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netcdf-c/ncdump/ncdump.c
Dennis Heimbigner f376c23329 Make utilities support NC_COMPACT 
re: https://github.com/Unidata/netcdf-c/issues/1642

Modify ncdump, nccopy, and ncgen to support the NC_COMPACT storage option.
Added test cases and added description to the man pages for the utilities.

1. ncdump: For compact storage variable, print special attribute __Storage_ as
````
    <var>: _Storage = "compact";
````

2. ncgen: parse and implement
````
    <var>: _Storage = "compact";
````
in a .cdl file

3. nccopy: Extend the chunk specification (-c flag) to support
   compact using the forms
````
nccopy ... -c <var>:compact
and
nccopy ... -c <var>:contiguous
````

Misc. other changes
1. cleanup the copy_chunking function in ncdump/nccopy.c
2020-02-29 12:06:21 -07:00

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/*! \file
Copyright 2018 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
#ifdef _MSC_VER /* Microsoft Compilers */
#include <io.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#ifdef HAVE_FCNTL_H
#include <fcntl.h>
#endif
#ifdef _MSC_VER
#define snprintf _snprintf
#include "XGetopt.h"
int opterr;
int optind;
#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 "netcdf_mem.h"
#include "netcdf_filter.h"
#include "netcdf_aux.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"
#include "nclog.h"
#include "ncwinpath.h"
#include "nclist.h"
#include "nc_provenance.h"
#ifdef USE_NETCDF4
#include "nc4internal.h" /* to get name of the special properties file */
#endif
#ifdef USE_DAP
extern int nc__testurl(const char*,char**);
#endif
#define XML_VERSION "1.0"
#define int64_t long long
#define uint64_t unsigned long long
/* If we have a variable named one of these:
we need to be careful about printing their attributes.
*/
static const char* keywords[] = {
"variable",
"dimension",
"data",
"group",
"types",
NULL
};
static int iskeyword(const char* kw)
{
const char** p;
for(p=keywords;*p;p++) {
if(strcmp(kw,*p)==0) return 1;
}
return 0;
}
/* 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\
[-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\n\
[-w] With client-side caching of variables for DAP URLs\n\
[-x] Output XML (NcML) instead of CDL\n\
[-Xp] Unconditionally suppress output of the properties attribute\n\
[-Ln] Set log level to n (>= 0); ignore if logging not enabled.\n\
file Name of netCDF file (or URL if DAP access enabled)\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] [-Ln] 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 delimiter */
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";
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";
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_OFFSET:
return "64-bit offset";
case NC_FORMAT_CDF5:
return "cdf5";
case NC_FORMAT_NETCDF4:
return "netCDF-4";
case NC_FORMAT_NETCDF4_CLASSIC:
return "netCDF-4 classic model";
default:
error("unrecognized file format: %d", kind);
return "unrecognized";
}
}
/* Return extended format string */
static const char *
kind_string_extended(int kind, int mode)
{
static char text[1024];
switch (kind) {
case NC_FORMATX_NC3:
if(mode & NC_CDF5)
snprintf(text,sizeof(text),"%s mode=%08x", "64-bit data",mode);
else if(mode & NC_64BIT_OFFSET)
snprintf(text,sizeof(text),"%s mode=%08x", "64-bit offset",mode);
else
snprintf(text,sizeof(text),"%s mode=%08x", "classic",mode);
break;
case NC_FORMATX_NC_HDF5:
snprintf(text,sizeof(text),"%s mode=%08x", "HDF5",mode);
break;
case NC_FORMATX_NC_HDF4:
snprintf(text,sizeof(text),"%s mode=%08x", "HDF4",mode);
break;
case NC_FORMATX_PNETCDF:
