v0.28.0dev#415
Draft
CPBridge wants to merge 18 commits into
Draft
Conversation
Add import_optional_dependency util function
* Remove packaging version specifier * Update packaging dependency version in pyproject.toml --------- Co-authored-by: Mason C. Cleveland <104479423+mccle@users.noreply.github.com>
* Add import_optional_dependency util function * Update optional import function. * Reformat code * Add module version compatibility check. * Move version incompatibility error raise location and update error message * Update src/highdicom/utils.py Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com> * Update src/highdicom/utils.py Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com> * Update src/highdicom/utils.py Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com> * Update src/highdicom/utils.py Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com> * Update src/highdicom/utils.py Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com> * Move to new utils file * Add packaging to requirements * add itk and sitk conversions * Add frame_of_reference_uid and coordinate_system arguments; update docstrings; reformat strings * remove channel argument * add noqa to work with flake8 * update type hints, minor tweaks to bool retyping * sync changes * flake8 * Add tests for sitk * flake8 * skip sitk test on failed import * fix url syntax * Fix itk conversion and add tests * Update .github/workflows/run_unit_tests.yml Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com> * Replace common url elements * Update docstrings and error messages * Update volume docs file * Update dtype tests with array equality and random values * Apply suggestion from @CPBridge Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com> * Reorganize and update docs files * Update docstrings * Fix multichannel check and add tests --------- Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com>
Co-authored-by: Chris Bridge <chrisbridge44@gmail.com>
* Add family and manufacturer to Algorithm Identification template * Linter fix --------- Co-authored-by: Chris Bridge <chrisbridge44@gmail.com>
Co-authored-by: Chris Bridge <chrisbridge44@gmail.com>
* Enforce volume datatypes must be a subtype of float, integer, or bool * Update docstrings to indicate optional dependency versions * Remove version numbers from docstrings * Update src/highdicom/volume.py Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com> * Separate dtype tests * fix variable name bug * Fix error string regex errors --------- Co-authored-by: Chris Bridge <chrisbridge44@googlemail.com>
… state IODs (#417) * Remove the content date and content time attributes from presentation state IODs * Linting
* newly designed multi-frame conversion based on pixelmed * mend * Flake8 verified code * Verified by mypy and flake8. Added stack module adder * mend * mend * mend * mend * Added frameset collection class * mend * mend * Debugged for exception on string conversion to DA, DT, TM * mend * mend * Fixed issues related to Marcus minor comments * mend * mend * mend * added logger for conversion * mend * Modified the way frameanatomysequence was added * mend * mend * mend * mend * Image/Frame-Type bug was fixed * changed the class structures for sop * modified the code to apply all major comments * mend * mend * Added tests to dicom legacy converter * mend * Modified code based on Markus's comments * Modified code based on Markus's comments * finished applying Markus's comments * Finished applying Markus/Andrey's commnets * modified commnets for 3rd round * Applied Chris's comments * Swapped voctors in normal calculation * Corrected how the normal vector was calculated * Moved FrameSet, FrameSetCollection and _DicomHelper classes into highdicom.utils * mend * made both FrameSet and FrameSetCollection classes private * applied Chris's comments for the 2nd round * Further tidy up * Flake8 fixes * Refactor modality-specific components to modality-specific subclasses * Minor refactor * refactor all lines ending in backslash * wip * Rename methods for clarity * Rebase on Image class, implement pixel data transcoding * Major refactor of legacy conversion * Improvements using validator * Implement BodyPartExamined -> AnatomicRegionSequence mapping * Fix standard JSON file packaging * Refactor handling of Enhanced X Image modules * Skip optional modules if not all attributes have values * Refactor to remove configs * Correct handling of private attributes * Improve functional group inclusion logic * Factor out common docstring * Improve error messages * Minor docstring improvements * Add logic to determine when to include frame anatomy information * Add min/max pixel values * Remove unused import * Refactor copy pixels method * Add checks on functional groups * Further tests and refactor to rmove test classes * Lint fixes * Further tests * Add missing keywork marks * Fix for aggregating ImageType, with test * Further tests and fix for inconsistent type 2 attribute * Linting * Set photometric interpretation based on transfer syntax * Add common instance reference module * Add tests for color transcoding * Add tests for from_datasets * Consolidate legacy classes, improve from_dataset * Add read functions * Fix specific character set * Add check for regularly volume * Add default series description * Improve handling of lossy image compression attributes * Move all standard data from python to JSON files * Adjust _module_utils imports * Remove outdated flake8 exclusion * Small bug fixes * Further exclusions * Further minor fixes * Add docs and quickstart page * Minor docs typo * Fix for re-encapsulating compressed pixel data * Add tests for decompressing to native transfer syntax * mypy fixes for legacy module * Remove sort_key parameter in favour of boolean sort option * Docstring improvements * Improvements to legacy doc page * remove print statement * Further exceptions * Add robustness to empty dates and times * Fix empty frame laterality * Fix timezone related errors * Work around ambiguous VR issues in source files * Add conversion of big endian to little endian * Add option to skip private attributes * Add strict parameter * Various bug fixes * Fix photometric interpretation * Add anatomical structure pairing info * Handle unrecognized body part examined * Issue warning for missing frame laterality * Move arguments to keyword only * Implement monochrome 1 conversion * Handle missing ImageType * Fix _AttributeConfig docstrings * Add dimension indexing * Update docs on legacy sorting * Fixes to legacy docs * Add note about future rearrangement of attributes * Add single lceread function * minor doc typos * Further docstring improvements * Fix limitation on different modality rescales per instance * Fix for largest/smallest pixel value * Fix for incosistent presence of reference image sequence * Fix spatial sorting * Add IDC examples to doc page --------- Co-authored-by: Afshin <akbarzadehm@gmail.com> Co-authored-by: Afshin Zade <42010605+afshinmessiah@users.noreply.github.com> Co-authored-by: Chris Bridge <chrisbridge44@gmail.com>
* Basic rebase * WIP rebasing PM * Refactor segmentation on common method * Rebase parametric map for creation * Support floating point pixel data in pixel transforms * Improve support for tiled full parametric maps * Switch to using BitsStored as a marker of float pixel data * Implementation of create_parametic_map_pyramid function * Fixes for ParametricMap docstrings * Add check for real world value map value range type * Index real world value map parameters * tests for pm from volume * Add more pm tests * Checks on volume LUTLabels * Consolidate multiframe image init methods * Refactor Image Pixel and General Image modules into _init_multiframe * Move pixel value transforms to general image init * Refactor dimension index sequence * Remove quantity code from index * Generalize dimension index sequence * Add tests for focal planes * Add series time and date to pyramids * Fix total pixel matrix size for irregular tiles * Use relative tolerance to compare pixel spacing * General tidy up * Remove test on volume reconstruction * Initial work on parametric map user guide * Make DimensionIndexSequence private * Add compression tests and docs section * Expand parametric maps docs * Further parametric maps docs * Docs tweaks * Change parametric map derivation code * Complete _init_multiframe docstring * linter * Misc tweaks from review * Add release note about deprecation of window center/width in pmap --------- Co-authored-by: Chris Bridge <chrisbridge44@gmail.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Version 0.28.0 release