-
Update CI workflow and add JUnit test reporting (#192,
8ccc0c0) -
CI/CD - Simplified GitHub Actions workflow to focus on main branch - Added JUnit test result summary reporting - Enhanced test job error handling
-
Development Tools - Updated pytest configuration for improved test reporting and caching - Refined linting configuration - Added new development task to clean cache and coverage files
A collection of tools for working with medical imaging data.
Options: -q, --quiet Suppress all logging except errors, overrides verbosity options. -v, --verbose
Increase verbosity of logging, overrides environment variable. (0-3: ERROR, WARNING, INFO, DEBUG).
--version Show the version and exit. -h, --help Show this message and exit.
Commands: dicomsort Sorts DICOM files into directories based on their tags. find-dicoms A tool to
find DICOM files. ```
versus using `med-imagetools[test]` ``` ❯ pixi run -e dev imgtools --help Usage: imgtools [OPTIONS]
COMMAND [ARGS]...
Commands: dicomsort Sorts DICOM files into directories based on their tags. find-dicoms A tool to
find DICOM files. testdata Download test data from the latest GitHub release.
-
New Features - Added GitHub release management functionality for medical imaging test data.
- Introduced new classes for handling GitHub releases and assets. - Implemented methods for downloading and extracting test datasets. - Enhanced command-line interface with a new command for downloading test datasets based on availability. - Expanded platform support in project configuration.
-
Documentation - Updated README with improved layout and badge presentation. - Enhanced project configuration in
pyproject.tomlandpixi.toml. -
Tests - Added comprehensive test suite for GitHub release data management. - Created fixtures and test methods to validate release retrieval and extraction. - Enhanced test coverage with additional scenarios for error handling.
This pull request introduces significant refactoring across multiple modules in the image tools
library, focusing on DICOM reading and processing functions. The changes centralize image reading
functionality into a new read_image utility function in the utils.py module, rename several
method signatures to use a more generic from_dicom approach, and improve the handling of DICOM
metadata across different image types like Dose, PET, and StructureSet. The modifications aim to
standardize the DICOM reading process and enhance code modularity.
| File | Changes | |------|---------| | src/imgtools/io/loaders/old_loaders.py | - Updated
read_dicom_rtstruct with optional roi_name_pattern parameter
- Modified method calls for
StructureSet, Dose, and PET object creation | | src/imgtools/modules/dose.py | - Removed
local read_image function
- Renamed from_dicom_rtdose to from_dicom
- Imported
read_image from .utils | | src/imgtools/modules/pet.py | - Removed local read_image
function
- Renamed from_dicom_pet to from_dicom
- Imported read_image from .utils |
| src/imgtools/modules/segmentation.py | - Added new from_dicom class method
- Added
from_dicom_seg alias method | | src/imgtools/modules/structureset.py | - Added from_dicom
method as alias for from_dicom_rtstruct
- Reintroduced roi_names and has_roi methods
-
Renamed _extract_metadata to utilize new RTSTRUCTMetadata type | |
src/imgtools/modules/utils.py | - Added new read_image utility function for DICOM series
reading |
-
Refactor find-dicom logic + docstring formatting, closes #149 (#186,
da363d6) -
Documentation - Improved docstring formatting for better readability in DICOM-related utility functions - Enhanced parameter descriptions in documentation
-
Chores - Reformatted code for improved readability - Slight modifications to code structure without changing core functionality
-
Remove unused imports for future re-introduction (#188,
cf5cbd0)
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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.
-
New Features - Added
PatternResolverfor parsing and resolving filename patterns. - EnhancedImageGeometrywith 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
iomodule. - Deleted thecommon.pyfile, removing obsolete functionality.
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.
- Bug Fixes - Improved image resampling and resizing functions with more precise rounding and type handling. - Enhanced parameter validation to ensure consistent integer conversion.
Co-authored-by: Joshua Siraj joshua.siraj@ryerson.ca
-
Improve logging, logic, and type annotations (#151,
ef4d0e7) -
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.
- Update .gitignore to exclude SQLite and database files
(
95a2179)
-
New Features - Enhanced
find_dicomsfunction to support limiting results and filtering by search input. -
Documentation - Updated installation instructions and expanded "Getting Started" section in the README. - Improved navigation structure in documentation, adding new entries for CLI reference.
-
Bug Fixes - Streamlined error handling and logging for various functions, ensuring clearer outputs and improved functionality.
-
Chores - Updated dependencies and configuration files for better management and performance.
-
Configure Git credentials for GitHub Actions and update documentation deployment step (
adf4e04) -
Update GitHub Actions workflow for concurrency and permissions; (
45cddb4)
Refactor logging code for improved maintainability by temporarily removing JSON logging functionality.
Update the .gitignore to exclude .dcm and .sqlite files.
Introduce an environment variable for debug logging and set the default log level based on this variable.
-
New Features - Introduced a new
LoggingManagerclass for structured logging management. - Added support for JSON logging configuration (currently commented out). - Added a new environment variable for logging level configuration in development. - New entries in.gitignoreto ignore.dcmand.sqlitefiles. - Enhanced CI/CD pipeline with new jobs for building and publishing documentation. -
Improvements - Enhanced logging control by utilizing environment variables for log levels. - Updated logging directory structure and default log filename for better organization. - Improved management of logging levels based on verbosity settings.
