def test_structuring_element8():
# check the output for a custom structuring element
r = np.array([[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 255, 0, 0, 0],
[0, 0, 255, 255, 255, 0], [0, 0, 0, 255, 255, 0],
[0, 0, 0, 0, 0, 0]])
# 8-bit
image = np.zeros((6, 6), dtype=np.uint8)
image[2, 2] = 255
elem = np.asarray([[1, 1, 0], [1, 1, 1], [0, 0, 1]], dtype=np.uint8)
out = np.empty_like(image)
mask = np.ones(image.shape, dtype=np.uint8)
rank.maximum(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=1,
shift_y=1)
assert_array_equal(r, out)
# 16-bit
image = np.zeros((6, 6), dtype=np.uint16)
image[2, 2] = 255
out = np.empty_like(image)
rank.maximum(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=1,
shift_y=1)
assert_array_equal(r, out)
def test_structuring_element8():
# check the output for a custom structuring element
r = np.array([[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 255, 0, 0, 0],
[0, 0, 255, 255, 255, 0],
[0, 0, 0, 255, 255, 0],
[0, 0, 0, 0, 0, 0]])
# 8-bit
image = np.zeros((6, 6), dtype=np.uint8)
image[2, 2] = 255
elem = np.asarray([[1, 1, 0], [1, 1, 1], [0, 0, 1]], dtype=np.uint8)
out = np.empty_like(image)
mask = np.ones(image.shape, dtype=np.uint8)
rank.maximum(image=image, selem=elem, out=out, mask=mask,
shift_x=1, shift_y=1)
assert_array_equal(r, out)
# 16-bit
image = np.zeros((6, 6), dtype=np.uint16)
image[2, 2] = 255
out = np.empty_like(image)
rank.maximum(image=image, selem=elem, out=out, mask=mask,
shift_x=1, shift_y=1)
assert_array_equal(r, out)
def test_smallest_selem16():
# check that min, max and mean returns identity if structuring element
# contains only central pixel
image = np.zeros((5, 5), dtype=np.uint16)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
elem = np.array([[1]], dtype=np.uint8)
rank.mean(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_array_equal(image, out)
rank.minimum(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_array_equal(image, out)
rank.maximum(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_array_equal(image, out)
def split_object(self, labeled_image):
""" split object when it's necessary
"""
labeled_image = labeled_image.astype(np.uint16)
labeled_mask = np.zeros_like(labeled_image, dtype=np.uint16)
labeled_mask[labeled_image != 0] = 1
#ift structuring element about center point. This only affects eccentric structuring elements (i.e. selem with even num===============================
labeled_image = skr.median(labeled_image, skm.disk(4))
labeled_mask = np.zeros_like(labeled_image, dtype=np.uint16)
labeled_mask[labeled_image != 0] = 1
distance = scipym.distance_transform_edt(labeled_image).astype(np.uint16)
#=======================================================================
# binary = np.zeros(np.shape(labeled_image))
# binary[labeled_image > 0] = 1
#=======================================================================
distance = skr.mean(distance, skm.disk(15))
l_max = skr.maximum(distance, skm.disk(5))
#l_max = skf.peak_local_max(distance, indices=False,labels=labeled_image, footprint=np.ones((3,3)))
l_max = l_max - distance <= 0
l_max = skr.maximum(l_max.astype(np.uint8), skm.disk(6))
marker = ndimage.label(l_max)[0]
split_image = skm.watershed(-distance, marker)
split_image[split_image[0,0] == split_image] = 0
return split_image
def test_empty_selem():
# check that min, max and mean returns zeros if structuring element is
# empty
image = np.zeros((5, 5), dtype=np.uint16)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
res = np.zeros_like(image)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
elem = np.array([[0, 0, 0], [0, 0, 0]], dtype=np.uint8)
rank.mean(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_array_equal(res, out)
rank.minimum(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_array_equal(res, out)
rank.maximum(image=image,
selem=elem,
out=out,
mask=mask,
shift_x=0,
shift_y=0)
assert_array_equal(res, out)
def test_compare_with_cmorph_dilate():
# compare the result of maximum filter with dilate
image = (np.random.rand(100, 100) * 256).astype(np.uint8)
out = np.empty_like(image)
mask = np.ones(image.shape, dtype=np.uint8)
for r in range(1, 20, 1):
elem = np.ones((r, r), dtype=np.uint8)
rank.maximum(image=image, selem=elem, out=out, mask=mask)
cm = cmorph._dilate(image=image, selem=elem)
assert_array_equal(out, cm)
def test_compare_with_cmorph_dilate():
# compare the result of maximum filter with dilate
image = (np.random.random((100, 100)) * 256).astype(np.uint8)
out = np.empty_like(image)
mask = np.ones(image.shape, dtype=np.uint8)
for r in range(1, 20, 1):
elem = np.ones((r, r), dtype=np.uint8)
rank.maximum(image=image, selem=elem, out=out, mask=mask)
cm = cmorph.dilate(image=image, selem=elem)
assert_array_equal(out, cm)
def test_percentile_max():
# check that percentile p0 = 1 is identical to local max
img = data.camera()
img16 = img.astype(np.uint16)
selem = disk(15)
# check for 8bit
img_p0 = rank.percentile(img, selem=selem, p0=1.)
