- New Features - Added an optional
overwriteparameter to correlation plotting functions - Enhanced control over file saving behavior when generating correlation plots - Users can now choose whether to replace existing plot files
Makes it easier to catch times when file exists without resolving the path twice
-
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.
add self and cross correlation plot functions
## 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.
-
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.
Didn't test updating from os to pathlib enough, but should be good now. Added basic test, needs to be expanded upon.
## 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.
-
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.
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.
## Summary by CodeRabbit-
New Features - Introduced a
CorrelationWriterclass 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
CorrelationWriterclass, covering various scenarios for saving correlation data.
Co-authored-by: Jermiah Joseph [email protected]
Updated include list to have the io/readers functions and updated the files so all ruff tests pass.
## Summary by CodeRabbit-
New Features - Enhanced flexibility in loading feature files by accepting both
Pathobjects 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.
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, andpandas. - 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 includeosx-64andwin-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.
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
-
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.
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.
## Summary by CodeRabbit-
New Features - Introduced an optional
segmentationLabelparameter 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
segmentationLabelparameter and to validate error handling for invalid inputs.
-
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.
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.
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
BaseWriterfor writing text and CSV files. - Introduced theNIFTIWriterclass for managing NIFTI file writing with validation and error handling. - Added newCSVWriterclass for saving data in CSV format.
closes bhklab/analyze_readii_outputs#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.
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
## 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.
negative_control_strategy(image, mask=mask, region=region_strategy)2. runs the__call__on thenegative_control_strategy3. which runs the__call__ofregion(image_array, mask_array)- the result of which is used to figure out what indices of the original image to apply the
transformmethod of theNegativeControlStrategyconcrete classes to 5. only replace the region indicesimage_array[mask_indices] = transformed_values
Resource on Strategy Pattern: https://refactoring.guru/design-patterns/strategy/python/example
Co-authored-by: Katy Scott [email protected]
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, andfeatureExtraction. -
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.
- 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
- Replace get_logger with imgtools inherited logging instance across modules
(
01bd13f)
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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
- Remove hatch config and streamline build settings in pyproject.toml for better package management
and deployment
(
0cf184c)
- Update CI/CD workflow for PyPI publishing; enhance publish step, remove TestPyPI, and configure
pixi.lock sha256
(
743ea52)
-
Correct version location in pyproject.toml configuration (
bdb49ea) -
Improve modality handling in loadSegmentation by reinforcing RTSTRUCT validation and simplifying modality checks (
5d1fef6) -
Update CI/CD workflow to trigger only on pushes to main branch (
2cc686f) -
Update ruff configuration and linting rules, switch docstring style to numpy, and enhance loader type annotations (
0142860)
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Add Codecov badge to README for improved visibility of test coverage (
9472ab6) -
Add Codecov step in CI/CD workflow to track coverage and report using coverage.xml (
fcbe561) -
Add Ruff linter to CI-CD workflow and update project config for linting and formatting tasks (
ecebe9a) -
Adjust CI-CD workflow to trigger on any branch for pull requests and comment out previous push configuration (
3c77975) -
Refine CI-CD workflow for Publish-To-PyPi and update pixi.lock SHA for dependency consistency (
3c904e1)
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Clean up .github/workflows/ci-cd.yml by removing unnecessary whitespace and ensuring proper formatting at end of file (
a6298ab) -
Update CI-CD workflow to include Ruff as a dependency for the Unit-Tests job before deployment to PyPI (
5d6a7f3)
- Update README with installation + badges
(
7bdf5d3)
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Enhance segmentation loading by adding validation for unsupported modalities in loadSegmentation function (
9ee6931) -
Expand pyproject.toml with publish-test command for deploying to test PyPI and add description for build task (
f309346) -
Rename job to Publish-To-Test-PyPi and add Test-TestPypi-Installation steps for verifying package deployment (
336185f) -
Update CI-CD workflow to include publishing to TestPyPI with new environment variables for authentication (
d645af1)
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Refactor CI/CD workflow with enhanced job structure and add basic config files for coverage and linting (
