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white_segments.py
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from PIL import Image
import numpy as np
#import matplotlib
#import matplotlib.pyplot as plt
import math
import random
#import pandas as pd
#import cv2 as cv
import skimage
import skimage.viewer
import csv
import time
Image.MAX_IMAGE_PIXELS = None
image1 = input('Enter thresholded image name with extension: ')
#path_in = ('shot7_bi.tif')
path_in = (str(image1))
#path_in = ('E:/Biology/Pancreas/thresholded_samples/' + str(image1))
#img=cv.imread(path_in)
img = Image.open(path_in)
image_type = input("Enter 'y' if the thresholded image is of manually tagged data: ")
time1 = time.time()
imarray = np.array(img)
img.close()
print(imarray.shape, imarray.size, len(imarray))
y_axis = imarray.shape[0] # 680 # size of each section
x_axis = imarray.shape[1]
s_size = 70 # size of each section (tile)
print('Tile size: ', s_size)
y_total = math.ceil(y_axis / s_size)
x_total = math.ceil(x_axis / s_size)
yx_total = y_total * x_total
section_items = []
segmented_areas = []
def combine_segments(section_n):
# combine segments xxx ooo
# xxxxxxxx
global segmented_areas
i1 = 0
while (i1 < len(segmented_areas[section_n])):
i2 = i1 + 1
while (i2 < len(segmented_areas[section_n])):
flag3 = 0
j2 = 2
while (j2 < len(segmented_areas[section_n][i2])):
j1 = 2
while (j1 < len(segmented_areas[section_n][i1])):
if abs(segmented_areas[section_n][i2][j2][0] - segmented_areas[section_n][i1][j1][0]) == 1:
if segmented_areas[section_n][i1][j1][1] <= segmented_areas[section_n][i2][j2][1] and segmented_areas[section_n][i1][j1][2] >= segmented_areas[section_n][i2][j2][1]:
flag3 = 1
elif segmented_areas[section_n][i2][j2][1] <= segmented_areas[section_n][i1][j1][1] and segmented_areas[section_n][i2][j2][2] >= segmented_areas[section_n][i1][j1][1]:
flag3 = 1
elif segmented_areas[section_n][i1][j1][0] > segmented_areas[section_n][i2][j2][0] + 1:
break
j1 = j1 + 1
j2 = j2 + 1
if flag3 == 1:
j2 = 2
while (j2 < len(segmented_areas[section_n][i2])):
j1 = 2
flag1 = 0
while (flag1 < 1):
if (j1 < len(segmented_areas[section_n][i1])):
if (j1 < len(segmented_areas[section_n][i1]) - 1):
if (segmented_areas[section_n][i1][j1][0] == segmented_areas[section_n][i2][j2][0]) and (segmented_areas[section_n][i1][j1 + 1][0] > segmented_areas[section_n][i2][j2][0]):
segmented_areas[section_n][i1].insert(j1 + 1, segmented_areas[section_n][i2][j2])
flag1 = 1
else:
segmented_areas[section_n][i1].append(segmented_areas[section_n][i2][j2])
flag1 = 1
j1 = j1 + 1
else:
flag1 = 1
j2 = j2 + 1
if segmented_areas[section_n][i1][1][1] < segmented_areas[section_n][i2][1][1]:
segmented_areas[section_n][i1][1][1] = segmented_areas[section_n][i2][1][1]
del segmented_areas[section_n][i2]
else:
i2 = i2 + 1
i1 = i1 + 1
def white_segments(y_axis, x_axis, s_size):
global section_items
global segmented_areas
print(y_total, x_total, yx_total)
section_items = []
for section_n in range(yx_total):
section_items.append([])
for i in range(s_size):
section_items[section_n].append([])
flag_0 = 0 # 1 when all sections are covered
#while (flag_0 == 0):
j1 = 0
j2 = 0
i1 = 0
while (i1 < y_total):
j = 0
while (j1 < (i1 * s_size) + s_size):
if j1 < y_axis:
j2 = 0
i2 = 0
while (i2 < x_total):
while (j2 < (i2 * s_size) + s_size):
if j2 < x_axis:
section_items[(i1 * x_total) + i2][j].append(imarray[j1][j2])
#section_items[(i1 * x_total) + i2][j].insert(0,imarray[j1][j2])
j2 = j2 + 1
else:
break
i2 = i2 + 1
j1 = j1 + 1
j = j + 1
else:
break
i1 = i1 + 1
# segment white areas
segmented_areas = [] # [[s_nos],[Yt,Yb,[Y,Xl,Xr]]]
y_pseudo_section = y_axis - ((y_total - 1) * s_size) # group of pixels left out whicha re unable to represent length of tile
x_pseudo_section = x_axis - ((x_total - 1) * s_size)
for section_n in range(len(section_items)):
segmented_areas.append([])
temp_areas = [] # segemented area in each row
if math.floor(section_n / x_total) < (y_total - 1):
i1 = 0
while (i1 < s_size):
if (section_n % x_total) < (x_total - 1):
i2 = 0
while (i2 < s_size):
