/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Purpose: A library for displaying the values of a dataset in a human * readable format. */ #include #include #include "h5tools.h" #include "h5tools_ref.h" #include "h5tools_utils.h" #include "H5private.h" #define SANITY_CHECK #define ALIGN(A,Z) ((((A) + (Z) - 1) / (Z)) * (Z)) /* global variables */ hid_t H5tools_ERR_CLS_g = -1; hid_t H5E_tools_g = -1; hid_t H5E_tools_min_id_g = -1; int compound_data; FILE *rawdatastream; /* should initialize to stdout but gcc moans about it */ int bin_output; /* binary output */ int bin_form; /* binary form */ int region_output; /* region output */ int packed_bits_num; /* number of packed bits to display */ int packed_data_offset; /* offset of packed bits to display */ unsigned long long packed_data_mask; /* mask in which packed bits to display */ static h5tool_format_t h5tools_dataformat = { 0, /*raw */ "", /*fmt_raw */ "%d", /*fmt_int */ "%u", /*fmt_uint */ "%hhd", /*fmt_schar */ "%u", /*fmt_uchar */ "%d", /*fmt_short */ "%u", /*fmt_ushort */ "%ld", /*fmt_long */ "%lu", /*fmt_ulong */ NULL, /*fmt_llong */ NULL, /*fmt_ullong */ "%g", /*fmt_double */ "%g", /*fmt_float */ 0, /*ascii */ 0, /*str_locale */ 0, /*str_repeat */ "[ ", /*arr_pre */ ",", /*arr_sep */ " ]", /*arr_suf */ 1, /*arr_linebreak */ "", /*cmpd_name */ ",\n", /*cmpd_sep */ "{\n", /*cmpd_pre */ "}", /*cmpd_suf */ "\n", /*cmpd_end */ ", ", /*vlen_sep */ "(", /*vlen_pre */ ")", /*vlen_suf */ "", /*vlen_end */ "%s", /*elmt_fmt */ ",", /*elmt_suf1 */ " ", /*elmt_suf2 */ "", /*idx_n_fmt */ "", /*idx_sep */ "", /*idx_fmt */ 80, /*line_ncols *//*standard default columns */ 0, /*line_per_line */ "", /*line_pre */ "%s", /*line_1st */ "%s", /*line_cont */ "", /*line_suf */ "", /*line_sep */ 1, /*line_multi_new */ " ", /*line_indent */ 1, /*skip_first */ 1, /*obj_hidefileno */ " "H5_PRINTF_HADDR_FMT, /*obj_format */ 1, /*dset_hidefileno */ "DATASET %s ", /*dset_format */ "%s", /*dset_blockformat_pre */ "%s", /*dset_ptformat_pre */ "%s", /*dset_ptformat */ 1, /*array indices */ 1 /*escape non printable characters */ }; static const h5tools_dump_header_t h5tools_standardformat = { "standardformat", /*name */ "HDF5", /*fileebgin */ "", /*fileend */ SUPER_BLOCK, /*bootblockbegin */ "", /*bootblockend */ H5_TOOLS_GROUP, /*groupbegin */ "", /*groupend */ H5_TOOLS_DATASET, /*datasetbegin */ "", /*datasetend */ ATTRIBUTE, /*attributebegin */ "", /*attributeend */ H5_TOOLS_DATATYPE, /*datatypebegin */ "", /*datatypeend */ DATASPACE, /*dataspacebegin */ "", /*dataspaceend */ DATA, /*databegin */ "", /*dataend */ SOFTLINK, /*softlinkbegin */ "", /*softlinkend */ EXTLINK, /*extlinkbegin */ "", /*extlinkend */ UDLINK, /*udlinkbegin */ "", /*udlinkend */ SUBSET, /*subsettingbegin */ "", /*subsettingend */ START, /*startbegin */ "", /*startend */ STRIDE, /*stridebegin */ "", /*strideend */ COUNT, /*countbegin */ "", /*countend */ BLOCK, /*blockbegin */ "", /*blockend */ "{", /*fileblockbegin */ "}", /*fileblockend */ "{", /*bootblockblockbegin */ "}", /*bootblockblockend */ "{", /*groupblockbegin */ "}", /*groupblockend */ "{", /*datasetblockbegin */ "}", /*datasetblockend */ "{", /*attributeblockbegin */ "}", /*attributeblockend */ "", /*datatypeblockbegin */ "", /*datatypeblockend */ "", /*dataspaceblockbegin */ "", /*dataspaceblockend */ "{", /*datablockbegin */ "}", /*datablockend */ "{", /*softlinkblockbegin */ "}", /*softlinkblockend */ "{", /*extlinkblockbegin */ "}", /*extlinkblockend */ "{", /*udlinkblockbegin */ "}", /*udlinkblockend */ "{", /*strblockbegin */ "}", /*strblockend */ "{", /*enumblockbegin */ "}", /*enumblockend */ "{", /*structblockbegin */ "}", /*structblockend */ "{", /*vlenblockbegin */ "}", /*vlenblockend */ "{", /*subsettingblockbegin */ "}", /*subsettingblockend */ "(", /*startblockbegin */ ");", /*startblockend */ "(", /*strideblockbegin */ ");", /*strideblockend */ "(", /*countblockbegin */ ");", /*countblockend */ "(", /*blockblockbegin */ ");", /*blockblockend */ "", /*dataspacedescriptionbegin */ "", /*dataspacedescriptionend */ "(", /*dataspacedimbegin */ ")", /*dataspacedimend */ }; static const h5tools_dump_header_t * h5tools_dump_header_format; /* local prototypes */ static int do_bin_output(FILE *stream, hid_t container, hsize_t nelmts, hid_t tid, void *_mem); static int render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem); static int render_bin_output_region_data_blocks(hid_t region_id, FILE *stream, hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata); static hbool_t render_bin_output_region_blocks(hid_t region_space, hid_t region_id, FILE *stream, hid_t container); static hbool_t render_bin_output_region_points(hid_t region_space, hid_t region_id, FILE *stream, hid_t container); static hbool_t h5tools_is_zero(const void *_mem, size_t size); hbool_t h5tools_render_element(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/, h5tools_str_t *buffer/*string into which to render */, hsize_t *curr_pos/*total data element position*/, size_t ncols, hsize_t local_elmt_counter/*element counter*/, hsize_t elmt_counter); hbool_t h5tools_render_region_element(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/, h5tools_str_t *buffer/*string into which to render */, hsize_t *curr_pos/*total data element position*/, size_t ncols, hsize_t *ptdata, hsize_t local_elmt_counter/*element counter*/, hsize_t elmt_counter); static int h5tools_print_region_data_blocks(hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t ctx, h5tools_str_t *buffer/*string into which to render */, size_t ncols, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata); hbool_t h5tools_dump_region_data_points(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/, h5tools_str_t *buffer/*string into which to render */, hsize_t *curr_pos/*total data element position*/, size_t ncols, hsize_t region_elmt_counter/*element counter*/, hsize_t elmt_counter); int h5tools_print_region_data_points(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t ctx, h5tools_str_t *buffer, size_t ncols, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata); hbool_t h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/, h5tools_str_t *buffer/*string into which to render */, hsize_t *curr_pos/*total data element position*/, size_t ncols, hsize_t region_elmt_counter/*element counter*/, hsize_t elmt_counter); /* module-scoped variables */ static int h5tools_init_g; /* if h5tools lib has been initialized */ #ifdef H5_HAVE_PARALLEL static int h5tools_mpi_init_g; /* if MPI_Init() has been called */ #endif /* H5_HAVE_PARALLEL */ /* Names of VFDs */ static const char *drivernames[]={ "sec2", "family", "split", "multi", #ifdef H5_HAVE_STREAM "stream", #endif /* H5_HAVE_STREAM */ #ifdef H5_HAVE_PARALLEL "mpio", "mpiposix" #endif /* H5_HAVE_PARALLEL */ }; /* This enum should match the entries in the above drivers_list since they * are indexes into the drivers_list array. */ enum { SEC2_IDX = 0 ,FAMILY_IDX ,SPLIT_IDX ,MULTI_IDX #ifdef H5_HAVE_STREAM ,STREAM_IDX #endif /* H5_HAVE_STREAM */ #ifdef H5_HAVE_PARALLEL ,MPIO_IDX ,MPIPOSIX_IDX #endif /* H5_HAVE_PARALLEL */ } driver_idx; #define NUM_DRIVERS (sizeof(drivernames) / sizeof(drivernames[0])) /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Initialize the H5 Tools library * Description: * 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 * Programmer: * Albert Cheng, 2000-10-31 * Modifications: *------------------------------------------------------------------------- */ void h5tools_init(void) { char lib_str[256]; if (!h5tools_init_g) { /* register the error class */ HDsnprintf(lib_str, sizeof(lib_str), "%d.%d.%d",H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE); H5TOOLS_INIT_ERROR() if (!rawdatastream) rawdatastream = stdout; h5tools_dump_header_format = &h5tools_standardformat; h5tools_init_g++; } } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Close the H5 Tools library * Description: * 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 * Programmer: * Albert Cheng, 2000-10-31 * Modifications: *------------------------------------------------------------------------- */ void h5tools_close(void) { if (h5tools_init_g) { if (rawdatastream && rawdatastream != stdout) { if (fclose(rawdatastream)) perror("closing rawdatastream"); else rawdatastream = 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; } } /*------------------------------------------------------------------------- * Audience: Private * Chapter: H5Tools Library * Purpose: Get a FAPL for a driver * Description: * Get a FAPL for a given VFL driver name. * Return: * None * Programmer: * Quincey Koziol, 2004-02-04 * Modifications: * Pedro Vicente Nunes, Thursday, July 27, 2006 * Added error return conditions for the H5Pset_fapl calls *------------------------------------------------------------------------- */ static hid_t h5tools_get_fapl(hid_t fapl, const char *driver, unsigned *drivernum) { hid_t new_fapl; /* Copy of file access property list passed in, or new property list */ /* 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) goto error; } /* end if */ else { if ((new_fapl = H5Pcopy(fapl)) < 0) goto error; } /* 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 (!strcmp(driver, drivernames[SEC2_IDX])) { /* SEC2 driver */ if (H5Pset_fapl_sec2(new_fapl) < 0) goto error; if (drivernum) *drivernum = SEC2_IDX; } else if (!strcmp(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) goto error; if (drivernum) *drivernum = FAMILY_IDX; } else if (!strcmp(driver, drivernames[SPLIT_IDX])) { /* SPLIT Driver */ if (H5Pset_fapl_split(new_fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT) < 0) goto error; if (drivernum) *drivernum = SPLIT_IDX; } else if (!strcmp(driver, drivernames[MULTI_IDX])) { /* MULTI Driver */ if (H5Pset_fapl_multi(new_fapl, NULL, NULL, NULL, NULL, TRUE) < 0) goto error; if(drivernum) *drivernum = MULTI_IDX; #ifdef H5_HAVE_STREAM } else if(!strcmp(driver, drivernames[STREAM_IDX])) { /* STREAM Driver */ if(H5Pset_fapl_stream(new_fapl, NULL) < 0) goto error; if(drivernum) *drivernum = STREAM_IDX; #endif /* H5_HAVE_STREAM */ #ifdef H5_HAVE_PARALLEL } else if(!strcmp(driver, drivernames[MPIO_IDX])) { /* MPI-I/O Driver */ /* check if MPI has been initialized. */ if(!h5tools_mpi_init_g) MPI_Initialized(&h5tools_mpi_init_g); if(h5tools_mpi_init_g) { if(H5Pset_fapl_mpio(new_fapl, MPI_COMM_WORLD, MPI_INFO_NULL) < 0) goto error; if(drivernum) *drivernum = MPIO_IDX; } /* end if */ } else if (!strcmp(driver, drivernames[MPIPOSIX_IDX])) { /* MPI-I/O Driver */ /* check if MPI has been initialized. */ if(!h5tools_mpi_init_g) MPI_Initialized(&h5tools_mpi_init_g); if(h5tools_mpi_init_g) { if(H5Pset_fapl_mpiposix(new_fapl, MPI_COMM_WORLD, TRUE) < 0) goto error; if(drivernum) *drivernum = MPIPOSIX_IDX; } /* end if */ #endif /* H5_HAVE_PARALLEL */ } else { goto error; } return(new_fapl); error: if(new_fapl != H5P_DEFAULT) H5Pclose(new_fapl); return -1; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Open a file with various VFL drivers. * Description: * 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 (and * the STREAM driver if H5_HAVE_STREAM is defined, that is). * * 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. * Programmer: * Lost in the mists of time. * Modifications: * Robb Matzke, 2000-06-23 * We only have to initialize driver[] on the first call, thereby * preventing memory leaks from repeated calls to H5Pcreate(). * * Robb Matzke, 2000-06-23 * Added DRIVERNAME_SIZE arg to prevent overflows when writing to * DRIVERNAME. * * Robb Matzke, 2000-06-23 * Added test to prevent coredump when the file could not be opened by * any driver. * * Robb Matzke, 2000-06-23 * Changed name from H5ToolsFopen() so it jives better with the names we * already have at the top of this source file. * * Thomas Radke, 2000-09-12 * Added Stream VFD to the driver[] array. * * Bill Wendling, 2001-01-10 * Changed macro behavior so that if we have a version other than 1.2.x * (i.e., > 1.2), then we do the drivers check. * * Bill Wendling, 2001-07-30 * Added DRIVER parameter so that the user can specify "try this driver" * instead of the default behaviour. If it fails to open the file with * that driver, this will fail completely (i.e., we won't try the other * drivers). We're assuming the user knows what they're doing. How UNIX * of us. *------------------------------------------------------------------------- */ 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; if (driver && *driver) { /* Get the correct FAPL for the given driver */ if ((my_fapl = h5tools_get_fapl(fapl, driver, &drivernum)) < 0) goto done; H5E_BEGIN_TRY { fid = H5Fopen(fname, flags, my_fapl); } H5E_END_TRY; if (fid == FAIL) goto done; } else { /* Try to open the file using each of the drivers */ for (drivernum = 0; drivernum < NUM_DRIVERS; drivernum++) { /* Get the correct FAPL for the given driver */ if((my_fapl = h5tools_get_fapl(fapl, drivernames[drivernum], NULL)) < 0) goto done; H5E_BEGIN_TRY { fid = H5Fopen(fname, flags, my_fapl); } H5E_END_TRY; if (fid != FAIL) break; else { /* Close the FAPL */ H5Pclose(my_fapl); my_fapl = H5P_DEFAULT; } /* end else */ } } /* Save the driver name */ if (drivername && drivername_size) { if (fid != FAIL) { strncpy(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; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Count the number of columns in a string. * Description: * Count the number of columns in a string. This is the number of * characters in the string not counting line-control characters. * Return: * On success, returns the width of the string. Otherwise this function * returns 0. * Programmer: * Robb Matzke, Tuesday, April 27, 1999 * Modifications: *------------------------------------------------------------------------- */ static size_t h5tools_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 conatains any variable length data * FALSE : type doesn't contain any variable length data * Negative value: error occur * * Programmer: Jonathan Kim March 18, 2011 *------------------------------------------------------------------------- */ htri_t h5tools_detect_vlen(hid_t tid) { htri_t ret; /* 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 conatains any variable length string * FALSE : type doesn't contain any variable length string * Negative value: error occur * *------------------------------------------------------------------------- */ 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) { int i = 0; int n = H5Tget_nmembers(tid); if(n < 0) { n = ret; goto done; } for(i = 0; i < n; i++) { hid_t mtid = H5Tget_member_type(tid, i); ret = h5tools_detect_vlen_str(mtid); if((ret == TRUE) || (ret < 0)) { H5Tclose(mtid); goto done; } H5Tclose(mtid); } } done: return ret; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Emit a simple prefix to STREAM. * Description: * 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 * Programmer: * Robb Matzke, Monday, April 26, 1999 * Modifications: * Robb Matzke, 1999-09-29 * If a new prefix is printed then the current element number is set back * to zero. * pvn, 2004-07-08 * Added support for printing array indices: * the indentation is printed before the prefix (printed one indentation * level before) *------------------------------------------------------------------------- */ static 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; int i, indentlevel = 0; if (!ctx->need_prefix) return; memset(&prefix, 0, sizeof(h5tools_str_t)); memset(&str, 0, sizeof(h5tools_str_t)); /* Terminate previous line, if any */ if (ctx->cur_column) { fputs(OPT(info->line_suf, ""), stream); putc('\n', stream); fputs(OPT(info->line_sep, ""), stream); } /* Calculate new prefix */ h5tools_str_prefix(&prefix, info, elmtno, ctx->ndims, 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 (i = 0; i < indentlevel - 1; i++) { fputs(h5tools_str_fmt(&str, 0, info->line_indent), stream); } } if (elmtno == 0 && secnum == 0 && info->line_1st) fputs(h5tools_str_fmt(&prefix, 0, info->line_1st), stream); else if (secnum && info->line_cont) fputs(h5tools_str_fmt(&prefix, 0, info->line_cont), stream); else fputs(h5tools_str_fmt(&prefix, 0, info->line_pre), stream); templength = h5tools_str_len(&prefix); for (i = 0; i < indentlevel; i++) { /*we already made the indent for the array indices case */ if (!info->pindex) { fputs(h5tools_str_fmt(&prefix, 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); } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Emit a simple prefix to STREAM. * Description: * 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 *------------------------------------------------------------------------- */ static 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; int i, indentlevel = 0; if (!ctx->need_prefix) return; memset(&prefix, 0, sizeof(h5tools_str_t)); memset(&str, 0, sizeof(h5tools_str_t)); /* Terminate previous line, if any */ if (ctx->cur_column) { fputs(OPT(info->line_suf, ""), stream); putc('\n', stream); fputs(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 (i = 0; i < indentlevel - 1; i++) { fputs(h5tools_str_fmt(&str, 0, info->line_indent), stream); } } if (elmtno == 0 && secnum == 0 && info->line_1st) fputs(h5tools_str_fmt(&prefix, 0, info->line_1st), stream); else if (secnum && info->line_cont) fputs(h5tools_str_fmt(&prefix, 0, info->line_cont), stream); else fputs(h5tools_str_fmt(&prefix, 0, info->line_pre), stream); templength = h5tools_str_len(&prefix); for (i = 0; i < indentlevel; i++) { /*we already made the indent for the array indices case */ if (!info->pindex) { fputs(h5tools_str_fmt(&prefix, 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); } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Prints NELMTS data elements to output STREAM. * Description: * Prints some (NELMTS) data elements to output STREAM. The elements are * stored in _MEM as type TYPE and are printed according to the format * described in INFO. The CTX struct contains context information shared * between calls to this function. The FLAGS is a bit field that * indicates whether the data supplied in this call falls at the * beginning or end of the total data to be printed (START_OF_DATA and * END_OF_DATA). * Return: * None * Programmer: * Robb Matzke, Monday, April 26, 1999 * Modifications: * Robb Matzke, 1999-06-04 * The `container' argument is the optional dataset for reference types. * * Robb Matzke, 1999-09-29 * Understands the `per_line' property which indicates that every Nth * element should begin a new line. * * Robb Matzke, LLNL, 2003-06-05 * Do not dereference the memory for a variable-length string here. * Deref in h5tools_str_sprint() instead so recursive types are * handled correctly. * * Pedro Vicente Nunes, The HDF Group, 2005-10-19 * 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 * new field sm_pos in h5tools_context_t, the current stripmine element position *------------------------------------------------------------------------- */ void h5tools_dump_simple_data(FILE *stream, const h5tool_format_t *info, hid_t container, h5tools_context_t *ctx/*in,out*/, unsigned flags, hsize_t nelmts, hid_t type, void *_mem) { unsigned char *mem = (unsigned char*) _mem; hsize_t i; /*element counter */ size_t size; /*size of each datum */ hid_t region_space; hid_t region_id; hbool_t dimension_break = TRUE; H5S_sel_type region_type; size_t ncols = 80; /*available output width */ h5tools_str_t buffer; /*string into which to render */ hsize_t curr_pos; /* total data element position */ hsize_t elmt_counter = 0;/*counts the # elements printed. *I (ptl?) needed something that *isn't going to get reset when a new *line is formed. I'm going to use *this var to count elements and *break after we see a number equal *to the ctx->size_last_dim. */ /* binary dump */ if (bin_output) { do_bin_output(rawdatastream, container, nelmts, type, _mem); } /* end if */ else { /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); size = H5Tget_size(type); if (info->line_ncols > 0) ncols = info->line_ncols; /* 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; for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) { void* memref = mem + i * size; if (region_output && H5Tequal(type, H5T_STD_REF_DSETREG)) { char ref_name[1024]; /* region data */ region_id = H5Rdereference(container, H5R_DATASET_REGION, memref); if (region_id >= 0) { region_space = H5Rget_region(container, H5R_DATASET_REGION, memref); if (region_space >= 0) { if (h5tools_is_zero(memref, H5Tget_size(type))) { h5tools_str_append(&buffer, "NULL"); } else { if(H5Rget_name(region_id, H5R_DATASET_REGION, memref, (char*) ref_name, 1024)<0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rget_name failed"); /* Render the region element begin */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, info->dset_format, ref_name); dimension_break = h5tools_render_element(stdout, info, ctx, &buffer, &curr_pos, ncols, i, elmt_counter); region_type = H5Sget_select_type(region_space); if(region_type==H5S_SEL_POINTS) /* Print point information */ dimension_break = h5tools_dump_region_data_points( region_space, region_id, stdout, info, ctx, &buffer, &curr_pos, ncols, i, elmt_counter); else if(region_type==H5S_SEL_HYPERSLABS) /* Print block information */ dimension_break = h5tools_dump_region_data_blocks( region_space, region_id, stdout, info, ctx, &buffer, &curr_pos, ncols, i, elmt_counter); else HERROR(H5E_tools_g, H5E_tools_min_id_g, "invalid region type"); /* Render the region element end */ } /* end else to if (h5tools_is_zero(... */ if(H5Sclose(region_space) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); } /* end if (region_space >= 0) */ else HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rget_region failed"); if(H5Dclose(region_id) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose failed"); } /* if (region_id >= 0) */ else HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rdereference failed"); ctx->need_prefix = TRUE; } /* end if (region_output... */ else { /* Render the data element begin*/ h5tools_str_reset(&buffer); h5tools_str_sprint(&buffer, info, container, type, memref, ctx); if (i + 1 < nelmts || (flags & END_OF_DATA) == 0) h5tools_str_append(&buffer, "%s", OPT(info->elmt_suf1, ",")); dimension_break = h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, ncols, i, elmt_counter); /* Render the data element end*/ } if(FALSE==dimension_break) elmt_counter = 0; } /* end for (i = 0; i < nelmts... */ h5tools_str_close(&buffer); }/* else bin */ } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Render an element to output STREAM. * Description: * 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, otherwise true * * 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; char *section; /*a section of output */ int secnum; /*section sequence number */ int multiline; /*datum was multiline */ s = h5tools_str_fmt(buffer, 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_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(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_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(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_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(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 = strtok(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 + strlen(section) + strlen(OPT(info->elmt_suf2, " ")) + strlen(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_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_simple_prefix(stream, info, ctx, *curr_pos, secnum); } else if ((local_elmt_counter || ctx->continuation) && secnum == 0) { fputs(OPT(info->elmt_suf2, " "), stream); ctx->cur_column += strlen(OPT(info->elmt_suf2, " ")); } /* Print the section */ fputs(section, stream); ctx->cur_column += strlen(section); } ctx->prev_multiline = multiline; return dimension_break; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Render a region element to output STREAM. * Description: * 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, otherwise true * * 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; char *section; /*a section of output */ int secnum; /*section sequence number */ int multiline; /*datum was multiline */ s = h5tools_str_fmt(buffer, 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_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(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_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(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_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(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 = strtok(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 + strlen(section) + strlen(OPT(info->elmt_suf2, " ")) + strlen(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_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_region_simple_prefix(stream, info, ctx, local_elmt_counter, ptdata, secnum); } else if ((local_elmt_counter || ctx->continuation) && secnum == 0) { fputs(OPT(info->elmt_suf2, " "), stream); ctx->cur_column += strlen(OPT(info->elmt_suf2, " ")); } /* Print the section */ fputs(section, stream); ctx->cur_column += strlen(section); } ctx->prev_multiline = multiline; return dimension_break; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Print the data values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to print the data in a region reference of type blocks. * * Return: * The function returns FAIL if there was an error, otherwise SUCEED * * 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 nblocks is the number of blocks in the region *------------------------------------------------------------------------- */ static int