994fd75) -
Update CI/CD workflow to use actions/checkout@v3, fix semantic-release task, and update pixi.lock (
790ae04)
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Add semantic-release workflow for automated versioning and update readii version to 1.11.0 with new author email (
92bc4d4) -
Update to use pixi and pyradiomics-bhklab (
6a67be4)
- feature_extraction: Actually raise an exception for negative control creation
(
e1a9888)
- feature_extraction: Add logging for error raised when cropping CT and segmentation
(
d9d8069)
- feature_extraction: Actually raise the error for the negative control creation Exception
(
f17fbbc)
- feature_extraction: Add try catch around cropping image step
(
fedf881)
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Add angular commit syntax to README (
c9f76df) -
Clean up angular commit formatting in README (
1f16ad1)
- feature_extraction: Add catch and logging around negative control creation
(
a90efac)
- Make output directory and parents as needed before saving radiomic output
(
bf7600c)
- Change output file from feature extraction without negative control to be
radiomicfeatures_original_datasetname.csv
(
7663ce8)
- test_feature_extraction: Updated for new original image feature extraction output
(
2e53bc8)
- Remove coloredlogs dependency and logging configuration from the project
(
ba8208f)
- Update lockfile
(
9c5fa18)
- Update ci-cd.yml
(
13cc197)
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Filter out None values and ensure feature results are properly formatted as lists in radiomicFeatureExtraction function (
53c68ff) -
Use Optional for pyradiomicsParamFilePath in feature extraction functions for older python versions (
a9aa977)
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Address some type annotation errors, and add logging (
79f342e) -
Simplify negative control region handling by removing unnecessary elif and raising ValueError in negative_controls.py (
17ad253) -
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)
- Update CI/CD workflow to specify supported platforms for Docker build, removing unsupported macOS
entries
(
d19bf9b)
- Update base image in Dockerfile to python:3.11-slim to fix docker image errors
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0e2cd3a)
- Using correct pyradiomics in pyproject
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980cdda)
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feature_extraction: Add try except around actual feature extraction call, add logging to end of feature extraction and file saving (
ba119ad) -
logging: Enhance metadata file logging output with update flag details and adjust logging level to INFO (
3705110)
- deps: Update dependencies
(
0296dbd)
- logging: Integrate logging for feature extraction and pipeline; replace print statements with
logger calls
(
ed6aed4)
- metadata: Add createImageMetadataFile function with logging for segmentation; improve error
handling and directory creation
(
7e3d07f)
- feature_extraction: Missed variable name change for non-cropped negative control
(
8d0d7bd)
- feature_extraction: Move cropping to after negative control creation
(
f6e840b)
- feature_extraction: Update negative control component splitting for non_roi options to
properly separate the type and region in singleRadiomicFeatureExtraction
(
3bb250e)
- feature_extraction: Negative control component split wouldn't work for
randomized_sampled_non_roi, so added specific fix for it for now until readii input is updated
(
241b202)
- negative_controls: Improved efficiency for ROI and Non-ROI negative control generation
(
00f3ab2)
- 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_negative_controls: Updated test functions to match new negative control generation
functions
(
fa78177)
- metadata: Drop _CT suffix from patient ID column in output of getCTWithSegmentation
(
5e31b73)
- metadata.py: Add saving out samples with segmentations to getCTWithSegmentation
(
b575f31)
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metdata.py: In matchCTtoSegmentation change outputDir to outputFilePath (
4219a1a) -
pipeline.py: Use new getCTWithSegmentation function, utilizes imgtools edges output (
f1dd879)
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test_metadata: Added tests for getCTWithSegmentation (
a7d3fc7) -
test_metadata: Fix outputFilePath argument for matchCTtoSegmentation, add output test for getCTWithSegmentation (
a9fec18)
- metadata: Update error message to say READII instead of YAREA
(
d6fc791)
- metadata.py: Using imgtools edges crawl output to get matched CT to RTSTRUCT list
(
dce17fc)
- Update docker image reference
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91b3c05)
- Force build
(
45cab79)
- Update dependencies and workflow for continuous deployment
(
d400520)
- Tag version in dockerfile
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1b06ed8)
- Add auto build docker
(
e1a58cd)
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feature_extraction: Added argument random seed for negative control creation (
053d542) -
pipeline: Added random seed command line argument for negative control creation (
405fa74)
- Install poetry
(
c1a905a)
- Update readme with docker link
(
4584af7)
fix: update readme with docker link
- Update readme with docker link
(
2f9a437)
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image_processing: Correctedroiimage was assigned to unused variabel, changed to segImage (
453402e) -
negative_controls: Cast result from randNumGen.integers to int for sitk SetPixel function to fix type error (
257c498) -
