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passing indices as argument to fit_file #90

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Merged
kushalbakshi merged 2 commits into from
Oct 12, 2023
Merged

passing indices as argument to fit_file #90

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697e804
add `validation` argument to dandi upload
Sep 6, 2023
b374a41
passing as argument to `fit_file`
ttngu207 Oct 12, 2023
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3 changes: 3 additions & 0 deletions element_interface/dandi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ def upload_to_dandi(
api_key: str = None,
sync: bool = False,
existing: str = "refresh",
validation: str = "required",
shell=True, # without this param, subprocess interprets first arg as file/dir
):
"""Upload NWB files to DANDI Archive
Expand All @@ -27,6 +28,7 @@ def upload_to_dandi(
sync (str, optional): If True, delete all files in archive that are not present
in the local directory.
existing (str, optional): see full description from `dandi upload --help`
validation (str, optional): [require|skip|ignore] see full description from `dandi upload --help`
"""

working_directory = working_directory or os.path.curdir
Expand Down Expand Up @@ -84,4 +86,5 @@ def upload_to_dandi(
dandi_instance="dandi-staging" if staging else "dandi",
existing=existing,
sync=sync,
validation=validation,
)
8 changes: 8 additions & 0 deletions element_interface/run_caiman.py
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Expand Up @@ -35,6 +35,13 @@ def run_caiman(
parameters["fnames"] = file_paths
parameters["fr"] = sampling_rate

if "indicies" in parameters:
indices = params.pop("indicies")
indicies = slice(*indices[0]), slice(*indices[1])
parameters['motion'] = {**parameters.get('motion', {}), "indicies": indicies}
else:
indicies = None

opts = params.CNMFParams(params_dict=parameters)

c, dview, n_processes = cm.cluster.setup_cluster(
Expand All @@ -45,6 +52,7 @@ def run_caiman(
cnm = CNMF(n_processes, params=opts, dview=dview)
cnmf_output, mc_output = cnm.fit_file(
motion_correct=True,
indices=indicies,
include_eval=True,
output_dir=output_dir,
return_mc=True,
Expand Down