added region_annotations #161
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This PR contains functions for several basic operations for spatial data analysis:
hp.sh.filter_by_morphology: Allows filtering a shapes layer based on morphological features (area, perimeter, circularity, ...). Can be used to clean cells after segmentation.
hp.sh.filter_by_shapes: Allows filtering a shapes layer based on a secondary shapes layer containing region annotation. Can be used to clean cells/polygons occurring in artifacts, outside of the tissue, etc..
hp.tb.filter_numerical: Allows filtering a table layer based on a numerical column in .obs. This is a generalization of hp.tb.filter_on_size.
hp.tb.filter_categorical: Allows filtering a table layer based on a categorical column in .obs.
hp.assign_cells_to_shapes: Allows determining whether a cell occurs in a region annotation. Creates a column or multiple columns in .obs.
hp.tb.compute_distance_to_shapes: Allows computing distances per cell to polygons in a shapes layer. Multiple modes are included to support different use-cases. E.g. computing distance of cell to nearest polygon, computing distances to all centroids of all polygons, ...
hp.sh.prep_region_annotations: Prepares region annotations in a shapes layer for
hp.sh.filter_by_morphology,hp.tb.assign_cells_to_shapesandhp.tb.compute_distance_to_shapes.These functions were tested for shapes and table layers occurring in the same coordinate space and no transformations were required. More challenging use-cases still need to be tested/supported.