void addToRoiManager(ImagePlus imp) {
if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
if (imp == null) return;
Roi roi = imp.getRoi();
if (roi == null) return;
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
RoiManager rm = (RoiManager) frame;
boolean altDown = IJ.altKeyDown();
IJ.setKeyUp(IJ.ALL_KEYS);
if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
if (roi.getState() == Roi.CONSTRUCTING) { // wait (up to 2 sec.) until ROI finished
long start = System.currentTimeMillis();
while (true) {
IJ.wait(10);
if (roi.getState() != Roi.CONSTRUCTING) break;
if ((System.currentTimeMillis() - start) > 2000) {
IJ.beep();
IJ.error("Add to Manager", "Selection is not complete");
return;
}
}
}
rm.runCommand("add");
IJ.setKeyUp(IJ.ALL_KEYS);
}
/**
* 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 String[] getOpenImageNames() {
int[] imageIDList = WindowManager.getIDList();
String[] imageNames = new String[imageIDList.length];
// imageNames[0] = "None";
if (!imageIDList.equals(null) && imageIDList.length > 1) {
for (int i = 0; i < imageIDList.length; i++) {
ImagePlus tempIMP = WindowManager.getImage(imageIDList[i]);
imageNames[i] = tempIMP.getTitle();
}
return imageNames;
} else {
imageNames[0] = "None";
return imageNames;
}
}
public void run(String arg) {
imp = WindowManager.getCurrentImage();
if (arg.equals("add")) {
addToRoiManager(imp);
return;
}
if (imp == null) {
IJ.noImage();
return;
}
if (arg.equals("all")) imp.setRoi(0, 0, imp.getWidth(), imp.getHeight());
else if (arg.equals("none")) imp.killRoi();
else if (arg.equals("restore")) imp.restoreRoi();
else if (arg.equals("spline")) fitSpline();
else if (arg.equals("circle")) fitCircle(imp);
else if (arg.equals("ellipse")) createEllipse(imp);
else if (arg.equals("hull")) convexHull(imp);
else if (arg.equals("mask")) createMask(imp);
else if (arg.equals("from")) createSelectionFromMask(imp);
else if (arg.equals("inverse")) invert(imp);
else if (arg.equals("toarea")) lineToArea(imp);
else if (arg.equals("toline")) areaToLine(imp);
else if (arg.equals("properties")) {
setProperties("Properties ", imp.getRoi());
imp.draw();
} else if (arg.equals("band")) makeBand(imp);
else if (arg.equals("tobox")) toBoundingBox(imp);
else runMacro(arg);
}
void createMask(ImagePlus imp) {
Roi roi = imp.getRoi();
boolean useInvertingLut = Prefs.useInvertingLut;
Prefs.useInvertingLut = false;
if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT)) {
createMaskFromThreshold(imp);
Prefs.useInvertingLut = useInvertingLut;
return;
}
ImagePlus maskImp = null;
Frame frame = WindowManager.getFrame("Mask");
if (frame != null && (frame instanceof ImageWindow))
maskImp = ((ImageWindow) frame).getImagePlus();
if (maskImp == null) {
ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
if (!Prefs.blackBackground) ip.invertLut();
maskImp = new ImagePlus("Mask", ip);
maskImp.show();
}
ImageProcessor ip = maskImp.getProcessor();
ip.setRoi(roi);
ip.setValue(255);
ip.fill(ip.getMask());
maskImp.updateAndDraw();
Prefs.useInvertingLut = useInvertingLut;
}
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);
}
void addToRoiManager(ImagePlus imp) {
if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
if (imp == null) return;
Roi roi = imp.getRoi();
if (roi == null) return;
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
RoiManager rm = (RoiManager) frame;
boolean altDown = IJ.altKeyDown();
IJ.setKeyUp(IJ.ALL_KEYS);
if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
rm.runCommand("add");
IJ.setKeyUp(IJ.ALL_KEYS);
}
boolean setProperties(String title, Roi roi) {
Frame f = WindowManager.getFrontWindow();
if (f != null && f.getTitle().indexOf("3D Viewer") != -1) return false;
if (roi == null) {
IJ.error("This command requires a selection.");
return false;
}
