MITK upgrade

[JostMigenda]

This combines work from the previous MITK upgrade effort and @alonsoJASL’s fork … and then rebased all of it onto of the current development branch. This was a bit of a painful rebase—going forward, we really should avoid having branches diverge for multiple years!—but José and I completed it this afternoon.

Next up, I’ll try to build it on my machine and see what further changes are needed. Therefore, I’ll leave this as a draft PR for now.

[github-actions]

⚡ Code Analysis Results ⚡

🔴 Cppcheck found 22 issues! Click here to see details.

CemrgApp/CemrgApp/Modules/CemrgAppModule/src/CemrgCommonUtils.cpp

Lines 1813 to 1818 in 0c691e3

	scalars = vtkFloatArray::SafeDownCast(surface->GetVtkPolyData()->GetCellData()->GetScalars());
	numObjects = surface->GetVtkPolyData()->GetNumberOfCells();
	} else{
	// surface->GetVtkPolyData()->GetCellData()->SetActiveScalars(fieldName.toStdString().c_str());
	scalars = vtkFloatArray::SafeDownCast(surface->GetVtkPolyData()->GetCellData()->GetScalars());
	numObjects = surface->GetVtkPolyData()->GetNumberOfCells();

!Line: 1813 - style: Redundant initialization for 'scalars'. The initialized value is overwritten before it is read. [redundantInitialization]

CemrgApp/CemrgApp/Modules/CemrgAppModule/src/CemrgCommonUtils.cpp

Lines 1806 to 1811 in 0c691e3

	vtkFloatArray *scalars = vtkFloatArray::New();
	vtkIdType numObjects;
	std::cout << "fieldName: " << fieldName.toStdString() << '\n';
	if (isElem){

!Line: 1806 - note: scalars is initialized

CemrgApp/CemrgApp/Modules/CemrgAppModule/src/CemrgCommonUtils.cpp

Lines 1813 to 1818 in 0c691e3

	scalars = vtkFloatArray::SafeDownCast(surface->GetVtkPolyData()->GetCellData()->GetScalars());
	numObjects = surface->GetVtkPolyData()->GetNumberOfCells();
	} else{
	// surface->GetVtkPolyData()->GetCellData()->SetActiveScalars(fieldName.toStdString().c_str());
	scalars = vtkFloatArray::SafeDownCast(surface->GetVtkPolyData()->GetCellData()->GetScalars());
	numObjects = surface->GetVtkPolyData()->GetNumberOfCells();

!Line: 1813 - note: scalars is overwritten

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

Lines 55 to 60 in 0c691e3

	class AtrialFibresClipperView : public QmitkAbstractView {
	// this is needed for all Qt objects that should have a Qt meta-object
	// (everything that derives from QObject and wants to have signal/slots)
	Q_OBJECT

!Line: 55 - style: The class 'AtrialFibresClipperView' does not have a constructor although it has private member variables. [noConstructor]

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

Lines 66 to 71 in 0c691e3

	class AtrialFibresView : public QmitkAbstractView {
	// this is needed for all Qt objects that should have a Qt meta-object
	// (everything that derives from QObject and wants to have signal/slots)
	Q_OBJECT

!Line: 66 - style: The class 'AtrialFibresView' does not have a constructor although it has private member variables. [noConstructor]

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

Lines 451 to 456 in 0c691e3

	radii = vtkDoubleArray::SafeDownCast(line->GetPointData()->GetArray("MaximumInscribedSphereRadius"));
	double adjust = ctrPlane->GetRadius() / radii->GetValue(position);
	//Adjust highlighted clipper
	for (unsigned int i=0; i<clipperActors.size(); i++)
	clipperActors.at(i)->GetProperty()->SetOpacity(i==(unsigned)index ? 1.0 : 0.1);

!Line: 451 - style: Redundant initialization for 'radii'. The initialized value is overwritten before it is read. [redundantInitialization]

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

Lines 450 to 455 in 0c691e3

	vtkSmartPointer<vtkDoubleArray> radii = vtkSmartPointer<vtkDoubleArray>::New();
	radii = vtkDoubleArray::SafeDownCast(line->GetPointData()->GetArray("MaximumInscribedSphereRadius"));
	double adjust = ctrPlane->GetRadius() / radii->GetValue(position);
	//Adjust highlighted clipper
	for (unsigned int i=0; i<clipperActors.size(); i++)

