/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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://support.hdfgroup.org/ftp/HDF5/releases. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Purpose: A library for displaying the values of a dataset in a human * readable format. */ #include #include "h5tools.h" #include "h5tools_dump.h" #include "h5tools_ref.h" #include "h5tools_utils.h" #include "H5private.h" /* global variables */ hid_t H5tools_ERR_STACK_g = 0; 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; int compound_data; 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 */ 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 */ /* This enum should match the entries in the below drivers_list since they * are indexes into the drivers_list array. */ typedef enum { SEC2_IDX = 0 ,FAMILY_IDX ,SPLIT_IDX ,MULTI_IDX #ifdef H5_HAVE_PARALLEL ,MPIO_IDX #endif /* H5_HAVE_PARALLEL */ ,SWMR_IDX } driver_idx; /* Names of VFDs */ static const char *drivernames[]={ [SEC2_IDX] = "sec2", [FAMILY_IDX] = "family", [SPLIT_IDX] = "split", [MULTI_IDX] = "multi", #ifdef H5_HAVE_PARALLEL [MPIO_IDX] = "mpio", #endif /* H5_HAVE_PARALLEL */ [SWMR_IDX] = "swmr", }; /* If h5tools_fopen() may try the i'th driver if its arguments do not * specify one and specified_only[i] is false. If specified_only[i] is * true, then the arguments must be specify the driver. */ static bool specified_only[] = { [SWMR_IDX] = true }; #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) { 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++; } } /*------------------------------------------------------------------------- * 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) { H5E_auto2_t tools_func; void *tools_edata; if (h5tools_init_g) { /* special case where only data is output to stdout */ if((rawoutstream == NULL) && rawdatastream && (rawdatastream == stdout)) HDfprintf(rawdatastream, "\n"); H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); if(tools_func!=NULL) 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(); 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; } static hid_t swmr_fapl_augment(hid_t fapl, const char *fname) { H5F_vfd_swmr_config_t *config = NULL; /* Configuration for VFD SWMR */ const char *dname; char *tname; /* * Set up to open the file with VFD SWMR configured. */ /* Enable page buffering */ if(H5Pset_page_buffer_size(fapl, 4096, 100, 0) < 0) { HDfprintf(rawerrorstream, "H5Pset_page_buffer_size failed\n"); return H5I_INVALID_HID; } /* Allocate memory for the configuration structure */ config = (H5F_vfd_swmr_config_t *)HDcalloc(1, sizeof(*config)); if(config == NULL) { HDfprintf(rawerrorstream, "VFD SWMR config allocation failed\n"); return H5I_INVALID_HID; } config->version = H5F__CURR_VFD_SWMR_CONFIG_VERSION; config->tick_len = 4; config->max_lag = 5; config->writer = FALSE; config->md_pages_reserved = 128; if ((tname = strdup(fname)) == NULL) { HDfprintf(rawerrorstream, "temporary string allocation failed\n"); return H5I_INVALID_HID; } dname = dirname(tname); snprintf(config->md_file_path, sizeof(config->md_file_path), "%s/my_md_file", dname); free(tname); /* Enable VFD SWMR configuration */ if(H5Pset_vfd_swmr_config(fapl, config) < 0) { HDfprintf(rawerrorstream, "H5Pset_vrd_swmr_config failed\n"); return H5I_INVALID_HID; } return fapl; } /*------------------------------------------------------------------------- * Function: h5tools_get_fapl * * Purpose: Get a FAPL for a given VFL driver name. * * Return: positive - succeeded * negative - failed *------------------------------------------------------------------------- */ static hid_t h5tools_get_fapl(hid_t fapl, const char *fname, const char *driver, unsigned *drivernum) { hid_t new_fapl = H5I_INVALID_HID; /* Copy of file access property list passed in, or new property list */ herr_t ret_value = SUCCEED; /* Make a copy of the FAPL, for the file open call to use, eventually */ if (fapl == H5P_DEFAULT) { if ((new_fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pcreate failed"); } /* end if */ else { if ((new_fapl = H5Pcopy(fapl)) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pcopy failed"); } /* end else */ /* Determine which driver the user wants to open the file with. Try * that driver. If it can't open it, then fail. */ if (!HDstrcmp(driver, drivernames[SWMR_IDX])) { /* SWMR driver */ if (swmr_fapl_augment(new_fapl, fname) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "swmr_fapl_augment failed"); if (drivernum) *drivernum = SWMR_IDX; } else if (!HDstrcmp(driver, drivernames[SEC2_IDX])) { /* SEC2 driver */ if (H5Pset_fapl_sec2(new_fapl) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_sec2 failed"); if (drivernum) *drivernum = SEC2_IDX; } else if (!HDstrcmp(driver, drivernames[FAMILY_IDX])) { /* FAMILY Driver */ /* Set member size to be 0 to indicate the current first member size * is the member size. */ if (H5Pset_fapl_family(new_fapl, (hsize_t) 0, H5P_DEFAULT) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_family failed"); if (drivernum) *drivernum = FAMILY_IDX; } else if (!HDstrcmp(driver, drivernames[SPLIT_IDX])) { /* SPLIT Driver */ if (H5Pset_fapl_split(new_fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_split failed"); if (drivernum) *drivernum = SPLIT_IDX; } else if (!HDstrcmp(driver, drivernames[MULTI_IDX])) { /* MULTI Driver */ if (H5Pset_fapl_multi(new_fapl, NULL, NULL, NULL, NULL, TRUE) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_multi failed"); if(drivernum) *drivernum = MULTI_IDX; } #ifdef H5_HAVE_PARALLEL else if(!HDstrcmp(driver, drivernames[MPIO_IDX])) { 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(new_fapl, MPI_COMM_WORLD, MPI_INFO_NULL) < 0) H5TOOLS_GOTO_ERROR(FAIL, "H5Pset_fapl_mpio failed"); if(drivernum) *drivernum = MPIO_IDX; } /* end if */ } #endif /* H5_HAVE_PARALLEL */ else ret_value = -1; done: if((new_fapl != H5P_DEFAULT) && (ret_value < 