All Classes and Interfaces

Class
Description
 
Abstract superclass for array-based color lookup tables.
Localizing Cursor on an ArrayImg.
A Type with arbitrary bit depth up to maximum 64 bits.
Provides basic infrastructure to implement Types based on single bits stored in a LongAccess
 
Abstract superclass for Img types that divide their underlying data into cells.
This interface is implemented by all samplers on the AbstractCellImg.
 
TODO
Abstract implementation of Composite.
TODO
TODO
TODO
TODO
TODO
 
TODO
TODO
Abstract implementation of Cursor.
Abstract implementation of Cursor.
 
Superclass of abstract EuclideanSpace implementations (accessors, containers, etc).
 
TODO
 
The performance of this type is traded off for the gain in memory storage.
TODO
Implementation of the Interval interface.
 
Abstract base class for Img that store pixels in a single linear array (an ArrayList or similar).In principle, the number of entities stored is limited to Integer.MAX_VALUE.
An abstract class that implements the Localizable interface using a long[] array to maintain position.
An abstract class that implements the Localizable interface using an int[] array to maintain position.
Abstract base class for localizing Cursors.
Abstract base class for localizing Cursors.
 
Abstract base class for Img that store pixels in a single linear list addressed by a long.
TODO
TODO
TODO
Abstract base class for a vector of NumericType scalars.
Abstract implementation of shared functions for mirroring out of bounds.
 
Bijective integer transform mapping between integer coordinates in [0,n-1].
A RealPositionable that drives a Positionable to somehow derived discrete coordinates.
Base class for 2D projectors.
Implementation of the RealInterval interface.
An abstract class that implements the RealLocalizable interface using an array of doubles to maintain position
TODO
Most simple case of a shear transform that just implements for a integer valued coordinate: coordinate[ shearDimension ] += coordinate[ referenceDimension ] (forward) coordinate[ shearDimension ] -= coordinate[ referenceDimension ] (backward) This abstract class holds the inverse and implements applyInverse in terms of inverse.apply
 
 
 
 
 
 
 
Abstract base class for VolatileNumericTypes that wrap a NumericType that is either VALID or INVALID.
Abstract base class for VolatileRealTypes that wrap RealType.
 
Convenient base class for IterableIntervals, RandomAccessibleIntervals, etc that forward the Interval interface to, for example, their source accessible.
Convenient base class for IterableRealIntervals, etc that forward the RealInterval interface to, for example, their source accessible.
 
 
Access the on channel of an ARGBType as an UnsignedByteType.
 
 
 
A native NumericType that encodes four channels at unsigned byte precision into one 32bit signed integer which is the format used in most display oriented image processing libraries such as AWT or ImageJ.
Interface for all ColorTable implementations that use an array to store their color table information.
Trivial interface for primitive array based data access implementations that can replicate themselves and return the underlying array.
ArrayImg<T extends NativeType<T>,A>
This Img stores an image in a single linear array of basic types.
An AWTScreenImage that is an ArrayImg.
 
Convenience factory methods for creation of ArrayImg instances with the most common pixel Type variants.
Fast implementation of a AbstractProjector2D that selects a 2D data plain from an ByteType ArrayImg.
Fast implementation of a AbstractProjector2D that selects a 2D data plain from an ShortType ArrayImg.
Localizing Cursor on an ArrayImg.
A ScreenImage that produces AWT Image objects.
Utility class to create AWTScreenImages.
Representation of base pairs using 3 bits per entry, supported characters: gap, N, A, T, G, C, U Bases are handled using the BasePairBitType.Base enumeration.
 
