public void run(ImageProcessor ip) {
if (enlarge && gd.wasOKed())
synchronized (this) {
if (!isEnlarged) {
enlargeCanvas();
isEnlarged = true;
}
}
if (isEnlarged) { // enlarging may have made the ImageProcessor invalid, also for the parallel
// threads
int slice = pfr.getSliceNumber();
if (imp.getStackSize() == 1) ip = imp.getProcessor();
else ip = imp.getStack().getProcessor(slice);
}
ip.setInterpolationMethod(interpolationMethod);
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) ip.setBackgroundValue(ip.getBestIndex(bgc));
else if (bitDepth == 24) ip.setBackgroundValue(bgc.getRGB());
} else ip.setBackgroundValue(0);
ip.rotate(angle);
if (!gd.wasOKed()) drawGridLines(gridLines);
if (isEnlarged && imp.getStackSize() == 1) {
imp.changes = true;
imp.updateAndDraw();
Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
}
}
void showResults() {
int count = rt.getCounter();
// if (count==0) return;
boolean lastSlice = !processStack || slice == imp.getStackSize();
if ((showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) && slice == 1 && count > 0)
imp.setOverlay(overlay);
else if (outlines != null && lastSlice) {
String title = imp != null ? imp.getTitle() : "Outlines";
String prefix;
if (showChoice == MASKS) prefix = "Mask of ";
else if (showChoice == ROI_MASKS) prefix = "Count Masks of ";
else prefix = "Drawing of ";
outlines.update(drawIP);
outputImage = new ImagePlus(prefix + title, outlines);
if (inSituShow) {
if (imp.getStackSize() == 1) Undo.setup(Undo.TRANSFORM, imp);
imp.setStack(null, outputImage.getStack());
} else if (!hideOutputImage) outputImage.show();
}
if (showResults && !processStack) {
TextPanel tp = IJ.getTextPanel();
if (beginningCount > 0 && tp != null && tp.getLineCount() != count) rt.show("Results");
Analyzer.firstParticle = beginningCount;
Analyzer.lastParticle = Analyzer.getCounter() - 1;
} else Analyzer.firstParticle = Analyzer.lastParticle = 0;
}
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) {
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();
}
/**
* 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(ImageProcessor ip) {
if (canceled) return;
slice++;
if (imp.getStackSize() > 1 && processStack) imp.setSlice(slice);
if (imp.getType() == ImagePlus.COLOR_RGB) {
ip = (ImageProcessor) imp.getProperty("Mask");
ip.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
}
if (!analyze(imp, ip)) canceled = true;
if (slice == imp.getStackSize()) {
imp.updateAndDraw();
if (saveRoi != null) imp.setRoi(saveRoi);
}
}
void updateSliceSummary() {
int slices = imp.getStackSize();
float[] areas = rt.getColumn(ResultsTable.AREA);
if (areas == null) areas = new float[0];
String label = imp.getTitle();
if (slices > 1) {
label = imp.getStack().getShortSliceLabel(slice);
label = label != null && !label.equals("") ? label : "" + slice;
}
String aLine = null;
double sum = 0.0;
int start = areas.length - particleCount;
if (start < 0) return;
for (int i = start; i < areas.length; i++) sum += areas[i];
int places = Analyzer.getPrecision();
Calibration cal = imp.getCalibration();
String total = "\t" + ResultsTable.d2s(sum, places);
String average = "\t" + ResultsTable.d2s(sum / particleCount, places);
String fraction = "\t" + ResultsTable.d2s(sum * 100.0 / totalArea, 1);
aLine = label + "\t" + particleCount + total + average + fraction;
aLine = addMeans(aLine, areas.length > 0 ? start : -1);
if (slices == 1) {
Frame frame = WindowManager.getFrame("Summary");
if (frame != null && (frame instanceof TextWindow) && summaryHdr.equals(prevHdr))
tw = (TextWindow) frame;
}
if (tw == null) {
String title = slices == 1 ? "Summary" : "Summary of " + imp.getTitle();
tw = new TextWindow(title, summaryHdr, aLine, 450, 300);
prevHdr = summaryHdr;
} else tw.append(aLine);
}
/**
* Saves statistics for one particle in a results table. This is a method subclasses may want to
* override.
*/
protected void saveResults(ImageStatistics stats, Roi roi) {
analyzer.saveResults(stats, roi);
if (recordStarts) {
rt.addValue("XStart", stats.xstart);
rt.addValue("YStart", stats.ystart);
}
if (addToManager) {
if (roiManager == null) {
if (Macro.getOptions() != null && Interpreter.isBatchMode())
roiManager = Interpreter.getBatchModeRoiManager();
if (roiManager == null) {
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) {
addToManager = false;
return;
}
roiManager = (RoiManager) frame;
}
if (resetCounter) roiManager.runCommand("reset");
}
if (imp.getStackSize() > 1) roi.setPosition(imp.getCurrentSlice());
if (lineWidth != 1) roi.setStrokeWidth(lineWidth);
roiManager.add(imp, roi, rt.getCounter());
}
if (showResults) rt.addResults();
}
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);
}
void scale(ImageProcessor ip) {
if (newWindow) {
Rectangle r = ip.getRoi();
ImagePlus imp2 = imp.createImagePlus();
imp2.setProcessor(title, ip.resize(newWidth, newHeight));
Calibration cal = imp2.getCalibration();
