def test_tv_denoise_2d(self):
"""
Apply the TV denoising algorithm on the lena image provided
by scipy
"""
# lena image
lena = color.rgb2gray(data.lena())[:256, :256]
# add noise to lena
lena += 0.5 * lena.std() * np.random.randn(*lena.shape)
# clip noise so that it does not exceed allowed range for float images.
lena = np.clip(lena, 0, 1)
# denoise
denoised_lena = filter.tv_denoise(lena, weight=60.0)
# which dtype?
assert denoised_lena.dtype in [np.float, np.float32, np.float64]
from scipy import ndimage
grad = ndimage.morphological_gradient(lena, size=((3, 3)))
grad_denoised = ndimage.morphological_gradient(
denoised_lena, size=((3, 3)))
# test if the total variation has decreased
assert np.sqrt(
(grad_denoised ** 2).sum()) < np.sqrt((grad ** 2).sum()) / 2
denoised_lena_int = filter.tv_denoise(img_as_uint(lena),
weight=60.0, keep_type=True)
assert denoised_lena_int.dtype is np.dtype('uint16')
def do_watershed(image, markers, tfile, shape, bstruct, algorithm, mg_size, use_ww_wl, wl, ww, q):
mask = np.memmap(tfile, shape=shape, dtype='uint8', mode='r+')
if use_ww_wl:
if algorithm == 'Watershed':
tmp_image = ndimage.morphological_gradient(
get_LUT_value(image, ww, wl).astype('uint16'),
mg_size)
tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)
else:
tmp_image = get_LUT_value(image, ww, wl).astype('uint16')
#tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)
#tmp_image = ndimage.morphological_gradient(
#get_LUT_value(image, ww, wl).astype('uint16'),
#self.config.mg_size)
tmp_mask = watershed_ift(tmp_image, markers.astype('int16'), bstruct)
else:
if algorithm == 'Watershed':
tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), mg_size)
tmp_mask = watershed(tmp_image, markers.astype('int16'), bstruct)
else:
tmp_image = (image - image.min()).astype('uint16')
#tmp_image = ndimage.gaussian_filter(tmp_image, self.config.mg_size)
#tmp_image = ndimage.morphological_gradient((image - image.min()).astype('uint16'), self.config.mg_size)
tmp_mask = watershed_ift(tmp_image, markers.astype('int8'), bstruct)
mask[:] = tmp_mask
mask.flush()
q.put(1)
def compute_sparsity(im):
l_x = len(im)
X, Y = np.ogrid[:l_x, :l_x]
mask = ((X - l_x/2)**2 + (Y - l_x/2)**2 <= (l_x/2)**2)
grad1 = ndimage.morphological_gradient(im, footprint=np.ones((3, 3)))
grad2 = ndimage.morphological_gradient(im, footprint=ndimage.generate_binary_structure(2, 1))
return (grad1[mask] > 0).mean(), (grad2[mask] > 0).mean()
def expand_watershed(self, pubsub_evt):
markers = self.matrix
image = self.viewer.slice_.matrix
self.viewer.slice_.do_threshold_to_all_slices()
mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:]
ww = self.viewer.slice_.window_width
wl = self.viewer.slice_.window_level
if BRUSH_BACKGROUND in markers and BRUSH_FOREGROUND in markers:
tmp_image = ndimage.morphological_gradient(get_LUT_value(image, ww, wl).astype('uint16'), self.mg_size)
tmp_mask = watershed(tmp_image, markers)
if self.viewer.overwrite_mask:
mask[:] = 0
mask[tmp_mask == 1] = 253
else:
mask[(tmp_mask==2) & ((mask == 0) | (mask == 2) | (mask == 253))] = 2
mask[(tmp_mask==1) & ((mask == 0) | (mask == 2) | (mask == 253))] = 253
#mask[:] = tmp_mask
self.viewer.slice_.current_mask.matrix[0] = 1
self.viewer.slice_.current_mask.matrix[:, 0, :] = 1
self.viewer.slice_.current_mask.matrix[:, :, 0] = 1
self.viewer.slice_.discard_all_buffers()
self.viewer.slice_.current_mask.clear_history()
Publisher.sendMessage('Reload actual slice')
def plot_wireframe(image, n_bubble=1):
