Highdicom

Patch release with a few bug fixes and documentation updates.

What's Changed
* Disallow measurement report with no measurement groups by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/325
* Fix spatial transformer `from_images` docstrings by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/326
* Enforce series description length by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/328
* Correctly format decimal string for spacing between slices by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/332
* add IDC acknowledgments by fedorov in https://github.com/ImagingDataCommons/highdicom/pull/331
* Allow reading from bytes objects by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/333
* Add docs section on working with remote filesystems by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/334


**Full Changelog**: https://github.com/ImagingDataCommons/highdicom/compare/v0.25.0...v0.25.1

New Features
* Add get_frames and get_stored_frames methods by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/320

Bug Fixes
* Critical bug fixes from the 0.24.0 release, including the implementation of the `Volume.match_geometry()`, `Volume.random_permute_spatial_axes()` and `Volume.random_flip_spatial()` methods, and greatly improve test coverage of the volume class by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/319
* Enforce monochrome 2 for input files to legacy conversion by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/321

Documentation
* New sections in the user guide on Images, Volumes, and Pixel Transforms
* Add channel section to volume user guide by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/322


**Full Changelog**: https://github.com/ImagingDataCommons/highdicom/compare/v0.24.0...v0.25.0

This is a significant release with several important new features added to the library.
The user guide will be updated soon with explanations of the new functionality.

Features

* Update internal DICOM standard information to 2024c
* Add support for the new LABELMAP segmentation type, introduced in DICOM 2024c. Labelmap segmentations store non-overlapping segments as an array in which pixel value indicates membership of a segment. This can be used simply by setting the `segmentation_type` parameter of the `highdicom.seg.Segmentation` constructor to `"LABELMAP"`. Parsing of Labelmap segmentations is also supported. By CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/234
* Add implementations of pixel transformations in new `highdicom.pixels` module and elsewhere, including real world value map, modality LUT, VOI LUT, presentation LUT, and Palette Color LUT.
* Add new general `highdicom.Image` class for reading frames from general DICOM images, and creating Volumes from general images. Methods on this class allow for reading frames with the above pixel transformations configurably applied.
* Add new `highdicom.Volume` class, representing an array of pixels in 3D space by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/277
* Several new functions in `highdicom.spatial` related to 3D volumes and affine matrices.
* Automatically set the DimensionOrganizationType attribute of a segmentation to 3D if the conditions are met.
* Add magic methods to allow segmentation objects to be pickled and unpickled
* Use pyupgrade to update all type hints to 3.10+ style
* Add ability to add spatial coordinates to a measurement by Fedalto in https://github.com/ImagingDataCommons/highdicom/pull/307
* Add support for python 3.13 by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/312


**Full Changelog**: https://github.com/ImagingDataCommons/highdicom/compare/v0.23.1...v0.24.0

Patch release with a few minor bug fixes

Bug Fixes
* Update docs to reflect python 3.10 dependency by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/308
* Allow searching SRs using LongCodeValue and URNCodeValue. Fix for 309 by rhaxton in https://github.com/ImagingDataCommons/highdicom/pull/310
* Fix for BOT construction with pydicom 3, by CPBridge in https://github.com/ImagingDataCommons/highdicom/pull/314
* Fix SR if `SpacingBetweenSlices` is not set, by Fedalto in https://github.com/ImagingDataCommons/highdicom/pull/315

New Contributors
* rhaxton made their first contribution in https://github.com/ImagingDataCommons/highdicom/pull/310

**Full Changelog**: https://github.com/ImagingDataCommons/highdicom/compare/v0.23.0...v0.23.1

Dependencies

- Highdicom now depends upon pydicom > 3.0.1. 301
- Highdicom now requires python > 3.10. This was necessitated by a similar move from pydicom. 301
- Remove references to `numpy.float_` to allow working with numpy>2

Tooling/Repo

- We have adopted the contributor covenant. 271
- Various style improvements 286 287 289 290 291 292
- We have moved to `pyproject.toml` metadata. 293
- Improve automated checks to enforce repo review rules 296

Features

- Further checks on graphic data for SRs 276
- Additional checks for microscopy bulk annotation coordinate types 281
- Further improvements in segmentation creation efficiency 285
- Allow creation of pyramid segmentations with floating point arrays, or with multiple segments 297
- Add options allowing to infer the subject context from an image 298
- Use pydicom 3 features to enable additional transfer syntaxes in compression.
- Add methods to get a list of images used as evidence within an SR 303
- Add a `further_source_images` option to the segmentation constructor 304

Fixes

- Minor fixes for microscopy bulk annotation graphic data 278
- Remove the JP2 wrapper from JPEG 2000 encoding

Docs

- Added a gitflow section to the developer guide. 272

Probably left this one far too long...

New Features
- New features for parsing existing Microscopy Bulk Annotations: `annread` function and `annotation_coordinate_type` property (230)
- Multiprocessing for frame encoding in segmentation construction (245)
- A major set of improvements for working with tiled segmentations including ability to pass in total pixel matrices to the segmentation constructor, the ability to create and read TILED_FULL segmentations, and the ability to construct segmentation total pixel matrices from tiled images (248)
- New function to create multiresolution segmentation pyramids (253)

Bug fixes
- Allow duplicate entries in the ReferencedSeriesSequence of a segmentation image (229)
- Remove plane orientation from the shared functional groups in the case of segs using the slide coordinate system (236), a DICOM compliance issue
- Exclude incompatible pydicom 2.4.0 in `setup.py` (238)
- Fixes to various value representations (239)
- Fix return type of `highdicom.seg.DimensionIndexSequence.get_plane_positions_of_image` (240)
- Correctly account for chrominance subsampling of natively encoded `YBR_FULL_422` images in the `ImageFileReader` (242)
- Work around pillow 10.0.0 breaking changes (244)
- Specimen description and preparation fixes within microscopy related content items (246)
- A number of style improvements (257 258 259 261 262 263 264 265 268)

Performance improvements
- Significant improvements to segmentation creation efficiency (227)

Documentation and tests
- Add `codespell` tool to check for spelling errors in the docs (237)
- Fix documentation links (250)
- Fix the readthedoc config (256)
- Fix to an incorrectly written frame encoding test (270)
- Use latest version of github actions (266)

New contributors

Thanks to yarikoptic thomas-albrecht elitalien and DimitriPapadopoulos for their first contributions to highdicom!