minor fixes for NifTK#344

- doc and unit test fixes for rgb hist. equil. - adding rgb_histogram_equilisation to regression app
JoonVan · May 4, 2019 · e0c5141 · e0c5141
1 parent 91fce3f
commit e0c5141
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/doc/source/config_spec.md b/doc/source/config_spec.md
@@ -407,7 +407,7 @@ More specifically:
  ---- | ---- | ------- | -------
 [normalisation](#normalisation) | `boolean` | `normalisation=True` | `False`
 [whitening](#whitening) | `boolean` | `whitening=True` | `False`
-[rgb_normalisation](#rgb_normalisation) | `boolean` | `rgb_normalisation=True` | `False`
+[rgb_normalisation](#rgb-normalisation) | `boolean` | `rgb_normalisation=True` | `False`
 [histogram_ref_file](#histogram-ref-file) | `string` | `histogram_ref_file=./hist_ref.txt` | `''`
 [norm_type](#norm-type) | `string` | `norm_type=percentile` | `percentile`
 [cutoff](#cutoff) | `float array (two elements)` | `cutoff=0.1, 0.9` | `0.01, 0.99`

diff --git a/niftynet/application/regression_application.py b/niftynet/application/regression_application.py
@@ -25,6 +25,8 @@
 from niftynet.layer.rand_flip import RandomFlipLayer
 from niftynet.layer.rand_rotation import RandomRotationLayer
 from niftynet.layer.rand_spatial_scaling import RandomSpatialScalingLayer
+from niftynet.layer.rgb_histogram_equilisation import \
+    RGBHistogramEquilisationLayer
 from niftynet.evaluation.regression_evaluator import RegressionEvaluator
 from niftynet.layer.rand_elastic_deform import RandomElasticDeformationLayer
 
@@ -100,12 +102,17 @@ def initialise_dataset_loader(
             name='hist_norm_layer') \
             if (self.net_param.histogram_ref_file and
                 self.net_param.normalisation) else None
+        rgb_normaliser = RGBHistogramEquilisationLayer(
+            image_name='image',
+            name='rbg_norm_layer') if self.net_param.rgb_normalisation else None
 
         normalisation_layers = []
         if histogram_normaliser is not None:
             normalisation_layers.append(histogram_normaliser)
         if mean_var_normaliser is not None:
             normalisation_layers.append(mean_var_normaliser)
+        if rgb_normaliser is not None:
+            normalisation_layers.append(rgb_normaliser)
 
         volume_padding_layer = []
         if self.net_param.volume_padding_size:

diff --git a/tests/rgb_histogram_equilisation_test.py b/tests/rgb_histogram_equilisation_test.py
@@ -117,7 +117,7 @@ def test_equilisation(self):
         cv2 = require_module('cv2', mandatory=False)
 
         if cv2 is None:
-            self.skipTest()
+            self.skipTest('requires cv2 module')
             return
 
         def _get_histogram(img):