dcopy.c

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#include "config.h"
#include "ncdispatch.h"
#include "nc_logging.h"
#include "nclist.h"
 
#ifdef USE_NETCDF4
 
static int searchgroup(int ncid1, int tid1, int grp, int* tid2);
static int searchgrouptree(int ncid1, int tid1, int grp, int* tid2);
 
static int
NC_compare_nc_types(int ncid1, int typeid1, int ncid2, int typeid2, int *equalp)
{
   int ret = NC_NOERR;
 
   /* If you don't care about the answer, neither do I! */
   if(equalp == NULL)
      return NC_NOERR;
 
   /* Assume the types are not equal. If we find any inequality, then
      exit with NC_NOERR and we're done. */
   *equalp = 0;
 
   /* Atomic types are so easy! */
   if (typeid1 <= NC_MAX_ATOMIC_TYPE)
   {
      if (typeid2 != typeid1)
     return NC_NOERR;
      *equalp = 1;
   }
   else
   {
      int i, ret, equal1;
      char name1[NC_MAX_NAME];
      char name2[NC_MAX_NAME];
      size_t size1, size2;
      nc_type base1, base2;
      size_t nelems1, nelems2;
      int class1, class2;
      void* value1 = NULL;
      void* value2 = NULL;
      size_t offset1, offset2;
      nc_type ftype1, ftype2;
      int ndims1, ndims2;
      int dimsizes1[NC_MAX_VAR_DIMS];
      int dimsizes2[NC_MAX_VAR_DIMS];
 
      /* Find out about the two types. */
      if ((ret = nc_inq_user_type(ncid1, typeid1, name1, &size1,
                  &base1, &nelems1, &class1)))
     return ret;
      if ((ret = nc_inq_user_type(ncid2, typeid2, name2, &size2,
                  &base2, &nelems2, &class2)))
     return ret;
 
      /* Check the obvious. */
      if(size1 != size2 || class1 != class2 || strcmp(name1,name2))
     return NC_NOERR;
 
      /* Check user-defined types in detail. */
      switch(class1)
      {
     case NC_VLEN:
        if((ret = NC_compare_nc_types(ncid1, base1, ncid2,
                      base1, &equal1)))
           return ret;
        if(!equal1)
           return NC_NOERR;
        break;
     case NC_OPAQUE:
        /* Already checked size above. */
        break;
     case NC_ENUM:
        if(base1 != base2 || nelems1 != nelems2) return NC_NOERR;
 
        if (!(value1 = malloc(size1)))
           return NC_ENOMEM;
        if (!(value2 = malloc(size2))) {
          free(value1);
          return NC_ENOMEM;
        }
 
        for(i = 0; i < nelems1; i++)
        {
           if ((ret = nc_inq_enum_member(ncid1, typeid1, i, name1,
                         value1)) ||
           (ret = nc_inq_enum_member(ncid2, typeid2, i, name2,
                         value2)) ||
           strcmp(name1, name2) || memcmp(value1, value2, size1))
           {
          free(value1);
          free(value2);
          return ret;
           }
        }
        free(value1);
        free(value2);
        break;
     case NC_COMPOUND:
        if(nelems1 != nelems2)
           return NC_NOERR;
 
        /* Compare each field. Each must be equal! */
        for(i = 0; i < nelems1; i++)
        {
           int j;
           if ((ret = nc_inq_compound_field(ncid1, typeid1, i, name1, &offset1,
                        &ftype1, &ndims1, dimsizes1)))
          return ret;
           if ((ret = nc_inq_compound_field(ncid2, typeid2, i, name2, &offset2,
                        &ftype2, &ndims2, dimsizes2)))
          return ret;
           if(ndims1 != ndims2)
          return NC_NOERR;
           for(j = 0; j < ndims1;j++)
          if(dimsizes1[j] != dimsizes2[j])
             return NC_NOERR;
 
