[Mne_analysis] -trans.fif

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Thu Feb 27 01:51:38 EST 2014
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Dan,

there is almost a test for everything see:

https://github.com/mne-tools/mne-python/blob/master/mne/tests/test_transforms.py#L33

and buildbot is green:

https://ci.inria.fr/mne-python/job/make/

So first make sure this test pass on your machine.

If it does your file may be corrupted or we have a bug
that you should report on github.

Best,
Alex


On Thu, Feb 27, 2014 at 4:42 AM, Eric Larson <larson.eric.d at gmail.com> wrote:
> Actually, I see that you're running version 0.7.1. Can you try latest
> master? We might need to backport a fix, but I'm curious whether the latest
> version works on your machine at least.
>
> Eric
>
>
>
> On Wed, Feb 26, 2014 at 7:40 PM, Eric Larson <larson.eric.d at gmail.com>
> wrote:
>>
>> Hey Dan,
>>
>> I just tried to replicate the problem, but the `trans` file read okay on
>> my machine. Which version of `mne` are you running?
>>
>> >>> import mne
>> >>> data_path = mne.datasets.sample.data_path()
>> >>> mri = data_path + '/MEG/sample/sample_audvis_raw-trans.fif'
>> >>> mne.read_trans(mri)
>> {'to': 5, 'dig': ...
>>
>> Eric
>>
>>
>>
>> On Wed, Feb 26, 2014 at 2:55 PM, dgw <dgwakeman at gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> I'm playing around with trans.fif files, and I have found some strange
>>> behavior. First, if you generate a quick trans.fif file with the
>>> sample data in mne_analyze. you cannot read it in with MNE-Python
>>> utilizing mne.read_trans . I am not sure if this problem is due to
>>> mne_analyze creating bad fif files or an MNE-Python bug.
>>>
>>> Here is the mne.read_trans error:
>>> test = mne.read_trans('sample_audvis_raw-trans.fif')
>>>
>>> ---------------------------------------------------------------------------
>>> IndexError                                Traceback (most recent call
>>> last)
>>> <ipython-input-6-8f82339f2100> in <module>()
>>> ----> 1 test = mne.read_trans('sample_audvis_raw-trans.fif')
>>>
>>>
>>> /usr/pubsw/packages/python/epd-7.3-1-rh5-x86_64/lib/python2.7/site-packages/mne-0.7.1-py2.7.egg/mne/transforms.pyc
>>> in read_trans(fname)
>>>     254     info = {}
>>>     255     fid, tree, _ = fiff_open(fname)
>>> --> 256     block = dir_tree_find(tree, FIFF.FIFFB_MNE)[0]
>>>     257
>>>     258     tag = find_tag(fid, block, FIFF.FIFF_COORD_TRANS)
>>>
>>> IndexError: list index out of range
>>>
>>> If I go into the file in either mne-python or mne-matlab, I find that
>>> the block number is 0. This looks a little suspicious to me, as I
>>> didn't believe block numbers could be 0, but I may be wrong. Any
>>> thoughts?
>>>
>>> D
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