/* Initialize iteration for a variable. Just a wrapper for
* nc_blkio_init() that makes the netCDF calls needed to initialize
* lower-level iterator. */
int
nc_get_iter(int ncid,
int varid,
size_t bufsize, /* size in bytes of memory buffer */
nciter_t **iterpp /* returned opaque iteration state */)
{
int stat = NC_NOERR;
nciter_t *iterp;
nc_type vartype;
size_t value_size = 0; /* size in bytes of each variable element */
int ndims; /* number of dimensions for variable */
int *dimids;
long long nvalues = 1;
int dim;
int chunked = 0;
/* Caller should free this by calling nc_free_iter(iterp) */
iterp = (nciter_t *) emalloc(sizeof(nciter_t));
memset((void*)iterp,0,sizeof(nciter_t)); /* make sure it is initialized */
NC_CHECK(nc_inq_varndims(ncid, varid, &ndims));
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
iterp->dimsizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
iterp->chunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
NC_CHECK(nc_inq_vardimid (ncid, varid, dimids));
for(dim = 0; dim < ndims; dim++) {
size_t len;
NC_CHECK(nc_inq_dimlen(ncid, dimids[dim], &len));
nvalues *= len;
iterp->dimsizes[dim] = len;
}
NC_CHECK(nc_inq_vartype(ncid, varid, &vartype));
NC_CHECK(inq_value_size(ncid, vartype, &value_size));
#ifdef USE_NETCDF4
{
int contig = 1;
if(ndims > 0) {
NC_CHECK(nc_inq_var_chunking(ncid, varid, &contig, NULL));
}
if(contig == 0) { /* chunked */
NC_CHECK(nc_inq_var_chunking(ncid, varid, &contig, iterp->chunksizes));
chunked = 1;
}
}
#endif /* USE_NETCDF4 */
NC_CHECK(nc_blkio_init(bufsize, value_size, ndims, chunked, iterp));
iterp->to_get = 0;
free(dimids);
*iterpp = iterp;
return stat;
}
/* Determine whether a variable named varname exists in any group in
an open netCDF file with id ncid. If so, return the count of how
many matching variables were found, else return a count of 0. The
variable name can be absolute such as "/foo" or "/GRP1/GRP1A/foo",
in which case there is only one group to look in, given by the path
from the root group. Alternatively, the variable name can be
relative, such as "foo" or "GRPA/GRPB/foo", in which case every
group is examined for a variable with that relative name. */
size_t
nc_inq_varname_count(int ncid, char *varname) {
/*
count = 0;
status = nc_inq_gvarid(ncid, varname, varid);
if (status == NC_NOERR)
count++;
for each subgroup gid {
count += nc_inq_varname_count(gid, varname);
}
return count;
*/
size_t count = 0;
int varid;
/* look in this group */
int status = nc_inq_gvarid(ncid, varname, &varid);
#ifdef USE_NETCDF4
int numgrps;
int *ncids;
int g;
#endif
if (status == NC_NOERR)
count++;
#ifdef USE_NETCDF4
/* if this group has subgroups, call recursively on each of them */
NC_CHECK( nc_inq_grps(ncid, &numgrps, NULL) );
/* Allocate memory to hold the list of group ids. */
ncids = emalloc((numgrps + 1) * sizeof(int));
/* Get the list of group ids. */
NC_CHECK( nc_inq_grps(ncid, NULL, ncids) );
/* Call this function for each group. */
for (g = 0; g < numgrps; g++) {
count += nc_inq_varname_count(ncids[g], varname);
}
free(ncids);
#endif /* USE_NETCDF4 */
return count;
}
/* Get parent id needed to define a new group from its full name in an
* open file identified by ncid. Assumes all intermediate groups are
* already defined. */
static int
nc_inq_parid(int ncid, const char *fullname, int *locidp) {
int stat = NC_NOERR;
char *parent = strdup(fullname);
char *slash = "/"; /* groupname separator */
char *last_slash;
if(parent == NULL) {
NC_CHECK(NC_ENOMEM);
}
last_slash = strrchr(parent, '/');
if(last_slash == parent) { /* parent is root */
free(parent);
parent = strdup(slash);
} else {
*last_slash = '\0'; /* truncate to get parent name */
}
NC_CHECK(nc_inq_grp_full_ncid(ncid, parent, locidp));
free(parent);
return stat;
}
/*
* copy a user-defined enum type in the group igrp to the group ogrp
*/
static int
copy_enum_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
nc_type otype;
nc_type basetype;
size_t basesize;
size_t nmembers;
char name[NC_MAX_NAME];
int i;
NC_CHECK(nc_inq_enum(igrp, itype, name, &basetype, &basesize, &nmembers));
NC_CHECK(nc_def_enum(ogrp, basetype, name, &otype));
for(i = 0; i < nmembers; i++) { /* insert enum members */
char ename[NC_MAX_NAME];
long long val; /* large enough to hold any integer type */
NC_CHECK(nc_inq_enum_member(igrp, itype, i, ename, &val));
NC_CHECK(nc_insert_enum(ogrp, otype, ename, &val));
}
return stat;
}
/*
* Get total number of groups (including the top-level group and all
* descendant groups, recursively) and all descendant subgroup ids
* (including the input rootid of the start group) for a group and
* all its descendants, in preorder.
