def compute_mask(self, params):
"""Creates the mask for the base image.
Needs the base image, an instance of imageloaderparams
and the clip area, which should be already defined
by the load_base_image method.
Creates the mask by improving the base mask created by the
compute_base_mask method. Applies the mask closing, dilation and
fill holes parameters.
"""
self.compute_base_mask(params)
mask = np.copy(self.base_mask)
closing_matrix = np.ones((params.mask_closing, params.mask_closing))
if params.mask_closing > 0:
# removes small dark spots and then small white spots
mask = img_as_float(morphology.closing(
mask, closing_matrix))
mask = 1 - \
img_as_float(morphology.closing(
1 - mask, closing_matrix))
for f in range(params.mask_dilation):
mask = morphology.erosion(mask, np.ones((3, 3)))
if params.mask_fill_holes:
# mask is inverted
mask = 1 - img_as_float(ndimage.binary_fill_holes(1.0 - mask))
self.mask = mask
self.overlay_mask_base_image()
def close_image(img, mask_length):
# Morphological closing on greyscale/binary image
img = img.astype(np.uint8)
img = closing(img, rectangle(mask_length,1))
return(img)
def getRegions():
"""Geocode address and retreive image centered
around lat/long"""
address = request.args.get('address')
results = Geocoder.geocode(address)
lat, lng = results[0].coordinates
zip_code = results[0].postal_code
map_url = 'https://maps.googleapis.com/maps/api/staticmap?center={0},{1}&size=640x640&zoom=19&sensor=false&maptype=roadmap&&style=visibility:simplified|gamma:0.1'
request_url = map_url.format(lat, lng)
req = urllib.urlopen(request_url)
img = io.imread(req.geturl(),flatten=True)
labels, numobjects = ndimage.label(img)
image = filter.canny(img, sigma=3)
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(3))
# remove artifacts connected to image border
cleared = bw.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(6, 6))
ax.imshow(image_label_overlay)
def scikit_example_plot_label():
image = data.coins()[50:-50, 50:-50]
# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(3))
# remove artifacts connected to image border
cleared = bw.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(6, 6))
ax.imshow(label_image, cmap='jet')
for region in regionprops(label_image, ['Area', 'BoundingBox']):
# skip small images
if region['Area'] < 100:
continue
# draw rectangle around segmented coins
minr, minc, maxr, maxc = region['BoundingBox']
rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
fill=False, edgecolor='red', linewidth=2)
ax.add_patch(rect)
plt.show()
def threshold_image(image, threshold=0): """ This function takes out any values in an image's RGB matrix that are below the threshold value. Inputs: - image: a matrix describing an image with only one channel represented. - threshold: a value, between 0 and 1, for which if an image matrix's value is below, will be set to 0, and if above, will be set to 1. If the threshold is set to 0, then an Otsu thresholding will be returned. Outputs: - thresholded_image: a matrix representation of the thresholded image. this is essentially a black and white image. - thresh: the threshold value To screen: the black-and-white image representation. - """ if threshold == 0: thresh = threshold_otsu(image) if threshold != 0: thresh = threshold thresholded_image = closing(image > thresh, square(3), out=None) imshow(thresholded_image) return thresholded_image, thresh
def segment_out_cells(base):
# TODO: try using OTSU for GFP thresholding
sel_elem = disk(2)
gfp_collector = np.sum(base, axis=0)
gfp_clustering_markers = np.zeros(gfp_collector.shape, dtype=np.uint8)
# random walker segment
gfp_clustering_markers[gfp_collector > np.mean(gfp_collector) * 2] = 2
gfp_clustering_markers[gfp_collector < np.mean(gfp_collector) * 0.20] = 1
labels = random_walker(gfp_collector, gfp_clustering_markers, beta=10, mode='bf')
# round up the labels and set the background to 0 from 1
labels = closing(labels, sel_elem)
labels -= 1
# prepare distances for the watershed
distance = ndi.distance_transform_edt(labels)
local_maxi = peak_local_max(distance,
indices=False, # we want the image mask, not peak position
min_distance=10, # about half of a bud with our size
threshold_abs=10, # allows to clear the noise
labels=labels)
# we fuse the labels that are close together that escaped the min distance in local_maxi
local_maxi = ndi.convolve(local_maxi, np.ones((5, 5)), mode='constant', cval=0.0)
# finish the watershed
expanded_maxi_markers = ndi.label(local_maxi, structure=np.ones((3, 3)))[0]
segmented_cells_labels = watershed(-distance, expanded_maxi_markers, mask=labels)
# log debugging data
running_debug_frame.gfp_collector = gfp_collector
running_debug_frame.gfp_clustering_markers = gfp_clustering_markers
running_debug_frame.labels = labels
running_debug_frame.segmented_cells_labels = segmented_cells_labels
return gfp_collector, segmented_cells_labels
def smooth(image):
filename_split = os.path.splitext(image)
filename_zero, fileext = filename_split
basename = os.path.basename(filename_zero)
im = np.array(Image.open(image))
with rasterio.open(image) as r:
im = r.read()
p = r.profile
im = im.squeeze()
selem = disk(1)
print("image min and max: ", im.min(),im.max())
dilated = skimage.morphology.dilation(im, selem)
print("dilated image min and max: ", dilated.min(),dilated.max())
eroded = skimage.morphology.erosion(im, selem)
print("eroded image min and max: ", eroded.min(),eroded.max())
opened = opening(im, selem)
print("opened image min and max: ", opened.min(),opened.max())
closed = closing(im, selem)
print("closed image min and max: ", closed.min(),closed.max())
#im[im==1]=0
#im[im==2]=1
median = cv2.medianBlur(im,9)
average = cv2.blur(im,(9,9))
#gaussian = cv2.GaussianBlur(im,(9,9),0)
gaussian = cv2.GaussianBlur(dilated,(9,9),0)
#bilateral = cv2.bilateralFilter(im,9,75,75)
bilateral = cv2.bilateralFilter(gaussian,9,75,75)
with rasterio.open(outPath+basename+fileext, 'w', **p) as dst:
dst.write(bilateral, 1)
color_outPath = outPath+'color/'
if not os.path.exists(color_outPath):
os.mkdir(color_outPath)
colored_image = color_outPath+basename+'.png'
os.system("gdaldem color-relief", bilateral, colorfile, colored_image)
return im, dilated, eroded, opened, closed, median, average, gaussian, bilateral
def plot_preprocessed_image(self):
"""
plots pre-processed image. The plotted image is the same as obtained at the end
of the get_text_candidates method.
"""
image = restoration.denoise_tv_chambolle(self.image, weight=0.1)
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(2))
cleared = bw.copy()
label_image = measure.label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(12, 12))
ax.imshow(image_label_overlay)
for region in regionprops(label_image):
if region.area < 10:
continue
minr, minc, maxr, maxc = region.bbox
rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
fill=False, edgecolor='red', linewidth=2)
ax.add_patch(rect)
plt.show()
def detectOpticDisc(image):
kernel = octagon(10, 10)
thresh = threshold_otsu(image[:,:,1])
binary = image > thresh
print binary.dtype
luminance = convertToHLS(image)[:,:,2]
t = threshold_otsu(luminance)
t = erosion(luminance, kernel)
labels = segmentation.slic(image[:,:,1], n_segments = 3)
out = color.label2rgb(labels, image[:,:,1], kind='avg')
skio.imshow(out)
x, y = computeCentroid(t)
print x, y
rows, cols, _ = image.shape
p1 = closing(image[:,:,1],kernel)
p2 = opening(p1, kernel)
p3 = reconstruction(p2, p1, 'dilation')
p3 = p3.astype(np.uint8)
#g = dilation(p3, kernel)-erosion(p3, kernel)
#g = rank.gradient(p3, disk(5))
g = cv2.morphologyEx(p3, cv2.MORPH_GRADIENT, kernel)
#markers = rank.gradient(p3, disk(5)) < 10
markers = drawCircle(rows, cols, x, y, 85)
#markers = ndimage.label(markers)[0]
#skio.imshow(markers)
g = g.astype(np.uint8)
#g = cv2.cvtColor(g, cv2.COLOR_GRAY2RGB)
w = watershed(g, markers)
print np.max(w), np.min(w)
w = w.astype(np.uint8)
#skio.imshow(w)
return w
def closing(gray_img, kernel=None):
"""Wrapper for scikit-image closing functions. Opening can remove small dark spots (i.e. pepper).
Inputs:
gray_img = input image (grayscale or binary)
kernel = optional neighborhood, expressed as an array of 1s and 0s. If None, use cross-shaped structuring element.
:param gray_img: ndarray
:param kernel = ndarray
:return filtered_img: ndarray
"""
params.device += 1
# Make sure the image is binary/grayscale
if len(np.shape(gray_img)) != 2:
fatal_error("Input image must be grayscale or binary")
# If image is binary use the faster method
if len(np.unique(gray_img)) == 2:
bool_img = morphology.binary_closing(image=gray_img, selem=kernel)
filtered_img = np.copy(bool_img.astype(np.uint8) * 255)
# Otherwise use method appropriate for grayscale images
else:
filtered_img = morphology.closing(gray_img, kernel)
if params.debug == 'print':
print_image(filtered_img, os.path.join(params.debug_outdir, str(params.device) + '_opening' + '.png'))
elif params.debug == 'plot':
plot_image(filtered_img, cmap='gray')
return filtered_img
def Mask_ROI_cl(im,disk_size,thresh=None,black_spots=None,with_morph=False):
l=np.array([0,0])
if not isinstance(im,l.__class__):
numpy_array=np.array(im)
else:
numpy_array=im
if len(numpy_array.shape)==3:
numpy_array=numpy_array[:,:,0:3].mean(axis=2)
selem = disk(disk_size)
closed = closing(numpy_array, selem)
if thresh is None:
thresh = threshold_otsu(closed)
binary = closed > thresh
if binary.dtype=='bool':
binary=binary+0
if black_spots is not None:
binary2 = closed > black_spots
binary2 = binary2 + 0
binary = binary - binary2
else:
binary -=1
binary=binary * -1
if with_morph:
return(binary,closed)
else:
return(binary)
def test_large_radius():
''' Compare execution time against scikit: single closing case
Here, our implementation does not take advantage of smaller radius results
so ours is slower than scikit, but it uses significantly less memory.
'''
base_dir = '/home/omar/data/DATA_NeoBrainS12/'
neo_subject = '30wCoronal/example2/'
# Read subject files
t2CurrentSubjectName = base_dir + 'trainingDataNeoBrainS12/'+neo_subject+'T2_1-1.nii.gz'
t2CurrentSubject_data = nib.load(t2CurrentSubjectName).get_data()
affineT2CS = nib.load(t2CurrentSubjectName).get_affine()
zoomsT2CS = nib.load(t2CurrentSubjectName).get_header().get_zooms()[:3]
# Step 1.4 - Resampling for isotropic voxels
n_zooms = (zoomsT2CS[0],zoomsT2CS[0],zoomsT2CS[0])
t2CurrentSubject_data,affineT2CS = reslice(t2CurrentSubject_data,affineT2CS,zoomsT2CS,n_zooms)
S = t2CurrentSubject_data.astype(np.float64)
###########compare times#########
# in-house
radius = 15
start = time.time()
d = isotropic_dilation(S, radius)
c = isotropic_erosion(d, radius)
end = time.time()
print('Elapsed (in-home): %f'%(end-start,))
# scikit
start = time.time()
expected = closing(S, ball(radius))
end = time.time()
print('Elapsed (scikit): %f'%(end-start,))
def removeChessboard(img):
# Get the major lines in the image
edges, dilatedEdges, (h, theta, d) = findLines(img)
# Create image with ones to fill inn lines
lines = np.ones(img.shape[:2])
# Add lines to image as zeroes
for _, angle, dist in zip(*hough_line_peaks(h, theta, d)):
y0 = (dist - 0 * np.cos(angle)) / np.sin(angle)
y1 = (dist - img.shape[1] * np.cos(angle)) / np.sin(angle)
x, y = line(int(y1), 0, int(y0), img.shape[1] - 1)
x = np.clip(x, 0, img.shape[0] - 1)
y = np.clip(y, 0, img.shape[1] - 1)
lines[x, y] = 0
# Remove border edges from image with all edges
w = 4
edges = np.pad(edges[w:img.shape[0] - w, w:img.shape[1] - w], w, mode='constant')
# Erode the lines bigger, such that they cover the original lines
lines = erosion(lines, square(13))
# Remove major lines and close shape paths
removedChessboard = closing(edges * lines, square(8))
return removedChessboard
def roofRegion(edge):
"""Estimate region based on edges of roofRegion
"""
# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(3))
# remove artifacts connected to image border
cleared = bw.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(6, 6))
ax.imshow(image_label_overlay)
for region in regionprops(label_image):
# skip small images
if region.area < 100:
continue
# draw rectangle around segmented coins
minr, minc, maxr, maxc = region.bbox
rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
fill=False, edgecolor='red', linewidth=2)
ax.add_patch(rect)
plt.show()
def get_valley_image(self, image):
valley_img = np.zeros_like(image)
for z in range(0, image.shape[0]):
valley_img[z, :, :] = closing(image[z, :, :], disk(5))
valley_img -= image
return valley_img
def Image_ws_tranche(image):
laser = Detect_laser(image)
laser_tranche = tranche_image(laser,60)
image_g = skimage.color.rgb2gray(image)
image_g = image_g * laser_tranche
image_med = rank2.median((image_g*255).astype('uint8'),disk(8))
image_clahe = exposure.equalize_adapthist(image_med, clip_limit=0.03)
image_clahe_stretch = exposure.rescale_intensity(image_clahe, out_range=(0, 256))
image_grad = rank2.gradient(image_clahe_stretch,disk(3))
image_grad_mark = image_grad<20
image_grad_forws = rank2.gradient(image_clahe_stretch,disk(1))
image_grad_mark_closed = closing(image_grad_mark,disk(1))
Labelised = (skimage.measure.label(image_grad_mark_closed,8,0))+1
Watersheded = watershed(image_grad_forws,Labelised)
cooc = coocurence_liste(Watersheded,laser,3)
x,y = compte_occurences(cooc)
return x,y
def morphOps( imgIn, sizeSE, sizeCC ):
imgOut = imgIn.astype(bool) #boolean image
imgOut = ~imgOut #img negative
imgOut = morphology.remove_small_objects( imgOut, sizeCC ) #cclargest
SE = morphology.selem.disk( sizeSE ) #structuring element
imgOut = morphology.closing(imgOut, SE)
return imgOut
def main():
for file_path in glob.glob("/home/lucas/Downloads/Lucas/GSK 10uM/*.JPG"):
img = data.imread(file_path, as_grey=True)
img = transform.resize(img, [600, 600])
img_color = transform.resize(data.imread(file_path), [600, 600])
img[img >img.mean()-0.1] = 0
# io.imshow(img)
# io.show()
#
edges = canny(img)
bordas_fechadas = closing(img > 0.1, square(15)) # fechando gaps
fill_cells = ndi.binary_fill_holes(bordas_fechadas)
# io.imshow(fill_cells)
# io.show()
img_label = label(fill_cells, background=0)
n= 0
for x in regionprops(img_label):
if x.area < 2000 and x.area > 300:
n +=1
print x.area
minr, minc, maxr, maxc = x.bbox
try:
out_path_name = file_path.split("/")[-1].rstrip(".JPG")
io.imsave("out/cell_{}_pic_{}_area_{}.png".format(n, out_path_name, str(round(x.area))),img_color[minr-3: maxr+3, minc-3: maxc+3])
#io.show()
except:
pass
def im_proc(im):
"""Apply series of morphological procedures on image."""
th = threshold_otsu(im)
im_bin = im > th
return(ndi.binary_fill_holes(
morphology.closing(
im_bin,np.ones((3,3)))))
def test_accuracy():
''' Verify that our implementation returns exactly the same as scikit
'''
base_dir = '/home/omar/data/DATA_NeoBrainS12/'
neo_subject = '30wCoronal/example2/'
# Read subject files
t2CurrentSubjectName = base_dir + 'trainingDataNeoBrainS12/'+neo_subject+'T2_1-1.nii.gz'
t2CurrentSubject_data = nib.load(t2CurrentSubjectName).get_data()
affineT2CS = nib.load(t2CurrentSubjectName).get_affine()
zoomsT2CS = nib.load(t2CurrentSubjectName).get_header().get_zooms()[:3]
n_zooms = (zoomsT2CS[0],zoomsT2CS[0],zoomsT2CS[0])
t2CurrentSubject_data,affineT2CS = reslice(t2CurrentSubject_data,affineT2CS,zoomsT2CS,n_zooms)
S = t2CurrentSubject_data.astype(np.float64)
max_radius = 4
D = SequencialSphereDilation(S)
for r in range(1, 1+max_radius):
D.expand(S)
expected = dilation(S, ball(r))
actual = D.get_current_dilation()
assert_array_equal(expected, actual)
expected = closing(S, ball(r))
actual = D.get_current_closing()
assert_array_equal(expected, actual)
def upsample_smooth(image):
filename_split = os.path.splitext(image)
filename_zero, fileext = filename_split
basename = os.path.basename(filename_zero)
upsampleRes = int(upsampleRes)
upsampled_image = outPath+basename+'_cubicSpline.png'
os.system("gdalwarp -tr", upsample_res, upsample_res," -r cubicspline ", image, upsampled_image)
im = np.array(Image.open(upsampled_image))
with rasterio.open(image) as r:
im = r.read()
p = r.profile
im = im.squeeze()
selem = disk(1)
print("image min and max: ", im.min(),im.max())
dilated = skimage.morphology.dilation(im, selem)
print("dilated image min and max: ", dilated.min(),dilated.max())
eroded = skimage.morphology.erosion(im, selem)
print("eroded image min and max: ", eroded.min(),eroded.max())
opened = opening(im, selem)
print("opened image min and max: ", opened.min(),opened.max())
closed = closing(im, selem)
print("closed image min and max: ", closed.min(),closed.max())
dilated = Image.fromarray(dilated)
dilated.save(outPath+basename+'.png')
with rasterio.open(outPath+basename+fileext, 'w', **p) as dst:
dst.write(dilated, 1)
color_outPath = outPath+'color/'
if not os.path.exists(color_outPath):
os.mkdir(color_outPath)
colored_image = color_outPath+basename+'.png'
os.system("gdaldem color-relief", dilated, colorfile, colored_image)
return im, dilated, eroded, opened, closed
def processOneImage(inputPath, outputPath):
image = io.imread(inputPath)
greyImage = rgb2grey(image)
threshold = threshold_otsu(greyImage)
imgout = closing(greyImage > threshold, square(1))
imgout = crop(imgout)
imgout = transform.resize(imgout, (max(imgout.shape), max(imgout.shape)))
io.imsave(outputPath, imgout)
def cloud_mask_kmeans(image, k=3):
image = np.array(image)
km = KMeans(k).fit(image.reshape(-1, 1))
labels, centers = km.labels_, km.cluster_centers_
cloud_center = np.argmax(centers)
mask = ((labels == cloud_center) & 1).reshape(image.shape)
mask = closing(mask, square(5))
del km, labels, centers, cloud_center
return np.array(mask)
def preprocess_image(self):
# Total-variation denoising
image = restoration.denoise_tv_chambolle(self.image, weight=0.1)
# Return threshold value based on Otsu's method
thresh = threshold_otsu(image)
# Increases contrast
self.bw = closing(image <= thresh, square(1))
self.cleared = self.bw.copy()
return self.cleared
def RemoveSpeckles(image,displayImages):
#opening and closing to remove the speckles in background and holes in background
radius = 5
selem = disk(radius)
opened = opening(image,selem=selem)
img_speckless = closing(opened,selem=disk(5))
if displayImages == 1 :
plt.figure(),plt.title('Opened and Closed Image'),plt.imshow(img_speckless,cmap='Greys')
return img_as_ubyte(img_speckless)
def crop_to_object(self, img):
img = img_as_ubyte(closing(img, square(5)))
ret,thresh = cv2.threshold(img,20,255,0)
_, lc, _ = cv2.findContours(thresh,cv2.RETR_TREE,cv2.CHAIN_APPROX_SIMPLE)
assert len(lc) == 1
rect = cv2.minAreaRect(lc[0])
img = rotate(img, rect[2], resize = True)
img = img_as_ubyte(img)
ret,thresh = cv2.threshold(img,20,255,0)
thresh = img_as_ubyte(closing(thresh, square(5)))
_, lc, _ = cv2.findContours(thresh,cv2.RETR_TREE,cv2.CHAIN_APPROX_SIMPLE)
assert len(lc) == 1
rect = cv2.minAreaRect(lc[0])
box = cv2.boxPoints(rect)
box = np.int0(box)
min_y, max_y = min(box[:,1]), max(box[:,1])
min_x, max_x = min(box[:,0]), max(box[:,0])
return img[min_y:max_y,min_x:max_x]
def process_image(image,
net,
get_rough_background,
get_accurate_background,
patch_size=128,
n_input_chanels=1,
binarization_threshold=0.3,
closing_filter_size=8,
minimal_crack_size=100):
image_h = image.shape[0]
image_w = image.shape[1]
plt.figure(figsize=(16, 24))
plt.subplot(3, 2, 1)
plt.imshow(image, cmap='gray')
rough_background = get_rough_background(image[np.newaxis,
np.newaxis, :, :] + 0.5)
accurate_background = get_accurate_background(rough_background)
plt.subplot(3, 2, 2)
plt.imshow(accurate_background[0, 0], cmap='gray')
prediction = predict_image(image[np.newaxis, :, :], accurate_background[0,
0],
net, patch_size, n_input_chanels)
plt.subplot(3, 2, 3)
plt.imshow(prediction, cmap='gray')
binarized = np.where(prediction > binarization_threshold, 1, 0)
plt.subplot(3, 2, 4)
plt.imshow(binarized, cmap='gray')
filtered = closing(binarized, square(closing_filter_size))
plt.subplot(3, 2, 5)
plt.imshow(filtered, cmap='gray')
blobs_labels = label(filtered, background=0)
labels, counts = np.unique(blobs_labels, return_counts=True)
final = np.where(
np.in1d(blobs_labels,
np.where(counts <= minimal_crack_size)[0]).reshape(
(image_h, image_w)), 0, filtered)
plt.subplot(3, 2, 6)
plt.imshow(np.where(
np.logical_and(accurate_background[0, 0] == 1, final == 0), 0.4,
final),
cmap='gray')
plt.show()
bins = np.arange(0, 180, 5)
area, length, weights = get_statistics(final, bins.size)
plt.hist(bins, bins=bins.size, weights=weights)
plt.show()
print 'area: ', area
print 'length: ', length
return final, (bins, weights)
def asf_n(I, order=3):
"""
"""
F = I.copy()
for r in np.arange(1, order + 1):
se = m.disk(r)
F = m.opening(m.closing(F, selem=se), selem=se)
return F
def morphological_filter(img):
thresh = threshold_otsu(img)
print(thresh, len(img[img >= thresh].ravel()) / len(img.ravel()))
binary = img >= thresh
make_figure(binary).show()
o_binary = opening(binary)
make_figure(o_binary).show()
c_binary = closing(o_binary)
make_figure(c_binary).show()
def getArea(address):
"""Geocode address and retreive image centered
around lat/long"""
address = address
results = Geocoder.geocode(address)
lat, lng = results[0].coordinates
zip_code = results[0].postal_code
map_url = 'https://maps.googleapis.com/maps/api/staticmap?center={0},{1}&size=640x640&zoom=19&sensor=false&maptype=roadmap&&style=visibility:simplified|gamma:0.1'
request_url = map_url.format(lat, lng)
req = urllib.urlopen(request_url)
img = io.imread(req.geturl(),flatten=True)
labels, numobjects = ndimage.label(img)
image = filter.canny(img, sigma=3)
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(3))
# remove artifacts connected to image border
cleared = bw.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
image_label_overlay = label2rgb(label_image, image=image)
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(6, 6))
ax.imshow(image_label_overlay)
dist = []
rp = regionprops(label_image)
rp = [x for x in rp if 100 < x.area <= 900]
for region in rp:
# skip small images
#if region.area < 100:
# continue
dist.append(sqrt( ( 320-region.centroid[0] )**2 + ( 320-region.centroid[1] )**2 ))
# draw rectangle around segmented coins
#minr, minc, maxr, maxc = region.bbox
#rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
# fill=False, edgecolor='red', linewidth=2)
#ax.add_patch(rect)
roof_index = dist.index(min(dist))
minr, minc, maxr, maxc = rp[roof_index].bbox
rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
fill=False, edgecolor='red', linewidth=2)
ax.add_patch(rect)
img = StringIO()
fig.savefig(img)
img.seek(0)
session['roof_area'] = rp[roof_index].area
roof_area = (rp[roof_index].area)*12
return(roof_area)
def applyMorph(result):
## Image morphic operation
# The morphological opening on an image is defined as an erosion followed by a dilation.
# Opening can remove small bright spots (i.e. “salt”) and connect small dark cracks.
# This tends to “open” up (dark) gaps between (bright) features.
result = sm.opening(result, sm.disk(2)) #用边长为2的圆形滤波器进行膨胀滤波
result = sm.dilation(result,sm.disk(tolerance)) #用边长为5的正方形滤波器进行膨胀滤波
result = sm.closing(result, sm.disk(2))
return result
def clicker(self, event, x, y, flags, param):
"""
Function to store the upper and lower color bounds for the mask at the
clicked location.
"""
# parse the parameters
bgr = param[0]
hsv = param[1]
resize_factor = param[2]
if event == cv2.EVENT_LBUTTONDOWN:
hsv = cv2.cvtColor(bgr, cv2.COLOR_BGR2HSV_FULL)
pixel = hsv[y, x]
# mask the following HSV (hue, saturation, brightness) ranges
upper = np.array([pixel[0] + 6, pixel[1] + 6, pixel[2] + 30])
lower = np.array([pixel[0] - 6, pixel[1] - 6, pixel[2] - 30])
# add the clicked value
self.lower = lower
self.upper = upper
# how does this mask look overlaid on the original image?
image_mask = cv2.inRange(hsv, lower, upper)
image_mask = np.invert(image_mask).astype(bool)
# clean it up
image_mask = morph.remove_small_holes(image_mask,
area_threshold=10,
connectivity=2)
image_mask = morph.opening(image_mask, selem=morph.selem.disk(1))
image_mask = morph.closing(image_mask, selem=morph.selem.disk(1))
image_mask = image_mask.astype(np.uint8)
image_mask[image_mask == 0] = 255
image_mask[image_mask == 1] = 0
image_mask = np.dstack((image_mask, image_mask, image_mask))
image_mask = cv2.addWeighted(image_mask, 0.6, bgr, 1, 0)
win_name = "Otsu Shadow Mask + Color Mask ('y' keep, 'n' to try another)"
cv2.namedWindow(win_name, cv2.WINDOW_NORMAL)
while cv2.getWindowProperty(win_name, 0) >= 0:
cv2.imshow(win_name, image_mask)
cv2.moveWindow(win_name, 0, 0)
cv2.resizeWindow(win_name,
resizeWin(image_mask, resize_factor)[0],
resizeWin(image_mask, resize_factor)[1])
k = cv2.waitKey(1)
# only keep the bounds if the 'y' key is pressed
if k == ord('y') & 0xFF:
cv2.destroyWindow(win_name)
self.closeWin = True
break
# ignore the clicked bounds if 'n' or window is closed
elif k == ord('n') & 0xFF:
self.lower = None
self.upper = None
cv2.destroyWindow(win_name)
break
elif cv2.getWindowProperty(win_name, 0) == -1:
self.lower = None
self.upper = None
break
def func(frame):
_dtype = frame.dtype
kernel = mor.disk(3)
frameWP = frame - mor.white_tophat(frame, kernel) * (mor.white_tophat(frame, kernel) > 1000).astype(float)
kernel = mor.rectangle(25, 1)
closed = mor.closing(frameWP, kernel)
opened = mor.opening(closed, kernel)
result = ((frameWP.astype(float) / opened.astype(float)) * 3000.0)
return result.astype(_dtype)
def apply_morphology(img):
selem = square(kernel_size)
return erosion(img,
selem), dilation(img, selem), opening(img, selem), closing(
img,
selem), ndimage.gaussian_filter(img,
sigma=(kernel_size,
kernel_size),
order=0)
def preprocess_image(self):
"""
Denoises and increases contrast.
