public void run(String arg) {
imp = IJ.getImage();
int stackSize = imp.getStackSize();
if (imp == null) {
IJ.noImage();
return;
}
// Make sure input image is a stack.
if (stackSize == 1) {
IJ.error("Z Project", "Stack required");
return;
}
// Check for inverting LUT.
if (imp.getProcessor().isInvertedLut()) {
if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return;
}
// Set default bounds.
int channels = imp.getNChannels();
int frames = imp.getNFrames();
int slices = imp.getNSlices();
isHyperstack =
imp.isHyperStack()
|| (ij.macro.Interpreter.isBatchMode()
&& ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize)));
boolean simpleComposite = channels == stackSize;
if (simpleComposite) isHyperstack = false;
startSlice = 1;
if (isHyperstack) {
int nSlices = imp.getNSlices();
if (nSlices > 1) stopSlice = nSlices;
else stopSlice = imp.getNFrames();
} else stopSlice = stackSize;
// Build control dialog
GenericDialog gd = buildControlDialog(startSlice, stopSlice);
gd.showDialog();
if (gd.wasCanceled()) return;
if (!imp.lock()) return; // exit if in use
long tstart = System.currentTimeMillis();
setStartSlice((int) gd.getNextNumber());
setStopSlice((int) gd.getNextNumber());
method = gd.getNextChoiceIndex();
Prefs.set(METHOD_KEY, method);
if (isHyperstack) {
allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false;
doHyperStackProjection(allTimeFrames);
} else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true);
else doProjection(true);
if (arg.equals("") && projImage != null) {
long tstop = System.currentTimeMillis();
projImage.setCalibration(imp.getCalibration());
if (simpleComposite) IJ.run(projImage, "Grays", "");
projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds");
}
imp.unlock();
IJ.register(ZProjector.class);
return;
}
/**
* This plugin performs a z-projection of the input stack. Type of output image is same as type of
* input image.
*
* @author Patrick Kelly <*****@*****.**>
*/
public class ZProjector implements PlugIn {
public static final int AVG_METHOD = 0;
public static final int MAX_METHOD = 1;
public static final int MIN_METHOD = 2;
public static final int SUM_METHOD = 3;
public static final int SD_METHOD = 4;
public static final int MEDIAN_METHOD = 5;
public static final String[] METHODS = {
"Average Intensity",
"Max Intensity",
"Min Intensity",
"Sum Slices",
"Standard Deviation",
"Median"
};
private static final String METHOD_KEY = "zproject.method";
private int method = (int) Prefs.get(METHOD_KEY, AVG_METHOD);
private static final int BYTE_TYPE = 0;
private static final int SHORT_TYPE = 1;
private static final int FLOAT_TYPE = 2;
public static final String lutMessage =
"Stacks with inverter LUTs may not project correctly.\n"
+ "To create a standard LUT, invert the stack (Edit/Invert)\n"
+ "and invert the LUT (Image/Lookup Tables/Invert LUT).";
/** Image to hold z-projection. */
private ImagePlus projImage = null;
/** Image stack to project. */
private ImagePlus imp = null;
/** Projection starts from this slice. */
private int startSlice = 1;
/** Projection ends at this slice. */
private int stopSlice = 1;
/** Project all time points? */
private boolean allTimeFrames = true;
private String color = "";
private boolean isHyperstack;
private int increment = 1;
private int sliceCount;
public ZProjector() {}
/** Construction of ZProjector with image to be projected. */
public ZProjector(ImagePlus imp) {
setImage(imp);
}
/**
* Explicitly set image to be projected. This is useful if ZProjection_ object is to be used not
* as a plugin but as a stand alone processing object.
*/
public void setImage(ImagePlus imp) {
this.imp = imp;
startSlice = 1;
stopSlice = imp.getStackSize();
}
public void setStartSlice(int slice) {
if (imp == null || slice < 1 || slice > imp.getStackSize()) return;
startSlice = slice;
}
public void setStopSlice(int slice) {
if (imp == null || slice < 1 || slice > imp.getStackSize()) return;
stopSlice = slice;
}
public void setMethod(int projMethod) {
method = projMethod;
}
/** Retrieve results of most recent projection operation. */
public ImagePlus getProjection() {
return projImage;
}
public void run(String arg) {
imp = IJ.getImage();
int stackSize = imp.getStackSize();
if (imp == null) {
IJ.noImage();
return;
}
// Make sure input image is a stack.
if (stackSize == 1) {
IJ.error("Z Project", "Stack required");
return;
}
// Check for inverting LUT.
