https://github.com/bhklab/readii - v1.34.3

v1.34.3 (2025-01-30)

Bug Fixes

• Pattern resolver update (#116, 39a6d6b)

PatternResolver in med-imagetools updated the input argument from pattern_parser to pattern_matcher, updated this to match here.

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

• Chores
• Updated parameter naming in the PatternResolver class for improved clarity and consistency.
• Modified the roiNames parameter format in segmentation loading tests for better structure and clarity.
• Adjusted expected output labels in segmentation tests to reflect new naming conventions.
• Reorganized import statements to source functions from a new module, maintaining accessibility. <!-- end of auto-generated comment: release notes by coderabbit.ai -->

---

Detailed Changes: v1.34.2...v1.34.3

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.34.2

v1.34.2 (2025-01-30)

Bug Fixes

• Axes labelling in plotCrossCorrHeatmap (#115, 49b38ce)

Swap vertical and horizontal feature labels on x and y axes of cross correlation heatmap

Summary by CodeRabbit

• Bug Fixes
• Corrected axis label assignments in cross-correlation heatmap visualization to improve accuracy of feature representation.

---

Detailed Changes: v1.34.1...v1.34.2

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.34.1

v1.34.1 (2025-01-15)

Bug Fixes

• Update toml to fix deprecated "depends_on" key (#109, 2c2c324)

---

Detailed Changes: v1.34.0...v1.34.1

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.34.0

v1.34.0 (2024-12-31)

Features

• Add overwrite variable to plot self and cross corr functions (#108, d1f9853)

Summary by CodeRabbit

• New Features
• Added an optional overwrite parameter to correlation plotting functions
• Enhanced control over file saving behavior when generating correlation plots
  • Users can now choose whether to replace existing plot files

---

Detailed Changes: v1.33.0...v1.34.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.33.0

v1.33.0 (2024-12-30)

Features

• Add error for when file output by CorrelationWriter already exists (#106, ef58923)

Makes it easier to catch times when file exists without resolving the path twice

Summary by CodeRabbit

• New Features

• Added a new, more specific exception for handling file existence scenarios during correlation writing.

• Documentation

  • Updated method documentation to reflect new error handling behavior.

---

Detailed Changes: v1.32.0...v1.33.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.32.0

v1.32.0 (2024-12-30)

Features

• Update plot correlation functions (#104, 9baffe9)

add self and cross correlation plot functions

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

• New Features
• Introduced functionality for plotting self and cross correlation heatmaps and histograms.
• Added methods for generating histograms with customizable parameters and optional saving options.
• Bug Fixes
• Enhanced error handling for plot saving to prevent overwriting existing files.
• Tests
• Added a comprehensive suite of unit tests for correlation plotting functionalities, ensuring correct outputs and file handling. <!-- end of auto-generated comment: release notes by coderabbit.ai -->

---

Detailed Changes: v1.31.0...v1.32.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.31.0

v1.31.0 (2024-12-19)

Features

• Update correlation functions to get subsections of matrix (#103, 343d876)

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

• New Features
• Enhanced correlation analysis methods for improved clarity and functionality.

• Introduced a new method to retrieve both self and cross correlations in a single call.

• Bug Fixes

• Improved error handling for cases with no matching features, providing specific error messages.

• Documentation

  • Updated public API to reflect new method names and signatures. <!-- end of auto-generated comment: release notes by coderabbit.ai -->

---

Detailed Changes: v1.30.0...v1.31.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.30.0

v1.30.0 (2024-12-19)

Features

• Fix loaders some more (#98, 6272a03)

Didn't test updating from os to pathlib enough, but should be good now. Added basic test, needs to be expanded upon.

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

• New Features
• Introduced a new variable for improved file path handling in the feature loading process.

• Added a comment for clarity on retrieving the full path to the feature file.

• Bug Fixes

• Updated logic for removing the image type file from the feature files list.

• Tests

• Added a new test function to validate the functionality of the feature loading function.

  • Implemented a fixture for testing with a temporary feature file. <!-- end of auto-generated comment: release notes by coderabbit.ai -->

---

Detailed Changes: v1.29.1...v1.30.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.29.1

v1.29.1 (2024-12-18)

Bug Fixes

• Look for image type in Path stem as Path is not iterable (#97, 875a6c3)

Summary by CodeRabbit

• New Features
• Improved file matching logic for identifying features based on image types.

• Enhanced clarity in handling scenarios for matching files with updated control flow.

• Bug Fixes

• Retained consistent error handling with appropriate logging for warnings and exceptions.

---

Detailed Changes: v1.29.0...v1.29.1

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.29.0

v1.29.0 (2024-12-18)

Features

• Add CorrelationWriter (#96, b241c42)

Created CorrelationWriter class for the analyze portion of the pipeline.

I think there will eventually be a FeatureSetWriter that this should probably inherit from, but I need the Correlation one now for Aerts.

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

• New Features - Introduced a CorrelationWriter class for managing the writing of correlation data to files with customizable paths and filenames. - Added support for saving correlation data in both CSV and Excel formats.

