private ImagePlus openImage(String directory, String name, String path) {
Object o = tryOpen(directory, name, path);
// if an image was returned, assume success
if (o instanceof ImagePlus) return (ImagePlus) o;
// try opening the file with LOCI Bio-Formats plugin - always check this last!
// Do not call Bio-Formats if File>Import>Image Sequence is opening this file.
if (o == null
&& (IJ.getVersion().compareTo("1.38j") < 0 || !IJ.redirectingErrorMessages())
&& (new File(path).exists())) {
Object loci = IJ.runPlugIn("loci.plugins.LociImporter", path);
if (loci != null) {
// plugin exists and was launched
try {
// check whether plugin was successful
Class c = loci.getClass();
boolean success = c.getField("success").getBoolean(loci);
boolean canceled = c.getField("canceled").getBoolean(loci);
if (success || canceled) {
width = IMAGE_OPENED;
return null;
}
} catch (Exception exc) {
}
}
}
return null;
} // openImage
/** Called from io/Opener.java. */
public void run(String path) {
if (path.equals("")) return;
File theFile = new File(path);
String directory = theFile.getParent();
String fileName = theFile.getName();
if (directory == null) directory = "";
// Try and recognise file type and load the file if recognised
ImagePlus imp = openImage(directory, fileName, path);
if (imp == null) {
IJ.showStatus("");
return; // failed to load file or plugin has opened and displayed it
}
ImageStack stack = imp.getStack();
// get the title from the stack (falling back to the fileName)
String title = imp.getTitle().equals("") ? fileName : imp.getTitle();
// set the stack of this HandleExtraFileTypes object
// to that attached to the ImagePlus object returned by openImage()
setStack(title, stack);
// copy over the calibration info since it doesn't come with the ImageProcessor
setCalibration(imp.getCalibration());
// also copy the Show Info field over if it exists
if (imp.getProperty("Info") != null) setProperty("Info", imp.getProperty("Info"));
// copy the FileInfo
setFileInfo(imp.getOriginalFileInfo());
// copy dimensions
if (IJ.getVersion().compareTo("1.38s") >= 0)
setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
if (IJ.getVersion().compareTo("1.41o") >= 0) setOpenAsHyperStack(imp.getOpenAsHyperStack());
}
void loadTransformation(String filename, ResultsTable res) {
try {
String line;
FileReader fr = new FileReader(filename);
BufferedReader br = new BufferedReader(fr);
if (!br.readLine().equals(" Z-Step Raw Width minus Heigh Calibration Width minus Height")) {
IJ.error("File does not seam to be an Astigmatism calibration file");
return;
}
// java.lang.String [] elements = new java.lang.String [3];
java.lang.String[] elements;
int counter = 1;
res.reset();
while ((line = br.readLine()) != null) {
IJ.showStatus("Loading element " + counter + "... sit back and relax.");
counter++;
line.trim();
elements = line.split("\t");
res.incrementCounter();
res.addValue("Z-Step", Double.parseDouble(elements[1]));
res.addValue("Raw Width minus Heigh", Double.parseDouble(elements[2]));
res.addValue("Calibration Width minus Height", Double.parseDouble(elements[3]));
}
fr.close();
} catch (FileNotFoundException e) {
IJ.error("File not found exception" + e);
return;
} catch (IOException e) {
IJ.error("IOException exception" + e);
return;
} catch (NumberFormatException e) {
IJ.error("Number format exception" + e);
return;
}
}
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.noImage();
return;
}
ImageStack stack1 = imp.getStack();
String fileName = imp.getTitle();
int endslice = stack1.getSize();
ImagePlus imp2 = duplicateStack(imp);
imp2.show();
String duplicateName = imp2.getTitle();
// IJ.showMessage("Box",fileName);
ImageStack stack2 = imp2.getStack();
stack1.deleteSlice(1);
stack2.deleteSlice(endslice);
String calculatorstring =
("image1='"
+ fileName
+ "' operation=Subtract image2="
+ imp2.getTitle()
+ " create stack");
