AnalyzeSkeleton update

[Ignacio Arganda-Carreras]

Dear all,

I just updated AnalyzeSkeleton to solve some problems that were slowing
terribly down the calculation of the actual number of junctions:

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:analyzeskeleton:start#download

Special thanks to Martina A K Johansson for remarking me the problem.

Any feedback is welcome!

cheers!

ignacio

--
Ignacio Arganda-Carreras, Ph.D.
Institute of Neuroinformatics
Uni/ETH Zurich
Winterthurerstrasse 190
Bau 55
Zurich 8057
[phone]

Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html<http://arantxa.ii.uam.es/%7Eiarganda/index_EN.html>

[David Webster]

Ah yes!!  Much Much faster on large images with many skeletons. Did you
update the RFiji version as well?

David Webster

On Wed, Aug 5, 2009 at 10:49 AM, Ignacio Arganda
<[hidden email]>wrote:

> Dear all,
>
> I just updated AnalyzeSkeleton to solve some problems that were slowing
> terribly down the calculation of the actual number of junctions:
>
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:analyzeskeleton:start#download
>
> Special thanks to Martina A K Johansson for remarking me the problem.
>
> Any feedback is welcome!
>
> cheers!
>
> ignacio
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Institute of Neuroinformatics
> Uni/ETH Zurich
> Winterthurerstrasse 190
> Bau 55
> Zurich 8057
> [phone]
>
> Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html<
> http://arantxa.ii.uam.es/%7Eiarganda/index_EN.html<http://arantxa.ii.uam.es/~iarganda/index_EN.html>
> >
>

[dscho]

Hi,

On Wed, 5 Aug 2009, David Webster wrote:

> Ah yes!!  Much Much faster on large images with many skeletons. Did you
> update the RFiji version as well?

No.  I need an explicit "good to go" from Ignacio for that...

Ciao,
Dscho

[Ignacio Arganda-Carreras]

Hello everyone,

The Fiji version is in the developer repository as Johannes commented and
very soon as a regular update :)

ignacio

On Wed, Aug 5, 2009 at 10:13 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Wed, 5 Aug 2009, David Webster wrote:
>
> > Ah yes!!  Much Much faster on large images with many skeletons. Did you
> > update the RFiji version as well?
>
> No.  I need an explicit "good to go" from Ignacio for that...
>
> Ciao,
> Dscho
>

--
Ignacio Arganda-Carreras, Ph.D.
Institute of Neuroinformatics
Uni/ETH Zurich
Winterthurerstrasse 190
Bau 55
Zurich 8057
[phone]

Website: http://arantxa.ii.uam.es/~iarganda/index_EN.html

[Michael Doube]

Ignacio, Johannes

I'd like to track the changes to the Fiji version of AnalyzeSkeleton_
and merge some bits with my BoneJ version, Analyze_Skeleton, which is
hosted on github (and of course in my local git repo).  What's a good
way to do that, better than what I'm doing now which is just reading
Ignacio's code and copy-pasting the bits I want?

Mike

Ignacio Arganda wrote:

> Hello everyone,
>
> The Fiji version is in the developer repository as Johannes commented and
> very soon as a regular update :)
>
> ignacio
>
> On Wed, Aug 5, 2009 at 10:13 PM, Johannes Schindelin <
> [hidden email]> wrote:
>
>> Hi,
>>
>> On Wed, 5 Aug 2009, David Webster wrote:
>>
>>> Ah yes!!  Much Much faster on large images with many skeletons. Did you
>>> update the RFiji version as well?
>> No.  I need an explicit "good to go" from Ignacio for that...
>>
>> Ciao,
>> Dscho
>>
>
>
>

[dscho]

Hi,

On Thu, 6 Aug 2009, Michael Doube wrote:

> I'd like to track the changes to the Fiji version of AnalyzeSkeleton_
> and merge some bits with my BoneJ version, Analyze_Skeleton, which is
> hosted on github (and of course in my local git repo).  What's a good
> way to do that, better than what I'm doing now which is just reading
> Ignacio's code and copy-pasting the bits I want?

Mini Git tutorial (as most of the list members are most likely pretty
disinterested in the issue):

Start tracking fiji.git in so-called "remote branches", i.e. locally
cached copies of branches on the remote repository:

$ git remote add -f fiji git://pacific.mpi-cbg.de/fiji.git

Have a look at the changes affecting Analyze_Skeleton:

$ gitk fiji/master -- src-plugins/AnalyzeSkeleton_/

Note the commit names (the 40-character strings identifying each commit
uniquely) of the changes you do not have yet.  Then pick those changes
into your current branch, one by one:

$ git cherry-pick <commit-name>

If you want to have interactive help: I'll be in #fiji-devel (that's an
IRC channel on freenode.net) next week (this week I am on holiday).

Ciao,
Dscho