Examples with DoubleType net.imglib2.type.numeric.real.DoubleType used on opensource projects

Example 6 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project bigwarp by saalfeldlab.

the class GridRealRandomAccess method main.

public static void main(String[] args) {
    GridRealRandomAccess<DoubleType> ra = new GridRealRandomAccess<DoubleType>(new double[] { 100.0, 100.0 }, new DoubleType(), null);
    ra.setMethod(GRID_TYPE.LINE);
    for (double x = 2.1; x < 5.0; x += 1.0) for (double y = 0.0; y < 5.0; y += 0.5) {
        ra.setPosition(new double[] { x, y });
        System.out.println("(" + x + "," + y + ") : " + ra.get());
    }
}

Example 7 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project imagej-ops by imagej.

the class LocalPhansalkarThreshold method unaryComputer.

@Override
protected CenterAwareComputerOp<T, BitType> unaryComputer(final T inClass, final BitType outClass) {
    final LocalThresholdMethod<T> op = new LocalThresholdMethod<T>() {

        private UnaryComputerOp<Iterable<T>, DoubleType> mean;

        private UnaryComputerOp<Iterable<T>, DoubleType> stdDeviation;

        @Override
        public void compute(final Iterable<T> neighborhood, final T center, final BitType output) {
            if (mean == null) {
                mean = Computers.unary(ops(), Ops.Stats.Mean.class, new DoubleType(), neighborhood);
            }
            if (stdDeviation == null) {
                stdDeviation = Computers.unary(ops(), Ops.Stats.StdDev.class, new DoubleType(), neighborhood);
            }
            final DoubleType meanValue = new DoubleType();
            mean.compute(neighborhood, meanValue);
            final DoubleType stdDevValue = new DoubleType();
            stdDeviation.compute(neighborhood, stdDevValue);
            double threshold = meanValue.get() * (1.0d + p * Math.exp(-q * meanValue.get()) + k * ((stdDevValue.get() / r) - 1.0));
            output.set(center.getRealDouble() >= threshold);
        }
    };
    op.setEnvironment(ops());
    return op;
}

Example 8 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project imagej-ops by imagej.

the class IntegralVariance method compute.

@Override
public void compute(final RectangleNeighborhood<Composite<I>> input, final DoubleType output) {
    // computation according to
    // https://en.wikipedia.org/wiki/Summed_area_table
    final IntegralCursor<Composite<I>> cursorS1 = new IntegralCursor<>(input);
    final int dimensions = input.numDimensions();
    // Compute \sum (-1)^{dim - ||cornerVector||_{1}} * I(x^{cornerVector})
    final DoubleType sum1 = new DoubleType();
    sum1.setZero();
    // Convert from input to return type
    final Converter<I, DoubleType> conv = new RealDoubleConverter<>();
    // Compute \sum (-1)^{dim - ||cornerVector||_{1}} * I(x^{cornerVector})
    final DoubleType sum2 = new DoubleType();
    sum2.setZero();
    final DoubleType valueAsDoubleType = new DoubleType();
    while (cursorS1.hasNext()) {
        final Composite<I> compositeValue = cursorS1.next();
        final I value1 = compositeValue.get(0).copy();
        conv.convert(value1, valueAsDoubleType);
        // Obtain the cursor position encoded as corner vector
        final int cornerInteger1 = cursorS1.getCornerRepresentation();
        // Determine if the value has to be added (factor==1) or subtracted
        // (factor==-1)
        final DoubleType factor = new DoubleType(Math.pow(-1.0d, dimensions - IntegralMean.norm(cornerInteger1)));
        valueAsDoubleType.mul(factor);
        sum1.add(valueAsDoubleType);
        final I value2 = compositeValue.get(1).copy();
        conv.convert(value2, valueAsDoubleType);
        // Determine if the value has to be added (factor==1) or subtracted
        // (factor==-1)
        valueAsDoubleType.mul(factor);
        sum2.add(valueAsDoubleType);
    }
    final int area = (int) Intervals.numElements(Intervals.expand(input, -1l));
    // NB: Reuse available DoubleType
    valueAsDoubleType.set(area);
    sum1.mul(sum1);
    // NB
    sum1.div(valueAsDoubleType);
    sum2.sub(sum1);
    // NB
    valueAsDoubleType.sub(new DoubleType(1));
    // NB
    sum2.div(valueAsDoubleType);
    output.set(sum2);
}

Example 9 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project imagej-ops by imagej.

the class BoxCount method calculate.

/**
 * Counts the number of boxes that have foreground in the interval repeatedly with
 * different size boxes
 *
 * @param input An n-dimensional binary interval.
 * @return A list of (log(foreground count), -log(box size))
 *         {@link ValuePair} objects for curve fitting
 */
@Override
public List<ValuePair<DoubleType, DoubleType>> calculate(final RandomAccessibleInterval<B> input) {
    if (scaling < 1.0 || (scaling == 1.0 && maxSize > minSize)) {
        throw new IllegalArgumentException("Scaling must be > 1.0 or algorithm won't stop.");
    }
    final List<ValuePair<DoubleType, DoubleType>> points = new ArrayList<>();
    final int dimensions = input.numDimensions();
    final long[] sizes = new long[dimensions];
    input.dimensions(sizes);
    for (long boxSize = maxSize; boxSize >= minSize; boxSize /= scaling) {
        final long numTranslations = limitTranslations(boxSize, 1 + gridMoves);
        final long translationAmount = boxSize / numTranslations;
        final Stream<long[]> translations = translationStream(numTranslations, translationAmount, dimensions - 1, new long[dimensions]);
        final LongStream foregroundCounts = countTranslatedGrids(input, translations, sizes, boxSize);
        final long foreground = foregroundCounts.min().orElse(0);
        final double logSize = -Math.log(boxSize);
        final double logCount = Math.log(foreground);
        final ValuePair<DoubleType, DoubleType> point = new ValuePair<>(new DoubleType(logSize), new DoubleType(logCount));
        points.add(point);
    }
    return points;
}

Example 10 with DoubleType

use of net.imglib2.type.numeric.real.DoubleType in project imagej-ops by imagej.

the class RidgeDetectionUtils method getMaxCoords.

protected static long[] getMaxCoords(RandomAccessibleInterval<DoubleType> input, boolean useAbsoluteValue) {
    long[] dims = new long[input.numDimensions()];
    double max = Double.MIN_VALUE;
    Cursor<DoubleType> cursor = Views.iterable(input).localizingCursor();
    while (cursor.hasNext()) {
        cursor.fwd();
        double current = useAbsoluteValue ? Math.abs(cursor.get().get()) : cursor.get().get();
        if (current > max) {
            max = current;
            for (int d = 0; d < input.numDimensions(); d++) {
                dims[d] = cursor.getLongPosition(d);
            }
        }
    }
    return dims;
}