[svn-r7962] Purpose:

h5repack new features

Description:
added the copy of referenced objects

Solution:

Platforms tested:
linux
solaris 2.7
IRIX

Misc. update:

1 files changed, 600 insertions, 0 deletions

diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
new file mode 100644
index 0000000..cd5fe80
--- /dev/null
+++ b/tools/h5repack/h5repack_refs.c
@@ -0,0 +1,600 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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;
+}