img_max = rank.maximum(img, selem=selem)
assert_array_equal(img_p0, img_max)
# check for 16bit
img_p0 = rank.percentile(img16, selem=selem, p0=1.)
img_max = rank.maximum(img16, selem=selem)
assert_array_equal(img_p0, img_max)
def test_percentile_max():
# check that percentile p0 = 1 is identical to local max
img = data.camera()
img16 = img.astype(np.uint16)
selem = disk(15)
# check for 8bit
img_p0 = rank.percentile(img, selem=selem, p0=1.)
img_max = rank.maximum(img, selem=selem)
assert_array_equal(img_p0, img_max)
# check for 16bit
img_p0 = rank.percentile(img16, selem=selem, p0=1.)
img_max = rank.maximum(img16, selem=selem)
assert_array_equal(img_p0, img_max)
def substract_background(data, radius, background='mean', show=0):
dmin, dmax = data.min(), data.max()
tmp = ((data - dmin) / (dmax - dmin) * 255).astype(np.uint8)
lforeground = rank.minimum(tmp, disk(radius // 2))
if background == 'mean':
lbackground = rank.mean(lforeground, disk(radius * 4)).astype(int)
elif background == 'median':
lbackground = rank.median(lforeground, disk(radius * 4)).astype(int)
elif background == 'maximum':
lbackground = rank.maximum(lforeground, disk(radius * 4)).astype(int)
else:
lbackground = rank.modal(lforeground, disk(radius * 4)).astype(int)
rdata = (lforeground - lbackground)
if show > 2:
fig, axes = plt.subplots(ncols=3, nrows=1, figsize=(30, 10))
for ax, im, title in zip(axes, [lforeground, lbackground, rdata],
['Foreground', 'Background', 'Substraction']):
ax.imshow(im, 'optiona')
ax.set_xticks([])
ax.set_yticks([])
ax.set_title(title)
plt.show()
return rdata
def test_16bit():
image = np.zeros((21, 21), dtype=np.uint16)
selem = np.ones((3, 3), dtype=np.uint8)
for bitdepth in range(17):
value = 2**bitdepth - 1
image[10, 10] = value
assert rank.minimum(image, selem)[10, 10] == 0
assert rank.maximum(image, selem)[10, 10] == value
assert rank.mean(image, selem)[10, 10] == int(value / selem.size)
def test_16bit():
image = np.zeros((21, 21), dtype=np.uint16)
selem = np.ones((3, 3), dtype=np.uint8)
for bitdepth in range(17):
value = 2 ** bitdepth - 1
image[10, 10] = value
assert rank.minimum(image, selem)[10, 10] == 0
assert rank.maximum(image, selem)[10, 10] == value
assert rank.mean(image, selem)[10, 10] == int(value / selem.size)
def test_smallest_selem16():
# check that min, max and mean returns identity if structuring element
# contains only central pixel
image = np.zeros((5, 5), dtype=np.uint16)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
elem = np.array([[1]], dtype=np.uint8)
rank.mean(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_array_equal(image, out)
rank.minimum(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_array_equal(image, out)
rank.maximum(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_array_equal(image, out)
def test_empty_selem():
# check that min, max and mean returns zeros if structuring element is empty
image = np.zeros((5, 5), dtype=np.uint16)
out = np.zeros_like(image)
mask = np.ones_like(image, dtype=np.uint8)
res = np.zeros_like(image)
image[2, 2] = 255
image[2, 3] = 128
image[1, 2] = 16
