Package net.preibisch.mvrecon.process.fusion.transformed.nonrigid

Class NonRigidTools

java.lang.Object

net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

public class NonRigidTools
extends Object

Constructor Summary

Constructors

Constructor	Description
NonRigidTools()

Method Summary

Modifier and Type	Method	Description
static Collection<CorrespondingIP>	assembleAllCorrespondingPoints(mpicbg.spim.data.sequence.ViewId viewId, InterestPoints ipList, Collection<? extends CorrespondingInterestPoints> cipList, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse, Map<? extends mpicbg.spim.data.sequence.ViewId,? extends ViewInterestPointLists> interestPointLists)
static HashMap<mpicbg.spim.data.sequence.ViewId,Collection<CorrespondingIP>>	assembleIPsForNonRigid(Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> viewInterestPoints, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse, List<String> labels)
static ArrayList<mpicbg.spim.data.sequence.ViewId>	assembleViewsToUse(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, boolean nonRigidAcrossTime)
static HashMap<mpicbg.spim.data.sequence.ViewId,ModelGrid>	computeGrids(Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, HashMap<? extends mpicbg.spim.data.sequence.ViewId,? extends Collection<? extends NonrigidIP>> uniquePoints, long[] controlPointDistance, double alpha, net.imglib2.Interval boundingBox, boolean virtual, ExecutorService service)
static net.imglib2.util.Pair<HashMap<mpicbg.spim.data.sequence.ViewId,ArrayList<SimpleReferenceIP>>,Double>	computeReferencePoints(Collection<mpicbg.spim.data.sequence.ViewId> views, ArrayList<HashSet<CorrespondingIP>> uniqueIPs)
static ArrayList<CorrespondingIP>	copyIPs(List<CorrespondingIP> in)
static HashSet<CorrespondingIP>	copyIPs(Set<CorrespondingIP> in)
static net.imglib2.util.Pair<ArrayList<net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>>,ArrayList<net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>>>	createNonRigidVirtualImages(mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader, Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.realtransform.AffineTransform3D> downsampledRegistrations, HashMap<mpicbg.spim.data.sequence.ViewId,ModelGrid> nonrigidGrids, net.imglib2.Interval bbDS, FusionGUI.FusionType fusionType, boolean displayDistances, int interpolation, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments, int overlapExpansion)
static int	defaultOverlapExpansion(double maxDistance)
static ArrayList<HashSet<CorrespondingIP>>	findUniqueInterestPoints(Collection<CorrespondingIP> pairs)
static ArrayList<HashSet<CorrespondingIP>>	findUniqueInterestPoints(Map<mpicbg.spim.data.sequence.ViewId,Collection<CorrespondingIP>> annotatedIps)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtualInterpolatedNonRigid(mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader, Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.realtransform.AffineTransform3D> viewRegistrations, Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> viewInterestPoints, Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse, ArrayList<String> labels, FusionGUI.FusionType fusionType, boolean displayDistances, long[] controlPointDistance, double alpha, boolean virtualGrid, int interpolation, net.imglib2.Interval boundingBox, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments, ExecutorService service)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	fuseVirtualInterpolatedNonRigid(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse, ArrayList<String> labels, FusionGUI.FusionType fusionType, boolean displayDistances, long[] controlPointDistance, double alpha, boolean virtualGrid, int interpolation, net.imglib2.Interval boundingBox1, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments, ExecutorService service)
protected static IPL	getIPL(Collection<IPL> ipls, String label)
static double	transformCorrespondingIPs(Collection<CorrespondingIP> aips, Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.realtransform.AffineTransform3D> models)
static ArrayList<HashSet<CorrespondingIP>>	transformUniqueIPs(ArrayList<HashSet<CorrespondingIP>> uniqueIPs, Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.realtransform.AffineTransform3D> downsampledRegistrations)
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	transformViewNonRigid(net.imglib2.RandomAccessibleInterval<T> input, Collection<? extends NonrigidIP> ips, double alpha, mpicbg.models.AffineModel3D invertedModelOpener, net.imglib2.Interval boundingBox, float outsideValue, int interpolation)
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	transformViewNonRigidInterpolated(net.imglib2.RandomAccessibleInterval<T> input, ModelGrid grid, mpicbg.models.AffineModel3D invertedModelOpener, net.imglib2.Interval boundingBox, float outsideValue, int interpolation)
static int[]	uniqueInterestPointCounts(List<HashSet<CorrespondingIP>> groups)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	visualizeDistancesViewNonRigidInterpolated(net.imglib2.Interval input, ModelGrid grid, net.imglib2.realtransform.AffineTransform3D originalTransform, net.imglib2.Interval boundingBox, float outsideValue, int interpolation)

Methods inherited from class java.lang.Object

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

Constructor Details

NonRigidTools

public NonRigidTools()

