Package net.preibisch.mvrecon.fiji.spimdata.imgloaders

Class LegacyLightSheetZ1ImgLoader

java.lang.Object

net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader

net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

All Implemented Interfaces:

mpicbg.spim.data.legacy.LegacyBasicImgLoader<net.imglib2.type.numeric.integer.UnsignedShortType>, mpicbg.spim.data.legacy.LegacyImgLoader<net.imglib2.type.numeric.integer.UnsignedShortType>

public class LegacyLightSheetZ1ImgLoader
extends AbstractImgFactoryImgLoader

Field Summary

Fields inherited from class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader

imgFactory1

Constructor Summary

Constructors

Constructor	Description
LegacyLightSheetZ1ImgLoader(File cziFile, net.imglib2.img.ImgFactory<? extends net.imglib2.type.NativeType<?>> imgFactory, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

Method Summary

Modifier and Type	Method	Description
static boolean	createOMEXMLMetadata(loci.formats.IFormatReader r)
void	finalize()
protected static mpicbg.spim.data.sequence.Angle	getAngle(mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> seqDesc, mpicbg.spim.data.sequence.ViewId view)
protected static mpicbg.spim.data.sequence.Angle	getAngle(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)
protected static mpicbg.spim.data.sequence.Channel	getChannel(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)
File	getCZIFile()
net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	getFloatImage(mpicbg.spim.data.sequence.ViewId view, boolean normalize)
protected static mpicbg.spim.data.sequence.Illumination	getIllumination(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)
net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.integer.UnsignedShortType>	getImage(mpicbg.spim.data.sequence.ViewId view)
protected static mpicbg.spim.data.sequence.Tile	getTile(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)
static loci.formats.IFormatReader	instantiateImageReader()
protected void	loadMetaData(mpicbg.spim.data.sequence.ViewId view)	Loads only the metadata from the image, should call updateMetaDataCache( ... )
protected <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> net.imglib2.img.Img<T>	openCZI(T type, mpicbg.spim.data.sequence.ViewId view)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readBytes(byte[] b, net.imglib2.Cursor<T> cursor, int width)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readBytesArray(byte[] b, net.imglib2.Cursor<T> cursor, int numPx)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readFloats(byte[] b, net.imglib2.Cursor<T> cursor, int width, boolean isLittleEndian)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readFloatsArray(byte[] b, net.imglib2.Cursor<T> cursor, int numPx, boolean isLittleEndian)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readSignedShorts(byte[] b, net.imglib2.Cursor<T> cursor, int width, boolean isLittleEndian)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readSignedShortsArray(byte[] b, net.imglib2.Cursor<T> cursor, int numPx, boolean isLittleEndian)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readUnsignedInts(byte[] b, net.imglib2.Cursor<T> cursor, int width, boolean isLittleEndian)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readUnsignedIntsArray(byte[] b, net.imglib2.Cursor<T> cursor, int numPx, boolean isLittleEndian)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readUnsignedShorts(byte[] b, net.imglib2.Cursor<T> cursor, int width, boolean isLittleEndian)
static final <T extends net.imglib2.type.numeric.RealType<T>> void	readUnsignedShortsArray(byte[] b, net.imglib2.Cursor<T> cursor, int numPx, boolean isLittleEndian)
String	toString()

Methods inherited from class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader

getImgFactory, setImgFactory

Methods inherited from class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

getImageSize, getImageType, getVoxelSize, updateMetaDataCache, updateXMLMetaData, updateXMLMetaData, updateXMLMetaData

Methods inherited from class java.lang.Object

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

Constructor Details

LegacyLightSheetZ1ImgLoader

public LegacyLightSheetZ1ImgLoader(File cziFile,
 net.imglib2.img.ImgFactory<? extends net.imglib2.type.NativeType<?>> imgFactory,
 mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

Method Details

getCZIFile

public File getCZIFile()

getFloatImage

public net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> getFloatImage(mpicbg.spim.data.sequence.ViewId view,
 boolean normalize)

getImage

public net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.integer.UnsignedShortType> getImage(mpicbg.spim.data.sequence.ViewId view)

loadMetaData

protected void loadMetaData(mpicbg.spim.data.sequence.ViewId view)

Description copied from class: AbstractImgLoader

Loads only the metadata from the image, should call updateMetaDataCache( ... )

Specified by:

loadMetaData in class AbstractImgLoader

Parameters:

view - - the view to load metadata for

finalize

public void finalize()

Overrides:

finalize in class Object

openCZI

protected <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
net.imglib2.img.Img<T> openCZI(T type,
 mpicbg.spim.data.sequence.ViewId view)
                        throws Exception

Throws:

Exception

readBytes

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readBytes(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int width)

readBytesArray

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readBytesArray(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int numPx)

readUnsignedShorts

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readUnsignedShorts(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int width,
 boolean isLittleEndian)

readUnsignedShortsArray

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readUnsignedShortsArray(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int numPx,
 boolean isLittleEndian)

readSignedShorts

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readSignedShorts(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int width,
 boolean isLittleEndian)

readSignedShortsArray

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readSignedShortsArray(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int numPx,
 boolean isLittleEndian)

readUnsignedInts

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readUnsignedInts(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int width,
 boolean isLittleEndian)

readUnsignedIntsArray

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readUnsignedIntsArray(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int numPx,
 boolean isLittleEndian)

readFloats

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readFloats(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int width,
 boolean isLittleEndian)

readFloatsArray

public static final <T extends net.imglib2.type.numeric.RealType<T>>
void readFloatsArray(byte[] b,
 net.imglib2.Cursor<T> cursor,
 int numPx,
 boolean isLittleEndian)

instantiateImageReader

public static loci.formats.IFormatReader instantiateImageReader()

createOMEXMLMetadata

public static boolean createOMEXMLMetadata(loci.formats.IFormatReader r)

getAngle

protected static mpicbg.spim.data.sequence.Angle getAngle(mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> seqDesc,
 mpicbg.spim.data.sequence.ViewId view)

getAngle

protected static mpicbg.spim.data.sequence.Angle getAngle(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)

getChannel

protected static mpicbg.spim.data.sequence.Channel getChannel(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)

getIllumination

protected static mpicbg.spim.data.sequence.Illumination getIllumination(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)

getTile

protected static mpicbg.spim.data.sequence.Tile getTile(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)

toString

public String toString()

Overrides:

toString in class Object