netcdf-c/ncgen/util.c
Dennis Heimbigner 68a98f6e81 Fix ncgen handling of big data sections
The current ncgen does not properly handle very large
data sections. Apparently this is very uncommon because
it was only discovered in testing the new zarr code.

The fix required a new approach to processing data sections.
Unfortunately, the resulting ncgen is slower than before
but at least it is, I think, now correct.

The added test cases are in libnczarr, and so will
not show up until that is incorporated into master.

Note also that fortran code generation changed, but
has not been tested here.

Misc. Changes
1. Cleanup error handling in ncgen -lc and -lb output
2. Cleanup Makefiles for ncgen to remove unused code
3. Added a program, ncgen/ncdumpchunks, to print
   the data for a .nc file on a per-chunk format.
4. Made the XGetOpt change in PR https://github.com/Unidata/netcdf-c/pull/1694
   for ncdump/ncvalidator
2020-05-14 11:20:46 -06:00

671 lines
14 KiB
C

/*********************************************************************
* Copyright 2018, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
* $Header: /upc/share/CVS/netcdf-3/ncgen/util.c,v 1.4 2010/04/14 22:04:59 dmh Exp $
*********************************************************************/
#include "includes.h"
/* Track primitive symbol instances (initialized in ncgen.y) */
Symbol* primsymbols[PRIMNO];
char*
append(const char* s1, const char* s2)
{
int len = (s1?strlen(s1):0)+(s2?strlen(s2):0);
char* result = (char*)ecalloc(len+1);
result[0] = '\0';
if(s1) strcat(result,s1);
if(s2) strcat(result,s2);
return result;
}
unsigned int
chartohex(char c)
{
switch (c) {
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
return (c - '0');
case 'A': case 'B': case 'C':
case 'D': case 'E': case 'F':
return (c - 'A') + 0x0a;
case 'a': case 'b': case 'c':
case 'd': case 'e': case 'f':
return (c - 'a') + 0x0a;
}
return 0;
}
/*
* For generated Fortran, change 'e' to 'd' in exponent of double precision
* constants.
*/
void
expe2d(
char *cp) /* string containing double constant */
{
char *expchar = strrchr(cp,'e');
if (expchar) {
*expchar = 'd';
}
}
/* Returns non-zero if n is a power of 2, 0 otherwise */
int
pow2(
int n)
{
int m = n;
int p = 1;
while (m > 0) {
m /= 2;
p *= 2;
}
return p == 2*n;
}
/*
* 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.
*/
void
tztrim(
char *ss /* returned string representing dd */
)
{
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;
}
static void
clearSpecialdata(Specialdata* data)
{
if(data == NULL) return;
reclaimdatalist(data->_Fillvalue);
if(data->_ChunkSizes)
efree(data->_ChunkSizes);
if(data->_Filters) {
int i;
for(i=0;i<data->nfilters;i++) {
NC4_Filterspec* f = (NC4_Filterspec*)data->_Filters[i];
efree(f->params);
efree(f);
}
efree(data->_Filters);
}
}
void
freeSymbol(Symbol* sym)
{
if(sym == NULL) return;
switch (sym->objectclass) {
case NC_VAR:
clearSpecialdata(&sym->var.special);
listfree(sym->var.attributes);
break;
