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GUI.cxx.in
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/*Qt classes*/
#include <QFileDialog>
#include <QMessageBox>
#include <QProcess>
#include <QFile>
#include <QTextStream>
#include <QShortcut>
#include <QCloseEvent>
#include <QDropEvent>
#include <QDragEnterEvent>
#include <QMimeData>
#include <QUrl>
#include <QSignalMapper>
#include <QDialog>
#include <QLabel>
#include <QComboBox>
#include <QStackedWidget>
#include <QLineEdit>
#include <QTimer>
#include <QDebug>
/*std classes*/
#include <stdio.h>
#include <stdlib.h>
#include <vector>
/*itk classes*/
#include "itkImage.h"
#include "itkImageFileReader.h"
#include <itksys/SystemTools.hxx> // for FindProgram() and GetFilenamePath()
/* ITK modes = same values than the C variables: F_OK W_OK R_OK X_OK */
mode_t ITKmode_F_OK = 0;
mode_t ITKmode_W_OK = 2;
mode_t ITKmode_R_OK = 4;
mode_t ITKmode_X_OK = 1;
/* DTIAB version check:
Version will be written in a log file when computing
to display a warning if a new compute is done afterwards with a newer version
1.0 : No version file
1.1 : Introducing version file
Renaming AW folder to Diffeomorphic folders (folders renamed in python script)
Renaming GreedyAtlas' Def Fields to HField
Renaming Final Def Fields to GlobalDisplacementField
*/
/* homemade */
#include "GUI.h"
#include "ScriptWriter.h"
// Q_OS_WIN32 Q_OS_LINUX Q_OS_MAC are Qt macros
#if defined Q_OS_WIN32
#define Platform "win"
#elif defined Q_OS_MAC
#define Platform "mac"
#elif defined Q_OS_LINUX
#define Platform "linux"
#endif
// DTIAtlasBuilder_BUILD_SLICER_EXTENSION is defined as preprocessor variable with CMake set_target_properties() in DTIAtlasBuilder.cmake
#define SlicerPythonExec "${SlicerPythonExec}" // configured in DTIAtlasBuilder.cmake
template< class T > std::string IntOrDoubleToStr(T IntOrDoubleVar) // T is int or double
{
std::ostringstream oss;
oss << IntOrDoubleVar;
return oss.str();
}
/////////////////////////////////////////
// CONSTRUCTOR //
/////////////////////////////////////////
// bool Testing: If automatic testing (constructor called from DTIAtllasBuilderGUITest.cxx), this flag will prevent any pop up window to show
GUI::GUI(std::string ParamFile, std::string ConfigFile, std::string CSVFile, bool overwrite, bool noGUI, bool Testing, std::string commandRan) : QMainWindow()
{
setupUi(this);
this->setAcceptDrops(true);
m_ErrorDetectedInConstructor=false;
/* Script writing object */
m_scriptwriter = new ScriptWriter; // delete in "void GUI::ExitProgram()"
/* Variables */
m_CSVseparator = QString(",");
m_ParamSaved=1;
m_lastCasePath="";
m_noGUI=noGUI;
m_Testing = Testing;
if( overwrite ) OverwritecheckBox->setChecked(true);
m_ScriptRunning=false;
m_ScriptQProcess = new QProcess;
QObject::connect(m_ScriptQProcess, SIGNAL(finished(int)), this, SLOT(ScriptQProcessDone(int)));
m_ScriptRunningQTimer = new QTimer(this);
QObject::connect(m_ScriptRunningQTimer, SIGNAL(timeout()), this, SLOT(UpdateScriptRunningGUIDisplay()));
/* Error message if windows or mac */
if ( !m_Testing )
{
if( (std::string)Platform == "mac" || (std::string)Platform == "win")
{
if(DTIAtlasBuilder_BUILD_SLICER_EXTENSION) QMessageBox::critical(this, "DTIAtlasBuilder not working", "This program is currently not working as it should on this platform.\nPlease do not hit the compute button, or the process will fail.\nYou can find other useful tools in Slicer:\n> DTI-Reg\n>Resample DTI Volume - log euclidean");
else QMessageBox::critical(this, "DTIAtlasBuilder not working", "This program is currently not working as it should on this platform.\nPlease do not hit the compute button, or the process will fail.\nIf the package was compiled or downloaded, you will find other useful tools in the specified install directory.");
}
}
/* Initialize the options */
InitOptions();
if(!m_noGUI)
{
/* Objects connections */
QObject::connect(ComputepushButton, SIGNAL(clicked()), this, SLOT(Compute()));
// Compute button triggered when user presses ENTER key
QShortcut* EnterShortcut = new QShortcut(QKeySequence(Qt::Key_Return), this); // ENTER on main keyboard (RETURN)
QObject::connect(EnterShortcut, SIGNAL(activated()), ComputepushButton, SLOT(click()));
QShortcut* NumPadEnterShortcut = new QShortcut(QKeySequence(Qt::Key_Enter), this); // ENTER on num pad
QObject::connect(NumPadEnterShortcut, SIGNAL(activated()), ComputepushButton, SLOT(click()));
QObject::connect(StoppushButton, SIGNAL(clicked()), this, SLOT(KillScriptQProcess()));
QObject::connect(BrowseCSVPushButton, SIGNAL(clicked()), this, SLOT(ReadCSVSlot()));
QObject::connect(SaveCSVPushButton, SIGNAL(clicked()), this, SLOT(SaveCSVDatasetBrowse()));
QObject::connect(BrowseOutputPushButton, SIGNAL(clicked()), this, SLOT(OpenOutputBrowseWindow()));
QObject::connect(BrowseDTIRegExtraPathPushButton, SIGNAL(clicked()), this, SLOT(OpenDTIRegExtraPathBrowseWindow()));
QObject::connect(TemplateBrowsePushButton, SIGNAL(clicked()), this, SLOT(OpenTemplateBrowseWindow()));
QObject::connect(AddPushButton, SIGNAL(clicked()), this, SLOT(OpenAddCaseBrowseWindow()));
// Remove button triggered when user presses PLUS key
QShortcut* PlusShortcut = new QShortcut(QKeySequence(Qt::Key_Plus), this);
QObject::connect(PlusShortcut, SIGNAL(activated()), AddPushButton, SLOT(click()));
QObject::connect(RemovePushButton, SIGNAL(clicked()), this, SLOT(RemoveSelectedCases()));
// Remove button triggered when user presses DEL or MINUS key
QShortcut* DelShortcut = new QShortcut(QKeySequence(Qt::Key_Delete), this); // DELETE key
QObject::connect(DelShortcut, SIGNAL(activated()), RemovePushButton, SLOT(click()));
QShortcut* MinusShortcut = new QShortcut(QKeySequence(Qt::Key_Minus), this); // MINUS key
QObject::connect(MinusShortcut, SIGNAL(activated()), RemovePushButton, SLOT(click()));
RemovePushButton->setEnabled(false);
ComputepushButton->setEnabled(false);
StoppushButton->setEnabled(false);
CleanOutputPushButton->setEnabled(false);
DisableQC(); // will be enable when cases are loaded