           /* Compare user-defined field types. */
           if((ret = NC_compare_nc_types(ncid1, ftype1, ncid2, ftype2,
                         &equal1)))
          return ret;
           if(!equal1)
          return NC_NOERR;
        }
        break;
     default:
        return NC_EINVAL;
      }
      *equalp = 1;
   }
   return ret;
}
 
static int
NC_rec_find_nc_type(int ncid1, nc_type tid1, int ncid2, nc_type* tid2)
{
    int ret = NC_NOERR;
    int parent;
 
    if((ret = searchgroup(ncid1,tid1,ncid2,tid2)))
        goto done;
    if(*tid2 != 0)
        goto done; /* found */
 
   /* Look in the parents of ncid2 upto the root */
   switch (ret = nc_inq_grp_parent(ncid2,&parent)) {
   case NC_NOERR:
    /* Recurse up using parent grp */
        ret = NC_rec_find_nc_type(ncid1, tid1, parent, tid2);
    break;
   case NC_ENOGRP:
    /* do the breadth-first pre-order search of the whole tree */
    /* ncid2 should be root group */
    ret = searchgrouptree(ncid1,tid1,ncid2,tid2);
    break;
   default: break;
   }
 
done:
    return ret;
}
 
static int
NC_find_equal_type(int ncid1, nc_type xtype1, int ncid2, nc_type *xtype2)
{
   int ret = NC_NOERR;
 
   /* Check input */
   if(xtype1 <= NC_NAT)
      return NC_EINVAL;
 
   /* Handle atomic types. */
   if (xtype1 <= NC_MAX_ATOMIC_TYPE)
   {
      if(xtype2)
     *xtype2 = xtype1;
      return NC_NOERR;
   }
 
   /* Recursively search group ncid2 and its children
      to find a type that is equal (using compare_type)
      to xtype1. */
   ret = NC_rec_find_nc_type(ncid1, xtype1 , ncid2, xtype2);
   return ret;
}
 
#endif /* USE_NETCDF4 */
 
int
nc_copy_var(int ncid_in, int varid_in, int ncid_out)
{
   char name[NC_MAX_NAME + 1];
   char att_name[NC_MAX_NAME + 1];
   nc_type xtype;
   int ndims, dimids_in[NC_MAX_VAR_DIMS], dimids_out[NC_MAX_VAR_DIMS], natts, real_ndims;
   int varid_out;
   int a, d;
   void *data = NULL;
   size_t *count = NULL, *start = NULL;
   size_t reclen = 1;
   size_t *dimlen = NULL;
   int retval = NC_NOERR;
   size_t type_size;
   int src_format, dest_format;
   char type_name[NC_MAX_NAME+1];
   char dimname_in[NC_MAX_NAME + 1];
   int i;
 
   /* Learn about this var. */
   if ((retval = nc_inq_var(ncid_in, varid_in, name, &xtype,
                            &ndims, dimids_in, &natts)))
      return retval;
   /* find corresponding dimids in the output file */
   for(i = 0; i < ndims; i++) {
      dimids_out[i] = dimids_in[i];
      if ((retval = nc_inq_dimname(ncid_in, dimids_in[i], dimname_in)))
         return retval;
      if ((retval = nc_inq_dimid(ncid_out, dimname_in, &dimids_out[i])))
         return retval;
   }
 
   LOG((2, "nc_copy_var: ncid_in 0x%x varid_in %d ncid_out 0x%x",
        ncid_in, varid_in, ncid_out));
 
   /* Make sure we are not trying to write into a netcdf-3 file
    * anything that won't fit in netcdf-3. */
   if ((retval = nc_inq_format(ncid_in, &src_format)))
      return retval;
   if ((retval = nc_inq_format(ncid_out, &dest_format)))
      return retval;
   if ((dest_format == NC_FORMAT_CLASSIC
        || dest_format == NC_FORMAT_64BIT_DATA
        || dest_format == NC_FORMAT_64BIT_OFFSET) &&
       src_format == NC_FORMAT_NETCDF4 && xtype > NC_DOUBLE)
      return NC_ENOTNC4;
 
