def degrade_line(im, eta=0, alpha=1.7, beta=1.7, alpha_0=1, beta_0=1):
"""
Degrades a line image by adding noise
Args:
im (PIL.Image): Input image
Returns:
PIL.Image in mode 'L'
"""
im = pil2array(im)
im = np.amax(im) - im
im = im * 1.0 / np.amax(im)
# foreground distance transform and flipping to white probability
fg_dist = distance_transform_cdt(im, metric='taxicab')
fg_prob = alpha_0 * np.exp(-alpha * (fg_dist**2)) + eta
fg_prob[im == 0] = 0
fg_flip = np.random.binomial(1, fg_prob)
# background distance transform and flipping to black probability
bg_dist = distance_transform_cdt(1 - im, metric='taxicab')
bg_prob = beta_0 * np.exp(-beta * (bg_dist**2)) + eta
bg_prob[im == 1] = 0
bg_flip = np.random.binomial(1, bg_prob)
# flip
im -= fg_flip
im += bg_flip
# use a circular kernel of size 3
sel = np.array([[1, 1], [1, 1]])
im = binary_closing(im, sel)
return array2pil(255 - im.astype('B') * 255)
def compute_error(self,
true_mask: Mask,
pred_mask: Mask,
c: int = 5,
p: float = 2):
""" Compute the Baddeley Error for binary images.
Note:
A.J. Baddeley - "An Error Metric for Binary Images"
"""
# Ensure that masks have binary values
true_mask = true_mask > 0
pred_mask = pred_mask > 0
# Handle masks filled with the same value
xor_mask = true_mask ^ pred_mask
if (~xor_mask).all(): # Masks equal
return 1.0
elif xor_mask.all(): # Masks completely different
return 0.0
# Compute metric
true_edt = distance_transform_cdt(true_mask,
metric='taxicab').astype(float)
true_edt = np.minimum(true_edt, c)
true_edt[true_edt <
0] = c # where a distance cannot be computed, set to maximum
pred_edt = distance_transform_cdt(pred_mask,
metric='taxicab').astype(float)
pred_edt = np.minimum(pred_edt, c)
pred_edt[pred_edt < 0] = c
dist = np.abs(true_edt - pred_edt)
dist /= c # c is the maximum possible distance
dist = (dist**p).mean()**(1 / p)
return 1.0 - dist
def __init__(self,
img_mask_name,
crop_sz=(64, 64),
num_data=10000,
transform=None):
"""
Args:
img_mask_name: list of name pairs of image and mask data, each pair is a tuple of (img_name, mask_name)
For mask, 1-positive samples, 0-negative samples
crop_sz: cropping size
num_data: generated sample size
transform: data augmentation
"""
self.img_all = {}
self.mask_all = {}
self.seg_all = {
} # segmented image, used as a reference to generate training samples by random cropping
self.num_pairs = len(img_mask_name)
for i in range(self.num_pairs):
curr_name = img_mask_name[i]
assert os.path.exists(curr_name[0]) and os.path.exists(curr_name[1]), \
'Image or mask does not exist!'
img = imread(curr_name[0])
thres = threshold_triangle(img)
seg_img = np.zeros(img.shape, dtype=img.dtype)
seg_img[img > thres] = 1
self.seg_all[str(i)] = seg_img
img = img.astype(float)
mu = img.mean(axis=(1, 2))
sigma = img.std(axis=(1, 2))
img = (img - mu.reshape(len(mu), 1, 1)) / sigma.reshape(
len(sigma), 1, 1)
self.img_all[str(i)] = img
msk_data = np.load(curr_name[1], allow_pickle=True).tolist()
mask = msk_data['masks']
mask[mask != -1] = 1
mask[mask == -1] = 0
obj_dist = distance_transform_cdt(mask, metric='chessboard')
bg = np.zeros(mask.shape, dtype=mask.dtype)
bg[mask == 0] = 1
bg_dist = distance_transform_cdt(bg, metric='chessboard')
bg_dist[bg_dist > 4] = 4
mask_dist = (obj_dist - bg_dist).astype(float)
self.mask_all[str(i)] = mask_dist
self.crop_sz = crop_sz
self.num_data = num_data
self.transform = transform
def create_dt_mask(self, pnum, grid_size):
batch_mask = np.zeros(
[pnum, grid_size * grid_size],
dtype=np.float32) # Initialize your array of zeros
for i in range(pnum):
mask = np.zeros([grid_size, grid_size],
dtype=np.float32) # Initialize your array of zeros
thera = 1.0 * i / pnum * 2 * 3.1416
x = np.cos(thera)
y = -np.sin(thera)
x = (0.7 * x + 1) / 2
y = (0.7 * y + 1) / 2
mask[np.clip(np.floor(y * (grid_size - 1)), 0, grid_size -
1).astype(int),
np.clip(np.floor(x * (grid_size - 1)), 0, grid_size -
1).astype(int)] = 1
dt_mask = grid_size - distance_transform_cdt(
1 - mask, metric='taxicab').astype(np.float32)
dt_mask[dt_mask < grid_size - 15] = 0
batch_mask[i] = dt_mask.reshape(-1)
return batch_mask
def get_weight(polygon_targets):
batch_targets = []
for b in range(polygon_targets.shape[0]):
target_ins = []
for p in polygon_targets[b]:
t = np.zeros(h * w + 1)
t[p] = 1
if p != h * w:
spatial_part = t[:-1].reshape(h, w)
spatial_part = -1 * (spatial_part - 1)
spatial_part = distance_transform_cdt(
spatial_part, metric='taxicab').astype(np.float32)
spatial_part = np.clip(spatial_part, 0, dt_threshold)
spatial_part /= dt_threshold
spatial_part = -1. * (spatial_part - 1.)
