def preprocess_image(im_path, n_levels, crop_shape=None, padding=None, aff_ref='FS', dist_map=False):
# read image and corresponding info
im, shape, aff, n_dims, n_channels, header, im_res = utils.get_volume_info(im_path, return_volume=True)
if padding:
im = edit_volumes.pad_volume(im, padding_shape=padding)
pad_shape = im.shape[:n_dims]
else:
pad_shape = shape
# check that patch_shape or im_shape are divisible by 2**n_levels
if crop_shape is not None:
crop_shape = utils.reformat_to_list(crop_shape, length=n_dims, dtype='int')
if not all([pad_shape[i] >= crop_shape[i] for i in range(len(pad_shape))]):
crop_shape = [min(pad_shape[i], crop_shape[i]) for i in range(n_dims)]
if not all([size % (2**n_levels) == 0 for size in crop_shape]):
crop_shape = [utils.find_closest_number_divisible_by_m(size, 2 ** n_levels) for size in crop_shape]
else:
if not all([size % (2**n_levels) == 0 for size in pad_shape]):
crop_shape = [utils.find_closest_number_divisible_by_m(size, 2 ** n_levels) for size in pad_shape]
# crop image if necessary
if crop_shape is not None:
im, crop_idx = edit_volumes.crop_volume(im, cropping_shape=crop_shape, return_crop_idx=True)
else:
crop_idx = None
# align image to training axes and directions
if n_dims > 2:
if aff_ref == 'FS':
aff_ref = np.array([[-1., 0., 0., 0.], [0., 0., 1., 0.], [0., -1., 0., 0.], [0., 0., 0., 1.]])
im = edit_volumes.align_volume_to_ref(im, aff, aff_ref=aff_ref, return_aff=False, n_dims=n_dims)
elif aff_ref == 'identity':
aff_ref = np.eye(4)
im = edit_volumes.align_volume_to_ref(im, aff, aff_ref=aff_ref, return_aff=False, n_dims=n_dims)
# normalise image
if n_channels == 1:
m = np.min(im)
M = np.max(im)
if M == m:
im = np.zeros(im.shape)
else:
im = (im - m) / (M - m)
else:
for i in range(im.shape[-1]):
if (not dist_map) | (dist_map & (i % 2 == 0)):
channel = im[..., i]
m = np.min(channel)
M = np.max(channel)
if M == m:
im[..., i] = np.zeros(channel.shape)
else:
im[..., i] = (channel - m) / (M - m)
# add batch and channel axes
im = utils.add_axis(im) if n_channels > 1 else utils.add_axis(im, axis=[0, -1])
return im, aff, header, im_res, n_channels, n_dims, shape, pad_shape, crop_idx
def generate_brain(self):
"""call this method when an object of this class has been instantiated to generate new brains"""
(image, labels) = next(self.brain_generator)
# put back images in native space
list_images = list()
list_labels = list()
for i in range(self.batchsize):
list_images.append(edit_volumes.align_volume_to_ref(image[i], np.eye(4),
aff_ref=self.aff, n_dims=self.n_dims))
list_labels.append(edit_volumes.align_volume_to_ref(labels[i], np.eye(4),
aff_ref=self.aff, n_dims=self.n_dims))
image = np.stack(list_images, axis=0)
labels = np.stack(list_labels, axis=0)
return image, labels
def postprocess(prediction, pad_shape, im_shape, crop, n_dims, labels,
keep_biggest_component, aff):
# get posteriors and segmentation
post_patch = np.squeeze(prediction)
seg_patch = post_patch.argmax(-1)
