def main(argv):
nc = len(argv) - 4
if len(argv) < 4:
print "usage:", argv[0], "record start duration [ coefficients ... ]"
sys.exit(1)
if nc < 1: nc = 1
c = [0.] * nc
for i in range(0, nc):
c[i] = float(argv[i+4])
nsig = wfdb.isigopen(argv[1], None, 0)
if nsig < 1: sys.exit(3)
s = wfdb.WFDB_SiginfoArray(nsig)
v = wfdb.WFDB_SampleArray(nsig)
if wfdb.isigopen(argv[1], s.cast(), nsig) != nsig: sys.exit(3)
if wfdb.isigsettime(wfdb.strtim(argv[2])) < 0: sys.exit(4)
nsamp = wfdb.strtim(argv[3])
if nsamp < 1:
print argv[0]+ ": inappropriate value for duration"
sys.exit(5)
if wfdb.osigopen("16l", s.cast(), nsig) != nsig: sys.exit(6)
wfdb.sample(0, 0)
for t in range(0, nsamp):
if not wfdb.sample_valid(): break
for j in range(0, nsig):
vv = 0
for i in range(0, nc):
if c[i] != 0.: vv += c[i] * wfdb.sample(j, t+i)
v[j] = int(vv)
if wfdb.putvec(v.cast()) < 0: break
wfdb.newheader("out")
wfdb.wfdbquit()
def setupWfdb(rec_name, annotator ):
nsig = openWfdbSignal(rec_name);
#Allocate memory for sig info array
#we can use siarray to access WFDB_Siginfo structure
siarray = wfdb.WFDB_SiginfoArray(nsig);
#Allocate memory for data
sdata = wfdb.WFDB_SampleArray(nsig);
#Open WFDB record
wfdb.isigopen(rec_name, siarray.cast(), nsig);
#read annotations from file
#WFDB_Anninfor() contains name and attributes of annotator .atr etc
a = wfdb.WFDB_Anninfo();
#WFDB_Annotation describes the attributes of signals
#declare object in c : WFDB_Annotation annot; see below for declaring object in python
annot = wfdb.WFDB_Annotation();
#read name and status of annotation file
#a.name="atr";
#a.name="ecg";
#a.name="output_annotator"
a.name=annotator;
a.stat = wfdb.WFDB_READ;
freq=wfdb.sampfreq(rec_name);
nsamp=siarray[0].nsamp;
print ("sampling frequency is: " + str(freq))
init_time=wfdb.timstr(0);
#print("strtim for starting value is: " + str(wfdb.strtim(init_time)));
##comment june 16
###### print signal specification #####
record_info=wfdb.getinfo(rec_name)
#print("getinfor is " + str(record_info));
# print("total num of samples: " + str(nsamp));
# print "Starting time of record is: "+ str(init_time);
# print("sampling frequency is:"+ str(freq));
########## READ ANNOTATION ##################
if wfdb.annopen(rec_name, a, 1) < 0:
print("cannot open aanopen");
exit();
return (nsamp, freq, annot, init_time,sdata);
def main(argv):
siarray = wfdb.isigopen("100s")
if siarray.nsig < 2: sys.exit(1)
v = wfdb.WFDB_SampleArray(2)
for i in range(0,10):
if wfdb.getvec(v.cast()) < 0: sys.exit(2)
print "\t%d\t%d" % (v[0], v[1])
def openWfdbSignal(rec_name):
#Find the number of signals in record
nsig = wfdb.isigopen(rec_name, None, 0);
if nsig<0:
print "number of signals < 0, error opening signal record";
exit();
print "Number of signals: " + str(nsig) +" in record: "+ rec_name;
return nsig;
def main(argv):
nsamp = 1000
if len(argv) < 2:
print "usage:", argv[0], "record"
sys.exit(1)
nsig = wfdb.isigopen(argv[1], None, 0)
if nsig <= 0: sys.exit(2)
s = wfdb.WFDB_SiginfoArray(nsig)
vin = wfdb.WFDB_SampleArray(nsig)
vout = wfdb.WFDB_SampleArray(nsig)
if wfdb.isigopen(argv[1], s.cast(), nsig) != nsig: sys.exit(2)
if wfdb.osigopen("8l", s.cast(), nsig) <= 0: sys.exit(3)
