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
if wfdb.annopen(argv[2], a, 1) < 0: sys.exit(2)
rrmax = 3 * wfdb.sampfreq(argv[2])
if rrmax <= 0: sys.exit(3)
rrhist = [0] * int(rrmax+1)
while 1:
if not (wfdb.getann(0,annot) == 0 and not wfdb.wfdb_isqrs(annot.anntyp)): break
t = annot.time
while wfdb.getann(0, annot) == 0:
if wfdb.wfdb_isqrs(annot.anntyp):
rr = annot.time - t
if rr > rrmax: rr = rrmax
rrhist[rr] += 1
t = annot.time
for rr in range(1, int(rrmax)):
print '%(rr)4d %(time)s' % {'rr': rrhist[rr], 'time': wfdb.mstimstr(rr)}
rr += 1
print '%(rr)4d %(time)s (or longer)' % {'rr': rrhist[rr], 'time': wfdb.mstimstr(rr)}
wfdb.wfdbquit()
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 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 _set_attributes(self):
#-------------------------
if self._siginfo is None: return
# wfdbname = wfdb.wfdbfile(None, None)
# recname = wfdbname[:-4] if wfdbname.endswith('.hea') else wfdbname
# if source.startswith('http://') or recname.startswith('ftp://'):
# source = wfdbname
# else:
# recname = file_uri(recname)
# source = file_uri(wfdbname)
# if not uri: uri = recname
##logging.debug('rec: %s, source: %s', recname, source)
self._framerate = wfdb.sampfreq(None)/wfdb.getspf()
start = wfdb.mstimstr(0)
if start[0] == '[':
self.starttime = dateutil.parser.parse(start[1:-1], dayfirst=True)
if self._siginfo[0].nsamp > 0:
self.duration = self._siginfo[0].nsamp/float(self._framerate)
##duration = dateutil.parser.parse(wfdb.mstimstr(wfdb.strtim('e')))
##print duration ## But has date...
self._framesize = 0
self.data_signals = [ ]
self.annotation_signals = [ ]
self._offsets = [ ]
offset = 0
for n in xrange(self._nsignals):
if self._siginfo[n].desc != 'EDF Annotations':
self.data_signals.append(n)
self.add_signal(WFDBSignal(n, self,
self._siginfo[n].units,
metadata =
{ 'label': self._siginfo[n].desc,
'rate': self._framerate*self._siginfo[n].spf,
} ))
else:
self.annotation_signals.append(n)
self._framesize += self._siginfo[n].spf
self._offsets.append((offset, self._framesize))
offset = self._framesize
self._sigpoints = np.ones(self._framesize, 'bool')
for n in xrange(self._nsignals):
if n in self.annotation_signals:
for i in xrange(*self._offsets[n]): self._sigpoints[i] = False
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):
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()
physig0 = []
physig1 = []
#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 = annotation
print a.name
a.stat = wfdb.WFDB_READ
freq = wfdb.sampfreq(rec_name)
nsamp = siarray[0].nsamp
init_time = wfdb.timstr(0)
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))
def gettime(sample_num, freq, init_time):
return float(sample_num) / float(freq)
#sample interval
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()
physig0=[];
physig1=[];
#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=annotation;
print a.name
a.stat = wfdb.WFDB_READ;
freq=wfdb.sampfreq(rec_name);
nsamp=siarray[0].nsamp;
init_time=wfdb.timstr(0);
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));
def gettime(sample_num, freq, init_time):
return float(sample_num)/float(freq)
#sample interval
