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[netCDF #CNJ-934792]: Possible bug in netCDF C-API
- Subject: [netCDF #CNJ-934792]: Possible bug in netCDF C-API
- Date: Mon, 19 Oct 2009 13:23:35 -0600
Lynton,
> I have been experiencing problems with the attached netcDF4 dataset
> "efitOut.nc". The ncdump programme crashes part way through
> interpreting this file.
>
> I suspect that the problem is due to unlimited dimensions.
A fix is in the next snapshot release, or you can use the attached ncdump.c.
Thanks again for the bug report.
--Russ
Russ Rew UCAR Unidata Program
address@hidden http://www.unidata.ucar.edu
Ticket Details
===================
Ticket ID: CNJ-934792
Department: Support netCDF
Priority: Normal
Status: Closed
/*********************************************************************
* Copyright 2008, University Corporation for Atmospheric Research
* See netcdf/README file for copying and redistribution conditions.
* $Header: /upc/share/CVS/netcdf-3/ncdump/ncdump.c,v 1.146 2009/10/19
19:16:11 russ Exp $
*********************************************************************/
#include <config.h>
#include <stdio.h>
#ifndef _WIN32
#include <unistd.h>
#endif
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <assert.h>
#include <math.h>
#ifdef HAVE_LOCALE_H
#include <locale.h>
#endif /* HAVE_LOCALE_H */
#include <netcdf.h>
#include "nctime.h" /* new iso time and calendar stuff */
#include "ncdump.h"
#include "dumplib.h"
#include "vardata.h"
#include "indent.h"
#include "isnan.h"
#include "cdl.h"
#define int64_t long long
#define uint64_t unsigned long long
#define STREQ(a, b) (*(a) == *(b) && strcmp((a), (b)) == 0)
char *progname;
static void
usage(void)
{
#define USAGE "\
[-c] Coordinate variable data and header information\n\
[-h] Header information only, no data\n\
[-v var1[,...]] Data for variable(s) <var1>,... only\n\
[-b [c|f]] Brief annotations for C or Fortran indices in data\n\
[-f [c|f]] Full annotations for C or Fortran indices in data\n\
[-l len] Line length maximum in data section (default 80)\n\
[-n name] Name for netCDF (default derived from file name)\n\
[-p n[,n]] Display floating-point values with less precision\n\
[-k] Output kind of netCDF file\n\
[-x] Output XML (NcML) instead of CDL\n\
[-s] Output special (virtual) attributes\n\
[-t] Output time data as ISO date-time strings\n\
file Name of netCDF file\n"
(void) fprintf(stderr,
"%s [-c|-h] [-v ...] [[-b|-f] [c|f]] [-l len] [-n name] [-p
n[,n]] [-x] [-k] [-s] [-t] file\n%s",
progname,
USAGE);
(void) fprintf(stderr,
"netcdf library version %s\n",
nc_inq_libvers());
}
/*
* convert pathname of netcdf file into name for cdl unit, by taking
* last component of path and stripping off any extension.
* DMH: add code to handle OPeNDAP url.
* DMH: I think this also works for UTF8.
*/
static char *
name_path(const char *path)
{
const char *cp;
char *new;
char *sp;
#ifdef vms
#define FILE_DELIMITER ']'
#endif
#if defined(WIN32) || defined(msdos)
#define FILE_DELIMITER '\\'
#endif
#ifndef FILE_DELIMITER /* default to unix */
#define FILE_DELIMITER '/'
#endif
#ifdef USE_DAP
/* See if this is a url */
{
char* base;
extern int nc__testurl(const char*,char**);
if(nc__testurl(path,&base)) {
return base; /* Looks like a url */
}
/* else fall thru and treat like a file path */
}
#endif /*USE_DAP*/
cp = strrchr(path, FILE_DELIMITER);
if (cp == 0) /* no delimiter */
cp = path;
else /* skip delimeter */
cp++;
new = (char *) emalloc((unsigned) (strlen(cp)+1));
(void) strncpy(new, cp, strlen(cp) + 1); /* copy last component of path
*/
if ((sp = strrchr(new, '.')) != NULL)
*sp = '\0'; /* strip off any extension */
return new;
}
/* Return primitive type name */
static const char *
prim_type_name(nc_type type)
{
switch (type) {
case NC_BYTE:
return "byte";
case NC_CHAR:
return "char";
case NC_SHORT:
return "short";
case NC_INT:
return "int";
case NC_FLOAT:
return "float";
case NC_DOUBLE:
return "double";
#ifdef USE_NETCDF4
case NC_UBYTE:
return "ubyte";
case NC_USHORT:
return "ushort";
case NC_UINT:
return "uint";
case NC_INT64:
return "int64";
case NC_UINT64:
return "uint64";
case NC_STRING:
return "string";
case NC_VLEN:
return "vlen";
case NC_OPAQUE:
return "opaque";
case NC_COMPOUND:
return "compound";
#endif /* USE_NETCDF4 */
default:
error("prim_type_name: bad type %d", type);
return "bogus";
}
}
/*
* Remove trailing zeros (after decimal point) but not trailing decimal
* point from ss, a string representation of a floating-point number that
* might include an exponent part.
*/
static void
tztrim(char *ss)
{
char *cp, *ep;
cp = ss;
if (*cp == '-')
cp++;
while(isdigit((int)*cp) || *cp == '.')
cp++;
if (*--cp == '.')
return;
ep = cp+1;
while (*cp == '0')
cp--;
cp++;
if (cp == ep)
return;
while (*ep)
*cp++ = *ep++;
*cp = '\0';
return;
}
/* Return file type string */
static const char *
kind_string(int kind)
{
switch (kind) {
case NC_FORMAT_CLASSIC:
return "classic";
case NC_FORMAT_64BIT:
return "64-bit offset";
case NC_FORMAT_NETCDF4:
return "netCDF-4";
case NC_FORMAT_NETCDF4_CLASSIC:
return "netCDF-4 classic model";
default:
error("unrecognized file format: %d");
return "unrecognized";
}
}
/*
* Emit kind of netCDF file
*/
static void
do_nckind(int ncid, const char *path)
{
int nc_kind;
/*nc_set_log_level(3);*/
NC_CHECK( nc_inq_format(ncid, &nc_kind) );
printf ("%s\n", kind_string(nc_kind));
NC_CHECK( nc_close(ncid) );
}
/*
* Emit initial line of output for NcML
*/
static void
pr_initx(int ncid, const char *path)
{
printf("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<netcdf
xmlns=\"http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2\";
location=\"%s\">\n",
path);
}
/*
* Print attribute string, for text attributes.
*/
static void
pr_att_string(
int kind,
size_t len,
const char *string
)
{
int iel;
const char *cp;
const char *sp;
unsigned char uc;
cp = string;
printf ("\"");
/* adjust len so trailing nulls don't get printed */
sp = cp + len - 1;
while (len != 0 && *sp-- == '\0')
len--;
for (iel = 0; iel < len; iel++)
switch (uc = *cp++ & 0377) {
case '\b':
printf ("\\b");
break;
case '\f':
printf ("\\f");
break;
case '\n':
/* Only generate linebreaks after embedded newlines for
* classic, 64-bit offset, or classic model files. For
* netCDF-4 files, don't generate linebreaks, because that
* would create an extra string in a list of strings. */
if (kind != NC_FORMAT_NETCDF4) {
printf ("\\n\",\n\t\t\t\"");
} else {
printf("\\n");
}
break;
case '\r':
printf ("\\r");
break;
case '\t':
printf ("\\t");
break;
case '\v':
printf ("\\v");
break;
case '\\':
printf ("\\\\");
break;
case '\'':
printf ("\\'");
break;
case '\"':
printf ("\\\"");
break;
default:
if (iscntrl(uc))
printf ("\\%03o",uc);
else
printf ("%c",uc);
break;
}
printf ("\"");
}
/*
* Print NcML attribute string, for text attributes.