while nsamp > 0 and wfdb.getvec(vin.cast()) > 0:
nsamp -= 1
for i in range(0, nsig): vout[i] -= vin[i]
if wfdb.putvec(vout.cast()) < 0: break
for i in range(0, nsig): vout[i] = vin[i]
wfdb.newheader("dif")
wfdb.wfdbquit()
def main(argv):
if len(argv) < 2:
print "usage:", argv[0], "record"
sys.exit(1)
nsig = wfdb.isigopen(argv[1], None, 0)
if nsig < 1: sys.exit(2)
s = wfdb.WFDB_SiginfoArray(nsig)
if wfdb.isigopen(argv[1], s.cast(), nsig) != nsig: sys.exit(2)
print "Record", argv[1]
print "Starting time:", wfdb.timstr(0)
print "Sampling frequency: %(sf)g Hz" % {'sf': wfdb.sampfreq(argv[1])}
print nsig, "signals"
for i in range(0,nsig):
print "Group %(g)d, Signal %(s)d:" % {'g': s[i].group, 's': i }
print " File:", s[i].fname
print " Description:", s[i].desc
print " Gain:",
if s[i].gain == 0.:
print "uncalibrated; assume", wfdb.WFDB_DEFGAIN,
else:
print "%(gain)g" % {'gain': s[i].gain},
if s[i].units is not None:
print "adu/" + s[i].units
else:
print "adu/mV"
print " Initial value:", s[i].initval
print " Storage format:", s[i].fmt
print " I/O:",
if s[i].bsize == 0:
print "can be unbuffered"
else:
print str(s[i].bsize) + "-byte blocks"
print " ADC resolution:", s[i].adcres, "bits"
print " ADC zero:", s[i].adczero
if s[i].nsamp > 0:
print " Length:", wfdb.timstr(s[i].nsamp), \
"(" + str(s[i].nsamp) + " sample intervals)"
print " Checksum:", s[i].cksum
else:
print " Length undefined"
wfdb.wfdbquit()
def main(argv):
record = ''
# Parse the arguments
try:
opts, args = getopt.getopt(argv, "hr:", ["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
# Read the number of signals in the record
nsig = wfdb.isigopen(record, None, 0)
# Exit if the record is not found, or there are no signals
if nsig < 1:
usage()
sys.exit(2)
siarray = wfdb.WFDB_SiginfoArray(nsig)
wfdb.isigopen(record, siarray, nsig)
n = 0
v = wfdb.intArray(nsig)
# Loop over each sample and print the signal values.
while wfdb.getvec(v) > 0:
print n,
for i in range(0,nsig):
print v[i],
print
n = n + 1
wfdb.wfdbquit()
def read(self , record = None):
if record == None:
if self.record == None:
sys.exit(1)
else:
record = self.record
else:
self.record = record
sig0 = []
sigt = []
siarray = wfdb.WFDB_SiginfoArray(2)
if (wfdb.isigopen(record , siarray.cast() , 2) < 1):
sys.exit(1)
v = wfdb.WFDB_SampleArray(2)
#Getting X Axes Interval
#Appending data to array
X_INTERVAL = 20
pause = 0
for i in range(siarray.cast().nsamp):
if ( wfdb.getvec(v.cast()) < 0 ):
break
sig0.append(v.__getitem__(0))
sigt.append(pause)
pause = pause + X_INTERVAL
pass
#High Pass Filtering
highpass_filter = HighpassFilter()
high_pass = highpass_filter.process(sig0,siarray.cast().nsamp)
#Low pass Filtering
lowpass_filter = LowpassFilter()
low_pass = lowpass_filter.process(high_pass, len(high_pass))
qrs = QRSDetector()
qrs_data = qrs.process(low_pass, len(low_pass))
feature_extractor = FeatureExtractor()
features = feature_extractor.get_RR_interval(sig0, qrs_data)
#sig0 = qrs_dat
wfdb.wfdbquit()
return sigt , sig0 , features
def read(self, record=None):
if record == None:
if self.record == None:
sys.exit(1)
else:
record = self.record
else:
self.record = record
sig0 = []
sigt = []
