[svn-r11443] Purpose:

new features

Description:

added support for the scale/offset filter
there is a new filter symbol 'SOFF'
-f SOFF=<scale_factor,scale_type>

scale_factor = integer
scale_type = 'IN' or 'DS'


Solution:

Platforms tested:
Linux
SunOS

Misc. update:

6 files changed, 132 insertions, 61 deletions

diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index 0ced373..dab4ece 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -30,7 +30,6 @@
 #define MAX_NC_NAME 256 /* max length of a name */
 #define MAX_VAR_DIMS 32 /* max per variable dimensions */
 
-
 /*-------------------------------------------------------------------------
  * data structures for command line options
  *-------------------------------------------------------------------------
@@ -44,11 +43,13 @@ typedef struct {
 /*
  the type of filter and additional parameter
  type can be one of the filters
- H5Z_FILTER_NONE       0,  uncompress if compressed
- H5Z_FILTER_DEFLATE	   1 , deflation like gzip
- H5Z_FILTER_SHUFFLE    2 , shuffle the data
- H5Z_FILTER_FLETCHER32 3 , letcher32 checksum of EDC
- H5Z_FILTER_SZIP       4 , szip compression
+ H5Z_FILTER_NONE        0,  uncompress if compressed
+ H5Z_FILTER_DEFLATE	    1 , deflation like gzip
+ H5Z_FILTER_SHUFFLE     2 , shuffle the data
+ H5Z_FILTER_FLETCHER32  3 , letcher32 checksum of EDC
+ H5Z_FILTER_SZIP        4 , szip compression
+	H5Z_FILTER_NBIT        5 , nbit compression              
+ H5Z_FILTER_SCALEOFFSET 6 , scaleoffset compression      
 */
 
 #define CDVALUES 2
@@ -56,11 +57,6 @@ typedef struct {
 typedef struct {
  H5Z_filter_t filtn;               /* filter identification number */
  int          cd_values[CDVALUES]; /* filter client data values */
- /* extra input for szip, selects the coding method
-    entropy coding method: EC=0
-    nearest neighbor coding method: NN=1
- */
- int          szip_coding;
 } filter_info_t;
 
 /* chunk lengths along each dimension and rank */
@@ -71,7 +67,7 @@ typedef struct {
 
 /* we currently define a maximum value for the filters array,
    that corresponds to the current library filters */
-#define H5_REPACK_MAX_NFILTERS 4
+#define H5_REPACK_MAX_NFILTERS 6
 
 /* information for one object, contains PATH, CHUNK info and FILTER info */
 typedef struct {
diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c
index db3277b..1f4c2d7 100644
--- a/tools/h5repack/h5repack_filters.c
+++ b/tools/h5repack/h5repack_filters.c
@@ -147,8 +147,6 @@ int aux_assign_obj(const char* name,            /* object name from traverse lis
 			tmp.nfilters=1;
 			tmp.filter[0]=options->filter_g;
 		}
-
-
 		if (options->all_layout)
 		{
 			/* assign the global layout info to the OBJ info */
@@ -163,10 +161,7 @@ int aux_assign_obj(const char* name,            /* object name from traverse lis
 			default:
 				break;
 			}/*switch*/
-
 		}
-
-
 	}
 
  *obj = tmp;
@@ -199,7 +194,6 @@ int apply_filters(const char* name,    /* object name from traverse list */
                   pack_opt_t *options) /* repack options */
 {
 	int          nfilters;       /* number of filters in DCPL */
- unsigned     aggression;     /* the deflate level */
  hsize_t      nelmts;         /* number of elements in dataset */
  size_t       size;           /* size of datatype in bytes */
  hsize_t      chsize[64];     /* chunk size in elements */
@@ -276,10 +270,7 @@ int apply_filters(const char* name,    /* object name from traverse list */
   }
  }
 
-
-
-
-	/*-------------------------------------------------------------------------
+/*-------------------------------------------------------------------------
  * the type of filter and additional parameter
  * type can be one of the filters
  * H5Z_FILTER_NONE       0,  uncompress if compressed
@@ -318,12 +309,16 @@ int apply_filters(const char* name,    /* object name from traverse list */
 				*-------------------------------------------------------------------------
 				*/
 			case H5Z_FILTER_DEFLATE:
-				aggression=obj.filter[i].cd_values[0];
-				/* set up for deflated data */
-				if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
-					return -1;
-				if(H5Pset_deflate(dcpl_id,aggression)<0)
-					return -1;
+				{
+					unsigned     aggression;     /* the deflate level */
+					
+					aggression = obj.filter[i].cd_values[0];
+					/* set up for deflated data */
+					if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+						return -1;
+					if(H5Pset_deflate(dcpl_id,aggression)<0)
+						return -1;
+				}
 				break;
 
