net.imglib2.algorithm.math

Class ImgMath

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()

Method Summary

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 net.imglib2.type.numeric.RealType<T>> BlockReadSource<T>	block(net.imglib2.RandomAccessible<T> src, long radius)
static <T extends net.imglib2.type.numeric.RealType<T>> BlockReadSource<T>	block(net.imglib2.RandomAccessible<T> src, long[] radius)
static <T extends net.imglib2.type.numeric.RealType<T>> BlockReadSource<T>	block(net.imglib2.RandomAccessible<T> src, long[][] corners)
static Compute	compute(IFunction operation)
static <I extends net.imglib2.type.numeric.RealType<I>> Compute	compute(net.imglib2.RandomAccessibleInterval<I> src)
static <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	computeInto(IFunction operation, net.imglib2.RandomAccessibleInterval<O> target)
static <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	computeInto(IFunction operation, net.imglib2.RandomAccessibleInterval<O> target, net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,O> converter)
static <O extends net.imglib2.type.NativeType<O> & net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	computeIntoArrayImg(IFunction operation)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	computeIntoFloats(IFunction operation)
static <O extends net.imglib2.type.NativeType<O> & net.imglib2.type.numeric.RealType<O>> net.imglib2.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 net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(net.imglib2.KDTree<T> kdtree, double radius)
static <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(net.imglib2.KDTree<T> kdtree, double radius, Object outside)
static <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(net.imglib2.KDTree<T> kdtree, double radius, Object outside, net.imglib2.Interval interval)
static <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(List<net.imglib2.Point> positions, List<T> values, double radius)
static <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(List<net.imglib2.Point> positions, List<T> values, double radius, Object outside)
static <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(List<net.imglib2.Point> positions, List<T> values, double radius, Object outside, net.imglib2.Interval interval)
static <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(List<net.imglib2.Point> positions, T value, double radius)
static <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(List<net.imglib2.Point> positions, T value, double radius, Object outside)
static <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T>	gen(List<net.imglib2.Point> positions, T value, double radius, Object outside, net.imglib2.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 net.imglib2.type.numeric.RealType<T>> ImgSource<T>	img(net.imglib2.RandomAccessibleInterval<T> rai)
static <T extends net.imglib2.type.numeric.RealType<T>> ImgSource<T>	intervalSource(net.imglib2.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 net.imglib2.type.numeric.RealType<T>> OffsetSource<T>	offset(IFunction f, long[] offset)
static <T extends net.imglib2.type.numeric.RealType<T>> RandomAccessibleSource<T>	offset(net.imglib2.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 net.imglib2.type.numeric.RealType<T>> IFunction	source(net.imglib2.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 net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O>	view(ViewableFunction operation) Almost all IFunction are also ViewableFunction.
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.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 net.imglib2.type.numeric.RealType<I>> Compute compute(net.imglib2.RandomAccessibleInterval<I> src)

computeIntoFloats

public static final net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> computeIntoFloats(IFunction operation)

computeInto

public static final <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> computeInto(IFunction operation,
                                                                                                                         net.imglib2.RandomAccessibleInterval<O> target)

computeInto

public static final <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> computeInto(IFunction operation,
                                                                                                                         net.imglib2.RandomAccessibleInterval<O> target,
                                                                                                                         net.imglib2.converter.Converter<net.imglib2.type.numeric.RealType<?>,O> converter)

computeIntoImg

public static final <O extends net.imglib2.type.NativeType<O> & net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> computeIntoImg(IFunction operation)

computeIntoArrayImg

public static final <O extends net.imglib2.type.NativeType<O> & net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> computeIntoArrayImg(IFunction operation)

view

public static final <O extends net.imglib2.type.numeric.RealType<O>> net.imglib2.RandomAccessibleInterval<O> view(ViewableFunction operation)

Almost all IFunction are also ViewableFunction.

Parameters:

operation -

Returns:

viewFloats

public static final net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.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 net.imglib2.type.numeric.RealType<T>> ImgSource<T> img(net.imglib2.RandomAccessibleInterval<T> rai)

intervalSource

public static final <T extends net.imglib2.type.numeric.RealType<T>> ImgSource<T> intervalSource(net.imglib2.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 net.imglib2.type.numeric.RealType<T>> BlockReadSource<T> block(net.imglib2.RandomAccessible<T> src,
                                                                                              long[] radius)

block

public static final <T extends net.imglib2.type.numeric.RealType<T>> BlockReadSource<T> block(net.imglib2.RandomAccessible<T> src,
                                                                                              long radius)

block

public static final <T extends net.imglib2.type.numeric.RealType<T>> BlockReadSource<T> block(net.imglib2.RandomAccessible<T> src,
                                                                                              long[][] corners)

offset

public static final <T extends net.imglib2.type.numeric.RealType<T>> RandomAccessibleSource<T> offset(net.imglib2.RandomAccessible<T> src,
                                                                                                      long[] offset)

offset

public static final <T extends net.imglib2.type.numeric.RealType<T>> OffsetSource<T> offset(IFunction f,
                                                                                            long[] offset)

source

public static final <T extends net.imglib2.type.numeric.RealType<T>> IFunction source(net.imglib2.RandomAccessible<T> src)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(List<net.imglib2.Point> positions,
                                                                                         T value,
                                                                                         double radius)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(List<net.imglib2.Point> positions,
                                                                                         T value,
                                                                                         double radius,
                                                                                         Object outside)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(List<net.imglib2.Point> positions,
                                                                                         T value,
                                                                                         double radius,
                                                                                         Object outside,
                                                                                         net.imglib2.Interval interval)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(List<net.imglib2.Point> positions,
                                                                                         List<T> values,
                                                                                         double radius)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(List<net.imglib2.Point> positions,
                                                                                         List<T> values,
                                                                                         double radius,
                                                                                         Object outside)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(List<net.imglib2.Point> positions,
                                                                                         List<T> values,
                                                                                         double radius,
                                                                                         Object outside,
                                                                                         net.imglib2.Interval interval)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(net.imglib2.KDTree<T> kdtree,
                                                                                         double radius)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(net.imglib2.KDTree<T> kdtree,
                                                                                         double radius,
                                                                                         Object outside)

gen

public static final <T extends net.imglib2.type.numeric.RealType<T>> KDTreeSource<T> gen(net.imglib2.KDTree<T> kdtree,
                                                                                         double radius,
                                                                                         Object outside,
                                                                                         net.imglib2.Interval interval)