   /* Later on, we will need to know the size of this type. */
   if ((retval = nc_inq_type(ncid_in, xtype, type_name, &type_size)))
      return retval;
   LOG((3, "type %s has size %d", type_name, type_size));
 
   /* Switch back to define mode, and create the output var. */
   retval = nc_redef(ncid_out);
   if (retval && retval != NC_EINDEFINE)
      BAIL(retval);
   if ((retval = nc_def_var(ncid_out, name, xtype,
                            ndims, dimids_out, &varid_out)))
      BAIL(retval);
 
   /* Copy the attributes. */
   for (a=0; a<natts; a++)
   {
      if ((retval = nc_inq_attname(ncid_in, varid_in, a, att_name)))
         BAIL(retval);
      if ((retval = nc_copy_att(ncid_in, varid_in, att_name,
                ncid_out, varid_out)))
         BAIL(retval);
   }
 
   /* End define mode, to write metadata and create file. */
   nc_enddef(ncid_out);
   nc_sync(ncid_out);
 
   /* Allocate memory for our start and count arrays. If ndims = 0
      this is a scalar, which I will treat as a 1-D array with one
      element. */
   real_ndims = ndims ? ndims : 1;
   if (!(start = malloc((size_t)real_ndims * sizeof(size_t))))
      BAIL(NC_ENOMEM);
   if (!(count = malloc((size_t)real_ndims * sizeof(size_t))))
      BAIL(NC_ENOMEM);
 
   /* The start array will be all zeros, except the first element,
      which will be the record number. Count will be the dimension
      size, except for the first element, which will be one, because
      we will copy one record at a time. For this we need the var
      shape. */
   if (!(dimlen = malloc((size_t)real_ndims * sizeof(size_t))))
      BAIL(NC_ENOMEM);
 
   /* Set to 0, to correct for an unlikely dereference
      error reported by clang/llvm. */
   dimlen[0] = 0;
 
   /* Find out how much data. */
   for (d=0; d<ndims; d++)
   {
      if ((retval = nc_inq_dimlen(ncid_in, dimids_in[d], &dimlen[d])))
         BAIL(retval);
      LOG((4, "nc_copy_var: there are %d data", dimlen[d]));
   }
 
   /* If this is really a scalar, then set the dimlen to 1. */
   if (ndims == 0)
      dimlen[0] = 1;
 
   for (d=0; d<real_ndims; d++)
   {
      start[d] = 0;
      count[d] = d ? dimlen[d] : 1;
      if (d) reclen *= dimlen[d];
   }
 
   /* If there are no records, we're done. */
   if (!dimlen[0])
      goto exit;
 
   /* Allocate memory for one record. */
   if (!(data = malloc(reclen * type_size))) {
     if(count) free(count);
     if(dimlen) free(dimlen);
     if(start) free(start);
     return NC_ENOMEM;
   }
 