IJ.run("Image Calculator...", calculatorstring);
ImagePlus imp3 = WindowManager.getCurrentImage();
imp3.setTitle(fileName + " DeltaF up");
imp2.getWindow().close();
imp.getWindow().close();
}
/** Handle menu events. */
public void actionPerformed(ActionEvent e) {
if ((e.getSource() instanceof MenuItem)) {
MenuItem item = (MenuItem) e.getSource();
String cmd = e.getActionCommand();
commandName = cmd;
ImagePlus imp = null;
if (item.getParent() == Menus.getOpenRecentMenu()) {
new RecentOpener(cmd); // open image in separate thread
return;
} else if (item.getParent() == Menus.getPopupMenu()) {
Object parent = Menus.getPopupMenu().getParent();
if (parent instanceof ImageCanvas) imp = ((ImageCanvas) parent).getImage();
}
int flags = e.getModifiers();
hotkey = false;
actionPerformedTime = System.currentTimeMillis();
long ellapsedTime = actionPerformedTime - keyPressedTime;
if (cmd != null && (ellapsedTime >= 200L || !cmd.equals(lastKeyCommand))) {
if ((flags & Event.ALT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_ALT);
if ((flags & Event.SHIFT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_SHIFT);
new Executer(cmd, imp);
}
lastKeyCommand = null;
if (IJ.debugMode) IJ.log("actionPerformed: time=" + ellapsedTime + ", " + e);
}
}
public synchronized void adjustmentValueChanged(AdjustmentEvent e) {
if (!checkImage()) {
IJ.beep();
IJ.showStatus("No Image");
return;
}
if (e.getSource() == minSlider) {
adjustMinHue((int) minSlider.getValue());
} else if (e.getSource() == maxSlider) {
adjustMaxHue((int) maxSlider.getValue());
} else if (e.getSource() == minSlider2) {
adjustMinSat((int) minSlider2.getValue());
} else if (e.getSource() == maxSlider2) {
adjustMaxSat((int) maxSlider2.getValue());
} else if (e.getSource() == minSlider3) {
adjustMinBri((int) minSlider3.getValue());
} else if (e.getSource() == maxSlider3) {
adjustMaxBri((int) maxSlider3.getValue());
}
originalB.setEnabled(true);
updateLabels();
updatePlot();
notify();
}
/** Called by ImageJ when the user selects Quit. */
public void quit() {
quitMacro = IJ.macroRunning();
Thread thread = new Thread(this, "Quit");
thread.setPriority(Thread.NORM_PRIORITY);
thread.start();
IJ.wait(10);
}
public Channels() {
super("Channels");
if (instance != null) {
instance.toFront();
return;
}
WindowManager.addWindow(this);
instance = this;
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
setLayout(gridbag);
int y = 0;
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.fill = GridBagConstraints.BOTH;
c.anchor = GridBagConstraints.CENTER;
int margin = 32;
if (IJ.isMacOSX()) margin = 20;
c.insets = new Insets(10, margin, 10, margin);
choice = new Choice();
for (int i = 0; i < modes.length; i++) choice.addItem(modes[i]);
choice.select(0);
choice.addItemListener(this);
add(choice, c);
CompositeImage ci = getImage();
int nCheckBoxes = ci != null ? ci.getNChannels() : 3;
if (nCheckBoxes > CompositeImage.MAX_CHANNELS) nCheckBoxes = CompositeImage.MAX_CHANNELS;
checkbox = new Checkbox[nCheckBoxes];
for (int i = 0; i < nCheckBoxes; i++) {
checkbox[i] = new Checkbox("Channel " + (i + 1), true);
c.insets = new Insets(0, 25, i < nCheckBoxes - 1 ? 0 : 10, 5);
c.gridy = y++;
add(checkbox[i], c);
checkbox[i].addItemListener(this);
}
c.insets = new Insets(0, 15, 10, 15);
c.fill = GridBagConstraints.NONE;
c.gridy = y++;
moreButton = new Button(moreLabel);
moreButton.addActionListener(this);
add(moreButton, c);
update();
pm = new PopupMenu();
for (int i = 0; i < menuItems.length; i++) addPopupItem(menuItems[i]);
add(pm);
addKeyListener(IJ.getInstance()); // ImageJ handles keyboard shortcuts
setResizable(false);
pack();
if (location == null) {
GUI.center(this);
location = getLocation();
} else setLocation(location);
show();
}
public void actionPerformed(ActionEvent e) {
String command = e.getActionCommand();
if (command == null) return;
if (command.equals(moreLabel)) {
Point bloc = moreButton.getLocation();
