ImageD/d__makro__cellcolonies_8h_source.html

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

 *   added:     20.11.2018          *

 *   author:    David Eilenstein    *

 *   contact:   D.Eilenstein@gsi.de *

 *   project:   ImageD              *

 *   facility:  GSI Darmstadt, Ger  *

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


#ifndef D_MAKRO_CELLCOLONIES_H

#define D_MAKRO_CELLCOLONIES_H


//own

#include <d_enum.h>

#include <d_error_handler.h>

#include <d_img_proc.h>

#include <d_plot.h>

#include <d_stat.h>

#include <d_viewer.h>

#include <d_storage.h>


//Qt

#include <QMainWindow>

#include <QFileDialog>

#include <QFileInfo>

#include <QFileInfoList>

#include <QDir>

#include <QDateTime>

#include <QComboBox>


//Qt::Charts

#include <QChartView>

#include <QChart>


//general

#include <iostream>

#include <sstream>

#include <fstream>

#include <vector>

#include <algorithm>


//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_CellColonies;

}


class D_MAKRO_CellColonies : public QMainWindow

{

    Q_OBJECT


public:

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

    ~D_MAKRO_CellColonies();


    void closeEvent(QCloseEvent *event);

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


private slots:


    //Load

    void Load_Images();


    //Save

    void Save_Stack();

    void Save_Analysis_Dialog();

    void Save_Analysis();

    void Save_Processing_Chain();

    void Save_Image(D_Viewer *viewer, QString name_default);

    void Save_Image_Cells();

    void Save_Image_Results_Color();

    void Save_Image_Results_Surrival();

    void Save_Image_Results_Segmentation();

    void Save_Image_Results_Attribute();

    void Save_Plot(QChartView *pCV_Save, QString name_default);

    void Save_Plot_Colony();

    void Save_Plot_Image();

    void Save_Plot_Surrival();

    void Save_Parameters();

    void Save_Results();

    void Save_Raw_Data();


    //View

    void Update_Views();

    void Update_View_Cells();

    void Update_View_Results();

    void Update_View_Surrival();

    void Update_View_Segmentation();

    void Update_View_Attribute();

    void Update_Ui();


    //Image

    void Update_Images();

    void Update_Image_Cells();

    void Update_Image_Results();

    void Update_Image_Surrival();

    void Update_Image_Segmentation();

    void Update_Image_Attribute();


    //Results

    void Update_Results();


    //Settings

    void Settings_Reset();


    //Image Processing

    void Update_ImgProc();

    void Update_ImgProc_Cells(int start_step);

    void Update_ImgProc_Results(int start_step);

    void Update_Step_Cells(int step);

    void Update_Step_Results(int step);


    //Calculation

    void Calc_All();

    void Calc_Colony_Values_Split();

    void Calc_Colony_Stats();

    void Calc_Colony_Attributes();

    void Calc_Image_Stats();

    void Calc_Colony_Survival();


    //Plot

    void Plot_Histogram_Colonies();

    void Plot_Stat_Compare();

    void Plot_MM_Colonies();

    void Plot_CSK_Colonies();

    void Plot_Quantiles_Colonies();

    void Plot_Histogram_Image();

    void Plot_Attribute_Compare();

    void Plot_Colony_Surrival();

    void Plot_Radial_Transmission_Colony();


    //Populate UI

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

    void Populate_CB_Stat();

    void Populate_CB_Attribute();

    void Populate_CB_Typ();


    //Trigger Image Proc

    void on_doubleSpinBox_ProcCon_ROI_X1_valueChanged(double arg1);

    void on_doubleSpinBox_ProcCon_ROI_Y1_valueChanged(double arg1);

    void on_doubleSpinBox_ProcCon_ROI_X2_valueChanged(double arg1);

    void on_doubleSpinBox_ProcCon_ROI_Y2_valueChanged(double arg1);

    void on_spinBox_ProcCon_ColGrab_H_Min_valueChanged(int arg1);

    void on_spinBox_ProcCon_ColGrab_S_Min_valueChanged(int arg1);

    void on_spinBox_ProcCon_ColGrab_V_Min_valueChanged(int arg1);

    void on_spinBox_ProcCon_ColGrab_H_Max_valueChanged(int arg1);

    void on_spinBox_ProcCon_ColGrab_S_Max_valueChanged(int arg1);

    void on_spinBox_ProcCon_ColGrab_V_Max_valueChanged(int arg1);

    void on_spinBox_ProcCon_CellCol_Black_Noise_valueChanged(int arg1);

