fix region padding based on gergelys feedback

.vscode/settings.json

 {
-    "python.formatting.provider": "black"
+    "python.formatting.provider": "black",
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        "./tests",
+        "-p",
+        "test*.py"
+    ],
+    "python.testing.pytestEnabled": false,
+    "python.testing.unittestEnabled": true
 }
\ No newline at end of file

PyNutil/processing/counting_and_load.py

@@ -209,7 +209,10 @@ def warp_image(image, triangulation, rescaleXY):
     newY[newY >= reg_h] = reg_h - 1
     newX[newX < 0] = 0
     newY[newY < 0] = 0
-    new_image = image[newY, newX]
+    new_image = np.zeros_like(image)
+    mask = (newX <= reg_w) & (newY <= reg_h) & (newX > 0) & (newY > 0)
+    new_image[mask] = image[mask]
+    new_image[~mask] = 0
     return new_image