private void undoglobalfit() {
for (int i = 0; i < ncurves; i++) {
for (int j = 0; j < nparams; j++) {
globalparams[i][j] = undoparams[i][j];
globalformulas[i][j] = undoformulas[i][j];
globalvflmatrix[i][j] = undovflmatrix[i][j];
}
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
fit[i][j][k] = undofit[i][j][k];
}
}
if (i == dispcurve) {
pwfit.updateSeries(fit[dispcurve], 1, true);
}
c2[i] = undoc2[i];
c2array[i].setText("" + (float) c2[i]);
}
globalc2 = undoglobalc2;
globalc2label.setText("Global chi^2 = " + (float) globalc2);
}
private void fitglobal() {
int nparams = 11;
int nsel = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
nsel++;
}
}
double[][] params = new double[nsel][nparams];
String[][] tempformulas = new String[nsel][nparams];
double[][][] constraints = new double[2][nsel][nparams];
int[][] vflmatrix = new int[nsel][nparams];
int counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < nparams; j++) {
params[counter][j] = globalparams[i][j];
tempformulas[counter][j] = globalformulas[i][j];
constraints[0][counter][j] = globalconstraints[0][i][j];
constraints[1][counter][j] = globalconstraints[1][i][j];
vflmatrix[counter][j] = globalvflmatrix[i][j];
}
counter++;
}
for (int j = 0; j < nparams; j++) {
undoparams[i][j] = globalparams[i][j];
undoformulas[i][j] = globalformulas[i][j];
undovflmatrix[i][j] = globalvflmatrix[i][j];
}
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
undofit[i][j][k] = fit[i][j][k];
}
}
undoc2[i] = c2[i];
}
undoglobalc2 = globalc2;
if (showglobalfitdialog(params, tempformulas, vflmatrix)) {
counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < nparams; j++) {
globalparams[i][j] = params[counter][j];
globalformulas[i][j] = tempformulas[counter][j];
globalvflmatrix[i][j] = vflmatrix[counter][j];
}
counter++;
}
}
double[] stats = new double[2];
float[][] tempdata = new float[nsel][xpts * ypts];
float[][] tempweights = new float[nsel][xpts * ypts];
counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]);
tempweights[counter][j + k * xpts] = weights[i][j][k];
}
}
counter++;
}
}
int tempmaxiter = globalfitclass.maxiter;
if (checkc2) {
globalfitclass.changemaxiter(0);
}
double[] tempc2vals = new double[nsel];
IJ.showStatus("Fitting Globally");
float[][] tempfit =
globalfitclass.fitdata(
params,
vflmatrix,
tempformulas,
paramsnames,
constraints,
tempdata,
tempweights,
stats,
tempc2vals,
false);
IJ.showStatus("Fit Complete");
globalfitclass.changemaxiter(tempmaxiter);
globalc2 = stats[1];
globalc2label.setText("Global chi^2 = " + (float) globalc2);
counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
fit[i][j][k] = tempfit[counter][j + xpts * k] * (float) nmeas[i];
}
}
if (i == dispcurve) {
pwfit.updateSeries(fit[dispcurve], 1, true);
}
for (int j = 0; j < nparams; j++) {
globalparams[i][j] = params[counter][j];
}
c2[i] = tempc2vals[counter];
c2array[i].setText("" + (float) c2[i]);
counter++;
}
}
float[] temp = pwfit.getLimits();
temp[4] = 1.0f;
pwfit.setLimits(temp);
}
}
void init(String[] names1, float[][][] pch1, int psfflag1) {
setLayout(null);
names = names1;
pch = pch1;
psfflag = psfflag1;
ncurves = pch.length;
nparams = 11;
xpts = pch[0].length;
ypts = pch[0][0].length;
checkarray = new Checkbox[ncurves];
include = new boolean[ncurves];
namearray = new TextField[ncurves + 1];
int1array = new TextField[ncurves + 1];
intensity1 = new double[ncurves + 1];
e1array = new TextField[ncurves + 1];
n1array = new TextField[ncurves + 1];
bright1 = new double[ncurves + 1];
number1 = new double[ncurves + 1];
int2array = new TextField[ncurves + 1];
intensity2 = new double[ncurves + 1];
e2array = new TextField[ncurves + 1];
n2array = new TextField[ncurves + 1];
bright2 = new double[ncurves + 1];
number2 = new double[ncurves + 1];
eccarray = new TextField[ncurves + 1];
brightcc = new double[ncurves + 1];
eminccarray = new TextField[ncurves + 1];
brightmincc = new double[ncurves + 1];
c2array = new TextField[ncurves + 1];
c2 = new double[ncurves + 1];
nmeas = new int[ncurves + 1];
avg = new float[xpts][ypts];
indices = new int[ncurves];
beta = 0.05;
getintbright();
for (int i = 0; i < ncurves; i++) {
include[i] = true;
indices[i] = i;
}
updateavg();
int starty = 60;
int startx = 10;
int yinc = 25;
for (int i = 0; i <= ncurves; i++) {
if (i != ncurves) {
checkarray[i] = new Checkbox("", include[i]);