spatial_part /= np.sum(spatial_part)
spatial_part = spatial_part.flatten()
t = np.concatenate([spatial_part, [0.]], axis=-1)
target_ins.append(t.astype(np.float32))
batch_targets.append(target_ins)
batch_targets = np.array(batch_targets).astype(np.float32)
batch_targets = torch.from_numpy(batch_targets).reshape(
batch_size, -1, h * w + 1).to(polygon_targets.device)
return batch_targets
def load(self, index):
if index < len(self.images) and index < len(
self.gt_segmentations) and index < len(self.gt_boundaries):
image = np.copy(self.images[index])
gt_segmentation = np.copy(self.gt_segmentations[index])
gt_boundary = np.copy(self.gt_boundaries[index])
else:
image = scipy.misc.imread(self.image_filenames[index],
flatten=False).astype(float)
if self.equalize_histogram:
histmin, histmax = get_isbi_dataset_intensity_min_max(
self.image_filenames[index])
image = do_equalize_histogram(image,
histmin=histmin,
histmax=histmax)
gt_segmentation = None
gt_boundary = None
if len(self.gt_filenames) > index:
gt_segmentation = scipy.misc.imread(self.gt_filenames[index],
flatten=False)
boundary_pixels = np.ones(gt_segmentation.shape, dtype=bool)
boundary_pixels[0:-1, :] &= (
gt_segmentation[0:-1, :] == gt_segmentation[1:, :])
boundary_pixels[1:, :] &= (
gt_segmentation[1:, :] == gt_segmentation[0:-1, :])
boundary_pixels[:, 0:-1] &= (
gt_segmentation[:, 0:-1] == gt_segmentation[:, 1:])
boundary_pixels[:, 1:] &= (
gt_segmentation[:, 1:] == gt_segmentation[:, 0:-1])
gt_boundary = distance_transform_cdt(
boundary_pixels, metric='taxicab').astype(float)
gt_boundary[gt_boundary > self.dt_bound] = self.dt_bound
gt_segmentation = (gt_segmentation > 0.5)
gt_segmentation = gt_segmentation.astype(float)
return (image, gt_segmentation, gt_boundary)
def skeleton2graph(dendrite_id, dendrite_folder, seg, res, shrink=False):
print('generate graph from skeleton ..')
skel = ReadSkeletons(dendrite_folder,
skeleton_algorithm='thinning',
downsample_resolution=res,
read_edges=True)[1]
sz = seg.shape
# bb = GetBbox(seg>0)
bb = GetBbox(seg == int(dendrite_id))
seg_b = seg[bb[0]:bb[1] + 1, bb[2]:bb[3] + 1, bb[4]:bb[5] + 1]
dt = distance_transform_cdt(seg_b, return_distances=True)
new_graph, wt_dict, th_dict, ph_dict = GetGraphFromSkeleton(
skel,
dt=dt,
dt_bb=[bb[x] for x in [0, 2, 4]],
modified_bfs=modified_bfs)
edge_list = GetEdgeList(new_graph, wt_dict, th_dict, ph_dict)
G = nx.Graph(shape=sz)
# add edge attributes
G.add_edges_from(edge_list)
if shrink == True: #shrink graph size
edgTh = [40, 1] # threshold
n0 = len(G.nodes())
G = ShrinkGraph_v2(G, threshold=edgTh)
n1 = len(G.nodes())
print('#nodes: %d -> %d' % (n0, n1))
return G, skel
def getEdgeDistByMask(self, mask3D, setID, sigma=4.5):
result = Preprocessor.loadThresholdMask(setID)
#result = generic_gradient_magnitude(result, sobel).astype(np.float32)
#result = nd.filters.gaussian_filter(result, sigma)
result = morph.distance_transform_cdt(result, metric='taxicab').astype(
np.float32)
return result[mask3D]
def get_indeces(image_path):
# Load image from path
Image = io.loadmat(image_path)
Label = np.zeros(Image['scanROI'].shape)
Label[Image['goldROI'] == 2] = 1
Scan = Image["scanROI"]
Dims = np.prod(Scan.shape)
# units = np.divide(Image['scanROI'].shape, 100.0)
# max = np.array([0.9854, 0.7775, 0.6922])
# min = np.array([0.4995, 0.1120, 0.0538])
# xl, yl, zl = np.around(np.multiply(Scan.shape, max))
# xu, yu, zu = np.int32(np.floor(np.multiply(Scan.shape, min)))
#
# cropped = np.squeeze(np.where(Label[xu:xl, yu:yl, zu:zl] >= 0))
# X = np.asarray([cropped[0] +xu, cropped[1]+yu , cropped[2] + zu])
B = morphology.distance_transform_cdt(np.absolute(Label - 1))
B = B.reshape(Dims)
X = np.squeeze(np.where(B < 6))
Inds = np.asarray(np.unravel_index(X, Scan.shape, order='C'))
return Inds.T, Label, Image
def CompactLabel(Label, Compaction=3):
"""Re-labels objects that have multiple non-contiguous portions to create
a new label image where each object is contiguous.
Parameters:
-----------
Label : array_like
A uint32 type label image generated by segmentation methods.
Compaction : int
Factor used in compacting objects to remove thin spurs. Refered to as
'd' in the reference below. Default value = 3.
Notes:
------
Implemented from the reference below.
Returns:
--------
Split : array_like
A uint32 label where discontiguous objects are split and relabeled.
See Also:
---------
AreaOpenLabel, CondenseLabel, ShuffleLabel, SplitLabel, WidthOpenLabel
References:
-----------
.. [1] S. Weinert et al "Detection and Segmentation of Cell Nuclei in
Virtual Microscopy Images: A Minimum-Model Approach" in Nature Scientific
Reports,vol.2,no.503, doi:10.1038/srep00503, 2012.
"""
# copy input image
Compact = Label.copy()
# generate distance map of label image
D = mp.distance_transform_cdt(Compact > 0, metric='taxicab')
# define 4-neighbors filtering kernel
Kernel = np.zeros((3, 3), dtype=np.bool)
Kernel[1, :] = True
Kernel[:, 1] = True
# sweep over distance values from d-1 to 1
for i in np.arange(Compaction-1, 0, -1):
# four-neighbor maxima of distance transform
MaxD = ft.maximum_filter(D, footprint=Kernel)
# identify pixels whose max 4-neighbor is less than i+1
Decrement = (D == i) & (MaxD < i+1)
# decrement non-compact pixels
D[Decrement] -= 1
# zero label pixels where D == 0
Compact[D == 0] = 0
return Compact
def Sampling(image_path):
"""
:param image_path: path to image generated by get_paths
:param patch_sizes: a list or array of patch sizes desired for convolution. Must be odd > 1.
