Fixed crashes when reloading images due to stale reference_pointer; a…

…lso weird 3d sphere rendering

GUI/Qt/View/QtVTKRenderWindowBox.cxx

@@ -175,37 +175,25 @@ class QtVTKOffscreenMesaWidget : public QWidget
 QtVTKRenderWindowBox::QtVTKRenderWindowBox(QWidget *parent) :
   QWidget(parent)
 {
-  // Create a sphere
-  sphereSource = vtkSmartPointer<vtkSphereSource>::New();
-  sphereSource->SetCenter(0.0, 0.0, 0.0);
-  sphereSource->SetRadius(5.0);
-  sphereSource->SetPhiResolution(100);
-  sphereSource->SetThetaResolution(100);
-
-  mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
-  mapper->SetInputConnection(sphereSource->GetOutputPort());
-
-  actor = vtkSmartPointer<vtkActor>::New();
-  actor->SetMapper(mapper);
-  actor->GetProperty()->SetColor(1.0, 0.0, 0.0);
-
+  /*
   renderer = vtkSmartPointer<vtkRenderer>::New();
   renderer->AddActor(actor);
   renderer->ResetCamera();
   renderer->SetBackground(0.2,0.2,0.0);
+  */
 
   // Create an internal GL rendering widget
 #ifndef VTK_OPENGL_HAS_OSMESA
   auto *iw = new QVTKOpenGLNativeWidgetWithScreenshot(this);
   iw->setRenderWindow(vtkNew<vtkGenericOpenGLRenderWindow>());
-  iw->renderWindow()->AddRenderer(renderer);
+  // iw->renderWindow()->AddRenderer(renderer);
   iw->setObjectName("internalWidget");
   m_InternalWidget = iw;
 
 #else
   auto *iw = new QtVTKOffscreenMesaWidget(this);
   vtkNew<vtkRenderWindow> rwin;
-  rwin->AddRenderer(renderer);
+  // rwin->AddRenderer(renderer);
 
   vtkNew<QVTKInteractor> inter;
   inter->SetRenderWindow(rwin);

GUI/Qt/View/QtVTKRenderWindowBox.h

@@ -71,11 +71,5 @@ public slots:
   // Enter and leave events
   virtual void enterEvent(QEnterEvent *) override;
   virtual void leaveEvent(QEvent *) override;
-
-  // TODO delete this stuff
-  vtkSmartPointer<vtkSphereSource> sphereSource;
-  vtkSmartPointer<vtkPolyDataMapper> mapper;
-  vtkSmartPointer<vtkActor> actor;
-  vtkSmartPointer<vtkRenderer> renderer;
 };
 #endif // QTVTKRENDERWINDOWBOX_H

Logic/Framework/GenericImageData.cxx

@@ -274,6 +274,21 @@ ::UnloadMainImage()
   m_TimePointProperties->Reset();
 }
 
+void GenericImageData::UpdateReferenceImageInAllLayers()
+{
+  for(LayerIterator lit(this); !lit.IsAtEnd(); ++lit)
+  {
+    auto *wrapper = lit.GetLayer();
+    if(wrapper && wrapper->IsInitialized())
+      {
+      if(wrapper->GetReferenceSpace() && wrapper->GetReferenceSpace() != wrapper->GetImageBase())
+        {
+        wrapper->SetReferenceSpace(this->GetMain()->GetImageBase());
+        }
+      }
+  }
+}
+
 
 
 void

Logic/Framework/GenericImageData.h

@@ -225,6 +225,9 @@ class GenericImageData : public itk::Object
   /** Unload the main image (and everything else) */
   virtual void UnloadMainImage();
 
+  /** Update the reference space after the reload of the main image */
+  virtual void UpdateReferenceImageInAllLayers();
+
   /**
    * Get the first segmentation image.
    */

Logic/Framework/ImageIODelegates.cxx

@@ -453,17 +453,29 @@ ::UpdateWrapperWithTraits()
   RescaleNativeImageToIntegralType<Image4DType> rescaler;
   typename Image4DType::Pointer image4d = rescaler(m_IO);
 
-  auto anatomicWrapper = dynamic_cast<WrapperType*>(m_Wrapper.GetPointer());
+  auto *aw = dynamic_cast<WrapperType*>(m_Wrapper.GetPointer());
 
-  if (!anatomicWrapper)
+  if (!aw)
     {
     std::ostringstream oss;
     oss << "Cannot cast wrapper to: \""
         << typeid(WrapperType).name() << "\"";
     throw IRISException("Error reloading image from file: %s", oss.str().c_str());
     }
 
