AnnotationRenderer#

class AnnotationRenderer(score_prop=None, mapper=None, where=None, score_fn=<function AnnotationRenderer.<lambda>>, max_scale=8)[source]#

Renderer containing information and methods to render annotations from an AnnotationStore to a tile.

Parameters:

  • score_prop (str) – A key that is present in the properties of annotations to be rendered that will be used to color rendered annotations.

  • mapper (str, Dict or List) – A dictionary or colormap used to color annotations according to the value of properties[score_prop] of an annotation. Should be either a matplotlib colormap, a string which is a name of a matplotlib colormap, a dict of possible property {value: color} pairs, or a list of categorical property values (in which case a dict will be created with a random color generated for each category).

  • where (str or Callable) – a callable or predicate which will be passed on to AnnotationStore.query() when fetching annotations to be rendered (see tiatoolbox.annotation.storage.AnnotationStore for more details).

  • score_fn (Callable) – an optional callable which will be called on the value of the property that will be used to generate the color before giving it to colormap. Use it for example to normalise property values if they do not fall into the range [0,1], as matplotlib colormap expects values in this range. i.e., roughly speaking annotation_color=mapper(score_fn(ann.properties[score_prop])).

  • max_scale (int) – downsample level above which Polygon geometries on crowded tiles will be rendered as a bounding box instead.

Methods

get_color

Get the color for an annotation.

render_line

Render a line annotation onto a tile using cv2.

render_poly

Render a polygon annotation onto a tile using cv2.

render_pt

Render a point annotation onto a tile using cv2.

render_rect

Render a box annotation onto a tile using cv2.

to_tile_coords

Return coords relative to top left of tile, as array suitable for cv2.
get_color(annotation)[source]#

Get the color for an annotation. :param annotation: Annotation to get color for. :type annotation: Annotation

Returns:

A color tuple (rgba).

Return type:

tuple

Parameters:

annotation (Annotation) –

render_line(tile, annotation, top_left, scale)[source]#

Render a line annotation onto a tile using cv2. :param tile: The rgb(a) tile image to render onto. :type tile: ndarray :param annotation: The annotation to render. :type annotation: Annotation :param top_left: The top left corner of the tile in wsi. :type top_left: tuple :param scale: The zoom scale at which we are rendering. :type scale: int

Parameters:
render_poly(tile, annotation, top_left, scale)[source]#

Render a polygon annotation onto a tile using cv2. :param tile: The rgb(a) tile image to render onto. :type tile: ndarray :param annotation: The annotation to render. :type annotation: Annotation :param top_left: The top left corner of the tile in wsi. :type top_left: tuple :param scale: The zoom scale at which we are rendering. :type scale: int

Parameters:
render_pt(tile, annotation, top_left, scale)[source]#

Render a point annotation onto a tile using cv2. :param tile: The rgb(a) tile image to render onto. :type tile: ndarray :param annotation: The annotation to render. :type annotation: Annotation :param top_left: The top left corner of the tile in wsi. :type top_left: tuple :param scale: The zoom scale at which we are rendering. :type scale: int

Parameters:
render_rect(tile, annotation, top_left, scale)[source]#

Render a box annotation onto a tile using cv2. :param tile: The rgb(a) tile image to render onto. :type tile: ndarray :param annotation: The annotation to render. :type annotation: Annotation :param top_left: The top left corner of the tile in wsi. :type top_left: tuple :param scale: The zoom scale at which we are rendering. :type scale: int

Parameters:
static to_tile_coords(coords, top_left, scale)[source]#

Return coords relative to top left of tile, as array suitable for cv2. :param coords: List of coordinates in the form [x, y]. :type coords: List :param top_left: The top left corner of the tile in wsi. :type top_left: tuple :param scale: The zoom scale at which we are rendering. :type scale: int

Returns:

Array of coordinates in tile space in the form [x, y].

Return type:

np.array

Parameters: