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e2dfb53df72ca884cb9225e738aef77135f92e68
hdf5/hl/src/H5TB.c
Scot Breitenfeld bac0fbe4d6 [svn-r23112] Brought revision 22610 from the trunk to the branch: 
svn merge -r 22609:22610 https://svn.hdfgroup.uiuc.edu/hdf5/trunk/hl .

Fixes bug HDFFV-8055 (and HDFFV-8278)
2012-12-20 00:44:13 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdlib.h>
#include <string.h>
#include "H5private.h"
#include "H5LTprivate.h"
#include "H5TBprivate.h"
/*-------------------------------------------------------------------------
*
* internal functions
*
*-------------------------------------------------------------------------
*/
static int H5TB_find_field(const char *field,
const char *field_list);
static herr_t H5TB_attach_attributes(const char *table_title,
hid_t loc_id,
const char *dset_name,
hsize_t nfields,
hid_t tid );
static hid_t H5TB_create_type(hid_t loc_id,
const char *dset_name,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
hid_t ftype_id);
/*-------------------------------------------------------------------------
*
* Create functions
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5TBmake_table
*
* Purpose: Make a table
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
* Quincey Koziol
*
* Date: January 17, 2001
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t H5TBmake_table( const char *table_title,
hid_t loc_id,
const char *dset_name,
hsize_t nfields,
hsize_t nrecords,
size_t type_size,
const char *field_names[],
const size_t *field_offset,
const hid_t *field_types,
hsize_t chunk_size,
void *fill_data,
int compress,
const void *buf )
{
hid_t did;
hid_t sid;
hid_t mem_type_id;
hid_t plist_id;
hsize_t dims[1];
hsize_t dims_chunk[1];
hsize_t maxdims[1] = { H5S_UNLIMITED };
char attr_name[255];
char *member_name;
hid_t attr_id;
char aux[255];
hsize_t i;
unsigned char *tmp_buf;
dims[0] = nrecords;
dims_chunk[0] = chunk_size;
/* create the memory data type. */
if ((mem_type_id = H5Tcreate (H5T_COMPOUND, type_size )) < 0)
return -1;
/* insert fields. */
for ( i = 0; i < nfields; i++)
{
if(H5Tinsert(mem_type_id, field_names[i], field_offset[i], field_types[i] ) < 0)
return -1;
}
/* create a simple data space with unlimited size */
if ((sid = H5Screate_simple( 1, dims, maxdims )) < 0)
return -1;
/* modify dataset creation properties, i.e. enable chunking */
plist_id = H5Pcreate(H5P_DATASET_CREATE);
if (H5Pset_chunk(plist_id, 1, dims_chunk) < 0)
return -1;
/* set the fill value using a struct as the data type. */
if (fill_data)
{
if(H5Pset_fill_value(plist_id, mem_type_id, fill_data) < 0)
return -1;
}
/*
dataset creation property list is modified to use
GZIP compression with the compression effort set to 6.
*/
if (compress)
{
if(H5Pset_deflate(plist_id, 6) < 0)
return -1;
}
/* create the dataset. */
if ((did = H5Dcreate2(loc_id, dset_name, mem_type_id, sid, H5P_DEFAULT, plist_id, H5P_DEFAULT)) < 0)
goto out;
/* only write if there is something to write */
if (buf)
{
/* Write data to the dataset. */
if (H5Dwrite( did, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf ) < 0)
goto out;
}
/* terminate access to the data space. */
if (H5Sclose(sid) < 0)
goto out;
/* end access to the dataset */
if (H5Dclose(did) < 0)
goto out;
/* end access to the property list */
if (H5Pclose(plist_id) < 0)
goto out;
/*-------------------------------------------------------------------------
* set the conforming table attributes
*-------------------------------------------------------------------------
*/
/* attach the CLASS attribute */
if (H5LTset_attribute_string( loc_id, dset_name, "CLASS", TABLE_CLASS ) < 0)
goto out;
/* attach the VERSION attribute */
if (H5LTset_attribute_string( loc_id, dset_name, "VERSION", TABLE_VERSION ) < 0)
goto out;
/* attach the TITLE attribute */
if (H5LTset_attribute_string( loc_id, dset_name, "TITLE", table_title ) < 0)
goto out;
/* attach the FIELD_ name attribute */
for ( i = 0; i < nfields; i++)
{
/* get the member name */
member_name = H5Tget_member_name( mem_type_id,(unsigned) i );
strcpy( attr_name, "FIELD_" );
sprintf( aux, "%d", (int)i );
strcat( attr_name, aux );
sprintf( aux, "%s", "_NAME" );
strcat( attr_name, aux );
/* attach the attribute */
if (H5LTset_attribute_string( loc_id, dset_name, attr_name, member_name ) < 0)
goto out;
free( member_name );
}
/* attach the FIELD_ fill value attribute */
if (fill_data )
{
tmp_buf = (unsigned char *) fill_data;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
if (( sid = H5Screate(H5S_SCALAR)) < 0)
goto out;
for ( i = 0; i < nfields; i++)
{
/* get the member name */
member_name = H5Tget_member_name(mem_type_id, (unsigned)i);
strcpy(attr_name, "FIELD_");
sprintf(aux, "%d", (int)i);
strcat(attr_name, aux);
sprintf(aux, "%s", "_FILL");
strcat(attr_name, aux);
if ((attr_id = H5Acreate2(did, attr_name, field_types[i], sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto out;
if (H5Awrite(attr_id, field_types[i], tmp_buf+field_offset[i]) < 0)
goto out;
if (H5Aclose(attr_id) < 0)
goto out;
free(member_name);
}
/* terminate access to the data space. */
if (H5Sclose(sid) < 0)
goto out;
/* end access to the dataset */
if (H5Dclose(did) < 0)
goto out;
}
/* release the datatype. */
if (H5Tclose( mem_type_id ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY {
H5Dclose(did);
H5Sclose(sid);
H5Pclose(plist_id);
H5Tclose(mem_type_id);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
*
* Write functions
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5TBappend_records
*
* Purpose: Appends records to a table
*
* Return: Success: 0, Failure: -1
*
* Programmers:
* Pedro Vicente, pvn@ncsa.uiuc.edu
* Quincey Koziol
*
* Date: November 19, 2001
*
* Comments: Uses memory offsets
*
* Modifications: April 1, 2004
* the FIELD_SIZES parameter is used to define the memory type ID
* returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
herr_t H5TBappend_records( hid_t loc_id,
const char *dset_name,
hsize_t nrecords,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
const void *buf )
{
hid_t did;
hid_t tid=-1;
hid_t mem_type_id=-1;
hid_t sid=-1;
hid_t m_sid=-1;
hsize_t nrecords_orig;
hsize_t nfields;
/* get the original number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords_orig ) < 0)
return -1;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
goto out;
/* get the datatypes */
if ((tid = H5Dget_type( did )) < 0)
goto out;
if ((mem_type_id=H5TB_create_type(loc_id,dset_name,type_size,field_offset,field_sizes,tid)) < 0)
goto out;
/* append the records */
if ((H5TB_common_append_records(did, mem_type_id, (size_t)nrecords, nrecords_orig, buf)) < 0)
goto out;
/* close */
if (H5Tclose( tid ) < 0)
return -1;
if (H5Tclose( mem_type_id ) < 0)
goto out;
if (H5Dclose( did ) < 0)
goto out;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(tid);
H5Sclose(m_sid);
H5Sclose(sid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBwrite_records
*
* Purpose: Writes records
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 19, 2001
*
* Comments: Uses memory offsets
*
* Modifications: April 1, 2004
* the FIELD_SIZES parameter is used to define the memory type ID
* returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
herr_t H5TBwrite_records( hid_t loc_id,
const char *dset_name,
hsize_t start,
hsize_t nrecords,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
const void *buf )
{
hid_t did;
hid_t tid;
hsize_t count[1];
hsize_t offset[1];
hid_t sid=-1;
hid_t m_sid=-1;
hsize_t mem_size[1];
hsize_t dims[1];
hid_t mem_type_id=-1;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* get the datatype */
if ((tid = H5Dget_type( did )) < 0)
goto out;
if ((mem_type_id=H5TB_create_type(loc_id,dset_name,type_size,field_offset,field_sizes,tid)) < 0)
goto out;
/* get the dataspace handle */
if ((sid = H5Dget_space( did )) < 0)
goto out;
/* get records */
if (H5Sget_simple_extent_dims( sid, dims, NULL) < 0)
goto out;
if (start + nrecords > dims[0] )
goto out;
/* define a hyperslab in the dataset of the size of the records */
offset[0] = start;
count[0] = nrecords;
if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if ((m_sid = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if (H5Dwrite( did, mem_type_id, m_sid, sid, H5P_DEFAULT, buf ) < 0)
goto out;
/* close */
if (H5Sclose( m_sid ) < 0)
goto out;
if (H5Sclose( sid ) < 0)
goto out;
if (H5Tclose( tid ) < 0)
goto out;
if (H5Tclose( mem_type_id ) < 0)
return -1;
if (H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(tid);
H5Sclose(m_sid);
H5Sclose(sid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBwrite_fields_name
*
* Purpose: Writes fields
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 21, 2001
*
* Comments:
*
* Modifications: April 1, 2004
* the FIELD_SIZES parameter is used to define a memory type ID
*
*-------------------------------------------------------------------------
*/
herr_t H5TBwrite_fields_name( hid_t loc_id,
const char *dset_name,
const char *field_names,
hsize_t start,
hsize_t nrecords,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
const void *buf )
{
hid_t did;
