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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 "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 *data )
{
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.
Note that compression can be used only when dataset is chunked.
*/
if(compress )
{
if(H5Pset_deflate( plist_id, 6) < 0)
return -1;
}
/* Create the dataset. */
if((did = H5Dcreate( loc_id, dset_name, mem_type_id, sid, plist_id )) < 0)
goto out;
/* Only write if there is something to write */
if(data )
{
/* Write data to the dataset. */
if(H5Dwrite( did, mem_type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, data ) < 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", "2.0" ) < 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 = fill_data;
/* Open the dataset. */
if((did = H5Dopen( loc_id, dset_name )) < 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, 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);
}
/* Close the dataset. */
H5Dclose( did );
/* Close data space. */
H5Sclose( sid );
}
/* Release the datatype. */
if(H5Tclose( mem_type_id ) < 0)
return -1;
return 0;
/* error zone, gracefully close */
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 DST_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 *data )
{
hid_t did;
hid_t tid=-1;
hid_t mem_type_id=-1;
hid_t sid=-1;
hid_t mem_space_id=-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 = H5Dopen( loc_id, dset_name )) < 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, data))<0)
goto out;
/* Release the datatype. */
if(H5Tclose( tid ) < 0)
return -1;
/* Release the datatype. */
if(H5Tclose( mem_type_id ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( did ) < 0)
goto out;
return 0;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(tid);
H5Sclose(mem_space_id);
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 DST_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 *data )
{
hid_t did;
hid_t tid;
hsize_t count[1];
hsize_t offset[1];
hid_t sid=-1;
hid_t mem_space_id=-1;
hsize_t mem_size[1];
hsize_t dims[1];
hid_t mem_type_id=-1;
/* Open the dataset. */
if((did = H5Dopen( loc_id, dset_name )) < 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((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if(H5Dwrite( did, mem_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 0)
goto out;
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( sid ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( tid ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( mem_type_id ) < 0)
return -1;
/* End access to the dataset */
if(H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(tid);
H5Sclose(mem_space_id);
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 DST_SIZES parameter is used to define the memory type ID
* returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
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 *data )
{
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 mem_space_id=-1;
hid_t file_space_id=-1;
char *member_name;
hssize_t nfields;
hssize_t i, j;
hid_t PRESERVE;
size_t size_native;
/* Create xfer properties to preserve initialized data */
if ((PRESERVE = H5Pcreate (H5P_DATASET_XFER))<0)
return -1;
if (H5Pset_preserve (PRESERVE, 1)<0)
return -1;
/* Open the dataset. */
if((did = H5Dopen( loc_id, dset_name )) < 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((mem_space_id = 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, mem_space_id, file_space_id, PRESERVE, data ) < 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 ) < 0)
return -1;
if(H5Sclose( file_space_id ) < 0)
return -1;
if(H5Sclose( mem_space_id ) < 0)
return -1;
return 0;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Pclose(PRESERVE);
H5Dclose(did);
H5Sclose(file_space_id);
H5Sclose(mem_space_id);
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 DST_SIZES parameter is used to define the memory type ID
* returned by H5TB_create_type
*
*-------------------------------------------------------------------------
*/
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 *data )
{
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 mem_space_id=-1;
hid_t file_space_id=-1;
char *member_name;
hsize_t i, j;
hid_t PRESERVE;
size_t size_native;
/* Create xfer properties to preserve initialized data */
if ((PRESERVE = H5Pcreate (H5P_DATASET_XFER))<0)
return -1;
if (H5Pset_preserve (PRESERVE, 1)<0)
return -1;
/* Open the dataset. */
if((did = H5Dopen( loc_id, dset_name )) < 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++)
{
j = field_index[i];
/* Get the member name */
member_name = H5Tget_member_name( tid, (unsigned) j );
/* Get the member type */
