int fetchannotations(void)
{
int afirst = 1, i;
WFDB_Anninfo ai;
WFDB_Time ta0, taf;
if (nann < 1) return (0);
if (tfreq != ffreq) {
ta0 = (WFDB_Time)(t0*tfreq/ffreq + 0.5);
taf = (WFDB_Time)(tf*tfreq/ffreq + 0.5);
}
else {
ta0 = t0;
taf = tf;
}
printf(" %c \"annotator\":\n [", nosig > 0 ? ' ' : '{');
setgvmode(WFDB_HIGHRES);
for (i = 0; i < nann; i++) {
ai.name = annotator[i];
ai.stat = WFDB_READ;
if (annopen(recpath, &ai, 1) >= 0) {
char *p;
int first = 1;
WFDB_Annotation annot;
if (ta0 > 0L) iannsettime(ta0);
if (!afirst) printf(",");
else afirst = 0;
printf("\n { \"name\": \"%s\",\n", annotator[i]);
printf(" \"annotation\":\n");
printf(" [");
while ((getann(0, &annot) == 0) && (taf <= 0 || annot.time < taf)) {
if (!first) printf(",");
else first = 0;
printf("\n { \"t\": %ld,\n", (long)(annot.time));
printf(" \"a\": %s,\n",
p = strjson(annstr(annot.anntyp)));
SFREE(p);
printf(" \"s\": %d,\n", annot.subtyp);
printf(" \"c\": %d,\n", annot.chan);
printf(" \"n\": %d,\n", annot.num);
if (annot.aux && *(annot.aux)) {
printf(" \"x\": %s\n", p = strjson(annot.aux+1));
SFREE(p);
}
else
printf(" \"x\": null\n");
printf(" }");
}
printf("\n ]\n }");
}
}
printf("\n ]\n }\n");
return (1);
}
INTEGER getann_(INTEGER *annotator, INTEGER *time, INTEGER *anntyp, INTEGER *subtyp, INTEGER *chan, INTEGER *num, char *aux)
{
static WFDB_Annotation iann;
int i, j;
i = getann((WFDB_Annotator)(*annotator), &iann);
if (i == 0) {
*time = iann.time;
*anntyp = iann.anntyp;
*subtyp = iann.subtyp;
*chan = iann.chan;
*num = iann.num;
aux = iann.aux;
}
return (i);
}
main()
{
WFDB_Anninfo an[2];
char record[8], iann[10], oann[10];
WFDB_Annotation annot;
printf("Type record name: ");
fgets(record, 8, stdin); record[strlen(record)-1] = '\0';
printf("Type input annotator name: ");
fgets(iann, 10, stdin); iann[strlen(iann)-1] = '\0';
printf("Type output annotator name: ");
fgets(oann, 10, stdin); oann[strlen(oann)-1] = '\0';
an[0].name = iann; an[0].stat = WFDB_READ;
an[1].name = oann; an[1].stat = WFDB_WRITE;
if (annopen(record, an, 2) < 0) exit(1);
while (getann(0, &annot) == 0)
if (isqrs(annot.anntyp)) {
annot.anntyp = NORMAL;
if (putann(0, &annot) < 0) break;
}
wfdbquit();
}
int main(int argc, char **argv)
{
int c;
int inflag = 0;
int dbg = 0;
int sr_ds = 200;
char * rec_name = "vfdb/427";
char * db_path = "/opt/physiobank/database";
size_t win_sec = 8;
/* r stands for record with folder
* p for path
* i for information of record
* s downsample sr
* w window length default:8
* d debug
*/
while ((c = getopt(argc, argv, "idr:p:s:w:")) != -1)
switch (c){
case 'i':
inflag = 1;
break;
case 'r':
rec_name = optarg;
break;
case 'p':
db_path = optarg;
break;
case 's':
sr_ds= atoi(optarg);
break;
case'w':
win_sec = atoi(optarg);
break;
case'd':
dbg = 1;
break;
default:
abort();
}
int i, j, nsig;
WFDB_Sample *v;
WFDB_Siginfo *s;
WFDB_Anninfo a;
setwfdb(db_path);
nsig = isigopen(rec_name, NULL, 0);
if (nsig < 1){
printf("nsig:%d\n",nsig);
exit(1);
}
s = (WFDB_Siginfo *)malloc(nsig * sizeof(WFDB_Siginfo));
if (isigopen(rec_name, s, nsig) != nsig)
exit(1);
v = (WFDB_Sample *)malloc(nsig * sizeof(WFDB_Sample));
int orig_sr = sampfreq(rec_name);
a.name = "atr"; a.stat = WFDB_READ;
if (wfdbinit(rec_name, &a, 1, s, nsig) != nsig) exit(3);
if(1 == inflag ){
printf("sr:%d\n",orig_sr);
printf("%d signals\n", nsig);
for (i = 0; i < nsig; i++) {
printf("Group %d, Signal %d:\n", s[i].group, i);
printf("File: %s\n", s[i].fname);
printf("Description: %s\n", s[i].desc);
printf("Gain: ");
if (s[i].gain == 0.)
