com.openinventor.imageviz.engines.imagefiltering.texturefilters

Class SoMultiscaleStructureEnhancementProcessing3d

java.lang.Object

com.openinventor.inventor.Inventor

com.openinventor.inventor.misc.SoBase

com.openinventor.inventor.fields.SoFieldContainer

com.openinventor.inventor.engines.SoEngine

com.openinventor.imageviz.engines.SoImageVizEngine

com.openinventor.imageviz.engines.imagefiltering.texturefilters.SoMultiscaleStructureEnhancementProcessing3d

All Implemented Interfaces:

SafeDisposable

public class SoMultiscaleStructureEnhancementProcessing3d
extends SoImageVizEngine

SoMultiscaleStructureEnhancementProcessing2d engine Overview

The purpose of this algorithm is to enhance structures of interest from an image using a multi scale analysis. The result of this algorithm is a score image that can be used with the goal of segmenting the input image.

The SoMultiscaleStructureEnhancement filters compute a score between 0 and 1 for each pixel, 1 representing a good matching with a structure model and 0 a background pixel. This provides a powerful technique for automatically identifying structures such as blood vessels. The score can be computed either on an Hessian matrix to detect ridge structures or on a Gradient tensor for object edges and corners. The structure models available are:

• Balls (circular structures with Hessian in 2D, spherical in 3D, object corners with Gradient tensor)
• Rods (linear structures)
• Plates (only available in 3D)

The principle of the algorithm can be summarized as follows :

• A set of tensor fields is extracted from the image by filtering the image at different scales.
• A score image is extracted from each tensor field by analyzing the eigenvalues of tensors.
• The final score is obtained by selecting the maximum of all score images.

The following publication describes this algorithm when applied to detect Rod structures with the Hessian matrix: A.F.Frangi, W.J.Niessen, K.L.Vincken, M.A.Viergever, "Multiscale vessel enhancement filtering", Lecture Notes in Computer Science(MICCAI), vol. 1496, pp. 130-137, 1998.

Tensor Extraction

2 modes are available for computing the tensor field; the GRADIENT mode and the HESSIAN mode. The first one is based on the gradient tensor the second one on the hessian matrix.

GRADIENT mode

In the GRADIENT mode, the gradient tensor is extracted. This tensor also referred to as structure tensor or second order moment matrix, is a matrix derived from the gradient of the image. This matrix summarizes the predominant directions of the gradient around the voxel of interest.

Where is a gaussian kernel controlling the scale of analysis.

HESSIAN mode

In this mode, the tensor field is based on the extraction of the hessian matrix of the image. This hessian matrix is computed by filtering the image with the derivative of a gaussian kernel.The standard deviation of the kernel controls the scale of analysis.

Feature extraction

The parameter structureType controls the type of structure that is extracted from the tensor field(ROD/BALL/PLANE). The computation is based on eigen values , and where .

Let first introduce

, and

The first ratio attains its maximum for blob-like structure. The second ratio distinguishes plate-like and line-like structures.

The score for StructureType3D.ROD corresponds to :

The score for StructureType3D.BALL is computed as follow :

The score for StructureType3D.PLANE is computed as follow :

where is the tensor norm , is a threshold which controls the flatness sensitivity, is a threshold which controls the blobness sensitivity, and is a sensitivity threshold which controls the noise influence. with the maximum Hessian norm in the image.

In the HESSIAN mode, the lightness parameter limits the feature extraction to dark or bright objects by analyzing the sign of eigenvalues. This parameter is ignored in GRADIENT mode where tensors are positive definite matrices.

See also:

SoMultiscaleStructureEnhancementProcessing2d.

File format/default:

MultiscaleStructureEnhancementProcessing3d {

inImage	NULL
tensorType	HESSIAN
standardDeviationRange	1.0f 3.0f
standardDeviationStep	1.0f
lightness	BRIGHT
structureType	ROD

}

Library references: structureenhancementfilter3d

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SoMultiscaleStructureEnhancementProcessing3d.LightnessType
static class	SoMultiscaleStructureEnhancementProcessing3d.StructureTypes
static class	SoMultiscaleStructureEnhancementProcessing3d.TensorTypes

Nested classes/interfaces inherited from class com.openinventor.imageviz.engines.SoImageVizEngine

SoImageVizEngine.ComputeModes, SoImageVizEngine.EventArg, SoImageVizEngine.Neighborhood3ds

Nested classes/interfaces inherited from class com.openinventor.inventor.Inventor

