public boolean beadCalibration3d() {
imp = IJ.getImage();
if (imp == null) {
IJ.noImage();
return false;
} else if (imp.getStackSize() == 1) {
IJ.error("Stack required");
return false;
} else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) {
// In order to support 32bit images, pict[] must be changed to float[], and getPixel(x, y);
// requires a Float.intBitsToFloat() conversion
IJ.error("8 or 16 bit greyscale image required");
return false;
}
width = imp.getWidth();
height = imp.getHeight();
nslices = imp.getStackSize();
imtitle = imp.getTitle();
models[0] = "*None*";
models[1] = "line";
models[2] = "2nd degree polynomial";
models[3] = "3rd degree polynomial";
models[4] = "4th degree polynomial";
GenericDialog gd = new GenericDialog("3D PALM calibration");
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0);
gd.addNumericField(
"Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0);
gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2);
gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0);
gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3]));
gd.addCheckbox(
"Show divergence of bead positions against model",
prefs.get("QuickPALM.3Dcal_showDivergence", false));
gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false));
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.pthrsh", pthrsh * 100);
cal_z = gd.getNextNumber();
prefs.set("QuickPALM.z-step", cal_z);
window = (int) gd.getNextNumber();
prefs.set("QuickPALM.window", window);
model = gd.getNextChoice();
prefs.set("QuickPALM.model", model);
part_divergence = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence);
part_extrainfo = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo);
return true;
}
/** Ask for parameters and then execute. */
public void run(String arg) {
// 1 - Obtain the currently active image:
ImagePlus imp = IJ.getImage();
if (null == imp) {
IJ.showMessage("There must be at least one image open");
return;
}
if (imp.getBitDepth() != 8) {
IJ.showMessage("Error", "Only 8-bit images are supported");
return;
}
// 2 - Ask for parameters:
GenericDialog gd = new GenericDialog("Auto Local Threshold");
String[] methods = {
"Try all",
"Bernsen",
"Contrast",
"Mean",
"Median",
"MidGrey",
"Niblack",
"Otsu",
"Phansalkar",
"Sauvola"
};
gd.addMessage("Auto Local Threshold v1.5");
gd.addChoice("Method", methods, methods[0]);
gd.addNumericField("Radius", 15, 0);
gd.addMessage("Special paramters (if different from default)");
gd.addNumericField("Parameter_1", 0, 0);
gd.addNumericField("Parameter_2", 0, 0);
gd.addCheckbox("White objects on black background", true);
if (imp.getStackSize() > 1) {
gd.addCheckbox("Stack", false);
}
gd.addMessage("Thresholded result is always shown in white [255].");
gd.showDialog();
if (gd.wasCanceled()) return;
// 3 - Retrieve parameters from the dialog
String myMethod = gd.getNextChoice();
int radius = (int) gd.getNextNumber();
double par1 = (double) gd.getNextNumber();
double par2 = (double) gd.getNextNumber();
boolean doIwhite = gd.getNextBoolean();
boolean doIstack = false;
int stackSize = imp.getStackSize();
if (stackSize > 1) doIstack = gd.getNextBoolean();
// 4 - Execute!
// long start = System.currentTimeMillis();
if (myMethod.equals("Try all")) {
ImageProcessor ip = imp.getProcessor();
int xe = ip.getWidth();
int ye = ip.getHeight();
int ml = methods.length;
ImagePlus imp2, imp3;
ImageStack tstack = null, stackNew;
if (stackSize > 1 && doIstack) {
boolean doItAnyway = true;
if (stackSize > 25) {
YesNoCancelDialog d =
new YesNoCancelDialog(
IJ.getInstance(),
"Auto Local Threshold",
"You might run out of memory.\n \nDisplay "
+ stackSize
+ " slices?\n \n \'No\' will process without display and\noutput results to the log window.");
if (!d.yesPressed()) {
// doIlog=true; //will show in the log window
doItAnyway = false;
}
if (d.cancelPressed()) return;
}
for (int j = 1; j <= stackSize; j++) {
imp.setSlice(j);
ip = imp.getProcessor();
tstack = new ImageStack(xe, ye);
for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate());
imp2 = new ImagePlus("Auto Threshold", tstack);
imp2.updateAndDraw();
for (int k = 1; k < ml; k++) {
imp2.setSlice(k);
Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite);
}
// if (doItAnyway){
CanvasResizer cr = new CanvasResizer();
stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1);
imp3 = new ImagePlus("Auto Threshold", stackNew);
imp3.updateAndDraw();
MontageMaker mm = new MontageMaker();
mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true); // 3 columns and 3 rows
}
imp.setSlice(1);
// if (doItAnyway)
IJ.run("Images to Stack", "method=[Copy (center)] title=Montage");
return;
} else { // single image try all
tstack = new ImageStack(xe, ye);
for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate());
imp2 = new ImagePlus("Auto Threshold", tstack);
imp2.updateAndDraw();
for (int k = 1; k < ml; k++) {
imp2.setSlice(k);
// IJ.log("analyzing slice with "+methods[k]);
Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite);
}
// imp2.setSlice(1);
CanvasResizer cr = new CanvasResizer();
stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1);
imp3 = new ImagePlus("Auto Threshold", stackNew);
imp3.updateAndDraw();
MontageMaker mm = new MontageMaker();
mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true);
return;
}
} else { // selected a method
if (stackSize > 1 && doIstack) { // whole stack
// if (doIstackHistogram) {// one global histogram
// Object[] result = exec(imp, myMethod, noWhite, noBlack, doIwhite, doIset, doIlog,
// doIstackHistogram );
// }
// else{ // slice by slice
for (int k = 1; k <= stackSize; k++) {
imp.setSlice(k);
Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite);
}
// }
imp.setSlice(1);
} else { // just one slice
Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite);
}
// 5 - If all went well, show the image:
// not needed here as the source image is binarised
}
}
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;
}