# keep biggest connected component (use it with smoothing!)
if keep_biggest_component:
left_mask = edit_volumes.get_largest_connected_component(
(seg_patch > 0) & (seg_patch < 6))
right_mask = edit_volumes.get_largest_connected_component(
seg_patch > 5)
seg_patch *= (left_mask | right_mask)
# paste patches back to matrix of original image size
if crop is not None:
seg = np.zeros(shape=pad_shape, dtype='int32')
posteriors = np.zeros(shape=[*pad_shape, labels.shape[0]])
posteriors[...,
0] = np.ones(pad_shape) # place background around patch
if n_dims == 2:
seg[crop[0]:crop[2], crop[1]:crop[3]] = seg_patch
posteriors[crop[0]:crop[2], crop[1]:crop[3], :] = post_patch
elif n_dims == 3:
seg[crop[0]:crop[3], crop[1]:crop[4], crop[2]:crop[5]] = seg_patch
posteriors[crop[0]:crop[3], crop[1]:crop[4],
crop[2]:crop[5], :] = post_patch
else:
seg = seg_patch
posteriors = post_patch
seg = labels[seg.astype('int')].astype('int')
if im_shape != pad_shape:
bounds = [int((p - i) / 2) for (p, i) in zip(pad_shape, im_shape)]
bounds += [p + i for (p, i) in zip(bounds, im_shape)]
seg = edit_volumes.crop_volume_with_idx(seg, bounds)
# align prediction back to first orientation
if n_dims > 2:
seg = edit_volumes.align_volume_to_ref(seg, np.eye(4), aff_ref=aff)
posteriors = edit_volumes.align_volume_to_ref(posteriors,
np.eye(4),
aff_ref=aff,
n_dims=n_dims)
return seg, posteriors
def postprocess(prediction, pad_shape, im_shape, crop, n_dims, labels, keep_biggest_component,
aff, aff_ref='FS', keep_biggest_of_each_group=True, n_neutral_labels=None):
# get posteriors and segmentation
post_patch = np.squeeze(prediction)
# reset posteriors to zero outside the largest connected component of each topological class
if keep_biggest_of_each_group:
topology_classes = np.array([0, 1, 2, 3, 4, 4, 5, 5, 6, 6, 7, 8, 9, 10, 11, 12, 13, 14, 5])
if n_neutral_labels != len(labels):
left = topology_classes[n_neutral_labels:]
topology_classes = np.concatenate([topology_classes, left + np.max(left) - np.min(left) + 1])
unique_topology_classes = np.unique(topology_classes)
post_patch_mask = post_patch > 0.2
for topology_class in unique_topology_classes[1:]:
tmp_topology_indices = np.where(topology_classes == topology_class)[0]
tmp_mask = np.any(post_patch_mask[..., tmp_topology_indices], axis=-1)
tmp_mask = edit_volumes.get_largest_connected_component(tmp_mask)
for idx in tmp_topology_indices:
post_patch[..., idx] *= tmp_mask
# renormalise posteriors and get hard segmentation
post_patch /= np.sum(post_patch, axis=-1)[..., np.newaxis]
seg_patch = post_patch.argmax(-1)
# keep biggest connected component (use it with smoothing!)
if keep_biggest_component:
mask = seg_patch > 0
mask = edit_volumes.get_largest_connected_component(mask)
seg_patch = seg_patch * mask
# align prediction back to first orientation
if n_dims > 2:
if aff_ref == 'FS':
aff_ref = np.array([[-1., 0., 0., 0.], [0., 0., 1., 0.], [0., -1., 0., 0.], [0., 0., 0., 1.]])
seg_patch = edit_volumes.align_volume_to_ref(seg_patch, aff_ref, aff_ref=aff, return_aff=False)
post_patch = edit_volumes.align_volume_to_ref(post_patch, aff_ref, aff_ref=aff, n_dims=n_dims)
elif aff_ref == 'identity':
aff_ref = np.eye(4)
seg_patch = edit_volumes.align_volume_to_ref(seg_patch, aff_ref, aff_ref=aff, return_aff=False)
post_patch = edit_volumes.align_volume_to_ref(post_patch, aff_ref, aff_ref=aff, n_dims=n_dims)
# paste patches back to matrix of original image size
if crop is not None:
seg = np.zeros(shape=pad_shape, dtype='int32')
posteriors = np.zeros(shape=[*pad_shape, labels.shape[0]])
posteriors[..., 0] = np.ones(pad_shape) # place background around patch
if n_dims == 2:
seg[crop[0]:crop[2], crop[1]:crop[3]] = seg_patch
posteriors[crop[0]:crop[2], crop[1]:crop[3], :] = post_patch
elif n_dims == 3:
seg[crop[0]:crop[3], crop[1]:crop[4], crop[2]:crop[5]] = seg_patch
posteriors[crop[0]:crop[3], crop[1]:crop[4], crop[2]:crop[5], :] = post_patch
else:
seg = seg_patch
posteriors = post_patch
seg = labels[seg.astype('int')].astype('int')
if im_shape != pad_shape:
bounds = [int((p-i)/2) for (p, i) in zip(pad_shape, im_shape)]
bounds += [p + i for (p, i) in zip(bounds, im_shape)]
seg = edit_volumes.crop_volume_with_idx(seg, bounds)
return seg, posteriors
# Do the actual work
print('Found %d images' % len(images_to_segment))
for idx, (path_image, path_prediction) in enumerate(
zip(images_to_segment, path_predictions)):
print(' Working on image %d ' % (idx + 1))
print(' ' + path_image)
im, aff, hdr = utils.load_volume(path_image, im_only=False, dtype='float')
if args['ct']:
im[im < 0] = 0
im[im > 80] = 80
im, aff = edit_volumes.resample_volume(im, aff, [1.0, 1.0, 1.0])
aff_ref = np.eye(4)
im, aff2 = edit_volumes.align_volume_to_ref(im,
aff,
aff_ref=aff_ref,
return_aff=True,
n_dims=3)
im = im - np.min(im)
im = im / np.max(im)
I = im[np.newaxis, ..., np.newaxis]
W = (np.ceil(np.array(I.shape[1:-1]) / 32.0) * 32).astype('int')
idx = np.floor((W - I.shape[1:-1]) / 2).astype('int')
S = np.zeros([1, *W, 1])
S[0, idx[0]:idx[0] + I.shape[1], idx[1]:idx[1] + I.shape[2],
idx[2]:idx[2] + I.shape[3], :] = I
output = unet_model.predict(S)
pred = np.squeeze(output)
pred = 255 * pred
pred[pred < 0] = 0
pred[pred > 128] = 128
# Do the actual work
print('Found %d images' % len(images_to_segment_t1))
for idx, (path_image_t1, path_image_t2, path_prediction) in enumerate(
zip(images_to_segment_t1, images_to_segment_t2, path_predictions)):
print(' Working on image %d ' % (idx + 1))
print(' ' + path_image_t1 + ', ' + path_image_t2)
im1, aff1, hdr1 = utils.load_volume(path_image_t1,
im_only=False,
dtype='float')
im1, aff1 = edit_volumes.resample_volume(im1, aff1, [1.0, 1.0, 1.0])
aff_ref = np.eye(4)
im1, aff1_mod = edit_volumes.align_volume_to_ref(im1,
aff1,
aff_ref=aff_ref,
return_aff=True,
n_dims=3)
im2, aff2, hdr2 = utils.load_volume(path_image_t2,
im_only=False,
dtype='float')
im2 = edit_volumes.resample_volume_like(im1, aff1_mod, im2, aff2)
minimum = np.min(im1)
im1 = im1 - minimum
spread = np.max(
im1) / 3.0 # don't ask, it's something I messed up at training
im1 = im1 / spread
im2 = im2 - np.min(im2)
im2 = im2 / np.max(
im2) * 2.0 # don't ask, it's something I messed up at training
def postprocess(post_patch,
pad_shape,
im_shape,
crop,
n_dims,
segmentation_labels,
lr_indices,
keep_biggest_component,
aff,
topology_classes=True,
post_patch_flip=None):
# get posteriors and segmentation
post_patch = np.squeeze(post_patch)
if post_patch_flip is not None:
post_patch_flip = edit_volumes.flip_volume(np.squeeze(post_patch_flip),
direction='rl',
aff=np.eye(4))
if lr_indices is not None:
post_patch_flip[..., lr_indices.flatten()] = post_patch_flip[
..., lr_indices[::-1].flatten()]
post_patch = 0.5 * (post_patch + post_patch_flip)