!Line: 450 - note: radii is initialized

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

Lines 451 to 456 in 0c691e3

	radii = vtkDoubleArray::SafeDownCast(line->GetPointData()->GetArray("MaximumInscribedSphereRadius"));
	double adjust = ctrPlane->GetRadius() / radii->GetValue(position);
	//Adjust highlighted clipper
	for (unsigned int i=0; i<clipperActors.size(); i++)
	clipperActors.at(i)->GetProperty()->SetOpacity(i==(unsigned)index ? 1.0 : 0.1);

!Line: 451 - note: radii is overwritten

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

Lines 53 to 58 in 0c691e3

	class AtrialFibresLandmarksView : public QmitkAbstractView {
	// this is needed for all Qt objects that should have a Qt meta-object
	// (everything that derives from QObject and wants to have signal/slots)
	Q_OBJECT

!Line: 53 - style: The class 'AtrialFibresLandmarksView' does not have a constructor although it has private member variables. [noConstructor]

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

Lines 392 to 397 in 0c691e3

	double distance;
	int pickedSeedId = -1;
	double minDistance = 1E10;
	for (int i=0; i<pickedCellPointIds->GetNumberOfIds(); i++) {
	distance = vtkMath::Distance2BetweenPoints(
	pickPosition, surface->GetVtkPolyData()->GetPoint(pickedCellPointIds->GetId(i)));

!Line: 392 - style: The scope of the variable 'distance' can be reduced. [variableScope]

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

Lines 248 to 253 in 0c691e3

	std::ofstream fileRefined, fileRough, fileRefinedLabels;
	MITK_INFO << "[SaveRefinedPoints] Saving TXT file.";
	fileRefined.open((prodPath + outname + ".txt").toStdString());
	fileRefinedLabels.open((prodPath + outname + "-Labels.txt").toStdString());

!Line: 248 - style: Unused variable: fileRough [unusedVariable]

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

Lines 50 to 55 in 0c691e3

	class AtrialFibresVisualiseView : public QmitkAbstractView {
	// this is needed for all Qt objects that should have a Qt meta-object
	// (everything that derives from QObject and wants to have signal/slots)
	Q_OBJECT

!Line: 50 - style: The class 'AtrialFibresVisualiseView' does not have a constructor although it has private member variables. [noConstructor]

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

Lines 1794 to 1799 in 0c691e3

	if(!userInputAccepted){
	QDialog* inputs = new QDialog(0, Qt::WindowFlags());
	m_UIEditLabels.setupUi(inputs);
	connect(m_UIEditLabels.buttonBox, SIGNAL(accepted()), inputs, SLOT(accept()));
	connect(m_UIEditLabels.buttonBox, SIGNAL(rejected()), inputs, SLOT(reject()));
	std::cout << "WHICH ATRIUM: " << uac_whichAtrium.toStdString() << '\n';

!Line: 1794 - style: Condition '!userInputAccepted' is always true [knownConditionTrueFalse]

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

Lines 1792 to 1797 in 0c691e3

	bool userInputAccepted=false;
	if(!userInputAccepted){
	QDialog* inputs = new QDialog(0, Qt::WindowFlags());
	m_UIEditLabels.setupUi(inputs);
	connect(m_UIEditLabels.buttonBox, SIGNAL(accepted()), inputs, SLOT(accept()));

!Line: 1792 - note: Assignment 'userInputAccepted=false', assigned value is 0

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

Lines 1794 to 1799 in 0c691e3

	if(!userInputAccepted){
	QDialog* inputs = new QDialog(0, Qt::WindowFlags());
	m_UIEditLabels.setupUi(inputs);
	connect(m_UIEditLabels.buttonBox, SIGNAL(accepted()), inputs, SLOT(accept()));
	connect(m_UIEditLabels.buttonBox, SIGNAL(rejected()), inputs, SLOT(reject()));
	std::cout << "WHICH ATRIUM: " << uac_whichAtrium.toStdString() << '\n';