RoiProperties rp = new RoiProperties(title, roi);
return rp.showDialog();
}
/** Sets the color used used for the ROI Manager "Show All" mode. */
public static void setShowAllColor(Color c) {
if (c == null) return;
showAllColor = c;
labelColor = null;
ImagePlus img = WindowManager.getCurrentImage();
if (img != null) {
ImageCanvas ic = img.getCanvas();
if (ic != null && ic.getShowAllROIs()) img.draw();
}
}
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;
}
void createMaskFromThreshold(ImagePlus imp) {
ImageProcessor ip = imp.getProcessor();
if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) {
IJ.error("Create Mask", "Area selection or thresholded image required");
return;
}
double t1 = ip.getMinThreshold();
double t2 = ip.getMaxThreshold();
IJ.run("Duplicate...", "title=mask");
ImagePlus imp2 = WindowManager.getCurrentImage();
ImageProcessor ip2 = imp2.getProcessor();
ip2.setThreshold(t1, t2, ImageProcessor.NO_LUT_UPDATE);
IJ.run("Convert to Mask");
}
void checkForCalibrationConflict(ImagePlus imp, Calibration cal) {
Calibration gcal = imp.getGlobalCalibration();
if (gcal == null || !showConflictMessage || IJ.isMacro()) return;
if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return;
GenericDialog gd = new GenericDialog(imp.getTitle());
gd.addMessage("The calibration of this image conflicts\nwith the current global calibration.");
gd.addCheckbox("Disable_Global Calibration", true);
gd.addCheckbox("Disable_these Messages", false);
gd.showDialog();
if (gd.wasCanceled()) return;
boolean disable = gd.getNextBoolean();
if (disable) {
imp.setGlobalCalibration(null);
imp.setCalibration(cal);
WindowManager.repaintImageWindows();
}
boolean dontShow = gd.getNextBoolean();
if (dontShow) showConflictMessage = false;
}
void createMask(ImagePlus imp) {
Roi roi = imp.getRoi();
boolean useInvertingLut = Prefs.useInvertingLut;
Prefs.useInvertingLut = false;
boolean selectAll =
roi != null
&& roi.getType() == Roi.RECTANGLE
&& roi.getBounds().width == imp.getWidth()
&& roi.getBounds().height == imp.getHeight()
&& imp.isThreshold();
if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT) || selectAll) {
createMaskFromThreshold(imp);
Prefs.useInvertingLut = useInvertingLut;
return;
}
ImagePlus maskImp = null;
Frame frame = WindowManager.getFrame("Mask");
if (frame != null && (frame instanceof ImageWindow))
maskImp = ((ImageWindow) frame).getImagePlus();
if (maskImp == null) {
ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
if (!Prefs.blackBackground) ip.invertLut();
maskImp = new ImagePlus("Mask", ip);
maskImp.show();
}
ImageProcessor ip = maskImp.getProcessor();
ip.setRoi(roi);
ip.setValue(255);
ip.fill(ip.getMask());
Calibration cal = imp.getCalibration();
if (cal.scaled()) {
Calibration cal2 = maskImp.getCalibration();
cal2.pixelWidth = cal.pixelWidth;
cal2.pixelHeight = cal.pixelHeight;
cal2.setUnit(cal.getUnit());
}
maskImp.updateAndRepaintWindow();
Prefs.useInvertingLut = useInvertingLut;
}
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
Calibration cal = imp.getCalibration();
GenericDialog gd = new GenericDialog("Options");
int subsize = 32;
gd.addNumericField("Subregion Size (pixels)?", subsize, 0);
int stepsize = 16;
gd.addNumericField("Step Size?", stepsize, 0);
int shift = 3;
gd.addNumericField("STICS temporal Shift?", shift, 0);
float xoffset = 0.0f;
gd.addNumericField("X_Offset", xoffset, 5, 15, null);
float yoffset = 0.0f;
gd.addNumericField("Y_Offset", yoffset, 5, 15, null);
float multiplier = 8.0f;
gd.addNumericField("Velocity Multiplier", multiplier, 5, 15, null);
float ftime = 1.0f;
gd.addNumericField("Frame_Time(min)", ftime, 5, 15, null);
float scaling = (float) cal.pixelWidth;
gd.addNumericField("Pixel_Size(um)", scaling, 5, 15, null);
boolean norm = true;
gd.addCheckbox("Normalize_Vector_lengths?", norm);