   /* Copy the var data one record at a time. */
   for (start[0]=0; !retval && start[0]<(size_t)dimlen[0]; start[0]++)
   {
      switch (xtype)
      {
     case NC_BYTE:
        retval = nc_get_vara_schar(ncid_in, varid_in, start, count,
                       (signed char *)data);
        if (!retval)
           retval = nc_put_vara_schar(ncid_out, varid_out, start, count,
                      (const signed char *)data);
        break;
     case NC_CHAR:
        retval = nc_get_vara_text(ncid_in, varid_in, start, count,
                      (char *)data);
        if (!retval)
           retval = nc_put_vara_text(ncid_out, varid_out, start, count,
                     (char *)data);
        break;
     case NC_SHORT:
        retval = nc_get_vara_short(ncid_in, varid_in, start, count,
                       (short *)data);
        if (!retval)
           retval = nc_put_vara_short(ncid_out, varid_out, start, count,
                      (short *)data);
        break;
     case NC_INT:
        retval = nc_get_vara_int(ncid_in, varid_in, start, count,
                     (int *)data);
        if (!retval)
           retval = nc_put_vara_int(ncid_out, varid_out, start, count,
                    (int *)data);
        break;
     case NC_FLOAT:
        retval = nc_get_vara_float(ncid_in, varid_in, start, count,
                       (float *)data);
        if (!retval)
           retval = nc_put_vara_float(ncid_out, varid_out, start, count,
                      (float *)data);
        break;
     case NC_DOUBLE:
        retval = nc_get_vara_double(ncid_in, varid_in, start, count,
                    (double *)data);
        if (!retval)
           retval = nc_put_vara_double(ncid_out, varid_out, start, count,
                       (double *)data);
        break;
     case NC_UBYTE:
        retval = nc_get_vara_uchar(ncid_in, varid_in, start, count,
                       (unsigned char *)data);
        if (!retval)
           retval = nc_put_vara_uchar(ncid_out, varid_out, start, count,
                      (unsigned char *)data);
        break;
     case NC_USHORT:
        retval = nc_get_vara_ushort(ncid_in, varid_in, start, count,
                    (unsigned short *)data);
        if (!retval)
           retval = nc_put_vara_ushort(ncid_out, varid_out, start, count,
                       (unsigned short *)data);
        break;
     case NC_UINT:
        retval = nc_get_vara_uint(ncid_in, varid_in, start, count,
                      (unsigned int *)data);
        if (!retval)
           retval = nc_put_vara_uint(ncid_out, varid_out, start, count,
                     (unsigned int *)data);
        break;
     case NC_INT64:
        retval = nc_get_vara_longlong(ncid_in, varid_in, start, count,
                      (long long *)data);
        if (!retval)
           retval = nc_put_vara_longlong(ncid_out, varid_out, start, count,
                         (long long *)data);
        break;
     case NC_UINT64:
        retval = nc_get_vara_ulonglong(ncid_in, varid_in, start, count,
                       (unsigned long long *)data);
        if (!retval)
           retval = nc_put_vara_ulonglong(ncid_out, varid_out, start, count,
                          (unsigned long long *)data);
        break;
     default:
        retval = NC_EBADTYPE;
      }
   }
 
  exit:
   if (data) free(data);
   if (dimlen) free(dimlen);
   if (start) free(start);
   if (count) free(count);
   return retval;
}
 
static int
NC_copy_att(int ncid_in, int varid_in, const char *name,
        int ncid_out, int varid_out)
{
   nc_type xtype;
   size_t len;
   void *data=NULL;
   int res;
 
   LOG((2, "nc_copy_att: ncid_in 0x%x varid_in %d name %s",
    ncid_in, varid_in, name));
 
   /* Find out about the attribute to be copied. */
   if ((res = nc_inq_att(ncid_in, varid_in, name, &xtype, &len)))
      return res;
 
#ifdef SEPDATA
   if (xtype < NC_STRING)
   {
      /* Handle non-string atomic types. */
      if (len)
      {
         size_t size = NC_atomictypelen(xtype);
 
         assert(size > 0);
     if (!(data = malloc(len * size)))
        return NC_ENOMEM;
      }
 
      res = nc_get_att(ncid_in, varid_in, name, data);
      if (!res)
     res = nc_put_att(ncid_out, varid_out, name, xtype,
              len, data);
      if (len)
     free(data);
   }
#ifdef USE_NETCDF4
   else if (xtype == NC_STRING)
   {
      /* Copy string attributes. */
      char **str_data;
      if (!(str_data = malloc(sizeof(char *) * len)))
     return NC_ENOMEM;
      res = nc_get_att_string(ncid_in, varid_in, name, str_data);
      if (!res)
     res = nc_put_att_string(ncid_out, varid_out, name, len,
                 (const char **)str_data);
      nc_free_string(len, str_data);
      free(str_data);
   }
   else
   {
      /* Copy user-defined type attributes. */
      int class;
      size_t size;
      void *data;
      nc_type xtype_out = NC_NAT;
 
