Python wfdb.rdann() Examples
The following are 6
code examples of wfdb.rdann().
You can vote up the ones you like or vote down the ones you don't like,
and go to the original project or source file by following the links above each example.
You may also want to check out all available functions/classes of the module
wfdb
, or try the search function
.
.
Example #1
| Source File: download_mit_arrhythmia.py From NeuroKit with MIT License | 7 votes |
|
def read_file(file, participant):
"""Utility function
"""
# Get signal
data = pd.DataFrame({"ECG": wfdb.rdsamp(file[:-4])[0][:, 0]})
data["Participant"] = "MIT-Arrhythmia_%.2i" %(participant)
data["Sample"] = range(len(data))
data["Sampling_Rate"] = 360
data["Database"] = "MIT-Arrhythmia-x" if "x_mitdb" in file else "MIT-Arrhythmia"
# getting annotations
anno = wfdb.rdann(file[:-4], 'atr')
anno = np.unique(anno.sample[np.in1d(anno.symbol, ['N', 'L', 'R', 'B', 'A', 'a', 'J', 'S', 'V', 'r', 'F', 'e', 'j', 'n', 'E', '/', 'f', 'Q', '?'])])
anno = pd.DataFrame({"Rpeaks": anno})
anno["Participant"] = "MIT-Arrhythmia_%.2i" %(participant)
anno["Sampling_Rate"] = 360
anno["Database"] = "MIT-Arrhythmia-x" if "x_mitdb" in file else "MIT-Arrhythmia"
return data, anno
Example #2
| Source File: tester_MITDB.py From py-ecg-detectors with GNU General Public License v3.0 | 5 votes |
|
def single_classifier_test(self, detector, tolerance=0):
max_delay_in_samples = 350 / 5
dat_files = []
for file in os.listdir(self.mitdb_dir):
if file.endswith(".dat"):
dat_files.append(file)
mit_records = [w.replace(".dat", "") for w in dat_files]
results = np.zeros((len(mit_records), 5), dtype=int)
i = 0
for record in mit_records:
progress = int(i/float(len(mit_records))*100.0)
print("MITDB progress: %i%%" % progress)
sig, fields = wfdb.rdsamp(self.mitdb_dir+'/'+record)
unfiltered_ecg = sig[:, 0]
ann = wfdb.rdann(str(self.mitdb_dir+'/'+record), 'atr')
anno = _tester_utils.sort_MIT_annotations(ann)
r_peaks = detector(unfiltered_ecg)
delay = _tester_utils.calcMedianDelay(r_peaks, unfiltered_ecg, max_delay_in_samples)
if delay > 1:
TP, FP, FN = _tester_utils.evaluate_detector(r_peaks, anno, delay, tol=tolerance)
TN = len(unfiltered_ecg)-(TP+FP+FN)
results[i, 0] = int(record)
results[i, 1] = TP
results[i, 2] = FP
results[i, 3] = FN
results[i, 4] = TN
i = i+1
return results
Example #3
| Source File: nsrdb.py From deepecg with MIT License | 5 votes |
|
def _get_sections(self):
"""Collect continuous normal sinus rhythm sections."""
# Empty dictionary for NSR sections
sections = list()
# Loop through recordings
for record_id in self.record_ids:
# Import recording
record = wfdb.rdrecord(os.path.join(self.raw_path, record_id))
# Import annotations
annotation = wfdb.rdann(os.path.join(self.raw_path, record_id), 'atr')
# Get sample frequency
fs = record.__dict__['fs']
# Get waveform
waveform = record.__dict__['p_signal']
# labels
labels = np.array(annotation.__dict__['symbol'])
# Samples
sample = annotation.__dict__['sample']
# Section counter
section_id = 0
# Loop through labels
for start, stop in self._contiguous_regions(labels == 'N'):
if stop - start >= self.min_labels:
sections.append({'label': 'N', 'section': section_id, 'record': record_id, 'fs': fs, 'channel': 1,
'db': self.db_name, 'waveform': waveform[sample[start]:sample[stop - 1], 0]})
sections.append({'label': 'N', 'section': section_id, 'record': record_id, 'fs': fs, 'channel': 2,
'db': self.db_name, 'waveform': waveform[sample[start]:sample[stop - 1], 1]})
section_id += 1
return sections
Example #4
| Source File: tester_MITDB.py From ecg-detectors with GNU General Public License v3.0 | 4 votes |
|
def single_classifier_test(self, detector, tolerance=0, print_results = True):
dat_files = []
for file in os.listdir(self.mitdb_dir):
if file.endswith(".dat"):
