Modifier and Type | Class and Description |
---|---|
class |
AbstractWrappedInterval<I extends Interval>
Convenient base class for
IterableIntervals ,
RandomAccessibleIntervals , etc that forward
the Interval interface to, for example, their source accessible. |
Modifier and Type | Interface and Description |
---|---|
interface |
IterableInterval<T>
An
IterableRealInterval whose elements are located at integer
coordinates. |
interface |
RandomAccessibleInterval<T>
f:{x∈Zn|[min,max]→T}
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractInterval
Implementation of the
Interval interface. |
class |
AbstractWrappedInterval<I extends Interval>
Convenient base class for
IterableIntervals ,
RandomAccessibleIntervals , etc that forward
the Interval interface to, for example, their source accessible. |
class |
FinalInterval
Implementation of the
Interval interface. |
class |
PointSampleList<T>
A list of data samples at explicit
integer coordinates . |
Modifier and Type | Method and Description |
---|---|
RandomAccess<T> |
RandomAccessible.randomAccess(Interval interval)
Create a random access sampler for integer coordinates.
|
Constructor and Description |
---|
AbstractInterval(Interval interval)
Creates a
AbstractInterval from another Interval |
FinalInterval(Interval interval)
Creates an Interval from another
Interval |
FlatIterationOrder(Interval interval) |
Modifier and Type | Field and Description |
---|---|
protected Interval |
BSplineLazyCoefficientsInterpolatorFactory.interval |
protected Interval |
BSplineDecomposition.originalInterval |
Modifier and Type | Method and Description |
---|---|
static IntervalIterator |
BSplineDecomposition.getIterator(Interval interval,
int dim) |
static IntervalIterator |
BSplineDecomposition.getIterator(Interval paddedInterval,
Interval originalInterval,
int dim) |
Constructor and Description |
---|
BSplineLazyCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int[] blockSize) |
BSplineLazyCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int order,
boolean clipping,
int[] blockSize) |
BSplineLazyCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int order,
boolean clipping,
S coefficientType,
int[] blockSize) |
BSplineLazyCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int order,
boolean clipping,
S coefficientType,
int[] blockSize,
OutOfBoundsFactory<? extends RealType<?>,?> oobFactory)
Creates a new
BSplineLazyCoefficientsInterpolatorFactory . |
BSplineLazyCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int order,
int[] blockSize) |
LazyCellImgFactory(BSplineDecomposition<T,S> decomposition,
Interval interval,
int[] blockSize,
S type) |
Modifier and Type | Method and Description |
---|---|
Interval |
MultiDimensionConvolution.requiredSourceInterval(Interval targetInterval) |
Interval |
LineConvolution.requiredSourceInterval(Interval targetInterval) |
Interval |
Convolution.requiredSourceInterval(Interval targetInterval)
Returns the required size for source image, to calculate the given target
interval.
|
Modifier and Type | Method and Description |
---|---|
Interval |
MultiDimensionConvolution.requiredSourceInterval(Interval targetInterval) |
Interval |
LineConvolution.requiredSourceInterval(Interval targetInterval) |
Interval |
Convolution.requiredSourceInterval(Interval targetInterval)
Returns the required size for source image, to calculate the given target
interval.
|
Modifier and Type | Field and Description |
---|---|
protected Interval |
DogDetection.interval |
Constructor and Description |
---|
DogDetection(RandomAccessible<T> input,
Interval interval,
double[] calibration,
double sigmaSmaller,
double sigmaLarger,
DogDetection.ExtremaType extremaType,
double minPeakValue,
boolean normalizeMinPeakValue)
Sets up a
DogDetection with the specified parameters (does not do
any computation yet). |
DogDetection(RandomAccessible<T> input,
Interval interval,
double[] calibration,
double sigmaSmaller,
double sigmaLarger,
DogDetection.ExtremaType extremaType,
double minPeakValue,
boolean normalizeMinPeakValue,
F computationType)
Sets up a
DogDetection with the specified parameters (does not do
any computation yet). |
Modifier and Type | Method and Description |
---|---|
static Interval |
FFTMethods.paddingIntervalCentered(Interval input,
Dimensions paddingDimensions)
Computes the padding interval required to perform an FFT when the padding
dimensions are known.
|
static Interval |
FFTMethods.unpaddingIntervalCentered(Interval fftDimensions,
Dimensions originalDimensions)
Computes the un-padding interval required to extract the original sized
image from an inverse FFT when padding was applying upon the FFT.
|
Modifier and Type | Method and Description |
---|---|
static Pair<Interval,Interval> |
FFTConvolution.setupFFTs(Interval imgInterval,
Interval kernelInterval,
long[] min,
long[] max) |
static Pair<Interval,Interval> |
FFTConvolution.setupFFTs(Interval imgInterval,
Interval kernelInterval,
long[] min,
long[] max) |
Modifier and Type | Method and Description |
---|---|
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessible<C> input,
Interval inputInterval,
ImgFactory<R> factory,
R type) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessible<C> input,
Interval inputInterval,
ImgFactory<R> factory,
R type,
ExecutorService service) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessible<C> input,
Interval inputInterval,
ImgFactory<R> factory,
R type,
int numThreads) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessible<C> input,
Interval inputInterval,
Interval outputDimensions,
ImgFactory<R> factory,
ExecutorService service) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessible<C> input,
Interval inputInterval,
Interval outputDimensions,
ImgFactory<R> factory,
R type) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessible<C> input,
Interval inputInterval,
Interval outputDimensions,
ImgFactory<R> factory,
R type,
ExecutorService service)
Deprecated.
|
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessible<C> input,
Interval inputInterval,
Interval outputDimensions,
ImgFactory<R> factory,
R type,
int numThreads) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessibleInterval<C> input,
Interval outputDimensions,
ImgFactory<R> factory,
R type) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessibleInterval<C> input,
Interval outputDimensions,
ImgFactory<R> factory,
R type,
ExecutorService service) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFT.complexToReal(RandomAccessibleInterval<C> input,
Interval outputDimensions,
ImgFactory<R> factory,
R type,
int numThreads) |
static <C extends ComplexType<C>,R extends RealType<R>> |
FFTMethods.complexToReal(RandomAccessibleInterval<C> input,
RandomAccessibleInterval<R> output,
Interval interval,
int dim)
Computes a complex-to-real inverse FFT transform of an n-dimensional
dataset in a certain dimension (typically dim = 0).
|
static <C extends ComplexType<C>,R extends RealType<R>> |
FFTMethods.complexToReal(RandomAccessibleInterval<C> input,
RandomAccessibleInterval<R> output,
Interval interval,
int dim,
boolean scale)
Computes a complex-to-real inverse FFT transform of an n-dimensional
dataset in a certain dimension (typically dim = 0).
|
static <C extends ComplexType<C>,R extends RealType<R>> |
FFTMethods.complexToReal(RandomAccessibleInterval<C> input,
RandomAccessibleInterval<R> output,
Interval interval,
int dim,
boolean scale,
ExecutorService service)
Computes a complex-to-real inverse FFT transform of an n-dimensional
dataset in a certain dimension (typically dim = 0).
|
static <C extends ComplexType<C>,R extends RealType<R>> |
FFTMethods.complexToReal(RandomAccessibleInterval<C> input,
RandomAccessibleInterval<R> output,
Interval interval,
int dim,
boolean scale,
int nThreads)
Computes a complex-to-real inverse FFT transform of an n-dimensional
dataset in a certain dimension (typically dim = 0).
|
static <R extends RealType<R>> |
FFTConvolution.computeImgFFT(Interval imgConvolutionInterval,
RandomAccessible<R> img,
ImgFactory<ComplexFloatType> fftFactory,
ExecutorService service) |
static <R extends RealType<R>> |
FFTConvolution.computeKernelFFT(Interval kernelConvolutionInterval,
long[] min,
long[] max,
boolean complexConjugate,
RandomAccessible<R> kernel,
ImgFactory<ComplexFloatType> fftFactory,
ExecutorService service) |
static <R extends RealType<R>> |
FFTConvolution.convolve(RandomAccessible<R> img,
Interval imgInterval,
RandomAccessible<R> kernel,
Interval kernelInterval,
RandomAccessibleInterval<R> output,
ImgFactory<ComplexFloatType> factory,
boolean div,
ExecutorService service) |
static boolean |
FFTMethods.dimensionsEqual(Interval interval,
long[] paddedDimensions)
A helper method to test if padding is actually necessary
|
static Interval |
FFTMethods.paddingIntervalCentered(Interval input,
Dimensions paddingDimensions)
Computes the padding interval required to perform an FFT when the padding
dimensions are known.
