[svn-r12884]

 h5repack support for H5Ocopy in the copy of objects. The old method
for recreating references was dropped (references recreated in a second
traversal of the file)
The logic for using H5Ocopy or not is
if the input DCPL has filters or non default layout OR these are
requested by the user THEN
use the old h5repack read / write
ELSE
use H5Ocopy

1 files changed, 0 insertions, 720 deletions

diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 7fce723..e01af2d 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -24,728 +24,8 @@ extern char  *progname;
 static const char* MapIdToName(hid_t refobj_id,
                                trav_table_t *travt);
 
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id);
 
 
-static int copy_refs_attr(hid_t loc_in,
-                          hid_t loc_out,
-                          pack_opt_t *options,
-                          trav_table_t *travt,
-                          hid_t fidout         /* for saving references */
-                          );
-
-/*-------------------------------------------------------------------------
- * Function: do_copy_refobjs
- *
- * Purpose: duplicate all referenced HDF5 objects in the file
- *  and create hard links
- *
- * 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,
-                    trav_table_t *travt,
-                    pack_opt_t *options) /* repack options */
-{
- hid_t     grp_in=-1;            /* read group ID */
- hid_t     grp_out=-1;           /* write group ID */
- hid_t     dset_in=-1;           /* read dataset ID */
- hid_t     dset_out=-1;          /* write dataset ID */
- hid_t     type_in=-1;           /* named type ID */
- hid_t     dcpl_id=-1;           /* dataset creation property list ID */
- hid_t     space_id=-1;          /* space ID */
- hid_t     ftype_id=-1;          /* file type ID */
- hid_t     wtype_id=-1;          /* read/write type ID */
- size_t    msize;             /* 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 */
- int       next;              /* external files */
- int       i, j;
-
-/*-------------------------------------------------------------------------
- * browse
- *-------------------------------------------------------------------------
- */
-
- for ( i = 0; i < travt->nobjs; i++)
- {
-  switch ( travt->objs[i].type )
-  {
- /*-------------------------------------------------------------------------
-  * H5G_GROUP
-  *-------------------------------------------------------------------------
-  */
-  case H5G_GROUP:
-
-   /*-------------------------------------------------------------------------
-    * check for hard links
-    *-------------------------------------------------------------------------
-    */
-
-   if (travt->objs[i].nlinks)
-   {
-    for ( j=0; j<travt->objs[i].nlinks; j++)
-    {
-      H5Glink(fidout,
-      H5L_TYPE_HARD,
-      travt->objs[i].name,
-      travt->objs[i].links[j].new_name);
-    }
-   }
-
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_DATASET
-   *-------------------------------------------------------------------------
-   */
-  case H5G_DATASET:
-
-   if ((dset_in=H5Dopen(fidin,travt->objs[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 (options->use_native==1)
-    wtype_id = h5tools_get_native_type(ftype_id);
-   else
-    wtype_id = H5Tcopy(ftype_id); 
-
-   if ((msize=H5Tget_size(wtype_id))==0)
-    goto error;
-
-/*-------------------------------------------------------------------------
- * check for external files
- *-------------------------------------------------------------------------
- */
-   if ((next=H5Pget_external_count (dcpl_id))<0)
-    goto error;
-/*-------------------------------------------------------------------------
- * check if the dataset creation property list has filters that
- * are not registered in the current configuration
- * 1) the external filters GZIP and SZIP might not be available
- * 2) the internal filters might be turned off
- *-------------------------------------------------------------------------
- */
-   if (next==0 && h5tools_canreadf((NULL),dcpl_id)==1)
-   {
-/*-------------------------------------------------------------------------
- * test for a valid output dataset
- *-------------------------------------------------------------------------
- */
-   dset_out = FAIL;
-
-/*-------------------------------------------------------------------------
- * object references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- *-------------------------------------------------------------------------
- */
-   if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
-   {
-    H5G_obj_t        obj_type;
-    hid_t            refobj_id;
-    hobj_ref_t       *refbuf=NULL; /* buffer for object references */
-    hobj_ref_t       *buf=NULL;
-    const char*      refname;
-    unsigned         u;
-
-   /*-------------------------------------------------------------------------
-    * read to memory
-    *-------------------------------------------------------------------------
-    */
-
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      error_msg(progname, "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Dread(dset_in,wtype_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){
-      error_msg(progname, "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( u=0; u<nelmts; u++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
-        continue;
-      } H5E_END_TRY;
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       /* create the reference, -1 parameter for objects */
