Preparation for 0.23.0 release #305
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* Add transformer constructors * Add PixelToPixelTransformer and ImageToImageTransformer * Add round_output option to ReferenceToPixelTransformer * Add drop_slice_coord and drop_slice_index to ReferenceToImageTransformer and ReferenceToImageTransformer, respectively * Move various functions from highdicom.utils to highdicom.spatial in order to avoid circular dependencies
* remove unnecessary resize in create_segmentation_pyramid * remove unnecessary resize in create_segmentation_pyramid * Fix in _add_slide_metadata * Some efficiency improvements for TILED_FULL * Encode incrementally with native encoding * Add check on length of plane_positions in case of tile_pixel_array * remove unnecessary checks on geometry, remove need for plane_positions * Remove dictionary tag lookups in _get_pffg_item * WIP faster method to calculate tile positions * Remove plane positions where not necessary * Avoid unnecessary calculation of source plane positions * Linter fixes
* Allow fractional and multisegment pyramids; add tests * Update docstring * Fix for labelmap style masks * Lint fix
* Import related fixes; remove fix_meta_info, now unnecessary * Drop support for python<3.10 * Fixes to codes and RLE encoding * Remove fix for resolved pydicom bug in decode_frame * Fix frame encoding and decoding, add further transfer syntaxes * Various fixes * Enforce repo-review rules (#296) * Enforce repo-review rule PP302 PP302: Sets a minimum pytest to at least 6 Must have a `minversion=`, and must be at least 6 (first version to support `pyproject.toml` configuration). * Enforce repo-review rule PP305 PP305: Specifies xfail_strict `xfail_strict` should be set. You can manually specify if a check should be strict when setting each xfail. * Enforce repo-review rule PP306 PP306: Specifies strict config `--strict-config` should be in `addopts = [...]`. This forces an error if a config setting is misspelled. * Enforce repo-review rule PP307 PP307: Specifies strict markers `--strict-markers` should be in `addopts = [...]`. This forces all markers to be specified in config, avoiding misspellings. * Enforce repo-review rule PP308 PP308: Specifies useful pytest summary An explicit summary flag like `-ra` should be in `addopts = [...]` (print summary of all fails/errors). * Enforce pytest ≥ 7.3.2 This is the first version to support Python 3.12: https://docs.pytest.org/en/stable/changelog.html#pytest-7-3-2-2023-06-10 * Enforce repo-review rule MY104 MY104: MyPy enables ignore-without-code Must have `"ignore-without-code"` in `enable_error_code = [...]`. This will force all skips in your project to include the error code, which makes them more readable, and avoids skipping something unintended. * Enforce repo-review rule MY105 MY105: MyPy enables redundant-expr Must have `"redundant-expr"` in `enable_error_code = [...]`. This helps catch useless lines of code, like checking the same condition twice. * Enforce repo-review rule MY106 MY106: MyPy enables truthy-bool Must have `"truthy-bool"` in `enable_error_code = []`. This catches mistakes in using a value as truthy if it cannot be falsy. * Remove pillow-jpls dependency as functionality now comes from pylibjpeg * Add details of single bit JPEG2000 to the docs * Better workaround for floating point pixel decoding * Adjust dependencies * Deprecate row_stack for vstack * Bump pydicom version to 3.0.1 * Error message typo --------- Co-authored-by: Dimitri Papadopoulos Orfanos <[email protected]>