• Bug Fixes - Implemented error handling for invalid correlation data, existing files, and filename format validation.

• Tests - Added a comprehensive suite of unit tests for the CorrelationWriter class, covering various scenarios for saving correlation data. <!-- end of auto-generated comment: release notes by coderabbit.ai -->

---

Co-authored-by: Jermiah Joseph jermiahjoseph98@gmail.com

---

Detailed Changes: v1.28.0...v1.29.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.28.0

v1.28.0 (2024-12-18)

Features

• Add io/readers to ruff config (#94, 7efc97b)

Updated include list to have the io/readers functions and updated the files so all ruff tests pass.

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

• New Features
• Enhanced flexibility in loading feature files by accepting both Path objects and strings.

• Improved error handling and logging for file loading and directory access.

• Bug Fixes

• Enhanced error handling and logging for file loading and directory access, providing clearer context for issues.

• Documentation

• Updated docstrings for functions to improve clarity and detail, including return type annotations. <!-- end of auto-generated comment: release notes by coderabbit.ai -->

---

Detailed Changes: v1.27.0...v1.28.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.27.0

v1.27.0 (2024-12-17)

Features

• Add analysis functions (#92, a57182c)

Includes correlation calculations and plotting those correlations as a heatmap and histogram

• New Features - Updated version number to 1.26.0 with new dependencies: numpy, seaborn, and pandas. - Introduced a new module for analyzing READII outputs with several correlation functions. - Added visualization functions for correlation data: heatmap and histogram. - New validation function for DataFrame dimensions added. - Expanded platform support to include osx-64 and win-64.

• Bug Fixes - Enhanced error handling in correlation calculations and plot saving processes. - Simplified exception handling in feature loading functions.

• Documentation - Improved docstrings for new functions and modules for better usability.

• Chores - Expanded linting configuration for broader coverage of Python files.

---

Detailed Changes: v1.26.0...v1.27.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.26.0

v1.26.0 (2024-12-16)

Features

• Expand platform support in pixi and CI/CD workflow (#91, 546fe5c)

This PR adds the windows platform and older mac platform to the pixi configuration so developers with those machines can be assured that they can contribute to this project without running into dependency issues

• also add a testing branch to test with windows across all configured python versions

Summary by CodeRabbit

• New Features

  • Expanded testing environment to include Windows support.
  • Updated project version to "1.25.0".
  • Added support for additional platforms: "osx-64" and "win-64".

• Bug Fixes

• Clarified the checkout process for the publishing jobs in the CI-CD workflow.

---

Detailed Changes: v1.25.0...v1.26.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.25.0

v1.25.0 (2024-12-16)

Features

• Add optional segmentationLabel input for singleRadiomifFetaureExtraction (#90, bebb8f3)

Discovered an edge case when processing ISPY2 SEG files that have multiple regions in them that are identified by numeric values in the mask.

Need READII to be able to take a specific value so the correct mask is used when checking the mask, cropping the image, and performing feature extraction.

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

• New Features - Introduced an optional segmentationLabel parameter in the feature extraction process for enhanced flexibility. - Improved error handling during segmentation mask validation and image cropping.

• Bug Fixes - Enhanced robustness by catching and logging exceptions related to feature extraction.

• Tests - Added new tests to verify behavior with the segmentationLabel parameter and to validate error handling for invalid inputs. <!-- end of auto-generated comment: release notes by coderabbit.ai -->

---

Detailed Changes: v1.24.0...v1.25.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.24.0

v1.24.0 (2024-12-16)

Features

• Add data functions used for analysis code (#89, 2eb6e1e)

Summary by CodeRabbit

• New Features
• Introduced functions for manipulating and analyzing patient data, including patient ID handling and time conversion.
• Added capabilities for selecting and filtering radiomic data within DataFrames.

• Implemented methods for replacing values and splitting DataFrames based on specified criteria.

• Bug Fixes

• Enhanced error handling across multiple functions to ensure robust performance and logging of issues.

---

Detailed Changes: v1.23.0...v1.24.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.23.0

v1.23.0 (2024-12-13)

Features

• Add io/loaders module (#83, 81fbd78)

Includes features, general, and images specific loading functions

• New Features
• Introduced a new module for loading various data types in the READII pipeline.
• Added functions for loading imaging feature sets, dataset configurations, and data files into DataFrames.

---

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

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.22.0

v1.22.0 (2024-12-13)

Features

• Add BaseWriter, and example NIFTIWriter with notebooks documenting them (#84, 7228770)

Mostly inspired and reusing logic from Med-ImageTools DICOMSorter design

• New Features
• Enhanced Jupyter notebooks for saving medical imaging data in NIFTI format and CSV metadata.
• Added examples for using subclasses of BaseWriter for writing text and CSV files.
• Introduced the NIFTIWriter class for managing NIFTI file writing with validation and error handling.
  • Added new CSVWriter class for saving data in CSV format.

---

Detailed Changes: v1.21.0...v1.22.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.21.0

v1.21.0 (2024-12-13)

Features

• Add readii-datasets CLI command and include orcestra-downloader dependency (#80, f760b68)

closes https://github.com/bhklab/analyzereadiioutputs/issues/6

the CLI in orcestra-downloader uses click and allows us to reuse the same user CLI API for just a subset of the data and so the readii-datasets entry point is just a renamed version of that one to prevent rewriting code.

---

Detailed Changes: v1.20.0...v1.21.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.20.0

v1.20.0 (2024-12-12)

Features

• Initialize documentation (#85, 3b2c294)

Start of documentation, mostly copied the core dependencies and plugins from med-imagetools

• Set up initial documentation structure using MkDocs, including configuration and integration of Markdown files for the README and CHANGELOG.

this "core" would be the base of the main vs 2.0 branch

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

• New Features - Added badges for project health and status in the README. - Expanded installation instructions with a new environment setup method. - Introduced a section for serving documentation locally.

• Documentation - Enhanced clarity and structure of the README, including command-line options and contributing guidelines. - Updated inclusion method for CHANGELOG and README in documentation. - Introduced a new configuration file for MkDocs documentation, improving navigation and usability.

• Bug Fixes - Corrected formatting for bash commands in the README to enhance readability.

• Chores - Updated project version and dependencies in the configuration files. <!-- end of auto-generated comment: release notes by coderabbit.ai -->

---

Detailed Changes: v1.19.0...v1.20.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.19.0

v1.19.0 (2024-12-11)

Features

• Add abstract and concrete classes for negative controls and regions (#81, c10a568)

4D-Lung

Order of operations

1. negative_control_strategy(image, mask=mask, region=region_strategy) 2. runs the __call__ on the negative_control_strategy 3. which runs the __call__ of region(image_array, mask_array) 4. the result of which is used to figure out what indices of the original image to apply the transform method of the NegativeControlStrategy concrete classes to 5. only replace the region indices image_array[mask_indices] = transformed_values

Resource on Strategy Pattern: https://refactoring.guru/design-patterns/strategy/python/example

---

Co-authored-by: Katy Scott k.l.scott16@gmail.com

Refactoring

• Update Ruff configuration and refactor codebase (#68, e88e704)

Enhance the Ruff configuration to include additional files and ignore specific PEP-8 naming conventions. Refactor the codebase by replacing os.path with pathlib, improving logging verbosity, adding type annotations, and organizing imports.

• Bug Fixes
• Improved error handling for image cropping and feature extraction processes, ensuring robustness and clearer logging.
• Chores
• Updated configuration settings to refine linting rules and file inclusions, optimizing code quality checks.

• Incremented Pixi version across CI-CD jobs for improved performance.

• feature-extraction: Extract-method refactor to simplify workflow, prepare for class-based feature extraction (#69, 3bcaa28)

summary: Refactor code to improve readability, logging, and type annotations while addressing various bugs and updating dependencies.

mostly extract-method refactoring to make following code flow a bit easier. - setting up to create a class for the module to save from passing around all the parameters

updates to code quality control tasks - for the most part will follow suit with med-imagetools configuration for qc - pixi run qc will run ruff format and lint on files included in ruff.toml - Enhance ruff configuration to include additional files and ignore specific PEP-8 naming conventions.

• New Features - Introduced new functions for enhanced radiomic feature extraction: generateNegativeControl, cropImageAndMask, and featureExtraction.

• Improvements - Enhanced error handling and logging for the feature extraction process. - Improved documentation and formatting in loaders for better readability.

• Configuration Updates - Updated linting configuration to include specific files for checks and clarified linting rules with detailed comments. - Updated project version to "1.18.0" and added new dependencies for Jupyter-related packages. - Streamlined CI-CD workflow by modifying linting commands and removing unnecessary jobs.

---

Detailed Changes: v1.18.0...v1.19.0

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.18.0

v1.18.0 (2024-11-28)

Features

• Add slicedim to displayimageslice (#67, c018de5)

• feat: add slice dimension variable for displayImageSlice

Allows user to indicate whether the slice index is first or last

• build: add libraries to run jupyter notebooks

• docs: fix variable type for sliceDim in displayImageSlice docstring

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.17.0

v1.17.0 (2024-11-22)

Features

• Replace get_logger with imgtools inherited logging instance across modules (01bd13f)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.16.0

- Jupyter Notebook
Published by jjjermiah over 1 year ago

https://github.com/bhklab/readii - v1.14.1

v1.14.1 (2024-11-07)

Bug Fixes

• fix: add readii cli entry point to pyproject (#58) (1710b72)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.14.0

v1.14.0 (2024-11-01)

Features

• feat: remove dicom-parser, update mit, deprecate padSeg (#51)

• fix: Update med-imagetools dependency and handle deprecated padSegToMatchCT function in feature_extraction.py with error logging

• chore: Update .gitignore to exclude .old, data, and trash directories for working dir

• Update src/readii/feature_extraction.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

• fix: change gitignore data

• better handling of data ignore

---

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> (a6658e7)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.13.2

v1.13.2 (2024-10-22)

