/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include #include "H5LTprivate.h" #include "H5TBprivate.h" /*------------------------------------------------------------------------- * * internal functions * *------------------------------------------------------------------------- */ static hbool_t H5TB_find_field(const char *field, const char *field_list); static herr_t H5TB_attach_attributes(const char *table_title, hid_t loc_id, const char *dset_name, hsize_t nfields, hid_t tid); static hid_t H5TB_create_type(hid_t loc_id, const char *dset_name, size_t type_size, const size_t *field_offset, const size_t *field_sizes, hid_t ftype_id); /*------------------------------------------------------------------------- * * Create functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBmake_table * * Purpose: Make a table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Quincey Koziol * * Date: January 17, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBmake_table(const char *table_title, hid_t loc_id, const char *dset_name, hsize_t nfields, hsize_t nrecords, size_t type_size, const char *field_names[], const size_t *field_offset, const hid_t *field_types, hsize_t chunk_size, void *fill_data, int compress, const void *buf) { hid_t did = H5I_BADID; hid_t sid = H5I_BADID; hid_t mem_type_id = H5I_BADID; hid_t plist_id = H5I_BADID; hid_t attr_id = H5I_BADID; hsize_t dims[1]; hsize_t dims_chunk[1]; hsize_t maxdims[1] = {H5S_UNLIMITED}; char attr_name[255]; char *member_name = NULL; unsigned char *tmp_buf = NULL; hsize_t i; herr_t ret_val = -1; /* check the arguments */ if (table_title == NULL) { goto out; } if (dset_name == NULL) { goto out; } if (field_names == NULL) { goto out; } dims[0] = nrecords; dims_chunk[0] = chunk_size; /* create the memory data type. */ if((mem_type_id = H5Tcreate(H5T_COMPOUND, type_size)) < 0) goto out; /* insert fields. */ for(i = 0; i < nfields; i++) if(H5Tinsert(mem_type_id, field_names[i], field_offset[i], field_types[i] ) < 0) goto out; /* create a simple data space with unlimited size */ if((sid = H5Screate_simple(1, dims, maxdims)) < 0) goto out; /* modify dataset creation properties, i.e. enable chunking */ if((plist_id = H5Pcreate(H5P_DATASET_CREATE)) < 0) goto out; if(H5Pset_chunk(plist_id, 1, dims_chunk) < 0) goto out; /* 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) goto out; /* 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) goto out; /* 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) 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; sid = H5I_BADID; /* end access to the dataset */ if(H5Dclose(did) < 0) goto out; did = H5I_BADID; /* end access to the property list */ if(H5Pclose(plist_id) < 0) goto out; plist_id = H5I_BADID; /*------------------------------------------------------------------------- * 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 */ if(NULL == (member_name = H5Tget_member_name(mem_type_id, (unsigned)i))) goto out; HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_NAME", (int)i); /* attach the attribute */ if(H5LTset_attribute_string(loc_id, dset_name, attr_name, member_name) < 0) goto out; H5free_memory(member_name); member_name = NULL; } /* end for */ /* attach the FIELD_ fill value attribute */ if(fill_data) { tmp_buf = (unsigned char *)fill_data; /* open the dataset. */ if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; if((sid = H5Screate(H5S_SCALAR)) < 0) goto out; for(i = 0; i < nfields; i++) { HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_FILL", (int)i); 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; attr_id = H5I_BADID; } /* end for */ /* terminate access to the data space. */ if(H5Sclose(sid) < 0) goto out; sid = H5I_BADID; /* end access to the dataset */ if(H5Dclose(did) < 0) goto out; did = H5I_BADID; } /* end if */ /* release the datatype. */ if(H5Tclose(mem_type_id) < 0) goto out; mem_type_id = H5I_BADID; ret_val = 0; out: if(member_name) H5free_memory(member_name); if(attr_id > 0) if(H5Aclose(attr_id) < 0) ret_val = -1; if(plist_id > 0) if(H5Pclose(plist_id) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; if(mem_type_id > 0) if(H5Tclose(mem_type_id) < 0) ret_val = -1; return ret_val; } /* end H5TBmake_table() */ /*------------------------------------------------------------------------- * * Write functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBappend_records * * Purpose: Appends records to a table * * Return: Success: 0, Failure: -1 * * Programmers: * Pedro Vicente, pvn@ncsa.uiuc.edu * Quincey Koziol * * Date: November 19, 2001 * * Comments: Uses memory offsets * *------------------------------------------------------------------------- */ herr_t H5TBappend_records(hid_t loc_id, const char *dset_name, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, const void *buf) { hid_t did = H5I_BADID; hid_t tid = H5I_BADID; hid_t mem_type_id = H5I_BADID; hsize_t nrecords_orig; hsize_t nfields; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /* get the original number of records and fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &nrecords_orig) < 0) goto out; /* 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; ret_val = 0; out: if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(mem_type_id > 0) if(H5Tclose(mem_type_id) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBappend_records() */ /*------------------------------------------------------------------------- * Function: H5TBwrite_records * * Purpose: Writes records * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: Uses memory offsets * *------------------------------------------------------------------------- */ herr_t H5TBwrite_records(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, const void *buf) { hid_t did = H5I_BADID; hid_t tid = H5I_BADID; hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hid_t mem_type_id = H5I_BADID; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; hsize_t dims[1]; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /* 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((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; ret_val = 0; out: if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(mem_type_id > 0) if(H5Tclose(mem_type_id) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBwrite_records() */ /*------------------------------------------------------------------------- * Function: H5TBwrite_fields_name * * Purpose: Writes fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 21, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBwrite_fields_name(hid_t loc_id, const char *dset_name, const char *field_names, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, const void *buf) { hid_t did = H5I_BADID; hid_t tid = H5I_BADID; hid_t write_type_id = H5I_BADID; hid_t member_type_id = H5I_BADID; hid_t nmtype_id = H5I_BADID; hid_t m_sid = H5I_BADID; hid_t file_space_id = H5I_BADID; hid_t preserve_id = H5I_BADID; hssize_t nfields; hssize_t i, j; hsize_t count[1]; hsize_t offset[1]; char *member_name = NULL; size_t size_native; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; if (field_names == NULL) 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; /* 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 though the members */ for(i = 0; i < nfields; i++) { /* get the member name */ if(NULL == (member_name = H5Tget_member_name(tid, (unsigned)i))) goto out; if(H5TB_find_field(member_name, field_names)) { /* 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; if(0 == (size_native = H5Tget_size(nmtype_id))) goto out; /* 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; } /* end if */ /* only one field */ else { if(H5Tinsert(write_type_id, member_name, (size_t)0, nmtype_id) < 0) goto out; } /* end