hdf5/tools/h5repack/h5repack_parse.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 <string.h>
#include <stdio.h>
#include <ctype.h>
#include "h5tools_utils.h"
#include "h5repack.h"

extern char  *progname;

/*-------------------------------------------------------------------------
 * Function: parse_filter
 *
 * Purpose: read filter information
 *
 * Return: a list of names, the number of names and its compression type
 *
 * <name of filter> can be:
 *  GZIP, to apply the HDF5 GZIP filter (GZIP compression)
 *  SZIP, to apply the HDF5 SZIP filter (SZIP compression)
 *  SHUF, to apply the HDF5 shuffle filter
 *  FLET, to apply the HDF5 checksum filter
 *  NBIT, to apply the HDF5 NBIT filter (NBIT compression)
 *  SOFF, to apply the HDF5 scale+offset filter (compression)
 *  NONE, to remove the filter
 *
 * Examples:
 * "GZIP=6"
 * "A,B:NONE"
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: September, 23, 2003
 *
 *-------------------------------------------------------------------------
 */


obj_list_t* parse_filter(const char *str,
                         int *n_objs,
                         filter_info_t *filt,
                         pack_opt_t *options)
{
 unsigned    i, u;
 char        c;
 size_t      len=strlen(str);
 int         j, m, n, k, l, end_obj=-1, no_param=0;
 char        sobj[MAX_NC_NAME];
 char        scomp[10];
 char        stype[5];
 char        smask[3];
 obj_list_t* obj_list=NULL;
 unsigned    pixels_per_block;

#if defined(PARSE_DEBUG)
 fprintf(stderr,"%s\n",str);
#endif

 /* initialize compression  info */
 memset(filt,0,sizeof(filter_info_t));

 /* check for the end of object list and number of objects */
 for ( i=0, n=0; i<len; i++)
 {
  c = str[i];
  if ( c==':' )
  {
   end_obj=i;
  }
  if ( c==',' )
  {
   n++;
  }
 }

 if (end_obj==-1) { /* missing : */
  /* apply to all objects */
  options->all_filter=1;
 }

 n++;
 obj_list=malloc(n*sizeof(obj_list_t));
 if (obj_list==NULL)
 {
  error_msg(progname, "could not allocate object list\n");
  return NULL;
 }
 *n_objs=n;

 /* get object list */
 for ( j=0, k=0, n=0; j<end_obj; j++,k++)
 {
  c = str[j];
  sobj[k]=c;
  if ( c==',' || j==end_obj-1)
  {
   if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0';
   strcpy(obj_list[n].obj,sobj);
   memset(sobj,0,sizeof(sobj));
   n++;
   k=-1;
  }
 }
 /* nothing after : */
 if (end_obj+1==(int)len)
 {
  if (obj_list) free(obj_list);
  error_msg(progname, "input Error: Invalid compression type in <%s>\n",str);
  exit(1);
 }


 /* get filter additional parameters */
 m=0;
 for ( i=end_obj+1, k=0, j=0; i<len; i++,k++)
 {
  c = str[i];
  scomp[k]=c;
  if ( c=='=' || i==len-1)
  {
   if ( c=='=') {      /*one more parameter */
    scomp[k]='\0';     /*cut space */

/*-------------------------------------------------------------------------
 * H5Z_FILTER_SZIP
 * szip has the format SZIP=<pixels per block,coding>
 * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN'
 * example SZIP=8,NN
 *-------------------------------------------------------------------------
 */
    if (strcmp(scomp,"SZIP")==0)
    {
     l=-1; /* mask index check */
     for ( m=0,u=i+1; u<len; u++,m++)
     {
      if (str[u]==',')
      {
       stype[m]='\0'; /* end digit of szip */
       l=0;  /* start EC or NN search */
       u++;  /* skip ',' */
      }
      c = str[u];
      if (!isdigit(c) && l==-1){
       if (obj_list) free(obj_list);
       error_msg(progname, "compression parameter not digit in <%s>\n",str);
       exit(1);
      }
      if (l==-1)
       stype[m]=c;
      else
      {
       smask[l]=c;
       l++;
       if (l==2)
       {
        smask[l]='\0';
        i=len-1; /* end */
        (*n_objs)--; /* we counted an extra ',' */
        if (strcmp(smask,"NN")==0)
         filt->cd_values[j++]=H5_SZIP_NN_OPTION_MASK;
        else if (strcmp(smask,"EC")==0)
         filt->cd_values[j++]=H5_SZIP_EC_OPTION_MASK;
        else
        {
         error_msg(progname, "szip mask must be 'NN' or 'EC' \n");
         exit(1);
        }

