3D Patch extraction from 3D input about medpy HOT 1 CLOSED

Well, extracting patches should be quite straight forward with numpy (remember: each image returned by medpy is, in fact, a numpy array).

You must first consider how to treat incomplete patches. The image won't always have dimension that are multiples of 32 (e.g., shape=363636). What do you do then? You must decide either to accept smaller left-over patches (e.g., shape=444). Or, alternatively, you can pad the patches. Or, third option, cropthe images to a size that is a multiple of 32 in all dimensions.

Next, should the patches be overlapping? And if yes, how far?

You can get some inspiration from Google (https://www.google.de/search?q=numpy+array+patches+extract+3d)

Medpy provides a few patch iterators for special cases: http://loli.github.io/medpy/iterators.html
For you, the CentredPatchIterator might be interesting: equally sized patches, automatically padded and non-overlapping. Us eit like

for patch i CentredPatchIterator(image, (32,32,32), cval=0):
   do_something_with_patch()

I hope I could be of help. If you have further questions, please write directly to my email, since the issue tracker is intended for bugs only.

from medpy.