if (imp.getProcessor().isInvertedLut()) {
if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return;
}
// Set default bounds.
int channels = imp.getNChannels();
int frames = imp.getNFrames();
int slices = imp.getNSlices();
isHyperstack =
imp.isHyperStack()
|| (ij.macro.Interpreter.isBatchMode()
&& ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize)));
boolean simpleComposite = channels == stackSize;
if (simpleComposite) isHyperstack = false;
startSlice = 1;
if (isHyperstack) {
int nSlices = imp.getNSlices();
if (nSlices > 1) stopSlice = nSlices;
else stopSlice = imp.getNFrames();
} else stopSlice = stackSize;
// Build control dialog
GenericDialog gd = buildControlDialog(startSlice, stopSlice);
gd.showDialog();
if (gd.wasCanceled()) return;
if (!imp.lock()) return; // exit if in use
long tstart = System.currentTimeMillis();
setStartSlice((int) gd.getNextNumber());
setStopSlice((int) gd.getNextNumber());
method = gd.getNextChoiceIndex();
Prefs.set(METHOD_KEY, method);
if (isHyperstack) {
allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false;
doHyperStackProjection(allTimeFrames);
} else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true);
else doProjection(true);
if (arg.equals("") && projImage != null) {
long tstop = System.currentTimeMillis();
projImage.setCalibration(imp.getCalibration());
if (simpleComposite) IJ.run(projImage, "Grays", "");
projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds");
}
imp.unlock();
IJ.register(ZProjector.class);
return;
}
public void doRGBProjection() {
doRGBProjection(imp.getStack());
}
// Added by Marcel Boeglin 2013.09.23
public void doRGBProjection(boolean handleOverlay) {
doRGBProjection(imp.getStack());
Overlay overlay = imp.getOverlay();
if (handleOverlay && overlay != null) projImage.setOverlay(projectRGBHyperStackRois(overlay));
}
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);
}
/**
* Builds dialog to query users for projection parameters.
*
* @param start starting slice to display
* @param stop last slice
*/
protected GenericDialog buildControlDialog(int start, int stop) {
GenericDialog gd = new GenericDialog("ZProjection", IJ.getInstance());
gd.addNumericField("Start slice:", startSlice, 0 /*digits*/);
gd.addNumericField("Stop slice:", stopSlice, 0 /*digits*/);
gd.addChoice("Projection type", METHODS, METHODS[method]);
if (isHyperstack && imp.getNFrames() > 1 && imp.getNSlices() > 1)
gd.addCheckbox("All time frames", allTimeFrames);
return gd;
}
/** Performs actual projection using specified method. */
public void doProjection() {
if (imp == null) return;
sliceCount = 0;
if (method < AVG_METHOD || method > MEDIAN_METHOD) method = AVG_METHOD;
for (int slice = startSlice; slice <= stopSlice; slice += increment) sliceCount++;
if (method == MEDIAN_METHOD) {
projImage = doMedianProjection();
return;
}
// Create new float processor for projected pixels.
FloatProcessor fp = new FloatProcessor(imp.getWidth(), imp.getHeight());
ImageStack stack = imp.getStack();
RayFunction rayFunc = getRayFunction(method, fp);
if (IJ.debugMode == true) {
IJ.log("\nProjecting stack from: " + startSlice + " to: " + stopSlice);
}
// Determine type of input image. Explicit determination of
// processor type is required for subsequent pixel
// manipulation. This approach is more efficient than the
// more general use of ImageProcessor's getPixelValue and
// putPixel methods.
int ptype;
if (stack.getProcessor(1) instanceof ByteProcessor) ptype = BYTE_TYPE;
else if (stack.getProcessor(1) instanceof ShortProcessor) ptype = SHORT_TYPE;
else if (stack.getProcessor(1) instanceof FloatProcessor) ptype = FLOAT_TYPE;
else {
IJ.error("Z Project", "Non-RGB stack required");
return;
}
// Do the projection.
for (int n = startSlice; n <= stopSlice; n += increment) {
IJ.showStatus("ZProjection " + color + ": " + n + "/" + stopSlice);
IJ.showProgress(n - startSlice, stopSlice - startSlice);
projectSlice(stack.getPixels(n), rayFunc, ptype);
}
// Finish up projection.
