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Clarified documentation for nc_inq_grp_ncid(), differentiating it from nc_inq_ncid(). Fixed problem returning values from functions declared void in some libsrc4/ test programs. Added test for bug in ncdump for dimensions with same name in nested groups, and fix for bug. Fixed nccopy bug involving dimensions with smae name in nested groups. Added code for specifying chunking by dimension to nccopy (but not implemented yet).

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This commit is contained in:
Russ Rew 2010-12-30 18:17:04 +00:00
parent 99496dd311
commit b37a176fa0
10 changed files with 141 additions and 50 deletions
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9
libsrc4/tst_converts.c
View File

@ -22,8 +22,8 @@
#define VAR2_NAME "var2"
void check_file(int format, unsigned char *uchar_out);
void create_file(int format, unsigned char *uchar_out);
int check_file(int format, unsigned char *uchar_out);
int create_file(int format, unsigned char *uchar_out);
int
main(int argc, char **argv)
@ -45,7 +45,7 @@ main(int argc, char **argv)
}
/* Create a test file with one var of type NC_BYTE. */
void
int
create_file(int format, unsigned char *uchar_out)
{
int ncid, varid, cflags=0, dimids[1];
@ -68,9 +68,10 @@ create_file(int format, unsigned char *uchar_out)
if ((format != NC_FORMAT_NETCDF4) && retval) ERR;
if ((format == NC_FORMAT_NETCDF4) && (retval != NC_ERANGE)) ERR;
if (nc_close(ncid)) ERR;
return NC_NOERR;
}
void
int
check_file(int format, unsigned char *uchar_out)
{

5
libsrc4/tst_files.c
View File

@ -14,7 +14,7 @@
#ifdef IGNORE
extern NC_FILE_INFO_T *nc_file;
#endif
void test_redef(int format);
int test_redef(int format);
#define FILE_NAME "tst_files.nc"
#define ATT1_NAME "MoneyOwned"
@ -359,7 +359,7 @@ main(int argc, char **argv)
#define NEW_CACHE_NELEMS 2000
#define NEW_CACHE_PREEMPTION .75
void
int
test_redef(int format)
{
int ncid, varid, dimids[REDEF_NDIMS], dimids_in[REDEF_NDIMS];
@ -527,6 +527,7 @@ test_redef(int format)
if (uchar_in != uchar_out) ERR;
if (nc_close(ncid)) ERR;
return NC_NOERR;
}

6
libsrc4/tst_utf8.c
View File

@ -34,7 +34,7 @@ struct comp {
/* Given an ncid, check the file to make sure it has all the objects I
* expect. */
void
int
check_nc4_file(int ncid)
{
int varid, dimid, attnum, grpid, grpid2, grpid3, numgrps;
@ -117,11 +117,12 @@ check_nc4_file(int ncid)
name_in[0] = 0;
if (nc_inq_compound_fieldname(grpid3, comp_typeid, 0, name_in)) ERR;
if (strncmp(norm_utf8, name_in, sizeof(norm_utf8))) ERR;
return NC_NOERR;
}
/* Given an ncid, check the file to make sure it has all the objects I
* expect. */
void
int
check_classic_file(int ncid)
{
int varid, dimid, attnum;
@ -161,6 +162,7 @@ check_classic_file(int ncid)
if (att_type != NC_CHAR || att_len != sizeof(name_utf8)) ERR;
if (nc_get_att_text(ncid, varid, norm_utf8, strings_in)) ERR;
if (strncmp(name_utf8, strings_in, sizeof(name_utf8))) ERR;
return NC_NOERR;
}
int

11
man4/netcdf-c.texi
View File

@ -3372,7 +3372,8 @@ An error was reported by the HDF5 layer.
@section Find a Group by Name: nc_inq_grp_ncid
@findex nc_inq_grp_parent
Given a group name an an ncid, find the ncid of the group id.
Given a group location id and the name of an immediate subgroup, find
the location id of the named subgroup.
@heading Usage
@ -3383,13 +3384,13 @@ int nc_inq_grp_ncid(int ncid, const char *grp_name, int *grp_ncid);
@table @code
@item ncid
The group id to look in.
The location id of the group in which to look.
@item grp_name
The name of the group that should be found.
The name of a subgroup.
@item grp_ncid
A pointer to int which will get the group id, if it is found.
A pointer to int which will get the group id of the named subgroup, if it is found.
@end table
@ -3409,7 +3410,7 @@ Bad group id.
No name provided or name longer than NC_MAX_NAME.
@item NC_ENOGRP
Named group not found.
Named subgroup not found.
@item NC_ENOTNC4
Attempting a netCDF-4 operation on a netCDF-3 file. NetCDF-4