*
* If grpids or numgrps is NULL, it will be ignored. So typical use
* is to call with grpids NULL to get numgrps, allocate enough space
* for the group ids, then call again to get them.
*/
int
nc_inq_grps_full(int rootid, int *numgrps, int *grpids)
{
int stat = NC_NOERR;
ncgiter_t *giter; /* pointer to group iterator */
int grpid;
size_t count;
NC_CHECK(nc_get_giter(rootid, &giter));
count = 0;
NC_CHECK(nc_next_giter(giter, &grpid));
while(grpid != 0) {
if(grpids)
grpids[count] = grpid;
count++;
NC_CHECK(nc_next_giter(giter, &grpid));
}
if(numgrps)
*numgrps = count;
nc_free_giter(giter);
return stat;
}
/*
* Get group id of next group. On first call gets start group id,
* subsequently returns other subgroup ids in preorder. Returns zero
* when no more groups left.
*/
int
nc_next_giter(ncgiter_t *iterp, int *grpidp) {
int stat = NC_NOERR;
int numgrps;
int *grpids;
int i;
if(gs_empty(iterp)) {
*grpidp = 0; /* not a group, signals iterator is done */
} else {
*grpidp = gs_pop(iterp);
NC_CHECK(nc_inq_grps2(*grpidp, &numgrps, NULL));
if(numgrps > 0) {
grpids = (int *)emalloc(sizeof(int) * numgrps);
NC_CHECK(nc_inq_grps2(*grpidp, &numgrps, grpids));
for(i = numgrps - 1; i >= 0; i--) { /* push ids on stack in reverse order */
gs_push(iterp, grpids[i]);
}
free(grpids);
}
}
return stat;
}
static void
pr_att(
int ncid,
int varid,
const char *varname,
int ia
)
{
struct ncatt att; /* attribute */
NC_CHECK( nc_inq_attname(ncid, varid, ia, att.name) );
Printf ("\t\t%s:%s = ", varname, att.name);
NC_CHECK( nc_inq_att(ncid, varid, att.name, &att.type, &att.len) );
if (att.len == 0) { /* show 0-length attributes as empty strings */
att.type = NC_CHAR;
att.len = 1;
}
switch (att.type) {
case NC_CHAR:
att.string = (char *) malloc(att.len);
if (!att.string) {
error("Out of memory!");
NC_CHECK( nc_close(ncid) );
return;
}
NC_CHECK( nc_get_att_text(ncid, varid, att.name, att.string ) );
pr_att_string(att.len, att.string);
free(att.string);
break;
default:
att.vals = (double *) malloc(att.len * sizeof(double));
if (!att.vals) {
error("Out of memory!");
NC_CHECK( nc_close(ncid) );
return;
}
NC_CHECK( nc_get_att_double(ncid, varid, att.name, att.vals ) );
pr_att_vals(att.type, att.len, att.vals);
free(att.vals);
break;
}
Printf (" ;\n");
}
/*
* copy a user-defined compound type in the group igrp to the group ogrp
*/
static int
copy_compound_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
char name[NC_MAX_NAME];
size_t size;
size_t nfields;
nc_type otype;
int fid;
NC_CHECK(nc_inq_compound(igrp, itype, name, &size, &nfields));
NC_CHECK(nc_def_compound(ogrp, size, name, &otype));
for (fid = 0; fid < nfields; fid++) {
char fname[NC_MAX_NAME];
char ftypename[NC_MAX_NAME];
size_t foff;
nc_type iftype, oftype;
int fndims;
NC_CHECK(nc_inq_compound_field(igrp, itype, fid, fname, &foff, &iftype, &fndims, NULL));
/* type ids in source don't necessarily correspond to same
* typeids in destination, so look up destination typeid by using
* field type name */
NC_CHECK(nc_inq_type(igrp, iftype, ftypename, NULL));
NC_CHECK(nc_inq_typeid(ogrp, ftypename, &oftype));
if(fndims == 0) {
NC_CHECK(nc_insert_compound(ogrp, otype, fname, foff, oftype));
} else { /* field is array type */
int *fdimsizes;
fdimsizes = (int *) emalloc((fndims + 1) * sizeof(int));
stat = nc_inq_compound_field(igrp, itype, fid, NULL, NULL, NULL,
NULL, fdimsizes);
NC_CHECK(nc_insert_array_compound(ogrp, otype, fname, foff, oftype, fndims, fdimsizes));
free(fdimsizes);
}
}
return stat;
}
/*
* return 1 if varid identifies a record variable
* else return 0
*/
int
isrecvar(int ncid, int varid)
{
int ndims;
int is_recvar = 0;
int *dimids;
NC_CHECK( nc_inq_varndims(ncid, varid, &ndims) );
#ifdef USE_NETCDF4
if (ndims > 0) {
int nunlimdims;
int *recdimids;
int dim, recdim;
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
NC_CHECK( nc_inq_unlimdims(ncid, &nunlimdims, NULL) );
recdimids = (int *) emalloc((nunlimdims + 1) * sizeof(int));
