diff options
Diffstat (limited to 'tools/h5repack/h5repack_copy.c')
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 133 |
1 files changed, 70 insertions, 63 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 9573ee8..b41f7be 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -5,12 +5,10 @@ * * * 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. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" @@ -76,36 +74,28 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t /*------------------------------------------------------------------------- * Function: copy_objects * - * Purpose: duplicate all HDF5 objects in the file + * Purpose: duplicate all HDF5 objects in the file * - * Return: 0, ok, -1 no + * Return: 0, ok, + * -1 no * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * * Date: October, 23, 2003 * - * Modification: - * Peter Cao, June 13, 2007 - * Add "-L, --latest" and other options to pack a file with the latest file format - * - * Peter Cao, September 25, 2007 - * Copy user block when repacking a file - * - * Pedro Vicente, August 20, 2008 - * Add a user block to file if requested - * *------------------------------------------------------------------------- */ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t fidin; - hid_t fidout = -1; - trav_table_t *travt = NULL; - hsize_t ub_size = 0; /* size of user block */ - hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ - hid_t fapl = H5P_DEFAULT; /* file access property list ID */ + int ret_value = 0; /* no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + hid_t fidin; + hid_t fidout = -1; + trav_table_t *travt = NULL; + hsize_t ub_size = 0; /* size of user block */ + hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */ + hid_t fapl = H5P_DEFAULT; /* file access property list ID */ + unsigned crt_order_flags; /* group creation order flag */ /*------------------------------------------------------------------------- * open input file @@ -119,6 +109,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) /* get user block size and file space strategy/threshold */ { hid_t fcpl_in; /* file creation property list ID for input file */ + hid_t grp_in = -1; /* group ID */ + hid_t gcpl_in = -1; /* group creation property list */ if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) { error_msg("failed to retrieve file creation property list\n"); @@ -130,6 +122,18 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); } + /* open root group */ + if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed"); + + /* get root group creation property list */ + if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed"); + + /* query and set the group creation properties */ + if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed"); + if (H5Pclose(fcpl_in) < 0) { error_msg("failed to close property list\n"); HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); @@ -300,6 +304,9 @@ print_user_block(fnamein, fidin); } } + if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed"); + /*------------------------------------------------------------------------- * create the output file *------------------------------------------------------------------------- @@ -328,6 +335,8 @@ print_user_block(fnamein, fidin); *------------------------------------------------------------------------- */ + /* Initialize indexing options */ + h5trav_set_index(sort_by, sort_order); /* init table */ trav_table_init(&travt); @@ -444,10 +453,10 @@ done: int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - int k; + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int k; H5D_layout_t dset_layout; - int rank_chunk; + int rank_chunk; hsize_t dims_chunk[H5S_MAX_RANK]; hsize_t size_chunk = 1; hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */ @@ -662,33 +671,33 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - hid_t grp_in = -1; /* group ID */ - hid_t grp_out = -1; /* group ID */ - hid_t dset_in = -1; /* read dataset ID */ + hid_t grp_in = -1; /* group ID */ + hid_t grp_out = -1; /* group ID */ + hid_t dset_in = -1; /* read dataset ID */ hid_t dset_out = -1; /* write dataset ID */ - hid_t gcpl_in = -1; /* group creation property list */ + hid_t gcpl_in = -1; /* group creation property list */ hid_t gcpl_out = -1; /* group creation property list */ - hid_t type_in = -1; /* named type ID */ + hid_t type_in = -1; /* named type ID */ hid_t type_out = -1; /* named type ID */ - hid_t dcpl_in = -1; /* dataset creation property list ID */ + hid_t dcpl_in = -1; /* dataset creation property list ID */ hid_t dcpl_out = -1; /* dataset creation property list ID */ hid_t f_space_id = -1; /* file space ID */ hid_t ftype_id = -1; /* file type ID */ hid_t wtype_id = -1; /* read/write type ID */ named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */ - size_t msize; /* size of type */ - hsize_t nelmts; /* number of elements in dataset */ + size_t msize; /* size of type */ + hsize_t nelmts; /* number of elements in dataset */ H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset */ - int rank; /* rank of dataset */ + int rank; /* rank of dataset */ hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */ - hsize_t dsize_in; /* input dataset size before filter */ - hsize_t dsize_out; /* output dataset size after filter */ - int apply_s; /* flag for apply filter to small dataset sizes */ - int apply_f; /* flag for apply filter to return error on H5Dcreate */ - void *buf = NULL; /* buffer for raw data */ + hsize_t dsize_in; /* input dataset size before filter */ + hsize_t dsize_out; /* output dataset size after filter */ + int apply_s; /* flag for apply filter to small dataset sizes */ + int apply_f; /* flag for apply filter to return error on H5Dcreate */ + void *buf = NULL; /* buffer for raw data */ void *hslab_buf = NULL; /* hyperslab buffer for raw data */ - int has_filter; /* current object has a filter */ - int req_filter; /* there was a request for a filter */ + int has_filter; /* current object has a filter */ + int req_filter; /* there was a request for a filter */ int req_obj_layout = 0; /* request layout to current object */ unsigned crt_order_flags; /* group creation order flag */ unsigned i; @@ -869,7 +878,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, /* wtype_id will have already been set if using a named dtype */ if (!is_named) { if (options->use_native == 1) - wtype_id = h5tools_get_native_type(ftype_id); + wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); else wtype_id = H5Tcopy(ftype_id); } /* end if */ @@ -1303,20 +1312,19 @@ done: * *------------------------------------------------------------------------- */ -static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, - int pr) +static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) { - char strfilter[255]; + char strfilter[255]; #if defined (PRINT_DEBUG ) - char temp[255]; + char temp[255]; #endif - int nfilters; /* number of filters */ - unsigned filt_flags; /* filter flags */ - H5Z_filter_t filtn; /* filter identification number */ - unsigned cd_values[20]; /* filter client data values */ - size_t cd_nelmts; /* filter client number of values */ - char f_objname[256]; /* filter objname */ - int i; + int nfilters; /* number of filters */ + unsigned filt_flags; /* filter flags */ + H5Z_filter_t filtn; /* filter identification number */ + unsigned cd_values[20]; /* filter client data values */ + size_t cd_nelmts; /* filter client number of values */ + char f_objname[256]; /* filter objname */ + int i; HDstrcpy(strfilter, "\0"); @@ -1415,10 +1423,9 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, * *------------------------------------------------------------------------- */ -static int copy_user_block(const char *infile, const char *outfile, - hsize_t size) +static int copy_user_block(const char *infile, const char *outfile, hsize_t size) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ int infid = -1, outfid = -1; /* File descriptors */ /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */ @@ -1495,12 +1502,12 @@ done: static void print_user_block(const char *filename, hid_t fid) { - int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ - int fh; /* file handle */ + int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */ + int fh; /* file handle */ hsize_t ub_size; /* user block size */ hsize_t size; /* size read */ - hid_t fcpl; /* file creation property list ID for HDF5 file */ - int i; + hid_t fcpl; /* file creation property list ID for HDF5 file */ + int i; /* get user block size */ if(( fcpl = H5Fget_create_plist(fid)) < 0) { |