Package net.preibisch.mvrecon.process.interestpointregistration

Class TransformationTools

java.lang.Object

net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

public class TransformationTools
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	debugMissingInterestPoints	When true, prints individual warnings for each view missing interest points.
static NumberFormat	f
static int	maxPerViewTransformLog	Maximum number of per-view 'Transformation Models:' lines to print from printAndSummarizeTransformations(java.lang.Iterable<? extends mpicbg.spim.data.sequence.ViewId>, java.util.Map<? extends mpicbg.spim.data.sequence.ViewId, ? extends mpicbg.models.Tile>) per call before output is suppressed.

Constructor Summary

Constructors

Constructor	Description
TransformationTools()

Method Summary

Modifier and Type	Method	Description
static boolean	affineTransformsEqual(net.imglib2.realtransform.AffineTransform3D tA, net.imglib2.realtransform.AffineTransform3D tB)
static Collection<InterestPoint>	applyTransformation(Collection<InterestPoint> list, net.imglib2.realtransform.AffineTransform3D m)
static HashMap<String,Collection<InterestPoint>>	applyTransformation(HashMap<String,Collection<InterestPoint>> lists, net.imglib2.realtransform.AffineTransform3D m)
static net.imglib2.realtransform.AffineTransform3D	averageTransforms(Collection<? extends net.imglib2.realtransform.AffineGet> models)
static double[]	averageVectors(Collection<double[]> vectors)
static net.imglib2.util.Pair<double[],String>	computeAverageCalibration(Iterable<? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> group, mpicbg.spim.data.registration.ViewRegistrations vrs)
static net.imglib2.util.Pair<double[],String>	computeCalibration(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd, mpicbg.spim.data.registration.ViewRegistrations vrs)
static net.imglib2.realtransform.AffineTransform3D	computeMapBackModel(net.imglib2.Dimensions size, net.imglib2.realtransform.AffineTransform3D mapBackViewRegistration, mpicbg.models.AbstractModel<?> computedModel, mpicbg.models.Model<?> mapBackModel)
static double[][]	cubeFor(net.imglib2.RealInterval r)
static void	filterForOverlappingInterestPoints(Map<mpicbg.spim.data.sequence.ViewId,HashMap<String,Collection<InterestPoint>>> interestpoints, Collection<? extends Group<mpicbg.spim.data.sequence.ViewId>> groups, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.sequence.ViewDescription> viewDescriptions)
static void	filterForOverlappingInterestPoints(Map<mpicbg.spim.data.sequence.ViewId,HashMap<String,Collection<InterestPoint>>> interestpoints, Collection<? extends Group<mpicbg.spim.data.sequence.ViewId>> groups, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.sequence.ViewDescription> viewDescriptions, int numThreads)
static mpicbg.models.AffineModel3D	getAffineModel3D(Transform3D transform)
static net.imglib2.realtransform.AffineTransform3D	getAffineTransform(mpicbg.models.Affine3D<?> model)
static <V> Map<V,HashMap<String,Collection<InterestPoint>>>	getAllInterestPoints(Collection<? extends V> viewIds, Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<V,ViewInterestPointLists> interestpoints, Map<V,HashMap<String,Double>> labelMap, boolean transform)
static <V> Map<V,HashMap<String,Collection<InterestPoint>>>	getAllInterestPoints(Collection<? extends V> viewIds, Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<V,ViewInterestPointLists> interestpoints, Map<V,HashMap<String,Double>> labelMap, boolean transform, int numThreads)
static <V> Map<V,HashMap<String,Collection<InterestPoint>>>	getAllTransformedInterestPoints(Collection<? extends V> viewIds, Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<V,ViewInterestPointLists> interestpoints, Map<V,HashMap<String,Double>> labelMap)
