Update Organoid_Analyzer_AI_zstack2_HF.py

Organoid_Analyzer_AI_zstack2_HF.py

@@ -354,13 +354,13 @@ def main(args):
         contours = list(contours["contour"])
         cv2.drawContours(mask, contours, -1, 255, thickness=cv2.FILLED)
         # Extract all ROIs from the source image at once
-        src_image = np.array(files[x])
+        src_image = pad(np.array(files[x]))
         roi = cv2.bitwise_and(src_image, src_image, mask=mask)
         # Paste the extracted regions onto the destination image
-        print("ROI Shape:", roi.shape)
-        print("img Shape:", img.shape)
-        print("mask Shape:", mask.shape)
-        print("mask Shape fixed:", mask.shape)    
+        #print("ROI Shape:", roi.shape)
+        #print("img Shape:", img.shape)
+        #print("mask Shape:", mask.shape)
+        #print("mask Shape fixed:", mask.shape)    
         np.copyto(img, roi, where=(mask== 255))
     try:
         del x, mask, src_image, roi, best, contours