mainwindow.cpp

#include "mainwindow.h"
#include "ui_mainwindow.h"
#include "editlist.h"
#include "editfeat.h"
#include "choosecombinations.h"
#include <QSpinBox>
#include <QMessageBox>
#include<QFileDialog>
#include<QJsonDocument>
#include<QJsonObject>
#include<QThread>
#include<QProcess>
MainWindow::MainWindow(QWidget *parent) :
    QMainWindow(parent),
    ui(new Ui::MainWindow)
{
//    Environment.currentEnv():{
    /*This is the main window which will appear as you run
     * the GUI. Some of the boxes have been checked false and some have
     * hidden according to the requirements of the program.
     *
     */

    ui->setupUi(this);
    ui->radioButton_Unprocessed->setChecked(true);
    ui->checkBox->setChecked(false);
    ui->checkBox_preprocFeat->setChecked(false);
    ui->checkBox_ROICorrs->setChecked(false);
    ui->checkBox_GSR->setChecked(false);
    ui->checkBox_GSR_2->setChecked(false);
    ui->spinBox->setRange(1,5);

    // Values set randomly for now. These are no of the threads which will
    // be executed. Can be changed later to some other value.
    ui->spinBox_threads->setRange(1,12);
    ui->spinBox_threads->setValue(4);


    ui->checkBox_wt_groups->setChecked(true);
    ui->checkBox_bw_groups->setChecked(false);
    ui->checkBox_bw_groups->hide();
    ui->chooseCombsButton->hide();
    ui->label_Hypothesis->hide();
    ui->radioButton_G1_gr_G2->hide();
    ui->radioButton_G1_gr_G2->setChecked(true);
    ui->radioButton_G2_gr_G1->hide();
    ui->radioButton_NormFischer->setChecked(true);
    ui->radioButton_reg_n->setChecked(true);
    ui->radioButton_Ank_Corr->setChecked(true);
    ui->checkBox_doStats->setChecked(true);
    ui->radioButton_SepFDRcorrect->setChecked(true);
    ui->lineEdit_highpass->hide();
    ui->lineEdit_lowpass->hide();
    ui->label_BET_Correct->hide();
    ui->checkBox_GSR_2->hide();
    ui->lineEdit_BET_correct_value->hide();
    ui->checkBox_RobustBET->setChecked(false);
    ui->checkBox_RobustBET->hide();

    //Here I set the default name for the Analysis. It can be changed accordingly.
    QString DefAnalysisName = "FConnectivityAnl";

    //In case 'FSLDIR' path exists, the box will get flooded.
    if (QDir(FSLDIR).exists()){
        ui->lineEdit_FSLDIR->setText(FSLDIR);
    }

    //OutDir stores the current directory we are in.
    ui->lineEdit_AnalysisName->setText(DefAnalysisName);
    ui->lineEdit_OutDir->setText(OutDir + "/"+DefAnalysisName);
}


MainWindow::~MainWindow()
{
    // Deletes the ui when we exit the mainwindow.
    delete ui;
}

void MainWindow::on_pushButton_chooseData_clicked()
{
    /*
     * Function to be performed when the 'Choose Data'
     * button is clicked. If the preprocessing has already been
     * done with FSL, then we just need to take the FEAT folders
     * else we need to display a different window where both
     * functional and structural files are to be given.
     */
    if (ui->radioButton_PreprocwFSL->isChecked()){
        // Preprocessing done with FSL
        // Displays the 'editFeat' window and set number of
        // groups equal to spinBoxvalue. At the end, we need to
        // get the Feat File names.
        editFeat editfeat;
        editfeat.setGroups(spinBoxValue);
        editfeat.setModal(true);
        editfeat.exec();
        FeatFileNames= editfeat.get_FileNames();
    }
    else {
        // No preprocessing done or done without FSL.
        // Displays the 'editlist' window and set number of
        // groups equal to spinBoxvalue. At the end, we need to get
        // lists of Functional and Structural files.
        EditList editlist;
        editlist.setGroups(spinBoxValue);
        editlist.setModal(true);
        editlist.exec();
        StructuralFileNames = editlist.get_StructuralFileNames();
        FunctionalFileNames = editlist.get_FunctionalFileNames();
    }

