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Ticket/2545/dev #2604

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merged 6 commits into from
Nov 17, 2022
Merged

Ticket/2545/dev #2604

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2bab3b5
added data object TargetImagingDepth
mikejhuang Nov 9, 2022
cfbd2db
Add target_imaging_depth to behavior_ophys_metadata, multiplane_metad…
mikejhuang Nov 10, 2022
3ff5c5a
lint
mikejhuang Nov 10, 2022
b6d9d21
rename target_imaging_depth to average_container_depth
mikejhuang Nov 14, 2022
6800f2a
added docstring and reformatted average_container_depth query
mikejhuang Nov 14, 2022
1df9a32
fix from_json method from imaging_depth and average_container_depth
mikejhuang Nov 15, 2022
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50 changes: 15 additions & 35 deletions allensdk/brain_observatory/behavior/behavior_ophys_experiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,44 +2,22 @@
import pandas as pd
from pynwb import NWBFile

from allensdk.brain_observatory.behavior.behavior_session import (
BehaviorSession)
from allensdk.brain_observatory.behavior.behavior_session import BehaviorSession # NOQA
from allensdk.brain_observatory.behavior.data_files import SyncFile
from allensdk.brain_observatory.behavior.data_files\
.rigid_motion_transform_file import \
RigidMotionTransformFile
from allensdk.brain_observatory.behavior.data_objects import \
BehaviorSessionId
from allensdk.brain_observatory.behavior.data_objects.cell_specimens \
.cell_specimens import \
CellSpecimens, EventsParams
from allensdk.brain_observatory.behavior.data_objects.metadata \
.behavior_metadata.date_of_acquisition import \
DateOfAcquisitionOphys, DateOfAcquisition
from allensdk.brain_observatory.behavior.data_objects.metadata\
.behavior_ophys_metadata import \
BehaviorOphysMetadata
from allensdk.brain_observatory.behavior.data_objects.metadata\
.ophys_experiment_metadata.multi_plane_metadata.imaging_plane_group \
import \
ImagingPlaneGroup
from allensdk.brain_observatory.behavior.data_objects.metadata\
.ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata \
import \
MultiplaneMetadata
from allensdk.brain_observatory.behavior.data_objects.motion_correction \
import \
MotionCorrection
from allensdk.brain_observatory.behavior.data_objects.projections import \
Projections
from allensdk.brain_observatory.behavior.data_objects.stimuli.util import \
calculate_monitor_delay
from allensdk.brain_observatory.behavior.data_objects.timestamps \
.ophys_timestamps import \
OphysTimestamps, OphysTimestampsMultiplane
from allensdk.brain_observatory.behavior.data_files.rigid_motion_transform_file import RigidMotionTransformFile # NOQA
from allensdk.brain_observatory.behavior.data_objects import BehaviorSessionId
from allensdk.brain_observatory.behavior.data_objects.cell_specimens.cell_specimens import CellSpecimens, EventsParams # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.date_of_acquisition import DateOfAcquisition, DateOfAcquisitionOphys # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.behavior_ophys_metadata import BehaviorOphysMetadata # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.imaging_plane_group import ImagingPlaneGroup # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata import MultiplaneMetadata # NOQA
from allensdk.brain_observatory.behavior.data_objects.motion_correction import MotionCorrection # NOQA
from allensdk.brain_observatory.behavior.data_objects.projections import Projections # NOQA
from allensdk.brain_observatory.behavior.data_objects.stimuli.util import calculate_monitor_delay # NOQA
from allensdk.brain_observatory.behavior.data_objects.timestamps.ophys_timestamps import OphysTimestamps, OphysTimestampsMultiplane # NOQA
from allensdk.brain_observatory.behavior.image_api import Image
from allensdk.core.auth_config import LIMS_DB_CREDENTIAL_MAP
from allensdk.deprecated import legacy
from allensdk.brain_observatory.behavior.image_api import Image
from allensdk.internal.api import db_connection_creator


Expand Down Expand Up @@ -426,6 +404,8 @@ def metadata(self):
'field_of_view_width':
self._metadata.ophys_metadata.field_of_view_shape.width,
'imaging_depth': self._metadata.ophys_metadata.imaging_depth,
'average_container_depth':
self._metadata.ophys_metadata.average_container_depth,
'imaging_plane_group':
self._metadata.ophys_metadata.imaging_plane_group
if isinstance(self._metadata.ophys_metadata,
Expand Down
24 changes: 6 additions & 18 deletions allensdk/brain_observatory/behavior/data_objects/metadata/behavior_ophys_metadata.py
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Expand Up @@ -2,26 +2,13 @@

