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.
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
 
AbstractBlockFilter - Class in mpicbg.ij.plugin
Abstract base class for variance and STD filters.
AbstractBlockFilter() - Constructor for class mpicbg.ij.plugin.AbstractBlockFilter
 
AbstractBlockStatistics - Class in mpicbg.ij.plugin
Abstract base class for variance and STD filters.
AbstractBlockStatistics() - Constructor for class mpicbg.ij.plugin.AbstractBlockStatistics
 
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.ByteInterpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.ByteInterpolator
 
AbstractTransformMapping.FloatInterpolator - Class in mpicbg.ij.stack
 
AbstractTransformMapping.FloatInterpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.FloatInterpolator
 
AbstractTransformMapping.Interpolator - Class in mpicbg.ij.stack
 
AbstractTransformMapping.Interpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.Interpolator
 
AbstractTransformMapping.RGBInterpolator - Class in mpicbg.ij.stack
 
AbstractTransformMapping.RGBInterpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.RGBInterpolator
 
AbstractTransformMapping.ShortInterpolator - Class in mpicbg.ij.stack
 
AbstractTransformMapping.ShortInterpolator() - Constructor for class mpicbg.ij.stack.AbstractTransformMapping.ShortInterpolator
 
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
Doesn not check for index < 0 for efficiency resons, 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
 
addHandle(int, int) - Method in class Transform_MovingLeastSquaresMesh
 
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
 
adjustmentValueChanged(AdjustmentEvent) - Method in class Stack_Rotate
 
affine - Variable in class mpicbg.models.InterpolatedAffineModel1D
 
affine - Variable in class mpicbg.models.InterpolatedAffineModel2D
 
affine - Variable in class mpicbg.models.InterpolatedAffineModel3D
 
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
 
afs - Variable in class mpicbg.models.InterpolatedAffineModel1D
 
afs - Variable in class mpicbg.models.InterpolatedAffineModel2D
 
afs - Variable in class mpicbg.models.InterpolatedAffineModel3D
 
AlignStacksWithLandmarks - Class in mpicbg.ij.plugin
 
AlignStacksWithLandmarks() - Constructor for class mpicbg.ij.plugin.AlignStacksWithLandmarks
 
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(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
 
apply() - Method in class Transform_SpringMesh
 
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 class mpicbg.models.InterpolatedAffineModel1D
 
applyInverse(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D
 
applyInverse(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D
 
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 a InvertibleModel 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.
bfs - Variable in class mpicbg.models.InterpolatedAffineModel1D
 
bfs - Variable in class mpicbg.models.InterpolatedAffineModel2D
 
bfs - Variable in class mpicbg.models.InterpolatedAffineModel3D
 
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.
blockRadius - Static variable in class mpicbg.ij.plugin.MSEBlockFlow
 
blockRadius - Static variable in class mpicbg.ij.plugin.PMCCBlockFlow
 
blockRadiusX - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter
 
blockRadiusX - Static variable in class mpicbg.ij.plugin.AbstractBlockFilter
 
blockRadiusX - Static variable in class mpicbg.ij.plugin.Mean
 
blockRadiusY - Variable in class mpicbg.ij.integral.AbstractInteractiveBlockFilter
 
blockRadiusY - Static variable in class mpicbg.ij.plugin.AbstractBlockFilter
 
blockRadiusY - Static variable in class mpicbg.ij.plugin.Mean
 
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
 
BlockStatistics.RowIntegrator(double[], double[], int, int, int) - Constructor for class mpicbg.ij.integral.BlockStatistics.RowIntegrator
 
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
brx - Variable in class mpicbg.ij.plugin.AbstractBlockFilter
 
bry - Variable in class mpicbg.ij.plugin.AbstractBlockFilter
 
bs - Static variable in class mpicbg.util.ColorStream
 
bss - Variable in class mpicbg.ij.plugin.AbstractBlockStatistics
 
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.