printf("uncalibrated; assume %g", WFDB_DEFGAIN);
else printf("%g", s[i].gain);
printf(" adu/%s\n", s[i].units ? s[i].units : "mV");
printf(" Initial value: %d\n", s[i].initval);
printf(" Storage format: %d\n", s[i].fmt);
printf(" I/O: ");
if (s[i].bsize == 0) printf("can be unbuffered\n");
else printf("%d-byte blocks\n", s[i].bsize);
printf(" ADC resolution: %d bits\n", s[i].adcres);
printf(" ADC zero: %d\n", s[i].adczero);
if (s[i].nsamp > 0L) {
printf(" Length: %s (%ld sample intervals)\n",
timstr(s[i].nsamp), s[i].nsamp);
printf(" Checksum: %d\n", s[i].cksum);
}
else printf(" Length undefined\n");
}
}
fifo_t fifo_ecg;
int fifo_ecg_buf[FIFO_SIZE];
fifo_init(&fifo_ecg, fifo_ecg_buf, FIFO_SIZE);
fifo_t fifo_bt;
int fifo_bt_buf[FIFO_SIZE];
fifo_init(&fifo_bt, fifo_bt_buf, FIFO_SIZE);
int tmp = 0;
int sr = 200;
WFDB_Time begin_samp = 0;
WFDB_Time end_samp = orig_sr*win_sec;
WFDB_Annotation begin_ann;
WFDB_Annotation end_ann;
getann(0, &begin_ann);
while(0 == getann(0, &end_ann))
if ((end_ann.aux != NULL && *end_ann.aux > 0)
||0 == strcmp(annstr(end_ann.anntyp), "[")
||0 == strcmp(annstr(end_ann.anntyp), "]")
||0 == strcmp(annstr(end_ann.anntyp), "~")
){
break;
}
int * pBt_len = (int*)calloc(win_sec,sizeof(int));
ResetBDAC();
for (; ;) {
if (getvec(v) < 0)
break;
// for (j = 0; j < nsig; j++){
// }
tmp = v[nsig-1];
tmp = v[0];
int vout1 = 0;
static int bt_i = 0;
static unsigned int samplecnt = 0;
int idx = 0;
if(down_sample(tmp, &vout1, orig_sr, sr)) {
samplecnt ++;
fifo_write(&fifo_ecg, &vout1, 1*sizeof(int));
int beatType, beatMatch;
long ltmp = vout1-s[0].adczero;
ltmp *= 200; ltmp /= s[0].gain;
int bdac_dly = BeatDetectAndClassify(ltmp, &beatType, &beatMatch);
idx = bt_i/sr;
if (0 != bdac_dly ) {
pBt_len[idx]++;
fifo_write(&fifo_bt, &beatType, sizeof(int));
}
bt_i = ++bt_i%(win_sec*sr);
}
double cm = 0.0;
int size = win_sec*sr;
if(fifo_len(&fifo_ecg)/sizeof(int) >= sr*win_sec){
int * win_data = (int*)malloc(win_sec*sr*sizeof(int));
int * ds_data = (int*)malloc(win_sec*sr_ds*sizeof(int));
int len = fifo_len(&fifo_bt)/sizeof(int);
int * p = (int*)calloc(len, sizeof(int));
if (0 != len){
//printf("bt_i:%d\n", bt_i);
fifo_read_steps(&fifo_bt, p, len*sizeof(int), pBt_len[bt_i/sr]*sizeof(int));
//for (i = 0;i< len;i++) printf("%d ", p[i]);
//printf("\n");
}
pBt_len[bt_i/sr] = 0;
fifo_read_steps(&fifo_ecg, win_data, size*sizeof(int), sr*sizeof(int));
filtering(win_data, size, sr);
int i = 0;
int ds_size = 0;
int vout;
for(i = 0;i < size;i++){
// if(down_sample(win_data[i], &vout, sr, sr_ds)) ds_data[ds_size++] = vout;
}
double dven = 0.0;
if (0 != len){
int tmp_cnt = 0;
for(i = 0; i < len ; i++){
if(5 == p[i]) dven ++;
}
//printf("div:%d %d\n", tmp_cnt, len);
dven /= len;
}
//cm = ecg_complexity_measure(win_data, size);
//cm = ecg_complexity_measure(ds_data, ds_size);
//cm = cpsd(ds_data, ds_size, 0.5*sr_ds);
//cm = calc_grid(ds_data, ds_size, 0.5*sr_ds);
cm = calc_grid(win_data, size, 0.5*sr);
if (-1 == cm ) continue;
//VT print 1;
//VF print 2;
int hr = (int)((double)(len*60)/win_sec+0.5);
