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added cropImages, registration and deformMesh
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@sagebei
sagebei committed Sep 13, 2024
1 parent c952b7b commit 3c4cdef
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Showing 4 changed files with 191 additions and 65 deletions.
12 changes: 8 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 @@ -38,6 +38,7 @@ PURPOSE. See the above copyright notices for more information.
#include <QDebug>
#include <QDir>
#include <QMessageBox>
#include <QThread>

// C++ Standard
#include <thread>
Expand Down Expand Up @@ -189,12 +190,13 @@ void CemrgCommandLine::ExecuteTracking(QString dir, QString imgTimes, QString pa
QStringList arguments;

if (apathd.exists()) {

QString threads = QString::number(QThread::idealThreadCount());
MITK_INFO << "Using " << threads.toStdString() << " CPU cores";
process->setWorkingDirectory(executablePath);
arguments << "-images" << imgTimesFilePath;
if (!param.isEmpty()) arguments << "-parin" << param;
arguments << "-dofout" << outAbsolutePath;
arguments << "-threads" << "12";
arguments << "-threads" << threads;
arguments << "-verbose" << "3";

} else {
Expand Down Expand Up @@ -1461,10 +1463,12 @@ void CemrgCommandLine::DockerAtrialStrainMotion(QString dir, QString function) {

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

ExecuteCommand(executableName, arguments, "", false);
/***
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177 changes: 117 additions & 60 deletions CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -129,42 +129,64 @@ void AtrialStrainMotionView::CreateQtPartControl(QWidget *parent)
// 1: Segment and Extract
connect(m_Controls.segment_extract, SIGNAL(clicked()), this, SLOT(SegmentExtract()));
m_Controls.segment_extract->setStyleSheet("Text-align:left");
// 4. Post processing
// 2. Post processing
// m_Controls.button_man4_2_postproc->setVisible(false);
connect(m_Controls.button_man4_2_postproc, SIGNAL(clicked()), this, SLOT(SegmentationPostprocessing()));
m_Controls.button_man4_2_postproc->setStyleSheet("Text-align:left");
// 5. Identify PVs
// 3. Identify PVs
connect(m_Controls.button_man5_idPV, SIGNAL(clicked()), this, SLOT(IdentifyPV()));
m_Controls.button_man5_idPV->setStyleSheet("Text-align:left");
// 6. Create Labelled Mesh
// 4. Create Labelled Mesh
connect(m_Controls.button_man6_labelmesh, SIGNAL(clicked()), this, SLOT(CreateLabelledMesh()));
m_Controls.button_man6_labelmesh->setStyleSheet("Text-align:left");
// 7. Mesh Preprocessing
// 5. Mesh Preprocessing
connect(m_Controls.button_auto4_meshpreproc, SIGNAL(clicked()), this, SLOT(MeshPreprocessing()));
m_Controls.button_auto4_meshpreproc->setStyleSheet("Text-align:left");
// 8. Verify Labels
// 6. Verify Labels
connect(m_Controls.button_0_3_checklabels, SIGNAL(clicked()), this, SLOT(UacCalculationVerifyLabels()));
m_Controls.button_0_3_checklabels->setStyleSheet("Text-align:left");
// 9. Clip PV
// 7. Clip PV
connect(m_Controls.button_man8_clipPV, SIGNAL(clicked()), this, SLOT(ClipperPV()));
m_Controls.button_man8_clipPV->setStyleSheet("Text-align:left");
// 10. Mesh Improvement
// 8. 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
// 9. Auto Landmark
connect(m_Controls.autoLM, SIGNAL(clicked()), this, SLOT(AutoLandMark()));
m_Controls.autoLM->setStyleSheet("Text-align:left");
// 12. UAC Stage 1
// 10. UAC Stage 1
connect(m_Controls.uac_stage_1, SIGNAL(clicked()), this, SLOT(UAC_Stage1()));
m_Controls.uac_stage_1->setStyleSheet("Text-align:left");
// 13. UAC Stage 2
// 11. UAC Stage 2
connect(m_Controls.uac_stage_2, SIGNAL(clicked()), this, SLOT(UAC_Stage2()));
m_Controls.uac_stage_2->setStyleSheet("Text-align:left");

// 14. Create Model
// 12. Create Model
connect(m_Controls.create_model, SIGNAL(clicked()), this, SLOT(CreateModel()));
m_Controls.create_model->setStyleSheet("Text-align:left");