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
 
cent - Variable in class mpicbg.ij.plugin.NormalizeLocalContrast
 
center - Static variable in class mpicbg.ij.plugin.NormalizeLocalContrast
 
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.plugin.MSEBlockFlow
 
colorCircle(ColorProcessor) - Static method in class mpicbg.ij.plugin.MSEGaussianFlow
 
colorCircle(ColorProcessor) - Static method in class mpicbg.ij.plugin.PMCCBlockFlow
 
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
 
copyParameters() - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
copyParameters() - Method in class mpicbg.ij.plugin.AbstractBlockStatistics
 
copyParameters() - Method in class mpicbg.ij.plugin.NormalizeLocalContrast
 
copyParameters() - Method in class mpicbg.ij.plugin.RemoveOutliers
 
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
 
createAlignedStack(ImagePlus, ImagePlus, Collection<PointMatch>, M) - Static method in class mpicbg.ij.plugin.AlignStacksWithLandmarks
 
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.
createFeatureDescriptorImage(String, Feature) - Static method in class MOPS_ExtractPointRoi
 
createFeatureDescriptorShape(Feature) - Static method in class MOPS_ExtractPointRoi
Create a Shape that illustrates the descriptor patch.
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
 
createMapping() - Method in class Transform_MovingLeastSquaresMesh
 
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
createModel(int) - Static method in class mpicbg.ij.plugin.ElasticAlign
 
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.

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
 
deserialize(String) - Static method in class mpicbg.ij.plugin.ElasticAlign
Attempts to find a file containing a serialized object.
deserialize(String) - Static method in class mpicbg.ij.plugin.ElasticMontage
Attempts to find a file containing a serialized object.
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.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class mpicbg.ij.plugin.Mean
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class mpicbg.ij.plugin.NormalizeLocalContrast
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class mpicbg.ij.plugin.RemoveOutliers
 
dialogTitle() - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
dialogTitle() - Method in class mpicbg.ij.plugin.NormalizeLocalContrast
 
dialogTitle() - Method in class mpicbg.ij.plugin.RemoveOutliers
 
dialogTitle() - Method in class mpicbg.ij.plugin.SampleVariance
 
dialogTitle() - Method in class mpicbg.ij.plugin.StandardDeviation
 
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
 
DiffusionMask - Class in mpicbg.ij.plugin
Diffuse
DiffusionMask() - Constructor for class mpicbg.ij.plugin.DiffusionMask
 
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
 
DoubleIntegralImage(FloatProcessor) - Constructor for class mpicbg.ij.integral.DoubleIntegralImage
 
DoubleIntegralImage(ImageProcessor) - Constructor for class mpicbg.ij.integral.DoubleIntegralImage
 
downsample(FloatArray2D, FloatArray2D) - Static method in class mpicbg.imagefeatures.FloatArray2DScaleOctave
downsample src by simply using every second pixel into dst For efficiency reasons, the dimensions of dst are not checked, that is, you have to take care, that dst.width == src.width / 2 + src.width % 2 && dst.height == src.height / 2 + src.height % 2 .
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
 
drawFeatureDescriptor(FloatProcessor, Feature) - Static method in class MOPS_ExtractPointRoi
 
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

ElasticAlign - Class in mpicbg.ij.plugin
 
ElasticAlign() - Constructor for class mpicbg.ij.plugin.ElasticAlign
 
ElasticMontage - Class in mpicbg.ij.plugin
 
ElasticMontage() - Constructor for class mpicbg.ij.plugin.ElasticMontage
 
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
 
exec(ImagePlus, ImagePlus, float, int, int, int, int, int, float, float, float, int) - Method in class SIFT_ExtractPointRoi
If unsure, just use default parameters by using exec(ImagePlus, ImagePlus, int) method, where only the model is specified.
exec(ImagePlus, ImagePlus, int) - Method in class SIFT_ExtractPointRoi
Execute with default parameters, except the model.
exec(ImagePlus, ImagePlus) - Method in class SIFT_ExtractPointRoi
Execute with default parameters (model is Rigid)
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
&lsquot;Contrast Limited Adaptive Histogram Equalization&rsquot; as described in
BibTeX:
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 How many samples per row and column
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 - Static variable in class mpicbg.ij.plugin.MSEGaussianFlow
 
