diff options
| -rw-r--r-- | tools/h5dump/h5dump.c | 55 | ||||
| -rw-r--r-- | tools/lib/h5tools.c | 379 |
2 files changed, 248 insertions, 186 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c index eaf56c9..c6b5708 100644 --- a/tools/h5dump/h5dump.c +++ b/tools/h5dump/h5dump.c @@ -390,9 +390,9 @@ struct handler_t { */ #if 0 /* binary: not implemented yet */ -static const char *s_opts = "hbBHvVa:d:g:l:t:w:xD:o:s:T:c:k:"; +static const char *s_opts = "hbBHvVa:d:g:l:t:w:xD:o:s:S:c:k:"; #else -static const char *s_opts = "hBHvVa:d:g:l:t:w:xD:o:s:T:c:k:"; +static const char *s_opts = "hBHvVa:d:g:l:t:w:xD:o:s:S:c:k:"; #endif /* 0 */ static struct long_options l_opts[] = { { "help", no_arg, 'h' }, @@ -1713,7 +1713,7 @@ dump_dims(hsize_t *s, int dims) register int i; for (i = 0; i < dims; i++) { - printf("%u", s[i]); + printf("%u", (unsigned int)s[i]); if (i + 1 != dims) printf(", "); @@ -2038,8 +2038,8 @@ parse_subset_params(char *dset) /* sanity check to make sure the [ isn't part of the dataset name */ if (brace > slash) { *brace++ = '\0'; - s = calloc(1, sizeof(struct subset_t)); + s = calloc(1, sizeof(struct subset_t)); s->start = parse_hsize_list(brace); while (*brace && *brace != ';') @@ -2103,6 +2103,45 @@ handle_datasets(hid_t fid, char *dset, void *data) return; } + if (sset) { + /* check that all of the subsetting parameters are okay */ + if (!sset->count) { + error_msg(progname, "`count' argument missing for subsetting\n"); + exit(EXIT_FAILURE); + } + + if (!sset->start || !sset->stride || !sset->block) { + /* they didn't specify a ``stride'' or ``block''. default to 1 in all + * dimensions */ + hid_t sid = H5Dget_space(dsetid); + unsigned int ndims = H5Sget_simple_extent_ndims(sid); + + H5Sclose(sid); + + if (!sset->start) + /* default to (0, 0, ...) for the start coord */ + sset->start = calloc(ndims, sizeof(hsize_t)); + + if (!sset->stride) { + unsigned int i; + + sset->stride = calloc(ndims, sizeof(hsize_t)); + + for (i = 0; i < ndims; i++) + sset->stride[i] = 1; + } + + if (!sset->block) { + unsigned int i; + + sset->block = calloc(ndims, sizeof(hsize_t)); + + for (i = 0; i < ndims; i++) + sset->block[i] = 1; + } + } + } + H5Gget_objinfo(dsetid, ".", TRUE, &statbuf); if (statbuf.nlink > 1) { @@ -2445,7 +2484,7 @@ parse_start: /** begin subsetting parameters **/ case 's': - case 'T': + case 'S': case 'c': case 'k': { struct subset_t *s; @@ -2471,7 +2510,7 @@ parse_start: * slightly convoluted, but...we are only interested in options * for subsetting: "--start", "--stride", "--count", and "--block" * which can come in any order. If we run out of parameters (EOF) - * or run into one which isn't a subsetting parameter (NOT s, T, + * or run into one which isn't a subsetting parameter (NOT s, S, * c, or K), then we exit the do-while look, set the subset_info * to the structure we've been filling. If we've reached the end * of the options, we exit the parsing (goto parse_end) otherwise, @@ -4465,15 +4504,17 @@ xml_print_strs(hid_t did, int source) ssiz *= H5Tget_size(type); buf = calloc((size_t)ssiz, sizeof(char)); + if (buf == NULL) { return FAIL; } + e = H5Dread(did, type, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); + if (e < 0) { free(buf); return FAIL; } - } else if (source == ATTRIBUTE_DATA) { space = H5Aget_space(did); ssiz = H5Sget_simple_extent_npoints(space); diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c index c76cdf4..2341c7f 100644 --- a/tools/lib/h5tools.c +++ b/tools/lib/h5tools.c @@ -28,7 +28,7 @@ #define H5TOOLS_BUFSIZE (1024 * 1024) #else #define H5TOOLS_BUFSIZE (1024) -#endif +#endif /* 1 */ #define ALIGN(A,Z) ((((A) + (Z) - 1) / (Z)) * (Z)) @@ -44,17 +44,17 @@ FILE *rawdatastream; /* should initialize to stdout but gcc moans about it static int h5tools_init_g; /* if h5tools lib has been initialized */ /*------------------------------------------------------------------------- - * Function: h5tools_init - * - * Purpose: Initialize the H5 Tools library. - * 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 - * + * 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: *------------------------------------------------------------------------- */ @@ -70,18 +70,18 @@ h5tools_init(void) } /*------------------------------------------------------------------------- - * Function: h5tools_close - * - * Purpose: Close the H5 Tools library by closing or releasing 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 - * + * 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: *------------------------------------------------------------------------- */ @@ -101,43 +101,47 @@ h5tools_close(void) } /*------------------------------------------------------------------------- - * Function: h5tools_fopen - * - * Purpose: Attempts to open a file with various VFL drivers. - * - * Return: Success: 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. - * - * Failure: -1. If DRIVERNAME is non-null then the - * first byte is set to the null terminator. - * + * 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). + * 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 + * 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 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 + * 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. + * 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. + * 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, 2001-01-10 + * 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. *------------------------------------------------------------------------- */ hid_t @@ -148,11 +152,11 @@ h5tools_fopen(const char *fname, char *drivername, size_t drivername_size) hid_t fapl; } driver[16]; static int ndrivers = 0; + register int