// Crop Image
connect(m_Controls.crop_images, SIGNAL(clicked()), this, SLOT(CropImage()));
m_Controls.crop_images->setStyleSheet("Text-align:left");
// Registration
connect(m_Controls.registration, SIGNAL(clicked()), this, SLOT(Registration()));
m_Controls.registration->setStyleSheet("Text-align:left");
// Deform Mesh
connect(m_Controls.deform_mesh, SIGNAL(clicked()), this, SLOT(DeformMesh()));
m_Controls.deform_mesh->setStyleSheet("Text-align:left");
// Generate Cell Area Strains
connect(m_Controls.generate_cell_area_strains, SIGNAL(clicked()), this, SLOT(GenerateCellAreaStrains()));
m_Controls.generate_cell_area_strains->setStyleSheet("Text-align:left");
// Jacobian Threshold
connect(m_Controls.jacobian_threshold, SIGNAL(clicked()), this, SLOT(JacobianThreshold()));
m_Controls.jacobian_threshold->setStyleSheet("Text-align:left");
// Plot Area Strain
connect(m_Controls.plot_area_strain, SIGNAL(clicked()), this, SLOT(PlotAreaStrain()));
m_Controls.plot_area_strain->setStyleSheet("Text-align:left");
// Calculate Fiber Strain
connect(m_Controls.calc_fiber_strains, SIGNAL(clicked()), this, SLOT(CalcFiberStrains()));
m_Controls.calc_fiber_strains->setStyleSheet("Text-align:left");
// Plot Fiber Strain
connect(m_Controls.plot_fibers_trains, SIGNAL(clicked()), this, SLOT(PlotFibersTrains()));
m_Controls.plot_fibers_trains->setStyleSheet("Text-align:left");


// Set default variables
Expand Down Expand Up @@ -199,47 +221,6 @@ void AtrialStrainMotionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /
*/
}

void AtrialStrainMotionView::DoImageProcessing()
{
QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
if (nodes.empty())
return;

mitk::DataNode *node = nodes.front();

if (!node)
{
// Nothing selected. Inform the user and return
QMessageBox::information(nullptr, "Template", "Please load and select an image before starting image processing.");
return;
}

// here we have a valid mitk::DataNode

// a node itself is not very useful, we need its data item (the image)
mitk::BaseData *data = node->GetData();
if (data)
{
// test if this data item is an image or not (could also be a surface or something totally different)
mitk::Image *image = dynamic_cast<mitk::Image *>(data);
if (image)
{
std::stringstream message;
std::string name;
message << "Performing image processing for image ";
if (node->GetName(name))
{
// a property called "name" was found for this DataNode
message << "'" << name << "'";
}
message << ".";
MITK_INFO << message.str();

// actually do something here...
}
}
}

bool AtrialStrainMotionView::GetUserAnalysisSelectorInputs(){
MITK_INFO << "[GetUserAnalysisSelectorInputs]";
QString metadata = Path("UAC_CT/prodMetadata.txt");
Expand Down Expand Up @@ -744,6 +725,11 @@ bool AtrialStrainMotionView::RequestProjectDirectoryFromUser() {
void AtrialStrainMotionView::SegmentExtract() {
if (!RequestProjectDirectoryFromUser()) return; // if the path was chosen incorrectly -> returns.

QDir q_directory(directory);
q_directory.mkdir("UAC_CT") ? MITK_INFO << "UAC_CT created" : MITK_INFO << "UAC_CT exists";
q_directory.mkdir("UAC_CT_aligned") ? MITK_INFO << "UAC_CT_aligned created" : MITK_INFO << "UAC_CT_aligned exists";
q_directory.mkdir("tracking") ? MITK_INFO << "tracking folder created" : MITK_INFO << "tracking folder exists";

// copy the first image and segment it
QDir nifti_dir = QDir(directory + "/nifti/");
QString input_file_name = nifti_dir.entryList(QDir::AllEntries | QDir::NoDotAndDotDot)[0];
Expand All @@ -752,12 +738,14 @@ void AtrialStrainMotionView::SegmentExtract() {

MITK_INFO(QFile::copy(nifti_dir.absolutePath() + "/" + input_file_name, input_file_path)) << "Copied " << input_file_name;

// extract LA
std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
cmd->SetUseDockerContainers(true);
QString pathToSegmentation = cmd->DockerCctaMultilabelSegmentation(directory, input_file_path, false);
MITK_INFO << pathToSegmentation;

// extract LA
// cmd->DockerAtrialStrainMotion(directory, "fix_vtk_metadata");

mitk::Image::Pointer segmentation = mitk::IOUtil::Load<mitk::Image>(pathToSegmentation.toStdString());

if (!segmentation) return ;
Expand Down Expand Up @@ -787,10 +775,6 @@ void AtrialStrainMotionView::SegmentExtract() {
// mitk::Surface::Pointer la_msh = mitk::IOUtil::Load<mitk::Surface>(la_msh_path.toStdString());
// CemrgCommonUtils::AddToStorage(la_msh, "la_msh", this->GetDataStorage());

QDir q_directory(directory);
q_directory.mkdir("UAC_CT") ? MITK_INFO << "UAC_CT created" : MITK_INFO << "UAC_CT exists";
q_directory.mkdir("UAC_CT_aligned") ? MITK_INFO << "UAC_CT_aligned created" : MITK_INFO << "UAC_CT_aligned exists";