siarray = wfdb.WFDB_SiginfoArray(2)
if (wfdb.isigopen(record, siarray.cast(), 2) < 1):
sys.exit(1)
v = wfdb.WFDB_SampleArray(2)
#Getting X Axes Interval
#Appending data to array
X_INTERVAL = 20
pause = 0
for i in range(siarray.cast().nsamp):
if (wfdb.getvec(v.cast()) < 0):
break
sig0.append(v.__getitem__(0))
sigt.append(pause)
pause = pause + X_INTERVAL
pass
#High Pass Filtering
highpass_filter = HighpassFilter()
high_pass = highpass_filter.process(sig0, siarray.cast().nsamp)
#Low pass Filtering
lowpass_filter = LowpassFilter()
low_pass = lowpass_filter.process(high_pass, len(high_pass))
qrs = QRSDetector()
qrs_data = qrs.process(low_pass, len(low_pass))
feature_extractor = FeatureExtractor()
features = feature_extractor.get_RR_interval(sig0, qrs_data)
#sig0 = qrs_dat
wfdb.wfdbquit()
return sigt, sig0, features
def initialise(self, **kwds):
#----------------------------
fname = str(self.dataset)
global _WFDBLock, _CurrentRecord, _RecordCount
with _WFDBLock:
if _CurrentRecord and _CurrentRecord != fname:
raise IOError("WFDB does not allow concurrent access to different recordings")
_CurrentRecord = fname
_RecordCount += 1
wfdb.setgvmode(wfdb.WFDB_HIGHRES)
## http: url needs .hea extension??
#logging.debug('Opening: %s (%s)', fname, uri)
if fname.startswith(PHYSIOBANK):
fname = fname[len(PHYSIOBANK):]
self._siginfo = wfdb.isigopen(fname)
if self._siginfo is None:
raise IOError("Cannot open header for '%s'" % fname)
self._nsignals = self._siginfo.nsig
for s in self.signals():
WFDBSignal.initialise_class(s)
def main(argv):
time = maxslope = nslope = scmin = 0
a = wfdb.WFDB_Anninfo()
annot = wfdb.WFDB_Annotation()
if len(argv) < 2:
print "usage:", argv[0], "record [threshold]"
sys.exit(1)
a.name = "qrs"
a.stat = wfdb.WFDB_WRITE
nsig = wfdb.isigopen(argv[1], None, 0)
if nsig < 1: sys.exit(2)
s = wfdb.WFDB_SiginfoArray(nsig)
v = wfdb.WFDB_SampleArray(nsig)
if wfdb.wfdbinit(argv[1], a, 1, s.cast(), nsig) != nsig: sys.exit(2)
if wfdb.sampfreq(None) < 240. or wfdb.sampfreq(None) > 260.:
wfdb.setifreq(250.)
if len(argv) > 2: scmin = wfdb.muvadu(0, argv[2])
if scmin < 1: scmin = wfdb.muvadu(0, 1000)
slopecrit = scmax = 10 * scmin
ms160 = wfdb.strtim("0.16")
ms200 = wfdb.strtim("0.2")
s2 = wfdb.strtim("2")
annot.subtyp = annot.chan = annot.num = 0
annot.aux = None
wfdb.getvec(v.cast())
t9 = t8 = t7 = t6 = t5 = t4 = t3 = t2 = t1 = v[0]
while 1:
t0 = v[0]
filter = t0 + 4*t1 + 6*t2 + 4*t3 + t4 - t5 - 4*t6 - 6*t7 - 4*t8 - t9
if time % s2 == 0:
if nslope == 0:
slopecrit -= slopecrit >> 4
if slopecrit < scmin: slopecrit = scmin
elif nslope >= 5:
slopecrit += slopecrit >> 4
if slopecrit > scmax: slopecrit = scmax
if nslope == 0 and abs(filter) > slopecrit:
nslope = 1
maxtime = ms160
if filter > 0:
sign = 1
else:
sign = -1
qtime = time
if nslope != 0:
if filter * sign < -slopecrit:
sign = -sign
nslope = nslope + 1
if nslope > 4:
maxtime = ms200
else:
maxtime = ms160
elif filter * sign > slopecrit and \
abs(filter) > maxslope:
maxslope = abs(filter)
if maxtime < 0:
if 2 <= nslope and nslope <= 4:
slopecrit += ((maxslope>>2) - slopecrit) >> 3
if slopecrit < scmin:
slopecrit = scmin
elif slopecrit > scmax:
slopecrit = scmax