if (cal.scaled()) {
cal.pixelWidth *= 1.0 / xscale;
cal.pixelHeight *= 1.0 / yscale;
}
imp2.show();
imp.trimProcessor();
imp2.trimProcessor();
imp2.changes = true;
} else {
if (processStack && imp.getStackSize() > 1) {
Undo.reset();
StackProcessor sp = new StackProcessor(imp.getStack(), ip);
sp.scale(xscale, yscale, bgValue);
} else {
ip.snapshot();
Undo.setup(Undo.FILTER, imp);
ip.setSnapshotCopyMode(true);
ip.scale(xscale, yscale);
ip.setSnapshotCopyMode(false);
}
imp.killRoi();
imp.updateAndDraw();
imp.changes = true;
}
}
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;
}
public String getImageInfo(ImagePlus imp, ImageProcessor ip) {
String infoProperty = null;
if (imp.getStackSize() > 1) {
ImageStack stack = imp.getStack();
String label = stack.getSliceLabel(imp.getCurrentSlice());
if (label != null && label.indexOf('\n') > 0) infoProperty = label;
}
if (infoProperty == null) {
infoProperty = (String) imp.getProperty("Info");
if (infoProperty == null) infoProperty = getExifData(imp);
}
String info = getInfo(imp, ip);
if (infoProperty != null) return infoProperty + "\n------------------------\n" + info;
else return info;
}
// at the very end - show output image (if the is a separate one)
private void showOutput() {
if (interrupted) return;
if (outStack != null) {
outImp = new ImagePlus(TITLE_PREFIX[processType] + imp.getShortTitle(), outStack);
int[] d = imp.getDimensions();
outImp.setDimensions(d[2], d[3], d[4]);
for (int i = 1; i <= imp.getStackSize(); i++)
outStack.setSliceLabel(imp.getStack().getSliceLabel(i), i);
}
if (outImageType != BYTE_OVERWRITE) {
ImageProcessor ip = outImp.getProcessor();
if (!Prefs.blackBackground) ip.invertLut();
ip.resetMinAndMax();
outImp.show();
}
}
void createNewStack(ImagePlus imp, ImageProcessor ip) {
int nSlices = imp.getStackSize();
int w = imp.getWidth(), h = imp.getHeight();
ImagePlus imp2 = imp.createImagePlus();
Rectangle r = ip.getRoi();
boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight();
ImageStack stack1 = imp.getStack();
ImageStack stack2 = new ImageStack(newWidth, newHeight);
ImageProcessor ip1, ip2;
int method = interpolationMethod;
if (w == 1 || h == 1) method = ImageProcessor.NONE;
for (int i = 1; i <= nSlices; i++) {
IJ.showStatus("Scale: " + i + "/" + nSlices);
ip1 = stack1.getProcessor(i);
String label = stack1.getSliceLabel(i);
if (crop) {
ip1.setRoi(r);
ip1 = ip1.crop();
}
ip1.setInterpolationMethod(method);
ip2 = ip1.resize(newWidth, newHeight, averageWhenDownsizing);
if (ip2 != null) stack2.addSlice(label, ip2);
IJ.showProgress(i, nSlices);
}
imp2.setStack(title, stack2);
Calibration cal = imp2.getCalibration();
if (cal.scaled()) {
cal.pixelWidth *= 1.0 / xscale;
cal.pixelHeight *= 1.0 / yscale;
}
IJ.showProgress(1.0);
int[] dim = imp.getDimensions();
imp2.setDimensions(dim[2], dim[3], dim[4]);
if (imp.isComposite()) {
imp2 = new CompositeImage(imp2, ((CompositeImage) imp).getMode());
((CompositeImage) imp2).copyLuts(imp);
}
if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true);
if (newDepth > 0 && newDepth != oldDepth)
imp2 = (new Resizer()).zScale(imp2, newDepth, interpolationMethod);
if (imp2 != null) {
imp2.show();
imp2.changes = true;
}
}
/**
* 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 void doRGBProjection(ImageStack stack) {
ImageStack[] channels = ChannelSplitter.splitRGB(stack, true);
ImagePlus red = new ImagePlus("Red", channels[0]);
ImagePlus green = new ImagePlus("Green", channels[1]);
ImagePlus blue = new ImagePlus("Blue", channels[2]);
imp.unlock();
ImagePlus saveImp = imp;
imp = red;
color = "(red)";
doProjection();
ImagePlus red2 = projImage;
imp = green;
color = "(green)";
doProjection();
ImagePlus green2 = projImage;
imp = blue;
color = "(blue)";
doProjection();
ImagePlus blue2 = projImage;
int w = red2.getWidth(), h = red2.getHeight(), d = red2.getStackSize();
if (method == SD_METHOD) {
ImageProcessor r = red2.getProcessor();
ImageProcessor g = green2.getProcessor();
ImageProcessor b = blue2.getProcessor();
double max = 0;
double rmax = r.getStatistics().max;
if (rmax > max) max = rmax;
double gmax = g.getStatistics().max;
if (gmax > max) max = gmax;
double bmax = b.getStatistics().max;
if (bmax > max) max = bmax;
double scale = 255 / max;
r.multiply(scale);
g.multiply(scale);
b.multiply(scale);
red2.setProcessor(r.convertToByte(false));
green2.setProcessor(g.convertToByte(false));
blue2.setProcessor(b.convertToByte(false));
}
RGBStackMerge merge = new RGBStackMerge();
ImageStack stack2 =
merge.mergeStacks(w, h, d, red2.getStack(), green2.getStack(), blue2.getStack(), true);
imp = saveImp;
projImage = new ImagePlus(makeTitle(), stack2);
}
public void run(String arg) {
imp = IJ.getImage();
Roi roi = imp.getRoi();
if (roi != null && !roi.isArea()) imp.killRoi(); // ignore any line selection
ImageProcessor ip = imp.getProcessor();
if (!showDialog(ip)) return;
