java.lang.Object
- gov.nih.mipav.view.renderer.WildMagic.AAM.CVisDVector
- - gov.nih.mipav.view.renderer.WildMagic.AAM.CDVector
  - - gov.nih.mipav.view.renderer.WildMagic.AAM.CAAMShape

```
public class CAAMShape
extends CDVector
```
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 $ Shape container. This class act as a container for a shape. Essentially it's just a set of 2D points stored in a vector in the format xxxyyy.

Author:

Ruida Cheng

Field Summary

Fields
Modifier and Type	Field	Description
`private boolean`	`m_bAbsPointCoordinates`	Indicates if the point coordinates is in relative or absolute format.
`private int`	`m_iNbPoints`	The number of points.
`private double[]`	`m_pData`	un-safe pointer to the first point data element.
`private java.lang.String`	`m_szASFVer`	Current ASF version number.
`private java.lang.String`	`m_szHostImage`	Optional 'host image' filename including full path.
`private java.util.Vector<CAAMPointInfo>`	`m_vPointAux`	Auxillary point data.
`private java.util.Vector<java.lang.Float>`	`m_vUser1`	User-defined field 1.
`private java.util.Vector<java.lang.Float>`	`m_vUser2`	User-defined field 2.
`private java.util.Vector<java.lang.Float>`	`m_vUser3`	User-defined field 3.
`private ModelImage`	`myHostImage`	host image.

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

Fields inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CVisDVector
m_data, m_fExternalStorage, m_length

