java.lang.Object
- gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMObject
- - gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMModel

Direct Known Subclasses:

C_AAMMODEL, CAAMModelMS, CAAMModelSeq
```
public class CAAMModel
extends CAAMObject
```
This is the Java modified version of C++ active appearance model API (AAM_API). It is modified with a subset of required functions for automatic MRI prostate segmentation. AAM-API LICENSE - file: license.txt This software is freely available for non-commercial use such as research and education. Please see the full disclaimer below. All publications describing work using this software should cite the reference given below. Copyright (c) 2000-2003 Mikkel B. Stegmann, mbs@imm.dtu.dk IMM, Informatics & Mathematical Modelling DTU, Technical University of Denmark Richard Petersens Plads, Building 321 DK-2800 Lyngby, Denmark http://www.imm.dtu.dk/~aam/ REFERENCES Please use the reference below, when writing articles, reports etc. where the AAM-API has been used. A draft version the article is available from the homepage. I will be happy to receive pre- or reprints of such articles. /Mikkel ------------- M. B. Stegmann, B. K. Ersboll, R. Larsen, "FAME -- A Flexible Appearance Modelling Environment", IEEE Transactions on Medical Imaging, IEEE, 2003 (to appear) ------------- 3RD PART SOFTWARE The software is partly based on the following libraries: - The Microsoft(tm) Vision Software Developers Kit, VisSDK - LAPACK DISCLAIMER This software is provided 'as-is', without any express or implied warranty. In no event will the author be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any non-commercial purpose, and to alter it, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. -- No guarantees of performance accompany this software, nor is any responsibility assumed on the part of the author or IMM. This software is provided by Mikkel B. Stegmann and IMM ``as is'' and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall IMM or Mikkel B. Stegmann be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage. $Revision: 1.4 $ $Date: 2003/04/23 14:49:15 $ The core Active Appearance Model object that hold all eigenmodels, prediction matrices etc. Build by a CAAMBuilder.

Author:

Ruida Cheng

Field Summary

Fields
Modifier and Type	Field	Description
`protected boolean`	`m_bUseConvexHull`	flag to use convexhull.
`protected boolean`	`m_bUseTangentSpace`	flag to use targent space.
`protected CAAMDeformPCA`	`m_CombinedPCA`	The combined PCA.
`protected double`	`m_dAddExtents`	flag to add extents.
`protected double`	`m_dAMFVersion`	The AMF format version.
`protected double`	`m_dBuildTime`	model build time.
`protected CAAMDeformPCA`	`m_DisplacementPCA`	deform displacement PCA.
`protected double`	`m_dMeanShapeSize`	mean shape size.
`protected int`	`m_iCombinedTrunc`	combined truncation.
`protected int`	`m_iLearningMethod`	which learning method to use.
`protected int`	`m_iModelReduction`	flag for model reduction.
`protected int`	`m_iNShapes`	the number of shapes.
`protected int`	`m_iShapeTrunc`	shape truncation.
`protected int`	`m_iTextureSamples`	The number of texture samples in the model.
`protected int`	`m_iTextureTrunc`	texture truncation.
`protected CDMatrix`	`m_mQgEV`	The texture part of the combined eigenvectors.
`protected CDMatrix`	`m_mQsEV`	The shape part of the combined eigenvectors.
`protected CDMatrix`	`m_mShape2PixelWeights`	The shape-to-pixel weights.
`protected CDMatrix`	`m_mShapeInstance`	Cache shape matrix.
`protected CDMatrix`	`m_mTextureInstance`	Cache texture matrix.
`protected CAAMAnalyzeSynthesize`	`m_pAnalyzeSynthesize`	AAM synthesize analysis.
`protected CAAMReferenceFrame`	`m_pReferenceFrame`	AAM reference frame.
`protected CAAMDeform`	`m_pShapeBasis`	The shape basis.
`protected CAAMDeform`	`m_pTextureBasis`	The texture basis.
`protected CAAMTransferFunction`	`m_pTextureTF`	The texture transfer function.
`protected CDMatrix`	`m_R_c`	The parameter prediction matrix
`protected CDMatrix`	`m_R_t`
`protected java.lang.String`	`m_sCurrentAnalyzeId`	Current analyzer name.
`protected CAAMDeformPCA`	`m_ShapePCA`	The shape PCA.
`protected CAAMShape`	`m_sMeanAShape`	Cached mean shape.
`protected CAAMDeformPCA`	`m_TexturePCA`	The texture PCA.
`protected CDVector`	`m_vMeanTexture`	The mean texture.
`protected CDVector`	`m_vMeanTextureOrg`	the mean texture original.
`protected CDVector`	`m_vPoseParameterUpdateConstraints`	pose parameters update.
`protected CDVector`	`m_vShapeParameterConstraintsMean`	shape parameters upate.
`protected CDVector`	`m_vShapeParameterConstraintsSD`
`protected CDVector`	`m_vTextureVar`	The variance of each normalized pixel in the texture model.

Constructor Summary

Constructors
Constructor Description

CAAMModel()
Constructor.

