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Quickfix: Run add_optogenetic_epochs #135

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Merged
merged 9 commits into from
Sep 3, 2025
Merged

Quickfix: Run add_optogenetic_epochs #135

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eb88067
add create optoggenetic epochs call to main function
samuelbray32 Sep 2, 2025
f08d6af
add better logging
samuelbray32 Sep 2, 2025
4eb1a6e
enforce same size spatial node arrays
samuelbray32 Sep 3, 2025
cd83f20
add data path for opto files
samuelbray32 Sep 3, 2025
18b708c
changelog and doc
samuelbray32 Sep 3, 2025
bf6a9ba
update expected npode size for padding
samuelbray32 Sep 3, 2025
37d684c
Update src/trodes_to_nwb/convert_optogenetics.py
samuelbray32 Sep 3, 2025
09fef98
fix formatting from copilot
samuelbray32 Sep 3, 2025
08f704a
explain shape in comment
samuelbray32 Sep 3, 2025
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3 changes: 2 additions & 1 deletion src/trodes_to_nwb/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
from trodes_to_nwb.convert_dios import add_dios
from trodes_to_nwb.convert_ephys import RecFileDataChunkIterator, add_raw_ephys
from trodes_to_nwb.convert_intervals import add_epochs, add_sample_count
from trodes_to_nwb.convert_optogenetics import add_optogenetics
from trodes_to_nwb.convert_optogenetics import add_optogenetic_epochs, add_optogenetics
from trodes_to_nwb.convert_position import add_associated_video_files, add_position
from trodes_to_nwb.convert_rec_header import (
add_header_device,
Expand Down Expand Up @@ -278,6 +278,7 @@ def _create_nwb(
nwb_file, metadata, session_df, video_directory, convert_video
)
add_optogenetics(nwb_file, metadata, device_metadata)
add_optogenetic_epochs(nwb_file, metadata)

if not behavior_only:
add_electrode_groups(
Expand Down
7 changes: 4 additions & 3 deletions src/trodes_to_nwb/convert_optogenetics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def add_optogenetics(nwbfile: NWBFile, metadata: dict, device_metadata: List[dic
return

# Add optogenetic experiment metadata

logger.info("Adding optogenetic experiment metadata")
virus, virus_injection = make_virus_injecton(
metadata.get("virus_injection"), device_metadata
)
Expand Down Expand Up @@ -306,11 +306,12 @@ def add_optogenetic_epochs(
file_dir : str, optional
Directory appended to the file path given in the metadata. Default is empty string.
"""

logger = logging.getLogger("convert")
opto_epochs_metadata = metadata.get("fs_gui_yamls", [])
if len(opto_epochs_metadata) == 0:
print("No optogenetic epochs found in metadata.")
logger.info("No optogenetic epochs found in metadata.")
return
logger.info(f"Adding {len(opto_epochs_metadata)} optogenetic epochs.")

from ndx_franklab_novela import FrankLabOptogeneticEpochsTable

Expand Down
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