QObject::connect(actionLoad_parameters, SIGNAL(triggered()), this, SLOT(LoadParametersSlot()));
QObject::connect(actionSave_parameters, SIGNAL(triggered()), this, SLOT(SaveParametersSlot()));
QObject::connect(actionExit, SIGNAL(triggered()), this, SLOT(ExitProgram()));
QObject::connect(actionLoad_Software_Configuration, SIGNAL(triggered()), this, SLOT(LoadConfigSlot()));
QObject::connect(actionSave_Software_Configuration, SIGNAL(triggered()), this, SLOT(SaveConfig()));
QObject::connect(actionRead_Me, SIGNAL(triggered()), this, SLOT(ReadMe()));
QObject::connect(actionKeyboard_Shortcuts, SIGNAL(triggered()), this, SLOT(KeyShortcuts()));
QObject::connect(InterpolTypeComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(InterpolTypeComboBoxChanged(int)));
QObject::connect(TensInterpolComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(TensorInterpolComboBoxChanged(int)));
QObject::connect(RegMethodcomboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(RegMethodComboBoxChanged(int)));
QObject::connect(DefaultButton, SIGNAL(clicked()), this, SLOT(ConfigDefault()));
QObject::connect(GAPath, SIGNAL(editingFinished()), this, SLOT(testGA())); // test the version of GreedyAtlas automatically when the text is changed manually ( not by a setText() )
QObject::connect(DTIRegPath, SIGNAL(editingFinished()), this, SLOT(testDTIReg())); // test the version of DTI-Reg automatically when the text is changed manually ( not by a setText() )
QObject::connect(GridProcesscheckBox, SIGNAL(stateChanged(int)), this, SLOT(GridProcesscheckBoxHasChanged(int)));
QObject::connect(OutputFolderLineEdit, SIGNAL(textChanged(QString)), this, SLOT(OutputFolderLineEditHasChanged(QString)));
QObject::connect(AffineQCButton, SIGNAL(clicked()), this, SLOT(DisplayAffineQC()));
QObject::connect(DeformQCButton, SIGNAL(clicked()), this, SLOT(DisplayDeformQC()));
QObject::connect(ResampQCButton, SIGNAL(clicked()), this, SLOT(DisplayResampQC()));
QObject::connect(CleanOutputPushButton, SIGNAL(clicked()), this, SLOT(CleanOutputFolder()));
/* Browse software path Buttons */
QSignalMapper *SoftButtonMapper = new QSignalMapper();
QObject::connect(SoftButtonMapper, SIGNAL(mapped(int)), this, SLOT( BrowseSoft(int) ));
QObject::connect(ImagemathButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(ImagemathButton,1);
QObject::connect(ResampButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(ResampButton,2);
QObject::connect(CropDTIButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(CropDTIButton,3);
QObject::connect(dtiprocButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(dtiprocButton,4);
QObject::connect(BRAINSFitButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(BRAINSFitButton,5);
QObject::connect(GAButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(GAButton,6);
QObject::connect(dtiavgButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(dtiavgButton,7);
QObject::connect(DTIRegButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(DTIRegButton,8);
QObject::connect(unuButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(unuButton,9);
QObject::connect(MriWatcherButton, SIGNAL(clicked()), SoftButtonMapper, SLOT(map()));
SoftButtonMapper->setMapping(MriWatcherButton,10);
/* Reset software path Buttons */
QSignalMapper *ResetSoftButtonMapper = new QSignalMapper();
QObject::connect(ResetSoftButtonMapper, SIGNAL(mapped(int)), this, SLOT( ResetSoft(int) ));
QObject::connect(ImagemathResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(ImagemathResetButton,1);
QObject::connect(ResampResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(ResampResetButton,2);
QObject::connect(CropDTIResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(CropDTIResetButton,3);
QObject::connect(dtiprocResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(dtiprocResetButton,4);
QObject::connect(BRAINSFitResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(BRAINSFitResetButton,5);
QObject::connect(GAResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(GAResetButton,6);
QObject::connect(dtiavgResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(dtiavgResetButton,7);
QObject::connect(DTIRegResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(DTIRegResetButton,8);
QObject::connect(unuResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(unuResetButton,9);
QObject::connect(MriWatcherResetButton, SIGNAL(clicked()), ResetSoftButtonMapper, SLOT(map()));
ResetSoftButtonMapper->setMapping(MriWatcherResetButton,10);
/* When any value changes, the value of m_ParamSaved is set to 0 */
QObject::connect(TemplateLineEdit, SIGNAL(textChanged(QString)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(OutputFolderLineEdit, SIGNAL(textChanged(QString)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(SafetyMargincheckBox, SIGNAL(stateChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(BFAffineTfmModecomboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(OverwritecheckBox, SIGNAL(stateChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(SL4checkBox, SIGNAL(stateChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(SL2checkBox, SIGNAL(stateChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(SL1checkBox, SIGNAL(stateChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(NbLoopsSpinBox, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(SL4spinBox, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(nbIter4SpinBox, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(alpha4DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(beta4DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(gamma4DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(maxPerturbation4DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(SL2spinBox, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(nbIter2SpinBox, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(alpha2DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(beta2DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(gamma2DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(maxPerturbation2DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(SL1spinBox, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(nbIter1SpinBox, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(alpha1DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(beta1DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(gamma1DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(maxPerturbation1DoubleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(TensTfmComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(InterpolTypeComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(TensInterpolComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(DTIRegExtraPathlineEdit, SIGNAL(textChanged(QString)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(RegMethodcomboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_windowComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_BSplineComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_nologComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_BRegTypeComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_TfmModeComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_NbPyrLevSpin, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_PyrLevItLine, SIGNAL(textChanged(QString)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_ARegTypeComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_TfmStepLine, SIGNAL(textChanged(QString)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_IterLine, SIGNAL(textChanged(QString)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_SimMetComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_SimParamDble, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_GSigmaDble, SIGNAL(valueChanged(double)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(m_SmoothOffCheck, SIGNAL(stateChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(NbThreadsSpinBox, SIGNAL(valueChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
QObject::connect(GridProcesscheckBox, SIGNAL(stateChanged(int)), this, SLOT(WidgetHasChangedParamNoSaved()));
} //if(!m_noGUI)
m_FromConstructor=1; // do not test GA path if 'Default' called from constructor -> test at the end of constructor
/* SET the soft config */
// get the directory where the running executable is
std::string DTIABExecutablePath = itksys::SystemTools::GetRealPath( itksys::SystemTools::GetFilenamePath(commandRan).c_str() );
if( DTIABExecutablePath=="" ) // if DTIAtlasBuilder called without path (e.g. $ DTIAtlasBuilder) => either found in the PATH or in the current dir => FindProgram will find it
{
DTIABExecutablePath = itksys::SystemTools::GetFilenamePath( itksys::SystemTools::FindProgram( itksys::SystemTools::GetFilenameName(commandRan).c_str() ).c_str() );
// get the name of the executable used (i.e. DTIAtlasBuilder, DTIAtlasBuilder_vX.X (GetFilenameName), then search it in the PATH or current dir (FindProgram) and get the parent dir (GetFilenamePath)
}
// set the path to the executable directory for FindProgram
m_FindProgramDTIABExecDirVec.push_back(DTIABExecutablePath); // FindProgram will search in the executable directory too
// If DTIAB is built as an SlicerExtension, give the path to the folder containing external non cli tools
// If no SicerExtension, find_program will just search there and find nothing -> not an issue
if((std::string)Platform == "linux" || (std::string)Platform == "win")
{
m_DTIABSlicerExtensionExternalBinDir = DTIABExecutablePath + "/../../../ExternalBin"; // the executable will be in Ext/lib/Slicer4.2/cli_modules and the tools will be in Ext/ExternalBin
}
else if((std::string)Platform == "mac")
{
m_DTIABSlicerExtensionExternalBinDir = DTIABExecutablePath + "/../ExternalBin";
}
m_FindProgramDTIABExecDirVec.push_back(m_DTIABSlicerExtensionExternalBinDir);
// On Mac if Slicer Ext, paths to BRAINS (compiled within Slicer) are not set in the PATH env var, so add it to the search vector
if(DTIAtlasBuilder_BUILD_SLICER_EXTENSION && (std::string)Platform=="mac")
{
std::string SlicerExtMacBRAINSPath = m_DTIABSlicerExtensionExternalBinDir + "/../../../cli_modules";
m_FindProgramDTIABExecDirVec.push_back(SlicerExtMacBRAINSPath);
}
// Because ANTS is in m_DTIABSlicerExtensionExternalBinDir when Slicer Ext
if(DTIAtlasBuilder_BUILD_SLICER_EXTENSION)
{
DTIRegExtraPathlineEdit->setText( QString( m_DTIABSlicerExtensionExternalBinDir.c_str() ));
}
// look for the programs with the itk function
ConfigDefault();
// Look for the config file in the executable directory
std::string SoftConfigPath= DTIABExecutablePath + "/DTIAtlasBuilderSoftConfig.txt";
if( itksys::SystemTools::GetPermissions(SoftConfigPath.c_str(),ITKmode_F_OK) )
{
if( LoadConfig(QString( SoftConfigPath.c_str() )) == -1 )
{
m_ErrorDetectedInConstructor=true; // if file exists
}
}
// Look for the config file in the current directory
std::string CurrentPath = itksys::SystemTools::GetRealPath( itksys::SystemTools::GetCurrentWorkingDirectory().c_str() ); //GetRealPath() to remove symlinks
SoftConfigPath = CurrentPath + "/DTIAtlasBuilderSoftConfig.txt";
if( itksys::SystemTools::GetPermissions( SoftConfigPath.c_str() , ITKmode_F_OK) )
{
if( LoadConfig(QString( SoftConfigPath.c_str() )) == -1 )
{
m_ErrorDetectedInConstructor=true; // if file exists
}
}
// Look for the config file in the env variable
const char * value = itksys::SystemTools::GetEnv("DTIAtlasBuilderSoftPath"); // C function = const char * getenv(const char *)
if (value!=NULL)
{
printf ("| Environment variable read. The config file is \'%s\'\n",value);
if( LoadConfig(QString(value)) == -1 )
{
m_ErrorDetectedInConstructor=true; // replace the paths by the paths given in the config file
}
}
else
{
std::cout<<"| No environment variable found"<<std::endl;
}
/* Look for the parameter file in the current directory */ // Load only if no param file given and if CSV file is given, only load the given CSV file.