CAAMModel(CAAMModel m)
Copy constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`AddExtents()`	Returns the amount shape extents added (warning: shape extents will be remove in later versions).
`boolean`	`ApproxExample(java.lang.String filename, ModelSimpleImage outImg)`	Doing model approximation of an (unseen) example.
`CAAMModel`	`assign(CAAMModel m)`	Assignment operator.
`void`	`Combined2ShapeParam(CDVector c, CDVector b_s)`	Converts combined model parameters to shape parameters.
`void`	`Combined2TexParam(CDVector c, CDVector b_g)`	Converts combined model parameters to texture parameters.
`CAAMDeformPCA`	`CombinedPCA()`	Returns the combined PCA.
`void`	`ConstrainSearchParameters(CDVector c, CDVector pose)`	Constrain the pose and model parameters to be within some reasonable limits.
`void`	`dispose()`	dispose memory
`boolean`	`EstimatePose(ModelSimpleImage image, CAAMShape shape, CDVector pose)`	Estimate the pose of a shape using the pose regression matrix.
`int`	`getNumberShapeParameters()`	Get the the number of eigen values in PCA.
`boolean`	`IsConvexHullUsed()`	Returns true if the texture model is based on the convex hull.
`CAAMShape`	`MeanShape()`	Returns the mean shape.
`double`	`MeanShapeSize()`	Returns the mean shape size, i.e. the size of the reference shape.
`CDVector`	`MeanTexture()`	Returns the mean texture.
`double`	`ModelEstimateTexDiff(ModelSimpleImage image, CDVector c, CAAMShape estimate, CDVector diff, int similaritym)`	Wrapper to calculate the pixel difference from a model instance and an image.
`double`	`ModelEstimateTexDiff(ModelSimpleImage image, CDVector c, CAAMShape estimate, CDVector diff, int similaritym, boolean useInterpolation)`	Calculates the pixel difference from a model instance and an image.
`void`	`ModelImage(CDVector c, ModelSimpleImage outImg, CAAMShape matchPose)`	Generate model instance (match pose to 'shape') and render the instance into the image 'img'.
`void`	`ModelImage(CDVector c, ModelSimpleImage outImg, CAAMShape matchPose, boolean fitTexture)`	Generates a model image based on the parameters in 'c' with various options.
`void`	`ModelImageEx(CAAMShape shape, CDVector texture, ModelSimpleImage outImg, boolean renderImage, boolean fitTexture)`	Generates a synthetic image from the AAM using the model parameters in 'c'.
`int`	`ModelReduction()`	Return model reduction.
`int`	`NBands()`	Returns the number of bands in the model
`void`	`NormalizeTexture(CDVector texture)`	Normalizes a texture vector.
`int`	`NTextureSamples()`	Returns the number of samples in the texture model.
`CAAMOptRes`	`OptimizeModel(ModelSimpleImage image, CAAMShape s, CDVector c)`	Wrapper for model optimization.
`CAAMOptRes`	`OptimizeModel(ModelSimpleImage image, CAAMShape s, CDVector c, int maxIterations, java.util.Vector<CAAMOptState> pOptStates)`	Wrapper for model optimization
`CAAMOptRes`	`OptimizeModel(ModelSimpleImage image, CAAMShape s, CDVector c, int maxIterations, java.util.Vector<CAAMOptState> pOptStates, boolean disableDamping)`	Performs AAM optimization of a shape containing initial pose and a set of model parameters (c).
`CAAMOptRes`	`OptimizeModelByFineTuning(ModelSimpleImage image, CAAMShape s, CDVector c, int maxIterations, int similaritym, int optimizer)`	Perform general-purpose optimization of the AAM using simulated annealing, conjugate gradient, steepest descent, BGFS or pattern search.
`CDMatrix`	`Qg()`	The texture part of the combined PCA eigenvectors.
`CDMatrix`	`Qs()`	The shape part of the combined PCA eigenvectors.
`CDMatrix`	`Rc()`	Texture parameter update prediction matrix.
`boolean`	`ReadModel(java.lang.String filename)`	Reads the complete AAMModel from disk.
`int`	`ReductionFactor()`	Returns the reduction factor of the training set that this model was