NC_CHECK( nc_inq_unlimdims(ncid, NULL, recdimids) );
for (dim = 0; dim < ndims && is_recvar == 0; dim++) {
for(recdim = 0; recdim < nunlimdims; recdim++) {
if(dimids[dim] == recdimids[recdim]) {
is_recvar = 1;
break;
}
}
}
free(dimids);
free(recdimids);
}
#else
if (ndims > 0) {
int recdimid;
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
NC_CHECK( nc_inq_unlimdim(ncid, &recdimid) );
if(dimids[0] == recdimid)
is_recvar = 1;
free(dimids);
}
#endif /* USE_NETCDF4 */
return is_recvar;
}
static void
do_ncdump(const char *path, struct fspec* specp)
{
int ndims; /* number of dimensions */
int nvars; /* number of variables */
int ngatts; /* number of global attributes */
int xdimid; /* id of unlimited dimension */
int dimid; /* dimension id */
int varid; /* variable id */
struct ncdim dims[NC_MAX_DIMS]; /* dimensions */
size_t vdims[NC_MAX_DIMS]; /* dimension sizes for a single variable */
struct ncvar var; /* variable */
struct ncatt att; /* attribute */
int id; /* dimension number per variable */
int ia; /* attribute number */
int iv; /* variable number */
int is_coord; /* true if variable is a coordinate variable */
int ncid; /* netCDF id */
vnode* vlist = 0; /* list for vars specified with -v option */
int nc_status; /* return from netcdf calls */
nc_status = nc_open(path, NC_NOWRITE, &ncid);
if (nc_status != NC_NOERR) {
error("%s: %s", path, nc_strerror(nc_status));
}
/*
* If any vars were specified with -v option, get list of associated
* variable ids
*/
if (specp->nlvars > 0) {
vlist = newvlist(); /* list for vars specified with -v option */
for (iv=0; iv < specp->nlvars; iv++) {
NC_CHECK( nc_inq_varid(ncid, specp->lvars[iv], &varid) );
varadd(vlist, varid);
}
}
/* if name not specified, derive it from path */
if (specp->name == (char *)0) {
specp->name = name_path (path);
}
Printf ("netcdf %s {\n", specp->name);
/*
* get number of dimensions, number of variables, number of global
* atts, and dimension id of unlimited dimension, if any
*/
NC_CHECK( nc_inq(ncid, &ndims, &nvars, &ngatts, &xdimid) );
/* get dimension info */
if (ndims > 0)
Printf ("dimensions:\n");
for (dimid = 0; dimid < ndims; dimid++) {
NC_CHECK( nc_inq_dim(ncid, dimid, dims[dimid].name, &dims[dimid].size) );
if (dimid == xdimid)
Printf ("\t%s = %s ; // (%ld currently)\n",dims[dimid].name,
"UNLIMITED", (long)dims[dimid].size);
else
Printf ("\t%s = %ld ;\n", dims[dimid].name, (long)dims[dimid].size);
}
if (nvars > 0)
Printf ("variables:\n");
/* get variable info, with variable attributes */
for (varid = 0; varid < nvars; varid++) {
NC_CHECK( nc_inq_var(ncid, varid, var.name, &var.type, &var.ndims,
var.dims, &var.natts) );
Printf ("\t%s %s", type_name(var.type), var.name);
if (var.ndims > 0)
Printf ("(");
for (id = 0; id < var.ndims; id++) {
Printf ("%s%s",
dims[var.dims[id]].name,
id < var.ndims-1 ? ", " : ")");
}
Printf (" ;\n");
/* get variable attributes */
for (ia = 0; ia < var.natts; ia++)
pr_att(ncid, varid, var.name, ia); /* print ia-th attribute */
}
/* get global attributes */
if (ngatts > 0)
Printf ("\n// global attributes:\n");
for (ia = 0; ia < ngatts; ia++)
pr_att(ncid, NC_GLOBAL, "", ia); /* print ia-th global attribute */
if (! specp->header_only) {
if (nvars > 0) {
Printf ("data:\n");
}
/* output variable data */
for (varid = 0; varid < nvars; varid++) {
/* if var list specified, test for membership */
if (specp->nlvars > 0 && ! varmember(vlist, varid))
continue;
NC_CHECK( nc_inq_var(ncid, varid, var.name, &var.type, &var.ndims,
var.dims, &var.natts) );
if (specp->coord_vals) {
/* Find out if this is a coordinate variable */
is_coord = 0;
for (dimid = 0; dimid < ndims; dimid++) {
if (strcmp(dims[dimid].name, var.name) == 0 &&
var.ndims == 1) {
is_coord = 1;
break;
}
}
if (! is_coord) /* don't get data for non-coordinate vars */
continue;
}
/*
* Only get data for variable if it is not a record variable,
* or if it is a record variable and at least one record has
* been written.