# Position the scan upright,
# so the head of the patient would be at the top facing the camera
#p = image.transpose(2,1,0)
R = measure.regionprops(image)
print 'total bubbles', len(R)
top_n = sorted([(r.area, r.label) for r in R])[::-1][:n_bubble]
top_n_R = [R[i-1] for a,i in top_n]
neighborhood = ndimage.morphology.generate_binary_structure(3, 2)
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111, projection='3d')
for r in top_n_R:
print r.label, r.area
p = r.image
outline = ndimage.morphological_gradient(p, structure=neighborhood)
print outline.shape
ax.plot_wireframe(np.where(outline))
ax.set_xlim(0, p.shape[0])
ax.set_ylim(0, p.shape[1])
ax.set_zlim(0, p.shape[2])
plt.show()
def test_denoise_tv_chambolle_2d():
# astronaut image
img = astro_gray.copy()
# add noise to astronaut
img += 0.5 * img.std() * np.random.rand(*img.shape)
# clip noise so that it does not exceed allowed range for float images.
img = np.clip(img, 0, 1)
# denoise
denoised_astro = restoration.denoise_tv_chambolle(img, weight=0.1)
# which dtype?
assert_(denoised_astro.dtype in [np.float, np.float32, np.float64])
from scipy import ndimage as ndi
grad = ndi.morphological_gradient(img, size=((3, 3)))
grad_denoised = ndi.morphological_gradient(denoised_astro, size=((3, 3)))
# test if the total variation has decreased
assert_(grad_denoised.dtype == np.float)
assert_(np.sqrt((grad_denoised**2).sum()) < np.sqrt((grad**2).sum()))
def test_denoise_tv_chambolle_2d():
# lena image
img = lena_gray
# add noise to lena
img += 0.5 * img.std() * np.random.random(img.shape)
# clip noise so that it does not exceed allowed range for float images.
img = np.clip(img, 0, 1)
# denoise
denoised_lena = restoration.denoise_tv_chambolle(img, weight=60.0)
# which dtype?
assert denoised_lena.dtype in [np.float, np.float32, np.float64]
from scipy import ndimage
grad = ndimage.morphological_gradient(img, size=((3, 3)))
grad_denoised = ndimage.morphological_gradient(denoised_lena, size=((3, 3)))
# test if the total variation has decreased
assert grad_denoised.dtype == np.float
assert np.sqrt((grad_denoised ** 2).sum()) < np.sqrt((grad ** 2).sum()) / 2
def test_tv_denoise_2d(self):
"""
Apply the TV denoising algorithm on the lena image provided
by scipy
"""
# lena image
lena = color.rgb2gray(data.lena())
# add noise to lena
lena += 0.5 * lena.std()*np.random.randn(*lena.shape)
# denoise
denoised_lena = filter.tv_denoise(lena, weight=60.0)
# which dtype?
assert denoised_lena.dtype in [np.float, np.float32, np.float64]
from scipy import ndimage
grad = ndimage.morphological_gradient(lena, size=((3,3)))
grad_denoised = ndimage.morphological_gradient(denoised_lena, size=((3,3)))
# test if the total variation has decreased
assert np.sqrt((grad_denoised**2).sum()) < np.sqrt((grad**2).sum()) / 2
denoised_lena_int = filter.tv_denoise(lena.astype(np.int32), \
weight=60.0, keep_type=True)
assert denoised_lena_int.dtype is np.dtype('int32')
def compute_best_J(im):
# A more precise computation of sisj could be done...
l_x = len(im)
X, Y = np.ogrid[:l_x, :l_x]
mask = ((X - l_x/2)**2 + (Y - l_x/2)**2 <= (l_x/2)**2)
grad = ndimage.morphological_gradient(im, footprint=np.ones((3, 3)))
sisj_average = 1 - (grad[mask] > 0).mean()
J1 = np.arctanh(sisj_average)
grad2 = np.abs(np.diff(im, axis=0))[:, :-1] + np.abs(np.diff(im, axis=1))[:-1]
sisj_average = 1 - 2*(grad2[mask[:-1, :-1]] > 0).mean()
J2 = np.arctanh(sisj_average)
return J1, J2
def separate_lungs(image, return_list=None, iteration=-1):
"""
This only takes in a 2D slice to make he lung segmentation and takes really long to run.
