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-rw-r--r--tools/h5repack/Makefile.in6
-rw-r--r--tools/h5repack/h5repack.c160
-rw-r--r--tools/h5repack/h5repack.h148
-rw-r--r--tools/h5repack/h5repack_copy.c111
-rw-r--r--tools/h5repack/h5repack_filters.c345
-rw-r--r--tools/h5repack/h5repack_main.c2
-rw-r--r--tools/h5repack/h5repack_opttable.c56
-rw-r--r--tools/h5repack/h5repack_parse.c134
-rw-r--r--tools/h5repack/h5repack_refs.c25
-rw-r--r--tools/h5repack/h5repack_verify.c241
-rw-r--r--tools/h5repack/testh5repack_dset.c3
-rw-r--r--tools/h5repack/testh5repack_filters.c385
-rw-r--r--tools/h5repack/testh5repack_main.c106
-rw-r--r--tools/h5repack/testh5repack_make.c318
14 files changed, 1532 insertions, 508 deletions
diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index dc4d686..5b3cbc0 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -50,10 +50,10 @@ MOSTLYCLEAN=*.h5
## Source and object files for programs...
##
-PROG_SRC=h5repack.c h5repack_copy.c h5repack_refs.c h5repack_list.c h5repack_main.c h5repack_opttable.c h5repack_parse.c testh5repack_attr.c testh5repack_dset.c testh5repack_filters.c testh5repack_main.c
+PROG_SRC=h5repack.c h5repack_copy.c h5repack_filters.c h5repack_refs.c h5repack_list.c h5repack_main.c h5repack_opttable.c h5repack_parse.c h5repack_verify.c testh5repack_attr.c testh5repack_dset.c testh5repack_filters.c testh5repack_main.c testh5repack_make.c
PROG_OBJ=$(PROG_SRC:.c=.lo)
-OBJS=h5repack.lo h5repack_copy.lo h5repack_refs.lo h5repack_list.lo h5repack_main.lo h5repack_opttable.lo h5repack_parse.lo
-TEST_OBJS=h5repack.lo h5repack_copy.lo h5repack_refs.lo h5repack_list.lo h5repack_opttable.lo h5repack_parse.lo testh5repack_attr.lo testh5repack_dset.lo testh5repack_filters.lo testh5repack_main.lo
+OBJS=h5repack.lo h5repack_filters.lo h5repack_copy.lo h5repack_refs.lo h5repack_list.lo h5repack_main.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo
+TEST_OBJS=h5repack.lo h5repack_filters.lo h5repack_copy.lo h5repack_refs.lo h5repack_list.lo h5repack_opttable.lo h5repack_parse.lo h5repack_verify.lo testh5repack_attr.lo testh5repack_dset.lo testh5repack_filters.lo testh5repack_main.lo testh5repack_make.lo
PRIVATE_HDR=
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 24a90f7..6ba20bd 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -97,7 +97,7 @@ int h5repack_end (pack_opt_t *options)
}
/*-------------------------------------------------------------------------
- * Function: h5repack_addcomp
+ * Function: h5repack_addfilter
*
* Purpose: add a compression -t option to table
* Example: -t "*:GZIP 6" , STR = "*:GZIP 6"
@@ -107,45 +107,34 @@ int h5repack_end (pack_opt_t *options)
*-------------------------------------------------------------------------
*/
-int h5repack_addcomp(const char* str,
- pack_opt_t *options)
+int h5repack_addfilter(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;
+ obj_list_t *obj_list=NULL; /*one object list for the -f and -c option entry */
+ filter_info_t filt; /*filter info for the current -f option entry */
+ int n_objs; /*number of objects in the current -f or -c option entry */
- if (options->all_comp==1){
- printf("Error: Invalid compression input: '*' is present with other objects <%s>\n",str);
+ if (options->all_filter==1){
+ printf("Error: Invalid compression input: all option is present \
+ with other objects <%s>\n",str);
return -1;
}
- /* parse the -t option */
- obj_list=parse_comp(str,&n_objs,&comp);
+ /* parse the -f option */
+ obj_list=parse_filter(str,&n_objs,&filt,options);
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;
- }
+ return -1;
}
- if (i>1)
+ if (options->all_filter==1)
{
- printf("\nError: '*' cannot be with other objects, <%s>. Exiting...\n",str);
- free(obj_list);
- options_table_free(options->op_tbl);
- return -1;
+ /* if we are compressing all set the global filter type */
+ options->filter_g=filt;
}
- if (options->all_comp==0)
- options_add_comp(obj_list,n_objs,comp,options->op_tbl);
+ if (options->all_filter==0)
+ options_add_filter(obj_list,n_objs,filt,options->op_tbl);
free(obj_list);
return 0;
@@ -172,7 +161,7 @@ int h5repack_addchunk(const char* str,
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;
+ int j;
if (options->all_chunk==1){
printf("Error: Invalid chunking input: '*' is present with other objects <%s>\n",str);
@@ -180,29 +169,16 @@ int h5repack_addchunk(const char* str,
}
/* parse the -c option */
- obj_list=parse_chunk(str,&n_objs,chunk_lengths,&chunk_rank);
+ obj_list=parse_chunk(str,&n_objs,chunk_lengths,&chunk_rank,options);
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)
+ if (options->all_chunk==1)
{
- printf("\nError: '*' cannot be with other objects, <%s>. Exiting...\n",str);
- free(obj_list);
- options_table_free(options->op_tbl);
- return -1;
+ /* if we are chunking all set the global chunking type */
+ options->chunk_g.rank=chunk_rank;
+ for (j = 0; j < chunk_rank; j++)
+ options->chunk_g.chunk_lengths[j] = chunk_lengths[j];
}
if (options->all_chunk==0)
@@ -230,6 +206,9 @@ static int check_options(pack_opt_t *options)
{
int i, k, j, has_cp=0, has_ck=0;
+ unsigned szip_options_mask=H5_SZIP_NN_OPTION_MASK;
+ unsigned szip_pixels_per_block;
+
/*-------------------------------------------------------------------------
* objects to chunk
*-------------------------------------------------------------------------
@@ -248,12 +227,12 @@ static int check_options(pack_opt_t *options)
for ( i = 0; i < options->op_tbl->nelems; i++)
{
- char* obj_name=options->op_tbl->objs[i].path;
+ char* 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);
+ printf("\t<%s> with chunk size ",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");
@@ -263,13 +242,14 @@ static int check_options(pack_opt_t *options)
else if (options->op_tbl->objs[i].chunk.rank==-2)
{
if (options->verbose)
- printf("\t%s %s\n",obj_name,"NONE");
+ printf("\t%s %s\n",name,"NONE");
has_ck=1;
}
}
if (options->all_chunk==1 && has_ck){
- printf("Error: Invalid chunking input: '*' is present with other objects\n");
+ printf("Error: Invalid chunking input: all option\
+ is present with other objects\n");
return -1;
}
@@ -280,23 +260,22 @@ static int check_options(pack_opt_t *options)
if (options->verbose)
{
- printf("Objects to compress are...\n");
- if (options->all_comp==1)
+ printf("Objects to filter are...\n");
+ if (options->all_filter==1)
{
- switch (options->comp_g.type)
+ H5Z_filter_t filtn=options->filter_g.filtn;
+ switch (filtn)
{
case H5Z_FILTER_NONE:
- printf("\tUncompress all %s\n",
- get_scomp(options->comp_g.type));
+ printf("\tUncompress all %s\n",get_sfilter(filtn));
break;
case H5Z_FILTER_SZIP:
- printf("\tCompress all with %s compression\n",
- get_scomp(options->comp_g.type));
+ printf("\tCompress all with %s compression\n",get_sfilter(filtn));
break;
case H5Z_FILTER_DEFLATE:
printf("\tCompress all with %s compression, parameter %d\n",
- get_scomp(options->comp_g.type),
- options->comp_g.info);
+ get_sfilter(filtn),
+ options->filter_g.cd_values[0]);
break;
};
}
@@ -304,22 +283,54 @@ static int check_options(pack_opt_t *options)
for ( i = 0; i < options->op_tbl->nelems; i++)
{
- pack_info_t obj=options->op_tbl->objs[i];
- if (obj.comp.type>0)
+ pack_info_t obj = options->op_tbl->objs[i];
+ char* name = obj.path;
+ if (obj.filter.filtn>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);
+ if (options->verbose)
+ {
+ printf("\t<%s> with %s filter",
+ name,
+ get_sfilter(obj.filter.filtn));
}
has_cp=1;
- }
- }
+
+ /*check for invalid combination of options */
+ switch (obj.filter.filtn)
+ {
+ default:
+ break;
+ case H5Z_FILTER_SZIP:
+
+ szip_pixels_per_block=obj.filter.cd_values[0];
+
+ /* check szip parameters */
+ if (check_szip(obj.chunk.rank,
+ obj.chunk.chunk_lengths,
+ 0, /* do not test size */
+ szip_options_mask,
+ szip_pixels_per_block)==0)
+ {
+ /* Return: 1=can apply the filter
+ 0=cannot apply the filter
+ Reset this object filter info
+ */
+
+ options->op_tbl->objs[i].filter.filtn=-1;
+ options->op_tbl->objs[i].chunk.rank=-1;
+ printf("\tObject <%s> cannot be filtered\n",name);
+
+
+ }
+
+ break;
+ } /* switch */
+ } /* filtn */
+ } /* i */
- if (options->all_comp==1 && has_cp){
- printf("Error: Invalid compression input: * is present with other objects\n");
+ if (options->all_filter==1 && has_cp){
+ printf("Error: Invalid compression input: all option\
+ is present with other objects\n");
return -1;
}
return 0;
@@ -342,6 +353,7 @@ static int check_options(pack_opt_t *options)
void read_info(const char *filename,
pack_opt_t *options)
{
+
char stype[10];
char comp_info[1024];
FILE *fp;
@@ -383,7 +395,7 @@ void read_info(const char *filename,
}
comp_info[i-1]='\0'; /*cut the last " */
