mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-12-03 02:32:04 +08:00
eab58732d8
Purpose: HDF5 now supports SZIP with no encoder. Description: SZIP can be configured to have both encoder and decoder or just to have the decoder. HDF5 can now query the configuration of any filter, and will throw errors if users try to write using a filter with encoding disabled. Solution: Added H5Zget_filter_info function, changed API for H5Pget_filter and H5P_get_filter_by_id. See SZIP RFC. Platforms tested: Copper (fortran, C++, parallel), Sleipnir (C++), Arabica (fortran, C++), Verbena (fortran, C++) Misc. update:
497 lines
13 KiB
C
497 lines
13 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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#include <stdlib.h>
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#include "h5repack.h"
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/*-------------------------------------------------------------------------
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* File: h5repack.c
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* Purpose: Public API functions
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*-------------------------------------------------------------------------
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*/
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static int check_options(pack_opt_t *options);
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/*-------------------------------------------------------------------------
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* Function: aux_initglb_filter
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*
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* Purpose: auxiliary function, initialize the options global filter
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*
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* Return: void
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*
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*-------------------------------------------------------------------------
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*/
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static void aux_initglb_filter(pack_opt_t *options)
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{
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int k;
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options->filter_g.filtn = -1;
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for ( k=0; k<CDVALUES; k++)
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options->filter_g.cd_values[k] = -1;
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}
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/*-------------------------------------------------------------------------
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* Function: h5repack
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*
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* Purpose: locate all high-level HDF5 objects in the file
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* and compress/chunk them using options
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*
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* Algorythm: 2 traversals are made to the file; the 1st builds a list of
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* the objects, the 2nd makes a copy of them, using the options;
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* the reason for the 1st traversal is to check for invalid
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* object name requests
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*
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* Return: 0, ok, -1, fail
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*
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* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
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*
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* Date: September, 22, 2003
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*
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*-------------------------------------------------------------------------
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*/
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int h5repack(const char* infile,
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const char* outfile,
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pack_opt_t *options)
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{
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/* check input */
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if (check_options(options)<0)
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return -1;
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/* check for objects in input that are in the file */
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if (check_objects(infile,options)<0)
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return -1;
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/* copy the objects */
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if (copy_objects(infile,outfile,options)<0)
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return -1;
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return 0;
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}
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/*-------------------------------------------------------------------------
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* Function: h5repack_init
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*
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* Purpose: initialize options
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*
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* Return: 0, ok, -1, fail
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*
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*-------------------------------------------------------------------------
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*/
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int h5repack_init (pack_opt_t *options,
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int verbose)
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{
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memset(options,0,sizeof(pack_opt_t));
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options->threshold = 1024;
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options->verbose = verbose;
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return (options_table_init(&(options->op_tbl)));
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}
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/*-------------------------------------------------------------------------
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* Function: h5repack_end
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*
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* Purpose: free options table
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*
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*-------------------------------------------------------------------------
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*/
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int h5repack_end (pack_opt_t *options)
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{
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return options_table_free(options->op_tbl);
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}
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/*-------------------------------------------------------------------------
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* Function: h5repack_addfilter
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*
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* Purpose: add a compression -f option to table
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* Example: -f dset:GZIP=6
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*
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* Return: 0, ok, -1, fail
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*
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*-------------------------------------------------------------------------
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*/
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int h5repack_addfilter(const char* str,
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pack_opt_t *options)
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{
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obj_list_t *obj_list=NULL; /*one object list for the -f and -c option entry */
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filter_info_t filt; /*filter info for the current -f option entry */
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int n_objs; /*number of objects in the current -f or -c option entry */
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if (options->all_filter==1){
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printf("Error: Invalid compression input: all option is present \
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with other objects <%s>\n",str);
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return -1;
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}
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/* parse the -f option */
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obj_list=parse_filter(str,&n_objs,&filt,options);
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if (obj_list==NULL)
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{
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return -1;
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}
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if (options->all_filter==1)
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{
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/* if we are compressing all set the global filter type */
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aux_initglb_filter(options);
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options->filter_g=filt;
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}
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if (options->all_filter==0)
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options_add_filter(obj_list,n_objs,filt,options->op_tbl);
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free(obj_list);
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return 0;
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}
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/*-------------------------------------------------------------------------
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* Function: h5repack_addlayout
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*
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* Purpose: add a layout option
