use of mpicbg.models.TranslationModel1D in project TrakEM2 by trakem2.
the class MatchIntensities method run.
/**
* @param layers
* @param radius
* @param scale
* @param numCoefficients
* @param lambda1
* @param lambda2
* @param neighborWeight
* @param roi
*/
public <M extends Model<M> & Affine1D<M>> void run(final List<Layer> layers, final int radius, final double scale, final int numCoefficients, final double lambda1, final double lambda2, final double neighborWeight, final Rectangle roi) throws InterruptedException, ExecutionException {
final int firstLayerIndex = layerset.getLayerIndex(layers.get(0).getId());
final int lastLayerIndex = layerset.getLayerIndex(layers.get(layers.size() - 1).getId());
// final PointMatchFilter filter = new RansacRegressionFilter();
final PointMatchFilter filter = new RansacRegressionReduceFilter();
/* collect patches */
Utils.log("Collecting patches ... ");
final ArrayList<Patch> patches = new ArrayList<Patch>();
for (final Layer layer : layers) patches.addAll((Collection) layer.getDisplayables(Patch.class, roi));
/* delete existing intensity coefficients */
Utils.log("Clearing existing intensity maps ... ");
for (final Patch p : patches) p.clearIntensityMap();
/* generate coefficient tiles for all patches
* TODO consider offering alternative models */
final HashMap<Patch, ArrayList<Tile<? extends M>>> coefficientsTiles = (HashMap) generateCoefficientsTiles(patches, new InterpolatedAffineModel1D<InterpolatedAffineModel1D<AffineModel1D, TranslationModel1D>, IdentityModel>(new InterpolatedAffineModel1D<AffineModel1D, TranslationModel1D>(new AffineModel1D(), new TranslationModel1D(), lambda1), new IdentityModel(), lambda2), numCoefficients * numCoefficients);
/* completed patches */
final HashSet<Patch> completedPatches = new HashSet<Patch>();
/* collect patch pairs */
Utils.log("Collecting patch pairs ... ");
final ArrayList<ValuePair<Patch, Patch>> patchPairs = new ArrayList<ValuePair<Patch, Patch>>();
for (final Patch p1 : patches) {
completedPatches.add(p1);
final Rectangle box1 = p1.getBoundingBox().intersection(roi);
final ArrayList<Patch> p2s = new ArrayList<Patch>();
/* across adjacent layers */
final int layerIndex = layerset.getLayerIndex(p1.getLayer().getId());
for (int i = Math.max(firstLayerIndex, layerIndex - radius); i <= Math.min(lastLayerIndex, layerIndex + radius); ++i) {
final Layer layer = layerset.getLayer(i);
if (layer != null)
p2s.addAll((Collection) layer.getDisplayables(Patch.class, box1));
}
for (final Patch p2 : p2s) {
/*
* if this patch had been processed earlier, all matches are
* already in
*/
if (completedPatches.contains(p2))
continue;
patchPairs.add(new ValuePair<Patch, Patch>(p1, p2));
}
}
final int numThreads = Integer.parseInt(layerset.getProperty("n_mipmap_threads", Integer.toString(Runtime.getRuntime().availableProcessors())));
Utils.log("Matching intensities using " + numThreads + " threads ... ");
final ExecutorService exec = Executors.newFixedThreadPool(numThreads);
final ArrayList<Future<?>> futures = new ArrayList<Future<?>>();
for (final ValuePair<Patch, Patch> patchPair : patchPairs) {
futures.add(exec.submit(new Matcher(roi, patchPair, (HashMap) coefficientsTiles, filter, scale, numCoefficients)));
}
for (final Future<?> future : futures) future.get();
/* connect tiles within patches */
Utils.log("Connecting coefficient tiles in the same patch ... ");
for (final Patch p1 : completedPatches) {
/* get the coefficient tiles */
final ArrayList<Tile<? extends M>> p1CoefficientsTiles = coefficientsTiles.get(p1);
for (int y = 1; y < numCoefficients; ++y) {
final int yr = numCoefficients * y;
final int yr1 = yr - numCoefficients;
for (int x = 0; x < numCoefficients; ++x) {
identityConnect(p1CoefficientsTiles.get(yr1 + x), p1CoefficientsTiles.get(yr + x), neighborWeight);
}
}
for (int y = 0; y < numCoefficients; ++y) {
final int yr = numCoefficients * y;
for (int x = 1; x < numCoefficients; ++x) {
final int yrx = yr + x;
identityConnect(p1CoefficientsTiles.get(yrx), p1CoefficientsTiles.get(yrx - 1), neighborWeight);
}
}
}
/* optimize */
Utils.log("Optimizing ... ");
final TileConfiguration tc = new TileConfiguration();
for (final ArrayList<Tile<? extends M>> coefficients : coefficientsTiles.values()) {
// for ( final Tile< ? > t : coefficients )
// if ( t.getMatches().size() == 0 )
// IJ.log( "bang" );
tc.addTiles(coefficients);
}
try {
tc.optimize(0.01f, iterations, iterations, 0.75f);
} catch (final NotEnoughDataPointsException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (final IllDefinedDataPointsException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
/* save coefficients */
final double[] ab = new double[2];
final FSLoader loader = (FSLoader) layerset.getProject().getLoader();
final String itsDir = loader.getUNUIdFolder() + "trakem2.its/";
for (final Entry<Patch, ArrayList<Tile<? extends M>>> entry : coefficientsTiles.entrySet()) {
final FloatProcessor as = new FloatProcessor(numCoefficients, numCoefficients);
final FloatProcessor bs = new FloatProcessor(numCoefficients, numCoefficients);
final Patch p = entry.getKey();
final double min = p.getMin();
final double max = p.getMax();
final ArrayList<Tile<? extends M>> tiles = entry.getValue();
for (int i = 0; i < numCoefficients * numCoefficients; ++i) {
final Tile<? extends M> t = tiles.get(i);
final Affine1D<?> affine = t.getModel();
affine.toArray(ab);
/* coefficients mapping into existing [min, max] */
as.setf(i, (float) ab[0]);
bs.setf(i, (float) ((max - min) * ab[1] + min - ab[0] * min));
}
final ImageStack coefficientsStack = new ImageStack(numCoefficients, numCoefficients);
coefficientsStack.addSlice(as);
coefficientsStack.addSlice(bs);
final String itsPath = itsDir + FSLoader.createIdPath(Long.toString(p.getId()), "it", ".tif");
new File(itsPath).getParentFile().mkdirs();
IJ.saveAs(new ImagePlus("", coefficientsStack), "tif", itsPath);
}
/* update mipmaps */
for (final Patch p : patches) p.getProject().getLoader().decacheImagePlus(p.getId());
final ArrayList<Future<Boolean>> mipmapFutures = new ArrayList<Future<Boolean>>();
for (final Patch p : patches) mipmapFutures.add(p.updateMipMaps());
for (final Future<Boolean> f : mipmapFutures) f.get();
Utils.log("Matching intensities done.");
}
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