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_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)
def extract_pwave(output_folder, record, rec_name, annotation, start_time,
end_time):
## time for which you want to read record ##
nsamp, freq, annot, init_time, sdata = ws.setupWfdb(rec_name, annotation)
#print("nsamp:"+str(nsamp)+" freq:"+str(freq));
rdann_file = output_folder + "ecgpu_output.txt"
s1_rdann_file = output_folder + "s1_ecgpu_output.txt"
output_ann = "output_annotator"
#ecgpu_path="/home/ubuntu/Documents/Thesis_work/ecgpuwave-1.3.2"
#change directory to output_folder
os.chdir(output_folder)
signal_0 = "0"
os.system("rm -f " + rdann_file)
cmd_create_ann = "ecgpuwave -r " + rec_name + " " + "-a" + " " + output_ann + " -f " + start_time + " -t " + end_time + " -i " + annotation + " -s " + signal_0
print(cmd_create_ann)
os.system(cmd_create_ann)
#use rdann to ouput annotations as a text file
cmd_disp_ann = "rdann -r " + rec_name + " -a output_annot"
#push output text to a file
print(cmd_disp_ann)
os.system(cmd_disp_ann + ">" + rdann_file)
s0_l_p_wave_times = [
] # this will contain p wave values for 1 rec and will be emptied everytime
## code for p wave time calculation goes here ####
f = open(rdann_file, 'r')
for line in f:
temp = line.split()
if (temp[2] == '(') and (temp[-1] == '0'):
start_sample_num = float(temp[1])
#print ("start sample num is : "+ str(start_sample_num))
elif (temp[2] == ')') and (temp[-1] == '0'):
end_sample_num = float(temp[1])
#print("end_sample_num is: " +str(end_sample_num))
p_duration_ms = (end_sample_num - start_sample_num) * (1000 / freq)
s0_l_p_wave_times.append(p_duration_ms)
#print ("pwave duration from signal 0 is : " + str(p_duration_ms))
##### extract p wave times for second signal
signal_1 = "1"
os.system("rm -f " + s1_rdann_file)
cmd_create_ann = "ecgpuwave -r " + rec_name + " " + "-a" + " " + output_ann + " -f " + start_time + " -t " + end_time + " -i " + annotation + " -s " + signal_1
print(cmd_create_ann)
os.system(cmd_create_ann)
#use rdann to ouput annotations as a text file
cmd_disp_ann = "rdann -r " + rec_name + " -a output_annot"
#push output text to a file
print(cmd_disp_ann)
os.system(cmd_disp_ann + ">" + s1_rdann_file)
s1_l_p_wave_times = [
] # this will contain p wave values for 1 rec and will be emptied everytime
## code for p wave time calculation goes here ####
f = open(s1_rdann_file, 'r')
for line in f:
temp = line.split()
if (temp[2] == '(') and (temp[-1] == '0'):
start_sample_num = float(temp[1])
#print ("start sample num is : "+ str(start_sample_num))
elif (temp[2] == ')') and (temp[-1] == '0'):
end_sample_num = float(temp[1])
#print("end_sample_num is: " +str(end_sample_num))
p_duration_ms = (end_sample_num - start_sample_num) * (1000 / freq)
#print ("pwave duration from signal 1 is : " + str(p_duration_ms))
s1_l_p_wave_times.append(p_duration_ms)
return s0_l_p_wave_times, s1_l_p_wave_times
def extract_wave_times(output_folder, record, rec_name, annotation, start_time,
end_time, signal_num):
##The num field of each WFON and WFOFF annotation designates the type of waveform with which it is associated: 0 for a P wave, 1 for a QRS complex, or 2 for a T wave.