if(( member_type_id = H5Tget_member_type( tid, (unsigned) 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((mem_space_id = 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, mem_space_id, file_space_id, PRESERVE, data ) < 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 ) < 0)
return -1;
if(H5Sclose( file_space_id ) < 0)
return -1;
if(H5Sclose( mem_space_id ) < 0)
return -1;
return 0;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Pclose(PRESERVE);
H5Dclose(did);
H5Sclose(file_space_id);
H5Sclose(mem_space_id);
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=H5Dopen(loc_id,dset_name))<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, gracefully close */
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 DST_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 *data )
{
hid_t did;
hid_t ftype_id;
hid_t mem_type_id=-1;
hsize_t count[1];
hsize_t offset[1];
hid_t sid=-1;
hsize_t dims[1];
hid_t mem_space_id=-1;
hsize_t mem_size[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 = H5Dopen( loc_id, dset_name )) < 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, data)) < 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((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
/* read */
if(H5Dread( did, mem_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 0)
goto out;
/* close */
if(H5Sclose( mem_space_id ) < 0)
goto out;
if(H5Sclose( sid ) < 0)
goto out;
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, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(ftype_id);
H5Sclose(mem_space_id);
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 DST_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 *data )
{
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 mem_space_id=-1;
hsize_t mem_size[1];
size_t size_native;
hssize_t i, j;
/* open the dataset */
if((did = H5Dopen( loc_id, dset_name )) < 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((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
/* read */
if(H5Dread( did, mem_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 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( mem_space_id ) < 0)
goto out;
if(H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(did);
H5Tclose(mem_type_id);
H5Tclose(ftype_id);
H5Sclose(mem_space_id);
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 DST_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 *data )
{
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 mem_space_id=-1;
hsize_t mem_size[1];
size_t size_native;
hsize_t i, j;
/* Open the dataset. */
if((did = H5Dopen( loc_id, dset_name )) < 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++)
{
j = field_index[i];
/* Get the member name */
member_name = H5Tget_member_name( tid, (unsigned) j );
/* Get the member type */
if(( member_type_id = H5Tget_member_type( tid, (unsigned) 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((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
/* Read */
if(H5Dread( did, read_type_id, mem_space_id, sid, H5P_DEFAULT, data ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( sid ) < 0)
goto out;
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id ) < 0)
goto out;
/* End access to the read id */
if(H5Tclose( read_type_id ) )
goto out;
/* Release the datatype. */
if(H5Tclose( tid ) < 0)
return -1;
/* End access to the dataset */
if(H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(did);
H5Tclose(read_type_id);
H5Tclose(tid);
H5Sclose(mem_space_id);
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;
hid_t tid;
hsize_t count[1];
hsize_t offset[1];
hid_t sid;
hid_t mem_space_id;
hsize_t mem_size[1];
unsigned char *tmp_buf;
size_t src_size;
size_t *src_offset;
size_t *src_sizes;
hsize_t nrows;
#if defined (SHRINK)
hsize_t dims[1];
#endif
/*-------------------------------------------------------------------------
* 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)
return -1;
src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t));
src_sizes = (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, src_sizes, src_offset, &src_size ) < 0)
return -1;
/*-------------------------------------------------------------------------
* Read the records after the deleted one(s)
*-------------------------------------------------------------------------
*/
read_start = start + nrecords;
read_nrecords = ntotal_records - read_start;
tmp_buf = (unsigned char *)calloc((size_t) read_nrecords, src_size );
if(tmp_buf == NULL )
return -1;
/* 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)
return -1;
/*-------------------------------------------------------------------------
* Write the records in another position
*-------------------------------------------------------------------------