int ret = check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(VT");
if (1 == ret){
printf("%d %lf %lf %d\n", 1, cm, dven, hr);
} else if (0 == ret) {
ret = check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(VFL");
int ret2 = check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "[");
if (1 == ret || 1 == ret2){
printf("%d %lf %lf %d\n", 2, cm, dven, hr);
} else if (0 == ret){
// ret = check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(N");
// int ret3 = check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "N");
// if ((1 == ret || 1 == ret3) && -1 != begin_ann.subtyp) printf ("%d %lf %lf %d\n", 0, cm, dven, hr);
if (1 == check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(AFIB")
|| 1 == check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(AFL")
|| 1 == check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(IVR")
|| 1 == check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(SVTA")
|| 1 == check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(SBR")
|| 1 == check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(BII")
) printf ("%d %lf %lf %d\n", 0, cm, dven, hr);
// int ret = check_ann(begin_samp, end_samp, &begin_ann, &end_ann, "(SVTA");
// if (1 == ret) printf ("%d %lf\n", 0, cm);
}
}
//iannsettime(begin_samp);
begin_samp += orig_sr;
end_samp += orig_sr;
if(end_ann.time < begin_samp){
begin_ann = end_ann;
while(1)
if (0 != getann(0, &end_ann)){
end_ann = begin_ann;
/*the last sample of the signal*/
end_ann.time = s[nsig-1].nsamp;
break;
}else if ((end_ann.aux != NULL && *end_ann.aux > 0)
||0 == strcmp(annstr(end_ann.anntyp), "[")
||0 == strcmp(annstr(end_ann.anntyp), "]")
||0 == strcmp(annstr(end_ann.anntyp), "~")
){
break;
}
if(dbg){
printf("begin tm:%s type:%s ", mstimstr(begin_ann.time), annstr(begin_ann.anntyp));
if(begin_ann.aux != NULL)
printf("begin aux:%s", begin_ann.aux+1);
printf("\n");
printf("end tm:%s type:%s ", mstimstr(end_ann.time), annstr(end_ann.anntyp));
if (end_ann.aux != NULL)
printf("end aux:%s", end_ann.aux+1);
printf("\n");
printf("begin sample:%s\n", mstimstr(begin_samp));
printf("ann diff:%s\n", mstimstr(end_ann.time-begin_ann.time));
}
}
free(p);
free(ds_data);
free(win_data);
}
}
free(pBt_len);
wfdbquit();
return 0;
}
main(int argc, char **argv)
{
char *oaname = "gqf";
double HR;
FILE *config = NULL;
int a0 = 0, a1 = 0, **count, dn, i, ibest, ichosen = 0, j, *mbuf,
n, niann = 0, nseg, tdn;
WFDB_Anninfo *a;
WFDB_Annotation annot;
WFDB_Frequency spm;
WFDB_Time t0, tf;
pname = prog_name(argv[0]);
for (i = 1; i < argc; i++) {
if (*argv[i] == '-') switch (*(argv[i]+1)) {
case 'a': /* input annotator names */
for (a0 = a1 = ++i; a1 < argc && *argv[a1] != '-'; a1++, i++)
;
if ((niann = a1 - a0) < 2) {
(void)fprintf(stderr,
"%s: input annotator names must follow -a\n",
pname);
cleanup(1);
}
break;
case 'c': /* configuration file */
if (++i >= argc) {
(void)fprintf(stderr,
"%s: name of configuration file must follow -c\n", pname);
cleanup(1);
}
if ((config = fopen(argv[i], "rt")) == NULL) {
(void)fprintf(stderr,
"%s: can't read configuration file %s\n", pname, argv[i]);
