MedPlotly.h

#pragma once
//
// Class to handle creation of charts using the plotly js package
//
// Main functionalities:
// (1) Configurable page content
// (2) Single signal charts
// (3) Panel charts
// (4) drugs heatmap
// (5) Major demographics table (TBD as a table)
// (6) Registries View (TBD)
// (7) ReadCodes View
//
//
 
 
 
#include <string>
#include <iostream>
#include <sstream>
#include <iomanip>
#include <boost/program_options.hpp>
#include <boost/algorithm/string/split.hpp>
#include <InfraMed/InfraMed/InfraMed.h>
#include <InfraMed/InfraMed/MedPidRepository.h>
#include <MedProcessTools/MedProcessTools/MedModel.h>
#include <MedTime/MedTime/MedTime.h>
 
#include <Logger/Logger/Logger.h>
#define LOCAL_SECTION LOG_APP
#define LOCAL_LEVEL LOG_DEF_LEVEL
using namespace std;
namespace po = boost::program_options;
 
 
//=========================================================================================================
namespace PlotlyColorDefaults {
 
 
    static const vector<string> bg_opaque_colors = { "rgba(162, 217, 206,0.333)" ,  "rgba(199, 210, 232, 0.333)" ,  "rgba(220, 199, 232,0.333)",
        "rgba(232, 199, 204,0.333)",  "rgba(200, 232, 199,0.333)",  "rgba(232, 217, 199,0.333)",  "rgba(215, 216, 192,0.333)" };
 
    static string get_bg_color(int i) { return PlotlyColorDefaults::bg_opaque_colors[i % (int)PlotlyColorDefaults::bg_opaque_colors.size()]; }
 
};
 
//=========================================================================================================
class SignalParams : public SerializableObject {
public:
    int null_zeros = 1;
    int log_scale = 1;
    int time_chan = 0;
    int val_chan = 0;
    bool get_ascenders_codes = false;
    int ascender_limit = 1;
    string filter_regex_codes = "";
    string remove_regex_codes = "";
 
    int init(map<string, string>& _map);
};
 
//=========================================================================================================
class PanelInfo : public SerializableObject {
public:
    string name = "";           // to be used when adding it
    string title = "";          // title of panel chart
    vector<string> sigs;        // sigs to be drawn on panel chart.
    vector<string> drugs;       // list of drug groups to visualize
    vector<string> drug_colors;         // bg colors to use. (when not initialized, will be initialized from a defaulted list).
    int null_zeros = -1;        // -1: means take default
    int log_scale = -1;         // -1: means take default
    int width = -1;
    int height = -1;
    int block_mode = -1;
 
    PanelInfo() {};
    PanelInfo(string _name, string _title, const vector<string> &_sigs, const vector<string> &_drugs, const vector<string> &_drug_colors, int _null_zeros, int _log_scale) {
        name = _name; title = _title; sigs = _sigs; drugs = _drugs; drug_colors = _drug_colors; null_zeros = _null_zeros; log_scale = _log_scale;
    }
 
    int init(map<string, string>& _map);
};
 
 
//=========================================================================================================
class DrugsHeatMapParams : public SerializableObject {
public:
    vector<string> drugs;
    string color0;
    string color1;
    int granularity_months = 1;
    int min_date = 20000101;
    string drug_sig = "Drug";
    int width = 1200;
    int height = 200;
 
 
    int init(map<string, string>& _map);
};
 
//=========================================================================================================
// General Params:
// Either defaulted , or read from a config file
//=========================================================================================================
class MedPlotlyParams : public SerializableObject {
public:
    string page_title = "Patient Report";
 
    // signal specific params
    map<string, SignalParams> sig_params;
 
    // Drugs groups
    map<string, vector<string>> drugs_groups;
 
    // Panels
    map<string, PanelInfo> panels;
 
    // drugs heatmap
    DrugsHeatMapParams dhm_params;
 
    // view order
    vector<string> views;
 
    // javascript
    string js_dir = "";
    vector<string> js_files;
 
    // zeros handling
    int null_zeros_default = 1; // in default we treat zeros as outliers and don't draw them.
    int log_scale_default = 1;
    int width_default = 600;
    int height_default = 400;
    int block_mode_default = 1;
 
    // time unit , currently supporting Date and Minutes
    int rep_time_unit = MedTime::Date; // default is Date.
 
