Examples with RandomAccessibleInterval net.imglib2.RandomAccessibleInterval used on opensource projects

Example 1 with RandomAccessibleInterval

use of net.imglib2.RandomAccessibleInterval in project vcell by virtualcell.

the class DeconstructGeometryCommand method run.

@Override
public void run() {
    // Crop to get a z-stack over time (remove channel dimension)
    long maxX = fluorData.max(fluorData.dimensionIndex(Axes.X));
    long maxY = fluorData.max(fluorData.dimensionIndex(Axes.Y));
    long maxZ = fluorData.max(fluorData.dimensionIndex(Axes.Z));
    long maxTime = fluorData.max(fluorData.dimensionIndex(Axes.TIME));
    Img fluorImg = fluorData.getImgPlus().getImg();
    FinalInterval intervals = Intervals.createMinMax(0, 0, 0, 0, 0, maxX, maxY, maxZ, 0, maxTime);
    RandomAccessibleInterval fluorImgCropped = ops.transform().crop(fluorImg, intervals, true);
    // Calculate scale factors
    double[] scaleFactors = { 1, 1, 1, 1 };
    for (int i = 0; i < geomData.numDimensions(); i++) {
        scaleFactors[i] = geomData.dimension(i) / (double) fluorImgCropped.dimension(i);
    }
    // Scale the fluorescence dataset to match the geometry
    NLinearInterpolatorFactory interpolatorFactory = new NLinearInterpolatorFactory();
    RandomAccessibleInterval fluorScaled = ops.transform().scale(fluorImgCropped, scaleFactors, interpolatorFactory);
    // Crop out the first slice of each z-stack in time series
    intervals = Intervals.createMinMax(0, 0, 0, 0, fluorScaled.dimension(0) - 1, fluorScaled.dimension(1) - 1, 0, fluorScaled.dimension(3) - 1);
    IntervalView fluorXYT = (IntervalView) ops.transform().crop(fluorScaled, intervals, true);
    // Create a blank image of the same X-Y-Time dimensions
    long[] dimensions = { fluorXYT.dimension(0), fluorXYT.dimension(1), fluorXYT.dimension(2) };
    Img<DoubleType> result = ops.create().img(dimensions);
    // Calculate constant d in TIRF exponential decay function
    theta = theta * 2 * Math.PI / 360;
    double n1 = 1.52;
    double n2 = 1.38;
    double d = lambda * Math.pow((Math.pow(n1, 2) * Math.pow(Math.sin(theta), 2) - Math.pow(n2, 2)), -0.5) / (4 * Math.PI);
    // Iterate through each time point, using 3D geometry to generate 2D intensities
    Cursor<DoubleType> cursor = fluorXYT.localizingCursor();
    RandomAccess fluorRA = fluorScaled.randomAccess();
    RandomAccess<RealType<?>> geomRA = geomData.randomAccess();
    RandomAccess<DoubleType> resultRA = result.randomAccess();
    maxZ = geomData.dimension(2) - 1;
    while (cursor.hasNext()) {
        cursor.fwd();
        int[] positionXYZ = { cursor.getIntPosition(0), cursor.getIntPosition(1), (int) maxZ - 1 };
        int[] positionXYZT = { cursor.getIntPosition(0), cursor.getIntPosition(1), (int) maxZ - 1, cursor.getIntPosition(2) };
        resultRA.setPosition(cursor);
        geomRA.setPosition(positionXYZ);
        double sum = 0.0;
        while (positionXYZ[2] >= 0 && geomRA.get().getRealDouble() != 0.0) {
            fluorRA.setPosition(positionXYZT);
            geomRA.setPosition(positionXYZ);
            sum += geomRA.get().getRealDouble() * Math.exp(-zSpacing * positionXYZ[2] / d);
            positionXYZ[2]--;
        }
        resultRA.get().set(sum);
    }
    System.out.println("done");
    displayService.createDisplay(result);
}

Example 2 with RandomAccessibleInterval

use of net.imglib2.RandomAccessibleInterval in project vcell by virtualcell.

the class PlotROIStats method run.