|
static <R extends RealType<R>,C extends ComplexType<C>> |
FFT.realToComplex(RandomAccessible<R> input,
Interval inputInterval,
ImgFactory<C> factory,
C type) |
static <R extends RealType<R>,C extends ComplexType<C>> |
FFT.realToComplex(RandomAccessible<R> input,
Interval inputInterval,
ImgFactory<C> factory,
C type,
ExecutorService service)
Deprecated.
|
static <R extends RealType<R>,C extends ComplexType<C>> |
FFT.realToComplex(RandomAccessible<R> input,
Interval inputInterval,
ImgFactory<C> factory,
C type,
int numThreads) |
static <R extends RealType<R>,C extends ComplexType<C>> |
FFT.realToComplex(RandomAccessible<R> input,
Interval inputInterval,
ImgFactory<C> factory,
ExecutorService service) |
static <R extends RealType<R>,C extends ComplexType<C>> |
FFTMethods.realToComplex(RandomAccessibleInterval<R> input,
RandomAccessibleInterval<C> output,
Interval interval,
int dim)
Computes a real-to-complex forward FFT transform of an n-dimensional
dataset in a certain dimension (typically dim = 0).
|
static <R extends RealType<R>,C extends ComplexType<C>> |
FFTMethods.realToComplex(RandomAccessibleInterval<R> input,
RandomAccessibleInterval<C> output,
Interval interval,
int dim,
boolean scale)
Computes a real-to-complex forward FFT transform of an n-dimensional
dataset in a certain dimension (typically dim = 0).
|
static <R extends RealType<R>,C extends ComplexType<C>> |
FFTMethods.realToComplex(RandomAccessibleInterval<R> input,
RandomAccessibleInterval<C> output,
Interval interval,
int dim,
boolean scale,
ExecutorService service)
Computes a real-to-complex forward FFT transform of an n-dimensional
dataset in a certain dimension (typically dim = 0).
|
static <R extends RealType<R>,C extends ComplexType<C>> |
FFTMethods.realToComplex(RandomAccessibleInterval<R> input,
RandomAccessibleInterval<C> output,
Interval interval,
int dim,
boolean scale,
int nThreads)
Computes a real-to-complex forward FFT transform of an n-dimensional
dataset in a certain dimension (typically dim = 0).
|
void |
FFTConvolution.setImg(RandomAccessible<R> img,
Interval imgInterval) |
void |
FFTConvolution.setKernel(RandomAccessible<R> kernel,
Interval kernelInterval) |
static Pair<Interval,Interval> |
FFTConvolution.setupFFTs(Interval imgInterval,
Interval kernelInterval,
long[] min,
long[] max) |
static Interval |
FFTMethods.unpaddingIntervalCentered(Interval fftDimensions,
Dimensions originalDimensions)
Computes the un-padding interval required to extract the original sized
image from an inverse FFT when padding was applying upon the FFT.
|
Constructor and Description |
---|
FFTConvolution(RandomAccessible<R> img,
Interval imgInterval,
RandomAccessible<R> kernel,
Interval kernelInterval,
ImgFactory<ComplexFloatType> factory)
Compute a Fourier space based convolution in-place (img will be replaced
by the convolved result).
|
FFTConvolution(RandomAccessible<R> img,
Interval imgInterval,
RandomAccessible<R> kernel,
Interval kernelInterval,
ImgFactory<ComplexFloatType> factory,
ExecutorService service)
Compute a Fourier space based convolution in-place (img will be replaced
by the convolved result).
|
FFTConvolution(RandomAccessible<R> img,
Interval imgInterval,
RandomAccessible<R> kernel,
Interval kernelInterval,
RandomAccessibleInterval<R> output,
ImgFactory<ComplexFloatType> factory)
Compute a Fourier space based convolution.
|
FFTConvolution(RandomAccessible<R> img,
Interval imgInterval,
RandomAccessible<R> kernel,
Interval kernelInterval,
RandomAccessibleInterval<R> output,
ImgFactory<ComplexFloatType> factory,
ExecutorService service)
Compute a Fourier space based convolution.
|
Modifier and Type | Method and Description |
---|---|
Interval |
AbstractGauss.getInputInterval() |
protected Interval |
AbstractGauss.getRange(int dim)
The area for the output/temp that needs to be convolved, always relative
to the input of the next convolution operation.
|
protected Interval |
AbstractGauss.getTemporaryImgSize() |
Modifier and Type | Method and Description |
---|---|
protected SamplingLineIterator<T> |
AbstractGauss.createInputLineSampler(int dim,
Interval range)
An
Iterator that samples a one dimensional line of input data for
the current dimension. |
protected WritableLineIterator<T> |
AbstractGauss.createOutputLineWriter(int dim,
Interval range,
SamplingLineIterator<T> inputLineSampler)
An
Iterator that samples a one dimensional line of output data
for the current dimension. |
static Img<DoubleType> |
GaussDouble.gauss(double[] sigma,
RandomAccessible<DoubleType> input,
Interval interval,
ImgFactory<DoubleType> factory)
Deprecated.
|
static void |
GaussDouble.gauss(double[] sigma,
RandomAccessible<DoubleType> input,
Interval interval,
RandomAccessible<DoubleType> output,
Localizable outputOffset,
ImgFactory<DoubleType> factory)
Deprecated.
|
static Img<FloatType> |
GaussFloat.gauss(double[] sigma,
RandomAccessible<FloatType> input,
Interval interval,
ImgFactory<FloatType> factory)
Deprecated.
|
static void |
GaussFloat.gauss(double[] sigma,
RandomAccessible<FloatType> input,
Interval interval,
RandomAccessible<FloatType> output,
Localizable outputOffset,
ImgFactory<FloatType> factory)
Deprecated.
|
static <T extends RealType<T>> |
Gauss.inDouble(double[] sigma,
RandomAccessible<T> img,
Interval interval,
RandomAccessible<T> output,
Localizable origin,
ImgFactory<DoubleType> imgFactory)
Deprecated.
Computes a Gaussian convolution with double precision on an infinite
RandomAccessible |
static <T extends RealType<T>> |
Gauss.inDouble(double sigma,
RandomAccessible<T> img,
Interval interval,
RandomAccessible<T> output,
Localizable origin,
ImgFactory<DoubleType> imgFactory)
Deprecated.
Computes a Gaussian convolution with double precision on an infinite
RandomAccessible |
static <T extends RealType<T>> |
Gauss.inFloat(double[] sigma,
RandomAccessible<T> img,
Interval interval,
RandomAccessible<T> output,
Localizable origin,
ImgFactory<FloatType> imgFactory)
Deprecated.
Computes a Gaussian convolution with float precision on an infinite
RandomAccessible |
static <T extends RealType<T>> |
Gauss.inFloat(double sigma,
RandomAccessible<T> img,
Interval interval,
RandomAccessible<T> output,
Localizable origin,
ImgFactory<FloatType> imgFactory)
Deprecated.
Computes a Gaussian convolution with float precision on an infinite
RandomAccessible |
static <T extends NumericType<T>> |
Gauss.inNumericType(double[] sigma,
RandomAccessible<T> img,
Interval interval,
RandomAccessible<T> output,
Localizable origin,
ImgFactory<T> imgFactory)
Deprecated.
Computes a Gaussian convolution with the precision of the type provided
on an infinite
RandomAccessible |
static <T extends NumericType<T>> |
Gauss.inNumericType(double sigma,
RandomAccessible<T> img,
Interval interval,
RandomAccessible<T> output,
Localizable origin,
ImgFactory<T> imgFactory)
Deprecated.
Computes a Gaussian convolution with the precision of the type provided
on an infinite
RandomAccessible |
protected void |
AbstractGauss.updateInputLineSampler(SamplingLineIterator<T> a,
Interval range,
long[] offset,
Localizable originalLocation)
Updates the current
SamplingLineIterator to the location of the
new line that is processed and clears the processing line (set all values
to zero) |
protected void |
AbstractGauss.updateOutputLineWriter(WritableLineIterator<T> a,
Interval range,
long[] offset,
Localizable originalLocation)
Updates the current
WritableLineIterator to the location of the
new line that is processed. |
Constructor and Description |
---|
AbstractGauss(double[] sigma,
RandomAccessible<T> input,
Interval inputInterval,
RandomAccessible<T> output,
Localizable outputOffset,
ImgFactory<T> factory,
T type) |
GaussDouble(double[] sigma,
RandomAccessible<DoubleType> input,
Interval interval,
ImgFactory<DoubleType> factory)
Deprecated.
Computes a Gaussian convolution with double precision on a
RandomAccessible of DoubleType in a certain
Interval and returns an Img defined by the
ImgFactory containing the result |
GaussDouble(double[] sigma,
RandomAccessible<DoubleType> input,
Interval interval,
RandomAccessible<DoubleType> output,
Localizable outputOffset,
ImgFactory<DoubleType> factory)
Deprecated.