      /* Find out if there is an equal type in the output file. */
      /* Note: original code used a libsrc4 specific internal function
     which we had to "duplicate" here */
      if ((res = NC_find_equal_type(ncid_in, xtype, ncid_out, &xtype_out)))
     return res;
      if (xtype_out)
      {
     /* We found an equal type! */
     if ((res = nc_inq_user_type(ncid_in, xtype, NULL, &size,
                    NULL, NULL, &class)))
        return res;
     if (class == NC_VLEN) /* VLENs are different... */
     {
        nc_vlen_t *vldata;
        int i;
        if (!(vldata = malloc(sizeof(nc_vlen_t) * len)))
           return NC_ENOMEM;
        if ((res = nc_get_att(ncid_in, varid_in, name, vldata)))
           return res;
        if ((res = nc_put_att(ncid_out, varid_out, name, xtype_out,
                 len, vldata)))
           return res;
        for (i = 0; i < len; i++)
           if((res = nc_free_vlen(&vldata[i])))
          return res;
        free(vldata);
         }
     else /* not VLEN */
     {
        if (!(data = malloc(size * len)))
           return NC_ENOMEM;
        res = nc_get_att(ncid_in, varid_in, name, data);
        if (!res)
           res = nc_put_att(ncid_out, varid_out, name, xtype_out, len, data);
        free(data);
         }
      }
   }
#endif 
#else 
   {
    /* Copy arbitrary attributes. */
        int class;
        size_t size;
        nc_type xtype_out = NC_NAT;
 
        if(xtype <= NC_MAX_ATOMIC_TYPE) {
        xtype_out = xtype;
        if((res = nc_inq_type(ncid_out,xtype_out,NULL,&size))) return res;
    } else { /* User defined type */
            /* Find out if there is an equal type in the output file. */
            /* Note: original code used a libsrc4 specific internal function
           which we had to "duplicate" here */
            if ((res = NC_find_equal_type(ncid_in, xtype, ncid_out, &xtype_out)))
            return res;
            if (xtype_out) {
        /* We found an equal type! */
        if ((res = nc_inq_user_type(ncid_in, xtype, NULL, &size, NULL, NULL, &class)))
            return res;
        }
    }
        if((data = malloc(size * len))==NULL) {return NC_ENOMEM;}
        res = nc_get_att(ncid_in, varid_in, name, data);
    if(!res)
        res = nc_put_att(ncid_out, varid_out, name, xtype_out, len, data);
    (void)nc_reclaim_data_all(ncid_out,xtype_out,data,len);
      }
#endif /*SEPDATA*/
 
   return res;
}
 
int
nc_copy_att(int ncid_in, int varid_in, const char *name,
        int ncid_out, int varid_out)
{
   int format, target_natts, target_attid;
   char att_name[NC_MAX_NAME + 1];
   int a, retval;
 
   /* What is the destination format? */
   if ((retval = nc_inq_format(ncid_out, &format)))
      return retval;
 
   /* Can't copy to same var in same file. */
   if (ncid_in == ncid_out && varid_in == varid_out)
      return NC_NOERR;
 
   /* For classic model netCDF-4 files, order of attributes must be
    * maintained during copies. We MUST MAINTAIN ORDER! */
   if (format == NC_FORMAT_NETCDF4_CLASSIC)
   {
      /* Does this attribute already exist in the target file? */
      retval = nc_inq_attid(ncid_out, varid_out, name, &target_attid);
      if (retval == NC_ENOTATT)
      {
     /* Attribute does not exist. No order to be preserved. */
     return NC_copy_att(ncid_in, varid_in, name, ncid_out, varid_out);
      }
      else if (retval == NC_NOERR)
      {
     /* How many atts for this var? */
     if ((retval = nc_inq_varnatts(ncid_out, varid_out, &target_natts)))
        return retval;
 