std::string ParamPath = CurrentPath + "/DTIAtlasBuilderParameters.txt";
if( ParamFile.empty() && itksys::SystemTools::GetPermissions( ParamPath.c_str() , ITKmode_F_OK) )
{
if( LoadParameters(QString( ParamPath.c_str() ), !CSVFile.empty()) == -1 )
{
m_ErrorDetectedInConstructor=true;
}
}
/* Load Parameters from Command Line => cmd line arguments a taking into account at last and change the parameters at last because they have priority */
if( !ParamFile.empty() )
{
if( LoadParameters(QString(ParamFile.c_str()), !CSVFile.empty()) == -1 )
{
m_ErrorDetectedInConstructor=true;
}
}
else if(m_noGUI) // no parameters and nogui => not possible
{
std::cout<<"| Please give a parameter file"<<std::endl; // command line display
m_ErrorDetectedInConstructor=true;
}
if( !CSVFile.empty() )
{
if( ReadCSV( QString(CSVFile.c_str())) == -1 )
{
m_ErrorDetectedInConstructor=true;
}
}
if( !ConfigFile.empty() )
{
if( LoadConfig( QString(ConfigFile.c_str())) == -1 )
{
m_ErrorDetectedInConstructor=true;
}
}
m_FromConstructor=0;
/* NOW that all the files have been loaded => test if all the paths are here */
bool GAFound=true;
bool DTIRegFound=true;
std::string notFound;
if(ImagemathPath->text().isEmpty()) notFound = notFound + "> ImageMath\n";
if(ResampPath->text().isEmpty()) notFound = notFound + "> ResampleDTIlogEuclidean\n";
if(CropDTIPath->text().isEmpty()) notFound = notFound + "> CropDTI\n";
if(dtiprocPath->text().isEmpty()) notFound = notFound + "> dtiprocess\n";
if(BRAINSFitPath->text().isEmpty()) notFound = notFound + "> BRAINSFit\n";
if(GAPath->text().isEmpty())
{
notFound = notFound + "> GreedyAtlas\n";
GAFound=false; // so it will not test the version
}
if(dtiavgPath->text().isEmpty()) notFound = notFound + "> dtiaverage\n";
if(DTIRegPath->text().isEmpty())
{
notFound = notFound + "> DTI-Reg\n";
DTIRegFound=false; // so it will not test the version
}
if(unuPath->text().isEmpty()) notFound = notFound + "> unu\n";
if(MriWatcherPath->text().isEmpty()) notFound = notFound + "> MriWatcher (Program will work, but QC will not be available)\n";
if( !notFound.empty() )
{
if(!m_noGUI && !m_Testing)
{
std::string text = "The following programs have not been found.\nPlease enter the path manually or open a configuration file:\n" + notFound;
QMessageBox::warning(this, "Program missing", QString(text.c_str()) );
}
else
{
std::cout<<"| The following programs have not been found. Please give a configuration file or modify it or enter the path manually in the GUI:\n"<< notFound <<std::endl;
}
}
if(GAFound)
{
testGA(); // test the version of GreedyAtlas only if found
}
if(DTIRegFound)
{
testDTIReg(); // test the version of DTI-Reg only if found
}
}
/////////////////////////////////////////
// INITIALIZATIONS //
/////////////////////////////////////////
void GUI::InitOptions()
{
/* Init options for Final AtlasBuilding param : Interpolation algo */
m_optionStackLayout = new QStackedWidget;
optionHLayout->addWidget(m_optionStackLayout);
QWidget *emptyWidget= new QWidget;
m_optionStackLayout->addWidget(emptyWidget);
QLabel *windowLabel = new QLabel("Type:", this);
m_windowComboBox = new QComboBox(this);
m_windowComboBox->addItem("Hamming");
m_windowComboBox->addItem("Cosine");
m_windowComboBox->addItem("Welch");
m_windowComboBox->addItem("Lanczos");
m_windowComboBox->addItem("Blackman");
m_windowComboBox->setCurrentIndex(1);
QHBoxLayout *windowLayout= new QHBoxLayout;
windowLayout->addWidget(windowLabel);
windowLayout->addWidget(m_windowComboBox);
QWidget *windowWidget= new QWidget;
windowWidget->setLayout(windowLayout);
m_optionStackLayout->addWidget(windowWidget);
QLabel *BSplineLabel = new QLabel("Order:", this);
m_BSplineComboBox = new QComboBox(this);
m_BSplineComboBox->addItem("0");
m_BSplineComboBox->addItem("1");
m_BSplineComboBox->addItem("2");
m_BSplineComboBox->addItem("3");
m_BSplineComboBox->addItem("4");
m_BSplineComboBox->addItem("5");
m_BSplineComboBox->setCurrentIndex(3);
QHBoxLayout *BSplineLayout= new QHBoxLayout;
BSplineLayout->addWidget(BSplineLabel);
BSplineLayout->addWidget(m_BSplineComboBox);
QWidget *BSplineWidget= new QWidget;
BSplineWidget->setLayout(BSplineLayout);
m_optionStackLayout->addWidget(BSplineWidget);
m_optionStackLayout->setCurrentIndex(0);
/* Init options for Final AtlasBuilding param : Tensor Interpolation */
m_logOptionStackLayout = new QStackedWidget;
logOptionHLayout->addWidget(m_logOptionStackLayout);
QWidget *logEmptyWidget= new QWidget;
m_logOptionStackLayout->addWidget(logEmptyWidget);