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 #filter(Collection, Collection, float, int) with minNumInliers = Model.getMinNumMatches().
filter(Collection<P>, Collection<P>) - Method in interface mpicbg.models.Model
Call #filter(Collection, Collection, float) 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 #filterRansac(List, Collection, int, float, float, int, float) with maxTrust = 4.
filterRansac(List<P>, Collection<P>, int, double, double, double) - Method in interface mpicbg.models.Model
Call #filterRansac(List, Collection, int, float, float, int, float) with minNumInliers = Model.getMinNumMatches().
filterRansac(List<P>, Collection<P>, int, double, double) - Method in interface mpicbg.models.Model
Call #filterRansac(List, Collection, int, float, float, float) with maxTrust = 4.
Find_PointRoi - Class in <Unnamed>
 
Find_PointRoi() - Constructor for class Find_PointRoi
 
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 - Static variable in class mpicbg.ij.plugin.AbstractBlockFilter
 
flags - Static variable in class mpicbg.ij.plugin.Mean
 
flags - Variable in class mpicbg.util.RealSum
 
Flat - Class in mpicbg.ij.clahe
&lsquot;Contrast Limited Adaptive Histogram Equalization&rsquot; as described in
BibTeX:
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
 
FloatArray2DMOPS.Param() - Constructor for class mpicbg.imagefeatures.FloatArray2DMOPS.Param
 
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
 
FloatArray2DSIFT.Param() - Constructor for class mpicbg.imagefeatures.FloatArray2DSIFT.Param
 
floatArray2DToFloatProcessor(FloatArray2D, FloatProcessor) - Static method in class mpicbg.imagefeatures.ImageArrayConverter
 
FloatArrayToImagePlus(FloatArray2D, String, float, float) - Static method in class mpicbg.imagefeatures.ImageArrayConverter
 
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
 
fps - Variable in class mpicbg.ij.plugin.AbstractBlockFilter
 

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
Doesn not check for index < 0 for efficiency resons, 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
 
getDoubleSum(int, int, int, int) - Method in class mpicbg.ij.integral.DoubleIntegralImage
 
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.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.ij.integral.LongRGBIntegralImage
 
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
 
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 .
illustrateSprings(ColorProcessor, double, double) - Method in class mpicbg.models.SpringMesh
Paint all into a ColorProcessor.
illustrateSprings(ColorProcessor, double, double, double, double) - Method in class mpicbg.models.SpringMesh
Paint all 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 MOPS_ExtractPointRoi
 
imageClosed(ImagePlus) - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform
 
imageClosed(ImagePlus) - Method in class mpicbg.ij.InteractiveMapping
 
imageOpened(ImagePlus) - Method in class MOPS_ExtractPointRoi
 
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 MOPS_ExtractPointRoi
 
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(ImagePlus) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
init(ImagePlus) - Method in class mpicbg.ij.plugin.AbstractBlockStatistics
 
init(ImagePlus) - Method in class mpicbg.ij.plugin.NormalizeLocalContrast
 
init(ImagePlus) - Method in class mpicbg.ij.plugin.RemoveOutliers
 
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.
init() - Method in class Transform_MovingLeastSquaresMesh
 
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, int, int, double[], double[], int) - Static method in class mpicbg.ij.integral.BlockStatistics
 