static double	getAverageAnisotropyFactor(mpicbg.spim.data.sequence.SequenceDescription seq, Collection<? extends mpicbg.spim.data.sequence.ViewId> views)
static double	getAverageAnisotropyFactor(mpicbg.spim.data.SpimData spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> views)
static <V> Collection<InterestPoint>	getCorrespondingInterestPoints(V viewId, Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<V,ViewInterestPointLists> interestpoints, Map<V,String> labelMap, boolean transform)
static <V> HashMap<String,Collection<InterestPoint>>	getInterestPoints(V viewId, Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<V,ViewInterestPointLists> interestpoints, Map<V,HashMap<String,Double>> labelMap, boolean transform)
static <V> HashMap<String,Collection<InterestPoint>>	getInterestPoints(V viewId, Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<V,ViewInterestPointLists> interestpoints, Map<V,HashMap<String,Double>> labelMap, boolean transform, ConcurrentHashMap<String,ConcurrentLinkedQueue<V>> missingInterestPoints)
static Matrix4d	getMatrix4d(mpicbg.models.AffineModel3D model)
static Matrix4d	getMatrix4d(mpicbg.models.RigidModel3D model)
static mpicbg.models.AffineModel3D	getModel(net.imglib2.realtransform.AffineGet affine)
static mpicbg.models.RigidModel3D	getRigidModel3D(Transform3D transform)
static String	getRotationAxis(mpicbg.models.RigidModel3D model)	WARNING: This fails on older MACs, in this case remove: Check if Apple's out-dated Java 3D version 1.3 is installed in System/Library/Java/Extensions/ on your Mac.
static String	getScaling(mpicbg.models.Affine3D<?> affine)
static void	getScaling(mpicbg.models.Affine3D<?> affine, double[] scale)
static String	getScaling(net.imglib2.realtransform.AffineGet affine)
static void	getScaling(net.imglib2.realtransform.AffineGet affine, double[] scale)
static String	getScaling(Transform3D t)
static void	getScaling(Transform3D t, double[] scale)
static <V> net.imglib2.realtransform.AffineTransform3D	getTransform(V viewId, Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations)
static <M extends mpicbg.models.AbstractAffineModel3D<M>> Transform3D	getTransform3D(M model)
static Transform3D	getTransform3D(mpicbg.models.Affine3D<?> affine)
static Transform3D	getTransform3D(net.imglib2.realtransform.AffineGet affine)
static <V> Collection<InterestPoint>	getTransformedCorrespondingInterestPoints(V viewId, Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<V,ViewInterestPointLists> interestpoints, Map<V,String> labelMap)
static boolean	isApproximatelyIdentity(mpicbg.models.Affine3D<?> model, double eps)
static String	printAffine3D(mpicbg.models.Affine3D<?> model)
static String	printAffine3D(net.imglib2.realtransform.AffineGet model)
static void	printAndSummarizeTransformations(Iterable<? extends mpicbg.spim.data.sequence.ViewId> views, Map<? extends mpicbg.spim.data.sequence.ViewId,? extends mpicbg.models.Tile> map)	Print per-view transformation models (capped at maxPerViewTransformLog) followed by a one-line summary of identity vs non-identity counts.
static String	printRealInterval(net.imglib2.RealInterval interval)	get String representation of RealInterval TODO: PR to ImgLib2 (Util) ?
static void	reCenterViews(bdv.BigDataViewer viewer, Collection<mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> selectedViews, mpicbg.spim.data.registration.ViewRegistrations viewRegistrations)
static net.imglib2.util.Pair<double[],net.imglib2.realtransform.AffineTransform3D>	scaling(net.imglib2.Dimensions dim, net.imglib2.realtransform.AffineTransform3D transformationModel)
static <V> void	storeTransformation(mpicbg.spim.data.registration.ViewRegistration vr, V viewId, mpicbg.models.Tile<?> tile, net.imglib2.realtransform.AffineGet mapBackModel, String modelDescription)
static double[][]	unitCube()

