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

```
public class CAAMInitializeStegmann
extends CAAMInitialize
```
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 $ Concrete class implementation of a simple initialization method.

Author:

Ruida Cheng

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`(package private) class`	`CAAMInitializeStegmann.CAAMInitCandidates`	Initialization candidate containiner.
`(package private) class`	`CAAMInitializeStegmann.CAAMInitEntry`	Container for initialization results.

Field Summary

Fields
Modifier and Type	Field	Description
`private double`	`m_dXmax`	search range, currently not used.
`private double`	`m_dXmin`	search range, currently not used.
`private double`	`m_dXspacing`	stepping length, currently not used.
`private double`	`m_dYmax`	search range, currently not used.
`private double`	`m_dYmin`	search range, currently not used.
`private double`	`m_dYspacing`	stepping length, currently not used.
`private int`	`m_nCandidates`	number of candidates.
`private int`	`m_nIterations1stPass`	number of iterations.
`private int`	`m_nIterations2ndPass`	number of iterations.
`CAAMShape`	`m_sCentredRefshape`	Centered reference shape.
`private java.util.Vector<CDVector>`	`m_vModelParameterSteps`	Model parameters changes steps.
`private CDVector`	`m_vRotationSteps`	model rotation steps.
`private CDVector`	`m_vScaleSteps`	model scale steps.
`poly`	`meanShapePolygon`	mean shape polygon.

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

Constructor Summary

Constructors
Constructor	Description
`CAAMInitializeStegmann(CAAMModel aammodel)`	Constructor.
`CAAMInitializeStegmann(CAAMModel aammodel, ModelImage targetImageSlice, ModelImage sampleImage, CAAMShape sampleShape)`	AAM initialization from given aam model, target imge, and sample image and VOI

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`counterClockwise(float[] x, float[] y, float[] z, int nPts)`	Change the given VOI to counter clock wise order.
`int`	`Initialize(ModelSimpleImage image, CAAMShape s, CDVector c)`	Performs a somewhat brute force initialization of an AAM.
`int`	`Initialize(ModelSimpleImage image, CAAMShape s, CDVector c, ModelImage targetImageSlice)`	Performs a somewhat brute force initialization of an AAM.
`static void`	`pause()`	Pause function for testing and debugging purpose.
`void`	`SetIterations1stPass(int i)`	Sets the number of iterations in the coarse search.
`void`	`SetIterations2ndPass(int i)`	Sets the number of iterations in the refinement search.
`void`	`SetModelParameterSteps(java.util.Vector<CDVector> av)`	Sets the number of model parameter steps.
`void`	`SetNCandidates(int i)`	Set the number of candidates
`void`	`SetRotationSteps(CDVector v)`	Sets the number of rotation steps.
`void`	`SetScaleSteps(CDVector v)`	Sets the number of scale steps.
`void`	`SetXYSpacing(double xs, double ys)`	Sets the spacing of the search grid in x and y.

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_sCentredRefshape
```
public CAAMShape m_sCentredRefshape
```
    Centered reference shape.
  - m_vScaleSteps
```
private CDVector m_vScaleSteps
```
    model scale steps.
  - m_vRotationSteps
```
private CDVector m_vRotationSteps
```
    model rotation steps.
  - m_vModelParameterSteps
```
private java.util.Vector<CDVector> m_vModelParameterSteps
```
    Model parameters changes steps.
  - m_dXspacing
```
private double m_dXspacing
```
    stepping length, currently not used.
  - m_dYspacing
```
private double m_dYspacing
```
    stepping length, currently not used.
  - m_dXmin
```
private double m_dXmin
```
    search range, currently not used.
  - m_dXmax
```
private double m_dXmax
```
    search range, currently not used.
  - m_dYmin
```
private double m_dYmin
```
    search range, currently not used.
  - m_dYmax
```
private double m_dYmax
```
    search range, currently not used.
  - m_nIterations1stPass
```
private int m_nIterations1stPass
```
    number of iterations.
  - m_nIterations2ndPass
```
private int m_nIterations2ndPass
```
    number of iterations.
  - m_nCandidates
```
private int m_nCandidates
```
    number of candidates.
  - meanShapePolygon
```
public poly meanShapePolygon
```
    mean shape polygon.
- Constructor Detail
  - CAAMInitializeStegmann
```
public CAAMInitializeStegmann(CAAMModel aammodel)
```
    Constructor.
    
