Package net.preibisch.mvrecon.process.fusion

Class FusionTools

java.lang.Object

net.preibisch.mvrecon.process.fusion.FusionTools

public class FusionTools
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	FusionTools.ImgDataType

Field Summary

Fields

Modifier and Type	Field	Description
static float	defaultBlendingBorder
static float	defaultBlendingRange
static double	defaultContentBasedSigma1
static double	defaultContentBasedSigma2
static String[]	imgDataTypeChoice

Constructor Summary

Constructors

Constructor	Description
FusionTools()

Method Summary

Modifier and Type	Method	Description
static void	adjustBlending(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd, float[] blending, float[] border, net.imglib2.realtransform.AffineTransform3D transformationModel)	Compute how much blending in the input has to be done so the target values blending and border are achieved in the fused image
static void	adjustBlending(net.imglib2.Dimensions dim, String name, float[] blending, float[] border, net.imglib2.realtransform.AffineTransform3D transformationModel)
static void	adjustContentBased(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd, double[] sigma1, double[] sigma2, double[] usedDownsampleFactors, double anisotropyFactor)	Compute how much sigma in the input has to be applied so the target values of sigma1 and 2 are achieved in the fused image
static final ArrayList<mpicbg.spim.data.sequence.ViewDescription>	assembleInputData(SpimData2 spimData, mpicbg.spim.data.sequence.TimePoint timepoint, mpicbg.spim.data.sequence.Channel channel, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
static <T extends net.imglib2.type.NativeType<T>, A extends net.imglib2.img.basictypeaccess.array.ArrayDataAccess<A>> net.imglib2.RandomAccessibleInterval<T>	cacheRandomAccessibleInterval(net.imglib2.RandomAccessibleInterval<T> input, long maxCacheSize, T type, int... cellDim)
static <T extends net.imglib2.type.NativeType<T>> net.imglib2.RandomAccessibleInterval<T>	cacheRandomAccessibleInterval(net.imglib2.RandomAccessibleInterval<T> input, T type, int... cellDim)
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	convertInput(net.imglib2.RandomAccessibleInterval<T> img)
static final <T extends net.imglib2.type.Type<T>> void	copyImg(long start, long loopSize, net.imglib2.RandomAccessibleInterval<T> source, net.imglib2.RandomAccessibleInterval<T> target)
static <T extends net.imglib2.type.Type<T>> net.imglib2.RandomAccessibleInterval<T>	copyImg(net.imglib2.RandomAccessibleInterval<T> input, net.imglib2.img.ImgFactory<T> factory, T type, ExecutorService service)
static <T extends net.imglib2.type.Type<T>> net.imglib2.RandomAccessibleInterval<T>	copyImg(net.imglib2.RandomAccessibleInterval<T> input, net.imglib2.img.ImgFactory<T> factory, T type, ExecutorService service, boolean showProgress)
static <T extends net.imglib2.type.Type<T>> void	copyImg(net.imglib2.RandomAccessibleInterval<T> input, net.imglib2.RandomAccessibleInterval<T> output, ExecutorService service)
static <T extends net.imglib2.type.Type<T>> void	copyImg(net.imglib2.RandomAccessibleInterval<T> input, net.imglib2.RandomAccessibleInterval<T> output, ExecutorService service, boolean showProgress)
static <T extends net.imglib2.type.Type<T>> net.imglib2.img.Img<T>	copyImgNoTranslation(net.imglib2.RandomAccessibleInterval<T> input, net.imglib2.img.ImgFactory<T> factory, T type, ExecutorService service)
static <T extends net.imglib2.type.Type<T>> net.imglib2.img.Img<T>	copyImgNoTranslation(net.imglib2.RandomAccessibleInterval<T> input, net.imglib2.img.ImgFactory<T> factory, T type, ExecutorService service, boolean showProgress)
static net.imglib2.util.Pair<net.imglib2.Interval,net.imglib2.realtransform.AffineTransform3D>	createAnisotropicBoundingBox(net.imglib2.Interval boundingBox, double anisotropy)	Creates an anisotropic bounding box by floor/ceil to include all data and provides the affine transformation to scale it to global coordinates
static net.imglib2.util.Pair<net.imglib2.Interval,net.imglib2.realtransform.AffineTransform3D>	createDownsampledBoundingBox(net.imglib2.Interval boundingBox, double downsampling)	Creates a downsampled bounding box by rounding and provides the affine transformation to scale it to global coordinates, which also corrects for the fact that the fused image is ZEROMIN (TODO: change that)
static ij.ImagePlus	display(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input, FusionTools.ImgDataType imgType)
static ij.ImagePlus	display(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input, FusionTools.ImgDataType imgType, double min, double max, int[] cellDim, int maxCacheSize)
static ij.ImagePlus	display(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input, FusionTools.ImgDataType imgType, int[] cellDim, int maxCacheSize)
static ij.ImagePlus	displayCached(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input)
static ij.ImagePlus	displayCached(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input, double min, double max)
static ij.ImagePlus	displayCached(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input, double min, double max, int[] cellDim, int maxCacheSize)
static ij.ImagePlus	displayCached(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input, int[] cellDim, int maxCacheSize)
