[bugfixes] Automatic segmentation fixed where labels would appear as doubles (e.g 2.99999 instead of 3).

Author: alonsoJASL

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

@@ -56,11 +56,12 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommonUtils {
 
     //Nifti Conversion Utils
     static bool ConvertToNifti(mitk::BaseData::Pointer oneNode, QString path2file, bool resample=false, bool reorient=false);
+    static void RoundPixelValues(QString pathToImage, QString outputPath="");
 
     //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 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

@@ -29,6 +29,7 @@ PURPOSE.  See the above copyright notices for more information.
 //ITK
 #include <itkNearestNeighborInterpolateImageFunction.h>
 #include <itkBSplineInterpolateImageFunction.h>
+#include <itkImageRegionIteratorWithIndex.h>
 #include <itkResampleImageFilter.h>
 #include <itkOrientImageFilter.h>
 
@@ -76,6 +77,7 @@ PURPOSE.  See the above copyright notices for more information.
 #include <QMessageBox>
 #include <QString>
 #include <QFile>
+#include <QFileInfo>
 #include <QTextStream>
 #include "CemrgCommonUtils.h"
 
@@ -265,6 +267,38 @@ bool CemrgCommonUtils::ConvertToNifti(mitk::BaseData::Pointer oneNode, QString p
     return successful;
 }
 
+void CemrgCommonUtils::RoundPixelValues(QString pathToImage, QString outputPath){
+    QFileInfo fi(pathToImage);
+    if(fi.exists()){
+        using ImageType = itk::Image<double, 3>;
+        using IteratorType = itk::ImageRegionIteratorWithIndex<ImageType>;
+
+        ImageType::Pointer im = ImageType::New();
+        mitk::CastToItkImage(mitk::IOUtil::Load<mitk::Image>(pathToImage.toStdString()), im);
+
+        IteratorType imIter(im, im->GetLargestPossibleRegion());
+
+        imIter.GoToBegin();
+        while(!imIter.IsAtEnd()){
+            double pixelValue = imIter.Get();
+            imIter.Set(std::round(pixelValue));
+
+            ++imIter;
+        }
+
+        QString writingPath = (outputPath.isEmpty()) ? pathToImage : outputPath;
+
+        mitk::Image::Pointer outputImg = mitk::Image::New();
+        mitk::CastToMitkImage(im, outputImg);
+
+        MITK_INFO(outputPath.isEmpty()) << ("Overwriting: " + pathToImage).toStdString();
+        mitk::IOUtil::Save(outputImg, writingPath.toStdString());
+
+    } else{
+        MITK_WARN << ("Path: " + pathToImage + " does not exist.").toStdString();
+    }
+}
+
 
 mitk::Surface::Pointer CemrgCommonUtils::LoadVTKMesh(std::string path) {
 

Version2.0/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarView.cpp

@@ -466,9 +466,13 @@ void AtrialScarView::AutomaticAnalysis() {
 
         timerLog->StartTimer();
         if (cnnPath.isEmpty()) {
+            MITK_INFO << "[AUTOMATIC_ANALYSIS] Computing automatic segmentation step.";
             cnnPath = cmd->DockerCemrgNetPrediction(mraPath);
         }
 
+        MITK_INFO << "Round pixel values from automatic segmentation.";
+        CemrgCommonUtils::RoundPixelValues(cnnPath);
+
         if (!cnnPath.isEmpty()) {
 
             MITK_INFO << ("Successful prediction with file "+cnnPath).toStdString();
@@ -867,20 +871,27 @@ void AtrialScarView::SegmentIMGS() {
                     this->BusyCursorOn();
                     mitk::ProgressBar::GetInstance()->AddStepsToDo(2);
 
-                    //CNN prediction
+                    MITK_INFO << "CNN prediction";
                     mraPath = directory + mitk::IOUtil::GetDirectorySeparator() + "test.nii";
                     mitk::IOUtil::Save(image, mraPath.toStdString());
                     std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
+
                     cmd->SetUseDockerContainers(true);
                     QString cnnPath = cmd->DockerCemrgNetPrediction(mraPath);
+
+                    MITK_INFO << "Round pixel values from automatic segmentation.";
+                    CemrgCommonUtils::RoundPixelValues(cnnPath);
                     mitk::ProgressBar::GetInstance()->Progress();
 
                     //Clean prediction
                     using ImageTypeCHAR = itk::Image<short, 3>;
                     using ConnectedComponentImageFilterType = itk::ConnectedComponentImageFilter<ImageTypeCHAR, ImageTypeCHAR>;
                     using LabelShapeKeepNObjImgFilterType = itk::LabelShapeKeepNObjectsImageFilter<ImageTypeCHAR>;
+
                     ImageTypeCHAR::Pointer orgSegImage = ImageTypeCHAR::New();
                     mitk::CastToItkImage(mitk::IOUtil::Load<mitk::Image>(cnnPath.toStdString()), orgSegImage);
+
+
                     ConnectedComponentImageFilterType::Pointer connected = ConnectedComponentImageFilterType::New();
                     connected->SetInput(orgSegImage);
                     connected->Update();