snprintf(text,sizeof(text),"%s mode=%08x", "PNETCDF",mode);
break;
case NC_FORMATX_DAP2:
snprintf(text,sizeof(text),"%s mode=%08x", "DAP2",mode);
break;
case NC_FORMATX_DAP4:
snprintf(text,sizeof(text),"%s mode=%08x", "DAP4",mode);
break;
case NC_FORMATX_UNDEFINED:
snprintf(text,sizeof(text),"%s mode=%08x", "unknown",mode);
break;
default:
error("unrecognized extended format: %d",kind);
snprintf(text,sizeof(text),"%s mode=%08x", "unrecognized",mode);
break;
}
return text;
}
#if 0
static int
fileopen(const char* path, void** memp, size_t* sizep)
{
int status = NC_NOERR;
int fd = -1;
int oflags = 0;
off_t size = 0;
void* mem = NULL;
off_t red = 0;
char* pos = NULL;
/* Open the file, but make sure we can write it if needed */
oflags = O_RDONLY;
#ifdef O_BINARY
oflags |= O_BINARY;
#endif
oflags |= O_EXCL;
#ifdef vms
fd = open(path, oflags, 0, "ctx=stm");
#else
fd = NCopen2(path, oflags);
#endif
if(fd < 0) {
status = errno;
goto done;
}
/* get current filesize = max(|file|,initialize)*/
size = lseek(fd,0,SEEK_END);
if(size < 0) {status = errno; goto done;}
/* move pointer back to beginning of file */
(void)lseek(fd,0,SEEK_SET);
mem = malloc(size);
if(mem == NULL) {status = NC_ENOMEM; goto done;}
/* Read the file into memory */
/* We need to do multiple reads because there is no
guarantee that the amount read will be the full amount */
red = size;
pos = (char*)mem;
while(red > 0) {
ssize_t count = read(fd, pos, red);
if(count < 0) {status = errno; goto done;}
if(count == 0) {status = NC_ENOTNC; goto done;}
/* assert(count > 0) */
red -= count;
pos += count;
}
done:
if(fd >= 0)
(void)close(fd);
if(status != NC_NOERR) {
#ifndef DEBUG
fprintf(stderr,"open failed: file=%s err=%d\n",path,status);
fflush(stderr);
#endif
}
if(status != NC_NOERR && mem != NULL) {
free(mem);
mem = NULL;
} else {
if(sizep) *sizep = size;
if(memp) {
*memp = mem;
} else if(mem) {
free(mem);
}
}
return status;
}
#endif
/*
* Emit initial line of output for NcML
*/
static void
pr_initx(int ncid, const char *path)
{
printf("<?xml version=\"%s\" encoding=\"UTF-8\"?>\n<netcdf xmlns=\"http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2\" location=\"%s\">\n",
XML_VERSION, 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, cdf5, 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(
const char* attname,
size_t len,
const char *string
)
{
int iel;
const char *cp;
const char *sp;
unsigned char uc;
int nulcount = 0;
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;
case '\0':
printf ("&#0;");
if(nulcount++ == 0)
fprintf(stderr,"Attribute: '%s'; value contains nul characters; producing illegal xml\n",attname);
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;
unsigned char uc;
unsigned short us;
unsigned int ui;
int64_t i64;
uint64_t ui64;
#ifdef USE_NETCDF4
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;
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 ("%lldLL%s", i64, delim);
break;
case NC_UINT64:
ui64 = ((uint64_t *) vals)[iel];
printf ("%lluULL%s", ui64, delim);
break;
#ifdef USE_NETCDF4
case NC_STRING:
stringp = ((char **) vals)[iel];
if(stringp)
pr_att_string(kind, strlen(stringp), stringp);
else
printf("NIL");
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;
unsigned int ui;
int64_t i64;
uint64_t ui64;
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;
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;
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) );
#ifdef USE_NETCDF4
if (ncid == getrootid(ncid)
&& varid == NC_GLOBAL
&& strcmp(att.name,NCPROPS)==0)
return; /* will be printed elsewhere */
#endif
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);
