/**
* Builds dialog to query users for projection parameters.
*
* @param start starting slice to display
* @param stop last slice
*/
protected GenericDialog buildControlDialog(int start, int stop) {
GenericDialog gd = new GenericDialog("ZProjection", IJ.getInstance());
gd.addNumericField("Start slice:", startSlice, 0 /*digits*/);
gd.addNumericField("Stop slice:", stopSlice, 0 /*digits*/);
gd.addChoice("Projection type", METHODS, METHODS[method]);
if (isHyperstack && imp.getNFrames() > 1 && imp.getNSlices() > 1)
gd.addCheckbox("All time frames", allTimeFrames);
return gd;
}
/** Quit using a separate thread, hopefully avoiding thread deadlocks. */
public void run() {
quitting = true;
boolean changes = false;
int[] wList = WindowManager.getIDList();
if (wList != null) {
for (int i = 0; i < wList.length; i++) {
ImagePlus imp = WindowManager.getImage(wList[i]);
if (imp != null && imp.changes == true) {
changes = true;
break;
}
}
}
Frame[] frames = WindowManager.getNonImageWindows();
if (frames != null) {
for (int i = 0; i < frames.length; i++) {
if (frames[i] != null && (frames[i] instanceof Editor)) {
if (((Editor) frames[i]).fileChanged()) {
changes = true;
break;
}
}
}
}
if (windowClosed
&& !changes
&& Menus.window.getItemCount() > Menus.WINDOW_MENU_ITEMS
&& !(IJ.macroRunning() && WindowManager.getImageCount() == 0)) {
GenericDialog gd = new GenericDialog("ImageJ", this);
gd.addMessage("Are you sure you want to quit ImageJ?");
gd.showDialog();
quitting = !gd.wasCanceled();
windowClosed = false;
}
if (!quitting) return;
if (!WindowManager.closeAllWindows()) {
quitting = false;
return;
}
// IJ.log("savePreferences");
if (applet == null) {
saveWindowLocations();
Prefs.savePreferences();
}
IJ.cleanup();
// setVisible(false);
// IJ.log("dispose");
dispose();
if (exitWhenQuitting) System.exit(0);
}
/** EdiDialog constructor comment. */
public void show() {
getContentPane().setLayout(new java.awt.BorderLayout());
JScrollPane center = new JScrollPane();
getContentPane().add(center, java.awt.BorderLayout.CENTER);
list = new JList();
list.setBackground(parentWindow.getBackground());
DefaultListModel model = new DefaultListModel();
list.setModel(model);
for (int i = 0; i < DesignFrame.processingElements.length; i++) {
model.addElement((String) DesignFrame.processingElements[i][0]);
}
// list.ActionListener((ActionListener) this);
center.setViewportView(list);
JPanel down = new JPanel();
getContentPane().add(down, java.awt.BorderLayout.SOUTH);
down.setLayout(new java.awt.FlowLayout(java.awt.FlowLayout.RIGHT, 2, 2));
bOK = new JButton("OK");
bOK.addActionListener(this);
bAdd = new JButton("Add");
bAdd.addActionListener(this);
bCancel = new JButton("Cancel");
bCancel.addActionListener(this);
down.add(bOK);
down.add(bAdd);
down.add(bCancel);
pack();
setSize(getWidth(), getHeight() * 2);
list.addKeyListener(this);
super.show();
}
/** EdiDialog constructor comment. */
public void keyReleased(java.awt.event.KeyEvent e) {
if (e.getSource() == list) {
switch (e.getKeyCode()) {
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
if (keys.length() > 0) keys.setLength(keys.length() - 1);
break;
case KeyEvent.VK_ESCAPE:
dispose();
break;
case KeyEvent.VK_ENTER:
dispose();
actionOK();
break;
case KeyEvent.VK_SPACE:
actionAdd();
break;
default:
// keys.append((char) e.getKeyChar());
list.ensureIndexIsVisible(list.getSelectedIndex());
}
// if (debug)
// System.out.println("keys: " + keys);
return;
}
switch (e.getKeyCode()) {
case KeyEvent.VK_ENTER:
case KeyEvent.VK_ESCAPE:
dispose();
break;
