/**************************************************************/
 /*  THEMIS ESA ION AND ELECTRON MOMENTS CDF -> DD netCDF      */
 /*                         04.01.2008                         */
 /*                           V 1.1                            */
 /*                                                            */
 /*   New CDF with ALL modes and new params                    */
 /*                   */
 /**************************************************************/

#include <stdio.h>
#include <stdlib.h>
#include <netcdf.h>
#include <cdf.h>
#include <DD.h>
#include <string.h>
#include <time.h>
#include <math.h>

#define TimeGap  1800000.0
#define Source "themis@cdpp2"
#define MAX_FILE_NAME_LEN  250                   // Max. file name length
#define MAX_VARS           250                   // Max # of VARS in CDF


/*************************************
   Global variables and structures
**************************************/
long   CDFDims,                                         // Number of dimensions in a CDF file
       CDFVars,                                            // Number of variables in a CDF file
       CDFDimSizes[CDF_MAX_DIMS],      // Dimension Sizes in a CDF file
       CDFencoding,                                    // Data encoding
       CDFmajority,                                      // Variable majority
       CDFmaxRec,                                     // max Record number
       CDFAttrs;                                          // number of CDF Attributes


struct cdfvar {                              // CDF variable structure
     char name[CDF_VAR_NAME_LEN+1];
     long num;                                //variable number
     long datatype;
     long numElem;                     // variable dimensionality
     long recVariance;                 // variable rec Variance
     long dimVariances[CDF_MAX_DIMS];  // # of data values in dimSizes
} cdfVar[MAX_VARS];

char mode[4];
int  ncID;
char ncFile[] = "peim000000000.nc";
int TimeDimID, TimeLengthID, DataID, Data2ID;
int TimeDimVector[2], DataDimVector[2],  Data2DimVector[2];      // netCDF Dim vectors
size_t Start[2] = {0L,0L};
size_t TimeCount[2] = {1L,TIMELENGTH};
size_t Data1Count[2] = {1L,1L};
size_t DataCount[2] = {1L,3L};
size_t Data2Count[2] = {1L,6L};

char Version[]="v01";
char ThemisID[]="tha\0";
char ThemisTime[]="tha_peim_time";
char PAR0[]="tha_peim_density";
char PAR1[]="tha_peim_ptot";
char PAR2[]="tha_peim_flux";
char PAR3[]="tha_peim_mftens"; // Momentum Flux Tensor DSL
char PAR4[]="tha_peim_eflux"; 
char PAR5[]="tha_peim_velocity_gse";
char PAR6[]="tha_peim_ptens"; // Pressure Tensor DSL 
char PAR7[]="tha_peim_mag";
char PAR8[]="tha_peim_velocity_mag";
char PAR9[]="tha_peim_t3_mag";  // Diagonilized Temperature
char PAR10[]="tha_peim_ptens_mag"; // 


int StartTimeID, StopTimeID;
int DeltaTID, DensID, PtotID;                    // 1D
int FluxID, EfluxID, VelID, MagID, VelMagID, TempMagID;       // 2D -> 3
int MfTensID, PtensID, PtensMagID ;                                                        // 2D -> 6
 
int TimeID;                                                                         // Time netCDF variable
 
  
char StartT[TIMELENGTH]; // Start time from  data
char StopT[TIMELENGTH];  // Stop time from  data
/**************************
   Function prototypes
**************************/
void usage();
void cdf_handle_error (CDFstatus);
void nc_handle_error (int);
void ncdefine();
/*--------------------------------------------------------------------------*/
void usage()
{
   printf ("\nDescription:\n");
   printf ("    This program converts a themis CDF file into a netCDF file.\n");
   printf ("\n");
   printf ("Usage: esa2nc <CDF file name> <ThemisID>\n");
   printf ("\n");
   printf ("Example: esa2nc testfile tha\n");
   printf ("\n");
   exit(1);
}
/*--------------------------------------------------------------------------
 *  Handles a CDF error.
 *--------------------------------------------------------------------------*/
void cdf_handle_error(CDFstatus status)
{

  char  message[CDF_STATUSTEXT_LEN+1];

