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slide.py
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from functools import partial
import os
import glob
import openslide as osli
import cv2 as cv
import numpy as np
from imageprocess import ImageProcess
from key_defs import *
class Slide:
def __init__(self, conf):
self.conf = conf
self.detector = ImageProcess(self.conf)
self.slide = self.load_image()
self.initialize_windows()
self.overview_factor, self.original_overview = self.generate_overview()
self.overview = self.original_overview.copy()
self.create_mask_window()
self.pixels_per_square_mm = ((float(self.slide.properties[osli.PROPERTY_NAME_MPP_X]) * 1000) ** 2)
self.current_iter = 0
self.current_printed = False
self.drawing = False
self.draw_points = []
self.overview_draw_points = []
self.update_overview = True
self.current_immune_cells = 0
self.draw_counter = 0
def initialize_windows(self):
self.overview_window = "Overview"
self.mask_window = "Mask"
self.original_window = "Original"
self.immunocells_window = "Detected immunocells"
self.hed_window = "Hematoxylin-Eosin-DAB"
self.conf.hed_window = "Hematoxylin-Eosin-DAB"
window_size = self.conf.options.window_size
cv.namedWindow(self.overview_window, cv.WINDOW_NORMAL)
cv.resizeWindow(self.overview_window, window_size, window_size)
cv.namedWindow(self.immunocells_window, cv.WINDOW_NORMAL)
cv.resizeWindow(self.immunocells_window, window_size, window_size)
cv.setMouseCallback(self.overview_window, self.mouse_draw_overview)
if self.conf.options.advanced:
cv.namedWindow(self.mask_window, cv.WINDOW_NORMAL)
cv.namedWindow(self.original_window, cv.WINDOW_NORMAL)
cv.namedWindow(self.hed_window, cv.WINDOW_NORMAL)
cv.resizeWindow(self.hed_window, window_size, window_size)
cv.resizeWindow(self.mask_window, window_size, window_size)
cv.resizeWindow(self.original_window, window_size, window_size)
def mouse_draw_overview(self, event, x, y, flags, param):
if event == cv.EVENT_MOUSEMOVE and self.drawing:
self.draw_counter += 1
if self.draw_counter > 5:
self.update_overview = True
self.draw_counter = 0
real_x = int((x * self.overview_factor) + int(self.slide.properties[osli.PROPERTY_NAME_BOUNDS_X]))
real_y = int((y * self.overview_factor) + int(self.slide.properties[osli.PROPERTY_NAME_BOUNDS_Y]))
self.draw_points.append([real_x, real_y])
self.overview_draw_points.append([x,y])
def generate_overview(self):
minx = int(self.slide.properties[osli.PROPERTY_NAME_BOUNDS_X])
miny = int(self.slide.properties[osli.PROPERTY_NAME_BOUNDS_Y])
level = self.conf.options.overview_downsample
factor = self.slide.level_downsamples[level]
width = int(float(self.slide.properties[osli.PROPERTY_NAME_BOUNDS_WIDTH]) / factor)
height = int(float(self.slide.properties[osli.PROPERTY_NAME_BOUNDS_HEIGHT]) / factor)
region = self.slide.read_region((minx, miny), level, (width,height)).convert('RGB')
overview = cv.cvtColor(np.array(region), cv.COLOR_RGB2BGR)
return factor, overview
def get_region_selection(self, selection, level = 0):
x,y,w,h = cv.boundingRect(selection)
return self.slide.read_region((x,y), level, (w, h)).convert('RGB')
def get_sections_selection(self, selection, level = 0):
x,y,w,h = cv.boundingRect(selection)
real_x = x - (x % 1000)
real_y = y - (y % 1000)
real_width = x + w + 1000 - ((x + w) % 1000)
real_height = y + h + 1000 - ((y + h) % 1000)
current_x = real_x
current_y = real_y
images = {}
while current_y < real_height:
while current_x < real_width:
if current_x not in images:
images[current_x] = {}
images[current_x][current_y] = self.slide.read_region((current_x, current_y), level, (1000,1000)).convert('RGB')
current_x += 1000
current_y += 1000
return images
def draw_overview_overlay(self):
if not self.update_overview:
return self.overview
self.update_overview = False
if len(self.overview_draw_points) > 4:
contours = np.array(self.overview_draw_points).reshape((-1,1,2)).astype(np.int32)
