Replace MIRTK: Surface creation

CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h

@@ -49,7 +49,7 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommandLine: public QObject {
     QDialog* GetDialog();
 
     //Execute Plugin Specific Functions
-    QString ExecuteSurf(QString dir, QString segPath, QString morphOperation = "close", int iter = 1, float th = 0.5, int blur = 0, int smth = 10);
+    QString ExecuteSurf(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);
@@ -58,9 +58,6 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommandLine: public QObject {
     void ExecuteSimpleTranslation(QString dir, QString sourceMeshP, QString targetMeshP, QString transformFileName = "init.dof", bool transformThePoints = true);
 
     //Execute MIRTK Specific Functions
-    QString ExecuteMorphologicalOperation(QString operation, QString dir, QString segPath, QString outputPath = "segmentation.s.nii", int iter = 1);
-    QString ExecuteExtractSurface(QString dir, QString segPath, QString outputPath = "segmentation.vtk", float th = 0.5, int blur = 0);
-    QString ExecuteSmoothSurface(QString dir, QString segPath, QString outputPath, int smth = 10);
     void ExecuteTransformationOnPoints(QString dir, QString meshFullPath, QString outputMeshFullPath, QString transformFileFullPath, double applyingIniTime = -100);
     void ExecuteResamplingOnNifti(QString niiFullPath, QString outputNiiFullPath, int isovalue);
 

CemrgApp/Modules/CemrgAppModule/include/CemrgCommonUtils.h

@@ -71,7 +71,7 @@ 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 mitk::Surface::Pointer ExtractSurfaceFromSegmentation(mitk::Image::Pointer image, double thresh=0.5, double blur=0.8, double smoothIterations=3, double decimation=0.0);
     static mitk::Surface::Pointer ClipWithSphere(mitk::Surface::Pointer surface, double x_c, double y_c, double z_c, double radius, QString saveToPath="");
     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");

CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp

@@ -44,6 +44,7 @@ PURPOSE.  See the above copyright notices for more information.
 #include <chrono>
 #include <sys/stat.h>
 #include "CemrgCommandLine.h"
+#include "CemrgCommonUtils.h"
 
 CemrgCommandLine::CemrgCommandLine() {
 
@@ -92,32 +93,22 @@ QDialog* CemrgCommandLine::GetDialog() {
  ****************** Execute Plugin Specific Functions **********************
  ***************************************************************************/
 
-QString CemrgCommandLine::ExecuteSurf(QString dir, QString segPath, QString morphOperation, int iter, float th, int blur, int smth) {
-
-    MITK_INFO << "[ATTENTION] SURFACE CREATION: Close -> Surface -> Smooth";
-
-    QString closeOutputPath, surfOutputPath;
-    QString outAbsolutePath = "ERROR_IN_PROCESSING";
-    closeOutputPath = ExecuteMorphologicalOperation(morphOperation, dir, segPath, "segmentation.s.nii", iter);
+QString CemrgCommandLine::ExecuteSurf(QString dir, QString segPath, float thresh, int blur, int smooth) {
+    MITK_INFO << "[ATTENTION] SURFACE CREATION: Surface -> Smooth";
 
+    // Load input image into memory
+    QString inputPath = segPath.contains(dir) ? segPath : dir + "/" + segPath;
     mitk::ProgressBar::GetInstance()->Progress();
-    if (QString::compare(closeOutputPath, "ERROR_IN_PROCESSING")!=0) {
-
-        surfOutputPath = ExecuteExtractSurface(dir, closeOutputPath, "segmentation.vtk", th, blur);
-        mitk::ProgressBar::GetInstance()->Progress();
+    mitk::Image::Pointer inputImage = mitk::IOUtil::Load<mitk::Image>(inputPath.toStdString());
 
