[Mne_analysis] how to use tutorials when mne is not installed in home directory?
Alexandre Gramfort
alexandre.gramfort at inria.fr
Fri Sep 11 03:12:43 EDT 2020
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'>
>
>
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