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Fitter |
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package ij.plugin.frame;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import java.io.*;
import ij.*;
import ij.plugin.*;
import ij.plugin.frame.*;
import ij.text.*;
import ij.gui.*;
import ij.util.*;
import ij.io.*;
import ij.process.*;
import ij.measure.*;
/** ImageJ plugin that does curve fitting using the modified CurveFitter class.
* Includes simplex settings dialog option.
*
* @author Kieran Holland (email: holki659@student.otago.ac.nz)
*/
public class Fitter extends PlugInFrame implements PlugIn, ItemListener, ActionListener {
Choice fit;
Button doIt, open, apply;
Checkbox settings;
String fitTypeStr = CurveFitter.fitList[0];
TextArea textArea;
double[] dx = {0,1,2,3,4,5};
double[] dy = {0,.9,4.5,8,18,24};
double[] x,y;
static CurveFitter cf;
static int fitType;
static String equation = "y = a + b*x + c*x*x";
static final int USER_DEFINED = 100;
public Fitter() {
super("Curve Fitter");
WindowManager.addWindow(this);
Panel panel = new Panel();
fit = new Choice();
for (int i=0; i<CurveFitter.fitList.length; i++)
fit.addItem(CurveFitter.fitList[i]);
fit.addItem("*User-defined*");
fit.addItemListener(this);
panel.add(fit);
doIt = new Button(" Fit ");
doIt.addActionListener(this);
panel.add(doIt);
open = new Button("Open");
open.addActionListener(this);
panel.add(open);
apply = new Button("Apply");
apply.addActionListener(this);
panel.add(apply);
settings = new Checkbox("Show settings", false);
panel.add(settings);
add("North", panel);
String text = "";
for (int i=0; i<dx.length; i++)
text += IJ.d2s(dx[i],2)+" "+IJ.d2s(dy[i],2)+"\n";
textArea = new TextArea("",15,30,TextArea.SCROLLBARS_VERTICAL_ONLY);
//textArea.setBackground(Color.white);
textArea.setFont(new Font("Monospaced", Font.PLAIN, 12));
if (IJ.isLinux()) textArea.setBackground(Color.white);
textArea.append(text);
add("Center", textArea);
pack();
GUI.center(this);
show();
IJ.register(Fitter.class);
}
public void doFit(int fitType) {
if (fitType>=CurveFitter.fitList.length)
fitType = USER_DEFINED;
this.fitType = fitType;
if (!getData())
return;
cf = new CurveFitter(x, y);
if (fitType==USER_DEFINED) {
String eqn = getEquation();
if (eqn==null) return;
int params = cf.doCustomFit(eqn, null, settings.getState());
if (params==0) return;
} else
cf.doFit(fitType, settings.getState());
IJ.log(cf.getResultString());
plot(cf);
}
String getEquation() {
GenericDialog gd = new GenericDialog("Formula");
gd.addStringField("Formula:", equation, 38);
gd.showDialog();
if (gd.wasCanceled())
return null;
equation = gd.getNextString();
return equation;
}
public static void plot(CurveFitter cf) {
double[] x = cf.getXPoints();
double[] y = cf.getYPoints();
double[] a = Tools.getMinMax(x);
double xmin=a[0], xmax=a[1];
a = Tools.getMinMax(y);
double ymin=a[0], ymax=a[1];
float[] px = new float[100];
float[] py = new float[100];
double inc = (xmax-xmin)/99.0;
double tmp = xmin;
for (int i=0; i<100; i++) {
px[i]=(float)tmp;
tmp += inc;
}
double[] params = cf.getParams();
for (int i=0; i<100; i++)
py[i] = (float)cf.f(params, px[i]);
a = Tools.getMinMax(py);
ymin = Math.min(ymin, a[0]);
ymax = Math.max(ymax, a[1]);
Plot plot = new Plot(cf.getFormula(),"X","Y",px,py);
plot.setLimits(xmin, xmax, ymin, ymax);
plot.addPoints(x, y, PlotWindow.CIRCLE);
double yloc = 0.1;
double yinc = 0.085;
plot.addLabel(0.02, yloc, cf.getName()); yloc+=yinc;
plot.addLabel(0.02, yloc, cf.getFormula()); yloc+=yinc;
double[] p = cf.getParams();
int n = cf.getNumParams();
char pChar = 'a';
for (int i = 0; i < n; i++) {
plot.addLabel(0.02, yloc, pChar+"="+IJ.d2s(p[i],4));
yloc+=yinc;
pChar++;
}
plot.addLabel(0.02, yloc, "R^2="+IJ.d2s(cf.getRSquared(),3)); yloc+=yinc;
plot.show();
}
double sqr(double x) {return x*x;}
boolean getData() {
textArea.selectAll();
String text = textArea.getText();
text = zapGremlins(text);
textArea.select(0,0);
StringTokenizer st = new StringTokenizer(text, " \t\n\r,");
int nTokens = st.countTokens();
if (nTokens<4 || (nTokens%2)!=0)
return false;
int n = nTokens/2;
x = new double[n];
y = new double[n];
for (int i=0; i<n; i++) {
x[i] = getNum(st);
y[i] = getNum(st);
}
return true;
}
void applyFunction() {
if (cf==null) {
IJ.error("No function available");
return;
}
ImagePlus img = WindowManager.getCurrentImage();
if (img==null) {
IJ.noImage();
return;
}
if (img.getTitle().startsWith("y=")) {
IJ.error("First select the image to be transformed");
return;
}
double[] p = cf.getParams();
int width = img.getWidth();
int height = img.getHeight();
int size = width*height;
float[] data = new float[size];
ImageProcessor ip = img.getProcessor();
float value;
for (int y=0; y<height; y++) {
for (int x=0; x<width; x++) {
value = ip.getPixelValue(x,y);
data[y*width+x] = (float)cf.f(p, value);
}
}
ImageProcessor ip2 = new FloatProcessor(width, height, data, ip.getColorModel());
new ImagePlus(img.getTitle()+"-transformed", ip2).show();
}
double getNum(StringTokenizer st) {
Double d;
String token = st.nextToken();
try {d = new Double(token);}
catch (NumberFormatException e){d = null;}
if (d!=null)
return(d.doubleValue());
else
return 0.0;
}
void open() {
OpenDialog od = new OpenDialog("Open Text File...", "");
String directory = od.getDirectory();
String name = od.getFileName();
if (name==null)
return;
String path = directory + name;
textArea.selectAll();
textArea.setText("");
try {
BufferedReader r = new BufferedReader(new FileReader(directory+name));
while (true) {
String s=r.readLine();
if (s==null) break;
if (s.length()>100) break;
textArea.append(s+"\n");
}
}
catch (Exception e) {
IJ.error(e.getMessage());
return;
}
}
public void itemStateChanged(ItemEvent e) {
fitTypeStr = fit.getSelectedItem();
}
public void actionPerformed(ActionEvent e) {
if (e.getSource()==doIt)
doFit(fit.getSelectedIndex());
else if (e.getSource()==apply)
applyFunction();
else
open();
//if(e.getSource()==doIt) {
// try {doFit(fit.getSelectedIndex());}
// catch (Exception ex) {IJ.write(ex.getMessage());}
//}
}
String zapGremlins(String text) {
char[] chars = new char[text.length()];
chars = text.toCharArray();
int count=0;
for (int i=0; i<chars.length; i++) {
char c = chars[i];
if (c!='\n' && c!='\t' && (c<32||c>127)) {
count++;
chars[i] = ' ';
}
}
if (count>0)
return new String(chars);
else
return text;
}
}
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Fitter |
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