- if (h5repack_addcomp(comp_info,options)==-1){
+ if (h5repack_addfilter(comp_info,options)==-1){
printf( "Could not add compression option. Exiting\n");
exit(1);
}
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index a372a6f..ae20cc4 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -42,16 +42,21 @@ typedef struct {
} obj_list_t;
/*
- the type of compression and additional parameter
+ 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_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
*/
+
+#define CDVALUES 2
+
typedef struct {
- int type;
- int info;
-} comp_info_t;
+ H5Z_filter_t filtn; /* filter identification number */
+ int cd_values[CDVALUES]; /* filter client data values */
+} filter_info_t;
/* chunk lengths along each dimension and rank */
typedef struct {
@@ -59,18 +64,18 @@ typedef struct {
int rank;
} chunk_info_t;
-/* information for one object, contains PATH, CHUNK info and COMP info */
+/* information for one object, contains PATH, CHUNK info and FILTER info */
typedef struct {
- char path[MAX_NC_NAME]; /* name of object */
- comp_info_t comp; /* compression information */
- chunk_info_t chunk; /* chunk information */
- hid_t refobj_id; /* object ID */
+ char path[MAX_NC_NAME]; /* name of object */
+ filter_info_t filter; /* filter information */
+ chunk_info_t chunk; /* chunk information */
+ hid_t refobj_id; /* object ID, references */
} pack_info_t;
/* store a table of all objects */
typedef struct {
- int size;
- int nelems;
+ int size;
+ int nelems;
pack_info_t *objs;
} pack_opttbl_t;
@@ -82,14 +87,13 @@ typedef struct {
/* all the above, ready to go to the hrepack call */
typedef struct {
- pack_opttbl_t *op_tbl; /*table with all -c and -t options */
- int all_chunk; /*chunk all objects, input of "*" */
- int all_comp; /*comp all objects, input of "*" */
- comp_info_t comp_g; /*global compress INFO for the ALL case */
+ pack_opttbl_t *op_tbl; /*table with all -c and -f options */
+ int all_chunk; /*chunk all objects */
+ int all_filter; /*filter all objects */
+ filter_info_t filter_g; /*global filter INFO for the ALL case */
chunk_info_t chunk_g; /*global chunk INFO for the ALL case */
int verbose; /*verbose mode */
int threshold; /*minimum size to compress, in bytes */
-
} pack_opt_t;
@@ -103,11 +107,12 @@ typedef struct {
extern "C" {
#endif
-int h5repack (const char* infile, const char* outfile, pack_opt_t *options);
-int h5repack_addcomp (const char* str, pack_opt_t *options);
-int h5repack_addchunk(const char* str, pack_opt_t *options);
-int h5repack_init (pack_opt_t *options, int verbose);
-int h5repack_end (pack_opt_t *options);
+int h5repack (const char* infile, const char* outfile, pack_opt_t *options);
+int h5repack_addfilter (const char* str, pack_opt_t *options);
+int h5repack_addchunk (const char* str, pack_opt_t *options);
+int h5repack_init (pack_opt_t *options, int verbose);
+int h5repack_end (pack_opt_t *options);
+int h5repack_verify (const char *fname,pack_opt_t *options);
#ifdef __cplusplus
}
@@ -139,14 +144,11 @@ int do_copy_file(hid_t fidin,
int copy_attr(hid_t loc_in,
hid_t loc_out,
- pack_opt_t *options,
- trav_table_t *travt,
- hid_t fidout /* for saving references */
+ pack_opt_t *options
);
const char* MapIdToName(hid_t refobj_id,
- trav_table_t *travt,
- pack_opt_t *options) /* repack options */;
+ trav_table_t *travt);
int do_copy_refobjs(hid_t fidin,
hid_t fidout,
@@ -163,6 +165,34 @@ int do_copy_refobjs_inattr(hid_t loc_in,
void read_info(const char *filename,pack_opt_t *options);
void close_obj(H5G_obj_t obj_type, hid_t obj_id);
+
+/*-------------------------------------------------------------------------
+ * filters
+ *-------------------------------------------------------------------------
+ */
+
+int apply_filter(hid_t dcpl_id,
+ size_t size, /* size of datatype in bytes */
+ pack_opt_t *options, /* repack options */
+ pack_info_t *obj); /* info about object to filter */
+
+int has_filter(hid_t dcpl_id,
+ H5Z_filter_t filtnin);
+
+int check_szip_params( unsigned bits_per_pixel,
+ unsigned pixels_per_block,
+ unsigned pixels_per_scanline,
+ hsize_t image_pixels);
+
+int check_szip(int rank, /* chunk rank */
+ hsize_t *dims, /* chunk dims */
+ size_t size, /* size of datatype in bytes */
+ unsigned szip_options_mask,
+ unsigned szip_pixels_per_block);
+
+
+
+
/*-------------------------------------------------------------------------
* options table
*-------------------------------------------------------------------------
@@ -174,9 +204,9 @@ int options_add_chunk ( obj_list_t *obj_list,
hsize_t *chunk_lengths,
int chunk_rank,
pack_opttbl_t *table );
-int options_add_comp ( obj_list_t *obj_list,
+int options_add_filter ( obj_list_t *obj_list,
int n_objs,
- comp_info_t comp,
+ filter_info_t filt,
pack_opttbl_t *table );
pack_info_t* options_get_object( const char *path,
pack_opttbl_t *table);
@@ -186,14 +216,16 @@ pack_info_t* options_get_object( const char *path,
*-------------------------------------------------------------------------
*/
-obj_list_t* parse_comp (const char *str,
+obj_list_t* parse_filter(const char *str,
int *n_objs,
- comp_info_t *comp);
+ filter_info_t *filt,
+ pack_opt_t *options);
obj_list_t* parse_chunk (const char *str,
int *n_objs,
hsize_t *chunk_lengths,
- int *chunk_rank);
-const char* get_scomp (int code);
+ int *chunk_rank,
+ pack_opt_t *options);
+const char* get_sfilter (H5Z_filter_t filtn);
int parse_number(char *str);
/*-------------------------------------------------------------------------
@@ -211,9 +243,7 @@ int parse_number(char *str);
#define FNAME4OUT "test4out.h5"
int make_testfiles(void);
-int make_all_objects(hid_t fid);
-int make_attributes(hid_t fid);
-int make_special_objects(hid_t loc_id);
+
int make_attr(hid_t fid);
int write_dset( hid_t loc_id,
int rank,
@@ -236,6 +266,48 @@ void write_dset_in(hid_t loc_id,
hid_t file_id,
int make_diffs /* flag to modify data buffers */);
+int make_deflate(hid_t loc_id);
+int make_szip(hid_t loc_id);
+int make_nofilters(hid_t loc_id);
+
+
+
+/*-------------------------------------------------------------------------
+ * check SZIP parameters
+ *-------------------------------------------------------------------------
+ */
+
+typedef struct
+{
+ int compression_mode;
+ int options_mask;
+ unsigned bits_per_pixel;
+ unsigned pixels_per_block;
+ unsigned pixels_per_scanline;
+ hsize_t pixels;
+
+}szip_comp_t;
+
+/* for SZIP */
+#if !defined (NN_OPTION_MASK)
+#define NN_OPTION_MASK 32
+#endif
+#if !defined (RAW_OPTION_MASK)
+#define RAW_OPTION_MASK 128
+#endif
+#if !defined (MAX_BLOCKS_PER_SCANLINE)
+#define MAX_BLOCKS_PER_SCANLINE 128
+#endif
+#if !defined (MAX_PIXELS_PER_BLOCK)
+#define MAX_PIXELS_PER_BLOCK 32
+#endif
+#if !defined (MAX_PIXELS_PER_SCANLINE)
+#define MAX_PIXELS_PER_SCANLINE (MAX_BLOCKS_PER_SCANLINE)*(MAX_PIXELS_PER_BLOCK)
+#endif
+#if !defined (NN_MODE)
+#define NN_MODE 1
+#endif
+
#endif /* H5REPACK_H__ */
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 2afc94b..4d56ae6 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -19,6 +19,11 @@
#include "H5private.h"
#include "h5repack.h"
+static int filter_this(const char* name,
+ pack_opt_t *options,
+ pack_info_t *obj); /* info about object to filter */
+
+
/*-------------------------------------------------------------------------
* Function: copy_file
*
@@ -39,7 +44,6 @@ int copy_file(const char* fnamein,
{
hid_t fidin;
hid_t fidout;
- int nobjects=0;
trav_table_t *travt=NULL;
/*-------------------------------------------------------------------------
@@ -161,6 +165,8 @@ int do_copy_file(hid_t fidin,
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ hsize_t dsize_in; /* input dataset size before filter */
+ hsize_t dsize_out; /* output dataset size after filter */
int i, j;
/*-------------------------------------------------------------------------
@@ -191,7 +197,7 @@ int do_copy_file(hid_t fidin,
* copy attrs
*-------------------------------------------------------------------------
*/
- if (copy_attr(grp_in,grp_out,options,travt,fidout)<0)
+ if (copy_attr(grp_in,grp_out,options)<0)
goto error;
if (H5Gclose(grp_out)<0)
@@ -239,6 +245,12 @@ int do_copy_file(hid_t fidin,
*/
if ( ! H5Tequal(mtype_id, H5T_STD_REF_OBJ) )
{
+
+ /* the information about the object to be filtered */
+ pack_info_t filt_obj;
+
+ /* get the storage size of the input dataset */
+ dsize_in=H5Dget_storage_size(dset_in);
/*-------------------------------------------------------------------------
* read to memory
@@ -254,21 +266,41 @@ int do_copy_file(hid_t fidin,
goto error;
/*-------------------------------------------------------------------------
+ * apply the filter; check first if the object is to be filtered.
