java.lang.Object
- com.pixelmed.geometry.GeometryOfSlice

Direct Known Subclasses:

GeometryOfSliceFromAttributeList
```
public class GeometryOfSlice
extends java.lang.Object
```
A class to describe the spatial geometry of a single cross-sectional image slice.

The 3D coordinate space used is the DICOM coordinate space, which is LPH+, that is, the x-axis is increasing to the left hand side of the patient, the y-axis is increasing to the posterior side of the patient, and the z-axis is increasing toward the head of the patient.

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`C`
`protected javax.vecmath.Vector3d`	`column`
`protected double[]`	`columnArray`
`protected javax.vecmath.Tuple3d`	`dimensions`
`protected javax.vecmath.Vector3d`	`normal`
`protected double[]`	`normalArray`
`protected int`	`R`
`protected javax.vecmath.Vector3d`	`row`
`protected double[]`	`rowArray`
`protected double`	`sliceThickness`
`protected javax.vecmath.Point3d`	`tlhc`
`protected double[]`	`tlhcArray`
`protected javax.vecmath.Tuple3d`	`voxelSpacing`
`protected double[]`	`voxelSpacingArray`

Constructor Summary

Constructors
Constructor	Description
`GeometryOfSlice()`	Construct an empty geometry.
`GeometryOfSlice(double[] rowArray, double[] columnArray, double[] tlhcArray, double[] voxelSpacingArray, double sliceThickness, double[] dimensions)`	Construct the geometry.
`GeometryOfSlice(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column, javax.vecmath.Point3d tlhc, javax.vecmath.Tuple3d voxelSpacing, double sliceThickness, javax.vecmath.Tuple3d dimensions)`	Construct the geometry.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static boolean`	`areSlicesParallel(GeometryOfSlice slice1, GeometryOfSlice slice2)`	Determine if two slices are parallel.
`protected void`	`findMaxComponents()`
`javax.vecmath.Vector3d`	`getColumn()`	Get the column direction.
`double[]`	`getColumnArray()`	Get the column direction.
`java.lang.String`	`getColumnOrientation()`	Get the letter representation of the orientation of the columns of this slice.
`java.lang.String`	`getColumnOrientation(boolean quadruped)`	Get the letter representation of the orientation of the columns of this slice.
`javax.vecmath.Tuple3d`	`getDimensions()`	Get the dimensions of the voxel.
`double`	`getDistanceAlongNormalFromOrigin()`	Given the present geometry, determine the distance along the normal to the plane of the slice of the TLHC of the image from the origin of the coordinate space (0,0,0).
`double`	`getDistanceAlongNormalFromOrigin(javax.vecmath.Point3d point)`	Given the present geometry, determine the distance along the normal to the plane of the slice of an arbitrary point (not necessarily in the plane of the image) from the origin of the coordinate space (0,0,0).
`javax.vecmath.Vector3d`	`getNormal()`	Get the normal direction.
`double[]`	`getNormalArray()`	Get the normal direction.
`static java.lang.String`	`getOrientation(double[] orientation)`	Get the letter representation of the orientation of a vector.
`static java.lang.String`	`getOrientation(double[] orientation, boolean quadruped)`	Get the letter representation of the orientation of a vector.
`javax.vecmath.Vector3d`	`getRow()`	Get the row direction.
`double[]`	`getRowArray()`	Get the row direction.
`java.lang.String`	`getRowOrientation()`	Get the letter representation of the orientation of the rows of this slice.
`java.lang.String`	`getRowOrientation(boolean quadruped)`	Get the letter representation of the orientation of the rows of this slice.
`double`	`getSliceThickness()`	Get the spacing between centers of the voxel in three dimension.
`javax.vecmath.Point3d`	`getTLHC()`	Get the position of the top left hand corner.
`double[]`	`getTLHCArray()`	Get the position of the top left hand corner.
`javax.vecmath.Tuple3d`	`getVoxelSpacing()`	Get the spacing between centers of the voxel in three dimension.
`double[]`	`getVoxelSpacingArray()`	Get the spacing between centers of the voxel in three dimension.
`boolean`	`isPointInSlicePlane(double[] location)`	Is an arbitrary point in the DICOM 3D coordinate space within the plane of the image.
`boolean`	`isPointInSlicePlane(javax.vecmath.Point3d point)`	Is an arbitrary point in the DICOM 3D coordinate space within the plane of the image.
`double[]`	`lookupImageCoordinate(double[] location)`	Given the present geometry, look up the location of a point specified in x,y and z coordinates of the point in the DICOM 3D coordinate space, and return the image coordinates (column and row offset).
`void`	`lookupImageCoordinate(double[] offsets, double[] location)`	Given the present geometry, look up the location of a point specified in x,y and z coordinates of the point in the DICOM 3D coordinate space, and return the image coordinates (column and row offset).
`void`	`lookupImageCoordinate(double[] location, double column, double row)`	Given the present geometry, look up the location of a point specified in image coordinates (column and row offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
`void`	`lookupImageCoordinate(double[] location, int column, int row)`	Given the present geometry, look up the location of a point specified in image coordinates (column and row offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
`double[]`	`lookupImageCoordinate(double column, double row)`	Given the present geometry, look up the location of a point specified in image coordinates (column and row offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
`double[]`	`lookupImageCoordinate(int column, int row)`	Given the present geometry, look up the location of a point specified in image coordinates (column and row offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
`protected void`	`makeNormal()`
`java.lang.String`	`toString()`	Get a human-readable rendering of the geometry.

