/* file: annxml.c G. Moody 28 June 2010
-------------------------------------------------------------------------------
heaxml: Convert a WFDB annotation file to XML format
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/).
_______________________________________________________________________________
*/
#include <stdio.h>
#include <wfdb/wfdb.h>
#include <wfdb/ecgcodes.h>
#define WFDBXMLPROLOG "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" \
"<?xml-stylesheet type=\"text/xsl\"" \
" href=\"wfdb.xsl\"?>\n" \
"<!DOCTYPE wfdbannotationset PUBLIC \"-//PhysioNet//DTD WFDB 1.0//EN\"" \
" \"http://physionet.org/physiobank/database/XML/wfdb.dtd\">\n"
char *token(char *p)
{
if (p) {
while (*p && *p != ' ' && *p != '\t' && *p != '\n')
p++; /* find whitespace */
while (*p && (*p == ' ' || *p == '\t' || *p == '\n'))
p++; /* find first non-whitespace */
if (*p == '\0') p = NULL;
}
return (p);
}
void output_xml(FILE *ofile, char *tag, char *p)
{
if (p) {
fprintf(ofile, "<%s>", tag);
while (*p) {
if (*p == '<') fprintf(ofile, "<");
else if (*p == '>') fprintf(ofile, ">");
else if (*p == '&') fprintf(ofile, "&");
else if (*p == '>') fprintf(ofile, ">");
else if (*p == '"') fprintf(ofile, """);
else if (*p == '\'') fprintf(ofile, "'");
else fprintf(ofile, "%c", *p);
p++;
}
fprintf(ofile, "</%s>", tag);
}
return;
}
int nsig;
FILE *ofile;
WFDB_Annotation annot;
WFDB_Frequency sfreq;
void process_start(char *tstring);
void process_anntab(void);
void process_annotation(void);
main(int argc, char **argv)
{
char *annotator, *ofname, *p, *pname, *record, *prog_name();
WFDB_Anninfo ai;
pname = prog_name(argv[0]);
if (argc < 3) {
(void)fprintf(stderr, "usage: %s RECORD ANNOTATOR\n", pname);
exit(1);
}
record = argv[1];
annotator = argv[2];
/* Discover the number of signals defined in the header. */
if ((nsig = isigopen(record, NULL, 0)) < 0) exit(2);
sfreq = sampfreq(record);
/* Open the input annotation file. */
ai.name = annotator;
ai.stat = WFDB_READ;
if (annopen(record, &ai, 1) < 0)
exit(3);
/* The name of the output file is of the form 'RECORD.ANNOTATOR.xml'. Any
directory separators (/) in the record name are replaced by hyphens (-)
in the output file name, so that the output file is always written into
the current directory. */
ofname = calloc(strlen(record)+strlen(annotator)+6, sizeof(char));
sprintf(ofname, "%s.%s.xml", record, annotator);
for (p = ofname; *p; p++)
if (*p == '/') *p = '-';
/* Open the output file and write the XML prolog. */
if ((ofile = fopen(ofname, "wt")) == NULL) {
fprintf(stderr, "%s: can't create %s\n", pname, ofname);
exit(4);
}
fprintf(ofile, WFDBXMLPROLOG);
(void)fprintf(ofile, "<wfdbannotationset annotator=\"%s\""
" record=\"%s\">\n", annotator, record);
process_start(mstimstr(0));
(void)fprintf(ofile, "<samplingfrequency>%.12g</samplingfrequency>\n",
sfreq);
while (getann(0, &annot) >= 0)
process_annotation();
process_anntab();
fprintf(ofile, "</wfdbannotationset>\n");
wfdbquit();
exit(0);
}
void process_start(char *p)
{
if (*p == '[') {
int day = -1, month = -1, year = -1;
double hour = -1.0, minute = -1.0, second = -1.0;
fprintf(ofile, "<start>\n");
sscanf(p+1, "%lf:%lf:%lf %d/%d/%d",
&hour, &minute, &second, &day, &month, &year);
if (year >= 0) {
if (year < 100) year += 1900;
if (year < 1975) year += 100;
fprintf(ofile, "<year>%d</year>\n", year);
}
if (month > 0) fprintf(ofile, "<month>%d</month>\n", month);
if (day > 0) fprintf(ofile, "<day>%d</day>\n", day);
if (second < 0) { /* incomplete start time in MM:SS or SS format */
if (minute < 0) { second = hour; hour = -1; } /* SS format */
else { second = minute; minute = hour; hour = -1; } /* MM:SS */
}
if (hour >= 0) fprintf(ofile, "<hour>%g</hour>\n", hour);
if (minute >= 0) fprintf(ofile, "<minute>%g</minute>\n", minute);
if (second >= 0) fprintf(ofile, "<second>%g</second>\n", second);
fprintf(ofile, "</start>\n");
}
}
static long anncount[ACMAX+1];
void process_anntab()
{
int i;
fprintf(ofile, "<anntab>");
for (i = 0; i <= ACMAX; i++) {
if (anncount[i]) {
fprintf(ofile, "<anntabentry><anntype>%d</anntype>", i);
output_xml(ofile, "anncode", annstr(i));
output_xml(ofile, "anndescription", anndesc(i));
fprintf(ofile, "<anncount>%ld</anncount></anntabentry>\n", anncount[i]);
}
}
fprintf(ofile, "</anntab>");
}
void process_annotation()
{
fprintf(ofile, "<annotation><time>%ld</time><anncode>%s</anncode>",
annot.time, annstr(annot.anntyp));
if (annot.subtyp) fprintf(ofile, "<subtype>%d</subtype>", annot.subtyp);
if (annot.chan) fprintf(ofile, "<chan>%d</chan>", annot.chan);
if (annot.num) fprintf(ofile, "<num>%d</num>", annot.num);
if (annot.aux) output_xml(ofile, "aux", annot.aux+1);
fprintf(ofile, "</annotation>\n");
anncount[annot.anntyp]++;
}
char *prog_name(s)
char *s;
{
char *p = s + strlen(s);
#ifdef MSDOS
while (p >= s && *p != '\\' && *p != ':') {
if (*p == '.')
*p = '\0'; /* strip off extension */
if ('A' <= *p && *p <= 'Z')
*p += 'a' - 'A'; /* convert to lower case */
p--;
}
#else
while (p >= s && *p != '/')
p--;
#endif
return (p+1);
}