jendelel · November 19, 2024 18:45 · jasminjahanpuspo · Jan 31, 2023 · shubham-pipada · Nov 6, 2024
diff --git a/load_inbreast_roi.py b/load_inbreast_roi.py
 from skimage.draw import polygon
 import numpy as np
 import plistlib

 def load_inbreast_mask(mask_path, imshape=(4084, 3328)):
    """
    This function loads a osirix xml region as a binary numpy array for INBREAST
    dataset

    @mask_path : Path to the xml file
    @imshape : The shape of the image as an array e.g. [4084, 3328]

    return: numpy array where positions in the roi are assigned a value of 1.

    """

    def load_point(point_string):
        x, y = tuple([float(num) for num in point_string.strip('()').split(',')])
        return y, x

    mask = np.zeros(imshape)
    with open(mask_path, 'rb') as mask_file:
        plist_dict = plistlib.load(mask_file, fmt=plistlib.FMT_XML)['Images'][0]
        numRois = plist_dict['NumberOfROIs']
        rois = plist_dict['ROIs']
        assert len(rois) == numRois
        for roi in rois:
            numPoints = roi['NumberOfPoints']
            points = roi['Point_px']
            assert numPoints == len(points)
            points = [load_point(point) for point in points]
            if len(points) <= 2:
                for point in points:
                    mask[int(point[0]), int(point[1])] = 1
            else:
                x, y = zip(*points)
                x, y = np.array(x), np.array(y)
                poly_x, poly_y = polygon(x, y, shape=imshape)
                mask[poly_x, poly_y] = 1
    return mask
	from skimage.draw import polygon
	import numpy as np
	import plistlib

	def load_inbreast_mask(mask_path, imshape=(4084, 3328)):
	"""
	This function loads a osirix xml region as a binary numpy array for INBREAST
	dataset

	@mask_path : Path to the xml file
	@imshape : The shape of the image as an array e.g. [4084, 3328]

	return: numpy array where positions in the roi are assigned a value of 1.

	"""

	def load_point(point_string):
	x, y = tuple([float(num) for num in point_string.strip('()').split(',')])
	return y, x

	mask = np.zeros(imshape)
	with open(mask_path, 'rb') as mask_file:
	plist_dict = plistlib.load(mask_file, fmt=plistlib.FMT_XML)['Images'][0]
	numRois = plist_dict['NumberOfROIs']
	rois = plist_dict['ROIs']
	assert len(rois) == numRois
	for roi in rois:
	numPoints = roi['NumberOfPoints']
	points = roi['Point_px']
	assert numPoints == len(points)
	points = [load_point(point) for point in points]
	if len(points) <= 2:
	for point in points:
	mask[int(point[0]), int(point[1])] = 1
	else:
	x, y = zip(*points)
	x, y = np.array(x), np.array(y)
	poly_x, poly_y = polygon(x, y, shape=imshape)
	mask[poly_x, poly_y] = 1
	return mask