File path not found sorting in container
See original GitHub issueThe filepats of my recording is not found when running sorting algorithm using a docker file.
sorting_TDC = ss.run_tridesclous(
recording,
output_folder="tridesclous_output",
docker_image="spikeinterface/tridesclous-base:1.6.4",
)
The way it tries to find it is by using this method (see #L170-L207)
def find_recording_folder(d):
if "kwargs" in d.keys():
# handle nested
kwargs = d["kwargs"]
nested_extractor_dict = None
for k, v in kwargs.items():
if isinstance(v, dict) and is_dict_extractor(v):
nested_extractor_dict = v
if nested_extractor_dict is None:
folder_to_mount = find_recording_folder(kwargs)
else:
folder_to_mount = find_recording_folder(nested_extractor_dict)
return folder_to_mount
else:
for k, v in d.items():
if "path" in k:
# paths can be str or list of str
if isinstance(v, str):
# one path
abs_path = Path(v)
if abs_path.is_file():
folder_to_mount = abs_path.parent
elif abs_path.is_dir():
folder_to_mount = abs_path
elif isinstance(v, list):
# list of path
relative_paths = []
folder_to_mount = None
for abs_path in v:
abs_path = Path(abs_path)
if folder_to_mount is None:
folder_to_mount = abs_path.parent
else:
assert folder_to_mount == abs_path.parent
else:
raise ValueError(
f'{k} key for path must be str or list[str]')
return folder_to_mount
But that gives me the following error:
UnboundLocalError: local variable 'folder_to_mount' referenced before assignment
d
in my case (neuropixel 2.0 dual recording) looks like this:
{'class': 'spikeinterface.extractors.neoextractors.openephys.OpenEphysBinaryRecordingExtractor',
'module': 'spikeinterface',
'kwargs': {'all_annotations': False,
'stream_id': '0',
'folder_path': '/Volumes/FK_Fileserver1/Project_NP_optogenetics/data/raw/NP6/2022-06-29_17-15-43'},
'dumpable': True,
'version': '0.94.1.dev0',
So I think the line return folder_to_mount
should be one tab up or outside the for loop
😃
Issue Analytics
- State:
- Created a year ago
- Comments:9 (6 by maintainers)
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@alejoe91 as far as I can tell now this works for me! thank you for the quick fix 👌
@yger a the same problem. I will have a look