else */ j++; /* close */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; if(H5Tclose(nmtype_id) < 0) goto out; nmtype_id = H5I_BADID; } /* end if */ H5free_memory(member_name); member_name = NULL; } /* end for */ /* 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; ret_val = 0; out: if(member_name) H5free_memory(member_name); if(preserve_id > 0) if(H5Pclose(preserve_id) < 0) ret_val = -1; if(write_type_id > 0) if(H5Tclose(write_type_id) < 0) ret_val = -1; if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(file_space_id > 0) if(H5Sclose(file_space_id) < 0) ret_val = -1; if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBwrite_fields_name() */ /*------------------------------------------------------------------------- * Function: H5TBwrite_fields_index * * Purpose: Writes fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 21, 2001 * * Comments: Uses memory offsets * *------------------------------------------------------------------------- */ herr_t H5TBwrite_fields_index(hid_t loc_id, const char *dset_name, hsize_t nfields, const int *field_index, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, const void *buf) { hid_t did = H5I_BADID; hid_t tid = H5I_BADID; hid_t write_type_id = H5I_BADID; hid_t member_type_id = H5I_BADID; hid_t nmtype_id = H5I_BADID; hid_t m_sid = H5I_BADID; hid_t file_space_id = H5I_BADID; hid_t preserve_id = H5I_BADID; hsize_t count[1]; hsize_t offset[1]; hsize_t i; size_t size_native; char *member_name = NULL; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) 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; /* open the dataset. */ if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /* get the datatype */ if((tid = H5Dget_type(did)) < 0) goto out; /* create a write id */ if((write_type_id = H5Tcreate(H5T_COMPOUND, type_size)) < 0) goto out; /* iterate tru the members */ for(i = 0; i < nfields; i++) { unsigned j; /* Range check value */ if(field_index[i] < 0) goto out; j = (unsigned)field_index[i]; /* get the member name */ if(NULL == (member_name = H5Tget_member_name(tid, j))) goto out; /* get the member type */ if((member_type_id = H5Tget_member_type(tid, j)) < 0) goto out; /* convert to native type */ if((nmtype_id = H5Tget_native_type(member_type_id,H5T_DIR_DEFAULT)) < 0) goto out; if(0 == (size_native = H5Tget_size(nmtype_id))) goto out; 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; } /* end if */ /* only one field */ else { if(H5Tinsert(write_type_id, member_name, (size_t)0, nmtype_id) < 0) goto out; } /* end else */ /* close */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; if(H5Tclose(nmtype_id) < 0) goto out; nmtype_id = H5I_BADID; H5free_memory(member_name); member_name = NULL; } /* end for */ /* 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; ret_val = 0; out: if(member_name) H5free_memory(member_name); if(preserve_id > 0) if(H5Pclose(preserve_id) < 0) ret_val = -1; if(write_type_id > 0) if(H5Tclose(write_type_id) < 0) ret_val = -1; if(member_type_id > 0) if(H5Tclose(member_type_id) < 0) ret_val = -1; if(nmtype_id > 0) if(H5Tclose(nmtype_id) < 0) ret_val = -1; if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(file_space_id > 0) if(H5Sclose(file_space_id) < 0) ret_val = -1; if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBwrite_fields_index() */ /*------------------------------------------------------------------------- * * Read functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBread_table * * Purpose: Reads a table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 20, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBread_table(hid_t loc_id, const char *dset_name, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *dst_buf) { hid_t did = H5I_BADID; hid_t ftype_id = H5I_BADID; hid_t mem_type_id = H5I_BADID; hid_t sid = H5I_BADID; hsize_t dims[1]; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /* open the dataset. */ if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /* 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; ret_val = 0; out: if(mem_type_id > 0) if(H5Tclose(mem_type_id) < 0) ret_val = -1; if(ftype_id > 0) if(H5Tclose(ftype_id) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBread_table() */ /*------------------------------------------------------------------------- * Function: H5TBread_records * * Purpose: Reads records * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBread_records(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *buf) { hid_t did = H5I_BADID; hid_t ftype_id = H5I_BADID; hid_t mem_type_id = H5I_BADID; hsize_t nrecords_orig; hsize_t nfields; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /* get the number of records and fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &nrecords_orig) < 0) goto out; /* open the dataset */ if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 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 the records */ if((H5TB_common_read_records(did, mem_type_id, start, (size_t)nrecords, nrecords_orig, buf)) < 0) goto out; ret_val = 0; out: if(mem_type_id > 0) if(H5Tclose(mem_type_id) < 0) ret_val = -1; if(ftype_id > 0) if(H5Tclose(ftype_id) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBread_records() */ /*------------------------------------------------------------------------- * Function: H5TBread_fields_name * * Purpose: Reads fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBread_fields_name(hid_t loc_id, const char *dset_name, const char *field_names, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *buf) { hid_t did = H5I_BADID; hid_t ftype_id = H5I_BADID; hid_t mem_type_id = H5I_BADID; hid_t mtype_id = H5I_BADID; hid_t nmtype_id = H5I_BADID; hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hssize_t nfields; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; size_t size_native; char *member_name = NULL; hssize_t i, j; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; if (field_names == NULL) goto out; /* 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 through the members */ for(i = 0, j = 0; i < nfields; i++) { /* get the member name */ if(NULL == (member_name = H5Tget_member_name(ftype_id, (unsigned)i))) goto out; if(H5TB_find_field(member_name, field_names)) { /* 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; if(0 == (size_native = H5Tget_size(nmtype_id))) goto out; 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; } /* end if */ else { if(H5Tinsert(mem_type_id, member_name, (size_t)0, nmtype_id) < 0) goto out; } /* end else */ /* close */ if(H5Tclose(mtype_id) < 0) goto out; mtype_id = H5I_BADID; if(H5Tclose(nmtype_id) < 0) goto out; nmtype_id = H5I_BADID; j++; } /* end if */ H5free_memory(member_name); member_name = NULL; } /* end for */ /* check to make sure field was found, no reason to continue if it does not exist */ if(j == 0) goto out; /* 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; ret_val = 0; out: if(member_name) H5free_memory(member_name); if(mtype_id > 0) if(H5Tclose(mtype_id) < 0) ret_val = -1; if(nmtype_id > 0) if(H5Tclose(nmtype_id) < 0) ret_val = -1; if(mem_type_id > 0) if(H5Tclose(mem_type_id) < 0) ret_val = -1; if(ftype_id > 0) if(H5Tclose(ftype_id) < 0) ret_val = -1; if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBread_fields_name() */ /*------------------------------------------------------------------------- * Function: H5TBread_fields_index * * Purpose: Reads fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBread_fields_index(hid_t loc_id, const char *dset_name, hsize_t nfields, const int *field_index, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *buf) { hid_t did = H5I_BADID; hid_t tid = H5I_BADID; hid_t read_type_id = H5I_BADID; hid_t member_type_id = H5I_BADID; hid_t nmtype_id = H5I_BADID; hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; hsize_t i; size_t size_native; char *member_name = NULL; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /* open the dataset. */ if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /* get the datatype */ if((tid = H5Dget_type(did)) < 0) goto out; /* create a read id */ if((read_type_id = H5Tcreate(H5T_COMPOUND, type_size)) < 0) goto out; /* iterate tru the members */ for(i = 0; i < nfields; i++) { unsigned j; /* Range check */ if(field_index[i] < 0) goto out; j = (unsigned)field_index[i]; /* get the member name */ if(NULL == (member_name = H5Tget_member_name(tid, (unsigned)j))) goto out; /* 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; if(0 == (size_native = H5Tget_size(nmtype_id))) goto out; 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; } /* end if */ else { if(H5Tinsert(read_type_id, member_name, (size_t)0, nmtype_id) < 0) goto out; } /* end else */ /* close the member type */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; if(H5Tclose(nmtype_id) < 0) goto out; nmtype_id = H5I_BADID; H5free_memory(member_name); member_name = NULL; } /* end for */ /* 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; ret_val = 0; out: if(member_name) H5free_memory(member_name); if(read_type_id > 0) if(H5Tclose(read_type_id) < 0) ret_val = -1; if(member_type_id > 0) if(H5Tclose(member_type_id) < 0) ret_val = -1; if(nmtype_id > 0) if(H5Tclose(nmtype_id) < 0) ret_val = -1; if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBread_fields_index() */ /*------------------------------------------------------------------------- * * Manipulation functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBdelete_record * * Purpose: Delete records from middle of table ("pulling up" all the records after it) * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 26, 2001 * *------------------------------------------------------------------------- */ herr_t H5TBdelete_record(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords) { hid_t did = H5I_BADID; hid_t tid = H5I_BADID; hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hid_t mem_type_id = H5I_BADID; hsize_t nfields; hsize_t ntotal_records; hsize_t read_start; hsize_t read_nrecords; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; hsize_t dims[1]; size_t src_size; size_t *src_offset = NULL; size_t *src_sizes = NULL; unsigned char *tmp_buf = NULL; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /*------------------------------------------------------------------------- * first we get information about type size and offsets on disk *------------------------------------------------------------------------- */ /* get the number of records and fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &ntotal_records) < 0) goto out; if(NULL == (src_offset = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t)))) goto out; if(NULL == (src_sizes = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t)))) goto out; /* get field info */ if(H5TBget_field_info(loc_id, dset_name, NULL, src_sizes, src_offset, &src_size) < 0) goto out; /* open the dataset. */ if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /*------------------------------------------------------------------------- * read the records after the deleted one(s) *------------------------------------------------------------------------- */ read_start = start + nrecords; read_nrecords = ntotal_records - read_start; if(read_nrecords) { if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t)read_nrecords, src_size))) goto out; /* read the records after the deleted one(s) */ if(H5TBread_records(loc_id, dset_name, read_start, read_nrecords, src_size, src_offset, src_sizes, tmp_buf) < 0) goto out; /*------------------------------------------------------------------------- * write the records in another position *------------------------------------------------------------------------- */ /* get the datatype */ if((tid = H5Dget_type(did)) < 0) goto out; /* get the dataspace handle */ if((sid = H5Dget_space(did)) < 0) goto out; /* create the memory data type. */ if((mem_type_id = H5TB_create_type( loc_id, dset_name, src_size, src_offset, src_sizes, tid)) < 0) goto out; /* define a hyperslab in the dataset of the size of the records */ offset[0] = start; count[0] = read_nrecords; if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) goto out; /* create a memory dataspace handle */ mem_size[0] = count[0]; if((m_sid = H5Screate_simple(1, mem_size, NULL)) < 0) goto out; if(H5Dwrite(did, mem_type_id, m_sid, sid, H5P_DEFAULT, tmp_buf) < 0) goto out; /* close */ if(H5Sclose(m_sid) < 0) goto out; m_sid = H5I_BADID; if(H5Tclose(mem_type_id) < 0) goto out; mem_type_id = H5I_BADID; if(H5Sclose(sid) < 0) goto out; sid = H5I_BADID; if(H5Tclose(tid) < 0) goto out; tid = H5I_BADID; } /* read_nrecords */ /*------------------------------------------------------------------------- * change the dataset dimension *------------------------------------------------------------------------- */ dims[0] = ntotal_records - nrecords; if(H5Dset_extent(did, dims) < 0) goto out; ret_val = 0; out: if(tmp_buf) HDfree(tmp_buf); if(src_offset) HDfree(src_offset); if(src_sizes) HDfree(src_sizes); if(mem_type_id > 0) if(H5Tclose(mem_type_id) < 0) ret_val = -1; if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBdelete_record() */ /*------------------------------------------------------------------------- * Function: H5TBinsert_record * * Purpose: Inserts records into middle of table ("pushing down" all the records after it) * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 26, 2001 * * Comments: Uses memory offsets * *------------------------------------------------------------------------- */ herr_t H5TBinsert_record(hid_t loc_id, const char *dset_name, hsize_t start, hsize_t nrecords, size_t type_size, const size_t *field_offset, const size_t *field_sizes, void *buf) { hid_t did = H5I_BADID; hid_t tid = H5I_BADID; hid_t mem_type_id = H5I_BADID; hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hsize_t nfields; hsize_t ntotal_records; hsize_t read_nrecords; hsize_t count[1]; hsize_t offset[1]; hsize_t dims[1]; hsize_t mem_dims[1]; unsigned char *tmp_buf = NULL; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /*------------------------------------------------------------------------- * read the records after the inserted one(s) *------------------------------------------------------------------------- */ /* get the dimensions */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &ntotal_records) < 0) goto out; /* 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; if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t) read_nrecords, type_size))) goto out; /* 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) goto out; /* 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) goto out; /* get the file data space */ if((sid = H5Dget_space(did)) < 0) goto out; /* 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; m_sid = H5I_BADID; if(H5Sclose(sid) < 0) goto out; sid = H5I_BADID; /*------------------------------------------------------------------------- * 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) goto out; /* get the file data space */ if((sid = H5Dget_space(did)) < 0) goto out; /* 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; ret_val = 0; out: if(tmp_buf) HDfree(tmp_buf); if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(mem_type_id > 0) if(H5Tclose(mem_type_id) < 0) ret_val = -1; if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBinsert_record() */ /*------------------------------------------------------------------------- * Function: H5TBadd_records_from * * Purpose: Add