Uses of Interface mpicbg.models.Model (Fiji Javadocs 0-SNAPSHOT API)

Packages that use Model
Package	Description
bigwarp.transforms
bunwarpj.trakem2.transform
lenscorrection
mpicbg.icp
mpicbg.ij
mpicbg.ij.blockmatching
mpicbg.models
mpicbg.pointdescriptor.model
mpicbg.spim.registration.detection
mpicbg.spim.registration.detection.descriptor
mpicbg.spim.registration.segmentation
mpicbg.stitching
mpicbg.trakem2.align
org.janelia.intensity
org.janelia.thickness.inference
process
spim.process.interestpointregistration
spim.process.interestpointregistration.optimizationtypes

Uses of Model in bigwarp.transforms

Methods in bigwarp.transforms that return Model
Modifier and Type	Method and Description
`Model<?>`	BigWarpTransform.`getModelType()`

Methods in bigwarp.transforms with parameters of type Model
Modifier and Type	Method and Description
`void`	BigWarpTransform.`fitModel(Model<?> model)`

Constructors in bigwarp.transforms with parameters of type Model
Constructor and Description
`ModelTransformSolver(Model<?> model)`

Uses of Model in bunwarpj.trakem2.transform

Classes in bunwarpj.trakem2.transform that implement Model
Modifier and Type	Class and Description
`class`	`CubicBSplineTransform` Class to implement elastic transforms based on cubic B-splines.

Uses of Model in lenscorrection

Classes in lenscorrection that implement Model
Modifier and Type	Class and Description
`class`	`PolynomialModel2D` A wrpper for `NonLinearTransform` and the `AbstractAffineModel2D` to which it is regularized.

Uses of Model in mpicbg.icp

Methods in mpicbg.icp with parameters of type Model
Modifier and Type	Method and Description
`void`	ICP.`estimateIntialModel(List<PointMatch> matches, Model<?> model)` Estimates an initial `Model` based on some given `PointMatch`es.
`void`	ICP.`runICPIteration(Model<?> lastModel, Model<?> newModel)` Performs one iteration of the `ICP`.
`void`	ICP.`runICPIteration(Model<?> lastModel, Model<?> newModel)` Performs one iteration of the `ICP`.

Uses of Model in mpicbg.ij

Classes in mpicbg.ij with type parameters of type Model
Modifier and Type	Class and Description
`class`	`InteractiveInvertibleCoordinateTransform<M extends Model<M> & InvertibleCoordinateTransform>` An interactive parent class for point based image deformation.

Uses of Model in mpicbg.ij.blockmatching

Methods in mpicbg.ij.blockmatching with parameters of type Model
Modifier and Type	Method and Description
`static void`	BlockMatching.`findMatches(ij.process.FloatProcessor source, ij.process.FloatProcessor target, ij.process.FloatProcessor sourceMask, ij.process.FloatProcessor targetMask, Model<?> initialModel, Class<? extends AbstractAffineModel2D<?>> localModelClass, float maxEpsilon, float maxScale, float minR, float rodR, float maxCurvatureR, int meshResolution, float alpha, Collection<PointMatch> sourceMatches)`

Uses of Model in mpicbg.models

Classes in mpicbg.models with type parameters of type Model
Modifier and Type	Class and Description
`class`	`ConstantAffineModel1D<A extends Model<A> & Affine1D<A> & InvertibleBoundable>` 1D affine specialization of `ConstantModel`.
`class`	`ConstantModel<A extends Model<A>,M extends ConstantModel<A,M>>` Wraps another models but does not pass through calls to `fit(float[][], float[][], float[])`.
`class`	`InterpolatedAffineModel1D<A extends Model<A> & Affine1D<A>,B extends Model<B> & Affine1D<B>>` 1D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedAffineModel1D<A extends Model<A> & Affine1D<A>,B extends Model<B> & Affine1D<B>>` 1D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedAffineModel2D<A extends Model<A> & Affine2D<A>,B extends Model<B> & Affine2D<B>>` 2D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedAffineModel2D<A extends Model<A> & Affine2D<A>,B extends Model<B> & Affine2D<B>>` 2D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedAffineModel3D<A extends Model<A> & Affine3D<A>,B extends Model<B> & Affine3D<B>>` 3D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedAffineModel3D<A extends Model<A> & Affine3D<A>,B extends Model<B> & Affine3D<B>>` 3D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedModel<A extends Model<A>,B extends Model<B>,M extends InterpolatedModel<A,B,M>>` Linearly interpolates between two independent models.
`class`	`InterpolatedModel<A extends Model<A>,B extends Model<B>,M extends InterpolatedModel<A,B,M>>` Linearly interpolates between two independent models.
`class`	`InvertibleConstantModel<A extends Model<A> & InvertibleCoordinateTransform,M extends InvertibleConstantModel<A,M>>` Invertible specialization of `ConstantModel`.
`class`	`InvertibleInterpolatedModel<A extends Model<A> & InvertibleCoordinateTransform,B extends Model<B> & InvertibleCoordinateTransform,M extends InvertibleInterpolatedModel<A,B,M>>` Invertible specialization of `InterpolatedModel`.
`class`	`InvertibleInterpolatedModel<A extends Model<A> & InvertibleCoordinateTransform,B extends Model<B> & InvertibleCoordinateTransform,M extends InvertibleInterpolatedModel<A,B,M>>` Invertible specialization of `InterpolatedModel`.
`interface`	`Model<M extends Model<M>>` `CoordinateTransform` whose parameters can be estimated through a least-squares(like) fit.
`class`	`Tile<M extends Model<M>>`

