Posted by
Sidnei Paciornik on
Oct 23, 2015; 4:16pm
URL: http://imagej.273.s1.nabble.com/kawa-script-using-mpicbg-1-0-2-jar-ERROR-tp5014635p5014742.html
Dear all, but specially Stephan Saafeld,
I was particularly shocked with the tone of some of your answers to doubts
posted regarding the mpcibg code.
I always took for granted that the nicest part of ImageJ and FIJI is the sense
of community and the fact that we can always help and be helped. Given the size
and diversity of this community, it is evident that all kinds of doubts, from
basic to sophisticated, will appear.
Granted, some developers might not want or have the time to answer to the doubts
regarding the code he/she developed. But if he/she is available to answer,
sentences such as “ if you want to keep doing what you propose which is clearly the result of not having spent sufficient time with it ” seem impatient or aggressive, and serve not purpose.
I don´t think we are part of part of this community to “teach lessons” (in the
repressive sense) to others. We are here to help and promote free software,
science and knowledge.
Sincerely Prof. Sidnei Paciornik Grupo de Análise de Imagens e Microscopia Digital
DEQM - Departamento de Engenharia Química e de Materiais
PUC-Rio
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: (55) (21)3527-1243
On Mon, Oct 19, 2015 at 3:28 PM, Saalfeld, Stephan <
[hidden email] > wrote:
Hi David,
> (1) "Linear Stack Alignment with SIFT" now works, _but_, iff I display images
on
> the screen, which is required to call "Images to Stack":
>
> (a) I want to open images in memory only and built the stack myself,
> example(s) [preferably kawa/clojure of course since I use kawa]
> welcome;
>
> (b) "Linear Stack Alignment with SIFT" does not expect/accept a stack
> argument, I would need, if possible, that you implement a version
> that accept a stack instead of 'magically' grab the one fiji creates
> when calling "Images to Stack" time:
>
> would that be possible?
>
No, it is unnecessary because the ImageJ and mpicbg API have lots of
public methods that allow fine grained access to all its functionality.
You will have to read about and learn it and then you will realize that
both (1) and (2) are strange things to ask for ;).
E.g., if you want to keep doing what you propose which is clearly the
result of not having spent sufficient time with it, you could call
http://rsb.info.nih.gov/ij/ developer/api/ij/IJ.html#run-
ij.ImagePlus-java.lang.String- java.lang.String-
as making an ImagePlus from an ImageStack is as simple as
http://rsb.info.nih.gov/ij/ developer/api/ij/ImagePlus.
html#ImagePlus-java.lang. String-ij.ImageStack-
and
> As you understood already, it is extremely important for us, I should say
mandatory
> actually, that absolutely everything happens in memory and no windows is/needs
to
> be opened during the execution of the script.
>
everything you're talking about happens in memory. If you do not want
UI, use the API directly instead of plugins whose sole purpose is to
provide a UI to some functions.
Good luck,
Stephan
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