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

- Field Detail
  - rowArray
```
protected double[] rowArray
```
  - row
```
protected javax.vecmath.Vector3d row
```
  - columnArray
```
protected double[] columnArray
```
  - column
```
protected javax.vecmath.Vector3d column
```
  - tlhc
```
protected javax.vecmath.Point3d tlhc
```
  - tlhcArray
```
protected double[] tlhcArray
```
  - voxelSpacing
```
protected javax.vecmath.Tuple3d voxelSpacing
```
  - voxelSpacingArray
```
protected double[] voxelSpacingArray
```
  - sliceThickness
```
protected double sliceThickness
```
  - dimensions
```
protected javax.vecmath.Tuple3d dimensions
```
  - normal
```
protected javax.vecmath.Vector3d normal
```
  - normalArray
```
protected double[] normalArray
```
  - R
```
protected int R
```
  - C
```
protected int C
```
- Constructor Detail
  - GeometryOfSlice
```
public GeometryOfSlice()
```
    Construct an empty geometry.
  - GeometryOfSlice
```
public GeometryOfSlice(javax.vecmath.Vector3d row,
                       javax.vecmath.Vector3d column,
                       javax.vecmath.Point3d tlhc,
                       javax.vecmath.Tuple3d voxelSpacing,
                       double sliceThickness,
                       javax.vecmath.Tuple3d dimensions)
```
    Construct the geometry.
    
    Parameters:
    
    row - the direction of the row as X, Y and Z components (direction cosines, unit vector) LPH+
    
    column - the direction of the column as X, Y and Z components (direction cosines, unit vector) LPH+
    
    tlhc - the position of the top left hand corner of the slice as a point (X, Y and Z) LPH+
    
    voxelSpacing - the row and column spacing and, if a volume, the slice interval (spacing between the centers of parallel slices) in mm
    
    sliceThickness - the slice thickness in mm
    
    dimensions - the row and column dimensions and 1 for the third dimension
  - GeometryOfSlice
```
public GeometryOfSlice(double[] rowArray,
                       double[] columnArray,
                       double[] tlhcArray,
                       double[] voxelSpacingArray,
                       double sliceThickness,
                       double[] dimensions)
```
    Construct the geometry.
    