Inventor.ConstructorCommand

Field Summary

Fields

Modifier and Type	Field and Description
static int	BALL Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.StructureTypes.BALL instead.
static int	BRIGHT Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.LightnessType.BRIGHT instead.
static int	DARK Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.LightnessType.DARK instead.
static int	GRADIENT Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.TensorTypes.GRADIENT instead.
static int	HESSIAN Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.TensorTypes.HESSIAN instead.
SoSFImageDataAdapter	inImage Input image.
SoSFEnum<SoMultiscaleStructureEnhancementProcessing3d.LightnessType>	lightness The lightness type of structures to enhance.
SoImageVizEngineOutput<SoSFImageDataAdapter,SoImageDataAdapter>	outImage Output image.
static int	PLANE Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.StructureTypes.PLANE instead.
static int	ROD Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.StructureTypes.ROD instead.
SoSFVec2f	standardDeviationRange Standard deviation of the Gaussian kernel at the minimum and maximum scale.
SoSFFloat	standardDeviationStep Standard deviation step.
SoSFEnum<SoMultiscaleStructureEnhancementProcessing3d.StructureTypes>	structureType Shape of structures to extract.
SoSFEnum<SoMultiscaleStructureEnhancementProcessing3d.TensorTypes>	tensorType Defines whether the command will use the gradient tensor or the hessian matrix.

Fields inherited from class com.openinventor.imageviz.engines.SoImageVizEngine

CONNECTIVITY_18, CONNECTIVITY_26, CONNECTIVITY_6, MODE_2D, MODE_3D, MODE_AUTO, onBegin, onEnd, onProgress

Fields inherited from class com.openinventor.inventor.Inventor

VERBOSE_LEVEL, ZeroHandle

Constructor Summary

Constructors

Constructor and Description
SoMultiscaleStructureEnhancementProcessing3d() Constructor.

Method Summary

Methods inherited from class com.openinventor.imageviz.engines.SoImageVizEngine

abortEvaluate, isEvaluating, startEvaluate, waitEvaluate

Methods inherited from class com.openinventor.inventor.engines.SoEngine

copy, getByName, getOutput, getOutputName

Methods inherited from class com.openinventor.inventor.fields.SoFieldContainer

copyFieldValues, copyFieldValues, enableNotify, fieldsAreEqual, get, getAllFields, getEventIn, getEventOut, getField, getFieldName, hasDefaultValues, isNotifyEnabled, set, setToDefaults

Methods inherited from class com.openinventor.inventor.misc.SoBase

dispose, getEXTERNPROTO, getName, getPROTO, isDisposable, isSynchronizable, setName, setSynchronizable, touch

Methods inherited from class com.openinventor.inventor.Inventor

getAddress, getNativeResourceHandle, startInternalThreads, stopInternalThreads

Methods inherited from class java.lang.Object

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

Field Detail

HESSIAN

@Deprecated
public static final int HESSIAN

Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.TensorTypes.HESSIAN instead.

GRADIENT

@Deprecated
public static final int GRADIENT

Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.TensorTypes.GRADIENT instead.

BRIGHT

@Deprecated
public static final int BRIGHT

Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.LightnessType.BRIGHT instead.

DARK

@Deprecated
public static final int DARK

Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.LightnessType.DARK instead.

ROD

@Deprecated
public static final int ROD

Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.StructureTypes.ROD instead.

BALL

@Deprecated
public static final int BALL

Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.StructureTypes.BALL instead.

PLANE

@Deprecated
public static final int PLANE

Deprecated. Use SoMultiscaleStructureEnhancementProcessing3d.StructureTypes.PLANE instead.

inImage

public final SoSFImageDataAdapter inImage

Input image. Type of the image can be integer or floating. Default value is NULL. Supported types include: grayscale image.

tensorType

public final SoSFEnum<SoMultiscaleStructureEnhancementProcessing3d.TensorTypes> tensorType

Defines whether the command will use the gradient tensor or the hessian matrix. . Default is HESSIAN

standardDeviationRange

public final SoSFVec2f standardDeviationRange

Standard deviation of the Gaussian kernel at the minimum and maximum scale. Default value is SbVec2f(1.0f,3.0f).

standardDeviationStep

public final SoSFFloat standardDeviationStep

Standard deviation step. Structures will be detected from min to max standard deviation at a pitch of this value. Default value is 1.0f.

lightness

public final SoSFEnum<SoMultiscaleStructureEnhancementProcessing3d.LightnessType> lightness

The lightness type of structures to enhance. . Default is BRIGHT

structureType

public final SoSFEnum<SoMultiscaleStructureEnhancementProcessing3d.StructureTypes> structureType

Shape of structures to extract. . Default is ROD

outImage

public final SoImageVizEngineOutput<SoSFImageDataAdapter,SoImageDataAdapter> outImage

Output image. Type of the output image is forced to float. Default value is NULL. Supported types include: grayscale image.

Constructor Detail

SoMultiscaleStructureEnhancementProcessing3d

public SoMultiscaleStructureEnhancementProcessing3d()

Constructor.