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Add included ROIs from fiber locations #16

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merged 3 commits into from
Jul 22, 2024
Merged

Add included ROIs from fiber locations #16

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ede5519
fix append mode backend configuration
weiglszonja Jul 17, 2024
0aaae64
add included from fiber locations excel file
weiglszonja Jul 17, 2024
9613489
override accepted_list in plane segmentation to use included from fib…
weiglszonja Jul 17, 2024
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7 changes: 4 additions & 3 deletions src/howe_lab_to_nwb/vu2024/utils/add_fiber_photometry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ def add_fiber_photometry_table(nwbfile: NWBFile, metadata: dict):
description="The fiber tip coordinates (AP, ML, DV) in Allen Brain Atlas coordinates",
)
fiber_photometry_table.add_column(
name="is_good_fiber",
name="included",
description="Whether this fiber has been successfully implanted.",
)

Expand Down Expand Up @@ -180,9 +180,9 @@ def add_fiber_photometry_series(
if default_series_name not in nwbfile.acquisition:
for fiber_ind in range(num_fibers):
brain_area = fiber_locations_metadata[fiber_ind]["location"]
is_good_fiber = True if brain_area else False
included = fiber_locations_metadata[fiber_ind]["included"]
fiber_photometry_table.add_row(
is_good_fiber=is_good_fiber,
included=included,
location=brain_area, # TODO: change this in the extension to brain_area
coordinates=fiber_locations_metadata[fiber_ind]["coordinates"],
allen_atlas_coordinates=fiber_locations_metadata[fiber_ind]["allen_atlas_coordinates"],
Expand Down Expand Up @@ -264,6 +264,7 @@ def get_fiber_locations(file_path: FilePathType) -> List[dict]:
allen_atlas_coordinates=allen_atlas_coordinates,
# TODO: rename to brain_area
location=brain_area,
included=row["included"],
)
fibers_metadata.append(fiber_metadata)

Expand Down
11 changes: 3 additions & 8 deletions src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
from typing import Union, Optional, List

from dateutil import tz
from neuroconv.tools.nwb_helpers import configure_and_write_nwbfile
from neuroconv.utils import load_dict_from_file, dict_deep_update
from pynwb import NWBFile

Expand Down Expand Up @@ -118,7 +119,7 @@ def single_wavelength_session_to_nwb(
)

# Add ROI segmentation
accepted_list = [fiber_ind for fiber_ind, fiber in enumerate(fiber_locations_metadata) if fiber["location"] != ""]
accepted_list = [fiber_ind for fiber_ind, fiber in enumerate(fiber_locations_metadata) if fiber["included"]]
roi_source_data = dict(
file_path=str(raw_fiber_photometry_file_path),
sampling_frequency=sampling_frequency,
Expand Down Expand Up @@ -209,13 +210,7 @@ def single_wavelength_session_to_nwb(
if nwbfile_path is None:
return nwbfile

converter.run_conversion(
nwbfile_path=nwbfile_path,
nwbfile=nwbfile,
metadata=metadata,
conversion_options=conversion_options,
overwrite=True,
)
configure_and_write_nwbfile(nwbfile=nwbfile, output_filepath=nwbfile_path)


if __name__ == "__main__":
Expand Down
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