Bug Fixes

• fix: Remove hatch config and streamline build settings in pyproject.toml for better package management and deployment (0cf184c)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.13.1

v1.13.1 (2024-10-22)

Bug Fixes

• fix: Update CI/CD workflow for PyPI publishing; enhance publish step, remove TestPyPI, and configure pixi.lock sha256 (743ea52)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.13.0

v1.13.0 (2024-10-22)

Bug Fixes

• fix: update CI/CD workflow to trigger only on pushes to main branch (2cc686f)

• fix: correct version location in pyproject.toml configuration (bdb49ea)

• fix: improve modality handling in loadSegmentation by reinforcing RTSTRUCT validation and simplifying modality checks (5d1fef6)

• fix: update ruff configuration and linting rules, switch docstring style to numpy, and enhance loader type annotations (0142860)

Chores

• chore: refine CI-CD workflow for Publish-To-PyPi and update pixi.lock SHA for dependency consistency (3c904e1)

• chore: add Ruff linter to CI-CD workflow and update project config for linting and formatting tasks (ecebe9a)

• chore: adjust CI-CD workflow to trigger on any branch for pull requests and comment out previous push configuration (3c77975)

• chore: add Codecov badge to README for improved visibility of test coverage (9472ab6)

• chore: add Codecov step in CI/CD workflow to track coverage and report using coverage.xml (fcbe561)

Continuous Integration

• ci: clean up .github/workflows/ci-cd.yml by removing unnecessary whitespace and ensuring proper formatting at end of file (a6298ab)

• ci: update CI-CD workflow to include Ruff as a dependency for the Unit-Tests job before deployment to PyPI (5d6a7f3)

Documentation

• docs: update README with installation + badges (7bdf5d3)

Features

• feat: enhance segmentation loading by adding validation for unsupported modalities in loadSegmentation function (9ee6931)

• feat: rename job to Publish-To-Test-PyPi and add Test-TestPypi-Installation steps for verifying package deployment (336185f)

• feat: update CI-CD workflow to include publishing to TestPyPI with new environment variables for authentication (d645af1)

• feat: expand pyproject.toml with publish-test command for deploying to test PyPI and add description for build task (f309346)

Unknown

• Merge pull request #42 from bhklab/jjjermiah/refactor/main

feat: Enhance CI/CD Workflow with TestPyPI Publishing, Linting Improvements, and minor docs update (376b414)

• doc: enhance docstrings in loaders.py, providing clearer descriptions and improving module documentation for DICOM and RTSTRUCT functions (249238c)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.12.0

v1.12.0 (2024-10-22)

Chores

• chore: update CI/CD workflow to use actions/checkout@v3, fix semantic-release task, and update pixi.lock (790ae04)

• chore: refactor CI/CD workflow with enhanced job structure and add basic config files for coverage and linting (994fd75)

Features

• feat: add semantic-release workflow for automated versioning and update readii version to 1.11.0 with new author email (92bc4d4)

• feat: update to use pixi and pyradiomics-bhklab (6a67be4)

Unknown

• Merge pull request #40 from bhklab/jjjermiah/add-pixi

feat: Use Pixi, pyradiomics fork (fd582a5)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.11.0

v1.11.0 (2024-09-25)

Feature

• feat(feature_extraction): add logging for error raised when cropping CT and segmentation (d9d8069)

Fix

• fix(feature_extraction): actually raise an exception for negative control creation (e1a9888)

Unknown

• Merge pull request #39 from bhklab/negativecontrolerror_handling

Negative control error handling (2bac7db)

• Merge branch 'main' of github.com:bhklab/yarea into main (556178e)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.9.0

v1.9.0 (2024-09-25)

Documentation

• docs: clean up angular commit formatting in README (1f16ad1)

• docs: add angular commit syntax to README (c9f76df)

Feature

• feat(feature_extraction): add catch and logging around negative control creation (a90efac)

Unknown

• Merge pull request #38 from bhklab/add_logging

Negative control error catching and angular commit syntax (8646cf0)

• Merge pull request #37 from bhklab/keeprunningflag

Created keep_running flag (0c95c80)

• Added logging (f666b4d)

• Created keep_running flag, which keeps pipeline running even if a single patient fails. (c1fe170)

- Jupyter Notebook
Published by github-actions[bot] over 1 year ago

https://github.com/bhklab/readii - v1.8.0

v1.8.0 (2024-09-17)

Feature

• feat: make output directory and parents as needed before saving radiomic output (bf7600c)

Refactor

• refactor: change output file from feature extraction without negative control to be radiomicfeaturesoriginaldatasetname.csv (7663ce8)

Test

• test(testfeatureextraction): updated for new original image feature extraction output (2e53bc8)

Unknown

• Merge pull request #36 from bhklab/change-original-image-output-name-convention

Change original image output name convention (d6af655)

- Jupyter Notebook
Published by github-actions[bot] almost 2 years ago

https://github.com/bhklab/readii - v1.7.7

v1.7.7 (2024-09-12)

Chore

• chore: update lockfile (9c5fa18)

Fix

• fix: Remove coloredlogs dependency and logging configuration from the project (ba8208f)

