Clean up legacy code in _models.py and related parts
#180
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yes! yes agree on all the points |
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I can pick this up |
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@melonora addressed the point on |
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LucaMarconato
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Mar 14, 2024
* Multi table (#196) * update napari dependency * change deprecated is_categorical_dtype * Iinitial table widget * add table_names to model * More self explainable function name * allow changing tables * fix some tests * Fixed tests * Revert "Multi table (#196)" (#197) This reverts commit aa56cca. * Avoid exception when registering shortcut (#201) * Fix undefined attribute _labels_key Accessing the property `model.labels_key` gave an `AttributeError("'ImageModel' object has no attribute '_labels_key'")` * Avoid exception when key binding collides with existing If the shortcut is already registered, Napari does not warn but raise an error. To avoid crashing Napari, we must provide the override argument (no matter whether preserving existing or overriding with the new command). * add color by in adata view * remove _scale from model * remove points coordinates * remove point_diameter * remove spot diameter --------- Co-authored-by: aeisenbarth <[email protected]> Co-authored-by: Luca Marconato <[email protected]>
melonora
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Mar 19, 2024
* Multi table (#198) * update napari dependency * change deprecated is_categorical_dtype * Iinitial table widget * add table_names to model * More self explainable function name * allow changing tables * fix some tests * Fixed tests * Multi table (#200) * update napari dependency * change deprecated is_categorical_dtype * Iinitial table widget * add table_names to model * More self explainable function name * allow changing tables * fix some tests * Fixed tests * remove legacy squidpy * remove legacy squidpy * remove coordinates * fix tests * silence warnings * fix last tests * fix mypy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Multi table (#202) * update napari dependency * change deprecated is_categorical_dtype * Iinitial table widget * add table_names to model * More self explainable function name * allow changing tables * fix some tests * Fixed tests * remove legacy squidpy * remove legacy squidpy * remove coordinates * fix tests * silence warnings * fix last tests * fix mypy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add table for adatascatter --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Fix adding layer without table * fix removing layer * fix wrong point size when affine specified (#193) * add color by in adata view (#204) * Issue #180 (#205) * Multi table (#196) * update napari dependency * change deprecated is_categorical_dtype * Iinitial table widget * add table_names to model * More self explainable function name * allow changing tables * fix some tests * Fixed tests * Revert "Multi table (#196)" (#197) This reverts commit aa56cca. * Avoid exception when registering shortcut (#201) * Fix undefined attribute _labels_key Accessing the property `model.labels_key` gave an `AttributeError("'ImageModel' object has no attribute '_labels_key'")` * Avoid exception when key binding collides with existing If the shortcut is already registered, Napari does not warn but raise an error. To avoid crashing Napari, we must provide the override argument (no matter whether preserving existing or overriding with the new command). * add color by in adata view * remove _scale from model * remove points coordinates * remove point_diameter * remove spot diameter --------- Co-authored-by: aeisenbarth <[email protected]> Co-authored-by: Luca Marconato <[email protected]> * Issue #192 (#207) * Multi table (#196) * update napari dependency * change deprecated is_categorical_dtype * Iinitial table widget * add table_names to model * More self explainable function name * allow changing tables * fix some tests * Fixed tests * Revert "Multi table (#196)" (#197) This reverts commit aa56cca. * Avoid exception when registering shortcut (#201) * Fix undefined attribute _labels_key Accessing the property `model.labels_key` gave an `AttributeError("'ImageModel' object has no attribute '_labels_key'")` * Avoid exception when key binding collides with existing If the shortcut is already registered, Napari does not warn but raise an error. To avoid crashing Napari, we must provide the override argument (no matter whether preserving existing or overriding with the new command). * add color by in adata view * remove _scale from model * remove points coordinates * remove point_diameter * remove spot diameter * fix #192 --------- Co-authored-by: aeisenbarth <[email protected]> Co-authored-by: Luca Marconato <[email protected]> * Test spatialelement table join (#208) * fixed all the non-cytassist images * refactor get_init_table_list * fix permutation * use join * use join for view * change hardcoded sample threshold * bunch of updates * adjust test * change into left join * change into left join * random hex colors * get actual index * change indices and adata * match rows left * fix joins * rename to vars * fix color by * fix radii * pass cs * fix _calc_default_radii() * fix tests * improve speed test * removed comments * added code to show circles as ellipses * correct point layer size after scaling * fix labels color by * fix mibitof example * last bug fixes * initial step points columns * add dask import back * fix points columns --------- Co-authored-by: wmv_hpomen <[email protected]> Co-authored-by: Wouter-Michiel Vierdag <[email protected]> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: LucaMarconato <[email protected]> Co-authored-by: aeisenbarth <[email protected]> Co-authored-by: Luca Marconato <[email protected]>
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CC @giovp, please comment on this.
_models.pycontains a lot of legacy code that makes the code fragile. In particular we should remove the following:_scale, not used anymore now that we have coordinate transformations_spot_diameter/_point_diameter, we should keep one of the two onlylabel_key(and relative methods, like the getter/setterlabels_key. This is in realityinstance_key, and for some reasons it's used only for labels. Theregion_key+instance_keylogic applies both to labels and shapes (shapes=circles or polygons/multipolygons). I suggest either to addregion_keyandinstance_keyto the model, or not put them in the model at all. I favor the second approach._spatial_key, not needed any moreIn this PR I would also make the following change:
_spot_diameterand_point_diameter, let's remove thepointswidget from the bottom right UI; it's never used.The text was updated successfully, but these errors were encountered: