/* file: rdsamp.c G. Moody 23 June 1983
Last revised: 11 December 2017
-------------------------------------------------------------------------------
rdsamp: Print an arbitrary number of samples from each signal
Copyright (C) 1983-2010 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>
/* values for timeunits */
#define SECONDS 1
#define MINUTES 2
#define HOURS 3
#define TIMSTR 4
#define MSTIMSTR 5
#define SHORTTIMSTR 6
#define HHMMSS 7
#define SAMPLES 8
#define WFDBXMLPROLOG "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" \
"<?xml-stylesheet type=\"text/xsl\"" \
" href=\"wfdb.xsl\"?>\n" \
"<!DOCTYPE wfdbsampleset PUBLIC \"-//PhysioNet//DTD WFDB 1.0//EN\"" \
" \"http://physionet.org/physiobank/database/XML/wfdb.dtd\">\n"
char *pname;
main(argc, argv)
int argc;
char *argv[];
{
char *record = NULL, *search = NULL, *escapify(), *prog_name();
char *invalid, *snfmt, *tfmt, *tnfmt, *tufmt, *vfmt, speriod[16], tustr[16];
int cflag = 0, highres = 0, i, isiglist, nsig, nosig = 0, pflag = 0, s,
*sig = NULL, timeunits = SECONDS, vflag = 0, xflag = 0;
WFDB_Frequency freq;
WFDB_Sample *v;
WFDB_Siginfo *si;
WFDB_Time from = 0L, maxl = 0L, to = 0L;
void help();
pname = prog_name(argv[0]);
for (i = 1 ; i < argc; i++) {
if (*argv[i] == '-') switch (*(argv[i]+1)) {
case 'c': /* output in CSV format */
cflag = 1;
break;
case 'f': /* starting time */
if (++i >= argc) {
(void)fprintf(stderr, "%s: time must follow -f\n", pname);
exit(1);
}
from = i;
break;
case 'h': /* help requested */
help();
exit(0);
break;
case 'H': /* select high-resolution mode */
highres = 1;
break;
case 'l': /* maximum length of output follows */
if (++i >= argc) {
(void)fprintf(stderr, "%s: max output length must follow -l\n",
pname);
exit(1);
}
maxl = i;
break;
case 'P': /* output in high-precision physical units */
++pflag; /* (fall through to case 'p') */
case 'p': /* output in physical units specified */
++pflag;
if (*(argv[i]+2) == 'd') timeunits = TIMSTR;
else if (*(argv[i]+2) == 'e') timeunits = HHMMSS;
else if (*(argv[i]+2) == 'h') timeunits = HOURS;
else if (*(argv[i]+2) == 'm') timeunits = MINUTES;
else if (*(argv[i]+2) == 'S') timeunits = SAMPLES;
else timeunits = SECONDS;
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 's': /* signal list follows */
isiglist = i+1; /* index of first argument containing a signal # */
while (i+1 < argc && *argv[i+1] != '-') {
i++;
nosig++; /* number of elements in signal list */
}
if (nosig == 0) {
(void)fprintf(stderr, "%s: signal list must follow -s\n",
pname);
exit(1);
}
break;
case 'S': /* search for valid sample of specified signal */
if (++i >= argc) {
(void)fprintf(stderr,
"%s: signal name or number must follow -S\n",
pname);
exit(1);
}
search = argv[i];
break;
case 't': /* end time */
if (++i >= argc) {
(void)fprintf(stderr, "%s: time must follow -t\n",pname);
exit(1);
}
to = i;
break;
case 'v': /* verbose output -- include column headings */
vflag = 1;
break;
case 'X': /* output in WFDB-XML format */
xflag = cflag = vflag = 1; /* format is CSV inside an XML wrapper */
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);
}
if ((nsig = isigopen(record, NULL, 0)) <= 0) exit(2);
if ((v = malloc(nsig * sizeof(WFDB_Sample))) == NULL ||
(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 = 0; i < nsig; i++)
if (si[i].gain == 0.0) si[i].gain = WFDB_DEFGAIN;
if (highres)
setgvmode(WFDB_HIGHRES);
freq = sampfreq(NULL);
if (from > 0L && (from = strtim(argv[from])) < 0L)
from = -from;
if (isigsettime(from) < 0)
exit(2);
if (to > 0L && (to = strtim(argv[to])) < 0L)
to = -to;
if (nosig) { /* print samples only from specified signals */
if ((sig = (int *)malloc((unsigned)nosig*sizeof(int))) == NULL) {
(void)fprintf(stderr, "%s: insufficient memory\n", pname);
exit(2);
}
for (i = 0; i < nosig; i++) {
if ((s = findsig(argv[isiglist+i])) < 0) {
(void)fprintf(stderr, "%s: can't read signal '%s'\n", pname,
argv[isiglist+i]);
exit(2);
}
sig[i] = s;