Computes a Gaussian convolution with double precision on a
RandomAccessible of DoubleType in a certain
Interval and writes it into a given RandomAccessible at a
specific Point |
GaussFloat(double[] sigma,
RandomAccessible<FloatType> input,
Interval interval,
ImgFactory<FloatType> factory)
Deprecated.
Computes a Gaussian convolution with float precision on a
RandomAccessible of FloatType in a certain
Interval and returns an Img defined by the
ImgFactory containing the result |
GaussFloat(double[] sigma,
RandomAccessible<FloatType> input,
Interval interval,
RandomAccessible<FloatType> output,
Localizable outputOffset,
ImgFactory<FloatType> factory)
Deprecated.
Computes a Gaussian convolution with float precision on a
RandomAccessible of FloatType in a certain
Interval and writes it into a given RandomAccessible at a
specific Point |
GaussGeneral(double[] sigma,
RandomAccessible<T> input,
Interval interval,
ImgFactory<T> factory,
T type)
Deprecated.
Computes a Gaussian convolution on a
RandomAccessible in a
certain Interval and returns an Img defined by the
ImgFactory containing the result. |
GaussGeneral(double[] sigma,
RandomAccessible<T> input,
Interval interval,
RandomAccessible<T> output,
Localizable outputOffset,
ImgFactory<T> factory,
T type)
Deprecated.
Computes a Gaussian convolution with any precision on a
RandomAccessible in a certain Interval and writes it into
a given RandomAccessible at a specific Point
WARNING: This is a very slow implementation as it is not written for
NativeType . |
GaussNativeType(double[] sigma,
RandomAccessible<T> input,
Interval interval,
ImgFactory<T> factory,
T type)
Deprecated.
Computes a Gaussian convolution on a
RandomAccessible in a
certain Interval and returns an Img defined by the
ImgFactory containing the result. |
GaussNativeType(double[] sigma,
RandomAccessible<T> input,
Interval interval,
RandomAccessible<T> output,
Localizable outputOffset,
ImgFactory<T> factory,
T type)
Deprecated.
Computes a Gaussian convolution with any precision on a
RandomAccessible in a certain Interval and writes it into
a given RandomAccessible at a specific Point |
Modifier and Type | Method and Description |
---|---|
AbstractConvertedRandomAccess<T,T> |
ScaleAsFunctionOfPosition.randomAccess(Interval interval) |
Constructor and Description |
---|
BSplineCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval) |
BSplineCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int order) |
BSplineCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int order,
boolean clipping) |
BSplineCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int order,
boolean clipping,
ImgFactory<S> coefficientFactory,
OutOfBoundsFactory<? extends RealType<?>,?> oobFactory)
Creates a new
BSplineCoefficientsInterpolatorFactory using the BSpline
interpolation in a certain window |
BSplineCoefficientsInterpolatorFactory(RandomAccessible<T> img,
Interval interval,
int order,
boolean clipping,
S coefficientType) |
Modifier and Type | Method and Description |
---|---|
RandomAccess<List<I>> |
VolumetricSearch.randomAccess(Interval interval) |
Modifier and Type | Method and Description |
---|---|
static <T> ToLongBiFunction<Localizable,T> |
ConnectedComponentAnalysis.idFromIntervalIndexer(Interval interval) |
Modifier and Type | Method and Description |
---|---|
static <T extends NativeType<T>> |
Lazy.generate(Interval targetInterval,
int[] blockSize,
T type,
Set<AccessFlags> accessFlags,
Consumer<RandomAccessibleInterval<T>> op)
Create a memory
CachedCellImg with a cell generator
Consumer . |
static <T> ArrayList<Future<T>> |
Caches.preFetch(RandomAccessible<T> source,
Interval interval,
long[] spacing,
ExecutorService exec)
Trigger pre-fetching of an
Interval in a RandomAccessible
by concurrent sampling of values at a sparse grid. |
Modifier and Type | Method and Description |
---|---|
static <P,T> List<P> |
LocalExtrema.findLocalExtrema(RandomAccessible<T> source,
Interval interval,
LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck)
Find pixels that are extrema in their local neighborhood.
|
static <P,T> List<P> |
LocalExtrema.findLocalExtrema(RandomAccessible<T> source,
Interval interval,
LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
Shape shape)
Find pixels that are extrema in their local neighborhood.
|
static <P,T> List<P> |
LocalExtrema.findLocalExtrema(RandomAccessible<T> source,
Interval interval,
LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
Shape shape,
ExecutorService service,
int numTasks)
Find pixels that are extrema in their local neighborhood.
|
static <P,T> List<P> |
LocalExtrema.findLocalExtrema(RandomAccessible<T> source,
Interval interval,
LocalExtrema.LocalNeighborhoodCheck<P,T> localNeighborhoodCheck,
Shape shape,
ExecutorService service,
int numTasks,
int splitDim)
Find pixels that are extrema in their local neighborhood.
|
static int |
LocalExtrema.getBiggestDimension(Interval interval) |
ArrayList<RefinedPeak<P>> |
SubpixelLocalization.process(List<P> peaks,
RandomAccessible<T> img,
Interval validInterval)
Refine a set of peaks to subpixel coordinates.
|
static <T extends RealType<T>,P extends Localizable> |
SubpixelLocalization.refinePeaks(List<P> peaks,
RandomAccessible<T> img,
Interval validInterval,
boolean returnInvalidPeaks,
int maxNumMoves,
boolean allowMaximaTolerance,
float maximaTolerance,
boolean[] allowedToMoveInDim)
Refine a set of peaks to subpixel coordinates.
|
static <T extends RealType<T>,P extends Localizable> |
SubpixelLocalization.refinePeaks(List<P> peaks,
RandomAccessible<T> img,
Interval validInterval,
boolean returnInvalidPeaks,
int maxNumMoves,
boolean allowMaximaTolerance,
float maximaTolerance,
boolean[] allowedToMoveInDim,
int numThreads)
Refine a set of peaks to subpixel coordinates.
|
Modifier and Type | Method and Description |
---|---|
Interval |
KDTreeSource.getInterval() |
Interval |
ImgSource.getInterval() |
Modifier and Type | Method and Description |
---|---|
static <T extends RealType<T>> |
ImgMath.gen(KDTree<T> kdtree,
double radius,
Object outside,
Interval interval) |
static <T extends RealType<T>> |
ImgMath.gen(List<Point> positions,
List<T> values,
double radius,
Object outside,
Interval interval) |
static <T extends RealType<T>> |
ImgMath.gen(List<Point> positions,
T value,
double radius,
Object outside,
Interval interval) |
<O extends RealType<O>> |
Compute.view(Interval interval) |
<O extends RealType<O>,C extends RealType<C>> |
Compute.view(Interval interval,
Converter<RealType<?>,C> inConverter,
C computingType,
O outputType,
Converter<C,O> outConverter) |
<O extends RealType<O>> |
Compute.view(Interval interval,
O outputType) |
Constructor and Description |
---|
KDTreeSource(KDTree<I> kdtree,
double radius,
Object outside,
Interval interval) |
KDTreeSource(List<Point> points,
I value,
double radius,
Object outside,
Interval interval) |
KDTreeSource(List<Point> points,
List<I> values,
double radius,
Object outside,
Interval interval) |
Modifier and Type | Method and Description |
---|---|
static Interval |
Util.findFirstInterval(IFunction f) |
Interval |
SourceInterval.getInterval() |
Modifier and Type | Class and Description |
---|---|
class |
IterableRandomAccessibleFunction<C extends RealType<C>,O extends RealType<O>>
|
class |
IterableRandomAccessibleFunctionDouble<O extends RealType<O>> |
Modifier and Type | Method and Description |
---|---|
RandomAccess<O> |
KDTreeRadiusSource.randomAccess(Interval interval) |
RandomAccess<O> |
IterableRandomAccessibleFunction.randomAccess(Interval interval) |
Constructor and Description |
---|
KDTreeRadiusSource(O scrap,
Converter<RealType<?>,O> converter,
KDTree<I> kdtree,
double radius,
I outside,
Interval interval) |
Modifier and Type | Method and Description |
---|---|
static <T extends RealType<T>> |
BlackTopHat.blackTopHatInPlace(RandomAccessible<T> source,
Interval interval,
List<? extends Shape> strels,
int numThreads)
|
static <T extends Type<T> & Comparable<T> & Sub<T>> |
BlackTopHat.blackTopHatInPlace(RandomAccessible<T> source,
Interval interval,
List<? extends Shape> strels,
T minVal,
T maxVal,
int numThreads)
Performs the black top-hat (or bottom-hat) morphological operation, using
a list of
Shape s as a flat structuring element. |
static <T extends RealType<T>> |
BlackTopHat.blackTopHatInPlace(RandomAccessible<T> source,
Interval interval,
Shape strel,
int numThreads)
|
static <T extends Type<T> & Comparable<T> & Sub<T>> |
BlackTopHat.blackTopHatInPlace(RandomAccessible<T> source,
Interval interval,
Shape strel,
T minVal,
T maxVal,
int numThreads)
Performs the black top-hat (or bottom-hat) morphological operation, using
a
Shape as a flat structuring element. |
static <T extends RealType<T>> |
Closing.closeInPlace(RandomAccessibleInterval<T> source,
Interval interval,
List<? extends Shape> strels,
int numThreads)
Performs the closing morphological operation, on a source
RandomAccessibleInterval using a list of Shape s as a flat
structuring element. |
static <T extends Type<T> & Comparable<T>> |
Closing.closeInPlace(RandomAccessibleInterval<T> source,
Interval interval,
List<? extends Shape> strels,
T minVal,
T maxVal,
int numThreads)
Performs the closing morphological operation, on a
RandomAccessibleInterval using a list of Shape s as a flat
structuring element. |
static <T extends RealType<T>> |
Closing.closeInPlace(RandomAccessibleInterval<T> source,
Interval interval,
Shape strel,
int numThreads)
Performs the closing morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends Type<T> & Comparable<T>> |
Closing.closeInPlace(RandomAccessibleInterval<T> source,
Interval interval,
Shape strel,
T minVal,
T maxVal,
int numThreads)
Performs the closing morphological operation, on a
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T> long[][] |
MorphologyUtils.computeTargetImageDimensionsAndOffset(Interval source,
Shape strel)
Static util to compute the final image dimensions and required offset
when performing a full dilation with the specified strel.
