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

Class LegacyFileMapImgLoaderLOCI

java.lang.Object

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

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

net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

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 LegacyFileMapImgLoaderLOCI
extends AbstractImgFactoryImgLoader

Field Summary

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

imgFactory1

Constructor Summary

Constructors

Constructor	Description
LegacyFileMapImgLoaderLOCI(Map<? extends mpicbg.spim.data.sequence.ViewId,FileMapEntry> fileMap, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)
LegacyFileMapImgLoaderLOCI(Map<? extends mpicbg.spim.data.sequence.ViewId,FileMapEntry> fileMap, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription, boolean zGrouped)

Method Summary

Modifier and Type	Method	Description
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>, IL extends mpicbg.spim.data.sequence.ImgLoader & FileMapGettable> void	checkAndRemoveZeroVolume(SpimData2 spimData, IL loader)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>, IL extends mpicbg.spim.data.sequence.ImgLoader & FileMapGettable> void	checkAndRemoveZeroVolume(SpimData2 spimData, IL loader, boolean filesArePatterns)	check if views in spimData contain zero-valued planes at the end of the z-axis.
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)
Map<mpicbg.spim.data.sequence.ViewId,FileMapEntry>	getFileMap()
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)
static long	getMaxNonzero(loci.formats.IFormatReader reader)
static <T extends net.imglib2.type.numeric.RealType<T>> long	getMaxNonzero(net.imglib2.RandomAccessibleInterval<T> img, int dim)	get the highest index in dimension dim where a hyperslice of img in that dimension contains nonzero values.
protected static mpicbg.spim.data.sequence.Tile	getTile(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd)
static <T extends net.imglib2.type.numeric.RealType<T>> boolean	isNonezero(net.imglib2.IterableInterval<T> slice)	check whether any pixel in slice is nonzero.
static boolean	isNonzero(byte[] buf)
static boolean	isZSizeEqualInEveryFile(SpimData2 spimData, FileMapGettable loader)	for every file in the dataset file list check if the z-size is equal for every series.
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.RandomAccessibleInterval<T>	openImg(T type, mpicbg.spim.data.sequence.ViewId view)

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

Constructor Details

LegacyFileMapImgLoaderLOCI

public LegacyFileMapImgLoaderLOCI(Map<? extends mpicbg.spim.data.sequence.ViewId,FileMapEntry> fileMap,
 mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

LegacyFileMapImgLoaderLOCI

public LegacyFileMapImgLoaderLOCI(Map<? extends mpicbg.spim.data.sequence.ViewId,FileMapEntry> fileMap,
 mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription,
 boolean zGrouped)

Method Details

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

openImg

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

Throws:

Exception

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)

getFileMap

public Map<mpicbg.spim.data.sequence.ViewId,FileMapEntry> getFileMap()

isZSizeEqualInEveryFile

public static boolean isZSizeEqualInEveryFile(SpimData2 spimData,
 FileMapGettable loader)

for every file in the dataset file list check if the z-size is equal for every series.

Parameters:

spimData - the dataset

loader - the associated loader

Returns:

true if z-sizes are equal in every file, false if they differ inside any file

checkAndRemoveZeroVolume

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>,
IL extends mpicbg.spim.data.sequence.ImgLoader & FileMapGettable>
void checkAndRemoveZeroVolume(SpimData2 spimData,
 IL loader,
 boolean filesArePatterns)

check if views in spimData contain zero-valued planes at the end of the z-axis. re-set ViewSetup dimensions to ignore the zero-volume (use this to fix "the BioFormats bug")

Type Parameters:

T - pixel type

IL - ImgLoader type

Parameters:

spimData - the SpimData to correct

loader - the imgLoader to use

filesArePatterns - whether file names contain patterns and should be grouped when opening

checkAndRemoveZeroVolume

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>,
IL extends mpicbg.spim.data.sequence.ImgLoader & FileMapGettable>
void checkAndRemoveZeroVolume(SpimData2 spimData,
 IL loader)

getMaxNonzero

public static <T extends net.imglib2.type.numeric.RealType<T>>
long getMaxNonzero(net.imglib2.RandomAccessibleInterval<T> img,
 int dim)

get the highest index in dimension dim where a hyperslice of img in that dimension contains nonzero values. NB: the result is in local image coordinates (i.e. we zero-min the input)

Type Parameters:

T - pixel type

Parameters:

img - the input image

dim - the dimension along which to check

Returns:

the highest index with nonzero pixels

getMaxNonzero

public static long getMaxNonzero(loci.formats.IFormatReader reader)

isNonzero

public static boolean isNonzero(byte[] buf)

isNonezero

public static <T extends net.imglib2.type.numeric.RealType<T>>
boolean isNonezero(net.imglib2.IterableInterval<T> slice)

check whether any pixel in slice is nonzero. NB: we do a raw floating point comparison here, so we might get false results if the image was operated on in any way due to numerical inaccuracies.

Type Parameters:

T - pixel type

Parameters:

slice - the input image

Returns:

true if slice has nonzero entries else false