/*
 * #%L
 * ImgLib2: a general-purpose, multidimensional image processing library.
 * %%
 * Copyright (C) 2009 - 2016 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
 * John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
 * Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
 * Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
 * Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
 * Jean-Yves Tinevez and Michael Zinsmaier.
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 * 
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
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 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
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 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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 */
import ij.ImageJ;

import io.scif.img.IO;
import io.scif.img.ImgIOException;

import net.imglib2.RandomAccessible;
import net.imglib2.algorithm.gauss3.Gauss3;
import net.imglib2.exception.IncompatibleTypeException;
import net.imglib2.img.Img;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.view.Views;

/**
 * Use of Gaussian Convolution on the Image
 * but convolve with a different outofboundsstrategy
 *
 * @author Stephan Preibisch
 * @author Stephan Saalfeld
 */
public class Example6a2
{
	public Example6a2() throws ImgIOException, IncompatibleTypeException
	{
		// open with SCIFIO as a FloatType
		Img< FloatType > image = IO.openImgs( "DrosophilaWing.tif",
			new FloatType() ).get( 0 );

		// perform gaussian convolution with float precision
		double[] sigma = new double[ image.numDimensions() ];

		for ( int d = 0; d < image.numDimensions(); ++d )
			sigma[ d ] = 8;

		// first extend the image to infinity, zeropad
		RandomAccessible< FloatType > infiniteImg = Views.extendValue( image, new FloatType() );

		// now we convolve the whole image manually in-place
		// note that is is basically the same as the call above, just called in a more generic way
		//
		// sigma .. the sigma
		// infiniteImg ... the RandomAccessible that is the source for the convolution
		// image ... defines the RandomAccessibleInterval that is the target of the convolution
		Gauss3.gauss( sigma, infiniteImg, image );

		// show the in-place convolved image (note the different outofboundsstrategy at the edges)
		ImageJFunctions.show( image );
	}

	public static void main( String[] args ) throws ImgIOException, IncompatibleTypeException
	{
		// open an ImageJ window
		new ImageJ();

		// run the example
		new Example6a2();
	}
}