if section_items[section_n][i1][i2][0] == 255:
if len(temp_areas) == 0:
temp_areas.append([[i1,i2,i2]])
else:
j1 = 0
while (j1 < len(temp_areas)):
if i2 + (s_size * 0) == temp_areas[j1][len(temp_areas[j1]) - 1][2] + 1:
temp_areas[j1][len(temp_areas[j1]) - 1][2] = temp_areas[j1][len(temp_areas[j1]) - 1][2] + 1
break
j1 = j1 + 1
if j1 == len(temp_areas):
temp_areas.append([[i1,i2,i2]])
i2 = i2 + 1
else:
i2 = 0
while (i2 < x_pseudo_section):
if section_items[section_n][i1][i2][0] == 255:
if len(temp_areas) == 0:
temp_areas.append([[i1,i2,i2]])
else:
j1 = 0
while (j1 < len(temp_areas)):
if i2 + (s_size * 0) == temp_areas[j1][len(temp_areas[j1]) - 1][2] + 1:
temp_areas[j1][len(temp_areas[j1]) - 1][2] = temp_areas[j1][len(temp_areas[j1]) - 1][2] + 1
break
j1 = j1 + 1
if j1 == len(temp_areas):
temp_areas.append([[i1,i2,i2]])
i2 = i2 + 1
if len(temp_areas) > 0:
i = 0
while (i < len(temp_areas)):
segmented_areas[section_n].append([[section_n],[i1,i1]])
i2 = 0
while(i2 < len(temp_areas[i])):
segmented_areas[section_n][len(segmented_areas[section_n]) - 1].append(temp_areas[i][i2])
i2 = i2 + 1
#segmented_areas.append(temp_areas[i])
temp_areas[i].insert(0, len(segmented_areas[section_n]) - 1)
i = i + 1
break
i1 = i1 + 1
else:
i1 = 0
while (i1 < y_pseudo_section):
if (section_n % x_total) < (x_total - 1):
i2 = 0
while (i2 < s_size):
if section_items[section_n][i1][i2][0] == 255:
if len(temp_areas) == 0:
temp_areas.append([[i1,i2,i2]])
else:
j1 = 0
while (j1 < len(temp_areas)):
if i2 + (s_size * 0) == temp_areas[j1][len(temp_areas[j1]) - 1][2] + 1:
temp_areas[j1][len(temp_areas[j1]) - 1][2] = temp_areas[j1][len(temp_areas[j1]) - 1][2] + 1
break
j1 = j1 + 1
if j1 == len(temp_areas):
temp_areas.append([[i1,i2,i2]])
i2 = i2 + 1
else:
i2 = 0
while (i2 < x_pseudo_section):
if section_items[section_n][i1][i2][0] == 255:
if len(temp_areas) == 0:
temp_areas.append([[i1,i2,i2]])
else:
j1 = 0
while (j1 < len(temp_areas)):
if i2 + (s_size * 0) == temp_areas[j1][len(temp_areas[j1]) - 1][2] + 1:
temp_areas[j1][len(temp_areas[j1]) - 1][2] = temp_areas[j1][len(temp_areas[j1]) - 1][2] + 1
break
j1 = j1 + 1
if j1 == len(temp_areas):
temp_areas.append([[i1,i2,i2]])
i2 = i2 + 1
if len(temp_areas) > 0:
i = 0
while (i < len(temp_areas)):
segmented_areas[section_n].append([[section_n],[i1,i1]])
i2 = 0
while(i2 < len(temp_areas[i])):
segmented_areas[section_n][len(segmented_areas[section_n]) - 1].append(temp_areas[i][i2])
i2 = i2 + 1
#segmented_areas.append(temp_areas[i])
temp_areas[i].insert(0, len(segmented_areas[section_n]) - 1)
i = i + 1
break
i1 = i1 + 1
temp_areas2 = []
if math.floor(section_n / x_total) < (y_total - 1):
i1 = i1 + 1
while (i1 < s_size):
if (section_n % x_total) < (x_total - 1):
i2 = 0
temp_areas2 = []
while (i2 < s_size):
if section_items[section_n][i1][i2][0] == 255:
if len(temp_areas2) == 0:
temp_areas2.append([[i1,i2,i2]])
else:
j1 = 0
while (j1 < len(temp_areas2)):
if i2 + (s_size * 0) == temp_areas2[j1][len(temp_areas2[j1]) - 1][2] + 1:
temp_areas2[j1][len(temp_areas2[j1]) - 1][2] = temp_areas2[j1][len(temp_areas2[j1]) - 1][2] + 1
break
j1 = j1 + 1
if j1 == len(temp_areas2):
temp_areas2.append([[i1,i2,i2]])
i2 = i2 + 1
else:
i2 = 0
temp_areas2 = []
while (i2 < x_pseudo_section):
if section_items[section_n][i1][i2][0] == 255:
if len(temp_areas2) == 0:
temp_areas2.append([[i1,i2,i2]])
else:
j1 = 0
while (j1 < len(temp_areas2)):
if i2 + (s_size * 0) == temp_areas2[j1][len(temp_areas2[j1]) - 1][2] + 1:
temp_areas2[j1][len(temp_areas2[j1]) - 1][2] = temp_areas2[j1][len(temp_areas2[j1]) - 1][2] + 1
break
j1 = j1 + 1
if j1 == len(temp_areas2):
temp_areas2.append([[i1,i2,i2]])
i2 = i2 + 1
j1 = 0
# find logic for xxxxx or x xx or xxxxx or xxx
# x xx xxxxx xxx xxxxx
new_areas = []
while (j1 < len(temp_areas2)):
j2 = 0
while (j2 < len(temp_areas)):
if (temp_areas[j2][1][1] >= temp_areas2[j1][0][1] and temp_areas[j2][1][1] <= temp_areas2[j1][0][2]) or \
(temp_areas[j2][1][2] <= temp_areas2[j1][0][2] and temp_areas[j2][1][2] >= temp_areas2[j1][0][1]) or \