if (ip.getWidth() > 1 && ip.getHeight() > 1) ip.setInterpolate(interpolate);
else ip.setInterpolate(false);
ip.setBackgroundValue(bgValue);
imp.startTiming();
try {
if (newWindow && imp.getStackSize() > 1 && processStack) createNewStack(imp, ip);
else scale(ip);
} catch (OutOfMemoryError o) {
IJ.outOfMemory("Scale");
}
IJ.showProgress(1.0);
}
void enlargeCanvas() {
imp.unlock();
if (imp.getStackSize() == 1) Undo.setup(Undo.COMPOUND_FILTER, imp);
IJ.run("Select All");
IJ.run("Rotate...", "angle=" + angle);
Roi roi = imp.getRoi();
Rectangle r = roi.getBounds();
if (r.width < imp.getWidth()) r.width = imp.getWidth();
if (r.height < imp.getHeight()) r.height = imp.getHeight();
IJ.showStatus("Rotate: Enlarging...");
IJ.run(
"Canvas Size...",
"width="
+ r.width
+ " height="
+ r.height
+ " position=Center "
+ (fillWithBackground ? "" : "zero"));
IJ.showStatus("Rotating...");
}
void createNewStack(ImagePlus imp, ImageProcessor ip) {
Rectangle r = ip.getRoi();
boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight();
int nSlices = imp.getStackSize();
ImageStack stack1 = imp.getStack();
ImageStack stack2 = new ImageStack(newWidth, newHeight);
ImageProcessor ip1, ip2;
boolean interp = interpolate;
if (imp.getWidth() == 1 || imp.getHeight() == 1) interp = false;
for (int i = 1; i <= nSlices; i++) {
IJ.showStatus("Scale: " + i + "/" + nSlices);
ip1 = stack1.getProcessor(i);
String label = stack1.getSliceLabel(i);
if (crop) {
ip1.setRoi(r);
ip1 = ip1.crop();
}
ip1.setInterpolate(interp);
ip2 = ip1.resize(newWidth, newHeight);
if (ip2 != null) stack2.addSlice(label, ip2);
IJ.showProgress(i, nSlices);
}
ImagePlus imp2 = imp.createImagePlus();
imp2.setStack(title, stack2);
Calibration cal = imp2.getCalibration();
if (cal.scaled()) {
cal.pixelWidth *= 1.0 / xscale;
cal.pixelHeight *= 1.0 / yscale;
}
int[] dim = imp.getDimensions();
imp2.setDimensions(dim[2], dim[3], dim[4]);
IJ.showProgress(1.0);
if (imp.isComposite()) {
imp2 = new CompositeImage(imp2, 0);
((CompositeImage) imp2).copyLuts(imp);
}
if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true);
imp2.show();
imp2.changes = true;
}
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();
}
public void run(String arg) {
imp = IJ.getImage();
if (imp == null) return;
stackSize = imp.getStackSize();
Roi roi = imp.getRoi();
Calibration cal = imp.getCalibration();
if (roi != null && roi.getBounds().equals(prevRoi) && cal.pixelWidth == prevPixelWidth)
roi = null;
if (roi != null) {
boolean rectOrOval =
roi != null && (roi.getType() == Roi.RECTANGLE || roi.getType() == Roi.OVAL);
oval = rectOrOval && (roi.getType() == Roi.OVAL); // Handle existing oval ROI
Rectangle r = roi.getBounds();
width = r.width;
height = r.height;
xRoi = r.x;
yRoi = r.y;
if (scaledUnits && cal.scaled()) {
xRoi = xRoi * cal.pixelWidth;
yRoi = yRoi * cal.pixelHeight;
width = width * cal.pixelWidth;
height = height * cal.pixelHeight;
}
if (centered) { // Make xRoi and yRoi consistent when centered mode is active
xRoi += width / 2.0;
yRoi += height / 2.0;
}
} else if (!validDialogValues()) {
width = imp.getWidth() / 2;
height = imp.getHeight() / 2;
xRoi = width / 2;
yRoi = height / 2;
}
iSlice = imp.getCurrentSlice();
showDialog();
}
void setCalibration(ImagePlus imp) {
if (fi.fileType == FileInfo.GRAY16_SIGNED) {
if (IJ.debugMode) IJ.log("16-bit signed");
double[] coeff = new double[2];
coeff[0] = -32768.0;
coeff[1] = 1.0;
imp.getLocalCalibration().setFunction(Calibration.STRAIGHT_LINE, coeff, "gray value");
}
Properties props = decodeDescriptionString(fi);
Calibration cal = imp.getCalibration();
boolean calibrated = false;
if (fi.pixelWidth > 0.0 && fi.unit != null) {
cal.pixelWidth = fi.pixelWidth;
cal.pixelHeight = fi.pixelHeight;
cal.pixelDepth = fi.pixelDepth;
cal.setUnit(fi.unit);
calibrated = true;
}
if (fi.valueUnit != null) {
int f = fi.calibrationFunction;
if ((f >= Calibration.STRAIGHT_LINE && f <= Calibration.RODBARD2 && fi.coefficients != null)
|| f == Calibration.UNCALIBRATED_OD) {
boolean zeroClip = props != null && props.getProperty("zeroclip", "false").equals("true");
cal.setFunction(f, fi.coefficients, fi.valueUnit, zeroClip);
calibrated = true;
}
}
if (calibrated) checkForCalibrationConflict(imp, cal);
if (fi.frameInterval != 0.0) cal.frameInterval = fi.frameInterval;
if (props == null) return;
cal.xOrigin = getDouble(props, "xorigin");
cal.yOrigin = getDouble(props, "yorigin");
cal.zOrigin = getDouble(props, "zorigin");
cal.info = props.getProperty("info");
cal.fps = getDouble(props, "fps");
cal.loop = getBoolean(props, "loop");
cal.frameInterval = getDouble(props, "finterval");
cal.setTimeUnit(props.getProperty("tunit", "sec"));
double displayMin = getDouble(props, "min");
double displayMax = getDouble(props, "max");
if (!(displayMin == 0.0 && displayMax == 0.0)) {
int type = imp.getType();
ImageProcessor ip = imp.getProcessor();
if (type == ImagePlus.GRAY8 || type == ImagePlus.COLOR_256)