if self.drawing:
cv.polylines(self.overview, [contours], False, (255,255,0),2)
else:
cv.drawContours(self.overview, [contours],0,(255,255,255),2)
return self.overview
def export_images(self, contour):
if self.conf.options.create_segments:
if not os.path.exists('selections'):
os.mkdir('selections')
dir_list = glob.glob('selections/*')
target_dir = 100
for i in range(1,100):
if "selections/{}".format(str(i)) not in dir_list and target_dir == 100:
target_dir = str(i)
os.mkdir("selections/{}".format(target_dir))
images = self.get_sections_selection(contour)
for x_value in images:
for y_value in images[x_value]:
# save image as 'selections/<selection_num>/<x>_<y>.png'
images[x_value][y_value].save("selections/{}/{}_{}.png".format(target_dir, x_value, y_value))
def __call__(self):
while True:
contour = np.array(self.draw_points).reshape((-1,1,2)).astype(np.int32)
x,y,w,h = cv.boundingRect(contour)
area = cv.contourArea(contour)
if not self.current_printed and len(self.draw_points) > 4 and not self.drawing:
self.export_images(contour)
img = self.get_region_selection(contour)
img = np.array(img)
immune_cells, mask, _ = self.detector.get_immune_cells(img)
inside_cells = []
for cell in immune_cells:
moment = cv.moments(cell)
center_x = int(moment['m10']/moment['m00']) + x
center_y = int(moment['m01']/moment['m00']) + y
if cv.pointPolygonTest(contour, (center_x, center_y), False) >= 0:
inside_cells.append(cell)
immune_cells = inside_cells
if not self.current_printed:
self.current_immune_cells = len(immune_cells)
print("Immune cells in selection: {}".format(len(immune_cells)))
self.current_printed = True
img = cv.cvtColor(img, cv.COLOR_RGB2BGR)
cvimg2 = img.copy()
cvimg2 = cv.drawContours(cvimg2, immune_cells, -1, (0,255,0))
updated_list = [[p[0] - x, p[1] - y] for p in self.draw_points]
updated_contour = np.array(updated_list).reshape((-1,1,2)).astype(np.int32)
cv.drawContours(cvimg2, [updated_contour], 0, (255,255,255), 4)
if self.conf.options.advanced:
cv.imshow(self.mask_window, mask)
cv.imshow(self.original_window, img)
cv.imshow(self.immunocells_window, cvimg2)
over = self.draw_overview_overlay()
cv.imshow(self.overview_window, over)
if area > 0:
cv.displayStatusBar(self.overview_window, "Immune cells in selection: {}, immune cells per square millimeter: {}".format(self.current_immune_cells, self.current_immune_cells / (area / self.pixels_per_square_mm)))
key = cv.waitKeyEx(100)
if key == KEY_ESC:
return
elif key == KEY_SPACE:
if self.drawing:
self.current_printed = False
self.update_overview = True
print("Stopped drawing")
self.drawing = False
self.overview = self.original_overview.copy()
else:
print("Started drawing")
self.drawing = True
self.draw_points = []
self.overview_draw_points = []
self.selected_regions = []
elif key != -1:
print("Button pressed {}".format(key))
def load_image(self):
return osli.OpenSlide(self.conf.options.input)
def create_mask_window(self):
update = partial(self.conf.update_configuration, self)
cv.createTrackbar('Min hematoxylin', 'Mask', self.conf.options.hue_min, 255, partial(update, "hue_min"))
cv.createTrackbar('Max hematoxylin', 'Mask', self.conf.options.hue_max, 255, partial(update, "hue_max"))
cv.createTrackbar('Min eosin', 'Mask', self.conf.options.sat_min, 255, partial(update, "sat_min"))
cv.createTrackbar('Max eosin', 'Mask', self.conf.options.sat_max, 255, partial(update, "sat_max"))
cv.createTrackbar('Min DAB', 'Mask', self.conf.options.val_min, 255, partial(update, "val_min"))
cv.createTrackbar('Max DAB', 'Mask', self.conf.options.val_max, 255, partial(update, "val_max"))
cv.createTrackbar('Min area', 'Mask', self.conf.options.area_min, 5000, partial(update, "area_min"))
cv.createTrackbar('Max area', 'Mask', self.conf.options.area_max, 5000, partial(update, "area_max"))
cv.createTrackbar('Min circularity', 'Mask', self.conf.options.circularity, 100, partial(update, "circularity"))