|
static <T extends RealType<T>> |
Dilation.dilateInPlace(RandomAccessibleInterval<T> source,
Interval interval,
List<? extends Shape> strels,
int numThreads)
Performs the dilation morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends Type<T> & Comparable<T>> |
Dilation.dilateInPlace(RandomAccessibleInterval<T> source,
Interval interval,
List<? extends Shape> strels,
T minVal,
int numThreads)
Performs the dilation morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends RealType<T>> |
Dilation.dilateInPlace(RandomAccessibleInterval<T> source,
Interval interval,
Shape strel,
int numThreads)
Performs the dilation morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends Type<T> & Comparable<T>> |
Dilation.dilateInPlace(RandomAccessibleInterval<T> source,
Interval interval,
Shape strel,
T minVal,
int numThreads)
Performs the dilation morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends RealType<T>> |
Erosion.erodeInPlace(RandomAccessible<T> source,
Interval interval,
List<? extends Shape> strels,
int numThreads)
Performs the erosion morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends RealType<T>> |
Erosion.erodeInPlace(RandomAccessible<T> source,
Interval interval,
Shape strel,
int numThreads)
Performs the erosion morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends Type<T> & Comparable<T>> |
Erosion.erodeInPlace(RandomAccessibleInterval<T> source,
Interval interval,
List<? extends Shape> strels,
T maxVal,
int numThreads)
Performs the erosion morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends Type<T> & Comparable<T>> |
Erosion.erodeInPlace(RandomAccessibleInterval<T> source,
Interval interval,
Shape strel,
T maxVal,
int numThreads)
Performs the erosion morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends RealType<T>> |
Opening.openInPlace(RandomAccessibleInterval<T> source,
Interval interval,
List<? extends Shape> strels,
int numThreads)
Performs the opening morphological operation, on a source
RandomAccessibleInterval using a list of Shape s as a flat
structuring element. |
static <T extends Type<T> & Comparable<T>> |
Opening.openInPlace(RandomAccessibleInterval<T> source,
Interval interval,
List<? extends Shape> strels,
T minVal,
T maxVal,
int numThreads)
Performs the opening morphological operation, on a
RandomAccessibleInterval using a list of Shape s as a flat
structuring element. |
static <T extends RealType<T>> |
Opening.openInPlace(RandomAccessibleInterval<T> source,
Interval interval,
Shape strel,
int numThreads)
Performs the opening morphological operation, on a
RealType
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends Type<T> & Comparable<T>> |
Opening.openInPlace(RandomAccessibleInterval<T> source,
Interval interval,
Shape strel,
T minVal,
T maxVal,
int numThreads)
Performs the opening morphological operation, on a
RandomAccessibleInterval using a Shape as a flat
structuring element. |
static <T extends RealType<T>> |
TopHat.topHatInPlace(RandomAccessible<T> source,
Interval interval,
List<? extends Shape> strels,
int numThreads)
|
static <T extends Type<T> & Comparable<T> & Sub<T>> |
TopHat.topHatInPlace(RandomAccessible<T> source,
Interval interval,
List<? extends Shape> strels,
T minVal,
T maxVal,
int numThreads)
Performs the top-hat (white top-hat) morphological operation, using a
list of
Shape s as a flat structuring element. |
static <T extends RealType<T>> |
TopHat.topHatInPlace(RandomAccessible<T> source,
Interval interval,
Shape strel,
int numThreads)
|
static <T extends Type<T> & Comparable<T> & Sub<T>> |
TopHat.topHatInPlace(RandomAccessible<T> source,
Interval interval,
Shape strel,
T minVal,
T maxVal,
int numThreads)
Performs the top-hat (white top-hat) morphological operation, using a
Shape as a flat structuring element. |
Modifier and Type | Method and Description |
---|---|
static int |
DistanceTransform.getLargestDimension(Interval interval)
Convenience method to find largest dimension of
Interval
interval. |
Modifier and Type | Interface and Description |
---|---|
interface |
Neighborhood<T> |
Modifier and Type | Field and Description |
---|---|
protected Interval |
RectangleNeighborhoodLocalizableSampler.sourceInterval |
protected Interval |
PeriodicLineNeighborhoodLocalizableSampler.sourceInterval |
protected Interval |
PairOfPointsNeighborhoodLocalizableSampler.sourceInterval |
protected Interval |
HypersphereNeighborhoodLocalizableSampler.sourceInterval |
protected Interval |
HorizontalLineNeighborhoodLocalizableSampler.sourceInterval |
protected Interval |
DiamondTipsNeighborhoodLocalizableSampler.sourceInterval |
protected Interval |
DiamondNeighborhoodLocalizableSampler.sourceInterval |
protected Interval |
RectangleNeighborhoodLocalizableSampler.span |
Modifier and Type | Method and Description |
---|---|
Neighborhood<T> |
RectangleNeighborhoodFactory.create(long[] position,
long[] currentMin,
long[] currentMax,
Interval span,
RandomAccess<T> sourceRandomAccess) |
RandomAccess<Neighborhood<T>> |
RectangleShape.NeighborhoodsAccessible.randomAccess(Interval interval) |
RandomAccess<Neighborhood<T>> |
PeriodicLineShape.NeighborhoodsAccessible.randomAccess(Interval interval) |
RandomAccess<Neighborhood<T>> |
PairOfPointsShape.NeighborhoodsAccessible.randomAccess(Interval interval) |
RandomAccess<Neighborhood<T>> |
HyperSphereShape.NeighborhoodsAccessible.randomAccess(Interval interval) |
RandomAccess<Neighborhood<T>> |
HorizontalLineShape.NeighborhoodsAccessible.randomAccess(Interval interval) |
RandomAccess<Neighborhood<T>> |
DiamondTipsShape.NeighborhoodsAccessible.randomAccess(Interval interval) |
RandomAccess<Neighborhood<T>> |
DiamondShape.NeighborhoodsAccessible.randomAccess(Interval interval) |
Modifier and Type | Class and Description |
---|---|
class |
HyperSphere<T>
TODO
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractNeighborhood<T>
A
Positionable IterableInterval that serves as a local
neighborhood, e.g. |
class |
BufferedRectangularNeighborhood<T extends Type<T>> |
class |
EllipseNeighborhood<T> |
class |
EllipsoidNeighborhood<T>
This class implements a
IterableInterval representing the volume of a
3D ellipsoid. |
class |
HyperSphereNeighborhoodGPL<T>
Deprecated.
|
class |
RectangleNeighborhoodGPL<T>
A
Positionable IterableInterval that serves as a local
neighborhood, e.g. |
Modifier and Type | Class and Description |
---|---|
class |
LocalNeighborhood<T>
Deprecated.
|
class |
LocalNeighborhood2<T>
Deprecated.