if(iskeyword(varname)) /* see discussion about escapes in ncgen man page*/
printf(" ");
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 = NULL;
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);
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;
default:
error("enum must have an integer base type: %d", base_nc_type);
}
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);
break;
default:
error("unrecognized class of user defined type: %d", class);
}
ncaux_reclaim_data(ncid,att.type,data,att.len);
free(data);
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
)
{
int contig = NC_CHUNKED;
/* No special variable attributes for classic or 64-bit offset data */
if(kind == 1 || kind == 2)
return;
/* _Chunking tests */
NC_CHECK( nc_inq_var_chunking(ncid, varid, &contig, NULL ) );
if(contig == NC_CONTIGUOUS) {
pr_att_name(ncid, varp->name, NC_ATT_STORAGE);
printf(" = \"contiguous\" ;\n");
} else if(contig == NC_COMPACT) {
pr_att_name(ncid, varp->name, NC_ATT_STORAGE);
printf(" = \"compact\" ;\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);
}
/* _Filter (including deflate and shuffle) */
{
size_t nparams, nfilters, nbytes;
int shuffle=NC_NOSHUFFLE;
unsigned int* filterids = NULL;
unsigned int* params = NULL;
int usedeflateatt = 0;
/* Get applicable filter ids */
NC_CHECK(nc_inq_var_filterids(ncid, varid, &nfilters, NULL));
/* Get set of filters for this variable */
if(nfilters > 0) {
filterids = (unsigned int*)malloc(sizeof(unsigned int)*nfilters);
if(filterids == NULL) NC_CHECK(NC_ENOMEM);
} else
filterids = NULL;
NC_CHECK(nc_inq_var_filterids(ncid, varid, &nfilters, filterids));
if(nfilters > 0) {
int k;
int pratt = 0;
for(k=0;k<nfilters;k++) {
NC_CHECK(nc_inq_var_filter_info(ncid, varid, filterids[k], &nparams, NULL));
if(nparams > 0) {
params = (unsigned int*)calloc(1,sizeof(unsigned int)*nparams);
NC_CHECK(nc_inq_var_filter_info(ncid, varid, filterids[k], &nbytes, params));
} else
params = NULL;
/* Use _Deflate if the first filter is zip */
if(k == 0 && filterids[k] == H5Z_FILTER_DEFLATE) {
pr_att_name(ncid, varp->name, NC_ATT_DEFLATE);
printf(" = %d", (int)params[0]);
pratt = 1;
usedeflateatt = 1;
nullfree(params); params = NULL;
continue;
}
if(pratt || k == 0) {
pr_att_name(ncid,varp->name,NC_ATT_FILTER);
printf(" = \"");
pratt = 0;
}
if(k > 0) printf("|");
printf("%u",filterids[k]);
if(nparams > 0) {
int i;
for(i=0;i<nparams;i++)
printf(",%u",params[i]);
}
nullfree(params); params = NULL;
}
if(!usedeflateatt) printf("\"");
printf(" ;\n");
}
if(filterids) free(filterids);
/* Finally, do Shuffle */
NC_CHECK( nc_inq_var_deflate(ncid, varid, &shuffle, NULL, NULL));
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 != NC_ENDIAN_NATIVE) { /* NC_ENDIAN_NATIVE is the default */
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;
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 */
static void
pr_att_hidden(
int ncid,
int kind
)
{
int stat;
size_t len;
/* No special variable attributes for classic or 64-bit offset data */
#if 0
if(kind == 1 || kind == 2) return;
#endif
/* Print out Selected hidden attributes */
/* NCPROPS */
stat = nc_inq_att(ncid,NC_GLOBAL,NCPROPS,NULL,&len);
if(stat == NC_NOERR) {
char* propdata = (char*)malloc(len+1);
if(propdata == NULL)
return;
stat = nc_get_att_text(ncid,NC_GLOBAL,NCPROPS,propdata);
if(stat == NC_NOERR) {
pr_att_name(ncid, "", NCPROPS);
/* make sure its null terminated */
propdata[len] = '\0';
printf(" = \"%s\" ;\n",propdata);
}
free(propdata);
}
/* _SuperblockVersion */
stat = nc_inq_att(ncid,NC_GLOBAL,SUPERBLOCKATT,NULL,&len);
if(stat == NC_NOERR && len == 1) {
int sbversion;
