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https://github.com/HDFGroup/hdf5.git
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931efcb5eb
1) new function for tools library 2) new test script for h5repack Description: 1) currently all the tools (h5dump, h5diff, etc) do not check if a filter is available for reading some dataset that might have a filter not available on the current configuration (the behaviour of the tools until now was to trigger a library error, saying that the dataset cannot be read due to the lack of the filter) Solution: 1) added a new function h5tools_canreadf that checks if a dataset can be read depending on the availability of filters. this function was added in calls for h5diff and h5repack. instead of triggering the library error, a message is printed, saying that the dataset cannot be read (the print is optional, it is on on verbose mode) 2) added a shell script that tests the commannd line tool behaviour of h5repack the script does a series of runs of h5repack with several options on the same file (this file test4.h5 was added to the testfiles dir). then, it runs the h5diff tool, with the input and output files , in each run. the goal of the test is also to check item 1) . the binary file was saved with filters that might not be available on other configurations Platforms tested: linux (all filters enabled) linux (some filters disabled) solaris (some filters disabled) AIX (some filters disabled) windows (all filters on and off ) Misc. update:
347 lines
11 KiB
C
347 lines
11 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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#ifndef H5REPACK_H__
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#define H5REPACK_H__
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#include "hdf5.h"
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#include "h5trav.h"
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#include "h5diff.h"
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#include "h5tools.h"
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#if 0
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#define H5_REPACK_DEBUG
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#endif
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#define H5FOPENERROR "unable to open file"
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#define PFORMAT "%-7s %-7s %-7s\n" /*chunk info, compression info, name*/
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#define PFORMAT1 "%-7s %-7s %-7s" /*chunk info, compression info, name*/
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#define MAX_NC_NAME 256 /* max length of a name */
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#define MAX_VAR_DIMS 32 /* max per variable dimensions */
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/*-------------------------------------------------------------------------
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* data structures for command line options
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*-------------------------------------------------------------------------
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*/
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/* a list of names */
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typedef struct {
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char obj[MAX_NC_NAME];
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} obj_list_t;
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/*
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the type of filter and additional parameter
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type can be one of the filters
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H5Z_FILTER_NONE 0, uncompress if compressed
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H5Z_FILTER_DEFLATE 1 , deflation like gzip
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H5Z_FILTER_SHUFFLE 2 , shuffle the data
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H5Z_FILTER_FLETCHER32 3 , letcher32 checksum of EDC
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H5Z_FILTER_SZIP 4 , szip compression
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*/
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#define CDVALUES 2
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typedef struct {
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H5Z_filter_t filtn; /* filter identification number */
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int cd_values[CDVALUES]; /* filter client data values */
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} filter_info_t;
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/* chunk lengths along each dimension and rank */
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typedef struct {
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hsize_t chunk_lengths[MAX_VAR_DIMS];
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int rank;
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} chunk_info_t;
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/* we currently define a maximum value for the filters array,
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that corresponds to the current library filters */
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#define H5_REPACK_MAX_NFILTERS 4
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/* information for one object, contains PATH, CHUNK info and FILTER info */
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typedef struct {
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char path[MAX_NC_NAME]; /* name of object */
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filter_info_t filter[H5_REPACK_MAX_NFILTERS]; /* filter array */
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int nfilters; /* current number of filters */
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H5D_layout_t layout; /* layout information */
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chunk_info_t chunk; /* chunk information */
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hid_t refobj_id; /* object ID, references */
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} pack_info_t;
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/* store a table of all objects */
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typedef struct {
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int size;
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int nelems;
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pack_info_t *objs;
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} pack_opttbl_t;
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/*-------------------------------------------------------------------------
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* command line options
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*-------------------------------------------------------------------------
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*/
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/* all the above, ready to go to the hrepack call */
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typedef struct {
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pack_opttbl_t *op_tbl; /*table with all -c and -f options */
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int all_layout; /*apply the layout to all objects */
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int all_filter; /*apply the filter to all objects */
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filter_info_t filter_g; /*global filter INFO for the ALL case */
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chunk_info_t chunk_g; /*global chunk INFO for the ALL case */
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H5D_layout_t layout_g; /*global layout information for the ALL case */
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int verbose; /*verbose mode */
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int threshold; /*minimum size to compress, in bytes */
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} pack_opt_t;
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/*-------------------------------------------------------------------------
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* public functions
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*-------------------------------------------------------------------------
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*/
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#ifdef __cplusplus
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extern "C" {
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#endif
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int h5repack (const char* infile, const char* outfile, pack_opt_t *options);
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int h5repack_addfilter (const char* str, pack_opt_t *options);
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int h5repack_addlayout (const char* str, pack_opt_t *options);
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int h5repack_init (pack_opt_t *options, int verbose);
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int h5repack_end (pack_opt_t *options);
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int h5repack_verify (const char *fname,pack_opt_t *options);
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int h5repack_cmpdcpl (const char *fname1,
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const char *fname2);
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#ifdef __cplusplus
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}
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#endif
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/*-------------------------------------------------------------------------
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* private functions
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*-------------------------------------------------------------------------
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*/
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int check_objects(const char* fname,
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pack_opt_t *options);
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int copy_objects(const char* fnamein,
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const char* fnameout,
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pack_opt_t *options);
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void print_objlist(const char *filename,
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int nobjects,
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trav_info_t *travi );
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int do_copy_objects(hid_t fidin,
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hid_t fidout,
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trav_table_t *travt,
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pack_opt_t *options);
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int copy_attr(hid_t loc_in,
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hid_t loc_out,
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pack_opt_t *options
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);
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int do_copy_refobjs(hid_t fidin,
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hid_t fidout,
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trav_table_t *travt,
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pack_opt_t *options); /* repack options */
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void read_info(const char *filename,pack_opt_t *options);
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void init_packobject(pack_info_t *obj);
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int print_filters(hid_t dcpl_id);
