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079c3a771c
netcdf-c/ncdump/ncdump.c
Russ Rew 08112a46ad Resolve NCF-129, update documentation.
2011-09-26 16:25:10 +00:00

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/*
Copyright 2011 University Corporation for Atmospheric
Research/Unidata. See \ref copyright file for more info. */
#include <config.h>
#include <stdio.h>
#ifdef HAVE_GETOPT_H
#include <getopt.h>
#endif
#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 "utils.h"
#include "nccomps.h"
#include "nctime0.h" /* new iso time and calendar stuff */
#include "dumplib.h"
#include "ncdump.h"
#include "vardata.h"
#include "indent.h"
#include "isnan.h"
#include "cdl.h"
#define int64_t long long
#define uint64_t unsigned long long
/* globals */
char *progname;
fspec_t formatting_specs = /* defaults, overridden by command-line options */
{
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, /* use 'T' separator between date and time values as strings? */
false, /* output special attributes, eg chunking? */
LANG_C, /* language conventions for indices */
false, /* for DAP URLs, client-side cache used */
0, /* if -v specified, number of variables in list */
0, /* if -v specified, list of variable names */
0, /* if -g specified, number of groups names in list */
0, /* if -g specified, list of group names */
0, /* if -g specified, list of matching grpids */
0 /* kind of netCDF file */
};
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 date-time strings\n\
[-i] Output time data as date-time strings with ISO-8601 'T' separator\n\
[-g grp1[,...]] Data and metadata for group(s) <grp1>,... only\
[-w] Without client-side caching of variables for DAP URLs\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]] [-k] [-x] [-s] [-t|-i] [-g ...] [-w] 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 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 ("&quot;");
break;
case '<':
printf ("&lt;");
break;
case '>':
printf ("&gt;");
break;
case '&':
printf ("&amp;");
break;
case '\n':
printf ("&#xA;");
break;
case '\r':
printf ("&#xD;");
break;
case '\t':
printf ("&#x9;");
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 (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 ("%huUS%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';
/* (1) Print normal list of attribute values. */
pr_att_valgs(kind, att.type, att.len, att.valgp);
printf (" ;"); /* terminator for normal list */
/* (2) If -t option, add list of date/time strings as CDL comments. */
if(formatting_specs.string_times) {
/* Prints text after semicolon and before final newline.
* Prints nothing if not qualified for time interpretation.
* Will include line breaks for longer lists. */
print_att_times(ncid, varid, att);
if(is_bounds_att(&att)) {
insert_bounds_info(ncid, varid, att);
}
}
#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 + 1) * sizeof(nc_vlen_t));
break;
case NC_OPAQUE:
data = emalloc((att.len + 1) * type_size);
break;
case NC_ENUM:
/* a long long is ample for all base types */
data = emalloc((att.len + 1) * sizeof(int64_t));
break;
case NC_COMPOUND:
data = emalloc((att.len + 1) * 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);
}
printf (" ;"); /* terminator for user defined types */
}
#endif /* USE_NETCDF4 */
printf ("\n"); /* final newline for all attribute types */
}
/* 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 + 1);
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;
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, NULL) );
/* 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) {
int *field_dim_sizes = (int *) emalloc((field_ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_compound_field(ncid, typeid, f, NULL,
NULL, NULL, NULL,
field_dim_sizes) );
printf("(");
for (d = 0; d < field_ndims-1; d++)
printf("%d, ", field_dim_sizes[d]);
printf("%d)", field_dim_sizes[field_ndims-1]);
free(field_dim_sizes);
}
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 = NULL;
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 + 1);
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;
free(fillvalp);
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;
free(fillvalp);
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;
free(fillvalp);
fillvalp = 0;
break;
}
}
vp->fillvalp = fillvalp;
}
/* Recursively dump the contents of a group. (Only netcdf-4 format
* files can have groups, so recursion will not take place for classic
* format files.)