boolean centered = true;
gd.addCheckbox("Center_Vectors?", centered);
float magthresh = 0.0f;
gd.addNumericField("Magnitude_Threshhold?", magthresh, 5, 15, null);
int rlength = 10;
gd.addNumericField("Running_avg_length", rlength, 0);
int inc = 5;
gd.addNumericField("Start_frame_increment", inc, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
subsize = (int) gd.getNextNumber();
stepsize = (int) gd.getNextNumber();
shift = (int) gd.getNextNumber();
xoffset = (float) gd.getNextNumber();
yoffset = (float) gd.getNextNumber();
multiplier = (float) gd.getNextNumber();
ftime = (float) gd.getNextNumber();
scaling = (float) gd.getNextNumber();
norm = gd.getNextBoolean();
centered = gd.getNextBoolean();
magthresh = (float) gd.getNextNumber();
rlength = (int) gd.getNextNumber();
inc = (int) gd.getNextNumber();
int width = imp.getWidth();
int xregions = 1 + (int) (((float) width - (float) subsize) / (float) stepsize);
int newwidth = xregions * subsize;
int height = imp.getHeight();
int yregions = 1 + (int) (((float) height - (float) subsize) / (float) stepsize);
int newheight = yregions * subsize;
ImageStack stack = imp.getStack();
int slices = imp.getNSlices();
int channels = imp.getNChannels();
int frames = imp.getNFrames();
if (frames == 1) {
frames = slices;
slices = 1;
}
Roi roi = imp.getRoi();
if (roi == null) {
roi = new Roi(0, 0, width, height);
}
STICS_map map = new STICS_map(subsize, stepsize);
Object[] tseries = jutils.get3DTSeries(stack, 0, 0, frames, slices, channels);
map.update_STICS_map(tseries, width, height, 0, rlength, roi.getPolygon(), shift);
FloatProcessor fp =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
ImageStack vector_stack = new ImageStack(fp.getWidth(), fp.getHeight());
vector_stack.addSlice("", fp);
float[][] vel = map.get_scaled_velocities(scaling, ftime, stepsize);
ImageStack velstack = new ImageStack(map.xregions, map.yregions);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
int velframes = 2;
IJ.showStatus("frame " + 0 + " calculated");
for (int i = inc; i < (frames - rlength); i += inc) {
map.update_STICS_map(tseries, width, height, i, rlength, roi.getPolygon(), shift);
FloatProcessor fp2 =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
vector_stack.addSlice("", fp2);
vel = map.get_scaled_velocities(scaling, ftime, stepsize);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
velframes += 2;
IJ.showStatus("frame " + i + " calculated");
}
(new ImagePlus("STICS Vectors", vector_stack)).show();
ImagePlus imp3 = new ImagePlus("Velocities", velstack);
imp3.setOpenAsHyperStack(true);
imp3.setDimensions(2, 1, velframes / 2);
new CompositeImage(imp3, CompositeImage.COLOR).show();
}
public BandAdjuster() {
super("Threshold Colour");
if (instance != null) {
instance.toFront();
return;
}
imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.beep();
IJ.showStatus("No image");
return;
}
IJ.run("Select None");
thread = new Thread(this, "BandAdjuster");
WindowManager.addWindow(this);
instance = this;
IJ.register(PasteController.class);
ij = IJ.getInstance();
Font font = new Font("SansSerif", Font.PLAIN, 10);
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
setLayout(gridbag);
int y = 0;
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
labelh = new Label("Hue", Label.CENTER);
add(labelh, c);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(7, 0, 0, 0);
labelf = new Label("Filter type", Label.RIGHT);
add(labelf, c);
// plot
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(plot, c);
// checkboxes
panelh = new Panel();
filterTypeH = new CheckboxGroup();
bandPassH = new Checkbox("Pass");
bandPassH.setCheckboxGroup(filterTypeH);
bandPassH.addItemListener(this);
panelh.add(bandPassH);
bandStopH = new Checkbox("Stop");
bandStopH.setCheckboxGroup(filterTypeH);