records from first table to second table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: December 5, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBadd_records_from(hid_t loc_id, const char *dset_name1, hsize_t start1, hsize_t nrecords, const char *dset_name2, hsize_t start2) { hid_t did = H5I_BADID; hid_t tid = H5I_BADID; hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; hsize_t nfields; hsize_t ntotal_records; size_t type_size1; size_t src_size; size_t *src_offset = NULL; size_t *src_sizes = NULL; unsigned char *tmp_buf = NULL; herr_t ret_val = -1; /* check the arguments */ if (dset_name1 == NULL) goto out; if (dset_name2 == NULL) goto out; /*------------------------------------------------------------------------- * first we get information about type size and offsets on disk *------------------------------------------------------------------------- */ /* get the number of records and fields */ if(H5TBget_table_info(loc_id, dset_name1, &nfields, &ntotal_records) < 0) goto out; if(NULL == (src_offset = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t)))) goto out; if(NULL == (src_sizes = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t)))) goto out; /* get field info */ if(H5TBget_field_info(loc_id, dset_name1, NULL, src_sizes, src_offset, &src_size) < 0) goto out; /*------------------------------------------------------------------------- * Get information about the first table and read it *------------------------------------------------------------------------- */ /* open the 1st dataset. */ if((did = H5Dopen2(loc_id, dset_name1, H5P_DEFAULT)) < 0) goto out; /* get the datatype */ if((tid = H5Dget_type(did)) < 0) goto out; /* get the dataspace handle */ if((sid = H5Dget_space(did)) < 0) goto out; /* get the size of the datatype */ if(0 == (type_size1 = H5Tget_size(tid))) goto out; if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t)nrecords, type_size1))) goto out; /* define a hyperslab in the dataset of the size of the records */ offset[0] = start1; count[0] = nrecords; if(H5Sselect_hyperslab(sid, 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, tid, m_sid, sid, 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; ret_val = 0; out: if(tmp_buf) HDfree(tmp_buf); if(src_offset) HDfree(src_offset); if(src_sizes) HDfree(src_sizes); if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBadd_records_from() */ /*------------------------------------------------------------------------- * Function: H5TBcombine_tables * * Purpose: Combine records from two tables into a third * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: December 10, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBcombine_tables(hid_t loc_id1, const char *dset_name1, hid_t loc_id2, const char *dset_name2, const char *dset_name3) { /* identifiers for the 1st dataset. */ hid_t did_1 = H5I_BADID; hid_t tid_1 = H5I_BADID; hid_t sid_1 = H5I_BADID; hid_t pid_1 = H5I_BADID; /* identifiers for the 2nd dataset. */ hid_t did_2 = H5I_BADID; hid_t tid_2 = H5I_BADID; hid_t sid_2 = H5I_BADID; hid_t pid_2 = H5I_BADID; /* identifiers for the 3rd dataset. */ hid_t did_3 = H5I_BADID; hid_t tid_3 = H5I_BADID; hid_t sid_3 = H5I_BADID; hid_t pid_3 = H5I_BADID; hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hid_t member_type_id = H5I_BADID; hid_t attr_id = H5I_BADID; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; hsize_t nfields; hsize_t nrecords; hsize_t dims[1]; hsize_t maxdims[1] = {H5S_UNLIMITED}; hsize_t i; size_t type_size; size_t member_offset; size_t src_size; size_t *src_offset = NULL; size_t *src_sizes = NULL; char attr_name[255]; unsigned char *tmp_buf = NULL; unsigned char *tmp_fill_buf = NULL; htri_t has_fill; herr_t ret_val = -1; /* check the arguments */ if (dset_name1 == NULL) goto out; if (dset_name2 == NULL) goto out; if (dset_name3 == NULL) goto out; /*------------------------------------------------------------------------- * first we get information about type size and offsets on disk *------------------------------------------------------------------------- */ /* get the number of records and fields */ if(H5TBget_table_info(loc_id1, dset_name1, &nfields, &nrecords) < 0) goto out; if(NULL == (src_offset = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t)))) goto out; if(NULL == (src_sizes = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t)))) goto out; /* get field info */ if(H5TBget_field_info(loc_id1, dset_name1, NULL, src_sizes, src_offset, &src_size) < 0) goto out; /*------------------------------------------------------------------------- * get information about the first table *------------------------------------------------------------------------- */ /* open the 1st dataset. */ if((did_1 = H5Dopen2(loc_id1, dset_name1, H5P_DEFAULT)) < 0) goto out; /* get the datatype */ if((tid_1 = H5Dget_type(did_1)) < 0) goto out; /* get the dataspace handle */ if((sid_1 = H5Dget_space(did_1)) < 0) goto out; /* get creation properties list */ if((pid_1 = H5Dget_create_plist(did_1)) < 0) goto out; /* get the dimensions */ if(H5TBget_table_info(loc_id1, dset_name1, &nfields, &nrecords) < 0) goto out; /*------------------------------------------------------------------------- * make the merged table with no data originally *------------------------------------------------------------------------- */ /* clone the property list */ if((pid_3 = H5Pcopy(pid_1)) < 0) goto out; /* clone the type id */ if((tid_3 = H5Tcopy(tid_1)) < 0) goto out; /*------------------------------------------------------------------------- * here we do not clone the file space from the 1st dataset, because we want to create * an empty table. Instead we create a new dataspace with zero records and expandable. *------------------------------------------------------------------------- */ dims[0] = 0; /* create a simple data space with unlimited size */ if((sid_3 = H5Screate_simple(1, dims, maxdims)) < 0) goto out; /* create the dataset */ if((did_3 = H5Dcreate2(loc_id1, dset_name3, tid_3, sid_3, H5P_DEFAULT, pid_3, H5P_DEFAULT)) < 0) goto out; /*------------------------------------------------------------------------- * attach the conforming table attributes *------------------------------------------------------------------------- */ if(H5TB_attach_attributes("Merge table", loc_id1, dset_name3, nfields, tid_3) < 0) goto out; /*------------------------------------------------------------------------- * get attributes *------------------------------------------------------------------------- */ if(0 == (type_size = H5Tget_size(tid_3))) goto out; /* alloc fill value attribute buffer */ if(NULL == (tmp_fill_buf = (unsigned char *)HDmalloc(type_size))) goto out; /* get the fill value attributes */ if((has_fill = H5TBAget_fill(loc_id1, dset_name1, did_1, tmp_fill_buf)) < 0) goto out; /*------------------------------------------------------------------------- * attach the fill attributes from previous table *------------------------------------------------------------------------- */ if(has_fill) { if((sid = H5Screate(H5S_SCALAR)) < 0) goto out; for(i = 0; i < nfields; i++) { /* get the member type */ if((member_type_id = H5Tget_member_type(tid_3, (unsigned)i)) < 0) goto out; /* get the member offset */ member_offset = H5Tget_member_offset(tid_3, (unsigned)i); HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_FILL", (int)i); if((attr_id = H5Acreate2(did_3, attr_name, member_type_id, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto out; if(H5Awrite(attr_id, member_type_id, tmp_fill_buf + member_offset) < 0) goto out; if(H5Aclose(attr_id) < 0) goto out; attr_id = H5I_BADID; if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; } /* end for */ /* close data space. */ if(H5Sclose(sid) < 0) goto