:param total_sample_size: sampled patches for convolution, and corresponding labels
:return: sampled patches for convolution, and corresponding labels
"""
# Load image from path
Image = io.loadmat(image_path)
# Extract total number of voxels
Dims = np.prod(Image['scan'].shape)
# Create 1 mask image
Label = (Image['Tibia'] + 2 * Image['Femur'])
np.place(Label, Label > 2, [2, 1])
if Image['isright'] == 0:
Scan = np.fliplr(Image["scan"])
Label = np.fliplr(Label)
else:
Scan = Image["scan"]
Label2 = (Image['Tibia'] + Image['Femur'])
B = morphology.distance_transform_cdt(np.absolute(Label2 - 1))
B = B.reshape(Dims)
X = np.float32(range(np.max(B), 3, -1)) / range(4, np.max(B) + 1, 1)
No_samples = 18000
Index = np.array([])
samples = np.divide(X, sum(X)) * No_samples
for i in range(4, np.max(B) + 1):
Index = np.int32(
np.append(
Index,
np.random.choice(np.squeeze(np.where(B == i)),
(samples[i - 4]),
replace=False)))
Label = Label.reshape(Dims)
# Find indexes of voxels to sample
Gold_ind = np.squeeze(np.where(Label == 1))
Silv_ind = np.squeeze(np.where(Label == 2))
Edge_ind = np.squeeze(np.where((B > 0) & (B <= 2)))
Index = np.hstack((Gold_ind, Silv_ind, Edge_ind, Index))
np.random.shuffle(Index)
Inds = np.asarray(np.unravel_index(Index, Scan.shape, order='C'))
Label_Sample = Label[Index]
return Scan, Label_Sample, Inds.T
def degrade_line(im, eta=0.0, alpha=1.5, beta=1.5, alpha_0=1.0, beta_0=1.0):
"""
Degrades a line image by adding noise.
For parameter meanings consult [1].
Args:
im (PIL.Image): Input image
eta (float):
alpha (float):
beta (float):
alpha_0 (float):
beta_0 (float):
Returns:
PIL.Image in mode '1'
"""
logger.debug('Inverting and normalizing input image')
im = pil2array(im)
im = np.amax(im) - im
im = im * 1.0 / np.amax(im)
logger.debug('Calculating foreground distance transform')
fg_dist = distance_transform_cdt(1 - im, metric='taxicab')
logger.debug('Calculating flip to white probability')
fg_prob = alpha_0 * np.exp(-alpha * (fg_dist**2)) + eta
fg_prob[im == 1] = 0
fg_flip = np.random.binomial(1, fg_prob)
logger.debug('Calculating background distance transform')
bg_dist = distance_transform_cdt(im, metric='taxicab')
logger.debug('Calculating flip to black probability')
bg_prob = beta_0 * np.exp(-beta * (bg_dist**2)) + eta
bg_prob[im == 0] = 0
bg_flip = np.random.binomial(1, bg_prob)
# flip
logger.debug('Flipping')
im -= bg_flip
im += fg_flip
logger.debug('Binary closing')
sel = np.array([[1, 1], [1, 1]])
im = binary_closing(im, sel)
logger.debug('Converting to image')
return array2pil(255 - im.astype('B') * 255)
def degrade_line(im, eta=0.0, alpha=1.5, beta=1.5, alpha_0=1.0, beta_0=1.0):
"""
Degrades a line image by adding noise.
For parameter meanings consult [1].
Args:
im (PIL.Image): Input image
eta (float):
alpha (float):
beta (float):
alpha_0 (float):
beta_0 (float):
Returns:
PIL.Image in mode '1'
"""
logger.debug(u'Inverting and normalizing input image')
im = pil2array(im)
im = np.amax(im)-im
im = im*1.0/np.amax(im)
logger.debug(u'Calculating foreground distance transform')
fg_dist = distance_transform_cdt(1-im, metric='taxicab')
logger.debug(u'Calculating flip to white probability')
fg_prob = alpha_0 * np.exp(-alpha * (fg_dist**2)) + eta
fg_prob[im == 1] = 0
fg_flip = np.random.binomial(1, fg_prob)
logger.debug(u'Calculating background distance transform')
bg_dist = distance_transform_cdt(im, metric='taxicab')
logger.debug(u'Calculating flip to black probability')
bg_prob = beta_0 * np.exp(-beta * (bg_dist**2)) + eta
bg_prob[im == 0] = 0
bg_flip = np.random.binomial(1, bg_prob)
# flip
logger.debug(u'Flipping')
im -= bg_flip
im += fg_flip
logger.debug(u'Binary closing')
sel = np.array([[1, 1], [1, 1]])
im = binary_closing(im, sel)
logger.debug(u'Converting to image')
return array2pil(255-im.astype('B')*255)
def Sampling(image_path):
"""
:param image_path: path to image generated by get_paths
:param patch_sizes: a list or array of patch sizes desired for convolution. Must be odd > 1.
