Examples with UnsignedShortType net.imglib2.type.numeric.integer.UnsignedShortType used on opensource projects

Example 1 with UnsignedShortType

use of net.imglib2.type.numeric.integer.UnsignedShortType in project imagej-ops by imagej.

the class InvertTest method testUnsignedShortTypeInvert.

@Test
public void testUnsignedShortTypeInvert() {
    final Img<UnsignedShortType> inUnsignedShortType = generateUnsignedShortArrayTestImg(true, 5, 5);
    final Img<UnsignedShortType> outUnsignedShortType = inUnsignedShortType.factory().create(inUnsignedShortType, new UnsignedShortType());
    assertDefaultInvert(inUnsignedShortType, outUnsignedShortType);
    assertDefaultInvertMinMaxProvided(inUnsignedShortType, outUnsignedShortType, new UnsignedShortType((short) 437), new UnsignedShortType((short) 8008));
}

Example 2 with UnsignedShortType

use of net.imglib2.type.numeric.integer.UnsignedShortType in project imagej-ops by imagej.

the class AbstractThresholdTest method initialize.

@Before
public void initialize() {
    final long[] dimensions = new long[] { xSize, ySize };
    final Random r = new Random(0xdeadbeef);
    // create image and output
    in = ArrayImgs.unsignedShorts(dimensions);
    final RandomAccess<UnsignedShortType> ra = in.randomAccess();
    // populate pixel values with a ramp function + a constant
    for (int x = 0; x < xSize; x++) {
        for (int y = 0; y < ySize; y++) {
            ra.setPosition(new int[] { x, y });
            ra.get().setReal(r.nextInt(65535));
        }
    }
}

Example 3 with UnsignedShortType

use of net.imglib2.type.numeric.integer.UnsignedShortType in project vcell by virtualcell.

the class ConstructTIRFGeometry method run.

@Override
public void run() {
    // Calculate constant d in TIRF exponential decay function
    // Angle of incidence in radians
    theta = theta * 2 * Math.PI / 360;
    // Refractive index of glass
    final double n1 = 1.52;
    // Refractive index of cytosol
    final double n2 = 1.38;
    final double d = lambda * Math.pow((Math.pow(n1, 2) * Math.pow(Math.sin(theta), 2) - Math.pow(n2, 2)), -0.5) / (4 * Math.PI);
    System.out.println("d: " + d);
    final double fluorPerMolecule = 250;
    // Get frame of interest to define geometry
    long maxX = data.dimension(0) - 1;
    long maxY = data.dimension(1) - 1;
    Interval interval = Intervals.createMinMax(0, 0, sliceIndex, maxX, maxY, sliceIndex);
    RandomAccessibleInterval<T> croppedRAI = ops.transform().crop(data, interval, true);
    // Subtract lowest pixel value
    IterableInterval<T> dataII = Views.iterable(croppedRAI);
    double min = ops.stats().min(dataII).getRealDouble();
    Cursor<T> dataCursor = dataII.cursor();
    while (dataCursor.hasNext()) {
        double val = dataCursor.next().getRealDouble();
        dataCursor.get().setReal(val - min);
    }
    // Perform Gaussian blur
    RandomAccessibleInterval<T> blurredRAI = ops.filter().gauss(croppedRAI, 2);
    IterableInterval<T> blurredII = Views.iterable(blurredRAI);
    // Segment slice by threshold and fill holes
    IterableInterval<BitType> thresholded = ops.threshold().huang(blurredII);
    Img<BitType> thresholdedImg = ops.convert().bit(thresholded);
    RandomAccessibleInterval<BitType> thresholdedRAI = ops.morphology().fillHoles(thresholdedImg);
    // Get the largest region
    RandomAccessibleInterval<LabelingType<ByteType>> labeling = ops.labeling().cca(thresholdedRAI, ConnectedComponents.StructuringElement.EIGHT_CONNECTED);
    LabelRegions<ByteType> labelRegions = new LabelRegions<>(labeling);
    Iterator<LabelRegion<ByteType>> iterator = labelRegions.iterator();
    LabelRegion<ByteType> maxRegion = iterator.next();
    while (iterator.hasNext()) {
        LabelRegion<ByteType> currRegion = iterator.next();
        if (currRegion.size() > maxRegion.size()) {
            maxRegion = currRegion;
        }
    }
    // Generate z index map
    double iMax = ops.stats().max(dataII).getRealDouble();
    Img<UnsignedShortType> dataImg = ops.convert().uint16(dataII);
    Img<UnsignedShortType> zMap = ops.convert().uint16(ops.create().img(dataII));
    LabelRegionCursor cursor = maxRegion.localizingCursor();
    RandomAccess<UnsignedShortType> zMapRA = zMap.randomAccess();
    RandomAccess<UnsignedShortType> dataRA = dataImg.randomAccess();
    while (cursor.hasNext()) {
        cursor.fwd();
        zMapRA.setPosition(cursor);
        dataRA.setPosition(cursor);
        double val = dataRA.get().getRealDouble();
        // Log of 0 is undefined
        if (val < 1) {
            val = 1;
        }
        int z = (int) Math.round(-d * Math.log(val / iMax) / zRes);
        zMapRA.get().set(z);
    }
    System.out.println("6");
    // Use map to construct 3D geometry
    // Add 5 slices of padding on top
    int maxZ = (int) ops.stats().max(zMap).getRealDouble() + 5;
    long[] resultDimensions = { maxX + 1, maxY + 1, maxZ };
    Img<BitType> result = new ArrayImgFactory<BitType>().create(resultDimensions, new BitType());
    RandomAccess<BitType> resultRA = result.randomAccess();
    System.out.println(maxZ);
    cursor.reset();
    while (cursor.hasNext()) {
        cursor.fwd();
        zMapRA.setPosition(cursor);
        int zIndex = zMapRA.get().get();
        int[] position = { cursor.getIntPosition(0), cursor.getIntPosition(1), zIndex };
        while (position[2] < maxZ) {
            resultRA.setPosition(position);
            resultRA.get().set(true);
            position[2]++;
        }
    }
    output = datasetService.create(result);
    CalibratedAxis[] axes = new DefaultLinearAxis[] { new DefaultLinearAxis(Axes.X), new DefaultLinearAxis(Axes.Y), new DefaultLinearAxis(Axes.Z) };
    output.setAxes(axes);
    System.out.println("Done constructing geometry");
}

Example 4 with UnsignedShortType

use of net.imglib2.type.numeric.integer.UnsignedShortType in project imagej-ops by imagej.

the class AbstractThresholdTest method assertThreshold.

protected void assertThreshold(final int expected, final Object actual) {
    final Object value = actual instanceof List ? ListUtils.first((List<?>) actual) : actual;
    assertTrue(value instanceof UnsignedShortType);
    final UnsignedShortType threshold = (UnsignedShortType) value;
    assertEquals(expected, threshold.get());
}

Example 5 with UnsignedShortType

use of net.imglib2.type.numeric.integer.UnsignedShortType in project imagej-ops by imagej.

the class ApplyManualThresholdTest method testApplyThreshold.

@Test
public void testApplyThreshold() throws IncompatibleTypeException {
    final Img<BitType> out = bitmap();
    final UnsignedShortType threshold = new UnsignedShortType(30000);
    ops.run(ApplyManualThreshold.class, out, in, threshold);
    assertCount(out, 54);
}