Package net.preibisch.mvrecon.fiji.plugin.fusion

Class DeconvolutionGUI

java.lang.Object

net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

All Implemented Interfaces:

FusionExportInterface

public class DeconvolutionGUI
extends Object
implements FusionExportInterface

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	additionalSmoothBlending
protected boolean	adjustBlending
protected boolean	adjustIntensities
protected float	blendingBorder
protected float	blendingRange
protected net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType>	blockFactory
static String[]	blocksChoice
protected int[]	blockSize
protected int	blockSizeIndex
protected int	boundingBox
protected int	cacheBlockSize
protected int	cacheMaxNumBlocks
protected int	cacheTypeInputImg
protected int	cacheTypeWeights
static String[]	computationOnChoice
protected ComputeBlockThreadFactory<?>	computeFactory
protected int	computeOnIndex
protected net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType>	copyFactory
protected int	debugInterval
protected boolean	debugMode
static boolean	defaultAdditionalSmoothBlending
static boolean	defaultAdjustBlending
static boolean	defaultAdjustIntensities
static int	defaultBB
static float	defaultBlendingBorder
static float	defaultBlendingRange
static int	defaultBlockSizeIndex
static int	defaultBlockSizeX
static int	defaultBlockSizeY
static int	defaultBlockSizeZ
static int	defaultCacheBlockSize
static int	defaultCacheMaxNumBlocks
static int	defaultComputeOnIndex
static int	defaultDebugInterval
static boolean	defaultDebugMode
static double	defaultDownsampling
static boolean	defaultGroupIllums
static boolean	defaultGroupTiles
static int	defaultImgExportAlgorithm
static int	defaultInputImgCacheType
static double	defaultLambda
static boolean	defaultMul
static int	defaultNumIterations
static double	defaultOsemSpeedup
static boolean	defaultPreciseAvgMax
static int	defaultPSFType
static int	defaultPsiCopyBlockSize
static int	defaultPsiInit
static String	defaultPsiStartFile
static int	defaultSplittingType
static boolean	defaultTestEmptyBlocks
static boolean	defaultUseTikhonovRegularization
static int	defaultWeightCacheType
protected double	downsampling
protected boolean	groupIllums
protected boolean	groupTiles
protected int	imgExport
static final String[]	imgExportDescriptions
protected double	lambda
protected long[]	maxBlock
protected boolean	mul
protected NonRigidParametersGUI	nrgui
protected int	numIterations
protected double	osemSpeedup
static String[]	osemspeedupChoice
protected boolean	preciseAvgMax
protected int	psfType
static String[]	psfTypeChoice
protected int	psiCopyBlockSize
protected net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType>	psiFactory
protected int	psiInit
static String[]	psiInitChoice
protected String	psiStartFile
protected final SpimData2	spimData
protected int	splittingType
static String[]	splittingTypes
static final ArrayList<ImgExport>	staticImgExportAlgorithms
protected boolean	testEmptyBlocks
protected boolean	useTikhonov

Constructor Summary

Constructors

Constructor	Description
DeconvolutionGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views, ExecutorService service)

Method Summary

Modifier and Type	Method	Description
boolean	adjustIntensities()
boolean	getAdditionalSmoothBlending()
double	getAnisotropyFactor()
protected boolean	getBlendingAndGrouping()
float	getBlendingBorder()
float	getBlendingRange()
net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType>	getBlockFactory()
protected boolean	getBlocks()
BoundingBox	getBoundingBox()
int	getCacheBlockSize()
int	getCacheMaxNumBlocks()
int[]	getComputeBlockSize()
ComputeBlockThreadFactory<?>	getComputeBlockThreadFactory()
protected boolean	getComputeDevice()
net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType>	getCopyFactory()
protected boolean	getDebug()
int	getDebugInterval()
boolean	getDebugMode()
List<Group<mpicbg.spim.data.sequence.ViewDescription>>	getDeconvolutionGrouping(Group<mpicbg.spim.data.sequence.ViewDescription> group)
net.imglib2.Interval	getDownsampledBoundingBox()
double	getDownsampling()
List<Group<mpicbg.spim.data.sequence.ViewDescription>>	getFusionGroups()
FusionTools.ImgDataType	getInputImgCacheType()
float	getLambda()
ImgExport	getNewExporterInstance()
NonRigidParametersGUI	getNonRigidParameters()
int	getNumIterations()
double	getOSEMSpeedUp()
int	getPixelType()	0 == "32-bit floating point", 1 == "16-bit unsigned integer"
HashMap<mpicbg.spim.data.sequence.ViewId,PointSpreadFunction>	getPSFs()
DeconViewPSF.PSFTYPE	getPSFType()
int	getPsiCopyBlockSize()
net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType>	getPsiFactory()
protected boolean	getPsiFile()
PsiInitFactory	getPsiInitFactory()
SpimData2	getSpimData()
int	getSplittingType()	0 == "Each timepoint & channel", 1 == "Each timepoint, channel & illumination", 2 == "All views together", 3 == "Each view"
boolean	getUseTikhonov()
List<mpicbg.spim.data.sequence.ViewId>	getViews()
FusionTools.ImgDataType	getWeightCacheType()
boolean	groupIllums()
boolean	groupTiles()
boolean	isImgLoaderVirtual()
boolean	isMultiplicative()
boolean	isMultiResolution()
static boolean	isPowerOfTwo(int value)
static boolean	isPowerOfTwo(int[] values)
static long[]	maxTransformedKernel(HashMap<mpicbg.spim.data.sequence.ViewId,PointSpreadFunction> psfs, mpicbg.spim.data.registration.ViewRegistrations vr)
boolean	queryDetails()
boolean	testEmptyBlocks()

