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/* The functions in this file are copies of some functions in 'ncdf4' package,
* in order for the bugfix in .ncvar_get_inner in easyNCDF to work. When ncdf4
* addresses this bug, these function will be removed from this package.
* This code belongs to David Pierce.
*/
#include <stdio.h>
#include <netcdf.h>
#include <string.h>
#include <stdlib.h>
#include <Rdefines.h>
#include <R_ext/Rdynload.h>
/* These same values are hard-coded into the R source. Don't change them!
* Note that they are not the same as values defined in the netcdf
* library headers, since I don't want my R code to depend on those
*/
#define R_NC_TYPE_SHORT 1
#define R_NC_TYPE_INT 2
#define R_NC_TYPE_FLOAT 3
#define R_NC_TYPE_DOUBLE 4
#define R_NC_TYPE_TEXT 5
#define R_NC_TYPE_BYTE 6
/* New types in netcdf version 4 */
#define R_NC_TYPE_UBYTE 7
#define R_NC_TYPE_USHORT 8
#define R_NC_TYPE_UINT 9
#define R_NC_TYPE_INT64 10
#define R_NC_TYPE_UINT64 11
#define R_NC_TYPE_STRING 12
int R_nc4_nctype_to_Rtypecode( nc_type nct );
void R_nc4_varsize( int *ncid, int *varid, int *ndims, int *varsize, int *retval );
void R_nc4_inq_vartype( int *ncid, int *varid, int *precint, int *retval );
void R_nc4_inq_varndims( int *ncid, int *varid, int *ndims, int *retval );
void R_nc4_open( char **filename, int *cmode, int *ncid, int *retval );
void R_nc4_get_vara_text( int *ncid, int *varid, int *start, int *count, char **tempstore, char **data, int *retval );
void R_nc4_close ( int *ncid );
SEXP Rsx_nc4_get_vara_double( SEXP sx_ncid, SEXP sx_varid, SEXP sx_start, SEXP sx_count, SEXP sx_fixmiss, SEXP sx_imvstate, SEXP sx_missval );
SEXP Rsx_nc4_get_vara_int ( SEXP sx_ncid, SEXP sx_varid, SEXP sx_start, SEXP sx_count, SEXP sx_byte_style );
SEXP R_nc4_blankstring(SEXP size);
SEXP R_nc4_get_vara_string( SEXP sx_nc, SEXP sx_varid, SEXP sx_start, SEXP sx_count );
void R_nc4_inq_varid_hier( int *ncid, char **varname, int *returned_grpid, int *returned_varid );
// Non-registered
int R_nc4_util_nslashes( char *s, int *idx_first_slash );
void R_nc4_inq_varid_hier_inner( int *ncid, char *varname, int *returned_grpid, int *returned_varid );
/* For C calls that don't use SEXP type args */
static const
R_CMethodDef cMethods[] = {
{"R_nc4_inq_varid_hier", (DL_FUNC) &R_nc4_inq_varid_hier, 4},
{"R_nc4_nctype_to_Rtypecode", (DL_FUNC) &R_nc4_nctype_to_Rtypecode, 1},
{"R_nc4_varsize", (DL_FUNC) &R_nc4_varsize, 5},
{"R_nc4_inq_vartype", (DL_FUNC) &R_nc4_inq_vartype, 4},
{"R_nc4_inq_varndims", (DL_FUNC) &R_nc4_inq_varndims, 4},
{"R_nc4_open", (DL_FUNC) &R_nc4_open, 4},
{"R_nc4_get_vara_text", (DL_FUNC) &R_nc4_get_vara_text, 7},
{"R_nc4_close", (DL_FUNC) &R_nc4_close, 1},
NULL
};
/* For C calls that use SEXP type args */
static const
R_CallMethodDef callMethods[] = {
{"Rsx_nc4_get_vara_double", (DL_FUNC) &Rsx_nc4_get_vara_double, 7},
{"Rsx_nc4_get_vara_int", (DL_FUNC) &Rsx_nc4_get_vara_int, 5},
{"R_nc4_blankstring", (DL_FUNC) &R_nc4_blankstring, 1},
{"R_nc4_get_vara_string", (DL_FUNC) &R_nc4_get_vara_string, 4},
NULL
};
/*********************************************************************
* Register our extnal routines for R
*/
void R_init_ncdf4( DllInfo *info )
{
R_registerRoutines( info, cMethods, callMethods, NULL, NULL );
R_useDynamicSymbols( info, FALSE );
}
/*********************************************************************
* Converts from type "nc_type" to an integer as defined in the beginning
* of this file. We do NOT use the raw nc_type integers because then the
* R code would have a dependency on the arbitrary values in the netcdf
* header files!
