@Override
public boolean process() {
final long startTime = System.currentTimeMillis();
final long imageSize = image.getNumPixels();
final AtomicInteger ai = new AtomicInteger(0);
final Thread[] threads = SimpleMultiThreading.newThreads(getNumThreads());
final Vector<Chunk> threadChunks = SimpleMultiThreading.divideIntoChunks(imageSize, numThreads);
final boolean isCompatible =
image.getContainer().compareStorageContainerCompatibility(output.getContainer());
for (int ithread = 0; ithread < threads.length; ++ithread)
threads[ithread] =
new Thread(
new Runnable() {
public void run() {
// Thread ID
final int myNumber = ai.getAndIncrement();
// get chunk of pixels to process
final Chunk myChunk = threadChunks.get(myNumber);
// check if all container types are comparable so that we can use simple iterators
// we assume transivity here
if (isCompatible) {
// we can simply use iterators
computeSimple(myChunk.getStartPosition(), myChunk.getLoopSize());
} else {
// we need a combination of Localizable and LocalizableByDim
computeAdvanced(myChunk.getStartPosition(), myChunk.getLoopSize());
}
}
});
SimpleMultiThreading.startAndJoin(threads);
processingTime = System.currentTimeMillis() - startTime;
return true;
}
/**
* Can be called with values[ 3 ], i.e. [initialsigma, sigma2, threshold] or values[ 2 ], i.e.
* [initialsigma, threshold]
*
* <p>The results are stored in the same array. If called with values[ 2 ], sigma2 changing will
* be disabled
*
* @param text - the text which is shown when asking for the file
* @param values - the initial values and also contains the result
* @param sigmaMax - the maximal sigma allowed by the interactive app
* @return {@link InteractiveDoG} - the instance for querying additional parameters
*/
public static InteractiveDoG getInteractiveDoGParameters(
final ImagePlus imp, final int channel, final double values[], final float sigmaMax) {
if (imp.isDisplayedHyperStack())
imp.setPosition(imp.getStackIndex(channel + 1, imp.getNSlices() / 2 + 1, 1));
else imp.setSlice(imp.getStackIndex(channel + 1, imp.getNSlices() / 2 + 1, 1));
imp.setRoi(0, 0, imp.getWidth() / 3, imp.getHeight() / 3);
final InteractiveDoG idog = new InteractiveDoG(imp, channel);
idog.setSigmaMax(sigmaMax);
idog.setLookForMaxima(defaultInteractiveMaxima);
idog.setLookForMinima(defaultInteractiveMinima);
if (values.length == 2) {
idog.setSigma2isAdjustable(false);
idog.setInitialSigma((float) values[0]);
idog.setThreshold((float) values[1]);
} else {
idog.setInitialSigma((float) values[0]);
idog.setThreshold((float) values[2]);
}
idog.run(null);
while (!idog.isFinished()) SimpleMultiThreading.threadWait(100);
if (values.length == 2) {
values[0] = idog.getInitialSigma();
values[1] = idog.getThreshold();
} else {
values[0] = idog.getInitialSigma();
values[1] = idog.getSigma2();
values[2] = idog.getThreshold();
}
// remove the roi
imp.killRoi();
defaultInteractiveMaxima = idog.getLookForMaxima();
defaultInteractiveMinima = idog.getLookForMinima();
return idog;
}
/**
* Execute the segmentation part.
*
* <p>This method looks for bright blobs: bright object of approximately spherical shape, whose
* expected diameter is given in argument. The method used for segmentation depends on the {@link
* SpotSegmenter} chosen, and set in {@link #settings};
*
* <p>This gives us a collection of spots, which at this stage simply wrap a physical center
* location. These spots are stored in a {@link SpotCollection} field, {@link #spots}, but
* listeners of this model are <b>not</b> notified when the process is over.