default:
break;
}
super.keyReleased(e);
}
public void run(String arg) {
GenericDialog gd = new GenericDialog("Options");
double sfreq = 20000.0;
gd.addNumericField("Sampling Frequency?", sfreq, 1, 10, null);
String[] psfchoice = {"3D Gaussian", "Gaus-Lorentz^2", "2D Gaussian"};
gd.addChoice("PSF Type?", psfchoice, psfchoice[0]);
String[] filetypechoice = {
"Confocor 3 raw", "Short binary trajectory", "PlotWindow trajectory", "Ascii Text File"
};
gd.addChoice("File Type?", filetypechoice, filetypechoice[0]);
boolean ch2green = true;
gd.addCheckbox("Ch2 is green?", ch2green);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
sfreq = gd.getNextNumber();
int psfflag = gd.getNextChoiceIndex();
int fileflag = gd.getNextChoiceIndex();
ch2green = gd.getNextBoolean();
int nfiles = 0;
Object[] histograms = null;
int xmax = 0;
int ymax = 0;
String[] names = null;
if (fileflag < 2) {
jdataio ioclass = new jdataio();
File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
if (filearray.length == 0) {
return;
}
String dir = filearray[0].getAbsolutePath();
int sepindex = dir.lastIndexOf(File.separator);
String newdir = dir.substring(0, sepindex + 1);
OpenDialog.setDefaultDirectory(newdir);
nfiles = filearray.length / 2;
if (nfiles > 25) {
nfiles = 25;
}
histograms = new Object[nfiles];
names = organize_c3_files(filearray);
for (int i = 0; i < nfiles; i++) {
try {
int length1 = (int) (((double) filearray[2 * i].length() - 128.0) / 4.0);
int length2 = (int) (((double) filearray[2 * i + 1].length() - 128.0) / 4.0);
int length3 = (int) (((double) filearray[2 * i].length()) / 2.0);
int length4 = (int) (((double) filearray[2 * i + 1].length()) / 2.0);
InputStream instream = new BufferedInputStream(new FileInputStream(filearray[2 * i]));
InputStream instream2 =
new BufferedInputStream(new FileInputStream(filearray[2 * i + 1]));
if (fileflag == 0) {
int[] pmdata = new int[length1];
int[] pmdata2 = new int[length2];
if (!ioclass.skipstreambytes(instream, 128)) {
showioerror();
instream.close();
return;
}
if (!ioclass.skipstreambytes(instream2, 128)) {
showioerror();
instream2.close();
return;
}
if (!ioclass.readintelintfile(instream, length1, pmdata)) {
showioerror();
instream.close();
return;
}
if (!ioclass.readintelintfile(instream2, length2, pmdata2)) {
showioerror();
instream2.close();
return;
}
if (ch2green) {
histograms[i] = (new pmodeconvert()).pm2pch(pmdata2, pmdata, sfreq, 20000000);
} else {
histograms[i] = (new pmodeconvert()).pm2pch(pmdata, pmdata2, sfreq, 20000000);
}
} else {
float[] tmdata = new float[length3];
float[] tmdata2 = new float[length4];
if (!ioclass.readintelshortfile(instream, length3, tmdata)) {
showioerror();
instream.close();
return;
}
if (!ioclass.readintelshortfile(instream2, length4, tmdata2)) {
showioerror();
instream2.close();
return;
}
if (ch2green) {
histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata2, tmdata);
} else {
histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata, tmdata2);
}
}
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
instream.close();
instream2.close();
} catch (IOException e) {
showioerror();
return;
}
}
} else {
if (fileflag == 2) {
ImageWindow iw = WindowManager.getCurrentWindow();
float[][] trajectories = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
float[][] tempxvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
sfreq = 1.0 / ((double) tempxvals[0][1]);
nfiles = trajectories.length / 2;
if (nfiles > 25) {
nfiles = 25;
}
names = new String[nfiles + 1];
names[nfiles] = "avg";
histograms = new Object[nfiles];
for (int i = 0; i < nfiles; i++) {
names[i] = "trajectory " + (i + 1);
if (ch2green) {
histograms[i] =
(new pmodeconvert())
.create_2Dhistogram(trajectories[2 * i + 1], trajectories[2 * i]);
} else {
histograms[i] =
(new pmodeconvert())
.create_2Dhistogram(trajectories[2 * i], trajectories[2 * i + 1]);
}
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
}
} else {
// here we read tab delimited lines from files
jdataio ioclass = new jdataio();
File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
if (filearray.length == 0) {
return;
}
String dir = filearray[0].getAbsolutePath();
int sepindex = dir.lastIndexOf(File.separator);
String newdir = dir.substring(0, sepindex + 1);
OpenDialog.setDefaultDirectory(newdir);
nfiles = filearray.length;
if (nfiles > 25) {
nfiles = 25;
}
histograms = new Object[nfiles];
names = new String[nfiles + 1];
names[nfiles] = "avg";
for (int i = 0; i < nfiles; i++) {
try {
names[i] = filearray[i].getName();
BufferedReader d = new BufferedReader(new FileReader(filearray[i]));
String[] lines = new String[256];
int counter = 0;
do {
lines[counter] = d.readLine();
counter++;
} while ((lines[counter - 1] != null && lines[counter - 1] != "") && counter < 256);
int numcolumns = 0;
for (int j = 0; j < counter - 1; j++) {
int temp = getncolumns(lines[j]);
if (temp > numcolumns) {
numcolumns = temp;
}
}
float[][] temphist2 = null;
if (ch2green) {
temphist2 = new float[numcolumns][counter - 1];
} else {
temphist2 = new float[counter - 1][numcolumns];
}
for (int k = 0; k < counter - 1; k++) {
float[] temp = tab_delim2float(lines[k]);
for (int j = 0; j < numcolumns; j++) {
if (ch2green) {
temphist2[j][k] = temp[j];
} else {
temphist2[k][j] = temp[j];
}
}
}
histograms[i] = temphist2;
d.close();
} catch (IOException e) {
showioerror();
return;
}
}
for (int i = 0; i < nfiles; i++) {
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
}
}
}
// note that here x is green and y is red
float[][][] pch = new float[nfiles][xmax][ymax];
for (int i = 0; i < nfiles; i++) {
for (int j = 0; j < ((float[][]) histograms[i]).length; j++) {
for (int k = 0; k < ((float[][]) histograms[i])[j].length; k++) {
pch[i][j][k] = ((float[][]) histograms[i])[j][k];
}
}
}
final PCH2DFitWindow cw = new PCH2DFitWindow();
cw.init(names, pch, psfflag);
final Frame f = new Frame("PCH 2D Analysis");
f.setLocation(10, 10);
f.addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent e) {
f.dispose();
}
});
f.add(cw);
f.pack();
f.setResizable(false);
Insets ins = f.getInsets();
cw.totalSize.height = PCH2DFitWindow.H + ins.bottom + ins.top + 65;
cw.totalSize.width = PCH2DFitWindow.WR + ins.left + ins.right;
f.setSize(cw.totalSize);
f.setVisible(true);
cw.requestFocus();
}
private void geterrors() {
GenericDialog gd = new GenericDialog("Options");
float conf = 0.67f;
gd.addNumericField("Confidence Limit", (int) (conf * 100.0f), 5, 10, null);
gd.addChoice("Error Parameter", paramsnames, paramsnames[0]);
double spacing = 0.01;
gd.addNumericField("Chi^2 plot spacing (% of value)?", spacing * 100.0, 2, 10, null);
boolean globalerror = false;
gd.addCheckbox("Global Fit Error?", globalerror);
int dataset = 0;
gd.addNumericField("Data Set (for Global Error)", dataset, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
conf = 0.01f * (float) gd.getNextNumber();
int paramindex = (int) gd.getNextChoiceIndex();
spacing = 0.01 * gd.getNextNumber();
globalerror = gd.getNextBoolean();
dataset = (int) gd.getNextNumber();
if (globalerror) {
