Package gov.nih.mipav.view.renderer.WildMagic.WormUntwisting

Class WormData

java.lang.Object

gov.nih.mipav.view.renderer.WildMagic.WormUntwisting.WormData

public class WormData
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	autoLatticeGenerationOutput
static java.lang.String	editLatticeOutput
static java.lang.String	editSeamCellOutput
private java.lang.String	imageName
static java.lang.String	integratedAnnotationOutput
static java.lang.String	namedSeamCellOutput
static java.lang.String	neuriteOutput
private java.lang.String	outputDirectory
private java.lang.String	outputImagesDirectory
static java.lang.String	straightenedAnnotations
static java.lang.String	straightenedLattice
static float	VoxelSize
private ModelImage	wormImage

Constructor Summary

Constructors

Constructor	Description
WormData(ModelImage image)

Method Summary

Modifier and Type	Method	Description
private void	checkParentDir(java.lang.String parentDir)	Creates the parent directory for the output images and data created by worm segmentation and untwisting:
private static boolean	checkSeamCells(java.lang.String outputDirectory)
static VOI	getIntegratedMarkerAnnotations(java.lang.String outputDirectory)
static java.lang.String	getIntegratedMarkerAnnotationsPath(java.lang.String outputDirectory)
static java.lang.String	getOutputDirectory(ModelImage image)
static java.lang.String	getStraightAnnotationsPath(java.lang.String outputDirectory)
static boolean	integratedExists(java.lang.String outputDirectory)
static void	openStraightAnnotations(java.lang.String dir, ModelImage image)
VOIVector	readFinalLattice()
private VOIVector	readFinalLattice(boolean convertLegacyXML)
static VOIVector	readFinalLattice(java.lang.String outputDirectory, boolean convertLegacyXML, ModelImage image)
private static VOIVector	readLegacyLattice(java.lang.String fileName, ModelImage wormImage)
static VOIVector	readStraightLattice(java.lang.String outputDirectory)
static void	saveIntegratedMarkerAnnotations(java.lang.String outputDirectory, VOI annotations)
static void	saveSeamAnnotations(java.lang.String outputDirectory, VOI annotations, boolean rename, boolean checkImage)

Methods inherited from class java.lang.Object

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

Field Detail

VoxelSize

public static float VoxelSize

editSeamCellOutput

public static final java.lang.String editSeamCellOutput

namedSeamCellOutput

public static final java.lang.String namedSeamCellOutput

autoLatticeGenerationOutput

public static final java.lang.String autoLatticeGenerationOutput

editLatticeOutput

public static final java.lang.String editLatticeOutput

integratedAnnotationOutput

public static final java.lang.String integratedAnnotationOutput

straightenedLattice

public static final java.lang.String straightenedLattice

straightenedAnnotations

public static final java.lang.String straightenedAnnotations

neuriteOutput

public static final java.lang.String neuriteOutput

imageName

private java.lang.String imageName

wormImage

private ModelImage wormImage

outputDirectory

private java.lang.String outputDirectory

outputImagesDirectory

private java.lang.String outputImagesDirectory

Constructor Detail

WormData

public WormData(ModelImage image)

Method Detail

getOutputDirectory

public static java.lang.String getOutputDirectory(ModelImage image)

integratedExists

public static boolean integratedExists(java.lang.String outputDirectory)

getIntegratedMarkerAnnotationsPath

public static java.lang.String getIntegratedMarkerAnnotationsPath(java.lang.String outputDirectory)

getStraightAnnotationsPath

public static java.lang.String getStraightAnnotationsPath(java.lang.String outputDirectory)

getIntegratedMarkerAnnotations

public static VOI getIntegratedMarkerAnnotations(java.lang.String outputDirectory)

openStraightAnnotations

public static void openStraightAnnotations(java.lang.String dir,
                                           ModelImage image)

readStraightLattice

public static VOIVector readStraightLattice(java.lang.String outputDirectory)

readFinalLattice

public VOIVector readFinalLattice()

readFinalLattice

private VOIVector readFinalLattice(boolean convertLegacyXML)

readFinalLattice

public static VOIVector readFinalLattice(java.lang.String outputDirectory,
                                         boolean convertLegacyXML,
                                         ModelImage image)

readLegacyLattice

private static VOIVector readLegacyLattice(java.lang.String fileName,
                                           ModelImage wormImage)

checkSeamCells

private static boolean checkSeamCells(java.lang.String outputDirectory)

saveIntegratedMarkerAnnotations

public static void saveIntegratedMarkerAnnotations(java.lang.String outputDirectory,
                                                   VOI annotations)

saveSeamAnnotations

public static void saveSeamAnnotations(java.lang.String outputDirectory,
                                       VOI annotations,
                                       boolean rename,
                                       boolean checkImage)

checkParentDir

private void checkParentDir(java.lang.String parentDir)

Creates the parent directory for the output images and data created by worm segmentation and untwisting:

Parameters:

parentDir -