Constructor Summary

Constructors
Constructor	Description
`CAAMShape()`	Default constructor.
`CAAMShape(int nbPoints)`	Constructs a shape with 'nbPoints' points.
`CAAMShape(CAAMShape s)`	Copy contructor.
`CAAMShape(CDVector v)`	Constructs a shape from a vector.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`Abs2Rel(int image_width, int image_height)`	Converts shape coordinates from absolute to relative.
`void`	`Abs2Rel(java.lang.String hostImagePath)`	Converts shape coordinates from absolute to relative by using the hostimage.
`CAAMShape`	`add(CVisDVector v)`	Plus operator.
`void`	`AddInterior(int interations)`	Add articifial interior points to the shape by making a Delaunay triangulation and adding the centroid of each triangle.
`void`	`AddPath(CAAMShape shape, CAAMPointInfo pointType)`	Adds a path to the shape.
`void`	`AddShapeExtends(int nPixels)`	Adds an extra outer path on each outer path in the distance of 'nPixels' along the point normal.
`double`	`AlignTo(CAAMShape ref)`	Wrapper to align this to ref.
`double`	`AlignTo(CAAMShape ref, double[] pTheta)`	Aligns this to 'ref' with respect to pose.
`void`	`AlignTransformation(CAAMShape ref, double[] scale, double[] theta, CAAMPoint t)`	Returns the transformation that aligns this to 'ref' with respect to pose.
`void`	`AllocateUserFields()`	Allocates room for the three user defined fields.
`double`	`Area()`
`double`	`Area(boolean use_covex_hull)`	Returns the total area of the shape (with holes excluded).
`CDVector`	`assign(double value)`	Assignment operator (double).
`CAAMShape`	`assign(CAAMShape s)`	Assignment operator (CAAMShape).
`CDVector`	`assign(CVisDVector vIn)`	Assignment operator (CAAMShape).
`CAAMShape`	`CalcConvexHull()`	Calculates the convex hull of each path in the shape.
`CAAMPoint`	`COG()`	Calculates the center of gravity of the shape (actually it's the center of the centroid).
`void`	`COG(double[] x, double[] y)`	Calculates the center of gravity of the shape (actually it's the center of the centroid).
`boolean`	`ConsistencyCheck()`	Tests if any interior points has gone outside outer path of the shape.
`boolean`	`ConvertASFfromVOI(VOIBase v)`	Convert ASF shape from VOI
`private void`	`CopyData(CAAMShape s)`	Copies all data from a shape to this.
`int`	`DEC_TO_ZERO(int a)`	Convert deciam number to 0
`void`	`Displace(CDVector poseVec)`	Displaces the shape around it's center of gravity using a displacement vector.
`void`	`dispose()`	dispose memory
`void`	`Expand(int nPixels)`	Expands the shape by moving each model point 'nPixels' perperdicular to the shape contour (that is: along the model point normal).
`CAAMShape`	`ExtractPath(int startPosition)`	Extracts one path from a shape into a new shape.
`void`	`FromFile(java.io.DataInputStream fh)`	Reads a shape from a file.
`boolean`	`generateVOImesh(ModelImage targetImageSlice)`	From the current shape, generate the corresponding triagnle meshes view.
`boolean`	`generateVOIs(ModelImage targetImageSlice)`	ASF writer version 0.90.
`ModelImage`	`getHostImage()`	Get host image.
`ModelSimpleImage`	`GetHostImage(ModelImage src, int rfactor)`	Retrives the image connected to the shape.
`ModelSimpleImage`	`GetHostImage(ModelSimpleImage dest, java.lang.String path, int rfactor)`	Retrives the image connected to the shape.
`java.util.Vector<java.lang.Integer>`	`GetPaths()`	Extracts the starting positions of each path in the shape by a simple linear search.
`CAAMPoint`	`GetPoint(int i)`	Returns the i'th point.
`int`	`GetPoint(int i, double[] x, double[] y)`	Returns the i'th point.
`void`	`GetPointUS(int i, double[] x, double[] y)`	un-safe (and dirty) since it depends on assumptions regarding the
`double`	`GetRotation(CAAMShape ref)`	Returns the rotation between ref and this (in radians).
`double`	`Height()`	Shape height
`java.lang.String`	`HostImage()`	Host image (if any).
`double`	`initAlignTo(CAAMShape ref)`	Init ref to this.
`double`	`initAlignTo(CAAMShape ref, double[] pTheta)`	Aligns this to 'ref' with respect to pose.
`boolean`	`IsAbs()`	Returns true if the shape is in absolute coordinates.
`boolean`	`IsConvex()`	Tests if the shap is convex w.r.t. each path.
`boolean`	`IsInside(CAAMPoint p)`	Wrapper to check is point p is inside the shape
`boolean`	`IsInside(CAAMPoint p, boolean bBoundTest)`	Tests if the point 'p' belongs to the shape.
`boolean`	`IsInsidePath(CAAMPoint p, int path_start)`	Tests if the point 'p' is inside the path starting at position 'path_start'.
`void`	`MakeBorderShape(int size)`	Converts a one path shape into a border shape by adding two symmetric borders: an inside (a hole) and an outside border.
`double`	`MaxX()`	Find the maximum x component of the shape.
`double`	`MaxY()`	Find the maximum y component of the shape.
`double`	`MinX()`	Find the maximum x component of the shape.
`double`	`MinY()`	Find the minimum y component of the shape.
`void`	`Normal(int i, CAAMPoint p1, CAAMPoint p2, double dist)`	Finds the normal to the i'th point on the shape.
`void`	`NormalDisplacement(int i, double dist)`	Displaces the i-th point along the normal.
`double`	`Normalize()`	Normalizes the shape by translating it's center of gravity to origo and scale by the reciprocal of the 2-norm.
`int`	`NPoints()`	The number of shape points.
`static void`	`Param2PoseVec(double scale, double theta, double tx, double ty, CDVector poseVec)`	Converts pose parameters: scale, theta, tx, ty to a pose vector.
`int`	`PathLen(int startPosition)`	Returns the length of a path.
`java.util.Vector<CAAMPointInfo>`	`PointAux()`	Returns the complete point aux vector of the shape.
`static void`	`PoseVec2Param(CDVector poseVec, double[] scale, double[] theta, double[] tx, double[] ty)`	Converts a pose vector to pose parameters: scale, theta, tx, ty.
`boolean`	`ReadASF(java.lang.String filename)`	Reads an ver. 0.90 .asf into relative coordinates.
`boolean`	`ReadASF0_90(java.lang.String filename)`	Reads an ver. 0.90 .asf into relative coordinates.
`boolean`	`ReadASFfromVOI(ModelImage image)`	Generate ASF shape from given VOI
`boolean`	`ReadASFfromVOI_init(ModelImage image)`
`void`	`Rel2Abs(int image_width, int image_height)`	Converts shape coordinates from relative to absolute.
`void`	`Rel2Abs(java.lang.String hostImagePath)`
`void`	`RemovePoint(int i)`	Removes the i-th point from the shape.
`void`	`Resize(int length, double[] storage)`	Change number of shape points in the shape.
`void`	`ReversePointOrder()`	Reverses the point point ordering.
`void`	`Rotate(double theta)`	rotate shape with given theta angle
`void`	`Rotate(double theta, boolean aroundCOG)`	Rotates the shape.
`void`	`Scale(double s)`	Scale the shape
`void`	`Scale(double s, boolean aroundCOG)`	Scales the shape.
`void`	`SetClosedPathConnectivity()`	Sets all point to be connected in one closed path.
`void`	`SetHostImage(java.lang.String hostImageFilename)`	Returns the host image (if any).
`int`	`SetPoint(int i, double x, double y)`	Overwrites the i'th point.
`int`	`SetPoint(int i, CAAMPoint p)`	Overwrites the i'th point.
`void`	`setPointAux(int index, CAAMPointInfo value)`	Set specific point info
`void`	`setPointAux(java.util.Vector<CAAMPointInfo> value)`	set point info vector
`void`	`SetPointInfoFlagsInPath(int startPosition, int flags)`	Sets all flags in one path to the same value.
`double`	`ShapeSize()`	Returns the 2-norm of this shape centralized.
`CAAMShape`	`sub(CVisDVector v)`	Minus operator.
`void`	`ToFile(java.io.DataOutputStream fh)`	Write the shape to a binary file.
`void`	`Translate(double x, double y)`	Translates the shape.
`void`	`Translate(CAAMPoint p)`	Translates the shape.
`java.util.Vector<java.lang.Float>`	`UserField(int field_nb)`	Returns the reference of the user defined field vector number 'field_nb'.
`double`	`Width()`	Shape width.
`boolean`	`WriteASF(java.lang.String filename, int image_width, int image_height)`	Writes the shape to a ASF file.
`boolean`	`WriteASF0_90(java.lang.String filename, int image_width, int image_height)`	ASF writer version 0.90.