hid_t tid=-1;
hid_t write_type_id=-1;
hid_t member_type_id;
hid_t nmtype_id;
hsize_t count[1];
hsize_t offset[1];
hid_t m_sid=-1;
hid_t file_space_id=-1;
char *member_name;
hssize_t nfields;
hssize_t i, j;
hid_t preserve_id;
size_t size_native;
/* create xfer properties to preserve initialized data */
if ((preserve_id = H5Pcreate (H5P_DATASET_XFER)) < 0)
return -1;
if (H5Pset_preserve (preserve_id, 1) < 0)
return -1;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if ((tid = H5Dget_type( did )) < 0)
goto out;
/* get the number of fields */
if (( nfields = H5Tget_nmembers( tid )) < 0)
goto out;
/* create a write id */
if (( write_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0)
goto out;
j = 0;
/* iterate tru the members */
for ( i = 0; i < nfields; i++)
{
/* get the member name */
member_name = H5Tget_member_name( tid, (unsigned)i );
if(H5TB_find_field( member_name, field_names ) > 0 )
{
/* get the member type */
if(( member_type_id = H5Tget_member_type( tid,(unsigned) i )) < 0)
goto out;
/* convert to native type */
if ((nmtype_id=H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT)) < 0)
goto out;
size_native=H5Tget_size(nmtype_id);
/* adjust, if necessary */
if (field_sizes[j]!=size_native)
{
if (H5Tset_size(nmtype_id, field_sizes[j]) < 0)
goto out;
}
/* the field in the file is found by its name */
if (field_offset )
{
if (H5Tinsert( write_type_id, member_name, field_offset[j], nmtype_id ) < 0)
goto out;
}
/* only one field */
else
{
if (H5Tinsert( write_type_id, member_name, (size_t)0, nmtype_id ) < 0)
goto out;
}
j++;
/* close */
if(H5Tclose( member_type_id ) < 0)
goto out;
if(H5Tclose( nmtype_id ) < 0)
goto out;
}
free( member_name );
}
/* get the dataspace handle */
if ((file_space_id = H5Dget_space( did )) < 0)
goto out;
if ((m_sid = H5Screate_simple(1, &nrecords, NULL)) < 0)
goto out;
/* define a hyperslab in the dataset */
offset[0] = start;
count[0] = nrecords;
if (H5Sselect_hyperslab( file_space_id, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* write */
if (H5Dwrite( did, write_type_id, m_sid, file_space_id, preserve_id, buf ) < 0)
goto out;
/* close */
if(H5Tclose( write_type_id ) )
goto out;
if(H5Tclose( tid ) < 0)
return -1;
if(H5Dclose( did ) < 0)
return -1;
if(H5Pclose( preserve_id ) < 0)
return -1;
if(H5Sclose( file_space_id ) < 0)
return -1;
if(H5Sclose( m_sid ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Pclose(preserve_id);
H5Dclose(did);
H5Sclose(file_space_id);
H5Sclose(m_sid);
H5Tclose(write_type_id);
H5Tclose(tid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBwrite_fields_index
*
* Purpose: Writes fields
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 21, 2001
*
* Comments: Uses memory offsets
*
* Modifications: April 1, 2004
* the FIELD_SIZES parameter is used to define a memory type ID
*
*-------------------------------------------------------------------------
*/
herr_t H5TBwrite_fields_index( hid_t loc_id,
const char *dset_name,
hsize_t nfields,
const int *field_index,
hsize_t start,
hsize_t nrecords,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
const void *buf )
{
hid_t did;
hid_t tid=-1;
hid_t write_type_id=-1;
hid_t member_type_id;
hid_t nmtype_id;
hsize_t count[1];
hsize_t offset[1];
hid_t m_sid=-1;
hid_t file_space_id=-1;
char *member_name;
hsize_t i;
hid_t preserve_id;
size_t size_native;
/* create xfer properties to preserve initialized data */
if ((preserve_id = H5Pcreate (H5P_DATASET_XFER)) < 0)
return -1;
if (H5Pset_preserve (preserve_id, 1) < 0)
return -1;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if ((tid = H5Dget_type( did )) < 0)
goto out;
/* create a write id */
if (( write_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0)
goto out;
/* iterate tru the members */
for ( i = 0; i < nfields; i++)
{
unsigned j;
/* Range check value */
if(field_index[i] < 0)
goto out;
j = (unsigned)field_index[i];
/* get the member name */
member_name = H5Tget_member_name( tid, j );
/* get the member type */
if (( member_type_id = H5Tget_member_type( tid, j )) < 0)
goto out;
/* convert to native type */
if ((nmtype_id = H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT)) < 0)
goto out;
size_native = H5Tget_size(nmtype_id);
if (field_sizes[i]!=size_native)
{
if (H5Tset_size(nmtype_id, field_sizes[i]) < 0)
goto out;
}
/* the field in the file is found by its name */
if ( field_offset )
{
if (H5Tinsert( write_type_id, member_name, field_offset[ i ], nmtype_id ) < 0)
goto out;
}
/* only one field */
else
{
if (H5Tinsert( write_type_id, member_name, (size_t)0, nmtype_id ) < 0)
goto out;
}
/* close */
if(H5Tclose( member_type_id ) < 0)
goto out;
if(H5Tclose( nmtype_id ) < 0)
goto out;
free( member_name );
}
/* get the dataspace handles */
if ((file_space_id = H5Dget_space( did )) < 0)
goto out;
if ((m_sid = H5Screate_simple(1, &nrecords, NULL)) < 0)
goto out;
/* define a hyperslab in the dataset */
offset[0] = start;
count[0] = nrecords;
if (H5Sselect_hyperslab( file_space_id, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* write */
if (H5Dwrite( did, write_type_id, m_sid, file_space_id, preserve_id, buf ) < 0)
goto out;
/* close */
if (H5Tclose( write_type_id ) )
goto out;
if (H5Tclose( tid ) < 0)
return -1;
if (H5Dclose( did ) < 0)
return -1;
if (H5Pclose( preserve_id ) < 0)
return -1;
if (H5Sclose( file_space_id ) < 0)
return -1;
if (H5Sclose( m_sid ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Pclose(preserve_id);
H5Dclose(did);
H5Sclose(file_space_id);
H5Sclose(m_sid);
H5Tclose(write_type_id);
H5Tclose(tid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
*
* Read functions
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5TBread_table
*
* Purpose: Reads a table
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 20, 2001
*
* Comments:
*
* Modifications: April 1, 2004
* used a memory type ID returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
herr_t H5TBread_table( hid_t loc_id,
const char *dset_name,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
void *dst_buf )
{
hid_t did;
hid_t ftype_id=-1;
hid_t mem_type_id=-1;
hid_t sid;
hsize_t dims[1];
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* get the dataspace handle */
if ((sid = H5Dget_space( did )) < 0)
goto out;
/* get dimensions */
if (H5Sget_simple_extent_dims( sid, dims, NULL) < 0)
goto out;
/* get the datatypes */
if ((ftype_id=H5Dget_type (did)) < 0)
goto out;
if ((mem_type_id=H5TB_create_type(loc_id,dset_name,type_size,field_offset,field_sizes,ftype_id)) < 0)
goto out;
/* read */
if (H5Dread( did, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, dst_buf) < 0)
goto out;
/* close */
if (H5Tclose( ftype_id ) < 0)
goto out;
if (H5Tclose( mem_type_id ) < 0)
goto out;
if (H5Sclose( sid ) < 0)
goto out;
if (H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(ftype_id);
H5Sclose(sid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBread_records
*
* Purpose: Reads records
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 19, 2001
*
* Comments:
*
* Modifications: April 1, 2004
* the FIELD_SIZES parameter is used to define the memory type ID
* returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
herr_t H5TBread_records( hid_t loc_id,
const char *dset_name,
hsize_t start,
hsize_t nrecords,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
void *buf )
{
hid_t did;
hid_t ftype_id;
hid_t mem_type_id=-1;
hid_t sid=-1;
hid_t m_sid=-1;
hsize_t nrecords_orig;
hsize_t nfields;
/* get the number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords_orig ) < 0)
return -1;
/* open the dataset */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* get the datatypes */
if ((ftype_id = H5Dget_type( did )) < 0)
goto out;
if ((mem_type_id=H5TB_create_type(loc_id,dset_name,type_size,field_offset,field_sizes,ftype_id)) < 0)
goto out;
/* read the records */
if ((H5TB_common_read_records(did, mem_type_id, start, (size_t)nrecords, nrecords_orig, buf)) < 0)
goto out;
/* close */
if (H5Tclose( ftype_id ) < 0)
return -1;
if (H5Tclose( mem_type_id ) < 0)
return -1;
if (H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY {
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(ftype_id);
H5Sclose(m_sid);
H5Sclose(sid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBread_fields_name
*
* Purpose: Reads fields
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 19, 2001
*
* Comments:
*
* Modifications: April 1, 2004
* the FIELD_SIZES parameter is used to define the memory type ID
* returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
herr_t H5TBread_fields_name( hid_t loc_id,
const char *dset_name,
const char *field_names,
hsize_t start,
hsize_t nrecords,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
void *buf )
{
hid_t did;
hid_t ftype_id=-1;
hid_t mem_type_id=-1;
hid_t mtype_id;
hid_t nmtype_id;
char *member_name;
hssize_t nfields;
hsize_t count[1];
hsize_t offset[1];
hid_t sid=-1;
hid_t m_sid=-1;
hsize_t mem_size[1];
size_t size_native;
hssize_t i, j;
/* open the dataset */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if ((ftype_id = H5Dget_type( did )) < 0)
goto out;
