[Mne_analysis] not understanding use of pick_types
Megan Schendel
mschendel at mrn.org
Wed Nov 6 18:49:34 EST 2019
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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>>
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