-        if (QString::compare(surfOutputPath, "ERROR_IN_PROCESSING")!=0) {
+    // TODO: check semantics of thresh/blur/smooth are identical
+    mitk::Surface::Pointer smoothedSurface = CemrgCommonUtils::ExtractSurfaceFromSegmentation(inputImage, (double)thresh, (double)blur, (double)smooth);
+    CemrgCommonUtils::FlipXYPlane(smoothedSurface, "", "");
 
-            outAbsolutePath = ExecuteSmoothSurface(dir, surfOutputPath, surfOutputPath, smth);
-            remove((dir + "/segmentation.s.nii").toStdString().c_str());
-            mitk::ProgressBar::GetInstance()->Progress();
-
-        } else {
-            mitk::ProgressBar::GetInstance()->Progress();
-        }//_if
-    } else {
-        mitk::ProgressBar::GetInstance()->Progress(2);
-    }//_if
+    // 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;
 }
@@ -364,151 +355,6 @@ void CemrgCommandLine::ExecuteSimpleTranslation(QString dir, QString sourceMeshP
  ****************** Execute MIRTK Specific Functions **********************
  ***************************************************************************/
 
-QString CemrgCommandLine::ExecuteMorphologicalOperation(QString operation, QString dir, QString segPath, QString outputPath, int iter) {
-
-    MITK_INFO << "[ATTENTION] Attempting Pointset transformation.";
-
-    QString commandName;
-
-    if (QString::compare(operation, "dilate", Qt::CaseInsensitive)==0) {
-        commandName = "dilate-image";
-    } else if (QString::compare(operation, "erode", Qt::CaseInsensitive)==0) {
-        commandName = "erode-image";
-    } else if (QString::compare(operation, "open", Qt::CaseInsensitive)==0) {
-        commandName = "open-image";
-    } else if (QString::compare(operation, "close", Qt::CaseInsensitive)==0) {
-        commandName = "close-image";
-    } else {
-        MITK_ERROR << ("Morphological operation: " + operation + " misspelled or not supported.").toStdString();
-        return "ERROR_IN_PROCESSING";
-    }
-
-    QString inputImgFullPath, outAbsolutePath;
-    QString prodPath = dir + "/";
-
-    inputImgFullPath = segPath.contains(dir, Qt::CaseSensitive) ? segPath : prodPath + segPath;
-    outAbsolutePath = outputPath.contains(dir, Qt::CaseSensitive) ? outputPath : prodPath + outputPath;
-
-    MITK_INFO << ("[...] OPERATION: " + operation).toStdString();
-    MITK_INFO << ("[...] INPUT IMAGE: " + inputImgFullPath).toStdString();
-    MITK_INFO << ("[...] OUTPUT IMAGE: " + outAbsolutePath).toStdString();
-
-    MITK_INFO << "Using static MIRTK libraries.";
-    QString executablePath = QCoreApplication::applicationDirPath() + "/MLib";
-    QString executableName = executablePath + "/" + commandName;
-    QDir apathd(executablePath);
-    QStringList arguments;
-
-    if (apathd.exists()) {
-
-        process->setWorkingDirectory(executablePath);
-        arguments << inputImgFullPath;
-        arguments << outAbsolutePath;
-        arguments << "-iterations" << QString::number(iter);
-
-    } else {
-        QMessageBox::warning(NULL, "Please check the LOG", "MIRTK libraries not found");
-        MITK_WARN << "MIRTK libraries not found. Please make sure the MLib folder is inside the directory;\n\t"+
-                        mitk::IOUtil::GetProgramPath();
-    }//_if
-
-    bool successful = ExecuteCommand(executableName, arguments, outAbsolutePath);
-    if (!successful) {
-        MITK_WARN << "Local MIRTK libraries did not produce a good outcome.";
-        return "ERROR_IN_PROCESSING";
-    } else {
-        return outAbsolutePath;
-    }
-}
-
-QString CemrgCommandLine::ExecuteExtractSurface(QString dir, QString segPath, QString outputPath,float th, int blur) {
-
