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;
}
}
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);
}
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;
}
/** Splits the specified image into separate channels. */
public static ImagePlus[] split(ImagePlus imp) {
if (imp.getType() == ImagePlus.COLOR_RGB) {
ImageStack[] stacks = splitRGB(imp.getStack(), true);
ImagePlus[] images = new ImagePlus[3];
images[0] = new ImagePlus("red", stacks[0]);
images[1] = new ImagePlus("green", stacks[1]);
images[2] = new ImagePlus("blue", stacks[2]);
return images;
}
int width = imp.getWidth();
int height = imp.getHeight();
int channels = imp.getNChannels();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int bitDepth = imp.getBitDepth();
int size = slices * frames;
Vector images = new Vector();
HyperStackReducer reducer = new HyperStackReducer(imp);
for (int c = 1; c <= channels; c++) {
ImageStack stack2 = new ImageStack(width, height, size); // create empty stack
stack2.setPixels(
imp.getProcessor().getPixels(), 1); // can't create ImagePlus will null 1st image
ImagePlus imp2 = new ImagePlus("C" + c + "-" + imp.getTitle(), stack2);
stack2.setPixels(null, 1);
imp.setPosition(c, 1, 1);
imp2.setDimensions(1, slices, frames);
imp2.setCalibration(imp.getCalibration());
reducer.reduce(imp2);
if (imp.isComposite() && ((CompositeImage) imp).getMode() == IJ.GRAYSCALE)
IJ.run(imp2, "Grays", "");
if (imp2.getNDimensions() > 3) imp2.setOpenAsHyperStack(true);
images.add(imp2);
}
ImagePlus[] array = new ImagePlus[images.size()];
return (ImagePlus[]) images.toArray(array);
}
/** Opens the image. Displays it if 'show' is true. Returns an ImagePlus object if successful. */
public ImagePlus open(boolean show) {
ImagePlus imp = null;
Object pixels;
ProgressBar pb = null;
ImageProcessor ip;
ColorModel cm = createColorModel(fi);
if (fi.nImages > 1) {
return openStack(cm, show);
}
switch (fi.fileType) {
case FileInfo.GRAY8:
case FileInfo.COLOR8:
case FileInfo.BITMAP:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.GRAY16_SIGNED:
case FileInfo.GRAY16_UNSIGNED:
case FileInfo.GRAY12_UNSIGNED:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ShortProcessor(width, height, (short[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.GRAY32_INT:
case FileInfo.GRAY32_UNSIGNED:
case FileInfo.GRAY32_FLOAT:
case FileInfo.GRAY24_UNSIGNED:
case FileInfo.GRAY64_FLOAT:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new FloatProcessor(width, height, (float[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.RGB:
case FileInfo.BGR:
case FileInfo.ARGB:
case FileInfo.ABGR:
case FileInfo.BARG:
case FileInfo.RGB_PLANAR:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ColorProcessor(width, height, (int[]) pixels);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.RGB48:
case FileInfo.RGB48_PLANAR:
boolean planar = fi.fileType == FileInfo.RGB48_PLANAR;
Object[] pixelArray = (Object[]) readPixels(fi);
if (pixelArray == null) return null;
ImageStack stack = new ImageStack(width, height);
stack.addSlice("Red", pixelArray[0]);
stack.addSlice("Green", pixelArray[1]);
stack.addSlice("Blue", pixelArray[2]);
imp = new ImagePlus(fi.fileName, stack);
imp.setDimensions(3, 1, 1);
if (planar) imp.getProcessor().resetMinAndMax();
imp.setFileInfo(fi);
int mode = CompositeImage.COMPOSITE;
if (fi.description != null) {
if (fi.description.indexOf("mode=color") != -1) mode = CompositeImage.COLOR;
else if (fi.description.indexOf("mode=gray") != -1) mode = CompositeImage.GRAYSCALE;
}
imp = new CompositeImage(imp, mode);
if (!planar && fi.displayRanges == null) {
for (int c = 1; c <= 3; c++) {
imp.setPosition(c, 1, 1);
imp.setDisplayRange(minValue, maxValue);
}
imp.setPosition(1, 1, 1);
}
break;
}
imp.setFileInfo(fi);
setCalibration(imp);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (fi.sliceLabels != null && fi.sliceLabels.length == 1 && fi.sliceLabels[0] != null)
imp.setProperty("Label", fi.sliceLabels[0]);
if (show) imp.show();
return imp;
}
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);
}
}
}
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();
}