Module io.scif

Package io.scif.img

Interface ImgUtilityService

All Superinterfaces:

Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Disposable, org.scijava.plugin.HasPluginInfo, org.scijava.Identifiable, org.scijava.Initializable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.Prioritized, org.scijava.plugin.RichPlugin, SCIFIOService, org.scijava.plugin.SciJavaPlugin, org.scijava.service.Service, org.scijava.Versioned

All Known Implementing Classes:

DefaultImgUtilityService

public interface ImgUtilityService
extends SCIFIOService

Helper methods for converting between SCIFIO and ImgLib2 data structures.

Author:

Stephan Preibisch, Stephan Saalfeld, Curtis Rueden

Method Summary

Modifier and Type	Method	Description
double	decodeWord(byte[] plane, int index, int pixelType, boolean little)
net.imglib2.img.array.ArrayImg<?,?>	getArrayAccess(net.imagej.ImgPlus<?> img)	Obtains array access instance backing the given img, if any.
long[]	getConstrainedLengths(Metadata m, int imageIndex, SCIFIOConfig config)	Returns an N-dimensional list of axis lengths from the given Metadata, constrained by the provided SubRegion (if present)
long[]	getDimLengths(Metadata m, int imageIndex, SCIFIOConfig config)	Compiles an N-dimensional list of axis lengths from the given Metadata.
int	getImageCount(org.scijava.io.location.Location source)
net.imglib2.img.basictypeaccess.PlanarAccess<net.imglib2.img.basictypeaccess.array.ArrayDataAccess<?>>	getPlanarAccess(net.imagej.ImgPlus<?> img)	Obtains planar access instance backing the given img, if any.
String	guessDimOrder(net.imagej.axis.CalibratedAxis[] axes, long[] dimLengths, long[] newLengths)	The ImgLib axes structure can contain multiple unknown axes.
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> boolean	isCompressible(net.imagej.ImgPlus<T> img)	Currently there are limits as to what types of Images can be saved.
<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> boolean	isCompressible(net.imglib2.img.Img<T> img)	see isCompressible(ImgPlus)
net.imglib2.img.basictypeaccess.array.ArrayDataAccess<?>	makeArray(Object array)	Wraps raw primitive array in ImgLib2 Array object.
<T> SCIFIOImgPlus<T>	makeSCIFIOImgPlus(net.imglib2.img.Img<T> img)	Convenience method for wrapping an Img as a SCIFIOImgPlus .
net.imglib2.type.Type<?>	makeType(int pixelType)	Converts SCIFIO pixel type to ImgLib2 Type object.
int	makeType(Object type)	Converts ImgLib2 Type object to SCIFIO pixel type.

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Disposable

dispose

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier, log

Methods inherited from interface org.scijava.service.Service

initialize, registerEventHandlers

Methods inherited from interface org.scijava.Versioned

getVersion

Method Detail

getPlanarAccess

net.imglib2.img.basictypeaccess.PlanarAccess<net.imglib2.img.basictypeaccess.array.ArrayDataAccess<?>> getPlanarAccess(net.imagej.ImgPlus<?> img)

Obtains planar access instance backing the given img, if any.

getArrayAccess

net.imglib2.img.array.ArrayImg<?,?> getArrayAccess(net.imagej.ImgPlus<?> img)

Obtains array access instance backing the given img, if any.

makeType

net.imglib2.type.Type<?> makeType(int pixelType)

Converts SCIFIO pixel type to ImgLib2 Type object.

makeType

int makeType(Object type)
      throws ImgIOException

Converts ImgLib2 Type object to SCIFIO pixel type.

Throws:

ImgIOException

makeArray

net.imglib2.img.basictypeaccess.array.ArrayDataAccess<?> makeArray(Object array)

Wraps raw primitive array in ImgLib2 Array object.

getDimLengths

long[] getDimLengths(Metadata m,
                     int imageIndex,
                     SCIFIOConfig config)

Compiles an N-dimensional list of axis lengths from the given Metadata.

getConstrainedLengths

long[] getConstrainedLengths(Metadata m,
                             int imageIndex,
                             SCIFIOConfig config)

Returns an N-dimensional list of axis lengths from the given Metadata, constrained by the provided SubRegion (if present)

getImageCount

int getImageCount(org.scijava.io.location.Location source)
           throws ImgIOException

Parameters:

source - - the location of the dataset to assess

Returns:

The number of images in the specified dataset.

Throws:

ImgIOException

isCompressible

<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> boolean isCompressible(net.imglib2.img.Img<T> img)

see isCompressible(ImgPlus)

isCompressible

<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> boolean isCompressible(net.imagej.ImgPlus<T> img)

Currently there are limits as to what types of Images can be saved. All images must ultimately adhere to an, at most, five-dimensional structure using the known axes X, Y, Z, Channel and Time. Unknown axes (U) can potentially be handled by coercing to the Channel axis. For example, X Y Z U C U T would be valid, as would X Y Z U T. But X Y C Z U T would not, as the unknown axis can not be compressed with Channel. This method will return true if the axes of the provided image can be represented with a valid 5D String, and false otherwise.

guessDimOrder

String guessDimOrder(net.imagej.axis.CalibratedAxis[] axes,
                     long[] dimLengths,
                     long[] newLengths)

The ImgLib axes structure can contain multiple unknown axes. This method will determine if the provided dimension order, obtained from an ImgLib AxisType array, can be converted to a 5-dimensional sequence compatible with SCIFIO, and returns that sequence if it exists and null otherwise.

Parameters:

newLengths - - updated to hold the lengths of the newly ordered axes

decodeWord

double decodeWord(byte[] plane,
                  int index,
                  int pixelType,
                  boolean little)

Parameters:

plane - - byte array from the desired plane

index - - pixel index into the plane (NOT an array index)

pixelType - - base pixel type of the plane's data

little - - endianness of the plane's bytes

Returns:

A double value for the specified pixel.

makeSCIFIOImgPlus

<T> SCIFIOImgPlus<T> makeSCIFIOImgPlus(net.imglib2.img.Img<T> img)

Convenience method for wrapping an Img as a SCIFIOImgPlus .

Parameters:

img - Img to wrap

Returns:

SCIFIOImgPlus wrapping the provided Img, or if the provided Img is a SCIFIOImgPlus, casts and returns.