diff options
| -rw-r--r-- | tools/h5tools.c | 273 |
1 files changed, 119 insertions, 154 deletions
diff --git a/tools/h5tools.c b/tools/h5tools.c index 78a8258..0a62934 100644 --- a/tools/h5tools.c +++ b/tools/h5tools.c @@ -26,7 +26,7 @@ int compound_data; int nCols = 80; FILE *rawdatastream; /* should initialize to stdout but gcc moans about it */ -static int h5tools_init_g = 0; /* if h5tools lib has been initialized */ +static int h5tools_init_g = 0; /* if h5tools lib has been initialized */ int print_data(hid_t oid, hid_t _p_type, int obj_data); @@ -126,9 +126,10 @@ static int h5dump_vlen_dset(FILE *, const h5dump_t *, hid_t, hid_t, int); void h5tools_init(void) { - if (!h5tools_init_g){ + if (!h5tools_init_g) { if (!rawdatastream) rawdatastream = stdout; + h5tools_init_g++; } } @@ -152,13 +153,14 @@ h5tools_init(void) void h5tools_close(void) { - if (h5tools_init_g){ - if (rawdatastream && rawdatastream != stdout){ + if (h5tools_init_g) { + if (rawdatastream && rawdatastream != stdout) { if (fclose(rawdatastream)) perror("closing rawdatastream"); else rawdatastream = NULL; } + h5tools_init_g = 0; } } @@ -584,12 +586,14 @@ h5dump_region(hid_t region, h5dump_str_t *str/*in,out*/, const h5dump_t *info) /* Print block information */ if (nblocks > 0) { - int i, j; + int i; ptdata = malloc(nblocks * ndims * 2 * sizeof(ptdata[0])); H5Sget_select_hyper_blocklist(region, 0, nblocks, ptdata); for (i = 0; i < nblocks; i++) { + int j; + h5dump_str_append(str, info->dset_blockformat_pre, i ? "," OPTIONAL_LINE_BREAK " " : "", (unsigned long)i); @@ -610,12 +614,14 @@ h5dump_region(hid_t region, h5dump_str_t *str/*in,out*/, const h5dump_t *info) /* Print point information */ if (npoints > 0) { - int i, j; + int i; ptdata = malloc(npoints * ndims * sizeof(ptdata[0])); H5Sget_select_elem_pointlist(region, 0, npoints, ptdata); for (i = 0; i < npoints; i++) { + int j; + h5dump_str_append(str, info->dset_ptformat_pre , i ? "," OPTIONAL_LINE_BREAK " " : "", (unsigned long)i); @@ -934,13 +940,12 @@ h5dump_sprint(h5dump_str_t *str/*in,out*/, const h5dump_t *info, * indentation. Be warned that column number calculations will be * incorrect and that object indices at the beginning of the line * will be missing (h5dump doesn't display them anyway). */ - if (ctx->indent_level >= 0 && - str->len && '\n'==str->s[str->len-1]) { + if (ctx->indent_level >= 0 && str->len && + str->s[str->len - 1] == '\n') { h5dump_str_append(str, OPT(info->line_pre, ""), ""); - for (x=0; x<ctx->indent_level+1; x++) { + for (x = 0; x < ctx->indent_level + 1; x++) h5dump_str_append(str, "%s", OPT(info->line_indent, "")); - } } /* The name */ @@ -997,13 +1002,12 @@ h5dump_sprint(h5dump_str_t *str/*in,out*/, const h5dump_t *info, * (h5dump doesn't display them anyway). */ h5dump_str_append(str, "%s", OPT(info->cmpd_end, "")); - if (ctx->indent_level >= 0 && - str->len && '\n'==str->s[str->len-1]) { + if (ctx->indent_level >= 0 && str->len && + str->s[str->len - 1] == '\n') { h5dump_str_append(str, OPT(info->line_pre, ""), ""); - for (x = 0; x < ctx->indent_level; x++) { + for (x = 0; x < ctx->indent_level; x++) h5dump_str_append(str, "%s", OPT(info->line_indent, "")); - } } h5dump_str_append(str, "%s", OPT(info->cmpd_suf, "}")); @@ -1273,7 +1277,7 @@ h5dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container, for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++){ /* Render the element */ h5dump_str_reset(&buffer); - h5dump_sprint(&buffer, info, container, type, mem+i*size, ctx); + h5dump_sprint(&buffer, info, container, type, mem + i * size, ctx); if (i + 1 < nelmts || 0 == (flags & END_OF_DATA)) h5dump_str_append(&buffer, "%s", OPT(info->elmt_suf1, ",")); @@ -1306,9 +1310,11 @@ h5dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container, } } - /* we need to break after each row of a dimension---> we should + /* + * 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 */ + * way the dumper did it before + */ if (info->arr_linebreak && ctx->cur_elmt){ if ((ctx->cur_elmt % ctx->size_last_dim) == 0) ctx->need_prefix = TRUE; @@ -1351,8 +1357,10 @@ h5dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container, * start a new line. */ - /* added the info->skip_first because the dumper does not want - * this check to happen for