Examples with AffineModel2D mpicbg.models.AffineModel2D used on opensource projects

Example 16 with AffineModel2D

use of mpicbg.models.AffineModel2D in project TrakEM2 by trakem2.

the class TransformMeshMappingWithMasks method map.

/**
 * Render source into master using alpha composition.
 * Interpolation is specified by the interpolation methods
 * set in source and alpha.
 *
 * Mapping for color images with alpha composition.
 *
 * @param source
 * @param alpha
 * @param target
 * @param targetMask
 * @param numThreads
 */
public final void map(final ColorProcessor source, final ByteProcessor alpha, final ColorProcessor target, final ByteProcessor targetMask, final int numThreads) {
    final List<AffineModel2D> l = new ArrayList<AffineModel2D>();
    l.addAll(transform.getAV().keySet());
    final AtomicInteger i = new AtomicInteger(0);
    final ArrayList<Thread> threads = new ArrayList<Thread>(numThreads);
    for (int k = 0; k < numThreads; ++k) {
        final Thread mtt = new MapColorAlphaTriangleThread(i, l, transform, source, alpha, target, targetMask);
        threads.add(mtt);
        mtt.start();
    }
    for (final Thread mtt : threads) {
        try {
            mtt.join();
        } catch (final InterruptedException e) {
        }
    }
}

Example 17 with AffineModel2D

use of mpicbg.models.AffineModel2D in project TrakEM2 by trakem2.

the class TransformMeshMappingWithMasks method map.

/**
 * Render source into target using alpha composition.
 * Interpolation is specified by the interpolation methods
 * set in source and alpha.
 *
 * @param source
 * @param alpha
 * @param target
 * @param numThreads
 */
public final void map(final ByteProcessor source, final ByteProcessor alpha, final ByteProcessor target, final ByteProcessor targetMask, final int numThreads) {
    final List<AffineModel2D> l = new ArrayList<AffineModel2D>();
    l.addAll(transform.getAV().keySet());
    final AtomicInteger i = new AtomicInteger(0);
    final ArrayList<Thread> threads = new ArrayList<Thread>(numThreads);
    for (int k = 0; k < numThreads; ++k) {
        final Thread mtt = new MapByteAlphaTriangleThread(i, l, transform, source, alpha, target, targetMask);
        threads.add(mtt);
        mtt.start();
    }
    for (final Thread mtt : threads) {
        try {
            mtt.join();
        } catch (final InterruptedException e) {
        }
    }
}

Example 18 with AffineModel2D

use of mpicbg.models.AffineModel2D in project TrakEM2 by trakem2.

the class MovingLeastSquaresTransform method init.

@Override
public final void init(final String data) throws NumberFormatException {
    matches.clear();
    final String[] fields = data.split("\\s+");
    if (fields.length > 3) {
        final int d = Integer.parseInt(fields[1]);
        if ((fields.length - 3) % (2 * d + 1) == 0) {
            if (d == 2) {
                if (fields[0].equals("translation"))
                    model = new TranslationModel2D();
                else if (fields[0].equals("rigid"))
                    model = new RigidModel2D();
                else if (fields[0].equals("similarity"))
                    model = new SimilarityModel2D();
                else if (fields[0].equals("affine"))
                    model = new AffineModel2D();
                else
                    throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
            } else if (d == 3) {
                if (fields[0].equals("affine"))
                    model = new AffineModel3D();
                else
                    throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
            } else
                throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
            alpha = Double.parseDouble(fields[2]);
            int i = 2;
            while (i < fields.length - 1) {
                final double[] p1 = new double[d];
                for (int k = 0; k < d; ++k) p1[k] = Double.parseDouble(fields[++i]);
                final double[] p2 = new double[d];
                for (int k = 0; k < d; ++k) p2[k] = Double.parseDouble(fields[++i]);
                final double weight = Double.parseDouble(fields[++i]);
                final PointMatch m = new PointMatch(new Point(p1), new Point(p2), weight);
                matches.add(m);
            }
        } else
            throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
    } else
        throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
}

Example 19 with AffineModel2D

use of mpicbg.models.AffineModel2D in project TrakEM2 by trakem2.

the class MovingLeastSquaresTransform2 method init2.

