void interpolate() {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Interpolate");
return;
}
if (roi.getType() == Roi.POINT) return;
if (IJ.isMacro() && Macro.getOptions() == null) Macro.setOptions("interval=1");
GenericDialog gd = new GenericDialog("Interpolate");
gd.addNumericField("Interval:", 1.0, 1, 4, "pixel");
gd.addCheckbox("Smooth", IJ.isMacro() ? false : smooth);
gd.showDialog();
if (gd.wasCanceled()) return;
double interval = gd.getNextNumber();
smooth = gd.getNextBoolean();
Undo.setup(Undo.ROI, imp);
FloatPolygon poly = roi.getInterpolatedPolygon(interval, smooth);
int t = roi.getType();
int type = roi.isLine() ? Roi.FREELINE : Roi.FREEROI;
if (t == Roi.POLYGON && interval > 1.0) type = Roi.POLYGON;
if ((t == Roi.RECTANGLE || t == Roi.OVAL || t == Roi.FREEROI) && interval >= 5.0)
type = Roi.POLYGON;
if ((t == Roi.LINE || t == Roi.FREELINE) && interval >= 5.0) type = Roi.POLYLINE;
if (t == Roi.POLYLINE && interval >= 1.0) type = Roi.POLYLINE;
ImageCanvas ic = imp.getCanvas();
if (poly.npoints <= 150 && ic != null && ic.getMagnification() >= 12.0)
type = roi.isLine() ? Roi.POLYLINE : Roi.POLYGON;
Roi p = new PolygonRoi(poly, type);
if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth());
p.setStrokeColor(roi.getStrokeColor());
p.setName(roi.getName());
transferProperties(roi, p);
imp.setRoi(p);
}
void fitSpline() {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Spline");
return;
}
int type = roi.getType();
boolean segmentedSelection = type == Roi.POLYGON || type == Roi.POLYLINE;
if (!(segmentedSelection
|| type == Roi.FREEROI
|| type == Roi.TRACED_ROI
|| type == Roi.FREELINE)) {
IJ.error("Spline", "Polygon or polyline selection required");
return;
}
if (roi instanceof EllipseRoi) return;
PolygonRoi p = (PolygonRoi) roi;
if (!segmentedSelection) {
if (p.subPixelResolution()) p = trimFloatPolygon(p, p.getUncalibratedLength());
else p = trimPolygon(p, p.getUncalibratedLength());
}
String options = Macro.getOptions();
if (options != null && options.indexOf("straighten") != -1) p.fitSplineForStraightening();
else if (options != null && options.indexOf("remove") != -1) p.removeSplineFit();
else p.fitSpline();
imp.draw();
LineWidthAdjuster.update();
}
void createEllipse(ImagePlus imp) {
IJ.showStatus("Fitting ellipse");
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Fit Ellipse");
return;
}
if (roi.isLine()) {
IJ.error("Fit Ellipse", "\"Fit Ellipse\" does not work with line selections");
return;
}
ImageProcessor ip = imp.getProcessor();
ip.setRoi(roi);
int options = Measurements.CENTROID + Measurements.ELLIPSE;
ImageStatistics stats = ImageStatistics.getStatistics(ip, options, null);
double dx = stats.major * Math.cos(stats.angle / 180.0 * Math.PI) / 2.0;
double dy = -stats.major * Math.sin(stats.angle / 180.0 * Math.PI) / 2.0;
double x1 = stats.xCentroid - dx;
double x2 = stats.xCentroid + dx;
double y1 = stats.yCentroid - dy;
double y2 = stats.yCentroid + dy;
double aspectRatio = stats.minor / stats.major;
imp.killRoi();
imp.setRoi(new EllipseRoi(x1, y1, x2, y2, aspectRatio));
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
Undo.setup(Undo.ROI, imp);
Roi roi2 = null;
if (roi.getType() == Roi.LINE) {
double width = roi.getStrokeWidth();
if (width <= 1.0) roi.setStrokeWidth(1.0000001);
FloatPolygon p = roi.getFloatPolygon();
roi.setStrokeWidth(width);
roi2 = new PolygonRoi(p, Roi.POLYGON);
roi2.setDrawOffset(roi.getDrawOffset());
} else {
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
roi.drawPixels(ip2);
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
roi2 = tts.convert(ip2);
}