*/
int R_nc4_nctype_to_Rtypecode( nc_type nct )
{
if( nct == NC_CHAR )
return(R_NC_TYPE_TEXT);
else if( nct == NC_SHORT )
return(R_NC_TYPE_SHORT);
else if( nct == NC_INT )
return(R_NC_TYPE_INT);
else if( nct == NC_FLOAT )
return(R_NC_TYPE_FLOAT);
else if( nct == NC_DOUBLE )
return(R_NC_TYPE_DOUBLE);
else if( nct == NC_BYTE )
return(R_NC_TYPE_BYTE);
else if( nct == NC_UBYTE )
return(R_NC_TYPE_UBYTE);
else if( nct == NC_USHORT )
return(R_NC_TYPE_USHORT);
else if( nct == NC_UINT )
return(R_NC_TYPE_UINT);
else if( nct == NC_INT64 )
return(R_NC_TYPE_INT64);
else if( nct == NC_UINT64 )
return(R_NC_TYPE_UINT64);
else if( nct == NC_STRING )
return(R_NC_TYPE_STRING);
else
return(-1);
}
/*********************************************************************/
/* Returns a vector of dim sizes for the variable.
* 'retval' is 0 for no error, or -1 for an error.
*/
void R_nc4_varsize( int *ncid, int *varid, int *ndims, int *varsize, int *retval )
{
int i, err, dimid[NC_MAX_DIMS];
size_t dimlen;
*retval = 0;
/* Get ndims */
err = nc_inq_varndims( *ncid, *varid, ndims );
if( err != NC_NOERR ) {
Rprintf( "Error in R_nc4_varsize on nc_inq_varndims call: %s\n",
nc_strerror(err) );
*retval = -1;
return;
}
/* Get dimids */
err = nc_inq_vardimid( *ncid, *varid, dimid );
if( err != NC_NOERR ) {
Rprintf( "Error in R_nc4_varsize on nc_inq_vardimid call: %s\n",
nc_strerror(err) );
*retval = -1;
return;
}
/* Get size of each dim */
for( i=0; i<(*ndims); i++ ) {
err = nc_inq_dimlen( *ncid, dimid[i], &dimlen );
if( err != NC_NOERR ) {
Rprintf( "Error in R_nc4_varsize on nc_inq_dimlen call: %s\n",
nc_strerror(err) );
*retval = -1;
return;
}
varsize[i] = (int)dimlen;
}
}
/*********************************************************************/
void R_nc4_inq_vartype( int *ncid, int *varid, int *precint, int *retval )
{
nc_type nct;
*retval = nc_inq_vartype( *ncid, *varid, &nct );
if( *retval != NC_NOERR )
Rprintf( "Error in R_nc4_inq_var: %s\n",
nc_strerror(*retval) );
*precint = R_nc4_nctype_to_Rtypecode(nct);
}
/*********************************************************************/
void R_nc4_inq_varndims( int *ncid, int *varid, int *ndims, int *retval )
{
*retval = nc_inq_varndims(*ncid, *varid, ndims );
if( *retval != NC_NOERR )
Rprintf( "Error in R_nc4_inq_varndims: %s\n",
nc_strerror(*retval) );
}
/*********************************************************************/
/* Inputs:
* sx_fixmiss : is 1 if we want to fix the missing values in this
* routine, and 0 otherwise
* sx_imvstate : 0=var has no missing value; 1=var has a NA for
* the missing value; 2=var has a valid, non-NA missing value
*
* Returns a list with elements:
* $error : 0 for success, -1 for error
* $data : array of integer values read in from the netcdf file
*/
SEXP Rsx_nc4_get_vara_double( SEXP sx_ncid, SEXP sx_varid, SEXP sx_start, SEXP sx_count,
SEXP sx_fixmiss, SEXP sx_imvstate, SEXP sx_missval )
{
SEXP sx_retval, sx_retnames, sx_reterr, sx_retdata;
int ncid, varid, i, err, ndims, fixmiss, imvstate, scalar_var;
double *p_data, missval, mvtol;
size_t s_start[MAX_NC_DIMS], s_count[MAX_NC_DIMS], tot_size;
char vn[2048];
/* Make space for our returned list, which will have