/* get the number of fields */
if (( nfields = H5Tget_nmembers( ftype_id )) < 0)
goto out;
/* create a memory read id */
if (( mem_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0)
goto out;
/* iterate tru the members */
for ( i=0,j=0; i<nfields; i++)
{
/* get the member name */
member_name = H5Tget_member_name( ftype_id, (unsigned)i );
if(H5TB_find_field( member_name, field_names ) > 0 )
{
/* get the member type */
if (( mtype_id = H5Tget_member_type( ftype_id, (unsigned) i )) < 0)
goto out;
/* convert to native type */
if ((nmtype_id=H5Tget_native_type(mtype_id,H5T_DIR_DEFAULT)) < 0)
goto out;
size_native=H5Tget_size(nmtype_id);
if (field_sizes[j]!=size_native)
{
if (H5Tset_size(nmtype_id, field_sizes[j]) < 0)
goto out;
}
/* the field in the file is found by its name */
if(field_offset )
{
if(H5Tinsert( mem_type_id, member_name, field_offset[j], nmtype_id ) < 0)
goto out;
}
else
{
if(H5Tinsert( mem_type_id, member_name, (size_t)0, nmtype_id ) < 0)
goto out;
}
/* close */
if(H5Tclose( mtype_id ) < 0)
goto out;
if(H5Tclose( nmtype_id ) < 0)
goto out;
j++;
}
free( member_name );
}
/* get the dataspace handle */
if ((sid = H5Dget_space( did )) < 0)
goto out;
/* define a hyperslab in the dataset */
offset[0] = start;
count[0] = nrecords;
if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if ((m_sid = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
/* read */
if (H5Dread( did, mem_type_id, m_sid, sid, H5P_DEFAULT, buf ) < 0)
goto out;
/* close */
if (H5Tclose( mem_type_id ) )
goto out;
if (H5Tclose( ftype_id ) < 0)
return -1;
if (H5Sclose( sid ) < 0)
goto out;
if (H5Sclose( m_sid ) < 0)
goto out;
if (H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(ftype_id);
H5Sclose(m_sid);
H5Sclose(sid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBread_fields_index
*
* Purpose: Reads fields
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 19, 2001
*
* Comments:
*
* Modifications: April 1, 2004
* the FIELD_SIZES parameter is used to define the memory type ID
* returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
herr_t H5TBread_fields_index( hid_t loc_id,
const char *dset_name,
hsize_t nfields,
const int *field_index,
hsize_t start,
hsize_t nrecords,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
void *buf )
{
hid_t did;
hid_t tid=-1;
hid_t read_type_id=-1;
hid_t member_type_id;
hid_t nmtype_id;
char *member_name;
hsize_t count[1];
hsize_t offset[1];
hid_t sid=-1;
hid_t m_sid=-1;
hsize_t mem_size[1];
size_t size_native;
hsize_t i;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if ((tid = H5Dget_type( did )) < 0)
goto out;
/* create a read id */
if (( read_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0)
goto out;
/* iterate tru the members */
for ( i = 0; i < nfields; i++)
{
unsigned j;
/* Range check */
if(field_index[i] < 0)
goto out;
j = (unsigned)field_index[i];
/* get the member name */
member_name = H5Tget_member_name( tid, j );
/* get the member type */
if (( member_type_id = H5Tget_member_type( tid, j )) < 0)
goto out;
/* get the member size */
if (H5Tget_size( member_type_id ) == 0 )
goto out;
/* convert to native type */
if ((nmtype_id=H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT)) < 0)
goto out;
size_native=H5Tget_size(nmtype_id);
if (field_sizes[i]!=size_native)
{
if (H5Tset_size(nmtype_id, field_sizes[i]) < 0)
goto out;
}
/* the field in the file is found by its name */
if (field_offset )
{
if(H5Tinsert( read_type_id, member_name, field_offset[i], nmtype_id ) < 0)
goto out;
}
else
{
if(H5Tinsert( read_type_id, member_name, (size_t)0, nmtype_id ) < 0)
goto out;
}
/* close the member type */
if (H5Tclose( member_type_id ) < 0)
goto out;
if (H5Tclose( nmtype_id ) < 0)
goto out;
free( member_name );
}
/* get the dataspace handle */
if ((sid = H5Dget_space( did )) < 0)
goto out;
/* define a hyperslab in the dataset */
offset[0] = start;
count[0] = nrecords;
if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if ((m_sid = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
/* read */
if (H5Dread( did, read_type_id, m_sid, sid, H5P_DEFAULT, buf ) < 0)
goto out;
/* close */
if (H5Sclose( sid ) < 0)
goto out;
if (H5Sclose( m_sid ) < 0)
goto out;
if (H5Tclose( read_type_id ) )
goto out;
if (H5Tclose( tid ) < 0)
return -1;
if (H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did);
H5Tclose(read_type_id);
H5Tclose(tid);
H5Sclose(m_sid);
H5Sclose(sid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
*
* Manipulation functions
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5TBdelete_record
*
* Purpose: Delete records from middle of table ("pulling up" all the records after it)
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 26, 2001
*
* Modifications: April 29, 2003
*
*
*-------------------------------------------------------------------------
*/
herr_t H5TBdelete_record( hid_t loc_id,
const char *dset_name,
hsize_t start,
hsize_t nrecords )
{
hsize_t nfields;
hsize_t ntotal_records;
hsize_t read_start;
hsize_t read_nrecords;
hid_t did=-1;
hid_t tid=-1;
hid_t sid=-1;
hid_t m_sid=-1;
hid_t mem_type_id=-1;
hsize_t count[1];
hsize_t offset[1];
hsize_t mem_size[1];
unsigned char *tmp_buf=NULL;
size_t src_size;
size_t *src_offset = NULL;
size_t *src_sizes = NULL;
hsize_t dims[1];
/*-------------------------------------------------------------------------
* first we get information about type size and offsets on disk
*-------------------------------------------------------------------------
*/
/* get the number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &ntotal_records ) < 0)
goto out;
if(NULL == (src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t))))
goto out;
if(NULL == (src_sizes = (size_t *)malloc((size_t)nfields * sizeof(size_t))))
goto out;
/* get field info */
if (H5TBget_field_info( loc_id, dset_name, NULL, src_sizes, src_offset, &src_size ) < 0)
goto out;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
goto out;
/*-------------------------------------------------------------------------
* read the records after the deleted one(s)
*-------------------------------------------------------------------------
*/
read_start = start + nrecords;
read_nrecords = ntotal_records - read_start;
if ( read_nrecords )
{
if(NULL == (tmp_buf = (unsigned char *)calloc((size_t) read_nrecords, src_size )))
goto out;
/* read the records after the deleted one(s) */
if (H5TBread_records( loc_id, dset_name, read_start, read_nrecords, src_size, src_offset, src_sizes, tmp_buf ) < 0)
goto out;
/*-------------------------------------------------------------------------
* write the records in another position
*-------------------------------------------------------------------------
*/
/* get the datatype */
if ((tid = H5Dget_type( did )) < 0)
goto out;
/* get the dataspace handle */
if ((sid = H5Dget_space( did )) < 0)
goto out;
/* create the memory data type. */
if ((mem_type_id=H5TB_create_type( loc_id, dset_name, src_size, src_offset, src_sizes, tid)) < 0)
goto out;
/* define a hyperslab in the dataset of the size of the records */
offset[0] = start;
count[0] = read_nrecords;
if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if ((m_sid = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if (H5Dwrite( did, mem_type_id, m_sid, sid, H5P_DEFAULT, tmp_buf ) < 0)
goto out;
/* close */
if (H5Sclose( m_sid ) < 0)
goto out;
if (H5Tclose( mem_type_id ) < 0)
goto out;
if (H5Sclose( sid ) < 0)
goto out;
if (H5Tclose( tid ) < 0)
goto out;
} /* read_nrecords */
/*-------------------------------------------------------------------------
* change the dataset dimension
*-------------------------------------------------------------------------
*/
dims[0] = ntotal_records - nrecords;
if (H5Dset_extent( did, dims ) < 0)
goto out;
/* close dataset */
if (H5Dclose( did ) < 0)
goto out;
if(tmp_buf)
free(tmp_buf);
if(src_offset)
free(src_offset);
if(src_sizes)
free(src_sizes);
return 0;
/* error zone */
out:
if(tmp_buf)
free(tmp_buf);
if(src_offset)
free(src_offset);
if(src_sizes)
free(src_sizes);
H5E_BEGIN_TRY
{
H5Tclose(mem_type_id);
H5Dclose(did);
H5Tclose(tid);
H5Sclose(sid);
H5Sclose(m_sid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBinsert_record
*
* Purpose: Inserts records into middle of table ("pushing down" all the records after it)
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 26, 2001
*
* Comments: Uses memory offsets
*
* Modifications: April 1, 2004
* the FIELD_SIZES parameter is used to define the memory type ID
* returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
herr_t H5TBinsert_record( hid_t loc_id,
const char *dset_name,
hsize_t start,
hsize_t nrecords,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
void *buf )
{
hsize_t nfields;
hsize_t ntotal_records;
hsize_t read_nrecords;
hid_t did;
hid_t tid=-1;
hid_t mem_type_id=-1;
hsize_t count[1];
hsize_t offset[1];
hid_t sid=-1;
hid_t m_sid=-1;
hsize_t dims[1];
hsize_t mem_dims[1];
unsigned char *tmp_buf;
/*-------------------------------------------------------------------------
* read the records after the inserted one(s)
