/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 COPYING file, which can be found at the root of the source code * * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Purpose: A library for routines that are common * amongst the various HDF5 tools. */ #include "h5tools.h" #include "h5tools_dump.h" #include "h5tools_ref.h" #include "h5tools_utils.h" #include "H5private.h" #ifdef H5_TOOLS_DEBUG /* global debug variables */ int H5tools_INDENT_g = 0; #endif /* global variables */ H5E_auto2_t lib_func; H5E_auto2_t tools_func; void * lib_edata; void * tools_edata; hid_t H5tools_ERR_STACK_g = H5I_INVALID_HID; hid_t H5tools_ERR_CLS_g = H5I_INVALID_HID; hid_t H5E_tools_g = H5I_INVALID_HID; hid_t H5E_tools_min_id_g = H5I_INVALID_HID; hid_t H5E_tools_min_info_id_g = H5I_INVALID_HID; hid_t H5E_tools_min_dbg_id_g = H5I_INVALID_HID; FILE *rawattrstream = NULL; /* should initialize to stdout but gcc moans about it */ FILE *rawdatastream = NULL; /* should initialize to stdout but gcc moans about it */ FILE *rawinstream = NULL; /* should initialize to stdin but gcc moans about it */ FILE *rawoutstream = NULL; /* should initialize to stdout but gcc moans about it */ FILE *rawerrorstream = NULL; /* should initialize to stderr but gcc moans about it */ int bin_output; /* binary output */ int bin_form = 0; /* binary form, default NATIVE */ int region_output; /* region output */ int oid_output; /* oid output */ int data_output; /* data output */ int attr_data_output; /* attribute data output */ int compound_data; unsigned packed_bits_num; /* number of packed bits to display */ unsigned packed_data_offset; /* offset of packed bits to display */ unsigned packed_data_length; /* length of packed bits to display */ unsigned long long packed_data_mask; /* mask in which packed bits to display */ int enable_error_stack = 0; /* re-enable error stack; disable=0 enable=1 */ /* sort parameters */ H5_index_t sort_by = H5_INDEX_NAME; /* sort_by [creation_order | name] */ H5_iter_order_t sort_order = H5_ITER_INC; /* sort_order [ascending | descending] */ /* module-scoped variables */ static int h5tools_init_g; /* if h5tools lib has been initialized */ /* Names of VFDs. These names are always available so that * the tools can emit special messages when a VFD is asked * for by name but is not compiled into the library or is * somehow otherwise not enabled. * */ const char *drivernames[] = { "sec2", "direct", "log", "windows", "stdio", "core", "family", "split", "multi", "mpio", "ros3", "hdfs", }; #define NUM_DRIVERS (sizeof(drivernames) / sizeof(drivernames[0])) /*------------------------------------------------------------------------- * Function: h5tools_init * * Purpose: This should be called before any other h5tools function is called. * Effect of any h5tools function called before this has been called is * undetermined. * * Return None *------------------------------------------------------------------------- */ void h5tools_init(void) { /* Disable error reporting */ H5Eget_auto2(H5E_DEFAULT, &lib_func, &lib_edata); H5Eset_auto2(H5E_DEFAULT, NULL, NULL); if (!h5tools_init_g) { H5TOOLS_INIT_ERROR(); if (!rawattrstream) rawattrstream = stdout; if (!rawdatastream) rawdatastream = stdout; if (!rawinstream) rawinstream = stdin; if (!rawoutstream) rawoutstream = stdout; if (!rawerrorstream) rawerrorstream = stderr; h5tools_dump_init(); h5tools_init_g++; } /* Disable tools error reporting */ H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); } /*------------------------------------------------------------------------- * Function: h5tools_error_report * * Purpose: Enable error stack reporting after command line is parsed. * * Return: None *------------------------------------------------------------------------- */ void h5tools_error_report(void) { if (h5tools_init_g) { if (enable_error_stack > 0) { H5Eset_auto2(H5E_DEFAULT, lib_func, lib_edata); H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); } } } /*------------------------------------------------------------------------- * Function: h5tools_close * * Purpose: Close or release resources such as files opened by the library. This * should be called after all other h5tools functions have been called. * Effect of any h5tools function called after this has been called is * undetermined. * * Return: None *------------------------------------------------------------------------- */ void h5tools_close(void) { if (h5tools_init_g) { /* special case where only data is output to stdout */ if ((rawoutstream == NULL) && rawdatastream && (rawdatastream == stdout)) HDfprintf(rawdatastream, "\n"); if (tools_func) H5Eprint2(H5tools_ERR_STACK_g, rawerrorstream); if (rawattrstream && rawattrstream != stdout) { if (fclose(rawattrstream)) perror("closing rawattrstream"); else rawattrstream = NULL; } if (rawdatastream && rawdatastream != stdout) { if (fclose(rawdatastream)) perror("closing rawdatastream"); else rawdatastream = NULL; } if (rawinstream && rawinstream != stdin) { if (fclose(rawinstream)) perror("closing rawinstream"); else rawinstream = NULL; } if (rawoutstream && rawoutstream != stdout) { if (fclose(rawoutstream)) perror("closing rawoutstream"); else rawoutstream = NULL; } if (rawerrorstream && rawerrorstream != stderr) { if (fclose(rawerrorstream)) perror("closing rawerrorstream"); else rawerrorstream = NULL; } /* Clean up the reference path table, if it's been used */ term_ref_path_table(); /* Restore error stacks from init */ H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); H5Eset_auto2(H5E_DEFAULT, lib_func, lib_edata); H5TOOLS_CLOSE_ERROR(); /* Shut down the library */ H5close(); h5tools_init_g = 0; } } /*------------------------------------------------------------------------- * Function: h5tools_set_data_output_file * * Purpose: Open fname as the output file for dataset raw data. * Set rawdatastream as its file stream. * * Return: 0 -- succeeded * negative -- failed *------------------------------------------------------------------------- */ int h5tools_set_data_output_file(const char *fname, int is_bin) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawdatastream is changed only when succeeded */ if (rawdatastream && rawdatastream != stdout) { if (HDfclose(rawdatastream)) HDperror("closing rawdatastream"); else rawdatastream = NULL; } /* First check if filename is string "NULL" */ if (fname != NULL) { /* binary output */ if (is_bin) { if ((f = HDfopen(fname, "wb")) != NULL) { rawdatastream = f; retvalue = SUCCEED; } } else { if ((f = HDfopen(fname, "w")) != NULL) { rawdatastream = f; retvalue = SUCCEED; } } } else { rawdatastream = NULL; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * Function: h5tools_set_attr_output_file * * Purpose: Open fname as the output file for attribute raw data. * Set rawattrstream as its file stream. * * Return: 0 -- succeeded * negative -- failed *------------------------------------------------------------------------- */ int h5tools_set_attr_output_file(const char *fname, int is_bin) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawattrstream is changed only when succeeded */ if (rawattrstream && rawattrstream != stdout) { if (HDfclose(rawattrstream)) HDperror("closing rawattrstream"); else rawattrstream = NULL; } /* First check if filename is string "NULL" */ if (fname != NULL) { /* binary output */ if (is_bin) { if ((f = HDfopen(fname, "wb")) != NULL) { rawattrstream = f; retvalue = SUCCEED; } } else { if ((f = HDfopen(fname, "w")) != NULL) { rawattrstream = f; retvalue = SUCCEED; } } } else { rawattrstream = NULL; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * Function: h5tools_set_input_file * * Purpose: Open fname as the input file for raw input. * Set rawinstream as its file stream. * * Return: 0 -- succeeded * negative -- failed * *------------------------------------------------------------------------- */ int h5tools_set_input_file(const char *fname, int is_bin) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawinstream is changed only when succeeded */ if (rawinstream && rawinstream != stdin) { if (HDfclose(rawinstream)) HDperror("closing rawinstream"); else rawinstream = NULL; } /* First check if filename is string "NULL" */ if (fname != NULL) { /* binary output */ if (is_bin) { if ((f = HDfopen(fname, "rb")) != NULL) { rawinstream = f; retvalue = SUCCEED; } } else { if ((f = HDfopen(fname, "r")) != NULL) { rawinstream = f; retvalue = SUCCEED; } } } else { rawinstream = NULL; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * Function: h5tools_set_output_file * * Purpose: Open fname as the output file for raw output. * Set rawoutstream as its file stream. * * Return: 0 -- succeeded * negative -- failed * *------------------------------------------------------------------------- */ int h5tools_set_output_file(const char *fname, int is_bin) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawoutstream is changed only when succeeded */ if (rawoutstream && rawoutstream != stdout) { if (HDfclose(rawoutstream)) HDperror("closing rawoutstream"); else rawoutstream = NULL; } /* First check if filename is string "NULL" */ if (fname != NULL) { /* binary output */ if (is_bin) { if ((f = HDfopen(fname, "wb")) != NULL) { rawoutstream = f; retvalue = SUCCEED; } } else { if ((f = HDfopen(fname, "w")) != NULL) { rawoutstream = f; retvalue = SUCCEED; } } } else { rawoutstream = NULL; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * Function: h5tools_set_error_file * * Purpose: Open fname as the error output file for dataset raw error. * Set rawerrorstream as its file stream. * * Return: 0 -- succeeded * negative -- failed *------------------------------------------------------------------------- */ int h5tools_set_error_file(const char *fname, int is_bin) { int retvalue = FAIL; FILE *f; /* temporary holding place for the stream pointer * so that rawerrorstream is changed only when succeeded */ if (rawerrorstream && rawerrorstream != stderr) { if (HDfclose(rawerrorstream)) HDperror("closing rawerrorstream"); else rawerrorstream = NULL; } /* First check if filename is string "NULL" */ if (fname != NULL) { /* binary output */ if (is_bin) { if ((f = HDfopen(fname, "wb")) != NULL) { rawerrorstream = f; retvalue = SUCCEED; } } else { if ((f = HDfopen(fname, "w")) != NULL) { rawerrorstream = f; retvalue = SUCCEED; } } } else { rawerrorstream = NULL; retvalue = SUCCEED; } return retvalue; } /*------------------------------------------------------------------------- * Function: h5tools_set_fapl_vfd * * Purpose: Given a VFL driver name, sets the appropriate driver on the * specified FAPL. * * Return: positive - succeeded * negative - failed *------------------------------------------------------------------------- */ static herr_t h5tools_set_fapl_vfd(hid_t fapl_id, h5tools_vfd_info_t *vfd_info) { herr_t ret_value = SUCCEED; /* Determine which driver the user wants to open the file with */ if (!HDstrcmp(vfd_info->name, drivernames[SEC2_VFD_IDX])) { /* SEC2 Driver */ if (H5Pset_fapl_sec2(fapl_id) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_sec2 failed"); } else if (!HDstrcmp(vfd_info->name, drivernames[DIRECT_VFD_IDX])) { #ifdef H5_HAVE_DIRECT /* Direct Driver */ if (H5Pset_fapl_direct(fapl_id, 1024, 4096, 8 * 4096) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_direct failed"); #else H5TOOLS_GOTO_ERROR(FAIL, "Direct VFD is not enabled"); #endif } else if (!HDstrcmp(vfd_info->name, drivernames[LOG_VFD_IDX])) { unsigned long long log_flags = H5FD_LOG_LOC_IO | H5FD_LOG_ALLOC; /* Log Driver */ if (H5Pset_fapl_log(fapl_id, NULL, log_flags, (size_t)0) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_log failed"); } else if (!HDstrcmp(vfd_info->name, drivernames[WINDOWS_VFD_IDX])) { #ifdef H5_HAVE_WINDOWS /* There is no Windows VFD - use SEC2 */ if (H5Pset_fapl_sec2(fapl_id) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_sec2 failed"); #else H5TOOLS_GOTO_ERROR(FAIL, "Windows VFD is not enabled"); #endif } else if (!HDstrcmp(vfd_info->name, drivernames[STDIO_VFD_IDX])) { /* Stdio Driver */ if (H5Pset_fapl_stdio(fapl_id) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_stdio failed"); } else if (!HDstrcmp(vfd_info->name, drivernames[CORE_VFD_IDX])) { /* Core Driver */ if (H5Pset_fapl_core(fapl_id, (size_t)H5_MB, TRUE) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_core failed"); } else if (!HDstrcmp(vfd_info->name, drivernames[FAMILY_VFD_IDX])) { /* FAMILY Driver */ /* Set member size to be 0 to indicate the current first member size * is the member size. */ if (H5Pset_fapl_family(fapl_id, (hsize_t)0, H5P_DEFAULT) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_family failed"); } else if (!HDstrcmp(vfd_info->name, drivernames[SPLIT_VFD_IDX])) { /* SPLIT Driver */ if (H5Pset_fapl_split(fapl_id, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_split failed"); } else if (!HDstrcmp(vfd_info->name, drivernames[MULTI_VFD_IDX])) { /* MULTI Driver */ if (H5Pset_fapl_multi(fapl_id, NULL, NULL, NULL, NULL, TRUE) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_multi failed"); } else if (!HDstrcmp(vfd_info->name, drivernames[MPIO_VFD_IDX])) { #ifdef H5_HAVE_PARALLEL int mpi_initialized, mpi_finalized; /* MPI-I/O Driver */ /* check if MPI is available. */ MPI_Initialized(&mpi_initialized); MPI_Finalized(&mpi_finalized); if (mpi_initialized && !mpi_finalized) { if (H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_mpio failed"); } #else H5TOOLS_GOTO_ERROR(FAIL, "MPI-I/O VFD is not enabled"); #endif /* H5_HAVE_PARALLEL */ } else if (!HDstrcmp(vfd_info->name, drivernames[ROS3_VFD_IDX])) { #ifdef H5_HAVE_ROS3_VFD if (!vfd_info->info) H5TOOLS_GOTO_ERROR(FAIL, "Read-only S3 VFD info is invalid"); if (H5Pset_fapl_ros3(fapl_id, (H5FD_ros3_fapl_t *)vfd_info->info) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_ros3() failed"); #else H5TOOLS_GOTO_ERROR(FAIL, "Read-only S3 VFD is not enabled"); #endif } else if (!HDstrcmp(vfd_info->name, drivernames[HDFS_VFD_IDX])) { #ifdef H5_HAVE_LIBHDFS if (!vfd_info->info) H5TOOLS_GOTO_ERROR(FAIL, "HDFS VFD info is invalid"); if (H5Pset_fapl_hdfs(fapl_id, (H5FD_hdfs_fapl_t *)vfd_info->info) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_hdfs() failed"); #else H5TOOLS_GOTO_ERROR(FAIL, "The HDFS VFD