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Colony_Analyzer_AI2_HF.py

@@ -220,7 +220,14 @@ def main(args):
     del z
     p = stitch(img_map)
     colonies = analyze_colonies(p, min_size, min_circ, np.array(args[0]))
-    
+    if len(colonies) <=0:
+    	caption = np.ones((150, 2048, 3), dtype=np.uint8) * 255  # Multiply by 255 to make it white
+    	cv2.putText(caption, 'No colonies detected.', (40, 40), cv2.FONT_HERSHEY_SIMPLEX, 1, (0, 0, 0), 3)
+    	cv2.imwrite('results.png', np.vstack((np.array(args[0]), caption)))
+    	colonies = pd.DataFrame({"Colony Number":[], 'Colony volume':[], "colony_area":[],'mean_pixel_value':[], "centroid":[], "necrotic_area":[],"percent_necrotic":[]})
+    	with pd.ExcelWriter('results.xlsx') as writer:
+        	colonies.to_excel(writer, sheet_name="Colony data", index=False)
+    	return(np.vstack((args[0], caption)), 'results.png', 'results.xlsx')
     img = np.array(args[0])
     img = cv2.copyMakeBorder(img,top=0, bottom=10,left=0,right=10, borderType=cv2.BORDER_CONSTANT,  value=[255, 255, 255]) 
     #print(colonies.to_string())

Colony_Analyzer_AI_zstack2_HF.py

@@ -263,6 +263,14 @@ def main(args):
             colonies = frame
         else:
            colonies = compare_frames(frame, colonies)
+    if len(colonies) <=0:
+    	caption = np.ones((150, 2048, 3), dtype=np.uint8) * 255  # Multiply by 255 to make it white
+    	cv2.putText(caption, 'No colonies detected.', (40, 40), cv2.FONT_HERSHEY_SIMPLEX, 1, (0, 0, 0), 3)
+    	cv2.imwrite('results.png', np.vstack((np.array(files[0]), caption)))
+    	colonies = pd.DataFrame({"Colony Number":[], 'Colony volume':[], "colony_area":[],'mean_pixel_value':[], "centroid":[], "necrotic_area":[],"percent_necrotic":[]})
+    	with pd.ExcelWriter('results.xlsx') as writer:
+            colonies.to_excel(writer, sheet_name="Colony data", index=False)
+    	return(np.vstack((files[0], caption)), 'results.png', 'results.xlsx')
     counts = {}
     for x in range(len(files)):
         counts[x] = list(colonies["source"]).count(x)