QLabel *nologLabel = new QLabel("Correction:", this);
m_nologComboBox = new QComboBox(this);
m_nologComboBox->addItem("Zero");
m_nologComboBox->addItem("None");
m_nologComboBox->addItem("Absolute Value");
m_nologComboBox->addItem("Nearest");
m_nologComboBox->setCurrentIndex(1);
QHBoxLayout *nologLayout= new QHBoxLayout;
nologLayout->addWidget(nologLabel);
nologLayout->addWidget(m_nologComboBox);
QWidget *nologWidget= new QWidget;
nologWidget->setLayout(nologLayout);
m_logOptionStackLayout->addWidget(nologWidget);
m_logOptionStackLayout->setCurrentIndex(0);
/* Init options for DTI-Reg: Reg Method */
m_DTIRegOptionStackLayout = new QStackedWidget;
DTIRegOptionsVLayout->addWidget(m_DTIRegOptionStackLayout);
/*BRAINS*/
QHBoxLayout *BRAINSHLayout = new QHBoxLayout;
QVBoxLayout *BRAINSLabelVLayout = new QVBoxLayout;
BRAINSHLayout->addLayout(BRAINSLabelVLayout);
QVBoxLayout *BRAINSWidgetVLayout = new QVBoxLayout;
BRAINSHLayout->addLayout(BRAINSWidgetVLayout);
QLabel *BRegTypeLabel = new QLabel("Registration Type:", this);
BRAINSLabelVLayout->addWidget(BRegTypeLabel);
m_BRegTypeComboBox = new QComboBox(this);
m_BRegTypeComboBox->addItem("None");
m_BRegTypeComboBox->addItem("Rigid");
m_BRegTypeComboBox->addItem("BSpline");
m_BRegTypeComboBox->addItem("Diffeomorphic");
m_BRegTypeComboBox->addItem("Demons");
m_BRegTypeComboBox->addItem("FastSymmetricForces");
m_BRegTypeComboBox->setCurrentIndex(3);
BRAINSWidgetVLayout->addWidget(m_BRegTypeComboBox);
QLabel *TfmModeLabel = new QLabel("Transform Mode:", this);
BRAINSLabelVLayout->addWidget(TfmModeLabel);
m_TfmModeComboBox = new QComboBox(this);
m_TfmModeComboBox->addItem("Off");
m_TfmModeComboBox->addItem("useMomentsAlign");
m_TfmModeComboBox->addItem("useCenterOfHeadAlign");
m_TfmModeComboBox->addItem("useGeometryAlign");
m_TfmModeComboBox->addItem("Use computed affine transform");
m_TfmModeComboBox->setCurrentIndex(4);
BRAINSWidgetVLayout->addWidget(m_TfmModeComboBox);
QLabel *NbPyrLevLabel = new QLabel("Number Of Pyramid Levels:", this);
BRAINSLabelVLayout->addWidget(NbPyrLevLabel);
m_NbPyrLevSpin = new QSpinBox(this);
m_NbPyrLevSpin->setValue(5);
BRAINSWidgetVLayout->addWidget(m_NbPyrLevSpin);
QLabel *PyrLevItLabel = new QLabel("Number Of Iterations for the Pyramid Levels:", this);
BRAINSLabelVLayout->addWidget(PyrLevItLabel);
m_PyrLevItLine = new QLineEdit(this);
m_PyrLevItLine->setText("300,50,30,20,15");
BRAINSWidgetVLayout->addWidget(m_PyrLevItLine);
QWidget *BRAINSWidget = new QWidget;
BRAINSWidget->setLayout(BRAINSHLayout);
m_DTIRegOptionStackLayout->addWidget(BRAINSWidget);
/*ANTS*/
QHBoxLayout *ANTSHLayout = new QHBoxLayout;
QVBoxLayout *ANTSLabelVLayout = new QVBoxLayout;
ANTSHLayout->addLayout(ANTSLabelVLayout);
QVBoxLayout *ANTSWidgetVLayout = new QVBoxLayout;
ANTSHLayout->addLayout(ANTSWidgetVLayout);
QLabel *ARegTypeLabel = new QLabel("Registration Type:", this);
ANTSLabelVLayout->addWidget(ARegTypeLabel);
m_ARegTypeComboBox = new QComboBox(this);
m_ARegTypeComboBox->addItem("None");
m_ARegTypeComboBox->addItem("Rigid");
m_ARegTypeComboBox->addItem("Elast");
m_ARegTypeComboBox->addItem("Exp");
m_ARegTypeComboBox->addItem("GreedyExp");
m_ARegTypeComboBox->addItem("GreedyDiffeo (SyN)");
m_ARegTypeComboBox->addItem("SpatioTempDiffeo (SyN)");
m_ARegTypeComboBox->setCurrentIndex(5);
QObject::connect(m_ARegTypeComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(ANTSRegTypeChanged( int )));
ANTSWidgetVLayout->addWidget(m_ARegTypeComboBox);
QLabel *TfmStepLabel = new QLabel("Transformation Step:", this);
ANTSLabelVLayout->addWidget(TfmStepLabel);
m_TfmStepLine = new QLineEdit(this);
m_TfmStepLine->setText("0.25");
ANTSWidgetVLayout->addWidget(m_TfmStepLine);
QLabel *IterLabel = new QLabel("Iterations:", this);
ANTSLabelVLayout->addWidget(IterLabel);
m_IterLine = new QLineEdit(this);
m_IterLine->setText("100x50x25");
ANTSWidgetVLayout->addWidget(m_IterLine);
QLabel *SimMetLabel = new QLabel("Similarity Metric:", this);
ANTSLabelVLayout->addWidget(SimMetLabel);
m_SimMetComboBox = new QComboBox(this);
m_SimMetComboBox->addItem("Cross-Correlation (CC)");
m_SimMetComboBox->addItem("Mutual Information (MI)");
m_SimMetComboBox->addItem("Mean Square Difference (MSQ)");
m_SimMetComboBox->setCurrentIndex(0);
QObject::connect(m_SimMetComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(SimMetChanged( int )));
ANTSWidgetVLayout->addWidget(m_SimMetComboBox);
m_SimParamLabel = new QLabel("Region Radius:", this);
