hdf5/tools/h5repack/h5repack.c

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the files COPYING and Copyright.html.  COPYING can be found at the root   *
 * of the source code distribution tree; Copyright.html can be found at the  *
 * root level of an installed copy of the electronic HDF5 document set and   *
 * is linked from the top-level documents page.  It can also be found at     *
 * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
 * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#include <stdlib.h>
#include "h5repack.h"

/*-------------------------------------------------------------------------
 * File: h5repack.c
 * Purpose: Public API functions 
 *-------------------------------------------------------------------------
 */

static int check_options(pack_opt_t *options);

/*-------------------------------------------------------------------------
 * Function: h5repack
 *
 * Purpose: locate all high-level HDF5 objects in the file 
 *  and compress/chunk them using options
 *
 * Algorythm: 2 traversals are made to the file; the 1st builds a list of
 *  the objects, the 2nd makes a copy of them, using the options;
 *  the reason for the 1st traversal is to check for invalid 
 *  object name requests
 *
 * Return: 0, ok, -1, fail
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: September, 22, 2003
 *
 *-------------------------------------------------------------------------
 */
int h5repack(const char* infile, 
             const char* outfile, 
             pack_opt_t *options)
{
 /* check input */
 if (check_options(options)<0)
  return -1;
 
 /* check for objects in input that are in the file */
 if (check_objects(infile,options)<0)
  return -1;
 
 /* copy the file  */
 if (copy_file(infile,outfile,options)<0)
  return -1;
 
 return 0;
}



/*-------------------------------------------------------------------------
 * Function: h5repack_init
 *
 * Purpose: initialize options
 *
 * Return: 0, ok, -1, fail
 *
 *-------------------------------------------------------------------------
 */

int h5repack_init (pack_opt_t *options, 
                   int verbose)
{
 memset(options,0,sizeof(pack_opt_t));
 options->threshold = 1024;
 options->verbose   = verbose;
 return (options_table_init(&(options->op_tbl)));
}

/*-------------------------------------------------------------------------
 * Function: h5repack_end
 *
 * Purpose: free options table
 *
 *-------------------------------------------------------------------------
 */

int h5repack_end  (pack_opt_t *options)
{
 return options_table_free(options->op_tbl);
}

/*-------------------------------------------------------------------------
 * Function: h5repack_addcomp
 *
 * Purpose: add a compression -t option to table 
 *   Example: -t "*:GZIP 6" , STR = "*:GZIP 6"
 *
 * Return: 0, ok, -1, fail
 *
 *-------------------------------------------------------------------------
 */

int h5repack_addcomp(const char* str, 
                     pack_opt_t *options)
{
 obj_list_t      *obj_list=NULL; /*one object list for the -t and -c option entry */
 comp_info_t     comp;           /*compression info for the current -t option entry */
 int             n_objs;         /*number of objects in the current -t or -c option entry */
 int             i;

 if (options->all_comp==1){
  printf("Error: Invalid compression input: '*' is present with other objects <%s>\n",str);
  return -1;
 }

 /* parse the -t option */
 obj_list=parse_comp(str,&n_objs,&comp);
 if (obj_list==NULL)
  return -1;

  /* searh for the "*" all objects character */
 for (i = 0; i < n_objs; i++) 
 {
  if (strcmp("*",obj_list[i].obj)==0)
  {
   /* if we are compressing all set the global comp type */
   options->all_comp=1;
   options->comp_g=comp;
  }
 }

 if (i>1)
 {
  printf("\nError: '*' cannot be with other objects, <%s>. Exiting...\n",str);
  free(obj_list);
  options_table_free(options->op_tbl);
  return -1;
 }

 if (options->all_comp==0)
  options_add_comp(obj_list,n_objs,comp,options->op_tbl);

 free(obj_list);
 return 0;
}


/*-------------------------------------------------------------------------
 * Function: h5repack_addchunk
 *
 * Purpose: add a chunk -c option to table 
 *   Example: -c "*:2x2" , STR = "*:2x2"
 *
 * Return: 0, ok, -1, fail
 *
 *-------------------------------------------------------------------------
 */


int h5repack_addchunk(const char* str, 
                      pack_opt_t *options)
{
  
 obj_list_t  *obj_list=NULL;     /*one object list for the -t and -c option entry */
 int         n_objs;             /*number of objects in the current -t or -c option entry */
 hsize_t     chunk_lengths[MAX_VAR_DIMS]; /* chunk lengths along each dimension */
 int         chunk_rank;         /*global rank for chunks */
 int         i, j;

 if (options->all_chunk==1){
  printf("Error: Invalid chunking input: '*' is present with other objects <%s>\n",str);
  return -1;
 }
 
 /* parse the -c option */
 obj_list=parse_chunk(str,&n_objs,chunk_lengths,&chunk_rank);
 if (obj_list==NULL)
  return -1;

  /* searh for the "*" all objects character */
 for (i = 0; i < n_objs; i++) 
 {
  if (strcmp("*",obj_list[i].obj)==0)
  {
   /* if we are chunking all set the global chunking type */
   options->all_chunk=1;
   options->chunk_g.rank=chunk_rank;
   for (j = 0; j < chunk_rank; j++) 
    options->chunk_g.chunk_lengths[j] = chunk_lengths[j];
  }
 }

 if (i>1)
 {
  printf("\nError: '*' cannot be with other objects, <%s>. Exiting...\n",str);
  free(obj_list);
  options_table_free(options->op_tbl);
  return -1;
 }

 if (options->all_chunk==0)
  options_add_chunk(obj_list,n_objs,chunk_lengths,chunk_rank,options->op_tbl);

 free(obj_list);
 return 0;
}


/*-------------------------------------------------------------------------
 * Function: check_options
 *
 * Purpose: print options, checks for invalid options
 *
 * Return: void, return -1 on error
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: September, 22, 2003
 *
 *-------------------------------------------------------------------------
 */
static int check_options(pack_opt_t *options)
{
 int   i, k, j, has_cp=0, has_ck=0;

