update to original repo

Author: zengyuy

connectomics/config/defaults.py

@@ -484,6 +484,7 @@
 # Do inference one-by-on (load a volume when needed).
 _C.INFERENCE.DO_SINGLY = False
 _C.INFERENCE.DO_SINGLY_START_INDEX = 0
+_C.INFERENCE.DO_SINGLY_STEP = 1
 
 _C.INFERENCE.PAD_SIZE = None
 _C.INFERENCE.UNPAD = True

connectomics/data/dataset/build.py

@@ -67,9 +67,12 @@ def _get_file_list(name: Union[str, List[str]],
         return name
 
     suffix = name.split('.')[-1]
-    if suffix == 'txt':  # a text file saving the absolute path
+    if suffix == 'txt':  # a text file saving the absolute or relative path
         with open(name) as file:
-            filelist = [line.rstrip('\n') for line in file]
+            if prefix is None:
+                filelist = [line.rstrip('\n') for line in file]
+            else:
+                filelist = [os.path.join(prefix, line.rstrip('\n')) for line in file]
         return filelist
 
     suffix = name.split('/')[-1]

connectomics/data/dataset/dataset_volume.py

@@ -164,7 +164,7 @@ def __init__(self,
             self.sample_num_a = np.sum(self.sample_num)
             self.sample_num_c = np.cumsum([0] + list(self.sample_num))
         """
-
+        
         if self.mode in ['val', 'test']:  # for validation and test
             self.sample_size_test = [
                 np.array([np.prod(x[1:3]), x[2]]) for x in self.sample_size]

connectomics/engine/trainer.py

@@ -274,31 +274,34 @@ def test(self):
 
     def test_singly(self):
         dir_name = _get_file_list(self.cfg.DATASET.INPUT_PATH)
-        img_name = _get_file_list(self.cfg.DATASET.IMAGE_NAME, prefix=dir_name[0])
         assert len(dir_name) == 1 # avoid ambiguity when DO_SINGLY is True
+        img_name = _get_file_list(self.cfg.DATASET.IMAGE_NAME, prefix=dir_name[0])
+        num_file = len(img_name)
+
+        if os.path.isfile(self.cfg.INFERENCE.OUTPUT_NAME):
+            output_name = _get_file_list(self.cfg.DATASET.OUTPUT_NAME, prefix=self.output_dir)
+        else:
+            # same filename but different location
+            if self.output_dir != dir_name[0]:
+                output_name = _get_file_list(self.cfg.DATASET.IMAGE_NAME, prefix=self.output_dir)
+            else:
+                output_name = [x+'_result.h5' for x in img_name]
 
-        # save input image names for further reference
+        # save input image names for future reference
         fw = open(os.path.join(self.output_dir, "images.txt"), "w")
         fw.write('\n'.join(img_name))
         fw.close()
 
-        num_file = len(img_name)
-        start_idx = self.cfg.INFERENCE.DO_SINGLY_START_INDEX
-        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()
+        for i in range(self.cfg.INFERENCE.DO_SINGLY_START_INDEX, num_file, self.cfg.INFERENCE.DO_SINGLY_STEP):
+            self.test_filename = output_name[i]
+            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