diff options
| -rw-r--r-- | hl/src/H5TB.c | 5849 | ||||
| -rw-r--r-- | hl/src/H5TBprivate.h | 1 | ||||
| -rw-r--r-- | hl/src/H5TBpublic.h | 20 |
3 files changed, 2879 insertions, 2991 deletions
diff --git a/hl/src/H5TB.c b/hl/src/H5TB.c index bbe9be5..bdf4cad 100644 --- a/hl/src/H5TB.c +++ b/hl/src/H5TB.c @@ -81,180 +81,186 @@ herr_t H5TBmake_table( const char *table_title, hsize_t chunk_size, void *fill_data, int compress, - const void *data ) + 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. - 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 = 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(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 = 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); - } - - /* 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 */ + + 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 = 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; - + H5E_BEGIN_TRY { + H5Dclose(did); + H5Sclose(sid); + H5Pclose(plist_id); + H5Tclose(mem_type_id); + } H5E_END_TRY; + return -1; + } /*------------------------------------------------------------------------- @@ -280,7 +286,7 @@ out: * Comments: Uses memory offsets * * Modifications: April 1, 2004 - * the DST_SIZES parameter is used to define the memory type ID + * the FIELD_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- @@ -292,60 +298,56 @@ herr_t H5TBappend_records( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *field_sizes, - const void *data ) + const void *buf ) { - 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 = 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, 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 */ + 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(mem_space_id); - H5Sclose(sid); - } H5E_END_TRY; - return -1; + H5E_BEGIN_TRY + { + H5Dclose(did); + H5Tclose(mem_type_id); + H5Tclose(tid); + H5Sclose(m_sid); + H5Sclose(sid); + } H5E_END_TRY; + return -1; } /*------------------------------------------------------------------------- @@ -362,7 +364,7 @@ out: * Comments: Uses memory offsets * * Modifications: April 1, 2004 - * the DST_SIZES parameter is used to define the memory type ID + * the FIELD_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- @@ -376,88 +378,80 @@ herr_t H5TBwrite_records( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *field_sizes, - const void *data ) + const void *buf ) { - - 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 = 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((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 */ + + 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(mem_space_id); - H5Sclose(sid); - } H5E_END_TRY; - return -1; + H5E_BEGIN_TRY + { + H5Dclose(did); + H5Tclose(mem_type_id); + H5Tclose(tid); + H5Sclose(m_sid); + H5Sclose(sid); + } H5E_END_TRY; + return -1; } /*------------------------------------------------------------------------- @@ -474,8 +468,7 @@ out: * Comments: * * Modifications: April 1, 2004 - * the DST_SIZES parameter is used to define the memory type ID - * returned by H5TB_create_type + * the FIELD_SIZES parameter is used to define a memory type ID * *------------------------------------------------------------------------- */ @@ -487,144 +480,144 @@ herr_t H5TBwrite_fields_name( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *field_sizes, - const void *data ) + 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 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 = 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((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 */ + 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); - H5Dclose(did); - H5Sclose(file_space_id); - H5Sclose(mem_space_id); - H5Tclose(write_type_id); - H5Tclose(tid); - } H5E_END_TRY; - return -1; - + 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; + } @@ -643,8 +636,7 @@ out: * 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 + * the FIELD_SIZES parameter is used to define a memory type ID * *------------------------------------------------------------------------- */ @@ -659,131 +651,131 @@ herr_t H5TBwrite_fields_index( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *field_sizes, - const void *data ) + 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 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 = 