Examples with DataRange net.imagej.autoscale.DataRange used on opensource projects

Example 1 with DataRange

use of net.imagej.autoscale.DataRange 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 2 with DataRange

use of net.imagej.autoscale.DataRange in project vcell by virtualcell.

the class InFrameDisplayService method autoscale.

/**
 * Scales the brightness and contrast for better display.
 * Does not change the underlying pixel intensities.
 * @param datasetView
 */
private void autoscale(DatasetView datasetView) {
    DataRange range = autoscaleService.getDefaultIntervalRange(datasetView.getData());
    datasetView.setChannelRanges(range.getMin(), range.getMax());
    datasetView.getProjector().map();
    datasetView.update();
}

Example 3 with DataRange

use of net.imagej.autoscale.DataRange in project imagej-plugins-commands by imagej.

the class BrightnessContrast method computeDataMinMax.

// -- Helper methods --
// TODO we have a couple refresh problems
// 1) right now if you bounce between two displays with this dialog open the
// dialog values (like min, max, and hist don't update)
// 2) even if you can fix 1) the fact that we don't change to a new
// HistogramBundle but rather tweak the existing one might cause refresh()
// probs also. Because the update() code checks if the T's are the same.
// This means there is a implicit requirement for object reference equality
// rather than using something like equals(). Or a isChanged() interface
// (since in this case equals() would not work either).
private void computeDataMinMax(final RandomAccessibleInterval<? extends RealType<?>> img) {
    // FIXME: Reconcile this with DefaultDatasetView.autoscale(int). There is
    // no reason to hardcode the usage of ComputeMinMax twice. Rather, there
    // should be a single entry point for obtain the channel min/maxes from
    // the metadata, and if they aren't there, then compute them. Probably
    // Dataset (not DatasetView) is a good place for it, because it is metadata
    // independent of the visualization settings.
    DataRange range = autoscaleService.getDefaultRandomAccessRange(img);
    dataMin = range.getMin();
    dataMax = range.getMax();
    final MutableModuleItem<Double> minItem = getInfo().getMutableInput("min", Double.class);
    minItem.setSoftMinimum(dataMin);
    minItem.setSoftMaximum(dataMax);
    final MutableModuleItem<Double> maxItem = getInfo().getMutableInput("max", Double.class);
    maxItem.setSoftMinimum(dataMin);
    maxItem.setSoftMaximum(dataMax);
    // System.out.println("IN HERE!!!!!!");
    // System.out.println(" dataMin = " + dataMin);
    // System.out.println(" dataMax = " + dataMax);
    @SuppressWarnings({ "unchecked", "rawtypes" }) Iterable<T> iterable = Views.iterable((RandomAccessibleInterval<T>) (RandomAccessibleInterval) img);
    BinMapper1d<T> mapper = new Real1dBinMapper<T>(dataMin, dataMax, 256, false);
    Histogram1d<T> histogram = new Histogram1d<T>(iterable, mapper);
    if (bundle == null) {
        bundle = new HistogramBundle(histogram);
    } else {
        bundle.setHistogram(0, histogram);
    }
    bundle.setDataMinMax(dataMin, dataMax);
    // bundle.setLineSlopeIntercept(1, 0);
    log().debug("computeDataMinMax: dataMin=" + dataMin + ", dataMax=" + dataMax);
// force a widget refresh to see new Hist (and also fill min and max fields)
// NOPE. HistBundle is unchanged. Only internals are. So no
// refresh called. Note that I changed InteractiveCommand::update() to
// always setValue() and still this did not work. !!!! Huh?
// update(getInfo().getMutableInput("bundle", HistogramBundle.class),
// bundle);
// NOPE
// getInfo().getInput("bundle", HistogramBundle.class).setValue(this,
// bundle);
// NOPE
// getInfo().setVisible(false);
// getInfo().setVisible(true);
// NOPE
// getInfo().getMutableInput("bundle",HistogramBundle.class).initialize(this);
// NOPE
// getInfo().getMutableInput("bundle",HistogramBundle.class).callback(this);
}

Example 4 with DataRange

use of net.imagej.autoscale.DataRange in project imagej-plugins-commands by imagej.

the class SaltAndPepper method setupWorkingData.

private void setupWorkingData() {
    selection = overlayService.getSelectionBounds(display);
    inputImage = input.getImgPlus();
    position = new long[inputImage.numDimensions()];
    accessor = inputImage.randomAccess();
    if (autoCalcMinMax) {
        DataRange range = autoscaleService.getDefaultIntervalRange(inputImage);
        pepperValue = range.getMin();
        saltValue = range.getMax();
        RealType<?> t = inputImage.firstElement();
        @SuppressWarnings({ "unchecked", "rawtypes" }) final ComputeMinMax<? extends RealType<?>> cmm = new ComputeMinMax(inputImage, t.createVariable(), t.createVariable());
        cmm.process();
        pepperValue = cmm.getMin().getRealDouble();
        saltValue = cmm.getMax().getRealDouble();
    }
}