|
Constructor and Description |
---|
ImageTransform(RandomAccessible<T> input,
Interval interval,
InvertibleBoundable transform,
InterpolatorFactory<T,RandomAccessible<T>> interpolatorFactory,
ImgFactory<T> outImgFactory) |
Modifier and Type | Method and Description |
---|---|
Interval |
Grids.CreateAndCropBlockToFitInterval.apply(long[] min) |
Modifier and Type | Method and Description |
---|---|
static List<Interval> |
Grids.collectAllContainedIntervals(long[] dimensions,
int[] blockSize)
Get all blocks of size
blockSize contained within an interval
specified by dimensions and their positions within a cell grid. |
static List<Interval> |
Grids.collectAllContainedIntervals(long[] min,
long[] max,
int[] blockSize)
Get all blocks of size
blockSize contained within an interval
specified by min , max and their positions within a cell
grid. |
static List<Pair<Interval,long[]>> |
Grids.collectAllContainedIntervalsWithGridPositions(long[] dimensions,
int[] blockSize)
Get all blocks of size
blockSize contained within an interval
specified by dimensions and their positions within a cell grid. |
static List<Pair<Interval,long[]>> |
Grids.collectAllContainedIntervalsWithGridPositions(long[] min,
long[] max,
int[] blockSize)
Get all blocks of size
blockSize contained within an interval
specified by min , max and their positions within a cell
grid. |
static Function<long[],Pair<Interval,long[]>> |
Grids.croppedIntervalAndGridPosition(long[] dimensions,
int[] blockSize) |
static Function<long[],Pair<Interval,long[]>> |
Grids.croppedIntervalAndGridPosition(long[] min,
long[] max,
int[] blockSize)
|
Modifier and Type | Method and Description |
---|---|
static <T> List<Future<List<T>>> |
ParallelizeOverBlocks.parallelize(Function<Interval,T> func,
Interval interval,
int[] blockSize,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
static <T> List<T> |
ParallelizeOverBlocks.parallelizeAndWait(Function<Interval,T> func,
Interval interval,
int[] blockSize,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
Modifier and Type | Method and Description |
---|---|
static <T> List<Future<List<T>>> |
ParallelizeOverBlocks.parallelize(Function<Interval,T> func,
Interval interval,
int[] blockSize,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
static <T> List<Future<List<T>>> |
ParallelizeOverBlocks.parallelize(Function<Interval,T> func,
List<Interval> blocks,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
static <T> List<Future<List<T>>> |
ParallelizeOverBlocks.parallelize(Function<Interval,T> func,
List<Interval> blocks,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
static <T> List<Future<List<T>>> |
ParallelizeOverBlocks.parallelize(Function<Interval,T> func,
long[] min,
long[] max,
int[] blockSize,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
static <T> List<T> |
ParallelizeOverBlocks.parallelizeAndWait(Function<Interval,T> func,
Interval interval,
int[] blockSize,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
static <T> List<T> |
ParallelizeOverBlocks.parallelizeAndWait(Function<Interval,T> func,
List<Interval> blocks,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
static <T> List<T> |
ParallelizeOverBlocks.parallelizeAndWait(Function<Interval,T> func,
List<Interval> blocks,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
static <T> List<T> |
ParallelizeOverBlocks.parallelizeAndWait(Function<Interval,T> func,
long[] min,
long[] max,
int[] blockSize,
ExecutorService es,
int numTasks)
Submit blocked tasks and wait for execution.
|
Constructor and Description |
---|
CreateAndCropBlockToFitInterval(int[] blockSize,
Interval interval)
Convenience constructor for
Interval . |
GetGridCoordinates(int[] blockSize,
Interval interval)
Convenience constructor for
Interval . |
Modifier and Type | Class and Description |
---|---|
class |
CachedCellImg<T extends NativeType<T>,A>
A
LazyCellImg that creates empty Cells lazily when they are accessed
and stores (modified) Cells in a disk cache when memory runs full. |
class |
DiskCachedCellImg<T extends NativeType<T>,A>
A
LazyCellImg that creates empty Cells lazily when they are accessed
and stores (modified) Cells in a disk cache when memory runs full. |
class |
SingleCellArrayImg<T extends NativeType<T>,A extends ArrayDataAccess<A>>
A
NativeImg representing a single cell of an AbstractCellImg . |
Modifier and Type | Method and Description |
---|---|
RandomAccess<T> |
SingleCellArrayImg.randomAccess(Interval interval) |
Constructor and Description |
---|
IntervalKeyLoaderAsLongKeyLoader(CellGrid grid,
Function<Interval,A> intervalKeyLoader) |
Modifier and Type | Class and Description |
---|---|
class |
AbstractConvertedIterableInterval<A,B>
TODO
|
class |
AbstractConvertedIterableRandomAccessibleInterval<A,B,S extends RandomAccessible<A> & IterableInterval<A>>
TODO
|
class |
AbstractConvertedRandomAccessibleInterval<A,B> |
Modifier and Type | Method and Description |
---|---|
abstract AbstractConvertedRandomAccess<A,B> |
AbstractConvertedRandomAccessibleInterval.randomAccess(Interval interval) |
abstract AbstractConvertedRandomAccess<A,B> |
AbstractConvertedRandomAccessible.randomAccess(Interval interval) |
abstract AbstractConvertedRandomAccess<A,B> |
AbstractConvertedIterableRandomAccessibleInterval.randomAccess(Interval interval) |
Modifier and Type | Class and Description |
---|---|
class |
BiConvertedIterableInterval<A,B,C extends Type<C>>
TODO
|
class |
BiConvertedRandomAccessibleInterval<A,B,C extends Type<C>>
TODO
|
class |
ConvertedIterableInterval<A,B extends Type<B>>
TODO
|
class |
ConvertedRandomAccessibleInterval<A,B extends Type<B>>
TODO
|
Modifier and Type | Method and Description |
---|---|
ConvertedRandomAccess<A,B> |
ConvertedRandomAccessibleInterval.randomAccess(Interval interval) |
ConvertedRandomAccess<A,B> |
ConvertedRandomAccessible.randomAccess(Interval interval) |
BiConvertedRandomAccess<A,B,C> |
BiConvertedRandomAccessibleInterval.randomAccess(Interval interval) |
BiConvertedRandomAccess<A,B,C> |
BiConvertedRandomAccessible.randomAccess(Interval interval) |
Modifier and Type | Class and Description |
---|---|
class |
WriteConvertedIterableInterval<A,B>
TODO
|
class |
WriteConvertedIterableRandomAccessibleInterval<A,B,S extends RandomAccessible<A> & IterableInterval<A>>
TODO
|
class |
WriteConvertedRandomAccessibleInterval<A,B>
TODO
|
Modifier and Type | Method and Description |
---|---|
WriteConvertedRandomAccess<A,B> |
WriteConvertedRandomAccessibleInterval.randomAccess(Interval interval) |
WriteConvertedRandomAccess<A,B> |
WriteConvertedRandomAccessible.randomAccess(Interval interval) |
WriteConvertedRandomAccess<A,B> |
WriteConvertedIterableRandomAccessibleInterval.randomAccess(Interval interval) |
Modifier and Type | Class and Description |
---|---|
class |
ARGBScreenImage |
class |
ArrayImgAWTScreenImage<T extends NativeType<T>,A>
An
AWTScreenImage that is an ArrayImg . |
class |
ByteAWTScreenImage
A
AWTScreenImage that is an ArrayImg<ByteType, ByteArray> . |
class |
DoubleAWTScreenImage
A
AWTScreenImage that is an ArrayImg<DoubleType, DoubleArray>
. |
class |
FloatAWTScreenImage
A
AWTScreenImage that is an ArrayImg<FloatType, FloatArray> . |
class |
IntAWTScreenImage
A
AWTScreenImage that is an ArrayImg<ShortType, ShortArray> . |
class |
ShortAWTScreenImage
A
AWTScreenImage that is an ArrayImg<ShortType, ShortArray> . |
class |
UnsignedByteAWTScreenImage
A
AWTScreenImage that is an
ArrayImg<UnsignedByteType, ByteArray> . |
class |
UnsignedIntAWTScreenImage
A
AWTScreenImage that is an ArrayImg<ShortType, ShortArray> . |
class |
UnsignedShortAWTScreenImage
A
AWTScreenImage that is an
ArrayImg<UnsignedShortType, ShortArray> . |
Modifier and Type | Class and Description |
---|---|
class |
DiscreteFrequencyDistribution
This class represents an n-dimensional set of counters.