*
* ncid: id of open file (first call) or group (subsequent recursive calls)
* path: file path name (first call)
*/
static void
do_ncdump_rec(int ncid, const char *path)
{
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 */
idnode_t* 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 */
int is_root = 1; /* true if ncid is root group or if netCDF-3 */
#ifdef USE_NETCDF4
if (nc_inq_grp_parent(ncid, NULL) != NC_ENOGRP)
is_root = 0;
#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 (formatting_specs.nlvars > 0) {
vlist = newidlist(); /* list for vars specified with -v option */
for (iv=0; iv < formatting_specs.nlvars; iv++) {
if(nc_inq_gvarid(ncid, formatting_specs.lvars[iv], &varid) == NC_NOERR)
idadd(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 + 1) * 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);
if (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 ; // (%lu currently)\n",
(unsigned long)dims[d_grp].size);
} else {
printf ("%lu ;\n", (unsigned long)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. */
memset((void*)&var,0,sizeof(var));
for (varid = 0; varid < nvars; varid++) {
NC_CHECK( nc_inq_varndims(ncid, varid, &var.ndims) );
if(var.dims != NULL) free(var.dims);
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++) {
/* 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) );
#ifdef USE_NETCDF4
/* 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 + 1);
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);
}
}
#endif /* USE_NETCDF4 */
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 (formatting_specs.special_atts) {
pr_att_specials(ncid, kind, varid, &var);
}
#endif /* USE_NETCDF4 */
}
/* get global attributes */
if (ngatts > 0 || formatting_specs.special_atts) {
printf ("\n");
indent_out();
if (is_root)
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 (is_root && formatting_specs.special_atts) { /* output special attribute
* for format variant */
pr_att_global_format(ncid, kind);
}
/* output variable data, unless "-h" option specified header only
* or this group is not in list of groups specified by "-g"
* option */
if (! formatting_specs.header_only && group_wanted(ncid) ) {
if (nvars > 0) {
indent_out();
printf ("data:\n");
}
for (varid = 0; varid < nvars; varid++) {
int no_data;
/* if var list specified, test for membership */
if (formatting_specs.nlvars > 0 && ! idmember(vlist, varid))
continue;
NC_CHECK( nc_inq_varndims(ncid, varid, &var.ndims) );
if(var.dims != NULL) free(var.dims);
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 (formatting_specs.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_data = 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_data = 1;
}
vdims[id] = len;
}
/* Don't get data for record variables if no records have
* been written yet */
if (no_data) {
free(vdims);
vdims = 0;
continue;
}
if(var.fillvalp != NULL) free(var.fillvalp);
get_fill_info(ncid, varid, &var); /* sets has_fillval, fillvalp mmbrs */
if(var.timeinfo != NULL) {
if(var.timeinfo->units) free(var.timeinfo->units);
free(var.timeinfo);
}
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);
if (vardata(&var, vdims, ncid, varid) == -1) {
error("can't output data for variable %s", var.name);
goto done;
}
}
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_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);
indent_out();
/* printf ("} // group %s\n", group_name); */
printf ("} // group ");
print_name (group_name);
printf ("\n");
indent_less();
}
free(ncids);
}
#endif /* USE_NETCDF4 */
done:
if(var.dims != NULL) free(var.dims);
if(var.fillvalp != NULL) free(var.fillvalp);
if(var.timeinfo != NULL) {
if(var.timeinfo->units) free(var.timeinfo->units);
free(var.timeinfo);
}
if (dims)
free(dims);
if (vlist)
free(vlist);
}
static void
do_ncdump(int ncid, const char *path)
{
char* esc_specname;
/* output initial line */
indent_init();
indent_out();
esc_specname=escaped_name(formatting_specs.name);
printf ("netcdf %s {\n", esc_specname);
free(esc_specname);
do_ncdump_rec(ncid, path);
indent_out();
printf ("}\n");
}
static void
do_ncdumpx(int ncid, const char *path)
{
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 */
idnode_t* vlist = 0; /* list for vars specified with -v option */
/*
