ImageD/d__bio__nucleuspedigree_8h_source.html

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

 *   added:     04.01.2021          *

 *   author:    David Eilenstein    *

 *   contact:   D.Eilenstein@gsi.de *

 *   project:   ImageD              *

 *   facility:  GSI Darmstadt, Ger  *

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


#ifndef D_BIO_NUCLEUSPEDIGREE_H

#define D_BIO_NUCLEUSPEDIGREE_H


//own

#include <d_enum.h>

#include <d_stat.h>

#include <d_math.h>

#include <d_bio_nucleuslife.h>

#include <d_bio_nucleusblob.h>

#include <d_bio_nucleusimage.h>

#include <d_bio_enum.h>

#include <d_bio_attribute_filter.h>

#include <d_viewer_plot_3d.h>

#include <d_viewer_3d.h>


//Qt

#include <QObject>

#include <QFileDialog>

#include <QFileInfo>

#include <QFileInfoList>

#include <QDir>

#include <QDateTime>

#include <QInputDialog>

#include <QMessageBox>


//general

#include <iostream>

#include <sstream>

#include <fstream>

#include <vector>

#include <algorithm>

#include <thread>


//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>


class D_Bio_NucleusPedigree : public QObject

{

    Q_OBJECT


public:

    D_Bio_NucleusPedigree();


    void clear();


    void set_size_time_and_mosaik(size_t t_size, size_t y_size, size_t x_size);

    void set_time_irradiation(double t_irr);

    size_t size_T()                                         {return size_time;}

    size_t size_Y()                                         {return size_mosaik_y;}

    size_t size_X()                                         {return size_mosaik_x;}

    Rect rect_RegularRange_px()                             {return FrameInMarginXY;}

    size_t nuclei_blob_count(size_t t, size_t y, size_t x);

    size_t nuclei_blob_count(size_t t);

    size_t nuclei_blob_count();


    size_t mosaik_index_non_empty_min_x();

    size_t mosaik_index_non_empty_max_x();

    size_t mosaik_index_non_empty_min_y();

    size_t mosaik_index_non_empty_max_y();


    QString info();

    void info_debug();

    void info_popup();


    D_Bio_NucleusBlob*          get_pNucleus(size_t t, size_t y_mosaic, size_t x_mosaic, size_t i);

    D_Bio_NucleusBlob*          get_pNucleus(size_t t, size_t y_mosaic_min, size_t x_mosaic_min, size_t y_mosaic_max, size_t x_mosaic_max, size_t y_pos_px, size_t x_pos_px);

    vector<D_Bio_NucleusBlob*>  get_pNuclei_FromNucLifes(bool filtered_only);


    size_t                      get_NucleusLifesCount(bool filtered);

    D_Bio_NucleusLife*          get_pNucleusLife(size_t index, bool filtered);


    bool load_nuclei_data(QString QS_path_NucDataMaster, QString QS_path_NucData, size_t nt, size_t ny, size_t nx, bool forget_contour, bool foci_are_part_of_nuc_files);

    bool add_nucleus_blob(size_t t, size_t y, size_t x, D_Bio_NucleusBlob nuc);


    bool initMatching(vector<double> score_weights, vector<double> score_maxima, double shift_limit, double max_rel_area_inc_to, double max_rel_area_dec_to, double max_age, double thres_tm1_go1, double thres_tm2_go1, double thres_tm3_go1, double thres_tm1_go2, double thres_tm2_go2, double thres_tm3_go2, double mitosis_mult_go1, double mitosis_mult_go2);


    int setPedigreeViewer_Plot3D( D_Viewer_Plot_3D *viewer);

    int updatePedigreeView_Plot3D(                          size_t points_per_edge, size_t t_min = 0, size_t t_max = size_t(INFINITY), double y_min_um = -INFINITY, double y_max_um = INFINITY, double x_min_um = -INFINITY, double x_max_um = INFINITY);

    int updatePedigreeView_Plot3D(D_Viewer_Plot_3D *viewer, size_t points_per_edge, size_t t_min = 0, size_t t_max = size_t(INFINITY), double y_min_um = -INFINITY, double y_max_um = INFINITY, double x_min_um = -INFINITY, double x_max_um = INFINITY);


    int setPedigreeViewer_Volumetric( D_Viewer_3D *viewer);

    int updatePedigreeView_Volumetric(                      size_t size_volT_px, size_t size_volY_px, size_t size_volX_px, size_t size_Node_px, size_t size_Edge_px, size_t size_Y_px_original, size_t size_X_px_original);

