net.imglib2.algorithm.math

Class Compute

java.lang.Object

net.imglib2.algorithm.math.Compute

public class Compute
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Compute.Parameters

Constructor Summary

Constructors

Constructor and Description
Compute(IFunction operation) Validate the {code operation}.

Method Summary

Modifier and Type	Method and Description
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O>	cursor() Returns a Cursor with the same type as the first input image found.
<C extends net.imglib2.type.numeric.RealType<C>,O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O>	cursor(C computeType, O outputType)
<C extends net.imglib2.type.numeric.RealType<C>,O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O>	cursor(net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter, C computeType, O outputType, net.imglib2.converter.Converter<C,O> outConverter)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O>	cursor(O outputType)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O>	cursorDouble() Returns a Cursor with the same type as the first input image found.
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O>	cursorDouble(O outputType)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O>	cursorDouble(O outputType, net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,O> converter)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	into(net.imglib2.RandomAccessibleInterval<O> target) Execute the computation and store the result into the target.
<O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	into(net.imglib2.RandomAccessibleInterval<O> target, C computingType)
<O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	into(net.imglib2.RandomAccessibleInterval<O> target, net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter, C computingType, net.imglib2.converter.Converter<C,O> outConverter)
<O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	into(net.imglib2.RandomAccessibleInterval<O> target, net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter, C computingType, net.imglib2.converter.Converter<C,O> outConverter, boolean printHierarchy) Execute the mathematical operations and store the result into the given RandomAccessibleInterval.
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	into(net.imglib2.RandomAccessibleInterval<O> target, net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,O> inConverter) Execute the mathematical operations and store the result into the given RandomAccessibleInterval.
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.img.array.ArrayImg<O,?>	intoArrayImg()
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C> & net.imglib2.type.NativeType<C>> net.imglib2.img.array.ArrayImg<O,?>	intoArrayImg(C computeType, O outputType)
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.img.array.ArrayImg<O,?>	intoArrayImg(O outputType)
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.RandomAccessibleInterval<O>	intoImg() Execute the computation and store the result into a newly created Img of the same Type (and kind, by ImgFactory) as one of the input images, using as the computation Type the type of that picked input image.
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	intoImg(C computeType, O outputType) Execute the computation and store the result into a newly created Img of the same kind, by ImgFactory, as one of the input images, but of type outputType, while using computeType for math operations, converting to the outputType to store the result.
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.RandomAccessibleInterval<O>	intoImg(O outputType) Execute the computation and store the result into a newly created Img of the same kind, by ImgFactory, as one of the input images, but of type outputType, which is also used as the computation Type.
<O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	parallelInto(net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter, C computeType, O outputType, net.imglib2.converter.Converter<C,O> outConverter, net.imglib2.RandomAccessibleInterval<O> target) Compute the result multithreaded into an ArrayImg of the given Type.
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	parallelInto(net.imglib2.RandomAccessibleInterval<O> target) Compute the result multithreaded into an ArrayImg of the given Type.
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.RandomAccessibleInterval<O>	parallelIntoArrayImg() Compute the result multithreaded into an ArrayImg of the same Type as the first image found, with mathematical operations using that same Type.
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	parallelIntoArrayImg(C computeType, O outputType) Compute the result multithreaded into an ArrayImg of the given Type.
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	parallelIntoArrayImg(net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter, C computeType, O outputType, net.imglib2.converter.Converter<C,O> outConverter) Compute the result multithreaded into an ArrayImg of the given Type.
<O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.RandomAccessibleInterval<O>	parallelIntoArrayImg(O outputType) Compute the result multithreaded into an ArrayImg of the given Type.
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O>	randomAccess() Returns a RandomAccess with the same type as the first input image found.
<C extends net.imglib2.type.numeric.RealType<C>,O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O>	randomAccess(C computeType, O outputType, net.imglib2.converter.Converter<C,O> outConverter)
<C extends net.imglib2.type.numeric.RealType<C>,O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O>	randomAccess(net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter, C computeType, O outputType, net.imglib2.converter.Converter<C,O> outConverter)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O>	randomAccess(O outputType)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O>	randomAccessDouble() Returns a RandomAccess with the same type as the first input image found.
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O>	randomAccessDouble(O outputType)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O>	randomAccessDouble(O outputType, net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,O> converter)
static Compute.Parameters	validate(IFunction f)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	view()
<O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	view(C computingType, O outputType) View the result of the computations as a RandomAccessibleInterval, i.e. there is no target image, instead any pixel can be viewed as the result of the computation applied to it, dynamically.
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	view(net.imglib2.Interval interval)
<O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O>	view(net.imglib2.Interval interval, net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter, C computingType, O outputType, net.imglib2.converter.Converter<C,O> outConverter)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	view(net.imglib2.Interval interval, O outputType)
<O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	view(O outputType)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Compute

public Compute(IFunction operation)

Validate the {code operation}.

