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transfer_annotation.py
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from openslide import OpenSlide
from PIL import Image, ImageDraw
import os
import cv2
import numpy
import magic
from xml.dom.minidom import parseString
import subprocess
def is_or_not_RGBA(img):
if img.mode == 'RGBA':
alpha = img.split()[3]
bgmask = alpha.point(lambda x: 255 - x)
img = img.convert('RGB')
# paste(color, box, mask)
img.paste((255, 255, 255), None, bgmask)
else:
img = img.convert('RGB')
return img
def draw_rangcle_jpg(file_dir):
mrxs_lst = []
if not os.path.isdir(file_dir):
mrxs_lst[0] = file_dir
else:
for i in os.listdir(file_dir):
if os.path.splitext(i)[-1] == '.mrxs':
mrxs_lst.append(os.path.join(file_dir, os.path.splitext(i)[0]))
for mrxs_fille_name in mrxs_lst:
#mrxs_fille_name = "/home/gytang/medicine/fake/DCB-003"
osr = OpenSlide(mrxs_fille_name + '.mrxs')
axis_list = []
find_file_flag = 0
file_list = os.listdir(mrxs_fille_name)
file_list.sort()
for i in file_list[::-1]:
a = magic.from_file(os.path.join(mrxs_fille_name, i))
print("{}: magic tool read file property: {}".format(i, a))
if a.find("ASCII text") != -1 or a.find("UTF-8 Unicode") != -1:
with open(os.path.join(mrxs_fille_name, i)) as f:
lines = f.readlines()
lines.reverse()
if lines[-1].find("<attributes>") == -1:
continue
if find_file_flag == 1:
print("There are already exsited a .dat label config file. The mrxs is not as normal as we occured.")
find_file_flag = 1
ID_name = []
res = []
for idx, line in enumerate(lines):
try:
line = parseString(line)
# print("ok:", line[0])
except:
#print("Can't analysis the {}th line".format(idx))
#print(line)
res.append(line)
continue
descript_lst = line.getElementsByTagName('descriptor')
for elements in descript_lst:
ID = elements.getAttribute('ID')[1:-1]
if ID not in ID_name:
ID_name.append(ID)
flag_lst = line.getElementsByTagName('slide_flag')
axis = []
sib_lst = line.getElementsByTagName('SimpleBookmark')
if sib_lst == []:
continue
label = sib_lst[0].getAttribute('Caption')
detail_label = sib_lst[0].getAttribute('Desc')
if label.find("Annotation") == 0 and detail_label != "":
#print("alter annotation label.")
for node in sib_lst:
node.setAttribute("Caption", detail_label)
label = detail_label
print("===============================================================================")
print("alter_caption :", label)
axis.append(flag_lst[0].getAttribute('brLeft'))
axis.append(flag_lst[0].getAttribute('brTop'))
axis.append(flag_lst[0].getAttribute('brRight'))
axis.append(flag_lst[0].getAttribute('brBottom'))
axis = [int(i) for i in axis]
ww = axis[2] - axis[0]
hh = axis[3] - axis[1]
w, h = osr.level_dimensions[0]
img = osr.read_region((max(axis[0]-100,0), max(axis[1]-100,0)), 0, (min(w,round(ww + 200)), min(h,round(hh + 200))))
#img.show()
img = is_or_not_RGBA(img)
img = numpy.array(img)
opencv_image = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
print(100, 100, round(ww),round(hh))
opencv_image = cv2.rectangle(opencv_image, (100, 100),(100 + round(ww), 100+round(hh)), (0, 0, 0), 10)
#imgdraw.rectangle((round(axis[0]),round(axis[1]),round(ww),round(hh)),None,outline=(0,0,0))
ratio = 512 / (ww+200)
opencv_image = cv2.resize(opencv_image, (512, int((hh+200) * ratio)))
#cv2.imshow("show", opencv_image)
#cv2.waitKey(1000)
while(1):
is_label = input("Is it a label?\n"
"(Enter means yes, or input 'n' or 'N' means that the box is not label):")
#cv2.destroyAllWindows()
if is_label == "" or is_label.lower() == "y" or is_label.lower() == "yes":
print("\nfile:",mrxs_fille_name,"axis:", axis, "ID:", ID, "label:", label)
axis_list.append({"axis": axis, "ID": ID, "label": label})
res.append(line)
break
elif is_label.lower() == "n" or is_label.lower() == "no":
break
else:
print("The format of input is wrong. Please input again.")