       }
      }

     }  /* u */
    } /*if */

/*-------------------------------------------------------------------------
 * H5Z_FILTER_SCALEOFFSET
    * scaleoffset has the format SOFF=<scale_factor,scale_type>
    * scale_type can be
    *   integer datatype, H5Z_SO_INT (IN)
    *   float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE  (DS)
    *   float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE  (ES) , not yet implemented
    * for integer datatypes, scale_factor denotes Minimum Bits
    * for float datatypes, scale_factor denotes decimal scale factor
 *  examples
    *  SOFF=31,IN
    *  SOFF=3,DF
 *-------------------------------------------------------------------------
 */

    else if (strcmp(scomp,"SOFF")==0)
    {
     l=-1; /* mask index check */
     for ( m=0,u=i+1; u<len; u++,m++)
     {
      if (str[u]==',')
      {
       stype[m]='\0'; /* end digit */
       l=0;  /* start 'IN' , 'DS', or 'ES' search */
       u++;  /* skip ',' */
      }
      c = str[u];
      if (!isdigit(c) && l==-1){
       if (obj_list) free(obj_list);
       error_msg(progname, "compression parameter is not a digit in <%s>\n",str);
       exit(1);
      }
      if (l==-1)
       stype[m]=c;
      else
      {
       smask[l]=c;
       l++;
       if (l==2)
       {
        smask[l]='\0';
        i=len-1; /* end */
        (*n_objs)--; /* we counted an extra ',' */
        if (strcmp(smask,"IN")==0)
                                    filt->cd_values[j++]=H5Z_SO_INT;
        else if (strcmp(smask,"DS")==H5Z_SO_FLOAT_DSCALE)
                                    filt->cd_values[j++]=H5Z_SO_FLOAT_DSCALE;
        else
        {
         error_msg(progname, "scale type must be 'IN' or 'DS' \n");
         exit(1);
        }

       }
      }

     }  /* u */
    } /*if */


/*-------------------------------------------------------------------------
 * all other filters
 *-------------------------------------------------------------------------
 */

    else
    {
     /* here we could have 1 or 2 digits  */
     for ( m=0,u=i+1; u<len; u++,m++)
     {
      c = str[u];
      if (!isdigit(c)){
       if (obj_list) free(obj_list);
       error_msg(progname, "compression parameter is not a digit in <%s>\n",str);
       exit(1);
      }
      stype[m]=c;
     } /* u */

     stype[m]='\0';
    } /*if */



    filt->cd_values[j++]=atoi(stype);
    i+=m; /* jump */
   }
   else if (i==len-1) { /*no more parameters */
    scomp[k+1]='\0';
    no_param=1;
   }

/*-------------------------------------------------------------------------
 * H5Z_FILTER_NONE
 *-------------------------------------------------------------------------
 */
   if (strcmp(scomp,"NONE")==0)
    filt->filtn=H5Z_FILTER_NONE;

/*-------------------------------------------------------------------------
 * H5Z_FILTER_DEFLATE
 *-------------------------------------------------------------------------
 */
   else if (strcmp(scomp,"GZIP")==0)
   {
    filt->filtn=H5Z_FILTER_DEFLATE;
    if (no_param) { /*no more parameters, GZIP must have parameter */
     if (obj_list) free(obj_list);
     error_msg(progname, "missing compression parameter in <%s>\n",str);
     exit(1);
    }
   }

/*-------------------------------------------------------------------------
 * H5Z_FILTER_SZIP
 *-------------------------------------------------------------------------
 */
   else if (strcmp(scomp,"SZIP")==0)
   {
    filt->filtn=H5Z_FILTER_SZIP;
    if (no_param) { /*no more parameters, SZIP must have parameter */
     if (obj_list) free(obj_list);
     error_msg(progname, "missing compression parameter in <%s>\n",str);
     exit(1);
    }
   }