*/
static void
pr_attx_string(
size_t len,
const char *string
)
{
int iel;
const char *cp;
const char *sp;
unsigned char uc;
cp = string;
printf ("\"");
/* adjust len so trailing nulls don't get printed */
sp = cp + len - 1;
while (len != 0 && *sp-- == '\0')
len--;
for (iel = 0; iel < len; iel++)
switch (uc = *cp++ & 0377) {
case '\"':
printf (""");
break;
case '<':
printf ("<");
break;
case '>':
printf (">");
break;
case '&':
printf ("&");
break;
case '\n':
printf ("
");
break;
case '\r':
printf ("
");
break;
case '\t':
printf ("	");
break;
default:
if (iscntrl(uc))
printf ("&#%d;",uc);
else
printf ("%c",uc);
break;
}
printf ("\"");
}
/*
* Print list of attribute values, for attributes of primitive types.
* Attribute values must be printed with explicit type tags for
* netCDF-3 primitive types, because CDL doesn't require explicit
* syntax to declare such attribute types.
*/
static void
pr_att_valgs(
int kind,
nc_type type,
size_t len,
const void *vals
)
{
int iel;
signed char sc;
short ss;
int ii;
char gps[PRIM_LEN];
float ff;
double dd;
#ifdef USE_NETCDF4
unsigned char uc;
unsigned short us;
unsigned int ui;
int64_t i64;
uint64_t ui64;
char *stringp;
#endif /* USE_NETCDF4 */
char *delim = ", "; /* delimiter between output values */
if (len == 0)
return;
if (type == NC_CHAR) {
char *cp = (char *) vals;
pr_att_string(kind, len, cp);
return;
}
/* else */
for (iel = 0; iel < len; iel++) {
if (iel == len - 1)
delim = "";
switch (type) {
case NC_BYTE:
sc = ((signed char *) vals)[iel];
printf ("%db%s", sc, delim);
break;
case NC_SHORT:
ss = ((short *) vals)[iel];
printf ("%ds%s", ss, delim);
break;
case NC_INT:
ii = ((int *) vals)[iel];
printf ("%d%s", ii, delim);
break;
case NC_FLOAT:
ff = ((float *) vals)[iel];
if(isfinite(ff)) {
int res;
res = snprintf(gps, PRIM_LEN, float_att_fmt, ff);
assert(res < PRIM_LEN);
tztrim(gps); /* trim trailing 0's after '.' */
printf ("%s%s", gps, delim);
} else {
if(isnan(ff)) {
printf("NaNf%s", delim);
} else if(isinf(ff)) {
if(ff < 0.0f) {
printf("-");
}
printf("Infinityf%s", delim);
}
}
break;
case NC_DOUBLE:
dd = ((double *) vals)[iel];
if(isfinite(dd)) {
int res;
res = snprintf(gps, PRIM_LEN, double_att_fmt, dd);
assert(res < PRIM_LEN);
tztrim(gps);
printf ("%s%s", gps, delim);
} else {
if(isnan(dd)) {
printf("NaN%s", delim);
} else if(isinf(dd)) {
if(dd < 0.0) {
printf("-");
}
printf("Infinity%s", delim);
}
}
break;
#ifdef USE_NETCDF4
case NC_UBYTE:
uc = ((unsigned char *) vals)[iel];
printf ("%uUB%s", uc, delim);
break;
case NC_USHORT:
us = ((unsigned short *) vals)[iel];
printf ("%hdUS%s", us, delim);
break;
case NC_UINT:
ui = ((unsigned int *) vals)[iel];
printf ("%uU%s", ui, delim);
break;
case NC_INT64:
i64 = ((int64_t *) vals)[iel];
printf ("%lldL%s", i64, delim);
break;
case NC_UINT64:
ui64 = ((uint64_t *) vals)[iel];
printf ("%lluUL%s", ui64, delim);
break;
case NC_STRING:
stringp = ((char **) vals)[iel];
pr_att_string(kind, strlen(stringp), stringp);
printf("%s", delim);
break;
#endif /* USE_NETCDF4 */
default:
error("pr_att_vals: bad type");
}
}
}
/*
* Print list of numeric attribute values to string for use in NcML output.
* Unlike CDL, NcML makes type explicit, so don't need type suffixes.
*/
static void
pr_att_valsx(
nc_type type,
size_t len,
const double *vals,
char *attvals, /* returned string */
size_t attvalslen /* size of attvals buffer, assumed
large enough to hold all len
blank-separated values */
)
{
int iel;
float ff;
double dd;
int ii;
#ifdef USE_NETCDF4
unsigned int ui;
int64_t i64;
uint64_t ui64;
#endif /* USE_NETCDF4 */
attvals[0]='\0';
if (len == 0)
return;
for (iel = 0; iel < len; iel++) {
char gps[PRIM_LEN];
int res;
switch (type) {
case NC_BYTE:
case NC_SHORT:
case NC_INT:
ii = vals[iel];
res = snprintf(gps, PRIM_LEN, "%d", ii);
assert(res < PRIM_LEN);
(void) strlcat(attvals, gps, attvalslen);
(void) strlcat(attvals, iel < len-1 ? " " : "", attvalslen);
break;
#ifdef USE_NETCDF4
case NC_UBYTE:
case NC_USHORT:
case NC_UINT:
ui = vals[iel];
res = snprintf(gps, PRIM_LEN, "%u", ui);
assert(res < PRIM_LEN);
(void) strlcat(attvals, gps, attvalslen);
(void) strlcat(attvals, iel < len-1 ? " " : "", attvalslen);
break;
case NC_INT64:
i64 = vals[iel];
res = snprintf(gps, PRIM_LEN, "%lld", i64);
assert(res < PRIM_LEN);
(void) strlcat(attvals, gps, attvalslen);
(void) strlcat(attvals, iel < len-1 ? " " : "", attvalslen);
break;
case NC_UINT64:
ui64 = vals[iel];
res = snprintf(gps, PRIM_LEN, "%llu", ui64);
assert(res < PRIM_LEN);
(void) strlcat(attvals, gps, attvalslen);
(void) strlcat(attvals, iel < len-1 ? " " : "", attvalslen);
break;
#endif /* USE_NETCDF4 */
case NC_FLOAT:
ff = vals[iel];
res = snprintf(gps, PRIM_LEN, float_attx_fmt, ff);
assert(res < PRIM_LEN);
tztrim(gps); /* trim trailing 0's after '.' */
(void) strlcat(attvals, gps, attvalslen);
(void) strlcat(attvals, iel < len-1 ? " " : "", attvalslen);
break;
case NC_DOUBLE:
dd = vals[iel];
res = snprintf(gps, PRIM_LEN, double_att_fmt, dd);
assert(res < PRIM_LEN);
tztrim(gps); /* trim trailing 0's after '.' */
(void) strlcat(attvals, gps, attvalslen);
(void) strlcat(attvals, iel < len-1 ? " " : "", attvalslen);
break;
default:
error("pr_att_valsx: bad type");
}
}
}
/*
* Print a variable attribute
*/
static void
pr_att(
int ncid,