* Enforce repo-review rules (#296) * Enforce repo-review rule PP302 PP302: Sets a minimum pytest to at least 6 Must have a `minversion=`, and must be at least 6 (first version to support `pyproject.toml` configuration). * Enforce repo-review rule PP305 PP305: Specifies xfail_strict `xfail_strict` should be set. You can manually specify if a check should be strict when setting each xfail. * Enforce repo-review rule PP306 PP306: Specifies strict config `--strict-config` should be in `addopts = [...]`. This forces an error if a config setting is misspelled. * Enforce repo-review rule PP307 PP307: Specifies strict markers `--strict-markers` should be in `addopts = [...]`. This forces all markers to be specified in config, avoiding misspellings. * Enforce repo-review rule PP308 PP308: Specifies useful pytest summary An explicit summary flag like `-ra` should be in `addopts = [...]` (print summary of all fails/errors). * Enforce pytest ≥ 7.3.2 This is the first version to support Python 3.12: https://docs.pytest.org/en/stable/changelog.html#pytest-7-3-2-2023-06-10 * Enforce repo-review rule MY104 MY104: MyPy enables ignore-without-code Must have `"ignore-without-code"` in `enable_error_code = [...]`. This will force all skips in your project to include the error code, which makes them more readable, and avoids skipping something unintended. * Enforce repo-review rule MY105 MY105: MyPy enables redundant-expr Must have `"redundant-expr"` in `enable_error_code = [...]`. This helps catch useless lines of code, like checking the same condition twice. * Enforce repo-review rule MY106 MY106: MyPy enables truthy-bool Must have `"truthy-bool"` in `enable_error_code = []`. This catches mistakes in using a value as truthy if it cannot be falsy. * Add get_evidence and get_evidence_series methods for _SR * Fix to docstrings --------- Co-authored-by: Dimitri Papadopoulos Orfanos <[email protected]>
* Add SubjectContextSpecimen.from_image() method * Import related fixes; remove fix_meta_info, now unnecessary * Drop support for python<3.10 * Fixes to codes and RLE encoding * Remove fix for resolved pydicom bug in decode_frame * Fix frame encoding and decoding, add further transfer syntaxes * Various fixes * Enforce repo-review rules (#296) * Enforce repo-review rule PP302 PP302: Sets a minimum pytest to at least 6 Must have a `minversion=`, and must be at least 6 (first version to support `pyproject.toml` configuration). * Enforce repo-review rule PP305 PP305: Specifies xfail_strict `xfail_strict` should be set. You can manually specify if a check should be strict when setting each xfail. * Enforce repo-review rule PP306 PP306: Specifies strict config `--strict-config` should be in `addopts = [...]`. This forces an error if a config setting is misspelled. * Enforce repo-review rule PP307 PP307: Specifies strict markers `--strict-markers` should be in `addopts = [...]`. This forces all markers to be specified in config, avoiding misspellings. * Enforce repo-review rule PP308 PP308: Specifies useful pytest summary An explicit summary flag like `-ra` should be in `addopts = [...]` (print summary of all fails/errors). * Enforce pytest ≥ 7.3.2 This is the first version to support Python 3.12: https://docs.pytest.org/en/stable/changelog.html#pytest-7-3-2-2023-06-10 * Enforce repo-review rule MY104 MY104: MyPy enables ignore-without-code Must have `"ignore-without-code"` in `enable_error_code = [...]`. This will force all skips in your project to include the error code, which makes them more readable, and avoids skipping something unintended. * Enforce repo-review rule MY105 MY105: MyPy enables redundant-expr Must have `"redundant-expr"` in `enable_error_code = [...]`. This helps catch useless lines of code, like checking the same condition twice. * Enforce repo-review rule MY106 MY106: MyPy enables truthy-bool Must have `"truthy-bool"` in `enable_error_code = []`. This catches mistakes in using a value as truthy if it cannot be falsy. * Remove pillow-jpls dependency as functionality now comes from pylibjpeg * Add details of single bit JPEG2000 to the docs * Better workaround for floating point pixel decoding * Adjust dependencies * Deprecate row_stack for vstack * Bump pydicom version to 3.0.1 * Error message typo * Add SubjectContext.for_image() method --------- Co-authored-by: Dimitri Papadopoulos Orfanos <[email protected]>
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Dependencies
numpy.float_to allow working with numpy>2Tooling/Repo
:afternoqa#289 Enforce ruff rules (RUF) #290 Enforce ruff/flynt rules (FLY) #291 Enforce ruff/flake8-pyi rules (PYI) #292pyproject.tomlmetadata. setup.py → pyproject.toml #293Features
further_source_imagesoption to the segmentation constructor Add further_source_images option to segmentation #304Fixes
Docs