Representation of base pairs using one char per entry, supported characters: gap, N, A, T, G, C, U Bases are handled using the BasePairBitType.Base enumeration.
TODO
Tools for setting up basic benchmarks.
An interface for defining a bin mapping algorithm.
Static utility methods to convert from a value to a bin, useful for dealing with histograms and LUTs.
TODO
BitAccess based on a Ntree<Boolean>.
TODO
A BooleanType wrapping a single primitive boolean variable.
Interface implemented by entities (Samplers, Positionables, Localizables) that can tell whether they are currently located outside of the image boundaries.
TODO
Implemented by Transforms that can transform (easily) a BoundingBox in the source space to a bounding box in the target space.
TODO
 
A AWTScreenImage that is an ArrayImg<ByteType, ByteArray>.
ByteAccess based on a Ntree<Byte>.
TODO
A cell of an AbstractCellImg.
CellCursor<T extends NativeType<T>,C extends Cell<?>>
Defines AbstractCellImg geometry and translates between image, cell, and grid coordinates.
CellImg<T extends NativeType<T>,A>
 
Factory for creating CellImgs.
Iteration order for a CellImg.
CellLocalizingCursor<T extends NativeType<T>,C extends Cell<?>>
Localizing Cursor on a AbstractCellImg.
CellRandomAccess<T extends NativeType<T>,C extends Cell<?>>
Convert UnsignedByteType into one channel of ARGBType.
 
TODO
 
CharAccess based on a Ntree<Char>.
 
16-bit color lookup table.
8-bit color lookup table.
TODO
TODO
Returns the imaginary value of a complex value
Computes the phase spectrum for a complex value
Computes the power spectrum for a complex value
Computes the generalized log of the power spectrum for a complex value
Returns the real value for of complex value
TODO
Map the components of the source vector to obtain the target vector, for instance transform (x,y,z) to (x,z,y).
Map the components of the source vector to obtain the target vector, for instance transform (x,y,z) to (x,z,y).
A Composite is a vector of scalars T.
A converter to extract one channel of a Composite.
A factory to create a Composite vector of scalars T given a RandomAccess.
CompositeView collapses the trailing dimension of a RandomAccessible of T into a Composite of T.
Creates a composite image from across multiple dimensional positions along an axis (typically, but not necessarily, channels).
Creates a composite image from across multiple dimensional positions along an axis (typically, but not necessarily, channels).
If T implements Concatenable<A> that means you can concatenate it with an A, usually resulting in another T.
Utilities for manipulating lists of (pre-)concatenable objects.
 
TODO
TODO
TODO
TODO
TODO
TODO
TODO
TODO
 
Convenience factory methods for sample conversion.
A Cursor iterates over a set of Localizable elements, for example the image values at the (integer) pixel positions of an image.
Defines an extent in n-dimensional discrete space.
Interface for objects that can be flagged dirty (useful for access objects that track if their content was modified)
 
 
 
 
 
 
 
This class represents an n-dimensional set of counters.
 
TODO
TODO
A AWTScreenImage that is an ArrayImg<DoubleType, DoubleArray> .
DoubleAccess based on a Ntree<Double>.
TODO
{Rn}: an N-dimensional Euclidean space.
An implementation of dimensionality that can wrap a long[] array.
Implementation of the Interval interface.
Implementation of the RealInterval interface.
A flat iteration order on an IterableInterval.
TODO
TODO
A AWTScreenImage that is an ArrayImg<FloatType, FloatArray>.
FloatAccess based on a Ntree<Float>.
TODO
A RealPositionable that drives a Positionable to its floor discrete coordinates.
RealRandomAccess to a RandomAccess by nearest floor interpolation (i.e., the value is sampled at floor(x)).
 
A RealPositionable that drives a Positionable to its floor discrete coordinates plus a discrete offset vector.
Implements the concept of fractions
Wrap a source RandomAccess which is related to this by a Mixed transformToSource.
Wrap a source RandomAccess which is related to this by a Slicing transformToSource.
TODO
A generic vector of scalars T.
 