Method Details

fuseVirtualInterpolatedNonRigid

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtualInterpolatedNonRigid(SpimData2 spimData,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse,
 ArrayList<String> labels,
 FusionGUI.FusionType fusionType,
 boolean displayDistances,
 long[] controlPointDistance,
 double alpha,
 boolean virtualGrid,
 int interpolation,
 net.imglib2.Interval boundingBox1,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments,
 ExecutorService service)

fuseVirtualInterpolatedNonRigid

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> fuseVirtualInterpolatedNonRigid(mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader,
 Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.realtransform.AffineTransform3D> viewRegistrations,
 Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> viewInterestPoints,
 Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse,
 ArrayList<String> labels,
 FusionGUI.FusionType fusionType,
 boolean displayDistances,
 long[] controlPointDistance,
 double alpha,
 boolean virtualGrid,
 int interpolation,
 net.imglib2.Interval boundingBox,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments,
 ExecutorService service)

defaultOverlapExpansion

public static int defaultOverlapExpansion(double maxDistance)

assembleViewsToUse

public static ArrayList<mpicbg.spim.data.sequence.ViewId> assembleViewsToUse(SpimData2 spimData,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse,
 boolean nonRigidAcrossTime)

assembleIPsForNonRigid

public static HashMap<mpicbg.spim.data.sequence.ViewId,Collection<CorrespondingIP>> assembleIPsForNonRigid(Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> viewInterestPoints,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse,
 List<String> labels)

createNonRigidVirtualImages

public static net.imglib2.util.Pair<ArrayList<net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>>,ArrayList<net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>>> createNonRigidVirtualImages(mpicbg.spim.data.generic.sequence.BasicImgLoader imgloader,
 Map<mpicbg.spim.data.sequence.ViewId,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> viewDescriptions,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse,
 Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.realtransform.AffineTransform3D> downsampledRegistrations,
 HashMap<mpicbg.spim.data.sequence.ViewId,ModelGrid> nonrigidGrids,
 net.imglib2.Interval bbDS,
 FusionGUI.FusionType fusionType,
 boolean displayDistances,
 int interpolation,
 Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments,
 int overlapExpansion)

transformViewNonRigidInterpolated

public static <T extends net.imglib2.type.numeric.RealType<T>>
net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> transformViewNonRigidInterpolated(net.imglib2.RandomAccessibleInterval<T> input,
 ModelGrid grid,
 mpicbg.models.AffineModel3D invertedModelOpener,
 net.imglib2.Interval boundingBox,
 float outsideValue,
 int interpolation)

transformViewNonRigid

public static <T extends net.imglib2.type.numeric.RealType<T>>
net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> transformViewNonRigid(net.imglib2.RandomAccessibleInterval<T> input,
 Collection<? extends NonrigidIP> ips,
 double alpha,
 mpicbg.models.AffineModel3D invertedModelOpener,
 net.imglib2.Interval boundingBox,
 float outsideValue,
 int interpolation)

visualizeDistancesViewNonRigidInterpolated

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> visualizeDistancesViewNonRigidInterpolated(net.imglib2.Interval input,
 ModelGrid grid,
 net.imglib2.realtransform.AffineTransform3D originalTransform,
 net.imglib2.Interval boundingBox,
 float outsideValue,
 int interpolation)

computeGrids

public static HashMap<mpicbg.spim.data.sequence.ViewId,ModelGrid> computeGrids(Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse,
 HashMap<? extends mpicbg.spim.data.sequence.ViewId,? extends Collection<? extends NonrigidIP>> uniquePoints,
 long[] controlPointDistance,
 double alpha,
 net.imglib2.Interval boundingBox,
 boolean virtual,
 ExecutorService service)

computeReferencePoints

public static net.imglib2.util.Pair<HashMap<mpicbg.spim.data.sequence.ViewId,ArrayList<SimpleReferenceIP>>,Double> computeReferencePoints(Collection<mpicbg.spim.data.sequence.ViewId> views,
 ArrayList<HashSet<CorrespondingIP>> uniqueIPs)

findUniqueInterestPoints

public static ArrayList<HashSet<CorrespondingIP>> findUniqueInterestPoints(Map<mpicbg.spim.data.sequence.ViewId,Collection<CorrespondingIP>> annotatedIps)

findUniqueInterestPoints

public static ArrayList<HashSet<CorrespondingIP>> findUniqueInterestPoints(Collection<CorrespondingIP> pairs)

copyIPs

public static ArrayList<CorrespondingIP> copyIPs(List<CorrespondingIP> in)

copyIPs

public static HashSet<CorrespondingIP> copyIPs(Set<CorrespondingIP> in)

transformUniqueIPs

public static ArrayList<HashSet<CorrespondingIP>> transformUniqueIPs(ArrayList<HashSet<CorrespondingIP>> uniqueIPs,
 Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.realtransform.AffineTransform3D> downsampledRegistrations)

transformCorrespondingIPs

public static double transformCorrespondingIPs(Collection<CorrespondingIP> aips,
 Map<mpicbg.spim.data.sequence.ViewId,net.imglib2.realtransform.AffineTransform3D> models)

assembleAllCorrespondingPoints

public static Collection<CorrespondingIP> assembleAllCorrespondingPoints(mpicbg.spim.data.sequence.ViewId viewId,
 InterestPoints ipList,
 Collection<? extends CorrespondingInterestPoints> cipList,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse,
 Map<? extends mpicbg.spim.data.sequence.ViewId,? extends ViewInterestPointLists> interestPointLists)

uniqueInterestPointCounts

public static int[] uniqueInterestPointCounts(List<HashSet<CorrespondingIP>> groups)

getIPL

protected static IPL getIPL(Collection<IPL> ipls,
 String label)