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;
}
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();
}