ANTSLabelVLayout->addWidget(m_SimParamLabel);
m_SimParamDble = new QDoubleSpinBox(this);
m_SimParamDble->setValue(2);
ANTSWidgetVLayout->addWidget(m_SimParamDble);
QLabel *GSigmaLabel = new QLabel("Gaussian Sigma:", this);
ANTSLabelVLayout->addWidget(GSigmaLabel);
m_GSigmaDble = new QDoubleSpinBox(this);
m_GSigmaDble->setValue(3);
ANTSWidgetVLayout->addWidget(m_GSigmaDble);
m_SmoothOffCheck = new QCheckBox("Gaussian Smoothing Off", this);
m_SmoothOffCheck->setChecked(false);
m_SmoothOffCheck->setLayoutDirection(Qt::RightToLeft);
ANTSLabelVLayout->addWidget(m_SmoothOffCheck);
QLabel *emptyL = new QLabel("", this);
ANTSWidgetVLayout->addWidget(emptyL);
QWidget *ANTSWidget = new QWidget;
ANTSWidget->setLayout(ANTSHLayout);
m_DTIRegOptionStackLayout->addWidget(ANTSWidget);
m_DTIRegOptionStackLayout->setCurrentIndex(0); //BRAINS is the default
}
/////////////////////////////////////////
// CASES //
/////////////////////////////////////////
bool GUI::FileIsParameterFile( std::string filepath ) // TODO
{
if( itksys::SystemTools::GetFilenameLastExtension( filepath ) != ".txt" )
{
return false;
}
QFile file(filepath.c_str());
if (file.open(QFile::ReadOnly))
{
QTextStream stream(&file);
QString line = stream.readLine();
QStringList list = line.split("=");
if( ! list.at(0).contains("DTIAtlasBuilderParameterFileVersion") )
{
return false;
}
}
return true;
}
bool GUI::FileIsSoftConfigFile( std::string filepath ) // TODO
{
if( itksys::SystemTools::GetFilenameLastExtension( filepath ) != ".txt" )
{
return false;
}
QFile file(filepath.c_str());
if (file.open(QFile::ReadOnly))
{
QTextStream stream(&file);
QString line = stream.readLine();
QStringList list = line.split("=");
if( ! list.at(0).contains("ImageMath") )
{
return false;
}
line = stream.readLine();
list = line.split("=");
if( ! list.at(0).contains("ResampleDTIlogEuclidean") )
{
return false;
}
}
return true;
}
void GUI::dragEnterEvent(QDragEnterEvent *event)
{
event->acceptProposedAction();
}
void GUI::dropEvent(QDropEvent* event)
{
const QMimeData* mimeData = event->mimeData();
// check for needed mime type, a file or a list of files
if( mimeData->hasUrls() )
{
QStringList pathList;
QList<QUrl> urlList = mimeData->urls();
// extract the local paths of the files
for (int i = 0; i < urlList.size(); ++i)
{
QString CurrentFile = urlList.at(i).toLocalFile();
if ( itksys::SystemTools::GetFilenameLastExtension( CurrentFile.toStdString() ) == ".csv" ) // load possible csv file(s)
{
ReadCSV( CurrentFile );
}
else if ( FileIsParameterFile( CurrentFile.toStdString() ) ) // load possible parameter file(s)
{
LoadParameters(CurrentFile,false);
}
else if ( FileIsSoftConfigFile( CurrentFile.toStdString() ) ) // load possible soft config file(s)
{
LoadConfig(CurrentFile);
}
else // other file -> maybe image: will be check in AddCasesToListWidget()
{
pathList.append( CurrentFile );
}
}
AddCasesToListWidget(pathList, QString(""));
} // if mimedata hasurls
} // dropEvent
void GUI::OpenAddCaseBrowseWindow() /*SLOT*/
{
QStringList CaseListBrowse = QFileDialog::getOpenFileNames(this, "Open Cases", m_lastCasePath, "ITK format Images (*.nrrd *.nhdr *.nii *.nii.gz *.*)");
AddCasesToListWidget(CaseListBrowse, QString(""));
}
void GUI::AddCasesToListWidget(QStringList CaseList, QString CSVfiletext) // called when drag&dropping any file or adding files with the + button or loading CSV file
{
bool SomeFilesAreNotImages = false;
// Add REAL PATH of cases to list
for(unsigned int i=0; i<CaseList.count() ; i++)
{
std::string CaseRealPath = itksys::SystemTools::GetRealPath( CaseList.at(i).toStdString().c_str() );
if( CheckCase( CaseRealPath, true ) ) // true for no display if error: just not add file
{
CaseListWidget->addItem( QString( CaseRealPath.c_str() ) );
}
else
{
SomeFilesAreNotImages = true; // to display warning
}
}
if( SomeFilesAreNotImages && !m_noGUI && !m_Testing )
{
QMessageBox::warning(this, "Not DTI Images", "Some of the files added were not DTI images.\nThese files have not been loaded into the list." );
}
if(!CaseList.isEmpty())
{
if( CaseListWidget->count()>0 )
{
RemovePushButton->setEnabled(true);
ComputepushButton->setEnabled(true);
if( ! OutputFolderLineEdit->text().isEmpty() )
{
EnableQC();
}
}
m_ParamSaved=0;
SelectCasesLabel->setText( CSVfiletext );
m_lastCasePath = CaseList.last();
CheckCasesIndex();
}
}
void GUI::RemoveSelectedCases() /*SLOT*/
{
int NbOfSelectedItems = (CaseListWidget->selectedItems()).size();
int NB=NbOfSelectedItems;
int ItemRow;
