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

```
public class CAAMModelSeq
extends CAAMModel
```
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 $ AAM sequence object. This is a generalization of a multi-scale model.

Author:

Ruida Cheng

Field Summary

Fields
Modifier and Type Field Description

protected java.util.Vector<java.lang.String> m_vACF
AAM configuration vector.

protected java.util.Vector<CAAMModel> m_vModels
model vector.
- Fields inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMModel
  m_bUseConvexHull, m_bUseTangentSpace, m_CombinedPCA, m_dAddExtents, m_dAMFVersion, m_dBuildTime, m_DisplacementPCA, m_dMeanShapeSize, m_iCombinedTrunc, m_iLearningMethod, m_iModelReduction, m_iNShapes, m_iShapeTrunc, m_iTextureSamples, m_iTextureTrunc, m_mQgEV, m_mQsEV, m_mShape2PixelWeights, m_mShapeInstance, m_mTextureInstance, m_pAnalyzeSynthesize, m_pReferenceFrame, m_pShapeBasis, m_pTextureBasis, m_pTextureTF, m_R_c, m_R_t, m_sCurrentAnalyzeId, m_ShapePCA, m_sMeanAShape, m_TexturePCA, m_vMeanTexture, m_vMeanTextureOrg, m_vPoseParameterUpdateConstraints, m_vShapeParameterConstraintsMean, m_vShapeParameterConstraintsSD, m_vTextureVar

Constructor Summary

Constructors
Constructor Description

CAAMModelSeq()
Default multi-scale constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`BuildFromSACF(java.lang.String SACF, java.lang.String inDir)`	Wrapper to build the sequential model from the given aam configuration files.
`void`	`BuildFromSACF(java.lang.String SACF, java.lang.String inDir, int excludeShape)`	Driver method for model generation.
`void`	`BuildFromSACF(java.lang.String SACF, java.util.Vector<java.lang.String> asfFiles, int excludeShape)`	Diver method for model generation.
`void`	`dispose()`	dispose memory
`CAAMModel`	`FinalModel()`	Get the final model
`CAAMModel`	`Model(int i)`	Get the model at level i.
`int`	`ModelScale(int i)`
`int`	`NModels()`	Get the number of models.
`boolean`	`ReadModels(java.lang.String samf)`	Reads the complete AAMModel from disk.
`void`	`ScaleShape2Final(int model, CAAMShape shape)`	Scale a shape defined in 'model' coordinates to 'FinalModel' coordinates.
`void`	`ScaleShape2Model(int model, CAAMShape shape)`	Scale a shape defined in 'FinalModel' coordinates to 'model' coordinates .
`boolean`	`WriteModels(java.lang.String filename)`	Wrapper to write the sequence AAM to disk
`boolean`	`WriteModels(java.lang.String filename, boolean txt_only)`	Writes the sequence AAM to disk as a set of .txt and .amf files.

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMModel
AddExtents, ApproxExample, assign, Combined2ShapeParam, Combined2TexParam, CombinedPCA, ConstrainSearchParameters, EstimatePose, getNumberShapeParameters, IsConvexHullUsed, MeanShape, MeanShapeSize, MeanTexture, ModelEstimateTexDiff, ModelEstimateTexDiff, ModelImage, ModelImage, ModelImageEx, ModelReduction, NBands, NormalizeTexture, NTextureSamples, OptimizeModel, OptimizeModel, OptimizeModel, OptimizeModelByFineTuning, Qg, Qs, Rc, ReadModel, ReductionFactor, ReferenceFrame, ReferenceShape, Rt, SampleShape, SampleShape, SampleShape, SampleShape, SetPoseParameterUpdateConstraints, SetShapeParameterUpdateConstraints, Shape2Combined, Shape2Param, Shape2PixelWeights, ShapeBasis, ShapeFreeImage, ShapeFreeImage, ShapeFreeImage, ShapeInstance, ShapePCA, ShapePCAInstance, ShapeTex2Combined, ShapeTex2Param, ShapeTexParam2Combined, ShapeTexParam2Combined, ShapeTexParam2Combined, TextureBasis, TextureInstance, TexturePCA, TextureTF, WriteModel, WriteModel, WriteVarianceMap

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_vModels
```
protected java.util.Vector<CAAMModel> m_vModels
```
    model vector.
  - m_vACF
```
protected java.util.Vector<java.lang.String> m_vACF
```
    AAM configuration vector.
- Constructor Detail
  - CAAMModelSeq
```
public CAAMModelSeq()
```
    Default multi-scale constructor.
- Method Detail
  - Model
```
public final CAAMModel Model(int i)
```
    Get the model at level i.
    