cleanup(1);
}
break;
case 'h': /* help requested */
help();
cleanup(0);
break;
case 'o': /* output annotator name */
if (++i >= argc) {
(void)fprintf(stderr,
"%s: output annotator name must follow -o\n",
pname);
cleanup(1);
}
oaname = argv[i];
break;
case 'r': /* record name */
if (++i >= argc) {
(void)fprintf(stderr, "%s: input record name must follow -r\n",
pname);
cleanup(1);
}
record = argv[i];
break;
default:
(void)fprintf(stderr, "%s: unrecognized option %s\n", pname,
argv[i]);
cleanup(1);
}
else {
(void)fprintf(stderr, "%s: unrecognized argument %s\n", pname,
argv[i]);
cleanup(1);
}
}
/* Quit unless record name and at least two annotator names specified. */
if (record == NULL || niann < 2) {
help();
cleanup(1);
}
/* Set up annotator info. */
a = gcalloc(sizeof(WFDB_Anninfo), niann+1);
for (i = a0, j = 0; i < a1; i++, j++) {
a[j].name = argv[i]; a[j].stat = WFDB_READ;
}
a[j].name = oaname; a[j].stat = WFDB_WRITE;
/* Read a priori physiologic parameters from the configuration file if
available. They can be adjusted in the configuration file for pediatric,
fetal, or animal ECGs. */
if (config) {
char buf[256], *p;
/* Read the configuration file a line at a time. */
while (fgets(buf, sizeof(buf), config)) {
/* Skip comments (empty lines and lines beginning with `#'). */
if (buf[0] == '#' || buf[0] == '\n') continue;
/* Set parameters. Each `getconf' below is executed once for
each non-comment line in the configuration file. */
getconf(HR, "%lf");
}
fclose(config);
}
/* If any a priori parameters were not specified in the configuration file,
initialize them here (using values chosen for adult human ECGs). */
if (HR == 0.0) HR = 75;
spm = 60.0 * sampfreq(record); /* sample intervals per minute */
nseg = strtim("e")/spm; /* number of complete 1-minute intervals */
/* Set up buffer for median calculation. */
mbuf = gcalloc(sizeof(int), niann + 1);
mbuf[niann] = HR; /* initial median is HR */
/* Set up arrays for HR minute-by-minute time series. */
count = gcalloc(sizeof(int *), niann + 1);
for (i = 0; i < niann; i++)
count[i] = gcalloc(sizeof(int), nseg+1);
/* Pass 1: Load the HR arrays. */
if (annopen(record, a, niann) < 0) cleanup(2);
for (i = 0; i < niann; i++) {
for (tf = spm, j = 0; j < nseg+1; tf += spm, j++) {
n = 0;
while (getann(i, &annot) == 0 && annot.time < tf)
if (isqrs(annot.anntyp)) n++;
count[i][j] = n;
}
}
wfdbquit();
/* Pass 2: Select the input annotations to be copied, and copy them. */
if (annopen(record, a, niann+1) < 0) cleanup(2);
for (j = 0, t0 = 0, tf = spm; j < nseg+1; j++, t0 = tf, tf += spm) {
for (i = 0; i < niann; i++)
mbuf[i] = count[i][j];
/* Note that the last element, mbuf[niann], is the previous median. */
qsort(mbuf, niann+1, sizeof(int), icomp);
/* If mbuf has an even number of members, the median is the mean of
the two central values. */
if (niann & 1) mbuf[niann] = (mbuf[(niann-1)/2] + mbuf[(niann+1)/2])/2;
/* Otherwise it's the single central value. */
else mbuf[niann] = mbuf[niann/2];
/* Find the input that best matches the prediction (the median). */
