java.lang.Object
- gov.nih.mipav.view.renderer.flythroughview.ModelImage3DLayout

```
public class ModelImage3DLayout
extends java.lang.Object
```
Used to store the information and layout which describes a volume of data.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`static class`	`ModelImage3DLayout.GradientNeighbors`	Stores the indexes into a linear array for the samples to use in computing finite difference based gradients as follows:

Field Summary

Fields
Modifier and Type	Field	Description
`private float[]`	`m_afDistanceNeighbors27`	Array of exact Euclidean distances (in sample coordinates) to each of the 26-connected neighbors corresponding to the relative indexes in m_aiOffsetNeighbors27 array.
`private float[]`	`m_afRealDistanceNeighbors27`	Array of exact Euclidean distances to each of the 26-connected neighbors scaled by the size of each sample along each axis and corresponding to the relative indexes in m_aiOffsetNeighbors27 array.
`private int[]`	`m_aiOffsetNeighbors27`	Array of 27 index offsets used by the getOffsetXYZNeighbors27 method.
`private int[]`	`m_aiOffsetNeighborsVoxel`	Array of 8 index offsets used by the getIndexNeighborsVoxel method.
`private Point3D[]`	`m_akOffsetXYZNeighbors27`	Array of 27 index offsets used by the getIndexNeighbors27 method.
`boolean`	`m_bReverseX`	Flag set to reverse order of "real" X coordinates assigned to samples.
`boolean`	`m_bReverseY`	Flag set to reverse order of "real" Y coordinates assigned to samples.
`boolean`	`m_bReverseZ`	Flag set to reverse order of "real" Z coordinates assigned to samples.
`float`	`m_fOffsetX`	"Real" coordinate of sample at the 0 index along the X axis.
`float`	`m_fOffsetY`	"Real" coordinate of sample at the 0 index along the X axis.
`float`	`m_fOffsetZ`	"Real" coordinate of sample at the 0 index along the X axis.
`float`	`m_fSpacingX`	Spacing between each sample along X axis.
`float`	`m_fSpacingY`	Spacing between each sample along Y axis.
`float`	`m_fSpacingZ`	Spacing between each sample along Z axis.
`int`	`m_iDimX`	Number of samples in volume along X axis.
`int`	`m_iDimY`	Number of samples in volume along Y axis.
`int`	`m_iDimZ`	Number of samples in volume along Z axis.
`private ModelImage3DLayout.GradientNeighbors`	`m_kOffsetNeighborsGradient`	Index offsets used by the getIndexNeighborsGradient method.

