A B C D E F G H I K L M N O P Q R S T U V W X Y Z

A

a - Variable in class mpicbg.models.InterpolatedCoordinateTransform

a - Variable in class mpicbg.models.InterpolatedModel

a - Variable in class mpicbg.models.PolynomialTransform2D

holds two coefficients for each polynomial coefficient, including 1 initialized at 0 order, i.e. translation, the order follows that specified at http://bishopw.loni.ucla.edu/AIR5/2Dnonlinear.html#polylist two times

AbstractAffineModel1D<M extends AbstractAffineModel1D<M>> - Class in mpicbg.models

AbstractAffineModel1D() - Constructor for class mpicbg.models.AbstractAffineModel1D

AbstractAffineModel2D<M extends AbstractAffineModel2D<M>> - Class in mpicbg.models

AbstractAffineModel2D() - Constructor for class mpicbg.models.AbstractAffineModel2D

AbstractAffineModel3D<M extends AbstractAffineModel3D<M>> - Class in mpicbg.models

AbstractAffineModel3D() - Constructor for class mpicbg.models.AbstractAffineModel3D

AbstractInteractiveBlockFilter - Class in mpicbg.ij.integral

AbstractInteractiveBlockFilter() - Constructor for class mpicbg.ij.integral.AbstractInteractiveBlockFilter

AbstractInteractiveBlockFilter.PaintThread - Class in mpicbg.ij.integral

AbstractModel<M extends AbstractModel<M>> - Class in mpicbg.models

Abstract class for arbitrary transformation models to be applied to Points in n-dimensional space.

AbstractModel() - Constructor for class mpicbg.models.AbstractModel

AbstractMovingLeastSquaresTransform - Class in mpicbg.models

Smooth coordinate transformation interpolating between a set of control points that are maped exactly on top of each other using landmark based deformation by means of Moving Least Squares as described by \citet{SchaeferAl06}.

AbstractMovingLeastSquaresTransform() - Constructor for class mpicbg.models.AbstractMovingLeastSquaresTransform

AbstractTransformMapping<T> - Class in mpicbg.ij.stack

Abstract base class Mapping from an source into an target.

AbstractTransformMapping(T) - Constructor for class mpicbg.ij.stack.AbstractTransformMapping

AbstractTransformMapping.ByteInterpolator - Class in mpicbg.ij.stack

AbstractTransformMapping.FloatInterpolator - Class in mpicbg.ij.stack

AbstractTransformMapping.Interpolator - Class in mpicbg.ij.stack

AbstractTransformMapping.RGBInterpolator - Class in mpicbg.ij.stack

AbstractTransformMapping.ShortInterpolator - Class in mpicbg.ij.stack

add(E) - Method in class mpicbg.models.CoordinateTransformList

add(double) - Method in class mpicbg.models.ErrorStatistic

add(E) - Method in class mpicbg.models.InverseCoordinateTransformList

add(E) - Method in class mpicbg.models.InvertibleCoordinateTransformList

add(E) - Method in interface mpicbg.models.TransformList

add(double, double) - Method in class mpicbg.util.RealStreamPMCC

add(double) - Method in class mpicbg.util.RealSum

Add an element to the sum.

add(T) - Method in class mpicbg.util.RingBuffer

add(int, T) - Method in class mpicbg.util.RingBuffer

Does not check for index < 0 for efficiency reasons, so be sure not to pass negative indices.

add(T) - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

addConnectedTile(Tile<?>) - Method in class mpicbg.models.Tile

Add a Tile to the set of connected tiles.

addFields(GenericDialog, FloatArray2DMOPS.Param) - Static method in class mpicbg.ij.MOPS

addFields(GenericDialog, FloatArray2DSIFT.Param) - Static method in class mpicbg.ij.SIFT

addHandle(int, int) - Method in class mpicbg.ij.InteractiveMapping

addMatch(PointMatch) - Method in class mpicbg.models.Tile

Add one PointMatch.

addMatches(Collection<PointMatch>) - Method in class mpicbg.models.Tile

Add more PointMatches.

addMatchWeightedByDistance(PointMatch, double) - Method in class mpicbg.models.MovingLeastSquaresMesh

Add a PointMatch to all Tiles weighted by its distance to the corresponding vertex.

addPassiveVertex(Vertex) - Method in class mpicbg.models.SpringMesh

Add a passive vertex.

addSpring(Vertex, Spring) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addSpring(Vertex, double[]) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addSpring(Vertex, double[], double) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addSpring(Vertex, double) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addSpring(Vertex, double, double) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addTile(Tile<?>) - Method in class mpicbg.models.TileConfiguration

Add a single Tile.

addTiles(Collection<? extends Tile<?>>) - Method in class mpicbg.models.TileConfiguration

Add a Collection of Tiles.

addTiles(TileConfiguration) - Method in class mpicbg.models.TileConfiguration

Add all Tiles of another TileConfiguration.

addTriangle(ArrayList<PointMatch>) - Method in class mpicbg.models.TransformMesh

Add a triangle defined by 3 PointMatches that defines an AffineTransform2D.

addVertex(Vertex, double) - Method in class mpicbg.models.SpringMesh

Add a Vertex to the mesh.

addVertexWeightedByDistance(Vertex, double, double) - Method in class mpicbg.models.SpringMesh

Add a Vertex to the mesh.

addWeight(double) - Method in class mpicbg.models.Spring

Affine1D<T extends Affine1D<T>> - Interface in mpicbg.models

Affine2D<T extends Affine2D<T>> - Interface in mpicbg.models

Affine3D<T extends Affine3D<T>> - Interface in mpicbg.models

AffineModel1D - Class in mpicbg.models

AffineModel1D() - Constructor for class mpicbg.models.AffineModel1D

AffineModel2D - Class in mpicbg.models

2d-affine transformation models to be applied to points in 2d-space.

AffineModel2D() - Constructor for class mpicbg.models.AffineModel2D

AffineModel3D - Class in mpicbg.models

3d-affine transformation models to be applied to points in 3d-space.

AffineModel3D() - Constructor for class mpicbg.models.AffineModel3D

alpha - Variable in class mpicbg.models.AbstractMovingLeastSquaresTransform

alpha - Variable in class mpicbg.models.ElasticMovingLeastSquaresMesh

apply(double[]) - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

apply(double[]) - Method in class mpicbg.models.AffineModel1D

apply(double[]) - Method in class mpicbg.models.AffineModel2D

apply(double[]) - Method in class mpicbg.models.AffineModel3D

apply(double[]) - Method in class mpicbg.models.ConstantModel

apply(double[]) - Method in interface mpicbg.models.CoordinateTransform

Apply the CoordinateTransform to a location.

apply(double[]) - Method in class mpicbg.models.CoordinateTransformList

apply(double[]) - Method in class mpicbg.models.CoordinateTransformMap2D

apply(double[]) - Method in class mpicbg.models.HomographyModel2D

apply(double[]) - Method in class mpicbg.models.IdentityModel

apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

apply(double[]) - Method in class mpicbg.models.InterpolatedCoordinateTransform

apply(double[]) - Method in class mpicbg.models.InterpolatedModel

apply(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

apply(CoordinateTransform) - Method in class mpicbg.models.MovingLeastSquaresMesh

Apply an arbitrary coordinate transformation to each Tile's PointMatches.

apply(CoordinateTransform) - Method in class mpicbg.models.Point

Apply a CoordinateTransform to the Point.

apply(CoordinateTransform, double) - Method in class mpicbg.models.Point

Apply a CoordinateTransform to the Point by a given amount.

apply(CoordinateTransform, Iterable<P>) - Static method in class mpicbg.models.Point

Apply a CoordinateTransform to an Iterable collection of Points.

apply(CoordinateTransform) - Method in class mpicbg.models.PointMatch

Apply a CoordinateTransform to PointMatch.p1, update distance.

apply(CoordinateTransform, double) - Method in class mpicbg.models.PointMatch

Apply a CoordinateTransform to PointMatch.p1 with a given amount, update distance.

apply(Collection<? extends PointMatch>, CoordinateTransform) - Static method in class mpicbg.models.PointMatch

Apply a CoordinateTransform to PointMatch.p1 a Collection of PointMatches, update their distances.

apply(double[]) - Method in class mpicbg.models.PolynomialTransform2D

apply(double[]) - Method in class mpicbg.models.RigidModel2D

apply(double[]) - Method in class mpicbg.models.RigidModel3D

apply(double[]) - Method in class mpicbg.models.SimilarityModel2D

apply(double[]) - Method in class mpicbg.models.SimilarityModel3D

apply() - Method in class mpicbg.models.Tile

Apply the current AbstractModel to all local point coordinates.

apply(double) - Method in class mpicbg.models.Tile

Apply the current AbstractModel to all local point coordinates.

apply() - Method in class mpicbg.models.TileConfiguration

Apply the model of each Tile to all its PointMatches.

apply(ThreadPoolExecutor) - Method in class mpicbg.models.TileConfiguration

Apply the model of each Tile to all its PointMatches using a given ThreadPoolExecutor.

apply(double[]) - Method in class mpicbg.models.TransformMesh

apply(double[]) - Method in class mpicbg.models.TranslationModel1D

apply(double[]) - Method in class mpicbg.models.TranslationModel2D

apply(double[]) - Method in class mpicbg.models.TranslationModel3D

applyInPlace(double[]) - Method in class mpicbg.models.AffineModel1D

applyInPlace(double[]) - Method in class mpicbg.models.AffineModel2D

applyInPlace(double[]) - Method in class mpicbg.models.AffineModel3D

applyInPlace(double[]) - Method in class mpicbg.models.ConstantModel

applyInPlace(double[]) - Method in interface mpicbg.models.CoordinateTransform

Apply the CoordinateTransform to a location.

applyInPlace(double[]) - Method in class mpicbg.models.CoordinateTransformList

applyInPlace(double[]) - Method in class mpicbg.models.CoordinateTransformMap2D

applyInPlace(double[]) - Method in class mpicbg.models.HomographyModel2D

applyInPlace(double[]) - Method in class mpicbg.models.IdentityModel

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedCoordinateTransform

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedModel

applyInPlace(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

applyInPlace(double[]) - Method in class mpicbg.models.MovingLeastSquaresTransform

applyInPlace(double[]) - Method in class mpicbg.models.MovingLeastSquaresTransform2

applyInPlace(double[]) - Method in class mpicbg.models.PolynomialTransform2D

applyInPlace(double[]) - Method in class mpicbg.models.RigidModel2D

applyInPlace(double[]) - Method in class mpicbg.models.RigidModel3D

applyInPlace(double[]) - Method in class mpicbg.models.SimilarityModel2D

applyInPlace(double[]) - Method in class mpicbg.models.SimilarityModel3D

applyInPlace(double[]) - Method in class mpicbg.models.TransformMesh

applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel1D

applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel2D

applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel3D

applyInverse(double[]) - Method in class mpicbg.models.AffineModel1D

applyInverse(double[]) - Method in class mpicbg.models.AffineModel2D

applyInverse(double[]) - Method in class mpicbg.models.AffineModel3D

applyInverse(double[]) - Method in class mpicbg.models.HomographyModel2D

applyInverse(double[]) - Method in class mpicbg.models.IdentityModel

applyInverse(double[]) - Method in interface mpicbg.models.InverseCoordinateTransform

Apply the inverse of the model to a point location

applyInverse(double[]) - Method in class mpicbg.models.InverseCoordinateTransformList

applyInverse(double[]) - Method in class mpicbg.models.InverseCoordinateTransformMap2D

applyInverse(double[]) - Method in class mpicbg.models.InvertibleConstantModel

applyInverse(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

applyInverse(double[]) - Method in class mpicbg.models.InvertibleInterpolatedModel

applyInverse(InverseCoordinateTransform) - Method in class mpicbg.models.Point

Apply the inverse of an InvertibleCoordinateTransform to the Point.

applyInverse(InverseCoordinateTransform, Iterable<Point>) - Static method in class mpicbg.models.Point

Apply an InverseCoordinateTransform to an Iterable collection of Points.

applyInverse(double[]) - Method in class mpicbg.models.RigidModel2D

applyInverse(double[]) - Method in class mpicbg.models.RigidModel3D

applyInverse(double[]) - Method in class mpicbg.models.SimilarityModel2D

applyInverse(double[]) - Method in class mpicbg.models.SimilarityModel3D

applyInverse(double[]) - Method in class mpicbg.models.TransformMesh

applyInverse(double[]) - Method in class mpicbg.models.TranslationModel1D

applyInverse(double[]) - Method in class mpicbg.models.TranslationModel2D

applyInverse(double[]) - Method in class mpicbg.models.TranslationModel3D

applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel1D

applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel2D

applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel3D

applyInverseInPlace(double[]) - Method in class mpicbg.models.HomographyModel2D

applyInverseInPlace(double[]) - Method in class mpicbg.models.IdentityModel

applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

applyInverseInPlace(double[]) - Method in interface mpicbg.models.InverseCoordinateTransform

apply the inverse of the model to a point location

applyInverseInPlace(double[]) - Method in class mpicbg.models.InverseCoordinateTransformList

applyInverseInPlace(double[]) - Method in class mpicbg.models.InverseCoordinateTransformMap2D

applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleConstantModel

applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleInterpolatedModel

applyInverseInPlace(double[]) - Method in class mpicbg.models.RigidModel2D

applyInverseInPlace(double[]) - Method in class mpicbg.models.RigidModel3D

applyInverseInPlace(double[]) - Method in class mpicbg.models.SimilarityModel2D

applyInverseInPlace(double[]) - Method in class mpicbg.models.SimilarityModel3D

applyInverseInPlace(double[]) - Method in class mpicbg.models.TransformMesh

applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel1D

applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel2D

applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel3D

apv - Variable in class mpicbg.models.SpringMesh

argb(int, int, int) - Static method in class mpicbg.util.ColorStream

av - Variable in class mpicbg.models.TransformMesh

B

b - Variable in class mpicbg.models.InterpolatedCoordinateTransform

b - Variable in class mpicbg.models.InterpolatedModel

bc - Variable in class mpicbg.ij.integral.InteractivePMCC

betterThan(M) - Method in class mpicbg.models.AbstractModel

"Less than" operater to make Models comparable.

betterThan(M) - Method in interface mpicbg.models.Model

"Less than" operater to make Models comparable.

BlockMatching - Class in mpicbg.ij.blockmatching

Methods for establishing block-based correspondences for given sets of source Points.

blockMean(FloatProcessor, int, int, int, int) - Static method in class mpicbg.ij.blockmatching.BlockMatching

Estimate the mean intensity of a block.

BlockPMCC - Class in mpicbg.ij.integral

Pearson's Product-Moment Correlation Coefficient (PMCC) for overlapping blocks of pixels in two single channel images accelerated by integral images.

BlockPMCC(int, int, FloatProcessor, FloatProcessor) - Constructor for class mpicbg.ij.integral.BlockPMCC

Special case constructor for fpX and fpY having equal dimensions.

BlockPMCC(int, int, FloatProcessor, FloatProcessor, int, int) - Constructor for class mpicbg.ij.integral.BlockPMCC

Special case constructor for fpX and fpY having equal dimensions.

BlockPMCC(FloatProcessor, FloatProcessor) - Constructor for class mpicbg.ij.integral.BlockPMCC

Two loops because fpX and fpY can have different dimensions.

BlockPMCC(FloatProcessor, FloatProcessor, int, int) - Constructor for class mpicbg.ij.integral.BlockPMCC

Two loops because fpX and fpY can have different dimensions.

blockRadiusX - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

blockRadiusY - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

BlockStatistics - Class in mpicbg.ij.integral

Basic statistical properties of a block of pixels that can be accelerated using integral images.

BlockStatistics(FloatProcessor) - Constructor for class mpicbg.ij.integral.BlockStatistics

BlockStatistics.RowIntegrator - Class in mpicbg.ij.integral

Deprecated.

blockVariance(FloatProcessor, int, int, int, int, float) - Static method in class mpicbg.ij.blockmatching.BlockMatching

Estimate the intensity variance of a block.

Boundable - Interface in mpicbg.models

A CoordinateTransform that, for a given source interval in n-space, can estimate the target interval in n-space.

bounds(double[], double[]) - Method in class mpicbg.models.TransformMesh

Calculate bounding box

bs - Static variable in class mpicbg.util.ColorStream

buffer - Variable in class mpicbg.util.RingBuffer

bufferIndex - Variable in class mpicbg.util.RingBuffer.RingBufferListIterator

build() - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

build the scale octave

buildStub() - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

build only the gaussian image with 2 * INITIAL_SIGMA Use this method for the partial creation of an octaved scale space without creating each scale octave.

ByteInterpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.ByteInterpolator

C

calculate() - Method in class mpicbg.ij.integral.InteractivePMCC

calculate() - Method in class mpicbg.ij.integral.InteractiveSquarePMCC

calculateBoundingBox(ArrayList<PointMatch>, double[], double[]) - Static method in class mpicbg.ij.TransformMeshMapping

calculateBoundingBoxInverse(ArrayList<PointMatch>, double[], double[]) - Static method in class mpicbg.ij.TransformMeshMapping

calculateForce(Point, Point, double[]) - Method in class mpicbg.models.Spring

Estimate the force vector effective to p1 if this Spring would connect both Vertices.

calculateForceAndSpeed(ErrorStatistic) - Method in class mpicbg.models.SpringMesh

Deprecated.

Remains for legacy compatibility

calculateWeight() - Method in class mpicbg.models.PointMatch

calculateWeight() - Method in class mpicbg.models.Spring

canDoNumDimension(int) - Method in class mpicbg.models.SimilarityModel3D

canvas - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

clear() - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

clear the scale octave to save memory

clear() - Method in class mpicbg.models.CoordinateTransformList

clear() - Method in class mpicbg.models.ErrorStatistic

clear() - Method in class mpicbg.models.InverseCoordinateTransformList

clear() - Method in class mpicbg.models.InvertibleCoordinateTransformList

clear() - Method in class mpicbg.models.TileConfiguration

Cleanup.

clear() - Method in interface mpicbg.models.TransformList

clear() - Method in class mpicbg.util.RingBuffer

clone() - Method in class mpicbg.imagefeatures.FloatArray

clone() - Method in class mpicbg.imagefeatures.FloatArray2D

clone() - Method in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

clone() - Method in class mpicbg.models.Point

Clone this Point instance.

clone() - Method in class mpicbg.util.Matrix3x3

cloneSourcePoints(Collection<PointMatch>, Collection<Point>) - Static method in class mpicbg.models.PointMatch

cloneTargetPoints(Collection<PointMatch>, Collection<Point>) - Static method in class mpicbg.models.PointMatch

colorCircle(ColorProcessor) - Static method in class mpicbg.ij.util.Util

Draw a color circle into a ColorProcessor.

ColorStream - Class in mpicbg.util

Generate a stream of `random' saturated RGB colors with all colors being maximally distinct from each other.

ColorStream() - Constructor for class mpicbg.util.ColorStream

colorVector(double, double) - Static method in class mpicbg.ij.util.Util

Generate an integer encoded 24bit RGB color that encodes a 2d vector with amplitude being intensity and color being orientation.

compareTo(Feature) - Method in class mpicbg.imagefeatures.Feature

Comparator for making Features sortable.

concatenate(M) - Method in class mpicbg.models.AbstractAffineModel2D

concatenate(T) - Method in interface mpicbg.models.Affine1D

concatenate(T) - Method in interface mpicbg.models.Affine2D

concatenate(T) - Method in interface mpicbg.models.Affine3D

concatenate(AffineModel1D) - Method in class mpicbg.models.AffineModel1D

concatenate(TranslationModel2D) - Method in class mpicbg.models.AffineModel2D

concatenate(AffineModel2D) - Method in class mpicbg.models.AffineModel2D

concatenate(AffineModel3D) - Method in class mpicbg.models.AffineModel3D

concatenate(TranslationModel3D) - Method in class mpicbg.models.AffineModel3D

concatenate(ConstantAffineModel1D<A>) - Method in class mpicbg.models.ConstantAffineModel1D

concatenate(IdentityModel) - Method in class mpicbg.models.IdentityModel

concatenate(AffineModel1D) - Method in class mpicbg.models.InterpolatedAffineModel1D

concatenate(InterpolatedAffineModel1D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel1D

concatenate(AffineModel2D) - Method in class mpicbg.models.InterpolatedAffineModel2D

concatenate(InterpolatedAffineModel2D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel2D

concatenate(InterpolatedAffineModel3D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel3D

concatenate(RigidModel2D) - Method in class mpicbg.models.RigidModel2D

concatenate(RigidModel3D) - Method in class mpicbg.models.RigidModel3D

concatenate(TranslationModel3D) - Method in class mpicbg.models.RigidModel3D

concatenate(SimilarityModel2D) - Method in class mpicbg.models.SimilarityModel2D

concatenate(SimilarityModel3D) - Method in class mpicbg.models.SimilarityModel3D

concatenate(TranslationModel1D) - Method in class mpicbg.models.TranslationModel1D

concatenate(TranslationModel2D) - Method in class mpicbg.models.TranslationModel2D

concatenate(TranslationModel3D) - Method in class mpicbg.models.TranslationModel3D

concatenate(Matrix3x3) - Method in class mpicbg.util.Matrix3x3

Concatenate a matrix: this = this × m

connect(Tile<?>, Collection<PointMatch>) - Method in class mpicbg.models.Tile

Connect two tiles by a set of point correspondences

connectedTiles - Variable in class mpicbg.models.Tile

A set of Tiles that share point correpondences with this Tile.

ConstantAffineModel1D<A extends Model<A> & Affine1D<A> & InvertibleBoundable> - Class in mpicbg.models

1D affine specialization of ConstantModel.

ConstantAffineModel1D(A) - Constructor for class mpicbg.models.ConstantAffineModel1D

ConstantModel<A extends Model<A>,M extends ConstantModel<A,M>> - Class in mpicbg.models

Wraps another models but does not pass through calls to Model.fit(float[][], float[][], float[]).

ConstantModel(A) - Constructor for class mpicbg.models.ConstantModel

containsIndex(int) - Method in class mpicbg.util.RingBuffer

convolveSeparable(FloatProcessor, float[], float[]) - Static method in class mpicbg.ij.util.Filter

Convolve an image with a horizontal and a vertical kernel simple straightforward, not optimized---replace this with a trusted better version soon

convolveSeparable(FloatArray2D, float[], float[]) - Static method in class mpicbg.imagefeatures.Filter

Convolve an image with a horizontal and a vertical kernel simple straightforward, not optimized---replace this with a trusted better version soon

CoordinateTransform - Interface in mpicbg.models

CoordinateTransformList<E extends CoordinateTransform> - Class in mpicbg.models

TODO Think about if it should really implement Boundable.

CoordinateTransformList() - Constructor for class mpicbg.models.CoordinateTransformList

CoordinateTransformMap2D - Class in mpicbg.models

A CoordinateTransform that is saved as a LUT on integer coordinates.

CoordinateTransformMap2D(float[][]) - Constructor for class mpicbg.models.CoordinateTransformMap2D

CoordinateTransformMap2D(CoordinateTransform, int, int) - Constructor for class mpicbg.models.CoordinateTransformMap2D

CoordinateTransformMap2D(FileInputStream) - Constructor for class mpicbg.models.CoordinateTransformMap2D

CoordinateTransformMesh - Class in mpicbg.models

CoordinateTransformMesh(CoordinateTransform, int, double, double) - Constructor for class mpicbg.models.CoordinateTransformMesh

copy() - Method in class mpicbg.models.AffineModel1D

copy() - Method in class mpicbg.models.AffineModel2D

copy() - Method in class mpicbg.models.AffineModel3D

copy() - Method in class mpicbg.models.ConstantAffineModel1D

copy() - Method in class mpicbg.models.ConstantModel

copy() - Method in class mpicbg.models.HomographyModel2D

copy() - Method in class mpicbg.models.IdentityModel

copy() - Method in class mpicbg.models.InterpolatedAffineModel1D

copy() - Method in class mpicbg.models.InterpolatedAffineModel2D

copy() - Method in class mpicbg.models.InterpolatedAffineModel3D

copy() - Method in class mpicbg.models.InterpolatedModel

copy() - Method in class mpicbg.models.InvertibleConstantModel

copy() - Method in class mpicbg.models.InvertibleInterpolatedModel

copy() - Method in interface mpicbg.models.Model

Clone the model.

copy() - Method in class mpicbg.models.RigidModel2D

copy() - Method in class mpicbg.models.RigidModel3D

copy() - Method in class mpicbg.models.SimilarityModel2D

copy() - Method in class mpicbg.models.SimilarityModel3D

copy() - Method in class mpicbg.models.TranslationModel1D

copy() - Method in class mpicbg.models.TranslationModel2D

copy() - Method in class mpicbg.models.TranslationModel3D

cos - Variable in class mpicbg.models.RigidModel2D

cost - Variable in class mpicbg.models.AbstractModel

The cost depends on what kind of algorithm is running.

cost - Variable in class mpicbg.models.Tile

The transfer error of this Tile's AbstractModel as estimated from weighted square point correspondence displacement.

create(ImageProcessor) - Static method in class mpicbg.ij.integral.DifferenceOfMean

Factory method that decides on the type of ip which DifferenceOfMean constructor to call.

create(ImageProcessor) - Static method in class mpicbg.ij.integral.Mean

Factory method that decides on the type of ip which Mean constructor to call.

create(ImageProcessor) - Static method in class mpicbg.ij.integral.Scale

Factory method that decides on the type of ip which Scale constructor to call.

create(ImageProcessor) - Static method in class mpicbg.ij.integral.Tilt

Factory method that decides on the type of ip which Tilt constructor to call.

createAffine() - Method in class mpicbg.models.AbstractAffineModel2D

Create an AffineTransform representing the current parameters the model.

createAffine() - Method in interface mpicbg.models.Affine2D

Create an AffineTransform representing the current parameters the model.

createAffine() - Method in class mpicbg.models.AffineModel2D

createAffine() - Method in class mpicbg.models.IdentityModel

createAffine() - Method in class mpicbg.models.InterpolatedAffineModel2D

createAffine() - Method in class mpicbg.models.RigidModel2D

createAffine() - Method in class mpicbg.models.SimilarityModel2D

createAffine() - Method in class mpicbg.models.TranslationModel2D

createAffineModel1D() - Method in class mpicbg.models.ConstantAffineModel1D

createAffineModel1D() - Method in class mpicbg.models.InterpolatedAffineModel1D

createAffineModel2D() - Method in class mpicbg.models.InterpolatedAffineModel2D

createAffineModel3D() - Method in class mpicbg.models.InterpolatedAffineModel3D

createConvolveSeparable(FloatProcessor, float[], float[]) - Static method in class mpicbg.ij.util.Filter

Create a convolved image with a horizontal and a vertical kernel simple straightforward, not optimized---replace this with a trusted better version soon

createDownsampled(FloatProcessor, double, float, float) - Static method in class mpicbg.ij.util.Filter

Create a downsampled FloatProcessor.

createDownsampled(ImageProcessor, double, float, float) - Static method in class mpicbg.ij.util.Filter

Create a downsampled ImageProcessor.

createGaussianKernel(float) - Static method in class mpicbg.ij.util.Filter

Create a non-normalized 1d-Gaussian kernel of appropriate size.

createGaussianKernel(double, boolean) - Static method in class mpicbg.imagefeatures.Filter

Create a 1d-Gaussian kernel of appropriate size.

createGaussianKernel(float, boolean) - Static method in class mpicbg.imagefeatures.Filter

Create a 1d-Gaussian kernel of appropriate size.

createGaussianKernelOffset(float, float, float, boolean) - Static method in class mpicbg.imagefeatures.Filter

Create a normalized 2d gaussian impulse with appropriate size with its center slightly moved away from the middle.

createGaussianKernelOffset(double, double, double, boolean) - Static method in class mpicbg.imagefeatures.Filter

Create a normalized 2d gaussian impulse with appropriate size with its center slightly moved away from the middle.

createGradients(FloatProcessor) - Static method in class mpicbg.ij.util.Filter

createGradients(FloatArray2D) - Static method in class mpicbg.imagefeatures.Filter

createInverse() - Method in class mpicbg.models.AbstractAffineModel2D

createInverse() - Method in interface mpicbg.models.Affine1D

createInverse() - Method in interface mpicbg.models.Affine2D

createInverse() - Method in interface mpicbg.models.Affine3D

createInverse() - Method in class mpicbg.models.AffineModel1D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.AffineModel2D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.AffineModel3D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.ConstantAffineModel1D

createInverse() - Method in class mpicbg.models.HomographyModel2D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.IdentityModel

TODO Not yet tested

createInverse() - Method in class mpicbg.models.InterpolatedAffineModel1D

createInverse() - Method in class mpicbg.models.InterpolatedAffineModel2D

createInverse() - Method in class mpicbg.models.InterpolatedAffineModel3D

createInverse() - Method in class mpicbg.models.InvertibleConstantModel

createInverse() - Method in interface mpicbg.models.InvertibleCoordinateTransform

createInverse() - Method in class mpicbg.models.InvertibleCoordinateTransformList

createInverse() - Method in class mpicbg.models.InvertibleInterpolatedModel

createInverse() - Method in class mpicbg.models.RigidModel2D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.RigidModel3D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.SimilarityModel2D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.SimilarityModel3D

createInverse() - Method in class mpicbg.models.TransformMesh

TODO Not yet tested

createInverse() - Method in class mpicbg.models.TranslationModel1D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.TranslationModel2D

TODO Not yet tested

createInverse() - Method in class mpicbg.models.TranslationModel3D

TODO Not yet tested

createInverse(double, double, double, double, double, double, double, double, double) - Static method in class mpicbg.util.Matrix3x3

createInverse(float, float, float, float, float, float, float, float, float) - Static method in class mpicbg.util.Matrix3x3

createInverseAffine() - Method in class mpicbg.models.AbstractAffineModel2D

Create an AffineTransform representing the inverse of the current parameters of the model.

createInverseAffine() - Method in interface mpicbg.models.Affine2D

Create an AffineTransform representing the inverse of the current parameters of the model.

createInverseAffine() - Method in class mpicbg.models.AffineModel2D

createInverseAffine() - Method in class mpicbg.models.IdentityModel

createInverseAffine() - Method in class mpicbg.models.InterpolatedAffineModel2D

createInverseAffine() - Method in class mpicbg.models.RigidModel2D

createInverseAffine() - Method in class mpicbg.models.SimilarityModel2D

createInverseAffine() - Method in class mpicbg.models.TranslationModel2D

createMapping() - Method in class mpicbg.ij.InteractiveMapping

createMatches(List<Feature>, List<Feature>, float) - Static method in class mpicbg.imagefeatures.FloatArray2DMOPS

Identify corresponding features

createMatches(List<Feature>, List<Feature>, double, HashMap<Point, Feature>, HashMap<Point, Feature>) - Static method in class mpicbg.imagefeatures.FloatArray2DMOPS

Identify corresponding features.

createMatches(List<Feature>, List<Feature>, double, AbstractModel<?>, double, double) - Static method in class mpicbg.imagefeatures.FloatArray2DMOPS

identify corresponding features using spatial constraints

createMatches(List<Feature>, List<Feature>, float) - Static method in class mpicbg.imagefeatures.FloatArray2DSIFT

Identify corresponding features

createMatches(List<Feature>, List<Feature>, double, AbstractModel<?>, double, double) - Static method in class mpicbg.imagefeatures.FloatArray2DSIFT

identify corresponding features using spatial constraints

createNormalizedGaussianKernel(float) - Static method in class mpicbg.ij.util.Filter

Create a normalized 1d-Gaussian kernel of appropriate size.

createNormalizedShiftedGaussianKernel(float, float, float) - Static method in class mpicbg.ij.util.Filter

Create a non-normalized 2d-Gaussian impulse with appropriate size whose center is slightly shifted away from the middle.

createPoint(double[]) - Method in interface mpicbg.models.PointFactory

createPointMatch(Point, Point) - Method in interface mpicbg.models.PointMatchFactory

createPointMatch(Point, Point, double) - Method in interface mpicbg.models.PointMatchFactory

createSaturatedColor(float, float) - Static method in class mpicbg.ij.util.Util

Create a saturated color in a periodic interval

createShiftedGaussianKernel(float, float, float) - Static method in class mpicbg.ij.util.Filter

Create a non-normalized 2d-Gaussian impulse with appropriate size whose center is slightly shifted away from the middle.

creatingInverseNotSupportedException - Static variable in class mpicbg.models.InvertibleInterpolatedModel

D

damp - Variable in class mpicbg.models.SpringMesh

data - Variable in class mpicbg.imagefeatures.FloatArray

DCT - Class in mpicbg.util

Naive Implementation of the Discrete Cosine Transform Type I.

DCT() - Constructor for class mpicbg.util.DCT

dct(float[], float[]) - Static method in class mpicbg.util.DCT

Transfer data values into DCT coefficients.

decimalFormat - Static variable in class mpicbg.models.TileConfiguration

decimalFormatSymbols - Static variable in class mpicbg.models.TileConfiguration

defaultPointFactory - Static variable in class mpicbg.models.TransformMesh

defaultPointMatchFactory - Static variable in class mpicbg.models.TransformMesh

descriptor - Variable in class mpicbg.imagefeatures.Feature

descriptorDistance(Feature) - Method in class mpicbg.imagefeatures.Feature

det() - Method in class mpicbg.util.Matrix3x3

Calculate the determinant.

det(double[]) - Static method in class mpicbg.util.Matrix3x3

Calculate the determinant of a matrix given as a double[] (row after row).

det(float[]) - Static method in class mpicbg.util.Matrix3x3

Calculate the determinant of a matrix given as a float[] (row after row).

det(double, double, double, double, double, double, double, double, double) - Static method in class mpicbg.util.Matrix3x3

Calculate the determinant of a matrix given by values.

det(float, float, float, float, float, float, float, float, float) - Static method in class mpicbg.util.Matrix3x3

Calculate the determinant of a matrix given by values.

DifferenceOfMean - Class in mpicbg.ij.integral

DifferenceOfMean(ColorProcessor) - Constructor for class mpicbg.ij.integral.DifferenceOfMean

DifferenceOfMean(ByteProcessor) - Constructor for class mpicbg.ij.integral.DifferenceOfMean

DifferenceOfMean(ShortProcessor) - Constructor for class mpicbg.ij.integral.DifferenceOfMean

DifferenceOfMean(FloatProcessor) - Constructor for class mpicbg.ij.integral.DifferenceOfMean

differenceOfMean(int, int, int, int) - Method in class mpicbg.ij.integral.DifferenceOfMean

differenceOfMean(int, int) - Method in class mpicbg.ij.integral.DifferenceOfMean

direction - Variable in class mpicbg.models.Vertex

The current moving direction of the Vertex.

distance() - Method in class mpicbg.models.Point

Estimate the Euclidean distance of local and world coordinates.

distance(Point, Point) - Static method in class mpicbg.models.Point

Estimate the Euclidean distance of two Points in world space.

div(float, float) - Static method in class mpicbg.util.Util

An equivalent to div for float

DoubleIntegralImage - Class in mpicbg.ij.integral

A 2d integral image (summed-area table) that allows for fast computation of the sum of pixel values in a rectangular area.

DoubleIntegralImage(FloatProcessor) - Constructor for class mpicbg.ij.integral.DoubleIntegralImage

Construct a new DoubleIntegralImage from a FloatProcessor.

DoubleIntegralImage(ImageProcessor) - Constructor for class mpicbg.ij.integral.DoubleIntegralImage

Construct a new DoubleIntegralImage from an ImageProcessor.

downsample(FloatArray2D, FloatArray2D) - Static method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

Downsample src by simply using every second pixel into dst.

draw() - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

draw() - Method in class mpicbg.ij.integral.InteractiveDifferenceOfMean

draw() - Method in class mpicbg.ij.integral.InteractiveMean

draw() - Method in class mpicbg.ij.integral.InteractivePMCC

draw() - Method in class mpicbg.ij.integral.InteractiveScale

draw() - Method in class mpicbg.ij.integral.InteractiveStandardDeviation

draw() - Method in class mpicbg.ij.integral.InteractiveTilt

draw() - Method in class mpicbg.ij.integral.InteractiveVariance

drawEpsilonCoordinates(ImageProcessor, Color, int) - Static method in class mpicbg.ij.visualization.PointVis

drawFeaturePoints(ImageProcessor, Iterable<? extends Feature>, Color, int, Rectangle, double) - Static method in class mpicbg.ij.visualization.PointVis

drawFeaturePoints(ImageProcessor, Collection<? extends Feature>, Color, int) - Static method in class mpicbg.ij.visualization.PointVis

drawLocalPointMatchLines(ImageProcessor, Collection<? extends PointMatch>, Color, int, Rectangle, Rectangle, double, double) - Static method in class mpicbg.ij.visualization.PointVis

drawLocalPoints(ImageProcessor, Collection<? extends Point>, Color, int, Rectangle, double) - Static method in class mpicbg.ij.visualization.PointVis

drawLocalPoints(ImageProcessor, Collection<? extends Point>, Color, int) - Static method in class mpicbg.ij.visualization.PointVis

drawWorldPointMatchLines(ImageProcessor, Collection<? extends PointMatch>, Color, int, Rectangle, Rectangle, double, double) - Static method in class mpicbg.ij.visualization.PointVis

drawWorldPoints(ImageProcessor, Collection<? extends Point>, Color, int, Rectangle, double) - Static method in class mpicbg.ij.visualization.PointVis

drawWorldPoints(ImageProcessor, Collection<? extends Point>, Color, int) - Static method in class mpicbg.ij.visualization.PointVis

E

ElasticMovingLeastSquaresMesh<M extends AbstractModel<M>> - Class in mpicbg.models

ElasticMovingLeastSquaresMesh(Class<M>, int, int, double, double, double) - Constructor for class mpicbg.models.ElasticMovingLeastSquaresMesh

ElasticMovingLeastSquaresMesh(Class<M>, int, double, double, double) - Constructor for class mpicbg.models.ElasticMovingLeastSquaresMesh

elementIndex - Variable in class mpicbg.util.RingBuffer.RingBufferIterator

elementIndex - Variable in class mpicbg.util.RingBuffer.RingBufferListIterator

enhance(FloatArray2D, float) - Static method in class mpicbg.imagefeatures.Filter

In place enhance all values of a FloatArray to fill the given range.

equals(FloatArray2DSIFT.Param) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

equals(Object) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

error - Variable in class mpicbg.models.MovingLeastSquaresMesh

error - Variable in class mpicbg.models.TileConfiguration

ErrorStatistic - Class in mpicbg.models

ErrorStatistic(int) - Constructor for class mpicbg.models.ErrorStatistic

estimateBounds(double[], double[]) - Method in class mpicbg.models.AbstractAffineModel1D

estimateBounds(double[], double[]) - Method in class mpicbg.models.AbstractAffineModel2D

estimateBounds(double[], double[]) - Method in class mpicbg.models.AbstractAffineModel3D

estimateBounds(double[], double[]) - Method in interface mpicbg.models.Boundable

Estimate the bounds of an n-dimensional interval [min,max] with min and max being n-dimensional vectors.

estimateBounds(double[], double[]) - Method in class mpicbg.models.ConstantAffineModel1D

estimateBounds(double[], double[]) - Method in class mpicbg.models.CoordinateTransformList

Estimate the bounds of an n-dimensional interval [min,max] with min and max being n-dimensional vectors.

estimateBounds(double[], double[]) - Method in class mpicbg.models.HomographyModel2D

estimateBounds(double[], double[]) - Method in class mpicbg.models.IdentityModel

estimateBounds(double[], double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

estimateBounds(double[], double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

estimateBounds(double[], double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

estimateBounds(double[], double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

Estimate the bounds of an n-dimensional interval [min,max] with min and max being n-dimensional vectors.

estimateBounds(double[], double[]) - Method in class mpicbg.models.TranslationModel3D

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.AbstractAffineModel1D

TODO not yet tested!

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.AbstractAffineModel2D

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.AbstractAffineModel3D

TODO not yet tested!

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.ConstantAffineModel1D

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.HomographyModel2D

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.IdentityModel

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

estimateInverseBounds(double[], double[]) - Method in interface mpicbg.models.InverseBoundable

Estimate the bounds of an n-dimensional interval [min,max] with min and max being n-dimensional vectors.

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.InverseCoordinateTransformList

Estimate the bounds of an n-dimensional interval [min,max] with min and max being n-dimensional vectors.

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

Estimate the bounds of an n-dimensional interval [min,max] with min and max being n-dimensional vectors.

estimateInverseBounds(double[], double[]) - Method in class mpicbg.models.TranslationModel3D

expand(double) - Method in class mpicbg.util.RealSum

export(FileOutputStream) - Method in class mpicbg.models.CoordinateTransformMap2D

export(FileOutputStream) - Method in class mpicbg.models.InverseCoordinateTransformMap2D

extractFeatures(ImageProcessor, Collection<Feature>) - Method in class mpicbg.ij.FeatureTransform

Extract features from an ImageProcessor

extractFeatures(ImageProcessor) - Method in class mpicbg.ij.FeatureTransform

extractFeatures(ImageProcessor, Collection<Feature>) - Method in class mpicbg.ij.MOPS

Extract MOPS features from an ImageProcessor

extractFeatures(ImageProcessor, Collection<Feature>) - Method in class mpicbg.ij.SIFT

Extract SIFT features from an ImageProcessor

extractFeatures(Collection<Feature>) - Method in class mpicbg.imagefeatures.FloatArray2DFeatureTransform

Detect features.

extractFeatures() - Method in class mpicbg.imagefeatures.FloatArray2DFeatureTransform

extractFeatures(Collection<Feature>) - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

extractFeatures(Collection<Feature>) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

F

FastFlat - Class in mpicbg.ij.clahe

"Contrast Limited Adaptive Histogram Equalization" as described in BibTeX: @article{zuiderveld94, author = {Zuiderveld, Karel}, title = {Contrast limited adaptive histogram equalization}, book = {Graphics gems IV}, year = {1994}, isbn = {0-12-336155-9}, pages = {474--485}, publisher = {Academic Press Professional, Inc.}, address = {San Diego, CA, USA}, } This version calculates the CDF for adjacent blocks and interpolates the respective CDF for each pixel location in between.

FastFlat() - Constructor for class mpicbg.ij.clahe.FastFlat

fdBins - Variable in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

Feature descriptor orientation bins How many bins per local histogram

fdSize - Variable in class mpicbg.imagefeatures.FloatArray2DMOPS.Param

Width of the feature descriptor square in samples.

fdSize - Variable in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

Feature descriptor size.

Feature - Class in mpicbg.imagefeatures

Local image feature TODO Replace the Transformation descriptors by a InverseCoordinateTransform.

Feature() - Constructor for class mpicbg.imagefeatures.Feature

Dummy constructor for Serialization to work properly.

Feature(double, double, double[], float[]) - Constructor for class mpicbg.imagefeatures.Feature

featureSizeHistogram(List<Feature>, double, double, int) - Static method in class mpicbg.imagefeatures.FloatArray2DMOPS

get a histogram of feature sizes

featureSizeHistogram(Vector<Feature>, double, double, int) - Static method in class mpicbg.imagefeatures.FloatArray2DSIFT

get a histogram of feature sizes

FeatureTransform<T extends FloatArray2DFeatureTransform<?>> - Class in mpicbg.ij

FeatureTransform(T) - Constructor for class mpicbg.ij.FeatureTransform

Constructor

fillWithNaN(FloatProcessor) - Static method in class mpicbg.ij.util.Util

fillWithNoise(ByteProcessor) - Static method in class mpicbg.ij.util.Util

fillWithNoise(FloatProcessor) - Static method in class mpicbg.ij.util.Util

Filter - Class in mpicbg.ij.util

Filter() - Constructor for class mpicbg.ij.util.Filter

Filter - Class in mpicbg.imagefeatures

Filter() - Constructor for class mpicbg.imagefeatures.Filter

filter(Collection<P>, Collection<P>, double, int) - Method in class mpicbg.models.AbstractModel

Estimate the AbstractModel and filter potential outliers by robust iterative regression.

filter(Collection<P>, Collection<P>, double) - Method in class mpicbg.models.AbstractModel

Call AbstractModel.filter(Collection, Collection, double, int) with minNumInliers = Model.getMinNumMatches().

filter(Collection<P>, Collection<P>) - Method in class mpicbg.models.AbstractModel

Call AbstractModel.filter(Collection, Collection, double) with maxTrust = 4 and minNumInliers = Model.getMinNumMatches().

filter(Collection<P>, Collection<P>, double, int) - Method in interface mpicbg.models.Model

Estimate the Model and filter potential outliers by robust iterative regression.

filter(Collection<P>, Collection<P>, double) - Method in interface mpicbg.models.Model

Call Model.filter(Collection, Collection, double, int) with minNumInliers = Model.getMinNumMatches().

filter(Collection<P>, Collection<P>) - Method in interface mpicbg.models.Model

Call Model.filter(Collection, Collection, double) with maxTrust = 4 and minNumInliers = Model.getMinNumMatches().

filterRansac(List<P>, Collection<P>, int, double, double, int, double) - Method in class mpicbg.models.AbstractModel

Estimate a AbstractModel from a set with many outliers by first filtering the worst outliers with RANSAC \citet[{FischlerB81} and filter potential outliers by robust iterative regression.

filterRansac(List<P>, Collection<P>, int, double, double, int) - Method in class mpicbg.models.AbstractModel

Call AbstractModel.filterRansac(List, Collection, int, double, double, int, double) with maxTrust = 4.

filterRansac(List<P>, Collection<P>, int, double, double, double) - Method in class mpicbg.models.AbstractModel

Call AbstractModel.filterRansac(List, Collection, int, double, double, int, double) with minNumInliers = Model.getMinNumMatches().

filterRansac(List<P>, Collection<P>, int, double, double) - Method in class mpicbg.models.AbstractModel

Call AbstractModel.filterRansac(List, Collection, int, double, double, double) with maxTrust = 4.

filterRansac(List<P>, Collection<P>, int, double, double, int, double) - Method in interface mpicbg.models.Model

Estimate a Model from a set with many outliers by first filtering the worst outliers with RANSAC \citet[{FischlerB81} and filter potential outliers by robust iterative regression.

filterRansac(List<P>, Collection<P>, int, double, double, int) - Method in interface mpicbg.models.Model

Call Model.filterRansac(List, Collection, int, double, double, int, double) with maxTrust = 4.

filterRansac(List<P>, Collection<P>, int, double, double, double) - Method in interface mpicbg.models.Model

Call Model.filterRansac(List, Collection, int, double, double, int, double) with minNumInliers = Model.getMinNumMatches().

filterRansac(List<P>, Collection<P>, int, double, double) - Method in interface mpicbg.models.Model

Call Model.filterRansac(List, Collection, int, double, double, double) with maxTrust = 4.

findClosest(double[]) - Method in class mpicbg.models.MovingLeastSquaresMesh

What to use this method for: If you want to add a PointMatch between two Tiles t and o do the following.

findClosestSourcePoint(double[]) - Method in class mpicbg.models.TransformMesh

Find the closest source point to a given coordinate.

findClosestSourceVertex(double[]) - Method in class mpicbg.models.SpringMesh

Find the closest Vertex to a given coordinate in terms of its source coordinates.

findClosestTargetPoint(double[]) - Method in class mpicbg.models.TransformMesh

Find the closest target point to a given coordinate.

findClosestTargetVertex(double[]) - Method in class mpicbg.models.SpringMesh

Find the closest Vertex to a given coordinate in terms of its target coordinates.

findConnectedTile(PointMatch) - Method in class mpicbg.models.Tile

Try to find the tile which is connected by a particular PointMatch.

findMatches(FloatProcessor, FloatProcessor, FloatProcessor, FloatProcessor, Model<?>, Class<? extends AbstractAffineModel2D<?>>, float, float, float, float, float, int, float, Collection<PointMatch>) - Static method in class mpicbg.ij.blockmatching.BlockMatching

fit(float[][], float[][], float[]) - Method in class mpicbg.models.AbstractModel

Default fit implementation using Model.fit(Collection).

fit(double[][], double[][], double[]) - Method in class mpicbg.models.AbstractModel

Default fit implementation using Model.fit(Collection).

fit(double[][], double[][], double[]) - Method in class mpicbg.models.AffineModel1D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(float[][], float[][], float[]) - Method in class mpicbg.models.AffineModel1D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(Collection<P>) - Method in class mpicbg.models.AffineModel1D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(double[][], double[][], double[]) - Method in class mpicbg.models.AffineModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(float[][], float[][], float[]) - Method in class mpicbg.models.AffineModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(Collection<P>) - Method in class mpicbg.models.AffineModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(double[][], double[][], double[]) - Method in class mpicbg.models.AffineModel3D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(float[][], float[][], float[]) - Method in class mpicbg.models.AffineModel3D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(Collection<P>) - Method in class mpicbg.models.AffineModel3D

Closed form weighted least squares solution as described by \citet{SchaeferAl06}.

fit(Collection<P>) - Method in class mpicbg.models.ConstantModel

fit(Collection<P>) - Method in class mpicbg.models.HomographyModel2D

fit(double[][], double[][], double[]) - Method in class mpicbg.models.IdentityModel

fit(float[][], float[][], float[]) - Method in class mpicbg.models.IdentityModel

fit(Collection<P>) - Method in class mpicbg.models.IdentityModel

fit(Collection<P>) - Method in class mpicbg.models.InterpolatedAffineModel1D

fit(Collection<P>) - Method in class mpicbg.models.InterpolatedAffineModel2D

fit(Collection<P>) - Method in class mpicbg.models.InterpolatedAffineModel3D

fit(Collection<P>) - Method in class mpicbg.models.InterpolatedModel

fit(float[][], float[][], float[]) - Method in interface mpicbg.models.Model

Fit the Model to a set of data points minimizing the global transfer error.

fit(double[][], double[][], double[]) - Method in interface mpicbg.models.Model

Fit the Model to a set of data points minimizing the global transfer error.

fit(Collection<P>) - Method in interface mpicbg.models.Model

Fit the Model to a set of data points minimizing the global transfer error.

fit(double[][], double[][], double[]) - Method in class mpicbg.models.RigidModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06} and implemented by Johannes Schindelin.

fit(float[][], float[][], float[]) - Method in class mpicbg.models.RigidModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06} and implemented by Johannes Schindelin.

fit(Collection<P>) - Method in class mpicbg.models.RigidModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06} and implemented by Johannes Schindelin.

fit(Collection<P>) - Method in class mpicbg.models.RigidModel3D

fit(double[][], double[][], double[]) - Method in class mpicbg.models.SimilarityModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06} and implemented by Johannes Schindelin.

fit(float[][], float[][], float[]) - Method in class mpicbg.models.SimilarityModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06} and implemented by Johannes Schindelin.

fit(Collection<P>) - Method in class mpicbg.models.SimilarityModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06} and implemented by Johannes Schindelin.

fit(float[][], float[][], float[]) - Method in class mpicbg.models.SimilarityModel3D

fit(double[][], double[][], double[]) - Method in class mpicbg.models.SimilarityModel3D

fit(Collection<P>) - Method in class mpicbg.models.SimilarityModel3D

fit(double[][], double[][], double[]) - Method in class mpicbg.models.TranslationModel1D

fit(float[][], float[][], float[]) - Method in class mpicbg.models.TranslationModel1D

fit(Collection<P>) - Method in class mpicbg.models.TranslationModel1D

fit(double[][], double[][], double[]) - Method in class mpicbg.models.TranslationModel2D

fit(float[][], float[][], float[]) - Method in class mpicbg.models.TranslationModel2D

fit(Collection<P>) - Method in class mpicbg.models.TranslationModel2D

fit(Collection<P>) - Method in class mpicbg.models.TranslationModel3D

fitModel() - Method in class mpicbg.models.Tile

Update the transformation AbstractModel.

fixedTiles - Variable in class mpicbg.models.ElasticMovingLeastSquaresMesh

fixedTiles - Variable in class mpicbg.models.TileConfiguration

fixedVertices - Variable in class mpicbg.models.SpringMesh

fixTile(Tile<M>) - Method in class mpicbg.models.ElasticMovingLeastSquaresMesh

fixTile(Tile<?>) - Method in class mpicbg.models.TileConfiguration

Fix a single Tile.

flags - Variable in class mpicbg.util.RealSum

Flat - Class in mpicbg.ij.clahe

"Contrast Limited Adaptive Histogram Equalization" as described in BibTeX: @article{zuiderveld94, author = {Zuiderveld, Karel}, title = {Contrast limited adaptive histogram equalization}, book = {Graphics gems IV}, year = {1994}, isbn = {0-12-336155-9}, pages = {474--485}, publisher = {Academic Press Professional, Inc.}, address = {San Diego, CA, USA}, }

Flat() - Constructor for class mpicbg.ij.clahe.Flat

flip(Collection<PointMatch>, Collection<PointMatch>) - Static method in class mpicbg.models.PointMatch

Flip all PointMatches from matches symmetrically and fill flippedMatches with them, weights remain unchanged.

flip(Collection<PointMatch>) - Static method in class mpicbg.models.PointMatch

Flip symmetrically, weights remains unchanged.

FloatArray - Class in mpicbg.imagefeatures

Simple float array that stores all values in one linear array.

FloatArray() - Constructor for class mpicbg.imagefeatures.FloatArray

FloatArray2D - Class in mpicbg.imagefeatures

Simple 2d float array that stores all values in one linear array.

FloatArray2D(int, int) - Constructor for class mpicbg.imagefeatures.FloatArray2D

FloatArray2D(float[], int, int) - Constructor for class mpicbg.imagefeatures.FloatArray2D

FloatArray2DFeatureTransform<P> - Class in mpicbg.imagefeatures

FloatArray2DFeatureTransform(P) - Constructor for class mpicbg.imagefeatures.FloatArray2DFeatureTransform

Constructor

FloatArray2DMOPS - Class in mpicbg.imagefeatures

This implementation actually uses the DoG-detector as described by \cite{Lowe04} and extracts local intensity patches from coarser scales similar to what was described by \cite{BrownAl05} as Multi-Scale Oriented Patches.

FloatArray2DMOPS(FloatArray2DMOPS.Param) - Constructor for class mpicbg.imagefeatures.FloatArray2DMOPS

Constructor

FloatArray2DMOPS.Param - Class in mpicbg.imagefeatures

FloatArray2DScaleOctave - Class in mpicbg.imagefeatures

single octave of a discrete FloatArray2DScaleSpace This class is optimized for the Difference Of Gaussian detector used in David Lowe's SIFT-algorithm \citep{Loew04}.

FloatArray2DScaleOctave(FloatArray2D, int, float) - Constructor for class mpicbg.imagefeatures.FloatArray2DScaleOctave

Constructor

FloatArray2DScaleOctave(FloatArray2D, float[], float[], float[][]) - Constructor for class mpicbg.imagefeatures.FloatArray2DScaleOctave

Constructor faster initialisation with precomputed gaussian kernels

FloatArray2DScaleOctave.State - Enum in mpicbg.imagefeatures

FloatArray2DScaleOctaveDoGDetector - Class in mpicbg.imagefeatures

Difference Of Gaussian detector on top of a scale space octave as described by Lowe (2004).

FloatArray2DScaleOctaveDoGDetector() - Constructor for class mpicbg.imagefeatures.FloatArray2DScaleOctaveDoGDetector

Constructor

FloatArray2DSIFT - Class in mpicbg.imagefeatures

Scale Invariant Feature Transform as described by David Lowe \cite{Loew04}.

FloatArray2DSIFT(FloatArray2DSIFT.Param) - Constructor for class mpicbg.imagefeatures.FloatArray2DSIFT

Constructor

FloatArray2DSIFT.Param - Class in mpicbg.imagefeatures

floatArray2DToFloatProcessor(FloatArray2D, FloatProcessor) - Static method in class mpicbg.imagefeatures.ImageArrayConverter

FloatArrayToImagePlus(FloatArray2D, String, float, float) - Static method in class mpicbg.imagefeatures.ImageArrayConverter

FloatInterpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.FloatInterpolator

force - Variable in class mpicbg.models.SpringMesh

force - Variable in class mpicbg.models.Vertex

The resulting force amplitude applied to this Vertex.

forceAmplitude - Variable in class mpicbg.models.Vertex

fp - Variable in class mpicbg.ij.integral.BlockStatistics

fpOriginal - Variable in class mpicbg.ij.integral.NormalizeLocalContrast

fpOriginal - Variable in class mpicbg.ij.integral.RemoveOutliers

G

generateIndependentGroups(Set<Tile<?>>, int) - Static method in class mpicbg.models.TileUtil

Returns a lazy collection of arrays of Tile, where none of the tiles of one specific array are connected to any of the tiles in that same array.

get(int, int) - Method in class mpicbg.imagefeatures.FloatArray2D

get(int) - Method in class mpicbg.models.CoordinateTransformList

get(int) - Method in class mpicbg.models.InverseCoordinateTransformList

get(int) - Method in class mpicbg.models.InvertibleCoordinateTransformList

get(int) - Method in interface mpicbg.models.TransformList

get(int) - Method in class mpicbg.util.RingBuffer

Does not check for index < 0 for efficiency reasons, so be sure not to pass negative indices.

getA() - Method in class mpicbg.models.InterpolatedCoordinateTransform

getA() - Method in class mpicbg.models.InterpolatedModel

getAlpha() - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

getAV() - Method in class mpicbg.models.TransformMesh

getB() - Method in class mpicbg.models.InterpolatedCoordinateTransform

getB() - Method in class mpicbg.models.InterpolatedModel

getCandidates() - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctaveDoGDetector

getConnectedTiles() - Method in class mpicbg.models.Tile

getConnectedVertices() - Method in class mpicbg.models.Vertex

Get all Vertices that are connected to this Vertex by a spring.

getConnectingPointMatches(Tile<?>, Tile<?>) - Method in class mpicbg.models.TileConfiguration

Returns an ArrayList of PointMatch that connect the targetTile and the referenceTile.

getCost() - Method in class mpicbg.models.AbstractModel

getCost() - Method in interface mpicbg.models.Model

getCost() - Method in class mpicbg.models.Tile

getD() - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

getD(int) - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

getDirection() - Method in class mpicbg.models.Vertex

getDistance() - Method in class mpicbg.models.PointMatch

getDistance() - Method in class mpicbg.models.Tile

getDoubleSum(int, int) - Method in class mpicbg.ij.integral.DoubleIntegralImage

Get the sum of the area from (0, 0) (inclusively) to (x, y) (inclusively).

getDoubleSum(int, int, int, int) - Method in class mpicbg.ij.integral.DoubleIntegralImage

Get the sum of the area from (xMin, yMin) (exclusively) to (xMax, yMax) (inclusively).

getError() - Method in class mpicbg.models.MovingLeastSquaresMesh

getError() - Method in class mpicbg.models.TileConfiguration

getFastInstance() - Static method in class mpicbg.ij.clahe.Flat

getFeatureObjectSize() - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

Returns the size in bytes of a Feature object.

getFeatureObjectSize(int) - Static method in class mpicbg.imagefeatures.FloatArray2DMOPS

getFixedTiles() - Method in class mpicbg.models.TileConfiguration

getForce() - Method in class mpicbg.models.SpringMesh

getForce() - Method in class mpicbg.models.Vertex

getForces() - Method in class mpicbg.models.Vertex

getForceSum() - Method in class mpicbg.models.Vertex

getHeight() - Method in class mpicbg.ij.integral.DoubleIntegralImage

getHeight() - Method in interface mpicbg.ij.integral.IntegralImage

getHeight() - Method in class mpicbg.ij.integral.IntIntegralImage

getHeight() - Method in class mpicbg.ij.integral.LongIntegralImage

getHeight() - Method in class mpicbg.ij.integral.LongRGBIntegralImage

getHeight() - Method in class mpicbg.models.CoordinateTransformMap2D

getHeight() - Method in class mpicbg.models.InverseCoordinateTransformMap2D

getHeight() - Method in class mpicbg.models.TransformMesh

getInitialSigma() - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

getInitialSigma() - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

getInstance() - Static method in class mpicbg.ij.clahe.Flat

getIntSum(int, int) - Method in class mpicbg.ij.integral.IntIntegralImage

getIntSum(int, int, int, int) - Method in class mpicbg.ij.integral.IntIntegralImage

getL() - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

getL(int) - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

getL() - Method in class mpicbg.models.Point

getL1(int) - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

get the gradients of the corresponding gaussian image, generates it on demand, if not yet available.

