def hm(img):
s1 = get_structure("rectangular")
s2 = get_structure("elliptical")
s3 = get_structure("cross-shaped")
result1 = ndimage.binary_hit_or_miss(img, structure1=s1).astype(np.int)
result2 = ndimage.binary_hit_or_miss(img, structure1=s2).astype(np.int)
result3 = ndimage.binary_hit_or_miss(img, structure1=s3).astype(np.int)
plt.subplot(2,2,1), plt.imshow(img, cmap="gray"), plt.title("Real Image")
plt.subplot(2,2,2), plt.imshow(result1, cmap="gray"), plt.title("rectangular kernel")
plt.subplot(2,2,3), plt.imshow(result2, cmap="gray"), plt.title("elliptical kernel")
plt.subplot(2,2,4), plt.imshow(result3, cmap="gray"), plt.title("cross-shaped kernel")
plt.show()
def fill(img):
"""both img and element should be binnary"""
e = np.ones((3,3), np.int)
e[1,1] = 0
interiorPoints = ndimage.binary_hit_or_miss(img, e).astype(np.int)
img = img + interiorPoints
return img.astype(np.uint8)
def clean(img):
"""both img and element should be binnary"""
e = np.zeros((3,3), np.int)
e[1,1] = 1
interiorPoints = ndimage.binary_hit_or_miss(img, e).astype(np.int)
img = img - interiorPoints
return img.astype(np.uint8)
def find1Cpixels(bwImage):
""" identifies 1-connected pixels in image """
# fills pixels matching the following neighborhoods:
hoods = [[[1, 0, 0],
[0, 1, 0],
[0, 0, 0]],
[[0, 1, 0],
[0, 1, 0],
[0, 0, 0]],
[[0, 0, 1],
[0, 1, 0],
[0, 0, 0]],
[[0, 0, 0],
[1, 1, 0],
[0, 0, 0]],
[[0, 0, 0],
[0, 1, 1],
[0, 0, 0]],
[[0, 0, 0],
[0, 1, 0],
[1, 0, 0]],
[[0, 0, 0],
[0, 1, 0],
[0, 1, 0]],
[[0, 0, 0],
[0, 1, 0],
[0, 0, 1]]]
output = np.zeros(bwImage.shape, dtype=np.bool)
# for each neighborhood, find matching pixels and set them to 1 in the img
for hood in hoods:
output = np.logical_or(output,
ndimage.binary_hit_or_miss(bwImage, hood))
return output
def drain_rois(img_data):
"""
Find all the ROIs in img_data and returns a similar volume with the ROIs
emptied, keeping only their border voxels.
This is useful for DTI tractography.
@param img_data: numpy array
@return:
an array of same shape as img_data
"""
out = np.zeros(img_data.shape, dtype=img_data.dtype)
if img_data.ndim == 2:
kernel = np.ones([3, 3], dtype=int)
elif img_data.ndim == 3:
kernel = np.ones([3, 3, 3], dtype=int)
elif img_data.ndim == 4:
kernel = np.ones([3, 3, 3, 3], dtype=int)
vals = np.unique(img_data)
vals = vals[vals != 0]
for i in vals:
roi = img_data == i
hits = scn.binary_hit_or_miss(roi, kernel)
roi[hits] = 0
out[roi > 0] = i
return out
def thining(img):
ss = []
s = np.array([ [1,1], [1,1]], 'uint8')
plt.subplot(1,2,1), plt.imshow(img, cmap="gray"), plt.title(str(2))
for i in range(12):
img = ndimage.binary_hit_or_miss(img, structure1=s).astype(np.uint8)
plt.subplot(1,2,2), plt.imshow(img, cmap="gray"), plt.title(str(2))
plt.show()
def __operationTask(self,input_var):
'''
perform respective moephological operation on input block.
Parameters
----------
input_var : type: 3d numpy array, ith block.
Returns
-------
output : type: 3d array, output of operation, ith block array.
'''
D=self.__operationArgumentDic
if self.__operation=="binary_closing":
return ndimage.binary_closing(input_var, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
elif self.__operation=="binary_dilation":
return ndimage.binary_dilation(input_var, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
elif self.__operation=="binary_erosion":
return ndimage.binary_erosion(input_var, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
elif self.__operation=="binary_fill_holes": #the output might be different then scipy.ndimage
return ndimage.binary_fill_holes(input_var, structure=D["structure"],output=D["output"], origin=D["origin"])
elif self.__operation=="binary_hit_or_miss":
return ndimage.binary_hit_or_miss(input_var, structure1=D["structure1"],structure2=D["structure2"],output=D["output"], origin1=D["origin1"], origin2=D["origin2"])
elif self.__operation=="binary_opening":
return ndimage.binary_opening(input_var, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
elif self.__operation=="binary_propagation":
return ndimage.binary_propagation(input_var, structure=D["structure"],output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"])
elif self.__operation=="black_tophat":
return ndimage.black_tophat(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
elif self.__operation=="grey_dilation":
return ndimage.grey_dilation(input_var, structure=D["structure"],size=D["size"], footprint=D["footprint"],output=D["output"], mode=D["mode"], cval=D["cval"], origin=D["origin"])
elif self.__operation=="grey_closing":
return ndimage.grey_closing(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
elif self.__operation=="grey_erosion":
return ndimage.grey_erosion(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
elif self.__operation=="grey_opening":
return ndimage.grey_opening(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
elif self.__operation=="morphological_gradient":
return ndimage.morphological_gradient(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
elif self.__operation=="morphological_laplace":
return ndimage.morphological_laplace(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
elif self.__operation=="white_tophat":
return ndimage.white_tophat(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
elif self.__operation=="multiply":
return input_var*D["scalar"]
else:
return input_var # no operation performed....
def return_ends(skeleton):
'''
Find the endpoints of the skeleton.
'''
end_points = []
for i, struct in enumerate(end_structs):
hits = nd.binary_hit_or_miss(skeleton, structure1=struct)
if not np.any(hits):
continue
for y, x in zip(*np.where(hits)):
end_points.append((y, x))
return end_points
def find1Cpixels(bwImage):
""" identifies 1-connected pixels in image """
# fills pixels matching the following neighborhoods:
hoods = [[[1, 0, 0], [0, 1, 0], [0, 0, 0]],
[[0, 1, 0], [0, 1, 0], [0, 0, 0]],
[[0, 0, 1], [0, 1, 0], [0, 0, 0]],
[[0, 0, 0], [1, 1, 0], [0, 0, 0]],
[[0, 0, 0], [0, 1, 1], [0, 0, 0]],
[[0, 0, 0], [0, 1, 0], [1, 0, 0]],
[[0, 0, 0], [0, 1, 0], [0, 1, 0]],
[[0, 0, 0], [0, 1, 0], [0, 0, 1]]]
output = np.zeros(bwImage.shape, dtype=np.bool)
# for each neighborhood, find matching pixels and set them to 1 in the img
for hood in hoods:
output = np.logical_or(output,
ndimage.binary_hit_or_miss(bwImage, hood))
return output
def return_ends(skeleton):
'''
Find the endpoints of the skeleton.
