Implemented background filling with user-specified value

xgymri · Apr 11, 2019 · ed63210 · ed63210
1 parent 7ba1dbc
commit ed63210
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Showing 4 changed files with 17 additions and 3 deletions.
diff --git a/niftynet/application/regression_application.py b/niftynet/application/regression_application.py
@@ -203,7 +203,8 @@ def initialise_grid_aggregator(self):
             output_path=self.action_param.save_seg_dir,
             window_border=self.action_param.border,
             interp_order=self.action_param.output_interp_order,
-            postfix=self.action_param.output_postfix)
+            postfix=self.action_param.output_postfix,
+            fill_constant=self.action_param.fill_constant)
 
     def initialise_resize_aggregator(self):
         self.output_decoder = ResizeSamplesAggregator(

diff --git a/niftynet/application/segmentation_application.py b/niftynet/application/segmentation_application.py
@@ -237,7 +237,8 @@ def initialise_grid_aggregator(self):
             output_path=self.action_param.save_seg_dir,
             window_border=self.action_param.border,
             interp_order=self.action_param.output_interp_order,
-            postfix=self.action_param.output_postfix)
+            postfix=self.action_param.output_postfix,
+            fill_constant=self.action_param.fill_constant)
 
     def initialise_resize_aggregator(self):
         self.output_decoder = ResizeSamplesAggregator(

diff --git a/niftynet/engine/windows_aggregator_grid.py b/niftynet/engine/windows_aggregator_grid.py
@@ -28,14 +28,16 @@ def __init__(self,
                  output_path=os.path.join('.', 'output'),
                  window_border=(),
                  interp_order=0,
-                 postfix='_niftynet_out'):
+                 postfix='_niftynet_out',
+                 fill_constant=0.0):
         ImageWindowsAggregator.__init__(
             self, image_reader=image_reader, output_path=output_path)
         self.name = name
         self.image_out = None
         self.window_border = window_border
         self.output_interp_order = interp_order
         self.postfix = postfix
+        self.fill_constant = fill_constant
 
     def decode_batch(self, window, location):
         n_samples = location.shape[0]
@@ -68,6 +70,10 @@ def _initialise_empty_image(self, image_id, n_channels, dtype=np.float):
         for layer in self.reader.preprocessors:
             if isinstance(layer, PadLayer):
                 empty_image, _ = layer(empty_image)
+
+        if self.fill_constant != 0.0:
+            empty_image[:] = self.fill_constant
+
         return empty_image
 
     def _save_current_image(self):

diff --git a/niftynet/utilities/user_parameters_default.py b/niftynet/utilities/user_parameters_default.py
@@ -148,6 +148,12 @@ def add_inference_args(parser):
         type=spatialnumarray,
         default=(0, 0, 0))
 
+    parser.add_argument(
+        "--fill-constant",
+        help="Output fill value used fill borders of output images.",
+        type=float,
+        default=0.0)
+
     return parser