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CDVector
__dbl_cmp_asc, __dbl_cmp_des, Abs, AlignTo, AlignTo, assign, assign, AutoCorrelation, Ceil, Clamp, CrossProduct, ElementDivide, ElementMultiply, Eq, Eq, Floor, FromFile, Ge, Ge, Gt, Gt, Le, Le, Linspace, Log, Lt, Lt, Max, Mean, Median, Min, Min, Ne, Ne, Norm1, Norm2, Normalize2, NormInf, Pow, quick_select, Rand, Rand, Range, Reverse, Round, Shuffle, Skewness, Sort, Sort, Sqr, Sqrt, Std, Sum, ToFile, ToMatlab, ToMatrix, ToString, Trim, TrimmedMean, TrimmedStd, TrimmedVar, Var, Var, VecCat

Methods inherited from class gov.nih.mipav.view.renderer.WildMagic.AAM.CVisDVector
add_into, div, div_into, EqDiff, EqProd, EqSum, equals, FreeBuffer, get, Length, less_than, mult, mult, mult_into, neg, not_equals, Resize, Resize, set, SetSize, SetSize, sub_into, VisCrossProduct, VisCrossProduct

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

- Field Detail
  - m_vPointAux
```
private java.util.Vector<CAAMPointInfo> m_vPointAux
```
    Auxillary point data.
  - m_vUser1
```
private java.util.Vector<java.lang.Float> m_vUser1
```
    User-defined field 1.
  - m_vUser2
```
private java.util.Vector<java.lang.Float> m_vUser2
```
    User-defined field 2.
  - m_vUser3
```
private java.util.Vector<java.lang.Float> m_vUser3
```
    User-defined field 3.
  - m_szASFVer
```
private java.lang.String m_szASFVer
```
    Current ASF version number.
  - m_iNbPoints
```
private int m_iNbPoints
```
    The number of points.
  - m_bAbsPointCoordinates
```
private boolean m_bAbsPointCoordinates
```
    Indicates if the point coordinates is in relative or absolute format.
  - m_szHostImage
```
private java.lang.String m_szHostImage
```
    Optional 'host image' filename including full path.
  - myHostImage
```
private ModelImage myHostImage
```
    host image.
  - m_pData
```
private double[] m_pData
```
    un-safe pointer to the first point data element.
- Constructor Detail
  - CAAMShape
```
public CAAMShape()
```
    Default constructor. Defaults to absolute shape coordinates and sets the number of points to zero. Notice that the user defined fields is *not* allocated by default. In order to preserved memory the user must to this explicitly by using AllocateUserFields();
  - CAAMShape
```
public CAAMShape(int nbPoints)
```
    Constructs a shape with 'nbPoints' points. Defaults to absolute point coordinates and single closed path connectivity.
    
    Parameters:
    
    nbPoints - The number of points the shape should contain.
    
    See Also:
    
    SetClosedPathConnectivity()
  - CAAMShape
```
public CAAMShape(CDVector v)
```
    Constructs a shape from a vector. Defaults to absolute point coordinates and single closed path connectivity.
    
    Parameters:
    
    v - The input vector.
    
    See Also:
    
    SetClosedPathConnectivity()
  - CAAMShape
```
public CAAMShape(CAAMShape s)
```
    Copy contructor.
    
    Parameters:
    
    s - The input shape.
- Method Detail
  - ToFile
```
public void ToFile(java.io.DataOutputStream fh)
```
    Write the shape to a binary file.
    