*/
if (var.ndims == 0
|| var.dims[0] != xdimid
|| dims[xdimid].size != 0) {
/* Collect variable's dim sizes */
for (id = 0; id < var.ndims; id++)
vdims[id] = dims[var.dims[id]].size;
var.has_fillval = 1; /* by default, but turn off for bytes */
/* get _FillValue attribute */
nc_status = nc_inq_att(ncid,varid,_FillValue,&att.type,&att.len);
if(nc_status == NC_NOERR &&
att.type == var.type && att.len == 1) {
if(var.type == NC_CHAR) {
char fillc;
NC_CHECK( nc_get_att_text(ncid, varid, _FillValue,
&fillc ) );
var.fillval = fillc;
} else {
NC_CHECK( nc_get_att_double(ncid, varid, _FillValue,
&var.fillval) );
}
} else {
switch (var.type) {
case NC_BYTE:
/* don't do default fill-values for bytes, too risky */
var.has_fillval = 0;
break;
case NC_CHAR:
var.fillval = NC_FILL_CHAR;
break;
case NC_SHORT:
var.fillval = NC_FILL_SHORT;
break;
case NC_INT:
var.fillval = NC_FILL_INT;
break;
case NC_FLOAT:
var.fillval = NC_FILL_FLOAT;
break;
case NC_DOUBLE:
var.fillval = NC_FILL_DOUBLE;
break;
default:
break;
}
}
if (vardata(&var, vdims, ncid, varid, specp) == -1) {
error("can't output data for variable %s", var.name);
NC_CHECK(
nc_close(ncid) );
if (vlist)
free(vlist);
return;
}
}
}
}
Printf ("}\n");
NC_CHECK(
nc_close(ncid) );
if (vlist)
free(vlist);
}
/* Output the data for a single variable, in CDL syntax. */
int
vardata(
const struct ncvar *vp, /* variable */
long vdims[], /* variable dimension sizes */
int ncid, /* netcdf id */
int varid, /* variable id */
const struct fspec* fsp /* formatting specs */
)
{
long cor[NC_MAX_DIMS]; /* corner coordinates */
long edg[NC_MAX_DIMS]; /* edges of hypercube */
long add[NC_MAX_DIMS]; /* "odometer" increment to next "row" */
#define VALBUFSIZ 1000
double vals[VALBUFSIZ] ; /* aligned buffer */
int gulp = VALBUFSIZ;
int id;
int ir;
long nels;
long ncols;
long nrows;
int vrank = vp->ndims;
static int initeps = 0;
/* printf format used to print each value */
char *fmt = get_fmt(ncid, varid, vp->type);
if (!initeps) { /* make sure epsilons get initialized */
init_epsilons();
initeps = 1;
}
nels = 1;
for (id = 0; id < vrank; id++) {
cor[id] = 0;
edg[id] = 1;
nels *= vdims[id]; /* total number of values for variable */
}
if (vrank <= 1) {
Printf("\n %s = ", vp->name);
set_indent ((int)strlen(vp->name) + 4);
} else {
Printf("\n %s =\n ", vp->name);
set_indent (2);
}
if (vrank < 1) {
ncols = 1;
} else {
ncols = vdims[vrank-1]; /* size of "row" along last dimension */
edg[vrank-1] = vdims[vrank-1];
for (id = 0; id < vrank; id++)
add[id] = 0;
if (vrank > 1)
add[vrank-2] = 1;
}
nrows = nels/ncols; /* number of "rows" */
for (ir = 0; ir < nrows; ir++) {
/*
* rather than just printing a whole row at once (which might exceed
* the capacity of MSDOS platforms, for example), we break each row
* into smaller chunks, if necessary.
*/
long corsav;
int left = (int)ncols;
boolean lastrow;
if (vrank > 0) {
corsav = cor[vrank-1];
if (fsp->brief_data_cmnts != false
&& vrank > 1
&& left > 0) { /* print brief comment with indices range */
Printf("// %s(",vp->name);
switch (fsp->data_lang) {
case LANG_C:
/* print brief comment with C variable indices */
for (id = 0; id < vrank-1; id++)
Printf("%lu,", (unsigned long)cor[id]);
if (vdims[vrank-1] == 1)
Printf("0");
else
Printf(" 0-%lu", (unsigned long)vdims[vrank-1]-1);
break;
case LANG_F:
/* print brief comment with Fortran variable indices */
if (vdims[vrank-1] == 1)
Printf("1");
else
Printf("1-%lu ", (unsigned long)vdims[vrank-1]);
for (id = vrank-2; id >=0 ; id--) {
Printf(",%lu", (unsigned long)(1 + cor[id]));
}
break;
}
Printf(")\n ");
set_indent(4);
}
}
lastrow = (boolean)(ir == nrows-1);