pm.show(this, bloc.x, bloc.y);
} else if (command.equals("Convert to RGB")) IJ.doCommand("Stack to RGB");
else IJ.doCommand(command);
}
public void run(String arg) {
ImageWindow iw = WindowManager.getCurrentWindow();
pw = jutils.getPW4SelCopy(iw);
String title = pw.getTitle();
float[][] yvals = pw.getYValues();
float[][] xvals = pw.getXValues();
int length = yvals[0].length;
if (pw.getShowErrors()) errs = pw.getErrors(0, false);
int[] colors = pw.getColors();
colors[0] = 0;
ScriptEngineManager manager = new ScriptEngineManager();
engine = manager.getEngineByName("js");
ce = (Compilable) engine;
// hitcounter=0;
c2 = 0.0f;
iterations = 0;
checkc2 = false;
double[] stats = new double[3];
tempx = new float[length];
tempdata = new float[length];
System.arraycopy(xvals[0], 0, tempx, 0, length);
System.arraycopy(yvals[0], 0, tempdata, 0, length);
pw.addPoints(tempx, new float[tempx.length], false);
series = pw.getNpts().length - 1;
double[] params = new double[10];
int[] fixes = {0, 0, 0, 1, 1, 1, 1, 1, 1, 1};
init_options(params, fixes);
if (!init_functions()) {
return;
}
while (showoptions(params, fixes)) {
NLLSfit_v2 fitclass;
if (checkc2) {
fitclass = new NLLSfit_v2(this, 0);
} else {
fitclass = new NLLSfit_v2(this, 0.0001, 50, 0.1);
}
float[] fit = fitclass.fitdata(params, fixes, constraints, yvals[0], weights, stats, true);
pw.updateSeries(fit, series, false);
c2 = (float) stats[1];
iterations = (int) stats[0];
}
IJ.log("Chi Squared = " + (float) stats[1]);
IJ.log("Iterations = " + (int) stats[0]);
for (int i = 0; i < 10; i++) {
IJ.log("P" + (i + 1) + " = " + (float) params[i] + " fixed = " + fixes[i]);
}
IJ.log("AIC = " + (float) stats[2]);
// IJ.log("hits = "+hitcounter);
set_options(params, fixes);
}
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;
}
private boolean checkImage() {
imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.beep();
IJ.showStatus("No image");
return false;
}
ip = setup(imp);
if (ip == null) return false;
return true;
}
public void run(String arg) {
int[] wList = WindowManager.getIDList();
if (wList == null) {
IJ.error("No images are open.");
return;
}
double thalf = 0.5;
boolean keep;
GenericDialog gd = new GenericDialog("Bleach correction");
gd.addNumericField("t½:", thalf, 1);
gd.addCheckbox("Keep source stack:", true);
gd.showDialog();
if (gd.wasCanceled()) return;
long start = System.currentTimeMillis();
thalf = gd.getNextNumber();
keep = gd.getNextBoolean();
if (keep) IJ.run("Duplicate...", "title='Bleach corrected' duplicate");
ImagePlus imp1 = WindowManager.getCurrentImage();
int d1 = imp1.getStackSize();
double v1, v2;
int width = imp1.getWidth();
int height = imp1.getHeight();
ImageProcessor ip1, ip2, ip3;
int slices = imp1.getStackSize();
ImageStack stack1 = imp1.getStack();
ImageStack stack2 = imp1.getStack();
int currentSlice = imp1.getCurrentSlice();
for (int n = 1; n <= slices; n++) {
ip1 = stack1.getProcessor(n);
ip3 = stack1.getProcessor(1);
ip2 = stack2.getProcessor(n);
for (int x = 0; x < width; x++) {
for (int y = 0; y < height; y++) {
v1 = ip1.getPixelValue(x, y);
v2 = ip3.getPixelValue(x, y);
// =B8/(EXP(-C$7*A8))
v1 = (v1 / Math.exp(-n * thalf));
ip2.putPixelValue(x, y, v1);
}
}
IJ.showProgress((double) n / slices);
IJ.showStatus(n + "/" + slices);
}
// stack2.show();
imp1.updateAndDraw();
}
boolean init_functions() {
GenericDialog gd = new GenericDialog("Fitting Options");
gd.addStringField("Extra Definitions", exdef, 50);
gd.addCheckbox("Weight Using Plot Errors", false);
gd.addStringField("Weighting Equation (y is for data)", weightfunction, 50);
gd.addStringField("Fit_Equation", function, 50);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
}
exdef = gd.getNextString();
boolean errweights = gd.getNextBoolean();
weightfunction = gd.getNextString();
function = gd.getNextString();
// first initialize the weights
weights = new float[tempdata.length];
if (errweights
