pythonimporteuropean-data-format

Import .edf file directly from online archive in python

Using pyedflib to import edf files, is it possible to import datasets directly from their source? Or is it always necessary to download data and import locally?

for example, I would like to do this:

pyedflib.EdfReader("https://www.physionet.org/pn6/chbmit/chb02/chb02_02.edf")

---------------------------------------------------------------------------
IOError                                   Traceback (most recent call last)
<ipython-input-64-d123ce671a2f> in <module>()
----> 1 pyedflib.EdfReader("https://www.physionet.org/pn6/chbmit/chb02/chb02_02.edf")

pyedflib/_extensions/_pyedflib.pyx in pyedflib._extensions._pyedflib.CyEdfReader.__init__()

pyedflib/_extensions/_pyedflib.pyx in pyedflib._extensions._pyedflib.CyEdfReader.open()

pyedflib/_extensions/_pyedflib.pyx in pyedflib._extensions._pyedflib.CyEdfReader.check_open_ok()

IOError: can not open file, no such file or directory
Solution

  • Answer received on GitHub page 

    import pyedflib
import os
url = "https://www.physionet.org/pn6/chbmit/chb01/chb01_01.edf"
filename = "./chb.edf"
try:
    from urllib import urlretrieve # Python 2

except ImportError:
    from urllib.request import urlretrieve # Python 3

urlretrieve(url,filename)
pyedflib.EdfReader(filename)
os.remove(filename)

    https://github.com/holgern/pyedflib/issues/22#issuecomment-341649760