|
class |
Histogram1d<T>
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
|
class |
HistogramNd<T>
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
|
Modifier and Type | Method and Description |
---|---|
RandomAccess<LongType> |
HistogramNd.randomAccess(Interval interval) |
RandomAccess<LongType> |
Histogram1d.randomAccess(Interval interval) |
RandomAccess<LongType> |
DiscreteFrequencyDistribution.randomAccess(Interval interval) |
Modifier and Type | Interface and Description |
---|---|
interface |
Img<T>
An
Img is a RandomAccessibleInterval that has its min at
0n and its max positive. |
interface |
NativeImg<T extends Type<T>,A>
TODO
|
interface |
NativeLongAccessImg<T extends Type<T>,A>
TODO
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractImg<T>
TODO
|
class |
AbstractNativeImg<T extends NativeType<T>,A>
TODO
|
class |
AbstractNativeLongAccessImg<T extends NativeLongAccessType<T>,A>
TODO
|
class |
ImgView<T extends Type<T>>
Allows a
RandomAccessibleInterval to be treated as an Img . |
Modifier and Type | Method and Description |
---|---|
Cursor<T> |
ImgView.cursor(Interval interval) |
Cursor<T> |
ImgView.localizingCursor(Interval interval) |
RandomAccess<T> |
AbstractImg.randomAccess(Interval interval) |
Object |
ImgView.subIntervalIterationOrder(Interval interval) |
boolean |
ImgView.supportsOptimizedCursor(Interval interval) |
Modifier and Type | Class and Description |
---|---|
class |
ArrayImg<T extends NativeType<T>,A>
This
Img stores an image in a single linear array of basic types. |
Modifier and Type | Method and Description |
---|---|
Cursor<T> |
ArrayImg.cursor(Interval interval)
|
Cursor<T> |
ArrayImg.localizingCursor(Interval interval)
|
ArrayRandomAccess<T> |
ArrayImg.randomAccess(Interval interval) |
Object |
ArrayImg.subIntervalIterationOrder(Interval interval)
Returns the iteration order given the interval.
|
boolean |
ArrayImg.supportsOptimizedCursor(Interval interval)
|
Modifier and Type | Class and Description |
---|---|
class |
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. |
class |
Cell<A>
A cell of an
AbstractCellImg . |
class |
CellImg<T extends NativeType<T>,A> |
class |
LazyCellImg<T extends NativeType<T>,A>
A
AbstractCellImg that obtains its Cells lazily when they are
accessed. |
static class |
LazyCellImg.LazyCells<T> |
Modifier and Type | Class and Description |
---|---|
class |
ByteImagePlus<T extends NativeType<T>>
ImagePlusImg for byte-stored data. |
class |
FloatImagePlus<T extends NativeType<T>>
ImagePlusImg for float-stored data. |
class |
ImagePlusImg<T extends NativeType<T>,A extends ArrayDataAccess<A>>
A container that stores data in an array of 2D slices each as a linear array
of basic types.
|
class |
IntImagePlus<T extends NativeType<T>>
ImagePlusImg for integer-stored data. |
class |
ShortImagePlus<T extends NativeType<T>>
ImagePlusImg for short-stored data. |
Modifier and Type | Class and Description |
---|---|
class |
AbstractListImg<T>
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 . |
class |
AbstractLongListImg<T>
Abstract base class for
Img that store pixels in a single linear
list addressed by a long. |
class |
ListImg<T>
|
Modifier and Type | Class and Description |
---|---|
class |
PlanarImg<T extends NativeType<T>,A extends ArrayDataAccess<A>>
A
NativeImg that stores data in an list of primitive arrays, one per
image plane. |
Modifier and Type | Method and Description |
---|---|
Cursor<T> |
PlanarImg.cursor(Interval interval)
|
Cursor<T> |
PlanarImg.localizingCursor(Interval interval)
|
Object |
PlanarImg.subIntervalIterationOrder(Interval interval)
Returns the iteration order given the interval.
|
boolean |
PlanarImg.supportsOptimizedCursor(Interval interval)
|
Constructor and Description |
---|
PlanarPlaneSubsetCursor(PlanarImg<T,?> container,
Interval interval)
Constructor
|
PlanarPlaneSubsetLocalizingCursor(PlanarImg<T,?> container,
Interval interval)
Constructor
|
Modifier and Type | Class and Description |
---|---|
class |
NtreeCursor<T extends NativeType<T>> |
class |
NtreeImg<T extends NativeType<T>,A extends NtreeAccess<?,A>> |
Modifier and Type | Class and Description |
---|---|
class |
UnsafeImg<T extends NativeLongAccessType<T>,A>
This
Img stores an image in a single linear array of basic types. |
Modifier and Type | Method and Description |
---|---|
UnsafeSubIntervalCursor<T> |
UnsafeImg.cursor(Interval interval)
|
UnsafeLocalizingSubIntervalCursor<T> |
UnsafeImg.localizingCursor(Interval interval)
|
UnsafeRandomAccess<T> |
UnsafeImg.randomAccess(Interval interval) |
Object |
UnsafeImg.subIntervalIterationOrder(Interval interval)
Returns the iteration order given the interval.
|
boolean |
UnsafeImg.supportsOptimizedCursor(Interval interval)
|
Modifier and Type | Class and Description |
---|---|
class |
IntervalIterator
Use this class to iterate a virtual
Interval in flat order, that is:
row by row, plane by plane, cube by cube, ... |
class |
LocalizingIntervalIterator
Use this class to iterate a virtual
Interval in flat order, that is:
row by row, plane by plane, cube by cube, ... |
class |
LocalizingZeroMinIntervalIterator
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, ... |
class |
OffsetableIntervalIterator
A
IntervalIterator that has an adjustable offset |
class |
OffsetableLocalizingIntervalIterator
A
LocalizingIntervalIterator that has an adjustable offset |
class |
ZeroMinIntervalIterator
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, ... |
Modifier and Type | Method and Description |
---|---|
static IntervalIterator |
IntervalIterator.create(Interval interval) |
Constructor and Description |
---|
IntervalIterator(Interval interval)
Iterates a given
Interval . |
LocalizingIntervalIterator(Interval interval) |
LocalizingZeroMinIntervalIterator(Interval interval) |
OffsetableIntervalIterator(Interval interval) |
OffsetableLocalizingIntervalIterator(Interval interval) |
ZeroMinIntervalIterator(Interval interval) |
Modifier and Type | Interface and Description |
---|---|
interface |
Labeling<T extends Comparable<T>>
Deprecated.
|
interface |
NativeLabeling<T extends Comparable<T>>
Deprecated.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractLabeling<T extends Comparable<T>>
Deprecated.
|
class |
AbstractNativeLabeling<T extends Comparable<T>>
Deprecated.
|
class |
LabelingView<L extends Comparable<L>>
Deprecated.
|
class |
NativeImgLabeling<T extends Comparable<T>,I extends IntegerType<I>>
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
Labeling<T> |
LabelingFactory.create(Interval interval)
Deprecated.
|
Cursor<LabelingType<T>> |
NativeImgLabeling.cursor(Interval interval)
Deprecated.
|
Cursor<LabelingType<L>> |
LabelingView.cursor(Interval interval)
Deprecated.
|
Cursor<LabelingType<T>> |
NativeImgLabeling.localizingCursor(Interval interval)
Deprecated.
|
Cursor<LabelingType<L>> |
LabelingView.localizingCursor(Interval interval)
Deprecated.
|
RandomAccess<LabelingType<T>> |
NativeImgLabeling.randomAccess(Interval interval)
Deprecated.
|
Object |
NativeImgLabeling.subIntervalIterationOrder(Interval interval)
Deprecated.
|
Object |
LabelingView.subIntervalIterationOrder(Interval interval)
Deprecated.
|
boolean |
NativeImgLabeling.supportsOptimizedCursor(Interval interval)
Deprecated.
|
boolean |
LabelingView.supportsOptimizedCursor(Interval interval)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static List<Interval> |
IntervalChunks.chunkInterval(Interval interval,
int numberOfChunks)
Returns a list of disjoint intervals, that covers the given interval.
|
Modifier and Type | Method and Description |
---|---|
static List<Interval> |
IntervalChunks.chunkInterval(Interval interval,
int numberOfChunks)
Returns a list of disjoint intervals, that covers the given interval.
|
Modifier and Type | Class and Description |
---|---|
class |
OutOfBoundsBorderFactory<T,F extends Interval & RandomAccessible<T>>
Strategy to repeat the boundary pixels (creates
OutOfBoundsBorder ). |
class |
OutOfBoundsConstantValueFactory<T,F extends Interval & RandomAccessible<T>> |
class |
OutOfBoundsMirrorExpWindowingFactory<T extends NumericType<T>,F extends Interval & RandomAccessible<T>>
TODO
|
class |
OutOfBoundsMirrorFactory<T,F extends Interval & RandomAccessible<T>>
Create appropriate strategies that virtually mirror a
RandomAccessible at its boundaries. |
class |
OutOfBoundsPeriodicFactory<T,F extends Interval & RandomAccessible<T>>
Create appropriate strategies that virtually extend a
RandomAccessibleInterval periodically. |
class |
OutOfBoundsRandomValueFactory<T extends RealType<T>,F extends Interval & RandomAccessible<T>> |
Modifier and Type | Method and Description |
---|---|
RandomAccess<LongType> |
PositionRandomAccessible.randomAccess(Interval interval) |
FunctionRandomAccessible.FunctionRandomAccess |
FunctionRandomAccessible.randomAccess(Interval interval) |
Modifier and Type | Method and Description |
---|---|
RealTransformRandomAccessible.RealTransformRandomAccess |
RealTransformRandomAccessible.randomAccess(Interval interval)
To be overridden for
RealTransform that can estimate the
boundaries of a transferred RealInterval . |
RandomAccess<LongType> |
PositionRandomAccessible.randomAccess(Interval interval) |
AffineRandomAccessible.AffineRandomAccess |
AffineRandomAccessible.randomAccess(Interval interval)
To be overridden for
RealTransform that can estimate the
boundaries of a transferred RealInterval . |
Modifier and Type | Interface and Description |
---|---|
interface |
IterableRegion<T extends BooleanType<T>>
A region that allows to iterate only the pixels contained in the region
(instead of all pixels in bounding box).
