v2.0.0-rc.7

v2.0.0-rc.7 (2025-02-14)

This release is published under the MIT License.

Bug Fixes

• Update SEG value for ISPY2 dataset in test configuration (d9a83d1)

---

Detailed Changes: v2.0.0-rc.6...v2.0.0-rc.7

v2.0.0-rc.6

v2.0.0-rc.6 (2025-02-14)

---

Detailed Changes: v2.0.0-rc.4...v2.0.0-rc.6

What's Changed

Bug Fixes

• Add function to handle out of bounds coordinates for a RegionBox in an image
  (#221,
  fc36464)

This works the same way as _adjust_negative_coordinates, but requires the image as an addition
input and modifies the RegionBox object directly.

A message is logged in the debugger if a dimension is adjusted.

I also updated the crop_image function to call this before applying the crop.

• Handle odd extra dimension values in expand_to_min_size
  (#220,
  881dcfc)

• Removed import
  (c9d3b4f)

• Replace Error with ValueError for task ID validation in AutoPipeline
  (7d911be)

• Update array_to_image function to require either a reference image or all spatial parameters
  (e35c842)

• Update import path for get_modality_metadata in old_loaders.py
  (93a16c1)

• Update testdata function to accept patterns for exclusion
  (d321275)

Chores

• Add Python 3.13 to classifiers and include project URLs in pyproject.toml
  (e1eca75)

• Deprecate
  (2d9d86d)

• Deprecate
  (e060e79)

• Deprecate
  (2123ed8)

• Deprecate autopipeutils and nifti_to_dicom modules
  (3cf82c9)

• Import sanitize_file_name and update all to include it
  (a28db1d)

• Ruff qc
  (2de2416)

• Update coverage and mypy configurations to reflect deprecation of modules and increase pytest max
  processes
  (bd32522)

• Update GitHub Actions workflow and modify semantic release configuration
  (d622168)

• Update GitHub Actions workflow to include Python 3.13 and upgrade pixi version to 0.41.1
  (1b767e1)

• Update GitHub Actions workflow to set locked option to false
  (53cc645)

• Update pixi toml and lock
  (ca942a0)

• Update pixi.lock to reflect dependency changes
  (9982560)

Documentation

• Update README.md so codecov badge takes you to codecov.io
  (b39528f)

Features

• Add desired_size to centroid bounding box generation
  (#219,
  066844d)

In old version, bounding box was a single voxel. Now is expanded to at least the minimum dimension
default.

• New Features - Now, users can optionally specify a desired size when generating image bounding
  boxes for enhanced control.

• Chores - Updated the software version from 1.21.1 to 1.22.0.

• Add DICOM metadata extraction functions for various modalities
  (fbfb509)

• Add index command to crawl and index DICOM images
  (0234fe0)

• Add optional import functionality and clean up dependencies
  (#217,
  072e6ce)

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.

• Enhance filename sanitization by removing disallowed characters at the edges and adding
  comprehensive tests
  (57283e2)

• Enhance RegionBox to support desired size in from_mask_centroid and adjust bounding box
  calculations
  (0e85352)

• Improve code structure and refactor image processing utilities
  (d036547)

• New Features - Introduced a new PET image type for enhanced imaging support. - Enabled
  automated dataset indexing and visualization for quicker data previews. - Expanded image
  input/output capabilities with versatile export options. - Enhanced scanning functionality with
  improved metadata and statistics. - Upgraded CLI worker allocation for more reliable performance.

• Refactor - Streamlined image processing operations and improved overall code clarity.

• Tests - Extended test coverage across image conversion and region handling functions.

Refactoring

• Remove structureset_helpers module and its utilities
  (cc68dc7)

• Simplify type hints and clean up mypy configuration
  (7c3c97a)

• Update dataset collections and enhance test coverage for shared data directory
  (22c8202)

Testing

• Add minimum release version check and improve test readability
  (576884b)

Full Changelog: v2.0.0-rc.4...v2.0.0-rc.6

v2.0.0-rc.4

v2.0.0-rc.4 (2025-02-10)

This release is published under the MIT License.

Bug Fixes

• Add function to handle out of bounds coordinates for a RegionBox in an image (#221, 9949a4f)

This works the same way as _adjust_negative_coordinates, but requires the image as an addition input and modifies the RegionBox object directly.

A message is logged in the debugger if a dimension is adjusted.

I also updated the crop_image function to call this before applying the crop.

---

Detailed Changes: v2.0.0-rc.3...v2.0.0-rc.4

v2.0.0-rc.3

v2.0.0-rc.3 (2025-02-07)

This release is published under the MIT License.

Chores

• Update lockfile (9069f4f)

---

Detailed Changes: v2.0.0-rc.2...v2.0.0-rc.3

v2.0.0-rc.2

v2.0.0-rc.2 (2025-02-07)

This release is published under the MIT License.

Chores

• Comment out PyPI publish step in CI workflow (c42f5eb)

• Update pixi.lock file (e2c2c5e)

Features

• Allow CI-CD workflow to run on development branch (d832db9)

• Update docs and lockfile (6e07540)

---

Detailed Changes: v2.0.0-rc.1...v2.0.0-rc.2

v2.0.0-rc.1

v2.0.0-rc.1 (2025-02-07)

Chores

• Update lockfile (f3c4837)

Features

• Add optional import functionality and clean up dependencies (#217, 9efc491)

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.

---

Detailed Changes: v1.21.1...v2.0.0-rc.1

v1.23.2

v1.23.2 (2025-02-07)

This release is published under the MIT License.

Bug Fixes

• Add function to handle out of bounds coordinates for a RegionBox in an image (#221, 155f59a)

This works the same way as _adjust_negative_coordinates, but requires the image as an addition input and modifies the RegionBox object directly.

A message is logged in the debugger if a dimension is adjusted.

I also updated the crop_image function to call this before applying the crop.

---

Detailed Changes: v1.23.1...v1.23.2

v1.23.1

v1.23.1 (2025-02-07)

This release is published under the MIT License.

Bug Fixes

• Handle odd extra dimension values in expand_to_min_size (#220, 6eb58ea)

---

Detailed Changes: v1.23.0...v1.23.1

v1.23.0

v1.23.0 (2025-02-07)

This release is published under the MIT License.

Features

• Add desired_size to centroid bounding box generation (#219, 30a129f)

In old version, bounding box was a single voxel. Now is expanded to at least the minimum dimension default.

• New Features

• Now, users can optionally specify a desired size when generating image bounding boxes for enhanced control.

• Chores

  • Updated the software version from 1.21.1 to 1.22.0.

---

Detailed Changes: v1.22.0...v1.23.0

v1.22.0

v1.22.0 (2025-02-07)

This release is published under the MIT License.

Features

• Add optional import functionality and clean up dependencies (#217, 9efc491)

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.

---

Detailed Changes: v1.21.1...v1.22.0