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

Example 6 with PointSet

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

the class StatisticsDemo method getRegion.

private PointSet getRegion() {
    Overlay overlay = oSrv.getActiveOverlay(display);
    if (overlay != null) {
        return new RoiPointSet(overlay.getRegionOfInterest());
    }
    long[] pt1 = new long[display.numDimensions()];
    long[] pt2 = new long[display.numDimensions()];
    // current plane only
    pt1[0] = 0;
    pt1[1] = 0;
    pt2[0] = display.dimension(0) - 1;
    pt2[1] = display.dimension(1) - 1;
    for (int i = 2; i < display.numDimensions(); i++) {
        pt1[i] = pt2[i] = display.getLongPosition(i);
    }
    return new HyperVolumePointSet(pt1, pt2);
}

Example 7 with PointSet

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

the class Binner method reduceData.

private void reduceData(Dataset ds, List<Integer> reductionFactors) {
    // make the correct Function from the dataset based upon valueMethod.
    Function<PointSet, T> func = function(ds);
    // setup neighborhood to calc from
    PointSet neigh = neighborhood(reductionFactors);
    // make new dimensioned data
    Dataset newDs = newData(ds, reductionFactors);
    // walk each pixel in new dimension, find neighborhood of related point in
    // original space, calc value, and set in newDs.
    long[] currPos = new long[newDs.numDimensions()];
    long[] lastPos = new long[newDs.numDimensions()];
    long[] translation = new long[ds.numDimensions()];
    @SuppressWarnings("unchecked") Cursor<T> cursor = (Cursor<T>) newDs.getImgPlus().localizingCursor();
    T var = cursor.get().createVariable();
    while (cursor.hasNext()) {
        cursor.next();
        cursor.localize(currPos);
        findTranslation(lastPos, currPos, reductionFactors, translation);
        for (int i = 0; i < lastPos.length; i++) {
            lastPos[i] = currPos[i];
        }
        neigh.translate(translation);
        func.compute(neigh, var);
        cursor.get().set(var);
    }
    // TODO
    // update scale of newData's axes?
    // HOW!!!!????
    // This might point out a way to say: setAxis(new ScaleAxis(getAxis())). Can
    // chain these. Thus any axis can be built up from others. It's a thought at
    // least.
    // update data
    ds.setImgPlus(newDs.getImgPlus());
}

Example 8 with PointSet

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

the class Binarize method planeData.

// returns a PointSet that represents the points in a plane of a dataset
private PointSet planeData(Dataset ds, long[] planePos) {
    long[] pt1 = new long[ds.numDimensions()];
    long[] pt2 = new long[ds.numDimensions()];
    int i = 0;
    for (int d = 0; d < ds.numDimensions(); d++) {
        AxisType type = ds.axis(d).type();
        if (type == Axes.X || type == Axes.Y) {
            pt1[d] = 0;
            pt2[d] = ds.dimension(d) - 1;
        } else {
            pt1[d] = planePos[i];
            pt2[d] = planePos[i];
            i++;
        }
    }
    return new HyperVolumePointSet(pt1, pt2);
}

Example 9 with PointSet

use of net.imglib2.ops.pointset.PointSet 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 10 with PointSet

use of net.imglib2.ops.pointset.PointSet 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);
    }
}