Upload Colony_Analyzer_AI_zstack2_HF.py

Colony_Analyzer_AI_zstack2_HF.py

@@ -301,6 +301,8 @@ def main(args):
     #nearby is a boolean list of whether a colony has overlapping colonies. If so, labelling positions change
     nearby = [False]*len(colonies)
     areas = list(colonies["colony_area"])
+    if img.ndim == 2:
+        img = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
     for i in range(len(colonies)): 
         cv2.drawContours(img, [list(colonies["contour"])[i]], -1, (0, 255, 0), 2)
         cv2.drawContours(img, list(colonies['nec_contours'])[i], -1, (0, 0, 255), 2)
@@ -357,7 +359,6 @@ def main(args):
 
     print('img ndim: ' +str(img.ndim))
     print('caption ndim: ' +str(caption.ndim))
-    if img.ndim == 2:
-        img = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
+
     cv2.imwrite('Group_analysis_results.png', np.vstack((img, caption)))
     return(np.vstack((img, caption)), 'Group_analysis_results.png', 'Group_analysis_results.xlsx')