Multispectral random walker segmentation

[Josh Warner]

Pull request is up!  I also fixed a bug in the fallback call of _solve_cg() 
if pyamg is not installed.  Comments appreciated.

Josh


On Monday, August 27, 2012 7:55:11 AM UTC-5, Emmanuelle Gouillart wrote:
>
> Hi Josh, 
>
> my changes have been merged, so if you pull from github they are in 
> the master branch now, you can add your changes and make a pull request! 
>
> Cheers, 
> Emmanuelle 
>
> On Thu, Aug 23, 2012 at 02:50:05PM -0700, Josh Warner wrote: 
> >    I'd be happy to include your suggested changes, if it's simpler to go 
> that 
> >    route than have two separate pull requests. �I don't want to step 
> on any 
> >    toes regarding attribution, though. � 
> >    Having the 'soft' probabilities available is definitely a useful 
> >    improvement (cleanup, fuzzy post-processing), and I'm glad you 
> implemented 
> >    that! � 
> >    Josh 
>
> >    On Monday, August 20, 2012 4:11:45 PM UTC-5, Emmanuelle Gouillart 
> wrote: 
>
> >      Hi Josh, 
>
> >      extending the random walker algorithm to multichannel images sounds 
> like 
> >      a very nice idea, and I'm sure that it would be useful for other 
> people 
> >      (including myself!). 
>
> >      In fact, I had started working on some improvements of the random 
> walker 
> >      code but didn't go as far as proposing the pull request. I have a 
> branch 
> >      for that on 
> >      [1]
> https://github.com/emmanuelle/scikits.image/tree/fix_random_walker, 
> >      maybe 
> >      you can include these changes when you contribute your changes? 
>
> >      Cheers, 
> >      Emmanuelle 
>
> >      On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner wrote: 
> >      > � �I have modified the existing random walker algorithm into 
> a fully 
> >      > � �backwards-compatible version which allows inclusion of 
> >      multispectral data, 
> >      > � �e.g. RGBA channels or different (registered) image 
> modalities. �I 
> >      really 
> >      > � �liked the existing algorithm, so I just extended it rather 
> than 
> >      write one 
> >      > � �from scratch for my own purposes. �The overhead is 
> minimal; 
> >      multispectral 
> >      > � �processing is triggered if data is passed as an iterable 
> of arrays 
> >      rather 
> >      > � �than just an array. � 
> >      > � �This amounts to combining image gradients as 
> sqrt(sum-of-squares) 
> >      and 
> >      > � �dividing by sqrt(#channels). �For obvious reasons, the 
> several 
> >      channels 
> >      > � �must be pre-processed to have data on similar ranges by 
> whitening 
> >      or a 
> >      > � �similar method. �Not usually a problem for RGB, but in 
> medical 
> >      imaging 
> >      > � �this rears its head. 
> >      > � �Would this be of interest to the community? �I'd be 
> happy to 
> >      contribute 
> >      > � �the changes if there is interest. 
>
> > References 
>
> >    Visible links 
> >    1. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker 
>
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