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//******************************************************************************
//
// File: R1Histogram.java
// Package: edu.rit.mri
// Unit: Class edu.rit.mri.R1Histogram
//
// 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.numeric.plot.Plot;
import java.io.File;
import java.text.DecimalFormat;
/**
* Class R1Histogram is a main program that displays the results of a spin
* relaxometry analysis of a magnetic resonance image.
* <P>
* The program displays a histogram of the computed spin-lattice relaxation
* rates <I>R</I>1 for all the tissues. The program reads the relaxation rates
* from a tissues data set file using class {@linkplain TissuesDataSetReader}.
* The relaxation rate lower and upper bounds and the number of intervals for
* the histogram are specified on the command line.
* <P>
* Usage: java edu.rit.mri.R1Histogram <I>tissuesfile</I> <I>R1_lower</I>
* <I>R1_upper</I> <I>N</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)
* <BR><I>N</I> = Number of intervals
*
* @author Alan Kaminsky
* @version 27-Jun-2008
*/
public class R1Histogram
{
// Prevent construction.
private R1Histogram()
{
}
// Main program.
static final DecimalFormat FMT1 = new DecimalFormat ("0.0");
static final DecimalFormat FMT2 = new DecimalFormat ("0.0E0");
/**
* Main program.
*/
public static void main
(String[] args)
throws Exception
{
// Parse command line arguments.
if (args.length != 4) usage();
File tissuesfile = new File (args[0]);
double R1_lower = Double.parseDouble (args[1]);
double R1_upper = Double.parseDouble (args[2]);
int N = Integer.parseInt (args[3]);
double binWidth = (R1_upper - R1_lower)/N;
// Set up histogram bins.
double[] x = new double [N+1];
double[] y = new double [N+1];
for (int i = 0; i <= N; ++ i)
{
x[i] = R1_lower + i*binWidth;
}
// Count all spin-lattice relaxation rates in the data set.
TissuesDataSetReader reader = new TissuesDataSetReader (tissuesfile);
int P = reader.getPixelCount();
for (int i = 0; i < P; ++ i)
{
PixelTissues tissues = reader.getPixelTissues(i);
if (tissues != null)
{
int L = tissues.numTissues();
for (int j = 0; j < L; ++ j)
{
double R1 = tissues.R1(j);
int k = (int) Math.floor((R1 - R1_lower)/binWidth);
if (0 <= k && k <= N) y[k] += 1.0;
}
}
}
// Create plot of histogram.
Plot plot = new Plot();
plot.plotTitle ("<I>R</I><SUB>1</SUB> Histogram")
.leftMargin (54)
.xAxisLength (800)
.xAxisStart (R1_lower)
.xAxisEnd (R1_upper)
.xAxisMajorDivisions (20)
.xAxisTickFormat (FMT2)
.xAxisTitle ("Spin-lattice relaxation rate, <I>R</I><SUB>1</SUB> (sec<SUP>\u20121</SUP>)")
.yAxisLength (400)
.yAxisMajorDivisions (10)
.yAxisTickFormat (FMT2)
.yAxisTitle ("Count")
.yAxisTitleOffset (42)
.xySeries (x, y);
// Display plot.
plot.getFrame().setVisible (true);
}
// Hidden operations.
/**
* Print a usage message and exit.
*/
private static void usage()
{
System.err.println ("Usage: java edu.rit.mri.R1Histogram <tissuesfile> <R1_lower> <R1_upper> <N>");
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.err.println ("<N> = Number of intervals");
System.exit (1);
}
}
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