is not enabled"); #endif } else H5TOOLS_GOTO_ERROR(FAIL, "invalid VFD name"); done: return ret_value; } /*------------------------------------------------------------------------- * Function: h5tools_get_fapl * * Purpose: Copies an input fapl and then sets a VFD on it. * * The returned fapl must be closed by the caller. * * Return: positive - succeeded * negative - failed *------------------------------------------------------------------------- */ hid_t h5tools_get_fapl(hid_t prev_fapl_id, h5tools_vfd_info_t *vfd_info) { hid_t new_fapl_id = H5I_INVALID_HID; hid_t ret_value = H5I_INVALID_HID; if (prev_fapl_id < 0) H5TOOLS_GOTO_ERROR(FAIL, "invalid FAPL"); /* Make a copy of the FAPL or create one if H5P_DEFAULT is specified. */ if (H5P_DEFAULT == prev_fapl_id) { if ((new_fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Pcreate failed"); } else { if ((new_fapl_id = H5Pcopy(prev_fapl_id)) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Pcopy failed"); } /* Set non-default virtual file driver, if requested */ if (vfd_info) if (h5tools_set_fapl_vfd(new_fapl_id, vfd_info) < 0) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to set VFD on FAPL"); ret_value = new_fapl_id; done: if ((new_fapl_id >= 0) && (ret_value < 0)) { H5Pclose(new_fapl_id); new_fapl_id = H5I_INVALID_HID; } return ret_value; } /*------------------------------------------------------------------------- * Function: h5tools_get_vfd_name * * Purpose: Given a FAPL, retrieves the name of the VFL driver set on it * if using a native-terminal VOL connector. If a * non-native-terminal VOL connector is set on the FAPL, the * first byte of the returned driver name will be set to the null * terminator. * * Return: SUCCEED/FAIL *------------------------------------------------------------------------- */ herr_t h5tools_get_vfd_name(hid_t fapl_id, char *drivername, size_t drivername_size) { herr_t ret_value = SUCCEED; if (fapl_id < 0) H5TOOLS_GOTO_ERROR(FAIL, "invalid FAPL"); if (!drivername) H5TOOLS_GOTO_ERROR(FAIL, "drivername is NULL"); if (drivername && !drivername_size) H5TOOLS_GOTO_ERROR(FAIL, "drivername_size must be non-zero"); /* Initialize the driver name */ drivername[0] = '\0'; if (fapl_id == H5P_DEFAULT) fapl_id = H5P_FILE_ACCESS_DEFAULT; if (fapl_id >= 0) { const char *driver_name; hid_t driver_id; if ((driver_id = H5Pget_driver(fapl_id)) < 0) H5TOOLS_GOTO_ERROR(FAIL, "failed to retrieve VFL driver ID from FAPL"); if (driver_id == H5FD_SEC2) driver_name = drivernames[SEC2_VFD_IDX]; #ifdef H5_HAVE_DIRECT else if (driver_id == H5FD_DIRECT) driver_name = drivernames[DIRECT_VFD_IDX]; #endif else if (driver_id == H5FD_LOG) driver_name = drivernames[LOG_VFD_IDX]; #ifdef H5_HAVE_WINDOWS else if (driver_id == H5FD_WINDOWS) driver_name = drivernames[WINDOWS_VFD_IDX]; #endif else if (driver_id == H5FD_STDIO) driver_name = drivernames[STDIO_VFD_IDX]; else if (driver_id == H5FD_CORE) driver_name = drivernames[CORE_VFD_IDX]; else if (driver_id == H5FD_FAMILY) driver_name = drivernames[FAMILY_VFD_IDX]; else if (driver_id == H5FD_MULTI) driver_name = drivernames[MULTI_VFD_IDX]; #ifdef H5_HAVE_PARALLEL else if (driver_id == H5FD_MPIO) driver_name = drivernames[MPIO_VFD_IDX]; #endif #ifdef H5_HAVE_ROS3_VFD else if (driver_id == H5FD_ROS3) driver_name = drivernames[ROS3_VFD_IDX]; #endif #ifdef H5_HAVE_LIBHDFS else if (driver_id == H5FD_HDFS) driver_name = drivernames[HDFS_VFD_IDX]; #endif else driver_name = "unknown"; HDstrncpy(drivername, driver_name, drivername_size); drivername[drivername_size - 1] = '\0'; } done: return ret_value; } /*------------------------------------------------------------------------- * Function: h5tools_fopen * * Purpose: Opens file FNAME using the specified flags and FAPL. * * The 'use_specific_driver' parameter is used to control the * VFD connector that this routine uses to open the file * with. If 'use_specific_driver' is set to TRUE, this routine * assumes that the caller has already set a specific VFD * connector on the given FAPL and will attempt to directly use * the FAPL for opening the file. We assume that the caller knows * what they are doing; if the file is unable to be opened using * that FAPL, this routine will return H5I_INVALID_HID. * * However, if 'use_specific_driver' is set to FALSE, this * routine assumes that the caller HAS NOT set a specific VFD * connector on the given FAPL and will instead loop through * the various available VFL drivers and VOL connectors trying to * open FNAME. * * The list of available VFL drivers is as follows: * - If the HDF5 library is version 1.2 or less, then we have * only the SEC2 driver to try out. * - If the HDF5 library is greater than version 1.2, then we * have the FAMILY, SPLIT, and MULTI drivers to play with. * * Return: * On success, returns a file ID for the opened file. If DRIVERNAME is * non-null then the first DRIVERNAME_SIZE-1 characters of the driver * name are copied into the DRIVERNAME array and null terminated. * * On failure, the function returns H5I_INVALID_HID and DRIVERNAME * will not be set. *------------------------------------------------------------------------- */ hid_t h5tools_fopen(const char *fname, unsigned flags, hid_t fapl_id, hbool_t use_specific_driver, char *drivername, size_t drivername_size) { hid_t fid = H5I_INVALID_HID; hid_t tmp_fapl_id = H5I_INVALID_HID; hid_t used_fapl_id = H5I_INVALID_HID; unsigned drivernum; hid_t ret_value = H5I_INVALID_HID; /* * First try to open the file using just the given FAPL. */ /* Allow error stack display if --enable-error-stack has optional arg number */ if (enable_error_stack > 1) { fid = H5Fopen(fname, flags, fapl_id); } else { H5E_BEGIN_TRY { fid = H5Fopen(fname, flags, fapl_id); } H5E_END_TRY; } /* If we succeeded in opening the file, we're done. */ if (fid >= 0) { used_fapl_id = fapl_id; H5TOOLS_GOTO_DONE(fid); } /* * If we failed to open the file and the caller specified 'use_specific_driver' * as TRUE, we should return failure now since the file couldn't be opened with * the VFL driver that was set on the FAPL by the caller. */ if (fid < 0 && use_specific_driver) H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to open file using specified FAPL"); for (drivernum = 0; drivernum < NUM_DRIVERS; drivernum++) { h5tools_vfd_info_t vfd_info; /* Skip the log VFD as it prints out to standard out * and is fundamentally SEC2 anyway. */ if (drivernum == LOG_VFD_IDX) continue; vfd_info.info = NULL; vfd_info.name = drivernames[drivernum]; /* Get a fapl reflecting the selected VFD */ if ((tmp_fapl_id = h5tools_get_fapl(fapl_id, &vfd_info)) < 0) continue; /* Can we open the file with this combo? */ if ((fid = h5tools_fopen(fname, flags, tmp_fapl_id, TRUE, drivername, drivername_size)) >= 0) { used_fapl_id = tmp_fapl_id; H5TOOLS_GOTO_DONE(fid); } else { /* Close the temporary fapl */ H5Pclose(tmp_fapl_id); tmp_fapl_id = H5I_INVALID_HID; } } /* File was unable to be opened at all */ ret_value = H5I_INVALID_HID; done: /* Save the driver name */ if (drivername && drivername_size && ret_value >= 0) if (used_fapl_id >= 0 && h5tools_get_vfd_name(used_fapl_id, drivername, drivername_size) < 