int kind,
int varid,
const char *varname,
int ia
)
{
ncatt_t att; /* attribute */
NC_CHECK( nc_inq_attname(ncid, varid, ia, att.name) );
NC_CHECK( nc_inq_att(ncid, varid, att.name, &att.type, &att.len) );
att.tinfo = get_typeinfo(att.type);
indent_out();
printf ("\t\t");
#ifdef USE_NETCDF4
if (is_user_defined_type(att.type) || att.type == NC_STRING)
#else
if (is_user_defined_type(att.type))
#endif
{
/* TODO: omit next two lines if att_type_name not needed
* because print_type_name() looks it up */
char att_type_name[NC_MAX_NAME + 1];
get_type_name(ncid, att.type, att_type_name);
/* printf ("\t\t%s ", att_type_name); */
/* ... but handle special characters in CDL names with escapes */
print_type_name(ncid, att.type);
printf(" ");
}
/* printf ("\t\t%s:%s = ", varname, att.name); */
print_name(varname);
printf(":");
print_name(att.name);
printf(" = ");
if (att.len == 0) { /* show 0-length attributes as empty strings */
att.type = NC_CHAR;
}
if (! is_user_defined_type(att.type) ) {
att.valgp = (void *) emalloc((att.len + 1) * att.tinfo->size );
NC_CHECK( nc_get_att(ncid, varid, att.name, att.valgp ) );
if(att.type == NC_CHAR) /* null-terminate retrieved text att value */
((char *)att.valgp)[att.len] = '\0';
pr_att_valgs(kind, att.type, att.len, att.valgp);
#ifdef USE_NETCDF4
/* If NC_STRING, need to free all the strings also */
if(att.type == NC_STRING) {
nc_free_string(att.len, att.valgp);
}
#endif /* USE_NETCDF4 */
free(att.valgp);
}
#ifdef USE_NETCDF4
else /* User-defined type. */
{
char type_name[NC_MAX_NAME + 1];
size_t type_size, nfields;
nc_type base_nc_type;
int class, i;
void *data;
NC_CHECK( nc_inq_user_type(ncid, att.type, type_name, &type_size,
&base_nc_type, &nfields, &class));
switch(class)
{
case NC_VLEN:
/* because size returned for vlen is base type size, but we
* need space to read array of vlen structs into ... */
data = emalloc(att.len * sizeof(nc_vlen_t));
break;
case NC_OPAQUE:
data = emalloc(att.len * type_size);
break;
case NC_ENUM:
/* a long long is ample for all base types */
data = emalloc(att.len * sizeof(int64_t));
break;
case NC_COMPOUND:
data = emalloc(att.len * type_size);
break;
default:
error("unrecognized class of user defined type: %d", class);
}
NC_CHECK( nc_get_att(ncid, varid, att.name, data));
switch(class) {
case NC_VLEN:
pr_any_att_vals(&att, data);
free(data);
break;
case NC_OPAQUE: {
char *sout = emalloc(2 * type_size + strlen("0X") + 1);
unsigned char *cp = data;
for (i = 0; i < att.len; i++) {
(void) ncopaque_val_as_hex(type_size, sout, cp);
printf("%s%s", sout, i < att.len-1 ? ", " : "");
cp += type_size;
}
free(sout);
}
break;
case NC_ENUM: {
int64_t value;
for (i = 0; i < att.len; i++) {
char enum_name[NC_MAX_NAME + 1];
switch(base_nc_type)
{
case NC_BYTE:
value = *((char *)data + i);
break;
case NC_UBYTE:
value = *((unsigned char *)data + i);
break;
case NC_SHORT:
value = *((short *)data + i);
break;
case NC_USHORT:
value = *((unsigned short *)data + i);
break;
case NC_INT:
value = *((int *)data + i);
break;
case NC_UINT:
value = *((unsigned int *)data + i);
break;
case NC_INT64:
value = *((int64_t *)data + i);
break;
case NC_UINT64:
value = *((uint64_t *)data + i);
break;
}
NC_CHECK( nc_inq_enum_ident(ncid, att.type, value,
enum_name));
/* printf("%s%s", enum_name, i < att.len-1 ? ", " : ""); */
print_name(enum_name);
printf("%s", i < att.len-1 ? ", " : "");
}
}
break;
case NC_COMPOUND:
pr_any_att_vals(&att, data);
free(data);
break;
default:
error("unrecognized class of user defined type: %d", class);
}
}
#endif /* USE_NETCDF4 */
printf (" ;\n");
}
/* Common code for printing attribute name */
static void
pr_att_name(
int ncid,
const char *varname,
const char *attname
)
{
indent_out();
printf ("\t\t");
print_name(varname);
printf(":");
print_name(attname);
}
/*
* Print special _Format global attribute, a virtual attribute not
* actually stored in the file.
*/
static void
pr_att_global_format(
int ncid,
int kind
)
{
pr_att_name(ncid, "", NC_ATT_FORMAT);
printf(" = ");
printf("\"%s\"", kind_string(kind));
printf (" ;\n");
}
#ifdef USE_NETCDF4
/*
* Print special reserved variable attributes, such as _Chunking,
* _DeflateLevel, ... These are virtual, not real, attributes
* generated from the result of inquire calls. They are of primitive
* type to fit into the classic model. Currently, these only exist
* for netCDF-4 data.
*/
static void
pr_att_specials(
int ncid,
int kind,
int varid,
const ncvar_t *varp
)
{
/* No special variable attributes for classic or 64-bit offset data */
if(kind == 1 || kind == 2)
return;
/* _Chunking */
if (varp->ndims > 0) { /* no chunking for scalar variables */
int contig = 0;
NC_CHECK( nc_inq_var_chunking(ncid, varid, &contig, NULL ) );
if(contig == 1) {
pr_att_name(ncid, varp->name, NC_ATT_STORAGE);
printf(" = \"contiguous\" ;\n");
} else {
size_t *chunkp;
int i;
pr_att_name(ncid, varp->name, NC_ATT_STORAGE);
printf(" = \"chunked\" ;\n");
chunkp = (size_t *) emalloc(sizeof(size_t) * varp->ndims + 1 );
NC_CHECK( nc_inq_var_chunking(ncid, varid, NULL, chunkp) );
/* print chunking, even if it is default */
pr_att_name(ncid, varp->name, NC_ATT_CHUNKING);
printf(" = ");
for(i = 0; i < varp->ndims; i++) {
printf("%lu%s", (unsigned long)chunkp[i], i+1 < varp->ndims ?