Methods inherited from class java.lang.Object

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

Field Details

f

public static NumberFormat f

debugMissingInterestPoints

public static boolean debugMissingInterestPoints

When true, prints individual warnings for each view missing interest points. When false (default), prints a consolidated summary per label.

maxPerViewTransformLog

public static int maxPerViewTransformLog

Maximum number of per-view 'Transformation Models:' lines to print from printAndSummarizeTransformations(java.lang.Iterable<? extends mpicbg.spim.data.sequence.ViewId>, java.util.Map<? extends mpicbg.spim.data.sequence.ViewId, ? extends mpicbg.models.Tile>) per call before output is suppressed. Set to Integer.MAX_VALUE to print everything (legacy behavior). The identity-vs-non-identity summary is always emitted regardless of this threshold. The cap is per-call (per "Transformation Models:" block), so in TWO_ROUND global opt round 1 and round 2 each get their own budget.

Constructor Details

TransformationTools

public TransformationTools()

Method Details

reCenterViews

public static void reCenterViews(bdv.BigDataViewer viewer,
 Collection<mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> selectedViews,
 mpicbg.spim.data.registration.ViewRegistrations viewRegistrations)

scaling

public static net.imglib2.util.Pair<double[],net.imglib2.realtransform.AffineTransform3D> scaling(net.imglib2.Dimensions dim,
 net.imglib2.realtransform.AffineTransform3D transformationModel)

averageTransforms

public static net.imglib2.realtransform.AffineTransform3D averageTransforms(Collection<? extends net.imglib2.realtransform.AffineGet> models)

averageVectors

public static double[] averageVectors(Collection<double[]> vectors)

getRotationAxis

public static String getRotationAxis(mpicbg.models.RigidModel3D model)

WARNING: This fails on older MACs, in this case remove: Check if Apple's out-dated Java 3D version 1.3 is installed in System/Library/Java/Extensions/ on your Mac. Remove all Java 3D 1.3 related files including vecmath.jar (jar, jnilib), they are useless.

Parameters:

model - - the model

Returns:

- String description of rot. axis

getScaling

public static void getScaling(mpicbg.models.Affine3D<?> affine,
 double[] scale)

getScaling

public static void getScaling(net.imglib2.realtransform.AffineGet affine,
 double[] scale)

getScaling

public static String getScaling(mpicbg.models.Affine3D<?> affine)

getScaling

public static String getScaling(net.imglib2.realtransform.AffineGet affine)

getScaling

public static String getScaling(Transform3D t)

getScaling

public static void getScaling(Transform3D t,
 double[] scale)

computeAverageCalibration

public static net.imglib2.util.Pair<double[],String> computeAverageCalibration(Iterable<? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> group,
 mpicbg.spim.data.registration.ViewRegistrations vrs)

computeCalibration

public static net.imglib2.util.Pair<double[],String> computeCalibration(mpicbg.spim.data.generic.sequence.BasicViewDescription<?> vd,
 mpicbg.spim.data.registration.ViewRegistrations vrs)

getTransform3D

public static Transform3D getTransform3D(mpicbg.models.Affine3D<?> affine)

getTransform3D

public static Transform3D getTransform3D(net.imglib2.realtransform.AffineGet affine)

getTransform3D

public static <M extends mpicbg.models.AbstractAffineModel3D<M>>
Transform3D getTransform3D(M model)

getAffineModel3D

public static mpicbg.models.AffineModel3D getAffineModel3D(Transform3D transform)

getRigidModel3D

public static mpicbg.models.RigidModel3D getRigidModel3D(Transform3D transform)

getMatrix4d

public static Matrix4d getMatrix4d(mpicbg.models.AffineModel3D model)

getMatrix4d

public static Matrix4d getMatrix4d(mpicbg.models.RigidModel3D model)

printAffine3D

public static String printAffine3D(mpicbg.models.Affine3D<?> model)

printAffine3D

public static String printAffine3D(net.imglib2.realtransform.AffineGet model)

getModel

public static mpicbg.models.AffineModel3D getModel(net.imglib2.realtransform.AffineGet affine)

computeMapBackModel

public static net.imglib2.realtransform.AffineTransform3D computeMapBackModel(net.imglib2.Dimensions size,
 net.imglib2.realtransform.AffineTransform3D mapBackViewRegistration,
 mpicbg.models.AbstractModel<?> computedModel,
 mpicbg.models.Model<?> mapBackModel)

Parameters:

size - - size of view which is used to map back

mapBackViewRegistration - - the registration model of this view before computing the new registration

computedModel - - the new model

mapBackModel - - which model to use to map back (e.g. rigid, translation)

Returns:

the transformation to map back, pre-concatenate this to all views that are registered

filterForOverlappingInterestPoints

public static void filterForOverlappingInterestPoints(Map<mpicbg.spim.data.sequence.ViewId,HashMap<String,Collection<InterestPoint>>> interestpoints,
 Collection<? extends Group<mpicbg.spim.data.sequence.ViewId>> groups,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.sequence.ViewDescription> viewDescriptions)

filterForOverlappingInterestPoints

public static void filterForOverlappingInterestPoints(Map<mpicbg.spim.data.sequence.ViewId,HashMap<String,Collection<InterestPoint>>> interestpoints,
 Collection<? extends Group<mpicbg.spim.data.sequence.ViewId>> groups,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.sequence.ViewDescription> viewDescriptions,
 int numThreads)

getAllTransformedInterestPoints

public static <V>
Map<V,HashMap<String,Collection<InterestPoint>>> getAllTransformedInterestPoints(Collection<? extends V> viewIds,
 Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<V,ViewInterestPointLists> interestpoints,
 Map<V,HashMap<String,Double>> labelMap)