+ * if the filter could not be applied, continue
+ *-------------------------------------------------------------------------
+ */
+ if (filter_this(travt->objs[i].name,options,&filt_obj))
+ {
+ if (apply_filter(dcpl_id,H5Tget_size(mtype_id),options,&filt_obj)<0)
+ continue;
+ }
+
+ /*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,ftype_id,space_id,dcpl_id))<0)
goto error;
- if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
- goto error;
+ if (dsize_in) {
+ if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+ goto error;
+ }
/*-------------------------------------------------------------------------
* copy attrs
*-------------------------------------------------------------------------
*/
- if (copy_attr(dset_in,dset_out,options,travt,fidout)<0)
+ if (copy_attr(dset_in,dset_out,options)<0)
goto error;
+
+ /*-------------------------------------------------------------------------
+ * store the storage sizes
+ *-------------------------------------------------------------------------
+ */
+ dsize_out=H5Dget_storage_size(dset_out);
+
/*close */
if (H5Dclose(dset_out)<0)
goto error;
@@ -317,7 +349,7 @@ int do_copy_file(hid_t fidin,
* copy attrs
*-------------------------------------------------------------------------
*/
- if (copy_attr(type_in,type_out,options,travt,fidout)<0)
+ if (copy_attr(type_in,type_out,options)<0)
goto error;
if (H5Tclose(type_in)<0)
@@ -372,8 +404,6 @@ int do_copy_file(hid_t fidin,
break;
}
}
-
-
/*-------------------------------------------------------------------------
* the root is a special case, we get an ID for the root group
@@ -389,7 +419,7 @@ int do_copy_file(hid_t fidin,
if ((grp_in = H5Gopen(fidin,"/"))<0)
goto error;
- if (copy_attr(grp_in,grp_out,options,travt,fidout)<0)
+ if (copy_attr(grp_in,grp_out,options)<0)
goto error;
if (H5Gclose(grp_out)<0)
@@ -438,9 +468,7 @@ error:
int copy_attr(hid_t loc_in,
hid_t loc_out,
- pack_opt_t *options,
- trav_table_t *travt,
- hid_t fidout /* for saving references */
+ pack_opt_t *options
)
{
hid_t attr_id; /* attr ID */
@@ -456,7 +484,6 @@ int copy_attr(hid_t loc_in,
char name[255];
int n, j;
unsigned u;
- int have_ref=0;
if ((n = H5Aget_num_attrs(loc_in))<0)
goto error;
@@ -576,3 +603,61 @@ error:
return -1;
}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: filter_this
+ *
+ * Purpose: find the object name NAME (got from the traverse list)
+ * in the repack options list; assign the filter information OBJ
+ *
+ * Return: 0 not found, 1 found
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 19, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static
+int filter_this(const char* name, /* object name from traverse list */
+ pack_opt_t *options, /* repack options */
+ pack_info_t *obj) /* info about object to filter */
+{
+ char *pdest;
+ int result;
+ int i;
+
+ /* if we are applying to all objects just return true */
+ if (options->all_filter)
+ {
+ /* assign the global filter and chunk info to the OBJ info */
+ obj->filter=options->filter_g;
+ obj->chunk=options->chunk_g;
+ return 1;
+ }
+
+ for ( i=0; i<options->op_tbl->nelems; i++)
+ {
+ if (strcmp(options->op_tbl->objs[i].path,name)==0)
+ {
+ *obj=options->op_tbl->objs[i];
+ return 1;
+ }
+
+ pdest = strstr(name,options->op_tbl->objs[i].path);
+ result = (int)(pdest - name);
+
+ /* found at position 1, meaning without '/' */
+ if( pdest != NULL && result==1 )
+ {
+ *obj=options->op_tbl->objs[i];
+ return 1;
+ }
+ }
+
+ return 0;
+}
+
diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c
new file mode 100644
index 0000000..6c88b51
--- /dev/null
+++ b/tools/h5repack/h5repack_filters.c
@@ -0,0 +1,345 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 "hdf5.h"
+#include "h5test.h"
+#include "h5repack.h"
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: apply_filter
+ *
+ * Purpose: apply a filter to the property list; do extra checking
+ * in the case of SZIP
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 19, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int apply_filter(hid_t dcpl_id,
+ size_t size, /* size of datatype in bytes */
+ pack_opt_t *options, /* repack options */
+ pack_info_t *obj) /* info about object to filter */
+{
+ int nfilters; /* number of filters */
+ unsigned filt_flags; /* filter flags */
+ H5Z_filter_t filtn; /* filter identification number */
+ unsigned cd_values[20]; /* filter client data values */
+ size_t cd_nelmts; /* filter client number of values */
+ size_t cd_num; /* filter client data counter */
+ char f_name[256]; /* filter/file name */
+ char s[64]; /* temporary string buffer */
+ int i;
+ unsigned aggression; /* the deflate level */
+ unsigned szip_options_mask=H5_SZIP_NN_OPTION_MASK;
+ unsigned szip_pixels_per_block;
+
+
+
+ /* get information about filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
+ return -1;
+
+ for (i=0; i<nfilters; i++)
+ {
+ cd_nelmts = NELMTS(cd_values);
+ filtn = H5Pget_filter(dcpl_id,
+ i,
+ &filt_flags,
+ &cd_nelmts,
+ cd_values,
+ sizeof(f_name),
+ f_name);
+
+ if (options->verbose)
+ {
+ f_name[sizeof(f_name)-1] = '\0';
+ sprintf(s, "Filter-%d:", i);
+ printf(" %-10s %s-%u %s {", s,
+ f_name[0]?f_name:"method",
+ (unsigned)filtn,
+ filt_flags & H5Z_FLAG_OPTIONAL?"OPT":"");
+ for (cd_num=0; cd_num<cd_nelmts; cd_num++) {
+ printf("%s%u", cd_num?", ":"", cd_values[cd_num]);
+ }
+ printf("}\n");
+ }
+ }
+
+
+/*
+ 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 , fletcher32 checksum of EDC
+ H5Z_FILTER_SZIP 4 , szip compression
+*/
+
+ switch (obj->filter.filtn)
+ {
+ case H5Z_FILTER_NONE:
+
+ break;
+
+
+ case H5Z_FILTER_DEFLATE:
+
+
+ aggression=obj->filter.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;
+
+
+ case H5Z_FILTER_SZIP:
+
+ szip_pixels_per_block=obj->filter.cd_values[0];
+
+ /* check szip parameters */
+ if (check_szip(obj->chunk.rank,
+ obj->chunk.chunk_lengths,
+ size,
+ szip_options_mask,
+ szip_pixels_per_block)==1)
+ {
+ /* set up for szip data */
+ if(H5Pset_chunk(dcpl_id,obj->chunk.rank,obj->chunk.chunk_lengths)<0)
+ return -1;
+ if (H5Pset_szip(dcpl_id, szip_options_mask, szip_pixels_per_block)<0)
+ return -1;
+
+ }
+ else
+ {
+ printf("SZIP filter cannot be applied\n");
+ }
+
+ break;
+
+
+ default:
+ break;
+
+ } /* switch */
+
+ return 0;
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: check_szip
+ *
+ * Purpose: utility to check SZIP parameters
+ *
+ * SZIP compresses data block by block, with a user-tunable block size.
+ * This block size is passed in the parameter pixels_per_block and must be even,
+ * with typical values being 8, 10, 16, and 32. The more pixel values vary,
+ * the smaller this number should be. For optimal performance, the number of
+ * pixels per scan line (i.e., the size of the fastest-changing dimension in the chunk)
+ * should be an even multiple of the number of pixels per block.