", " : " ;\n");
}
free(chunkp);
}
}
/*_Deflate, _Shuffle */
{
int shuffle=NC_NOSHUFFLE, deflate=0, deflate_level=0;
NC_CHECK( nc_inq_var_deflate(ncid, varid, &shuffle,
&deflate, &deflate_level) );
if(deflate != 0) {
pr_att_name(ncid, varp->name, NC_ATT_DEFLATE);
printf(" = %d ;\n", deflate_level);
}
if(shuffle != NC_NOSHUFFLE) {
pr_att_name(ncid, varp->name, NC_ATT_SHUFFLE);
printf(" = \"true\" ;\n");
}
}
/* _Checksum */
{
int fletcher32 = 0;
NC_CHECK( nc_inq_var_fletcher32(ncid, varid, &fletcher32) );
if(fletcher32 != 0) {
pr_att_name(ncid, varp->name, NC_ATT_CHECKSUM);
printf(" = \"true\" ;\n");
}
}
/* _Endianness */
if(varp->tinfo->size > 1) /* Endianness is meaningless for 1-byte types */
{
int endianness = 0;
NC_CHECK( nc_inq_var_endian(ncid, varid, &endianness) );
if(endianness != 0) {
pr_att_name(ncid, varp->name, NC_ATT_ENDIANNESS);
printf(" = ");
switch (endianness) {
case NC_ENDIAN_LITTLE:
printf("\"little\"");
break;
case NC_ENDIAN_BIG:
printf("\"big\"");
break;
case NC_ENDIAN_NATIVE:
printf("\"native\"");
break;
default:
error("pr_att_specials: bad endianness: %d", endianness);
break;
}
printf(" ;\n");
}
}
{
int no_fill = 0;
/* Don't get the fill_value, it's set explicitly with
* _FillValue attribute, because nc_def_var_fill() creates a
* _FillValue attribute, if needed, and it's value gets
* displayed elsewhere as a normal (not special virtual)
* attribute. */
NC_CHECK( nc_inq_var_fill(ncid, varid, &no_fill, NULL) );
if(no_fill != 0) {
pr_att_name(ncid, varp->name, NC_ATT_NOFILL);
printf(" = \"true\" ;\n");
}
}
/* TODO: handle _Nbit when inquire function is available */
/* TODO: handle _ScaleOffset when inquire is available */
/* TODO: handle _Szip when szip inquire function is available */
}
#endif /* USE_NETCDF4 */
/*
* Print a variable attribute for NcML
*/
static void
pr_attx(
int ncid,
int varid,
int ia
)
{
ncatt_t att; /* attribute */
char *attvals;
int attvalslen = 0;
NC_CHECK( nc_inq_attname(ncid, varid, ia, att.name) );
NC_CHECK( nc_inq_att(ncid, varid, att.name, &att.type, &att.len) );
att.tinfo = get_typeinfo(att.type);
/* Put attribute values into a single string, with blanks in between */
switch (att.type) {
case NC_CHAR:
attvals = (char *) emalloc(att.len + 1);
attvalslen = att.len;
attvals[att.len] = '\0';
NC_CHECK( nc_get_att_text(ncid, varid, att.name, attvals ) );
break;
#ifdef USE_NETCDF4
case NC_STRING:
/* TODO: this only prints first string value, need to handle
multiple strings? */
attvals = (char *) emalloc(att.len + 1);
attvals[att.len] = '\0';
NC_CHECK( nc_get_att_text(ncid, varid, att.name, attvals ) );
break;
case NC_VLEN:
/* TODO */
break;
case NC_OPAQUE:
/* TODO */
break;
case NC_COMPOUND:
/* TODO */
break;
#endif /* USE_NETCDF4 */
default:
att.vals = (double *) emalloc((att.len + 1) * sizeof(double));
NC_CHECK( nc_get_att_double(ncid, varid, att.name, att.vals ) );
attvalslen = 20*att.len; /* max 20 chars for each value and blank
separator */
attvals = (char *) emalloc(attvalslen + 1);
pr_att_valsx(att.type, att.len, att.vals, attvals, attvalslen);
free(att.vals);
break;
}
/* Don't output type for string attributes, since that's default type */
if(att.type == NC_CHAR
#ifdef USE_NETCDF4
|| att.type == NC_CHAR
#endif /* USE_NETCDF4 */
) {
/* TODO: XML-ish escapes for special chars in names */
printf ("%s <attribute name=\"%s\" value=",
varid != NC_GLOBAL ? " " : "",
att.name);
/* print attvals as a string with XML escapes */
pr_attx_string(attvalslen, attvals);
} else { /* non-string attribute */
char att_type_name[NC_MAX_NAME + 1];
get_type_name(ncid, att.type, att_type_name);
/* TODO: print full type name with group prefix, when needed */
printf ("%s <attribute name=\"%s\" type=\"%s\" value=\"",
varid != NC_GLOBAL ? " " : "",
att.name,
att_type_name);
printf("%s\"",attvals);
}
printf (" />\n");
free (attvals);
}
/* Print optional NcML attribute for a variable's shape */
static void
pr_shape(ncvar_t* varp, ncdim_t *dims)
{
char *shape;
int shapelen = 0;
int id;
if (varp->ndims == 0)
return;
for (id = 0; id < varp->ndims; id++) {
shapelen += strlen(dims[varp->dims[id]].name) + 1;
}
shape = (char *) emalloc(shapelen);
shape[0] = '\0';
for (id = 0; id < varp->ndims; id++) {
/* TODO: XML-ish escapes for special chars in dim names */
strlcat(shape, dims[varp->dims[id]].name, shapelen);
strlcat(shape, id < varp->ndims-1 ? " " : "", shapelen);
}
printf (" shape=\"%s\"", shape);
free(shape);
}
#ifdef USE_NETCDF4
/* Print an enum type declaration */
static void
print_enum_type(int ncid, nc_type typeid) {
char type_name[NC_MAX_NAME + 1];
size_t type_size;
nc_type base_nc_type;
size_t type_nfields;
int type_class;
char base_type_name[NC_MAX_NAME + 1];
int f;
int64_t memval;
char memname[NC_MAX_NAME + 1];
/* extra space for escapes, and punctuation */
#define SAFE_BUF_LEN 4*NC_MAX_NAME+30
char safe_buf[SAFE_BUF_LEN];
char *delim;
int64_t data; /* space for data of any primitive type */
char *esc_btn;
char *esc_tn;
char *esc_mn;
int res;
NC_CHECK( nc_inq_user_type(ncid, typeid, type_name, &type_size,
&base_nc_type,
&type_nfields, &type_class) );
get_type_name(ncid, base_nc_type, base_type_name);
indent_out();
esc_btn = escaped_name(base_type_name);
esc_tn = escaped_name(type_name);
res = snprintf(safe_buf, SAFE_BUF_LEN,"%s enum %s {", esc_btn, esc_tn);
assert(res < SAFE_BUF_LEN);
free(esc_btn);
free(esc_tn);
lput(safe_buf);
delim = ", ";
for (f = 0; f < type_nfields; f++) {
if (f == type_nfields - 1)
delim = "} ;\n";
NC_CHECK( nc_inq_enum_member(ncid, typeid, f, memname, &data) );
switch (base_nc_type) {
case NC_BYTE:
memval = *(char *)&data;
break;
case NC_SHORT:
memval = *(short *)&data;
break;
case NC_INT:
memval = *(int *)&data;
break;
#ifdef USE_NETCDF4
case NC_UBYTE:
memval = *(unsigned char *)&data;
break;
case NC_USHORT:
memval = *(unsigned short *)&data;
break;
case NC_UINT:
memval = *(unsigned int *)&data;
break;
case NC_INT64:
memval = *(int64_t *)&data;
break;
case NC_UINT64:
memval = *(uint64_t *)&data;
break;
#endif /* USE_NETCDF4 */
default:
error("Bad base type for enum!");
break;
}
esc_mn = escaped_name(memname);
res = snprintf(safe_buf, SAFE_BUF_LEN, "%s = %lld%s", memname,