while(NbOfSelectedItems>0)
{
ItemRow = CaseListWidget->row( CaseListWidget->selectedItems().at(0) );
CaseListWidget->takeItem(ItemRow);
delete CaseListWidget->selectedItems().at(0);
NbOfSelectedItems--;
}
if( NB>0 ) // only if some items were removed
{
if ( CaseListWidget->count()==0 )
{
RemovePushButton->setEnabled(false);
ComputepushButton->setEnabled(false);
DisableQC();
}
m_ParamSaved=0;
SelectCasesLabel->setText( QString("") );
CheckCasesIndex();
}
}
void GUI::CheckCasesIndex() /* Check duplicates Change ids at the begining of the lines */
{
// Check IDs at the beginning of the lines
std::string text;
for(int i=0; i < CaseListWidget->count() ;i++)
{
if( CaseListWidget->item(i)->text().contains(": ") ) text = IntOrDoubleToStr<int>(i+1) + ": " + CaseListWidget->item(i)->text().toStdString().substr( CaseListWidget->item(i)->text().split(":").at(0).size()+2 ); // from pos to the end
else text = IntOrDoubleToStr<int>(i+1) + ": " + CaseListWidget->item(i)->text().toStdString();
CaseListWidget->item(i)->setText( QString( text.c_str() ) );
}
// Check and remove possible duplicates in the list
std::vector< std::string > UniqueCaseVector; // contains only one of each
unsigned int NbUniqueCases = CaseListWidget->count();
bool RemoveDuplicatesWarningDisplayed = false; // to display popup only once
for(unsigned int i=0; i<NbUniqueCases; i++)
{
std::string CurrentCase = CaseListWidget->item(i)->text().toStdString().substr( CaseListWidget->item(i)->text().split(":").at(0).size()+2 );
// substr: keep only what is after "id: " (.size() returns the nb of digits of the id and +2 is for ": " after the id number)
// search and remove
if( std::find( UniqueCaseVector.begin(), UniqueCaseVector.end(), CurrentCase ) != UniqueCaseVector.end() ) // not the only one: if found => != end
{
if( !m_noGUI && !m_Testing && !RemoveDuplicatesWarningDisplayed ) // for the first duplicate found, ask if want to remove, if no break
{
int ret = QMessageBox::warning(this,"Remove duplicates","Duplicated cases have been detected in the list.\nDo you want to remove these duplicates?",QMessageBox::No | QMessageBox::Yes);
if(ret == QMessageBox::No) break; // if no remove break the for loop HERE so nothing removed
RemoveDuplicatesWarningDisplayed = true;
}
CaseListWidget->takeItem(i); //remove current
i--;
NbUniqueCases--;
}
else // first one
{
UniqueCaseVector.push_back( CurrentCase );
}
}
} // CheckCasesIndex()
/////////////////////////////////////////
// OUTPUT //
/////////////////////////////////////////
void GUI::OpenOutputBrowseWindow() /*SLOT*/
{
// If already an output folder, browse from this location
QString CurrentOutputFolder = "";
if( !OutputFolderLineEdit->text().isEmpty() )
{
CurrentOutputFolder = OutputFolderLineEdit->text();
}
QString OutputBrowse = QFileDialog::getExistingDirectory( this, "Find Directory", CurrentOutputFolder );
if(!OutputBrowse.isEmpty())
{
OutputFolderLineEdit->setText(OutputBrowse);
}
}
void GUI::CleanOutputFolder() /*SLOT*/
{
// Remove all useless temporary images
std::string PopupText = "This action will remove the content of all these folders:\n" + OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/1_Affine_Registration\n" + OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/2_NonLinear_Registration\n" + OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/3_Diffeomorphic_Atlas\n" + OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/4_Final_Resampling/First_Resampling\n\nDo you really want to remove them?";
int ret = QMessageBox::warning(this, "Remove Files", QString( PopupText.c_str() ), QMessageBox::No | QMessageBox::Yes );
if (ret == QMessageBox::Yes)
{
std::cout<<"| Cleaning output folder...";
std::vector< std::string > PathsToRemove;
PathsToRemove.push_back(OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/1_Affine_Registration");
PathsToRemove.push_back(OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/2_NonLinear_Registration");
PathsToRemove.push_back(OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/3_Diffeomorphic_Atlas");
PathsToRemove.push_back(OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/4_Final_Resampling/First_Resampling");
for( unsigned int i = 0 ; i < PathsToRemove.size() ; ++i )
{
if( itksys::SystemTools::GetPermissions( PathsToRemove[i].c_str(), ITKmode_F_OK ) )
{
itksys::SystemTools::RemoveADirectory( PathsToRemove[i].c_str() );
}
}
// itksys::SystemTools::RemoveFile(const char* source);
std::cout<<"DONE"<<std::endl;