*-------------------------------------------------------------------------
*/
/* get the dimensions */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &ntotal_records ) < 0)
return -1;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if ((tid = H5Dget_type( did )) < 0)
goto out;
/* create the memory data type. */
if ((mem_type_id=H5TB_create_type(loc_id,dset_name,type_size,field_offset,field_sizes,tid)) < 0)
goto out;
read_nrecords = ntotal_records - start;
tmp_buf = (unsigned char *)calloc((size_t) read_nrecords, type_size);
/* read the records after the inserted one(s) */
if (H5TBread_records( loc_id, dset_name, start, read_nrecords, type_size, field_offset, field_sizes, tmp_buf ) < 0)
return -1;
/* extend the dataset */
dims[0] = ntotal_records + nrecords;
if (H5Dset_extent(did, dims) < 0)
goto out;
/*-------------------------------------------------------------------------
* write the inserted records
*-------------------------------------------------------------------------
*/
/* create a simple memory data space */
mem_dims[0] = nrecords;
if ((m_sid = H5Screate_simple(1, mem_dims, NULL)) < 0)
return -1;
/* get the file data space */
if ((sid = H5Dget_space( did )) < 0)
return -1;
/* define a hyperslab in the dataset to write the new data */
offset[0] = start;
count[0] = nrecords;
if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
if (H5Dwrite( did, mem_type_id, m_sid, sid, H5P_DEFAULT, buf ) < 0)
goto out;
/* terminate access to the dataspace */
if (H5Sclose( m_sid ) < 0)
goto out;
if (H5Sclose( sid ) < 0)
goto out;
/*-------------------------------------------------------------------------
* write the "pushed down" records
*-------------------------------------------------------------------------
*/
/* create a simple memory data space */
mem_dims[0]=read_nrecords;
if ((m_sid = H5Screate_simple( 1, mem_dims, NULL )) < 0)
return -1;
/* get the file data space */
if ((sid = H5Dget_space( did )) < 0)
return -1;
/* define a hyperslab in the dataset to write the new data */
offset[0] = start + nrecords;
count[0] = read_nrecords;
if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
if (H5Dwrite( did, mem_type_id, m_sid, sid, H5P_DEFAULT, tmp_buf ) < 0)
goto out;
/* close */
if (H5Sclose( m_sid ) < 0)
goto out;
if (H5Sclose( sid ) < 0)
goto out;
if (H5Tclose( tid ) < 0)
return -1;
if (H5Tclose( mem_type_id ) < 0)
return -1;
if (H5Dclose( did ) < 0)
return -1;
free( tmp_buf );
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did);
H5Sclose(sid);
H5Sclose(m_sid);
H5Tclose(mem_type_id);
H5Tclose(tid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBadd_records_from
*
* Purpose: Add records from first table to second table
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December 5, 2001
*
* Comments:
*
* Modifications:
*
*
*-------------------------------------------------------------------------
*/
herr_t H5TBadd_records_from( hid_t loc_id,
const char *dset_name1,
hsize_t start1,
hsize_t nrecords,
const char *dset_name2,
hsize_t start2 )
{
hid_t did_1;
hid_t tid_1;
hid_t sid_1=-1;
hid_t msid_1=-1;
size_t type_size1;
hsize_t count[1];
hsize_t offset[1];
hsize_t mem_size[1];
hsize_t nfields;
hsize_t ntotal_records;
unsigned char *tmp_buf = NULL;
size_t src_size;
size_t *src_offset = NULL;
size_t *src_sizes = NULL;
/*-------------------------------------------------------------------------
* first we get information about type size and offsets on disk
*-------------------------------------------------------------------------
*/
/* get the number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name1, &nfields, &ntotal_records ) < 0)
goto out;
if(NULL == (src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t))))
goto out;
if(NULL == (src_sizes = (size_t *)malloc((size_t)nfields * sizeof(size_t))))
goto out;
/* get field info */
if (H5TBget_field_info( loc_id, dset_name1, NULL, src_sizes, src_offset, &src_size ) < 0)
goto out;
/*-------------------------------------------------------------------------
* Get information about the first table and read it
*-------------------------------------------------------------------------
*/
/* open the 1st dataset. */
if ((did_1 = H5Dopen2(loc_id, dset_name1, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if ((tid_1 = H5Dget_type( did_1 )) < 0)
goto out;
/* get the dataspace handle */
if ((sid_1 = H5Dget_space( did_1 )) < 0)
goto out;
/* get the size of the datatype */
if (( type_size1 = H5Tget_size( tid_1 )) == 0 )
goto out;
if(NULL == (tmp_buf = (unsigned char *)calloc((size_t)nrecords, type_size1 )))
goto out;
/* define a hyperslab in the dataset of the size of the records */
offset[0] = start1;
count[0] = nrecords;
if (H5Sselect_hyperslab( sid_1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if ((msid_1 = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if (H5Dread( did_1, tid_1, msid_1, sid_1, H5P_DEFAULT, tmp_buf ) < 0)
goto out;
/*-------------------------------------------------------------------------
* add to the second table
*-------------------------------------------------------------------------
*/
if (H5TBinsert_record(loc_id,dset_name2,start2,nrecords,src_size,src_offset,src_sizes,tmp_buf ) < 0)
goto out;
/*-------------------------------------------------------------------------
* close resources for table 1
*-------------------------------------------------------------------------
*/
if (H5Sclose( msid_1 ) < 0)
goto out;
if (H5Sclose( sid_1 ) < 0)
goto out;
if (H5Tclose( tid_1 ) < 0)
goto out;
if (H5Dclose( did_1 ) < 0)
goto out;
if(tmp_buf)
free(tmp_buf);
if(src_offset)
free(src_offset);
if(src_sizes)
free(src_sizes);
return 0;
/* error zone */
out:
if(tmp_buf)
free(tmp_buf);
if(src_offset)
free(src_offset);
if(src_sizes)
free(src_sizes);
H5E_BEGIN_TRY
{
H5Dclose(did_1);
H5Sclose(sid_1);
H5Sclose(msid_1);
H5Tclose(tid_1);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBcombine_tables
*
* Purpose: Combine records from two tables into a third
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December 10, 2001
*
* Comments:
*
* Modifications:
*
*
*-------------------------------------------------------------------------
*/
herr_t H5TBcombine_tables(hid_t loc_id1,
const char *dset_name1,
hid_t loc_id2,
const char *dset_name2,
const char *dset_name3)
{
/* identifiers for the 1st dataset. */
hid_t did_1 = H5I_BADID;
hid_t tid_1 = H5I_BADID;
hid_t sid_1 = H5I_BADID;
hid_t pid_1 = H5I_BADID;
/* identifiers for the 2nd dataset. */
hid_t did_2 = H5I_BADID;
hid_t tid_2 = H5I_BADID;
hid_t sid_2 = H5I_BADID;
hid_t pid_2 = H5I_BADID;
/* identifiers for the 3rd dataset. */
hid_t did_3 = H5I_BADID;
hid_t tid_3 = H5I_BADID;
hid_t sid_3 = H5I_BADID;
hid_t pid_3 = H5I_BADID;
hid_t sid = H5I_BADID;
hid_t m_sid = H5I_BADID;
hid_t member_type_id = H5I_BADID;
hid_t attr_id = H5I_BADID;
hsize_t count[1];
hsize_t offset[1];
hsize_t mem_size[1];
hsize_t nfields;
hsize_t nrecords;
hsize_t dims[1];
hsize_t maxdims[1] = {H5S_UNLIMITED};
hsize_t i;
size_t type_size;
size_t member_offset;
size_t src_size;
size_t *src_offset = NULL;
size_t *src_sizes = NULL;
char attr_name[255];
char aux[255];
unsigned char *tmp_buf = NULL;
unsigned char *tmp_fill_buf = NULL;
htri_t has_fill;
int ret_val = -1;
/*-------------------------------------------------------------------------
* first we get information about type size and offsets on disk
*-------------------------------------------------------------------------
*/
/* get the number of records and fields */
if(H5TBget_table_info(loc_id1, dset_name1, &nfields, &nrecords) < 0)
goto out;
if(NULL == (src_offset = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t))))
goto out;
if(NULL == (src_sizes = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t))))
goto out;
/* get field info */
if(H5TBget_field_info(loc_id1, dset_name1, NULL, src_sizes, src_offset, &src_size) < 0)
goto out;
/*-------------------------------------------------------------------------
* get information about the first table
*-------------------------------------------------------------------------
*/
/* open the 1st dataset. */
if((did_1 = H5Dopen2(loc_id1, dset_name1, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if((tid_1 = H5Dget_type(did_1)) < 0)
goto out;
/* get the dataspace handle */
if((sid_1 = H5Dget_space(did_1)) < 0)
goto out;
/* get creation properties list */
if((pid_1 = H5Dget_create_plist(did_1)) < 0)
goto out;
/* get the dimensions */
if(H5TBget_table_info(loc_id1, dset_name1, &nfields, &nrecords) < 0)
goto out;
/*-------------------------------------------------------------------------
* make the merged table with no data originally
*-------------------------------------------------------------------------
*/
/* clone the property list */
if((pid_3 = H5Pcopy(pid_1)) < 0)
goto out;
/* clone the type id */
if((tid_3 = H5Tcopy(tid_1)) < 0)
goto out;
/*-------------------------------------------------------------------------
* here we do not clone the file space from the 1st dataset, because we want to create
* an empty table. Instead we create a new dataspace with zero records and expandable.
