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authorPedro Vicente Nunes <pvn@hdfgroup.org>2003-12-16 18:08:45 (GMT)
committerPedro Vicente Nunes <pvn@hdfgroup.org>2003-12-16 18:08:45 (GMT)
commitdc4f40f02f16d182ffad1fcbfa3dfdaf0d9426b9 (patch)
tree9914f9b0c661d5bdd73e83f559a4048fe6975724 /tools/h5repack/h5repack_refs.c
parent991bd6c9e3f590104269c70c4e7becb55770091f (diff)
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[svn-r7962] Purpose:
h5repack new features Description: added the copy of referenced objects Solution: Platforms tested: linux solaris 2.7 IRIX Misc. update:
Diffstat (limited to 'tools/h5repack/h5repack_refs.c')
-rw-r--r--tools/h5repack/h5repack_refs.c600
1 files changed, 600 insertions, 0 deletions
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
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+++ b/tools/h5repack/h5repack_refs.c
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+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the files COPYING and Copyright.html. COPYING can be found at the root *
+ * of the source code distribution tree; Copyright.html can be found at the *
+ * root level of an installed copy of the electronic HDF5 document set and *
+ * is linked from the top-level documents page. It can also be found at *
+ * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
+ * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include "H5private.h"
+#include "h5repack.h"
+
+
+/*-------------------------------------------------------------------------
+ * Function: do_copy_refobjs
+ *
+ * Purpose: duplicate all referenced HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December, 10, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int do_copy_refobjs(hid_t fidin,
+ hid_t fidout,
+ int nobjects, /* number of objects */
+ trav_info_t *travi, /* array of object names */
+ pack_opt_t *options) /* repack options */
+{
+ 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 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 */
+ hsize_t nelmts; /* number of elements in dataset */
+ int rank; /* rank of dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ int i, j;
+
+ /* initialize to test for non reference cases */
+
+/*-------------------------------------------------------------------------
+ * browse
+ *-------------------------------------------------------------------------
+ */
+
+ for ( i = 0; i < nobjects; i++)
+ {
+
+ switch ( travi[i].type )
+ {
+ /*-------------------------------------------------------------------------
+ * H5G_GROUP
+ *-------------------------------------------------------------------------
+ */
+ case H5G_GROUP:
+
+ if((grp_in = H5Gopen (fidin,travi[i].name))<0)
+ goto error;
+
+ if (H5Gclose(grp_in)<0)
+ goto error;
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5G_DATASET
+ *-------------------------------------------------------------------------
+ */
+ case H5G_DATASET:
+
+ if ((dset_in=H5Dopen(fidin,travi[i].name))<0)
+ goto error;
+ if ((space_id=H5Dget_space(dset_in))<0)
+ goto error;
+ if ((ftype_id=H5Dget_type (dset_in))<0)
+ goto error;
+ if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
+ goto error;
+ if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
+ goto error;
+ if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
+ goto error;
+ 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;
+
+
+/*-------------------------------------------------------------------------
+ * object references are a special case
+ * we cannot just copy the buffers, but instead we recreate the reference
+ *-------------------------------------------------------------------------
+ */
+ if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
+ {
+ H5G_obj_t obj_type;
+ hid_t refobj_id;
+ hobj_ref_t *refbuf;
+ const char* refname;
+ hobj_ref_t *buf;
+
+ /*-------------------------------------------------------------------------
+ * read to memory
+ *-------------------------------------------------------------------------
+ */
+
+ buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+ if ( buf==NULL){
+ printf( "cannot read into memory\n" );
+ goto error;
+ }
+ if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+ goto error;
+
+
+ if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