-    MITK_INFO << "[ATTENTION] Attempting Surface extraction.";
-
-    QString commandName = "extract-surface";
-    QString inputImgFullPath, outAbsolutePath;
-    QString prodPath = dir + "/";
-
-    inputImgFullPath = segPath.contains(dir, Qt::CaseSensitive) ? segPath : prodPath + segPath;
-    outAbsolutePath = outputPath.contains(dir, Qt::CaseSensitive) ? outputPath : prodPath + outputPath;
-
-    MITK_INFO << ("[...] INPUT IMAGE: " + inputImgFullPath).toStdString();
-    MITK_INFO << ("[...] OUTPUT MESH: " + outAbsolutePath).toStdString();
-
-    MITK_INFO << "Using static MIRTK libraries.";
-    QString executablePath = QCoreApplication::applicationDirPath() + "/MLib";
-    QString executableName = executablePath + "/" + commandName;
-    QDir apathd(executablePath);
-    QStringList arguments;
-
-    if (apathd.exists()) {
-
-        process->setWorkingDirectory(executablePath);
-        arguments << inputImgFullPath;
-        arguments << outAbsolutePath;
-        arguments << "-isovalue" << QString::number(th);
-        arguments << "-blur" << QString::number(blur);
-        arguments << "-ascii";
-        arguments << "-verbose" << "3";
-
-    } else {
-        QMessageBox::warning(NULL, "Please check the LOG", "MIRTK libraries not found");
-        MITK_WARN << "MIRTK libraries not found. Please make sure the MLib folder is inside the directory;\n\t"+
-                        mitk::IOUtil::GetProgramPath();
-    }//_if
-
-    bool successful = ExecuteCommand(executableName, arguments, outAbsolutePath);
-    if (!successful) {
-        MITK_WARN << "Local MIRTK libraries did not produce a good outcome.";
-        return "ERROR_IN_PROCESSING";
-    } else {
-        return outAbsolutePath;
-    }
-}
-
-QString CemrgCommandLine::ExecuteSmoothSurface(QString dir, QString segPath, QString outputPath, int smth) {
-
-    MITK_INFO << "[ATTENTION] Attempting Surface extraction.";
-
-    QString commandName = "smooth-surface";
-    QString inputMeshFullPath, outAbsolutePath;
-    QString prodPath = dir + "/";
-
-    inputMeshFullPath = segPath.contains(dir, Qt::CaseSensitive) ? segPath : prodPath + segPath;
-    outAbsolutePath = outputPath.contains(dir, Qt::CaseSensitive) ? outputPath : prodPath + outputPath;
-
-    MITK_INFO << ("[...] INPUT IMAGE: " + inputMeshFullPath).toStdString();
-    MITK_INFO << ("[...] OUTPUT MESH: " + outAbsolutePath).toStdString();
-
-    MITK_INFO << "Using static MIRTK libraries.";
-    QString executablePath = QCoreApplication::applicationDirPath() + "/MLib";
-    QString executableName = executablePath + "/" + commandName;
-    QDir apathd(executablePath);
-    QStringList arguments;
-
-    if (apathd.exists()) {
-
-        process->setWorkingDirectory(executablePath);
-        arguments << inputMeshFullPath;
-        arguments << outAbsolutePath;
-        arguments << "-iterations" << QString::number(smth);
-        arguments << "-verbose" << "3";
-
-    } else {
-        QMessageBox::warning(NULL, "Please check the LOG", "MIRTK libraries not found");
-        MITK_WARN << "MIRTK libraries not found. Please make sure the MLib folder is inside the directory;\n\t"+
-                        mitk::IOUtil::GetProgramPath();
-    }//_if
-
-    bool successful = ExecuteCommand(executableName, arguments, outAbsolutePath);
-    if (!successful) {
-        MITK_WARN << "Local MIRTK libraries did not produce a good outcome.";
-        return "ERROR_IN_PROCESSING";
-    } else {
-        return outAbsolutePath;
-    }
-}
-
 void CemrgCommandLine::ExecuteTransformationOnPoints(QString dir, QString meshFullPath, QString outputMeshFullPath, QString transformFileFullPath, double applyingIniTime) {
 
