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;
}
/** 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);
}
public boolean analyseParticles(MyFunctions f) {
GenericDialog gd = new GenericDialog("Analyse PALM/STORM Particles");
gd.addNumericField("Minimum SNR", prefs.get("QuickPALM.snr", 5), 2);
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.fwhm", 4), 0);
gd.addNumericField("Image plane pixel size (nm)", prefs.get("QuickPALM.pixelsize", 106), 2);
gd.addCheckbox("Smart SNR", prefs.get("QuickPALM.smartsnr", true));
gd.addCheckbox(
"3D PALM (astigmatism) - will require calibration file",
prefs.get("QuickPALM.is3d", false));
gd.addCheckbox("Online rendering", prefs.get("QuickPALM.view", true));
gd.addCheckbox("Attach to running acquisition", prefs.get("QuickPALM.attach", false));
gd.addCheckbox("Stream particle info directly into file", prefs.get("QuickPALM.stream", true));
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Online rendering settings (used only if selected) --");
gd.addMessage("\n");
gd.addNumericField("Pixel size of rendered image (nm)", 30, 2);
gd.addNumericField("Accumulate last (0 to accumulate all frames)", 0, 0);
gd.addNumericField("Update every (frames)", 10, 0);
// gd.addNumericField("Allow color saturation (%)", 50, 0);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Attach to running acquisition settings (used only if selected) --");
gd.addMessage("\n");
gd.addStringField(
"_Image name pattern (NN...NN represents the numerical change)",
prefs.get("QuickPALM.pattern", "imgNNNNNNNNN.tif"),
20);
gd.addNumericField("Start NN...NN with", 0, 0);
gd.addNumericField("In acquisition max. wait time for new image (ms)", 50, 0);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Advanced settings (don't normally need to be changed) --");
gd.addMessage("\n");
gd.addNumericField("_Minimum symmetry (%)", prefs.get("QuickPALM.symmetry", 50), 0);
gd.addNumericField(
"Local threshold (% maximum intensity)", prefs.get("QuickPALM.lthreshold", 20), 0);
gd.addNumericField("_Maximum iterations per frame", prefs.get("QuickPALM.maxiter", 1000), 0);
gd.addNumericField(
"Threads (each takes ~3*[frame size] in memory)", prefs.get("QuickPALM.nthreads", 50), 0);
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
snr = (int) gd.getNextNumber();
prefs.set("QuickPALM.snr", snr);
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.fwhm", fwhm);
pixelsize = gd.getNextNumber();
prefs.set("QuickPALM.pixelsize", pixelsize);
smartsnr = gd.getNextBoolean();
prefs.set("QuickPALM.smartsnr", smartsnr);
is3d = gd.getNextBoolean();
prefs.set("QuickPALM.is3d", is3d);
view = gd.getNextBoolean();
prefs.set("QuickPALM.view", view);
attach = gd.getNextBoolean();
prefs.set("QuickPALM.attach", attach);
if (gd.getNextBoolean()) {
f.psave = new ParticleSaver();
f.psave.setup();
prefs.set("QuickPALM.stream", true);
} else prefs.set("QuickPALM.stream", false);
// --
magn = pixelsize / gd.getNextNumber();
viewer_accumulate = (int) gd.getNextNumber();
viewer_update = (int) gd.getNextNumber();
// --
pattern = gd.getNextString().trim();
prefs.set("QuickPALM.pattern", pattern);
prefix = pattern.substring(0, pattern.indexOf("N"));
sufix = pattern.substring(pattern.lastIndexOf("N") + 1, pattern.length());
nimchars = pattern.split("N").length - 1;
nimstart = (int) gd.getNextNumber();
waittime = (int) gd.getNextNumber();
// --
symmetry = gd.getNextNumber() / 100;
prefs.set("QuickPALM.symmetry", symmetry);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.lthreshold", pthrsh * 100);
maxpart = (int) gd.getNextNumber();
prefs.set("QuickPALM.maxiter", maxpart);
threads = (int) gd.getNextNumber();
prefs.set("QuickPALM.nthreads", threads);
return true;
}
public boolean reconstructDataset() {
view_modes[0] = "3D color";