checkarray[i].setBounds(startx, starty + i * yinc, 20, 20);
checkarray[i].addItemListener(this);
add(checkarray[i]);
}
namearray[i] = new TextField(names[i]);
namearray[i].setBounds(startx + 30, starty + i * yinc, 200, 20);
add(namearray[i]);
int1array[i] = new TextField("" + (float) intensity1[i]);
int1array[i].setBounds(startx + 30 + 210, starty + i * yinc, 40, 20);
add(int1array[i]);
e1array[i] = new TextField("" + (float) bright1[i]);
e1array[i].setBounds(startx + 30 + 210 + 50, starty + i * yinc, 40, 20);
add(e1array[i]);
n1array[i] = new TextField("" + (float) number1[i]);
n1array[i].setBounds(startx + 30 + 210 + 50 + 50, starty + i * yinc, 40, 20);
add(n1array[i]);
int2array[i] = new TextField("" + (float) intensity2[i]);
int2array[i].setBounds(startx + 30 + 210 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(int2array[i]);
e2array[i] = new TextField("" + (float) bright2[i]);
e2array[i].setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(e2array[i]);
n2array[i] = new TextField("" + (float) number2[i]);
n2array[i].setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(n2array[i]);
eccarray[i] = new TextField("" + (float) brightcc[i]);
eccarray[i].setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(eccarray[i]);
eminccarray[i] = new TextField("" + (float) brightmincc[i]);
eminccarray[i].setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50, starty + i * yinc, 40, 20);
add(eminccarray[i]);
c2[i] = 0.0;
c2array[i] = new TextField("" + (float) c2[i]);
c2array[i].setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50 + 50, starty + i * yinc, 80, 20);
add(c2array[i]);
}
namelabel = new Label("Filename");
namelabel.setBounds(startx + 30, starty - 25, 100, 20);
add(namelabel);
intlabel = new Label("<Ig>");
intlabel.setBounds(startx + 30 + 210, starty - 25, 40, 20);
add(intlabel);
brightlabel = new Label("<eg>");
brightlabel.setBounds(startx + 30 + 210 + 50, starty - 25, 40, 20);
add(brightlabel);
nlabel = new Label("<Ng>");
nlabel.setBounds(startx + 30 + 210 + 50 + 50, starty - 25, 40, 20);
add(nlabel);
int2label = new Label("<Ir>");
int2label.setBounds(startx + 30 + 210 + 50 + 50 + 50, starty - 25, 40, 20);
add(int2label);
bright2label = new Label("<er>");
bright2label.setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50, starty - 25, 40, 20);
add(bright2label);
n2label = new Label("<Nr>");
n2label.setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50 + 50, starty - 25, 40, 20);
add(n2label);
brightcclabel = new Label("<ecc>");
brightcclabel.setBounds(startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50, starty - 25, 40, 20);
add(brightcclabel);
brightccminlabel = new Label("min");
brightccminlabel.setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50, starty - 25, 40, 20);
add(brightccminlabel);
c2label = new Label("chi^2");
c2label.setBounds(
startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50 + 50, starty - 25, 80, 20);
add(c2label);
int buttonsx = startx + 30 + 210 + 50 + 50 + 50 + 50 + 50 + 50 + 50 + 50 + 90;
fitavgbutton = new Button("Fit Avg");
fitavgbutton.setBounds(buttonsx, starty - 25, 100, 40);
fitavgbutton.addActionListener(this);
add(fitavgbutton);
fitglobalbutton = new Button("Fit Global");
fitglobalbutton.setBounds(buttonsx, starty - 25 + 50, 100, 40);
fitglobalbutton.addActionListener(this);
add(fitglobalbutton);
clearparamsbutton = new Button("Reset Fit Params");
clearparamsbutton.setBounds(buttonsx, starty - 25 + 50 + 50, 100, 40);
clearparamsbutton.addActionListener(this);
add(clearparamsbutton);
checkc2 = false;
fitclass = new NLLSfit(this, 0.0001, 50, 0.1);
globalfitclass = new NLLSglobalfit(this, 0.0001, 50, 0.1);
pchfunc = new pch2D((int) ((double) xpts * 1.5), (int) ((double) ypts * 1.5), psfflag);
avgfit = new float[xpts][ypts];
fit = new float[ncurves][xpts][ypts];
xvals = new float[ncurves][xpts][ypts];
for (int i = 0; i < ncurves; i++) {
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
xvals[i][j][k] = (float) k;
fit[i][j][k] = 1.0f;
}
}
}
globalc2label = new Label("Global chi^2 = " + (float) 0.0);
globalc2label.setBounds(buttonsx, starty - 25 + 50 + 50 + 50, 140, 20);
add(globalc2label);
dispcurvelabel = new Label("Display Fit #");
dispcurvelabel.setBounds(buttonsx, starty - 25 + 50 + 50 + 50 + 30, 70, 20);
add(dispcurvelabel);