support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, true, 0.1);
int[] erindeces = {paramindex, dataset};
// need to set up all the matrices
int nsel = 0;
int nparams = 11;
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];
float[][] tempdata = new float[nsel][xpts * ypts];
float[][] tempweights = new float[nsel][xpts * ypts];
int nfit = 0;
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];
if (vflmatrix[counter][j] == 0 || (j == 0 && vflmatrix[counter][j] == 2)) {
nfit++;
}
}
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 dofnum = xpts * ypts * nsel - (nfit - 1) - 1;
int dofden = xpts * ypts * nsel - nfit - 1;
// double flim=FLimit(dofnum,dofden,(double)conf);
double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
IJ.log("FLimit = " + (float) flim);
if (flim == Double.NaN && flim < 1.0) {
IJ.showMessage("Invalid Limiting F Value");
return;
}
double truespacing = Math.abs(params[erindeces[1]][erindeces[0]] * spacing);
double[][] c2plot =
erclass.geterrorsglobal(
params,
vflmatrix,
tempformulas,
paramsnames,
constraints,
tempdata,
tempweights,
flim,
truespacing,
erindeces);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
int templength = c2plot[0].length;
float[][] c2plotf = new float[2][templength - 1];
for (int i = 0; i < (templength - 1); i++) {
c2plotf[0][i] = (float) c2plot[0][i + 1];
c2plotf[1][i] = (float) c2plot[1][i + 1];
}
new PlotWindow4(
"c2 plot",
paramsnames[paramindex] + "[" + dataset + "]",
"Chi^2",
c2plotf[0],
c2plotf[1])
.draw();
} else {
support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, false, 0.1);
int errindex = paramindex;
float[] tempdata = new float[xpts * ypts];
float[] tempweights = new float[xpts * ypts];
for (int i = 0; i < xpts; i++) {
for (int j = 0; j < ypts; j++) {
tempdata[i + j * xpts] = (float) ((double) avg[i][j] / (double) nmeas[ncurves]);
tempweights[i + j * xpts] = avgweights[i][j];
}
}
int nfit = 0;
for (int i = 0; i < 7; i++) {
if (avgfixes[i] == 0) {
nfit++;
}
}
int dofnum = xpts * ypts - (nfit - 1) - 1;
int dofden = xpts * ypts - nfit - 1;
double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
IJ.log("FLimit = " + (float) flim);
if (flim == Double.NaN && flim < 1.0) {
IJ.showMessage("Invalid Limiting F Value");
return;
}
double truespacing = Math.abs(avgparams[errindex] * spacing);
double[][] c2plot =
erclass.geterrors(
avgparams,
avgfixes,
avgconstraints,
tempdata,
tempweights,
flim,
truespacing,
errindex);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
int templength = c2plot[0].length;
float[][] c2plotf = new float[2][templength - 1];
for (int i = 0; i < (templength - 1); i++) {
c2plotf[0][i] = (float) c2plot[0][i + 1];
c2plotf[1][i] = (float) c2plot[1][i + 1];
}
new PlotWindow4("c2 plot", paramsnames[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
}
}
/** Invoked when an action occurs. */
public void locateOnComponent(int x, int y, java.awt.Component f) {
cX = x;
cY = y;
super.locateOnComponent(x, y, f);
}
boolean showDialog(ImageProcessor ip) {
int bitDepth = imp.getBitDepth();
boolean isStack = imp.getStackSize() > 1;
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale (0.05-25):", xstr);
gd.addStringField("Y Scale (0.05-25):", ystr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
fields = gd.getStringFields();
for (int i = 0; i < 3; i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
fieldWithFocus = xField;
gd.addCheckbox("Interpolate", interpolate);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with Background Color", fillWithBackground);