annot.time = wfdb.strtim("i") - (time - qtime) - 4
annot.anntyp = wfdb.NORMAL
wfdb.putann(0, annot)
time = 0
elif nslope >= 5:
annot.time = wfdb.strtim("i") - (time - qtime) - 4
annot.anntyp = wfdb.ARFCT
wfdb.putann(0, annot)
nslope = 0
maxtime = maxtime - 1
t9 = t8
t8 = t7
t7 = t6
t6 = t5
t5 = t4
t4 = t3
t3 = t2
t2 = t1
t1 = t0
time = time + 1
if not wfdb.getvec(v.cast()) > 0: break
wfdb.wfdbquit()
def main(argv):
db_path = "/opt/physiobank/database"
record = ''
wfdb.setwfdb(db_path)
# Parse the arguments
try:
opts, args = getopt.getopt(argv, "hr:", ["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
# Read the number of signals in the record
nsig = wfdb.isigopen(record, None, 0)
# Exit if the record is not found, or there are no signals
if nsig < 1:
usage()
sys.exit(2)
siarray = wfdb.WFDB_SiginfoArray(nsig)
wfdb.isigopen(record, siarray, nsig)
n = 0
v = wfdb.intArray(nsig)
lf = bf_math.intArray(siarray[0].nsamp)
global sld_samp
global ln
global y_axes
global sr_ds
global subplt
sr = (int)(wfdb.sampfreq(record))
print "sr:",sr
sr_ds = 50
# Loop over each sample and print the signal values.
while wfdb.getvec(v) > 0:
for i in range(0,1):
lf[n] = v[i]
n = n + 1
bf_math.filtering(lf,siarray[0].nsamp,sr)
_nsamp = siarray[0].nsamp
x_axes = xrange(_nsamp*sr_ds/sr)
print "x_axes:", _nsamp*sr_ds/sr
y_axes = []
for i in xrange(_nsamp):
b, val = bf_math.down_sample(lf[i], sr, sr_ds)
if (b):
y_axes.append(val)
print "y_axes:", len(y_axes)
plt.figure(1)
subplt = plt.subplot(111)
ln, = plt.plot(xrange(0,5*sr_ds), y_axes[0:5*sr_ds] )
#plt.axis([-100, 100])
plt.ylim(-300,300)
#subplt.autoscale_view(True,True,True)
axcolor = 'lightgoldenrodyellow'
axsamp = plt.axes([0.25, 0.15, 0.65, 0.03], axisbg=axcolor)
sld_samp = Slider(axsamp, 'samp', 0.1, 33*60, valinit=1)
sld_samp.on_changed(update)
plt.show()
wfdb.wfdbquit()
sig_time = []
count = 0
ann_graph = []
split_time0 = []
annotator_array = []
#Database and record name
db_name = "afpdb"
annotation = dload_annotator_names(db_name)[0]
#rec_name=dload_rec_names(db_name)[0];
record = "n08"
rec_name = "afpdb/" + record
#Find the number of signals in record
nsig = wfdb.isigopen(rec_name, None, 0)
if nsig < 0:
print "error opening signal record"
exit()
print "Number of signals: " + str(nsig) + " in record: " + rec_name
#Allocate memory for sig info array
#we can use siarray to access WFDB_Siginfo structure
siarray = wfdb.WFDB_SiginfoArray(nsig)
#Allocate memory for data
sdata = wfdb.WFDB_SampleArray(nsig)
#Open WFDB record
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()
count=0;
ann_graph=[];
split_time0=[];
annotator_array=[];
#Database and record name
db_name="afpdb";
annotation=dload_annotator_names(db_name)[0];
#rec_name=dload_rec_names(db_name)[0];
record="n08"
rec_name = "afpdb/"+record
#Find the number of signals in record
nsig = wfdb.isigopen(rec_name, None, 0);
if nsig<0:
print "error opening signal record";
exit();
print "Number of signals: " + str(nsig) +" in record: "+ rec_name;
#Allocate memory for sig info array
#we can use siarray to access WFDB_Siginfo structure
siarray = wfdb.WFDB_SiginfoArray(nsig);
#Allocate memory for data
sdata = wfdb.WFDB_SampleArray(nsig);
#Open WFDB record