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added UAC stage 1 and 2, with issues
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@sagebei
sagebei committed Sep 6, 2024
1 parent 383a41e commit e883956
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Showing 5 changed files with 227 additions and 4 deletions.
3 changes: 3 additions & 0 deletions CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h
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Expand Up @@ -112,6 +112,9 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommandLine: public QObject {

QString DockerCctaMultilabelSegmentation(QString dir, QString path_to_f, bool saveas_nifti);

// TODO: added a function to run the afmotion image
void DockerAtrialStrainMotion(QString dir, QString function);

protected slots:

void UpdateStdText();
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40 changes: 36 additions & 4 deletions CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -786,20 +786,25 @@ QString CemrgCommandLine::DockerUacMainMode(QString dir, QString stage, QString
arguments << "--noraa";
}

arguments << QString::number(scale);
arguments << "--scale" << QString::number(scale);

QStringList outputs;
if (stage.compare("1")) {

if (stage.compare("1") == 0) {
MITK_INFO << "------------------------------Stage 1-------------------------------";
outputs << "LSbc1.vtx" << "LSbc2.vtx" << "PAbc1.vtx" << "PAbc2.vtx";

} else if (stage.compare("2a")){
} else if (stage.compare("2a") == 0){
MITK_INFO << "------------------------------Stage 2a-------------------------------";
outputs << "AnteriorMesh.elem" << "AnteriorMesh.pts" << "PosteriorMesh.elem" << "PosteriorMesh.pts";

} else if (stage.compare("2b")){
} else if (stage.compare("2b") == 0){
MITK_INFO << "------------------------------Stage 2b-------------------------------";
outputs << "Labelled_Coords_2D_Rescaling_v3_C.elem" << "Labelled_Coords_2D_Rescaling_v3_C.pts";
}

QString outPath = home.absolutePath() + "/" + outputs.at(0);
MITK_INFO << "outPath: " << outPath.toStdString();
bool successful = ExecuteCommand(executableName, arguments, outPath);

if(successful){
Expand Down Expand Up @@ -1443,3 +1448,30 @@ QString CemrgCommandLine::DockerCctaMultilabelSegmentation(QString dir, QString
}
return res;
}


void CemrgCommandLine::DockerAtrialStrainMotion(QString dir, QString function) {
// docker run --rm --volume=./UAC_CT:/data/UAC_CT afmotion autoLM
SetDockerImage("afmotion");
QString executablePath = "";
#if defined(__APPLE__)
executablePath = "/usr/local/bin/";
#endif
QString executableName = executablePath + "docker";

QStringList arguments;
arguments << "run" << "--rm";
arguments << "--volume="+dir+":/data/UAC_CT/";
arguments << "afmotion";
arguments << function;

ExecuteCommand(executableName, arguments, "", false);
/***
if (successful) {
MITK_INFO << "Successful " << function.toStdString();
} else {
MITK_WARN << "Unsuccessful " << function.toStdString();
}
***/

}
163 changes: 163 additions & 0 deletions CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.cpp
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Expand Up @@ -157,6 +157,15 @@ void AtrialStrainMotionView::CreateQtPartControl(QWidget *parent)
// 10. Mesh Improvement
connect(m_Controls.btn_mesh_improvement, SIGNAL(clicked()), this, SLOT(MeshImprovement()));
m_Controls.btn_mesh_improvement->setStyleSheet("Text-align:left");
// 11. Auto Landmark
connect(m_Controls.autoLM, SIGNAL(clicked()), this, SLOT(AutoLandMark()));
m_Controls.autoLM->setStyleSheet("Text-align:left");
// 12. UAC Stage 1
connect(m_Controls.uac_stage_1, SIGNAL(clicked()), this, SLOT(UAC_Stage1()));
m_Controls.uac_stage_1->setStyleSheet("Text-align:left");
// 12. UAC Stage 1
connect(m_Controls.uac_stage_2, SIGNAL(clicked()), this, SLOT(UAC_Stage2()));
m_Controls.uac_stage_2->setStyleSheet("Text-align:left");



Expand Down Expand Up @@ -707,6 +716,34 @@ bool AtrialStrainMotionView::GetUserEditLabelsInputs(){
return userInputAccepted;
}

bool AtrialStrainMotionView::IsOutputFileCorrect(QString dir, QStringList filenames){
bool success = true;

int countfails = 0;
QString checkOutputMsg = "";

std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
for (int ix = 0; ix < filenames.size(); ix++) {
bool okSingleTest = cmd->IsOutputSuccessful(dir + "/" + filenames.at(ix));

if (!okSingleTest){
MITK_ERROR << ("File(s) not created - " + filenames.at(ix)).toStdString();
countfails++;
checkOutputMsg += (countfails==1) ? "File(s) not created: " : "";
checkOutputMsg += "\n " + filenames.at(ix);
}
}

if (!checkOutputMsg.isEmpty()){
std::string msg = checkOutputMsg.toStdString();
QMessageBox::warning(NULL, "Warning", msg.c_str());
success = false;
}

return success;

