Examples with RealComposite net.imglib2.view.composite.RealComposite used on opensource projects

Example 1 with RealComposite

use of net.imglib2.view.composite.RealComposite in project imagej-ops by imagej.

the class PartialDerivativeFilterTest method testAllDerivatives.

@Test
public void testAllDerivatives() {
    Img<FloatType> img = generateFloatArrayTestImg(false, new long[] { 20, 20, 3 });
    Cursor<FloatType> cursorImg = img.cursor();
    int counterX = 0;
    int counterY = 0;
    while (cursorImg.hasNext()) {
        if (counterX > 8 && counterX < 12 || counterY > 8 && counterY < 12) {
            cursorImg.next().setOne();
        } else {
            cursorImg.next().setZero();
        }
        counterX++;
        if (counterX % 20 == 0) {
            counterY++;
        }
        if (counterX == 20) {
            counterX = 0;
        }
        if (counterY == 20) {
            counterY = 0;
        }
    }
    CompositeIntervalView<FloatType, RealComposite<FloatType>> out = ops.filter().allPartialDerivatives(img);
    CompositeView<FloatType, RealComposite<FloatType>>.CompositeRandomAccess outRA = out.randomAccess();
    FloatType type = Util.getTypeFromInterval(img).createVariable();
    // position 9,8 in all dimensions
    outRA.setPosition(new int[] { 9, 8, 0 });
    RealComposite<FloatType> outvalue = outRA.get();
    Float[] correctValues = new Float[] { 12.0f, 4.0f, 0.0f };
    int i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    outRA.setPosition(new int[] { 9, 8, 1 });
    outvalue = outRA.get();
    correctValues = new Float[] { 12.0f, 4.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    outRA.setPosition(new int[] { 9, 8, 2 });
    outvalue = outRA.get();
    correctValues = new Float[] { 12.0f, 4.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    // position 9,9 in all dimensions
    outRA.setPosition(new int[] { 9, 9, 0 });
    outvalue = outRA.get();
    correctValues = new Float[] { 4.0f, 4.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    outRA.setPosition(new int[] { 9, 9, 1 });
    outvalue = outRA.get();
    correctValues = new Float[] { 4.0f, 4.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    outRA.setPosition(new int[] { 9, 9, 2 });
    outvalue = outRA.get();
    correctValues = new Float[] { 4.0f, 4.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    // position 9,10 in all dimensions
    outRA.setPosition(new int[] { 9, 10, 0 });
    outvalue = outRA.get();
    correctValues = new Float[] { 0.0f, 0.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    outRA.setPosition(new int[] { 9, 10, 1 });
    outvalue = outRA.get();
    correctValues = new Float[] { 0.0f, 0.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    outRA.setPosition(new int[] { 9, 10, 2 });
    outvalue = outRA.get();
    correctValues = new Float[] { 0.0f, 0.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    // position 9,11 in all dimensions
    outRA.setPosition(new int[] { 9, 11, 0 });
    outvalue = outRA.get();
    correctValues = new Float[] { 4.0f, -4.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    outRA.setPosition(new int[] { 9, 11, 1 });
    outvalue = outRA.get();
    correctValues = new Float[] { 4.0f, -4.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
    outRA.setPosition(new int[] { 9, 11, 2 });
    outvalue = outRA.get();
    correctValues = new Float[] { 4.0f, -4.0f, 0.0f };
    i = 0;
    for (FloatType value : outvalue) {
        type.set(correctValues[i]);
        assertEquals(type, value);
        i++;
    }
}

Example 2 with RealComposite

use of net.imglib2.view.composite.RealComposite in project TrakEM2 by trakem2.

the class LinearIntensityMap method mapARGB.

protected static final <T extends RealType<T>> void mapARGB(final IterableInterval<ARGBType> image, final IterableInterval<RealComposite<T>> coefficients) {
    final Cursor<ARGBType> cs = image.cursor();
    final Cursor<RealComposite<T>> ct = coefficients.cursor();
    while (cs.hasNext()) {
        final RealComposite<T> t = ct.next();
        final double alpha = t.get(0).getRealDouble();
        final double beta = t.get(1).getRealDouble();
        final ARGBType s = cs.next();
        final int argb = s.get();
        final int a = ((argb >> 24) & 0xff);
        final double r = ((argb >> 16) & 0xff) * alpha + beta;
        final double g = ((argb >> 8) & 0xff) * alpha + beta;
        final double b = (argb & 0xff) * alpha + beta;
        s.set((a << 24) | ((r < 0 ? 0 : r > 255 ? 255 : (int) (r + 0.5)) << 16) | ((g < 0 ? 0 : g > 255 ? 255 : (int) (g + 0.5)) << 8) | (b < 0 ? 0 : b > 255 ? 255 : (int) (b + 0.5)));
    }
}

Example 3 with RealComposite

use of net.imglib2.view.composite.RealComposite in project imagej-ops by imagej.

the class CollapseRealViewTest method defaultCollapseRealTest.

