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[WARNING] Not overwriting name 'Groovy':
	proposed = org.scijava.plugins.scripting.groovy.GroovyScriptLanguage
	existing = org.scijava.plugins.scripting.groovy.GroovyScriptLanguage
[WARNING] Not overwriting name 'groovy':
	proposed = org.scijava.plugins.scripting.groovy.GroovyScriptLanguage
	existing = org.scijava.plugins.scripting.groovy.GroovyScriptLanguage
[WARNING] Not overwriting extension 'groovy':
	proposed = org.scijava.plugins.scripting.groovy.GroovyScriptLanguage
	existing = org.scijava.plugins.scripting.groovy.GroovyScriptLanguage
[WARNING] Not overwriting name 'BeanShell':

tpietzsch

package bdv;

import java.awt.Color;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionListener;
import java.io.File;

import bdv.export.ProgressWriterConsole;

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/**
 * This is an adaption of the algorithm described in <a href=
 * "http://www.geometrictools.com/Documentation/DistancePointEllipseEllipsoid.pdf">
 * "Distance from a Point to an Ellipse, an Ellipsoid, or a Hyperellipsoid" by
 * David Eberly</a> and available as a C++ implementation from
 * <a href="http://www.geometrictools.com">www.geometrictools.com</a> under the
 * <a href="http://www.boost.org/LICENSE_1_0.txt">Boost License</a>
 *
 * @author Tobias Pietzsch &lt;tobias.pietzsch@gmail.com&gt;
 */

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package net.imglib2.algorithm.fitting;

import net.imglib2.util.LinAlgHelpers;
import Jama.CholeskyDecomposition;
import Jama.Matrix;

/**
 * Adapted from BoneJ's FitEllipsoid.
 *
 * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>

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	public static < T extends Type< T > & Comparable< T > >
	void maxFilterBox(
			final RandomAccessibleInterval< T > input,
			final RandomAccessibleInterval< T > output,
			final ImgFactory< T > imgFactory, final T type,
			final int span )
	{
		final int n = input.numDimensions();

		final long[][] tmpdims = new long[ n ][];

tpietzsch

	public static void main( final String[] args )
	{
		final Img< IntType > img = PlanarImgs.ints( 1000, 1000 );
//		final Img< IntType > img = ArrayImgs.ints( 1000, 1000 );
		final RandomAccess< IntType > a = img.randomAccess();
		final IterableInterval< IntType > iterable = Views.flatIterable( Views.interval( img, Intervals.createMinMax( 0, 100, 999, 199 ) ) );
		final Cursor< IntType > c = iterable.localizingCursor();
		c.fwd();
		System.out.println( Util.printCoordinates( c ) );
		a.setPosition( c );

tpietzsch

package com.indago.segment.features;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import net.imagej.ops.Op;
import net.imagej.ops.OpEnvironment;

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package bdv.examples.boundingbox;

import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.WindowEvent;

import javax.swing.AbstractAction;
import javax.swing.ActionMap;
import javax.swing.InputMap;
import javax.swing.JButton;

tpietzsch

import ij.ImageJ;
import ij.ImagePlus;
import ij.io.Opener;

import java.io.File;
import java.util.ArrayList;

import net.imglib2.Cursor;
import net.imglib2.ExtendedRandomAccessibleInterval;
import net.imglib2.FinalInterval;