hdf5_histogram.c

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#include <string.h>
#include <stdlib.h>
#include <hdf5.h>
#include <hdf5_hl.h>
#include "../consts.h"
#include "../diag/hist.h"
#include "hdf5_histogram.h"

int hdf5_hist_write(hid_t f, char* path, histogram* hist) {
    int ordinate_dim = 1;
    int abscissa_dim = 0;
    for(int i = 0; i < HIST_ALLDIM; i++) {
        abscissa_dim += hist->axes[i].n ? 1 : 0;
    }
 
    int* abscissa_n_slots = (int*) malloc(abscissa_dim * sizeof(int));
    double* abscissa_min = (double*) malloc(abscissa_dim * sizeof(double));
    double* abscissa_max = (double*) malloc(abscissa_dim * sizeof(double));
    char** abscissa_names = (char**) malloc(abscissa_dim * sizeof(char*));
    char** abscissa_units = (char**) malloc(abscissa_dim * sizeof(char*));
 
    int k = 0;
    for(int i = 0; i < HIST_ALLDIM; i++) {
        if(!hist->axes[i].n) {
            continue;
        }
        abscissa_min[k] = hist->axes[i].min;
        abscissa_max[k] = hist->axes[i].max;
        abscissa_n_slots[k] = hist->axes[i].n;
 
        switch (hist->axes[i].name)
        {
        case R:
            abscissa_names[k] = "r";
            abscissa_units[k] = "m";
            break;
        case PHI:
            abscissa_names[k] = "phi";
            abscissa_units[k] = "deg";
            abscissa_min[k] *= 180.0/CONST_PI;
            abscissa_max[k] *= 180.0/CONST_PI;
            break;
        case Z:
            abscissa_names[k] = "z";
            abscissa_units[k] = "m";
            break;
        case RHO:
            abscissa_names[k] = "rho";
            abscissa_units[k] = "1";
            break;
        case THETA:
            abscissa_names[k] = "theta";
            abscissa_units[k] = "deg";
            break;
        case PPAR:
            abscissa_names[k] = "ppar";
            abscissa_units[k] = "kg*m/s";
            break;
        case PPERP:
            abscissa_names[k] = "pperp";
            abscissa_units[k] = "kg*m/s";
            break;
        case PR:
            abscissa_names[k] = "pr";
            abscissa_units[k] = "kg*m/s";
            break;
        case PPHI:
            abscissa_names[k] = "pphi";
            abscissa_units[k] = "kg*m/s";
            break;
        case PZ:
            abscissa_names[k] = "pz";
            abscissa_units[k] = "kg*m/s";
            break;
        case EKIN:
            abscissa_names[k] = "ekin";
            abscissa_units[k] = "eV";
            abscissa_min[k] /= CONST_E;
            abscissa_max[k] /= CONST_E;
            break;
        case XI:
            abscissa_names[k] = "pitch";
            abscissa_units[k] = "1";
            break;
        case MU:
            abscissa_names[k] = "mu";
            abscissa_units[k] = "T/eV";
            break;
        case PTOR:
            abscissa_names[k] = "ptor";
            abscissa_units[k] = "kg*m/s";
            break;
        case TIME:
            abscissa_names[k] = "time";
            abscissa_units[k] = "s";
            break;
        case CHARGE:
            abscissa_names[k] = "charge";
            abscissa_units[k] = "e";
            break;
        }
        k++;
    }
    char* ordinate_names[] = { "distribution" };
    char* ordinate_units[] = { "s/(m^5*kg^2*deg*e)" };
 
    /* Create a group for this distribution and write the data in it */
    int retval = hdf5_histogram_write_uniform_double(
        f, path, abscissa_dim, ordinate_dim, abscissa_n_slots, abscissa_min,
        abscissa_max, abscissa_units, abscissa_names, ordinate_units,
        ordinate_names, hist->bins);
    free(abscissa_n_slots);
    free(abscissa_min);
    free(abscissa_max);
    free(abscissa_names);
    free(abscissa_units);
 
    return retval;
}

int hdf5_histogram_write_uniform_double(
    hid_t f, const char *path, int abscissaDim, int ordinateDim,
    int *abscissaNslots, double *abscissaMin, double *abscissaMax,
    char **abscissaUnits, char **abscissaNames,
    char **ordinateUnits, char **ordinateNames, double *ordinate) {
 
    char temppath[256]; /* Helper variable */
 
    /* Create histogram group */
    hid_t histogram = H5Gcreate2(f, path, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    if(histogram < 0) {
        return 1;
    }
 
    /* Dimensions of ordinate data to be written */
    hsize_t dims[100];
    dims[0] = ordinateDim;
    for (int i=0; i<abscissaDim; i++) {
        dims[i+1] = abscissaNslots[i];
    }
 
    /* Write ordinate including its names and units */
    herr_t err;
    err = H5LTmake_dataset_double(histogram , "ordinate", abscissaDim+1,
                                  dims, ordinate);
    if(err){
        H5Gclose(histogram);
        return err;
    }
    for(int i=0; i<ordinateDim; i++) {
        sprintf(temppath, "name_%02d", i);
        H5LTset_attribute_string(histogram, "ordinate", temppath,
                                 ordinateNames[i]);
        sprintf(temppath, "unit_%02d", i);
        H5LTset_attribute_string(histogram, "ordinate", temppath,
                                 ordinateUnits[i]);
    }
 
 
    /* Write ordinate and abscissa dimensions */
    hsize_t dimsize = 1;
    err = H5LTmake_dataset_int(histogram , "ordinate_ndim", 1, &dimsize,
                               &ordinateDim);
    if(err){
        H5Gclose(histogram);
        return 1;
    }
    err = H5LTmake_dataset_int(histogram , "abscissa_ndim", 1, &dimsize,
                               &abscissaDim);
    if(err){
        H5Gclose(histogram);
        return 1;
    }
 
    /* Write abscissae */
    for (int i=0; i<abscissaDim; i++) {
 
        double* abscissavec = (double *) malloc( (dims[i+1]+1)*sizeof(double) );
        for(int j=0; j<dims[i+1]+1; j++) {
            abscissavec[j] =
                abscissaMin[i] + j * ( (abscissaMax[i] - abscissaMin[i])
                                       / abscissaNslots[i] );
        }
 
        /* Vector */
        char abscissapath[256];
        sprintf(abscissapath, "abscissa_vec_%02d",i+1);
        hsize_t abscissasize[1] = {abscissaNslots[i]+1};
        err = H5LTmake_dataset_double(histogram , abscissapath, 1, abscissasize,
                                      abscissavec);
        free(abscissavec);
        if(err){
            H5Gclose(histogram);
            return 1;
        }
 
        /* Vector length */
        sprintf(temppath, "abscissa_nbin_%02d", i+1);
        err = H5LTmake_dataset_int(histogram, temppath, 1, &dimsize,
                                   &(abscissaNslots[i]));
        if(err){
            H5Gclose(histogram);
            return 1;
        }
 
        /* Name and unit */
        sprintf(temppath, "name_%02d", i);
        H5LTset_attribute_string(histogram, abscissapath, temppath,
                                 abscissaNames[i]);
        sprintf(temppath, "unit_%02d", i);
        H5LTset_attribute_string(histogram, abscissapath, temppath,
                                 abscissaUnits[i]);
 
    }
 
    H5Gclose(histogram);
 
    return 0;
}