Classes in mpicbg.models that implement Model
Modifier and Type	Class and Description
`class`	`AbstractAffineModel1D<M extends AbstractAffineModel1D<M>>`
`class`	`AbstractAffineModel2D<M extends AbstractAffineModel2D<M>>`
`class`	`AbstractAffineModel3D<M extends AbstractAffineModel3D<M>>`
`class`	`AbstractModel<M extends AbstractModel<M>>` Abstract class for arbitrary transformation models to be applied to `Points` in n-dimensional space.
`class`	`AffineModel1D`
`class`	`AffineModel2D` 2d-affine transformation models to be applied to points in 2d-space.
`class`	`AffineModel3D` 3d-affine transformation models to be applied to points in 3d-space.
`class`	`ConstantAffineModel1D<A extends Model<A> & Affine1D<A> & InvertibleBoundable>` 1D affine specialization of `ConstantModel`.
`class`	`ConstantModel<A extends Model<A>,M extends ConstantModel<A,M>>` Wraps another models but does not pass through calls to `fit(float[][], float[][], float[])`.
`class`	`HomographyModel2D` 2d-homography `AbstractModel` to be applied to points in 2d-space.
`class`	`IdentityModel` nd-identity `AbstractModel`.
`class`	`InterpolatedAffineModel1D<A extends Model<A> & Affine1D<A>,B extends Model<B> & Affine1D<B>>` 1D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedAffineModel2D<A extends Model<A> & Affine2D<A>,B extends Model<B> & Affine2D<B>>` 2D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedAffineModel3D<A extends Model<A> & Affine3D<A>,B extends Model<B> & Affine3D<B>>` 3D affine specialization of `InterpolatedModel`.
`class`	`InterpolatedModel<A extends Model<A>,B extends Model<B>,M extends InterpolatedModel<A,B,M>>` Linearly interpolates between two independent models.
`class`	`InvertibleConstantModel<A extends Model<A> & InvertibleCoordinateTransform,M extends InvertibleConstantModel<A,M>>` Invertible specialization of `ConstantModel`.
`class`	`InvertibleInterpolatedModel<A extends Model<A> & InvertibleCoordinateTransform,B extends Model<B> & InvertibleCoordinateTransform,M extends InvertibleInterpolatedModel<A,B,M>>` Invertible specialization of `InterpolatedModel`.
`class`	`RigidModel2D` 2d-rigid transformation models to be applied to points in 2d-space.
`class`	`RigidModel3D`
`class`	`SimilarityModel2D` 2d-similarity transformation models to be applied to points in 2d-space.
`class`	`SimilarityModel3D` 3d-rigid transformation models to be applied to points in 3d-space.
`class`	`TranslationModel1D` 1d-translation `AbstractModel` to be applied to points in 1d-space.
`class`	`TranslationModel2D` 2d-translation `AbstractModel` to be applied to points in 2d-space.
`class`	`TranslationModel3D`

Fields in mpicbg.models declared as Model
Modifier and Type	Field and Description
`protected A`	InterpolatedModel.`a`
`protected B`	InterpolatedModel.`b`
`protected M`	Tile.`model` The transformation `AbstractModel` of the `Tile`.
`protected A`	ConstantModel.`model`
`protected Model<?>`	AbstractMovingLeastSquaresTransform.`model`

Methods in mpicbg.models that return Model
Modifier and Type	Method and Description
`Model<?>`	AbstractMovingLeastSquaresTransform.`getModel()`

Methods in mpicbg.models with parameters of type Model
Modifier and Type	Method and Description
`void`	AbstractMovingLeastSquaresTransform.`setModel(Model<?> model)`

Method parameters in mpicbg.models with type arguments of type Model
Modifier and Type	Method and Description
`void`	AbstractMovingLeastSquaresTransform.`setModel(Class<? extends Model<?>> modelClass)`