'''
end_points = []
for i, struct in enumerate(end_structs):
hits = nd.binary_hit_or_miss(skeleton, structure1=struct)
if not np.any(hits):
continue
for y, x in zip(*np.where(hits)):
end_points.append((y, x))
return end_points
def finalPruning(self, skeleton):
removedBranches = []
prunedSkeleton = skeleton
for i in xrange(0, len(finalPruningKernel)):
removedBranches.append(
ndimage.binary_hit_or_miss(prunedSkeleton,
finalPruningKernel[i]).astype(int))
finalRemovedBranches = removedBranches[0]
for i in xrange(1, len(removedBranches)):
finalRemovedBranches = np.logical_or(
finalRemovedBranches, removedBranches[i]).astype(int)
prunedSkeleton = np.logical_and(
skeleton,
np.logical_not(finalRemovedBranches).astype(int)).astype(int)
return prunedSkeleton
def pruning(self, skeleton):
prunedSkeleton = skeleton
removedBranches = []
for i in xrange(0, len(pruningHitKernel)):
removedBranches.append(
ndimage.binary_hit_or_miss(
prunedSkeleton,
structure1=pruningHitKernel[i],
structure2=pruningMissKernel[i]).astype(int))
finalRemovedBranches = removedBranches[0]
for k in xrange(1, len(removedBranches)):
finalRemovedBranches = np.logical_or(
finalRemovedBranches, removedBranches[k]).astype(int)
prunedSkeleton = np.logical_and(
skeleton,
np.logical_not(finalRemovedBranches).astype(int)).astype(int)
return prunedSkeleton
def bwdiagfill(bwimage):
""" clone of matlab's bwmorph(image,'diag') function? """
# fills pixels matching the following neighborhoods:
hoods = [[[0, 1, 0],
[1, 0, 0],
[0, 0, 0]],
[[0, 0, 0],
[1, 0, 0],
[0, 1, 0]],
[[0, 0, 0],
[0, 0, 1],
[0, 1, 0]],
[[0, 1, 0],
[0, 0, 1],
[0, 0, 0]]]
output = bwimage.copy()
# for each neighborhood, find matching pixels and set them to 1 in the img
for hood in hoods:
output = np.logical_or(output,
ndimage.binary_hit_or_miss(bwimage, hood))
return output
def skel(img):
"""skeletonize image"""
print("Skel")
hits = [ np.array([[0, 0, 0], [0, 1, 0], [1, 1, 1]]),
np.array([[0, 0, 0], [1, 1, 0], [0, 1, 0]]) ]
misses = [ np.array([[1, 1, 1], [0, 0, 0], [0, 0, 0]]),
np.array([[0, 1, 1], [0, 0, 1], [0, 0, 0]]) ]
for i in range(6):
hits.append(np.transpose(hits[-2])[::-1, ...])
misses.append(np.transpose(misses[-2])[::-1, ...])
filters = zip(hits,misses)
while True:
prev = img
for hit, miss in filters:
filtered = ndimage.binary_hit_or_miss(img, hit, miss)
img = np.logical_and(img, np.logical_not(filtered))
if np.abs(prev-img).max() == 0:
break
return img
def operationTask(input): D=operationArgumentDic #self.M.add_mem()#..................................................................................................... if operation=="binary_closing": return ndimage.binary_closing(input, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"]) elif operation=="binary_dilation": return ndimage.binary_dilation(input, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"]) elif operation=="binary_erosion": return ndimage.binary_erosion(input, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"]) elif operation=="binary_fill_holes": return ndimage.binary_fill_holes(input, structure=D["structure"],output=D["output"], origin=D["origin"]) elif operation=="binary_hit_or_miss": return ndimage.binary_hit_or_miss(input, structure1=D["structure1"],structure2=D["structure2"],output=D["output"], origin1=D["origin1"], origin2=D["origin2"]) elif operation=="binary_opening": return ndimage.binary_opening(input, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"]) elif operation=="binary_propagation": return ndimage.binary_propagation(input, structure=D["structure"],output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"]) elif operation=="black_tophat": return ndimage.black_tophat(input, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"]) elif operation=="grey_dilation": return ndimage.grey_dilation(input, structure=D["structure"],size=D["size"], footprint=D["footprint"],output=D["output"], mode=D["mode"], cval=D["cval"], origin=D["origin"]) elif operation=="grey_closing": return ndimage.grey_closing(input, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"]) elif operation=="grey_erosion": return ndimage.grey_erosion(input, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"]) elif operation=="grey_opening": return ndimage.grey_opening(input, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"]) elif operation=="morphological_gradient": return ndimage.morphological_gradient(input, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"]) elif operation=="morphological_laplace": return ndimage.morphological_laplace(input, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"]) elif operation=="white_tophat": return ndimage.white_tophat(input, structure=D["structure"], size=D["size"], footprint=D["footprint"], output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"]) elif operation=="intMultiply": return input*D["scalar"] else: return input
def skeleton(img):
h1 = np.array([[0, 0, 0], [0, 1, 0], [1, 1, 1]])
m1 = np.array([[1, 1, 1], [0, 0, 0], [0, 0, 0]])
h2 = np.array([[0, 0, 0], [1, 1, 0], [0, 1, 0]])
m2 = np.array([[0, 0, 1], [0, 0, 1], [0, 0, 0]])
hit_list = []
miss_list = []
for k in range(4):
hit_list.append(np.rot90(h1, k))
hit_list.append(np.rot90(h2, k))
miss_list.append(np.rot90(m1, k))
miss_list.append(np.rot90(m2, k))
img = img.copy()
while True:
last = img
for hit, miss in zip(hit_list, miss_list):
hm = binary_hit_or_miss(img, hit, miss)
# 删除白色点
img = np.logical_and(img, np.logical_not(hm))
if np.all(img == last):
break
return img
def drain_rois(img):
"""Find all the ROIs in img and returns a similar volume with the ROIs
emptied, keeping only their border voxels.
This is useful for DTI tractography.
Parameters
----------
img: img-like object or str
Can either be:
- a file path to a Nifti image
- any object with get_data() and get_affine() methods, e.g., nibabel.Nifti1Image.
If niimg is a string, consider it as a path to Nifti image and
call nibabel.load on it. If it is an object, check if get_data()
and get_affine() methods are present, raise TypeError otherwise.