-       if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
-        goto error;
-       if (options->verbose)
-        printf("object <%s> object reference created to <%s>\n",
-        travt->objs[i].name,
-        refname);
-      }/*refname*/
-      close_obj(obj_type,refobj_id);
-     }/*  u */
-    }/*nelmts*/
-
-    /*-------------------------------------------------------------------------
-     * create/write dataset/close
-     *-------------------------------------------------------------------------
-     */
-    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
-     goto error;
-    if (nelmts) {
-     if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
-      goto error;
-    }
-
-    if (buf)
-     free(buf);
-    if (refbuf)
-     free(refbuf);
-
-   }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
-   else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
-   {
-    H5G_obj_t        obj_type;
-    hid_t            refobj_id;
-    hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
-    hdset_reg_ref_t  *buf=NULL;    /* output buffer */
-    const char*      refname;
-    unsigned         u;
-
-   /*-------------------------------------------------------------------------
-    * read input to memory
-    *-------------------------------------------------------------------------
-    */
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      error_msg(progname, "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
-      goto error;
-     if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
-      goto error;
-
-     /*-------------------------------------------------------------------------
-      * create output
-      *-------------------------------------------------------------------------
-      */
-
-     refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
-     if ( refbuf==NULL){
-      error_msg(progname, "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( u=0; u<nelmts; u++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
-        continue;
-      } H5E_END_TRY;
-
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       hid_t region_id;    /* region id of the referenced dataset */
-       if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
-        goto error;
-       /* create the reference, we need the space_id */
-       if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
-        goto error;
-       if (H5Sclose(region_id)<0)
-        goto error;
-       if (options->verbose)
-        printf("object <%s> region reference created to <%s>\n",
-        travt->objs[i].name,
-        refname);
-      }/*refname*/
-      close_obj(obj_type,refobj_id);
-     }/*  u */
-    }/*nelmts*/
-
-    /*-------------------------------------------------------------------------
-     * create/write dataset/close
-     *-------------------------------------------------------------------------
-     */
-    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,space_id,dcpl_id))<0)
-     goto error;
-    if (nelmts) {
-     if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
-      goto error;
-    }
-
-    if (buf)
-     free(buf);
-    if (refbuf)
-     free(refbuf);
-   } /* H5T_STD_REF_DSETREG */
-
-
-/*-------------------------------------------------------------------------
- * not references, open previously created object in 1st traversal
- *-------------------------------------------------------------------------
- */
-   else
-   {
-    if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
-     goto error;
-   }
-
-   assert(dset_out!=FAIL);
-
-/*-------------------------------------------------------------------------
- * copy referenced objects in attributes
- *-------------------------------------------------------------------------
- */
-   if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
-    goto error;
-
-
-/*-------------------------------------------------------------------------
- * check for hard links
- *-------------------------------------------------------------------------
- */
-   if (travt->objs[i].nlinks)
-   {
-    for ( j=0; j<travt->objs[i].nlinks; j++){
-     H5Glink(fidout,
-      H5L_TYPE_HARD,
-      travt->objs[i].name,
-      travt->objs[i].links[j].new_name);
-    }
-   }
-
-   if (H5Dclose(dset_out)<0)
-    goto error;
-
-   }/*can_read*/
-
-   /*-------------------------------------------------------------------------
-    * close
-    *-------------------------------------------------------------------------
-    */
-
-   if (H5Tclose(ftype_id)<0)
-    goto error;
-   if (H5Tclose(wtype_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;
-
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_TYPE
-   *-------------------------------------------------------------------------
-   */
-  case H5G_TYPE:
-
-   if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
-    goto error;
-
-   if (H5Tclose(type_in)<0)
-    goto error;
-
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_LINK
-   * H5G_UDLINK
-   *-------------------------------------------------------------------------
-   */
-
-  case H5G_LINK:
-  case H5G_UDLINK:
-
-   /*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 (copy_refs_attr(grp_in,grp_out,options,travt,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(wtype_id);
-  H5Tclose(type_in);
- } H5E_END_TRY;
- return -1;
-
-}
-
-
-/*-------------------------------------------------------------------------
- * Function: copy_refs_attr
- *
- * Purpose: duplicate all referenced HDF5 located in attributes