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((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 */ + 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); - H5Dclose(did); - H5Sclose(file_space_id); - H5Sclose(mem_space_id); - H5Tclose(write_type_id); - H5Tclose(tid); - } H5E_END_TRY; - return -1; + 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; } @@ -821,56 +813,57 @@ herr_t H5TBread_table( hid_t loc_id, 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, gracefully close */ + 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; + H5E_BEGIN_TRY + { + H5Dclose(did); + H5Tclose(mem_type_id); + H5Tclose(ftype_id); + H5Sclose(sid); + } H5E_END_TRY; + return -1; } /*------------------------------------------------------------------------- @@ -887,7 +880,7 @@ out: * Comments: * * Modifications: April 1, 2004 - * the DST_SIZES parameter is used to define the memory type ID + * the FIELD_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- @@ -901,91 +894,57 @@ herr_t H5TBread_records( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *field_sizes, - void *data ) + void *buf ) { - - 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 = 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, 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 */ + + 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(mem_space_id); - H5Sclose(sid); - } H5E_END_TRY; - return -1; - + H5E_BEGIN_TRY { + H5Dclose(did); + H5Tclose(mem_type_id); + H5Tclose(ftype_id); + H5Sclose(m_sid); + H5Sclose(sid); + } H5E_END_TRY; + return -1; + } @@ -1003,7 +962,7 @@ out: * Comments: * * Modifications: April 1, 2004 - * the DST_SIZES parameter is used to define the memory type ID + * the FIELD_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- @@ -1018,129 +977,130 @@ herr_t H5TBread_fields_name( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *field_sizes, - void *data ) + 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 mem_space_id=-1; - hsize_t mem_size[1]; - size_t size_native; - hssize_t i, j; - - /* open the dataset */ - if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) - goto out; - - /* get the datatype */ - if((ftype_id = H5Dget_type( did )) < 0) - goto out; - - /* get the number of fields */ - if(( nfields = H5Tget_nmembers( ftype_id )) < 0) - goto out; - - /* create a memory read id */ - if(( mem_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0) - goto out; - - /* iterate tru the members */ - for ( i=0,j=0; i<nfields; i++) - { - /* get the member name */ - member_name = H5Tget_member_name( ftype_id, (unsigned)i ); - - if(H5TB_find_field( member_name, field_names ) > 0 ) - { - /* get the member type */ - if(( mtype_id = H5Tget_member_type( ftype_id, (unsigned) i )) < 0) - goto out; - - /* convert to native type */ - if ((nmtype_id=H5Tget_native_type(mtype_id,H5T_DIR_DEFAULT)) < 0) - goto out; - - size_native=H5Tget_size(nmtype_id); - - if (field_sizes[j]!=size_native) - { - if (H5Tset_size(nmtype_id, field_sizes[j]) < 0) - goto out; - } - /* the field in the file is found by its name */ - if(field_offset ) - { - if(H5Tinsert( mem_type_id, member_name, field_offset[j], nmtype_id ) < 0) - goto out; - } - else - { - if(H5Tinsert( mem_type_id, member_name, (size_t)0, nmtype_id ) < 0) - goto out; - } - - /* close */ - if(H5Tclose( mtype_id ) < 0) - goto out; - if(H5Tclose( nmtype_id ) < 0) - goto out; - j++; - } - free( member_name ); - } - - /* get the dataspace handle */ - if((sid = H5Dget_space( did )) < 0) - goto out; - - /* define a hyperslab in the dataset */ - offset[0] = start; - count[0] = nrecords; - if(H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) - goto out; - - /* create a memory dataspace handle */ - mem_size[0] = count[0]; - if((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 */ + hid_t did; + hid_t ftype_id=-1; + hid_t mem_type_id=-1; + hid_t mtype_id; + hid_t nmtype_id; + char *member_name; + hssize_t nfields; + hsize_t count[1]; + hsize_t offset[1]; + hid_t sid=-1; + hid_t m_sid=-1; + hsize_t mem_size[1]; + size_t size_native; + hssize_t i, j; + + /* open the dataset */ + if ((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) + goto out; + + /* get the datatype */ + if ((ftype_id = H5Dget_type( did )) < 0) + goto out; + + /* get the number of fields */ + if (( nfields = H5Tget_nmembers( ftype_id )) < 0) + goto out; + + /* create a memory read id */ + if (( mem_type_id = H5Tcreate( H5T_COMPOUND, type_size )) < 0) + goto out; + + /* iterate tru the members */ + for ( i=0,j=0; i<nfields; i++) + { + /* get the member name */ + member_name = H5Tget_member_name( ftype_id, (unsigned)i ); + + if(H5TB_find_field( member_name, field_names ) > 0 ) + { + /* get the member type */ + if (( mtype_id = H5Tget_member_type( ftype_id, (unsigned) i )) < 0) + goto out; + + /* convert to native type */ + if ((nmtype_id=H5Tget_native_type(mtype_id,H5T_DIR_DEFAULT)) < 0) + goto out; + + size_native=H5Tget_size(nmtype_id); + + if (field_sizes[j]!