memval, delim);
assert(res < SAFE_BUF_LEN);
free(esc_mn);
lput(safe_buf);
}
}
/* Print a user-defined type declaration */
static void
print_ud_type(int ncid, nc_type typeid) {
char type_name[NC_MAX_NAME + 1];
char base_type_name[NC_MAX_NAME + 1];
size_t type_nfields, type_size;
nc_type base_nc_type;
int f, type_class;
NC_CHECK( nc_inq_user_type(ncid, typeid, type_name, &type_size,
&base_nc_type,
&type_nfields, &type_class) );
switch(type_class) {
case NC_VLEN:
/* TODO: don't bother getting base_type_name if
* print_type_name looks it up anyway */
get_type_name(ncid, base_nc_type, base_type_name);
indent_out();
/* printf("%s(*) %s ;\n", base_type_name, type_name); */
print_type_name(ncid, base_nc_type);
printf("(*) ");
print_type_name(ncid, typeid);
printf(" ;\n");
break;
case NC_OPAQUE:
indent_out();
/* printf("opaque(%d) %s ;\n", (int)type_size, type_name); */
printf("opaque(%d) ", (int)type_size);
print_type_name(ncid, typeid);
printf(" ;\n");
break;
case NC_ENUM:
print_enum_type(ncid, typeid);
break;
case NC_COMPOUND:
{
char field_name[NC_MAX_NAME + 1];
char field_type_name[NC_MAX_NAME + 1];
size_t field_offset;
nc_type field_type;
int field_ndims, field_dim_sizes[NC_MAX_DIMS];
int d;
indent_out();
/* printf("compound %s {\n", type_name); */
printf("compound ");
print_type_name(ncid, typeid);
printf(" {\n");
for (f = 0; f < type_nfields; f++)
{
NC_CHECK( nc_inq_compound_field(ncid, typeid, f,
field_name,
&field_offset, &field_type,
&field_ndims,
field_dim_sizes) );
/* TODO: don't bother if field_type_name not needed here */
get_type_name(ncid, field_type, field_type_name);
indent_out();
/* printf(" %s %s", field_type_name, field_name); */
printf(" ");
print_type_name(ncid, field_type);
printf(" ");
print_name(field_name);
if (field_ndims > 0) {
printf("(");
for (d = 0; d < field_ndims-1; d++)
printf("%d, ", field_dim_sizes[d]);
printf("%d)", field_dim_sizes[field_ndims-1]);
}
printf(" ;\n");
}
indent_out();
/* printf("}; // %s\n", type_name); */
printf("}; // ");
print_type_name(ncid, typeid);
printf("\n");
}
break;
default:
error("Unknown class of user-defined type!");
}
}
#endif /* USE_NETCDF4 */
static void
get_fill_info(int ncid, int varid, ncvar_t *vp) {
ncatt_t att; /* attribute */
int nc_status; /* return from netcdf calls */
void *fillvalp;
vp->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);
fillvalp = emalloc(vp->tinfo->size);
if(nc_status == NC_NOERR &&
att.type == vp->type && att.len == 1) {
NC_CHECK(nc_get_att(ncid, varid, _FillValue, fillvalp));
} else {
switch (vp->type) {
case NC_BYTE:
/* don't do default fill-values for bytes, too risky */
vp->has_fillval = 0;
fillvalp = 0;
break;
case NC_CHAR:
*(char *)fillvalp = NC_FILL_CHAR;
break;
case NC_SHORT:
*(short *)fillvalp = NC_FILL_SHORT;
break;
case NC_INT:
*(int *)fillvalp = NC_FILL_INT;
break;
case NC_FLOAT:
*(float *)fillvalp = NC_FILL_FLOAT;
break;
case NC_DOUBLE:
*(double *)fillvalp = NC_FILL_DOUBLE;
break;
#ifdef USE_NETCDF4
case NC_UBYTE:
/* don't do default fill-values for bytes, too risky */
vp->has_fillval = 0;
fillvalp = 0;
break;
case NC_USHORT:
*(unsigned short *)fillvalp = NC_FILL_USHORT;
break;
case NC_UINT:
*(unsigned int *)fillvalp = NC_FILL_UINT;
break;
case NC_INT64:
*(int64_t *)fillvalp = NC_FILL_INT64;
break;
case NC_UINT64:
*(uint64_t *)fillvalp = NC_FILL_UINT64;
break;
case NC_STRING:
*((char **)fillvalp) = NC_FILL_STRING;
break;
#endif /* USE_NETCDF4 */
default: /* no default fill values for NC_NAT
or user-defined types */
vp->has_fillval = 0;
fillvalp = 0;
break;
}
}
vp->fillvalp = fillvalp;
}
/* Check for optional "calendar" attribute and return specified
* calendar type, if present. */
cdCalenType
calendar_type(int ncid, int varid) {
int ctype;
int stat;
ncatt_t catt;
static struct {
char* attname;
int type;
} calmap[] = {
{"gregorian", cdMixed},
{"standard", cdMixed}, /* synonym */
{"proleptic_gregorian", cdStandard},
{"noleap", cdNoLeap},
{"no_leap", cdNoLeap},
{"365_day", cdNoLeap}, /* synonym */
{"allleap", cd366},
{"all_leap", cd366}, /* synonym */
{"366_day", cd366}, /* synonym */
{"360_day", cd360},
{"julian", cdJulian},
{"none", cdClim} /* TODO: test this */
};
#define CF_CAL_ATT_NAME "calendar"
int ncals = (sizeof calmap)/(sizeof calmap[0]);
ctype = cdMixed; /* default mixed Gregorian/Julian ala udunits */
stat = nc_inq_att(ncid, varid, CF_CAL_ATT_NAME, &catt.type, &catt.len);
if(stat == NC_NOERR && catt.type == NC_CHAR && catt.len > 0) {
char *calstr = (char *)emalloc(catt.len + 1);
int itype;
NC_CHECK(nc_get_att(ncid, varid, CF_CAL_ATT_NAME, calstr));
calstr[catt.len] = '\0';
for(itype = 0; itype < ncals; itype++) {
if(strncmp(calstr, calmap[itype].attname, catt.len) == 0) {
ctype = calmap[itype].type;
break;
}
}
free(calstr);
}
return ctype;
}
static void
get_timeinfo(int ncid, int varid, ncvar_t *vp) {
ncatt_t uatt; /* units attribute */
int nc_status; /* return from netcdf calls */
char *units;
vp->has_timeval = false; /* by default, turn on if criteria met */
vp->timeinfo = 0;
/* time variables must have appropriate units attribute */
nc_status = nc_inq_att(ncid, varid, "units", &uatt.type, &uatt.len);
if(nc_status == NC_NOERR && uatt.type == NC_CHAR) { /* TODO: NC_STRING? */
units = emalloc(uatt.len + 1);
NC_CHECK(nc_get_att(ncid, varid, "units", units));
units[uatt.len] = '\0';
/* check for calendar attribute (not required even for time vars) */
vp->timeinfo = (timeinfo_t *)emalloc(sizeof(timeinfo_t));
vp->timeinfo->calendar = calendar_type(ncid, varid);
/* Parse relative units, returning the unit and base component time. */
if(cdParseRelunits(vp->timeinfo->calendar, units,
&vp->timeinfo->unit, &vp->timeinfo->origin) != 0) {
/* error parsing units so just treat as not a time variable */
free(vp->timeinfo);
free(units);
return;
}
/* Currently this gets reparsed for every value, need function
* like cdRel2Comp that resuses parsed units? */
vp->timeinfo->units = strdup(units);
vp->has_timeval = true;
free(units);
}
return;
}
/* Recursively dump the contents of a group. (Recall that only
* netcdf-4 format files can have groups. On all other formats, there
* is just a root group, so recursion will not take place.)
