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Copy pathN-ary-Mask-Generator.py
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N-ary-Mask-Generator.py
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# -*- coding: utf-8 -*-
"""
Created on Fri Nov 10 15:10:46 2023
@author: Olivier-Rukundo - Modifications by [email protected] - Olivier Rukundo Ph.D.
"""
# @original script: https://github.com/ruchikaverma-iitg/MoNuSAC/blob/master/n-ary_mask_generation.ipynb
# Errors generated by the original script: ValueError: A linearring requires at least 4 coordinates.
# Corrections or updates made (see lines):
# if len(regions[0]) >= 4:
# poly = Polygon(regions[0])
.
.
.
# else:
# print("Skipping creation of Polygon. Insufficient coordinates.")
# Additional problems with the original script: The original script saved images as .tif format, which resulted in huge size of saved masks and masks without metadata.
# Additional updates: I consided using a more common format (like PNG) to automatically handle metadata more consistently with our expectations (see lines):
# cv2.imwrite(sub_image_loc[:-4]+'.png', np.array(img.read_region((0,0),0,img.level_dimensions[0])))
# mask_path = sub_path+'/'+str(count)+'_mask.png'
import os # OR added this to find the openslide DLL file
os.add_dll_directory(r'C:\Users\...\openslide-win64-20231011\openslide-win64-20231011\bin')
import openslide
# from xml.dom import minidom
import numpy as np
# import openslide
# from openslide import open_slide
from glob import glob
import cv2
# import matplotlib.pyplot as plt
# import scipy.io as sio
# from PIL import Image
# import scipy
# import scipy.ndimage
from shapely.geometry import Polygon
from skimage import draw
import xml.etree.ElementTree as ET
# Read svs files from the desired path
count = 0
data_path = r'C:\Users\...\TrainingData\MoNuSAC_images_and_annotations' #Path to read data from
destination_path = r'C:\Users\...\NaryMaskTrainingData' # Path to save n-ary masks corresponding to xml files
os.chdir(destination_path)
try:
os.mkdir(destination_path+'\MoNuSAC_masks')
except OSError:
print ("Creation of the mask directory %s failed" % destination_path)
os.chdir(destination_path+'\MoNuSAC_masks')#Create folder named as MoNuSAC_masks
patients = [x[0] for x in os.walk(data_path)]#Total patients in the data_path
len(patients)
for patient_loc in patients:
patient_name = patient_loc[len(data_path)+1:]#Patient name
print(patient_name)
## To make patient's name directory in the destination folder
try:
os.mkdir(patient_name)
except OSError:
print ("\n Creation of the patient's directory %s failed" % patient_name)
## Read sub-images of each patient in the data path
sub_images = glob(patient_loc+'/*.svs')
for sub_image_loc in sub_images:
gt = 0
sub_image_name = sub_image_loc[len(data_path)+len(patient_name)+1:-4]
print(sub_image_name)
## To make sub_image directory under the patient's folder
sub_image = './'+patient_name+'/'+sub_image_name #Destination path
try:
os.mkdir(sub_image)
except OSError:
print ("\n Creation of the patient's directory %s failed" % sub_image)
image_name = sub_image_loc
img = openslide.OpenSlide(image_name)
# If svs image needs to save in tif
cv2.imwrite(sub_image_loc[:-4]+'.png', np.array(img.read_region((0,0),0,img.level_dimensions[0])))
# Read xml file
xml_file_name = image_name[:-4]
xml_file_name = xml_file_name+'.xml'
tree = ET.parse(xml_file_name)
root = tree.getroot()
#Generate n-ary mask for each cell-type
for k in range(len(root)):
label = [x.attrib['Name'] for x in root[k][0]]
label = label[0]
for child in root[k]:
for x in child:
r = x.tag
if r == 'Attribute':
count = count+1
print(count)
label = x.attrib['Name']
n_ary_mask = np.transpose(np.zeros((img.read_region((0,0),0,img.level_dimensions[0]).size)))
print(label)
# Create directory for each label
sub_path = sub_image+'/'+label
try:
os.mkdir(sub_path)
except OSError:
print ("Creation of the directory %s failed" % label)
else:
print ("Successfully created the directory %s " % label)
if r == 'Region':
regions = []
vertices = x[1]
coords = np.zeros((len(vertices), 2))
for i, vertex in enumerate(vertices):
coords[i][0] = vertex.attrib['X']
coords[i][1] = vertex.attrib['Y']
regions.append(coords)
# poly = Polygon(regions[0])
if len(regions[0]) >= 4: # I added this condition to check if there are fewer than 4 coordinates or else to print a skipping message
poly = Polygon(regions[0])
vertex_row_coords = regions[0][:,0]
vertex_col_coords = regions[0][:,1]
fill_row_coords, fill_col_coords = draw.polygon(vertex_col_coords, vertex_row_coords, n_ary_mask.shape)
gt = gt+1 #Keep track of giving unique value to each instance in an image
n_ary_mask[fill_row_coords, fill_col_coords] = gt
mask_path = sub_path+'/'+str(count)+'_mask.png'
cv2.imwrite(mask_path, n_ary_mask)
else:
print("Skipping creation of Polygon. Insufficient coordinates.")