h5tools_print_region_data_blocks(hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t ctx, h5tools_str_t *buffer/*string into which to render */, size_t ncols, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata) { hbool_t dimension_break = TRUE; hsize_t *dims1 = NULL; hsize_t *start = NULL; hsize_t *count = NULL; size_t numelem; hsize_t total_size[H5S_MAX_RANK]; hsize_t elmtno; /* elemnt index */ unsigned int region_flags; /* buffer extent flags */ hsize_t curr_pos; int jndx; size_t indx; int type_size; hid_t mem_space = -1; void *region_buf = NULL; int blkndx; hid_t sid1 = -1; int ret_value = SUCCEED; /* Get the dataspace of the dataset */ if((sid1 = H5Dget_space(region_id)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); /* Allocate space for the dimension array */ if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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(ndims, dims1, NULL)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed"); if((type_size = H5Tget_size(type_id)) == 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); if((region_buf = HDmalloc(type_size * numelem)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for start"); if((count = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for count"); curr_pos = 0; for (blkndx = 0; blkndx < nblocks; blkndx++) { ctx.ndims = ndims; ctx.need_prefix = TRUE; ctx.cur_elmt = 0; 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) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dread failed"); ctx.indent_level++; if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); /* assume entire data space to be printed */ for (indx = 0; indx < (size_t) ctx.ndims; indx++) ctx.p_min_idx[indx] = start[indx]; init_acc_pos(&ctx, total_size); /* print the data */ region_flags = START_OF_DATA; if (blkndx == nblocks - 1) region_flags |= END_OF_DATA; for (indx = 0; indx < (size_t)ctx.ndims; indx++) ctx.p_max_idx[indx] = dims1[indx]; curr_pos = 0; ctx.sm_pos = blkndx*2*ndims; ctx.size_last_dim = dims1[ndims-1]; h5tools_region_simple_prefix(stream, info, &ctx, curr_pos, ptdata, 0); elmtno = 0; for (indx = 0; indx < numelem; indx++, elmtno++, ctx.cur_elmt++) { /* Render the region data element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "%s", indx ? OPTIONAL_LINE_BREAK "" : ""); h5tools_str_sprint(buffer, info, region_id, type_id, ((char*)region_buf + indx * type_size), &ctx); if (indx + 1 < numelem || (region_flags & END_OF_DATA) == 0) h5tools_str_append(buffer, "%s", OPT(info->elmt_suf1, ",")); dimension_break = h5tools_render_region_element(stream, info, &ctx, buffer, &curr_pos, ncols, ptdata, indx, elmtno); /* Render the region data element end */ if(FALSE == dimension_break) elmtno = 0; } /* end for (indx = 0; indx < numelem; indx++, region_elmtno++, ctx.cur_elmt++) */ ctx.indent_level--; } /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */ done: HDfree(start); HDfree(count); HDfree(region_buf); HDfree(dims1); if(H5Sclose(mem_space) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); if(H5Sclose(sid1) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Print some values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to dump a region reference using blocks. * * Return: * The function returns False if the last dimension has been reached, otherwise True * * In/Out: * h5tools_context_t *ctx * 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 region_elmt_counter is the region element loop counter * hsize_t elmt_count is the data element loop counter *------------------------------------------------------------------------- */ hbool_t h5tools_dump_region_data_blocks(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx/*in,out*/, h5tools_str_t *buffer/*string into which to render */, hsize_t *curr_pos/*total data element position*/, size_t ncols, hsize_t region_elmt_counter/*element counter*/, hsize_t elmt_counter) { HERR_INIT(hbool_t, TRUE) hbool_t dimension_break = TRUE; hssize_t nblocks; hsize_t alloc_size; hsize_t *ptdata = NULL; int ndims; hid_t dtype; hid_t type_id; int i; if((nblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0) H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed"); /* Print block information */ if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); /* Render the region { element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "{"); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the region { element end */ /* Render the region datatype info and indices element begin */ h5tools_str_reset(buffer); ctx->indent_level++; ctx->need_prefix = TRUE; h5tools_str_append(buffer, "REGION_TYPE BLOCK "); alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); assert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/ if((ptdata = (hsize_t*) malloc((size_t) alloc_size)) == NULL) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could not allocate buffer for ptdata"); H5_CHECK_OVERFLOW(nblocks, hssize_t, hsize_t); if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "H5Rget_select_hyper_blocklist failed"); for (i = 0; i < nblocks; i++) { int j; h5tools_str_append(buffer, info->dset_blockformat_pre, i ? "," OPTIONAL_LINE_BREAK " " : "", (unsigned long) i); /* Start coordinates and opposite corner */ for (j = 0; j < ndims; j++) h5tools_str_append(buffer, "%s%lu", j ? "," : "(", (unsigned long) ptdata[i * 2 * ndims + j]); for (j = 0; j < ndims; j++) h5tools_str_append(buffer, "%s%lu", j ? "," : ")-(", (unsigned long) ptdata[i * 2 * ndims + j + ndims]); h5tools_str_append(buffer, ")"); } /* end for (i = 0; i < nblocks; i++) */ dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the region datatype info and indices element end */ ctx->need_prefix = TRUE; if((dtype = H5Dget_type(region_id)) < 0) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "H5Dget_type failed"); if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "H5Tget_native_type failed"); /* Render the datatype element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->datatypebegin, h5tools_dump_header_format->datatypeblockbegin); h5tools_print_datatype(buffer, info, ctx, dtype); if (HDstrlen(h5tools_dump_header_format->datatypeblockend)) { h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeblockend); if (HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(buffer, " "); } if (HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeend); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the datatype element end */ ctx->need_prefix = TRUE; /* Render the dataspace element begin */ h5tools_str_reset(buffer); ctx->need_prefix = TRUE; h5tools_str_append(buffer, "%s ", h5tools_dump_header_format->dataspacebegin); h5tools_print_dataspace(buffer, region_space); if (HDstrlen(h5tools_dump_header_format->dataspaceblockend)) { h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend); if (HDstrlen(h5tools_dump_header_format->dataspaceend)) h5tools_str_append(buffer, " "); } if (HDstrlen(h5tools_dump_header_format->dataspaceend)) h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the dataspace element end */ ctx->need_prefix = TRUE; /* Render the databegin element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->databegin, h5tools_dump_header_format->datablockbegin); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the databegin element end */ ctx->need_prefix = TRUE; h5tools_print_region_data_blocks(region_id, rawdatastream, info, *ctx, buffer, ncols, ndims, type_id, nblocks, ptdata); done: free(ptdata); if(H5Tclose(type_id) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(dtype) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); ctx->need_prefix = TRUE; /* Render the dataend element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->dataend, h5tools_dump_header_format->datablockend); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the dataend element end */ ctx->indent_level--; ctx->need_prefix = TRUE; /* Render the region } element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "}"); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the region } element end */ H5_LEAVE(dimension_break) CATCH return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: 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 h5tools_print_region_data_points(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t ctx, h5tools_str_t *buffer, size_t ncols, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata) { hbool_t dimension_break = TRUE; hsize_t *dims1 = NULL; hsize_t elmtno; /* elemnt index */ unsigned int region_flags; /* buffer extent flags */ hsize_t curr_pos; size_t indx; int jndx; int type_size; hid_t mem_space = -1; void *region_buf = NULL; int ret_value = SUCCEED; if((type_size = H5Tget_size(type_id)) == 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); if((region_buf = HDmalloc(type_size * npoints)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for region"); /* Allocate space for the dimension array */ if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for dims"); dims1[0] = npoints; if((mem_space = H5Screate_simple(1, dims1, NULL)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed"); if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); elmtno = 0; curr_pos = 0; for (jndx = 0; jndx < npoints; jndx++, elmtno++) { ctx.ndims = ndims; ctx.need_prefix = TRUE; ctx.cur_elmt = 0; /* points are always 0 */ /* Render the point element begin */ h5tools_str_reset(buffer); ctx.indent_level++; /* assume entire data space to be printed */ for (indx = 0; indx < (size_t) ctx.ndims; indx++) ctx.p_min_idx[indx] = 0; if(H5Sget_simple_extent_dims(region_space, ctx.p_max_idx, NULL) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); if (ctx.ndims > 0) { ctx.size_last_dim = (int) (ctx.p_max_idx[ctx.ndims - 1]); } else ctx.size_last_dim = 0; if (ctx.ndims > 0) init_acc_pos(&ctx, ctx.p_max_idx); /* print the data */ region_flags = START_OF_DATA; if (jndx == npoints - 1) region_flags |= END_OF_DATA; curr_pos = 0; /* points requires constant 0 */ ctx.sm_pos = jndx * ndims; h5tools_region_simple_prefix(stream, info, &ctx, curr_pos, ptdata, 0); h5tools_str_sprint(buffer, info, region_id, type_id, ((char*)region_buf + jndx * type_size), &ctx); if (jndx + 1 < npoints || (region_flags & END_OF_DATA) == 0) h5tools_str_append(buffer, "%s", OPT(info->elmt_suf1, ",")); dimension_break = h5tools_render_region_element(stream, info, &ctx, buffer, &curr_pos, ncols, ptdata, (hsize_t)0, elmtno); /* Render the point element end */ ctx.indent_level--; if(FALSE == dimension_break) elmtno = 0; } /* end for (jndx = 0; jndx < npoints; jndx++, region_elmtno++) */ done: HDfree(region_buf); HDfree(dims1); if(H5Sclose(mem_space) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Print some values from a dataset referenced by region points. * * Description: * This is a special case subfunction to dump a region reference using points. * * Return: * The function returns False if the last dimension has been reached, otherwise True * * In/Out: * h5tools_context_t *ctx * 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 region_elmt_counter is the region element loop counter * hsize_t elmt_count is the data element loop counter *------------------------------------------------------------------------- */ hbool_t h5tools_dump_region_data_points(hid_t region_space, hid_t region_id, FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, h5tools_str_t *buffer, hsize_t *curr_pos, size_t ncols, hsize_t region_elmt_counter, hsize_t elmt_counter) { HERR_INIT(hbool_t, TRUE) hbool_t dimension_break = TRUE; hssize_t npoints; hsize_t alloc_size; hsize_t *ptdata; int ndims; hssize_t indx; hid_t dtype; hid_t type_id; if((npoints = H5Sget_select_elem_npoints(region_space)) <= 0) H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed"); /* Allocate space for the dimension array */ if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5E_THROW(dimension_break, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); /* Render the region { element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "{"); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the region { element end */ /* Render the region datatype info and indices element begin */ h5tools_str_reset(buffer); ctx->indent_level++; ctx->need_prefix = TRUE; h5tools_str_append(buffer, "REGION_TYPE POINT "); alloc_size = npoints * ndims * sizeof(ptdata[0]); assert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/ if(NULL == (ptdata = (hsize_t *)HDmalloc((size_t) alloc_size))) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could not allocate buffer for ptdata"); H5_CHECK_OVERFLOW(npoints, hssize_t, hsize_t); if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "H5Sget_select_elem_pointlist failed"); for (indx = 0; indx < npoints; indx++) { int loop_indx; h5tools_str_append(buffer, info->dset_ptformat_pre, indx ? "," OPTIONAL_LINE_BREAK " " : "", (unsigned long) indx); for (loop_indx = 0; loop_indx < ndims; loop_indx++) h5tools_str_append(buffer, "%s%lu", loop_indx ? "," : "(", (unsigned long) (ptdata[indx * ndims + loop_indx])); h5tools_str_append(buffer, ")"); } /* end for (indx = 0; indx < npoints; indx++) */ dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the region datatype info and indices element end */ ctx->need_prefix = TRUE; if((dtype = H5Dget_type(region_id)) < 0) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "H5Dget_type failed"); if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "H5Tget_native_type failed"); /* Render the datatype element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->datatypebegin, h5tools_dump_header_format->datatypeblockbegin); h5tools_print_datatype(buffer, info, ctx, dtype); if (HDstrlen(h5tools_dump_header_format->datatypeblockend)) { h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeblockend); if (HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(buffer, " "); } if (HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(buffer, "%s", h5tools_dump_header_format->datatypeend); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the datatype element end */ ctx->need_prefix = TRUE; /* Render the dataspace element begin */ h5tools_str_reset(buffer); ctx->need_prefix = TRUE; h5tools_str_append(buffer, "%s ", h5tools_dump_header_format->dataspacebegin); h5tools_print_dataspace(buffer, region_space); if (HDstrlen(h5tools_dump_header_format->dataspaceblockend)) { h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend); if (HDstrlen(h5tools_dump_header_format->dataspaceend)) h5tools_str_append(buffer, " "); } if (HDstrlen(h5tools_dump_header_format->dataspaceend)) h5tools_str_append(buffer, "%s", h5tools_dump_header_format->dataspaceblockend); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the dataspace element end */ ctx->need_prefix = TRUE; /* Render the databegin element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->databegin, h5tools_dump_header_format->datablockbegin); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the databegin element end */ ctx->need_prefix = TRUE; h5tools_print_region_data_points(region_space, region_id, rawdatastream, info, *ctx, buffer, ncols, ndims, type_id, npoints, ptdata); done: free(ptdata); if(H5Tclose(type_id) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(dtype) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); ctx->need_prefix = TRUE; /* Render the dataend element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "%s %s ", h5tools_dump_header_format->dataend, h5tools_dump_header_format->datablockend); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the dataend element end*/ ctx->indent_level--; ctx->need_prefix = TRUE; /* Render the region } element begin */ h5tools_str_reset(buffer); h5tools_str_append(buffer, "}"); dimension_break = h5tools_render_element(stream, info, ctx, buffer, curr_pos, ncols, region_elmt_counter, elmt_counter); /* Render the region } element end */ H5_LEAVE(dimension_break) CATCH return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: print out the data for a subset of a dataset. * Description: * * Select a hyperslab from the dataset DSET using the parameters * specified in SSET. Dump this out to STREAM. * * Hyperslabs select "count" blocks of size "block", spaced "stride" elements * from each other, starting at coordinate "start". * * Return: * On success, return SUCCEED. Otherwise, the function returns FAIL. * * Algorithm * * The parameters from SSET are translated into temporary * variables so that 1 row is printed at a time (getting the coordinate indices * at each row). * We define the stride, count and block to be 1 in the row dimension to achieve * this and advance until all points are printed. * * The element position is obtained from the matrix according to: * Given an index I(z,y,x) its position from the beginning of an array * of sizes A(size_z, size_y,size_x) is given by * Position of I(z,y,x) = index_z * size_y * size_x * + index_y * size_x * + index_x * *------------------------------------------------------------------------- */ static herr_t h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset, hid_t p_type, struct subset_t *sset, hid_t f_space, hsize_t hyperslab_count, hsize_t *temp_start,/* start inside offset count loop */ hsize_t *temp_count,/* count inside offset count loop */ hsize_t *temp_block,/* block size used in loop */ hsize_t *temp_stride,/* stride size used in loop */ hsize_t *total_size,/* total size of dataset */ unsigned int row_dim/* index of row_counter dimension */) { HERR_INIT(herr_t, SUCCEED) size_t i; /* counters */ size_t j; /* counters */ hsize_t zero[1] = {0}; /* vector of zeros */ unsigned int flags; /* buffer extent flags */ hsize_t elmtno; /* elemnt index */ hsize_t low[H5S_MAX_RANK]; /* low bound of hyperslab */ hsize_t high[H5S_MAX_RANK]; /* higher bound of hyperslab */ size_t p_type_nbytes; /* size of memory type */ hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ hsize_t sm_nbytes; /* bytes per stripmine */ hssize_t ssm_nelmts; /* elements per stripmine*/ hsize_t sm_nelmts; /* elements per stripmine*/ unsigned char *sm_buf = NULL; /* buffer for raw data */ hid_t sm_space = -1; /* stripmine data space */ hsize_t size_row_block; /* size for blocks along rows */ hsize_t row_counter = 0; /* VL data special information */ unsigned int vl_data = 0; /* contains VL datatypes */ if ((size_t) ctx->ndims > NELMTS(sm_size)) H5E_THROW(FAIL, H5E_tools_min_id_g, "ndims and sm_size comparision failed"); if (ctx->ndims > 0) init_acc_pos(ctx, total_size); size_row_block = sset->block.data[row_dim]; /* Check if we have VL data in the dataset's datatype */ if (h5tools_detect_vlen_str(p_type) == TRUE) vl_data = TRUE; if (H5Tdetect_class(p_type, H5T_VLEN) == TRUE) vl_data = TRUE; /* display loop */ for (; hyperslab_count > 0; temp_start[row_dim] += temp_stride[row_dim], hyperslab_count--) { /* jump rows if size of block exceeded cases where block > 1 only and stride > block */ if (size_row_block > 1 && row_counter == size_row_block && sset->stride.data[row_dim] > sset->block.data[row_dim]) { hsize_t increase_rows = sset->stride.data[row_dim] - sset->block.data[row_dim]; temp_start[row_dim] += increase_rows; row_counter = 0; } row_counter++; /* calculate the potential number of elements we're going to print */ if(H5Sselect_hyperslab(f_space, H5S_SELECT_SET, temp_start, temp_stride, temp_count, temp_block) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); if((ssm_nelmts = H5Sget_select_npoints(f_space)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_select_npoints failed"); sm_nelmts = (hsize_t)ssm_nelmts; if (sm_nelmts > 0) { /* * determine the strip mine size and allocate a buffer. the strip mine is * a hyperslab whose size is manageable. */ if((sm_nbytes = p_type_nbytes = H5Tget_size(p_type)) == 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); if (ctx->ndims > 0) for (i = ctx->ndims; i > 0; --i) { hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes; if (size == 0) /* datum size > H5TOOLS_BUFSIZE */ size = 1; sm_size[i - 1] = MIN(total_size[i - 1], size); sm_nbytes *= sm_size[i - 1]; assert(sm_nbytes > 0); } assert(sm_nbytes == (hsize_t) ((size_t) sm_nbytes)); /*check for overflow*/ if(NULL == (sm_buf = (unsigned char *)HDmalloc((size_t) sm_nelmts * p_type_nbytes))) H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for strip-mine"); if((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed"); if(H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &sm_nelmts, NULL) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); /* read the data */ if(H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dread failed"); /* print the data */ flags = START_OF_DATA; if (hyperslab_count == 1) flags |= END_OF_DATA; for (i = 0; i < ctx->ndims; i++) ctx->p_max_idx[i] = ctx->p_min_idx[i] + MIN(total_size[i], sm_size[i]); /* print array indices. get the lower bound of the hyperslab and calulate the element position at the start of hyperslab */ if(H5Sget_select_bounds(f_space, low, high) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_select_bounds failed"); elmtno = 0; for (i = 0; i < (size_t) ctx->ndims - 1; i++) { hsize_t offset = 1; /* accumulation of the previous dimensions */ for (j = i + 1; j < (size_t) ctx->ndims; j++) offset *= total_size[j]; elmtno += low[i] * offset; } elmtno += low[ctx->ndims - 1]; /* initialize the current stripmine position; this is necessary to print the array indices */ ctx->sm_pos = elmtno; h5tools_dump_simple_data(stream, info, dset, ctx, flags, sm_nelmts, p_type, sm_buf); /* Reclaim any VL memory, if necessary */ if (vl_data) H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf); if(H5Sclose(sm_space) < 0) H5E_THROW(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); if(sm_buf) HDfree(sm_buf); sm_buf = NULL; } else H5E_THROW(SUCCEED, H5E_tools_min_id_g, "nothing to print"); /* we need to jump to next line and update the index */ ctx->need_prefix = 1; ctx->continuation++; } /* hyperslab_count loop */ CATCH if(sm_buf) HDfree(sm_buf); return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: print out the data for a subset of a dataset. * Description: * * Select a hyperslab from the dataset DSET using the parameters * specified in SSET. Dump this out to STREAM. * * Hyperslabs select "count" blocks of size "block", spaced "stride" elements * from each other, starting at coordinate "start". * * Return: * On success, return SUCCEED. Otherwise, the function returns FAIL. * * Algorithm * * The parameters from SSET are translated into temporary * variables so that 1 row is printed at a time (getting the coordinate indices * at each row). * We define the stride, count and block to be 1 in the row dimension to achieve * this and advance until all points are printed. * * The element position is obtained from the matrix according to: * Given an index I(z,y,x) its position from the beginning of an array * of sizes A(size_z, size_y,size_x) is given by * Position of I(z,y,x) = index_z * size_y * size_x * + index_y * size_x * + index_x * *------------------------------------------------------------------------- */ static herr_t h5tools_display_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset, hid_t p_type, struct subset_t *sset, hid_t f_space, hsize_t *total_size) { size_t i; /* counters */ hsize_t n; /* counters */ hsize_t count; /* hyperslab count */ hsize_t outer_count; /* offset count */ unsigned int row_dim; /* index of row_counter dimension */ int current_outer_dim; /* dimension for start */ hsize_t temp_start[H5S_MAX_RANK];/* temporary start inside offset count loop */ hsize_t max_start[H5S_MAX_RANK]; /* maximum start inside offset count loop */ hsize_t temp_count[H5S_MAX_RANK];/* temporary count inside offset count loop */ hsize_t temp_block[H5S_MAX_RANK];/* temporary block size used in loop */ hsize_t temp_stride[H5S_MAX_RANK];/* temporary stride size used in loop */ int reset_dim; herr_t ret_value = SUCCEED; if (ctx->ndims == 1) row_dim = 0; else row_dim = ctx->ndims - 2; /* get the offset count */ outer_count = 1; if (ctx->ndims > 2) for (i = 0; i < (size_t) ctx->ndims - 2; i++) { /* consider block size */ outer_count = outer_count * sset->count.data[i] * sset->block.data[i]; } /* initialize temporary start, count and maximum start */ for (i = 0; i < (size_t) ctx->ndims; i++) { temp_start[i] = sset->start.data[i]; temp_count[i] = sset->count.data[i]; temp_block[i] = sset->block.data[i]; temp_stride[i] = sset->stride.data[i]; max_start[i] = 0; } if (ctx->ndims > 2) { for (i = 0; i < (size_t) ctx->ndims - 2; i++) { max_start[i] = temp_start[i] + sset->count.data[i]; temp_count[i] = 1; } } /* offset loop */ for (n = 0; n < outer_count; n++) { /* number of read iterations in inner loop, read by rows, to match 2D display */ if (ctx->ndims > 1) { /* count is the number of iterations to display all the rows, the block size count times */ count = sset->count.data[row_dim] * sset->block.data[row_dim]; /* always 1 row_counter at a time, that is a block of size 1, 1 time */ temp_count[row_dim] = 1; temp_block[row_dim] = 1; /* advance 1 row_counter at a time */ if (sset->block.data[row_dim] > 1) temp_stride[row_dim] = 1; } /* for the 1D case */ else { count = 1; } h5tools_print_simple_subset(stream, info, ctx, dset, p_type, sset, f_space, count, temp_start, temp_count, temp_block, temp_stride, total_size, row_dim); if (ctx->ndims > 2) { /* dimension for start */ current_outer_dim = (ctx->ndims - 2) - 1; /* set start to original from current_outer_dim up */ for (i = current_outer_dim + 1; i < ctx->ndims; i++) { temp_start[i] = sset->start.data[i]; } /* increment start dimension */ do { reset_dim = 0; temp_start[current_outer_dim]++; if (temp_start[current_outer_dim] >= max_start[current_outer_dim]) { temp_start[current_outer_dim] = sset->start.data[current_outer_dim]; /* consider