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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.*;
import ij.process.*;
import ij.gui.*;
import ij.plugin.frame.Recorder;
import java.awt.*;
import java.awt.event.*;

/** Implements the Analyze/Plot Profile and Edit/Options/Profile Plot Options commands. */
public class Profiler implements PlugIn, PlotMaker {
	ImagePlus imp;
	boolean firstTime = true;
	boolean plotVertically;

	public void run(String arg) {
		if (arg.equals("set"))
			{doOptions(); return;}
		imp = IJ.getImage();
		if (firstTime)
			plotVertically = Prefs.verticalProfile || IJ.altKeyDown();
		Plot plot = getPlot();
		firstTime = false;
		if (plot==null)
			return;
		plot.setPlotMaker(this);
		plot.show();
		Roi roi = imp.getRoi();
		if (roi!=null && roi.getType()==Roi.RECTANGLE)
			plot.getImagePlus().setProperty ("Label", plotVertically ? "vertical" : "horizontal");
	}
	
	public Plot getPlot() {
		Roi roi = imp.getRoi();
		if (roi==null || !(roi.isLine()||roi.getType()==Roi.RECTANGLE)) {
			if (firstTime)
				IJ.error("Plot Profile", "Line or rectangular selection required");
			return null;
		}
		ProfilePlot pp = new ProfilePlot(imp, plotVertically);
		return pp.getPlot();
	}
	
	public ImagePlus getSourceImage() {
		return imp;
	}

	public void doOptions() {
		double ymin = ProfilePlot.getFixedMin();
		double ymax = ProfilePlot.getFixedMax();
		boolean fixedScale = ymin!=0.0 || ymax!=0.0;
		boolean wasFixedScale = fixedScale;			
		GenericDialog gd = new GenericDialog("Plot Defaults");
		gd.setInsets(4,0,0);
		gd.addMessage("---------- Plot Defaults ---------");
		gd.addNumericField("Width:", PlotWindow.plotWidth, 0);
		gd.addNumericField("Height:", PlotWindow.plotHeight, 0);
		gd.addNumericField("Font size:", PlotWindow.getDefaultFontSize());
		gd.setInsets(5,20,0); //distance to previous
		//gd.addCheckbox("Draw grid lines", !PlotWindow.noGridLines);
		gd.addCheckbox("Draw_ticks", !PlotWindow.noTicks);
		gd.addCheckbox("Auto-close", PlotWindow.autoClose);
		gd.addCheckbox("List values", PlotWindow.listValues);		
		gd.setInsets(15,0,0);
		gd.addMessage("------- Profile Plot Options -------");
		gd.setInsets(5,20,0);
		gd.addCheckbox("Fixed y-axis scale", fixedScale);
		gd.addNumericField("Minimum Y:", ymin, 2);
		gd.addNumericField("Maximum Y:", ymax, 2);
		gd.setInsets(10,20,0);
		gd.addCheckbox("Vertical profile", Prefs.verticalProfile);
		gd.addCheckbox("Interpolate line profiles", PlotWindow.interpolate);
		gd.addHelp(IJ.URL+"/docs/menus/edit.html#plot-options");
		gd.showDialog();
		if (gd.wasCanceled())
			return;
		int w = (int)gd.getNextNumber();
		int h = (int)gd.getNextNumber();
		if (wymax) {
			double tmp = ymin;
			ymin = ymax;
			ymax = tmp;
		}
		ProfilePlot.setMinAndMax(ymin, ymax);
		if (!Recorder.scriptMode())
			Recorder.recordString("setOption(\"InterpolateLines\", "+PlotWindow.interpolate+");\n");
	}
		
}