netcdf-c/libdispatch/nclist.c
Dennis Heimbigner 11fe00ea05 Add filter support to NCZarr
Filter support has three goals:

1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled

Detailed usage directions are define in docs/filters.md.

For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.

This is a big change since filters affect many parts of the code.

In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.

### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.

### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.

### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-02 17:04:26 -06:00

295 lines
5.9 KiB
C

/* Copyright 2018, UCAR/Unidata and OPeNDAP, Inc.
See the COPYRIGHT file for more information. */
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "nclist.h"
#ifdef _WIN32
#define strcasecmp _stricmp
#endif
int nclistnull(void* e) {return e == NULL;}
#ifndef TRUE
#define TRUE 1
#endif
#ifndef FALSE
#define FALSE 0
#endif
#define DEFAULTALLOC 16
#define ALLOCINCR 16
NClist* nclistnew(void)
{
NClist* l;
/*
if(!ncinitialized) {
memset((void*)&ncDATANULL,0,sizeof(void*));
ncinitialized = 1;
}
*/
l = (NClist*)malloc(sizeof(NClist));
if(l) {
l->alloc=0;
l->length=0;
l->content=NULL;
}
return l;
}
int
nclistfree(NClist* l)
{
if(l) {
l->alloc = 0;
if(l->content != NULL) {free(l->content); l->content = NULL;}
free(l);
}
return TRUE;
}
/*
Free a list and its contents
*/
int
nclistfreeall(NClist* l)
{
nclistclearall(l);
return nclistfree(l);
}
/*
Free the contents of a list
*/
int
nclistclearall(NClist* l)
{
size_t i,len;
if(l == NULL) return TRUE;
len = l->length;
for(i=0;i<len;i++) {
void* value = l->content[i];
if(value != NULL) free(value);
}
nclistsetlength(l,0);
return TRUE;
}
int
nclistsetalloc(NClist* l, size_t sz)
{
void** newcontent = NULL;
if(l == NULL) return FALSE;
if(sz <= 0) {sz = (l->length?2*l->length:DEFAULTALLOC);}
if(l->alloc >= sz) {return TRUE;}
newcontent=(void**)calloc(sz,sizeof(void*));
if(newcontent != NULL && l->alloc > 0 && l->length > 0 && l->content != NULL) {
memcpy((void*)newcontent,(void*)l->content,sizeof(void*)*l->length);
}
if(l->content != NULL) free(l->content);
l->content=newcontent;
l->alloc=sz;
return TRUE;
}
int
nclistsetlength(NClist* l, size_t newlen)
{
if(l == NULL) return FALSE;
if(newlen > l->alloc && !nclistsetalloc(l,newlen)) return FALSE;
if(newlen > l->length) {
/* clear any extension */
memset(&l->content[l->length],0,(newlen - l->length)*sizeof(void*));
}
l->length = newlen;
return TRUE;
}
void*
nclistget(NClist* l, size_t index)
{
if(l == NULL || l->length == 0) return NULL;
if(index >= l->length) return NULL;
return l->content[index];
}
/* Insert at position i of l; will overwrite previous value;
guarantees alloc and length
*/
int
nclistset(NClist* l, size_t index, void* elem)
{
if(l == NULL) return FALSE;
if(!nclistsetalloc(l,index+1)) return FALSE;
if(index >= l->length) {
if(!nclistsetlength(l,index+1)) return FALSE;
}
l->content[index] = elem;
return TRUE;
}
/* Insert at position i of l; will push up elements i..|seq|. */
int
nclistinsert(NClist* l, size_t index, void* elem)
{
long i; /* do not make unsigned */
if(l == NULL) return FALSE;
if(index > l->length) return FALSE;
nclistsetalloc(l,0);
for(i=(long)l->length;i>index;i--) l->content[i] = l->content[i-1];
l->content[index] = elem;
l->length++;
return TRUE;
}
int
nclistpush(NClist* l, const void* elem)
{
if(l == NULL) return FALSE;
if(l->length >= l->alloc) nclistsetalloc(l,0);
l->content[l->length] = (void*)elem;
l->length++;
return TRUE;
}
void*
nclistpop(NClist* l)
{
if(l == NULL || l->length == 0) return NULL;
l->length--;
return l->content[l->length];
}
void*
nclisttop(NClist* l)
{
if(l == NULL || l->length == 0) return NULL;
return l->content[l->length - 1];
}
void*
nclistremove(NClist* l, size_t i)
{
size_t len;
void* elem;
if(l == NULL || (len=l->length) == 0) return NULL;
if(i >= len) return NULL;
elem = l->content[i];
for(i+=1;i<len;i++) l->content[i-1] = l->content[i];
l->length--;
return elem;
}
int
nclistcontains(NClist* l, void* elem)
{
size_t i;
for(i=0;i<nclistlength(l);i++) {
if(elem == nclistget(l,i)) return 1;
}
return 0;
}
/* Return 1/0 */
int
nclistmatch(NClist* l, const char* elem, int casesensitive)
{
size_t i;
for(i=0;i<nclistlength(l);i++) {
const char* candidate = (const char*)nclistget(l,i);
int match;
if(casesensitive)
match = strcmp(elem,candidate);
else
match = strcasecmp(elem,candidate);
if(match == 0) return 1;
}
return 0;
}
/* Remove element by value; only removes first encountered */
int
nclistelemremove(NClist* l, void* elem)
{
size_t len;
size_t i;
int found = 0;
if(l == NULL || (len=l->length) == 0) return 0;
for(i=0;i<nclistlength(l);i++) {
void* candidate = l->content[i];
if(elem == candidate) {
for(i+=1;i<len;i++) l->content[i-1] = l->content[i];
l->length--;
found = 1;
break;
}
}
return found;
}
/* Extends nclist to include a unique operator
which remove duplicate values; NULL values removed
return value is always 1.
*/
int
nclistunique(NClist* l)
{
size_t i,j,k,len;
void** content;
if(l == NULL || l->length == 0) return 1;
len = l->length;
content = l->content;
for(i=0;i<len;i++) {
for(j=i+1;j<len;j++) {
if(content[i] == content[j]) {
/* compress out jth element */
for(k=j+1;k<len;k++) content[k-1] = content[k];
len--;
}
}
}
l->length = len;
return 1;
}
/* Duplicate a list and if deep is true, assume the contents
are char** and duplicate those also */
NClist*
nclistclone(NClist* l, int deep)
{
NClist* clone = NULL;
if(l == NULL) goto done;
clone = nclistnew();
nclistsetalloc(clone,l->length+1); /* make room for final null */
if(!deep) {
nclistsetlength(clone,l->length);
memcpy((void*)clone->content,(void*)l->content,sizeof(void*)*l->length);
} else { /*deep*/
int i;
for(i=0;i<nclistlength(l);i++) {
char* dups = strdup(nclistget(l,i));
if(dups == NULL) {nclistfreeall(clone); clone = NULL; goto done;}
nclistpush(clone,dups);
}
}
clone->content[l->length] = (void*)0;
done:
return clone;
}
void*
nclistextract(NClist* l)
{
void* result = l->content;
l->alloc = 0;
l->length = 0;
l->content = NULL;
return result;
}