def generate_raw_db(self): """Generate the raw version of the QT database in the 'raw' folder.""" LOGGER.info('Generating Raw QT Database...\nSave path: {}'.format( self.raw_path)) wfdb.dl_database(self.db_name, self.raw_path) self.record_names = self._get_record_names() LOGGER.info('Complete!')
def downloadDB(name): # Download WFDB record as requested by the user path = (os.getcwd() + '\\' + name) if os.path.exists(path): return name + " is already exist" else: wfdb.dl_database(name, path) return "Done"
def dl_all_db(db_dir=None): if not db_dir: db_dir = _gen_default_dbdir() dbs = wfdb.get_dbs() for db in dbs: db_name = db[0] print('downloading db: ', db[0], ' ', db[1]) wfdb.dl_database(db_name + '/', dl_dir=os.path.join(db_dir, db_name))
def generate_raw_db(self): """Generate the raw version of the MIT-BIH Atrial Fibrillation database in the 'raw' folder.""" print('Generating Raw MIT-BIH Atrial Fibrillation Database ...') # Download database wfdb.dl_database(self.db_name, self.raw_path) # Get list of recordings self.record_ids = [ file.split('.')[0] for file in os.listdir(self.raw_path) if '.dat' in file ] print('Complete!\n')
def downloadData(): ''' Downloads data from physionet ''' try: # creating necessary directories os.mkdir('database') os.mkdir('database/cudb') os.mkdir('database/mitMVAdb') except: pass wfdb.dl_database('vfdb', dl_dir='database/mitMVAdb') # download mitMVAdb wfdb.dl_database('cudb', dl_dir='database/cudb') # download cudb
def main(): # Command line argument parser parser = argparse.ArgumentParser( description='Download PTB Diagnostic Database') parser.add_argument('--download_path', type=str, required=False, default="../data/", help='Path to download the dataset to.') args = parser.parse_args() download_path = args.download_path print("Downloading the PTB Diagnostic Database into {}".format( download_path)) wfdb.dl_database('ptbdb', download_path) print("Dataset successfully downloaded!")
def test_dl_database_with_dat_file(self): wfdb.dl_database('afdb', './download-tests/', ['04015'])
def test_dl_database_no_dat_file(self): wfdb.dl_database('afdb', './download-tests/', ['00735'])
def download(): print('Downloading data...') download_dir = os.path.join(DATASET_ROOT, 'download') wfdb.dl_database('mitdb', dl_dir=download_dir)
def download_all_files(): wfdb.dl_database(DB, DESTINATION_PATH)
def dl_dbs(dbs, db_dir=None): if not db_dir: db_dir = _gen_default_dbdir() for db in dbs: wfdb.dl_database(db + '/', dl_dir=os.path.join(db_dir, db))
# this script convert the full dataset mitdb (data and annotatiosn) to text files from os import listdir, makedirs, system, getcwd from os.path import isfile, isdir, join, exists import wfdb #dir = 'ediagnostic/wfdb/'#'mitdb/' # dir = getcwd() + '/database/mitdb/' dir = 'database/mitdb/' #Create folder dir_out = dir + 'csv/' if not exists(dir_out): makedirs(dir_out) wfdb.dl_database('mitdb', getcwd() + '/database/mitdb/', overwrite=True) records = [ f for f in listdir(dir) if isfile(join(dir, f)) if (f.find('.dat') != -1) ] #print records for r in records: command = 'rdsamp -r ' + dir + r[: -4] + ' -c -H -f 0 -v >' + dir_out + r[: -4] + '.csv' print(command) system(command) command_annotations = 'rdann -r ' + dir + r[: -4] + ' -f 0 -a atr -v >' + dir_out + r[:
import matplotlib.pyplot as plt import numpy as np import pandas as pd import tensorflow as tf from tensorflow import keras from tensorflow.keras import layers from sklearn.metrics import confusion_matrix import seaborn as sn os.chdir('C:\\Users\\Jerry\\Desktop\\Jerry\\projects\\heartbeat_python') #%% download all the files test = wfdb.get_dbs() wfdb.get_record_list('mitdb') wfdb.dl_database( 'mitdb', 'C:\\Users\\Jerry\\Desktop\\Jerry\\projects\\Heartbeat Python\\data') #%% building a loop to read in data and annotations then cutting the ECG into heartbeats def simple_plot(x, alpha=1, grid=True): plt.plot(np.arange(0, len(x)), x, alpha=alpha) if grid: plt.grid(True) sample = wfdb.rdsamp('data\\101')[0][:, 0] # read in the record annotation = wfdb.rdann('data\\101', 'atr', return_label_elements=['description'
def download_data(): if not exists(dir_out): makedirs(dir_out) wfdb.dl_database('mitdb', getcwd() + '/database/', overwrite=False) wfdb.dl_database('edb', getcwd() + '/database/', overwrite=False)
import os import numpy as np import wfdb # download dataset dataset_root = './dataset' download_dir = os.path.join(dataset_root, 'data') wfdb.dl_database('mitdb', dl_dir=download_dir) # setting window_size = 720 # 2 seconds sample_rate = 360 # 360 Hz # list train_record_list = [ '101', '106', '108', '109', '112', '115', '116', '118', '119', '122', '124', '201', '203', '205', '207', '208', '209', '215', '220', '223', '230' ] test_record_list = [ '100', '103', '105', '111', '113', '117', '121', '123', '200', '210', '212', '213', '214', '219', '221', '222', '228', '231', '232', '233', '234' ] # annotation labels = ['N', 'V'] valid_symbols = ['N', 'L', 'R', 'e', 'j', 'V', 'E'] label_map = { 'N': 'N', 'L': 'N', 'R': 'N', 'e': 'N',
import wfdb # for physionet tools import os # for downloading samples from databases from IPython.display import display # for displaying physionet libraries if __name__ == '__main__': # Make download directories in your current working directory current_working_directory = os.getcwd() # the download directory for the arrhythmia database directory_database1 = os.path.join(current_working_directory, 'mitdb') # the download directory for the hypertension database directory_database2 = os.path.join(current_working_directory, 'shareedb') # Download all the WFDB content wfdb.dl_database('mitdb', dl_dir=directory_database1) wfdb.dl_database('shareedb', dl_dir=directory_database2) # Display the downloaded content in the folders display(os.listdir(directory_database1)) display(os.listdir(directory_database2))
def download(): try: wfdb.dl_database('mitdb', os.getcwd() +'\mitdb') except: print("donwload f****d")