def wfdbAnnotation(e):
#=====================
import wfdb
mark = wfdb.annstr(int(e))
## text = "Pacing on" if t < 100 else "Pacing off" ########
## chart.annotate(text, t, 0.0, textpos=(t, 1.05))
if mark in "NLRBAaJSVrFejnE/fQ?":
if mark == 'N': mark = u'\u2022' # Unicode bullet
return (mark, wfdb.anndesc(int(e)))
return ('', '')
def main(argv):
a = wfdb.WFDB_Anninfo()
annot = wfdb.WFDB_Annotation()
if len(argv) < 3:
print "usage:", argv[0], "annotator record"
sys.exit(1)
a.name = argv[1]
a.stat = wfdb.WFDB_READ
wfdb.sampfreq(argv[2])
if wfdb.annopen(argv[2], a, 1) < 0:
sys.exit(2)
while wfdb.getann(0, annot) == 0:
if annot.aux is not None:
aux = annot.aux[1:]
else:
aux = ""
print wfdb.timstr(-annot.time), "(" + str(annot.time) + ")", wfdb.annstr(
annot.anntyp
), annot.subtyp, annot.chan, annot.num, aux
wfdb.wfdbquit()
def get_ecg_signal(rec_name, annotation, start_time, end_time):
#variables and arrays
iteration = []
sig_time = []
#count=0;
#ann_graph=[];
#split_time0=[];
#annotator_array=[];
nsamp, freq, annot, init_time, sdata = ws.setupWfdb(rec_name, annotation)
sig0 = []
sig1 = []
#physig0 is array with physical units
physig0 = []
physig1 = []
print type(init_time)
#print("strtim for starting value is: " + str(wfdb.strtim(init_time)));
#print("total num of samples: " + str(nsamp));
#print "Starting time of record is: "+ str(init_time);
#print("sampling frequency is:"+ str(freq));
#sample interval
#required length of signal in seconds
#num_sample_start=start_time*60*freq
num_sample_end = end_time * 60 * freq
loop_iteration = int(math.floor(num_sample_end))
#print("loop iteration = " +str(loop_iteration));
# loop runs for loop_iteration times to extract signal samples
num_value = loop_iteration
for i in range(0, num_value):
if wfdb.getvec(sdata.cast()) < 0:
print "ERROR: getvec() < 0"
exit()
else:
#signal values in adu units:
sig0.append(sdata[0])
sig1.append(sdata[1])
sig_time.append(gettime(i, freq, init_time))
#print("time for sample " + str(i) + "is: " + str(sig_time[i]));
#convert adu units to physical units and save in physig0 and 1 (later generalise it for n number of signals)
physig0.append(aduphys(0, sig0[i]))
physig1.append(aduphys(1, sig1[i]))
#append iteration number as value in
iteration.append(i)
#getann reads next annotation and returns 0 when successful
while wfdb.getann(0, annot) == 0:
if annot.time > num_value:
#print("annot.time>number of samples extracted");
break
# annot.time is time of the annotation, in samples from the beginning of the record.
print wfdb.timstr(-annot.time), "(" + str(
annot.time) + ")", wfdb.annstr(
annot.anntyp), annot.subtyp, annot.chan, annot.num
print("signal value at this annotation is : " +
str(physig0[annot.time]) + " " + str(sig_time[annot.time]))
return (physig0, physig1, sig_time)
# #append iteration number as value in
# iteration.append(i);
########## READ ANNOTATION ##################
if wfdb.annopen(rec_name, a, 1) < 0:
print("cannot open aanopen")
exit()
#getann reads next annotation and returns 0 when successful
while wfdb.getann(0, annot) == 0:
if annot.time > num_value:
#if annot.time>=start_val and annot.time<=end_val:
print("annot.time>number of samples extracted")