static ij.ImagePlus	displayCopy(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input)
static ij.ImagePlus	displayCopy(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input, double min, double max)
static ij.ImagePlus	displayVirtually(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input)
static ij.ImagePlus	displayVirtually(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input, double min, double max)
static final Vector<ImagePortion>	divideIntoPortions(long imageSize)
static final void	execTasks(ArrayList<Callable<Void>> tasks, int nThreads, String jobDescription)
static final void	execTasks(ArrayList<Callable<Void>> tasks, ExecutorService taskExecutor, String jobDescription)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtual(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> views, FusionGUI.FusionType fusionType, int interpolation, net.imglib2.Interval boundingBox, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtual(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, FusionGUI.FusionType fusionType, net.imglib2.Interval bb)	Virtually fuses views
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtual(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, FusionGUI.FusionType fusionType, net.imglib2.Interval bb, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)	Virtually fuses views
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtual(mpicbg.spim.data.generic.AbstractSpimData<? extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,? extends mpicbg.spim.data.sequence.ImgLoader>> spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, FusionGUI.FusionType fusionType)	Virtually fuses views using a maximal bounding box around all views
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtual(mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader, Map<mpicbg.spim.data.sequence.ViewId,? extends net.imglib2.realtransform.AffineTransform3D> registrations, Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions, Collection<? extends mpicbg.spim.data.sequence.ViewId> views, FusionGUI.FusionType fusionType, int interpolation, net.imglib2.Interval boundingBox, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtual(mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader, Map<mpicbg.spim.data.sequence.ViewId,? extends net.imglib2.realtransform.AffineTransform3D> registrations, Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions, Collection<? extends mpicbg.spim.data.sequence.ViewId> views, FusionGUI.FusionType fusionType, net.imglib2.Interval bb)	Virtually fuses views
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtual(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, FusionGUI.FusionType fusionType, boolean adjustIntensities)	Virtually fuses views using a maximal bounding box around all views
static String	getAngleName(List<mpicbg.spim.data.sequence.Angle> anglesToProcess)
static net.imglib2.Interval	getFusedZeroMinInterval(net.imglib2.Interval bbDS)
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	getFusionMinMax(net.imglib2.RandomAccessibleInterval<T> img, double min, double max)
static String	getIllumName(List<mpicbg.spim.data.sequence.Illumination> illumsToProcess)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> ij.ImagePlus	getImagePlusInstance(net.imglib2.RandomAccessibleInterval<T> img, boolean virtualDisplay, String title, double min, double max, ExecutorService service)
static double	getMinRes(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> desc)
static boolean	is2d(Collection<? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> views)
static <T extends net.imglib2.type.numeric.RealType<T>> float[]	minMax(net.imglib2.RandomAccessibleInterval<T> img)
static <T extends net.imglib2.type.numeric.RealType<T>> float[]	minMax(net.imglib2.RandomAccessibleInterval<T> img, ExecutorService service)
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	minMaxApprox(net.imglib2.RandomAccessibleInterval<T> img)	Deprecated.
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	minMaxApprox1(net.imglib2.RandomAccessibleInterval<T> img)
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	minMaxApprox1(net.imglib2.RandomAccessibleInterval<T> img, int numPixels)
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	minMaxApprox1(net.imglib2.RandomAccessibleInterval<T> img, Random rnd, int numPixels)
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	minMaxAvgApprox1(net.imglib2.RandomAccessibleInterval<T> img, Random rnd, int numPixels)
static boolean	normalizeImage(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> img)	Normalizes the image to the range [0...1]
static boolean	normalizeImage(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> img, float min, float max)	Normalizes the image to the range [0...1]
static boolean	normalizeImage(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> img, float min, float max, ExecutorService service)	Normalizes the image to the range [0...1]
static long	numPixels(long[] dim, double downsampling)
static long	numPixels(long[] min, long[] max, double downsampling)
static long	numPixels(net.imglib2.Interval bb, double downsampling)
static void	runThreads(Thread[] threads)
static <T> net.imglib2.RandomAccessibleInterval<T>	translateIfNecessary(net.imglib2.Interval original, net.imglib2.RandomAccessibleInterval<T> copy)