while (left > 0) {
long toget = left < gulp ? left : gulp;
if (vrank > 0)
edg[vrank-1] = toget;
switch(vp->type) {
case NC_CHAR:
NC_CHECK(
ncvarget(ncid, varid, cor, edg, (char *)vals) );
pr_tvals(vp, toget, fmt, left > toget, lastrow,
(char *) vals, fsp, cor);
break;
case NC_BYTE:
NC_CHECK(
ncvarget(ncid, varid, cor, edg, (signed char *)vals) );
pr_bvals(vp, toget, fmt, left > toget, lastrow,
(signed char *) vals, fsp, cor);
break;
case NC_SHORT:
NC_CHECK(
ncvarget(ncid, varid, cor, edg, (short *)vals) );
pr_svals(vp, toget, fmt, left > toget, lastrow,
(short *) vals, fsp, cor);
break;
case NC_INT:
NC_CHECK(
ncvarget(ncid, varid, cor, edg, (int *)vals) );
pr_ivals(vp, toget, fmt, left > toget, lastrow,
(int *) vals, fsp, cor);
break;
case NC_FLOAT:
NC_CHECK(
ncvarget(ncid, varid, cor, edg, (float *)vals) );
pr_fvals(vp, toget, fmt, left > toget, lastrow,
(float *) vals, fsp, cor);
break;
case NC_DOUBLE:
NC_CHECK(
ncvarget(ncid, varid, cor, edg, (double *)vals) );
pr_dvals(vp, toget, fmt, left > toget, lastrow,
(double *) vals, fsp, cor);
break;
default:
error("vardata: bad type");
}
left -= toget;
if (vrank > 0)
cor[vrank-1] += toget;
}
if (vrank > 0)
cor[vrank-1] = corsav;
if (ir < nrows-1)
if (!upcorner(vdims,vp->ndims,cor,add))
error("vardata: odometer overflowed!");
set_indent(2);
}
return 0;
}
int main(int argc, char ** argv)
{
int ncid, dimid, varid;
MPI_Init(&argc, &argv);
MPI_Datatype vtype, rtype, usertype;
MPI_Aint lb, extent;
int userbufsz, *userbuf, *cmpbuf, i, errs=0;
int count = 25;
double pi = 3.14159;
MPI_Offset start, acount;
ncmpi_create(MPI_COMM_WORLD, "vectors.nc", NC_CLOBBER, MPI_INFO_NULL,
&ncid);
ncmpi_def_dim(ncid, "50k", 1024*50, &dimid);
ncmpi_def_var(ncid, "vector", NC_DOUBLE, 1, &dimid, &varid);
ncmpi_enddef(ncid);
MPI_Type_vector(VECCOUNT, BLOCKLEN, STRIDE, MPI_INT, &vtype);
MPI_Type_create_resized(vtype, 0, STRIDE*VECCOUNT*sizeof(int), &rtype);
MPI_Type_contiguous(count, rtype, &usertype);
MPI_Type_commit(&usertype);
MPI_Type_free(&vtype);
MPI_Type_free(&rtype);
MPI_Type_get_extent(usertype, &lb, &extent);
userbufsz = extent;
userbuf = malloc(userbufsz);
cmpbuf = calloc(userbufsz, 1);
for (i=0; i< userbufsz/sizeof(int); i++) {
userbuf[i] = pi*i;
}
start = 10; acount = count*12;
ncmpi_begin_indep_data(ncid);
ncmpi_put_vara(ncid, varid, &start, &acount,
userbuf, 1, usertype);
ncmpi_close(ncid);
NC_CHECK(ncmpi_open(MPI_COMM_WORLD, "vectors.nc", NC_NOWRITE,
MPI_INFO_NULL, &ncid));
ncmpi_begin_indep_data(ncid);
NC_CHECK(ncmpi_inq_varid(ncid, "vector", &varid));
NC_CHECK(ncmpi_get_vara(ncid, varid, &start, &acount,
cmpbuf, 1, usertype));
ncmpi_close(ncid);
for (i=0; errs < 10 && i < acount; i++) {
/* vector of 4,3,5, so skip 4th and 5th items of every block */
if (i%STRIDE >= BLOCKLEN) continue;
if (userbuf[i] != cmpbuf[i]) {
errs++;
fprintf(stderr, "%d: expected 0x%x got 0x%x\n",
i, userbuf[i], cmpbuf[i]);
}
}
free(userbuf);
free(cmpbuf);
MPI_Type_free(&usertype);
MPI_Finalize();
return 0;
}
/* Output the data for a single variable, in NcML syntax.
* TODO: currently not called, need option for NcML with values ... */
int
vardatax(
const ncvar_t *vp, /* variable */
size_t vdims[], /* variable dimension sizes */
int ncid, /* netcdf id */
int varid /* variable id */
)
{
size_t *cor; /* corner coordinates */
size_t *edg; /* edges of hypercube */
size_t *add; /* "odometer" increment to next "row" */
void *vals;
int id;
int ir;
size_t nels;
size_t ncols;
size_t nrows;
int vrank = vp->ndims;
cor = (size_t *) emalloc((vrank + 1) * sizeof(size_t));
edg = (size_t *) emalloc((vrank + 1) * sizeof(size_t));
