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src/roiextractors/__init__.py

@@ -1,4 +1,5 @@
 """Python-based module for extracting from, converting between, and handling recorded and optical imaging data from several file formats."""
+
 # Keeping __version__ accessible only to maintain backcompatability.
 # Modern appraoch (Python >= 3.8) is to use importlib
 try:

src/roiextractors/example_datasets/__init__.py

@@ -10,4 +10,5 @@
 toy_example
     Create a toy example of an ImagingExtractor and a SegmentationExtractor.
 """
+
 from .toy_example import toy_example

src/roiextractors/example_datasets/toy_example.py

@@ -5,6 +5,7 @@
 toy_example
     Create a toy example of an ImagingExtractor and a SegmentationExtractor.
 """
+
 import numpy as np
 
 from ..extractors.numpyextractors import (

src/roiextractors/extraction_tools.py

@@ -5,6 +5,7 @@
 VideoStructure
     A data class for specifying the structure of a video.
 """
+
 import sys
 import importlib.util
 from functools import wraps

src/roiextractors/extractorlist.py

@@ -1,4 +1,5 @@
 """Listing of available formats for extraction."""
+
 from .extractors.caiman import CaimanSegmentationExtractor
 from .extractors.hdf5imagingextractor import Hdf5ImagingExtractor
 from .extractors.numpyextractors import (

src/roiextractors/extractors/caiman/__init__.py

@@ -10,4 +10,5 @@
 CaimanSegmentationExtractor
     A class for extracting segmentation from Caiman output.
 """
+
 from .caimansegmentationextractor import CaimanSegmentationExtractor

src/roiextractors/extractors/caiman/caimansegmentationextractor.py

@@ -5,6 +5,7 @@
 CaimanSegmentationExtractor
     A class for extracting segmentation from CaImAn output.
 """
+
 from pathlib import Path
 
 try:

src/roiextractors/extractors/hdf5imagingextractor/__init__.py

@@ -11,4 +11,5 @@
 Hdf5ImagingExtractor
     An imaging extractor for HDF5.
 """
+
 from .hdf5imagingextractor import Hdf5ImagingExtractor

src/roiextractors/extractors/hdf5imagingextractor/hdf5imagingextractor.py

@@ -5,6 +5,7 @@
 Hdf5ImagingExtractor
     An imaging extractor for HDF5.
 """
+
 from pathlib import Path
 from typing import Optional, Tuple
 from warnings import warn

src/roiextractors/extractors/memmapextractors/__init__.py

@@ -14,5 +14,6 @@
 NumpyMemmapImagingExtractor
     The class for reading optical imaging data stored in a binary format with numpy.memmap.
 """
+
 from .memmapextractors import MemmapImagingExtractor
 from .numpymemampextractor import NumpyMemmapImagingExtractor

src/roiextractors/extractors/memmapextractors/memmapextractors.py

@@ -5,6 +5,7 @@
 MemmapImagingExtractor
     The base class for memmapable imaging extractors.
 """
+
 from pathlib import Path
 
 import numpy as np

src/roiextractors/extractors/memmapextractors/numpymemampextractor.py

@@ -5,6 +5,7 @@
 NumpyMemmapImagingExtractor
     The class for reading optical imaging data stored in a binary format with numpy.memmap.
 """
+
 import os
 from pathlib import Path
 from typing import Tuple, Dict

src/roiextractors/extractors/miniscopeimagingextractor/__init__.py

@@ -10,4 +10,5 @@
 MiniscopeImagingExtractor
     An ImagingExtractor for the Miniscope video (.avi) format.
 """
+
 from .miniscopeimagingextractor import MiniscopeImagingExtractor

src/roiextractors/extractors/miniscopeimagingextractor/miniscopeimagingextractor.py

@@ -5,6 +5,7 @@
 MiniscopeImagingExtractor
     An ImagingExtractor for the Miniscope video (.avi) format.
 """
+
 import json
 import re
 from pathlib import Path

src/roiextractors/extractors/numpyextractors/__init__.py

@@ -12,4 +12,5 @@
 NumpySegmentationExtractor
     A Segmentation extractor specified by image masks and traces .npy files.
 """
+
 from .numpyextractors import NumpyImagingExtractor, NumpySegmentationExtractor

src/roiextractors/extractors/numpyextractors/numpyextractors.py

@@ -7,6 +7,7 @@
 NumpySegmentationExtractor
     A Segmentation extractor specified by image masks and traces .npy files.
 """
+
 from pathlib import Path
 from typing import Optional, Tuple
 

src/roiextractors/extractors/nwbextractors/__init__.py

@@ -12,4 +12,5 @@
 NwbSegmentationExtractor
     Extracts segmentation data from NWB files.
 """
+
 from .nwbextractors import NwbImagingExtractor, NwbSegmentationExtractor

src/roiextractors/extractors/nwbextractors/nwbextractors.py

@@ -7,6 +7,7 @@
 NwbSegmentationExtractor
     Extracts segmentation data from NWB files.
 """
+
 from pathlib import Path
 from typing import Union, Optional, Iterable, Tuple
 

src/roiextractors/extractors/sbximagingextractor/__init__.py

@@ -10,4 +10,5 @@
 SbxImagingExtractor
     An ImagingExtractor for Scanbox Image files.
 """
+
 from .sbximagingextractor import SbxImagingExtractor

