ImageD/d__makro__mitochondrien_8h_source.html

/************************************

 *   added:     09.10.2018          *

 *   author:    David Eilenstein    *

 *   contact:   D.Eilenstein@gsi.de *

 *   project:   ImageD              *

 *   facility:  GSI Darmstadt, Ger  *

 ************************************/


#ifndef D_MAKRO_MITOCHONDRIEN_H

#define D_MAKRO_MITOCHONDRIEN_H


//own

#include <d_enum.h>

#include <scenemousetrack.h>

#include <d_img_proc.h>

#include <d_plot.h>

#include <d_storage.h>

#include <d_stat.h>

#include <d_error_handler.h>

#include <d_viewer.h>


//general

#include <iostream>

#include <sstream>

#include <fstream>

#include <vector>

#include <algorithm>

#include <iomanip>


//Qt

#include <QMainWindow>

#include <QImage>

#include <QPixmap>

#include <QGraphicsScene>

#include <QFileInfo>

#include <QDir>

#include <QString>

#include <QDebug>

#include <QMessageBox>

#include <QFileDialog>

#include <QFileInfo>

#include <QBuffer>

#include <QSpacerItem>

#include <QElapsedTimer>

#include <QTextDocument>

#include <QTextBlock>

#include <QGridLayout>

#include <QResizeEvent>

#include <QMouseEvent>

#include <QDateTime>

#include <QDesktopServices>

#include <QUrl>

#include <QComboBox>


//openCV

#include <opencv2/core/core.hpp>

#include <opencv2/highgui/highgui.hpp>

#include <opencv2/imgproc/imgproc.hpp>


//namespaces

using namespace std;

//using namespace cv; (prohibited because of abigous names with qtdatavisualization)

#include <d_opencv_typedefs.h>


namespace Ui {

class D_MAKRO_Mitochondrien;

}


class D_MAKRO_Mitochondrien : public QMainWindow

{

    Q_OBJECT


public:

    explicit D_MAKRO_Mitochondrien(D_Storage *pStorage, QWidget *parent = 0);

    ~D_MAKRO_Mitochondrien();


    void closeEvent(QCloseEvent *event);

    void set_ClosingPossible(bool closeable)     {ClosingPossible = closeable;}


public slots:

    void Update_ImgProc_All();


private slots:

    void mousePressEvent(QMouseEvent *event);

    void resizeEvent(QResizeEvent *event);


    void Populate_CB_Single(QComboBox *CB, QStringList QSL, int index_init);


    void Update_ImgProc_Photons(unsigned int start_step);

    void Update_ImgProc_Parameters();

    void Convert_Parameters_8bit_All();

    void Convert_Parameters_8bit_RoI();

    void Update_ImgProc_Results(unsigned int start_step);

    void Update_Step_Photons(unsigned int step);


    void Update_Results_Proc();

    void Update_Results_Proc_Force();


    void Update_Step_Results(unsigned int step);


    void Update_Combi_Results();

    void Update_Math_Image();


    void Update_Plot_Hist_Img();

    void Update_Plot_Hist_Cells();


    void Update_Plot_Parameter_Pixel();

    void Update_Plot_Parameter_Cells();


    void Update_Plot_Stat_MeanMedian();

    void Update_Plot_Stat_CvSkewKurt();

    void Update_Plot_Stat_Quantiles();


    void Calc_Data_All();

    int  Calc_Data_Split_Img2vv();

    void Calc_Data_Parameter_Stats();


    void Calc_T2_Handling();

    void Calc_NADPH_NADH_All();

    void Calc_NADPH_NADH();

    void Calc_NADH();

    void Calc_NADPH();


    void Stream_Stats_Start();

    void Stream_Init();

    void Stream_Stats();

    void Stream_ImagesPlots();

    void Stream_Settings();

    void Stream_Stats_End();


    void Update_Views();

    void Update_View_Photons();

    void Update_View_Parameters();

    void Update_View_Results();

    void Update_View(QImage *QI_Show, Mat *MA_Show, QPixmap *PX_Show, SceneMouseTrack *SC_Show, QGraphicsView *GV_Show, double *x_factor, double *y_factor);

    void Update_Ui();


    void Populate_CB_Style();

    void Update_Style();


    void Load_Directory();

    void Load_Images();

    void Clear_Queue();

    void Next_Image();


    void Save_Image_Photons();

    void Save_Image_Parameters();

    void Save_Image_Results();

    void Save_Image(QImage *QI_Save, QString name_default);

    void Save_Image(D_Viewer *ViewerSave, QString name_default);

    void Save_Plot();

    void Save_Plot(QChartView *pCV_Save, QString name_default);


    //Manual RoI

    void Get_Click_Pos(int x, int y);

    void Draw_Line();

    void Fill_Background();

    void CellSep_Undo();

    void CellSep_Load();

    void CellSep_Save();

    void CellSep_Open();

    void Set_Scale_Factor_View(QImage *QI, QGraphicsView *GV);

    void Init_Cell_Regions();

    void Export_Cell_Regions();


