trakem2_exportAreaLists.bsh

trakem2_exportAreaLists.bsh

import ij.IJ;
import ij.ImagePlus;

import java.util.ArrayList;

import ini.trakem2.Project;
import ini.trakem2.tree.ProjectThing;

import ini.trakem2.display.Display;
import ini.trakem2.display.AreaList;

destdir="/home/john/tmp/tem2/";
type = ImagePlus.GRAY8;


/*
 * This function starts at the root Project thing
 * and recursively finds AreaLists.
 * When it does, it writes a tif file to the 'destdir', 
 * where the tif file name consists of the titles of all
 * project things
 */
void writeArealists( ProjectThing root, String prefix )
{
	// put a check here to be sure root is okay
	if( root == null )
		return;

	// add this object's title to the file name
	thisprefix = prefix + "_" + root.getTitle();

	// get this project's object and see if it's an AreaList
	obj = root.getObject();
	if( obj instanceof AreaList )
	{	
		// if so, write a tif
		ip = ((AreaList)obj).getStack( type, 1.0 );
		IJ.save( ip, destdir + thisprefix + ".tif" );
	}

	// recurse
	children = root.getChildren();
	if( children != null )
	{
		for( int i = 0; i < children.size(); i++ )
		{
			c = children.get( i );
			writeArealists( c, thisprefix );
		}
	}
}

// get the root ProjectThing
project = Project.getProjects().get(0);
root = project.getRootProjectThing();

// call the function
writeArealists( root, "" );