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

A

a - Variable in class mpicbg.trakem2.util.Downsampler.Pair

a - Variable in class mpicbg.trakem2.util.Pair

a - Variable in class mpicbg.trakem2.util.Triple

AffineModel2D - Class in mpicbg.trakem2.transform

AffineModel2D() - Constructor for class mpicbg.trakem2.transform.AffineModel2D

AffineModel3D - Class in mpicbg.trakem2.transform

AffineModel3D() - Constructor for class mpicbg.trakem2.transform.AffineModel3D

append(StringBuilder, HashSet<String>, String) - Static method in class mpicbg.trakem2.transform.DTD

apply(double[]) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

apply(double[]) - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform

applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform

applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

Multi-threading safe version of the original applyInPlace method.

applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform

applyInverseInPlace(double[]) - Method in class mpicbg.trakem2.transform.TransformMesh

Catch non-invertible locations outside of the meshes boundaries and transfer them with the affine defined by the `closest' affine (the affine whose summed up control points distances to location are smallest).

B

b - Variable in class mpicbg.trakem2.util.Downsampler.Pair

b - Variable in class mpicbg.trakem2.util.Pair

b - Variable in class mpicbg.trakem2.util.Triple

beta - Variable in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

boundingBox - Variable in class mpicbg.trakem2.transform.TransformMesh

C

c - Variable in class mpicbg.trakem2.util.Triple

closestSourceAffine(double[]) - Method in class mpicbg.trakem2.transform.TransformMesh

Return the AffineModel2D used by the triangle enclosing or closest to the passed target location.

closestTargetAffine(double[]) - Method in class mpicbg.trakem2.transform.TransformMesh

Return the AffineModel2D used by the triangle enclosing or closest to the passed target location.

CoordinateTransform - Interface in mpicbg.trakem2.transform

InvertibleCoordinateTransform with String import and export as used in TrakEM2.

CoordinateTransformList<E extends CoordinateTransform> - Class in mpicbg.trakem2.transform

CoordinateTransformList() - Constructor for class mpicbg.trakem2.transform.CoordinateTransformList

copy() - Method in class mpicbg.trakem2.transform.AffineModel2D

copy() - Method in class mpicbg.trakem2.transform.AffineModel3D

copy() - Method in interface mpicbg.trakem2.transform.CoordinateTransform

copy() - Method in class mpicbg.trakem2.transform.CoordinateTransformList

copy() - Method in class mpicbg.trakem2.transform.HomographyModel2D

copy() - Method in interface mpicbg.trakem2.transform.InvertibleCoordinateTransform

copy() - Method in class mpicbg.trakem2.transform.InvertibleCoordinateTransformList

copy() - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform

copy() - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

copy() - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

TODO Make this more efficient

copy() - Method in class mpicbg.trakem2.transform.PolynomialTransform2D

copy() - Method in class mpicbg.trakem2.transform.RigidModel2D

copy() - Method in class mpicbg.trakem2.transform.SimilarityModel2D

copy() - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform

copy() - Method in class mpicbg.trakem2.transform.TranslationModel2D

copy() - Method in class mpicbg.trakem2.transform.TranslationModel3D

createInverse() - Method in class mpicbg.trakem2.transform.AffineModel2D

TODO Not yet tested

createInverse() - Method in class mpicbg.trakem2.transform.AffineModel3D

createInverseMappedImage(ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping

createInverseMappedImageInterpolated(ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping

createMappedImage(ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping

createMappedImageInterpolated(ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping

createMappedMaskedImage(ImageProcessor, ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping

createMappedMaskedImageInterpolated(ImageProcessor, ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping

D

data - Variable in class mpicbg.trakem2.util.Downsampler.Entry

dimension - Variable in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

downsampleAlphaAndOutside(ByteProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

Combine an alpha and outside mask into a downsampled alpha and outside mask.

downsampleByteProcessor(ByteProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

downsampleByteProcessor(ByteProcessor, int) - Static method in class mpicbg.trakem2.util.Downsampler

downsampleColor(ColorProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

Create a downsampled version of a ColorProcessor and the mapping of its red, green and blue channels into three unsigned byte arrays.