*/
/* Open the dataset. */
if((did = H5Dopen( loc_id, dset_name )) < 0)
return -1;
/* Get the datatype */
if((tid = H5Dget_type( did )) < 0)
goto out;
/* Get the dataspace handle */
if((sid = H5Dget_space( did )) < 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((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if(H5Dwrite( did, tid, mem_space_id, sid, H5P_DEFAULT, tmp_buf ) < 0)
goto out;
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( sid ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( tid ) < 0)
goto out;
/*-------------------------------------------------------------------------
* Change the table dimension
*-------------------------------------------------------------------------
*/
#if defined (SHRINK)
dims[0] = ntotal_records - nrecords;
if(H5Dset_extent( did, dims ) < 0)
goto out;
#endif
/* End access to the dataset */
if(H5Dclose( did ) < 0)
return -1;
free( tmp_buf );
free( src_offset );
free( src_sizes );
/*-------------------------------------------------------------------------
* Store the new dimension as an attribute
*-------------------------------------------------------------------------
*/
nrows = ntotal_records - nrecords;
/* Set the attribute */
if (H5LT_set_attribute_numerical(loc_id,dset_name,"NROWS",(size_t)1,
H5T_NATIVE_LLONG,&nrows)<0)
return -1;
return 0;
out:
H5Dclose( did );
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 DST_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 *data )
{
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 mem_space_id=-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 = H5Dopen( loc_id, dset_name )) < 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((mem_space_id = 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, mem_space_id, sid, H5P_DEFAULT, data ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( mem_space_id ) < 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((mem_space_id = 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, mem_space_id, sid, H5P_DEFAULT, tmp_buf ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( mem_space_id ) < 0)
goto out;
if(H5Sclose( sid ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( tid ) < 0)
return -1;
/* Release the datatype. */
if(H5Tclose( mem_type_id ) < 0)
return -1;
/* End access to the dataset */
if(H5Dclose( did ) < 0)
return -1;
free( tmp_buf );
return 0;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(did);
H5Sclose(sid);
H5Sclose(mem_space_id);
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 )
{
/* Identifiers for the 1st dataset. */
hid_t dataset_id1;
hid_t type_id1;
hid_t space_id1=-1;
hid_t mem_space_id1=-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;
size_t src_size;
size_t *src_offset;
size_t *src_sizes;
/*-------------------------------------------------------------------------
* 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)
return -1;
src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t));
src_sizes = (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_name1, NULL, src_sizes, src_offset, &src_size ) < 0)
return -1;
/*-------------------------------------------------------------------------
* Get information about the first table and read it
*-------------------------------------------------------------------------
*/
/* Open the 1st dataset. */
if((dataset_id1 = H5Dopen( loc_id, dset_name1 )) < 0)
return -1;
/* Get the datatype */
if((type_id1 = H5Dget_type( dataset_id1 )) < 0)
goto out;
/* Get the dataspace handle */
if((space_id1 = H5Dget_space( dataset_id1 )) < 0)
goto out;
/* Get the size of the datatype */
if(( type_size1 = H5Tget_size( type_id1 )) == 0 )
goto out;
tmp_buf = (unsigned char *)calloc((size_t)nrecords, type_size1 );
/* Define a hyperslab in the dataset of the size of the records */
offset[0] = start1;
count[0] = nrecords;
if(H5Sselect_hyperslab( space_id1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* Create a memory dataspace handle */
mem_size[0] = count[0];
if((mem_space_id1 = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if(H5Dread( dataset_id1, type_id1, mem_space_id1, space_id1, 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
*-------------------------------------------------------------------------
*/
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id1 ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( space_id1 ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( type_id1 ) < 0)
return -1;
/* End access to the dataset */
if(H5Dclose( dataset_id1 ) < 0)
return -1;
free( tmp_buf );
free( src_offset );
free( src_sizes );
return 0;
/* error zone, gracefully close */
out:
H5E_BEGIN_TRY {
H5Dclose(dataset_id1);