getLambda() - Method in class mpicbg.models.InterpolatedCoordinateTransform

getLambda() - Method in class mpicbg.models.InterpolatedModel

getLength() - Method in class mpicbg.models.Spring

getList(List<E>) - Method in class mpicbg.models.CoordinateTransformList

getList(List<E>) - Method in class mpicbg.models.InverseCoordinateTransformList

getList(List<E>) - Method in class mpicbg.models.InvertibleCoordinateTransformList

getList(List<E>) - Method in interface mpicbg.models.TransformList

getLongSum(int, int) - Method in class mpicbg.ij.integral.LongIntegralImage

getLongSum(int, int, int, int) - Method in class mpicbg.ij.integral.LongIntegralImage

getMatches() - Method in class mpicbg.models.MovingLeastSquaresTransform

getMatches() - Method in class mpicbg.models.Tile

getMatrix(double[]) - Method in class mpicbg.models.AbstractAffineModel1D

getMatrix(double[]) - Method in class mpicbg.models.AbstractAffineModel3D

getMatrix(double[]) - Method in class mpicbg.models.AffineModel1D

getMatrix(double[]) - Method in class mpicbg.models.AffineModel3D

getMatrix(double[]) - Method in class mpicbg.models.RigidModel3D

getMatrix(double[]) - Method in class mpicbg.models.SimilarityModel3D

getMatrix(double[]) - Method in class mpicbg.models.TranslationModel1D

getMatrix(double[]) - Method in class mpicbg.models.TranslationModel3D

getMaxError() - Method in class mpicbg.models.TileConfiguration

getMaxOctaveSize() - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

getMaxOctaveSize() - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

getMeanX() - Method in class mpicbg.util.RealStreamPMCC

getMeanY() - Method in class mpicbg.util.RealStreamPMCC

getMedian() - Method in class mpicbg.models.ErrorStatistic

getMinError() - Method in class mpicbg.models.TileConfiguration

getMinNumMatches() - Method in class mpicbg.models.AffineModel1D

getMinNumMatches() - Method in class mpicbg.models.AffineModel2D

getMinNumMatches() - Method in class mpicbg.models.AffineModel3D

getMinNumMatches() - Method in class mpicbg.models.ConstantModel

getMinNumMatches() - Method in class mpicbg.models.HomographyModel2D

getMinNumMatches() - Method in class mpicbg.models.IdentityModel

getMinNumMatches() - Method in class mpicbg.models.InterpolatedModel

getMinNumMatches() - Method in interface mpicbg.models.Model

getMinNumMatches() - Method in class mpicbg.models.RigidModel2D

getMinNumMatches() - Method in class mpicbg.models.RigidModel3D

getMinNumMatches() - Method in class mpicbg.models.SimilarityModel2D

getMinNumMatches() - Method in class mpicbg.models.SimilarityModel3D

getMinNumMatches() - Method in class mpicbg.models.TranslationModel1D

getMinNumMatches() - Method in class mpicbg.models.TranslationModel2D

getMinNumMatches() - Method in class mpicbg.models.TranslationModel3D

getModel() - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

getModel() - Method in class mpicbg.models.ConstantModel

getModel() - Method in class mpicbg.models.Tile

getModelClass() - Method in class mpicbg.models.MovingLeastSquaresMesh

getN() - Method in class mpicbg.util.RealStreamPMCC

getOctave(int) - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

getOctave(int) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

getOctaves() - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

getOctaves() - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

getP1() - Method in class mpicbg.models.PointMatch

getP2() - Method in class mpicbg.models.PointMatch

getPMCC() - Method in class mpicbg.util.RealStreamPMCC

getScaledSum(int, int, int, int, float) - Method in class mpicbg.ij.integral.DoubleIntegralImage

getScaledSum(int, int, int, int, float) - Method in interface mpicbg.ij.integral.IntegralImage

getScaledSum(int, int, int, int, float) - Method in class mpicbg.ij.integral.IntIntegralImage

getScaledSum(int, int, int, int, float) - Method in class mpicbg.ij.integral.LongIntegralImage

getScaledSum(int, int, int, int, float) - Method in class mpicbg.ij.integral.LongRGBIntegralImage

getSpeed() - Method in class mpicbg.models.Vertex

getSpring(Vertex) - Method in class mpicbg.models.Vertex

Get the Spring that connects this Vertex to a given other Vertex if any.

getSprings() - Method in class mpicbg.models.Vertex

getSum(int, int, int, int) - Method in class mpicbg.ij.integral.DoubleIntegralImage

getSum(int, int, int, int) - Method in interface mpicbg.ij.integral.IntegralImage

getSum(int, int, int, int) - Method in class mpicbg.ij.integral.IntIntegralImage

getSum(int, int, int, int) - Method in class mpicbg.ij.integral.LongIntegralImage

getSum(int, int, int, int) - Method in class mpicbg.ij.integral.LongRGBIntegralImage

getSum() - Method in class mpicbg.util.RealSum

Get the current sum by summing up all intermediate sums.

getTargetProcessor() - Method in class mpicbg.ij.integral.BlockPMCC

getTiles() - Method in class mpicbg.models.TileConfiguration

getTransform() - Method in interface mpicbg.ij.InverseMapping

getTransform() - Method in class mpicbg.ij.InverseTransformMapping

getTransform() - Method in class mpicbg.ij.InvertibleTransformMapping

getTransform() - Method in interface mpicbg.ij.Mapping

getTransform() - Method in class mpicbg.ij.stack.AbstractTransformMapping

getTransform() - Method in interface mpicbg.ij.stack.Mapping

getTransform() - Method in class mpicbg.ij.TransformMapping

getTranslation() - Method in class mpicbg.models.TranslationModel1D

getTranslation() - Method in class mpicbg.models.TranslationModel2D

getTranslation() - Method in class mpicbg.models.TranslationModel3D

getVA() - Method in class mpicbg.models.TransformMesh

getVarX() - Method in class mpicbg.util.RealStreamPMCC

getVarY() - Method in class mpicbg.util.RealStreamPMCC

getVerticeModelMap() - Method in class mpicbg.models.MovingLeastSquaresMesh

getVertices() - Method in class mpicbg.models.MovingLeastSquaresMesh

getVertices() - Method in class mpicbg.models.SpringMesh

getW() - Method in class mpicbg.models.Point

getWeight() - Method in class mpicbg.models.PointMatch

getWeight() - Method in class mpicbg.models.Spring

getWeights() - Method in class mpicbg.models.PointMatch

getWeights() - Method in class mpicbg.models.Spring

getWideSlope(int) - Method in class mpicbg.models.ErrorStatistic

getWidth() - Method in class mpicbg.ij.integral.DoubleIntegralImage

getWidth() - Method in interface mpicbg.ij.integral.IntegralImage

getWidth() - Method in class mpicbg.ij.integral.IntIntegralImage

getWidth() - Method in class mpicbg.ij.integral.LongIntegralImage

getWidth() - Method in class mpicbg.ij.integral.LongRGBIntegralImage

getWidth() - Method in class mpicbg.models.CoordinateTransformMap2D

getWidth() - Method in class mpicbg.models.InverseCoordinateTransformMap2D

getWidth() - Method in class mpicbg.models.TransformMesh

goldenRatio - Static variable in class mpicbg.util.ColorStream

gs - Static variable in class mpicbg.util.ColorStream

H

handles - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

handles - Variable in class mpicbg.ij.InteractiveMapping

hasNext() - Method in class mpicbg.util.RingBuffer.RingBufferIterator

hasNext() - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

hasPrevious() - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

height - Variable in class mpicbg.imagefeatures.FloatArray2D

height - Variable in class mpicbg.imagefeatures.FloatArray2DScaleOctave

height - Variable in class mpicbg.models.CoordinateTransformMap2D

height - Variable in class mpicbg.models.InverseCoordinateTransformMap2D

height - Variable in class mpicbg.models.TransformMesh

HomographyModel2D - Class in mpicbg.models

2d-homography AbstractModel to be applied to points in 2d-space.

HomographyModel2D() - Constructor for class mpicbg.models.HomographyModel2D

hooks - Variable in class mpicbg.ij.InteractiveMapping

I

i - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator

Deprecated.

i00 - Variable in class mpicbg.models.AffineModel1D

i00 - Variable in class mpicbg.models.AffineModel2D

i00 - Variable in class mpicbg.models.AffineModel3D

i00 - Variable in class mpicbg.models.HomographyModel2D

i00 - Variable in class mpicbg.models.RigidModel3D

i00 - Variable in class mpicbg.models.SimilarityModel3D

i01 - Variable in class mpicbg.models.AffineModel1D

i01 - Variable in class mpicbg.models.AffineModel2D

i01 - Variable in class mpicbg.models.AffineModel3D

i01 - Variable in class mpicbg.models.HomographyModel2D

i01 - Variable in class mpicbg.models.RigidModel3D

i01 - Variable in class mpicbg.models.SimilarityModel3D

i02 - Variable in class mpicbg.models.AffineModel2D

i02 - Variable in class mpicbg.models.AffineModel3D

i02 - Variable in class mpicbg.models.HomographyModel2D

i02 - Variable in class mpicbg.models.RigidModel3D

i02 - Variable in class mpicbg.models.SimilarityModel3D

i03 - Variable in class mpicbg.models.AffineModel3D

i03 - Variable in class mpicbg.models.RigidModel3D

i03 - Variable in class mpicbg.models.SimilarityModel3D

i10 - Variable in class mpicbg.models.AffineModel2D

i10 - Variable in class mpicbg.models.AffineModel3D

i10 - Variable in class mpicbg.models.HomographyModel2D

i10 - Variable in class mpicbg.models.RigidModel3D

i10 - Variable in class mpicbg.models.SimilarityModel3D

i11 - Variable in class mpicbg.models.AffineModel2D

i11 - Variable in class mpicbg.models.AffineModel3D

i11 - Variable in class mpicbg.models.HomographyModel2D

i11 - Variable in class mpicbg.models.RigidModel3D

i11 - Variable in class mpicbg.models.SimilarityModel3D

i12 - Variable in class mpicbg.models.AffineModel2D

i12 - Variable in class mpicbg.models.AffineModel3D

i12 - Variable in class mpicbg.models.HomographyModel2D

i12 - Variable in class mpicbg.models.RigidModel3D

i12 - Variable in class mpicbg.models.SimilarityModel3D

i13 - Variable in class mpicbg.models.AffineModel3D

i13 - Variable in class mpicbg.models.RigidModel3D

i13 - Variable in class mpicbg.models.SimilarityModel3D

i20 - Variable in class mpicbg.models.AffineModel3D

i20 - Variable in class mpicbg.models.HomographyModel2D

i20 - Variable in class mpicbg.models.RigidModel3D

i20 - Variable in class mpicbg.models.SimilarityModel3D

i21 - Variable in class mpicbg.models.AffineModel3D

i21 - Variable in class mpicbg.models.HomographyModel2D

i21 - Variable in class mpicbg.models.RigidModel3D

i21 - Variable in class mpicbg.models.SimilarityModel3D

i22 - Variable in class mpicbg.models.AffineModel3D

i22 - Variable in class mpicbg.models.HomographyModel2D

i22 - Variable in class mpicbg.models.RigidModel3D

i22 - Variable in class mpicbg.models.SimilarityModel3D

i23 - Variable in class mpicbg.models.AffineModel3D

i23 - Variable in class mpicbg.models.RigidModel3D

i23 - Variable in class mpicbg.models.SimilarityModel3D

icp(List<Point>, List<Point>) - Method in class mpicbg.models.AbstractModel

Estimate the best model in terms of the Iterative Closest Point Algorithm \cite{Zhang94} for matching two point clouds into each other.

icp(List<Point>, List<Point>) - Method in interface mpicbg.models.Model

Estimate the best model in terms of the Iterative Closest Point Algorithm \cite{Zhang94} for matching two point clouds into each other.

idct(float[], float, float) - Static method in class mpicbg.util.DCT

Reconstruct a sample from DCT coefficients.

idct(float[], float[]) - Static method in class mpicbg.util.DCT

Reconstruct data values from DCT coefficients.

identifyConnectedGraphs(Collection<? extends Tile<?>>) - Static method in class mpicbg.models.Tile

Identify the set of connected graphs that contains all given tiles.

IdentityModel - Class in mpicbg.models

nd-identity AbstractModel.

IdentityModel() - Constructor for class mpicbg.models.IdentityModel

ij - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

IllDefinedDataPointsException - Exception in mpicbg.models

Signalizes that there were not enough data points available to estimate the AbstractModel.

IllDefinedDataPointsException() - Constructor for exception mpicbg.models.IllDefinedDataPointsException

IllDefinedDataPointsException(String) - Constructor for exception mpicbg.models.IllDefinedDataPointsException

IllDefinedDataPointsException(Throwable) - Constructor for exception mpicbg.models.IllDefinedDataPointsException

IllDefinedDataPointsException(String, Throwable) - Constructor for exception mpicbg.models.IllDefinedDataPointsException

illegalStateException - Static variable in class mpicbg.util.RingBuffer

illustrateBestRigidSVG() - Method in class mpicbg.models.TransformMesh

Create an SVG path that illustrates the best regid approximation of the mesh as a rotated square.

illustrateMatches(Collection<PointMatch>) - Static method in class mpicbg.ij.blockmatching.BlockMatching

Create a Shape that illustrates a Collection of PointMatches.

illustrateMesh() - Method in class mpicbg.models.SpringMesh

Create a Shape that illustrates the mesh.

illustrateMesh() - Method in class mpicbg.models.TransformMesh

Create a Shape that illustrates the mesh.

illustrateMeshSVG() - Method in class mpicbg.models.TransformMesh

Create an SVG path that illustrates the mesh.

illustratePointMatchDisplacements() - Method in class mpicbg.models.ElasticMovingLeastSquaresMesh

Create a Shape that illustrates the displacements of PointMatches.

illustratePointMatches() - Method in class mpicbg.models.ElasticMovingLeastSquaresMesh

Create a Shape that illustrates the PointMatches.

illustrateSprings() - Method in class mpicbg.models.SpringMesh

Create a Shape that illustrates the Springs.

illustrateSprings(ColorProcessor, double, double) - Method in class mpicbg.models.SpringMesh

Paint all Springs into a ColorProcessor.

illustrateSprings(ColorProcessor, double, double, double, double) - Method in class mpicbg.models.SpringMesh

Paint all Springs into a ColorProcessor.

illustrateTriangle(AffineModel2D, GeneralPath) - Method in class mpicbg.models.TransformMesh

ImageArrayConverter - Class in mpicbg.imagefeatures

ImageArrayConverter() - Constructor for class mpicbg.imagefeatures.ImageArrayConverter

imageClosed(ImagePlus) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

imageClosed(ImagePlus) - Method in class mpicbg.ij.InteractiveMapping

imageOpened(ImagePlus) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

imageOpened(ImagePlus) - Method in class mpicbg.ij.InteractiveMapping

imageProcessorToFloatArray2D(ImageProcessor, FloatArray2D) - Static method in class mpicbg.imagefeatures.ImageArrayConverter

imageProcessorToFloatArray2DCropAndNormalize(ImageProcessor, FloatArray2D) - Static method in class mpicbg.imagefeatures.ImageArrayConverter

Convert an arbitrary ImageProcessor into a FloatArray2D mapping min and max into [0.0,1.0] cropping larger and smaller values.

imageUpdated(ImagePlus) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

imageUpdated(ImagePlus) - Method in class mpicbg.ij.InteractiveMapping

imp - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

imp - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

imp - Variable in class mpicbg.ij.InteractiveMapping

imp - Variable in class mpicbg.ij.MappingThread

imp - Variable in class mpicbg.ij.PaintInvertibleCoordinateTransformThread

index - Variable in class mpicbg.util.RingBuffer.RingBufferIterator

indexOutOfBounds(int) - Method in class mpicbg.util.RingBuffer

indexOutOfBoundsException - Static variable in class mpicbg.util.RingBuffer

init() - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

init() - Method in class mpicbg.ij.integral.InteractiveDifferenceOfMean

init() - Method in class mpicbg.ij.integral.InteractiveMean

init() - Method in class mpicbg.ij.integral.InteractivePMCC

init() - Method in class mpicbg.ij.integral.InteractiveScale

init() - Method in class mpicbg.ij.integral.InteractiveStandardDeviation

init() - Method in class mpicbg.ij.integral.InteractiveTilt

init() - Method in class mpicbg.ij.integral.InteractiveVariance

init() - Method in class mpicbg.ij.InteractiveMapping

init(FloatArray2D) - Method in class mpicbg.imagefeatures.FloatArray2DFeatureTransform

Initialize the feature transform.

init(FloatArray2D) - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

initialize the scale space as a scale pyramid having octave stubs only

init(FloatArray2D) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

initialize the scale space as a scale pyramid having octave stubs only

init(CoordinateTransform) - Method in class mpicbg.models.SpringMesh

TODO Not yet tested

init(CoordinateTransform) - Method in class mpicbg.models.TransformMesh

Initialize the mesh with a CoordinateTransform.

initialSigma - Variable in class mpicbg.imagefeatures.FloatArray2DMOPS.Param

initialSigma - Variable in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

Initial sigma of each Scale Octave

IntegralImage - Interface in mpicbg.ij.integral

A 2d integral image (summed-area table) as described by Crow (1984).

integrateColumns(int, int, double[], double[]) - Static method in class mpicbg.ij.integral.BlockStatistics

integrateRows(int, int, double[], double[]) - Method in class mpicbg.ij.integral.BlockStatistics

integrateRowsParallel(int, int, int, int, double[], double[]) - Method in class mpicbg.ij.integral.BlockStatistics

Deprecated.

InteractiveDifferenceOfMean - Class in mpicbg.ij.integral

InteractiveDifferenceOfMean() - Constructor for class mpicbg.ij.integral.InteractiveDifferenceOfMean

InteractiveInvertibleCoordinateTransform<M extends Model<M> & InvertibleCoordinateTransform> - Class in mpicbg.ij

An interactive parent class for point based image deformation.

InteractiveInvertibleCoordinateTransform() - Constructor for class mpicbg.ij.InteractiveInvertibleCoordinateTransform

InteractiveInvertibleCoordinateTransform.Tuple - Class in mpicbg.ij

InteractiveMapping - Class in mpicbg.ij

An interactive parent class for point based image deformation.

InteractiveMapping() - Constructor for class mpicbg.ij.InteractiveMapping

InteractiveMean - Class in mpicbg.ij.integral

InteractiveMean() - Constructor for class mpicbg.ij.integral.InteractiveMean

InteractivePMCC - Class in mpicbg.ij.integral

InteractivePMCC() - Constructor for class mpicbg.ij.integral.InteractivePMCC

InteractiveScale - Class in mpicbg.ij.integral

InteractiveScale() - Constructor for class mpicbg.ij.integral.InteractiveScale

InteractiveSquarePMCC - Class in mpicbg.ij.integral

InteractiveSquarePMCC() - Constructor for class mpicbg.ij.integral.InteractiveSquarePMCC

InteractiveStandardDeviation - Class in mpicbg.ij.integral

InteractiveStandardDeviation() - Constructor for class mpicbg.ij.integral.InteractiveStandardDeviation

InteractiveTilt - Class in mpicbg.ij.integral

Fake the tilt-lens effect as used for 'Smallgantics' pictures by applying gradually increasing smooth from a 'focal line'.

InteractiveTilt() - Constructor for class mpicbg.ij.integral.InteractiveTilt

InteractiveVariance - Class in mpicbg.ij.integral

InteractiveVariance() - Constructor for class mpicbg.ij.integral.InteractiveVariance

interpolate - Static variable in class mpicbg.ij.InteractiveMapping

interpolate - Variable in class mpicbg.ij.MappingThread

interpolate(int, int, double) - Method in class mpicbg.ij.stack.AbstractTransformMapping.ByteInterpolator

interpolate(int, int, double) - Method in class mpicbg.ij.stack.AbstractTransformMapping.FloatInterpolator

interpolate(int, int, double) - Method in class mpicbg.ij.stack.AbstractTransformMapping.Interpolator

interpolate(float, float, float) - Static method in class mpicbg.ij.stack.AbstractTransformMapping.Interpolator

interpolate(double, double, double) - Static method in class mpicbg.ij.stack.AbstractTransformMapping.Interpolator

interpolate(int, int, double) - Method in class mpicbg.ij.stack.AbstractTransformMapping.RGBInterpolator

interpolate(int, int, double) - Method in class mpicbg.ij.stack.AbstractTransformMapping.ShortInterpolator

interpolate() - Method in class mpicbg.models.InterpolatedAffineModel1D

interpolate() - Method in class mpicbg.models.InterpolatedAffineModel2D

interpolate() - Method in class mpicbg.models.InterpolatedAffineModel3D

interpolate(double[], int, int, double, double) - Static method in class mpicbg.util.ColorStream

InterpolatedAffineModel1D<A extends Model<A> & Affine1D<A>,B extends Model<B> & Affine1D<B>> - Class in mpicbg.models

1D affine specialization of InterpolatedModel.

