Update dialog boxes after removing iter argument to ExecuteSurf

OpenHeartDevelopers · Jul 11, 2024 · 21870a6 · 21870a6
1 parent ba8542d
commit 21870a6
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Showing 11 changed files with 55 additions and 92 deletions.
diff --git a/CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h b/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, 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);

diff --git a/CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp b/CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp
@@ -93,7 +93,7 @@ QDialog* CemrgCommandLine::GetDialog() {
  ****************** Execute Plugin Specific Functions **********************
  ***************************************************************************/
 
-QString CemrgCommandLine::ExecuteSurf(QString dir, QString segPath, int iter, float thresh, int blur, int smooth) {
+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

diff --git a/CemrgApp/Modules/CemrgAppModule/test/CemrgCommandLineTest.cpp b/CemrgApp/Modules/CemrgAppModule/test/CemrgCommandLineTest.cpp
@@ -123,15 +123,14 @@ void TestCemrgCommandLine::cleanupTestCase() {
 
 void TestCemrgCommandLine::ExecuteSurf_data() {
     QTest::addColumn<QString>("segPath");
-    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>, 2> surfData { {
-        {"sphere_initial.nii", 1, 0.5, 0, 10, "/surf_expected_1.vtk"},
-        {"sphere_shifted.nii", 1, 0.5, 0, 10, "/surf_expected_2.vtk"},
+        {"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++)
@@ -140,13 +139,12 @@ void TestCemrgCommandLine::ExecuteSurf_data() {
 
 void TestCemrgCommandLine::ExecuteSurf() {
     QFETCH(QString, segPath);
-    QFETCH(int, iterations);
     QFETCH(float, threshold);
     QFETCH(int, blur);
     QFETCH(int, smoothness);
     QFETCH(QString, result);
 
-    QString surfOutput = cemrgCommandLine->ExecuteSurf(dataPath, segPath, 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!");
 }
 

diff --git a/CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresView.cpp b/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"), 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"), 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"), 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;

diff --git a/CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresView.h b/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;

diff --git a/CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresViewUIMeshing.ui b/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">

diff --git a/CemrgApp/Plugins/kcl.cemrgapp.mmcwplugin/src/internal/MmcwView.cpp b/CemrgApp/Plugins/kcl.cemrgapp.mmcwplugin/src/internal/MmcwView.cpp
@@ -564,25 +564,23 @@ void MmcwView::CreateSurf() {
     //Act on dialog return code
     if (dialogCode == QDialog::Accepted) {
 
-        bool ok1, ok2, ok3, ok4;
-        int iter = m_UIMeshing.lineEdit_1->text().toInt(&ok1);
-        float th = m_UIMeshing.lineEdit_2->text().toFloat(&ok2);
-        int blur = m_UIMeshing.lineEdit_3->text().toInt(&ok3);
-        int smth = m_UIMeshing.lineEdit_4->text().toInt(&ok4);
+        bool ok1, ok2, ok3;
+        float th = m_UIMeshing.lineEdit_1->text().toFloat(&ok1);
+        int blur = m_UIMeshing.lineEdit_2->text().toInt(&ok2);
+        int smth = m_UIMeshing.lineEdit_3->text().toInt(&ok3);
 
         //Set default values
-        if (!ok1 || !ok2 || !ok3 || !ok4)
+        if (!ok1 || !ok2 || !ok3)
             QMessageBox::warning(NULL, "Attention", "Reverting to default parameters!");
-        if (!ok1) iter = 1;
-        if (!ok2) th = 0.5;
-        if (!ok3) blur = 0;
-        if (!ok4) smth = 10;
+        if (!ok1) th = 0.5;
+        if (!ok2) blur = 0;
+        if (!ok3) smth = 10;
         //_if
 
         this->BusyCursorOn();
         mitk::ProgressBar::GetInstance()->AddStepsToDo(3);
         std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
-        QString output = cmd->ExecuteSurf(directory, path, iter, th, blur, smth);
+        QString output = cmd->ExecuteSurf(directory, path, th, blur, smth);
         QMessageBox::information(NULL, "Attention", "Command Line Operations Finished!");
         this->BusyCursorOff();
 

diff --git a/CemrgApp/Plugins/kcl.cemrgapp.mmcwplugin/src/internal/MmcwViewUIMeshing.ui b/CemrgApp/Plugins/kcl.cemrgapp.mmcwplugin/src/internal/MmcwViewUIMeshing.ui
@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>216</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">
@@ -50,30 +50,20 @@
      <property name="text">
       <string/>
      </property>
-     <property name="placeholderText">
-      <string>Iteration (default = 1)</string>
-     </property>
-    </widget>
-   </item>
-   <item>
-    <widget class="QLineEdit" name="lineEdit_2">
      <property name="placeholderText">
       <string>Threshold (default = 0.5)</string>
      </property>
     </widget>
    </item>
    <item>
-    <widget class="QLineEdit" name="lineEdit_3">
+    <widget class="QLineEdit" name="lineEdit_2">
      <property name="placeholderText">
       <string>Blur (default = 0)</string>
      </property>
     </widget>
    </item>
    <item>
-    <widget class="QLineEdit" name="lineEdit_4">
-     <property name="text">
-      <string/>
-     </property>
+    <widget class="QLineEdit" name="lineEdit_3">
      <property name="placeholderText">
       <string>Smooth (default = 10)</string>
      </property>

diff --git a/CemrgApp/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarClipperView.cpp b/CemrgApp/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarClipperView.cpp
@@ -190,28 +190,27 @@ void AtrialScarClipperView::iniPreSurf() {
             //Act on dialog return code
             if (dialogCode == QDialog::Accepted) {
 