Constructor Summary

Constructors
Constructor	Description
`ModelImage3DLayout(int iDimX, int iDimY, int iDimZ, float fSpacingX, float fSpacingY, float fSpacingZ, float fOffsetX, float fOffsetY, float fOffsetZ)`	Create a volume with the specified dimensions.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`getDistanceNeighbors27(float[] afDistances)`	Fill an array of distances to the 26-connected neighbors for any given sample where the distances are the Euclidean distances in sample coordinates.
`int`	`getIndex(int iX, int iY, int iZ)`	Compute the index in a linear data array dimensioned to store all the samples of this volume.
`int`	`getIndexChecked(int iX, int iY, int iZ)`	Compute the index in a linear data array dimensioned to store all the samples of this volume.
`int`	`getIndexIncX()`	Get the amount to increment the linear array index for each increment in the x coordinate index.
`int`	`getIndexIncY()`	Get the amount to increment the linear array index for each increment in the y coordinate index.
`int`	`getIndexIncZ()`	Get the amount to increment the linear array index for each increment in the z coordinate index.
`void`	`getIndexNeighbors27(int iIndexCenter, int[] aiIndexes)`	Fill an array of indexes for a linear array of volume values.
`void`	`getIndexNeighbors27(int iX, int iY, int iZ, int[] aiIndexes)`	Fill an array of indexes for a linear array of volume values.
`void`	`getIndexNeighborsGradient(int iX, int iY, int iZ, ModelImage3DLayout.GradientNeighbors kNeighbors)`	Retrieve the indexes for the 6-connected neighbors of the specified sample which are used to compute the gradient.
`void`	`getIndexNeighborsVoxel(int iX, int iY, int iZ, int[] aiIndexes)`	Fill an array of indexes for a linear array of volume values.
`int`	`getIndexX(int iIndex)`	Get X sample coordinate from a linear array index for volume data.
`int`	`getIndexY(int iIndex)`	Get Y sample coordinate from a linear array index for volume data.
`int`	`getIndexZ(int iIndex)`	Get Z sample coordinate from a linear array index for volume data.
`int`	`getNumSamples()`	Query the total number of samples for a volume with these parameters.
`void`	`getOffsetXYZNeighbors27(Point3D[] akOffsetXYZ)`	Fill in the array of offsets to the 26-connected neighbors for any given sample in the volume.
`float`	`getRealDistance(int iX1, int iY1, int iZ1, int iX2, int iY2, int iZ2)`	Given the coordinates of two points in sample space of the volume, compute the real distance betwen them by taking into consideration the spacing between samples in the volume along each axis.
`void`	`getRealDistanceNeighbors27(float[] afDistances)`	Fill an array of distances to the 26-connected neighbors for any given sample where the distances are the real Euclidean distances scaled by the size of the sample along each axis.
`void`	`getRealPoint(int iX, int iY, int iZ, WildMagic.LibFoundation.Mathematics.Vector3f kPoint)`	Compute the "real" coordinates of the sample in the volume at the specified sample coordinate indexes.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getSamplePoint(float x, float y, float z)`	Convert the input "real" coordinates into sample coordinates.

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

- Field Detail
  - m_bReverseX
```
public final boolean m_bReverseX
```
    Flag set to reverse order of "real" X coordinates assigned to samples.
  - m_bReverseY
```
public final boolean m_bReverseY
```
    Flag set to reverse order of "real" Y coordinates assigned to samples.
  - m_bReverseZ
```
public final boolean m_bReverseZ
```
    Flag set to reverse order of "real" Z coordinates assigned to samples.
  - m_fOffsetX
```
public final float m_fOffsetX
```
    "Real" coordinate of sample at the 0 index along the X axis.
  - m_fOffsetY
```
public final float m_fOffsetY
```
    "Real" coordinate of sample at the 0 index along the X axis.
  - m_fOffsetZ
```
public final float m_fOffsetZ
```
    "Real" coordinate of sample at the 0 index along the X axis.
  - m_fSpacingX
```
public final float m_fSpacingX
```
    Spacing between each sample along X axis.
  - m_fSpacingY
```
public final float m_fSpacingY
```
    Spacing between each sample along Y axis.
  - m_fSpacingZ
```
public final float m_fSpacingZ
```
    Spacing between each sample along Z axis.
  - m_iDimX
```
public final int m_iDimX
```
    Number of samples in volume along X axis.
  - m_iDimY
```
public final int m_iDimY
```
    Number of samples in volume along Y axis.
  - m_iDimZ
```
public final int m_iDimZ
```
    Number of samples in volume along Z axis.
  - m_afDistanceNeighbors27
```
private final float[] m_afDistanceNeighbors27
```
    Array of exact Euclidean distances (in sample coordinates) to each of the 26-connected neighbors corresponding to the relative indexes in m_aiOffsetNeighbors27 array.
  - m_afRealDistanceNeighbors27
```
private final float[] m_afRealDistanceNeighbors27
```
    Array of exact Euclidean distances to each of the 26-connected neighbors scaled by the size of each sample along each axis and corresponding to the relative indexes in m_aiOffsetNeighbors27 array.
  - m_aiOffsetNeighbors27
```
private final int[] m_aiOffsetNeighbors27
```
    Array of 27 index offsets used by the getOffsetXYZNeighbors27 method.
  - m_aiOffsetNeighborsVoxel
```
private final int[] m_aiOffsetNeighborsVoxel
```
    Array of 8 index offsets used by the getIndexNeighborsVoxel method.
  - m_akOffsetXYZNeighbors27
```
private final Point3D[] m_akOffsetXYZNeighbors27
```
    Array of 27 index offsets used by the getIndexNeighbors27 method.
  - m_kOffsetNeighborsGradient
```
private final ModelImage3DLayout.GradientNeighbors m_kOffsetNeighborsGradient
```
    Index offsets used by the getIndexNeighborsGradient method.
- Constructor Detail
  - ModelImage3DLayout
```
public ModelImage3DLayout(int iDimX,
                          int iDimY,
                          int iDimZ,
                          float fSpacingX,
                          float fSpacingY,
                          float fSpacingZ,
                          float fOffsetX,
                          float fOffsetY,
                          float fOffsetZ)
```
    Create a volume with the specified dimensions.
    