if (isStack) gd.addCheckbox("Process Entire Stack", processStack);
gd.addCheckbox("Create New Window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Invalid width or height entered");
return false;
}
if (xscale > 25.0) xscale = 25.0;
if (yscale > 25.0) yscale = 25.0;
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
interpolate = gd.getNextBoolean();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
if (isStack) processStack = gd.getNextBoolean();
newWindow = gd.getNextBoolean();
if (!newWindow && xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else {
if (bitDepth == 8) bgValue = ip.isInvertedLut() ? 0.0 : 255.0; // white
else if (bitDepth == 24) bgValue = 0xffffffff; // white
}
return true;
}
boolean showDialog(ImageProcessor ip) {
String macroOptions = Macro.getOptions();
if (macroOptions != null) {
if (macroOptions.indexOf(" interpolate") != -1)
macroOptions.replaceAll(" interpolate", " interpolation=Bilinear");
else if (macroOptions.indexOf(" interpolation=") == -1)
macroOptions = macroOptions + " interpolation=None";
Macro.setOptions(macroOptions);
}
int bitDepth = imp.getBitDepth();
int stackSize = imp.getStackSize();
boolean isStack = stackSize > 1;
oldDepth = stackSize;
if (isStack) {
xstr = "1.0";
ystr = "1.0";
zstr = "1.0";
}
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
zscale = 1.0;
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale:", xstr);
gd.addStringField("Y Scale:", ystr);
if (isStack) gd.addStringField("Z Scale:", zstr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
if (isStack) {
String label = "Depth (images):";
if (imp.isHyperStack()) {
int slices = imp.getNSlices();
int frames = imp.getNFrames();
if (slices == 1 && frames > 1) {
label = "Depth (frames):";
oldDepth = frames;
} else {
label = "Depth (slices):";
oldDepth = slices;
}
}
gd.addStringField(label, "" + oldDepth);
}
fields = gd.getStringFields();
for (int i = 0; i < fields.size(); i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
if (isStack) {
zField = (TextField) fields.elementAt(2);
widthField = (TextField) fields.elementAt(3);
heightField = (TextField) fields.elementAt(4);
depthField = (TextField) fields.elementAt(5);
} else {
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
}
fieldWithFocus = xField;
gd.addChoice("Interpolation:", methods, methods[interpolationMethod]);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with background color", fillWithBackground);
gd.addCheckbox("Average when downsizing", averageWhenDownsizing);
boolean hyperstack = imp.isHyperStack() || imp.isComposite();
if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack);
gd.addCheckbox("Create new window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (isStack) {
zstr = gd.getNextString();
zscale = Tools.parseDouble(ystr, 0.0);
}
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Scaler", "Width or height is 0");
return false;
}
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0);
interpolationMethod = gd.getNextChoiceIndex();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
averageWhenDownsizing = gd.getNextBoolean();
if (isStack && !hyperstack) processStack = gd.getNextBoolean();
if (hyperstack) processStack = true;
newWindow = gd.getNextBoolean();
if (xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else bgValue = 0.0;
return true;
}
/**
* Creates a dialog box, allowing the user to enter the requested width, height, x & y
* coordinates, slice number for a Region Of Interest, option for oval, and option for whether x &
* y coordinates to be centered.