TODO
Abstract superclass for Long types.
Abstract base class for native IntegerTypes that encode their value into a 16bit short.
A Histogram1d is a histogram that tracks up to four kinds of values: 1) values in the center of the distribution 2) values to the left of the center of the distribution (lower tail) 3) values to the right of the center of the distribution (upper tail) 4) values outside the other areas
A HistogramNd is an n-dimensional histogram that tracks up to four kinds of values: 1) values in the center of the distribution 2) values to the left of the center of the distribution (lower tail) 3) values to the right of the center of the distribution (upper tail) 4) values outside the other areas
 
An Img is a RandomAccessibleInterval that has its min at 0n and its max positive.
TODO
 
This class contains static methods for copying image data to and from Img instances.
ImgView<T extends Type<T>>
Allows a RandomAccessibleInterval to be treated as an Img.
Is thrown if a Type is not supported.
TODO
 
A AWTScreenImage that is an ArrayImg<ShortType, ShortArray>.
Maps integer values into a 1-d set of bins.
TODO
A RealRandomAccessible that is generated through interpolation.
 
{x∈Zn|mindxdmaxd;d∈{0… n-1}}
N-dimensional data is often stored in a flat 1-dimensional array.
Use this class to iterate a virtual Interval in flat order, that is: row by row, plane by plane, cube by cube, ...
Convenience methods for manipulating Intervals.
allows stepwise access to a preselected projected dimension.
IntervalView is a view that puts Interval boundaries on its source RandomAccessible.
IntAccess based on a Ntree<Integer>.
TODO
RealRandomAccess to a KNearestNeighborSearch whose sample value is generated by weighting the k nearest neighbors of a query real coordinate by their inverse distance to an arbitrary power p.
Factory for InverseDistanceWeightingInterpolator instances that work on a KNearestNeighborSearch.
Backward implementation of the most simple case of a shear transform: coordinate[ shearDimension ] -= coordinate[ referenceDimension ]
Final implementation of the inverse of an InvertibleTransform that simply replaces apply by applyInverse and conversely.
Invertible transformation from Zn to Zm .
An IterableRealInterval whose elements are located at integer coordinates.
A general 2D Projector that uses two dimensions as input to create the 2D result.
An Iterable which is backed by two other Iterables, whose iteration produces a Pair of objects corresponding to those given by the two respective iterations of the backing Iterables.
Generates Cursors that iterate a RandomAccessibleInterval in flat order, that is: row by row, plane by plane, cube by cube, ...
f:Rn∈[0,s]→T
Simplifies View cascades to provide the most efficient Cursor.
The Iterator interface provides basic functionality for iterating over a set of elements.
KDTree to access values at RealLocalizable positions.
Compare RealLocalizables by comparing their coordinates in dimension d.
A KDTreeNode that stores it's value as a Sampler.
A KDTreeNode that stores it's value as a reference.
Abstract base class for nodes in a KDTree.
k-nearest-neighbor search in an Euclidean space.
k-nearest-neighbor search on IterableRealInterval implemented as linear search.
Implementation of KNearestNeighborSearch search for kd-trees.
TODO
n-dimensional double-based Lanczos Interpolation
TODO
A AbstractCellImg that obtains its Cells lazily when they are accessed.
 
 
Basic vector and matrix operations implemented on double[] and double[][].
 
This Img stores an image in a single linear ArrayList.
ImgFactory for ListImg of any type T.
Localizing Cursor on a ListImg.
The Localizable interface can localize itself in an n-dimensional discrete space.
Use this class to iterate a virtual Interval in flat order, that is: row by row, plane by plane, cube by cube, ...
Use this class to iterate a virtual rectangular Interval whose min coordinates are at 0n in flat order, that is: row by row, plane by plane, cube by cube, ...
TODO
 
LongAccess based on a Ntree<Longeger>.
TODO
Mixed transform allows to express common integer view transformations such as translation, rotation, rotoinversion, and projection.
Wrap a source RandomAccess which is related to this by a Mixed transformToSource.
Mixed transform allows to express common integer view transformations such as translation, rotation, rotoinversion, and projection.
TODO
 
 
 
NativeImg<T extends Type<T>,A>
TODO
TODO
A NativeType is a Type that that provides access to data stored in Java primitive arrays.
RealRandomAccess to a RandomAccess by nearest neighbor interpolation.
 
