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-rw-r--r--tools/h5repack/h5repack.h4
-rw-r--r--tools/h5repack/h5repack_list.c257
-rw-r--r--tools/h5repack/h5repack_list.h5
-rw-r--r--tools/h5repack/test_h5repack_main.c2
4 files changed, 245 insertions, 23 deletions
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index a661e76..01eef14 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -24,7 +24,9 @@
#define MAX_NC_NAME 256 /* max length of a name */
#define MAX_VAR_DIMS 32 /* max per variable dimensions */
-
+#if 1
+#define H5_REPACK_DEBUG
+#endif
/*-------------------------------------------------------------------------
diff --git a/tools/h5repack/h5repack_list.c b/tools/h5repack/h5repack_list.c
index f444218..8358221 100644
--- a/tools/h5repack/h5repack_list.c
+++ b/tools/h5repack/h5repack_list.c
@@ -193,15 +193,14 @@ int copy_file(char* fnamein,
return -1;
}
+
+
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
do_copy_file(fidin,fidout,nobjects,info,options);
-
-
-
/*-------------------------------------------------------------------------
* free
@@ -241,19 +240,19 @@ void print_objlist(char *filename,
switch ( info[i].type )
{
case H5G_GROUP:
- printf("%s %20s\n", info[i].name, "group" );
+ printf(" %-10s %s\n", "group", info[i].name );
break;
case H5G_DATASET:
- printf("%s %20s\n", info[i].name, "dataset" );
+ printf(" %-10s %s\n", "dataset", info[i].name );
break;
case H5G_TYPE:
- printf("%s %20s\n", info[i].name, "datatype" );
+ printf(" %-10s %s\n", "datatype", info[i].name );
break;
case H5G_LINK:
- printf("%s %20s\n", info[i].name, "link" );
+ printf(" %-10s %s\n", "link", info[i].name );
break;
default:
- printf("%s %20s\n", info[i].name, "User defined object" );
+ printf(" %-10s %s\n", "User defined object", info[i].name );
break;
}
}
@@ -281,18 +280,21 @@ int do_copy_file(hid_t fidin,
trav_info_t *info,
pack_opt_t *options)
{
- hid_t grp_id; /* group ID */
+ hid_t grp_in; /* group ID */
+ hid_t grp_out; /* group ID */
hid_t dset_in; /* read dataset ID */
hid_t dset_out; /* write dataset ID */
+ hid_t type_in; /* named type ID */
+ hid_t type_out; /* named type ID */
hid_t dcpl_id; /* dataset creation property list ID */
hid_t space_id; /* space ID */
hid_t ftype_id; /* file data type ID */
hid_t mtype_id; /* memory data type ID */
size_t msize; /* memory size of memory type */
void *buf=NULL; /* data buffer */
- hsize_t nelmts; /* number of elements in dataaset */
+ hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
- hsize_t dims[32]; /* dimansions of dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
int i, j;
for ( i = 0; i < nobjects; i++)
@@ -305,11 +307,26 @@ int do_copy_file(hid_t fidin,
*/
case H5G_GROUP:
if (options->verbose)
- printf("%s %20s\n", info[i].name, "group" );
+ printf(" %-10s %s\n", "group",info[i].name );
- if ((grp_id=H5Gcreate(fidout, info[i].name, 0))<0)
+ if ((grp_out=H5Gcreate(fidout, info[i].name, 0))<0)
goto error;
- if (H5Gclose(grp_id)<0)
+
+ if((grp_in = H5Gopen (fidin, info[i].name))<0)
+ goto error;
+
+/*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+
+ copy_attr(grp_in,
+ grp_out,
+ options);
+
+ if (H5Gclose(grp_out)<0)
+ goto error;
+ if (H5Gclose(grp_in)<0)