ip.setMinAndMax(displayMin, displayMax);
else if (type == ImagePlus.GRAY16 || type == ImagePlus.GRAY32) {
if (ip.getMin() != displayMin || ip.getMax() != displayMax)
ip.setMinAndMax(displayMin, displayMax);
}
}
int stackSize = imp.getStackSize();
if (stackSize > 1) {
int channels = (int) getDouble(props, "channels");
int slices = (int) getDouble(props, "slices");
int frames = (int) getDouble(props, "frames");
if (channels == 0) channels = 1;
if (slices == 0) slices = 1;
if (frames == 0) frames = 1;
// IJ.log("setCalibration: "+channels+" "+slices+" "+frames);
if (channels * slices * frames == stackSize) {
imp.setDimensions(channels, slices, frames);
if (getBoolean(props, "hyperstack")) imp.setOpenAsHyperStack(true);
}
}
}
String getInfo(ImagePlus imp, ImageProcessor ip) {
String s = new String("\n");
s += "Title: " + imp.getTitle() + "\n";
Calibration cal = imp.getCalibration();
int stackSize = imp.getStackSize();
int channels = imp.getNChannels();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int digits = imp.getBitDepth() == 32 ? 4 : 0;
if (cal.scaled()) {
String unit = cal.getUnit();
String units = cal.getUnits();
s +=
"Width: "
+ IJ.d2s(imp.getWidth() * cal.pixelWidth, 2)
+ " "
+ units
+ " ("
+ imp.getWidth()
+ ")\n";
s +=
"Height: "
+ IJ.d2s(imp.getHeight() * cal.pixelHeight, 2)
+ " "
+ units
+ " ("
+ imp.getHeight()
+ ")\n";
if (slices > 1)
s += "Depth: " + IJ.d2s(slices * cal.pixelDepth, 2) + " " + units + " (" + slices + ")\n";
double xResolution = 1.0 / cal.pixelWidth;
double yResolution = 1.0 / cal.pixelHeight;
int places = Tools.getDecimalPlaces(xResolution, yResolution);
if (xResolution == yResolution)
s += "Resolution: " + IJ.d2s(xResolution, places) + " pixels per " + unit + "\n";
else {
s += "X Resolution: " + IJ.d2s(xResolution, places) + " pixels per " + unit + "\n";
s += "Y Resolution: " + IJ.d2s(yResolution, places) + " pixels per " + unit + "\n";
}
} else {
s += "Width: " + imp.getWidth() + " pixels\n";
s += "Height: " + imp.getHeight() + " pixels\n";
if (stackSize > 1) s += "Depth: " + slices + " pixels\n";
}
if (stackSize > 1)
s +=
"Voxel size: "
+ d2s(cal.pixelWidth)
+ "x"
+ d2s(cal.pixelHeight)
+ "x"
+ d2s(cal.pixelDepth)
+ " "
+ cal.getUnit()
+ "\n";
else
s +=
"Pixel size: "
+ d2s(cal.pixelWidth)
+ "x"
+ d2s(cal.pixelHeight)
+ " "
+ cal.getUnit()
+ "\n";
s += "ID: " + imp.getID() + "\n";
String zOrigin = stackSize > 1 || cal.zOrigin != 0.0 ? "," + d2s(cal.zOrigin) : "";
s += "Coordinate origin: " + d2s(cal.xOrigin) + "," + d2s(cal.yOrigin) + zOrigin + "\n";
int type = imp.getType();
switch (type) {
case ImagePlus.GRAY8:
s += "Bits per pixel: 8 ";
String lut = "LUT";
if (imp.getProcessor().isColorLut()) lut = "color " + lut;
else lut = "grayscale " + lut;
if (imp.isInvertedLut()) lut = "inverting " + lut;
s += "(" + lut + ")\n";
if (imp.getNChannels() > 1) s += displayRanges(imp);
else s += "Display range: " + (int) ip.getMin() + "-" + (int) ip.getMax() + "\n";
break;
case ImagePlus.GRAY16:
case ImagePlus.GRAY32:
if (type == ImagePlus.GRAY16) {
String sign = cal.isSigned16Bit() ? "signed" : "unsigned";
s += "Bits per pixel: 16 (" + sign + ")\n";
} else s += "Bits per pixel: 32 (float)\n";
if (imp.getNChannels() > 1) s += displayRanges(imp);
else {
s += "Display range: ";
double min = ip.getMin();
double max = ip.getMax();
if (cal.calibrated()) {
min = cal.getCValue((int) min);
max = cal.getCValue((int) max);
}
s += IJ.d2s(min, digits) + " - " + IJ.d2s(max, digits) + "\n";
}
break;
case ImagePlus.COLOR_256:
s += "Bits per pixel: 8 (color LUT)\n";
break;
case ImagePlus.COLOR_RGB:
s += "Bits per pixel: 32 (RGB)\n";
break;
}
double interval = cal.frameInterval;
double fps = cal.fps;
if (stackSize > 1) {
ImageStack stack = imp.getStack();
int slice = imp.getCurrentSlice();
String number = slice + "/" + stackSize;
String label = stack.getShortSliceLabel(slice);
if (label != null && label.length() > 0) label = " (" + label + ")";
else label = "";
if (interval > 0.0 || fps != 0.0) {
s += "Frame: " + number + label + "\n";
if (fps != 0.0) {
String sRate =
Math.abs(fps - Math.round(fps)) < 0.00001 ? IJ.d2s(fps, 0) : IJ.d2s(fps, 5);
s += "Frame rate: " + sRate + " fps\n";
}
if (interval != 0.0)
s +=
"Frame interval: "
+ ((int) interval == interval ? IJ.d2s(interval, 0) : IJ.d2s(interval, 5))
+ " "
+ cal.getTimeUnit()
+ "\n";
} else s += "Image: " + number + label + "\n";
if (imp.isHyperStack()) {
if (channels > 1) s += " Channel: " + imp.getChannel() + "/" + channels + "\n";
if (slices > 1) s += " Slice: " + imp.getSlice() + "/" + slices + "\n";
if (frames > 1) s += " Frame: " + imp.getFrame() + "/" + frames + "\n";
}
if (imp.isComposite()) {
if (!imp.isHyperStack() && channels > 1) s += " Channels: " + channels + "\n";
String mode = ((CompositeImage) imp).getModeAsString();
s += " Composite mode: \"" + mode + "\"\n";
}
}
if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) s += "No Threshold\n";