@Test
public void defaultCollapseRealTest() {
    Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 10, 10 }, new DoubleType());
    CompositeIntervalView<DoubleType, RealComposite<DoubleType>> il2 = Views.collapseReal((RandomAccessibleInterval<DoubleType>) img);
    CompositeIntervalView<DoubleType, RealComposite<DoubleType>> opr = ops.transform().collapseRealView((RandomAccessibleInterval<DoubleType>) img);
    assertEquals(il2.numDimensions(), opr.numDimensions());
    CompositeView<DoubleType, RealComposite<DoubleType>> il2_2 = Views.collapseReal((RandomAccessible<DoubleType>) img, 1);
    CompositeView<DoubleType, RealComposite<DoubleType>> opr_2 = ops.transform().collapseRealView((RandomAccessible<DoubleType>) img, 1);
    assertEquals(il2_2.numDimensions(), opr_2.numDimensions());
}

Example 4 with RealComposite

use of net.imglib2.view.composite.RealComposite in project imagej-ops by imagej.

the class HessianFilterTest method test.

@Test
public void test() {
    Img<FloatType> img = generateFloatArrayTestImg(false, new long[] { 50, 50 });
    Cursor<FloatType> cursorImg = img.cursor();
    int counterX = 0;
    int counterY = 0;
    while (cursorImg.hasNext()) {
        if (counterX > 20 && counterX < 30 || counterY > 20 && counterY < 30) {
            cursorImg.next().setOne();
        } else {
            cursorImg.next().setZero();
        }
        counterX++;
        if (counterX % 50 == 0) {
            counterY++;
        }
        if (counterX == 50) {
            counterX = 0;
        }
        if (counterY == 50) {
            counterY = 0;
        }
    }
    CompositeIntervalView<FloatType, RealComposite<FloatType>> out = ops.filter().hessian(img);
    Cursor<RealComposite<FloatType>> outCursor = Views.iterable(out).cursor();
    while (outCursor.hasNext()) {
        RealComposite<FloatType> values = outCursor.next();
        assertEquals(values.get(1), values.get(2));
    }
    CompositeView<FloatType, RealComposite<FloatType>>.CompositeRandomAccess outRA = out.randomAccess();
    // two numbers represent a coordinate: 20|0 ; 21|0 ...
    int[] positions = new int[] { 20, 0, 21, 0, 19, 31, 19, 30 };
    float[] valuesXX = new float[] { 16.0f, -16.0f, 15.0f, 11.0f };
    float[] valuesXY = new float[] { 0.0f, 0.0f, 1.0f, 3.0f };
    float[] valuesYY = new float[] { 0.0f, 0.0f, 15.0f, 15.0f };
    FloatType type = Util.getTypeFromInterval(img).createVariable();
    int i = 0;
    int j = 0;
    while (i < positions.length - 1) {
        int[] pos = new int[2];
        pos[0] = positions[i];
        pos[1] = positions[i + 1];
        outRA.setPosition(pos);
        type.set(valuesXX[j]);
        assertEquals(type, outRA.get().get(0));
        outRA.setPosition(pos);
        type.set(valuesXY[j]);
        assertEquals(type, outRA.get().get(1));
        outRA.setPosition(pos);
        type.set(valuesYY[j]);
        assertEquals(type, outRA.get().get(3));
        i += 2;
        j++;
    }
}

Example 5 with RealComposite

use of net.imglib2.view.composite.RealComposite in project TrakEM2 by trakem2.

the class LinearIntensityMap method run.

@SuppressWarnings({ "rawtypes", "unchecked" })
public <S extends NumericType<S>> void run(final RandomAccessibleInterval<S> image) {
    assert image.numDimensions() == dimensions.numDimensions() : "Number of dimensions do not match.";
    final double[] s = new double[dimensions.numDimensions()];
    for (int d = 0; d < s.length; ++d) s[d] = image.dimension(d) / dimensions.dimension(d);
    final Scale scale = new Scale(s);
    // System.out.println( "translation-n " + translation.numDimensions() );
    final RandomAccessibleInterval<RealComposite<T>> stretchedCoefficients = Views.offsetInterval(Views.raster(RealViews.transform(RealViews.transform(coefficients, translation), scale)), image);
    /* decide on type which mapping to use */
    final S t = image.randomAccess().get();
    if (ARGBType.class.isInstance(t))
        mapARGB(Views.flatIterable((RandomAccessibleInterval<ARGBType>) image), Views.flatIterable(stretchedCoefficients));
    else if (RealComposite.class.isInstance(t))
        mapComposite(Views.flatIterable((RandomAccessibleInterval) image), Views.flatIterable(stretchedCoefficients));
    else if (RealType.class.isInstance(t)) {
        final RealType<?> r = (RealType) t;
        if (r.getMinValue() > -Double.MAX_VALUE || r.getMaxValue() < Double.MAX_VALUE)
            // TODO Bug in javac does not enable cast from RandomAccessibleInterval< S > to RandomAccessibleInterval< RealType >, remove when fixed
            mapCrop(Views.flatIterable((RandomAccessibleInterval<RealType>) (Object) image), Views.flatIterable(stretchedCoefficients));
        else
            // TODO Bug in javac does not enable cast from RandomAccessibleInterval< S > to RandomAccessibleInterval< RealType >, remove when fixed
            map(Views.flatIterable((RandomAccessibleInterval<RealType>) (Object) image), Views.flatIterable(stretchedCoefficients));
    }
}