|
interface |
MaskInterval
A bounded
Mask , that is, the mask predicate evaluates to
false outside the bounds interval. |
interface |
PositionableIterableInterval<T>
An
IterableInterval that can be moved around. |
interface |
PositionableIterableRegion<T extends BooleanType<T>>
An
IterableRegion that can be moved around. |
Modifier and Type | Class and Description |
---|---|
protected class |
AbstractIterableRegionOfInterest.AROIClippedIterableInterval<T extends Type<T>>
Deprecated.
|
protected class |
AbstractIterableRegionOfInterest.AROIIterableInterval<T extends Type<T>>
Deprecated.
|
protected class |
BinaryMaskRegionOfInterest.BMROIIterableInterval<TT extends Type<TT>>
Deprecated.
|
static class |
Bounds.AbstractAdaptingInterval
|
static class |
Bounds.IntersectionInterval
The intersection of two intervals.
|
static class |
Bounds.SmallestContainingInterval
Represents the smallest
Interval completely containing a
specified RealInterval . |
static class |
Bounds.UnionInterval
The union of two intervals.
|
Modifier and Type | Method and Description |
---|---|
static Interval |
Masks.emptyInterval(int numDims)
Creates an
Interval which has min > max for all dimensions. |
protected Interval |
AbstractIterableRegionOfInterest.AROIClippedIterableInterval.getSrcInterval() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
AbstractIterableRegionOfInterest.jumpFwd(long totalSteps,
long[] position,
long[] end,
Interval interval)
Deprecated.
Jump forward a certain number of steps from the given position.
|
protected boolean |
AbstractIterableRegionOfInterest.nextRaster(long[] position,
long[] end,
Interval interval)
Deprecated.
Advance the position to the next raster, taking care that the raster is
wholly within the given interval.
|
static Bounds.IntBounds |
Bounds.IntBounds.of(Interval i) |
Constructor and Description |
---|
IntBounds(Interval interval) |
IntersectionInterval(Interval i1,
Interval i2) |
UnionInterval(Interval i1,
Interval i2) |
Modifier and Type | Class and Description |
---|---|
class |
Boundary<T extends BooleanType<T>>
An
IterableRegion of the boundary pixels of a source boolean
RandomAccessibleInterval . |
Modifier and Type | Method and Description |
---|---|
RandomAccess<BoolType> |
Boundary.randomAccess(Interval interval) |
Modifier and Type | Class and Description |
---|---|
class |
DefaultBinaryCompositeMaskInterval
A
MaskInterval which results from an operation on two
Predicate s. |
class |
DefaultUnaryCompositeMaskInterval
A
MaskInterval which is the result of an operation on a
Predicate . |
Constructor and Description |
---|
DefaultBinaryCompositeMaskInterval(Operators.BinaryMaskOperator operator,
Predicate<? super Localizable> arg0,
Predicate<? super Localizable> arg1,
Interval interval,
BoundaryType boundaryType,
BinaryOperator<KnownConstant> knownConstantOp) |
DefaultUnaryCompositeMaskInterval(Operators.UnaryMaskOperator operator,
Predicate<? super Localizable> arg0,
Interval interval,
BoundaryType boundaryType,
UnaryOperator<KnownConstant> knownConstantOp) |
Modifier and Type | Method and Description |
---|---|
static Interval |
GeomMaths.getBounds(Collection<? extends Localizable> vertices) |
Modifier and Type | Class and Description |
---|---|
class |
IterableLine
An immutable line sampled on integer position.
|
Modifier and Type | Class and Description |
---|---|
class |
BoundingBox
A bounding box
Interval around a region that is build by
aggregating positions contained in the region. |
class |
ImgLabeling<T,I extends IntegerType<I>>
A labeling backed by a
image of integer
indices. |
class |
LabelRegion<T>
Present pixels of a given label in a
ImgLabeling as a
PositionableIterableRegion . |
Modifier and Type | Method and Description |
---|---|
Cursor<LabelingType<T>> |
ImgLabeling.cursor(Interval interval) |
Cursor<LabelingType<T>> |
ImgLabeling.localizingCursor(Interval interval) |
RandomAccess<BoolType> |
LabelRegion.randomAccess(Interval interval) |
RandomAccess<LabelingType<T>> |
ImgLabeling.randomAccess(Interval interval) |
Object |
ImgLabeling.subIntervalIterationOrder(Interval interval) |
boolean |
ImgLabeling.supportsOptimizedCursor(Interval interval) |
Constructor and Description |
---|
LabelRegionRandomAccess(LabelRegion<T> region,
Interval interval,
long[] offset) |
Modifier and Type | Class and Description |
---|---|
class |
DefaultMaskInterval |
class |
MaskIntervalAsRandomAccessibleInterval<B extends BooleanType<B>>
This class takes a
MaskInterval and wraps it as a
RandomAccessibleInterval . |
class |
RandomAccessibleIntervalAsMaskInterval<B extends BooleanType<B>>
Wraps a
RandomAccessibleInterval as a MaskInterval . |
Modifier and Type | Method and Description |
---|---|
RandomAccess<B> |
MaskIntervalAsRandomAccessibleInterval.randomAccess(Interval interval) |
RandomAccess<B> |
MaskAsRandomAccessible.randomAccess(Interval interval) |
Constructor and Description |
---|
DefaultMaskInterval(Interval interval,
BoundaryType boundaryType,
Predicate<? super Localizable> predicate,
KnownConstant knownConstant) |
Modifier and Type | Class and Description |
---|---|
class |
IterableRandomAccessibleRegion<T extends BooleanType<T>>
Deprecated.
|
class |
IterableRegionOnBooleanRAI<T extends BooleanType<T>>
Wrap a boolean
RandomAccessibleInterval as a IterableRegion . |
class |
PositionableInterval
An interval that can be moved around.
|
class |
PositionableWrappedIterableInterval<T,S extends IterableInterval<T>>
Makes a
IterableInterval Positionable by wrapping its cursors
with an offset. |
class |
PositionableWrappedIterableRegion<T extends BooleanType<T>>
Makes a
IterableRegion Positionable by wrapping its accessors
with an offset. |
class |
RandomAccessibleRegionCursor<T extends BooleanType<T>>
Deprecated.
|
class |
SamplingIterableInterval<T> |
Modifier and Type | Method and Description |
---|---|
RandomAccess<T> |
PositionableWrappedIterableRegion.randomAccess(Interval interval) |
RandomAccess<T> |
IterableRegionOnBooleanRAI.randomAccess(Interval interval) |
RandomAccess<T> |
IterableRandomAccessibleRegion.randomAccess(Interval interval)
Deprecated.
|
Constructor and Description |
---|
PositionableInterval(Interval initial) |
Modifier and Type | Method and Description |
---|---|
static void |
ImgLib2Assert.assertIntervalEquals(Interval expected,
Interval actual)
Throws an AssertionError, if the two Intervals differ.
|
<T extends NativeType<T>> |
RandomImgs.nextImage(T type,
Interval interval)
Creates an image with randomized content.
|
Modifier and Type | Method and Description |
---|---|
Interval |
BoundingBox.getInterval() |
Constructor and Description |
---|
BoundingBox(Interval interval) |
Modifier and Type | Method and Description |
---|---|
static boolean |
PermutationTransform.checkInterval(Interval interval,
int[] lut)
Test whether a given lut can be applied to an interval.
|
Modifier and Type | Method and Description |
---|---|
static <T,F extends Interval & RandomAccessible<T>> |
Util.getTypeFromInterval(F rai)
Gets an instance of T from the
RandomAccessibleInterval by
querying the value at the min coordinate |
Modifier and Type | Method and Description |
---|---|
static Interval |
Intervals.largestContainedInterval(RealInterval ri)
Compute the largest
Interval that is contained in the specified
RealInterval . |
static Interval |
Intervals.smallestContainingInterval(RealInterval ri)
Compute the smallest
Interval containing the specified
RealInterval . |
Modifier and Type | Method and Description |
---|---|
static FinalInterval |
Intervals.addDimension(Interval interval,
long minOfNewDim,
long maxOfNewDim)
Create new interval by adding a dimension to the source
Interval . |
static <T> RandomAccessibleInterval<T> |
ConstantUtils.constantRandomAccessibleInterval(T constant,
Interval interval) |
static <T> RandomAccessibleInterval<T> |
ConstantUtils.constantRandomAccessibleInterval(T constant,
int numDimensions,
Interval interval)
Deprecated.
