Uses of Class mpicbg.trakem2.align.AbstractAffineTile2D (Fiji Javadocs 0-SNAPSHOT API)

Packages that use AbstractAffineTile2D
Package Description

ini.trakem2.imaging

mpicbg.trakem2.align

Packages that use AbstractAffineTile2D
Package	Description
ini.trakem2.imaging
mpicbg.trakem2.align

Uses of AbstractAffineTile2D in ini.trakem2.imaging

Method parameters in ini.trakem2.imaging with type arguments of type AbstractAffineTile2D
Modifier and Type	Method and Description
`static void`	StitchingTEM.`optimizeTileConfiguration(ArrayList<AbstractAffineTile2D<?>> tiles, ArrayList<AbstractAffineTile2D<?>> fixed_tiles, StitchingTEM.PhaseCorrelationParam param)` Optimize tile configuration by removing bad matches
`static void`	StitchingTEM.`optimizeTileConfiguration(ArrayList<AbstractAffineTile2D<?>> tiles, ArrayList<AbstractAffineTile2D<?>> fixed_tiles, StitchingTEM.PhaseCorrelationParam param)` Optimize tile configuration by removing bad matches

Uses of AbstractAffineTile2D in mpicbg.trakem2.align

Subclasses of AbstractAffineTile2D in mpicbg.trakem2.align
Modifier and Type	Class and Description
`class`	`AffineTile2D`
`class`	`GenericAffineTile2D<A extends Model<A> & Affine2D<A>>`
`class`	`RigidTile2D`
`class`	`SimilarityTile2D`
`class`	`TranslationTile2D`

Fields in mpicbg.trakem2.align with type parameters of type AbstractAffineTile2D
Modifier and Type	Field and Description
`protected List<AbstractAffineTile2D<?>>`	Align.ExtractFeaturesThread.`tiles`
`protected List<AbstractAffineTile2D<?>>`	Align.MatchFeaturesAndFindModelThread.`tiles`

Methods in mpicbg.trakem2.align with type parameters of type AbstractAffineTile2D
Modifier and Type	Method and Description
`static <AAT extends AbstractAffineTile2D<?>> void`	AbstractAffineTile2D.`pairOverlappingTiles(List<AAT> tiles, List<AbstractAffineTile2D<?>[]> tilePairs)` Search a `List` of `Tiles` for overlapping pairs.
`static <AAT extends AbstractAffineTile2D<?>> void`	AbstractAffineTile2D.`pairOverlappingTiles(List<AAT> tiles, List<AbstractAffineTile2D<?>[]> tilePairs, boolean sloppyOverlapTest)` Search a `List` of `Tiles` for overlapping pairs.

Methods in mpicbg.trakem2.align with parameters of type AbstractAffineTile2D
Modifier and Type	Method and Description
`protected static Collection<Feature>`	Align.`deserializeFeatures(Align.Param p, AbstractAffineTile2D<?> t)` Retrieve the features only if saved with the exact same relevant SIFT parameters.
`protected static Collection<PointMatch>`	Align.`deserializePointMatches(Align.Param p, AbstractAffineTile2D<?> t1, AbstractAffineTile2D<?> t2)`
`protected static Collection<PointMatch>`	Align.`deserializePointMatches(Align.Param p, AbstractAffineTile2D<?> t1, AbstractAffineTile2D<?> t2)`
`protected static Collection<Feature>`	Align.`fetchFeatures(Align.Param p, AbstractAffineTile2D<?> t)`
`protected static Collection<PointMatch>`	Align.`fetchPointMatches(Align.Param p, AbstractAffineTile2D<?> t1, AbstractAffineTile2D<?> t2)` Fetch a `Collection` of corresponding `SIFT-features`.
`protected static Collection<PointMatch>`	Align.`fetchPointMatches(Align.Param p, AbstractAffineTile2D<?> t1, AbstractAffineTile2D<?> t2)` Fetch a `Collection` of corresponding `SIFT-features`.
`boolean`	AbstractAffineTile2D.`intersects(AbstractAffineTile2D<?> t)`
`boolean`	AbstractAffineTile2D.`intersects(AbstractAffineTile2D<?> t, boolean sloppy)`
`void`	AbstractAffineTile2D.`makeVirtualConnection(AbstractAffineTile2D<?> t)` Add a virtual connection between two Tiles.
`protected static void`	Align.`pairwiseAlign(AbstractAffineTile2D<?> tile, Set<AbstractAffineTile2D<?>> visited)`
`protected static boolean`	Align.`serializeFeatures(Align.Param p, AbstractAffineTile2D<?> t, Collection<Feature> f)`
`protected static boolean`	Align.`serializePointMatches(Align.Param p, AbstractAffineTile2D<?> t1, AbstractAffineTile2D<?> t2, Collection<PointMatch> m)` Save a `Collection` of `PointMatches` two-sided.
`protected static boolean`	Align.`serializePointMatches(Align.Param p, AbstractAffineTile2D<?> t1, AbstractAffineTile2D<?> t2, Collection<PointMatch> m)` Save a `Collection` of `PointMatches` two-sided.

