v0.5.0

v0.5.0

Back-compatability break

• The orientation of traces in all SegmentationExtractors has been standardized to have time (frames) as the first axis, and ROIs as the final axis. PR #200

Features

• Add support for newer versions of EXTRACT output files. PR #170
  The ExtractSegmentationExtractor class is now abstract and redirects to the newer or older
  extractor depending on the version of the file. PR #170
• The ExtractSegmentationExtractor.write_segmentation method has now been deprecated. PR #170

Improvements

• Add frame_to_time to SegmentationExtractor, get_roi_ids is now a class method. PR #187
• Add set_times to SegmentationExtractor. PR #188
• Updated the test for segmentation images to check all images for the given segmentation extractors. PR #190
• Refactored the NwbSegmentationExtractor to be more flexible with segmentation images and keep up
  with the change in catalystneuro/neuoroconv#41
  of trace names. PR #191
• Implemented a more efficient case of the base ImagingExtractor.get_frames through get_video when the indices are contiguous. PR #195
• Removed max_frame check on MultiImagingExtractor.get_video() to adhere to upper-bound slicing semantics. PR #195
• Improved the MultiImagingExtractor.get_video() to no longer rely on get_frames. PR #195
• Added dtype consistency check across MultiImaging components as well as a direct override method. PR #195
• Added the FrameSliceSegmentationExtractor class and corresponding Segmentation.frame_slice(...) method. PR #201
• Changed the output_struct_name argument to optional in ExtractSegmentationExtractor.
  to allow more flexible usage for the user and better error message when it cannot be found in the file.
  For consistency, output_struct_name argument has been also added to the legacy extractor.
  The orientation of segmentation images are transposed for consistency in image orientation (height x width). PR #210
• Relaxed rounding of ImagingExtractor.frame_to_time(...) and SegmentationExtractor.frame_to_time(...) to be more consistent with SpikeInterface. PR #212

Fixes

• Fixed the reference to the proper mov_field in Hdf5ImagingExtractor. PR #195
• Updated the name of the ROICentroids column for the NwbSegmentationExtractor to be up-to-date with NeuroConv v0.2.0 write_segmentation. PR #208
• Updated the trace orientation for the NwbSegmentationExtractor. PR #208

v0.4.18

Improvements

• get_video is now an abstract method in ImagingExtractor PR #180

Features

• Add dummy segmentation extractor PR #176

Testing

• Added unittests to the get_frames method from ImagingExtractors to assert that they are consistent with numpy
  indexing behavior. PR #154
• Tests for spikeinterface like-behavior for the get_video function PR #181

v0.4.17

New features

• Adds MultiImagingExtractor for combining multiple imaging extractors.
• Adds ScanImageTiffExtractor for reading .tiff files output from ScanImage
• Adds NumpyImagingExtractor for extracting raw video data as memmaps.
• Added frame slicing capabilities for imaging extractors.

Minor changes

• Suite2P argument has become folder_path instead of file_path, file_path deprecation scheduled for august or later.
• Improved docstrings across many extractors.

Testing changes

• Added checks and debugs that all sampling frequencies returns are floats
• Round trip testing working for all extractors that have a working write method.

v0.4.1

v0.4.1

Bug Fix

Allows the TiffImagingInterface to read from non-memmap files.

v0.4.0

v0.4.0 removes the NWB write functions from the project; these are now incorporated into the nwb_conversion_tools project. A deprecation message is left on any attempt to use the related functions.

v0.3.1

Additional support for .sbx files