integrateRows(int, 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
 
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
 
interpolate - Variable in class Stack_Rotate.MappingThread
 
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
 
IntIntegralImage - Class in mpicbg.ij.integral
 
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 MOPS_ExtractPointRoi
 
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
 
keyPressed(KeyEvent) - Method in class mpicbg.ij.plugin.ElasticAlign
 
keyPressed(KeyEvent) - Method in class mpicbg.ij.plugin.MSEGaussianFlow
 
keyPressed(KeyEvent) - Method in class SIFT_Align
 
keyPressed(KeyEvent) - Method in class Stack_Rotate
 
keyPressed(KeyEvent) - Method in class Transform_SpringMesh
 
keyReleased(KeyEvent) - Method in class MOPS_ExtractPointRoi
 
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
 
keyReleased(KeyEvent) - Method in class mpicbg.ij.plugin.ElasticAlign
 
keyReleased(KeyEvent) - Method in class mpicbg.ij.plugin.MSEGaussianFlow
 
keyReleased(KeyEvent) - Method in class SIFT_Align
 
keyReleased(KeyEvent) - Method in class Stack_Rotate
 
keyReleased(KeyEvent) - Method in class Transform_SpringMesh
 
keyTyped(KeyEvent) - Method in class MOPS_ExtractPointRoi
 
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
 
keyTyped(KeyEvent) - Method in class mpicbg.ij.plugin.ElasticAlign
 
keyTyped(KeyEvent) - Method in class mpicbg.ij.plugin.MSEGaussianFlow
 
keyTyped(KeyEvent) - Method in class SIFT_Align
 
keyTyped(KeyEvent) - Method in class Stack_Rotate
 
keyTyped(KeyEvent) - Method in class Transform_SpringMesh
 

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(!) integer value.
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
 
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
 
man - Static variable in class Transform_MovingLeastSquaresMesh
 
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.
mapping - Variable in class Transform_SpringMesh
 
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.
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(List<Feature>, List<Feature>, List<PointMatch>, double) - Static method in class mpicbg.imagefeatures.Feature
Identify corresponding features
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 - Static variable in class mpicbg.ij.plugin.MSEBlockFlow
 
maxDistance - Static variable in class mpicbg.ij.plugin.MSEGaussianFlow
 
maxDistance - Static variable in class mpicbg.ij.plugin.PMCCBlockFlow
 
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 - Class in mpicbg.ij.plugin
Apply a mean filter.
Mean() - Constructor for class mpicbg.ij.plugin.Mean
 
mean - Variable in class mpicbg.ij.plugin.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
mesh - Variable in class Transform_MovingLeastSquaresMesh
 
mesh - Variable in class Transform_SpringMesh
 
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.
model - Variable in class Transform_Affine
 
model - Variable in class Transform_Perspective
 
model - Variable in class Transform_RegularizedAffine
 
model - Variable in class Transform_Rigid
 
model - Variable in class Transform_Similarity
 
modelClass - Variable in class mpicbg.models.MovingLeastSquaresMesh
 
modifiers(int) - Static method in class MOPS_ExtractPointRoi
 
modifiers(int) - Static method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform
 
modifiers(int) - Static method in class mpicbg.ij.InteractiveMapping
 
modifiers(int) - Static method in class Stack_Rotate
 
modifiers(int) - Static method in class Transform_SpringMesh
 
MOPS - Class in mpicbg.ij
 
MOPS(FloatArray2DMOPS) - Constructor for class mpicbg.ij.MOPS
Constructor
MOPS_ExtractPointRoi - Class in <Unnamed>
Extract landmark correspondences in two images as PointRoi.
MOPS_ExtractPointRoi() - Constructor for class MOPS_ExtractPointRoi
 