src/roiextractors/extractors/sbximagingextractor/sbximagingextractor.py

@@ -5,6 +5,7 @@
 SbxImagingExtractor
     An ImagingExtractor for Scanbox Image files.
 """
+
 from multiprocessing.sharedctypes import Value
 import os
 from pathlib import Path

src/roiextractors/extractors/schnitzerextractor/__init__.py

@@ -18,6 +18,7 @@
 LegacyExtractSegmentationExtractor
     Extractor for reading the segmentation data that results from calls to older versions of EXTRACT.
 """
+
 from .cnmfesegmentationextractor import CnmfeSegmentationExtractor
 from .extractsegmentationextractor import (
     LegacyExtractSegmentationExtractor,

src/roiextractors/extractors/schnitzerextractor/cnmfesegmentationextractor.py

@@ -5,6 +5,7 @@
 CnmfeSegmentationExtractor
     A segmentation extractor for CNMF-E ROI segmentation method.
 """
+
 from pathlib import Path
 
 try:

src/roiextractors/extractors/schnitzerextractor/extractsegmentationextractor.py

@@ -9,6 +9,7 @@
 LegacyExtractSegmentationExtractor
     Extractor for reading the segmentation data that results from calls to older versions of EXTRACT.
 """
+
 from abc import ABC
 from pathlib import Path
 from typing import Optional

src/roiextractors/extractors/simaextractor/__init__.py

@@ -10,4 +10,5 @@
 SimaSegmentationExtractor
     A segmentation extractor for Sima.
 """
+
 from .simasegmentationextractor import SimaSegmentationExtractor

src/roiextractors/extractors/simaextractor/simasegmentationextractor.py

@@ -5,6 +5,7 @@
 SimaSegmentationExtractor
     A segmentation extractor for Sima.
 """
+
 import os
 import pickle
 import re

src/roiextractors/extractors/suite2p/__init__.py

@@ -10,4 +10,5 @@
 Suite2pSegmentationExtractor
     A segmentation extractor for Suite2p.
 """
+
 from .suite2psegmentationextractor import Suite2pSegmentationExtractor

src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py

@@ -5,6 +5,7 @@
 Suite2pSegmentationExtractor
     A segmentation extractor for Suite2p.
 """
+
 import shutil
 from pathlib import Path
 from typing import Optional

src/roiextractors/extractors/tiffimagingextractors/__init__.py

@@ -28,6 +28,7 @@
 MicroManagerTiffImagingExtractor
     Specialized extractor for reading TIFF files produced via Micro-Manager.
 """
+
 from .tiffimagingextractor import TiffImagingExtractor
 from .scanimagetiffimagingextractor import (
     ScanImageTiffImagingExtractor,

src/roiextractors/extractors/tiffimagingextractors/brukertiffimagingextractor.py

@@ -7,6 +7,7 @@
 BrukerTiffMultiPlaneImagingExtractor
     A MultiImagingExtractor for TIFF files produced by Bruker with multiple planes.
 """
+
 import logging
 import re
 from collections import Counter

src/roiextractors/extractors/tiffimagingextractors/scanimagetiff_utils.py

@@ -1,4 +1,5 @@
 """Utility functions for ScanImage TIFF Extractors."""
+
 import numpy as np
 import json
 from ...extraction_tools import PathType, get_package

src/roiextractors/extractors/tiffimagingextractors/scanimagetiffimagingextractor.py

@@ -5,6 +5,7 @@
 ScanImageTiffImagingExtractor
     Specialized extractor for reading TIFF files produced via ScanImage.
 """
+
 from pathlib import Path
 from typing import Optional, Tuple, List, Iterable
 from warnings import warn

src/roiextractors/extractors/tiffimagingextractors/tiffimagingextractor.py

@@ -5,6 +5,7 @@
 TiffImagingExtractor
     A TIFF imaging extractor for TIFF files.
 """
+
 from pathlib import Path
 from typing import Optional
 from warnings import warn

src/roiextractors/imagingextractor.py

@@ -7,6 +7,7 @@
 FrameSliceImagingExtractor
     Class to get a lazy frame slice.
 """
+
 from abc import ABC, abstractmethod
 from typing import Union, Optional, Tuple
 from copy import deepcopy

src/roiextractors/multiimagingextractor.py

@@ -5,6 +5,7 @@
 MultiImagingExtractor
     This class is used to combine multiple ImagingExtractor objects by frames.
 """
+
 from collections import defaultdict
 from typing import Tuple, List, Iterable, Optional
 

src/roiextractors/multisegmentationextractor.py

@@ -5,6 +5,7 @@
 MultiSegmentationExtractor
     This class is used to combine multiple SegmentationExtractor objects by frames.
 """
+
 import numpy as np
 
 from .segmentationextractor import SegmentationExtractor

src/roiextractors/segmentationextractor.py

@@ -9,6 +9,7 @@
 FrameSliceSegmentationExtractor
     Class to get a lazy frame slice.
 """
+
 from abc import ABC, abstractmethod
 from typing import Union, Optional, Tuple, Iterable, List
 

src/roiextractors/testing.py

@@ -1,4 +1,5 @@
 """Testing utilities for the roiextractors package."""
+
 from collections.abc import Iterable
 from typing import Tuple, Optional