    void on_spinBox_ProcCon_CellCol_White_Noise_valueChanged(int arg1);

    void on_spinBox_ProcCon_Seed_Blur_Size_valueChanged(int arg1);

    void on_doubleSpinBox_ProcCon_Seed_Blur_Sigma_valueChanged(double arg1);

    void on_spinBox_ProcCon_Thres_Size_valueChanged(int arg1);

    void on_doubleSpinBox_ProcCon_Thres_Offset_valueChanged(double arg1);

    void on_spinBox_ProcCon_Seed_Open_Size_valueChanged(int arg1);

    void on_checkBox_ProcCon_Watershed_Border_stateChanged(int arg1);

    void on_checkBox_ProcCon_Watershed_nSeed_stateChanged(int arg1);

    void on_spinBox_ProcCon_Ref_Blur_Size_valueChanged(int arg1);

    void on_doubleSpinBox_ProcCon_Ref_Blur_Sigma_valueChanged(double arg1);


    //Stack

    void on_action_Last_Image_triggered();

    void on_action_Next_Image_triggered();


    //Update Results

    void on_comboBox_ProcView_Image_currentIndexChanged(const QString &arg1);


    //Trigger Surrival Calculation


    void on_doubleSpinBox_Extract_Asphere_Thres_valueChanged(double arg1);


    void on_doubleSpinBox_Separtate_Asphere_Thres_valueChanged(double arg1);


    void on_doubleSpinBox_Measure_Base_valueChanged(double arg1);


    void on_doubleSpinBox_Measure_Factor_valueChanged(double arg1);


    void on_doubleSpinBox_Sur_CellCount_valueChanged(double arg1);


private:

    Ui::D_MAKRO_CellColonies *ui;


    bool                    ClosingPossible = false;


    //Store

    D_Storage       *pStore;


    //Paths

    QDir            DIR_Input_Dir;

    QFileInfoList   FIL_Input_Images;

    QFileInfo       FI_Reference_Image;

    QString         QS_BaseName_Current = "";


    //Images

    Mat             MA_Reference;

    vector<Mat>     vMA_Cells;

    vector<Mat>     vMA_Results;

    Mat             MA_Result_Color;

    Mat             MA_Result_Surrival;

    Mat             MA_Result_Segmentation;

    Mat             MA_Result_Attribute;

    bool            Loaded_FileInfos = false;


    //Stats

    vector<vector<vector<double>>>  vvvd_TypColVal;

    vector<vector<vector<double>>>  vvvd_TypColSta;

    vector<vector<double>>          vvd_AttCol_new;

    vector<vector<double>>          vvd_AttSta_new;

    vector<int>                     vi_ColSur_new;

    bool                            Calced_TypColVal = false;

    bool                            Calced_TypColSta = false;

    bool                            Calced_AttCol_new = false;

    bool                            Calced_AttSta_new = false;

    bool                            Calced_ColSur_new = false;


    //Plot

    QChartView  *pChartView_Colony;

    QChartView  *pChartView_Image;

    QChartView  *pChartView_Surrival;

    QChart      *pChart_Colony;

    QChart      *pChart_Image;

    QChart      *pChart_Surrival;

    void        Init_Plot();


    //View

    D_Viewer    Viewer_Cells;

    D_Viewer    Viewer_Results;

    D_Viewer    Viewer_Surrival;

    D_Viewer    Viewer_Segmentation;

    D_Viewer    Viewer_Attribute;


    //Statusbar

    QLabel      *L_SB_ValAtPos;


    //Surrival

    int         count_detected;

    int         count_surrival;

    int         count_dead;

    double      prz_surrival;

    double      prz_dead;


    //Save

    bool        stream_active = false;

    bool        stack_proc_active = false;

    QDir        DIR_Stream;

    QDir        DIR_Stream_Processing;

    QDir        DIR_Stream_Stack;

    QDir        DIR_Stream_Stack_Labeling;

    QDir        DIR_Stream_Stack_Surrival;

    QDir        DIR_Stream_Stack_Attribute;

    ofstream    OS_Parameters;

    ofstream    OS_Results;

    ofstream    OS_Raw_Data;

    ofstream    OS_Stack;

    ofstream    OS_Stack_Summary;