Method parameters in mpicbg.trakem2.align with type arguments of type AbstractAffineTile2D
Modifier and Type	Method and Description
`static void`	Align.`alignTileCollections(Align.Param p, Collection<AbstractAffineTile2D<?>> a, Collection<AbstractAffineTile2D<?>> b)` Align two collections of tiles
`static void`	Align.`alignTileCollections(Align.Param p, Collection<AbstractAffineTile2D<?>> a, Collection<AbstractAffineTile2D<?>> b)` Align two collections of tiles
`static void`	AlignTask.`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn)`
`static void`	AlignTask.`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn)`
`static void`	AlignTask.`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn, boolean sloppyOverlapTest)`
`static void`	AlignTask.`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn, boolean sloppyOverlapTest)`
`static void`	Align.`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, boolean tilesAreInPlace, int numThreads)` Align a set of `tiles` using the following procedure: Extract `SIFT-features` from all `tiles`. Establish `point-correspondences` from consistent sets of `feature` matches among tile pairs, optionally inspect only those that are already overlapping. Globally align the tile configuration. Both `feature extraction` and `matching` are executed in multiple `Threads`, with the number of `Threads` being a parameter of the method.
`static void`	Align.`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, boolean tilesAreInPlace, int numThreads)` Align a set of `tiles` using the following procedure: Extract `SIFT-features` from all `tiles`. Establish `point-correspondences` from consistent sets of `feature` matches among tile pairs, optionally inspect only those that are already overlapping. Globally align the tile configuration. Both `feature extraction` and `matching` are executed in multiple `Threads`, with the number of `Threads` being a parameter of the method.
`static void`	Align.`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, int numThreads)` Align a set of overlapping `tiles` using the following procedure: Extract `SIFT-features` from all `tiles`. Establish `point-correspondences` from consistent sets of `feature` matches among overlapping tiles. Globally align the tile configuration. Both `feature extraction` and `matching` are executed in multiple `Threads`, with the number of `Threads` being a parameter of the method.
`static void`	Align.`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, int numThreads)` Align a set of overlapping `tiles` using the following procedure: Extract `SIFT-features` from all `tiles`. Establish `point-correspondences` from consistent sets of `feature` matches among overlapping tiles. Globally align the tile configuration. Both `feature extraction` and `matching` are executed in multiple `Threads`, with the number of `Threads` being a parameter of the method.
`static void`	Align.`connectTilePairs(Align.Param p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>[]> tilePairs, int numThreads)` Connect a `List` of `Tiles` by geometrically consistent `SIFT-feature` correspondences.
`static void`	Align.`connectTilePairs(Align.Param p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>[]> tilePairs, int numThreads, boolean multipleHypotheses)` Connect a `List` of `Tiles` by geometrically consistent `SIFT-feature` correspondences.
`protected static void`	ElasticMontage.`extractAndSaveFeatures(List<AbstractAffineTile2D<?>> tiles, FloatArray2DSIFT.Param siftParam, boolean clearCache)` Extract SIFT features and save them into the project folder.
