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remove unused morphOperation argument to ExecuteSurf
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Delete superfluous test case (which only differed in the morphOperation from the first test case)
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@JostMigenda
JostMigenda committed Jul 10, 2024
1 parent 7de0a86 commit ba8542d
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Showing 8 changed files with 15 additions and 18 deletions.
2 changes: 1 addition & 1 deletion CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h
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Expand Up @@ -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, int iter = 1, 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);
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2 changes: 1 addition & 1 deletion CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp
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Expand Up @@ -93,7 +93,7 @@ QDialog* CemrgCommandLine::GetDialog() {
****************** Execute Plugin Specific Functions **********************
***************************************************************************/

QString CemrgCommandLine::ExecuteSurf(QString dir, QString segPath, QString morphOperation, int iter, float thresh, int blur, int smooth) {
QString CemrgCommandLine::ExecuteSurf(QString dir, QString segPath, int iter, float thresh, int blur, int smooth) {
MITK_INFO << "[ATTENTION] SURFACE CREATION: Surface -> Smooth";

// Load input image into memory
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11 changes: 4 additions & 7 deletions CemrgApp/Modules/CemrgAppModule/test/CemrgCommandLineTest.cpp
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Expand Up @@ -123,17 +123,15 @@ 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", 1, 0.5, 0, 10, "/surf_expected_1.vtk"},
{"sphere_shifted.nii", 1, 0.5, 0, 10, "/surf_expected_2.vtk"},
} };

for (size_t i = 0; i < surfData.size(); i++)
Expand All @@ -142,14 +140,13 @@ 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, iterations, threshold, blur, smoothness);
QVERIFY2(EqualFiles(surfOutput, dataPath + result), "The function output is different from the expected output!");
}

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Binary file removed CemrgApp/Modules/CemrgAppModule/test/Data/CommandLine/surf_expected_3.vtk
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6 changes: 3 additions & 3 deletions CemrgApp/Plugins/kcl.cemrgapp.atrialfibres/src/internal/AtrialFibresView.cpp
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Expand Up @@ -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_iter, uiMesh_th, uiMesh_bl, uiMesh_smth);
atrium->ProjectTagsOnExistingSurface(tagAtriumAuto, directory, tagName+".vtk");

MITK_INFO << "[AUTOMATIC_PIPELINE] Add the mesh to storage";
Expand Down Expand Up @@ -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_iter, uiMesh_th, uiMesh_bl, uiMesh_smth);

//Add the mesh to storage
std::string meshName = segNode->GetName() + "-Mesh";
Expand Down Expand Up @@ -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_iter, uiMesh_th, uiMesh_bl, uiMesh_smth);
atrium->ProjectTagsOnExistingSurface(pveins, directory, tagName+".vtk");

MITK_INFO << "Add the mesh to storage";
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2 changes: 1 addition & 1 deletion CemrgApp/Plugins/kcl.cemrgapp.mmcwplugin/src/internal/MmcwView.cpp
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Expand Up @@ -582,7 +582,7 @@ void MmcwView::CreateSurf() {
this->BusyCursorOn();
mitk::ProgressBar::GetInstance()->AddStepsToDo(3);
std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
QString output = cmd->ExecuteSurf(directory, path, "close", iter, th, blur, smth);
QString output = cmd->ExecuteSurf(directory, path, iter, th, blur, smth);
QMessageBox::information(NULL, "Attention", "Command Line Operations Finished!");
this->BusyCursorOff();

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2 changes: 1 addition & 1 deletion CemrgApp/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarClipperView.cpp
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Expand Up @@ -211,7 +211,7 @@ void AtrialScarClipperView::iniPreSurf() {
mitk::IOUtil::Save(image, path.toStdString());
mitk::ProgressBar::GetInstance()->AddStepsToDo(3);
std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
QString output = cmd->ExecuteSurf(directory, path, "close", iter, th, blur, smth);
QString output = cmd->ExecuteSurf(directory, path, iter, th, blur, smth);
QMessageBox::information(NULL, "Attention", "Command Line Operations Finished!");
this->BusyCursorOff();

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8 changes: 4 additions & 4 deletions CemrgApp/Plugins/kcl.cemrgapp.scar/src/internal/AtrialScarView.cpp
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Expand Up @@ -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, "close", 1, .5, 0, 10);
QString output1 = cmd->ExecuteSurf(direct, segCleanPath, 1, .5, 0, 10);
mitk::Surface::Pointer shell = mitk::IOUtil::Load<mitk::Surface>(output1.toStdString());
vtkSmartPointer<vtkDecimatePro> deci = vtkSmartPointer<vtkDecimatePro>::New();
deci->SetInputData(shell->GetVtkPolyData());
Expand Down Expand Up @@ -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"), "close", 1, .5, 0, 10);
QString output2 = cmd->ExecuteSurf(direct, (direct + "/PVeinsCroppedImage.nii"), 1, .5, 0, 10);
mitk::Surface::Pointer LAShell = mitk::IOUtil::Load<mitk::Surface>(output2.toStdString());

MITK_INFO << "[AUTOMATIC_ANALYSIS][9] Clip the mitral valve";
Expand Down Expand Up @@ -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", "close", 1, 0.5, 0, 10);
QString mviShellPath = cmd->ExecuteSurf(direct, "prodMVI.nii", 1, 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();
Expand Down Expand Up @@ -1197,7 +1197,7 @@ void AtrialScarView::CreateSurf() {
mitk::ProgressBar::GetInstance()->AddStepsToDo(3);
std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
cmd->SetUseDockerContainers(_useDockerInPlugin);
path = cmd->ExecuteSurf(directory, pathTemp, "close", iter, th, blur, smth);
path = cmd->ExecuteSurf(directory, pathTemp, iter, th, blur, smth);
QMessageBox::information(NULL, "Attention", "Command Line Operations Finished!");
this->BusyCursorOff();

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