Merge branch 'T24641-FibCrash'

Author: peterneher

Applications/Diffusion/CMakeLists.txt

@@ -49,7 +49,7 @@ set(_plugins
   org.mitk.gui.qt.diffusionimaging.reconstruction
   org.mitk.gui.qt.diffusionimaging.tractography
   org.mitk.gui.qt.diffusionimaging.registration
-#  org.mitk.gui.qt.diffusionimaging.python
+  org.mitk.gui.qt.diffusionimaging.python
   org.mitk.gui.qt.diffusionimaging.denoising
 #  org.mitk.gui.qt.matchpoint.algorithm.browser
 #  org.mitk.gui.qt.matchpoint.algorithm.control

Applications/Diffusion/target_libraries.cmake

@@ -22,7 +22,7 @@ set(target_libraries
   org_mitk_gui_qt_diffusionimaging_reconstruction
   org_mitk_gui_qt_diffusionimaging_tractography
   org_mitk_gui_qt_diffusionimaging_registration
-#  org_mitk_gui_qt_diffusionimaging_python
+  org_mitk_gui_qt_diffusionimaging_python
   org_mitk_gui_qt_diffusionimaging_denoising
 #  org_mitk_gui_qt_matchpoint_algorithm_browser
 #  org_mitk_gui_qt_matchpoint_algorithm_control

Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt

@@ -15,5 +15,6 @@ mitkAddCustomModuleTest(mitkMachineLearningTrackingTest mitkMachineLearningTrack
 mitkAddCustomModuleTest(mitkStreamlineTractographyTest mitkStreamlineTractographyTest)
 mitkAddCustomModuleTest(mitkFiberProcessingTest mitkFiberProcessingTest)
 mitkAddCustomModuleTest(mitkFiberFitTest mitkFiberFitTest)
+mitkAddCustomModuleTest(mitkFiberMapper3DTest mitkFiberMapper3DTest)
 
 ENDIF()

Modules/DiffusionImaging/FiberTracking/Testing/files.cmake

@@ -10,6 +10,7 @@ SET(MODULE_CUSTOM_TESTS
   mitkMachineLearningTrackingTest.cpp
   mitkFiberProcessingTest.cpp
   mitkFiberFitTest.cpp
+  mitkFiberMapper3DTest.cpp
 )
 
 

Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberMapper3DTest.cpp

@@ -0,0 +1,109 @@
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include <mitkNodePredicateDataType.h>
+#include <mitkRenderingTestHelper.h>
+#include <mitkSmartPointerProperty.h>
+#include <mitkTestingMacros.h>
+
+#include <vtkSmartPointer.h>
+#include <vtkTexturedSphereSource.h>
+
+
+/*===================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center,
+Division of Medical and Biological Informatics.
+All rights reserved.
+
+This software is distributed WITHOUT ANY WARRANTY; without
+even the implied warranty of MERCHANTABILITY or FITNESS FOR
+A PARTICULAR PURPOSE.
+
+See LICENSE.txt or http://www.mitk.org for details.
+
+===================================================================*/
+
+#include "mitkTestingMacros.h"
+#include <mitkFiberBundle.h>
+#include <itksys/SystemTools.hxx>
+#include <mitkTestingConfig.h>
+#include <mitkIOUtil.h>
+#include <omp.h>
+#include <mitkTestFixture.h>
+#include <mitkPreferenceListReaderOptionsFunctor.h>
+
+class mitkFiberMapper3DTestSuite : public mitk::TestFixture
+{
+
+  CPPUNIT_TEST_SUITE(mitkFiberMapper3DTestSuite);
+  MITK_TEST(Test1);
+  CPPUNIT_TEST_SUITE_END();
+
+  typedef itk::Image<float, 3> ItkFloatImgType;
+
+private:
+
+  /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
+
+  mitk::FiberBundle::Pointer fib;
+
+public:
+
+  void setUp() override
+  {
+    fib = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberFit/Cluster_0.fib"));
+  }
+
+  void tearDown() override
+  {
+
+  }
+
+  void AddGeneratedDataToStorage(mitk::DataStorage *dataStorage)
+  {
+    auto node = mitk::DataNode::New();
+    node->SetData(fib);
+
+    dataStorage->Add(node);
+  }
+
+  void Test1()
+  {
+    omp_set_num_threads(1);
+
+    auto node = mitk::DataNode::New();
+    node->SetData(fib);
+
+    MITK_INFO << "TEST 1";
+    mitk::RenderingTestHelper renderingHelper(640, 480);
+    renderingHelper.AddNodeToStorage(node);
+
+    MITK_INFO << "TEST 2";
+    renderingHelper.SetMapperID(mitk::BaseRenderer::Standard3D);
+    renderingHelper.GetVtkRenderer()->SetBackground(0.0, 0.0, 0.0);
+
+    MITK_INFO << "TEST 3";
+    mitk::RenderingManager::GetInstance()->InitializeViews(fib->GetGeometry(), mitk::RenderingManager::RequestType::REQUEST_UPDATE_ALL);
+    renderingHelper.SaveReferenceScreenShot(mitk::IOUtil::GetTempPath()+"fib_renderingtest.png");
+    MITK_INFO << "TEST 4";
+  }
+
+};
+
+MITK_TEST_SUITE_REGISTRATION(mitkFiberMapper3D)

Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/Sift2WeightCopy.cpp

@@ -52,9 +52,9 @@ int main(int argc, char* argv[])
 {
     mitkCommandLineParser parser;
 
-    parser.setTitle("Sift2 Fiber Weight Import");
+    parser.setTitle("SIFT2 Fiber Weight Import");
     parser.setCategory("Fiber Tracking and Processing Methods");
-    parser.setDescription("Import sift2 fiber weights.");
+    parser.setDescription("Import SIFT2 fiber weights.");
     parser.setContributor("MIC");
 
     parser.setArgumentPrefix("--", "-");

Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.cpp

@@ -48,4 +48,5 @@ void  QmitkDwiPreprocessingPerspective::CreateInitialLayout(berry::IPageLayout::
     left->AddView("org.mitk.views.denoisingview");
     left->AddView("org.mitk.views.simpleregistrationview");
     left->AddView("org.mitk.views.headmotioncorrectionview");
+    left->AddView("org.mitk.views.brainextraction");
 }