add = (size_t *) emalloc((vrank + 1) * sizeof(size_t));
nels = 1;
for (id = 0; id < vrank; id++) {
cor[id] = 0;
edg[id] = 1;
nels *= vdims[id]; /* total number of values for variable */
}
printf(" <values>\n ");
set_indent (7);
if (vrank < 1) {
ncols = 1;
} else {
ncols = vdims[vrank-1]; /* size of "row" along last dimension */
edg[vrank-1] = vdims[vrank-1];
for (id = 0; id < vrank; id++)
add[id] = 0;
if (vrank > 1)
add[vrank-2] = 1;
}
nrows = nels/ncols; /* number of "rows" */
vals = emalloc(ncols * vp->tinfo->size);
for (ir = 0; ir < nrows; ir++) {
size_t corsav;
bool_t lastrow;
if (vrank > 0) {
corsav = cor[vrank-1];
}
lastrow = (bool_t)(ir == nrows-1);
if (vrank > 0)
edg[vrank-1] = ncols;
NC_CHECK(nc_get_vara(ncid, varid, cor, edg, vals) );
/* Test if we should treat array of chars as a string */
if(vp->type == NC_CHAR &&
(vp->fmt == 0 || STREQ(vp->fmt,"%s") || STREQ(vp->fmt,""))) {
pr_tvalsx(vp, ncols, 0, lastrow, (char *) vals);
} else {
pr_any_valsx(vp, ncols, 0, lastrow, vals);
}
if (vrank > 0)
cor[vrank-1] += ncols;
if (vrank > 0)
cor[vrank-1] = corsav;
if (ir < nrows-1)
if (!upcorner(vdims,vp->ndims,cor,add))
error("vardata: odometer overflowed!");
set_indent(2);
}
printf(" </values>\n");
free(vals);
free(cor);
free(edg);
free(add);
return 0;
}
/* Output the data for a single variable, in CDL syntax. */
int
vardata(
const ncvar_t *vp, /* variable */
size_t vdims[], /* variable dimension sizes */
int ncid, /* netcdf id */
int varid /* variable id */
)
{
size_t *cor; /* corner coordinates */
size_t *edg; /* edges of hypercube */
size_t *add; /* "odometer" increment to next "row" */
void *vals;
int id;
int ir;
size_t nels;
size_t ncols;
size_t nrows;
int vrank = vp->ndims;
cor = (size_t *) emalloc((1 + vrank) * sizeof(size_t));
edg = (size_t *) emalloc((1 + vrank) * sizeof(size_t));
add = (size_t *) emalloc((1 + vrank) * sizeof(size_t));
nels = 1;
if(vrank == 0) { /*scalar*/
cor[0] = 0;
edg[0] = 1;
} else {
for (id = 0; id < vrank; id++) {
cor[id] = 0;
edg[id] = 1;
nels *= vdims[id]; /* total number of values for variable */
}
}
printf("\n");
indent_out();
printf(" ");
print_name(vp->name);
if (vrank <= 1) {
printf(" = ");
set_indent ((int)strlen(vp->name) + 4 + indent_get());
} else {
printf(" =\n ");
set_indent (2 + indent_get());
}
if (vrank == 0) {
ncols = 1;
} else {
ncols = vdims[vrank-1]; /* size of "row" along last dimension */
edg[vrank-1] = ncols;
for (id = 0; id < vrank; id++)
add[id] = 0;
if (vrank > 1)
add[vrank-2] = 1;
}
nrows = nels/ncols; /* number of "rows" */
vals = emalloc(ncols * vp->tinfo->size);
/* Test if we should treat array of chars as a string */
if(vp->type == NC_CHAR && (vp->fmt == 0 || STREQ(vp->fmt,"%s") || STREQ(vp->fmt,""))) {
for (ir = 0; ir < nrows; ir++) {
if (vrank > 0) {
if (formatting_specs.brief_data_cmnts != false && vrank > 1 && ncols > 0) {
annotate_brief(vp, cor, vdims);
}
}
NC_CHECK(nc_get_vara(ncid, varid, cor, edg, vals));
pr_tvals(vp, ncols, (ir == nrows-1), (char *) vals, cor);
if (ir < nrows-1)
if (!upcorner(vdims, vp->ndims, cor, add))
error("vardata: odometer overflowed!");
set_indent(2);
}
} else {
int level = 0;
int rank = vp->ndims;
int marks_pending = 0;
NC_CHECK(print_rows(level, ncid, varid, vp, ncols, rank, vdims, cor, edg,
vals, marks_pending));
}
free(vals);
free(cor);
free(edg);
free(add);
return 0;
}
/* Print data values for variable varid.
*
* Recursive to handle possibility of variables with multiple
* unlimited dimensions, for which the CDL syntax requires use of "{"
* and "}" in data section to disambiguate the size of nested records
* in a simple linear list of values.