# ## doing wave num encoding here:
# if wave_name == 'p':
# wave_num = '0'
# elif wave_name == 'r':
# wave_num = '1'
# elif wave_name =='t':
# wave_num = '2'
## time for which you want to read record ##
nsamp, freq, annot, init_time, sdata = ws.setupWfdb(rec_name, annotation)
rdann_file = output_folder + "ecgpu_output.txt"
output_ann = "output_annotator"
os.chdir(output_folder)
signal = signal_num
os.system("rm -f " + rdann_file)
cmd_create_ann = "ecgpuwave -r " + rec_name + " " + "-a" + " " + output_ann + " -f " + start_time + " -t " + end_time + " -i " + annotation + " -s " + signal
print(cmd_create_ann)
os.system(cmd_create_ann)
#use rdann to ouput annotations as a text file
cmd_disp_ann = "rdann -r " + rec_name + " -a output_annot"
#push output text to a file
print(cmd_disp_ann)
os.system(cmd_disp_ann + ">" + rdann_file)
## features we want to extract:
# p_dur=p_off-p_on
# p_ini=p_p_peak-p_on
# p_ter = p_off - p_peak
# p_asy=p_ter/p_ini
#pr_on
#pr_peak
#r_off
l_wave_dur_time = [
] # this will contain p/t wave values for 1 rec and will be emptied everytime
l_wave_ini_time = []
l_wave_ter_time = []
l_wave_asy_time = []
l_pr_on_time = []
l_pr_peak_time = []
l_pr_off_time = []
l_pp_on_time = []
## code for p wave time calculation goes here ####
f = open(rdann_file, 'r')
p_true = 0
for line in f:
temp = line.split()
if (temp[2] == '(') and (temp[-1] == '0'):
start_sample_num = float(temp[1])
#print ("start sample num is : "+ str(start_sample_num))
elif (temp[2] == 'p') and (temp[-1] == '0'):
peak_sample_num = float(temp[1])
p_true = 1
elif (temp[2] == ')') and (temp[-1] == '0'):
end_sample_num = float(temp[1])
#print("end_sample_num is: " +str(end_sample_num))
wave_duration_ms = (end_sample_num - start_sample_num) * (1000 /
freq)
wave_ini_ms = (peak_sample_num - start_sample_num) * (1000 / freq)
wave_ter_ms = (end_sample_num - peak_sample_num) * (1000 / freq)
wave_asy_ms = wave_ter_ms / wave_ini_ms
l_wave_dur_time.append(wave_duration_ms)
l_wave_ini_time.append(wave_ini_ms)
l_wave_ter_time.append(wave_ter_ms)
l_wave_asy_time.append(wave_asy_ms)
if (temp[2] == 'N') and (temp[-1] == '0') and (
p_true == 1
): # this is looking for r peakvand making sure that p wave was calculated previously
r_peak_sample = float(temp[1])
pr_on_ms = (r_peak_sample - start_sample_num) * (1000 / freq)
pr_peak_ms = (r_peak_sample - peak_sample_num) * (1000 / freq)
pr_off_ms = (r_peak_sample - end_sample_num) * (1000 / freq)
p_true = 0
l_pr_on_time.append(pr_on_ms)
l_pr_peak_time.append(pr_peak_ms)
l_pr_off_time.append(pr_off_ms)
for i in range(len(l_wave_dur_time) - 1):
pp_on_ms = l_wave_dur_time[i + 1] - l_wave_dur_time[i]
l_pp_on_time.append(pp_on_ms)
#print ("pwave duration from signal 0 is : " + str(p_duration_ms))
##### extract p wave times for second signal
all_time_features = [
l_wave_dur_time, l_wave_ini_time, l_wave_ter_time, l_wave_asy_time,
l_pr_on_time, l_pr_peak_time, l_pr_off_time
]
return all_time_features
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_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)
def extract_pwave(output_folder,record,rec_name,annotation,start_time,end_time):
## time for which you want to read record ##
nsamp, freq, annot, init_time,sdata=ws.setupWfdb(rec_name, annotation)
#print("nsamp:"+str(nsamp)+" freq:"+str(freq));
rdann_file=output_folder+"ecgpu_output.txt"
s1_rdann_file=output_folder+"s1_ecgpu_output.txt"
output_ann="output_annotator"
#ecgpu_path="/home/ubuntu/Documents/Thesis_work/ecgpuwave-1.3.2"
#change directory to output_folder
os.chdir(output_folder)
signal_0="0";
os.system("rm -f "+rdann_file)
cmd_create_ann="ecgpuwave -r "+rec_name +" "+"-a"+" "+output_ann+ " -f "+start_time+" -t "+ end_time +" -i "+annotation+" -s "+signal_0
print(cmd_create_ann)
os.system(cmd_create_ann)
#use rdann to ouput annotations as a text file
cmd_disp_ann="rdann -r "+rec_name+" -a output_annot"
#push output text to a file
print (cmd_disp_ann)
os.system(cmd_disp_ann +">" +rdann_file)
s0_l_p_wave_times=[] # this will contain p wave values for 1 rec and will be emptied everytime
## code for p wave time calculation goes here ####
f=open(rdann_file,'r')
for line in f:
temp=line.split()
if (temp[2] == '(') and (temp[-1] =='0'):
start_sample_num=float(temp[1])
#print ("start sample num is : "+ str(start_sample_num))
elif (temp[2] == ')') and (temp[-1] =='0'):
end_sample_num=float(temp[1])
#print("end_sample_num is: " +str(end_sample_num))
p_duration_ms=(end_sample_num-start_sample_num) *(1000/freq);
s0_l_p_wave_times.append(p_duration_ms)
#print ("pwave duration from signal 0 is : " + str(p_duration_ms))
##### extract p wave times for second signal
signal_1="1";
os.system("rm -f "+s1_rdann_file)
cmd_create_ann="ecgpuwave -r "+rec_name +" "+"-a"+" "+output_ann+ " -f "+start_time+" -t "+ end_time +" -i "+annotation+" -s "+signal_1
print(cmd_create_ann)
os.system(cmd_create_ann)
#use rdann to ouput annotations as a text file
cmd_disp_ann="rdann -r "+rec_name+" -a output_annot"
#push output text to a file
print (cmd_disp_ann)
os.system(cmd_disp_ann +">" +s1_rdann_file)
s1_l_p_wave_times=[] # this will contain p wave values for 1 rec and will be emptied everytime
## code for p wave time calculation goes here ####
f=open(s1_rdann_file,'r')
for line in f:
temp=line.split()
if (temp[2] == '(') and (temp[-1] =='0'):
start_sample_num=float(temp[1])
#print ("start sample num is : "+ str(start_sample_num))
elif (temp[2] == ')') and (temp[-1] =='0'):
end_sample_num=float(temp[1])
#print("end_sample_num is: " +str(end_sample_num))
p_duration_ms=(end_sample_num-start_sample_num) *(1000/freq);
#print ("pwave duration from signal 1 is : " + str(p_duration_ms))
s1_l_p_wave_times.append(p_duration_ms)
return s0_l_p_wave_times,s1_l_p_wave_times
def extract_wave_times(output_folder,record,rec_name,annotation,start_time,end_time,signal_num):
##The num field of each WFON and WFOFF annotation designates the type of waveform with which it is associated: 0 for a P wave, 1 for a QRS complex, or 2 for a T wave.