(temp_areas2[j1][0][1] <= temp_areas[j2][1][1] and temp_areas2[j1][0][2] >= temp_areas[j2][1][2]) or \
(temp_areas[j2][1][1] <= temp_areas2[j1][0][1] and temp_areas[j2][1][2] >= temp_areas2[j1][0][2]):
segmented_areas[section_n][temp_areas[j2][0]].append(temp_areas2[j1][0])
if segmented_areas[section_n][temp_areas[j2][0]][1][1] < temp_areas2[j1][0][0]: # update Yb
segmented_areas[section_n][temp_areas[j2][0]][1][1] = temp_areas2[j1][0][0]
if isinstance(temp_areas2[j1][0], list):
temp_areas2[j1].insert(0, temp_areas[j2][0])
break
j2 = j2 + 1
if j2 == len(temp_areas):
new_areas.append(j1)
j1 = j1 + 1
# append new areas to segmented_areas
i = 0
while (i < len(new_areas)):
segmented_areas[section_n].append([[section_n],[i1,i1]])
i2 = 0
while(i2 < len(temp_areas2[new_areas[i]])):
segmented_areas[section_n][len(segmented_areas[section_n]) - 1].append(temp_areas2[new_areas[i]][i2])
i2 = i2 + 1
#segmented_areas.append(temp_areas[i])
temp_areas2[new_areas[i]].insert(0, len(segmented_areas[section_n]) - 1)
i = i + 1
temp_areas = []
for i in temp_areas2:
temp_areas.append(i)
i1 = i1 + 1
else:
i1 = i1 + 1
while (i1 < y_pseudo_section):
if (section_n % x_total) < (x_total - 1):
i2 = 0
temp_areas2 = []
while (i2 < s_size):
if section_items[section_n][i1][i2][0] == 255:
if len(temp_areas2) == 0:
temp_areas2.append([[i1,i2,i2]])
else:
j1 = 0
while (j1 < len(temp_areas2)):
if i2 + (s_size * 0) == temp_areas2[j1][len(temp_areas2[j1]) - 1][2] + 1:
temp_areas2[j1][len(temp_areas2[j1]) - 1][2] = temp_areas2[j1][len(temp_areas2[j1]) - 1][2] + 1
break
j1 = j1 + 1
if j1 == len(temp_areas2):
temp_areas2.append([[i1,i2,i2]])
i2 = i2 + 1
else:
i2 = 0
temp_areas2 = []
while (i2 < x_pseudo_section):
if section_items[section_n][i1][i2][0] == 255:
if len(temp_areas2) == 0:
temp_areas2.append([[i1,i2,i2]])
else:
j1 = 0
while (j1 < len(temp_areas2)):
if i2 + (s_size * 0) == temp_areas2[j1][len(temp_areas2[j1]) - 1][2] + 1:
temp_areas2[j1][len(temp_areas2[j1]) - 1][2] = temp_areas2[j1][len(temp_areas2[j1]) - 1][2] + 1
break
j1 = j1 + 1
if j1 == len(temp_areas2):
temp_areas2.append([[i1,i2,i2]])
i2 = i2 + 1
j1 = 0
# find logic for xxxxx or x xx or xxxxx or xxx
# x xx xxxxx xxx xxxxx
new_areas = []
while (j1 < len(temp_areas2)):
j2 = 0
while (j2 < len(temp_areas)):
if (temp_areas[j2][1][1] >= temp_areas2[j1][0][1] and temp_areas[j2][1][1] <= temp_areas2[j1][0][2]) or \
(temp_areas[j2][1][2] <= temp_areas2[j1][0][2] and temp_areas[j2][1][2] >= temp_areas2[j1][0][1]) or \
(temp_areas2[j1][0][1] <= temp_areas[j2][1][1] and temp_areas2[j1][0][2] >= temp_areas[j2][1][2]) or \
(temp_areas[j2][1][1] <= temp_areas2[j1][0][1] and temp_areas[j2][1][2] >= temp_areas2[j1][0][2]):
segmented_areas[section_n][temp_areas[j2][0]].append(temp_areas2[j1][0])
if segmented_areas[section_n][temp_areas[j2][0]][1][1] < temp_areas2[j1][0][0]: # update Yb
segmented_areas[section_n][temp_areas[j2][0]][1][1] = temp_areas2[j1][0][0]
if isinstance(temp_areas2[j1][0], list):
temp_areas2[j1].insert(0, temp_areas[j2][0])
break
j2 = j2 + 1
if j2 == len(temp_areas):
new_areas.append(j1)
j1 = j1 + 1
# append new areas to segmented_areas
i = 0
while (i < len(new_areas)):
segmented_areas[section_n].append([[section_n],[i1,i1]])
i2 = 0
while(i2 < len(temp_areas2[new_areas[i]])):
segmented_areas[section_n][len(segmented_areas[section_n]) - 1].append(temp_areas2[new_areas[i]][i2])
i2 = i2 + 1
#segmented_areas.append(temp_areas[i])
temp_areas2[new_areas[i]].insert(0, len(segmented_areas[section_n]) - 1)
i = i + 1
temp_areas = []
for i in temp_areas2:
temp_areas.append(i)
i1 = i1 + 1
temp1 = 0
flag1 = 0
while (flag1 == 0):
combine_segments(section_n)
#print('len:', len(segmented_areas))
if temp1 != len(segmented_areas[section_n]):
temp1 = len(segmented_areas[section_n])
else:
flag1 = 1
# sections in boundary of segments
section_boundary = []
y_pseudo_section = y_axis - ((y_total - 1) * s_size)
x_pseudo_section = x_axis - ((x_total - 1) * s_size)
for section_n in range(len(segmented_areas)):
section_boundary.append([section_n])
if len(segmented_areas[section_n]) > 0:
if (section_n + 1) % x_total == 0:
x_length = x_pseudo_section - 1
else:
x_length = s_size - 1
if int(section_n / x_total) == y_total - 1:
y_length = y_pseudo_section - 1
else:
y_length = s_size - 1
i = 0 # top boundary -> 0
while (i < len(segmented_areas[section_n])):
flag1 = 0 # 1 if any section is present in boundary
i0 = 2
while (i0 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i0][0] > 0:
break
else:
section_boundary[section_n].append([0,[i, segmented_areas[section_n][i][i0][1], segmented_areas[section_n][i][i0][2]]]) # [i, left, right]
flag1 = 1
i0 = i0 + 1
break
if flag1 == 1:
while (i0 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i0][0] > 0:
break
else:
section_boundary[section_n][len(section_boundary[section_n]) - 1].append([i, segmented_areas[section_n][i][i0][1], segmented_areas[section_n][i][i0][2]]) # [i, left, right]
i0 = i0 + 1
i = i + 1
break
else:
i = i + 1
while (i < len(segmented_areas[section_n])):
i0 = 2
while (i0 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i0][0] > 0:
break
else:
section_boundary[section_n][len(section_boundary[section_n]) - 1].append([i, segmented_areas[section_n][i][i0][1], segmented_areas[section_n][i][i0][2]]) # [i, left, right]
i0 = i0 + 1
i = i + 1
i = 0 # bottom boundary -> 1
while (i < len(segmented_areas[section_n])):
flag1 = 0 # 1 if any section is present in boundary
i0 = len(segmented_areas[section_n][i]) - 1
while (i0 > 1):
if segmented_areas[section_n][i][i0][0] < y_length:
break
else:
section_boundary[section_n].append([1,[i, segmented_areas[section_n][i][i0][1], segmented_areas[section_n][i][i0][2]]]) # [i, left, right]
flag1 = 1
i0 = i0 - 1
break
if flag1 == 1:
while (i0 > 1):
if segmented_areas[section_n][i][i0][0] < y_length:
break
else:
section_boundary[section_n][len(section_boundary[section_n]) - 1].append([i, segmented_areas[section_n][i][i0][1], segmented_areas[section_n][i][i0][2]]) # [i, left, right]
i0 = i0 - 1
i = i + 1
break
else:
i = i + 1
while (i < len(segmented_areas[section_n])):
i0 = len(segmented_areas[section_n][i]) - 1
while (i0 > 1):
if segmented_areas[section_n][i][i0][0] < y_length:
break
else:
section_boundary[section_n][len(section_boundary[section_n]) - 1].append([i, segmented_areas[section_n][i][i0][1], segmented_areas[section_n][i][i0][2]]) # [i, left, right]
i0 = i0 - 1
i = i + 1
flag1 = 0 # 1 if any section is present in boundary
temp2 = 0 # index of one section in boundary
i = 0 # left boundary -> 2
while (i < len(segmented_areas[section_n])):
i0 = 2
while (i0 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i0][1] == 0:
section_boundary[section_n].append([2,[i, segmented_areas[section_n][i][i0][0]]])
temp1 = segmented_areas[section_n][i][i0][0]
temp2 = len(section_boundary[section_n][len(section_boundary[section_n]) - 1]) - 1
temp3 = segmented_areas[section_n][i][i0][0]
i1 = i0 + 1
while (i1 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i1][0] > temp3 + 1:
break
elif segmented_areas[section_n][i][i1][1] == 0:
temp1 = segmented_areas[section_n][i][i1][0]
temp3 = temp3 + 1
i1 = i1 + 1
section_boundary[section_n][len(section_boundary[section_n]) - 1][temp2].append(temp1)
flag1 = 1
i0 = i1
break
else:
i0 = i0 + 1
if flag1 == 1:
while (i0 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i0][1] == 0:
section_boundary[section_n][len(section_boundary[section_n]) - 1].append([i, segmented_areas[section_n][i][i0][0]])
temp1 = segmented_areas[section_n][i][i0][0]
temp2 = len(section_boundary[section_n][len(section_boundary[section_n]) - 1]) - 1
temp3 = segmented_areas[section_n][i][i0][0]
i1 = i0 + 1
while (i1 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i1][0] > temp3 + 1:
break
elif segmented_areas[section_n][i][i1][1] == 0:
temp1 = segmented_areas[section_n][i][i1][0]
temp3 = temp3 + 1
i1 = i1 + 1
section_boundary[section_n][len(section_boundary[section_n]) - 1][temp2].append(temp1)
i0 = i1
else:
i0 = i0 + 1
i = i + 1
break
else:
i = i + 1
while (i < len(segmented_areas[section_n])):
i0 = 2
while (i0 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i0][1] == 0:
section_boundary[section_n][len(section_boundary[section_n]) - 1].append([i, segmented_areas[section_n][i][i0][0]])
temp1 = segmented_areas[section_n][i][i0][0]
temp2 = len(section_boundary[section_n][len(section_boundary[section_n]) - 1]) - 1
temp3 = segmented_areas[section_n][i][i0][0]
i1 = i0 + 1
while (i1 < len(segmented_areas[section_n][i])):
if segmented_areas[section_n][i][i1][0] > temp3 + 1:
break
elif segmented_areas[section_n][i][i1][1] == 0:
temp1 = segmented_areas[section_n][i][i1][0]
temp3 = temp3 + 1
i1 = i1 + 1
section_boundary[section_n][len(section_boundary[section_n]) - 1][temp2].append(temp1)
i0 = i1
else:
i0 = i0 + 1
i = i + 1
flag1 = 0 # 1 if any section is present in boundary
temp2 = 0 # index of one section in boundary
i = 0 # right boundary -> 3
while (i < len(segmented_areas[section_n])):
i0 = len(segmented_areas[section_n][i]) - 1
while (i0 > 1):
if segmented_areas[section_n][i][i0][2] == x_length:
section_boundary[section_n].append([3,[i, segmented_areas[section_n][i][i0][0]]])
temp1 = segmented_areas[section_n][i][i0][0]
temp2 = len(section_boundary[section_n][len(section_boundary[section_n]) - 1]) - 1
temp3 = segmented_areas[section_n][i][i0][0]
i1 = i0 - 1
while (i1 > 1):
if segmented_areas[section_n][i][i1][0] < temp3 - 1:
break
elif segmented_areas[section_n][i][i1][2] == x_length:
temp1 = segmented_areas[section_n][i][i1][0]
temp3 = temp3 - 1
i1 = i1 - 1
section_boundary[section_n][len(section_boundary[section_n]) - 1][temp2].insert(1,temp1)
flag1 = 1
i0 = i1
break
else:
i0 = i0 - 1
if flag1 == 1:
while (i0 > 1):
if segmented_areas[section_n][i][i0][2] == x_length:
section_boundary[section_n][len(section_boundary[section_n]) - 1].append([i, segmented_areas[section_n][i][i0][0]])
temp1 = segmented_areas[section_n][i][i0][0]
temp2 = len(section_boundary[section_n][len(section_boundary[section_n]) - 1]) - 1
temp3 = segmented_areas[section_n][i][i0][0]
i1 = i0 - 1
while (i1 > 1):
if segmented_areas[section_n][i][i1][0] < temp3 - 1:
break
elif segmented_areas[section_n][i][i1][2] == x_length:
temp1 = segmented_areas[section_n][i][i1][0]
temp3 = temp3 - 1
i1 = i1 - 1
section_boundary[section_n][len(section_boundary[section_n]) - 1][temp2].insert(1,temp1)
i0 = i1
else:
i0 = i0 - 1
i = i + 1
break
else:
i = i + 1
while (i < len(segmented_areas[section_n])):
i0 = len(segmented_areas[section_n][i]) - 1
while (i0 > 1):
if segmented_areas[section_n][i][i0][2] == x_length:
section_boundary[section_n][len(section_boundary[section_n]) - 1].append([i, segmented_areas[section_n][i][i0][0]])
temp1 = segmented_areas[section_n][i][i0][0]
temp2 = len(section_boundary[section_n][len(section_boundary[section_n]) - 1]) - 1
temp3 = segmented_areas[section_n][i][i0][0]
i1 = i0 - 1
while (i1 > 1):
if segmented_areas[section_n][i][i1][0] < temp3 - 1:
break
elif segmented_areas[section_n][i][i1][2] == x_length:
temp1 = segmented_areas[section_n][i][i1][0]
temp3 = temp3 - 1
i1 = i1 - 1
section_boundary[section_n][len(section_boundary[section_n]) - 1][temp2].insert(1,temp1)
i0 = i1
else:
i0 = i0 - 1
i = i + 1
# combine segments across sections
print('section_boundary, yx_total: ', len(section_boundary), yx_total)
combine_seg_sec = []
for section_n in range(len(section_boundary)):
if len(section_boundary[section_n]) > 0:
for j in range(1,len(section_boundary[section_n])):
if section_boundary[section_n][j][0] == 2:
# section_n - 1
if section_n % x_total != 0: # == 0 indicates leftmost section
for i in range(1,len(section_boundary[section_n - 1])):
if section_boundary[section_n - 1][i][0] == 3:
j1 = 1
while (j1 < len(section_boundary[section_n][j])):
i1 = 1
while (i1 < len(section_boundary[section_n - 1][i])):
if section_boundary[section_n - 1][i][i1][1] <= section_boundary[section_n][j][j1][1] and section_boundary[section_n - 1][i][i1][2] >= section_boundary[section_n][j][j1][1]:
combine_seg_sec.append([[section_n, section_boundary[section_n][j][0], section_boundary[section_n][j][j1]], [section_n - 1, section_boundary[section_n - 1][i][0], section_boundary[section_n - 1][i][i1]]])