for (i = 0, dn = 9999; i < niann; i++) {
tdn = mbuf[niann] - count[i][j];
if (tdn < 0) tdn = -tdn;
if (tdn < dn) { dn = tdn; ibest = i; }
}
/* If the best match is not the previously chosen input, avoid switching
the input unless it's more than 2 beats further from the median. */
if (ibest != ichosen) {
tdn = mbuf[niann] - count[ichosen][j];
if (tdn < 0) tdn = -tdn;
if (tdn < dn + 3) ibest = ichosen;
}
ichosen = ibest;
/* Copy the chosen annotations for this one-minute segment. */
n = 0;
while (getann(ichosen, &annot) == 0 && n <= count[ichosen][j]) {
if (annot.time >= t0 && isqrs(annot.anntyp)) {
putann(0, &annot);
n++;
}
}
ungetann(ichosen, &annot);
}
cleanup(0);
}
void gettest() /* get next test annotation */
{
static long tt; /* time of previous test beat annotation */
static struct WFDB_ann annot;
tt = t;
t = tprime;
a = aprime;
/* See comments on the similar code in getref(), above. */
if (tt == 0L || t == huge_time ||
(tt <= vfontest && vfontest < t) ||
(tt <= sdontest && sdontest < t) ||
(tt <= pvfontest && pvfontest < t) ||
(tt <= psdontest && psdontest < t))
rr = 0L;
else
rr = t - tt;
if (oflag) test_annot = annot;
while (getann(1, &annot) == 0) {
if (isqrs(annot.anntyp) || Oflag) {
tprime = annot.time;
aprime = amap(annot.anntyp);
return;
}
if (annot.anntyp == NOISE) {
if ((annot.subtyp & 0x30) == 0x30) {
psdontest = sdontest;
psdofftest = sdofftest;
sdontest = annot.time;
if (getann(1, &annot) < 0) {
tprime = huge_time;
aprime = '*';
if (end_time > 0L)
shut_down += end_time - sdontest;
else {
(void)fprintf(stderr,
"%s: unterminated shutdown starting at %s in record %s, annotator %s\n",
pname, timstr(sdontest), record, an[1].name);
(void)fprintf(stderr,
" (not included in shutdown duration measurement)\n");
}
return;
}
if (annot.anntyp == NOISE &&
(annot.subtyp & 0x30) != 0x30)
sdofftest = annot.time;
else {
if (vfofftest > t) sdontest = vfofftest + match_dt;
else sdontest = t + match_dt;
sdofftest = annot.time - match_dt;
if (sdontest > sdofftest) sdontest = sdofftest;
(void)ungetann(0, &annot);
}
/* update shutdown duration tally */
shut_down += sdofftest - sdontest;
}
}
else if (annot.anntyp == VFON) {
pvfontest = vfontest;
pvfofftest = vfofftest;
vfontest = annot.time;
do {
if (getann(1, &annot) < 0) {
tprime = huge_time;
aprime = '*';
return;
}
} while (annot.anntyp != VFOFF);
vfofftest = annot.time;
}
}
tprime = huge_time;
aprime = '*';
}
void getref() /* get next reference beat annotation */
{
static long TT; /* time of previous reference beat annotation */
static struct WFDB_ann annot;
TT = T;
T = Tprime;
A = Aprime;
/* T-TT is not a valid RR interval if T is the time of the first beat,
if TT is the time of the last beat, or if a period of VF or shutdown
occurs between TT and T. */
if (TT == 0L || T == huge_time ||
(TT <= vfonref && vfonref < T) ||
(TT <= sdonref && sdonref < T) ||
(TT <= pvfonref && pvfonref < T) ||
(TT <= psdonref && psdonref < T))
RR = 0L;
else
RR = T - TT;
if (oflag) ref_annot = annot;
/* Read reference annotations until a beat annotation is read, or EOF.