    Parameters:
    
    iDimX - number of samples along the X axis
    
    iDimY - number of samples along the Y axis
    
    iDimZ - number of samples along the Z axis
    
    fSpacingX - spacing between samples along the X axis. Value can be negative to indicated a reverse direction for real coords.
    
    fSpacingY - spacing between samples along the Y axis Value can be negative to indicated a reverse direction for real coords.
    
    fSpacingZ - spacing between samples along the Z axis Value can be negative to indicated a reverse direction for real coords.
    
    fOffsetX - X coordinate of samples at X sample index 0
    
    fOffsetY - Y coordinate of samples at Y sample index 0
    
    fOffsetZ - Z coordinate of samples at Z sample index 0
- Method Detail
  - getDistanceNeighbors27
```
public void getDistanceNeighbors27(float[] afDistances)
```
    Fill an array of distances to the 26-connected neighbors for any given sample where the distances are the Euclidean distances in sample coordinates.
    
    Parameters:
    
    afDistances - must be an array with at least 27 entries where these entries will be filled in with the Euclidean distances for the 26-connected neighbors of any given sample in the volume. The ordering of the distances corresponds to the ordering of the relative linear array indexes returned by the getOffsetNeighbors27 method. Note that the [0] entry is for the center sample (always a distance of zero), and the remaining 26 entries are for the neighbor samples distances.
  - getIndex
```
public int getIndex(int iX,
                    int iY,
                    int iZ)
```
    Compute the index in a linear data array dimensioned to store all the samples of this volume. The index is determined by the specified 3D coordinate indexes. No checking is made to ensure that the coordinate indexes are in their respective ranges.
    
    Parameters:
    
    iX - sample X coordinate index
    
    iY - sample Y coordinate index
    
    iZ - sample Z coordinate index
    
    Returns:
    
    1D index into linear array
  - getIndexChecked
```
public int getIndexChecked(int iX,
                           int iY,
                           int iZ)
```
    Compute the index in a linear data array dimensioned to store all the samples of this volume. The index is determined by the specified 3D coordinate indexes. Each coordinate index is checked to ensure that it is within its respective coordinate ranges.
    
    Parameters:
    
    iX - sample X coordinate index
    
    iY - sample Y coordinate index
    
    iZ - sample Z coordinate index
    
    Returns:
    
    1D index into linear array or -1 if any of the indexes are outside their respective coordinate ranges
  - getIndexIncX
```
public int getIndexIncX()
```
    Get the amount to increment the linear array index for each increment in the x coordinate index.
    
    Returns:
    
    int Positive linear array index increment.
  - getIndexIncY
```
public int getIndexIncY()
```
    Get the amount to increment the linear array index for each increment in the y coordinate index.
    
    Returns:
    
    int Positive linear array index increment.
  - getIndexIncZ
```
public int getIndexIncZ()
```
    Get the amount to increment the linear array index for each increment in the z coordinate index.
    
    Returns:
    
    int Positive linear array index increment.
  - getIndexNeighbors27
```
public void getIndexNeighbors27(int iIndexCenter,
                                int[] aiIndexes)
```
    Fill an array of indexes for a linear array of volume values. These indexes are for the specified sample and the indexes of the immediate 26-connected neighbors.
    Unexpected results occur, e.g. invalid sample indexes, if the center sample specified by the indexes is for one on the border of the volume.
    
