camitk vs. mitk vs. slicer?

2015-02-22 Thread Steve M. Robbins
Hi, I'm about to dive into a small surgical planning project that will use some ITK algorithms (e.g. vesselness) and require visualization. For rapid prototyping the application, what is recommended today? I have used slicer in the past, though not for prototyping, and I've vaguely heard of m

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Andreas Tille
Hi Emmanuel, On Sun, Feb 22, 2015 at 10:31:13PM +0100, Emmanuel Bourg wrote: > Le 22/02/2015 22:06, Andreas Tille a écrit : > > > As far as I understand ftpmaster everything needs to be removed in > > src/hep/aida (including bin and ref). > > Yes they are right, but except for the src/hep/aida/b

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Emmanuel Bourg
Le 22/02/2015 22:06, Andreas Tille a écrit : > As far as I understand ftpmaster everything needs to be removed in > src/hep/aida (including bin and ref). Yes they are right, but except for the src/hep/aida/bin classes the src/hep/aida ones can be replaced by their equivalent in freehep. I conduc

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Andreas Tille
Hi Sune, On Sun, Feb 22, 2015 at 06:12:55PM +, Sune Vuorela wrote: > On 2015-02-22, Andreas Tille wrote: > > I tried the stupid approach and simply replaced the affected files > > > > IAxis.java IHistogram*.java > > > > by the equally named files I found in SVN. But this was probably to >

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Sune Vuorela
On 2015-02-22, Andreas Tille wrote: > I tried the stupid approach and simply replaced the affected files > > IAxis.java IHistogram*.java > > by the equally named files I found in SVN. But this was probably to > simple and did not build. I guess this approached needs somebody who > has some ba

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Andreas Tille
Hi Emmanuel, On Sun, Feb 22, 2015 at 11:19:37AM +0100, Emmanuel Bourg wrote: > There is something else you could try, you may remove the non free parts > of colt and try rebuilding the reverse dependencies with this stripped > down version. If it works you could then derive a new colt-free package

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Andreas Tille
Hi Markus, On Sun, Feb 22, 2015 at 06:11:47PM +0100, Markus Koschany wrote: > I think Emmanuel has already pointed in the right directions. Just to > clarify what exactly is controversial or difficult and has to be done. > > The *.java files under src/hep/aida/ in Colt belong to the freehep-aida

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Markus Koschany
On 22.02.2015 09:47, Andreas Tille wrote: [...] > Whatever helps to get a free functionality of libcolt-java would be > really helpful. > I think Emmanuel has already pointed in the right directions. Just to clarify what exactly is controversial or difficult and has to be done. The *.java files

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Emmanuel Bourg
There is something else you could try, you may remove the non free parts of colt and try rebuilding the reverse dependencies with this stripped down version. If it works you could then derive a new colt-free package from this version. Emmanuel Bourg -- To UNSUBSCRIBE, email to debian-med-requ..

Express upload seems to be broken

2015-02-22 Thread Andreas Tille
Hi Steffen, I tried to rebuild the current status of express. It seems the main package (not the new doc package is basically empty). I simply wanted to check for the name conflict claimed in the ITP bug which is not yet solved - or did I missed anything? Kind regards Andreas. -- ht

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Andreas Tille
Hi Emmanuel, On Sun, Feb 22, 2015 at 09:52:48AM +0100, Emmanuel Bourg wrote: > Le 22/02/2015 09:41, Andreas Tille a écrit : > > > This would be really good news. I'd be really happy about this but I > > personally have no idea what exactly needs to be done to approach it. > > Any help would be m

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Emmanuel Bourg
Le 22/02/2015 09:41, Andreas Tille a écrit : > This would be really good news. I'd be really happy about this but I > personally have no idea what exactly needs to be done to approach it. > Any help would be more than welcome. The classes of the Mahout fork reside in a different package. If they

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Andreas Tille
Hi Markus, thanks for checking this. On Sun, Feb 22, 2015 at 12:47:00AM +0100, Markus Koschany wrote: > > Where could one find the aida code replacement on java.freehep.org? So > far I found As far as I understood Emmanuel he has answered the question in his mail. > http://aida.freehep.org/li

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Andreas Tille
On Sun, Feb 22, 2015 at 01:40:22AM +0100, Emmanuel Bourg wrote: > I just found out the Apache Mahout project maintains a fork of Colt [1], > they kept only the free bits. Maybe it could be used as a replacement > for the projects based on Colt that don't use the non free part? This would be really

Re: Please help freeing libcolt-java [Was: Update on Trinityrnaseq packaging]

2015-02-22 Thread Andreas Tille
Hi Emmanuel, On Sun, Feb 22, 2015 at 01:01:39AM +0100, Emmanuel Bourg wrote: > > I got a quick look and it seems some of these classes are available in > the aida and jaida modules of freehep. The main issue seems to be the > hep.aida.bin package, it doesn't exist in freehep and depends on Colt >

Re: Update on Trinityrnaseq packaging

2015-02-22 Thread Andreas Tille
On Sun, Feb 22, 2015 at 08:50:37AM +0100, Andreas Tille wrote: > > That could be a workaround. Since you can not create such binary > packages from one source package you need to create different source > packages. I admit I'm fine if you ignore the contrib part for the > moment if you only need