public void init2(final String s) throws Exception {
    // WARNING: assumes all whitespace is single
    final int len = s.length();
    int i = 0;
    // Advance to the first white space
    while (' ' != s.charAt(++i)) {
    }
    // Interpret model by the last letter of the name
    final char modelLastChar = s.charAt(i - 1);
    // Determine dimension 2 or 3
    final int n = (s.charAt(i + 1)) - 48;
    switch(n) {
        case 3:
            model = new AffineModel3D();
            break;
        case 2:
            switch(modelLastChar) {
                case // translation
                'n':
                    model = new TranslationModel2D();
                    break;
                case // rigid
                'd':
                    model = new RigidModel2D();
                    break;
                case // similarity
                'y':
                    model = new SimilarityModel2D();
                    break;
                case // affine
                'e':
                    model = new AffineModel2D();
                    break;
                default:
                    throw new Exception("Unknown model " + s.substring(0, i));
            }
            break;
        default:
            throw new NumberFormatException("Unsupported model dimensions: " + n + " for " + this.getClass().getCanonicalName());
    }
    // 'i' is at whitespace before n
    // Move i to whitespace before alpha
    i += 2;
    // Mark last char before whitespace
    int cut = i - 1;
    // 'i' ends up at the whitespace after alpha
    while (' ' != s.charAt(++i)) {
    }
    // Parse alpha
    float[] f = new float[1];
    parse(s, cut, i - 1, f, 0);
    this.alpha = f[0];
    // Count numbers by counting one whitespace before each number
    int nVals = 0;
    for (int k = i; k < len; ++k) {
        if (' ' == s.charAt(k))
            ++nVals;
    }
    // The size of a unit of numbers
    final int cell = n + n + 1;
    // Detect inconsistency:
    if (0 != nVals % cell) {
        throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
    }
    // Create arrays
    this.p = new float[n][nVals / cell];
    this.q = new float[n][this.p[0].length];
    this.w = new float[this.p[0].length];
    // Mark the whitespace char before the first number
    cut = i - 1;
    // Start parsing from the end
    i = len - 1;
    int count = 0;
    if (2 == n) {
        while (i > cut) {
            // Determine which array from {p,q,w} and which position in the array, using n and count:
            switch(// n for dimensions, +1 for the weight
            count % cell) {
                case 0:
                    f = this.w;
                    break;
                case 1:
                    f = this.q[1];
                    break;
                case 2:
                    f = this.q[0];
                    break;
                case 3:
                    f = this.p[1];
                    break;
                case 4:
                    f = this.p[0];
                    break;
            }
            i = parse(s, cut, i, f, this.w.length - (count / cell) - 1);
            ++count;
        }
    } else {
        while (i > cut) {
            // Determine which array from {p,q,w} and which position in the array, using n and count:
            switch(// n for dimensions, +1 for the weight
            count % (n + n + 1)) {
                case 0:
                    f = this.w;
                    break;
                case 1:
                    f = this.q[2];
                    break;
                case 2:
                    f = this.q[1];
                    break;
                case 3:
                    f = this.q[0];
                    break;
                case 4:
                    f = this.p[2];
                    break;
                case 5:
                    f = this.p[1];
                    break;
                case 6:
                    f = this.p[0];
                    break;
            }
            i = parse(s, cut, i, f, this.w.length - (count / cell) - 1);
            ++count;
        }
    }
}

Example 20 with AffineModel2D

use of mpicbg.models.AffineModel2D in project TrakEM2 by trakem2.

the class Distortion_Correction method extractSIFTPointsThreaded.

protected static void extractSIFTPointsThreaded(final int index, final List<Feature>[] siftFeatures, final List<PointMatch>[] inliers, final AbstractAffineModel2D<?>[] models) {
    // save all matching candidates
    final List<PointMatch>[] candidates = new List[siftFeatures.length - 1];
    final Thread[] threads = MultiThreading.newThreads();
    // start at second
    final AtomicInteger ai = new AtomicInteger(0);
    for (int ithread = 0; ithread < threads.length; ++ithread) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                setPriority(Thread.NORM_PRIORITY);
                for (int j = ai.getAndIncrement(); j < candidates.length; j = ai.getAndIncrement()) {
                    final int i = (j < index ? j : j + 1);
                    candidates[j] = FloatArray2DSIFT.createMatches(siftFeatures[index], siftFeatures[i], 1.5f, null, Float.MAX_VALUE, 0.5f);
                }
            }
        };
    }
    MultiThreading.startAndJoin(threads);
    // get rid of the outliers and save the rigid transformations to match
    // the inliers
    final AtomicInteger ai2 = new AtomicInteger(0);
    for (int ithread = 0; ithread < threads.length; ++ithread) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                setPriority(Thread.NORM_PRIORITY);
                for (int i = ai2.getAndIncrement(); i < candidates.length; i = ai2.getAndIncrement()) {
                    final List<PointMatch> tmpInliers = new ArrayList<PointMatch>();
                    // RigidModel2D m =
                    // RigidModel2D.estimateBestModel(candidates.get(i),
                    // tmpInliers, sp.min_epsilon, sp.max_epsilon,
                    // sp.min_inlier_ratio);
                    final AbstractAffineModel2D<?> m;
                    switch(sp.expectedModelIndex) {
                        case 0:
                            m = new TranslationModel2D();
                            break;
                        case 1:
                            m = new RigidModel2D();
                            break;
                        case 2:
                            m = new SimilarityModel2D();
                            break;
                        case 3:
                            m = new AffineModel2D();
                            break;
                        default:
                            return;
                    }
                    boolean modelFound = false;
                    try {
                        modelFound = m.filterRansac(candidates[i], tmpInliers, 1000, sp.maxEpsilon, sp.minInlierRatio, 10);
                    } catch (final NotEnoughDataPointsException e) {
                        modelFound = false;
                    }
                    if (modelFound)
                        IJ.log("Model found:\n  " + candidates[i].size() + " candidates\n  " + tmpInliers.size() + " inliers\n  " + String.format("%.2f", m.getCost()) + "px average displacement");
                    else
                        IJ.log("No Model found.");
                    inliers[index * (sp.numberOfImages - 1) + i] = tmpInliers;
                    models[index * (sp.numberOfImages - 1) + i] = m;
                // System.out.println("**** MODEL ADDED: " +
                // (index*(sp.numberOfImages-1)+i));
                }
            }
        };
    }
    MultiThreading.startAndJoin(threads);
}