`CAAMReferenceFrame`	`ReferenceFrame()`	Returns the reference frame of the model.
`CAAMShape`	`ReferenceShape()`	Returns the reference shape where all texture sampling and comparison should be done.
`CDMatrix`	`Rt()`	Pose parameter update prediction matrix.
`int`	`SampleShape(ModelSimpleImage image, CAAMShape shape, CDVector textureSamples)`	Wrapper to build a texture vector from an image and a shape.
`int`	`SampleShape(ModelSimpleImage image, CAAMShape shape, CDVector textureSamples, boolean normalize)`	Wrapper to build a texture vector from an image and a shape.
`int`	`SampleShape(ModelSimpleImage image, CAAMShape shape, CDVector textureSamples, boolean normalize, boolean useInterpolation)`	Wrapper to build a texture vector from an image and a shape.
`int`	`SampleShape(ModelSimpleImage image, CAAMShape shape, CDVector textureSamples, boolean normalize, boolean useInterpolation, boolean map)`	Builds a texture vector from an image and a shape.
`void`	`SetPoseParameterUpdateConstraints(CDVector pc)`	Sets constraints on the pose parameter updates.
`void`	`SetShapeParameterUpdateConstraints(CDVector mean, CDVector sd)`	Sets user-specified shape parameter update constraints.
`void`	`Shape2Combined(CAAMShape shape, ModelSimpleImage image, CDVector c)`	Projects a shape into a set of c parameters.
`void`	`Shape2Param(CAAMShape shape, CDVector b_s)`	Projects a shape into a set of shape parameters,
`CDMatrix`	`Shape2PixelWeights()`	Return shape to pixel weight.
`CAAMDeform`	`ShapeBasis()`	Returns the shape PCA.
`ModelSimpleImage`	`ShapeFreeImage(CDVector textureSamples, ModelSimpleImage outImg)`	Wrapper to generates a shape free image using a vector of texture samples.
`ModelSimpleImage`	`ShapeFreeImage(CDVector textureSamples, ModelSimpleImage outImg, boolean deMap)`	Generates a shape free image (that is; a mean shape image) using a vector of texture samples.
`void`	`ShapeFreeImage(CDVector textureSamples, CDMatrix m, boolean deMap, boolean normalize)`	Generates a shape free image (that is; a mean shape image) using a vector of texture samples.
`void`	`ShapeInstance(CDVector c, CAAMShape outShape)`	Generates a shape based on a set of model parameters.
`CAAMDeformPCA`	`ShapePCA()`	Returns the shape PCA.
`void`	`ShapePCAInstance(CDVector b_s, CAAMShape outShape)`	Generates a shape based on a set of shape b-parameters.
`void`	`ShapeTex2Combined(CAAMShape shape, CDVector texture, CDVector c)`	Projects the shape and texture into c-space i.e. the combined model parameters.
`void`	`ShapeTex2Param(CAAMShape shape, CDVector texture, CDVector b)`	Extract the b-parameters from a shape and corresponding texture by inverting the shape and texture pca projection.
`void`	`ShapeTexParam2Combined(CDVector b, CDVector c)`	Transforms the concatenated b-parameters into combined model parameters.
`void`	`ShapeTexParam2Combined(CDVector b_s, CDVector b_g, CDVector c)`	Projects shape and texture parameters into the combined eigenspace.
`void`	`ShapeTexParam2Combined(java.util.Vector<CDVector> bVectors, java.util.Vector<CDVector> cVectors)`	Converts a set of b-vectors to combined model parameters (c-vectors).
`CAAMDeform`	`TextureBasis()`	Returns the texture PCA.
`void`	`TextureInstance(CDVector c, CDVector outTexture)`	Generates a texture based on a set of model parameters.
`CAAMDeformPCA`	`TexturePCA()`	Returns the texture PCA.
`CAAMTransferFunction`	`TextureTF()`	Return texture transfer function.
`boolean`	`WriteModel(java.lang.String filename)`	Write the AAM model to text file or binary file.
`boolean`	`WriteModel(java.lang.String filename, boolean txt_only)`	Writes the complete AAMModel to disk as a .txt and an .amf file.
`void`	`WriteVarianceMap(java.lang.String filename)`	Plots the variance of each pixel in the model over the training set into the mean shape and saves the image.