    Parameters:
    
    aammodel - The model to initialize.
  - CAAMInitializeStegmann
```
public CAAMInitializeStegmann(CAAMModel aammodel,
                              ModelImage targetImageSlice,
                              ModelImage sampleImage,
                              CAAMShape sampleShape)
```
    AAM initialization from given aam model, target imge, and sample image and VOI
    
    Parameters:
    
    aammodel - aam model
    
    targetImageSlice - target image
    
    sampleImage - sample image
    
    sampleShape - sample VOI
- Method Detail
  - pause
```
public static void pause()
```
    Pause function for testing and debugging purpose.
  - counterClockwise
```
private void counterClockwise(float[] x,
                              float[] y,
                              float[] z,
                              int nPts)
```
    Change the given VOI to counter clock wise order.
    
    Parameters:
    
    x - VOI x coordinate array
    
    y - VOI y coordinate array
    
    z - VOI z coordinate array
    
    nPts - number of VOI points
  - Initialize
```
public int Initialize(ModelSimpleImage image,
                      CAAMShape s,
                      CDVector c)
```
    Performs a somewhat brute force initialization of an AAM.
    
    Specified by:
    
    Initialize in class CAAMInitialize
    
    Parameters:
    
    image - The image beeing searched in.
    
    s - The output shape after initialization.
    
    c - The output model parameters after initialization.
    
    Returns:
    
    0 on succes, non-zero on errors.
  - Initialize
```
public int Initialize(ModelSimpleImage image,
                      CAAMShape s,
                      CDVector c,
                      ModelImage targetImageSlice)
```
    Performs a somewhat brute force initialization of an AAM.
    
    Parameters:
    
    image - The image being searched in.
    
    s - The output shape after initialization.
    
    c - The output model parameters after initialization.
    
    Returns:
    
    0 on succes, non-zero on errors.
  - SetNCandidates
```
public void SetNCandidates(int i)
```
    Set the number of candidates
    
    Parameters:
    
    i - candidiate index
  - SetIterations1stPass
```
public void SetIterations1stPass(int i)
```
    Sets the number of iterations in the coarse search.
    
    Parameters:
    
    i - iteration number
  - SetIterations2ndPass
```
public void SetIterations2ndPass(int i)
```
    Sets the number of iterations in the refinement search.
    
    Parameters:
    
    i - number of iterations
  - SetXYSpacing
```
public void SetXYSpacing(double xs,
                         double ys)
```
    Sets the spacing of the search grid in x and y.
    
    Parameters:
    
    xs - x coordinate step
    
    ys - y coordinate step
  - SetScaleSteps
```
public void SetScaleSteps(CDVector v)
```
    Sets the number of scale steps.
    
    Parameters:
    
    v - scale vector
  - SetRotationSteps
```
public void SetRotationSteps(CDVector v)
```
    Sets the number of rotation steps.
    
    Parameters:
    
    v - rotation vector
  - SetModelParameterSteps
```
public void SetModelParameterSteps(java.util.Vector<CDVector> av)
```
    Sets the number of model parameter steps.
    
    Parameters:
    
    av - parameters change vector

Class CAAMInitializeStegmann

Nested Class Summary

Field Summary

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

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_sCentredRefshape

m_vScaleSteps

m_vRotationSteps

m_vModelParameterSteps

m_dXspacing

m_dYspacing

m_dXmin

m_dXmax

m_dYmin

m_dYmax

m_nIterations1stPass

m_nIterations2ndPass

m_nCandidates

meanShapePolygon

Constructor Detail

CAAMInitializeStegmann

CAAMInitializeStegmann

Method Detail

pause

counterClockwise

Initialize

Initialize

SetNCandidates

SetIterations1stPass

SetIterations2ndPass

SetXYSpacing

SetScaleSteps

SetRotationSteps

SetModelParameterSteps