If an expanded output annotation file is required, all annotations
are treated as if they were beat annotations. */
while (getann(0, &annot) == 0) {
if (isqrs(annot.anntyp) || Oflag) { /* beat annotation */
Tprime = annot.time;
Aprime = amap(annot.anntyp);
return;
}
/* Shutdown occurs when neither signal is readable; the beginning of
shutdown is indicated by a NOISE annotation in which bits 4 and 5
of the subtyp field are set, and the end of shutdown is indicated
by a NOISE annotation with any value of `subtyp' for which at least
one of bits 4 and 5 is zero. In AHA DB reference annotation files,
shutdown is indicated by a single shutdown annotation placed roughly
in the middle of the shutdown interval; in this case, shutdown is
assumed to begin match_dt samples after the previous beat annotation
or VFOFF annotation, and is assumed to end match_dt samples before
the next annotation.
*/
else if (annot.anntyp == NOISE) {
if ((annot.subtyp & 0x30) == 0x30) {
psdonref = sdonref;
psdoffref = sdoffref;
sdonref = annot.time;
/* Read next annotation, which should mark end of shutdown. */
if (getann(0, &annot) < 0) { /* EOF before end of shutdown */
Tprime = sdoffref = huge_time;
Aprime = '*';
return;
}
if (annot.anntyp == NOISE &&
(annot.subtyp & 0x30) != 0x30)
sdoffref = annot.time;
else {
if (vfoffref > T) sdonref = vfoffref + match_dt;
else sdonref = T + match_dt;
sdoffref = annot.time - match_dt;
if (sdonref > sdoffref) sdonref = sdoffref;
(void)ungetann(0, &annot);
}
}
}
/* The beginning of ventricular fibrillation is indicated by a VFON
annotation, and its end by a VFOFF annotation; any annotations
between VFON and VFOFF are read and ignored. */
else if (annot.anntyp == VFON) {
pvfonref = vfonref;
pvfoffref = vfoffref;
vfonref = annot.time;
/* Read additional annotations, until end of VF or EOF. */
do {
if (getann(0, &annot) < 0) { /* EOF before end of VF */
Tprime = huge_time;
Aprime = '*';
return;
}
} while (annot.anntyp != VFOFF);
vfoffref = annot.time;
}
}
/* When this statement is reached, there are no more annotations in the
reference annotation file. */
Tprime = huge_time;
Aprime = '*';
}
int rtorrent(char *torrent){
int ret;
ret = readtorr(torrent);
if (ret < 0) {
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = getann();
if (ret < 0) {
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = ismulti();
if (ret < 0) {
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = getpilen();
if (ret < 0) {
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = getpihash();
if (ret < 0) {
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = getfname();
if (ret < 0) {
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = getflap();
if (ret < 0){
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = getflen();
if (ret < 0){
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = getinhash();
if (ret < 0){
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
ret = getpeid();
if (ret < 0){
printf("%s:%d wrong:",__FILE__,__LINE__);
return -1;
}
return 0;
}
