def getParams(self):
img = self.ch1
hist, bins = np.histogram(img.ravel(), 256, [0, np.max(img)])
#plt.hist(img.ravel(),256,[0,np.max(img)]); plt.show()
zero = np.argmax(hist)
img = img - bins[zero]
im = np.abs(img)
threshold = threshold_isodata(im)
im = im > threshold
filled = binary_fill_holes(im).astype(int)
filled = binary_closing(filled)
A1 = np.count_nonzero(filled)
P1 = perimeter(filled, neighbourhood=16)
C1 = 4 * 3.14 * A1 / (P1 * P1)
img = self.ch6
hist, bins = np.histogram(img.ravel(), 256, [0, np.max(img)])
#plt.hist(img.ravel(),256,[0,np.max(img)]); plt.show()
zero = np.argmax(hist)
img = img - bins[zero]
im = np.abs(img)
threshold = threshold_isodata(im)
im = im > threshold
filled = binary_fill_holes(im).astype(int)
filled = binary_closing(filled)
A2 = np.count_nonzero(filled)
P2 = perimeter(filled, neighbourhood=16)
C2 = 4 * 3.14 * A2 / (P2 * P2)
params = np.array([A1, P1, C1, A2, P2, C2])
return params
def cluster_process(labels, original, activations):
rbase = np.zeros(labels.shape)
rubase = np.zeros(labels.shape)
rubase[range(0,20),:] = 1
rubase[:,range(0,20)] = 1
rubase[range(-20,-1),:] = 1
rubase[:,range(-20,-1)] = 1
for i in range(1, int(np.max(labels))+1):
base = np.zeros(labels.shape)
base[labels==i] = 1
li = len(base.nonzero()[0])
if li>0:
hull = convex_hull_image(base)
lh =len(hull.nonzero()[0])
sel_org = base*original
sel_act = base*activations
cond = (li > 4000 and float(lh) / float(li) < 1.07 and perimeter(base)**2.0 / li < 30) or np.max(base * rubase) > 0.5
# print li>4000 and float(lh)/float(li)<1.07, perimeter(base)**2.0/li<30, np.max(base*rubase)>0.5, np.min(original[base>0])
hard_array =[li > 4000, float(lh) / float(li) < 1.07]
optional_array = [perimeter(base)**2.0/li < 25,
np.percentile(sel_org[sel_org>0], 5) > 0.2,
np.percentile(sel_act, 90) - np.percentile(sel_act, 90)]
print hard_array, optional_array
if debug and li>1000:
rs(base,'subspread cluster')
if cond:
rbase = rbase + base
rbase[rubase.astype(np.bool)] = 1
return dilation(rbase, selem)
def peri_area_series(self, levels):
perimeters = np.zeros(len(levels)-1)
areas = np.zeros(len(levels)-1)
for i, level in enumerate(levels):
mask_image = np.ma.masked_inside(self.data,levels[i],levels[i+1])
mask_image_outer = np.ma.masked_greater_equal(self.data,levels[i])
mask_image_inner = np.ma.masked_greater_equal(self.data,levels[i+1])
perimeters.append((perimeter(mask_image_outer.mask)+perimeter(mask_image_inner.mask)))
areas.append((self.__len__-np.nansum(mask_image.mask)))
self.areas = areas
self.perimeters = perimeters
def ComputePerimeter(binarizedImage):
perim = measure.perimeter(binarizedImage)
print('Perimeter calculation complete >>')
print('Perimeter is:', perim, 'pixels.')
print('Dimensions of preimeter variable is:', perim.shape)
print('Perimeter Type:', type(perim))
return perim
def give_Aver(self, srt, name):
filename = os.path.join(skimage.data_dir, srt + name)
image = io.imread(filename)
image_g = rgb2gray(image)
edges = feature.canny(image_g, sigma=self.sigma)
aver = measure.perimeter(edges)
return aver
def compute_blocky_metric(mtx, kernel_size, sd_thresh, remove_size):
'''
Compute perimeter of all connected components for an input matrix after uniform
smoothing, Z-standardization, and cleaning for small components.
input:
mtx - n * n matrix
kernel_size - size of kernel used in smoothing
sd_thresh - threshold to use for binarization
remove_size - filter on number of cells required in connected components
output:
dict of all intermediary quantities (standardized matrix, binarized matrix, cleaned
matrix) and the perimeter of the clean matrix.
'''
mtx_smooth = smooth(Z, kernel_size)
Z = standardize(mtx_smooth)
Z_threshold = binarize(Z, sd_thresh)
labels = measure.label(Z_threshold)
Z_clean = remove_small_clusters(Z_threshold, labels, remove_size)
blockyness = measure.perimeter(Z_clean, neighbourhood=4)
## prepare output dict
out = {}
out['mtx_standardize'] = Z
out['mtx_binarized'] = Z_threshold
out['mtx_clean'] = Z_clean
out['perimeter'] = blockyness
return(out)
def shape_measures(image):
"""Returns features about the 'basic' shape measures:
* scaled area
* Solidity
* Extend
* Major and minor axes lengths
* Centroid displacement
Look at 'http://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.regionprops' for more informations about these measures."""
# make image binary
new_im = image
new_im[new_im > 0] = 1
per = perimeter(new_im)
lbs = label(new_im)
properties = regionprops(lbs)
# extract properties of interest
if len(properties) > 0:
ratio = properties[0].area / (per * per) # scaled area
solidity = properties[0].solidity
extent = properties[0].extent
major_axis_scaled = properties[0].major_axis_length / per
minor_axis_scaled = properties[0].minor_axis_length / per
else:
ratio = 0
solidity = 0
extent = 0
major_axis_scaled = 0
minor_axis_scaled = 0
return [ratio, solidity, extent, major_axis_scaled, minor_axis_scaled]
def perimeter(self):
"""
The perimeter of the source segment, approximated lines through
the centers of the border pixels using a 4-connectivity.
"""
from skimage.measure import perimeter
return perimeter(self._cutout_segment_bool, 4) * u.pix
def getChar(self):
if not self.isPrepared:
self.preparerMedian()
print(u'Image en préparation automatique, attention aux paramètres')
self.char['taux'] = 100*np.sum(self.ready)/float(self.size)
self.char['temp'],self.char['time'] = finddata(self.filename)
self.char['perimeter']=measure.perimeter(self.ready)
def perimeter(self):
"""
The perimeter of the source segment, approximated lines through
the centers of the border pixels using a 4-connectivity.
"""
from skimage.measure import perimeter
return perimeter(self._cutout_segment_bool, 4) * u.pix
def batch_loss_perim(y_batch, p_batch):
print 'blp'
m = float(y_batch.shape[0])
bce_loss = sum(bce(y, p) for (y, p) in zip(y_batch, p_batch)) / m
perim_loss = sum(
perimeter(np.round(p)) / np.count_nonzero(np.round(p))
for p in p_batch) / m
return bce_loss + perim_loss
def circularity(spot, area):
if not area:
return 0
perim = perimeter(spot)
if perim != 0:
return (4 * np.pi * area) / (perim * perim)
return 0
def measure(self, img, m_type: int) -> float:
mask = img.get_mask(m_type)
mask_one = mask / mask.max()
label_img = label(mask_one)
region = regionprops(label_img)
area = region[0].area
per = perimeter(mask_one)
value = (4 * math.pi * area) / (per**2)
return value
def extractFeature(name, showall, showbb, flag):
(img, regions, ax, rthre, cthre) = extractImage(name, showall, showbb,
flag)
Features = []
boxes = []
for props in regions:
tmp = []
minr, minc, maxr, maxc = props.bbox
if maxc - minc < cthre or maxr - minr < rthre or maxc - minc > cthre * 9 or maxr - minr > rthre * 9:
continue
tmp.append(minr)
tmp.append(minc)
tmp.append(maxr)
tmp.append(maxc)
boxes.append(tmp)
if showbb == 1:
ax.add_patch(
Rectangle((minc, minr),
maxc - minc,
maxr - minr,
fill=False,
edgecolor='red',
linewidth=1))
# computing hu moments and removing small components
roi = img[minr:maxr, minc:maxc]
m = moments(roi)
cr = m[0, 1] / m[0, 0]
cc = m[1, 0] / m[0, 0]
mu = moments_central(roi, cr, cc)
nu = moments_normalized(mu)
hu = moments_hu(nu)
area = (maxr - minr) * (maxc - minc)
# add convexity
p = perimeter(img[minr:maxr, minc:maxc])
con = (area / (p * p)) * 4 * math.pi
convex = np.array([con])
hu = np.concatenate((hu, convex))
# add density
den = area / float(props.convex_area)
dense = np.array([den])
hu = np.concatenate((hu, dense))
Features.append(hu)
# print boxes
plt.title('Bounding Boxes')
if showbb == 1:
io.show()
return Features, boxes,
def perimeter_calculation(label_mask):
perimeter_val=[]
for slice in range(label_mask.shape[-1]):
perimeter_val.append(perimeter(label_mask[:,:,slice]))
average_perimeter = np.sum(perimeter_val)/label_mask.shape[-1]
return average_perimeter
def main():
data = bf.load_image("test2.h5")
thres = np.quantile(data.ravel(), 0.65)
bindata = data // thres
op_selem = disk(6)
close_selem = disk(12)
opened = opening(bindata, op_selem)
closed = closing(opened, close_selem)
peri = perimeter(closed)
area = np.count_nonzero(closed == 1)
compact = 4 * np.pi * area / (peri**2)
print(peri, area, compact)
bf.show_images([data, bindata, opened, closed, canny(closed)])
def perimeter(mask, invert=False):
'''
Calculate total perimeter of all objects in binary image.
calculates the perimeter of binary 2D shapes
if background is white and the region of interest black,
invert should be True.
Parameters
----------
mask : array_like
binary image
'''
if invert:
zeroidx = mask == 0
onesidx = mask == 255
maskinvert = np.copy(mask)
maskinvert[zeroidx] = 255
maskinvert[onesidx] = 0
return measure.perimeter(maskinvert > 110)
else:
return measure.perimeter(mask > 110)
def get_perimeter(img):
"""
1. Import the image:
"as_gray=True" is needed to reshape the original 3D array to a 2D array.
The perimeter function only accepts 2D arrays.
2. Invert the grayscale. I did this because the standard grayscale image
gave me a value of 0.0
"""
img = io.imread('Rothko_AI/' + img, as_gray=True)
img = invert(img)
return perimeter(img, neighbourhood=4)
def imageFeatures(s):
tmparr = s.pixel_array
threshold_mask = tmparr > 800
tmpmask = ndimage.binary_erosion(threshold_mask, iterations=6)
closedmask = ndimage.binary_fill_holes(tmpmask)
n_pixels = np.sum(tmpmask)
nf_pixels = np.sum(closedmask) ## # pixels above threshold
v_pixel = s.PixelSpacing[0] * s.PixelSpacing[1] * s.SliceThickness * 10**(
-6) # volume 1 pixel in leters
size = nf_pixels * v_pixel
size_hollow = n_pixels * v_pixel
perimeter = measure.perimeter(closedmask) * s.PixelSpacing[0]
meanhu = np.mean(tmparr[closedmask])
return [size, size_hollow, perimeter, meanhu]
def get_shape_analysis(data,
show_plot): # returns shape analysis features and plots
thres = np.quantile(data.ravel(), 0.65)
bindata = data // thres
op_selem = disk(6)
close_selem = disk(12)
opened = opening(bindata, op_selem)
closed = closing(opened, close_selem)
peri = perimeter(closed)
area = np.count_nonzero(closed == 1)
compact = (peri**2) / (4 * np.pi * area)
if show_plot:
bf.show_images([data, bindata, opened, closed, canny(closed)])
return ([peri, area, compact])
def circularThresholdLabels(labelImg, circularRange):
particleList = numpy.unique(labelImg[1:])
for particle in particleList:
bImgLabelN = labelImg==particle
circularity = 0
area = bImgLabelN.sum()
perimeter = measure.perimeter(bImgLabelN)
if (perimeter>0):
circularity = (4*numpy.pi*area)/(perimeter**2)
if (circularity>1):
circularity=1/circularity
if not(circularity>=circularRange[0] and circularity<=circularRange[1]):
labelImg[bImgLabelN]=0
return labelImg
def circularity(I):
"""
Circularity criterion
4*pi*A/P**2
returns crofton and classic
"""
P = perimCrofton(I)
print("Perimeter by crofton: ", P)
A = np.sum(I)
C = np.pi*4*A/P**2
p = measure.perimeter(I, neighbourhood=4)
print("Usual perimeter: ", p)
c = np.pi*4*A/p**2
return C, c
def get_sub_compacity(self, sub_images):
compacities = []
for index in range(len(sub_images)):
compacities.append([])
for index2, im in enumerate(sub_images[index]):
#contour = measure.find_contours(im, level=0.8)
#print(contour)
#exit(0)
perimeter = measure.perimeter(im, neighbourhood=4)
area = np.count_nonzero(im)
compacity = perimeter**2 / area
if compacity < 4 * np.pi:
print("Compacity is too small {} < {}".format(
compacity, 4 * np.pi))
compacity = 100