Methods inherited from class java.lang.Object

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

Field Details

imgDataTypeChoice

public static String[] imgDataTypeChoice

defaultBlendingRange

public static float defaultBlendingRange

defaultBlendingBorder

public static float defaultBlendingBorder

defaultContentBasedSigma1

public static double defaultContentBasedSigma1

defaultContentBasedSigma2

public static double defaultContentBasedSigma2

Constructor Details

FusionTools

public FusionTools()

Method Details

numPixels

public static long numPixels(net.imglib2.Interval bb,
 double downsampling)

numPixels

public static long numPixels(long[] dim,
 double downsampling)

numPixels

public static long numPixels(long[] min,
 long[] max,
 double downsampling)

fuseVirtual

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtual(mpicbg.spim.data.generic.AbstractSpimData<? extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,? extends mpicbg.spim.data.sequence.ImgLoader>> spimData,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 FusionGUI.FusionType fusionType)

Virtually fuses views using a maximal bounding box around all views

Parameters:

spimData - - an AbstractSpimData object

viewIds - - which viewIds to fuse (be careful to remove not present one's first)

fusionType - - how to combine pixels

Returns:

a virtually fused zeroMin RandomAccessibleInterval and the transformation to map it to global coordinates

fuseVirtual

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtual(SpimData2 spimData,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 FusionGUI.FusionType fusionType,
 boolean adjustIntensities)

Virtually fuses views using a maximal bounding box around all views

Parameters:

spimData - - an AbstractSpimData object

viewIds - - which viewIds to fuse (be careful to remove not present one's first)

fusionType - - how to combine pixels

adjustIntensities - - adjust intensities according to whats stored in the spimdata

Returns:

a virtually fused zeroMin RandomAccessibleInterval

fuseVirtual

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtual(mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader,
 Map<mpicbg.spim.data.sequence.ViewId,? extends net.imglib2.realtransform.AffineTransform3D> registrations,
 Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> views,
 FusionGUI.FusionType fusionType,
 net.imglib2.Interval bb)

Virtually fuses views

Parameters:

imgloader - - an imgloader

registrations - - all (updated) registrations

viewDescriptions - - all viewdescriptions

views - - which viewIds to fuse (be careful to remove not present one's first)

fusionType - - how to combine pixels

bb - - the bounding box in world coordinates (can be loaded from XML or defined through one of the BoundingBoxEstimation implementations)

Returns:

a virtually fused zeroMin RandomAccessibleInterval and the transformation to map it to global coordinates

fuseVirtual

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtual(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 FusionGUI.FusionType fusionType,
 net.imglib2.Interval bb)

