Merge pull request #2 from CemrgDevelopers/feature/plugin/atrialfibres

Feature/plugin/atrialfibres

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/include/CemrgCommandLine.h

@@ -97,7 +97,7 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommandLine: public QObject {
     inline void SetDockerImage(QString dockerimage) {_dockerimage = dockerimage;};
     inline QString GetDockerImage() {return _dockerimage;};
     inline void SetDockerImageOpenCarp(){_dockerimage = "docker.opencarp.org/opencarp/opencarp:latest";};
-    inline void SetDockerImageUac(){_dockerimage = "cemrg/uac:v1.1";};// modify when docker image has been pushed to hub
+    inline void SetDockerImageUac(){_dockerimage = "cemrg/uac:latest";};// modify when docker image has been pushed to hub
     QStringList GetDockerArguments(QString volume, QString dockerexe = "");
     QStringList GetOpenCarpDockerDefaultArguments(QString volume);
 

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);

CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresView.cpp

@@ -1185,7 +1185,7 @@ void AtrialFibresView::UacCalculationRough(){
         outputFiles << "LSbc1.vtx" << "LSbc2.vtx";
         outputFiles << "PAbc1.vtx" << "PAbc2.vtx";
 
-        if (!IsUacOutputCorrect(directory, outputFiles)){
+        if (!IsOutputFileCorrect(directory, outputFiles)){
             MITK_INFO << "TIMELOG|UacCalculation_Stage1| End (FAIL)";
             return;
         }
@@ -1203,7 +1203,7 @@ void AtrialFibresView::UacCalculationRough(){
         paLapSolve = cmd->OpenCarpDocker(directory, pa_par, "PA_UAC_N2");
         MITK_INFO << "TIMELOG|UacCalculation_Stage1| openCARP end";
 
-        bool uacOutputSuccess = IsUacOutputCorrect(directory, outputFiles);
+        bool uacOutputSuccess = IsOutputFileCorrect(directory, outputFiles);
         MITK_ERROR(!uacOutputSuccess) << ("Problem with " + uaccmd).toStdString();
         std::string msg = "UAC Calculation - Stage 1 ";
         msg += (uacOutputSuccess) ? "successful" : "failed";
@@ -1271,7 +1271,7 @@ void AtrialFibresView::UacCalculationRefined(){
         uacOutput = cmd->DockerUniversalAtrialCoordinates(directory, uaccmd, fibreAtlas, uacMeshName, uiLabels, path2landmarks);
         MITK_INFO << "TIMELOG|UacCalculation_Stage2| UAC 2.1 - End";
 
-        if (!IsUacOutputCorrect(directory, outputFiles)){
+        if (!IsOutputFileCorrect(directory, outputFiles)){
             MITK_INFO << "TIMELOG|UacCalculation_Stage2| End (FAILED)";
             return;
         }
@@ -1308,7 +1308,7 @@ void AtrialFibresView::UacCalculationRefined(){
         uacOutput = cmd->DockerUniversalAtrialCoordinates(directory, uaccmd, fibreAtlas, uacMeshName, uiLabels, "");
         MITK_INFO << "TIMELOG|UacCalculation_Stage2| UAC 2.2 - End";
 
-        bool uacOutputSuccess = IsUacOutputCorrect(directory, outputFiles);
+        bool uacOutputSuccess = IsOutputFileCorrect(directory, outputFiles);
         MITK_ERROR(!uacOutputSuccess) << ("Problem with " + uaccmd).toStdString();
         std::string msg = "UAC Calculation - Stage 2 ";
         msg += (uacOutputSuccess) ? "successful" : "failed";
@@ -1355,7 +1355,7 @@ void AtrialFibresView::UacFibreMapping(){
     outputFiles << "Labelled_Coords_2D_Rescaling_v3_C.vtk";
     outputFiles << "Labelled_Coords_2D_Rescaling_v3_C.elem";
     outputFiles << "Labelled_Coords_2D_Rescaling_v3_C.pts";
-    if (!IsUacOutputCorrect(directory, outputFiles)) return;
+    if (!IsOutputFileCorrect(directory, outputFiles)) return;
 
     std::cout << "[uac_fibreField]" << uac_fibreField.toStdString() << '\n';
     std::cout << "[output]" << uac_fibreFieldOutputName.toStdString() << '\n';
@@ -1479,7 +1479,7 @@ void AtrialFibresView::UacCalculationVerifyLabels(){
     MITK_INFO << "TIMELOG|VerifyLabels| End";
 }
 
-bool AtrialFibresView::IsUacOutputCorrect(QString dir, QStringList filenames){
+bool AtrialFibresView::IsOutputFileCorrect(QString dir, QStringList filenames){
     bool success = true;
     bool okSingleTest;
     int countfails = 0;
@@ -2295,7 +2295,7 @@ QString AtrialFibresView::UserIncludeLgeAnalysis(QString segPath, ImageType::Poi
 
 void AtrialFibresView::SetLgeAnalysis(bool b){
     analysisOnLge = b;
-    m_Controls.button_z_scar->setEnabled(b);
+    // m_Controls.button_z_scar->setEnabled(b);
 }
 
 void AtrialFibresView::CheckLoadedMeshQuality(){

CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresView.h

@@ -110,7 +110,7 @@ class AtrialFibresView : public QmitkAbstractView {
     inline std::string StdStringPath(QString fnameExt=""){return (Path(fnameExt).toStdString());};
 
     QString LandmarkFilesCreated(QString defaultName, QString type);
-    bool IsUacOutputCorrect(QString dir, QStringList filenames);
+    bool IsOutputFileCorrect(QString dir, QStringList filenames);
 
 protected slots:
 

CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresViewControls.ui

@@ -26,7 +26,7 @@
       <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
      </property>
      <property name="text">
-      <string>Atrial Fibress Pipeline</string>
+      <string>Atrial Fibres Pipeline</string>
      </property>
      <property name="alignment">
       <set>Qt::AlignCenter</set>

CemrgApp/Plugins/kcl.cemrgapp.mainapp/src/internal/QmitkCemrgAppCommonTools.cpp

@@ -301,7 +301,7 @@ void QmitkCemrgAppCommonTools::BinariseImage(){
     }
 
     QFileInfo fi(pathToImage);
-    QString outPath = fi.absolutePath() + "/" + fi.baseName() + "-bin" + fi.suffix();
+    QString outPath = fi.absolutePath() + "/" + fi.baseName() + "-bin." + fi.suffix();
 
     mitk::Image::Pointer im = mitk::IOUtil::Load<mitk::Image>(pathToImage.toStdString());
     mitk::Image::Pointer outIm = CemrgCommonUtils::ReturnBinarised(im);