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMObject
FromFile, ToFile

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - m_pAnalyzeSynthesize
```
protected CAAMAnalyzeSynthesize m_pAnalyzeSynthesize
```
    AAM synthesize analysis.
  - m_pReferenceFrame
```
protected CAAMReferenceFrame m_pReferenceFrame
```
    AAM reference frame.
  - m_pShapeBasis
```
protected CAAMDeform m_pShapeBasis
```
    The shape basis.
  - m_pTextureBasis
```
protected CAAMDeform m_pTextureBasis
```
    The texture basis.
  - m_ShapePCA
```
protected CAAMDeformPCA m_ShapePCA
```
    The shape PCA.
  - m_TexturePCA
```
protected CAAMDeformPCA m_TexturePCA
```
    The texture PCA.
  - m_CombinedPCA
```
protected CAAMDeformPCA m_CombinedPCA
```
    The combined PCA.
  - m_mShape2PixelWeights
```
protected CDMatrix m_mShape2PixelWeights
```
    The shape-to-pixel weights.
  - m_dAMFVersion
```
protected double m_dAMFVersion
```
    The AMF format version.
  - m_mQsEV
```
protected CDMatrix m_mQsEV
```
    The shape part of the combined eigenvectors.
  - m_mQgEV
```
protected CDMatrix m_mQgEV
```
    The texture part of the combined eigenvectors.
  - m_vMeanTexture
```
protected CDVector m_vMeanTexture
```
    The mean texture.
  - m_vMeanTextureOrg
```
protected CDVector m_vMeanTextureOrg
```
    the mean texture original.
  - m_sMeanAShape
```
protected CAAMShape m_sMeanAShape
```
    Cached mean shape.
  - m_mShapeInstance
```
protected CDMatrix m_mShapeInstance
```
    Cache shape matrix.
  - m_mTextureInstance
```
protected CDMatrix m_mTextureInstance
```
    Cache texture matrix.
  - m_vTextureVar
```
protected CDVector m_vTextureVar
```
    The variance of each normalized pixel in the texture model.
  - m_iTextureSamples
```
protected int m_iTextureSamples
```
    The number of texture samples in the model.
  - m_iNShapes
```
protected int m_iNShapes
```
    the number of shapes.
  - m_dMeanShapeSize
```
protected double m_dMeanShapeSize
```
    mean shape size.
  - m_R_c
```
protected CDMatrix m_R_c
```
    The parameter prediction matrix
  - m_R_t
```
protected CDMatrix m_R_t
```
  - m_pTextureTF
```
protected CAAMTransferFunction m_pTextureTF
```
    The texture transfer function.
  - m_iModelReduction
```
protected int m_iModelReduction
```
    flag for model reduction.
  - m_dAddExtents
```
protected double m_dAddExtents
```
    flag to add extents.
  - m_bUseConvexHull
```
protected boolean m_bUseConvexHull
```
    flag to use convexhull.
  - m_bUseTangentSpace
```
protected boolean m_bUseTangentSpace
```
    flag to use targent space.
  - m_iLearningMethod
```
protected int m_iLearningMethod
```
    which learning method to use.
  - m_iShapeTrunc
```
protected int m_iShapeTrunc
```
    shape truncation.
  - m_iTextureTrunc
```
protected int m_iTextureTrunc
```
    texture truncation.
  - m_iCombinedTrunc
```
protected int m_iCombinedTrunc
```
    combined truncation.
  - m_sCurrentAnalyzeId
```
protected java.lang.String m_sCurrentAnalyzeId
```
    Current analyzer name.
  - m_dBuildTime
```
protected double m_dBuildTime
```
    model build time.
  - m_vPoseParameterUpdateConstraints
```
protected CDVector m_vPoseParameterUpdateConstraints
```
    pose parameters update.
  - m_vShapeParameterConstraintsMean
```
protected CDVector m_vShapeParameterConstraintsMean
```
    shape parameters upate.
  - m_vShapeParameterConstraintsSD
```
protected CDVector m_vShapeParameterConstraintsSD
```
  - m_DisplacementPCA
```
protected CAAMDeformPCA m_DisplacementPCA
```
    deform displacement PCA.
- Constructor Detail
  - CAAMModel
```
public CAAMModel()
```
    Constructor. Set up the default settings.
  - CAAMModel
```
public CAAMModel(CAAMModel m)
```
    Copy constructor.
    
    Parameters:
    
    m - Object to copy from.
- Method Detail
  - Rc
```
public CDMatrix Rc()
```
    Texture parameter update prediction matrix.
    
    Returns:
    
    texture prediction matrix
  - Rt
```
public CDMatrix Rt()
```
    Pose parameter update prediction matrix.
    
    Returns:
    
    pose prediction matrix
  - Qg
```
public CDMatrix Qg()
```
    The texture part of the combined PCA eigenvectors.
    
    Returns:
    
    combined texture PCA
  - Qs
```
public CDMatrix Qs()
```
    The shape part of the combined PCA eigenvectors.
    
    Returns:
    
    combined shape PCA
  - ReferenceFrame
```
public CAAMReferenceFrame ReferenceFrame()
```
    Returns the reference frame of the model.
    
    Returns:
    
    refrence frame
  - NBands
```
public int NBands()
```
    Returns the number of bands in the model
    
    Returns:
    
    single channel to represent the gray scal intensity.
  - TextureTF
```
public CAAMTransferFunction TextureTF()
```
    Return texture transfer function.
    
    Returns:
    
    return texture transfer function
  - NTextureSamples
```
public int NTextureSamples()
```
    Returns the number of samples in the texture model.
    
    Returns:
    
    sample numbers
  - IsConvexHullUsed
```
public boolean IsConvexHullUsed()
```
    Returns true if the texture model is based on the convex hull.
    
    Returns:
    
    ture convex hull, false not
  - AddExtents
```
public double AddExtents()
```
    Returns the amount shape extents added (warning: shape extents will be remove in later versions).
    
    Returns:
    
    shape extents
  - MeanShape
```
public CAAMShape MeanShape()
```
    Returns the mean shape.
    
    Returns:
    
    mean shape
  - MeanTexture
```
public CDVector MeanTexture()
```
    Returns the mean texture.
    
    Returns:
    
    mean texture
  - Shape2PixelWeights
```
public CDMatrix Shape2PixelWeights()
```
    Return shape to pixel weight.
    
    Returns:
    
    weight
  - ShapePCA
```
public final CAAMDeformPCA ShapePCA()
```
    Returns the shape PCA.
    
    Returns:
    
    shape PCA
  - TexturePCA
```
public final CAAMDeformPCA TexturePCA()
```
    Returns the texture PCA.
    