negative_controls: Set random generated pixel value to int to work with SetPixel (
8d9b071) -
test_negative_controls: Makerandomimage test was using incorrect function (shuffleImage) (
143712a)
- poetry.lock: Updated package versions
(
811b748)
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feature_extraction: Fix typo in randomizeImageFromDistributionSampling import (
79dc539) -
negative_controls: Fix spelling of distribution in randomizeImageFromDistributionSampling (
4a01f5c)
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example.ipynb: Update notebook to use med-imagetools CT DICOM loader (
e6339b7) -
negative_controls: Add random seed description to shuffleImage function header (
df9a7d3)
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negative_controls: Add random seed to shuffleNonROI (
a402ee5) -
negative_controls: Add random seed to shuffleROI (
826b00d) -
negative_controls: Added random seed to all random functions and the apply negative control function (
280b465) -
negative_controls: Added random seed to shuffleImage function, now using numpy RNG and shuffle function (
a2556ae)
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negative_controls: Add random seed in shuffleROI test (
d12ac25) -
negative_controls: Add random seed to make random image (
6979ac6) -
negative_controls: Add random seed to shuffle image test (
c07c50e) -
negative_controls: Added pixel check for centre of ROI, updated failed assertion message for randomSeed pixel checks (
ed3bb17) -
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) -
negative_controls: Added random seed to shuffleROI and randomROI tests, updated negative control image variable to be clearer (
e09c142) -
negative_controls: Added tests for no roiLabel input for ROI and non-ROI negative control functions (
c083878) -
negative_controls: Fix the shuffle check that the same values exist in the new image in shuffleROI (
6de291d) -
negative_controls: In makeRandomImage, added ROI voxel check, removed random pixel check as its covered by the randomSeed checks (
17ca738) -
negative_controls: Removed redundant random pixel checks and added some checks for any change in the negative controls, updated some assertion failure messages (
4ca434b) -
negative_controls: Update assertion comment in shuffle ROI (
0c542f4) -
negative_controls: Update whole image pixel checks and remove random pixel checks in shuffleNonROI and makeRandomRoi (
b970cbe) -
negative_controls: Updated nsclcCropped fixture to use getCroppedImages function (
24dafff) -
negative_controls: Updated shuffle pixel check that values are the same as original (
52dda33)
- No development branch
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e3349db)
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Add pytest-xdist for development parallel tests (
d52a5a3) -
Fix formatting in ci-cd.yml and add back unit tests. Rename jobs for better clarity (
b4d49d5) -
Update poetry lock (
6999f20) -
Update pytest command to run tests in parallel (
e8f67b9)
- feature_extraction.py: Changed some function call spacing
(
09331a3)
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Explicit imports from readii.metadata module for performance (
f91afa4) -
Explicitly import all, nested import * can lead to performance issues (
8054799) -
Fixes, updates, formatting (
998f299)
refactor: Fixes, updates, formatting
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Format with black (
07d04d8) -
Format with black, explicit imports, and update type annotations (
04bada5) -
Refactor saveDataframeCSV and matchCTtoSegmentation functions, add type hints, and improve error handling, format with black (
16a83b9) -
Refactor type check in test_radiomicFeatureExtraction (
bc0d18d) -
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) -
Update type annotations. (
c6ee885) -
Update version variables in pyproject.toml (
5776e5f)
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Test builds and update toml to include this branch (
af61beb) -
Test deployment (
aa1dcb4) -
Wrong group in toml (
b55baab)
- Adding dockerfile and gha to build and deploy
(
b7d6b73)
- pipeline: Need to exit when catching the no segmentation type error
(
bd1a93b)
- Updating package versions
(
3f3a593)
- Update README with randomized sampled negative controls, add description of negative controls
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eaff95d)
- Update version number
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3b90606)
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Add pyarrow as dependency for pandas (
0050dc1) -
Changed pyradiomics dependency to 3.0.1 as 3.1.0 has installation issues (
9c89227) -
Update dependencies versions (
8b1af18) -
Updated med-imagetools dependency (
ed58b9c) -
Updated pyradiomics dependency tp 3.0.1a3 (
d780b27)
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image_processing: Moved crop to top of displayOverlay function to get correct centre slice index and array conversion happens after crop (
c1037d9) -
negative_controls: Fixed function call for randomized_sample_full in applyNegativeControl (
06a2f9c) -
pipeline: Fixed check for existing radiomic features file, had incorrect file name (
1819d3d)
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image_processing: Add option to display CT and segmentation cropped to ROI (
120524c) -
image_processing: Made cropping CT and segmentation its own function (
5202cc2)
- Changed package name from YAREA to READII
(
3bcb4f9)
BREAKING CHANGE: yarea name no longer used
- README: Update package headline for READII acronym
(
1294d44)
- pipeline: Change parallel input argument to be false by default
(
3f8c46a)