    Overrides:
    
    ToFile in class CDVector
    
    Parameters:
    
    sFilename - Destination filename.
  - FromFile
```
public void FromFile(java.io.DataInputStream fh)
```
    Reads a shape from a file.
    
    Overrides:
    
    FromFile in class CDVector
    
    Parameters:
    
    fh - An open file handle.
  - SetClosedPathConnectivity
```
public void SetClosedPathConnectivity()
```
    Sets all point to be connected in one closed path. Manipulates the aux point info such that the shape points is interpreted as one closed outer path defined clock-wise with repect to it's normals.
  - assign
```
public CDVector assign(double value)
```
    Assignment operator (double). Sets all x and y compoments of a shape equal to a double. [Actually only used when calculating a mean shape -- since we want to accumulate in an empty shape].
    
    Overrides:
    
    assign in class CDVector
    
    Parameters:
    
    value - The value to set all shape points to.
    
    Returns:
    
    This.
  - assign
```
public CAAMShape assign(CAAMShape s)
```
    Assignment operator (CAAMShape). Set one shape equal another.
    
    Parameters:
    
    s - The shape to copy.
  - CopyData
```
private void CopyData(CAAMShape s)
```
    Copies all data from a shape to this. Called from the assignment operator.
    
    Parameters:
    
    s - Shape to copy data from.
  - assign
```
public CDVector assign(CVisDVector vIn)
```
    Assignment operator (CAAMShape). Set the shape to be equal an xxx-yyy formatted vector. NOTE: this method does not manipulate any connectivity (i.e. point aux) info. So, if the shape beforehand was empty one should call SetClosedPathConnectivity() afterwards this call to obtain sensible point aux info.
    
    Overrides:
    
    assign in class CDVector
    
    Parameters:
    
    vIn - xxx-yyy formatted vector.
    
    Returns:
    
    This.
  - dispose
```
public void dispose()
```
    dispose memory
    
    Overrides:
    
    dispose in class CVisDVector
  - Rotate
```
public void Rotate(double theta)
```
    rotate shape with given theta angle
    
    Parameters:
    
    theta -
  - Rotate
```
public void Rotate(double theta,
                   boolean aroundCOG)
```
    Rotates the shape. Rotates the shape 'theta' radians.
    
    Parameters:
    
    theta - Rotation angle in radians.
    
    aroundCOG - If true the rotation is being done around the cog of the shape instead of around the global center.
  - Translate
```
public void Translate(CAAMPoint p)
```
    Translates the shape.
    
    Parameters:
    
    p - The offset to translate.
  - Translate
```
public void Translate(double x,
                      double y)
```
    Translates the shape.
    
    Parameters:
    
    x - X-translation.
    
    y - Y-translation.
  - ShapeSize
```
public double ShapeSize()
```
    Returns the 2-norm of this shape centralized.
    
    Returns:
    
    The 2-norm.
  - MinX
```
public double MinX()
```
    Find the maximum x component of the shape.
    
    Returns:
    
    The x-maximum.
  - MaxX
```
public double MaxX()
```
    Find the maximum x component of the shape.
    
    Returns:
    
    The x-maximum.
  - MinY
```
public double MinY()
```
    Find the minimum y component of the shape.
    
    Returns:
    
    The y-minimum.
  - MaxY
```
public double MaxY()
```
    Find the maximum y component of the shape.
    
    Returns:
    
    The y-maximum.
  - Scale
```
public void Scale(double s)
```
    Scale the shape
    
    Parameters:
    
    s -
  - Scale
```
public void Scale(double s,
                  boolean aroundCOG)
```
    Scales the shape.
    
    Parameters:
    
    s - Scale factor.
    
    aroundCOG - If true the scale is being done around the cog of the shape instead of around the global center.
  - COG
```
public CAAMPoint COG()
```
    Calculates the center of gravity of the shape (actually it's the center of the centroid).
    
    Parameters:
    
    p - cog output.
  - COG
```
public void COG(double[] x,
                double[] y)
```
    Calculates the center of gravity of the shape (actually it's the center of the centroid).
    
    Parameters:
    
    x - X cog output.
    
    y - X cog output.
  - Normalize
```
public double Normalize()
```
    Normalizes the shape by translating it's center of gravity to origo and scale by the reciprocal of the 2-norm.
    
    Returns:
    
    The 2-norm of the shape seen as a 2*nbPoint vector after the translation to orig.
  - SetPoint
```
public int SetPoint(int i,
                    double x,
                    double y)
```
    Overwrites the i'th point.
    
    Returns:
    
    Zero.
  - SetPoint
```
public int SetPoint(int i,
                    CAAMPoint p)
```
    Overwrites the i'th point. If the point doesn't exists, non-zero is returned.
    