    Parameters:
    
    rowArray - the direction of the row as X, Y and Z components (direction cosines, unit vector) LPH+
    
    columnArray - the direction of the column as X, Y and Z components (direction cosines, unit vector) LPH+
    
    tlhcArray - the position of the top left hand corner of the slice as a point (X, Y and Z) LPH+
    
    voxelSpacingArray - the row and column spacing and, if a volume, the slice interval (spacing between the centers of parallel slices) in mm
    
    sliceThickness - the slice thickness in mm
    
    dimensions - the row and column dimensions and 1 for the third dimension
- Method Detail
  - makeNormal
```
protected final void makeNormal()
```
  - getRow
```
public final javax.vecmath.Vector3d getRow()
```
    Get the row direction.
    
    Returns:
    
    the direction of the row as X, Y and Z components (direction cosines, unit vector) LPH+
  - getRowArray
```
public final double[] getRowArray()
```
    Get the row direction.
    
    Returns:
    
    the direction of the row as X, Y and Z components (direction cosines, unit vector) LPH+
  - getColumn
```
public final javax.vecmath.Vector3d getColumn()
```
    Get the column direction.
    
    Returns:
    
    the direction of the column as X, Y and Z components (direction cosines, unit vector) LPH+
  - getColumnArray
```
public final double[] getColumnArray()
```
    Get the column direction.
    
    Returns:
    
    the direction of the column as X, Y and Z components (direction cosines, unit vector) LPH+
  - getNormal
```
public final javax.vecmath.Vector3d getNormal()
```
    Get the normal direction.
    
    Returns:
    
    the direction of the normal to the plane of the slices, as X, Y and Z components (direction cosines, unit vector) LPH+
  - getNormalArray
```
public final double[] getNormalArray()
```
    Get the normal direction.
    
    Returns:
    
    the direction of the normal to the plane of the slices, as X, Y and Z components (direction cosines, unit vector) LPH+
  - getTLHC
```
public final javax.vecmath.Point3d getTLHC()
```
    Get the position of the top left hand corner.
    
    Returns:
    
    the position of the top left hand corner of the slice as a point (X, Y and Z) LPH+
  - getTLHCArray
```
public final double[] getTLHCArray()
```
    Get the position of the top left hand corner.
    
    Returns:
    
    the position of the top left hand corner of the slice as a point (X, Y and Z) LPH+
  - getVoxelSpacing
```
public final javax.vecmath.Tuple3d getVoxelSpacing()
```
    Get the spacing between centers of the voxel in three dimension.
    
    Returns:
    
    the row and column spacing and, if a volume, the slice interval (spacing between the centers of parallel slices) in mm
  - getVoxelSpacingArray
```
public final double[] getVoxelSpacingArray()
```
    Get the spacing between centers of the voxel in three dimension.
    
    Returns:
    
    the row and column spacing and, if a volume, the slice interval (spacing between the centers of parallel slices) in mm
  - getSliceThickness
```
public final double getSliceThickness()
```
    Get the spacing between centers of the voxel in three dimension.
    
    Returns:
    
    the slice thickness in mm
  - getDimensions
```
public final javax.vecmath.Tuple3d getDimensions()
```
    Get the dimensions of the voxel.
    
    Returns:
    
    the row and column dimensions and 1 for the third dimension
  - lookupImageCoordinate
```
public final double[] lookupImageCoordinate(int column,
                                            int row)
```
    Given the present geometry, look up the location of a point specified in image coordinates (column and row offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
    
    Parameters:
    
    column - the offset along the column from the top left hand corner, zero being no offset
    
    row - the offset along the row from the top left hand corner, zero being no offset
    
    Returns:
    
    the x, y and z location in 3D space
  - lookupImageCoordinate
```
public final void lookupImageCoordinate(double[] location,
                                        int column,
                                        int row)
```
    Given the present geometry, look up the location of a point specified in image coordinates (column and row offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
    