Returns
-------
np.ndarray
an array of same shape as img_data
"""
img_data = get_img_data(img)
out = np.zeros(img_data.shape, dtype=img_data.dtype)
krn_dim = [3] * img_data.ndim
kernel = np.ones(krn_dim, dtype=int)
vals = np.unique(img_data)
vals = vals[vals != 0]
for i in vals:
roi = img_data == i
hits = scn.binary_hit_or_miss(roi, kernel)
roi[hits] = 0
out[roi > 0] = i
return out
def my_thinning(img: np.ndarray, se: np.ndarray) -> np.ndarray:
"""
"""
return np.bitwise_xor(img, ndi.binary_hit_or_miss(img, se))
def _fill_gaps(wires, out):
"""Fill 1-minute gaps."""
mask = np.array([[1, 0, 1]])
return np.logical_or(wires,
ndimage.binary_hit_or_miss(wires, mask),
out=out)
def find_interestpoints(skeleton, plotFlag):
B1 = np.array([[0, 1, 0], [1, 1, 1], [0, 1, 0]])
B2 = np.array([[1, 0, 1], [0, 1, 0], [1, 0, 1]])
B3 = np.array([[0, 1, 0], [1, 1, 1], [0, 0, 0]])
B4 = np.array([[1, 0, 1], [0, 1, 0], [1, 0, 0]])
B5 = np.array([[0, 1, 0], [1, 1, 0], [0, 1, 0]])
B6 = np.array([[1, 0, 0], [0, 1, 0], [1, 0, 1]])
B7 = np.array([[0, 0, 0], [1, 1, 1], [0, 1, 0]])
B8 = np.array([[0, 0, 1], [0, 1, 0], [1, 0, 1]])
B9 = np.array([[0, 1, 0], [0, 1, 1], [0, 1, 0]])
B10 = np.array([[1, 0, 1], [0, 1, 0], [0, 0, 1]])
B11 = np.array([[1, 0, 1], [0, 1, 0], [0, 1, 0]])
B12 = np.array([[0, 1, 0], [1, 1, 0], [0, 0, 1]])
B13 = np.array([[1, 0, 0], [0, 1, 1], [1, 0, 0]])
B14 = np.array([[0, 0, 1], [1, 1, 0], [0, 1, 0]])
B15 = np.array([[0, 1, 0], [0, 1, 0], [1, 0, 1]])
B16 = np.rot90(B14)
B17 = np.rot90(B15)
B18 = np.rot90(B16)
IMhit_mis = (
binary_hit_or_miss(skeleton, B1) + binary_hit_or_miss(skeleton, B2) +
binary_hit_or_miss(skeleton, B3) + binary_hit_or_miss(skeleton, B4) +
binary_hit_or_miss(skeleton, B5) + binary_hit_or_miss(skeleton, B6) +
binary_hit_or_miss(skeleton, B7) + binary_hit_or_miss(skeleton, B8) +
binary_hit_or_miss(skeleton, B9) + binary_hit_or_miss(skeleton, B10) +
binary_hit_or_miss(skeleton, B11) + binary_hit_or_miss(skeleton, B12) +
binary_hit_or_miss(skeleton, B13) + binary_hit_or_miss(skeleton, B14) +
binary_hit_or_miss(skeleton, B15) + binary_hit_or_miss(skeleton, B16) +
binary_hit_or_miss(skeleton, B17) + binary_hit_or_miss(skeleton, B18))
IMhit_mis_bin = IMhit_mis.astype(np.int)
coordinates = np.nonzero(IMhit_mis_bin)
if (plotFlag == 1):
plt.figure(3)
plt.imshow(skeleton)
plt.scatter(x=coordinates[1],
y=coordinates[0],
c='r',
s=20,
marker='x')
plt.show()
return coordinates
def binary_hit_or_miss_transform(A, B=None, D=None):
if B is None:
B = np.ones((3, 3))
output = ndimage.binary_hit_or_miss(A, structure1=B).astype(np.uint8)
return output
def test_binary_hit_or_miss_operation_dense_input_default_value(self):
print("\n test_binary_hit_or_miss_operation_dense_input_default_value...")
v_output = vc.binary_hit_or_miss(input_dvar, structure1=structure1, make_float32=False)
d_output = ndimage.binary_hit_or_miss(input_dvar, structure1=structure1,)
msgs = "test_binary_hit_or_miss_operation_dense_input_default_value"
self.assertTrue((d_output==v_output).all(), msg=msgs)
def lengths(skeleton, verbose=False):
'''
Length finding via morphology.
'''
# 4-connected labels
four_labels = label(skeleton, 4, background=0)
four_sizes = nd.sum(skeleton, four_labels, range(np.max(four_labels) + 1))
# Lengths is the number of pixels minus number of objects with more
# than 1 pixel.
four_length = np.sum(four_sizes[four_sizes > 1]) - len(
four_sizes[four_sizes > 1])
# Find pixels which a 4-connected and subtract them off the skeleton
four_objects = np.where(four_sizes > 1)[0]
skel_copy = copy(skeleton)
for val in four_objects:
skel_copy[np.where(four_labels == val)] = 0
# Remaining pixels are only 8-connected
# Lengths is same as before, multiplied by sqrt(2)
eight_labels = label(skel_copy, 8, background=0)
eight_sizes = nd.sum(skel_copy, eight_labels,
range(np.max(eight_labels) + 1))
eight_length = (
(np.sum(eight_sizes) - 1) - np.max(eight_labels)) * np.sqrt(2)
# If there are no 4-connected pixels, we don't need the hit-miss portion.
if four_length == 0.0:
conn_length = 0.0
else:
# Check 4 to 8-connected elements
struct1 = np.array([[1, 0, 0], [0, 1, 1], [0, 0, 0]])
struct2 = np.array([[0, 0, 1], [1, 1, 0], [0, 0, 0]])
# Next check the three elements which will be double counted
check1 = np.array([[1, 1, 0, 0], [0, 0, 1, 1]])
check2 = np.array([[0, 0, 1, 1], [1, 1, 0, 0]])
check3 = np.array([[1, 1, 0], [0, 0, 1], [0, 0, 1]])
store = np.zeros(skeleton.shape)
# Loop through the 4 rotations of the structuring elements
for k in range(0, 4):
hm1 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(struct1, k=k))
store += hm1
hm2 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(struct2, k=k))
store += hm2
hm_check3 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(check3, k=k))
store -= hm_check3
if k <= 1:
hm_check1 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(check1,
k=k))
store -= hm_check1
hm_check2 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(check2,
k=k))
store -= hm_check2
conn_length = np.sqrt(2) * np.sum(np.sum(store, axis=1),
axis=0) # hits
if verbose:
print "Four Length: %s" % (four_length)
print "Eight Length: %s" % (eight_length)
print "Connect Length: %s" % (conn_length)
return conn_length + eight_length + four_length
def main():
structure = np.ones((3, 3, 3))
#.............test1. dense.......
filename = 'gyroidUniform.npy'
input = np.load(filename, mmap_mode="r")
print(
"..............................dense.............................................."
)
#0.Nothing..............
print("\n nothing testing...")
output = vc.nothing(input, blockSize=50, fakeGhost=4, makeFloat32=False)
print("\nresult: ", (input == output).all())
print(output.dtype, input.dtype)
#1.grey_dilation..............
print("\ngrey_dilation VoxelProcessind")
output = vc.grey_dilation(input, structure=structure, makeFloat32=False)
print("\ngrey_dilation Default")
d = ndimage.grey_dilation(input, structure=structure)
print("\nresult: ", (d == output).all())
print(output.dtype, input.dtype)
#2.grey_erosion..............
print("\ngrey_erosion VoxelProcessind")
output = vc.grey_erosion(input,
makeFloat32=False,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\ngrey_erosion Default")
d = ndimage.grey_erosion(input,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nresult: ", (d == output).all())
#3.grey_closing..............
print("\ngrey_closing VoxelProcessind")
output = vc.grey_closing(input,
makeFloat32=False,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\ngrey_closing Default")
d = ndimage.grey_closing(input,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nresult: ", (d == output).all())
print(output.dtype, input.dtype)
#4.grey_opening..............
