Examples with Pair net.imglib2.util.Pair used on opensource projects

Example 31 with Pair

use of net.imglib2.util.Pair in project repseqio by repseqio.

the class MarkovInsertModel method create.

@Override
public InsertGenerator create(RandomGenerator random, final boolean v, List<VDJCGene> vGenes, List<VDJCGene> dGenes, List<VDJCGene> jGenes, List<VDJCGene> cGenes) {
    Map<Byte, List<Pair<Byte, Double>>> distParams = new HashMap<>();
    for (Map.Entry<String, Double> s : distribution.entrySet()) {
        String[] split = s.getKey().split(">");
        if (split.length != 2 || split[0].length() != 1 || split[1].length() != 1)
            throw new IllegalArgumentException("Illegal distribution key: " + s.getKey() + ". " + "Expected something like \"A>C\"");
        byte codeFrom = NucleotideSequence.ALPHABET.symbolToCode(split[0].charAt(0));
        byte codeTo = NucleotideSequence.ALPHABET.symbolToCode(split[1].charAt(0));
        if (codeFrom == -1 || codeTo == -1)
            throw new IllegalArgumentException("Illegal nucleotide in: " + s.getKey() + ".");
        List<Pair<Byte, Double>> pairs = distParams.get(codeFrom);
        if (pairs == null)
            distParams.put(codeFrom, pairs = new ArrayList<>());
        pairs.add(new Pair<>(codeTo, s.getValue()));
    }
    final Map<Byte, EnumeratedDistribution<Byte>> dists = new HashMap<>();
    for (byte from = 0; from < NucleotideSequence.ALPHABET.basicSize(); from++) {
        List<Pair<Byte, Double>> d = distParams.get(from);
        if (d == null)
            throw new IllegalArgumentException("No distribution for letter: " + NucleotideSequence.ALPHABET.codeToSymbol(from));
        dists.put(from, new EnumeratedDistribution<>(random, d));
    }
    final IndependentIntGenerator lengthDist = lengthDistribution.create(random);
    return new InsertGenerator() {

        @Override
        public NucleotideSequence generate(GGene gene) {
            ReferencePoint point = beginPoint(fromLeft, v);
            int pointPosition = gene.getPartitioning().getPosition(point);
            if (pointPosition == -1)
                throw new RuntimeException("Point " + point + " is not available for gene " + gene);
            byte letter = gene.getSequence(new Range(pointPosition, pointPosition + 1)).codeAt(0);
            int length = lengthDist.sample();
            byte[] array = new byte[length];
            for (int i = 0; i < length; i++) {
                byte cLetter = dists.get(letter).sample();
                array[i] = cLetter;
                letter = cLetter;
            }
            if (!fromLeft)
                ArraysUtils.reverse(array);
            return NucleotideSequence.ALPHABET.createBuilder().ensureCapacity(length).append(array).createAndDestroy();
        }
    };
}

Example 32 with Pair

use of net.imglib2.util.Pair in project androidApp by InspectorIncognito.

the class GetBusesRequest method processResult.

@NonNull
@Override
public Pair<ArrayList<MapBus>, ArrayList<Event>> processResult(@NonNull String result) {
    ArrayList<MapBus> busResponse = new ArrayList<>();
    ArrayList<Event> eventResponse = new ArrayList<>();
    try {
        JSONObject response = new JSONObject(result);
        JSONArray buses = response.getJSONArray("servicios");
        JSONArray events = response.getJSONArray("eventos");
        Log.d("Callback events", events.toString());
        for (int i = 0; i < buses.length(); i++) {
            try {
                MapBus bus = new MapBus(buses.getJSONObject(i));
                busResponse.add(bus);
            } catch (JSONException ignored) {
            }
        }
        for (int i = 0; i < events.length(); i++) {
        // Event event = new Event(events.getJSONObject(i));
        // eventResponse.add(event);
        }
        return new Pair<>(busResponse, eventResponse);
    } catch (JSONException e) {
        e.printStackTrace();
        Log.e("GetBusesRequest", result);
    }
    return new Pair<>(busResponse, eventResponse);
}

Example 33 with Pair

use of net.imglib2.util.Pair in project TrakEM2 by trakem2.

the class ExportARGB method makeFlatImageARGBFromOriginals.

