/* file: xmlann.c G. Moody 22 August 2010
Last revised: 11 December 2017
-------------------------------------------------------------------------------
xmlann: Convert a WFDB-XML file to a WFDB-compatible annotation file
Copyright (C) 2010 George B. Moody
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program; if not, see <http://www.gnu.org/licenses/>.
You may contact the author by e-mail (wfdb@physionet.org) or postal mail
(MIT Room E25-505A, Cambridge, MA 02139 USA). For updates to this software,
please visit PhysioNet (http://www.physionet.org/).
_______________________________________________________________________________
The input to xmlann should be an XML file containing a <wfdbannotationset>,
as specified by 'wfdb.dtd'; see '100s.atr.xml' for a sample in this format.
The inverse transformation can be performed by 'annxml'.
TODO: collect anntabentry items and write anntab (rearrange in annhea
so this can be done in one pass). Optionally write a simple header
file and include sampling frequency/length/start attributes in it.
Define and handle new annotation dur and url items. */
#include <stdio.h>
#include <string.h>
#include <wfdb/wfdb.h>
#include "xmlproc.h" /* provides main(), process(), DATALEN, qflag, vflag */
char *content;
int depth, plen, output_not_open;
WFDB_Anninfo ai;
WFDB_Annotation a;
char *record, *rec;
double sps;
void XMLCALL start(void *data, const char *el, const char **attr)
{
int i;
sprintf(data + strlen(data), "/%s", el);
if (vflag) {
printf("\n%s", (char *) data);
for (i = 0; attr[i]; i += 2)
printf(" %s='%s'", attr[i], attr[i + 1]);
fflush(stdout);
}
if (strcmp("wfdbannotationset", el) == 0) {
if (depth) {
fprintf(stderr, "Malformed input: wfdbannotationset not at root\n");
// exit(1);
}
for (i = 0; attr[i]; i += 2) {
if (attr[i] && strcmp("annotator", attr[i]) == 0)
SSTRCPY(ai.name, attr[i+1]);
if (attr[i] && strcmp("record", attr[i]) == 0)
SSTRCPY(record, attr[i+1]);
}
if (ai.name == NULL || record == NULL) {
fprintf(stderr, "Malformed input: wfdbannotationset is missing a"
" required annotator or record attribute\n");
// exit(1);
}
for (rec = record + strlen(record); rec > record; rec--)
if (*rec == '/') { rec++; break; }
output_not_open = 1;
}
depth++;
}
void XMLCALL middle(void *data, const char *el, int len)
{
if (plen == 0) { /* not in the same element as last time */
if (len == 1 && *el == '\n')
return; /* ignore newlines outside of tags */
SALLOC(content, plen = len + 1, sizeof(char));
strncpy(content, el, len);
}
else {
SREALLOC(content, plen + len, sizeof(char));
strncpy(content + plen - 1, el, len);
plen += len;
}
if (vflag) { printf("\t|%s|", content); fflush(stdout); }
}
void XMLCALL end(void *data, const char *el)
{
char *p;
int i;
long t;
depth--;
if (depth == 0) {
if (strcmp("wfdbannotationset", el) == 0) {
wfdbquit();
if (!qflag) printf("%s.%s\n", rec, ai.name);
}
else if (record) {
fprintf(stderr, "Malformed input ends without /wfdbannotationset\n");
// exit(1);
}
else {
fprintf(stderr, "No wfdbannotationset in input\n");
// exit(1);
}
}
else if (strcmp("samplingfrequency", el) == 0)
sscanf(content, "%lf", &sps);
else if (strcmp("/wfdbannotationset/annotation", data) == 0) {
if (output_not_open) {
if (sps > 0) setafreq(sps);
ai.stat = WFDB_WRITE;
annopen(rec, &ai, 1);
output_not_open = 0;
}
putann(0, &a);
a.anntyp = a.subtyp = a.chan = a.num = 0;
a.aux = NULL;
}
else if (strcmp("/wfdbannotationset/annotation/time", data) == 0) {
sscanf(content, "%ld", &t);
a.time = t;
}
else if (strcmp("/wfdbannotationset/annotation/anncode", data) == 0) {
a.anntyp = strann(content);
}
else if (strcmp("/wfdbannotationset/annotation/subtype", data) == 0) {
sscanf(content, "%d", &i);
a.subtyp = i;
}
else if (strcmp("/wfdbannotationset/annotation/chan", data) == 0) {
sscanf(content, "%d", &i);
a.chan = i;
}
else if (strcmp("/wfdbannotationset/annotation/num", data) == 0) {
sscanf(content, "%d", &i);
a.num = i;
}
else if (strcmp("/wfdbannotationset/annotation/aux", data) == 0) {
static char auxbuf[256];
if ((i = strlen(content)) > 254) { i = 254; }
a.aux = auxbuf;
auxbuf[0] = i;
strncpy(auxbuf+1, content, i);
auxbuf[i+1] = '\0';
}
plen = 0;
for (p = data + strlen(data) - 1; p > (char *)data; p--)
if (*p == '/') { *p = '\0'; break; }
if (vflag) { printf("."); fflush(stdout); }
}
void cleanup()
{
content = NULL;
depth = plen = output_not_open = 0;
ai.name = NULL;
a.anntyp = a.subtyp = a.chan = a.num = 0;
a.aux = record = rec = NULL;
sps = 0;
}
void help()
{
fprintf(stderr, "usage: %s [ OPTION ...] [ FILE ... ]\n", pname);
fprintf(stderr, " OPTIONs may include:\n"
" -h print this usage summary\n"
" -q quiet mode (print errors only)\n"
" -v verbose mode\n"
" FILE is the name of a WFDB-XML annotation file to be converted\n"
" into one or more WFDB annotation files, or '-' to convert the\n"
" standard input.\n");
exit(1);
}