print("\ngrey_opening VoxelProcessind")
output = vc.grey_opening(input,
makeFloat32=False,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\ngrey_opening Default")
d = ndimage.grey_opening(input,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nresult: ", (d == output).all())
#5.binary_closing..............
print("\nbinary_closing VoxelProcessind")
output = vc.binary_closing(input,
makeFloat32=False,
structure=None,
iterations=1,
output=None,
origin=0,
mask=None,
border_value=0,
brute_force=False)
print("\nbinary_closing Default")
d = ndimage.binary_closing(input,
structure=None,
iterations=1,
output=None,
origin=0,
mask=None,
border_value=0,
brute_force=False)
print("\nresult: ", (d == output).all())
print(output[151][151][151])
#6.binary_opening..............
print("\nbinary_opening VoxelProcessind")
output = vc.binary_opening(input,
structure=None,
iterations=1,
output=None,
origin=0,
mask=None,
border_value=0,
brute_force=False)
print("\nbinary_opening Default")
d = ndimage.binary_opening(input,
structure=None,
iterations=1,
output=None,
origin=0,
mask=None,
border_value=0,
brute_force=False)
print("\nresult: ", (d == output).all())
#7.binary_dilation..............
print("\nbinary_dilation VoxelProcessind")
output = vc.binary_dilation(input,
makeFloat32=False,
structure=structure,
iterations=1,
mask=None,
output=None,
border_value=0,
origin=0,
brute_force=False)
print("\nbinary_dilation Default")
d = ndimage.binary_dilation(input,
structure=structure,
iterations=1,
mask=None,
output=None,
border_value=0,
origin=0,
brute_force=False)
print("\nresult: ", (d == output).all())
#8.binary_erosion..............
print("\nbinary_erosion VoxelProcessind")
output = vc.binary_erosion(input,
makeFloat32=False,
structure=None,
iterations=1,
mask=None,
output=None,
border_value=0,
origin=0,
brute_force=False)
print("\nbinary_erosion Default")
d = ndimage.binary_erosion(input,
structure=None,
iterations=1,
mask=None,
output=None,
border_value=0,
origin=0,
brute_force=False)
print("\nresult: ", (d == output).all())
#9.binary_fill_holes..............
print("\nbinary_fill_holes VoxelProcessind")
output = vc.binary_fill_holes(input,
makeFloat32=False,
structure=None,
output=None,
origin=0)
print("\nbinary_fill_holes Default")
d = ndimage.binary_fill_holes(input, structure=None, output=None, origin=0)
print("\nresult: ", (d == output).all())
#10.binary_hit_or_miss..............
print("\nbinary_hit_or_miss VoxelProcessind")
output = vc.binary_hit_or_miss(input,
makeFloat32=False,
structure1=None,
structure2=None,
output=None,
origin1=0,
origin2=None)
print("\nbinary_hit_or_miss Default")
d = ndimage.binary_hit_or_miss(input,
structure1=None,
structure2=None,
output=None,
origin1=0,
origin2=None)
print("\nresult: ", (d == output).all())
#11.binary_propagation..............
print("\nbinary_propagation VoxelProcessind")
output = vc.binary_propagation(input,
makeFloat32=False,
structure=None,
mask=None,
output=None,
border_value=0,
origin=0)
print("\nbinary_propagation Default")
d = ndimage.binary_propagation(input,
structure=None,
mask=None,
output=None,
border_value=0,
origin=0)
print("\nresult: ", (d == output).all())
#12.black_tophat..............
print("\nblack_tophat VoxelProcessind")
output = vc.black_tophat(input,
makeFloat32=False,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nblack_tophat Default")
d = ndimage.black_tophat(input,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nresult: ", (d == output).all())
#13.morphological_gradient..............
print("\nmorphological_gradient VoxelProcessind")
output = vc.morphological_gradient(input,
makeFloat32=False,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nmorphological_gradient Default")
d = ndimage.morphological_gradient(input,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nresult: ", (d == output).all())
#14.morphological_laplace..............
print("\nmorphological_laplace VoxelProcessind")
output = vc.morphological_laplace(input,
makeFloat32=False,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nmorphological_laplace Default")
d = ndimage.morphological_laplace(input,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nresult: ", (d == output).all())
#15.white_tophat..............
print("\nwhite_tophat VoxelProcessind")
output = vc.white_tophat(input,
makeFloat32=False,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nwhite_tophat VoxelProcessind Default")
d = ndimage.white_tophat(input,
size=None,
footprint=None,
structure=structure,
output=None,
mode='reflect',
cval=0.0,
origin=0)
print("\nresult: ", (d == output).all())
#16.intMultiply..............
print("\nintMultiply VoxelProcessind")
output = vc.intMultiply(input,
makeFloat32=False,
blockSize=50,
fakeGhost=1,
scalar=10)
print("\nintMultiply Default")
d = input * 10
print("\nresult: ", (d == output).all())
print(
"..............................Sparse.............................................."
)
input = random(400, 80000, density=0.3, dtype="float64")
input = input.todense()
input = np.array(input)
input = np.reshape(input, (400, 200, 400))
#0.Nothing..............
print("\n nothing testing...")
output = vc.nothing(input, makeFloat32=False)
print("\nresult: ", (input == output).all())
print(output.dtype, input.dtype)
#1.grey_dilation..............
print("\ngrey_dilation VoxelProcessind")
output = vc.grey_dilation(input, structure=structure, makeFloat32=False)
print("\ngrey_dilation Default")
d = ndimage.grey_dilation(input, structure=structure)
print("\nresult: ", (d == output).all())
print(output.dtype, input.dtype)
#2.grey_erosion..............
print("\ngrey_erosion VoxelProcessind")
output = vc.grey_erosion(input, makeFloat32=False, structure=structure)
print("\ngrey_erosion Default")
d = ndimage.grey_erosion(input, structure=structure)
print("\nresult: ", (d == output).all())
#3.grey_closing..............
print("\ngrey_closing VoxelProcessind")
output = vc.grey_closing(input, makeFloat32=False, structure=structure)
print("\ngrey_closing Default")
d = ndimage.grey_closing(input, structure=structure)
print("\nresult: ", (d == output).all())
print(output.dtype, input.dtype)
#4.grey_opening..............
print("\ngrey_opening VoxelProcessind")
output = vc.grey_opening(input, makeFloat32=False, structure=structure)
print("\ngrey_opening Default")
d = ndimage.grey_opening(input, structure=structure)
print("\nresult: ", (d == output).all())
#5.binary_closing..............
print("\nbinary_closing VoxelProcessind")
output = vc.binary_closing(input, makeFloat32=False)
print("\nbinary_closing Default")
d = ndimage.binary_closing(input)
print("\nresult: ", (d == output).all())
#6.binary_opening..............
print("\nbinary_opening VoxelProcessind")
output = vc.binary_opening(input, makeFloat32=False)
print("\nbinary_opening Default")
d = ndimage.binary_opening(input)
print("\nresult: ", (d == output).all())
#7.binary_dilation..............
print("\nbinary_dilation VoxelProcessind")
output = vc.binary_dilation(input, makeFloat32=False, structure=structure)
print("\nbinary_dilation Default")
d = ndimage.binary_dilation(input, structure=structure)
print("\nresult: ", (d == output).all())
#8.binary_erosion..............