case NC_TYPE:
if(sym->typ.econst)
reclaimconstant(sym->typ.econst);
if(sym->typ._Fillvalue)
reclaimdatalist(sym->typ._Fillvalue);
break;
case NC_GRP:
if(sym->file.filename)
efree(sym->file.filename);
break;
default: break;
}
/* Universal */
if(sym->name) efree(sym->name);
if(sym->fqn) efree(sym->fqn);
listfree(sym->prefix);
if(sym->data)
reclaimdatalist(sym->data);
listfree(sym->subnodes);
efree(sym);
}
char* nctypenames[17] = {
"NC_NAT",
"NC_BYTE", "NC_CHAR", "NC_SHORT", "NC_INT",
"NC_FLOAT", "NC_DOUBLE",
"NC_UBYTE", "NC_USHORT", "NC_UINT",
"NC_INT64", "NC_UINT64",
"NC_STRING",
"NC_VLEN", "NC_OPAQUE", "NC_ENUM", "NC_COMPOUND"
};
char* nctypenamesextend[9] = {
"NC_GRP", "NC_DIM", "NC_VAR", "NC_ATT", "NC_TYPE",
"NC_ECONST","NC_FIELD", "NC_ARRAY","NC_PRIM"
};
char*
nctypename(nc_type nctype)
{
char* s;
if(nctype >= NC_NAT && nctype <= NC_COMPOUND)
return nctypenames[nctype];
if(nctype >= NC_GRP && nctype <= NC_PRIM)
return nctypenamesextend[(nctype - NC_GRP)];
if(nctype == NC_FILLVALUE) return "NC_FILL";
if(nctype == NC_NIL) return "NC_NIL";
s = poolalloc(128);
sprintf(s,"NC_<%d>",nctype);
return s;
}
/* These are the augmented NC_ values (0 based from NC_GRP)*/
char* ncclassnames[9] = {
"NC_GRP", "NC_DIM", "NC_VAR", "NC_ATT",
"NC_TYP", "NC_ECONST", "NC_FIELD", "NC_ARRAY",
"NC_PRIM"
};
char*
ncclassname(nc_class ncc)
{
char* s;
if(ncc >= NC_NAT && ncc <= NC_COMPOUND)
return nctypename((nc_type)ncc);
if(ncc == NC_FILLVALUE) return "NC_FILL";
if(ncc >= NC_GRP && ncc <= NC_PRIM)
return ncclassnames[ncc - NC_GRP];
s = poolalloc(128);
sprintf(s,"NC_<%d>",ncc);
return s;
}
int ncsizes[17] = {
0,
1,1,2,4,
4,8,
1,2,4,
8,8,
sizeof(char*),
sizeof(nc_vlen_t),
0,0,0
};
int
ncsize(nc_type nctype)
{
if(nctype >= NC_NAT && nctype <= NC_COMPOUND)
return ncsizes[nctype];
return 0;
}
int
hasunlimited(Dimset* dimset)
{
int i;
for(i=0;i<dimset->ndims;i++) {
Symbol* dim = dimset->dimsyms[i];
if(dim->dim.declsize == NC_UNLIMITED) return 1;
}
return 0;
}
/* return 1 if first dimension is unlimited*/
int
isunlimited0(Dimset* dimset)
{
return (dimset->ndims > 0 && dimset->dimsyms[0]->dim.declsize == NC_UNLIMITED);
}
/* True only if dim[0] is unlimited all rest are bounded*/
/* or all are bounded*/
int
classicunlimited(Dimset* dimset)
{
int i;
int last = -1;
for(i=0;i<dimset->ndims;i++) {
Symbol* dim = dimset->dimsyms[i];
if(dim->dim.declsize == NC_UNLIMITED) last = i;
}
return (last < 1);
}
/* True only iff no dimension is unlimited*/
int
isbounded(Dimset* dimset)
{
int i;
for(i=0;i<dimset->ndims;i++) {
Symbol* dim = dimset->dimsyms[i];
if(dim->dim.declsize == NC_UNLIMITED) return 0;
}
return 1;
}
int
signedtype(nc_type nctype)
{
switch (nctype) {
case NC_BYTE:
case NC_SHORT:
case NC_INT:
case NC_INT64:
return nctype;
case NC_UBYTE: return NC_BYTE;
case NC_USHORT: return NC_SHORT;
case NC_UINT: return NC_INT;
case NC_UINT64: return NC_INT64;
default: break;
}
return nctype;
}
int
unsignedtype(nc_type nctype)
{
switch (nctype) {
case NC_UBYTE:
case NC_USHORT:
case NC_UINT:
case NC_UINT64:
return nctype;
case NC_BYTE: return NC_UBYTE;
case NC_SHORT: return NC_USHORT;
case NC_INT: return NC_UINT;
case NC_INT64: return NC_UINT64;
default: break;
}
return nctype;
}
int
isinttype(nc_type nctype)
{
return (nctype != NC_CHAR)
&& ((nctype >= NC_BYTE && nctype <= NC_INT)
|| (nctype >= NC_UBYTE && nctype <= NC_UINT64));
}
int
isuinttype(nc_type t)
{
return isinttype(t)
&& t >= NC_UBYTE
&& t <= NC_UINT64
&& t != NC_INT64;
}
int
isfloattype(nc_type nctype)
{
return (nctype == NC_FLOAT || nctype <= NC_DOUBLE);
}
int
isclassicprim(nc_type nctype)
{
return (nctype >= NC_BYTE && nctype <= NC_DOUBLE)
;
}
int
isclassicprimplus(nc_type nctype)
{
return (nctype >= NC_BYTE && nctype <= NC_DOUBLE)
|| (nctype == NC_STRING)
;
}
int
isprim(nc_type nctype)
{
return (nctype >= NC_BYTE && nctype <= NC_STRING)
;
}
int
isprimplus(nc_type nctype)
{
return (nctype >= NC_BYTE && nctype <= NC_STRING)
|| (nctype == NC_ECONST)
|| (nctype == NC_OPAQUE)
;
}
void
collectpath(Symbol* grp, List* grpstack)
{
while(grp != NULL) {
listpush(grpstack,(void*)grp);
grp = grp->container;
}
}
#ifdef USE_NETCDF4
/* Result is pool'd*/
char*
prefixtostring(List* prefix, char* separator)
{
int slen=0;
int plen;
int i;
char* result;
if(prefix == NULL) return pooldup("");
plen = prefixlen(prefix);
if(plen == 0) { /* root prefix*/
slen=0;
/* slen += strlen(separator);*/
slen++; /* for null terminator*/
result = poolalloc(slen);
result[0] = '\0';
/*strcat(result,separator);*/
} else {
for(i=0;i<plen;i++) {
Symbol* sym = (Symbol*)listget(prefix,i);
slen += (strlen(separator)+strlen(sym->name));
}
slen++; /* for null terminator*/
result = poolalloc(slen);
result[0] = '\0';
for(i=0;i<plen;i++) {
Symbol* sym = (Symbol*)listget(prefix,i);
strcat(result,separator);
strcat(result,sym->name); /* append "/<prefix[i]>"*/
}
}
return result;
}
#endif
/* Result is pool'd*/
char*
fullname(Symbol* sym)
{
#ifdef USE_NETCDF4
char* s1;
char* result;
char* prefix;
prefix = prefixtostring(sym->prefix,PATHSEPARATOR);
s1 = poolcat(prefix,PATHSEPARATOR);
result = poolcat(s1,sym->name);
return result;
#else
return nulldup(sym->name);
#endif
}
int
prefixeq(List* x1, List* x2)
{
Symbol** l1;
Symbol** l2;
int len,i;
if((len=listlength(x1)) != listlength(x2)) return 0;
l1=(Symbol**)listcontents(x1);
l2=(Symbol**)listcontents(x2);
for(i=0;i<len;i++) {
if(strcmp(l1[i]->name,l2[i]->name) != 0) return 0;
}
return 1;
}
List*
prefixdup(List* prefix)
{
List* dupseq;
int i;
if(prefix == NULL) return listnew();
dupseq = listnew();
listsetalloc(dupseq,listlength(prefix));
for(i=0;i<listlength(prefix);i++) listpush(dupseq,listget(prefix,i));
return dupseq;
}
/*
Many of the generate routines need to construct
heap strings for short periods. Remembering to
free such space is error prone, so provide a
pseudo-GC to handle these short term requests.
The idea is to have a fixed size pool
tracking malloc requests and automatically
releasing when the pool gets full.
