Source code for WSI.annotation
"""
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Created on Fri Feb 4 11:42:52 2023
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**Title:** ValidPath Toolbox - Annotation Extraction Module
**Description:** This is the Annotation Extraction module for the ValidPath toolbox. It is includes AnnotationExtractor class and several methods.
**Classes:** AnnotationExtractor
**Methods:** AnnotationExtractor.extract_ann (Save_dir: str,XMLs: array , WSIs: array)
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Author: SeyedM.MousaviKahaki (seyed.kahaki@fda.hhs.gov)
Version ='1.0'
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"""
import cv2
import numpy as np
import os
#import openslide
import lxml.etree as ET
import matplotlib.pyplot as plt
from glob import glob
from skimage.io import imsave, imread
from PIL import Image
import math
highsize = False
[docs]
class AnnotationExtractor :
def __init__(self):
pass
[docs]
def make_folder(self,directory):
"""
This method creates a directory if not exist.
:Parameters:
directory : string
Directory to be created.
:Returns:
None : None
None.
"""
if not os.path.exists(directory):
os.makedirs(directory)
[docs]
def extract_ann(self,save_dir,XMLs,WSIs,vis=False,save_mask=False):
"""
This method extracts different types for annotations from Whole Slide Images.
It can save the extracted annottions to the output directory as defined in inputs.
This code also handles several annotations per slide.
The output directory will be generated based on the strucutr of the input directories.
:Parameters:
save_dir : string
The path to the directory in order to save the annotations
WSIs : list
List of whole slide image files
XMLs : list
List of annotation files in XML format
:Returns:
Image (array) – annotation files
"""
plt.rcParams.update({'font.size': 6})
# go over all WSI
for idx, XML in enumerate(XMLs):
annotationID=0
tree = ET.parse(XML)
root = tree.getroot()
annot = root.findall("./Annotation")
for annotation in annot:
final_x=[]
final_y=[]
annotationID=annotation.attrib.get('Id') #annotationID+1
Regions = root.findall("./Annotation[@Id='" + str(annotationID) + "']/Regions/Region")
print("there are ",len(Regions) , "Regions in this annotation")
bounds = []
masks = []
lbl = annotation.attrib['Name']
region_number=0
print('opening: a region of ' + WSIs[idx])
pas_img = openslide.OpenSlide(WSIs[idx])
sw= True
for num , Region in enumerate(Regions):
if vis==True and save_mask ==False and sw==True :
#fig,axes = plt.subplots(nrows = 1, ncols = len(Regions))
#fig.tight_layout(pad=5.0)
sw = False
if vis==True and save_mask ==True and sw==True :
#fig,axes = plt.subplots(nrows = len(Regions), ncols = 2)
#fig.tight_layout(pad=5.0)
sw = False
print("\n Region numer ",num)
Vertices = Region.findall("./Vertices/Vertex")
x = []
y = []
for Vertex in Vertices:
x.append(int(np.float32(Vertex.attrib['X'])))
y.append(int(np.float32(Vertex.attrib['Y'])))
x1=x
y1=y
if highsize== True:
x = [ math.floor(number/4) for number in x]
y = [math.floor(number/4) for number in y]
final_x.append(max(x) - min(x))
final_y.append(max(y) - min(y))
bounds.append([min(x1), min(y1)])
points = np.stack([np.asarray(x), np.asarray(y)], axis=1)
points[:,1] = np.int32(np.round(points[:,1] - min(y) ))
points[:,0] = np.int32(np.round(points[:,0] - min(x) ))
mask = np.zeros([final_y[region_number], final_x[region_number]], dtype=np.int8)
if(len(x)>3): #polygon
print("....poly")
cv2.fillPoly(mask, [points], color=(255,255,255))
if(len(x)==2): # cirlce or ellipse
x_c_int = int(points[1,0]/2)
y_c_int =int(points[1,1]/2)
center_coordinates=(x_c_int,y_c_int)
if(points[:,0][1]==points[:,1][1]): #cirlce
print("....circle ")
cv2.circle(img=mask, center =center_coordinates, radius=x_c_int , color =(255,255,255), thickness=-1)
else: # ellipse
print("....ellipse ")
axesLength = (x_c_int, y_c_int)
angle =0
startAngle = 0
endAngle = 360
image = cv2.ellipse(mask, center_coordinates, axesLength, angle, startAngle, endAngle, (255,255,255), thickness=-1)
basename = os.path.basename(XML)
basename = os.path.splitext(basename)[0]
subdirm = '{}/{}/'.format(save_dir,basename)
if save_mask == True :
cv2.imwrite(subdirm+basename+"_anno_"+str(annotationID)+"_reg_"+str(region_number+1)+"_mask_"+lbl+".jpg",mask)
print('saved <mask>')
print(subdirm+basename+"_anno_"+str(annotationID)+"_reg_"+str(region_number+1)+"_mask_"+lbl+".jpg")
if vis==True :
#fig = plt.figure(figsize=(2, 2))
plt.imshow(mask)
plt.show()
#axes[num,1].imshow(mask)
#axes[num,1].set_title('Mask number : {}'.format(num))
masks.append(mask)
mask = masks[region_number]
if highsize== True:
PAS = pas_img.read_region((int(bounds[region_number][0]),
int(bounds[region_number][1])),
1,(final_x[region_number],final_y[region_number]))
# plt.imshow(PAS)
else:
PAS = pas_img.read_region((int(bounds[region_number][0]),
int(bounds[region_number][1])),
0, (final_x[region_number],final_y[region_number]))
# plt.imshow(PAS)
coord = (int(bounds[region_number][0]),int(bounds[region_number][1]))
# PAS = pas_img.read_region((int(bounds[region_number][0]),int(bounds[region_number][1])), 0, (final_x[region_number],final_y[region_number]))
PAS = np.array(PAS)[:,:,0:3]
for channel in range(3):
PAS_ = PAS[:,:,channel]
PAS_[masks[region_number] == 0] = 255
PAS[:,:,channel] = PAS_
subdir = '{}/{}/'.format(save_dir,basename)
self.make_folder(subdir)
#imsave(subdir + basename + '_anno_' + str(annotationID) +"_reg_"+str(region_number+1)+lblmber+1)+lbl+ "_coord_" + str(coord[0]) + "_" + str(coord[1]) + '.jpg', PAS)
imsave(subdir + basename + '_anno_' + str(annotationID) +"_reg_"+str(region_number+1)+lbl+ "_coord_" + str(coord[0]) + "_" + str(coord[1]) + '.jpg', PAS)
print('saved <region> of annotationID : ' + str(annotationID))
region_number = region_number + 1
if vis==True and save_mask==True :
plt.imshow(PAS)
plt.show()
#axes[num,0].imshow(PAS)
#axes[num,0].set_title('Region number : {}'.format(num))
if vis==True and save_mask ==False:
plt.imshow(PAS)
plt.show()
#axes[num].imshow(PAS)
#axes[num].set_title('Region number : {}'.format(num))
#plt.show()