Re: Threshold Segmentation in TrakEM2

Posted by Albert Cardona-2 on Dec 26, 2013; 1:45pm
URL: http://imagej.273.s1.nabble.com/Threshold-Segmentation-in-TrakEM2-tp5004623p5005989.html

2013/12/25 arjundayal <[hidden email]>

> Hi Albert,
>
> Thank you very much for your help! I wrote Java code that creates an Area
> object out of the yellow areas. How do I proceed to add it to the active
> AreaList in TrakEM2? Is there anything simpler than using Jython to call my
> Java code?
>
> Thanks,
> Arjun
>

Arjun,

from java itself, or from jython: it doesn't matter.

From java you'd do, to add a specific Area to a Layer with id layer_id, to
all AreaList existing in the project:

import ini.trakem2.Project;
import ini.trakem2.display.*;

Project p = Project.getProjects().get(0);
LayerSet ls = p.getRootLayerSet();

Area a = ... ; // in world coordinates
long layer_id = ...;

for (AreaList ali : ls.getAll(AreaList.class)) {
  Area local = new Area(a);
  local.transform(ali.getAffineTransform());
  ali.addArea(layer_id, local);
}


Hope the above helps.

Albert

>
>
>
> -----
> Arjun Dayal
> M.D. Class of 2016
> University of Chicago - Pritzker School of Medicine
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