stat = nc_get_att_int(ncid,NC_GLOBAL,SUPERBLOCKATT,&sbversion);
if(stat == NC_NOERR) {
pr_att_name(ncid, "", SUPERBLOCKATT);
printf(" = %d ;\n",sbversion);
}
}
/* _IsNetcdf4 */
stat = nc_inq_att(ncid,NC_GLOBAL,ISNETCDF4ATT,NULL,&len);
if(stat == NC_NOERR && len == 1) {
int isnc4;
stat = nc_get_att_int(ncid,NC_GLOBAL,ISNETCDF4ATT,&isnc4);
if(stat == NC_NOERR) {
pr_att_name(ncid, "", ISNETCDF4ATT);
printf(" = %d ;\n",isnc4?1:0);
}
}
}
/*
* Print a variable attribute for NcML
*/
static void
pr_attx(
int ncid,
int varid,
int ia
)
{
ncatt_t att; /* attribute */
char *attvals = NULL;
int attvalslen = 0;
NC_CHECK( nc_inq_attname(ncid, varid, ia, att.name) );
#ifdef USE_NETCDF4
if (ncid == getrootid(ncid)
&& varid == NC_GLOBAL
&& strcmp(att.name,NCPROPS)==0
&& (!formatting_specs.special_atts
|| !formatting_specs.xopt_props)
)
return;
#endif
NC_CHECK( nc_inq_att(ncid, varid, att.name, &att.type, &att.len) );
/* 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 = PRIM_LEN * att.len; /* max 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(att.name, 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");
if(attvals != NULL)
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 */
void* raw;
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) );
raw = (void*)&data;
switch (base_nc_type) {
case NC_BYTE:
memval = *(char *)raw;
break;
case NC_SHORT:
memval = *(short *)raw;
break;
case NC_INT:
memval = *(int *)raw;
break;
case NC_UBYTE:
memval = *(unsigned char *)raw;
break;
case NC_USHORT:
memval = *(unsigned short *)raw;
break;
case NC_UINT:
memval = *(unsigned int *)raw;
break;
case NC_INT64:
memval = *(int64_t *)raw;
break;
case NC_UINT64:
memval = *(uint64_t *)raw;
break;
default:
error("Bad base type for enum!");
break;
}
esc_mn = escaped_name(memname);
res = snprintf(safe_buf, SAFE_BUF_LEN, "%s = %lld%s", esc_mn,
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();
#if 0
printf("}; // %s\n", type_name);
#else
printf("}; // ");
#endif
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 = ecalloc(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;
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;
#ifdef USE_NETCDF4
case NC_STRING: {
char* s;
size_t len = strlen(NC_FILL_STRING);
#if 0
/* In order to avoid mem leak, allocate this string as part of fillvalp */
fillvalp = erealloc(fillvalp, vp->tinfo->size + 1 + len + 1);
s = ((char*)fillvalp) + vp->tinfo->size + 1;
#else
s = malloc(len+1);
#endif
memcpy(s,NC_FILL_STRING,len);
s[len] = '\0';
*((char **)fillvalp) = s;
} 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 = NULL; /* 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 ("%llu ;\n", (unsigned long long)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 and cdf5 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) );
memset((void*)&var,0,sizeof(var));
/* For each var, get and print out info. */
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 target_dimid; /* from variable dim list */
int locid; /* group id where dimension is defined */
/*Locate the innermost definition of a dimension with given name*/
NC_CHECK( nc_inq_dimid(ncid, dim_name, &dimid_test) );
/* Now, starting with current group, walk the parent chain
upward looking for the target dim_id */
target_dimid = var.dims[id];
locid = ncid;
while(target_dimid != dimid_test) {/*not in locid, try ancestors*/
int parent_id;
NC_CHECK( nc_inq_grp_parent(locid, &parent_id) );
locid = parent_id;
/* Is dim of this name defined in this group or higher? */
NC_CHECK( nc_inq_dimid(locid, dim_name, &dimid_test) );
}
/* innermost dimid with given name is in group locid.
