Module org.scijava.ops.image

Package org.scijava.ops.image.coloc.saca

Class SACASigMask

java.lang.Object

org.scijava.ops.image.coloc.saca.SACASigMask

All Implemented Interfaces:

Computers.Arity6<RandomAccessibleInterval<DoubleType>,Double,Double,Double,Boolean,Boolean,RandomAccessibleInterval<BitType>>, Consumers.Arity7<RandomAccessibleInterval<DoubleType>,Double,Double,Double,Boolean,Boolean,RandomAccessibleInterval<BitType>>

public class SACASigMask
extends Object
implements Computers.Arity6<RandomAccessibleInterval<DoubleType>,Double,Double,Double,Boolean,Boolean,RandomAccessibleInterval<BitType>>

Author:

Shulei Wang, Curtis Rueden, Ellen TA Dobson, Edward Evans

Implementation Note:

op names='coloc.saca.sigMask', priority='100.'

Constructor Summary

Constructors

Constructor	Description
SACASigMask()

Method Summary

Modifier and Type	Method	Description
void	compute(RandomAccessibleInterval<DoubleType> heatmap, Double alpha, Double mean, Double sd, Boolean lowerTail, Boolean logP, RandomAccessibleInterval<BitType> result)	Spatially Adaptive Colocalization Analysis (SACA) significant pixel mask.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.function.Computers.Arity6

accept

Methods inherited from interface org.scijava.function.Consumers.Arity7

andThen

Constructor Detail

SACASigMask

public SACASigMask()

Method Detail

compute

public void compute(RandomAccessibleInterval<DoubleType> heatmap,
                    Double alpha,
                    Double mean,
                    Double sd,
                    Boolean lowerTail,
                    Boolean logP,
                    RandomAccessibleInterval<BitType> result)

Spatially Adaptive Colocalization Analysis (SACA) significant pixel mask. This Op returns a binary mask of the significantly colocalized pixels from the input Z-score heatmap produced by the SACA framework. SACA was adapted from Shulei's java code for AdaptiveSmoothedKendallTau in his RKColocal package (https://github.com/lakerwsl/RKColocal/blob/master/RKColocal_0.0.1.0000.tar.gz).

Specified by:

compute in interface Computers.Arity6<RandomAccessibleInterval<DoubleType>,Double,Double,Double,Boolean,Boolean,RandomAccessibleInterval<BitType>>

Parameters:

heatmap - input Z-score heatmap returned from 'coloc.saca.heatmapZScore'

alpha - significance cuttoff, type 1 error (default=0.05)

mean - mean value (default=0)

sd - standard div (default=1)

lowerTail - lower tail (default=false)

logP - log P (default=false)

result - BitType significant pixel mask