Examples with PointSetIterator net.imglib2.ops.pointset.PointSetIterator used on opensource projects

Example 1 with PointSetIterator

use of net.imglib2.ops.pointset.PointSetIterator in project imagej-plugins-commands by imagej.

the class ConvertToMask method run.

// -- Command methods --
@Override
@SuppressWarnings({ "rawtypes", "unchecked" })
public void run() {
    if (!threshSrv.hasThreshold(input)) {
        cancel("This command requires a thresholded image.");
        return;
    }
    ThresholdOverlay thresh = threshSrv.getThreshold(input);
    PointSetIterator iter = thresh.getPointsWithin().iterator();
    if (!iter.hasNext()) {
        cancel("No pixels are within the threshold");
        return;
    }
    Dataset ds = dispSrv.getActiveDataset(input);
    final int numDims = ds.numDimensions();
    final long[] dimensions = new long[numDims];
    final long[] min = new long[numDims];
    /*
		 * First pass - find minima and maxima so we can use a shrunken image in some cases.
		 */
    for (int i = 0; i < numDims; i++) {
        min[i] = (long) Math.floor(thresh.realMin(i));
        dimensions[i] = (long) Math.floor(thresh.realMax(i) - thresh.realMin(i) + 1);
    }
    final ArrayImg<BitType, LongArray> arrayMask = ArrayImgs.bits(dimensions);
    final BitType t = new BitType(arrayMask);
    arrayMask.setLinkedType(t);
    final IntervalView<BitType> mask = Views.translate(arrayMask, min);
    final RandomAccess<BitType> raMask = mask.randomAccess();
    iter.reset();
    while (iter.hasNext()) {
        long[] pos = iter.next();
        raMask.setPosition(pos);
        raMask.get().set(true);
    }
    output = new BinaryMaskOverlay(context, new BinaryMaskRegionOfInterest<BitType, IntervalView<BitType>>(mask));
    output.setAlpha(alpha);
    output.setFillColor(color);
    for (int i = 0; i < numDims; i++) {
        output.setAxis(ds.axis(i), i);
    }
}

Example 2 with PointSetIterator

use of net.imglib2.ops.pointset.PointSetIterator in project imagej-plugins-commands by imagej.

the class Binarize method run.

// -- Command methods --
@Override
@SuppressWarnings("unchecked")
public void run() {
    long[] dims = Intervals.dimensionsAsLongArray(inputData);
    String err = checkInputMask(inputMask, dims);
    if (err != null) {
        cancel(err);
        return;
    }
    CalibratedAxis[] axes = new CalibratedAxis[dims.length];
    inputData.axes(axes);
    AxisType[] types = new AxisType[dims.length];
    for (int i = 0; i < dims.length; i++) {
        types[i] = axes[i].type();
    }
    Dataset mask = inputMask != null ? inputMask : datasetSrv.create(new BitType(), dims, "Mask", types, isVirtual(inputData));
    mask.setAxes(axes);
    RandomAccess<BitType> maskAccessor = (RandomAccess<BitType>) mask.getImgPlus().randomAccess();
    RandomAccess<? extends RealType<?>> dataAccessor = inputData.getImgPlus().randomAccess();
    DataRange minMax = calcDataRange(inputData);
    Histogram1d<T> histogram = null;
    boolean testLess = maskPixels.equals(INSIDE);
    DoubleType val = new DoubleType();
    // Better performance? Especially for CellImgs?
    if (thresholdEachPlane && planeCount(inputData) > 1) {
        // threshold each plane separately
        long[] planeSpace = planeSpace(inputData);
        PointSetIterator pIter = new HyperVolumePointSet(planeSpace).iterator();
        while (pIter.hasNext()) {
            long[] planePos = pIter.next();
            histogram = buildHistogram(inputData, planePos, minMax, histogram);
            double cutoffVal = cutoff(histogram, method, testLess, val);
            PointSet planeData = planeData(inputData, planePos);
            PointSetIterator iter = planeData.iterator();
            while (iter.hasNext()) {
                updateMask(iter.next(), testLess, cutoffVal, dataAccessor, maskAccessor);
            }
        }
    } else {
        // threshold entire dataset once
        histogram = buildHistogram(inputData, null, minMax, null);
        double cutoffVal = cutoff(histogram, method, testLess, val);
        PointSet fullData = fullData(dims);
        PointSetIterator iter = fullData.iterator();
        while (iter.hasNext()) {
            updateMask(iter.next(), testLess, cutoffVal, dataAccessor, maskAccessor);
        }
    }
    assignColorTables(mask);
    if (changeInput) {
        // TODO - should inputData be ItemIO.BOTH????
        inputData.setImgPlus(mask.getImgPlus());
    } else
        outputMask = mask;
}

Example 3 with PointSetIterator

use of net.imglib2.ops.pointset.PointSetIterator in project imagej-plugins-commands by imagej.

the class NanBackground method assignPixels.

private void assignPixels() {
    ThresholdOverlay thresh = threshSrv.getThreshold(display);
    PointSet ps = thresh.getPointsOutside();
    PointSetIterator iter = ps.iterator();
    RandomAccess<? extends RealType<?>> accessor = input.getImgPlus().randomAccess();
    while (iter.hasNext()) {
        long[] pos = iter.next();
        accessor.setPosition(pos);
        accessor.get().setReal(Double.NaN);
    }
}

Example 4 with PointSetIterator

use of net.imglib2.ops.pointset.PointSetIterator in project imagej-plugins-commands by imagej.

the class ImageCalculator method copyDataInto.

// -- private helpers --
private void copyDataInto(final Img<? extends RealType<?>> out, final Img<? extends RealType<?>> in, final long[] span) {
    final RandomAccess<? extends RealType<?>> src = in.randomAccess();
    final RandomAccess<? extends RealType<?>> dst = out.randomAccess();
    final HyperVolumePointSet ps = new HyperVolumePointSet(span);
    final PointSetIterator iter = ps.iterator();
    long[] pos = null;
    while (iter.hasNext()) {
        pos = iter.next();
        src.setPosition(pos);
        dst.setPosition(pos);
        final double value = src.get().getRealDouble();
        dst.get().setReal(value);
    }
}

Example 5 with PointSetIterator

use of net.imglib2.ops.pointset.PointSetIterator in project imagej-plugins-commands by imagej.

the class PointSetDemo method run.

@Override
public void run() {
    TextSpecifiedPointSet pointSet = new TextSpecifiedPointSet(specification);
    if (pointSet.getErrorString() != null) {
        cancel(pointSet.getErrorString());
        return;
    }
    long[] minBound = new long[pointSet.numDimensions()];
    long[] maxBound = new long[pointSet.numDimensions()];
    pointSet.min(minBound);
    pointSet.max(maxBound);
    for (int i = 0; i < minBound.length; i++) {
        if ((minBound[i] < 0) || (maxBound[i] < 0)) {
            cancel("For now won't handle negative space with this test plugin");
            return;
        }
        // make a border around the maximum bound
        maxBound[i] += 10;
    }
    output = ds.create(maxBound, "PointSet", null, 8, false, false);
    ImgPlus<? extends RealType<?>> imgplus = output.getImgPlus();
    RandomAccess<? extends RealType<?>> accessor = imgplus.randomAccess();
    PointSetIterator iter = pointSet.iterator();
    while (iter.hasNext()) {
        long[] pos = iter.next();
        accessor.setPosition(pos);
        accessor.get().setReal(255);
    }
}