transferProperties(roi, roi2);
roi2.setStrokeWidth(0);
Color c = roi2.getStrokeColor();
if (c != null) // remove any transparency
roi2.setStrokeColor(new Color(c.getRed(), c.getGreen(), c.getBlue()));
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
if (roi.getType() == Roi.LINE && roi.getStrokeWidth() == 1) {
IJ.error("Line to Area", "Straight line width must be > 1");
return;
}
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
if (roi.getType() == Roi.LINE) ip2.fillPolygon(roi.getPolygon());
else {
roi.drawPixels(ip2);
// BufferedImage bi = new BufferedImage(imp.getWidth(), imp.getHeight(),
// BufferedImage.TYPE_BYTE_GRAY);
// Graphics g = bi.getGraphics();
// Roi roi2 = (Roi)roi.clone();
// roi2.setStrokeColor(Color.white);
// roi2.drawOverlay(g);
// ip2 = new ByteProcessor(bi);
}
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
Roi roi2 = tts.convert(ip2);
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
void toBoundingBox(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("To Bounding Box");
return;
}
Rectangle r = roi.getBounds();
imp.killRoi();
imp.setRoi(new Roi(r.x, r.y, r.width, r.height));
}
private boolean ignoreArrowKeys(ImagePlus imp) {
Frame frame = WindowManager.getFrontWindow();
String title = frame.getTitle();
if (title != null && title.equals("ROI Manager")) return true;
// Control Panel?
if (frame != null && frame instanceof javax.swing.JFrame) return true;
ImageWindow win = imp.getWindow();
// LOCI Data Browser window?
if (imp.getStackSize() > 1 && win != null && win.getClass().getName().startsWith("loci"))
return true;
return false;
}
void invert(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isArea()) {
IJ.error("Inverse", "Area selection required");
return;
}
ShapeRoi s1, s2;
if (roi instanceof ShapeRoi) s1 = (ShapeRoi) roi;
else s1 = new ShapeRoi(roi);
s2 = new ShapeRoi(new Roi(0, 0, imp.getWidth(), imp.getHeight()));
imp.setRoi(s1.xor(s2));
}
void toBoundingBox(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("To Bounding Box");
return;
}
Undo.setup(Undo.ROI, imp);
Rectangle r = roi.getBounds();
imp.deleteRoi();
Roi roi2 = new Roi(r.x, r.y, r.width, r.height);
transferProperties(roi, roi2);
imp.setRoi(roi2);
}
void createMaskFromThreshold(ImagePlus imp) {
ImageProcessor ip = imp.getProcessor();
if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) {
IJ.error("Create Mask", "Area selection or thresholded image required");
return;
}
double t1 = ip.getMinThreshold();
double t2 = ip.getMaxThreshold();
IJ.run("Duplicate...", "title=mask");
ImagePlus imp2 = WindowManager.getCurrentImage();
ImageProcessor ip2 = imp2.getProcessor();
ip2.setThreshold(t1, t2, ImageProcessor.NO_LUT_UPDATE);
IJ.run("Convert to Mask");
}
void convexHull(ImagePlus imp) {
Roi roi = imp.getRoi();
int type = roi != null ? roi.getType() : -1;
if (!(type == Roi.FREEROI
|| type == Roi.TRACED_ROI
|| type == Roi.POLYGON
|| type == Roi.POINT)) {
IJ.error("Convex Hull", "Polygonal or point selection required");
return;
}
if (roi instanceof EllipseRoi) return;
Polygon p = roi.getConvexHull();
if (p != null) imp.setRoi(new PolygonRoi(p.xpoints, p.ypoints, p.npoints, roi.POLYGON));
}
void addToRoiManager(ImagePlus imp) {
if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
if (imp == null) return;
Roi roi = imp.getRoi();
if (roi == null) return;
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
RoiManager rm = (RoiManager) frame;
boolean altDown = IJ.altKeyDown();
IJ.setKeyUp(IJ.ALL_KEYS);
if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
if (roi.getState() == Roi.CONSTRUCTING) { // wait (up to 2 sec.) until ROI finished
