Ship fsaverage5 with nilearn

[GaelVaroquaux]

We now need fsaverage5 for basic interactive plotting functionality. It is retrieved via datasets.fetch_surf_fsaverage.

However, as any Internet access, this is brittle and can fail. For example:
https://ci.appveyor.com/project/nilearn-ci/nilearn/build/1.0.2612/job/0bn4wduir9icwafu

I suggest that we embed in nilearn the files needed for plotting, after compression with "gzip --best". It gives the following sizes:

$ ll -h
total 784K
-rw-r--r-- 1 varoquau varoquau 196K Jul 26 14:49 pial_inflated.left.gii.gz
-rw-r--r-- 1 varoquau varoquau 196K Jul 26 14:49 pial_inflated.right.gii.gz
-rw-r--r-- 1 varoquau varoquau 196K Jul 26 14:49 pial.left.gii.gz
-rw-r--r-- 1 varoquau varoquau 196K Jul 26 14:49 pial.right.gii.gz

This will make the download bigger by 784K, but the addition of the javascript libraries already added 1.3M (coming mostly from plotly-gl3d-latest.min.js).

The code of datasets.fetch_surf_fsaverage will need to be modified to load these files when it is fsaverage5 pial.

[GaelVaroquaux]

This has become a major issue: it is breaking all our CI. We unfortunately need to address it urgently.

@KamalakerDadi : do you have some spare cycles?

[KamalakerDadi]

What are files needed to be shipped ? Everything surface plotting uses ?

[GaelVaroquaux]

Listed above. And they need to be gzipped with best compression.

[KamalakerDadi]

Ok. I am on it.

[GaelVaroquaux]

Thank you so much Kamalakar!

[KamalakerDadi]

Shall we do the same for brainomics localizer data. Shipping only part of data where examples are dependant on ?

Right now it is down again http://brainomics.cea.fr/localizer

[GaelVaroquaux]

No: fsaverge affects the tests, more than the examples. Brainnomics will be addressed by @bthirion in a separate PR. ⁣Sent from my phone. Please forgive typos and briefness.​

…

On Jul 31, 2018, 19:14, at 19:14, KamalakerDadi ***@***.***> wrote: Shall we do the same for brainomics localizer data. Shipping only part of data where examples are dependant on ? Right now it is down again http://brainomics.cea.fr/localizer -- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: #1705 (comment)

[KamalakerDadi]

Does this needs to be uncompressed in home directory in nilearn_data folder ?

[GaelVaroquaux]

Does this needs to be uncompressed in home directory in nilearn_data folder ?

No, shipped like the template, avg152T1_brain.nii.gz in datasets/data. They can be gzipped separately, and then they don't need to be unzipped: nibabel knows how to read from gzipped files.

[KamalakerDadi]

They can be gzipped separately, and then they don't need to be unzipped: nibabel knows how to read from gzipped files.

Meaning if I give directly the gzipped files to plotting functions it should work, right ?

[KamalakerDadi]

gzipped gifti files doesn't work with nibabel.load or gifti.read ?

[GaelVaroquaux]

Meaning if I give directly the gzipped files to plotting functions it should work, right ?

Yes