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*
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* Return: 0, ok, -1, fail
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*
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*-------------------------------------------------------------------------
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*/
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int h5repack_addlayout(const char* str,
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pack_opt_t *options)
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{
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obj_list_t *obj_list=NULL; /*one object list for the -t and -c option entry */
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int n_objs; /*number of objects in the current -t or -c option entry */
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pack_info_t pack; /*info about layout to extract from parse */
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int j;
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init_packobject(&pack);
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if (options->all_layout==1){
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printf("Error: Invalid layout input: all option \
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is present with other objects <%s>\n",str);
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return -1;
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}
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/* parse the layout option */
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obj_list=parse_layout(str,&n_objs,&pack,options);
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if (obj_list==NULL)
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return -1;
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/* set global layout option */
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if (options->all_layout==1 )
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{
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options->layout_g=pack.layout;
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if (pack.layout==H5D_CHUNKED) {
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/* if we are chunking all set the global chunking type */
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options->chunk_g.rank=pack.chunk.rank;
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for (j = 0; j < pack.chunk.rank; j++)
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options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j];
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}
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}
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if (options->all_layout==0)
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options_add_layout(obj_list,
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n_objs,
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&pack,
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options->op_tbl);
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free(obj_list);
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return 0;
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}
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/*-------------------------------------------------------------------------
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* Function: check_options
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*
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* Purpose: print options, checks for invalid options
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*
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* Return: void, return -1 on error
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*
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* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
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*
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* Date: September, 22, 2003
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*
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*-------------------------------------------------------------------------
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*/
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static int check_options(pack_opt_t *options)
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{
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int i, k, j, has_cp=0, has_ck=0;
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unsigned szip_options_mask=H5_SZIP_NN_OPTION_MASK;
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unsigned szip_pixels_per_block;
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/*-------------------------------------------------------------------------
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* objects to layout
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*-------------------------------------------------------------------------
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*/
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if (options->verbose)
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{
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printf("\n");
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printf("Objects to modify are...\n");
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if (options->all_layout==1) {
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printf("\tApply layout to all\n ");
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if (H5D_CHUNKED==options->layout_g) {
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printf("with dimension [");
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for ( j = 0; j < options->chunk_g.rank; j++)
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printf("%d ",(int)options->chunk_g.chunk_lengths[j]);
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printf("]\n");
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}
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}
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}/* verbose */
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for ( i = 0; i < options->op_tbl->nelems; i++)
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{
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char* name=options->op_tbl->objs[i].path;
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if (options->op_tbl->objs[i].chunk.rank>0)
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{
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if (options->verbose){
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printf("\t<%s> with chunk size ",name);
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for ( k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
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printf("%d ",(int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
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printf("\n");
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}
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has_ck=1;
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}
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else if (options->op_tbl->objs[i].chunk.rank==-2)
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{
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if (options->verbose)
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printf("\t%s %s\n",name,"NONE");
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has_ck=1;
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}
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}
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if (options->all_layout==1 && has_ck){
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printf("Error: Invalid chunking input: all option\
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is present with other objects\n");
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return -1;
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}
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/*-------------------------------------------------------------------------
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* objects to compress/uncompress
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*-------------------------------------------------------------------------
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*/
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if (options->verbose)
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{
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printf("Objects to filter are...\n");
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if (options->all_filter==1)
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{
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H5Z_filter_t filtn=options->filter_g.filtn;
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switch (filtn)
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{
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case H5Z_FILTER_NONE:
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printf("\tUncompress all %s\n",get_sfilter(filtn));
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break;
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case H5Z_FILTER_SZIP:
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printf("\tCompress all with %s compression\n",get_sfilter(filtn));
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break;
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case H5Z_FILTER_DEFLATE:
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printf("\tCompress all with %s compression, parameter %d\n",
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get_sfilter(filtn),
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options->filter_g.cd_values[0]);
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break;
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};
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}
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} /* verbose */
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for ( i = 0; i < options->op_tbl->nelems; i++)
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{
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pack_info_t pack = options->op_tbl->objs[i];
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char* name = pack.path;
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for ( j=0; j<pack.nfilters; j++)
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{
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if (options->verbose)
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{
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printf("\t<%s> with %s filter",
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name,
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get_sfilter(pack.filter[j].filtn));
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}