|| weightfunction.equals("")
|| weightfunction == null
|| weightfunction == "1.0") {
if (errweights) {
for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f / (errs[i] * errs[i]);
} else {
for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f;
}
} else {
for (int i = 0; i < tempdata.length; i++) {
String script =
"y =" + tempdata[i] + "; " + "x =" + tempx[i] + "; " + "retval=" + weightfunction + ";";
Double temp = new Double(0.0);
try {
temp = (Double) engine.eval(script);
} catch (Exception e) {
IJ.log(e.getMessage());
}
if (!(temp.isInfinite() || temp.isNaN())) {
weights[i] = temp.floatValue();
}
}
}
// now compile the function script
try {
String script1 = exdef + "; retval=" + function + ";";
cs = ce.compile(script1);
} catch (Exception e) {
IJ.log(e.toString());
return false;
}
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 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();
}
/**
* Prepare for processing; also called at the very end with argument 'final' to show any newly
* created output image.
*/
public int setup(String arg, ImagePlus imp) {
if (arg.equals("final")) {
showOutput();
return DONE;
}
this.imp = imp;
// 'arg' is processing type; default is 'EDM' (0)
if (arg.equals("watershed")) {
processType = WATERSHED;
flags += KEEP_THRESHOLD;
} else if (arg.equals("points")) processType = UEP;
else if (arg.equals("voronoi")) processType = VORONOI;
// output type
if (processType != WATERSHED) // Watershed always has output BYTE_OVERWRITE=0
outImageType = outputType; // otherwise use the static variable from setOutputType
if (outImageType != BYTE_OVERWRITE) flags |= NO_CHANGES;
// check image and prepare
if (imp != null) {
ImageProcessor ip = imp.getProcessor();
if (!ip.isBinary()) {
IJ.error("8-bit binary image (0 and 255) required.");
return DONE;
}
ip.resetRoi();
// processing routines assume background=0; image may be otherwise
boolean invertedLut = imp.isInvertedLut();
background255 =
(invertedLut && Prefs.blackBackground) || (!invertedLut && !Prefs.blackBackground);
}
return flags;
} // public int setup
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
if (!(imp instanceof Image5D)) {
IJ.error("Current Image is not an Image5D.");
return;
}
IJ.register(Add_Empty_Slice.class);
Image5D i5d = (Image5D) imp;
Image5DWindow win = ((Image5DWindow) i5d.getWindow());
int n = i5d.getNSlices();
i5d.expandDimension(3, n + 1, true);
win.updateSliceSelector();
}
public double[] fitfunc(double[] fitparams) {
Bindings b = engine.createBindings();
for (int i = 0; i < 10; i++) b.put("P" + (i + 1), fitparams[i]);
/*String script1="P1="+fitparams[0]+"; "+
"P2="+fitparams[1]+"; "+
"P3="+fitparams[2]+"; "+
"P4="+fitparams[3]+"; "+
"P5="+fitparams[4]+"; "+
"P6="+fitparams[5]+"; "+
"P7="+fitparams[6]+"; "+
"P8="+fitparams[7]+"; "+
"P9="+fitparams[8]+"; "+
"P10="+fitparams[9]+"; "+
exdef+"; x=";
String script2="; retval="+function+";";*/
try {
double[] temp = new double[tempx.length];
for (int i = 0; i < tempx.length; i++) {
// temp[i]=((Double)engine.eval(script1+(double)tempx[i]+script2)).doubleValue();
b.put("x", tempx[i]);
b.put("y", tempdata[i]);
temp[i] = (Double) cs.eval(b);
}
return temp;
} catch (Exception e) {
IJ.log(e.getMessage());
return null;
}
}
public boolean checkBeads() {
rmanager = RoiManager.getInstance();
if (IJ.versionLessThan("1.26i")) return false;
else if (rmanager == null) {
IJ.error("Add bead ROIs to the RoiManager first (select region then press [t]).");
return false;
}
nrois = rmanager.getCount();
if (nrois == 0) {
IJ.error("Add bead ROIs to the RoiManager first (select region then press [t]).");
return false;
}
rois = rmanager.getRoisAsArray();
return true;
}
public String getInfo() {
return version()
+ System.getProperty("os.name")
+ " "
+ System.getProperty("os.version")
+ "; "
+ IJ.freeMemory();
}
/**
* Execute the plugin functionality: duplicate and scale the given image.