}
nsig = nosig;
}
else { /* print samples from all signals */
if ((sig = (int *)malloc((unsigned)nsig*sizeof(int))) == NULL) {
(void)fprintf(stderr, "%s: insufficient memory\n", pname);
exit(2);
}
for (i = 0; i < nsig; i++)
sig[i] = i;
}
/* Reset 'from' if a search was requested. */
if (search &&
((s = findsig(search)) < 0 || (from = tnextvec(s, from)) < 0)) {
(void)fprintf(stderr, "%s: can't read signal '%s'\n", pname, search);
exit(2);
}
/* Reset 'to' if a duration limit was specified. */
if (maxl > 0L && (maxl = strtim(argv[maxl])) < 0L)
maxl = -maxl;
if (maxl && (to == 0L || to > from + maxl))
to = from + maxl;
/* Adjust timeunits if starting time or date is undefined. */
if (timeunits == TIMSTR) {
char *p = timstr(0L);
if (*p != '[') timeunits = HHMMSS;
else if (strlen(p) < 16) timeunits = SHORTTIMSTR;
else if (freq > 1.0) timeunits = MSTIMSTR;
}
if (timeunits == HOURS) freq *= 3600.;
else if (timeunits == MINUTES) freq *= 60.;
/* Set formats for output. */
if (cflag) { /* CSV output selected */
snfmt = ",'%s'";
if (pflag) { /* output in physical units */
switch (timeunits) {
case SAMPLES: tnfmt = "'sample interval'";
sprintf(tustr, "'%g sec'", 1./freq);
tufmt = tustr; break;
case SHORTTIMSTR: tnfmt = "'Time'";
tufmt = "'hh:mm:ss.mmm'"; break;
case TIMSTR: tnfmt = "'Time and date'";
tufmt = "'hh:mm:ss dd/mm/yyyy'"; break;
case MSTIMSTR: tnfmt = "'Time and date'";
tufmt = "'hh:mm:ss.mmm dd/mm/yyyy'"; break;
case HHMMSS: tnfmt = "'Elapsed time'";
tufmt = "'hh:mm:ss.mmm'"; break;
case HOURS: tnfmt = "'Elapsed time'";
tufmt = "'hours'"; break;
case MINUTES: tnfmt = "'Elapsed time'";
tufmt = "'minutes'"; break;
default:
case SECONDS: tnfmt = "'Elapsed time'";
tufmt = "'seconds'"; break;
}
invalid = ",-";
if (pflag > 1) /* output in high-precision physical units */
vfmt = ",%.8lf";
else
vfmt = ",%.3lf";
}
else { /* output in raw units */
tnfmt = "'sample #'";
tfmt = "%ld";
vfmt = ",%d";
}
}
else { /* output in tab-separated columns selected */
if (pflag) { /* output in physical units */
switch (timeunits) {
case SAMPLES: tnfmt = "sample interval";
sprintf(speriod, "(%g", 1./freq);
speriod[10] = '\0';
sprintf(tustr, "%10s sec)", speriod);
tufmt = tustr; break;
case SHORTTIMSTR: tnfmt = " Time";
tufmt = "(hh:mm:ss.mmm)"; break;
case TIMSTR: tnfmt = " Time Date ";
tufmt = "(hh:mm:ss dd/mm/yyyy)"; break;
case MSTIMSTR: tnfmt = " Time Date ";
tufmt = "(hh:mm:ss.mmm dd/mm/yyyy)"; break;
case HHMMSS: tnfmt = " Elapsed time";
tufmt = " hh:mm:ss.mmm"; break;
case HOURS: tnfmt = " Elapsed time";
tufmt = " (hours)"; break;
case MINUTES: tnfmt = " Elapsed time";
tufmt = " (minutes)"; break;
default:
case SECONDS: tnfmt = " Elapsed time";
tufmt = " (seconds)"; break;
}
if (pflag > 1) { /* output in high-precision physical units */
snfmt = "\t%15s";
invalid = "\t -";
vfmt = "\t%15.8lf";
}
else {
snfmt = "\t%7s";
invalid = "\t -";
vfmt = "\t%7.3lf";
}
}
else { /* output in raw units */
snfmt = "\t%7s";
tnfmt = " sample #";
tfmt = "%15ld";
vfmt = "\t%7d";
}
}
/* Print WFDB-XML prolog if '-x' option selected. */
if (xflag) {
printf(WFDBXMLPROLOG);
printf("<wfdbsampleset>\n"
"<samplingfrequency>%g</samplingfrequency>\n"
"<signals>%d</signals>\n<description>",
freq, nsig);
}
/* Print column headers if '-v' option selected. */
if (vflag) {
char *p, *t;
int j, l;
(void)printf("%s", tnfmt);
for (i = 0; i < nsig; i++) {
/* Check if a default signal description was provided by looking
for the string ", signal " in the desc field. If so, replace it
with a shorter string. */
p = si[sig[i]].desc;
if (strstr(p, ", signal ")) {
char *t;
if (t = malloc(10*sizeof(char))) {
(void)sprintf(t, "sig %d", sig[i]);
p = t;
}
}
if (cflag == 0) {
l = strlen(p);
if (pflag > 1) {
if (l > 15) p += l - 15;
}
else {
if (l > 7) p+= l - 7;
}
}
else
p = escapify(p);
(void)printf(snfmt, p);
}
if (xflag) (void)printf("</description>");
(void)printf("\n");
}
/* Print data in physical units if '-p' option selected. */