long start = System.currentTimeMillis();
while (true) {
IJ.wait(10);
if (roi.getState() != Roi.CONSTRUCTING) break;
if ((System.currentTimeMillis() - start) > 2000) {
IJ.beep();
IJ.error("Add to Manager", "Selection is not complete");
return;
}
}
}
rm.runCommand("add");
IJ.setKeyUp(IJ.ALL_KEYS);
}
void runMacro(String arg) {
Roi roi = imp.getRoi();
if (IJ.macroRunning()) {
String options = Macro.getOptions();
if (options != null
&& (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) {
IJ.run("Rotate... ", options); // run Image>Transform>Rotate
return;
}
}
if (roi == null) {
noRoi("Rotate>Selection");
return;
}
roi = (Roi) roi.clone();
if (arg.equals("rotate")) {
double d = Tools.parseDouble(angle);
if (Double.isNaN(d)) angle = "15";
String value = IJ.runMacroFile("ij.jar:RotateSelection", angle);
if (value != null) angle = value;
} else if (arg.equals("enlarge")) {
String value = IJ.runMacroFile("ij.jar:EnlargeSelection", enlarge);
if (value != null) enlarge = value;
Roi.previousRoi = roi;
}
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
if (roi.getType() == Roi.LINE && roi.getStrokeWidth() > 1) ip2.fillPolygon(roi.getPolygon());
else roi.drawPixels(ip2);
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
Roi roi2 = tts.convert(ip2);
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
private void enlarge(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi != null) {
Undo.setup(Undo.ROI, imp);
roi = (Roi) roi.clone();
(new RoiEnlarger()).run("");
} else noRoi("Enlarge");
}
void createMask(ImagePlus imp) {
Roi roi = imp.getRoi();
boolean useInvertingLut = Prefs.useInvertingLut;
Prefs.useInvertingLut = false;
if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT)) {
createMaskFromThreshold(imp);
Prefs.useInvertingLut = useInvertingLut;
return;
}
ImagePlus maskImp = null;
Frame frame = WindowManager.getFrame("Mask");
if (frame != null && (frame instanceof ImageWindow))
maskImp = ((ImageWindow) frame).getImagePlus();
if (maskImp == null) {
ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
if (!Prefs.blackBackground) ip.invertLut();
maskImp = new ImagePlus("Mask", ip);
maskImp.show();
}
ImageProcessor ip = maskImp.getProcessor();
ip.setRoi(roi);
ip.setValue(255);
ip.fill(ip.getMask());
maskImp.updateAndDraw();
Prefs.useInvertingLut = useInvertingLut;
}
public void run(String arg) {
imp = WindowManager.getCurrentImage();
if (arg.equals("add")) {
addToRoiManager(imp);
return;
}
if (imp == null) {
IJ.noImage();
return;
}
if (arg.equals("all")) imp.setRoi(0, 0, imp.getWidth(), imp.getHeight());
else if (arg.equals("none")) imp.killRoi();
else if (arg.equals("restore")) imp.restoreRoi();
else if (arg.equals("spline")) fitSpline();
else if (arg.equals("circle")) fitCircle(imp);
else if (arg.equals("ellipse")) createEllipse(imp);
else if (arg.equals("hull")) convexHull(imp);
else if (arg.equals("mask")) createMask(imp);
else if (arg.equals("from")) createSelectionFromMask(imp);
else if (arg.equals("inverse")) invert(imp);
else if (arg.equals("toarea")) lineToArea(imp);
else if (arg.equals("toline")) areaToLine(imp);
else if (arg.equals("properties")) {
setProperties("Properties ", imp.getRoi());
imp.draw();
} else if (arg.equals("band")) makeBand(imp);
else if (arg.equals("tobox")) toBoundingBox(imp);
else runMacro(arg);
}
// Finds the index of the upper right point that is guaranteed to be on convex hull
int findFirstPoint(int[] xCoordinates, int[] yCoordinates, int n, ImagePlus imp) {
int smallestY = imp.getHeight();
int x, y;
for (int i = 0; i < n; i++) {
y = yCoordinates[i];
