netcdf-c/libnczarr/zclose.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

297 lines
7.5 KiB
C

/*********************************************************************
* Copyright 1993, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
#include "zincludes.h"
#include "zfilter.h"
/* Forward */
static int zclose_group(NC_GRP_INFO_T*);
static int zclose_gatts(NC_GRP_INFO_T*);
static int zclose_vars(NC_GRP_INFO_T*);
static int zclose_dims(NC_GRP_INFO_T*);
static int zclose_types(NC_GRP_INFO_T*);
static int zclose_type(NC_TYPE_INFO_T* type);
static int zwrite_vars(NC_GRP_INFO_T *grp);
/**************************************************/
/**
* @internal This function will recurse through an open ZARR file and
* release resources. All ZARR annotations reclaimed
*
* @param file Pointer to ZARR file info struct.
* @param abort True if this is an abort.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENCZARR could not close the file.
* @author Dennis Heimbigner
*/
int
ncz_close_file(NC_FILE_INFO_T* file, int abort)
{
int stat = NC_NOERR;
NCZ_FILE_INFO_T* zinfo = NULL;
ZTRACE(2,"file=%s abort=%d",file->hdr.name,abort);
if(!abort) {
/* Flush | create all chunks for all vars */
if((stat=zwrite_vars(file->root_grp))) goto done;
}
/* Internal close to reclaim zarr annotations */
if((stat = zclose_group(file->root_grp)))
goto done;
zinfo = file->format_file_info;
if((stat = nczmap_close(zinfo->map,(abort && zinfo->created)?1:0)))
goto done;
NCZ_freestringvec(0,zinfo->envv_controls);
NC_authfree(zinfo->auth);
nullfree(zinfo);
done:
return ZUNTRACE(stat);
}
/**************************************************/
/**
* @internal Recursively free zarr annotations for a group (and everything
* it contains).
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
zclose_group(NC_GRP_INFO_T *grp)
{
int stat = NC_NOERR;
NCZ_GRP_INFO_T* zgrp;
int i;
assert(grp && grp->format_grp_info != NULL);
LOG((3, "%s: grp->name %s", __func__, grp->hdr.name));
/* Recursively call this function for each child, if any, stopping
* if there is an error. */
for(i=0; i<ncindexsize(grp->children); i++) {
if ((stat = zclose_group((NC_GRP_INFO_T*)ncindexith(grp->children,i))))
goto done;
}
/* Close resources associated with global attributes. */
if ((stat = zclose_gatts(grp)))
goto done;
/* Close resources associated with vars. */
if ((stat = zclose_vars(grp)))
goto done;
/* Close resources associated with dims. */
if ((stat = zclose_dims(grp)))
goto done;
/* Close resources associated with types. */
if ((stat = zclose_types(grp)))
goto done;
/* Close the zgroup. */
zgrp = grp->format_grp_info;
LOG((4, "%s: closing group %s", __func__, grp->hdr.name));
nullfree(zgrp);
grp->format_grp_info = NULL; /* avoid memory errors */
done:
return stat;
}
/**
* @internal Close resources for global atts in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
zclose_gatts(NC_GRP_INFO_T* grp)
{
int stat = NC_NOERR;
NC_ATT_INFO_T *att;
int a;
for(a = 0; a < ncindexsize(grp->att); a++) {
NCZ_ATT_INFO_T* zatt = NULL;
att = (NC_ATT_INFO_T* )ncindexith(grp->att, a);
assert(att && att->format_att_info != NULL);
zatt = att->format_att_info;
nullfree(zatt);
att->format_att_info = NULL; /* avoid memory errors */
}
return stat;
}
/**
* @internal Close resources for vars in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
zclose_vars(NC_GRP_INFO_T* grp)
{
int stat = NC_NOERR;
NC_VAR_INFO_T* var;
NCZ_VAR_INFO_T* zvar;
NC_ATT_INFO_T* att;
int a, i;
for(i = 0; i < ncindexsize(grp->vars); i++) {
var = (NC_VAR_INFO_T*)ncindexith(grp->vars, i);
assert(var && var->format_var_info);
zvar = var->format_var_info;;
for(a = 0; a < ncindexsize(var->att); a++) {
NCZ_ATT_INFO_T* zatt;
att = (NC_ATT_INFO_T*)ncindexith(var->att, a);
assert(att && att->format_att_info);
zatt = att->format_att_info;
nullfree(zatt);
att->format_att_info = NULL; /* avoid memory errors */
}
/* Reclaim filters */
if(var->filters != NULL) {
(void)NCZ_filter_freelist(var);
}
var->filters = NULL;
/* Reclaim the type */
(void)zclose_type(var->type_info);
NCZ_free_chunk_cache(zvar->cache);
/* reclaim xarray */
nclistfreeall(zvar->xarray);
nullfree(zvar);
var->format_var_info = NULL; /* avoid memory errors */
}
return stat;
}
/**
* @internal Close resources for dims in a group.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
zclose_dims(NC_GRP_INFO_T* grp)
{
int stat = NC_NOERR;
NC_DIM_INFO_T* dim;
int i;
for(i = 0; i < ncindexsize(grp->dim); i++) {
NCZ_DIM_INFO_T* zdim;
dim = (NC_DIM_INFO_T*)ncindexith(grp->dim, i);
assert(dim && dim->format_dim_info);
zdim = dim->format_dim_info;
nullfree(zdim);
dim->format_dim_info = NULL; /* avoid memory errors */
}
return stat;
}
/**
* @internal Close resources for a single type. Set values to
* 0 after closing types. Because of type reference counters, these
* closes can be called multiple times.
*
* @param type Pointer to type struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
zclose_type(NC_TYPE_INFO_T* type)
{
int stat = NC_NOERR;
NCZ_TYPE_INFO_T* ztype;
assert(type && type->format_type_info != NULL);
/* Get Zarr-specific type info. */
ztype = type->format_type_info;
nullfree(ztype);
type->format_type_info = NULL; /* avoid memory errors */
return stat;
}
/**
* @internal Close resources for types in a group. Set values to
* 0 after closing types. Because of type reference counters, these
* closes can be called multiple times.
* Warning: note that atomic types are not covered here; this
* is only for user-defined types.
*
* @param grp Pointer to group info struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
zclose_types(NC_GRP_INFO_T* grp)
{
int stat = NC_NOERR;
int i;
NC_TYPE_INFO_T* type;
for(i = 0; i < ncindexsize(grp->type); i++)
{
type = (NC_TYPE_INFO_T*)ncindexith(grp->type, i);
if((stat = zclose_type(type))) goto done;
}
done:
return stat;
}
/**
* @internal Recursively flush/create all data for all vars.
*
* @param grp Pointer to group info struct whose vars need to be written
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
zwrite_vars(NC_GRP_INFO_T *grp)
{
int stat = NC_NOERR;
int i;
assert(grp && grp->format_grp_info != NULL);
LOG((3, "%s: grp->name %s", __func__, grp->hdr.name));
/* Write all vars for this group breadth first */
for(i = 0; i < ncindexsize(grp->vars); i++) {
NC_VAR_INFO_T* var = (NC_VAR_INFO_T*)ncindexith(grp->vars, i);
if((stat = ncz_write_var(var))) goto done;
}
/* Recursively call this function for each child group, if any, stopping
* if there is an error. */
for(i=0; i<ncindexsize(grp->children); i++) {
if ((stat = zwrite_vars((NC_GRP_INFO_T*)ncindexith(grp->children,i))))
goto done;
}
done:
return stat;
}