/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * 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_str.h" #include "h5tools_utils.h" #include "hdf5.h" #include "H5private.h" /* * The output functions need a temporary buffer to hold a piece of the * dataset while it's being printed. This constant sets the limit on the * size of that temporary buffer in bytes. For efficiency's sake, choose the * largest value suitable for your machine (for testing use a small value). */ #if 1 #define H5TOOLS_BUFSIZE (1024 * 1024) #else #define H5TOOLS_BUFSIZE (1024) #endif /* 1 */ #define ALIGN(A,Z) ((((A) + (Z) - 1) / (Z)) * (Z)) #define START_OF_DATA 0x0001 #define END_OF_DATA 0x0002 /* global variables */ int indent; int compound_data; FILE *rawdatastream; /* should initialize to stdout but gcc moans about it */ /* module-scoped variables */ static int h5tools_init_g; /* if h5tools lib has been initialized */ /*------------------------------------------------------------------------- * 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) { if (!h5tools_init_g) { if (!rawdatastream) rawdatastream = stdout; 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; } h5tools_init_g = 0; } } /*------------------------------------------------------------------------- * 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, const char *driver, char *drivername, size_t drivername_size) { static struct d_list { const char *name; hid_t fapl; } drivers_list[] = { { "sec2", FAIL } ,{ "family", FAIL } ,{ "split", FAIL } ,{ "multi", FAIL } #ifdef H5_HAVE_STREAM ,{ "stream", FAIL } #endif /* H5_HAVE_STREAM */ }; /* 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 */ }; #define NUM_DRIVERS (sizeof(drivers_list) / sizeof(struct d_list)) static int initialized = 0; size_t drivernum; hid_t fid = FAIL; #ifndef VERSION12 hid_t fapl = H5P_DEFAULT; #endif /* !VERSION12 */ if (!initialized) { /* Build a list of file access property lists which we should try * when opening the file. Eventually we'd like some way for the * user to augment/replace this list interactively. */ ++initialized; /* SEC2 Driver */ drivers_list[SEC2_IDX].fapl = H5P_DEFAULT; #ifndef VERSION12 /* FAMILY Driver */ drivers_list[FAMILY_IDX].fapl = fapl = H5Pcreate(H5P_FILE_ACCESS); H5Pset_fapl_family(fapl, (hsize_t)0, H5P_DEFAULT); /* SPLIT Driver */ drivers_list[SPLIT_IDX].fapl = fapl = H5Pcreate(H5P_FILE_ACCESS); H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT); /* MULTI Driver */ drivers_list[MULTI_IDX].fapl = fapl = H5Pcreate(H5P_FILE_ACCESS); H5Pset_fapl_multi(fapl, NULL, NULL, NULL, NULL, TRUE); #ifdef H5_HAVE_STREAM /* STREAM Driver */ drivers_list[STREAM_IDX].fapl = fapl = H5Pcreate(H5P_FILE_ACCESS); H5Pset_fapl_stream(fapl, NULL); #endif /* H5_HAVE_STREAM */ #endif /* !VERSION12 */ } if (driver && *driver) { /* 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, drivers_list[SEC2_IDX].name)) { H5E_BEGIN_TRY { fid = H5Fopen(fname, H5F_ACC_RDONLY, drivers_list[SEC2_IDX].fapl); } H5E_END_TRY; if (fid == FAIL) goto done; drivernum = SEC2_IDX; } else if (!strcmp(driver, drivers_list[FAMILY_IDX].name)) { H5E_BEGIN_TRY { fid = H5Fopen(fname, H5F_ACC_RDONLY, drivers_list[FAMILY_IDX].fapl); } H5E_END_TRY; if (fid == FAIL) goto done; drivernum = FAMILY_IDX; } else if (!strcmp(driver, drivers_list[SPLIT_IDX].name)) { H5E_BEGIN_TRY { fid = H5Fopen(fname, H5F_ACC_RDONLY, drivers_list[SPLIT_IDX].fapl); } H5E_END_TRY; if (fid == FAIL) goto done; drivernum = SPLIT_IDX; } else if (!strcmp(driver, drivers_list[MULTI_IDX].name)) { H5E_BEGIN_TRY { fid = H5Fopen(fname, H5F_ACC_RDONLY, drivers_list[MULTI_IDX].fapl); } H5E_END_TRY; if (fid == FAIL) goto done; drivernum = MULTI_IDX; #ifdef H5_HAVE_STREAM } else if (!strcmp(driver, drivers_list[STREAM_IDX].name)) { H5E_BEGIN_TRY { fid = H5Fopen(fname, H5F_ACC_RDONLY, drivers_list[STREAM_IDX].fapl); } H5E_END_TRY; if (fid == FAIL) goto done; drivernum = STREAM_IDX; #endif /* H5_HAVE_STREAM */ } else { goto done; } } else { /* Try to open the file using each of the drivers */ for (drivernum = 0; drivernum < NUM_DRIVERS; drivernum++) { H5E_BEGIN_TRY { fid = H5Fopen(fname, H5F_ACC_RDONLY, drivers_list[drivernum].fapl); } H5E_END_TRY; if (fid != FAIL) break; } } /* Save the driver name */ if (drivername && drivername_size) { if (fid != FAIL) { strncpy(drivername, drivers_list[drivernum].name, drivername_size); drivername[drivername_size - 1] = '\0'; } else { /*no file opened*/ drivername[0] = '\0'; } } done: 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; } /*------------------------------------------------------------------------- * 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. *------------------------------------------------------------------------- */ static void h5tools_simple_prefix(FILE *stream, const h5dump_t *info, h5tools_context_t *ctx, hsize_t elmtno, int secnum) { h5tools_str_t prefix; size_t templength = 0; int i, indentlevel = 0; if (!ctx->need_prefix) return; memset(&prefix, 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->p_min_idx, ctx->p_max_idx); /* 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; } 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++){ fputs(h5tools_str_fmt(&prefix, 0, info->line_indent), stream); templength += h5tools_str_len(&prefix); } ctx->cur_column = ctx->prev_prefix_len = templength; ctx->cur_elmt = 0; ctx->need_prefix = 0; /* Free string */ h5tools_str_close(&prefix); } /*------------------------------------------------------------------------- * 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. *------------------------------------------------------------------------- */ static void h5tools_dump_simple_data(FILE *stream, const h5dump_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 */ char *s, *section; /*a section of output */ int secnum; /*section sequence number */ size_t size; /*size of each datum */ size_t ncols = 80; /*available output width */ h5tools_str_t buffer; /*string into which to render */ int multiline; /*datum was multiline */ int 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. */ /* Setup */ memset(&buffer, 0, sizeof(h5tools_str_t)); size = H5Tget_size(type); if (info->line_ncols > 0) ncols = info->line_ncols; h5tools_simple_prefix(stream, info, ctx, (hsize_t)0, 0); for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) { /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_sprint(&buffer, info, container, type, mem + i * size, ctx); if (i + 1 < nelmts || (flags & END_OF_DATA) == 0) h5tools_str_append(&buffer, "%s", OPT(info->elmt_suf1, ",")); 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; elmt_counter = 0; } } /* * 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. */ 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 || i) && (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++; h5tools_simple_prefix(stream, info, ctx, i, secnum); } else if ((i || 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; } h5tools_str_close(&buffer); } /*------------------------------------------------------------------------- * 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. * Return: * On success, return SUCCEED. Otherwise, the function returns FAIL. * Programmer: * Bill Wendling, Wednesday, 07. March 2001 * Modifications: *------------------------------------------------------------------------- */ static herr_t h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, struct subset_t *sset, int indentlevel) { herr_t ret; /*the value to return */ hid_t f_space; /*file data space */ hsize_t i; /*counters */ hssize_t zero = 0; /*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 */ /* 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 */ hsize_t count; ret = FAIL; /* be pessimistic */ f_space = H5Dget_space(dset); if (f_space == FAIL) goto done; /* * 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; ctx.ndims = H5Sget_simple_extent_ndims(f_space); if ((size_t)ctx.ndims > NELMTS(sm_size)) goto done_close; /* assume entire data space to be printed */ if (ctx.ndims > 0) for (i = 0; i < (hsize_t)ctx.ndims; i++) ctx.p_min_idx[i] = 0; H5Sget_simple_extent_dims(f_space, total_size, NULL); ctx.size_last_dim = (int)total_size[ctx.ndims - 1]; count = sset->count[ctx.ndims - 1]; sset->count[ctx.ndims - 1] = 1; for (; count > 0; sset->start[ctx.ndims - 1] += sset->stride[ctx.ndims - 1], count--) { /* calculate