If this is not current group, then use fully qualified
name (fqn) for the dimension name by prefixing dimname
with group name */
if(locid != ncid) { /* We need to use fqn */
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 */
}
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_hidden(ncid, kind);
pr_att_global_format(ncid, kind);
}
fflush(stdout);
/* 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, formatting_specs.nlgrps, formatting_specs.grpids) ) {
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;
}
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(var.fillvalp != NULL)
{ncaux_reclaim_data(ncid,var.tinfo->tid,var.fillvalp,1); free(var.fillvalp); var.fillvalp = NULL;}
}
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) {
/* Release any data hanging off of fillvalp */
ncaux_reclaim_data(ncid,var.tinfo->tid,var.fillvalp,1);
free(var.fillvalp);
var.fillvalp = NULL;
}
if(var.timeinfo != NULL) {
if(var.timeinfo->units) free(var.timeinfo->units);
free(var.timeinfo);
}
if (dims)
free(dims);
if (vlist)
freeidlist(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 = NULL; /* 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)
freeidlist(vlist);
if(dims)
free(dims);
if(var.dims != NULL)
free(var.dims);
}
/*
* 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);
}
#ifdef USE_DAP
#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));
if(tmp_path) free(tmp_path);
if(*path) free(*pathp);
*pathp = path;
return;
}
#endif
int
main(int argc, char *argv[])
{
int ncstat = NC_NOERR;
int c;
int i;
int max_len = 80; /* default maximum line length */
int nameopt = 0;
bool_t xml_out = false; /* if true, output NcML instead of CDL */
bool_t kind_out = false; /* if true, just output kind of netCDF file */
bool_t kind_out_extended = false; /* output inq_format vs inq_format_extended */
int Xp_flag = 0; /* indicate that -Xp flag was set */
char* path = NULL;
char errmsg[4096];
errmsg[0] = '\0';
#if defined(_WIN32) || defined(msdos) || defined(WIN64)
putenv("PRINTF_EXPONENT_DIGITS=2"); /* Enforce unix/linux style exponent formatting. */
#endif
#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();
exit(EXIT_SUCCESS);
}
while ((c = getopt(argc, argv, "b:cd:f:g:hikl:n:p:stv:xwKL:X:")) != 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((int)optarg[0])) {
case 'c':
formatting_specs.data_lang = LANG_C;
break;
case 'f':
formatting_specs.data_lang = LANG_F;
break;
default:
snprintf(errmsg,sizeof(errmsg),"invalid value for -b option: %s", optarg);
goto fail;
}
break;
case 'f': /* full comments in data section */
formatting_specs.full_data_cmnts = true;
switch (tolower((int)optarg[0])) {
case 'c':
formatting_specs.data_lang = LANG_C;
break;
case 'f':
formatting_specs.data_lang = LANG_F;
break;
default:
snprintf(errmsg,sizeof(errmsg),"invalid value for -f option: %s", optarg);
goto fail;
}
break;
case 'l': /* maximum line length */
max_len = (int) strtol(optarg, 0, 0);
if (max_len < 10) {
snprintf(errmsg,sizeof(errmsg),"unreasonably small line length specified: %d", max_len);
goto fail;
}
break;
case 'v': /* variable names */
/* make list of names of variables specified */
make_lvars (optarg, &formatting_specs.nlvars, &formatting_specs.lvars);
break;
case 'g': /* group names */
/* make list of names of groups specified */
make_lgrps (optarg, &formatting_specs.nlgrps, &formatting_specs.lgrps,