/*-------------------------------------------------------------------------
 * H5Z_FILTER_SHUFFLE
 *-------------------------------------------------------------------------
 */
   else if (strcmp(scomp,"SHUF")==0)
   {
    filt->filtn=H5Z_FILTER_SHUFFLE;
    if (m>0){ /*shuffle does not have parameter */
     if (obj_list) free(obj_list);
     error_msg(progname, "extra parameter in SHUF <%s>\n",str);
     exit(1);
    }
   }
/*-------------------------------------------------------------------------
 * H5Z_FILTER_FLETCHER32
 *-------------------------------------------------------------------------
 */
   else if (strcmp(scomp,"FLET")==0)
   {
    filt->filtn=H5Z_FILTER_FLETCHER32;
    if (m>0){ /*shuffle does not have parameter */
     if (obj_list) free(obj_list);
     error_msg(progname, "extra parameter in FLET <%s>\n",str);
     exit(1);
    }
   }
/*-------------------------------------------------------------------------
 * H5Z_FILTER_NBIT
 *-------------------------------------------------------------------------
 */
   else if (strcmp(scomp,"NBIT")==0)
   {
    filt->filtn=H5Z_FILTER_NBIT;
    if (m>0){ /*nbit does not have parameter */
     if (obj_list) free(obj_list);
     error_msg(progname, "extra parameter in NBIT <%s>\n",str);
     exit(1);
    }
   }
/*-------------------------------------------------------------------------
 * H5Z_FILTER_SCALEOFFSET
 *-------------------------------------------------------------------------
 */
   else if (strcmp(scomp,"SOFF")==0)
   {
    filt->filtn=H5Z_FILTER_SCALEOFFSET;
    if (no_param) { /*no more parameters, SOFF must have parameter */
     if (obj_list) free(obj_list);
     error_msg(progname, "missing compression parameter in <%s>\n",str);
     exit(1);
    }
   }
   else {
    if (obj_list) free(obj_list);
    error_msg(progname, "invalid filter type in <%s>\n",str);
    exit(1);
   }
  }
 } /*i*/

/*-------------------------------------------------------------------------
 * check valid parameters
 *-------------------------------------------------------------------------
 */

 switch (filt->filtn)
 {

 case H5Z_FILTER_DEFLATE:
  if (filt->cd_values[0]<0 || filt->cd_values[0]>9 ){
   if (obj_list) free(obj_list);
   error_msg(progname, "invalid compression parameter in <%s>\n",str);
   exit(1);
  }
  break;


 case H5Z_FILTER_SZIP:
  pixels_per_block=filt->cd_values[0];
  if ((pixels_per_block%2)==1) {
   if (obj_list) free(obj_list);
   error_msg(progname, "pixels_per_block is not even in <%s>\n",str);
   exit(1);
  }
  if (pixels_per_block>H5_SZIP_MAX_PIXELS_PER_BLOCK) {
   if (obj_list) free(obj_list);
   error_msg(progname, "pixels_per_block is too large in <%s>\n",str);
   exit(1);
  }
  if ( (strcmp(smask,"NN")!=0) && (strcmp(smask,"EC")!=0) ) {
   if (obj_list) free(obj_list);
   error_msg(progname, "szip mask must be 'NN' or 'EC' \n");
   exit(1);
  }
  break;
 case H5Z_FILTER_SCALEOFFSET:
  if (filt->cd_values[0]<0 ){
   if (obj_list) free(obj_list);
   error_msg(progname, "invalid compression parameter in <%s>\n",str);
   exit(1);
  }
  break;
 };

 return obj_list;
}


/*-------------------------------------------------------------------------
 * Function: get_sfilter
 *
 * Purpose: return the filter as a string name
 *
 * Return: name of filter, exit on error
 *
 *-------------------------------------------------------------------------
 */

const char* get_sfilter(H5Z_filter_t filtn)
{
 if (filtn==H5Z_FILTER_NONE)
  return "NONE";
 else if (filtn==H5Z_FILTER_DEFLATE)
  return "GZIP";
 else if (filtn==H5Z_FILTER_SZIP)
  return "SZIP";
 else if (filtn==H5Z_FILTER_SHUFFLE)
  return "SHUFFLE";
 else if (filtn==H5Z_FILTER_FLETCHER32)
  return "FLETCHER32";
 else if (filtn==H5Z_FILTER_NBIT)
  return "NBIT";
 else if (filtn==H5Z_FILTER_SCALEOFFSET)
  return "SOFF";
 else {
  error_msg(progname, "input error in filter type\n");
  exit(1);
 }
 return NULL;
}


/*-------------------------------------------------------------------------
 * Function: parse_layout
 *
 * Purpose: read layout info
 *
 * Return: a list of names, the number of names and its chunking info for
 *  chunked. NULL, on error
 * the layout type can be:
 *  CHUNK, to apply chunking layout
 *  CONTI, to apply continuous layout
 *  COMPA, to apply compact layout
 *
 * Example:
 * "AA,B,CDE:CHUNK=10X10"
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: December 30, 2003
 *
 *-------------------------------------------------------------------------
 */
obj_list_t* parse_layout(const char *str,
                         int *n_objs,
                         pack_info_t *pack,    /* info about layout needed */
                         pack_opt_t *options)
{
 obj_list_t* obj_list=NULL;
 unsigned    i;
 char        c;
 size_t      len=strlen(str);
 int         j, n, k, end_obj=-1, c_index;
 char        sobj[MAX_NC_NAME];
 char        sdim[10];
 char        slayout[10];


 memset(sdim, '\0', sizeof(sdim));
 memset(sobj, '\0', sizeof(sobj));
 memset(slayout, '\0', sizeof(slayout));