downsampleColorProcessor(ColorProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

downsampleColorProcessor(ColorProcessor, int) - Static method in class mpicbg.trakem2.util.Downsampler

downsampleFloat(FloatProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

Create a downsampled version of a FloatProcessor and the mapping of its [min,max] range into an unsigned byte array.

downsampleFloatProcessor(FloatProcessor, int) - Static method in class mpicbg.trakem2.util.Downsampler

downsampleFloatProcessor(FloatProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

downsampleImageProcessor(ImageProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

Convenience call for abstract ImageProcessor.

downsampleImageProcessor(ImageProcessor, int) - Static method in class mpicbg.trakem2.util.Downsampler

Convenience call for abstract ImageProcessor.

downsampleOutside(ByteProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

Downsample and outside mask.

Downsampler - Class in mpicbg.trakem2.util

Downsampler() - Constructor for class mpicbg.trakem2.util.Downsampler

Downsampler.Entry - Class in mpicbg.trakem2.util

Downsampler.Pair<A,B> - Class in mpicbg.trakem2.util

downsampleShort(ShortProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

Create a downsampled version of a ShortProcessor and the mapping of its [min,max] range into an unsigned byte array.

downsampleShortProcessor(ShortProcessor) - Static method in class mpicbg.trakem2.util.Downsampler

DTD - Class in mpicbg.trakem2.transform

E

Entry(int, int, byte[][]) - Constructor for class mpicbg.trakem2.util.Downsampler.Entry

Entry(int, int, int) - Constructor for class mpicbg.trakem2.util.Downsampler.Entry

ExportedTile - Class in mpicbg.trakem2.transform

ExportedTile(ShortProcessor, int, int, double, double) - Constructor for class mpicbg.trakem2.transform.ExportedTile

G

getBoundingBox() - Method in class mpicbg.trakem2.transform.TransformMesh

getHeight() - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks

getP() - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

getQ() - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

getWeight() - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

getWidth() - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks

H

height - Variable in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

height - Variable in class mpicbg.trakem2.util.Downsampler.Entry

HomographyModel2D - Class in mpicbg.trakem2.transform

HomographyModel2D() - Constructor for class mpicbg.trakem2.transform.HomographyModel2D

I

ImageProcessorWithMasks(ImageProcessor, ImageProcessor, ByteProcessor) - Constructor for class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks

init(String) - Method in class mpicbg.trakem2.transform.AffineModel2D

init(String) - Method in class mpicbg.trakem2.transform.AffineModel3D

init(String) - Method in interface mpicbg.trakem2.transform.CoordinateTransform

Initialize the properties of the CoordinateTransform from a data string as generated by CoordinateTransform.toDataString().

init(String) - Method in class mpicbg.trakem2.transform.CoordinateTransformList

init(String) - Method in class mpicbg.trakem2.transform.HomographyModel2D

init(String) - Method in class mpicbg.trakem2.transform.InvertibleCoordinateTransformList

init(String) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform

init(String) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

init(String) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

init(String) - Method in class mpicbg.trakem2.transform.PolynomialTransform2D

init(String) - Method in class mpicbg.trakem2.transform.RigidModel2D

init(String) - Method in class mpicbg.trakem2.transform.SimilarityModel2D

init(String) - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform

init(String) - Method in class mpicbg.trakem2.transform.TranslationModel2D

init(String) - Method in class mpicbg.trakem2.transform.TranslationModel3D

init2(String) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

InvertibleCoordinateTransform - Interface in mpicbg.trakem2.transform

InvertibleCoordinateTransform with String import and export as used in TrakEM2.