!Line: 1794 - note: Condition '!userInputAccepted' is always true

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

Lines 2339 to 2344 in 0c691e3

	segImage = atrium->LoadImage(segRegPath);
	resultString = segRegPath;
	tagName += "-reg";
	SetLgeAnalysis(true);

!Line: 2339 - style: Variable 'segImage' is assigned a value that is never used. [unreadVariable]

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

Lines 192 to 197 in 0c691e3

	reply1 = Ask("Question", "Use alternative DICOM reader?");
	#endif
	if (reply1 == QMessageBox::Yes) {
	QString dicomFolder = QFileDialog::getExistingDirectory(NULL, "Open folder with DICOMs.", mitk::IOUtil::GetProgramPath().c_str(), QFileDialog::ShowDirsOnly|QFileDialog::DontUseNativeDialog);

!Line: 192 - style: Redundant initialization for 'reply1'. The initialized value is overwritten before it is read. [redundantInitialization]

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

Lines 189 to 194 in 0c691e3

	int reply1 = QMessageBox::No;
	#if defined(__APPLE__)
	MITK_INFO << "Ask user about alternative DICOM reader";
	reply1 = Ask("Question", "Use alternative DICOM reader?");
	#endif

!Line: 189 - note: reply1 is initialized

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

Lines 192 to 197 in 0c691e3

	reply1 = Ask("Question", "Use alternative DICOM reader?");
	#endif
	if (reply1 == QMessageBox::Yes) {
	QString dicomFolder = QFileDialog::getExistingDirectory(NULL, "Open folder with DICOMs.", mitk::IOUtil::GetProgramPath().c_str(), QFileDialog::ShowDirsOnly|QFileDialog::DontUseNativeDialog);

!Line: 192 - note: reply1 is overwritten

CemrgApp/CemrgApp/Plugins/kcl.cemrgapp.mmcwplugin/src/internal/MmcwView.cpp

Lines 723 to 728 in 0c691e3

	if (dcm_path_fix) {
	MITK_INFO << "[ATTENTION] Saving imgTimes.lst file to project directory.";
	time = directory + "/imgTimes.lst";
	file.open(time.toStdString(), std::ofstream::binary);
	file << "dcm- .nii\n";
	}

!Line: 723 - style: Condition 'dcm_path_fix' is always true [knownConditionTrueFalse]

CemrgApp/CemrgApp/Plugins/kcl.cemrgapp.mmcwplugin/src/internal/MmcwView.cpp

Lines 722 to 727 in 0c691e3

	bool dcm_path_fix = true;
	if (dcm_path_fix) {
	MITK_INFO << "[ATTENTION] Saving imgTimes.lst file to project directory.";
	time = directory + "/imgTimes.lst";
	file.open(time.toStdString(), std::ofstream::binary);
	file << "dcm- .nii\n";

!Line: 722 - note: Assignment 'dcm_path_fix=true', assigned value is 1

CemrgApp/CemrgApp/Plugins/kcl.cemrgapp.mmcwplugin/src/internal/MmcwView.cpp

Lines 723 to 728 in 0c691e3

	if (dcm_path_fix) {
	MITK_INFO << "[ATTENTION] Saving imgTimes.lst file to project directory.";
	time = directory + "/imgTimes.lst";
	file.open(time.toStdString(), std::ofstream::binary);
	file << "dcm- .nii\n";
	}

!Line: 723 - note: Condition 'dcm_path_fix' is always true

[alonsoJASL]

Changes look OK.

[LouiseABowler]

This is looking really good @JostMigenda! 🚀

I've left a couple of comments but go ahead and merge this when you're ready, those comments won't need any further review.

I have also given this PR a go on my Linux machine today. Mixed results there - it builds fine, but the applcation won't open. I suspect any fixes will inolve the setup instructions rather than the code, do don't let that block this PR 👍

[LouiseABowler]

Thanks for the revisions @JostMigenda, this looks good to me 🙌

[JostMigenda]

Test’s are failing during the “Download precompiled Build folder” step; no logs for that step is available, but the error message for the overall workflow run says:
System.IO.IOException: No space left on device
Is it possible that the downloaded build folder (plus the CemrgApp repo itself) exceeds the 14 GB disk space limit on GitHub’s runners?

Anyway, since the tests already fail on the head of the development branch, this shouldn’t stop us from merging this PR.