Uses of Model in mpicbg.pointdescriptor.model

Classes in mpicbg.pointdescriptor.model that implement Model
Modifier and Type	Class and Description
`class`	`FixedModel` This model just applies some other `TranslationInvariantModel` without computing anything.
`class`	`TranslationInvariantAffineModel3D` 3d-affine transformation models to be applied to points in 3d-space.
`class`	`TranslationInvariantFixedModel` This model just applies some other `TranslationInvariantModel` without computing anything.
`class`	`TranslationInvariantModel<M extends TranslationInvariantModel<M>>` This class is a subtle hint that `Model`s which are used to fit `AbstractPointDescriptor`s should be translation invariant.
`class`	`TranslationInvariantRigidModel2D` 2d-rigid transformation models to be applied to points in 2d-space.
`class`	`TranslationInvariantRigidModel3D` 3d-rigid transformation models to be applied to points in 3d-space.
`class`	`TranslationInvariantSimilarityModel3D` 3d-rigid transformation models to be applied to points in 3d-space.

Uses of Model in mpicbg.spim.registration.detection

Methods in mpicbg.spim.registration.detection with parameters of type Model
Modifier and Type	Method and Description
`static <S extends DetectionIdentification<S,T>,T extends DetectionView<S,T>> String`	DetectionRegistration.`computeRANSAC(ArrayList<PointMatchGeneric<T>> correspondenceCandidates, ArrayList<PointMatchGeneric<T>> inlierList, Model<?> model)` Computes the RANSAC with reasonable parameters
`static <S extends DetectionIdentification<S,T>,T extends DetectionView<S,T>> String`	DetectionRegistration.`computeRANSAC(ArrayList<PointMatchGeneric<T>> correspondenceCandidates, ArrayList<PointMatchGeneric<T>> inlierList, Model<?> model, float maxEpsilon, float minInlierRatio, float minNumberInlierFactor, int numIterations)`

Uses of Model in mpicbg.spim.registration.detection.descriptor

Classes in mpicbg.spim.registration.detection.descriptor with type parameters of type Model
Modifier and Type	Class and Description
`class`	`SparseCorrespondenceExtraction<M extends Model<M>,T extends DetectionView<?,T>>`

Uses of Model in mpicbg.spim.registration.segmentation

Methods in mpicbg.spim.registration.segmentation with parameters of type Model
Modifier and Type	Method and Description
`TranslationInvariantFixedModel`	NucleiConfiguration.`getFixedModel(Model ransacModel)`
`FixedModel`	NucleiConfiguration.`getFixedTranslationModel(Model ransacModel)`

Uses of Model in mpicbg.stitching

Methods in mpicbg.stitching that return Model
Modifier and Type	Method and Description
`Model<?>`	ImageCollectionElement.`getModel()`
`Model<?>`	ComparePair.`getModel1()`
`Model<?>`	ComparePair.`getModel2()`

Methods in mpicbg.stitching with parameters of type Model
Modifier and Type	Method and Description
`void`	ImageCollectionElement.`setModel(Model<?> model)`

Constructors in mpicbg.stitching with parameters of type Model
Constructor and Description
`ImagePlusTimePoint(ij.ImagePlus imp, int impId, int timepoint, Model model, ImageCollectionElement element)`

Uses of Model in mpicbg.trakem2.align

Classes in mpicbg.trakem2.align with type parameters of type Model
Modifier and Type	Class and Description
`class`	`AbstractAffineTile2D<A extends Model<A> & Affine2D<A>>`
`class`	`GenericAffineTile2D<A extends Model<A> & Affine2D<A>>`

Methods in mpicbg.trakem2.align with parameters of type Model
Modifier and Type	Method and Description
`static boolean`	Align.`findModel(Model<?> model, List<PointMatch> candidates, Collection<PointMatch> inliers, float maxEpsilon, float minInlierRatio, int minNumInliers, boolean rejectIdentity, float identityTolerance)`
`static boolean`	Align.`findModel(Model<?> model, List<PointMatch> candidates, Collection<PointMatch> inliers, float maxEpsilon, float minInlierRatio, int minNumInliers, boolean rejectIdentity, float identityTolerance, boolean multipleHypotheses)`

Uses of Model in org.janelia.intensity

Fields in org.janelia.intensity declared as Model
Modifier and Type	Field and Description
`protected Model<?>`	RansacRegressionReduceFilter.`model`
`protected Model<?>`	RansacRegressionFilter.`model`

Methods in org.janelia.intensity with type parameters of type Model
Modifier and Type	Method and Description
`protected static <T extends Model<T> & Affine1D<T>> HashMap<Patch,ArrayList<Tile<T>>>`	MatchIntensities.`generateCoefficientsTiles(Collection<Patch> patches, T template, int nCoefficients)`
`<M extends Model<M> & Affine1D<M>> void`	MatchIntensities.`run(List<Layer> layers, int radius, double scale, int numCoefficients, double lambda1, double lambda2, double neighborWeight, Rectangle roi)`

