public void mouseMoved(MouseEvent e) {
// if (ij==null) return;
int sx = e.getX();
int sy = e.getY();
int ox = offScreenX(sx);
int oy = offScreenY(sy);
flags = e.getModifiers();
setCursor(sx, sy, ox, oy);
IJ.setInputEvent(e);
Roi roi = imp.getRoi();
if (roi != null
&& (roi.getType() == Roi.POLYGON
|| roi.getType() == Roi.POLYLINE
|| roi.getType() == Roi.ANGLE)
&& roi.getState() == roi.CONSTRUCTING) {
PolygonRoi pRoi = (PolygonRoi) roi;
pRoi.handleMouseMove(ox, oy);
} else {
if (ox < imageWidth && oy < imageHeight) {
ImageWindow win = imp.getWindow();
// Cursor must move at least 12 pixels before text
// displayed using IJ.showStatus() is overwritten.
if ((sx - sx2) * (sx - sx2) + (sy - sy2) * (sy - sy2) > 144) showCursorStatus = true;
if (win != null && showCursorStatus) win.mouseMoved(ox, oy);
} else IJ.showStatus("");
}
}
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 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 fitSpline() {
Roi roi = imp.getRoi();
if (roi == null) {
IJ.error("Spline", "Selection required");
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) 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 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();
}
/** 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);
}
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 int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
this.pfr = pfr;
String macroOptions = Macro.getOptions();
if (macroOptions != null) {
if (macroOptions.indexOf(" interpolate") != -1)
macroOptions.replaceAll(" interpolate", " interpolation=Bilinear");
else if (macroOptions.indexOf(" interpolation=") == -1)
macroOptions = macroOptions + " interpolation=None";
Macro.setOptions(macroOptions);
}
gd = new GenericDialog("Rotate", IJ.getInstance());
gd.addNumericField("Angle (degrees):", angle, (int) angle == angle ? 1 : 2);
gd.addNumericField("Grid Lines:", gridLines, 0);
gd.addChoice("Interpolation:", methods, methods[interpolationMethod]);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with Background Color", fillWithBackground);
if (canEnlarge) gd.addCheckbox("Enlarge Image to Fit Result", enlarge);
else enlarge = false;
gd.addPreviewCheckbox(pfr);
gd.addDialogListener(this);
gd.showDialog();
drawGridLines(0);
if (gd.wasCanceled()) {
return DONE;
}
if (!enlarge) flags |= KEEP_PREVIEW; // standard filter without enlarge
else if (imp.getStackSize() == 1) flags |= NO_CHANGES; // undoable as a "compound filter"
return IJ.setupDialog(imp, flags);
}
/* Are we tracing a one pixel wide line? Makes Legacy mode 8-connected instead of 4-connected */
private boolean isLine(int xs, int ys) {
int r = 5;
int xmin = xs;
int xmax = xs + 2 * r;
if (xmax >= width) xmax = width - 1;
int ymin = ys - r;
if (ymin < 0) ymin = 0;
int ymax = ys + r;
if (ymax >= height) ymax = height - 1;
int area = 0;
int insideCount = 0;
for (int x = xmin; (x <= xmax); x++)
for (int y = ymin; y <= ymax; y++) {
area++;
if (inside(x, y)) insideCount++;
}
if (IJ.debugMode)
IJ.log(
(((double) insideCount) / area < 0.25 ? "line " : "blob ")
+ insideCount
+ " "
+ area
+ " "
+ IJ.d2s(((double) insideCount) / area));
return ((double) insideCount) / area < 0.25;
}
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
if (doOptions) {
this.imp = imp;
this.pfr = pfr;
GenericDialog gd = new GenericDialog("Binary Options");
gd.addNumericField("Iterations (1-" + MAX_ITERATIONS + "):", iterations, 0, 3, "");
gd.addNumericField("Count (1-8):", count, 0, 3, "");
gd.addCheckbox("Black background", Prefs.blackBackground);
gd.addCheckbox("Pad edges when eroding", Prefs.padEdges);
gd.addChoice("EDM output:", outputTypes, outputTypes[EDM.getOutputType()]);
if (imp != null) {
gd.addChoice("Do:", operations, operation);
gd.addPreviewCheckbox(pfr);
gd.addDialogListener(this);
previewing = true;
}
gd.addHelp(IJ.URL + "/docs/menus/process.html#options");
gd.showDialog();
previewing = false;
if (gd.wasCanceled()) return DONE;
if (imp == null) { // options dialog only, no do/preview