82
ncdump/nccopy.c
View File

@ -540,7 +540,7 @@ free_var_chunk_cache(int igrp, int varid)
/* Copy dimensions from group igrp to group ogrp */
static int
copy_dims(int igrp, int ogrp)
copy_dims(int igrp, int ogrp, int *dimmap)
{
int stat = NC_NOERR;
int ndims;
@ -581,36 +581,38 @@ copy_dims(int igrp, int ogrp)
size_t length;
int is_unlim;
int uld;
int dimid;
int idimid, odimid;
is_unlim = 0;
#ifdef USE_NETCDF4
dimid = dimids[dgrp];
idimid = dimids[dgrp];
for (uld = 0; uld < nunlims; uld++) {
if(dimid == unlimids[uld]) {
if(idimid == unlimids[uld]) {
is_unlim = 1;
break;
}
}
#else
dimid = dgrp;
if(unlimid != -1 && (dimid == unlimid)) {
idimid = dgrp;
if(unlimid != -1 && (idimid == unlimid)) {
is_unlim = 1;
}
#endif /* USE_NETCDF4 */
stat = nc_inq_dim(igrp, dimid, name, &length);
stat = nc_inq_dim(igrp, idimid, name, &length);
if (stat == NC_EDIMSIZE && sizeof(size_t) < 8) {
fprintf(stderr, "dimension \"%s\" requires 64-bit platform\n",
name);
}
CHECK(stat, nc_inq_dim);
if(is_unlim && !option_fix_unlimdims) {
stat = nc_def_dim(ogrp, name, NC_UNLIMITED, NULL);
stat = nc_def_dim(ogrp, name, NC_UNLIMITED, &odimid);
} else {
stat = nc_def_dim(ogrp, name, length, NULL);
stat = nc_def_dim(ogrp, name, length, &odimid);
}
CHECK(stat, nc_def_dim);
CHECK(stat, nc_def_dim);
/* Store (idimid, odimid) mapping for later use */
dimmap[idimid] = odimid;
}
#ifdef USE_NETCDF4
free(dimids);
@ -644,7 +646,7 @@ copy_atts(int igrp, int ivar, int ogrp, int ovar)
/* copy the schema for a single variable in group igrp to group ogrp */
static int
copy_var(int igrp, int varid, int ogrp)
copy_var(int igrp, int varid, int ogrp, int *dimmap)
{
int stat = NC_NOERR;
int ndims;
@ -678,11 +680,7 @@ copy_var(int igrp, int varid, int ogrp)
/* get the corresponding dimids in the output file */
odimids = (int *) emalloc((ndims + 1) * sizeof(int));
for(i = 0; i < ndims; i++) {
char dimname[NC_MAX_NAME];
stat = nc_inq_dimname(igrp, idimids[i], dimname);
CHECK(stat, nc_inq_dimname);
stat = nc_inq_dimid(ogrp, dimname, &odimids[i]);
CHECK(stat, nc_inq_dimid);
odimids[i] = dimmap[idimids[i]];
}
/* define the output variable */
@ -722,7 +720,7 @@ copy_var(int igrp, int varid, int ogrp)
/* copy the schema for all the variables in group igrp to group ogrp */
static int
copy_vars(int igrp, int ogrp)
copy_vars(int igrp, int ogrp, int *dimmap)
{
int stat = NC_NOERR;
int nvars;
@ -731,16 +729,17 @@ copy_vars(int igrp, int ogrp)
stat = nc_inq_nvars(igrp, &nvars);
CHECK(stat, nc_inq_nvars);
for (varid = 0; varid < nvars; varid++) {
stat = copy_var(igrp, varid, ogrp);
stat = copy_var(igrp, varid, ogrp, dimmap);
CHECK(stat, copy_var);
}
return stat;
}
/* Copy the schema in a group and all its subgroups, recursively, from
* group igrp in input to parent group ogrp in destination. */
* group igrp in input to parent group ogrp in destination. Use
* dimmap array to map input dimids to output dimids. */
static int
copy_schema(int igrp, int ogrp)
copy_schema(int igrp, int ogrp, int *dimmap)
{
int stat = NC_NOERR;
int ogid; /* like igrp but in output file */
@ -751,11 +750,11 @@ copy_schema(int igrp, int ogrp)
stat = get_grpid(igrp, ogrp, &ogid);
CHECK(stat, get_grpid);