* two elements, named $error and $data
*/
PROTECT( sx_retval = allocVector( VECSXP, 2 )); /* 2 elements in returned list */
/* Set names for the returned list */
PROTECT( sx_retnames = allocVector( STRSXP, 2 ));
SET_STRING_ELT( sx_retnames, 0, mkChar("error") );
SET_STRING_ELT( sx_retnames, 1, mkChar("data" ) );
setAttrib( sx_retval, R_NamesSymbol, sx_retnames );
UNPROTECT(1); /* done with sx_retnames */
/* Set provisional 'no error' retval */
PROTECT(sx_reterr = allocVector( INTSXP, 1 ));
INTEGER(sx_reterr)[0] = 0;
ncid = INTEGER(sx_ncid )[0];
varid = INTEGER(sx_varid )[0];
fixmiss = INTEGER(sx_fixmiss )[0];
imvstate = INTEGER(sx_imvstate)[0];
missval = REAL (sx_missval )[0];
/* Get number of dimensions in this variable */
err = nc_inq_varndims( ncid, varid, &ndims );
if( err != NC_NOERR ) {
Rprintf( "Error in R_nc4_get_vara_double while getting ndims: %s\n",
nc_strerror(err) );
INTEGER(sx_reterr)[0] = -1;
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
UNPROTECT(2);
return( sx_retval );
}
/* Sanity check -- number of start and count elements must
match number of dims in the var
*/
scalar_var = ((ndims==0) && (GET_LENGTH(sx_start)==1) && (INTEGER(sx_start)[0]==0) && (INTEGER(sx_count)[0]==1));
if( (!scalar_var) && (ndims != GET_LENGTH(sx_start))) {
Rprintf( "Error in R_nc4_get_vara_double: I think var has %d dimensions, but passed start array is length %d. They must be the same!\n",
ndims, GET_LENGTH(sx_start) );
INTEGER(sx_reterr)[0] = -1;
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
UNPROTECT(2);
return( sx_retval );
}
if( (!scalar_var) && (ndims != GET_LENGTH(sx_count))) {
Rprintf( "Error in R_nc4_get_vara_double: I think var has %d dimensions, but passed count array is length %d. They must be the same!\n",
ndims, GET_LENGTH(sx_count) );
INTEGER(sx_reterr)[0] = -1;
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
UNPROTECT(2);
return( sx_retval );
}
/* Get total number of elements we will be reading so we can
* allocate R space
*/
tot_size = 1L;
for( i=0; i<ndims; i++ ) {
s_start[i] = (size_t)(INTEGER(sx_start)[i]);
s_count[i] = (size_t)(INTEGER(sx_count)[i]);
tot_size *= s_count[i];
}
/* Make space for the returned data */
PROTECT( sx_retdata = allocVector(REALSXP, tot_size));
p_data = REAL( sx_retdata );
/* Actually read in the data now */
err = nc_get_vara_double( ncid, varid, s_start, s_count, p_data );
if( err != NC_NOERR ) {
nc_inq_varname( ncid, varid, vn );
Rprintf( "Error in Rsx_nc4_get_vara_double: %s\n",
nc_strerror( err ) );
Rprintf( "Var: %s Ndims: %d Start: ", vn, ndims );
for( i=0; i<ndims; i++ ) {
Rprintf( "%u", (unsigned int)s_start[i] );
if( i < ndims-1 )
Rprintf( "," );
}
Rprintf( " " );
Rprintf( "Count: " );
for( i=0; i<ndims; i++ ) {
Rprintf( "%u", (unsigned int)s_count[i] );
if( i < ndims-1 )
Rprintf( "," );
}
Rprintf( "\n" );
INTEGER(sx_reterr)[0] = -1;
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
UNPROTECT(3);
return( sx_retval );
}
/* We only do this for imvstate==2, which is a valid, non-NA
* missing value. If the variable has NO missing value
* (imvstate==0) or a NA missing value (imvstate==1) then
* we skip this block.
