//******************************************************************************
//
// File: Test06.java
// Package: edu.rit.mri.test
// Unit: Class edu.rit.mri.test.Test06
//
// 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.
//
// 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.test;
import edu.rit.mri.PixelAnalysis;
import edu.rit.mri.PixelSignal;
import edu.rit.mri.SignalDataSetReader;
import edu.rit.mri.SpinSignal;
import edu.rit.numeric.AggregateXYSeries;
import edu.rit.numeric.ArraySeries;
import edu.rit.numeric.ListXYSeries;
import edu.rit.numeric.Series;
import edu.rit.numeric.plot.Dots;
import edu.rit.numeric.plot.Plot;
import edu.rit.numeric.plot.Strokes;
import java.awt.Color;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
/**
* Class Test06 is a unit test main program for class {@linkplain
* edu.rit.mri.PixelAnalysis edu.rit.mri.PixelAnalysis}. Using an instance of
* class {@linkplain edu.rit.mri.SignalDataSetReader
* edu.rit.mri.SignalDataSetReader}, the program reads the data for a specified
* pixel index. The program does a spin relaxometry analysis on the data set.
* The program displays a plot of the data set along with the reconstructed spin
* signal.
*
* Usage: java edu.rit.mri.test.Test06 signalfile R1_lower
* R1_upper N index
*
signalfile = Input spin signal data set file
*
R1_lower = Lower R1 spin-lattice relaxation rate (1/sec)
*
R1_upper = Upper R1 spin-lattice relaxation rate (1/sec)
*
N = Number of R1 intervals
*
index = Pixel index
*
* @author Alan Kaminsky
* @version 21-Jun-2008
*/
public class Test06
{
// Prevent construction.
private Test06()
{
}
// Main program.
/**
* Main program.
*/
public static void main
(String[] args)
throws Exception
{
// Parse command line arguments.
if (args.length != 5) usage();
File signalfile = new File (args[0]);
double R1_lower = Double.parseDouble (args[1]);
double R1_upper = Double.parseDouble (args[2]);
int N = Integer.parseInt (args[3]);
int index = Integer.parseInt (args[4]);
// Set up spin signal data set reader.
SignalDataSetReader reader = new SignalDataSetReader (signalfile);
// Get data X-Y series.
Series t_series = reader.getTimeSeries();
int M = t_series.length();
PixelSignal signal = reader.getPixelSignal (index);
if (signal == null)
{
System.err.println ("Test06: Pixel "+index+" has no data");
System.exit (0);
}
Series S_series = signal.S_measured();
// // Print data X-Y series.
// System.out.println ("Measured t, S(t)");
// for (int i = 0; i < M; ++ i)
// {
// System.out.print (tseries.x(i));
// System.out.print ('\t');
// System.out.print (dseries.x(i));
// System.out.println();
// }
// Compute spin relaxation rates.
double[] R1 = new double [N+1];
double log_R1_lower = Math.log (R1_lower);
double log_R1_upper = Math.log (R1_upper);
double interval = (log_R1_upper - log_R1_lower)/N;
for (int j = 0; j <= N; ++ j)
{
R1[j] = Math.exp (log_R1_lower + j*interval);
}
ArraySeries R1_series = new ArraySeries (R1);
// Compute design matrix.
double[][] A = new double [M] [N+1];
for (int i = 0; i < M; ++ i)
{
double[] A_i = A[i];
double t_i = t_series.x(i);
for (int j = 0; j <= N; ++ j)
{
A_i[j] = SpinSignal.S (R1[j], t_i);
}
}
// Do the spin relaxometry analysis.
ArrayList rho_list = new ArrayList();
ArrayList R1_list = new ArrayList();
PixelAnalysis.analyze
(t_series, S_series, R1_series, A, rho_list, R1_list);
// Print solution.
printSolution (t_series, S_series, rho_list, R1_list);
// Create plot with data X-Y series.
Plot plot = new Plot();
plot.xAxisLength (1200)
.xAxisMajorDivisions (20)
.yAxisLength (600)
.yAxisMajorDivisions (10)
.seriesDots (Dots.circle (Color.BLACK, null, null, 5))
.seriesColor (Color.BLACK)
.seriesStroke (Strokes.solid (2))
.xySeries (new AggregateXYSeries (t_series, S_series));
// If we found a plausible solution, generate model spin signal X-Y
// series and add to plot.
int L = rho_list.size();
if (L > 0)
{
ListXYSeries signal_series = new ListXYSeries();
for (int i = 0; i < M; ++ i)
{
double t_i = t_series.x(i);
double s_i = 0.0;
for (int j = 0; j < L; ++ j)
{
s_i += SpinSignal.S (rho_list.get(j), R1_list.get(j), t_i);
}
signal_series.add (t_i, s_i);
}
plot.seriesDots (null)
.seriesColor (Color.RED)
.seriesStroke (Strokes.solid (1))
.xySeries (signal_series);
}
// Display plot.
plot.getFrame().setVisible (true);
}
// Hidden operations.
/**
* Print the given solution.
*/
private static void printSolution
(Series t_series,
Series S_series,
List rho_list,
List R1_list)
{
int M = t_series.length();
int L = rho_list.size();
if (L == 0)
{
System.out.println ("Test06: Could not find solution");
}
else
{
System.out.println ("rho\tR1\tT1");
for (int i = 0; i < L; ++ i)
{
System.out.print (rho_list.get(i));
System.out.print ('\t');
System.out.print (R1_list.get(i));
System.out.print ('\t');
System.out.print (1.0/R1_list.get(i));
System.out.println();
}
double chisqr =
computeChiSqr (t_series, S_series, rho_list, R1_list);
System.out.print ("chi^2 = ");
System.out.print (chisqr);
System.out.println();
int dof = M - 2*L;
System.out.print ("dof = ");
System.out.print (dof);
System.out.println();
double sigma = Math.sqrt(chisqr/dof);
System.out.print ("sigma = ");
System.out.print (sigma);
System.out.println();
}
}
/**
* Calculate chi^2 between the measured data series and the model function
* determined by the given parameters.
*/
private static double computeChiSqr
(Series t_series,
Series S_series,
List rho_list,
List R1_list)
{
int M = t_series.length();
int L = rho_list.size();
double chisqr = 0.0;
for (int i = 0; i < M; ++ i)
{
double t_i = t_series.x(i);
double s_i = 0.0;
for (int j = 0; j < L; ++ j)
{
s_i += SpinSignal.S (rho_list.get(j), R1_list.get(j), t_i);
}
double d = s_i - S_series.x(i);
chisqr += d*d;
}
return chisqr;
}
/**
* Print a usage message and exit.
*/
private static void usage()
{
System.err.println ("Usage: java edu.rit.mri.test.Test06 ");
System.err.println (" = Input spin signal data set file");
System.err.println (" = Lower R1 spin-lattice relaxation rate (1/sec)");
System.err.println (" = Upper R1 spin-lattice relaxation rate (1/sec)");
System.err.println (" = Number of R1 intervals");
System.err.println (" = Pixel index");
System.exit (1);
}
}
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