} // if (ret == QMessageBox::Yes)
}
/////////////////////////////////////////
// DTI-Reg //
/////////////////////////////////////////
void GUI::OpenDTIRegExtraPathBrowseWindow() /*SLOT*/
{
QString DTIRegExtraPathBrowse=QFileDialog::getExistingDirectory(this);
if(!DTIRegExtraPathBrowse.isEmpty())
{
DTIRegExtraPathlineEdit->setText(DTIRegExtraPathBrowse);
}
}
/////////////////////////////////////////
// TEMPLATE //
/////////////////////////////////////////
void GUI::OpenTemplateBrowseWindow() /*SLOT*/
{
QString TemplateBrowse=QFileDialog::getOpenFileName(this, "Open Atlas FA Template", QString(), "ITK format Images (*.nrrd *.nhdr *.nii *.nii.gz *.*)");
if(!TemplateBrowse.isEmpty())
{
TemplateLineEdit->setText(TemplateBrowse);
}
}
/////////////////////////////////////////
// QUALITY CONTROL //
/////////////////////////////////////////
void GUI::DisplayAffineQC() /*SLOT*/
{
std::string program = MriWatcherPath->text().toStdString() + " --viewAll";
std::string pathList="";
std::string path;
for(int i=0; i < CaseListWidget->count() ;i++)
{
path = OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/1_Affine_Registration/Loop" + IntOrDoubleToStr<int>(NbLoopsSpinBox->value()) + "/" + itksys::SystemTools::GetFilenameWithoutExtension( CaseListWidget->item(i)->text().toStdString() ) + "_Loop" + IntOrDoubleToStr<int>(NbLoopsSpinBox->value()) + "_FinalFA.nrrd";
if( itksys::SystemTools::GetPermissions(path.c_str(), ITKmode_F_OK) ) pathList = pathList + " " + path;
}
if(NbLoopsSpinBox->value()>0)
{
path = OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/1_Affine_Registration/Loop" + IntOrDoubleToStr<int>(NbLoopsSpinBox->value()-1) + "/Loop" + IntOrDoubleToStr<int>(NbLoopsSpinBox->value()-1) + "_FAAverage.nrrd";
}
else // if no looping (NbLoopsSpinBox->value()==0), an average is computed anyway for QC
{
path = OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/1_Affine_Registration/Loop0/Loop0_FAAverage.nrrd";
}
if( itksys::SystemTools::GetPermissions(path.c_str(), ITKmode_F_OK) ) pathList = pathList + " " + path;
if( pathList != "" )
{
program = program + pathList;
std::cout<<"| Starting: "<<program<<std::endl;
QProcess* QCQProcess = new QProcess;
QCQProcess->start(program.c_str());
}
else
{
if(!m_noGUI && !m_Testing)
{
std::string text = "None of the images to be displayed have been found.\nPlease check that these files exist:\n" + OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/1_Affine_Registration/Loop" + IntOrDoubleToStr<int>(NbLoopsSpinBox->value()) + "/*_Loop" + IntOrDoubleToStr<int>(NbLoopsSpinBox->value()) + "_FinalFA.nrrd";
QMessageBox::warning(this, "No images found", text.c_str() );
}
else
{
std::cout<<"| None of the images to be displayed have been found. Please check that these files exist: "<< OutputFolderLineEdit->text().toStdString() << "/DTIAtlas/1_Affine_Registration/Loop" << IntOrDoubleToStr<int>(NbLoopsSpinBox->value()) << "/*_Loop" << IntOrDoubleToStr<int>(NbLoopsSpinBox->value()) << "_FinalFA.nrrd" <<std::endl;
}
}
}
void GUI::DisplayDeformQC() /*SLOT*/
{
std::string program = MriWatcherPath->text().toStdString() + " --viewAll";
std::string pathList="";
std::string path;
for(int i=0; i < CaseListWidget->count() ;i++)
{
path = OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/3_Diffeomorphic_Atlas/" + itksys::SystemTools::GetFilenameWithoutExtension( CaseListWidget->item(i)->text().toStdString() ) + "_DiffeomorphicFA.nrrd";
if( itksys::SystemTools::GetPermissions(path.c_str(), ITKmode_F_OK) ) pathList = pathList + " " + path;
}
path = OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/3_Diffeomorphic_Atlas/DiffeomorphicAtlasFA.nrrd";
if( itksys::SystemTools::GetPermissions(path.c_str(), ITKmode_F_OK) ) pathList = pathList + " " + path;
if( pathList != "" )
{
program = program + pathList;
std::cout<<"| Starting: "<<program<<std::endl;
QProcess* QCQProcess = new QProcess;
QCQProcess->start(program.c_str());
}
else
{
if(!m_noGUI && !m_Testing)
{
std::string text = "None of the images to be displayed have been found.\nPlease check that these files exist:\n" + OutputFolderLineEdit->text().toStdString() + "/DTIAtlas/3_Diffeomorphic_Atlas/*_DiffeomorphicFA.nrrd";
QMessageBox::warning(this, "No images found", text.c_str() );
}
else
{
std::cout<<"| None of the images to be displayed have been found. Please check that these files exist: "<< OutputFolderLineEdit->text().toStdString() << "/DTIAtlas/3_Diffeomorphic_Atlas/*_DiffeomorphicFA.nrrd" <<std::endl;
}
}