*/
/* Max number of allocated pool items*/
#define POOLMAX 100
static char* pool[POOLMAX];
static int poolindex = -1;
#define POOL_DEFAULT 256
char*
poolalloc(size_t length)
{
if(poolindex == -1) { /* initialize*/
memset((void*)pool,0,sizeof(pool));
poolindex = 0;
}
if(poolindex == POOLMAX) poolindex=0;
if(length == 0) length = POOL_DEFAULT;
if(pool[poolindex] != NULL) efree(pool[poolindex]);
pool[poolindex] = (char*)ecalloc(length);
return pool[poolindex++];
}
char*
pooldup(const char* s)
{
char* sdup = poolalloc(strlen(s)+1);
strncpy(sdup,s,(strlen(s)+1));
return sdup;
}
char*
poolcat(const char* s1, const char* s2)
{
int len1, len2;
char* cat;
if(s1 == NULL && s2 == NULL) return NULL;
len1 = (s1?strlen(s1):0);
len2 = (s2?strlen(s2):0);
cat = poolalloc(len1+len2+1);
cat[0] = '\0';
if(s1 != NULL) strcat(cat,s1);
if(s2 != NULL) strcat(cat,s2);
return cat;
}
/* Result is malloc'd*/
unsigned char*
makebytestring(char* s, size_t* lenp)
{
unsigned char* bytes;
unsigned char* b;
size_t slen = strlen(s); /* # nibbles */
size_t blen = slen/2; /* # bytes */
int i;
ASSERT((slen%2) == 0);
ASSERT(blen > 0);
bytes = (unsigned char*)ecalloc(blen);
b = bytes;
for(i=0;i<slen;i+=2) {
unsigned int digit1 = chartohex(*s++);
unsigned int digit2 = chartohex(*s++);
unsigned int byte = (digit1 << 4) | digit2;
*b++ = byte;
}
if(lenp) *lenp = blen;
return bytes;
}
int
getpadding(int offset, int alignment)
{
int rem = (alignment==0?0:(offset % alignment));
int pad = (rem==0?0:(alignment - rem));
return pad;
}
static void
reclaimSymbols(void)
{
int i;
for(i=0;i<listlength(symlist);i++) {
Symbol* sym = listget(symlist,i);
freeSymbol(sym);
}
}
void
cleanup()
{
reclaimSymbols();
listfree(symlist);
listfree(grpdefs);
listfree(dimdefs);
listfree(attdefs);
listfree(gattdefs);
listfree(xattdefs);
listfree(typdefs);
listfree(vardefs);
filldatalist->readonly = 0;
freedatalist(filldatalist);
}
/* compute the total n-dimensional size as 1 long array;
if stop == 0, then stop = dimset->ndims.
*/
size_t
crossproduct(Dimset* dimset, int start, int stop)
{
size_t totalsize = 1;
int i;
for(i=start;i<stop;i++) {
totalsize = totalsize * dimset->dimsyms[i]->dim.declsize;
}
return totalsize;
}
/* Do the "complement" of crossproduct;
compute the total n-dimensional size of an array
starting at 0 thru the 'last' array index.
stop if we encounter an unlimited dimension
*/
size_t
prefixarraylength(Dimset* dimset, int last)
{
return crossproduct(dimset,0,last+1);
}
#ifdef USE_HDF5
extern int H5Eprint1(FILE * stream);
#endif
void
check_err(const int stat, const int line, const char* file, const char* func)
{
check_err2(stat,-1,line,file,func);
}
void check_err2(const int stat, const int cdlline, const int line, const char* file, const char* func)
{
if (stat != NC_NOERR) {
if(cdlline >= 0)
fprintf(stderr, "ncgen: cdl line %d; %s\n", cdlline, nc_strerror(stat));
else
fprintf(stderr, "ncgen: %s\n", nc_strerror(stat));
fprintf(stderr, "\t(%s:%s:%d)\n", file,func,line);
#ifdef USE_HDF5
H5Eprint1(stderr);
#endif
fflush(stderr);
finalize_netcdf(1);
}
}
/**
Find the index of the first unlimited
dimension at or after 'start'.
If no unlimited exists, return |dimset|
*/
int
findunlimited(Dimset* dimset, int start)
{
for(;start<dimset->ndims;start++) {
if(dimset->dimsyms[start]->dim.isunlimited)
return start;
}
return dimset->ndims;
}
/**
Find the index of the last unlimited
dimension.
If no unlimited exists, return |dimset|
*/
int
findlastunlimited(Dimset* dimset)
{
int i;
for(i=dimset->ndims-1;i>=0;i--) {
if(dimset->dimsyms[i]->dim.isunlimited)
return i;
}
return dimset->ndims;
}
/**
Count the number of unlimited dimensions.
*/
int
countunlimited(Dimset* dimset)
{
int i, count;
for(count=0,i=dimset->ndims-1;i>=0;i--) {
if(dimset->dimsyms[i]->dim.isunlimited)
count++;
}
return count;
}
/* Return standard format string */
const char *
kind_string(int kind)
{
switch (kind) {
case 1: return "classic";
case 2: return "64-bit offset";
case 3: return "netCDF-4";
case 4: return "netCDF-4 classic model";
default:
derror("Unknown format index: %d\n",kind);
}
return NULL;
}