Nearest-neighbor search in an Euclidean space.
Nearest-neighbor interpolation implemented by NearestNeighborSearch.
Factory for NearestNeighborSearchInterpolator instances that work on a NearestNeighborSearch.
k-nearest-neighbor search on IterableRealInterval implemented as linear search.
Implementation of NearestNeighborSearch search for kd-trees.
Performs multi-linear interpolation.
 
 
 
N-linear interpolator for ARGB values with overflow check.
 
 
Ntree<T extends Comparable<T>>
N-dimensional equivalent of a quad/oct-tree.
 
NtreeAccess<L extends Comparable<L>,A extends NtreeAccess<L,A>>
 
 
NtreeImg<T extends NativeType<T>,A extends NtreeAccess<?,A>>
 
 
 
IntAccess based on a Ntree<Integer>.
 
A vector of NumericType scalars.
 
TODO
A IntervalIterator that has an adjustable offset
A LocalizingIntervalIterator that has an adjustable offset
 
Repeat the boundary pixels.
Strategy to repeat the boundary pixels (creates OutOfBoundsBorder).
 
 
 
Coordinates out of image bounds are mirrored between boundary coordinates.
Adds a exponential windowing to the mirrored content outside the Interval boundaries
TODO
Create appropriate strategies that virtually mirror a RandomAccessible at its boundaries.
 
Coordinates out of image bounds are mirrored at boundary coordinates.
Coordinates out of image bounds are periodically repeated.
Create appropriate strategies that virtually extend a RandomAccessibleInterval periodically.
Return a random value in a certain range when outside of the Interval
 
 
TODO
Bijective integer transform mapping between integer coordinates in [0,n-1].
Interface allowing access to data on a plane-by-plane basis.
Basic Iterator for PlanarContainers
Basic Iterator for 1d PlanarContainers
Basic Iterator for 2d PlanarContainers
A NativeImg that stores data in an list of primitive arrays, one per image plane.
This interface is implemented by all samplers on the PlanarImg.
Helps to sample a planar image by keeping track of the current slice.
Factory that creates an appropriate PlanarImg.
Convenience factory methods for creation of PlanarImg instances with the most common pixel Type variants.
Fast implementation of a AbstractProjector2D that selects a 2D data plain from a ByteType PlanarImg.
Fast implementation of a AbstractProjector2D that selects a 2D data plain from an ShortType PlanarImg.
Localizing Iterator for a PlanarContainers
TODO
TODO
Basic Iterator for PlanarContainers
Cursor optimized for one plane in an PlanarImg.
RandomAccess for a 1-dimensional PlanarImg.
A Point is a position in Euclidean space specified in integer coordinates.
A list of data samples at explicit integer coordinates.
An element that can be positioned in n-dimensional discrete space.
If T implements PreConcatenable<A> that means you can pre-concatenate it with an A, usually resulting in another T.
provides samples from a projected (SamplingProjector2D) dimension.
 
Radius neighbor search in an Euclidean space.
Implementation of RadiusNeighborSearch search for kd-trees.
 
f:Zn→T
f:{x∈Zn|[min,max]→T}
A Cursor that iterates any RandomAccessibleInterval by moving a RandomAccess in flat iteration order.
A RandomAccessible over two independent RandomAccessibles whose type is the Pair of corresponding values at the same coordinates in either of the two sources.
A general 2D Projector that uses two dimensions as input to create the 2D result.
Maps real values into a 1-d set of bins.
 
A vector of RealType scalars.
 
A RealCursor iterates over a set of RealLocalizable elements, for example intensity values sampled at a finite set of arbitrary real positions.
Converts any RealType to a DoubleType.
TODO
 
TODO
{x∈Rn|mindxdmaxd;d∈{0… n-1}}
The RealLocalizable interface can localize itself in an n-dimensional real space.
RealLUTConverter contains a ColorTable8, through which samples are filtered.
 
