Python wfdb.rdann方法代码示例

# 需要导入模块: import wfdb [as 别名]
# 或者: from wfdb import rdann [as 别名]
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 

# 需要导入模块: import wfdb [as 别名]
# 或者: from wfdb import rdann [as 别名]
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 

# 需要导入模块: import wfdb [as 别名]
# 或者: from wfdb import rdann [as 别名]
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 

# 需要导入模块: import wfdb [as 别名]
# 或者: from wfdb import rdann [as 别名]
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 

# 需要导入模块: import wfdb [as 别名]
# 或者: from wfdb import rdann [as 别名]
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 

# 需要导入模块: import wfdb [as 别名]
# 或者: from wfdb import rdann [as 别名]
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