polygons

get_reduced_coords(coords, angle_th, distance_th)

Given polygon vertices coordinates, deletes those that are too close or that form a too small angle.

Parameters:

Name	Type	Description	Default
coords	NDArray[Any, 2, Number]	array of coordinates.	required
angle_th	float	minimum angle (in degrees) formed by 3 consecutives vertices. If the angle is too small, the middle vertex will be deleted.	required
distance_th	float	minimum distance between vertices. If 2 consecutive sides of the polygon are too small, the middle vertex will be deleted.	required

Returns:

Type	Description
NDArray[Any, 2, int]	Array of polygon coordinates with small and flat sides pruned.

hovernet_to_wkt(infile, outfile, slide_height=None)

Take a hovernet json output file and convert it to a wkt file. Optionally convert coordinates to cytomine format.

Parameters:

Name	Type	Description	Default
infile	PathLike	path to input hovernet json file.	required
outfile	PathLike	path to output wkt file.	required
slide_height	Optional[int]	height of the slide on which hovernet was used. If given, coordinates will be converted to cytomine format (y = slide_height - y).	None

mask_to_polygons_layer(mask, angle_th=2, distance_th=3)

Convert mask array into :class:shapely.geometry.MultiPolygon.

Parameters:

Name	Type	Description	Default
mask	NDBoolMask	input mask array.	required

Returns:

Type	Description
MultiPolygon	class:shapely.geometry.MultiPolygon where polygons are extracted from
MultiPolygon	positive areas in the mask.

reduce_polygon(polygon, angle_th=0, distance_th=0)

Given a :class:shapely.geometry.Polygon, delete vertices that create small or flat sides on the interior and on the exterior.

Parameters:

Name	Type	Description	Default
polygon	Polygon	input polygon.	required
angle_th	float	minimum angle (in degrees) formed by 3 consecutives vertices. If the angle is too small, the middle vertex will be deleted.	0
distance_th	float	minimum distance between vertices. If 2 consecutive sides of the polygon are too small, the middle vertex will be deleted.	0

Returns:

Type	Description
Polygon	Reduced polygon.