Highdicom

Bug fixes

* Fix Dimension Organization of Segmentation instances (92).

Major changes

* Deprecate `Segmentation.add_segments()` method (92). All segments now need to be passed to the constructor method. See more detailed release notes about this issue [here](https://highdicom.readthedocs.io/en/latest/release_notes.html#deprecation-of-add-segments-method).

Improvements

* Improve import logic for subpackages and modules to allow:
python
import highdicom as hd
seg_image = hd.seg.Segmentation(...)

* Update API documentation to reflect namespaces of public API
* Add unit tests and increase test coverage

Improvements

* Increase test coverage of `highdicom.sr.templates` and `highdicom.sr.content` modules
* Add hyperlinks for context groups (CIDs) and templates (TIDs) to docstrings
* Add checks to ensure that argument `segment_number` of `highdicom.seg.sop.Segmentation.add_segments` method is a positive number
* Add checks to ensure that segments added to Segmentation instance via `highdicom.seg.sop.Segmentation.add_segments` are ordered correctly
* Add checks to prevent Content Sequence in Finding Sites from being empty
* Make tests stricter by enforcing valid value representation in pydicom
* Add alternative constructor methods for `highdicom.sr.content` classes

Bug fixes

* Make `algorithm_identification` parameter of `highdicom.seg.content.SegmentDescription` constructor optional to support manual segmentation
* Make `laterality` parameter `highdicom.sc.sop.SCImage` constructor optional
* Fix referencing segments in Planar/Volumetric ROI Measurements and Qualitative Evaluations templates
* Fix Code Value in `highdicom.sr.templates.DeviceObserverIdentifyingAttributes`
* Include documentation of `highdicom.uid` module
* Fix constructor of `highdicom.sr.templates.TimePointContext`

Bug fixes

* Fix addition of segments to Segmentation image with different plane positions

Improvements

* Increase unit test coverage

New features

* Implement image file reader for efficient frame-level access (`highdicom.io.ImageFileReader`)
* Add support for spatial coordinate transformations (`highdicom.spatial.ImageToReferenceTransformer` and `highdicom.spatial.ReferenceToImageTransformer`)
* Add support for color management based on ICC Profiles (`highdicom.color.ColorManager`)
* Add utilities for encoding and decoding of frames (`highdicom.frame.decode_frame` and `highdicom.frame.encode_frame`)
* Add new content item `geometric_purpose` to structured reporting templates (`highdicom.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations` and `highdicom.sr.templates.VolumetricROIMeasurementsAndQualitativeEvaluations`)

Improvements

* Add more segmentation test datasets
* Apply stricter flake8 coding style rules

Bug fixes

* Fix copying of specimen attributes in derived objects (`highdicom.base.SOPClass`)
* Fix docstring in structured reporting template (`highdicom.sr.templates.Measurement`)

Bug fixes

* Remove optional Total Pixel Matrix Focal Planes attribute from Segmentation SOP class
* Fix typing errors reported by newer mypy versions