mouseClicked(MouseEvent) - Method in class MOPS_ExtractPointRoi
 
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
 
mouseClicked(MouseEvent) - Method in class Stack_Rotate
 
mouseClicked(MouseEvent) - Method in class Transform_SpringMesh
 
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
 
mouseDragged(MouseEvent) - Method in class Stack_Rotate
 
mouseDragged(MouseEvent) - Method in class Transform_SpringMesh
 
mouseEntered(MouseEvent) - Method in class MOPS_ExtractPointRoi
 
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
 
mouseEntered(MouseEvent) - Method in class Stack_Rotate
 
mouseEntered(MouseEvent) - Method in class Transform_SpringMesh
 
mouseExited(MouseEvent) - Method in class MOPS_ExtractPointRoi
 
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
 
mouseExited(MouseEvent) - Method in class Stack_Rotate
 
mouseExited(MouseEvent) - Method in class Transform_SpringMesh
 
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
 
mouseMoved(MouseEvent) - Method in class Stack_Rotate
 
mouseMoved(MouseEvent) - Method in class Transform_SpringMesh
 
mousePressed(MouseEvent) - Method in class MOPS_ExtractPointRoi
 
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
 
mousePressed(MouseEvent) - Method in class Stack_Rotate
 
mousePressed(MouseEvent) - Method in class Transform_SpringMesh
 
mouseReleased(MouseEvent) - Method in class MOPS_ExtractPointRoi
 
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
 
mouseReleased(MouseEvent) - Method in class Stack_Rotate
 
mouseReleased(MouseEvent) - Method in class Transform_SpringMesh
 
mouseWheelMoved(MouseWheelEvent) - Method in class mpicbg.ij.integral.InteractiveDifferenceOfMean
 
mouseWheelMoved(MouseWheelEvent) - Method in class Stack_Rotate
 
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.plugin - package mpicbg.ij.plugin
 
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
 
MSEBlockFlow - Class in mpicbg.ij.plugin
Transfer an image sequence into an optic flow field
MSEBlockFlow() - Constructor for class mpicbg.ij.plugin.MSEBlockFlow
 
MSEGaussianFlow - Class in mpicbg.ij.plugin
Transfer an image sequence into an optic flow field
MSEGaussianFlow() - Constructor for class mpicbg.ij.plugin.MSEGaussianFlow
 
myModel() - Method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform
 
myModel() - Method in class Transform_Affine
 
myModel() - Method in class Transform_Perspective
 
myModel() - Method in class Transform_RegularizedAffine
 
myModel() - Method in class Transform_Rigid
 
myModel() - Method in class Transform_Similarity
 

N

n - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator
 
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
 
NL - Static variable in class Transform_MovingLeastSquaresMesh
 
nlcs - Variable in class mpicbg.ij.plugin.NormalizeLocalContrast
 
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
 
NormalizeLocalContrast - Class in mpicbg.ij.plugin
Normalize contrast based on per-pixel mean and STD.
NormalizeLocalContrast() - Constructor for class mpicbg.ij.plugin.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
 
onReturn() - Method in class Transform_Affine
 
onReturn() - Method in class Transform_RegularizedAffine
 
onReturn() - Method in class Transform_Rigid
 
onReturn() - Method in class Transform_Similarity
 
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
 
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
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
 
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.ij.plugin.MSEBlockFlow
 
pingPong(int, int) - Static method in class mpicbg.ij.plugin.MSEGaussianFlow
 
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 ...
pip - Variable in class mpicbg.ij.plugin.AbstractBlockFilter
 
pip - Variable in class mpicbg.ij.plugin.Mean
 
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
 
PlugIn - Class in mpicbg.ij.clahe
&lsquot;Contrast Limited Adaptive Histogram Equalization&rsquot; as described in
BibTeX:
PlugIn() - Constructor for class mpicbg.ij.clahe.PlugIn
 
PMCCBlockFlow - Class in mpicbg.ij.plugin
Transfer an image sequence into an optic flow field
PMCCBlockFlow() - Constructor for class mpicbg.ij.plugin.PMCCBlockFlow
 
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
 
process(int) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
process(int) - Method in class mpicbg.ij.plugin.NormalizeLocalContrast
 
process(int) - Method in class mpicbg.ij.plugin.RemoveOutliers
 
process(int) - Method in class mpicbg.ij.plugin.SampleVariance
 
process(int) - Method in class mpicbg.ij.plugin.StandardDeviation
 
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 rXY 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
Doesn not check for index < 0 for efficiency resons, so be sure not to pass negative indices.
remove() - Method in class mpicbg.util.RingBuffer.RingBufferIterator
TODO Should we implement this? It is very random, where an iterator ...
remove() - Method in class mpicbg.util.RingBuffer.RingBufferListIterator
 
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
 
RemoveOutliers - Class in mpicbg.ij.plugin
Remove saturated pixels by diffusing the neighbors in.
RemoveOutliers() - Constructor for class mpicbg.ij.plugin.RemoveOutliers
 
removePassiveVertex(Vertex) - Method in class mpicbg.models.SpringMesh
Remove a passive vertex.
RemoveSaturated - Class in mpicbg.ij.plugin
Remove saturated pixels by diffusing the neighbors in.
RemoveSaturated() - Constructor for class mpicbg.ij.plugin.RemoveSaturated
 