&formatting_specs.grpids);
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 'K': /* extended format info */
kind_out_extended = 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 'X': /* special options */
switch (tolower((int)optarg[0])) {
case 'm':
formatting_specs.xopt_inmemory = 1;
break;
case 'p': /* suppress the properties attribute */
Xp_flag = 1; /* record that this flag was set */
break;
default:
snprintf(errmsg,sizeof(errmsg),"invalid value for -X option: %s", optarg);
goto fail;
}
break;
case 'L':
#ifdef LOGGING
{
int level = atoi(optarg);
if(level >= 0)
nc_set_log_level(level);
}
#endif
ncsetlogging(1);
break;
case '?':
usage();
exit(EXIT_FAILURE);
}
/* Decide xopt_props */
if(formatting_specs.special_atts && Xp_flag == 1)
formatting_specs.xopt_props = 0;
else if(formatting_specs.special_atts && Xp_flag == 0)
formatting_specs.xopt_props = 1;
else if(!formatting_specs.special_atts)
formatting_specs.xopt_props = 0;
else
formatting_specs.xopt_props = 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();
exit(EXIT_FAILURE);
}
i = 0;
init_epsilons();
path = strdup(argv[i]);
if(!path) {
snprintf(errmsg,sizeof(errmsg),"out of memory copying argument %s", argv[i]);
goto fail;
}
if (!nameopt)
formatting_specs.name = name_path(path);
if (argc > 0) {
int ncid;
/* 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 */
if(nc__testurl(path, NULL)) /* See if this is a url */
adapt_url_for_cache(&path);
/* else fall thru and treat like a file path */
}
#endif /*USE_DAP*/
if(formatting_specs.xopt_inmemory) {
#if 0
size_t size = 0;
void* mem = NULL;
ncstat = fileopen(path,&mem,&size);
if(ncstat == NC_NOERR)
ncstat = nc_open_mem(path,NC_INMEMORY,size,mem,&ncid);
#else
ncstat = nc_open(path,NC_DISKLESS|NC_NOWRITE,&ncid);
#endif
} else /* just a file */
ncstat = nc_open(path, NC_NOWRITE, &ncid);
if (ncstat != NC_NOERR) goto fail;
NC_CHECK( nc_inq_format(ncid, &formatting_specs.nc_kind) );
NC_CHECK( nc_inq_format_extended(ncid,
&formatting_specs.nc_extended,
&formatting_specs.nc_mode) );
if (kind_out) {
printf ("%s\n", kind_string(formatting_specs.nc_kind));
} else if (kind_out_extended) {
printf ("%s\n", kind_string_extended(formatting_specs.nc_extended,formatting_specs.nc_mode));
} else {
/* Initialize list of types. */
init_types(ncid);
/* Check if any vars in -v don't exist */
if(missing_vars(ncid, formatting_specs.nlvars, formatting_specs.lvars)) {
snprintf(errmsg,sizeof(errmsg),"-v: non-existent variables");
goto fail;
}
if(formatting_specs.nlgrps > 0) {
if(formatting_specs.nc_kind != NC_FORMAT_NETCDF4)
goto fail;
/* Check if any grps in -g don't exist */
if(grp_matches(ncid, formatting_specs.nlgrps, formatting_specs.lgrps, formatting_specs.grpids) == 0)
goto fail;
}
if (xml_out) {
if(formatting_specs.nc_kind == NC_FORMAT_NETCDF4) {
snprintf(errmsg,sizeof(errmsg),"NcML output (-x) currently only permitted for netCDF classic model");
goto fail;
}
do_ncdumpx(ncid, path);
} else {
do_ncdump(ncid, path);
}
}
NC_CHECK( nc_close(ncid) );
}
if(path) {free(path); path = NULL;}
exit(EXIT_SUCCESS);
fail: /* ncstat failures */
path = (path?path:strdup("<unknown>"));
if(ncstat && strlen(errmsg) == 0)
snprintf(errmsg,sizeof(errmsg),"%s: %s", path, nc_strerror(ncstat));
if(strlen(errmsg) > 0)
error("%s: %s", path, errmsg);
if(path) free(path);
exit(EXIT_FAILURE);
}
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