    Parameters:
    
    iIndexCenter - linear volume data array index center sample
    
    aiIndexes - must be an array with at least 27 entries where these entries will be filled in with the indexes for linear volume data array for the specified sample and its 26-connected neighbors. Note that the [0] entry is for the center sample, but there is no specified ordering for the 26 neighbor samples.
  - getIndexNeighbors27
```
public void getIndexNeighbors27(int iX,
                                int iY,
                                int iZ,
                                int[] aiIndexes)
```
    Fill an array of indexes for a linear array of volume values. These indexes are for the specified sample and the indexes of the immediate 26-connected neighbors.
    Unexpected results occur, e.g. invalid sample indexes, if the center sample specified by the indexes is for one on the border of the volume.
    
    Parameters:
    
    iX - sample X coordinate index for center sample
    
    iY - sample Y coordinate index for center sample
    
    iZ - sample Z coordinate index for center sample
    
    aiIndexes - must be an array with at least 27 entries where these entries will be filled in with the indexes for linear volume data array for the specified sample and its 26-connected neighbors. Note that the [0] entry is for the center sample, but there is no specified ordering for the 26 neighbor samples.
  - getIndexNeighborsGradient
```
public void getIndexNeighborsGradient(int iX,
                                      int iY,
                                      int iZ,
                                      ModelImage3DLayout.GradientNeighbors kNeighbors)
```
    Retrieve the indexes for the 6-connected neighbors of the specified sample which are used to compute the gradient. If the sample is along any border of the volume, then the indexes for a forward/reverse finite difference are returned which would involve the sample itself but only for the axis where the sample is along its corresponding border. Otherwise, the samples are returned for computing finite central difference.
    Unexpected results occur, e.g. invalid sample indexes, if the center sample specified by the indexes is for one on the border of the volume.
    
    Parameters:
    
    iX - sample X coordinate index for center sample
    
    iY - sample Y coordinate index for center sample
    
    iZ - sample Z coordinate index for center sample
    
    kNeighbors - contains the indexes for the 6-connected neighbors used to compute the gradient
  - getIndexNeighborsVoxel
```
public void getIndexNeighborsVoxel(int iX,
                                   int iY,
                                   int iZ,
                                   int[] aiIndexes)
```
    Fill an array of indexes for a linear array of volume values. These indexes are for the specified sample and the indexes of the immediate neighbor samples that comprise a voxel. Of the 8 neighboring samples returned for a voxel, the specified sample will have the smallest of the coordinate indexes, i.e., the "minimum" corner sample.
    Unexpected results occur, e.g. invalid sample indexes, if the specified sample is along any of the maximum borders of the volume (given by an sample coordinate index being the maximum for the corresponding axis).
    
    Parameters:
    
    iX - sample X coordinate index for "minimum" corner sample
    
    iY - sample Y coordinate index for "minimum" corner sample
    
    iZ - sample Z coordinate index for "minimum" corner sample
    
    aiIndexes - must be an array with at least 8 entries where these entries will be filled in with the indexes for linear volume data array for the specified sample and its voxel neighbors. Note that the [0] entry is for the specified sample, but there is no specified ordering for the other 7 neighbor samples.
  - getIndexX
```
public int getIndexX(int iIndex)
```
    Get X sample coordinate from a linear array index for volume data.
    
    Parameters:
    
    iIndex - linear array index
    
    Returns:
    
    X sample coordinate
  - getIndexY
```
public int getIndexY(int iIndex)
```
    Get Y sample coordinate from a linear array index for volume data.
    
    Parameters:
    
    iIndex - linear array index
    
    Returns:
    
    Y sample coordinate
  - getIndexZ
```
public int getIndexZ(int iIndex)
```
    Get Z sample coordinate from a linear array index for volume data.
    
    Parameters:
    
    iIndex - linear array index
    
    Returns:
    
    Z sample coordinate
  - getNumSamples
```
public int getNumSamples()
```
    Query the total number of samples for a volume with these parameters.
    