:param total_sample_size: sampled patches for convolution, and corresponding labels
:return: sampled patches for convolution, and corresponding labels
"""
# Load image from path
Image = io.loadmat(image_path)
# Extract total number of voxels
Dims = np.prod(Image['scanROI'].shape)
# Create 1 mask image
Label = np.zeros(Image['scanROI'].shape)
Label[Image['goldROI'] == 2] = 1
Scan = Image["scanROI"]
#max = np.array([0.9854, 0.7775, 0.6922])
#min = np.array([0.4995, 0.1120, 0.0538])
#xl, yl, zl =np.int32(np.around(np.multiply(Scan.shape, max)))
#xu, yu, zu = np.int32(np.floor(np.multiply(Scan.shape, min)))
#cropped = np.squeeze(np.where(Label[xu:xl, yu:yl, zu:zl] >= 0))
#X = np.asarray([cropped[0] +xu, cropped[1]+yu , cropped[2] + zu])
# MM = np.ravel_multi_index(X, np.asarray(Scan.shape))
B = morphology.distance_transform_cdt(np.absolute(Label - 1))
B = B.reshape(Dims)
# Gold_ind = np.squeeze(np.where(Label == 1 ))
# X = np.float32(range(np.max(B), 1, -1))/range(2, np.max(B)+1, 1)
# No_samples = np.shape(Gold_ind)[1]
# A = B[MM]
# Index = np.array([])
# samples = np.divide(X, sum(X))*No_samples
# for i in range(2, np.max(A)):
# Index = np.int32(np.append(Index, np.random.choice(np.squeeze(np.where(A == i)),(np.floor(samples)[i-1]), replace=False)))
Label = Label.reshape(Dims)
# Find indexes of voxels to sample
Gold_ind = np.squeeze(np.where(Label == 1))
Indeg = np.int32(
np.random.choice(np.squeeze(Gold_ind), 1000, replace=False))
P_ind = np.squeeze(np.where(np.logical_and(B > 0, B < 6)))
Index = np.int32(np.random.choice(np.squeeze(P_ind), 1000, replace=False))
Index = np.hstack((Index, Indeg))
np.random.shuffle(Index)
Inds = np.asarray(np.unravel_index(Index, Scan.shape, order='C'))
Indie = Inds.reshape(3, 1, Inds.shape[1]).T
Label_Sample = Label[Index]
return Scan, Label_Sample, Inds.T
def roi_track_counts(fdpy,fref,fatlas,roi_no,dist_transf=True,fres=None):
dpr=Dpy(fdpy,'r')
T=dpr.read_tracks()
dpr.close()
img=nib.load(fref)
affine=img.get_affine()
zooms = img.get_header().get_zooms()
iaffine=np.linalg.inv(affine)
T2=[]
#go back to volume space
for t in T:
T2.append(np.dot(t,iaffine[:3,:3].T)+iaffine[:3,3])
del T
tcs,tes=track_counts(T2,img.get_shape(),zooms,True)
atlas_img=nib.load(fatlas)
atlas=atlas_img.get_data()
roi=atlas.copy()
roi[atlas!=roi_no]=0
if dist_transf:
roi2=distance_transform_cdt(roi)
roi[roi2!=roi2.max()]=0
I=np.array(np.where(roi==roi_no)).T
else:
I=np.array(np.where(roi==roi_no)).T
"""
if erosion_level>0:
roi2=binary_erosion(roi,cross,erosion_level)
I=np.array(np.where(roi2==True)).T
else:
roi2=distance_transform_cdt(roi)
I=np.array(np.where(roi==roi_no)).T
"""
#print I.shape
#nib.save(nib.Nifti1Image(roi2,affine),'/tmp/test.nii.gz')
Ttes=[]
for iroi in I:
try:
Ttes.append(tes[tuple(iroi)])
except KeyError:
pass
Ttes=list(set(list(chain.from_iterable(Ttes))))
T2n=np.array(T2,dtype=np.object)
res=list(T2n[Ttes])
#back to world space
res2=[]
for t in res:
res2.append(np.dot(t,affine[:3,:3].T)+affine[:3,3])
np.save(fres,np.array(res2,dtype=np.object))
def main():
H, W = MAP()
A = [INPUT() for _ in range(H)]
# A : 2 次元 numpy 配列. 白マス -> True, 黒マス -> False
A = np.array([[(Ai[j] != "#") for j in range(W)] for Ai in A])
# distance_transform_cdt(X) : 2 次元 numpy 配列 X の要素 0 からの距離を要素に持つ 2 次元 numpy 配列を返す.
# [metric] taxicab : マンハッタン距離 (4 近傍), chessboard : チェビシェフ距離 (8 近傍)
print(distance_transform_cdt(A, metric="taxicab").max())
def Sampling(image_path):
"""
:param image_path: path to image generated by get_paths
:param patch_sizes: a list or array of patch sizes desired for convolution. Must be odd > 1.
:param total_sample_size: sampled patches for convolution, and corresponding labels
:return: sampled patches for convolution, and corresponding labels
"""
# Load image from path
Image = io.loadmat(image_path)
# Extract total number of voxels
Dims = np.prod(Image['scanROI'].shape)
# Create 1 mask image
Label = np.zeros(Image['scanROI'].shape)
# Label[Image['classIm'] == 1] = 1
Label[Image['classIm'] == 1] = 1
if Image['isright'] == 0:
Scan = np.fliplr(Image["scanROI"])
Label = np.fliplr(Label)
else:
Scan = Image["scanROI"]
Gold_ind = np.squeeze(np.where(Label == 1))
B = morphology.distance_transform_cdt(np.absolute(Label - 1))
B = B.reshape(Dims)
X = np.float32(range(np.max(B), 1, -1)) / range(2, np.max(B) + 1, 1)
No_samples = Gold_ind.shape[1]
Index = np.array([])
samples = np.divide(X, sum(X)) * No_samples
for i in range(2, np.max(B)):
Index = np.int32(
np.append(
Index,
np.random.choice(np.squeeze(np.where(B == i)),
(samples[i - 1]),
replace=False)))
Label = Label.reshape(Dims)
# Find indexes of voxels to sample
Gold_ind = np.squeeze(np.where(Label == 1))
P_ind = np.squeeze(np.where(B > 1) & (B < 5))
Index = np.hstack((Gold_ind, Index, P_ind))
print Index.shape
np.random.shuffle(Index)
Inds = np.asarray(np.unravel_index(Index, Scan.shape, order='C'))
Label_Sample = Label[Index]
return Scan, Label_Sample, Inds.T
def DistanceWithoutNormalise(bin_image):
res = np.zeros_like(bin_image)
for j in range(1, bin_image.max() + 1):
one_cell = np.zeros_like(bin_image)
one_cell[bin_image == j] = 1
one_cell = distance_transform_cdt(one_cell)
res[bin_image == j] = one_cell[bin_image == j]
res = res.astype('uint8')
return res
def DistanceWithoutNormalise(bin_image):
res = np.zeros_like(bin_image)
for j in range(1, bin_image.max() + 1):
one_cell = np.zeros_like(bin_image)
one_cell[bin_image == j] = 1
one_cell = distance_transform_cdt(one_cell)
res[bin_image == j] = one_cell[bin_image == j]
res = res.astype('uint8')
return res
def process(inp):
(indir, outdir, basename) = inp
print(inp)
labelmap = np.array(Image.open(osp.join(indir, basename)
).convert("P")).astype(np.int16)
labelmap = _encode_label(labelmap)
depth_map = np.zeros(labelmap.shape, dtype=np.float32)
dir_map = np.zeros((*labelmap.shape, 2), dtype=np.float32)
for id in range(255):
labelmap_i = (labelmap == id).astype(np.uint8)
if labelmap_i.sum() < 100:
continue
if args.metric == 'euc':
depth_i = distance_transform_edt(labelmap_i)
elif args.metric == 'taxicab':
