def label_image_postprocessing(self, image):
"""
Processes label instance segmentation np arrays. Smoothes the image, if self.label_gaussian_blur_sigma > 0.
:param image: The instance segmentation np array.
:return: The processed np array.
"""
channel_axis = self.get_channel_axis(image, self.data_format)
if self.label_gaussian_blur_sigma > 0.0: # and self.label_gaussian_blur_sigma != 1.0:
images, labels = split_label_image_with_unknown_labels(np.squeeze(image, axis=channel_axis), dtype=np.uint16)
gaussians = [0, self.label_gaussian_blur_sigma, self.label_gaussian_blur_sigma] if image.ndim == 4 else [self.label_gaussian_blur_sigma, self.label_gaussian_blur_sigma]
images = smooth_label_images(images, gaussians, dtype=np.uint16)
image = np.expand_dims(merge_label_images(images, labels), channel_axis)
return image
def label_image_postprocessing(self, image):
"""
Processes label instance segmentation np arrays. Smoothes the image, if self.label_gaussian_blur_sigma > 0.
:param image: The instance segmentation np array.
:return: The processed np array.
"""
if self.label_gaussian_blur_sigma > 0:
images, labels = split_label_image_with_unknown_labels(
image, dtype=np.uint16)
images = smooth_label_images(images,
self.label_gaussian_blur_sigma,
dtype=np.uint16)
image = merge_label_images(images, labels)
return image
def relabel_seg(seg, tra):
seg_label_images, _ = split_label_image_with_unknown_labels(seg)
tra_label_images, tra_labels = split_label_image_with_unknown_labels(tra)
del tra_label_images[0]
del tra_labels[0]
new_seg_labels = [0]
for i in range(1, len(seg_label_images)):
seg_label_image = seg_label_images[i]
tra_label_overlap = [
(tra_label,
np.sum(np.bitwise_and(seg_label_image == 1,
tra_label_image == 1)))
for tra_label_image, tra_label in zip(tra_label_images, tra_labels)
]
best_tra_label, best_overlap = max(tra_label_overlap,
key=lambda x: x[1])
new_seg_labels.append(best_tra_label)
assert len(
np.unique(new_seg_labels)) == len(new_seg_labels), 'duplicate labels'
new_seg = merge_label_images(seg_label_images, new_seg_labels)
return new_seg