# keep biggest connected component (use it with smoothing!)
if keep_biggest_component:
tmp_post_patch = post_patch[..., 1:]
post_patch_mask = np.sum(tmp_post_patch, axis=-1) > 0.25
post_patch_mask = edit_volumes.get_largest_connected_component(
post_patch_mask)
post_patch_mask = np.stack([post_patch_mask] *
tmp_post_patch.shape[-1],
axis=-1)
tmp_post_patch = edit_volumes.mask_volume(tmp_post_patch,
mask=post_patch_mask)
post_patch[..., 1:] = tmp_post_patch
# reset posteriors to zero outside the largest connected component of each topological class
if topology_classes is not None:
post_patch_mask = post_patch > 0.25
for topology_class in np.unique(topology_classes)[1:]:
tmp_topology_indices = np.where(
topology_classes == topology_class)[0]
tmp_mask = np.any(post_patch_mask[..., tmp_topology_indices],
axis=-1)
tmp_mask = edit_volumes.get_largest_connected_component(tmp_mask)
for idx in tmp_topology_indices:
post_patch[..., idx] *= tmp_mask
# renormalise posteriors and get hard segmentation
if (post_patch_flip is not None) | keep_biggest_component | (
topology_classes is not None):
post_patch /= np.sum(post_patch, axis=-1)[..., np.newaxis]
seg_patch = post_patch.argmax(-1)
# paste patches back to matrix of original image size
if crop is not None:
seg = np.zeros(shape=pad_shape, dtype='int32')
posteriors = np.zeros(shape=[*pad_shape, segmentation_labels.shape[0]])
posteriors[...,
0] = np.ones(pad_shape) # place background around patch
if n_dims == 2:
seg[crop[0]:crop[2], crop[1]:crop[3]] = seg_patch
posteriors[crop[0]:crop[2], crop[1]:crop[3], :] = post_patch
elif n_dims == 3:
seg[crop[0]:crop[3], crop[1]:crop[4], crop[2]:crop[5]] = seg_patch
posteriors[crop[0]:crop[3], crop[1]:crop[4],
crop[2]:crop[5], :] = post_patch
else:
seg = seg_patch
posteriors = post_patch
seg = segmentation_labels[seg.astype('int')].astype('int')
if im_shape != pad_shape:
bounds = [int((p - i) / 2) for (p, i) in zip(pad_shape, im_shape)]
bounds += [p + i for (p, i) in zip(bounds, im_shape)]
seg = edit_volumes.crop_volume_with_idx(seg, bounds)
posteriors = edit_volumes.crop_volume_with_idx(posteriors,
bounds,
n_dims=n_dims)
# align prediction back to first orientation
if n_dims > 2:
seg = edit_volumes.align_volume_to_ref(seg,
aff=np.eye(4),
aff_ref=aff,
n_dims=n_dims,
return_aff=False)
posteriors = edit_volumes.align_volume_to_ref(posteriors,
aff=np.eye(4),
aff_ref=aff,
n_dims=n_dims)
return seg, posteriors
def preprocess_image(im_path,
n_levels,
target_res,
crop=None,
padding=None,
flip=False,
path_resample=None):
# read image and corresponding info
im, _, aff, n_dims, n_channels, header, im_res = utils.get_volume_info(
im_path, True)
# resample image if necessary
if target_res is not None:
target_res = np.squeeze(
utils.reformat_to_n_channels_array(target_res, n_dims))
if np.any((im_res > target_res + 0.05) | (im_res < target_res - 0.05)):
im_res = target_res
im, aff = edit_volumes.resample_volume(im, aff, im_res)
if path_resample is not None:
utils.save_volume(im, aff, header, path_resample)
# align image
im = edit_volumes.align_volume_to_ref(im,