`static void`	Align.`optimizeTileConfiguration(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles)` Align a set of `tiles` that are interconnected by `point-correspondences`.
`static void`	Align.`optimizeTileConfiguration(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles)` Align a set of `tiles` that are interconnected by `point-correspondences`.
`static void`	AbstractAffineTile2D.`pairOverlappingTiles(List<AbstractAffineTile2D<?>> tilesA, List<AbstractAffineTile2D<?>> tilesB, List<AbstractAffineTile2D<?>[]> tilePairs)` Search two `Lists` of `Tiles` for overlapping pairs.
`static void`	AbstractAffineTile2D.`pairOverlappingTiles(List<AbstractAffineTile2D<?>> tilesA, List<AbstractAffineTile2D<?>> tilesB, List<AbstractAffineTile2D<?>[]> tilePairs)` Search two `Lists` of `Tiles` for overlapping pairs.
`static void`	AbstractAffineTile2D.`pairOverlappingTiles(List<AbstractAffineTile2D<?>> tilesA, List<AbstractAffineTile2D<?>> tilesB, List<AbstractAffineTile2D<?>[]> tilePairs, boolean sloppyOverlapTest)` Search two `Lists` of `Tiles` for overlapping pairs.
`static void`	AbstractAffineTile2D.`pairOverlappingTiles(List<AbstractAffineTile2D<?>> tilesA, List<AbstractAffineTile2D<?>> tilesB, List<AbstractAffineTile2D<?>[]> tilePairs, boolean sloppyOverlapTest)` Search two `Lists` of `Tiles` for overlapping pairs.
`static void`	AbstractAffineTile2D.`pairTiles(List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>[]> tilePairs)` Pair all `Tiles` from a `List`.
`static void`	AbstractAffineTile2D.`pairTiles(List<AbstractAffineTile2D<?>> tilesA, List<AbstractAffineTile2D<?>> tilesB, List<AbstractAffineTile2D<?>[]> tilePairs)` Pair all `Tiles` from two `Lists`.
`static void`	AbstractAffineTile2D.`pairTiles(List<AbstractAffineTile2D<?>> tilesA, List<AbstractAffineTile2D<?>> tilesB, List<AbstractAffineTile2D<?>[]> tilePairs)` Pair all `Tiles` from two `Lists`.
`protected static void`	Align.`pairwiseAlign(AbstractAffineTile2D<?> tile, Set<AbstractAffineTile2D<?>> visited)`
`static void`	Align.`pairwiseAlignTileConfiguration(List<AbstractAffineTile2D<?>> tiles)`
`static void`	Align.`tilesFromPatches(Align.Param p, List<? extends Patch> patches, Collection<? extends Patch> fixedPatches, List<AbstractAffineTile2D<?>> tiles, Collection<AbstractAffineTile2D<?>> fixedTiles)` If a Patch is locked or in fixedPatches, its corresponding Tile is added to fixedTiles.
`static void`	Align.`tilesFromPatches(Align.Param p, List<? extends Patch> patches, Collection<? extends Patch> fixedPatches, List<AbstractAffineTile2D<?>> tiles, Collection<AbstractAffineTile2D<?>> fixedTiles)` If a Patch is locked or in fixedPatches, its corresponding Tile is added to fixedTiles.

Constructor parameters in mpicbg.trakem2.align with type arguments of type AbstractAffineTile2D
Constructor and Description
`ExtractFeaturesThread(Align.Param p, List<AbstractAffineTile2D<?>> tiles, AtomicInteger ai, AtomicInteger ap, int steps)`
`MatchFeaturesAndFindModelThread(Align.Param p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>[]> tilePairs, AtomicInteger ai, AtomicInteger ap, int steps)`
`MatchFeaturesAndFindModelThread(Align.Param p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>[]> tilePairs, AtomicInteger ai, AtomicInteger ap, int steps, boolean multipleHypotheses)`

Uses of Classmpicbg.trakem2.align.AbstractAffineTile2D

Uses of AbstractAffineTile2D in ini.trakem2.imaging

Uses of AbstractAffineTile2D in mpicbg.trakem2.align

Uses of Class
mpicbg.trakem2.align.AbstractAffineTile2D