InvertibleCoordinateTransformList<E extends InvertibleCoordinateTransform> - Class in mpicbg.trakem2.transform

InvertibleCoordinateTransformList() - Constructor for class mpicbg.trakem2.transform.InvertibleCoordinateTransformList

ip - Variable in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks

K

kernelExpand(double[]) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

L

length - Variable in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

M

map(TransformMeshMappingWithMasks.ImageProcessorWithMasks, TransformMeshMappingWithMasks.ImageProcessorWithMasks, int) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

map(TransformMeshMappingWithMasks.ImageProcessorWithMasks, TransformMeshMappingWithMasks.ImageProcessorWithMasks) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

map(ShortProcessor, ByteProcessor, ShortProcessor, int) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

Render source into target using alpha composition.

map(ShortProcessor, ByteProcessor, ShortProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

Render source into master using alpha composition.

map(ColorProcessor, ByteProcessor, ColorProcessor, ByteProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

Render source into master using alpha composition.

map(ColorProcessor, ByteProcessor, ColorProcessor, ByteProcessor, int) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

Render source into master using alpha composition.

map(ByteProcessor, ByteProcessor, ByteProcessor, ByteProcessor, int) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

Render source into target using alpha composition.

map(ByteProcessor, ByteProcessor, ByteProcessor, ByteProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

Render source into master using alpha composition.

mapByteAlphaTriangle(TransformMesh, AffineModel2D, ByteProcessor, ByteProcessor, ByteProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

mapColorAlphaTriangle(TransformMesh, AffineModel2D, ColorProcessor, ByteProcessor, ColorProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

Mapping for color images with alpha composition.

mapInterpolated(TransformMeshMappingWithMasks.ImageProcessorWithMasks, TransformMeshMappingWithMasks.ImageProcessorWithMasks, int) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

mapInterpolated(TransformMeshMappingWithMasks.ImageProcessorWithMasks, TransformMeshMappingWithMasks.ImageProcessorWithMasks) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

mapShortAlphaTriangle(TransformMesh, AffineModel2D, ShortProcessor, ByteProcessor, ShortProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

mapTriangle(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

mapTriangle(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor, ImageProcessor, ImageProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

mapTriangleInterpolated(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

mapTriangleInterpolated(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor, ImageProcessor, ImageProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

Does not do alpha composition.

mask - Variable in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks

max - Variable in class mpicbg.trakem2.transform.ExportedTile

min - Variable in class mpicbg.trakem2.transform.ExportedTile

MovingLeastSquaresTransform - Class in mpicbg.trakem2.transform

MovingLeastSquaresTransform() - Constructor for class mpicbg.trakem2.transform.MovingLeastSquaresTransform

MovingLeastSquaresTransform2 - Class in mpicbg.trakem2.transform

MovingLeastSquaresTransform2() - Constructor for class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

mpicbg.trakem2.transform - package mpicbg.trakem2.transform

mpicbg.trakem2.util - package mpicbg.trakem2.util

multiply(double[][], double[]) - Static method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

N

NonLinearCoordinateTransform - Class in mpicbg.trakem2.transform

NonLinearCoordinateTransform() - Constructor for class mpicbg.trakem2.transform.NonLinearCoordinateTransform

normMean - Variable in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

normVar - Variable in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

O

outside - Variable in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks

P

Pair(A, B) - Constructor for class mpicbg.trakem2.util.Downsampler.Pair

Pair<A,B> - Class in mpicbg.trakem2.util

Pair(A, B) - Constructor for class mpicbg.trakem2.util.Pair

PolynomialTransform2D - Class in mpicbg.trakem2.transform

n-th order 2d polynomial transform.

PolynomialTransform2D() - Constructor for class mpicbg.trakem2.transform.PolynomialTransform2D

R

RigidModel2D - Class in mpicbg.trakem2.transform

RigidModel2D() - Constructor for class mpicbg.trakem2.transform.RigidModel2D

S

SimilarityModel2D - Class in mpicbg.trakem2.transform

SimilarityModel2D() - Constructor for class mpicbg.trakem2.transform.SimilarityModel2D

sp - Variable in class mpicbg.trakem2.transform.ExportedTile

T

ThinPlateSplineTransform - Class in mpicbg.trakem2.transform

ThinPlateSplineTransform() - Constructor for class mpicbg.trakem2.transform.ThinPlateSplineTransform