elem = np.array([[0, 0, 0], [0, 0, 0]], dtype=np.uint8)
rank.mean(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_array_equal(res, out)
rank.minimum(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_array_equal(res, out)
rank.maximum(image=image, selem=elem, out=out, mask=mask,
shift_x=0, shift_y=0)
assert_array_equal(res, out)
def run(self, workspace):
cell_object = workspace.object_set.get_objects(self.primary_objects.value)
cell_labeled = cell_object.get_segmented()
cell_image = cell_object.get_parent_image()
cell_image = (cell_image * 1000).astype(np.uint16)
# object_count = cell_labeled.max()
maxi = skr.maximum(cell_image.astype(np.uint8), skm.disk(10))
local_max = maxi - cell_image < 10
local_max_labelize, object_count = scipy.ndimage.label(local_max, np.ones((3, 3), bool))
histo_local_max, not_use = np.histogram(local_max_labelize, range(object_count + 2))
old = local_max_labelize.copy()
# filter in intensity mean
# =======================================================================
#
# regionprops_result = skmes.regionprops(local_max_labelize, intensity_image=cell_image)
#
# for region in regionprops_result:
# if region["mean_intensity"]
# =======================================================================
# filter on size
for i in range(object_count + 1):
value = histo_local_max[i]
if value > self.range_size.max or value < self.range_size.min:
local_max_labelize[local_max_labelize == i] = 0
# split granule for each cell
cell_labeled = skm.label(cell_labeled)
cell_count = np.max(cell_labeled)
for cell_object_value in range(1, cell_count):
cell_object_mask = cell_labeled == cell_object_value
granule_in_cell = np.logical_and(cell_object_mask, local_max_labelize)
granule_in_cell = skm.label(granule_in_cell)
# ===================================================================
# plt.imshow(granule_in_cell + cell_object_mask)
# plt.show()
# ===================================================================
#
# get the filename
#
measurements = workspace.measurements
file_name_feature = self.source_file_name_feature
filename = measurements.get_current_measurement("Image", file_name_feature)
print "filename = ", filename
.. note::
`skimage.dilate` and `skimage.erode` are equivalent filters (see below for
comparison).
Here is an example of the classical morphological gray-level filters: opening,
closing and morphological gradient.
"""
from skimage.filter.rank import maximum, minimum, gradient
noisy_image = img_as_ubyte(data.camera())
closing = maximum(minimum(noisy_image, disk(5)), disk(5))
opening = minimum(maximum(noisy_image, disk(5)), disk(5))
grad = gradient(noisy_image, disk(5))
# display results
fig = plt.figure(figsize=[10, 7])
plt.subplot(2, 2, 1)
plt.imshow(noisy_image, cmap=plt.cm.gray)
plt.title('Original')
plt.axis('off')
plt.subplot(2, 2, 2)
plt.imshow(closing, cmap=plt.cm.gray)
plt.title('Gray-level closing')
plt.axis('off')
.. note::
`skimage.dilate` and `skimage.erode` are equivalent filters (see below for
comparison).
Here is an example of the classical morphological greylevel filters: opening,
closing and morphological gradient.