*/
if( (fixmiss == 1) && (imvstate == 2)) {
if( missval == 0.0 )
mvtol = 1.e-10; /* arbitrary -- what are you supposed to use?? */
else
mvtol = fabs( missval ) * 1.e-5;
for( i=0L; i<tot_size; i++ ) {
if( fabs( p_data[i] - missval ) < mvtol )
p_data[i] = NA_REAL;
}
}
/* OK we can successfully return now */
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
SET_VECTOR_ELT( sx_retval, 1, sx_retdata );
UNPROTECT(3);
return( sx_retval );
}
/*********************************************************************/
/* Input value byte_style is 1 for signed, 2 for unsigned
*
* Returns a list with elements:
* $error : 0 for success, -1 for error
* $data : array of integer values read in from the netcdf file
*/
SEXP Rsx_nc4_get_vara_int( SEXP sx_ncid, SEXP sx_varid, SEXP sx_start,
SEXP sx_count, SEXP sx_byte_style )
{
SEXP sx_retval, sx_retnames, sx_reterr, sx_retdata;
int ncid, varid, byte_style, i, err, ndims, *p_data, scalar_var;
size_t s_start[MAX_NC_DIMS], s_count[MAX_NC_DIMS], tot_size, k;
char vn[2048];
nc_type nct;
/* Make space for our returned list, which will have
* two elements, named $error and $data
*/
PROTECT( sx_retval = allocVector( VECSXP, 2 )); /* 2 elements in returned list */
/* Set names for the returned list */
PROTECT( sx_retnames = allocVector( STRSXP, 2 ));
SET_STRING_ELT( sx_retnames, 0, mkChar("error") );
SET_STRING_ELT( sx_retnames, 1, mkChar("data" ) );
setAttrib( sx_retval, R_NamesSymbol, sx_retnames );
UNPROTECT(1); /* done with sx_retnames */
/* Set provisional 'no error' retval */
PROTECT(sx_reterr = allocVector( INTSXP, 1 ));
INTEGER(sx_reterr)[0] = 0;
ncid = INTEGER(sx_ncid )[0];
varid = INTEGER(sx_varid )[0];
byte_style = INTEGER(sx_byte_style)[0];
/* Get number of dimensions in this variable */
err = nc_inq_varndims( ncid, varid, &ndims );
if( err != NC_NOERR ) {
Rprintf( "Error in R_nc4_get_vara_int while getting ndims: %s\n",
nc_strerror(err) );
INTEGER(sx_reterr)[0] = -1;
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
UNPROTECT(2);
return( sx_retval );
}
/* Sanity check -- number of start and count elements must
match number of dims in the var
*/
scalar_var = ((ndims==0) && (GET_LENGTH(sx_start)==1) && (INTEGER(sx_start)[0]==0) && (INTEGER(sx_count)[0]==1));
if( (!scalar_var) && (ndims != GET_LENGTH(sx_start))) {
Rprintf( "Error in R_nc4_get_vara_int: I think var has %d dimensions, but passed start array is length %d. They must be the same!\n",
ndims, GET_LENGTH(sx_start) );
INTEGER(sx_reterr)[0] = -1;
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
UNPROTECT(2);
return( sx_retval );
}
if( (!scalar_var) && (ndims != GET_LENGTH(sx_count))) {
Rprintf( "Error in R_nc4_get_vara_int: I think var has %d dimensions, but passed count array is length %d. They must be the same!\n",
ndims, GET_LENGTH(sx_count) );
INTEGER(sx_reterr)[0] = -1;
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
UNPROTECT(2);
return( sx_retval );
}
/* Get total number of elements we will be reading so we can
* allocate R space
*/
tot_size = 1L;
for( i=0; i<ndims; i++ ) {
