add ExecuteSurf variant that returns surface immediately

Skip round trip to disk for simplicity and performance.

Author: JostMigenda

CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h

@@ -29,6 +29,8 @@ PURPOSE.  See the above copyright notices for more information.
 #ifndef CemrgCommandLine_h
 #define CemrgCommandLine_h
 
+#include <mitkSurface.h>
+
 // Qt
 #include <memory>
 #include <QProcess>
@@ -50,6 +52,7 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommandLine: public QObject {
 
     //Execute Plugin Specific Functions
     QString ExecuteSurf(QString dir, QString segPath, float th = 0.5, int blur = 0, int smth = 10);
+    mitk::Surface::Pointer ExecuteSurf_new(QString dir, QString segPath, float th = 0.5, int blur = 0, int smth = 10);
     QString ExecuteCreateCGALMesh(QString dir, QString outputName, QString paramsFullPath, QString segmentationName = "converted.inr");
     void ExecuteTracking(QString dir, QString imgTimes, QString param, QString output = "tsffd.dof");
     void ExecuteApplying(QString dir, QString inputMesh, double iniTime, QString dofin, int noFrames, int smooth);

CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp

@@ -94,6 +94,14 @@ QDialog* CemrgCommandLine::GetDialog() {
  ***************************************************************************/
 
 QString CemrgCommandLine::ExecuteSurf(QString dir, QString segPath, float thresh, int blur, int smooth) {
+    // Calling code expects a QString of the file path as return value, not the Surface pointer itself.
+    mitk::Surface::Pointer surface = CemrgCommandLine::ExecuteSurf_new(dir, segPath, thresh, blur, smooth);
+    QString outAbsolutePath = dir + "/segmentation.vtk";
+    mitk::IOUtil::Save(surface, outAbsolutePath.toStdString());
+    return outAbsolutePath;
+}
+
+mitk::Surface::Pointer CemrgCommandLine::ExecuteSurf_new(QString dir, QString segPath, float thresh, int blur, int smooth) {
     MITK_INFO << "[ATTENTION] SURFACE CREATION: Surface -> Smooth";
 
     // Load input image into memory
@@ -105,12 +113,8 @@ QString CemrgCommandLine::ExecuteSurf(QString dir, QString segPath, float thresh
     mitk::Surface::Pointer smoothedSurface = CemrgCommonUtils::ExtractSurfaceFromSegmentation(inputImage, (double)thresh, (double)blur, (double)smooth);
     CemrgCommonUtils::FlipXYPlane(smoothedSurface, "", "");
 
-    // Calling code expects a QString of the file path as return value, not the Surface pointer itself.
-    QString outAbsolutePath = dir + "/segmentation.vtk";
-    mitk::IOUtil::Save(smoothedSurface, outAbsolutePath.toStdString());
     mitk::ProgressBar::GetInstance()->Progress(2);
-
-    return outAbsolutePath;
+    return smoothedSurface;
 }
 
 QString CemrgCommandLine::ExecuteCreateCGALMesh(QString dir, QString outputName, QString paramsFullPath, QString segmentationName) {

CemrgApp/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarClipperView.cpp

@@ -209,12 +209,11 @@ void AtrialScarClipperView::iniPreSurf() {
                 mitk::IOUtil::Save(image, path.toStdString());
                 mitk::ProgressBar::GetInstance()->AddStepsToDo(3);
                 std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
-                QString output = cmd->ExecuteSurf(directory, path, th, blur, smth);
+                mitk::Surface::Pointer shell = cmd->ExecuteSurf_new(directory, path, th, blur, smth);
                 QMessageBox::information(NULL, "Attention", "Command Line Operations Finished!");
                 this->BusyCursorOff();
 
                 //Decimate the mesh to visualise
-                mitk::Surface::Pointer shell = mitk::IOUtil::Load<mitk::Surface>(output.toStdString());
                 vtkSmartPointer<vtkDecimatePro> deci = vtkSmartPointer<vtkDecimatePro>::New();
                 deci->SetInputData(shell->GetVtkPolyData());
                 deci->SetTargetReduction(ds);

CemrgApp/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarView.cpp

@@ -540,8 +540,7 @@ void AtrialScarView::AutomaticAnalysis() {
             MITK_INFO << ("[...][3.1] Saved file: " + segCleanPath).toStdString();
 
             MITK_INFO << "[AUTOMATIC_ANALYSIS][4] Vein clipping mesh";
-            QString output1 = cmd->ExecuteSurf(direct, segCleanPath, .5, 0, 10);
-            mitk::Surface::Pointer shell = mitk::IOUtil::Load<mitk::Surface>(output1.toStdString());
+            mitk::Surface::Pointer shell = cmd->ExecuteSurf_new(direct, segCleanPath, .5, 0, 10);
             vtkSmartPointer<vtkDecimatePro> deci = vtkSmartPointer<vtkDecimatePro>::New();
             deci->SetInputData(shell->GetVtkPolyData());
             deci->SetTargetReduction(0.1);
@@ -662,8 +661,7 @@ void AtrialScarView::AutomaticAnalysis() {
             MITK_INFO << "[...][7.3] ClipVeinsImage finished .";
 
             MITK_INFO << "[AUTOMATIC_ANALYSIS][8] Create a mesh from clipped segmentation of veins";
-            QString output2 = cmd->ExecuteSurf(direct, (direct + "/PVeinsCroppedImage.nii"), .5, 0, 10);
-            mitk::Surface::Pointer LAShell = mitk::IOUtil::Load<mitk::Surface>(output2.toStdString());
+            mitk::Surface::Pointer LAShell = cmd->ExecuteSurf_new(direct, "PVeinsCroppedImage.nii", .5, 0, 10);
 
             MITK_INFO << "[AUTOMATIC_ANALYSIS][9] Clip the mitral valve";
             ImageTypeCHAR::Pointer mvImage = ImageTypeCHAR::New();
@@ -693,9 +691,8 @@ void AtrialScarView::AutomaticAnalysis() {
             mitk::IOUtil::Save(mitk::ImportItkImage(mvImage), (direct + "/prodMVI.nii").toStdString());
 
             // Make vtk of prodMVI
-            QString mviShellPath = cmd->ExecuteSurf(direct, "prodMVI.nii", 0.5, 0, 10);
+            mitk::Surface::Pointer ClipperSurface = cmd->ExecuteSurf_new(direct, "prodMVI.nii", 0.5, 0, 10);
             // Implement code from command line tool
-            mitk::Surface::Pointer ClipperSurface = mitk::IOUtil::Load<mitk::Surface>(mviShellPath.toStdString());
             vtkSmartPointer<vtkImplicitPolyDataDistance> implicitFn = vtkSmartPointer<vtkImplicitPolyDataDistance>::New();
             implicitFn->SetInput(ClipperSurface->GetVtkPolyData());
             vtkMTimeType mtime = implicitFn->GetMTime();
@@ -725,9 +722,9 @@ void AtrialScarView::AutomaticAnalysis() {
             clean->SetInputConnection(lrgRegion->GetOutputPort());
             clean->Update();
 
-            MITK_INFO << ("[...][9.4] Saving to file: " + output2).toStdString();
+            MITK_INFO << ("[...][9.4] Saving to file: " + direct + "/segmentation.vtk").toStdString();
             LAShell->SetVtkPolyData(clean->GetOutput());
-            mitk::IOUtil::Save(LAShell, output2.toStdString());
+            mitk::IOUtil::Save(LAShell, (direct + "/segmentation.vtk").toStdString());
 
             MITK_INFO << "[AUTOMATIC_ANALYSIS][10] Scar projection";
             int minStep = minStep_UI;