else {
double lower = ip.getMinThreshold();
double upper = ip.getMaxThreshold();
int dp = digits;
if (cal.calibrated()) {
lower = cal.getCValue((int) lower);
upper = cal.getCValue((int) upper);
dp = cal.isSigned16Bit() ? 0 : 4;
}
s += "Threshold: " + IJ.d2s(lower, dp) + "-" + IJ.d2s(upper, dp) + "\n";
}
ImageCanvas ic = imp.getCanvas();
double mag = ic != null ? ic.getMagnification() : 1.0;
if (mag != 1.0) s += "Magnification: " + IJ.d2s(mag, 2) + "\n";
if (cal.calibrated()) {
s += " \n";
int curveFit = cal.getFunction();
s += "Calibration Function: ";
if (curveFit == Calibration.UNCALIBRATED_OD) s += "Uncalibrated OD\n";
else if (curveFit == Calibration.CUSTOM) s += "Custom lookup table\n";
else s += CurveFitter.fList[curveFit] + "\n";
double[] c = cal.getCoefficients();
if (c != null) {
s += " a: " + IJ.d2s(c[0], 6) + "\n";
s += " b: " + IJ.d2s(c[1], 6) + "\n";
if (c.length >= 3) s += " c: " + IJ.d2s(c[2], 6) + "\n";
if (c.length >= 4) s += " c: " + IJ.d2s(c[3], 6) + "\n";
if (c.length >= 5) s += " c: " + IJ.d2s(c[4], 6) + "\n";
}
s += " Unit: \"" + cal.getValueUnit() + "\"\n";
} else s += "Uncalibrated\n";
FileInfo fi = imp.getOriginalFileInfo();
if (fi != null) {
if (fi.url != null && !fi.url.equals("")) s += "URL: " + fi.url + "\n";
else if (fi.directory != null && fi.fileName != null)
s += "Path: " + fi.directory + fi.fileName + "\n";
}
ImageWindow win = imp.getWindow();
if (win != null) {
Point loc = win.getLocation();
Dimension screen = IJ.getScreenSize();
s +=
"Screen location: "
+ loc.x
+ ","
+ loc.y
+ " ("
+ screen.width
+ "x"
+ screen.height
+ ")\n";
}
Overlay overlay = imp.getOverlay();
if (overlay != null) {
String hidden = imp.getHideOverlay() ? " (hidden)" : " ";
int n = overlay.size();
String elements = n == 1 ? " element" : " elements";
s += "Overlay: " + n + elements + (imp.getHideOverlay() ? " (hidden)" : "") + "\n";
} else s += "No Overlay\n";
Roi roi = imp.getRoi();
if (roi == null) {
if (cal.calibrated()) s += " \n";
s += "No Selection\n";
} else if (roi instanceof EllipseRoi) {
s += "\nElliptical Selection\n";
double[] p = ((EllipseRoi) roi).getParams();
double dx = p[2] - p[0];
double dy = p[3] - p[1];
double major = Math.sqrt(dx * dx + dy * dy);
s += " Major: " + IJ.d2s(major, 2) + "\n";
s += " Minor: " + IJ.d2s(major * p[4], 2) + "\n";
s += " X1: " + IJ.d2s(p[0], 2) + "\n";
s += " Y1: " + IJ.d2s(p[1], 2) + "\n";
s += " X2: " + IJ.d2s(p[2], 2) + "\n";
s += " Y2: " + IJ.d2s(p[3], 2) + "\n";
s += " Aspect ratio: " + IJ.d2s(p[4], 2) + "\n";
} else {
s += " \n";
s += roi.getTypeAsString() + " Selection";
String points = null;
if (roi instanceof PointRoi) {
int npoints = ((PolygonRoi) roi).getNCoordinates();
String suffix = npoints > 1 ? "s)" : ")";
points = " (" + npoints + " point" + suffix;
}
String name = roi.getName();
if (name != null) {
s += " (\"" + name + "\")";
if (points != null) s += "\n " + points;
} else if (points != null) s += points;
s += "\n";
Rectangle r = roi.getBounds();
if (roi instanceof Line) {
Line line = (Line) roi;
s += " X1: " + IJ.d2s(line.x1d * cal.pixelWidth) + "\n";
s += " Y1: " + IJ.d2s(yy(line.y1d, imp) * cal.pixelHeight) + "\n";
s += " X2: " + IJ.d2s(line.x2d * cal.pixelWidth) + "\n";
s += " Y2: " + IJ.d2s(yy(line.y2d, imp) * cal.pixelHeight) + "\n";
} else if (cal.scaled()) {
s += " X: " + IJ.d2s(cal.getX(r.x)) + " (" + r.x + ")\n";
s += " Y: " + IJ.d2s(cal.getY(r.y, imp.getHeight())) + " (" + r.y + ")\n";
s += " Width: " + IJ.d2s(r.width * cal.pixelWidth) + " (" + r.width + ")\n";
s += " Height: " + IJ.d2s(r.height * cal.pixelHeight) + " (" + r.height + ")\n";
} else {
s += " X: " + r.x + "\n";
s += " Y: " + yy(r.y, imp) + "\n";
s += " Width: " + r.width + "\n";
s += " Height: " + r.height + "\n";
}
}
return s;
}
ImageProcessor setup(ImagePlus imp) {
ImageProcessor ip;
int type = imp.getType();
if (type != ImagePlus.COLOR_RGB) return null;
ip = imp.getProcessor();
int id = imp.getID();
int slice = imp.getCurrentSlice();
if ((id != previousImageID) | (slice != previousSlice) | (flag)) {
flag = false; // if true, flags a change from HSB to RGB or viceversa
numSlices = imp.getStackSize();
stack = imp.getStack();
width = stack.getWidth();
height = stack.getHeight();
numPixels = width * height;
hSource = new byte[numPixels];
sSource = new byte[numPixels];
bSource = new byte[numPixels];
// restore = (int[])ip.getPixelsCopy(); //This runs into trouble sometimes, so do it the
// long way:
int[] temp = (int[]) ip.getPixels();
restore = new int[numPixels];
for (int i = 0; i < numPixels; i++) restore[i] = temp[i];
fillMask = new int[numPixels];
// Get hsb or rgb from image.
ColorProcessor cp = (ColorProcessor) ip;
IJ.showStatus("Gathering data");
if (isRGB) cp.getRGB(hSource, sSource, bSource);
else cp.getHSB(hSource, sSource, bSource);
IJ.showStatus("done");
// Create a spectrum ColorModel for the Hue histogram plot.