}

void MainWindow::on_pushButton_7_clicked()
{
    // Displays the help information
    QMessageBox::information(this,"Help", "Put the reference MNI structural file here.");
}

void MainWindow::on_pushButton_3_clicked()
{
    QApplication::quit();
}

//void MainWindow::on_pushButton_6_clicked()
//{
//    QApplication::quit();
//}

void MainWindow::on_pushButton_12_clicked()
{
    QApplication::quit();
}

void MainWindow::on_pushButton_18_clicked()
{
    QMessageBox::information(this,"Help", "If correlation files given, then there is no requirement of input.");

}

void MainWindow::on_commandLinkButton_Reference_clicked()
{
    /*
     * Sets the Reference MNI space File in the lineEdit box.
     */
    QString new_input;

    // Get the input already present in the cell.
    QString already_input = ui->lineEdit_Reference->text();
    QFile Fout(already_input) ;

    if (Fout.exists())
    {
        // If such file exists, then opne the Directory chooser from that path.
        new_input=QFileDialog::getOpenFileName(
                                                    this,
                                                    tr("Open File"),
                                                    already_input,
                                                    "Nifti File (*.nii.gz);;All files (*.*)"
                                                       );
    }
    else
    {
        // else open it from the default path.
        new_input=QFileDialog::getOpenFileName(
                                                this,
                                                tr("Open File"),
                                                CommonDir,
                                                "Nifti File (*.nii.gz);;All files (*.*)"
                                                   );
    }
    if (new_input!=NULL){
        // It is used for handling the CANCEL button. In case the cancel is clicked in
        // directory chooser, then we need to set it to previous input else the new input.
    ui->lineEdit_Reference->setText(new_input);
    }
    else {
        ui->lineEdit_Reference->setText(already_input);
    }
}

void MainWindow::on_commandLinkButton_OutDir_clicked()
{
    /*
     * The function is same as that of Reference File Command button.
     * There's a difference just in populating the box. We need to add the Analysis Name
     * at the end. This function is used for giving the Output Directory.
     */
    QString new_Dir;

    if (QDir(OutDir).exists())
    {
        new_Dir=QFileDialog::getExistingDirectory(
                                                    this,
                                                    tr("Choose Directory"),
                                                    OutDir);
    }
    else {
        new_Dir =QFileDialog::getExistingDirectory(
                                                this,
                                                tr("Choose Directory"),
                                                CommonDir);
    }
    if (new_Dir!=NULL){
        ui->lineEdit_OutDir->setText(new_Dir +"/"+ ui->lineEdit_AnalysisName->text());
        OutDir = new_Dir+"/";
    }
    else{
        ui->lineEdit_OutDir->setText(OutDir + ui->lineEdit_AnalysisName->text());
    }
}

void MainWindow::on_commandLinkButton_ROIFile_clicked()
{
    /*
     * This function is also same as that of Reference File command button.
     * It is used for selecting the ROI file input.
     */
    QString new_input;
    QString already_input = ui->lineEdit_ROIFile->text();
    QFile Fout(already_input) ;

    if (Fout.exists())
    {
        already_input=QFileDialog::getOpenFileName(
                                                    this,
                                                    tr("Open File"),
                                                    already_input,
                                                    "Nifti File (*.nii.gz);;All files (*.*)"
                                                       );
    }
    else
    {
        already_input=QFileDialog::getOpenFileName(
                                                this,
                                                tr("Open File"),
                                                CommonDir,
                                                "Nifti File (*.nii.gz);;All files (*.*)"
                                                   );
    }
    if (new_input!=NULL){
        ui->lineEdit_ROIFile->setText(new_input);

