Multispectral random walker segmentation

[Josh Warner]

I noticed a documentation inconsistency in `labels` for random_walker; it 
hadn't been updated with the rest of the file and still said `labels` 
should be the same shape as `data`. This is true for the single-channel 
case, but for multichannel input `labels` should look like a single channel 
(missing the final dimension in `data`). Proposed docfix is submitted in a 
PR.  

Josh 

On Monday, August 27, 2012 4:27:33 PM UTC-5, Emmanuelle Gouillart wrote:
>
> Wow, that was quick :-), thanks! 
>
> I'll have a look tomorrow, I'm just back from Brussels and Euroscipy! 
>
> Emmanuelle 
>
> On Mon, Aug 27, 2012 at 02:18:22PM -0700, Josh Warner wrote: 
> >    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][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. 
> >      [2]
> https://github.com/emmanuelle/scikits.image/tree/fix_random_walker 
>
> > References 
>
> >    Visible links 
> >    1. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker 
> >    2. https://github.com/emmanuelle/scikits.image/tree/fix_random_walker 
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20120917/8e7186ee/attachment.html>