* If any vars were specified with -v option, get list of associated
* variable ids
*/
if (formatting_specs.nlvars > 0) {
vlist = newidlist(); /* list for vars specified with -v option */
for (iv=0; iv < formatting_specs.nlvars; iv++) {
NC_CHECK( nc_inq_varid(ncid, formatting_specs.lvars[iv], &varid) );
idadd(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 */
memset((void*)&var,0,sizeof(var));
for (varid = 0; varid < nvars; varid++) {
NC_CHECK( nc_inq_varndims(ncid, varid, &var.ndims) );
if(var.dims != NULL) free(var.dims);
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 */
(formatting_specs.header_only) ||
/* list of variables specified and this variable not in list */
(formatting_specs.nlvars > 0 && !idmember(vlist, varid)) ||
/* coordinate vars only and this is not a coordinate variable */
(formatting_specs.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");
if (vlist)
free(vlist);
if(dims)
free(dims);
}
static void
make_lvars(char *optarg)
{
char *cp = optarg;
int nvars = 1;
char ** cpp;
/* compute number of variable names in comma-delimited list */
formatting_specs.nlvars = 1;
while (*cp++)
if (*cp == ',')
nvars++;
formatting_specs.nlvars = nvars;
formatting_specs.lvars = (char **) emalloc(nvars * sizeof(char*));
cpp = formatting_specs.lvars;
/* copy variable names into list */
for (cp = strtok(optarg, ","); cp != NULL; cp = strtok((char *) NULL, ",")) {
*cpp = strdup(cp);
cpp++;
}
}
static void
make_lgrps(char *optarg)
{
char *cp = optarg;
int ngrps = 1;
char ** cpp;
/* compute number of group names in comma-delimited list */
while (*cp++)
if (*cp == ',')
ngrps++;
formatting_specs.nlgrps = ngrps;
formatting_specs.lgrps = (char **) emalloc(ngrps * sizeof(char*));
cpp = formatting_specs.lgrps;
/* copy group names into list */
for (cp = strtok(optarg, ","); cp != NULL; cp = strtok((char *) NULL, ",")) {
*cpp = strdup(cp);
cpp++;
}
/* make empty list of grpids, to be filled in after input file opened */
formatting_specs.grpids = newidlist();
}
/*
* 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 && *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 && *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);
#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;
}
/* 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) {
int iv;
for (iv=0; iv < formatting_specs.nlvars; iv++) {
if(nc_inq_varname_count(ncid, formatting_specs.lvars[iv]) == 0) {
error("%s: No such variable", formatting_specs.lvars[iv]);
}
}
return 0;
}
/* Determine whether a group named formatting_specs.lgrps[igrp] exists
* in a netCDF file or group with id ncid. If so, return the count of
* how many matching groups were found, else return a count of 0. If
* the name begins with "/", it is interpreted as an absolute group
* name, in which case only 0 or 1 is returned. Otherwise, interpret
* it as a relative name, and the total number of occurrences within
* the file/group identified by ncid is returned.
*
* Also has side effect of updating the ngrpids and the associate
* grpids array that represent the group list specified by the -g
* option. TODO: put this in its own function instead.
*/
static size_t
nc_inq_grpname_count(int ncid, int igrp) {
size_t count = 0;
int numgrps;
int *ncids;
int g;
int grpid;
int status;
char *grpname=formatting_specs.lgrps[igrp];
/* permit empty string to also designate root group */
if(grpname[0] == '\0' || STREQ(grpname,"/")) {
count = 1;
idadd(formatting_specs.grpids, ncid);
return count;
}
#ifdef USE_NETCDF4
/* Handle absolute group names */
if(grpname[0] == '/') {
int grpid;
status = nc_inq_grp_full_ncid(ncid, grpname, &grpid);
if(status == NC_NOERR) {
count = 1;
idadd(formatting_specs.grpids, grpid);
} else if(status == NC_ENOGRP) {
count = 0;
} else {
error("when looking up group %s: %s ", grpname, nc_strerror(status));
}
return count;
}
/* look in this group */
status = nc_inq_grp_ncid(ncid, grpname, &grpid);
if (status == NC_NOERR) {
count++;
idadd(formatting_specs.grpids, grpid);
}
/* if this group has subgroups, call recursively on each of them */
NC_CHECK( nc_inq_grps(ncid, &numgrps, NULL) );
if(numgrps > 0) {
/* Allocate memory to hold the list of group ids. */
ncids = emalloc(numgrps * sizeof(int));
/* Get the list of group ids. */