*/
void showDialog() {
Calibration cal = imp.getCalibration();
int digits = 0;
if (scaledUnits && cal.scaled()) digits = 2;
Roi roi = imp.getRoi();
if (roi == null) drawRoi();
GenericDialog gd = new GenericDialog("Specify");
gd.addNumericField("Width:", width, digits);
gd.addNumericField("Height:", height, digits);
gd.addNumericField("X coordinate:", xRoi, digits);
gd.addNumericField("Y coordinate:", yRoi, digits);
if (stackSize > 1) gd.addNumericField("Slice:", iSlice, 0);
gd.addCheckbox("Oval", oval);
gd.addCheckbox("Constrain square/circle", square);
gd.addCheckbox("Centered", centered);
if (cal.scaled()) {
boolean unitsMatch = cal.getXUnit().equals(cal.getYUnit());
String units = unitsMatch ? cal.getUnits() : cal.getXUnit() + " x " + cal.getYUnit();
gd.addCheckbox("Scaled units (" + units + ")", scaledUnits);
}
fields = gd.getNumericFields();
gd.addDialogListener(this);
gd.showDialog();
if (gd.wasCanceled()) {
if (roi == null) imp.deleteRoi();
else // *ALWAYS* restore initial ROI when cancelled
imp.setRoi(roi);
}
}
public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
if (IJ.isMacOSX()) IJ.wait(50);
Calibration cal = imp.getCalibration();
width = gd.getNextNumber();
height = gd.getNextNumber();
xRoi = gd.getNextNumber();
yRoi = gd.getNextNumber();
if (stackSize > 1) iSlice = (int) gd.getNextNumber();
oval = gd.getNextBoolean();
square = gd.getNextBoolean();
centered = gd.getNextBoolean();
if (cal.scaled()) scaledUnits = gd.getNextBoolean();
if (gd.invalidNumber() || width <= 0 || height <= 0) return false;
//
Vector numFields = gd.getNumericFields();
Vector checkboxes = gd.getCheckboxes();
boolean newWidth = false, newHeight = false, newXY = false;
if (e != null && e.getSource() == checkboxes.get(SQUARE) && square) {
width = 0.5 * (width + height); // make square: same width&height
height = width;
newWidth = true;
newHeight = true;
}
if (e != null && e.getSource() == checkboxes.get(CENTERED)) {
double shiftBy = centered ? 0.5 : -0.5; // 'centered' changed:
xRoi += shiftBy * width; // shift x, y to keep roi the same
yRoi += shiftBy * height;
newXY = true;
}
if (square && width != height && e != null) { // in 'square' mode, synchronize width&height
if (e.getSource() == numFields.get(WIDTH)) {
height = width;
newHeight = true;
} else if (e.getSource() == numFields.get(HEIGHT)) {
width = height;
newWidth = true;
}
}
if (e != null && cal.scaled() && e.getSource() == checkboxes.get(SCALED_UNITS)) {
double xFactor = scaledUnits ? cal.pixelWidth : 1. / cal.pixelWidth;
double yFactor = scaledUnits ? cal.pixelHeight : 1. / cal.pixelHeight;
width *= xFactor; // transform everything to keep roi the same
height *= yFactor;
xRoi *= xFactor;
yRoi *= yFactor;
newWidth = true;
newHeight = true;
newXY = true;
}
int digits = (scaledUnits || (int) width != width) ? 2 : 0;
if (newWidth) ((TextField) (numFields.get(WIDTH))).setText(IJ.d2s(width, digits));
if (newHeight) ((TextField) (numFields.get(HEIGHT))).setText(IJ.d2s(height, digits));
digits = (scaledUnits || (int) xRoi != xRoi || (int) yRoi != yRoi) ? 2 : 0;
if (newXY) {
((TextField) (numFields.get(X_ROI))).setText(IJ.d2s(xRoi, digits));
((TextField) (numFields.get(Y_ROI))).setText(IJ.d2s(yRoi, digits));
}
if (stackSize > 1 && iSlice > 0 && iSlice <= stackSize) imp.setSlice(iSlice);
if (!newWidth && !newHeight && !newXY) // don't draw if an update will come immediately
drawRoi();
return true;
}
public void itemStateChanged(ItemEvent e) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) return;
if (!imp.isComposite()) {