break
# annot.time is time of the annotation, in samples from the beginning of the record.
print wfdb.timstr(-annot.time), "(" + str(annot.time) + ")", wfdb.annstr(
annot.anntyp), annot.subtyp, annot.chan, annot.num
# print ("signal value at this annotation is : " + str(physig0[annot.time])+" "+ str(sig_time[annot.time]));
#else:
#print("getann not working");
#exit();
#write signals to file
# f=open('/home/ubuntu/Documents/eclispe_workspace/test_one/my_first_pyproj/sig_file.txt','a');
# f.write("sig_time values: \t signal 0 values: \t signal 1 values: \n");
# for i in range(0,len(physig0)):
# f.write(str(sig_time[i])+ "\t");
# f.write(str(physig0[i]) + "\t");
# f.write(str(physig1[i]) + "\n");
# # #f.write(str(ann_graph));
def main(argv):
nbeats = stoptime = 0
a = wfdb.WFDB_Anninfo()
annot = wfdb.WFDB_Annotation()
if len(argv) < 3:
print "usage:", argv[0], "annotator record [beat-type from to]",
sys.exit(1)
a.name = argv[1]
a.stat = wfdb.WFDB_READ
nsig = wfdb.isigopen(argv[2], None, 0)
if nsig < 1: sys.exit(2)
s = wfdb.WFDB_SiginfoArray(nsig)
v = wfdb.WFDB_SampleArray(nsig)
vb = wfdb.WFDB_SampleArray(nsig)
sum = [None] * nsig
if wfdb.wfdbinit(argv[2], a, 1, s.cast(), nsig) != nsig: sys.exit(3)
hwindow = wfdb.strtim(".05")
window = 2*hwindow + 1
for i in range(nsig):
sum[i] = [0] * window
if len(argv) > 3:
btype = wfdb.strann(argv[3])
else:
btype = wfdb.NORMAL
if len(argv) > 4: wfdb.iannsettime(wfdb.strtim(argv[4]))
if len(argv) > 5:
stoptime = wdfb.strtim(argv[5])
if stoptime < 0:
stoptime = -stoptime
if s[0].nsamp > 0 and stoptime > s[0].nsamp:
stoptime = s[0].nsamp
else:
stoptime = s[0].nsamp
if stoptime > 0: stoptime -= hwindow
while 1:
if not (wfdb.getann(0, annot) == 0 and annot.time < hwindow): break
while 1:
if annot.anntyp == btype:
wfdb.isigsettime(annot.time - hwindow - 1)
wfdb.getvec(vb.cast())
j=0
while j < window and wfdb.getvec(v.cast()) > 0:
for i in range(nsig):
sum[i][j] += v[i] - vb[i]
j += 1
nbeats += 1
if not (wfdb.getann(0, annot) == 0 and \
(stoptime == 0L or annot.time < stoptime)): break
if nbeats < 1:
print argv[0] + ": no `" + wfdb.annstr(btype) + "' beats found"
sys.exit(4)
print "Average of", nbeats, "`" + wfdb.annstr(btype) + "' beats:"
for j in range(window):
for i in range(nsig):
print "%(av)g" % {'av': float(sum[i][j])/nbeats},
sys.stdout.write("") # surpress next space
if i < nsig-1:
print "\t",
else:
print
wfdb.wfdbquit()
def main(argv):
record = ''
annotator = ''
# parse the arguments
try:
opts, args = getopt.getopt(argv, "hr:a:", ["help"])
except getopt.GetoptError:
usage()
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"):
usage()
sys.exit()
elif opt == '-r':
record = arg
elif opt == '-a':
annotator = arg
if len(record) == 0 or len(annotator) == 0:
usage()
sys.exit(2)
# set the sampling frequency
sps = wfdb.sampfreq(record)
if sps < 0:
sps = wfdb.WFDB_DEFFREQ
wfdb.setsampfreq(sps)
# get a new anninfo object
ai = wfdb.WFDB_Anninfo()
# set ai fields
ai.name = annotator
ai.stat = wfdb.WFDB_READ
# open the annotation
result = wfdb.annopen( record, ai, 1 )
if result < 0:
usage()
sys.exit(2)
# get a new annotation object
annot = wfdb.WFDB_Annotation()
while wfdb.getann(0, annot) == 0:
# remove first char from aux string, if there is one
if annot.aux is not None:
aux = annot.aux[1:]
else:
aux = ""
print "%s\t%d\t%s\t%d\t%d\t%d\t%s" % ( \
wfdb.mstimstr(-annot.time), \
annot.time, \
wfdb.annstr(annot.anntyp),
annot.subtyp,
annot.chan, \
annot.num, \
aux)
wfdb.wfdbquit()
# #append iteration number as value in
# iteration.append(i);
########## READ ANNOTATION ##################
if wfdb.annopen(rec_name, a, 1) < 0:
print("cannot open aanopen");
exit();
#getann reads next annotation and returns 0 when successful
while wfdb.getann(0,annot) ==0:
if annot.time>num_value:
#if annot.time>=start_val and annot.time<=end_val:
print("annot.time>number of samples extracted");
break;