    Returns:
    
    texture PCA
  - ShapeBasis
```
public CAAMDeform ShapeBasis()
```
    Returns the shape PCA.
    
    Returns:
    
    shape PCA.
  - TextureBasis
```
public CAAMDeform TextureBasis()
```
    Returns the texture PCA.
    
    Returns:
    
    texture PCA.
  - CombinedPCA
```
public CAAMDeformPCA CombinedPCA()
```
    Returns the combined PCA.
    
    Returns:
    
    combined PCA.
  - ModelReduction
```
public int ModelReduction()
```
    Return model reduction.
    
    Returns:
    
    flag for model reduction.
  - MeanShapeSize
```
public double MeanShapeSize()
```
    Returns the mean shape size, i.e. the size of the reference shape.
    
    Returns:
    
    mean shape size.
  - dispose
```
public void dispose()
```
    dispose memory
  - ApproxExample
```
public boolean ApproxExample(java.lang.String filename,
                             ModelSimpleImage outImg)
```
    Doing model approximation of an (unseen) example. Synthesizes an unseen example by projecting the shape and (normalized) texture into c-parameter space, generating a model instance and assigning it the appropriate pose (incl. denormalization).
    
    Parameters:
    
    filename - The base filename of an annotation. Ex. "scan.asf"
    
    outImg - The output image where the model approximation has been overlaid.
    
    Returns:
    
    true on success, false if the image and/or annotation could not be read.
  - SetPoseParameterUpdateConstraints
```
public void SetPoseParameterUpdateConstraints(CDVector pc)
```
    Sets constraints on the pose parameter updates. NOTICE: Currently, these are *not* saved along with the model and thus must be set each time a model is loaded.
    
    Parameters:
    
    pc - Parameter constraints (in absolute numbers).
  - SetShapeParameterUpdateConstraints
```
public void SetShapeParameterUpdateConstraints(CDVector mean,
                                               CDVector sd)
```
    Sets user-specified shape parameter update constraints. NOTICE: These are currently not saved with the model.
    
    Parameters:
    
    mean - Some shape parameter configuration.
    
    sd - The standard diviations of the 'mean'.
  - ConstrainSearchParameters
```
public void ConstrainSearchParameters(CDVector c,
                                      CDVector pose)
```
    Constrain the pose and model parameters to be within some reasonable limits.
    
    Parameters:
    
    c - The model parameters.
    
    pose - The pose parameters.
  - EstimatePose
```
public boolean EstimatePose(ModelSimpleImage image,
                            CAAMShape shape,
                            CDVector pose)
```
    Estimate the pose of a shape using the pose regression matrix.
    
    Parameters:
    
    image - The image to search in.
    
    shape - The shape to determine the pose from.
    
    pose - The output pose vector.
    
    Returns:
    
    True is ok, false if the shape is outside the image.
  - ModelImage
```
public void ModelImage(CDVector c,
                       ModelSimpleImage outImg,
                       CAAMShape matchPose)
```
    Generate model instance (match pose to 'shape') and render the instance into the image 'img'.
    
    Parameters:
    
    c - combined model parameters
    
    outImg - result image
    
    matchPose - matched shape
  - ModelImage
```
public void ModelImage(CDVector c,
                       ModelSimpleImage outImg,
                       CAAMShape matchPose,
                       boolean fitTexture)
```
    Generates a model image based on the parameters in 'c' with various options.
    
    Parameters:
    
    c - A set of model parameters.
    
    outImg - The output imge.
    
    matchPose - A pointer to a shape. If not NULL the model generated by the set of c-parameters will be aligned wrt. pose to this shape.
    
    fitTexture - If matchPose is not NULL, the de-mapped and de-normalized texture will be fitted in a least squares sense to the texture in outImg given by the shape. Default true.
  - ModelImageEx
```
public void ModelImageEx(CAAMShape shape,
                         CDVector texture,
                         ModelSimpleImage outImg,
                         boolean renderImage,
                         boolean fitTexture)
```
    Generates a synthetic image from the AAM using the model parameters in 'c'.
    
    Parameters:
    
    shape - The shape the texture vector should be mapped to.
    
    textureSamples - The texture vector to be warped into an image. Will be de-mapped and de-normalized.
    
    outImg - The output image (sized correctly inside this method, if renderInImage is false).
    
    renderImage - If true: 1) outImg is expected to be allocated. 2) the model is rendered with it's pose unchanged, thus the shape is expected to lie within the outImg This option is used for drawing the final optimization into the image or to draw a model approximation into the image 'outImg'. Default false.
    
    fitTexture - If renderImage is true, the de-mapped and de-normalized texture will be fitted in a least squares sense to the texture in outImg given by the shape. Default true.
  - ShapeFreeImage
```
public ModelSimpleImage ShapeFreeImage(CDVector textureSamples,
                                       ModelSimpleImage outImg)
```
    Wrapper to generates a shape free image using a vector of texture samples.
    