depth_i = distance_transform_cdt(labelmap_i, metric='taxicab')
else:
raise RuntimeError
depth_map += depth_i
dir_i_before = dir_i = np.zeros_like(dir_map)
dir_i = torch.nn.functional.conv2d(torch.from_numpy(depth_i).float().view(
1, 1, *depth_i.shape), sobel_ker, padding=ksize//2).squeeze().permute(1, 2, 0).numpy()
# The following line is necessary
dir_i[(labelmap_i == 0), :] = 0
dir_map += dir_i
depth_map[depth_map > 250] = 250
depth_map = depth_map.astype(np.uint8)
deg_reduce = 2
dir_deg_map = np.degrees(np.arctan2(
dir_map[:, :, 0], dir_map[:, :, 1])) + 180
dir_deg_map = (dir_deg_map / deg_reduce)
print(dir_deg_map.min(), dir_deg_map.max())
dir_deg_map = dir_deg_map.astype(np.uint8)
io.savemat(
osp.join(outdir, basename.replace("png", "mat")),
{"dir_deg": dir_deg_map, "depth": depth_map, 'deg_reduce': deg_reduce},
do_compression=True,
)
try:
io.loadmat(osp.join(outdir, basename.replace("png", "mat")),)
except Exception as e:
print(e)
io.savemat(
osp.join(outdir, basename.replace("png", "mat")),
{"dir_deg": dir_deg_map, "depth": depth_map, 'deg_reduce': deg_reduce},
do_compression=False,
)
def process(inp):
(indir, outdir, basename) = inp
print(inp)
labelmap = np.array(Image.open(osp.join(indir, basename)))
depth_map = np.ones(labelmap.shape) * 0
dir_map = np.zeros((*labelmap.shape, 2))
ignore_id_list = set(range(256)) - label_list
for id in ignore_id_list:
labelmap[labelmap == id] = 255
labelmap_flattened = np.unique(labelmap)
print(labelmap_flattened)
for id in labelmap_flattened:
labelmap_i = labelmap.copy()
labelmap_i[labelmap != id] = 0
labelmap_i[labelmap == id] = 1
# if labelmap_i.sum() < 100:
# continue
if args.metric == 'euc':
depth_i = distance_transform_edt(labelmap_i)
elif args.metric == 'taxicab':
depth_i = distance_transform_cdt(labelmap_i, metric='taxicab')
else:
raise RuntimeError
depth_map[labelmap_i == 1] = depth_i[labelmap_i == 1]
dir_i_before = dir_i = np.zeros_like(dir_map)
dir_i = torch.nn.functional.conv2d(
torch.from_numpy(depth_i).float().view(1, 1, *depth_i.shape),
sobel_ker,
padding=ksize // 2).squeeze().permute(1, 2, 0).numpy()
# The following line is necessary
dir_i[(labelmap_i == 0), :] = 0
dir_map += dir_i
depth_map[depth_map > 250] = 250
depth_map = depth_map.astype(np.uint8)
# print(np.unique(depth_map))
deg_reduce = 2
dir_deg_map = np.degrees(np.arctan2(dir_map[:, :, 0], dir_map[:, :,
1])) + 180
dir_deg_map = (dir_deg_map / deg_reduce)
print(dir_deg_map.min(), dir_deg_map.max())
dir_deg_map = dir_deg_map.astype(np.uint8)
dct = {
"dir_deg": dir_deg_map,
"depth": depth_map,
'deg_reduce': deg_reduce
}
safe_savemat(osp.join(outdir, basename.replace("png", "mat")), dct)
def get_skeleton(seg_fn, out_folder, bfs, res, edgTh, modified_bfs, opt):
if opt == '0': # mesh -> skeleton
seg = ReadH5(seg_fn, 'main')
CreateSkeleton(seg, out_folder, res, res)
elif opt == '1': # skeleton -> dense graph
import networkx as nx
print('read skel')
skel = ReadSkeletons(out_folder,
skeleton_algorithm='thinning',
downsample_resolution=res,
read_edges=True)[1]
print('save node positions')
node_pos = np.stack(skel.get_nodes()).astype(int)
WriteH5(out_folder + 'node_pos.h5', node_pos)
print('generate dt for edge width')
seg = ReadH5(seg_fn, 'main')
sz = seg.shape
bb = GetBbox(seg > 0)
seg_b = seg[bb[0]:bb[1] + 1, bb[2]:bb[3] + 1, bb[4]:bb[5] + 1]
dt = distance_transform_cdt(seg_b, return_distances=True)
print('generate graph')
new_graph, wt_dict, th_dict, ph_dict = GetGraphFromSkeleton(skel, dt=dt, dt_bb=[bb[x] for x in [0,2,4]],\
modified_bfs=modified_bfs)
print('save as a networkx object')
edge_list = GetEdgeList(new_graph, wt_dict, th_dict, ph_dict)
G = nx.Graph(shape=sz)
# add edge attributes
G.add_edges_from(edge_list)
nx.write_gpickle(G, out_folder + 'graph-%s.obj' % (bfs))
elif opt == '2': # reduced graph
import networkx as nx
G = nx.read_gpickle(out_folder + 'graph-%s.obj' % (bfs))
n0 = len(G.nodes())
G = ShrinkGraph_v2(G, threshold=edgTh)
n1 = len(G.nodes())
print('#nodes: %d -> %d' % (n0, n1))
nx.write_gpickle(
G,
out_folder + 'graph-%s-%d-%d.obj' % (bfs, edgTh[0], 10 * edgTh[1]))
elif opt == '3': # generate h5 for visualization
import networkx as nx
G = nx.read_gpickle(out_folder + 'graph-%s-%d-%d.obj' %
(bfs, edgTh[0], 10 * edgTh[1]))
pos = ReadH5(out_folder + 'node_pos.h5', 'main')
vis = Graph2H5(G, pos)
WriteH5(
out_folder + 'graph-%s-%d-%d.h5' % (bfs, edgTh[0], 10 * edgTh[1]),
vis)
def Symlink_Mask(r, dst_rgb, dst_mask):
rgb = r['path_to_image']
#print rgb
mask_name = r['path_to_label']
symlink(rgb, join(dst_rgb, basename(rgb)))
mask = imread(mask_name)
line = generate_wsl(mask)
mask[mask > 0] = 1
mask[line > 0] = 0
mask = distance_transform_cdt(mask)
imsave(join(dst_mask, basename(mask_name)), mask)
def dt_image(shape, vertices, thresh=5):
"""
Create a distance transform image given the size of
the canvas and vertices of the polygon. Any distance
less than the threshold is set to 0
"""
mask = create_polygon(shape, vertices, perimeter=True)
# Invert
mask = 1 - mask
dt_mask = distance_transform_cdt(mask, metric='taxicab').astype(np.float32)
dt_mask[dt_mask < thresh] = 0
return dt_mask
def DistanceBinNormalise(bin_image):
bin_image = label(bin_image)
result = np.zeros_like(bin_image, dtype="float")
for k in range(1, bin_image.max() + 1):
tmp = np.zeros_like(result, dtype="float")
tmp[bin_image == k] = 1
dist = distance_transform_cdt(tmp)
MAX = dist.max()
dist = dist.astype(float) / MAX
result[bin_image == k] = dist[bin_image == k]
result = result * 255
result = result.astype('uint8')
return result
def DistanceBinNormalise(bin_image):
bin_image = label(bin_image)
result = np.zeros_like(bin_image, dtype="float")
for k in range(1, bin_image.max() + 1):
tmp = np.zeros_like(result, dtype="float")
tmp[bin_image == k] = 1
dist = distance_transform_cdt(tmp)
MAX = dist.max()
dist = dist.astype(float) / MAX
result[bin_image == k] = dist[bin_image == k]
result = result * 255
result = result.astype('uint8')
return result
def dist_image(imf):
'''
Return the distance image 'imd' of 'imf'
imd[r,c] is the distance of pixel (r,c) to the closest edge pixel.
