/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include #include #include "H5private.h" #include "h5tools.h" #include "h5tools_dump.h" #include "h5tools_utils.h" #include "h5tools_ref.h" #include "h5trav.h" #include "h5dump_extern.h" #include "h5dump_ddl.h" typedef struct { hid_t fid; /* File ID being traversed */ char *op_name; /* Object name wanted */ } trav_handle_udata_t; typedef struct { char *path; /* Path of object being searched */ char *op_name; /* Object name wanted */ } trav_attr_udata_t; /* callback function used by H5Literate() */ static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void *op_data); static int dump_extlink(hid_t group, const char *linkname, const char *objname); /*------------------------------------------------------------------------- * Function: dump_datatype * * Purpose: Dump the datatype. Datatype can be HDF5 predefined * atomic datatype or committed/transient datatype. * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *------------------------------------------------------------------------- */ void dump_datatype(hid_t type) { h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; h5dump_type_table = type_table; h5tools_dump_datatype(rawoutstream, outputformat, &ctx, type); h5dump_type_table = NULL; } /*------------------------------------------------------------------------- * Function: dump_dataspace * * Purpose: Dump the dataspace. Dataspace can be named dataspace, * array, or others. * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *------------------------------------------------------------------------- */ void dump_dataspace(hid_t space) { h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; h5tools_dump_dataspace(rawoutstream, outputformat, &ctx, space); } /*------------------------------------------------------------------------- * Function: dump_attr_cb * * Purpose: attribute function callback called by H5Aiterate2, displays the attribute * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Ruey-Hsia Li * * Modifications: Pedro Vicente, October 4, 2007 * Added H5A_info_t parameter to conform with H5Aiterate2 * *------------------------------------------------------------------------- */ herr_t dump_attr_cb(hid_t oid, const char *attr_name, const H5A_info_t UNUSED *info, void UNUSED *_op_data) { h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; hid_t attr_id; herr_t ret = SUCCEED; HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT); oid_output = display_oid; data_output = display_data; attr_data_output = display_attr_data; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; string_dataformat.fmt_float = fp_format; } if (h5tools_nCols==0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; h5dump_type_table = type_table; h5tools_dump_attribute(rawoutstream, outputformat, &ctx, attr_name, attr_id, display_ai, display_char); h5dump_type_table = NULL; if(attr_id < 0) { h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } return ret; } /*------------------------------------------------------------------------- * Function: dump_all_cb * * Purpose: function callback called by H5Literate, * displays everything in the specified object * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Ruey-Hsia Li * * Modifications: * RMcG, November 2000 * Added XML support. Also, optionally checks the op_data argument * * PVN, May 2008 * Dump external links * *------------------------------------------------------------------------- */ static herr_t dump_all_cb(hid_t group, const char *name, const H5L_info_t *linfo, void UNUSED *op_data) { hid_t obj; herr_t ret = SUCCEED; char *obj_path = NULL; /* Full path of object */ h5tools_str_t buffer; /* string into which to render */ h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; hsize_t curr_pos = 0; /* total data element position */ /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; string_dataformat.fmt_float = fp_format; } if (h5tools_nCols==0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; /* Build the object's path name */ obj_path = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2); if(!obj_path) { ret = FAIL; goto done; } HDstrcpy(obj_path, prefix); HDstrcat(obj_path, "/"); HDstrcat(obj_path, name); if(linfo->type == H5L_TYPE_HARD) { H5O_info_t oinfo; /* Stat the object */ if(H5Oget_info_by_name(group, name, &oinfo, H5P_DEFAULT) < 0) { error_msg("unable to get object information for \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; goto done; } /* end if */ switch(oinfo.type) { case H5O_TYPE_GROUP: if((obj = H5Gopen2(group, name, H5P_DEFAULT)) < 0) { error_msg("unable to dump group \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { char *old_prefix; /* Pointer to previous prefix */ /* Keep copy of prefix before iterating into group */ old_prefix = HDstrdup(prefix); HDassert(old_prefix); /* Append group name to prefix */ add_prefix(&prefix, &prefix_len, name); /* Iterate into group */ dump_function_table->dump_group_function(obj, name); /* Restore old prefix name */ HDstrcpy(prefix, old_prefix); HDfree(old_prefix); /* Close group */ H5Gclose(obj); } break; case H5O_TYPE_DATASET: if((obj = H5Dopen2(group, name, H5P_DEFAULT)) >= 0) { if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(dset_table, oinfo.addr); if(found_obj == NULL) { ctx.indent_level++; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->datasetbegin, name, h5tools_dump_header_format->datasetblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->datasetblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetblockend); if(HDstrlen(h5tools_dump_header_format->datasetend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->datasetend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; h5tools_setstatus(EXIT_FAILURE); ret = FAIL; H5Dclose(obj); goto done; } else if(found_obj->displayed) { ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->datasetbegin, name, h5tools_dump_header_format->datasetblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\"", HARDLINK, found_obj->objname); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->datasetblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetblockend); if(HDstrlen(h5tools_dump_header_format->datasetend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->datasetend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); H5Dclose(obj); goto done; } else { found_obj->displayed = TRUE; } } /* end if */ dump_function_table->dump_dataset_function(obj, name, NULL); H5Dclose(obj); } else { error_msg("unable to dump dataset \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } break; case H5O_TYPE_NAMED_DATATYPE: if((obj = H5Topen2(group, name, H5P_DEFAULT)) < 0) { error_msg("unable to dump datatype \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { dump_function_table->dump_named_datatype_function(obj, name); H5Tclose(obj); } break; default: error_msg("unknown object \"%s\"\n", name); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } } /* end if */ else { char *targbuf; switch(linfo->type) { case H5L_TYPE_SOFT: targbuf = (char *)HDmalloc(linfo->u.val_size); HDassert(targbuf); ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->softlinkbegin, name, h5tools_dump_header_format->softlinkblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { error_msg("unable to get link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { /* print the value of a soft link */ /* Standard DDL: no modification */ ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "LINKTARGET \"%s\"", targbuf); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } ctx.indent_level--; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->softlinkblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkblockend); if(HDstrlen(h5tools_dump_header_format->softlinkend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->softlinkend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->softlinkend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(targbuf); break; case H5L_TYPE_EXTERNAL: targbuf = (char *)HDmalloc(linfo->u.val_size); HDassert(targbuf); ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->extlinkbegin, name, h5tools_dump_header_format->extlinkblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); if(H5Lget_val(group, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) { indentation(dump_indent); error_msg("unable to get external link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } /* end if */ else { const char *filename; const char *targname; if(H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &targname) < 0) { indentation(dump_indent); error_msg("unable to unpack external link value\n"); h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } /* end if */ else { ctx.indent_level++; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "TARGETFILE \"%s\"", filename); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "TARGETPATH \"%s\"", targname); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* dump the external link */ dump_extlink(group, name, targname); ctx.indent_level--; } /* end else */ } /* end else */ ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->extlinkblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkblockend); if(HDstrlen(h5tools_dump_header_format->extlinkend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->extlinkend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->extlinkend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); HDfree(targbuf); break; default: ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->udlinkbegin, name, h5tools_dump_header_format->udlinkblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "LINKCLASS %d", linfo->type); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->udlinkblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->udlinkblockend); if(HDstrlen(h5tools_dump_header_format->udlinkend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->udlinkend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->udlinkend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); break; } /* end switch */ } /* end else */ done: h5tools_str_close(&buffer); if(obj_path) HDfree(obj_path); return ret; } /*------------------------------------------------------------------------- * Function: attr_iteration * * Purpose: Iterate and display attributes within the specified group * * Return: void * *------------------------------------------------------------------------- */ void attr_iteration(hid_t gid, unsigned attr_crt_order_flags) { /* attribute iteration: if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group for attributes, then, sort by creation order, otherwise by name */ if(include_attrs) { if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) { if(H5Aiterate2(gid, sort_by, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end if */ else { if(H5Aiterate2(gid, H5_INDEX_NAME, sort_order, NULL, dump_attr_cb, NULL) < 0) { error_msg("error getting attribute information\n"); h5tools_setstatus(EXIT_FAILURE); } /* end if */ } /* end else */ } } /*------------------------------------------------------------------------- * Function: link_iteration * * Purpose: Iterate and display links within the specified group * * Return: void * *------------------------------------------------------------------------- */ void link_iteration(hid_t gid, unsigned crt_order_flags) { /* if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set in the group, then, sort by creation order, otherwise by name */ if((sort_by == H5_INDEX_CRT_ORDER) && (crt_order_flags & H5P_CRT_ORDER_TRACKED)) H5Literate(gid, sort_by, sort_order, NULL, dump_all_cb, NULL); else H5Literate(gid, H5_INDEX_NAME, sort_order, NULL, dump_all_cb, NULL); } /*------------------------------------------------------------------------- * Function: dump_named_datatype * * Purpose: Dump named datatype * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * Pedro Vicente, March 27, 2006 * added display of attributes * Pedro Vicente, October 4, 2007, added parameters to H5Aiterate2() to allow for * other iteration orders * *------------------------------------------------------------------------- */ void dump_named_datatype(hid_t tid, const char *name) { H5O_info_t oinfo; unsigned attr_crt_order_flags; hid_t tcpl_id = -1; /* datatype creation property list ID */ 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 = &h5tools_dataformat; h5tool_format_t string_dataformat; /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; string_dataformat.fmt_float = fp_format; } if (h5tools_nCols==0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; if ((tcpl_id = H5Tget_create_plist(tid)) < 0) { error_msg("error in getting creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the creation properties for attributes */ if (H5Pget_attr_creation_order(tcpl_id, &attr_crt_order_flags) < 0) { error_msg("error in getting creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } if(H5Pclose(tcpl_id) < 0) { error_msg("error in closing creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->datatypebegin, name, h5tools_dump_header_format->datatypeblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); H5Oget_info(tid, &oinfo); /* Must check for uniqueness of all objects if we've traversed an elink, * otherwise only check if the reference count > 1. */ if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(type_table, oinfo.addr); if (found_obj == NULL) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); goto done; } else if (found_obj->displayed) { /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\"", HARDLINK, found_obj->objname); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); goto done; } else found_obj->displayed = TRUE; } /* end if */ /* Render the element */ h5tools_str_reset(&buffer); h5tools_print_datatype(rawoutstream, &buffer, outputformat, &ctx, tid, FALSE); if(H5Tget_class(tid) != H5T_COMPOUND) { h5tools_str_append(&buffer, ";"); } h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); /* print attributes */ dump_indent += COL; attr_iteration(tid, attr_crt_order_flags); dump_indent -= COL; done: /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->datatypeblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeblockend); if(HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->datatypeend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datatypeend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } /*------------------------------------------------------------------------- * Function: dump_group * * Purpose: Dump everything within the specified group * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * * Call to dump_all_cb -- add parameter to select everything. * * Pedro Vicente, October 1, 2007 * handle several iteration orders for attributes and groups * *------------------------------------------------------------------------- */ void dump_group(hid_t gid, const char *name) { H5O_info_t oinfo; hid_t dset; hid_t type; hid_t gcpl_id; unsigned crt_order_flags; unsigned attr_crt_order_flags; char type_name[1024]; h5tools_str_t buffer; /* string into which to render */ h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; hsize_t curr_pos = 0; /* total data element position */ if ((gcpl_id = H5Gget_create_plist(gid)) < 0) { error_msg("error in getting group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the group creation properties for attributes */ if (H5Pget_attr_creation_order(gcpl_id, &attr_crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the group creation properties */ if(H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } if(H5Pclose(gcpl_id) < 0) { error_msg("error in closing group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; string_dataformat.fmt_float = fp_format; } if (h5tools_nCols==0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->groupbegin, name, h5tools_dump_header_format->groupblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level++; dump_indent += COL; if(!HDstrcmp(name, "/") && unamedtype) { unsigned u; /* Local index variable */ /* dump unamed type in root group */ for(u = 0; u < type_table->nobjs; u++) if(!type_table->objs[u].recorded) { dset = H5Dopen2(gid, type_table->objs[u].objname, H5P_DEFAULT); type = H5Dget_type(dset); sprintf(type_name, "#"H5_PRINTF_HADDR_FMT, type_table->objs[u].objno); dump_function_table->dump_named_datatype_function(type, type_name); H5Tclose(type); H5Dclose(dset); } } /* end if */ if(display_oid) { h5tools_dump_oid(rawoutstream, outputformat, &ctx, gid); } h5tools_dump_comment(rawoutstream, outputformat, &ctx, gid); H5Oget_info(gid, &oinfo); /* Must check for uniqueness of all objects if we've traversed an elink, * otherwise only check if the reference count > 1. */ if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(group_table, oinfo.addr); if (found_obj == NULL) { error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__); h5tools_setstatus(EXIT_FAILURE); } else if (found_obj->displayed) { ctx.need_prefix = TRUE; /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\"", HARDLINK, found_obj->objname); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); } else { found_obj->displayed = TRUE; attr_iteration(gid, attr_crt_order_flags); link_iteration(gid, crt_order_flags); } } else { attr_iteration(gid, attr_crt_order_flags); link_iteration(gid, crt_order_flags); } dump_indent -= COL; ctx.indent_level--; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->groupblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->groupblockend); if(HDstrlen(h5tools_dump_header_format->groupend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->groupend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->groupend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } /*------------------------------------------------------------------------- * Function: dump_dataset * * Purpose: Dump the specified data set * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * Pedro Vicente, 2004, added dataset creation property list display * Pedro Vicente, October 4, 2007, added parameters to H5Aiterate2() to allow for * other iteration orders * *------------------------------------------------------------------------- */ void dump_dataset(hid_t did, const char *name, struct subset_t *sset) { h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; hid_t type, space; unsigned attr_crt_order_flags; hid_t dcpl_id; /* dataset creation property list ID */ h5tools_str_t buffer; /* string into which to render */ hsize_t curr_pos = 0; /* total data element position */ HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; string_dataformat.fmt_float = fp_format; } if (h5tools_nCols==0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; if ((dcpl_id = H5Dget_create_plist(did)) < 0) { error_msg("error in getting creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the creation properties for attributes */ if (H5Pget_attr_creation_order(dcpl_id, &attr_crt_order_flags) < 0) { error_msg("error in getting creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->datasetbegin, name, h5tools_dump_header_format->datasetblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_dump_comment(rawoutstream, outputformat, &ctx, did); dump_indent += COL; ctx.indent_level++; type = H5Dget_type(did); h5dump_type_table = type_table; h5tools_dump_datatype(rawoutstream, outputformat, &ctx, type); h5dump_type_table = NULL; space = H5Dget_space(did); h5tools_dump_dataspace(rawoutstream, outputformat, &ctx, space); H5Sclose(space); if(display_oid) { h5tools_dump_oid(rawoutstream, outputformat, &ctx, did); } if(display_dcpl) { h5dump_type_table = type_table; h5tools_dump_dcpl(rawoutstream, outputformat, &ctx, dcpl_id, type, did); h5dump_type_table = NULL; } H5Pclose(dcpl_id); if(display_data) { int data_loop = 1; int i; if(display_packed_bits) data_loop = packed_bits_num; for(i=0; iline_ncols, (hsize_t)0, (hsize_t)0); } switch(H5Tget_class(type)) { case H5T_TIME: ctx.indent_level++; ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "DATA{ not yet implemented.}"); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); ctx.indent_level--; break; case H5T_INTEGER: case H5T_FLOAT: case H5T_STRING: case H5T_BITFIELD: case H5T_OPAQUE: case H5T_COMPOUND: case H5T_REFERENCE: case H5T_ENUM: case H5T_VLEN: case H5T_ARRAY: { h5tools_dump_data(rawoutstream, outputformat, &ctx, did, TRUE, sset, display_ai, display_char); } break; default: break; } /* end switch */ } /* for(i=0;idatasetblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetblockend); if(HDstrlen(h5tools_dump_header_format->datasetend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->datasetend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->datasetend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); } /*------------------------------------------------------------------------- * Function: dump_data * * Purpose: Dump attribute or dataset data * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: pvn, print the matrix indices * Albert Cheng, 2004/11/18 * Add --string printing for attributes too. * *------------------------------------------------------------------------- */ void dump_data(hid_t obj_id, int obj_data, struct subset_t *sset, int display_index) { h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; int print_dataset = FALSE; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; string_dataformat.fmt_float = fp_format; } if (h5tools_nCols==0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; if(obj_data == DATASET_DATA) print_dataset = TRUE; h5tools_dump_data(rawoutstream, outputformat, &ctx, obj_id, print_dataset, sset, display_index, display_char); } /*------------------------------------------------------------------------- * Function: dump_fcpl * * Purpose: prints file creation property list information * * Return: void * * Programmer: pvn * * Modifications: * *------------------------------------------------------------------------- */ void dump_fcpl(hid_t fid) { hid_t fcpl; /* file creation property list ID */ hsize_t userblock; /* userblock size retrieved from FCPL */ size_t off_size; /* size of offsets in the file */ size_t len_size; /* size of lengths in the file */ unsigned super; /* superblock version # */ unsigned freelist; /* free list version # */ unsigned stab; /* symbol table entry version # */ unsigned shhdr; /* shared object header version # */ #ifdef SHOW_FILE_DRIVER hid_t fapl; /* file access property list ID */ hid_t fdriver; /* file driver */ char dname[32]; /* buffer to store driver name */ #endif unsigned sym_lk; /* symbol table B-tree leaf 'K' value */ unsigned sym_ik; /* symbol table B-tree internal 'K' value */ unsigned istore_ik; /* indexed storage B-tree internal 'K' value */ fcpl=H5Fget_create_plist(fid); H5Pget_version(fcpl, &super, &freelist, &stab, &shhdr); H5Pget_userblock(fcpl,&userblock); H5Pget_sizes(fcpl,&off_size,&len_size); H5Pget_sym_k(fcpl,&sym_ik,&sym_lk); H5Pget_istore_k(fcpl,&istore_ik); H5Pclose(fcpl); #ifdef SHOW_FILE_DRIVER fapl=h5_fileaccess(); fdriver=H5Pget_driver(fapl); H5Pclose(fapl); #endif /*------------------------------------------------------------------------- * SUPER_BLOCK *------------------------------------------------------------------------- */ PRINTSTREAM(rawoutstream, "\n%s %s\n",SUPER_BLOCK, BEGIN); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s %u\n","SUPERBLOCK_VERSION", super); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s %u\n","FREELIST_VERSION", freelist); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s %u\n","SYMBOLTABLE_VERSION", stab); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s %u\n","OBJECTHEADER_VERSION", shhdr); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream,"%s %zu\n","OFFSET_SIZE", off_size); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream,"%s %zu\n","LENGTH_SIZE", len_size); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s %u\n","BTREE_RANK", sym_ik); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s %d\n","BTREE_LEAF", sym_lk); #ifdef SHOW_FILE_DRIVER if(H5FD_CORE==fdriver) HDstrcpy(dname,"H5FD_CORE"); #ifdef H5_HAVE_DIRECT else if(H5FD_DIRECT==fdriver) HDstrcpy(dname,"H5FD_DIRECT"); #endif else if(H5FD_FAMILY==fdriver) HDstrcpy(dname,"H5FD_FAMILY"); else if(H5FD_LOG==fdriver) HDstrcpy(dname,"H5FD_LOG"); else if(H5FD_MPIO==fdriver) HDstrcpy(dname,"H5FD_MPIO"); else if(H5FD_MULTI==fdriver) HDstrcpy(dname,"H5FD_MULTI"); else if(H5FD_SEC2==fdriver) HDstrcpy(dname,"H5FD_SEC2"); else if(H5FD_STDIO==fdriver) HDstrcpy(dname,"H5FD_STDIO"); else HDstrcpy(dname,"Unknown driver"); /* Take out this because the driver used can be different from the * standard output. */ /*indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s %s\n","FILE_DRIVER", dname);*/ #endif indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s %u\n","ISTORE_K", istore_ik); /*------------------------------------------------------------------------- * USER_BLOCK *------------------------------------------------------------------------- */ indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "USER_BLOCK %s\n",BEGIN); indentation(dump_indent + COL + COL); PRINTSTREAM(rawoutstream,"%s %Hu\n","USERBLOCK_SIZE", userblock); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s\n",END); PRINTSTREAM(rawoutstream, "%s",END); } /*------------------------------------------------------------------------- * Function: dump_fcontents * * Purpose: prints all objects * * Return: void * * Programmer: pvn * * Modifications: * *------------------------------------------------------------------------- */ void dump_fcontents(hid_t fid) { PRINTSTREAM(rawoutstream, "%s %s\n",FILE_CONTENTS, BEGIN); /* special case of unamed types in root group */ if (unamedtype) { unsigned u; for (u = 0; u < type_table->nobjs; u++) { if (!type_table->objs[u].recorded) PRINTSTREAM(rawoutstream, " %-10s /#"H5_PRINTF_HADDR_FMT"\n", "datatype", type_table->objs[u].objno); } } /* print objects in the files */ h5trav_print(fid); PRINTSTREAM(rawoutstream, " %s\n",END); } static herr_t attr_search(hid_t oid, const char *attr_name, const H5A_info_t UNUSED *ainfo, void *_op_data) { herr_t ret = SUCCEED; int i; int j; int k; char *obj_op_name; char *obj_name; trav_attr_udata_t *attr_data = (trav_attr_udata_t*)_op_data; char *buf = attr_data->path; char *op_name = attr_data->op_name; j = (int)HDstrlen(op_name) - 1; /* find the last / */ while(j >= 0) { if (op_name[j] == '/' && (j==0 || (j>0 && op_name[j-1]!='\\'))) break; j--; } obj_op_name = h5tools_str_replace(op_name + j + 1, "\\/", "/"); if(obj_op_name == NULL) { h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { if(HDstrcmp(attr_name, obj_op_name)==0) { /* object name */ i = (int)HDstrlen(buf); j = (int)HDstrlen(op_name); k = (size_t)i + 1 + (size_t)j + 1 + 2; obj_name = (char *)HDmalloc((size_t)k); if(obj_name == NULL) { h5tools_setstatus(EXIT_FAILURE); ret = FAIL; } else { HDmemset(obj_name, '\0', (size_t)k); if(op_name[0] != '/') { HDstrncat(obj_name, buf, (size_t)i + 1); if(buf[i-1] != '/') HDstrncat(obj_name, "/", (size_t)2); } HDstrncat(obj_name, op_name, (size_t)j + 1); handle_attributes(oid, obj_name, NULL, 0, NULL); HDfree(obj_name); } } HDfree(obj_op_name); } return ret; } /* end attr_search() */ static herr_t obj_search(const char *path, const H5O_info_t *oi, const char UNUSED *already_visited, void *_op_data) { trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; char *op_name = (char*)handle_data->op_name; trav_attr_udata_t attr_data; attr_data.path = (char*)path; attr_data.op_name = op_name; H5Aiterate_by_name(handle_data->fid, path, H5_INDEX_NAME, H5_ITER_INC, NULL, attr_search, (void*)&attr_data, H5P_DEFAULT); if(HDstrcmp(path, op_name)==0) { switch(oi->type) { case H5O_TYPE_GROUP: handle_groups(handle_data->fid, path, NULL, 0, NULL); break; case H5O_TYPE_DATASET: handle_datasets(handle_data->fid, path, NULL, 0, NULL); break; case H5O_TYPE_NAMED_DATATYPE: handle_datatypes(handle_data->fid, path, NULL, 0, NULL); break; case H5O_TYPE_UNKNOWN: case H5O_TYPE_NTYPES: default: error_msg("unknown object type value\n"); h5tools_setstatus(EXIT_FAILURE); } /* end switch */ } return 0; } /* end obj_search() */ static herr_t lnk_search(const char *path, const H5L_info_t *li, void *_op_data) { int search_len; int k; char *search_name; trav_handle_udata_t *handle_data = (trav_handle_udata_t*)_op_data; char *op_name = (char*)handle_data->op_name; search_len = HDstrlen(op_name); if(search_len > 0 && op_name[0] != '/') { k = 2; } else k = 1; search_name = (char *)HDmalloc((size_t)(search_len + k)); if(search_name == NULL) { error_msg("creating temporary link\n"); h5tools_setstatus(EXIT_FAILURE); } else { if (k == 2) { HDstrcpy(search_name, "/"); HDstrncat(search_name, op_name, (size_t)search_len + 1); } else HDstrncpy(search_name, op_name, (size_t)search_len + 1); search_name[search_len + k - 1] = '\0'; if(HDstrcmp(path, search_name) == 0) { switch(li->type) { case H5L_TYPE_SOFT: case H5L_TYPE_EXTERNAL: handle_links(handle_data->fid, op_name, NULL, 0, NULL); break; case H5L_TYPE_HARD: case H5L_TYPE_MAX: case H5L_TYPE_ERROR: default: error_msg("unknown link type value\n"); h5tools_setstatus(EXIT_FAILURE); break; } /* end switch() */ } HDfree(search_name); } return 0; } /* end lnk_search() */ /*------------------------------------------------------------------------- * Function: handle_paths * * Purpose: Handle objects from the command. * * Return: void * *------------------------------------------------------------------------- */ void handle_paths(hid_t fid, const char *path_name, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name) { hid_t gid = -1; if((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0) { error_msg("unable to open root group\n"); h5tools_setstatus(EXIT_FAILURE); } else { hid_t gcpl_id; unsigned crt_order_flags; unsigned attr_crt_order_flags; trav_handle_udata_t handle_udata; /* User data for traversal */ if ((gcpl_id = H5Gget_create_plist(gid)) < 0) { error_msg("error in getting group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the group creation properties for attributes */ if (H5Pget_attr_creation_order(gcpl_id, &attr_crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } /* query the group creation properties */ if(H5Pget_link_creation_order(gcpl_id, &crt_order_flags) < 0) { error_msg("error in getting group creation properties\n"); h5tools_setstatus(EXIT_FAILURE); } if(H5Pclose(gcpl_id) < 0) { error_msg("error in closing group creation property list ID\n"); h5tools_setstatus(EXIT_FAILURE); } handle_udata.fid = fid; handle_udata.op_name = (char*)path_name; if(h5trav_visit(fid, "/", TRUE, TRUE, obj_search, lnk_search, &handle_udata) < 0) { error_msg("error traversing information\n"); h5tools_setstatus(EXIT_FAILURE); } } } /*------------------------------------------------------------------------- * Function: handle_attributes * * Purpose: Handle the attributes from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * * PVN, May 2008 * add an extra parameter PE, to allow printing/not printing of error messages * *------------------------------------------------------------------------- */ void handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name) { hid_t oid = -1; hid_t attr_id = -1; char *obj_name; char *attr_name; int j; h5tools_str_t buffer; /* string into which to render */ h5tools_context_t ctx; /* print context */ h5tool_format_t *outputformat = &h5tools_dataformat; h5tool_format_t string_dataformat; hsize_t curr_pos = 0; /* total data element position */ j = (int)HDstrlen(attr) - 1; obj_name = (char *)HDmalloc((size_t)j + 2); if(obj_name == NULL) goto error; /* find the last / */ while(j >= 0) { if (attr[j] == '/' && (j==0 || (j>0 && attr[j-1]!='\\'))) break; j--; } /* object name */ if(j == -1) HDstrcpy(obj_name, "/"); else { HDstrncpy(obj_name, attr, (size_t)j + 1); obj_name[j + 1] = '\0'; } /* end else */ dump_indent += COL; HDmemset(&ctx, 0, sizeof(ctx)); ctx.indent_level = dump_indent/COL; ctx.cur_column = dump_indent; string_dataformat = *outputformat; if (fp_format) { string_dataformat.fmt_double = fp_format; string_dataformat.fmt_float = fp_format; } if (h5tools_nCols==0) { string_dataformat.line_ncols = 65535; string_dataformat.line_per_line = 1; } else string_dataformat.line_ncols = h5tools_nCols; string_dataformat.do_escape = display_escape; outputformat = &string_dataformat; attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/"); /* handle error case: cannot open the object with the attribute */ if((oid = H5Oopen(fid, obj_name, H5P_DEFAULT)) < 0) { /* setup */ HDmemset(&buffer, 0, sizeof(h5tools_str_t)); ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); h5tools_str_append(&buffer, "%s \"%s\" %s", h5tools_dump_header_format->attributebegin, attr, h5tools_dump_header_format->attributeblockbegin); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); error_msg("unable to open object \"%s\"\n", obj_name); ctx.need_prefix = TRUE; h5tools_simple_prefix(rawoutstream, outputformat, &ctx, (hsize_t)0, 0); /* Render the element */ h5tools_str_reset(&buffer); if(HDstrlen(h5tools_dump_header_format->attributeblockend)) { h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->attributeblockend); if(HDstrlen(h5tools_dump_header_format->attributeend)) h5tools_str_append(&buffer, " "); } if(HDstrlen(h5tools_dump_header_format->attributeend)) h5tools_str_append(&buffer, "%s", h5tools_dump_header_format->attributeend); h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0); h5tools_str_close(&buffer); goto error; } /* end if */ attr_id = H5Aopen(oid, attr_name, H5P_DEFAULT); oid_output = display_oid; data_output = display_data; attr_data_output = display_attr_data; h5dump_type_table = type_table; h5tools_dump_attribute(rawoutstream, outputformat, &ctx, attr_name, attr_id, display_ai, display_char); h5dump_type_table = NULL; if(attr_id < 0) { goto error; } /* Close object */ if(H5Oclose(oid) < 0) { goto error; } /* end if */ HDfree(obj_name); HDfree(attr_name); dump_indent -= COL; return; error: h5tools_setstatus(EXIT_FAILURE); if(obj_name) HDfree(obj_name); if (attr_name) HDfree(attr_name); H5E_BEGIN_TRY { H5Oclose(oid); H5Aclose(attr_id); } H5E_END_TRY; dump_indent -= COL; } /*------------------------------------------------------------------------- * Function: handle_datasets * * Purpose: Handle the datasets from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * Pedro Vicente, Tuesday, January 15, 2008 * check for block overlap\ * * Pedro Vicente, May 8, 2008 * added a flag PE that prints/not prints error messages * added for cases of external links not found, to avoid printing of * objects not found, since external links are dumped on a trial error basis * *------------------------------------------------------------------------- */ void handle_datasets(hid_t fid, const char *dset, void *data, int pe, const char *display_name) { H5O_info_t oinfo; hid_t dsetid; struct subset_t *sset = (struct subset_t *)data; const char *real_name = display_name ? display_name : dset; if((dsetid = H5Dopen2(fid, dset, H5P_DEFAULT)) < 0) { if (pe) { handle_links(fid, dset, data, pe, display_name); } return; } /* end if */ if(sset) { unsigned int i; unsigned int ndims; hid_t sid = H5Dget_space(dsetid); int ndims_res = H5Sget_simple_extent_ndims(sid); H5Sclose(sid); if(ndims_res < 0) { error_msg("H5Sget_simple_extent_ndims failed\n"); h5tools_setstatus(EXIT_FAILURE); return; } else ndims = ndims_res; if(!sset->start.data || !sset->stride.data || !sset->count.data || !sset->block.data) { /* they didn't specify a ``stride'' or ``block''. default to 1 in all * dimensions */ if(!sset->start.data) { /* default to (0, 0, ...) for the start coord */ sset->start.data = (hsize_t *)HDcalloc((size_t)ndims, sizeof(hsize_t)); sset->start.len = ndims; } if(!sset->stride.data) { sset->stride.data = (hsize_t *)HDcalloc((size_t)ndims, sizeof(hsize_t)); sset->stride.len = ndims; for (i = 0; i < ndims; i++) sset->stride.data[i] = 1; } if(!sset->count.data) { sset->count.data = (hsize_t *)HDcalloc((size_t)ndims, sizeof(hsize_t)); sset->count.len = ndims; for (i = 0; i < ndims; i++) sset->count.data[i] = 1; } if(!sset->block.data) { sset->block.data = (hsize_t *)HDcalloc((size_t)ndims, sizeof(hsize_t)); sset->block.len = ndims; for (i = 0; i < ndims; i++) sset->block.data[i] = 1; } } /*------------------------------------------------------------------------- * check for dimension overflow *------------------------------------------------------------------------- */ if(sset->start.len > ndims) { error_msg("number of start dims (%u) exceed dataset dims (%u)\n", sset->start.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } if(sset->stride.len > ndims) { error_msg("number of stride dims (%u) exceed dataset dims (%u)\n", sset->stride.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } if(sset->count.len > ndims) { error_msg("number of count dims (%u) exceed dataset dims (%u)\n", sset->count.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } if(sset->block.len > ndims) { error_msg("number of block dims (%u) exceed dataset dims (%u)\n", sset->block.len, ndims); h5tools_setstatus(EXIT_FAILURE); return; } /*------------------------------------------------------------------------- * check for block overlap *------------------------------------------------------------------------- */ for(i = 0; i < ndims; i++) { if(sset->count.data[i] > 1) { if(sset->stride.data[i] < sset->block.data[i]) { error_msg("wrong subset selection; blocks overlap\n"); h5tools_setstatus(EXIT_FAILURE); return; } /* end if */ } /* end if */ } /* end for */ } /* end if */ H5Oget_info(dsetid, &oinfo); if(oinfo.rc > 1 || hit_elink) { obj_t *found_obj; /* Found object */ found_obj = search_obj(dset_table, oinfo.addr); if(found_obj) { if (found_obj->displayed) { PRINTVALSTREAM(rawoutstream, "\n"); indentation(dump_indent); begin_obj(h5tools_dump_header_format->datasetbegin, real_name, h5tools_dump_header_format->datasetblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(dump_indent + COL); PRINTSTREAM(rawoutstream, "%s \"%s\"\n", HARDLINK, found_obj->objname); indentation(dump_indent); end_obj(h5tools_dump_header_format->datasetend, h5tools_dump_header_format->datasetblockend); } else { found_obj->displayed = TRUE; dump_indent += COL; dump_dataset(dsetid, real_name, sset); dump_indent -= COL; } } else h5tools_setstatus(EXIT_FAILURE); } else { dump_indent += COL; dump_dataset(dsetid, real_name, sset); dump_indent -= COL; } if(H5Dclose(dsetid) < 0) h5tools_setstatus(EXIT_FAILURE); } /*------------------------------------------------------------------------- * Function: handle_groups * * Purpose: Handle the groups from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: Pedro Vicente, September 26, 2007 * handle creation order * * Pedro Vicente, May 8, 2008 * added a flag PE that prints/not prints error messages * added for cases of external links not found, to avoid printing of * objects not found, since external links are dumped on a trial error basis * *------------------------------------------------------------------------- */ void handle_groups(hid_t fid, const char *group, void UNUSED *data, int pe, const char *display_name) { hid_t gid; const char *real_name = display_name ? display_name : group; if((gid = H5Gopen2(fid, group, H5P_DEFAULT)) < 0) { if (pe) { PRINTVALSTREAM(rawoutstream, "\n"); begin_obj(h5tools_dump_header_format->groupbegin, real_name, h5tools_dump_header_format->groupblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(COL); error_msg("unable to open group \"%s\"\n", real_name); end_obj(h5tools_dump_header_format->groupend, h5tools_dump_header_format->groupblockend); h5tools_setstatus(EXIT_FAILURE); } } else { size_t new_len = HDstrlen(group) + 1; if(prefix_len <= new_len) { prefix_len = new_len; prefix = (char *)HDrealloc(prefix, prefix_len); } /* end if */ HDstrcpy(prefix, group); dump_indent += COL; dump_group(gid, real_name); dump_indent -= COL; if(H5Gclose(gid) < 0) h5tools_setstatus(EXIT_FAILURE); } /* end else */ } /* end handle_groups() */ /*------------------------------------------------------------------------- * Function: handle_links * * Purpose: Handle soft or UD links from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * *------------------------------------------------------------------------- */ void handle_links(hid_t fid, const char *links, void UNUSED * data, int UNUSED pe, const char UNUSED *display_name) { H5L_info_t linfo; if(H5Lget_info(fid, links, &linfo, H5P_DEFAULT) < 0) { error_msg("unable to get link info from \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } else if(linfo.type == H5L_TYPE_HARD) { error_msg("\"%s\" is a hard link\n", links); h5tools_setstatus(EXIT_FAILURE); } else { char *buf = (char *)HDmalloc(linfo.u.val_size); PRINTVALSTREAM(rawoutstream, "\n"); switch(linfo.type) { case H5L_TYPE_SOFT: /* Soft link */ begin_obj(h5tools_dump_header_format->softlinkbegin, links, h5tools_dump_header_format->softlinkblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(COL); if(H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0) PRINTSTREAM(rawoutstream, "LINKTARGET \"%s\"\n", buf); else { error_msg("h5dump error: unable to get link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } end_obj(h5tools_dump_header_format->softlinkend, h5tools_dump_header_format->softlinkblockend); break; case H5L_TYPE_EXTERNAL: begin_obj(h5tools_dump_header_format->udlinkbegin, links, h5tools_dump_header_format->udlinkblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(COL); begin_obj(h5tools_dump_header_format->extlinkbegin, links, h5tools_dump_header_format->extlinkblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); if(H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0) { const char *elink_file; const char *elink_path; if(H5Lunpack_elink_val(buf, linfo.u.val_size, NULL, &elink_file, &elink_path)>=0) { indentation(COL); PRINTSTREAM(rawoutstream, "LINKCLASS %d\n", linfo.type); indentation(COL); PRINTSTREAM(rawoutstream, "TARGETFILE \"%s\"\n", elink_file); indentation(COL); PRINTSTREAM(rawoutstream, "TARGETPATH \"%s\"\n", elink_path); } else { error_msg("h5dump error: unable to unpack external link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } } else { error_msg("h5dump error: unable to get external link value for \"%s\"\n", links); h5tools_setstatus(EXIT_FAILURE); } end_obj(h5tools_dump_header_format->extlinkend, h5tools_dump_header_format->extlinkblockend); break; default: begin_obj(h5tools_dump_header_format->udlinkbegin, links, h5tools_dump_header_format->udlinkblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(COL); begin_obj(h5tools_dump_header_format->udlinkbegin, links, h5tools_dump_header_format->udlinkblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(COL); PRINTSTREAM(rawoutstream, "LINKCLASS %d\n", linfo.type); end_obj(h5tools_dump_header_format->udlinkend, h5tools_dump_header_format->udlinkblockend); break; } /* end switch */ HDfree(buf); } /* end else */ } /*------------------------------------------------------------------------- * Function: handle_datatypes * * Purpose: Handle the datatypes from the command. * * Return: void * * Programmer: Bill Wendling * Tuesday, 9. January 2001 * * Modifications: * * Pedro Vicente, May 8, 2008 * added a flag PE that prints/not prints error messages * added for cases of external links not found, to avoid printing of * objects not found, since external links are dumped on a trial error basis * *------------------------------------------------------------------------- */ void handle_datatypes(hid_t fid, const char *type, void UNUSED * data, int pe, const char *display_name) { hid_t type_id; const char *real_name = display_name ? display_name : type; if((type_id = H5Topen2(fid, type, H5P_DEFAULT)) < 0) { /* check if type is unamed datatype */ unsigned idx = 0; while(idx < type_table->nobjs ) { char name[128]; if(!type_table->objs[idx].recorded) { /* unamed datatype */ sprintf(name, "/#"H5_PRINTF_HADDR_FMT, type_table->objs[idx].objno); if(!HDstrcmp(name, real_name)) break; } /* end if */ idx++; } /* end while */ if(idx == type_table->nobjs) { if (pe) { /* unknown type */ PRINTVALSTREAM(rawoutstream, "\n"); begin_obj(h5tools_dump_header_format->datatypebegin, real_name, h5tools_dump_header_format->datatypeblockbegin); PRINTVALSTREAM(rawoutstream, "\n"); indentation(COL); error_msg("unable to open datatype \"%s\"\n", real_name); end_obj(h5tools_dump_header_format->datatypeend, h5tools_dump_header_format->datatypeblockend); h5tools_setstatus(EXIT_FAILURE); } } else { hid_t dsetid = H5Dopen2(fid, type_table->objs[idx].objname, H5P_DEFAULT); type_id = H5Dget_type(dsetid); dump_indent += COL; dump_named_datatype(type_id, real_name); dump_indent -= COL; H5Tclose(type_id); H5Dclose(dsetid); } } else { dump_indent += COL; dump_named_datatype(type_id, real_name); dump_indent -= COL; if(H5Tclose(type_id) < 0) h5tools_setstatus(EXIT_FAILURE); } } /*------------------------------------------------------------------------- * Function: dump_extlink * * made by: PVN * * Purpose: Dump an external link * Since external links are soft links, they are dumped on a trial error * basis, attempting to dump as a dataset, as a group and as a named datatype * Error messages are supressed * * Modifications: * Neil Fortner * 13 October 2008 * Function basically rewritten. No longer directly opens the target file, * now initializes a new set of tables for the external file. No longer * dumps on a trial and error basis, but errors are still suppressed. * *------------------------------------------------------------------------- */ static int dump_extlink(hid_t group, const char *linkname, const char *objname) { hid_t oid; H5O_info_t oi; table_t *old_group_table = group_table; table_t *old_dset_table = dset_table; table_t *old_type_table = type_table; hbool_t old_hit_elink; ssize_t idx; /* Open target object */ if ((oid = H5Oopen(group, linkname, H5P_DEFAULT)) < 0) goto fail; /* Get object info */ if (H5Oget_info(oid, &oi) < 0) { H5Oclose(oid); goto fail; } /* Check if we have visited this file already */ if ((idx = table_list_visited(oi.fileno)) < 0) { /* We have not visited this file, build object tables */ if ((idx = table_list_add(oid, oi.fileno)) < 0) { H5Oclose(oid); goto fail; } } /* Do not recurse through an external link into the original file (idx=0) */ if (idx) { /* Update table pointers */ group_table = table_list.tables[idx].group_table; dset_table = table_list.tables[idx].dset_table; type_table = table_list.tables[idx].type_table; /* We will now traverse the external link, set this global to indicate this */ old_hit_elink = hit_elink; hit_elink = TRUE; /* add some indentation to distinguish that these objects are external */ dump_indent += COL; /* Recurse into the external file */ switch (oi.type) { case H5O_TYPE_GROUP: handle_groups(group, linkname, NULL, 0, objname); break; case H5O_TYPE_DATASET: handle_datasets(group, linkname, NULL, 0, objname); break; case H5O_TYPE_NAMED_DATATYPE: handle_datatypes(group, linkname, NULL, 0, objname); break; default: h5tools_setstatus(EXIT_FAILURE); } dump_indent -= COL; /* Reset table pointers */ group_table = old_group_table; dset_table = old_dset_table; type_table = old_type_table; /* Reset hit_elink */ hit_elink = old_hit_elink; } /* end if */ if (H5Idec_ref(oid) < 0) h5tools_setstatus(EXIT_FAILURE); return SUCCEED; fail: return FAIL; }