Unknown

• Merge pull request #35 from bhklab/removecoloredlogs

fix: Remove coloredlogs dependency and logging configuration from the project (7616d88)

- Jupyter Notebook
Published by github-actions[bot] almost 2 years ago

https://github.com/bhklab/readii - v1.7.6

v1.7.6 (2024-08-27)

Fix

• fix: Update ci-cd.yml (13cc197)

- Jupyter Notebook
Published by github-actions[bot] almost 2 years ago

https://github.com/bhklab/readii - v1.7.5

v1.7.5 (2024-08-20)

Unknown

• Merge pull request #34 from bhklab/add_logging

fix(feature_extraction): add try except around actual feature extract… (3e6f211)

• Merge branch 'main' into add_logging (e36ac1b)

- Jupyter Notebook
Published by github-actions[bot] almost 2 years ago

https://github.com/bhklab/readii - v1.7.4

v1.7.4 (2024-08-19)

Fix

• fix: use Optional for pyradiomicsParamFilePath in feature extraction functions for older python versions (a9aa977)

• fix: filter out None values and ensure feature results are properly formatted as lists in radiomicFeatureExtraction function (53c68ff)

Refactor

• refactor: simplify negative control region handling by removing unnecessary elif and raising ValueError in negative_controls.py (17ad253)

• refactor: update logging format for better clarity in log messages, put the function name at the end of message in brackets to make it easier to read (bb8aa14)

• refactor: address some type annotation errors, and add logging (79f342e)

Unknown

• Merge pull request #33 from bhklab/featureextractiontypeannt

fix: type annotations & refactor typing issues (b1ce1ed)

- Jupyter Notebook
Published by github-actions[bot] almost 2 years ago

https://github.com/bhklab/readii - v1.7.3

v1.7.3 (2024-08-19)

Fix

• fix: update CI/CD workflow to specify supported platforms for Docker build, removing unsupported macOS entries (d19bf9b)

- Jupyter Notebook
Published by github-actions[bot] almost 2 years ago

https://github.com/bhklab/readii - v1.7.2

v1.7.2 (2024-08-19)

Fix

• fix: update base image in Dockerfile to python:3.11-slim to fix docker image errors (0e2cd3a)

- Jupyter Notebook
Published by github-actions[bot] almost 2 years ago

https://github.com/bhklab/readii - v1.7.1

v1.7.1 (2024-08-19)

Fix

• fix: using correct pyradiomics in pyproject (980cdda)

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https://github.com/bhklab/readii - v1.7.0

v1.7.0 (2024-08-19)

Chore

• chore(deps): update dependencies (0296dbd)

Feature

• feat(logging): integrate logging for feature extraction and pipeline; replace print statements with logger calls (ed6aed4)

Fix

• fix(logging): enhance metadata file logging output with update flag details and adjust logging level to INFO (3705110)

Refactor

• refactor(metadata): add createImageMetadataFile function with logging for segmentation; improve error handling and directory creation (7e3d07f)

Unknown

• Merge pull request #31 from bhklab/add_logging

feat: Add_logging (1255e97)

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https://github.com/bhklab/readii - v1.6.4

v1.6.4 (2024-08-14)

Fix

• fix(feature_extraction): missed variable name change for non-cropped negative control (8d0d7bd)

Refactor

• refactor(feature_extraction): move cropping to after negative control creation (f6e840b)

Unknown

• Merge pull request #30 from bhklab/development_katy

fix(feature_extraction): missed variable name change for non-cropped … (ffe6e47)

• Merge pull request #29 from bhklab/development_katy

refactor(feature_extraction): move cropping to after negative control… (f8db5b0)

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https://github.com/bhklab/readii - v1.6.3

v1.6.3 (2024-08-08)

Fix

• fix(featureextraction): update negative control component splitting for nonroi options to properly separate the type and region in singleRadiomicFeatureExtraction (3bb250e)

Unknown

• Merge pull request #28 from bhklab/development_katy

fix(feature_extraction): update negative control component splitting … (fc6d13d)

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https://github.com/bhklab/readii - v1.6.2

v1.6.2 (2024-08-07)

Fix

• fix(featureextraction): negative control component split wouldn't work for randomizedsamplednonroi, so added specific fix for it for now until readii input is updated (241b202)

Unknown

• Merge pull request #27 from bhklab/development_katy

fix(feature_extraction): negative control component split wouldn't wo… (55dac25)

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https://github.com/bhklab/readii - v1.6.1

v1.6.1 (2024-08-06)

Performance

• perf(negative_controls): improved efficiency for ROI and Non-ROI negative control generation (00f3ab2)

Refactor

• refactor(feature_extraction): update for new negative control functions, remove unnecessary imports, add print statement when starting feature extraction to differentiate from negative control creation (5669919)

Test

• test(testnegativecontrols): updated test functions to match new negative control generation functions (fa78177)

Unknown

• Merge pull request #26 from bhklab/development_katy

Improved efficiency negative control functions (8d9bcb6)