print("\nbinary_erosion VoxelProcessind")
output = vc.binary_erosion(input, makeFloat32=False)
print("\nbinary_erosion Default")
d = ndimage.binary_erosion(input)
print("\nresult: ", (d == output).all())
#9.binary_fill_holes..............
print("\nbinary_fill_holes VoxelProcessind")
output = vc.binary_fill_holes(input, makeFloat32=False)
print("\nbinary_fill_holes Default")
d = ndimage.binary_fill_holes(input)
print("\nresult: ", (d == output).all())
#10.binary_hit_or_miss..............
print("\nbinary_hit_or_miss VoxelProcessind")
output = vc.binary_hit_or_miss(input, makeFloat32=False)
print("\nbinary_hit_or_miss Default")
d = ndimage.binary_hit_or_miss(input)
print("\nresult: ", (d == output).all())
#11.binary_propagation..............
print("\nbinary_propagation VoxelProcessind")
output = vc.binary_propagation(input, makeFloat32=False)
print("\nbinary_propagation Default")
d = ndimage.binary_propagation(input)
print("\nresult: ", (d == output).all())
#12.black_tophat..............
print("\nblack_tophat VoxelProcessind")
output = vc.black_tophat(input, makeFloat32=False, structure=structure)
print("\nblack_tophat Default")
d = ndimage.black_tophat(input, structure=structure)
print("\nresult: ", (d == output).all())
#13.morphological_gradient..............
print("\nmorphological_gradient VoxelProcessind")
output = vc.morphological_gradient(
input,
structure=structure,
makeFloat32=False,
)
print("\nmorphological_gradient Default")
d = ndimage.morphological_gradient(input, structure=structure)
print("\nresult: ", (d == output).all())
#14.morphological_laplace..............
print("\nmorphological_laplace VoxelProcessind")
output = vc.morphological_laplace(input,
structure=structure,
makeFloat32=False)
print("\nmorphological_laplace Default")
d = ndimage.morphological_laplace(input, structure=structure)
print("\nresult: ", (d == output).all())
#15.white_tophat..............
print("\nwhite_tophat VoxelProcessind")
output = vc.white_tophat(input, makeFloat32=False, structure=structure)
print("\nwhite_tophat VoxelProcessind Default")
d = ndimage.white_tophat(input, structure=structure)
print("\nresult: ", (d == output).all())
#16.intMultiply..............
print("\nintMultiply VoxelProcessind")
output = vc.intMultiply(input, makeFloat32=False, scalar=10)
print("\nintMultiply Default")
d = input * 10
print("\nresult: ", (d == output).all())
B10 = np.array([[1, 0, 1], [0, 1, 0], [0, 0, 1]])
B11 = np.array([[1, 0, 1], [0, 1, 0], [0, 1, 0]])
B12 = np.array([[0, 1, 0], [1, 1, 0], [0, 0, 1]])
B13 = np.array([[1, 0, 0], [0, 1, 1], [1, 0, 0]])
B14 = np.array([[0, 0, 1], [1, 1, 0], [0, 1, 0]])
B15 = np.array([[0, 1, 0], [0, 1, 0], [1, 0, 1]])
B16 = np.rot90(B14)
B17 = np.rot90(B15)
B18 = np.rot90(B16)
IMhit_mis = (
binary_hit_or_miss(skeleton, B1) + binary_hit_or_miss(skeleton, B2) +
binary_hit_or_miss(skeleton, B3) + binary_hit_or_miss(skeleton, B4) +
binary_hit_or_miss(skeleton, B5) + binary_hit_or_miss(skeleton, B6) +
binary_hit_or_miss(skeleton, B7) + binary_hit_or_miss(skeleton, B8) +
binary_hit_or_miss(skeleton, B9) + binary_hit_or_miss(skeleton, B10) +
binary_hit_or_miss(skeleton, B11) + binary_hit_or_miss(skeleton, B12) +
binary_hit_or_miss(skeleton, B13) + binary_hit_or_miss(skeleton, B14) +
binary_hit_or_miss(skeleton, B15) + binary_hit_or_miss(skeleton, B16) +
binary_hit_or_miss(skeleton, B17) + binary_hit_or_miss(skeleton, B18))
IMhit_mis_bin = IMhit_mis.astype(np.int)
coordinates = np.nonzero(IMhit_mis_bin)
coordinates = np.nonzero(IMhit_mis_bin)
plt.figure(3)
def _getnodes(Xin):
# hits
structures = []
structures.append([[1, 0, 0], [0, 1, 0], [0, 0, 0]])
structures.append([[0, 1, 0], [0, 1, 0], [0, 0, 0]])
structures.append([[0, 0, 1], [0, 1, 0], [0, 0, 0]])
structures.append([[0, 0, 0], [0, 1, 1], [0, 0, 0]])
structures.append([[0, 0, 0], [0, 1, 0], [0, 0, 1]])
structures.append([[0, 0, 0], [0, 1, 0], [0, 1, 0]])
structures.append([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
structures.append([[0, 0, 0], [1, 1, 0], [0, 0, 0]])
#structures.append([[1, 1, 1], [0, 1, 1], [1, 0, 0]])
#structures.append([[1, 1, 1], [1, 1, 0], [0, 0, 1]])
#structures.append([[1, 0, 0], [0, 1, 1], [1, 1, 1]])
#structures.append([[0, 0, 1], [1, 1, 0], [1, 1, 1]])
crossings = [[0, 1, 0, 1, 0, 0, 1, 0], [0, 0, 1, 0, 1, 0, 0, 1],
[1, 0, 0, 1, 0, 1, 0, 0], [0, 1, 0, 0, 1, 0, 1, 0],
[0, 0, 1, 0, 0, 1, 0, 1], [1, 0, 0, 1, 0, 0, 1, 0],
[0, 1, 0, 0, 1, 0, 0, 1], [1, 0, 1, 0, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 1, 0, 1], [0, 1, 0, 1, 0, 0, 0, 1],
[0, 1, 0, 1, 0, 1, 0, 0], [0, 0, 0, 1, 0, 1, 0, 1],
[1, 0, 1, 0, 0, 0, 1, 0], [1, 0, 1, 0, 1, 0, 0, 0],
[0, 0, 1, 0, 1, 0, 1, 0], [1, 0, 0, 0, 1, 0, 1, 0],
[1, 0, 0, 1, 1, 1, 0, 0], [0, 0, 1, 0, 0, 1, 1, 1],
[1, 1, 0, 0, 1, 0, 0, 1], [0, 1, 1, 1, 0, 0, 1, 0],
[1, 0, 1, 1, 0, 0, 1, 0], [1, 0, 1, 0, 0, 1, 1, 0],
[1, 0, 1, 1, 0, 1, 1, 0], [0, 1, 1, 0, 1, 0, 1, 1],
[1, 1, 0, 1, 1, 0, 1, 0], [1, 1, 0, 0, 1, 0, 1, 0],
[0, 1, 1, 0, 1, 0, 1, 0], [0, 0, 1, 0, 1, 0, 1, 1],
[1, 0, 0, 1, 1, 0, 1, 0], [1, 0, 1, 0, 1, 1, 0, 1],
[1, 0, 1, 0, 1, 1, 0, 0], [1, 0, 1, 0, 1, 0, 0, 1],
[0, 1, 0, 0, 1, 0, 1, 1], [0, 1, 1, 0, 1, 0, 0, 1],
[1, 1, 0, 1, 0, 0, 1, 0], [0, 1, 0, 1, 1, 0, 1, 0],
[0, 0, 1, 0, 1, 1, 0, 1], [1, 0, 1, 0, 0, 1, 0, 1],
[1, 0, 0, 1, 0, 1, 1, 0], [1, 0, 1, 1, 0, 1, 0, 0],
[0, 1, 1, 1, 1, 0, 0, 1], [1, 1, 0, 1, 0, 1, 1, 1],
[1, 1, 1, 1, 0, 1, 0, 0], [0, 1, 0, 0, 1, 1, 1, 1]]
for i in range(len(crossings)):
A = crossings[i]
B = np.ones((3, 3))
B[1, 0] = A[0]
B[0, 0] = A[1]
B[0, 1] = A[2]
B[0, 2] = A[3]
B[1, 2] = A[4]
B[2, 2] = A[5]
B[2, 1] = A[6]
B[2, 0] = A[7]
structures.append(B.tolist())
nodes = []
for i in range(len(structures)):
structure1 = np.array(structures[i])
X0 = spim.binary_hit_or_miss(Xin,
structure1=structure1).astype(int)
r0, c0 = np.nonzero(X0 == 1)
for j in range(len(r0)):
nodes.append([c0[j], r0[j]])
nodes = np.array(nodes)
return nodes
# hit and miss transform for detecting branched point and endpoint in scikit-image from scipy import ndimage ndimage.binary_hit_or_miss(...)
