All Classes and Interfaces
Class
Description
Abstract superclass for array-based color lookup tables.
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
AbstractCellImg<T extends NativeType<T>,A,C extends Cell<A>,I extends RandomAccessible<C> & IterableInterval<C>>
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
AbstractConvertedIterableRandomAccessibleInterval<A,B,S extends RandomAccessible<A> & IterableInterval<A>>
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 positionTODO
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.
This
Img stores an image in a single linear array of basic types.An
AWTScreenImage that is an ArrayImg.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
AbstractArrayLocalizingCursor on an ArrayImg.RandomAccess 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.Cursor on a AbstractCellImg.Defines
AbstractCellImg geometry and translates between image, cell,
and grid coordinates.Factory for creating
CellImgs.Iteration order for a
CellImg.Localizing
Cursor on a AbstractCellImg.RandomAccess on a AbstractCellImg.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.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)
A
ByteArray with an DirtyVolatileByteArray.isDirty() and an AbstractVolatileByteArray.isValid()
flag.A
CharArray with an DirtyVolatileCharArray.isDirty() and an AbstractVolatileCharArray.isValid()
flag.A
DoubleArray with an DirtyVolatileDoubleArray.isDirty() and an AbstractVolatileDoubleArray.isValid()
flag.A
FloatArray with an DirtyVolatileFloatArray.isDirty() and an AbstractVolatileFloatArray.isValid()
flag.A
LongArray with an DirtyVolatileLongArray.isDirty() and an AbstractVolatileLongArray.isValid()
flag.A
ShortArray with an DirtyVolatileShortArray.isDirty() and an AbstractVolatileShortArray.isValid()
flag.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.
Implements
RealRandomAccessible for a
RealRandomAccessibleRealInterval through an
RealOutOfBoundsFactory.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
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.
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|mind≤
xd≤maxd;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.
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[][].
ImgFactory for ListImg of any type T.RandomAccess 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.
Mixed transform allows to express common integer view transformations such as
translation, rotation, rotoinversion, and projection.
TODO
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.
N-dimensional equivalent of a quad/oct-tree.
IntAccess based on a
Ntree<Integer>.A vector of
NumericType scalars.TODO
A
IntervalIterator that has an adjustable offsetA
LocalizingIntervalIterator that has an adjustable offsetRepeat 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
OutOfBoundsMirrorExpWindowingFactory<T extends NumericType<T>,F extends Interval & RandomAccessible<T>>
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
PlanarContainersBasic Iterator for 1d
PlanarContainersBasic Iterator for 2d
PlanarContainersA
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.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
PlanarContainersTODO
TODO
Basic Iterator for
PlanarContainersCursor optimized for one plane in an PlanarImg.
RandomAccess on a 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|mind≤
xd≤maxd;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.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.
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.A
RandomAccess on a StackView.A
RandomAccess on a StackView.Describes how a
RandomAccess on the (n+1)-dimensional
StackView maps position changes into position changes of the
underlying n-dimensional RandomAccesses.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.TODO
TODO
TODO
The
Type interface is responsible for accessing and manipulating
(pixel) values.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.
IterableIntervalProjector2D for Volatile input.A basic type access that can contain valid or invalid data.
An
ArrayDataAccess that can contain valid or invalid data.A
ByteArray with an AbstractVolatileByteArray.isValid() flag.A
CharArray with an AbstractVolatileCharArray.isValid() flag.A
DoubleArray with an AbstractVolatileDoubleArray.isValid() flag.A
FloatArray with an AbstractVolatileFloatArray.isValid() flag.A
IntArray with an AbstractVolatileIntArray.isValid() flag.A
LongArray with an AbstractVolatileLongArray.isValid() flag.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.A
ShortArray with an AbstractVolatileShortArray.isValid() flag.An object that wraps an
Img somehow.TODO
TODO
WriteConvertedIterableRandomAccessibleInterval<A,B,S extends RandomAccessible<A> & IterableInterval<A>>
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, ...