 				/*-------------------------------------------------------------------------
@@ -335,12 +330,9 @@ int apply_filters(const char* name,    /* object name from traverse list */
 					unsigned  options_mask;
 					unsigned  pixels_per_block;
 
-					pixels_per_block=obj.filter[i].cd_values[0];
-					if (obj.filter[i].szip_coding==0)
-						options_mask=H5_SZIP_NN_OPTION_MASK;
-					else
-						options_mask=H5_SZIP_EC_OPTION_MASK;
-
+					options_mask     = obj.filter[i].cd_values[0]; 
+					pixels_per_block = obj.filter[i].cd_values[1];
+		
 					/* set up for szip data */
 					if(H5Pset_chunk(dcpl_id,obj.chunk.rank,obj.chunk.chunk_lengths)<0)
 						return -1;
@@ -385,15 +377,20 @@ int apply_filters(const char* name,    /* object name from traverse list */
 				* H5Z_FILTER_SCALEOFFSET , scale+offset compression
 				*-------------------------------------------------------------------------
 				*/
+
 			case H5Z_FILTER_SCALEOFFSET:
-				aggression=obj.filter[i].cd_values[0];
-				if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
-					return -1;
-                                /* The following line  needs to be changed in the future,
-                                   H5_SO_INT needs to be passed as a parameter, it can
-                                   be either H5_SO_FLOAT_DSCALE or H5_SO_INT. KY, 2005/8/31 */ 
-				if (H5Pset_scaleoffset(dcpl_id,H5Z_SO_INT,aggression)<0)
-					return -1;
+				{
+					H5Z_SO_scale_type_t scale_type; 
+     int                 scale_factor;      
+					
+					scale_type   = obj.filter[i].cd_values[0];
+					scale_factor = obj.filter[i].cd_values[1];
+					
+					if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+						return -1;
+					if (H5Pset_scaleoffset(dcpl_id,scale_type,scale_factor)<0)
+						return -1;
+				}
 				break;
 			} /* switch */
 		}/*i*/
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 665f8e1..96eb787 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -136,9 +136,12 @@ void usage(void)
  printf("-i input          Input HDF5 File\n");
  printf("-o output         Output HDF5 File\n");
  printf("[-h]              Print usage message\n");
- printf("[-v]              Verbose mode. Print output (list of objects, filters, warnings)\n");
+ printf("[-v]              Verbose mode. Print more output (list of objects,\n");
+	printf("                   filters, warnings)\n");
  printf("[-f 'filter']     Filter type: 'filter' is a string with the format\n");
+	printf("\n");
  printf("     <list of objects> : <name of filter> = <filter parameters>\n");
+	printf("\n");
  printf("     <list of objects> is a comma separated list of object names\n");
  printf("       meaning apply compression only to those objects.\n");
  printf("       if no object names are specified, the filter is applied to all objects\n");
@@ -148,15 +151,24 @@ void usage(void)
  printf("       SHUF, to apply the HDF5 shuffle filter\n");
  printf("       FLET, to apply the HDF5 checksum filter\n");
  printf("       NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
+	printf("       SOFF, to apply the HDF5 Scale/Offset filter\n");
  printf("       NONE, to remove the filter\n");
  printf("     <filter parameters> is optional compression info\n");
  printf("       SHUF (no parameter)\n");
  printf("       FLET (no parameter)\n");
  printf("       NBIT (no parameter)\n");
  printf("       GZIP=<deflation level> from 1-9\n");
- printf("       SZIP=<pixels per block,coding> (pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN')\n");
+ printf("       SZIP=<pixels per block,coding>\n");
+	printf("            (pixels per block is a even number in 2-32 and coding method\n");
+	printf("            is 'EC' or 'NN')\n");
+	printf("       SOFF=<scale_factor,scale_type>\n");
+	printf("            (scale_factor is an integer and scale_type is either 'IN'\n");
+	printf("             for integer type, or 'DS', for floating point type\n");
+	printf("             using the D-scaling method)\n");
  printf("[-l 'layout']     Layout type. 'layout' is a string with the format\n");
+ printf("\n");
  printf("     <list of objects> : <layout type>\n");
+ printf("\n");
  printf("     <list of objects> is a comma separated list of object names,\n");
  printf("       meaning that layout information is supplied for those objects.\n");
  printf("       if no object names are specified, the layout is applied to all objects\n");
@@ -169,8 +181,9 @@ void usage(void)
  printf("       <dim_1 x dim_2 x ... dim_n>\n");
  printf("\n");
  printf("-e file           File with the -f and -l options (only filter and layout flags)\n");
- printf("-m number         Do not apply the filter to objects which size in bytes is smaller than number.\n");
- printf("                  If no size is specified a minimum of 1024 bytes is assumed.\n");
+ printf("-m size           Do not apply the filter to objects which size in bytes\n");
+	printf("                   is smaller than number. If no size is specified a minimum of\n");
+ printf("                   1024 bytes is assumed.\n");
  printf("\n");
  printf("Examples of use:\n");
  printf("\n");
@@ -188,4 +201,3 @@ void usage(void)
  printf("\n");
 }
 