-                bool ok1, ok2, ok3, ok4;
-                int iter = m_UIMeshing.lineEdit_1->text().toInt(&ok1);
-                float th = m_UIMeshing.lineEdit_2->text().toFloat(&ok2);
-                int blur = m_UIMeshing.lineEdit_3->text().toInt(&ok3);
-                int smth = m_UIMeshing.lineEdit_4->text().toInt(&ok4);
+                bool ok1, ok2, ok3;
+                // TODO: iter parameter is no longer used; remove from dialog box
+                float th = m_UIMeshing.lineEdit_1->text().toFloat(&ok1);
+                int blur = m_UIMeshing.lineEdit_2->text().toInt(&ok2);
+                int smth = m_UIMeshing.lineEdit_3->text().toInt(&ok3);
                 float ds = 0.1;
 
                 //Set default values
-                if (!ok1 || !ok2 || !ok3 || !ok4)
+                if (!ok1 || !ok2 || !ok3)
                     QMessageBox::warning(NULL, "Attention", "Reverting to default parameters!");
-                if (!ok1) iter = 1;
-                if (!ok2) th = 0.5;
-                if (!ok3) blur = 0;
-                if (!ok4) smth = 10;
+                if (!ok1) th = 0.5;
+                if (!ok2) blur = 0;
+                if (!ok3) smth = 10;
                 //_if
 
                 this->BusyCursorOn();
                 path = directory + "/temp.nii";
                 mitk::IOUtil::Save(image, path.toStdString());
                 mitk::ProgressBar::GetInstance()->AddStepsToDo(3);
                 std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
-                QString output = cmd->ExecuteSurf(directory, path, iter, th, blur, smth);
+                QString output = cmd->ExecuteSurf(directory, path, th, blur, smth);
                 QMessageBox::information(NULL, "Attention", "Command Line Operations Finished!");
                 this->BusyCursorOff();
 

diff --git a/CemrgApp/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarView.cpp b/CemrgApp/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarView.cpp
@@ -540,7 +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, 1, .5, 0, 10);
+            QString output1 = cmd->ExecuteSurf(direct, segCleanPath, .5, 0, 10);
             mitk::Surface::Pointer shell = mitk::IOUtil::Load<mitk::Surface>(output1.toStdString());
             vtkSmartPointer<vtkDecimatePro> deci = vtkSmartPointer<vtkDecimatePro>::New();
             deci->SetInputData(shell->GetVtkPolyData());
@@ -662,7 +662,7 @@ 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"), 1, .5, 0, 10);
+            QString output2 = cmd->ExecuteSurf(direct, (direct + "/PVeinsCroppedImage.nii"), .5, 0, 10);
             mitk::Surface::Pointer LAShell = mitk::IOUtil::Load<mitk::Surface>(output2.toStdString());
 
             MITK_INFO << "[AUTOMATIC_ANALYSIS][9] Clip the mitral valve";
@@ -693,7 +693,7 @@ void AtrialScarView::AutomaticAnalysis() {
             mitk::IOUtil::Save(mitk::ImportItkImage(mvImage), (direct + "/prodMVI.nii").toStdString());
 
             // Make vtk of prodMVI
-            QString mviShellPath = cmd->ExecuteSurf(direct, "prodMVI.nii", 1, 0.5, 0, 10);
+            QString mviShellPath = cmd->ExecuteSurf(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();
@@ -1176,19 +1176,17 @@ void AtrialScarView::CreateSurf() {
             //Act on dialog return code
             if (dialogCode == QDialog::Accepted) {
 
-                bool ok1, ok2, ok3, ok4;
-                int iter = m_UIMeshing.lineEdit_1->text().toInt(&ok1);
-                float th = m_UIMeshing.lineEdit_2->text().toFloat(&ok2);
-                int blur = m_UIMeshing.lineEdit_3->text().toInt(&ok3);
-                int smth = m_UIMeshing.lineEdit_4->text().toInt(&ok4);
+                bool ok1, ok2, ok3;
+                float th = m_UIMeshing.lineEdit_1->text().toFloat(&ok1);
+                int blur = m_UIMeshing.lineEdit_2->text().toInt(&ok2);
+                int smth = m_UIMeshing.lineEdit_3->text().toInt(&ok3);
 
                 //Set default values
-                if (!ok1 || !ok2 || !ok3 || !ok4)
+                if (!ok1 || !ok2 || !ok3)
                     QMessageBox::warning(NULL, "Attention", "Reverting to default parameters!");
-                if (!ok1) iter = 1;
-                if (!ok2) th = 0.5;
-                if (!ok3) blur = 0;
-                if (!ok4) smth = 10;
+                if (!ok1) th = 0.5;
+                if (!ok2) blur = 0;
+                if (!ok3) smth = 10;
                 //_if
 
                 this->BusyCursorOn();
@@ -1197,7 +1195,7 @@ void AtrialScarView::CreateSurf() {
                 mitk::ProgressBar::GetInstance()->AddStepsToDo(3);
                 std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
                 cmd->SetUseDockerContainers(_useDockerInPlugin);
-                path = cmd->ExecuteSurf(directory, pathTemp, iter, th, blur, smth);
+                path = cmd->ExecuteSurf(directory, pathTemp, th, blur, smth);
                 QMessageBox::information(NULL, "Attention", "Command Line Operations Finished!");
                 this->BusyCursorOff();