*-------------------------------------------------------------------------
*/
dims[0] = 0;
/* create a simple data space with unlimited size */
if((sid_3 = H5Screate_simple(1, dims, maxdims)) < 0)
goto out;
/* create the dataset */
if((did_3 = H5Dcreate2(loc_id1, dset_name3, tid_3, sid_3, H5P_DEFAULT, pid_3, H5P_DEFAULT)) < 0)
goto out;
/*-------------------------------------------------------------------------
* attach the conforming table attributes
*-------------------------------------------------------------------------
*/
if(H5TB_attach_attributes("Merge table", loc_id1, dset_name3, nfields, tid_3) < 0)
goto out;
/*-------------------------------------------------------------------------
* get attributes
*-------------------------------------------------------------------------
*/
type_size = H5Tget_size(tid_3);
/* alloc fill value attribute buffer */
if(NULL == (tmp_fill_buf = (unsigned char *)HDmalloc(type_size)))
goto out;
/* get the fill value attributes */
if((has_fill = H5TBAget_fill(loc_id1, dset_name1, did_1, tmp_fill_buf)) < 0)
goto out;
/*-------------------------------------------------------------------------
* attach the fill attributes from previous table
*-------------------------------------------------------------------------
*/
if(has_fill) {
if((sid = H5Screate(H5S_SCALAR)) < 0)
goto out;
for(i = 0; i < nfields; i++) {
/* get the member type */
if((member_type_id = H5Tget_member_type(tid_3, (unsigned)i)) < 0)
goto out;
/* get the member offset */
member_offset = H5Tget_member_offset(tid_3, (unsigned)i);
HDstrncpy(attr_name, "FIELD_", 6);
HDsnprintf(aux, 12, "%d", (int)i);
HDstrncat(attr_name, aux, 12);
HDsnprintf(aux, 6, "%s", "_FILL");
HDstrncat(attr_name, aux, 7);
if((attr_id = H5Acreate2(did_3, attr_name, member_type_id, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto out;
if(H5Awrite(attr_id, member_type_id, tmp_fill_buf + member_offset) < 0)
goto out;
if(H5Aclose(attr_id) < 0)
goto out;
attr_id = H5I_BADID;
if(H5Tclose(member_type_id) < 0)
goto out;
member_type_id = H5I_BADID;
}
/* close data space. */
if(H5Sclose(sid) < 0)
goto out;
sid = H5I_BADID;
}
/*-------------------------------------------------------------------------
* read data from 1st table
*-------------------------------------------------------------------------
*/
if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t)nrecords, type_size)))
goto out;
/* define a hyperslab in the dataset of the size of the records */
offset[0] = 0;
count[0] = nrecords;
if(H5Sselect_hyperslab(sid_1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if((m_sid = H5Screate_simple(1, mem_size, NULL)) < 0)
goto out;
if(H5Dread(did_1, tid_1, m_sid, sid_1, H5P_DEFAULT, tmp_buf) < 0)
goto out;
/*-------------------------------------------------------------------------
* save data from 1st table into new table
*-------------------------------------------------------------------------
*/
/* append the records to the new table */
if(H5TBappend_records(loc_id1, dset_name3, nrecords, src_size, src_offset, src_sizes, tmp_buf) < 0)
goto out;
/*-------------------------------------------------------------------------
* release resources from 1st table
*-------------------------------------------------------------------------
*/
if(H5Sclose(m_sid) < 0)
goto out;
m_sid = H5I_BADID;
if(H5Sclose(sid_1) < 0)
goto out;
sid_1 = H5I_BADID;
if(H5Tclose(tid_1) < 0)
goto out;
tid_1 = H5I_BADID;
if(H5Pclose(pid_1) < 0)
goto out;
pid_1 = H5I_BADID;
if(H5Dclose(did_1) < 0)
goto out;
did_1 = H5I_BADID;
/* Release resources. */
free(tmp_buf);
tmp_buf = NULL;
/*-------------------------------------------------------------------------
* get information about the 2nd table
*-------------------------------------------------------------------------
*/
/* open the dataset. */
if((did_2 = H5Dopen2(loc_id2, dset_name2, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if((tid_2 = H5Dget_type(did_2)) < 0)
goto out;
/* get the dataspace handle */
if((sid_2 = H5Dget_space(did_2)) < 0)
goto out;
/* get the property list handle */
if((pid_2 = H5Dget_create_plist(did_2)) < 0)
goto out;
/* get the dimensions */
if(H5TBget_table_info(loc_id2, dset_name2, &nfields, &nrecords) < 0)
goto out;
/*-------------------------------------------------------------------------
* read data from 2nd table
*-------------------------------------------------------------------------
*/
if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t)nrecords, type_size)))
goto out;
/* define a hyperslab in the dataset of the size of the records */
offset[0] = 0;
count[0] = nrecords;
if(H5Sselect_hyperslab(sid_2, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if((m_sid = H5Screate_simple(1, mem_size, NULL)) < 0)
goto out;
if(H5Dread(did_2, tid_2, m_sid, sid_2, H5P_DEFAULT, tmp_buf) < 0)
goto out;
/*-------------------------------------------------------------------------
* save data from 2nd table into new table
*-------------------------------------------------------------------------
*/
/* append the records to the new table */
if(H5TBappend_records(loc_id1, dset_name3, nrecords, src_size, src_offset, src_sizes, tmp_buf) < 0)
goto out;
/*-------------------------------------------------------------------------
* release resources from 2nd table
*-------------------------------------------------------------------------
*/
if(H5Sclose(m_sid) < 0)
goto out;
m_sid = H5I_BADID;
if(H5Sclose(sid_2) < 0)
goto out;
sid_2 = H5I_BADID;
if(H5Tclose(tid_2) < 0)
goto out;
tid_2 = H5I_BADID;
if(H5Pclose(pid_2) < 0)
goto out;
pid_2 = H5I_BADID;
if(H5Dclose(did_2) < 0)
goto out;
did_2 = H5I_BADID;
/*-------------------------------------------------------------------------
* release resources from 3rd table
*-------------------------------------------------------------------------
*/
if(H5Sclose(sid_3) < 0)
goto out;
sid_3 = H5I_BADID;
if(H5Tclose(tid_3) < 0)
goto out;
tid_3 = H5I_BADID;
if(H5Pclose(pid_3) < 0)
goto out;
pid_3 = H5I_BADID;
if(H5Dclose(did_3) < 0)
goto out;
did_3 = H5I_BADID;
ret_val = 0;
out:
if(tmp_buf)
free(tmp_buf);
if(tmp_fill_buf)
free(tmp_fill_buf);
if(src_offset)
free(src_offset);
if(src_sizes)
free(src_sizes);
H5E_BEGIN_TRY {
if(member_type_id > 0)
H5Tclose(member_type_id);
if(attr_id > 0)
H5Aclose(attr_id);
if(sid > 0)
H5Sclose(sid);
if(m_sid > 0)
H5Sclose(m_sid);
if(pid_1 > 0)
H5Pclose(pid_1);
if(tid_1 > 0)
H5Tclose(tid_1);
if(sid_1 > 0)
H5Sclose(sid_1);
if(did_1 > 0)
H5Dclose(did_1);
if(pid_2 > 0)
H5Pclose(pid_2);
if(tid_2 > 0)
H5Tclose(tid_2);
if(sid_2 > 0)
H5Sclose(sid_2);
if(did_2 > 0)
H5Dclose(did_2);
if(pid_3 > 0)
H5Pclose(pid_3);
if(tid_3 > 0)
H5Tclose(tid_3);
if(sid_3 > 0)
H5Sclose(sid_3);
if(did_3 > 0)
H5Dclose(did_3);
} H5E_END_TRY;
return ret_val;
}
/*-------------------------------------------------------------------------
* Function: H5TBinsert_field
*
* Purpose: Inserts a field
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: January 30, 2002
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t H5TBinsert_field( hid_t loc_id,
const char *dset_name,
const char *field_name,
hid_t field_type,
hsize_t position,
const void *fill_data,
const void *buf )
{
/* identifiers for the 1st, original dataset */
hid_t did_1;
hid_t tid_1;
hid_t sid_1;
hid_t pid_1;
hid_t msid_1;
/* identifiers for the 2nd, new dataset */
hid_t did_2;
hid_t tid_2;
hid_t sid_2;
hid_t pid_2;
hid_t msid_2;
hid_t member_type_id;
size_t member_size;
size_t new_member_size = 0;
char *member_name;
size_t total_size;
hsize_t nfields;
hsize_t nrecords;
hsize_t dims_chunk[1];
hsize_t dims[1];
hsize_t maxdims[1] = { H5S_UNLIMITED };
hsize_t count[1];
hsize_t offset[1];
hsize_t mem_size[1];
hid_t write_type_id;
hid_t preserve_id;
size_t curr_offset;
int inserted;
hsize_t idx;
char table_title[255];
size_t member_offset;
char attr_name[255];
hid_t attr_id;
char aux[255];
unsigned char *tmp_buf;
unsigned char *tmp_fill_buf;
hsize_t i;
/* get the number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0)
return -1;
/*-------------------------------------------------------------------------
* get information about the old data type
*-------------------------------------------------------------------------
*/
/* open the dataset. */
if ((did_1 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* get creation properties list */
if ((pid_1 = H5Dget_create_plist( did_1 )) < 0)
goto out;
/* get the datatype */
if ((tid_1 = H5Dget_type( did_1 )) < 0)
goto out;
/* get the size of the datatype */
if (( total_size = H5Tget_size( tid_1 )) == 0 )
goto out;
/* get the dataspace handle */
if ((sid_1 = H5Dget_space( did_1 )) < 0)
goto out;
/* get dimension */
if (H5Sget_simple_extent_dims( sid_1, dims, NULL) < 0)
goto out;
/*-------------------------------------------------------------------------
* get attributes
*-------------------------------------------------------------------------
*/
/* get the table title */
if ((H5TBAget_title( did_1, table_title )) < 0)
goto out;
/* alloc fill value attribute buffer */
tmp_fill_buf = (unsigned char *)malloc(total_size );
/* get the fill value attributes */
if ((H5TBAget_fill( loc_id, dset_name, did_1, tmp_fill_buf )) < 0)
goto out;
/*-------------------------------------------------------------------------
* create a new data type
*-------------------------------------------------------------------------
*/
/* get the new member size */
member_size = H5Tget_size( field_type );
/* create the data type. */
if (( tid_2 = H5Tcreate (H5T_COMPOUND,(size_t)(total_size + member_size) )) < 0)
goto out;
curr_offset = 0;
inserted = 0;
/* insert the old fields, counting with the new one */
for ( i = 0; i < nfields + 1; i++)
{
idx = i;
if (inserted )
idx = i - 1;
if (i == position )
{
/* get the new member size */
new_member_size = H5Tget_size( field_type );
/* insert the new field type */
if (H5Tinsert( tid_2, field_name, curr_offset, field_type ) < 0)
goto out;
curr_offset += new_member_size;
inserted = 1;
continue;
}
/* get the member name */
member_name = H5Tget_member_name( tid_1, (unsigned)idx );