But supposedly will get all corner cases. Not sure if mask from this is very good.
Looks like the mask might be too dilated.
:param image:
:param return_list:
:param iteration:
:return:
"""
#Creation of the markers as shown above:
marker_internal, marker_external, marker_watershed = generate_markers(
image)
#Creation of the Sobel-Gradient
sobel_filtered_dx = ndimage.sobel(image, 1)
sobel_filtered_dy = ndimage.sobel(image, 0)
sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
sobel_gradient *= 255.0 / np.max(sobel_gradient)
#Watershed algorithm
watershed = morphology.watershed(sobel_gradient, marker_watershed)
#Reducing the image created by the Watershed algorithm to its outline
outline = ndimage.morphological_gradient(watershed, size=(3, 3))
outline = outline.astype(bool)
#Performing Black-Tophat Morphology for reinclusion
#Creation of the disk-kernel and increasing its size a bit
blackhat_struct = [[0, 0, 1, 1, 1, 0, 0], [0, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1], [0, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 0, 0]]
blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
#Perform the Black-Hat
outline += ndimage.black_tophat(outline, structure=blackhat_struct)
#Use the internal marker and the Outline that was just created to generate the lungfilter
lungfilter = np.bitwise_or(marker_internal, outline)
#Close holes in the lungfilter
#fill_holes is not used here, since in some slices the heart would be reincluded by accident
lungfilter = ndimage.morphology.binary_closing(lungfilter,
structure=np.ones((5, 5)),
iterations=3)
# #Apply the lungfilter (note the filtered areas being assigned -2000 HU)
# segmented = np.where(lungfilter == 1, image, -2000*np.ones((512, 512)))
if iteration >= 0 and return_list:
return_list[iteration] = lungfilter
else:
return lungfilter
def get_segmented_lungs(image):
#Creation of the markers as shown above:
marker_internal, marker_external, marker_watershed = generate_markers(image)
#Creation of the Sobel-Gradient
sobel_filtered_dx = ndimage.sobel(image, 1)
sobel_filtered_dy = ndimage.sobel(image, 0)
sobel_gradient = np.hypot(sobel_filtered_dx, sobel_filtered_dy)
sobel_gradient *= 255.0 / np.max(sobel_gradient)
#Watershed algorithm
watershed = morphology.watershed(sobel_gradient, marker_watershed)
#Reducing the image created by the Watershed algorithm to its outline
outline = ndimage.morphological_gradient(watershed, size=(3,3))
outline = outline.astype(bool)
#Performing Black-Tophat Morphology for reinclusion
#Creation of the disk-kernel and increasing its size a bit
blackhat_struct = [[0, 0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 0, 0]]
#blackhat_struct = ndimage.iterate_structure(blackhat_struct, 8)
blackhat_struct = ndimage.iterate_structure(blackhat_struct, 14) # <- retains more of the area, 12 works well. Changed to 14, 12 still excluded some parts.