-
Bug Fixes - Improved handling of logging level discrepancies with user-specified settings.
-
Documentation - Updated docstrings and comments for clarity on new logging setup and features.
- Pipeline entry no longer needs to manually configure loglevel
(
66f8119)
- deps: Update med-imagetools to version 1.9.1 and update sha256 checksum
(
ab77c58)
- logging: Simplify logger configuration and enhance environment variable handling
(
c1f624b)
- Downstream bug where datagraph.py was missing from wheel due to data* being ignored in .gitignore
(
2dbb245)
- Fix broken images
(
a7d0e3a)
-
docs: add mkdocs-include-markdown plugin for Markdown file inclusion
-
docs: add tag helpers documentation for DICOM utilities
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docs: add documentation for finding DICOM files
-
Update src/imgtools/cli/dicomfind.py
-
feat: add regex filtering and improved logging for dicom_finder function
-
chore: exclude CLI files from coverage reporting
- Update README with new CLI point and reorganize, and formatting
(
96c6ab6)
- Common prefix for tree
(
a940969)
- Add dicomsorting cli entry
(
d435f93)
-
feat(logging): add structlog integration with custom processors and example logger
-
chore: remove star imports
-
feat(lint): update ruff configuration to include new linting rules and extend exclusions
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refactor: update pixi.lock and pixi.toml for ruff command structure and remove unused betapipeline entry
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refactor(logging): standardize string quotes and improve logger configuration handling
-
feat(logging): integrate structured logging and enhance debug information in AutoPipeline and StructureSet
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fix: #134 (comment)
-
fix: #134 (comment)
-
fix: #134 (comment)
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refactor(logging): streamline logging configuration and ensure log directory creation
-
chore: add log files to .gitignore to prevent tracking of generated logs
-
fix: Update src/imgtools/logging/init.py
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
-
fix: #134 (comment)
-
chore: update .gitignore to include log files in imgtools directory
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feat(datagraph): integrate logging for edge table processing and visualization
-
feat(ops): add timing for graph formation and update DataGraph initialization
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chore: rename workflow from Test to CI-CD and restrict push triggers to main branch
-
feat(crawl): integrate logging for folder crawling and data saving processes
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fix(structureset): enhance logging for ROI point retrieval errors
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fix(autopipeline): update logger level to use environment variable for flexibility
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fix(logging): streamline error handling for log directory creation
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fix: #134 (comment)
-
refactor(logging): enhance logging configuration and streamline JSON setup
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chore(pixi.lock): add license_family field for clarity
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refactor(logging): enhance LoggingManager with valid log levels and improve JSON logging setup
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refactor(logging): enhance documentation and improve LoggingManager configuration options
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refactor(logging): validate log level assignment before setting self.level
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feat(logging): add mypy and type-checking support; refactor logging manager and improve error handling
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refactor(logging): remove unused Optional import from typing
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feat: started port to pixi
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feat: updated test suite for pixi and started refactor of cicd
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build: added coverage to gha
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fix: explicitly direct location of package code and update pixi in pipeline
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fix: added linux to pixi
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chore: update GitHub Actions workflow for improved deployment process
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chore: clean up GitHub Actions workflow by removing commented-out jobs and updating dependencies
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chore: update GitHub Actions workflow to deploy from both main and devel branches, and refresh dependencies in pixi.lock
-
chore(sem-ver): 1.6.0-rc.1
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fix: update version_toml path in pyproject.toml for semantic release
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chore(sem-ver): 1.6.0-rc.2
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chore: remove requirements.txt file and poetry.lock
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chore: update authors and maintainers in pyproject.toml, and add version in init.py
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chore: remove setup.py file as part of project restructuring
-
chore: update pixi.lock and add ruff configuration for linting
-
chore: fix some recommendations from coderabbit
Co-authored-by: semantic-release
-
fix(datagraph): update edge_types to 8 and handle new edge type for SEG->CT/MR mapping in final dataframe processing
-
fix(pyproject): update attrs version constraint to allow all 23.x versions and above
- Ci-cd - add id in release for pypi step
(
7abd175)
- Update ci to release to pypi
(
a92a41f)
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fix: remove deprecated pydicom.dicomdir.DicomDir variable type option
-
style: removed Union since dicom_data can only be a FileDataset
-
refactor: remove Union import for linting
- Update ci to use semver bot
(
98e3bd0)
-
chore: bump artifact action version
-
refactor: update StructureSetToSegmentation docstring and remove unused dev group in pyproject.toml
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chore: fix download action in workflow to use correct artifact version
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chore: correct instantiation reference and update parameter description in StructureSetToSegmentation docstring
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chore: enhance StructureSetToSegmentation docstring to support None as a roi_names option for loading all ROIs
- Upload latest version to pypi
(
1debad3)
- Format toml
(
269f55d)
- Bump version
(
58ec67f)
-
feat: semantic release
-
fix: if statement issue