getAllInterestPoints

public static <V>
Map<V,HashMap<String,Collection<InterestPoint>>> getAllInterestPoints(Collection<? extends V> viewIds,
 Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<V,ViewInterestPointLists> interestpoints,
 Map<V,HashMap<String,Double>> labelMap,
 boolean transform)

getAllInterestPoints

public static <V>
Map<V,HashMap<String,Collection<InterestPoint>>> getAllInterestPoints(Collection<? extends V> viewIds,
 Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<V,ViewInterestPointLists> interestpoints,
 Map<V,HashMap<String,Double>> labelMap,
 boolean transform,
 int numThreads)

getInterestPoints

public static <V>
HashMap<String,Collection<InterestPoint>> getInterestPoints(V viewId,
 Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<V,ViewInterestPointLists> interestpoints,
 Map<V,HashMap<String,Double>> labelMap,
 boolean transform)

getInterestPoints

public static <V>
HashMap<String,Collection<InterestPoint>> getInterestPoints(V viewId,
 Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<V,ViewInterestPointLists> interestpoints,
 Map<V,HashMap<String,Double>> labelMap,
 boolean transform,
 ConcurrentHashMap<String,ConcurrentLinkedQueue<V>> missingInterestPoints)

getTransformedCorrespondingInterestPoints

public static <V> Collection<InterestPoint> getTransformedCorrespondingInterestPoints(V viewId,
 Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<V,ViewInterestPointLists> interestpoints,
 Map<V,String> labelMap)

getCorrespondingInterestPoints

public static <V> Collection<InterestPoint> getCorrespondingInterestPoints(V viewId,
 Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<V,ViewInterestPointLists> interestpoints,
 Map<V,String> labelMap,
 boolean transform)

getTransform

public static <V>
net.imglib2.realtransform.AffineTransform3D getTransform(V viewId,
 Map<V,mpicbg.spim.data.registration.ViewRegistration> registrations)

applyTransformation

public static HashMap<String,Collection<InterestPoint>> applyTransformation(HashMap<String,Collection<InterestPoint>> lists,
 net.imglib2.realtransform.AffineTransform3D m)

applyTransformation

public static Collection<InterestPoint> applyTransformation(Collection<InterestPoint> list,
 net.imglib2.realtransform.AffineTransform3D m)

storeTransformation

public static <V> void storeTransformation(mpicbg.spim.data.registration.ViewRegistration vr,
 V viewId,
 mpicbg.models.Tile<?> tile,
 net.imglib2.realtransform.AffineGet mapBackModel,
 String modelDescription)

getAffineTransform

public static net.imglib2.realtransform.AffineTransform3D getAffineTransform(mpicbg.models.Affine3D<?> model)

printAndSummarizeTransformations

public static void printAndSummarizeTransformations(Iterable<? extends mpicbg.spim.data.sequence.ViewId> views,
 Map<? extends mpicbg.spim.data.sequence.ViewId,? extends mpicbg.models.Tile> map)

Print per-view transformation models (capped at maxPerViewTransformLog) followed by a one-line summary of identity vs non-identity counts. Replaces the inlined print loop that GlobalOpt and GlobalOptIterative used to have.

Parameters:

views - ordered iterable of ViewIds (the print order)

map - mapping from ViewId to its solved Tile (raw Tile accepted to support both HashMap<ViewId, Tile<M>> and the raw-typed HashMap<ViewId, Tile> callers that exist in BBS)

isApproximatelyIdentity

public static boolean isApproximatelyIdentity(mpicbg.models.Affine3D<?> model,
 double eps)

Returns:

true iff every element of the affine 3x4 matrix is within eps of the 3D identity matrix (diag(1,1,1) with zero translation).

affineTransformsEqual

public static boolean affineTransformsEqual(net.imglib2.realtransform.AffineTransform3D tA,
 net.imglib2.realtransform.AffineTransform3D tB)

getAverageAnisotropyFactor

public static double getAverageAnisotropyFactor(mpicbg.spim.data.SpimData spimData,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> views)

getAverageAnisotropyFactor

public static double getAverageAnisotropyFactor(mpicbg.spim.data.sequence.SequenceDescription seq,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> views)

unitCube

public static double[][] unitCube()

cubeFor

public static double[][] cubeFor(net.imglib2.RealInterval r)

printRealInterval

public static String printRealInterval(net.imglib2.RealInterval interval)

get String representation of RealInterval TODO: PR to ImgLib2 (Util) ?

Parameters:

interval - the interval

Returns:

String representation