    Parameters:
    
    textureSamples - texture samples
    
    outImg - result image
    
    Returns:
    
    shape free image
  - ShapeFreeImage
```
public ModelSimpleImage ShapeFreeImage(CDVector textureSamples,
                                       ModelSimpleImage outImg,
                                       boolean deMap)
```
    Generates a shape free image (that is; a mean shape image) using a vector of texture samples.
    
    Parameters:
    
    textureSamples - The texture vector to be warped into an image. De-normalizes (and demaps) inside this method.
    
    outImg - A reference to an output image. Resize of the image is done inside this method.
    
    Returns:
    
    shape free image.
  - ShapeFreeImage
```
public void ShapeFreeImage(CDVector textureSamples,
                           CDMatrix m,
                           boolean deMap,
                           boolean normalize)
```
    Generates a shape free image (that is; a mean shape image) using a vector of texture samples.
    
    Parameters:
    
    textureSamples - The texture vector to be warped into an image. De-normalizes (and demaps) inside this method.
    
    m - A reference to an output image on matrix form. Resize of the matrix is done inside this method.
    
    deMap -
  - ModelEstimateTexDiff
```
public double ModelEstimateTexDiff(ModelSimpleImage image,
                                   CDVector c,
                                   CAAMShape estimate,
                                   CDVector diff,
                                   int similaritym)
```
    Wrapper to calculate the pixel difference from a model instance and an image.
    
    Parameters:
    
    image - model image
    
    c - parameter vector
    
    estimate - estimaed shape
    
    diff - difference vector
    
    similaritym - similarity measure type
    
    Returns:
    
    similarity measure
  - ModelEstimateTexDiff
```
public double ModelEstimateTexDiff(ModelSimpleImage image,
                                   CDVector c,
                                   CAAMShape estimate,
                                   CDVector diff,
                                   int similaritym,
                                   boolean useInterpolation)
```
    Calculates the pixel difference from a model instance and an image.
    
    Parameters:
    
    image - The image (input)
    
    c - Model parameters (in/output).
    
    estimate - The shape estimate (in/output).
    
    diff - The pixel difference vector (output) Resized inside.
    
    similaritym - Set the used similarity measure: 0 Non-normalised L_2 norm (default) 1 The "Mahalanobis" distance (texture samples are regarded independent to increase performance). 2 The Lorentzian error norm. 3 Absolute auto correlation of the residuals.
    
    Returns:
    
    The similarity measure.
  - NormalizeTexture
```
public void NormalizeTexture(CDVector texture)
```
    Normalizes a texture vector.
    
    Parameters:
    
    texture - Texture to be normalized.
  - OptimizeModel
```
public CAAMOptRes OptimizeModel(ModelSimpleImage image,
                                CAAMShape s,
                                CDVector c)
```
    Wrapper for model optimization.
    
    Parameters:
    
    image - search image
    
    s - init shape
    
    c - init model parameters
    
    Returns:
    
    optimization result
  - OptimizeModel
```
public CAAMOptRes OptimizeModel(ModelSimpleImage image,
                                CAAMShape s,
                                CDVector c,
                                int maxIterations,
                                java.util.Vector<CAAMOptState> pOptStates)
```
    Wrapper for model optimization
    
    Parameters:
    
    image - search image
    
    s - init shape
    
    c - init parameters
    
    maxIterations - max iterations
    
    pOptStates - optimization state
    
    Returns:
    
    optimization result
  - OptimizeModel
```
public CAAMOptRes OptimizeModel(ModelSimpleImage image,
                                CAAMShape s,
                                CDVector c,
                                int maxIterations,
                                java.util.Vector<CAAMOptState> pOptStates,
                                boolean disableDamping)
```
    Performs AAM optimization of a shape containing initial pose and a set of model parameters (c).
    
    Parameters:
    
    image - The image to search in.
    
    s - The initial shape (also containing the inital pose, thus; not a normalized shape). Actually only the pose of 's' is used (to align the reference shape as the initial shape). NOTE: The optimal shape is returned in 's' after execution.
    
    c - The initial model parameters. If this vector is empty, it is resized correctly and set equal to zero, thus the mean model. NOTE: The optimal model parameters are returned in 'c' after execution.
    
    maxIterations - The maximum iterations allowed.
    
    pOptStates - Optional parameter all convergence info can be returned in. See CAAMOptState.
    
    disableDamping - Disables the damping steps (default false).
    
    Returns:
    
    The results of the optimization in the form of a 'CAAMOptRes' instance.
  - OptimizeModelByFineTuning
```
public CAAMOptRes OptimizeModelByFineTuning(ModelSimpleImage image,
                                            CAAMShape s,
                                            CDVector c,
                                            int maxIterations,
                                            int similaritym,
                                            int optimizer)
```
    Perform general-purpose optimization of the AAM using simulated annealing, conjugate gradient, steepest descent, BGFS or pattern search.
    