continue
with open(os.path.join(mrxs_fille_name, i), 'w') as fd:
if res is not None:
res.reverse()
for re in res:
try:
# print("ok:", line[0])
line = re.toxml() + '\n'
if line.find('<?xml version="1.0" ?>') == 0:
line = line.replace('<?xml version="1.0" ?>', '')
#print(line)
fd.write(line)
except:
#print("Can't analysis the {}th line")
#print(re)
fd.write(re)
continue
break
if find_file_flag == 0:
print("No .dat label file in mrxs {} which searched by magic tool.".format(mrxs_fille_name))
osr.close()
#return axis_list
def alter_capption_main(file_dir):
mrxs_lst = []
if not os.path.isdir(file_dir):
mrxs_lst[0] = file_dir
else:
for i in os.listdir(file_dir):
if os.path.splitext(i)[-1] == '.mrxs':
print(os.path.join(file_dir, os.path.splitext(i)[0]))
mrxs_lst.append(os.path.join(file_dir, os.path.splitext(i)[0]))
for mrxs_fille_name in mrxs_lst:
#mrxs_fille_name = "/home/gytang/medicine/fake/DCB-003"
osr = OpenSlide(mrxs_fille_name + '.mrxs')
axis_list = []
find_file_flag = 0
file_list = os.listdir(mrxs_fille_name)
file_list.sort()
for i in file_list[::-1]:
a = magic.from_file(os.path.join(mrxs_fille_name, i))
print("{}: magic tool read file property: {}".format(i, a))
if a.find("ASCII text") != -1 or a.find("UTF-8 Unicode") != -1:
with open(os.path.join(mrxs_fille_name, i)) as f:
lines = f.readlines()
lines.reverse()
if lines[-1].find("<attributes>") == -1:
continue
if find_file_flag == 1:
print("There are already exsited a .dat label config file. The mrxs is not as normal as we occured.")
find_file_flag = 1
ID_name = []
res = []
for idx, line in enumerate(lines):
try:
line = parseString(line)
# print("ok:", line[0])
except:
#print("Can't analysis the {}th line".format(idx))
#print(line)
res.append(line)
continue
descript_lst = line.getElementsByTagName('descriptor')
for elements in descript_lst:
ID = elements.getAttribute('ID')[1:-1]
if ID not in ID_name:
ID_name.append(ID)
flag_lst = line.getElementsByTagName('slide_flag')
axis = []
sib_lst = line.getElementsByTagName('SimpleBookmark')
if sib_lst == []:
continue
label = sib_lst[0].getAttribute('Caption')
detail_label = sib_lst[0].getAttribute('Desc')
if label.find("Annotation") == 0 and detail_label != "":
#print("alter annotation label.")