'''
imf_inv = 1 - (skimage.img_as_ubyte(imf) != 0)
imd = distance_transform_cdt(imf_inv)
# imd = cv2.distanceTransform(imf_inv ,cv2.DIST_L2,5)
# plt.imshow(imf_inv)
# plt.title('imf_inv')
# plt.figure()
# plt.imshow(imd)
# plt.title('imd')
# plt.colorbar()
return imd
def stringify_board(board):
t = {0: '*', 1: '.', 2: '.', 3: 'c'}
stringified_board = ['']
dt = distance_transform_cdt(board)
try:
candidate = np.argwhere(dt > 1)[0]
board[candidate[0], candidate[1]] = 3
except IndexError:
board[0, 0] = 3
for l in board:
stringified_board.append("".join([t[e] for e in l]))
return "\n".join(stringified_board)
def _augment(self, img, _):
img = np.copy(img)
orig_ann = img[..., 0] # instance ID map
fixed_ann = self._fix_mirror_padding(orig_ann)
# re-cropping with fixed instance id map
crop_ann = cropping_center(fixed_ann, self.crop_shape)
orig_dst = np.zeros(orig_ann.shape, dtype=np.float32)
inst_list = list(np.unique(crop_ann))
inst_list.remove(0) # 0 is background
for inst_id in inst_list:
inst_map = np.array(fixed_ann == inst_id, np.uint8)
inst_box = bounding_box(inst_map)
# expand the box by 2px
inst_box[0] -= 2
inst_box[2] -= 2
inst_box[1] += 2
inst_box[3] += 2
inst_map = inst_map[inst_box[0]:inst_box[1],
inst_box[2]:inst_box[3]]
if inst_map.shape[0] < 2 or \
inst_map.shape[1] < 2:
continue
# chessboard distance map generation
# normalize distance to 0-1
inst_dst = distance_transform_cdt(inst_map)
inst_dst = inst_dst.astype('float32')
if self.inst_norm:
max_value = np.amax(inst_dst)
if max_value <= 0:
continue # HACK: temporay patch for divide 0 i.e no nuclei (how?)
inst_dst = (inst_dst / np.amax(inst_dst))
####
dst_map_box = orig_dst[inst_box[0]:inst_box[1],
inst_box[2]:inst_box[3]]
dst_map_box[inst_map > 0] = inst_dst[inst_map > 0]
#
img = img.astype('float32')
img = np.dstack([img, orig_dst])
return img
def dt_targets_from_class(poly, grid_size, dt_threshold):
# grid_size: 28
# poly: 即Ground Truth, [bs, seq_len], 每行一个poly, seq_len个值, 每个值是在grid*gird中的index
"""
NOTE: numpy function!
poly: [bs, time_steps], each value in [0, grid*size**2+1)
grid_size: size of the grid the polygon is in
dt_threshold: threshold for smoothing in dt targets
returns:
full_targets: [bs, time_steps, grid_size**2+1] array containing
dt smoothed targets to be used for the polygon loss function
"""
full_targets = []
for b in range(poly.shape[0]):
targets = []
for p in poly[b]:
t = np.zeros(grid_size**2 + 1, dtype=np.int32)
t[p] += 1
if p != grid_size**2: #EOS
spatial_part = t[:-1]
spatial_part = np.reshape(spatial_part,
[grid_size, grid_size, 1])
# Invert image
spatial_part = -1 * (spatial_part - 1)
# Compute distance transform
spatial_part = distance_transform_cdt(spatial_part,
metric='taxicab').astype(
np.float32)
# Threshold
spatial_part = np.clip(spatial_part, 0, dt_threshold)
# Normalize
spatial_part /= dt_threshold
# Invert back
spatial_part = -1. * (spatial_part - 1.)