if (method == SUM_METHOD) {
fp.resetMinAndMax();
projImage = new ImagePlus(makeTitle(), fp);
} else if (method == SD_METHOD) {
rayFunc.postProcess();
fp.resetMinAndMax();
projImage = new ImagePlus(makeTitle(), fp);
} else {
rayFunc.postProcess();
projImage = makeOutputImage(imp, fp, ptype);
}
if (projImage == null) IJ.error("Z Project", "Error computing projection.");
}
// Added by Marcel Boeglin 2013.09.23
/**
* Performs actual projection using specified method. If handleOverlay, adds stack overlay
* elements from startSlice to stopSlice to projection
*/
public void doProjection(boolean handleOverlay) {
doProjection();
Overlay overlay = imp.getOverlay();
if (handleOverlay && overlay != null) projImage.setOverlay(projectStackRois(overlay));
}
// Added by Marcel Boeglin 2013.09.23
private Overlay projectStackRois(Overlay overlay) {
if (overlay == null) return null;
Overlay overlay2 = new Overlay();
Roi roi;
int s;
for (Roi r : overlay.toArray()) {
s = r.getPosition();
roi = (Roi) r.clone();
if (s >= startSlice && s <= stopSlice || s == 0) {
roi.setPosition(s);
overlay2.add(roi);
}
}
return overlay2;
}
public void doHyperStackProjection(boolean allTimeFrames) {
int start = startSlice;
int stop = stopSlice;
int firstFrame = 1;
int lastFrame = imp.getNFrames();
if (!allTimeFrames) firstFrame = lastFrame = imp.getFrame();
ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
int channels = imp.getNChannels();
int slices = imp.getNSlices();
if (slices == 1) {
slices = imp.getNFrames();
firstFrame = lastFrame = 1;
}
int frames = lastFrame - firstFrame + 1;
increment = channels;
boolean rgb = imp.getBitDepth() == 24;
for (int frame = firstFrame; frame <= lastFrame; frame++) {
for (int channel = 1; channel <= channels; channel++) {
startSlice = (frame - 1) * channels * slices + (start - 1) * channels + channel;
stopSlice = (frame - 1) * channels * slices + (stop - 1) * channels + channel;
if (rgb) doHSRGBProjection(imp);
else doProjection();
stack.addSlice(null, projImage.getProcessor());
}
}
projImage = new ImagePlus(makeTitle(), stack);
projImage.setDimensions(channels, 1, frames);
if (channels > 1) {
projImage = new CompositeImage(projImage, 0);
((CompositeImage) projImage).copyLuts(imp);
if (method == SUM_METHOD || method == SD_METHOD)
((CompositeImage) projImage).resetDisplayRanges();
}
if (frames > 1) projImage.setOpenAsHyperStack(true);
Overlay overlay = imp.getOverlay();
if (overlay != null) {
startSlice = start;
stopSlice = stop;
if (imp.getType() == ImagePlus.COLOR_RGB)
projImage.setOverlay(projectRGBHyperStackRois(overlay));
else projImage.setOverlay(projectHyperStackRois(overlay));
}
IJ.showProgress(1, 1);
}
// Added by Marcel Boeglin 2013.09.22
private Overlay projectRGBHyperStackRois(Overlay overlay) {
if (overlay == null) return null;
int frames = projImage.getNFrames();
int t1 = imp.getFrame();
Overlay overlay2 = new Overlay();
Roi roi;
int c, z, t;
for (Roi r : overlay.toArray()) {
c = r.getCPosition();
z = r.getZPosition();
t = r.getTPosition();
roi = (Roi) r.clone();
if (z >= startSlice && z <= stopSlice || z == 0 || c == 0 || t == 0) {
if (frames == 1 && t != t1 && t != 0) // current time frame
continue;
roi.setPosition(t);
overlay2.add(roi);
}
}
return overlay2;
}
// Added by Marcel Boeglin 2013.09.22
private Overlay projectHyperStackRois(Overlay overlay) {
if (overlay == null) return null;
int t1 = imp.getFrame();
int channels = projImage.getNChannels();
int slices = 1;
int frames = projImage.getNFrames();
Overlay overlay2 = new Overlay();
Roi roi;
int c, z, t;
int size = channels * slices * frames;
for (Roi r : overlay.toArray()) {
c = r.getCPosition();
z = r.getZPosition();
t = r.getTPosition();
roi = (Roi) r.clone();
if (size == channels) { // current time frame
if (z >= startSlice && z <= stopSlice && t == t1 || c == 0) {
roi.setPosition(c);
overlay2.add(roi);
}
} else if (size == frames * channels) { // all time frames
if (z >= startSlice && z <= stopSlice) roi.setPosition(c, 1, t);
else if (z == 0) roi.setPosition(c, 0, t);
else continue;
overlay2.add(roi);
}
}
return overlay2;
}
private void doHSRGBProjection(ImagePlus rgbImp) {
ImageStack stack = rgbImp.getStack();
ImageStack stack2 = new ImageStack(stack.getWidth(), stack.getHeight());
for (int i = startSlice; i <= stopSlice; i++) stack2.addSlice(null, stack.getProcessor(i));
startSlice = 1;
stopSlice = stack2.getSize();
doRGBProjection(stack2);
}
private RayFunction getRayFunction(int method, FloatProcessor fp) {
switch (method) {
case AVG_METHOD:
case SUM_METHOD:
return new AverageIntensity(fp, sliceCount);
case MAX_METHOD:
return new MaxIntensity(fp);
case MIN_METHOD:
return new MinIntensity(fp);
case SD_METHOD:
return new StandardDeviation(fp, sliceCount);
default:
IJ.error("Z Project", "Unknown method.");
return null;
}
}
/** Generate output image whose type is same as input image. */
private ImagePlus makeOutputImage(ImagePlus imp, FloatProcessor fp, int ptype) {
int width = imp.getWidth();
int height = imp.getHeight();
float[] pixels = (float[]) fp.getPixels();
ImageProcessor oip = null;
// Create output image consistent w/ type of input image.
