ImgMath (ImgLib2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- net.imglib2.algorithm.math.ImgMath

public class ImgMath
extends Object

An easy yet high performance way to perform pixel-wise math on one or more RandomAccessibleInterval instances. Peak performance is within 1.2X - 1.8X of manually writing a loop using ImgLib2's low-level Cursor or RandomAccess with native math + / - * and flow if else operators and in-loop variable declarations. Input images can be of different Type as long as all of them extend RealType. An example in java:

 
 
 import static net.imglib2.algorithm.math.ImgMath.*;
 
 RandomAccessibleInterval<A> img1 = ...
 RandomAccessibleInterval<B> img2 = ...
 RandomAccessibleInterval<C> img3 = ...
 
 RandomAccessibleInterval<O> result = ...
 
 compute( div( max( img1, img2, img3 ), 3.0 ) ).into( result );

Another example, illustrating variable declaration with Let and also if/then/else flow control, to compute the saturation of an RGB image:

 
 import static net.imglib2.algorithm.math.ImgMath.*;
 
 RandomAccessible< ARGBType > rgb = ...
 
 final RandomAccessibleInterval< UnsignedByteType >
		    red = Converters.argbChannel( rgb, 1 ),
			green = Converters.argbChannel( rgb, 2 ),
			blue = Converters.argbChannel( rgb, 3 );
 
 RandomAccessibleInterval< FloatType > saturation = new ArrayImgFactory< FloatType >( new FloatType() ).create( rgb );
 
 compute( let( "red", red,
				 "green", green,
				 "blue", blue,
				 "max", max( var( "red" ), var( "green" ), var( "blue" ) ),
				 "min", min( var( "red" ), var( "green" ), var( "blue" ) ),
				 IF ( EQ( 0, var( "max" ) ),
				   THEN( 0 ),
				   ELSE( div( sub( var( "max" ), var( "min" ) ),
					          var( "max" ) ) ) ) ) )
		  .into( saturation );

Author:: Albert Cardona

Constructor Summary

Constructors
Constructor and Description

ImgMath()

