MenuWindow.cpp

#include "MenuWindow.h"
#include "biologicalprocess.h"
#include "colocalisation.h"
#include "ui_MenuWindow.h"
#include "qcustomplot.cpp"
#include <iostream>
#include <QMessageBox>
#include <QtDataVisualization>



MenuWindow::MenuWindow(QWidget *parent) :
    QMainWindow(parent),
    ui(new Ui::MenuWindow)
{
    ui->setupUi(this);

//    Q3DScatter *scatter = new Q3DScatter();

//    QWidget *container = QWidget::createWindowContainer(scatter);

//    ui->horizontalLayout->addWidget(container, 1);
}

MenuWindow::~MenuWindow()
{
    delete ui;
}

void MenuWindow::makePlot(Eigen::MatrixXd m) {

    qputenv("QSG_RHI_BACKEND", "opengl");
//    QGuiApplication app(argc, argv);


//    Eigen::MatrixXf m(4,3);
//    m(0,0) = 3;
//    m(1,0) = 2.5;
//    m(2,0) = 5;
//    m(3,0) = 4;
//    m(0,1) = 5;
//    m(1,1) = 0.5;
//    m(2,1) = 3.5;
//    m(3,1) = 4;
//    m(0,2) = 34;
//    m(1,2) = 5;
//    m(2,2) = 2;
//    m(3,2) = 65;
    std::cout << m << std::endl;
    std::cout << m.rows() <<std::endl;


    scatter = new Q3DScatter();

    QWidget *container = QWidget::createWindowContainer(scatter);

    ui->horizontalLayout->addWidget(container, 1);

    std::cout << "Initialized scatter object";
    scatter->setFlags(scatter->flags() ^ Qt::FramelessWindowHint);
    QScatter3DSeries *series = new QScatter3DSeries;
    QScatterDataArray data;
    for (int i = 0; i < m.rows(); i++){
        data << QVector3D(m(i,0), m(i,2), m(i,1));
        }
   series->dataProxy()->addItems(data);
   scatter->addSeries(series);
   scatter->show();
//    // allow rescaling the color scale by dragging/zooming
//    ui->customPlot->setInteractions(QCP::iRangeDrag|QCP::iRangeZoom);
//    // configure axis rect
//    ui->customPlot->axisRect()->setupFullAxesBox(true);
//    // set the axis labels
//    ui->customPlot->xAxis->setLabel("x");
//    ui->customPlot->yAxis->setLabel("y");

//    // set up the QCPColorMap
//    QCPColorMap *colorMap = new QCPColorMap(ui->customPlot->xAxis, ui->customPlot->yAxis);

//    // get matrix dimensions
//    int number_rows = m.rows();
//    int number_cols = m.cols(); // should be 3
//    // set data size
//    int data_size = number_rows; // just the third column

//    // find max, min value
//    double maxValx = m.col(0).maxCoeff(); // biggest x- value
//    double minValx = m.col(0).minCoeff(); // smalles x- value
//    double maxValy = m.col(1).maxCoeff(); // biggest y- value
//    double minValy = m.col(1).minCoeff(); // smallest y- value

//    // print out the values (test)
//    std::cout << "Datasize :"<< data_size << std::endl;
//    std::cout << "NumberCols :"<< number_cols << std::endl;
//    std::cout << "NumberRows :"<< number_rows << std::endl;

//    std::cout << "maxValx :"<< maxValx << std::endl;
//    std::cout << "minValx :"<< minValx << std::endl;
//    std::cout << "maxValy :"<< maxValy << std::endl;
//    std::cout << "minValy :"<< minValy << std::endl;

//    // set the size of the data
//    colorMap->data()->setSize(data_size,data_size);

//    // set range of color map using max and min values
//    colorMap->data()->setRange(QCPRange(minValx, maxValx), QCPRange(minValy, maxValy)); //set the range of the HeatMap;



//    //95 PERCENT CONFIDENCE interval
//    //calculate mean
//    double mean = 0.0;
//    for(int i= 0; i<data_size; i++){
//           mean += m(i,2); };//only the third column
//    mean /= data_size;

//    //calculate standard deviation
//    double sd = 0.0;
//    for(int i= 0; i<data_size; i++){
//           sd += pow(m(i,2) - mean,2);} // only third column

//    //standart error
//    sd = sqrt(sd/(data_size));

//    //margin of error
//    double ci = 2* sd;

//    double q1 = mean-ci;
//    double q3 = mean+ci;

//    //print confidence interval
//    std::cout << "95% Confidence Interval: [" << q1 << ", " << q3 << "]" << std::endl;


//    // assign some data, by accessing the QCPColorMapData instance of the color map
//    for(int i = 0; i < number_rows; i++){
//        if(m(i,2)>q1 && m(i,2)<q3){
//            colorMap->data()->setData(m(i,0),m(i,1),m(i,2));
//        }
//    }

//    // assign data with cell and with confidence level
//    /*for(int i = 0; i < number_rows; i++){
//           i f(m(i,2)>q1 && m(i,2)<q3){ // if the third value of the row is in the confidence interval
//                colorMap->data()->setCell(int(m(i,0)),int(m(i,1)), m(i,2)); // plot only data between q1 and q3 here we want quantile
//                  }
//            else{colorMap->data()->setCell(m(i,0),m(i,1), m(i,2));} //assign 0
//    }*/



//   /* Ticks and Labels: The following code is just an example hot it works
//   QSharedPointer<QCPAxisTickerText> textTickerx(new QCPAxisTickerText);

//   // tick strategy. readability is more important
//   textTickerx->setTickStepStrategy(QCPAxisTicker::tssReadability);
//   textTickerx->setTickOrigin(0);// sets origin (not necessary)
//   textTickerx->setTickCount(3);

//   QSharedPointer<QCPAxisTickerText> textTickery(new QCPAxisTickerText);

//   // tick strategy. readability is more important
//   textTickery->setTickStepStrategy(QCPAxisTicker::tssReadability);
//   textTickery->setTickOrigin(0);// sets origin (not necessary)
//   textTickery->setTickCount(4);

//   //assign the labels using vectors
//   QVector<QString> xgenenames;
//   QVector<double> xpositions;
//   for(int i = 0; i < number_cols; i++){
//       xgenenames.append("Bacteria");
//       xpositions.append(i);
//   };

//   QVector<QString> ygenenames;
//   QVector<double> ypositions;
//   for(int i = 0; i < number_cols; i++){
//       ygenenames.append("Bacteria");
//       ypositions.append(i);
//   };


//   textTickerx->setTicks(xpositions, xgenenames);
//   textTickery->setTicks(ypositions, ygenenames);

//   ///assign each label individually
//   for(int i = 0; i < number_cols; i++){
//       textTickerx->addTick(i, "Bacteria");}; // Here we need the gene names

//   for(int j = 0; j< number_rows; j++){
//       textTickery->addTick(j, "Bacteria");}; // Here we need the gene names



//   //set x-axis ticker
//   ui->customPlot->xAxis->setTicker(textTickerx);
//   ui->customPlot->xAxis->setTickLabelPadding(8); //Sets the distance between the axis base line
//   ui->customPlot->xAxis->setTickLabelColor(QColorConstants::Red); //Sets the color of the tick labels.
//   ui->customPlot->xAxis->setTickLabelRotation(-90.0); //Sets the rotation of the tick labels.

//   //set y-axis ticker
//   ui->customPlot->yAxis->setTicker(textTickery);
//   ui->customPlot->yAxis->setTickLabelColor(QColorConstants::Red); //Sets the color of the tick labels. */


//   // color scale
//   // create color scale
//   QCPColorScale *colorScale = new QCPColorScale(ui->customPlot);
//   // add it to the right of the main axis rect
//   ui->customPlot->plotLayout()->addElement(0, 1, colorScale);
//   // scale shall be vertical bar with tick/axis labels right
//   colorScale->setType(QCPAxis::atRight);
//   // set width of scale
//   colorScale->setBarWidth(8);
//   // allos to drag the data range
//   colorScale->setRangeDrag(&free);
//   // associate the color map with the color scale
//   colorMap->setColorScale(colorScale);
//   // set label of color scale
//   colorScale->axis()->setLabel("Intensity");



//   // color gradient
//   // empty gradient with no defined colour stops
//   QCPColorGradient gradient;
//   //Hue variation similar to a spectrum, often used in numerical visualization (creates banding illusion but allows more precise magnitude estimates)
//   //In between these color stops, the color is interpolated according to setColorInterpolation.
//   gradient.setColorInterpolation(QCPColorGradient::ciRGB);
//   gradient.setColorStopAt(0, QColor(0, 0, 100));
//   gradient.setColorStopAt(0.15, QColor(0, 50, 255));
//   gradient.setColorStopAt(0.35, QColor(0, 255, 255));
//   gradient.setColorStopAt(0.65, QColor(255, 255, 0));
//   gradient.setColorStopAt(0.85, QColor(255, 30, 0));
//   gradient.setColorStopAt(1, QColor(100, 0, 0));
//   // NaN data points as the transparent
//   gradient.setNanHandling(QCPColorGradient::nhTransparent);
//   // set the number of discretization levels of the color gradient to n (max. n = 350)
//   gradient.setLevelCount(350);
//   //assign it to the heatmap
//   colorMap->setGradient(gradient);


//   // set interpolation: True or False
//   colorMap->setInterpolate(false);

//   // make sure the axis rect and color scale synchronize their bottom and top margins (so they line up)
//   QCPMarginGroup *marginGroup = new QCPMarginGroup(ui->customPlot);
//   ui->customPlot->axisRect()->setMarginGroup(QCP::msBottom|QCP::msTop, marginGroup);
//   colorScale->setMarginGroup(QCP::msBottom|QCP::msTop, marginGroup);

//   // rescale the data dimension (color) such that all data points lie in the span visualized by the color gradient
//   colorMap->rescaleDataRange();

//   // rescale the key (x) and value (y) axes so the whole color map is visible
//   ui->customPlot->rescaleAxes();

}

void MenuWindow::on_ColocalizationButton_clicked()
{

    /* This function creates an instance of colocalizationwindow and shows it when the button is pressed.
     * It also sets all of the data in the object of colocalizationwindow to be the data from the file and
     * calls makeHeatMap() to generate the heatmap.
     */


    coWindow = new colocalizationwindow(this); //creates the instance of colocalizationWindow
    connect(coWindow, &colocalizationwindow::MenuWindow, this, &MenuWindow::show); //connects menuwindow and colocalizationwindow so that we can navigate between them

    coWindow->setFileObject(files);


    this->hide(); //hides menuwindow
    coWindow->show(); //shows colocalizationwindow


}


void MenuWindow::on_BiologicalButton_clicked()
{

    /* This function creates an instance of bioprocesswindow and shows it when the button is pressed.
     * It also sets all of the data in the object of bioprocesswindow to be the data from the file and
     * calls makeHeatMap() to generate the heatmap. It also calls setProcessToAnalyze(), but that will
     * be deleted later on.
     */

    biochooseWindow = new BioChooser(this); //creates the instance of colocalizationWindow
    connect(biochooseWindow, &BioChooser::MenuWindow, this, &MenuWindow::show); //connects menuwindow and colocalizationwindow so that we can navigate between them


    biochooseWindow->setFileObject(files);
    this->hide(); //hides menuwindow
    biochooseWindow->show(); //shows biowindow
    //bioWindow->makeHeatMap(); //generates the heatmap

}


void MenuWindow::on_UploadWindowButton_clicked()
{
    this->close();
    emit UploadWindow(); //returns to uploadwindow
}