def get_annotation(sample, ann_type, ann_fs, start, end):
try:
annotation = wfdb.rdann(sample, ann_type, sampfrom=start*ann_fs, sampto=end*ann_fs)
except Exception as e:
annotation = wfdb.Annotation(sample, ann_type, [], [])
print("Error getting annotation for sample ", sample, ann_type, e)
return annotation
def get_ecg_data(datfile):
## convert .dat/q1c to numpy arrays
recordname=os.path.basename(datfile).split(".dat")[0]
recordpath=os.path.dirname(datfile)
cwd=os.getcwd()
os.chdir(recordpath) ## somehow it only works if you chdir.
annotator='q1c'
annotation = wfdb.rdann(recordname, extension=annotator, sampfrom=0,sampto = None, pbdir=None)
Lstannot=list(zip(annotation.sample,annotation.symbol,annotation.aux_note))
FirstLstannot=min( i[0] for i in Lstannot)
LastLstannot=max( i[0] for i in Lstannot)-1
print("first-last annotation:", FirstLstannot,LastLstannot)
record = wfdb.rdsamp(recordname, sampfrom=FirstLstannot,sampto = LastLstannot) #wfdb.showanncodes()
annotation = wfdb.rdann(recordname, annotator, sampfrom=FirstLstannot,sampto = LastLstannot) ## get annotation between first and last.
annotation2 = wfdb.Annotation(recordname='sel32', extension='niek', sample=(annotation.sample-FirstLstannot), symbol = annotation.symbol, aux_note=annotation.aux_note)
Vctrecord=np.transpose(record.p_signals)
VctAnnotationHot=np.zeros( (6,len(Vctrecord[1])), dtype=np.int)
VctAnnotationHot[5]=1 ## inverse of the others
#print("ecg, 2 lead of shape" , Vctrecord.shape)
#print("VctAnnotationHot of shape" , VctAnnotationHot.shape)
#print('plotting extracted signal with annotation')
#wfdb.plotrec(record, annotation=annotation2, title='Record 100 from MIT-BIH Arrhythmia Database', timeunits = 'seconds')
VctAnnotations=list(zip(annotation2.sample,annotation2.symbol)) ## zip coordinates + annotations (N),(t) etc)
#print(VctAnnotations)
for i in range(len(VctAnnotations)):
#print(VctAnnotations[i]) # Print to display annotations of an ecg
try:
if VctAnnotations[i][1]=="p":
if VctAnnotations[i-1][1]=="(":
pstart=VctAnnotations[i-1][0]
if VctAnnotations[i+1][1]==")":
pend=VctAnnotations[i+1][0]
if VctAnnotations[i+3][1]=="N":
rpos=VctAnnotations[i+3][0]
if VctAnnotations[i+2][1]=="(":
qpos=VctAnnotations[i+2][0]
if VctAnnotations[i+4][1]==")":
spos=VctAnnotations[i+4][0]
for ii in range(0,8): ## search for t (sometimes the "(" for the t is missing )
if VctAnnotations[i+ii][1]=="t":
tpos=VctAnnotations[i+ii][0]
if VctAnnotations[i+ii+1][1]==")":
tendpos=VctAnnotations[i+ii+1][0]
# #print(ppos,qpos,rpos,spos,tendpos)
VctAnnotationHot[0][pstart:pend]=1 #P segment
VctAnnotationHot[1][pend:qpos]=1 #part "nothing" between P and Q, previously left unnanotated, but categorical probably can't deal with that
VctAnnotationHot[2][qpos:rpos]=1 #QR
VctAnnotationHot[3][rpos:spos]=1 #RS
VctAnnotationHot[4][spos:tendpos]=1 #ST (from end of S to end of T)
VctAnnotationHot[5][pstart:tendpos]=0 #tendpos:pstart becomes 1, because it is inverted above
except IndexError:
pass
Vctrecord=np.transpose(Vctrecord) # transpose to (timesteps,feat)
VctAnnotationHot=np.transpose(VctAnnotationHot)
os.chdir(cwd)
return Vctrecord, VctAnnotationHot
def my_get_ecg_data(datfile):
## convert .dat/q1c to numpy arrays
recordname = os.path.basename(datfile).split(".dat")[0]
recordpath = os.path.dirname(datfile)
cwd = os.getcwd()
os.chdir(recordpath) ## somehow it only works if you chdir.
annotator = annot_type
annotation = wfdb.rdann(recordname, extension=annotator, sampfrom=0, sampto=None, pb_dir=None) # read annotation
Lstannot = list(zip(annotation.sample, annotation.symbol, annotation.aux_note))
FirstLstannot = min(i[0] for i in Lstannot) # annot start
LastLstannot = max(i[0] for i in Lstannot) - 1 # annot end
print("first-last annotation:", FirstLstannot, LastLstannot)
record = wfdb.rdsamp(recordname, sampfrom=FirstLstannot, sampto=LastLstannot) # read signal
annotation = wfdb.rdann(recordname, annotator, sampfrom=FirstLstannot,
sampto=LastLstannot) ## get annotation between first and last.
# this make annotation from 0 to end
annotation2 = wfdb.Annotation(record_name=recordname, extension=annot_type,
sample=(annotation.sample - FirstLstannot),
symbol=annotation.symbol, aux_note=annotation.aux_note)
Vctrecord = np.transpose(record[0])
VctAnnotationHot = np.zeros((6, len(Vctrecord[1])),
dtype=np.int) # 6 annotation type: 0: P, 1: PQ, 2: QR, 3: RS, 4: ST, 5: ISO (TP)
#VctAnnotationHot[3] = 1 ## inverse of the others
# print("ecg, 2 lead of shape" , Vctrecord.shape)
# print("VctAnnotationHot of shape" , VctAnnotationHot.shape)
# print('plotting extracted signal with annotation')
# wfdb.plotrec(record, annotation=annotation2, title='Record 100 from MIT-BIH Arrhythmia Database', timeunits = 'seconds')
VctAnnotations = list(zip(annotation2.sample, annotation2.symbol)) ## zip coordinates + annotations (N),(t) etc)
# print(VctAnnotations)
annsamp = []
anntype = []
for i in range(len(VctAnnotations)):
annsamp.append(VctAnnotations[i][0])
anntype.append(VctAnnotations[i][1])
length = len(annsamp)
begin = -1
end = -1
s = 'none'
states = {'N': 0, 'st': 1, 't': 2, 'iso': 3, 'p': 4, 'pq': 5}
annot_expand = -1 * np.ones(length)
for j, samp in enumerate(annsamp):
if anntype[j] == '(':
begin = samp
if (end > 0) & (s != 'none'):
if s == 'N':
VctAnnotationHot[1][end:begin] = 1
#annot_expand[end:begin] = states['st']
elif s == 't':
VctAnnotationHot[3][end:begin] = 1
#annot_expand[end:begin] = states['iso']
elif s == 'p':
VctAnnotationHot[5][end:begin] = 1
#annot_expand[end:begin] = states['pq']
elif anntype[j] == ')':
end = samp
if (begin >= 0) & (s != 'none'):
VctAnnotationHot[states[s]][begin:end] = 1
#annot_expand[begin:end] = states[s]
else:
s = anntype[j]
Vctrecord = np.transpose(Vctrecord) # transpose to (timesteps,feat)
VctAnnotationHot = np.transpose(VctAnnotationHot)
os.chdir(cwd)
return Vctrecord, VctAnnotationHot