def data_extract(self):
list_img = os.listdir(self.input_slide_dir)
list_obj_mask = os.listdir(self.obj_dir)
list_obj_Tissue = os.listdir(self.tissue_mask_dir)
list_img = sorted(list_img, key=natural_key)
list_obj_mask = sorted(list_obj_mask, key=natural_key)
list_obj_Tissue = sorted(list_obj_Tissue, key=natural_key)
voronoi_dir = 'voronoi'
if os.path.exists(os.path.join(self.output_dir, voronoi_dir)) is False:
os.makedirs(os.path.join(self.output_dir, voronoi_dir))
for p1 in range(len(list_img)):
file_name = list_img[p1]
img = cv2.imread(os.path.join(self.input_slide_dir, list_img[p1]))
img_orig = img.copy()
file1 = os.path.join(self.obj_dir, list_obj_mask[p1])
file2 = os.path.join(self.tissue_mask_dir, list_obj_Tissue[p1])
x1 = []
y1 = []
points11 = []
x1, y1 = centroids1(file1)
for i in range(0, len(x1)):
points11.append([x1[i], y1[i]])
points = np.array(points11)
vor = Voronoi(points)
regions, vertices = voronoi_finite_polygons_2d(vor)
cnts_img_t = Contours(file2)
point_t = []
for c1 in cnts_img_t:
point_t.append([c1[0][0], c1[0][1]])
point_t = np.array(point_t)
pts = MultiPoint([Point(i) for i in point_t])
mask = pts.convex_hull
print("mask=", mask.bounds)
new_vertices = []
a = 0
for region in regions:
print("a=", a)
a = a + 1
polygon = vertices[region]
shape = list(polygon.shape)
shape[0] += 1
p = Polygon(np.append(
polygon, polygon[0]).reshape(*shape)).intersection(mask)
print("p=", p.bounds)
print("lk=", int(p.length))
l1 = int(p.length)
if (l1 > 0):
poly = np.array(
list(
zip(p.boundary.coords.xy[0][:-1],
p.boundary.coords.xy[1][:-1])))
new_vertices.append(poly)
new_vertices.append(poly)
for p1 in new_vertices:
pts = np.array(p1, np.int32)
pts = pts.reshape((-1, 1, 2))
cv2.polylines(img, [pts], True, (0, 0, 0), 3)
for p1 in points11:
cv2.circle(img, (p1[0], p1[1]), 13, (0, 255, 0), cv2.FILLED,
cv2.LINE_AA, 0)
#
cv2.imwrite(os.path.join(self.output_dir, voronoi_dir, file_name),
img)
new_vert = []
for i in range(len(new_vertices)):
new_vert.append(new_vertices[i].tolist())
write_voronoi_detail(self.output_dir, file_name, new_vert)
