@Override
public final void run() {
while (!isInterrupted()) {
final boolean b;
synchronized (this) {
b = pleaseRepaint;
pleaseRepaint = keepPainting;
}
if (b) {
final long t = System.currentTimeMillis();
lambda += dt * dLambda;
phi += dt * dPhi;
this.camera.setOrientation(lambda, phi, rho);
mapper.map(temp);
final Object targetPixels = target.getPixels();
target.setPixels(temp.getPixels());
temp.setPixels(targetPixels);
impTarget.updateAndDraw();
if (visualize) visualize(impSource, temp.getWidth(), temp.getHeight(), p);
dt = (System.currentTimeMillis() - t) / 1000f;
}
synchronized (this) {
try {
if (!pleaseRepaint) wait();
} catch (final InterruptedException e) {
}
}
}
}
/**
* Returns an ImageProcessor for the specified slice, were 1<=n<=nslices. Returns null if the
* stack is empty.
*/
public ImageProcessor getProcessor(int n) {
ImageProcessor ip;
if (n < 1 || n > nSlices) throw new IllegalArgumentException(outOfRange + n);
if (nSlices == 0) return null;
if (stack[0] == null) throw new IllegalArgumentException("Pixel array is null");
if (stack[0] instanceof byte[]) ip = new ByteProcessor(width, height, null, cm);
else if (stack[0] instanceof short[]) ip = new ShortProcessor(width, height, null, cm);
else if (stack[0] instanceof int[]) ip = new ColorProcessor(width, height, null);
else if (stack[0] instanceof float[]) ip = new FloatProcessor(width, height, null, cm);
else throw new IllegalArgumentException("Unknown stack type");
ip.setPixels(stack[n - 1]);
if (min != Double.MAX_VALUE && ip != null && !(ip instanceof ColorProcessor))
ip.setMinAndMax(min, max);
if (cTable != null) ip.setCalibrationTable(cTable);
return ip;
}
/**
* Converts a binary image into a 8-bit grayscale Euclidean Distance Map (EDM). Each foreground
* (nonzero) pixel in the binary image is assigned a value equal to its distance from the nearest
* background (zero) pixel.
*/
public void toEDM(ImageProcessor ip) {
ip.setPixels(0, makeFloatEDM(ip, 0, false));
ip.resetMinAndMax();
}
/** Called by the PlugInFilterRunner to process the image or one frame of a stack */
public void run(ImageProcessor ip) {
if (interrupted) return;
int width = ip.getWidth();
int height = ip.getHeight();
int backgroundValue =
(processType == VORONOI)
? (background255 ? 0 : (byte) 255)
: // Voronoi needs EDM of the background
(background255 ? (byte) 255 : 0); // all others do EDM of the foreground
if (USES_WATERSHED[processType]) nPasses = 0; // watershed has its own progress bar
FloatProcessor floatEdm = makeFloatEDM(ip, backgroundValue, false);
ByteProcessor maxIp = null;
if (USES_MAX_FINDER[processType]) {
if (processType == VORONOI) floatEdm.multiply(-1); // Voronoi starts from minima of EDM
int maxOutputType =
USES_WATERSHED[processType] ? MaximumFinder.SEGMENTED : MaximumFinder.SINGLE_POINTS;
boolean isEDM = processType != VORONOI;
maxIp =
maxFinder.findMaxima(
floatEdm,
MAXFINDER_TOLERANCE,
ImageProcessor.NO_THRESHOLD,
maxOutputType,
false,
isEDM);
if (maxIp == null) { // segmentation cancelled by user?
interrupted = true;
return;
} else if (processType != WATERSHED) {
if (processType == VORONOI) floatEdm.multiply(-1);
resetMasked(floatEdm, maxIp, processType == VORONOI ? -1 : 0);
}
}
ImageProcessor outIp = null;
if (processType == WATERSHED) {
if (background255) maxIp.invert();
ip.copyBits(maxIp, 0, 0, Blitter.COPY);
ip.setBinaryThreshold();
} else
switch (outImageType) { // for all these, output contains the values of the EDM
case FLOAT:
outIp = floatEdm;
break;
case SHORT:
floatEdm.setMinAndMax(0., 65535.);
outIp = floatEdm.convertToShort(true);
break;
case BYTE:
floatEdm.setMinAndMax(0., 255.);
outIp = floatEdm.convertToByte(true);
break;
case BYTE_OVERWRITE:
ip.setPixels(0, floatEdm);
if (floatEdm.getMax() > 255.) ip.resetMinAndMax(); // otherwise we have max of floatEdm
}
if (outImageType != BYTE_OVERWRITE) { // new output image
if (outStack == null) {
outImp = new ImagePlus(TITLE_PREFIX[processType] + imp.getShortTitle(), outIp);
} else outStack.setPixels(outIp.getPixels(), pfr.getSliceNumber());
}
} // public void run
/** Apply a local Binary Partition filter */
public static void localBinaryPartition(ImageProcessor processor) {
LocalBinaryPartitionFilter localbinary =
new LocalBinaryPartitionFilter(processor.convertToByte(true));
byte[] bytes = localbinary.performExtraction();
processor.setPixels(bytes);
}
/**
* @param ip
* @param v
*/
public static void run(final ImageProcessor ip, final float v) {
final int w = ip.getWidth();
final int h = ip.getHeight();
final int wh = w * h;
final ImageProcessor ipTarget = ip.duplicate();
int numSaturatedPixels = 0;
do {
numSaturatedPixels = 0;
for (int i = 0; i < wh; ++i)
if (ip.getf(i) == v) {
++numSaturatedPixels;
final int y = i / w;
final int x = i % w;
float s = 0;
float n = 0;
if (y > 0) {
if (x > 0) {
final float tl = ip.getf(x - 1, y - 1);
if (tl != v) {
s += 0.5f * tl;
n += 0.5f;
}
}
final float t = ip.getf(x, y - 1);
if (t != v) {
s += t;
n += 1;
}
if (x < w - 1) {
final float tr = ip.getf(x + 1, y - 1);
if (tr != v) {
s += 0.5f * tr;
n += 0.5f;
}
}
}
if (x > 0) {
final float l = ip.getf(x - 1, y);
if (l != v) {
s += l;
n += 1;
}
}
if (x < w - 1) {
final float r = ip.getf(x + 1, y);
if (r != v) {
s += r;
n += 1;
}
}
if (y < h - 1) {
if (x > 0) {
final float bl = ip.getf(x - 1, y + 1);
if (bl != v) {
s += 0.5f * bl;
n += 0.5f;
}
}
final float b = ip.getf(x, y + 1);
if (b != v) {
s += b;
n += 1;
}
if (x < w - 1) {
final float br = ip.getf(x + 1, y + 1);
if (br != v) {
s += 0.5f * br;
n += 0.5f;
}
}
}
if (n > 0) ipTarget.setf(i, s / n);
}
ip.setPixels(ipTarget.getPixelsCopy());
} while (numSaturatedPixels > 0);
}