These are chat archives for freeman-lab/discussion

17th
Jul 2016
Davis Bennett
@d-v-b
Jul 17 2016 17:29
This message was deleted
@freeman-lab @jwittenbach is anyone working on that lucas kanade matlab translation? Otherwise I'll take a stab at it.
Jeremy Freeman
@freeman-lab
Jul 17 2016 17:45
i say go for it!
@d-v-b
you can start a branch of thunder-registration
Davis Bennett
@d-v-b
Jul 17 2016 17:45
hmm for the moment i'm just going to directly copy this guy's (2-d) function
i'm a little surprised that I've never seen an optic flow-style algorithm used in the big medical imaging alignment packages
Jeremy Freeman
@freeman-lab
Jul 17 2016 17:47
cool yeah good place to start
will be easy to fold in
if it works well
Davis Bennett
@d-v-b
Jul 17 2016 17:48
what do your attitude regarding potential algorithms with external dependencies in thunder-registration
the registration method i've put together for my own data uses SimpleITK, which wraps a ton of c++ code
Jeremy Freeman
@freeman-lab
Jul 17 2016 17:49
well, generally wary of things that lead to complex installation process
Davis Bennett
@d-v-b
Jul 17 2016 17:49
agreed
Jeremy Freeman
@freeman-lab
Jul 17 2016 17:49
if packages are available through conda
Davis Bennett
@d-v-b
Jul 17 2016 17:49
...which simpleitk is not
Jeremy Freeman
@freeman-lab
Jul 17 2016 17:49
even if they have a lot of compiled dependencies
it's not so bad
the other option is having optional dependencies
but i don't love that either
Davis Bennett
@d-v-b
Jul 17 2016 17:52
all the libs for aligning medical images are compiled C/C++ with interfaces to python
*all the ones worth considering for our purposes, that is
and I don't think any of them are on conda
Jeremy Freeman
@freeman-lab
Jul 17 2016 17:53
so replicating this little matlab translation thing? does that require any of those libraries?
Davis Bennett
@d-v-b
Jul 17 2016 17:54
no no, from what I can tell this should be a simple numpy thing
i'm thinking further down the road
like if I wanted to bring my current registration pipeline, or mika's, into thunder-registration
or if you wanted to get some mri people using thunder-registration
the external dependencies would be an issue