"""
from skimage.filter.rank import maximum, minimum, gradient
ima = data.camera()
closing = maximum(minimum(ima, disk(5)), disk(5))
opening = minimum(maximum(ima, disk(5)), disk(5))
grad = gradient(ima, disk(5))
# display results
fig = plt.figure(figsize=[10, 7])
plt.subplot(2, 2, 1)
plt.imshow(ima, cmap=plt.cm.gray)
plt.xlabel('original')
plt.subplot(2, 2, 2)
plt.imshow(closing, cmap=plt.cm.gray)
plt.xlabel('greylevel closing')
plt.subplot(2, 2, 3)
plt.imshow(opening, cmap=plt.cm.gray)
plt.xlabel('greylevel opening')
plt.subplot(2, 2, 4)
plt.imshow(out_pile)
try:
io.imsave('C:/users/attialex/Desktop/out_pile_3.png',
skimage.img_as_uint(out_pile))
io.imsave('C:/users/attialex/Desktop/out_cell_3.png',
skimage.img_as_uint(out_cell))
except Exception as e:
print e.message
try:
bg = normalize3Chan(imex * 1.)
fg_c = normalize3Chan(out_cell)
fg_p = normalize3Chan(out_pile)
fg_c[:, :, 0] = 0
fg_c[:, :, 2] = 0
s1 = cv2.addWeighted(bg, .8, fg_c, .2, 0)
cv2.imshow('cell', s1)
s2 = cv2.addWeighted(bg, .8, fg_p, .2, 0)
cv2.imshow('pile', s2)
cv2.waitKey()
except Exception as e:
print e.message
max_pile = maximum(out_pile, np.ones((40, 40)))
unique_pile = np.unique(max_pile)
max_cell = maximum(out_cell, np.ones((40, 40)))
unique_cell = np.unique(max_cell)
plt.show()
def run(self, workspace):
'''Run the algorithm on one image set'''
#
# Get the image as a binary image
#
image_set = workspace.image_set
image = image_set.get_image(self.image_name.value, must_be_binary=True)
mask = image.pixel_data
if image.has_mask:
mask = mask & image.mask
angle_count = self.angle_count.value
#
# We collect the i,j and angle of pairs of points that
# are 3-d adjacent after erosion.
#
# i - the i coordinate of each point found after erosion
# j - the j coordinate of each point found after erosion
# a - the angle of the structuring element for each point found
#
i = np.zeros(0, int)
j = np.zeros(0, int)
a = np.zeros(0, int)
ig, jg = np.mgrid[0:mask.shape[0], 0:mask.shape[1]]
#this_idx = 0
for angle_number in range(angle_count):
angle = float(angle_number) * np.pi / float(angle_count)
strel = self.get_diamond(angle)
erosion = binary_erosion(mask, strel)
#
# Accumulate the count, i, j and angle for all foreground points
# in the erosion
#
this_count = np.sum(erosion)
i = np.hstack((i, ig[erosion]))
j = np.hstack((j, jg[erosion]))
a = np.hstack((a, np.ones(this_count, float) * angle))
#
# Find connections based on distances, not adjacency
#
first, second = self.find_adjacent_by_distance(i, j, a)
#
# Do all connected components.
#
if len(first) > 0:
ij_labels = all_connected_components(first, second) + 1
nlabels = np.max(ij_labels)
label_indexes = np.arange(1, nlabels + 1)
#
# Compute the measurements
#
center_x = fix(mean_of_labels(j, ij_labels, label_indexes))
center_y = fix(mean_of_labels(i, ij_labels, label_indexes))