0) H5TOOLS_ERROR(H5I_INVALID_HID, "failed to retrieve name of VFD used to open file"); if (tmp_fapl_id >= 0) H5Pclose(tmp_fapl_id); return ret_value; } /*------------------------------------------------------------------------- * Function: h5tools_count_ncols * * Purpose: Count the number of columns in a string. This is the number of * characters in the string not counting line-control characters. * * Return: success - returns the width of the string. * failure - 0. *------------------------------------------------------------------------- */ static size_t h5tools_count_ncols(const char *s) { register size_t i; for (i = 0; *s; s++) if (*s >= ' ') i++; return i; } /*------------------------------------------------------------------------- * Function: h5tools_detect_vlen * * Purpose: Recursive check for any variable length data in given type. * * Return: TRUE : type contains any variable length data * FALSE : type doesn't contain any variable length data * Negative value: failed *------------------------------------------------------------------------- */ htri_t h5tools_detect_vlen(hid_t tid) { htri_t ret = FALSE; /* recursive detect any vlen data values in type (compound, array ...) */ ret = H5Tdetect_class(tid, H5T_VLEN); if ((ret == TRUE) || (ret < 0)) goto done; /* recursive detect any vlen string in type (compound, array ...) */ ret = h5tools_detect_vlen_str(tid); if ((ret == TRUE) || (ret < 0)) goto done; done: return ret; } /*------------------------------------------------------------------------- * Function: h5tools_detect_vlen_str * * Purpose: Recursive check for variable length string of a datatype. * * Return: TRUE : type contains any variable length string * FALSE : type doesn't contain any variable length string * Negative value: failed *------------------------------------------------------------------------- */ htri_t h5tools_detect_vlen_str(hid_t tid) { H5T_class_t tclass = -1; htri_t ret = FALSE; ret = H5Tis_variable_str(tid); if ((ret == TRUE) || (ret < 0)) goto done; tclass = H5Tget_class(tid); if (tclass == H5T_ARRAY || tclass == H5T_VLEN) { hid_t btid = H5Tget_super(tid); if (btid < 0) { ret = (htri_t)btid; goto done; } ret = h5tools_detect_vlen_str(btid); if ((ret == TRUE) || (ret < 0)) { H5Tclose(btid); goto done; } } else if (tclass == H5T_COMPOUND) { unsigned nmembs; int snmembs = H5Tget_nmembers(tid); unsigned u; if (snmembs < 0) { ret = FAIL; goto done; } nmembs = (unsigned)snmembs; for (u = 0; u < nmembs; u++) { hid_t mtid = H5Tget_member_type(tid, u); ret = h5tools_detect_vlen_str(mtid); if ((ret == TRUE) || (ret < 0)) { H5Tclose(mtid); goto done; } H5Tclose(mtid); } } done: return ret; } /*------------------------------------------------------------------------- * Function: h5tools_simple_prefix * * Purpose: If /ctx->need_prefix/ is set then terminate the current line (if * applicable), calculate the prefix string, and display it at the start * of a line. * * Return: None *------------------------------------------------------------------------- */ void h5tools_simple_prefix(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hsize_t elmtno, int secnum) { h5tools_str_t prefix; h5tools_str_t str; /*temporary for indentation */ size_t templength = 0; unsigned u, indentlevel = 0; if (stream == NULL) return; if (!ctx->need_prefix) return; H5TOOLS_START_DEBUG(" "); HDmemset(&prefix, 0, sizeof(h5tools_str_t)); HDmemset(&str, 0, sizeof(h5tools_str_t)); /* Terminate previous line, if any */ H5TOOLS_DEBUG("before CR elmtno=%ld, ctx->cur_column=%d, info->idx_fmt=%s, info->line_suf=%s", elmtno, ctx->cur_column, info->idx_fmt, info->line_suf); if (ctx->cur_column) { PUTSTREAM(OPT(info->line_suf, ""), stream); HDputc('\n', stream); PUTSTREAM(OPT(info->line_sep, ""), stream); } H5TOOLS_DEBUG("after CR elmtno=%ld, ctx->ndims=%d", elmtno, ctx->ndims); /* Calculate new prefix */ h5tools_str_prefix(&prefix, info, elmtno, ctx); H5TOOLS_DEBUG("prefix=%s - str=%s", prefix.s, str.s); /* Write new prefix to output */ if (ctx->indent_level > 0) indentlevel = ctx->indent_level; else /* * This is because sometimes we don't print out all the header * info for the data (like the tattr-2.ddl example). If that happens * the ctx->indent_level is negative so we need to skip the above and * just print out the default indent levels. */ indentlevel = ctx->default_indent_level; /* when printing array indices, print the indentation before the prefix the prefix is printed one indentation level before */ if (info->pindex) for (u = 0; u < indentlevel - 1; u++) PUTSTREAM(h5tools_str_fmt(&str, (size_t)0, info->line_indent), stream); if (elmtno == 0 && secnum == 0 && info->line_1st) PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_1st), stream); else if (secnum && info->line_cont) PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_cont), stream); else PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_pre), stream); templength = h5tools_str_len(&prefix); H5TOOLS_DEBUG("prefix=%s - templength=%d", prefix.s, templength); for (u = 0; u < indentlevel; u++) { /*we already made the indent for the array indices case */ if (!info->pindex) { PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_indent), stream); templength += h5tools_str_len(&prefix); } else { /*we cannot count the prefix for the array indices case */ templength += h5tools_str_len(&str); } } H5TOOLS_DEBUG("prefix=%s - templength=%d", prefix.s, templength); ctx->cur_column = ctx->prev_prefix_len = templength; ctx->cur_elmt = 0; ctx->need_prefix = 0; H5TOOLS_DEBUG("prefix=%s - str=%s", prefix.s, str.s); /* Free string */ h5tools_str_close(&prefix); h5tools_str_close(&str); H5TOOLS_ENDDEBUG(" "); } /*------------------------------------------------------------------------- * Function: h5tools_region_simple_prefix * * Purpose: If /ctx->need_prefix/ is set then terminate the current line (if * applicable), calculate the prefix string, and display it at the start * of a line. Calls region specific function. * * Return: None *------------------------------------------------------------------------- */ void h5tools_region_simple_prefix(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hsize_t elmtno, hsize_t *ptdata, int secnum) { h5tools_str_t prefix; h5tools_str_t str; /*temporary for indentation */ size_t templength = 0; unsigned u, indentlevel = 0; if (stream == NULL) return; if (!ctx->need_prefix) return; HDmemset(&prefix, 0, sizeof(h5tools_str_t)); HDmemset(&str, 0, sizeof(h5tools_str_t)); /* Terminate previous line, if any */ if (ctx->cur_column) { PUTSTREAM(OPT(info->line_suf, ""), stream); HDputc('\n', stream); PUTSTREAM(OPT(info->line_sep, ""), stream); } /* Calculate new prefix */ h5tools_str_region_prefix(&prefix, info, elmtno, ptdata, ctx); /* Write new prefix to output */ if (ctx->indent_level > 0) indentlevel = ctx->indent_level; else /* * This is because sometimes we don't print out all the header * info for the data (like the tattr-2.ddl example). If that happens * the ctx->indent_level is negative so we need to skip the above and * just print out the default indent levels. */ indentlevel = ctx->default_indent_level; /* when