*/
static int
print_rows(
int level, /* 0 at top-level, incremented for each recursive level */
int ncid, /* netcdf id */
int varid, /* variable id */
const ncvar_t *vp, /* variable */
size_t ncols, /* number of values in a row */
int rank, /* number of elements in following 3 arrays */
size_t vdims[], /* variable dimension sizes */
size_t cor[], /* corner coordinates */
size_t edg[], /* edges of hypercube */
void *vals, /* allocated buffer for ncols values in a row */
int marks_pending /* number of pending closing "}" record markers */
)
{
int d0 = 0;
size_t inc = 1;
int i;
bool_t mark_record = (level > 0 && is_unlim_dim(ncid, vp->dims[level]));
safebuf_t *sb = sbuf_new();
if (rank > 0)
d0 = vdims[level];
for(i = level + 1; i < rank; i++) {
inc *= vdims[i];
}
if(mark_record) { /* the whole point of this recursion is printing these "{}" */
lput("{");
marks_pending++; /* matching "}"s to emit after last "row" */
}
if(rank - level > 1) { /* this level is just d0 next levels */
size_t *local_cor = emalloc((rank + 1) * sizeof(size_t));
size_t *local_edg = emalloc((rank + 1) * sizeof(size_t));
for(i = 0; i < rank; i++) {
local_cor[i] = cor[i];
local_edg[i] = edg[i];
}
local_cor[level] = 0;
local_edg[level] = 1;
for(i = 0; i < d0 - 1; i++) {
print_rows(level + 1, ncid, varid, vp, ncols, rank, vdims,
local_cor, local_edg, vals, 0);
local_cor[level] += 1;
}
print_rows(level + 1, ncid, varid, vp, ncols, rank, vdims,
local_cor, local_edg, vals, marks_pending);
free(local_edg);
free(local_cor);
} else { /* bottom out of recursion */
char *valp = vals;
bool_t lastrow;
int j;
if(formatting_specs.brief_data_cmnts && rank > 1) {
annotate_brief(vp, cor, vdims);
}
NC_CHECK(nc_get_vara(ncid, varid, cor, edg, (void *)valp));
for(i=0; i < d0 - 1; i++) {
print_any_val(sb, vp, (void *)valp);
valp += vp->tinfo->size; /* next value according to type */
if (formatting_specs.full_data_cmnts) {
printf("%s, ", sb->buf);
annotate (vp, cor, i);
} else {
sbuf_cat(sb, ", ");
lput(sbuf_str(sb));
}
}
print_any_val(sb, vp, (void *)valp);
/* determine if this is the last row */
lastrow = true;
for(j = 0; j < rank - 1; j++) {
if (cor[j] != vdims[j] - 1) {
lastrow = false;
break;
}
}
if (formatting_specs.full_data_cmnts) {
for (j = 0; j < marks_pending; j++) {
sbuf_cat(sb, "}");
}
printf("%s", sbuf_str(sb));
lastdelim (0, lastrow);
annotate (vp, cor, i);
} else {
for (j = 0; j < marks_pending; j++) {
sbuf_cat(sb, "}");
}
lput(sbuf_str(sb));
lastdelim2 (0, lastrow);
}
}
sbuf_free(sb);
return NC_NOERR;
}
/* Output the data for a single variable, in NcML syntax.
* TODO: currently not called, need option for NcML with values ... */
int
vardatax(
const ncvar_t *vp, /* variable */
size_t vdims[], /* variable dimension sizes */
int ncid, /* netcdf id */
int varid, /* variable id */
const fspec_t *fsp /* formatting specs */
)
{
size_t cor[NC_MAX_DIMS]; /* corner coordinates */
size_t edg[NC_MAX_DIMS]; /* edges of hypercube */
size_t add[NC_MAX_DIMS]; /* "odometer" increment to next "row" */
size_t gulp;
void *vals;
int id;
int ir;
size_t nels;
size_t ncols;
size_t nrows;
int vrank = vp->ndims;
nels = 1;
for (id = 0; id < vrank; id++) {
cor[id] = 0;
edg[id] = 1;
nels *= vdims[id]; /* total number of values for variable */
}
printf(" <values>\n ");
set_indent (7);
if (vrank < 1) {
ncols = 1;
} else {
ncols = vdims[vrank-1]; /* size of "row" along last dimension */
edg[vrank-1] = vdims[vrank-1];
for (id = 0; id < vrank; id++)
add[id] = 0;
if (vrank > 1)
add[vrank-2] = 1;
}
nrows = nels/ncols; /* number of "rows" */
gulp = ncols < VALBUFSIZ ? VALBUFSIZ : ncols;
vals = emalloc(gulp * vp->tinfo->size);
for (ir = 0; ir < nrows; ir++) {
/*
* rather than just printing a whole row at once (which might
* exceed the capacity of some platforms), we break each row
* into smaller chunks, if necessary.
*/
size_t corsav;
int left = (int)ncols;
boolean lastrow;
if (vrank > 0) {
corsav = cor[vrank-1];
}
lastrow = (boolean)(ir == nrows-1);
while (left > 0) {
size_t toget = left < gulp ? left : gulp;
if (vrank > 0)
edg[vrank-1] = toget;
NC_CHECK(nc_get_vara(ncid, varid, cor, edg, vals) );
/* Test if we should treat array of chars as a string */
if(vp->type == NC_CHAR &&
(vp->fmt == 0 || STREQ(vp->fmt,"%s") || STREQ(vp->fmt,""))) {
pr_tvalsx(vp, toget, left > toget, lastrow, (char *) vals);
} else {
pr_any_valsx(vp, toget, left > toget, lastrow, vals);
}
left -= toget;
if (vrank > 0)
cor[vrank-1] += toget;
}
if (vrank > 0)
cor[vrank-1] = corsav;
if (ir < nrows-1)
if (!upcorner(vdims,vp->ndims,cor,add))
error("vardata: odometer overflowed!");
set_indent(2);
}
printf(" </values>\n");
free(vals);
return 0;
}
/* Output the data for a single variable, in CDL syntax. */
int
vardata(
const ncvar_t *vp, /* variable */
size_t vdims[], /* variable dimension sizes */
int ncid, /* netcdf id */
int varid, /* variable id */
const fspec_t *fsp /* formatting specs */
)
{
size_t cor[NC_MAX_DIMS]; /* corner coordinates */
size_t edg[NC_MAX_DIMS]; /* edges of hypercube */
size_t add[NC_MAX_DIMS]; /* "odometer" increment to next "row" */
size_t gulp;
void *vals;
int id;
int ir;
size_t nels;
size_t ncols;
size_t nrows;
int vrank = vp->ndims;
nels = 1;
for (id = 0; id < vrank; id++) {
cor[id] = 0;
edg[id] = 1;
nels *= vdims[id]; /* total number of values for variable */
}
printf("\n");
indent_out();
/* printf(" %s = ", vp->name); */
/* or */
/* printf(" %s =\n ", vp->name); */
printf(" ");
print_name(vp->name);
if (vrank <= 1) {
printf(" = ");
set_indent ((int)strlen(vp->name) + 4 + indent_get());
} else {
printf(" =\n ");
set_indent (2 + indent_get());
}
if (vrank < 1) {
ncols = 1;
} else {
ncols = vdims[vrank-1]; /* size of "row" along last dimension */
edg[vrank-1] = vdims[vrank-1];
for (id = 0; id < vrank; id++)
add[id] = 0;
if (vrank > 1)
add[vrank-2] = 1;
}
nrows = nels/ncols; /* number of "rows" */
gulp = ncols < VALBUFSIZ ? ncols : VALBUFSIZ;
vals = emalloc(gulp * vp->tinfo->size);
for (ir = 0; ir < nrows; ir++) {
/*
* rather than just printing a whole row at once (which might
* exceed the capacity of some platforms), we break each row
* into smaller chunks, if necessary.
