public void run(String arg) {
ImageJ ij = IJ.getInstance();
ij.setDropTarget(null);
new DropTarget(ij, this);
new DropTarget(Toolbar.getInstance(), this);
new DropTarget(ij.getStatusBar(), this);
}
public void dragOver(DropTargetDragEvent e) {
if (IJ.debugMode) IJ.log("DragOver: " + e.getLocation());
Point loc = e.getLocation();
int buttonSize = Toolbar.getButtonSize();
int width = IJ.getInstance().getSize().width;
openAsVirtualStack = width - loc.x <= buttonSize;
if (openAsVirtualStack) IJ.showStatus("<<Open as Virtual Stack>>");
else IJ.showStatus("<<Drag and Drop>>");
}
// Miscellaneous Options
void miscOptions() {
String key = IJ.isMacintosh() ? "command" : "control";
GenericDialog gd = new GenericDialog("Miscellaneous Options", IJ.getInstance());
gd.addStringField("Divide by zero value:", "" + FloatBlitter.divideByZeroValue, 10);
gd.addCheckbox("Use pointer cursor", Prefs.usePointerCursor);
gd.addCheckbox("Hide \"Process Stack?\" dialog", IJ.hideProcessStackDialog);
gd.addCheckbox("Require " + key + " key for shortcuts", Prefs.requireControlKey);
gd.addCheckbox("Move isolated plugins to Misc. menu", Prefs.moveToMisc);
if (!IJ.isMacOSX()) gd.addCheckbox("Run single instance listener", Prefs.runSocketListener);
gd.addCheckbox("Enhanced line tool", Prefs.enhancedLineTool);
gd.addCheckbox("Reverse CZT order of \">\" and \"<\"", Prefs.reverseNextPreviousOrder);
gd.addCheckbox("Debug mode", IJ.debugMode);
gd.addHelp(IJ.URL + "/docs/menus/edit.html#misc");
gd.showDialog();
if (gd.wasCanceled()) return;
String divValue = gd.getNextString();
if (divValue.equalsIgnoreCase("infinity") || divValue.equalsIgnoreCase("infinite"))
FloatBlitter.divideByZeroValue = Float.POSITIVE_INFINITY;
else if (divValue.equalsIgnoreCase("NaN")) FloatBlitter.divideByZeroValue = Float.NaN;
else if (divValue.equalsIgnoreCase("max")) FloatBlitter.divideByZeroValue = Float.MAX_VALUE;
else {
Float f;
try {
f = new Float(divValue);
} catch (NumberFormatException e) {
f = null;
}
if (f != null) FloatBlitter.divideByZeroValue = f.floatValue();
}
IJ.register(FloatBlitter.class);
Prefs.usePointerCursor = gd.getNextBoolean();
IJ.hideProcessStackDialog = gd.getNextBoolean();
Prefs.requireControlKey = gd.getNextBoolean();
Prefs.moveToMisc = gd.getNextBoolean();
if (!IJ.isMacOSX()) Prefs.runSocketListener = gd.getNextBoolean();
Prefs.enhancedLineTool = gd.getNextBoolean();
Prefs.reverseNextPreviousOrder = gd.getNextBoolean();
IJ.setDebugMode(gd.getNextBoolean());
}
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 static void main(String args[]) {
if (System.getProperty("java.version").substring(0, 3).compareTo("1.5") < 0) {
javax.swing.JOptionPane.showMessageDialog(
null, "ImageJ " + VERSION + " requires Java 1.5 or later.");
System.exit(0);
}
boolean noGUI = false;
int mode = STANDALONE;
arguments = args;
// System.setProperty("file.encoding", "UTF-8");
int nArgs = args != null ? args.length : 0;
boolean commandLine = false;
for (int i = 0; i < nArgs; i++) {
String arg = args[i];
if (arg == null) continue;
if (args[i].startsWith("-")) {
if (args[i].startsWith("-batch")) noGUI = true;
else if (args[i].startsWith("-debug")) IJ.setDebugMode(true);
else if (args[i].startsWith("-ijpath") && i + 1 < nArgs) {
if (IJ.debugMode) IJ.log("-ijpath: " + args[i + 1]);
Prefs.setHomeDir(args[i + 1]);
commandLine = true;
args[i + 1] = null;
} else if (args[i].startsWith("-port")) {
int delta = (int) Tools.parseDouble(args[i].substring(5, args[i].length()), 0.0);
commandLine = true;
if (delta == 0) mode = EMBEDDED;
else if (delta > 0 && DEFAULT_PORT + delta < 65536) port = DEFAULT_PORT + delta;
}
}
}
// If existing ImageJ instance, pass arguments to it and quit.