elif section_boundary[section_n][j][j1][1] <= section_boundary[section_n - 1][i][i1][1] and section_boundary[section_n][j][j1][2] >= section_boundary[section_n - 1][i][i1][1]:
combine_seg_sec.append([[section_n, section_boundary[section_n][j][0], section_boundary[section_n][j][j1]], [section_n - 1, section_boundary[section_n - 1][i][0], section_boundary[section_n - 1][i][i1]]])
i1 = i1 + 1
j1 = j1 + 1
break
elif section_boundary[section_n][j][0] == 3:
# section_n + 1
if (section_n + 1) % x_total != 0: # == 0 indicates rightmost section
for i in range(1,len(section_boundary[section_n + 1])):
if section_boundary[section_n + 1][i][0] == 2:
j1 = 1
while (j1 < len(section_boundary[section_n][j])):
i1 = 1
while (i1 < len(section_boundary[section_n + 1][i])):
if section_boundary[section_n + 1][i][i1][1] <= section_boundary[section_n][j][j1][1] and section_boundary[section_n + 1][i][i1][2] >= section_boundary[section_n][j][j1][1]:
combine_seg_sec.append([[section_n, section_boundary[section_n][j][0], section_boundary[section_n][j][j1]], [section_n + 1, section_boundary[section_n + 1][i][0], section_boundary[section_n + 1][i][i1]]])
elif section_boundary[section_n][j][j1][1] <= section_boundary[section_n + 1][i][i1][1] and section_boundary[section_n][j][j1][2] >= section_boundary[section_n + 1][i][i1][1]:
combine_seg_sec.append([[section_n, section_boundary[section_n][j][0], section_boundary[section_n][j][j1]], [section_n + 1, section_boundary[section_n + 1][i][0], section_boundary[section_n + 1][i][i1]]])
i1 = i1 + 1
j1 = j1 + 1
break
elif section_boundary[section_n][j][0] == 0:
# section_n - x_total
if (section_n - x_total) >= 0: # indicates topmost section
for i in range(1,len(section_boundary[section_n - x_total])):
if section_boundary[section_n - x_total][i][0] == 1:
j1 = 1
while (j1 < len(section_boundary[section_n][j])):
i1 = 1
while (i1 < len(section_boundary[section_n - x_total][i])):
if section_boundary[section_n - x_total][i][i1][1] <= section_boundary[section_n][j][j1][1] and section_boundary[section_n - x_total][i][i1][2] >= section_boundary[section_n][j][j1][1]:
combine_seg_sec.append([[section_n, section_boundary[section_n][j][0], section_boundary[section_n][j][j1]], [section_n - x_total, section_boundary[section_n - x_total][i][0], section_boundary[section_n - x_total][i][i1]]])
elif section_boundary[section_n][j][j1][1] <= section_boundary[section_n - x_total][i][i1][1] and section_boundary[section_n][j][j1][2] >= section_boundary[section_n - x_total][i][i1][1]:
combine_seg_sec.append([[section_n, section_boundary[section_n][j][0], section_boundary[section_n][j][j1]], [section_n - x_total, section_boundary[section_n - x_total][i][0], section_boundary[section_n - x_total][i][i1]]])
i1 = i1 + 1
j1 = j1 + 1
break
elif section_boundary[section_n][j][0] == 1:
# section_n + x_total
if (section_n + x_total) <= (yx_total) - 1: # indicates bottommost section
for i in range(1,len(section_boundary[section_n + x_total])):
if section_boundary[section_n + x_total][i][0] == 0:
j1 = 1
while (j1 < len(section_boundary[section_n][j])):
i1 = 1
while (i1 < len(section_boundary[section_n + x_total][i])):
if section_boundary[section_n + x_total][i][i1][1] <= section_boundary[section_n][j][j1][1] and section_boundary[section_n + x_total][i][i1][2] >= section_boundary[section_n][j][j1][1]:
combine_seg_sec.append([[section_n, section_boundary[section_n][j][0], section_boundary[section_n][j][j1]], [section_n + x_total, section_boundary[section_n + x_total][i][0], section_boundary[section_n + x_total][i][i1]]])
elif section_boundary[section_n][j][j1][1] <= section_boundary[section_n + x_total][i][i1][1] and section_boundary[section_n][j][j1][2] >= section_boundary[section_n + x_total][i][i1][1]:
combine_seg_sec.append([[section_n, section_boundary[section_n][j][0], section_boundary[section_n][j][j1]], [section_n + x_total, section_boundary[section_n + x_total][i][0], section_boundary[section_n + x_total][i][i1]]])
i1 = i1 + 1
j1 = j1 + 1
break
final_seg_sec = []
combine_seg_sec_covered = []