aff,
aff_ref=np.eye(4),
n_dims=n_dims)
shape = list(im.shape)
# pad image if specified
if padding:
im = edit_volumes.pad_volume(im, padding_shape=padding)
pad_shape = im.shape[:n_dims]
else:
pad_shape = shape
# check that patch_shape or im_shape are divisible by 2**n_levels
if crop is not None:
crop = utils.reformat_to_list(crop, length=n_dims, dtype='int')
if not all([pad_shape[i] >= crop[i] for i in range(len(pad_shape))]):
crop = [min(pad_shape[i], crop[i]) for i in range(n_dims)]
if not all([size % (2**n_levels) == 0 for size in crop]):
crop = [
utils.find_closest_number_divisible_by_m(size, 2**n_levels)
for size in crop
]
else:
if not all([size % (2**n_levels) == 0 for size in pad_shape]):
crop = [
utils.find_closest_number_divisible_by_m(size, 2**n_levels)
for size in pad_shape
]
# crop image if necessary
if crop is not None:
im, crop_idx = edit_volumes.crop_volume(im,
cropping_shape=crop,
return_crop_idx=True)
else:
crop_idx = None
# normalise image
if n_channels == 1:
im = edit_volumes.rescale_volume(im,
new_min=0.,
new_max=1.,
min_percentile=0.5,
max_percentile=99.5)
else:
for i in range(im.shape[-1]):
im[..., i] = edit_volumes.rescale_volume(im[..., i],
new_min=0.,
new_max=1.,
min_percentile=0.5,
max_percentile=99.5)
# flip image along right/left axis
if flip & (n_dims > 2):
im_flipped = edit_volumes.flip_volume(im,
direction='rl',
aff=np.eye(4))
im_flipped = utils.add_axis(
im_flipped) if n_channels > 1 else utils.add_axis(im_flipped,
axis=[0, -1])
else:
im_flipped = None
# add batch and channel axes
im = utils.add_axis(im) if n_channels > 1 else utils.add_axis(im,
axis=[0, -1])
return im, aff, header, im_res, n_channels, n_dims, shape, pad_shape, crop_idx, im_flipped
def postprocess(prediction, crop_shape, pad_shape, im_shape, crop, n_dims, labels, keep_biggest_component,
aff, aff_ref='FS'):
# get posteriors and segmentation
post_patch = np.squeeze(prediction)
seg_patch = post_patch.argmax(-1)
# keep biggest connected component (use it with smoothing!)
if keep_biggest_component:
components, n_components = label(seg_patch)
if n_components > 1:
unique_components = np.unique(components)
size = 0
mask = None
for comp in unique_components[1:]:
tmp_mask = components == comp
tmp_size = np.sum(tmp_mask)
if tmp_size > size:
size = tmp_size
mask = tmp_mask
seg_patch[np.logical_not(mask)] = 0
# align prediction back to first orientation
if n_dims > 2:
if aff_ref == 'FS':
aff_ref = np.array([[-1., 0., 0., 0.], [0., 0., 1., 0.], [0., -1., 0., 0.], [0., 0., 0., 1.]])
seg_patch = edit_volumes.align_volume_to_ref(seg_patch, aff_ref, aff_ref=aff, return_aff=False)
post_patch = edit_volumes.align_volume_to_ref(post_patch, aff_ref, aff_ref=aff, n_dims=n_dims)
elif aff_ref == 'identity':
aff_ref = np.eye(4)
seg_patch = edit_volumes.align_volume_to_ref(seg_patch, aff_ref, aff_ref=aff, return_aff=False)
post_patch = edit_volumes.align_volume_to_ref(post_patch, aff_ref, aff_ref=aff, n_dims=n_dims)
elif aff_ref == 'MS':
aff_ref = np.array([[-1., 0., 0., 0.], [0., -1., 0., 0.], [0., 0., 1., 0.], [0., 0., 0., 1.]])