MITK_INFO(QFile::copy(la_msh_path, directory + "/UAC_CT" + "/LA_msh.vtk")) << "Copied LA_msh.vtk";

// Analysis Selector
Expand Down Expand Up @@ -821,6 +805,7 @@ void AtrialStrainMotionView::SegmentExtract() {
CemrgCommonUtils::AddToStorage(im, tagName.toStdString(), this->GetDataStorage());

}

}

void AtrialStrainMotionView::SegmentationPostprocessing(){
Expand Down Expand Up @@ -1253,6 +1238,7 @@ void AtrialStrainMotionView::CreateModel() {

// generateLabelledMsh
cmd->ExecuteTouch(Path("UAC_CT/") + "clean-Labelled-refined-aligned.vtk");
cmd->ExecuteTouch(Path("UAC_CT/") + "clean-Labelled-refined-aligned.vtp");
cmd->DockerAtrialStrainMotion(Path(), "generateLabelledMsh");

// appendFibres
Expand All @@ -1263,4 +1249,75 @@ void AtrialStrainMotionView::CreateModel() {

// alignMesh
cmd->DockerAtrialStrainMotion(Path(), "alignMesh");
}
}




void AtrialStrainMotionView::CropImage() {
MITK_INFO << "crop image";
// TODO: automate finding x_start, y_start, z_start ...
if (!RequestProjectDirectoryFromUser()) return;

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

for (int frame = 0; frame <= 20; frame ++) {
QString cropped_img_name = "dcm-crop-" + QString::number(frame) + ".nii";
cmd->ExecuteTouch(Path("nifti/") + cropped_img_name);
}

cmd->DockerAtrialStrainMotion(Path(), "cropImages");
}

void AtrialStrainMotionView::Registration() {
MITK_INFO << "Registration";
if (!RequestProjectDirectoryFromUser()) return;
std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
cmd->SetUseDockerContainers(true);

cmd->ExecuteTouch(Path("tracking/") + "Final.cfg");
cmd->ExecuteTouch(Path("tracking/") + "imgTimes.lst");

cmd->DockerAtrialStrainMotion(Path(), "registration");

cmd->ExecuteTracking(Path(), Path("tracking/imgTimes.lst"), Path("tracking/Final.cfg"), Path("tracking/tsffd.dof"));
}

void AtrialStrainMotionView::DeformMesh() {
MITK_INFO << "DeformMesh";
if (!RequestProjectDirectoryFromUser()) return;
std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
cmd->SetUseDockerContainers(true);
for (int frame = 0; frame < 10; frame ++) {
cmd->ExecuteTransformationOnPoints(directory,
Path("UAC_CT/clean-Labelled-refined-aligned.vtp"),
QString("tracking/cLr-aligned-") + QString::number(frame) + ".vtp",
QString("tracking/tsffd.dof"),
frame * 10);
}


}

void AtrialStrainMotionView::GenerateCellAreaStrains() {
MITK_INFO << "GenerateCellAreaStrains";
}

void AtrialStrainMotionView::JacobianThreshold() {
MITK_INFO << "JacobianThreshold";
}

void AtrialStrainMotionView::PlotAreaStrain() {
MITK_INFO << "PlotAreaStrain";
}

void AtrialStrainMotionView::CalcFiberStrains() {
MITK_INFO << "CalcFiberStrains";
}

void AtrialStrainMotionView::PlotFibersTrains() {
MITK_INFO << "PlotFibersTrains";
}


11 changes: 10 additions & 1 deletion CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.h
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Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ class AtrialStrainMotionView : public QmitkAbstractView {


protected slots:
void DoImageProcessing();
// Model creation pipeline
void SegmentExtract();
void SegmentationPostprocessing();
void IdentifyPV();
Expand All @@ -130,6 +130,15 @@ protected slots:
void UAC_Stage1();
void UAC_Stage2();
void CreateModel();
// motion tracking pipeline
void CropImage();
void Registration();
void DeformMesh();
void GenerateCellAreaStrains();
void JacobianThreshold();
void PlotAreaStrain();
void CalcFiberStrains();
void PlotFibersTrains();

private:
double uiMesh_th, uiMesh_bl, uiMesh_smth, uiMesh_iter;
Expand Down
56 changes: 56 additions & 0 deletions ...pp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionViewControls.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,62 @@
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="crop_images">
<property name="text">
<string>Crop Images</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="registration">
<property name="text">
<string>registration</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="deform_mesh">
<property name="text">
<string>Deform Mesh</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="generate_cell_area_strains">
<property name="text">
<string>Generate Cell Area Strains</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="jacobian_threshold">
<property name="text">
<string>jacobianThreshold</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="plot_area_strain">
<property name="text">
<string>plotAreaStrain</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="calc_fiber_strains">
<property name="text">
<string>Calc Fiber Strains</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="plot_fibers_trains">
<property name="text">
<string>plot Fiber Strains</string>
</property>
</widget>
</item>
<item>
<spacer name="spacer1">
<property name="orientation">
Expand Down

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