Constructors
Constructor and Description
`ImgMath()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static Add`	`add(Object... obs)`
`static Add`	`add(Object o1, Object o2)`
`static AndLogical`	`AND(Object... o)`
`static AndLogical`	`AND(Object o1, Object o2)`
`static <T extends RealType<T>> BlockReadSource<T>`	`block(RandomAccessible<T> src, long radius)`
`static <T extends RealType<T>> BlockReadSource<T>`	`block(RandomAccessible<T> src, long[] radius)`
`static <T extends RealType<T>> BlockReadSource<T>`	`block(RandomAccessible<T> src, long[][] corners)`
`static Compute`	`compute(IFunction operation)`
`static <I extends RealType<I>> Compute`	`compute(RandomAccessibleInterval<I> src)`
`static <O extends RealType<O>> RandomAccessibleInterval<O>`	`computeInto(IFunction operation, RandomAccessibleInterval<O> target)`
`static <O extends RealType<O>> RandomAccessibleInterval<O>`	`computeInto(IFunction operation, RandomAccessibleInterval<O> target, Converter<RealType<?>,O> converter)`
`static <O extends NativeType<O> & RealType<O>> RandomAccessibleInterval<O>`	`computeIntoArrayImg(IFunction operation)`
`static RandomAccessibleInterval<FloatType>`	`computeIntoFloats(IFunction operation)`
`static <O extends NativeType<O> & RealType<O>> RandomAccessibleInterval<O>`	`computeIntoImg(IFunction operation)`
`static Div`	`div(Object... obs)`
`static Div`	`div(Object o1, Object o2)`
`static Else`	`ELSE(Object o)`
`static Equal`	`EQ(Object o1, Object o2)`
`static Equal`	`equal(Object o1, Object o2)`
`static Exp`	`exp(Object o1)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(KDTree<T> kdtree, double radius)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(KDTree<T> kdtree, double radius, Object outside)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(KDTree<T> kdtree, double radius, Object outside, Interval interval)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(List<Point> positions, List<T> values, double radius)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(List<Point> positions, List<T> values, double radius, Object outside)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(List<Point> positions, List<T> values, double radius, Object outside, Interval interval)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(List<Point> positions, T value, double radius)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(List<Point> positions, T value, double radius, Object outside)`
`static <T extends RealType<T>> KDTreeSource<T>`	`gen(List<Point> positions, T value, double radius, Object outside, Interval interval)`
`static GreaterThan`	`greaterThan(Object o1, Object o2)`
`static GreaterThan`	`GT(Object o1, Object o2)`
`static If`	`IF(Object o1, Object o2, Object o3)`
`static <T extends RealType<T>> ImgSource<T>`	`img(RandomAccessibleInterval<T> rai)`
`static <T extends RealType<T>> ImgSource<T>`	`intervalSource(RandomAccessibleInterval<T> rai)` Synonym of `img(RandomAccessibleInterval)`, given that `img` is a widely used variable name.
`static LessThan`	`lessThan(Object o1, Object o2)`
`static Let`	`let(Object... obs)`
`static Let`	`let(Object[] pairs, Object body)`
`static Let`	`let(String varName, Object varValue, Object body)`
`static Log`	`log(Object o1)`
`static Log`	`logarithm(Object o1)`
`static LessThan`	`LT(Object o1, Object o2)`
`static Max`	`max(Object... obs)`
`static Max`	`max(Object o1, Object o2)`
`static Max`	`maximum(Object... obs)`
`static Max`	`maximum(Object o1, Object o2)`
`static Min`	`min(Object... obs)`
`static Min`	`min(Object o1, Object o2)`
`static Min`	`minimum(Object... obs)`
`static Min`	`minimum(Object o1, Object o2)`
`static Minus`	`minus(Object o1)`
`static Mul`	`mul(Object... obs)`
`static Mul`	`mul(Object o1, Object o2)`
`static NotEqual`	`NEQ(Object o1, Object o2)`
`static NotLogical`	`NOT(Object o)`
`static NotEqual`	`notEqual(Object o1, Object o2)`
`static NumberSource`	`number(Number number)`
`static <T extends RealType<T>> OffsetSource<T>`	`offset(IFunction f, long[] offset)`
`static <T extends RealType<T>> RandomAccessibleSource<T>`	`offset(RandomAccessible<T> src, long[] offset)`
`static OrLogical`	`OR(Object... o)`
`static OrLogical`	`OR(Object o1, Object o2)`
`static Pow`	`pow(Object o1, Object o2)`
`static Pow`	`power(Object o1, Object o2)`
`static <T extends RealType<T>> IFunction`	`source(RandomAccessible<T> src)`
`static Sub`	`sub(Object... obs)`
`static Sub`	`sub(Object o1, Object o2)`
`static Then`	`THEN(Object o)`
`static Var`	`var(String name)`
`static <O extends RealType<O>> RandomAccessibleInterval<O>`	`view(ViewableFunction operation)` Almost all `IFunction` are also `ViewableFunction`.
`static RandomAccessibleInterval<FloatType>`	`viewFloats(ViewableFunction operation)` Almost all `IFunction` are also `ViewableFunction`.
`static XorLogical`	`XOR(Object... o)`
`static XorLogical`	`XOR(Object o1, Object o2)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail
- ImgMath
```
public ImgMath()
```

Method Detail

compute

public static final Compute compute(IFunction operation)

compute

public static final <I extends RealType<I>> Compute compute(RandomAccessibleInterval<I> src)

computeIntoFloats

public static final RandomAccessibleInterval<FloatType> computeIntoFloats(IFunction operation)

computeInto

public static final <O extends RealType<O>> RandomAccessibleInterval<O> computeInto(IFunction operation,
                                                                                    RandomAccessibleInterval<O> target)

computeInto

public static final <O extends RealType<O>> RandomAccessibleInterval<O> computeInto(IFunction operation,
                                                                                    RandomAccessibleInterval<O> target,
                                                                                    Converter<RealType<?>,O> converter)

computeIntoImg

public static final <O extends NativeType<O> & RealType<O>> RandomAccessibleInterval<O> computeIntoImg(IFunction operation)

computeIntoArrayImg

public static final <O extends NativeType<O> & RealType<O>> RandomAccessibleInterval<O> computeIntoArrayImg(IFunction operation)

view

public static final <O extends RealType<O>> RandomAccessibleInterval<O> view(ViewableFunction operation)

Almost all IFunction are also ViewableFunction.

Parameters:: operation -
Returns:

viewFloats

public static final RandomAccessibleInterval<FloatType> viewFloats(ViewableFunction operation)

Almost all IFunction are also ViewableFunction.