for i in range(len(combine_seg_sec)):
combine_seg_sec_covered.append(0)
# sequentially combine the combine_seg_sec groups (tiled image to single image)
i1 = 0
while (i1 < len(combine_seg_sec)):
#print(i1, len(combine_seg_sec))
temp1 = 0
final_seg_sec.append([[combine_seg_sec[i1][0][0], combine_seg_sec[i1][0][2][0]], [combine_seg_sec[i1][1][0], combine_seg_sec[i1][1][2][0]]])
i2 = i1 + 1
while (i2 < len(combine_seg_sec)):
if combine_seg_sec[i1][0][0] == combine_seg_sec[i2][0][0] and combine_seg_sec[i1][0][2][0] == combine_seg_sec[i2][0][2][0]:
final_seg_sec[len(final_seg_sec) - 1].append([combine_seg_sec[i2][0][0], combine_seg_sec[i2][0][2][0]])
final_seg_sec[len(final_seg_sec) - 1].append([combine_seg_sec[i2][1][0], combine_seg_sec[i2][1][2][0]])
temp1 = 1
elif combine_seg_sec[i1][1][0] == combine_seg_sec[i2][0][0] and combine_seg_sec[i1][1][2][0] == combine_seg_sec[i2][0][2][0]:
final_seg_sec[len(final_seg_sec) - 1].append([combine_seg_sec[i2][0][0], combine_seg_sec[i2][0][2][0]])
final_seg_sec[len(final_seg_sec) - 1].append([combine_seg_sec[i2][1][0], combine_seg_sec[i2][1][2][0]])
temp1 = 1
if combine_seg_sec[i1][0][0] == combine_seg_sec[i2][1][0] and combine_seg_sec[i1][0][2][0] == combine_seg_sec[i2][1][2][0]:
final_seg_sec[len(final_seg_sec) - 1].append([combine_seg_sec[i2][0][0], combine_seg_sec[i2][0][2][0]])
final_seg_sec[len(final_seg_sec) - 1].append([combine_seg_sec[i2][1][0], combine_seg_sec[i2][1][2][0]])
temp1 = 1
elif combine_seg_sec[i1][1][0] == combine_seg_sec[i2][1][0] and combine_seg_sec[i1][1][2][0] == combine_seg_sec[i2][1][2][0]:
final_seg_sec[len(final_seg_sec) - 1].append([combine_seg_sec[i2][0][0], combine_seg_sec[i2][0][2][0]])
final_seg_sec[len(final_seg_sec) - 1].append([combine_seg_sec[i2][1][0], combine_seg_sec[i2][1][2][0]])
temp1 = 1
if temp1 == 1:
combine_seg_sec_covered[i2] = 1
i2 = i2 + 1
i1 = i1 + 1
i = 0
while (i < len(final_seg_sec)):
i1 = 0
while (i1 < len(final_seg_sec[i])):
i2 = i1 + 1
while (i2 < len(final_seg_sec[i])):
if final_seg_sec[i][i1] == final_seg_sec[i][i2]:
del final_seg_sec[i][i2]
else:
i2 = i2 + 1
i1 = i1 + 1
i = i + 1
#identify and append the combine_seg_sec groups which are not covered
flag1 = 0
while (flag1 == 0):
i1 = 0
temp2 = 0
while (i1 < len(combine_seg_sec)):
if combine_seg_sec_covered[i1] == 0:
temp1 = 0
j1 = 0
while (j1 < len(final_seg_sec)):
j2 = 0
while (j2 < len(final_seg_sec[j1])):
if combine_seg_sec[i1][0][0] == final_seg_sec[j1][j2][0] and combine_seg_sec[i1][0][2][0] == final_seg_sec[j1][j2][1]:
final_seg_sec[j1].append([combine_seg_sec[i1][0][0], combine_seg_sec[i1][0][2][0]])
final_seg_sec[j1].append([combine_seg_sec[i1][1][0], combine_seg_sec[i1][1][2][0]])
temp1 = 1
temp2 = 1
combine_seg_sec_covered[i1] = temp1
break
elif combine_seg_sec[i1][1][0] == final_seg_sec[j1][j2][0] and combine_seg_sec[i1][1][2][0] == final_seg_sec[j1][j2][1]:
final_seg_sec[j1].append([combine_seg_sec[i1][0][0], combine_seg_sec[i1][0][2][0]])
final_seg_sec[j1].append([combine_seg_sec[i1][1][0], combine_seg_sec[i1][1][2][0]])
temp1 = 1
temp2 = 1
combine_seg_sec_covered[i1] = temp1
break
j2 = j2 + 1
if temp1 == 1:
break
j1 = j1 + 1
i1 = i1 + 1
if temp2 == 0:
flag1 = 1
i = 0
while (i < len(final_seg_sec)):
i1 = 0
while (i1 < len(final_seg_sec[i])):
i2 = i1 + 1
while (i2 < len(final_seg_sec[i])):
if final_seg_sec[i][i1] == final_seg_sec[i][i2]:
del final_seg_sec[i][i2]
else:
i2 = i2 + 1
i1 = i1 + 1
i = i + 1
combine_seg_sec = []
# combine the related final_seg_sec groups
flag1 = 0
while (flag1 == 0):
temp2 = 0
i = 0
while (i < len(final_seg_sec)):
j = i + 1
while (j < len(final_seg_sec)):
temp1 = 0
j1 = 0
while (j1 < len(final_seg_sec[j])):
if final_seg_sec[i].__contains__(final_seg_sec[j][j1]) == True:
j2 = 0
while (j2 < len(final_seg_sec[j])):
final_seg_sec[i].append(final_seg_sec[j][j2])
j2 = j2 + 1
temp1 = 1
temp2 = 1
break
j1 = j1 + 1
if temp1 == 1:
del final_seg_sec[j]
else:
j = j + 1
i = i + 1
if temp2 == 0:
flag1 = 1
i = 0
while (i < len(final_seg_sec)):
i1 = 0
while (i1 < len(final_seg_sec[i])):
i2 = i1 + 1