Parameters:

operation -

Method Detail

intoArrayImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.img.array.ArrayImg<O,?> intoArrayImg()

intoArrayImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C> & net.imglib2.type.NativeType<C>> net.imglib2.img.array.ArrayImg<O,?> intoArrayImg(C computeType,
                                                                                                                                                                                                                          O outputType)

intoArrayImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.img.array.ArrayImg<O,?> intoArrayImg(O outputType)

intoImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.RandomAccessibleInterval<O> intoImg()

Execute the computation and store the result into a newly created Img of the same Type (and kind, by ImgFactory) as one of the input images, using as the computation Type the type of that picked input image. This approach is appropriate when e.g. all input images are of the same type, and operations aren't expected to overflow the Type or it doesn't matter whether they do.

Returns:

A newly created Img with the result of the computation.

intoImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.RandomAccessibleInterval<O> intoImg(O outputType)

Execute the computation and store the result into a newly created Img of the same kind, by ImgFactory, as one of the input images, but of type outputType, which is also used as the computation Type.

Parameters:

outputType - The Type of the returned Img and used for computing.

Returns:

A newly created Img with the result of the computation.

intoImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> intoImg(C computeType,
                                                                                                                                                                                        O outputType)

Execute the computation and store the result into a newly created Img of the same kind, by ImgFactory, as one of the input images, but of type outputType, while using computeType for math operations, converting to the outputType to store the result.

Parameters:

computeType - The Type used to perform mathematical operations.

outputType - The Type of the returned Img.

Returns:

A newly created Img with the result of the computation.

into

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> into(net.imglib2.RandomAccessibleInterval<O> target)

Execute the computation and store the result into the target. The computation is done using Type-based math, with the Type of the target defining the specific math implementation and numerical precision that will be used.

Parameters:

target - The RandomAccessibleInterval into which to store the computation; note its Type determines the precision of the computation and the specific implementation of the mathematical operations.

Returns:

The target.

into

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> into(net.imglib2.RandomAccessibleInterval<O> target,
                                                                                                     net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,O> inConverter)

Execute the mathematical operations and store the result into the given RandomAccessibleInterval.

Parameters:

target - The RandomAccessibleInterval into which to store the computation; note its Type determines the precision of the computation and the specific implementation of the mathematical operations.

inConverter - The Converter that transfers all input Type to the Type of the target; when null, will create one that uses double floating-point precision; but note that if the Type of an input RandomAccessibleInterval is the same as that of the target, the converter will not be used.

Returns:

The target.

into

public <O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> into(net.imglib2.RandomAccessibleInterval<O> target,
                                                                                                                                                    C computingType)

into

public <O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> into(net.imglib2.RandomAccessibleInterval<O> target,
                                                                                                                                                    net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter,
                                                                                                                                                    C computingType,
                                                                                                                                                    net.imglib2.converter.Converter<C,O> outConverter)

into

public <O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> into(net.imglib2.RandomAccessibleInterval<O> target,
                                                                                                                                                    net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter,
                                                                                                                                                    C computingType,
                                                                                                                                                    net.imglib2.converter.Converter<C,O> outConverter,
                                                                                                                                                    boolean printHierarchy)

Execute the mathematical operations and store the result into the given RandomAccessibleInterval. Takes into account whether all images involved in the computation are iterable in a compatible way.

Parameters:

target - The RandomAccessibleInterval into which to store the computation.

inConverter - The Converter that transfers all input Type to the Type of the target; when null, will create one that uses double floating-point precision; but note that if the Type of an input RandomAccessibleInterval is the same as that of the target, the converter will not be used.

computingType - The Type that determines the precision of the computation and the specific implementation of the mathematical operations.

outConverter - The Converter that transfers the computingType to the Type of the target; will not be used if the computeType is the same as the Type of the output; when null, a new one is created, which is the identity when the computingType equal the Type of the target, and a generic RealType converter that uses floating-point values (with RealType#setReal(double)) created with Util#genericRealTypeConverter() is used.

printHierarchy - Emits to stdout the hierarchy of OFunction types.

Returns:

The target.

view

public <O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> view(net.imglib2.Interval interval,
                                                                                                                                                    net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter,
                                                                                                                                                    C computingType,
                                                                                                                                                    O outputType,
                                                                                                                                                    net.imglib2.converter.Converter<C,O> outConverter)

view

public <O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> view(C computingType,
                                                                                                                                                    O outputType)

View the result of the computations as a RandomAccessibleInterval, i.e. there is no target image, instead any pixel can be viewed as the result of the computation applied to it, dynamically. Conversion between the input and computing type is done with an appropriate converter or none when types are the same. See also ViewableFunction and methods below related to Compute#randomAccess() and Compute#cursor(). The key difference is that, here, the computing and the output type can be different.

