#include <math.h>

#include <hdf5.h>

#include <netcdf.h>

#include <stdio.h>

#include <stdlib.h>

#include <string.h>

#define DX .01 // Interval size in x direction

#define DY .01 // Interval size in y direction

#define SECTION 50 // Value of z-plane slab

//// #define STEPS 500 // Timesteps to compute

#define STEPS 50

// Filename hdf5

#define H5_FILE_NAME_HDF5 "data.h5"

#define ERR_HDF5 { H5Eprint( H5E_DEFAULT, stdout ); exit(2); }

// Filename NetCDF

#define NC_FILE_NAME_NETCDF "data.nc"

#define ERR_NETCDF(e) { printf( "Error: %s\n", nc_strerror(e) ); exit(2); }

int main() {

double *data_out; // buffer

int nx = 1/DX; // hyperslab and output buffer dimensions

int ny = 1/DY;

// int i, j;

// Allocate memory for data

if((data_out = (double *)malloc(STEPS * nx * ny * sizeof(double))) == NULL)

printf("Error malloc matrix data_out[%d]\n",nx * ny);

// Create NetCDF file. NC_CLOBBER tells NetCDF to overwrite this file, if it already exists

int ncid, retval;

// if( retval = nc_create( NC_FILE_NAME_NETCDF, NC_CLOBBER|NC_NETCDF4, &ncid ) ) {

if( retval = nc_create( NC_FILE_NAME_NETCDF, NC_CLOBBER, &ncid ) ) {

ERR_NETCDF(retval);

}

// Define the x and y dimensions. NetCDF will hand back and ID for each.

int x_dimid, y_dimid, t_dimid;

if( retval = nc_def_dim( ncid, "x", nx, &x_dimid ) ) {

ERR_NETCDF(retval);

}

if( retval = nc_def_dim( ncid, "y", ny, &y_dimid ) ) {

ERR_NETCDF(retval);

}

// Define the t dimension at NetCDF.

if( retval = nc_def_dim( ncid, "t", NC_UNLIMITED, &t_dimid ) ) {

ERR_NETCDF(retval);

}

// Define coordinate variables for x and y at NetCDF

int x_varid, y_varid, t_varid;

if( retval = nc_def_var( ncid, "x", NC_DOUBLE, 1, &x_dimid, &x_varid ) ) {

ERR_NETCDF(retval);

}

if( retval = nc_def_var( ncid, "y", NC_DOUBLE, 1, &y_dimid, &y_varid ) ) {

ERR_NETCDF(retval);

}

if( retval = nc_def_var( ncid, "t", NC_DOUBLE, 1, &t_dimid, &t_varid ) ) {

ERR_NETCDF(retval);

}

// Define the nc-variable to store temperature data. The t dimension should be the one which varies more slowly at NetCDF.

int varid;

int dimids[3] = { t_dimid, x_dimid, y_dimid };

if( retval = nc_def_var( ncid, "temperature", NC_DOUBLE, 3, dimids, &varid )){

ERR_NETCDF(retval);

}

// Write x, y, t and temperature units at NetCDF

char * space_units = "meters";

char * time_units = "seconds since start of the experiment";

char * temp_units = "kelvin";

if( retval = nc_put_att_text( ncid, x_varid, "units", strlen(space_units), space_units ) ) {

ERR_NETCDF(retval);

}

if( retval = nc_put_att_text( ncid, y_varid, "units", strlen(space_units), space_units ) ) {

ERR_NETCDF(retval);

}

if( retval = nc_put_att_text( ncid, t_varid, "units", strlen(time_units), time_units ) ) {

ERR_NETCDF(retval);

}

if( retval = nc_put_att_text( ncid, varid, "units", strlen(temp_units), temp_units ) ) {

ERR_NETCDF(retval);

}

double scale_factor = 300.0;

if( retval = nc_put_att_double( ncid, varid, "scale_factor", NC_DOUBLE, 1, &scale_factor ) ) {

ERR_NETCDF(retval);

}

// End define mode: this tells NetCDF that we are done defining metadata at NetCDF

if( retval = nc_enddef( ncid ) ) {

ERR_NETCDF(retval);

}

// Write x coordinates at NetCDF

size_t pos;

for( pos = 0; pos < nx; ++pos ) {

double x = DX*pos;

if( retval = nc_put_var1_double( ncid, x_varid, &pos, &x ) ) {

ERR_NETCDF(retval);

}

}

// Write y coordinates at NetCDF

for( pos = 0; pos < ny; ++pos ) {

double y = DY*pos;

if( retval = nc_put_var1_double( ncid, y_varid, &pos, &y ) ) {

ERR_NETCDF(retval);

}

}

// Open an existing HDF5 file for Output buffer

hid_t file_id = H5Fopen(H5_FILE_NAME_HDF5, H5F_ACC_RDONLY, H5P_DEFAULT);

if( file_id < 0 ) { ERR_HDF5; }

// Open an existing HDF5 dataset

hid_t tempD = H5Dopen(file_id, "temperature", H5P_DEFAULT);

if( tempD < 0 ) { ERR_HDF5; }

// Returns an identifier for a copy of the dataspace for a dataset HDF5

hid_t tempSel = H5Dget_space (tempD); /* dataspace handle */

if( tempSel < 0 ) { ERR_HDF5; }

// Returns the number of dimensions in the HDF5 dataspace if successful; otherwise returns a negative value

int rank;

rank = H5Sget_simple_extent_ndims (tempSel);

// Retrieves dataspace dimension size and maximum size HDF5

hsize_t dims_out[2]; // HDF5 dataset dimensions

hid_t status_n = H5Sget_simple_extent_dims (tempSel, dims_out, NULL);

if( status_n < 0 ) { ERR_HDF5; }

// Display the number of dimensions in the HDF5 dataspace and the dataspace dimension size and maximum size

printf("\nRank: %d\nDimensions: %lu x %lu \n", rank, (unsigned long)(dims_out[0]), (unsigned long)(dims_out[1]));

// Define hyperslab in the dataset HDF5

hsize_t sel_offset_in[4] = {0,0,0,SECTION}; // The temperature value for the last interaction (STEPS) is chosen

hsize_t sel_length_in[4] = {STEPS, nx, ny, 1};

H5Sselect_hyperslab( tempSel, H5S_SELECT_SET, sel_offset_in, NULL, sel_length_in, NULL );

if( tempSel < 0 ) { ERR_HDF5; }

// Define the memory dataspace HDF5

hsize_t memSdim[4]={STEPS,nx,ny};

hid_t memS = H5Screate_simple( 3, memSdim, NULL );

if( memS < 0 ) { ERR_HDF5; }

// Define memory HDF5 hyperslab

hsize_t sel_offset_out[3] = {0,0,0};

hsize_t sel_length_out[3] = {STEPS, nx, ny};

H5Sselect_hyperslab( memS, H5S_SELECT_SET, sel_offset_out, NULL, sel_length_out, NULL );

if( memS < 0 ) { ERR_HDF5; }

// Read dataset tempD data from HDF5 hyperslab in the file into the hyperslab in memory

hsize_t status = H5Dread (tempD, H5T_NATIVE_DOUBLE, memS, tempSel, H5P_DEFAULT, data_out);

if( status < 0 ) { ERR_HDF5; }

// printf ("Data:\n ");

// for( i = 0; i < nx; ++i ) {

// for( j = 0; j < ny; ++j ) {

// printf("%f ", data_out[i*ny+j]);

// }

// printf("\n ");

// }

// printf("\n");

// Write the data to the NETCDF file

size_t corner_vector[3] = {0,0,0};

size_t edge_lengths[3] = {STEPS, nx, ny};

if(retval = nc_put_vara_double(ncid, varid, corner_vector, edge_lengths, data_out)){

ERR_NETCDF(retval);

}

pos = 0;

double tval = 0;

if( retval = nc_put_var1_double( ncid, t_varid, &pos, &tval ) ) {

ERR_NETCDF(retval);

}

// Close the HDF5 memspace

if( H5Sclose( memS ) < 0 ) { ERR_HDF5; }

// Close the HDF5 dataspace

if( H5Sclose( tempSel ) < 0 ) { ERR_HDF5; }

// Close the HDF5 dataset

if( H5Dclose( tempD ) < 0 ) { ERR_HDF5; }

// Close the HDF5 file

if( H5Fclose( file_id ) < 0 ) { ERR_HDF5; }

// Close the file. This frees up any internal NetCDF resources associated with the file, and flushes any buffers

if( retval = nc_close( ncid ) ) {

ERR_NETCDF(retval);

}

// Free memory

free(data_out);

return 0;

}