• notebook(optimizenegativecontrols): code to develop improved negative control functions (d5c396b)

• Coded up improved speed functions for ROI and Non-ROI negative control generation using matrix math (bc825cd)

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https://github.com/bhklab/readii - v1.6.0

v1.6.0 (2024-07-31)

Feature

• feat(metadata.py): add saving out samples with segmentations to getCTWithSegmentation (b575f31)

Fix

• fix(metadata): drop _CT suffix from patient ID column in output of getCTWithSegmentation (5e31b73)

Refactor

• refactor(pipeline.py): use new getCTWithSegmentation function, utilizes imgtools edges output (f1dd879)

• refactor(metdata.py): in matchCTtoSegmentation change outputDir to outputFilePath (4219a1a)

Test

• test(test_metadata): fix outputFilePath argument for matchCTtoSegmentation, add output test for getCTWithSegmentation (a9fec18)

• test(test_metadata): added tests for getCTWithSegmentation (a7d3fc7)

Unknown

• Merge pull request #25 from bhklab/development_katy

New get CT with RTSTRUCTs function (5c31b26)

• getCTWithSegmentation works for RTSTRUCT (6c69b8a)

• getCTWithSegmentation works for RTSTRUCT (bd8d0a0)

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https://github.com/bhklab/readii - v1.5.0

v1.5.0 (2024-07-31)

Feature

• feat(metadata.py): using imgtools edges crawl output to get matched CT to RTSTRUCT list (dce17fc)

Style

• style(metadata): Update error message to say READII instead of YAREA (d6fc791)

Unknown

• Merge pull request #24 from bhklab/development_katy

New CT to RTSTRUCT matching method and start of testing new negative control generation method (c3533a0)

• notebooks: create general notebook for debugging (9df7b73)

• notebooks: working on improving efficiency of negative control generation (bccb4f5)

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https://github.com/bhklab/readii - v1.4.4

v1.4.4 (2024-05-30)

Fix

• fix: update docker image reference (91b3c05)

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https://github.com/bhklab/readii - v1.4.3

v1.4.3 (2024-05-30)

Chore

• chore: update dependencies and workflow for continuous deployment (d400520)

Fix

• fix: force build (45cab79)

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https://github.com/bhklab/readii - v1.4.2

v1.4.2 (2024-05-30)

Fix

• fix: tag version in dockerfile (1b06ed8)

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https://github.com/bhklab/readii - v1.4.1

v1.4.1 (2024-05-30)

Fix

• fix: add auto build docker (e1a58cd)

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https://github.com/bhklab/readii - v1.4.0

v1.4.0 (2024-05-29)

Feature

• feat(pipeline): added random seed command line argument for negative control creation (405fa74)

• feat(feature_extraction): added argument random seed for negative control creation (053d542)

Unknown

• Merge pull request #23 from bhklab/development_katy

Adding negative control to main pipeline and feature extraction functions (0afc838)

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https://github.com/bhklab/readii - v1.3.4

v1.3.4 (2024-05-16)

Fix

• fix: poetry lock (0632d5a)

• fix: pyradiomics original (4ab6aa7)

• fix: pyradiomics original (9513427)

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https://github.com/bhklab/readii - v1.3.3

v1.3.3 (2024-05-16)

Fix

• fix: install poetry (c1a905a)

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https://github.com/bhklab/readii - v1.3.2

v1.3.2 (2024-05-16)

Fix

• fix: update lock (18054bd)

• fix: no docker buils (e0a8e63)

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https://github.com/bhklab/readii - v1.3.1

v1.3.1 (2024-05-16)

Fix

• fix: update readme with docker link

fix: update readme with docker link (4584af7)

• fix: update readme with docker link (2f9a437)

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https://github.com/bhklab/readii - v1.3.0

v1.3.0 (2024-05-16)

Build

• build(poetry.lock): updated package versions (811b748)

Documentation

• docs(negative_controls): add random seed description to shuffleImage function header (df9a7d3)

• docs(example.ipynb): update notebook to use med-imagetools CT DICOM loader (e6339b7)

Feature

• feat(negative_controls): added random seed to all random functions and the apply negative control function (280b465)

• feat(negative_controls): add random seed to shuffleNonROI (a402ee5)

• feat(negative_controls): add random seed to shuffleROI (826b00d)

• feat(negative_controls): added random seed to shuffleImage function, now using numpy RNG and shuffle function (a2556ae)

Fix

• fix(negative_controls): set random generated pixel value to int to work with SetPixel (8d9b071)

• fix(negative_controls): cast result from randNumGen.integers to int for sitk SetPixel function to fix type error (257c498)

• fix(image_processing): correctedROIImage was assigned to unused variabel, changed to segImage (453402e)

• fix(testnegativecontrols): makeRandomImage test was using incorrect function (shuffleImage) (143712a)

Style

• style(feature_extraction): fix typo in randomizeImageFromDistributionSampling import (79dc539)

• style(negative_controls): fix spelling of distribution in randomizeImageFromDistributionSampling (4a01f5c)

Test

• test(negative_controls): added tests for no roiLabel input for ROI and non-ROI negative control functions (c083878)

