def preprocessing(pixels): print "-------------Preprocessing phase--------------" #Gaussian filter print "Passing gaussian filter." pixels = filters.gaussian(pixels) #define threshold to binarization of image k = util.otsu_thresholding(pixels) print "Threshold used in the binarization: %d" % (k) #binarize image using the threshold k print "Getting binarized image." pixels = util.binarization(pixels, k) print "Closing operator." pixels = morphology.binary_closing(pixels) print "Opening operator." pixels = morphology.binary_opening(pixels) return pixels
def gray2otsu(gray_im, verbose=1):
''' Otsu thresholding '''
otsu_im, o_th = otsu_thresholding(gray_im)
if verbose:
print 'Otsu threshold: ', o_th
return otsu_im
def gray2otsu(gray_im, verbose=1):
''' Otsu thresholding '''
otsu_im, o_th = otsu_thresholding(gray_im)
if verbose:
logger.info('Otsu threshold: {}'.format(o_th))
return otsu_im
slide.level_dimensions[slide_level])
#center of slide
c_x, c_y = center_of_slide_level(slide, slide_level)
print "center of x : {0} , center of y : {0}".format(c_x, c_y)
#slide padding size
padding = 10
#read_region
tile_0255 = slide.read_region((0, 0), slide_level, (s_level_w, s_level_h))
im_rgba = np.array(tile_0255)
#convert to gray from rgba
im_gray = cv2.cvtColor(im_rgba, cv2.COLOR_RGBA2GRAY)
im_rgb = cv2.cvtColor(im_rgba, cv2.COLOR_RGBA2RGB)
#apply atsu thresholding
im_gray_ostu, x = otsu_thresholding(im_gray)
temp = im_gray
#cv2.drawContours(im_gray,im_gray_ostu,-1,255,-1)
#cv2.findContours(im_gray,)
print "ostu image max value : {0}".format(np.max(im_gray_ostu))
print "otsu threaholding :{0}\n".format(x)
#image_labels = measure.label(im_gray_ostu)
print "image_labels \n"
print "gray image shape:", im_gray.shape
#apply mopology
kernel = np.ones((2, 2), np.uint8)
kernel_1 = np.ones((5, 5), np.uint8)
opening = cv2.morphologyEx(im_gray_ostu, cv2.MORPH_OPEN, kernel)
opening_1 = cv2.morphologyEx(im_gray_ostu, cv2.MORPH_OPEN, kernel_1)
closing = cv2.morphologyEx(im_gray_ostu, cv2.MORPH_CLOSE, kernel)
print "WSI Dimensions (width , hight) : {0}".format(slide.dimensions)
"""Slide.read reagion"""
slide_level = 3
rgba_im = slide.read_region((0, 0), slide_level,
slide.level_dimensions[slide_level])
rgba_im = np.array(rgba_im)
rgb_im = cv2.cvtColor(rgba_im, cv2.COLOR_RGBA2RGB)
"""Slide image convert to gray"""
gray_im = cv2.cvtColor(rgb_im, cv2.COLOR_RGB2GRAY)
"""Slide image apply atsu thresholding"""
otsu_im, o_th = otsu_thresholding(gray_im)
"""Slide image Draw Contours"""
#cont_im = rgb_im
#cv2.drawContours(cont_im,otsu_im,-1,(0,255,0),-1)
"""mopology """
kernel_o = np.ones((5, 5), np.uint8)
#kernel_c = np.ones((1,1),np.uint8)
morp_im = cv2.morphologyEx(otsu_im, cv2.MORPH_OPEN, kernel_o)
#morp_im = cv2.morphologyEx(otsu_im,cv2.MORPH_CLOSE,kernel_c)
print morp_im.shape
morp_im = morp_im == 0
morp_im = (morp_im).astype(float)
"""patch size,leveled patch size """