#print("{}.{}:".format(index, index2), perimeter, area, compacity)
compacities[index].append(compacity)
return compacities
def minkoMeasured(G, sigma, hmin, hmax):
H = np.arange(hmin, hmax, .1)
A = []
P = []
E = []
bar = progressbar.ProgressBar()
for h in bar(H):
levelset = G >= h
# A[i] = np.sum(levelset);
# P[i] = measure.perimeter(levelset);# perimeter in 4-neighborhood
# E[i] = eulerNb4(levelset) # euler number
a, p, e = bwminko(levelset)
p = measure.perimeter(levelset)
A.append(a)
P.append(p)
E.append(e)
return A, P, E
def _extract_features(self, labels, intensity):
self.ndim = labels.ndim
self.spacing = np.broadcast_to(np.array(self.spacing), self.ndim)
self.isotropic = np.all(self.spacing == self.spacing[0])
# map 2D feature names if 3D image
if self.ndim == 3:
# skimage regions props uses 2D feature names (e.g. perimeter, area instead of surface, volume respectively)
features = {
self._name_mapping_3D_2D.get(f, f)
for f in self.features
}
else:
features = self.features
# special case pre: extract "convex_image" to compute missing "convex_perimeter" feature
if 'convex_perimeter' in features:
features = [
'convex_image' if x == 'convex_perimeter' else x
for x in features
]
# extract actual features
props = regionprops_table(labels,
intensity_image=intensity,
properties=features,
separator='-')
# special case post: extract compute missing "convex_perimeter" feature
convex_images = props.pop('convex_image', None)
if convex_images is not None:
props['convex_perimeter'] = [
perimeter(hull) for hull in convex_images
]
# map back 3D feature names if 3D image
if self.ndim == 3:
props = {
self._name_mapping_2D_3D.get(key, key): val
for key, val in props.items()
}
return props
def relperimeterthresh(image, exponent = 2):
try:
#Lowering the exponent increases tolerance for rough image edges, and is more suitable when
#there is a large variance in foreground brightness
lothresh = filters.threshold_triangle(image)
hithresh = filters.threshold_otsu(image)
if lothresh > hithresh:
lothresh = hithresh // 2
threshqual = []
threshsearch = []
for thresh in range(lothresh, hithresh +10, max((hithresh-lothresh)//5, 1)):
sample = image > thresh
threshqual.append((measure.perimeter(sample) ** exponent)/np.sum(sample))
threshsearch.append(thresh)
goodthresh = threshsearch[np.argmin(threshqual)]
return goodthresh
except:
try:
return filters.threshold_otsu(image)
except ValueError:
return np.nan
def selective_search(im_orig,
scale=40.0,
sigma=0.8,
min_size=40,
gp=[0.5, 0.5]):
'''Selective Search
Parameters
----------
im_orig : ndarray
Input image
scale : int
Free parameter. Higher means larger clusters in felzenszwalb segmentation.
sigma : float
Width of Gaussian kernel for felzenszwalb segmentation.
min_size : int
Minimum component size for felzenszwalb segmentation.
Returns
-------
img : ndarray
image with region label
region label is stored in the 4th value of each pixel [r,g,b,(region)]
regions : array of dict
[
{
'rect': (left, top, width, height),
'labels': [...],
'size': component_size
},
...