printing array indices, print the indentation before the prefix the prefix is printed one indentation level before */ if (info->pindex) for (u = 0; u < indentlevel - 1; u++) PUTSTREAM(h5tools_str_fmt(&str, (size_t)0, info->line_indent), stream); if (elmtno == 0 && secnum == 0 && info->line_1st) PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_1st), stream); else if (secnum && info->line_cont) PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_cont), stream); else PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_pre), stream); templength = h5tools_str_len(&prefix); for (u = 0; u < indentlevel; u++) /*we already made the indent for the array indices case */ if (!info->pindex) { PUTSTREAM(h5tools_str_fmt(&prefix, (size_t)0, info->line_indent), stream); templength += h5tools_str_len(&prefix); } else { /*we cannot count the prefix for the array indices case */ templength += h5tools_str_len(&str); } ctx->cur_column = ctx->prev_prefix_len = templength; ctx->cur_elmt = 0; ctx->need_prefix = 0; /* Free string */ h5tools_str_close(&prefix); h5tools_str_close(&str); } /*------------------------------------------------------------------------- * Function: h5tools_render_element * * Purpose: Prints the string buffer to the output STREAM. The string is * printed according to the format described in INFO. The CTX struct * contains context information shared between calls to this function. * * Return: False if a dimension end is reached * True otherwise * * In/Out: * h5tools_context_t *ctx * h5tools_str_t *buffer * hsize_t *curr_pos * * Parameters Description: * h5tools_str_t *buffer is the string into which to render * hsize_t curr_pos is the total data element position * size_t ncols * hsize_t local_elmt_counter is the local element loop counter * hsize_t elmt_count is the data element loop counter *------------------------------------------------------------------------- */ hbool_t h5tools_render_element(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, h5tools_str_t *buffer, hsize_t *curr_pos, size_t ncols, hsize_t local_elmt_counter, hsize_t elmt_counter) { hbool_t dimension_break = TRUE; char * s = NULL; char * section = NULL; /* a section of output */ int secnum; /* section sequence number */ int multiline; /* datum was multiline */ if (stream == NULL) return dimension_break; H5TOOLS_START_DEBUG(" need_prefix=%d", ctx->need_prefix); H5TOOLS_DEBUG("elmt_counter=%ld - local_elmt_counter=%ld", elmt_counter, local_elmt_counter); s = h5tools_str_fmt(buffer, (size_t)0, "%s"); H5TOOLS_DEBUG("s=%s", s); /* * If the element would split on multiple lines if printed at our * current location... */ if (info->line_multi_new == 1 && (ctx->cur_column + h5tools_count_ncols(s) + HDstrlen(OPT(info->elmt_suf2, " ")) + HDstrlen(OPT(info->line_suf, ""))) > ncols) { if (ctx->prev_multiline) { /* * ... and the previous element also occupied more than one * line, then start this element at the beginning of a line. */ ctx->need_prefix = TRUE; } else if ((ctx->prev_prefix_len + h5tools_count_ncols(s) + HDstrlen(OPT(info->elmt_suf2, " ")) + HDstrlen(OPT(info->line_suf, ""))) <= ncols) { /* * ...but *could* fit on one line otherwise, then we * should end the current line and start this element on its * own line. */ ctx->need_prefix = TRUE; } H5TOOLS_DEBUG("ctx->need_prefix=%d", ctx->need_prefix); } /* * We need to break after each row of a dimension---> we should * break at the end of the each last dimension well that is the * way the dumper did it before */ if (info->arr_linebreak && ctx->cur_elmt) { if (ctx->size_last_dim && (ctx->cur_elmt % ctx->size_last_dim) == 0) ctx->need_prefix = TRUE; if (elmt_counter == ctx->size_last_dim) { ctx->need_prefix = TRUE; dimension_break = FALSE; } H5TOOLS_DEBUG("ctx->need_prefix=%d", ctx->need_prefix); } H5TOOLS_DEBUG("elmt_counter=%ld - ctx->size_last_dim=%ld info->line_suf=%s", elmt_counter, ctx->size_last_dim, info->line_suf); /* * If the previous element occupied multiple lines and this element * is too long to fit on a line then start this element at the * beginning of the line. */ if (info->line_multi_new == 1 && ctx->prev_multiline && (ctx->cur_column + h5tools_count_ncols(s) + HDstrlen(OPT(info->elmt_suf2, " ")) + HDstrlen(OPT(info->line_suf, ""))) > ncols) ctx->need_prefix = TRUE; H5TOOLS_DEBUG("ctx->need_prefix=%d", ctx->need_prefix); /* * If too many elements have already been printed then we need to * start a new line. */ if (info->line_per_line > 0 && ctx->cur_elmt >= info->line_per_line) ctx->need_prefix = TRUE; H5TOOLS_DEBUG("ctx->need_prefix=%d", ctx->need_prefix); /* * Each OPTIONAL_LINE_BREAK embedded in the rendered string can cause * the data to split across multiple lines. We display the sections * one-at a time. */ multiline = 0; for (secnum = 0, multiline = 0; (section = HDstrtok(secnum ? NULL : s, OPTIONAL_LINE_BREAK)); secnum++) { /* * If the current section plus possible suffix and end-of-line * information would cause the output to wrap then we need to * start a new line. */ /* * check for displaying prefix for each section */ if ((ctx->cur_column + HDstrlen(section) + HDstrlen(OPT(info->elmt_suf2, " ")) + HDstrlen(OPT(info->line_suf, ""))) > ncols) ctx->need_prefix = 1; /* * Print the prefix or separate the beginning of this element * from the previous element. */ H5TOOLS_DEBUG("ctx->need_prefix=%d", ctx->need_prefix); if (ctx->need_prefix) { if (secnum) multiline++; /* pass to the prefix in h5tools_simple_prefix the total * position instead of the current stripmine position i; * this is necessary to print the array indices */ *curr_pos = ctx->sm_pos + local_elmt_counter; H5TOOLS_DEBUG("curr_pos=%ld - ctx->sm_pos=%ld - ctx->ndims=%ld", *curr_pos, ctx->sm_pos, ctx->ndims); h5tools_simple_prefix(stream, info, ctx, *curr_pos, secnum); } else if ((local_elmt_counter || ctx->continuation) && secnum == 0) { PUTSTREAM(OPT(info->elmt_suf2, " "), stream); ctx->cur_column += HDstrlen(OPT(info->elmt_suf2, " ")); } H5TOOLS_DEBUG("section=%s", section); /* Print the section */ PUTSTREAM(section, stream); ctx->cur_column += HDstrlen(section); } ctx->prev_multiline = multiline; H5TOOLS_ENDDEBUG(" "); return dimension_break; } /*------------------------------------------------------------------------- * Function: h5tools_render_region_element * * Purpose: Prints the string buffer to the output STREAM. The string is * printed according to the format described in INFO. The CTX struct * contains context information shared between calls to this function. * * Return: * False if a dimension end is reached * True otherwise * * In/Out: * h5tools_context_t *ctx * h5tools_str_t *buffer * hsize_t *curr_pos * * Parameters Description: * h5tools_str_t *buffer is the string into which to render * hsize_t curr_pos is the total data element position * size_t ncols * hsize_t *ptdata * hsize_t local_elmt_counter is the local element loop counter * hsize_t elmt_count is the data element loop counter *------------------------------------------------------------------------- */ hbool_t h5tools_render_region_element(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, h5tools_str_t *buffer, hsize_t *curr_pos, size_t ncols, hsize_t *ptdata, hsize_t local_elmt_counter, hsize_t elmt_counter) { hbool_t dimension_break = TRUE; char * s = NULL; char * section = NULL; /* a section of output */ int secnum; /* section sequence number */ int multiline; /* datum was multiline */ H5TOOLS_START_DEBUG(" "); H5TOOLS_DEBUG("elmt_counter=%ld - local_elmt_counter=%ld", elmt_counter, local_elmt_counter); s = h5tools_str_fmt(buffer, (size_t)0, "%s"); /* * If the element would split on multiple lines if printed at our * current location... */ if (info->line_multi_new == 1 && (ctx->cur_column + h5tools_count_ncols(s) + HDstrlen(OPT(info->elmt_suf2, " ")) + HDstrlen(OPT(info->line_suf, ""))) > ncols) { if (ctx->prev_multiline) { /* * ... and the previous element also occupied more than one * line, then start this element at the beginning of a line. */ ctx->need_prefix = TRUE; } else if ((ctx->prev_prefix_len + h5tools_count_ncols(s) + HDstrlen(OPT(info->elmt_suf2, " ")) + HDstrlen(OPT(info->line_suf, ""))) <= ncols) { /* * ...but *could* fit on one line otherwise, then we * should end the current line and start this element on its * own line. */ ctx->need_prefix = TRUE; } } /* * We need to break after each row of a dimension---> we should * break at the end of the each last dimension well that is the * way the dumper did it before */ if (info->arr_linebreak && ctx->cur_elmt) { if (ctx->size_last_dim && (ctx->cur_elmt % ctx->size_last_dim) == 0) ctx->need_prefix = TRUE; if (elmt_counter == ctx->size_last_dim) { ctx->need_prefix = TRUE; dimension_break = FALSE; } } /* * If the previous element occupied multiple lines and this element * is too long to fit on a line then start this element at the * beginning of the line. */ if (info->line_multi_new == 1 && ctx->prev_multiline && (ctx->cur_column + h5tools_count_ncols(s) + HDstrlen(OPT(info->elmt_suf2, " ")) + HDstrlen(OPT(info->line_suf, ""))) > ncols) ctx->need_prefix = TRUE; /* * If too many elements have already been printed then we need to * start a new line. */ if (info->line_per_line > 0 && ctx->cur_elmt >= info->line_per_line) ctx->need_prefix = TRUE; /* * Each OPTIONAL_LINE_BREAK embedded in the rendered string can cause * the data to split across multiple lines. We display the sections * one-at a time. */ multiline = 0; for (secnum = 0, multiline = 0; (section = HDstrtok(secnum ? NULL : s, OPTIONAL_LINE_BREAK)); secnum++) { /* * If the current section plus possible suffix and end-of-line * information would cause the output to wrap then we need to * start a new line. */ /* * Added the info->skip_first because the dumper does not want * this check to happen for the first line */ if ((!info->skip_first || local_elmt_counter) && (ctx->cur_column + HDstrlen(section) + HDstrlen(OPT(info->elmt_suf2, " ")) + HDstrlen(OPT(info->line_suf, ""))) > ncols) ctx->need_prefix = 1; /* * Print the prefix or separate the beginning of this element * from the previous element. */ if (ctx->need_prefix) { if (secnum) multiline++; /* pass to the prefix in h5tools_region_simple_prefix the total * position instead of the current stripmine position i; * this is necessary to print the array indices */ *curr_pos = ctx->sm_pos + local_elmt_counter; H5TOOLS_DEBUG("curr_pos=%ld - ctx->sm_pos=%ld", *curr_pos, ctx->sm_pos); h5tools_region_simple_prefix(stream, info, ctx, local_elmt_counter, ptdata, secnum); } else if ((local_elmt_counter || ctx->continuation) && secnum == 0) { PUTSTREAM(OPT(info->elmt_suf2, " "), stream); ctx->cur_column += HDstrlen(OPT(info->elmt_suf2, " ")); } /* Print the section */ PUTSTREAM(section, stream); ctx->cur_column += HDstrlen(section); } ctx->prev_multiline = multiline; H5TOOLS_ENDDEBUG(" "); return dimension_break; } /*------------------------------------------------------------------------- * Function: init_acc_pos * * Purpose: initialize accumulator and matrix position * * Return: void *------------------------------------------------------------------------- */ void init_acc_pos(unsigned ndims, hsize_t *dims, hsize_t *acc, hsize_t *pos, hsize_t *p_min_idx) { int i; unsigned j; H5TOOLS_START_DEBUG(" "); for (i = 0; (unsigned)i < ndims; i++) p_min_idx[i] = 0; if (ndims > 0) { acc[ndims - 1] = 1; for (i = ((int)ndims - 2); i >= 0; i--) { acc[i] = acc[i + 1] * dims[i + 1]; H5TOOLS_DEBUG("acc[%d]=%ld", i, acc[i]); } for (j = 0; j < ndims; j++) pos[j] = 0; } H5TOOLS_ENDDEBUG(" "); } /*------------------------------------------------------------------------- * Function: calc_acc_pos * * Purpose: Calculate the number of elements represented by a unit change * in a certain index position. * * Return: void *------------------------------------------------------------------------- */ hsize_t calc_acc_pos(unsigned ndims, hsize_t elmtno, hsize_t *acc, hsize_t *pos) { int i; hsize_t curr_pos = elmtno; H5TOOLS_START_DEBUG(" "); if (ndims > 0) { for (i = 0; i < (int)ndims; i++) { if (curr_pos > 0) { H5TOOLS_DEBUG("curr_pos=%ld - ctx->acc[%d]=%ld", curr_pos, i, acc[i]); pos[i] = curr_pos / acc[i]; curr_pos -= acc[i] * pos[i]; } else pos[i] = 0; H5TOOLS_DEBUG("curr_pos=%ld - pos[%d]=%ld - acc[%d]=%ld", curr_pos, i, pos[i], i, acc[i]); } } H5TOOLS_ENDDEBUG(" "); return curr_pos; } /*------------------------------------------------------------------------- * Function: render_bin_output * * Purpose: Write one element of memory buffer to a binary file stream * * Return: Success: SUCCEED * Failure: FAIL *------------------------------------------------------------------------- */ int render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t block_nelmts) { unsigned char *mem = (unsigned char *)_mem; size_t size; /* datum size */ hsize_t block_index; H5T_class_t type_class; hbool_t past_catch = FALSE; int ret_value = 0; H5TOOLS_START_DEBUG(" "); if ((size = H5Tget_size(tid)) == 0) H5TOOLS_THROW((-1), "H5Tget_size failed"); if ((type_class = H5Tget_class(tid)) < 0) H5TOOLS_THROW((-1), "H5Tget_class failed"); switch (type_class) { case H5T_INTEGER: case H5T_FLOAT: case H5T_ENUM: case H5T_BITFIELD: H5TOOLS_DEBUG("numbers"); block_index = block_nelmts * size; while (block_index > 0) { size_t bytes_in = 0; /* # of bytes to write */ size_t bytes_wrote = 0; /* # of bytes written */ if (block_index > sizeof(size_t)) bytes_in = sizeof(size_t); else bytes_in = (size_t)block_index; bytes_wrote = HDfwrite(mem, 1, bytes_in, stream); if (bytes_wrote != bytes_in || (0 == bytes_wrote && HDferror(stream))) H5TOOLS_THROW((-1), "fwrite failed"); block_index -= (hsize_t)bytes_wrote; mem = mem + bytes_wrote; } break; case H5T_STRING: { unsigned int i; H5T_str_t pad; char * s = NULL; unsigned char tempuchar; H5TOOLS_DEBUG("H5T_STRING"); pad = H5Tget_strpad(tid); for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char *)_mem) + block_index * size; if (H5Tis_variable_str(tid)) { s = *(char **)((void *)mem); if (s != NULL) size = HDstrlen(s); else H5TOOLS_THROW((-1), "NULL string"); } else { s = (char *)mem; } for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) { HDmemcpy(&tempuchar, &s[i], sizeof(unsigned char)); if (1 != HDfwrite(&tempuchar, sizeof(unsigned char), 1, stream)) H5TOOLS_THROW((-1), "fwrite failed"); } /* i */ } /* for (block_index = 0; block_index < block_nelmts; block_index++) */ } break; case H5T_COMPOUND: { int snmembs; unsigned nmembs; H5TOOLS_DEBUG("H5T_COMPOUND"); if ((snmembs = H5Tget_nmembers(tid)) < 0) H5TOOLS_THROW((-1), "H5Tget_nmembers of compound failed"); nmembs = (unsigned)snmembs; for (block_index = 0; block_index < block_nelmts; block_index++) { unsigned j; mem = ((unsigned char *)_mem) + block_index * size; for (j = 0; j < nmembs; j++) { hid_t memb = H5I_INVALID_HID; size_t offset; offset = H5Tget_member_offset(tid, j); memb = H5Tget_member_type(tid, j); if (render_bin_output(stream, container, memb, mem + offset, 1) < 0) { H5Tclose(memb); H5TOOLS_THROW((-1), "render_bin_output of compound member failed"); } H5Tclose(memb); } } } break; case H5T_ARRAY: { int k, ndims; hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts = 0; hid_t memb = H5I_INVALID_HID; H5TOOLS_DEBUG("H5T_ARRAY"); /* get the array's base datatype for each element */ memb = H5Tget_super(tid); ndims = H5Tget_array_ndims(tid); H5Tget_array_dims2(tid, dims); if (ndims >= 1 && ndims <= H5S_MAX_RANK) { /* calculate the number of array elements */ for (k = 0, nelmts = 1; k < ndims; k++) { temp_nelmts = nelmts; temp_nelmts *= dims[k]; nelmts = (size_t)temp_nelmts; } } else { H5Tclose(memb); H5TOOLS_THROW((-1), "calculate the number of array elements failed"); } for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char *)_mem) + block_index * size; /* dump the array element */ if (render_bin_output(stream, container, memb, mem, nelmts) < 0) { H5Tclose(memb); H5TOOLS_THROW((-1), "render_bin_output failed"); } } H5Tclose(memb); } break; case H5T_VLEN: { hsize_t nelmts; hid_t memb = H5I_INVALID_HID; H5TOOLS_DEBUG("H5T_VLEN"); /* get the VL sequences's base datatype for each element */ memb = H5Tget_super(tid); for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char *)_mem) + block_index * size; /* Get the number of sequence elements */ nelmts = ((hvl_t *)((void *)mem))->len; /* dump the array element */ if (render_bin_output(stream, container, memb, ((char *)(((hvl_t *)((void *)mem))->p)), nelmts) < 0) { H5Tclose(memb); H5TOOLS_THROW((-1), "render_bin_output failed"); } } H5Tclose(memb); } break; case H5T_REFERENCE: { H5TOOLS_DEBUG("reference class type"); if (size == H5R_DSET_REG_REF_BUF_SIZE) { /* if (H5Tequal(tid, H5T_STD_REF_DSETREG)) */ H5TOOLS_DEBUG("H5T_STD_REF_DSETREG"); if (region_output) { /* region data */ hid_t region_id = H5I_INVALID_HID; hid_t region_space = H5I_INVALID_HID; H5S_sel_type region_type; for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char *)_mem) + block_index * size; region_id = H5Rdereference(container, H5R_DATASET_REGION, mem); if (region_id >= 0) { region_space = H5Rget_region(container, H5R_DATASET_REGION, mem); if (region_space >= 0) { region_type = H5Sget_select_type(region_space); if (region_type == H5S_SEL_POINTS) render_bin_output_region_points(region_space, region_id, stream, container); else render_bin_output_region_blocks(region_space, region_id, stream, container); H5Sclose(region_space); } /* end if (region_space >= 0) */ H5Dclose(region_id); } } } /* end if (region_output... */ } else if (size == H5R_OBJ_REF_BUF_SIZE) { /* if (H5Tequal(tid, H5T_STD_REF_OBJ)) */ H5TOOLS_DEBUG("H5T_STD_REF_OBJ"); } } break; case H5T_TIME: case H5T_OPAQUE: H5TOOLS_DEBUG("H5T_OPAQUE"); for (block_index = 0; block_index < block_nelmts; block_index++) { mem = ((unsigned char *)_mem) + block_index * size; if (size != HDfwrite(mem, sizeof(char), size, stream)) H5TOOLS_THROW((-1), "fwrite failed"); } /* end for */ break; case H5T_NO_CLASS: case H5T_NCLASSES: default: /* Badness */ H5TOOLS_THROW((-1), "bad type class"); break; } /* end switch */ CATCH H5TOOLS_ENDDEBUG(" "); return ret_value; } /*------------------------------------------------------------------------- * Function: render_bin_output_region_data_blocks * * Purpose: Print the data values from a dataset referenced by region blocks. * This is a special case subfunction to print the data in a region reference of type blocks. * * Return: FAIL if there was an error * SUCCEED otherwise * *------------------------------------------------------------------------- */ int render_bin_output_region_data_blocks(hid_t region_id, FILE *stream, hid_t container, unsigned ndims, hid_t type_id, hsize_t nblocks, hsize_t *ptdata) { hsize_t *dims1 = NULL; hsize_t *start = NULL; hsize_t *count = NULL; hsize_t numelem; hsize_t total_size[H5S_MAX_RANK]; unsigned jndx; size_t type_size; hid_t mem_space = H5I_INVALID_HID; void * region_buf = NULL; hbool_t past_catch = FALSE; hsize_t blkndx; hid_t sid1 = H5I_INVALID_HID; int ret_value = -1; H5TOOLS_START_DEBUG(" "); /* Get the dataspace of the dataset */ if ((sid1 = H5Dget_space(region_id)) < 0) H5TOOLS_THROW((-1), "H5Dget_space failed"); /* Allocate space for the dimension array */ if ((dims1 = (hsize_t *)HDmalloc(sizeof(hsize_t) * ndims)) == NULL) H5TOOLS_THROW((-1), "Could not allocate buffer for dims"); /* find the dimensions of each data space from the block coordinates */ numelem = 1; for (jndx = 0; jndx < ndims; jndx++) { dims1[jndx] = ptdata[jndx + ndims] - ptdata[jndx] + 1; numelem = dims1[jndx] * numelem; } /* Create dataspace for reading buffer */ if ((mem_space = H5Screate_simple((int)ndims, dims1, NULL)) < 0) H5TOOLS_THROW((-1), "H5Screate_simple failed"); if ((type_size = H5Tget_size(type_id)) == 0) H5TOOLS_THROW((-1), "H5Tget_size failed"); if ((region_buf = HDmalloc(type_size * (size_t)numelem)) == NULL) H5TOOLS_THROW((-1), "Could not allocate region buffer"); /* Select (x , x , ..., x ) x (y , y , ..., y ) hyperslab for reading memory dataset */ /* 1 2 n 1 2 n */ if ((start = (hsize_t *)HDmalloc(sizeof(hsize_t) * ndims)) == NULL) H5TOOLS_THROW((-1), "Could not allocate buffer for start"); if ((count = (hsize_t *)HDmalloc(sizeof(hsize_t) * ndims)) == NULL) H5TOOLS_THROW((-1), "Could not allocate buffer for count"); for (blkndx = 0; blkndx < nblocks; blkndx++) { for (jndx = 0; jndx < ndims; jndx++) { start[jndx] = ptdata[jndx + blkndx * ndims * 2]; count[jndx] = dims1[jndx]; } if (H5Sselect_hyperslab(sid1, H5S_SELECT_SET, start, NULL, count, NULL) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sselect_hyperslab failed"); if (H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); if (H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); if (render_bin_output(stream, container, type_id, (char *)region_buf, numelem) < 0) H5TOOLS_GOTO_ERROR((-1), "render_bin_output of data region failed"); /* Render the region data element end */ done:; } /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */ CATCH HDfree(start); HDfree(count); HDfree(region_buf); HDfree(dims1); if (H5Sclose(mem_space) < 0) H5TOOLS_ERROR((-1), "H5Sclose failed"); if (H5Sclose(sid1) < 0) H5TOOLS_ERROR((-1), "H5Sclose failed"); H5TOOLS_ENDDEBUG(" "); return ret_value; } /*------------------------------------------------------------------------- * Function: render_bin_output_region_blocks * * Purpose: Print