From 5731bb69e450b703fe3dcc29627fe0873bbcb05d Mon Sep 17 00:00:00 2001
From: Christian Herz <christianherz1985@googlemail.com>
Date: Mon, 18 Sep 2017 12:11:58 -0400
Subject: [PATCH 1/2] BUG: fixes wrong api calls caused by Slicer Core changes
 (issue #197)

---
 DICOMPlugins/DICOMSegmentationPlugin.py | 34 ++++++++++++-------------
 QuantitativeReporting.py                | 10 +-------
 2 files changed, 18 insertions(+), 26 deletions(-)

diff --git a/DICOMPlugins/DICOMSegmentationPlugin.py b/DICOMPlugins/DICOMSegmentationPlugin.py
index 90a0aa7..354defd 100644
--- a/DICOMPlugins/DICOMSegmentationPlugin.py
+++ b/DICOMPlugins/DICOMSegmentationPlugin.py
@@ -177,15 +177,14 @@ def load(self,loadable):
           regionModCode, regionModCodingScheme, regionModCodeMeaning = \
             self.getValuesFromCodeSequence(segment, "AnatomicRegionModifierSequence")
 
-          dummyTerminologyWidget = slicer.qSlicerTerminologyNavigatorWidget() # Still cannot call static methods from python
-          segmentTerminologyTag = dummyTerminologyWidget.serializeTerminologyEntry(
-                                          loadable.name,
-                                          categoryCode, categoryCodingScheme, categoryCodeMeaning,
-                                          typeCode, typeCodingScheme, typeCodeMeaning,
-                                          typeModCode, typeModCodingScheme, typeModCodeMeaning,
-                                          loadable.name,
-                                          regionCode, regionCodingScheme, regionCodeMeaning,
-                                          regionModCode, regionModCodingScheme, regionModCodeMeaning)
+          segmentTerminologyTag = terminologiesLogic.SerializeTerminologyEntry(
+                                    loadable.name,
+                                    categoryCode, categoryCodingScheme, categoryCodeMeaning,
+                                    typeCode, typeCodingScheme, typeCodeMeaning,
+                                    typeModCode, typeModCodingScheme, typeModCodeMeaning,
+                                    loadable.name,
+                                    regionCode, regionCodingScheme, regionCodeMeaning,
+                                    regionModCode, regionModCodingScheme, regionModCodeMeaning)
           # end of processing a line of terminology
 
           # TODO: Create logic class that both CLI and this plugin uses so that we don't need to have temporary NRRD
@@ -334,6 +333,15 @@ class EmptySegmentsFoundError(ValueError):
   class NoNonEmptySegmentsFoundError(ValueError):
       pass
 
+  @staticmethod
+  def getDeserializedTerminologyEntry(vtkSegment):
+    terminologyEntry = slicer.vtkSlicerTerminologyEntry()
+    tag = vtk.mutable("")
+    vtkSegment.GetTag(vtkSegment.GetTerminologyEntryTagName(), tag)
+    terminologyLogic = slicer.modules.terminologies.logic()
+    terminologyLogic.DeserializeTerminologyEntry(tag, terminologyEntry)
+    return terminologyEntry
+
   @staticmethod
   def saveJSON(data, destination):
     with open(os.path.join(destination), 'w') as outfile:
@@ -551,14 +559,6 @@ def checkTerminologyOfSegments(self, segmentIDs):
       if any(v is None for v in [category, propType]):
         raise ValueError("Segment {} has missing attributes. Make sure to set terminology.".format(segment.GetName()))
 
-  def getDeserializedTerminologyEntry(self, vtkSegment):
-    terminologyWidget = slicer.qSlicerTerminologyNavigatorWidget()
-    terminologyEntry = slicer.vtkSlicerTerminologyEntry()
-    tag = vtk.mutable("")
-    vtkSegment.GetTag(vtkSegment.GetTerminologyEntryTagName(), tag)
-    terminologyWidget.deserializeTerminologyEntry(tag, terminologyEntry)
-    return terminologyEntry
-
   def createJSONFromTerminologyContext(self, terminologyEntry):
     segmentData = dict()
 
diff --git a/QuantitativeReporting.py b/QuantitativeReporting.py
index 0533fb9..5fcde9b 100644
--- a/QuantitativeReporting.py
+++ b/QuantitativeReporting.py
@@ -973,7 +973,7 @@ def generateJSON4DcmSR(self, dcmSegmentationFile, sourceVolumeNode):
       data["segmentationSOPInstanceUID"] = segmentationSOPInstanceUID
       segment = self.segmentationNode.GetSegmentation().GetSegment(segmentID)
 
-      terminologyEntry = self.getDeserializedTerminologyEntry(segment)
+      terminologyEntry = DICOMSegmentationExporter.getDeserializedTerminologyEntry(segment)
 
       data["Finding"] = self.createJSONFromTerminologyContext(terminologyEntry)["SegmentedPropertyTypeCodeSequence"]
       anatomicContext = self.createJSONFromAnatomicContext(terminologyEntry)
@@ -1005,14 +1005,6 @@ def _createCodeSequence(self, vtkStringifiedCodedEntry):
       codeSequence[key] = value
     return codeSequence
 
-  def getDeserializedTerminologyEntry(self, segment):
-    terminologyWidget = slicer.qSlicerTerminologyNavigatorWidget()
-    terminologyEntry = slicer.vtkSlicerTerminologyEntry()
-    tag = vtk.mutable("")
-    segment.GetTag(segment.GetTerminologyEntryTagName(), tag)
-    terminologyWidget.deserializeTerminologyEntry(tag, terminologyEntry)
-    return terminologyEntry
-
 
 class CustomDICOMDetailsWidget(DICOMDetailsWidget, ParameterNodeObservationMixin):
 

From 151ddc46e61502853a99976aa80f287419988055 Mon Sep 17 00:00:00 2001
From: Christian Herz <christianherz1985@googlemail.com>
Date: Mon, 18 Sep 2017 14:43:04 -0400
Subject: [PATCH 2/2] ENH: hiding Segmentations... button

---
 QuantitativeReporting.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/QuantitativeReporting.py b/QuantitativeReporting.py
index 5fcde9b..6200f74 100644
--- a/QuantitativeReporting.py
+++ b/QuantitativeReporting.py
@@ -760,6 +760,7 @@ def setup(self):
     super(QuantitativeReportingSegmentEditorWidget, self).setup()
     if self.developerMode:
       self.reloadCollapsibleButton.hide()
+    self.editor.switchToSegmentationsButtonVisible = False
     self.editor.segmentationNodeSelectorVisible = False
     self.editor.setEffectButtonStyle(qt.Qt.ToolButtonIconOnly)
     self.clearSegmentationEditorSelectors()