Merge pull request #52 from MStarmans91/development

Fix documentation building

.readthedocs.yml

@@ -5,8 +5,12 @@ version: 2
 sphinx:
   configuration: WORC/doc/conf.py
 
+formats: []
+
 python:
   version: 3.7
   install:
-    - requirements: WORC/doc/doc_requirements.txt
     - requirements: requirements.txt
+    - method: pip
+      path: .
+  system_packages: true

WORC/WORC.py

@@ -207,10 +207,10 @@ def defaultconfig(self):
         config['Preprocessing']['Clipping_Range'] = '-1000.0, 3000.0'
         config['Preprocessing']['Normalize'] = 'True'
         config['Preprocessing']['Normalize_ROI'] = 'Full'
+        config['Preprocessing']['Method'] = 'z_score'
         config['Preprocessing']['ROIDetermine'] = 'Provided'
         config['Preprocessing']['ROIdilate'] = 'False'
         config['Preprocessing']['ROIdilateradius'] = '10'
-        config['Preprocessing']['Method'] = 'z_score'
         config['Preprocessing']['Resampling'] = 'False'
         config['Preprocessing']['Resampling_spacing'] = '1, 1, 1'
         config['Preprocessing']['BiasCorrection'] = 'False'

WORC/processing/preprocessing.py

@@ -60,8 +60,19 @@ def preprocess(imagefile, config, metadata=None, mask=None):
 
         if image.GetSpacing() == (1, 1, 1):
             print('Detected 1x1x1 spacing, overwriting with DICOM metadata.')
-            slice_thickness = metadata[0x18, 0x50].value
-            pixel_spacing = metadata[0x28, 0x30].value
+            if [0x18, 0x50] in list(metadata.keys()):
+                slice_thickness = metadata[0x18, 0x50].value
+            elif [0x18, 0x88] in list(metadata.keys()):
+                # Take spacing between slices
+                slice_thickness = metadata[0x18, 0x88].value
+            else:
+                slice_thickness = 1.0
+
+            if [0x28, 0x30] in list(metadata.keys()):
+                pixel_spacing = metadata[0x28, 0x30].value
+            else:
+                pixel_spacing = [1.0, 1.0]
+
             spacing = (float(pixel_spacing[0]),
                        float(pixel_spacing[1]),
                        float(slice_thickness))

WORC/tools/Evaluate.py

@@ -449,7 +449,25 @@ def create_links_Addon(self):
         self.node_Ranked_Posteriors.inputs['estimator'] = prediction
         self.node_Ranked_Posteriors.inputs['pinfo'] = pinfo
 
-        if self.parent.sources_images_train:
+        if self.parent.sources_images_test:
+            images = self.parent.sources_images_test[label].output
+            segmentations =\
+                self.parent.sources_segmentations_test[label].output
+            self.link_images_perc =\
+                self.network.create_link(images, self.node_Ranked_Percentages.inputs['images'])
+            self.link_images_perc.collapse = 'test'
+            self.link_segmentations_perc =\
+                self.network.create_link(segmentations, self.node_Ranked_Percentages.inputs['segmentations'])
+            self.link_segmentations_perc.collapse = 'test'
+
+            self.link_images_post =\
+                self.network.create_link(images, self.node_Ranked_Posteriors.inputs['images'])
+            self.link_images_post.collapse = 'test'
+            self.link_segmentations_post =\
+                self.network.create_link(segmentations, self.node_Ranked_Posteriors.inputs['segmentations'])
+            self.link_segmentations_post.collapse = 'test'
+
+        elif self.parent.sources_images_train:
             self.link_images_perc =\
                 self.network.create_link(images, self.node_Ranked_Percentages.inputs['images'])
             self.link_images_perc.collapse = 'train'