Update app.py

app.py

@@ -3,46 +3,7 @@ import openslide
 
 from PIL import Image, ImageDraw
 from xml.etree import ElementTree as ET
-
-# accept slide thumbnail, x, y and annotation 
-def get_mask_from_xml(xml_path, image_size, image_shrinking_factor):
-    tree = ET.parse(xml_path)
-    root = tree.getroot()
-    image = Image.new("L", image_size, "white")
-    draw = ImageDraw.Draw(image)
-    draw.fill = True
-    label2grayscale_color = {"bg": 0, "tissue": 1, "tisuue": 1}
-    for i in root[0]:
-        annotation_type = i.attrib["Type"]
-        annotation_label = i.attrib["PartOfGroup"]
-        # there is roi rectangle
-        if annotation_type not in ["Spline", "Polygon", "Rectangle"]:
-            print(f"Annotation type must be either Spline, Rectangle or Polygon but found: {annotation_type}")
-            continue
-            
-        if annotation_label not in label2grayscale_color:
-            print(f"Annotation label must be either tissue or bg but found: {annotation_label}")
-            continue
-        
-        coordinates = [(i.attrib["X"], i.attrib["Y"]) for i in i[0]]
-        coordinates = [(str2float(x), str2float(y)) for x, y in coordinates]
-        coordinates = [(x*image_shrinking_factor, y*image_shrinking_factor) for x, y in coordinates]
-        
-        if annotation_type in ["Spline", "Polygon"]:
-            draw.polygon(coordinates, fill=label2grayscale_color[annotation_label])
-        elif annotation_type == "Rectangle":
-            # ^
-            # |         point 1 is bigger than point 3
-            # | 0 1
-            # | 3 2 
-            # |------->
-            draw.rectangle([coordinates[3], coordinates[1]], fill=label2grayscale_color[annotation_label])
-#         if annotation_type == "Spline":
-#             draw.line(coordinates, fill=label2grayscale_color[annotation_label], width=1)
-#         elif annotation_type == "Polygon":
-#             draw.polygon(coordinates, fill=label2grayscale_color[annotation_label])
-    return image
-
+from project_utils.preprocessing import get_mask_from_xml
 
 # output as png or npy 
 def process(x, y, annotation_size, annotation):