boolean passArgs = mode == STANDALONE && !noGUI;
if (IJ.isMacOSX() && !commandLine) passArgs = false;
if (passArgs && isRunning(args)) return;
ImageJ ij = IJ.getInstance();
if (!noGUI && (ij == null || (ij != null && !ij.isShowing()))) {
ij = new ImageJ(null, mode);
ij.exitWhenQuitting = true;
}
int macros = 0;
for (int i = 0; i < nArgs; i++) {
String arg = args[i];
if (arg == null) continue;
if (arg.startsWith("-")) {
if ((arg.startsWith("-macro") || arg.startsWith("-batch")) && i + 1 < nArgs) {
String arg2 = i + 2 < nArgs ? args[i + 2] : null;
Prefs.commandLineMacro = true;
if (noGUI && args[i + 1].endsWith(".js")) Interpreter.batchMode = true;
IJ.runMacroFile(args[i + 1], arg2);
break;
} else if (arg.startsWith("-eval") && i + 1 < nArgs) {
String rtn = IJ.runMacro(args[i + 1]);
if (rtn != null) System.out.print(rtn);
args[i + 1] = null;
} else if (arg.startsWith("-run") && i + 1 < nArgs) {
IJ.run(args[i + 1]);
args[i + 1] = null;
}
} else if (macros == 0 && (arg.endsWith(".ijm") || arg.endsWith(".txt"))) {
IJ.runMacroFile(arg);
macros++;
} else if (arg.length() > 0 && arg.indexOf("ij.ImageJ") == -1) {
File file = new File(arg);
IJ.open(file.getAbsolutePath());
}
}
if (IJ.debugMode && IJ.getInstance() == null) new JavaProperties().run("");
if (noGUI) System.exit(0);
}
String getInfo(ImagePlus imp, ImageProcessor ip) {
String s = new String("");
if (IJ.getInstance() != null) s += IJ.getInstance().getInfo() + "\n \n";
s += "Title: " + imp.getTitle() + "\n";
Calibration cal = imp.getCalibration();
int stackSize = imp.getStackSize();
int channels = imp.getNChannels();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int digits = imp.getBitDepth() == 32 ? 4 : 0;
int dp, dp2;
boolean nonUniformUnits = !cal.getXUnit().equals(cal.getYUnit());
String xunit = cal.getXUnit();
String yunit = cal.getYUnit();
String zunit = cal.getZUnit();
if (cal.scaled()) {
String xunits = cal.getUnits();
String yunits = xunits;
String zunits = xunits;
if (nonUniformUnits) {
xunits = xunit;
yunits = yunit;
zunits = zunit;
}
double pw = imp.getWidth() * cal.pixelWidth;
double ph = imp.getHeight() * cal.pixelHeight;
s += "Width: " + d2s(pw) + " " + xunits + " (" + imp.getWidth() + ")\n";
s += "Height: " + d2s(ph) + " " + yunits + " (" + imp.getHeight() + ")\n";
if (slices > 1) {
double pd = slices * cal.pixelDepth;
s += "Depth: " + d2s(pd) + " " + zunits + " (" + slices + ")\n";
}
s += "Size: " + ImageWindow.getImageSize(imp) + "\n";
double xResolution = 1.0 / cal.pixelWidth;
double yResolution = 1.0 / cal.pixelHeight;
if (xResolution == yResolution)
s += "Resolution: " + d2s(xResolution) + " pixels per " + xunit + "\n";
else {
s += "X Resolution: " + d2s(xResolution) + " pixels per " + xunit + "\n";
s += "Y Resolution: " + d2s(yResolution) + " pixels per " + yunit + "\n";
}
} else {
s += "Width: " + imp.getWidth() + " pixels\n";
s += "Height: " + imp.getHeight() + " pixels\n";
if (stackSize > 1) s += "Depth: " + slices + " pixels\n";
s += "Size: " + ImageWindow.getImageSize(imp) + "\n";
}
if (stackSize > 1) {
String vunit = cal.getUnit() + "^3";
if (nonUniformUnits) vunit = "(" + xunit + " x " + yunit + " x " + zunit + ")";
s +=
"Voxel size: "
+ d2s(cal.pixelWidth)
+ "x"
+ d2s(cal.pixelHeight)
+ "x"
+ d2s(cal.pixelDepth)
+ " "
+ vunit
+ "\n";
} else {