"""
#image = restoration.denoise_tv_chambolle(self.image, weight=0.1)
thresh = filter.threshold_adaptive(self.image, 21)
self.bw = closing(self.image > thresh, square(2))
self.cleared = self.bw.copy()
return self.cleared
def preprocess_image(self):
"""
Denoises and increases contrast.
"""
image = restoration.denoise_tv_chambolle(self.image, weight=0.1)
thresh = threshold_otsu(image)
self.bw = closing(image > thresh, square(2))
self.cleared = self.bw.copy()
return self.cleared
def processOneImage(inputPath, outputPaths):
image = io.imread(inputPath)
greyImage = rgb2grey(image)
threshold = threshold_otsu(greyImage)
imgout = closing(greyImage > threshold, square(1))
imgout = crop(imgout)
imgout = transform.resize(imgout, (max(imgout.shape), max(imgout.shape)))
for outputPath in outputPaths:
io.imsave(outputPath, imgout)
def get_open_close_info(im, sz):
o_area = img_area(im)
a = np.zeros((2 * sz))
for i in range(sz):
im_c = morpho.opening(im, morpho.disk(i + 1))
a[i] = (o_area - img_area(im_c)) / o_area
im_c = morpho.closing(im, morpho.disk(i + 1))
a[i + sz] = (o_area - img_area(im_c)) / o_area
return a
def morph_version(grey_im, im):
Thresh = filters.threshold_otsu(grey_im)
io.imsave("test1.png", grey_im)
print(Thresh)
print(grey_im)
picBW = grey_im < Thresh
print(picBW)
Strel = morph.disk(2)
Strel2 = morph.disk(5)
BWimg_dil = morph.dilation(picBW, Strel)
BWimg_close = morph.closing(BWimg_dil, Strel2)
foreground = morph.closing(grey_im > Thresh, morph.square(3))
io.imsave("test.png", img_as_uint(foreground))
L = label(BWimg_close)
half_length = int(np.floor(np.size(L, 1) / 2))
L_cntr = L[half_length, half_length]
print("Label of blob that contains the center pixel: {}".format(L_cntr))
cropped_images = []
pad = 20
top_ten_areas = sorted(regionprops(L), key=lambda x: x.area,
reverse=True)[:10]
for region_index, region in enumerate(top_ten_areas):
print("area: ", region.area)
# draw a rectangle around the segmented articles
# bbox describes: min_row, min_col, max_row, max_col
minr, minc, maxr, maxc = region.bbox
# use those bounding box coordinates to crop the image
cropped_images.append(im[minr - pad:maxr + pad, minc - pad:maxc + pad])
# create a directory in which to store cropped images
out_dir = "segmented_articles/"
if not os.path.exists(out_dir):
os.makedirs(out_dir)
# save each cropped image by its index number
for c, cropped_image in enumerate(cropped_images):
io.imsave(out_dir + str(c) + ".png", cropped_image)
def get_label_image(image=None,
min_pixels=50,
square_width=3,
thresh=None,
connectivity=None,
semantic_segmentation=None,
min_thresh=0.1,
label_size_max_portion=0.5,
plot=False,
figsize=(20, 10)):
"""Use skimage to filter background and get labels
Args:
image: 2-D numpy array or torch.Tenor
Returns:
label_image: same size with image
regions: skimage.measure.regionprops(image)
"""
from skimage.measure import label, regionprops
from skimage.morphology import closing, square
from skimage.filters import threshold_otsu
if semantic_segmentation is None:
if isinstance(image, torch.Tensor):
image = image.detach().cpu().numpy()
if thresh is None:
# apply threshold
thresh = threshold_otsu(image)
if min_thresh is not None:
thresh = max(thresh, min_thresh)
semantic_segmentation = closing(image > thresh,
square(width=square_width))
if plot:
plt.figure(figsize=figsize)
plt.imshow(semantic_segmentation)
plt.title(f'Semantic segmentation with threshold={thresh:.2f}')
plt.show()
# label image regions
label_image = label(semantic_segmentation, connectivity=connectivity)
if plot:
plt.figure(figsize=figsize)
plt.imshow(label_image)
plt.title(
f'label image ({collections.Counter(label_image.reshape(-1))} before post-processing)'
)
plt.show()
for k in np.unique(label_image):
loc = label_image == k
if loc.sum() < min_pixels or loc.sum(
) > label_image.size * label_size_max_portion:
label_image[loc] = 0
for i, k in enumerate(sorted(np.unique(label_image))):
if i < k:
label_image[label_image == k] = i
regions = regionprops(label_image)
return label_image, regions
def get_bounding_box(self, img):
'''
Find the bounding box of the blue barrel
call other functions in this class if needed
Inputs:
img - original image
Outputs:
boxes - a list of lists of bounding boxes. Each nested list is a bounding box in the form of [x1, y1, x2, y2]
where (x1, y1) and (x2, y2) are the top left and bottom right coordinate respectively. The order of bounding boxes in the list
is from left to right in the image.