Methods inherited from class java.lang.Object

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

Field Details

staticImgExportAlgorithms

public static final ArrayList<ImgExport> staticImgExportAlgorithms

imgExportDescriptions

public static final String[] imgExportDescriptions

computationOnChoice

public static String[] computationOnChoice

osemspeedupChoice

public static String[] osemspeedupChoice

blocksChoice

public static String[] blocksChoice

psfTypeChoice

public static String[] psfTypeChoice

psiInitChoice

public static String[] psiInitChoice

splittingTypes

public static String[] splittingTypes

defaultBB

public static int defaultBB

defaultInputImgCacheType

public static int defaultInputImgCacheType

defaultWeightCacheType

public static int defaultWeightCacheType

defaultDownsampling

public static double defaultDownsampling

defaultAdjustIntensities

public static boolean defaultAdjustIntensities

defaultMul

public static boolean defaultMul

defaultPSFType

public static int defaultPSFType

defaultPsiInit

public static int defaultPsiInit

defaultOsemSpeedup

public static double defaultOsemSpeedup

defaultNumIterations

public static int defaultNumIterations

defaultDebugMode

public static boolean defaultDebugMode

defaultDebugInterval

public static int defaultDebugInterval

defaultUseTikhonovRegularization

public static boolean defaultUseTikhonovRegularization

defaultLambda

public static double defaultLambda

defaultBlockSizeIndex

public static int defaultBlockSizeIndex

defaultBlockSizeX

public static int defaultBlockSizeX

defaultBlockSizeY

public static int defaultBlockSizeY

defaultBlockSizeZ

public static int defaultBlockSizeZ

defaultTestEmptyBlocks

public static boolean defaultTestEmptyBlocks

defaultCacheBlockSize

public static int defaultCacheBlockSize

defaultCacheMaxNumBlocks

public static int defaultCacheMaxNumBlocks

defaultPsiCopyBlockSize

public static int defaultPsiCopyBlockSize

defaultComputeOnIndex

public static int defaultComputeOnIndex

defaultAdjustBlending

public static boolean defaultAdjustBlending

defaultBlendingRange

public static float defaultBlendingRange

defaultBlendingBorder

public static float defaultBlendingBorder

defaultAdditionalSmoothBlending

public static boolean defaultAdditionalSmoothBlending

defaultGroupTiles

public static boolean defaultGroupTiles

defaultGroupIllums

public static boolean defaultGroupIllums

defaultSplittingType

public static int defaultSplittingType

defaultImgExportAlgorithm

public static int defaultImgExportAlgorithm

defaultPsiStartFile

public static String defaultPsiStartFile

defaultPreciseAvgMax

public static boolean defaultPreciseAvgMax

boundingBox

protected int boundingBox

downsampling

protected double downsampling

adjustIntensities

protected boolean adjustIntensities

mul

protected boolean mul

cacheTypeInputImg

protected int cacheTypeInputImg

cacheTypeWeights

protected int cacheTypeWeights

psfType

protected int psfType

psiInit

protected int psiInit

osemSpeedup

protected double osemSpeedup

numIterations

protected int numIterations

debugMode

protected boolean debugMode

debugInterval

protected int debugInterval

useTikhonov

protected boolean useTikhonov

lambda

protected double lambda

blockSizeIndex

protected int blockSizeIndex

blockSize

protected int[] blockSize

testEmptyBlocks

protected boolean testEmptyBlocks

cacheBlockSize

protected int cacheBlockSize

cacheMaxNumBlocks

protected int cacheMaxNumBlocks

psiCopyBlockSize

protected int psiCopyBlockSize

computeOnIndex

protected int computeOnIndex

psiFactory

protected net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> psiFactory

copyFactory

protected net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> copyFactory

blockFactory

protected net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> blockFactory

computeFactory

protected ComputeBlockThreadFactory<?> computeFactory

adjustBlending

protected boolean adjustBlending

blendingRange

protected float blendingRange

blendingBorder

protected float blendingBorder

additionalSmoothBlending

protected boolean additionalSmoothBlending

groupTiles

protected boolean groupTiles

groupIllums

protected boolean groupIllums

splittingType

protected int splittingType

imgExport

protected int imgExport

maxBlock

protected long[] maxBlock

psiStartFile

protected String psiStartFile

preciseAvgMax

protected boolean preciseAvgMax

nrgui

protected NonRigidParametersGUI nrgui

spimData

protected final SpimData2 spimData

Constructor Details

DeconvolutionGUI

public DeconvolutionGUI(SpimData2 spimData,
 List<mpicbg.spim.data.sequence.ViewId> views,
 ExecutorService service)