the first 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, " ")) + @@ -1438,13 +1446,12 @@ h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, #endif /* - * Check that everything looks okay. The dimensionality must not be too + * 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.indent_level = indentlevel; ctx.need_prefix = 1; f_space = H5Dget_space(dset); ctx.ndims = H5Sget_simple_extent_ndims(f_space); @@ -1467,13 +1474,13 @@ h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, ctx.size_last_dim = total_size[ctx.ndims - 1]; /* - * Determine the strip mine size and allocate a buffer. The strip mine is + * Determine the strip mine size and allocate a buffer. The strip mine is * a hyperslab whose size is manageable. */ p_type_nbytes = H5Tget_size(p_type); for (i = ctx.ndims, sm_nbytes = p_type_nbytes; i > 0; --i) { - sm_size[i - 1] = MIN (total_size[i - 1], H5DUMP_BUFSIZE / sm_nbytes); + sm_size[i - 1] = MIN(total_size[i - 1], H5DUMP_BUFSIZE / sm_nbytes); sm_nbytes *= sm_size[i - 1]; assert(sm_nbytes > 0); } @@ -1490,7 +1497,7 @@ h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, /* 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]); + 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]; } @@ -1504,7 +1511,7 @@ h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, H5Sselect_all(sm_space); hs_nelmts = 1; } - + /* Read the data */ if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0) return -1; @@ -1573,13 +1580,14 @@ h5dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t type, * 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(space); if ((size_t)ctx.ndims > NELMTS(ctx.p_min_idx)) return -1; + 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; @@ -1593,7 +1601,6 @@ h5dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t type, return 0; /*nothing to print*/ ctx.size_last_dim = ctx.p_max_idx[ctx.ndims - 1]; - ctx.indent_level = indentlevel; /* Print it */ h5dump_simple_data(stream, info, -1/*no dataset*/, &ctx, @@ -1702,7 +1709,7 @@ h5dump_fixtype(hid_t f_type) memb = calloc(nmembs, sizeof(hid_t)); name = calloc(nmembs, sizeof(char *)); ndims = calloc(nmembs, sizeof(int)); - dims = calloc(nmembs*4, sizeof(size_t)); + dims = calloc(nmembs * 4, sizeof(size_t)); for (i = 0, size = 0; i < nmembs; i++) { int j; @@ -1890,94 +1897,64 @@ done: return status; } -static -void *vlcustom_alloc(size_t size, void *info) -{ - void *ret_value = NULL; - int *mem_used = (int *)info; - size_t extra = MAX(sizeof(void *), sizeof(size_t)); - - if ((ret_value = HDmalloc(extra + size)) != NULL) { - *(size_t *)ret_value = size; - *mem_used += size; - } - - ret_value = ((unsigned char *)ret_value) + extra; - return ret_value; -} - -static -void vlcustom_free(void *_mem, void *info) -{ - if (_mem) { - int *mem_used = (int *)info; - size_t extra = MAX(sizeof(void *), sizeof(size_t)); - unsigned char *mem = ((unsigned char *)_mem) - extra; - - *mem_used -= *(size_t *)mem; - HDfree(mem); - } -} - +/*------------------------------------------------------------------------- + * Function: h5dump_vlen_dset + * + * Purpose: Dump variable length datatypes to the STREAM. We can only + * support atomic, 1-dimensional variable length data since other + * types would be way too complicated to dump. + * + * Return: Success: 0 + * + * Failure: FAIL + * + * Programmer: Bill Wendling + * Wednesday, November 8, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ static int h5dump_vlen_dset(FILE *stream, const h5dump_t *info, hid_t dset, hid_t type, int indentlevel) { - hvl_t *rdata = NULL; /*information to read in */ + h5dump_context_t ctx; /*print context */ hid_t base_type; /*the base type of the VL data */ hid_t xfer_pid; /*dataset transfer property list id */ hid_t f_space; /*file data space */ hsize_t dims[H5S_MAX_RANK]; /*size of the dimensions */ + hid_t mem_space; const char *bad_type; - hsize_t mem_needed; - size_t ncols = 80; herr_t ret; - - /* Print info */ - size_t size; /*size of memory type */ - hsize_t p_nelmts; /*total selected elmts */ - int mem_used = 0; + hssize_t start = 0, count = 1; unsigned int i; - base_type = H5Tget_super(type); - xfer_pid = H5Pcreate(H5P_DATA_XFER); - - if (xfer_pid == FAIL) - return FAIL; - - ret = H5Pset_vlen_mem_manager(xfer_pid, vlcustom_alloc, &mem_used, - vlcustom_free, &mem_used); - - if (ret == FAIL) { - H5Pclose(xfer_pid); - return FAIL; - } - + memset(&ctx, 0, sizeof(h5dump_context_t)); + ctx.indent_level = indentlevel; + ctx.need_prefix = 1; f_space = H5Dget_space(dset); + ctx.ndims = H5Sget_simple_extent_ndims(f_space); - if ((size_t)H5Sget_simple_extent_ndims(f_space) > 1) { - fprintf(stream, - "Multidimensional variable length datatypes not supported\n"); + if (ctx.ndims > 1) { ret = FAIL; - goto done; + goto free_space; } - H5Dvlen_get_buf_size(dset, type, f_space, &mem_needed); - - H5Sget_simple_extent_dims(f_space, dims, NULL); - rdata = HDmalloc(dims[0] * sizeof(hvl_t)); + base_type = H5Tget_super(type); + xfer_pid = H5Pcreate(H5P_DATA_XFER); - if (!rdata) { + if (xfer_pid == FAIL) { ret = FAIL; - goto done; + goto free_xfer; } - ret = H5Dread(dset, type, H5S_ALL, H5S_ALL, xfer_pid, rdata); - - if (info->line_ncols > 0) - ncols = info->line_ncols; + H5Sget_simple_extent_dims(f_space, dims, NULL); + ctx.size_last_dim = dims[ctx.ndims - 1]; - size = H5Tget_size(base_type); + /* Assume entire data space to be printed */ + for (i = 0; i < (hsize_t)ctx.ndims; i++) + ctx.p_min_idx[i] = 0; recheck: switch (H5Tget_class(base_type)) { @@ -2016,78 +1993,66 @@ recheck: bad_type = "H5T_TIME"; default: fprintf(stream, - "Dumper doesn't support %s variable length datatype at this time\n", - bad_type ? bad_type : "(null)"); - goto done; + "Dumper doesn't support %s variable length datatype at this time.\n", + OPT(bad_type, "(null)")); + goto free_xfer; } + /* Create a simple memory space so that we can read in the hvl_t object */ + mem_space = H5Screate_simple(0, NULL, NULL); + for (i = 0; i < dims[0]; i++) { - hsize_t j; - - p_nelmts = rdata[i].len; - -#define OUTPUT_ELEMENTS(type, fmt) { \ - unsigned char *_data = (unsigned char *)rdata[i].p; \ - \ - indentation(indent + COL); \ - for (j = 0; j < p_nelmts; j++, _data += size) { \ - fprintf(stream, "%" ## fmt ## "%s", *(type *)_data, \ - j == p_nelmts - 1 ? "\n" : ", "); \ - } \ -} + unsigned char *buffer; + hsize_t mem_needed; + herr_t ret; + hvl_t *vldata; + h5dump_context_t tmp; - switch (H5Tget_class(base_type)) { - case H5T_INTEGER: - if (H5Tget_sign(base_type) == H5T_SGN_NONE) { - if (size <= sizeof(unsigned char)) { - OUTPUT_ELEMENTS(unsigned char, "c"); - } else if (size <= sizeof(unsigned short)) { - OUTPUT_ELEMENTS(unsigned short, "dhu"); - } else if (size <= sizeof(unsigned int)) { - OUTPUT_ELEMENTS(unsigned int, "u"); - } else if (size <= sizeof(unsigned long)) { - OUTPUT_ELEMENTS(unsigned long, "lu"); - } else { - OUTPUT_ELEMENTS(unsigned long_long, PRINTF_LL_WIDTH "u"); - } - } else { - if (size <= sizeof(char)) { - OUTPUT_ELEMENTS(char, "c"); - } else if (size <= sizeof(short)) { - OUTPUT_ELEMENTS(short, "dh"); - } else if (size <= sizeof(int)) { - OUTPUT_ELEMENTS(int, "d"); - } else if (size <= sizeof(long)) { - OUTPUT_ELEMENTS(long, "ld"); - } else { - OUTPUT_ELEMENTS(long_long, PRINTF_LL_WIDTH "d"); - } - } + start = i; + ret = H5Sselect_hyperslab(f_space, H5S_SELECT_SET, &start, NULL, &count, NULL); - break; + if (ret == FAIL) + goto free_mem; - case H5T_FLOAT: - if (size <= sizeof(float)) { - OUTPUT_ELEMENTS(float, "e"); - } else if (size <= sizeof(double)) { - OUTPUT_ELEMENTS(double, "e"); - } else { - OUTPUT_ELEMENTS(long double, "e"); - } + ret = H5Dvlen_get_buf_size(dset, type, f_space, &mem_needed); - break; + if (ret == FAIL) + goto free_mem; - default: - break; + mem_needed += sizeof(hvl_t); + buffer = calloc(mem_needed, 1); + + if (!buffer) { + indentation(indentlevel); + fprintf(stream, + "Unable to allocate %ld bytes for variable length data.\n", + (long)mem_needed); + continue; } - } - ret = H5Dvlen_reclaim(type, f_space, xfer_pid, rdata); + ret = H5Dread(dset, type, mem_space, f_space, H5P_DEFAULT, buffer); -done: + if (ret == FAIL) + goto free_mem; + + vldata = (hvl_t *)buffer; + + /* I cast, therefore, I think I know what I am doing */ + tmp = ctx; + h5dump_simple_data(stream, info, dset, &ctx, + START_OF_DATA | END_OF_DATA, + vldata->len, base_type, (void *)vldata->p); + ctx = tmp; + fputs("\n", stream); + free(buffer); + } + +free_mem: + H5Sclose(mem_space); +free_xfer: H5Pclose(xfer_pid); +free_space: H5Sclose(f_space); - free(rdata); return ret; } |