H5Sclose(space_id1);
H5Sclose(mem_space_id1);
H5Tclose(type_id1);
} 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 dataset_id1;
hid_t type_id1;
hid_t space_id1;
hid_t plist_id1;
/* Identifiers for the 2nd dataset. */
hid_t dataset_id2;
hid_t type_id2;
hid_t space_id2;
hid_t plist_id2;
/* Identifiers for the 3rd dataset. */
hid_t dataset_id3;
hid_t type_id3;
hid_t space_id3;
hid_t plist_id3;
hsize_t count[1];
hsize_t offset[1];
hid_t mem_space_id;
hsize_t mem_size[1];
hsize_t nfields;
hsize_t nrecords;
hsize_t dims[1];
hsize_t maxdims[1] = { H5S_UNLIMITED };
size_t type_size;
hid_t sid;
hid_t member_type_id;
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;
size_t src_size;
size_t *src_offset;
size_t *src_sizes;
int has_fill=0;
/*-------------------------------------------------------------------------
* 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)
return -1;
src_offset = (size_t *)malloc((size_t)nfields * sizeof(size_t));
src_sizes = (size_t *)malloc((size_t)nfields * sizeof(size_t));
if(src_offset == NULL )
return -1;
/* Get field info */
if(H5TBget_field_info( loc_id1, dset_name1, NULL, src_sizes, src_offset, &src_size ) < 0)
return -1;
/*-------------------------------------------------------------------------
* Get information about the first table
*-------------------------------------------------------------------------
*/
/* Open the 1st dataset. */
if((dataset_id1 = H5Dopen( loc_id1, dset_name1 )) < 0)
goto out;
/* Get the datatype */
if((type_id1 = H5Dget_type( dataset_id1 )) < 0)
goto out;
/* Get the dataspace handle */
if((space_id1 = H5Dget_space( dataset_id1 )) < 0)
goto out;
/* Get creation properties list */
if((plist_id1 = H5Dget_create_plist( dataset_id1 )) < 0)
goto out;
/* Get the dimensions */
if(H5TBget_table_info ( loc_id1, dset_name1, &nfields, &nrecords ) < 0)
return -1;
/*-------------------------------------------------------------------------
* Make the merged table with no data originally
*-------------------------------------------------------------------------
*/
/* Clone the property list */
if(( plist_id3 = H5Pcopy( plist_id1 )) < 0)
goto out;
/* Clone the type id */
if(( type_id3 = H5Tcopy( type_id1 )) < 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((space_id3 = H5Screate_simple( 1, dims, maxdims )) < 0)
return -1;
/* Create the dataset */
if((dataset_id3 = H5Dcreate( loc_id1, dset_name3, type_id3, space_id3, plist_id3 )) < 0)
goto out;
/*-------------------------------------------------------------------------
* Attach the conforming table attributes
*-------------------------------------------------------------------------
*/
if(H5TB_attach_attributes( "Merge table", loc_id1, dset_name3, nfields, type_id3 ) < 0)
goto out;
/*-------------------------------------------------------------------------
* Get attributes
*-------------------------------------------------------------------------
*/
type_size = H5Tget_size( type_id3 );
/* alloc fill value attribute buffer */
tmp_fill_buf = (unsigned char *)malloc((size_t) type_size );
/* Get the fill value attributes */
has_fill=H5TBAget_fill( loc_id1, dset_name1, dataset_id1, tmp_fill_buf );
/*-------------------------------------------------------------------------
* Attach the fill attributes from previous table
*-------------------------------------------------------------------------
*/
if(has_fill == 1 )
{
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( type_id3, (unsigned) i )) < 0)
goto out;
/* Get the member offset */
member_offset = H5Tget_member_offset(type_id3, (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(dataset_id3, ".", attr_name, member_type_id, sid, H5P_DEFAULT, 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;
if(H5Tclose(member_type_id) < 0)
goto out;
}
/* Close data space. */
if(H5Sclose( sid ) < 0)
goto out;
}
/*-------------------------------------------------------------------------
* Read data from 1st table
*-------------------------------------------------------------------------
*/
tmp_buf = (unsigned char *)calloc((size_t) nrecords, type_size );
/* Define a hyperslab in the dataset of the size of the records */
offset[0] = 0;
count[0] = nrecords;
if(H5Sselect_hyperslab( space_id1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* Create a memory dataspace handle */
mem_size[0] = count[0];
if((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if(H5Dread( dataset_id1, type_id1, mem_space_id, space_id1, 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
*-------------------------------------------------------------------------
*/
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( space_id1 ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( type_id1 ) < 0)
