Examples with N5Reader org.janelia.saalfeldlab.n5.N5Reader used on opensource projects

Example 1 with N5Reader

use of org.janelia.saalfeldlab.n5.N5Reader in project bigwarp by saalfeldlab.

the class BigWarpInit method loadN5Source.

public static Source<?> loadN5Source(final String n5Root, final String n5Dataset) {
    final N5Reader n5;
    try {
        n5 = new N5Factory().openReader(n5Root);
    } catch (IOException e) {
        e.printStackTrace();
        return null;
    }
    final N5MetadataParser<?>[] PARSERS = new N5MetadataParser[] { new ImagePlusLegacyMetadataParser(), new N5CosemMetadataParser(), new N5SingleScaleMetadataParser(), new CanonicalMetadataParser(), new N5GenericSingleScaleMetadataParser() };
    final N5MetadataParser<?>[] GROUP_PARSERS = new N5MetadataParser[] { new N5CosemMultiScaleMetadata.CosemMultiScaleParser(), new N5ViewerMultiscaleMetadataParser(), new CanonicalMetadataParser() };
    N5Metadata meta = null;
    try {
        final N5DatasetDiscoverer discoverer = new N5DatasetDiscoverer(n5, N5DatasetDiscoverer.fromParsers(PARSERS), N5DatasetDiscoverer.fromParsers(GROUP_PARSERS));
        final N5TreeNode node = discoverer.discoverAndParseRecursive(n5Dataset);
        meta = node.getMetadata();
    } catch (IOException e) {
    }
    if (meta instanceof MultiscaleMetadata) {
        return openAsSourceMulti(n5, (MultiscaleMetadata<?>) meta, true);
    } else {
        return openAsSource(n5, meta, true);
    }
}

Example 2 with N5Reader

use of org.janelia.saalfeldlab.n5.N5Reader in project bigwarp by saalfeldlab.

the class BigWarpInit method openAsSource.

@SuppressWarnings({ "unchecked", "rawtypes" })
public static <T extends N5Metadata> Source<?> openAsSource(final N5Reader n5, final T meta, final boolean isVolatile) {
    final RandomAccessibleInterval imageRaw;
    final RandomAccessibleInterval image;
    try {
        if (isVolatile)
            imageRaw = to3d(N5Utils.openVolatile(n5, meta.getPath()));
        else
            imageRaw = to3d(N5Utils.open(n5, meta.getPath()));
        if (meta instanceof N5ImagePlusMetadata && ((N5ImagePlusMetadata) meta).getType() == ImagePlus.COLOR_RGB && Util.getTypeFromInterval(imageRaw) instanceof UnsignedIntType) {
            image = toColor(imageRaw);
        } else
            image = imageRaw;
        if (meta instanceof SpatialMetadata) {
            final String unit = ((SpatialMetadata) meta).unit();
            final AffineTransform3D srcXfm = ((SpatialMetadata) meta).spatialTransform3d();
            final FinalVoxelDimensions voxelDims = new FinalVoxelDimensions(unit, new double[] { srcXfm.get(0, 0), srcXfm.get(1, 1), srcXfm.get(2, 2) });
            return new BwRandomAccessibleIntervalSource(image, Util.getTypeFromInterval(image), srcXfm, meta.getPath(), voxelDims);
        } else
            return new BwRandomAccessibleIntervalSource(image, Util.getTypeFromInterval(image), new AffineTransform3D(), meta.getPath());
    } catch (IOException e) {
        e.printStackTrace();
    }
    return null;
}

Example 3 with N5Reader

use of org.janelia.saalfeldlab.n5.N5Reader in project mars-fx by duderstadt-lab.

the class MarsBdvFrame method loadN5Source.