    Parameters:
    
    i - level
    
    Returns:
    
    corresponding model in model vetor
  - NModels
```
public final int NModels()
```
    Get the number of models.
    
    Returns:
    
    number of models
  - FinalModel
```
public final CAAMModel FinalModel()
```
    Get the final model
    
    Returns:
    
    last element
  - ModelScale
```
public int ModelScale(int i)
```
  - dispose
```
public void dispose()
```
    dispose memory
    
    Overrides:
    
    dispose in class CAAMModel
  - BuildFromSACF
```
public void BuildFromSACF(java.lang.String SACF,
                          java.lang.String inDir)
```
    Wrapper to build the sequential model from the given aam configuration files.
    
    Parameters:
    
    SACF - aam configuration sequential file
    
    inDir - file dir
  - BuildFromSACF
```
public void BuildFromSACF(java.lang.String SACF,
                          java.lang.String inDir,
                          int excludeShape)
```
    Driver method for model generation. This method automates the model generation as much as possible by using the various class methods for all the sequences in the task of producing a model.
    
    Parameters:
    
    SACF - Filename of a sequence ACF, which is a file containing a list of acfs, one per line. E.g. scale4_convex_hull.acf scale4_whiskers.acf scale4.acf scale2.acf scale1.acf
    
    inDir - Input directory where annotations (.asf) resides.
    
    excludeShape - Excludes one shape number 'excludeShape' from the input directory. Default -1, i.e. no shapes are removed. Used to perform leave-one-out testing.
  - BuildFromSACF
```
public void BuildFromSACF(java.lang.String SACF,
                          java.util.Vector<java.lang.String> asfFiles,
                          int excludeShape)
```
    Diver method for model generation. This method automates the model generation as much as possible by using the various class methods for all the sequences in the task of producing a model.
    
    Parameters:
    
    SACF - Filename of a sequence ACF, which is a file containing a list of acfs, one per line. E.g. scale4_convex_hull.acf scale4_whiskers.acf scale4.acf scale2.acf scale1.acf
    
    asfFiles - Vector of asf filenames.
    
    excludeShape - Excludes one shape number 'excludeShape' from the input directory. Default -1, i.e. no shapes are removed. Used to perform leave-one-out testing.
  - WriteModels
```
public boolean WriteModels(java.lang.String filename)
```
    Wrapper to write the sequence AAM to disk
    
    Parameters:
    
    filename - file name
    
    Returns:
    
    success or not
  - WriteModels
```
public boolean WriteModels(java.lang.String filename,
                           boolean txt_only)
```
    Writes the sequence AAM to disk as a set of .txt and .amf files. Filenames are determined from the ACF file names.
    
    Parameters:
    
    filename - Filename of the output .samf-file.
    
    txt_only - If true, binary model data is not written.
    
    Returns:
    
    true on success, false on file errors.
  - ReadModels
```
public boolean ReadModels(java.lang.String samf)
```
    Reads the complete AAMModel from disk.
    
    Parameters:
    
    filename - Input filename (.samf).
    
    Returns:
    
    true on success, false on file errors.
  - ScaleShape2Model
```
public void ScaleShape2Model(int model,
                             CAAMShape shape)
```
    Scale a shape defined in 'FinalModel' coordinates to 'model' coordinates .
    
    Parameters:
    
    model - The model the input shape are scaled to.
    
    shape - Input shape, which going to be scaled.
  - ScaleShape2Final
```
public void ScaleShape2Final(int model,
                             CAAMShape shape)
```
    Scale a shape defined in 'model' coordinates to 'FinalModel' coordinates.
    
    Parameters:
    
    model - The model the input shape are scaled from.
    
    shape - Input shape, which going to be scaled.

Modifier and Type	Field	Description
`protected java.util.Vector<java.lang.String>`	`m_vACF`	AAM configuration vector.
`protected java.util.Vector<CAAMModel>`	`m_vModels`	model vector.

Class CAAMModelSeq

Field Summary

Fields inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMModel

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Detail

m_vModels

m_vACF

Constructor Detail

CAAMModelSeq

Method Detail

Model

NModels

FinalModel

ModelScale

dispose

BuildFromSACF

BuildFromSACF

BuildFromSACF

WriteModels

WriteModels

ReadModels

ScaleShape2Model

ScaleShape2Final