@Override
public void run() {
    Plot plot = new ColorPlot("ROI Mean Intensity", "Time", "Mean Intensity");
    StringBuilder legendLabels = new StringBuilder();
    for (RandomAccessibleInterval<T> data : datasetROIsMap.keySet()) {
        if (data instanceof Dataset) {
            legendLabels.append(((Dataset) data).getName());
            legendLabels.append(": ");
        }
        List<Overlay> overlays = datasetROIsMap.get(data);
        for (int i = 0; i < overlays.size(); i++) {
            Overlay overlay = overlays.get(i);
            RandomAccessibleInterval<T> cropped = crop(data, overlay);
            Pair<double[], double[]> xyPair = (Pair<double[], double[]>) ops.run("imageStatsForPlotting", ImageStatsForPlotting.MEAN, cropped);
            plot.addPoints(xyPair.getA(), xyPair.getB(), Plot.LINE);
            legendLabels.append("ROI ");
            legendLabels.append(i + 1);
            legendLabels.append("\n");
        }
    }
    plot.addLegend(legendLabels.toString());
    plot.show();
}

Example 3 with RandomAccessibleInterval

use of net.imglib2.RandomAccessibleInterval in project vcell by virtualcell.

the class PlotROIStats method crop.

private RandomAccessibleInterval<T> crop(RandomAccessibleInterval<T> data, Overlay overlay) {
    int numDimensions = data.numDimensions();
    long[] minDimensions = new long[numDimensions];
    long[] maxDimensions = new long[numDimensions];
    if (numDimensions > 0) {
        minDimensions[0] = (long) overlay.realMin(0);
        maxDimensions[0] = (long) overlay.realMax(0);
    }
    if (numDimensions > 1) {
        minDimensions[1] = (long) overlay.realMin(0);
        maxDimensions[1] = (long) overlay.realMax(0);
    }
    for (int i = 2; i < numDimensions; i++) {
        minDimensions[i] = 0;
        maxDimensions[i] = data.dimension(i) - 1;
    }
    FinalInterval interval = new FinalInterval(minDimensions, maxDimensions);
    RandomAccessibleInterval<T> cropped = ops.transform().crop(data, interval);
    return cropped;
}

Example 4 with RandomAccessibleInterval

use of net.imglib2.RandomAccessibleInterval in project vcell by virtualcell.

the class CompareController method getMaskFromGeometry.

private RandomAccessibleInterval<BitType> getMaskFromGeometry() {
    DatasetSelectionPanel panel = new DatasetSelectionPanel();
    List<Dataset> geometryList = model.getProject().getGeometry();
    final String description = "Geometry: ";
    panel.addComboBox(geometryList.toArray(new Dataset[geometryList.size()]), description);
    int returnVal = JOptionPane.showConfirmDialog(view, panel, "Select cell geometry", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
    if (returnVal == JOptionPane.OK_OPTION) {
        Dataset geometry = panel.getSelectedDatasetForDescription(description);
        @SuppressWarnings("unchecked") RandomAccessibleInterval<BitType> mask = (RandomAccessibleInterval<BitType>) opService.run("largestRegionSlice", geometry);
        return mask;
    }
    return null;
}

Example 5 with RandomAccessibleInterval

use of net.imglib2.RandomAccessibleInterval in project vcell by virtualcell.

the class PlotImageStats method run.

@Override
public void run() {
    Plot plot = new ColorPlot("Frame mean intensity", "Time", "Mean intensity");
    StringBuilder legendLabels = new StringBuilder();
    for (int i = 0; i < datasets.size(); i++) {
        RandomAccessibleInterval<T> data = datasets.get(i);
        if (data instanceof Dataset) {
            legendLabels.append(((Dataset) data).getName());
            legendLabels.append(": ");
        }
        Pair<double[], double[]> xyPair = (Pair<double[], double[]>) ops.run("imageStatsForPlotting", ImageStatsForPlotting.MEAN, data, mask);
        plot.addPoints(xyPair.getA(), xyPair.getB(), Plot.LINE);
        legendLabels.append("ROI ");
        legendLabels.append(i + 1);
        legendLabels.append("\n");
    }
    plot.addLegend(legendLabels.toString());
    plot.show();
}