add everything

app.py

@@ -1,15 +1,69 @@
 import gradio as gr
 import openslide
 
+from PIL import Image, ImageDraw
+from xml.etree import ElementTree as ET
 
-def process(text):
-    return text[::-1]
+# 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
+
+
+# output as png or npy 
+def process(x, y, annotation_size, annotation):
+    image_shrinking_factor = annotation_size / min(x, y)
+
+    # get thumbnail
+    image = get_mask_from_xml(annotation, (annotation_size, annotation_size), image_shrinking_factor)
+    image.save("mask.png")
+    return "mask.png"
 
 
 demo = gr.Interface(
     fn=process,
-    inputs="text",
-    outputs="text",
+    inputs=[
+        # gr.File(label="Slide thumbnail", type="file", accept=".png"),
+        gr.Number(label="X", default=10_000),
+        gr.Number(label="Y", default=10_000),
+        gr.Number(label="Thumbnail size", default=500),
+        gr.File(label="ASAP Annotation", type="file", accept=".xml"),
+    ],
+    outputs="image",
     title="Reverse Text",
     description="Reverses the text entered by the user",