changed to torch_em standardize

Author: lufre1

synapse_net/inference/cristae.py

@@ -42,6 +42,7 @@ def segment_cristae(
     return_predictions: bool = False,
     scale: Optional[List[float]] = None,
     mask: Optional[np.ndarray] = None,
+    **kwargs
 ) -> Union[np.ndarray, Tuple[np.ndarray, np.ndarray]]:
     """Segment cristae in an input volume.
 
@@ -61,6 +62,8 @@ def segment_cristae(
         The segmentation mask as a numpy array, or a tuple containing the segmentation mask
         and the predictions if return_predictions is True.
     """
+    with_channels = kwargs.pop("with_channels", True)
+    channels_to_standardize = kwargs.pop("channels_to_standardize", [0])
     if verbose:
         print("Segmenting cristae in volume of shape", input_volume.shape)
     # Create the scaler to handle prediction with a different scaling factor.
@@ -72,7 +75,7 @@ def segment_cristae(
         mask = scaler.scale_input(mask, is_segmentation=True)
     pred = get_prediction(
         input_volume, model_path=model_path, model=model, mask=mask,
-        tiling=tiling, with_channels=True, verbose=verbose
+        tiling=tiling, with_channels=with_channels, channels_to_standardize=channels_to_standardize, verbose=verbose
     )
     foreground, boundaries = pred[:2]
     seg = _run_segmentation(foreground, verbose=verbose, min_size=min_size)

synapse_net/inference/util.py

@@ -85,7 +85,7 @@ def get_prediction(
     model: Optional[torch.nn.Module] = None,
     verbose: bool = True,
     with_channels: bool = False,
-    channels_to_normalize: Optional[List[int]] = [0],
+    channels_to_standardize: Optional[List[int]] = None,
     mask: Optional[np.ndarray] = None,
 ) -> np.ndarray:
     """Run prediction on a given volume.
@@ -100,7 +100,7 @@ def get_prediction(
         tiling: The tiling configuration for the prediction.
         verbose: Whether to print timing information.
         with_channels: Whether to predict with channels.
-        channels_to_normalize: List of channels to normalize. Defaults to 0.
+        channels_to_standardize: List of channels to standardize. Defaults to None.
         mask: Optional binary mask. If given, the prediction will only be run in
             the foreground region of the mask.
 
@@ -123,9 +123,12 @@ def get_prediction(
     # If we have channels then the standardization is done independently per channel.
     if with_channels:
         input_volume = input_volume.astype(np.float32, copy=False)
+        channels_to_standardize = None
         # TODO Check that this is the correct axis.
-        for ch in channels_to_normalize:
-            input_volume[ch] = torch_em.transform.raw.normalize(input_volume[ch])
+        if channels_to_standardize is None:  # assume all channels
+            channels_to_standardize = range(input_volume.shape[0])
+        for ch in channels_to_standardize:
+            input_volume[ch] = torch_em.transform.raw.standardize(input_volume[ch])
     else:
         input_volume = torch_em.transform.raw.standardize(input_volume)