     MITK_INFO << "[ATTENTION] Attempting Pointset transformation.";

CemrgApp/Modules/CemrgAppModule/test/CemrgCommandLineTest.cpp

@@ -123,17 +123,14 @@ void TestCemrgCommandLine::cleanupTestCase() {
 
 void TestCemrgCommandLine::ExecuteSurf_data() {
     QTest::addColumn<QString>("segPath");
-    QTest::addColumn<QString>("morphOperation");
-    QTest::addColumn<int>("iterations");
     QTest::addColumn<float>("threshold");
     QTest::addColumn<int>("blur");
     QTest::addColumn<int>("smoothness");
     QTest::addColumn<QString>("result");
 
-    const array<tuple<QString, QString, int, float, int, int, QString>, 3> surfData { {
-        {"sphere_initial.nii", "close", 1, 0.5, 0, 10, "/surf_expected_1.vtk"},
-        {"sphere_shifted.nii", "dilate", 1, 0.5, 0, 10, "/surf_expected_2.vtk"},
-        {"sphere_initial.nii", "erode", 1, 0.5, 0, 10, "/surf_expected_3.vtk"}
+    const array<tuple<QString, QString, int, float, int, int, QString>, 2> surfData { {
+        {"sphere_initial.nii", 0.5, 0, 10, "/surf_expected_1.vtk"},
+        {"sphere_shifted.nii", 0.5, 0, 10, "/surf_expected_2.vtk"},
     } };
 
     for (size_t i = 0; i < surfData.size(); i++)
@@ -142,14 +139,12 @@ void TestCemrgCommandLine::ExecuteSurf_data() {
 
 void TestCemrgCommandLine::ExecuteSurf() {
     QFETCH(QString, segPath);
-    QFETCH(QString, morphOperation);
-    QFETCH(int, iterations);
     QFETCH(float, threshold);
     QFETCH(int, blur);
     QFETCH(int, smoothness);
     QFETCH(QString, result);
 
-    QString surfOutput = cemrgCommandLine->ExecuteSurf(dataPath, segPath, morphOperation, iterations, threshold, blur, smoothness);
+    QString surfOutput = cemrgCommandLine->ExecuteSurf(dataPath, segPath, threshold, blur, smoothness);
     QVERIFY2(EqualFiles(surfOutput, dataPath + result), "The function output is different from the expected output!");
 }
 

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

@@ -472,7 +472,7 @@ void AtrialFibresView::AutomaticAnalysis(){
         std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
         cmd->SetUseDockerContainers(true);
 
-        cmd->ExecuteSurf(directory, Path("prodClean.nii"), "close", uiMesh_iter, uiMesh_th, uiMesh_bl, uiMesh_smth);
+        cmd->ExecuteSurf(directory, Path("prodClean.nii"), uiMesh_th, uiMesh_bl, uiMesh_smth);
         atrium->ProjectTagsOnExistingSurface(tagAtriumAuto, directory, tagName+".vtk");
 
         MITK_INFO << "[AUTOMATIC_PIPELINE] Add the mesh to storage";
@@ -673,7 +673,7 @@ void AtrialFibresView::IdentifyPV(){
                     std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
                     cmd->SetUseDockerContainers(true);
 
-                    cmd->ExecuteSurf(directory, Path("prodClean.nii"), "close", uiMesh_iter, uiMesh_th, uiMesh_bl, uiMesh_smth);
+                    cmd->ExecuteSurf(directory, Path("prodClean.nii"), uiMesh_th, uiMesh_bl, uiMesh_smth);
 
                     //Add the mesh to storage
                     std::string meshName = segNode->GetName() + "-Mesh";
@@ -728,7 +728,7 @@ void AtrialFibresView::CreateLabelledMesh(){
         std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
         cmd->SetUseDockerContainers(true);
 
-        cmd->ExecuteSurf(directory, Path("prodClean.nii"), "close", uiMesh_iter, uiMesh_th, uiMesh_bl, uiMesh_smth);
+        cmd->ExecuteSurf(directory, Path("prodClean.nii"), uiMesh_th, uiMesh_bl, uiMesh_smth);
         atrium->ProjectTagsOnExistingSurface(pveins, directory, tagName+".vtk");
 
         MITK_INFO << "Add the mesh to storage";
@@ -1996,7 +1996,6 @@ bool AtrialFibresView::GetUserMeshingInputs(){
 
     if(userHasSetMeshingParams){
         QString msg = "The parameters have been set already, change them?\n";
-        msg += "close iter= " + QString::number(uiMesh_iter) + '\n';
         msg += "threshold= " + QString::number(uiMesh_th) + '\n';
         msg += "blur= " + QString::number(uiMesh_bl) + '\n';
         msg += "smooth iter= " + QString::number(uiMesh_smth);
@@ -2017,19 +2016,17 @@ bool AtrialFibresView::GetUserMeshingInputs(){
         //Act on dialog return code
         if (dialogCode == QDialog::Accepted) {
 
-            bool ok1, ok2, ok3, ok4;
+            bool ok1, ok2, ok3;
             uiMesh_th= m_UIMeshing.lineEdit_1->text().toDouble(&ok1);
             uiMesh_bl= m_UIMeshing.lineEdit_2->text().toDouble(&ok2);
             uiMesh_smth= m_UIMeshing.lineEdit_3->text().toDouble(&ok3);
-            uiMesh_iter= m_UIMeshing.lineEdit_4->text().toDouble(&ok4);
 
             //Set default values
-            if (!ok1 || !ok2 || !ok3 || !ok4)
+            if (!ok1 || !ok2 || !ok3)
             QMessageBox::warning(NULL, "Attention", "Reverting to default parameters!");
             if (!ok1) uiMesh_th=0.5;
             if (!ok2) uiMesh_bl=0.0;
             if (!ok3) uiMesh_smth=10;
-            if (!ok4) uiMesh_iter=0;
 
             inputs->deleteLater();
             userInputAccepted=true;

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

@@ -173,7 +173,7 @@ protected slots:
     bool automaticPipeline, analysisOnLge, resurfaceMesh, userHasSetMeshingParams;
 
     // user-defined parameters
-    double uiMesh_th, uiMesh_bl, uiMesh_smth, uiMesh_iter;
+    double uiMesh_th, uiMesh_bl, uiMesh_smth;
     double uiRemesh_max, uiRemesh_avrg, uiRemesh_min, uiRemesh_surfcorr;
     bool uiRemesh_isscalar, uiRemesh_extractParts, uiRemesh_cleanmesh;
     int uiScar_minStep, uiScar_maxStep, uiScar_projectionMethod, uiScar_thresholdMethod, uiFormat_scale;

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

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>222</width>
-    <height>196</height>
+    <height>160</height>
    </rect>
   </property>
   <property name="sizePolicy">
@@ -19,13 +19,13 @@
   <property name="minimumSize">
    <size>
     <width>0</width>
-    <height>196</height>
+    <height>160</height>
    </size>
   </property>
   <property name="maximumSize">
    <size>
     <width>16777215</width>
-    <height>196</height>
+    <height>160</height>
    </size>
   </property>
   <property name="windowTitle">
@@ -45,13 +45,6 @@
      </property>
     </widget>
    </item>
-   <item>
-    <widget class="QLineEdit" name="lineEdit_4">
-     <property name="placeholderText">
-      <string>'Close' iterations (default=0)</string>
-     </property>
-    </widget>
-   </item>
    <item>
     <widget class="QLineEdit" name="lineEdit_1">
      <property name="placeholderText">