[bugfix] manual - binarise image

Author: alonsoJASL

CemrgApp/Modules/CemrgAppModule/include/CemrgAtrialTools.h

@@ -165,6 +165,7 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgAtrialTools {
     ImFilterType::Pointer ImOpenFilter(ImageType::Pointer input, uint16_t radius);
     ShortImageType::Pointer Uint16ToShort(ImageType::Pointer im);
     mitk::Image::Pointer ImErode(ImageType::Pointer input, int vxls=3);
+    void QuickBinarise(ImageType::Pointer imToBin);
     void SaveImageToDisk(ImageType::Pointer im, QString dir, QString imName);
     vtkSmartPointer<vtkConnectivityFilter> GetLabelConnectivity(mitk::Surface::Pointer externalSurface, double label, bool colourRegions=false);
 

CemrgApp/Modules/CemrgAppModule/src/CemrgAtrialTools.cpp

@@ -213,16 +213,23 @@ ImageType::Pointer CemrgAtrialTools::RemoveNoiseFromAutomaticSegmentation(QStrin
     keepObjs->SetAttribute(LabelShapeKeepNObjImgFilterType::LabelObjectType::NUMBER_OF_PIXELS);
     keepObjs->Update();
 
-    return keepObjs->GetOutput();
-}
+    ImageType::Pointer outIm = keepObjs->GetOutput();
+    IteratorType imIter(outIm, outIm->GetLargestPossibleRegion());
 
-ImageType::Pointer CemrgAtrialTools::CleanAutomaticSegmentation(QString dir, QString segName, QString cleanName){
-    QString inputPath = dir + "/" + segName;
-    ImageType::Pointer orgSegImage = LoadImage(inputPath);
-    ImageType::Pointer atriumCoarse = RemoveNoiseFromAutomaticSegmentation(dir, segName);
+    imIter.GoToBegin();
+    while(!imIter.IsAtEnd()){
+        float value = (imIter.Get() > 0) ? 1 : 0;
+        imIter.Set(value);
+
+        ++imIter;
+    }
 
+    return outIm;
+}
+
+void CemrgAtrialTools::QuickBinarise(ImageType::Pointer imToBin){
     // binarise to 1, 0
-    IteratorType imIter(atriumCoarse, atriumCoarse->GetLargestPossibleRegion());
+    IteratorType imIter(imToBin, imToBin->GetLargestPossibleRegion());
 
     imIter.GoToBegin();
     while(!imIter.IsAtEnd()){
@@ -231,6 +238,12 @@ ImageType::Pointer CemrgAtrialTools::CleanAutomaticSegmentation(QString dir, QSt
 
         ++imIter;
     }
+}
+
+ImageType::Pointer CemrgAtrialTools::CleanAutomaticSegmentation(QString dir, QString segName, QString cleanName){
+    QString inputPath = dir + "/" + segName;
+    ImageType::Pointer orgSegImage = LoadImage(inputPath);
+    ImageType::Pointer atriumCoarse = RemoveNoiseFromAutomaticSegmentation(dir, segName);
 
     if(!cleanName.isEmpty()){
         SaveImageToDisk(atriumCoarse, dir, cleanName);