*
* ncid: id of open file (first call) or group (subsequent recursive calls)
* path: file path name (first call) or NULL if called for a group
* specp: formatting spec
*/
static void
do_ncdump_rec(int ncid, const char *path, fspec_t* specp)
{
int ndims; /* number of dimensions */
int nvars; /* number of variables */
int ngatts; /* number of global attributes */
int xdimid; /* id of unlimited dimension */
int varid; /* variable id */
ncdim_t *dims; /* dimensions */
size_t *vdims=0; /* dimension sizes for a single variable */
ncvar_t var; /* variable */
int id; /* dimension number per variable */
int ia; /* attribute number */
int iv; /* variable number */
vnode* vlist = 0; /* list for vars specified with -v option */
char type_name[NC_MAX_NAME + 1];
int kind; /* strings output differently for nc4 files */
char dim_name[NC_MAX_NAME + 1];
#ifdef USE_NETCDF4
int *dimids_grp; /* dimids of the dims in this group. */
int *unlimids; /* dimids of unlimited dimensions in this group
*/
int d_grp, ndims_grp;
int ntypes, *typeids;
int nunlim;
#else
int dimid; /* dimension id */
#endif /* USE_NETCDF4 */
/*
* If any vars were specified with -v option, get list of
* associated variable ids relative to this group. Assume vars
* specified with syntax like "grp1/grp2/varname" or
* "/grp1/grp2/varname" if they are in groups.
*/
if (specp->nlvars > 0) {
vlist = newvlist(); /* list for vars specified with -v option */
for (iv=0; iv < specp->nlvars; iv++) {
if(nc_inq_gvarid(ncid, specp->lvars[iv], &varid) == NC_NOERR)
varadd(vlist, varid);
}
}
#ifdef USE_NETCDF4
/* Are there any user defined types in this group? */
NC_CHECK( nc_inq_typeids(ncid, &ntypes, NULL) );
if (ntypes)
{
int t;
typeids = emalloc(ntypes * sizeof(int));
NC_CHECK( nc_inq_typeids(ncid, &ntypes, typeids) );
indent_out();
printf("types:\n");
indent_more();
for (t = 0; t < ntypes; t++)
{
print_ud_type(ncid, typeids[t]); /* print declaration of user-defined
type */
}
indent_less();
free(typeids);
}
#endif /* USE_NETCDF4 */
/*
* 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 */
dims = (ncdim_t *) emalloc((ndims + 1) * sizeof(ncdim_t));
if (ndims > 0) {
indent_out();
printf ("dimensions:\n");
}
#ifdef USE_NETCDF4
/* In netCDF-4 files, dimids will not be sequential because they
* may be defined in various groups, and we are only looking at one
* group at a time. */
/* Find the number of dimids defined in this group. */
NC_CHECK( nc_inq_ndims(ncid, &ndims_grp) );
dimids_grp = (int *)emalloc((ndims_grp + 1) * sizeof(int));
/* Find the dimension ids in this group. */
NC_CHECK( nc_inq_dimids(ncid, 0, dimids_grp, 0) );
/* Find the number of unlimited dimensions and get their IDs */
NC_CHECK( nc_inq_unlimdims(ncid, &nunlim, NULL) );
unlimids = (int *)emalloc((nunlim + 1) * sizeof(int));
NC_CHECK( nc_inq_unlimdims(ncid, &nunlim, unlimids) );
/* For each dimension defined in this group, get and print out info. */
for (d_grp = 0; d_grp < ndims_grp; d_grp++)
{
int dimid = dimids_grp[d_grp];
int is_unlimited = 0;
int uld;
int stat;
for (uld = 0; uld < nunlim; uld++) {
if(dimid == unlimids[uld]) {
is_unlimited = 1;
break;
}
}
stat = nc_inq_dim(ncid, dimid, dims[d_grp].name, &dims[d_grp].size);
/* TODO: settle issue whether NC_EBADDIM or NC_EDIMSIZE used for
very-large dimensions */
if ((stat == NC_EBADDIM || stat == NC_EDIMSIZE) && SIZEOF_SIZE_T < 8) {
error("dimension \"%s\" too large for 32-bit platform, try 64-bit
version", dims[d_grp].name);
} else {
NC_CHECK (stat);
}
indent_out();
printf ("\t");
print_name(dims[d_grp].name);
printf (" = ");
if(SIZEOF_SIZE_T >= 8) {
if (is_unlimited) {
printf ("UNLIMITED ; // (%llu currently)\n",
dims[d_grp].size);
} else {
printf ("%llu ;\n", dims[d_grp].size);
}
} else { /* 32-bit platform */
if (is_unlimited) {
printf ("UNLIMITED ; // (%u currently)\n",
(unsigned int)dims[d_grp].size);
} else {
printf ("%u ;\n", (unsigned int)dims[d_grp].size);
}
}
}
if(unlimids)
free(unlimids);
if(dimids_grp)
free(dimids_grp);
#else /* not using netCDF-4 */
for (dimid = 0; dimid < ndims; dimid++) {
NC_CHECK( nc_inq_dim(ncid, dimid, dims[dimid].name, &dims[dimid].size) );
indent_out();
printf ("\t");
print_name(dims[dimid].name);
printf (" = ");
if (dimid == xdimid) {
printf ("UNLIMITED ; // (%u currently)\n",
(unsigned int)dims[dimid].size);
} else {
printf ("%u ;\n", (unsigned int)dims[dimid].size);
}
}
#endif /* USE_NETCDF4 */
if (nvars > 0) {
indent_out();
printf ("variables:\n");
}
/* Because netCDF-4 can have a string attribute with multiple
* string values, we can't output strings with embedded newlines
* as what look like multiple strings, as we do for classic and
* 64-bit offset files. So we need to know the output file type
* to know how to print strings with embedded newlines. */
NC_CHECK( nc_inq_format(ncid, &kind) );
/* For each var, get and print out info. */
for (varid = 0; varid < nvars; varid++) {
NC_CHECK( nc_inq_varndims(ncid, varid, &var.ndims) );
var.dims = (int *) emalloc((var.ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_var(ncid, varid, var.name, &var.type, 0,
var.dims, &var.natts) );
/* TODO: don't bother if type name not needed here */
get_type_name(ncid, var.type, type_name);
var.tinfo = get_typeinfo(var.type);
indent_out();
/* printf ("\t%s %s", type_name, var.name); */
printf ("\t");
/* TODO: if duplicate type name and not just inherited, print
* full type name. */
print_type_name (ncid, var.type);
printf (" ");
print_name (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 ? ", " :
")"); */
/* 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) );
print_name (dim_name);
printf ("%s", id < var.ndims-1 ? ", " : ")");
}
printf (" ;\n");
/* print variable attributes */
for (ia = 0; ia < var.natts; ia++) { /* print ia-th attribute */
pr_att(ncid, kind, varid, var.name, ia);
}
#ifdef USE_NETCDF4
/* Print special (virtual) attributes, if option specified */
if (specp->special_atts) {
pr_att_specials(ncid, kind, varid, &var);
}
free(var.dims);
#endif /* USE_NETCDF4 */
}
/* get global attributes */
if (ngatts > 0 || specp->special_atts) {
printf ("\n");
indent_out();
if (path != NULL) /* top-level, root group */
printf("// global attributes:\n");
else
printf("// group attributes:\n");
}
for (ia = 0; ia < ngatts; ia++) { /* print ia-th global attribute */
pr_att(ncid, kind, NC_GLOBAL, "", ia);
}
if (path != NULL && specp->special_atts) { /* output special attribute
* for format variant */
pr_att_global_format(ncid, kind);
}
/* output variable data */
if (! specp->header_only) {
if (nvars > 0) {
indent_out();
printf ("data:\n");
}
for (varid = 0; varid < nvars; varid++) {
int no_records;
/* if var list specified, test for membership */
if (specp->nlvars > 0 && ! varmember(vlist, varid))
continue;
NC_CHECK( nc_inq_varndims(ncid, varid, &var.ndims) );
var.dims = (int *) emalloc((var.ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_var(ncid, varid, var.name, &var.type, 0,
var.dims, &var.natts) );
var.tinfo = get_typeinfo(var.type);
/* If coords-only option specified, don't get data for
* non-coordinate vars */
if (specp->coord_vals && !iscoordvar(ncid,varid)) {
continue;
}
/* Collect variable's dim sizes */
if (vdims) {
free(vdims);
vdims = 0;
}
vdims = (size_t *) emalloc((var.ndims + 1) * SIZEOF_SIZE_T);
no_records = 0;
for (id = 0; id < var.ndims; id++) {
size_t len;
NC_CHECK( nc_inq_dimlen(ncid, var.dims[id], &len) );
if(len == 0) {
no_records = 1;
}
vdims[id] = len;
}
/* Don't get data for record variables if no records have
* been written yet */
if (no_records) {
free(vdims);
vdims = 0;
continue;
}
get_fill_info(ncid, varid, &var); /* sets has_fillval, fillvalp mmbrs
*/
get_timeinfo(ncid, varid, &var); /* sets has_timeval, timeinfo mmbrs */
/* printf format used to print each value */
var.fmt = get_fmt(ncid, varid, var.type);
var.locid = ncid;
set_tostring_func(&var, specp);
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;
}
}
if (vdims) {
free(vdims);
vdims = 0;
}
}
#ifdef USE_NETCDF4
/* For netCDF-4 compiles, check to see if the file has any
* groups. If it does, this function is called recursively on each
* of them. */
{
int g, numgrps, *ncids;
char group_name[NC_MAX_NAME + 1];
/* See how many groups there are. */
NC_CHECK( nc_status = 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++)
{
NC_CHECK( nc_inq_grpname(ncids[g], group_name) );
printf ("\n");
indent_out();
/* printf ("group: %s {\n", group_name); */
printf ("group: ");
print_name (group_name);
printf (" {\n");
indent_more();
do_ncdump_rec(ncids[g], NULL, specp);
indent_out();
/* printf ("} // group %s\n", group_name); */
printf ("} // group ");
print_name (group_name);
printf ("\n");
indent_less();
}
free(ncids);
}
#endif /* USE_NETCDF4 */
if (vlist)
free(vlist);
if (dims)
free(dims);
}
static void
do_ncdump(int ncid, const char *path, fspec_t* specp)
{
char* esc_specname;
/* output initial line */
indent_init();
indent_out();
esc_specname=escaped_name(specp->name);
printf ("netcdf %s {\n", esc_specname);
free(esc_specname);
do_ncdump_rec(ncid, path, specp);
indent_out();
printf ("}\n");
NC_CHECK( nc_close(ncid) );
}
static void
do_ncdumpx(int ncid, const char *path, fspec_t* 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 */
ncdim_t *dims; /* dimensions */
ncvar_t var; /* variable */
int ia; /* attribute number */
int iv; /* variable number */
vnode* vlist = 0; /* list for vars specified with -v option */
/*
* 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);
}
}
/* output initial line */
pr_initx(ncid, path);
/*
* get number of dimensions, number of variables, number of global
* atts, and dimension id of unlimited dimension, if any
*/
/* TODO: print names with XML-ish escapes fopr special chars */
NC_CHECK( nc_inq(ncid, &ndims, &nvars, &ngatts, &xdimid) );
/* get dimension info */
dims = (ncdim_t *) emalloc((ndims + 1) * sizeof(ncdim_t));
for (dimid = 0; dimid < ndims; dimid++) {
NC_CHECK( nc_inq_dim(ncid, dimid, dims[dimid].name, &dims[dimid].size)
);
if (dimid == xdimid)
printf(" <dimension name=\"%s\" length=\"%d\" isUnlimited=\"true\"
/>\n",
dims[dimid].name, (int)dims[dimid].size);
else
printf (" <dimension name=\"%s\" length=\"%d\" />\n",
dims[dimid].name, (int)dims[dimid].size);
}
/* get global attributes */
for (ia = 0; ia < ngatts; ia++)
pr_attx(ncid, NC_GLOBAL, ia); /* print ia-th global attribute */
/* get variable info, with variable attributes */
for (varid = 0; varid < nvars; varid++) {
NC_CHECK( nc_inq_varndims(ncid, varid, &var.ndims) );
var.dims = (int *) emalloc((var.ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_var(ncid, varid, var.name, &var.type, 0,
var.dims, &var.natts) );
printf (" <variable name=\"%s\"", var.name);
pr_shape(&var, dims);
/* handle one-line variable elements that aren't containers
for attributes or data values, since they need to be
rendered as <variable ... /> instead of <variable ..>
... </variable> */
if (var.natts == 0) {
if (
/* header-only specified */
(specp->header_only) ||
/* list of variables specified and this variable not in list */
(specp->nlvars > 0 && !varmember(vlist, varid)) ||
/* coordinate vars only and this is not a coordinate variable */
(specp->coord_vals && !iscoordvar(ncid, varid)) ||
/* this is a record variable, but no records have been written
*/
(isrecvar(ncid,varid) && dims[xdimid].size == 0)
) {
printf (" type=\"%s\" />\n", prim_type_name(var.type));
continue;
}
}
/* else nest attributes values, data values in <variable> ...
</variable> */
printf (" type=\"%s\">\n", prim_type_name(var.type));
/* get variable attributes */
for (ia = 0; ia < var.natts; ia++) {
pr_attx(ncid, varid, ia); /* print ia-th attribute */
}
printf (" </variable>\n");
}
printf ("</netcdf>\n");
NC_CHECK(
nc_close(ncid) );
if (vlist)
free(vlist);
if(dims)
free(dims);
}
static void
make_lvars(char *optarg, fspec_t* fspecp)
{
char *cp = optarg;
int nvars = 1;
char ** cpp;
/* compute number of variable names in comma-delimited list */
fspecp->nlvars = 1;
while (*cp++)
if (*cp == ',')
nvars++;
fspecp->lvars = (char **) emalloc(nvars * sizeof(char*));
cpp = fspecp->lvars;
/* copy variable names into list */
for (cp = strtok(optarg, ",");
cp != NULL;
cp = strtok((char *) NULL, ",")) {
size_t bufsiz = strlen(cp) + 1;
*cpp = (char *) emalloc(bufsiz);
strncpy(*cpp, cp, bufsiz);
cpp++;
}
fspecp->nlvars = nvars;
}
/*
* Extract the significant-digits specifiers from the (deprecated and
* undocumented) -d argument on the command-line and update the
* default data formats appropriately. This only exists because an
* old version of ncdump supported the "-d" flag which did not
* override the C_format attributes (if any).
