/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 <stdio.h>
#include <stdlib.h>
#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"
/*-------------------------------------------------------------------------
* 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, oid, 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
*
*-------------------------------------------------------------------------
*/
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, 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, outputformat->line_ncols, 0, 0);
error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 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, 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, outputformat->line_ncols, 0, 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, outputformat->line_ncols, 0, 0);
ctx.indent_level--;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 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, outputformat->line_ncols, 0, 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, 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, outputformat->line_ncols, 0, 0);
}
ctx.indent_level--;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 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, 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, outputformat->line_ncols, 0, 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, 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, outputformat->line_ncols, 0, 0);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 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, 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, outputformat->line_ncols, 0, 0);
HDfree(targbuf);
break;
default:
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 0);
ctx.indent_level++;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 0);
ctx.indent_level--;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 0);
break;
} /* end switch */
} /* end else */
done:
h5tools_str_close(&buffer);
if(obj_path)
HDfree(obj_path);
return ret;
}
/*-------------------------------------------------------------------------
* 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, outputformat->line_ncols, 0, 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, outputformat->line_ncols, 0, 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, outputformat->line_ncols, 0, 0);
/* print attributes */
dump_indent += COL;
/* attribute iteration: if there is a request to do H5_INDEX_CRT_ORDER and tracking order is set
in the datatype's create property list for attributes, then, sort by creation order, otherwise by name */
if((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) {
if(H5Aiterate2(tid, 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(tid, 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 */
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, outputformat->line_ncols, 0, 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, outputformat->line_ncols, 0, 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, outputformat->line_ncols, 0, 0);
}
else {
found_obj->displayed = TRUE;
/* 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((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 */
/* 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);
}
}
else {
/* 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((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 */
/* 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);
}
dump_indent -= COL;
ctx.indent_level--;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 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, 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, outputformat->line_ncols, 0, 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; i<data_loop; i++) {
if(display_packed_bits) {
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 0, 0);
/* Render the element */
h5tools_str_reset(&buffer);
packed_data_mask = packed_mask[i];
packed_data_offset = packed_offset[i];
packed_data_length = packed_length[i];
h5tools_print_packed_bits(&buffer, type);
h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos, outputformat->line_ncols, 0, 0);
}
switch(H5Tget_class(type)) {
case H5T_TIME:
ctx.indent_level++;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 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;i<data_loop;i++) */
}
H5Tclose(type);
if (!bin_output) {
/* 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((sort_by == H5_INDEX_CRT_ORDER) && (attr_crt_order_flags & H5P_CRT_ORDER_TRACKED)) {
if(H5Aiterate2(did, 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(did, 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 */
}
ctx.indent_level--;
dump_indent -= COL;
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 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
*-------------------------------------------------------------------------
*/
HDfprintf(rawoutstream, "\n%s %s\n",SUPER_BLOCK, BEGIN);
indentation(dump_indent + COL);
HDfprintf(rawoutstream, "%s %u\n","SUPERBLOCK_VERSION", super);