goto error;
break;
@@ -320,7 +337,7 @@ int do_copy_file(hid_t fidin,
*/
case H5G_DATASET:
if (options->verbose)
- printf("%s %20s\n", info[i].name, "dataset" );
+ printf(" %-10s %s\n", "dataset",info[i].name );
if ((dset_in=H5Dopen(fidin,info[i].name))<0)
goto error;
@@ -363,6 +380,22 @@ int do_copy_file(hid_t fidin,
if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
+
+/*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+
+ copy_attr(dset_in,
+ dset_out,
+ options);
+
+
+/*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
if (H5Tclose(ftype_id)<0)
goto error;
if (H5Tclose(mtype_id)<0)
@@ -375,7 +408,9 @@ int do_copy_file(hid_t fidin,
goto error;
if (H5Dclose(dset_out)<0)
goto error;
-
+
+ if (buf)
+ free(buf);
break;
@@ -384,18 +419,68 @@ int do_copy_file(hid_t fidin,
*-------------------------------------------------------------------------
*/
case H5G_TYPE:
+
+ if ((type_in = H5Topen (fidin, info[i].name))<0)
+ goto error;
+
+ if ((type_out = H5Tcopy(type_in))<0)
+ goto error;
+
+ if ((H5Tcommit(fidout, info[i].name, type_out))<0)
+ goto error;
+
+/*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+
+ copy_attr(type_in,
+ type_out,
+ options);
+
+ if (H5Tclose(type_in)<0)
+ goto error;
+ if (H5Tclose(type_out)<0)
+ goto error;
+
if (options->verbose)
- printf("%s %20s\n", info[i].name, "datatype" );
+ printf(" %-10s %s\n", "datatype",info[i].name );
+
break;
case H5G_LINK:
- if (options->verbose)
- printf("%s %20s\n", info[i].name, "link" );
+
+ {
+
+ H5G_stat_t statbuf;
+ char *targbuf=NULL;
+
+ if (H5Gget_objinfo(fidin,info[i].name,FALSE,&statbuf)<0)
+ goto error;
+
+ targbuf = malloc(statbuf.linklen);
+
+ if (H5Gget_linkval(fidin,info[i].name,statbuf.linklen,targbuf)<0)
+ goto error;
+
+ if (H5Glink(fidout,
+ H5G_LINK_SOFT,
+ targbuf, /* current name of object */
+ info[i].name /* new name of object */
+ )<0)
+ goto error;
+
+ free(targbuf);
+
+ if (options->verbose)
+ printf(" %-10s %s\n", "link",info[i].name );
+
+ }
break;
default:
if (options->verbose)
- printf("%s %20s\n", info[i].name, "User defined object" );
+ printf(" %-10s %s\n", "User defined object", info[i].name);
break;
}
}
@@ -404,16 +489,146 @@ int do_copy_file(hid_t fidin,
error:
H5E_BEGIN_TRY {
- H5Gclose(grp_id);
+ H5Gclose(grp_in);
+ H5Gclose(grp_out);
H5Pclose(dcpl_id);
H5Sclose(space_id);
H5Dclose(dset_in);
H5Dclose(dset_out);
H5Tclose(ftype_id);
H5Tclose(mtype_id);
+ H5Tclose(type_in);
+ H5Tclose(type_out);
+ if (buf)
+ free(buf);
} H5E_END_TRY;
return -1;
}
+/*-------------------------------------------------------------------------
+ * Function: copy_attr
+ *
+ * Purpose: copy attributes located in LOC_IN, which is obtained either from
+ * loc_id = H5Gopen( fid, name);
+ * loc_id = H5Dopen( fid, name);
+ * loc_id = H5Topen( fid, name);
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 28, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int copy_attr(hid_t loc_in,
+ hid_t loc_out,
+ pack_opt_t *options
+ )
+{
+ hid_t attr_id; /* attr ID */
+ hid_t attr_out; /* attr ID */
+ hid_t space_id; /* space ID */
+ hid_t ftype_id; /* file data type ID */
+ hid_t mtype_id; /* memory data type ID */
+ size_t msize; /* memory size of memory type */