Parameters:

computingType - The Type that defines the math to use.

outputType - The @{code Type} of the constructed and returned RandomAccessibleInterval. return A RandomAccessibleInterval view of the result of the computations.

view

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> view(O outputType)

view

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> view()

view

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> view(net.imglib2.Interval interval)

view

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> view(net.imglib2.Interval interval,
                                                                                                     O outputType)

parallelIntoArrayImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.RandomAccessibleInterval<O> parallelIntoArrayImg()

Compute the result multithreaded into an ArrayImg of the same Type as the first image found, with mathematical operations using that same Type.

parallelIntoArrayImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>> net.imglib2.RandomAccessibleInterval<O> parallelIntoArrayImg(O outputType)

Compute the result multithreaded into an ArrayImg of the given Type.

Parameters:

outputType - The Type used for both computations and the output image.

parallelIntoArrayImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> parallelIntoArrayImg(C computeType,
                                                                                                                                                                                                     O outputType)

Compute the result multithreaded into an ArrayImg of the given Type. Uses generic RealType converters where appropriate as provided by Util#genericRealTypeConverter().

Parameters:

computeType - The Type used for computations.

outputType - The Type used for the output image.

parallelIntoArrayImg

public <O extends net.imglib2.type.numeric.RealType<O> & net.imglib2.type.NativeType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> parallelIntoArrayImg(net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter,
                                                                                                                                                                                                     C computeType,
                                                                                                                                                                                                     O outputType,
                                                                                                                                                                                                     net.imglib2.converter.Converter<C,O> outConverter)

Compute the result multithreaded into an ArrayImg of the given Type.

Parameters:

inConverter - From input to computeType, or when null, uses Util#genericRealTypeConverter().

computeType - The Type used for computations.

outputType - The Type used for the output image.

outConverter - From computeType to outputType, or when null, uses Util#genericRealTypeConverter().

parallelInto

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> parallelInto(net.imglib2.RandomAccessibleInterval<O> target)

Compute the result multithreaded into an ArrayImg of the given Type. Uses generic RealType converters where appropriate as provided by Util#genericRealTypeConverter().

Parameters:

target - To store the result of the computation, with its Type defining both the output Type and the Type used for computations.

parallelInto

public <O extends net.imglib2.type.numeric.RealType<O>,C extends net.imglib2.type.numeric.RealType<C>> net.imglib2.RandomAccessibleInterval<O> parallelInto(net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter,
                                                                                                                                                            C computeType,
                                                                                                                                                            O outputType,
                                                                                                                                                            net.imglib2.converter.Converter<C,O> outConverter,
                                                                                                                                                            net.imglib2.RandomAccessibleInterval<O> target)

Compute the result multithreaded into an ArrayImg of the given Type.

Parameters:

inConverter - From input to computeType, or when null, uses Util#genericRealTypeConverter().

computeType - The Type used for computations.

outputType - The Type used for the output image.

outConverter - From computeType to outputType, or when null, uses Util#genericRealTypeConverter().

validate

public static Compute.Parameters validate(IFunction f)

randomAccess

public <C extends net.imglib2.type.numeric.RealType<C>,O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O> randomAccess(net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter,
                                                                                                                                                C computeType,
                                                                                                                                                O outputType,
                                                                                                                                                net.imglib2.converter.Converter<C,O> outConverter)

randomAccess

public <C extends net.imglib2.type.numeric.RealType<C>,O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O> randomAccess(C computeType,
                                                                                                                                                O outputType,
                                                                                                                                                net.imglib2.converter.Converter<C,O> outConverter)

randomAccess

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O> randomAccess(O outputType)

randomAccess

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O> randomAccess()

Returns a RandomAccess with the same type as the first input image found.

cursor

public <C extends net.imglib2.type.numeric.RealType<C>,O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O> cursor(net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,C> inConverter,
                                                                                                                                    C computeType,
                                                                                                                                    O outputType,
                                                                                                                                    net.imglib2.converter.Converter<C,O> outConverter)

cursor

public <C extends net.imglib2.type.numeric.RealType<C>,O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O> cursor(C computeType,
                                                                                                                                    O outputType)

cursor

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O> cursor(O outputType)

cursor

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O> cursor()

Returns a Cursor with the same type as the first input image found.

randomAccessDouble

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O> randomAccessDouble(O outputType,
                                                                                                       net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,O> converter)

randomAccessDouble

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O> randomAccessDouble(O outputType)

randomAccessDouble

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccess<O> randomAccessDouble()

Returns a RandomAccess with the same type as the first input image found.

cursorDouble

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O> cursorDouble(O outputType,
                                                                                           net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,O> converter)

cursorDouble

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O> cursorDouble(O outputType)

cursorDouble

public <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.Cursor<O> cursorDouble()

Returns a Cursor with the same type as the first input image found.