def get_RR_interval(rec_name, annotation, start_time, end_time):
#setup wfdb (change annotator here)
rr_int = 0
t = 0
beats = 0
sig_time = []
#change annotations
nsamp, freq, annot, init_time, sdata = ws.setupWfdb(rec_name, annotation)
RR_sec_func = []
#num_sample_end=38400; # this translates to 230339 annot time which means 30 mins of data ## check this
num_sample_start = start_time * 60 * freq
num_sample_end = end_time * 60 * freq
###### check if its the same record or new. if new , shift annot.time
# annot.time
#getann reads next annotation and returns 0 when successful
# annot.time is time of the annotation, in samples from the beginning of the record.
#when getting samples for cross-validation and testing, just adjust annot.time so it starts reading samples from there
t = annot.time
##comment june 16
#print ("annot.time at the beginning is: " + str(annot.time))
#annot_file=open('/home/ubuntu/Documents/eclispe_workspace/test_one/my_first_pyproj/research_March17/annot_type' +str(record)+'.txt','a');
while wfdb.getann(0, annot) == 0:
if annot.time > num_sample_start and annot.time < num_sample_end:
#code for extracting time:
time = wfdb.timstr(-annot.time)
split_time = time.split(":")
hr_time = split_time[0]
minute_time = split_time[1]
if len(split_time) > 2:
sec_time = split_time[2]
if wfdb.wfdb_isqrs(annot.anntyp):
# if same_as_prev[record] == 1 and int(hr_time) >= 1 and int(hr_time) < 23:
#annot.time=annot.time + prev_annot_time;
rr_int = annot.time - t
beats = beats + 1
rr_sec = rr_int / freq
rr_sec_rounded = round(rr_sec, 3)
###############testing here############################
############################################
RR_sec_func.append(rr_sec_rounded)
# sampling intervals (e.g., if the original recording was sampled at 128 samples per second, then an
t = annot.time
#print ("annot.time after rr interval is: " + str(t))
#print ("-annot.time after rr interval is: " + wfdb.timstr(-annot.time))
#print ("annot.time in if is: " + str(annot.time))
#prev_annot_time.append(annot.time)
#print ("beats = "+ str(beats))
return RR_sec_func
def get_RR_interval(rec_name,annotation,start_time,end_time):
#setup wfdb (change annotator here)
rr_int=0;
t=0;
beats=0;
sig_time=[];
#change annotations
nsamp, freq, annot, init_time = setupWfdb(rec_name,annotation);
RR_sec_func=[];
#num_sample=38400; # this translates to 230339 annot time which means 30 mins of data ## check this
num_sample=end_time*60*freq
###### check if its the same record or new. if new , shift annot.time
# annot.time
#getann reads next annotation and returns 0 when successful
# annot.time is time of the annotation, in samples from the beginning of the record.
#when getting samples for cross-validation and testing, just adjust annot.time so it starts reading samples from there
t = annot.time;
##comment june 16
#print ("annot.time at the beginning is: " + str(annot.time))
#annot_file=open('/home/ubuntu/Documents/eclispe_workspace/test_one/my_first_pyproj/research_March17/annot_type' +str(record)+'.txt','a');
while wfdb.getann(0, annot) == 0 and annot.time<num_sample:
#code for extracting time:
time=wfdb.timstr(-annot.time)
split_time=time.split(":")
hr_time=split_time[0];
minute_time=split_time[1];
if len(split_time) >2:
sec_time=split_time[2];
if wfdb.wfdb_isqrs(annot.anntyp):
# if same_as_prev[record] == 1 and int(hr_time) >= 1 and int(hr_time) < 23:
#annot.time=annot.time + prev_annot_time;
rr_int = annot.time - t
beats=beats+1;
rr_sec=rr_int/freq
rr_sec_rounded=round(rr_sec,3);
RR_sec_func.append(rr_sec_rounded);
# sampling intervals (e.g., if the original recording was sampled at 128 samples per second, then an
t = annot.time
#print ("annot.time after rr interval is: " + str(t))
#print ("-annot.time after rr interval is: " + wfdb.timstr(-annot.time))
#print ("annot.time in if is: " + str(annot.time))
#prev_annot_time.append(annot.time)
#print ("beats = "+ str(beats))
return RR_sec_func
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 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 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 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)
#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
#required length of signal in seconds
#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
#required length of signal in seconds
siglength_sec=1;
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)