]
'''
assert im_orig.shape[2] == 3, "3ch image is expected"
# load image and get smallest regions
# region label is stored in the 4th value of each pixel [r,g,b,(region)]
img = _generate_segments(im_orig, scale, sigma, min_size)
if img is None:
return None, {}
imsize = img.shape[0] * img.shape[1]
R = _extract_regions(img)
# extract neighbouring information
neighbours = _extract_neighbours(R)
# calculate initial similarities
S = {}
for (ai, ar), (bi, br) in neighbours:
S[(ai, bi)] = _calc_sim(ar, br, imsize)
# hierarchal search
while S != {}:
# get highest similarity
i, j = sorted(S.items(), key=lambda i: i[1])[-1][0]
# merge corresponding regions
t = max(R.keys()) + 1.0
R[t] = _merge_regions(R[i], R[j])
# mark similarities for regions to be removed
key_to_delete = []
for k, v in list(S.items()):
if (i in k) or (j in k):
key_to_delete.append(k)
# remove old similarities of related regions
for k in key_to_delete:
del S[k]
# calculate similarity set with the new region
for k in [a for a in key_to_delete if a != (i, j)]:
n = k[1] if k[0] in (i, j) else k[0]
S[(t, n)] = _calc_sim(R[t], R[n], imsize)
regions = []
gp[0] = gp[0] * img.shape[1]
gp[1] = gp[1] * img.shape[0]
for k, r in list(R.items()):
# x is width
width = r['max_x'] - r['min_x']
height = r['max_y'] - r['min_y']
if (gp[0]>r['min_x']-0.25*width) and \
(gp[1]>r['min_y']-0.25*height) and \
(gp[0]<r['max_x']+width*0.25) and \
(gp[1]<r['max_y']+height*0.25):
regions.append({
'rect': (r['min_x'], r['min_y'], r['max_x'] - r['min_x'],
r['max_y'] - r['min_y']),
'd':
math.sqrt((gp[0] - (r['min_x'] + r['max_x']) / 2)**2 +
(gp[1] - (r['min_y'] + r['max_y']) / 2)**2),
'size':
r['size'],
'labels':
r['labels'],
'masks':
r['masks'],
'hist_c':
r['hist_c'],
'hist_t':
r['hist_t'],
'objectness':
perimeter(r['masks']) / (regionprops(r['masks'].astype(
numpy.uint8))[0].major_axis_length + regionprops(
r['masks'].astype(numpy.uint8))[0].minor_axis_length),
})
return regions
date1 = str(year)+'-01-01T00:00:00'
date2 = str(year)+'-12-31T23:00:00'
it_tot = index_date(MSEAtl.time,date1)[0]
Nt = MSEAtl.time.sel({'time':slice(date1,date2)}).shape[0]
L_CONTOUR[str(year)] = np.zeros((Nt,))
for it in range(Nt):
print('it=',it,' & it_tot=',it_tot,' ',end='\r')
MSE_tmp = MSEAtl[it_tot,:,:]
# Contour = curve.get_contours(MSE_tmp>np.percentile(MSE_tmp,80))
# L = 0
# for j,contour in enumerate(Contour):
# plt.plot(lonAtl[contour[:,1].astype(int)],latAtl[contour[:,0].astype(int)],color='k')
# L += np.sum(contour*dx)
MSE_binary = np.zeros(np.shape(MSE_tmp))
MSE_binary[MSE_tmp>np.percentile(MSE_tmp, per_thresh)] = 1
binary_boundary=np.copy(MSE_binary)
binary_boundary[:,1:-1]=0
L = dx*(measure.perimeter(MSE_binary,8)- np.sum(binary_boundary))
L_CONTOUR[str(year)][it] = L
it_tot+=1
#### Save the contour length in a pickle file
path_PKL = '/users/jwindmil/2019_WMI/dev/jwindmiller/PKL_DATA/'
hf = open(path_PKL+'10_2_CONTOURL_%i'%(per_thresh)+str(year)+'.pkl','wb')
CONdata = {"Tot_Contour_km":L_CONTOUR,"time":MSEAtl.time}
pickle.dump(CONdata,hf)
hf.close()
im_crop = get_roi(bw_img)
dist_map = get_roi(bw_dmap)
node_id_image = get_roi(ws_labels)
ax1.imshow(im_crop)
node_dict = {}
for c_node in np.unique(node_id_image[node_id_image > 0]):
y_n, x_n = np.where(node_id_image == c_node)
node_dict[c_node] = {
"x": np.mean(x_n),
"y": np.mean(y_n),
"width": np.mean(dist_map[node_id_image == c_node]),
"perimeter": perimeter(node_id_image == c_node),
}
ax1.plot(np.mean(x_n), np.mean(y_n), "rs")
edge_dict = {}
for i in node_dict.keys():
i_grow = dilation(node_id_image == i, np.ones((3, 3)))
for j in node_dict.keys():
if i < j:
j_grow = dilation(node_id_image == j, np.ones((3, 3)))
interface_length = np.sum(i_grow & j_grow)
if interface_length > 0:
v_nodes = [i, j]
edge_dict[(i, j)] = {
def get_ratio_properties(self, smallest_size, theMask, ratio_intensity,
threshold, Img_after, i, j):
# remove artifacts connected to image border
self.Labelmask = theMask
self.ratioImag = ratio_intensity
self.row_num = i
self.column_num = j
self.threshold = threshold
self.originimg = Img_after
cleared = self.Labelmask.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
#image_label_overlay = label2rgb(label_image, image=image)
#fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(6, 6))
