v0.2.2

[0.2.2] - 2024-08-07

Major

• New disk format for shapes using GeoParquet (the change is backward compatible) #542

Minor

• Add return_background as argument to get_centroids and get_element_instances #621
• Ability to save data using older disk formats #542

Fixed

• Circles validation now checks for inf or nan radii #653
• Bug with table name in torch dataset #654 @LLehner

v0.2.1

[0.2.1] - 2024-07-04

Minor

• Relaxing spatial-image package requirement #616

v0.2.0

[0.2.0] - 2024-07-03

Changed

• Using DataArray directly instead of the subclass SpatialImage (removed install constraint for the spatial_image package) #587
• Using DataTree directly instead of the subclass MultiscaleSpatialImage (removed install constraint for the multiscale_spatial_image package) #587

Major

• Added operation: to_polygons() @quentinblampey #560
• Extended rasterize() to support all the data types @quentinblampey #566
• Added operation: rasterize_bins() @quentinblampey #578
• Added operation: map_raster() to apply functions block-wise to raster data @ArneDefauw #588

Minor

• Removed pygeos dependency @omsai #545
• Channel coordinate annotations on images now persist through rasterize() @clwgg #544
• Added datasets module
• Extended get_values() to AnnData tables #579
• Added get_element_instances() (replaces _get_unique_label_values_as_index()) #582
• Added get_element_annotators(), retrieving the tables that annotate a particular SpatialElement #595

Fixed

• Preserve channel names of multi-scale images in transform (#379)

v0.2.0rc1

Update pyproject.toml

v0.2.0rc0

pre-release, changelog will appear in the release

v0.1.2

[0.1.2] - 2024-03-30

Minor

• Made get_channels() public.
• Added utils force_2d() to force 3D shapes to 2D (this is a temporary solution until .force_2d() is available in geopandas).

v0.1.1

[0.1.1] - 2024-03-28

Added

• Added method update_annotated_regions_metadata() which updates the regionvalue automatically from theregion_key` columns

Changed

• Renamed join_sdata_spatialelement_table to join_spatialelement_table, and made it work also without SpatialData objects.

v0.1.0-rc0

[0.1.0] - 2024-03-24

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

v0.1.0

updated notebooks

v0.1.0-pre0

Fixes on dataloaders (#439)

* wip fixes

* fix docstring

* wip

* refactored torch dataset; before code cleanup

* support for multiscale images

* code cleanup

* removed comments

* always returning a single-scale image