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
 
repaint() - Method in class Stack_Rotate.MappingThread
 
reset() - Method in class mpicbg.util.Matrix3x3
Set to identity.
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.RingBufferIterator() - Constructor for class mpicbg.util.RingBuffer.RingBufferIterator
 
RingBuffer.RingBufferListIterator - Class in mpicbg.util
 
RingBuffer.RingBufferListIterator() - Constructor for class mpicbg.util.RingBuffer.RingBufferListIterator
 
RingBuffer.RingBufferListIterator(int) - Constructor for class mpicbg.util.RingBuffer.RingBufferListIterator
 
rmos - Variable in class mpicbg.ij.plugin.RemoveOutliers
 
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
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 rXY2 for the current offset with given radius.
rSignedSquare(int) - Method in class mpicbg.ij.integral.BlockPMCC
 
run(String) - Method in class Find_PointRoi
 
run(String) - Method in class MOPS_ExtractPointRoi
 
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(String) - Method in class mpicbg.ij.clahe.PlugIn
PlugIn access
run(ImagePlus) - Static method in class mpicbg.ij.clahe.PlugIn
Process an ImagePlus with the static parameters.
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
 
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(ImageProcessor) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
run(String) - Method in class mpicbg.ij.plugin.AlignStacksWithLandmarks
 
run(ImageProcessor, FloatProcessor, int) - Static method in class mpicbg.ij.plugin.DiffusionMask
 
run(String) - Method in class mpicbg.ij.plugin.DiffusionMask
 
run(String) - Method in class mpicbg.ij.plugin.ElasticAlign
 
run() - Method in class mpicbg.ij.plugin.ElasticAlign
 
run(String) - Method in class mpicbg.ij.plugin.ElasticMontage
 
run() - Method in class mpicbg.ij.plugin.ElasticMontage
 
run(ImageProcessor) - Method in class mpicbg.ij.plugin.Mean
 
run(String) - Method in class mpicbg.ij.plugin.MSEBlockFlow
 
run(String) - Method in class mpicbg.ij.plugin.MSEGaussianFlow
 
run(ImageProcessor, int, int, float, boolean, boolean) - Static method in class mpicbg.ij.plugin.NormalizeLocalContrast
Apply local contrast enhancement to and ImageProcessor.
run(String) - Method in class mpicbg.ij.plugin.PMCCBlockFlow
 
run(ImageProcessor, int, int, float) - Static method in class mpicbg.ij.plugin.RemoveOutliers
Remove outlier pixels from an ImageProcessor.
run(ImageProcessor, float) - Static method in class mpicbg.ij.plugin.RemoveSaturated
 
run(String) - Method in class mpicbg.ij.plugin.RemoveSaturated
 
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
run(String) - Method in class SIFT_Align
 
run(String) - Method in class SIFT_ExtractPointRoi
 
run(String) - Method in class SIFT_Test
 
run() - Method in class Stack_Rotate.MappingThread
 
run(String) - Method in class Stack_Rotate
 
run(String) - Method in class Transform_Roi
 
run(String) - Method in class Transform_SpringMesh
 
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.
SampleVariance - Class in mpicbg.ij.plugin
Sample variance block filter.
SampleVariance() - Constructor for class mpicbg.ij.plugin.SampleVariance
 