if (y < smallestY) smallestY = y;
}
int smallestX = imp.getWidth();
int p1 = 0;
for (int i = 0; i < n; i++) {
x = xCoordinates[i];
y = yCoordinates[i];
if (y == smallestY && x < smallestX) {
smallestX = x;
p1 = i;
}
}
return p1;
}
public void run(String arg) {
ImagePlus imp = WindowManager.getImage(id);
if (imp != null && imp.getWindow() != null) {
imp.getWindow().toFront();
return;
}
int colorWidth = 22;
int colorHeight = 16;
int columns = 5;
int rows = 20;
int width = columns * colorWidth;
int height = rows * colorHeight;
ColorGenerator cg = new ColorGenerator(width, height, new int[width * height], this);
cg.drawColors(colorWidth, colorHeight, columns, rows);
setProcessor("CP", cg);
id = getID();
show();
IJ.register(ColorPicker.class);
}
private boolean showDialog() {
String[] types = {"RAW", "JPEG", "ZLIB"};
GenericDialog gd = new GenericDialog("Generate Bricks");
gd.addChoice("FileType", types, filetype);
gd.addNumericField("JPEG quality", jpeg_quality, 0);
gd.addNumericField("Max file size (MB)", bdsizelimit, 0);
int[] wlist = WindowManager.getIDList();
if (wlist == null) return false;
String[] titles = new String[wlist.length];
for (int i = 0; i < wlist.length; i++) titles[i] = "";
int tnum = 0;
for (int i = 0; i < wlist.length; i++) {
ImagePlus imp = WindowManager.getImage(wlist[i]);
if (imp != null) {
titles[tnum] = imp.getTitle();
tnum++;
}
}
gd.addChoice("Source image: ", titles, titles[0]);
gd.showDialog();
if (gd.wasCanceled()) return false;
filetype = types[gd.getNextChoiceIndex()];
jpeg_quality = (int) gd.getNextNumber();
if (jpeg_quality > 100) jpeg_quality = 100;
if (jpeg_quality < 0) jpeg_quality = 0;
bdsizelimit = (int) gd.getNextNumber();
int id = gd.getNextChoiceIndex();
lvImgTitle = new ArrayList<String>();
lvImgTitle.add(titles[id]);
Prefs.set("filetype.string", filetype);
Prefs.set("jpeg_quality.int", jpeg_quality);
Prefs.set("bdsizelimit.int", bdsizelimit);
return true;
}
private boolean deleteOverlayRoi(ImagePlus imp) {
if (imp == null) return false;
Overlay overlay = null;
ImageCanvas ic = imp.getCanvas();
if (ic != null) overlay = ic.getShowAllList();
if (overlay == null) overlay = imp.getOverlay();
if (overlay == null) return false;
Roi roi = imp.getRoi();
for (int i = 0; i < overlay.size(); i++) {
Roi roi2 = overlay.get(i);
if (roi2 == roi) {
overlay.remove(i);
imp.deleteRoi();
ic = imp.getCanvas();
if (ic != null) ic.roiManagerSelect(roi, true);
return true;
}
}
return false;
}
public void refreshBackground() {
// Boundary for Background Selection
setColor(0x444444);
drawRect((w * 2) - 12, 276, (w * 2) + 4, (h * 2) + 4);
setColor(0x999999);
drawRect((w * 2) - 11, 277, (w * 2) + 2, (h * 2) + 2);
setRoi((w * 2) - 10, 278, w * 2, h * 2); // Paints the Background Color
setColor(Toolbar.getBackgroundColor());
fill();
imp.updateAndDraw();
}
public void refreshForeground() {
// Boundary for Foreground Selection
setColor(0x444444);
drawRect(8, 266, (w * 2) + 4, (h * 2) + 4);
setColor(0x999999);
drawRect(9, 267, (w * 2) + 2, (h * 2) + 2);
setRoi(10, 268, w * 2, h * 2); // Paints the Foreground Color
setColor(Toolbar.getForegroundColor());
fill();
imp.updateAndDraw();
}
void areaToLine(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isArea()) {
IJ.error("Area to Line", "Area selection required");
return;
}
Polygon p = roi.getPolygon();
if (p == null) return;
int type1 = roi.getType();
if (type1 == Roi.COMPOSITE) {
IJ.error("Area to Line", "Composite selections cannot be converted to lines.");
return;
}
int type2 = Roi.POLYLINE;
if (type1 == Roi.OVAL
|| type1 == Roi.FREEROI
|| type1 == Roi.TRACED_ROI