s_start[i] = (size_t)(INTEGER(sx_start)[i]);
s_count[i] = (size_t)(INTEGER(sx_count)[i]);
tot_size *= s_count[i];
}
/* Make space for the returned data */
PROTECT( sx_retdata = allocVector(INTSXP, tot_size));
p_data = INTEGER( sx_retdata );
/* Actually read in the data now */
err = nc_get_vara_int( ncid, varid, s_start, s_count, p_data );
if( err != NC_NOERR ) {
nc_inq_varname( ncid, varid, vn );
Rprintf( "Error in Rsx_nc4_get_vara_int: %s\n",
nc_strerror( err ) );
Rprintf( "Var: %s Ndims: %d Start: ", vn, ndims );
for( i=0; i<ndims; i++ ) {
Rprintf( "%u", (unsigned int)s_start[i] );
if( i < ndims-1 )
Rprintf( "," );
}
Rprintf( " Count: " );
for( i=0; i<ndims; i++ ) {
Rprintf( "%u", (unsigned int)s_count[i] );
if( i < ndims-1 )
Rprintf( "," );
}
Rprintf( "\n" );
INTEGER(sx_reterr)[0] = -1;
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
UNPROTECT(3);
return( sx_retval );
}
err = nc_inq_vartype( ncid, varid, &nct );
if( nct == NC_BYTE ) {
/* netcdf library for reading from byte to int, as we do here,
* is SIGNED. So, if user requests signed, we don't have to
* do anything; only adjust if user asks for unsigned.
*/
if( byte_style == 2 ) { /* unsigned */
for( k=0L; k<tot_size; k++ ) {
if( p_data[k] < 0 )
p_data[k] += 256;
}
}
}
/* OK we can successfully return now */
SET_VECTOR_ELT( sx_retval, 0, sx_reterr );
SET_VECTOR_ELT( sx_retval, 1, sx_retdata );
UNPROTECT(3);
return( sx_retval );
}
/*********************************************************************/
void R_nc4_get_vara_text( int *ncid, int *varid, int *start,
int *count, char **tempstore, char **data, int *retval )
{
int i, err, ndims;
size_t s_start[MAX_NC_DIMS], s_count[MAX_NC_DIMS], nstr, slen;
char vn[2048];
err = nc_inq_varndims(*ncid, *varid, &ndims );
if( err != NC_NOERR )
Rprintf( "Error in R_nc4_get_vara_text while getting ndims: %s\n",
nc_strerror(*retval) );
nstr = 1L;
for( i=0; i<ndims; i++ ) {
s_start[i] = (size_t)start[i];
s_count[i] = (size_t)count[i];
if( i < (ndims-1) )
nstr *= s_count[i];
}
slen = s_count[ndims-1];
*retval = nc_get_vara_text(*ncid, *varid, s_start, s_count, tempstore[0] );
if( *retval != NC_NOERR ) {
nc_inq_varname( *ncid, *varid, vn );
Rprintf( "Error in R_nc4_get_vara_text: %s\n",
nc_strerror(*retval) );
Rprintf( "Var: %s Ndims: %d Start: ", vn, ndims );
for( i=0; i<ndims; i++ ) {
Rprintf( "%u", (unsigned int)s_start[i] );
if( i < ndims-1 )
Rprintf( "," );
}
Rprintf( " Count: " );
for( i=0; i<ndims; i++ ) {
Rprintf( "%u", (unsigned int)s_count[i] );
if( i < ndims-1 )
Rprintf( "," );
}
Rprintf( "\n" );
}
/* Now copy each string over to the final data array */
for( i=0; i<nstr; i++ ) {
strncpy( data[i], tempstore[0]+i*slen, slen );
data[i][slen] = '\0';
}
}
/*********************************************************************/
/* Code kindly donated by Martin Morgan of the Fred Hutchinson
* Cancer Research Center
*/
SEXP R_nc4_blankstring(SEXP size)
{
int i, len;
char *str;
SEXP blank, string;
if (!IS_INTEGER(size) || LENGTH(size)!=1)
Rf_error("'size' must be 'integer(1)'");
len = INTEGER(size)[0];
