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

Example 1 with PointSet

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

the class MeasurementDemo method getNestedNeighborhoods.

// this returns a list of PointSets that are progressively bigger.
// for illustration.
private List<PointSet> getNestedNeighborhoods(long delta) {
    long[] zeroOrigin = new long[2];
    long[] tmpNeg = new long[] { delta, delta };
    long[] tmpPos = new long[] { delta, delta };
    List<PointSet> regions = new ArrayList<PointSet>();
    for (int i = 0; i < 5; i++) {
        PointSet ps = new HyperVolumePointSet(zeroOrigin, tmpNeg, tmpPos);
        regions.add(ps);
        tmpNeg = tmpNeg.clone();
        tmpPos = tmpPos.clone();
        tmpNeg[0]++;
        tmpNeg[1]++;
        tmpPos[0]++;
        tmpPos[1]++;
    }
    return regions;
}

Example 2 with PointSet

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

the class MeasurementDemo method example5.

// measuring a custom set of data using an aggregating class
private void example5() {
    Dataset ds = getTestData();
    DoubleType output = new DoubleType();
    RealImageFunction<?, DoubleType> imgFunc = mSrv.imgFunction(ds, output);
    BasicStatsFunction<DoubleType> statFunc = new BasicStatsFunction<DoubleType>(imgFunc, new DoubleType());
    PointSet region = new HyperVolumePointSet(Intervals.dimensionsAsLongArray(ds));
    BasicStats stats = new BasicStats();
    mSrv.measure(statFunc, region, stats);
    System.out.println("mean = " + stats.getXBar());
    System.out.println("var = " + stats.getS2n1());
}

Example 3 with PointSet

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

the class MeasurementDemo method example3.

// a measurement that has a metric with nondefault constructor and oob
private void example3() {
    Dataset ds = getTestData();
    DoubleType output = new DoubleType();
    OutOfBoundsFactory<UnsignedByteType, RandomAccessibleInterval<UnsignedByteType>> oobFactory = getOobFactory();
    @SuppressWarnings("unchecked") RealImageFunction<?, DoubleType> imgFuncWithOOB = new RealImageFunction<UnsignedByteType, DoubleType>((Img<UnsignedByteType>) ds.getImgPlus(), oobFactory, output);
    // force to (0,0) - tests that oob code is working
    // ds.dimension(0) / 2;
    long ctrX = 0;
    // ds.dimension(1) / 2;
    long ctrY = 0;
    long[] posDeltas = new long[] { 3, 3 };
    long[] negDeltas = new long[] { 3, 3 };
    List<PointSet> pointSets = getNestedNeighborhoods(3);
    RealAdaptiveMedianFunction<DoubleType> adapMedFunc = new RealAdaptiveMedianFunction<DoubleType>(imgFuncWithOOB, pointSets);
    PointSet region = new HyperVolumePointSet(new long[] { ctrX, ctrY }, negDeltas, posDeltas);
    mSrv.measure(adapMedFunc, region, output);
    System.out.println("adaptive median is " + output.getRealDouble());
}

Example 4 with PointSet

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

the class MeasurementDemo method example2.

// a basic measurement with out of bounds data handling
private void example2() {
    Dataset ds = getTestData();
    DoubleType output = new DoubleType();
    OutOfBoundsFactory<UnsignedByteType, RandomAccessibleInterval<UnsignedByteType>> oobFactory = getOobFactory();
    @SuppressWarnings("unchecked") RealImageFunction<?, DoubleType> imgFuncWithOOB = new RealImageFunction<UnsignedByteType, DoubleType>((Img<UnsignedByteType>) ds.getImgPlus(), oobFactory, output);
    RealMaxFunction<DoubleType> maxFunc = new RealMaxFunction<DoubleType>(imgFuncWithOOB);
    PointSet region = new HyperVolumePointSet(Intervals.dimensionsAsLongArray(ds));
    mSrv.measure(maxFunc, region, output);
    System.out.println("max is " + output.getRealDouble());
}

Example 5 with PointSet

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

the class MeasurementDemo method calc.

// -- private helpers --
private void calc() {
    PointSet points;
    Overlay overlay = oSrv.getActiveOverlay(display);
    if (overlay != null) {
        points = new RoiPointSet(overlay.getRegionOfInterest());
    } else {
        long[] dims = Intervals.dimensionsAsLongArray(display);
        // 1st plane only
        for (int i = 2; i < dims.length; i++) {
            dims[i] = 1;
        }
        points = new HyperVolumePointSet(dims);
    }
    DoubleType output = new DoubleType();
    mSrv.measure(function, points, output);
    sSrv.showStatus(funcName + " of selected region is " + output.getRealDouble());
}