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

Class LegacyStackImgLoaderIJ

java.lang.Object

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

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

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

net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

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 LegacyStackImgLoaderIJ
extends LegacyStackImgLoader

Field Summary

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

fileNamePattern, layoutAngles, layoutChannels, layoutIllum, layoutTiles, layoutTP, numDigitsAngles, numDigitsChannels, numDigitsIlluminations, numDigitsTiles, numDigitsTimepoints, path, replaceAngles, replaceChannels, replaceIlluminations, replaceTiles, replaceTimepoints, sequenceDescription

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

imgFactory1

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	getFloatImage(mpicbg.spim.data.sequence.ViewId view, boolean normalize)	Get FloatType image normalized to the range [0,1].
net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.integer.UnsignedShortType>	getImage(mpicbg.spim.data.sequence.ViewId view)	Get UnsignedShortType un-normalized image.
protected void	loadMetaData(mpicbg.spim.data.sequence.ViewId view)	Loads only the metadata from the image, should call updateMetaDataCache( ... )
static ij.ImagePlus	open(File file)
protected static Generic_Resave_HDF5.ParametersResaveHDF5	queryParameters()
String	toString()
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	updateAndGetMinMax(net.imglib2.RandomAccessibleInterval<T> img, Generic_Resave_HDF5.ParametersResaveHDF5 params)

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

getFile, getFileNamePattern, getLayoutAngles, getLayoutChannels, getLayoutIlluminations, getLayoutTiles, getLayoutTimePoints, getPath, init, instantiateImg

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, wait, wait, wait

Constructor Details

LegacyStackImgLoaderIJ

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

Method Details

open

public static ij.ImagePlus open(File file)

getFloatImage

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

Get FloatType image normalized to the range [0,1].

Parameters:

view - timepoint and setup for which to retrieve the image.

normalize - if the image should be normalized to [0,1] or not

Returns:

FloatType image normalized to range [0,1]

getImage

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

Get UnsignedShortType un-normalized image.

Parameters:

view - timepoint and setup for which to retrieve the image.

Returns:

UnsignedShortType image.

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

toString

public String toString()

Overrides:

toString in class Object

queryParameters

protected static Generic_Resave_HDF5.ParametersResaveHDF5 queryParameters()

updateAndGetMinMax

public static <T extends net.imglib2.type.numeric.RealType<T>>
double[] updateAndGetMinMax(net.imglib2.RandomAccessibleInterval<T> img,
 Generic_Resave_HDF5.ParametersResaveHDF5 params)