Uses of Model in org.janelia.thickness.inference

Constructors in org.janelia.thickness.inference with parameters of type Model
Constructor and Description
`BorderRegularization(Model<?> m, int length)`
`IdentityRegularization(Model<?> m, int length)`
`ModelRegularization(Model<?> m, double[] regularizationValues, double[] weights)`

Uses of Model in process

Fields in process declared as Model
Modifier and Type	Field and Description
`Model<?>`	ComparePair.`model`

Methods in process that return Model
Modifier and Type	Method and Description
`protected static Model<?>`	Matching.`pairwiseMatching(ArrayList<PointMatch> finalInliers, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks1, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks2, float zStretching1, float zStretching2, DescriptorParameters params, String explanation)`

Methods in process with parameters of type Model
Modifier and Type	Method and Description
`protected static String`	Matching.`computeRANSAC(ArrayList<PointMatch> candidates, ArrayList<PointMatch> inliers, Model<?> model, float maxEpsilon)`
`protected static ArrayList<DifferenceOfGaussianPeak<FloatType>>`	Matching.`filterForROI(Roi roi, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks, Model<?> model)`
`protected static ArrayList<PointMatch>`	Matching.`getCorrespondenceCandidates(double nTimesBetter, Matcher matcher, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks1, ArrayList<DifferenceOfGaussianPeak<FloatType>> peaks2, Model<?> model, int dimensionality, float zStretching1, float zStretching2, String explanation)`
`protected static void`	Matching.`writePoints(ArrayList<PointMatch> finalInliers, DescriptorParameters params, Model<?> finalModel, PrintWriter out)`

Constructors in process with parameters of type Model
Constructor and Description
`ComparePair(int indexA, int indexB, Model<?> model)`

Uses of Model in spim.process.interestpointregistration

Methods in spim.process.interestpointregistration with type parameters of type Model
Modifier and Type	Method and Description
`protected static <M extends Model<M>> TileConfiguration`	GlobalOpt.`addAndFixTiles(List<ViewId> views, HashMap<ViewId,Tile<M>> map, GlobalOptimizationType registrationType, GlobalOptimizationSubset subset, boolean considerTimePointsAsUnit)`
`protected static <M extends Model<M>> HashMap<ViewId,Tile<M>>`	GlobalOpt.`assignViewsToTiles(M model, List<ViewId> views, boolean considerTimePointsAsUnit)`
`static <M extends Model<M>> HashMap<ViewId,Tile<M>>`	GlobalOpt.`compute(M model, GlobalOptimizationType registrationType, GlobalOptimizationSubset subset, boolean considerTimePointsAsUnit)` Computes a global optimization based on the corresponding points

Methods in spim.process.interestpointregistration with parameters of type Model
Modifier and Type	Method and Description
`static Pair<String,Double>`	RANSAC.`computeRANSAC(ArrayList<PointMatchGeneric<Detection>> correspondenceCandidates, ArrayList<PointMatchGeneric<Detection>> inlierList, Model<?> model, double maxEpsilon, double minInlierRatio, double minNumberInlierFactor, int numIterations)`

Uses of Model in spim.process.interestpointregistration.optimizationtypes

Methods in spim.process.interestpointregistration.optimizationtypes with type parameters of type Model
Modifier and Type	Method and Description
`<M extends Model<M>> boolean`	GlobalOptimizationSubset.`computeGlobalOpt(M model, GlobalOptimizationType type, SpimData2 spimData, List<ChannelProcess> channelsToProcess, String description)`
`protected <M extends Model<M>> AffineTransform3D`	GlobalOptimizationSubset.`computeMapBackModel(HashMap<ViewId,Tile<M>> tiles, GlobalOptimizationType type, SpimData2 spimData)`

Uses of Interfacempicbg.models.Model

Uses of Model in bigwarp.transforms

Uses of Model in bunwarpj.trakem2.transform

Uses of Model in lenscorrection

Uses of Model in mpicbg.icp

Uses of Model in mpicbg.ij

Uses of Model in mpicbg.ij.blockmatching

Uses of Model in mpicbg.models

Uses of Model in mpicbg.pointdescriptor.model

Uses of Model in mpicbg.spim.registration.detection

Uses of Model in mpicbg.spim.registration.detection.descriptor

Uses of Model in mpicbg.spim.registration.segmentation

Uses of Model in mpicbg.stitching

Uses of Model in mpicbg.trakem2.align

Uses of Model in org.janelia.intensity

Uses of Model in org.janelia.thickness.inference

Uses of Model in process

Uses of Model in spim.process.interestpointregistration

Uses of Model in spim.process.interestpointregistration.optimizationtypes

Uses of Interface
mpicbg.models.Model