seg_patch = edit_volumes.align_volume_to_ref(seg_patch, aff_ref, aff_ref=aff, return_aff=False)
post_patch = edit_volumes.align_volume_to_ref(post_patch, aff_ref, aff_ref=aff, n_dims=n_dims)
# paste patches back to matrix of original image size
if crop_shape is not None:
seg = np.zeros(shape=pad_shape, dtype='int32')
posteriors = np.zeros(shape=[*pad_shape, labels.shape[0]])
posteriors[..., 0] = np.ones(pad_shape) # place background around patch
if n_dims == 2:
seg[crop[0]:crop[2], crop[1]:crop[3]] = seg_patch
posteriors[crop[0]:crop[2], crop[1]:crop[3], :] = post_patch
elif n_dims == 3:
seg[crop[0]:crop[3], crop[1]:crop[4], crop[2]:crop[5]] = seg_patch
posteriors[crop[0]:crop[3], crop[1]:crop[4], crop[2]:crop[5], :] = post_patch
else:
seg = seg_patch
posteriors = post_patch
seg = labels[seg.astype('int')].astype('int')
if im_shape != pad_shape:
lower_bound = [int((p-i)/2) for (p, i) in zip(pad_shape, im_shape)]
upper_bound = [p-int((p-i)/2) for (p, i) in zip(pad_shape, im_shape)]
if n_dims == 2:
seg = seg[lower_bound[0]:upper_bound[0], lower_bound[1]:upper_bound[1]]
elif n_dims == 3:
seg = seg[lower_bound[0]:upper_bound[0], lower_bound[1]:upper_bound[1], lower_bound[2]:upper_bound[2]]
return seg, posteriors
def preprocess_image(im_path, n_levels, crop_shape=None, padding=None, aff_ref='FS'):
# read image and corresponding info
im, shape, aff, n_dims, n_channels, header, im_res = utils.get_volume_info(im_path, return_volume=True)
if padding:
if n_channels == 1:
im = np.pad(im, padding, mode='constant')
pad_shape = im.shape
else:
im = np.pad(im, tuple([(padding, padding)] * n_dims + [(0, 0)]), mode='constant')
pad_shape = im.shape[:-1]
else:
pad_shape = shape
# check that patch_shape or im_shape are divisible by 2**n_levels
if crop_shape is not None:
crop_shape = utils.reformat_to_list(crop_shape, length=n_dims, dtype='int')
if not all([pad_shape[i] >= crop_shape[i] for i in range(len(pad_shape))]):
crop_shape = [min(pad_shape[i], crop_shape[i]) for i in range(n_dims)]
print('cropping dimensions are higher than image size, changing cropping size to {}'.format(crop_shape))
if not all([size % (2**n_levels) == 0 for size in crop_shape]):
crop_shape = [utils.find_closest_number_divisible_by_m(size, 2 ** n_levels) for size in crop_shape]
else:
if not all([size % (2**n_levels) == 0 for size in pad_shape]):
crop_shape = [utils.find_closest_number_divisible_by_m(size, 2 ** n_levels) for size in pad_shape]
# crop image if necessary
if crop_shape is not None:
crop_idx = np.round((pad_shape - np.array(crop_shape)) / 2).astype('int')
crop_idx = np.concatenate((crop_idx, crop_idx + crop_shape), axis=0)
im = edit_volumes.crop_volume_with_idx(im, crop_idx=crop_idx)
else:
crop_idx = None
# align image to training axes and directions
if n_dims > 2:
if aff_ref == 'FS':
aff_ref = np.array([[-1., 0., 0., 0.], [0., 0., 1., 0.], [0., -1., 0., 0.], [0., 0., 0., 1.]])
im = edit_volumes.align_volume_to_ref(im, aff, aff_ref=aff_ref, return_aff=False)
elif aff_ref == 'identity':
aff_ref = np.eye(4)
im = edit_volumes.align_volume_to_ref(im, aff, aff_ref=aff_ref, return_aff=False)
elif aff_ref == 'MS':
aff_ref = np.array([[-1., 0., 0., 0.], [0., -1., 0., 0.], [0., 0., 1., 0.], [0., 0., 0., 1.]])
im = edit_volumes.align_volume_to_ref(im, aff, aff_ref=aff_ref, return_aff=False)
# normalise image
if n_channels == 1:
m = np.min(im)
M = np.max(im)
if M == m:
im = np.zeros(im.shape)
else:
im = (im - m) / (M - m)
if n_channels > 1:
for i in range(im.shape[-1]):
channel = im[..., i]
m = np.min(channel)
M = np.max(channel)
if M == m:
im[..., i] = np.zeros(channel.shape)
else:
im[..., i] = (channel - m) / (M - m)
# add batch and channel axes
if n_channels > 1:
im = utils.add_axis(im)
else:
im = utils.add_axis(im, -2)
return im, aff, header, im_res, n_channels, n_dims, shape, pad_shape, crop_shape, crop_idx