if (pflag) {
char *p;
/* Print units as a second line of column headers if '-v' selected. */
if (vflag) {
char s[12];
if (xflag) (void)printf("<units>");
(void)printf("%s", tufmt);
for (i = 0; i < nsig; i++) {
p = si[sig[i]].units;
if (p == NULL) p = "mV";
if (cflag == 0) {
char ustring[16];
int len;
len = strlen(p);
if (pflag > 1) { if (len > 13) len = 13; }
else if (len > 5) len = 5;
ustring[0] = '(';
strncpy(ustring+1, p, len);
ustring[len+1] = '\0';
(void)printf(pflag > 1 ? "\t%14s)" : "\t%6s)", ustring);
}
else {
p = escapify(p);
(void)printf(",'%s'", p);
}
}
if (xflag) (void)printf("</units>");
(void)printf("\n");
}
if (xflag) (void)printf("<samplevectors>\n");
while ((to == 0L || from < to) && getvec(v) >= 0) {
if (cflag == 0) {
switch (timeunits) {
case TIMSTR: (void)printf("%s", timstr(-from)); break;
case SHORTTIMSTR:
case MSTIMSTR: (void)printf("%s", mstimstr(-from)); break;
case HHMMSS: (void)printf("%15s", from == 0L ?
"0:00.000" : mstimstr(from)); break;
case SAMPLES: (void)printf("%15ld", from); break;
default:
case SECONDS: (void)printf("%15.3lf",(double)from/freq); break;
case MINUTES: (void)printf("%15.5lf",(double)from/freq); break;
case HOURS: (void)printf("%15.7lf",(double)from/freq); break;
}
}
else {
switch (timeunits) {
case TIMSTR:
for (p = timstr(-from); *p == ' '; p++)
;
(void)printf("'%s'", p); break;
case SHORTTIMSTR:
case MSTIMSTR:
for (p = mstimstr(-from); *p == ' '; p++)
;
(void)printf("'%s'", p); break;
case HHMMSS:
if (from == 0L) printf("'0:00.000'");
else {
for (p = mstimstr(from); *p == ' '; p++)
;
(void)printf("'%s'", p); break;
}
break;
case SAMPLES: (void)printf("%ld", from); break;
default:
case SECONDS: (void)printf("%.3lf",(double)from/freq); break;
case MINUTES: (void)printf("%.5lf",(double)from/freq); break;
case HOURS: (void)printf("%.7lf",(double)from/freq); break;
}
}
from++;
for (i = 0; i < nsig; i++) {
if (v[sig[i]] != WFDB_INVALID_SAMPLE)
(void)printf(vfmt,
((double)v[sig[i]] - si[sig[i]].baseline)/si[sig[i]].gain);
else
(void)printf("%s", invalid);
}
(void)printf("\n");
}
}
else { /* output in raw units */
if (xflag) (void)printf("<samplevectors>\n");
while ((to == 0L || from < to) && getvec(v) >= 0) {
(void)printf(tfmt, from++);
for (i = 0; i < nsig; i++)
(void)printf(vfmt, v[sig[i]]);
(void)printf("\n");
}
}
if (xflag) /* print trailer if WFDB-XML output was selected */
printf("</samplevectors>\n</wfdbsampleset>\n");
exit(0);
}
char *escapify(char *s)
{
char *p = s, *q = s, *r;
int c = 0;
while (*p) {
if (*p == '\'' || *p == '\\')
c++;
p++;
}
if (c > 0 && (p = r = calloc(p-s+c, sizeof(char))) != NULL) {
while (*q) {
if (*q == '\'' || *q == '\\')
*q++ = '\\';
*p++ = *q;
}
q = r;
}
return (q);
}
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 record, and OPTIONS may include:",
" -c use CSV (comma-separated value) output format",
" -f TIME begin at specified time",
" -h print this usage summary",
" -H read multifrequency signals in high resolution mode",
" -l INTERVAL truncate output after the specified time interval (hh:mm:ss)",
" -p print times and samples in physical units (default: raw units)",
" -P same as -p, but with greater precision",
" -p and -P may be followed by a character to choose a time",
" format; choices are:",
" -pd (or -Pd) print time of day and date if known",
" -pe (or -Pe) print elapsed time as <hours>:<minutes>:<seconds>",
" -ph (or -Ph) print elapsed time in hours",
" -pm (or -Pm) print elapsed time in minutes",
" -ps (or -Ps) print elapsed time in seconds",
" -pS (or -PS) print elapsed time in sample intervals",
" -s SIGNAL [SIGNAL ...] print only the specified signal(s)",
" -S SIGNAL search for a valid sample of the specified SIGNAL at or after",
" the time specified with -f, and begin printing then",
" -t TIME stop at specified time",
" -v print column headings",
" -X output in WFDB-XML format",
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]);
}