spatial_part /= np.sum(spatial_part)
spatial_part = spatial_part.flatten()
t = np.concatenate([spatial_part, [0.]], axis=-1)
targets.append(t.astype(np.float32))
full_targets.append(targets)
return np.array(full_targets, dtype=np.float32)
def from_t2(t2, mask, data_img, split, edge_n=None, grp_target=None):
""" scales effect with observations
Args:
t2 (float): ratio of effect to population variance
mask (Mask): effect location
data_img (DataImage):
grp_target: grp that effect is applied to
split (dict): keys are grp labels, values are sbj_list
edge_n (int): number of voxels on edge of mask (taxicab erosion)
which have a 'scaled' effect. For example, if edge_n
= 1, then the outermost layer of voxels has only half
the delta applied. see Effect.scale
"""
# get grp_tuple, grp_tuple[1] has effect applied
assert len(split) == 2, 'invalid split'
grp_tuple = sorted(split.keys())
if grp_target is not None:
assert grp_target in grp_tuple
if grp_target is not grp_tuple[1]:
grp_tuple = reversed(grp_tuple)
# get fs_dict
fs_dict = dict()
for grp, sbj_list in split.items():
fs_dict[grp] = data_img.get_fs(sbj_list=sbj_list, mask=mask)
delta, cov_pool, _, _ = get_t2_stats(fs_dict, grp_tuple=grp_tuple)
# compute scale
if edge_n is None:
scale = mask
else:
scale = distance_transform_cdt(mask,
metric='taxicab') / (edge_n + 1)
scale[scale >= 1] = 1
# build effect with proper direction
# todo: refactor all pool_cov -> cov_pool
eff = EffectConstant(mask=mask,
delta=delta,
pool_cov=cov_pool,
scale=scale)
# scale to given t2
return eff.to_t2(t2)
def fitAndDivide(roi_mask, brain_mask, t_map, nii, workdir, iteration):
if not os.path.exists(workdir + str(iteration)):
os.mkdir(workdir + str(iteration))
flat_data = t_map[roi_mask].ravel().squeeze()
(flat_active, selected_model) = fitMixture(flat_data)
print "winning model: %s"%selected_model
active_map = np.zeros(t_map.shape) == 1
active_map[roi_mask] = flat_active
new_img = nb.Nifti1Image(active_map, nii.get_affine(), nii.get_header())
nb.save(new_img, os.path.join(workdir + str(iteration), 'thr_map.nii'))
plt.show()
#26 connectivity
labeled_map, n_regions = label(active_map, generate_binary_structure(3,3))
print "%d disconnected regions"%n_regions
distances, indices = distance_transform_cdt(np.logical_not(active_map), metric='chessboard', return_distances=True, return_indices=True)
new_img = nb.Nifti1Image(distances, nii.get_affine(), nii.get_header())
nb.save(new_img, os.path.join(workdir+ str(iteration), 'distances.nii'))
labels = labeled_map[indices[0,:], indices[1,:], indices[2,:]]
for region_id in range(1,n_regions+1):
sub_roi_mask = np.zeros(t_map.shape) == 1
sub_roi_mask[np.logical_and(labels == region_id, roi_mask)] = True
activity_within_roi = (labeled_map == region_id)
new_img = nb.Nifti1Image(sub_roi_mask, nii.get_affine(), nii.get_header())
nb.save(new_img, os.path.join(workdir+ str(iteration), 'sub%d_roi_mask.nii'%region_id))
new_sub_roi_mask = extendROIMask(sub_roi_mask, activity_within_roi, brain_mask)
new_img = nb.Nifti1Image(new_sub_roi_mask, nii.get_affine(), nii.get_header())
nb.save(new_img, os.path.join(workdir+ str(iteration), 'new_sub%d_roi_mask.nii'%region_id))
if new_sub_roi_mask != sub_roi_mask:
fitAndDivide(new_sub_roi_mask, brain_mask, t_map, nii, workdir += , iteration+1)
def find_seed_centroids(stack):
"""Find seeds in given binary stack, returning dictionary containing seed
centroids."""
distances = distance_transform_cdt(stack)
seeds = distances > 10
seed_label_array = label(seeds)
seed_labels = {}
for seed_label in np.unique(seed_label_array):
float_center = map(np.mean, np.where(seed_label_array==seed_label))
int_center = map(int, float_center)
seed_name = 'seed{}'.format(seed_label)
seed_labels[seed_name] = int_center
return seed_labels
def get_roi_new(roi_no,dist_transf=False):
atlas_img=nib.load(fatlas)
atlas=atlas_img.get_data()
roiaff=atlas_img.get_affine()
roi=atlas.copy()
roi[atlas!=roi_no]=0
if dist_transf:
roi2=distance_transform_cdt(roi)
roi[roi2!=roi2.max()]=0
I=np.array(np.where(roi==roi_no)).T
else:
I=np.array(np.where(roi==roi_no)).T
wI=np.dot(roiaff[:3,:3],I.T).T+roiaff[:3,3]
wI=wI.astype('f4')
return wI
def spike_dt(data_file):
pm = PathManager(data_file, working_base='/localscratch/ct_analysis')
stack_path = pm.spath('raw_stack.stack')
z = 273
filename = "z{}.png".format(z)
full_path = os.path.join(stack_path, filename)
plane = Image.from_file(full_path)
threshold = threshold_otsu(plane)
thresholded = plane > threshold
imsave('t.png', thresholded)
dt = distance_transform_cdt(thresholded)
imsave('dt.png', dt)
print dt.max()
tdt = dt > 70
imsave('tdt.png', tdt)
def Sampling(image_path):
"""
:param image_path: path to image generated by get_paths
:param patch_sizes: a list or array of patch sizes desired for convolution. Must be odd > 1.
:param total_sample_size: sampled patches for convolution, and corresponding labels
:return: sampled patches for convolution, and corresponding labels
"""
Image = io.loadmat(image_path)
Scan = Image['Scan']
Label = np.zeros(Image['Label'].shape)
Label[Image['Label'] > 0] = 1
Gold_ind = np.squeeze(np.where(Label >= 1))
Dims = np.prod(Scan.shape)
B = morphology.distance_transform_cdt(np.absolute(Label - 1))
B = B.reshape(Dims)
X = np.float32(range(np.max(B), 1, -1)) / range(2, np.max(B) + 1, 1)
No_samples = Gold_ind.shape[1]
Index = np.array([])
samples = np.divide(X, sum(X)) * No_samples
for i in range(2, np.max(B)):
Index = np.int32(
np.append(
Index,
np.random.choice(np.squeeze(np.where(B == i)),
(samples[i - 1]),
replace=False)))
Label = Label.reshape(Dims)
Gold_ind = np.squeeze(np.where(Label >= 1))
# Find indexes of voxels to sample
P_ind = np.squeeze(np.where(B == 1))
Index = np.hstack((Gold_ind, Index, P_ind))
np.random.shuffle(Index)
Inds = np.asarray(np.unravel_index(Index, Scan.shape, order='C'))
Label_Sample = Label[Index]
return Scan, Label_Sample, Inds.T
def _get_surface_distance(self, y_pred_edges, y_edges):
"""
Calculate the surface distances from `y_pred_edges` to `y_edges`.
Args:
y_pred_edges (np.ndarray): the edge of the predictions.
y_edges (np.ndarray): the edge of the ground truth.