    }
    else {
        ui->lineEdit_ROIFile->setText(already_input);
    }
}

void MainWindow::on_commandLinkButton_FSLDIR_clicked()
{
    /*
     * TO BE REVIEWED. THE FN IS NOT YET COMPLETE.
     */
    QString new_Dir;

    if (QDir(FSLDIR).exists())
    {
        new_Dir=QFileDialog::getExistingDirectory(
                                                    this,
                                                    tr("Choose Directory"),
                                                    FSLDIR);
    }
    else {
        new_Dir =QFileDialog::getExistingDirectory(
                                                this,
                                                tr("Choose Directory"),
                                                CommonDir);
    }
    if (new_Dir!=NULL){
        ui->lineEdit_FSLDIR->setText(new_Dir);
        FSLDIR = new_Dir;
    }
    else{
        ui->lineEdit_OutDir->setText(FSLDIR);
    }
    QString filename=QFileDialog::getExistingDirectory(
                                                this,
                                                tr("Choose Directory"),
                                                CommonDir);
    ui->lineEdit_FSLDIR->setText(filename);
}



void MainWindow::on_commandLinkButton_CorrFile_clicked()
{

    QString new_input;
    QString already_input = ui->lineEdit_CorrFile->text();
    QFile Fout(already_input) ;

    if (Fout.exists())
    {
      already_input=QFileDialog::getOpenFileName(
                                                    this,
                                                    tr("Open File"),
                                                    already_input,
                                                    "Nifti File (*.nii.gz);;All files (*.*)"
                                                       );
    }
    else
    {
        already_input=QFileDialog::getOpenFileName(
                                                this,
                                                tr("Open File"),
                                                CommonDir,
                                                "Nifti File (*.nii.gz);;All files (*.*)"
                                                   );
    }
    if (new_input!=NULL){
        ui->lineEdit_CorrFile->setText(new_input);

    }
    else {
        ui->lineEdit_CorrFile->setText(already_input);
    }
}

void MainWindow::on_help_ROIFile_clicked()
{
    QMessageBox::information(this,"Caution", "This file must be registered to reference.");
}


void MainWindow::on_lineEdit_AnalysisName_textEdited(const QString &arg1)
{
    ui->lineEdit_OutDir->setText(OutDir +"/"+ arg1);

}







void MainWindow::on_chooseCombsButton_clicked()
{
    /*
     * For testing purpose
    QList<int> list;
    list<<100<<500;
    */

    QString AB;
    chooseCombinations choosecombinations;
    choosecombinations.setCheckboxes(spinBoxValue);
    choosecombinations.setModal(true);
    choosecombinations.exec();
    mirrored_checkStates = choosecombinations.checkedGroups;
    int GroupB = 2;
    int lastOne =1;
    for (int i = 0; i < mirrored_checkStates.size(); ++i) {
        combinations.append(mirrored_checkStates.at(i)/2);
        if (mirrored_checkStates.at(i) == 2){

            AB+= "Group_" + QString::number(lastOne) + "_vs_Group_" + QString::number(GroupB) +",";
        }
        GroupB++;
        if (GroupB>spinBoxValue){
            lastOne++;
            GroupB =lastOne + 1;
        }
    }
    QMessageBox::information(this,"Help",AB);
}

void MainWindow::on_spinBox_valueChanged(int arg1)
{
    bool check_bw_groups = ui->checkBox_bw_groups->isChecked();
    spinBoxValue = arg1;
    FeatFileNames.clear();
    FunctionalFileNames.clear();
    StructuralFileNames.clear();
    if (arg1==1){
        ui->checkBox_wt_groups->setChecked(true);
        ui->checkBox_bw_groups->hide();
        on_checkBox_bw_groups_clicked(false);
    }
    else if (arg1==2){
        ui->checkBox_bw_groups->show();
        on_checkBox_bw_groups_clicked(check_bw_groups);
        ui->checkBox_AllCombs->hide();
        ui->chooseCombsButton->hide();
        if (check_bw_groups){
            ui->label_Hypothesis->show();
            ui->radioButton_G1_gr_G2->show();
            ui->radioButton_G2_gr_G1->show();
            ui->radioButton_G1_gr_G2->setChecked(true);
        }
    }
    else {
        ui->checkBox_bw_groups->show();
        on_checkBox_bw_groups_clicked(check_bw_groups);
        if (check_bw_groups){
            ui->checkBox_AllCombs->show();
            ui->checkBox_AllCombs->setChecked(true);
            ui->label_Hypothesis->hide();
            ui->radioButton_G1_gr_G2->hide();
            ui->radioButton_G2_gr_G1->hide();
        }

