Med-imagetools

Chores

- Update lockfile
([`9069f4f`](https://github.com/bhklab/med-imagetools/commit/9069f4fe3bcc2f2344d2e6148cb1b7dd614d09c0))

Bug Fixes

- Push release candidates to pypi
([`2120f9f`](https://github.com/bhklab/med-imagetools/commit/2120f9f3160f1230f782fd50d209ec69dda653a6))

Chores

- Comment out PyPI publish step in CI workflow
([`c42f5eb`](https://github.com/bhklab/med-imagetools/commit/c42f5eb848b254d2389fe58810f43cce389192b7))

- Update pixi.lock file
([`e2c2c5e`](https://github.com/bhklab/med-imagetools/commit/e2c2c5e75d1b30db2f4d4e5edb45cffcdff869ae))

Features

- Allow CI-CD workflow to run on development branch
([`d832db9`](https://github.com/bhklab/med-imagetools/commit/d832db9bf165daefab5c849b16c81493799f89b7))

- Update docs and lockfile
([`6e07540`](https://github.com/bhklab/med-imagetools/commit/6e075408fd1ef5e4da4ec84000c558d8fa117e59))

Chores

- Update lockfile
([`f3c4837`](https://github.com/bhklab/med-imagetools/commit/f3c4837e14ca692f68eba2f0d27c30cab2cf7a7c))

Features

- Add optional import functionality and clean up dependencies
([217](https://github.com/bhklab/med-imagetools/pull/217),
[`9efc491`](https://github.com/bhklab/med-imagetools/commit/9efc491ef6e6ded596b7880eca810ce24c8a6647))

Introduce optional import functionality for h5py and pynrrd, while removing unused dependencies and
refactoring the codebase for better maintainability.

- Documentation • Updated installation instructions with new environment setup commands and
streamlined guidance.

- Refactor • Removed legacy imaging processing and indexing functionalities to simplify the toolset.

- New Features • Enhanced error handling for optional dependencies to offer clearer messaging when
modules are missing.

Bug Fixes

- Refactor DICOM utilities and enhance documentation
([216](https://github.com/bhklab/med-imagetools/pull/216),
[`1ed8de6`](https://github.com/bhklab/med-imagetools/commit/1ed8de6d0f373837a24b36653df30338d66cea0c))

Remove unnecessary sanitization functionality, improve DICOM exception handling, and introduce new
utilities for loading and extracting ROI metadata. Update documentation to include references for
the new DICOM utilities.

- **New Features** - Enhanced support for processing various DICOM file formats with improved
metadata extraction and robust error handling. - Introduced cross-platform support for determining
optimal file path and filename lengths, along with secure filename sanitization.

- **Refactor** - Streamlined DICOM processing by removing legacy parameters and simplifying function
interfaces for consistent performance.

- **Tests** - Updated the testing suite for improved type safety and reliability, ensuring smoother
interactions when handling DICOM files.

Documentation

- Enhance RegionBox with flexible padding options and module updates
([215](https://github.com/bhklab/med-imagetools/pull/215),
[`5f38f49`](https://github.com/bhklab/med-imagetools/commit/5f38f4994c14dcabf79a3400000f560de1c798cc))

Introduce the BoxPadMethod enum for padding flexibility in RegionBox. Update import paths and remove
deprecated modules to streamline the codebase.

Chores

- Update lockfile
([`3ff9ca1`](https://github.com/bhklab/med-imagetools/commit/3ff9ca1da86a3f2d481a6fd151dec42b90245836))

Features

- Improve AbstractBaseWriter with indexing and add docs (176)
([189](https://github.com/bhklab/med-imagetools/pull/189),
[`e147629`](https://github.com/bhklab/med-imagetools/commit/e147629c0f2f055d02609cde6f1f2f4be5e260c0))

- **New Features** - Introduced a unified file writing framework that streamlines saving image and
array data across various formats (e.g., HDF5, NIFTI, NumPy). - Enhanced file handling with
improved validations for naming, compression levels, and managing existing files, ensuring smooth
data export and logging.

- **Tests** - Added comprehensive testing to verify file saving operations, error handling, and file
indexing, ensuring robust performance across different usage scenarios. <!-- end of auto-generated
comment: release notes by coderabbit.ai -->

Refactoring

- Remove Vector3D; update Coordinate3D and enhance RegionBox
([210](https://github.com/bhklab/med-imagetools/pull/210),
[`c16ae7c`](https://github.com/bhklab/med-imagetools/commit/c16ae7c04695e2b5f15d3d8a8fe54209b9024dd7))

Remove the Vector3D class, integrating its functionality into Coordinate3D. Update documentation and
improve the calculate_image_boundaries function to support world coordinates. Rename variables for
clarity and consistency.

- **New Features** - Introduced a cropping capability that allows simultaneous cropping of images
and their corresponding masks. - Added an optional parameter to select the coordinate system when
computing image boundaries. - Added new functions to retrieve example dataset paths and images.

- **Enhancements** - Improved 3D coordinate operations to now support integer arithmetic as well as
equality and ordering comparisons. - Updated documentation and diagrams to provide a clearer,
simplified view of class relationships.

- **Refactor** - Removed a legacy 3D vector type to streamline the available coordinate types.

- **Bug Fixes** - Simplified exception handling and improved clarity in the
`BoundingBoxOutsideImageError` class.

- **Tests** - Expanded test coverage for the new `Coordinate3D` class, including equality and
comparison operations, while removing tests for the deprecated `Vector3D`. - Added a new test for
validating example dataset images.

Features

- Add examples module for image dataset tools
([212](https://github.com/bhklab/med-imagetools/pull/212),
[`a882574`](https://github.com/bhklab/med-imagetools/commit/a8825741006650fae3f36fd5bbe270768b87965a))

- **New Features** - Introduced new functions for streamlined access to example dataset resources,
mapping key identifiers to their corresponding file paths and images. - Added a dynamic capability
to conditionally include functionalities based on the availability of test data. - **Bug Fixes**
- Enhanced error handling for missing dataset files. - **Tests** - Added a new test function to
verify the integrity and presence of example dataset images.