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* add test data from ngff * remove config * readme test data * correct naming * add note readme test data rfc5 * rename * add initial models * add model validator * parse Identity Co-authored-by: m.lucalmer@gmail.com * parse Identity Co-authored-by: m.lucalmer@gmail.com * move coordinate systems Co-authored-by: m.lucalmer@gmail.com * check input output in cs names * improve coordinate system validation; add more examples from ngff * wip towards a first full example with the new specs * added code skeleton * add rfc5 image test * add tests (skipped) for example data * wip add tests placeholder for zarr * add skipped tests for all data files; test_image() now creates a Zarr group * add new user stories examples * fix precommit * remove SpatialMapper * add pyperclip test dependency * allow test run on windows os * wip test ensure_scale_translation * avoid pytest not recognizing pydantic core ValidationError * fix validation tests, removed pyperclip, restored old pytest.raises * finished multiscale validators * using submodule for new data from John * remove old data form repo; add sparse checkout submodule * fix submodule * fixed paths * new sparse checkout instructions * updated git sparse checkout instructions * added link to rfc5 data readme in docs * update submodule; add validation axes dims; pytest.raises with match * fix tests dimensionality datasets * add test ensure ordered scales * improve README for data download; fix small issues * run pre-commit * fix pre-commit * fix pre-commit * fix pre-commit * change tuple to list in Sequence * remove discriminator for CoordinateTransformationType * better comment class inside before validator * add ABC to CoordinateTransformation; fix types tuple -> list; add validation input-output for CoordinateTransformation; add test for mismatching scale+translation in Dataset * add comment for test * simplified validators (comments from David) * Apply suggestions from code review Co-authored-by: David Stansby <dstansby@gmail.com> * fix typo in code review suggestions * wip fix tests * fix tests * fix docs; restore type ignore * fix docs * addressed most review comments * Fix mypy * Checkout submodules in tests * Remove .gitmodules * Skip RFC5 tests for now * Migrate RFC5 work to v06 * Strip out external tests * Remove gitignore update * Add comment about non-empty name validation * Use Axis instead of Axes * Use tuples instead of floats --------- Co-authored-by: Wouter-Michiel Vierdag <michiel.vierdag@embl.de> Co-authored-by: Luca Marconato <m.lucalmer@gmail.com> Co-authored-by: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com>
* Add RFC5 example tests * Fix gitmodule paths to be relative * Sort list of files * Make relative import absolute
* Minor changes to coordinate transform object naming * Transformation > Transform
* Define remaining transform models * Use more ndim
* Get two of the RFC5 examples working. * Error if list out of date * Put back xfail
* Add support for coordinate metadata path metadata * Add test for missing parameters * Ignore mypy
* Re-implement Image.new() for RFC 5 * Set discrete * Add translation to test
* Fix inverse field name * Update examples commit * xfail broken example * Update path inference in Collection * Enable some more example tests * Remove print statement
* Fix image paths * Fix long lines
* Add TransformGraph class * Script to generate all transform graphs * Add coordinate systems to graph explicitly * Output graphs to another repository * Fix output path * Change font name * Expand compound transforms in graph * Generate graphs for collections * Add links between default system and path * Set font for all text * Label top level collection * Unskip images * Only add label when in a collection * Make lines between groups dashed * Discover groups stored in output paths * Add a CLI for rendering a transform graph * Fix paths in tests * Add smoke test for graphviz
* Add code to transform points * Add inverse transform method * Add some inverse transform tests * Implement affine transform * Validate row lengths in Affine * Add a point type * Add method to get inverse transforms * Remove inverse_transform_point * Clean up old comment * Add notes about transform_point impelmentation * Add test for affine dimension mismatch * Implement rotation transform * Test sequence transform * Fixes to read in metadata examples * Remove duplicate property * Remove old method
* Fix dataset transform type * Fix pre-commit
* add Collection.new() method * fix mypy errors * change images input to dict[str,Image]
…#368) * Validate output of transforms in multiscale datasets * Update output system validation
* Update RFC5 examples * Implement scene * Simplify multiscale transform validation * Fix transformation validation
* Add Scene to top level namespace * Fix image API docs * Add separate scene and coordinate doc pages * Doc build fixes
* Add separate scene and coordinate doc pages * Doc build fixes * Improve base transform model documentation * Fix output description * Add descriptions to Affine * Add sub-sections to coordinate API docs * Show headings * Better API docs for CoordinateSystem and CoordinateSystemIdentifier * Add descriptions for Axis parameters * Add more transform parameter definitions * Fix typo Co-authored-by: Jan Eglinger <jan.eglinger@gmail.com> * Fix line length --------- Co-authored-by: Jan Eglinger <jan.eglinger@gmail.com>
* Allow path=None in coordinate system identifiers * Allow None path in transform graph implementation
- implement `from_version` and `to_version` for v05 Multiscales - implement `from_version` and `to_version` for v04 Multiscales - add tests for both converters
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
fix parameter passage in v06 metadata conversion
fix version conversion for 0.4 metadata
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Follow-up for #398 for 0.6 metadata