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has_cp=1;
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/*check for invalid combination of options */
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switch (pack.filter[j].filtn)
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{
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default:
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break;
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case H5Z_FILTER_SZIP:
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szip_pixels_per_block=pack.filter[j].cd_values[0];
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/* check szip parameters */
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if ( pack.chunk.rank!=-1 /*
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it means a layout was not input, so there is no
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case to try to check it
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*/
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&& check_szip(0, /* do not test size */
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pack.chunk.rank,
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pack.chunk.chunk_lengths,
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szip_options_mask,
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&szip_pixels_per_block,
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options)==0)
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{
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/* Return: 1=can apply the filter
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0=cannot apply the filter
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Reset this object filter info
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*/
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options->op_tbl->objs[i].filter[j].filtn=-1;
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options->op_tbl->objs[i].chunk.rank=-1;
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printf("\tObject <%s> cannot be filtered\n",name);
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}
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break;
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} /* switch */
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} /* j */
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} /* i */
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if (options->all_filter==1 && has_cp){
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printf("Error: Invalid compression input: all option\
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is present with other objects\n");
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return -1;
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}
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return 0;
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}
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/*-------------------------------------------------------------------------
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* Function: read_info
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*
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* Purpose: read comp and chunk options from file
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*
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* Return: void, exit on error
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*
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* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
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*
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* Date: September, 22, 2003
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*
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*-------------------------------------------------------------------------
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*/
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void read_info(const char *filename,
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pack_opt_t *options)
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{
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char stype[10];
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char comp_info[1024];
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FILE *fp;
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char c;
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int i, rc=1;
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char *srcdir = getenv("srcdir"); /* the source directory */
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char data_file[512]=""; /* buffer to hold name of existing file */
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/* compose the name of the file to open, using the srcdir, if appropriate */
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if (srcdir){
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strcpy(data_file,srcdir);
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strcat(data_file,"/");
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}
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strcat(data_file,filename);
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if ((fp = fopen(data_file, "r")) == (FILE *)NULL) {
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printf( "Cannot open options file %s", filename);
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exit(1);
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}
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/* cycle until end of file reached */
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while( 1 )
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{
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rc=fscanf(fp, "%s", stype);
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if (rc==-1)
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break;
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/*-------------------------------------------------------------------------
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* filter
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*-------------------------------------------------------------------------
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*/
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if (strcmp(stype,"-f") == 0) {
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/* find begining of info */
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i=0; c='0';
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while( c!=' ' )
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{
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fscanf(fp, "%c", &c);
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if (feof(fp)) break;
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}
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c='0';
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/* go until end */
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while( c!=' ' )
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{
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fscanf(fp, "%c", &c);
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comp_info[i]=c;
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i++;
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if (feof(fp)) break;
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if (c==10 /*eol*/) break;
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}
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comp_info[i-1]='\0'; /*cut the last " */
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if (h5repack_addfilter(comp_info,options)==-1){
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printf( "Could not add compression option. Exiting\n");
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exit(1);
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}
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}
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/*-------------------------------------------------------------------------
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* layout
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*-------------------------------------------------------------------------
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*/
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else if (strcmp(stype,"-l") == 0) {
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/* find begining of info */
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i=0; c='0';
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while( c!=' ' )
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{
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fscanf(fp, "%c", &c);
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if (feof(fp)) break;
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}
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c='0';
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/* go until end */
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while( c!=' ' )
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{
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fscanf(fp, "%c", &c);
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comp_info[i]=c;
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i++;
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if (feof(fp)) break;
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if (c==10 /*eol*/) break;
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}
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comp_info[i-1]='\0'; /*cut the last " */
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if (h5repack_addlayout(comp_info,options)==-1){
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printf( "Could not add chunck option. Exiting\n");
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exit(1);
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}
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}
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/*-------------------------------------------------------------------------
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* not valid
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*-------------------------------------------------------------------------
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*/
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else {
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printf( "Bad file format for %s", filename);
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exit(1);
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}
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}
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fclose(fp);
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return;
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}
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