[Mne_analysis] not understanding use of pick_types
Megan Schendel
mschendel at mrn.org
Wed Nov 6 19:08:50 EST 2019
External Email - Use Caution
Hi Dan,
I was just coming around to that conclusion, too.
I read the epochs from a pre-existing file, first.
Then I've been using a .pick_types(meg=True) to get just the meg channels,
then the two subsequent pick_types(meg='mag') and pick_types(meg='grad')
were failing.
However, if I use the read epochs function and follow it immediately by the
pick_types(meg='mag') it seems to work. Then I can do the read epochs
function again and follow that by the pick_types(meg='grad') it works.
However something about the sequence of my commands seems to be altering
the epochs object so it doesn't have all the channels which is causing the
later pick_types functions to fail.
Could you give me a quick example of how to use the epochs.copy() line to
make this work for me?
Thanks!
Megan
MEG Technician
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106
On Wed, Nov 6, 2019 at 5:07 PM Dan McCloy <dan.mccloy at gmail.com> wrote:
> External Email - Use Caution
>
> could you show us how you created the `epochs` variable, and anything you
> did to it before this failing line? I'm not sure, but it looks like maybe
> you've got an earlier step in which you needed to include an
> `epochs.copy()` before doing a pick... many (all?) of the picking methods
> operate in-place, so if you do first do something like
> epochs.pick_types(meg=False, eeg=True) then subsequent calls to
> epochs.pick_types(meg='mag') will fail because after the EEG picking,
> `epochs` now only contains EEG channels.
>
> On Wed, Nov 6, 2019 at 3:50 PM Megan Schendel <mschendel at mrn.org> wrote:
>
>> External Email - Use Caution
>>
>> Hi all,
>> Now I'm using mne version 0.19, but I'm still getting pick errors using
>> .pick_types(meg='mag') and (meg='grad').
>> See below for commands and errors. Any help would be appreciated!
>> Thanks,
>> Megan
>>
>> In [26]: mne.__version__
>> Out[26]: '0.19.1'
>>
>> In [27]: mag_epochs = epochs.pick_types(meg='mag')
>> ...:
>>
>> ---------------------------------------------------------------------------
>> IndexError Traceback (most recent call
>> last)
>> <ipython-input-27-b02891c6983c> in <module>
>> ----> 1 mag_epochs = epochs.pick_types(meg='mag')
>>
>> </export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-31>
>> in pick_types(self, meg, eeg, stim, eog, ecg, emg, ref_meg, misc, resp,
>> chpi, exci, ias, syst, seeg, dipole, gof, bio, ecog, fnirs, include,
>> exclude, selection, verbose)
>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/utils/_logging.py
>> in wrapper(*args, **kwargs)
>> 88 with use_log_level(verbose_level):
>> 89 return function(*args, **kwargs)
>> ---> 90 return function(*args, **kwargs)
>> 91 return FunctionMaker.create(
>> 92 function, 'return decfunc(%(signature)s)',
>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/channels/channels.py
>> in pick_types(self, meg, eeg, stim, eog, ecg, emg, ref_meg, misc, resp,
>> chpi, exci, ias, syst, seeg, dipole, gof, bio, ecog, fnirs, include,
>> exclude, selection, verbose)
>> 673 ecog=ecog, fnirs=fnirs, include=include,
>> exclude=exclude,
>> 674 selection=selection)
>> --> 675 return self._pick_drop_channels(idx)
>> 676
>> 677 def pick_channels(self, ch_names):
>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/channels/channels.py
>> in _pick_drop_channels(self, idx)
>> 813
>> 814 if getattr(self, 'picks', None) is not None:
>> --> 815 self.picks = self.picks[idx]
>> 816
>> 817 if hasattr(self, '_cals'):
>>
>> IndexError: index 0 is out of bounds for axis 0 with size 0
>>
>>
>> In [28]: grad_epochs = epochs.pick_types(meg='grad')
>>
>> ---------------------------------------------------------------------------
>> ValueError Traceback (most recent call
>> last)
>> <ipython-input-28-ed060676757b> in <module>
>> ----> 1 grad_epochs = epochs.pick_types(meg='grad')
>>
>> </export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-31>
>> in pick_types(self, meg, eeg, stim, eog, ecg, emg, ref_meg, misc, resp,
>> chpi, exci, ias, syst, seeg, dipole, gof, bio, ecog, fnirs, include,
>> exclude, selection, verbose)
>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/utils/_logging.py
>> in wrapper(*args, **kwargs)
>> 88 with use_log_level(verbose_level):
>> 89 return function(*args, **kwargs)
>> ---> 90 return function(*args, **kwargs)
>> 91 return FunctionMaker.create(
>> 92 function, 'return decfunc(%(signature)s)',
>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/channels/channels.py
>> in pick_types(self, meg, eeg, stim, eog, ecg, emg, ref_meg, misc, resp,
>> chpi, exci, ias, syst, seeg, dipole, gof, bio, ecog, fnirs, include,
>> exclude, selection, verbose)
>> 673 ecog=ecog, fnirs=fnirs, include=include,
>> exclude=exclude,
>> 674 selection=selection)
>> --> 675 return self._pick_drop_channels(idx)
>> 676
>> 677 def pick_channels(self, ch_names):
>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/channels/channels.py
>> in _pick_drop_channels(self, idx)
>> 818 self._cals = self._cals[idx]
>> 819
>> --> 820 pick_info(self.info, idx, copy=False)
>> 821
>> 822 if getattr(self, '_projector', None) is not None:
>>
>> </export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-8>
>> in pick_info(info, sel, copy, verbose)
>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/utils/_logging.py
>> in wrapper(*args, **kwargs)
>> 88 with use_log_level(verbose_level):
>> 89 return function(*args, **kwargs)
>> ---> 90 return function(*args, **kwargs)
>> 91 return FunctionMaker.create(
>> 92 function, 'return decfunc(%(signature)s)',
>>
>> /export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/io/pick.py
>> in pick_info(info, sel, copy, verbose)
>> 447 return info
>> 448 elif len(sel) == 0:
>> --> 449 raise ValueError('No channels match the selection.')