from pynwb import NWBFile

from allensdk.core import DataObject
from allensdk.brain_observatory.behavior.data_objects import BehaviorSessionId
from allensdk.core import \
JsonReadableInterface, NwbReadableInterface, \
LimsReadableInterface
from allensdk.core import \
NwbWritableInterface
from allensdk.brain_observatory.behavior.data_objects.metadata\
.behavior_metadata.behavior_metadata import \
BehaviorMetadata
from allensdk.brain_observatory.behavior.data_objects.metadata\
.ophys_experiment_metadata.multi_plane_metadata\
.multi_plane_metadata import \
MultiplaneMetadata
from allensdk.brain_observatory.behavior.data_objects.metadata\
.ophys_experiment_metadata.ophys_experiment_metadata import \
OphysExperimentMetadata
from allensdk.brain_observatory.behavior.schemas import \
OphysBehaviorMetadataSchema
from allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.behavior_metadata import BehaviorMetadata # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata import MultiplaneMetadata # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata import OphysExperimentMetadata # NOQA
from allensdk.brain_observatory.behavior.schemas import OphysBehaviorMetadataSchema # NOQA
from allensdk.brain_observatory.nwb import load_pynwb_extension
from allensdk.core import DataObject, JsonReadableInterface, LimsReadableInterface, NwbReadableInterface, NwbWritableInterface # NOQA
from allensdk.internal.api import PostgresQueryMixin


Expand Down Expand Up @@ -158,6 +145,7 @@ def to_nwb(self, nwbfile: NWBFile) -> NWBFile:
session_type=behavior_meta.session_type,
equipment_name=behavior_meta.equipment.value,
imaging_depth=ophys_meta.imaging_depth,
average_container_depth=ophys_meta.average_container_depth,
behavior_session_uuid=str(behavior_meta.behavior_session_uuid),
behavior_session_id=behavior_meta.behavior_session_id
)
Expand Down
58 changes: 58 additions & 0 deletions ...atory/behavior/data_objects/metadata/ophys_experiment_metadata/average_container_depth.py
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@@ -0,0 +1,58 @@
from pynwb import NWBFile

from allensdk.core import DataObject, JsonReadableInterface, LimsReadableInterface, NwbReadableInterface # NOQA
from allensdk.internal.api import PostgresQueryMixin


class AverageContainerDepth(
DataObject,
LimsReadableInterface,
NwbReadableInterface,
JsonReadableInterface,
):
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"""Data object loads and stores the average `imaging_depth`s
(microns) across experiments in the container that an experiment is
associated with.
"""
def __init__(self, average_container_depth: int):
super().__init__(
name="average_container_depth", value=average_container_depth
)

@classmethod
def from_lims(
cls, ophys_experiment_id: int, lims_db: PostgresQueryMixin
) -> "AverageContainerDepth":
query_container_id = """
SELECT visual_behavior_experiment_container_id
FROM ophys_experiments_visual_behavior_experiment_containers
WHERE ophys_experiment_id = {}
""".format(
ophys_experiment_id
)

container_id = lims_db.fetchone(query_container_id, strict=True)

query_depths = """
SELECT AVG(imd.depth)
FROM ophys_experiments_visual_behavior_experiment_containers ec
JOIN ophys_experiments oe ON oe.id = ec.ophys_experiment_id
LEFT JOIN imaging_depths imd ON imd.id = oe.imaging_depth_id
WHERE ec.visual_behavior_experiment_container_id = {};
""".format(
container_id
)

average_container_depth = int(lims_db.fetchone(query_depths))
return cls(average_container_depth=average_container_depth)

@classmethod
def from_json(cls, dict_repr: dict) -> "AverageContainerDepth":
# TODO remove all of the from_json loading and validation step
# ticket 2607
return cls(average_container_depth=dict_repr["targeted_depth"])

@classmethod
def from_nwb(cls, nwbfile: NWBFile) -> "AverageContainerDepth":
metadata = nwbfile.lab_meta_data["metadata"]
return cls(average_container_depth=metadata.average_container_depth)
10 changes: 8 additions & 2 deletions ...ain_observatory/behavior/data_objects/metadata/ophys_experiment_metadata/imaging_depth.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,24 +8,30 @@

class ImagingDepth(DataObject, LimsReadableInterface, NwbReadableInterface,
JsonReadableInterface):
"""Data object loads and stores the imaging_depth (microns) for an
experiments. This is the calculated difference between measured
z-depths of the surface and imaging_depth.
"""
def __init__(self, imaging_depth: int):
super().__init__(name='imaging_depth', value=imaging_depth)

@classmethod
def from_lims(cls, ophys_experiment_id: int,
lims_db: PostgresQueryMixin) -> "ImagingDepth":
query = """
SELECT id.depth
SELECT imd.depth
FROM ophys_experiments oe
JOIN ophys_sessions os ON oe.ophys_session_id = os.id
LEFT JOIN imaging_depths id ON id.id = oe.imaging_depth_id
LEFT JOIN imaging_depths imd ON imd.id = oe.imaging_depth_id
WHERE oe.id = {};
""".format(ophys_experiment_id)
imaging_depth = lims_db.fetchone(query, strict=True)
return cls(imaging_depth=imaging_depth)