#Perform the Black-Hat
outline += ndimage.black_tophat(outline, structure=blackhat_struct)
#Use the internal marker and the Outline that was just created to generate the lungfilter
lungfilter = np.bitwise_or(marker_internal, outline)
#Close holes in the lungfilter
#fill_holes is not used here, since in some slices the heart would be reincluded by accident
lungfilter = ndimage.morphology.binary_closing(lungfilter, structure=np.ones((5,5)), iterations=3)
#Apply the lungfilter (note the filtered areas being assigned threshold_min HU)
segmented = np.where(lungfilter == 1, image, threshold_min*np.ones(image.shape))
#return segmented, lungfilter, outline, watershed, sobel_gradient, marker_internal, marker_external, marker_watershed
return segmented
def OnBrushRelease(self, evt, obj):
n = self.viewer.slice_data.number
self.viewer.slice_.discard_all_buffers()
if self.orientation == 'AXIAL':
image = self.viewer.slice_.matrix[n]
mask = self.viewer.slice_.current_mask.matrix[n+1, 1:, 1:]
self.viewer.slice_.current_mask.matrix[n+1, 0, 0] = 1
markers = self.matrix[n]
elif self.orientation == 'CORONAL':
image = self.viewer.slice_.matrix[:, n, :]
mask = self.viewer.slice_.current_mask.matrix[1:, n+1, 1:]
self.viewer.slice_.current_mask.matrix[0, n+1, 0]
markers = self.matrix[:, n, :]
elif self.orientation == 'SAGITAL':
image = self.viewer.slice_.matrix[:, :, n]
mask = self.viewer.slice_.current_mask.matrix[1: , 1:, n+1]
self.viewer.slice_.current_mask.matrix[0 , 0, n+1]
markers = self.matrix[:, :, n]
ww = self.viewer.slice_.window_width
wl = self.viewer.slice_.window_level
if BRUSH_BACKGROUND in markers and BRUSH_FOREGROUND in markers:
tmp_image = ndimage.morphological_gradient(get_LUT_value(image, ww, wl).astype('uint16'), self.mg_size)
tmp_mask = watershed(tmp_image, markers)
if self.viewer.overwrite_mask:
mask[:] = 0
mask[tmp_mask == 1] = 253
else:
mask[(tmp_mask==2) & ((mask == 0) | (mask == 2) | (mask == 253))] = 2
mask[(tmp_mask==1) & ((mask == 0) | (mask == 2) | (mask == 253))] = 253
self.viewer.slice_.current_mask.was_edited = True
self.viewer.slice_.current_mask.clear_history()
Publisher.sendMessage('Reload actual slice')
else:
self.viewer.OnScrollBar(update3D=False)
def get_training_data( file_img, file_mask, r ):
# create mask
input_mask = irtk.imread( file_mask )
x_min, y_min, z_min, x_max, y_max, z_max = (input_mask == 0).bbox()
background = irtk.zeros( input_mask.get_header(), dtype='uint8' )
background[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1] = 1
background = nd.morphological_gradient( background, size=7)
n = background[z_min+1:z_max,
y_min+1:y_max,
x_min+1:x_max].sum()
z = np.random.randint(low=0, high=input_mask.shape[0],size=1.25*n)
y = np.random.randint(low=0, high=input_mask.shape[1],size=1.25*n)
x = np.random.randint(low=0, high=input_mask.shape[2],size=1.25*n)
background[z,y,x] = 1
background[z_min+1:z_max,
y_min+1:y_max,
x_min+1:x_max] = 0
foreground = (input_mask == 1).astype('uint8')
new_mask = irtk.zeros( input_mask.get_header(), dtype='uint8' )
new_mask[foreground == 1] = 1
new_mask[background != 0] = 2
img = irtk.imread( file_img, dtype='float32' )
X = []
Y = []
for z in xrange(img.shape[0]):
YX = np.transpose( np.nonzero( foreground[z] ) )
if DEBUG:
YX = YX[::10]
else:
YX = YX[::2]
if YX.shape[0] == 0:
continue
patches = extract_patches2D( img[z], r, YX )
patches = np.reshape( patches, (patches.shape[0],patches.shape[1]*patches.shape[2]) )
print patches.shape, YX.shape
X.extend( patches )
Y.extend( [1]*len(YX) )
for z in xrange(img.shape[0]):
YX = np.transpose( np.nonzero( background[z] ) )
if DEBUG:
YX = YX[::10]
else:
YX = YX[::2]
if YX.shape[0] == 0:
continue
patches = extract_patches2D( img[z], r, YX )
patches = np.reshape( patches, (patches.shape[0],patches.shape[1]*patches.shape[2]) )
print patches.shape, YX.shape
X.extend( patches )
Y.extend( [0]*len(YX) )
return X, Y
def mask_image( file_img, file_mask, ga, r, neigh, output_dir ):
img = irtk.imread( file_img, dtype='float32' )
input_mask = irtk.imread( file_mask )
print "predicting..."