Color c;
byte[] reds = new byte[256];
byte[] greens = new byte[256];
byte[] blues = new byte[256];
for (int i = 0; i < 256; i++) {
c = Color.getHSBColor(i / 255f, 1f, 1f);
reds[i] = (byte) c.getRed();
greens[i] = (byte) c.getGreen();
blues[i] = (byte) c.getBlue();
}
ColorModel cm = new IndexColorModel(8, 256, reds, greens, blues);
// Make an image with just the hue from the RGB image and the spectrum LUT.
// This is just for a hue histogram for the plot. Do not show it.
// ByteProcessor bpHue = new ByteProcessor(width,height,h,cm);
ByteProcessor bpHue = new ByteProcessor(width, height, hSource, cm);
ImagePlus impHue = new ImagePlus("Hue", bpHue);
// impHue.show();
ByteProcessor bpSat = new ByteProcessor(width, height, sSource, cm);
ImagePlus impSat = new ImagePlus("Sat", bpSat);
// impSat.show();
ByteProcessor bpBri = new ByteProcessor(width, height, bSource, cm);
ImagePlus impBri = new ImagePlus("Bri", bpBri);
// impBri.show();
plot.setHistogram(impHue, 0);
splot.setHistogram(impSat, 1);
bplot.setHistogram(impBri, 2);
updateLabels();
updatePlot();
updateScrollBars();
imp.updateAndDraw();
}
previousImageID = id;
previousSlice = slice;
return ip;
}
/** 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 keyPressed(KeyEvent e) {
// if (e.isConsumed()) return;
int keyCode = e.getKeyCode();
IJ.setKeyDown(keyCode);
hotkey = false;
if (keyCode == KeyEvent.VK_CONTROL || keyCode == KeyEvent.VK_SHIFT) return;
char keyChar = e.getKeyChar();
int flags = e.getModifiers();
if (IJ.debugMode)
IJ.log(
"keyPressed: code="
+ keyCode
+ " ("
+ KeyEvent.getKeyText(keyCode)
+ "), char=\""
+ keyChar
+ "\" ("
+ (int) keyChar
+ "), flags="
+ KeyEvent.getKeyModifiersText(flags));
boolean shift = (flags & KeyEvent.SHIFT_MASK) != 0;
boolean control = (flags & KeyEvent.CTRL_MASK) != 0;
boolean alt = (flags & KeyEvent.ALT_MASK) != 0;
boolean meta = (flags & KeyEvent.META_MASK) != 0;
String cmd = null;
ImagePlus imp = WindowManager.getCurrentImage();
boolean isStack = (imp != null) && (imp.getStackSize() > 1);
if (imp != null
&& !control
&& ((keyChar >= 32 && keyChar <= 255) || keyChar == '\b' || keyChar == '\n')) {
Roi roi = imp.getRoi();
if (roi instanceof TextRoi) {
if ((flags & KeyEvent.META_MASK) != 0 && IJ.isMacOSX()) return;
if (alt) {
switch (keyChar) {
case 'u':
case 'm':
keyChar = IJ.micronSymbol;
break;
case 'A':
keyChar = IJ.angstromSymbol;
break;
default:
}
}
((TextRoi) roi).addChar(keyChar);
return;
}
}
// Handle one character macro shortcuts
if (!control && !meta) {
Hashtable macroShortcuts = Menus.getMacroShortcuts();
if (macroShortcuts.size() > 0) {
if (shift) cmd = (String) macroShortcuts.get(new Integer(keyCode + 200));
else cmd = (String) macroShortcuts.get(new Integer(keyCode));
if (cmd != null) {
// MacroInstaller.runMacroCommand(cmd);
commandName = cmd;
MacroInstaller.runMacroShortcut(cmd);
return;
}
}
}
if ((!Prefs.requireControlKey || control || meta) && keyChar != '+') {
Hashtable shortcuts = Menus.getShortcuts();
if (shift) cmd = (String) shortcuts.get(new Integer(keyCode + 200));
else cmd = (String) shortcuts.get(new Integer(keyCode));
}
if (cmd == null) {
switch (keyChar) {
case '<':
case ',':
if (isStack) cmd = "Previous Slice [<]";
break;
case '>':
case '.':
case ';':
if (isStack) cmd = "Next Slice [>]";
break;
case '+':
case '=':
cmd = "In [+]";
break;
case '-':
cmd = "Out [-]";
break;
case '/':
cmd = "Reslice [/]...";
break;
default:
}
}
if (cmd == null) {
switch (keyCode) {
case KeyEvent.VK_TAB:
WindowManager.putBehind();
return;
case KeyEvent.VK_BACK_SPACE: // delete
if (deleteOverlayRoi(imp)) return;
cmd = "Clear";
hotkey = true;
break;
// case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start
// Animation"; break;
case KeyEvent.VK_EQUALS:
cmd = "In [+]";
break;
case KeyEvent.VK_MINUS:
cmd = "Out [-]";
break;
case KeyEvent.VK_SLASH:
case 0xbf:
cmd = "Reslice [/]...";
break;
case KeyEvent.VK_COMMA:
case 0xbc:
if (isStack) cmd = "Previous Slice [<]";
break;
case KeyEvent.VK_PERIOD:
case 0xbe:
if (isStack) cmd = "Next Slice [>]";
break;
case KeyEvent.VK_LEFT:
case KeyEvent.VK_RIGHT:
case KeyEvent.VK_UP:
case KeyEvent.VK_DOWN: // arrow keys
if (imp == null) return;
Roi roi = imp.getRoi();
if (IJ.shiftKeyDown() && imp == Orthogonal_Views.getImage()) return;
boolean stackKey = imp.getStackSize() > 1 && (roi == null || IJ.shiftKeyDown());
boolean zoomKey = roi == null || IJ.shiftKeyDown() || IJ.controlKeyDown();
if (stackKey && keyCode == KeyEvent.VK_RIGHT) cmd = "Next Slice [>]";
else if (stackKey && keyCode == KeyEvent.VK_LEFT) cmd = "Previous Slice [<]";
else if (zoomKey
&& keyCode == KeyEvent.VK_DOWN
&& !ignoreArrowKeys(imp)
&& Toolbar.getToolId() < Toolbar.SPARE6) cmd = "Out [-]";
else if (zoomKey
&& keyCode == KeyEvent.VK_UP
&& !ignoreArrowKeys(imp)
&& Toolbar.getToolId() < Toolbar.SPARE6) cmd = "In [+]";