    //Statusbar

    void Update_SB_ValAtPos(int x, int y, Mat *pMA);


    //UI adapt

    void AdaptUI_NADH_p_NADPH_MinMax();

    void AdaptUI_Results();


    void ERR(int err, QString func = "no specified", QString detail = "no specified");


    void on_spinBox_PhoCon_Blur_Size_valueChanged(int arg1);


    void on_doubleSpinBox_PhoCon_Blur_Sigma_valueChanged(double arg1);


    void on_spinBox_PhoCon_Thres_Size_valueChanged(int arg1);


    void on_doubleSpinBox_PhoCon_Thres_Offset_valueChanged(double arg1);


    void on_comboBox_PhoVie_Step_currentIndexChanged(int index);


    void on_spinBox_PhoCon_EdgCon_Size_valueChanged(int arg1);


    void on_pushButton_PhoCon_Paint_Reset_clicked();


    void on_pushButton_ResCon_Zoom_Reset_clicked();


    void on_spinBox_His_ClassCount_valueChanged(int arg1);


    void on_comboBox_ResCon_Rubberband_currentIndexChanged(int index);


    void on_pushButton_RessCon_Zoom_In_clicked();


    void on_pushButton_ResCon_Zoom_Out_clicked();


    void on_spinBox_ParAll_ClassCount_valueChanged(int arg1);


    void on_action_Autoselect_Save_Filename_triggered(bool checked);


    void on_doubleSpinBox_ParCon_T2_Min_Const_valueChanged(double arg1);


    void on_doubleSpinBox_ParCon_T2_Max_Const_valueChanged(double arg1);


    void on_doubleSpinBox_ParCon_T2_Min_Thres_valueChanged(double arg1);


    void on_doubleSpinBox_ParCon_T2_Max_Thres_valueChanged(double arg1);


    void on_action_Show_Photons_triggered(bool checked);


    void on_action_Show_Parameters_triggered(bool checked);


    void on_action_Show_Results_triggered(bool checked);


    void on_comboBox_AnalysedImage_currentIndexChanged(int index);


    void on_radioButton_PhoCon_Paint_Line_clicked(bool checked);


    void on_comboBox_PhoCon_Paint_FillStep_currentIndexChanged(int index);


    void on_radioButton_PhoCon_Paint_Fill_clicked(bool checked);


private:

    Ui::D_MAKRO_Mitochondrien *ui;


    bool                    ClosingPossible = false;


    //Data Storage

    Mat             MA_Init;

    D_Storage       *pStore;

    unsigned int    pos_dest;


    //Files

    QDir            DIR_Input_Dir;

    QFileInfoList   FIL_Input_Images;

    QString         QS_Image_BasePath;

    QString         QS_Image_BaseName;

    bool            Auto_SaveName = false;


    //Photons

    vector<Mat>     vMA_Photons;


    //Parameters

    vector<Mat>     vMA_Parameter_All_Float;

    vector<Mat>     vMA_Parameter_All_8Bit;

    vector<Mat>     vMA_Parameter_RoI_Float;

    vector<Mat>     vMA_Parameter_RoI_8Bit;

    QStringList     QSL_Parameter_Suffixes;

    unsigned int    PARAMETERS;

    unsigned int    PARAMETERS_only_input;

    bool            param_set = false;

    void            Init_Parameters();

    void            Read_Parameters_From_UI();

    void            Populate_CB_Parameters();

    void            Init_vMA_Parameter();


    //Shading Correct

    Mat             MA_Reference;

    void            Load_Reference();

    QFileInfo       FI_Reference;

    bool            Exist_Refernce = false;


    //Output Data

    bool                            Calc_Done = false;

    bool                            CB_Cells_Updated = false;

    unsigned int                    CellCount = 0;

    vector<int>                     CellColor_LUT;

    vector<vector<vector<double>>>  vvv_Data_ParNucPix;

    vector<vector<vector<double>>>  vvv_Stat_ParNucSta;

    void                            Populate_CB_Cells();

    void                            Check_Parameter_Existence();

    void                            Norm_Parameters();

    bool                            Exist_photons = false;

    bool                            Exist_t1 = false;

    bool                            Exist_t2 = false;

    bool                            Exist_a1 = false;

    bool                            Exist_a2 = false;

    bool                            Exist_chi = false;

    bool                            Calced_NADPH_NADH = false;

    bool                            Calced_NADH = false;

    bool                            Calced_NADPH = false;

    //vector<double>                  v_NADH;

    //vector<double>                  v_NADPH;

    //vector<double>                  v_NADPH_NADH;

    void                            Populate_CB_Stat();

    QStringList                     QSL_Stats;