    Parameters:
    
    location - an array in which to return the x, y and z location in 3D space
    
    column - the offset along the column from the top left hand corner, zero being no offset
    
    row - the offset along the row from the top left hand corner, zero being no offset
  - lookupImageCoordinate
```
public final double[] lookupImageCoordinate(double column,
                                            double row)
```
    Given the present geometry, look up the location of a point specified in image coordinates (column and row offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
    
    Parameters:
    
    column - the offset along the column from the top left hand corner, zero being no offset
    
    row - the offset along the row from the top left hand corner, zero being no offset
    
    Returns:
    
    the x, y and z location in 3D space
  - lookupImageCoordinate
```
public final void lookupImageCoordinate(double[] location,
                                        double column,
                                        double row)
```
    Given the present geometry, look up the location of a point specified in image coordinates (column and row offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
    
    Parameters:
    
    location - an array in which to return the x, y and z location in 3D space
    
    column - the offset along the column from the top left hand corner, zero being no offset
    
    row - the offset along the row from the top left hand corner, zero being no offset
  - lookupImageCoordinate
```
public final double[] lookupImageCoordinate(double[] location)
```
    Given the present geometry, look up the location of a point specified in x,y and z coordinates of the point in the DICOM 3D coordinate space, and return the image coordinates (column and row offset).
    
    Parameters:
    
    location - the x, y and z location in 3D space
    
    Returns:
    
    the column and row offsets from the top left hand corner of the image
  - findMaxComponents
```
protected final void findMaxComponents()
```
  - lookupImageCoordinate
```
public final void lookupImageCoordinate(double[] offsets,
                                        double[] location)
```
    Given the present geometry, look up the location of a point specified in x,y and z coordinates of the point in the DICOM 3D coordinate space, and return the image coordinates (column and row offset).
    
    Parameters:
    
    offsets - an array in which to return the column and row offsets from the top left hand corner of the image
    
    location - the x, y and z location in 3D space
  - getDistanceAlongNormalFromOrigin
```
public final double getDistanceAlongNormalFromOrigin(javax.vecmath.Point3d point)
```
    Given the present geometry, determine the distance along the normal to the plane of the slice of an arbitrary point (not necessarily in the plane of the image) from the origin of the coordinate space (0,0,0).
    
    Parameters:
    
    point - the point
    
    Returns:
    
    the distance of the point from the origin along the normal axis
  - getDistanceAlongNormalFromOrigin
```
public final double getDistanceAlongNormalFromOrigin()
```
    Given the present geometry, determine the distance along the normal to the plane of the slice of the TLHC of the image from the origin of the coordinate space (0,0,0).
    
    Returns:
    
    the distance of the TLHC from the origin along the normal axis
  - isPointInSlicePlane
```
public final boolean isPointInSlicePlane(javax.vecmath.Point3d point)
```
    Is an arbitrary point in the DICOM 3D coordinate space within the plane of the image.
    
    Slice thickness is not considered, only floating point rounding precision tolerance is permitted.
    
    Parameters:
    
    point - the point
    
    Returns:
    
    true if within the plane of the image
  - isPointInSlicePlane
```
public final boolean isPointInSlicePlane(double[] location)
```
    Is an arbitrary point in the DICOM 3D coordinate space within the plane of the image.
    
    Slice thickness is not considered, only floating point rounding precision tolerance is permitted.
    
    Parameters:
    
    location - the point
    
    Returns:
    
    true if within the plane of the image
  - areSlicesParallel
```
public static final boolean areSlicesParallel(GeometryOfSlice slice1,
                                              GeometryOfSlice slice2)
```
    Determine if two slices are parallel.
    
    Parameters:
    
    slice1 - the geometry of one slice
    
    slice2 - the geometry of the other slice
    
    Returns:
    
    true if slices are parallel
  - toString
```
public final java.lang.String toString()
```
    Get a human-readable rendering of the geometry.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    the string rendering of the geometry
  - getOrientation
```
public static final java.lang.String getOrientation(double[] orientation,
                                                    boolean quadruped)
```
    Get the letter representation of the orientation of a vector.
    