    Returns:
    
    Zero on success, non-zero if the point doesn't exists.
  - GetPoint
```
public int GetPoint(int i,
                    double[] x,
                    double[] y)
```
    Returns the i'th point.
    
    Returns:
    
    Zero.
  - GetPoint
```
public CAAMPoint GetPoint(int i)
```
    Returns the i'th point.
    
    Returns:
    
    The i'th point.
  - Resize
```
public void Resize(int length,
                   double[] storage)
```
    Change number of shape points in the shape. Note: Destroys *all* current point data and point info data.
    
    Overrides:
    
    Resize in class CVisDVector
    
    Parameters:
    
    length -
    
    storage -
  - AlignTransformation
```
public void AlignTransformation(CAAMShape ref,
                                double[] scale,
                                double[] theta,
                                CAAMPoint t)
```
    Returns the transformation that aligns this to 'ref' with respect to pose.
    
    Parameters:
    
    ref - The reference shape.
  - initAlignTo
```
public double initAlignTo(CAAMShape ref)
```
    Init ref to this.
    
    Parameters:
    
    ref -
    
    Returns:
    
    2-norm of the shape
  - initAlignTo
```
public double initAlignTo(CAAMShape ref,
                          double[] pTheta)
```
    Aligns this to 'ref' with respect to pose.
    
    Parameters:
    
    ref - The reference shape.
    
    pTheta - Optional pointer to return the rotation carried out on this.
    
    Returns:
    
    The 2-norm of the this shape seen as a 2*nbPoint vector after the translation to orig but before the scale done to fit 'ref'.
  - AlignTo
```
public double AlignTo(CAAMShape ref)
```
    Wrapper to align this to ref.
    
    Parameters:
    
    ref -
    
    Returns:
  - AlignTo
```
public double AlignTo(CAAMShape ref,
                      double[] pTheta)
```
    Aligns this to 'ref' with respect to pose.
    
    Parameters:
    
    ref - The reference shape.
    
    pTheta - Optional pointer to return the rotation carried out on this.
    
    Returns:
    
    The 2-norm of the this shape seen as a 2*nbPoint vector after the translation to origo but before the scale done to fit 'ref'.
  - GetRotation
```
public double GetRotation(CAAMShape ref)
```
    Returns the rotation between ref and this (in radians). Get the rotation between two shapes by minimizing the sum of squared point distances, as described by Goodall (and Bookstein) using Singular Value Decomposition (SVD). Note that both shapes must be normalized with respect to scale and position beforehand. This could be done by using CAAMSAhape::Normalize().
    
    Returns:
    
    The estimated angle, theta, between the two shapes.
  - Param2PoseVec
```
public static void Param2PoseVec(double scale,
                                 double theta,
                                 double tx,
                                 double ty,
                                 CDVector poseVec)
```
    Converts pose parameters: scale, theta, tx, ty to a pose vector. The pose vector will be in the format: [ s, theta, tx, ty ] where s = scale-1
    
    Parameters:
    
    scale - Scale input.
    
    theta - Rotational input.
    
    tx - X translation input.
    
    ty - Y translation input.
    
    poseVec - The output pose vector.
  - PoseVec2Param
```
public static void PoseVec2Param(CDVector poseVec,
                                 double[] scale,
                                 double[] theta,
                                 double[] tx,
                                 double[] ty)
```
    Converts a pose vector to pose parameters: scale, theta, tx, ty. The pose vector are expected to be in the format: [ s, theta, tx, ty ] where s = scale-1
    
    Parameters:
    
    poseVec - The input pose vector.
    
    scale - Scale output.
    
    theta - Rotational output.
    
    tx - X translation output.
    
    ty - Y translation output.
  - Displace
```
public void Displace(CDVector poseVec)
```
    Displaces the shape around it's center of gravity using a displacement vector.
    
    Parameters:
    
    poseVec - The input pose vector.
  - IsInsidePath
```
public boolean IsInsidePath(CAAMPoint p,
                            int path_start)
```
    Tests if the point 'p' is inside the path starting at position 'path_start'. Rarely used. Primary a helper function to IsInside.
    
    Parameters:
    
    p - The point to test for.
    
    path_start - The point index where a path starts
    
    Returns:
    
    True if 'p' is inside
  - IsInside
```
public boolean IsInside(CAAMPoint p)
```
    Wrapper to check is point p is inside the shape
    
    Parameters:
    
    p - point
    
    Returns:
    
    inside or not
  - IsInside
```
public boolean IsInside(CAAMPoint p,
                        boolean bBoundTest)
```
    Tests if the point 'p' belongs to the shape. In the current version all shape points are assumes to be ordered points in a n-point polygon with no holes. For example used to clean up the meshes (removing unwanted triangles from the triangulisation).
    