InterpolatedAffineModel1D(A, B, double) - Constructor for class mpicbg.models.InterpolatedAffineModel1D

InterpolatedAffineModel2D<A extends Model<A> & Affine2D<A>,B extends Model<B> & Affine2D<B>> - Class in mpicbg.models

2D affine specialization of InterpolatedModel.

InterpolatedAffineModel2D(A, B, double) - Constructor for class mpicbg.models.InterpolatedAffineModel2D

InterpolatedAffineModel3D<A extends Model<A> & Affine3D<A>,B extends Model<B> & Affine3D<B>> - Class in mpicbg.models

3D affine specialization of InterpolatedModel.

InterpolatedAffineModel3D(A, B, double) - Constructor for class mpicbg.models.InterpolatedAffineModel3D

InterpolatedCoordinateTransform<A extends CoordinateTransform,B extends CoordinateTransform> - Class in mpicbg.models

Linearly interpolates between two independent CoordinateTransforms.

InterpolatedCoordinateTransform(A, B, double) - Constructor for class mpicbg.models.InterpolatedCoordinateTransform

InterpolatedModel<A extends Model<A>,B extends Model<B>,M extends InterpolatedModel<A,B,M>> - Class in mpicbg.models

Linearly interpolates between two independent models.

InterpolatedModel(A, B, double) - Constructor for class mpicbg.models.InterpolatedModel

Interpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.Interpolator

IntIntegralImage - Class in mpicbg.ij.integral

A 2d integral image (summed-area table) that allows for fast computation of the sum of pixel values in a rectangular area.

IntIntegralImage(ImageProcessor) - Constructor for class mpicbg.ij.integral.IntIntegralImage

InverseBoundable - Interface in mpicbg.models

An InverseCoordinateTransform that, for a given source interval in n-space, can estimate the target interval in n-space.

InverseCoordinateTransform - Interface in mpicbg.models

InverseCoordinateTransformList<E extends InverseCoordinateTransform> - Class in mpicbg.models

TODO Think about if it should really implement InverseBoundable.

InverseCoordinateTransformList() - Constructor for class mpicbg.models.InverseCoordinateTransformList

InverseCoordinateTransformMap2D - Class in mpicbg.models

An InverseCoordinateTransform that is saved as a LUT on integer coordinates.

InverseCoordinateTransformMap2D(float[][]) - Constructor for class mpicbg.models.InverseCoordinateTransformMap2D

InverseCoordinateTransformMap2D(InverseCoordinateTransform, int, int) - Constructor for class mpicbg.models.InverseCoordinateTransformMap2D

InverseCoordinateTransformMap2D(FileInputStream) - Constructor for class mpicbg.models.InverseCoordinateTransformMap2D

InverseMapping<T extends CoordinateTransform> - Interface in mpicbg.ij

Describes an inverse mapping from source into target.

InverseTransformMapping<T extends InverseCoordinateTransform> - Class in mpicbg.ij

Use an InverseCoordinateTransform to map source into target which is a Mapping.

InverseTransformMapping(T) - Constructor for class mpicbg.ij.InverseTransformMapping

InverseTransformMapping<T extends InverseCoordinateTransform> - Class in mpicbg.ij.stack

Use an InverseCoordinateTransform to map source into target which is a projective Mapping.

InverseTransformMapping(T) - Constructor for class mpicbg.ij.stack.InverseTransformMapping

invert() - Method in class mpicbg.models.AffineModel1D

invert() - Method in class mpicbg.models.AffineModel2D

invert() - Method in class mpicbg.models.AffineModel3D

invert() - Method in class mpicbg.models.RigidModel3D

invert() - Method in class mpicbg.models.SimilarityModel2D

invert() - Method in class mpicbg.models.SimilarityModel3D

invert() - Method in class mpicbg.util.Matrix3x3

invert(double[]) - Static method in class mpicbg.util.Matrix3x3

invert(float[]) - Static method in class mpicbg.util.Matrix3x3

InvertibleBoundable - Interface in mpicbg.models

InvertibleConstantModel<A extends Model<A> & InvertibleCoordinateTransform,M extends InvertibleConstantModel<A,M>> - Class in mpicbg.models

Invertible specialization of ConstantModel.

InvertibleConstantModel(A) - Constructor for class mpicbg.models.InvertibleConstantModel

InvertibleCoordinateTransform - Interface in mpicbg.models

InvertibleCoordinateTransformList<E extends InvertibleCoordinateTransform> - Class in mpicbg.models

InvertibleCoordinateTransformList() - Constructor for class mpicbg.models.InvertibleCoordinateTransformList

InvertibleInterpolatedModel<A extends Model<A> & InvertibleCoordinateTransform,B extends Model<B> & InvertibleCoordinateTransform,M extends InvertibleInterpolatedModel<A,B,M>> - Class in mpicbg.models

Invertible specialization of InterpolatedModel.

InvertibleInterpolatedModel(A, B, double) - Constructor for class mpicbg.models.InvertibleInterpolatedModel

InvertibleMapping<T extends InvertibleCoordinateTransform> - Interface in mpicbg.ij

Describes an invertible (bidirectional) mapping from source into target.

InvertibleTransformMapping<T extends InvertibleCoordinateTransform> - Class in mpicbg.ij

Use an InvertibleCoordinateTransform to map source into target which is a Mapping.

InvertibleTransformMapping(T) - Constructor for class mpicbg.ij.InvertibleTransformMapping

isIdentity(CoordinateTransform, Iterable<Point>, double) - Static method in class mpicbg.models.Transforms

Check if a CoordinateTransform is the identity transform with respect to a set of Points and a given tolerance.

isInConvexTargetPolygon(ArrayList<PointMatch>, double[]) - Static method in class mpicbg.models.TransformMesh

Checks if a location is inside a given polygon at the target side or not.

isInSourcePolygon(ArrayList<PointMatch>, double[]) - Static method in class mpicbg.models.TransformMesh

Checks if a location is inside a given polygon at the source side or not.

isInTriangle(double, double, double, double, double, double, double, double) - Static method in class mpicbg.ij.TransformMeshMapping

Checks if a location is inside a given triangle.

isInvertible - Variable in class mpicbg.models.AffineModel1D

isInvertible - Variable in class mpicbg.models.AffineModel3D

isInvertible - Variable in class mpicbg.models.RigidModel3D

isInvertible - Variable in class mpicbg.models.SimilarityModel3D

iterator() - Method in class mpicbg.util.RingBuffer

itx - Variable in class mpicbg.models.RigidModel2D

ity - Variable in class mpicbg.models.RigidModel2D

K

keyPressed(KeyEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

keyPressed(KeyEvent) - Method in class mpicbg.ij.integral.InteractiveDifferenceOfMean

keyPressed(KeyEvent) - Method in class mpicbg.ij.integral.InteractivePMCC

keyPressed(KeyEvent) - Method in class mpicbg.ij.integral.InteractiveStandardDeviation

keyPressed(KeyEvent) - Method in class mpicbg.ij.integral.InteractiveVariance

keyPressed(KeyEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

keyPressed(KeyEvent) - Method in class mpicbg.ij.InteractiveMapping

keyReleased(KeyEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

keyReleased(KeyEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

keyReleased(KeyEvent) - Method in class mpicbg.ij.InteractiveMapping

keyTyped(KeyEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

keyTyped(KeyEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

keyTyped(KeyEvent) - Method in class mpicbg.ij.InteractiveMapping

L

l - Variable in class mpicbg.models.Point

Local coordinates

l1 - Variable in class mpicbg.models.InterpolatedModel

lambda - Variable in class mpicbg.models.InterpolatedCoordinateTransform

lambda - Variable in class mpicbg.models.InterpolatedModel

lastIndex() - Method in class mpicbg.util.RingBuffer

ldu(int) - Static method in class mpicbg.util.Util

(Hopefully) fast floor log₂ of an unsigned(!)

length - Variable in class mpicbg.models.Spring

length(double[], double[]) - Static method in class mpicbg.models.Spring

listIterator() - Method in class mpicbg.util.RingBuffer

listIterator(int) - Method in class mpicbg.util.RingBuffer

localDistance(Point, Point) - Static method in class mpicbg.models.Point

Estimate the Euclidean distance of two Points in local space.

localSmoothnessFilter(Collection<P>, Collection<P>, double, double, double) - Method in class mpicbg.models.AbstractModel

Default implementation of AbstractModel.localSmoothnessFilter(Collection, Collection, double, double, double).

localSmoothnessFilter(Collection<P>, Collection<P>, double, double, double) - Method in interface mpicbg.models.Model

Filter a Collection of PointMatches by the smoothness of their support for the given Model.

location - Variable in class mpicbg.imagefeatures.Feature

LongIntegralImage - Class in mpicbg.ij.integral

Summed area table using 64bit signed integer precision.

LongIntegralImage(ImageProcessor) - Constructor for class mpicbg.ij.integral.LongIntegralImage

LongRGBIntegralImage - Class in mpicbg.ij.integral

A 2d integral image (summed-area table) that allows for fast computation of the sum of pixel values in a rectangular area.

LongRGBIntegralImage(ColorProcessor) - Constructor for class mpicbg.ij.integral.LongRGBIntegralImage

longSums(long[], int, int) - Method in class mpicbg.ij.integral.LongRGBIntegralImage

Write the r,g,b sums at a specified x,y location into a passed array with ≥3 fields.

longSums(long[], int, int, int, int) - Method in class mpicbg.ij.integral.LongRGBIntegralImage

Write the r,g,b sums in a specified rectangle into a passed array with ≥3 fields.

M

m - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

m - Variable in class mpicbg.ij.InteractiveMapping

m00 - Variable in class mpicbg.models.AffineModel1D

m00 - Variable in class mpicbg.models.AffineModel2D

m00 - Variable in class mpicbg.models.AffineModel3D

m00 - Variable in class mpicbg.models.HomographyModel2D

m00 - Variable in class mpicbg.models.RigidModel3D

m00 - Variable in class mpicbg.models.SimilarityModel3D

m00 - Variable in class mpicbg.util.Matrix3x3

m01 - Variable in class mpicbg.models.AffineModel1D

m01 - Variable in class mpicbg.models.AffineModel2D

m01 - Variable in class mpicbg.models.AffineModel3D

m01 - Variable in class mpicbg.models.HomographyModel2D

m01 - Variable in class mpicbg.models.RigidModel3D

m01 - Variable in class mpicbg.models.SimilarityModel3D

m01 - Variable in class mpicbg.util.Matrix3x3

m02 - Variable in class mpicbg.models.AffineModel2D

m02 - Variable in class mpicbg.models.AffineModel3D

m02 - Variable in class mpicbg.models.HomographyModel2D

m02 - Variable in class mpicbg.models.RigidModel3D

m02 - Variable in class mpicbg.models.SimilarityModel3D

m02 - Variable in class mpicbg.util.Matrix3x3

m03 - Variable in class mpicbg.models.AffineModel3D

m03 - Variable in class mpicbg.models.RigidModel3D

m03 - Variable in class mpicbg.models.SimilarityModel3D

m10 - Variable in class mpicbg.models.AffineModel2D

m10 - Variable in class mpicbg.models.AffineModel3D

m10 - Variable in class mpicbg.models.HomographyModel2D

m10 - Variable in class mpicbg.models.RigidModel3D

m10 - Variable in class mpicbg.models.SimilarityModel3D

m10 - Variable in class mpicbg.util.Matrix3x3

m11 - Variable in class mpicbg.models.AffineModel2D

m11 - Variable in class mpicbg.models.AffineModel3D

m11 - Variable in class mpicbg.models.HomographyModel2D

m11 - Variable in class mpicbg.models.RigidModel3D

m11 - Variable in class mpicbg.models.SimilarityModel3D

m11 - Variable in class mpicbg.util.Matrix3x3

m12 - Variable in class mpicbg.models.AffineModel2D

m12 - Variable in class mpicbg.models.AffineModel3D

m12 - Variable in class mpicbg.models.HomographyModel2D

m12 - Variable in class mpicbg.models.RigidModel3D

m12 - Variable in class mpicbg.models.SimilarityModel3D

m12 - Variable in class mpicbg.util.Matrix3x3

m13 - Variable in class mpicbg.models.AffineModel3D

m13 - Variable in class mpicbg.models.RigidModel3D

m13 - Variable in class mpicbg.models.SimilarityModel3D

m20 - Variable in class mpicbg.models.AffineModel3D

m20 - Variable in class mpicbg.models.HomographyModel2D

m20 - Variable in class mpicbg.models.RigidModel3D

m20 - Variable in class mpicbg.models.SimilarityModel3D

m20 - Variable in class mpicbg.util.Matrix3x3

m21 - Variable in class mpicbg.models.AffineModel3D

m21 - Variable in class mpicbg.models.HomographyModel2D

m21 - Variable in class mpicbg.models.RigidModel3D

m21 - Variable in class mpicbg.models.SimilarityModel3D

m21 - Variable in class mpicbg.util.Matrix3x3

m22 - Variable in class mpicbg.models.AffineModel3D

m22 - Variable in class mpicbg.models.HomographyModel2D

m22 - Variable in class mpicbg.models.RigidModel3D

m22 - Variable in class mpicbg.models.SimilarityModel3D

m22 - Variable in class mpicbg.util.Matrix3x3

m23 - Variable in class mpicbg.models.AffineModel3D

m23 - Variable in class mpicbg.models.RigidModel3D

m23 - Variable in class mpicbg.models.SimilarityModel3D

main(String...) - Static method in class mpicbg.models.PolynomialTransform2D

map(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.InverseTransformMapping

map(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.InvertibleTransformMapping

map(ImageProcessor, ImageProcessor) - Method in interface mpicbg.ij.Mapping

Map source into target

map(ImageStack, ImageProcessor) - Method in class mpicbg.ij.stack.InverseTransformMapping

map(ImageStack, ImageProcessor) - Method in interface mpicbg.ij.stack.Mapping

Map source into target

map(ImageStack, ImageProcessor) - Method in class mpicbg.ij.stack.TransformMapping

map(ImageProcessor, ImageProcessor, int) - Method in class mpicbg.ij.TransformMeshMapping

map(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.TransformMeshMapping

map - Variable in class mpicbg.models.CoordinateTransformMap2D

target coordinates addressed interleaved as map[ row ][ 2 * column ] = x map[ row ][ 2 * column + 1 ] = y

map - Variable in class mpicbg.models.InverseCoordinateTransformMap2D

target coordinates addressed interleaved as map[ row ][ 2 * column ] = x map[ row ][ 2 * column + 1 ] = y

mapInterpolated(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.InverseTransformMapping

mapInterpolated(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.InvertibleTransformMapping

mapInterpolated(ImageProcessor, ImageProcessor) - Method in interface mpicbg.ij.Mapping

Map source into target using bilinear interpolation.

mapInterpolated(ImageStack, ImageProcessor) - Method in class mpicbg.ij.stack.InverseTransformMapping

mapInterpolated(ImageStack, ImageProcessor) - Method in interface mpicbg.ij.stack.Mapping

Map source into target using bilinear interpolation.

mapInterpolated(ImageStack, ImageProcessor) - Method in class mpicbg.ij.stack.TransformMapping

mapInterpolated(ImageProcessor, ImageProcessor, int) - Method in class mpicbg.ij.TransformMeshMapping

mapInterpolated(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.TransformMeshMapping

mapInverse(ImageProcessor, ImageProcessor) - Method in interface mpicbg.ij.InverseMapping

Map inversely source into target

mapInverse(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.InvertibleTransformMapping

mapInverse(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.TransformMapping

mapInverse(ImageProcessor, ImageProcessor, int) - Method in class mpicbg.ij.TransformMeshMapping

mapInverse(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.TransformMeshMapping

mapInverseInterpolated(ImageProcessor, ImageProcessor) - Method in interface mpicbg.ij.InverseMapping

Map inversely source into target using bilinear interpolation.

mapInverseInterpolated(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.InvertibleTransformMapping

mapInverseInterpolated(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.TransformMapping

mapInverseInterpolated(ImageProcessor, ImageProcessor, int) - Method in class mpicbg.ij.TransformMeshMapping

mapInverseInterpolated(ImageProcessor, ImageProcessor) - Method in class mpicbg.ij.TransformMeshMapping

mapping - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

mapping - Variable in class mpicbg.ij.InteractiveMapping

Mapping<T extends InverseCoordinateTransform> - Interface in mpicbg.ij

Describes a mapping from source into target.

mapping - Variable in class mpicbg.ij.MappingThread

mapping - Variable in class mpicbg.ij.PaintInvertibleCoordinateTransformThread

Mapping<T> - Interface in mpicbg.ij.stack

Describes a mapping from source into target.

MappingThread - Class in mpicbg.ij

MappingThread(ImagePlus, ImageProcessor, ImageProcessor, AtomicBoolean, Mapping<?>, boolean, int) - Constructor for class mpicbg.ij.MappingThread

MappingThread(ImagePlus, ImageProcessor, ImageProcessor, AtomicBoolean, Mapping<?>, boolean) - Constructor for class mpicbg.ij.MappingThread

mapTriangle(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor) - Static method in class mpicbg.ij.TransformMeshMapping

mapTriangleInterpolated(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor) - Static method in class mpicbg.ij.TransformMeshMapping

mapTriangleInverse(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor) - Static method in class mpicbg.ij.TransformMeshMapping

mapTriangleInverseInterpolated(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor) - Static method in class mpicbg.ij.TransformMeshMapping

matchByMaximalPMCC(FloatProcessor, FloatProcessor, int, int, int, int, float, float, float, Collection<PointMatch>, Collection<PointMatch>) - Static method in class mpicbg.ij.blockmatching.BlockMatching

matchByMaximalPMCC(FloatProcessor, FloatProcessor, FloatProcessor, FloatProcessor, double, CoordinateTransform, int, int, int, int, float, float, float, Collection<? extends Point>, Collection<PointMatch>, ErrorStatistic) - Static method in class mpicbg.ij.blockmatching.BlockMatching

Estimate point correspondences for a Collection of Points among two images that are approximately related by an InvertibleCoordinateTransform using the Pearson product-moment correlation coefficient (PMCC) r of pixel intensities as similarity measure.

matchByMaximalPMCC(FloatProcessor, FloatProcessor, FloatProcessor, FloatProcessor, float, CoordinateTransform, int, int, int, int, Collection<? extends Point>, Collection<PointMatch>, ErrorStatistic) - Static method in class mpicbg.ij.blockmatching.BlockMatching

Estimate point correspondences for a Collection of Points among two images that are approximately related by an InvertibleCoordinateTransform using the Pearson product-moment correlation coefficient (PMCC) r of pixel intensities as similarity measure.

matchByMaximalPMCCFromPreScaledImages(FloatProcessor, FloatProcessor, double, int, int, int, int, float, float, float, Collection<? extends Point>, Collection<PointMatch>) - Static method in class mpicbg.ij.blockmatching.BlockMatching

Estimate point correspondences for a Collection of Points among two images that are approximately related by an InvertibleCoordinateTransform using the Pearson product-moment correlation coefficient (PMCC) r of pixel intensities as similarity measure.

matchByMinimalSquareDifference(FloatProcessor, FloatProcessor, InvertibleCoordinateTransform, int, int, int, int, Collection<? extends Point>, Collection<PointMatch>) - Static method in class mpicbg.ij.blockmatching.BlockMatching

Estimate point correspondences for a Collection of Points among two images that are approximately related by an InvertibleCoordinateTransform using the square difference of pixel intensities as a similarity measure.

matches - Variable in class mpicbg.models.MovingLeastSquaresTransform

matches - Variable in class mpicbg.models.Tile

A set of point correspondences with p1 being a local point in this Tile and p2 being the corresponding local point in another Tile.

matchFeatures(Collection<Feature>, Collection<Feature>, List<PointMatch>, float) - Static method in class mpicbg.ij.FeatureTransform

Identify corresponding features

matchFeatures(Collection<Feature>, Collection<Feature>, float) - Static method in class mpicbg.ij.FeatureTransform

Identify corresponding features

matchFeatures(List<Feature>, List<Feature>, List<PointMatch>, double) - Static method in class mpicbg.imagefeatures.Feature

Deprecated.

matchFeaturesLocally(Collection<Feature>, Collection<Feature>, double, float) - Static method in class mpicbg.ij.FeatureTransform

Identify corresponding features with locations within a given radius

Matrix3x3 - Class in mpicbg.util

Basic operations on 3x3 double matrices.

