Med-imagetools

Features

- Add dockerfile and update lockfile ([177](https://github.com/bhklab/med-imagetools/pull/177),
[`6cf5515`](https://github.com/bhklab/med-imagetools/commit/6cf551529ebb7bfb432d868f4859c0631ec413a8))

Features

- Refactor utility modules, add patternresolver, formt
([170](https://github.com/bhklab/med-imagetools/pull/170),
[`dcc5aad`](https://github.com/bhklab/med-imagetools/commit/dcc5aadc9c053e581877b7561828a97c0de122ec))

Introduce image utilities and a new PatternResolver class, along with updated dependencies and
configuration adjustments. This enhances the project's capabilities for handling image processing
and pattern resolution.

Release Notes

- **New Features** - Added `PatternResolver` for parsing and resolving filename patterns. - Enhanced
`ImageGeometry` with a spacing attribute. - Introduced a new method to extract ROI names from
DICOM files.

- **Improvements** - Updated dependency specifications for numpy, pandas, and rich. - Improved code
formatting across multiple files. - Expanded linting coverage for additional Python files. -
Enhanced error handling and flexibility in ROI extraction from DICOM files.

- **Documentation** - Improved docstrings and code comments for better readability.

- **Chores** - Updated CI/CD workflow to support additional branches. - Reformatted configuration
files for consistency. - Removed unused import from the `io` module. - Deleted the `common.py`
file, removing obsolete functionality.

Features

- Improve structureset and crawl modules, Refactor tests and improve dataset handling
([165](https://github.com/bhklab/med-imagetools/pull/165),
[`5333a80`](https://github.com/bhklab/med-imagetools/commit/5333a80c6b2242c12d384846a3649a94a9eea60f))

Bug Fixes

- Replaced capturing regex terms with non capturing in datagraph
([162](https://github.com/bhklab/med-imagetools/pull/162),
[`3237b21`](https://github.com/bhklab/med-imagetools/commit/3237b21957adc5bc3efffe42d589bdeb4f27bc57))

Bug Fixes

- Rounding error in resample function ([163](https://github.com/bhklab/med-imagetools/pull/163),
[`f57a747`](https://github.com/bhklab/med-imagetools/commit/f57a7473b2dd5e14b12f4cdd833b9ecc1b60e6ad))

When output_size was not provided to `resample` function, the size was determined based on the
spacing but was floored. This would sometimes incorrectly shrink the image size. Changed to use
`np.round` instead.

Additionally, added the `output_size` argument to the `resample` call in the `resize` function. The
output size is already available in the function as `new_size`, so it doesn't make sense to
recalculate it in the `resample` function.

<!-- This is an auto-generated comment: release notes by coderabbit.ai -->

Summary by CodeRabbit

- **Bug Fixes** - Improved image resampling and resizing functions with more precise rounding and
type handling. - Enhanced parameter validation to ensure consistent integer conversion.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Features

- Minor grade refactoring ([158](https://github.com/bhklab/med-imagetools/pull/158),
[`0dff0f4`](https://github.com/bhklab/med-imagetools/commit/0dff0f403d802d517614105b50f1c4008945e32d))

Co-authored-by: Joshua Siraj <joshua.sirajryerson.ca>

Refactoring

- Improve logging, logic, and type annotations
([151](https://github.com/bhklab/med-imagetools/pull/151),
[`ef4d0e7`](https://github.com/bhklab/med-imagetools/commit/ef4d0e7c8f6b5e52c395916d0235645517a7ca03))

- **New Features** - Enhanced logging flexibility with new parameters for specifying logger names. -
Improved progress reporting in the folder crawling process with descriptive progress bars.

- **Bug Fixes** - Updated error handling for invalid file actions and DICOM tag checks for clearer
user feedback.

- **Documentation** - Improved docstring clarity and formatting across multiple functions.

- **Refactor** - Streamlined configuration files for testing and linting processes. - Restructured
class and function definitions for better readability and maintainability.

- **Style** - Consistent formatting applied to function signatures and docstrings.

- Modules/datagraph.py ([153](https://github.com/bhklab/med-imagetools/pull/153),
[`41a7c88`](https://github.com/bhklab/med-imagetools/commit/41a7c88992525c8cdfd690ef287ab5f76dc8e588))