drivernum; hid_t fid = -1; #ifndef VERSION12 hid_t fapl = H5P_DEFAULT; #endif /* !VERSION12 */ - int drivernum; if (!ndrivers) { /* Build a list of file access property lists which we should try @@ -203,7 +207,8 @@ h5tools_fopen(const char *fname, char *drivername, size_t drivername_size) strncpy(drivername, driver[drivernum].name, drivername_size); drivername[drivername_size - 1] = '\0'; } else { - drivername[0] = '\0'; /*no file opened*/ + /*no file opened*/ + drivername[0] = '\0'; } } @@ -211,21 +216,18 @@ h5tools_fopen(const char *fname, char *drivername, size_t drivername_size) } /*------------------------------------------------------------------------- - * Function: h5tools_ncols - * - * Purpose: Count the number of columns in a string. This is the number - * of characters in the string not counting line-control - * characters. - * - * Return: Success: Width of string. - * - * Failure: 0 - * - * Programmer: Robb Matzke - * Tuesday, April 27, 1999 - * + * 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 @@ -241,21 +243,21 @@ h5tools_ncols(const char *s) } /*------------------------------------------------------------------------- - * Function: h5tools_simple_prefix - * - * Purpose: If ctx->need_prefix is set then terminate the current line - * (if applicable), calculate the prefix string, and display it - * at the start of a line. - * - * Return: void - * - * Programmer: Robb Matzke - * Monday, April 26, 1999 - * + * 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. + * Robb Matzke, 1999-09-29 + * If a new prefix is printed then the current element number is set back + * to zero. *------------------------------------------------------------------------- */ static void @@ -287,10 +289,10 @@ h5tools_simple_prefix(FILE *stream, const h5dump_t *info, indentlevel = ctx->indent_level; } else { /* - * this is because sometimes we dont print out all the header - * info for the data(like the tattr-2.ddl example. if that happens - * the ctx->indent_level a negative so we need to skip the above - * and just print out the default indent levels. + * 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; } @@ -318,31 +320,28 @@ h5tools_simple_prefix(FILE *stream, const h5dump_t *info, } /*------------------------------------------------------------------------- - * Function: h5tools_dump_simple_data - * - * Purpose: 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: void - * - * Programmer: Robb Matzke - * Monday, April 26, 1999 - * + * 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, 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 @@ -494,19 +493,17 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container, } /*------------------------------------------------------------------------- - * Function: h5tools_dump_simple_subset - * - * Purpose: - * - * Return: Success: SUCCEED - * - * Failure: FAIL - * - * Programmer: Bill Wendling - * Wednesday, 07. March 2001 - * + * 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 @@ -524,7 +521,6 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset, /* 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 */ @@ -533,6 +529,8 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset, 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); @@ -560,54 +558,80 @@ h5tools_dump_simple_subset(FILE *stream, const h5dump_t *info, hid_t dset, H5Sget_simple_extent_dims(f_space, total_size, NULL); ctx.size_last_dim = total_size[ctx.ndims - 1]; - /* calculate the potential number of elements we're going to print */ - H5Sselect_hyperslab(f_space, H5S_SELECT_SET, sset->start, sset->stride, - sset->count, sset->block); - p_nelmts = H5Sget_select_npoints(f_space); + count = sset->count[ctx.ndims - 1]; + sset->count[ctx.ndims - 1] = 1; - if (p_nelmts == 0) { - /* nothing to print */ - ret = SUCCEED; - goto done_close; - } + 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, sset->start, sset->stride, + sset->count, sset->block); + sm_nelmts = H5Sget_select_npoints(f_space); - /* - * 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); + /* + * 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 (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); + if (sm_nelmts == 0) { + /* nothing to print */ + ret = SUCCEED; + goto done_close; } - assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/ - sm_buf = malloc((size_t)p_nelmts * p_type_nbytes); - sm_nelmts = p_nelmts; - sm_space = H5Screate_simple(1, &sm_nelmts, NULL); + /* + * 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); - H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, &zero, NULL, &sm_nelmts, NULL); + 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); + } - /* 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; - } + 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); - /* Print the data */ - flags = START_OF_DATA | END_OF_DATA; + H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, &zero, NULL, &sm_nelmts, NULL); - 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]); - } + /* 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; - h5tools_dump_simple_data(stream, info, dset, &ctx, flags, sm_nelmts, - p_type, sm_buf); + 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) { @@ -625,24 +649,21 @@ done: } /*------------------------------------------------------------------------- - * Function: h5tools_dump_simple_dset - * + * Audience: Public + * Chapter: H5Tools Library * Purpose: Print some values from a dataset with a simple data space. - * 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: Success: SUCCEED - * - * Failure: FAIL - * - * Programmer: Robb Matzke - * Thursday, July 23, 1998 - * + * 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 |