goto out;
/* Terminate access to a property list */
if(H5Pclose( plist_id1 ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( dataset_id1 ) < 0)
goto out;
/* Release resources. */
free( tmp_buf );
/*-------------------------------------------------------------------------
* Get information about the 2nd table
*-------------------------------------------------------------------------
*/
/* Open the dataset. */
if((dataset_id2 = H5Dopen( loc_id2, dset_name2 )) < 0)
goto out;
/* Get the datatype */
if((type_id2 = H5Dget_type( dataset_id2 )) < 0)
goto out;
/* Get the dataspace handle */
if((space_id2 = H5Dget_space( dataset_id2 )) < 0)
goto out;
/* Get the property list handle */
if((plist_id2 = H5Dget_create_plist( dataset_id2 )) < 0)
goto out;
/* Get the dimensions */
if(H5TBget_table_info ( loc_id2, dset_name2, &nfields, &nrecords ) < 0)
return -1;
/*-------------------------------------------------------------------------
* Read data from 2nd table
*-------------------------------------------------------------------------
*/
tmp_buf = (unsigned char *)calloc((size_t) nrecords, type_size );
/* Define a hyperslab in the dataset of the size of the records */
offset[0] = 0;
count[0] = nrecords;
if(H5Sselect_hyperslab( space_id2, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* Create a memory dataspace handle */
mem_size[0] = count[0];
if((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if(H5Dread( dataset_id2, type_id2, mem_space_id, space_id2, 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
*-------------------------------------------------------------------------
*/
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( space_id2 ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( type_id2 ) < 0)
return -1;
/* Terminate access to a property list */
if(H5Pclose( plist_id2 ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( dataset_id2 ) < 0)
return -1;
/*-------------------------------------------------------------------------
* Release resources from 3rd table
*-------------------------------------------------------------------------
*/
/* Terminate access to the dataspace */
if(H5Sclose( space_id3 ) < 0)
return -1;
/* Release the datatype. */
if(H5Tclose( type_id3 ) < 0)
return -1;
/* Terminate access to a property list */
if(H5Pclose( plist_id3 ) < 0)
return -1;
/* End access to the dataset */
if(H5Dclose( dataset_id3 ) < 0)
return -1;
/* Release resources. */
free( tmp_buf );
free( tmp_fill_buf );
free( src_offset );
free( src_sizes );
return 0;
out:
H5Dclose( dataset_id1 );
return -1;
}
/*-------------------------------------------------------------------------
* 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 *data )
{
/* Identifiers for the 1st, original dataset */
hid_t dataset_id1;
hid_t type_id1;
hid_t space_id1;
hid_t plist_id1;
hid_t mem_space_id1;
/* Identifiers for the 2nd, new dataset */
hid_t dataset_id2;
hid_t type_id2;
hid_t space_id2;
hid_t plist_id2;
hid_t mem_space_id2;
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;
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((dataset_id1 = H5Dopen( loc_id, dset_name )) < 0)
return -1;
/* Get creation properties list */
if((plist_id1 = H5Dget_create_plist( dataset_id1 )) < 0)
goto out;
/* Get the datatype */
if((type_id1 = H5Dget_type( dataset_id1 )) < 0)
goto out;
/* Get the size of the datatype */
if(( total_size = H5Tget_size( type_id1 )) == 0 )
goto out;
/* Get the dataspace handle */
if((space_id1 = H5Dget_space( dataset_id1 )) < 0)
goto out;
/* Get dimension */
if(H5Sget_simple_extent_dims( space_id1, dims, NULL) < 0)
goto out;
/*-------------------------------------------------------------------------
* Get attributes
*-------------------------------------------------------------------------
*/
/* Get the table title */
if((H5TBAget_title( dataset_id1, 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, dataset_id1, 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 (( type_id2 = 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( type_id2, 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( type_id1, (unsigned)idx );
/* Get the member type */
if(( member_type_id = H5Tget_member_type( type_id1,(unsigned)idx )) < 0)
goto out;
/* Get the member size */
member_size = H5Tget_size( member_type_id );
/* Insert it into the new type */
if(H5Tinsert( type_id2, 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( plist_id1, 1, dims_chunk ) < 0)
goto out;
/* Create a new simple data space with unlimited size, using the dimension */
if(( space_id2 = H5Screate_simple( 1, dims, maxdims )) < 0)
return -1;
/* Modify dataset creation properties, i.e. enable chunking */