*/
size_t corsav = 0;
int left = (int)ncols;
boolean lastrow;
if (vrank > 0) {
corsav = cor[vrank-1];
if (fsp->brief_data_cmnts != false
&& vrank > 1
&& left > 0) { /* print brief comment with indices range */
/* printf("// %s(",vp->name); */
printf("// ");
printf(vp->name);
printf("(");
switch (fsp->data_lang) {
case LANG_C:
/* print brief comment with C variable indices */
for (id = 0; id < vrank-1; id++)
printf("%lu,", (unsigned long)cor[id]);
if (vdims[vrank-1] == 1)
printf("0");
else
printf(" 0-%lu", (unsigned long)vdims[vrank-1]-1);
break;
case LANG_F:
/* print brief comment with Fortran variable indices */
if (vdims[vrank-1] == 1)
printf("1");
else
printf("1-%lu ", (unsigned long)vdims[vrank-1]);
for (id = vrank-2; id >=0 ; id--) {
printf(",%lu", (unsigned long)(1 + cor[id]));
}
break;
}
printf(")\n");
indent_out();
printf(" ");
set_indent(4 + indent_get());
}
}
lastrow = (boolean)(ir == nrows-1);
while (left > 0) {
size_t toget = left < gulp ? left : gulp;
if (vrank > 0)
edg[vrank-1] = toget;
NC_CHECK(nc_get_vara(ncid, varid, cor, edg, vals) );
/* Test if we should treat array of chars as a string */
if(vp->type == NC_CHAR &&
(vp->fmt == 0 || STREQ(vp->fmt,"%s") || STREQ(vp->fmt,""))) {
pr_tvals(vp, toget, left > toget, lastrow, (char *) vals,
fsp, cor);
} else {
pr_any_vals(vp, toget, left > toget, lastrow, vals, fsp, cor);
}
left -= toget;
if (vrank > 0)
cor[vrank-1] += toget;
}
if (vrank > 0)
cor[vrank-1] = corsav;
if (ir < nrows-1)
if (!upcorner(vdims,vp->ndims,cor,add))
error("vardata: odometer overflowed!");
set_indent(2);
}
free(vals);
return 0;
}
/* Output the data for a single variable, in CDL syntax. */
int
vardata(
const ncvar_t *vp, /* variable */
size_t vdims[], /* variable dimension sizes */
int ncid, /* netcdf id */
int varid /* variable id */
)
{
size_t *cor; /* corner coordinates */
size_t *edg; /* edges of hypercube */
size_t *add; /* "odometer" increment to next "row" */
void *vals;
int id;
size_t nels;
size_t ncols;
size_t nrows;
int vrank = vp->ndims;
int level = 0;
int marks_pending = 0;
cor = (size_t *) emalloc((1 + vrank) * sizeof(size_t));
edg = (size_t *) emalloc((1 + vrank) * sizeof(size_t));
add = (size_t *) emalloc((1 + vrank) * sizeof(size_t));
nels = 1;
if(vrank == 0) { /*scalar*/
cor[0] = 0;
edg[0] = 1;
} else {
for (id = 0; id < vrank; id++) {
cor[id] = 0;
edg[id] = 1;
nels *= vdims[id]; /* total number of values for variable */
}
}
printf("\n");
indent_out();
printf(" ");
print_name(vp->name);
if (vrank <= 1) {
printf(" = ");
set_indent ((int)strlen(vp->name) + 4 + indent_get());
} else {
printf(" =\n ");
set_indent (2 + indent_get());
}
if (vrank == 0) {
ncols = 1;
} else {
ncols = vdims[vrank-1]; /* size of "row" along last dimension */
edg[vrank-1] = ncols;
for (id = 0; id < vrank; id++)
add[id] = 0;
if (vrank > 1)
add[vrank-2] = 1;
}
nrows = nels/ncols; /* number of "rows" */
vals = emalloc(ncols * vp->tinfo->size);
NC_CHECK(print_rows(level, ncid, varid, vp, vdims, cor, edg, vals, marks_pending));
free(vals);
free(cor);
free(edg);
free(add);
return 0;
}