# ## doing wave num encoding here:
# if wave_name == 'p':
# wave_num = '0'
# elif wave_name == 'r':
# wave_num = '1'
# elif wave_name =='t':
# wave_num = '2'
## time for which you want to read record ##
nsamp, freq, annot, init_time,sdata=ws.setupWfdb(rec_name, annotation)
rdann_file=output_folder+"ecgpu_output.txt"
output_ann="output_annotator"
os.chdir(output_folder)
signal=signal_num;
os.system("rm -f "+rdann_file)
cmd_create_ann="ecgpuwave -r "+rec_name +" "+"-a"+" "+output_ann+ " -f "+start_time+" -t "+ end_time +" -i "+annotation+" -s "+signal
print(cmd_create_ann)
os.system(cmd_create_ann)
#use rdann to ouput annotations as a text file
cmd_disp_ann="rdann -r "+rec_name+" -a output_annot"
#push output text to a file
print (cmd_disp_ann)
os.system(cmd_disp_ann +">" +rdann_file)
## features we want to extract:
# p_dur=p_off-p_on
# p_ini=p_p_peak-p_on
# p_ter = p_off - p_peak
# p_asy=p_ter/p_ini
#pr_on
#pr_peak
#r_off
l_wave_dur_time=[] # this will contain p/t wave values for 1 rec and will be emptied everytime
l_wave_ini_time=[]
l_wave_ter_time=[]
l_wave_asy_time=[]
l_pr_on_time=[]
l_pr_peak_time=[]
l_pr_off_time=[]
l_pp_on_time=[]
## code for p wave time calculation goes here ####
f=open(rdann_file,'r')
p_true=0
for line in f:
temp=line.split()
if (temp[2] == '(') and (temp[-1] =='0'):
start_sample_num=float(temp[1])
#print ("start sample num is : "+ str(start_sample_num))
elif (temp[2] == 'p') and (temp[-1] =='0'):
peak_sample_num=float(temp[1])
p_true=1;
elif (temp[2] == ')') and (temp[-1] =='0'):
end_sample_num=float(temp[1])
#print("end_sample_num is: " +str(end_sample_num))
wave_duration_ms=(end_sample_num-start_sample_num) *(1000/freq);
wave_ini_ms=(peak_sample_num-start_sample_num)*(1000/freq)
wave_ter_ms=(end_sample_num-peak_sample_num)*(1000/freq)
wave_asy_ms=wave_ter_ms/wave_ini_ms
l_wave_dur_time.append(wave_duration_ms)
l_wave_ini_time.append(wave_ini_ms)
l_wave_ter_time.append(wave_ter_ms)
l_wave_asy_time.append(wave_asy_ms)
if (temp[2] == 'N') and (temp[-1] =='0') and (p_true== 1): # this is looking for r peakvand making sure that p wave was calculated previously
r_peak_sample=float(temp[1])
pr_on_ms=(r_peak_sample -start_sample_num)*(1000/freq)
pr_peak_ms=(r_peak_sample-peak_sample_num)*(1000/freq)
pr_off_ms=(r_peak_sample-end_sample_num)*(1000/freq)
p_true=0;
l_pr_on_time.append(pr_on_ms)
l_pr_peak_time.append(pr_peak_ms)
l_pr_off_time.append(pr_off_ms)
for i in range(len(l_wave_dur_time)-1):
pp_on_ms=l_wave_dur_time[i+1]- l_wave_dur_time[i]
l_pp_on_time.append(pp_on_ms)
#print ("pwave duration from signal 0 is : " + str(p_duration_ms))
##### extract p wave times for second signal
all_time_features=[l_wave_dur_time,l_wave_ini_time,l_wave_ter_time,l_wave_asy_time,l_pr_on_time,l_pr_peak_time,l_pr_off_time]
return all_time_features