    For bipeds, L or R, A or P, H or F.
    
    For quadrupeds, Le or Rt, V or D, Cr or Cd (with lower case; use toUpperCase() to produce valid CodeString for PatientOrientation).
    
    Parameters:
    
    orientation - the orientation
    
    quadruped - true if subject is a quadruped rather than a biped
    
    Returns:
    
    a string rendering of the orientation, more than one letter if oblique to the orthogonal axes, or empty string (not null) if fails
  - getOrientation
```
public static final java.lang.String getOrientation(double[] orientation)
```
    Get the letter representation of the orientation of a vector.
    
    Assumes a biped rather than a quadruped, so returns L or R, A or P, H or F.
    
    Parameters:
    
    orientation - the orientation
    
    Returns:
    
    a string rendering of the orientation, more than one letter if oblique to the orthogonal axes, or empty string (not null) if fails
  - getRowOrientation
```
public final java.lang.String getRowOrientation(boolean quadruped)
```
    Get the letter representation of the orientation of the rows of this slice.
    
    For bipeds, L or R, A or P, H or F.
    
    For quadrupeds, Le or Rt, V or D, Cr or Cd (with lower case; use toUpperCase() to produce valid CodeString for PatientOrientation).
    
    Parameters:
    
    quadruped - true if subject is a quadruped rather than a biped
    
    Returns:
    
    a string rendering of the row orientation, more than one letter if oblique to the orthogonal axes, or empty string (not null) if fails
  - getColumnOrientation
```
public final java.lang.String getColumnOrientation(boolean quadruped)
```
    Get the letter representation of the orientation of the columns of this slice.
    
    For bipeds, L or R, A or P, H or F.
    
    For quadrupeds, Le or Rt, V or D, Cr or Cd (with lower case; use toUpperCase() to produce valid CodeString for PatientOrientation).
    
    Parameters:
    
    quadruped - true if subject is a quadruped rather than a biped
    
    Returns:
    
    a string rendering of the column orientation, more than one letter if oblique to the orthogonal axes, or empty string (not null) if fails
  - getRowOrientation
```
public final java.lang.String getRowOrientation()
```
    Get the letter representation of the orientation of the rows of this slice.
    
    Assumes a biped rather than a quadruped, so returns L or R, A or P, H or F.
    
    Returns:
    
    a string rendering of the row orientation, more than one letter if oblique to the orthogonal axes, or empty string (not null) if fails
  - getColumnOrientation
```
public final java.lang.String getColumnOrientation()
```
    Get the letter representation of the orientation of the columns of this slice.
    
    Assumes a biped rather than a quadruped, so returns L or R, A or P, H or F.
    
    Returns:
    
    a string rendering of the column orientation, more than one letter if oblique to the orthogonal axes, or empty string (not null) if fails

Class GeometryOfSlice

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

rowArray

row

columnArray

column

tlhc

tlhcArray

voxelSpacing

voxelSpacingArray

sliceThickness

dimensions

normal

normalArray

R

C

Constructor Detail

GeometryOfSlice

GeometryOfSlice

GeometryOfSlice

Method Detail

makeNormal

getRow

getRowArray

getColumn

getColumnArray

getNormal

getNormalArray

getTLHC

getTLHCArray

getVoxelSpacing

getVoxelSpacingArray

getSliceThickness

getDimensions

lookupImageCoordinate

lookupImageCoordinate

lookupImageCoordinate

lookupImageCoordinate

lookupImageCoordinate

findMaxComponents

lookupImageCoordinate

getDistanceAlongNormalFromOrigin

getDistanceAlongNormalFromOrigin

isPointInSlicePlane

isPointInSlicePlane

areSlicesParallel

toString

getOrientation

getOrientation

getRowOrientation

getColumnOrientation

getRowOrientation

getColumnOrientation