for node in sib_lst:
node.setAttribute("Caption", detail_label)
label = detail_label
print("===============================================================================")
print("alter_caption :", label)
axis.append(flag_lst[0].getAttribute('brLeft'))
axis.append(flag_lst[0].getAttribute('brTop'))
axis.append(flag_lst[0].getAttribute('brRight'))
axis.append(flag_lst[0].getAttribute('brBottom'))
axis = [int(i) for i in axis]
ww = axis[2] - axis[0]
hh = axis[3] - axis[1]
print("\nfile:", mrxs_fille_name, "axis:", axis, "ID:", ID, "label:", label)
axis_list.append({"axis": axis, "ID": ID, "label": label})
res.append(line)
w, h = osr.level_dimensions[0]
img = osr.read_region((max(axis[0]-100,0), max(axis[1]-100,0)), 0, (min(w,round(ww + 200)), min(h,round(hh + 200))))
#img.show()
img = is_or_not_RGBA(img)
img = numpy.array(img)
opencv_image = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
print(100, 100, round(ww),round(hh))
opencv_image = cv2.rectangle(opencv_image, (100, 100),(100 + round(ww), 100+round(hh)), (0, 0, 0), 10)
#imgdraw.rectangle((round(axis[0]),round(axis[1]),round(ww),round(hh)),None,outline=(0,0,0))
ratio = 512 / (ww+200)
opencv_image = cv2.resize(opencv_image, (512, int((hh+200) * ratio)))
cv2.imshow("show", opencv_image)
cv2.waitKey(1000)
while(1):
is_label = input("Is it a label?\n"
"(Enter means yes, or input 'n' or 'N' means that the box is not label):")
#cv2.destroyAllWindows()
if is_label == "" or is_label.lower() == "y" or is_label.lower() == "yes":
print("\nfile:",mrxs_fille_name,"axis:", axis, "ID:", ID, "label:", label)
axis_list.append({"axis": axis, "ID": ID, "label": label})
res.append(line)
break
elif is_label.lower() == "n" or is_label.lower() == "no":
break
else:
print("The format of input is wrong. Please input again.")
continue
with open(os.path.join(mrxs_fille_name, i), 'w') as fd:
if res is not None:
res.reverse()
for re in res:
try:
# print("ok:", line[0])
line = re.toxml() + '\n'
if line.find('<?xml version="1.0" ?>') == 0:
line = line.replace('<?xml version="1.0" ?>', '')
#print(line)
fd.write(line)
except:
#print("Can't analysis the {}th line")
#print(re)
fd.write(re)
continue
break
if find_file_flag == 0:
print("No .dat label file in mrxs {} which searched by magic tool.".format(mrxs_fille_name))
osr.close()
def save_label_alter_caption_main(file_dir):
mrxs_lst = []
if not os.path.isdir(file_dir):
mrxs_lst[0] = file_dir
else:
for i in os.listdir(file_dir):
if os.path.splitext(i)[-1] == '.mrxs':
print(os.path.join(file_dir, os.path.splitext(i)[0]))
mrxs_lst.append(os.path.join(file_dir, os.path.splitext(i)[0]))
for mrxs_fille_name in mrxs_lst:
# mrxs_fille_name = "/home/gytang/medicine/fake/DCB-003"
osr = OpenSlide(mrxs_fille_name + '.mrxs')
axis_list = []
find_file_flag = 0
file_list = os.listdir(mrxs_fille_name)
file_list.sort()
for i in file_list[::-1]:
a = magic.from_file(os.path.join(mrxs_fille_name, i))
print("{}: magic tool read file property: {}".format(i, a))
if a.find("ASCII text") != -1 or a.find("UTF-8 Unicode") != -1:
with open(os.path.join(mrxs_fille_name, i)) as f:
lines = f.readlines()
lines.reverse()
if lines[-1].find("<attributes>") == -1:
continue
if find_file_flag == 1:
print(
"There are already exsited a .dat label config file. The mrxs is not as normal as we occured.")
find_file_flag = 1
ID_name = []
res = []
for idx, line in enumerate(lines):
try:
line = parseString(line)
# print("ok:", line[0])
except:
# print("Can't analysis the {}th line".format(idx))
# print(line)
res.append(line)
continue
descript_lst = line.getElementsByTagName('descriptor')
for elements in descript_lst:
ID = elements.getAttribute('ID')[1:-1]
if ID not in ID_name:
ID_name.append(ID)
flag_lst = line.getElementsByTagName('slide_flag')
axis = []
sib_lst = line.getElementsByTagName('SimpleBookmark')
if sib_lst == []:
continue
label = sib_lst[0].getAttribute('Caption')
detail_label = sib_lst[0].getAttribute('Desc')
if label.find("Annotation") == 0 and detail_label != "":