if (len < 0)
Rf_error("'size' must be >= 0");
str = R_alloc(len + 1, sizeof(char));
for (i = 0; i < len; ++i)
str[i] = ' ';
str[len] = '\0';
blank = PROTECT(NEW_CHARACTER(1));
string = PROTECT(mkChar(str));
SET_STRING_ELT(blank, 0, string);
UNPROTECT(2);
return(blank);
}
/*********************************************************************************
* Read vlen strings given the numeric varid, start, and count to use
*/
SEXP R_nc4_get_vara_string( SEXP sx_nc, SEXP sx_varid, SEXP sx_start, SEXP sx_count )
{
SEXP sx_retval, sx_retnames, sx_retstrings, sx_reterror;
int i, ierr, nchar, varid, ncid, ndims, count_int[MAX_NC_DIMS], start_int[MAX_NC_DIMS], len_count, len_start;
size_t count[MAX_NC_DIMS], start[MAX_NC_DIMS], tot_count, isz;
char **ss;
/* Convert passed parameters (which are in R format) into C format */
ncid = INTEGER(sx_nc )[0];
varid = INTEGER(sx_varid)[0];
len_start = length(sx_start);
for( i=0; i<len_start; i++ ) {
start_int[i] = INTEGER(sx_start)[i];
start [i] = (size_t)(start_int[i]);
}
len_count = length(sx_count);
for( i=0; i<len_count; i++ ) {
count_int[i] = INTEGER(sx_count)[i];
count [i] = (size_t)(count_int[i]);
}
PROTECT( sx_retval = allocVector( VECSXP, 2 )); /* 2 elements in the returned list: $error, $strings */
/* Set the names for the returned list */
PROTECT( sx_retnames = allocVector( STRSXP, 2 )); /* 2 elements in the returned list */
SET_STRING_ELT( sx_retnames, 0, mkChar("error") );
SET_STRING_ELT( sx_retnames, 1, mkChar("data") );
setAttrib( sx_retval, R_NamesSymbol, sx_retnames );
UNPROTECT(1);
/* Set the return error code */
PROTECT( sx_reterror = allocVector( INTSXP, 1 ));
INTEGER( sx_reterror)[0] = 0;
/* Get number of dims in the var */
ierr = nc_inq_varndims( ncid, varid, &ndims );
/*--------------------------------------------------------------
* At this point we have all the C values we need:
* ncid
* varid (numeric)
* ndims
* start
* count
*---------------------------------------------------------------*/
tot_count = 1L;
for( i=0; i<ndims; i++ )
tot_count *= count[i];
ss = (char **)malloc( sizeof( char *) * tot_count );
if( ss == NULL ) {
INTEGER( sx_reterror)[0] = -1;
error("ncdf4 library: routine R_nc4_get_vara_string: Error trying to allocate space to read the vlen strings: total count of strings requested: %ld\n", tot_count );
}
if( (ierr = nc_get_vara_string( ncid, varid, start, count, ss )) != 0 ) {
INTEGER( sx_reterror)[0] = -2;
error("ncdf4 library: routine R_nc4_get_vara_string: Error reading vlen strings: %s\n",
nc_strerror(ierr));
}
PROTECT( sx_retstrings = allocVector( STRSXP, tot_count ));
for( isz=0L; isz<tot_count; isz++ ) {
nchar = strlen( ss[isz] );
SET_STRING_ELT( sx_retstrings, isz, mkChar(ss[isz]) );
}
SET_VECTOR_ELT( sx_retval, 0, sx_reterror );
SET_VECTOR_ELT( sx_retval, 1, sx_retstrings );
UNPROTECT(3);
/* Free netcdf string storage */
nc_free_string( tot_count, ss );
return( sx_retval );
}
/*********************************************************************/
/* cmode is 0 for read only, 1 for write access.