/*-------------------------------------------------------------------------
 * objects to chunk
 *-------------------------------------------------------------------------
 */
 if (options->verbose) 
 {
  printf("\n");
  printf("Objects to chunk are...\n");
  if (options->all_chunk==1)  {
   printf("\tChunk all with dimension [");
   for ( j = 0; j < options->chunk_g.rank; j++)  
    printf("%d ",(int)options->chunk_g.chunk_lengths[j]);
   printf("]\n");
  }
 }/* verbose */

 for ( i = 0; i < options->op_tbl->nelems; i++) 
 {
  char* obj_name=options->op_tbl->objs[i].path;
  
  if (options->op_tbl->objs[i].chunk.rank>0)
  {
   if (options->verbose){
    printf("\t<%s> with chunk size ",obj_name); 
    for ( k = 0; k < options->op_tbl->objs[i].chunk.rank; k++) 
     printf("%d ",(int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
    printf("\n");
   }
   has_ck=1;
  }
  else if (options->op_tbl->objs[i].chunk.rank==-2)
  {
   if (options->verbose)
    printf("\t%s %s\n",obj_name,"NONE"); 
   has_ck=1;
  }
 }
 
 if (options->all_chunk==1 && has_ck){
  printf("Error: Invalid chunking input: '*' is present with other objects\n");
  return -1;
 }
 
/*-------------------------------------------------------------------------
 * objects to compress/uncompress
 *-------------------------------------------------------------------------
 */
 
 if (options->verbose) 
 {
  printf("Objects to compress are...\n");
  if (options->all_comp==1) 
  {
   switch (options->comp_g.type)
   {
   case H5Z_FILTER_NONE:
     printf("\tUncompress all %s\n",
     get_scomp(options->comp_g.type));
    break;
   case H5Z_FILTER_SZIP:
     printf("\tCompress all with %s compression\n",
     get_scomp(options->comp_g.type));
    break;
   case H5Z_FILTER_DEFLATE:
     printf("\tCompress all with %s compression, parameter %d\n",
     get_scomp(options->comp_g.type),
     options->comp_g.info);
    break;
   };
  }
 } /* verbose */

 for ( i = 0; i < options->op_tbl->nelems; i++) 
 {
  pack_info_t obj=options->op_tbl->objs[i];
  if (obj.comp.type>0)
  {
   char* obj_name=obj.path;
   if (options->verbose) {
    printf("\t<%s> with %s compression, parameter %d\n",
     obj_name,
     get_scomp(obj.comp.type),
     obj.comp.info);
   }
   has_cp=1;
  }
 }
 
 if (options->all_comp==1 && has_cp){
  printf("Error: Invalid compression input: * is present with other objects\n");
  return -1;
 }
 return 0;
}

/*-------------------------------------------------------------------------
 * Function: read_info
 *
 * Purpose: read comp and chunk options from file
 *
 * Return: void, exit on error
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: September, 22, 2003
 *
 *-------------------------------------------------------------------------
 */

void read_info(const char *filename,
               pack_opt_t *options) 
{
 char stype[10];
 char comp_info[1024];
 FILE *fp;
 char c;
 int  i, rc=1;

 
 if ((fp = fopen(filename, "r")) == (FILE *)NULL) {
  printf( "Cannot open options file %s", filename);
  exit(1);
 }

 /* Cycle until end of file reached */
 while( 1 )
 {
  rc=fscanf(fp, "%s", stype);
  if (rc==-1)
   break;
   
 /*-------------------------------------------------------------------------
  * comp
  *-------------------------------------------------------------------------
  */
  if (strcmp(stype,"-t") == 0) { 

   /* find begining of info */
   i=0; c='0';
   while( c!='"' )
   {
    fscanf(fp, "%c", &c);
   }
   c='0';
   /* go until end */
   while( c!='"' )
   {
    fscanf(fp, "%c", &c);
    comp_info[i]=c;
    i++;
   }
   comp_info[i-1]='\0'; /*cut the last " */    

   if (h5repack_addcomp(comp_info,options)==-1){
    printf( "Could not add compression option. Exiting\n");
    exit(1);
   }
  }
 /*-------------------------------------------------------------------------
  * chunk
  *-------------------------------------------------------------------------
  */
  else if (strcmp(stype,"-c") == 0) { 
   
   /* find begining of info */
   i=0; c='0';
   while( c!='"' )
   {
    fscanf(fp, "%c", &c);
   }
   c='0';
   /* go until end */
   while( c!='"' )
   {
    fscanf(fp, "%c", &c);
    comp_info[i]=c;
    i++;
   }
   comp_info[i-1]='\0'; /*cut the last " */    

   if (h5repack_addchunk(comp_info,options)==-1){
    printf( "Could not add chunck option. Exiting\n");
    exit(1);
   }
  }
 /*-------------------------------------------------------------------------
  * not valid
  *-------------------------------------------------------------------------
  */
  else {
   printf( "Bad file format for %s", filename);
   exit(1);
  }
 }

 fclose(fp);
 return;
}