*
* @return an Object[] array with the name and the scaled ImagePlus. Does NOT show the new, image;
* just returns it.
*/
public Object[] exec(
ImagePlus imp, String myMethod, int radius, double par1, double par2, boolean doIwhite) {
// 0 - Check validity of parameters
if (null == imp) return null;
ImageProcessor ip = imp.getProcessor();
int xe = ip.getWidth();
int ye = ip.getHeight();
// int [] data = (ip.getHistogram());
IJ.showStatus("Thresholding...");
long startTime = System.currentTimeMillis();
// 1 Do it
if (imp.getStackSize() == 1) {
ip.snapshot();
Undo.setup(Undo.FILTER, imp);
}
// Apply the selected algorithm
if (myMethod.equals("Bernsen")) {
Bernsen(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Contrast")) {
Contrast(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Mean")) {
Mean(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Median")) {
Median(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("MidGrey")) {
MidGrey(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Niblack")) {
Niblack(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Otsu")) {
Otsu(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Phansalkar")) {
Phansalkar(imp, radius, par1, par2, doIwhite);
} else if (myMethod.equals("Sauvola")) {
Sauvola(imp, radius, par1, par2, doIwhite);
}
// IJ.showProgress((double)(255-i)/255);
imp.updateAndDraw();
imp.getProcessor().setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
// 2 - Return the threshold and the image
IJ.showStatus("\nDone " + (System.currentTimeMillis() - startTime) / 1000.0);
return new Object[] {imp};
}
private String version() {
return "ImageJ "
+ VERSION
+ BUILD
+ "; "
+ "Java "
+ System.getProperty("java.version")
+ (IJ.is64Bit() ? " [64-bit]; " : " [32-bit]; ");
}
void Bernsen(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
// Bernsen recommends WIN_SIZE = 31 and CONTRAST_THRESHOLD = 15.