=size_native) + { + if (H5Tset_size(nmtype_id, field_sizes[j]) < 0) + goto out; + } + /* the field in the file is found by its name */ + if(field_offset ) + { + if(H5Tinsert( mem_type_id, member_name, field_offset[j], nmtype_id ) < 0) + goto out; + } + else + { + if(H5Tinsert( mem_type_id, member_name, (size_t)0, nmtype_id ) < 0) + goto out; + } + + /* close */ + if(H5Tclose( mtype_id ) < 0) + goto out; + if(H5Tclose( nmtype_id ) < 0) + goto out; + j++; + } + free( member_name ); + } + + /* get the dataspace handle */ + if ((sid = H5Dget_space( did )) < 0) + goto out; + + /* define a hyperslab in the dataset */ + offset[0] = start; + count[0] = nrecords; + if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) + goto out; + + /* create a memory dataspace handle */ + mem_size[0] = count[0]; + if ((m_sid = H5Screate_simple( 1, mem_size, NULL )) < 0) + goto out; + + /* read */ + if (H5Dread( did, mem_type_id, m_sid, sid, H5P_DEFAULT, buf ) < 0) + goto out; + + /* close */ + if (H5Tclose( mem_type_id ) ) + goto out; + if (H5Tclose( ftype_id ) < 0) + return -1; + if (H5Sclose( sid ) < 0) + goto out; + if (H5Sclose( m_sid ) < 0) + goto out; + if (H5Dclose( did ) < 0) + return -1; + + return 0; + + /* error zone */ out: - H5E_BEGIN_TRY { - H5Dclose(did); - H5Tclose(mem_type_id); - H5Tclose(ftype_id); - H5Sclose(mem_space_id); - H5Sclose(sid); - } H5E_END_TRY; - return -1; - + H5E_BEGIN_TRY + { + H5Dclose(did); + H5Tclose(mem_type_id); + H5Tclose(ftype_id); + H5Sclose(m_sid); + H5Sclose(sid); + } H5E_END_TRY; + return -1; + } @@ -1158,7 +1118,7 @@ out: * Comments: * * Modifications: April 1, 2004 - * the DST_SIZES parameter is used to define the memory type ID + * the FIELD_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- @@ -1174,136 +1134,129 @@ herr_t H5TBread_fields_index( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *field_sizes, - void *data ) + 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 mem_space_id=-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((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 */ + + 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(mem_space_id); - H5Sclose(sid); - } H5E_END_TRY; - return -1; - + H5E_BEGIN_TRY + { + H5Dclose(did); + H5Tclose(read_type_id); + H5Tclose(tid); + H5Sclose(m_sid); + H5Sclose(sid); + } H5E_END_TRY; + return -1; + } @@ -1336,141 +1289,122 @@ herr_t H5TBdelete_record( hid_t loc_id, 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; - 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; - - /* 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 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 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 - *------------------------------------------------------------------------- - */ - dims[0] = ntotal_records - nrecords; - if(H5Dset_extent( did, dims ) < 0) - goto out; - - /* 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; - + + 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 m_sid; + hsize_t mem_size[1]; + unsigned char *tmp_buf; + 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; + + /* 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 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 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 ((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; + + + /*------------------------------------------------------------------------- + * 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; + + free( tmp_buf ); + free( src_offset ); + free( src_sizes ); + + + return 0; + out: - H5Dclose( did ); - return -1; + H5Dclose( did ); + return -1; } /*------------------------------------------------------------------------- @@ -1487,7 +1421,7 @@ out: * Comments: Uses memory offsets * * Modifications: April 1, 2004 - * the DST_SIZES parameter is used to define the memory type ID + * the