    Parameters:
    
    bBoundTest - Flags wheather a bounding box test should be performed prior to the exact test.
    
    Returns:
    
    True if 'p' is inside.
  - Expand
```
public void Expand(int nPixels)
```
    Expands the shape by moving each model point 'nPixels' perperdicular to the shape contour (that is: along the model point normal). This function will expand each outer (closed) path of the shape. No tests for crossing contours are being made as of now.
    
    Parameters:
    
    nPixels - The number of pixel to expand the shape with.
  - Normal
```
public void Normal(int i,
                   CAAMPoint p1,
                   CAAMPoint p2,
                   double dist)
```
    Finds the normal to the i'th point on the shape. If the point should be a single point the normal points is defined to be equal to the point it self.
    
    Parameters:
    
    i - Index of point.
    
    p1 - Reference to the outside normal point.
    
    p2 - Reference to the inside normal point.
    
    dist - The desired distance from p[1|2] to the i-th point.
  - NormalDisplacement
```
public void NormalDisplacement(int i,
                               double dist)
```
    Displaces the i-th point along the normal.
    
    Parameters:
    
    i - Index of point.
    
    dist - The distance to move the point (>0 move point outwards,
  - WriteASF
```
public boolean WriteASF(java.lang.String filename,
                        int image_width,
                        int image_height)
```
    Writes the shape to a ASF file. Remember asf's are always in relative coordinates. Se format description else where.
    
    Parameters:
    
    filename - Output filename.
    
    image_width - The image the coord. is relative to.
    
    image_height - The image the coord. is relative to.
    
    Returns:
    
    true on success, false on errors
  - WriteASF0_90
```
public boolean WriteASF0_90(java.lang.String filename,
                            int image_width,
                            int image_height)
```
    ASF writer version 0.90. Writes the shape to a ver. 0.90 ASF file. Remember asf's are always in relative coordinates. Se format description else where.
    
    Parameters:
    
    filename - Output filename.
    
    image_width - The image the coord. is relative to.
    
    image_height - The image the coord. is relative to.
    
    Returns:
    
    true on success, false on errors
  - generateVOIs
```
public boolean generateVOIs(ModelImage targetImageSlice)
```
    ASF writer version 0.90. Writes the shape to a ver. 0.90 ASF file. Remember asf's are always in relative coordinates. Se format description else where.
    
    Parameters:
    
    filename - Output filename.
    
    image_width - The image the coord. is relative to.
    
    image_height - The image the coord. is relative to.
    
    Returns:
    
    true on success, false on errors
  - generateVOImesh
```
public boolean generateVOImesh(ModelImage targetImageSlice)
```
    From the current shape, generate the corresponding triagnle meshes view. VOIs is used to display the mesh.
    
    Parameters:
    
    targetImageSlice -
    
    Returns:
    
    true by default
  - ReadASF
```
public boolean ReadASF(java.lang.String filename)
```
    Reads an ver. 0.90 .asf into relative coordinates. Se format description else where.
    
    Parameters:
    
    filename - Input filename.
    
    Returns:
    
    true on success, false on errors
  - ReadASF0_90
```
public boolean ReadASF0_90(java.lang.String filename)
```
    Reads an ver. 0.90 .asf into relative coordinates. Se format description else where.
    
    Parameters:
    
    filename - Input filename.
    
    Returns:
    
    true on success, false on errors
  - ReadASFfromVOI
```
public boolean ReadASFfromVOI(ModelImage image)
```
    Generate ASF shape from given VOI
    
    Parameters:
    
    image - image with VOI.
    
    Returns:
    
    success or not
  - ConvertASFfromVOI
```
public boolean ConvertASFfromVOI(VOIBase v)
```
    Convert ASF shape from VOI
    
    Parameters:
    
    v - VOI
    
    Returns:
    
    success or not.
  - ReadASFfromVOI_init
```
public boolean ReadASFfromVOI_init(ModelImage image)
```
  - Abs2Rel
```
public void Abs2Rel(java.lang.String hostImagePath)
```
    Converts shape coordinates from absolute to relative by using the hostimage.
  - IsAbs
```
public boolean IsAbs()
```
    Returns true if the shape is in absolute coordinates.
    
    Returns:
    
    is abs coordinate or not
  - Rel2Abs
```
public void Rel2Abs(java.lang.String hostImagePath)
```
  - Abs2Rel
```
public void Abs2Rel(int image_width,
                    int image_height)
```
    Converts shape coordinates from absolute to relative. Relative coordinates are specified as: x_relative = x_abs/image_width y_relative = y_abs/image_height
    
    Parameters:
    
    image_width - The image the coord. should be relative to.
    
    image_height - The image the coord. should be relative to.
    
    See Also:
    
    Rel2Abs(java.lang.String)
  - Rel2Abs
```
public void Rel2Abs(int image_width,
                    int image_height)
```
    Converts shape coordinates from relative to absolute. Relative coordinates are specified as: x_relative = x_abs/image_width y_relative = y_abs/image_height
    
    Parameters:
    
    image_width - The image the coord. is relative to.
    
    image_height - The image the coord. is relative to.
    
    See Also:
    
    Abs2Rel(java.lang.String)
  - AddPath
```
public void AddPath(CAAMShape shape,
                    CAAMPointInfo pointType)
```
    Adds a path to the shape. All added point inherits the given pointtype.
    
    Parameters:
    
    shape - A shape containing one path.
    
    pointType - The pointtype of the added points.
  - ReversePointOrder
```
public void ReversePointOrder()
```
    Reverses the point point ordering. Used when a clock-wise outer path shall converted to a counter-clock wise hole.
  - GetPaths
```
public java.util.Vector<java.lang.Integer> GetPaths()
```
    Extracts the starting positions of each path in the shape by a simple linear search. The starting position is identified by a change in path id (saved in the m_vPointAux member).
    
    Returns:
    
    A vector of path starting positions.
  - PathLen
```
public int PathLen(int startPosition)
```
    Returns the length of a path.
    
    Parameters:
    
    startPosition - The starting position of the path.
    
    Returns:
    
    The path length.
    
    See Also:
    
    GetPaths()
  - ExtractPath
```
public CAAMShape ExtractPath(int startPosition)
```
    Extracts one path from a shape into a new shape.
    
    Parameters:
    
    startPosition - The starting position of the path.
    
    Returns:
    
    The path as a new shape.
  - AddShapeExtends
```
public void AddShapeExtends(int nPixels)
```
    Adds an extra outer path on each outer path in the distance of 'nPixels' along the point normal. This method is primary used in conjunction with the "do not use the convex hull" feature. In such a case one often still wants a certain neighborhood of the shape to be included in the model.
    
    Parameters:
    
    nPixels - The size of the extents.
  - SetPointInfoFlagsInPath
```
public void SetPointInfoFlagsInPath(int startPosition,
                                    int flags)
```
    Sets all flags in one path to the same value.
    
    Parameters:
    
    startPosition - Starting position of the path.
    
    flags - The flags.
  - AddInterior
```
public void AddInterior(int interations)
```
    Add articifial interior points to the shape by making a Delaunay triangulation and adding the centroid of each triangle. This is done iteratively. Default is one iteration
    
    Parameters:
    
    interations - Controls the number of artificial points. One iteration equals one triangulation.
  - ConsistencyCheck
```
public boolean ConsistencyCheck()
```
    Tests if any interior points has gone outside outer path of the shape.
    
    Returns:
    
    True if the shape looks ok, false if not.
  - MakeBorderShape
```
public void MakeBorderShape(int size)
```
    Converts a one path shape into a border shape by adding two symmetric borders: an inside (a hole) and an outside border. No checks for folding paths are done as of now.
    
    Parameters:
    
    size - The size of the border in pixels.
  - add
```
public CAAMShape add(CVisDVector v)
```
    Plus operator.
    
    Overrides:
    
    add in class CVisDVector
    
    Parameters:
    
    v - Vector to add.
    
    Returns:
    
    The addition of this and 'v'.
  - sub
```
public CAAMShape sub(CVisDVector v)
```
    Minus operator.
    
    Overrides:
    
    sub in class CVisDVector
    
    Parameters:
    
    v - Vector to add.
    
    Returns:
    
    The subtraction of this and 'v'.
  - GetHostImage
```
public ModelSimpleImage GetHostImage(ModelSimpleImage dest,
                                     java.lang.String path,
                                     int rfactor)
```
    Retrives the image connected to the shape. As of now it's loaded from disk using the HostImage() member in the shape.
    
    Parameters:
    
    dest - The destination image.
    
    path - The path to the .asf file.
    
    rfactor - Optional reduction factor. Performs a scaling of the the shape by 1/rfactor. Default 1 i.e. no scaling.
    
    Returns:
    
    refactored image.
  - GetHostImage
```
public ModelSimpleImage GetHostImage(ModelImage src,
                                     int rfactor)
```
    Retrives the image connected to the shape. As of now it's loaded from disk using the HostImage() member in the shape.
    
    Parameters:
    
    src - source image
    
    rfactor - reduction factor
    
    Returns:
    
    refactored iamge.
  - Area
```
public double Area()
```
  - Area
```
public double Area(boolean use_covex_hull)
```
    Returns the total area of the shape (with holes excluded).
    