   CDFerror (status, message);              /* Get the appropriate message */
   fprintf  (stderr, "CDF: %s\n", message);
//   exit(1);
}
/*--------------------------------------------------------------------------
 *  Handles a netCDF error.
 *--------------------------------------------------------------------------*/
void nc_handle_error(int status)
{
  fprintf(stderr, "%s\n", nc_strerror(status));
  exit(1);
}
 
 
/*--------------------------------------------------------------------------
 *  NetCDF File Definition  *
 *--------------------------------------------------------------------------*/
 void ncdefine(double Time)
 {
    char *s;
    time_t p;
    int status;
    char *STime;

/*********************** Create netCDF file *****************************/     
      memcpy(&(ncFile[0]),&(mode[0]),4);
      STime = Double2DD_Time(Time);
      memcpy(&(ncFile[4]),&(STime[2]), 9);
      if ((status = nc_create(ncFile, NC_CLOBBER, &ncID)) != NC_NOERR)
                                                      nc_handle_error(status);
/******************netCDF Dimensions *******************************/
        nc_def_dim (ncID, "Time", NC_UNLIMITED, &TimeDimID);
        nc_def_dim (ncID, "TimeLength", TIMELENGTH, &TimeLengthID);
        nc_def_dim (ncID, "Data",3L, &DataID); 
        nc_def_dim (ncID, "Data2",6L, &Data2ID);
  
/********************netCDF Variables ******************/
       TimeDimVector[0] = TimeDimID;
       DataDimVector[0] = TimeDimID;
       Data2DimVector[0] = TimeDimID;
       TimeDimVector[1] = TimeLengthID;
       DataDimVector[1] = DataID;
       
       Data2DimVector[1] = Data2ID;

//ModeID, DensID, VelID, TempID;
       nc_def_var (ncID, "Time", NC_CHAR, 2, TimeDimVector, &TimeID);
       nc_def_var (ncID, "Density", NC_DOUBLE, 1, &TimeDimID, &DensID);
       nc_def_var (ncID, "Ptot", NC_DOUBLE, 1, &TimeDimID, &PtotID);
       nc_def_var (ncID, "Flux", NC_DOUBLE, 2, DataDimVector, &FluxID);
       nc_def_var (ncID, "MfTens", NC_DOUBLE, 2, Data2DimVector, &MfTensID);
       nc_def_var (ncID, "Eflux", NC_DOUBLE, 2, DataDimVector, &EfluxID);
       nc_def_var (ncID, "Velocity", NC_DOUBLE, 2, DataDimVector, &VelID);
       nc_def_var (ncID, "Ptens", NC_DOUBLE, 2, Data2DimVector, &PtensID);
       nc_def_var (ncID, "Mag", NC_DOUBLE, 2, DataDimVector, &MagID); 
       nc_def_var (ncID, "VelocityMag", NC_DOUBLE, 2, DataDimVector, &VelMagID);
       nc_def_var (ncID, "TempMag", NC_DOUBLE, 2, DataDimVector, &TempMagID);
       nc_def_var (ncID, "PtensMag", NC_DOUBLE, 2, Data2DimVector, &PtensMagID);
     
       nc_def_var (ncID, "StartTime",NC_CHAR, 1, &TimeLengthID, &StartTimeID);
       nc_def_var (ncID, "StopTime",NC_CHAR, 1, &TimeLengthID , &StopTimeID);
 