-
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index 7bb6d10..d4c2532 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -17,7 +17,6 @@
 #include "h5repack.h"
 
 
-
 /*-------------------------------------------------------------------------
  * Function: init_packobject
  *
@@ -36,7 +35,6 @@ void init_packobject(pack_info_t *obj)
  for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
  {
   obj->filter[j].filtn        = -1;
-  obj->filter[j].szip_coding  = -1;
   for ( k=0; k<CDVALUES; k++)
    obj->filter[j].cd_values[k] = -1;
  }
diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c
index 7e82fde..1c67216 100644
--- a/tools/h5repack/h5repack_parse.c
+++ b/tools/h5repack/h5repack_parse.c
@@ -35,7 +35,7 @@
  *  SHUF, to apply the HDF5 shuffle filter
  *  FLET, to apply the HDF5 checksum filter
  *  NBIT, to apply the HDF5 NBIT filter (NBIT compression)
- *  S+O, to apply the HDF5 scale+offset filter (compression)
+ *  SOFF, to apply the HDF5 scale+offset filter (compression)
  *  NONE, to remove the filter
  *
  * Examples:
@@ -135,11 +135,13 @@ obj_list_t* parse_filter(const char *str,
    if ( c=='=') {      /*one more parameter */
     scomp[k]='\0';     /*cut space */
 
-     /*SZIP is a special case , it can be
-      SZIP=8,EC
-      SZIP=8,NN
-      */
-
+/*-------------------------------------------------------------------------
+ * 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 */
@@ -169,9 +171,9 @@ obj_list_t* parse_filter(const char *str,
         i=len-1; /* end */
         (*n_objs)--; /* we counted an extra ',' */
         if (strcmp(smask,"NN")==0)
-         filt->szip_coding=0;
+									filt->cd_values[j++]=H5_SZIP_NN_OPTION_MASK;
         else if (strcmp(smask,"EC")==0)
-         filt->szip_coding=1;
+									filt->cd_values[j++]=H5_SZIP_EC_OPTION_MASK;
         else
         {
          printf("Input Error: szip mask must be 'NN' or 'EC' \n");
@@ -184,6 +186,71 @@ obj_list_t* parse_filter(const char *str,
      }  /* 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);
+       printf("Input Error: 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,"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
+        {
+         printf("Input Error: scale type must be 'IN' or 'DS' \n");
+         exit(1);
+        }
+
+       }
+      }
+
+     }  /* u */
+    } /*if */
+
+
+/*-------------------------------------------------------------------------
+ * all other filters
+ *-------------------------------------------------------------------------
+ */
+
     else
     {
      /* here we could have 1 or 2 digits  */
@@ -289,10 +356,10 @@ obj_list_t* parse_filter(const char *str,
  * H5Z_FILTER_SCALEOFFSET
  *-------------------------------------------------------------------------
  */
-   else if (strcmp(scomp,"S+O")==0)
+   else if (strcmp(scomp,"SOFF")==0)
    {
     filt->filtn=H5Z_FILTER_SCALEOFFSET;
-    if (no_param) { /*no more parameters, S+O must have parameter */
+    if (no_param) { /*no more parameters, SOFF must have parameter */
      if (obj_list) free(obj_list);
      printf("Input Error: Missing compression parameter in <%s>\n",str);
      exit(1);
@@ -379,7 +446,7 @@ const char* get_sfilter(H5Z_filter_t filtn)
  else if (filtn==H5Z_FILTER_NBIT)
   return "NBIT";
  else if (filtn==H5Z_FILTER_SCALEOFFSET)
-  return "S+O";
+  return "SOFF";
  else {
   printf("Input error in filter type\n");
   exit(1);
diff --git a/tools/h5repack/testh5repack_main.c b/tools/h5repack/testh5repack_main.c
index 26dcfc7..ab6c09e 100644
--- a/tools/h5repack/testh5repack_main.c
+++ b/tools/h5repack/testh5repack_main.c
@@ -1052,12 +1052,13 @@ if (szip_can_encode) {
  SKIPPED();
 #endif
 
+
   TESTING("    adding scaleoffset filter");
 
 #ifdef H5_HAVE_FILTER_SCALEOFFSET
  if (h5repack_init (&pack_options, 0)<0)
   TEST_ERROR;
- if (h5repack_addfilter("dset_none:S+O=31",&pack_options)<0)
+ if (h5repack_addfilter("dset_none:SOFF=31,IN",&pack_options)<0)
   TEST_ERROR;
  if (h5repack(FNAME13,FNAME13OUT,&pack_options)<0)
   TEST_ERROR;