• test(negative_controls): removed redundant random pixel checks and added some checks for any change in the negative controls, updated some assertion failure messages (4ca434b)

• test(negative_controls): update whole image pixel checks and remove random pixel checks in shuffleNonROI and makeRandomRoi (b970cbe)

• test(negative_controls): update assertion comment in shuffle ROI (0c542f4)

• test(negative_controls): fix the shuffle check that the same values exist in the new image in shuffleROI (6de291d)

• test(negative_controls): in makeRandomImage, added ROI voxel check, removed random pixel check as its covered by the randomSeed checks (17ca738)

• test(negative_controls): Added pixel check for centre of ROI, updated failed assertion message for randomSeed pixel checks (ed3bb17)

• test(negative_controls): updated shuffle pixel check that values are the same as original (52dda33)

• test(negative_controls): added random seed to rest of functions, changed conversion to pixels to include whole image not just region that's been altered (28db728)

• test(negative_controls): added random seed to shuffleROI and randomROI tests, updated negative control image variable to be clearer (e09c142)

• test(negative_controls): add random seed in shuffleROI test (d12ac25)

• test(negative_controls): updated nsclcCropped fixture to use getCroppedImages function (24dafff)

• test(negative_controls): add random seed to make random image (6979ac6)

• test(negative_controls): add random seed to shuffle image test (c07c50e)

Unknown

• Merge pull request #19 from bhklab/addrandomseed

Adding random seed to all negative controls for reproducible results (26d8cbc)

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https://github.com/bhklab/readii - v1.2.1

v1.2.1 (2024-03-27)

Build

• build: Update pytest command to run tests in parallel (e8f67b9)

• build: update poetry lock (6999f20)

• build: Fix formatting in ci-cd.yml and add back unit tests. Rename jobs for better clarity (b4d49d5)

• build: add pytest-xdist for development parallel tests (d52a5a3)

Fix

• fix: no development branch (e3349db)

Refactor

• refactor: format with black, explicit imports, and update type annotations (04bada5)

• refactor: Fixes, updates, formatting

refactor: Fixes, updates, formatting (998f299)

• refactor: format with black (07d04d8)

• refactor: explicit imports from readii.metadata module for performance (f91afa4)

• refactor: Refactor type check in test_radiomicFeatureExtraction (bc0d18d)

• refactor: Refactor saveDataframeCSV and matchCTtoSegmentation functions, add type hints, and improve error handling, format with black (16a83b9)

• refactor: Update version variables in pyproject.toml (5776e5f)

• refactor: explicitly import all, nested import * can lead to performance issues (8054799)

• refactor: update type annotations. (c6ee885)

• refactor: update type annotations to handle optional parameters, format with black for readability, refactor applyNegativeControl function to raise AssertionErrror for optional baseROI, handle edge case and raise error if none of the nc_types. (11f0d92)

Style

• style(feature_extraction.py): changed some function call spacing (09331a3)

Unknown

• Merge pull request #15 from bhklab/dockerfile

Refactor: Add dockerfile, fix some type errors, update type annotations, add some error-handling, formatting (20f8d54)

• fixed wrong docker repo (8ca1a93)

• Merge branch 'dockerfile' of github.com:bhklab/readii into dockerfile (6bb042d)

• Update ci-cd.yml and pyproject.toml (fa35141)

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https://github.com/bhklab/readii - v1.2.0

v1.2.0 (2024-03-15)

Feature

• feat: adding dockerfile and gha to build and deploy (b7d6b73)

Fix

• fix: wrong group in toml (b55baab)

• fix: test builds and update toml to include this branch (af61beb)

• fix: test deployment (aa1dcb4)

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https://github.com/bhklab/readii - v1.1.3

v1.1.3 (2024-03-06)

Build

• build: updating package versions (3f3a593)

Fix

• fix(pipeline): need to exit when catching the no segmentation type error (bd1a93b)

Unknown

• Merge pull request #14 from bhklab/development_katy

Another fix for catching no segmentation type error (6e3e8fc)

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https://github.com/bhklab/readii - v1.1.1

v1.1.1 (2024-02-08)

Build

• build: add pyarrow as dependency for pandas (0050dc1)

• build: updated pyradiomics dependency tp 3.0.1a3 (d780b27)

• build: updated med-imagetools dependency (ed58b9c)

• build: changed pyradiomics dependency to 3.0.1 as 3.1.0 has installation issues (9c89227)

• build: update dependencies versions (8b1af18)

Fix

• fix: update version number (3b90606)

Unknown

• Merge pull request #10 from bhklab/development_katy

fix: update version number (2923f7a)

• fix version number (36e8ff8)

• patch: use pyradiomics 3.0.1a3 (98d5e91)

• Merge pull request #9 from bhklab/development_katy

Development katy (0f1cc66)

• bug(image_processing): force ROI voxel label to int to be compatible with pyradiomics 3.0.1a3 (38e7653)

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https://github.com/bhklab/readii - v1.1.0

v1.1.0 (2024-01-31)