# annot.time is time of the annotation, in samples from the beginning of the record.
print wfdb.timstr(-annot.time),"(" + str(annot.time)+ ")",wfdb.annstr(annot.anntyp), annot.subtyp,annot.chan, annot.num
# print ("signal value at this annotation is : " + str(physig0[annot.time])+" "+ str(sig_time[annot.time]));
#else:
#print("getann not working");
#exit();
#write signals to file
# f=open('/home/ubuntu/Documents/eclispe_workspace/test_one/my_first_pyproj/sig_file.txt','a');
# f.write("sig_time values: \t signal 0 values: \t signal 1 values: \n");
# for i in range(0,len(physig0)):
# f.write(str(sig_time[i])+ "\t");
# f.write(str(physig0[i]) + "\t");
# f.write(str(physig1[i]) + "\n");
def get_ecg_signal(rec_name,annotation,start_time,end_time):
#variables and arrays
iteration=[];
sig_time=[];
#count=0;
#ann_graph=[];
#split_time0=[];
#annotator_array=[];
nsamp, freq, annot, init_time,sdata = ws.setupWfdb(rec_name,annotation);
sig0 = [];
sig1 = [];
#physig0 is array with physical units
physig0=[];
physig1=[];
print type(init_time);
#print("strtim for starting value is: " + str(wfdb.strtim(init_time)));
#print("total num of samples: " + str(nsamp));
#print "Starting time of record is: "+ str(init_time);
#print("sampling frequency is:"+ str(freq));
#sample interval
#required length of signal in seconds
#num_sample_start=start_time*60*freq
num_sample_end=end_time*60*freq
loop_iteration=int(math.floor(num_sample_end));
#print("loop iteration = " +str(loop_iteration));
# loop runs for loop_iteration times to extract signal samples
num_value=loop_iteration;
for i in range(0,num_value):
if wfdb.getvec(sdata.cast()) < 0:
print "ERROR: getvec() < 0";
exit();
else:
#signal values in adu units:
sig0.append(sdata[0]);
sig1.append(sdata[1]);
sig_time.append(gettime(i, freq, init_time));
#print("time for sample " + str(i) + "is: " + str(sig_time[i]));
#convert adu units to physical units and save in physig0 and 1 (later generalise it for n number of signals)
physig0.append(aduphys(0,sig0[i]));
physig1.append(aduphys(1,sig1[i]));
#append iteration number as value in
iteration.append(i);
#getann reads next annotation and returns 0 when successful
while wfdb.getann(0,annot) ==0:
if annot.time>num_value:
#print("annot.time>number of samples extracted");
break;
# annot.time is time of the annotation, in samples from the beginning of the record.
print wfdb.timstr(-annot.time),"(" + str(annot.time)+ ")",wfdb.annstr(annot.anntyp), annot.subtyp,annot.chan, annot.num
print ("signal value at this annotation is : " + str(physig0[annot.time])+" "+ str(sig_time[annot.time]));
return(physig0,physig1,sig_time)