org.hkijena.jipipe.plugins.ilastik.utils.hdf5

Class Hdf5

java.lang.Object

org.hkijena.jipipe.plugins.ilastik.utils.hdf5.Hdf5

public final class Hdf5
extends Object

Method Summary

Modifier and Type	Method and Description
static List<DatasetDescription>	datasets(File file) Return descriptions of supported datasets in an HDF5 file, sorted by their paths.
static <T extends net.imglib2.type.NativeType<T>> net.imagej.ImgPlus<T>	readDataset(File file, String path) readDataset(java.io.File, java.lang.String) with Ilastik ImgUtils DEFAULT_AXES and without callback.
static <T extends net.imglib2.type.NativeType<T>> net.imagej.ImgPlus<T>	readDataset(File file, String path, List<net.imagej.axis.AxisType> axes) readDataset(java.io.File, java.lang.String) without callback.
static <T extends net.imglib2.type.NativeType<T>> net.imagej.ImgPlus<T>	readDataset(File file, String path, List<net.imagej.axis.AxisType> axes, LongConsumer callback) Read HDF5 dataset contents.
static <T extends net.imglib2.type.NativeType<T>> void	writeDataset(File file, String path, net.imagej.ImgPlus<T> img) writeDataset(java.io.File, java.lang.String, net.imagej.ImgPlus<T>) without compression, axis reordering and callback.
static <T extends net.imglib2.type.NativeType<T>> void	writeDataset(File file, String path, net.imagej.ImgPlus<T> img, int compressionLevel) writeDataset(java.io.File, java.lang.String, net.imagej.ImgPlus<T>) without axis reordering and callback.
static <T extends net.imglib2.type.NativeType<T>> void	writeDataset(File file, String path, net.imagej.ImgPlus<T> img, int compressionLevel, List<net.imagej.axis.AxisType> axes) writeDataset(java.io.File, java.lang.String, net.imagej.ImgPlus<T>) without callback.
static <T extends net.imglib2.type.NativeType<T>> void	writeDataset(File file, String path, net.imagej.ImgPlus<T> img, int compressionLevel, List<net.imagej.axis.AxisType> axes, LongConsumer callback) Write image contents to HDF5 dataset, creating/overwriting file and dataset if needed.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

datasets

public static List<DatasetDescription> datasets(File file)

Return descriptions of supported datasets in an HDF5 file, sorted by their paths.

readDataset

public static <T extends net.imglib2.type.NativeType<T>> net.imagej.ImgPlus<T> readDataset(File file,
                                                                                           String path)

readDataset(java.io.File, java.lang.String) with Ilastik ImgUtils DEFAULT_AXES and without callback.

readDataset

public static <T extends net.imglib2.type.NativeType<T>> net.imagej.ImgPlus<T> readDataset(File file,
                                                                                           String path,
                                                                                           List<net.imagej.axis.AxisType> axes)

readDataset(java.io.File, java.lang.String) without callback.

readDataset

public static <T extends net.imglib2.type.NativeType<T>> net.imagej.ImgPlus<T> readDataset(File file,
                                                                                           String path,
                                                                                           List<net.imagej.axis.AxisType> axes,
                                                                                           LongConsumer callback)

Read HDF5 dataset contents.

Only 2D-5D datasets with types enumerated in DatasetType are supported.

If not null, callback will be invoked between block writes (N + 1 invocations for N blocks). The callback accepts the total number of bytes written so far. This is useful for progress reporting.

writeDataset

public static <T extends net.imglib2.type.NativeType<T>> void writeDataset(File file,
                                                                           String path,
                                                                           net.imagej.ImgPlus<T> img)

writeDataset(java.io.File, java.lang.String, net.imagej.ImgPlus<T>) without compression, axis reordering and callback.

writeDataset

public static <T extends net.imglib2.type.NativeType<T>> void writeDataset(File file,
                                                                           String path,
                                                                           net.imagej.ImgPlus<T> img,
                                                                           int compressionLevel)

writeDataset(java.io.File, java.lang.String, net.imagej.ImgPlus<T>) without axis reordering and callback.

writeDataset

public static <T extends net.imglib2.type.NativeType<T>> void writeDataset(File file,
                                                                           String path,
                                                                           net.imagej.ImgPlus<T> img,
                                                                           int compressionLevel,
                                                                           List<net.imagej.axis.AxisType> axes)

writeDataset(java.io.File, java.lang.String, net.imagej.ImgPlus<T>) without callback.

writeDataset

public static <T extends net.imglib2.type.NativeType<T>> void writeDataset(File file,
                                                                           String path,
                                                                           net.imagej.ImgPlus<T> img,
                                                                           int compressionLevel,
                                                                           List<net.imagej.axis.AxisType> axes,
                                                                           LongConsumer callback)

Write image contents to HDF5 dataset, creating/overwriting file and dataset if needed.

Only 2D-5D datasets with types enumerated in DatasetType are supported. As a special case, ARGBType is supported too, but its use is discouraged.

if axes are specified, image will be written in the specified axis order.

If not null, callback will be invoked between block writes (N + 1 invocations for N blocks). The callback accepts the total number of bytes written so far. This is useful for progress reporting.