res = irtk.zeros( img.get_header(), dtype='float32' )
res2 = irtk.zeros( img.get_header(), dtype='float32' )
res3 = irtk.zeros( img.get_header(), dtype='float32' )
res4 = irtk.zeros( img.get_header(), dtype='uint8' )
mask = irtk.ones( input_mask.get_header(), dtype='uint8' )
mask[input_mask == 2] = 0
for z in xrange(img.shape[0]):
print z
YX = np.transpose( np.nonzero( mask[z] ) )
if YX.shape[0] == 0:
continue # this slice does not intersect the box
patches = extract_patches2D( img[z], r, YX )
patches = np.reshape( patches, (patches.shape[0],patches.shape[1]*patches.shape[2]) )
predictions = neigh.predict_proba(patches)[:,1]
res[z,YX[:,0],YX[:,1]] = predictions
x_min, y_min, z_min, x_max, y_max, z_max = mask.bbox()
proba = res[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1]
if args.mass:
BV = get_BV( args.ga )
box_volume = (z_max-z_min)*img.header['pixelSize'][2]*(y_max-y_min)*img.header['pixelSize'][1]*(x_max-x_min)*img.header['pixelSize'][0]
ratio = float(BV) / float(box_volume)
print "ratio", ratio
q0,q1 = mquantiles( proba.flatten(), prob=[0.5*(1.0-ratio),
1.0-0.5*ratio] )
print "threshold", q0,q1
#threshold = max(0.5,threshold)
# labels = res[z_min:z_max+1,
# y_min:y_max+1,
# x_min:x_max+1] > threshold
#res = 1 / (np.exp(-(res-threshold)/(res.max()-res.min())))
res[res<q0] = q0
res[res>q1] = q1
res -= res.min()
res /= res.max()
labels = res[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1] > 0.5
proba = res[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1]
cropped_img = img[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1]
if args.do_3D:
labels = irtk.crf( cropped_img,
labels,
proba,
l=args.l,
sigma=get_noiseXY(cropped_img),
sigmaZ=get_noiseZ(cropped_img) )
# elif args.do_patchZ:
# labels = irtk.crf_patchZ( cropped_img,
# labels,
# proba,
# l=10.0 )
# else:
# for z in xrange(z_min,z_max+1):
# labels[z] = irtk.crf( cropped_img[z],
# labels[z],
# proba[z],
# l=1.0 )
print "MAX LABEL:", labels.max()
irtk.imwrite(output_dir + "/bare_"+os.path.basename(file_img), labels )
tmp = irtk.zeros( img.get_header(), dtype='uint8' )
tmp[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1] = labels
( min_x_bare, min_y_bare, min_z_bare,
max_x_bare, max_y_bare, max_z_bare ) = tmp.bbox()
if not args.no_cleaning:
# clean by fitting ellipses enlarged of 10%
for z in xrange(labels.shape[0]):
edges = nd.morphological_gradient( labels[z] > 0,size=5 )
points = np.transpose(edges.nonzero())[:,::-1]
if len(points) == 0:
continue
points = np.array(map(lambda x:[x],points),dtype='int32')
ellipse = cv2.fitEllipse(points)
cv2.ellipse( labels[z], (ellipse[0],
(1.1*ellipse[1][0],1.1*ellipse[1][1]),
ellipse[2]) , 1, -1 )
irtk.imwrite(output_dir + "/seg_"+os.path.basename(file_img), labels )
irtk.imwrite(output_dir + "/res_"+os.path.basename(file_img), res )
# re-read the image in case we processed it
img = irtk.imread( file_img, dtype='float32' )
cropped_img = img[z_min:z_max+1,
y_min:y_max+1,
x_min:x_max+1]
cropped_img[labels==0] = -1
masked = cropped_img.bbox(crop=True)
irtk.imwrite(output_dir + "/masked_"+os.path.basename(file_img), masked )
# re-read the image in case we processed it
img = irtk.imread( file_img, dtype='float32' )
x0 = min_x_bare + (max_x_bare - min_x_bare) / 2
y0 = min_y_bare + (max_y_bare - min_y_bare) / 2