    MedModel model_rep_processors;
    bool load_dynamically = true;
    vector<string> phisical_read_sigs;
    vector<string> all_need_sigs;
 
    int read_config(const string &config_fname);
 
};
 
//=========================================================================================================
// Used in order to be able to mark some interesting times on generated charts
class ChartTimeSign : public SerializableObject {
public:
    int time;
    string name;
    string color = ""; // if empty will use default color lists
 
    ChartTimeSign() {};
    ChartTimeSign(int t, const string &_name, const string _color) { time = t; name = _name; color = _color; }
    int init(map<string, string>& _map);
 
    // example of how to initialize a vector:
    //vector<ChartTimeSign> vec = { ChartTimeSign(1,"a","b") , ChartTimeSign(2,"d","e") };
 
};
 
class LocalViewsParams {
public:
    LocalViewsParams() {};
    LocalViewsParams(int _pid, int _from, int _to) { pid = _pid; from_date = _from; to_date = _to; }
    int pid = 0;
    int from_date = 0;
    int to_date = 0;
 
 
};
 
class PidDataRec {
public:
    PidRec rec_static;
    PidDynamicRec rec_dynamic;
    bool use_dynamic = false;
 
    void uget(int sid, UniversalSigVec &usv) {
        if (use_dynamic)
            rec_dynamic.uget(sid, rec_dynamic.get_n_versions() - 1, usv);
        else
            rec_static.uget(sid, usv);
    }
    void uget(const string &sid, UniversalSigVec &usv) {
        if (use_dynamic)
            rec_dynamic.uget(sid, rec_dynamic.get_n_versions() - 1, usv);
        else
            rec_static.uget(sid, usv);
    }
    void *get(const string &sid, int &len) {
        if (use_dynamic)
            return rec_dynamic.get(sid, rec_dynamic.get_n_versions() - 1, len);
        else
            return rec_static.get(sid, len);
    }
    int pid() {
        if (use_dynamic)
            return rec_dynamic.pid;
        else
            return rec_static.pid;
    }
    MedRepository *my_base_rep() {
        if (use_dynamic)
            return rec_dynamic.my_base_rep;
        else
            return rec_static.my_base_rep;
    }
};
 
//=========================================================================================================
// MedPatientPlotlyDate:
// - Built to handle date based repositories
// - allows configurable viewing of a given PidRec
//=========================================================================================================
class MedPatientPlotlyDate {
 
public:
    MedPlotlyParams params;
 
    int read_config(const string &config_name) { return params.read_config(config_name); }
 
    // gets a pid record and returns a string representing the html for its view page based on configuration
    // mode is either file (for an html file:/// version) or server (for use with a web server returning it)
    int get_rec_html(string &shtml, LocalViewsParams &lvp, PidDataRec &rec, const string &mode, const vector<ChartTimeSign> &sign_times, const vector<string> &view);
    int get_rec_html(string &shtml, LocalViewsParams &lvp, PidDataRec &rec, const string &mode, const vector<ChartTimeSign> &sign_times) {
        return get_rec_html(shtml, lvp, rec, mode, sign_times, params.views);
    }
 
    int init_rep_processors(MedPidRepository &rep, const string &rep_conf);
 
private:
    // builders for html
    int add_html_header(string &shtml, const string &mode);
    int add_basic_demographics(string &shtml, PidDataRec &rec, vector<ChartTimeSign> &times);
    int add_panel_chart(string &shtml, LocalViewsParams &lvp, PidDataRec &rec, const PanelInfo &pi, const vector<ChartTimeSign> &times);
    int add_drugs_heatmap(string &shtml, PidDataRec &rec);
 
    // THIN_RC report
    bool add_categorical_chart(string &shtml, PidDataRec &rec, const vector<ChartTimeSign> &times, 
        const string &sig_name, string &div_name, bool show_legend, int channel);
 
    void add_search_box(string &shtml, const string &sig_name, const string &div_chart, const string &div_table, int channel);
 
    // categorical signal , add as table
    bool add_categorical_table(string sig, string &shtml, PidDataRec &rec, const vector<ChartTimeSign> &times, string &div_name);
 
    // heatmap creation
    void get_drugs_heatmap(PidDataRec &rec, vector<int> &_xdates, vector<string> &_sets_names, vector<vector<float>> &_hmap, const vector<string> &drugs);
 
 
    // adding a specific dataset of a sepcific sig + channel
    void add_xy_js(string &shtml, vector<int> &dates, vector<float> &vals, int null_zeros_flag, string prefix);
    void add_xy_js(string &shtml, UniversalSigVec &usv, int time_chan, int chan, int null_zeros_flag, string prefix);
 
    void add_dataset_js(string &html, UniversalSigVec &usv, int time_chan, int chan, int null_zeros_flag, string prefix, string sname, int yaxis, string sig);
    void add_bg_dataset_js(string &shtml, vector<int> &dates, vector<float> &vals, int null_zeros_flag, string color, string prefix, string sname, int yaxis, string name);
 
    // helpers
    string  date_to_string(int date, bool fix_days_valid = false);
    string  time_to_string(int time, int time_unit);
    string  time_to_string(int time) { return time_to_string(time, params.rep_time_unit); }
    void get_usv_min_max(UniversalSigVec &usv, float &vmin, float &vmax);
 
};