/* get the member type */
if (( member_type_id = H5Tget_member_type( tid_1,(unsigned)idx )) < 0)
goto out;
/* get the member size */
member_size = H5Tget_size( member_type_id );
/* insert it into the new type */
if (H5Tinsert( tid_2, member_name, curr_offset, member_type_id ) < 0)
goto out;
curr_offset += member_size;
free( member_name );
/* close the member type */
if(H5Tclose( member_type_id ) < 0)
goto out;
} /* i */
/*-------------------------------------------------------------------------
* create a new temporary dataset
*-------------------------------------------------------------------------
*/
/* retrieve the size of chunk */
if (H5Pget_chunk(pid_1, 1, dims_chunk) < 0)
goto out;
/* create a new simple data space with unlimited size, using the dimension */
if ((sid_2 = H5Screate_simple( 1, dims, maxdims)) < 0)
return -1;
/* modify dataset creation properties, i.e. enable chunking */
pid_2 = H5Pcreate(H5P_DATASET_CREATE);
if (H5Pset_chunk(pid_2, 1, dims_chunk) < 0)
return -1;
/* create the dataset. */
if ((did_2 = H5Dcreate2(loc_id, "new", tid_2, sid_2, H5P_DEFAULT, pid_2, H5P_DEFAULT)) < 0)
goto out;
/*-------------------------------------------------------------------------
* read data from 1st table
*-------------------------------------------------------------------------
*/
tmp_buf = (unsigned char *)calloc((size_t)nrecords, (size_t)total_size);
/* define a hyperslab in the dataset of the size of the records */
offset[0] = 0;
count[0] = nrecords;
if (H5Sselect_hyperslab(sid_1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if ((msid_1 = H5Screate_simple(1, mem_size, NULL)) < 0)
goto out;
if (H5Dread(did_1, tid_1, msid_1, H5S_ALL, H5P_DEFAULT, tmp_buf) < 0)
goto out;
/*-------------------------------------------------------------------------
* save data from 1st table into new table, using the 1st type id
*-------------------------------------------------------------------------
*/
/* write */
if (H5Dwrite( did_2, tid_1, msid_1, H5S_ALL, H5P_DEFAULT, tmp_buf ) < 0)
goto out;
/*-------------------------------------------------------------------------
* save the function supplied data of the new field
*-------------------------------------------------------------------------
*/
/* create a write id */
if (( write_type_id = H5Tcreate( H5T_COMPOUND, (size_t)new_member_size )) < 0)
goto out;
/* the field in the file is found by its name */
if (H5Tinsert( write_type_id, field_name, (size_t)0, field_type ) < 0)
goto out;
/* create xfer properties to preserve initialized data */
if ((preserve_id = H5Pcreate (H5P_DATASET_XFER)) < 0)
goto out;
if (H5Pset_preserve (preserve_id, 1) < 0)
goto out;
/* only write if there is something to write */
if ( buf )
{
/* create a memory dataspace handle */
if ((msid_2 = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
/* write */
if (H5Dwrite( did_2, write_type_id, msid_2, sid_2, preserve_id, buf ) < 0)
goto out;
/* terminate access to the memory dataspace */
if (H5Sclose( msid_2 ) < 0)
goto out;
}
/* end access to the property list */
if (H5Pclose( preserve_id ) < 0)
goto out;
/*-------------------------------------------------------------------------
* release resources from 1st table
*-------------------------------------------------------------------------
*/
if (H5Sclose( msid_1 ) < 0)
goto out;
if (H5Tclose( tid_1 ) < 0)
goto out;
if (H5Pclose( pid_1 ) < 0)
goto out;
if (H5Sclose( sid_1 ) < 0)
goto out;
if (H5Dclose( did_1 ) < 0)
goto out;
/*-------------------------------------------------------------------------
* release resources from 2nd table
*-------------------------------------------------------------------------
*/
if (H5Sclose( sid_2 ) < 0)
goto out;
if (H5Tclose( tid_2 ) < 0)
goto out;
if (H5Pclose( pid_2 ) < 0)
goto out;
if (H5Dclose( did_2 ) < 0)
goto out;
/*-------------------------------------------------------------------------
* delete 1st table
*-------------------------------------------------------------------------
*/
if (H5Ldelete( loc_id, dset_name, H5P_DEFAULT ) < 0)
return -1;
/*-------------------------------------------------------------------------
* rename 2nd table
*-------------------------------------------------------------------------
*/
if (H5Lmove( loc_id, "new", H5L_SAME_LOC, dset_name, H5P_DEFAULT, H5P_DEFAULT ) < 0)
return -1;
/*-------------------------------------------------------------------------
* attach the conforming table attributes
*-------------------------------------------------------------------------
*/
/* get the number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0)
return -1;
/* open the dataset. */
if ((did_1 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* get the datatype */
if ((tid_1 = H5Dget_type( did_1 )) < 0)
goto out;
/* set the attributes */
if (H5TB_attach_attributes( table_title, loc_id, dset_name,(hsize_t) nfields, tid_1 ) < 0)
return -1;
/*-------------------------------------------------------------------------
* attach the fill attributes from previous table
*-------------------------------------------------------------------------
*/
if (( sid_1 = H5Screate(H5S_SCALAR)) < 0)
goto out;
for ( i = 0; i < nfields-1; i++)
{
/* get the member type */
if(( member_type_id = H5Tget_member_type( tid_1, (unsigned) i )) < 0)
goto out;
/* get the member offset */
member_offset = H5Tget_member_offset(tid_1, (unsigned)i);
strcpy(attr_name, "FIELD_");
sprintf(aux, "%d", (int)i);
strcat(attr_name, aux);
sprintf(aux, "%s", "_FILL");
strcat(attr_name, aux);
if ((attr_id = H5Acreate2(did_1, attr_name, member_type_id, sid_1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto out;
if (H5Awrite(attr_id, member_type_id, tmp_fill_buf+member_offset) < 0)
goto out;
if (H5Aclose(attr_id) < 0)
goto out;
/* close the member type */
if (H5Tclose(member_type_id) < 0)
goto out;
}
/*-------------------------------------------------------------------------
* attach the fill attribute from the new field, if present
*-------------------------------------------------------------------------
*/
if (fill_data)
{
strcpy(attr_name, "FIELD_");
sprintf(aux, "%d",(int)(nfields - 1));
strcat(attr_name, aux);
sprintf(aux, "%s", "_FILL");
strcat(attr_name, aux);
/* get the member type */
if ((member_type_id = H5Tget_member_type(tid_1, (unsigned)nfields - 1)) < 0)
goto out;
if ((attr_id = H5Acreate2(did_1, attr_name, member_type_id, sid_1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto out;
if (H5Awrite(attr_id, member_type_id, fill_data) < 0)
goto out;
if (H5Aclose(attr_id) < 0)
goto out;
if (H5Tclose(member_type_id) < 0)
goto out;
}
/* close */
if (H5Sclose( sid_1 ) < 0)
goto out;
if (H5Tclose( tid_1 ) < 0)
goto out;
if (H5Dclose( did_1 ) < 0)
goto out;
/* release resources. */
free ( tmp_buf );
free ( tmp_fill_buf );
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did_1);
H5Sclose(sid_1);
H5Tclose(tid_1);
H5Pclose(pid_1);
H5Dclose(did_2);
H5Sclose(sid_2);
H5Tclose(tid_2);
H5Pclose(pid_2);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBdelete_field
*
* Purpose: Deletes a field
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: January 30, 2002
*
* Comments:
*
* Modifications:
*
*
*-------------------------------------------------------------------------
*/
herr_t H5TBdelete_field( hid_t loc_id,
const char *dset_name,
const char *field_name )
{
/* identifiers for the 1st original dataset */
hid_t did_1;
hid_t tid_1;
hid_t sid_1;
hid_t pid_1;
/* identifiers for the 2nd new dataset */
hid_t did_2;
hid_t tid_2;
hid_t sid_2;
hid_t pid_2;
hid_t member_type_id;
size_t member_size;
char *member_name;
size_t type_size1;
size_t type_size2;
hsize_t nfields;
hsize_t nrecords;
hsize_t dims_chunk[1];
hsize_t dims[1];
hsize_t maxdims[1] = { H5S_UNLIMITED };
hid_t preserve_id;
size_t curr_offset;
size_t delete_member_size = 0;
hid_t read_type_id;
hid_t write_type_id;
unsigned char *tmp_buf;
unsigned char *tmp_fill_buf;
char attr_name[255];
char aux[255];
char table_title[255];
size_t member_offset;
hid_t attr_id;
hsize_t i;
htri_t has_fill = 0;
/* get the number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0)
return -1;
/*-------------------------------------------------------------------------
* get information about the old data type
*-------------------------------------------------------------------------
*/
/* open the dataset. */
if ((did_1 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* get creation properties list */
if ((pid_1 = H5Dget_create_plist( did_1 )) < 0)
goto out;
/* get the datatype */
if ((tid_1 = H5Dget_type( did_1 )) < 0)
goto out;
/* get the size of the datatype */
type_size1 = H5Tget_size( tid_1 );
/* get the dataspace handle */
if ((sid_1 = H5Dget_space( did_1 )) < 0)
goto out;
/* get dimension */
if (H5Sget_simple_extent_dims( sid_1, dims, NULL) < 0)
goto out;
/*-------------------------------------------------------------------------
* create a new data type; first we find the size of the datatype to delete
*-------------------------------------------------------------------------
*/
/* check out the field */
for ( i = 0; i < nfields; i++)
{
/* get the member name */
member_name = H5Tget_member_name( tid_1,(unsigned) i );
/* we want to find the field to delete */
if (H5TB_find_field( member_name, field_name ) > 0 )
{
/* get the member type */
if (( member_type_id = H5Tget_member_type( tid_1,(unsigned) i )) < 0)
goto out;
/* get the member size */
delete_member_size = H5Tget_size( member_type_id );
/* close the member type */
if (H5Tclose( member_type_id ) < 0)
goto out;
free( member_name );
break;
}
free( member_name );
} /* i */
/* no field to delete was found */
if (delete_member_size == 0 )
goto out;
/*-------------------------------------------------------------------------
* create a new data type; we now insert all the fields into the new type
*-------------------------------------------------------------------------
*/
type_size2 = type_size1 - delete_member_size;
/* create the data type. */
if (( tid_2 = H5Tcreate (H5T_COMPOUND, type_size2 )) < 0)
goto out;
curr_offset = 0;