+ goto error;
+ refbuf=HDmalloc((unsigned)nelmts*msize);
+ if ( refbuf==NULL){
+ printf( "cannot allocate memory\n" );
+ goto error;
+ }
+ for ( j=0; j<nelmts; j++)
+ {
+ if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[j]))<0)
+ goto error;
+
+ /* get the name. a valid name could only occur in the
+ second traversal of the file */
+ if ((refname=MapIdToName(refobj_id,nobjects,travi,options))!=NULL)
+ {
+ /* create the reference */
+ if (H5Rcreate(&refbuf[j],fidout,refname,H5R_OBJECT,-1)<0)
+ goto error;
+
+ if (options->verbose)
+ printf("object <%s> reference created to <%s>\n",travi[i].name,refname);
+ }
+ close_obj(obj_type,refobj_id);
+ }/* j */
+
+
+
+ /*-------------------------------------------------------------------------
+ * create/write dataset/close
+ *-------------------------------------------------------------------------
+ */
+ if ((dset_out=H5Dcreate(fidout,travi[i].name,ftype_id,space_id,dcpl_id))<0)
+ goto error;
+ if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
+ goto error;
+
+ free(buf);
+ free(refbuf);
+
+ }/*H5T_STD_REF_OBJ*/
+
+
+ /*-------------------------------------------------------------------------
+ * open previously created object in 1st traversal
+ *-------------------------------------------------------------------------
+ */
+
+ else
+ {
+ if ((dset_out=H5Dopen(fidout,travi[i].name))<0)
+ goto error;
+ }
+
+ /*-------------------------------------------------------------------------
+ * copy referenced objects in attributes
+ *-------------------------------------------------------------------------
+ */
+
+ if (do_copy_refobjs_inattr(dset_in,dset_out,options,nobjects,travi,fidout)<0)
+ goto error;
+
+
+ /*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ if (H5Tclose(ftype_id)<0)
+ goto error;
+ if (H5Tclose(mtype_id)<0)
+ goto error;
+ if (H5Pclose(dcpl_id)<0)
+ goto error;
+ if (H5Sclose(space_id)<0)
+ goto error;
+ if (H5Dclose(dset_in)<0)
+ goto error;
+ if (H5Dclose(dset_out)<0)
+ goto error;
+
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5G_TYPE
+ *-------------------------------------------------------------------------
+ */
+ case H5G_TYPE:
+
+ if ((type_in = H5Topen (fidin,travi[i].name))<0)
+ goto error;
+
+ if (H5Tclose(type_in)<0)
+ goto error;
+
+
+ break;
+
+
+ /*-------------------------------------------------------------------------
+ * H5G_LINK
+ *-------------------------------------------------------------------------
+ */
+
+ case H5G_LINK:
+
+ /*nothing to do */
+ break;
+
+ default:
+
+ break;
+ }
+ }
+
+
+
+/*-------------------------------------------------------------------------
+ * the root is a special case, we get an ID for the root group
+ * and copy its attributes using that ID
+ * it must be done last, because the attributes might contain references to
+ * objects in the object list
+ *-------------------------------------------------------------------------
+ */
+
+ if ((grp_out = H5Gopen(fidout,"/"))<0)
+ goto error;
+
+ if ((grp_in = H5Gopen(fidin,"/"))<0)
+ goto error;
+
+ if (do_copy_refobjs_inattr(grp_in,grp_out,options,nobjects,travi,fidout)<0)
+ goto error;
+
+ if (H5Gclose(grp_out)<0)
+ goto error;
+ if (H5Gclose(grp_in)<0)
+ goto error;
+
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ 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);
+ } H5E_END_TRY;
+ return -1;
+
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: do_copy_refobjs_inattr
+ *
+ * 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 do_copy_refobjs_inattr(hid_t loc_in,
+ hid_t loc_out,
+ pack_opt_t *options,
+ int nobjects, /* number of objects */
+ trav_info_t *travi, /* array of object names */
+ hid_t fidout /* for saving references */
+ )
+{
+ 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 type */
+ 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, j;
+ unsigned u;
+
+ if ((n = H5Aget_num_attrs(loc_in))<0)
+ goto error;
+
+ for ( u = 0; u < (unsigned)n; u++)
+ {
+
+/*-------------------------------------------------------------------------
+ * open
+ *-------------------------------------------------------------------------
+ */
+ /* open attribute */
+ if ((attr_id = H5Aopen_idx(loc_in, u))<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;
+
+
+ /*-------------------------------------------------------------------------