stat = copy_dims(igrp, ogid);
stat = copy_dims(igrp, ogid, dimmap);
CHECK(stat, copy_dims);
stat = copy_atts(igrp, NC_GLOBAL, ogid, NC_GLOBAL);
CHECK(stat, copy_atts);
stat = copy_vars(igrp, ogid);
stat = copy_vars(igrp, ogid, dimmap);
CHECK(stat, copy_vars);
#ifdef USE_NETCDF4
{
@ -768,7 +767,7 @@ copy_schema(int igrp, int ogrp)
CHECK(stat, nc_inq_grps);
for(i = 0; i < numgrps; i++) {
stat = copy_schema(grpids[i], ogid);
stat = copy_schema(grpids[i], ogid, dimmap);
CHECK(stat, copy_schema);
}
free(grpids);
@ -947,6 +946,30 @@ copy_data(int igrp, int ogrp, size_t copybuf_size)
return stat;
}
/* Allocate an int array for mapping input dimids to output dimids, to
* be filled in and used later, with odimid = dimmap[idimid]. */
void
dimmap_init(int ncid, int** dimmap_p) {
int stat = NC_NOERR;
int numgrps;
int *grpids;
int igrp, idim;
int ndims=0;
/* get total number of groups and their ids, including all descendants */
stat = nc_inq_grps_full(ncid, &numgrps, NULL);
CHECK(stat, nc_inq_grps_full);
grpids = emalloc(numgrps * sizeof(int));
stat = nc_inq_grps_full(ncid, NULL, grpids);
CHECK(stat, nc_inq_grps_full);
for(igrp = 0; igrp < numgrps; igrp++) {
int ndims_local;
nc_inq_ndims(grpids[igrp], &ndims_local);
ndims += ndims_local;
}
*dimmap_p = (int *) emalloc(ndims * sizeof(int));
free(grpids);
}
/* copy infile to outfile using netCDF API, kind specifies which
* netCDF format for output: -1 -> same as input, 1 -> classic, 2 ->
@ -961,6 +984,7 @@ copy(char* infile, char* outfile, int kind, size_t copybuf_size)
int stat = NC_NOERR;
int igrp, ogrp;
int inkind, outkind;
int *dimmap; /* array for mapping dimids from input to output */
stat = nc_open(infile,NC_NOWRITE,&igrp);
CHECK(stat,nc_open);
@ -1020,8 +1044,10 @@ copy(char* infile, char* outfile, int kind, size_t copybuf_size)
}
#endif /* USE_NETCDF4 */
stat = copy_schema(igrp, ogrp);
dimmap_init(igrp, &dimmap); /* alloc and initialize dimid mapping from igrp to ogrp */
stat = copy_schema(igrp, ogrp, dimmap);
CHECK(stat,copy_schema);
free(dimmap);
stat = nc_enddef(ogrp);
CHECK(stat, nc_enddef);
stat = copy_data(igrp, ogrp, copybuf_size);
@ -1042,13 +1068,14 @@ usage(void)
1 classic, 2 64-bit offset, 3 netCDF-4, 4 netCDF-4 classic model\n\
[-d n] deflation compression level, default same as input (0=none 9=max)\n\
[-s] adds shuffle option to deflation compression\n\
[-c chunkspec] specifies chunking for dimensions like \"dim1/N1,dim2/N2,...\"\n\
[-u] converts unlimited dimensions to fixed-size dimensions in output copy\n\
[-m n] size in bytes of copy buffer, default is 5000000 bytes\n\
infile name of netCDF input file\n\
outfile name for netCDF output file\n"
(void) fprintf(stderr,
"%s [-k n] [-d n] [-s] [-u] [-m n] infile outfile\n%s",
"%s [-k n] [-d n] [-s] [-c chunkspec] [-u] [-m n] infile outfile\n%s",
progname,
USAGE);
}
@ -1144,6 +1171,11 @@ main(int argc, char**argv)
case 's': /* shuffling, may improve compression */
option_shuffle_vars = NC_SHUFFLE;
break;
case 'c': /* optional chunking spec for each dimension in list */
{
/* parse chunkspec string into (dimid, chunklen) structure */
}
break;
case 'u': /* convert unlimited dimensions to fixed size */
option_fix_unlimdims = 1;
break;