else if (roi != null) {
if ((flags & KeyEvent.ALT_MASK) != 0) roi.nudgeCorner(keyCode);
else roi.nudge(keyCode);
return;
}
break;
case KeyEvent.VK_ESCAPE:
abortPluginOrMacro(imp);
return;
case KeyEvent.VK_ENTER:
WindowManager.toFront(this);
return;
default:
break;
}
}
if (cmd != null && !cmd.equals("")) {
commandName = cmd;
if (cmd.equals("Fill") || cmd.equals("Draw")) hotkey = true;
if (cmd.charAt(0) == MacroInstaller.commandPrefix) MacroInstaller.runMacroShortcut(cmd);
else {
doCommand(cmd);
keyPressedTime = System.currentTimeMillis();
lastKeyCommand = cmd;
}
}
}
boolean showDialog(ImageProcessor ip) {
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);
}
int bitDepth = imp.getBitDepth();
int stackSize = imp.getStackSize();
boolean isStack = stackSize > 1;
oldDepth = stackSize;
if (isStack) {
xstr = "1.0";
ystr = "1.0";
zstr = "1.0";
}
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
zscale = 1.0;
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale:", xstr);
gd.addStringField("Y Scale:", ystr);
if (isStack) gd.addStringField("Z Scale:", zstr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
if (isStack) {
String label = "Depth (images):";
if (imp.isHyperStack()) {
int slices = imp.getNSlices();
int frames = imp.getNFrames();
if (slices == 1 && frames > 1) {
label = "Depth (frames):";
oldDepth = frames;
} else {
label = "Depth (slices):";
oldDepth = slices;
}
}
gd.addStringField(label, "" + oldDepth);
}
fields = gd.getStringFields();
for (int i = 0; i < fields.size(); i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
if (isStack) {
zField = (TextField) fields.elementAt(2);
widthField = (TextField) fields.elementAt(3);
heightField = (TextField) fields.elementAt(4);
depthField = (TextField) fields.elementAt(5);
} else {
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
}
fieldWithFocus = xField;
gd.addChoice("Interpolation:", methods, methods[interpolationMethod]);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with background color", fillWithBackground);
gd.addCheckbox("Average when downsizing", averageWhenDownsizing);
boolean hyperstack = imp.isHyperStack() || imp.isComposite();
if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack);
gd.addCheckbox("Create new window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (isStack) {
zstr = gd.getNextString();
zscale = Tools.parseDouble(ystr, 0.0);
}
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Scaler", "Width or height is 0");
return false;
}
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0);
interpolationMethod = gd.getNextChoiceIndex();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
averageWhenDownsizing = gd.getNextBoolean();
if (isStack && !hyperstack) processStack = gd.getNextBoolean();
if (hyperstack) processStack = true;
newWindow = gd.getNextBoolean();
if (xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else bgValue = 0.0;
return true;
}
/**
* Performs particle analysis on the specified ImagePlus and ImageProcessor. Returns false if
* there is an error.
*/
public boolean analyze(ImagePlus imp, ImageProcessor ip) {
if (this.imp == null) this.imp = imp;
showResults = (options & SHOW_RESULTS) != 0;
excludeEdgeParticles = (options & EXCLUDE_EDGE_PARTICLES) != 0;
resetCounter = (options & CLEAR_WORKSHEET) != 0;
showProgress = (options & SHOW_PROGRESS) != 0;
floodFill = (options & INCLUDE_HOLES) == 0;
recordStarts = (options & RECORD_STARTS) != 0;
addToManager = (options & ADD_TO_MANAGER) != 0;
displaySummary = (options & DISPLAY_SUMMARY) != 0;
inSituShow = (options & IN_SITU_SHOW) != 0;
outputImage = null;
ip.snapshot();
ip.setProgressBar(null);
if (Analyzer.isRedirectImage()) {
redirectImp = Analyzer.getRedirectImage(imp);
if (redirectImp == null) return false;
int depth = redirectImp.getStackSize();
if (depth > 1 && depth == imp.getStackSize()) {
ImageStack redirectStack = redirectImp.getStack();
redirectIP = redirectStack.getProcessor(imp.getCurrentSlice());
} else redirectIP = redirectImp.getProcessor();
} else if (imp.getType() == ImagePlus.COLOR_RGB) {
ImagePlus original = (ImagePlus) imp.getProperty("OriginalImage");
if (original != null
&& original.getWidth() == imp.getWidth()
&& original.getHeight() == imp.getHeight()) {
redirectImp = original;
redirectIP = original.getProcessor();
}
}
if (!setThresholdLevels(imp, ip)) return false;
width = ip.getWidth();
height = ip.getHeight();
if (!(showChoice == NOTHING || showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS)) {
blackBackground = Prefs.blackBackground && inSituShow;
if (slice == 1) outlines = new ImageStack(width, height);
if (showChoice == ROI_MASKS) drawIP = new ShortProcessor(width, height);
else drawIP = new ByteProcessor(width, height);
drawIP.setLineWidth(lineWidth);
if (showChoice == ROI_MASKS) {
} // Place holder for now...