    }
}

void MainWindow::on_checkBox_AllCombs_clicked(bool checked)
{
    if (!checked){
        ui->chooseCombsButton->show();
    }
    else {
        ui->chooseCombsButton->hide();
    }
}

void MainWindow::writeStats(QJsonObject &json) const
{
    if (ui->checkBox_wt_groups->isChecked()){
        json["Analysis within Groups"] = true;
    }
    if (ui->checkBox_bw_groups->isChecked()){
        json["Analysis between Groups"] = true;
        if (spinBoxValue ==2)
            json["Gr1>Gr2"] = ui->radioButton_G1_gr_G2->isChecked();
        else{
            json["Combinations"] = combinations;
        }
    }
    json["AnalysisType"] = ui->comboBox_StatType->currentIndex();
    /*
     * Fisher Types are :
     * False: MaxMinFisher,
     * True: Normal Fisher
     *
     * FDR Correction:
     * False: Joint FDR
     * True: Separate FDR for each ROI
    */

    json["doNormalFisher"] = ui->radioButton_NormFischer->isChecked();
    json["Separate FDR"] = ui->radioButton_SepFDRcorrect->isChecked();

}
void MainWindow::writeReferImgpath(QJsonObject &json) const
{
    QString FilePath;
    QJsonObject ReferSummary;
    ReferSummary["Info"] = QString("It tells the path of the file used for reference.");
    ReferSummary["ReferImgPath"] = ui->lineEdit_Reference->text();
    json["ReferSummary"] = ReferSummary;


    QString MaskFile = ui->lineEdit_Mask->text();
    QFile Mask(MaskFile);
    if (Mask.exists()){
    json["MaskNotProvided"] = false;
    json["UseMaskFile"] = MaskFile;
    }
    else {
        json["MaskNotProvided"] = true;
    }

    QJsonObject ProcessingType;
    ProcessingType["Info"] = QString("The inputs can be of 3 types: "
                                      "#0 : Unprocessed "
                                      "#1 : Preprocessed without FSL "
                                      "#2 : Preprocessed with FSL");
    ProcessingType["ProcessingWay"] = ProcessingWay;
    json["ProcessingType"] = ProcessingType;
    json["No of Groups"] = spinBoxValue;
    json["Repetition Time"] = ui->lineEdit_TR->text().toFloat();
    if (ProcessingWay ==2){
        QJsonObject FeatList;
        FeatList["Info"] = QString("This is for case 2. We shall require the list of only the feat directories.");
        QJsonArray FeatFilesArray;
        for (int i=1 ; i<=FeatFileNames.size() ; i++)
        {
            FilePath = OutChosenPath + "/"+ ui->lineEdit_AnalysisName->text() + "_Group_" + QString::number(i)+"_FeatDirs.txt";
            QFile::copy(FeatFileNames.at(i-1), FilePath );
            QFile file(FeatFileNames.at(i-1));
            file.remove();
            FeatFilesArray.append(FilePath);
        }
        FeatList["FeatFilePaths"] = FeatFilesArray;
        json["FeatFilesInfo"] = FeatList;
    }

    else{
        QJsonObject FilesInfo;
        FilesInfo["Info"] = QString("This is for case 0 and case 1. We shall require the list of functional files. In case the corresponding structural"
                                    " files are also present, please also provide them for proper registration.");
        QJsonArray StructuralArray;
        QJsonArray FunctionalArray;
        for (int i=1 ; i<=FunctionalFileNames.size() ; i++)
        {
            FilePath = OutChosenPath + "/"+ ui->lineEdit_AnalysisName->text() + "_Group_" + QString::number(i)+"_FunctionalFiles.txt";
            QFile::copy(FunctionalFileNames.at(i-1), FilePath);
            QFile file(FunctionalFileNames.at(i-1));
            file.remove();
            FunctionalArray.append(FilePath);
        }
        for (int i=1 ; i<=StructuralFileNames.size() ; i++)
        {
            FilePath = OutChosenPath + "/"+ ui->lineEdit_AnalysisName->text() + "_Group_" + QString::number(i)+"_StructuralFiles.txt";
            QFile::copy(StructuralFileNames.at(i-1), FilePath);
            QFile file(StructuralFileNames.at(i-1));
            file.remove();
            StructuralArray.append(FilePath);
        }
        FilesInfo["FunctionalFilePaths"] = FunctionalArray;
        FilesInfo["StructuralFilePaths"] = StructuralArray;
        json["FilesInfo"] = FilesInfo;
    }

    QJsonObject OutputInfo;
    OutputInfo["Info"] = QString("This tells the output directory where files are to be saved.");
    OutputInfo["OutDirectory"] = OutChosenPath;
    OutputInfo["Save preprocessed .feat"] = ui->checkBox_preprocFeat->isChecked();
    OutputInfo["Save 4D ROI wise Corrs"] = ui->checkBox_ROICorrs->isChecked();
    json["OutputInfo"] = OutputInfo;

    json["ROIFilePath"] = ui->lineEdit_ROIFile->text();
    json["FSLDirectory"] = ui->lineEdit_FSLDIR->text();

    if (ProcessingWay == 0){
        QJsonObject MotionCrt;
        MotionCrt["Info"] = QString("The motion Correction can be of two types:"
                               " #0 : None, "
                               "#1 : MCFlirt"
                               );
        QJsonObject SliceCorrect;
        SliceCorrect["Info"]= QString("The Slice Time Correction can be of 5 types: "
                               "#0 : None, "
                               "#1 : Regular Up, "
                               "#2 : Regular Down, "
                               "#3 : Interleaved, "
                               "#4 : Use Slice Order File, "
                               "#5 : Use Slice timings File.");
        json["Registration"] = ui->radioButton_reg_y->isChecked();
        MotionCrt["Type"] = ui->comboBox_MCorrect->currentIndex();
        json["Motion Correction"] = MotionCrt;
        json["B0 Unwarping"] = ui->checkBox_B0->isChecked();
        SliceCorrect["Type"] = ui->comboBox_STimeCorrect->currentIndex();
        json["Slice Time Correct"] = SliceCorrect;
        json["BET Brain Extract"] = ui->checkBox_BET->isChecked();
        if (ui->checkBox_BET->isChecked()){
            QJsonObject BET;
            BET["Info"] = QString("To do Brain Extraction, the key #BET Brain Extract should be true. BET Correction Value can range between 0 and 1. "
                                  "doRobustBET uses recursive brain extraction which may vary in various cases.");
            BET["BET Correction Value"] = ui->lineEdit_BET_correct_value->text().toFloat();
            BET["doRobustBET"] = ui->checkBox_RobustBET->isChecked();
            json["BETParams"] = BET;
        }

        json["FWHM"] = ui->doubleSpinBox_FWHM->value();
        json["Intensity Normalization"] = ui->checkBox_IntensityNorm->isChecked();
        json["Temporal Filtering"] = (ui->checkBox_HighPass->isChecked())||(ui->checkBox_LowPass->isChecked());
        QJsonObject tempfilt;
        tempfilt["Info"] = QString("High pass value and low pass value are required for temporal filtering. These are written in units of sigma. In case "
                                   "you don't want to apply high pass or low pass, simply replace the values with -1.");
        tempfilt["High Pass Value (in sigma)"] = ui->checkBox_HighPass->isChecked() ? ui->lineEdit_highpass->text().toFloat()/(2*ui->lineEdit_TR->text().toFloat()) : float(-1);

        tempfilt["Low Pass Value (in sigma)"] = ui->checkBox_LowPass->isChecked() ? ui->lineEdit_lowpass->text().toFloat()/(2*ui->lineEdit_TR->text().toFloat()) : float(-1);
        json["FilteringParams"] = tempfilt;
        json["applyGSR"] = ui->checkBox_GSR->isChecked();

        json["Melodic ICA"] = ui->checkBox_MelodicICA->isChecked();
    }
    else if (ProcessingWay ==1){
        json["Registration"] = ui->radioButton_reg_y->isChecked();
    }
    else {
        json["Registration"] = ui->radioButton_reg_y->isChecked();
        json["applyGSR"] = ui->checkBox_GSR_2->isChecked();
    }

    bool doCorr = true;
    json["doCorr"] = doCorr;
    json["CorrFunction"] = ui->radioButton_Ank_Corr->isChecked();
    if (doCorr){
        bool doStats = ui->checkBox_doStats->isChecked();
        json["doStats"] = doStats;
        if (doStats){
            QJsonObject StatsObj;
            writeStats(StatsObj);
            json["Stats"] = StatsObj;
        }
    }
}


void MainWindow::writeAnalysisName(QJsonObject &json) const
{
    /*
     * The above JSON file making has been done till preprocessing.
     * I haven't yet added some blocks for preprocessing such as
     * Text box for Custom Slice Time Correction File.
     * Other Functions for Perfusion subtraction also.
     *
     */
    json["Analysis Name"] = ui->lineEdit_AnalysisName->text();
    json["No of threads"] = ui->spinBox_threads->value();
    json["WorkingDir"] = WorkingDir;
    QJsonObject ReferenceImgpath;
    writeReferImgpath(ReferenceImgpath);
    json["AnalysisParams"] = ReferenceImgpath;
}

void MainWindow::runProgram(QString JSONFile){
    QString program( "python" );
    QStringList args = QStringList() << "read_json.py"<<JSONFile;
    QProcess p;
    p.setWorkingDirectory(WorkingDir);
    int exitCode = p.execute( program, args );
}

void MainWindow::on_pushButton_Go_clicked()
{
    int lenFuncFiles= FunctionalFileNames.size();
    int lenFeatFiles = FeatFileNames.size();
//    if (((lenFuncFiles!=spinBoxValue)||(lenStructFiles!=spinBoxValue)) && (lenFeatFiles != spinBoxValue)){
    if ((lenFuncFiles!=spinBoxValue) && (lenFeatFiles != spinBoxValue)){
        QMessageBox::warning(this,"Title","You haven't specified the complete 4D data files.");
    }
    else{
        OutChosenPath = ui->lineEdit_OutDir->text();
        QString JSONFile= OutChosenPath + QString( "/"+ui->lineEdit_AnalysisName->text()+"Design.json");
        if (!QDir(OutChosenPath).exists()){
            QDir dir;
            bool created = dir.mkdir(OutChosenPath);
            if (!created){
                QMessageBox::warning(this,"Help","Not able to create Directory: "+ OutChosenPath);
                return;
            }
        }

        QFile saveFile( JSONFile);
        if (!saveFile.open(QIODevice::WriteOnly)) {
            qWarning("Couldn't open save file.");
        }
        QJsonObject Object;
        writeAnalysisName(Object);
        QJsonDocument saveDoc(Object);
        saveFile.write(saveDoc.toJson());
        saveFile.close();

        runProgram(JSONFile);

//        QString cmd_qt = QString("python %1 %2").arg("read_json.py").arg(JSONFile);

//        const char* cmd = cmd_qt.toLatin1().constData();
//        system(cmd);


    }
}


void MainWindow::on_radioButton_Unprocessed_clicked()
{
    ProcessingWay = 0;
    ui->tabWidget->setTabEnabled(1,true);
    ui->tabWidget->setTabEnabled(2,true);
    ui->checkBox_GSR_2->hide();
}

void MainWindow::on_radioButton_PreprocwtFSL_clicked()
{
    ProcessingWay = 1;
    ui->tabWidget->setTabEnabled(1,false);
    ui->tabWidget->setTabEnabled(2,true);

    ui->checkBox_GSR_2->hide();
}

void MainWindow::on_radioButton_PreprocwFSL_clicked()
{
    ProcessingWay = 2;
    ui->tabWidget->setTabEnabled(1,false);
    ui->tabWidget->setTabEnabled(2,true);

    ui->checkBox_GSR_2->show();
}

void MainWindow::on_checkBox_HighPass_clicked(bool checked)
{
    if (checked)
        ui->lineEdit_highpass->show();
    else
        ui->lineEdit_highpass->hide();
}

void MainWindow::on_checkBox_LowPass_clicked(bool checked)
{
    if (checked)
        ui->lineEdit_lowpass->show();
    else
        ui->lineEdit_lowpass->hide();
}

void MainWindow::on_commandLinkButton_Mask_clicked()
{
    /*
     * Sets the Mask File in the lineEdit box.
     */
    QString new_input;

    // Get the input already present in the cell.
    QString already_input = ui->lineEdit_Mask->text();
    QFile Fout(already_input) ;

    if (Fout.exists())
    {
        // If such file exists, then opne the Directory chooser from that path.
        new_input=QFileDialog::getOpenFileName(
                                                    this,
                                                    tr("Open File"),
                                                    already_input,
                                                    "Nifti File (*.nii.gz);;All files (*.*)"
                                                       );
    }
    else
    {
        // else open it from the default path.
        new_input=QFileDialog::getOpenFileName(
                                                this,
                                                tr("Open File"),
                                                CommonDir,
                                                "Nifti File (*.nii.gz);;All files (*.*)"
                                                   );
    }
    if (new_input!=NULL){
        // It is used for handling the CANCEL button. In case the cancel is clicked in
        // directory chooser, then we need to set it to previous input else the new input.
    ui->lineEdit_Mask->setText(new_input);
    }
    else {
        ui->lineEdit_Mask->setText(already_input);
    }
}

void MainWindow::on_pushButton_Go3_clicked()
{
    on_pushButton_Go_clicked();
}

void MainWindow::on_checkBox_BET_clicked(bool checked)
{
    if (checked){
        ui->label_BET_Correct->show();
        ui->lineEdit_BET_correct_value->show();
        ui->checkBox_RobustBET->show();
    }
    else{
        ui->label_BET_Correct->hide();
        ui->lineEdit_BET_correct_value->hide();
        ui->checkBox_RobustBET->hide();
    }
}

void MainWindow::on_checkBox_doStats_clicked(bool checked)
{
    ui->tabWidget->setTabEnabled(3,checked);
}



void MainWindow::on_checkBox_bw_groups_clicked(bool checked)
{

    if (checked){
        if (spinBoxValue == 2){

            ui->label_Hypothesis->show();
            ui->radioButton_G1_gr_G2->show();
            ui->radioButton_G2_gr_G1->show();
        }
        else{
            ui->checkBox_AllCombs->show();
            ui->checkBox_AllCombs->setChecked(true);
        }
     }
    else
    {
        ui->chooseCombsButton->hide();
        ui->checkBox_AllCombs->hide();
        ui->label_Hypothesis->hide();
        ui->radioButton_G1_gr_G2->hide();
        ui->radioButton_G2_gr_G1->hide();
    }
}

void MainWindow::on_pushButton_Save1_clicked()
{
    int lenFuncFiles= FunctionalFileNames.size();
    int lenFeatFiles = FeatFileNames.size();
//    if (((lenFuncFiles!=spinBoxValue)||(lenStructFiles!=spinBoxValue)) && (lenFeatFiles != spinBoxValue)){
    if ((lenFuncFiles!=spinBoxValue) && (lenFeatFiles != spinBoxValue)){
        QMessageBox::warning(this,"Title","You haven't specified the complete 4D data files.");
    }
    OutChosenPath = ui->lineEdit_OutDir->text();
    QString JSONFile= OutChosenPath + QString( "/"+ui->lineEdit_AnalysisName->text()+"Design.json");
    if (!QDir(OutChosenPath).exists()){
        QDir dir;
        bool created = dir.mkdir(OutChosenPath);
        if (!created){
            QMessageBox::warning(this,"Help","Not able to create Directory: "+ OutChosenPath);
            return;
            }

    }


    QFile saveFile( JSONFile);
    if (!saveFile.open(QIODevice::WriteOnly)) {
        qWarning("Couldn't open save file.");
    }
    QJsonObject Object;
    writeAnalysisName(Object);
    QJsonDocument saveDoc(Object);
    saveFile.write(saveDoc.toJson());
    saveFile.close();
}

void MainWindow::on_pushButton_Save_clicked()
{
    on_pushButton_Save1_clicked();
}