Our solution uses xy-coordinate instead of rc-coordinate. More information: http://scikit-image.org/docs/dev/user_guide/numpy_images.html#coordinate-conventions
'''
boxes = []
threshold = 0.65
binary_img = self.segment_image(img)
binary_img_cp = np.copy(binary_img)
mean_b = np.mean(binary_img_cp, dtype=float)
std_b = np.std(binary_img_cp, dtype=float)
while not boxes:
threshold = threshold + 0.08 * np.log(mean_b / std_b)
idx = (binary_img_cp >= threshold)
binary_img = np.uint8(idx)
selem = disk(10)
binary_img = closing(binary_img, selem=selem)
#clean up image
#find connected components
contours, hierarchy = cv2.findContours(binary_img,
cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_SIMPLE)
#iterate through all the top-level contours,
#draw each connected component with its own random color
for idx in range(len(contours)):
color = 255 * np.random.random([3])
cv2.drawContours(binary_img, contours, idx, color, -1)
#go through each region
#find apply shape statistic to include or exclude as barrel
props = regionprops(binary_img)
for reg in props:
print(reg.area)
#make sure area seen is sizable enough
if reg.area > 400:
major = reg.major_axis_length
minor = reg.minor_axis_length + 0.001
ratio = major / minor
print(ratio)
#make sure area is shaped like barrel (longer than wider)
if ratio <= 4.2 and ratio >= 1.1:
y1, x1, y2, x2 = reg.bbox
boxes.append([x1 - 7, y1 + 5, x2 + 7, y2 + 5])
boxes.sort(key=itemgetter(1))
boxes = boxes[:2]
return boxes
def plot_preprocessed_image(self):
'''plots pre-processed image and returns crops of chars.'''
rects = []
image = restoration.denoise_tv_chambolle(self.image, weight=0.2)
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(2))
cleared = bw.copy()
label_image = measure.label(cleared)
#borders = np.logical_xor(bw, cleared)
#label_image[borders] = -1
#image_label_overlay = label2rgb(label_image, image=image)
#fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(12, 12))
#ax.imshow(image_label_overlay)
for region in regionprops(label_image):
if region.area < 10:
continue
minr, minc, maxr, maxc = region.bbox
if minr >= 2:
minr -= 2
if minc >= 2:
minc -= 3
maxr += 1
maxc += 2
rects.append([minc, minr, maxc, maxr]) #EXTREMELY IMPORTANT LINE, [x1, y1, x2, y2]
#rect = mpatches.Rectangle((minc, minr), maxc - minc, maxr - minr,
#fill=False, edgecolor='red', linewidth=2)
#ax.add_patch(rect)
#plt.show()
def is_nested(rects, i, j):
return (rects[j][0] >= rects[i][0] and rects[j][2] <= rects[i][2] and rects[j][1] >= rects[i][1] and rects[j][3] <= rects[i][3]) or (rects[j][0] <= rects[i][0] and rects[j][2] >= rects[i][2] and rects[j][1] <= rects[i][1] and rects[j][3] >= rects[i][3])
# makes list of indices of nested rectangles in rects
deletes = []
for i in range(len(rects)-1):
for j in range(i+1, len(rects)):
if (is_nested(rects, i, j)):
deletes.append(j)
# deletes nested rectangles in rects
num_dels = 0
for d in deletes:
del rects[d-num_dels]
num_dels += 1
print 'successful deletion'
return rects
def widens_mask(img):
""" Morphological operators on img """
img = closing(img, disk(2))
img = opening(img, disk(1))
img = remove_little_holes(img,
destructive=False) # remove little black holes
neg = ~img
img = ~remove_little_holes(
neg, destructive=False) # remove little white elements
return dilation(img, disk(1))
def post_process(output_tensor,no_closing): #b,c,h,w->h,w
out = torch.sigmoid(output_tensor[0])
out_numpy = out.max(0)[1].cpu().numpy()
out_numpy = np.array(out_numpy).astype('uint8')
if not no_closing:
out_numpy=sm.closing(out_numpy,sm.square(3))
out_numpy_ske=sm.skeletonize(out_numpy)#骨架化
out_numpy_ske=out_numpy_ske.astype('uint8')
results={'out':out_numpy,'out_ske':out_numpy_ske}
return results
def preprocess_image(self):
'''
Denoise and increase contrast
'''
image = restoration.denoise_tv_chambolle(self.gray, weight=0.1)
thresh = threshold_otsu(image)
self.bw = closing(image > thresh, square(2))
self.cleared = self.bw.copy()
return self.cleared
def prefilter(self, img, rec_size=20, se_size=3):
se = morphology.disk(se_size)
im1 = self.morpho_rec(img, rec_size)
im2 = self.morpho_rec2(im1, int(rec_size / 2))
im3 = morphology.closing(im2, se)
return im3
def get_enhanced_image_(self, raw_data: RawData, img: array) -> array:
image = sobel(img)
image = threshold(image, threshold_otsu(image))
image = closing(image)
if self.debug_level >= DebugLevel.ALL:
imshow(image, cmap="gray")
self.savers_['enhanced'].save(raw_data.name)
return image
def close(self, alpha=ALPHA):
'''performs normal closing operation'''
try:
seed = (min(len(self.altered_image), len(self.altered_image[0]))**
2) / 10000
print(seed)
assert seed < 50 # to prevent lags
self.altered_image = morphology.opening(
self.altered_image, morphology.disk(seed / alpha))
self.altered_image = morphology.closing(
self.altered_image, morphology.disk(seed / alpha))
except AssertionError as e:
self.altered_image = morphology.opening(
self.altered_image, morphology.disk(seed / (alpha**2)))
self.altered_image = morphology.closing(
self.altered_image, morphology.disk(seed / (alpha**2)))
print("seed size too big: {}! \nresize image please!".format(seed))
print(e)
def refine_mask(mask, type="calc"):
if type == "calc":
#mask = dilation(mask, square(9))
return mask
elif type == "mass":
mask = closing(mask, square(9))
else:
raise TypeError("Unknown lesion type!")