#ax.imshow(label_image)
#contours = find_contours(original_intensity, self.threshold)
dtype = [('Row index', 'i4'), ('Column index', 'i4'),
('Mean intensity', float), ('Circularity', float),
('Mean intensity in contour', float)]
region_mean_intensity_list = []
region_circularit_list = []
region_meanintensity_contour_list = []
loopmun = 0
dirforcellprp = {}
for region in regionprops(label_image, intensity_image=self.ratioImag):
# skip small images
if region.area > smallest_size:
# 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)
#centroidint1 = int(region.centroid[0])
#centroidint2 = int(region.centroid[1])
#ax.text(centroidint1+50, centroidint2+55, round(region.mean_intensity,3),fontsize=15, style='italic',bbox={'facecolor':'red', 'alpha':0.5, 'pad':10})
region_mean_intensity = region.mean_intensity #mean intensity of the region, 0 pixels are omitted.
#allpixelnum = region.bbox_area
#labeledpixelnum = region.area #number of pixels in region omitting 0.
filledimg = region.filled_image
filledperimeter = perimeter(filledimg)
#Sliced_binary_region_image = region.image
intensityimage = region.intensity_image
singlethresh = threshold_otsu(filledimg)
#print(region.area)
#print(region.bbox_area)
#print(region_mean_intensity)
s = imageanalysistoolbox()
contourimage = s.contour(filledimg, intensityimage,
singlethresh)
self.contour_mask = s.inwarddilationmask(
contourimage, filledimg, 3)
filledimg = region.filled_image #Binary region image with filled holes which has the same size as bounding box.
filledperimeter = perimeter(filledimg)
regioncircularity = (4 * math.pi * region.filled_area) / (
filledperimeter * filledperimeter
) # region.perimeter will count in perimeters from the holes inside
self.contour_origin_image = self.contour_mask * intensityimage
contourprops = regionprops(self.contour_mask, intensityimage)
contour_mean = contourprops[0].mean_intensity
#print('contour_mean:'+str(contour_mean))
#print(region_mean_intensity)
region_mean_intensity_list.append(region_mean_intensity)
region_circularit_list.append(regioncircularity)
region_meanintensity_contour_list.append(contour_mean)
dirforcellprp[loopmun] = (self.row_num, self.column_num,
region_mean_intensity,
regioncircularity, contour_mean)
loopmun = loopmun + 1
cell_properties = np.zeros(len(region_mean_intensity_list),
dtype=dtype)
for p in range(loopmun):
cell_properties[p] = dirforcellprp[p]
return region_mean_intensity_list, cell_properties, self.contour_origin_image
dapi=pixels[0,:,:] plt.imshow(dapi) GFP=pixels[1,:,:] plt.imshow(GFP) block_size = 21 nmask = threshold_local(dapi, block_size,offset=0.0004) nmask2 = dapi > nmask plt.imshow(nmask2) nmask3 = binary_opening(nmask2, structure=np.ones((3,3))).astype(np.float64) plt.imshow(nmask3) nmask4 = binary_fill_holes(nmask3) plt.imshow(nmask4) perimeter(nmask4, neighbourhood=4) all_labels = measure.label(nmask4) plt.imshow(all_labels) label_objects, nb_labels = label(all_labels) plt.imshow(label_objects) sizes = np.bincount(label_objects.ravel()) #np.histogram(sizes, bins=10, range=None) #plt.hist(sizes, bins='auto') #plt.show() mask_sizes = sizes > 250 #all the values larger than 250 is True mask_sizes[0] = 0 #column 0, False will get the value of zero gsegg = mask_sizes[label_objects] gsegg, nb_labels = label(gsegg) plt.imshow(gsegg)
def get_cell_dictionary(self, smallest_size, theMask, threshold,
intensity_bef, intensty_aft, i, j, contour_thres,
contour_dilationparameter):
# remove artifacts connected to image border
self.Labelmask = theMask
self.Imagbef = intensity_bef
self.Imageaft = intensty_aft
self.row_num = i
self.column_num = j
self.threshold = threshold
self.contour_thres = contour_thres
self.contour_dilationparameter = contour_dilationparameter
cleared = self.Labelmask.copy()
clear_border(cleared)
# label image regions
label_image = label(cleared)
self.individual_cell_dic_bef = {}
self.individual_cell_dic_aft = {}
loopmun = 0
for region in regionprops(label_image, intensity_image=self.Imagbef
): # USE image before perfusion as template
# skip small images
if region.area > smallest_size:
# draw rectangle around segmented coins
minr, minc, maxr, maxc = region.bbox
region_mean_intensity = region.mean_intensity #mean intensity of the region, 0 pixels in label are omitted.
