private void openDirectory(File f, String path) {
if (path == null) return;
if (!(path.endsWith(File.separator) || path.endsWith("/"))) path += File.separator;
String[] names = f.list();
names = (new FolderOpener()).trimFileList(names);
if (names == null) return;
String msg = "Open all " + names.length + " images in \"" + f.getName() + "\" as a stack?";
GenericDialog gd = new GenericDialog("Open Folder");
gd.setInsets(10, 5, 0);
gd.addMessage(msg);
gd.setInsets(15, 35, 0);
gd.addCheckbox("Convert to RGB", convertToRGB);
gd.setInsets(0, 35, 0);
gd.addCheckbox("Use Virtual Stack", virtualStack);
gd.enableYesNoCancel();
gd.showDialog();
if (gd.wasCanceled()) return;
if (gd.wasOKed()) {
convertToRGB = gd.getNextBoolean();
virtualStack = gd.getNextBoolean();
String options = " sort";
if (convertToRGB) options += " convert_to_rgb";
if (virtualStack) options += " use";
IJ.run("Image Sequence...", "open=[" + path + "]" + options);
DirectoryChooser.setDefaultDirectory(path);
} else {
for (int k = 0; k < names.length; k++) {
IJ.redirectErrorMessages();
if (!names[k].startsWith(".")) (new Opener()).open(path + names[k]);
}
}
IJ.register(DragAndDrop.class);
}
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;
}
void addSelection() {
ImagePlus imp = IJ.getImage();
String macroOptions = Macro.getOptions();
if (macroOptions != null && IJ.macroRunning() && macroOptions.indexOf("remove") != -1) {
imp.setOverlay(null);
return;
}
Roi roi = imp.getRoi();
if (roi == null && imp.getOverlay() != null) {
GenericDialog gd = new GenericDialog("No Selection");
gd.addMessage("\"Overlay>Add\" requires a selection.");
gd.setInsets(15, 40, 0);
gd.addCheckbox("Remove existing overlay", false);
gd.showDialog();
if (gd.wasCanceled()) return;
if (gd.getNextBoolean()) imp.setOverlay(null);
return;
}
if (roi == null) {
IJ.error("This command requires a selection.");
return;
}
roi = (Roi) roi.clone();
if (roi.getStrokeColor() == null) roi.setStrokeColor(Toolbar.getForegroundColor());
int width = Line.getWidth();
Rectangle bounds = roi.getBounds();
boolean tooWide = width > Math.max(bounds.width, bounds.height) / 3.0;
if (roi.getStroke() == null && width > 1 && !tooWide) roi.setStrokeWidth(Line.getWidth());
Overlay overlay = imp.getOverlay();
if (overlay != null && overlay.size() > 0 && !roi.isDrawingTool()) {
Roi roi2 = overlay.get(overlay.size() - 1);
if (roi.getStroke() == null) roi.setStrokeWidth(roi2.getStrokeWidth());
if (roi.getFillColor() == null) roi.setFillColor(roi2.getFillColor());
}
boolean points = roi instanceof PointRoi && ((PolygonRoi) roi).getNCoordinates() > 1;
if (points) roi.setStrokeColor(Color.red);
if (!IJ.altKeyDown() && !(roi instanceof Arrow)) {
RoiProperties rp = new RoiProperties("Add to Overlay", roi);
if (!rp.showDialog()) return;
}
String name = roi.getName();
boolean newOverlay = name != null && name.equals("new-overlay");
if (overlay == null || newOverlay) overlay = new Overlay();
overlay.add(roi);
imp.setOverlay(overlay);
overlay2 = overlay;
if (points || (roi instanceof ImageRoi) || (roi instanceof Arrow)) imp.killRoi();
Undo.setup(Undo.OVERLAY_ADDITION, imp);
}
int showDialog(String[] versions) {
GenericDialog gd = new GenericDialog("ImageJ Updater");
gd.addChoice("Upgrade To:", versions, versions[0]);
String msg =
"You are currently running v"
+ version()
+ ".\n"
+ " \n"
+ "If you click \"OK\", ImageJ will quit\n"
+ "and you will be running the upgraded\n"
+ "version after you restart ImageJ.\n";
gd.addMessage(msg);
gd.showDialog();
if (gd.wasCanceled()) return -1;
else return gd.getNextChoiceIndex();