Feature

• feat(image_processing): made cropping CT and segmentation its own function (5202cc2)

• feat(image_processing): add option to display CT and segmentation cropped to ROI (120524c)

Fix

• fix(pipeline): fixed check for existing radiomic features file, had incorrect file name (1819d3d)

• fix(negativecontrols): fixed function call for randomizedsample_full in applyNegativeControl (06a2f9c)

• fix(image_processing): moved crop to top of displayOverlay function to get correct centre slice index and array conversion happens after crop (c1037d9)

Unknown

• Merge pull request #8 from bhklab/development_katy

Added display functions for CT and CT with segmentation overlaid Fixed function call for randomized sample full image Fixed check for existing radiomic features file (ba4a9fe)

• Merge pull request #7 from bhklab/development_mogtaba

Fixed CTtoSegmentation merge issue and fixed negative control settings (7bbf3b7)

• fixed merge between SEGs and CTs, in matchCTtoSegmentation (fc1dda1)

• added new negative controls to --negative_control flag (9aaf76c)

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https://github.com/bhklab/readii - v1.0.0

v1.0.0 (2024-01-26)

Breaking

• build: changed package name from YAREA to READII

BREAKING CHANGE: yarea name no longer used (3bcb4f9)

Documentation

• docs(README): update package headline for READII acronym (1294d44)

Unknown

• Merge pull request #6 from bhklab/name_change

Name change from yarea to readii (2374af4)

• Merge branch 'main' into name_change (480b596)

• Merge pull request #5 from bhklab/development_mogtaba

Created 3 new negative controls by sampling original image and tests (2f95cf7)

• Created 3 new negative controls by sampling original image and added tests for them (ec3dd21)

• merged changes (db63a6c)

• Removed test that doesn't take into account shuffling edge case. (28ab19e)

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https://github.com/bhklab/readii - v0.6.0

v0.6.0 (2024-01-19)

Feature

• feat(pipeline): change parallel input argument to be false by default (3f8c46a)

Unknown

• Merge pull request #4 from bhklab/development_katy

feat(pipeline): change parallel input argument to be false by default (8d0626d)

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https://github.com/bhklab/readii -

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https://github.com/bhklab/readii - v0.4.0

v0.4.0 (2024-01-17)

Build

• build: add publish to PyPI back in (e7f182e)

Documentation

• docs: add installation and usage details to README (4281620)

Feature

• feat: added command line example runs to notebook (48d8d40)

Unknown

• add tests/output/ to gitignore to not commit output files (fa713ff)

• Merge branch 'main' of github.com:bhklab/yarea into main (1327e22)

• Add ci pass requirement back in (b678d4a)

• Fixed error with the path for CT and SEG files in the tests for negative controls (5ea6e2c)

• Fixed feature_extraction error where padSegToMatchCT function was being called incorrectly (82ad022)

• Merge pull request #1 from bhklab/negativecontroltests

Created testing suite for negative controls and fixed errors in imageprocessing.py and negativecontrols.py (f0fdd02)

• merged conflicts (d78fb5f)

• Finished testing suite for the negative controls (6d81739)

• Merge branch 'main' of github.com:bhklab/yarea into main (cee3c0f)

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https://github.com/bhklab/readii - v0.3.0

v0.3.0 (2023-12-21)

Build

• build: updated semantic release variables (5e24044)

• build: updated semantic release and added package build steps (5a51e07)

• build: remove publish to PyPI (f276b76)

Documentation

• docs(pipeline): fixed typo in data directory help message (7a19b5a)

Feature

• feat: add ability to run pipeline using poetry run (ced5e67)

• feat(gitignore): ignore vscode directory with configurations (7e30be2)

• feat(pipeline): main pipeline function to run radiomic feature extraction (929573d)

• feat(metadata): added check for csv type on imgFileListPath argument (ac09625)

• feat(metadata): made function to find the segmentation type from the list of image files (8dd4ddf)

Fix

• fix(testfeatureextraction): fixed expected output path for radiomicFeatureExtraction (53c9db3)

• fix(image_processing): fixed usage of ctDirPath variable in padSegToMatchCT (892c8d7)

• fix: move size mismatch handling back to radiomicFeatureExtraction because image file paths are available in that function (ccbe852)

• fix(feature_extraction): moved error handling into singleRadiomicFeatureExtraction and added catch for wrong pyradiomics parameter file (41a3901)

• fix: change radiomic features file output name (ea0b963)

• fix(feature_extraction): add check for None in pyradiomics parameter file spot, use default if that's the case (5340f57)

• fix(yarea): renamed this file because it had import issues being named the same as the package (833c5b4)

Style

• style(feature_extraction): changed ctFolderPath to ctDirPath for consistency (b7b452e)

Test

• test(test_metadata): testing for getSegmentationType function (57768cf)

Unknown

• remove files from tutorial (5afac9a)

• updated version (3a063cf)

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https://github.com/bhklab/readii - Version 0.2.0

See the CHANGELOG for details.

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https://github.com/bhklab/readii - Version 0.1.0

First release of area!

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