38
ncdump/ncdump.c
View File

@ -1500,10 +1500,44 @@ do_ncdump_rec(int ncid, const char *path, fspec_t* specp)
if (var.ndims > 0)
printf ("(");
for (id = 0; id < var.ndims; id++) {
/* printf ("%s%s", dims[var.dims[id]].name, id < var.ndims-1 ? ", " : ")"); */
/* This dim may be in a parent group, so let's look up the
* name. */
NC_CHECK( nc_inq_dimname(ncid, var.dims[id], dim_name) );
/* Subtlety: The following code block is needed because
* nc_inq_dimname() currently returns only a simple dimension
* name, without a prefix identifying the group it came from.
* That's OK unless the dimid identifies a dimension in an
* ancestor group that has the same simple name as a
* dimension in the current group (or some intermediate
* group), in which case the simple name is ambiguous. This
* code tests for that case and provides an absolute dimname
* only in the case where a simple name would be
* ambiguous. */
{
int dimid_test; /* to see if dimname is ambiguous */
int locid; /* group id where dimension is defined */
NC_CHECK( nc_inq_dimid(ncid, dim_name, &dimid_test) );
locid = ncid;
while(var.dims[id] != dimid_test) { /* not in locid, try ancestors */
int parent_id;
NC_CHECK( nc_inq_grp_parent(locid, &parent_id); );
locid = parent_id;
NC_CHECK( nc_inq_dimid(locid, dim_name, &dimid_test) );
}
/* dimid is in group locid, prefix dimname with group name if needed */
if(locid != ncid) {
size_t len;
char *locname; /* the group name */
NC_CHECK( nc_inq_grpname_full(locid, &len, NULL) );
locname = emalloc(len);
NC_CHECK( nc_inq_grpname_full(locid, &len, locname) );
print_name (locname);
if(strcmp("/", locname) != 0) { /* not the root group */
printf("/"); /* ensure a trailing slash */
}
free(locname);
}
}
print_name (dim_name);
printf ("%s", id < var.ndims-1 ? ", " : ")");
}
@ -1569,8 +1603,6 @@ do_ncdump_rec(int ncid, const char *path, fspec_t* specp)
no_data = 0;
for (id = 0; id < var.ndims; id++) {
size_t len;
/* bug, wrong length value returned if dimension
* inherited from ancestor group */
NC_CHECK( nc_inq_dimlen(ncid, var.dims[id], &len) );
if(len == 0) {
no_data = 1;

11
ncdump/ref_tst_group_data.cdl
View File

@ -44,12 +44,23 @@ group: g2 {
variables:
float var(dim) ;
var:units = "mm/msec" ;
float var2(/dim, /g2/dim, dim) ;
// group attributes:
:title = "in third group" ;
data:
var = 1, 2, 3 ;
var2 =
1, 2, 3,
4, 5, 6,
7, 8, 9,
10, 11, 12,
13, 14, 15,
16, 17, 18,
19, 20, 21,
22, 23, 24 ;
} // group g3
} // group g2
}

1
ncdump/ref_tst_group_data_v23.cdl
View File

@ -38,6 +38,7 @@ group: g2 {
variables:
float var(dim) ;
var:units = "mm/msec" ;
float var2(/dim, /g2/dim, dim) ;
// group attributes:
:title = "in third group" ;