bandStopH.addItemListener(this);
panelh.add(bandStopH);
bandPassH.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panelh, c);
// minHue slider
minSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider, c);
minSlider.addAdjustmentListener(this);
minSlider.setUnitIncrement(1);
// minHue slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label1 = new Label(" ", Label.LEFT);
label1.setFont(font);
add(label1, c);
// maxHue sliderHue
maxSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider, c);
maxSlider.addAdjustmentListener(this);
maxSlider.setUnitIncrement(1);
// maxHue slider label
c.gridx = 1;
c.gridwidth = 1;
c.gridy = y++;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label2 = new Label(" ", Label.LEFT);
label2.setFont(font);
add(label2, c);
// =====
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(10, 0, 0, 0);
labels = new Label("Saturation", Label.CENTER);
add(labels, c);
// plot
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(splot, c);
// checkboxes
panels = new Panel();
filterTypeS = new CheckboxGroup();
bandPassS = new Checkbox("Pass");
bandPassS.setCheckboxGroup(filterTypeS);
bandPassS.addItemListener(this);
panels.add(bandPassS);
bandStopS = new Checkbox("Stop");
bandStopS.setCheckboxGroup(filterTypeS);
bandStopS.addItemListener(this);
panels.add(bandStopS);
bandPassS.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panels, c);
// minSat slider
minSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider2, c);
minSlider2.addAdjustmentListener(this);
minSlider2.setUnitIncrement(1);
// minSat slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label3 = new Label(" ", Label.LEFT);
label3.setFont(font);
add(label3, c);
// maxSat slider
maxSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider2, c);
maxSlider2.addAdjustmentListener(this);
maxSlider2.setUnitIncrement(1);
// maxSat slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label4 = new Label(" ", Label.LEFT);
label4.setFont(font);
add(label4, c);
// =====
c.gridx = 0;
c.gridwidth = 1;
c.gridy = y++;
c.weightx = 0;
c.insets = new Insets(10, 0, 0, 0);
labelb = new Label("Brightness", Label.CENTER);
add(labelb, c);
c.gridx = 0;
c.gridwidth = 1;
c.gridy = y;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(bplot, c);
// checkboxes
panelb = new Panel();
filterTypeB = new CheckboxGroup();
bandPassB = new Checkbox("Pass");
bandPassB.setCheckboxGroup(filterTypeB);
bandPassB.addItemListener(this);
panelb.add(bandPassB);
bandStopB = new Checkbox("Stop");
bandStopB.setCheckboxGroup(filterTypeB);
bandStopB.addItemListener(this);
panelb.add(bandStopB);
bandPassB.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panelb, c);
// minBri slider
minSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider3, c);
minSlider3.addAdjustmentListener(this);
minSlider3.setUnitIncrement(1);
// minBri slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label5 = new Label(" ", Label.LEFT);
label5.setFont(font);
add(label5, c);
// maxBri slider
maxSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider3, c);
maxSlider3.addAdjustmentListener(this);
maxSlider3.setUnitIncrement(1);
// maxBri slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label6 = new Label(" ", Label.LEFT);
label6.setFont(font);
add(label6, c);
// =====
panelt = new Panel();
threshold = new Checkbox("Threshold");
threshold.addItemListener(this);
panelt.add(threshold);
invert = new Checkbox("Invert");
invert.addItemListener(this);
panelt.add(invert);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panelt, c);
// buttons
panel = new Panel();
// panel.setLayout(new GridLayout(2, 2, 0, 0));
originalB = new Button("Original");
originalB.setEnabled(false);
originalB.addActionListener(this);
originalB.addKeyListener(ij);
