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removed class section of module docstrings
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pauladkisson committed May 23, 2024
1 parent fbae508 commit 4c96f57
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8 changes: 1 addition & 7 deletions src/roiextractors/extraction_tools.py
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"""Various tools for extraction of ROIs from imaging data.
Classes
-------
VideoStructure
A data class for specifying the structure of a video.
"""
"""Various tools for extraction of ROIs from imaging data."""

import sys
import importlib.util
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10 changes: 1 addition & 9 deletions src/roiextractors/extractors/nwbextractors/nwbextractors.py
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"""Imaging and segmentation extractors for NWB files.
Classes
-------
NwbImagingExtractor
Extracts imaging data from NWB files.
NwbSegmentationExtractor
Extracts segmentation data from NWB files.
"""
"""Imaging and segmentation extractors for NWB files."""

from pathlib import Path
from typing import Union, Optional, Iterable, Tuple
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"""Imaging Extractors for Scanbox files.
Classes
-------
SbxImagingExtractor
An ImagingExtractor for Scanbox Image files.
"""
"""Imaging Extractors for Scanbox files."""

from multiprocessing.sharedctypes import Value
import os
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"""A segmentation extractor for CNMF-E ROI segmentation method.
Classes
-------
CnmfeSegmentationExtractor
A segmentation extractor for CNMF-E ROI segmentation method.
"""
"""A segmentation extractor for CNMF-E ROI segmentation method."""

from pathlib import Path

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"""Extractor for reading the segmentation data that results from calls to EXTRACT.
Classes
-------
ExtractSegmentationExtractor
Abstract class that defines which extractor class to use for a given file.
NewExtractSegmentationExtractor
Extractor for reading the segmentation data that results from calls to newer versions of EXTRACT.
LegacyExtractSegmentationExtractor
Extractor for reading the segmentation data that results from calls to older versions of EXTRACT.
"""
"""Extractor for reading the segmentation data that results from calls to EXTRACT."""

from abc import ABC
from pathlib import Path
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"""A segmentation extractor for Sima.
Classes
-------
SimaSegmentationExtractor
A segmentation extractor for Sima.
"""
"""A segmentation extractor for Sima."""

import os
import pickle
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"""A segmentation extractor for Suite2p.
Classes
-------
Suite2pSegmentationExtractor
A segmentation extractor for Suite2p.
"""
"""A segmentation extractor for Suite2p."""

import shutil
from pathlib import Path
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"""ImagingExtractors for the TIFF image format produced by Bruker.
Classes
-------
BrukerTiffSinglePlaneImagingExtractor
A ImagingExtractor for TIFF files produced by Bruker with only 1 plane.
BrukerTiffMultiPlaneImagingExtractor
A MultiImagingExtractor for TIFF files produced by Bruker with multiple planes.
"""
"""ImagingExtractors for the TIFF image format produced by Bruker."""

import logging
import re
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"""A ImagingExtractor for TIFF files produced by Micro-Manager.
Classes
-------
MicroManagerTiffImagingExtractor
A ImagingExtractor for TIFF files produced by Micro-Manager.
"""
"""A ImagingExtractor for TIFF files produced by Micro-Manager."""

import json
import logging
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"""Specialized extractor for reading TIFF files produced via ScanImage.
Classes
-------
ScanImageTiffImagingExtractor
Specialized extractor for reading TIFF files produced via ScanImage.
"""
"""Specialized extractor for reading TIFF files produced via ScanImage."""

from pathlib import Path
from typing import Optional, Tuple, List, Iterable
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"""A TIFF imaging extractor for TIFF files.
Classes
-------
TiffImagingExtractor
A TIFF imaging extractor for TIFF files.
"""
"""A TIFF imaging extractor for TIFF files."""

from pathlib import Path
from typing import Optional
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10 changes: 1 addition & 9 deletions src/roiextractors/imagingextractor.py
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"""Base class definitions for all ImagingExtractors.
Classes
-------
ImagingExtractor
Abstract class that contains all the meta-data and input data from the imaging data.
FrameSliceImagingExtractor
Class to get a lazy frame slice.
"""
"""Base class definitions for all ImagingExtractors."""

from abc import ABC, abstractmethod
from typing import Union, Optional, Tuple
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8 changes: 1 addition & 7 deletions src/roiextractors/multiimagingextractor.py
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"""Defines the MultiImagingExtractor class.
Classes
-------
MultiImagingExtractor
This class is used to combine multiple ImagingExtractor objects by frames.
"""
"""Defines the MultiImagingExtractor class."""

from collections import defaultdict
from typing import Tuple, List, Iterable, Optional
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8 changes: 1 addition & 7 deletions src/roiextractors/multisegmentationextractor.py
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"""Defines the MultiSegmentationExtractor class.
Classes
-------
MultiSegmentationExtractor
This class is used to combine multiple SegmentationExtractor objects by frames.
"""
"""Defines the MultiSegmentationExtractor class."""

import numpy as np

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12 changes: 1 addition & 11 deletions src/roiextractors/segmentationextractor.py
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"""Base segmentation extractors.
Classes
-------
SegmentationExtractor
Abstract class that contains all the meta-data and output data from the ROI segmentation operation when applied to
the pre-processed data. It also contains methods to read from and write to various data formats output from the
processing pipelines like SIMA, CaImAn, Suite2p, CNMF-E.
FrameSliceSegmentationExtractor
Class to get a lazy frame slice.
"""
"""Base segmentation extractors."""

from abc import ABC, abstractmethod
from typing import Union, Optional, Tuple, Iterable, List
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