block */ if (sset->block.data[current_outer_dim] > 1) temp_start[current_outer_dim]++; current_outer_dim--; reset_dim = 1; } } while (current_outer_dim >= 0 && reset_dim); } /* ctx.ndims > 1 */ } /* outer_count */ return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Dump out a subset of a dataset. * Description: * * Select a hyperslab from the dataset DSET using the parameters * specified in SSET. Dump this out to STREAM. * * Hyperslabs select "count" blocks of size "block", spaced "stride" elements * from each other, starting at coordinate "start". * * Return: * On success, return SUCCEED. Otherwise, the function returns FAIL. * * Original programmer: * Bill Wendling, Wednesday, March 07, 2001 * * Rewritten with modified algorithm by: * Pedro Vicente, Wednesday, January 16, 2008, contributions from Quincey Koziol * * Algorithm * * In a inner loop, the parameters from SSET are translated into temporary * variables so that 1 row is printed at a time (getting the coordinate indices * at each row). * We define the stride, count and block to be 1 in the row dimension to achieve * this and advance until all points are printed. * An outer loop for cases where dimensionality is greater than 2D is made. * In each iteration, the 2D block is displayed in the inner loop. The remaining * slower dimensions above the first 2 are incremented one at a time in the outer loop * * The element position is obtained from the matrix according to: * Given an index I(z,y,x) its position from the beginning of an array * of sizes A(size_z, size_y,size_x) is given by * Position of I(z,y,x) = index_z * size_y * size_x * + index_y * size_x * + index_x * *------------------------------------------------------------------------- */ static herr_t h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, hid_t dset, hid_t p_type, struct subset_t *sset, int indentlevel) { HERR_INIT(herr_t, SUCCEED) int sndims; hid_t f_space = -1; /* file data space */ size_t i; /* counters */ hsize_t total_size[H5S_MAX_RANK];/* total size of dataset*/ h5tools_context_t ctx; /* print context */ if((f_space = H5Dget_space(dset)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); /* * check that everything looks okay. the dimensionality must not be too * great and the dimensionality of the items selected for printing must * match the dimensionality of the dataset. */ memset(&ctx, 0, sizeof(ctx)); ctx.indent_level = indentlevel; ctx.need_prefix = 1; if((sndims = H5Sget_simple_extent_ndims(f_space)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); ctx.ndims = (unsigned)sndims; /* assume entire data space to be printed */ if (ctx.ndims > 0) for (i = 0; i < (size_t) ctx.ndims; i++) ctx.p_min_idx[i] = 0; if(H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); ctx.size_last_dim = total_size[ctx.ndims - 1]; h5tools_display_simple_subset(stream, info, &ctx, dset, p_type, sset, f_space, total_size); /* Terminate the output */ if (ctx.cur_column) { fputs(OPT(info->line_suf, ""), stdout); putc('\n', stdout); fputs(OPT(info->line_sep, ""), stdout); } CATCH if(f_space >= 0 && H5Sclose(f_space) < 0) H5E_THROW(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Print some values from a dataset with a simple data space. * Description: * This is a special case of h5tools_dump_dset(). This function only * intended for dumping datasets -- it does strip mining and some other * things which are unnecessary for smaller objects such as attributes * (to print small objects like attributes simply read the attribute and * call h5tools_dump_simple_mem()). * Return: * On success, the function returns SUCCEED. Otherwise, the function * returns FAIL. *------------------------------------------------------------------------- */ static int h5tools_dump_simple_dset(FILE *stream, const h5tool_format_t *info, hid_t dset, hid_t p_type, int indentlevel) { hid_t f_space; /* file data space */ hsize_t elmtno; /* counter */ size_t i; /* counter */ int carry; /* counter carry value */ hsize_t zero[8]; /* vector of zeros */ unsigned int flags; /* buffer extent flags */ hsize_t total_size[H5S_MAX_RANK]; /* total size of dataset*/ /* Print info */ h5tools_context_t ctx; /* print context */ size_t p_type_nbytes; /* size of memory type */ hsize_t p_nelmts; /* total selected elmts */ /* Stripmine info */ hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */ hsize_t sm_nbytes; /* bytes per stripmine */ hsize_t sm_nelmts; /* elements per stripmine*/ unsigned char *sm_buf = NULL; /* buffer for raw data */ hid_t sm_space; /* stripmine data space */ /* Hyperslab info */ hsize_t hs_offset[H5S_MAX_RANK]; /* starting offset */ hsize_t hs_size[H5S_MAX_RANK]; /* size this pass */ hsize_t hs_nelmts; /* elements in request */ /* VL data special information */ unsigned int vl_data = 0; /* contains VL datatypes */ f_space = H5Dget_space(dset); if (f_space == FAIL) return FAIL; /* * Check that everything looks okay. The dimensionality must not be too * great and the dimensionality of the items selected for printing must * match the dimensionality of the dataset. */ memset(&ctx, 0, sizeof(ctx)); ctx.ndims = H5Sget_simple_extent_ndims(f_space); if ((size_t)ctx.ndims > NELMTS(sm_size)) { H5Sclose(f_space); return FAIL; } ctx.indent_level = indentlevel; ctx.need_prefix = 1; /* Assume entire data space to be printed */ if (ctx.ndims > 0) for (i = 0; i < (size_t)ctx.ndims; i++) ctx.p_min_idx[i] = 0; H5Sget_simple_extent_dims(f_space, total_size, NULL); /* calculate the number of elements we're going to print */ p_nelmts = 1; if (ctx.ndims > 0) { for (i = 0; i < ctx.ndims; i++) p_nelmts *= total_size[i]; ctx.size_last_dim = (total_size[ctx.ndims - 1]); } /* end if */ else ctx.size_last_dim = 0; if (p_nelmts == 0) { /* nothing to print */ H5Sclose(f_space); return SUCCEED; } /* Check if we have VL data in the dataset's datatype */ if (h5tools_detect_vlen_str(p_type) == TRUE) vl_data = TRUE; if (H5Tdetect_class(p_type, H5T_VLEN) == TRUE) vl_data = TRUE; /* * Determine the strip mine size and allocate a buffer. The strip mine is * a hyperslab whose size is manageable. */ sm_nbytes = p_type_nbytes = H5Tget_size(p_type); if (ctx.ndims > 0) { for (i = ctx.ndims; i > 0; --i) { hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes; if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */ size = 1; sm_size[i - 1] = MIN(total_size[i - 1], size); sm_nbytes *= sm_size[i - 1]; assert(sm_nbytes > 0); } } if(!sm_nbytes) goto done; assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/ sm_buf = (unsigned char *)HDmalloc((size_t)sm_nbytes); sm_nelmts = sm_nbytes / p_type_nbytes; sm_space = H5Screate_simple(1, &sm_nelmts, NULL); if (ctx.ndims > 0) init_acc_pos(&ctx, total_size); /* The stripmine loop */ memset(hs_offset, 0, sizeof hs_offset); memset(zero, 0, sizeof zero); for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) { /* Calculate the hyperslab size */ if (ctx.ndims > 0) { for (i = 0, hs_nelmts = 1; i < ctx.ndims; i++) { hs_size[i] = MIN(total_size[i] - hs_offset[i], sm_size[i]); ctx.p_max_idx[i] = ctx.p_min_idx[i] + hs_size[i]; hs_nelmts *= hs_size[i]; } H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL); H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL); } else { H5Sselect_all(f_space); H5Sselect_all(sm_space); hs_nelmts = 1; } /* Read the data */ if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) { H5Sclose(f_space); H5Sclose(sm_space); free(sm_buf); return FAIL; } /* Print the data */ flags = (elmtno == 0) ? START_OF_DATA : 0; flags |= ((elmtno + hs_nelmts) >= p_nelmts) ? END_OF_DATA : 0; /* initialize the current stripmine position; this is necessary to print the array indices */ ctx.sm_pos = elmtno; h5tools_dump_simple_data(stream, info, dset, &ctx, flags, hs_nelmts, p_type, sm_buf); /* Reclaim any VL memory, if necessary */ if (vl_data) H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf); /* Calculate the next hyperslab offset */ for (i = ctx.ndims, carry = 1; i > 0 && carry; --i) { ctx.p_min_idx[i - 1] = ctx.p_max_idx[i - 1]; hs_offset[i - 1] += hs_size[i - 1]; if (hs_offset[i - 1] == total_size[i - 1]) hs_offset[i - 1] = 0; else carry = 0; } ctx.continuation++; } /* Terminate the output */ if (ctx.cur_column) { fputs(OPT(info->line_suf, ""), stream); putc('\n', stream); fputs(OPT(info->line_sep, ""), stream); } HDfree(sm_buf); done: H5Sclose(sm_space); H5Sclose(f_space); return SUCCEED; } /*------------------------------------------------------------------------- * Function: h5tools_dump_simple_mem * * Purpose: Print some values from memory with a simple data space. * This is a special case of h5tools_dump_mem(). * * Return: Success: SUCCEED * Failure: FAIL * *------------------------------------------------------------------------- */ static int h5tools_dump_simple_mem(FILE *stream, const h5tool_format_t *info, hid_t obj_id, hid_t type, hid_t space, void *mem, int indentlevel) { int i; /*counters */ hsize_t nelmts; /*total selected elmts */ h5tools_context_t ctx; /*printing context */ /* * Check that everything looks okay. The dimensionality must not be too * great and the dimensionality of the items selected for printing must * match the dimensionality of the dataset. */ memset(&ctx, 0, sizeof(ctx)); ctx.ndims = H5Sget_simple_extent_ndims(space); if ((size_t) ctx.ndims > NELMTS(ctx.p_min_idx)) return FAIL; ctx.indent_level = indentlevel; ctx.need_prefix = 1; /* Assume entire data space to be printed */ for (i = 0; i < ctx.ndims; i++) ctx.p_min_idx[i] = 0; H5Sget_simple_extent_dims(space, ctx.p_max_idx, NULL); for (i = 0, nelmts = 1; ctx.ndims != 0 && i < ctx.ndims; i++) nelmts *= ctx.p_max_idx[i] - ctx.p_min_idx[i]; if (nelmts == 0) return SUCCEED; /*nothing to print*/ if (ctx.ndims > 0) { assert(ctx.p_max_idx[ctx.ndims - 1] == (hsize_t) ((int) ctx.p_max_idx[ctx.ndims - 1])); ctx.size_last_dim = (int) (ctx.p_max_idx[ctx.ndims - 1]); } /* end if */ else ctx.size_last_dim = 0; if (ctx.ndims > 0) init_acc_pos(&ctx, ctx.p_max_idx); /* Print it */ h5tools_dump_simple_data(stream, info, obj_id, &ctx, START_OF_DATA | END_OF_DATA, nelmts, type, mem); /* Terminate the output */ if (ctx.cur_column) { fputs(OPT(info->line_suf, ""), stream); putc('\n', stream); fputs(OPT(info->line_sep, ""), stream); } return SUCCEED; } /*------------------------------------------------------------------------- * Function: h5tools_dump_dset * * Purpose: Print some values from a dataset DSET to the file STREAM * after converting all types to P_TYPE (which should be a * native type). If P_TYPE is a negative value then it will be * computed from the dataset type using only native types. * * Note: This function is intended only for datasets since it does * some things like strip mining which are unnecessary for * smaller objects such as attributes. The easiest way to print * small objects is to read the object into memory and call * h5tools_dump_mem(). * * Return: Success: SUCCEED * Failure: FAIL * * Modifications: * Robb Matzke, 1999-06-07 * If info->raw is set then the memory datatype will be the same * as the file datatype. * * Bill Wendling, 2001-02-27 * Renamed to ``h5tools_dump_dset'' and added the subsetting * parameter. * *------------------------------------------------------------------------- */ int h5tools_dump_dset(FILE *stream, const h5tool_format_t *info, hid_t dset, hid_t _p_type, struct subset_t *sset, int indentlevel) { hid_t f_space; hid_t p_type = _p_type; hid_t f_type; H5S_class_t space_type; int status = FAIL; h5tool_format_t info_dflt; /* Use default values */ if (!stream) stream = stdout; if (!info) { memset(&info_dflt, 0, sizeof info_dflt); info = &info_dflt; } if (p_type < 0) { f_type = H5Dget_type(dset); if (info->raw || bin_form == 1) p_type = H5Tcopy(f_type); else if (bin_form == 2) p_type = h5tools_get_little_endian_type(f_type); else if (bin_form == 3) p_type = h5tools_get_big_endian_type(f_type); else p_type = h5tools_get_native_type(f_type); H5Tclose(f_type); if (p_type < 0) goto done; } /* Check the data space */ f_space = H5Dget_space(dset); space_type = H5Sget_simple_extent_type(f_space); /* Print the data */ if (space_type == H5S_SIMPLE || space_type == H5S_SCALAR) { if(!sset) status = h5tools_dump_simple_dset(rawdatastream, info, dset, p_type, indentlevel); else status = h5tools_dump_simple_subset(rawdatastream, info, dset, p_type, sset, indentlevel); } else /* space is H5S_NULL */ status = SUCCEED; /* Close the dataspace */ H5Sclose(f_space); done: if (p_type != _p_type) H5Tclose(p_type); return status; } /*------------------------------------------------------------------------- * Function: h5tools_dump_mem * * Purpose: Displays the data contained in MEM. MEM must have the * specified data TYPE and SPACE. Currently only simple data * spaces are allowed and only the `all' selection. * * Return: Success: SUCCEED * Failure: FAIL * *------------------------------------------------------------------------- */ int h5tools_dump_mem(FILE *stream, const h5tool_format_t *info, hid_t obj_id, hid_t type, hid_t space, void *mem, int indentlevel) { HERR_INIT(int, SUCCEED) h5tool_format_t info_dflt; /* Use default values */ if (!stream) stream = stdout; if (!info) { memset(&info_dflt, 0, sizeof(info_dflt)); info = &info_dflt; } /* Check the data space */ if (H5Sis_simple(space) <= 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sis_simple failed") H5_LEAVE(h5tools_dump_simple_mem(stream, info, obj_id, type, space, mem, indentlevel)) CATCH return ret_value; } /*------------------------------------------------------------------------- * Function: print_datatype * * Purpose: print the datatype. * * Return: void * * In/Out: h5tools_str_t *buffer * h5tools_context_t *ctx * *------------------------------------------------------------------------- */ int h5tools_print_datatype(h5tools_str_t *buffer, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t type) { HERR_INIT(int, SUCCEED) char *mname; hid_t mtype, str_type; int snmembers; unsigned nmembers; int sndims; unsigned i; size_t size = 0; hsize_t dims[H5TOOLS_DUMP_MAX_RANK]; H5T_str_t str_pad; H5T_cset_t cset; H5T_order_t order; H5T_class_t type_class; hid_t super; hid_t tmp_type; htri_t is_vlstr = FALSE; const char *order_s = NULL; /* byte order string */ H5T_sign_t sign; /* sign scheme value */ const char *sign_s = NULL; /* sign scheme string */ if((type_class = H5Tget_class(type)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_class failed"); switch (type_class) { case H5T_INTEGER: if (H5Tequal(type, H5T_STD_I8BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_I8BE"); } else if (H5Tequal(type, H5T_STD_I8LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_I8LE"); } else if (H5Tequal(type, H5T_STD_I16BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_I16BE"); } else if (H5Tequal(type, H5T_STD_I16LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_I16LE"); } else if (H5Tequal(type, H5T_STD_I32BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_I32BE"); } else if (H5Tequal(type, H5T_STD_I32LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_I32LE"); } else if (H5Tequal(type, H5T_STD_I64BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_I64BE"); } else if (H5Tequal(type, H5T_STD_I64LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_I64LE"); } else if (H5Tequal(type, H5T_STD_U8BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_U8BE"); } else if (H5Tequal(type, H5T_STD_U8LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_U8LE"); } else if (H5Tequal(type, H5T_STD_U16BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_U16BE"); } else if (H5Tequal(type, H5T_STD_U16LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_U16LE"); } else if (H5Tequal(type, H5T_STD_U32BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_U32BE"); } else if (H5Tequal(type, H5T_STD_U32LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_U32LE"); } else if (H5Tequal(type, H5T_STD_U64BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_U64BE"); } else if (H5Tequal(type, H5T_STD_U64LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_U64LE"); } else if (H5Tequal(type, H5T_NATIVE_SCHAR) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_SCHAR"); } else if (H5Tequal(type, H5T_NATIVE_UCHAR) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_UCHAR"); } else if (H5Tequal(type, H5T_NATIVE_SHORT) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_SHORT"); } else if (H5Tequal(type, H5T_NATIVE_USHORT) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_USHORT"); } else if (H5Tequal(type, H5T_NATIVE_INT) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_INT"); } else if (H5Tequal(type, H5T_NATIVE_UINT) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_UINT"); } else if (H5Tequal(type, H5T_NATIVE_LONG) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_LONG"); } else if (H5Tequal(type, H5T_NATIVE_ULONG) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_ULONG"); } else if (H5Tequal(type, H5T_NATIVE_LLONG) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_LLONG"); } else if (H5Tequal(type, H5T_NATIVE_ULLONG) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_ULLONG"); } else { /* byte order */ if (H5Tget_size(type) > 1) { order = H5Tget_order(type); if (H5T_ORDER_LE == order) { order_s = " little-endian"; } else if (H5T_ORDER_BE == order) { order_s = " big-endian"; } else if (H5T_ORDER_VAX == order) { order_s = " mixed-endian"; } else { order_s = " unknown-byte-order"; } } else { order_s = ""; } /* sign */ if ((sign = H5Tget_sign(type)) >= 0) { if (H5T_SGN_NONE == sign) { sign_s = " unsigned"; } else if (H5T_SGN_2 == sign) { sign_s = ""; } else { sign_s = " unknown-sign"; } } else { sign_s = " unknown-sign"; } /* print size, order, and sign */ h5tools_str_append(buffer, "%lu-bit%s%s integer", (unsigned long) (8 * H5Tget_size(type)), order_s, sign_s); } break; case H5T_FLOAT: if (H5Tequal(type, H5T_IEEE_F32BE) == TRUE) { h5tools_str_append(buffer, "H5T_IEEE_F32BE"); } else if (H5Tequal(type, H5T_IEEE_F32LE) == TRUE) { h5tools_str_append(buffer, "H5T_IEEE_F32LE"); } else if (H5Tequal(type, H5T_IEEE_F64BE) == TRUE) { h5tools_str_append(buffer, "H5T_IEEE_F64BE"); } else if (H5Tequal(type, H5T_IEEE_F64LE) == TRUE) { h5tools_str_append(buffer, "H5T_IEEE_F64LE"); } else if (H5Tequal(type, H5T_VAX_F32) == TRUE) { h5tools_str_append(buffer, "H5T_VAX_F32"); } else if (H5Tequal(type, H5T_VAX_F64) == TRUE) { h5tools_str_append(buffer, "H5T_VAX_F64"); } else if (H5Tequal(type, H5T_NATIVE_FLOAT) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_FLOAT"); } else if (H5Tequal(type, H5T_NATIVE_DOUBLE) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_DOUBLE"); #if H5_SIZEOF_LONG_DOUBLE !=0 } else if (H5Tequal(type, H5T_NATIVE_LDOUBLE) == TRUE) { h5tools_str_append(buffer, "H5T_NATIVE_LDOUBLE"); #endif } else { /* byte order */ if (H5Tget_size(type) > 1) { order = H5Tget_order(type); if (H5T_ORDER_LE == order) { order_s = " little-endian"; } else if (H5T_ORDER_BE == order) { order_s = " big-endian"; } else if (H5T_ORDER_VAX == order) { order_s = " mixed-endian"; } else { order_s = " unknown-byte-order"; } } else { order_s = ""; } /* print size and byte order */ h5tools_str_append(buffer, "%lu-bit%s floating-point", (unsigned long) (8 * H5Tget_size(type)), order_s); } break; case H5T_TIME: h5tools_str_append(buffer, "H5T_TIME: not yet implemented"); break; case H5T_STRING: /* Make a copy of type in memory in case when TYPE is on disk, the size * will be bigger than in memory. This makes it easier to compare * types in memory. */ tmp_type = H5Tcopy(type); size = H5Tget_size(tmp_type); str_pad = H5Tget_strpad(tmp_type); cset = H5Tget_cset(tmp_type); is_vlstr = H5Tis_variable_str(tmp_type); h5tools_str_append(buffer, "H5T_STRING %s\n", h5tools_dump_header_format->strblockbegin); ctx->indent_level++; if (is_vlstr) h5tools_str_append(buffer, "%s H5T_VARIABLE;\n", STRSIZE); else h5tools_str_append(buffer, "%s %d;\n", STRSIZE, (int) size); h5tools_str_append(buffer, "%s ", STRPAD); if (str_pad == H5T_STR_NULLTERM) h5tools_str_append(buffer, "H5T_STR_NULLTERM;\n"); else if (str_pad == H5T_STR_NULLPAD) h5tools_str_append(buffer, "H5T_STR_NULLPAD;\n"); else if (str_pad == H5T_STR_SPACEPAD) h5tools_str_append(buffer, "H5T_STR_SPACEPAD;\n"); else h5tools_str_append(buffer, "H5T_STR_ERROR;\n"); h5tools_str_append(buffer, "%s ", CSET); if (cset == H5T_CSET_ASCII) h5tools_str_append(buffer, "H5T_CSET_ASCII;\n"); else h5tools_str_append(buffer, "unknown_cset;\n"); str_type = H5Tcopy(H5T_C_S1); if (is_vlstr) H5Tset_size(str_type, H5T_VARIABLE); else H5Tset_size(str_type, size); H5Tset_cset(str_type, cset); H5Tset_strpad(str_type, str_pad); h5tools_str_append(buffer, "%s ", CTYPE); /* Check C variable-length string first. Are the two types equal? */ if (H5Tequal(tmp_type, str_type)) { h5tools_str_append(buffer, "H5T_C_S1;\n"); goto done; } /* Change the endianness and see if they're equal. */ order = H5Tget_order(tmp_type); if (order == H5T_ORDER_LE) H5Tset_order(str_type, H5T_ORDER_LE); else if (order == H5T_ORDER_BE) H5Tset_order(str_type, H5T_ORDER_BE); if (H5Tequal(tmp_type, str_type)) { h5tools_str_append(buffer, "H5T_C_S1;\n"); goto done; } /* If not equal to C variable-length string, check Fortran type. */ if(H5Tclose(str_type) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); str_type = H5Tcopy(H5T_FORTRAN_S1); H5Tset_cset(str_type, cset); H5Tset_size(str_type, size); H5Tset_strpad(str_type, str_pad); /* Are the two types equal? */ if (H5Tequal(tmp_type, str_type)) { h5tools_str_append(buffer, "H5T_FORTRAN_S1;\n"); goto done; } /* Change the endianness and see if they're equal. */ order = H5Tget_order(tmp_type); if (order == H5T_ORDER_LE) H5Tset_order(str_type, H5T_ORDER_LE); else if (order == H5T_ORDER_BE) H5Tset_order(str_type, H5T_ORDER_BE); if (H5Tequal(tmp_type, str_type)) { h5tools_str_append(buffer, "H5T_FORTRAN_S1;\n"); goto done; } /* Type doesn't match any of above. */ h5tools_str_append(buffer, "unknown_one_character_type;\n "); done: if(H5Tclose(str_type) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(tmp_type) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); ctx->indent_level--; h5tools_str_append(buffer, "%s", h5tools_dump_header_format->strblockend); break; case H5T_BITFIELD: if (H5Tequal(type, H5T_STD_B8BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_B8BE"); } else if (H5Tequal(type, H5T_STD_B8LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_B8LE"); } else if (H5Tequal(type, H5T_STD_B16BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_B16BE"); } else if (H5Tequal(type, H5T_STD_B16LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_B16LE"); } else if (H5Tequal(type, H5T_STD_B32BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_B32BE"); } else if (H5Tequal(type, H5T_STD_B32LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_B32LE"); } else if (H5Tequal(type, H5T_STD_B64BE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_B64BE"); } else if (H5Tequal(type, H5T_STD_B64LE) == TRUE) { h5tools_str_append(buffer, "H5T_STD_B64LE"); } else { h5tools_str_append(buffer, "undefined bitfield"); } break; case H5T_OPAQUE: h5tools_str_append(buffer, "\n"); h5tools_str_append(buffer, "H5T_OPAQUE;\n"); { char *ttag = H5Tget_tag(type); h5tools_str_append(buffer, "OPAQUE_TAG \"%s\";\n", ttag); if (ttag) HDfree(ttag); } break; case H5T_COMPOUND: if((snmembers = H5Tget_nmembers(type)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed"); nmembers = (unsigned)snmembers; h5tools_str_append(buffer, "H5T_COMPOUND %s\n", h5tools_dump_header_format->structblockbegin); for (i = 0; i < nmembers; i++) { mname = H5Tget_member_name(type, i); if((mtype = H5Tget_member_type(type, i))>=0) { if (H5Tget_class(mtype) == H5T_COMPOUND) ctx->indent_level++; h5tools_print_datatype(buffer, info, ctx, mtype); if (H5Tget_class(mtype) == H5T_COMPOUND) ctx->indent_level--; h5tools_str_append(buffer, " \"%s\";\n", mname); if(H5Tclose(mtype) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); } else HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tget_member_type failed"); free(mname); } h5tools_str_append(buffer, "%s", h5tools_dump_header_format->structblockend); break; case H5T_REFERENCE: h5tools_str_append(buffer, "H5T_REFERENCE"); if(region_output) { if (H5Tequal(type, H5T_STD_REF_DSETREG) == TRUE) { h5tools_str_append(buffer, " { H5T_STD_REF_DSETREG }"); } else { h5tools_str_append(buffer, " { H5T_STD_REF_OBJECT }"); } } break; case H5T_ENUM: if((super = H5Tget_super(type)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed"); h5tools_str_append(buffer, "H5T_ENUM %s\n", h5tools_dump_header_format->enumblockbegin); ctx->indent_level++; h5tools_print_datatype(buffer, info, ctx, super); if(H5Tclose(super) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); h5tools_str_append(buffer, ";\n"); h5tools_print_enum(buffer, type); ctx->indent_level--; h5tools_str_append(buffer, "%s", h5tools_dump_header_format->enumblockend); break; case H5T_VLEN: if((super = H5Tget_super(type)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed"); h5tools_str_append(buffer, "H5T_VLEN %s ", h5tools_dump_header_format->vlenblockbegin); h5tools_print_datatype(buffer, info, ctx, super); if(H5Tclose(super) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); h5tools_str_append(buffer, "%s", h5tools_dump_header_format->vlenblockend); break; case H5T_ARRAY: h5tools_str_append(buffer, "H5T_ARRAY { "); /* Get array information */ if((sndims = H5Tget_array_ndims(type)) >= 0) { unsigned ndims = (unsigned)sndims; if(H5Tget_array_dims2(type, dims) >= 0) { /* Print array dimensions */ for (i = 0; i < ndims; i++) h5tools_str_append(buffer, "[%d]", (int) dims[i]); h5tools_str_append(buffer, " "); } else HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tget_array_dims2 