Napari to shapeley

napari_shapely.py

import numpy as np

from shapely.geometry.polygon import Polygon
from shapely.geometry import GeometryCollection, LineString


def napari_shape_to_shapely(coords: np.ndarray, shape_type: str = "polygon"):
    """
    Convert an individual napari shape from a shapes layer to a shapely object
    There is no direct correspondence between a 'rectangle' in napari and a 'box' in
    shapely. The command for creating a box only requires minimum and maximum x and y
    coordinates, i.e. this is for axis aligned rectangles. In contrast, a napari rectangle
    can be arbitrarily rotated and still be a rectangle.
    So for converting a rectangle from napari to shapely we have to go to a polygon
    """
    _coords = coords[:, ::-1].copy()  # shapely has col,row order, numpy row,col
    _coords[:, 1] *= -1  # axis direction flipped between shapely and napari
    if shape_type in ("rectangle", "polygon", "ellipse"):
        return Polygon(_coords)
    elif shape_type in ("line", "path"):
        return LineString(_coords)
    else:
        raise ValueError


def napari_shape_layer_to_shapely(s):
    """
    Convert all shapes in a napari shape layer to shapely objects
    and return a GeometryCollection
    """
    shapes = []
    for _coord, _st in zip(s.data, s.shape_type):
        shapes.append(napari_shape_to_shapely(_coord, _st))
    return GeometryCollection(shapes)