Method Details

getSpimData

public SpimData2 getSpimData()

Specified by:

getSpimData in interface FusionExportInterface

getViews

public List<mpicbg.spim.data.sequence.ViewId> getViews()

Specified by:

getViews in interface FusionExportInterface

getBoundingBox

public BoundingBox getBoundingBox()

getDownsampledBoundingBox

public net.imglib2.Interval getDownsampledBoundingBox()

Specified by:

getDownsampledBoundingBox in interface FusionExportInterface

getPixelType

public int getPixelType()

Description copied from interface: FusionExportInterface

0 == "32-bit floating point", 1 == "16-bit unsigned integer"

Specified by:

getPixelType in interface FusionExportInterface

Returns:

the pixel type

getDownsampling

public double getDownsampling()

Specified by:

getDownsampling in interface FusionExportInterface

Returns:

the downsampling used for the fusion, or Double.NaN if no downsampling

getAnisotropyFactor

public double getAnisotropyFactor()

Specified by:

getAnisotropyFactor in interface FusionExportInterface

Returns:

the average anisotropy factor in z of all views used to "flatten" the fused image, or Double.NaN if no change

adjustIntensities

public boolean adjustIntensities()

getSplittingType

public int getSplittingType()

Description copied from interface: FusionExportInterface

0 == "Each timepoint & channel", 1 == "Each timepoint, channel & illumination", 2 == "All views together", 3 == "Each view"

Specified by:

getSplittingType in interface FusionExportInterface

Returns:

- how the views that are processed are split up

getInputImgCacheType

public FusionTools.ImgDataType getInputImgCacheType()

getWeightCacheType

public FusionTools.ImgDataType getWeightCacheType()

getPSFType

public DeconViewPSF.PSFTYPE getPSFType()

getOSEMSpeedUp

public double getOSEMSpeedUp()

getNumIterations

public int getNumIterations()

getDebugMode

public boolean getDebugMode()

getDebugInterval

public int getDebugInterval()

getUseTikhonov

public boolean getUseTikhonov()

getLambda

public float getLambda()

getComputeBlockSize

public int[] getComputeBlockSize()

testEmptyBlocks

public boolean testEmptyBlocks()

getCacheBlockSize

public int getCacheBlockSize()

getCacheMaxNumBlocks

public int getCacheMaxNumBlocks()

getPsiCopyBlockSize

public int getPsiCopyBlockSize()

getBlockFactory

public net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> getBlockFactory()

getPsiFactory

public net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> getPsiFactory()

getCopyFactory

public net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> getCopyFactory()

getComputeBlockThreadFactory

public ComputeBlockThreadFactory<?> getComputeBlockThreadFactory()

isMultiplicative

public boolean isMultiplicative()

getBlendingRange

public float getBlendingRange()

getBlendingBorder

public float getBlendingBorder()

getAdditionalSmoothBlending

public boolean getAdditionalSmoothBlending()

groupTiles

public boolean groupTiles()

groupIllums

public boolean groupIllums()

getNonRigidParameters

public NonRigidParametersGUI getNonRigidParameters()

getPsiInitFactory

public PsiInitFactory getPsiInitFactory()

getNewExporterInstance

public ImgExport getNewExporterInstance()

Specified by:

getNewExporterInstance in interface FusionExportInterface

Returns:

- creates a new instance of the exporter object

queryDetails

public boolean queryDetails()

isImgLoaderVirtual

public boolean isImgLoaderVirtual()

isMultiResolution

public boolean isMultiResolution()

getFusionGroups

public List<Group<mpicbg.spim.data.sequence.ViewDescription>> getFusionGroups()

Specified by:

getFusionGroups in interface FusionExportInterface

getDeconvolutionGrouping

public List<Group<mpicbg.spim.data.sequence.ViewDescription>> getDeconvolutionGrouping(Group<mpicbg.spim.data.sequence.ViewDescription> group)

getPSFs

public HashMap<mpicbg.spim.data.sequence.ViewId,PointSpreadFunction> getPSFs()

getPsiFile

protected boolean getPsiFile()

getDebug

protected boolean getDebug()

getBlocks

protected boolean getBlocks()

isPowerOfTwo

public static boolean isPowerOfTwo(int[] values)

isPowerOfTwo

public static boolean isPowerOfTwo(int value)

getComputeDevice

protected boolean getComputeDevice()

getBlendingAndGrouping

protected boolean getBlendingAndGrouping()

maxTransformedKernel

public static long[] maxTransformedKernel(HashMap<mpicbg.spim.data.sequence.ViewId,PointSpreadFunction> psfs,
 mpicbg.spim.data.registration.ViewRegistrations vr)