NC_CHECK( nc_inq_grps(ncid, NULL, ncids) );
/* Call this function recursively for each group. */
for (g = 0; g < numgrps; g++) {
count += nc_inq_grpname_count(ncids[g], igrp);
}
free(ncids);
}
#endif /* USE_NETCDF4 */
return count;
}
/* Check if any group names specified with "-g grp1,...,grpn" are
* missing. Returns total number of matching groups if no missing
* groups detected, otherwise exits. */
static int
grp_matches(int ncid) {
int ig;
size_t total = 0;
for (ig=0; ig < formatting_specs.nlgrps; ig++) {
size_t count = nc_inq_grpname_count(ncid, ig);
if(count == 0) {
error("%s: No such group", formatting_specs.lgrps[ig]);
return 0;
}
total += count;
}
return total;
}
#define DAP_CLIENT_CACHE_DIRECTIVE "[cache]"
/* replace path string with same string prefixed by
* DAP_CLIENT_NCDUMP_DIRECTIVE */
static
void adapt_url_for_cache(char **pathp) {
char prefix[] = DAP_CLIENT_CACHE_DIRECTIVE;
char* path = *pathp;
char *tmp_path = strdup(path);
path = (char *)emalloc(strlen(prefix) + strlen(tmp_path) + 1);
path[0] = '\0';
strncat(path, prefix, strlen(prefix));
strncat(path, tmp_path, strlen(tmp_path));
free(tmp_path);
*pathp = path;
return;
}
/**
The ncdump tool generates the CDL text representation of a netCDF
dataset on standard output, optionally excluding some or all of the
variable data in the output. The output from ncdump is intended to be
acceptable as input to ncgen. Thus ncdump and ncgen can be used as
inverses to transform data representation between binary and text
representations.
As of netCDF version 4.1, ncdump can also access DAP data sources if
DAP support is enabled in the underlying netCDF library. Instead of
specifying a file name as argument to ncdump, the user specifies a URL
to a DAP source.
ncdump may also be used as a simple browser for netCDF datasets, to
display the dimension names and lengths; variable names, types, and
shapes; attribute names and values; and optionally, the values of data
for all variables or selected variables in a netCDF dataset.
ncdump defines a default format used for each type of netCDF variable
data, but this can be overridden if a C_format attribute is defined
for a netCDF variable. In this case, ncdump will use the C_format
attribute to format values for that variable. For example, if
floating-point data for the netCDF variable Z is known to be accurate
to only three significant digits, it might be appropriate to use this
variable attribute:
\code
Z:C_format = "%.3g"
\endcode
Ncdump uses '_' to represent data values that are equal to the
_FillValue attribute for a variable, intended to represent data that
has not yet been written. If a variable has no _FillValue attribute,
the default fill value for the variable type is used unless the
variable is of byte type.
UNIX syntax for invoking ncdump:
\code
ncdump [-c | -h] [-v var1,...] [-g grp1,...] [-b lang] [-f lang]
[-l len] [-n name] [-p fdig[,ddig]] [-x] [-s] [-t] input-file
\endcode
or
\code
ncdump -k input-file
\endcode
where:
-c Show the values of coordinate variables (variables that are also
dimensions) as well as the declarations of all dimensions, variables,
and attribute values. Data values of non-coordinate variables are not
included in the output. This is often the most suitable option to use
for a brief look at the structure and contents of a netCDF file.
-h Show only the header information in the output, that is, output
only the declarations for the netCDF dimensions, variables, and
attributes of the input file, but no data values for any
variables. The output is identical to using the '-c' option except
that the values of coordinate variables are not included. (At most
one of '-c' or '-h' options may be present.)
-v var1,... The output will include data values for the specified
variables, in addition to the declarations of all dimensions,
variables, and attributes. One or more variables must be specified by
name in the comma-delimited list following this option. The list must
be a single argument to the command, hence cannot contain blanks or
other white space characters. The named variables must be valid
netCDF variables in the input-file. The default, without this option
and in the absence of the '-c' or '-h' options, is to include data
values for all variables in the output.