Virtually fuses views

Parameters:

spimData - - an AbstractSpimData object

viewIds - - which viewIds to fuse (be careful to remove not present one's first)

fusionType - - how to combine pixels

bb - - the bounding box in world coordinates (can be loaded from XML or defined through one of the BoundingBoxEstimation implementations)

Returns:

a virtually fused zeroMin RandomAccessibleInterval and the transformation to map it to global coordinates

fuseVirtual

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtual(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 FusionGUI.FusionType fusionType,
 net.imglib2.Interval bb,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)

Virtually fuses views

Parameters:

spimData - - an AbstractSpimData object

viewIds - - which viewIds to fuse (be careful to remove not present one's first)

fusionType - - how to combine pixels

bb - - the bounding box in world coordinates (can be loaded from XML or defined through one of the BoundingBoxEstimation implementations)

intensityAdjustments - - the intensityadjustsments or null

Returns:

a virtually fused zeroMin RandomAccessibleInterval

fuseVirtual

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtual(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> views,
 FusionGUI.FusionType fusionType,
 int interpolation,
 net.imglib2.Interval boundingBox,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)

createAnisotropicBoundingBox

public static net.imglib2.util.Pair<net.imglib2.Interval,net.imglib2.realtransform.AffineTransform3D> createAnisotropicBoundingBox(net.imglib2.Interval boundingBox,
 double anisotropy)

Creates an anisotropic bounding box by floor/ceil to include all data and provides the affine transformation to scale it to global coordinates

Parameters:

boundingBox - - the bounding box to scale

anisotropy - - the desired anisotropy

Returns:

a downsampled interval and the corresponding affine transform to map it to global coordinates or a copy if anisotropy == Double.NaN or 1.0

createDownsampledBoundingBox

public static net.imglib2.util.Pair<net.imglib2.Interval,net.imglib2.realtransform.AffineTransform3D> createDownsampledBoundingBox(net.imglib2.Interval boundingBox,
 double downsampling)

Creates a downsampled bounding box by rounding and provides the affine transformation to scale it to global coordinates, which also corrects for the fact that the fused image is ZEROMIN (TODO: change that)

Parameters:

boundingBox - - the bounding box to scale

downsampling - - the desired downsampling

Returns:

a downsampled interval and the corresponding affine transform to map it to global coordinates or a copy if downsampling == Double.NaN or 1.0

getFusedZeroMinInterval

public static net.imglib2.Interval getFusedZeroMinInterval(net.imglib2.Interval bbDS)

is2d

public static boolean is2d(Collection<? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> views)

fuseVirtual

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtual(mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader,
 Map<mpicbg.spim.data.sequence.ViewId,? extends net.imglib2.realtransform.AffineTransform3D> registrations,
 Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> views,
 FusionGUI.FusionType fusionType,
 int interpolation,
 net.imglib2.Interval boundingBox,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)

convertInput

public static <T extends net.imglib2.type.numeric.RealType<T>>
net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> convertInput(net.imglib2.RandomAccessibleInterval<T> img)

displayVirtually

public static ij.ImagePlus displayVirtually(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input)

displayVirtually

public static ij.ImagePlus displayVirtually(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input,
 double min,
 double max)

displayCopy

public static ij.ImagePlus displayCopy(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input)

displayCopy

public static ij.ImagePlus displayCopy(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input,
 double min,
 double max)

displayCached

public static ij.ImagePlus displayCached(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input,
 int[] cellDim,
 int maxCacheSize)

displayCached

public static ij.ImagePlus displayCached(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input,
 double min,
 double max,
 int[] cellDim,
 int maxCacheSize)

displayCached

public static ij.ImagePlus displayCached(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input)

displayCached

public static ij.ImagePlus displayCached(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input,
 double min,
 double max)

display

public static ij.ImagePlus display(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input,
 FusionTools.ImgDataType imgType)