+ * elements
+ *-------------------------------------------------------------------------
+ */
+ 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;
+
+
+
+/*-------------------------------------------------------------------------
+ * object references are a special case
+ * we cannot just copy the buffers, but instead we recreate the reference
+ *-------------------------------------------------------------------------
+ */
+ if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
+ {
+ H5G_obj_t obj_type;
+ hid_t refobj_id;
+ hobj_ref_t *refbuf;
+ int i;
+ const char* refname;
+ hobj_ref_t *buf;
+
+
+ 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;
+
+ if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0)
+ goto error;
+ refbuf=HDmalloc((unsigned)nelmts*msize);
+ if ( refbuf==NULL){
+ printf( "cannot allocate memory\n" );
+ goto error;
+ }
+ for ( i=0; i<nelmts; i++)
+ {
+ if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[i]))<0)
+ goto error;
+
+ /* get the name. a valid name could only occur in the
+ second traversal of the file */
+ if ((refname=MapIdToName(refobj_id,nobjects,travi,options))!=NULL)
+ {
+ /* create the reference */
+ if (H5Rcreate(&refbuf[i],fidout,refname,H5R_OBJECT,-1)<0)
+ goto error;
+
+ if (options->verbose)
+ printf("object <%s> reference created to <%s>\n",name,refname);
+ }
+ close_obj(obj_type,refobj_id);
+ }/* i */
+
+
+ /*-------------------------------------------------------------------------
+ * copy
+ *-------------------------------------------------------------------------
+ */
+
+ if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
+ goto error;
+ if(H5Awrite(attr_out,mtype_id,refbuf)<0)
+ goto error;
+
+ if (H5Aclose(attr_out)<0)
+ goto error;
+
+ free(refbuf);
+ free(buf);
+
+ }/*H5T_STD_REF_OBJ*/
+
+
+/*-------------------------------------------------------------------------
+ * 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;
+ } /* u */
+
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Tclose(ftype_id);
+ H5Tclose(mtype_id);
+ H5Sclose(space_id);
+ H5Aclose(attr_id);
+ H5Aclose(attr_out);
+ } H5E_END_TRY;
+ return -1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: close_obj
+ *
+ * Purpose: Auxiliary function to close an object
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
+{
+
+ switch (obj_type) {
+ case H5G_GROUP:
+ H5Gclose(obj_id);
+ break;
+ case H5G_DATASET:
+ H5Dclose(obj_id);
+ break;
+ case H5G_TYPE:
+ H5Tclose(obj_id);
+ break;
+ default:
+ assert(0);
+ break;
+ }
+}
+
+/*-------------------------------------------------------------------------
+ * Function: MapIdToName
+ *
+ * Purpose: map an object ID to a name
+ *
+ *-------------------------------------------------------------------------
+ */
+
+const char* MapIdToName(hid_t refobj_id,
+ int nobjects, /* number of objects */
+ trav_info_t *travi, /* array of object names */
+ pack_opt_t *options) /* repack options */
+{
+ hid_t id;
+ hid_t fid;
+ int i;
+
+ if ((fid = H5Iget_file_id(refobj_id))<0)
+ {
+ assert(0);
+ return NULL;
+ }
+
+
+ for ( i=0; i<nobjects; i++)
+ {
+ switch ( travi[i].type )
+ {
+
+ /*-------------------------------------------------------------------------
+ * H5G_GROUP
+ *-------------------------------------------------------------------------
+ */
+
+ case H5G_GROUP:
+
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5G_DATASET
+ *-------------------------------------------------------------------------
+ */
+
+ case H5G_DATASET:
+
+ if ((id = H5Dopen(fid,travi[i].name))<0)
+ {
+ assert(0);
+ return NULL;
+ }
+
+ if (H5Dclose(id)<0)
+ {
+ assert(0);
+ return NULL;
+ }
+
+ if (id==refobj_id)
+ {
+ H5Fclose(fid);
+ return travi[i].name;
+ }
+
+
+ break;
+
+ /*-------------------------------------------------------------------------
+ * H5G_TYPE
+ *-------------------------------------------------------------------------
+ */
+
+ case H5G_TYPE:
+
+
+
+ break;
+
+
+ /*-------------------------------------------------------------------------
+ * H5G_LINK
+ *-------------------------------------------------------------------------
+ */
+
+ case H5G_LINK:
+ break;
+
+ default:
+ assert(0);
+ break;
+
+ }
+
+
+ } /* i */
+
+ if (H5Fclose(fid)<0)
+ return NULL;
+
+ return NULL;
+}