plist_id2 = H5Pcreate (H5P_DATASET_CREATE);
if(H5Pset_chunk ( plist_id2, 1, dims_chunk ) < 0)
return -1;
/* Create the dataset. */
if(( dataset_id2 = H5Dcreate( loc_id, "new", type_id2, space_id2, plist_id2 )) < 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( space_id1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* Create a memory dataspace handle */
mem_size[0] = count[0];
if((mem_space_id1 = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if(H5Dread( dataset_id1, type_id1, mem_space_id1, 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( dataset_id2, type_id1, mem_space_id1, 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 = H5Pcreate (H5P_DATASET_XFER))<0)
goto out;
if (H5Pset_preserve (PRESERVE, 1)<0)
goto out;
/* Only write if there is something to write */
if(data )
{
/* Create a memory dataspace handle */
if((mem_space_id2 = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
/* Write */
if(H5Dwrite( dataset_id2, write_type_id, mem_space_id2, space_id2, PRESERVE, data ) < 0)
goto out;
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id2 ) < 0)
goto out;
}
/* End access to the property list */
if(H5Pclose( PRESERVE ) < 0)
goto out;
/*-------------------------------------------------------------------------
* Release resources from 1st table
*-------------------------------------------------------------------------
*/
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id1 ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( type_id1 ) < 0)
goto out;
/* Terminate access to a property list */
if(H5Pclose( plist_id1 ) < 0)
goto out;
/* Terminate access to the data space */
if(H5Sclose( space_id1 ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( dataset_id1 ) < 0)
goto out;
/*-------------------------------------------------------------------------
* Release resources from 2nd table
*-------------------------------------------------------------------------
*/
/* Terminate access to the dataspace */
if(H5Sclose( space_id2 ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( type_id2 ) < 0)
return -1;
/* Terminate access to a property list */
if(H5Pclose( plist_id2 ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( dataset_id2 ) < 0)
return -1;
/*-------------------------------------------------------------------------
* 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((dataset_id1 = H5Dopen( loc_id, dset_name )) < 0)
return -1;
/* Get the datatype */
if((type_id1 = H5Dget_type( dataset_id1 )) < 0)
goto out;
/* Set the attributes */
if(H5TB_attach_attributes( table_title, loc_id, dset_name,(hsize_t) nfields, type_id1 ) < 0)
return -1;
/*-------------------------------------------------------------------------
* Attach the fill attributes from previous table
*-------------------------------------------------------------------------
*/
if (( space_id1 = H5Screate(H5S_SCALAR)) < 0)
goto out;
for ( i = 0; i < nfields-1; i++)
{
/* Get the member type */
if(( member_type_id = H5Tget_member_type( type_id1, (unsigned) i )) < 0)
goto out;
/* Get the member offset */
member_offset = H5Tget_member_offset(type_id1, (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(dataset_id1, ".", attr_name, member_type_id, space_id1, H5P_DEFAULT, 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(type_id1, (unsigned)nfields - 1)) < 0)
goto out;
if((attr_id = H5Acreate2(dataset_id1, ".", attr_name, member_type_id, space_id1, H5P_DEFAULT, 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 data space. */
if(H5Sclose( space_id1 ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( type_id1 ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( dataset_id1 ) < 0)
goto out;
/* Release resources. */
free ( tmp_buf );
free ( tmp_fill_buf );
return 0;
out:
H5Dclose( dataset_id1 );
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 dataset_id1;
hid_t type_id1;
hid_t space_id1;
hid_t plist_id1;
/* Identifiers for the 2nd new dataset */
hid_t dataset_id2;
hid_t type_id2;
hid_t space_id2;
hid_t plist_id2;
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;
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;
int 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((dataset_id1 = H5Dopen( loc_id, dset_name )) < 0)
return -1;
/* Get creation properties list */
if((plist_id1 = H5Dget_create_plist( dataset_id1 )) < 0)
goto out;
/* Get the datatype */
if((type_id1 = H5Dget_type( dataset_id1 )) < 0)
goto out;
/* Get the size of the datatype */
type_size1 = H5Tget_size( type_id1 );
/* Get the dataspace handle */
if((space_id1 = H5Dget_space( dataset_id1 )) < 0)
goto out;
/* Get dimension */