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
 
serialize(Object, String) - Static method in class mpicbg.ij.plugin.ElasticAlign
Serializes the given object into the path.
serialize(Object, String) - Static method in class mpicbg.ij.plugin.ElasticMontage
Serializes the given object into the path.
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(double, double) - Method in class mpicbg.models.AffineModel1D
Initialize the model such that the respective affine transform is:
set(AffineModel2D) - 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(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:
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
Initialize the model such that the respective affine transform is:
set(InterpolatedAffineModel2D<A, B>) - Method in class mpicbg.models.InterpolatedAffineModel2D
 
set(double, double, double, double, double, double) - Method in class mpicbg.models.InterpolatedAffineModel2D
Initialize the model such that the respective affine transform is:
set(AffineTransform) - Method in class mpicbg.models.InterpolatedAffineModel2D
Initialize the model with the parameters of an AffineTransform.
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(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(double, double, double, double, double, double, double, double, double, double, double, double) - Method in class mpicbg.models.RigidModel3D
Initialize the model such that the respective affine transform is:
set(SimilarityModel2D) - 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:
set(SimilarityModel3D) - 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
 
setHandles() - Method in class Transform_Affine
 
setHandles() - Method in class Transform_Perspective
 
setHandles() - Method in class Transform_RegularizedAffine
 
setHandles() - Method in class Transform_Rigid
 
setHandles() - Method in class Transform_Similarity
 
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
 
setNPasses(int) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
setNPasses(int) - Method in class mpicbg.ij.plugin.Mean
 
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:
setSlice(float) - Method in class mpicbg.ij.stack.AbstractTransformMapping
 
setSlice(float) - Method in interface mpicbg.ij.stack.Mapping
Set the slice
setup(String, ImagePlus) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
setup(String, ImagePlus) - Method in class mpicbg.ij.plugin.Mean
 
setup() - Method in class Transform_Roi
 
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.
showColors - Static variable in class mpicbg.ij.plugin.MSEBlockFlow
 
showColors - Static variable in class mpicbg.ij.plugin.MSEGaussianFlow
 
showColors - Static variable in class mpicbg.ij.plugin.PMCCBlockFlow
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class mpicbg.ij.plugin.Mean
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class mpicbg.ij.plugin.NormalizeLocalContrast
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class mpicbg.ij.plugin.RemoveOutliers
 
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
SIFT_Align - Class in <Unnamed>
Align a stack consecutively using automatically extracted robust landmark correspondences.
SIFT_Align() - Constructor for class SIFT_Align
 
SIFT_ExtractPointRoi - Class in <Unnamed>
Extract landmark correspondences in two images as PointRoi.
SIFT_ExtractPointRoi() - Constructor for class SIFT_ExtractPointRoi
 
SIFT_Test - Class in <Unnamed>
Extract and display Scale Invariant Features after the method of David Lowe \cite{Lowe04} in an image.
SIFT_Test() - Constructor for class SIFT_Test
 
sigma - Static variable in class mpicbg.ij.plugin.MSEGaussianFlow
 
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
 
source - Variable in class Stack_Rotate.MappingThread
 
source - Variable in class Transform_Roi
 
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 with v1 being this Vertex and v2 being the Vertex at the other side of the Spring.
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
 
Stack_Rotate - Class in <Unnamed>
 
Stack_Rotate() - Constructor for class Stack_Rotate
 
Stack_Rotate.MappingThread - Class in <Unnamed>
 
Stack_Rotate.MappingThread(ImageStack, ImageProcessor, boolean) - Constructor for class Stack_Rotate.MappingThread
 
stackIndex - Variable in class mpicbg.ij.MappingThread
 
StandardDeviation - Class in mpicbg.ij.plugin
STD block filter.
StandardDeviation() - Constructor for class mpicbg.ij.plugin.StandardDeviation
 
standardDeviations - Static variable in class mpicbg.ij.plugin.NormalizeLocalContrast
 
standardDeviations - Static variable in class mpicbg.ij.plugin.RemoveOutliers
 
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
 
stds - Variable in class mpicbg.ij.plugin.NormalizeLocalContrast
 
stds - Variable in class mpicbg.ij.plugin.RemoveOutliers
 
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
 
stret - Variable in class mpicbg.ij.plugin.NormalizeLocalContrast
 
stretch - Static variable in class mpicbg.ij.plugin.NormalizeLocalContrast
 
sum - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator
 
sum - Variable in class mpicbg.ij.integral.IntIntegralImage
 
sum - Variable in class mpicbg.ij.integral.LongIntegralImage
 
sumB - Variable in class mpicbg.ij.integral.LongRGBIntegralImage
 
sumG - Variable in class mpicbg.ij.integral.LongRGBIntegralImage
 
sumOfSquares - Variable in class mpicbg.ij.integral.BlockStatistics.RowIntegrator
 
