TODO for nipy development

This document will serve to organize current development work on nipy. It will include current sprint items, future feature ideas, and design discussions, etc…

Documentation

  • Create NIPY sidebar with links to all project related websites.

  • Create a Best Practices document.

  • Create a rst doc for Request a review process.

Tutorials

Tutorials are an excellent way to document and test the software. Some ideas for tutorials to write in our Sphinx documentation (in no specific order):

  • Slice timing

  • Image resampling

  • Image IO

  • Registration using SPM/FSL

  • FMRI analysis

  • Making one 4D image from many 3D images, and vice versa. Document ImageList and FmriImageList.

  • Apply SPM registration .mat to a NIPY image.

  • Create working example out of this TRAC pca page. Should also be a rest document.

  • Add analysis pipeline(s) blueprint.

Bugs

These should be moved to the nipy bug section on github. Placed here until they can be input.

  • Fix possible precision error in fixes.scipy.ndimage.test_registration function test_autoalign_nmi_value_2. See FIXME.

  • Fix error in test_segment test_texture2 functions (fixes.scipy.ndimage). See FIXME.

  • import nipy.algorithms is very slow! Find and fix. The shared library is slow.

  • base class for all new-style classes should be object; preliminary search with grin "class +[a-zA-Z0-9]+ *:"

Refactorings

  • image.save function should accept filename or file-like object. If I have an open file I would like to be able to pass that in also, instead of fp.name. Happens in test code a lot.

  • image._open function should accept Image objects in addition to ndarrays and filenames. Currently the save function has to call np.asarray(img) to get the data array out of the image and pass them to _open in order to create the output image.

  • Add dtype options when saving. When saving images it uses the native dtype for the system. Should be able to specify this. in the test_file_roundtrip, self.img is a uint8, but is saved to tmpfile as float64. Adding this would allow us to save images without the scaling being applied.

  • In image._open(url, …), should we test if the “url” is a PyNiftiIO object already? This was in the tests from ‘old code’ and passed:

    new = Image(self.img._data, self.img.grid)

    img._data is a PyNIftiIO object. It works, but we should verify it’s harmless otherwise prevent it from happening.

  • Look at image.merge_image function. Is it still needed? Does it fit into the current api?

  • FmriImageList.emptycopy() - Is there a better way to do this? Matthew proposed possibly implementing Gael’s dress/undress metadata example.

  • Verify documentation of the image generators. Create a simple example using them.

  • Use python 2.5 feature of being able to reset the generator?

  • Add test data where volumes contain intensity ramps. Slice with generator and test ramp values.

  • Implement fmriimagelist blueprint.

Code Design Thoughts

A central location to dump thoughts that could be shared by the developers and tracked easily.

Future Features

Put ideas here for features nipy should have but are not part of our current development. These features will eventually be added to a weekly sprint log.

  • Auto backup script for nipy repos to run as weekly cron job. We should setup a machine to perform regular branch builds and tests. This would also provide an on-site backup.

  • See if we can add bz2 support to nifticlib.

  • Should image.load have an optional squeeze keyword to squeeze a 4D image with one frame into a 3D image?