+ void *buf=NULL; /* data buffer */
+ hsize_t nelmts; /* number of elements in dataset */
+ int rank; /* rank of dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ char name[255];
+ int n, i, j;
+
+ if ((n = H5Aget_num_attrs(loc_in))<0)
+ goto error;
+
+ for ( i = 0; i < n; i++)
+ {
+/*-------------------------------------------------------------------------
+ * open
+ *-------------------------------------------------------------------------
+ */
+ /* open attribute */
+ if ((attr_id = H5Aopen_idx(loc_in, i))<0)
+ goto error;
+
+ /* get name */
+ if (H5Aget_name( attr_id, 255, name )<0)
+ goto error;
+
+ /* get the file datatype */
+ if ((ftype_id = H5Aget_type( attr_id )) < 0 )
+ goto error;
+
+ /* get the dataspace handle */
+ if ((space_id = H5Aget_space( attr_id )) < 0 )
+ goto error;
+
+ /* get dimensions */
+ if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
+ goto error;
+
+/*-------------------------------------------------------------------------
+ * read to memory
+ *-------------------------------------------------------------------------
+ */
+ nelmts=1;
+ for (j=0; j<rank; j++)
+ nelmts*=dims[j];
+ if ((mtype_id=H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<0)
+ goto error;
+ if ((msize=H5Tget_size(mtype_id))<0)
+ goto error;
+ buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+ if ( buf==NULL){
+ printf( "cannot read into memory\n" );
+ goto error;
+ }
+ if (H5Aread(attr_id,mtype_id,buf)<0)
+ goto error;
+
+
+/*-------------------------------------------------------------------------
+ * copy
+ *-------------------------------------------------------------------------
+ */
+
+ if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
+ goto error;
+ if(H5Awrite(attr_out,mtype_id,buf)<0)
+ goto error;
+
+ if (options->verbose)
+ printf(" %-13s %s\n", "attr", name);
+
+/*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ if (H5Tclose(ftype_id)<0) goto error;
+ if (H5Tclose(mtype_id)<0) goto error;
+ if (H5Sclose(space_id)<0) goto error;
+ if (H5Aclose(attr_id)<0) goto error;
+ if (H5Aclose(attr_out)<0) goto error;
+ if (buf)
+ free(buf);
+ } /* i */
+
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Tclose(ftype_id);
+ H5Tclose(mtype_id);
+ H5Sclose(space_id);
+ H5Aclose(attr_id);
+ H5Aclose(attr_out);
+ if (buf)
+ free(buf);
+ } H5E_END_TRY;
+ return -1;
+}
diff --git a/tools/h5repack/h5repack_list.h b/tools/h5repack/h5repack_list.h
index 905057e..fd10c6b 100644
--- a/tools/h5repack/h5repack_list.h
+++ b/tools/h5repack/h5repack_list.h
@@ -44,6 +44,11 @@ int do_copy_file(hid_t fidin,
trav_info_t *info,
pack_opt_t *options);
+int copy_attr(hid_t loc_in,
+ hid_t loc_out,
+ pack_opt_t *options
+ );
+
diff --git a/tools/h5repack/test_h5repack_main.c b/tools/h5repack/test_h5repack_main.c
index 828bc3a..b647427 100644
--- a/tools/h5repack/test_h5repack_main.c
+++ b/tools/h5repack/test_h5repack_main.c
@@ -60,7 +60,7 @@ test()
TEST_ERROR;
if (h5repack_end (&pack_options)<0)
TEST_ERROR;
- if (h5diff(FILENAME,FILENAME,NULL,NULL,diff_options) == 1)
+ if (h5diff(FILENAME,FILENAME,NULL,NULL,&diff_options) == 1)
TEST_ERROR;
PASSED();
generated by cgit v0.12 at 2024-11-04 20:48:10 (GMT)