if(H5Sget_simple_extent_dims( space_id1, 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( type_id1,(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( type_id1,(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 (( type_id2 = 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( dataset_id1, 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( type_id1, (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( type_id1, (unsigned)i )) < 0)
goto out;
/* Get the member size */
member_size = H5Tget_size( member_type_id );
/* Insert it into the new type */
if(H5Tinsert( type_id2, 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( dataset_id1, attr_name );
/* Get it */
if(has_fill == 1 )
{
if(H5LT_get_attribute_disk( dataset_id1, 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( plist_id1, 1, dims_chunk ) < 0)
goto out;
/* Create a new simple data space with unlimited size, using the dimension */
if(( space_id2 = H5Screate_simple( 1, dims, maxdims )) < 0)
return -1;
/* Modify dataset creation properties, i.e. enable chunking */
plist_id2 = H5Pcreate (H5P_DATASET_CREATE);
if(H5Pset_chunk ( plist_id2, 1, dims_chunk ) < 0)
return -1;
/* Create the dataset. */
if(( dataset_id2 = H5Dcreate( loc_id, "new", type_id2, space_id2, plist_id2 )) < 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( type_id1,(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( type_id1, (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( dataset_id1, 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 = H5Pcreate (H5P_DATASET_XFER))<0)
goto out;
if (H5Pset_preserve (PRESERVE, 1)<0)
goto out;
/* Write */
if(H5Dwrite( dataset_id2, write_type_id, H5S_ALL, H5S_ALL, PRESERVE, tmp_buf ) < 0)
goto out;
/* End access to the property list */
if(H5Pclose( PRESERVE ) < 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
*-------------------------------------------------------------------------
*/
/* Release the datatype. */
if(H5Tclose( type_id1 ) < 0)
goto out;
/* Terminate access to a property list */
if(H5Pclose( plist_id1 ) < 0)
goto out;
/* Terminate access to the data space */
if(H5Sclose( space_id1 ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( dataset_id1 ) < 0)
goto out;
/*-------------------------------------------------------------------------
* Release resources from 2nd table
*-------------------------------------------------------------------------
*/
/* Terminate access to the dataspace */
if(H5Sclose( space_id2 ) < 0)
goto out;
/* Release the datatype. */
if(H5Tclose( type_id2 ) < 0)
return -1;
/* Terminate access to a property list */
if(H5Pclose( plist_id2 ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( dataset_id2 ) < 0)
return -1;
/*-------------------------------------------------------------------------
* 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((dataset_id1 = H5Dopen( loc_id, dset_name )) < 0)
return -1;
/* Get the datatype */
if((type_id1 = H5Dget_type( dataset_id1 )) < 0)
goto out;
/* Set the attributes */
if(H5TB_attach_attributes( table_title, loc_id, dset_name, nfields, type_id1 ) < 0)
return -1;
/*-------------------------------------------------------------------------
* Attach the fill attributes from previous table
*-------------------------------------------------------------------------
*/
if(has_fill == 1)
{
if((space_id1 = H5Screate(H5S_SCALAR)) < 0)
goto out;
for(i = 0; i < nfields; i++)
{
/* Get the member type */
if(( member_type_id = H5Tget_member_type( type_id1, (unsigned)i )) < 0)
goto out;
/* Get the member offset */
member_offset = H5Tget_member_offset(type_id1, (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(dataset_id1, ".", attr_name, member_type_id, space_id1, H5P_DEFAULT, 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(space_id1) < 0)
goto out;
} /*has_fill*/
/* Release the datatype. */
if(H5Tclose( type_id1 ) < 0)
goto out;
/* End access to the dataset */
if(H5Dclose( dataset_id1 ) < 0)
goto out;
/* Release resources. */
free ( tmp_fill_buf );
return 0;
out:
H5Dclose( dataset_id1 );
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: 0, Failure: -1
*
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Date: January 30, 2002
*
* Comments:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_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"
*
*
*-------------------------------------------------------------------------
*/
herr_t H5TBget_table_info ( hid_t loc_id,
const char *dset_name,
hsize_t *nfields,
hsize_t *nrecords )
{
hid_t tid;
hid_t sid=-1;
hid_t did;
int num_members;
hsize_t dims[1];
int has_attr;
hsize_t n[1];
/* Open the dataset. */
if((did = H5Dopen( loc_id, dset_name )) < 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;
if (nfields)
*nfields = num_members;
