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);
}
/** 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");
}
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(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();
}