+ *
+ * Return: 1=can apply the filter
+ * 0=cannot apply the filter
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int check_szip(int rank, /* chunk rank */
+ hsize_t *dims, /* chunk dims */
+ size_t size, /* size of datatype in bytes */
+ unsigned szip_options_mask,
+ unsigned szip_pixels_per_block)
+{
+ szip_comp_t szip;
+ int i;
+
+ /*
+ pixels_per_scanline = size of the fastest-changing dimension
+ Must be <= MAX_PIXELS_PER_SCANLINE and <= pixels
+ */
+ szip.pixels_per_scanline = (unsigned)dims[rank-1];
+ szip.pixels = 1;
+ for ( i = 0; i < rank; i++)
+ {
+ szip.pixels *= dims[i];
+ }
+
+ if (szip.pixels_per_scanline > MAX_PIXELS_PER_SCANLINE)
+ {
+ printf("Warning: in SZIP setting, pixels per scanline was set to <%d>, \
+ MAX_PIXELS_PER_SCANLINE\n",MAX_PIXELS_PER_SCANLINE);
+ szip.pixels_per_scanline = MAX_PIXELS_PER_SCANLINE;
+ }
+
+ /*
+ pixels_per_block must be an even number, and <= pixels_per_scanline
+ and <= MAX_PIXELS_PER_BLOCK
+ */
+ szip.pixels_per_block=szip_pixels_per_block;
+
+ if (szip.pixels_per_block > szip.pixels_per_scanline)
+ {
+ printf("\n\tWarning: in SZIP setting, pixels per block <%d>, \
+ cannot be greater than pixels per scanline<%d>\n",
+ szip.pixels_per_block, szip.pixels_per_scanline);
+ return 0;
+ }
+
+ szip.options_mask = szip_options_mask;
+ szip.compression_mode = NN_MODE;
+
+ /*
+ bits_per_pixel
+ Must be in range 1..24,32,64
+ */
+ switch(size)
+ {
+ case 0:
+ /* size was not provided for test */
+ szip.bits_per_pixel = 0;
+ break;
+ case 1:
+ szip.bits_per_pixel = 8;
+ break;
+ case 2:
+ szip.bits_per_pixel = 16;
+ break;
+ case 4:
+ szip.bits_per_pixel = 32;
+ break;
+ case 8:
+ szip.bits_per_pixel = 64;
+ break;
+ default:
+ printf("Error: Bad numeric type of size <%d> in SZIP\n",size);
+ return 0;
+ }
+
+ return check_szip_params( szip.bits_per_pixel,
+ szip.pixels_per_block,
+ szip.pixels_per_scanline,
+ szip.pixels);
+
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: check_szip_params
+ *
+ * Purpose: Adapted from rice.c. Checks the SZIP parameters
+ *
+ * Return: 1=can apply the filter
+ * 0=cannot apply the filter
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int check_szip_params( unsigned bits_per_pixel,
+ unsigned pixels_per_block,
+ unsigned pixels_per_scanline,
+ hsize_t image_pixels)
+{
+
+ if (pixels_per_block & 1)
+ {
+ printf("Pixels per block must be even.\n");
+ return 0;
+ }
+
+ if (pixels_per_block > pixels_per_scanline)
+ {
+ printf("Pixels per block is greater than pixels per scanline.\n");
+ return 0;
+ }
+
+ if (bits_per_pixel) /* if provided for test */
+ {
+ if (bits_per_pixel >= 1 && bits_per_pixel <= 24)
+ ;
+ else if (bits_per_pixel == 32 || bits_per_pixel == 64)
+ ;
+ else
+ {
+ printf("bits per pixel must be in range 1..24,32,64");
+ return 0;
+ }
+ }
+
+ if (pixels_per_block > MAX_PIXELS_PER_BLOCK)
+ {
+ printf("maximum pixels per block exceeded");
+ return 0;
+ }
+
+ if (pixels_per_block & 1)
+ {
+ printf("pixels per block must be even");
+ return 0;
+ }
+
+ if (pixels_per_block > pixels_per_scanline)
+ {
+ printf("pixels per block > pixels per scanline");
+ return 0;
+ }
+
+ if (pixels_per_scanline > MAX_PIXELS_PER_SCANLINE)
+ {
+ printf("maximum pixels per scanline exceeded");
+ return 0;
+ }
+
+ if (image_pixels < pixels_per_scanline)
+ {
+ printf("image pixels less than pixels per scanline");
+ return 0;
+ }
+
+ if (image_pixels % pixels_per_scanline)
+ {
+ printf("Pixels (%d) must be integer multiple of pixels per scanline (%d)\n",
+ (unsigned)image_pixels,pixels_per_scanline);
+ return 0;
+ }
+
+#if 0
+ if (pixels_per_scanline % pixels_per_block)
+ {
+ printf("Pixels per scanline (%d) must be an integer multiple of pixels per block (%d)\n",
+ pixels_per_scanline, pixels_per_block);
+ return 0;
+ }
+#endif
+
+ return 1;
+}
+
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 5a5bb78..b7dd9bf 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -51,7 +51,7 @@ int main(int argc, char **argv)
else if (strcmp(argv[i], "-t") == 0) {
/* add the -t option */
- h5repack_addcomp(argv[i+1],&options);
+ h5repack_addfilter(argv[i+1],&options);
/* jump to next */
++i;
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index 0dcebd4..0571656 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -30,7 +30,7 @@
int options_table_init( pack_opttbl_t **tbl )
{
- int i;
+ int i, j;
pack_opttbl_t* table = (pack_opttbl_t*) malloc(sizeof(pack_opttbl_t));
if (table==NULL) {
printf("Error: not enough memory for options table\n");
@@ -45,11 +45,13 @@ int options_table_init( pack_opttbl_t **tbl )
return -1;
}
- for (i = 0; i < table->size; i++) {
+ for ( i=0; i<table->size; i++) {
strcpy(table->objs[i].path,"\0");
- table->objs[i].comp.info = -1;
- table->objs[i].comp.type = -1;
+ table->objs[i].filter.filtn = -1;
+ for ( j=0; j<CDVALUES; j++)
+ table->objs[i].filter.cd_values[j] = -1;
table->objs[i].chunk.rank = -1;
+ table->objs[i].refobj_id = -1;
}
*tbl = table;
@@ -101,9 +103,11 @@ int options_add_chunk( obj_list_t *obj_list,
}
for (i = table->nelems; i < table->size; i++) {
strcpy(table->objs[i].path,"\0");
- table->objs[i].comp.info = -1;
- table->objs[i].comp.type = -1;
+ table->objs[i].filter.filtn = -1;
+ for ( j=0; j<CDVALUES; j++)
+ table->objs[i].filter.cd_values[j] = -1;
table->objs[i].chunk.rank = -1;
+ table->objs[i].refobj_id = -1;
}
}
@@ -173,19 +177,19 @@ int options_add_chunk( obj_list_t *obj_list,
/*-------------------------------------------------------------------------
- * Function: options_add_comp
+ * Function: options_add_filter
*
- * Purpose: add a compression -t option to the option list
+ * Purpose: add a compression -f option to the option list
*
* Return: 0, ok, -1, fail
*
*-------------------------------------------------------------------------
*/
-int options_add_comp( obj_list_t *obj_list,
- int n_objs,
- comp_info_t comp,
- pack_opttbl_t *table )
+int options_add_filter(obj_list_t *obj_list,
+ int n_objs,
+ filter_info_t filt,
+ pack_opttbl_t *table )
{
int i, j, I, added=0, found=0;
@@ -199,9 +203,11 @@ int options_add_comp( obj_list_t *obj_list,
}
for (i = table->nelems; i < table->size; i++) {
strcpy(table->objs[i].path,"\0");
- table->objs[i].comp.info = -1;
- table->objs[i].comp.type = -1;
+ table->objs[i].filter.filtn = -1;
+ for ( j=0; j<CDVALUES; j++)
+ table->objs[i].filter.cd_values[j] = -1;
table->objs[i].chunk.rank = -1;
+ table->objs[i].refobj_id = -1;
}
}
@@ -217,19 +223,11 @@ int options_add_comp( obj_list_t *obj_list,
/*already on the table */
if (strcmp(obj_list[j].obj,table->objs[i].path)==0)
{
- /* already COMP info inserted for this one; exit */
- if (table->objs[i].comp.type>0)
- {
- printf("Input Error: compression information already inserted for <%s>\n",obj_list[j].obj);
- exit(1);
- }
- /* insert the comp info */
- else
- {
- table->objs[i].comp = comp;
- found=1;
- break;
- }
+ /* insert */
+
+ table->objs[i].filter = filt;
+ found=1;
+ break;
} /* if */
} /* i */
@@ -239,7 +237,7 @@ int options_add_comp( obj_list_t *obj_list,
I = table->nelems + added;
added++;
strcpy(table->objs[I].path,obj_list[j].obj);
- table->objs[I].comp = comp;
+ table->objs[I].filter = filt;
}
} /* j */
}
@@ -253,7 +251,7 @@ int options_add_comp( obj_list_t *obj_list,
I = table->nelems + added;
added++;
strcpy(table->objs[I].path,obj_list[j].obj);
- table->objs[I].comp = comp;
+ table->objs[I].filter = filt;
}
}
diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c
index f401e1c..9f331b2 100644
--- a/tools/h5repack/h5repack_parse.c
+++ b/tools/h5repack/h5repack_parse.c
@@ -20,15 +20,13 @@
/*-------------------------------------------------------------------------
- * Function: parse_comp
+ * Function: parse_filter
*
- * Purpose: read compression info
+ * Purpose: read filter information
*
* Return: a list of names, the number of names and its compression type
- * NULL, on error
*
* Examples:
- * "AA,B,CDE:RLE"
* "GZIP 6"
* "A,B:NONE"
*
@@ -40,9 +38,10 @@
*/
-obj_list_t* parse_comp(const char *str,
- int *n_objs,
- comp_info_t *comp)
+obj_list_t* parse_filter(const char *str,
+ int *n_objs,
+ filter_info_t *filt,
+ pack_opt_t *options)
{
unsigned i, u;
char c;
@@ -52,9 +51,10 @@ obj_list_t* parse_comp(const char *str,
char scomp[10];
char stype[5];
obj_list_t* obj_list=NULL;
+ unsigned pixels_per_block;
/* initialize compression info */
- memset(comp,0,sizeof(comp_info_t));
+ 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++)
@@ -71,8 +71,8 @@ obj_list_t* parse_comp(const char *str,
}
if (end_obj==-1) { /* missing : */
- printf("Input Error: Invalid compression input in <%s>\n",str);
- exit(1);
+ /* apply to all objects */
+ options->all_filter=1;
}
n++;
@@ -107,9 +107,9 @@ obj_list_t* parse_comp(const char *str,
}
- /* get compression type */
+ /* get filter additional parameters */
m=0;
- for ( i=end_obj+1, k=0; i<len; i++,k++)
+ for ( i=end_obj+1, k=0, j=0; i<len; i++,k++)
{
c = str[i];
scomp[k]=c;
@@ -129,7 +129,7 @@ obj_list_t* parse_comp(const char *str,
stype[m]=c;
}
stype[m]='\0';
- comp->info=atoi(stype);