display

public static ij.ImagePlus display(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input,
 FusionTools.ImgDataType imgType,
 int[] cellDim,
 int maxCacheSize)

display

public static ij.ImagePlus display(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> input,
 FusionTools.ImgDataType imgType,
 double min,
 double max,
 int[] cellDim,
 int maxCacheSize)

getFusionMinMax

public static <T extends net.imglib2.type.numeric.RealType<T>>
double[] getFusionMinMax(net.imglib2.RandomAccessibleInterval<T> img,
 double min,
 double max)

getImagePlusInstance

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
ij.ImagePlus getImagePlusInstance(net.imglib2.RandomAccessibleInterval<T> img,
 boolean virtualDisplay,
 String title,
 double min,
 double max,
 ExecutorService service)

adjustBlending

public static void adjustBlending(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd,
 float[] blending,
 float[] border,
 net.imglib2.realtransform.AffineTransform3D transformationModel)

Compute how much blending in the input has to be done so the target values blending and border are achieved in the fused image

Parameters:

vd - - which view

blending - - the target blending range, e.g. 40

border - - the target blending border, e.g. 0

transformationModel - - the transformation model used to map from the (downsampled) input to the output

adjustBlending

public static void adjustBlending(net.imglib2.Dimensions dim,
 String name,
 float[] blending,
 float[] border,
 net.imglib2.realtransform.AffineTransform3D transformationModel)

adjustContentBased

public static void adjustContentBased(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd,
 double[] sigma1,
 double[] sigma2,
 double[] usedDownsampleFactors,
 double anisotropyFactor)

Compute how much sigma in the input has to be applied so the target values of sigma1 and 2 are achieved in the fused image

Parameters:

vd - - which view

sigma1 - - the target sigma1 for entropy approximation, e.g. 20

sigma2 - - the target sigma2 for entropy approximation, e.g. 40

usedDownsampleFactors - - the downsampling factors used to load the input image

anisotropyFactor - - anisotropyFactor or Double.NaN

getMinRes

public static double getMinRes(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> desc)

getIllumName

public static String getIllumName(List<mpicbg.spim.data.sequence.Illumination> illumsToProcess)

getAngleName

public static String getAngleName(List<mpicbg.spim.data.sequence.Angle> anglesToProcess)

assembleInputData

public static final ArrayList<mpicbg.spim.data.sequence.ViewDescription> assembleInputData(SpimData2 spimData,
 mpicbg.spim.data.sequence.TimePoint timepoint,
 mpicbg.spim.data.sequence.Channel channel,
 List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)

cacheRandomAccessibleInterval

public static <T extends net.imglib2.type.NativeType<T>>
net.imglib2.RandomAccessibleInterval<T> cacheRandomAccessibleInterval(net.imglib2.RandomAccessibleInterval<T> input,
 T type,
 int... cellDim)

cacheRandomAccessibleInterval

public static <T extends net.imglib2.type.NativeType<T>,
A extends net.imglib2.img.basictypeaccess.array.ArrayDataAccess<A>>
net.imglib2.RandomAccessibleInterval<T> cacheRandomAccessibleInterval(net.imglib2.RandomAccessibleInterval<T> input,
 long maxCacheSize,
 T type,
 int... cellDim)

copyImg

public static <T extends net.imglib2.type.Type<T>>
net.imglib2.RandomAccessibleInterval<T> copyImg(net.imglib2.RandomAccessibleInterval<T> input,
 net.imglib2.img.ImgFactory<T> factory,
 T type,
 ExecutorService service)

copyImg

public static <T extends net.imglib2.type.Type<T>>
net.imglib2.RandomAccessibleInterval<T> copyImg(net.imglib2.RandomAccessibleInterval<T> input,
 net.imglib2.img.ImgFactory<T> factory,
 T type,
 ExecutorService service,
 boolean showProgress)