    Parameters:
    
    use_covex_hull - Use the convex hull of the shape for area calculation (default false).
    
    Returns:
    
    The area.
  - CalcConvexHull
```
public CAAMShape CalcConvexHull()
```
    Calculates the convex hull of each path in the shape. The calulation is built upon the geometrical fact that the homogenous point matrix: [ p1x p2x p3x ; p1y p2y p3y ; 1 1 1 ] is positive if p1, p2, p3 is a convex segment and negative if concave. Note: this holds for a clock-wise ordering of p1,p2,p3. Any open paths are considered cyclic in the concavity calulation. Remember that paths should be defined clock-wise in the asf format. BUG COMMENT: This does not seem to work with multiple paths.
    
    Returns:
    
    A convex version of this shape w.r.t. each path.
  - IsConvex
```
public boolean IsConvex()
```
    Tests if the shap is convex w.r.t. each path. This call is rather expensive, since it spaws a call to CalcConvexHull().
    
    Returns:
    
    True on convex, false on concave.
  - RemovePoint
```
public void RemovePoint(int i)
```
    Removes the i-th point from the shape. Since this require massive reordering of the preceeding point connectivity this is actually a very expensive call [a fairly ugly in it's implementation] :-(
    
    Parameters:
    
    i - The index of the point to remove.
  - DEC_TO_ZERO
```
public int DEC_TO_ZERO(int a)
```
    Convert deciam number to 0
    
    Parameters:
    
    a - int number
    
    Returns:
  - UserField
```
public java.util.Vector<java.lang.Float> UserField(int field_nb)
```
    Returns the reference of the user defined field vector number 'field_nb'.
    
    Parameters:
    
    field_nb - Field number [1-3].
    
    Returns:
    
    A reference to the specified field vector.
  - AllocateUserFields
```
public void AllocateUserFields()
```
    Allocates room for the three user defined fields. Notice that the user defined fields is *not* allocated by default. In order to preserved memory the user must to this explicitly by using AllocateUserFields();
  - HostImage
```
public final java.lang.String HostImage()
```
    Host image (if any).
    
    Returns:
    
    host image
  - SetHostImage
```
public void SetHostImage(java.lang.String hostImageFilename)
```
    Returns the host image (if any).
    
    Parameters:
    
    hostImageFilename -
  - Width
```
public double Width()
```
    Shape width.
    
    Returns:
    
    shape width
  - Height
```
public double Height()
```
    Shape height
    
    Returns:
    
    shape height
  - NPoints
```
public final int NPoints()
```
    The number of shape points.
    
    Returns:
    
    number of points on shape
  - GetPointUS
```
public void GetPointUS(int i,
                       double[] x,
                       double[] y)
```
    un-safe (and dirty) since it depends on assumptions regarding the
    
    Parameters:
    
    i - index
    
    x - x coordinate pointer
    
    y - y conrdinate pointer
  - PointAux
```
public java.util.Vector<CAAMPointInfo> PointAux()
```
    Returns the complete point aux vector of the shape.
    
    Returns:
    
    point info vector
  - setPointAux
```
public void setPointAux(java.util.Vector<CAAMPointInfo> value)
```
    set point info vector
    
    Parameters:
    
    value -
  - setPointAux
```
public void setPointAux(int index,
                        CAAMPointInfo value)
```
    Set specific point info
    
    Parameters:
    
    index -
    
    value -
  - getHostImage
```
public ModelImage getHostImage()
```
    Get host image.
    
    Returns:
    
    image

Class CAAMShape

Field Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Detail

m_vPointAux

m_vUser1

m_vUser2

m_vUser3

m_szASFVer

m_iNbPoints

m_bAbsPointCoordinates

m_szHostImage

myHostImage

m_pData

Constructor Detail

CAAMShape

CAAMShape

CAAMShape

CAAMShape

Method Detail

ToFile

FromFile

SetClosedPathConnectivity

assign

assign

CopyData

assign

dispose

Rotate

Rotate

Translate

Translate

ShapeSize

MinX

MaxX

MinY

MaxY

Scale

Scale

COG

COG

Normalize

SetPoint

SetPoint

GetPoint

GetPoint

Resize

AlignTransformation

initAlignTo

initAlignTo

AlignTo

AlignTo

GetRotation

Param2PoseVec

PoseVec2Param

Displace

IsInsidePath

IsInside

IsInside

Expand

Normal

NormalDisplacement

WriteASF

WriteASF0_90

generateVOIs

generateVOImesh

ReadASF

ReadASF0_90

ReadASFfromVOI

ConvertASFfromVOI

ReadASFfromVOI_init

Abs2Rel

IsAbs

Rel2Abs