Matrix3x3() - Constructor for class mpicbg.util.Matrix3x3

Initialize and identity matrix.

Matrix3x3(double, double, double, double, double, double, double, double, double) - Constructor for class mpicbg.util.Matrix3x3

Initialize a matrix.

Matrix3x3(double[]) - Constructor for class mpicbg.util.Matrix3x3

Initialize a matrix with a double[].

max - Variable in class mpicbg.models.ErrorStatistic

max(float[], float[]) - Static method in class mpicbg.util.Util

Writes max(a,b) into a

max(double[], double[]) - Static method in class mpicbg.util.Util

Writes max(a,b) into a

maxDistance(Collection<PointMatch>) - Static method in class mpicbg.models.PointMatch

maxError - Variable in class mpicbg.models.TileConfiguration

maxForce - Variable in class mpicbg.models.SpringMesh

maxOctaveSize - Variable in class mpicbg.imagefeatures.FloatArray2DMOPS.Param

maxOctaveSize - Variable in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

Size limits for scale octaves in px: minOctaveSize < octave < maxOctaveSize

maxSpeed - Variable in class mpicbg.models.SpringMesh

maxStretch - Variable in class mpicbg.models.Spring

mean(int, int) - Method in class mpicbg.ij.integral.BlockStatistics

Set all pixels in ip to their block mean for a block with given radius.

mean(int) - Method in class mpicbg.ij.integral.BlockStatistics

Mean - Class in mpicbg.ij.integral

Mean(ColorProcessor) - Constructor for class mpicbg.ij.integral.Mean

Mean(ByteProcessor) - Constructor for class mpicbg.ij.integral.Mean

Mean(ShortProcessor) - Constructor for class mpicbg.ij.integral.Mean

Mean(FloatProcessor) - Constructor for class mpicbg.ij.integral.Mean

mean(int, int) - Method in class mpicbg.ij.integral.Mean

mean(int) - Method in class mpicbg.ij.integral.Mean

mean - Variable in class mpicbg.models.ErrorStatistic

meanDistance(Collection<PointMatch>) - Static method in class mpicbg.models.PointMatch

memset(byte[], byte) - Static method in class mpicbg.util.Util

For Java, the fastest way doing memset(x) Found at http://burks.brighton.ac.uk/burks/language/java/jprogfaq/faq_b.htm

memset(short[], short) - Static method in class mpicbg.util.Util

For Java, the fastest way doing memset(x) Found at http://burks.brighton.ac.uk/burks/language/java/jprogfaq/faq_b.htm

memset(int[], int) - Static method in class mpicbg.util.Util

For Java, the fastest way doing memset(x) Found at http://burks.brighton.ac.uk/burks/language/java/jprogfaq/faq_b.htm

memset(long[], long) - Static method in class mpicbg.util.Util

For Java, the fastest way doing memset(x) Found at http://burks.brighton.ac.uk/burks/language/java/jprogfaq/faq_b.htm

memset(float[], float) - Static method in class mpicbg.util.Util

For Java, the fastest way doing memset(x) Found at http://burks.brighton.ac.uk/burks/language/java/jprogfaq/faq_b.htm

memset(double[], double) - Static method in class mpicbg.util.Util

For Java, the fastest way doing memset(x) Found at http://burks.brighton.ac.uk/burks/language/java/jprogfaq/faq_b.htm

memset(boolean[], boolean) - Static method in class mpicbg.util.Util

For Java, the fastest way doing memset(x) Found at http://burks.brighton.ac.uk/burks/language/java/jprogfaq/faq_b.htm

memset(char[], char) - Static method in class mpicbg.util.Util

For Java, the fastest way doing memset(x) Found at http://burks.brighton.ac.uk/burks/language/java/jprogfaq/faq_b.htm

min - Variable in class mpicbg.models.ErrorStatistic

min(float[], float[]) - Static method in class mpicbg.util.Util

Writes min(a,b) into a

min(double[], double[]) - Static method in class mpicbg.util.Util

Writes min(a,b) into a

MIN_NUM_MATCHES - Static variable in class mpicbg.models.AffineModel1D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.AffineModel2D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.AffineModel3D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.HomographyModel2D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.IdentityModel

MIN_NUM_MATCHES - Static variable in class mpicbg.models.RigidModel2D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.RigidModel3D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.SimilarityModel2D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.SimilarityModel3D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.TranslationModel1D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.TranslationModel2D

MIN_NUM_MATCHES - Static variable in class mpicbg.models.TranslationModel3D

minError - Variable in class mpicbg.models.TileConfiguration

minForce - Variable in class mpicbg.models.SpringMesh

minOctaveSize - Variable in class mpicbg.imagefeatures.FloatArray2DMOPS.Param

minOctaveSize - Variable in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

mod(float, float) - Static method in class mpicbg.util.Util

An equivalent to % for float

model - Variable in class mpicbg.models.AbstractMovingLeastSquaresTransform

model - Variable in class mpicbg.models.ConstantModel

Model<M extends Model<M>> - Interface in mpicbg.models

CoordinateTransform whose parameters can be estimated through a least-squares(like) fit.

model - Variable in class mpicbg.models.Tile

The transformation AbstractModel of the Tile.

modelClass - Variable in class mpicbg.models.MovingLeastSquaresMesh

modifiers(int) - Static method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

modifiers(int) - Static method in class mpicbg.ij.InteractiveMapping

MOPS - Class in mpicbg.ij

MOPS(FloatArray2DMOPS) - Constructor for class mpicbg.ij.MOPS

Constructor

mouseClicked(MouseEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

mouseClicked(MouseEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

mouseClicked(MouseEvent) - Method in class mpicbg.ij.InteractiveMapping

mouseDragged(MouseEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

mouseDragged(MouseEvent) - Method in class mpicbg.ij.integral.InteractiveDifferenceOfMean

mouseDragged(MouseEvent) - Method in class mpicbg.ij.integral.InteractivePMCC

mouseDragged(MouseEvent) - Method in class mpicbg.ij.integral.InteractiveTilt

mouseDragged(MouseEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

mouseDragged(MouseEvent) - Method in class mpicbg.ij.InteractiveMapping

mouseEntered(MouseEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

mouseEntered(MouseEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

mouseEntered(MouseEvent) - Method in class mpicbg.ij.InteractiveMapping

mouseExited(MouseEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

mouseExited(MouseEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

mouseExited(MouseEvent) - Method in class mpicbg.ij.InteractiveMapping

mouseMoved(MouseEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

mouseMoved(MouseEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

mouseMoved(MouseEvent) - Method in class mpicbg.ij.InteractiveMapping

mousePressed(MouseEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

mousePressed(MouseEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

mousePressed(MouseEvent) - Method in class mpicbg.ij.InteractiveMapping

mouseReleased(MouseEvent) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

mouseReleased(MouseEvent) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

mouseReleased(MouseEvent) - Method in class mpicbg.ij.InteractiveMapping

mouseWheelMoved(MouseWheelEvent) - Method in class mpicbg.ij.integral.InteractiveDifferenceOfMean

move(double) - Method in class mpicbg.models.Vertex

Move the vertex for a given time.

MovingLeastSquaresMesh<M extends AbstractModel<M>> - Class in mpicbg.models

A transformation mesh that implements a landmark based deformation by means of Moving Least Squares as described by \citet{SchaeferAl06} inspired by the implementation of Johannes Schindelin.

MovingLeastSquaresMesh(Class<M>, int, int, double, double) - Constructor for class mpicbg.models.MovingLeastSquaresMesh

MovingLeastSquaresMesh(Class<M>, int, double, double) - Constructor for class mpicbg.models.MovingLeastSquaresMesh

MovingLeastSquaresTransform - Class in mpicbg.models

Smooth coordinate transformation interpolating between a set of control points that are maped exactly on top of each other using landmark based deformation by means of Moving Least Squares as described by \citet{SchaeferAl06}.

MovingLeastSquaresTransform() - Constructor for class mpicbg.models.MovingLeastSquaresTransform

MovingLeastSquaresTransform2 - Class in mpicbg.models

Alternative implementation of the smooth coordinate transformation interpolating between a set of control points that are maped exactly on top of each other using landmark based deformation by means of Moving Least Squares as described by \citet{SchaeferAl06}.

MovingLeastSquaresTransform2() - Constructor for class mpicbg.models.MovingLeastSquaresTransform2

mpicbg.ij - package mpicbg.ij

mpicbg.ij.blockmatching - package mpicbg.ij.blockmatching

mpicbg.ij.clahe - package mpicbg.ij.clahe

mpicbg.ij.integral - package mpicbg.ij.integral

mpicbg.ij.stack - package mpicbg.ij.stack

mpicbg.ij.util - package mpicbg.ij.util

mpicbg.ij.visualization - package mpicbg.ij.visualization

mpicbg.imagefeatures - package mpicbg.imagefeatures

mpicbg.models - package mpicbg.models

mpicbg.util - package mpicbg.util

myModel() - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

N

n - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator

Deprecated.

n() - Method in class mpicbg.models.ErrorStatistic

N - Variable in class mpicbg.models.SimilarityModel3D

n - Variable in class mpicbg.util.RealStreamPMCC

next() - Static method in class mpicbg.util.ColorStream

next() - Method in class mpicbg.util.RingBuffer.RingBufferIterator

next() - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

nextBufferIndex - Variable in class mpicbg.util.RingBuffer

nextIndex() - Method in class mpicbg.util.RingBuffer

nextIndex() - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

nextRealIndex - Variable in class mpicbg.util.RingBuffer

NL - Static variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

NoninvertibleModelException - Exception in mpicbg.models

Signalizes that a AbstractModel is not invertible.

NoninvertibleModelException() - Constructor for exception mpicbg.models.NoninvertibleModelException

NoninvertibleModelException(String) - Constructor for exception mpicbg.models.NoninvertibleModelException

NoninvertibleModelException(Throwable) - Constructor for exception mpicbg.models.NoninvertibleModelException

NoninvertibleModelException(String, Throwable) - Constructor for exception mpicbg.models.NoninvertibleModelException

normalize(float[]) - Static method in class mpicbg.ij.util.Filter

Normalize data numerically such that the sum of all fields is 1.0

normalizeContrast(FloatProcessor) - Static method in class mpicbg.ij.util.Util

Normalize the dynamic range of a FloatProcessor to the interval [0,1].

NormalizeLocalContrast - Class in mpicbg.ij.integral

Normalize contrast based on per-pixel mean and STD.

NormalizeLocalContrast(FloatProcessor) - Constructor for class mpicbg.ij.integral.NormalizeLocalContrast

noSuchElementException - Static variable in class mpicbg.util.RingBuffer

NotEnoughDataPointsException - Exception in mpicbg.models

Signalizes that there were not enough data points available to estimate the AbstractModel.

NotEnoughDataPointsException() - Constructor for exception mpicbg.models.NotEnoughDataPointsException

NotEnoughDataPointsException(String) - Constructor for exception mpicbg.models.NotEnoughDataPointsException

NotEnoughDataPointsException(Throwable) - Constructor for exception mpicbg.models.NotEnoughDataPointsException

NotEnoughDataPointsException(String, Throwable) - Constructor for exception mpicbg.models.NotEnoughDataPointsException

numPolTerms(int) - Static method in class mpicbg.models.PolynomialTransform2D

Calculate the number of polynomial terms for a 2d polynomial transform of given order.

numVertices() - Method in class mpicbg.models.MovingLeastSquaresMesh

numVertices() - Method in class mpicbg.models.SpringMesh

numY(int, double, double) - Static method in class mpicbg.models.TransformMesh

O

onReturn() - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

optimize(double, int, int) - Method in class mpicbg.models.ElasticMovingLeastSquaresMesh

Minimize the displacement of all PointMatches of all tiles.

optimize(double, int, int) - Method in class mpicbg.models.SpringMesh

Optimize the mesh.

optimize(double, int, int, double) - Method in class mpicbg.models.TileConfiguration

Minimize the displacement of all Correspondence pairs of all Tiles and tell about it.

optimize(double, int, int) - Method in class mpicbg.models.TileConfiguration

Minimize the displacement of all Correspondence pairs of all Tiles and tell about it.

optimize(ErrorStatistic, double, int, int, double) - Method in class mpicbg.models.TileConfiguration

Minimize the displacement of all Correspondence pairs of all Tiles and tell about it.

optimizeAndFilter(double, int, int, double, double) - Method in class mpicbg.models.TileConfiguration

optimizeAndFilter(double, int, int, double) - Method in class mpicbg.models.TileConfiguration

optimizeByStrength(double, int, int, ByteProcessor, ImagePlus) - Method in class mpicbg.models.ElasticMovingLeastSquaresMesh

Minimize the displacement of all PointMatches of all tiles.

optimizeConcurrently(ErrorStatistic, double, int, int, double, TileConfiguration, Set<Tile<?>>, Set<Tile<?>>, int) - Static method in class mpicbg.models.TileUtil

optimizeConcurrently(ErrorStatistic, double, int, int, double, TileConfiguration, Set<Tile<?>>, Set<Tile<?>>, int, boolean) - Static method in class mpicbg.models.TileUtil

optimizeIteration(ErrorStatistic) - Method in class mpicbg.models.ElasticMovingLeastSquaresMesh

Performs one optimization iteration and writes its error into the ErrorStatistics

optimizeIteration() - Method in class mpicbg.models.ElasticMovingLeastSquaresMesh

Performs one optimization iteration.

optimizeMeshes(Collection<SpringMesh>, double, int, int) - Static method in class mpicbg.models.SpringMesh

Optimize a Collection of connected SpringMeshes.

optimizeMeshes(Collection<SpringMesh>, double, int, int, boolean) - Static method in class mpicbg.models.SpringMesh

Optimize a Collection of connected SpringMeshes.

optimizeMeshes(Collection<SpringMesh>, double, int, int, double, boolean) - Static method in class mpicbg.models.SpringMesh

Optimize a Collection of connected SpringMeshes.

optimizeMeshes2(Collection<SpringMesh>, double, int, int) - Static method in class mpicbg.models.SpringMesh

Deprecated.

Remains for reproducing legacy results

optimizeMeshes2(Collection<SpringMesh>, double, int, int, boolean) - Static method in class mpicbg.models.SpringMesh

Deprecated.

Remains for reproducing legacy results

optimizeSilently(ErrorStatistic, double, int, int) - Method in class mpicbg.models.TileConfiguration

Minimize the displacement of all Correspondence pairs of all Tiles

optimizeSilently(ErrorStatistic, double, int, int, double) - Method in class mpicbg.models.TileConfiguration

Minimize the displacement of all Correspondence pairs of all Tiles

optimizeSilentlyConcurrent(ErrorStatistic, double, int, int, double) - Method in class mpicbg.models.TileConfiguration

optimizeStep(ErrorStatistic) - Method in class mpicbg.models.SpringMesh

Performs one optimization step.

order - Variable in class mpicbg.models.PolynomialTransform2D

order of the polynomial transform

orderOf(int) - Static method in class mpicbg.models.PolynomialTransform2D

Calculate the maximum order of a polynom whose number of polyynomial terms is smaller or equal a given number.

orientation - Variable in class mpicbg.imagefeatures.Feature

P

p - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

p - Variable in class mpicbg.ij.InteractiveMapping

p - Variable in class mpicbg.imagefeatures.FloatArray2DFeatureTransform

p - Variable in class mpicbg.models.MovingLeastSquaresTransform2

p1 - Variable in class mpicbg.models.PointMatch

p2 - Variable in class mpicbg.models.PointMatch

painter - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

painter - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform.Tuple

painter - Variable in class mpicbg.ij.InteractiveMapping

PaintInvertibleCoordinateTransformThread - Class in mpicbg.ij

PaintInvertibleCoordinateTransformThread(ImagePlus, ImageProcessor, ImageProcessor, AtomicBoolean, InverseCoordinateTransform) - Constructor for class mpicbg.ij.PaintInvertibleCoordinateTransformThread

paintMeshes(Collection<SpringMesh>, double) - Static method in class mpicbg.models.SpringMesh

paintSprings(Collection<SpringMesh>, double, double) - Static method in class mpicbg.models.SpringMesh

paintSprings(Collection<SpringMesh>, int, int, double) - Static method in class mpicbg.models.SpringMesh

Param() - Constructor for class mpicbg.imagefeatures.FloatArray2DMOPS.Param

Param() - Constructor for class mpicbg.imagefeatures.FloatArray2DSIFT.Param

pattern - Variable in class mpicbg.imagefeatures.FloatArray2DMOPS

pickInterpolator(ImageProcessor) - Static method in class mpicbg.ij.stack.AbstractTransformMapping

pingPong(int, int) - Static method in class mpicbg.util.Util

Return an unsigned integer that bounces in a ping pong manner in the range [0 ... mod - 1].

pleaseRepaint - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform.Tuple

pleaseRepaint - Variable in class mpicbg.ij.InteractiveMapping

pleaseRepaint - Variable in class mpicbg.ij.MappingThread

pleaseRepaint - Variable in class mpicbg.ij.PaintInvertibleCoordinateTransformThread

Point - Class in mpicbg.models

An n-dimensional point.

Point(double[], double[]) - Constructor for class mpicbg.models.Point

Constructor Sets Point.l to the given double[] reference.

Point(double[]) - Constructor for class mpicbg.models.Point

Constructor Sets Point.l to the given double[] reference.

PointFactory<P extends Point> - Interface in mpicbg.models

PointMatch - Class in mpicbg.models

A link between two Points that are expected to be ideally at the same location in the world coordinate space.

PointMatch(Point, Point, double[], double) - Constructor for class mpicbg.models.PointMatch

Constructor Create a PointMatch with an Array of weights and a strength.

PointMatch(Point, Point, double[]) - Constructor for class mpicbg.models.PointMatch

Constructor Create a PointMatch with an Array of weights.

PointMatch(Point, Point, double) - Constructor for class mpicbg.models.PointMatch

Constructor Create a PointMatch with one weight.

PointMatch(Point, Point, double, double) - Constructor for class mpicbg.models.PointMatch

Constructor Create a PointMatch with one weight and strength.

PointMatch(Point, Point) - Constructor for class mpicbg.models.PointMatch

Constructor Create a PointMatch without weight.

PointMatchFactory<M extends PointMatch> - Interface in mpicbg.models

pointRoisToPointMatches(PointRoi, PointRoi) - Static method in class mpicbg.ij.util.Util

pointRoiToPoints(PointRoi) - Static method in class mpicbg.ij.util.Util

pointsToPointRoi(Collection<? extends Point>) - Static method in class mpicbg.ij.util.Util

Create an ImageJ PointRoi from a Collection of Points.