#allpixelnum = region.bbox_area
#labeledpixelnum = region.area #number of pixels in region omitting 0.
filledimg = region.filled_image
filledperimeter = perimeter(filledimg)
#Sliced_binary_region_image = region.image
self.intensityimage_intensity = region.intensity_image # need a copy of this cause region will be altered by s.contour
#self.regionimage_before = self.intensityimage_intensity.copy()
#self.regionimage_after = self.Imageaft[minr:maxr, minc:maxc]
#Get 2 more pixels out of boundary box in case of cell movements
#We need to add 2 rows and columns of 0 to the whole FOV in case cells detected at the edge
expanded_image_container_bef = np.zeros(
(self.Imagbef.shape[0] + 4, self.Imagbef.shape[1] + 4))
expanded_image_container_bef[2:self.Imagbef.shape[0] + 2,
2:self.Imagbef.shape[1] +
2] = self.Imagbef
expanded_image_container_aft = np.zeros(
(self.Imageaft.shape[0] + 4, self.Imageaft.shape[1] + 4))
expanded_image_container_aft[2:self.Imageaft.shape[0] + 2,
2:self.Imageaft.shape[1] +
2] = self.Imageaft
self.regionimage_before = expanded_image_container_bef[minr -
2:maxr +
2,
minc -
2:maxc +
2]
self.regionimage_after = expanded_image_container_aft[minr -
2:maxr +
2, minc -
2:maxc +
2]
self.regionimage_before_for_contour = self.regionimage_before.copy(
)
self.regionimage_after_for_contour = self.regionimage_after.copy(
)
self.individual_cell_dic_bef[str(
loopmun
)] = self.regionimage_before_for_contour # put each cell region into a dictionary
self.individual_cell_dic_aft[str(
loopmun)] = self.regionimage_after_for_contour
loopmun = loopmun + 1
return self.individual_cell_dic_bef, self.individual_cell_dic_aft
def compactness(labelled, label):
return 4 * np.pi * np.sum(labelled == label) / (perimeter(
labelled == label)**2)
# EXTRACAO DE CARACTERISTICAS
f_1 = [0, 0, 0]
f_2 = [0, 0, 0]
img_1 = np.divide(img_1, 255.0)
img_2 = np.divide(img_2, 255.0)
prop1 = img_1.shape[0]*img_1.shape[1]
prop2 = img_2.shape[0]*img_2.shape[1]
# AREAS
f_1[0] = np.sum(img_1)/prop1
f_2[0] = np.sum(img_2)/prop2
# PERIMETROS
f_1[1] = perimeter(img_1)/prop1
f_2[1] = perimeter(img_2)/prop2
f_1[2] = dist_1/prop1
f_2[2] = dist_2/prop2
person = pearsonr(f_1, f_2)
dist = (distance.euclidean(f_1, f_2))*100
print np.abs((person[0]*100)-dist)
plt.subplot(121), plt.imshow(img_1, cmap='gray')
plt.title(''), plt.xticks([]), plt.yticks([])
plt.subplot(122), plt.imshow(img_2, cmap='gray')
plt.title(''), plt.xticks([]), plt.yticks([])
def morphologyStats(image, res):
perim = (float(perimeter(image)) / res) * (2.0 + 35.0/64.0)
area = (float(np.sum(image != 0)) / (res**2)) * ((2.0 + 35.0/64.0)**2)
dissection = (4 * area) / (perim ** 2)
compactness = (perim ** 2) / area
return (perim, area, dissection, compactness)