*/
static void
set_sigdigs(const char *optarg)
{
char *ptr1 = 0;
char *ptr2 = 0;
int flt_digits = FLT_DIGITS; /* default floating-point digits */
int dbl_digits = DBL_DIGITS; /* default double-precision digits */
if (optarg != 0 && (int) strlen(optarg) > 0 && optarg[0] != ',')
flt_digits = (int)strtol(optarg, &ptr1, 10);
if (flt_digits < 1 || flt_digits > 20) {
error("unreasonable value for float significant digits: %d",
flt_digits);
}
if (*ptr1 == ',')
dbl_digits = (int)strtol(ptr1+1, &ptr2, 10);
if (ptr2 == ptr1+1 || dbl_digits < 1 || dbl_digits > 20) {
error("unreasonable value for double significant digits: %d",
dbl_digits);
}
set_formats(flt_digits, dbl_digits);
}
/*
* Extract the significant-digits specifiers from the -p argument on the
* command-line, set flags so we can override C_format attributes (if any),
* and update the default data formats appropriately.
*/
static void
set_precision(const char *optarg)
{
char *ptr1 = 0;
char *ptr2 = 0;
int flt_digits = FLT_DIGITS; /* default floating-point digits */
int dbl_digits = DBL_DIGITS; /* default double-precision digits */
if (optarg != 0 && (int) strlen(optarg) > 0 && optarg[0] != ',') {
flt_digits = (int)strtol(optarg, &ptr1, 10);
float_precision_specified = 1;
}
if (flt_digits < 1 || flt_digits > 20) {
error("unreasonable value for float significant digits: %d",
flt_digits);
}
if (*ptr1 == ',') {
dbl_digits = (int) strtol(ptr1+1, &ptr2, 10);
double_precision_specified = 1;
}
if (ptr2 == ptr1+1 || dbl_digits < 1 || dbl_digits > 20) {
error("unreasonable value for double significant digits: %d",
dbl_digits);
}
set_formats(flt_digits, dbl_digits);
}
/* 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);
int numgrps;
int *ncids;
int g;
if (status == NC_NOERR)
count++;
#ifdef USE_NETCDF4
/* if this group has subgroups, call recursively on each of them */
NC_CHECK( nc_status = 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;
}
/* Check if any variable names specified with "-v var1,...,varn" are
* missing. Returns 0 if no missing variables detected, otherwise
* exits. */
static int
missing_vars(int ncid, fspec_t *specp) {
int iv;
for (iv=0; iv < specp->nlvars; iv++) {
if(nc_inq_varname_count(ncid, specp->lvars[iv]) == 0) {
error("%s: No such variable", specp->lvars[iv]);
}
}
return 0;
}
int
main(int argc, char *argv[])
{
extern int optind;
extern int opterr;
extern char *optarg;
static fspec_t fspec = /* defaults, overridden on command line */
{
0, /* construct netcdf name from file name */
false, /* print header info only, no data? */
false, /* just print coord vars? */
false, /* brief comments in data section? */
false, /* full annotations in data section? */
false, /* human-readable output for date-time values */
false, /* output special attributes, eg chunking? */
LANG_C, /* language conventions for indices */
0, /* if -v specified, number of variables */
0 /* if -v specified, list of variable names */
};
int c;
int i;
int max_len = 80; /* default maximum line length */
int nameopt = 0;
boolean xml_out = false; /* if true, output NcML instead of CDL */
boolean kind_out = false; /* if true, just output kind of netCDF file */
#ifdef HAVE_LOCALE_H
setlocale(LC_ALL, "C"); /* CDL may be ambiguous with other locales */
#endif /* HAVE_LOCALE_H */
opterr = 1;
progname = argv[0];
set_formats(FLT_DIGITS, DBL_DIGITS); /* default for float, double data */
/* If the user called ncdump without arguments, print the usage
* message and return peacefully. */
if (argc <= 1)
{
usage();
#ifdef vms
exit(EXIT_SUCCESS);
#else
return EXIT_SUCCESS;
#endif
}
while ((c = getopt(argc, argv, "b:cd:f:hkl:n:p:stv:x")) != EOF)
switch(c) {
case 'h': /* dump header only, no data */
fspec.header_only = true;
break;
case 'c': /* header, data only for coordinate dims */
fspec.coord_vals = true;
break;
case 'n': /*
* provide different name than derived from
* file name
*/
fspec.name = optarg;
nameopt = 1;
break;
case 'b': /* brief comments in data section */
fspec.brief_data_cmnts = true;
switch (tolower(optarg[0])) {
case 'c':
fspec.data_lang = LANG_C;
break;
case 'f':
fspec.data_lang = LANG_F;
break;
default:
error("invalid value for -b option: %s", optarg);
}
break;
case 'f': /* full comments in data section */
fspec.full_data_cmnts = true;
switch (tolower(optarg[0])) {
case 'c':
fspec.data_lang = LANG_C;
break;
case 'f':
fspec.data_lang = LANG_F;
break;
default:
error("invalid value for -f option: %s", optarg);
}
break;
case 'l': /* maximum line length */
max_len = (int) strtol(optarg, 0, 0);
if (max_len < 10) {
error("unreasonably small line length specified: %d", max_len);
}
break;
case 'v': /* variable names */
/* make list of names of variables specified */
make_lvars (optarg, &fspec);
break;
case 'd': /* specify precision for floats (deprecated,
undocumented) */
set_sigdigs(optarg);
break;
case 'p': /* specify precision for floats, overrides
attribute specs */
set_precision(optarg);
break;
case 'x': /* XML output (NcML) */
xml_out = true;
break;
case 'k': /* just output what kind of netCDF file */
kind_out = true;
break;
case 't': /* human-readable strings for time values */
fspec.iso_times = true;
break;
case 's': /* output special (virtual) attributes for
* netCDF-4 files and variables, including
* _DeflateLevel, _Chunking, _Endianness,
* _Format, _Checksum, _NoFill */
fspec.special_atts = true;
break;
case '?':
usage();
return 0;
}
set_max_len(max_len);
argc -= optind;
argv += optind;
/* If no file arguments left or more than one, print usage message. */
if (argc != 1)
{
usage();
return 0;
}
i = 0;
init_epsilons();
{
char *path = argv[i];
if (!nameopt)
fspec.name = name_path(path);
if (argc > 0) {
int ncid, nc_status;
nc_status = nc_open(path, NC_NOWRITE, &ncid);
if (nc_status != NC_NOERR) {
error("%s: %s", path, nc_strerror(nc_status));
}
if (kind_out) {
do_nckind(ncid, path);
} else {
/* Initialize list of types. */
init_types(ncid);
/* Check if any vars in -v don't exist */
if(missing_vars(ncid, &fspec))
return EXIT_FAILURE;
if (xml_out) {
do_ncdumpx(ncid, path, &fspec);
} else {
do_ncdump(ncid, path, &fspec);
}
}
}
}
#ifdef vms
exit(EXIT_SUCCESS);
#else
return EXIT_SUCCESS;
#endif
}
