Roiextractors

Deprecations

* Remove support for Python 3.8: [PR 325](https://github.com/catalystneuro/roiextractors/pull/325)

Features

* Add InscopixImagingExtractor: [276](https://github.com/catalystneuro/roiextractors/pull/276)
* Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: [PR 317](https://github.com/catalystneuro/roiextractors/pull/317)
* Added API documentation: [337](https://github.com/catalystneuro/roiextractors/pull/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](https://github.com/catalystneuro/roiextractors/pull/344)

Fixes

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

Improvements

* The `Suite2PSegmentationExtractor` now produces an error when a required sub-file is missin: [330](https://github.com/catalystneuro/roiextractors/pull/330)
* Added `_image_mask` initialization in `BaseSegmentationExtractor`; combined `abstractmethod`s into top of file: [327](https://github.com/catalystneuro/roiextractors/pull/327)
* Optimize parsing of xml with `lxml` library for Burker extractors: [346](https://github.com/catalystneuro/roiextractors/pull/346)
* Protect sima and dill export [351](https://github.com/catalystneuro/roiextractors/pull/351)
* Improve error message when `TiffImagingExtractor` is not able to form memmap [353](https://github.com/catalystneuro/roiextractors/pull/353)
* Updated Check Docstrings workflow to use new github action: [354](https://github.com/catalystneuro/roiextractors/pull/354)

Testing

* Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: [PR 317](https://github.com/catalystneuro/roiextractors/pull/317)
* Added daily testing workflow and fixed bug with python 3.12 by upgrading scanimage-tiff-reader version: [PR 321](https://github.com/catalystneuro/roiextractors/pull/321)
* Remove wheel from requirements and move CI dependencies to test requirements [PR 348](https://github.com/catalystneuro/roiextractors/pull/348)
* Use Spikeinterface instead of Spikeextractors for toy_example [PR 349](https://github.com/catalystneuro/roiextractors/pull/349)

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](https://github.com/catalystneuro/roiextractors/pull/304).

* Fixed bug with automatic changelog test that was causing it to fail for daily tests: [PR 310](https://github.com/catalystneuro/roiextractors/pull/310)

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

Features

* Add support to get background components: add `get_background_ids()`, `get_background_image_masks()`, `get_background_pixel_masks()` to `SegmentationExtractor`. [PR 291](https://github.com/catalystneuro/roiextractors/pull/291)

* Add distinction for raw roi response and denoised roi response in `CaimanSegmentationExtractor`: [PR 291](https://github.com/catalystneuro/roiextractors/pull/291)

* Bug fix for the `CaimanSegmentationExtractor`: correctly extract temporal and spatial background components [PR 291](https://github.com/catalystneuro/roiextractors/pull/291)

* Added automatic version update workflow file that will run after publishing a new release to pypi: [PR 290](https://github.com/catalystneuro/roiextractors/pull/290)

* Added `ScanImageTiffSinglePlaneMultiFileImagingExtractor` and `ScanImageTiffMultiPlaneMultiFileImagingExtractor`: [PR 297](https://github.com/catalystneuro/roiextractors/pull/297/files)

* Added automatic changelog checking in the test workflow: [PR 302](https://github.com/catalystneuro/roiextractors/pull/302)

Fixes

* Improved xml parsing with Bruker [PR 267](https://github.com/catalystneuro/roiextractors/pull/267)

* Fixed a bug with `ScanImageTiffSinglePlaneImagingExtractor` in which `frames_per_slice` would be set to `_num_frames`: [PR 294](https://github.com/catalystneuro/roiextractors/pull/294)

Features

* Added support for red channel (anatomical) ROIs from suite2p in Suite2pSegmentationExtractor: [PR 270](https://github.com/catalystneuro/roiextractors/pull/270)

* Added support for RoiGroup metadata in the `extract_extra_metadata` function for ScanImageTiff files: [PR 272](https://github.com/catalystneuro/roiextractors/pull/272)

* Updated documentation and Readme PRs: [283](https://github.com/catalystneuro/roiextractors/pull/283) [#282](https://github.com/catalystneuro/roiextractors/pull/282) [#280](https://github.com/catalystneuro/roiextractors/pull/280)

Features

* Updated `Suite2pSegmentationExtractor` to support multi channel and multi plane data. [PR 242](https://github.com/catalystneuro/roiextractors/pull/242)

Fixes

* Fixed `MicroManagerTiffImagingExtractor` private extractor's dtype to not override the parent's dtype. [PR 257](https://github.com/catalystneuro/roiextractors/pull/257)
* Fixed override of `channel_name` in `Suite2pSegmentationExtractor`. [PR 263](https://github.com/catalystneuro/roiextractors/pull/263)

Features

* Added volumetric and multi-channel support for Bruker format. [PR 230](https://github.com/catalystneuro/roiextractors/pull/230)