panel.add(originalB);
filteredB = new Button("Filtered");
filteredB.setEnabled(false);
filteredB.addActionListener(this);
filteredB.addKeyListener(ij);
panel.add(filteredB);
stackB = new Button("Stack");
stackB.addActionListener(this);
stackB.addKeyListener(ij);
panel.add(stackB);
helpB = new Button("Help");
helpB.addActionListener(this);
helpB.addKeyListener(ij);
panel.add(helpB);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panel, c);
panelMode = new Panel();
sampleB = new Button("Sample");
sampleB.addActionListener(this);
sampleB.addKeyListener(ij);
panelMode.add(sampleB);
colourMode = new CheckboxGroup();
hsb = new Checkbox("HSB");
hsb.setCheckboxGroup(colourMode);
hsb.addItemListener(this);
panelMode.add(hsb);
hsb.setState(true);
rgb = new Checkbox("RGB");
rgb.setCheckboxGroup(colourMode);
rgb.addItemListener(this);
panelMode.add(rgb);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panelMode, c);
addKeyListener(ij); // ImageJ handles keyboard shortcuts
pack();
GUI.center(this);
setVisible(true);
ip = setup(imp);
if (ip == null) {
imp.unlock();
IJ.beep();
IJ.showStatus("RGB image cannot be thresholded");
return;
}
thread.start();
}
public void run(ImageProcessor ip) {
String[] imageNames = getOpenImageNames();
if (imageNames[0] == "None") {
IJ.error("need at least 2 binary open images");
return;
}
double previousMinOverlap = Prefs.get("BVTB.BinaryFeatureExtractor.minOverlap", 0);
boolean previousCombine = Prefs.get("BVTB.BinaryFeatureExtractor.combine", false);
GenericDialog gd = new GenericDialog("Binary Feature Extractor");
gd.addChoice("Objects image", imageNames, imageNames[0]);
gd.addChoice("Selector image", imageNames, imageNames[1]);
gd.addNumericField("Object_overlap in % (0=off)", previousMinOverlap, 0, 9, "");
gd.addCheckbox("Combine objects and selectors", previousCombine);
gd.addCheckbox("Count output", true);
gd.addCheckbox("Analysis tables", false);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
String objectsImgTitle = gd.getNextChoice();
String selectorsImgTitle = gd.getNextChoice();
double minOverlap = gd.getNextNumber();
boolean combineImages = gd.getNextBoolean();
boolean showCountOutput = gd.getNextBoolean();
boolean showAnalysis = gd.getNextBoolean();
if (gd.invalidNumber() || minOverlap < 0 || minOverlap > 100) {
IJ.error("invalid number");
return;
}
Prefs.set("BVTB.BinaryFeatureExtractor.minOverlap", minOverlap);
Prefs.set("BVTB.BinaryFeatureExtractor.combine", combineImages);
if (objectsImgTitle.equals(selectorsImgTitle)) {
IJ.error("images need to be different");
return;
}
ImagePlus objectsImp = WindowManager.getImage(objectsImgTitle);
ImageProcessor objectsIP = objectsImp.getProcessor();
ImagePlus selectorsImp = WindowManager.getImage(selectorsImgTitle);
ImageProcessor selectorsIP = selectorsImp.getProcessor();
if (!objectsIP.isBinary() || !selectorsIP.isBinary()) {
IJ.error("works with 8-bit binary images only");
return;
}
if ((objectsImp.getWidth() != selectorsImp.getWidth())
|| objectsImp.getHeight() != selectorsImp.getHeight()) {
IJ.error("images need to be of the same size");
return;
}
// close any existing RoiManager before instantiating a new one for this analysis
RoiManager oldRM = RoiManager.getInstance2();
if (oldRM != null) {
oldRM.close();
}
RoiManager objectsRM = new RoiManager(true);
ResultsTable objectsRT = new ResultsTable();
ParticleAnalyzer analyzeObjects =
new ParticleAnalyzer(analyzerOptions, measurementFlags, objectsRT, 0.0, 999999999.9);
analyzeObjects.setRoiManager(objectsRM);
analyzeObjects.analyze(objectsImp);
objectsRM.runCommand("Show None");
int objectNumber = objectsRT.getCounter();
Roi[] objectRoi = objectsRM.getRoisAsArray();
ResultsTable measureSelectorsRT = new ResultsTable();
Analyzer overlapAnalyzer = new Analyzer(selectorsImp, measurementFlags, measureSelectorsRT);
