[Mne_analysis] how to use tutorials when mne is not installed in home directory?

Megan Schendel mschendel at mrn.org
Fri Sep 11 19:44:26 EDT 2020
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        External Email - Use Caution        

Hi all,
Thanks very much, Alex and Dan!  That works.

Megan
MEG Technician
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106



On Fri, Sep 11, 2020 at 8:52 AM Dan McCloy <dan at mccloy.info> wrote:

>         External Email - Use Caution
>
> Adding to what Alex said, you can configure globally where you want
> datasets to be stored (and where MNE-Python will look for them when loading
> the datasets) using the MNE_DATA config variable. For example:
>
> mne.set_config('MNE_DATA', '/opt/data')
>
> will cause datasets to be downloaded to /opt/data/MNE-sample-data,
> /opt/data/MNE-fnirs-motor-data, etc.
>
> -- dan
> Daniel McCloy
> https://dan.mccloy.info
> Research Scientist
> Institute for Learning and Brain Sciences
> University of Washington
>
> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
> On Friday, September 11, 2020 2:12 AM, Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
>
> > External Email - Use Caution
> >
> > hi Megan,
> >
> > you can install mne anywhere you like but when it downloads
> > data it tries to put them in your home directory by default.
> >
> > see doc:
> https://mne.tools/stable/generated/mne.datasets.sample.data_path.html
> >
> > you can specify what path you want.
> >
> > HTH
> > Alex
> >
> > On Thu, Sep 10, 2020 at 11:32 PM Megan Schendel mschendel at mrn.org wrote:
> >
> > >         External Email - Use Caution
> > >
> > >
> > > Hi all,
> > > Still working on my upgrade issue, but in the meantime, I have a
> question about the sample data.
> > > I'm trying the tutorial for source timec ourse visualization...
> > >
> https://mne.tools/stable/auto_tutorials/source-modeling/plot_visualize_stc.html#sphx-glr-auto-tutorials-source-modeling-plot-visualize-stc-py
> > > ... but when I try
> > > data_path = sample.data_path()
> > > I get an error. It looks to me like it's looking for sample in my user
> home directory, but I have mne installed in a shared directory. If I
> understood better what the sample path should be, I could just create the
> data path string. Or perhaps I don't have the sample data at all because of
> the discrepancy between mne path and sample path?
> > > Thanks for your help, see the error below.
> > > Megan
> > >
> > > data_path = sample.data_path()
> > > Downloading archive MNE-sample-data-processed.tar.gz to
> /na/homes/mschendel/mne_data
> > > Downloading
> https://files.osf.io/v1/resources/rxvq7/providers/osfstorage/59c0e26f9ad5a1025c4ab159?version=5&action=download&direct
> (1.54 GB)
> > > Error while fetching file https://osf.io/86qa2/download?version=5.
> Dataset fetching aborted. ?B/s]
> > >
> > >
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> > >
> > > FileNotFoundError Traceback (most recent call last)
> > > <ipython-input-6-a3504eb0c729> in <module>
> > > ----> 1 data_path = sample.data_path()
> > > <decorator-gen-407> in data_path(path, force_update, update_path,
> download, verbose)
> > >
> /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne20/lib/python3.8/site-packages/mne/datasets/sample/sample.py
> in data_path(path, force_update, update_path, download, verbose)
> > > 17 def data_path(path=None, force_update=False, update_path=True,
> download=True,
> > > 18 verbose=None): # noqa: D103
> > > ---> 19 return _data_path(path=path, force_update=force_update,
> > > 20 update_path=update_path, name='sample',
> > > 21 download=download)
> > >
> /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne20/lib/python3.8/site-packages/mne/datasets/utils.py
> in data_path(path, force_update, update_path, download, name,
> check_version, return_version, archive_name)
> > > 393 full_name = list()
> > > 394 for u, an, h, fo in zip(url, archive_name, hash, folder_orig):-->
> 395 remove_archive, full = _download(path, u, an, h)
> > > 396 full_name.append(full)
> > > 397 del archive_name
> > >
> /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne20/lib/python3.8/site-packages/mne/datasets/utils.py
> in download(path, url, archive_name, hash, hash_type)
> > > 450 if fetch_archive:
> > > 451 logger.info('Downloading archive %s to %s' % (archive_name, path))
> > > --> 452 fetch_file(url, full_name, print_destination=False,
> > > 453 hash=hash_, hash_type=hash_type)454 return remove_archive,
> full_name
> > > <decorator-gen-3> in fetch_file(url, file_name, print_destination,
> resume, hash, timeout, hash_type, verbose)
> > >
> /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne20/lib/python3.8/site-packages/mne/utils/fetching.py
> in fetch_file(url, file_name, print_destination, resume, hash, timeout,
> hash_type, verbose)
> > > 115 else:
> > > 116 initial_size = 0
> > > --> 117 _get_http(url, temp_file_name, initial_size, timeout,
> verbose_bool)
> > > 118
> > > 119 # check hash sum eg md5sum
> > >
> /export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne20/lib/python3.8/site-packages/mne/utils/fetching.py
> in _get_http(failed resolving arguments)
> > > 53 del file_size
> > > 54 chunk_size = 8192 # 2 ** 13
> > > ---> 55 with open(temp_file_name, mode) as local_file:
> > > 56 while True:
> > > 57 t0 = time.time()
> > > FileNotFoundError: [Errno 2] No such file or directory:
> '/na/homes/mschendel/mne_data/MNE-sample-data-processed.tar.gz.part'
> > > In [7]: sample
> > > Out[7]: <module 'mne.datasets.sample' from
> '/export/research/analysis/human/jstephen/shared/programs/python/anaconda_072020/new/envs/mne20/lib/python3.8/site-packages/mne/datasets/sample/init.py'>
> > > MEG Technician
> > > The Mind Research Network
> > > 1101 Yale Blvd. NE
> > > Albuquerque, New Mexico 87106
> > >
> > > Mne_analysis mailing list
> > > Mne_analysis at nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
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>
>
>
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