+ filt->cd_values[j++]=atoi(stype);
i+=m; /* jump */
}
else if (i==len-1) { /*no more parameters */
@@ -142,7 +142,7 @@ obj_list_t* parse_comp(const char *str,
*-------------------------------------------------------------------------
*/
if (strcmp(scomp,"NONE")==0)
- comp->type=H5Z_FILTER_NONE;
+ filt->filtn=H5Z_FILTER_NONE;
/*-------------------------------------------------------------------------
* H5Z_FILTER_DEFLATE
@@ -150,7 +150,7 @@ obj_list_t* parse_comp(const char *str,
*/
else if (strcmp(scomp,"GZIP")==0)
{
- comp->type=H5Z_FILTER_DEFLATE;
+ filt->filtn=H5Z_FILTER_DEFLATE;
if (no_param) { /*no more parameters, GZIP must have parameter */
if (obj_list) free(obj_list);
printf("Input Error: Missing compression parameter in <%s>\n",str);
@@ -164,60 +164,108 @@ obj_list_t* parse_comp(const char *str,
*/
else if (strcmp(scomp,"SZIP")==0)
{
- comp->type=H5Z_FILTER_SZIP;
- if (m>0){ /*SZIP does not have parameter */
+ filt->filtn=H5Z_FILTER_SZIP;
+ if (no_param) { /*no more parameters, SZIP must have parameter */
if (obj_list) free(obj_list);
- printf("Input Error: Extra compression parameter in SZIP <%s>\n",str);
+ printf("Input Error: 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);
+ printf("Input Error: 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);
+ printf("Input Error: Extra parameter in FLET <%s>\n",str);
exit(1);
}
}
else {
if (obj_list) free(obj_list);
- printf("Input Error: Invalid compression type in <%s>\n",str);
+ printf("Input Error: Invalid filter type in <%s>\n",str);
exit(1);
}
}
} /*i*/
+/*-------------------------------------------------------------------------
+ * check valid parameters
+ *-------------------------------------------------------------------------
+ */
- /* check valid parameters */
- switch (comp->type)
- {
- case H5Z_FILTER_DEFLATE:
- if (comp->info<0 || comp->info>9 ){
- if (obj_list) free(obj_list);
- printf("Input Error: Invalid compression parameter in <%s>\n",str);
- exit(1);
- }
- break;
- case H5Z_FILTER_SZIP:
- break;
- };
+ switch (filt->filtn)
+ {
+
+ case H5Z_FILTER_DEFLATE:
+ if (filt->cd_values[0]<0 || filt->cd_values[0]>9 ){
+ if (obj_list) free(obj_list);
+ printf("Input Error: 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);
+ printf("Input Error: 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);
+ printf("Input Error: pixels_per_block is too large in <%s>\n",str);
+ exit(1);
+ }
+ break;
+ };
return obj_list;
}
/*-------------------------------------------------------------------------
- * Function: get_scomp
+ * Function: get_sfilter
*
- * Purpose: return the compression type as a string
+ * Purpose: return the filter as a string name
*
* Return: name of filter, exit on error
*
*-------------------------------------------------------------------------
*/
-const char* get_scomp(int code)
+const char* get_sfilter(H5Z_filter_t filtn)
{
- if (code==H5Z_FILTER_NONE)
+ if (filtn==H5Z_FILTER_NONE)
return "NONE";
- else if (code==H5Z_FILTER_DEFLATE)
+ else if (filtn==H5Z_FILTER_DEFLATE)
return "GZIP";
- else if (code==H5Z_FILTER_SZIP)
+ else if (filtn==H5Z_FILTER_SZIP)
return "SZIP";
+ else if (filtn==H5Z_FILTER_SHUFFLE)
+ return "SHUFFLE";
+ else if (filtn==H5Z_FILTER_FLETCHER32)
+ return "FLETCHERP";
else {
- printf("Input Error in compression type\n");
+ printf("Input error in filter type\n");
exit(1);
}
return NULL;
@@ -247,7 +295,8 @@ const char* get_scomp(int code)
obj_list_t* parse_chunk(const char *str,
int *n_objs,
hsize_t *chunk_lengths,
- int *chunk_rank)
+ int *chunk_rank,
+ pack_opt_t *options)
{
obj_list_t* obj_list=NULL;
unsigned i;
@@ -271,9 +320,8 @@ obj_list_t* parse_chunk(const char *str,
}
}
- if (end_obj==-1) { /* missing : */
- printf("Input Error: Invalid chunking input in <%s>\n",str);
- exit(1);
+ if (end_obj==-1) { /* missing : chunk all */
+ options->all_chunk=1;
}
n++;
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 81bafab..d02038d 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -130,6 +130,8 @@ int do_copy_refobjs(hid_t fidin,
hobj_ref_t *refbuf;
const char* refname;
hobj_ref_t *buf;
+ unsigned u;
+
/*-------------------------------------------------------------------------
* read to memory
@@ -152,17 +154,17 @@ int do_copy_refobjs(hid_t fidin,
printf( "cannot allocate memory\n" );
goto error;
}
- for ( j=0; j<nelmts; j++)
+ for ( u=0; u<nelmts; u++)
{
- if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[j]))<0)
+ if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
goto error;
/* get the name. a valid name could only occur in the
second traversal of the file */
- if ((refname=MapIdToName(refobj_id,travt,options))!=NULL)
+ if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
/* create the reference */
- if (H5Rcreate(&refbuf[j],fidout,refname,H5R_OBJECT,-1)<0)
+ if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
goto error;
if (options->verbose)
@@ -412,7 +414,7 @@ int do_copy_refobjs_inattr(hid_t loc_in,
H5G_obj_t obj_type;
hid_t refobj_id;
hobj_ref_t *refbuf;
- int i;
+ unsigned k;
const char* refname;
hobj_ref_t *buf;
@@ -432,17 +434,17 @@ int do_copy_refobjs_inattr(hid_t loc_in,
printf( "cannot allocate memory\n" );
goto error;
}
- for ( i=0; i<nelmts; i++)
+ for ( k=0; k<nelmts; k++)
{
- if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[i]))<0)
+ if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0)
goto error;
/* get the name. a valid name could only occur in the
second traversal of the file */
- if ((refname=MapIdToName(refobj_id,travt,options))!=NULL)
+ if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
/* create the reference */
- if (H5Rcreate(&refbuf[i],fidout,refname,H5R_OBJECT,-1)<0)
+ if (H5Rcreate(&refbuf[k],fidout,refname,H5R_OBJECT,-1)<0)
goto error;
if (options->verbose)
@@ -503,7 +505,7 @@ error:
*-------------------------------------------------------------------------
*/
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
+void close_obj(H5G_obj_t obj_type, hid_t obj_id)
{
switch (obj_type) {
@@ -531,8 +533,7 @@ static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
*/
const char* MapIdToName(hid_t refobj_id,
- trav_table_t *travt,
- pack_opt_t *options) /* repack options */
+ trav_table_t *travt)
{
hid_t id;
hid_t fid;
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
new file mode 100644
index 0000000..f3c1583
--- /dev/null
+++ b/tools/h5repack/h5repack_verify.c
@@ -0,0 +1,241 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 "hdf5.h"
+#include "h5test.h"
+#include "h5repack.h"
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: has_filter
+ *
+ * Purpose: verify if a filter is present in the property list DCPL_ID
+ *
+ * Return: 1 has, 0 does not, -1 error
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 19, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int has_filter(hid_t dcpl_id,
+ H5Z_filter_t filtnin)
+{
+
+ int nfilters; /* number of filters */
+ unsigned filt_flags; /* filter flags */
+ H5Z_filter_t filtn; /* filter identification number */
+ unsigned cd_values[20]; /* filter client data values */
+ size_t cd_nelmts; /* filter client number of values */
+ char f_name[256]; /* filter name */
+ int have=0; /* flag, filter is present */
+ hsize_t chsize[64]; /* chunk size in elements */
+ H5D_layout_t layout; /* layout */
+ int rank; /* rank */
+ int i; /* index */
+
+ /* if no information about the input filter is requested return exit */
+ if (filtnin==-1)
+ return 1;
+
+ /* get information about filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
+ return -1;
+
+/*
+ H5D_COMPACT = 0
+ H5D_CONTIGUOUS = 1
+ H5D_CHUNKED = 2
+ */
+ layout = H5Pget_layout(dcpl_id);
+ if (layout==H5D_CHUNKED)
+ {
+ if ((rank = H5Pget_chunk(dcpl_id,NELMTS(chsize),chsize/*out*/))<0)
+ return -1;
+ }
+
+ for (i=0; i<nfilters; i++)
+ {
+ cd_nelmts = NELMTS(cd_values);
+ filtn = H5Pget_filter(dcpl_id,
+ i,
+ &filt_flags,
+ &cd_nelmts,
+ cd_values,
+ sizeof(f_name),
+ f_name);
+
+ if (filtnin==filtn)
+ have=1;
+
+ }
+
+ return have;
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: h5repack_verify
+ *
+ * Purpose: verify if the filters specified in the options list are
+ * present on the output file
+ *
+ * Return: 1=filter present, 0=filter not present, -1=error
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December 19, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_verify(const char *fname,
+ pack_opt_t *options)
+{
+ hid_t fid; /* file ID */
+ hid_t dset_id; /* dataset ID */
+ hid_t dcpl_id; /* dataset creation property list ID */
+ hid_t space_id; /* space ID */
+ int ret=1, i;
+ trav_table_t *travt=NULL;
+
+ /* open the file */
+ if ((fid=H5Fopen(fname,H5F_ACC_RDONLY,H5P_DEFAULT))<0 )
+ return -1;
+
+ for ( i=0; i<options->op_tbl->nelems; i++)
+ {
+ char* name=options->op_tbl->objs[i].path;
+ pack_info_t obj=options->op_tbl->objs[i];
+
+/*-------------------------------------------------------------------------
+ * open
+ *-------------------------------------------------------------------------
+ */
+ if ((dset_id=H5Dopen(fid,name))<0)