}

bool AtrialStrainMotionView::RequestProjectDirectoryFromUser() {

bool succesfulAssignment = true;
Expand Down Expand Up @@ -1127,4 +1164,130 @@ void AtrialStrainMotionView::MeshImprovement() {

}

void AtrialStrainMotionView::AutoLandMark() {
if (!RequestProjectDirectoryFromUser()) return;

std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
cmd->SetUseDockerContainers(true);

QString outputFullPath = Path("UAC_CT/") + "prodRefinedLandmarks.txt";
cmd->ExecuteTouch(outputFullPath);
cmd->DockerAtrialStrainMotion(Path("UAC_CT/"), "autoLM");

QFileInfo finfo(outputFullPath);
bool fileExists = finfo.exists();

MITK_INFO << (fileExists ? "Final decision: Done" : "Final decision: Output file not found.");
}

void AtrialStrainMotionView::UAC_Stage1(){
if (!RequestProjectDirectoryFromUser()) return;
// docker run --rm --volume=/home/bzhou6/Desktop/V-0005/UAC_CT:/data cemrg/uac:3.0-beta uac --uac-stage 1 --atrium la --layer endo --fibre l --msh clean-Labelled-refined --tags 1 19 11 13 15 17 --landmarks prodRefinedLandmarks.txt --scale 1000

MITK_INFO << "TIMELOG|UacCalculation_Stage1| Start";
// Cemrg CMD
std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
cmd->SetUseDockerContainers(true);
MITK_INFO << "Do Rough UAC code from Docker";

QString uacOutput;
QStringList outputFiles;

QStringList tags;
tags << "1" << "19" << "11" << "13" << "15" << "17";
QStringList landmarks;
landmarks << "prodRefinedLandmarks.txt";
uacOutput = cmd->DockerUacMainMode(directory + "/UAC_CT", "1", "la", "endo", "l", "clean-Labelled-refined", tags, landmarks, false, false, 1000);
MITK_INFO << ("TIMELOG|UacCalculation_Stage1| UAC 1 end " + uacOutput).toStdString();

outputFiles << "LSbc1.vtx" << "LSbc2.vtx";
outputFiles << "PAbc1.vtx" << "PAbc2.vtx";

if (!IsOutputFileCorrect(directory + "/UAC_CT", outputFiles)){
MITK_INFO << "TIMELOG|UacCalculation_Stage1| End (FAIL)";
return;
}

//TODO: remove -parab_options_file ilu_cg_opts -ellip_options_file amg_cg_opts --> Unable to access file ilu_cg_opts
MITK_INFO << "Create Laplace Solve files for LR and PA SOLVES";
QString lr_par, pa_par;
MITK_INFO << "TIMELOG|UacCalculation_Stage1| openCARP start";
lr_par = CemrgCommonUtils::OpenCarpParamFileGenerator(directory + "/UAC_CT", "carpf_laplace_LS.par", "clean-Labelled-refined", "LSbc1", "LSbc2");
pa_par = CemrgCommonUtils::OpenCarpParamFileGenerator(directory + "/UAC_CT", "carpf_laplace_PA.par", "clean-Labelled-refined", "PAbc1", "PAbc2");

MITK_INFO << "Do Laplace Solves using Docker";
cmd->SetDockerImageOpenCarp();
QString lrLapSolve, paLapSolve;
lrLapSolve = cmd->OpenCarpDocker(directory + "/UAC_CT", lr_par, "LR_UAC_N2");
paLapSolve = cmd->OpenCarpDocker(directory + "/UAC_CT" , pa_par, "PA_UAC_N2");
MITK_INFO << ("TIMELOG|UacCalculation_Stage1| openCARP end " + lrLapSolve + " - " + paLapSolve).toStdString();

bool uacOutputSuccess = IsOutputFileCorrect(directory + "/UAC_CT", outputFiles);
MITK_ERROR(!uacOutputSuccess) << "problem in UAC_Stage1";
std::string msg = "UAC Calculation - Stage 1 ";
msg += (uacOutputSuccess) ? "successful" : "failed";
QMessageBox::information(NULL, "Attention", msg.c_str());
MITK_INFO << "TIMELOG|UacCalculation_Stage1| End";
}

void AtrialStrainMotionView::UAC_Stage2(){
if (!RequestProjectDirectoryFromUser()) return;
// Cemrg CMD
std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
cmd->SetUseDockerContainers(true);
MITK_INFO << "Do Rough UAC code from Docker";

QStringList outputFiles;
outputFiles << "AnteriorMesh.elem" << "PosteriorMesh.elem";
outputFiles << "Ant_Strength_Test_PA1.vtx" << "Ant_Strength_Test_LS1.vtx";
outputFiles << "Post_Strength_Test_PA1.vtx" << "Post_Strength_Test_LS1.vtx";
MITK_INFO << "TIMELOG|UacCalculation_Stage2| UAC 2.1 - Start";

QStringList tags;
tags << "1" << "19" << "11" << "13" << "15" << "17";
QStringList landmarks;
landmarks << "prodRefinedLandmarks.txt";
QString uacOutput = cmd->DockerUacMainMode(directory + "/UAC_CT", "2a", "la", "endo", "l", "clean-Labelled-refined", tags, landmarks, false, false, 1000);
MITK_INFO << ("TIMELOG|UacCalculation_Stage2| UAC 2.1 - End " + uacOutput).toStdString();

if (!IsOutputFileCorrect(directory + "/UAC_CT", outputFiles)){
MITK_INFO << "TIMELOG|UacCalculation_Stage2| End (FAILED)";
return;
}

QString lrp_par, udp_par, lra_par, uda_par;
QString carpf_lr = "carpf_laplace_single_LR";
QString carpf_ud = "carpf_laplace_single_UD";

MITK_INFO << "TIMELOG|UacCalculation_Stage2| openCARP - Start";
lrp_par = CemrgCommonUtils::OpenCarpParamFileGenerator(directory + "/UAC_CT", carpf_lr+"_P.par", "PosteriorMesh", "", "Post_Strength_Test_LS1");
udp_par = CemrgCommonUtils::OpenCarpParamFileGenerator(directory + "/UAC_CT", carpf_ud+"_P.par", "PosteriorMesh", "", "Post_Strength_Test_PA1");
lra_par = CemrgCommonUtils::OpenCarpParamFileGenerator(directory + "/UAC_CT", carpf_lr+"_A.par", "AnteriorMesh", "", "Ant_Strength_Test_LS1");
uda_par = CemrgCommonUtils::OpenCarpParamFileGenerator(directory + "/UAC_CT", carpf_ud+"_A.par", "AnteriorMesh", "", "Ant_Strength_Test_PA1");

cmd->SetDockerImageOpenCarp();

QString lrpLapSolve, udpLapSolve, lraLapSolve, udaLapSolve;
lrpLapSolve = cmd->OpenCarpDocker(directory + "/UAC_CT", lrp_par, "LR_Post_UAC");
udpLapSolve = cmd->OpenCarpDocker(directory + "/UAC_CT", udp_par, "UD_Post_UAC");
lraLapSolve = cmd->OpenCarpDocker(directory + "/UAC_CT", lra_par, "LR_Ant_UAC");
udaLapSolve = cmd->OpenCarpDocker(directory + "/UAC_CT", uda_par, "UD_Ant_UAC");
MITK_INFO << ("TIMELOG|UacCalculation_Stage2| openCARP - End " + lrpLapSolve + "-" + udpLapSolve + "-" + lraLapSolve + "-" + udaLapSolve).toStdString();


outputFiles.clear();
outputFiles << "Labelled_Coords_2D_Rescaling_v3_C.vtk";
outputFiles << "Labelled_Coords_2D_Rescaling_v3_C.elem";
outputFiles << "Labelled_Coords_2D_Rescaling_v3_C.pts";
MITK_INFO << "TIMELOG|UacCalculation_Stage2| UAC 2.2 - Start";
uacOutput = cmd->DockerUacMainMode(directory + "/UAC_CT", "2b", "la", "endo", "l", "clean-Labelled-refined", tags, landmarks, false, false, 1000);
MITK_INFO << "TIMELOG|UacCalculation_Stage2| UAC 2.2 - End";

bool uacOutputSuccess = IsOutputFileCorrect(directory + "/UAC_CT", outputFiles);
MITK_ERROR(!uacOutputSuccess) << "Problem with UAC_Stage2";
std::string msg = "UAC Calculation - Stage 2 ";
msg += (uacOutputSuccess) ? "successful" : "failed";
QMessageBox::information(NULL, "Attention", msg.c_str());

MITK_INFO << ("TIMELOG|UacCalculation_Stage2| End " + uacOutput).toStdString();
}
4 changes: 4 additions & 0 deletions CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.h
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Expand Up @@ -95,6 +95,7 @@ class AtrialStrainMotionView : public QmitkAbstractView {
QString UserIncludeLgeAnalysis(QString segPath, ImageType::Pointer seg);
bool GetUserUacOptionsInputs(bool enableFullUiOptions=true);
bool GetUserEditLabelsInputs();
bool IsOutputFileCorrect(QString dir, QStringList filenames);

protected:
virtual void CreateQtPartControl(QWidget *parent) override;
Expand Down Expand Up @@ -127,6 +128,9 @@ protected slots:
void ClipperMV();
void UacCalculationVerifyLabels();
void MeshImprovement();
void AutoLandMark();
void UAC_Stage1();
void UAC_Stage2();

private:
double uiMesh_th, uiMesh_bl, uiMesh_smth, uiMesh_iter;
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21 changes: 21 additions & 0 deletions ...pp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionViewControls.ui
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Expand Up @@ -100,6 +100,27 @@
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="autoLM">
<property name="text">
<string>11. Auto Landmark</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="uac_stage_1">
<property name="text">
<string>12. UAC Stage 1</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="uac_stage_2">
<property name="text">
<string>13. UAC Stage 2</string>
</property>
</widget>
</item>
<item>
<spacer name="spacer1">
<property name="orientation">
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