*
* @see #getSpots()
*/
public void execSegmentation() {
final Settings settings = model.getSettings();
final int segmentationChannel = settings.segmentationChannel;
final Logger logger = model.getLogger();
final ImagePlus imp = settings.imp;
if (null == imp) {
logger.error("No image to operate on.\n");
return;
}
if (null == settings.segmenter) {
logger.error("No segmenter selected.\n");
return;
}
if (null == settings.segmenterSettings) {
logger.error("No segmenter settings set.\n");
return;
}
if (!settings
.segmenterSettings
.getClass()
.equals(settings.segmenter.createDefaultSettings().getClass())) {
logger.error(
String.format(
"Segmenter settings class does not match segmenter class: %s vs %s.\n",
settings.segmenterSettings.getClass().getSimpleName(),
settings.segmenter.createDefaultSettings().getClass().getSimpleName()));
return;
}
final int numFrames = settings.tend - settings.tstart + 1;
final SpotCollection spots = new SpotCollection();
final AtomicInteger spotFound = new AtomicInteger(0);
final AtomicInteger progress = new AtomicInteger(0);
final Thread[] threads;
if (useMultithreading) {
threads = SimpleMultiThreading.newThreads();
} else {
threads = SimpleMultiThreading.newThreads(1);
}
// Prepare the thread array
final AtomicInteger ai = new AtomicInteger(settings.tstart);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] =
new Thread(
"TrackMate spot feature calculating thread " + (1 + ithread) + "/" + threads.length) {
public void run() {
for (int i = ai.getAndIncrement(); i <= settings.tend; i = ai.getAndIncrement()) {
Image<? extends RealType<?>> img =
TMUtils.getCroppedSingleFrameAsImage(
imp,
i,
segmentationChannel,
settings); // will be cropped according to settings
List<Spot> s = execSingleFrameSegmentation(img, settings, i);
// Add segmentation feature other than position
for (Spot spot : s) {
spot.putFeature(Spot.POSITION_T, i * settings.dt);
}
spots.put(i, s);
spotFound.addAndGet(s.size());
logger.setProgress(progress.incrementAndGet() / (float) numFrames);
} // Finished looping over frames
}
};
}
logger.setStatus("Segmenting...");
logger.setProgress(0);
SimpleMultiThreading.startAndJoin(threads);
model.setSpots(spots, true);
logger.log("Found " + spotFound.get() + " spots.\n");
logger.setProgress(1);
logger.setStatus("");
return;
}
/**
* Fuse one slice/volume (one channel)
*
* @param output - same the type of the ImagePlus input
* @param input - FloatType, because of Interpolation that needs to be done
* @param transform - the transformation
*/
public static <T extends RealType<T>> void fuseChannel(
final Image<T> output,
final Image<FloatType> input,
final float[] offset,
final InvertibleCoordinateTransform transform,
final InterpolatorFactory<FloatType> factory) {
final int dims = output.getNumDimensions();
long imageSize = output.getDimension(0);
for (int d = 1; d < output.getNumDimensions(); ++d) imageSize *= output.getDimension(d);
// run multithreaded
final AtomicInteger ai = new AtomicInteger(0);
final Thread[] threads = SimpleMultiThreading.newThreads();
final Vector<Chunk> threadChunks =
SimpleMultiThreading.divideIntoChunks(imageSize, threads.length);
for (int ithread = 0; ithread < threads.length; ++ithread)
threads[ithread] =
new Thread(
new Runnable() {
public void run() {
// Thread ID
final int myNumber = ai.getAndIncrement();
// get chunk of pixels to process
final Chunk myChunk = threadChunks.get(myNumber);
final long startPos = myChunk.getStartPosition();
final long loopSize = myChunk.getLoopSize();
final LocalizableCursor<T> out = output.createLocalizableCursor();
final Interpolator<FloatType> in = input.createInterpolator(factory);
final float[] tmp = new float[input.getNumDimensions()];
try {
// move to the starting position of the current thread
out.fwd(startPos);
// do as many pixels as wanted by this thread
for (long j = 0; j < loopSize; ++j) {
out.fwd();
for (int d = 0; d < dims; ++d) tmp[d] = out.getPosition(d) + offset[d];
transform.applyInverseInPlace(tmp);
in.setPosition(tmp);
out.getType().setReal(in.getType().get());
}
} catch (NoninvertibleModelException e) {
IJ.log("Cannot invert model, qutting.");
return;
}
}
});
SimpleMultiThreading.startAndJoin(threads);
/*
final LocalizableCursor<T> out = output.createLocalizableCursor();
final Interpolator<FloatType> in = input.createInterpolator( factory );
final float[] tmp = new float[ input.getNumDimensions() ];
try
{
while ( out.hasNext() )
{
out.fwd();
for ( int d = 0; d < dims; ++d )
tmp[ d ] = out.getPosition( d ) + offset[ d ];
transform.applyInverseInPlace( tmp );
in.setPosition( tmp );
out.getType().setReal( in.getType().get() );
}
}
catch (NoninvertibleModelException e)
{
IJ.log( "Cannot invert model, qutting." );
return;
}
*/
}