else if (showChoice == MASKS && !blackBackground) drawIP.invertLut();
else if (showChoice == OUTLINES) {
if (!inSituShow) {
if (customLut == null) makeCustomLut();
drawIP.setColorModel(customLut);
}
drawIP.setFont(new Font("SansSerif", Font.PLAIN, fontSize));
if (fontSize > 12 && inSituShow) drawIP.setAntialiasedText(true);
}
outlines.addSlice(null, drawIP);
if (showChoice == ROI_MASKS || blackBackground) {
drawIP.setColor(Color.black);
drawIP.fill();
drawIP.setColor(Color.white);
} else {
drawIP.setColor(Color.white);
drawIP.fill();
drawIP.setColor(Color.black);
}
}
calibration = redirectImp != null ? redirectImp.getCalibration() : imp.getCalibration();
if (rt == null) {
rt = Analyzer.getResultsTable();
analyzer = new Analyzer(imp);
} else analyzer = new Analyzer(imp, measurements, rt);
if (resetCounter && slice == 1) {
if (!Analyzer.resetCounter()) return false;
}
beginningCount = Analyzer.getCounter();
byte[] pixels = null;
if (ip instanceof ByteProcessor) pixels = (byte[]) ip.getPixels();
if (r == null) {
r = ip.getRoi();
mask = ip.getMask();
if (displaySummary) {
if (mask != null) totalArea = ImageStatistics.getStatistics(ip, AREA, calibration).area;
else totalArea = r.width * calibration.pixelWidth * r.height * calibration.pixelHeight;
}
}
minX = r.x;
maxX = r.x + r.width;
minY = r.y;
maxY = r.y + r.height;
if (r.width < width || r.height < height || mask != null) {
if (!eraseOutsideRoi(ip, r, mask)) return false;
}
int offset;
double value;
int inc = Math.max(r.height / 25, 1);
int mi = 0;
ImageWindow win = imp.getWindow();
if (win != null) win.running = true;
if (measurements == 0) measurements = Analyzer.getMeasurements();
if (showChoice == ELLIPSES) measurements |= ELLIPSE;
measurements &= ~LIMIT; // ignore "Limit to Threshold"
roiNeedsImage =
(measurements & PERIMETER) != 0
|| (measurements & SHAPE_DESCRIPTORS) != 0
|| (measurements & FERET) != 0;
particleCount = 0;
wand = new Wand(ip);
pf = new PolygonFiller();
if (floodFill) {
ImageProcessor ipf = ip.duplicate();
ipf.setValue(fillColor);
ff = new FloodFiller(ipf);
}
roiType = Wand.allPoints() ? Roi.FREEROI : Roi.TRACED_ROI;
for (int y = r.y; y < (r.y + r.height); y++) {
offset = y * width;
for (int x = r.x; x < (r.x + r.width); x++) {
if (pixels != null) value = pixels[offset + x] & 255;
else if (imageType == SHORT) value = ip.getPixel(x, y);
else value = ip.getPixelValue(x, y);
if (value >= level1 && value <= level2) analyzeParticle(x, y, imp, ip);
}
if (showProgress && ((y % inc) == 0)) IJ.showProgress((double) (y - r.y) / r.height);
if (win != null) canceled = !win.running;
if (canceled) {
Macro.abort();
break;
}
}
if (showProgress) IJ.showProgress(1.0);
if (showResults) rt.updateResults();
imp.killRoi();
ip.resetRoi();
ip.reset();
if (displaySummary && IJ.getInstance() != null) updateSliceSummary();
if (addToManager && roiManager != null) roiManager.setEditMode(imp, true);
maxParticleCount = (particleCount > maxParticleCount) ? particleCount : maxParticleCount;
totalCount += particleCount;
if (!canceled) showResults();
return true;
}
public void textValueChanged(TextEvent e) {
Object source = e.getSource();
double newXScale = xscale;
double newYScale = yscale;
double newZScale = zscale;
if (source == xField && fieldWithFocus == xField) {
String newXText = xField.getText();
newXScale = Tools.parseDouble(newXText, 0);
if (newXScale == 0) return;
if (newXScale != xscale) {
int newWidth = (int) (newXScale * r.width);
widthField.setText("" + newWidth);
if (constainAspectRatio) {
yField.setText(newXText);
int newHeight = (int) (newXScale * r.height);
heightField.setText("" + newHeight);
}
}
} else if (source == yField && fieldWithFocus == yField) {
String newYText = yField.getText();
newYScale = Tools.parseDouble(newYText, 0);
if (newYScale == 0) return;
if (newYScale != yscale) {
int newHeight = (int) (newYScale * r.height);
heightField.setText("" + newHeight);
}
} else if (source == zField && fieldWithFocus == zField) {
String newZText = zField.getText();
newZScale = Tools.parseDouble(newZText, 0);
if (newZScale == 0) return;
if (newZScale != zscale) {
int nSlices = imp.getStackSize();
if (imp.isHyperStack()) {
int slices = imp.getNSlices();
int frames = imp.getNFrames();
if (slices == 1 && frames > 1) nSlices = frames;
else nSlices = slices;
}
int newDepth = (int) (newZScale * nSlices);
depthField.setText("" + newDepth);
}
} else if (source == widthField && fieldWithFocus == widthField) {
int newWidth = (int) Tools.parseDouble(widthField.getText(), 0.0);
if (newWidth != 0) {
int newHeight = (int) (newWidth * (double) r.height / r.width);
heightField.setText("" + newHeight);
xField.setText("-");
yField.setText("-");
newXScale = 0.0;
newYScale = 0.0;
}
} else if (source == depthField && fieldWithFocus == depthField) {
int newDepth = (int) Tools.parseDouble(depthField.getText(), 0.0);
if (newDepth != 0) {
zField.setText("-");
newZScale = 0.0;
}
}
xscale = newXScale;
yscale = newYScale;
zscale = newZScale;
}
boolean showDialog(ImageProcessor ip) {
int bitDepth = imp.getBitDepth();
boolean isStack = imp.getStackSize() > 1;
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale (0.05-25):", xstr);
gd.addStringField("Y Scale (0.05-25):", ystr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
fields = gd.getStringFields();
for (int i = 0; i < 3; i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
fieldWithFocus = xField;
gd.addCheckbox("Interpolate", interpolate);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with Background Color", fillWithBackground);
if (isStack) gd.addCheckbox("Process Entire Stack", processStack);
gd.addCheckbox("Create New Window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Invalid width or height entered");
return false;
}
if (xscale > 25.0) xscale = 25.0;
if (yscale > 25.0) yscale = 25.0;
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
interpolate = gd.getNextBoolean();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
if (isStack) processStack = gd.getNextBoolean();
newWindow = gd.getNextBoolean();
if (!newWindow && xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else {
if (bitDepth == 8) bgValue = ip.isInvertedLut() ? 0.0 : 255.0; // white
else if (bitDepth == 24) bgValue = 0xffffffff; // white
}
return true;
}