Parameters:: operation -
Returns:

add

public static final Add add(Object o1,
                            Object o2)

add

public static final Add add(Object... obs)

sub

public static final Sub sub(Object o1,
                            Object o2)

sub

public static final Sub sub(Object... obs)

minus

public static final Minus minus(Object o1)

mul

public static final Mul mul(Object o1,
                            Object o2)

mul

public static final Mul mul(Object... obs)

div

public static final Div div(Object o1,
                            Object o2)

div

public static final Div div(Object... obs)

pow

public static final Pow pow(Object o1,
                            Object o2)

power

public static final Pow power(Object o1,
                              Object o2)

max

public static final Max max(Object o1,
                            Object o2)

max

public static final Max max(Object... obs)

maximum

public static final Max maximum(Object o1,
                                Object o2)

maximum

public static final Max maximum(Object... obs)

min

public static final Min min(Object o1,
                            Object o2)

min

public static final Min min(Object... obs)

minimum

public static final Min minimum(Object o1,
                                Object o2)

minimum

public static final Min minimum(Object... obs)

log

public static final Log log(Object o1)

logarithm

public static final Log logarithm(Object o1)

exp

public static final Exp exp(Object o1)

let

public static final Let let(String varName,
                            Object varValue,
                            Object body)

let

public static final Let let(Object[] pairs,
                            Object body)

let

public static final Let let(Object... obs)

var

public static final Var var(String name)

EQ

public static final Equal EQ(Object o1,
                             Object o2)

equal

public static final Equal equal(Object o1,
                                Object o2)

NEQ

public static final NotEqual NEQ(Object o1,
                                 Object o2)

notEqual

public static final NotEqual notEqual(Object o1,
                                      Object o2)

LT

public static final LessThan LT(Object o1,
                                Object o2)

lessThan

public static final LessThan lessThan(Object o1,
                                      Object o2)

GT

public static final GreaterThan GT(Object o1,
                                   Object o2)

greaterThan

public static final GreaterThan greaterThan(Object o1,
                                            Object o2)

IF

public static final If IF(Object o1,
                          Object o2,
                          Object o3)

THEN

public static final Then THEN(Object o)

ELSE

public static final Else ELSE(Object o)

AND

public static final AndLogical AND(Object o1,
                                   Object o2)

AND

public static final AndLogical AND(Object... o)

OR

public static final OrLogical OR(Object o1,
                                 Object o2)

OR

public static final OrLogical OR(Object... o)

XOR

public static final XorLogical XOR(Object o1,
                                   Object o2)

XOR

public static final XorLogical XOR(Object... o)

NOT

public static final NotLogical NOT(Object o)

img

public static final <T extends RealType<T>> ImgSource<T> img(RandomAccessibleInterval<T> rai)

intervalSource

public static final <T extends RealType<T>> ImgSource<T> intervalSource(RandomAccessibleInterval<T> rai)

Synonym of img(RandomAccessibleInterval), given that img is a widely used variable name.

number

public static final NumberSource number(Number number)

block

public static final <T extends RealType<T>> BlockReadSource<T> block(RandomAccessible<T> src,
                                                                     long[] radius)

block

public static final <T extends RealType<T>> BlockReadSource<T> block(RandomAccessible<T> src,
                                                                     long radius)

block

public static final <T extends RealType<T>> BlockReadSource<T> block(RandomAccessible<T> src,
                                                                     long[][] corners)

offset

public static final <T extends RealType<T>> RandomAccessibleSource<T> offset(RandomAccessible<T> src,
                                                                             long[] offset)

offset

public static final <T extends RealType<T>> OffsetSource<T> offset(IFunction f,
                                                                   long[] offset)

source

public static final <T extends RealType<T>> IFunction source(RandomAccessible<T> src)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(List<Point> positions,
                                                                T value,
                                                                double radius)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(List<Point> positions,
                                                                T value,
                                                                double radius,
                                                                Object outside)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(List<Point> positions,
                                                                T value,
                                                                double radius,
                                                                Object outside,
                                                                Interval interval)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(List<Point> positions,
                                                                List<T> values,
                                                                double radius)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(List<Point> positions,
                                                                List<T> values,
                                                                double radius,
                                                                Object outside)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(List<Point> positions,
                                                                List<T> values,
                                                                double radius,
                                                                Object outside,
                                                                Interval interval)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(KDTree<T> kdtree,
                                                                double radius)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(KDTree<T> kdtree,
                                                                double radius,
                                                                Object outside)

gen

public static final <T extends RealType<T>> KDTreeSource<T> gen(KDTree<T> kdtree,
                                                                double radius,
                                                                Object outside,
                                                                Interval interval)

Class ImgMath

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ImgMath

Method Detail

compute

compute

computeIntoFloats

computeInto

computeInto

computeIntoImg

computeIntoArrayImg

view

viewFloats

add

add

sub

sub

minus

mul

mul

div

div

pow

power

max

max

maximum

maximum

min

min

minimum

minimum

log

logarithm

exp

let

let

let

var

EQ

equal

NEQ

notEqual

LT

lessThan

GT

greaterThan

IF

THEN

ELSE

AND

AND

OR

OR

XOR

XOR

NOT

img

intervalSource

number

block

block

block

offset

offset

source

gen

gen

gen

gen

gen

gen

gen

gen

gen