/* alloc fill value attribute buffer */
tmp_fill_buf = (unsigned char *)malloc((size_t) type_size2 );
/*-------------------------------------------------------------------------
* get attributes from previous table in the process
*-------------------------------------------------------------------------
*/
/* get the table title */
if ((H5TBAget_title( did_1, table_title )) < 0)
goto out;
/* insert the old fields except the one to delete */
for ( i = 0; i < nfields; i++)
{
/* get the member name */
member_name = H5Tget_member_name( tid_1, (unsigned) i );
/* we want to skip the field to delete */
if (H5TB_find_field( member_name, field_name ) > 0 )
{
free( member_name );
continue;
}
/* get the member type */
if (( member_type_id = H5Tget_member_type( tid_1, (unsigned)i )) < 0)
goto out;
/* get the member size */
member_size = H5Tget_size( member_type_id );
/* insert it into the new type */
if (H5Tinsert( tid_2, member_name, curr_offset, member_type_id ) < 0)
goto out;
/*-------------------------------------------------------------------------
* get the fill value information
*-------------------------------------------------------------------------
*/
strcpy( attr_name, "FIELD_" );
sprintf( aux, "%d", (int)i );
strcat( attr_name, aux );
sprintf( aux, "%s", "_FILL" );
strcat( attr_name, aux );
/* check if we have the _FILL attribute */
has_fill = H5LT_find_attribute( did_1, attr_name );
/* get it */
if (has_fill == 1 )
{
if(H5LT_get_attribute_disk( did_1, attr_name, tmp_fill_buf+curr_offset ) < 0)
goto out;
}
curr_offset += member_size;
free(member_name);
/* close the member type */
if (H5Tclose(member_type_id) < 0)
goto out;
} /* i */
/*-------------------------------------------------------------------------
* create a new temporary dataset
*-------------------------------------------------------------------------
*/
/* retrieve the size of chunk */
if (H5Pget_chunk(pid_1, 1, dims_chunk) < 0)
goto out;
/* create a new simple data space with unlimited size, using the dimension */
if ((sid_2 = H5Screate_simple(1, dims, maxdims)) < 0)
return -1;
/* modify dataset creation properties, i.e. enable chunking */
pid_2 = H5Pcreate(H5P_DATASET_CREATE);
if (H5Pset_chunk(pid_2, 1, dims_chunk) < 0)
return -1;
/* create the dataset. */
if ((did_2 = H5Dcreate2(loc_id, "new", tid_2, sid_2, H5P_DEFAULT, pid_2, H5P_DEFAULT)) < 0)
goto out;
/*-------------------------------------------------------------------------
* we have to read field by field of the old dataset and save it into the new one
*-------------------------------------------------------------------------
*/
for ( i = 0; i < nfields; i++)
{
/* get the member name */
member_name = H5Tget_member_name(tid_1, (unsigned)i);
/* skip the field to delete */
if (H5TB_find_field(member_name, field_name) > 0)
{
free(member_name);
continue;
}
/* get the member type */
if ((member_type_id = H5Tget_member_type(tid_1, (unsigned)i)) < 0)
goto out;
/* get the member size */
member_size = H5Tget_size(member_type_id);
/* create a read id */
if ((read_type_id = H5Tcreate(H5T_COMPOUND, member_size)) < 0)
goto out;
/* insert it into the new type */
if (H5Tinsert( read_type_id, member_name, (size_t)0, member_type_id ) < 0)
goto out;
tmp_buf = (unsigned char *)calloc((size_t) nrecords, member_size );
/* read */
if (H5Dread( did_1, read_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, tmp_buf ) < 0)
goto out;
/* create a write id */
if (( write_type_id = H5Tcreate( H5T_COMPOUND, member_size )) < 0)
goto out;
/* the field in the file is found by its name */
if (H5Tinsert( write_type_id, member_name, (size_t)0, member_type_id ) < 0)
goto out;
/* create xfer properties to preserve initialized data */
if ((preserve_id = H5Pcreate (H5P_DATASET_XFER)) < 0)
goto out;
if (H5Pset_preserve (preserve_id, 1) < 0)
goto out;
/* write */
if(H5Dwrite( did_2, write_type_id, H5S_ALL, H5S_ALL, preserve_id, tmp_buf ) < 0)
goto out;
/* end access to the property list */
if (H5Pclose( preserve_id ) < 0)
goto out;
/* close the member type */
if (H5Tclose( member_type_id ) < 0)
goto out;
/* close the read type */
if (H5Tclose( read_type_id ) < 0)
goto out;
/* close the write type */
if (H5Tclose( write_type_id ) < 0)
goto out;
/* release resources. */
free( member_name );
free ( tmp_buf );
} /* i */
/*-------------------------------------------------------------------------
* release resources from 1st table
*-------------------------------------------------------------------------
*/
if (H5Tclose( tid_1 ) < 0)
goto out;
if (H5Pclose( pid_1 ) < 0)
goto out;
if (H5Sclose( sid_1 ) < 0)
goto out;
if (H5Dclose( did_1 ) < 0)
goto out;
/*-------------------------------------------------------------------------
* release resources from 2nd table
*-------------------------------------------------------------------------
*/
if (H5Sclose( sid_2 ) < 0)
goto out;
if (H5Tclose( tid_2 ) < 0)
goto out;
if (H5Pclose( pid_2 ) < 0)
goto out;
if (H5Dclose( did_2 ) < 0)
goto out;
/*-------------------------------------------------------------------------
* delete 1st table
*-------------------------------------------------------------------------
*/
if (H5Ldelete( loc_id, dset_name, H5P_DEFAULT ) < 0)
return -1;
/*-------------------------------------------------------------------------
* rename 2nd table
*-------------------------------------------------------------------------
*/
if (H5Lmove( loc_id, "new", H5L_SAME_LOC, dset_name, H5P_DEFAULT, H5P_DEFAULT ) < 0)
return -1;
/*-------------------------------------------------------------------------
* attach the conforming table attributes
*-------------------------------------------------------------------------
*/
/* get the number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0)
return -1;
/* open the dataset. */
if ((did_1 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* get the datatype */
if ((tid_1 = H5Dget_type( did_1 )) < 0)
goto out;
/* set the attributes */
if (H5TB_attach_attributes( table_title, loc_id, dset_name, nfields, tid_1 ) < 0)
return -1;
/*-------------------------------------------------------------------------
* attach the fill attributes from previous table
*-------------------------------------------------------------------------
*/
if (has_fill == 1)
{
if((sid_1 = H5Screate(H5S_SCALAR)) < 0)
goto out;
for(i = 0; i < nfields; i++)
{
/* get the member type */
if (( member_type_id = H5Tget_member_type( tid_1, (unsigned)i )) < 0)
goto out;
/* get the member offset */
member_offset = H5Tget_member_offset(tid_1, (unsigned)i);
strcpy(attr_name, "FIELD_");
sprintf(aux, "%d", (int)i);
strcat(attr_name, aux);
sprintf(aux, "%s", "_FILL");
strcat(attr_name, aux);
if ((attr_id = H5Acreate2(did_1, attr_name, member_type_id, sid_1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto out;
if (H5Awrite(attr_id, member_type_id, tmp_fill_buf+member_offset) < 0)
goto out;
if (H5Aclose(attr_id) < 0)
goto out;
/* close the member type */
if (H5Tclose(member_type_id) < 0)
goto out;
}
/* close data space. */
if (H5Sclose(sid_1) < 0)
goto out;
} /*has_fill*/
/* release the datatype. */
if (H5Tclose( tid_1 ) < 0)
goto out;
/* end access to the dataset */
if (H5Dclose( did_1 ) < 0)
goto out;
/* Release resources. */
free ( tmp_fill_buf );
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did_1);
H5Sclose(sid_1);
H5Tclose(tid_1);
H5Pclose(pid_1);
H5Dclose(did_2);
H5Sclose(sid_2);
H5Tclose(tid_2);
H5Pclose(pid_2);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
*
* Table attribute functions
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5TBAget_title
*
* Purpose: Read the table title
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: January 30, 2001
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t H5TBAget_title( hid_t loc_id,
char *table_title )
{
/* Get the TITLE attribute */
if(H5LT_get_attribute_disk( loc_id, "TITLE", table_title ) < 0)
return -1;
return 0;
}
/*-------------------------------------------------------------------------
* Function: H5TBAget_fill
*
* Purpose: Read the table attribute fill values
*
* Return: Success: TRUE/FALSE, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: January 30, 2002
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
htri_t H5TBAget_fill(hid_t loc_id,
const char *dset_name,
hid_t dset_id,
unsigned char *dst_buf)
{
hsize_t nfields;
hsize_t nrecords;
char attr_name[255];
char aux[255];
hsize_t i;
size_t *src_offset;
int has_fill=0;
/* get the number of records and fields */
if (H5TBget_table_info ( loc_id, dset_name, &nfields, &nrecords ) < 0)
return -1;
src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t));
if (src_offset == NULL )
return -1;
/* get field info */
if (H5TBget_field_info( loc_id, dset_name, NULL, NULL, src_offset, NULL ) < 0)
goto out;
for ( i = 0; i < nfields; i++)
{
strcpy( attr_name, "FIELD_" );
sprintf( aux, "%d", (int)i );
strcat( attr_name, aux );
sprintf( aux, "%s", "_FILL" );
strcat( attr_name, aux );
/* check if we have the _FILL attribute */
has_fill = H5LT_find_attribute( dset_id, attr_name );
/* get it */
if (has_fill == 1 )
{
if(H5LT_get_attribute_disk( dset_id, attr_name, dst_buf+src_offset[i] ) < 0)
goto out;
}
}
free( src_offset );
return has_fill;
out:
free( src_offset );
return -1;
}
/*-------------------------------------------------------------------------
*
* Inquiry functions
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5TBget_table_info
*
* Purpose: Gets the number of records and fields of a table
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 19, 2001
*
* Comments:
*
* Modifications:
* May 08, 2003
* In version 2.0 of Table, the number of records is stored as an
* attribute "NROWS"
* November 24, 2008
* In version 3.0 of Table, "NROWS" was deprecated
*
*
*-------------------------------------------------------------------------
*/
herr_t H5TBget_table_info ( hid_t loc_id,
const char *dset_name,
hsize_t *nfields,
hsize_t *nrecords )
{
hid_t tid=-1;
hid_t sid=-1;
hid_t did=-1;
int num_members;
hsize_t dims[1];
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* get the datatype */
