lazyslide.io.export_annotations#
- export_annotations(wsi, key, *, in_bounds=False, classes=None, colors=None, format='qupath', file=None)#
Export the annotations
- Parameters:
- wsi
WSIData The WSIData object to work on.
- keystr
The key to export. Must exist in wsi.shapes.
- in_boundsbool, default: False
Whether to move the annotations to the slide bounds.
- classesstr, default: None
The column to use for the classification. If None, the classification will be ignored. If provided, must exist in the GeoDataFrame.
- colorsstr | Mapping | Sequence, default: None
The column to use for the color, or a mapping from class values to colors, or a sequence of colors to be assigned to unique class values. If None, default colors will be used.
- formatstr, default: ‘qupath’
The format to export. Currently only ‘qupath’ is supported.
- filestr | Path, default: None
The file to save the annotations. If None, the annotations will not be saved. If provided, the parent directory will be created if it doesn’t exist.
- wsi
- Returns:
- GeoDataFrame
The exported annotations.
- Raises:
- ValueError
If key doesn’t exist in wsi.shapes. If classes is provided but doesn’t exist in the GeoDataFrame. If colors is provided but is not a string, mapping, or sequence.