/**
 * Limited to 2GB arrays for the requested image.
 *
 * @param patches
 * @param roi
 * @param backgroundValue
 * @param scale
 * @return
 */
public static final Pair<ColorProcessor, ByteProcessor> makeFlatImageARGBFromOriginals(final List<Patch> patches, final Rectangle roi, final double backgroundValue, final double scale) {
    final ColorProcessor target = new ColorProcessor((int) (roi.width * scale), (int) (roi.height * scale));
    target.setInterpolationMethod(ImageProcessor.BILINEAR);
    final ByteProcessor targetMask = new ByteProcessor(target.getWidth(), target.getHeight());
    targetMask.setInterpolationMethod(ImageProcessor.NEAREST_NEIGHBOR);
    for (final Patch patch : patches) {
        final Patch.PatchImage pai = patch.createTransformedImage();
        final ColorProcessor fp = (ColorProcessor) pai.target.convertToRGB();
        final ByteProcessor alpha;
        System.out.println("IMAGE:" + patch.getTitle());
        System.out.println("mask: " + pai.mask);
        System.out.println("outside: " + pai.outside);
        if (null == pai.mask) {
            if (null == pai.outside) {
                alpha = new ByteProcessor(fp.getWidth(), fp.getHeight());
                // fully opaque
                Arrays.fill((byte[]) alpha.getPixels(), (byte) 255);
            } else {
                alpha = pai.outside;
            }
        } else {
            alpha = pai.mask;
        }
        // The affine to apply
        final AffineTransform atc = new AffineTransform();
        atc.scale(scale, scale);
        atc.translate(-roi.x, -roi.y);
        final AffineTransform at = new AffineTransform();
        at.preConcatenate(atc);
        at.concatenate(patch.getAffineTransform());
        final AffineModel2D aff = new AffineModel2D();
        aff.set(at);
        final CoordinateTransformMesh mesh = new CoordinateTransformMesh(aff, patch.getMeshResolution(), fp.getWidth(), fp.getHeight());
        final TransformMeshMappingWithMasks<CoordinateTransformMesh> mapping = new TransformMeshMappingWithMasks<CoordinateTransformMesh>(mesh);
        fp.setInterpolationMethod(ImageProcessor.BILINEAR);
        // no interpolation
        alpha.setInterpolationMethod(ImageProcessor.NEAREST_NEIGHBOR);
        mapping.map(fp, alpha, target, targetMask);
    }
    return new Pair<ColorProcessor, ByteProcessor>(target, targetMask);
}

Example 34 with Pair

use of net.imglib2.util.Pair in project TrakEM2 by trakem2.

the class ExportBestFlatImage method makeFlatColorImage.

public Pair<ColorProcessor, ByteProcessor> makeFlatColorImage() {
    printInfo();
    if (canUseAWTImage()) {
        // less than 0.5 GB array size
        final ColorProcessor cp = new ColorProcessor(createAWTImage(ImagePlus.COLOR_RGB));
        final ByteProcessor alpha = new ByteProcessor(cp.getWidth(), cp.getHeight(), cp.getChannel(4));
        return new Pair<ColorProcessor, ByteProcessor>(cp, alpha);
    }
    if (!isSmallerThan2GB()) {
        Utils.log("Cannot create an image larger than 2 GB.");
        return null;
    }
    if (loader.isMipMapsRegenerationEnabled()) {
        return ExportARGB.makeFlatImageARGBFromMipMaps(patches, finalBox, 0, scale);
    }
    // No mipmaps: create an image as large as possible, then downsample it
    final Pair<ColorProcessor, ByteProcessor> pair = ExportARGB.makeFlatImageARGBFromOriginals(patches, finalBox, 0, scaleUP);
    final double sigma = computeSigma(pair.a.getWidth(), pair.a.getHeight());
    new GaussianBlur().blurGaussian(pair.a, sigma, sigma, 0.0002);
    new GaussianBlur().blurGaussian(pair.b, sigma, sigma, 0.0002);
    return pair;
}

Example 35 with Pair

use of net.imglib2.util.Pair in project TrakEM2 by trakem2.

the class ExportBestFlatImage method makeFlatFloatGrayImageAndAlpha.

/**
 * While the data is in the 8-bit range, the format is as a FloatProcessor.
 */
public Pair<FloatProcessor, FloatProcessor> makeFlatFloatGrayImageAndAlpha() {
    printInfo();
    if (canUseAWTImage()) {
        // In color to preserve the alpha channel present in mipmaps
        final Image img = createAWTImage(ImagePlus.COLOR_RGB);
        final int width = img.getWidth(null);
        final int height = img.getHeight(null);
        final int[] pixels = new int[width * height];
        PixelGrabber pg = new PixelGrabber(img, 0, 0, width, height, pixels, 0, width);
        try {
            pg.grabPixels();
        } catch (InterruptedException e) {
        }
        ;
        final float[] grey = new float[pixels.length];
        final float[] alpha = new float[pixels.length];
        for (int i = 0; i < pixels.length; ++i) {
            final int p = pixels[i];
            alpha[i] = ((p & 0xff000000) >> 24);
            grey[i] = (((p & 0x00ff0000) >> 16) + ((p & 0x0000ff00) >> 8) + (p & 0x000000ff)) / 3f;
        }
        return new Pair<FloatProcessor, FloatProcessor>(new FloatProcessor(width, height, grey, null), new FloatProcessor(width, height, alpha, null));
    }
    if (!isSmallerThan2GB()) {
        Utils.log("Cannot create an image larger than 2 GB.");
        return null;
    }
    if (loader.isMipMapsRegenerationEnabled()) {
        // Use mipmaps directly: they are already Gaussian-downsampled
        final Pair<ByteProcessor, ByteProcessor> pair = ExportUnsignedByte.makeFlatImageFromMipMaps(patches, finalBox, 0, scale);
        return new Pair<FloatProcessor, FloatProcessor>(pair.a.convertToFloatProcessor(), pair.b.convertToFloatProcessor());
    }
    // Else: no mipmaps
    loader.releaseAll();
    // Use originals and Gaussian-downsample them, then map them onto the target image
    final Pair<ByteProcessor, ByteProcessor> pair = ExportUnsignedByte.makeFlatImageFromOriginals(patches, finalBox, 0, scale);
    return new Pair<FloatProcessor, FloatProcessor>(pair.a.convertToFloatProcessor(), pair.b.convertToFloatProcessor());
}