    int updatePedigreeView_Volumetric(D_Viewer_3D *viewer,  size_t size_volT_px, size_t size_volY_px, size_t size_volX_px, size_t size_Node_px, size_t size_Edge_px, size_t size_Y_px_original, size_t size_X_px_original);

private:

    static int updatePedigreeView_Volumetric_TimeThread(D_VisDat_Obj *pVD_Target, vector<vector<vector<vector<D_Bio_NucleusBlob>>>> *pvvvvNucsTYXI, double score_range, double score_min, size_t size_Node_px, size_t size_Edge_px, size_t size_Y_px_original, size_t size_X_px_original, Rect frame_legit, size_t t_plane);

public:


    void set_scale_px2um(double scale)                                      {if(scale > 0) scale_px_to_um = scale;}

    void set_scale_T2h(double scale)                                        {if(scale > 0) scale_t_to_h = scale;}

    void set_scale_nodes(double scale)                                      {if(scale > 0 && scale <= 1) scale_nodes = scale;}

    void set_scale_edges(double scale)                                      {if(scale > 0 && scale <= 1) scale_edges = scale;}

    void set_FrameInMargin_XY(int x_min, int x_max, int y_min, int y_max)   {int w = x_max - x_min; int h = y_max - y_min; if(w > 0 && h > 0) set_FrameInMargin_XY(Rect(x_min, y_min, w, h));}

    void set_FrameInMargin_XY(Rect FrameInRange)                            {FrameInMarginXY = FrameInRange;}

    void set_FrameBorder_XY(Rect FrameBorder);

    void set_earliest_mitoses_allowed(size_t t_earliest)                    {match_earliest_mitosis_allowed = t_earliest;}

    void set_channels(QStringList channels_foc, QStringList channels_val)   {QSL_Channels_Foci = channels_foc; QSL_Channels_Values = channels_val;}


    bool set_attrib_filter_ui(QGroupBox* box_foci, QGroupBox* box_nucblobs, QGroupBox* box_nuclifes);

    bool set_attrib_filter_path(QDir* pDir_Save);

    bool set_attrib_filter_channels(QStringList channels_foc, QStringList channels_val);

    bool set_attrib_filter_scaling();

    bool set_attrib_filter(size_t filter_mode, size_t i_filt, bool is_active, size_t i_att, size_t i_comp, size_t i_ch, double thres_val);


    bool calc_NucLifes();

    bool calc_NucLifes_Filtered();


    vector<double>  attrib_data(size_t i_data_pt_lvl, size_t i_att_lvl_nuclife, size_t i_att_lvl_nucblob, /*size_t i_att_lvl_foc,*/ size_t i_att_nuclife, size_t i_att_nucblob, size_t i_att_foc, size_t ch_val, size_t ch_foc, size_t stat_low, size_t stat_high);

    //vector<double>  attrib_data(size_t i_data_point_level, size_t i_attrib_level, size_t i_attrib, size_t ch_val, size_t ch_foc, size_t stat_low, size_t stat_high);

    vector<double>  attrib_nuclife(size_t i_attrib);

    vector<double>  attrib_nucblob(size_t i_attrib, size_t ch_val);

    vector<double>  attrib_foci(size_t i_attrib, size_t ch_val);

    vector<double>  attrib_foci(size_t i_attrib, size_t ch_val, size_t ch_foc);


    bool save_analysis(QString QS_SavePath);

private:

    bool data_filtered_exists(size_t data_level);

    bool save_attribs_raw(QDir DIR_SaveMaster);

    bool save_attribs_raw(QFileInfo FI_SaveCsv, size_t data_level);

    bool save_attribs_stats_1D(QDir DIR_SaveMaster);

    bool save_attribs_stats_1D(QFileInfo FI_SaveCsv, size_t data_level);

    bool save_attribs_stats_2D(QDir DIR_SaveMaster);

    bool save_attribs_stats_2D_NucLifes(QDir DIR_SaveAttribsStats2D);

    bool save_attribs_stats_2D_NucBlobs(QDir DIR_SaveAttribsStats2D);

    bool save_attribs_stats_2D_Foci(QDir DIR_SaveAttribsStats2D, QString subset_name);


public:

    void match_all();

    void match_all_go1();

    void match_all_go2();


    void match_time_go1(size_t t);

    void match_time_go2(size_t t);

    void match_time_correct_mitosis_go1(size_t t);

    void match_time_correct_mitosis_go2(size_t t);


    bool match_save_results(QString QS_path);

    bool match_load_data_and_matches(QString QS_path_NucDataMaster, QString QS_path_NucData, QString QS_path_NucLifes, size_t nt, size_t ny, size_t nx, bool forget_contour, bool foci_are_part_of_nuc_files);