def lengths(skeleton, verbose=False):
'''
Length finding via morphology.
'''
# 4-connected labels
four_labels = label(skeleton, 4, background=0)
four_sizes = nd.sum(skeleton, four_labels, range(np.max(four_labels) + 1))
# Lengths is the number of pixels minus number of objects with more
# than 1 pixel.
four_length = np.sum(
four_sizes[four_sizes > 1]) - len(four_sizes[four_sizes > 1])
# Find pixels which a 4-connected and subtract them off the skeleton
four_objects = np.where(four_sizes > 1)[0]
skel_copy = copy(skeleton)
for val in four_objects:
skel_copy[np.where(four_labels == val)] = 0
# Remaining pixels are only 8-connected
# Lengths is same as before, multiplied by sqrt(2)
eight_labels = label(skel_copy, 8, background=0)
eight_sizes = nd.sum(
skel_copy, eight_labels, range(np.max(eight_labels) + 1))
eight_length = (
(np.sum(eight_sizes) - 1) - np.max(eight_labels)) * np.sqrt(2)
# If there are no 4-connected pixels, we don't need the hit-miss portion.
if four_length == 0.0:
conn_length = 0.0
else:
# Check 4 to 8-connected elements
struct1 = np.array([[1, 0, 0],
[0, 1, 1],
[0, 0, 0]])
struct2 = np.array([[0, 0, 1],
[1, 1, 0],
[0, 0, 0]])
# Next check the three elements which will be double counted
check1 = np.array([[1, 1, 0, 0],
[0, 0, 1, 1]])
check2 = np.array([[0, 0, 1, 1],
[1, 1, 0, 0]])
check3 = np.array([[1, 1, 0],
[0, 0, 1],
[0, 0, 1]])
store = np.zeros(skeleton.shape)
# Loop through the 4 rotations of the structuring elements
for k in range(0, 4):
hm1 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(struct1, k=k))
store += hm1
hm2 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(struct2, k=k))
store += hm2
hm_check3 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(check3, k=k))
store -= hm_check3
if k <= 1:
hm_check1 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(check1, k=k))
store -= hm_check1
hm_check2 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(check2, k=k))
store -= hm_check2
conn_length = np.sqrt(
2) * np.sum(np.sum(store, axis=1), axis=0) # hits
if verbose:
print "Four Length: %s" % (four_length)
print "Eight Length: %s" % (eight_length)
print "Connect Length: %s" % (conn_length)
return conn_length + eight_length + four_length
def test_binary_hit_or_miss_operation_sparse_input_blocks_ten(self):
print("\n test_binary_hit_or_miss_operation_sparse_input_blocks_ten...")
v_output = vc.binary_hit_or_miss(input_svar, structure1=structure1, no_of_blocks=10,make_float32=False)
d_output = ndimage.binary_hit_or_miss(input_svar, structure1=structure1,)
msgs = "test_binary_hit_or_miss_operation_sparse_input_blocks_ten"
self.assertTrue((d_output==v_output).all(), msg=msgs)
def skeleton_length(skeleton):
'''
Length finding via morphological operators. We use the differences in
connectivity between 4 and 8-connected to split regions. Connections
between 4 and 8-connected regions are found using a series of hit-miss
operators.
The inputted skeleton MUST have no intersections otherwise the returned
length will not be correct!
Parameters
----------
skeleton : numpy.ndarray
Array containing the skeleton.
Returns
-------
length : float
Length of the skeleton.
'''
# 4-connected labels
four_labels = nd.label(skeleton)[0]
four_sizes = nd.sum(skeleton, four_labels, range(np.max(four_labels) + 1))
# Lengths is the number of pixels minus number of objects with more
# than 1 pixel.
four_length = np.sum(
four_sizes[four_sizes > 1]) - len(four_sizes[four_sizes > 1])
# Find pixels which a 4-connected and subtract them off the skeleton
four_objects = np.where(four_sizes > 1)[0]
skel_copy = copy.copy(skeleton)
for val in four_objects:
skel_copy[np.where(four_labels == val)] = 0
# Remaining pixels are only 8-connected
# Lengths is same as before, multiplied by sqrt(2)
eight_labels = nd.label(skel_copy, eight_con())[0]
eight_sizes = nd.sum(
skel_copy, eight_labels, range(np.max(eight_labels) + 1))
eight_length = (
np.sum(eight_sizes) - np.max(eight_labels)) * np.sqrt(2)
