Added
Major
- Implemented support in SpatialData for storing multiple tables. These tables can annotate a SpatialElement but not
necessarily so.
- Added SQL like joins that can be executed by calling one public function `join_sdata_spatialelement_table`. The
following joins are supported: `left`, `left_exclusive`, `right`, `right_exclusive` and `inner`. The function has
an option to match rows. For `left` only matching `left` is supported and for `right` join only `right` matching of
rows is supported. Not all joins are supported for `Labels` elements.
- Added function `match_element_to_table` which allows the user to perform a right join of `SpatialElement`(s) with a
table with rows matching the row order in the table.
- Increased in-memory vs on-disk control: changes performed in-memory (e.g. adding a new image) are not automatically
performed on-disk.
Minor
- Added public helper function get_table_keys in spatialdata.models to retrieve annotation information of a given
table.
- Added public helper function check_target_region_column_symmetry in spatialdata.models to check whether annotation
metadata in table.uns['spatialdata_attrs'] corresponds with respective columns in table.obs.
- Added function validate_table_in_spatialdata in SpatialData to validate the annotation target of a table being
present in the SpatialData object.
- Added function get_annotated_regions in SpatialData to get the regions annotated by a given table.
- Added function get_region_key_column in SpatialData to get the region_key column in table.obs.
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
a table in a given SpatialData object.
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
- Added gen_elements generator in SpatialData to generate elements of a SpatialData object including tables.
- added SpatialData.subset() API
- added SpatialData.locate_element() API
- added utils function: transform_to_data_extent()
- added utils function: are_extents_equal()
- added utils function: postpone_transformation()
- added utils function: remove_transformations_to_coordinate_system()
- added utils function: get_centroids()
- added utils function: deepcopy()
- added operation: to_circles()
- added testing utilities: assert_spatial_data_objects_are_identical(), assert_elements_are_identical(),
assert_elements_dict_are_identical()
Changed
Major
- refactored data loader for deep learning
Minor
- Changed the string representation of SpatialData to reflect the changes in regard to multiple tables.
Fixed
Major
- improved usability and robustness of sdata.write() when overwrite=True aeisenbarth
- generalized queries to any combination of 2D/3D data and 2D/3D query region 409
- fixed warnings for categorical dtypes in tables in TableModel and PointsModel