CommonTestingTools.h

#ifndef __COMMONTESTINGTOOLS_H
#define __COMMONTESTINGTOOLS_H
 
#include <AlgoMarker/AlgoMarker/AlgoMarker.h>
#include <AlgoMarker/DynAMWrapper/DynAMWrapper.h>
#include <AlgoMarker/CommonTestingTools/CommonTestingTools.h>
#include <Logger/Logger/Logger.h>
#include <MedProcessTools/MedProcessTools/MedModel.h>
#include <MedProcessTools/MedProcessTools/MedSamples.h>
#include <MedIO/MedIO/MedIO.h>
#include <json/json.hpp>
 
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/json_parser.hpp>
#include <boost/algorithm/string/predicate.hpp>
#include <boost/algorithm/string.hpp>
#include <algorithm>
#include <string>
#include <vector>
#include "DataLoader.h"
 
 
#ifdef __linux__ 
#include <wordexp.h>
#elif _WIN32
#include "windows.h" 
#endif
 
namespace CommonTestingTools {
 
    class DataLoader;
 
    const map<int, int> code_to_status_tbl = {
        { 300, 2 },
    { 301, 2 },
    { 310, 2 },
    { 311, 2 },
    { 320, 1 },
    { 321, 2 },
    { 390, 0 },
    { 391, 1 },
    { 392, 2 }
    };
 
    const map<string, string> units_tbl = {
        { "BMI" , "kg/m^2" },
    { "Glucose" , "mg/dL" },
    { "HbA1C" , "%" },
    { "HDL" , "mg/dL" },
    { "Triglycerides" , "mg/dL" },
    { "ALT" , "U/L" },
    { "RBC" , "10^6/uL" },
    { "Na" , "mmol/L" },
    { "Weight" , "Kg" },
    { "WBC" , "10^3/uL" },
    { "Basophils#" , "#" },
    { "Basophils%" , "%" },
    { "Eosinophils#" , "#" },
    { "Eosinophils%" , "%" },
    { "Hematocrit" , "%" },
    { "Hemoglobin" , "g/dL" },
    { "Lymphocytes#" , "#" },
    { "Lymphocytes%" , "%" },
    { "MCH" , "pg/cell" },
    { "MCHC-M" , "g/dL" },
    { "MCV" , "fL" },
    { "Monocytes#" , "#" },
    { "Monocytes%" , "%" },
    { "MPV" , "mic*3" },
    { "Neutrophils#" , "#" },
    { "Neutrophils%" , "%" },
    { "Platelets" , "10^3/uL" },
    { "RDW" , "%" },
    { "MSG" , "#" }
    };
 
 
    using namespace std;
 
    string precision_float_to_string(float val);
    json read_json_array_next_chunk(ifstream& infile, bool& in_array);
 
    //Expand string with embedded Environment variables in it
    string expandEnvVars(const string &str);
 
    // convert a C++ vector of strings to a char**
    class charpp_adaptor : public vector<string> {
    protected:
        char** charpp_arr;
        char* charpp_buf;
    public:
        void init() {
            charpp_arr = (char**)malloc(1);
            charpp_buf = (char*)malloc(1);
        }
        ~charpp_adaptor() {
            free(charpp_arr);
            free(charpp_buf);
        };
        charpp_adaptor() : vector<string>() { init(); };
        charpp_adaptor(int capacity) : vector<string>(capacity) { init(); };
        charpp_adaptor(const charpp_adaptor& other) : vector<string>(other) { init(); };
 
        char** get_charpp();
    };
 
    // get a malloc'ed read-write copy of a vector's .data() pointer
    template<typename T>
    class get_volatile_data_adaptor {
    protected:
        T * data_p;
        size_t data_p_size;
        int n_elem;
    public:
        ~get_volatile_data_adaptor() {
            free(data_p);
        };
 
        T* from_vec(const vector<T>& orig) {
            n_elem = (int)orig.size();
            data_p_size = n_elem * sizeof(T);
            if (data_p_size == 0)
                return nullptr;
            data_p = (T*)realloc(data_p, data_p_size);
            memcpy(data_p, orig.data(), data_p_size);
            return data_p;
        };
 
        get_volatile_data_adaptor(const vector<T>& orig) : n_elem(0), data_p_size(0) { data_p = (T*)malloc(1); from_vec(orig); }
 
        T* get_volatile_data() {
            if (data_p_size == 0)
                return nullptr;
            return data_p;
        }
    };
 
    json json_AddData(const char *signalName, int TimeStamps_len, long long* TimeStamps, int Values_len, float* Values, int n_time_channels, int n_val_channels);
    json json_AddDataStr(const char *signalName, int TimeStamps_len, long long* TimeStamps, int Values_len, char** Values, int n_time_channels, int n_val_channels);
 
    int get_preds_from_algomarker(AlgoMarker *am, vector<MedSample> &res, bool print_msgs, DataLoader& d, bool force_add_data, ofstream& msgs_stream, vector<string> ignore_sig, bool extended_score=false);
    int get_preds_from_algomarker_single(AlgoMarker *am, vector<MedSample> &res, bool print_msgs, DataLoader& d, bool force_add_data, ofstream& msgs_stream, vector<string> ignore_sig, ofstream& json_reqfile_stream, bool extended_score=false);
    void save_sample_vec(vector<MedSample> sample_vec, const string& fname);
}
 
#endif // __COMMONTESTINGTOOLS_H