indentation(dump_indent + COL);
HDfprintf(rawoutstream, "%s %u\n","FREELIST_VERSION", freelist);
indentation(dump_indent + COL);
HDfprintf(rawoutstream, "%s %u\n","SYMBOLTABLE_VERSION", stab);
indentation(dump_indent + COL);
HDfprintf(rawoutstream, "%s %u\n","OBJECTHEADER_VERSION", shhdr);
indentation(dump_indent + COL);
HDfprintf(rawoutstream,"%s %Hd\n","OFFSET_SIZE", (long long)off_size);
indentation(dump_indent + COL);
HDfprintf(rawoutstream,"%s %Hd\n","LENGTH_SIZE", (long long)len_size);
indentation(dump_indent + COL);
HDfprintf(rawoutstream, "%s %u\n","BTREE_RANK", sym_ik);
indentation(dump_indent + COL);
HDfprintf(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");
#ifdef H5_HAVE_STREAM
else if (H5FD_STREAM==fdriver)
HDstrcpy(dname,"H5FD_STREAM");
#endif
else
HDstrcpy(dname,"Unknown driver");
/* Take out this because the driver used can be different from the
* standard output. */
/*indentation(dump_indent + COL);
HDfprintf(rawoutstream, "%s %s\n","FILE_DRIVER", dname);*/
#endif
indentation(dump_indent + COL);
HDfprintf(rawoutstream, "%s %u\n","ISTORE_K", istore_ik);
/*-------------------------------------------------------------------------
* USER_BLOCK
*-------------------------------------------------------------------------
*/
indentation(dump_indent + COL);
HDfprintf(rawoutstream, "USER_BLOCK %s\n",BEGIN);
indentation(dump_indent + COL + COL);
HDfprintf(rawoutstream,"%s %Hu\n","USERBLOCK_SIZE", userblock);
indentation(dump_indent + COL);
HDfprintf(rawoutstream, "%s\n",END);
HDfprintf(rawoutstream, "%s",END);
}
/*-------------------------------------------------------------------------
* Function: dump_fcontents
*
* Purpose: prints all objects
*
* Return: void
*
* Programmer: pvn
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void
dump_fcontents(hid_t fid)
{
HDfprintf(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)
HDfprintf(rawoutstream, " %-10s /#"H5_PRINTF_HADDR_FMT"\n", "datatype", type_table->objs[u].objno);
}
}
/* print objects in the files */
h5trav_print(fid);
HDfprintf(rawoutstream, " %s\n",END);
}
/*-------------------------------------------------------------------------
* 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;
const 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] == '/')
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 = attr + j + 1;
/* 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, 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, outputformat->line_ncols, 0, 0);
error_msg("unable to open object \"%s\"\n", obj_name);
ctx.need_prefix = TRUE;
h5tools_simple_prefix(rawoutstream, outputformat, &ctx, 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, outputformat->line_ncols, 0, 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, oid, attr, 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);
dump_indent -= COL;
return;
error:
h5tools_setstatus(EXIT_FAILURE);
if(obj_name)
HDfree(obj_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;
hid_t sid = H5Dget_space(dsetid);
int ndims = H5Sget_simple_extent_ndims(sid);
H5Sclose(sid);
if(ndims < 0) {
error_msg("H5Sget_simple_extent_ndims failed\n");
h5tools_setstatus(EXIT_FAILURE);
return;
}
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) {
HDfprintf(rawoutstream, "\n");
indentation(dump_indent);
begin_obj(h5tools_dump_header_format->datasetbegin, real_name, h5tools_dump_header_format->datasetblockbegin);
HDfprintf(rawoutstream, "\n");
indentation(dump_indent + COL);
HDfprintf(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) {
HDfprintf(rawoutstream, "\n");
begin_obj(h5tools_dump_header_format->groupbegin, real_name, h5tools_dump_header_format->groupblockbegin);
HDfprintf(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);
HDfprintf(rawoutstream, "\n");
switch(linfo.type) {
case H5L_TYPE_SOFT: /* Soft link */
begin_obj(h5tools_dump_header_format->softlinkbegin, links, h5tools_dump_header_format->softlinkblockbegin);
HDfprintf(rawoutstream, "\n");
indentation(COL);
if(H5Lget_val(fid, links, buf, linfo.u.val_size, H5P_DEFAULT) >= 0)
HDfprintf(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);
HDfprintf(rawoutstream, "\n");
indentation(COL);
begin_obj(h5tools_dump_header_format->extlinkbegin, links, h5tools_dump_header_format->extlinkblockbegin);
HDfprintf(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);
HDfprintf(rawoutstream, "LINKCLASS %d\n", linfo.type);
indentation(COL);
HDfprintf(rawoutstream, "TARGETFILE \"%s\"\n", elink_file);
indentation(COL);
HDfprintf(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);
HDfprintf(rawoutstream, "\n");
indentation(COL);
begin_obj(h5tools_dump_header_format->udlinkbegin, links, h5tools_dump_header_format->udlinkblockbegin);
HDfprintf(rawoutstream, "\n");
indentation(COL);
HDfprintf(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 */
HDfprintf(rawoutstream, "\n");
begin_obj(h5tools_dump_header_format->datatypebegin, real_name, h5tools_dump_header_format->datatypeblockbegin);
HDfprintf(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;
}