//******************************************************************************
//
// File: PlotPixel.java
// Package: edu.rit.mri
// Unit: Class edu.rit.mri.PlotPixel
//
// 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;
import edu.rit.numeric.AggregateXYSeries;
import edu.rit.numeric.Series;
import edu.rit.numeric.plot.Dots;
import edu.rit.numeric.plot.Plot;
import edu.rit.numeric.plot.Strokes;
import edu.rit.numeric.plot.impl.LinearAxis;
import java.awt.Color;
import java.io.File;
import java.text.DecimalFormat;
/**
* Class PlotPixel is a main program that displays the results of a spin
* relaxometry analysis of a magnetic resonance image.
*
* The program displays a plot of the measured spin signal for the pixel at a
* given index. The program reads the spin signal from a spin signal data set
* file using class {@linkplain SignalDataSetReader}.
*
* The program includes a plot of the fitted spin signal for the pixel as
* determined by the spin relaxometry analysis. The program reads the analysis
* results from a tissues data set file using class {@linkplain
* TissuesDataSetReader}. The program also prints the tissues' computed spin
* densities ρj, spin-lattice relaxation rates
* R1j, and spin-lattice relaxation times
* T1j. The program prints χ2,
* the sum of the squared differences between the measured spin signal and the
* fitted spin signal; the degrees of freedom (dof) in χ2;
* and the standard deviation σ of the errors in the measured
* signal derived from χ2.
*
* If no tissues data set file is specified, the analysis results are not
* plotted or printed.
*
* Usage: java edu.rit.mri.PlotPixel signalfile [ tissuesfile ]
* index
*
signalfile = Spin signal data set file
*
tissuesfile = Tissues data set file
*
index = Pixel index
*
* @author Alan Kaminsky
* @version 21-Jun-2008
*/
public class PlotPixel
{
// Prevent construction.
private PlotPixel()
{
}
// Main program.
/**
* Main program.
*/
public static void main
(String[] args)
throws Exception
{
// Parse command line arguments.
File signalfile = null;
File tissuesfile = null;
int index = 0;
if (args.length == 2)
{
signalfile = new File (args[0]);
index = Integer.parseInt (args[1]);
}
else if (args.length == 3)
{
signalfile = new File (args[0]);
tissuesfile = new File (args[1]);
index = Integer.parseInt (args[2]);
}
else
{
usage();
}
// Read time series and pixel signal for the given pixel.
SignalDataSetReader signalReader = new SignalDataSetReader (signalfile);
Series t_series = signalReader.getTimeSeries();
PixelSignal signal = signalReader.getPixelSignal (index);
signalReader.close();
if (signal == null)
{
System.err.println ("PlotPixel: Pixel "+index+" has no data");
System.exit (0);
}
Series S_measured = signal.S_measured();
int M = t_series.length();
// Read pixel tissues for the given pixel.
int L = 0;
Series S_computed = null;
if (tissuesfile != null)
{
TissuesDataSetReader tissuesReader =
new TissuesDataSetReader (tissuesfile);
PixelTissues tissues = tissuesReader.getPixelTissues (index);
tissuesReader.close();
if (tissues == null)
{
System.out.println ("No solution found");
}
else
{
L = tissues.numTissues();
if (L == 0)
{
System.out.println ("No solution found");
}
else
{
// Get computed spin signal.
S_computed = tissues.S_series (t_series);
// Print analysis results.
System.out.println ("rho\tR1\tT1");
for (int i = 0; i < L; ++ i)
{
System.out.print (tissues.rho(i));
System.out.print ('\t');
System.out.print (tissues.R1(i));
System.out.print ('\t');
System.out.print (1.0/tissues.R1(i));
System.out.println();
}
double chisqr = 0.0;
for (int i = 0; i < M; ++ i)
{
double d = S_measured.x(i) - S_computed.x(i);
chisqr += d*d;
}
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();
}
}
}
// Create plot with measured spin signal X-Y series.
double maxY = 0.0;
maxY = Math.max (maxY, Math.abs (S_measured.minX()));
maxY = Math.max (maxY, Math.abs (S_measured.maxX()));
if (L > 0)
{
maxY = Math.max (maxY, Math.abs (S_computed.minX()));
maxY = Math.max (maxY, Math.abs (S_computed.maxX()));
}
maxY = LinearAxis.autoscale (maxY);
Plot plot = new Plot();
plot.plotTitle ("Spin Signal vs. Time for Pixel "+index)
.leftMargin (72)
.xAxisLength (576)
.xAxisMajorDivisions (20)
.yAxisLength (288)
.xAxisTitle ("Time, t (sec)")
.yAxisMajorDivisions (10)
.yAxisStart (-maxY)
.yAxisEnd (+maxY)
.yAxisTickFormat (new DecimalFormat ("0.0E0"))
.yAxisTitle ("Spin signal, S (t)")
.yAxisTitleOffset (54)
.seriesDots (Dots.circle (Color.BLACK, null, null, 5))
.seriesColor (Color.BLACK)
//.seriesStroke (Strokes.solid (1))
.seriesStroke (null)
.xySeries (new AggregateXYSeries (t_series, S_measured));
// If we found a solution, add computed spin signal X-Y series to plot.
if (L > 0)
{
plot.seriesDots (null)
.seriesColor (Color.BLACK)
.seriesStroke (Strokes.solid (2))
.xySeries (new AggregateXYSeries (t_series, S_computed));
}
// 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.PlotPixel [] ");
System.err.println (" = Spin signal data set file");
System.err.println (" = Tissues data set file");
System.err.println (" = Pixel index");
System.exit (1);
}
}
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