#
# The angles are wierdly complicated because of the wrap-around.
# You can imagine some horrible cases, like a circular patch of
# "linear object" in which all angles are represented or a gentle "U"
# curve.
#
# For now, I'm going to use the following heuristic:
#
# Compute two different "angles". The angles of one go
# from 0 to 180 and the angles of the other go from -90 to 90.
# Take the variance of these from the mean and
# choose the representation with the lowest variance.
#
# An alternative would be to compute the variance at each possible
# dividing point. Another alternative would be to actually trace through
# the connected components - both overkill for such an inconsequential
# measurement I hope.
#
angles = fix(mean_of_labels(a, ij_labels, label_indexes))
vangles = fix(
mean_of_labels((a - angles[ij_labels - 1])**2, ij_labels,
label_indexes))
aa = a.copy()
aa[a > np.pi / 2] -= np.pi
aangles = fix(mean_of_labels(aa, ij_labels, label_indexes))
vaangles = fix(
mean_of_labels((aa - aangles[ij_labels - 1])**2, ij_labels,
label_indexes))
aangles[aangles < 0] += np.pi
angles[vaangles < vangles] = aangles[vaangles < vangles]
else:
center_x = np.zeros(0, int)
center_y = np.zeros(0, int)
angles = np.zeros(0)
nlabels = 0
label_indexes = np.zeros(0, int)
labels = np.zeros(mask.shape, int)
ifull = []
jfull = []
ij_labelsfull = []
labeldict = {}
for label_id in np.unique(label_indexes):
r = np.array(i) * (ij_labels == label_id)
r = r[r != 0]
c = np.array(j) * (ij_labels == label_id)
c = c[c != 0]
rect_strel = self.get_rectangle(angles[label_id - 1])
seedmask = np.zeros_like(mask, int)
seedmask[r, c] = label_id
reconstructedlinearobject = maximum(seedmask, rect_strel)
reconstructedlinearobject = reconstructedlinearobject * mask
if self.overlap_within_angle == False:
itemp, jtemp = np.where(reconstructedlinearobject == label_id)
ifull += list(itemp)
jfull += list(jtemp)
ij_labelsfull += [label_id] * len(itemp)
else:
itemp, jtemp = np.where(reconstructedlinearobject == label_id)
labeldict[label_id] = zip(itemp, jtemp)
if self.overlap_within_angle == True:
angledict = {}
for eachangle in range(len(angles)):
angledict[eachangle + 1] = [angles[eachangle]]
nmerges = 1
while nmerges != 0:
nmerges = sum([
self.mergeduplicates(firstlabel, secondlabel, labeldict,
angledict)
for firstlabel in label_indexes
for secondlabel in label_indexes
if firstlabel != secondlabel
])
newlabels = labeldict.keys()
newlabels.sort()
newangles = angledict.keys()
newangles.sort()
angles = []
for eachnewlabel in range(len(newlabels)):
ifull += [
int(eachloc[0])
for eachloc in labeldict[newlabels[eachnewlabel]]
]
jfull += [
int(eachloc[1])
for eachloc in labeldict[newlabels[eachnewlabel]]
]
ij_labelsfull += [eachnewlabel + 1] * len(
labeldict[newlabels[eachnewlabel]])
angles.append(np.mean(angledict[newlabels[eachnewlabel]]))
angles = np.array(angles)
ijv = np.zeros([len(ifull), 3], dtype=int)
ijv[:, 0] = ifull
ijv[:, 1] = jfull
ijv[:, 2] = ij_labelsfull
#
# Make the objects
#
object_set = workspace.object_set
object_name = self.object_name.value
assert isinstance(object_set, cpo.ObjectSet)
objects = cpo.Objects()
objects.ijv = ijv
objects.parent_image = image
object_set.add_objects(objects, object_name)
if self.show_window:
workspace.display_data.mask = mask
workspace.display_data.overlapping_labels = [
l for l, idx in objects.get_labels()
]
if self.overlap_within_angle == True:
center_x = np.bincount(ijv[:, 2],
ijv[:, 1])[objects.indices] / objects.areas
center_y = np.bincount(ijv[:, 2],
ijv[:, 0])[objects.indices] / objects.areas
m = workspace.measurements
assert isinstance(m, cpmeas.Measurements)
m.add_measurement(object_name, I.M_LOCATION_CENTER_X, center_x)
m.add_measurement(object_name, I.M_LOCATION_CENTER_Y, center_y)
m.add_measurement(object_name, M_ANGLE, angles * 180 / np.pi)
m.add_measurement(object_name, I.M_NUMBER_OBJECT_NUMBER, label_indexes)
m.add_image_measurement(I.FF_COUNT % object_name, nlabels)
probs = sv.predict(td)
out_cell = np.reshape(probs,(winds.shape[0],winds.shape[1]))
plt.figure()
plt.subplot(121)
plt.imshow(out_cell)
try:
io.imsave('C:/users/attialex/Desktop/out_cell_4.png',skimage.img_as_uint(out_cell))
except Exception as e:
print e.message
try:
bg = normalize3Chan(imex*1.)
fg_c = normalize3Chan(out_cell)
fg_c[:,:,0]=0;
fg_c[:,:,2]=0;
s1 = cv2.addWeighted(bg,.8,fg_c,.2,0)
cv2.imshow('cell',s1)
cv2.waitKey()
except Exception as e:
print e.message
max_cell = maximum(out_cell,np.ones((40,40)))
unique_cell = np.unique(max_cell)
plt.show()
.. note::
`skimage.dilate` and `skimage.erode` are equivalent filters (see below for
comparison).