dialogItemChanged(gd, null); // read dialog result
return DONE;
}
return operation.equals(NO_OPERATION) ? DONE : IJ.setupDialog(imp, flags);
} else { // no dialog, 'arg' is operation type
if (!((ByteProcessor) imp.getProcessor()).isBinary()) {
IJ.error("8-bit binary (black and white only) image required.");
return DONE;
}
return IJ.setupDialog(imp, flags);
}
}
public Zipper<Map<Integer, MZipper<RoiContainer>>> exec(
Zipper<Map<Integer, MZipper<RoiContainer>>> z, int frame) {
JFileChooser fc = new JFileChooser();
int returnVal = fc.showOpenDialog(WindowManager.getCurrentWindow().getCanvas());
Map<Integer, MZipper<RoiContainer>> newRois;
if (returnVal == JFileChooser.APPROVE_OPTION) {
try {
FileInputStream f = new FileInputStream(fc.getSelectedFile().getCanonicalPath());
MroiLisp parser = new MroiLisp(f);
parser.ReInit(f);
newRois = parser.roiFile();
// z.rights.clear();
// z.rights.add(newRois);
// z = z.right();
// return z;
return z.insertAndStep(newRois);
} catch (IOException e) {
IJ.error("Couldn't open from " + fc.getSelectedFile().getName() + ": " + e.getMessage());
} catch (mroi.ParseException e) {
IJ.error("Failed in parsing: " + e.getMessage());
} catch (Exception e) {
IJ.error("Malformed input file: " + e.getMessage());
}
}
return z;
}
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));
}
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();
}
/**
* Creates a new GenericDialog with the specified title. Uses the current image image window as
* the parent frame or the ImageJ frame if no image windows are open. Dialog parameters are
* recorded by ImageJ's command recorder but this requires that the first word of each label be
* unique.
*/
public GenericDialog(String title) {
this(
title,
WindowManager.getCurrentImage() != null
? (Frame) WindowManager.getCurrentImage().getWindow()
: IJ.getInstance() != null ? IJ.getInstance() : new Frame());
}
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);
}
/**
* Notify any DialogListeners of changes having occurred If a listener returns false, do not call
* further listeners and disable the OK button and preview Checkbox (if it exists). For
* PlugInFilters, this ensures that the PlugInFilterRunner, which listens as the last one, is not
* called if the PlugInFilter has detected invalid parameters. Thus, unnecessary calling the
* run(ip) method of the PlugInFilter for preview is avoided in that case.
*/
private void notifyListeners(AWTEvent e) {
if (dialogListeners == null) return;
boolean everythingOk = true;
for (int i = 0; everythingOk && i < dialogListeners.size(); i++)
try {
resetCounters();
if (!((DialogListener) dialogListeners.elementAt(i)).dialogItemChanged(this, e))
everythingOk = false;
} // disable further listeners if false (invalid parameters) returned
catch (Exception err) { // for exceptions, don't cover the input by a window but
IJ.beep(); // show them at in the "Log"
IJ.log(
"ERROR: "
+ err
+ "\nin DialogListener of "
+ dialogListeners.elementAt(i)
+ "\nat "
+ (err.getStackTrace()[0])
+ "\nfrom "
+ (err.getStackTrace()[1])); // requires Java 1.4
}
boolean workaroundOSXbug = IJ.isMacOSX() && okay != null && !okay.isEnabled() && everythingOk;
if (previewCheckbox != null) previewCheckbox.setEnabled(everythingOk);
if (okay != null) okay.setEnabled(everythingOk);
if (workaroundOSXbug) repaint(); // OSX 10.4 bug delays update of enabled until the next input
}
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();
}
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
public void reduceHyperstack(ImagePlus imp, int factor, boolean reduceSlices) {
int channels = imp.getNChannels();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int zfactor = reduceSlices ? factor : 1;
int tfactor = reduceSlices ? 1 : factor;
ImageStack stack = imp.getStack();
ImageStack stack2 = new ImageStack(imp.getWidth(), imp.getHeight());
boolean virtual = stack.isVirtual();
int slices2 = slices / zfactor + ((slices % zfactor) != 0 ? 1 : 0);
int frames2 = frames / tfactor + ((frames % tfactor) != 0 ? 1 : 0);