copyImgNoTranslation

public static <T extends net.imglib2.type.Type<T>>
net.imglib2.img.Img<T> copyImgNoTranslation(net.imglib2.RandomAccessibleInterval<T> input,
 net.imglib2.img.ImgFactory<T> factory,
 T type,
 ExecutorService service)

copyImgNoTranslation

public static <T extends net.imglib2.type.Type<T>>
net.imglib2.img.Img<T> copyImgNoTranslation(net.imglib2.RandomAccessibleInterval<T> input,
 net.imglib2.img.ImgFactory<T> factory,
 T type,
 ExecutorService service,
 boolean showProgress)

translateIfNecessary

public static <T>
net.imglib2.RandomAccessibleInterval<T> translateIfNecessary(net.imglib2.Interval original,
 net.imglib2.RandomAccessibleInterval<T> copy)

copyImg

public static <T extends net.imglib2.type.Type<T>>
void copyImg(net.imglib2.RandomAccessibleInterval<T> input,
 net.imglib2.RandomAccessibleInterval<T> output,
 ExecutorService service)

copyImg

public static <T extends net.imglib2.type.Type<T>>
void copyImg(net.imglib2.RandomAccessibleInterval<T> input,
 net.imglib2.RandomAccessibleInterval<T> output,
 ExecutorService service,
 boolean showProgress)

execTasks

public static final void execTasks(ArrayList<Callable<Void>> tasks,
 int nThreads,
 String jobDescription)

execTasks

public static final void execTasks(ArrayList<Callable<Void>> tasks,
 ExecutorService taskExecutor,
 String jobDescription)

copyImg

public static final <T extends net.imglib2.type.Type<T>>
void copyImg(long start,
 long loopSize,
 net.imglib2.RandomAccessibleInterval<T> source,
 net.imglib2.RandomAccessibleInterval<T> target)

minMax

public static <T extends net.imglib2.type.numeric.RealType<T>>
float[] minMax(net.imglib2.RandomAccessibleInterval<T> img)

minMax

public static <T extends net.imglib2.type.numeric.RealType<T>>
float[] minMax(net.imglib2.RandomAccessibleInterval<T> img,
 ExecutorService service)

minMaxApprox1

public static <T extends net.imglib2.type.numeric.RealType<T>>
double[] minMaxApprox1(net.imglib2.RandomAccessibleInterval<T> img)

minMaxApprox

@Deprecated
public static <T extends net.imglib2.type.numeric.RealType<T>>
double[] minMaxApprox(net.imglib2.RandomAccessibleInterval<T> img)

Deprecated.

minMaxApprox1

public static <T extends net.imglib2.type.numeric.RealType<T>>
double[] minMaxApprox1(net.imglib2.RandomAccessibleInterval<T> img,
 int numPixels)

minMaxApprox1

public static <T extends net.imglib2.type.numeric.RealType<T>>
double[] minMaxApprox1(net.imglib2.RandomAccessibleInterval<T> img,
 Random rnd,
 int numPixels)

minMaxAvgApprox1

public static <T extends net.imglib2.type.numeric.RealType<T>>
double[] minMaxAvgApprox1(net.imglib2.RandomAccessibleInterval<T> img,
 Random rnd,
 int numPixels)

normalizeImage

public static boolean normalizeImage(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> img)

Normalizes the image to the range [0...1]

Parameters:

img - - the image to normalize

Returns:

- normalized array

normalizeImage

public static boolean normalizeImage(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> img,
 float min,
 float max)

Normalizes the image to the range [0...1]

Parameters:

img - - the image to normalize

min - - min value

max - - max value

Returns:

- normalized array

normalizeImage

public static boolean normalizeImage(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> img,
 float min,
 float max,
 ExecutorService service)

Normalizes the image to the range [0...1]

Parameters:

img - - the image to normalize

min - - min value

max - - max value

service - - the ExecutorService (can be null)

Returns:

- normalized array

divideIntoPortions

public static final Vector<ImagePortion> divideIntoPortions(long imageSize)

runThreads

public static void runThreads(Thread[] threads)