@classmethod
def from_json(cls, dict_repr: dict) -> "ImagingDepth":
# TODO remove all of the from_json loading and validation step
# ticket 2607
return cls(imaging_depth=dict_repr['targeted_depth'])

@classmethod
Expand Down
41 changes: 16 additions & 25 deletions ...a_objects/metadata/ophys_experiment_metadata/multi_plane_metadata/multi_plane_metadata.py
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Original file line number Diff line number Diff line change
@@ -1,27 +1,13 @@
from pynwb import NWBFile

from allensdk.brain_observatory.behavior.data_objects.metadata \
.ophys_experiment_metadata.ophys_container_id import \
OphysContainerId
from allensdk.brain_observatory.behavior.data_objects.metadata \
.ophys_experiment_metadata.field_of_view_shape import \
FieldOfViewShape
from allensdk.brain_observatory.behavior.data_objects.metadata \
.ophys_experiment_metadata.imaging_depth import \
ImagingDepth
from allensdk.brain_observatory.behavior.data_objects.metadata \
.ophys_experiment_metadata.multi_plane_metadata \
.imaging_plane_group import \
ImagingPlaneGroup
from allensdk.brain_observatory.behavior.data_objects.metadata \
.ophys_experiment_metadata.ophys_experiment_metadata import \
OphysExperimentMetadata
from allensdk.brain_observatory.behavior.data_objects.metadata \
.ophys_experiment_metadata.ophys_session_id import \
OphysSessionId
from allensdk.brain_observatory.behavior.data_objects.metadata \
.ophys_experiment_metadata.project_code import \
ProjectCode
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.field_of_view_shape import FieldOfViewShape # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_depth import ImagingDepth # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.imaging_plane_group import ImagingPlaneGroup # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_container_id import OphysContainerId # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata import OphysExperimentMetadata # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_session_id import OphysSessionId # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.project_code import ProjectCode # NOQA
from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.average_container_depth import AverageContainerDepth # NOQA
from allensdk.internal.api import PostgresQueryMixin


Expand All @@ -32,6 +18,7 @@ def __init__(self,
ophys_container_id: OphysContainerId,
field_of_view_shape: FieldOfViewShape,
imaging_depth: ImagingDepth,
average_container_depth: AverageContainerDepth,
imaging_plane_group: ImagingPlaneGroup,
project_code: ProjectCode):
super().__init__(
Expand All @@ -40,6 +27,7 @@ def __init__(self,
ophys_container_id=ophys_container_id,
field_of_view_shape=field_of_view_shape,
imaging_depth=imaging_depth,
average_container_depth=average_container_depth,
project_code=project_code
)
self._imaging_plane_group = imaging_plane_group
Expand All @@ -55,9 +43,10 @@ def from_lims(
return cls(
ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
ophys_session_id=ophys_experiment_metadata._ophys_session_id,
ophys_container_id=ophys_experiment_metadata._ophys_container_id, # noqa E501
ophys_container_id=ophys_experiment_metadata._ophys_container_id,
field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
imaging_depth=ophys_experiment_metadata._imaging_depth,
average_container_depth=ophys_experiment_metadata._average_container_depth, # noqa E501
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Does black really not split this line and the others like it?

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There's been a ticket open for this on the black repository since 2018 and it hasn't been resolved yet.
psf/black#510

A black collaborator acknowledged the issue needs to be fixed in 2020
psf/black#1582 (comment)

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huh, if you fix it by hand, does black just revert it?

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Yes, it gets reverted.

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okay, guess we'll live with it.

project_code=ophys_experiment_metadata._project_code,
imaging_plane_group=imaging_plane_group
)
Expand All @@ -69,9 +58,10 @@ def from_json(cls, dict_repr: dict) -> "MultiplaneMetadata":
return cls(
ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
ophys_session_id=ophys_experiment_metadata._ophys_session_id,
ophys_container_id=ophys_experiment_metadata._ophys_container_id, # noqa E501
ophys_container_id=ophys_experiment_metadata._ophys_container_id,
field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
imaging_depth=ophys_experiment_metadata._imaging_depth,
average_container_depth=ophys_experiment_metadata._average_container_depth, # noqa E501
project_code=ophys_experiment_metadata._project_code,
imaging_plane_group=imaging_plane_group
)
Expand All @@ -83,9 +73,10 @@ def from_nwb(cls, nwbfile: NWBFile) -> "MultiplaneMetadata":
return cls(
ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
ophys_session_id=ophys_experiment_metadata._ophys_session_id,
ophys_container_id=ophys_experiment_metadata._ophys_container_id, # noqa E501
ophys_container_id=ophys_experiment_metadata._ophys_container_id,
field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
imaging_depth=ophys_experiment_metadata._imaging_depth,
average_container_depth=ophys_experiment_metadata._average_container_depth, # noqa E501
project_code=ophys_experiment_metadata._project_code,
imaging_plane_group=imaging_plane_group
)
Expand Down
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