ImagePlus outputImp =
IJ.createImage("output", "8-bit black", objectsImp.getWidth(), objectsImp.getHeight(), 1);
ImageProcessor outputIP = outputImp.getProcessor();
double[] measuredOverlap = new double[objectNumber];
outputIP.setValue(255.0);
for (int o = 0; o < objectNumber; o++) {
selectorsImp.killRoi();
selectorsImp.setRoi(objectRoi[o]);
overlapAnalyzer.measure();
measuredOverlap[o] = measureSelectorsRT.getValue("%Area", o);
if (minOverlap != 0.0 && measuredOverlap[o] >= minOverlap) {
outputIP.fill(objectRoi[o]);
finalCount++;
} else if (minOverlap == 0.0 && measuredOverlap[o] > 0.0) {
outputIP.fill(objectRoi[o]);
finalCount++;
}
}
// measureSelectorsRT.show("Objects");
selectorsImp.killRoi();
RoiManager selectorRM = new RoiManager(true);
ResultsTable selectorRT = new ResultsTable();
ParticleAnalyzer.setRoiManager(selectorRM);
ParticleAnalyzer analyzeSelectors =
new ParticleAnalyzer(analyzerOptions, measurementFlags, selectorRT, 0.0, 999999999.9);
analyzeSelectors.analyze(selectorsImp);
selectorRM.runCommand("Show None");
int selectorNumber = selectorRT.getCounter();
if (combineImages) {
outputImp.updateAndDraw();
Roi[] selectorRoi = selectorRM.getRoisAsArray();
ResultsTable measureObjectsRT = new ResultsTable();
Analyzer selectorAnalyzer = new Analyzer(outputImp, measurementFlags, measureObjectsRT);
double[] selectorOverlap = new double[selectorNumber];
outputIP.setValue(255.0);
for (int s = 0; s < selectorNumber; s++) {
outputImp.killRoi();
outputImp.setRoi(selectorRoi[s]);
selectorAnalyzer.measure();
selectorOverlap[s] = measureObjectsRT.getValue("%Area", s);
if (selectorOverlap[s] > 0.0d) {
outputIP.fill(selectorRoi[s]);
}
}
selectorRoi = null;
selectorAnalyzer = null;
measureObjectsRT = null;
}
// selectorRT.show("Selectors");
outputImp.killRoi();
String outputImageTitle = WindowManager.getUniqueName("Extracted_" + objectsImgTitle);
outputImp.setTitle(outputImageTitle);
outputImp.show();
outputImp.changes = true;
if (showCountOutput) {
String[] openTextWindows = WindowManager.getNonImageTitles();
boolean makeNewTable = true;
for (int w = 0; w < openTextWindows.length; w++) {
if (openTextWindows[w].equals("BFE_Results")) {
makeNewTable = false;
}
}
TextWindow existingCountTable = ResultsTable.getResultsWindow();
if (makeNewTable) {
countTable = new ResultsTable();
countTable.setPrecision(0);
countTable.setValue("Image", 0, outputImageTitle);
countTable.setValue("Objects", 0, objectNumber);
countTable.setValue("Selectors", 0, selectorNumber);
countTable.setValue("Extracted", 0, finalCount);
countTable.show("BFE_Results");
} else {
IJ.renameResults("BFE_Results", "Results");
countTable = ResultsTable.getResultsTable();
countTable.setPrecision(0);
countTable.incrementCounter();
countTable.addValue("Image", outputImageTitle);
countTable.addValue("Objects", objectNumber);
countTable.addValue("Selectors", selectorNumber);
countTable.addValue("Extracted", finalCount);
IJ.renameResults("Results", "BFE_Results");
countTable.show("BFE_Results");
}
}
if (showAnalysis) {
ResultsTable extractedRT = new ResultsTable();
ParticleAnalyzer analyzeExtracted =
new ParticleAnalyzer(
ParticleAnalyzer.CLEAR_WORKSHEET | ParticleAnalyzer.RECORD_STARTS,
measurementFlags,
extractedRT,
0.0,
999999999.9);
analyzeExtracted.analyze(outputImp);
objectsRT.show("Objects");
selectorRT.show("Selectors");
extractedRT.show("Extracted");
} else {
objectsRT = null;
selectorRT = null;
}
objectsRM = null;
measureSelectorsRT = null;
analyzeObjects = null;
overlapAnalyzer = null;
objectRoi = null;
selectorRM = null;
objectsImp.killRoi();
objectsImp.changes = false;
selectorsImp.changes = false;
}
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;
}
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;
}