dispcurvechoice = new Choice();
for (int i = 0; i < ncurves; i++) {
dispcurvechoice.add("" + (i + 1));
}
dispcurve = 0;
dispcurvechoice.select(0);
dispcurvechoice.setBounds(buttonsx + 80, starty - 25 + 50 + 50 + 50 + 30, 40, 20);
dispcurvechoice.addItemListener(this);
add(dispcurvechoice);
betalabel = new Label("Bleedthrough f");
betalabel.setBounds(buttonsx, starty - 25 + 50 + 50 + 50 + 30 + 30, 100, 20);
add(betalabel);
betaval = new TextField("" + (float) beta);
betaval.setBounds(buttonsx + 110, starty - 25 + 50 + 50 + 50 + 30 + 30, 40, 20);
betaval.addActionListener(this);
add(betaval);
beta = Double.parseDouble(betaval.getText());
updatebeta();
undobutton = new Button("Undo Global Fit");
undobutton.setBounds(buttonsx, starty - 25 + 50 + 50 + 50 + 30 + 30 + 50, 100, 40);
undobutton.addActionListener(this);
add(undobutton);
geterrorsbutton = new Button("Get Errors");
geterrorsbutton.setBounds(buttonsx, starty - 25 + 50 + 50 + 50 + 30 + 30 + 50 + 50, 100, 40);
geterrorsbutton.addActionListener(this);
add(geterrorsbutton);
copylabel = new Label("copyright 2009 Jay Unruh ([email protected]) non-profit use only");
copylabel.setBounds(10, 790, 400, 20);
add(copylabel);
n_b_label = new Label("N and B Analysis");
n_b_label.setBounds(250, 10, 100, 20);
add(n_b_label);
pwavg = new PlotWindow3D("Avg", "kg", "kr", "Frequency", avg, 0);
pwavg.setLogAxes(false, false, true);
pwavg.draw();
pwavg.addPoints(avgfit, true, 0);
float[] temp = pwavg.getLimits();
temp[4] = 1.0f;
pwavg.setLimits(temp);
float[][] temppch = new float[xpts][ypts];
for (int i = 0; i < xpts; i++) {
System.arraycopy(pch[dispcurve][i], 0, temppch[i], 0, ypts);
}
pwfit = new PlotWindow3D("Selected Curve", "kg", "kr", "Frequency", temppch, 0);
pwfit.setLogAxes(false, false, true);
pwfit.draw();
pwfit.addPoints(fit[dispcurve], true, 0);
float[] temp2 = pwfit.getLimits();
temp2[4] = 1.0f;
pwfit.setLimits(temp2);
resetparams();
repaint();
}
void showStatus(String s) {
statusLine.setText(s);
}
/**
* If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is
* ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ.
*/
public ImageJ(java.applet.Applet applet, int mode) {
super("ImageJ");
embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW);
this.applet = applet;
String err1 = Prefs.load(this, applet);
if (IJ.isLinux()) {
backgroundColor = new Color(240, 240, 240);
setBackground(backgroundColor);
}
Menus m = new Menus(this, applet);
String err2 = m.addMenuBar();
m.installPopupMenu(this);
setLayout(new GridLayout(2, 1));
// Tool bar
toolbar = new Toolbar();
toolbar.addKeyListener(this);
add(toolbar);
// Status bar
statusBar = new Panel();
statusBar.setLayout(new BorderLayout());
statusBar.setForeground(Color.black);
statusBar.setBackground(backgroundColor);
statusLine = new Label();
statusLine.setFont(SansSerif12);
statusLine.addKeyListener(this);
statusLine.addMouseListener(this);
statusBar.add("Center", statusLine);
progressBar = new ProgressBar(120, 20);
progressBar.addKeyListener(this);
progressBar.addMouseListener(this);
statusBar.add("East", progressBar);
statusBar.setSize(toolbar.getPreferredSize());
add(statusBar);
IJ.init(this, applet);
addKeyListener(this);
addWindowListener(this);
setFocusTraversalKeysEnabled(false);
Point loc = getPreferredLocation();
Dimension tbSize = toolbar.getPreferredSize();
int ijWidth = tbSize.width + 10;
int ijHeight = 100;
setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
if (mode != NO_SHOW) {
if (IJ.isWindows())
try {
setIcon();
} catch (Exception e) {
}
setBounds(loc.x, loc.y, ijWidth, ijHeight); // needed for pack to work
setLocation(loc.x, loc.y);
pack();
setResizable(!(IJ.isMacintosh() || IJ.isWindows())); // make resizable on Linux
show();
}
if (err1 != null) IJ.error(err1);
if (err2 != null) {
IJ.error(err2);
IJ.runPlugIn("ij.plugin.ClassChecker", "");
}
m.installStartupMacroSet();
if (IJ.isMacintosh() && applet == null) {
Object qh = null;
qh = IJ.runPlugIn("MacAdapter", "");
if (qh == null) IJ.runPlugIn("QuitHandler", "");
}
if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", "");
String str = m.getMacroCount() == 1 ? " macro" : " macros";
IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str);
// if (applet==null && !embedded && Prefs.runSocketListener)
// new SocketListener();
configureProxy();
if (applet == null) loadCursors();
}