v0.5.9

Deprecations

• Remove support for Python 3.8: PR #325

Features

• Add InscopixImagingExtractor: #276
• Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: PR #317
• Added API documentation: #337
• Optimized get_streams for BrukerTiffSinglePlaneImagingExtractor by introducing a static function get_available_channels which uses lazy parsing of the XML to fetch the available channels: #344

Fixes

• Remove unnecessary scipy import error handling: #315
• Fixed the typing returned by the InscopixImagingExtractor.get_dtype method: #326
• Detect Changelog Updates was moved to its own dedicated workflow to avoid daily testing failures: #336
• Fixed the Daily testing workflows by passing along the appropriate secrets: #340
• Change the criteria of determining if Bruker data is volumetric #342
• Fixes a bug that assumes the channel name is is on the tiff file for BrukerTiffSinglePlaneImagingExtractor #343
• Including packaging explicitly in minimal requirements #347
• Updated requirements to include cv2 and update dev testing locations for neuroconv: #357

Improvements

• The Suite2PSegmentationExtractor now produces an error when a required sub-file is missin: #330
• Added _image_mask initialization in BaseSegmentationExtractor; combined abstractmethods into top of file: #327
• Optimize parsing of xml with lxml library for Burker extractors: #346
• Protect sima and dill export #351
• Improve error message when TiffImagingExtractor is not able to form memmap #353
• Updated Check Docstrings workflow to use new github action: #354

Testing

• Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: PR #317
• Added daily testing workflow and fixed bug with python 3.12 by upgrading scanimage-tiff-reader version: PR #321
• Remove wheel from requirements and move CI dependencies to test requirements PR #348
• Use Spikeinterface instead of Spikeextractors for toy_example PR #349

v0.5.8

Fixes

• The triggering workflow name for update version was incorrectly set to auto-publish (the name of the yaml file). It has been renamed to Upload Package to PyPI (the name field of the workflow): PR #304.

• Fixed bug with automatic changelog test that was causing it to fail for daily tests: PR #310

• Updated zenodo to get a DOI on each release: No PR

v0.5.7

Features

• Add support to get background components: add get_background_ids(), get_background_image_masks(), get_background_pixel_masks() to SegmentationExtractor. PR #291

• Add distinction for raw roi response and denoised roi response in CaimanSegmentationExtractor: PR #291

• Bug fix for the CaimanSegmentationExtractor: correctly extract temporal and spatial background components PR #291

• Added automatic version update workflow file that will run after publishing a new release to pypi: PR #290

• Added ScanImageTiffSinglePlaneMultiFileImagingExtractor and ScanImageTiffMultiPlaneMultiFileImagingExtractor: PR #297

• Added automatic changelog checking in the test workflow: PR #302

Fixes

• Improved xml parsing with Bruker PR #267

• Fixed a bug with ScanImageTiffSinglePlaneImagingExtractor in which frames_per_slice would be set to _num_frames: PR #294

v0.5.6

Features

• Added support for red channel (anatomical) ROIs from suite2p in Suite2pSegmentationExtractor PR #270
• Added support for RoiGroup metadata in the extract_extra_metadata function for ScanImageTiff files PR #272
• Updated documentation and Readme PRs #283 #282 #280

v0.5.5

v0.5.5

Features

• Updated Suite2pSegmentationExtractor to support multi channel and multi plane data. PR #242

Fixes

• Fixed MicroManagerTiffImagingExtractor private extractor's dtype to not override the parent's dtype. PR #257
• Fixed override of channel_name in Suite2pSegmentationExtractor. PR #263

v0.5.4

v0.5.4

Features

• Added volumetric and multi-channel support for Bruker format. PR #230

v0.5.3

v0.5.3

Features

• Added support for Miniscope AVI files with the MiniscopeImagingExtractor. PR #225

v0.5.2

v0.5.2

Features

• Added support for MicroManager TIFF files with the MicroManagerTiffImagingExtractor. PR #222
• Added support for Bruker TIFF files with the BrukerTiffImagingExtractor. PR #220

v0.5.1

Features

• Added a has_time_vector function for ImagingExtractors and SegmentationExtractors, similar to the SpikeInterface API for detecting if timestamps have been set. PR #216

Fixes

• Fixed two issues with the SubFrameSegementation class: (i) attempting to set the private attribute _image_masks even when this was not present in the parent, and (ii) not calling the parent function for get_pixel_masks and instead using the base method even in cases where this had been overridden by the parent. PR #215

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