    bool match_load_matches(QString QS_path_NucLifes);


    bool event_find(QString* QS_FoundEventType, int* t_found, int* y_found, int* x_found, vector<int> vType_Search, vector<int> vType_Param, int t_min, int y_min, int x_greater_than, bool filter_use_t_after, int filter_param_t_after, bool filter_use_t_before, int filter_param_t_before, bool filter_use_range, int filter_param_x_min, int filter_param_x_max, int filter_param_y_min, int filter_param_y_max, bool filter_no_excluded);

    bool event_find(int* t_found, int* y_found, int* x_found, int type, int param, int t_min, int y_min, int x_greater_than, bool filter_use_t_after, int filter_param_t_after, bool filter_use_t_before, int filter_param_t_before, bool filter_use_range, int filter_param_x_min, int filter_param_x_max, int filter_param_y_min, int filter_param_y_max, bool filter_no_excluded);

    bool event_check(int* t_event, int* y_event, int* event_x, D_Bio_NucleusLife* pNucLifeTest, int type, int param);

    vector<size_t> event_counts(vector<int> vType_Param, int t_min, int y_min, int x_greater_than, bool filter_use_t_after, int filter_param_t_after, bool filter_use_t_before, int filter_param_t_before, bool filter_use_range, int filter_param_x_min, int filter_param_x_max, int filter_param_y_min, int filter_param_y_max, bool filter_no_excluded);


public slots:

    void SetAttribFilterToNeedUpdate();


private:


    static bool match_save_results_time_thread(vector<vector<vector<vector<D_Bio_NucleusBlob>>>> *pvvvvNucsTYXI, QDir DirSaveMaster, size_t t_thread);

    static bool load_time_nuclei_data_thread(vector<vector<vector<vector<D_Bio_NucleusBlob>>>> *pvvvvNucsTYXI, QDir DirLoadMaster, QDir DirLoadNucs, size_t t_thread, bool forget_contour, bool foci_are_part_of_nuc_files, int *err);

    static bool load_time_nuclei_matches_thread(vector<vector<vector<vector<D_Bio_NucleusBlob>>>> *pvvvvNucsTYXI, QDir DirLoadNucLifes, size_t t_thread, int *err);


    void        match_correct_mitosis(  size_t t_parents, size_t t_childs, double score_multiplier, bool allow_new_mitosis);

    void        match_times(            size_t t_parents, size_t t_childs, double score_thresh,     bool allow_new_mitosis);


    void        match_find_possible_matches(            vector<vector<double>> *vvPossibleMatches,              size_t t_parents, size_t t_childs, double score_thresh, bool allow_new_mitosis);

    void        match_find_possible_mitosis_corrections(vector<vector<double>> *vvPossibleMitosisCorrections,   size_t t_parents, size_t t_childs, double score_multiplier, bool allow_new_mitoses);


    static void match_find_possible_matches_thread(vector<vector<vector<vector<D_Bio_NucleusBlob>>>> *pvvvvNucsTYXI, vector<vector<double>> *vvPossibleMatches,                         size_t t_parents, size_t t_childs, double score_thresh, bool allow_new_mitosis, vector<size_t> *pvScoreRelevantCriteria, vector<double> *pvScoreWeights, vector<double> *pvScoreMax, double max_area_increase_to_rel, double max_area_decrease_to_rel, double max_shift, size_t y_toProc);

    static void match_find_possible_mitosis_corrections_thread(vector<vector<vector<vector<D_Bio_NucleusBlob>>>> *pvvvvNucsTYXI, vector<vector<double>> *vvPossibleMitosisCorrections, size_t t_parents, size_t t_childs, double mitosis_score_muliplier, bool allow_new_mitoses,              vector<size_t> *pvScoreRelevantCriteria, vector<double> *pvScoreWeights, vector<double> *pvScoreMax, double max_area_increase_to_rel, double max_area_decrease_to_rel, double max_shift, size_t y_toProc);


    void        match_accept_matches(vector<vector<double>> *vvPossibleMatches, bool allow_new_mitosis);

    void        match_accept_mitosis_corrections(vector<vector<double>> *vvPossibleMitosisCorrections, bool allow_new_mitosis);


    void        calc_PlotVol(vector<Point3d> vNodesCoord, vector<Point3d> vEdgeCoordBegins, vector<Point3d> vEdgeCoordEnds, vector<QColor> vNodeColor, vector<QColor> vEdgeColor, int size_T_px, int size_Y_px, int size_X_px, int size_nodes = 3, int size_edge = 1);


