How to use the wfdb.rdsamp function in wfdb

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github berndporr / py-ecg-detectors / tester_MITDB.py View on Github external
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
github neuropsychology / NeuroKit.py / utils / ecg_signal_quality_model_creation / data_creation.py View on Github external
- patient001/
    - patient002/
    - ...
"""


#==============================================================================
# Extracting
#==============================================================================
data={"Control": {}, "Patient": {}}
participants = [x for x in os.listdir("./data/") if 'patient' in x]
for participant in participants:
    files = os.listdir("./data/" + participant)
    if len([x for x in files if '.dat' in x]) > 0:
        file = [x for x in files if '.dat' in x][0].split(".")[0]
        signals, info = wfdb.rdsamp("data/" + participant + "/" + file)

        signals = pd.DataFrame(signals)
        signals.columns = info["sig_name"]

        data_participant = {}
        data_participant["Signals"] = signals
        data_participant["sampling_rate"] = info["fs"]


        for key in info["comments"]:
            try:
                data_participant[key.split(": ")[0]] = key.split(": ")[1]
            except IndexError:
                data_participant[key.split(":")[0]] = np.nan

        if data_participant["Reason for admission"] in ["n/a", "Healthy control"]:
github gogowenzhang / ECG_Detector / src / data_processing.py View on Github external
def load_data(signal_filename, label_filename):
    '''
    Load signal file and label file. One-hot encoding of labels. 
    Input: signal filename, label filename
    Output: list of signals, numpy array of labels
    '''

    signals = []
    records_file = open(signal_filename, 'r')
    for record_name in records_file:
        record = wfdb.rdsamp('data/training2017/{}'.format(record_name.strip())) 
        d_signal = record.adc()[:,0]
        signals.append(d_signal)

    labels = pd.read_csv(label_filename, header=None, names=['id', 'label'])
    y = labels['label']
    y[y=='N'] = 0
    y[y=='A'] = 1
    y[y=='O'] = 2
    y[y=='~'] = 3
    y = keras.utils.to_categorical(y)
    return signals, y
github gogowenzhang / ECG_Detector / src / demo_predict_one.py View on Github external
def load_data(record_name):
    '''
    Load signal file
    Input: signal file
    Output: list of signals
    '''    
    record = wfdb.rdsamp('data/training2017/{}'.format(record_name.strip())) 
    signal = record.adc()[:,0]
    return signal
github Nospoko / qrs-tutorial / utils / plotters.py View on Github external
def show_path(path):
    """ As a plot """
    # Read in the data
    record = wf.rdsamp(path)
    annotation = wf.rdann(path, 'atr')
    data = record.p_signals
    cha = data[:, 0]
    print 'Channel type:', record.signame[0]
    times = np.arange(len(cha), dtype = float)
    times /= record.fs
    plt.plot(times, cha)
    plt.xlabel('Time [s]')
    plt.show()
github gogowenzhang / ECG_Detector / src / predict.py View on Github external
def load_data(filename):
    '''
    Load signal file
    Input: signal file
    Output: list of signals
    '''
    signals = []
    records_file = open(filename, 'r')
    for record_name in records_file:
        record = wfdb.rdsamp('data/training2017/{}'.format(record_name.strip())) 
        d_signal = record.adc()[:,0]
        signals.append(d_signal)
    return signals
github Nospoko / qrs-tutorial / utils / plotters.py View on Github external
def show_objective_part2():
    """ For the model """
    # Choose a record
    records = dm.get_records()
    path = records[13]
    record = wf.rdsamp(path)
    ann = wf.rdann(path, 'atr')

    chid = 0
    print 'File:', path
    print 'Channel:', record.signame[chid]

    cha = record.p_signals[:, chid]

    # These were found manually
    sta = 184000
    end = sta + 1000
    times = np.arange(end-sta, dtype = 'float')
    times /= record.fs

    # Extract the annotations for that fragment
    where = (sta < ann.annsamp) & (ann.annsamp < end)
github Nospoko / qrs-tutorial / datasets / mitdb.py View on Github external
def make_dataset(records, width, savepath):
    """ Inside an array """
    # Prepare containers
    signals, labels = [], []

    # Iterate files
    for path in records:
        print 'Processing file:', path
        record = wf.rdsamp(path)
        annotations = wf.rdann(path, 'atr')

        # Extract pure signals
        data = record.p_signals

        # Convert each channel into labeled fragments
        signal, label = convert_data(data, annotations, width)

        # Cumulate
        signals.append(signal)
        labels.append(label)

    # Convert to one huge numpy.array
    signals = np.vstack(signals)
    labels = np.vstack(labels)
github Nospoko / qrs-tutorial / utils / plotters.py View on Github external
def show_annotations(path):
    """ Exemplary code """
    record = wf.rdsamp(path)
    annotation = wf.rdann(path, 'atr')

    # Get data and annotations for the first 2000 samples
    howmany = 2000
    channel = record.p_signals[:howmany, 0]

    # Extract all of the annotation related infromation
    where = annotation.annsamp < howmany
    samp = annotation.annsamp[where]

    # Convert to numpy.array to get fancy indexing access
    types = np.array(annotation.anntype)
    types = types[where]

    times = np.arange(howmany, dtype = 'float') / record.fs
    plt.plot(times, channel)

wfdb

The WFDB Python package: tools for reading, writing, and processing physiologic signals and annotations.

MIT
Latest version published 1 year ago

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