the potential number of elements we're going to print */ H5Sselect_hyperslab(f_space, H5S_SELECT_SET, (hssize_t*)sset->start, (hsize_t*)sset->stride, (hsize_t*)sset->count, (hsize_t*)sset->block); sm_nelmts = H5Sget_select_npoints(f_space); /* * start (0, 0) * block (2, 2) * stride (15, 5) * count (4, 3) * * make: * * for up to "count" times. * * start (0, += stride[last_dim]) * block (2, 2) * stride (15, 5) * count (4, 1) */ if (sm_nelmts == 0) { /* nothing to print */ ret = SUCCEED; goto done_close; } /* * 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) { sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes); sm_nbytes *= sm_size[i - 1]; assert(sm_nbytes > 0); } assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/ sm_buf = malloc((size_t)sm_nelmts * p_type_nbytes); sm_space = H5Screate_simple(1, &sm_nelmts, NULL); H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, &zero, NULL, &sm_nelmts, NULL); /* 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 = START_OF_DATA; if (count == 1) flags |= END_OF_DATA; for (i = 0; i < (hsize_t)ctx.ndims; i++) { ctx.p_max_idx[i] = ctx.p_min_idx[i] + MIN(total_size[i], sm_size[i]); } h5tools_dump_simple_data(stream, info, dset, &ctx, flags, sm_nelmts, p_type, sm_buf); free(sm_buf); ctx.continuation++; } /* Terminate the output */ if (ctx.cur_column) { fputs(OPT(info->line_suf, ""), stream); putc('\n', stream); fputs(OPT(info->line_sep, ""), stream); } ret = SUCCEED; done_close: H5Sclose(f_space); done: return ret; } /*------------------------------------------------------------------------- * 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. * Programmer: * Robb Matzke, Thursday, July 23, 1998 * Modifications: *------------------------------------------------------------------------- */ static int h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int indentlevel) { hid_t f_space; /*file data space */ hsize_t elmtno, i; /*counters */ int carry; /*counter carry value */ hssize_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 */ hssize_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.indent_level = indentlevel; ctx.need_prefix = 1; ctx.ndims = H5Sget_simple_extent_ndims(f_space); if ((size_t)ctx.ndims > NELMTS(sm_size)) { H5Sclose(f_space); return FAIL; } /* Assume entire data space to be printed */ if (ctx.ndims > 0) for (i = 0; i < (hsize_t)ctx.ndims; i++) ctx.p_min_idx[i] = 0; H5Sget_simple_extent_dims(f_space, total_size, NULL); ctx.size_last_dim = (int)total_size[ctx.ndims - 1]; /* calculate the number of elements we're going to print */ p_nelmts = 1; if (ctx.ndims > 0) for (i = 0, p_nelmts = 1; i < (hsize_t)ctx.ndims; i++) p_nelmts *= total_size[i]; if (p_nelmts == 0) { /* nothing to print */ H5Sclose(f_space); return SUCCEED; } /* Check if we have VL data in the dataset's datatype */ 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) { sm_size[i - 1] = MIN(total_size[i - 1], H5TOOLS_BUFSIZE / sm_nbytes); sm_nbytes *= sm_size[i - 1]; assert(sm_nbytes > 0); } } assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/ sm_buf = malloc((size_t)sm_nbytes); sm_nelmts = sm_nbytes / p_type_nbytes; sm_space = H5Screate_simple(1, &sm_nelmts, NULL); /* 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 < (hsize_t)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; 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] == (hssize_t)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); } H5Sclose(sm_space); H5Sclose(f_space); free(sm_buf); 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 * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static int h5tools_dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t obj_id, hid_t type, hid_t space, void *mem, int indentlevel) { hsize_t 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 < (hsize_t)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 < (hsize_t)ctx.ndims; i++) nelmts *= ctx.p_max_idx[i] - ctx.p_min_idx[i]; if (nelmts == 0) return SUCCEED; /*nothing to print*/ ctx.size_last_dim = (int)(ctx.p_max_idx[ctx.ndims - 1]); /* 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_fixtype * * Purpose: Given a file data type choose a memory data type which is * appropriate for printing the data. * * Return: Success: Memory data type * * Failure: FAIL * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Modifications: * Robb Matzke, 1999-06-04 * Added support for references. * *------------------------------------------------------------------------- */ hid_t h5tools_fixtype(hid_t f_type) { hid_t m_type = FAIL, f_memb; hid_t *memb = NULL; char **name = NULL; int nmembs = 0, i; int ndims; hsize_t dim[H5S_MAX_RANK]; size_t size, offset; hid_t array_base; /* H5T_str_t strpad; */ size = H5Tget_size(f_type); switch (H5Tget_class(f_type)) { case H5T_INTEGER: /* * Use the smallest native integer type of the same sign as the file * such that the memory type is at least as large as the file type. * If there is no memory type large enough then use the largest * memory type available. */ if (size <= sizeof(char)) { m_type = H5Tcopy(H5T_NATIVE_SCHAR); } else if (size <= sizeof(short)) { m_type = H5Tcopy(H5T_NATIVE_SHORT); } else if (size <= sizeof(int)) { m_type = H5Tcopy(H5T_NATIVE_INT); } else if (size <= sizeof(long)) { m_type = H5Tcopy(H5T_NATIVE_LONG); } else { m_type = H5Tcopy(H5T_NATIVE_LLONG); } H5Tset_sign(m_type, H5Tget_sign(f_type)); break; case H5T_FLOAT: /* * Use the smallest native floating point type available such that * its size is at least as large as the file type. If there is not * native type large enough then use the largest native type. */ if (size <= sizeof(float)) { m_type = H5Tcopy(H5T_NATIVE_FLOAT); } else if (size <= sizeof(double)) { m_type = H5Tcopy(H5T_NATIVE_DOUBLE); } else { m_type = H5Tcopy(H5T_NATIVE_LDOUBLE); } break; case H5T_STRING: /* * This is needed because the function in dumputil.c is the case where * strDUAction == TRUE. if it is false we will do the original action * here. */ m_type = H5Tcopy(f_type); H5Tset_cset(m_type, H5T_CSET_ASCII); break; case H5T_COMPOUND: /* * We have to do this in two steps. The first step scans the file * type and converts the members to native types and remembers all * their names and sizes, computing the size of the memory compound * type at the same time. Then we create the memory compound type * and add the members. */ nmembs = H5Tget_nmembers(f_type); assert(nmembs > 0); memb = calloc((size_t)nmembs, sizeof(hid_t)); name = calloc((size_t)nmembs, sizeof(char *)); for (i = 0, size = 0; i < nmembs; i++) { /* Get the member type and fix it */ f_memb = H5Tget_member_type(f_type, i); #ifdef WANT_H5_V1_2_COMPAT /* v1.2 returns the base type of an array field, work around this */ { hid_t new_f_memb; /* datatype for array, if necessary */ int arrndims; /* Array rank for reading */ size_t dims[H5S_MAX_RANK]; /* Array dimensions for reading */ hsize_t arrdims[H5S_MAX_RANK]; /* Array dimensions for reading */ int j; /* Local index variable */ /* Get the array dimensions */ arrndims=H5Tget_member_dims(f_type,i,dims,NULL); /* Patch up array information */ if(arrndims>0) { for(j=0; j= 0) H5Tclose(memb[j]); if (name[j]) free(name[j]); } free(memb); free(name); } return m_type; } /*------------------------------------------------------------------------- * 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 * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * 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 h5dump_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; int status = FAIL; h5dump_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) p_type = H5Tcopy(f_type); else p_type = h5tools_fixtype(f_type); H5Tclose(f_type); if (p_type < 0) goto done; } /* Check the data space */ f_space = H5Dget_space(dset); /* Print the data */ if (H5Sis_simple(f_space) > 0) { 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); } /* 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 * * Programmer: Robb Matzke * Wednesday, January 20, 1999 * * Modifications: * *------------------------------------------------------------------------- */ int h5tools_dump_mem(FILE *stream, const h5dump_t *info, hid_t obj_id, hid_t type, hid_t space, void *mem, int indentlevel) { h5dump_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) return -1; return h5tools_dump_simple_mem(stream, info, obj_id, type, space, mem, indentlevel); }