    //viewer

    D_Viewer_Plot_3D *pViewerPedigree_Plot3D;

    D_Viewer_3D *pViewerPedigree_Volumetric;


    //Plot_Volume for volumetric plot

    D_VisDat_Obj VD_PlotVol;


    //dimension

    size_t size_time = 0;

    size_t size_mosaik_y = 0;

    size_t size_mosaik_x = 0;


    //irradiation

    double time_irradiation = 0;


    //channels

    QStringList QSL_Channels_Foci;

    QStringList QSL_Channels_Values;


    //data

    vector<vector<vector<vector<D_Bio_NucleusBlob>>>> vvvvNucBlobs_TYXI;

    vector<D_Bio_NucleusLife> vNucLifes;

    vector<D_Bio_NucleusLife> vNucLifes_Filtered;


    //weights for score calc

    vector<size_t>                  vScoreCriteria_Relevant;

    vector<double>                  vScoreWeights_Relevant;

    vector<double>                  vScoreMaxima_Relevant;

    double                          match_thresh_max_area_increase_to = 1.25;

    double                          match_thresh_max_area_decrease_to = 0.35;

    double                          match_thresh_max_shift = 200;

    double                          match_max_age = 35;

    double                          match_score_thres_tm1_go1 = 0.50;

    double                          match_score_thres_tm2_go1 = 0.55;

    double                          match_score_thres_tm3_go1 = 0.60;

    double                          match_score_thres_tm1_go2 = 0.20;

    double                          match_score_thres_tm2_go2 = 0.25;

    double                          match_score_thres_tm3_go2 = 0.30;

    double                          match_score_multiplier_mitosis_go1 = 0.20;

    double                          match_score_multiplier_mitosis_go2 = 0.70;

    size_t                          match_earliest_mitosis_allowed = 0;


    //scaling XYT to rteal world coords

    double                          scale_px_to_um = 0.1;

    double                          scale_t_to_h = 1.0;

    double                          scale_nodes = 1;

    double                          scale_edges = 1;


    //XY range no border

    Rect                            FrameBorderXY = Rect(0, 0, INT_MAX, INT_MAX);

    Rect                            FrameInMarginXY = Rect(0, 0, INT_MAX, INT_MAX);


    //states

    bool                            state_ScoreWeightsAndMaxSet = false;

    bool                            state_PedigreeViewer_Plot3D_Set = false;

    bool                            state_PedigreeViewer_Volumetric_Set = false;

    bool                            state_AttribFiltersSet = false;

    bool                            state_NucLifesCalced = false;

    bool                            state_NucLifesFilteredCalced = false;

    bool                            state_NucLifeFilteringRunning = false;


    //attribute filter

    D_Bio_Attribute_Filter*         pAttribFilter_Foci = nullptr;

    D_Bio_Attribute_Filter*         pAttribFilter_NucBlobs = nullptr;

    D_Bio_Attribute_Filter*         pAttribFilter_NucLifes = nullptr;


    //match attribs

    enum MATCH_ATTRIB_INDEX {

        MATCH_ATTRIB_INDEX_SCORE,

        MATCH_ATTRIB_INDEX_PARENT_T,

        MATCH_ATTRIB_INDEX_PARENT_Y,

        MATCH_ATTRIB_INDEX_PARENT_X,

        MATCH_ATTRIB_INDEX_PARENT_I,

        MATCH_ATTRIB_INDEX_CHILD_T,

        MATCH_ATTRIB_INDEX_CHILD_Y,

        MATCH_ATTRIB_INDEX_CHILD_X,

        MATCH_ATTRIB_INDEX_CHILD_I,

        MATCH_ATTRIB_INDEX_NUMBER_OF

    };


public:

    enum EVENT_TYPE {

        EVENT_TYPE_LARGE_DIST_BETWEEN_NUC,

        EVENT_TYPE_MITOSIS,

        EVENT_TYPE_EXCLUDED,

        EVENT_TYPE_SHORT_LIFE_ISOLATED,

        EVENT_TYPE_SHORT_LIFE_LOOSE_START,

        EVENT_TYPE_SHORT_LIFE_LOOSE_END,

        EVENT_TYPE_SHORT_LIFE_BETWEEN_MITOSES,

        EVENT_TYPE_NUMBER_OF

    };

    const QStringList QSL_EventType = {

        "large dist between nuclei",

        "mitosis",

        "excluded",

        "short life (isolated)",

        "short life (loose start)",

        "short life (loose end)",

        "short life (between mitoses)"

    };

};


#endif // D_BIO_NUCLEUSPEDIGREE_H