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/*-------------------------------------------------------------------------
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* filters
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*-------------------------------------------------------------------------
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*/
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int filter_this(const char* name,
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pack_opt_t *options,
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pack_info_t *pack); /* info about object to filter */
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int apply_filters(const char* name, /* object name from traverse list */
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int rank, /* rank of dataset */
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hsize_t *dims, /* dimensions of dataset */
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hid_t dcpl_id, /* dataset creation property list */
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hid_t type_id, /* datatype */
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pack_opt_t *options, /* repack options */
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pack_info_t *obj); /* info about object to filter */
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int has_filter(hid_t dcpl_id,
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H5Z_filter_t filtnin);
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int check_szip_params( unsigned bits_per_pixel,
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unsigned pixels_per_block,
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unsigned pixels_per_scanline,
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hsize_t image_pixels);
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int check_szip(hid_t type_id, /* dataset datatype */
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int rank, /* chunk rank */
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hsize_t *dims, /* chunk dims */
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unsigned szip_options_mask /*IN*/,
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unsigned *szip_pixels_per_block /*IN,OUT*/,
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pack_opt_t *options);
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int can_read(const char* name, /* object name from traverse list */
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hid_t dcpl_id, /* dataset creation property list */
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pack_opt_t *options); /* repack options */
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/*-------------------------------------------------------------------------
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* layout functions
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*-------------------------------------------------------------------------
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*/
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int has_layout(hid_t dcpl_id,
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pack_info_t *obj);
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int layout_this(hid_t dcpl_id, /* DCPL from input object */
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const char* name, /* object name from traverse list */
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pack_opt_t *options, /* repack options */
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pack_info_t *pack /*OUT*/) /* object to apply layout */;
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int apply_layout(hid_t dcpl_id,
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pack_info_t *pack); /* info about object */
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/*-------------------------------------------------------------------------
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* options table
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*-------------------------------------------------------------------------
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*/
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int options_table_init( pack_opttbl_t **tbl );
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int options_table_free( pack_opttbl_t *table );
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int options_add_layout( obj_list_t *obj_list,
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int n_objs,
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pack_info_t *pack,
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pack_opttbl_t *table );
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int options_add_filter ( obj_list_t *obj_list,
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int n_objs,
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filter_info_t filt,
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pack_opttbl_t *table );
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pack_info_t* options_get_object( const char *path,
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pack_opttbl_t *table);
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/*-------------------------------------------------------------------------
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* parse functions
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*-------------------------------------------------------------------------
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*/
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obj_list_t* parse_filter(const char *str,
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int *n_objs,
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filter_info_t *filt,
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pack_opt_t *options);
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obj_list_t* parse_layout(const char *str,
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int *n_objs,
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pack_info_t *pack, /* info about object */
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pack_opt_t *options);
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const char* get_sfilter (H5Z_filter_t filtn);
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int parse_number(char *str);
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/*-------------------------------------------------------------------------
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* tests
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*-------------------------------------------------------------------------
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*/
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#define FNAME1 "test1.h5"
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#define FNAME1OUT "test1out.h5"
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#define FNAME2 "test2.h5"
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#define FNAME2OUT "test2out.h5"
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#define FNAME3 "test3.h5"
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#define FNAME3OUT "test3out.h5"
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#define FNAME4 "test4.h5"
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#define FNAME4OUT "test4out.h5"
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int make_testfiles(void);
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int make_attr(hid_t fid);
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int write_dset( hid_t loc_id,
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int rank,
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hsize_t *dims,
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const char *dset_name,
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hid_t type_id,
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void *buf );
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int write_attr(hid_t loc_id,
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int rank,
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hsize_t *dims,
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const char *attr_name,
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hid_t type_id,
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void *buf);
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void write_attr_in(hid_t loc_id,
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const char* dset_name, /* for saving reference to dataset*/
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hid_t fid, /* for reference create */
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int make_diffs /* flag to modify data buffers */);
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void write_dset_in(hid_t loc_id,
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const char* dset_name, /* for saving reference to dataset*/
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hid_t file_id,
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int make_diffs /* flag to modify data buffers */);
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int make_filters(hid_t loc_id);
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/*-------------------------------------------------------------------------
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* check SZIP parameters
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*-------------------------------------------------------------------------
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*/
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typedef struct
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{
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int compression_mode;
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int options_mask;
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unsigned bits_per_pixel;
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unsigned pixels_per_block;
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unsigned pixels_per_scanline;
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hsize_t pixels;
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}szip_comp_t;
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/* for SZIP */
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#if !defined (NN_OPTION_MASK)
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#define NN_OPTION_MASK 32
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#endif
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#if !defined (RAW_OPTION_MASK)
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#define RAW_OPTION_MASK 128
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#endif
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#if !defined (MAX_BLOCKS_PER_SCANLINE)
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#define MAX_BLOCKS_PER_SCANLINE 128
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#endif
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#if !defined (MAX_PIXELS_PER_BLOCK)
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#define MAX_PIXELS_PER_BLOCK 32
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#endif
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#if !defined (MAX_PIXELS_PER_SCANLINE)
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#define MAX_PIXELS_PER_SCANLINE (MAX_BLOCKS_PER_SCANLINE)*(MAX_PIXELS_PER_BLOCK)
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#endif
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#if !defined (NN_MODE)
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#define NN_MODE 1
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#endif
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#endif /* H5REPACK_H__ */
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