org.hkijena.jipipe.plugins.ilastik.utils

Class ImgUtils

java.lang.Object

org.hkijena.jipipe.plugins.ilastik.utils.ImgUtils

public final class ImgUtils
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static List<net.imagej.axis.AxisType>	DEFAULT_AXES Supported ImageJ axes in the default order.
static String	DEFAULT_STRING_AXES Supported axes in the character format, in the same order as DEFAULT_AXES.

Method Summary

Modifier and Type	Method and Description
static net.imagej.ImgPlus<net.imglib2.type.numeric.integer.UnsignedByteType>	argbToMultiChannel(net.imagej.ImgPlus<net.imglib2.type.numeric.ARGBType> img) Treat alpha, red, green, and blue values in ARGBType image as a separate, last channel dimension.
static List<net.imagej.axis.AxisType>	axesOf(net.imagej.ImgPlus<?> img) Extract axes from ImgPlus.
static List<net.imagej.axis.AxisType>	guessAxes(long[] dims) Guess axes from image dimensions.
static int[]	inputBlockDims(long[] dims, int[] chunkDims) Compute block dimensions suitable for reading.
static void	outputDims(long[] dims, List<net.imagej.axis.AxisType> axes, DatasetType type, int[] chunkDims, int[] blockDims) Compute chunk and block dimensions suitable for writing.
static List<net.imagej.axis.AxisType>	parseJsonAxes(String json) Parse axes from JSON string.
static int[]	reversed(int[] a) Return a new reversed array.
static long[]	reversed(long[] a) Return a new reversed array.
static String	reversed(String s) Return a reversed string.
static List<net.imagej.axis.AxisType>	toImagejAxes(String axes) Convert string with chars from DEFAULT_STRING_AXES to axes from DEFAULT_AXES.
static String	toStringAxes(List<net.imagej.axis.AxisType> axes) Convert axes from DEFAULT_AXES to string with chars from DEFAULT_STRING_AXES.
static <T extends net.imglib2.type.Type<T>> net.imglib2.img.Img<T>	transformDims(net.imglib2.img.Img<T> img, List<net.imagej.axis.AxisType> srcAxes) transformDims(net.imglib2.img.Img<T>, java.util.List<net.imagej.axis.AxisType>) to DEFAULT_AXES.
static <T extends net.imglib2.type.Type<T>> net.imglib2.img.Img<T>	transformDims(net.imglib2.img.Img<T> img, List<net.imagej.axis.AxisType> srcAxes, List<net.imagej.axis.AxisType> dstAxes) Change dimensions of the image with the given source axes to match destination axes.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_AXES

public static final List<net.imagej.axis.AxisType> DEFAULT_AXES

Supported ImageJ axes in the default order.

DEFAULT_STRING_AXES

public static final String DEFAULT_STRING_AXES

Supported axes in the character format, in the same order as DEFAULT_AXES.

See Also:

Constant Field Values

Method Detail

toStringAxes

public static String toStringAxes(List<net.imagej.axis.AxisType> axes)

Convert axes from DEFAULT_AXES to string with chars from DEFAULT_STRING_AXES.

toImagejAxes

public static List<net.imagej.axis.AxisType> toImagejAxes(String axes)

Convert string with chars from DEFAULT_STRING_AXES to axes from DEFAULT_AXES.

reversed

public static int[] reversed(int[] a)

Return a new reversed array.

reversed

public static long[] reversed(long[] a)

Return a new reversed array.

reversed

public static String reversed(String s)

Return a reversed string.

outputDims

public static void outputDims(long[] dims,
                              List<net.imagej.axis.AxisType> axes,
                              DatasetType type,
                              int[] chunkDims,
                              int[] blockDims)

Compute chunk and block dimensions suitable for writing.

Chunk dimensions are used for HDF5 chunking. Block dimensions are used for tiling input dataset.

inputBlockDims

public static int[] inputBlockDims(long[] dims,
                                   int[] chunkDims)

Compute block dimensions suitable for reading.

axesOf

public static List<net.imagej.axis.AxisType> axesOf(net.imagej.ImgPlus<?> img)

Extract axes from ImgPlus.

guessAxes

public static List<net.imagej.axis.AxisType> guessAxes(long[] dims)

Guess axes from image dimensions.

transformDims

public static <T extends net.imglib2.type.Type<T>> net.imglib2.img.Img<T> transformDims(net.imglib2.img.Img<T> img,
                                                                                        List<net.imagej.axis.AxisType> srcAxes)

transformDims(net.imglib2.img.Img<T>, java.util.List<net.imagej.axis.AxisType>) to DEFAULT_AXES.

transformDims

public static <T extends net.imglib2.type.Type<T>> net.imglib2.img.Img<T> transformDims(net.imglib2.img.Img<T> img,
                                                                                        List<net.imagej.axis.AxisType> srcAxes,
                                                                                        List<net.imagej.axis.AxisType> dstAxes)

Change dimensions of the image with the given source axes to match destination axes.

Existing axes are transposed to match the new order, new axes are inserted as singletons.

parseJsonAxes

public static List<net.imagej.axis.AxisType> parseJsonAxes(String json)

Parse axes from JSON string.

JSON string {"axes": [{"key": "y"}, {"key": "x}]} produces axes XY. Note the reversed axis order.

Throws:

org.json.JSONException - if JSON is malformed/invalid, or if axes are invalid.

argbToMultiChannel

public static net.imagej.ImgPlus<net.imglib2.type.numeric.integer.UnsignedByteType> argbToMultiChannel(net.imagej.ImgPlus<net.imglib2.type.numeric.ARGBType> img)

Treat alpha, red, green, and blue values in ARGBType image as a separate, last channel dimension.