"""
if not np.any(y_pred_edges):
return np.array([])
if not np.any(y_edges):
dis = np.inf * np.ones_like(y_edges)
else:
if self.distance_metric == "euclidean":
dis = morphology.distance_transform_edt(~y_edges)
elif self.distance_metric == "chessboard" or self.distance_metric == "taxicab":
dis = morphology.distance_transform_cdt(~y_edges, metric=self.distance_metric)
surface_distance = dis[y_pred_edges]
return surface_distance
def _get_surface_distance(self, y_pred_edges, y_edges):
"""
Calculate the surface distances from `y_pred_edges` to `y_edges`.
Args:
y_pred_edges (np.ndarray): the edge of the predictions.
y_edges (np.ndarray): the edge of the ground truth.
"""
if not np.any(y_pred_edges):
return np.array([])
if not np.any(y_edges):
dis = np.full(y_edges.shape, np.inf)
else:
if self.distance_metric == "euclidean":
dis = morphology.distance_transform_edt(~y_edges)
elif self.distance_metric in self.distance_metric_list[-2:]:
dis = morphology.distance_transform_cdt(~y_edges, metric=self.distance_metric)
surface_distance = dis[y_pred_edges]
return surface_distance
print('read skel')
skel = ReadSkeletons(out_folder,
skeleton_algorithm='thinning',
downsample_resolution=res,
read_edges=True)[1]
print('save node positions')
node_pos = np.stack(skel.get_nodes()).astype(int)
WriteH5(out_folder + 'node_pos.h5', node_pos)
print('generate dt for edge width')
seg = ReadH5(seg_fn, 'main')
sz = seg.shape
bb = GetBbox(seg > 0)
seg_b = seg[bb[0]:bb[1] + 1, bb[2]:bb[3] + 1, bb[4]:bb[5] + 1]
dt = distance_transform_cdt(seg_b, return_distances=True)
print('generate graph')
new_graph, wt_dict, th_dict, ph_dict = GetGraphFromSkeleton(skel, dt=dt, dt_bb=[bb[x] for x in [0,2,4]],\
modified_bfs=modified_bfs)
print('save as a networkx object')
edge_list = GetEdgeList(new_graph, wt_dict, th_dict, ph_dict)
G = nx.Graph(shape=sz)
# add edge attributes
G.add_edges_from(edge_list)
nx.write_gpickle(G, out_folder + 'graph-%s.obj' % (bfs))
elif opt == '2': # reduced graph
import networkx as nx
G = nx.read_gpickle(out_folder + 'graph-%s.obj' % (bfs))
def dthresh(image):
thresh = threshold_otsu(image)
thresholded = image > thresh
dt = distance_transform_cdt(thresholded)
return dt > 18
def dt_and_threshold(input_plane, threshold=75):
t_otsu = threshold_otsu(input_plane)
thresholded = input_plane > t_otsu
dt = distance_transform_cdt(thresholded)
return dt > threshold
def compact(im_label, compaction=3):
"""Performs a thinning operation on a label image to remove thin
protrusions from objects that are in contact with the background. Applies a
distance transform and sequentially removes pixels with small distances to
background that are not connected to higher distance pixels.
Parameters
----------
im_label : array_like
A labeled segmentation mask
compaction : int
Factor used in compacting objects to remove thin protrusions. Refered
to as d in the reference below. Default value = 3.
Notes
-----
Implemented from the reference below.
Returns
-------
im_compact : array_like
A labeled segmentation mask with thin protrusions removed.
See Also
--------
histomicstk.segmentation.label.area_open,
histomicstk.segmentation.label.condense,
histomicstk.segmentation.label.shuffle,
histomicstk.segmentation.label.split,
histomicstk.segmentation.label.width_open
References
----------
.. [1] S. Weinert et al "Detection and Segmentation of Cell Nuclei in
Virtual Microscopy Images: A Minimum-Model Approach" in Nature
Scientific Reports,vol.2,no.503, doi:10.1038/srep00503, 2012.
"""
# copy input image
im_compact = im_label.copy()
# generate distance map of label image
D = mp.distance_transform_cdt(im_compact > 0, metric='taxicab')
# define 4-neighbors filtering kernel
Kernel = np.zeros((3, 3), dtype=np.bool)
Kernel[1, :] = True
Kernel[:, 1] = True
# sweep over distance values from d-1 to 1
for i in np.arange(compaction-1, 0, -1):
# four-neighbor maxima of distance transform
MaxD = ft.maximum_filter(D, footprint=Kernel)
# identify pixels whose max 4-neighbor is less than i+1
Decrement = (D == i) & (MaxD < i+1)
# decrement non-compact pixels
D[Decrement] -= 1
# zero label pixels where D == 0
im_compact[D == 0] = 0
return im_compact
def width_open(im_label, width):
"""Removes thin objects from label image using maximum of distance
transform values within each object.
Parameters
----------
im_label : array_like
A uint32 type label image generated by segmentation methods.
width : int
width threshold for objects. Objects with fewer than 'Area' pixels will
be zeroed to merge with background.
Notes
-----
Objects are assumed to have positive nonzero values. A binary mask is
generated for each object setting all other objects to the background value
(0). The maximum chamfered distance transform value of this mask is used
to represent the object width.
Returns
-------
im_thinned : array_like
A uint32 label where objects with pixels < Area are removed.
See Also
--------
histomicstk.segmentation.label.condense,
histomicstk.segmentation.label.shuffle,
histomicstk.segmentation.label.split,
histomicstk.segmentation.label.area_open
"""
# copy input image
im_thinned = im_label.copy()
# condense label image
if np.unique(im_thinned).size-1 != im_thinned.max():
im_thinned = condense(im_thinned)
# get locations of objects in initial label image
Locations = ms.find_objects(im_thinned)
# iterate through objects, calculating distances where needed
for i in np.arange(1, len(Locations)+1):
# extract object from label image
W = im_thinned[Locations[i-1]]
# embed into mask with boundary
Mask = np.zeros((W.shape[0]+2, W.shape[1]+2), dtype=np.bool)
Mask[1:-1, 1:-1] = W == i
# calculate distance transform of mask
D = mp.distance_transform_cdt(Mask, metric='taxicab')
# get max distance
Max = D.max()
# zero label mask of object 'i'
if Max < width:
W[W == i] = 0
# condense to fill gaps
im_thinned = condense(im_thinned)
return im_thinned