    Returns:
    
    number of voxels
  - getOffsetXYZNeighbors27
```
public void getOffsetXYZNeighbors27(Point3D[] akOffsetXYZ)
```
    Fill in the array of offsets to the 26-connected neighbors for any given sample in the volume.
    
    Parameters:
    
    akOffsetXYZ - must be an array with at least 27 enties where these entries will be filled in with the XYZ index offsets for the 26-connected neighbors of any given sample in the volume. The ordering of the offsets corresponds to the ordering of the relative linear array indexes returned by the getIndexNeighbors27 method. Note that the [0] entry is for the center sample (always XYZ offsets of zero), and the remaining 26 entries are for the neighbor samples.
  - getRealDistance
```
public float getRealDistance(int iX1,
                             int iY1,
                             int iZ1,
                             int iX2,
                             int iY2,
                             int iZ2)
```
    Given the coordinates of two points in sample space of the volume, compute the real distance betwen them by taking into consideration the spacing between samples in the volume along each axis.
    
    Parameters:
    
    iX1 - X-axis sample coordinate of first point
    
    iY1 - Y-axis sample coordinate of first point
    
    iZ1 - Z-axis sample coordinate of first point
    
    iX2 - X-axis sample coordinate of second point
    
    iY2 - Y-axis sample coordinate of second point
    
    iZ2 - Z-axis sample coordinate fo second point
    
    Returns:
    
    computed "real" distance between two samples in volume
  - getRealDistanceNeighbors27
```
public void getRealDistanceNeighbors27(float[] afDistances)
```
    Fill an array of distances to the 26-connected neighbors for any given sample where the distances are the real Euclidean distances scaled by the size of the sample along each axis.
    
    Parameters:
    
    afDistances - must be an array with at least 27 entries where these entries will be filled in with the Euclidean distances for the 26-connected neighbors of any given sample in the volume. The ordering of the distances corresponds to the ordering of the relative linear array indexes returned by the getOffsetNeighbors27 method. Note that the [0] entry is for the center sample (always a distance of zero), and the remaining 26 entries are for the neighbor samples distances.
  - getRealPoint
```
public void getRealPoint(int iX,
                         int iY,
                         int iZ,
                         WildMagic.LibFoundation.Mathematics.Vector3f kPoint)
```
    Compute the "real" coordinates of the sample in the volume at the specified sample coordinate indexes.
    
    Parameters:
    
    iX - sample X coordinate index
    
    iY - sample Y coordinate index
    
    iZ - sample Z coordinate index
    
    kPoint - Point3f into which the computed coordinates are stored
  - getSamplePoint
```
public WildMagic.LibFoundation.Mathematics.Vector3f getSamplePoint(float x,
                                                                   float y,
                                                                   float z)
```
    Convert the input "real" coordinates into sample coordinates.
    
    Parameters:
    
    kRealPoint - Point3f These are the "real" coordinates.
    
    Returns:
    
    Point3f This is a new instance containing the interpolated sample coordinates converted from the input real coordinates.

Class ModelImage3DLayout

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

m_bReverseX

m_bReverseY

m_bReverseZ

m_fOffsetX

m_fOffsetY

m_fOffsetZ

m_fSpacingX

m_fSpacingY

m_fSpacingZ

m_iDimX

m_iDimY

m_iDimZ

m_afDistanceNeighbors27

m_afRealDistanceNeighbors27

m_aiOffsetNeighbors27

m_aiOffsetNeighborsVoxel

m_akOffsetXYZNeighbors27

m_kOffsetNeighborsGradient

Constructor Detail

ModelImage3DLayout

Method Detail

getDistanceNeighbors27

getIndex

getIndexChecked

getIndexIncX

getIndexIncY

getIndexIncZ

getIndexNeighbors27

getIndexNeighbors27

getIndexNeighborsGradient

getIndexNeighborsVoxel

getIndexX

getIndexY

getIndexZ

getNumSamples

getOffsetXYZNeighbors27

getRealDistance

getRealDistanceNeighbors27

getRealPoint

getSamplePoint