       

       nc_put_att_text(ncID, NC_GLOBAL, "Themis", 3, ThemisID);
       nc_put_att_text(ncID, NC_GLOBAL, "Source", 12, Source);
       nc_put_att_text(ncID, DensID, "Units", 5, "cm^-3");
       
       
       time(&p);
       s = ctime(&p);
       nc_put_att_text(ncID, NC_GLOBAL, "Created", 24, s); 
        
       nc_enddef(ncID);
        
       nc_put_vara_text(ncID, StartTimeID, &(Start[1]), &(TimeCount[1]), Double2DD_Time(Time));
        ;
 }
/*--------------------------------------------------------------------------*/
int main(int argc, char *argv[])
{
    long RecStart = 0, RecCount, RecCountF = 1, RecInt = 1, MaxRec;
    long indices[1] = {0}, counts[1] = {3}, counts2[1] = {6}, intervals[1] = {1};
    long countsE[1] = {1}, indicesF[2]={0,3}, indicesF2[2]={0,6};
    double *value;
    float *value_f;
    size_t numElem;
    long dimN, varN, par0, par1, par2, par3, par4, par5, par6, par7, par8, par9, par10;
    CDFstatus   cstatus;           // CDF status code
    CDFid id;
    int i, j, status;
    char  fileName[MAX_FILE_NAME_LEN];
    dd_tmstr_t *dtm;
    int First = 1;

    char *UT;
    char data_set[8]="thx_peim";
/*-------------------------------- Arguments Decoding ----------------------------------------*/
     if (argc <= 2) usage();       // CDF input file name and THEMIS Number not specified
     else
     {
           strcpy(fileName, argv[1]);
           strncpy(ThemisID,argv[2],3);
           strncpy(mode,argv[3],4); 
      }
      
/*------------------------------------------ CDF Variables Names Updated according to THEMIS Number -------------*/
        memcpy(&(data_set[2]),&(ThemisID[2]),1); 
        memcpy(&(data_set[6]),&(mode[2]),2);
      
        memcpy(&(ThemisTime[0]),&(data_set[0]),8);
        memcpy(&(PAR0[0]),&(data_set[0]),8); 
        memcpy(&(PAR1[0]),&(data_set[0]),8); 
        memcpy(&(PAR2[0]),&(data_set[0]),8); 
        memcpy(&(PAR3[0]),&(data_set[0]),8); 
        memcpy(&(PAR4[0]),&(data_set[0]),8); 
        memcpy(&(PAR5[0]),&(data_set[0]),8); 
        memcpy(&(PAR6[0]),&(data_set[0]),8); 
        memcpy(&(PAR7[0]),&(data_set[0]),8);
        memcpy(&(PAR8[0]),&(data_set[0]),8);
        memcpy(&(PAR9[0]),&(data_set[0]),8);
        memcpy(&(PAR10[0]),&(data_set[0]),8); 
    
/*********************** Open CDF file *****************************/
     if ((cstatus = CDFopen(fileName, &id))  != CDF_OK)
                                      cdf_handle_error(cstatus);
     printf(" THEMIS  %s \n", ThemisID);

/*********** treat all vars as zVars with eliminated false dimensionality **********/
    
     if ((cstatus = CDFlib(SELECT_, CDF_zMODE_, zMODEon2, NULL_)) != CDF_OK)
                                                   cdf_handle_error (cstatus);
 

/************************ Get CDF Data  ************************************/

   cstatus = CDFlib(GET_, zVAR_NUMBER_, ThemisTime, &varN, NULL_);
   cstatus = CDFlib( SELECT_, zVAR_, varN, GET_, zVAR_MAXREC_, &MaxRec, NULL_);
 
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR0, &par0, NULL_);    
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR1, &par1, NULL_); 
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR2, &par2, NULL_); 
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR3, &par3, NULL_);
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR4, &par4, NULL_);
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR5, &par5, NULL_);
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR6, &par6, NULL_);
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR7, &par7, NULL_);
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR8, &par8, NULL_);
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR9, &par9, NULL_);
   cstatus = CDFlib(GET_, zVAR_NUMBER_, PAR10, &par10, NULL_);
 