if ((tid = H5Dget_type( did )) < 0)
goto out;
/* get the number of members */
if ((num_members = H5Tget_nmembers( tid )) < 0)
goto out;
/*-------------------------------------------------------------------------
* get number of nfields
*-------------------------------------------------------------------------
*/
if (nfields)
*nfields = (hsize_t)num_members;
/*-------------------------------------------------------------------------
* get number of records
*-------------------------------------------------------------------------
*/
if (nrecords)
{
/* get the dataspace handle */
if ((sid = H5Dget_space( did )) < 0)
goto out;
/* get dimension */
if (H5Sget_simple_extent_dims( sid, dims, NULL) < 0)
goto out;
/* terminate access to the dataspace */
if (H5Sclose( sid ) < 0)
goto out;
*nrecords = dims[0];
}
/* close */
if (H5Tclose( tid ) < 0)
goto out;
if (H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did);
H5Sclose(sid);
H5Tclose(tid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TBget_field_info
*
* Purpose: Get information about fields
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 19, 2001
*
* Comments:
*
* Modifications:
*
*
*-------------------------------------------------------------------------
*/
herr_t H5TBget_field_info( hid_t loc_id,
const char *dset_name,
char *field_names[],
size_t *field_sizes,
size_t *field_offsets,
size_t *type_size )
{
hid_t did = -1; /* dataset ID */
hid_t tid = -1; /* file type ID */
hid_t n_tid = -1; /* native type ID */
hid_t m_tid = -1; /* member type ID */
hid_t nm_tid = -1; /* native member ID */
hssize_t nfields;
hssize_t i;
/* open the dataset. */
if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
goto out;
/* get the datatype */
if (( tid = H5Dget_type( did )) < 0)
goto out;
if ((n_tid = H5Tget_native_type(tid, H5T_DIR_DEFAULT)) < 0)
goto out;
/* get the type size */
if(type_size)
*type_size = H5Tget_size(n_tid);
/* get the number of members */
if (( nfields = H5Tget_nmembers( tid )) < 0)
goto out;
/* iterate tru the members */
for ( i = 0; i < nfields; i++) {
/* get the member name */
if(field_names) {
char *member_name;
member_name = H5Tget_member_name(tid, (unsigned)i);
strcpy(field_names[i], member_name);
free(member_name);
} /* end if */
/* get the member type */
if(( m_tid = H5Tget_member_type( tid,(unsigned) i )) < 0)
goto out;
if((nm_tid = H5Tget_native_type(m_tid,H5T_DIR_DEFAULT)) < 0)
goto out;
/* get the member size */
if(field_sizes)
field_sizes[i] = H5Tget_size(nm_tid);
/* get the member offset */
if(field_offsets)
field_offsets[i] = H5Tget_member_offset(n_tid, (unsigned) i);
/* close the member types */
if (H5Tclose( m_tid ) < 0)
goto out;
if (H5Tclose( nm_tid ) < 0)
goto out;
} /* i */
/* close */
if (H5Tclose( tid ) < 0)
goto out;
if (H5Tclose( n_tid ) < 0)
goto out;
if (H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Dclose(did);
H5Tclose(tid);
H5Tclose(n_tid);
H5Tclose(m_tid);
H5Tclose(nm_tid);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
*
* internal functions
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5TB_find_field
*
* Purpose: Find a string field
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: November 19, 2001
*
*-------------------------------------------------------------------------
*/
static
int H5TB_find_field( const char *field, const char *field_list )
{
const char *start = field_list;
const char *end;
while ( (end = HDstrstr( start, "," )) != 0 )
{
ptrdiff_t count = end - start;
if(HDstrncmp(start, field, (size_t)count) == 0 && (size_t)count == HDstrlen(field) )
return 1;
start = end + 1;
}
if(HDstrcmp( start, field ) == 0 )
return 1;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TB_attach_attributes
*
* Purpose: Private function that creates the conforming table attributes;
* Used by H5TBcombine_tables; not used by H5TBmake_table, which does not read
* the fill value attributes from an existing table
*
* Return: Success: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: December 6, 2001
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static
herr_t H5TB_attach_attributes( const char *table_title,
hid_t loc_id,
const char *dset_name,
hsize_t nfields,
hid_t tid )
{
char attr_name[255];
char *member_name;
char aux[255];
hsize_t i;
/* attach the CLASS attribute */
if (H5LTset_attribute_string( loc_id, dset_name, "CLASS", TABLE_CLASS ) < 0)
goto out;
/* attach the VERSION attribute */
if (H5LTset_attribute_string( loc_id, dset_name, "VERSION", TABLE_VERSION ) < 0)
goto out;
/* attach the TITLE attribute */
if (H5LTset_attribute_string( loc_id, dset_name, "TITLE", table_title ) < 0)
goto out;
/* attach the FIELD_ name attribute */
for ( i = 0; i < nfields; i++)
{
/* get the member name */
member_name = H5Tget_member_name( tid, (unsigned)i );
strcpy( attr_name, "FIELD_" );
sprintf( aux, "%d", (int)i );
strcat( attr_name, aux );
sprintf( aux, "%s", "_NAME" );
strcat( attr_name, aux );
/* attach the attribute */
if (H5LTset_attribute_string( loc_id, dset_name, attr_name, member_name ) < 0)
goto out;
free( member_name );
}
return 0;
out:
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TB_create_type
*
* Purpose: Private function that creates a memory type ID
*
* Return: Success: the memory type ID, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: March 31, 2004
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static
hid_t H5TB_create_type(hid_t loc_id,
const char *dset_name,
size_t type_size,
const size_t *field_offset,
const size_t *field_sizes,
hid_t ftype_id)
{
hid_t mem_type_id;
hid_t mtype_id=-1;
hid_t nmtype_id=-1;
size_t size_native;
hsize_t nfields;
char **fnames;
unsigned i;
/* get the number of fields */
if (H5TBget_table_info(loc_id,dset_name,&nfields,NULL) < 0)
return -1;
if ((fnames = (char**) malloc(sizeof(char*)*(size_t)nfields))==NULL)
return -1;
for ( i = 0; i < nfields; i++)
{
if ((fnames[i] = (char*) malloc(sizeof(char)*HLTB_MAX_FIELD_LEN))==NULL)
{
free(fnames);
return -1;
}
}
/* get field info */
if (H5TBget_field_info(loc_id,dset_name,fnames,NULL,NULL,NULL) < 0)
goto out;
/* create the memory data type */
if ((mem_type_id=H5Tcreate(H5T_COMPOUND,type_size)) < 0)
goto out;
/* get each field ID and adjust its size, if necessary */
for ( i = 0; i < nfields; i++)
{
if ((mtype_id = H5Tget_member_type(ftype_id,i)) < 0)
goto out;
if ((nmtype_id = H5Tget_native_type(mtype_id,H5T_DIR_DEFAULT)) < 0)
goto out;
size_native = H5Tget_size(nmtype_id);
if (field_sizes[i]!=size_native)
{
if (H5Tset_size(nmtype_id,field_sizes[i]) < 0)
goto out;
}
if (H5Tinsert(mem_type_id,fnames[i],field_offset[i],nmtype_id) < 0)
goto out;
if (H5Tclose(mtype_id) < 0)
goto out;
if (H5Tclose(nmtype_id) < 0)
goto out;
}
for ( i=0; i<nfields; i++)
{
free (fnames[i]);
}
free (fnames);
return mem_type_id;
/* error zone */
out:
H5E_BEGIN_TRY
{
H5Tclose(mtype_id);
H5Tclose(nmtype_id);
} H5E_END_TRY;
for ( i=0; i<nfields; i++)
{
if (fnames[i])
free (fnames[i]);
}
if (fnames)
free (fnames);
return -1;
}
/*-------------------------------------------------------------------------
*
* Functions shared between H5TB and H5PT
*
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* Function: H5TB_common_append_records
*
* Purpose: Common code for reading records shared between H5PT and H5TB
*
* Return: Success: 0, Failure: -1
*
* Programmer: Nat Furrer, nfurrer@ncsa.uiuc.edu
* James Laird, jlaird@ncsa.uiuc.edu
*
* Date: March 8, 2004
*
* Comments: Called by H5TBappend_records and H5PTappend_records
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t H5TB_common_append_records( hid_t dataset_id,
hid_t mem_type_id,
size_t nrecords,
hsize_t orig_table_size,
const void * buf)
{
hsize_t count[1];
hsize_t offset[1];
hid_t sid = H5I_BADID;
hid_t m_sid = H5I_BADID;
hsize_t dims[1];
hsize_t mem_dims[1];
/* extend the dataset */
dims[0] = nrecords + orig_table_size;
if (H5Dset_extent(dataset_id, dims) < 0)
goto out;
/* create a simple memory data space */
mem_dims[0] = nrecords;
if((m_sid = H5Screate_simple(1, mem_dims, NULL)) < 0)
goto out;
/* get a copy of the new file data space for writing */
if ((sid = H5Dget_space(dataset_id)) < 0)
goto out;
/* define a hyperslab in the dataset */
offset[0] = orig_table_size;
count[0] = nrecords;
if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* write the records */
if (H5Dwrite( dataset_id, mem_type_id, m_sid, sid, H5P_DEFAULT, buf ) < 0)
goto out;
/* close */
if (H5Sclose( m_sid ) < 0)
goto out;
if (H5Sclose( sid ) < 0)
goto out;
return 0;
out:
H5E_BEGIN_TRY
{
H5Sclose(m_sid);
H5Sclose(sid);
}
H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: H5TB_common_read_records
*
* Purpose: Common code for reading records shared between H5PT and H5TB
*
* Return: Success: 0, Failure: -1
*
* Programmer: Nat Furrer, nfurrer@ncsa.uiuc.edu
* James Laird, jlaird@ncsa.uiuc.edu
*
* Date: March 8, 2004
*
* Comments: Called by H5TBread_records and H5PTread_records
*
* Modifications:
*
*
*-------------------------------------------------------------------------
*/
herr_t H5TB_common_read_records( hid_t dataset_id,
hid_t mem_type_id,
hsize_t start,
size_t nrecords,
hsize_t table_size,
void *buf)
{
hsize_t count[1];
hsize_t offset[1];
hid_t sid = H5I_BADID;
hid_t m_sid = H5I_BADID;
hsize_t mem_size[1];
/* make sure the read request is in bounds */
if (start + nrecords > table_size )
goto out;
/* get the dataspace handle */
if ((sid = H5Dget_space( dataset_id )) < 0)
goto out;
/* define a hyperslab in the dataset of the size of the records */
offset[0] = start;
count[0] = nrecords;
if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* create a memory dataspace handle */
mem_size[0] = count[0];
if ((m_sid = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if ((H5Dread( dataset_id, mem_type_id, m_sid, sid, H5P_DEFAULT, buf)) < 0)
goto out;
/* close */
if (H5Sclose( m_sid ) < 0)
goto out;
if (H5Sclose( sid ) < 0)
goto out;
return 0;
out:
H5E_BEGIN_TRY
{
H5Sclose(sid);
H5Sclose(m_sid);
}
H5E_END_TRY;
return -1;
}
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