>> 450 n_unique =
>> len(np.unique(np.arange(len(info['ch_names']))[sel]))
>> 451 if n_unique != len(sel):
>>
>> ValueError: No channels match the selection.
>>
>>
>>
>> MEG Technician
>> The Mind Research Network
>> 1101 Yale Blvd. NE
>> Albuquerque, New Mexico 87106
>>
>>
>>
>> On Wed, Nov 6, 2019 at 4:23 PM Megan Schendel <mschendel at mrn.org> wrote:
>>
>>> Thanks, Dan! That worked and will keep me moving!
>>> Megan
>>> MEG Technician
>>> The Mind Research Network
>>> 1101 Yale Blvd. NE
>>> Albuquerque, New Mexico 87106
>>>
>>>
>>>
>>> On Wed, Nov 6, 2019 at 3:24 PM Dan McCloy <dan.mccloy at gmail.com> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> I don't know why --only-binary is failing there, but something you
>>>> could try to get going quickly is to clone one of the existing conda
>>>> environments, activate the cloned environment, and then do `pip install
>>>> --upgrade mne` in the new cloned env.
>>>> -- dan
>>>>
>>>> Daniel McCloy
>>>> http://dan.mccloy.info/
>>>> Research Scientist
>>>> Institute for Learning and Brain Sciences
>>>> University of Washington
>>>>
>>>>
>>>> On Wed, Nov 6, 2019 at 2:10 PM Megan Schendel <mschendel at mrn.org>
>>>> wrote:
>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> Hello again,
>>>>> I'm having trouble trying to update my version of mne.
>>>>> I'm following instructions from
>>>>> https://mne.tools/stable/install/mne_python.html and I'm trying to
>>>>> use a new anaconda environment so I don't disturb other users who have
>>>>> working scripts with older versions. I didn't get an error with the curl
>>>>> command, but when I try
>>>>> conda env create --name mne19 --file environment.yml
>>>>> I get
>>>>> Using Anaconda Cloud api site https://api.anaconda.org
>>>>> Fetching package metadata ...........
>>>>> Solving package specifications: .
>>>>> glib-2.63.1-h5 100%
>>>>> |###########################################################################################|
>>>>> Time: 0:00:00 7.00 MB/s
>>>>> pillow-6.2.1-p 100%
>>>>> |###########################################################################################|
>>>>> Time: 0:00:00 6.81 MB/s
>>>>> jupyter_core-4 100%
>>>>> |###########################################################################################|
>>>>> Time: 0:00:00 9.71 MB/s
>>>>> nbconvert-5.6. 100%
>>>>> |###########################################################################################|
>>>>> Time: 0:00:00 9.09 MB/s
>>>>> ERROR: Invalid requirement: 'dipy --only-binary dipy'
>>>>>
>>>>> CondaValueError: pip returned an error.
>>>>>
>>>>> I know you don't support anaconda, but any insights you could give to
>>>>> this error would be helpful! Or another way to just update the mne install
>>>>> and not the whole anaconda one.
>>>>>
>>>>> Thanks,
>>>>> Megan
>>>>>
>>>>> MEG Technician
>>>>> The Mind Research Network
>>>>> 1101 Yale Blvd. NE
>>>>> Albuquerque, New Mexico 87106
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Nov 1, 2019 at 5:03 PM Megan Schendel <mschendel at mrn.org>
>>>>> wrote:
>>>>>
>>>>>> Thank you for your help!
>>>>>> Megan
>>>>>> MEG Technician
>>>>>> The Mind Research Network
>>>>>> 1101 Yale Blvd. NE
>>>>>> Albuquerque, New Mexico 87106
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Oct 30, 2019 at 3:47 AM Alexandre Gramfort <
>>>>>> alexandre.gramfort at inria.fr> wrote:
>>>>>>
>>>>>>> External Email - Use Caution
>>>>>>>
>>>>>>> hi Megan
>>>>>>>
>>>>>>> your version of MNE python is too old to pick with a string.
>>>>>>>
>>>>>>> you need to update or use the old documentation:
>>>>>>>
>>>>>>> https://mne.tools/0.15/index.html
>>>>>>>
>>>>>>> we are now at version 0.19.1
>>>>>>>
>>>>>>> Alex
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Mne_analysis mailing list
>>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>
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