extract_patch.py

# -*- coding: utf-8 -*-
import cv2
from tqdm import tqdm
import csv
from glob import glob
import os

CSVDIR='./CSVResults' #input
PATCHDIR='./Patches/Z_expanded' #output

#%%
z_offsets = ['z0', 'z400', 'z-400', 'z800', 'z-800', 'z1200', 'z-1200', 'z1600', 'z-1600', 'z2000', 'z-2000']
#%%
def generate_patch(w=80):
	"""    
	Arguments:
	w -- window size for patches
	
	Returns:
	total_num -- total number of predicted nucleus patches
	"""        
	total_num = 0
	# generate patches only for the sub-images with nuclei detected
	for csv_path in tqdm(glob(CSVDIR+'/*.csv')):
		# extract image name without extension, and separate without z value
		img_name = os.path.basename(csv_path)[:-len('.csv')]
		img_name_l = img_name[:img_name.rindex('z0')]
		img_name_r = img_name[img_name.rindex('z0') + len('z0'):]
		
		for z_offset in z_offsets:
			img_z_name = img_name_l + z_offset + img_name_r + '.jpg'
			try:
				img = cv2.imread('./JPEGImages/' + img_z_name)
			except:
				print('Failed reading: '+'./JPEGImages/' + img_z_name)
				raise

			with open(csv_path) as f:
				f_csv = csv.reader(f)
				headers = next(f_csv)
				i = 0
				for row in f_csv:
					center = [round(float(row[-2])), round(float(row[-1]))]
					box = [center[0] - int(w/2), center[1] - int(w/2), 
						   center[0] + int(w/2), center[1] + int(w/2)]
					cropped = img[box[1]:box[1]+w, box[0]:box[0]+w]    # [Ymin:Ymax , Xmin:Xmax]
					if cropped.shape[0:2]==(w,w):
						outpath=PATCHDIR+"/{}_{}_{}.jpg".format(img_name, '0'*(4 - len(str(i))) + str(i), z_offset)
						try:
							cv2.imwrite(outpath, cropped, [int(cv2.IMWRITE_JPEG_QUALITY), 100])
						except:
							print('Failed writing: '+outpath)
							print(row)
							raise
					else:
						if z_offset==z_offsets[0]: #Print only once
					 		print('Ignoring partial patch of size'+str(cropped.shape))
					i += 1
				total_num += (f_csv.line_num - 1)
				
	return total_num

#%%
if __name__ == '__main__':
	print('#'*30)
	print('Generating predicted patches at all Z level.')
	print('#'*30)
	total_num = generate_patch()