-  anatomicWrapper->SetImage4D(image4d);
+  // Maintain the reference space and transform when reloading an image
+  auto *old_tform = aw->GetITKTransform();
+  auto *old_refspace = aw->GetReferenceSpace();
+  if(old_refspace == aw->GetImageBase())
+    old_refspace = nullptr;
+  aw->SetImage4D(image4d,
+                 old_refspace,
+                 const_cast<typename WrapperType::ITKTransformType *>(old_tform));
+
+  // This line takes care of stale pointers to reference_space in image wrappers
+  if(m_Wrapper == m_Driver->GetCurrentImageData()->GetMain())
+    m_Driver->GetCurrentImageData()->UpdateReferenceImageInAllLayers();
+
   m_Driver->SetCursorPosition(m_Driver->GetCursorPosition(), true);
   m_Driver->InvokeEvent(LayerChangeEvent()); // important, to trigger renderer rebuild assemblies
 }

Logic/ImageWrapper/ImageWrapper.cxx

@@ -1648,6 +1648,14 @@ ::SetITKTransform(ImageBaseType *refSpace, ITKTransformType *transform)
   this->InvokeEvent(WrapperDisplayMappingChangeEvent());
 }
 
+template<class TTraits>
+void
+ImageWrapper<TTraits>
+::SetReferenceSpace(ImageBaseType *referenceSpace)
+{
+  this->SetITKTransform(referenceSpace, m_AffineTransform);
+}
+
 template<class TTraits>
 const typename ImageWrapper<TTraits>::ITKTransformType *
 ImageWrapper<TTraits>

Logic/ImageWrapper/ImageWrapper.h

@@ -524,6 +524,11 @@ class ImageWrapper : public TTraits::WrapperBaseType
    */
   virtual void SetITKTransform(ImageBaseType *referenceSpace, ITKTransformType *transform) ITK_OVERRIDE;
 
+  /**
+   * Set the reference image without changing the transform
+   */
+  virtual void SetReferenceSpace(ImageBaseType *referenceSpace) ITK_OVERRIDE;
+
   /**
    * Get the ITK transform between this layer and its reference space
    */

Logic/ImageWrapper/ImageWrapperBase.h

@@ -477,6 +477,11 @@ class ImageWrapperBase : public WrapperBase
    */
   virtual void SetITKTransform(ImageBaseType *referenceSpace, ITKTransformType *transform) = 0;
 
+  /**
+   * Set the reference image without changing the transform
+   */
+  virtual void SetReferenceSpace(ImageBaseType *referenceSpace) = 0;
+
   /**
    * Get the ITK transform between this image and the reference space
    */

Logic/ImageWrapper/VectorImageWrapper.cxx

@@ -360,10 +360,18 @@ VectorImageWrapper<TTraits>
 ::SetITKTransform(ImageBaseType *referenceSpace, ITKTransformType *transform)
 {
   Superclass::SetITKTransform(referenceSpace, transform);
-  for(ScalarRepIterator it = m_ScalarReps.begin(); it != m_ScalarReps.end(); ++it)
-    {
-    it->second->SetITKTransform(referenceSpace, transform);
-    }
+  for(auto &it : m_ScalarReps)
+    it.second->SetITKTransform(referenceSpace, transform);
+}
+
+template<class TTraits>
+void
+VectorImageWrapper<TTraits>
+::SetReferenceSpace(ImageBaseType *referenceSpace)
+{
+  Superclass::SetReferenceSpace(referenceSpace);
+  for(auto &it : m_ScalarReps)
+    it.second->SetReferenceSpace(referenceSpace);
 }
 
 

Logic/ImageWrapper/VectorImageWrapper.h

@@ -183,6 +183,11 @@ class VectorImageWrapper : public ImageWrapper<TTraits>
   virtual void CopyImageCoordinateTransform(const ImageWrapperBase *source) ITK_OVERRIDE;
 
   virtual void SetSticky(bool value) ITK_OVERRIDE;
+
+  virtual void SetITKTransform(ImageBaseType *referenceSpace, ITKTransformType *transform) ITK_OVERRIDE;
+
+  virtual void SetReferenceSpace(ImageBaseType *referenceSpace) ITK_OVERRIDE;
+
 protected:
 
   /**
@@ -200,8 +205,6 @@ class VectorImageWrapper : public ImageWrapper<TTraits>
                                    ImageBaseType *refSpace = NULL,
                                    ITKTransformType *tran = NULL) ITK_OVERRIDE;
 
-  virtual void SetITKTransform(ImageBaseType *referenceSpace, ITKTransformType *transform) ITK_OVERRIDE;
-
   /** Destructor */
   virtual ~VectorImageWrapper();