failed"); } else HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tget_array_ndims failed"); /* Get array base type */ if((super = H5Tget_super(type)) >= 0) { /* Print base type */ h5tools_print_datatype(buffer, info, ctx, super); /* Close array base type */ if(H5Tclose(super) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); } else HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tget_super failed"); h5tools_str_append(buffer, " }"); break; default: h5tools_str_append(buffer, "unknown datatype"); break; } CATCH return ret_value; } /*------------------------------------------------------------------------- * Function: print_dataspace * * Purpose: print the dataspace. * * Return: void * * In/Out: h5tools_str_t *buffer * h5tools_context_t *ctx * *------------------------------------------------------------------------- */ int h5tools_print_dataspace(h5tools_str_t *buffer, hid_t space) { HERR_INIT(int, SUCCEED) hsize_t size[H5TOOLS_DUMP_MAX_RANK]; hsize_t maxsize[H5TOOLS_DUMP_MAX_RANK]; int ndims = -1; H5S_class_t space_type = -1; int i; if((ndims = H5Sget_simple_extent_dims(space, size, maxsize)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); if((space_type = H5Sget_simple_extent_type(space)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_type failed"); switch(space_type) { case H5S_SCALAR: /* scalar dataspace */ h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedescriptionbegin, S_SCALAR); break; case H5S_SIMPLE: /* simple dataspace */ h5tools_str_append(buffer, "%s %s { %s %" H5_PRINTF_LL_WIDTH "u", h5tools_dump_header_format->dataspacedescriptionbegin, S_SIMPLE, h5tools_dump_header_format->dataspacedimbegin, size[0]); for(i = 1; i < ndims; i++) h5tools_str_append(buffer, ", %" H5_PRINTF_LL_WIDTH "u", size[i]); h5tools_str_append(buffer, " %s / ", h5tools_dump_header_format->dataspacedimend); if(maxsize[0] == H5S_UNLIMITED) h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedimbegin, "H5S_UNLIMITED"); else h5tools_str_append(buffer, "%s %" H5_PRINTF_LL_WIDTH "u", h5tools_dump_header_format->dataspacedimbegin, maxsize[0]); for(i = 1; i < ndims; i++) if(maxsize[i] == H5S_UNLIMITED) h5tools_str_append(buffer, ", %s", "H5S_UNLIMITED"); else h5tools_str_append(buffer, ", %" H5_PRINTF_LL_WIDTH "u", maxsize[i]); h5tools_str_append(buffer, " %s }", h5tools_dump_header_format->dataspacedimend); break; case H5S_NULL: /* null dataspace */ h5tools_str_append(buffer, "%s %s", h5tools_dump_header_format->dataspacedescriptionbegin, S_NULL); break; case H5S_NO_CLASS: default: h5tools_str_append(buffer, "%s unknown dataspace %s\n", BEGIN, END); break; } /* end switch */ CATCH return ret_value; } /*------------------------------------------------------------------------- * Function: print_enum * * Purpose: prints the enum data * * Return: void * * In/Out: h5tools_str_t *buffer * h5tools_context_t *ctx * *-----------------------------------------------------------------------*/ int h5tools_print_enum(h5tools_str_t *buffer, hid_t type) { HERR_INIT(int, SUCCEED) char **name = NULL; /*member names */ unsigned char *value = NULL; /*value array */ unsigned char *copy = NULL; /*a pointer to value array */ unsigned nmembs = 0; /*number of members */ int nchars; /*number of output characters */ hid_t super = -1; /*enum base integer type */ hid_t native = -1; /*native integer datatype */ H5T_sign_t sign_type; /*sign of value type */ size_t type_size; /*value type size */ size_t dst_size; /*destination value type size */ int snmembs; unsigned i; if((snmembs = H5Tget_nmembers(type)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers failed"); nmembs = (unsigned)snmembs; assert(nmembs > 0); if((super = H5Tget_super(type)) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_super failed"); if((type_size = H5Tget_size(type)) <= 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size(type) failed"); /* * Determine what datatype to use for the native values. To simplify * things we entertain three possibilities: * 1. long long -- the largest native signed integer * 2. unsigned long long -- the largest native unsigned integer * 3. raw format */ if(type_size <= sizeof(long long)) { dst_size = sizeof(long long); if((sign_type = H5Tget_sign(type))<0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_sign failed"); if(H5T_SGN_NONE == sign_type) native = H5T_NATIVE_ULLONG; else native = H5T_NATIVE_LLONG; } /* end if */ else dst_size = type_size; /* Get the names and raw values of all members */ if(NULL == (name = (char **)HDcalloc(nmembs, sizeof(char *)))) H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for member name"); if(NULL == (value = (unsigned char *)HDcalloc(nmembs, MAX(type_size, dst_size)))) H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for member value"); for (i = 0; i < nmembs; i++) { name[i] = H5Tget_member_name(type, i); if(H5Tget_member_value(type, i, value + i * type_size) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_member_value failed"); } /* Convert values to native datatype */ if (native > 0) if(H5Tconvert(super, native, nmembs, value, NULL, H5P_DEFAULT) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tconvert failed"); /* * Sort members by increasing value * ***not implemented yet*** */ /* Print members */ for (i = 0; i < nmembs; i++) { h5tools_str_append(buffer, "\"%s\"", name[i]); nchars = strlen(name[i]); h5tools_str_append(buffer, "%*s ", MAX(0, 16 - nchars), ""); if (native < 0) { size_t j; h5tools_str_append(buffer, "0x"); for (j = 0; j < dst_size; j++) h5tools_str_append(buffer, "%02x", value[i * dst_size + j]); } else if (H5T_SGN_NONE == H5Tget_sign(native)) { /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" *strangely, unless use another pointer "copy".*/ copy = value + i * dst_size; h5tools_str_append(buffer, "%" H5_PRINTF_LL_WIDTH "u", *((unsigned long long *) ((void *) copy))); } else { /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size" *strangely, unless use another pointer "copy".*/ copy = value + i * dst_size; h5tools_str_append(buffer, "%" H5_PRINTF_LL_WIDTH "d", *((long long *) ((void *) copy))); } h5tools_str_append(buffer, ";\n"); } CATCH if(name) { /* Release resources */ for(i = 0; i < nmembs; i++) if(name[i]) free(name[i]); free(name); } /* end if */ if(value) free(value); if(super >= 0 && H5Tclose(super) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not close datatype's super class"); if(0 == nmembs) h5tools_str_append(buffer, "\n"); return ret_value; } /*------------------------------------------------------------------------- * Function: dump_datatype * * Purpose: Dump the datatype. Datatype can be HDF5 predefined * atomic datatype or committed/transient datatype. * * Return: void * * In/Out: h5tools_context_t *ctx *------------------------------------------------------------------------- */ void h5tools_dump_datatype(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t type) { size_t ncols = 80; /* available output width */ h5tools_str_t buffer; /* string into which to render */ hsize_t curr_pos; /* total data element position */ hsize_t elmt_counter = 0;/* counts the # elements printed.*/ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); if (info->line_ncols > 0) ncols = info->line_ncols; /* 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; h5tools_simple_prefix(stream, info, ctx, curr_pos, 0); /* Render the element */ h5tools_str_reset(&buffer); ctx->indent_level++; h5tools_str_append(&buffer, "%s %s ", h5tools_dump_header_format->datatypebegin, h5tools_dump_header_format->datatypeblockbegin); h5tools_print_datatype(&buffer, info, ctx, type); if (HDstrlen(h5tools_dump_header_format->datatypeblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeblockend); if (HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(&buffer, " "); } if (HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeend); h5tools_str_append(&buffer, "\n"); curr_pos = h5tools_render_element(stream, info, ctx, &buffer, &curr_pos, ncols, elmt_counter, 0); ctx->need_prefix = TRUE; ctx->indent_level--; } /*------------------------------------------------------------------------- * 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; assert(ctx->ndims); ctx->acc[ctx->ndims - 1] = 1; for (i = (ctx->ndims - 2); i >= 0; i--) { ctx->acc[i] = ctx->acc[i + 1] * dims[i + 1]; } for (i = 0; i < ctx->ndims; i++) ctx->pos[i] = 0; } /*------------------------------------------------------------------------- * Function: do_bin_output * * Purpose: Dump memory buffer to a binary file stream * * Return: Success: SUCCEED * Failure: FAIL *------------------------------------------------------------------------- */ static int do_bin_output(FILE *stream, hid_t container, hsize_t nelmts, hid_t tid, void *_mem) { HERR_INIT(int, SUCCEED) unsigned char *mem = (unsigned char*)_mem; size_t size; /* datum size */ hsize_t i; /* element counter */ if((size = H5Tget_size(tid)) == 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); for (i = 0; i < nelmts; i++) { if (render_bin_output(stream, container, tid, mem + i * size) < 0) { printf("\nError in writing binary stream\n"); return FAIL; } } CATCH return ret_value; } /*------------------------------------------------------------------------- * Function: render_bin_output * * Purpose: Write one element of memory buffer to a binary file stream * * Return: Success: SUCCEED * Failure: FAIL *------------------------------------------------------------------------- */ static int render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem) { HERR_INIT(int, SUCCEED) unsigned char *mem = (unsigned char*)_mem; size_t size; /* datum size */ float tempfloat; double tempdouble; unsigned long long tempullong; long long templlong; unsigned long tempulong; long templong; unsigned int tempuint; int tempint; unsigned short tempushort; short tempshort; unsigned char tempuchar; char tempschar; #if H5_SIZEOF_LONG_DOUBLE !=0 long double templdouble; #endif #ifdef DEBUG_H5DUMP_BIN static char fmt_llong[8], fmt_ullong[8]; if (!fmt_llong[0]) { sprintf(fmt_llong, "%%%sd", H5_PRINTF_LL_WIDTH); sprintf(fmt_ullong, "%%%su", H5_PRINTF_LL_WIDTH); } #endif if((size = H5Tget_size(tid)) == 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); if (H5Tequal(tid, H5T_NATIVE_FLOAT)) { memcpy(&tempfloat, mem, sizeof(float)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%g ", tempfloat); #else if (1 != fwrite(&tempfloat, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_DOUBLE)) { memcpy(&tempdouble, mem, sizeof(double)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%g ", tempdouble); #else if (1 != fwrite(&tempdouble, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } #if H5_SIZEOF_LONG_DOUBLE !=0 else if (H5Tequal(tid, H5T_NATIVE_LDOUBLE)) { memcpy(&templdouble, mem, sizeof(long double)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%Lf ", templdouble); #else if (1 != fwrite(&templdouble, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } #endif else if (H5T_STRING == H5Tget_class(tid)) { unsigned int i; H5T_str_t pad; char *s; pad = H5Tget_strpad(tid); if (H5Tis_variable_str(tid)) { s = *(char**) mem; if (s != NULL) size = HDstrlen(s); } else { s = (char *) mem; if((size = H5Tget_size(tid)) == 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); } for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) { memcpy(&tempuchar, &s[i], sizeof(unsigned char)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%d", tempuchar); #else if (1 != fwrite(&tempuchar, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } /* i */ } else if (H5Tequal(tid, H5T_NATIVE_INT)) { memcpy(&tempint, mem, sizeof(int)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%d ", tempint); #else if (1 != fwrite(&tempint, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_UINT)) { memcpy(&tempuint, mem, sizeof(unsigned int)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%u ", tempuint); #else if (1 != fwrite(&tempuint, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_SCHAR)) { memcpy(&tempschar, mem, sizeof(char)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%d ", tempschar); #else if (1 != fwrite(&tempschar, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_UCHAR)) { memcpy(&tempuchar, mem, sizeof(unsigned char)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%u ", tempuchar); #else if (1 != fwrite(&tempuchar, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_SHORT)) { memcpy(&tempshort, mem, sizeof(short)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%d ", tempshort); #else if (1 != fwrite(&tempshort, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_USHORT)) { memcpy(&tempushort, mem, sizeof(unsigned short)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%u ", tempushort); #else if (1 != fwrite(&tempushort, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_LONG)) { memcpy(&templong, mem, sizeof(long)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%ld ", templong); #else if (1 != fwrite(&templong, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_ULONG)) { memcpy(&tempulong, mem, sizeof(unsigned long)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%lu ", tempulong); #else if (1 != fwrite(&tempulong, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_LLONG)) { memcpy(&templlong, mem, sizeof(long long)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, fmt_llong, templlong); #else if (1 != fwrite(&templlong, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_ULLONG)) { memcpy(&tempullong, mem, sizeof(unsigned long long)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, fmt_ullong, tempullong); #else if (1 != fwrite(&tempullong, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (H5Tequal(tid, H5T_NATIVE_HSSIZE)) { if (sizeof(hssize_t) == sizeof(int)) { memcpy(&tempint, mem, sizeof(int)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%d ", tempint); #else if (1 != fwrite(&tempint, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (sizeof(hssize_t) == sizeof(long)) { memcpy(&templong, mem, sizeof(long)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%ld ", templong); #else if (1 != fwrite(&templong, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else { memcpy(&templlong, mem, sizeof(long long)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, fmt_llong, templlong); #else if (1 != fwrite(&templlong, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } } else if (H5Tequal(tid, H5T_NATIVE_HSIZE)) { if (sizeof(hsize_t) == sizeof(int)) { memcpy(&tempuint, mem, sizeof(unsigned int)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%u ", tempuint); #else if (1 != fwrite(&tempuint, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else if (sizeof(hsize_t) == sizeof(long)) { memcpy(&tempulong, mem, sizeof(unsigned long)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%lu ", tempulong); #else if (1 != fwrite(&tempulong, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else { memcpy(&tempullong, mem, sizeof(unsigned long long)); #ifdef DEBUG_H5DUMP_BIN fprintf(stream, fmt_ullong, tempullong); #else if (1 != fwrite(&tempullong, size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } } else if (H5Tget_class(tid) == H5T_COMPOUND) { unsigned j; hid_t memb; unsigned nmembs; size_t offset; nmembs = H5Tget_nmembers(tid); for (j = 0; j < nmembs; j++) { offset = H5Tget_member_offset(tid, j); memb = H5Tget_member_type(tid, j); if (render_bin_output(stream, container, memb, mem + offset) < 0) return FAIL; H5Tclose(memb); } } else if (H5Tget_class(tid) == H5T_ENUM) { unsigned int i; if (1 == size) { #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "0x%02x", mem[0]); #else if (1 != fwrite(&mem[0], size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else { for (i = 0; i < size; i++) { #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%s%02x", i?":":"", mem[i]); #else if (1 != fwrite(&mem[i], sizeof(char), 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } /*i*/ }/*else 1 */ } else if (H5Tget_class(tid) == H5T_ARRAY) { int k, ndims; hsize_t i, dims[H5S_MAX_RANK], temp_nelmts, nelmts; hid_t memb; /* get the array's base datatype for each element */ memb = H5Tget_super(tid); size = H5Tget_size(memb); ndims = H5Tget_array_ndims(tid); H5Tget_array_dims2(tid, dims); assert(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; } /* dump the array element */ for (i = 0; i < nelmts; i++) { if (render_bin_output(stream, container, memb, mem + i * size) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed"); } H5Tclose(memb); } else if (H5Tget_class(tid) == H5T_VLEN) { unsigned int i; hsize_t nelmts; hid_t memb; /* get the VL sequences's base datatype for each element */ memb = H5Tget_super(tid); size = H5Tget_size(memb); /* Get the number of sequence elements */ nelmts = ((hvl_t *) mem)->len; for (i = 0; i < nelmts; i++) { /* dump the array element */ if (render_bin_output(stream, container, memb, ((char *) (((hvl_t *) mem)->p)) + i * size) < 0) H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed"); } H5Tclose(memb); } else if (H5Tequal(tid, H5T_STD_REF_DSETREG)) { if (region_output) { /* region data */ hid_t region_id, region_space; H5S_sel_type region_type; 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_id >= 0) */ } /* end if (region_output... */ } else if (H5Tequal(tid, H5T_STD_REF_OBJ)) { } else { size_t i; if (1 == size) { #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "0x%02x", mem[0]); #else if (1 != fwrite(&mem[0], size, 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } else { for (i = 0; i < size; i++) { #ifdef DEBUG_H5DUMP_BIN fprintf(stream, "%s%02x", i?":":"", mem[i]); #else if (1 != fwrite(&mem[i], sizeof(char), 1, stream)) H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed"); #endif } /*i*/ }/*else 1 */ } CATCH return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Print the data values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to print the data in a region reference of type blocks. * * Return: * The function returns FAIL if there was an error, otherwise SUCEED * *------------------------------------------------------------------------- */ static int render_bin_output_region_data_blocks(hid_t region_id, FILE *stream, hid_t container, int ndims, hid_t type_id, hssize_t nblocks, hsize_t *ptdata) { hsize_t *dims1 = NULL; hsize_t *start = NULL; hsize_t *count = NULL; size_t numelem; hsize_t total_size[H5S_MAX_RANK]; int jndx; int type_size; hid_t mem_space = -1; void *region_buf = NULL; int blkndx; hid_t sid1 = -1; int ret_value = SUCCEED; /* Get the dataspace of the dataset */ if((sid1 = H5Dget_space(region_id)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed"); /* Allocate space for the dimension array */ if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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(ndims, dims1, NULL)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed"); if((type_size = H5Tget_size(type_id)) == 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); if((region_buf = HDmalloc(type_size * numelem)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for start"); if((count = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "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) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); if(H5Dread(region_id, type_id, mem_space, sid1, H5P_DEFAULT, region_buf) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dread failed"); if(H5Sget_simple_extent_dims(mem_space, total_size, NULL) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); for (jndx = 0; jndx < numelem; jndx++) { render_bin_output(stream, container, type_id, ((char*)region_buf + jndx * type_size)); /* Render the region data element end */ } /* end for (jndx = 0; jndx < numelem; jndx++) */ } /* end for (blkndx = 0; blkndx < nblocks; blkndx++) */ done: HDfree(start); HDfree(count); HDfree(region_buf); HDfree(dims1); if(H5Sclose(mem_space) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); if(H5Sclose(sid1) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Print some values from a dataset referenced by region blocks. * * Description: * This is a special case subfunction to dump a region reference using blocks. * * Return: * The function returns False if ERROR, otherwise True * *------------------------------------------------------------------------- */ static hbool_t render_bin_output_region_blocks(hid_t region_space, hid_t region_id, FILE *stream, hid_t container) { HERR_INIT(hbool_t, TRUE) hssize_t nblocks; hsize_t alloc_size; hsize_t *ptdata = NULL; int ndims; hid_t dtype; hid_t type_id; if((nblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0) H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed"); /* Print block information */ if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]); assert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/ if((ptdata = (hsize_t*) malloc((size_t) alloc_size)) == NULL) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata"); H5_CHECK_OVERFLOW(nblocks, hssize_t, hsize_t); if(H5Sget_select_hyper_blocklist(region_space, (hsize_t) 0, (hsize_t) nblocks, ptdata) < 0) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Rget_select_hyper_blocklist failed"); if((dtype = H5Dget_type(region_id)) < 0) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed"); if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Tget_native_type failed"); render_bin_output_region_data_blocks(region_id, stream, container, ndims, type_id, nblocks, ptdata); done: free(ptdata); if(H5Tclose(type_id) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(dtype) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); H5_LEAVE(TRUE) CATCH return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: 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, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata) { hsize_t *dims1 = NULL; int jndx; int type_size; hid_t mem_space = -1; void *region_buf = NULL; int ret_value = SUCCEED; if((type_size = H5Tget_size(type_id)) == 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); if((region_buf = HDmalloc(type_size * npoints)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for region"); /* Allocate space for the dimension array */ if((dims1 = (hsize_t *) HDmalloc(sizeof(hsize_t) * ndims)) == NULL) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not allocate buffer for dims"); dims1[0] = npoints; if((mem_space = H5Screate_simple(1, dims1, NULL)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Screate_simple failed"); if(H5Dread(region_id, type_id, mem_space, region_space, H5P_DEFAULT, region_buf) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); for (jndx = 0; jndx < npoints; jndx++) { if(H5Sget_simple_extent_dims(region_space, dims1, NULL) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed"); render_bin_output(stream, container, type_id, ((char*)region_buf + jndx * type_size)); } /* end for (jndx = 0; jndx < npoints; jndx++) */ done: HDfree(region_buf); HDfree(dims1); if(H5Sclose(mem_space) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose failed"); return ret_value; } /*------------------------------------------------------------------------- * Audience: Public * Chapter: H5Tools Library * Purpose: Print some values from a dataset referenced by region points. * * Description: * This is a special case subfunction to dump a region reference using points. * * Return: * The function returns False if the last dimension has been reached, otherwise True * *------------------------------------------------------------------------- */ static hbool_t render_bin_output_region_points(hid_t region_space, hid_t region_id, FILE *stream, hid_t container) { HERR_INIT(hbool_t, TRUE) hssize_t npoints; hsize_t alloc_size; hsize_t *ptdata; int ndims; hid_t dtype; hid_t type_id; if((npoints = H5Sget_select_elem_npoints(region_space)) <= 0) H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed"); /* Allocate space for the dimension array */ if((ndims = H5Sget_simple_extent_ndims(region_space)) < 0) H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); alloc_size = npoints * ndims * sizeof(ptdata[0]); assert(alloc_size == (hsize_t) ((size_t) alloc_size)); /*check for overflow*/ if(NULL == (ptdata = (hsize_t *)HDmalloc((size_t) alloc_size))) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "Could not allocate buffer for ptdata"); H5_CHECK_OVERFLOW(npoints, hssize_t, hsize_t); if(H5Sget_select_elem_pointlist(region_space, (hsize_t) 0, (hsize_t) npoints, ptdata) < 0) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_pointlist failed"); if((dtype = H5Dget_type(region_id)) < 0) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Dget_type failed"); if((type_id = H5Tget_native_type(dtype, H5T_DIR_DEFAULT)) < 0) HGOTO_ERROR(FALSE, H5E_tools_min_id_g, "H5Tget_native_type failed"); render_bin_output_region_data_points(region_space, region_id, stream, container, ndims, type_id, npoints, ptdata); done: free(ptdata); if(H5Tclose(type_id) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); if(H5Tclose(dtype) < 0) HERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Tclose failed"); H5_LEAVE(ret_value) CATCH 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 *------------------------------------------------------------------------- */ static 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. * * Programmer: Peter Cao * 4/27/2011 * *------------------------------------------------------------------------- */ 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 = 0; if ( name1 && strcmp(name1, ".")) H5Oget_info_by_name(loc_id1, name1, &oinfo1, H5P_DEFAULT); else H5Oget_info(loc_id1, &oinfo1); if ( name2 && strcmp(name2, ".")) 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; }