# print("alter annotation label.")
for node in sib_lst:
node.setAttribute("Caption", detail_label)
label = detail_label
print("===============================================================================")
print("alter_caption :", label)
axis.append(flag_lst[0].getAttribute('brLeft'))
axis.append(flag_lst[0].getAttribute('brTop'))
axis.append(flag_lst[0].getAttribute('brRight'))
axis.append(flag_lst[0].getAttribute('brBottom'))
axis = [int(i) for i in axis]
ww = axis[2] - axis[0]
hh = axis[3] - axis[1]
print("ww:", ww, ",hh:", hh)
print("\nfile:", mrxs_fille_name, "axis:", axis, "ID:", ID, "label:", label)
axis_list.append({"axis": axis, "ID": ID, "label": label})
res.append(line)
level_t = 0
w, h = osr.level_dimensions[level_t]
print("w:",w,",h:", h)
x = max(axis[0] - 100, 0)
y = max(axis[1] - 100, 0)
crop_x = min(int(w-x), int(ww + 200))
crop_y = min(int(h-y), int(hh + 200))
print(x, y, crop_x, crop_y)
#add
if crop_x > 10000 or crop_y > 10000:
level_t = int(crop_x/10000)
crop_x = int(crop_x/(2**level_t))
crop_y = int(crop_y/(2**level_t))
x = int(x/(2**level_t))
y = int(y/(2**level_t))
print("resize:", x, y, crop_x, crop_y)
img = osr.read_region((x, y), level_t,
(crop_x, crop_y))
# img.show()
img = is_or_not_RGBA(img)
img = numpy.array(img)
opencv_image = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
opencv_image = cv2.rectangle(opencv_image, (int(100/(level_t+1)), int(100/(level_t+1))),
(int((100 + round(ww))/(level_t+1)), int((100 + round(hh))/(level_t+1))), (0, 0, 0), 10)
# imgdraw.rectangle((round(axis[0]),round(axis[1]),round(ww),round(hh)),None,outline=(0,0,0))
ratio = 512 / ((ww + 200)/(level_t+1))
opencv_image = cv2.resize(opencv_image, (512, int((hh + 200)/(level_t+1) * ratio)))
save_label_path = os.path.join(os.path.dirname(mrxs_fille_name), "label", os.path.basename(mrxs_fille_name))
if not os.path.isdir(save_label_path):
os.makedirs(save_label_path)
# mrxs_fille_name = "/home/gytang/medicine/fake/DCB-003"
cv2.imwrite(os.path.join(save_label_path,label + '_' + ID + '.jpg'), opencv_image)
# cv2.imshow("show", opencv_image)
# cv2.waitKey(1000)
# while (1):
# is_label = input("Is it a label?\n"
# "(Enter means yes, or input 'n' or 'N' means that the box is not label):")
# # cv2.destroyAllWindows()
# if is_label == "" or is_label.lower() == "y" or is_label.lower() == "yes":
# print("\nfile:", mrxs_fille_name, "axis:", axis, "ID:", ID, "label:", label)
# axis_list.append({"axis": axis, "ID": ID, "label": label})
# res.append(line)
# break
# elif is_label.lower() == "n" or is_label.lower() == "no":
# break
# else:
# print("The format of input is wrong. Please input again.")
# continue
#
# with open(os.path.join(mrxs_fille_name, i), 'w') as fd:
# if res is not None:
# res.reverse()
# for re in res:
# try:
# # print("ok:", line[0])
# line = re.toxml() + '\n'
# if line.find('<?xml version="1.0" ?>') == 0:
# line = line.replace('<?xml version="1.0" ?>', '')
# # print(line)
# fd.write(line)
# except:
# # print("Can't analysis the {}th line")
# # print(re)
# fd.write(re)
# continue
break
if find_file_flag == 0:
print("No .dat label file in mrxs {} which searched by magic tool.".format(mrxs_fille_name))
osr.close()
#return axis_list
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('file_dir', type=str, help="The location of the mrxs file directory, as: /home/gytang/medicine/annotion/anotation-test-image/SHE .")
args = parser.parse_args()
#draw_rangcle_jpg(args.file_dir)
#delete_label_annotion(args.file_dir)
save_label_alter_caption_main(args.file_dir)
#alter_caption_main("/home/gytang/Downloads/res/other/")