fix issue for empty map

CryoREAD/data_processing/Resize_Map.py

@@ -9,6 +9,10 @@ def my_reform_1a(input_mrc, output_mrc, use_gpu=False):
     with torch.no_grad() and torch.cuda.amp.autocast(enabled=use_gpu):
 
         with mrcfile.open(input_mrc, permissive=True) as orig_map:
+
+            if np.allclose(orig_map.data, 0.0):
+                print("Input map is all zeros, exiting")
+                exit()
 
             orig_voxel_size = np.array([orig_map.voxel_size.x, orig_map.voxel_size.y, orig_map.voxel_size.z])
 

CryoREAD/main.py

@@ -60,9 +60,11 @@ def init_save_path(origin_map_path):
         os.chdir(running_dir)
         from data_processing.Unify_Map import Unify_Map
 
+        print("Unifying map", cur_map_path, "to", os.path.join(save_path, map_name + "_unified.mrc"))
         cur_map_path = Unify_Map(cur_map_path, os.path.join(save_path, map_name + "_unified.mrc"))
         from data_processing.Resize_Map import Resize_Map
 
+        print("Resizing map", cur_map_path, "to", os.path.join(save_path, map_name + ".mrc"))
         cur_map_path = Resize_Map(cur_map_path, os.path.join(save_path, map_name + ".mrc"))
         if params["contour"] < 0:
             # change contour level to 0 and increase all the density

main.py

@@ -71,9 +71,17 @@
                     break
                 if err:
                     logger.error(err.strip())  # Log stderr
-
-        real_space_cc = calc_map_ccc(seg_map_path, prot_prob_path)[0]
-        x, fsc, cutoff_05, cutoff_0143 = calculate_fsc(seg_map_path, prot_prob_path)
+        try:
+            real_space_cc = calc_map_ccc(seg_map_path, prot_prob_path)[0]
+        except:
+            logger.warning("Failed to calculate real space CC, maybe the map is empty")
+            real_space_cc = 0.0
+
+        try:
+            x, fsc, cutoff_05, cutoff_0143 = calculate_fsc(seg_map_path, prot_prob_path)
+        except:
+            logger.warning("Failed to calculate FSC, maybe the map is empty")
+            cutoff_05 = 0.0
         map_list.append([mrc_file, real_space_cc, cutoff_05])
 
     map_list.sort(key=lambda x: x[1], reverse=True)