// 1) Bernsen J. (1986) "Dynamic Thresholding of Grey-Level Images"
// Proc. of the 8th Int. Conf. on Pattern Recognition, pp. 1251-1255
// 2) Sezgin M. and Sankur B. (2004) "Survey over Image Thresholding
// Techniques and Quantitative Performance Evaluation" Journal of
// Electronic Imaging, 13(1): 146-165
// http://citeseer.ist.psu.edu/sezgin04survey.html
// Ported to ImageJ plugin from E Celebi's fourier_0.8 routines
// This version uses a circular local window, instead of a rectagular one
ImagePlus Maximp, Minimp;
ImageProcessor ip = imp.getProcessor(), ipMax, ipMin;
int contrast_threshold = 15;
int local_contrast;
int mid_gray;
byte object;
byte backg;
int temp;
if (par1 != 0) {
IJ.log("Bernsen: changed contrast_threshold from :" + contrast_threshold + " to:" + par1);
contrast_threshold = (int) par1;
}
if (doIwhite) {
object = (byte) 0xff;
backg = (byte) 0;
} else {
object = (byte) 0;
backg = (byte) 0xff;
}
Maximp = duplicateImage(ip);
ipMax = Maximp.getProcessor();
RankFilters rf = new RankFilters();
rf.rank(ipMax, radius, rf.MAX); // Maximum
// Maximp.show();
Minimp = duplicateImage(ip);
ipMin = Minimp.getProcessor();
rf.rank(ipMin, radius, rf.MIN); // Minimum
// Minimp.show();
byte[] pixels = (byte[]) ip.getPixels();
byte[] max = (byte[]) ipMax.getPixels();
byte[] min = (byte[]) ipMin.getPixels();
for (int i = 0; i < pixels.length; i++) {
local_contrast = (int) ((max[i] & 0xff) - (min[i] & 0xff));
mid_gray = (int) ((min[i] & 0xff) + (max[i] & 0xff)) / 2;
temp = (int) (pixels[i] & 0x0000ff);
if (local_contrast < contrast_threshold)
pixels[i] = (mid_gray >= 128) ? object : backg; // Low contrast region
else pixels[i] = (temp >= mid_gray) ? object : backg;
}
// imp.updateAndDraw();
return;
}
void applyStack() {
// int minKeepH = minHue, maxKeepH = maxHue; //GL not needed?
// int minKeepS = minSat, maxKeepS = maxSat;
// int minKeepB = minBri, maxKeepB = maxBri;
for (int i = 1; i <= numSlices; i++) {
imp.setSlice(i);
if (!checkImage()) {
IJ.beep();
IJ.showStatus("No Image");
return;
}
// minHue = minKeepH;
// maxHue = maxKeepH;
// minSat = minKeepS;
// maxSat = maxKeepS;
// minBri = minKeepB;
// maxBri = maxKeepB;
apply(imp, ip);
}
}
public void run(String arg) {
if (IJ.versionLessThan("1.49d")) return;
if (!showDialog()) return;
SaveDialog sd = new SaveDialog("Save as Bricks...", "", "");
basename = sd.getFileName();
directory = sd.getDirectory();
if (basename == null || directory == null) return;
build_bricks();
}
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();
}
/**
* Called by the PlugInFilterRunner after setup. Asks the user in case of a stack and prepares a
* separate ouptut stack if required
*/
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
this.pfr = pfr;
int width = imp.getWidth();
int height = imp.getHeight();
// ask whether to process all slices of stack & prepare stack
// (if required) for writing into it in parallel threads
flags = IJ.setupDialog(imp, flags);
if ((flags & DOES_STACKS) != 0 && outImageType != BYTE_OVERWRITE) {
outStack = new ImageStack(width, height, imp.getStackSize());
maxFinder.setNPasses(imp.getStackSize());
}
return flags;
} // public int showDialog
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.noImage();
return;
}
if (imp.getStackSize() > 1) {
IJ.error("This command requires a montage");
return;
}
GenericDialog gd = new GenericDialog("Stack Maker");
gd.addNumericField("Images_per_row: ", w, 0);
gd.addNumericField("Images_per_column: ", h, 0);
gd.addNumericField("Border width: ", b, 0);
gd.showDialog();
if (gd.wasCanceled()) return;
w = (int) gd.getNextNumber();
h = (int) gd.getNextNumber();
b = (int) gd.getNextNumber();
ImageStack stack = makeStack(imp.getProcessor(), w, h, b);
new ImagePlus("Stack", stack).show();
}
/**
* Attempts to open the specified path with the given plugin. If the plugin extends the ImagePlus
* class (e.g., BioRad_Reader), set extendsImagePlus to true, otherwise (e.g., LSM_Reader) set it
* to false.
*
* @return A reference to the plugin, if it was successful.
*/
private Object tryPlugIn(String className, String path) {
Object o = IJ.runPlugIn(className, path);
if (o instanceof ImagePlus) {
// plugin extends ImagePlus class
ImagePlus imp = (ImagePlus) o;
if (imp.getWidth() == 0) o = null; // invalid image
else width = IMAGE_OPENED; // success
} else {
// plugin does not extend ImagePlus; assume success
width = IMAGE_OPENED;
}
return o;
}