      RecCount = (long)(MaxRec+1);
      printf(" Max Rec %d\n", MaxRec);
    if (  RecCount > 0) {
       value = (double *)malloc(sizeof(double)* RecCount);
       if ((cstatus = CDFlib (SELECT_,
		     zVAR_, varN,
		     zVAR_RECNUMBER_, RecStart ,
		     zVAR_RECCOUNT_, RecCount,
		     zVAR_RECINTERVAL_, RecInt,
		     zVAR_DIMINDICES_, indices,
		     zVAR_DIMCOUNTS_, countsE,
	             zVAR_DIMINTERVALS_, intervals,
                     GET_, zVAR_HYPERDATA_, value,  NULL_) )
                                             != CDF_OK) cdf_handle_error(cstatus);

         for (i = 0; i < RecCount; i++) {
                    UT = Double2DD_Time(value[i]); 
                    dtm =  ReadTime(UT); 
                    if (First == 1) {
                       ncdefine(dtm->times);
                       First = 0;
                     }   
                    nc_put_vara_text(ncID, TimeID, Start, TimeCount, UT);
                    
                    Start[0]++;

         }
         nc_put_vara_text(ncID,StopTimeID, &Start[1], &TimeCount[1], UT); 
          
  
// Density        
            if ((cstatus = CDFlib (SELECT_, zVAR_, par0,
                                zVAR_RECNUMBER_, RecStart,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indices,
                                zVAR_DIMCOUNTS_, countsE,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
                       
               nc_put_var_double(ncID, DensID, value);
// Ion Total Pressure
             if ((cstatus = CDFlib (SELECT_, zVAR_, par1,
                                zVAR_RECNUMBER_, RecStart,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indices,
                                zVAR_DIMCOUNTS_, countsE,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
                       
               nc_put_var_double(ncID, PtotID, value); 
            
             free(value); 
             value = (double *)malloc(sizeof(double)* RecCount * 3);
 // flux
              if ((cstatus = CDFlib (SELECT_, zVAR_, par2,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);

            nc_put_var_double(ncID, FluxID, value);

// Energy Flux
         if ((cstatus = CDFlib (SELECT_, zVAR_, par4,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
          nc_put_var_double(ncID, EfluxID,value);

// Velocity GSE
          if ((cstatus = CDFlib (SELECT_, zVAR_, par5,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
 
           nc_put_var_double(ncID, VelID,  value);
  
// Magnetic Field Vector DSL
           if ((cstatus = CDFlib (SELECT_, zVAR_, par7,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
              
                        
            nc_put_var_double(ncID, MagID, value);
           
// Velocity Mag
           if ((cstatus = CDFlib (SELECT_, zVAR_, par8,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
              
                        
            nc_put_var_double(ncID, VelMagID, value);

 // Temperature Mag
           if ((cstatus = CDFlib (SELECT_, zVAR_, par9,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
              
                        
            nc_put_var_double(ncID, TempMagID, value);
         
            free(value);
            value = (double *)malloc(sizeof(double)* RecCount * 6);
  
// Momentum Flux Tensor
           if ((cstatus = CDFlib (SELECT_, zVAR_, par3,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF2,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
              
                        
            nc_put_var_double(ncID, MfTensID, value);

// Pressure Tensor
           if ((cstatus = CDFlib (SELECT_, zVAR_, par6,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF2,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
              
                        
            nc_put_var_double(ncID, PtensID, value);

// Pressure Tensor Mag
           if ((cstatus = CDFlib (SELECT_, zVAR_, par10,
                                zVAR_RECNUMBER_, RecStart ,
                                zVAR_RECCOUNT_, RecCount,
                                zVAR_RECINTERVAL_, RecInt,
                                zVAR_DIMINDICES_, indicesF2,
                                zVAR_DIMCOUNTS_, counts,
                                zVAR_DIMINTERVALS_, intervals,
                                GET_, zVAR_HYPERDATA_, value, NULL_))
                                              != CDF_OK)  cdf_handle_error(cstatus);
              
                        
            nc_put_var_double(ncID, PtensMagID, value);



         free(value);
/********************Close Files******************/
    if ((status = nc_close(ncID)) != NC_NOERR) nc_handle_error(status); 
  }
       if ((cstatus = CDFlib(CLOSE_, CDF_, NULL_)) != CDF_OK)
                            cdf_handle_error (cstatus);

       
       
}