/*
 * #%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.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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 * #L%
 */
import ij.ImageJ;

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

import net.imglib2.RandomAccessibleInterval;
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
 *
 * @author Stephan Preibisch
 * @author Stephan Saalfeld
 */
public class Example6a4
{
	public Example6a4() throws ImgIOException, IncompatibleTypeException
	{
		// open with ImgOpener as a FloatType
		Img< FloatType > image = IO.openImgs( "DrosophilaWing.tif",
			new FloatType() ).get( 0 );

		// perform all (n-1)-dimensional gaussian (in this case it means 1d) on
		// some of the row/columns
		double[] sigma = new double[ image.numDimensions() - 1 ];

		for ( int d = 0; d < sigma.length; ++d )
			sigma[ d ] = 16;

		// iterate over all dimensions, take always a hyperslice
		for ( int dim = 0; dim < image.numDimensions(); ++dim )
			// iterate over all possible hyperslices
			for ( long pos = 0; pos < image.dimension( dim ); ++pos )
				// convolve a subset of the 1-dimensional views
				if ( pos/30 % 2 == 1 )
				{
					// get the n-1 dimensional "slice"
					RandomAccessibleInterval< FloatType > view =
						Views.hyperSlice( image, dim, pos );

					// compute the gauss in-place on the view
					Gauss3.gauss( sigma, Views.extendMirrorSingle( view ), view );
				}

		// show the result
		ImageJFunctions.show( image );
	}

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

		// run the example
		new Example6a4();
	}
}