Examples with SpimSource bdv.SpimSource used on opensource projects

Example 1 with SpimSource

use of bdv.SpimSource in project mars-fx by duderstadt-lab.

the class MarsBdvFrame method loadAsSpimDataMinimal.

private Source<T> loadAsSpimDataMinimal(MarsBdvSource source, MarsMetadata meta) {
    SpimDataMinimal spimData;
    try {
        spimData = new XmlIoSpimDataMinimal().load(source.getPath());
        // Add transforms to spimData...
        Map<ViewId, ViewRegistration> registrations = spimData.getViewRegistrations().getViewRegistrations();
        for (ViewId id : registrations.keySet()) {
            if (source.getCorrectDrift()) {
                double dX = meta.getPlane(0, 0, 0, id.getTimePointId()).getXDrift();
                double dY = meta.getPlane(0, 0, 0, id.getTimePointId()).getYDrift();
                registrations.get(id).getModel().set(source.getAffineTransform3D(dX, dY));
            } else
                registrations.get(id).getModel().set(source.getAffineTransform3D());
        }
        if (spimData.getSequenceDescription().getTimePoints().size() > numTimePoints)
            numTimePoints = spimData.getSequenceDescription().getTimePoints().size();
        return new SpimSource<T>(spimData, 0, source.getName());
    } catch (SpimDataException e) {
        e.printStackTrace();
    }
    return null;
}

Example 2 with SpimSource

use of bdv.SpimSource in project imagej-utils by embl-cba.

the class BdvToVoxelGridImageConverter method setSourceImageAndTransform.

private void setSourceImageAndTransform(String sourceBdvFilePath, InterpolationType interpolationType) {
    final SpimData spimData = openSpimData(sourceBdvFilePath);
    final SpimSource<T> spimSource = new SpimSource<>(spimData, 0, "");
    int level = getClosestSourceLevel(targetVoxelSpacing, spimData);
    sourceVoxelSpacing = BdvUtils.getVoxelSpacings(spimData, 0).get(level);
    interpolatedSource = spimSource.getInterpolatedSource(0, level, getBdvInterpolation(interpolationType));
    sourceTransform = new AffineTransform3D();
    spimSource.getSourceTransform(0, level, sourceTransform);
    final double[] scalingFactors = Arrays.stream(targetVoxelSpacing).map(x -> 1.0 / x).toArray();
    scaleToVoxelGrid = new Scale3D(scalingFactors);
    transformedSourceInterval = Intervals.largestContainedInterval(IntervalUtils.scale(targetRealInterval, scalingFactors));
    sourceTransform.preConcatenate(scaleToVoxelGrid);
}