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Revert accidental push.
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@morriscb
morriscb committed May 16, 2023
1 parent 38e186b commit 5c54dd8
Showing 1 changed file with 29 additions and 67 deletions.
96 changes: 29 additions & 67 deletions allensdk/brain_observatory/behavior/data_objects/cell_specimens/cell_specimens.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@
from pynwb import NWBFile, ProcessingModule
from pynwb.ophys import OpticalChannel, ImageSegmentation

from allensdk import OneResultExpectedError
import allensdk.brain_observatory.roi_masks as roi
from allensdk.brain_observatory.behavior.data_files.neuropil_corrected_file \
import NeuropilCorrectedFile
Expand Down Expand Up @@ -190,19 +189,18 @@ def __init__(
name="cell_specimen_table", value=None, is_value_self=True
)

if len(cell_specimen_table) > 0:
# Validate ophys timestamps, traces
ophys_timestamps = ophys_timestamps.validate(
number_of_frames=dff_traces.get_number_of_frames()
)
self._validate_traces(
ophys_timestamps=ophys_timestamps,
dff_traces=dff_traces,
demixed_traces=demixed_traces,
neuropil_traces=neuropil_traces,
corrected_fluorescence_traces=corrected_fluorescence_traces,
cell_roi_ids=cell_specimen_table["cell_roi_id"].values,
)
ophys_timestamps = ophys_timestamps.validate(
number_of_frames=dff_traces.get_number_of_frames()
)
self._validate_traces(
ophys_timestamps=ophys_timestamps,
dff_traces=dff_traces,
demixed_traces=demixed_traces,
neuropil_traces=neuropil_traces,
corrected_fluorescence_traces=corrected_fluorescence_traces,
cell_roi_ids=cell_specimen_table["cell_roi_id"].values,
)

if exclude_invalid_rois:
cell_specimen_table = cell_specimen_table[
Expand All @@ -222,20 +220,18 @@ def __init__(
neuropil_traces.filter_and_reorder(
roi_ids=cell_specimen_table["cell_roi_id"].values
)
if corrected_fluorescence_traces is not None:
corrected_fluorescence_traces.filter_and_reorder(
roi_ids=cell_specimen_table["cell_roi_id"].values
)
corrected_fluorescence_traces.filter_and_reorder(
roi_ids=cell_specimen_table["cell_roi_id"].values
)

# Note: setting raise_if_rois_missing to False for events, since
# there seem to be cases where cell_specimen_table contains rois not in
# events
# See ie https://app.zenhub.com/workspaces/allensdk-10-5c17f74db59cfb36f158db8c/issues/alleninstitute/allensdk/2139 # noqa
if events is not None:
events.filter_and_reorder(
roi_ids=cell_specimen_table["cell_roi_id"].values,
raise_if_rois_missing=False,
)
events.filter_and_reorder(
roi_ids=cell_specimen_table["cell_roi_id"].values,
raise_if_rois_missing=False,
)

self._meta = meta
self._cell_specimen_table = cell_specimen_table
Expand All @@ -244,12 +240,9 @@ def __init__(
self._neuropil_traces = neuropil_traces
self._corrected_fluorescence_traces = corrected_fluorescence_traces
self._events = events
if len(cell_specimen_table) > 0:
self._segmentation_mask_image = self._get_segmentation_mask_image(
spacing=segmentation_mask_image_spacing
)
else:
self._segmentation_mask_image = None
self._segmentation_mask_image = self._get_segmentation_mask_image(
spacing=segmentation_mask_image_spacing
)

@property
def table(self) -> pd.DataFrame:
Expand Down Expand Up @@ -416,10 +409,7 @@ def _get_ophys_cell_segmentation_run_id() -> int:
""".format(
ophys_experiment_id
)
try:
return lims_db.fetchone(query, strict=True)
except OneResultExpectedError:
return -1
return lims_db.fetchone(query, strict=True)

def _get_cell_specimen_table():
ophys_cell_seg_run_id = _get_ophys_cell_segmentation_run_id()
Expand All @@ -430,10 +420,7 @@ def _get_cell_specimen_table():
""".format(
ophys_cell_seg_run_id
)
try:
initial_cs_table = pd.read_sql(query, lims_db.get_connection())
except OneResultExpectedError:
return pd.DataFrame()
initial_cs_table = pd.read_sql(query, lims_db.get_connection())
cst = initial_cs_table.rename(
columns={"id": "cell_roi_id", "mask_matrix": "roi_mask"}
)
Expand Down Expand Up @@ -491,29 +478,19 @@ def _get_events():
frame_rate_hz=meta.imaging_plane.ophys_frame_rate,
)

try:
cell_specimen_table = _get_cell_specimen_table()
except OneResultExpectedError:
cell_specimen_table = pd.DataFrame()
cell_specimen_table = _get_cell_specimen_table()

meta = CellSpecimenMeta.from_lims(
ophys_experiment_id=ophys_experiment_id,
lims_db=lims_db,
ophys_timestamps=ophys_timestamps,
)

if len(cell_specimen_table) > 0:
dff_traces = _get_dff_traces()
demixed_traces = _get_demixed_traces()
neuropil_traces = _get_neuropil_traces()
corrected_fluorescence_traces = _get_corrected_fluorescence_traces()
events = _get_events()
else:
dff_traces = None
demixed_traces = None
neuropil_traces = None
corrected_fluorescence_traces = None
events = None
dff_traces = _get_dff_traces()
demixed_traces = _get_demixed_traces()
neuropil_traces = _get_neuropil_traces()
corrected_fluorescence_traces = _get_corrected_fluorescence_traces()
events = _get_events()

return CellSpecimens(
cell_specimen_table=cell_specimen_table,
Expand Down Expand Up @@ -614,19 +591,6 @@ def from_nwb(
image_seg = ophys_module.data_interfaces["image_segmentation"]
plane_segmentations = image_seg.plane_segmentations
cell_specimen_table = plane_segmentations["cell_specimen_table"]
if len(cell_specimen_table.to_dataframe()) <= 0:
return CellSpecimens(
cell_specimen_table=df,
meta=meta,
dff_traces=None,
demixed_traces=None,
neuropil_traces=None,
corrected_fluorescence_traces=None,
events=None,
ophys_timestamps=None,
segmentation_mask_image_spacing=None,
exclude_invalid_rois=exclude_invalid_rois,
)

def _read_table(cell_specimen_table):
df = cell_specimen_table.to_dataframe()
Expand Down Expand Up @@ -692,8 +656,6 @@ def to_nwb(
:param ophys_timestamps
ophys timestamps
"""
if len(self.table) <= 0:
return nwbfile
# 1. Add cell specimen table
cell_roi_table = self.table.reset_index().set_index("cell_roi_id")
metadata = nwbfile.lab_meta_data["metadata"]
Expand Down

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