diff options
Diffstat (limited to 'tools/src/h5ls/h5ls.c')
| -rw-r--r-- | tools/src/h5ls/h5ls.c | 660 |
1 files changed, 539 insertions, 121 deletions
diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c index 5c9c693..6c21782 100644 --- a/tools/src/h5ls/h5ls.c +++ b/tools/src/h5ls/h5ls.c @@ -91,7 +91,7 @@ static h5tool_format_t ls_dataformat = { "", /*line_suf */ "", /*line_sep */ 1, /*line_multi_new */ - "", /*line_indent */ + " ", /*line_indent */ 0, /*skip_first */ @@ -132,7 +132,6 @@ static hbool_t no_dangling_link_g = FALSE; /* treat dangling link is error */ static hbool_t follow_elink_g = FALSE; /* follow external links */ static hbool_t grp_literal_g = FALSE; /* list group, not contents */ static hbool_t hexdump_g = FALSE; /* show data as raw hexadecimal */ -static hbool_t show_errors_g = FALSE; /* print HDF5 error messages */ static hbool_t simple_output_g = FALSE; /* make output more machine-readable */ static hbool_t show_file_name_g = FALSE; /* show file name for full names */ static hbool_t no_line_wrap_g = FALSE; /* show data content without line wrap */ @@ -193,7 +192,7 @@ usage (void) PRINTVALSTREAM(rawoutstream, " --no-dangling-links\n"); PRINTVALSTREAM(rawoutstream, " Must be used with --follow-symlinks option;\n"); PRINTVALSTREAM(rawoutstream, " otherwise, h5ls shows error message and returns an exit\n"); - PRINTVALSTREAM(rawoutstream, " code of 1. \n"); + PRINTVALSTREAM(rawoutstream, " code of 1.\n"); PRINTVALSTREAM(rawoutstream, " Check for any symbolic links (soft links or external links)\n"); PRINTVALSTREAM(rawoutstream, " that do not resolve to an existing object (dataset, group,\n"); PRINTVALSTREAM(rawoutstream, " or named datatype).\n"); @@ -228,11 +227,8 @@ usage (void) PRINTVALSTREAM(rawoutstream, " \"%%05d\" to open a file family.\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " Deprecated Options\n"); - PRINTVALSTREAM(rawoutstream, " The following options have been deprecated in HDF5. While they remain\n"); - PRINTVALSTREAM(rawoutstream, " available, they have been superseded as indicated and may be removed\n"); - PRINTVALSTREAM(rawoutstream, " from HDF5 in the future. Use the indicated replacement option in all\n"); - PRINTVALSTREAM(rawoutstream, " new work; where possible, existing scripts, et cetera, should also be\n"); - PRINTVALSTREAM(rawoutstream, " updated to use the replacement option.\n"); + PRINTVALSTREAM(rawoutstream, " The following options have been removed in HDF5 1.12. Use the indicated\n"); + PRINTVALSTREAM(rawoutstream, " replacement option in all work.\n"); PRINTVALSTREAM(rawoutstream, "\n"); PRINTVALSTREAM(rawoutstream, " -E or --external Follow external links.\n"); PRINTVALSTREAM(rawoutstream, " Replaced by --follow-symlinks.\n"); @@ -918,6 +914,7 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind) H5free_memory(name[i]); HDfree(name); HDfree(value); + H5Tclose(super); return FALSE; } @@ -1082,7 +1079,10 @@ print_reference_type(h5tools_str_t *buffer, hid_t type, int H5_ATTR_UNUSED ind) if (H5T_REFERENCE != H5Tget_class(type)) return FALSE; - if (H5Tequal(type, H5T_STD_REF_OBJ) == TRUE) { + if (H5Tequal(type, H5T_STD_REF) == TRUE) { + h5tools_str_append(buffer, "standard reference"); + } + else if (H5Tequal(type, H5T_STD_REF_OBJ) == TRUE) { h5tools_str_append(buffer, "object reference"); } else if (H5Tequal(type, H5T_STD_REF_DSETREG) == TRUE) { @@ -1285,6 +1285,233 @@ print_type(h5tools_str_t *buffer, hid_t type, int ind) h5tools_str_append(buffer,"%lu-byte class-%u unknown", (unsigned long)H5Tget_size(type), (unsigned)data_class); } +/* + * + */ +static void +dump_reference(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t container, H5R_ref_t *ref_buf, int ndims) +{ + H5TOOLS_ERR_INIT(int, SUCCEED) + hid_t new_obj_id = H5I_INVALID_HID; + hid_t new_obj_sid = H5I_INVALID_HID; + hsize_t elmt_counter = 0; /*counts the # elements printed. */ + size_t ncols = 80; /* available output width */ + size_t i; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t