Package net.preibisch.mvrecon.process.deconvolution.util

Class ProcessInputImages<V extends mpicbg.spim.data.sequence.ViewId>

java.lang.Object

net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages<V>

public class ProcessInputImages<V extends mpicbg.spim.data.sequence.ViewId>
extends Object

Constructor Summary

Constructors

Constructor	Description
ProcessInputImages(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, Collection<Group<V>> groups, ExecutorService service, net.imglib2.Interval bb, double downsampling, boolean useWeightsFusion, float blendingRangeFusion, float blendingBorderFusion, boolean useWeightsDecon, float blendingRangeDeconvolution, float blendingBorderDeconvolution, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)
ProcessInputImages(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, Collection<Group<V>> groups, ExecutorService service, net.imglib2.Interval bb, double downsampling, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)
ProcessInputImages(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, Collection<Group<V>> groups, ExecutorService service, net.imglib2.Interval bb, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)

Method Summary

Modifier and Type	Method	Description
void	cacheImages()
void	cacheImages(int cellDim, int maxCacheSize)
void	cacheNormalizedWeights()
void	cacheNormalizedWeights(int cellDim, int maxCacheSize)
static <V extends mpicbg.spim.data.sequence.ViewId> void	cacheRandomAccessibleInterval(Collection<Group<V>> groups, int cellDim, int maxCacheSize, HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> images)
void	cacheUnnormalizedWeights()
void	cacheUnnormalizedWeights(int cellDim, int maxCacheSize)
void	copyImages()
void	copyImages(net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> imgFactory)
void	copyNormalizedWeights()
void	copyNormalizedWeights(net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> imgFactory)
static <V extends mpicbg.spim.data.sequence.ViewId> void	copyRandomAccessibleInterval(Collection<Group<V>> groups, ExecutorService service, net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> factory, HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> images)
void	copyUnnormalizedWeights()
void	copyUnnormalizedWeights(net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> imgFactory)
void	fuseGroups()
static <V extends mpicbg.spim.data.sequence.ViewId> net.imglib2.Interval	fuseGroups(mpicbg.spim.data.generic.AbstractSpimData<?> spimData, HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> tImgs, HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> tWeights, HashMap<V,net.imglib2.realtransform.AffineTransform3D> models, Collection<Group<V>> groups, net.imglib2.Interval boundingBox, double downsampling, float[] blendingRangeFusion, float[] blendingBorderFusion, float[] blendingRangeDecon, float[] blendingBorderDecon, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)
net.imglib2.Interval	getBoundingBox()
net.imglib2.Interval	getDownsampledBoundingBox()
HashMap<V,net.imglib2.realtransform.AffineTransform3D>	getDownsampledModels()
ArrayList<Group<V>>	getGroups()
HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>>	getImages()
HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>>	getNormalizedWeights()
HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>>	getUnnormalizedWeights()
void	normalizeWeights()
void	normalizeWeights(double osemspeedup)
void	normalizeWeights(double osemspeedup, boolean additionalSmoothBlending, float maxDiffRange, float scalingRange)
static <V extends mpicbg.spim.data.sequence.ViewId> HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>>	normalizeWeights(HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> unnormalizedWeights, List<Group<V>> groups, double osemspeedup, boolean additionalSmoothBlending, float maxDiffRange, float scalingRange)

Methods inherited from class java.lang.Object

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

Constructor Details

ProcessInputImages

public ProcessInputImages(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 Collection<Group<V>> groups,
 ExecutorService service,
 net.imglib2.Interval bb,
 double downsampling,
 boolean useWeightsFusion,
 float blendingRangeFusion,
 float blendingBorderFusion,
 boolean useWeightsDecon,
 float blendingRangeDeconvolution,
 float blendingBorderDeconvolution,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)

ProcessInputImages

public ProcessInputImages(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 Collection<Group<V>> groups,
 ExecutorService service,
 net.imglib2.Interval bb,
 double downsampling,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)

ProcessInputImages

public ProcessInputImages(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 Collection<Group<V>> groups,
 ExecutorService service,
 net.imglib2.Interval bb,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)

Method Details

getGroups

public ArrayList<Group<V>> getGroups()

getBoundingBox

public net.imglib2.Interval getBoundingBox()

getDownsampledBoundingBox

public net.imglib2.Interval getDownsampledBoundingBox()

getDownsampledModels

public HashMap<V,net.imglib2.realtransform.AffineTransform3D> getDownsampledModels()

getImages

public HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> getImages()

getNormalizedWeights

public HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> getNormalizedWeights()

getUnnormalizedWeights

public HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> getUnnormalizedWeights()

fuseGroups

public void fuseGroups()

cacheImages

public void cacheImages(int cellDim,
 int maxCacheSize)

cacheImages

public void cacheImages()

copyImages

public void copyImages(net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> imgFactory)

copyImages

public void copyImages()

cacheUnnormalizedWeights

public void cacheUnnormalizedWeights(int cellDim,
 int maxCacheSize)

cacheUnnormalizedWeights

public void cacheUnnormalizedWeights()

copyUnnormalizedWeights

public void copyUnnormalizedWeights(net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> imgFactory)

copyUnnormalizedWeights

public void copyUnnormalizedWeights()

cacheNormalizedWeights

public void cacheNormalizedWeights(int cellDim,
 int maxCacheSize)

cacheNormalizedWeights

public void cacheNormalizedWeights()

copyNormalizedWeights

public void copyNormalizedWeights(net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> imgFactory)

copyNormalizedWeights

public void copyNormalizedWeights()

normalizeWeights

public void normalizeWeights()

normalizeWeights

public void normalizeWeights(double osemspeedup)

normalizeWeights

public void normalizeWeights(double osemspeedup,
 boolean additionalSmoothBlending,
 float maxDiffRange,
 float scalingRange)

normalizeWeights

public static <V extends mpicbg.spim.data.sequence.ViewId>
HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> normalizeWeights(HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> unnormalizedWeights,
 List<Group<V>> groups,
 double osemspeedup,
 boolean additionalSmoothBlending,
 float maxDiffRange,
 float scalingRange)

cacheRandomAccessibleInterval

public static <V extends mpicbg.spim.data.sequence.ViewId>
void cacheRandomAccessibleInterval(Collection<Group<V>> groups,
 int cellDim,
 int maxCacheSize,
 HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> images)

copyRandomAccessibleInterval

public static <V extends mpicbg.spim.data.sequence.ViewId>
void copyRandomAccessibleInterval(Collection<Group<V>> groups,
 ExecutorService service,
 net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> factory,
 HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> images)

fuseGroups

public static <V extends mpicbg.spim.data.sequence.ViewId>
net.imglib2.Interval fuseGroups(mpicbg.spim.data.generic.AbstractSpimData<?> spimData,
 HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> tImgs,
 HashMap<Group<V>,net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>> tWeights,
 HashMap<V,net.imglib2.realtransform.AffineTransform3D> models,
 Collection<Group<V>> groups,
 net.imglib2.Interval boundingBox,
 double downsampling,
 float[] blendingRangeFusion,
 float[] blendingBorderFusion,
 float[] blendingRangeDecon,
 float[] blendingBorderDecon,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments)