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

Example 11 with PointSet

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

the class AbstractNoiseReducerPlugin method run.

@Override
public void run() {
    Neighborhood neighborhood = determineNeighborhood(input.numDimensions());
    if (neighborhood == null)
        return;
    @SuppressWarnings("unchecked") ImgPlus<U> inputImg = (ImgPlus<U>) input.getImgPlus();
    OutOfBoundsMirrorFactory<U, RandomAccessibleInterval<U>> oobFactory = new OutOfBoundsMirrorFactory<U, RandomAccessibleInterval<U>>(Boundary.DOUBLE);
    Function<long[], DoubleType> otherFunc = new RealImageFunction<U, DoubleType>(inputImg, oobFactory, new DoubleType());
    PointSet ps = neighborhood.getPoints();
    Reducer<U, DoubleType> reducer = new Reducer<U, DoubleType>(getContext(), inputImg, getFunction(otherFunc), ps);
    output = reducer.reduceNoise(neighborhood.getDescription());
}

Example 12 with PointSet

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

the class NoiseReductionAdaptiveMedian method run.

// -- NoiseReductionAdaptiveMedian methods --
@Override
public void run() {
    @SuppressWarnings("unchecked") final ImgPlus<U> inputImg = (ImgPlus<U>) input.getImgPlus();
    final OutOfBoundsMirrorFactory<U, RandomAccessibleInterval<U>> oobFactory = new OutOfBoundsMirrorFactory<U, RandomAccessibleInterval<U>>(Boundary.DOUBLE);
    final Function<long[], DoubleType> otherFunc = new RealImageFunction<U, DoubleType>(inputImg, oobFactory, new DoubleType());
    final List<PointSet> pointSets = getNeighborhoods(input.numDimensions());
    final Reducer<U, DoubleType> reducer = new Reducer<U, DoubleType>(context, inputImg, getFunction(otherFunc, pointSets), pointSets.get(0));
    output = reducer.reduceNoise("Adaptive window neighborhood");
}

Example 13 with PointSet

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

the class MeasurementDemo method example1.

// -- Other examples --
// standard ways of measuring various values.
// a basic measurement
private void example1() {
    Dataset ds = getTestData();
    DoubleType output = new DoubleType();
    RealImageFunction<?, DoubleType> imgFunc = mSrv.imgFunction(ds, output);
    RealArithmeticMeanFunction<DoubleType> meanFunc = new RealArithmeticMeanFunction<DoubleType>(imgFunc);
    PointSet region = new HyperVolumePointSet(Intervals.dimensionsAsLongArray(ds));
    mSrv.measure(meanFunc, region, output);
    System.out.println("arithmetic mean is " + output.getRealDouble());
}

Example 14 with PointSet

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

the class MeasurementDemo method example4.

// measuring multiple things at a time
private void example4() {
    Dataset ds = getTestData();
    DoubleType output = new DoubleType();
    RealImageFunction<?, DoubleType> imgFunc = mSrv.imgFunction(ds, output);
    RealArithmeticMeanFunction<DoubleType> meanFunc = new RealArithmeticMeanFunction<DoubleType>(imgFunc);
    RealMinFunction<DoubleType> minFunc = new RealMinFunction<DoubleType>(imgFunc);
    RealMaxFunction<DoubleType> maxFunc = new RealMaxFunction<DoubleType>(imgFunc);
    List<Function<PointSet, DoubleType>> funcList = new ArrayList<Function<PointSet, DoubleType>>();
    List<DoubleType> outputList = new ArrayList<DoubleType>();
    funcList.add(meanFunc);
    funcList.add(minFunc);
    funcList.add(maxFunc);
    outputList.add(new DoubleType());
    outputList.add(new DoubleType());
    outputList.add(new DoubleType());
    PointSet region = new HyperVolumePointSet(Intervals.dimensionsAsLongArray(ds));
    mSrv.measure(funcList, region, outputList);
    System.out.println("mean = " + outputList.get(0).getRealDouble());
    System.out.println("min = " + outputList.get(1).getRealDouble());
    System.out.println("max = " + outputList.get(2).getRealDouble());
}

Example 15 with PointSet

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

the class MeasurementDemo method example6.

// measuring a user defined function with the service
private void example6() {
    Dataset ds = getTestData();
    IntType output = new IntType();
    RealImageFunction<?, IntType> imgFunc = mSrv.imgFunction(ds, output);
    CustomFunction func = new CustomFunction(imgFunc);
    PointSet region = new HyperVolumePointSet(Intervals.dimensionsAsLongArray(ds));
    mSrv.measure(func, region, output);
    System.out.println("total 7's = " + output.get());
}