|| ((roi instanceof PolygonRoi) && ((PolygonRoi) roi).isSplineFit())) type2 = Roi.FREELINE;
Roi roi2 = new PolygonRoi(p.xpoints, p.ypoints, p.npoints, type2);
imp.setRoi(roi2);
}
private void rotate(ImagePlus imp) {
Roi roi = imp.getRoi();
if (IJ.macroRunning()) {
String options = Macro.getOptions();
if (options != null
&& (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) {
IJ.run("Rotate... ", options); // run Image>Transform>Rotate
return;
}
}
(new RoiRotator()).run("");
}
void abortPluginOrMacro(ImagePlus imp) {
if (imp != null) {
ImageWindow win = imp.getWindow();
if (win != null) {
win.running = false;
win.running2 = false;
}
}
Macro.abort();
Interpreter.abort();
if (Interpreter.getInstance() != null) IJ.beep();
}
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;
}
public void run() {
while (!done) {
synchronized (this) {
try {
wait();
} catch (InterruptedException e) {
}
reset(imp, ip); // GL
apply(imp, ip); // GL
imp.updateAndDraw(); // GL
}
}
}
void runMacro(String arg, ImagePlus imp) {
boolean rotate = arg.equals("rotate");
Roi roi = imp.getRoi();
if (rotate && IJ.macroRunning()) {
String options = Macro.getOptions();
if (options != null
&& (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) {
IJ.run("Rotate... ", options); // run Image>Transform>Rotate
return;
}
}
if (roi == null) {
noRoi(rotate ? "Rotate" : "Enlarge");
return;
}
double dangle = Tools.parseDouble(angle);
if (Double.isNaN(dangle)) {
dangle = 15;
angle = "" + dangle;
}
if (rotate && (roi instanceof ImageRoi)) {
dangle = IJ.getNumber("Angle (degrees):", dangle);
((ImageRoi) roi).rotate(dangle);
imp.draw();
angle = "" + dangle;
return;
}
Undo.setup(Undo.ROI, imp);
roi = (Roi) roi.clone();
if (rotate) {
String value = IJ.runMacroFile("ij.jar:RotateSelection", angle);
Roi roi2 = imp.getRoi();
transferProperties(roi, roi2);
imp.setRoi(roi2);
if (value != null) angle = value;
} else if (arg.equals("enlarge")) (new RoiEnlarger()).run("");
}
public void actionPerformed(ActionEvent e) {
Button b = (Button) e.getSource();
if (b == null) return;
boolean imageThere = checkImage();
if (imageThere) {
if (b == originalB) {
reset(imp, ip);
filteredB.setEnabled(true);
} else if (b == filteredB) {
apply(imp, ip);
} else if (b == sampleB) {
reset(imp, ip);
sample();
apply(imp, ip);
} else if (b == stackB) {
applyStack();
} else if (b == helpB) {
IJ.showMessage(
"Help",
"Threshold Colour v1.0\n \n"
+ "Modification of Bob Dougherty's BandPass2 plugin by G.Landini to\n"
+ "threshold 24 bit RGB images based on Hue, Saturation and Brightness\n"
+ "or Red, Green and Blue components.\n \n"
+ "Pass: Band-pass filter (anything within range is displayed).\n \n"
+ "Stop: Band-reject filter (anything within range is NOT displayed).\n \n"
+ "Original: Shows the original image and updates the buffer when\n"
+ " switching to another image.\n \n"
+ "Filtered: Shows the filtered image.\n \n"
+ "Stack: Processes the rest of the slices in the stack (if any)\n"
+ " using the current settings.\n \n"
+ "Threshold: Shows the object/background in the foreground and\n"
+ " background colours selected in the ImageJ toolbar.\n \n"
+ "Invert: Swaps the fore/background colours.\n \n"
+ "Sample: (experimental) Sets the ranges of the filters based on the\n"
+ " pixel value componentd in a rectangular, user-defined, ROI.\n \n"
+ "HSB RGB: Selects HSB or RGB space and resets all the filters.\n \n"
+ "Note that the \'thresholded\' image is RGB, not 8 bit grey.");
}
updatePlot();
updateLabels();
imp.updateAndDraw();
} else {
IJ.beep();
IJ.showStatus("No Image");
}
notify();
}