 /* check for the end of object list and number of objects */
 for ( i=0, n=0; i<len; i++)
 {
  c = str[i];
  if ( c==':' )
  {
   end_obj=i;
  }
  if ( c==',' )
  {
   n++;
  }
 }

 if (end_obj==-1) { /* missing : chunk all */
  options->all_layout=1;
 }

 n++;
 obj_list=malloc(n*sizeof(obj_list_t));
 if (obj_list==NULL)
 {
  error_msg(progname, "could not allocate object list\n");
  return NULL;
 }
 *n_objs=n;

 /* get object list */
 for ( j=0, k=0, n=0; j<end_obj; j++,k++)
 {
  c = str[j];
  sobj[k]=c;
  if ( c==',' || j==end_obj-1)
  {
   if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0';
   strcpy(obj_list[n].obj,sobj);
   memset(sobj,0,sizeof(sobj));
   n++;
   k=-1;
  }
 }

 /* nothing after : */
 if (end_obj+1==(int)len)
 {
  if (obj_list) free(obj_list);
  error_msg(progname, "in parse layout, no characters after : in <%s>\n",str);
  exit(1);
 }

 /* get layout info */
 for ( j=end_obj+1, n=0; n<=5; j++,n++)
 {
  if (n==5)
  {
   slayout[n]='\0';  /*cut string */
   if (strcmp(slayout,"COMPA")==0)
    pack->layout=H5D_COMPACT;
   else if (strcmp(slayout,"CONTI")==0)
    pack->layout=H5D_CONTIGUOUS;
   else if (strcmp(slayout,"CHUNK")==0)
    pack->layout=H5D_CHUNKED;
   else {
    error_msg(progname, "in parse layout, not a valid layout in <%s>\n",str);
    exit(1);
   }
  }
  else
  {
   c = str[j];
   slayout[n]=c;
  }
 } /* j */


 if ( pack->layout==H5D_CHUNKED )
 {

/*-------------------------------------------------------------------------
 * get chunk info
 *-------------------------------------------------------------------------
 */
   k=0;

   if (j>(int)len)
   {
    if (obj_list) free(obj_list);
    error_msg(progname, "in parse layout,  <%s> Chunk dimensions missing\n",str);
    exit(1);
   }

   for ( i=j, c_index=0; i<len; i++)
   {
    c = str[i];
    sdim[k]=c;
    k++; /*increment sdim index */

    if (!isdigit(c) && c!='x'
     && c!='N' && c!='O' && c!='N' && c!='E'
     ){
     if (obj_list) free(obj_list);
     error_msg(progname, "in parse layout, <%s> Not a valid character in <%s>\n",
      sdim,str);
     exit(1);
    }

    if ( c=='x' || i==len-1)
    {
     if ( c=='x') {
      sdim[k-1]='\0';
      k=0;
      pack->chunk.chunk_lengths[c_index]=atoi(sdim);
      if (pack->chunk.chunk_lengths[c_index]==0) {
       if (obj_list) free(obj_list);
       error_msg(progname, "in parse layout, <%s> conversion to number in <%s>\n",
        sdim,str);
       exit(1);
      }
      c_index++;
     }
     else if (i==len-1) { /*no more parameters */
      sdim[k]='\0';
      k=0;
      if (strcmp(sdim,"NONE")==0)
      {
       pack->chunk.rank=-2;
      }
      else
      {
       pack->chunk.chunk_lengths[c_index]=atoi(sdim);
       if (pack->chunk.chunk_lengths[c_index]==0){
        if (obj_list) free(obj_list);
        error_msg(progname, "in parse layout, <%s> conversion to number in <%s>\n",
         sdim,str);
        exit(1);
       }
       pack->chunk.rank=c_index+1;
      }
     } /*if */
    } /*if c=='x' || i==len-1 */
   } /*i*/


 } /*H5D_CHUNKED*/


 return obj_list;
}



/*-------------------------------------------------------------------------
 * Function: parse_number
 *
 * Purpose: read a number from command line argument
 *
 * Return: number, -1 for FAIL
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: September, 23, 2003
 *
 *-------------------------------------------------------------------------
 */


int parse_number(char *str)
{
 unsigned    i;
 int         n;
 char        c;
 size_t      len=strlen(str);

 for ( i=0; i<len; i++)
 {
  c = str[i];
  if (!isdigit(c)){
   return -1;
  }
 }
 str[i]='\0';
 n=atoi(str);
 return n;
}