    Parameters:
    
    image - The image beeing searched in.
    
    s - The inital shape pose.
    
    c - The initial model parameters.
    
    maxIterations - The maximum allowed number of iterations.
    
    similaritym - The used similarity measure for the optimization: 0 Non-normalized L_2 norm (default). 1 The "Mahalanobis" distance (texture samples are regarded independent to increase performance). 2 The Lorentzian error norm.
    
    optimizer - Sets the optimer to use: 1 Steepest Descent (default) 2 Conjugate Gradient 3 Quasi-Newton, BFGS 4 Pattern search 5 Simulated annealing
    
    Returns:
    
    The final fit.
  - ReadModel
```
public boolean ReadModel(java.lang.String filename)
```
    Reads the complete AAMModel from disk.
    
    Parameters:
    
    filename - Input filename without any extension. E.g. if the files on disk are 'model.txt' & 'model.amf' -> filename = 'model'
    
    Returns:
    
    true on success, false on file errors.
  - ReductionFactor
```
public int ReductionFactor()
```
    Returns the reduction factor of the training set that this model was
    
    Returns:
    
    model reduction
  - SampleShape
```
public int SampleShape(ModelSimpleImage image,
                       CAAMShape shape,
                       CDVector textureSamples)
```
    Wrapper to build a texture vector from an image and a shape.
    
    Parameters:
    
    image - model image
    
    shape - voi
    
    textureSamples - texture samples
    
    Returns:
    
    shape inside or outside the image
  - SampleShape
```
public int SampleShape(ModelSimpleImage image,
                       CAAMShape shape,
                       CDVector textureSamples,
                       boolean normalize)
```
    Wrapper to build a texture vector from an image and a shape.
    
    Parameters:
    
    image - model image
    
    shape - VIO
    
    textureSamples - texture samples
    
    normalize - normalization
    
    Returns:
    
    shape inside or outside the image
  - SampleShape
```
public int SampleShape(ModelSimpleImage image,
                       CAAMShape shape,
                       CDVector textureSamples,
                       boolean normalize,
                       boolean useInterpolation)
```
    Wrapper to build a texture vector from an image and a shape.
    
    Parameters:
    
    image - model image
    
    shape - VIO
    
    textureSamples - texture samples
    
    normalize - normalization
    
    useInterpolation - interpolation or not.
    
    Returns:
    
    shape inside or outside the image
  - SampleShape
```
public int SampleShape(ModelSimpleImage image,
                       CAAMShape shape,
                       CDVector textureSamples,
                       boolean normalize,
                       boolean useInterpolation,
                       boolean map)
```
    Builds a texture vector from an image and a shape.
    
    Parameters:
    
    image - The image to sample in.
    
    textureSamples - The normalized destination texture vector.
    
    shape - The shape to sample from (in image coordinates).
    
    normalize - Perform normalization after sampling. Default true.
    
    map - Perform mapping after sampling. Default true.
    
    Returns:
    
    The number of samples done (zero if the shape is outside the image).
  - ShapeInstance
```
public void ShapeInstance(CDVector c,
                          CAAMShape outShape)
```
    Generates a shape based on a set of model parameters.
    
    Parameters:
    
    c - Input model parameters.
    
    outShape - The generated shape (resizing are done inside this method).
  - TextureInstance
```
public void TextureInstance(CDVector c,
                            CDVector outTexture)
```
    Generates a texture based on a set of model parameters.
    
    Parameters:
    
    c - Input model parameters.
    
    outShape - The generated texture (resizing are done inside this method).
  - ShapePCAInstance
```
public void ShapePCAInstance(CDVector b_s,
                             CAAMShape outShape)
```
    Generates a shape based on a set of shape b-parameters.
    
    Parameters:
    
    b_s - Shape parameters
    
    outShape - Output shape (resized inside method).
  - ShapeTex2Combined
```
public void ShapeTex2Combined(CAAMShape shape,
                              CDVector texture,
                              CDVector c)
```
    Projects the shape and texture into c-space i.e. the combined model parameters.
    
    Parameters:
    
    shape - The input shape aligned to the (aligned) mean shape.
    
    texture - The corresponding normalized texture.
    
    c - The resulting model parameters.
  - ShapeTex2Param
```
public void ShapeTex2Param(CAAMShape shape,
                           CDVector texture,
                           CDVector b)
```
    Extract the b-parameters from a shape and corresponding texture by inverting the shape and texture pca projection. Assumes that the shape and texture PCA are done beforehand.
    
    Parameters:
    
    shape - The input shape aligned to the (aligned) mean shape.
    
    texture - The corresponding normalized texture.
    
    b - The resulting concatenated b vector.
  - ShapeTexParam2Combined
```
public void ShapeTexParam2Combined(CDVector b,
                                   CDVector c)
```
    Transforms the concatenated b-parameters into combined model parameters.
    
    Parameters:
    
    b - Concatenated shape (weighted) and texture parameters
    
    c - Combined model parameters (resized inside function).
    
    See Also:
    
    ShapeTex2Param(gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMShape,gov.nih.mipav.view.renderer.WildMagic.AAM.CDVector,gov.nih.mipav.view.renderer.WildMagic.AAM.CDVector)
  - WriteModel
```
public boolean WriteModel(java.lang.String filename)
```
    Write the AAM model to text file or binary file.
    
