[svn-r8396] This commit was manufactured by cvs2svn to create branch 'hdf5_1_6'.

1 files changed, 620 insertions, 0 deletions

diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
new file mode 100644
index 0000000..7763bd2
--- /dev/null
+++ b/tools/h5repack/h5repack_copy.c
@@ -0,0 +1,620 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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: copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file 
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int copy_objects(const char* fnamein, 
+                 const char* fnameout,
+                 pack_opt_t *options)
+{
+ hid_t         fidin; 
+ hid_t         fidout; 
+ trav_table_t  *travt=NULL;
+
+/*-------------------------------------------------------------------------
+ * open the files 
+ *-------------------------------------------------------------------------
+ */
+
+ /* disable error reporting */
+ H5E_BEGIN_TRY {
+ 
+ /* Open the files */
+ if ((fidin=H5Fopen(fnamein,H5F_ACC_RDONLY,H5P_DEFAULT))<0 ){
+  printf("h5repack: <%s>: %s\n", fnamein, H5FOPENERROR );
+  exit(1);
+ }
+ if ((fidout=H5Fcreate(fnameout,H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0 ){
+  printf("h5repack: <%s>: Could not create file\n", fnameout );
+  exit(1);
+ }
+ /* enable error reporting */
+ } H5E_END_TRY;
+
+ 
+ if (options->verbose)
+  printf("Making file <%s>...\n",fnameout);
+
+
+ /* init table */
+ trav_table_init(&travt);
+
+ /* get the list of objects in the file */
+ if (h5trav_gettable(fidin,travt)<0)
+  goto out;
+
+/*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+ if(do_copy_objects(fidin,fidout,travt,options)<0) {
+  printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
+  goto out;
+ }
+
+/*-------------------------------------------------------------------------
+ * do the copy of referenced objects
+ * and create hard links
+ *-------------------------------------------------------------------------
+ */
+ if(do_copy_refobjs(fidin,fidout,travt,options)<0) {
+  printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
+  goto out;
+ }
+
+ /* free table */
+ trav_table_free(travt);
+
+/*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+ return 0;
+
+/*-------------------------------------------------------------------------
+ * out
+ *-------------------------------------------------------------------------
+ */
+
+out:
+ H5E_BEGIN_TRY {
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+ trav_table_free(travt);
+ } H5E_END_TRY;
+
+ return -1;
+}
+
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: do_copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file 
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int do_copy_objects(hid_t fidin, 
+                    hid_t fidout, 
+                    trav_table_t *travt,
+                    pack_opt_t *options) /* repack options */
+{
+ hid_t     grp_in=-1;       /* group ID */ 
+ hid_t     grp_out=-1;      /* 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     type_out=-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 data type ID */ 
+ hid_t     mtype_id=-1;     /* 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 */
+ hsize_t   dsize_in;     /* input dataset size before filter */
+#ifdef LATER
+ hsize_t   dsize_out;    /* output dataset size after filter */
+#endif /* LATER */
+ int       i, j;
+
+/*-------------------------------------------------------------------------
+ * copy the suppplied object list
+ *-------------------------------------------------------------------------
+ */
+
+ for ( i = 0; i < travt->nobjs; i++)
+ {
+
+  buf=NULL;
+  switch ( travt->objs[i].type )
+  {
+/*-------------------------------------------------------------------------
+ * H5G_GROUP
+ *-------------------------------------------------------------------------
+ */
+  case H5G_GROUP:
+   if (options->verbose)
+    printf(" %-10s %s\n", "group",travt->objs[i].name );
+
+   if ((grp_out=H5Gcreate(fidout,travt->objs[i].name, 0))<0) 
+    goto error;
+
+   if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0) 
+    goto error;
+
+   /*-------------------------------------------------------------------------
+    * copy attrs
+    *-------------------------------------------------------------------------
+    */
+   if (copy_attr(grp_in,grp_out,options)<0) 
+    goto error;
+   
+   if (H5Gclose(grp_out)<0) 
+    goto error;
+   if (H5Gclose(grp_in)<0) 
+    goto error;
+
+
+   break;
+
+/*-------------------------------------------------------------------------
+ * H5G_DATASET
+ *-------------------------------------------------------------------------
+ */
+  case H5G_DATASET:
+   if (options->verbose)
+    printf(" %-10s %s\n", "dataset",travt->objs[i].name );
+
+   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;
+   HDmemset(dims, 0, sizeof dims);
+   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;
+
+   if (options->verbose)
+    print_filters(dcpl_id);
+
+/*-------------------------------------------------------------------------
+ * 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 (h5tools_canreadf((options->verbose?travt->objs[i].name:NULL),dcpl_id)==1)
+   {
+
+/*-------------------------------------------------------------------------
+ * references are a special case
+ * we cannot just copy the buffers, but instead we recreate the reference
+ * in a second traversal of the output file
+ *-------------------------------------------------------------------------
+ */
+   if ( (H5T_REFERENCE!=H5Tget_class(mtype_id)))
+   {
+    /* the information about the object to be filtered/"layouted" */
+    pack_info_t obj;
+    init_packobject(&obj);
+   
+    /* get the storage size of the input dataset */
+    dsize_in=H5Dget_storage_size(dset_in);
+  
+  /*-------------------------------------------------------------------------
+   * read to memory
+   *-------------------------------------------------------------------------
+   */
+    if (nelmts)
+    {
+     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;
+     
+     /*-------------------------------------------------------------------------
+      * apply the layout; check first if the object is to be modified.
