package examples;

import java.util.Random;

import cmd.RenderImage;

import data.STData;

import data.STDataStatistics;

import filter.FilterFactory;

import filter.Filters;

import filter.GaussianFilterFactory;

import gui.bdv.AddedGene.Rendering;

import ij.ImageJ;

import ij.ImagePlus;

import ij.ImageStack;

import net.imglib2.IterableRealInterval;

import net.imglib2.RandomAccessibleInterval;

import net.imglib2.img.display.imagej.ImageJFunctions;

import net.imglib2.realtransform.AffineTransform2D;

import net.imglib2.type.numeric.real.DoubleType;

public class RunFilter

{

public static void main( String[] args )

{

final Rendering rendering = Rendering.Gauss;// Rendering.Linear;

final double renderFactor = 1.5;// 15;

// a pseudo-random number generator

final Random rnd = new Random( 124 );

// create random STData object

final STData data = CreateSTData.createRandomSTDATA( rnd );

// render an image for the raw data

final RandomAccessibleInterval<DoubleType> raw = RenderImage.display(

data,

new STDataStatistics( data ),

new AffineTransform2D(),

rendering,

renderFactor,

null,

data.getGeneNames().get( 0 ),

data.getRenderInterval( 10 ) );

// show raw image

new ImageJ();

ImageJFunctions.show( raw );

// filter with an increasing radius

ImageStack stack = new ImageStack();

for ( int radius = 1; radius <= 15; ++radius )

{

System.out.println( "Radius = " + radius );

// create Gaussian filter

final FilterFactory<DoubleType, DoubleType> filter =

new GaussianFilterFactory< DoubleType, DoubleType >( new DoubleType( 0 ), radius );

// filter first gene

final IterableRealInterval<DoubleType> filteredInterval =

Filters.filter( data.getExprData( data.getGeneNames().get( 0 ) ), filter );

// render an image for the raw data

final RandomAccessibleInterval<DoubleType> filterRendering = RenderImage.display(

filteredInterval,

new STDataStatistics( data ).getMedianDistance(),

new AffineTransform2D(),

rendering,

renderFactor,

data.getRenderInterval( 10 ) );

stack.addSlice( ImageJFunctions.wrap( filterRendering, "r=" + radius ).getProcessor() );

}

// show stack

ImagePlus imp = new ImagePlus( "increasing filtering", stack );

imp.resetDisplayRange();

imp.show();

}

}