int size = pixels.length;
switch (ptype) {
case BYTE_TYPE:
oip = imp.getProcessor().createProcessor(width, height);
byte[] pixels8 = (byte[]) oip.getPixels();
for (int i = 0; i < size; i++) pixels8[i] = (byte) pixels[i];
break;
case SHORT_TYPE:
oip = imp.getProcessor().createProcessor(width, height);
short[] pixels16 = (short[]) oip.getPixels();
for (int i = 0; i < size; i++) pixels16[i] = (short) pixels[i];
break;
case FLOAT_TYPE:
oip = new FloatProcessor(width, height, pixels, null);
break;
}
// Adjust for display.
// Calling this on non-ByteProcessors ensures image
// processor is set up to correctly display image.
oip.resetMinAndMax();
// Create new image plus object. Don't use
// ImagePlus.createImagePlus here because there may be
// attributes of input image that are not appropriate for
// projection.
return new ImagePlus(makeTitle(), oip);
}
/**
* Handles mechanics of projection by selecting appropriate pixel array type. We do this rather
* than using more general ImageProcessor getPixelValue() and putPixel() methods because direct
* manipulation of pixel arrays is much more efficient.
*/
private void projectSlice(Object pixelArray, RayFunction rayFunc, int ptype) {
switch (ptype) {
case BYTE_TYPE:
rayFunc.projectSlice((byte[]) pixelArray);
break;
case SHORT_TYPE:
rayFunc.projectSlice((short[]) pixelArray);
break;
case FLOAT_TYPE:
rayFunc.projectSlice((float[]) pixelArray);
break;
}
}
String makeTitle() {
String prefix = "AVG_";
switch (method) {
case SUM_METHOD:
prefix = "SUM_";
break;
case MAX_METHOD:
prefix = "MAX_";
break;
case MIN_METHOD:
prefix = "MIN_";
break;
case SD_METHOD:
prefix = "STD_";
break;
case MEDIAN_METHOD:
prefix = "MED_";
break;
}
return WindowManager.makeUniqueName(prefix + imp.getTitle());
}
ImagePlus doMedianProjection() {
IJ.showStatus("Calculating median...");
ImageStack stack = imp.getStack();
ImageProcessor[] slices = new ImageProcessor[sliceCount];
int index = 0;
for (int slice = startSlice; slice <= stopSlice; slice += increment)
slices[index++] = stack.getProcessor(slice);
ImageProcessor ip2 = slices[0].duplicate();
ip2 = ip2.convertToFloat();
float[] values = new float[sliceCount];
int width = ip2.getWidth();
int height = ip2.getHeight();
int inc = Math.max(height / 30, 1);
for (int y = 0; y < height; y++) {
if (y % inc == 0) IJ.showProgress(y, height - 1);
for (int x = 0; x < width; x++) {
for (int i = 0; i < sliceCount; i++) values[i] = slices[i].getPixelValue(x, y);
ip2.putPixelValue(x, y, median(values));
}
}
if (imp.getBitDepth() == 8) ip2 = ip2.convertToByte(false);
IJ.showProgress(1, 1);
return new ImagePlus(makeTitle(), ip2);
}
float median(float[] a) {
Arrays.sort(a);
int middle = a.length / 2;
if ((a.length & 1) == 0) // even
return (a[middle - 1] + a[middle]) / 2f;
else return a[middle];
}
/**
* Abstract class that specifies structure of ray function. Preprocessing should be done in
* derived class constructors.
*/
abstract class RayFunction {
/** Do actual slice projection for specific data types. */
public abstract void projectSlice(byte[] pixels);
public abstract void projectSlice(short[] pixels);
public abstract void projectSlice(float[] pixels);
/** Perform any necessary post processing operations, e.g. averging values. */
public void postProcess() {}
} // end RayFunction
/** Compute average intensity projection. */
class AverageIntensity extends RayFunction {
private float[] fpixels;
private int num, len;
/**
* Constructor requires number of slices to be projected. This is used to determine average at
* each pixel.
*/
public AverageIntensity(FloatProcessor fp, int num) {
fpixels = (float[]) fp.getPixels();
len = fpixels.length;
this.num = num;
}
public void projectSlice(byte[] pixels) {
for (int i = 0; i < len; i++) fpixels[i] += (pixels[i] & 0xff);
}
public void projectSlice(short[] pixels) {
for (int i = 0; i < len; i++) fpixels[i] += pixels[i] & 0xffff;
}
public void projectSlice(float[] pixels) {
for (int i = 0; i < len; i++) fpixels[i] += pixels[i];
}
public void postProcess() {
float fnum = num;
for (int i = 0; i < len; i++) fpixels[i] /= fnum;
}
} // end AverageIntensity
/** Compute max intensity projection. */
class MaxIntensity extends RayFunction {
private float[] fpixels;
private int len;
/** Simple constructor since no preprocessing is necessary. */
public MaxIntensity(FloatProcessor fp) {
fpixels = (float[]) fp.getPixels();
len = fpixels.length;
for (int i = 0; i < len; i++) fpixels[i] = -Float.MAX_VALUE;
}
public void projectSlice(byte[] pixels) {
for (int i = 0; i < len; i++) {
if ((pixels[i] & 0xff) > fpixels[i]) fpixels[i] = (pixels[i] & 0xff);
}
}
public void projectSlice(short[] pixels) {
for (int i = 0; i < len; i++) {
if ((pixels[i] & 0xffff) > fpixels[i]) fpixels[i] = pixels[i] & 0xffff;
}
}
public void projectSlice(float[] pixels) {
for (int i = 0; i < len; i++) {
if (pixels[i] > fpixels[i]) fpixels[i] = pixels[i];
}
}
} // end MaxIntensity
/** Compute min intensity projection. */
class MinIntensity extends RayFunction {
private float[] fpixels;
private int len;
/** Simple constructor since no preprocessing is necessary. */
public MinIntensity(FloatProcessor fp) {
fpixels = (float[]) fp.getPixels();
len = fpixels.length;
for (int i = 0; i < len; i++) fpixels[i] = Float.MAX_VALUE;
}
public void projectSlice(byte[] pixels) {
for (int i = 0; i < len; i++) {
if ((pixels[i] & 0xff) < fpixels[i]) fpixels[i] = (pixels[i] & 0xff);
}
}
public void projectSlice(short[] pixels) {
for (int i = 0; i < len; i++) {
if ((pixels[i] & 0xffff) < fpixels[i]) fpixels[i] = pixels[i] & 0xffff;
}
}
public void projectSlice(float[] pixels) {
for (int i = 0; i < len; i++) {
if (pixels[i] < fpixels[i]) fpixels[i] = pixels[i];
}
}
} // end MaxIntensity
/** Compute standard deviation projection. */
class StandardDeviation extends RayFunction {
private float[] result;
private double[] sum, sum2;
private int num, len;
public StandardDeviation(FloatProcessor fp, int num) {
result = (float[]) fp.getPixels();
len = result.length;
this.num = num;
sum = new double[len];
sum2 = new double[len];
}
public void projectSlice(byte[] pixels) {
int v;
for (int i = 0; i < len; i++) {
v = pixels[i] & 0xff;
sum[i] += v;
sum2[i] += v * v;
}
}
public void projectSlice(short[] pixels) {
double v;
for (int i = 0; i < len; i++) {
v = pixels[i] & 0xffff;
sum[i] += v;
sum2[i] += v * v;
}
}
public void projectSlice(float[] pixels) {
double v;
for (int i = 0; i < len; i++) {
v = pixels[i];
sum[i] += v;
sum2[i] += v * v;
}
}
public void postProcess() {
double stdDev;
double n = num;
for (int i = 0; i < len; i++) {
if (num > 1) {
stdDev = (n * sum2[i] - sum[i] * sum[i]) / n;
if (stdDev > 0.0) result[i] = (float) Math.sqrt(stdDev / (n - 1.0));
else result[i] = 0f;
} else result[i] = 0f;
}
}
} // end StandardDeviation
} // end ZProjection
