[Mne_analysis] how to use tutorials when mne is not installed in home directory?
Megan Schendel
mschendel at mrn.org
Thu Sep 10 17:30:10 EDT 2020
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
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