# If there are no 4-connected pixels, we don't need the hit-miss portion.
if four_length == 0.0:
conn_length = 0.0
else:
store = np.zeros(skeleton.shape)
# Loop through the 4 rotations of the structuring elements
for k in range(0, 4):
hm1 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(struct1, k=k))
store += hm1
hm2 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(struct2, k=k))
store += hm2
hm_check3 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(check3, k=k))
store -= hm_check3
if k <= 1:
hm_check1 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(check1, k=k))
store -= hm_check1
hm_check2 = nd.binary_hit_or_miss(
skeleton, structure1=np.rot90(check2, k=k))
store -= hm_check2
conn_length = np.sqrt(2) * \
np.sum(np.sum(store, axis=1), axis=0) # hits
return conn_length + eight_length + four_length
def branchedPoints(skel):
# defining branch shapes to locate nodes
# overexplained this section a bit
xbranch0 = np.array([[1, 0, 1], [0, 1, 0], [1, 0, 1]])
xbranch1 = np.array([[0, 1, 0], [1, 1, 1], [0, 1, 0]])
tbranch0 = np.array([[0, 0, 0], [1, 1, 1], [0, 1, 0]])
# flipud is flipping them up-down
# tbranch2 is tbranch0 transposed, which permutes it in all directions (might not be using that word right)
# tbranch3 is tbranch2 flipped left right
# those 3 functions are used to create all possible branches with just a few starting arrays below
tbranch1 = np.flipud(tbranch0)
tbranch2 = tbranch0.T
tbranch3 = np.fliplr(tbranch2)
tbranch4 = np.array([[1, 0, 1], [0, 1, 0], [1, 0, 0]])
tbranch5 = np.flipud(tbranch4)
tbranch6 = np.fliplr(tbranch4)
tbranch7 = np.fliplr(tbranch5)
ybranch0 = np.array([[1, 0, 1], [0, 1, 0], [0, 1, 0]])
ybranch1 = np.flipud(ybranch0)
ybranch2 = ybranch0.T
ybranch3 = np.fliplr(ybranch2)
ybranch4 = np.array([[0, 1, 0], [1, 1, 0], [0, 0, 1]])
ybranch5 = np.flipud(ybranch4)
ybranch6 = np.fliplr(ybranch4)
ybranch7 = np.fliplr(ybranch5)
offbranch0 = np.array([[0, 1, 0], [1, 1, 0], [1, 0, 1]])
offbranch1 = np.flipud(offbranch0)
offbranch2 = np.fliplr(offbranch0)
offbranch3 = np.fliplr(offbranch1)
offbranch4 = offbranch0.T
offbranch5 = np.flipud(offbranch4)
offbranch6 = np.fliplr(offbranch4)
offbranch7 = np.fliplr(offbranch5)
clustbranch0 = np.array([[0, 1, 1], [0, 1, 1], [1, 0, 0]])
clustbranch1 = np.flipud(clustbranch0)
clustbranch2 = np.fliplr(clustbranch0)
clustbranch3 = np.fliplr(clustbranch1)
clustbranch4 = np.array([[1, 1, 1], [0, 1, 1], [1, 0, 0]])
clustbranch5 = np.flipud(clustbranch4)
clustbranch6 = np.fliplr(clustbranch4)
clustbranch7 = np.fliplr(clustbranch5)
clustbranch8 = np.array([[1, 1, 1], [0, 1, 1], [1, 0, 1]])
clustbranch9 = np.flipud(clustbranch8)
clustbranch10 = np.fliplr(clustbranch8)
clustbranch11 = np.fliplr(clustbranch9)
crossbranch0 = np.array([[1, 0, 0], [1, 1, 1], [0, 1, 0]])
crossbranch1 = np.flipud(crossbranch0)
crossbranch2 = np.fliplr(crossbranch0)
crossbranch3 = np.fliplr(crossbranch1)
crossbranch4 = crossbranch0.T
crossbranch5 = np.flipud(crossbranch4)
crossbranch6 = np.fliplr(crossbranch4)
crossbranch7 = np.fliplr(crossbranch5)
# finding the location of all the branch points based on the arrays above
br1 = ndimage.binary_hit_or_miss(skel, xbranch0)
br2 = ndimage.binary_hit_or_miss(skel, xbranch1)
br3 = ndimage.binary_hit_or_miss(skel, tbranch0)
br4 = ndimage.binary_hit_or_miss(skel, tbranch1)
br5 = ndimage.binary_hit_or_miss(skel, tbranch2)
br6 = ndimage.binary_hit_or_miss(skel, tbranch3)
br7 = ndimage.binary_hit_or_miss(skel, tbranch4)
br8 = ndimage.binary_hit_or_miss(skel, tbranch5)
br9 = ndimage.binary_hit_or_miss(skel, tbranch6)
br10 = ndimage.binary_hit_or_miss(skel, tbranch7)
br11 = ndimage.binary_hit_or_miss(skel, ybranch0)
br12 = ndimage.binary_hit_or_miss(skel, ybranch1)
br13 = ndimage.binary_hit_or_miss(skel, ybranch2)
br14 = ndimage.binary_hit_or_miss(skel, ybranch3)
br15 = ndimage.binary_hit_or_miss(skel, ybranch4)
br16 = ndimage.binary_hit_or_miss(skel, ybranch5)
br17 = ndimage.binary_hit_or_miss(skel, ybranch6)
br18 = ndimage.binary_hit_or_miss(skel, ybranch7)
br19 = ndimage.binary_hit_or_miss(skel, offbranch0)
br20 = ndimage.binary_hit_or_miss(skel, offbranch1)
br21 = ndimage.binary_hit_or_miss(skel, offbranch2)
br22 = ndimage.binary_hit_or_miss(skel, offbranch3)
br23 = ndimage.binary_hit_or_miss(skel, offbranch4)
br24 = ndimage.binary_hit_or_miss(skel, offbranch5)
br25 = ndimage.binary_hit_or_miss(skel, offbranch6)
br26 = ndimage.binary_hit_or_miss(skel, offbranch7)
br27 = ndimage.binary_hit_or_miss(skel, clustbranch0)
br28 = ndimage.binary_hit_or_miss(skel, clustbranch1)
br29 = ndimage.binary_hit_or_miss(skel, clustbranch2)
br30 = ndimage.binary_hit_or_miss(skel, clustbranch3)
br31 = ndimage.binary_hit_or_miss(skel, clustbranch4)
br32 = ndimage.binary_hit_or_miss(skel, clustbranch5)
br33 = ndimage.binary_hit_or_miss(skel, clustbranch6)
br34 = ndimage.binary_hit_or_miss(skel, clustbranch7)
br35 = ndimage.binary_hit_or_miss(skel, clustbranch8)
br36 = ndimage.binary_hit_or_miss(skel, clustbranch9)
br37 = ndimage.binary_hit_or_miss(skel, clustbranch10)
br38 = ndimage.binary_hit_or_miss(skel, clustbranch11)
br39 = ndimage.binary_hit_or_miss(skel, crossbranch0)
br40 = ndimage.binary_hit_or_miss(skel, crossbranch1)
br41 = ndimage.binary_hit_or_miss(skel, crossbranch2)
br42 = ndimage.binary_hit_or_miss(skel, crossbranch3)
br43 = ndimage.binary_hit_or_miss(skel, crossbranch4)
br44 = ndimage.binary_hit_or_miss(skel, crossbranch5)
br45 = ndimage.binary_hit_or_miss(skel, crossbranch6)
br46 = ndimage.binary_hit_or_miss(skel, crossbranch7)
br = br1+br2+br3+br4+br5+br6+br7+br8+br9+br10+br11+br12+br13+br14+br15+br16+br17+br18+br19+br20+br21+br22+br23+br24\
+br25+br26+br27+br28+br29+br30+br31+br32+br33+br34+br35+br36+br37+br38+br39+br40+br41+br42+br43+br44+br45+br46
return br
#10.binary_hit_or_miss..............
print("\nbinary_hit_or_miss VoxelProcessing")
start_time = t.time()
output = vc.binary_hit_or_miss(input_var,
make_float32=False,
structure1=structure,
structure2=None,
output=None,
origin1=0,
origin2=None)
print("vc binary_hit_or_miss: ", (t.time() - start_time), " sec")
print("\nbinary_hit_or_miss Default")
start_time = t.time()
d = ndimage.binary_hit_or_miss(input_var,
structure1=structure,
structure2=None,
output=None,
origin1=0,
origin2=None)
print("scipy binary_hit_or_miss: ", (t.time() - start_time), " sec")
print("\nresult: ", (d == output).all())
#11.binary_propagation..............
print("\nbinary_propagation VoxelProcessing")
start_time = t.time()
output = vc.binary_propagation(input_var,
make_float32=False,
structure=structure,
mask=None,
output=None,
border_value=0,
origin=0)
def skeleton_length(skeleton):
'''
Length finding via morphological operators. We use the differences in
connectivity between 4 and 8-connected to split regions. Connections
between 4 and 8-connected regions are found using a series of hit-miss
operators.