+ goto error;
+ if ((space_id=H5Dget_space(dset_id))<0)
+ goto error;
+ if ((dcpl_id=H5Dget_create_plist(dset_id))<0)
+ goto error;
+
+/*-------------------------------------------------------------------------
+ * filter check
+ *-------------------------------------------------------------------------
+ */
+ if (has_filter(dcpl_id,obj.filter.filtn)==0)
+ ret=0;
+
+/*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if (H5Pclose(dcpl_id)<0)
+ goto error;
+ if (H5Sclose(space_id)<0)
+ goto error;
+ if (H5Dclose(dset_id)<0)
+ goto error;
+
+ }
+
+
+/*-------------------------------------------------------------------------
+ * check for the "all" objects option
+ *-------------------------------------------------------------------------
+ */
+
+ if (options->all_filter==1)
+ {
+
+ /* init table */
+ trav_table_init(&travt);
+
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fid,travt)<0)
+ goto error;
+
+ for ( i=0; i<travt->nobjs; i++)
+ {
+ char* name=travt->objs[i].name;
+
+ switch ( travt->objs[i].type )
+ {
+ case H5G_DATASET:
+
+ /*-------------------------------------------------------------------------
+ * open
+ *-------------------------------------------------------------------------
+ */
+ if ((dset_id=H5Dopen(fid,name))<0)
+ goto error;
+ if ((space_id=H5Dget_space(dset_id))<0)
+ goto error;
+ if ((dcpl_id=H5Dget_create_plist(dset_id))<0)
+ goto error;
+
+ /*-------------------------------------------------------------------------
+ * filter check
+ *-------------------------------------------------------------------------
+ */
+ if (has_filter(dcpl_id,options->filter_g.filtn)==0)
+ ret=0;
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+ if (H5Pclose(dcpl_id)<0)
+ goto error;
+ if (H5Sclose(space_id)<0)
+ goto error;
+ if (H5Dclose(dset_id)<0)
+ goto error;
+
+ break;
+ default:
+ break;
+ } /* switch */
+
+ } /* i */
+
+ /* free table */
+ trav_table_free(travt);
+ }
+
+/*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ if (H5Fclose(fid)<0)
+ return -1;
+
+ return ret;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Pclose(dcpl_id);
+ H5Sclose(space_id);
+ H5Dclose(dset_id);
+ H5Fclose(fid);
+ trav_table_free(travt);
+ } H5E_END_TRY;
+ return -1;
+}
+
diff --git a/tools/h5repack/testh5repack_dset.c b/tools/h5repack/testh5repack_dset.c
index 88363f7..42ad644 100644
--- a/tools/h5repack/testh5repack_dset.c
+++ b/tools/h5repack/testh5repack_dset.c
@@ -16,6 +16,9 @@
#include "h5test.h"
#include "h5repack.h"
+
+
+
/*-------------------------------------------------------------------------
* Function: write_dset
*
diff --git a/tools/h5repack/testh5repack_filters.c b/tools/h5repack/testh5repack_filters.c
index 9067ff0..5a35d67 100644
--- a/tools/h5repack/testh5repack_filters.c
+++ b/tools/h5repack/testh5repack_filters.c
@@ -16,80 +16,110 @@
#include "h5test.h"
#include "h5repack.h"
+#define DIM1 40
+#define DIM2 20
+#define CDIM1 DIM1/2
+#define CDIM2 DIM2/2
+#define RANK 2
+
+
/*-------------------------------------------------------------------------
* Function: make_deflate
*
- * Purpose: make a dataset using DEFLATE (GZIP) compression in FID
+ * Purpose: make a dataset using DEFLATE (GZIP) compression in LOC_ID
*
*-------------------------------------------------------------------------
*/
-static int
-make_deflate(hid_t fid)
+int make_deflate(hid_t loc_id)
{
hid_t dcpl; /* dataset creation property list */
hid_t dsid; /* dataset ID */
hid_t sid; /* dataspace ID */
- int rank=2;
- hsize_t dims[2]={4,2};
- hsize_t chunk_dims[2]={2,1};
- int buf[4][2]={{1,2},{3,4},{5,6},{7,8}};
+ hsize_t dims[RANK]={DIM1,DIM2};
+ hsize_t chunk_dims[RANK]={CDIM1,CDIM2};
+ int buf[40][20];
+ int i, j, n=0;
+
+ for (i=0; i<DIM1; i++){
+ for (j=0; j<DIM2; j++){
+ buf[i][j]=n++;
+ }
+ }
/* create a space */
- if((sid = H5Screate_simple(rank, dims, NULL))<0)
- TEST_ERROR;
+ if((sid = H5Screate_simple(RANK, dims, NULL))<0)
+ return -1;
/* create the dataset creation property list */
if ((dcpl = H5Pcreate(H5P_DATASET_CREATE))<0)
- TEST_ERROR;
+ goto out;
/* set up for deflated data */
- if(H5Pset_chunk(dcpl, rank, chunk_dims)<0)
- TEST_ERROR;
+ if(H5Pset_chunk(dcpl, RANK, chunk_dims)<0)
+ goto out;
if(H5Pset_deflate(dcpl, 9)<0)
- TEST_ERROR;
+ goto out;
/* create the dataset */
- if((dsid = H5Dcreate (fid, "dset_gzip", H5T_NATIVE_INT, sid, dcpl))<0)
- TEST_ERROR;
+ if((dsid = H5Dcreate (loc_id, "dset_gzip", H5T_NATIVE_INT, sid, dcpl))<0)
+ goto out;
/* write the data to the dataset */
if(H5Dwrite(dsid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)<0)
- TEST_ERROR;
+ goto out;
/* close */
if(H5Dclose(dsid)<0)
- TEST_ERROR;
- if(H5Pclose(dcpl)<0)
- TEST_ERROR;
+ goto out;
+
+/*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
if(H5Sclose(sid)<0)
- TEST_ERROR;
+ goto out;
+ if(H5Pclose(dcpl)<0)
+ goto out;
return 0;
-error:
- return 1;
+out:
+ H5E_BEGIN_TRY {
+ H5Dclose(dsid);
+ H5Pclose(dcpl);
+ H5Sclose(sid);
+ } H5E_END_TRY;
+ return -1;
}
/*-------------------------------------------------------------------------
* Function: make_szip
*
- * Purpose: make a dataset using SZIP compression in FID
+ * Purpose: make a dataset using SZIP compression in LOC_ID
*
*-------------------------------------------------------------------------
*/
-static int
-make_szip(hid_t fid)
+int make_szip(hid_t loc_id)
{
hid_t dcpl; /* dataset creation property list */
hid_t dsid; /* dataset ID */
hid_t sid; /* dataspace ID */
- int rank=2;
- hsize_t dims[2]={4,2};
- hsize_t chunk_dims[2]={2,1};
- int buf[4][2]={{1,2},{3,4},{5,6},{7,8}};
unsigned szip_options_mask=H5_SZIP_ALLOW_K13_OPTION_MASK|H5_SZIP_NN_OPTION_MASK;
unsigned szip_pixels_per_block;
+ hsize_t dims[RANK]={DIM1,DIM2};
+ hsize_t chunk_dims[RANK]={CDIM1,CDIM2};
+ int buf[40][20];
+ int i, j, n=0;
+
+ for (i=0; i<DIM1; i++){
+ for (j=0; j<DIM2; j++){
+ buf[i][j]=n++;
+ }
+ }
+
+ memset(buf,0,sizeof buf);
/*
pixels_per_block must be an even number, and <= pixels_per_scanline
@@ -98,295 +128,76 @@ make_szip(hid_t fid)
szip_pixels_per_block=16;
/* create a space */
- if((sid = H5Screate_simple(rank, dims, NULL))<0)
- TEST_ERROR;
+ if((sid = H5Screate_simple(RANK, dims, NULL))<0)
+ return -1;
/* create the dataset creation property list */
if ((dcpl = H5Pcreate(H5P_DATASET_CREATE))<0)
- TEST_ERROR;
+ goto out;
/* set up for sziped data */
- if(H5Pset_chunk(dcpl, rank, chunk_dims)<0)
- TEST_ERROR;
+ if(H5Pset_chunk(dcpl, RANK, chunk_dims)<0)
+ goto out;
if(H5Pset_szip (dcpl, szip_options_mask, szip_pixels_per_block)<0)
- TEST_ERROR;
+ goto out;
/* create the dataset */
- if((dsid = H5Dcreate (fid, "dset_szip", H5T_NATIVE_INT, sid, dcpl))<0)
- TEST_ERROR;
+ if((dsid = H5Dcreate (loc_id, "dset_szip", H5T_NATIVE_INT, sid, dcpl))<0)
+ goto out;
/* write the data to the dataset */
if(H5Dwrite(dsid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf)<0)
- TEST_ERROR;
+ goto out;
/* close */
if(H5Dclose(dsid)<0)
- TEST_ERROR;
+ goto out;
if(H5Pclose(dcpl)<0)
- TEST_ERROR;
+ goto out;
if(H5Sclose(sid)<0)
- TEST_ERROR;
+ goto out;
return 0;
-error:
- return 1;
+out:
+ H5E_BEGIN_TRY {
+ H5Dclose(dsid);
+ H5Pclose(dcpl);
+ H5Sclose(sid);
+ } H5E_END_TRY;
+ return -1;
}
/*-------------------------------------------------------------------------
- * Function: make_testfiles
+ * Function: make_nofilters
*
- * Purpose: make a test file with all types of HDF5 objects,
- * datatypes and filters
+ * Purpose: make several dataset with no filters
*
*-------------------------------------------------------------------------
*/
-int make_testfiles(void)
+int make_nofilters(hid_t loc_id)
{
- hid_t fid; /* file ID */
- int nerrors=0;
-
- TESTING(" generating datasets");
-
- /* create a file for general copy test */
- if((fid = H5Fcreate(FNAME1,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
- TEST_ERROR;
- nerrors += make_all_objects(fid);
- /* close */
- if(H5Fclose(fid)<0)
- TEST_ERROR;
-
- /* create a file for attributes copy test */
- if((fid = H5Fcreate(FNAME2,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
- TEST_ERROR;
- nerrors += make_attributes(fid);
- /* close */
- if(H5Fclose(fid)<0)
- TEST_ERROR;
-
- /* create a file for special items test */
- if((fid = H5Fcreate(FNAME3,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
- TEST_ERROR;
- nerrors += make_special_objects(fid);
- /* close */
- if(H5Fclose(fid)<0)
- TEST_ERROR;
-
- /* create a file for the filters test */
- if((fid = H5Fcreate(FNAME4,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
- TEST_ERROR;
- nerrors += make_deflate(fid);
- nerrors += make_szip(fid);
- /* close */
- if(H5Fclose(fid)<0)
- TEST_ERROR;
-
- if (nerrors)
- goto error;
-
- PASSED();
- return 0;
-
-error:
- return 1;
-}
-
-
-/*-------------------------------------------------------------------------
- * Function: make_all_objects
- *
- * Purpose: make a test file with all types of HDF5 objects, datatypes
- *
- *-------------------------------------------------------------------------
- */
-int make_all_objects(hid_t fid)
-{
- hid_t dset_id;
- hid_t group_id;