     /* If this is the last attribute in the target file, we are
      * off the hook. */
     if (target_attid == target_natts - 1)
        return NC_copy_att(ncid_in, varid_in, name, ncid_out, varid_out);
 
     /* Order MUST BE MAINTAINED! Copy all existing atts in the target
      * file, stopping at our target att. */
     for (a = 0; a < target_natts; a++)
     {
        if (a == target_attid)
        {
           if ((retval = NC_copy_att(ncid_in, varid_in, name, ncid_out, varid_out)))
          return retval;
        }
        else
        {
           if ((retval = nc_inq_attname(ncid_out, varid_out, a, att_name)))
          return retval;
           if ((retval = NC_copy_att(ncid_out, varid_out, att_name,
                     ncid_out, varid_out)))
          return retval;
        }
     }
      }
      else
     return retval; /* Some other error occurred. */
   }
   else
      return NC_copy_att(ncid_in, varid_in, name, ncid_out, varid_out);
 
   return NC_NOERR;
}
 
#ifdef USE_NETCDF4
 
/* Helper function for NC_rec_find_nc_type();
   search a specified group for matching type.
*/
static int
searchgroup(int ncid1, int tid1, int grp, int* tid2)
{
    int i,ret = NC_NOERR;
    int nids;
    int* ids = NULL;
 
    /* Get all types in grp */
    if(tid2)
    *tid2 = 0;
    if ((ret = nc_inq_typeids(grp, &nids, NULL)))
    goto done;
    if (nids)
    {
    if (!(ids = (int *)malloc((size_t)nids * sizeof(int))))
        {ret = NC_ENOMEM; goto done;}
    if ((ret = nc_inq_typeids(grp, &nids, ids)))
        goto done;
    for(i = 0; i < nids; i++)
        {
        int equal = 0;
        if ((ret = NC_compare_nc_types(ncid1, tid1, grp, ids[i], &equal)))
            goto done;
        if(equal)
        {
        if(tid2)
            *tid2 = ids[i];
        goto done;
        }
    }
    }
 
done:
    nullfree(ids);
    return ret;
}
 
/* Helper function for NC_rec_find_nc_type();
   search a tree of groups for a matching type
   using a breadth first queue
*/
static int
searchgrouptree(int ncid1, int tid1, int grp, int* tid2)
{
    int i,ret = NC_NOERR;
    int nids;
    int* ids = NULL;
    NClist* queue = nclistnew();
    int gid;
    uintptr_t id;
 
    id = grp;
    nclistpush(queue,(void*)id); /* prime the queue */
    while(nclistlength(queue) > 0) {
        id = (uintptr_t)nclistremove(queue,0);
    gid  = (int)id;
        if((ret = searchgroup(ncid1,tid1,gid,tid2)))
            goto done;
        if(*tid2 != 0)
            goto done; /*we found it*/
    /* Get subgroups of gid and push onto front of the queue (for breadth first) */
        if((ret = nc_inq_grps(gid,&nids,NULL)))
            goto done;
        if (!(ids = (int *)malloc((size_t)nids * sizeof(int))))
        {ret = NC_ENOMEM; goto done;}
        if ((ret = nc_inq_grps(gid, &nids, ids)))
            goto done;
    /* push onto the end of the queue */
        for(i=0;i<nids;i++) {
        id = ids[i];
        nclistpush(queue,(void*)id);
    }
    free(ids); ids = NULL;
    }
    /* Not found */
    ret = NC_EBADTYPE;
 
done:
    nclistfree(queue);
    nullfree(ids);
    return ret;
}
 
#endif