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-rw-r--r--tools/h5repack/h5repack_copy.c516
1 files changed, 516 insertions, 0 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
new file mode 100644
index 0000000..5c28b17
--- /dev/null
+++ b/tools/h5repack/h5repack_copy.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: copy_file
+ *
+ * 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_file(const char* fnamein,
+ const char* fnameout,
+ pack_opt_t *options)
+{
+ hid_t fidin;
+ hid_t fidout;
+ int nobjects;
+ trav_info_t *info=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>: No such file or directory\n", fnamein );
+ 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);
+
+
+/*-------------------------------------------------------------------------
+ * get the number of objects in the file
+ *-------------------------------------------------------------------------
+ */
+
+ if ((nobjects = h5trav_getinfo(fidin, NULL ))<0) {
+ printf("h5repack: <%s>: Could not obtain object list\n", fnamein );
+ return -1;
+ }
+
+/*-------------------------------------------------------------------------
+ * get the list of objects in the file
+ *-------------------------------------------------------------------------
+ */
+
+ if ((info = (trav_info_t*) malloc( nobjects * sizeof(trav_info_t)))==NULL){
+ printf("h5repack: <%s>: Could not allocate object list\n", fnamein );
+ return -1;
+ }
+ if (h5trav_getinfo(fidin, info )<0) {
+ printf("h5repack: <%s>: Could not obtain object list\n", fnamein );
+ return -1;
+ }
+
+/*-------------------------------------------------------------------------
+ * do the copy
+ *-------------------------------------------------------------------------
+ */
+
+ if(do_copy_file(fidin,fidout,nobjects,info,options)<0) {
+ printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
+ return -1;
+ }
+
+/*-------------------------------------------------------------------------
+ * free
+ *-------------------------------------------------------------------------
+ */
+ H5Fclose(fidin);
+ H5Fclose(fidout);
+ h5trav_freeinfo(info,nobjects);
+ return 0;
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: do_copy_file
+ *
+ * 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_file(hid_t fidin,
+ hid_t fidout,
+ int nobjects,
+ trav_info_t *info,
+ pack_opt_t *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 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 dataset */
+ int rank; /* rank of dataset */
+ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+ int i, j;
+
+
+/*-------------------------------------------------------------------------
+ * copy the suppplied object list
+ *-------------------------------------------------------------------------
+ */
+
+ for ( i = 0; i < nobjects; i++)
+ {
+ switch ( info[i].type )
+ {
+/*-------------------------------------------------------------------------
+ * H5G_GROUP
+ *-------------------------------------------------------------------------
+ */
+ case H5G_GROUP:
+ if (options->verbose)
+ printf(" %-10s %s\n", "group",info[i].name );
+
+ if ((grp_out=H5Gcreate(fidout, info[i].name, 0))<0)
+ goto error;
+
+ if((grp_in = H5Gopen (fidin, info[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",info[i].name );
+
+ if ((dset_in=H5Dopen(fidin,info[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;
+
+/*-------------------------------------------------------------------------
+ * 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 (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+ goto error;
+
+/*-------------------------------------------------------------------------
+ * create/write dataset/close
+ *-------------------------------------------------------------------------
+ */
+ if ((dset_out=H5Dcreate(fidout,info[i].name,ftype_id,space_id,dcpl_id))<0)
+ goto error;
+ 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;
+
+/*-------------------------------------------------------------------------
+ * 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;
+
+ if (buf)
+ free(buf);
+
+ break;
+
+/*-------------------------------------------------------------------------
+ * H5G_TYPE
+ *-------------------------------------------------------------------------
+ */
+ 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
+ *-------------------------------------------------------------------------
+ */
+ 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",info[i].name );
+
+ break;
+
+ case H5G_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(" %-10s %s\n", "User defined object", info[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; /* 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, 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;
+
+/*-------------------------------------------------------------------------
+ * 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);
+ } /* 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;
+}
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