some values from a dataset referenced by region blocks. * This is a special case subfunction to dump a region reference using blocks. * * Return: False if ERROR * True otherwise *------------------------------------------------------------------------- */ hbool_t render_bin_output_region_blocks(hid_t region_space, hid_t region_id, FILE *stream, hid_t container) { hssize_t snblocks; hsize_t nblocks; hsize_t alloc_size; hsize_t *ptdata = NULL; int sndims; unsigned ndims; hid_t dtype = H5I_INVALID_HID; hid_t type_id = H5I_INVALID_HID; hbool_t past_catch = FALSE; hbool_t ret_value = TRUE; H5TOOLS_START_DEBUG(" "); if ((snblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0) H5TOOLS_THROW(FALSE, "H5Sget_select_hyper_nblocks failed"); nblocks = (hsize_t)snblocks; /* Print block information */ if ((sndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5TOOLS_THROW(FALSE, "H5Sget_simple_extent_ndims failed"); ndims = (unsigned)sndims; alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); if ((ptdata = (hsize_t *)HDmalloc((size_t)alloc_size)) == NULL) H5TOOLS_GOTO_ERROR(FALSE, "Could not allocate buffer for ptdata"); if (H5Sget_select_hyper_blocklist(region_space, (hsize_t)0, nblocks, ptdata) < 0) H5TOOLS_GOTO_ERROR(FALSE, "H5Rget_select_hyper_blocklist failed"); if ((dtype = H5Dget_type(region_id)) < 0) H5TOOLS_GOTO_ERROR(FALSE, "H5Dget_type failed"); if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR(FALSE, "H5Tget_native_type failed"); render_bin_output_region_data_blocks(region_id, stream, container, ndims, type_id, nblocks, ptdata); done: HDfree(ptdata); if (type_id > 0 && H5Tclose(type_id) < 0) H5TOOLS_ERROR(FALSE, "H5Tclose failed"); if (dtype > 0 && H5Tclose(dtype) < 0) H5TOOLS_ERROR(FALSE, "H5Tclose failed"); H5_LEAVE(TRUE) CATCH H5TOOLS_ENDDEBUG(" "); return ret_value; } /*------------------------------------------------------------------------- * Function: H5Tools Library * Purpose: Print the data values from a dataset referenced by region points. * * Description: * This is a special case subfunction to print the data in a region reference of type points. * * Return: * The function returns FAIL on error, otherwise SUCCEED * * Parameters Description: * h5tools_str_t *buffer is the string into which to render * size_t ncols * int ndims is the number of dimensions of the region element * hssize_t npoints is the number of points in the region *------------------------------------------------------------------------- */ int render_bin_output_region_data_points(hid_t region_space, hid_t region_id, FILE *stream, hid_t container, unsigned ndims, hid_t type_id, hsize_t npoints) { hsize_t *dims1 = NULL; size_t type_size; hid_t mem_space = H5I_INVALID_HID; void * region_buf = NULL; int ret_value = 0; H5TOOLS_START_DEBUG(" "); if ((type_size = H5Tget_size(type_id)) == 0) H5TOOLS_GOTO_ERROR((-1), "H5Tget_size failed"); if ((region_buf = HDmalloc(type_size * (size_t)npoints)) == NULL) H5TOOLS_GOTO_ERROR((-1), "Could not allocate buffer for region"); /* Allocate space for the dimension array */ if ((dims1 = (hsize_t *)HDmalloc(sizeof(hsize_t) * ndims)) == NULL) H5TOOLS_GOTO_ERROR((-1), "Could not allocate buffer for dims"); dims1[0] = npoints; if ((mem_space = H5Screate_simple(1, dims1, NULL)) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Screate_simple failed"); if (H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Dread failed"); if (H5Sget_simple_extent_dims(region_space, dims1, NULL) < 0) H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed"); if (render_bin_output(stream, container, type_id, (char *)region_buf, npoints) < 0) H5TOOLS_GOTO_ERROR((-1), "render_bin_output of data points failed"); done: HDfree(region_buf); HDfree(dims1); if (H5Sclose(mem_space) < 0) H5TOOLS_ERROR((-1), "H5Sclose failed"); H5TOOLS_ENDDEBUG(" "); return ret_value; } /*------------------------------------------------------------------------- * Function: render_bin_output_region_points * * Purpose: Print some values from a dataset referenced by region points. * This is a special case function to dump a region reference using points. * * Return: False if the last dimension has been reached * True otherwise *------------------------------------------------------------------------- */ hbool_t render_bin_output_region_points(hid_t region_space, hid_t region_id, FILE *stream, hid_t container) { hssize_t snpoints; hsize_t npoints; int sndims; unsigned ndims; hid_t dtype = H5I_INVALID_HID; hid_t type_id = H5I_INVALID_HID; hbool_t past_catch = FALSE; hbool_t ret_value = TRUE; H5TOOLS_START_DEBUG(" "); if ((snpoints = H5Sget_select_elem_npoints(region_space)) <= 0) H5TOOLS_THROW(FALSE, "H5Sget_select_elem_npoints failed"); npoints = (hsize_t)snpoints; /* Allocate space for the dimension array */ if ((sndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5TOOLS_THROW(FALSE, "H5Sget_simple_extent_ndims failed"); ndims = (unsigned)sndims; if ((dtype = H5Dget_type(region_id)) < 0) H5TOOLS_GOTO_ERROR(FALSE, "H5Dget_type failed"); if ((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) H5TOOLS_GOTO_ERROR(FALSE, "H5Tget_native_type failed"); render_bin_output_region_data_points(region_space, region_id, stream, container, ndims, type_id, npoints); done: if (type_id > 0 && H5Tclose(type_id) < 0) H5TOOLS_ERROR(FALSE, "H5Tclose failed"); if (dtype > 0 && H5Tclose(dtype) < 0) H5TOOLS_ERROR(FALSE, "H5Tclose failed"); H5_LEAVE(ret_value) CATCH H5TOOLS_ENDDEBUG(" "); return ret_value; } /*------------------------------------------------------------------------- * Function: h5tools_is_zero * * Purpose: Determines if memory is initialized to all zero bytes. * * Return: TRUE if all bytes are zero * FALSE otherwise *------------------------------------------------------------------------- */ hbool_t h5tools_is_zero(const void *_mem, size_t size) { const unsigned char *mem = (const unsigned char *)_mem; while (size-- > 0) if (mem[size]) return FALSE; return TRUE; } /*------------------------------------------------------------------------- * Function: h5tools_is_obj_same * * Purpose: Check if two given object IDs or link names point to the same object. * * Parameters: * hid_t loc_id1: location of the first object * char *name1: link name of the first object. * Use "." or NULL if loc_id1 is the object to be compared. * hid_t loc_id2: location of the second object * char *name1: link name of the first object. * Use "." or NULL if loc_id2 is the object to be compared. * * Return: TRUE if it is the same object * FALSE otherwise. *------------------------------------------------------------------------- */ hbool_t h5tools_is_obj_same(hid_t loc_id1, const char *name1, hid_t loc_id2, const char *name2) { H5O_info_t oinfo1, oinfo2; hbool_t ret_val = FALSE; if (name1 && HDstrcmp(name1, ".") != 0) H5Oget_info_by_name(loc_id1, name1, &oinfo1, H5P_DEFAULT); else H5Oget_info(loc_id1, &oinfo1); if (name2 && HDstrcmp(name2, ".") != 0) H5Oget_info_by_name(loc_id2, name2, &oinfo2, H5P_DEFAULT); else H5Oget_info(loc_id2, &oinfo2); if (oinfo1.fileno == oinfo2.fileno && oinfo1.addr == oinfo2.addr) ret_val = 1; return ret_val; }