-g grp1,... The output will include data values only for the specified
groups. One or more groups must be specified by name in the
comma-delimited list following this option. The list must be a single
argument to the command. The named groups must be valid netCDF groups in the
input-file. The default, without this option and in the absence of
the '-c' or '-h' options, is to include data values for all groups in
the output.
-b lang A brief annotation in the form of a CDL comment (text
beginning with the characters '//') will be included in the data
section of the output for each 'row' of data, to help identify data
values for multidimensional variables. If lang begins with 'C' or
'c', then C language conventions will be used (zero-based indices,
last dimension varying fastest). If lang begins with 'F' or 'f', then
FORTRAN language conventions will be used (one-based indices, first
dimension varying fastest). In either case, the data will be
presented in the same order; only the annotations will differ. This
option may be useful for browsing through large volumes of
multidimensional data.
-f lang Full annotations in the form of trailing CDL comments (text
beginning with the characters '//') for every data value (except
individual characters in character arrays) will be included in the
data section. If lang begins with 'C' or 'c', then C language
conventions will be used. If lang begins with 'F' or 'f', then FORTRAN language
conventions will be used. In either case, the data will be presented in the same
order; only the annotations will differ. This option may be useful
for piping data into other filters, since each data value appears on
a separate line, fully identified. (At most one of '-b' or '-f'
options may be present.)
-l len Changes the default maximum line length (80) used in formatting
lists of non-character data values.
-p float_digits[,double_digits] Specifies default precision (number of
significant digits) to use in displaying floating-point or double
precision data values for attributes and variables. If specified, this
value overrides the value of the C_format attribute, if any, for a
variable. Floating-point data will be displayed with float_digits
significant digits. If double_digits is also specified,
double-precision values will be displayed with that many significant
digits. In the absence of any '-p' specifications, floating-point and
double-precision data are displayed with 7 and 15 significant digits
respectively. CDL files can be made smaller if less precision is
required. If both floating-point and double precisions are specified,
the two values must appear separated by a comma (no blanks) as a
single argument to the command.
-s Specifies that special virtual attributes should be output for the
file format variant and for variable properties such as compression,
chunking, and other properties specific to the format implementation
that are primarily related to performance rather than the logical
schema of the data. All the special virtual attributes begin with '_'
followed by an upper-case letter. Currently they include the global
attribute “_Format” and the variable attributes “_Fletcher32”,
“_ChunkSizes”, “_Endianness”, “_DeflateLevel”, “_Shuffle”, “_Storage”,
and “_NoFill”. The ncgen utility recognizes these attributes and
supports them appropriately.
-t Controls display of time data, if stored in a variable that uses a
udunits compliant time representation such as “days since 1970-01-01”
or “seconds since 2009-03-15 12:01:17”. If this option is specified,
time values are displayed as human-readable date-time strings rather
than numerical values, interpreted in terms of a “calendar” variable
attribute, if specified. Calendar attribute values interpreted with
this option include the CF Conventions values “gregorian” or
“standard”, “proleptic_gregorian”, “noleap” or “365_day”, “all_leap”
or “366_day”, “360_day”, and “julian”.
-n name CDL requires a name for a netCDF file, for use by 'ncgen
-b' in generating a default netCDF file name. By default, ncdump
constructs this name from the last component of the file name of the
input netCDF file by stripping off any extension it has. Use the
'-n' option to specify a different name. Although the output file name
used by 'ncgen -b' can be specified, it may be wise to have ncdump
change the default name to avoid inadvertently overwriting a valuable
netCDF file when using ncdump, editing the resulting CDL file, and
using 'ncgen -b' to generate a new netCDF file from the edited CDL
file.
\section Examples
Look at the structure of the data in the netCDF file foo.nc:
\code
ncdump -c foo.nc
\endcode
Produce an annotated CDL version of the structure and data in the
netCDF file foo.nc, using C-style indexing for the annotations:
\code
ncdump -b c foo.nc > foo.cdl
\endcode
Output data for only the variables uwind and vwind from the netCDF
file foo.nc, and show the floating-point data with only three
significant digits of precision:
\code
ncdump -v uwind,vwind -p 3 foo.nc
\endcode
Produce a fully-annotated (one data value per line) listing of the
data for the variable omega, using FORTRAN conventions for indices,
and changing the netCDF file name in the resulting CDL file to
omega:
\code
ncdump -v omega -f fortran -n omega foo.nc > Z.cdl
\endcode
Examine the translated DDS for the DAP source from the specified URL.