- hid_t type_id;
- hid_t root_id;
- hid_t space_id;
- hsize_t dims[1]={2};
- /* Compound datatype */
- typedef struct s_t
+ char name[5];
+ hsize_t dims[RANK]={DIM1,DIM2};
+ int buf[40][20];
+ int i, j, n=0;
+
+ for (i=0; i<DIM1; i++){
+ for (j=0; j<DIM2; j++){
+ buf[i][j]=n++;
+ }
+ }
+
+ for (i=0; i<4; i++)
{
- int a;
- float b;
- } s_t;
-
-/*-------------------------------------------------------------------------
- * H5G_DATASET
- *-------------------------------------------------------------------------
- */
-
- space_id = H5Screate_simple(1,dims,NULL);
- dset_id = H5Dcreate(fid,"dset_ref",H5T_NATIVE_INT,space_id,H5P_DEFAULT);
- H5Sclose(space_id);
-
-/*-------------------------------------------------------------------------
- * H5G_GROUP
- *-------------------------------------------------------------------------
- */
- group_id = H5Gcreate(fid,"g1",0);
- root_id = H5Gopen(fid, "/");
-
-/*-------------------------------------------------------------------------
- * H5G_TYPE
- *-------------------------------------------------------------------------
- */
+ sprintf(name,"dset%d",i+1);
+ if (write_dset(loc_id,RANK,dims,name,H5T_NATIVE_INT,buf)<0)
+ return -1;
+ }
- /* Create a memory compound datatype */
- type_id = H5Tcreate (H5T_COMPOUND, sizeof(s_t));
- H5Tinsert(type_id, "a", HOFFSET(s_t, a), H5T_NATIVE_INT);
- H5Tinsert(type_id, "b", HOFFSET(s_t, b), H5T_NATIVE_FLOAT);
- /* Commit compound datatype and close it */
- H5Tcommit(fid, "type", type_id);
- H5Tclose(type_id);
-
-/*-------------------------------------------------------------------------
- * H5G_LINK
- *-------------------------------------------------------------------------
- */
-
- H5Glink(fid, H5G_LINK_SOFT, "dset", "link");
-/*-------------------------------------------------------------------------
- * write a series of datasetes on the group, and root group
- *-------------------------------------------------------------------------
- */
-
- write_dset_in(root_id,"dset_ref",fid,0);
- write_dset_in(group_id,"dset_ref",fid,0);
-
-
- /* Close */
- H5Dclose(dset_id);
- H5Gclose(group_id);
- H5Gclose(root_id);
-
- return 0;
-
+ return 0;
}
-/*-------------------------------------------------------------------------
- * Function: make_attributes
- *
- * Purpose: make a test file with all types of attributes
- *
- *-------------------------------------------------------------------------
- */
-int make_attributes(hid_t fid)
-{
- hid_t dset_id;
- hid_t group_id;
- hid_t root_id;
- hid_t space_id;
- hsize_t dims[1]={2};
-
-/*-------------------------------------------------------------------------
- * H5G_DATASET
- *-------------------------------------------------------------------------
- */
-
- space_id = H5Screate_simple(1,dims,NULL);
- dset_id = H5Dcreate(fid,"dset",H5T_NATIVE_INT,space_id,H5P_DEFAULT);
- H5Sclose(space_id);
-
-/*-------------------------------------------------------------------------
- * H5G_GROUP
- *-------------------------------------------------------------------------
- */
- group_id = H5Gcreate(fid,"g1",0);
- root_id = H5Gopen(fid, "/");
-
-/*-------------------------------------------------------------------------
- * write a series of attributes on the dataset, group, and root group
- *-------------------------------------------------------------------------
- */
-
- write_attr_in(dset_id,"dset",fid,0);
- write_attr_in(group_id,"dset",fid,0);
- write_attr_in(root_id,"dset",fid,0);
-
- /* Close */
- H5Dclose(dset_id);
- H5Gclose(group_id);
- H5Gclose(root_id);
-
- return 0;
-
-}
-
-
-
-/*-------------------------------------------------------------------------
- * Function: make_special_objects
- *
- * Purpose: make a test file with non common items
- *
- *-------------------------------------------------------------------------
- */
-int make_special_objects(hid_t loc_id)
-{
- hid_t group1_id;
- hid_t group2_id;
- hid_t group3_id;
- hsize_t dims[1]={2};
- int buf[2]= {1,2};
-
-/*-------------------------------------------------------------------------
- * create a dataset and some hard links to it
- *-------------------------------------------------------------------------
- */
-
- if (write_dset(loc_id,1,dims,"dset",H5T_NATIVE_INT,buf)<0)
- return -1;
- if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link1 to dset")<0)
- return -1;
- if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link2 to dset")<0)
- return -1;
- if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link3 to dset")<0)
- return -1;
-
-
-/*-------------------------------------------------------------------------
- * create a group and some hard links to it
- *-------------------------------------------------------------------------
- */
-
- if ((group1_id = H5Gcreate(loc_id,"g1",0))<0)
- return -1;
- if ((group2_id = H5Gcreate(group1_id,"g2",0))<0)
- return -1;
- if ((group3_id = H5Gcreate(group2_id,"g3",0))<0)
- return -1;
-
- /*
- H5Glink2(curr_loc_id, current_name, link_type, new_loc_id, new_name )
- hid_t curr_loc_id
- IN: The file or group identifier for the original object.
- const char * current_name
- IN: Name of the existing object if link is a hard link.
- H5G_link_t link_type
- IN: Link type. Possible values are H5G_LINK_HARD and H5G_LINK_SOFT.
- hid_t new_loc_id
- IN: The file or group identifier for the new link.
- const char * new_name
- IN: New name for the object.
- */
-
- if (H5Glink2(loc_id, "g1", H5G_LINK_HARD, group2_id, "link1 to g1")<0)
- return -1;
- if (H5Glink2(group1_id, "g2", H5G_LINK_HARD, group3_id, "link1 to g2")<0)
- return -1;
-
- H5Gclose(group1_id);
- H5Gclose(group2_id);
- H5Gclose(group3_id);
-
- return 0;
-
-}
-
diff --git a/tools/h5repack/testh5repack_main.c b/tools/h5repack/testh5repack_main.c
index 83b9b77..e46dd53 100644
--- a/tools/h5repack/testh5repack_main.c
+++ b/tools/h5repack/testh5repack_main.c
@@ -81,17 +81,15 @@ error:
}
-
-
/*-------------------------------------------------------------------------
* Function: test_filter_deflate
*
* Purpose:
*
- * 1) compress/chunk FILENAME with teh DEFLATE filter
+ * 1) compress/chunk FILENAME with the DEFLATE filter
* 2) use the h5diff utility to compare the input and output file;
* it returns RET==0 if the objects have the same data
- * 3) use API functions to verify the compression/chunking input on the otput file
+ * 3) use API functions to verify the compression/chunking input on the output file
*
* Return: Success: zero
* Failure: 1
@@ -109,30 +107,119 @@ test_filter_deflate(void)
pack_opt_t pack_options;
diff_opt_t diff_options;
memset(&diff_options, 0, sizeof (diff_opt_t));
+ memset(&pack_options, 0, sizeof (pack_opt_t));
TESTING(" deflate filter");
+#ifdef H5_HAVE_FILTER_DEFLATE
+
+ if (h5repack_init (&pack_options, 0)<0)
+ TEST_ERROR;
+ if (h5repack_addfilter("dset1:GZIP 9",&pack_options)<0)
+ TEST_ERROR;
+ if (h5repack_addchunk("dset1:20x10",&pack_options)<0)
+ TEST_ERROR;
+ if (h5repack(FNAME4,FNAME4OUT,&pack_options)<0)
+ TEST_ERROR;
+ if (h5diff(FNAME4,FNAME4OUT,NULL,NULL,&diff_options) == 1)
+ TEST_ERROR;
+ if (h5repack_verify(FNAME4OUT,&pack_options)<=0)
+ TEST_ERROR;
+ if (h5repack_end (&pack_options)<0)
+ TEST_ERROR;
+
if (h5repack_init (&pack_options, 0)<0)
TEST_ERROR;
- if (h5repack_addcomp("dset_gzip:GZIP 9",&pack_options)<0)
+ if (h5repack_addfilter("GZIP 9",&pack_options)<0)
TEST_ERROR;
- if (h5repack_addchunk("dset_gzip:5x4",&pack_options)<0)
+ if (h5repack_addchunk("20x10",&pack_options)<0)
TEST_ERROR;
if (h5repack(FNAME4,FNAME4OUT,&pack_options)<0)
TEST_ERROR;
+ if (h5diff(FNAME4,FNAME4OUT,NULL,NULL,&diff_options) == 1)
+ TEST_ERROR;
+ if (h5repack_verify(FNAME4OUT,&pack_options)<=0)
+ TEST_ERROR;
if (h5repack_end (&pack_options)<0)
TEST_ERROR;
+
+ PASSED();
+#else
+ SKIPPED();
+#endif
+ return 0;
+
+#ifdef H5_HAVE_FILTER_DEFLATE
+error:
+ return 1;
+#endif
+
+
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: test_filter_szip
+ *
+ * Purpose:
+ *
+ * 1) compress/chunk FILENAME with the SZIP filter
+ * 2) use the h5diff utility to compare the input and output file;
+ * it returns RET==0 if the objects have the same data
+ * 3) use API functions to verify the compression/chunking input on the output file
+ *
+ * Return: Success: zero
+ * Failure: 1
+ *
+ * Programmer: Pedro Vicente <pvn@ncsa.uiuc.edu>
+ * December, 19, 2003
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+test_filter_szip(void)
+{
+ pack_opt_t pack_options;
+ diff_opt_t diff_options;
+ memset(&diff_options, 0, sizeof (diff_opt_t));
+ memset(&pack_options, 0, sizeof (pack_opt_t));
+
+ TESTING(" szip filter");
+
+#ifdef H5_HAVE_FILTER_SZIP
+
+ if (h5repack_init (&pack_options, 0)<0)
+ TEST_ERROR;
+ if (h5repack_addfilter("dset2:SZIP 8",&pack_options)<0)
+ TEST_ERROR;
+ if (h5repack_addchunk("dset2:20x10",&pack_options)<0)
+ TEST_ERROR;
+ if (h5repack(FNAME4,FNAME4OUT,&pack_options)<0)
+ TEST_ERROR;
if (h5diff(FNAME4,FNAME4OUT,NULL,NULL,&diff_options) == 1)
TEST_ERROR;
+ if (h5repack_verify(FNAME4OUT,&pack_options)<=0)
+ TEST_ERROR;
+ if (h5repack_end (&pack_options)<0)
+ TEST_ERROR;