Here is an example of the classical morphological gray-level filters: opening,
closing and morphological gradient.
"""
from skimage.filter.rank import maximum, minimum, gradient
noisy_image = img_as_ubyte(data.camera())
closing = maximum(minimum(noisy_image, disk(5)), disk(5))
opening = minimum(maximum(noisy_image, disk(5)), disk(5))
grad = gradient(noisy_image, disk(5))
# display results
fig = plt.figure(figsize=[10, 7])
plt.subplot(2, 2, 1)
plt.imshow(noisy_image, cmap=plt.cm.gray)
plt.title('Original')
plt.axis('off')
plt.subplot(2, 2, 2)
plt.imshow(closing, cmap=plt.cm.gray)
plt.title('Gray-level closing')
plt.axis('off')
.. note::
`skimage.dilate` and `skimage.erode` are equivalent filters (see below for
comparison).
Here is an example of the classical morphological greylevel filters: opening,
closing and morphological gradient.
"""
from skimage.filter.rank import maximum, minimum, gradient
ima = data.camera()
closing = maximum(minimum(ima, disk(5)), disk(5))
opening = minimum(maximum(ima, disk(5)), disk(5))
grad = gradient(ima, disk(5))
# display results
fig = plt.figure(figsize=[10, 7])
plt.subplot(2, 2, 1)
plt.imshow(ima, cmap=plt.cm.gray)
plt.xlabel('original')
plt.subplot(2, 2, 2)
plt.imshow(closing, cmap=plt.cm.gray)
plt.xlabel('greylevel closing')
plt.subplot(2, 2, 3)
plt.imshow(opening, cmap=plt.cm.gray)
plt.xlabel('greylevel opening')
plt.subplot(2, 2, 4)
plt.subplot(122)
plt.imshow(out_pile)
try:
io.imsave('C:/users/attialex/Desktop/out_pile_3.png',skimage.img_as_uint(out_pile))
io.imsave('C:/users/attialex/Desktop/out_cell_3.png',skimage.img_as_uint(out_cell))
except Exception as e:
print e.message
try:
bg = normalize3Chan(imex*1.)
fg_c = normalize3Chan(out_cell)
fg_p = normalize3Chan(out_pile)
fg_c[:,:,0]=0;
fg_c[:,:,2]=0;
s1 = cv2.addWeighted(bg,.8,fg_c,.2,0)
cv2.imshow('cell',s1)
s2 = cv2.addWeighted(bg,.8,fg_p,.2,0)
cv2.imshow('pile',s2)
cv2.waitKey()
except Exception as e:
print e.message
max_pile = maximum(out_pile,np.ones((40,40)))
unique_pile = np.unique(max_pile)
max_cell = maximum(out_cell,np.ones((40,40)))
unique_cell = np.unique(max_cell)
plt.show()
def cr_max(image, selem):
return maximum(image=image, selem=selem)
def cr_max(image, selem):
return maximum(image=image, selem=selem)
counter += 1
print 'predicting'
probs = sv.predict(td)
out_cell = np.reshape(probs, (winds.shape[0], winds.shape[1]))
plt.figure()
plt.subplot(121)
plt.imshow(out_cell)
try:
io.imsave('C:/users/attialex/Desktop/out_cell_4.png',
skimage.img_as_uint(out_cell))
except Exception as e:
print e.message
try:
bg = normalize3Chan(imex * 1.)
fg_c = normalize3Chan(out_cell)
fg_c[:, :, 0] = 0
fg_c[:, :, 2] = 0
s1 = cv2.addWeighted(bg, .8, fg_c, .2, 0)
cv2.imshow('cell', s1)
cv2.waitKey()
except Exception as e:
print e.message
max_cell = maximum(out_cell, np.ones((40, 40)))
unique_cell = np.unique(max_cell)
plt.show()