view_modes[1] = "2D histogram";
view_modes[2] = "2D particle intensity (16-bit)";
view_modes[3] = "2D particle intensity (8-bit)";
GenericDialog gd = new GenericDialog("Reconstruct PALM/STORM Dataset");
gd.addNumericField(
"Target pixel size for the rendered image (nm)",
prefs.get("QuickPALM.viewer_tpixelsize", 30),
2);
gd.addNumericField("Original image width (px)", prefs.get("QuickPALM.viewer_owidth", 512), 2);
gd.addNumericField("Original image height (px)", prefs.get("QuickPALM.viewer_oheight", 512), 2);
gd.addChoice("View mode", view_modes, prefs.get("QuickPALM.view_mode", view_modes[1]));
// gd.addNumericField("Allow image saturation (%)", prefs.get("QuickPALM.saturation", 50), 0);
gd.addCheckbox(
"Simulate sub-difraction spot (gaussian convolution - only 2D)",
prefs.get("QuickPALM.viewer_doConvolve", true));
// gd.addCheckbox("Make 3D stack", prefs.get("QuickPALM.viewer_do3d", false));
// gd.addCheckbox("Make movie", prefs.get("QuickPALM.viewer_doMovie", false));
gd.addCheckbox("Make 3D stack", false);
gd.addCheckbox("Make movie", false);
// gd.addCheckbox("Save only and don't show", prefs.get("QuickPALM.viewer_doSave", false));
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Simulate sub-difraction spot settings (used only if selected) --");
gd.addNumericField("FWHM of the spot", prefs.get("QuickPALM.viewer_fwhm", 30), 2);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Make 3D stack settings (used only if selected) --");
gd.addNumericField("Z-spacing between slices (nm)", prefs.get("QuickPALM.viewer_zstep", 50), 2);
gd.addNumericField(
"Merge particle Z-position above (nm - 0 for full Z range)",
prefs.get("QuickPALM.viewer_mergeabove", 0),
2);
gd.addNumericField(
"Merge particle Z-position bellow (nm - 0 for full Z range)",
prefs.get("QuickPALM.viewer_mergebellow", 0),
2);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Make movie settings (used only if selected) --");
gd.addNumericField(
"Make a reconstruction in every N frames", prefs.get("QuickPALM.viewer_update", 10), 0);
gd.addNumericField(
"Accumulate N neighboring frames for each reconstruction\n(set to 0 to accumulate all the preceding frames)",
prefs.get("QuickPALM.viewer_accumulate", 100),
0);
gd.showDialog();
if (gd.wasCanceled()) return false;
viewer_tpixelsize = gd.getNextNumber();
prefs.set("QuickPALM.viewer_tpixelsize", viewer_tpixelsize);
viewer_owidth = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_owidth", viewer_owidth);
viewer_oheight = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_oheight", viewer_oheight);
view_mode = gd.getNextChoice();
prefs.set("QuickPALM.view_mode", view_mode);
viewer_doConvolve = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_doConvolve", viewer_doConvolve);
viewer_do3d = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_do3d", viewer_do3d);
viewer_doMovie = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_doMovie", viewer_doMovie);
// viewer_doSave = gd.getNextBoolean();
// prefs.set("QuickPALM.viewer_doSave", viewer_doSave);
// -- Simulate sub-difraction spot
viewer_fwhm = gd.getNextNumber();
prefs.set("QuickPALM.viewer_fwhm", viewer_fwhm);
// -- Show B&W
// viewer_is8bit = gd.getNextBoolean();
// prefs.set("QuickPALM.viewer_is8bit", viewer_is8bit);
// -- Make 3D stack
viewer_zstep = gd.getNextNumber();
prefs.set("QuickPALM.viewer_zstep", viewer_zstep);
viewer_mergeabove = gd.getNextNumber();
prefs.set("QuickPALM.viewer_mergeabove", viewer_mergeabove);
viewer_mergebellow = gd.getNextNumber();
prefs.set("QuickPALM.viewer_mergebellow", viewer_mergebellow);
// -- Make Movie
viewer_update = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_update", viewer_update);
viewer_accumulate = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_accumulate", viewer_accumulate);
return true;
}