- *  relative to 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
- *
- *-------------------------------------------------------------------------
- */
-
-static int copy_refs_attr(hid_t loc_in,
-                          hid_t loc_out,
-                          pack_opt_t *options,
-                          trav_table_t *travt,
-                          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 type ID */
- hid_t      wtype_id;     /* read/write type ID */
- size_t     msize;        /* 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 (options->use_native==1)
-   wtype_id = h5tools_get_native_type(ftype_id);
-  else
-   wtype_id = H5Tcopy(ftype_id); 
-
-  if ((msize=H5Tget_size(wtype_id))==0)
-   goto error;
-
-/*-------------------------------------------------------------------------
- * object references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- *-------------------------------------------------------------------------
- */
-   if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
-   {
-    H5G_obj_t   obj_type;
-    hid_t       refobj_id;
-    hobj_ref_t  *refbuf=NULL;
-    unsigned    k;
-    const char* refname;
-    hobj_ref_t  *buf=NULL;
-
-   /*-------------------------------------------------------------------------
-    * read input to memory
-    *-------------------------------------------------------------------------
-    */
-
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      error_msg(progname, "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Aread(attr_id,wtype_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){
-      error_msg(progname, "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( k=0; k<nelmts; k++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0)
-        goto error;
-      } H5E_END_TRY;
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       /* create the reference */
-       if (H5Rcreate(&refbuf[k],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);
-     }/*  k */
-    }/*nelmts*/
-
-    /*-------------------------------------------------------------------------
-     * copy
-     *-------------------------------------------------------------------------
-     */
-
-    if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
-     goto error;
-    if (nelmts) {
-     if(H5Awrite(attr_out,wtype_id,refbuf)<0)
-      goto error;
-    }
-
-    if (H5Aclose(attr_out)<0)
-     goto error;
-
-    if (refbuf)
-     free(refbuf);
-    if (buf)
-     free(buf);
-
-   }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
-   else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
-   {
-    H5G_obj_t        obj_type;
-    hid_t            refobj_id;
-    hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
-    hdset_reg_ref_t  *buf=NULL;    /* output buffer */
-    const char*      refname;
-    unsigned         k;
-
-   /*-------------------------------------------------------------------------
-    * read input to memory
-    *-------------------------------------------------------------------------
-    */
-
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      error_msg(progname, "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Aread(attr_id,wtype_id,buf)<0)
-      goto error;
-     if ((obj_type = H5Rget_obj_type(attr_id,H5R_DATASET_REGION,buf))<0)
-      goto error;
-
-    /*-------------------------------------------------------------------------
-     * create output
-     *-------------------------------------------------------------------------
-     */
-
-     refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
-     if ( refbuf==NULL){
-      error_msg(progname, "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( k=0; k<nelmts; k++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
-        continue;
-      } H5E_END_TRY;
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       hid_t region_id;    /* region id of the referenced dataset */
-       if ((region_id = H5Rget_region(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
-        goto error;
-       /* create the reference, we need the space_id */
-       if (H5Rcreate(&refbuf[k],fidout,refname,H5R_DATASET_REGION,region_id)<0)
-        goto error;
-       if (H5Sclose(region_id)<0)
-        goto error;
-       if (options->verbose)
-        printf("object <%s> region reference created to <%s>\n",name,refname);
-      }
-      close_obj(obj_type,refobj_id);
-     }/*  k */
-    }/*nelmts */
-
-    /*-------------------------------------------------------------------------
-     * copy
-     *-------------------------------------------------------------------------
-     */
-
-    if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
-     goto error;
-    if (nelmts) {
-     if(H5Awrite(attr_out,wtype_id,refbuf)<0)
-      goto error;
-    }
-    if (H5Aclose(attr_out)<0)
-     goto error;
-    if (refbuf)
-     free(refbuf);
-    if (buf)
-     free(buf);
-   } /* H5T_STD_REF_DSETREG */
-
-/*-------------------------------------------------------------------------
- * close
- *-------------------------------------------------------------------------
- */
-
-  if (H5Tclose(ftype_id)<0) goto error;
-  if (H5Tclose(wtype_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(wtype_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)
-{
- H5E_BEGIN_TRY
- {
-  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:
-   break;
-  }
- } H5E_END_TRY;
-}
 
 /*-------------------------------------------------------------------------
  * Function: MapIdToName