boolean setProperties(String title, Roi roi) {
Frame f = WindowManager.getFrontWindow();
if (f != null && f.getTitle().indexOf("3D Viewer") != -1) return false;
if (roi == null) {
IJ.error("This command requires a selection.");
return false;
}
RoiProperties rp = new RoiProperties(title, roi);
return rp.showDialog();
}
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();
}
public BandAdjuster() {
super("Threshold Colour");
if (instance != null) {
instance.toFront();
return;
}
imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.beep();
IJ.showStatus("No image");
return;
}
IJ.run("Select None");
thread = new Thread(this, "BandAdjuster");
WindowManager.addWindow(this);
instance = this;
IJ.register(PasteController.class);
ij = IJ.getInstance();
Font font = new Font("SansSerif", Font.PLAIN, 10);
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
setLayout(gridbag);
int y = 0;
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
labelh = new Label("Hue", Label.CENTER);
add(labelh, c);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(7, 0, 0, 0);
labelf = new Label("Filter type", Label.RIGHT);
add(labelf, c);
// plot
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(plot, c);
// checkboxes
panelh = new Panel();
filterTypeH = new CheckboxGroup();
bandPassH = new Checkbox("Pass");
bandPassH.setCheckboxGroup(filterTypeH);
bandPassH.addItemListener(this);
panelh.add(bandPassH);
bandStopH = new Checkbox("Stop");
bandStopH.setCheckboxGroup(filterTypeH);
bandStopH.addItemListener(this);
panelh.add(bandStopH);
bandPassH.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panelh, c);
// minHue slider
minSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider, c);
minSlider.addAdjustmentListener(this);
minSlider.setUnitIncrement(1);
// minHue slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label1 = new Label(" ", Label.LEFT);
label1.setFont(font);
add(label1, c);
// maxHue sliderHue
maxSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider, c);
maxSlider.addAdjustmentListener(this);
maxSlider.setUnitIncrement(1);
// maxHue slider label
c.gridx = 1;
c.gridwidth = 1;
c.gridy = y++;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label2 = new Label(" ", Label.LEFT);
label2.setFont(font);
add(label2, c);
// =====
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(10, 0, 0, 0);
labels = new Label("Saturation", Label.CENTER);
add(labels, c);
// plot
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(splot, c);
// checkboxes
panels = new Panel();
filterTypeS = new CheckboxGroup();
bandPassS = new Checkbox("Pass");
bandPassS.setCheckboxGroup(filterTypeS);
bandPassS.addItemListener(this);
panels.add(bandPassS);
bandStopS = new Checkbox("Stop");
bandStopS.setCheckboxGroup(filterTypeS);
bandStopS.addItemListener(this);
panels.add(bandStopS);
bandPassS.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panels, c);
// minSat slider
minSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider2, c);
minSlider2.addAdjustmentListener(this);
minSlider2.setUnitIncrement(1);
// minSat slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label3 = new Label(" ", Label.LEFT);
label3.setFont(font);
add(label3, c);
// maxSat slider
maxSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider2, c);
maxSlider2.addAdjustmentListener(this);
maxSlider2.setUnitIncrement(1);
// maxSat slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label4 = new Label(" ", Label.LEFT);
label4.setFont(font);
add(label4, c);
// =====
c.gridx = 0;
c.gridwidth = 1;
c.gridy = y++;
c.weightx = 0;
c.insets = new Insets(10, 0, 0, 0);
labelb = new Label("Brightness", Label.CENTER);
add(labelb, c);
c.gridx = 0;
c.gridwidth = 1;
c.gridy = y;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(bplot, c);
// checkboxes
panelb = new Panel();
filterTypeB = new CheckboxGroup();
bandPassB = new Checkbox("Pass");
bandPassB.setCheckboxGroup(filterTypeB);
bandPassB.addItemListener(this);
panelb.add(bandPassB);
bandStopB = new Checkbox("Stop");
bandStopB.setCheckboxGroup(filterTypeB);
bandStopB.addItemListener(this);
panelb.add(bandStopB);
bandPassB.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panelb, c);
// minBri slider
minSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider3, c);
minSlider3.addAdjustmentListener(this);
minSlider3.setUnitIncrement(1);
// minBri slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label5 = new Label(" ", Label.LEFT);
label5.setFont(font);
add(label5, c);
// maxBri slider
maxSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider3, c);
maxSlider3.addAdjustmentListener(this);
maxSlider3.setUnitIncrement(1);
// maxBri slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label6 = new Label(" ", Label.LEFT);
label6.setFont(font);
add(label6, c);
// =====
panelt = new Panel();
threshold = new Checkbox("Threshold");
threshold.addItemListener(this);
panelt.add(threshold);
invert = new Checkbox("Invert");
invert.addItemListener(this);
panelt.add(invert);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panelt, c);
// buttons
panel = new Panel();
// panel.setLayout(new GridLayout(2, 2, 0, 0));
originalB = new Button("Original");
originalB.setEnabled(false);
originalB.addActionListener(this);
originalB.addKeyListener(ij);
panel.add(originalB);
filteredB = new Button("Filtered");
filteredB.setEnabled(false);
filteredB.addActionListener(this);
filteredB.addKeyListener(ij);
panel.add(filteredB);
stackB = new Button("Stack");
stackB.addActionListener(this);
stackB.addKeyListener(ij);
panel.add(stackB);
helpB = new Button("Help");
helpB.addActionListener(this);
helpB.addKeyListener(ij);
panel.add(helpB);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panel, c);
panelMode = new Panel();
sampleB = new Button("Sample");
sampleB.addActionListener(this);
sampleB.addKeyListener(ij);
panelMode.add(sampleB);
colourMode = new CheckboxGroup();
hsb = new Checkbox("HSB");
hsb.setCheckboxGroup(colourMode);
hsb.addItemListener(this);
panelMode.add(hsb);
hsb.setState(true);
rgb = new Checkbox("RGB");
rgb.setCheckboxGroup(colourMode);
rgb.addItemListener(this);
panelMode.add(rgb);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panelMode, c);
addKeyListener(ij); // ImageJ handles keyboard shortcuts
pack();
GUI.center(this);
setVisible(true);
ip = setup(imp);
if (ip == null) {
imp.unlock();
IJ.beep();
IJ.showStatus("RGB image cannot be thresholded");
return;
}
thread.start();
}