int channels = imp.getNChannels();
if (channels == 1 && imp.getStackSize() <= 4) channels = imp.getStackSize();
if (imp.getBitDepth() == 24 || (channels > 1 && channels < CompositeImage.MAX_CHANNELS)) {
GenericDialog gd = new GenericDialog(imp.getTitle());
gd.addMessage("Convert to multi-channel composite image?");
gd.showDialog();
if (gd.wasCanceled()) return;
else IJ.doCommand("Make Composite");
} else {
IJ.error(
"Channels",
"A composite image is required (e.g., "
+ moreLabel
+ " Open HeLa Cells),\nor create one using "
+ moreLabel
+ " Make Composite.");
return;
}
}
if (!imp.isComposite()) return;
CompositeImage ci = (CompositeImage) imp;
Object source = e.getSource();
if (source == choice) {
int index = ((Choice) source).getSelectedIndex();
switch (index) {
case 0:
ci.setMode(IJ.COMPOSITE);
break;
case 1:
ci.setMode(IJ.COLOR);
break;
case 2:
ci.setMode(IJ.GRAYSCALE);
break;
}
ci.updateAndDraw();
if (Recorder.record) {
String mode = null;
switch (index) {
case 0:
mode = "composite";
break;
case 1:
mode = "color";
break;
case 2:
mode = "grayscale";
break;
}
Recorder.record("Stack.setDisplayMode", mode);
}
} else if (source instanceof Checkbox) {
for (int i = 0; i < checkbox.length; i++) {
Checkbox cb = (Checkbox) source;
if (cb == checkbox[i]) {
if (ci.getMode() == IJ.COMPOSITE) {
boolean[] active = ci.getActiveChannels();
active[i] = cb.getState();
if (Recorder.record) {
String str = "";
for (int c = 0; c < ci.getNChannels(); c++) str += active[c] ? "1" : "0";
Recorder.record("Stack.setActiveChannels", str);
Recorder.record("//Stack.toggleChannel", imp.getChannel());
}
} else {
imp.setPosition(i + 1, imp.getSlice(), imp.getFrame());
if (Recorder.record) Recorder.record("Stack.setChannel", i + 1);
}
ci.updateAndDraw();
return;
}
}
}
}
public void run(String arg) {
imp = IJ.getImage();
int stackSize = imp.getStackSize();
if (imp == null) {
IJ.noImage();
return;
}
// Make sure input image is a stack.
if (stackSize == 1) {
IJ.error("Z Project", "Stack required");
return;
}
// Check for inverting LUT.
if (imp.getProcessor().isInvertedLut()) {
if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return;
}
// Set default bounds.
int channels = imp.getNChannels();
int frames = imp.getNFrames();
int slices = imp.getNSlices();
isHyperstack =
imp.isHyperStack()
|| (ij.macro.Interpreter.isBatchMode()
&& ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize)));
boolean simpleComposite = channels == stackSize;
if (simpleComposite) isHyperstack = false;
startSlice = 1;
if (isHyperstack) {
int nSlices = imp.getNSlices();
if (nSlices > 1) stopSlice = nSlices;
else stopSlice = imp.getNFrames();
} else stopSlice = stackSize;
// Build control dialog
GenericDialog gd = buildControlDialog(startSlice, stopSlice);
gd.showDialog();
if (gd.wasCanceled()) return;
if (!imp.lock()) return; // exit if in use
long tstart = System.currentTimeMillis();
setStartSlice((int) gd.getNextNumber());
setStopSlice((int) gd.getNextNumber());
method = gd.getNextChoiceIndex();
Prefs.set(METHOD_KEY, method);
if (isHyperstack) {
allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false;
doHyperStackProjection(allTimeFrames);
} else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true);
else doProjection(true);
if (arg.equals("") && projImage != null) {
long tstop = System.currentTimeMillis();
projImage.setCalibration(imp.getCalibration());
if (simpleComposite) IJ.run(projImage, "Grays", "");
projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds");
}
imp.unlock();
IJ.register(ZProjector.class);
return;
}