    Parameters:
    
    filename - file name
    
    Returns:
    
    success or not
  - WriteModel
```
public boolean WriteModel(java.lang.String filename,
                          boolean txt_only)
```
    Writes the complete AAMModel to disk as a .txt and an .amf file.
    
    Parameters:
    
    filename - Output filename without any extension.
    
    txt_only - If true binary model data is not written.
    
    Returns:
    
    true on success, false on file errors.
  - getNumberShapeParameters
```
public int getNumberShapeParameters()
```
    Get the the number of eigen values in PCA.
    
    Returns:
    
    number of eigen values in PCA
  - WriteVarianceMap
```
public void WriteVarianceMap(java.lang.String filename)
```
    Plots the variance of each pixel in the model over the training set into the mean shape and saves the image.
    
    Parameters:
    
    filename - Output image filename.
  - ReferenceShape
```
public final CAAMShape ReferenceShape()
```
    Returns the reference shape where all texture sampling and comparison should be done. The reference shape is defined as the mean shape size to mean size and moved to the fourth quadrant.
    
    Returns:
    
    The reference shape.
  - ShapeTexParam2Combined
```
public void ShapeTexParam2Combined(java.util.Vector<CDVector> bVectors,
                                   java.util.Vector<CDVector> cVectors)
```
    Converts a set of b-vectors to combined model parameters (c-vectors).
    
    Parameters:
    
    bVectors - The input b-vectors.
    
    cVectors - The output c-vectors.
  - assign
```
public CAAMModel assign(CAAMModel m)
```
    Assignment operator.
    
    Parameters:
    
    m - Object to copy from.
    
    Returns:
    
    This;
  - Shape2Combined
```
public void Shape2Combined(CAAMShape shape,
                           ModelSimpleImage image,
                           CDVector c)
```
    Projects a shape into a set of c parameters.
    
    Parameters:
    
    shape - The input shape (assumed to be in abs coordinates).
    
    image - The image where the shape is placed.
    
    c - The output combined model parameters.
  - Shape2Param
```
public void Shape2Param(CAAMShape shape,
                        CDVector b_s)
```
    Projects a shape into a set of shape parameters,
    
    Parameters:
    
    shape - The input shape (assumed to be in abs parameters).
    
    b - The output shape model parameters.
  - Combined2ShapeParam
```
public void Combined2ShapeParam(CDVector c,
                                CDVector b_s)
```
    Converts combined model parameters to shape parameters.
    
    Parameters:
    
    c - Combined model parameters.
    
    b_s - Output non-weighted shape parameters.
  - Combined2TexParam
```
public void Combined2TexParam(CDVector c,
                              CDVector b_g)
```
    Converts combined model parameters to texture parameters.
    
    Parameters:
    
    c - Combined model parameters.
    
    b_g - Output texture parameters.
  - ShapeTexParam2Combined
```
public void ShapeTexParam2Combined(CDVector b_s,
                                   CDVector b_g,
                                   CDVector c)
```
    Projects shape and texture parameters into the combined eigenspace.
    
    Parameters:
    
    b_s - Input shape parameters.
    
    b_g - Input texture parameters.
    
    c - Resulting combined model parameters.

Constructor	Description
`CAAMModel()`	Constructor.
`CAAMModel(CAAMModel m)`	Copy constructor.

Class CAAMModel

Field Summary

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMObject

Methods inherited from class java.lang.Object

Field Detail

m_pAnalyzeSynthesize

m_pReferenceFrame

m_pShapeBasis

m_pTextureBasis

m_ShapePCA

m_TexturePCA

m_CombinedPCA

m_mShape2PixelWeights

m_dAMFVersion

m_mQsEV

m_mQgEV

m_vMeanTexture

m_vMeanTextureOrg

m_sMeanAShape

m_mShapeInstance

m_mTextureInstance

m_vTextureVar

m_iTextureSamples

m_iNShapes

m_dMeanShapeSize

m_R_c

m_R_t

m_pTextureTF

m_iModelReduction

m_dAddExtents

m_bUseConvexHull

m_bUseTangentSpace

m_iLearningMethod

m_iShapeTrunc

m_iTextureTrunc

m_iCombinedTrunc

m_sCurrentAnalyzeId

m_dBuildTime

m_vPoseParameterUpdateConstraints

m_vShapeParameterConstraintsMean

m_vShapeParameterConstraintsSD

m_DisplacementPCA

Constructor Detail

CAAMModel

CAAMModel

Method Detail

Rc

Rt

Qg

Qs

ReferenceFrame

NBands

TextureTF

NTextureSamples

IsConvexHullUsed

AddExtents

MeanShape

MeanTexture

Shape2PixelWeights

ShapePCA

TexturePCA

ShapeBasis

TextureBasis

CombinedPCA

ModelReduction

MeanShapeSize

dispose

ApproxExample

SetPoseParameterUpdateConstraints

SetShapeParameterUpdateConstraints

ConstrainSearchParameters

EstimatePose

ModelImage

ModelImage

ModelImageEx

ShapeFreeImage

ShapeFreeImage

ShapeFreeImage