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ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.

There is a newer version: 1.54m

package ij.plugin;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.*;
import ij.gui.Roi;
import ij.plugin.filter.ThresholdToSelection;
import ij.plugin.frame.RoiManager;
import java.awt.Rectangle;
import java.util.ArrayList;

/** This class interpolates between ROIs in the ROI Manager.
 * @author Michael Doube
 * @author Johannes Schindelin
*/
public class RoiInterpolator implements PlugIn {
	int[][] idt;
	int w, h;

	public void run(String arg) {
		RoiManager roiman = RoiManager.getInstance();
		if (roiman==null || roiman.getCount()<2){
			IJ.error("RoiInterpolator", "Please populate the ROI Manager with at least two ROIs");
			return;
		}
		Roi[] rois = roiman.getRoisAsArray();
		int xmax = 0;
		int xmin = Integer.MAX_VALUE;
		int ymax = 0;
		int ymin = Integer.MAX_VALUE;
		int zmax = 1;
		int zmin = Integer.MAX_VALUE;
		ArrayList templateSlices = new ArrayList();
		for (Roi roi : rois){
			int slice = roiman.getSliceNumber(roi.getName());
			if (!templateSlices.contains(new Integer(slice)))
				templateSlices.add(new Integer(slice));
			if (slice==0) //ignore non-slice associated ROIs
				continue;
			zmin = Math.min(slice, zmin);
			zmax = Math.max(slice, zmax);
			Rectangle bounds = roi.getBounds();
			xmin = Math.min(xmin, bounds.x);
			ymin = Math.min(ymin, bounds.y);
			xmax = Math.max(xmax, bounds.x + bounds.width);
			ymax = Math.max(ymax, bounds.y + bounds.height);
		}
		if (templateSlices.size()<2) {
			IJ.error("RoiInterpolator", "ROIs are all on the same slice, nothing to interpolate");
			return;
		}
		//create the binary stack
		final int stackW = xmax - xmin + 1;
		final int stackH = ymax - ymin + 1;
		final int nSlices = zmax - zmin + 1;
		ImageStack stack = new ImageStack(stackW, stackH);
		for (int s=0; s