/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 #include #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, 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; /* 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 ((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 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, j; /* 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++) { 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 ((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; 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; size_t *src_sizes; 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) 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; if (src_sizes == NULL ) return -1; /* get field info */ if (H5TBget_field_info( loc_id, dset_name, NULL, src_sizes, src_offset, &src_size ) < 0) return -1; /* open the dataset. */ if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) return -1; /*------------------------------------------------------------------------- * read the records after the deleted one(s) *------------------------------------------------------------------------- */ read_start = start + nrecords; read_nrecords = ntotal_records - read_start; if ( read_nrecords ) { 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 *------------------------------------------------------------------------- */ /* 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 ((m_sid = H5Screate_simple( 1, mem_size, NULL )) < 0) goto out; if (H5Dwrite( did, tid, 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) 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) return -1; if (tmp_buf !=NULL) free( tmp_buf ); free( src_offset ); free( src_sizes ); return 0; /* error zone */ out: if (tmp_buf !=NULL ) free( tmp_buf ); H5E_BEGIN_TRY { H5Dclose(did); H5Tclose(tid); H5Sclose(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; 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 ((did_1 = H5Dopen2(loc_id, dset_name1, H5P_DEFAULT)) < 0) return -1; /* 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; 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( 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) return -1; if (H5Dclose( did_1 ) < 0) return -1; free( tmp_buf ); free( src_offset ); free( src_sizes ); return 0; /* error zone */ out: 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=-1; hid_t tid_1=-1; hid_t sid_1=-1; hid_t pid_1=-1; /* identifiers for the 2nd dataset. */ hid_t did_2=-1; hid_t tid_2=-1; hid_t sid_2=-1; hid_t pid_2=-1; /* identifiers for the 3rd dataset. */ hid_t did_3=-1; hid_t tid_3=-1; hid_t sid_3=-1; hid_t pid_3=-1; hsize_t count[1]; hsize_t offset[1]; hid_t m_sid; 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 ((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) return -1; /*------------------------------------------------------------------------- * 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) return -1; /* 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 */ tmp_fill_buf = (unsigned char *)malloc(type_size); /* get the fill value attributes */ has_fill = H5TBAget_fill(loc_id1, dset_name1, did_1, 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( tid_3, (unsigned) i )) < 0) goto out; /* get the member offset */ member_offset = H5Tget_member_offset(tid_3, (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_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; 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( 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; if(H5Sclose( sid_1 ) < 0) goto out; if(H5Tclose( tid_1 ) < 0) goto out; if(H5Pclose( pid_1 ) < 0) goto out; if(H5Dclose( did_1 ) < 0) goto out; /* Release resources. */ free( tmp_buf ); /*------------------------------------------------------------------------- * 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) 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( 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; if (H5Sclose( sid_2 ) < 0) goto out; if (H5Tclose( tid_2 ) < 0) return -1; if (H5Pclose( pid_2 ) < 0) goto out; if (H5Dclose( did_2 ) < 0) return -1; /*------------------------------------------------------------------------- * release resources from 3rd table *------------------------------------------------------------------------- */ if (H5Sclose( sid_3 ) < 0) return -1; if (H5Tclose( tid_3 ) < 0) return -1; if (H5Pclose( pid_3 ) < 0) return -1; if (H5Dclose( did_3 ) < 0) return -1; /* Release resources. */ free( tmp_buf ); free( tmp_fill_buf ); free( src_offset ); free( src_sizes ); 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); H5Dclose(did_3); H5Sclose(sid_3); H5Tclose(tid_3); H5Pclose(pid_3); } H5E_END_TRY; 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 *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; 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 ((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: 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" * 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 = 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 = 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", 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 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; }