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Refactor Miniscope Extractor Naming #374

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merged 6 commits into from
Oct 22, 2024
Merged

Refactor Miniscope Extractor Naming #374

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daf62dc
rename legacy extractor
h-mayorquin Oct 9, 2024
9e9dfcf
Merge branch 'main' into new_miniscope_interface
weiglszonja Oct 12, 2024
d4bc98d
docstring and name correction
h-mayorquin Oct 17, 2024
f6ec161
name change on init
h-mayorquin Oct 17, 2024
bdd857e
Merge branch 'main' into new_miniscope_interface
weiglszonja Oct 22, 2024
c194d02
changelog
h-mayorquin Oct 22, 2024
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2 changes: 1 addition & 1 deletion src/roiextractors/extractors/miniscopeimagingextractor/__init__.py
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Expand Up @@ -11,4 +11,4 @@
An ImagingExtractor for the Miniscope video (.avi) format.
"""

from .miniscopeimagingextractor import MiniscopeImagingExtractor
from .miniscopeimagingextractor import MiniscopeImagingExtractor, MiniscopeMultiSegmentExtractor
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Is this a typo? This is still an imaging extractor and not a segmentation right?

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@h-mayorquin h-mayorquin Oct 12, 2024 •
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[EDIT]

Sorry, no, it was nos a typo.

I am thinking on the concept of multi segment in spikeinterface when a session of the same data is divided with possible gaps in between. That said, it is missing the imaging word on it.

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@weiglszonja thanks for pointing this out. Now that I think about it, MultiSegment is also a bad name because in Spikeinterface multi-segment recordings do not extract the different recordings within the session as a single continuous recording. I settled for MiniscopeMultiRecordingImagingExtractor to avoid this possible confusion.

Can you take a look at the new naming and the new docstrings to see if it makes sense?

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24 changes: 14 additions & 10 deletions src/roiextractors/extractors/miniscopeimagingextractor/miniscopeimagingextractor.py
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Expand Up @@ -18,14 +18,14 @@
from ...extraction_tools import PathType, DtypeType, get_package


class MiniscopeImagingExtractor(MultiImagingExtractor): # TODO: rename to MiniscopeMultiImagingExtractor
class MiniscopeMultiSegmentExtractor(MultiImagingExtractor):
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Suggested change
class MiniscopeMultiSegmentExtractor(MultiImagingExtractor):
class MiniscopeMultiImagingExtractor(MultiImagingExtractor):

"""An ImagingExtractor for the Miniscope video (.avi) format.

This format consists of video (.avi) file(s) and configuration files (.json).
One _MiniscopeImagingExtractor is created for each video file and then combined into the MiniscopeImagingExtractor.
One _MiniscopeSingleVideoExtractor is created for each video file and then combined into the MiniscopeImagingExtractor.
"""

extractor_name = "MiniscopeImaging"
extractor_name = "MiniscopeMultiImaging"
is_writable = True
mode = "folder"

Expand Down Expand Up @@ -58,24 +58,28 @@ def __init__(self, folder_path: PathType):

imaging_extractors = []
for file_path in miniscope_avi_file_paths:
extractor = _MiniscopeImagingExtractor(file_path=file_path)
extractor = _MiniscopeSingleVideoExtractor(file_path=file_path)
extractor._sampling_frequency = self._sampling_frequency
imaging_extractors.append(extractor)

super().__init__(imaging_extractors=imaging_extractors)


class _MiniscopeImagingExtractor(ImagingExtractor):
"""An ImagingExtractor for the Miniscope video (.avi) format.
# Temporal renaming to keep backwards compatibility
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MiniscopeImagingExtractor = MiniscopeMultiSegmentExtractor
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class _MiniscopeSingleVideoExtractor(ImagingExtractor):
"""An auxiliar extractor to get data from a single Miniscope video (.avi) file.

This format consists of a single video (.avi) file and configuration file (.json).
Multiple _MiniscopeImagingExtractor are combined into the MiniscopeImagingExtractor for public access.
This format consists of a single video (.avi)
Multiple _MiniscopeSingleVideoExtractor are combined into the MiniscopeImagingExtractor for public access.
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Suggested change
Multiple _MiniscopeSingleVideoExtractor are combined into the MiniscopeImagingExtractor for public access.
Multiple _MiniscopeSingleVideoExtractor are combined into the MiniscopeMultiImagingExtractor for public access.

"""

extractor_name = "_MiniscopeImaging"
extractor_name = "_MiniscopeSingleVideo"

def __init__(self, file_path: PathType):
"""Create a _MiniscopeImagingExtractor instance from a file path.
"""Create a _MiniscopeSingleVideoExtractor instance from a file path.

Parameters
----------
Expand Down
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