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 test_dl_database_with_dat_file(self):
wfdb.dl_database('afdb', './download-tests/', ['04015'])
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[:
def test_dl_database_no_dat_file(self):
wfdb.dl_database('afdb', './download-tests/', ['00735'])
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")