PointVis - Class in mpicbg.ij.visualization

PointVis() - Constructor for class mpicbg.ij.visualization.PointVis

polTerms - Variable in class mpicbg.models.PolynomialTransform2D

register to hold all polynomial terms during applyInPlace following the order specified at http://bishopw.loni.ucla.edu/AIR5/2Dnonlinear.html#polylist excluding 1 because we want to avoid repeated multiplication with 1

PolynomialTransform2D - Class in mpicbg.models

PolynomialTransform2D() - Constructor for class mpicbg.models.PolynomialTransform2D

populateTerms(double, double) - Method in class mpicbg.models.PolynomialTransform2D

popWeight() - Method in class mpicbg.models.PointMatch

Get the last weights element and remove it from the list.

pow(int, int) - Static method in class mpicbg.util.Util

Integer version of Math.pow(double, double).

pow(float, int) - Static method in class mpicbg.util.Util

Float/Integer version of Math.pow(double, double).

pow(double, int) - Static method in class mpicbg.util.Util

Double/Integer version of Math.pow(double, double).

preAlign() - Method in class mpicbg.models.TileConfiguration

Computes a pre-alignemnt of all non-fixed Tiles by propagating the pairwise models.

preConcatenate(M) - Method in class mpicbg.models.AbstractAffineModel2D

preConcatenate(T) - Method in interface mpicbg.models.Affine1D

preConcatenate(T) - Method in interface mpicbg.models.Affine2D

preConcatenate(T) - Method in interface mpicbg.models.Affine3D

preConcatenate(AffineModel1D) - Method in class mpicbg.models.AffineModel1D

preConcatenate(AffineModel2D) - Method in class mpicbg.models.AffineModel2D

preConcatenate(TranslationModel2D) - Method in class mpicbg.models.AffineModel2D

preConcatenate(AffineModel3D) - Method in class mpicbg.models.AffineModel3D

preConcatenate(TranslationModel3D) - Method in class mpicbg.models.AffineModel3D

preConcatenate(ConstantAffineModel1D<A>) - Method in class mpicbg.models.ConstantAffineModel1D

preConcatenate(IdentityModel) - Method in class mpicbg.models.IdentityModel

preConcatenate(InterpolatedAffineModel1D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel1D

preConcatenate(AffineModel1D) - Method in class mpicbg.models.InterpolatedAffineModel1D

preConcatenate(InterpolatedAffineModel2D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel2D

preConcatenate(AffineModel2D) - Method in class mpicbg.models.InterpolatedAffineModel2D

preConcatenate(InterpolatedAffineModel3D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel3D

preConcatenate(RigidModel2D) - Method in class mpicbg.models.RigidModel2D

preConcatenate(RigidModel3D) - Method in class mpicbg.models.RigidModel3D

preConcatenate(TranslationModel3D) - Method in class mpicbg.models.RigidModel3D

preConcatenate(SimilarityModel2D) - Method in class mpicbg.models.SimilarityModel2D

preConcatenate(SimilarityModel3D) - Method in class mpicbg.models.SimilarityModel3D

preConcatenate(TranslationModel1D) - Method in class mpicbg.models.TranslationModel1D

preConcatenate(TranslationModel2D) - Method in class mpicbg.models.TranslationModel2D

preConcatenate(TranslationModel3D) - Method in class mpicbg.models.TranslationModel3D

preConcatenate(Matrix3x3) - Method in class mpicbg.util.Matrix3x3

Pre-concatenate a matrix: this = m × this

previous() - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

previousIndex() - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

println(String) - Static method in class mpicbg.models.SpringMesh

println(String) - Method in class mpicbg.models.TileConfiguration

printTerms() - Method in class mpicbg.models.PolynomialTransform2D

processCandidate(double[], int, List<Feature>) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

assign orientation to the given candidate, if more than one orientations found, duplicate the feature for each orientation estimate the feature descriptor for each of those candidates

pt - Variable in class mpicbg.models.MovingLeastSquaresMesh

Tiles are a collection of PointMatches that share a common transformation model.

pushWeight(double) - Method in class mpicbg.models.PointMatch

Append a new element to the right side of the weights list.

pv - Variable in class mpicbg.models.SpringMesh

pva - Variable in class mpicbg.models.SpringMesh

Q

q - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

q - Variable in class mpicbg.ij.InteractiveMapping

q - Variable in class mpicbg.models.MovingLeastSquaresTransform2

R

r(int, int) - Method in class mpicbg.ij.integral.BlockPMCC

Set all pixels in ip to their block PMCC r_XY for the current offset with given radius.

r(int) - Method in class mpicbg.ij.integral.BlockPMCC

ransac(List<P>, Collection<P>, int, double, double, int) - Method in class mpicbg.models.AbstractModel

Find the AbstractModel of a set of PointMatch candidates containing a high number of outliers using RANSAC \citet[{FischlerB81}.

ransac(List<P>, Collection<P>, int, double, double) - Method in class mpicbg.models.AbstractModel

Call AbstractModel.ransac(List, Collection, int, double, double, int) with minNumInliers = Model.getMinNumMatches().

ransac(List<P>, Collection<P>, int, double, double, int) - Method in interface mpicbg.models.Model

Find the Model of a set of PointMatch candidates containing a high number of outliers using RANSAC \citet[{FischlerB81}.

ransac(List<P>, Collection<P>, int, double, double) - Method in interface mpicbg.models.Model

Call Model.ransac(List, Collection, int, double, double, int) with minNumInliers = Model.getMinNumMatches().

readFields(GenericDialog, FloatArray2DMOPS.Param) - Static method in class mpicbg.ij.MOPS

readFields(GenericDialog, FloatArray2DSIFT.Param) - Static method in class mpicbg.ij.SIFT

realIndex - Variable in class mpicbg.util.RingBuffer.RingBufferListIterator

RealStreamPMCC - Class in mpicbg.util

Calculate the PMMC of a stream of double pairs by tracking the required sums.

RealStreamPMCC() - Constructor for class mpicbg.util.RealStreamPMCC

RealSum - Class in mpicbg.util

RealSum implements a method to reduce numerical instabilities when summing up a very large number of double precision numbers.

RealSum() - Constructor for class mpicbg.util.RealSum

Create a new RealSum.

RealSum(int) - Constructor for class mpicbg.util.RealSum

Create a new RealSum.

remove(E) - Method in class mpicbg.models.CoordinateTransformList

remove(int) - Method in class mpicbg.models.CoordinateTransformList

remove(E) - Method in class mpicbg.models.InverseCoordinateTransformList

remove(int) - Method in class mpicbg.models.InverseCoordinateTransformList

remove(E) - Method in class mpicbg.models.InvertibleCoordinateTransformList

remove(int) - Method in class mpicbg.models.InvertibleCoordinateTransformList

remove(E) - Method in interface mpicbg.models.TransformList

remove(int) - Method in interface mpicbg.models.TransformList

remove(int) - Method in class mpicbg.util.RingBuffer

Does not check for index < 0 for efficiency reasons, so be sure not to pass negative indices.

remove() - Method in class mpicbg.util.RingBuffer.RingBufferIterator

TODO Should we implement this?

remove() - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

removeAmbiguousMatches(List<PointMatch>) - Static method in class mpicbg.ij.FeatureTransform

Remove ambiguous matches from a list of matches.

removeConnectedTile(Tile<?>) - Method in class mpicbg.models.Tile

Remove a Tile from the set of connected Tiles.

removeMatch(PointMatch) - Method in class mpicbg.models.Tile

Remove a PointMatch.

RemoveOutliers - Class in mpicbg.ij.integral

Remove saturated pixels by diffusing the neighbors in.

RemoveOutliers(FloatProcessor) - Constructor for class mpicbg.ij.integral.RemoveOutliers

removeOutliers(int, int, float) - Method in class mpicbg.ij.integral.RemoveOutliers

removePassiveVertex(Vertex) - Method in class mpicbg.models.SpringMesh

Remove a passive vertex.

removeUnsafe(int) - Method in class mpicbg.util.RingBuffer

removeWeight(int) - Method in class mpicbg.models.Spring

render(int, int, int, int) - Method in class mpicbg.ij.integral.Tilt

repaint() - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter.PaintThread

reset() - Method in class mpicbg.models.AffineModel1D

reset() - Method in class mpicbg.models.AffineModel2D

reset() - Method in class mpicbg.models.AffineModel3D

reset() - Method in class mpicbg.models.RigidModel2D

reset() - Method in class mpicbg.models.RigidModel3D

reset() - Method in class mpicbg.models.SimilarityModel2D

reset() - Method in class mpicbg.models.SimilarityModel3D

reset() - Method in class mpicbg.util.Matrix3x3

Set to identity.

RGBInterpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.RGBInterpolator

RigidModel2D - Class in mpicbg.models

2d-rigid transformation models to be applied to points in 2d-space.

RigidModel2D() - Constructor for class mpicbg.models.RigidModel2D

RigidModel3D - Class in mpicbg.models

RigidModel3D() - Constructor for class mpicbg.models.RigidModel3D

RingBuffer<T> - Class in mpicbg.util

RingBuffer(int) - Constructor for class mpicbg.util.RingBuffer

RingBuffer.RingBufferIterator - Class in mpicbg.util

RingBuffer.RingBufferListIterator - Class in mpicbg.util

RingBufferIterator() - Constructor for class mpicbg.util.RingBuffer.RingBufferIterator

RingBufferListIterator() - Constructor for class mpicbg.util.RingBuffer.RingBufferListIterator

RingBufferListIterator(int) - Constructor for class mpicbg.util.RingBuffer.RingBufferListIterator

rnd - Static variable in class mpicbg.models.AbstractModel

rnd - Static variable in class mpicbg.models.Spring

rotate(int, double) - Method in class mpicbg.models.AffineModel3D

Rotate

rotate(int, double) - Method in class mpicbg.models.RigidModel3D

Rotate

round(float) - Static method in class mpicbg.util.Util

Round a

round(double) - Static method in class mpicbg.util.Util

Round a

roundPos(float) - Static method in class mpicbg.util.Util

Round a positive a

roundPos(double) - Static method in class mpicbg.util.Util

Round a positive a

RowIntegrator(double[], double[], int, int, int) - Constructor for class mpicbg.ij.integral.BlockStatistics.RowIntegrator

Deprecated.

rs - Static variable in class mpicbg.util.ColorStream

rSignedSquare(int, int) - Method in class mpicbg.ij.integral.BlockPMCC

Set all pixels in ip to their signed square block PMCC r_XY² for the current offset with given radius.

rSignedSquare(int) - Method in class mpicbg.ij.integral.BlockPMCC

run(ImagePlus, int, int, float, ByteProcessor) - Static method in class mpicbg.ij.clahe.FastFlat

Deprecated.

Use the instance method Flat.getInstance().Flat.run(ImagePlus, int, int, float, ByteProcessor, boolean) instead.

run(ImagePlus, int, int, float, int, int, int, int, ByteProcessor, ByteProcessor, ByteProcessor, ImageProcessor, boolean, ArrayList<Apply<?>>) - Method in class mpicbg.ij.clahe.FastFlat

The actual implementation

run(ImagePlus, int, int, float, ByteProcessor) - Static method in class mpicbg.ij.clahe.Flat

Deprecated.

Use the instance method Flat.getInstance().Flat.run(ImagePlus, int, int, float, ByteProcessor, boolean) instead.

run(ImagePlus, int, int, float, ByteProcessor, boolean) - Method in class mpicbg.ij.clahe.Flat

Process and ImagePlus with a given set of parameters.

run(ImagePlus, int, int, float, Rectangle, ByteProcessor, boolean) - Method in class mpicbg.ij.clahe.Flat

Process and ImagePlus with a given set of parameters including the bounding box and mask.

run(ImagePlus, int, int, float, int, int, int, int, ByteProcessor, ByteProcessor, ByteProcessor, ImageProcessor, boolean, ArrayList<Apply<?>>) - Method in class mpicbg.ij.clahe.Flat

The actual implementation

run() - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter.PaintThread

run(String) - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

run() - Method in class mpicbg.ij.integral.BlockStatistics.RowIntegrator

Deprecated.

run(String) - Method in class mpicbg.ij.integral.InteractivePMCC

run(String) - Method in class mpicbg.ij.integral.InteractiveTilt

run(int, int, float, boolean, boolean) - Method in class mpicbg.ij.integral.NormalizeLocalContrast

run(String) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

run(String) - Method in class mpicbg.ij.InteractiveMapping

run() - Method in class mpicbg.ij.MappingThread

run() - Method in class mpicbg.ij.PaintInvertibleCoordinateTransformThread

run() - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

Detect features in all scale octaves.

run(int) - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

Detect features in all scale octaves.

run(FloatArray2DScaleOctave) - Method in class mpicbg.imagefeatures.FloatArray2DScaleOctaveDoGDetector

run() - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

detect features in all scale octaves

run(int) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

detect features in all scale octaves

runCenter(int, int) - Method in class mpicbg.ij.integral.NormalizeLocalContrast

runCenterStretch(int, int, float) - Method in class mpicbg.ij.integral.NormalizeLocalContrast

runOctave(int) - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

detect features in the specified scale octave

runStretch(int, int, float) - Method in class mpicbg.ij.integral.NormalizeLocalContrast

S

sampleVariance(int, int) - Method in class mpicbg.ij.integral.BlockStatistics

Set all pixels in ip to their block sample variance for a block with given radius.

sampleVariance(int) - Method in class mpicbg.ij.integral.BlockStatistics

Set all pixels in ip to their block sample variance for a block with given radius.

Scale - Class in mpicbg.ij.integral

Scale(ColorProcessor) - Constructor for class mpicbg.ij.integral.Scale

Scale(ByteProcessor) - Constructor for class mpicbg.ij.integral.Scale

Scale(ShortProcessor) - Constructor for class mpicbg.ij.integral.Scale

Scale(FloatProcessor) - Constructor for class mpicbg.ij.integral.Scale

scale(int, int) - Method in class mpicbg.ij.integral.Scale

scale(double) - Method in class mpicbg.ij.integral.Scale

scale(ImageProcessor, float) - Static method in class mpicbg.ij.util.Filter

Scale an image with good quality in both up and down direction

scale - Variable in class mpicbg.imagefeatures.Feature

scale(double) - Method in class mpicbg.models.SpringMesh

TODO Not yet tested

scale(double) - Method in class mpicbg.models.TransformMesh

Scale all vertex coordinates

scos - Variable in class mpicbg.models.SimilarityModel2D

set(float, int, int) - Method in class mpicbg.imagefeatures.FloatArray2D

set(FloatArray2DSIFT.Param) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

set(AffineModel1D) - Method in class mpicbg.models.AffineModel1D

set(TranslationModel1D) - Method in class mpicbg.models.AffineModel1D

set(double, double) - Method in class mpicbg.models.AffineModel1D

Initialize the model such that the respective affine transform is: m00 m01 0 1

set(AffineModel2D) - Method in class mpicbg.models.AffineModel2D

set(TranslationModel2D) - Method in class mpicbg.models.AffineModel2D

set(RigidModel2D) - Method in class mpicbg.models.AffineModel2D

set(SimilarityModel2D) - Method in class mpicbg.models.AffineModel2D

set(double, double, double, double, double, double) - Method in class mpicbg.models.AffineModel2D

Initialize the model such that the respective affine transform is: m00 m01 m02 m10 m11 m12 0 0 1

set(AffineTransform) - Method in class mpicbg.models.AffineModel2D

Initialize the model with the parameters of an AffineTransform.

set(AffineModel3D) - Method in class mpicbg.models.AffineModel3D

set(TranslationModel3D) - Method in class mpicbg.models.AffineModel3D

set(RigidModel3D) - Method in class mpicbg.models.AffineModel3D

set(SimilarityModel3D) - Method in class mpicbg.models.AffineModel3D

set(double, double, double, double, double, double, double, double, double, double, double, double) - Method in class mpicbg.models.AffineModel3D

Initialize the model such that the respective affine transform is: m00 m01 m02 m03 m10 m11 m12 m13 m20 m21 m22 m23 0 0 0 1

set(M) - Method in class mpicbg.models.ConstantModel

set(double, double, double, double, double, double, double, double, double) - Method in class mpicbg.models.HomographyModel2D

set(HomographyModel2D) - Method in class mpicbg.models.HomographyModel2D

set(IdentityModel) - Method in class mpicbg.models.IdentityModel

set(InterpolatedAffineModel1D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel1D

set(float, float) - Method in class mpicbg.models.InterpolatedAffineModel1D

Deprecated.

set(InterpolatedAffineModel2D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel2D

set(double, double, double, double, double, double) - Method in class mpicbg.models.InterpolatedAffineModel2D

Deprecated.

set(AffineTransform) - Method in class mpicbg.models.InterpolatedAffineModel2D

Deprecated.

set(InterpolatedAffineModel3D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel3D

set(M) - Method in class mpicbg.models.InterpolatedModel

set(M) - Method in interface mpicbg.models.Model

Set the model to m

set(double...) - Method in class mpicbg.models.PolynomialTransform2D

Set the coefficients.

set(RigidModel2D) - Method in class mpicbg.models.RigidModel2D

set(TranslationModel2D) - Method in class mpicbg.models.RigidModel2D

set(double, double, double) - Method in class mpicbg.models.RigidModel2D

Initialize the model such that the respective affine transform is: cos(θ) -sin(θ) tx sin(θ) cos(θ) ty 0 0 1

set(double, double, double, double) - Method in class mpicbg.models.RigidModel2D

Initialize the model such that the respective affine transform is: cos -sin tx sin cos ty 0 0 1

set(RigidModel3D) - Method in class mpicbg.models.RigidModel3D

set(TranslationModel3D) - Method in class mpicbg.models.RigidModel3D

set(double, double, double, double, double, double, double, double, double, double, double, double) - Method in class mpicbg.models.RigidModel3D

Deprecated.

set(SimilarityModel2D) - Method in class mpicbg.models.SimilarityModel2D

set(TranslationModel2D) - Method in class mpicbg.models.SimilarityModel2D

set(RigidModel2D) - Method in class mpicbg.models.SimilarityModel2D

set(double, double, double, double) - Method in class mpicbg.models.SimilarityModel2D

Initialize the model such that the respective affine transform is: scos -sin tx sin scos ty 0 0 1

set(SimilarityModel3D) - Method in class mpicbg.models.SimilarityModel3D

set(TranslationModel3D) - Method in class mpicbg.models.SimilarityModel3D

set(RigidModel3D) - Method in class mpicbg.models.SimilarityModel3D

set(TranslationModel1D) - Method in class mpicbg.models.TranslationModel1D

set(double) - Method in class mpicbg.models.TranslationModel1D

Initialize the model with an offset

set(TranslationModel2D) - Method in class mpicbg.models.TranslationModel2D

set(double, double) - Method in class mpicbg.models.TranslationModel2D

Initialize the model such that the respective affine transform is: 1 0 tx 0 1 ty 0 0 1

set(double, double, double) - Method in class mpicbg.models.TranslationModel3D

set(TranslationModel3D) - Method in class mpicbg.models.TranslationModel3D

set(Matrix3x3) - Method in class mpicbg.util.Matrix3x3

set(T) - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

setAlpha(double) - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

setCost(double) - Method in class mpicbg.models.AbstractModel

setCost(double) - Method in interface mpicbg.models.Model

setHandles() - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

setInitialSigma(float) - Method in class mpicbg.imagefeatures.FloatArray2DMOPS

setInitialSigma(float) - Method in class mpicbg.imagefeatures.FloatArray2DSIFT

setLambda(float) - Method in class mpicbg.models.InterpolatedCoordinateTransform

setLambda(double) - Method in class mpicbg.models.InterpolatedModel

setLength(double) - Method in class mpicbg.models.Spring

setMatches(Collection<PointMatch>) - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

setMatches(Collection<PointMatch>) - Method in class mpicbg.models.MovingLeastSquaresTransform

setMatches(Collection<PointMatch>) - Method in class mpicbg.models.MovingLeastSquaresTransform2

Set the control points.

setMatches(float[][], float[][], float[]) - Method in class mpicbg.models.MovingLeastSquaresTransform2

Set the control points passing them as arrays that are used by reference.

setModel(Model<?>) - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

setModel(Class<? extends Model<?>>) - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

setModel(M) - Method in class mpicbg.models.Tile

setOffset(int, int) - Method in class mpicbg.ij.integral.BlockPMCC

Set the offset and re-calculate sumsXY respectively.

setScaleRotationTranslation(double, double, double, double) - Method in class mpicbg.models.SimilarityModel2D

Initialize the model such that the respective affine transform is: s * cos(θ) -sin(θ) tx sin(θ) s * cos(θ) ty 0 0 1

setSlice(float) - Method in class mpicbg.ij.stack.AbstractTransformMapping

setSlice(float) - Method in interface mpicbg.ij.stack.Mapping

Set the slice

setWeight(int, double) - Method in class mpicbg.models.PointMatch

setWeight(int, double) - Method in class mpicbg.models.Spring

setWeights(double[]) - Method in class mpicbg.models.PointMatch

setWeights(double[]) - Method in class mpicbg.models.Spring

shiftWeight() - Method in class mpicbg.models.PointMatch

Get the first weights element and remove it from the list.

ShortInterpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.ShortInterpolator

showHelp() - Method in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

showHelp() - Method in class mpicbg.ij.integral.InteractiveDifferenceOfMean

showHelp() - Method in class mpicbg.ij.integral.InteractiveMean

showHelp() - Method in class mpicbg.ij.integral.InteractivePMCC

showHelp() - Method in class mpicbg.ij.integral.InteractiveScale

showHelp() - Method in class mpicbg.ij.integral.InteractiveSquarePMCC

showHelp() - Method in class mpicbg.ij.integral.InteractiveStandardDeviation

showHelp() - Method in class mpicbg.ij.integral.InteractiveTilt

showHelp() - Method in class mpicbg.ij.integral.InteractiveVariance

showIllustration - Static variable in class mpicbg.ij.InteractiveMapping

showPreview - Static variable in class mpicbg.ij.InteractiveMapping

SIFT - Class in mpicbg.ij

SIFT(FloatArray2DSIFT) - Constructor for class mpicbg.ij.SIFT

Constructor

SIGMA - Variable in class mpicbg.imagefeatures.FloatArray2DScaleOctave

sigma of gaussian kernels corresponding to the steps of the octave the first member is the sigma of the gaussian kernel that is assumed to be the generating kernel of the first gaussian image instance of the octave

SimilarityModel2D - Class in mpicbg.models

2d-similarity transformation models to be applied to points in 2d-space.

