/* file: rdedfann.c G. Moody 14 March 2008
Last revised: 5 March 2014
-------------------------------------------------------------------------------
rdedfann: Print annotations from an EDF+ file
Copyright (C) 2008-2014 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/).
_______________________________________________________________________________
This program prints the annotations from an EDF+ file in the same format as
'rdann' does for WFDB-compatible annotation files. Note, however, that the
annotation mnemonics in EDF+ files do not in general match those used in
WFDB-compatible annotation files, so that it will usually be necessary to
translate those that come from EDF+ file before the text can be converted
by 'wrann'. For example, this command can be used to extract annotations
from 'foo.edf', change the EDF+ annotation type "QRS" to the WFDB type "N",
and then produce a WFDB-compatible annotation file 'foo.edf.qrs':
rdedf -r foo.edf | sed "s/QRS/ N" | wrann -r foo.edf -a qrs
*/
#include <stdio.h>
#include <wfdb/wfdb.h>
char *pname;
double sfreq = 0.0;
int state;
main(int argc, char **argv)
{
char *record = NULL, *prog_name();
int aindex = 0, alen = 0, framelen = 0, i, nsig, s, vflag = 0, xflag = 0;
WFDB_Sample *frame;
WFDB_Siginfo *si;
void help();
pname = prog_name(argv[0]);
for (i = 1; i < argc; i++) {
if (*argv[i] == '-') switch (*(argv[i]+1)) {
case 'F':
if (++i >= argc) {
(void)fprintf(stderr, "%s: sampling frequency must follow -F\n",
pname);
exit(1);
}
sscanf(argv[i], "%lf", &sfreq);
if (sfreq <= 0.0) sfreq = 1.0;
break;
case 'h': /* help requested */
help();
exit(0);
break;
case 'r': /* record name */
if (++i >= argc) {
(void)fprintf(stderr, "%s: record name must follow -r\n",
pname);
exit(1);
}
record = argv[i];
break;
case 'v': /* verbose output -- include column headings */
vflag = 1;
break;
case 'x': /* save EDF annotation text in aux rather than anntyp */
xflag = 1;
break;
default:
(void)fprintf(stderr, "%s: unrecognized option %s\n", pname,
argv[i]);
exit(1);
}
else {
(void)fprintf(stderr, "%s: unrecognized argument %s\n", pname,
argv[i]);
exit(1);
}
}
if (record == NULL) {
help();
exit(1);
}
setgvmode(WFDB_HIGHRES);
if ((nsig = isigopen(record, NULL, 0)) <= 0) exit(2);
if ((si = malloc(nsig * sizeof(WFDB_Siginfo))) == NULL) {
(void)fprintf(stderr, "%s: insufficient memory\n", pname);
exit(2);
}
if ((nsig = isigopen(record, si, nsig)) <= 0)
exit(2);
for (i = framelen = 0; i < nsig; i++) {
if (strcmp(si[i].desc, "EDF Annotations") == 0) {
aindex = framelen;
alen = si[i].spf;
}
framelen += si[i].spf;
}
if (alen == 0) {
(void)fprintf(stderr, "%s: record %s has no EDF annotations\n",
pname, record);
(void)free(si);
wfdbquit();
exit(3);
}
if ((frame = (int *)malloc((unsigned)framelen*sizeof(WFDB_Sample)))==NULL) {
(void)fprintf(stderr, "%s: insufficient memory\n", pname);
(void)free(si);
exit(2);
}
if (sfreq > 0.0) {
setgvmode(WFDB_LOWRES);
setsampfreq(sfreq);
}
else
sfreq = sampfreq(NULL);
/* Print column headers if '-v' option selected. */
if (vflag)
(void)printf(" Time Sample # Type Sub Chan Num\tAux\n");
while (getframe(frame) > 0) {
WFDB_Sample *p;
state = 0;
for (i = 0, p = (frame + aindex); i < alen; i++, p++) {
if (*p || state) {
proc(*p, xflag);
proc(*p >> 8, xflag);
}
else
break;
}
}
(void)free(frame);
(void)free(si);
wfdbquit();
exit(0); /*NOTREACHED*/
}
proc(int x, int xflag)
{
static char onset[1024], duration[1024], text[1024];
static char *onsetp, *durationp, *textp;
x &= 0xff;
switch (state) {
case 0: /* looking for a new TAL */
if (x == '\0')
break;
if (x != '+')
fprintf(stderr, "%s: unexpected character '%c' in input\n",
pname, x);
else {
state = 1;
onsetp = onset;
durationp = duration;
textp = text;
*textp = 0;
}
break;
case 1: /* accumulate characters from onset until 024 or 025 */
if (x == '\025') { /* end of onset, start of duration */
x = 0;
state = 2;
}
else if (x == '\024') { /* end of onset, start of annotation */
x = 0;
state = 3;
}
*(onsetp++) = x;
break;
case 2: /* accumulate characters from duration until 024 */
if (x == '\024') { /* end of onset, start of annotation */
x = 0;
state = 3;
}
*(durationp++) = x;
break;
case 3: /* accumulate characters from annotation until 024 */
if (x == '\024') { /* end of annotation */
x = 0;
state = 4;
}
*(textp++) = x;
break;
case 4: /* annot just ended, there may be another */
if (text[0]) { /* the annotation was not empty -- output it */
long t = (long)(atof(onset) * sfreq + 0.5);
/* replace whitespace with '_' */
for (textp = text; *textp; textp++)
if (*textp == ' ' || *textp == '\t') *textp = '_';
printf("%s %7ld %5s%5d%5d%5d\t%s",
t ? mstimstr(t) : " 0:00.000", t,
xflag ? "\"" : text, 0, 0, 0, xflag ? text : "");
if (duration[0])
printf("%cduration: %s", xflag ? ' ' : '\t', duration);
printf("\n");
}
if (x) {
text[0] = x;
textp = text + 1;
state = 3;
}
else /* end of TAL */
state = 0;
break;
}
}
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);
}
static char *help_strings[] = {
"usage: %s -r RECORD [OPTIONS ...]\n",
"where RECORD is the name of the input EDF+ record, and OPTIONS may include:",
" -F FREQ set the sampling frequency to FREQ Hz\n",
" -h print this usage summary",
" -v print column headings",
" -x print EDF+ annotation text in aux (default: print in anntyp)",
NULL
};
void help()
{
int i;
(void)fprintf(stderr, help_strings[0], pname);
for (i = 1; help_strings[i] != NULL; i++)
(void)fprintf(stderr, "%s\n", help_strings[i]);
}