    //CONSTANTS


    //Cells

    static unsigned const int

    c_ST_REFERENCE_LOAD     = 0,

    c_ST_REFERENCE_CROP     = 1,

    c_ST_REFERENCE_BLUR     = 2,

    c_ST_INPUT_LOAD         = 3,

    c_ST_INPUT_CROP         = 4,

    c_ST_INPUT_ANTI_SHADE   = 5,

    c_ST_CELLS_GRAB_COLOR   = 6,

    c_ST_CELLS_BINARY       = 7,

    c_ST_CELLS_NOISE_BLACK  = 8,

    c_ST_CELLS_NOISE_WHITE  = 9,

    c_ST_SEED_HSV           = 10,

    c_ST_SEED_SATURATION    = 11,

    c_ST_SEED_BLUR          = 12,

    c_ST_SEED_THRESH        = 13,

    c_ST_SEED_OPEN          = 14,

    c_ST_SEED_SPHERICITY_INV= 15,

    c_ST_SEED_ASPH_EXTRACT  = 16,

    c_ST_SEED_ASPH_DISTANCE = 17,

    c_ST_SEED_ASPH_SEPARATE = 18,

    c_ST_SEED_SPHERE_EXTRACT= 19,

    c_ST_SEED_ALL_SEEDS     = 20,

    c_ST_SEGM_WATERSHED     = 21,

    c_ST_SEGM_BINARY        = 22,

    c_ST_MEASURE_DIFF       = 23,

    c_ST_MEASURE_HSV        = 24,

    c_ST_MEASURE_VALUE      = 25,

    c_ST_MEASURE_VALUE_MASK = 26,

    c_ST_MEASURE_ABSORPTION = 27,

    c_ST_MEASURE_TRANSMISSON= 28,

    c_ST_MEASURE_CELL_COUNT = 29,

    c_CELLS_STEPS           = 30;


    //Results

    static unsigned const int

    c_ST_C_RGB              = 0,

    c_ST_C_RGB_ANTISHADE    = 1,

    c_ST_C_RGB_DIFFERENCE   = 2,

    c_ST_C_HSV_INPUT        = 3,

    c_ST_C_HSV_DIFFERENCE   = 4,

    c_ST_G_INPUT_SAT        = 5,

    c_ST_G_DIFF_VAL         = 6,

    c_ST_B_EDGES            = 7,

    c_ST_B_NUMBERS          = 8,

    c_ST_B_EDGES_NUMBERS    = 9,

    c_ST_B_ROI_OUT          = 10,

    c_ST_B_ROI_IN           = 11,

    c_RESULTS_STEPS         = 12;


    static unsigned const int

    c_ATT_SIZE_AREA             = 0,

    c_ATT_SIZE_RADIUS           = 1,

    c_ATT_SIZE_DIAMETER         = 2,

    c_ATT_ABSORB_MEAN           = 3,

    c_ATT_ABSORB_MEDIAN         = 4,

    c_ATT_ABSORB_SUM            = 5,

    c_ATT_TRANS_MEAN            = 6,

    c_ATT_TRANS_MEDIAN          = 7,

    c_ATT_TRANS_SUM             = 8,

    c_ATT_TRANS_RADIAL_MEAN     = 9,

    c_ATT_TRANS_RADIAL_MEDIAN   = 10,

    c_ATT_TRANS_RADIAL_SUM      = 11,

    c_ATT_CELL_DENSITY_MEAN     = 12,

    c_ATT_CELL_DENSITY_MEDIAN   = 13,

    c_ATT_CELL_DENSITY_SUM      = 14,

    c_ATT_COUNT                 = 15;

    QStringList QSL_Attrib      = {

        "Size_Area",                    "Size_Radius",                  "Size_Diameter",

        "Absorption_Mean",              "Absorption_Median",            "Absorption_Sum",

        "Transmission_Mean",            "Transmission_Median",          "Transmission_Sum",

        "Transmission_Radial_Mean",     "Transmission_Radial_Median",   "Transmission_Radial_Sum",

        "Aprox_Cell_Density_pPx_Mean",  "Aprox_Cell_Density_pPx_Median","Aprox_Cell_Count"

    };


    //Calculation

    static unsigned const int

    c_TYP_ABS               = 0,

    c_TYP_TRANS             = 1,

    c_TYP_TRANS_RADIAL      = 2,

    c_TYP_CELL_DENSITY      = 3,

    c_TYP_NUMBER_OF         = 4;

    QStringList QSL_Types   = {"Absorption", "Transmission", "Transmission_Radial", "Aprox_Cell_Density_per_Pixel"};


    //error handling

    D_Error_Handler ER;

    void ERR(int err, QString func = "not specified", QString detail = "not specified");


};


#endif // D_MAKRO_CELLCOLONIES_H