io.scif.img

Class DefaultImgUtilityService

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

org.scijava.service.AbstractService

io.scif.img.DefaultImgUtilityService

All Implemented Interfaces:

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

public class DefaultImgUtilityService
extends org.scijava.service.AbstractService
implements ImgUtilityService

Helper methods for converting between SCIFIO and ImgLib2 data structures.

Author:

Stephan Preibisch, Stephan Saalfeld, Curtis Rueden

Constructor Summary

Constructors

Constructor and Description
DefaultImgUtilityService()

Method Summary

Modifier and Type	Method and 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 reader.
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.imglib2.img.Img<T> img) see isCompressible(ImgPlus)
<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.
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 class org.scijava.service.AbstractService

getContext, setContext, toString

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority

Methods inherited from class org.scijava.AbstractContextual

context

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.service.Service

initialize, registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier, log

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface org.scijava.Versioned

getVersion

Methods inherited from interface org.scijava.Disposable

dispose

Constructor Detail

DefaultImgUtilityService

public DefaultImgUtilityService()

Method Detail

getDimLengths

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

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

Specified by:

getDimLengths in interface ImgUtilityService

getConstrainedLengths

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

Description copied from interface: ImgUtilityService

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

Specified by:

getConstrainedLengths in interface ImgUtilityService

getImageCount

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

Specified by:

getImageCount in interface ImgUtilityService

Parameters:

source - - the location of the dataset to assess

Returns:

The number of images in the specified dataset.

Throws:

ImgIOException

getPlanarAccess

public 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.

Specified by:

getPlanarAccess in interface ImgUtilityService

getArrayAccess

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

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

Specified by:

getArrayAccess in interface ImgUtilityService

makeType

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

Converts SCIFIO pixel type to ImgLib2 Type object.

Specified by:

makeType in interface ImgUtilityService

makeType

public int makeType(Object type)
             throws ImgIOException

Converts ImgLib2 Type object to SCIFIO pixel type.

Specified by:

makeType in interface ImgUtilityService

Throws:

ImgIOException

makeArray

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

Wraps raw primitive array in ImgLib2 Array object.

Specified by:

makeArray in interface ImgUtilityService

isCompressible

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

see isCompressible(ImgPlus)

Specified by:

isCompressible in interface ImgUtilityService

isCompressible

public <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.

Specified by:

isCompressible in interface ImgUtilityService

guessDimOrder

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

Description copied from interface: ImgUtilityService

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.

Specified by:

guessDimOrder in interface ImgUtilityService

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

decodeWord

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

Specified by:

decodeWord in interface ImgUtilityService

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

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

Description copied from interface: ImgUtilityService

Convenience method for wrapping an Img as a SCIFIOImgPlus .

Specified by:

makeSCIFIOImgPlus in interface ImgUtilityService

Parameters:

img - Img to wrap

Returns:

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