ||
| NwbReadableInterface, | ||
| JsonReadableInterface, | ||
| ): | ||
| def __init__(self, target_imaging_depth: int): | ||
| super().__init__(name='target_imaging_depth', value=target_imaging_depth) | ||
| super().__init__( | ||
| name="target_imaging_depth", value=target_imaging_depth | ||
| ) | ||
|
|
||
| @classmethod | ||
| def from_lims(cls, ophys_experiment_id: int, | ||
| lims_db: PostgresQueryMixin) -> "TargetImagingDepth": | ||
| def from_lims( | ||
| cls, ophys_experiment_id: int, lims_db: PostgresQueryMixin | ||
| ) -> "TargetImagingDepth": | ||
| query_container_id = """ | ||
| SELECT visual_behavior_experiment_container_id | ||
| FROM ophys_experiments_visual_behavior_experiment_containers | ||
| WHERE ophys_experiment_id = {} | ||
| """.format(ophys_experiment_id) | ||
|
|
||
| SELECT visual_behavior_experiment_container_id | ||
| FROM ophys_experiments_visual_behavior_experiment_containers | ||
| WHERE ophys_experiment_id = {} | ||
| """.format( | ||
| ophys_experiment_id | ||
| ) | ||
|
|
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| container_id = lims_db.fetchone(query_container_id, strict=True) | ||
|
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| query_depths = """ | ||
| SELECT id.depth | ||
| FROM ophys_experiments_visual_behavior_experiment_containers ec | ||
| JOIN ophys_experiments oe ON oe.id = ec.ophys_experiment_id | ||
| JOIN ophys_sessions os ON oe.ophys_session_id = os.id | ||
| LEFT JOIN imaging_depths id ON id.id = oe.imaging_depth_id | ||
| WHERE ec.visual_behavior_experiment_container_id = {}; | ||
| """.format(container_id) | ||
|
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||
| SELECT id.depth | ||
| FROM ophys_experiments_visual_behavior_experiment_containers ec | ||
| JOIN ophys_experiments oe ON oe.id = ec.ophys_experiment_id | ||
| JOIN ophys_sessions os ON oe.ophys_session_id = os.id | ||
| LEFT JOIN imaging_depths id ON id.id = oe.imaging_depth_id | ||
| WHERE ec.visual_behavior_experiment_container_id = {}; | ||
| """.format( | ||
| container_id | ||
| ) | ||
|
|
||
| imaging_depths = lims_db.fetchall(query_depths) | ||
| target_imaging_depth = sum(imaging_depths)/len(imaging_depths) | ||
| target_imaging_depth = sum(imaging_depths) / len(imaging_depths) | ||
| return cls(target_imaging_depth=target_imaging_depth) | ||
|
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||
| @classmethod | ||
| def from_json(cls, dict_repr: dict) -> "TargetImagingDepth": | ||
| return cls(target_imaging_depth=dict_repr['targeted_imaging_depth']) | ||
| return cls(target_imaging_depth=dict_repr["targeted_imaging_depth"]) | ||
|
|
||
| @classmethod | ||
| def from_nwb(cls, nwbfile: NWBFile) -> "TargetImagingDepth": | ||
| metadata = nwbfile.lab_meta_data['metadata'] | ||
| metadata = nwbfile.lab_meta_data["metadata"] | ||
| return cls(target_imaging_depth=metadata.target_imaging_depth) |
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