[Neuroimaging] Nibabel API change - always read as float

[vanessa sochat]

I don't like the modification, because there are plenty of images that
should be returned as int16. It's much more reasonable to have a workflow
like:

data = img.get_data()

*look at, think about, your data*
*make decisions* (cast as float, don't, etc)

Possibly we can have an intermediate solution of leaving the default
behavior and adding a to_float parameter, as Christopher suggested. But I'm
not sure how that is any better or different than float(data).


On Mon, Jul 6, 2015 at 9:13 AM, Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> On Mon, Jul 6, 2015 at 5:03 PM, Ben Cipollini <bcipolli at ucsd.edu> wrote:
> > I agree with Gael.
> >
> > I would also add, it also seems to be solving a problem that doesn't
> seem to
> > exist in the wild. There's never a report of hitting this issue, right?
> > Users using sum() or other raw operations are likely familiar with numpy,
> > and more ready/capable to debug their error.
>
> Basically any numpy operation on the returned array can give you weird
> errors.
>
> I did precisely run into this when teaching the students.  I was
> teaching them to run diagnostics, and the script I wrote used the sum.
> This worked fine on one set of functional images, but gave a
> completely wrong answer on another set of images, and it took me a
> little while to work out what had gone wrong.  Part of the problem is
> that nifti images are often int16, so it's easy to run into silent
> horrors just by adding or subtracting.  My feeling is that dealing
> with any operations on int16 arrays is for advanced users.  Advanced
> users will know to do `to_float=False`.
>
> > Adding complexity can potentially introduce confusion for all users,
> > including relatively numpy-naive ones. Then we potentially have to
> support
> > new questions, and I'm not sure there's any practical benefit.
>
> I think this is reducing complexity for basic use (you don't have to
> think about your data types, until you want to think about your data
> types).  At the moment, when you see this:
>
> data = img.get_data()
>
> you have to think 'oh wait, at the moment I can't easily predict what
> data type this is.  If I want to do stuff with this array, I will
> probably have to cast to float for safety'.
>
> Cheers,
>
> Matthew
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-- 
Vanessa Villamia Sochat
Stanford University
(603) 321-0676
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