Clean CPU examples - Githubissues

mind-inria / mri-nufft

Doing non-Cartesian MR Imaging has never been so easy.

https://mind-inria.github.io/mri-nufft/

BSD 3-Clause "New" or "Revised" License

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Clean CPU examples #196

Closed Daval-G closed 1 month ago

Daval-G commented 2 months ago

This PR cleans the CPU examples in several ways:

Change brain orientations to the medical standard
Reduce blank spaces around images
Remove some overlaps in figures
Split script-specific code from the utils and data preparation
Homogeneize parts and subparts names & structures
Homogeneize one-line descriptions
Homogeneize capitalizations, punctuations
Apply isort to clean imports
Fix a bunch of typos
Fix paragraph irregularities
Fix a few cross references
Break lines sometimes
Remove a few dead parts
Remove many useless outputs
Remove references to MFI in off-resonance operator (we don't do MFI but the opposite)

I will try to do the same for GPU examples later. Note that trajectory examples are barely touched, not because they are perfect but the opposite as I plan to break them into smaller examples as discussed in #118.

Daval-G commented 2 months ago

By the way, how can we change the examples order in the gallery ? It doesn't make sense

paquiteau commented 2 months ago

By the way, how can we change the examples order in the gallery ? It doesn't make sense

RTFM :upside_down_face: https://sphinx-gallery.github.io/stable/configuration.html#within-gallery-order

there are multiple possibilities; I guess FileNameSortKey and a proper naming scheme (example_01_...) could do the trick.

Daval-G commented 2 months ago

Very nice improvements, thanks!

If you wish, you can also tackle #182 in this as well.

Done

Daval-G commented 2 months ago

By the way, how can we change the examples order in the gallery ? It doesn't make sense

RTFM 🙃 https://sphinx-gallery.github.io/stable/configuration.html#within-gallery-order

there are multiple possibilities; I guess FileNameSortKey and a proper naming scheme (example_01_...) could do the trick.

For now let's sort by example name rather than filename, until we decide of a specific order

Daval-G commented 2 months ago

@paquiteau I cleaned the new CG example who seem to be problematic even on the main branch, but even after fixing it doesn't work as intended on my side (image not showing because the algorithm doesn't converge). I moved it to GPU examples because it uses gpuNUFFT even though I doubt it is a requirement, but since it didn't work on my side I didn't want to change too many things