return mask
def delsmall( img0 ):
img =color.rgb2gray(img0)
thresh = filters.threshold_otsu(img) #用otsu算法确定最佳分割阈值
bwimg =(img>=(thresh)) #用阈值进行分割，生成二值图像
labels = measure.label(bwimg) #标记连通域
bw =morphology.closing(img < thresh, morphology.square(2))
#img1 = morphology.remove_small_objects(labels, min_size=5, connectivity=1)
img2= morphology.remove_small_objects(bw, min_size=200, connectivity=1)
return img2
def processing(path):
img = imread(path)
gray = rgb2gray(img)
binary = 1 - (gray > 0.5)
binary = closing(binary)
binary = opening(binary)
labeled, nr_objects = ndimage.label(binary)
return nr_objects
def apply(self, img, param=None):
"""
see Filter.apply()
"""
if param['bin'] is not None and param['bin'] == 'y':
result = binary_closing(img, selem=disk(param['size']))
else:
result = closing(img, selem=disk(param['size']))
return result
def post_process_my(Test_predicted):
struc_element = disk(4)
total = Test_predicted.shape[0]
post_predicted = np.zeros((total, 128, 128, 1), dtype=np.uint8)
for j in range(total):
myimage = Test_predicted[j] #to uint8
opened = closing(myimage[:, :, 0], struc_element)
openedd = np.expand_dims(opened, axis=-1)
post_predicted[j, :, :, :] = openedd
return post_predicted
def prefilter(self, img, rec_size=20, se_size=3):
se = morphology.disk(se_size)
im1 = self.morpho_rec(img, rec_size)
im2 = self.morpho_rec2(im1, int(rec_size / 2))
im3 = morphology.closing(im2, se)
return im3
def _get_membrane_cube_data(self):
self._bdr_cube_data = np.zeros(self._cube_shape, dtype='bool')
for i in range(self._cube_shape[0]):
bdr_slice = mask_and_boundary_related.get_all_cell_boundary(
utils.label_to_rgb_ndarray(self._label_cube_data[i, :, :]))
self._bdr_cube_data[
i, :, :] = self._bdr_cube_data[i, :, :] | closing(bdr_slice)
for i in range(self._cube_shape[1]):
bdr_slice = mask_and_boundary_related.get_all_cell_boundary(
utils.label_to_rgb_ndarray(self._label_cube_data[:, i, :]))
self._bdr_cube_data[:,
i, :] = self._bdr_cube_data[:, i, :] | closing(
bdr_slice)
for i in range(self._cube_shape[2]):
bdr_slice = mask_and_boundary_related.get_all_cell_boundary(
utils.label_to_rgb_ndarray(self._label_cube_data[:, :, i]))
self._bdr_cube_data[:, :,
i] = self._bdr_cube_data[:, :, i] | closing(
bdr_slice)
def morph(X, strel, operation="opening"):
if operation == "erosion":
X_out = erosion(X)
elif operation == "dilation":
X_out = dilation(X)
elif operation == "closing":
X_out = closing(X)
else:
X_out = opening(X)
return X_out
def postprocess_bladder_mask(mask):
selem = morphology.ball(3)
mask = morphology.opening(mask, selem)
labels = measure.label(mask)
l_max = largest_label_volume(labels, bg=0)
if l_max is not None:
mask[labels != l_max] = 0
mask = morphology.closing(mask, selem)
return mask
def ApplyThresholdToImageRegion(image2, Tb, Bb, Lb, Rb,shouldThresholdImage):
image = rgb2gray(image2)
global foregroundPixelValue
global backgroundPixelValue
thresholdValue = threshold_otsu(image)
NumberOfRows = image.shape[0]
NumberOfColumns = image.shape[1]
numberOfBlackPixels = 0
numberOfWhitePixels = 0
selem = disk(3)
# simpe thresholding
for y in range(NumberOfRows):
for x in range(NumberOfColumns):
isWithinBoundary = IsWithinBoundary(y,x,image2, Tb, Bb, Lb, Rb,shouldThresholdImage)
if (isWithinBoundary):
if image[y,x] > thresholdValue:
#black
image[y,x] = 0
numberOfBlackPixels += 1
else:
#white
image[y,x] = 1
numberOfWhitePixels += 1
# assume foreground has more pixels in face region
if (numberOfWhitePixels > numberOfBlackPixels):
foregroundPixelValue = 1
backgroundPixelValue = 0
#print("foreground color is white")
else:
foregroundPixelValue = 0
backgroundPixelValue = 1
#print("foreground color is black")
image = opening(image,selem)
if (foregroundPixelValue == 0):
image = opening(image,selem)
else:
image = closing(image,selem)
if drawFaceImages:
io.imshow(image)
io.show()
return image
def parse_image(self):
self.m_print("Parsing panel image",0)
thresh = threshold_otsu(self.i_file)
bw = closing(self.i_file > thresh, square(3))
# remove artifacts connected to image border
cleared = bw.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
borders = np.logical_xor(bw, cleared)
label_image[borders] = -1
return label2rgb(label_image, image=self.i_file),label_image
def prefilter_new(self, img, rec_size=20, se_size=3):
img_cc = ccore.numpy_to_image(img, copy=True)
im1 = ccore.diameter_open(img_cc, rec_size, 8)
im2 = ccore.diameter_close(im1, int(rec_size / 2), 8)
#im1 = self.morpho_rec(img, rec_size)
#im2 = self.morpho_rec2(im1, int(rec_size / 2))
se = morphology.disk(se_size)
im3 = morphology.closing(im2.toArray(), se)
return im3