\code
ncdump -h http://test.opendap.org:8080/dods/dts/test.01
\endcode
*/
int
main(int argc, char *argv[])
{
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:g:hijkl:n:p:stv:xw")) != EOF)
switch(c) {
case 'h': /* dump header only, no data */
formatting_specs.header_only = true;
break;
case 'c': /* header, data only for coordinate dims */
formatting_specs.coord_vals = true;
break;
case 'n': /*
* provide different name than derived from
* file name
*/
formatting_specs.name = optarg;
nameopt = 1;
break;
case 'b': /* brief comments in data section */
formatting_specs.brief_data_cmnts = true;
switch (tolower(optarg[0])) {
case 'c':
formatting_specs.data_lang = LANG_C;
break;
case 'f':
formatting_specs.data_lang = LANG_F;
break;
default:
error("invalid value for -b option: %s", optarg);
}
break;
case 'f': /* full comments in data section */
formatting_specs.full_data_cmnts = true;
switch (tolower(optarg[0])) {
case 'c':
formatting_specs.data_lang = LANG_C;
break;
case 'f':
formatting_specs.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);
break;
case 'g': /* group names */
/* make list of names of groups specified */
make_lgrps (optarg);
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 date-time values */
formatting_specs.string_times = true;
formatting_specs.iso_separator = false;
break;
case 'i': /* human-readable strings for data-time values with 'T' separator */
formatting_specs.string_times = true;
formatting_specs.iso_separator = true;
break;
case 's': /* output special (virtual) attributes for
* netCDF-4 files and variables, including
* _DeflateLevel, _Chunking, _Endianness,
* _Format, _Checksum, _NoFill */
formatting_specs.special_atts = true;
break;
case 'w': /* with client-side cache for DAP URLs */
formatting_specs.with_cache = 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 = strdup(argv[i]);
if(!path)
error("out of memory copying argument %s", argv[i]);
if (!nameopt)
formatting_specs.name = name_path(path);
if (argc > 0) {
int ncid, nc_status;
/* If path is a URL, prefix with client-side directive to
* make ncdump reasonably efficient */
#ifdef USE_DAP
if(formatting_specs.with_cache) /* by default, don't use cache directive */
{
extern int nc__testurl(const char*,char**);
/* See if this is a url */
if(nc__testurl(path, NULL)) {
adapt_url_for_cache(&path);
}
/* else fall thru and treat like a file path */
}
#endif /*USE_DAP*/
nc_status = nc_open(path, NC_NOWRITE, &ncid);
if (nc_status != NC_NOERR) {
error("%s: %s", path, nc_strerror(nc_status));
}
NC_CHECK( nc_inq_format(ncid, &formatting_specs.nc_kind) );
if (kind_out) {
printf ("%s\n", kind_string(formatting_specs.nc_kind));
} else {
/* Initialize list of types. */
init_types(ncid);
/* Check if any vars in -v don't exist */
if(missing_vars(ncid))
return EXIT_FAILURE;
if(formatting_specs.nlgrps > 0) {
if(formatting_specs.nc_kind != NC_FORMAT_NETCDF4) {
error("Group list (-g ...) only permitted for netCDF-4 file");
return EXIT_FAILURE;
}
/* Check if any grps in -g don't exist */
if(grp_matches(ncid) == 0)
return EXIT_FAILURE;
}
if (xml_out) {
if(formatting_specs.nc_kind == NC_FORMAT_NETCDF4) {
error("NcML output (-x) currently only permitted for netCDF classic model");
return EXIT_FAILURE;
}
do_ncdumpx(ncid, path);
} else {
do_ncdump(ncid, path);
}
}
NC_CHECK( nc_close(ncid) );
}
free(path);
}
#ifdef vms
exit(EXIT_SUCCESS);
#else
return EXIT_SUCCESS;
#endif
}
END_OF_MAIN();
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