org.hkijena.jipipe.extensions.imagejalgorithms.ij1.colocalization

Class CustomColoc2<T extends RealType<T> & NativeType<T>>

java.lang.Object

sc.fiji.coloc.Coloc_2<T>

org.hkijena.jipipe.extensions.imagejalgorithms.ij1.colocalization.CustomColoc2<T>

Type Parameters:

T - img type

All Implemented Interfaces:

ij.plugin.PlugIn

public class CustomColoc2<T extends RealType<T> & NativeType<T>>
extends Coloc_2<T>

Customized version of Coloc_2 because many properties are protected

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CustomColoc2.ColocResult<T extends RealType<T> & NativeType<T>>

Nested classes/interfaces inherited from class sc.fiji.coloc.Coloc_2

Coloc_2.BoundingBox, Coloc_2.MaskInfo, Coloc_2.RoiConfiguration

Field Summary

Fields inherited from class sc.fiji.coloc.Coloc_2

autoSavePdf, Ch1Name, Ch2Name, costesSignificance, displayImages, histogram2D, img1, img1Channel, img2, img2Channel, index1, index2, indexMask, indexRegr, indexRoi, kendallTau, liHistogramCh1, liHistogramCh2, liICQ, mandersCorrelation, masks, pearsonsCorrelation, PREF_KEY, regressions, roiConfig, SpearmanRankCorrelation

Constructor Summary

Constructors

Constructor and Description
CustomColoc2(JIPipeProgressInfo progressInfo)

Method Summary

Modifier and Type	Method and Description
CustomColoc2.ColocResult<T>	customColocalise(Img<T> image1, Img<T> image2, Coloc_2.BoundingBox roi, Img<T> mask, List<ResultHandler<T>> extraHandlers) Call this method to run a whole colocalisation configuration, all selected algorithms get run on the supplied images.
ArrayList<Coloc_2.MaskInfo>	getMaskInfos()
boolean	initializeSettings(ij.ImagePlus imp1, ij.ImagePlus imp2, ij.ImagePlus mask, AutoThresholdRegression.Implementation thresholdRegression, boolean gdDisplayShuffledCostes, boolean gdUseLiCh1, boolean gdUseLiCh2, boolean gdUseLiICQ, boolean gdUseSpearmanRank, boolean gdUseManders, boolean gdUseKendallTau, boolean gdUseScatterplot, boolean gdUseCostes, int gdPsf, int gdNrCostesRandomisations)
List<CustomColoc2.ColocResult<T>>	runColocalization()
void	setChannelNames(String ch1Name, String ch2Name)

Methods inherited from class sc.fiji.coloc.Coloc_2

addIfValid, clip, colocalise, colocalise, createMaskImage, createMasksAndRois, createMasksFromImage, createMasksFromRoiManager, getBoundingBoxOfMask, hasValidRoi, initializeSettings, run, showDialog, split

Methods inherited from class java.lang.Object

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

Constructor Detail

CustomColoc2

public CustomColoc2(JIPipeProgressInfo progressInfo)

Method Detail

getMaskInfos

public ArrayList<Coloc_2.MaskInfo> getMaskInfos()

setChannelNames

public void setChannelNames(String ch1Name,
                            String ch2Name)

runColocalization

public List<CustomColoc2.ColocResult<T>> runColocalization()

customColocalise

public CustomColoc2.ColocResult<T> customColocalise(Img<T> image1,
                                                    Img<T> image2,
                                                    Coloc_2.BoundingBox roi,
                                                    Img<T> mask,
                                                    List<ResultHandler<T>> extraHandlers)
                                             throws MissingPreconditionException

Call this method to run a whole colocalisation configuration, all selected algorithms get run on the supplied images. You can specify the data further by supplying appropriate information in the mask structure.

Parameters:

image1 - First image.

image2 - Second image.

roi - Region of interest to which analysis is confined.

mask - Mask to which analysis is confined.

extraHandlers - additional objects to be notified of analysis results.

Returns:

Data structure housing the results.

Throws:

MissingPreconditionException

initializeSettings

public boolean initializeSettings(ij.ImagePlus imp1,
                                  ij.ImagePlus imp2,
                                  ij.ImagePlus mask,
                                  AutoThresholdRegression.Implementation thresholdRegression,
                                  boolean gdDisplayShuffledCostes,
                                  boolean gdUseLiCh1,
                                  boolean gdUseLiCh2,
                                  boolean gdUseLiICQ,
                                  boolean gdUseSpearmanRank,
                                  boolean gdUseManders,
                                  boolean gdUseKendallTau,
                                  boolean gdUseScatterplot,
                                  boolean gdUseCostes,
                                  int gdPsf,
                                  int gdNrCostesRandomisations)