- PASSED();
+ PASSED();
+#else
+ SKIPPED();
+#endif
return 0;
+#ifdef H5_HAVE_FILTER_SZIP
error:
return 1;
+#endif
+
}
+
/*-------------------------------------------------------------------------
* Function: main
*
@@ -157,7 +244,8 @@ int main (void)
puts("Testing h5repack:");
/* make the test files */
- nerrors += make_testfiles();
+ if (make_testfiles()<0)
+ goto error;
/* test a copy with no filters */
nerrors += test_copy();
@@ -165,6 +253,8 @@ int main (void)
/* test a copy with the deflate filter */
nerrors += test_filter_deflate();
+ /* test a copy with the szip filter */
+ nerrors += test_filter_szip();
/* check for errors */
if (nerrors)
diff --git a/tools/h5repack/testh5repack_make.c b/tools/h5repack/testh5repack_make.c
new file mode 100644
index 0000000..34d3029
--- /dev/null
+++ b/tools/h5repack/testh5repack_make.c
@@ -0,0 +1,318 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 "hdf5.h"
+#include "h5test.h"
+#include "h5repack.h"
+
+
+int make_all_objects(hid_t loc_id);
+int make_attributes(hid_t loc_id);
+int make_special_objects(hid_t loc_id);
+
+
+/*-------------------------------------------------------------------------
+ * Function: make_testfiles
+ *
+ * Purpose: make a test file with all types of HDF5 objects,
+ * datatypes and filters
+ *
+ *-------------------------------------------------------------------------
+ */
+int make_testfiles(void)
+{
+ hid_t loc_id; /* file ID */
+
+ TESTING(" generating datasets");
+
+ /* create a file for general copy test */
+ if((loc_id = H5Fcreate(FNAME1,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
+ return -1;
+
+ if (make_all_objects(loc_id)<0)
+ goto out;
+
+ /* close */
+ if(H5Fclose(loc_id)<0)
+ return -1;
+
+ /* create a file for attributes copy test */
+ if((loc_id = H5Fcreate(FNAME2,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
+ return -1;
+
+ if (make_attributes(loc_id)<0)
+ goto out;
+
+ /* close */
+ if(H5Fclose(loc_id)<0)
+ return -1;
+
+ /* create a file for special items test */
+ if((loc_id = H5Fcreate(FNAME3,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
+ return -1;
+
+ if (make_special_objects(loc_id)<0)
+ goto out;
+
+ /* close */
+ if(H5Fclose(loc_id)<0)
+ return -1;
+
+ /* create a file for the filters test */
+ if((loc_id = H5Fcreate(FNAME4,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT))<0)
+ return -1;
+
+ if (make_nofilters(loc_id)<0)
+ goto out;
+
+ if (make_deflate(loc_id)<0)
+ goto out;
+
+ if (make_szip(loc_id)<0)
+ goto out;
+
+ /* close */
+ if(H5Fclose(loc_id)<0)
+ return -1;
+
+ PASSED();
+ return 0;
+
+out:
+ H5E_BEGIN_TRY {
+ H5Fclose(loc_id);
+ } H5E_END_TRY;
+ return -1;
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: make_all_objects
+ *
+ * Purpose: make a test file with all types of HDF5 objects, datatypes
+ *
+ *-------------------------------------------------------------------------
+ */
+int make_all_objects(hid_t loc_id)
+{
+ hid_t dset_id;
+ hid_t group_id;
+ hid_t type_id;
+ hid_t root_id;
+ hid_t space_id;
+ hsize_t dims[1]={2};
+ /* Compound datatype */
+ typedef struct s_t
+ {
+ int a;
+ float b;
+ } s_t;
+
+/*-------------------------------------------------------------------------
+ * H5G_DATASET
+ *-------------------------------------------------------------------------
+ */
+
+ space_id = H5Screate_simple(1,dims,NULL);
+ dset_id = H5Dcreate(loc_id,"dset_ref",H5T_NATIVE_INT,space_id,H5P_DEFAULT);
+ H5Sclose(space_id);
+
+/*-------------------------------------------------------------------------
+ * H5G_GROUP
+ *-------------------------------------------------------------------------
+ */
+ group_id = H5Gcreate(loc_id,"g1",0);
+ root_id = H5Gopen(loc_id, "/");
+
+/*-------------------------------------------------------------------------
+ * H5G_TYPE
+ *-------------------------------------------------------------------------
+ */
+
+ /* Create a memory compound datatype */
+ type_id = H5Tcreate (H5T_COMPOUND, sizeof(s_t));
+ H5Tinsert(type_id, "a", HOFFSET(s_t, a), H5T_NATIVE_INT);
+ H5Tinsert(type_id, "b", HOFFSET(s_t, b), H5T_NATIVE_FLOAT);
+ /* Commit compound datatype and close it */
+ H5Tcommit(loc_id, "type", type_id);
+ H5Tclose(type_id);
+
+/*-------------------------------------------------------------------------
+ * H5G_LINK
+ *-------------------------------------------------------------------------
+ */
+
+ H5Glink(loc_id, H5G_LINK_SOFT, "dset", "link");
+
+/*-------------------------------------------------------------------------
+ * write a series of datasetes on the group, and root group
+ *-------------------------------------------------------------------------
+ */
+
+ write_dset_in(root_id,"dset_ref",loc_id,0);
+ write_dset_in(group_id,"dset_ref",loc_id,0);
+
+
+ /* Close */
+ H5Dclose(dset_id);
+ H5Gclose(group_id);
+ H5Gclose(root_id);
+
+ return 0;
+
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: make_attributes
+ *
+ * Purpose: make a test file with all types of attributes
+ *
+ *-------------------------------------------------------------------------
+ */
+int make_attributes(hid_t loc_id)
+{
+ hid_t dset_id;
+ hid_t group_id;
+ hid_t root_id;
+ hid_t space_id;
+ hsize_t dims[1]={2};
+
+
+/*-------------------------------------------------------------------------
+ * H5G_DATASET
+ *-------------------------------------------------------------------------
+ */
+
+ space_id = H5Screate_simple(1,dims,NULL);
+ dset_id = H5Dcreate(loc_id,"dset",H5T_NATIVE_INT,space_id,H5P_DEFAULT);
+ H5Sclose(space_id);
+
+/*-------------------------------------------------------------------------
+ * H5G_GROUP
+ *-------------------------------------------------------------------------
+ */
+ group_id = H5Gcreate(loc_id,"g1",0);
+ root_id = H5Gopen(loc_id, "/");
+
+/*-------------------------------------------------------------------------
+ * write a series of attributes on the dataset, group, and root group
+ *-------------------------------------------------------------------------
+ */
+
+ write_attr_in(dset_id,"dset",loc_id,0);
+ write_attr_in(group_id,"dset",loc_id,0);
+ write_attr_in(root_id,"dset",loc_id,0);
+
+ /* Close */
+ H5Dclose(dset_id);
+ H5Gclose(group_id);
+ H5Gclose(root_id);
+
+ return 0;
+
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: make_special_objects
+ *
+ * Purpose: make a test file with non common items
+ *
+ *-------------------------------------------------------------------------
+ */
+int make_special_objects(hid_t loc_id)
+{
+ hid_t group1_id;
+ hid_t group2_id;
+ hid_t group3_id;
+ hsize_t dims[2]={3,2};
+ int buf[3][2]= {{1,1},{1,2},{2,2}};
+ hid_t dset_id;
+ hid_t space_id;
+ hid_t plist_id;
+ herr_t status;
+ int fillvalue=2;
+
+/*-------------------------------------------------------------------------
+ * create a dataset and some hard links to it
+ *-------------------------------------------------------------------------
+ */
+
+ if (write_dset(loc_id,2,dims,"dset",H5T_NATIVE_INT,buf)<0)
+ return -1;
+ if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link1 to dset")<0)
+ return -1;
+ if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link2 to dset")<0)
+ return -1;
+ if (H5Glink(loc_id, H5G_LINK_HARD, "dset", "link3 to dset")<0)
+ return -1;
+
+
+/*-------------------------------------------------------------------------
+ * create a group and some hard links to it
+ *-------------------------------------------------------------------------
+ */
+
+ if ((group1_id = H5Gcreate(loc_id,"g1",0))<0)
+ return -1;
+ if ((group2_id = H5Gcreate(group1_id,"g2",0))<0)
+ return -1;
+ if ((group3_id = H5Gcreate(group2_id,"g3",0))<0)
+ return -1;
+
+ /*
+ H5Glink2(curr_loc_id, current_name, link_type, new_loc_id, new_name )
+ hid_t curr_loc_id
+ IN: The file or group identifier for the original object.
+ const char * current_name
+ IN: Name of the existing object if link is a hard link.
+ H5G_link_t link_type
+ IN: Link type. Possible values are H5G_LINK_HARD and H5G_LINK_SOFT.
+ hid_t new_loc_id
+ IN: The file or group identifier for the new link.
+ const char * new_name
+ IN: New name for the object.
+ */
+
+ if (H5Glink2(loc_id, "g1", H5G_LINK_HARD, group2_id, "link1 to g1")<0)
+ return -1;
+ if (H5Glink2(group1_id, "g2", H5G_LINK_HARD, group3_id, "link1 to g2")<0)
+ return -1;
+
+ H5Gclose(group1_id);
+ H5Gclose(group2_id);
+ H5Gclose(group3_id);
+
+/*-------------------------------------------------------------------------
+ * H5T_INTEGER, write a fill value
+ *-------------------------------------------------------------------------
+ */
+
+ plist_id = H5Pcreate(H5P_DATASET_CREATE);
+ status = H5Pset_fill_value(plist_id, H5T_NATIVE_INT, &fillvalue);
+ space_id = H5Screate_simple(2,dims,NULL);
+ dset_id = H5Dcreate(loc_id,"dset_fill",H5T_NATIVE_INT,space_id,plist_id);
+ status = H5Dwrite(dset_id,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf);
+ status = H5Pclose(plist_id);
+ status = H5Dclose(dset_id);
+ status = H5Sclose(space_id);
+
+ return 0;
+
+}
+
+
generated by cgit v0.12 at 2024-12-27 05:39:45 (GMT)