/**
* Adds a popup menu.
*
* @param label the label
* @param items the menu items
* @param defaultItem the menu item initially selected
*/
public void addChoice(String label, String[] items, String defaultItem) {
String label2 = label;
if (label2.indexOf('_') != -1) label2 = label2.replace('_', ' ');
Label theLabel = makeLabel(label2);
c.gridx = 0;
c.gridy = y;
c.anchor = GridBagConstraints.EAST;
c.gridwidth = 1;
if (choice == null) {
choice = new Vector(4);
c.insets = getInsets(5, 0, 5, 0);
} else c.insets = getInsets(0, 0, 5, 0);
grid.setConstraints(theLabel, c);
add(theLabel);
Choice thisChoice = new Choice();
thisChoice.addKeyListener(this);
thisChoice.addItemListener(this);
for (int i = 0; i < items.length; i++) thisChoice.addItem(items[i]);
thisChoice.select(defaultItem);
c.gridx = 1;
c.gridy = y;
c.anchor = GridBagConstraints.WEST;
grid.setConstraints(thisChoice, c);
add(thisChoice);
choice.addElement(thisChoice);
if (Recorder.record || macro) saveLabel(thisChoice, label);
y++;
}
public Channels() {
super("Channels");
if (instance != null) {
instance.toFront();
return;
}
WindowManager.addWindow(this);
instance = this;
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
setLayout(gridbag);
int y = 0;
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.fill = GridBagConstraints.BOTH;
c.anchor = GridBagConstraints.CENTER;
int margin = 32;
if (IJ.isMacOSX()) margin = 20;
c.insets = new Insets(10, margin, 10, margin);
choice = new Choice();
for (int i = 0; i < modes.length; i++) choice.addItem(modes[i]);
choice.select(0);
choice.addItemListener(this);
add(choice, c);
CompositeImage ci = getImage();
int nCheckBoxes = ci != null ? ci.getNChannels() : 3;
if (nCheckBoxes > CompositeImage.MAX_CHANNELS) nCheckBoxes = CompositeImage.MAX_CHANNELS;
checkbox = new Checkbox[nCheckBoxes];
for (int i = 0; i < nCheckBoxes; i++) {
checkbox[i] = new Checkbox("Channel " + (i + 1), true);
c.insets = new Insets(0, 25, i < nCheckBoxes - 1 ? 0 : 10, 5);
c.gridy = y++;
add(checkbox[i], c);
checkbox[i].addItemListener(this);
}
c.insets = new Insets(0, 15, 10, 15);
c.fill = GridBagConstraints.NONE;
c.gridy = y++;
moreButton = new Button(moreLabel);
moreButton.addActionListener(this);
add(moreButton, c);
update();
pm = new PopupMenu();
for (int i = 0; i < menuItems.length; i++) addPopupItem(menuItems[i]);
add(pm);
addKeyListener(IJ.getInstance()); // ImageJ handles keyboard shortcuts
setResizable(false);
pack();
if (location == null) {
GUI.center(this);
location = getLocation();
} else setLocation(location);
show();
}
/** Returns the index of the selected item in the next popup menu. */
public int getNextChoiceIndex() {
if (choice == null) return -1;
Choice thisChoice = (Choice) (choice.elementAt(choiceIndex));
int index = thisChoice.getSelectedIndex();
if (macro) {
String label = (String) labels.get((Object) thisChoice);
String oldItem = thisChoice.getSelectedItem();
int oldIndex = thisChoice.getSelectedIndex();
String item = Macro.getValue(macroOptions, label, oldItem);
if (item != null && item.startsWith("&")) // value is macro variable
item = getChoiceVariable(item);
thisChoice.select(item);
index = thisChoice.getSelectedIndex();
if (index == oldIndex && !item.equals(oldItem)) {
// is value a macro variable?
Interpreter interp = Interpreter.getInstance();
String s = interp != null ? interp.getStringVariable(item) : null;
if (s == null)
IJ.error(getTitle(), "\"" + item + "\" is not a valid choice for \"" + label + "\"");
else item = s;
}
}
if (recorderOn) {
int defaultIndex = ((Integer) (defaultChoiceIndexes.elementAt(choiceIndex))).intValue();
if (!(smartRecording && index == defaultIndex)) {
String item = thisChoice.getSelectedItem();
if (!(item.equals("*None*") && getTitle().equals("Merge Channels")))
recordOption(thisChoice, thisChoice.getSelectedItem());
}
}
choiceIndex++;
return index;
}
/** Returns the selected item in the next popup menu. */
public String getNextChoice() {
if (choice == null) return "";
Choice thisChoice = (Choice) (choice.elementAt(choiceIndex));
String item = thisChoice.getSelectedItem();
if (macro) {
String label = (String) labels.get((Object) thisChoice);
item = Macro.getValue(macroOptions, label, item);
if (item != null && item.startsWith("&")) // value is macro variable
item = getChoiceVariable(item);
}
if (recorderOn) recordOption(thisChoice, item);
choiceIndex++;
return item;
}
public void update() {
CompositeImage ci = getImage();
if (ci == null || checkbox == null) return;
int n = checkbox.length;
int nChannels = ci.getNChannels();
if (nChannels != n && nChannels <= CompositeImage.MAX_CHANNELS) {
instance = null;
location = getLocation();
close();
new Channels();
return;
}
boolean[] active = ci.getActiveChannels();
for (int i = 0; i < checkbox.length; i++) checkbox[i].setState(active[i]);
int index = 0;
switch (ci.getMode()) {
case IJ.COMPOSITE:
index = 0;
break;
case IJ.COLOR:
index = 1;
break;
case IJ.GRAYSCALE:
index = 2;
break;
}
choice.select(index);
}
public void itemStateChanged(ItemEvent e) {
beta = Double.parseDouble(betaval.getText());
updatebeta();
boolean avgchanged = false;
for (int i = 0; i < ncurves; i++) {
if (checkarray[i].getState() != include[i]) {
avgchanged = true;
if (include[i]) {
include[i] = false;
} else {
include[i] = true;
}
}
}
if (avgchanged) {
updateavg();
updatebeta();
int1array[ncurves].setText("" + (float) intensity1[ncurves]);
e1array[ncurves].setText("" + (float) bright1[ncurves]);
n1array[ncurves].setText("" + (float) number1[ncurves]);
int2array[ncurves].setText("" + (float) intensity2[ncurves]);
e2array[ncurves].setText("" + (float) bright2[ncurves]);
n2array[ncurves].setText("" + (float) number2[ncurves]);
eccarray[ncurves].setText("" + (float) brightcc[ncurves]);
pwavg.updateSeries(avg, 0, true);
float[] temp = pwavg.getLimits();
temp[4] = 1.0f;
pwavg.setLimits(temp);
}
if (e.getSource() == dispcurvechoice) {
dispcurve = dispcurvechoice.getSelectedIndex();
pwfit.updateSeries(pch[dispcurve], 0, true);
pwfit.updateSeries(fit[dispcurve], 1, true);
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();
}