[feature] CemrgCommonUtils Extract surface static function using mitk libraries

Author: alonsoJASL

Version2.0/Modules/CemrgAppModule/CMakeLists.txt

@@ -1,5 +1,5 @@
 mitk_create_module(CemrgAppModule
-  DEPENDS PUBLIC MitkQtWidgetsExt MitkQtWidgets MitkAlgorithmsExt MitkCore
+  DEPENDS PUBLIC MitkSegmentation MitkQtWidgetsExt MitkQtWidgets MitkAlgorithmsExt MitkCore
   PACKAGE_DEPENDS PRIVATE VMTK ITK
 )
 

Version2.0/Modules/CemrgAppModule/include/CemrgCommonUtils.h

@@ -59,6 +59,8 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommonUtils {
 
     //Mesh Utils
     static mitk::Surface::Pointer LoadVTKMesh(std::string path);
+    static mitk::Surface::Pointer ExtractSurfaceFromSegmentation(mitk::Image::Pointer image, double thresh=0.5, double blur=0.8, double smoothIterations=3, double decimation=0.5);
+    static void FlipXYPlane(mitk::Surface::Pointer surf, QString dir, QString vtkname="segmentation.vtk"); 
     static QString M3dlibParamFileGenerator(QString dir, QString filename="param-template.par", QString thicknessCalc="0");
     static void ConvertToCarto(std::string vtkPath, std::vector<double>, double, double, int, bool);
     static void CalculatePolyDataNormals(vtkSmartPointer<vtkPolyData>& pd, bool celldata=true);

Version2.0/Modules/CemrgAppModule/src/CemrgCommonUtils.cpp

@@ -67,6 +67,9 @@ PURPOSE.  See the above copyright notices for more information.
 #include <mitkITKImageImport.h>
 #include <mitkIOUtil.h>
 #include <mitkDataStorage.h>
+#include <mitkImagePixelReadAccessor.h>
+#include <mitkImageToSurfaceFilter.h>
+#include <mitkManualSegmentationToSurfaceFilter.h>
 #include <mitkRenderingManager.h>
 
 //Qt
@@ -304,6 +307,43 @@ mitk::Surface::Pointer CemrgCommonUtils::LoadVTKMesh(std::string path) {
     }//_catch
 }
 
+mitk::Surface::Pointer CemrgCommonUtils::ExtractSurfaceFromSegmentation(mitk::Image::Pointer image, double thresh, double blur, double smooth, double decimation){
+    auto im2surf = mitk::ManualSegmentationToSurfaceFilter::New();
+
+    im2surf->SetInput(image);
+    im2surf->SetThreshold(thresh);
+    im2surf->SetUseGaussianImageSmooth(true);
+    im2surf->SetSmooth(true);
+    im2surf->SetMedianFilter3D(true);
+    im2surf->InterpolationOn();
+    im2surf->SetGaussianStandardDeviation(blur);
+    im2surf->SetMedianKernelSize(smooth, smooth, smooth);
+    im2surf->SetDecimate(mitk::ImageToSurfaceFilter::QuadricDecimation);
+    im2surf->SetTargetReduction(decimation);
+    im2surf->UpdateLargestPossibleRegion();
+
+    mitk::Surface::Pointer shell = im2surf->GetOutput();
+    return shell;
+}
+
+void CemrgCommonUtils::FlipXYPlane(mitk::Surface::Pointer surf, QString dir, QString vtkname){
+
+    //Prepare points for MITK visualisation - (CemrgCommonUtils::LoadVTKMesh)
+    vtkSmartPointer<vtkPolyData> pd = surf->GetVtkPolyData();
+    for (int ix=0; ix<pd->GetNumberOfPoints(); ix++) {
+        double* point = pd->GetPoint(ix);
+        point[0] = -point[0];
+        point[1] = -point[1];
+        pd->GetPoints()->SetPoint(ix, point);
+    }
+
+    if(!vtkname.isEmpty()){
+        vtkname += (!vtkname.contains(".vtk")) ? ".vtk" : "";
+        QString path = dir + mitk::IOUtil::GetDirectorySeparator()+vtkname;
+        mitk::IOUtil::Save(surf, path.toStdString());
+    }
+}
+
 QString CemrgCommonUtils::M3dlibParamFileGenerator(QString dir, QString filename, QString thicknessCalc) {
 
     QString path2file = dir + mitk::IOUtil::GetDirectorySeparator() + filename;