org.hkijena.jipipe.plugins.ij3d

Class IJ3DUtils

java.lang.Object

org.hkijena.jipipe.plugins.ij3d.IJ3DUtils

public class IJ3DUtils
extends Object

Constructor Summary

Constructors

Constructor and Description
IJ3DUtils()

Method Summary

Modifier and Type	Method and Description
static List<org.jogamp.vecmath.Point3f>	convertMesh(List<org.scijava.vecmath.Point3f> list)
static mcib3d.geom.Object3D	duplicateObject3D(mcib3d.geom.Object3D other) Duplicates an Object3D
static ij.ImagePlus	forEach3DIn5DGenerate(ij.ImagePlus sourceImage, org.apache.commons.lang3.function.TriFunction<mcib3d.image3d.ImageHandler,ImageSliceIndex,JIPipeProgressInfo,mcib3d.image3d.ImageHandler> operation, JIPipeProgressInfo progressInfo)
static void	forEach3DIn5DIO(ij.ImagePlus imagePlus, TriConsumer<mcib3d.image3d.ImageHandler,ImageSliceIndex,JIPipeProgressInfo> operation, JIPipeProgressInfo progressInfo)
static void	generateRoi3dRelationRowMeasurements(mcib3d.image3d.ImageHandler reference, int roi1Index, int roi2Index, int measurements, boolean physicalUnits, ResultsTableData target, ROI3D roi1, ROI3D roi2, int row, String columnPrefix)
static void	generateRoi3dRowMeasurements(mcib3d.image3d.ImageHandler referenceImage, int index, ROI3D roi3D, int measurements, boolean physicalUnits, ResultsTableData target, int row, String columnPrefix)
static List<org.scijava.vecmath.Point3f>	jogAmpToSciJava(List<org.jogamp.vecmath.Point3f> points)
static void	measureRoi3d(mcib3d.image3d.ImageHandler referenceImage, ROI3DListData roiList, int measurements, boolean physicalUnits, String columnPrefix, ResultsTableData target, JIPipeProgressInfo progressInfo)
static void	measureRoi3dRelation(mcib3d.image3d.ImageHandler referenceImage, ROI3DListData roi1List, ROI3DListData roi2List, int measurements, boolean physicalUnits, boolean requireColocalization, boolean preciseColocalization, boolean ignoreC, boolean ignoreT, String columnPrefix, ResultsTableData target, JIPipeProgressInfo progressInfo)
static void	putToMap(mcib3d.image3d.ImageHandler imageHandler, int c, int t, Map<ImageSliceIndex,ij.process.ImageProcessor> sliceMap)
static ROI3DListData	roi2DtoRoi3D(ROI2DListData roi2DList, boolean force2D, boolean fast, Neighborhood3D neighborhood, JIPipeProgressInfo progressInfo) Converts 2D ROI to 3D ROI
static List<org.jogamp.vecmath.Point3f>	sciJavaToJogAmp(List<org.scijava.vecmath.Point3f> points)
static mcib3d.image3d.ImageHandler	wrapImage(ImagePlusData imagePlusData)

Methods inherited from class java.lang.Object

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

Constructor Detail

IJ3DUtils

public IJ3DUtils()

Method Detail

jogAmpToSciJava

public static List<org.scijava.vecmath.Point3f> jogAmpToSciJava(List<org.jogamp.vecmath.Point3f> points)

sciJavaToJogAmp

public static List<org.jogamp.vecmath.Point3f> sciJavaToJogAmp(List<org.scijava.vecmath.Point3f> points)

forEach3DIn5DIO

public static void forEach3DIn5DIO(ij.ImagePlus imagePlus,
                                   TriConsumer<mcib3d.image3d.ImageHandler,ImageSliceIndex,JIPipeProgressInfo> operation,
                                   JIPipeProgressInfo progressInfo)

forEach3DIn5DGenerate

public static ij.ImagePlus forEach3DIn5DGenerate(ij.ImagePlus sourceImage,
                                                 org.apache.commons.lang3.function.TriFunction<mcib3d.image3d.ImageHandler,ImageSliceIndex,JIPipeProgressInfo,mcib3d.image3d.ImageHandler> operation,
                                                 JIPipeProgressInfo progressInfo)

roi2DtoRoi3D

public static ROI3DListData roi2DtoRoi3D(ROI2DListData roi2DList,
                                         boolean force2D,
                                         boolean fast,
                                         Neighborhood3D neighborhood,
                                         JIPipeProgressInfo progressInfo)

Converts 2D ROI to 3D ROI

Parameters:

roi2DList - the 2D ROI list

force2D - force the creation of 2D ROI. always true if the fast mode is inactive

fast - use masks instead of processing the ROI per component. if false, automatically implies false2D

neighborhood - the neighborhood

progressInfo - the progress info

Returns:

the 3D ROI

wrapImage

public static mcib3d.image3d.ImageHandler wrapImage(ImagePlusData imagePlusData)

duplicateObject3D

public static mcib3d.geom.Object3D duplicateObject3D(mcib3d.geom.Object3D other)

Duplicates an Object3D

Parameters:

other - the object to copy

Returns:

the copied object

measureRoi3d

public static void measureRoi3d(mcib3d.image3d.ImageHandler referenceImage,
                                ROI3DListData roiList,
                                int measurements,
                                boolean physicalUnits,
                                String columnPrefix,
                                ResultsTableData target,
                                JIPipeProgressInfo progressInfo)

measureRoi3dRelation

public static void measureRoi3dRelation(mcib3d.image3d.ImageHandler referenceImage,
                                        ROI3DListData roi1List,
                                        ROI3DListData roi2List,
                                        int measurements,
                                        boolean physicalUnits,
                                        boolean requireColocalization,
                                        boolean preciseColocalization,
                                        boolean ignoreC,
                                        boolean ignoreT,
                                        String columnPrefix,
                                        ResultsTableData target,
                                        JIPipeProgressInfo progressInfo)

generateRoi3dRelationRowMeasurements

public static void generateRoi3dRelationRowMeasurements(mcib3d.image3d.ImageHandler reference,
                                                        int roi1Index,
                                                        int roi2Index,
                                                        int measurements,
                                                        boolean physicalUnits,
                                                        ResultsTableData target,
                                                        ROI3D roi1,
                                                        ROI3D roi2,
                                                        int row,
                                                        String columnPrefix)

generateRoi3dRowMeasurements

public static void generateRoi3dRowMeasurements(mcib3d.image3d.ImageHandler referenceImage,
                                                int index,
                                                ROI3D roi3D,
                                                int measurements,
                                                boolean physicalUnits,
                                                ResultsTableData target,
                                                int row,
                                                String columnPrefix)

putToMap

public static void putToMap(mcib3d.image3d.ImageHandler imageHandler,
                            int c,
                            int t,
                            Map<ImageSliceIndex,ij.process.ImageProcessor> sliceMap)

convertMesh

public static List<org.jogamp.vecmath.Point3f> convertMesh(List<org.scijava.vecmath.Point3f> list)