 
 
A point is a location in EuclideanSpace.
A list of data samples at explicit real coordinates.
An element that can be positioned in n-dimensional real space.
 
f:Rn→T
f:{x∈Rn|[min,max]→T}
RealSum implements a method to reduce numerical instabilities when summing up a very large number of double precision numbers.
RealType<T extends RealType<T>>
TODO
 
 
A RealPositionable that drives a Positionable to its round discrete coordinates: f = r < 0 ? (long)( r - 0.5 ) : (long)( r + 0.5 )
The Sampler interface provides access to a value whose type is specified by the generic parameter T.
TODO
A general 2D Projector that uses three dimensions as input to create the 2D result.
Toplevel interface for screen images.
Provides access to a set of predefined positions of a projected dimension
Transform n-dimensional to m-dimensional coordinates (m<n) by flattening dimensions >m.
 
 
Forward implementation of the most simple case of a shear transform: coordinate[ shearDimension ] += coordinate[ referenceDimension ]
TODO
 
A AWTScreenImage that is an ArrayImg<ShortType, ShortArray>.
 
TODO
DataBuffer that stores signed bytes.
DataBuffer that stores signed shorts.
 
TODO
Wrap a cursor that runs on a hyperslice and apply coordinate transform on localize calls.
Wrap a source RandomAccess which is related to this by a Slicing transformToSource.
Map the components of the source vector to a slice of the target space, for instance transform (x,y) to (x,C,y) where C is a constant.
A stack of n-dimensional RandomAccessibleIntervals, forming a (n+1)-dimensional RandomAccessibleInterval.
Describes how a RandomAccess on the (n+1)-dimensional StackView maps position changes into position changes of the underlying n-dimensional RandomAccesses.
 
Implementing this interface enables the implementor to return optimized Cursors for certain Intervals
SubsampleIntervalView is a view that provides access to only every sdth value of a source RandomAccessibleInterval.
SubsampleView is a view that provides access to only every sdth value of a source RandomAccessible.
Transformation from Zn to Zm.
A class is transformable if it can produce a copy of itself in the transformed space using the supplied transform.
The "brain" of the Views framework.
A view of a RandomAccessible which is related by a coordinate Transform to its source.
Wrap a source RandomAccess which is related to this by a generic Transform transformToSource.
Wrap a source RandomAccessible which is related to this by a generic Transform transformToSource.
TODO
TODO
TODO
Type<T extends Type<T>>
The Type interface is responsible for accessing and manipulating (pixel) values.
TypeIdentity<T extends Type<T>>
TODO
A Type with a bit depth of 128.
A 12-bit Type whose data is stored in a LongAccess.
A Type with a bit depth of 2.
A Type with a bit depth of 4.
A AWTScreenImage that is an ArrayImg<UnsignedByteType, ByteArray>.
TODO
A AWTScreenImage that is an ArrayImg<ShortType, ShortArray>.
DataBuffer that stores unsigned ints.
TODO
TODO
A AWTScreenImage that is an ArrayImg<UnsignedShortType, ShortArray>.
TODO
A Type with arbitrary bit depth up to maximum 64 bits.
TODO
Tests equivalency of values.
TODO
An interface which marks an object that is a lightweight wrapper or "view" around actual data.
Create light-weight views into RandomAccessibles.
Something volatile that has a value and is either VALID or INVALID.
A basic type access that can contain valid or invalid data.
An ArrayDataAccess that can contain valid or invalid data.
 
 
 
 
 
 
Something volatile that has a value and is either VALID or INVALID.
Something volatile that has a value and is either VALID or INVALID.
Converts a VolatileRealType to an ARGBType.
 
An object that wraps an Img somehow.
TODO
TODO
TODO
TODO
TODO
TODO
Use this class to iterate a virtual rectangular Interval whose min coordinates are at 0n in flat order, that is: row by row, plane by plane, cube by cube, ...