update syn compute

Author: donglaiw

connectomics/data/dataset/dataset_volume.py

@@ -138,8 +138,8 @@ def __init__(self,
         self.valid_mask = valid_mask
         self.valid_ratio = valid_ratio
         # precompute valid region
-        self.valid_pos = [None] * len(self.valid_mask) 
         if self.valid_mask is not None:
+            self.valid_pos = [None] * len(self.valid_mask) 
             for i, x in enumerate(self.valid_mask):
                 if x is not None:
                     self.valid_pos[i] = get_valid_pos(x, sample_volume_size, valid_ratio)

connectomics/engine/trainer.py

@@ -284,21 +284,20 @@ def test_singly(self):
 
         num_file = len(img_name)
         start_idx = self.cfg.INFERENCE.DO_SINGLY_START_INDEX
+        digits = int(math.log10(num_file))+1
         for i in range(start_idx, num_file):
-            dataset = get_dataset(
-                self.cfg, self.augmentor, self.mode, self.rank,
-                dir_name_init=dir_name, img_name_init=[img_name[i]])
-            self.dataloader = build_dataloader(
-                self.cfg, self.augmentor, self.mode, dataset, self.rank)
-            self.dataloader = iter(self.dataloader)
-
-            digits = int(math.log10(num_file))+1
             self.test_filename = self.cfg.INFERENCE.OUTPUT_NAME + \
                 '_' + str(i).zfill(digits) + '.h5'
             self.test_filename = self.augmentor.update_name(
                 self.test_filename)
-
-            self.test()
+            if not os.path.exists(self.test_filename):
+                dataset = get_dataset(
+                    self.cfg, self.augmentor, self.mode, self.rank,
+                    dir_name_init=dir_name, img_name_init=[img_name[i]])
+                self.dataloader = build_dataloader(
+                    self.cfg, self.augmentor, self.mode, dataset, self.rank)
+                self.dataloader = iter(self.dataloader)
+                self.test()
 
     # -----------------------------------------------------------------------------
     # Misc functions

connectomics/utils/process.py

@@ -269,10 +269,14 @@ def polarity2instance(
         thres = int(255.0 * thres)
         temp = (volume > thres) # boolean array
 
-    syn_pre = np.logical_and(temp[0], temp[2])
+    del volume
+    syn_pre = temp[0]
+    syn_pre &= temp[2]    
     syn_pre = remove_small_objects(syn_pre,
                 min_size=thres_small, connectivity=1)
-    syn_post = np.logical_and(temp[1], temp[2])
+    
+    syn_post = temp[1]
+    syn_post &= temp[2]
     syn_post = remove_small_objects(syn_post,
                 min_size=thres_small, connectivity=1)
 
@@ -291,7 +295,9 @@ def polarity2instance(
         # Since non-zero pixels in seg_pos and seg_neg are subsets of temp[2],
         # they are naturally subsets of non-zero pixels in foreground.
         seg_pre = (foreground*2 - 1) * syn_pre.astype(foreground.dtype)
+        del syn_pre
         seg_post = (foreground*2) * syn_post.astype(foreground.dtype)
+        del syn_post
         segm = np.maximum(seg_pre, seg_post)
 
         # Report the number of synapses