while (i2 < len(final_seg_sec[i])):
if final_seg_sec[i][i1] == final_seg_sec[i][i2]:
del final_seg_sec[i][i2]
else:
i2 = i2 + 1
i1 = i1 + 1
i = i + 1
i = 0
while (i < len(final_seg_sec)):
i1 = 0
while (i1 < len(final_seg_sec[i])):
i2 = i1 + 1
while (i2 < len(final_seg_sec[i])):
if final_seg_sec[i][i1] == final_seg_sec[i][i2]:
del final_seg_sec[i][i2]
else:
i2 = i2 + 1
i1 = i1 + 1
i = i + 1
section_boundary = []
combined_areas = [] # combine areas as per final_seg_sec
for line in final_seg_sec:
combined_areas.append([])
temp1 = len(combined_areas) - 1
temp2 = -1
for line1 in line:
combined_areas[temp1].append([line1])
temp2 = temp2 + 1
temp3 = len(segmented_areas[line1[0]][line1[1]])
for i in range(2,temp3):
if len(segmented_areas[line1[0]][line1[1]][i]) == 3:
combined_areas[temp1][temp2].append(segmented_areas[line1[0]][line1[1]][i])
segmented_areas[line1[0]][line1[1]].append([-1])
#print(segmented_areas[2])
i1 = 0
temp1 = len(segmented_areas)
while (i1 < temp1):
i2 = 0
while (i2 < len(segmented_areas[i1])):
if segmented_areas[i1][i2][len(segmented_areas[i1][i2]) - 1] == [-1]:
del segmented_areas[i1][i2]
else:
i2 = i2 + 1
i1 = i1 + 1
# apply colors
for section_n in range(len(section_items)):
i1 = 0
while (i1 < len(segmented_areas[section_n])):
random_colorR = random.randint(40,255)
random_colorG = random.randint(40,255)
random_colorB = random.randint(40,255)
i2 = 2
while (i2 < len(segmented_areas[section_n][i1])):
i = segmented_areas[section_n][i1][i2][1]
while (i <= segmented_areas[section_n][i1][i2][2]):
section_items[section_n][segmented_areas[section_n][i1][i2][0]][i][0] = random_colorR
section_items[section_n][segmented_areas[section_n][i1][i2][0]][i][1] = random_colorG
section_items[section_n][segmented_areas[section_n][i1][i2][0]][i][2] = random_colorB
i = i + 1
i2 = i2 + 1
i1 = i1 + 1
for section_n in range(len(combined_areas)):
random_colorR = random.randint(40,255)
random_colorG = random.randint(40,255)
random_colorB = random.randint(40,255)
i1 = 0
while (i1 < len(combined_areas[section_n])):
i2 = 1 # doubtful
while (i2 < len(combined_areas[section_n][i1])):
i = combined_areas[section_n][i1][i2][1]
while (i <= combined_areas[section_n][i1][i2][2]):
section_items[combined_areas[section_n][i1][0][0]][combined_areas[section_n][i1][i2][0]][i][0] = random_colorR
section_items[combined_areas[section_n][i1][0][0]][combined_areas[section_n][i1][i2][0]][i][1] = random_colorG
section_items[combined_areas[section_n][i1][0][0]][combined_areas[section_n][i1][i2][0]][i][2] = random_colorB
i = i + 1
i2 = i2 + 1
i1 = i1 + 1
# arrange sections as per original order for display
section_items_final = []
j1 = 0
i = 0
while (j1 < y_total):
j = 0
while (j < s_size):
if i < y_axis:
section_items_final.append([])
j2 = 0
while (j2 < x_total):
i1 = 0
while (i1 < len(section_items[(j1 * x_total) + j2][j])):
section_items_final[i].append(section_items[(j1 * x_total) + j2][j][i1])
i1 = i1 + 1
j2 = j2 + 1
j = j + 1
i = i + 1
else:
break
j1 = j1 + 1
print('len',len(section_items_final))
print('Time taken: ' + str(time.time() - time1) + ' seconds')
viewer = skimage.viewer.ImageViewer(np.array(section_items_final))
viewer.show()
if image_type == 'y':
output_file_open = open('white_groups_combined_manual.csv', 'w', newline='', encoding='utf16')
csv_write1 = csv.writer(output_file_open, delimiter = ',')
output_file_open = open('white_groups_segmented_manual.csv', 'w', newline='', encoding='utf16')
csv_write2 = csv.writer(output_file_open, delimiter = ',')
else:
output_file_open = open('white_groups_combined.csv', 'w', newline='', encoding='utf16')
csv_write1 = csv.writer(output_file_open, delimiter = ',')
output_file_open = open('white_groups_segmented.csv', 'w', newline='', encoding='utf16')
csv_write2 = csv.writer(output_file_open, delimiter = ',')
# write to csv file
for i in combined_areas:
for i1 in i:
for i2 in i1:
csv_write1.writerow(i2)
csv_write1.writerow('')
for i in segmented_areas:
for i1 in i:
for i2 in i1:
csv_write2.writerow(i2)
csv_write2.writerow('')
return 0
white_segments(y_axis, x_axis, s_size)