change segments in get perfusion and script can now update existing csv file

mu_map/polar_map/get_perfusion.py

@@ -16,23 +16,23 @@ class PolarMapSegment:
 
 # see https://www.ahajournals.org/doi/full/10.1161/hc0402.102975
 SEGMENTS = [
-    PolarMapSegment( id=1,  location="basal",      name="anterior", rect=( 29, 302,  53, 328)),
-    PolarMapSegment( id=2,  location="basal",  name="anteroseptal", rect=(166,  61, 190,  91)),
-    PolarMapSegment( id=3,  location="basal",  name="inferoseptal", rect=(438,  63, 463,  91)),
-    PolarMapSegment( id=4,  location="basal",      name="inferior", rect=(577, 299, 600, 329)),
-    PolarMapSegment( id=5,  location="basal", name="inferolateral", rect=(439, 539, 463, 565)),
-    PolarMapSegment( id=6,  location="basal", name="anterolateral", rect=(166, 539, 191, 567)),
-    PolarMapSegment( id=7,    location="mid",      name="anterior", rect=(107, 301, 131, 329)),
-    PolarMapSegment( id=8,    location="mid",  name="anteroseptal", rect=(205, 131, 230, 159)),
-    PolarMapSegment( id=9,    location="mid",  name="inferoseptal", rect=(399, 132, 425, 159)),
-    PolarMapSegment(id=10,    location="mid",      name="inferior", rect=(498, 301, 522, 328)),
-    PolarMapSegment(id=11,    location="mid", name="inferolateral", rect=(400, 471, 425, 498)),
-    PolarMapSegment(id=12,    location="mid", name="anterolateral", rect=(206, 471, 228, 497)),
-    PolarMapSegment(id=13, location="apical",      name="anterior", rect=(185, 302, 209, 328)),
-    PolarMapSegment(id=14, location="apical",        name="septal", rect=(304, 184, 328, 210)),
-    PolarMapSegment(id=15, location="apical",      name="inferior", rect=(421, 301, 445, 327)),
-    PolarMapSegment(id=16, location="apical",       name="lateral", rect=(303, 418, 328, 445)),
-    PolarMapSegment(id=17,   location="apex",          name="apex", rect=(304, 302, 329, 329)),
+    PolarMapSegment( id=1,  location="basal",      name="anterior", rect=( 27, 281,  27+22, 281+29)),
+    PolarMapSegment( id=2,  location="basal",  name="anteroseptal", rect=(156, 59, 156+22, 59+30)),
+    PolarMapSegment( id=3,  location="basal",  name="inferoseptal", rect=(411, 58, 411+22, 58+29)),
+    PolarMapSegment( id=4,  location="basal",      name="inferior", rect=(540, 280, 540+22,280+29)),
+    PolarMapSegment( id=5,  location="basal", name="inferolateral", rect=(411, 503, 411+22, 503+29)),
+    PolarMapSegment( id=6,  location="basal", name="anterolateral", rect=(156, 503, 156+22, 503+29)),
+    PolarMapSegment( id=7,    location="mid",      name="anterior", rect=(100, 281, 100+22, 281+29)),
+    PolarMapSegment( id=8,    location="mid",  name="anteroseptal", rect=(192, 122, 192+22, 122+29)),
+    PolarMapSegment( id=9,    location="mid",  name="inferoseptal", rect=(375, 122, 372+22, 122+29)),
+    PolarMapSegment(id=10,    location="mid",      name="inferior", rect=(467, 280, 467+22, 280+29)),
+    PolarMapSegment(id=11,    location="mid", name="inferolateral", rect=(375, 439, 375+22, 439+29)),
+    PolarMapSegment(id=12,    location="mid", name="anterolateral", rect=(192, 439, 192+22, 439+29)),
+    PolarMapSegment(id=13, location="apical",      name="anterior", rect=(174, 281, 174+22, 281+29)),
+    PolarMapSegment(id=14, location="apical",        name="septal", rect=(284, 171, 284+22, 171+29)),
+    PolarMapSegment(id=15, location="apical",      name="inferior", rect=(394, 280, 394+22, 280+30)),
+    PolarMapSegment(id=16, location="apical",       name="lateral", rect=(284, 391, 284+22, 391+29)),
+    PolarMapSegment(id=17,   location="apex",          name="apex", rect=(284, 281, 284+22, 281+29)),
 ]
 
 
@@ -87,20 +87,31 @@ if __name__ == "__main__":
     data = pd.read_csv(args.csv)
     data = data[data[headers.segments]]
 
-    rows = []
+    if os.path.isfile(args.perfusion_csv):
+        perfusion = pd.read_csv(args.perfusion_csv)
+    else:
+        perfusion = pd.DataFrame()
+
     for i in range(len(data)):
         row = data.iloc[i]
         _id = row[headers.id]
-        _file = os.path.join(args.images_dir, row[headers.file])
+        _file = row[headers.file]
+
+        if _file in perfusion["file"].values:
+            print(f"SKIP file {_file} as perfusion scores are already in {args.perfusion_csv}")
+            continue
+        else:
+            print(f"Process {_file} ...")
 
-        polar_map = cv.imread(_file)
+        polar_map = cv.imread(os.path.join(args.images_dir, _file))
         for segment in SEGMENTS:
             # extract number segment
             top, left, bottom, right = segment.rect
             img_number = polar_map[top:bottom, left:right]
 
             # process segment for improved automatic number detection
-            img_number = cv.resize(img_number, (args.number_res, args.number_res))
+            scale = args.number_res / img_number.shape[1]
+            img_number = cv.resize(img_number, None, fx=scale, fy=scale)
             img_number = cv.cvtColor(img_number, cv.COLOR_BGR2HSV)
             img_number = cv.inRange(img_number, hsv_green_lower, hsv_green_upper)
             img_number = cv.morphologyEx(img_number, cv.MORPH_CLOSE, np.ones((4, 4), np.uint8))
@@ -116,7 +127,8 @@ if __name__ == "__main__":
             _polar_map = cv.rectangle(_polar_map, (left, top), (right, bottom), (255, 255, 255), 1)
             _polar_map = cv.resize(_polar_map, (512, 512))
             img_number = img_number.repeat(3).reshape((*img_number.shape, 3))
-            img_number = cv.resize(img_number, (512, 512))
+            scale = 512 / img_number.shape[0]
+            img_number = cv.resize(img_number, None, fx=scale, fy=scale)
             space_h = np.full((512, 10, 3), 239, np.uint8)
 
             cv.imshow("Polar Map - Segment", np.hstack((_polar_map, space_h, img_number)))
@@ -138,7 +150,8 @@ if __name__ == "__main__":
 
             _value = pd.Series({f"segment_{segment.id}": number})
             row = pd.concat([row, _value])
-        rows.append(row)
-        pd.DataFrame(rows).to_csv(args.perfusion_csv)
+        perfusion = perfusion.append(row, ignore_index=True)
+        perfusion = perfusion.sort_values(by=["id", "file"])
+        perfusion.to_csv(args.perfusion_csv, index=False)