dat_files.append(file)
mit_records = [w.replace(".dat", "") for w in dat_files]
results = np.zeros((len(mit_records), 5), dtype=int)
i = 0
for record in mit_records:
progress = int(i/float(len(mit_records))*100.0)
print("Progress: %i%%" % progress)
sig, fields = wfdb.rdsamp(self.mitdb_dir/record)
unfiltered_ecg = sig[:, 0]
ann = wfdb.rdann(str(self.mitdb_dir/record), 'atr')
anno = tester_utils.sort_MIT_annotations(ann)
r_peaks = detector(unfiltered_ecg)
TP, FP, FN = tester_utils.evaluate_detector(r_peaks, anno, tol=tolerance)
TN = len(unfiltered_ecg)-(TP+FP+FN)
results[i, 0] = int(record)
results[i, 1] = TP
results[i, 2] = FP
results[i, 3] = FN
results[i, 4] = TN
i = i+1
if print_results:
total_tp = np.sum(results[:, 1])
total_fp = np.sum(results[:, 2])
total_fn = np.sum(results[:, 3])
se = total_tp/(total_tp+total_fn)*100.0
ppv = total_tp/(total_tp+total_fp)*100.0
f1 = (2*total_tp)/((2*total_tp)+total_fp+total_fn)*100.0
print("\nSensitivity: %.2f%%" % se)
print("PPV: %.2f%%" % ppv)
print("F1 Score: %.2f%%\n" % f1)
return results
Example #5
| Source File: tester_MITDB.py From ecg-detectors with GNU General Public License v3.0 | 4 votes |
|
def mcnemars_test(self, detector1, detector2, tolerance=0, print_results = True):
dat_files = []
for file in os.listdir(self.mitdb_dir):
if file.endswith(".dat"):
dat_files.append(file)
mit_records = [w.replace(".dat", "") for w in dat_files]
a = 0 #neg/neg
b = 0 #pos/neg
c = 0 #neg/pos
d = 0 #pos/pos
i = 0
for record in mit_records:
progress = int(i/float(len(mit_records))*100)
print("Progress: %i%%" % progress)
sig, fields = wfdb.rdsamp(self.mitdb_dir/record)
unfiltered_ecg = sig[:, 0]
ann = wfdb.rdann(str(self.mitdb_dir/record), 'atr')
anno = tester_utils.sort_MIT_annotations(ann)
r_peaks1 = detector1(unfiltered_ecg)
r_peaks2 = detector2(unfiltered_ecg)
for sample in anno:
result1 = np.any(np.in1d(sample, r_peaks1))
result2 = np.any(np.in1d(sample, r_peaks2))
if result1 and result2:
d+=1
elif result1 and not result2:
b+=1
elif not result1 and result2:
c+=1
elif not result1 and not result2:
a+=1
i+=1
table = np.array([[a, b], [c, d]])
if b==0 or c==0:
Z = 0
else:
Z = (abs(b-c)-1)/np.sqrt(b+c)
if print_results:
print("\n2x2 Table")
print(table)
print("\nZ score: %.4f\n" % Z)
return Z
Example #6
| Source File: afdb.py From deepecg with MIT License | 4 votes |
|
def _get_sections(self):
"""Collect continuous arrhythmia sections."""
# Empty dictionary for arrhythmia sections
sections = list()
# Loop through records
for record_id in self.record_ids:
# Import recording
record = wfdb.rdrecord(os.path.join(self.raw_path, record_id))
# Import annotations
annotation = wfdb.rdann(os.path.join(self.raw_path, record_id), 'atr')
# Get sample frequency
fs = record.__dict__['fs']
# Get waveform
waveform = record.__dict__['p_signal']
# labels
labels = [label[1:] for label in annotation.__dict__['aux_note']]
# Samples
sample = annotation.__dict__['sample']
# Loop through labels and collect sections
for idx, label in enumerate(labels):
if any(label in val for val in list(self.label_dict.keys())):
if idx != len(labels) - 1:
sections.append({'label': label, 'section': idx, 'record': record_id, 'fs': fs, 'channel': 0,
'db': self.db_name, 'waveform': waveform[sample[idx]:sample[idx + 1], 0]})
sections.append({'label': label, 'section': idx, 'record': record_id, 'fs': fs, 'channel': 1,
'db': self.db_name, 'waveform': waveform[sample[idx]:sample[idx + 1], 1]})
elif idx == len(labels) - 1:
sections.append({'label': label, 'section': idx, 'record': record_id, 'fs': fs, 'channel': 0,
'db': self.db_name, 'waveform': waveform[sample[idx]:, 0]})
sections.append({'label': label, 'section': idx, 'record': record_id, 'fs': fs, 'channel': 1,
'db': self.db_name, 'waveform': waveform[sample[idx]:, 1]})
return sections