}
// DICOM options
void dicom() {
GenericDialog gd = new GenericDialog("DICOM Options");
gd.addCheckbox("Open as 32-bit float", Prefs.openDicomsAsFloat);
// gd.addCheckbox("Calculate voxel depth", Prefs.calculateDicomVoxelDepth);
gd.addMessage("Orthogonal Views");
gd.setInsets(5, 40, 0);
gd.addCheckbox("Rotate YZ", Prefs.rotateYZ);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Flip XZ", Prefs.flipXZ);
gd.showDialog();
if (gd.wasCanceled()) return;
Prefs.openDicomsAsFloat = gd.getNextBoolean();
// Prefs.calculateDicomVoxelDepth = gd.getNextBoolean();
Prefs.rotateYZ = gd.getNextBoolean();
Prefs.flipXZ = gd.getNextBoolean();
}
// Input/Output options
void io() {
GenericDialog gd = new GenericDialog("I/O Options");
gd.addNumericField("JPEG quality (0-100):", FileSaver.getJpegQuality(), 0, 3, "");
gd.addNumericField("GIF and PNG transparent index:", Prefs.getTransparentIndex(), 0, 3, "");
gd.addStringField(
"File extension for tables (.txt, .xls or .csv):", Prefs.get("options.ext", ".csv"), 4);
gd.addCheckbox("Use JFileChooser to open/save", Prefs.useJFileChooser);
if (!IJ.isMacOSX())
gd.addCheckbox("Use_file chooser to import sequences", Prefs.useFileChooser);
gd.addCheckbox("Save TIFF and raw in Intel byte order", Prefs.intelByteOrder);
gd.addCheckbox("Skip dialog when opening .raw files", Prefs.skipRawDialog);
gd.setInsets(15, 20, 0);
gd.addMessage("Results Table Options");
gd.setInsets(3, 40, 0);
gd.addCheckbox("Copy_column headers", Prefs.copyColumnHeaders);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Copy_row numbers", !Prefs.noRowNumbers);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Save_column headers", !Prefs.dontSaveHeaders);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Save_row numbers", !Prefs.dontSaveRowNumbers);
gd.showDialog();
if (gd.wasCanceled()) return;
int quality = (int) gd.getNextNumber();
if (quality < 0) quality = 0;
if (quality > 100) quality = 100;
FileSaver.setJpegQuality(quality);
int transparentIndex = (int) gd.getNextNumber();
Prefs.setTransparentIndex(transparentIndex);
String extension = gd.getNextString();
if (!extension.startsWith(".")) extension = "." + extension;
Prefs.set("options.ext", extension);
Prefs.useJFileChooser = gd.getNextBoolean();
if (!IJ.isMacOSX()) Prefs.useFileChooser = gd.getNextBoolean();
Prefs.intelByteOrder = gd.getNextBoolean();
Prefs.skipRawDialog = gd.getNextBoolean();
Prefs.copyColumnHeaders = gd.getNextBoolean();
Prefs.noRowNumbers = !gd.getNextBoolean();
Prefs.dontSaveHeaders = !gd.getNextBoolean();
Prefs.dontSaveRowNumbers = !gd.getNextBoolean();
return;
}
void checkForCalibrationConflict(ImagePlus imp, Calibration cal) {
Calibration gcal = imp.getGlobalCalibration();
if (gcal == null || !showConflictMessage || IJ.isMacro()) return;
if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return;
GenericDialog gd = new GenericDialog(imp.getTitle());
gd.addMessage("The calibration of this image conflicts\nwith the current global calibration.");
gd.addCheckbox("Disable_Global Calibration", true);
gd.addCheckbox("Disable_these Messages", false);
gd.showDialog();
if (gd.wasCanceled()) return;
boolean disable = gd.getNextBoolean();
if (disable) {
imp.setGlobalCalibration(null);
imp.setCalibration(cal);
WindowManager.repaintImageWindows();
}
boolean dontShow = gd.getNextBoolean();
if (dontShow) showConflictMessage = false;
}
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;
}
/** 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 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;
}
}
}
}