error filtering biosemi imported file

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1

Hi everybody,
I'm working with some biosemi EEG files

the following code:

raw = read_raw_edf('bdf_file.bdf', hpts = 'hpts_file.hpts')
fraw = filter.band_pass_filter(raw, 1024, 30, 1)

gives me the error:

Traceback (most recent call last):
  File
"C:\Users\Mauricio\Documents\Dropbox\PhD\scripts\mne-python\preprocessing.py",
line 9, in <module>
    fraw = filter.band_pass_filter(raw, 1024, 30, 1)
  File "<string>", line 2, in band_pass_filter
  File "C:\Python33\lib\site-packages\mne-0.8.git-py3.3.egg\mne\utils.py",
line 387, in verbose
    ret = function(*args, **kwargs)
  File "C:\Python33\lib\site-packages\mne-0.8.git-py3.3.egg\mne\filter.py",
line 624, in band_pass_filter
    xf = _filter(x, Fs, freq, gain, filter_length, picks, n_jobs, copy)
  File "C:\Python33\lib\site-packages\mne-0.8.git-py3.3.egg\mne\filter.py",
line 276, in _filter
    x, orig_shape, picks = _prep_for_filtering(x, copy, picks)
  File "C:\Python33\lib\site-packages\mne-0.8.git-py3.3.egg\mne\filter.py",
line 226, in _prep_for_filtering
    orig_shape = x.shape
AttributeError: 'RawEDF' object has no attribute 'shape'

Could somebody tell me what I'm doing wrong?
What is the right pipeline importing and filtering .bdf files?

All the best,
Mauricio.
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2

Hey Mauricio,

You should be able to do "raw.filter(...) " directly on the Raw instance
(as a method of Raw). Does that make sense?

http://martinos.org/mne/stable/generated/mne.fiff.Raw.html#mne.fiff.Raw.filter

Eric

3

Thanks Eric,
do I have to type something like this?

raw = read_raw_edf('bdf_file.bdf', hpts = 'hpts_file.hpts')
raw.filter(30, 1)

in that case, I have to use
raw = read_raw_edf('bdf_file.bdf', hpts = 'hpts_file.hpts', preload =
'True')

Isn't it? But it's strange because when I read the bdf with preload =
'True' I don't know if the program crushes or it will take a lot of time
(I'm loading a 128 channels 50 min EEG on a PC with 8 GB RAM and two 3.4
GHz processors... it takes to EEGLab just 3 min). I waited for 1 hr and the
bdf didn't load.

All the best,
Mauricio.

2014/1/14 Eric Larson <larson.eric.d at gmail.com>

Hey Mauricio,

You should be able to do "raw.filter(...) " directly on the Raw instance
(as a method of Raw). Does that make sense?

http://martinos.org/mne/stable/generated/mne.fiff.Raw.html#mne.fiff.Raw.filter

Eric

Hi everybody,
I'm working with some biosemi EEG files

the following code:

raw = read_raw_edf('bdf_file.bdf', hpts = 'hpts_file.hpts')
fraw = filter.band_pass_filter(raw, 1024, 30, 1)

gives me the error:

Traceback (most recent call last):
  File
"C:\Users\Mauricio\Documents\Dropbox\PhD\scripts\mne-python\preprocessing.py",
line 9, in <module>
    fraw = filter.band_pass_filter(raw, 1024, 30, 1)
  File "<string>", line 2, in band_pass_filter
  File
"C:\Python33\lib\site-packages\mne-0.8.git-py3.3.egg\mne\utils.py", line
387, in verbose
    ret = function(*args, **kwargs)
  File
"C:\Python33\lib\site-packages\mne-0.8.git-py3.3.egg\mne\filter.py", line
624, in band_pass_filter
    xf = _filter(x, Fs, freq, gain, filter_length, picks, n_jobs, copy)
  File
"C:\Python33\lib\site-packages\mne-0.8.git-py3.3.egg\mne\filter.py", line
276, in _filter
    x, orig_shape, picks = _prep_for_filtering(x, copy, picks)
  File
"C:\Python33\lib\site-packages\mne-0.8.git-py3.3.egg\mne\filter.py", line
226, in _prep_for_filtering
    orig_shape = x.shape
AttributeError: 'RawEDF' object has no attribute 'shape'

Could somebody tell me what I'm doing wrong?
What is the right pipeline importing and filtering .bdf files?

All the best,
Mauricio.

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4

Hey Mauricio,

This sounds like it might be an issue with our preloading routines. If you
can upload a sample EDF file and start an issue on Github with a minimum
example (it looks like those lines would be it) of the problem, we can work
out a solution:

https://github.com/mne-tools/mne-python/issues?state=open

Thanks,
Eric

5

hi,

yes please share the file.

Just to make sure did you type:

raw = read_raw_edf('bdf_file.bdf', hpts = 'hpts_file.hpts', preload = 'True')

or

raw = read_raw_edf('bdf_file.bdf', hpts = 'hpts_file.hpts', preload = True)

?

ie. without the '' around the True.

the later is the good way.

Alex