String punit = cal.getUnit() + "^2";
if (nonUniformUnits) punit = "(" + xunit + " x " + yunit + ")";
dp = Tools.getDecimalPlaces(cal.pixelWidth, cal.pixelHeight);
s += "Pixel size: " + d2s(cal.pixelWidth) + "x" + d2s(cal.pixelHeight) + " " + punit + "\n";
}
s += "ID: " + imp.getID() + "\n";
int type = imp.getType();
switch (type) {
case ImagePlus.GRAY8:
s += "Bits per pixel: 8 ";
String lut = "LUT";
if (imp.getProcessor().isColorLut()) lut = "color " + lut;
else lut = "grayscale " + lut;
if (imp.isInvertedLut()) lut = "inverting " + lut;
s += "(" + lut + ")\n";
if (imp.getNChannels() > 1) s += displayRanges(imp);
else s += "Display range: " + (int) ip.getMin() + "-" + (int) ip.getMax() + "\n";
break;
case ImagePlus.GRAY16:
case ImagePlus.GRAY32:
if (type == ImagePlus.GRAY16) {
String sign = cal.isSigned16Bit() ? "signed" : "unsigned";
s += "Bits per pixel: 16 (" + sign + ")\n";
} else s += "Bits per pixel: 32 (float)\n";
if (imp.getNChannels() > 1) s += displayRanges(imp);
else {
s += "Display range: ";
double min = ip.getMin();
double max = ip.getMax();
if (cal.calibrated()) {
min = cal.getCValue((int) min);
max = cal.getCValue((int) max);
}
s += d2s(min) + " - " + d2s(max) + "\n";
}
break;
case ImagePlus.COLOR_256:
s += "Bits per pixel: 8 (color LUT)\n";
break;
case ImagePlus.COLOR_RGB:
s += "Bits per pixel: 32 (RGB)\n";
break;
}
double interval = cal.frameInterval;
double fps = cal.fps;
if (stackSize > 1) {
ImageStack stack = imp.getStack();
int slice = imp.getCurrentSlice();
String number = slice + "/" + stackSize;
String label = stack.getShortSliceLabel(slice);
if (label != null && label.length() > 0) label = " (" + label + ")";
else label = "";
if (interval > 0.0 || fps != 0.0) {
s += "Frame: " + number + label + "\n";
if (fps != 0.0) {
String sRate =
Math.abs(fps - Math.round(fps)) < 0.00001 ? IJ.d2s(fps, 0) : IJ.d2s(fps, 5);
s += "Frame rate: " + sRate + " fps\n";
}
if (interval != 0.0)
s +=
"Frame interval: "
+ ((int) interval == interval ? IJ.d2s(interval, 0) : IJ.d2s(interval, 5))
+ " "
+ cal.getTimeUnit()
+ "\n";
} else s += "Image: " + number + label + "\n";
if (imp.isHyperStack()) {
if (channels > 1) s += " Channel: " + imp.getChannel() + "/" + channels + "\n";
if (slices > 1) s += " Slice: " + imp.getSlice() + "/" + slices + "\n";
if (frames > 1) s += " Frame: " + imp.getFrame() + "/" + frames + "\n";
}
if (imp.isComposite()) {
if (!imp.isHyperStack() && channels > 1) s += " Channels: " + channels + "\n";
String mode = ((CompositeImage) imp).getModeAsString();
s += " Composite mode: \"" + mode + "\"\n";
}
}
if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) s += "No threshold\n";
else {
double lower = ip.getMinThreshold();
double upper = ip.getMaxThreshold();
if (cal.calibrated()) {
lower = cal.getCValue((int) lower);
upper = cal.getCValue((int) upper);
}
s += "Threshold: " + d2s(lower) + "-" + d2s(upper) + "\n";
}
ImageCanvas ic = imp.getCanvas();
double mag = ic != null ? ic.getMagnification() : 1.0;
if (mag != 1.0) s += "Magnification: " + IJ.d2s(mag, 2) + "\n";
if (cal.calibrated()) {
s += " \n";
int curveFit = cal.getFunction();
s += "Calibration function: ";
if (curveFit == Calibration.UNCALIBRATED_OD) s += "Uncalibrated OD\n";
else if (curveFit == Calibration.CUSTOM) s += "Custom lookup table\n";
else s += CurveFitter.fList[curveFit] + "\n";
