[Mne_analysis] error when initiating a raw object
Alexandre Gramfort
gramfort at nmr.mgh.harvard.edu
Wed Jan 9 11:06:05 EST 2013
hi Andy,
for whatever reason you have an empty Tag in your fiff file.
this patch should fix the problem:
https://github.com/mne-tools/mne-python/pull/356
let me know if it does so we can accept this patch.
Best,
Alex
On Wed, Jan 9, 2013 at 2:22 PM, Dykstra, Andrew
<Andrew.Dykstra at med.uni-heidelberg.de> wrote:
> Hi Alex,
>
> Yes, I can open the file with mne_browse_raw and can create evoked
> responses from it via mne_process_raw which themselves can be read via
> mne.fiff.read_evoked.
>
> An additional piece of information I just discovered: I can open the
> raw file straight from the acquisition. The file that I can cannot open
> was written via a modified version of fiff_write_raw_segment.m (buffer
> adjusted from 30 to 0.5 seconds) after some preprocessing in MATLAB. I
> haven't run into this issue with other subjects processed using the
> exact same stream. There are links to three files below. The first two
> are from the troublesome subject. The last is a raw file, after MATLAB
> preprocessing, that can be opened with mne.fiff.Raw.
>
> http://ubuntuone.com/69KPvr8lU4Goz7Hkm7MPJH
>
> http://ubuntuone.com/3QiiHgl7Oxr5astCIFwv6K
>
> http://ubuntuone.com/2kcJZjdCZJg2xpdAymGcI3
>
> Thanks for the help,
> Andy
>
> p.s. happy to learn that ICA has now been incorporated into the python
> package. This closes my data analysis loop to keep me in shell/python.
> Thanks Alex/Denis.
>
> --
> Andrew R. Dykstra, PhD
> Auditory Cognition Lab
> Neurologie und Poliklinik
> Universitätsklinikum Heidelberg
> Im Neuenheimer Feld 400
> 69120 Heidelberg
>
> "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov
>
> On 01/08/2013 07:09 PM, Alexandre Gramfort wrote:
>> hi Andy,
>>
>> can you read this file otherwise with mne_browse_raw or mne_process_raw?
>>
>> if yes can you share the file via dropbox or any other service?
>>
>> thanks
>> Alex
>>
>> On Tue, Jan 8, 2013 at 6:14 PM, Dykstra, Andrew
>> <Andrew.Dykstra at med.uni-heidelberg.de> wrote:
>>> Dear MNE community,
>>>
>>> I am experiencing an error that I don't understand when trying to create
>>> a raw object in Python. The traceback is below, and I only get this
>>> with the raw files from one subject. I initially thought that it could
>>> be due to the abnormally large file sizes of this subject's raw data
>>> (~700 Mb), but I have one other subject whose raw data were comparable
>>> and I can create raw objects from those data without issue.
>>>
>>> Has anyone experienced this?
>>>
>>> Cheers,
>>> Andy
>>>
>>> error Traceback (most recent call last)
>>> /home/andrew/Experiments/Awareness_wo_Attention/<ipython-input-8-5fbcd28d6772>
>>> in <module>()
>>> ----> 1
>>> runfile(r'/home/andrew/Experiments/Awareness_wo_Attention/py_tmp_check_dataset_channels.py',
>>> wdir=r'/home/andrew/Experiments/Awareness_wo_Attention')
>>>
>>> /usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.pyc
>>> in runfile(filename, args, wdir, namespace)
>>> 485 pass
>>> 486 os.chdir(wdir)
>>> --> 487 execfile(filename, namespace)
>>> 488 sys.argv = ['']
>>> 489 namespace.pop('__file__')
>>>
>>> /home/andrew/Experiments/Awareness_wo_Attention/py_tmp_check_dataset_channels.py
>>> in <module>()
>>> 48 for block in range(2):
>>> 49 fname.append(data_path + '/' + subject + '/meg/' +
>>> subject + '_block' + str(block+1) + '_cleaned_raw.fif')
>>> ---> 50 raw.append(mne.fiff.Raw(fname[block]))
>>> 51 chan.append(raw[block].ch_names)
>>> 52 chan.append([x for x in chan[0] if x not in set(chan[1])])
>>>
>>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/utils.pyc
>>> in dec(*args, **kwargs)
>>> 263 return ret
>>> 264 else:
>>> --> 265 return function(*args, **kwargs)
>>> 266
>>> 267 # set __wrapped__ attribute so ?? in IPython gets the right
>>> source
>>>
>>>
>>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/fiff/raw.pyc
>>> in __init__(self, fnames, allow_maxshield, preload, verbose, proj_active)
>>> 83
>>> 84 raws = [self._read_raw_file(fname, allow_maxshield,
>>> preload)
>>> ---> 85 for fname in fnames]
>>> 86
>>> 87 _check_raw_compatibility(raws)
>>>
>>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/utils.pyc
>>> in dec(*args, **kwargs)
>>> 263 return ret
>>> 264 else:
>>> --> 265 return function(*args, **kwargs)
>>> 266
>>> 267 # set __wrapped__ attribute so ?? in IPython gets the right
>>> source
>>>
>>>
>>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/fiff/raw.pyc
>>> in _read_raw_file(self, fname, allow_maxshield, preload, verbose)
>>> 137 ext = os.path.splitext(fname)[1].lower()
>>> 138 whole_file = preload if '.gz' in ext else False
>>> --> 139 fid, tree, _ = fiff_open(fname, preload=whole_file)
>>> 140
>>> 141 # Read the measurement info
>>>
>>>
>>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/utils.pyc
>>> in dec(*args, **kwargs)
>>> 263 return ret
>>> 264 else:
>>> --> 265 return function(*args, **kwargs)
>>> 266
>>> 267 # set __wrapped__ attribute so ?? in IPython gets the right
>>> source
>>>
>>>
>>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/fiff/open.pyc
>>> in fiff_open(fname, preload, verbose)
>>> 83 while tag.next >= 0:
>>> 84 pos = fid.tell()
>>> ---> 85 tag = read_tag_info(fid)
>>> 86 tag.pos = pos
>>> 87 directory.append(tag)
>>>
>>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/fiff/tag.pyc
>>> in read_tag_info(fid)
>>> 67 """
>>> 68 s = fid.read(4 * 4)
>>> ---> 69 tag = Tag(*struct.unpack(">iiii", s))
>>> 70 if tag.next == 0:
>>> 71 fid.seek(tag.size, 1)
>>>
>>> error: unpack requires a string argument of length 16
>>>
>>> --
>>> Andrew R. Dykstra, PhD
>>> Auditory Cognition Lab
>>> Neurologie und Poliklinik
>>> Universitätsklinikum Heidelberg
>>> Im Neuenheimer Feld 400
>>> 69120 Heidelberg
>>>
>>> "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov
>>>
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