*/
void R_nc4_open( char **filename, int *cmode, int *ncid, int *retval )
{
int nc_mode;
if( *cmode == 0 )
nc_mode = 0;
else if( *cmode == 1 )
nc_mode = NC_WRITE;
else
{
Rprintf( "Error in R_nc4_open: bad mode passed. Must be 0 (read) or 1 (write)\n");
*retval = -1;
return;
}
*retval = nc_open(R_ExpandFileName(filename[0]), nc_mode, ncid);
if( *retval != NC_NOERR )
Rprintf( "Error in R_nc4_open: %s\n",
nc_strerror(*retval) );
}
/*********************************************************************/
void R_nc4_close( int *ncid )
{
int err;
err = nc_close(*ncid);
if( err != NC_NOERR )
Rprintf( "Error in R_nc4_close: %s\n",
nc_strerror(err) );
}
/************************************************************************************************/
/* Returned index_first_slash is 0-based counting
*/
int R_nc4_util_nslashes( char *s, int *idx_first_slash )
{
int i, nslashes;
nslashes = 0;
*idx_first_slash = -1;
for( i=0; i<strlen(s); i++ ) {
if( s[i] == '/' ) {
nslashes++;
if( *idx_first_slash == -1 )
*idx_first_slash = i;
}
}
return( nslashes );
}
/****************************************************************************************/
void R_nc4_inq_varid_hier_inner( int *ncid, char *varname, int *returned_grpid, int *returned_varid )
{
int ierr, nslashes, idx_first_slash, gid;
char gname[MAX_NC_NAME];
/* Rprintf("R_nc4_inq_varid_hier_inner: Entering with varname=>%s<\n", varname ); */
/* Passed var name must not start with a slash */
if( varname[0] == '/' ) {
Rprintf( "Error in R_nc4_varid_hier: passed varname must not start with a slash!\n" );
*returned_varid = -1;
*returned_grpid = -1;
return;
}
/* If there are no forward slashes in the name, then it is a simple var name */
nslashes = R_nc4_util_nslashes( varname, &idx_first_slash );
/* Rprintf("R_nc4_inq_varid_hier_inner: varname >%s< has nslashes=%d and idx first slash=%d\n", varname, nslashes, idx_first_slash ); */
if( nslashes == 0 ) {
*returned_grpid = *ncid;
ierr = nc_inq_varid(*ncid, varname, returned_varid );
if( ierr != NC_NOERR ) {
*returned_varid = -1;
*returned_grpid = -1;
}
/* Rprintf("R_nc4_inq_varid_hier_inner: Found id for var >%s< varid:%d gid:%d\n", varname, *returned_varid, *returned_grpid ); */
return;
}
/* If we get here then the varname must have at least one slash, which indicates
* a group name under the current group name. Get the ID of that group
*/
strncpy( gname, varname, idx_first_slash );
gname[ idx_first_slash ] = '\0';
ierr = nc_inq_grp_ncid( *ncid, gname, &gid );
if( ierr != NC_NOERR ) {
Rprintf( "Error in R_nc4_varid_hier: extracted groupname not found: >%s< (coding error?)\n", gname );
*returned_varid = -1;
*returned_grpid = -1;
return;
}
/* Call ourselves recursively with the subgroup id and the varname stripped
* of its leading group name
*/
/* Rprintf("R_nc4_inq_varid_hier_inner: calling myself recursively with varname=>%s<\n", varname+idx_first_slash+1 ); */
R_nc4_inq_varid_hier_inner( &gid, varname+idx_first_slash+1, returned_grpid, returned_varid );
}
/****************************************************************************************/
/* This version of inq_varid works with hierarchial var names such as "model1/TS" and
* returns both the group ID and the var ID in that group, given the root group id
* (netcdf file ID).
*
* If the passed var is not found in the file, then -1 is returned.
*
* The passed slash-ful varname must not start or end with a slash.
*/
void R_nc4_inq_varid_hier( int *ncid, char **varname, int *returned_grpid, int *returned_varid )
{
/* Rprintf("R_nc4_inq_varid_hier: entering for var >%s<\n", varname[0] ); */
R_nc4_inq_varid_hier_inner( ncid, varname[0], returned_grpid, returned_varid );
}