0)) { H5Pclose(new_fapl); new_fapl = H5I_INVALID_HID; } return(new_fapl); } /*------------------------------------------------------------------------- * Function: h5tools_fopen * * Purpose: Loop through the various types of VFL drivers trying to open FNAME. * 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. * * If DRIVER is non-NULL, then it will try to open the file with that * driver first. We assume that the user knows what they are doing so, if * we fail, then we won't try other file drivers. * * 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. * * Otherwise, the function returns FAIL. If DRIVERNAME is non-null then * the first byte is set to the null terminator. *------------------------------------------------------------------------- */ hid_t h5tools_fopen(const char *fname, unsigned flags, hid_t fapl, const char *driver, char *drivername, size_t drivername_size) { unsigned drivernum; hid_t fid = FAIL; hid_t my_fapl = H5P_DEFAULT; /* Try to open the file using every eligible driver. */ for (drivernum = 0; drivernum < NUM_DRIVERS; drivernum++) { if (driver == NULL && specified_only[drivernum]) continue; if (driver != NULL && strcmp(drivernames[drivernum], driver) != 0) continue; /* Get the correct FAPL for the given driver */ if((my_fapl = h5tools_get_fapl(fapl, fname, drivernames[drivernum], NULL)) < 0) goto done; /* allow error stack display if enable-error-stack has optional arg number */ if (enable_error_stack > 1) { fid = H5Fopen(fname, flags, my_fapl); } else { H5E_BEGIN_TRY { fid = H5Fopen(fname, flags, my_fapl); } H5E_END_TRY; } if (fid != FAIL) break; /* Close the FAPL */ H5Pclose(my_fapl); my_fapl = H5P_DEFAULT; } /* Save the driver name */ if (drivername && drivername_size) { if (fid != FAIL) { HDstrncpy(drivername, drivernames[drivernum], drivername_size); drivername[drivername_size - 1] = '\0'; } else { /*no file opened*/ drivername[0] = '\0'; } } done: if(my_fapl != H5P_DEFAULT) H5Pclose(my_fapl); return fid; } /*------------------------------------------------------------------------- * 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. *------------------------------------------------------------------------- */ H5_ATTR_PURE 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_DEBUG("enter"); 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->ndims, 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("exit"); } /*------------------------------------------------------------------------- * 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->ndims, ctx->p_max_idx, 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_DEBUG("enter 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("exit"); 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_DEBUG("enter"); 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("exit"); return dimension_break; } /*------------------------------------------------------------------------- * Function: init_acc_pos * * Purpose: initialize accumulator and matrix position * * Return: void *------------------------------------------------------------------------- */ void init_acc_pos(h5tools_context_t *ctx, hsize_t *dims) { int i; unsigned j; H5TOOLS_DEBUG("enter"); if(ctx->ndims > 0) { ctx->acc[ctx->ndims - 1] = 1; for (i = ((int)ctx->ndims - 2); i >= 0; i--) { ctx->acc[i] = ctx->acc[i + 1] * dims[i + 1]; H5TOOLS_DEBUG("ctx->acc[%d]=%ld", i, ctx->acc[i]); } for (j = 0; j < ctx->ndims; j++) ctx->pos[j] = 0; } H5TOOLS_ENDDEBUG("exit"); } /*------------------------------------------------------------------------- * 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_DEBUG("enter"); 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; 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 (H5Tequal(tid, H5T_STD_REF)) { H5TOOLS_DEBUG("H5T_STD_REF"); 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; if((region_id = H5Ropen_object((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) < 0) H5TOOLS_INFO("H5Ropen_object H5T_STD_REF failed"); else { if((region_space = H5Ropen_region((const H5R_ref_t *)mem, H5P_DEFAULT, H5P_DEFAULT)) >= 0) { if (!h5tools_is_zero(mem, H5Tget_size(H5T_STD_REF))) { 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); } else { H5TOOLS_INFO("H5Ropen_object H5T_STD_REF NULL"); } H5Sclose(region_space); } /* end if (region_space >= 0) */ H5Dclose(region_id); } } } /* end if (region_output... */ } else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { /* if (size == H5R_DSET_REG_REF_BUF_SIZE) */ H5TOOLS_DEBUG("H5T_STD_REF_DSETREG"); } else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { /* if (size == H5R_OBJ_REF_BUF_SIZE) */ 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("exit"); 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; /* 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("exit"); 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; 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("exit"); 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; 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("exit"); 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; 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("exit"); 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 *------------------------------------------------------------------------- */ H5_ATTR_PURE 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_info2_t oinfo1, oinfo2; hbool_t ret_val = FALSE; if ( name1 && HDstrcmp(name1, ".")) H5Oget_info_by_name3(loc_id1, name1, &oinfo1, H5O_INFO_BASIC, H5P_DEFAULT); else H5Oget_info3(loc_id1, &oinfo1, H5O_INFO_BASIC); if ( name2 && HDstrcmp(name2, ".")) H5Oget_info_by_name3(loc_id2, name2, &oinfo2, H5O_INFO_BASIC, H5P_DEFAULT); else H5Oget_info3(loc_id2, &oinfo2, H5O_INFO_BASIC); if (oinfo1.fileno == oinfo2.fileno) { int token_cmp_val; H5Otoken_cmp(loc_id1, &oinfo1.token, &oinfo2.token, &token_cmp_val); if(!token_cmp_val) ret_val = TRUE; } return ret_val; }