out; sid = H5I_BADID; } /* end if */ /*------------------------------------------------------------------------- * read data from 1st table *------------------------------------------------------------------------- */ if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t)nrecords, type_size))) goto out; /* define a hyperslab in the dataset of the size of the records */ offset[0] = 0; count[0] = nrecords; if(H5Sselect_hyperslab(sid_1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) goto out; /* create a memory dataspace handle */ mem_size[0] = count[0]; if((m_sid = H5Screate_simple(1, mem_size, NULL)) < 0) goto out; if(H5Dread(did_1, tid_1, m_sid, sid_1, H5P_DEFAULT, tmp_buf) < 0) goto out; /*------------------------------------------------------------------------- * save data from 1st table into new table *------------------------------------------------------------------------- */ /* append the records to the new table */ if(H5TBappend_records(loc_id1, dset_name3, nrecords, src_size, src_offset, src_sizes, tmp_buf) < 0) goto out; /*------------------------------------------------------------------------- * release temporary resources *------------------------------------------------------------------------- */ if(H5Sclose(m_sid) < 0) goto out; m_sid = H5I_BADID; HDfree(tmp_buf); tmp_buf = NULL; /*------------------------------------------------------------------------- * get information about the 2nd table *------------------------------------------------------------------------- */ /* open the dataset. */ if((did_2 = H5Dopen2(loc_id2, dset_name2, H5P_DEFAULT)) < 0) goto out; /* get the datatype */ if((tid_2 = H5Dget_type(did_2)) < 0) goto out; /* get the dataspace handle */ if((sid_2 = H5Dget_space(did_2)) < 0) goto out; /* get the property list handle */ if((pid_2 = H5Dget_create_plist(did_2)) < 0) goto out; /* get the dimensions */ if(H5TBget_table_info(loc_id2, dset_name2, &nfields, &nrecords) < 0) goto out; /*------------------------------------------------------------------------- * read data from 2nd table *------------------------------------------------------------------------- */ if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t)nrecords, type_size))) goto out; /* define a hyperslab in the dataset of the size of the records */ offset[0] = 0; count[0] = nrecords; if(H5Sselect_hyperslab(sid_2, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) goto out; /* create a memory dataspace handle */ mem_size[0] = count[0]; if((m_sid = H5Screate_simple(1, mem_size, NULL)) < 0) goto out; if(H5Dread(did_2, tid_2, m_sid, sid_2, H5P_DEFAULT, tmp_buf) < 0) goto out; /*------------------------------------------------------------------------- * save data from 2nd table into new table *------------------------------------------------------------------------- */ /* append the records to the new table */ if(H5TBappend_records(loc_id1, dset_name3, nrecords, src_size, src_offset, src_sizes, tmp_buf) < 0) goto out; ret_val = 0; out: if(tmp_buf) HDfree(tmp_buf); if(tmp_fill_buf) HDfree(tmp_fill_buf); if(src_offset) HDfree(src_offset); if(src_sizes) HDfree(src_sizes); if(member_type_id > 0) if(H5Tclose(member_type_id) < 0) ret_val = -1; if(attr_id > 0) if(H5Aclose(attr_id) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(sid_1 > 0) if(H5Sclose(sid_1) < 0) ret_val = -1; if(tid_1 > 0) if(H5Tclose(tid_1) < 0) ret_val = -1; if(pid_1 > 0) if(H5Pclose(pid_1) < 0) ret_val = -1; if(did_1 > 0) if(H5Dclose(did_1) < 0) ret_val = -1; if(sid_2 > 0) if(H5Sclose(sid_2) < 0) ret_val = -1; if(tid_2 > 0) if(H5Tclose(tid_2) < 0) ret_val = -1; if(pid_2 > 0) if(H5Pclose(pid_2) < 0) ret_val = -1; if(did_2 > 0) if(H5Dclose(did_2) < 0) ret_val = -1; if(sid_3 > 0) if(H5Sclose(sid_3) < 0) ret_val = -1; if(tid_3 > 0) if(H5Tclose(tid_3) < 0) ret_val = -1; if(pid_3 > 0) if(H5Pclose(pid_3) < 0) ret_val = -1; if(did_3 > 0) if(H5Dclose(did_3) < 0) ret_val = -1; return ret_val; } /* end H5TBcombine_tables() */ /*------------------------------------------------------------------------- * Function: H5TBinsert_field * * Purpose: Inserts a field * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: January 30, 2002 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBinsert_field(hid_t loc_id, const char *dset_name, const char *field_name, hid_t field_type, hsize_t position, const void *fill_data, const void *buf) { /* identifiers for the 1st, original dataset */ hid_t did_1 = H5I_BADID; hid_t tid_1 = H5I_BADID; hid_t sid_1 = H5I_BADID; hid_t pid_1 = H5I_BADID; hid_t msid_1 = H5I_BADID; /* identifiers for the 2nd, new dataset */ hid_t did_2 = H5I_BADID; hid_t tid_2 = H5I_BADID; hid_t sid_2 = H5I_BADID; hid_t pid_2 = H5I_BADID; hid_t msid_2 = H5I_BADID; /* identifiers for the 3rd, final dataset */ hid_t did_3 = H5I_BADID; hid_t tid_3 = H5I_BADID; hid_t sid_3 = H5I_BADID; hid_t member_type_id = H5I_BADID; hid_t write_type_id = H5I_BADID; hid_t preserve_id = H5I_BADID; hid_t attr_id = H5I_BADID; size_t member_size; size_t new_member_size = 0; size_t total_size; size_t curr_offset; 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]; hsize_t i; char table_title[255]; char attr_name[255]; char *member_name = NULL; unsigned char *tmp_buf = NULL; unsigned char *tmp_fill_buf = NULL; hbool_t inserted; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; if (field_name == NULL) goto out; /* get the number of records and fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &nrecords) < 0) goto out; /*------------------------------------------------------------------------- * get information about the old data type *------------------------------------------------------------------------- */ /* open the dataset. */ if((did_1 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /* 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(0 == (total_size = H5Tget_size(tid_1))) 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 */ if(NULL == (tmp_fill_buf = (unsigned char *)HDmalloc(total_size))) goto out; /* 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 */ if(0 == (member_size = H5Tget_size(field_type))) goto out; /* create the data type. */ if((tid_2 = H5Tcreate(H5T_COMPOUND, (size_t)(total_size + member_size))) < 0) goto out; curr_offset = 0; inserted = FALSE; /* insert the old fields, counting with the new one */ for(i = 0; i < nfields + 1; i++) { hsize_t idx; idx = i; if(inserted) idx = i - 1; if(i == position) { /* get the new member size */ if(0 == (new_member_size = H5Tget_size(field_type))) goto out; /* insert the new field type */ if(H5Tinsert(tid_2, field_name, curr_offset, field_type) < 0) goto out; curr_offset += new_member_size; inserted = TRUE; } /* end if */ else { /* get the member name */ if(NULL == (member_name = H5Tget_member_name(tid_1, (unsigned)idx))) goto out; /* get the member type */ if((member_type_id = H5Tget_member_type(tid_1, (unsigned)idx)) < 0) goto out; /* get the member size */ if(0 == (member_size = H5Tget_size(member_type_id))) goto out; /* insert it into the new type */ if(H5Tinsert(tid_2, member_name, curr_offset, member_type_id) < 0) goto out; curr_offset += member_size; H5free_memory(member_name); member_name = NULL; /* close the member type */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; } /* end else */ } /* end for */ /*------------------------------------------------------------------------- * 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) goto out; /* modify dataset creation properties, i.e. enable chunking */ if((pid_2 = H5Pcreate(H5P_DATASET_CREATE)) < 0) goto out; if(H5Pset_chunk(pid_2, 1, dims_chunk) < 0) goto out; /* 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 *------------------------------------------------------------------------- */ if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t)nrecords, (size_t)total_size))) goto out; /* define a hyperslab in the dataset of the size of the records */ offset[0] = 0; count[0] = nrecords; if(H5Sselect_hyperslab(sid_1, H5S_SELECT_SET, offset, NULL, count, NULL) < 0) goto out; /* create a memory dataspace handle */ mem_size[0] = count[0]; if((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; } /* end if */ /*------------------------------------------------------------------------- * delete 1st table *------------------------------------------------------------------------- */ if(H5Ldelete(loc_id, dset_name, H5P_DEFAULT) < 0) goto out; /*------------------------------------------------------------------------- * rename 2nd table *------------------------------------------------------------------------- */ if(H5Lmove(loc_id, "new", H5L_SAME_LOC, dset_name, H5P_DEFAULT, H5P_DEFAULT) < 0) goto out; /*------------------------------------------------------------------------- * attach the conforming table attributes *------------------------------------------------------------------------- */ /* get the number of records and fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &nrecords) < 0) goto out; /* open the dataset. */ if((did_3 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /* get the datatype */ if((tid_3 = H5Dget_type(did_3)) < 0) goto out; /* set the attributes */ if(H5TB_attach_attributes(table_title, loc_id, dset_name, (hsize_t)nfields, tid_3) < 0) goto out; /*------------------------------------------------------------------------- * attach the fill attributes from previous table *------------------------------------------------------------------------- */ if((sid_3 = H5Screate(H5S_SCALAR)) < 0) goto out; for(i = 0; i < (nfields - 1); i++) { size_t member_offset; /* 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); HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_FILL", (int)i); if((attr_id = H5Acreate2(did_3, attr_name, member_type_id, sid_3, H5P_DEFAULT, H5P_DEFAULT)) < 0) goto out; if(H5Awrite(attr_id, member_type_id, tmp_fill_buf + member_offset) < 0) goto out; if(H5Aclose(attr_id) < 0) goto out; attr_id = H5I_BADID; /* close the member type */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; } /* end for */ /*------------------------------------------------------------------------- * attach the fill attribute from the new field, if present *------------------------------------------------------------------------- */ if(fill_data) { HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_FILL", (int)(nfields - 1)); /* get the member type */ if((member_type_id = H5Tget_member_type(tid_3, (unsigned)nfields - 1)) < 0) goto out; if((attr_id = H5Acreate2(did_3, attr_name, member_type_id, sid_3, 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; attr_id = H5I_BADID; if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; } /* end fill_data */ ret_val = 0; out: if(member_name) H5free_memory(member_name); if(tmp_buf) HDfree(tmp_buf); if(tmp_fill_buf) HDfree(tmp_fill_buf); if(preserve_id > 0) if(H5Pclose(preserve_id) < 0) ret_val = -1; if(msid_1 > 0) if(H5Sclose(msid_1) < 0) ret_val = -1; if(tid_1 > 0) if(H5Tclose(tid_1) < 0) ret_val = -1; if(pid_1 > 0) if(H5Pclose(pid_1) < 0) ret_val = -1; if(sid_1 > 0) if(H5Sclose(sid_1) < 0) ret_val = -1; if(did_1 > 0) if(H5Dclose(did_1) < 0) ret_val = -1; if(msid_2 > 0) if(H5Sclose(msid_2) < 0) ret_val = -1; if(sid_2 > 0) if(H5Sclose(sid_2) < 0) ret_val = -1; if(tid_2 > 0) if(H5Tclose(tid_2) < 0) ret_val = -1; if(pid_2 > 0) if(H5Pclose(pid_2) < 0) ret_val = -1; if(did_2 > 0) if(H5Dclose(did_2) < 0) ret_val = -1; if(sid_3 > 0) if(H5Sclose(sid_3) < 0) ret_val = -1; if(tid_3 > 0) if(H5Tclose(tid_3) < 0) ret_val = -1; if(did_3 > 0) if(H5Dclose(did_3) < 0) ret_val = -1; return ret_val; } /* end H5TBinsert_field() */ /*------------------------------------------------------------------------- * Function: H5TBdelete_field * * Purpose: Deletes a field * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: January 30, 2002 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBdelete_field(hid_t loc_id, const char *dset_name, const char *field_name) { /* identifiers for the 1st original dataset */ hid_t did_1 = H5I_BADID; hid_t tid_1 = H5I_BADID; hid_t sid_1 = H5I_BADID; hid_t pid_1 = H5I_BADID; /* identifiers for the 2nd new dataset */ hid_t did_2 = H5I_BADID; hid_t tid_2 = H5I_BADID; hid_t sid_2 = H5I_BADID; hid_t pid_2 = H5I_BADID; /* identifiers for the 3rd final dataset */ hid_t did_3 = H5I_BADID; hid_t tid_3 = H5I_BADID; hid_t member_type_id = H5I_BADID; hid_t preserve_id = H5I_BADID; hid_t read_type_id = H5I_BADID; hid_t write_type_id = H5I_BADID; hid_t attr_id = H5I_BADID; size_t member_size; size_t type_size1; size_t type_size2; size_t curr_offset; size_t delete_member_size = 0; size_t member_offset; hsize_t nfields; hsize_t nrecords; hsize_t dims_chunk[1]; hsize_t dims[1]; hsize_t maxdims[1] = { H5S_UNLIMITED }; hsize_t i; char attr_name[255]; char table_title[255]; char *member_name = NULL; unsigned char *tmp_buf = NULL; unsigned char *tmp_fill_buf = NULL; htri_t has_fill = FALSE; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; if (field_name == NULL) goto out; /* get the number of records and fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &nrecords) < 0) goto out; /*------------------------------------------------------------------------- * get information about the old data type *------------------------------------------------------------------------- */ /* open the dataset. */ if((did_1 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /* 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(0 == (type_size1 = H5Tget_size(tid_1))) 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; /*------------------------------------------------------------------------- * 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 */ if(NULL == (member_name = H5Tget_member_name(tid_1, (unsigned)i))) goto out; /* we want to find the field to delete */ if(H5TB_find_field(member_name, field_name)) { /* get the member type */ if((member_type_id = H5Tget_member_type(tid_1, (unsigned)i)) < 0) goto out; /* get the member size */ if(0 == (delete_member_size = H5Tget_size(member_type_id))) goto out; /* close the member type */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; H5free_memory(member_name); member_name = NULL; break; } /* end if */ H5free_memory(member_name); member_name = NULL; } /* end for */ /* 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 */ if(NULL == (tmp_fill_buf = (unsigned char *)HDmalloc((size_t)type_size2))) goto out; /*------------------------------------------------------------------------- * 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 */ if(NULL == (member_name = H5Tget_member_name(tid_1, (unsigned)i))) goto out; /* we want to skip the field to delete */ if(!H5TB_find_field(member_name, field_name)) { /* get the member type */ if((member_type_id = H5Tget_member_type(tid_1, (unsigned)i)) < 0) goto out; /* get the member size */ if(0 == (member_size = H5Tget_size(member_type_id))) goto out; /* 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 *------------------------------------------------------------------------- */ HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_FILL", (int)i); /* check if we have the _FILL attribute */ if((has_fill = H5LT_find_attribute(did_1, attr_name)) < 0) goto out; /* get it */ if(has_fill) if(H5LT_get_attribute_disk(did_1, attr_name, tmp_fill_buf + curr_offset) < 0) goto out; curr_offset += member_size; /* close the member type */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; } /* end if */ H5free_memory(member_name); member_name = NULL; } /* end for */ /*------------------------------------------------------------------------- * 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) goto out; /* modify dataset creation properties, i.e. enable chunking */ pid_2 = H5Pcreate(H5P_DATASET_CREATE); if(H5Pset_chunk(pid_2, 1, dims_chunk) < 0) goto out; /* 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 */ if(NULL == (member_name = H5Tget_member_name(tid_1, (unsigned)i))) goto out; /* skip 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 */ if(0 == (member_size = H5Tget_size(member_type_id))) goto out; /* 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; if(NULL == (tmp_buf = (unsigned char *)HDcalloc((size_t)nrecords, member_size))) goto out; /* 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; preserve_id = H5I_BADID; /* close the member type */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; /* close the read type */ if(H5Tclose(read_type_id) < 0) goto out; read_type_id = H5I_BADID; /* close the write type */ if(H5Tclose(write_type_id) < 0) goto out; write_type_id = H5I_BADID; HDfree(tmp_buf); tmp_buf = NULL; } /* end if */ /* release resources. */ H5free_memory(member_name); member_name = NULL; } /* end for */ /*------------------------------------------------------------------------- * delete 1st table *------------------------------------------------------------------------- */ if(H5Ldelete(loc_id, dset_name, H5P_DEFAULT) < 0) goto out; /*------------------------------------------------------------------------- * rename 2nd table *------------------------------------------------------------------------- */ if(H5Lmove(loc_id, "new", H5L_SAME_LOC, dset_name, H5P_DEFAULT, H5P_DEFAULT) < 0) goto out; /*------------------------------------------------------------------------- * attach the conforming table attributes *------------------------------------------------------------------------- */ /* get the number of records and fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &nrecords) < 0) goto out; /* open the dataset. */ if((did_3 = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /* get the datatype */ if((tid_3 = H5Dget_type(did_3)) < 0) goto out; /* set the attributes */ if(H5TB_attach_attributes(table_title, loc_id, dset_name, nfields, tid_3) < 0) goto out; /*------------------------------------------------------------------------- * attach the fill attributes from previous table *------------------------------------------------------------------------- */ if(has_fill) { 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_3, (unsigned)i)) < 0) goto out; /* get the member offset */ member_offset = H5Tget_member_offset(tid_3, (unsigned)i); HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_FILL", (int)i); if((attr_id = H5Acreate2(did_3, 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; attr_id = H5I_BADID; /* close the member type */ if(H5Tclose(member_type_id) < 0) goto out; member_type_id = H5I_BADID; } /* end for */ /* close data space. */ if(H5Sclose(sid_1) < 0) goto out; sid_1 = H5I_BADID; } /* end if */ ret_val = 0; out: if(member_name) H5free_memory(member_name); if(tmp_fill_buf) HDfree(tmp_fill_buf); if(tmp_buf) HDfree(tmp_buf); if(attr_id > 0) if(H5Aclose(attr_id) < 0) ret_val = -1; if(preserve_id > 0) if(H5Pclose(preserve_id) < 0) ret_val = -1; if(member_type_id > 0) if(H5Tclose(member_type_id) < 0) ret_val = -1; if(read_type_id > 0) if(H5Tclose(read_type_id) < 0) ret_val = -1; if(write_type_id > 0) if(H5Tclose(write_type_id) < 0) ret_val = -1; if(tid_1 > 0) if(H5Tclose(tid_1) < 0) ret_val = -1; if(pid_1 > 0) if(H5Pclose(pid_1) < 0) ret_val = -1; if(sid_1 > 0) if(H5Sclose(sid_1) < 0) ret_val = -1; if(did_1 > 0) if(H5Dclose(did_1) < 0) ret_val = -1; if(sid_2 > 0) if(H5Sclose(sid_2) < 0) ret_val = -1; if(tid_2 > 0) if(H5Tclose(tid_2) < 0) ret_val = -1; if(pid_2 > 0) if(H5Pclose(pid_2) < 0) ret_val = -1; if(did_2 > 0) if(H5Dclose(did_2) < 0) ret_val = -1; if(tid_3 > 0) if(H5Tclose(tid_3) < 0) ret_val = -1; if(did_3 > 0) if(H5Dclose(did_3) < 0) ret_val = -1; return ret_val; } /* end H5TBdelete_field() */ /*------------------------------------------------------------------------- * * Table attribute functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBAget_title * * Purpose: Read the table title * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: January 30, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBAget_title(hid_t loc_id, char *table_title) { /* Get the TITLE attribute */ if(H5LT_get_attribute_disk(loc_id, "TITLE", table_title) < 0) return -1; return 0; } /*------------------------------------------------------------------------- * Function: H5TBAget_fill * * Purpose: Read the table attribute fill values * * Return: Success: TRUE/FALSE, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: January 30, 2002 * * Comments: * *------------------------------------------------------------------------- */ htri_t H5TBAget_fill(hid_t loc_id, const char *dset_name, hid_t dset_id, unsigned char *dst_buf) { hsize_t nfields; hsize_t nrecords; hsize_t i; size_t *src_offset = NULL; char attr_name[255]; htri_t has_fill = FALSE; htri_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /* get the number of records and fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, &nrecords) < 0) goto out; if(NULL == (src_offset = (size_t *)HDmalloc((size_t)nfields * sizeof(size_t)))) goto out; /* 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++) { HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_FILL", (int)i); /* check if we have the _FILL attribute */ if((has_fill = H5LT_find_attribute(dset_id, attr_name)) < 0) goto out; /* get it */ if(has_fill) if(H5LT_get_attribute_disk(dset_id, attr_name, dst_buf + src_offset[i]) < 0) goto out; } /* end for */ ret_val = has_fill; out: if(src_offset) HDfree(src_offset); return ret_val; } /* end H5TBAget_fill() */ /*------------------------------------------------------------------------- * * Inquiry functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TBget_table_info * * Purpose: Gets the number of records and fields of a table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBget_table_info(hid_t loc_id, const char *dset_name, hsize_t *nfields, hsize_t *nrecords) { hid_t tid = H5I_BADID; hid_t sid = H5I_BADID; hid_t did = H5I_BADID; hsize_t dims[1]; int num_members; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /* 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 members */ if((num_members = H5Tget_nmembers(tid)) < 0) goto out; /*------------------------------------------------------------------------- * get number of nfields *------------------------------------------------------------------------- */ if(nfields) *nfields = (hsize_t)num_members; /*------------------------------------------------------------------------- * get number of records *------------------------------------------------------------------------- */ if(nrecords) { /* get the dataspace handle */ if((sid = H5Dget_space(did)) < 0) goto out; /* get dimension */ if(H5Sget_simple_extent_dims(sid, dims, NULL) < 0) goto out; /* terminate access to the dataspace */ if(H5Sclose(sid) < 0) goto out; sid = H5I_BADID; *nrecords = dims[0]; } /* end if */ ret_val = 0; out: if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBget_table_info() */ /*------------------------------------------------------------------------- * Function: H5TBget_field_info * * Purpose: Get information about fields * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * * Comments: * *------------------------------------------------------------------------- */ herr_t H5TBget_field_info(hid_t loc_id, const char *dset_name, char *field_names[], size_t *field_sizes, size_t *field_offsets, size_t *type_size) { hid_t did = H5I_BADID; /* dataset ID */ hid_t tid = H5I_BADID; /* file type ID */ hid_t n_tid = H5I_BADID; /* native type ID */ hid_t m_tid = H5I_BADID; /* member type ID */ hid_t nm_tid = H5I_BADID; /* native member ID */ hssize_t nfields; hssize_t i; herr_t ret_val = -1; /* check the arguments */ if (dset_name == NULL) goto out; /* open the dataset. */ if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0) goto out; /* get the datatype */ if((tid = H5Dget_type(did)) < 0) goto out; if((n_tid = H5Tget_native_type(tid, H5T_DIR_DEFAULT)) < 0) goto out; /* get the type size */ if(type_size) if(0 == (*type_size = H5Tget_size(n_tid))) goto out; /* get the number of members */ if((nfields = H5Tget_nmembers(tid)) < 0) goto out; /* iterate tru the members */ for(i = 0; i < nfields; i++) { /* get the member name */ if(field_names) { char *member_name; if(NULL == (member_name = H5Tget_member_name(tid, (unsigned)i))) goto out; strcpy(field_names[i], member_name); H5free_memory(member_name); } /* end if */ /* get the member type */ if((m_tid = H5Tget_member_type(tid, (unsigned)i)) < 0) goto out; if((nm_tid = H5Tget_native_type(m_tid, H5T_DIR_DEFAULT)) < 0) goto out; /* get the member size */ if(field_sizes) if(0 == (field_sizes[i] = H5Tget_size(nm_tid))) goto out; /* get the member offset */ if(field_offsets) field_offsets[i] = H5Tget_member_offset(n_tid, (unsigned) i); /* close the member types */ if(H5Tclose(m_tid) < 0) goto out; m_tid = H5I_BADID; if(H5Tclose(nm_tid) < 0) goto out; nm_tid = H5I_BADID; } /* end for */ ret_val = 0; out: if(tid > 0) if(H5Tclose(tid) < 0) ret_val = -1; if(n_tid > 0) if(H5Tclose(n_tid) < 0) ret_val = -1; if(m_tid > 0) if(H5Tclose(m_tid) < 0) ret_val = -1; if(nm_tid > 0) if(H5Tclose(nm_tid) < 0) ret_val = -1; if(did > 0) if(H5Dclose(did) < 0) ret_val = -1; return ret_val; } /* end H5TBget_field_info() */ /*------------------------------------------------------------------------- * * internal functions * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TB_find_field * * Purpose: Find a string field * * Return: Success: TRUE/FALSE, Failure: N/A * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: November 19, 2001 * *------------------------------------------------------------------------- */ static hbool_t H5TB_find_field(const char *field, const char *field_list) { const char *start = field_list; const char *end; /* check the arguments */ if (field == NULL) return FALSE; if (field_list == NULL) return FALSE; while((end = HDstrstr(start, ",")) != 0) { ptrdiff_t count = end - start; if(HDstrncmp(start, field, (size_t)count) == 0 && (size_t)count == HDstrlen(field)) return TRUE; start = end + 1; } /* end while */ if(HDstrncmp(start, field, HDstrlen(field)) == 0) return TRUE; return FALSE; } /* end H5TB_find_field() */ /*------------------------------------------------------------------------- * Function: H5TB_attach_attributes * * Purpose: Private function that creates the conforming table attributes; * Used by H5TBcombine_tables; not used by H5TBmake_table, which does not read * the fill value attributes from an existing table * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: December 6, 2001 * * Comments: * *------------------------------------------------------------------------- */ static herr_t H5TB_attach_attributes(const char *table_title, hid_t loc_id, const char *dset_name, hsize_t nfields, hid_t tid) { char attr_name[255]; char *member_name = NULL; hsize_t i; herr_t ret_val = -1; /* 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 */ if(NULL == (member_name = H5Tget_member_name(tid, (unsigned)i))) goto out; HDsnprintf(attr_name, sizeof(attr_name), "FIELD_%d_NAME", (int)i); /* attach the attribute */ if(H5LTset_attribute_string(loc_id, dset_name, attr_name, member_name) < 0) goto out; H5free_memory(member_name); member_name = NULL; } /* end for */ ret_val = 0; out: if(member_name) H5free_memory(member_name); return ret_val; } /* end H5TB_attach_attributes() */ /*------------------------------------------------------------------------- * Function: H5TB_create_type * * Purpose: Private function that creates a memory type ID * * Return: Success: the memory type ID, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: March 31, 2004 * * Comments: * *------------------------------------------------------------------------- */ static hid_t H5TB_create_type(hid_t loc_id, const char *dset_name, size_t type_size, const size_t *field_offset, const size_t *field_sizes, hid_t ftype_id) { hid_t mem_type_id = H5I_BADID; hid_t mtype_id = H5I_BADID; hid_t nmtype_id = H5I_BADID; size_t size_native; hsize_t nfields = 0; char **fnames = NULL; unsigned i; hid_t ret_val = -1; /* get the number of fields */ if(H5TBget_table_info(loc_id, dset_name, &nfields, NULL) < 0) goto out; if(NULL == (fnames = (char**)HDcalloc(sizeof(char*), (size_t)nfields))) goto out; for(i = 0; i < nfields; i++) if(NULL == (fnames[i] = (char*)HDmalloc(HLTB_MAX_FIELD_LEN))) goto out; /* 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; if(0 == (size_native = H5Tget_size(nmtype_id))) goto out; 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; mtype_id = H5I_BADID; if(H5Tclose(nmtype_id) < 0) goto out; nmtype_id = H5I_BADID; } /* end for */ ret_val = mem_type_id; out: if(fnames) { for(i = 0; i < nfields; i++) if(fnames[i]) HDfree(fnames[i]); HDfree(fnames); } /* end if */ if(mtype_id > 0) if(H5Tclose(mtype_id) < 0) ret_val = -1; if(nmtype_id > 0) if(H5Tclose(nmtype_id) < 0) ret_val = -1; if(ret_val < 0 && mem_type_id > 0) H5Tclose(mem_type_id); return ret_val; } /* end H5TB_create_type() */ /*------------------------------------------------------------------------- * * Functions shared between H5TB and H5PT * *------------------------------------------------------------------------- */ /*------------------------------------------------------------------------- * Function: H5TB_common_append_records * * Purpose: Common code for reading records shared between H5PT and H5TB * * Return: Success: 0, Failure: -1 * * Programmer: Nat Furrer, nfurrer@ncsa.uiuc.edu * James Laird, jlaird@ncsa.uiuc.edu * * Date: March 8, 2004 * * Comments: Called by H5TBappend_records and H5PTappend_records * *------------------------------------------------------------------------- */ herr_t H5TB_common_append_records(hid_t dataset_id, hid_t mem_type_id, size_t nrecords, hsize_t orig_table_size, const void *buf) { hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hsize_t count[1]; hsize_t offset[1]; hsize_t dims[1]; hsize_t mem_dims[1]; herr_t ret_val = -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; ret_val = 0; out: if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; return ret_val; } /* end H5TB_common_append_records() */ /*------------------------------------------------------------------------- * Function: H5TB_common_read_records * * Purpose: Common code for reading records shared between H5PT and H5TB * * Return: Success: 0, Failure: -1 * * Programmer: Nat Furrer, nfurrer@ncsa.uiuc.edu * James Laird, jlaird@ncsa.uiuc.edu * * Date: March 8, 2004 * * Comments: Called by H5TBread_records and H5PTread_records * *------------------------------------------------------------------------- */ herr_t H5TB_common_read_records(hid_t dataset_id, hid_t mem_type_id, hsize_t start, size_t nrecords, hsize_t table_size, void *buf) { hid_t sid = H5I_BADID; hid_t m_sid = H5I_BADID; hsize_t count[1]; hsize_t offset[1]; hsize_t mem_size[1]; herr_t ret_val = -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; ret_val = 0; out: if(m_sid > 0) if(H5Sclose(m_sid) < 0) ret_val = -1; if(sid > 0) if(H5Sclose(sid) < 0) ret_val = -1; return ret_val; } /* end H5TB_common_read_records() */