ThinPlateSplineTransform(ThinPlateR2LogRSplineKernelTransform) - Constructor for class mpicbg.trakem2.transform.ThinPlateSplineTransform

toDataString() - Method in class mpicbg.trakem2.transform.AffineModel2D

toDataString() - Method in class mpicbg.trakem2.transform.AffineModel3D

toDataString() - Method in interface mpicbg.trakem2.transform.CoordinateTransform

Create a String representation of the properties of the CoordinateTransform that can be used to re-create itself with CoordinateTransform.init(String).

toDataString() - Method in class mpicbg.trakem2.transform.CoordinateTransformList

toDataString() - Method in class mpicbg.trakem2.transform.HomographyModel2D

toDataString() - Method in class mpicbg.trakem2.transform.InvertibleCoordinateTransformList

toDataString() - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform

toDataString() - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

toDataString() - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

toDataString() - Method in class mpicbg.trakem2.transform.PolynomialTransform2D

toDataString() - Method in class mpicbg.trakem2.transform.RigidModel2D

toDataString() - Method in class mpicbg.trakem2.transform.SimilarityModel2D

toDataString() - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform

toDataString() - Method in class mpicbg.trakem2.transform.TranslationModel2D

toDataString() - Method in class mpicbg.trakem2.transform.TranslationModel3D

toString() - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

toXML(String) - Method in class mpicbg.trakem2.transform.AffineModel2D

toXML(String) - Method in class mpicbg.trakem2.transform.AffineModel3D

toXML(String) - Method in interface mpicbg.trakem2.transform.CoordinateTransform

Create an XML-export of the CoordinateTransform for use in TrakEM2.

toXML(String) - Method in class mpicbg.trakem2.transform.CoordinateTransformList

toXML(String) - Method in class mpicbg.trakem2.transform.HomographyModel2D

toXML(String) - Method in class mpicbg.trakem2.transform.InvertibleCoordinateTransformList

toXML(String) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform

toXML(String) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

toXML(String) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

toXML(String) - Method in class mpicbg.trakem2.transform.PolynomialTransform2D

toXML(String) - Method in class mpicbg.trakem2.transform.RigidModel2D

toXML(String) - Method in class mpicbg.trakem2.transform.SimilarityModel2D

toXML(String) - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform

toXML(String) - Method in class mpicbg.trakem2.transform.TranslationModel2D

toXML(String) - Method in class mpicbg.trakem2.transform.TranslationModel3D

TransformMesh - Class in mpicbg.trakem2.transform

TransformMesh(CoordinateTransform, int, double, double) - Constructor for class mpicbg.trakem2.transform.TransformMesh

TransformMeshMapping - Class in mpicbg.trakem2.transform

Creates automatically cropped mappings and inverse mappings of images using a TransformMesh.

TransformMeshMapping(TransformMesh) - Constructor for class mpicbg.trakem2.transform.TransformMeshMapping

TransformMeshMappingWithMasks<T extends mpicbg.models.TransformMesh> - Class in mpicbg.trakem2.transform

Specialized TransformMapping for Patches, that is, rendering the image, outside mask and mask in one go instead three.

TransformMeshMappingWithMasks(T) - Constructor for class mpicbg.trakem2.transform.TransformMeshMappingWithMasks

TransformMeshMappingWithMasks.ImageProcessorWithMasks - Class in mpicbg.trakem2.transform

TranslationModel2D - Class in mpicbg.trakem2.transform

TranslationModel2D() - Constructor for class mpicbg.trakem2.transform.TranslationModel2D

TranslationModel3D - Class in mpicbg.trakem2.transform

TranslationModel3D() - Constructor for class mpicbg.trakem2.transform.TranslationModel3D

Triple<A,B,C> - Class in mpicbg.trakem2.util

Triple(A, B, C) - Constructor for class mpicbg.trakem2.util.Triple

W

width - Variable in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

width - Variable in class mpicbg.trakem2.util.Downsampler.Entry

X

x - Variable in class mpicbg.trakem2.transform.ExportedTile

Y

y - Variable in class mpicbg.trakem2.transform.ExportedTile

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