/*-------------------------------------------------------------------------
* Get number of records
*-------------------------------------------------------------------------
*/
if (nrecords)
{
/* Try to find the attribute "NROWS" */
has_attr = H5LT_find_attribute( did, "NROWS" );
/* It exists, get it */
if(has_attr == 1 )
{
/* Get the attribute */
if(H5LTget_attribute(loc_id,dset_name,"NROWS",H5T_NATIVE_LLONG,n)<0)
return -1;
/**nrecords = *n;*/
*nrecords = n[0];
}
else
{
/* 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;
/* Terminate access to the dataspace */
if(H5Sclose( sid ) < 0)
goto out;
*nrecords = dims[0];
}
}/*nrecords*/
/* close */
if(H5Tclose( tid ) < 0)
goto out;
if(H5Dclose( did ) < 0)
return -1;
return 0;
/* error zone, gracefully close */
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;
hid_t ftype_id;
hid_t native_type_id;
hssize_t nfields;
char *member_name;
hid_t member_type_id;
hid_t nativem_type_id;
size_t member_size;
size_t member_offset;
size_t size;
hssize_t i;
/* Open the dataset. */
if(( did = H5Dopen( loc_id, dset_name )) < 0)
goto out;
/* Get the datatype */
if(( ftype_id = H5Dget_type( did )) < 0)
goto out;
if ((native_type_id = H5Tget_native_type(ftype_id,H5T_DIR_DEFAULT))<0)
goto out;
/* Get the type size */
size = H5Tget_size( native_type_id );
if(type_size )
*type_size = size;
/* Get the number of members */
if(( nfields = H5Tget_nmembers( ftype_id )) < 0)
goto out;
/* Iterate tru the members */
for ( i = 0; i < nfields; i++)
{
/* Get the member name */
member_name = H5Tget_member_name( ftype_id, (unsigned)i );
if(field_names )
strcpy( field_names[i], member_name );
/* Get the member type */
if(( member_type_id = H5Tget_member_type( ftype_id,(unsigned) i )) < 0)
goto out;
if ((nativem_type_id = H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT))<0)
goto out;
/* Get the member size */
member_size = H5Tget_size( nativem_type_id );
if(field_sizes )
field_sizes[i] = member_size;
/* Get the member offset */
member_offset = H5Tget_member_offset( native_type_id,(unsigned) i );
if(field_offsets )
field_offsets[i] = member_offset;
/* Close the member type */
if(H5Tclose( member_type_id ) < 0)
goto out;
if(H5Tclose( nativem_type_id ) < 0)
goto out;
free( member_name );
} /* i */
/* Release the datatype. */
if(H5Tclose( ftype_id ) < 0)
return -1;
if(H5Tclose( native_type_id ) < 0)
return -1;
/* End access to the dataset */
if(H5Dclose( did ) < 0)
return -1;
return 0;
out:
H5Dclose( did );
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 = strstr( start, "," )) != 0 )
{
size_t count = end - start;
if(strncmp(start, field, count) == 0 && count == strlen(field) )
return 1;
start = end + 1;
}
if(strcmp( 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", "2.0" ) < 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=malloc(sizeof(char*)*(size_t)nfields))==NULL)
return -1;
for ( i=0; i<nfields; i++)
{
if ((fnames[i]=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, gracefully close and free */
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 * data)
{
hsize_t count[1];
hsize_t offset[1];
hid_t space_id = H5I_BADID;
hid_t mem_space_id = 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((mem_space_id = H5Screate_simple(1, mem_dims, NULL)) < 0)
goto out;
/* Get a copy of the new file data space for writing */
if((space_id = H5Dget_space(dataset_id)) < 0)
goto out;
/* Define a hyperslab in the dataset */
offset[0] = orig_table_size;
count[0] = nrecords;
if(H5Sselect_hyperslab( space_id, H5S_SELECT_SET, offset, NULL, count, NULL)<0)
goto out;
/* Write the records */
if(H5Dwrite( dataset_id, mem_type_id, mem_space_id, space_id, H5P_DEFAULT, data )<0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( mem_space_id ) < 0)
goto out;
if(H5Sclose( space_id ) < 0)
goto out;
return 0;
out:
H5E_BEGIN_TRY
H5Sclose(mem_space_id);
H5Sclose(space_id);
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 *data)
{
hsize_t count[1];
hsize_t offset[1];
hid_t space_id = H5I_BADID;
hid_t mem_space_id = 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((space_id = 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( space_id, H5S_SELECT_SET, offset, NULL, count, NULL) < 0)
goto out;
/* Create a memory dataspace handle */
mem_size[0] = count[0];
if ((mem_space_id = H5Screate_simple( 1, mem_size, NULL )) < 0)
goto out;
if ((H5Dread( dataset_id, mem_type_id, mem_space_id, space_id, H5P_DEFAULT, data))<0)
goto out;
/* Terminate access to the memory dataspace */
if(H5Sclose( mem_space_id ) < 0)
goto out;
/* Terminate access to the dataspace */
if(H5Sclose( space_id ) < 0)
goto out;
return 0;
out:
H5E_BEGIN_TRY
H5Sclose(space_id);
H5Sclose(mem_space_id);
H5E_END_TRY
return -1;
}
|