The inputted skeleton MUST have no intersections otherwise the returned
length will not be correct!
Parameters
----------
skeleton : numpy.ndarray
Array containing the skeleton.
Returns
-------
length : float
Length of the skeleton.
'''
# 4-connected labels
four_labels = nd.label(skeleton)[0]
four_sizes = nd.sum(skeleton, four_labels, range(np.max(four_labels) + 1))
# Lengths is the number of pixels minus number of objects with more
# than 1 pixel.
four_length = np.sum(four_sizes[four_sizes > 1]) - len(
four_sizes[four_sizes > 1])
# Find pixels which a 4-connected and subtract them off the skeleton
four_objects = np.where(four_sizes > 1)[0]
skel_copy = copy.copy(skeleton)
for val in four_objects:
skel_copy[np.where(four_labels == val)] = 0
# Remaining pixels are only 8-connected
# Lengths is same as before, multiplied by sqrt(2)
eight_labels = nd.label(skel_copy, eight_con())[0]
eight_sizes = nd.sum(skel_copy, eight_labels,
range(np.max(eight_labels) + 1))
eight_length = (np.sum(eight_sizes) - np.max(eight_labels)) * np.sqrt(2)
# If there are no 4-connected pixels, we don't need the hit-miss portion.
if four_length == 0.0:
conn_length = 0.0
else:
store = np.zeros(skeleton.shape)
# Loop through the 4 rotations of the structuring elements
for k in range(0, 4):
hm1 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(struct1, k=k))
store += hm1
hm2 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(struct2, k=k))
store += hm2
hm_check3 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(check3, k=k))
store -= hm_check3
if k <= 1:
hm_check1 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(check1,
k=k))
store -= hm_check1
hm_check2 = nd.binary_hit_or_miss(skeleton,
structure1=np.rot90(check2,
k=k))
store -= hm_check2
conn_length = np.sqrt(2) * \
np.sum(np.sum(store, axis=1), axis=0) # hits
return conn_length + eight_length + four_length
ifname = args.input.strip()
ofname = args.output.strip()
ofname = add_extension_if_needed(ofname, '.nii.gz')
aff = nib.load(ifname).get_affine()
vol = nib.load(ifname).get_data()
out = np.zeros(vol.shape, dtype=vol.dtype)
if vol.ndim == 2:
kernel = np.ones([3,3], dtype=int)
elif vol.ndim == 3:
kernel = np.ones([3,3,3], dtype=int)
elif vol.ndim == 4:
kernel = np.ones([3,3,3,3], dtype=int)
vals = np.unique(vol)
vals = vals[vals != 0]
for i in vals:
roi = vol == i
hits = scn.binary_hit_or_miss (roi, kernel)
roi[hits] = 0
out[roi > 0] = i
ni = nib.Nifti1Image(out, aff)
nib.save(ni, ofname)
#-------------------------------------------------------------------------------
if __name__ == "__main__":
sys.exit(main())
def test_binary_hit_or_miss_operation_sparse_input_fakeghost_four(self):
print("\n test_binary_hit_or_miss_operation_sparse_input_fakeghost_four...")
v_output = vc.binary_hit_or_miss(input_svar,structure1=structure1, fakeghost=4,make_float32=False)
d_output = ndimage.binary_hit_or_miss(input_svar,structure1=structure1,)
msgs = "test_binary_hit_or_miss_operation_sparse_input_fakeghost_four"
self.assertTrue((d_output==v_output).all(), msg=msgs)
def endPoints(skel):
##
# Function returns boolen array that contains True values in the coordinates that fit as the endpoint of the fibers.
# arguments:
# - ‘skel’: array with skeletonized fibers
# function returns:
# - 'endp': boolen array that contains True values in the coordinates that fit as the endpoint of the fibers
##
epoint1 = np.array([[0, 0, 0], [0, 1, 0], [0, 1, 0]])
epoint2 = np.array([[0, 0, 0], [0, 1, 0], [0, 0, 1]])
epoint3 = np.array([[0, 0, 0], [0, 1, 1], [0, 0, 0]])
epoint4 = np.array([[0, 0, 1], [0, 1, 0], [0, 0, 0]])
epoint5 = np.array([[0, 1, 0], [0, 1, 0], [0, 0, 0]])
epoint6 = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 0]])
epoint7 = np.array([[0, 0, 0], [1, 1, 0], [0, 0, 0]])
epoint8 = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]])
epoint9 = np.array([[0, 0, 0], [0, 1, 0], [1, 1, 0]])
epoint10 = np.array([[0, 0, 0], [0, 1, 0], [0, 1, 1]])
epoint11 = np.array([[0, 0, 0], [0, 1, 1], [0, 0, 1]])
epoint12 = np.array([[0, 0, 1], [0, 1, 1], [0, 0, 0]])
epoint13 = np.array([[0, 1, 1], [0, 1, 0], [0, 0, 0]])
epoint14 = np.array([[1, 1, 0], [0, 1, 0], [0, 0, 0]])
epoint15 = np.array([[1, 0, 0], [1, 1, 0], [0, 0, 0]])
epoint16 = np.array([[0, 0, 0], [1, 1, 0], [1, 0, 0]])
endp1 = binary_hit_or_miss(skel, structure1=epoint1)
endp2 = binary_hit_or_miss(skel, structure1=epoint2)
endp3 = binary_hit_or_miss(skel, structure1=epoint3)
endp4 = binary_hit_or_miss(skel, structure1=epoint4)
endp5 = binary_hit_or_miss(skel, structure1=epoint5)
endp6 = binary_hit_or_miss(skel, structure1=epoint6)
endp7 = binary_hit_or_miss(skel, structure1=epoint7)
endp8 = binary_hit_or_miss(skel, structure1=epoint8)
endp9 = binary_hit_or_miss(skel, structure1=epoint9)
endp10 = binary_hit_or_miss(skel, structure1=epoint10)
endp11 = binary_hit_or_miss(skel, structure1=epoint11)
endp12 = binary_hit_or_miss(skel, structure1=epoint12)
endp13 = binary_hit_or_miss(skel, structure1=epoint13)
endp14 = binary_hit_or_miss(skel, structure1=epoint14)
endp15 = binary_hit_or_miss(skel, structure1=epoint15)
endp16 = binary_hit_or_miss(skel, structure1=epoint16)
endp = endp1 + \
endp2 + \
endp3 + \
endp4 + \
endp5 + \
endp6 + \
endp7 + \
endp8 + \
endp9 + \
endp10 + \
endp11 + \
endp12 + \
endp13 + \
endp14 + \
endp15 + \
endp16
return endp