26
ncdump/tst_group_data.c
View File

@ -19,6 +19,8 @@
#define DIM_LEN3 3
#define VAR_NAME "var"
#define VAR_RANK 1
#define VAR2_NAME "var2"
#define VAR2_RANK 3
#define ATT_NAME "units"
#define ATT_VAL "m/s"
#define ATT_VAL1 "km/hour"
@ -35,10 +37,13 @@
int
main(int argc, char **argv) {
int ncid, dimid, varid;
int var_dims[VAR_RANK];
int ncid, dimid, dimid1, dimid2, dimid3, varid, var2id;
int var_dims[VAR_RANK], var2_dims[VAR2_RANK];
int g1id, g2id, g3id;
float vals[] = {1.0, 2.0, 3.0, 4.0};
float vals2[] = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24};
int stat;
printf("\n*** Testing groups.\n");
printf("*** creating nested group file %s...", FILE_NAME);
@ -57,8 +62,8 @@ main(int argc, char **argv) {
/* put dim, var, atts with same names in a group */
if (nc_def_grp(ncid, G1_NAME, &g1id)) ERR;
if (nc_def_dim(g1id, DIM_NAME, DIM_LEN1, &dimid)) ERR;
var_dims[0] = dimid;
if (nc_def_dim(g1id, DIM_NAME, DIM_LEN1, &dimid1)) ERR;
var_dims[0] = dimid1;
if (nc_def_var(g1id, VAR_NAME, NC_FLOAT, VAR_RANK, var_dims, &varid)) ERR;
if (nc_put_att_text(g1id, varid, ATT_NAME, strlen(ATT_VAL1), ATT_VAL1)) ERR;
if (nc_put_att_text(g1id, NC_GLOBAL, GATT_NAME, strlen(GATT_VAL1),
@ -68,8 +73,8 @@ main(int argc, char **argv) {
/* put dim, var, atts with same names in a second group */
if (nc_def_grp(ncid, G2_NAME, &g2id)) ERR;
if (nc_def_dim(g2id, DIM_NAME, DIM_LEN2, &dimid)) ERR;
var_dims[0] = dimid;
if (nc_def_dim(g2id, DIM_NAME, DIM_LEN2, &dimid2)) ERR;
var_dims[0] = dimid2;
if (nc_def_var(g2id, VAR_NAME, NC_FLOAT, VAR_RANK, var_dims, &varid)) ERR;
if (nc_put_att_text(g2id, varid, ATT_NAME, strlen(ATT_VAL2), ATT_VAL2)) ERR;
if (nc_put_att_text(g2id, NC_GLOBAL, GATT_NAME, strlen(GATT_VAL2),
@ -79,14 +84,19 @@ main(int argc, char **argv) {
/* put dim, var, atts with same names in a subgroup of second group */
if (nc_def_grp(g2id, G3_NAME, &g3id)) ERR;
if (nc_def_dim(g3id, DIM_NAME, DIM_LEN3, &dimid)) ERR;
var_dims[0] = dimid;
if (nc_def_dim(g3id, DIM_NAME, DIM_LEN3, &dimid3)) ERR;
var_dims[0] = dimid3;
if (nc_def_var(g3id, VAR_NAME, NC_FLOAT, VAR_RANK, var_dims, &varid)) ERR;
if (nc_put_att_text(g3id, varid, ATT_NAME, strlen(ATT_VAL3), ATT_VAL3)) ERR;
if (nc_put_att_text(g3id, NC_GLOBAL, GATT_NAME, strlen(GATT_VAL3),
GATT_VAL3)) ERR;
var2_dims[0] = dimid;
var2_dims[1] = dimid2;
var2_dims[2] = dimid3;
if (nc_def_var(g3id, VAR2_NAME, NC_FLOAT, VAR2_RANK, var2_dims, &var2id)) ERR;
if (nc_enddef(g3id)) ERR;
if (nc_put_var_float(g3id, varid, vals)) ERR;
if (nc_put_var_float(g3id, var2id, vals2)) ERR;
if (nc_close(ncid)) ERR;

2
ncdump/tst_netcdf4.sh
View File

@ -40,7 +40,7 @@ echo "*** testing -v option with absolute name and groups..."
echo "*** comparing tst_group_data.cdl with ref_tst_group_data_v23.cdl..."
diff tst_group_data.cdl $srcdir/ref_tst_group_data_v23.cdl
echo "*** testing -v option with relative name and groups..."
./ncdump -v var tst_group_data.nc > tst_group_data.cdl
./ncdump -v var,var2 tst_group_data.nc > tst_group_data.cdl
echo "*** comparing tst_group_data.cdl with ref_tst_group_data.cdl..."
diff tst_group_data.cdl $srcdir/ref_tst_group_data.cdl
echo "*** dumping tst_enum_data.nc to tst_enum_data.cdl..."