FIELD_SIZES parameter is used to define the memory type ID * returned by H5TB_create_type * *------------------------------------------------------------------------- @@ -1501,143 +1435,136 @@ herr_t H5TBinsert_record( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *field_sizes, - void *data ) + 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 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 = 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((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 */ + + 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(mem_space_id); - H5Tclose(mem_type_id); - H5Tclose(tid); - } H5E_END_TRY; - return -1; + H5E_BEGIN_TRY + { + H5Dclose(did); + H5Sclose(sid); + H5Sclose(m_sid); + H5Tclose(mem_type_id); + H5Tclose(tid); + } H5E_END_TRY; + return -1; } /*------------------------------------------------------------------------- @@ -1666,124 +1593,115 @@ herr_t H5TBadd_records_from( hid_t loc_id, 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 = H5Dopen2(loc_id, dset_name1, H5P_DEFAULT)) < 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 */ + 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(dataset_id1); - H5Sclose(space_id1); - H5Sclose(mem_space_id1); - H5Tclose(type_id1); - } H5E_END_TRY; - return -1; - + H5E_BEGIN_TRY + { + H5Dclose(did_1); + H5Sclose(sid_1); + H5Sclose(msid_1); + H5Tclose(tid_1); + } H5E_END_TRY; + return -1; + } /*------------------------------------------------------------------------- @@ -1810,363 +1728,344 @@ herr_t H5TBcombine_tables( hid_t loc_id1, 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 = H5Dopen2(loc_id1, dset_name1, H5P_DEFAULT)) < 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 = H5Dcreate2(loc_id1, dset_name3, type_id3, space_id3, H5P_DEFAULT, plist_id3, H5P_DEFAULT)) < 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(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)) < 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 = H5Dopen2(loc_id2, dset_name2, H5P_DEFAULT)) < 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; - + + /* 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: - H5Dclose( dataset_id1 ); - return -1; - + 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 * @@ -2191,430 +2090,415 @@ herr_t H5TBinsert_field( hid_t loc_id, hid_t field_type, hsize_t position, const void *fill_data, - const void *data ) + const void *buf ) { - - /* 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 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 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 = H5Dcreate2(loc_id, "new", type_id2, space_id2, H5P_DEFAULT, plist_id2, 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(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 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 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)) < 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)) < 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; - + /* 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: - H5Dclose( dataset_id1 ); - return -1; + 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 * @@ -2638,437 +2522,432 @@ 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 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 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 = H5Dcreate2(loc_id, "new", type_id2, space_id2, H5P_DEFAULT, plist_id2, 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(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 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 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)) < 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; - + /* 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: - H5Dclose( dataset_id1 ); - return -1; + 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 @@ -3097,14 +2976,14 @@ out: 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; - + + /* Get the TITLE attribute */ + if(H5LT_get_attribute_disk( loc_id, "TITLE", table_title ) < 0) + return -1; + + + return 0; + } /*------------------------------------------------------------------------- @@ -3131,56 +3010,56 @@ herr_t H5TBAget_fill( hid_t loc_id, 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; - + + 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; - + free( src_offset ); + return -1; + } @@ -3204,9 +3083,12 @@ out: * * Comments: * - * Modifications: May 08, 2003 + * 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 * * *------------------------------------------------------------------------- @@ -3217,85 +3099,75 @@ herr_t H5TBget_table_info ( hid_t loc_id, 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 = 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; - - 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 */ + 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; - + H5E_BEGIN_TRY + { + H5Dclose(did); + H5Sclose(sid); + H5Tclose(tid); + } H5E_END_TRY; + return -1; + } /*------------------------------------------------------------------------- @@ -3323,92 +3195,104 @@ herr_t H5TBget_field_info( hid_t loc_id, 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 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 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; - + hid_t did; /* dataset ID */ + hid_t tid; /* file type ID */ + hid_t n_tid; /* native type ID */ + hid_t m_tid; /* member type ID */ + hid_t nm_tid; /* native member ID */ + hssize_t nfields; + char *member_name; + size_t member_size; + size_t member_offset; + size_t size; + 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 */ + size = H5Tget_size( n_tid ); + + if ( type_size ) + { + *type_size = size; + } + + /* 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 */ + member_name = H5Tget_member_name( tid, (unsigned)i ); + + if (field_names ) + { + strcpy( field_names[i], member_name ); + } + + /* 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 */ + member_size = H5Tget_size( nm_tid ); + + if(field_sizes ) + { + field_sizes[i] = member_size; + } + + /* get the member offset */ + member_offset = H5Tget_member_offset( n_tid,(unsigned) i ); + + if(field_offsets ) + { + field_offsets[i] = member_offset; + } + + /* close the member types */ + if (H5Tclose( m_tid ) < 0) + goto out; + if (H5Tclose( nm_tid ) < 0) + goto out; + + free( member_name ); + + } /* 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: - H5Dclose( did ); - return -1; - + H5E_BEGIN_TRY + { + H5Dclose(did); + H5Tclose(tid); + H5Tclose(n_tid); + } H5E_END_TRY; + return -1; + } /*------------------------------------------------------------------------- @@ -3437,7 +3321,7 @@ 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; @@ -3445,12 +3329,12 @@ int H5TB_find_field( const char *field, const char *field_list ) return 1; start = end + 1; } - + if(strcmp( start, field ) == 0 ) return 1; - + return -1; - + } @@ -3481,50 +3365,50 @@ herr_t H5TB_attach_attributes( const char *table_title, 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; - + + 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; - + return -1; + } /*------------------------------------------------------------------------- @@ -3553,81 +3437,83 @@ hid_t H5TB_create_type(hid_t loc_id, 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 */ + 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 */ 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; - + 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; + } @@ -3657,57 +3543,58 @@ out: *------------------------------------------------------------------------- */ 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) + hid_t mem_type_id, + size_t nrecords, + hsize_t orig_table_size, + const void * buf) { - hsize_t count[1]; - hsize_t offset[1]; - hid_t 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; - + hsize_t count[1]; + hsize_t offset[1]; + hid_t sid = H5I_BADID; + hid_t m_sid = H5I_BADID; + hsize_t dims[1]; + hsize_t mem_dims[1]; + + /* extend the dataset */ + dims[0] = nrecords + orig_table_size; + if (H5Dset_extent(dataset_id, dims) < 0) + goto out; + + /* create a simple memory data space */ + mem_dims[0] = nrecords; + if((m_sid = H5Screate_simple(1, mem_dims, NULL)) < 0) + goto out; + + /* get a copy of the new file data space for writing */ + if ((sid = H5Dget_space(dataset_id)) < 0) + goto out; + + /* define a hyperslab in the dataset */ + offset[0] = orig_table_size; + count[0] = nrecords; + if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) + goto out; + + /* write the records */ + if (H5Dwrite( dataset_id, mem_type_id, m_sid, sid, H5P_DEFAULT, buf ) < 0) + goto out; + + /* close */ + if (H5Sclose( m_sid ) < 0) + goto out; + if (H5Sclose( sid ) < 0) + goto out; + + return 0; + out: - H5E_BEGIN_TRY - H5Sclose(mem_space_id); - H5Sclose(space_id); - H5E_END_TRY - return -1; + H5E_BEGIN_TRY + { + H5Sclose(m_sid); + H5Sclose(sid); + } + H5E_END_TRY; + return -1; } @@ -3731,54 +3618,54 @@ out: *------------------------------------------------------------------------- */ 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) + hid_t mem_type_id, + hsize_t start, + size_t nrecords, + hsize_t table_size, + void *buf) { - hsize_t count[1]; - hsize_t offset[1]; - hid_t 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; - + hsize_t count[1]; + hsize_t offset[1]; + hid_t sid = H5I_BADID; + hid_t m_sid = H5I_BADID; + hsize_t mem_size[1]; + + /* make sure the read request is in bounds */ + if (start + nrecords > table_size ) + goto out; + + /* get the dataspace handle */ + if ((sid = H5Dget_space( dataset_id )) < 0) + goto out; + + /* define a hyperslab in the dataset of the size of the records */ + offset[0] = start; + count[0] = nrecords; + if (H5Sselect_hyperslab( sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) + goto out; + + /* create a memory dataspace handle */ + mem_size[0] = count[0]; + if ((m_sid = H5Screate_simple( 1, mem_size, NULL )) < 0) + goto out; + if ((H5Dread( dataset_id, mem_type_id, m_sid, sid, H5P_DEFAULT, buf)) < 0) + goto out; + + /* close */ + if (H5Sclose( m_sid ) < 0) + goto out; + if (H5Sclose( sid ) < 0) + goto out; + + return 0; + out: - H5E_BEGIN_TRY - H5Sclose(space_id); - H5Sclose(mem_space_id); - H5E_END_TRY - return -1; + H5E_BEGIN_TRY + { + H5Sclose(sid); + H5Sclose(m_sid); + } + H5E_END_TRY; + return -1; } diff --git a/hl/src/H5TBprivate.h b/hl/src/H5TBprivate.h index d4e5635..e2b668d 100644 --- a/hl/src/H5TBprivate.h +++ b/hl/src/H5TBprivate.h @@ -24,6 +24,7 @@ #define TABLE_CLASS "TABLE" +#define TABLE_VERSION "3.0" #define HLTB_MAX_FIELD_LEN 255 /*------------------------------------------------------------------------- diff --git a/hl/src/H5TBpublic.h b/hl/src/H5TBpublic.h index 143ceeb..4dd17bb 100644 --- a/hl/src/H5TBpublic.h +++ b/hl/src/H5TBpublic.h @@ -41,7 +41,7 @@ H5_HLDLL herr_t H5TBmake_table( const char *table_title, hsize_t chunk_size, void *fill_data, int compress, - const void *data ); + const void *buf ); /*------------------------------------------------------------------------- @@ -57,7 +57,7 @@ H5_HLDLL herr_t H5TBappend_records( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *dst_sizes, - const void *data ); + const void *buf ); H5_HLDLL herr_t H5TBwrite_records( hid_t loc_id, const char *dset_name, @@ -66,7 +66,7 @@ H5_HLDLL herr_t H5TBwrite_records( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *dst_sizes, - const void *data ); + const void *buf ); H5_HLDLL herr_t H5TBwrite_fields_name( hid_t loc_id, @@ -77,7 +77,7 @@ H5_HLDLL herr_t H5TBwrite_fields_name( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *dst_sizes, - const void *data ); + const void *buf ); H5_HLDLL herr_t H5TBwrite_fields_index( hid_t loc_id, const char *dset_name, @@ -88,7 +88,7 @@ H5_HLDLL herr_t H5TBwrite_fields_index( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *dst_sizes, - const void *data ); + const void *buf ); /*------------------------------------------------------------------------- @@ -116,7 +116,7 @@ H5_HLDLL herr_t H5TBread_fields_name( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *dst_sizes, - void *data ); + void *buf ); H5_HLDLL herr_t H5TBread_fields_index( hid_t loc_id, const char *dset_name, @@ -127,7 +127,7 @@ H5_HLDLL herr_t H5TBread_fields_index( hid_t loc_id, size_t type_size, const size_t *field_offset, const size_t *dst_sizes, - void *data ); + void *buf ); H5_HLDLL herr_t H5TBread_records( hid_t loc_id, @@ -137,7 +137,7 @@ H5_HLDLL herr_t H5TBread_records( hid_t loc_id, size_t type_size, const size_t *dst_offset, const size_t *dst_sizes, - void *data ); + void *buf ); /*------------------------------------------------------------------------- * @@ -181,7 +181,7 @@ H5_HLDLL herr_t H5TBinsert_record( hid_t loc_id, size_t dst_size, const size_t *dst_offset, const size_t *dst_sizes, - void *data ); + void *buf ); H5_HLDLL herr_t H5TBadd_records_from( hid_t loc_id, const char *dset_name1, @@ -202,7 +202,7 @@ H5_HLDLL herr_t H5TBinsert_field( hid_t loc_id, hid_t field_type, hsize_t position, const void *fill_data, - const void *data ); + const void *buf ); H5_HLDLL herr_t H5TBdelete_field( hid_t loc_id, const char *dset_name, |