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//******************************************************************************
//
// File: R1Image.java
// Package: edu.rit.mri
// Unit: Class edu.rit.mri.R1Image
//
// This Java source file is copyright (C) 2008 by Alan Kaminsky. All rights
// reserved. For further information, contact the author, Alan Kaminsky, at
// ark@cs.rit.edu.
//
// This Java source file is part of the Parallel Java Library ("PJ"). PJ is free
// software; you can redistribute it and/or modify it under the terms of the GNU
// General Public License as published by the Free Software Foundation; either
// version 3 of the License, or (at your option) any later version.
//
// PJ is distributed in the hope that it will be useful, but WITHOUT ANY
// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
// A PARTICULAR PURPOSE. See the GNU General Public License for more details.
//
// Linking this library statically or dynamically with other modules is making a
// combined work based on this library. Thus, the terms and conditions of the
// GNU General Public License cover the whole combination.
//
// As a special exception, the copyright holders of this library give you
// permission to link this library with independent modules to produce an
// executable, regardless of the license terms of these independent modules, and
// to copy and distribute the resulting executable under terms of your choice,
// provided that you also meet, for each linked independent module, the terms
// and conditions of the license of that module. An independent module is a
// module which is not derived from or based on this library. If you modify this
// library, you may extend this exception to your version of the library, but
// you are not obligated to do so. If you do not wish to do so, delete this
// exception statement from your version.
//
// A copy of the GNU General Public License is provided in the file gpl.txt. You
// may also obtain a copy of the GNU General Public License on the World Wide
// Web at http://www.gnu.org/licenses/gpl.html.
//
//******************************************************************************
package edu.rit.mri;
import edu.rit.image.PJGGrayImage;
import edu.rit.numeric.AggregateXYSeries;
import edu.rit.numeric.Interpolation;
import edu.rit.numeric.Series;
import edu.rit.swing.DisplayableFrame;
import java.io.File;
import javax.swing.JFrame;
/**
* Class R1Image is a program that displays an image depicting the locations of
* tissues with certain spin-lattice relaxation rates in a magnetic resonance
* image data set. A range of relaxation rates is specified on the command line.
* The program displays an image. Pixels with no data are black. Pixels with no
* tissues with relaxation rates in the given range are dark gray. Pixels with
* one or more tissues with relaxation rates in the given range are medium gray
* to white, depending on the spin densities; medium gray is a low spin density,
* white is a high spin density. The program uses class {@linkplain
* SignalDataSetReader} to read the data set.
* <P>
* Usage: java edu.rit.mri.test.R1Image <I>tissuesfile</I> <I>R1_lower</I>
* <I>R1_upper</I>
* <BR><I>tissuesfile</I> = Tissues data set file
* <BR><I>R1_lower</I> = Lower <I>R</I>1 spin-lattice relaxation rate (1/sec)
* <BR><I>R1_upper</I> = Upper <I>R</I>1 spin-lattice relaxation rate (1/sec)
*
* @author Alan Kaminsky
* @version 28-Jun-2008
*/
public class R1Image
{
// Prevent construction.
private R1Image()
{
}
// Main program.
/**
* Main program.
*/
public static void main
(String[] args)
throws Exception
{
// Parse command line arguments.
if (args.length != 3) usage();
File tissuesfile = new File (args[0]);
double R1_lower = Double.parseDouble (args[1]);
double R1_upper = Double.parseDouble (args[2]);
// Set up tissues data set reader.
TissuesDataSetReader reader = new TissuesDataSetReader (tissuesfile);
// Set up storage for image to be displayed.
int H = reader.getHeight();
int W = reader.getWidth();
double[][] rhosum = new double [H] [W];
byte[][] matrix = new byte [H] [W];
PJGGrayImage image = new PJGGrayImage (H, W, matrix);
// For each pixel, compute sum of spin densities of tissues having
// R1_lower <= R1 < R1_upper.
double rhomin = Double.POSITIVE_INFINITY;
double rhomax = Double.NEGATIVE_INFINITY;
for (int r = 0; r < H; ++ r)
{
for (int c = 0; c < W; ++ c)
{
PixelTissues tissues =
reader.getPixelTissues (reader.indexFor (r, c));
if (tissues != null)
{
image.setPixel (r, c, 0.25f);
double rho = 0.0;
for (int i = 0; i < tissues.numTissues(); ++ i)
{
double R1 = tissues.R1(i);
if (R1_lower <= R1 && R1 <= R1_upper)
{
rho += tissues.rho(i);
}
}
if (rho > 0.0)
{
rhomin = Math.min (rhomin, rho);
rhomax = Math.max (rhomax, rho);
rhosum[r][c] = rho;
}
}
}
}
// Set the gray shade of each pixel.
for (int r = 0; r < H; ++ r)
{
for (int c = 0; c < W; ++ c)
{
if (rhosum[r][c] > 0.0)
{
image.setPixel (r, c,
(float)((rhosum[r][c]-rhomin)/(rhomax-rhomin)*0.5+0.5));
}
}
}
// Close tissues data set.
reader.close();
// Display plot.
new DisplayableFrame
("Tissues with "+args[1]+" <= R1 < "+args[2],
image.getDisplayable(),
JFrame.EXIT_ON_CLOSE)
.setVisible (true);
}
// Hidden operations.
/**
* Print a usage message and exit.
*/
private static void usage()
{
System.err.println ("Usage: java edu.rit.mri.test.R1Image <tissuesfile> <R1_lower> <R1_upper>");
System.err.println ("<tissuesfile> = Tissues data set file");
System.err.println ("<R1_lower> = Lower R1 spin-lattice relaxation rate (1/sec)");
System.err.println ("<R1_upper> = Upper R1 spin-lattice relaxation rate (1/sec)");
System.exit (1);
}
}
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