Examples with Dimensions net.imglib2.Dimensions used on opensource projects

Example 26 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class Outline method createOutput.

@Override
public RandomAccessibleInterval<BitType> createOutput(final RandomAccessibleInterval<B> input, final Boolean input2) {
    final long[] dims = new long[input.numDimensions()];
    input.dimensions(dims);
    final FinalDimensions dimensions = new FinalDimensions(dims);
    return ops().create().img(dimensions, new BitType());
}

Example 27 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class IntegralMean 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>> cursor = new IntegralCursor<>(input);
    final int dimensions = input.numDimensions();
    // Compute \sum (-1)^{dim - ||cornerVector||_{1}} * I(x^{cornerVector})
    final DoubleType sum = new DoubleType();
    sum.setZero();
    // Convert from input to return type
    final Converter<I, DoubleType> conv = new RealDoubleConverter<>();
    final DoubleType valueAsDoubleType = new DoubleType();
    while (cursor.hasNext()) {
        final I value = cursor.next().get(0).copy();
        conv.convert(value, valueAsDoubleType);
        // Obtain the cursor position encoded as corner vector
        final int cornerInteger = cursor.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(cornerInteger)));
        valueAsDoubleType.mul(factor);
        sum.add(valueAsDoubleType);
    }
    final int area = (int) Intervals.numElements(Intervals.expand(input, -1l));
    // Compute mean by dividing the sum divided by the number of elements
    // NB: Reuse DoubleType
    valueAsDoubleType.set(area);
    sum.div(valueAsDoubleType);
    output.set(sum);
}

Example 28 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class IntegralSum method compute.

@Override
public void compute(final RectangleNeighborhood<I> input, final DoubleType output) {
    // computation according to
    // https://en.wikipedia.org/wiki/Summed_area_table
    final IntegralCursor<I> cursor = new IntegralCursor<>(input);
    final int dimensions = input.numDimensions();
    // Compute \sum (-1)^{dim - ||cornerVector||_{1}} * I(x^{cornerVector})
    final DoubleType sum = new DoubleType();
    sum.setZero();
    // Convert from input to return type
    final Converter<I, DoubleType> conv = new RealDoubleConverter<>();
    final DoubleType valueAsDoubleType = new DoubleType();
    while (cursor.hasNext()) {
        final I value = cursor.next().copy();
        conv.convert(value, valueAsDoubleType);
        // Obtain the cursor position encoded as corner vector
        final int cornerInteger = cursor.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(cornerInteger)));
        valueAsDoubleType.mul(factor);
        sum.add(valueAsDoubleType);
    }
    output.set(sum);
}

Example 29 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class PadInputFFT method calculate.

@Override
@SuppressWarnings("unchecked")
public O calculate(final I input, final Dimensions paddedDimensions) {
    Dimensions paddedFFTInputDimensions;
    // if an fftsize op has been set recompute padded size
    if (fftSizeOp != null) {
        long[][] sizes = fftSizeOp.calculate(paddedDimensions);
        paddedFFTInputDimensions = new FinalDimensions(sizes[0]);
    } else {
        paddedFFTInputDimensions = paddedDimensions;
    }
    if (obf == null) {
        obf = new OutOfBoundsConstantValueFactory<>(Util.getTypeFromInterval(input).createVariable());
    }
    Interval inputInterval = paddingIntervalCentered.calculate(input, paddedFFTInputDimensions);
    return (O) Views.interval(Views.extend(input, obf), inputInterval);
}

Example 30 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class PadShiftKernel method calculate.

@Override
@SuppressWarnings("unchecked")
public O calculate(final I kernel, final Dimensions paddedDimensions) {
    Dimensions paddedFFTInputDimensions;
    // if an fftsize op has been set recompute padded size
    if (fftSizeOp != null) {
        long[][] sizes = fftSizeOp.calculate(paddedDimensions);
        paddedFFTInputDimensions = new FinalDimensions(sizes[0]);
    } else {
        paddedFFTInputDimensions = paddedDimensions;
    }
    // compute where to place the final Interval for the kernel so that the
    // coordinate in the center
    // of the kernel is shifted to position (0,0).
    final Interval kernelConvolutionInterval = paddingIntervalCentered.calculate(kernel, paddedFFTInputDimensions);
    final Interval kernelConvolutionIntervalOrigin = paddingIntervalOrigin.calculate(kernel, kernelConvolutionInterval);
    return (O) Views.interval(Views.extendPeriodic(Views.interval(Views.extendValue(kernel, Util.getTypeFromInterval(kernel).createVariable()), kernelConvolutionInterval)), kernelConvolutionIntervalOrigin);
}