int n = channels * slices2 * frames2;
int count = 1;
for (int t = 1; t <= frames; t += tfactor) {
for (int z = 1; z <= slices; z += zfactor) {
for (int c = 1; c <= channels; c++) {
int i = imp.getStackIndex(c, z, t);
IJ.showProgress(i, n);
ImageProcessor ip = stack.getProcessor(imp.getStackIndex(c, z, t));
// IJ.log(count++ +" "+i+" "+c+" "+z+" "+t);
stack2.addSlice(stack.getSliceLabel(i), ip);
}
}
}
imp.setStack(stack2, channels, slices2, frames2);
Calibration cal = imp.getCalibration();
if (cal.scaled()) cal.pixelDepth *= zfactor;
if (virtual) imp.setTitle(imp.getTitle());
IJ.showProgress(1.0);
}
/** 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());
}
/** 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 int setup(String arg, ImagePlus imp) {
this.arg = arg;
this.imp = imp;
IJ.register(ParticleAnalyzer.class);
if (imp == null) {
IJ.noImage();
return DONE;
}
if (imp.getBitDepth() == 24 && !isThresholdedRGB(imp)) {
IJ.error(
"Particle Analyzer",
"RGB images must be thresholded using\n" + "Image>Adjust>Color Threshold.");
return DONE;
}
if (!showDialog()) return DONE;
int baseFlags = DOES_ALL + NO_CHANGES + NO_UNDO;
int flags = IJ.setupDialog(imp, baseFlags);
processStack = (flags & DOES_STACKS) != 0;
slice = 0;
saveRoi = imp.getRoi();
if (saveRoi != null && saveRoi.getType() != Roi.RECTANGLE && saveRoi.isArea())
polygon = saveRoi.getPolygon();
imp.startTiming();
nextFontSize = defaultFontSize;
nextLineWidth = 1;
return flags;
}
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();
}
void write16BitStack(OutputStream out, Object[] stack) throws IOException {
showProgressBar = false;
for (int i = 0; i < fi.nImages; i++) {
IJ.showStatus("Writing: " + (i + 1) + "/" + fi.nImages);
write16BitImage(out, (short[]) stack[i]);
IJ.showProgress((double) (i + 1) / fi.nImages);
}
}
public void dragOver(DropTargetDragEvent e) {
if (IJ.debugMode) IJ.log("DragOver: " + e.getLocation());
Point loc = e.getLocation();
int buttonSize = Toolbar.getButtonSize();
int width = IJ.getInstance().getSize().width;
openAsVirtualStack = width - loc.x <= buttonSize;
if (openAsVirtualStack) IJ.showStatus("<<Open as Virtual Stack>>");
else IJ.showStatus("<<Drag and Drop>>");
}
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);
}
void handleMouseMove(int sx, int sy) {
// Do rubber banding
int tool = Toolbar.getToolId();
if (!(tool == Toolbar.POLYGON || tool == Toolbar.POLYLINE || tool == Toolbar.ANGLE)) {
imp.deleteRoi();
imp.draw();
return;
}
drawRubberBand(sx, sy);
degrees = Double.NaN;
double len = -1;
if (nPoints > 1) {
double x1, y1, x2, y2;
if (xpf != null) {
x1 = xpf[nPoints - 2];
y1 = ypf[nPoints - 2];
x2 = xpf[nPoints - 1];
y2 = ypf[nPoints - 1];
} else {
x1 = xp[nPoints - 2];
y1 = yp[nPoints - 2];
x2 = xp[nPoints - 1];
y2 = yp[nPoints - 1];
}
degrees =
getAngle(
(int) Math.round(x1),
(int) Math.round(y1),
(int) Math.round(x2),
(int) Math.round(y2));
if (tool != Toolbar.ANGLE) {
Calibration cal = imp.getCalibration();
double pw = cal.pixelWidth, ph = cal.pixelHeight;
if (IJ.altKeyDown()) {
pw = 1.0;
ph = 1.0;
}
len = Math.sqrt((x2 - x1) * pw * (x2 - x1) * pw + (y2 - y1) * ph * (y2 - y1) * ph);
}
}
if (tool == Toolbar.ANGLE) {
if (nPoints == 2) angle1 = degrees;
else if (nPoints == 3) {
double angle2 = getAngle(xp[1], yp[1], xp[2], yp[2]);
degrees = Math.abs(180 - Math.abs(angle1 - angle2));
if (degrees > 180.0) degrees = 360.0 - degrees;
}
}
String length = len != -1 ? ", length=" + IJ.d2s(len) : "";
double degrees2 =
tool == Toolbar.ANGLE && nPoints == 3 && Prefs.reflexAngle ? 360.0 - degrees : degrees;
String angle = !Double.isNaN(degrees) ? ", angle=" + IJ.d2s(degrees2) : "";
int ox = ic != null ? ic.offScreenX(sx) : sx;
int oy = ic != null ? ic.offScreenY(sy) : sy;
IJ.showStatus(imp.getLocationAsString(ox, oy) + length + angle);
}
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(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);
}
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;
}