qupath_to_domain#
- qupath_to_domain(qupath_json_file, domain_name='a_qupath_domain', add_cells_as_points=True, pixel_size=[1, 1], properties_to_ignore=['isLocked', 'objectType', 'color'], specific_properties_as_labels=[], simplify_shapes=True, simplify_shapes_kwargs={'algorithm': 'Visvalingam-Whyatt', 'epsilon': 10}, print_summary=True)#
Import a QuPath GeoJSON file to a muspan domain. All metadata from the GeoJSON file is added as labels to the domain object. Only scalar and categorical metadata is supported.
- Parameters:
- qupath_json_filestr
Path to the QuPath GeoJSON file.
- domain_namestr, optional
Name of the domain, by default ‘a_qupath_domain’.
- add_cells_as_pointsbool, optional
Whether to add cells as points, by default True.
- pixel_sizelist, optional
Pixel size for scaling coordinates with x and y respectively, by default [1, 1].
- properties_to_ignorelist, optional
List of properties to ignore, by default [‘isLocked’, ‘objectType’, ‘color’].
- specific_properties_as_labelslist, optional
List of properties to be added as labels, by default [].
- simplify_shapesbool, optional
Whether to simplify shapes, by default True.
- simplify_shapes_kwargsdict, optional
Additional arguments for shape simplification, by default dict(algorithm=’Visvalingam-Whyatt’, epsilon=30).
- print_summarybool, optional
If True, print a summary of the resulting domain, by default True.
- Returns:
- domainmuspan domain
The muspan domain created from the QuPath GeoJSON file.
- Raises:
- ValueError
If qupath_json_file is not a string or if the GeoJSON file does not contain the expected structure output by QuPath.
Notes
Shape boundaries are simplfied by default using the Visvalingam-Whyatt algorithm with an epsilon of 10. This can be disabled by setting ``simplify_shapes’’ to False. See domain.simplify_shape_boundaries for more information.
Currently line colllections are not supported via import and will be ignore if present in the GeoJSON file.
If objects have multiple labels under the same property, only the first label will be added.