SimilarityModel2D() - Constructor for class mpicbg.models.SimilarityModel2D

SimilarityModel3D - Class in mpicbg.models

3d-rigid transformation models to be applied to points in 3d-space.

SimilarityModel3D() - Constructor for class mpicbg.models.SimilarityModel3D

sin - Variable in class mpicbg.models.RigidModel2D

size - Variable in class mpicbg.util.RingBuffer

size() - Method in class mpicbg.util.RingBuffer

slope - Variable in class mpicbg.models.ErrorStatistic

smoothForScale(FloatProcessor, double, float, float) - Static method in class mpicbg.ij.util.Filter

Smooth with a Gaussian kernel that represents downsampling at a given scale factor and sourceSigma.

smoothForScale(ImageProcessor, double, float, float) - Static method in class mpicbg.ij.util.Filter

Smooth with a Gaussian kernel that represents downsampling at a given scale factor and sourceSigma.

sortedValues - Variable in class mpicbg.models.ErrorStatistic

source - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform.Tuple

source - Variable in class mpicbg.ij.InteractiveMapping

source - Variable in class mpicbg.ij.MappingThread

source - Variable in class mpicbg.ij.PaintInvertibleCoordinateTransformThread

sourcePoints(Collection<PointMatch>, Collection<Point>) - Static method in class mpicbg.models.PointMatch

speed - Variable in class mpicbg.models.Vertex

Spring - Class in mpicbg.models

A simple spring model.

Spring(double, double[]) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring with an Array of weights.

Spring(double, double[], double) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring with an Array of weights.

Spring(double, double) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring with one weight.

Spring(double, double, double) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring with one weight.

Spring(double) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring without weight.

Spring(Point, Point, double[]) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring between two Points with an Array of weights.

Spring(Point, Point, double[], double) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring between two Points with an Array of weights.

Spring(Point, Point, double) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring between two Points with one weight.

Spring(Point, Point, double, double) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring between two Points with one weight.

Spring(Point, Point) - Constructor for class mpicbg.models.Spring

Constructor Create a Spring between two Points without weight.

SpringMesh - Class in mpicbg.models

A TransformMesh with all Vertices being interconnected by springs.

SpringMesh(int, int, double, double, double, double, double) - Constructor for class mpicbg.models.SpringMesh

SpringMesh(int, double, double, double, double, double) - Constructor for class mpicbg.models.SpringMesh

springs - Variable in class mpicbg.models.Vertex

A set of Springs.

SQRT2 - Static variable in class mpicbg.util.Util

squareDistance() - Method in class mpicbg.models.Point

Estimate the square distance of local and world coordinates.

squareDistance(Point, Point) - Static method in class mpicbg.models.Point

Estimate the square Euclidean distance of two Points in world space.

squareLength(double[], double[]) - Static method in class mpicbg.models.Spring

squareLocalDistance(Point, Point) - Static method in class mpicbg.models.Point

Estimate the square Euclidean distance of two Points in local space.

ssin - Variable in class mpicbg.models.SimilarityModel2D

stackIndex - Variable in class mpicbg.ij.MappingThread

start() - Method in class mpicbg.util.Timer

state - Variable in class mpicbg.imagefeatures.FloatArray2DScaleOctave

std(int, int) - Method in class mpicbg.ij.integral.BlockStatistics

Set all pixels in ip to their block STD for a block with given radius.

std(int) - Method in class mpicbg.ij.integral.BlockStatistics

Set all pixels in ip to their block STD for a block with given radius.

std - Variable in class mpicbg.models.ErrorStatistic

std0 - Variable in class mpicbg.models.ErrorStatistic

steps - Variable in class mpicbg.imagefeatures.FloatArray2DMOPS.Param

STEPS - Variable in class mpicbg.imagefeatures.FloatArray2DScaleOctave

steps per octave an octave consists of STEPS + 3 images to be

steps - Variable in class mpicbg.imagefeatures.FloatArray2DSIFT.Param

Steps per Scale Octave

stop() - Method in class mpicbg.util.Timer

strength - Variable in class mpicbg.models.PointMatch

sum - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator

Deprecated.

sumOfSquares - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator

Deprecated.

sums - Variable in class mpicbg.ij.integral.BlockStatistics

sums - Variable in class mpicbg.util.RealSum

sumsOfSquares - Variable in class mpicbg.ij.integral.BlockStatistics

sumX - Variable in class mpicbg.util.RealStreamPMCC

sumXX - Variable in class mpicbg.util.RealStreamPMCC

sumXY - Variable in class mpicbg.util.RealStreamPMCC

sumY - Variable in class mpicbg.util.RealStreamPMCC

sumYY - Variable in class mpicbg.util.RealStreamPMCC

T

t - Variable in class mpicbg.ij.FeatureTransform

t - Variable in class mpicbg.models.TranslationModel1D

target - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform.Tuple

target - Variable in class mpicbg.ij.InteractiveMapping

target - Variable in class mpicbg.ij.MappingThread

target - Variable in class mpicbg.ij.PaintInvertibleCoordinateTransformThread

targetIndex - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

targetIndex - Variable in class mpicbg.ij.InteractiveMapping

targetPoints(Collection<PointMatch>, Collection<Point>) - Static method in class mpicbg.models.PointMatch

temp - Variable in class mpicbg.ij.MappingThread

test(Collection<P>, Collection<P>, double, double, int) - Method in class mpicbg.models.AbstractModel

Test the AbstractModel for a set of PointMatch candidates.

test(Collection<P>, Collection<P>, double, double) - Method in class mpicbg.models.AbstractModel

Call AbstractModel.test(Collection, Collection, double, double, int) with minNumInliers = Model.getMinNumMatches().

test(Collection<P>, Collection<P>, double, double, int) - Method in interface mpicbg.models.Model

Test the Model for a set of PointMatch candidates.

test(Collection<P>, Collection<P>, double, double) - Method in interface mpicbg.models.Model

Call Model.test(Collection, Collection, double, double, int) with minNumInliers = Model.getMinNumMatches().

Tile<M extends Model<M>> - Class in mpicbg.models

Tile(M) - Constructor for class mpicbg.models.Tile

Constructor

TileConfiguration - Class in mpicbg.models

A configuration of tiles.

TileConfiguration() - Constructor for class mpicbg.models.TileConfiguration

tiles - Variable in class mpicbg.models.TileConfiguration

TileUtil - Class in mpicbg.models

TileUtil() - Constructor for class mpicbg.models.TileUtil

tilt - Variable in class mpicbg.ij.integral.InteractiveTilt

Tilt - Class in mpicbg.ij.integral

Tilt(ColorProcessor) - Constructor for class mpicbg.ij.integral.Tilt

Tilt(ByteProcessor) - Constructor for class mpicbg.ij.integral.Tilt

Tilt(ShortProcessor) - Constructor for class mpicbg.ij.integral.Tilt

Tilt(FloatProcessor) - Constructor for class mpicbg.ij.integral.Tilt

Timer - Class in mpicbg.util

Timer() - Constructor for class mpicbg.util.Timer

toArray(double[]) - Method in interface mpicbg.models.Affine1D

Write the 2 parameters of the affine into a double array.

toArray(double[]) - Method in interface mpicbg.models.Affine2D

Write the 6 parameters of the affine into a double array.

toArray(double[]) - Method in interface mpicbg.models.Affine3D

Write the 12 parameters of the affine into a double array.

toArray(double[]) - Method in class mpicbg.models.AffineModel1D

toArray(double[]) - Method in class mpicbg.models.AffineModel2D

toArray(double[]) - Method in class mpicbg.models.AffineModel3D

toArray(double[]) - Method in class mpicbg.models.ConstantAffineModel1D

toArray(double[]) - Method in class mpicbg.models.IdentityModel

toArray(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

toArray(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

toArray(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

toArray(double[]) - Method in class mpicbg.models.RigidModel2D

toArray(double[]) - Method in class mpicbg.models.RigidModel3D

toArray(double[]) - Method in class mpicbg.models.SimilarityModel2D

toArray(double[]) - Method in class mpicbg.models.SimilarityModel3D

toArray(double[]) - Method in class mpicbg.models.TranslationModel1D

toArray(double[]) - Method in class mpicbg.models.TranslationModel2D

toArray(double[]) - Method in class mpicbg.models.TranslationModel3D

toArray() - Method in class mpicbg.util.RingBuffer

toMatrix(double[][]) - Method in interface mpicbg.models.Affine1D

Write the 2 parameters of the affine into a 2x1 double array.

toMatrix(double[][]) - Method in interface mpicbg.models.Affine2D

Write the 6 parameters of the affine into a 3x2 double array.

toMatrix(double[][]) - Method in interface mpicbg.models.Affine3D

Write the 12 parameters of the affine into a 4x3 double array.

toMatrix(double[][]) - Method in class mpicbg.models.AffineModel1D

toMatrix(double[][]) - Method in class mpicbg.models.AffineModel2D

toMatrix(double[][]) - Method in class mpicbg.models.AffineModel3D

toMatrix(double[][]) - Method in class mpicbg.models.ConstantAffineModel1D

toMatrix(double[][]) - Method in class mpicbg.models.IdentityModel

toMatrix(double[][]) - Method in class mpicbg.models.InterpolatedAffineModel1D

toMatrix(double[][]) - Method in class mpicbg.models.InterpolatedAffineModel2D

toMatrix(double[][]) - Method in class mpicbg.models.InterpolatedAffineModel3D

toMatrix(double[][]) - Method in class mpicbg.models.RigidModel2D

toMatrix(double[][]) - Method in class mpicbg.models.RigidModel3D

toMatrix(double[][]) - Method in class mpicbg.models.SimilarityModel2D

toMatrix(double[][]) - Method in class mpicbg.models.SimilarityModel3D

toMatrix(double[][]) - Method in class mpicbg.models.TranslationModel1D

toMatrix(double[][]) - Method in class mpicbg.models.TranslationModel2D

toMatrix(double[][]) - Method in class mpicbg.models.TranslationModel3D

toProcessor() - Method in class mpicbg.ij.integral.DoubleIntegralImage

toString() - Method in class mpicbg.models.AbstractAffineModel2D

toString() - Method in class mpicbg.models.AffineModel1D

toString() - Method in class mpicbg.models.AffineModel3D

toString() - Method in class mpicbg.models.HomographyModel2D

toString() - Method in class mpicbg.models.RigidModel3D

toString() - Method in class mpicbg.models.SimilarityModel3D

toString() - Method in class mpicbg.models.TranslationModel3D

traceConnectedGraph(Set<Tile<?>>) - Method in class mpicbg.models.Tile

Find all Tiles that represent one connectivity graph by recursively tracing the Tile.connectedTiles.

traceConnectedGraph(Set<Vertex>) - Method in class mpicbg.models.Vertex

Find all Vertices that represent one connectivity graph by recursively tracing the Vertex.springs.

transferValue(int, int[]) - Static method in class mpicbg.ij.clahe.Util

Transfer a value.

transferValue(int, int[], int[], int) - Static method in class mpicbg.ij.clahe.Util

Transfer a value through contrast limited histogram equalization.

transform - Variable in class mpicbg.ij.InverseTransformMapping

transform - Variable in class mpicbg.ij.InvertibleTransformMapping

transform - Variable in class mpicbg.ij.PaintInvertibleCoordinateTransformThread

transform - Variable in class mpicbg.ij.stack.AbstractTransformMapping

transform - Variable in class mpicbg.ij.TransformMapping

TransformList<E> - Interface in mpicbg.models

A generic list of transforms

TransformMapping<T extends CoordinateTransform> - Class in mpicbg.ij.stack

Use a CoordinateTransform to map source into target which is a projective Mapping.

TransformMapping(T) - Constructor for class mpicbg.ij.stack.TransformMapping

TransformMapping<T extends CoordinateTransform> - Class in mpicbg.ij

Use a CoordinateTransform to map source into target which is an InverseMapping.

TransformMapping(T) - Constructor for class mpicbg.ij.TransformMapping

TransformMesh - Class in mpicbg.models

Triangular transformation mesh.

TransformMesh(int, int, double, double, PointFactory<?>, PointMatchFactory<?>) - Constructor for class mpicbg.models.TransformMesh

TransformMesh(int, int, double, double) - Constructor for class mpicbg.models.TransformMesh

TransformMesh(int, double, double) - Constructor for class mpicbg.models.TransformMesh

TransformMeshMap2D - Class in mpicbg.models

TransformMeshMap2D(TransformMesh, int, int) - Constructor for class mpicbg.models.TransformMeshMap2D

TransformMeshMapping<T extends TransformMesh> - Class in mpicbg.ij

Use a TransformMesh to map and map inversely source into target which is an InvertibleMapping.

TransformMeshMapping(T) - Constructor for class mpicbg.ij.TransformMeshMapping

transforms - Variable in class mpicbg.models.CoordinateTransformList

transforms - Variable in class mpicbg.models.InvertibleCoordinateTransformList

Transforms - Class in mpicbg.models

Exclusively static methods that would ideally be implemented in CoordinateTransform and related interfaces, but well---this is Java where multiple inheritance is considered evil...

translation - Variable in class mpicbg.models.TranslationModel3D

TranslationModel1D - Class in mpicbg.models

1d-translation AbstractModel to be applied to points in 1d-space.

TranslationModel1D() - Constructor for class mpicbg.models.TranslationModel1D

TranslationModel2D - Class in mpicbg.models

2d-translation AbstractModel to be applied to points in 2d-space.

TranslationModel2D() - Constructor for class mpicbg.models.TranslationModel2D

TranslationModel3D - Class in mpicbg.models

TranslationModel3D() - Constructor for class mpicbg.models.TranslationModel3D

tuples - Variable in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

tx - Variable in class mpicbg.models.RigidModel2D

tx - Variable in class mpicbg.models.SimilarityModel2D

tx - Variable in class mpicbg.models.TranslationModel2D

ty - Variable in class mpicbg.models.RigidModel2D

ty - Variable in class mpicbg.models.SimilarityModel2D

ty - Variable in class mpicbg.models.TranslationModel2D

U

unshiftWeight(double) - Method in class mpicbg.models.PointMatch

Append a new element to the left side of the weights list.

update(double) - Method in class mpicbg.models.ElasticMovingLeastSquaresMesh

Update all PointMatches in all tiles and estimate the average displacement by weight of the PointMatch.

update(double) - Method in class mpicbg.models.SpringMesh

Move all vertices for a given Δt

update() - Method in class mpicbg.models.Tile

Apply the current AbstractModel to all local point coordinates.

update(double) - Method in class mpicbg.models.Tile

Apply the current AbstractModel to all local point coordinates by weight.

update() - Method in class mpicbg.models.TileConfiguration

Update all Correspondences in all Tiles and estimate the average displacement.

update(double, double) - Method in class mpicbg.models.Vertex

Calculate the current force, direction and speed.

update(double) - Method in class mpicbg.models.Vertex

Deprecated.

Remains for legacy compatibility

updateAffine(PointMatch) - Method in class mpicbg.models.TransformMesh

Update all affine transformations that would have been affected by a given Vertex.

updateAffines() - Method in class mpicbg.models.SpringMesh

updateAffines() - Method in class mpicbg.models.TransformMesh

Update all affine transformations.

updateCost() - Method in class mpicbg.models.Tile

Update Tile.cost and Tile.distance.

updateDirection(double) - Method in class mpicbg.models.SpringMesh

Calculate motion vectors for all vertices.

updateDirection(double, double) - Method in class mpicbg.models.Vertex

Calculate the current direction and speed.

updateErrors() - Method in class mpicbg.models.TileConfiguration

Estimate min/max/average displacement of all PointMatches in all Tiles.

updateErrors(ThreadPoolExecutor) - Method in class mpicbg.models.TileConfiguration

Estimate min/max/average displacement of all PointMatches in all Tiles using a given ThreadPoolExecutor.

updateForce(ErrorStatistic) - Method in class mpicbg.models.SpringMesh

Update force vectors for all vertices.

updateForce() - Method in class mpicbg.models.Vertex

Calculate the current force.

updateHandles(int, int) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

updateHandles(int, int) - Method in class mpicbg.ij.InteractiveMapping

updateIllustration() - Method in class mpicbg.ij.InteractiveMapping

updateMapping() - Method in class mpicbg.ij.InteractiveMapping

updateModels() - Method in class mpicbg.models.MovingLeastSquaresMesh

Updates each vertex' transformation model by means of moving least squares.

updatePassiveVertices() - Method in class mpicbg.models.SpringMesh

updateRoi() - Method in class mpicbg.ij.InteractiveMapping

upsample(FloatArray2D, FloatArray2D) - Static method in class mpicbg.imagefeatures.FloatArray2DScaleOctave

Upsample src by linearly interpolating into dst.

useRoi(float[], float[]) - Static method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform

Util - Class in mpicbg.ij.clahe

"Contrast Limited Adaptive Histogram Equalization" as described in BibTeX: @article{zuiderveld94, author = {Zuiderveld, Karel}, title = {Contrast limited adaptive histogram equalization}, book = {Graphics gems IV}, year = {1994}, isbn = {0-12-336155-9}, pages = {474--485}, publisher = {Academic Press Professional, Inc.}, address = {San Diego, CA, USA}, }

Util() - Constructor for class mpicbg.ij.clahe.Util

Util - Class in mpicbg.ij.util

Util - Class in mpicbg.util

Methods collection for general purpose that do not have a common context

V

va - Variable in class mpicbg.models.TransformMesh

valueOf(String) - Static method in enum mpicbg.imagefeatures.FloatArray2DScaleOctave.State

Returns the enum constant of this type with the specified name.

values() - Static method in enum mpicbg.imagefeatures.FloatArray2DScaleOctave.State

Returns an array containing the constants of this enum type, in the order they are declared.

values - Variable in class mpicbg.models.ErrorStatistic

var - Variable in class mpicbg.models.ErrorStatistic

var0 - Variable in class mpicbg.models.ErrorStatistic

variance(int, int) - Method in class mpicbg.ij.integral.BlockStatistics

Set all pixels in ip to their block variance for a block with given radius.

variance(int) - Method in class mpicbg.ij.integral.BlockStatistics

Set all pixels in ip to their block variance for a block with given radius.

Vertex - Class in mpicbg.models

An n-dimensional Vertex being connected to other Vertices by Springs

Vertex(double[]) - Constructor for class mpicbg.models.Vertex

Constructor

Vertex(double[], double[]) - Constructor for class mpicbg.models.Vertex

Constructor

Vertex(Point) - Constructor for class mpicbg.models.Vertex

Constructor The Vertex takes over the coordinates of the Point by pointer.

vertices - Variable in class mpicbg.models.SpringMesh

vp - Variable in class mpicbg.models.SpringMesh

W

w - Variable in class mpicbg.models.MovingLeastSquaresTransform2

w - Variable in class mpicbg.models.Point

World coordinates

w1 - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator

Deprecated.

weigh(double) - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

weigh(double, double) - Method in class mpicbg.models.MovingLeastSquaresMesh

weigh(double, double) - Method in class mpicbg.models.SpringMesh

weight - Variable in class mpicbg.models.PointMatch

weight - Variable in class mpicbg.models.Spring

weights - Variable in class mpicbg.models.PointMatch

weights - Variable in class mpicbg.models.Spring

width - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator

Deprecated.

width - Variable in class mpicbg.imagefeatures.FloatArray2D

width - Variable in class mpicbg.imagefeatures.FloatArray2DScaleOctave

width - Variable in class mpicbg.models.CoordinateTransformMap2D

width - Variable in class mpicbg.models.InverseCoordinateTransformMap2D

width - Variable in class mpicbg.models.TransformMesh

window - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter

X

x1 - Variable in class mpicbg.ij.integral.InteractiveTilt

x2 - Variable in class mpicbg.ij.integral.InteractiveTilt

Y

y1 - Variable in class mpicbg.ij.integral.InteractiveTilt

y2 - Variable in class mpicbg.ij.integral.InteractiveTilt

Z

z - Variable in class mpicbg.ij.stack.AbstractTransformMapping

A B C D E F G H I K L M N O P Q R S T U V W X Y Z