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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.2.6] - TBD

Added

  • Added set_channel_names method to SpatialData to change the channel names of an image element in SpatialData
  • Added write_channel_names method to SpatialData to overwrite channel metadata on disk without overwriting the image array itself.

Changed

  • get_channels is marked for deprecation in SpatialData v0.3.0. Function is replaced by get_channel_names

Fixed

  • Updated deprecated default stages of pre-commit #771

[0.2.5] - 2024-06-11

Fixed

  • Incompatibility issues due to newest release of multiscale-spatial-image #760

[0.2.4] - 2024-06-11

Major

  • Enable vectorization of bounding_box_query for all SpatialData elements. #699

Minor

  • Added shortest_path parameter to get_transformation_between_coordinate_systems #714
  • Added get_pyramid_levels() utils API #719
  • Improved ergonomics of concatenate() when element names are non-unique #720
  • Improved performance of writing images with multiscales #577

[0.2.3] - 2024-09-25

Minor

  • Added clip: bool = False parameter to polygon_query() #670
  • Add sort parameter to PointsModel.parse() #672

Fixed

  • Fix interpolation artifact multiscale computation for labels #697

[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

[0.2.1] - 2024-07-04

Minor

  • Relaxing spatial-image package requirement #616

[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
  • Changed elementparameter (deprecation in v0.3.0) of transform_element_to_coordinate_system to a string element_name #611

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)
  • Fix filter_by_coordinate_system with SpatialData object having a table not annotating an element (#619)

[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).

[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.

[0.1.0] - 2024-03-24

Added

Major

  • Implemented support in SpatialData for storing multiple tables.

  • These tables can annotate a SpatialElement but now not necessarily so.

  • Deprecated .table attribute in favor of .tables dict-like accessor.

  • Added join operations

  • 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.

  • Incremental IO of data and metadata:

  • Increased in-memory vs on-disk control: changes performed in-memory (e.g. adding a new image) are not automatically performed on-disk.

  • Deprecated add_image(), add_labels(), add_shapes(), add_points() in favor of .images, .labels, .shapes, .points dict-like accessors.

  • new methods write_element(), write_transformations(), write_metadata(), remove_element_from_disk()

  • new methods write_consolidated_metadata() and has_consolidated_metadata()

  • deprecated save_transformations()

  • improved __repr__() with information on Zarr storage and Dask-backed files

  • new utils is_self_contained(), describe_elements_are_self_contained()

  • new utils element_paths_in_memory(), element_paths_on_disk()

Minor

  • Multiple table helper functions

  • 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 method get_annotated_regions() in SpatialData to get the regions annotated by a given table.

  • Added method get_region_key_column() in SpatialData to get the region_key column in table.obs.

  • Added method get_instance_key_column() in SpatialData to get the instance_key column in table.obs.

  • Added method 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.

  • Utils

  • 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: get_centroids()

  • added utils function: deepcopy()

  • added operation: to_circles()

  • documented previously-added get_channels() to retrieve the channel names of a raster element indepently of it being single or multi-scale

  • Transformations-related

    • 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 testing utilities: assert_spatial_data_objects_are_identical(), assert_elements_are_identical(), assert_elements_dict_are_identical()

Changed/fixed

Major

  • refactored data loader for deep learning
  • refactored SpatialData.write() to be more robust
  • generalized spatial queries to any combination of 2D/3D data and 2D/3D query region #409

Minor

  • Changed the string representation of SpatialData to reflect the changes in regard to multiple tables and incremental IO.
  • improved usability and robustness of sdata.write() when overwrite=True @aeisenbarth
  • fixed warnings for categorical dtypes in tables in TableModel and PointsModel
  • fixed wrong order of points after spatial queries

[0.0.14] - 2023-10-11

Added

Minor

  • new API: sdata.rename_coordinate_systems()

Technical

  • decompose affine transformation into simpler transformations
  • remove padding for blobs()

Major

  • get_extent() function to compute bounding box of the data

Minor

  • testing against pre-release packages

Fixed

  • Fixed bug with get_values(): ignoring background channel in labels

[0.0.13] - 2023-10-02

Added

  • polygon_query() support for images #358

Fixed

  • Fix missing c_coords argument in blobs multiscale #342
  • Replaced hardcoded string with instance_key #346

[0.0.12] - 2023-06-24

Added

  • Add multichannel blobs sample data (by @melonora)

[0.0.11] - 2023-06-21

Improved

  • Aggregation APIs.

[0.0.10] - 2023-06-06

Fixed

  • Fix blobs (#282)

[0.0.9] - 2023-05-23

Updated

  • Update napari-spatialdata pin (#279)
  • pin typing-extensions

[0.0.8] - 2023-05-22

Merged

  • Merge pull request #271 from scverse/fix/aggregation

[0.0.7] - 2023-05-20

Updated

  • Update readme

[0.0.6] - 2023-05-10

Added

  • This release adds polygon spatial query.

[0.0.5] - 2023-05-05

Fixed

  • fix tests badge (#242)

[0.0.4] - 2023-05-04

Tested

  • This release tests distribution via pypi

[0.0.3] - 2023-05-02

Added

  • This is an alpha release to test the release process.

[0.0.2] - 2023-05-02

Added

  • make version dynamic

[0.0.1.dev1] - 2023-03-25

Added

  • Dev version, not official release yet