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Fix of the dartsort parameter such that it uses scratch_dir #26

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Fix of the dartsort parameter such that it uses scratch_dir #26

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8 changes: 3 additions & 5 deletions src/ephysatlas/features.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ def get_feature_cmin(feature_name):
class DartParameters(pydantic.BaseModel):
localization_radius: pydantic.PositiveFloat = 150
chunk_length_samples: pydantic.PositiveInt = 2**15
trough_offset: pydantic.PositiveInt = (42,)
trough_offset: pydantic.PositiveInt = 42
scratch_dir: Path | str | None = pydantic.Field(
default=None,
description="Scratch directory for temporary files. If None, will use system defaults.",
Expand Down Expand Up @@ -409,12 +409,10 @@ def spikes(
:param params:
:return:
"""

params = DartParameters() if params is None else DartParameters(**params)
logger.info("Starting spike detection")
# Update params with scratch_dir if provided
if scratch_dir is not None:
params.scratch_dir = scratch_dir
df_spikes_, d_waveforms = dart_subtraction_numpy(data, fs, geometry, params=params)
df_spikes_, d_waveforms = dart_subtraction_numpy(data, fs, geometry, scratch_dir=scratch_dir, params=params)
logger.info("Spike detection completed")
df_waveforms = ibldsp.waveforms.compute_spike_features(d_waveforms["denoised"])
df_spikes = df_spikes_.merge(df_waveforms, left_index=True, right_index=True)
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