|
static boolean |
Intervals.contains(Interval containing,
Interval contained)
Test whether the
containing interval completely contains the
contained interval. |
static boolean |
Intervals.contains(Interval containing,
Localizable contained)
Test whether the
containing interval contains the
contained point. |
static boolean |
Intervals.equalDimensions(Interval a,
Interval b)
Deprecated.
|
static boolean |
Intervals.equals(Interval a,
Interval b)
Tests whether two intervals are equal in their min / max.
|
static FinalInterval |
Intervals.expand(Interval interval,
Dimensions border)
Grow/shrink an interval in all dimensions.
|
static FinalInterval |
Intervals.expand(Interval interval,
long... border)
Grow/shrink an interval in all dimensions.
|
static FinalInterval |
Intervals.expand(Interval interval,
long border)
Grow/shrink an interval in all dimensions.
|
static FinalInterval |
Intervals.expand(Interval interval,
long border,
int d)
Grow/shrink an interval in one dimensions.
|
static FinalInterval |
Intervals.hyperSlice(Interval interval,
int d)
Take a (n-1)-dimensional slice of a n-dimensional interval, dropping the
d axis.
|
static void |
IntervalIndexer.indexToPositionForInterval(long index,
Interval interval,
Positionable position) |
static FinalInterval |
Intervals.intersect(Interval intervalA,
Interval intervalB)
Compute the intersection of two intervals.
|
static FinalInterval |
Intervals.invertAxis(Interval interval,
int d)
Invert the bounds on the d-axis of the given interval
|
static boolean |
Intervals.isEmpty(Interval interval)
Check whether the given interval is empty, that is, the maximum is
smaller than the minimum in some dimension.
|
static int[] |
Intervals.maxAsIntArray(Interval interval)
Create a
int[] with the maximum of an Interval . |
static long[] |
Intervals.maxAsLongArray(Interval interval)
Create a
long[] with the maximum of an Interval . |
static int[] |
Intervals.minAsIntArray(Interval interval)
Create a
int[] with the minimum of an Interval . |
static long[] |
Intervals.minAsLongArray(Interval interval)
Create a
long[] with the minimum of an Interval . |
static FinalInterval |
Intervals.moveAxis(Interval interval,
int fromAxis,
int toAxis)
Create an interval with permuted axes.
|
static FinalInterval |
Intervals.permuteAxes(Interval interval,
int fromAxis,
int toAxis)
Create an interval with permuted axes.
|
static RandomAccessibleInterval<Localizable> |
Intervals.positions(Interval interval)
Returns an image, where each pixel value is the position of the pixel
represented as
Localizable . |
static long |
IntervalIndexer.positionToIndexForInterval(Localizable position,
Interval interval) |
static String |
Util.printInterval(Interval interval) |
static RandomAccessibleInterval<Localizable> |
Localizables.randomAccessibleInterval(Interval interval) |
static FinalInterval |
Intervals.rotate(Interval interval,
int fromAxis,
int toAxis)
Create an interval that is rotated by 90 degrees.
|
static String |
Intervals.toString(Interval value)
Returns a string that contains min, max and the dimensions of the
Interval . |
static FinalInterval |
Intervals.translate(Interval interval,
long... translation)
Translate an interval.
|
static FinalInterval |
Intervals.translate(Interval interval,
long t,
int d)
Translate an interval in one dimension.
|
static FinalInterval |
Intervals.translateInverse(Interval interval,
long... translation)
Translate an interval by
-translation . |
static FinalInterval |
Intervals.union(Interval intervalA,
Interval intervalB)
Compute the smallest interval that contains both input intervals.
|
static FinalInterval |
Intervals.zeroMin(Interval interval)
Returns an
Interval with the same dimensions as the given
interval, but min is all zero. |
Modifier and Type | Class and Description |
---|---|
class |
IntervalView<T>
IntervalView is a view that puts
Interval boundaries on its source
RandomAccessible . |
class |
IterableRandomAccessibleInterval<T>
Generates
Cursors that iterate a
RandomAccessibleInterval in flat order, that is: row by row, plane by
plane, cube by cube, ... |
class |
RandomAccessibleIntervalCursor<T>
A
Cursor that iterates any RandomAccessibleInterval by moving
a RandomAccess in flat iteration order. |
class |
StackView<T>
A stack of n-dimensional
RandomAccessibleInterval s, forming
a (n+1)-dimensional RandomAccessibleInterval . |
class |
SubsampleIntervalView<T>
SubsampleIntervalView is a view that provides access to only every
sdth value of a source
RandomAccessibleInterval . |
Modifier and Type | Method and Description |
---|---|
static <S> RandomAccessible<S> |
TransformBuilder.getEfficientRandomAccessible(Interval interval,
RandomAccessible<S> randomAccessible)
Get a RandomAccessible which provides RandomAccess to the specified
interval of randomAccessible . |
static <T> IntervalView<T> |
Views.interval(RandomAccessible<T> randomAccessible,
Interval interval)
Define an interval on a RandomAccessible.
|
static boolean |
Views.isZeroMin(Interval interval)
test whether the source interval starts at (0,0,...,0)
|
static <T> IntervalView<T> |
Views.offsetInterval(RandomAccessible<T> randomAccessible,
Interval interval)
Define an interval on a RandomAccessible and translate it such that the
min corner is at the origin.
|
RandomAccess<T> |
TransformView.randomAccess(Interval interval) |
RandomAccess<T> |
SubsampleView.randomAccess(Interval interval) |
RandomAccess<T> |
StackView.randomAccess(Interval interval) |
RandomAccessiblePair.RandomAccess |
RandomAccessiblePair.randomAccess(Interval interval) |
RandomAccess<T> |
RandomAccessibleOnRealRandomAccessible.randomAccess(Interval interval) |
RandomAccess<T> |
MixedTransformView.randomAccess(Interval interval) |
RandomAccess<T> |
IterableRandomAccessibleInterval.randomAccess(Interval i) |
RandomAccess<T> |
IntervalView.randomAccess(Interval interval) |
HyperSlicesView.HyperSlicesViewRandomAccess |
HyperSlicesView.randomAccess(Interval interval) |
RandomAccess<T> |
HyperSlice.randomAccess(Interval interval) |
RandomAccess<T> |
ExtendedRandomAccessibleInterval.randomAccess(Interval interval) |
static <T> IntervalView<T> |
Views.shear(RandomAccessible<T> source,
Interval interval,
int shearDimension,
int referenceDimension)
Positive shear transform of a RandomAccessible using
ShearTransform , i.e. |
static <T> IntervalView<T> |
Views.unshear(RandomAccessible<T> source,
Interval interval,
int shearDimension,
int referenceDimension)
Negative shear transform of a RandomAccessible using
InverseShearTransform , i.e. |
static MixedTransform |
ViewTransforms.zeroMin(Interval interval)
Returns the transformation that is used by
Views.zeroMin(RandomAccessibleInterval) . |
Constructor and Description |
---|
DefaultRA(RandomAccessibleInterval<T>[] slices,
Interval interval) |
HyperSliceRandomAccess(Interval interval) |
IntervalView(RandomAccessible<T> source,
Interval interval)
Create a view that defines an interval on a source.
|
MoveAllSlicesRA(RandomAccessibleInterval<T>[] slices,
Interval interval) |
SubsampleRandomAccess(Interval interval) |
TransformBuilder(Interval interval,
RandomAccessible<T> randomAccessible)
Create a new TransformBuilder.
|
Modifier and Type | Class and Description |
---|---|
class |
CompositeIntervalView<T,C extends Composite<T>>
|
Modifier and Type | Method and Description |
---|---|
CompositeView.CompositeRandomAccess |
CompositeView.randomAccess(Interval interval) |
Modifier and Type | Field and Description |
---|---|
protected Interval |
IterableTransformBuilder.interval
The interval which should be iterated.
|
Modifier and Type | Method and Description |
---|---|
Cursor<T> |
SubIntervalIterable.cursor(Interval interval)
|
static <S> IterableInterval<S> |
IterableTransformBuilder.getEfficientIterableInterval(Interval interval,
RandomAccessible<S> randomAccessible)
|
Cursor<T> |
SubIntervalIterable.localizingCursor(Interval interval)
|
Object |
SubIntervalIterable.subIntervalIterationOrder(Interval interval)
Returns the iteration order given the interval.
|
boolean |
SubIntervalIterable.supportsOptimizedCursor(Interval interval)
|
Constructor and Description |
---|
IterableTransformBuilder(Interval interval,
RandomAccessible<T> randomAccessible)
Create a new IterableTransformBuilder.
|
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