private Source<T> loadN5Source(MarsBdvSource source, MarsMetadata meta) throws IOException {
    N5Reader reader;
    if (n5Readers.containsKey(source.getPath())) {
        reader = n5Readers.get(source.getPath());
    } else {
        reader = new N5Importer.N5ViewerReaderFun().apply(source.getPath());
        n5Readers.put(source.getPath(), reader);
    }
    @SuppressWarnings("rawtypes") final RandomAccessibleInterval wholeImage = N5Utils.open(reader, source.getN5Dataset());
    // wholeImage should be XYT or XYCT. If XYCT, we hyperSlice to get one
    // channel.
    // XYZCT should also be supported
    int dims = wholeImage.numDimensions();
    @SuppressWarnings("rawtypes") final RandomAccessibleInterval image = (dims > 3) ? Views.hyperSlice(wholeImage, wholeImage.numDimensions() - 2, source.getChannel()) : wholeImage;
    int tSize = (int) image.dimension(image.numDimensions() - 1);
    if (tSize > numTimePoints)
        numTimePoints = tSize;
    @SuppressWarnings("rawtypes") final RandomAccessibleInterval[] images = new RandomAccessibleInterval[1];
    images[0] = image;
    if (source.getSingleTimePointMode()) {
        AffineTransform3D[] transforms = new AffineTransform3D[tSize];
        // Drift should be corrected against them
        for (int t = 0; t < tSize; t++) transforms[t] = source.getAffineTransform3D();
        int singleTimePoint = source.getSingleTimePoint();
        @SuppressWarnings("unchecked") final MarsSingleTimePointN5Source<T> n5Source = new MarsSingleTimePointN5Source<>((T) Util.getTypeFromInterval(image), source.getName(), images, transforms, singleTimePoint);
        return n5Source;
    } else {
        AffineTransform3D[] transforms = new AffineTransform3D[tSize];
        for (int t = 0; t < tSize; t++) {
            if (source.getCorrectDrift()) {
                double dX = meta.getPlane(0, 0, 0, t).getXDrift();
                double dY = meta.getPlane(0, 0, 0, t).getYDrift();
                transforms[t] = source.getAffineTransform3D(dX, dY);
            } else
                transforms[t] = source.getAffineTransform3D();
        }
        @SuppressWarnings("unchecked") final MarsN5Source<T> n5Source = new MarsN5Source<>((T) Util.getTypeFromInterval(image), source.getName(), images, transforms);
        return n5Source;
    }
}

Example 4 with N5Reader

use of org.janelia.saalfeldlab.n5.N5Reader in project mars-fx by duderstadt-lab.

the class MarsBdvFrame method loadN5VolatileSource.

private Source<T> loadN5VolatileSource(MarsBdvSource source, MarsMetadata meta) throws IOException {
    N5Reader reader;
    if (n5Readers.containsKey(source.getPath())) {
        reader = n5Readers.get(source.getPath());
    } else {
        reader = new N5Importer.N5ViewerReaderFun().apply(source.getPath());
        n5Readers.put(source.getPath(), reader);
    }
    @SuppressWarnings("rawtypes") final RandomAccessibleInterval wholeImage = N5Utils.openVolatile(reader, source.getN5Dataset());
    // wholeImage should be XYT or XYCT. If XYCT, we hyperSlice to get one
    // channel.
    // XYZCT should also be supported
    int dims = wholeImage.numDimensions();
    @SuppressWarnings("rawtypes") final RandomAccessibleInterval image = (dims > 3) ? Views.hyperSlice(wholeImage, wholeImage.numDimensions() - 2, source.getChannel()) : wholeImage;
    int tSize = (int) image.dimension(image.numDimensions() - 1);
    if (tSize > numTimePoints)
        numTimePoints = tSize;
    @SuppressWarnings("rawtypes") final RandomAccessibleInterval[] images = new RandomAccessibleInterval[1];
    images[0] = image;
    if (source.getSingleTimePointMode()) {
        AffineTransform3D[] transforms = new AffineTransform3D[tSize];
        // Drift should be corrected against them
        for (int t = 0; t < tSize; t++) transforms[t] = source.getAffineTransform3D();
        int singleTimePoint = source.getSingleTimePoint();
        @SuppressWarnings("unchecked") final MarsSingleTimePointN5Source<T> n5Source = new MarsSingleTimePointN5Source<>((T) Util.getTypeFromInterval(image), source.getName(), images, transforms, singleTimePoint);
        return (Source<T>) n5Source.asVolatile(sharedQueue);
    } else {
        AffineTransform3D[] transforms = new AffineTransform3D[tSize];
        for (int t = 0; t < tSize; t++) {
            if (source.getCorrectDrift()) {
                double dX = meta.getPlane(0, 0, 0, t).getXDrift();
                double dY = meta.getPlane(0, 0, 0, t).getYDrift();
                transforms[t] = source.getAffineTransform3D(dX, dY);
            } else
                transforms[t] = source.getAffineTransform3D();
        }
        @SuppressWarnings("unchecked") final MarsN5Source<T> n5Source = new MarsN5Source<>((T) Util.getTypeFromInterval(image), source.getName(), images, transforms);
        return (Source<T>) n5Source.asVolatile(sharedQueue);
    }
}