    //Results

    vector<Mat>     vMA_Results;

    Mat             MA_Color;

    QStringList     QSL_Results;

    void            Init_QSL_Results();

    void            Populate_CB_Results();

    void            Init_MatVector(vector<Mat> *vec, unsigned int l);


    //Math

    Mat             MA_Math;


    //Manual Seperation of cells

    //Mat             MA_Cell_Regions;

    bool            ManSep_Manip = false;

    bool            ManSep_Line_Begin = true;

    double          ManSep_Scale_Factor = 1.0;

    QPoint          ManSep_Pos_Last;

    QPoint          ManSep_Pos_Curr;

    QDir            DIR_CellSep;

    QDir            DIR_CellSep_Img;

    QFileInfo       FI_CellSep;

    bool            ManSep_FromFile;

    Mat             MA_CellSep_Last;


    //Display images

    D_Viewer        Viewer_Photons;

    D_Viewer        Viewer_Parameters;

    D_Viewer        Viewer_Results;

    /*QImage          QI_Photons;

    QImage          QI_Parameters;

    QImage          QI_Results;

    QPixmap         PX_Photons;

    QPixmap         PX_Parameters;

    QPixmap         PX_Results;

    SceneMouseTrack SC_Photons;

    SceneMouseTrack SC_Parameters;

    SceneMouseTrack SC_Results;

    void            Init_GraphicsView(QGraphicsView *view, SceneMouseTrack *scene);

    double          scale_factor_x_photons;

    double          scale_factor_y_photons;

    double          scale_factor_x_parameters;

    double          scale_factor_y_parameters;

    double          scale_factor_x_results;

    double          scale_factor_y_results;*/


    //Display plot

    QChartView      *ChartView_Plot;

    QChart          *Chart_Plot;

    void            Init_Plot();


    //stream to output data

    bool            Stream_Open = false;

    ofstream        OS_Stream_Summary;

    vector<ofstream>OS_Stream_Parameters;

    QDir            DIR_Stream;

    bool            Auto_ResultsProc_blocked = false;


    //Statusbar

    QLabel          *L_SB_ValAtPos;

    QLabel          *L_SB_Size;


    //CONSTANTS


    D_Error_Handler ER;


    //Result types

    static const unsigned int

    c_RT_IMAGE              = 0,

    c_RT_PLOT               = 1;

    static const unsigned int

    c_RT_IMAGE_COLOR        = 0,

    c_RT_IMAGE_MATH         = 1;

    static const unsigned int

    c_RT_PLOT_HIST_IMG      = 0,

    c_RT_PLOT_HIST_CELL     = 1,

    c_RT_PLOT_PAR_PIXEL     = 2,

    c_RT_PLOT_PAR_CELL      = 3,

    c_RT_PLOT_STAT_MM       = 4,

    c_RT_PLOT_STAT_CSK      = 5,

    c_RT_PLOT_STAT_QUANT    = 6;


    //Counts

    static const unsigned int

    c_SC_PHOTONS            = 11,

    c_SC_PARAMETERS         = 2,

    c_SC_RESULTS            = 7;


    //Photon Steps

    static const unsigned int

    c_ST_PH_LOAD            = 0,

    c_ST_PH_SHADE_CORRECT   = 1,

    c_ST_PH_INPUT_CONV_8bit = 2,

    c_ST_PH_INPUT_CONTRAST  = 3,

    c_ST_PH_INPUT_BLUR      = 4,

    c_ST_PH_BIN_THRES       = 5,

    c_ST_PH_REGIONS_EDGES   = 6,

    c_ST_PH_REGIONS_CONNECT = 7,

    c_ST_PH_REGIONS_SEP_VIEW= 8,

    c_ST_PH_REGIONS_LABEL   = 9,

    c_ST_PH_ROI_MITO        = 10;


    //Parameter Steps

    static const unsigned int

    c_ST_PA_ALL             = 0,

    c_ST_PA_ROI             = 1;

    unsigned int           //const after first load of images

    INDEX_NADPH_NADH        = 0,

    INDEX_NADH              = 0,

    INDEX_NADPH             = 0,

    INDEX_T1                = 0,

    INDEX_T2                = 0,

    INDEX_PHOTONS           = 0,

    INDEX_A2                = 0,

    INDEX_A1                = 0,

    INDEX_CHI               = 0;


    //Results Steps

    static const unsigned int

    c_ST_RE_EMPTY           = 0,

    c_ST_RE_PH_INPUT        = 1,

    c_ST_RE_PH_CONTRAST     = 2,

    c_ST_RE_PH_BINARY       = 3,

    c_ST_RE_PH_EDGES        = 4,

    c_ST_RE_PH_LABEL_NUMBER = 5,

    c_ST_RE_PH_EDGES_NUMBER = 6;

};


#endif // D_MAKRO_MITOCHONDRIEN_H