datactx; /* print context */ + + H5TOOLS_PUSH_STACK(); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "enter"); + + datactx = *ctx; /* print context */ + /* Assume entire data space to be printed */ + if (datactx.ndims > 0) + for (i = 0; i < (size_t)datactx.ndims; i++) + datactx.p_min_idx[i] = 0; + datactx.need_prefix = TRUE; + + HDmemset(&buffer, 0, sizeof(h5tools_str_t)); + for(i = 0; i < ndims; i++, datactx.cur_elmt++, elmt_counter++) { + H5O_type_t obj_type; /* Object type */ + H5R_type_t ref_type; /* Reference type */ + + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "reference loop:%d with curr_pos=%ld", i, curr_pos); + + datactx.need_prefix = TRUE; + h5tools_str_reset(&buffer); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "reference loop - h5tools_str_sprint with H5T_STD_REF:%d", i); + h5tools_str_sprint(&buffer, info, container, H5T_STD_REF, &ref_buf[i], &datactx); + h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)i, (hsize_t)ndims); + + ref_type = H5Rget_type((const H5R_ref_t *)&ref_buf[i]); + switch (ref_type) { + case H5R_OBJECT1: + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ref_type is H5R_OBJECT1"); + if (H5Rget_obj_type3((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, &obj_type) >= 0) { + switch (obj_type) { + case H5O_TYPE_DATASET: + if((new_obj_id = H5Ropen_object((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) { + datactx.indent_level++; + h5tools_dump_dset(stream, info, &datactx, new_obj_id); + datactx.indent_level--; + if(H5Dclose(new_obj_id) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose H5R_OBJECT1:H5O_TYPE_DATASET failed"); + if(H5Rdestroy(&ref_buf[i]) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rdestroy H5R_OBJECT1:H5O_TYPE_DATASET failed"); + } + else + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Ropen_object H5R_OBJECT1:H5O_TYPE_DATASET failed"); + break; + + case H5O_TYPE_GROUP: + case H5O_TYPE_NAMED_DATATYPE: + case H5O_TYPE_MAP: + case H5O_TYPE_UNKNOWN: + case H5O_TYPE_NTYPES: + default: + break; + } /* end switch */ + } + else + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rget_obj_type3 H5R_OBJECT1 failed"); + break; + case H5R_DATASET_REGION1: + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ref_type is H5R_DATASET_REGION1"); + if((new_obj_id = H5Ropen_object((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) { + datactx.indent_level++; + h5tools_dump_dset(stream, info, &datactx, new_obj_id); + datactx.indent_level--; + if(H5Dclose(new_obj_id) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose H5R_DATASET_REGION1 failed"); + if(H5Rdestroy(&ref_buf[i]) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rdestroy H5R_DATASET_REGION1 failed"); + } + else + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Ropen_object H5R_DATASET_REGION1 failed"); + break; + case H5R_OBJECT2: + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ref_type is H5R_OBJECT2"); + if (H5Rget_obj_type3((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, &obj_type) >= 0) { + switch (obj_type) { + case H5O_TYPE_GROUP: + break; + + case H5O_TYPE_DATASET: + if((new_obj_id = H5Ropen_object((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) { + datactx.indent_level++; + h5tools_dump_dset(stream, info, &datactx, new_obj_id); + datactx.indent_level--; + if(H5Oclose(new_obj_id) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Oclose H5R_OBJECT2 failed"); + if(H5Rdestroy(&ref_buf[i]) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rdestroy H5R_OBJECT2 failed"); + } + else + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Ropen_object H5R_OBJECT2 failed"); + break; + + case H5O_TYPE_NAMED_DATATYPE: + break; + + case H5O_TYPE_MAP: + case H5O_TYPE_UNKNOWN: + case H5O_TYPE_NTYPES: + default: + break; + } /* end switch */ + } + else + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rget_obj_type3 H5R_OBJECT2 failed"); + break; + case H5R_DATASET_REGION2: + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ref_type is H5R_DATASET_REGION2"); + + if (info->line_ncols > 0) + ncols = info->line_ncols; + + /* if (new_obj_id < 0) - could mean that no reference was written do not throw failure */ + if((new_obj_id = H5Ropen_object((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) < 0) + H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, + "H5Ropen_object H5R_DATASET_REGION2 failed"); + else { + if((new_obj_sid = H5Ropen_region((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) { + if (h5tools_is_zero(&ref_buf[i], H5Tget_size(H5T_STD_REF))) { + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "NULL H5R_DATASET_REGION2"); + + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " {"); + h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + + datactx.need_prefix = TRUE; + datactx.indent_level++; + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "NULL"); + h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + datactx.indent_level--; + datactx.need_prefix = TRUE; + + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "}"); + h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + } + else { + H5S_sel_type region_type; + + region_type = H5Sget_select_type(new_obj_sid); + if(region_type == H5S_SEL_POINTS) { + /* Print point information */ + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "H5S_SEL_POINTS H5R_DATASET_REGION2"); + h5tools_dump_region_data_points(new_obj_sid, new_obj_id, stream, info, &datactx, + &buffer, &curr_pos, ncols, i, elmt_counter); + } + else if(region_type == H5S_SEL_HYPERSLABS) { + /* Print block information */ + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "H5S_SEL_HYPERSLABS H5R_DATASET_REGION2"); + h5tools_dump_region_data_blocks(new_obj_sid, new_obj_id, stream, info, &datactx, + &buffer, &curr_pos, ncols, i, elmt_counter); + } + else + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "invalid region type"); + } /* end else to if (h5tools_is_zero(... */ + if(H5Sclose(new_obj_sid) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Sclose H5R_DATASET_REGION2 failed"); + } + else + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Ropen_region H5R_DATASET_REGION2 failed"); + if(H5Dclose(new_obj_id) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Dclose H5R_DATASET_REGION2 failed"); + if(H5Rdestroy(&ref_buf[i]) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rdestroy H5R_DATASET_REGION2 failed"); + } + break; + case H5R_ATTR: + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ref_type is H5R_ATTR"); + if((new_obj_id = H5Ropen_attr((const H5R_ref_t *)&ref_buf[i], H5P_DEFAULT, H5P_DEFAULT)) >= 0) { + h5tools_dump_region_attribute(new_obj_id, stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + if(H5Aclose(new_obj_id) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Aclose H5R_ATTR failed"); + if(H5Rdestroy(&ref_buf[i]) < 0) + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Rdestroy H5R_ATTR failed"); + } + else { + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "NULL H5R_ATTR"); + + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " {"); + h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + + datactx.need_prefix = TRUE; + datactx.indent_level++; + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "NULL"); + h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + datactx.indent_level--; + datactx.need_prefix = TRUE; + + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, "}"); + h5tools_render_element(stream, info, &datactx, &buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0); + + H5TOOLS_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Ropen_attr H5R_ATTR failed"); + } + break; + case H5R_BADTYPE: + case H5R_MAXTYPE: + default: + break; + } /* end switch */ + + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "finished reference loop:%d",i); + } /* end for(i = 0; i < ndims; i++, ctx->cur_elmt++, elmt_counter++) */ +done: + h5tools_str_close(&buffer); + + PRINTVALSTREAM(stream, "\n"); + + H5TOOLS_ENDDEBUG(H5E_tools_min_dbg_id_g, "exit"); + H5TOOLS_POP_STACK(); +} /*------------------------------------------------------------------------- * Function: dump_dataset_values @@ -1297,6 +1524,12 @@ print_type(h5tools_str_t *buffer, hid_t type, int ind) static void dump_dataset_values(hid_t dset) { + H5TOOLS_ERR_INIT(herr_t, SUCCEED) + hid_t f_type = H5I_INVALID_HID; + hid_t space = H5I_INVALID_HID; + hsize_t total_size[H5S_MAX_RANK]; + int ndims; + size_t i; char string_prefix[64]; static char fmt_double[16]; static char fmt_float[16]; @@ -1305,15 +1538,20 @@ dump_dataset_values(hid_t dset) h5tools_context_t ctx; /* print context */ h5tool_format_t outputformat; h5tool_format_t *info = &ls_dataformat; + H5R_ref_t *ref_buf = NULL; - hid_t f_type = H5Dget_type(dset); - size_t size = H5Tget_size(f_type); + H5TOOLS_PUSH_STACK(); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "enter"); + + f_type = H5Dget_type(dset); + space = H5Dget_space(dset); HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); outputformat = *info; outputformat.line_1st = NULL; + outputformat.idx_fmt = ""; if (simple_output_g) { outputformat.idx_fmt = ""; outputformat.line_per_line = 1; @@ -1345,9 +1583,10 @@ dump_dataset_values(hid_t dset) else { outputformat.line_ncols = (unsigned)width_g; } - if (label_g) outputformat.cmpd_name = "%s="; + if (label_g) + outputformat.cmpd_name = "%s="; outputformat.line_pre = " %s "; - outputformat.line_cont = " %s "; + outputformat.line_cont = " %s "; outputformat.str_repeat = 8; outputformat.arr_pre = NULL; @@ -1375,7 +1614,7 @@ dump_dataset_values(hid_t dset) * command line switch was given. */ outputformat.raw = TRUE; } - else if (string_g && 1 == size && H5T_INTEGER == H5Tget_class(f_type)) { + else if (string_g && H5Tget_size(f_type) == 1 && (H5Tget_class(f_type) == H5T_INTEGER)) { /* Print 1-byte integer data as an ASCI character string instead of * integers if the `-s' or `--string' command-line option was given. */ outputformat.ascii = TRUE; @@ -1387,29 +1626,244 @@ dump_dataset_values(hid_t dset) } info = &outputformat; - ctx.indent_level = 2; + ctx.indent_level = 1; ctx.cur_column = (size_t)curr_pos; /* Print all the values. */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " Data:\n"); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + ctx.need_prefix = TRUE; ctx.cur_column = (size_t)curr_pos; - if (h5tools_dump_dset(rawoutstream, info, &ctx, dset, NULL) < 0) { - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " Unable to print data."); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + if (H5Tget_class(f_type) == H5T_REFERENCE) { + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "reference class type"); + if (!H5Tequal(f_type, H5T_STD_REF) && !H5Tequal(f_type, H5T_STD_REF_DSETREG) && !H5Tequal(f_type, H5T_STD_REF_OBJ)) { + HGOTO_DONE(SUCCEED); + } + + ndims = (int)H5Sget_simple_extent_npoints(space); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ndims=%d - ctx.ndims=%d", ndims, ctx.ndims); + + /* 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(space, total_size, NULL); + if (ctx.ndims > 0) + init_acc_pos(&ctx, total_size); + ctx.need_prefix = TRUE; + + if (NULL != (ref_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), ndims))) { + H5TOOLS_DEBUG(H5E_tools_min_id_g, "H5Dread reference read"); + if(H5Dread(dset, H5T_STD_REF, H5S_ALL, H5S_ALL, H5P_DEFAULT, ref_buf) < 0) { + HDfree(ref_buf); + H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread reference failed"); + } + dump_reference(rawoutstream, info, &ctx, dset, ref_buf, ndims); + HDfree(ref_buf); + } } - + else { + if (h5tools_dump_dset(rawoutstream, info, &ctx, dset) < 0) { + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " Unable to print data."); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + } + } +done: + H5Sclose(space); H5Tclose(f_type); h5tools_str_close(&buffer); PRINTVALSTREAM(rawoutstream, "\n"); + + H5TOOLS_ENDDEBUG(H5E_tools_min_dbg_id_g, "exit"); + H5TOOLS_POP_STACK(); } /*------------------------------------------------------------------------- + * Function: dump_attribute_values + * + * Purpose: Prints all values of a attribute. + * + * Return: void + *------------------------------------------------------------------------- + */ +static void +dump_attribute_values(hid_t attr, const char *attr_name) +{ + H5TOOLS_ERR_INIT(herr_t, SUCCEED) + hid_t f_type = H5I_INVALID_HID; + hid_t space = H5I_INVALID_HID; + hsize_t total_size[H5S_MAX_RANK]; + int ndims; + size_t i; + char string_prefix[64]; + static char fmt_double[16]; + static char fmt_float[16]; + hsize_t curr_pos = 0; /* total data element position */ + h5tools_str_t buffer; /* string into which to render */ + h5tools_context_t ctx; /* print context */ + h5tool_format_t outputformat; + h5tool_format_t *info = &ls_dataformat; + H5R_ref_t *ref_buf = NULL; + + H5TOOLS_PUSH_STACK(); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "enter"); + + f_type = H5Aget_type(attr); + space = H5Aget_space(attr); + + HDmemset(&ctx, 0, sizeof(ctx)); + HDmemset(&buffer, 0, sizeof(h5tools_str_t)); + + outputformat = *info; + outputformat.line_1st = NULL; + outputformat.idx_fmt = ""; + if (simple_output_g) { + outputformat.idx_fmt = ""; + outputformat.line_per_line = 1; + outputformat.line_multi_new = 0; + outputformat.line_pre = " "; + outputformat.line_cont = " "; + + outputformat.arr_pre = ""; + outputformat.arr_suf = ""; + outputformat.arr_sep = " "; + + if (!label_g) { + outputformat.cmpd_pre = ""; + outputformat.cmpd_suf = ""; + } + outputformat.cmpd_sep = " "; + + if (label_g) + outputformat.cmpd_name = "%s="; + + outputformat.elmt_suf1 = " "; + outputformat.str_locale = ESCAPE_HTML; + + } + else { + if (no_line_wrap_g) { + outputformat.line_per_line = 1; + } + else { + outputformat.line_ncols = (unsigned)width_g; + } + if (label_g) + outputformat.cmpd_name = "%s="; + outputformat.line_pre = " %s "; + outputformat.line_cont = " %s "; + outputformat.str_repeat = 8; + + outputformat.arr_pre = NULL; + outputformat.arr_suf = NULL; + outputformat.arr_sep = NULL; + + outputformat.cmpd_pre = NULL; + outputformat.cmpd_suf = NULL; + outputformat.cmpd_sep = NULL; + + outputformat.vlen_sep = NULL; + outputformat.vlen_pre = NULL; + outputformat.vlen_suf = NULL; + outputformat.vlen_end = NULL; + } + outputformat.arr_linebreak = 0; + /* Floating point types should display full precision */ + HDsnprintf(fmt_float, sizeof(fmt_float), "%%1.%dg", FLT_DIG); + outputformat.fmt_float = fmt_float; + HDsnprintf(fmt_double, sizeof(fmt_double), "%%1.%dg", DBL_DIG); + outputformat.fmt_double = fmt_double; + + if (hexdump_g) { + /* Print all data in hexadecimal format if the `-x' or `--hexdump' + * command line switch was given. */ + outputformat.raw = TRUE; + } + else if (string_g && H5Tget_size(f_type) == 1 && (H5Tget_class(f_type) == H5T_INTEGER)) { + /* Print 1-byte integer data as an ASCI character string instead of + * integers if the `-s' or `--string' command-line option was given. */ + outputformat.ascii = TRUE; + outputformat.elmt_suf1 = ""; + outputformat.elmt_suf2 = ""; + HDsnprintf(string_prefix, sizeof(string_prefix), "%s\"", outputformat.line_pre); + outputformat.line_pre = string_prefix; + outputformat.line_suf = "\""; + } + info = &outputformat; + + ctx.indent_level = 2; + ctx.cur_column = (size_t)curr_pos; + + /* Print all the values. */ + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " Data:\n"); + + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + + ctx.need_prefix = TRUE; + ctx.cur_column = (size_t)curr_pos; + if (H5Tget_class(f_type) == H5T_REFERENCE) { + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "reference class type"); + if (!H5Tequal(f_type, H5T_STD_REF) && !H5Tequal(f_type, H5T_STD_REF_DSETREG) && !H5Tequal(f_type, H5T_STD_REF_OBJ)) { + HGOTO_DONE(SUCCEED); + } + + ndims = (int)H5Sget_simple_extent_npoints(space); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "ndims=%d - ctx.ndims=%d", ndims, ctx.ndims); + + /* 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(space, total_size, NULL); + if (ctx.ndims > 0) + init_acc_pos(&ctx, total_size); + ctx.need_prefix = TRUE; + + if (NULL != (ref_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), ndims))) { + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "H5Aread reference read"); + if(H5Aread(attr, H5T_STD_REF, ref_buf) < 0) { + HDfree(ref_buf); + H5TOOLS_GOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread reference failed"); + } + ctx.indent_level++; + dump_reference(rawoutstream, info, &ctx, attr, ref_buf, ndims); + ctx.indent_level--; + HDfree(ref_buf); + } + } + else { + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute data read"); + ctx.indent_level++; + if (h5tools_dump_mem(rawoutstream, info, &ctx, attr) < 0) { + h5tools_str_reset(&buffer); + h5tools_str_append(&buffer, " Unable to print data."); + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + } + ctx.indent_level--; + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute data read complete"); + } +done: + H5Sclose(space); + H5Tclose(f_type); + + h5tools_str_close(&buffer); + + PRINTVALSTREAM(rawoutstream, "\n"); + + H5TOOLS_ENDDEBUG(H5E_tools_min_dbg_id_g, "exit"); + H5TOOLS_POP_STACK(); +} + +/*------------------------------------------------------------------------- * Function: list_attr * * Purpose: Prints information about attributes. @@ -1422,39 +1876,43 @@ static herr_t list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ainfo, void H5_ATTR_UNUSED *op_data) { + H5TOOLS_ERR_INIT(herr_t, SUCCEED) hid_t attr = H5I_INVALID_HID; hid_t space = H5I_INVALID_HID; hid_t type = H5I_INVALID_HID; - hid_t p_type = H5I_INVALID_HID; hsize_t size[H5S_MAX_RANK]; hsize_t nelmts = 1; - hsize_t temp_need; - size_t need; int ndims; int i; - void *buf; H5S_class_t space_type; hsize_t curr_pos = 0; /* total data element position */ h5tools_str_t buffer; /* string into which to render */ h5tools_context_t ctx; /* print context */ h5tool_format_t *info = &ls_dataformat; - h5tool_format_t outputformat; + + H5TOOLS_PUSH_STACK(); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "enter"); HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); + ctx.indent_level = 2; + ctx.cur_column = (size_t)curr_pos; + h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " Attribute: "); print_string(&buffer, attr_name, TRUE); - if ((attr = H5Aopen(obj, attr_name, H5P_DEFAULT))) { + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute name:%s", attr_name); + if ((attr = H5Aopen(obj, attr_name, H5P_DEFAULT)) >= 0) { space = H5Aget_space(attr); type = H5Aget_type(attr); /* Data space */ ndims = H5Sget_simple_extent_dims(space, size, NULL); space_type = H5Sget_simple_extent_type(space); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute ndims:%d", ndims); switch(space_type) { case H5S_SCALAR: /* scalar dataspace */ @@ -1489,100 +1947,26 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ain /* Data type */ h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " Type: "); + h5tools_str_append(&buffer, " %-10s ", "Type:"); print_type(&buffer, type, 15); h5tools_str_append(&buffer, "\n"); h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); - /* Data */ - outputformat = *info; - - if (nelmts < 5) { - outputformat.idx_fmt = ""; - outputformat.line_1st = " Data: "; - outputformat.line_pre = " "; - outputformat.line_cont = " "; - outputformat.str_repeat = 8; - - } - else { - h5tools_str_reset(&buffer); - h5tools_str_append(&buffer, " Data:\n"); - h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); - outputformat.line_1st = NULL; - outputformat.line_pre = " %s "; - outputformat.line_cont = " %s "; - outputformat.str_repeat = 8; - } - - outputformat.line_ncols = (unsigned)width_g; - if (label_g) - outputformat.cmpd_name = "%s="; - if (string_g && 1 == H5Tget_size(type) && H5T_INTEGER == H5Tget_class(type)) { - outputformat.ascii = TRUE; - outputformat.elmt_suf1 = ""; - outputformat.elmt_suf2 = ""; - outputformat.line_pre = " %s \""; - outputformat.line_suf = "\""; - } /* end if */ - - - outputformat.arr_pre = NULL; - outputformat.arr_suf = NULL; - outputformat.arr_sep = NULL; - - outputformat.cmpd_pre = NULL; - outputformat.cmpd_suf = NULL; - outputformat.cmpd_sep = NULL; - - outputformat.vlen_sep = NULL; - outputformat.vlen_pre = NULL; - outputformat.vlen_suf = NULL; - outputformat.vlen_end = NULL; - - info = &outputformat; - - if (space_type != H5S_NULL && space_type != H5S_NO_CLASS) { - if (hexdump_g) - p_type = H5Tcopy(type); - else - p_type = H5Tget_native_type(type, H5T_DIR_DEFAULT); - - if (p_type >= 0) { - /* VL data special information */ - unsigned int vl_data = 0; /* contains VL datatypes */ - - /* Check if we have VL data in the dataset's datatype */ - if (h5tools_detect_vlen(p_type) == TRUE) - vl_data = TRUE; - - temp_need = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)); - need = (size_t)temp_need; - if((buf = HDmalloc(need)) != NULL) { - if(H5Aread(attr, p_type, buf) >= 0) { - ctx.need_prefix = TRUE; - ctx.indent_level = 2; - ctx.cur_column = (size_t)curr_pos; - h5tools_dump_mem(rawoutstream, info, &ctx, attr, p_type, space, buf); - } - - /* Reclaim any VL memory, if necessary */ - if (vl_data) - H5Treclaim(p_type, space, H5P_DEFAULT, buf); - - HDfree(buf); - } - H5Tclose(p_type); - } /* end if */ - } - H5Sclose(space); H5Tclose(type); + + h5tools_str_close(&buffer); + + if (data_g) + dump_attribute_values(attr, attr_name); H5Aclose(attr); } - h5tools_str_close(&buffer); - - PRINTVALSTREAM(rawoutstream, "\n"); + else { + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Attribute open failed"); + h5tools_str_close(&buffer); + } + H5TOOLS_ENDDEBUG(H5E_tools_min_dbg_id_g, "exit"); + H5TOOLS_POP_STACK(); return 0; } @@ -1796,7 +2180,10 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) break; case H5T_REFERENCE: - if (H5Tequal(type, H5T_STD_REF_DSETREG)) { + if (H5Tequal(dset, H5T_STD_REF)) { + h5tools_str_append(&buffer, "reference information not available"); + } + else if (H5Tequal(dset, H5T_STD_REF_DSETREG)) { h5tools_str_append(&buffer, "information not available"); } break; @@ -1835,8 +2222,10 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name) h5tools_str_append(&buffer, "}\n"); } /* end for */ } /* end if */ + h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); /* Print data type */ + h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " %-10s ", "Type:"); print_type(&buffer, type, 15); h5tools_str_append(&buffer, "\n"); @@ -1908,6 +2297,7 @@ datatype_list2(hid_t type, const char H5_ATTR_UNUSED *name) static herr_t list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void *_iter) { + H5TOOLS_ERR_INIT(herr_t, SUCCEED) H5O_type_t obj_type = oinfo->type; /* Type of the object */ iter_t *iter = (iter_t*)_iter; hsize_t curr_pos = 0; /* total data element position */ @@ -1915,11 +2305,15 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void h5tools_context_t ctx; /* print context */ h5tool_format_t *info = &ls_dataformat; + H5TOOLS_PUSH_STACK(); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "enter"); + HDmemset(&ctx, 0, sizeof(ctx)); HDmemset(&buffer, 0, sizeof(h5tools_str_t)); h5tools_str_reset(&buffer); + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Object name:%s", name); /* Print the link's name, either full name or base name */ if (!iter->symlink_target) print_obj_name(&buffer, iter, name, ""); @@ -1951,6 +2345,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void /* Open the object. Not all objects can be opened. If this is the case * then return right away. */ + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Open object name=%s", name); if (obj_type >= 0 && (obj = H5Oopen(iter->fid, name, H5P_DEFAULT)) < 0) { h5tools_str_reset(&buffer); h5tools_str_append(&buffer, " *ERROR*\n"); @@ -1959,6 +2354,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void } /* end if */ /* List the first line of information for the object. */ + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Object type:%d", obj_type); if (obj_type >= 0 && dispatch_g[obj_type].list1) (dispatch_g[obj_type].list1)(obj); if (!iter->symlink_target || (verbose_g > 0)) { @@ -1975,6 +2371,7 @@ list_obj(const char *name, const H5O_info_t *oinfo, const char *first_seen, void ssize_t cmt_bufsize = -1; /* Display attributes */ + H5TOOLS_DEBUG(H5E_tools_min_dbg_id_g, "Display attributes"); if (obj_type >= 0) H5Aiterate2(obj, H5_INDEX_NAME, H5_ITER_INC, NULL, list_attr, NULL); @@ -2042,6 +2439,9 @@ done: } h5tools_str_close(&buffer); + H5TOOLS_ENDDEBUG(H5E_tools_min_dbg_id_g, "exit"); + H5TOOLS_POP_STACK(); + return 0; } /* end list_obj() */ @@ -2445,6 +2845,10 @@ main(int argc, const char *argv[]) const char *preferred_driver = NULL; int err_exit = 0; hid_t fapl_id = H5P_DEFAULT; + H5E_auto2_t func; + H5E_auto2_t tools_func; + void *edata; + void *tools_edata; #ifdef H5_HAVE_ROS3_VFD /* default "anonymous" s3 configuration */ @@ -2472,9 +2876,17 @@ main(int argc, const char *argv[]) h5tools_setprogname(PROGRAMNAME); h5tools_setstatus(EXIT_SUCCESS); + /* Disable error reporting */ + H5Eget_auto2(H5E_DEFAULT, &func, &edata); + H5Eset_auto2(H5E_DEFAULT, NULL, NULL); + /* Initialize h5tools lib */ h5tools_init(); + /* Disable tools error reporting */ + H5Eget_auto2(H5tools_ERR_STACK_g, &tools_func, &tools_edata); + H5Eset_auto2(H5tools_ERR_STACK_g, NULL, NULL); + /* Build object display table */ DISPATCH(H5O_TYPE_GROUP, "Group", NULL, NULL); DISPATCH(H5O_TYPE_DATASET, "Dataset", dataset_list1, dataset_list2); @@ -2501,11 +2913,11 @@ main(int argc, const char *argv[]) data_g = TRUE; } else if (!HDstrcmp(argv[argno], "--enable-error-stack")) { - show_errors_g = TRUE; + enable_error_stack = 1; /* deprecated --errors */ } else if (!HDstrcmp(argv[argno], "--errors")) { - show_errors_g = TRUE; + enable_error_stack = 1; } else if (!HDstrcmp(argv[argno], "--follow-symlinks")) { follow_symlink_g = TRUE; @@ -2754,7 +3166,7 @@ main(int argc, const char *argv[]) /* deprecated -e */ case 'e': /* --errors */ - show_errors_g = TRUE; + enable_error_stack = 1; break; case 'E': /* --external */ @@ -2862,10 +3274,10 @@ main(int argc, const char *argv[]) } } /* preferred_driver defined */ - /* Turn off HDF5's automatic error printing unless you're debugging h5ls */ - if(!show_errors_g) - H5Eset_auto2(H5E_DEFAULT, NULL, NULL); - + if (enable_error_stack > 0) { + H5Eset_auto2(H5E_DEFAULT, func, edata); + H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata); + } /* Each remaining argument is an hdf5 file followed by an optional slash * and object name. @@ -2929,6 +3341,7 @@ main(int argc, const char *argv[]) x = oname; if (NULL == (oname = HDstrdup(oname))) { HDfprintf(rawerrorstream, "memory allocation failed\n"); + H5Eset_auto2(H5E_DEFAULT, func, edata); leave(EXIT_FAILURE); } *x = '\0'; @@ -2973,6 +3386,7 @@ main(int argc, const char *argv[]) h5tools_str_reset(&buffer); print_obj_name(&buffer, &iter, oname, "**NOT FOUND**"); h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols, (hsize_t)0, (hsize_t)0); + H5Eset_auto2(H5E_DEFAULT, func, edata); leave(EXIT_FAILURE); } /* end if */ } /* end if */ @@ -2981,8 +3395,10 @@ main(int argc, const char *argv[]) /* Open the object and display it's information */ if (li.type == H5L_TYPE_HARD) { - if (visit_obj(file, oname, &iter) < 0) + if (visit_obj(file, oname, &iter) < 0) { + H5Eset_auto2(H5E_DEFAULT, func, edata); leave(EXIT_FAILURE); + } } /* end if(li.type == H5L_TYPE_HARD) */ else { /* Specified name is not for object -- list that link */ @@ -3011,10 +3427,12 @@ main(int argc, const char *argv[]) if (fapl_id != H5P_DEFAULT) { if (0 < H5Pclose(fapl_id)) { HDfprintf(rawerrorstream, "Error: Unable to set close fapl entry\n\n"); + H5Eset_auto2(H5E_DEFAULT, func, edata); leave(EXIT_FAILURE); } } + H5Eset_auto2(H5E_DEFAULT, func, edata); if (err_exit) leave(EXIT_FAILURE); else |