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

Class LegacyStackImgLoader

java.lang.Object

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

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

net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

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>

Direct Known Subclasses:

LegacyStackImgLoaderIJ, LegacyStackImgLoaderLOCI

public abstract class LegacyStackImgLoader
extends AbstractImgFactoryImgLoader

Field Summary

Fields

Modifier and Type	Field	Description
protected String	fileNamePattern
protected int	layoutAngles
protected int	layoutChannels
protected int	layoutIllum
protected int	layoutTiles
protected int	layoutTP
protected int	numDigitsAngles
protected int	numDigitsChannels
protected int	numDigitsIlluminations
protected int	numDigitsTiles
protected int	numDigitsTimepoints
protected File	path
protected String	replaceAngles
protected String	replaceChannels
protected String	replaceIlluminations
protected String	replaceTiles
protected String	replaceTimepoints
protected mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?>	sequenceDescription

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

imgFactory1

Constructor Summary

Constructors

Constructor	Description
LegacyStackImgLoader(File path, String fileNamePattern, int layoutTP, int layoutChannels, int layoutIllum, int layoutAngles, int layoutTiles, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)	For a local initialization without the XML

Method Summary

Modifier and Type	Method	Description
protected File	getFile(mpicbg.spim.data.sequence.ViewId view)
String	getFileNamePattern()
int	getLayoutAngles()
int	getLayoutChannels()
int	getLayoutIlluminations()
int	getLayoutTiles()
int	getLayoutTimePoints()
File	getPath()
protected void	init()
protected <T extends net.imglib2.type.NativeType<T>> net.imglib2.img.Img<T>	instantiateImg(long[] dim, T type)

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, loadMetaData, updateMetaDataCache, updateXMLMetaData, updateXMLMetaData, updateXMLMetaData

Methods inherited from class java.lang.Object

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

Methods inherited from interface mpicbg.spim.data.legacy.LegacyBasicImgLoader

getImage

Methods inherited from interface mpicbg.spim.data.legacy.LegacyImgLoader

getFloatImage

Field Details

path

protected File path

fileNamePattern

protected String fileNamePattern

replaceTimepoints

protected String replaceTimepoints

replaceChannels

protected String replaceChannels

replaceIlluminations

protected String replaceIlluminations

replaceAngles

protected String replaceAngles

replaceTiles

protected String replaceTiles

numDigitsTimepoints

protected int numDigitsTimepoints

numDigitsChannels

protected int numDigitsChannels

numDigitsIlluminations

protected int numDigitsIlluminations

numDigitsAngles

protected int numDigitsAngles

numDigitsTiles

protected int numDigitsTiles

layoutTP

protected int layoutTP

layoutChannels

protected int layoutChannels

layoutIllum

protected int layoutIllum

layoutAngles

protected int layoutAngles

layoutTiles

protected int layoutTiles

sequenceDescription

protected mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription

Constructor Details

LegacyStackImgLoader

public LegacyStackImgLoader(File path,
 String fileNamePattern,
 int layoutTP,
 int layoutChannels,
 int layoutIllum,
 int layoutAngles,
 int layoutTiles,
 mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> sequenceDescription)

For a local initialization without the XML

Parameters:

path - - the path

fileNamePattern - - the filename pattern

layoutTP - - 0 == one, 1 == one per file, 2 == all in one file

layoutChannels - - 0 == one, 1 == one per file, 2 == all in one file

layoutIllum - - 0 == one, 1 == one per file, 2 == all in one file

layoutAngles - - 0 == one, 1 == one per file, 2 == all in one file

layoutTiles - - 0 == one, 1 == one per file, 2 == all in one file

sequenceDescription - - the sequence description

Method Details

getPath

public File getPath()

getFileNamePattern

public String getFileNamePattern()

getLayoutTimePoints

public int getLayoutTimePoints()

getLayoutChannels

public int getLayoutChannels()

getLayoutIlluminations

public int getLayoutIlluminations()

getLayoutAngles

public int getLayoutAngles()

getLayoutTiles

public int getLayoutTiles()

instantiateImg

protected <T extends net.imglib2.type.NativeType<T>>
net.imglib2.img.Img<T> instantiateImg(long[] dim,
 T type)

getFile

protected File getFile(mpicbg.spim.data.sequence.ViewId view)

init

protected void init()