sumR - Variable in class mpicbg.ij.integral.LongRGBIntegralImage
 
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
 
target - Variable in class Stack_Rotate.MappingThread
 
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
 
temp - Variable in class Stack_Rotate.MappingThread
 
template - Variable in class Transform_Roi
 
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
 
toByte(byte[]) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
toByte(byte[]) - Method in class mpicbg.ij.plugin.SampleVariance
 
toggleInterpolation() - Method in class Stack_Rotate.MappingThread
 
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
 
toRGB(int[]) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
toRGB(int[]) - Method in class mpicbg.ij.plugin.SampleVariance
 
toShort(short[]) - Method in class mpicbg.ij.plugin.AbstractBlockFilter
 
toShort(short[]) - Method in class mpicbg.ij.plugin.SampleVariance
 
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
 
transform(CoordinateTransform, ImageProcessor, ImageProcessor) - Static method in class Transform_Roi
 
Transform_Affine - Class in <Unnamed>
 
Transform_Affine() - Constructor for class Transform_Affine
 
Transform_MovingLeastSquaresMesh - Class in <Unnamed>
Smooth image deformation using landmark based deformation by means of Moving Least Squares as described by \citet{SchaeferAl06} inspired by the implementation of Johannes Schindelin.
Transform_MovingLeastSquaresMesh() - Constructor for class Transform_MovingLeastSquaresMesh
 
Transform_Perspective - Class in <Unnamed>
 
Transform_Perspective() - Constructor for class Transform_Perspective
 
Transform_RegularizedAffine - Class in <Unnamed>
 
Transform_RegularizedAffine() - Constructor for class Transform_RegularizedAffine
 
Transform_Rigid - Class in <Unnamed>
 
Transform_Rigid() - Constructor for class Transform_Rigid
 
Transform_Roi - Class in <Unnamed>
Use two sets of landmarks selected in two images to map one image to the other.
Transform_Roi() - Constructor for class Transform_Roi
 
Transform_Similarity - Class in <Unnamed>
 
Transform_Similarity() - Constructor for class Transform_Similarity
 
Transform_SpringMesh - Class in <Unnamed>
 
Transform_SpringMesh() - Constructor for class Transform_SpringMesh
 
transformInterpolated(CoordinateTransform, ImageProcessor, ImageProcessor) - Static method in class Transform_Roi
 
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.
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
 
updateHandles(int, int) - Method in class Transform_Affine
 
updateHandles(int, int) - Method in class Transform_MovingLeastSquaresMesh
 
updateHandles(int, int) - Method in class Transform_Perspective
 
updateHandles(int, int) - Method in class Transform_RegularizedAffine
 
updateHandles(int, int) - Method in class Transform_Rigid
 
updateHandles(int, int) - Method in class Transform_Similarity
 
updateIllustration() - Method in class mpicbg.ij.InteractiveMapping
 
updateIllustration() - Method in class Transform_MovingLeastSquaresMesh
 
updateMapping() - Method in class mpicbg.ij.InteractiveMapping
 
updateMapping() - Method in class Transform_MovingLeastSquaresMesh
 
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 For efficiency reasons, the dimensions of dst are not checked, that is, you have to take care, that src.width == dst.width / 2 + dst.width % 2 && src.height == dst.height / 2 + dst.height % 2 .
useRoi(float[], float[]) - Static method in class mpicbg.ij.InteractiveInvertibleCoordinateTransform
 
Util - Class in mpicbg.ij.clahe
&lsquot;Contrast Limited Adaptive Histogram Equalization&rsquot; as described in
BibTeX:
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.ij.integral.LongRGBIntegralImage
 
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
 
w1 - Variable in class mpicbg.ij.integral.LongRGBIntegralImage
 
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
 
width - Variable in class mpicbg.ij.integral.LongRGBIntegralImage
 
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
 

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