- Yarea name no longer used
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image_processing: Fixed image vs. imgArray variable mixup in displayImageSlice (
c9ea3d6) -
image_processing: Fixed remaining instances of imgArray variable (
84de500)
- Updated dependency versions
(
44de606)
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Require python 3.9 in conda env setup (
480b199) -
image_processing: Wrote docstring for displayCTSegOverlay (
2f69dab) -
pipeline: Indicate whether flags are true or false by default in help message of parallel and update (
311dd5e)
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image_processing: Add function to display CT slice with segmentation overlaid (
73342ef) -
image_processing: Add function to find center slice and coordinates of ROI in image (
78d69b2)
- test_image_processing: Added test for getROICenterCoords
(
8745fe7)
- Add installation and usage details to README
(
4281620)
- Added command line example runs to notebook
(
48d8d40)
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Change radiomic features file output name (
ea0b963) -
Move size mismatch handling back to radiomicFeatureExtraction because image file paths are available in that function (
ccbe852) -
feature_extraction: Add check for None in pyradiomics parameter file spot, use default if that's the case (
5340f57) -
feature_extraction: Moved error handling into singleRadiomicFeatureExtraction and added catch for wrong pyradiomics parameter file (
41a3901) -
image_processing: Fixed usage of ctDirPath variable in padSegToMatchCT (
892c8d7) -
test_feature_extraction: Fixed expected output path for radiomicFeatureExtraction (
53c9db3) -
yarea: Renamed this file because it had import issues being named the same as the package (
833c5b4)
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Add publish to PyPI back in (
e7f182e) -
Remove publish to PyPI (
f276b76) -
Updated semantic release and added package build steps (
5a51e07) -
Updated semantic release variables (
5e24044)
- feature_extraction: Changed ctFolderPath to ctDirPath for consistency
(
b7b452e)
- pipeline: Fixed typo in data directory help message
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7a19b5a)
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Add ability to run pipeline using poetry run (
ced5e67) -
gitignore: Ignore vscode directory with configurations (
7e30be2) -
metadata: Added check for csv type on imgFileListPath argument (
ac09625) -
metadata: Made function to find the segmentation type from the list of image files (
8dd4ddf) -
pipeline: Main pipeline function to run radiomic feature extraction (
929573d)
- test_metadata: Testing for getSegmentationType function
(
57768cf)
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Fixed default Pyradiomics parameter file path (
84f16db) -
Fixed inconsistencies and mistakes in variable names (
7dd0d30) -
Fixed pyradiomics parameter file path and moved print statement of which ROI is processed back to radiomicFeatureExtraction (
427eff7) -
Forgot to import pytest (
6e978ca) -
Incorrect indent in saveDataframeCSV (
dd6d2f5) -
Missing pytest import and passing flattened SEG to alignImages (
bab47e4) -
Need to see test outputs for actions (
6e95d0e) -
Rtstruct loader had incorrect variable for baseImageDirPath (
6cfb08c) -
Updated image file paths (
588ba46) -
Was missing pytest import (
b38e7a4)
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Add med-imagetools as a dependency (
84aef0f) -
Add PSR as dev dependency (
17cb2da) -
Add pyradiomics dependency (
cb11289)
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Add function to match CTs and segmentations in medimagetools output and function to save out dataframe as csv (
2f169e9) -
Add negative control generator functions (
da6d9c0) -
Add seg label finder function (
d575dee) -
Added check for input not being a dataframe for saveDataframeCSV (
69a0d84) -
Added example pyradiomics config (
2dee2eb) -
Changed input variable to outputDirPath to have consistent output file name (
a0b3336) -
Changed outputFilePath to outputDirPath so output files can be standardized (
d3ad8e8) -
Check that output file is a csv before starting any feature extraction (
d2390f5) -
Function for extraction of radiomic features from a single CT and segmentation pair (
ecb5d5b) -
Function to run radiomic feature extraction, including negative control and parallel options (
aeb6efd) -
Ignore unit test output files (
a3fd21e)
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Add getROIVoxelLabel test (
2571cea) -
Add load segmentation module tests (
6137f61) -
Added image path fixtures and error check test (
2b69fa1) -
Added image_processing unit tests (
587eb2a) -
Added incorrect object passed to saveDataframeCSV and fixed outputFilePath error test function call (
281637b) -
Added test for full radiomicFeatureExtraction function (
ade890c) -
Added tests for matchCTtoSegmentation function (
c66d24c) -
Check output from radiomicFeatureExtraction (
c525247) -
Functions for singleRadiomicFeatureExtraction (
37ec5d6) -
Started writing tests for radiomic feature extraction functions (
cd31b86) -
Test csv error in saveDataframeCSV (
3a9929a) -
Test output saving for matchCTtoSegmentation (
995726d) -
Updated test for radiomicFeatureExtraction to use default pyradiomics parameter file (
617abbc)
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Add loading and image processing dependencies (
96fd62f) -
Add pytest and pytest-cov as dev dependencies (
152b825) -
Added dev dependencies for docs (
0e87a13) -
Remove upper bound on dependency versions (
62ba9f8)
- Add unit test for loadDicomSITK
(
bef39f7)