double[] c = cal.getCoefficients();
if (c != null) {
s += " a: " + IJ.d2s(c[0], 6) + "\n";
s += " b: " + IJ.d2s(c[1], 6) + "\n";
if (c.length >= 3) s += " c: " + IJ.d2s(c[2], 6) + "\n";
if (c.length >= 4) s += " c: " + IJ.d2s(c[3], 6) + "\n";
if (c.length >= 5) s += " c: " + IJ.d2s(c[4], 6) + "\n";
}
s += " Unit: \"" + cal.getValueUnit() + "\"\n";
} else s += "Uncalibrated\n";
FileInfo fi = imp.getOriginalFileInfo();
if (fi != null) {
if (fi.url != null && !fi.url.equals("")) s += "URL: " + fi.url + "\n";
else if (fi.directory != null && fi.fileName != null)
s += "Path: " + fi.directory + fi.fileName + "\n";
}
ImageWindow win = imp.getWindow();
if (win != null) {
Point loc = win.getLocation();
Dimension screen = IJ.getScreenSize();
s +=
"Screen location: "
+ loc.x
+ ","
+ loc.y
+ " ("
+ screen.width
+ "x"
+ screen.height
+ ")\n";
}
String zOrigin = stackSize > 1 || cal.zOrigin != 0.0 ? "," + d2s(cal.zOrigin) : "";
String origin = d2s(cal.xOrigin) + "," + d2s(cal.yOrigin) + zOrigin;
if (!origin.equals("0,0") || cal.getInvertY()) s += "Coordinate origin: " + origin + "\n";
if (cal.getInvertY()) s += "Inverted y coordinates\n";
Overlay overlay = imp.getOverlay();
if (overlay != null) {
String hidden = imp.getHideOverlay() ? " (hidden)" : " ";
int n = overlay.size();
String elements = n == 1 ? " element" : " elements";
s += "Overlay: " + n + elements + (imp.getHideOverlay() ? " (hidden)" : "") + "\n";
} else s += "No overlay\n";
Roi roi = imp.getRoi();
if (roi == null) {
if (cal.calibrated()) s += " \n";
s += "No selection\n";
} else if (roi instanceof EllipseRoi) {
s += "\nElliptical selection\n";
double[] p = ((EllipseRoi) roi).getParams();
double dx = p[2] - p[0];
double dy = p[3] - p[1];
double major = Math.sqrt(dx * dx + dy * dy);
s += " Major: " + IJ.d2s(major, 2) + "\n";
s += " Minor: " + IJ.d2s(major * p[4], 2) + "\n";
s += " X1: " + IJ.d2s(p[0], 2) + "\n";
s += " Y1: " + IJ.d2s(p[1], 2) + "\n";
s += " X2: " + IJ.d2s(p[2], 2) + "\n";
s += " Y2: " + IJ.d2s(p[3], 2) + "\n";
s += " Aspect ratio: " + IJ.d2s(p[4], 2) + "\n";
} else {
s += " \n";
s += roi.getTypeAsString() + " Selection";
String points = null;
if (roi instanceof PointRoi) {
int npoints = ((PolygonRoi) roi).getNCoordinates();
String suffix = npoints > 1 ? "s)" : ")";
points = " (" + npoints + " point" + suffix;
}
String name = roi.getName();
if (name != null) {
s += " (\"" + name + "\")";
if (points != null) s += "\n " + points;
} else if (points != null) s += points;
s += "\n";
Rectangle r = roi.getBounds();
if (roi instanceof Line) {
Line line = (Line) roi;
s += " X1: " + IJ.d2s(line.x1d * cal.pixelWidth) + "\n";
s += " Y1: " + IJ.d2s(yy(line.y1d, imp) * cal.pixelHeight) + "\n";
s += " X2: " + IJ.d2s(line.x2d * cal.pixelWidth) + "\n";
s += " Y2: " + IJ.d2s(yy(line.y2d, imp) * cal.pixelHeight) + "\n";
} else if (cal.scaled()) {
s += " X: " + IJ.d2s(cal.getX(r.x)) + " (" + r.x + ")\n";
s += " Y: " + IJ.d2s(cal.getY(r.y, imp.getHeight())) + " (" + r.y + ")\n";
s += " Width: " + IJ.d2s(r.width * cal.pixelWidth) + " (" + r.width + ")\n";
s += " Height: " + IJ.d2s(r.height * cal.pixelHeight) + " (" + r.height + ")\n";
} else {
s += " X: " + r.x + "\n";
s += " Y: " + yy(r.y, imp) + "\n";
s += " Width: " + r.width + "\n";
s += " Height: " + r.height + "\n";
}
}
return s;
}