+      *-------------------------------------------------------------------------
+      */
+     if (layout_this(dcpl_id,travt->objs[i].name,options,&obj))
+     {
+      obj.chunk.rank=rank;
+      if (apply_layout(dcpl_id,&obj)<0)
+       goto error;
+     }
+
+    /*-------------------------------------------------------------------------
+     * apply the filter; check if the object is to be filtered.
+     *-------------------------------------------------------------------------
+     */
+     if (apply_filters(travt->objs[i].name,rank,dims,dcpl_id,mtype_id,options,&obj)<0)
+      goto error;
+
+    }/*nelmts*/
+    
+    /*-------------------------------------------------------------------------
+     * create/write dataset/close
+     *-------------------------------------------------------------------------
+     */
+    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0) 
+     goto error;
+    if (dsize_in && nelmts) {
+     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)<0) 
+     goto error;
+
+#ifdef LATER
+    /*-------------------------------------------------------------------------
+     * store the storage sizes
+     *-------------------------------------------------------------------------
+     */
+    
+    dsize_out=H5Dget_storage_size(dset_out);
+#endif /* LATER */
+
+    /*close */
+    if (H5Dclose(dset_out)<0) 
+     goto error;
+    
+    if (buf)
+     free(buf);
+    
+   }/*H5T_STD_REF_OBJ*/
+   }/*can_read*/
+
+
+/*-------------------------------------------------------------------------
+ * 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;
+   
+   break;
+
+/*-------------------------------------------------------------------------
+ * H5G_TYPE
+ *-------------------------------------------------------------------------
+ */
+  case H5G_TYPE:
+
+   if ((type_in = H5Topen (fidin,travt->objs[i].name))<0) 
+    goto error;
+
+   if ((type_out = H5Tcopy(type_in))<0) 
+    goto error;
+
+   if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<0) 
+    goto error;
+
+/*-------------------------------------------------------------------------
+ * copy attrs
+ *-------------------------------------------------------------------------
+ */
+   if (copy_attr(type_in,type_out,options)<0) 
+    goto error;
+   
+   if (H5Tclose(type_in)<0) 
+    goto error;
+   if (H5Tclose(type_out)<0) 
+    goto error;
+
+   if (options->verbose)
+    printf(" %-10s %s\n","datatype",travt->objs[i].name );
+
+   break;
+
+
+/*-------------------------------------------------------------------------
+ * H5G_LINK
+ *-------------------------------------------------------------------------
+ */
+
+  case H5G_LINK:
+   {
+    H5G_stat_t  statbuf;
+    char        *targbuf=NULL;
+    
+    if (H5Gget_objinfo(fidin,travt->objs[i].name,FALSE,&statbuf)<0)
+     goto error;
+    
+    targbuf = malloc(statbuf.linklen);
+    
+    if (H5Gget_linkval(fidin,travt->objs[i].name,statbuf.linklen,targbuf)<0)
+     goto error;
+
+    if (H5Glink(fidout,
+     H5G_LINK_SOFT,
+     targbuf,        /* current name of object */
+     travt->objs[i].name   /* new name of object */
+     )<0) 
+     goto error;
+    
+    free(targbuf);
+      
+    if (options->verbose)
+     printf(" %-10s %s\n","link",travt->objs[i].name );
+
+   }
+   break;
+
+  default:
+   if (options->verbose)
+    printf(" %-10s %s\n","User defined object",travt->objs[i].name);
+   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_attr(grp_in,grp_out,options)<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);
+  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=-1;      /* attr ID */ 
+ hid_t      attr_out=-1;     /* attr ID */ 
+ hid_t      space_id=-1;     /* space ID */ 
+ hid_t      ftype_id=-1;     /* file data type ID */ 
+ hid_t      mtype_id=-1;     /* memory data type ID */
+ size_t     msize;        /* memory size of 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, j;
+ unsigned   u;
+
+ if ((n = H5Aget_num_attrs(loc_in))<0) 
+  goto error;
+ 
+ for ( u = 0; u < (unsigned)n; u++)
+ {
+
+  /* set data buffer to NULL each iteration 
+     we might not use it in the case of references 
+   */
+   buf=NULL;    
+/*-------------------------------------------------------------------------
+ * 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;
+  
+  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 
+ * this is done on a second sweep of the file that just copies 
+ * the referenced objects
+ *-------------------------------------------------------------------------
+ */
+  if ( ! H5Tequal(mtype_id, H5T_STD_REF_OBJ)) 
+  {
+   
+   
+ /*-------------------------------------------------------------------------
+  * read to memory
+  *-------------------------------------------------------------------------
+  */
+   
+   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;
+   
+   /*close*/
+   if (H5Aclose(attr_out)<0) 
+    goto error;
+   
+   
+   if (buf)
+    free(buf);
+   
+   
+  } /*H5T_STD_REF_OBJ*/
+
+      
+  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;
+
+ } /* u */
+ 
+  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;
+}
+