ofd = get_OFD(ga)/img.header['pixelSize'][0]
cropped_img = img[min_z_bare:max_z_bare+1,
max(0,int(round(y0-ofd/2))):min(img.shape[1],int(round(y0+ofd/2+1))),
max(0,int(round(x0-ofd/2))):min(img.shape[2],int(round(x0+ofd/2+1)))].copy()
irtk.imwrite(output_dir + "/very_large_"+os.path.basename(file_img),
cropped_img )
cropped_proba = res[min_z_bare:max_z_bare+1,
max(0,int(round(y0-ofd/2))):min(img.shape[1],int(round(y0+ofd/2+1))),
max(0,int(round(x0-ofd/2))):min(img.shape[2],int(round(x0+ofd/2+1)))].copy()
irtk.imwrite(output_dir + "/proba_"+os.path.basename(file_img),
cropped_proba )
def extract_features(image_path_list):
'''
This function takes a list of image paths and computes several features of each
image in order to classify them. This include both basic properties like size
and aspect ratio as well as doing object recognition and counting. This runs at
about 1/s/core on a quad-core with HT 2.93 GHz i7.
'''
feature_list = []
name_list = []
file_list = []
#iterate through all the image paths
for image_path in image_path_list:
image_array = imread(image_path)
feature = []
feature.append(image_array.size)
shape = image_array.shape
#check if the image isblack or white
if len(shape) > 2:
feature.append(1)
#convert color images to grey so they can be compared with greyscale ones
image_array = color.rgb2grey(image_array)
'''
# Can't use these because there is nothing comparable for black and
# white images
feature.append(sum(sum(image_array[:,:,0])))
feature.append(sum(sum(image_array[:,:,1])))
feature.append(sum(sum(image_array[:,:,2])))
hsv = color.rgb2hsv(img_as_float(image_array))
feature.append(sum(sum(hsv[:,:,0])))
feature.append(sum(sum(hsv[:,:,1])))
feature.append(sum(sum(hsv[:,:,2])))
'''
else:
feature.append(0)
#print "bw: ", image_path
#determine basic image shape properties
feature.append(shape[0])
feature.append(shape[1])
feature.append(shape[0]/shape[1])
#compute the amount of different shades of grey and their ratios
black = np.average(image_array.flat <= 0.25 )
darkgrey = np.average((image_array.flat > 0.25) & (image_array.flat <= 0.5))
lightgrey = np.average((image_array.flat > 0.5) & (image_array.flat <= 0.75))
white = np.average(image_array.flat > 0.75)
feature.append(black)
feature.append(darkgrey)
feature.append(lightgrey)
feature.append(white)
feature.append(black/(white+1))
feature.append(lightgrey/(darkgrey+1))
feature.append(lightgrey/(black+1))
# compute the average of several common filter outputs
feature.append(np.average(flt.sobel(image_array)))
feature.append(np.average(ndimage.morphological_gradient(image_array, size=(2,2))))
feature.append(np.average(flt.prewitt(image_array)))
feature.append(np.average(flt.canny(image_array)))
#Use the canny filter to delineate object and then count the objects and
#their average size
p = flt.canny(image_array)
#plt.imshow(p,cmap=plt.cm.gray,interpolation='nearest')
#plt.show()
labels, count = ndimage.label(p)
area = np.sum((labels>0))/count
feature.append(area)
feature.append(count)
#determine the filename for the results file and the image type for the
#training set.
filename = image_path.split("/")[-1]
file_list.append(filename)
image = filename.split('_')[0]
name_list.append(image)
feature_list.append(feature)
return name_list, feature_list, file_list
