com.pixelmed.geometry

Class LocalizerPoster

java.lang.Object

com.pixelmed.geometry.LocalizerPoster

public abstract class LocalizerPoster
extends java.lang.Object

An abstract class that provides the basis for posting the position of specified slices and volumes on (usually orthogonal) localizer images.

This base class provides the interface, common storage and various utility methods, and specific methods of performing the localization operation are performed by concrete sub-classes, instantiated through a factory class.

Typically this would b used as follows, to get outlines in the form of a vector of shapes whose coordinates are those of the localizer image:

GeometryOfSlice localizerGeometry = new GeometryOfSliceFromAttributeList(localizerAttributeList);
GeometryOfSlice postImageGeometry = new GeometryOfSliceFromAttributeList(postImageAttributeList);
LocalizerPoster localizerPoster = LocalizerPosterFactory.getLocalizerPoster(false,false);
localizerPoster.setLocalizerGeometry(localizerGeometry);
Vector shapes = localizerPoster.getOutlineOnLocalizerForThisGeometry(postImageGeometry);
 

See Also:

LocalizerPosterFactory, GeometryOfSlice, GeometryOfSliceFromAttributeList

Field Summary

Fields

Modifier and Type	Field and Description
protected javax.vecmath.Vector3d	localizerColumn
protected javax.vecmath.Tuple3d	localizerDimensions
protected double[]	localizerDimensionsArray
protected javax.vecmath.Vector3d	localizerNormal
protected javax.vecmath.Vector3d	localizerRow
protected javax.vecmath.Point3d	localizerTLHC
protected javax.vecmath.Tuple3d	localizerVoxelSpacing
protected double[]	localizerVoxelSpacingArray
protected javax.vecmath.Matrix3d	rotateIntoLocalizerSpace

Method Summary

Modifier and Type	Method and Description
protected static boolean	classifyCornersIntoEdgeCrossingZPlane(javax.vecmath.Point3d startCorner, javax.vecmath.Point3d endCorner)
protected void	doCommonConstructorStuff()
protected java.util.Vector	drawLinesBetweenAnyPointsWhichIntersectPlaneWhereZIsZero(javax.vecmath.Point3d[] corners)
protected java.util.Vector	drawOutlineOnLocalizer(javax.vecmath.Point3d[] corners)
protected java.util.Vector	drawOutlineOnLocalizer(java.util.Vector corners)
static java.awt.Rectangle	getBoundsOfContainedRectangle(javax.vecmath.Point3d[] containedRectangle, javax.vecmath.Point3d[] wholeRectangle, java.awt.Rectangle boundsOfWholeRectangle)
static javax.vecmath.Point3d[]	getCornersOfSourceCubeInSourceSpace(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column, javax.vecmath.Point3d originalTLHC, javax.vecmath.Tuple3d voxelSpacing, double sliceThickness, javax.vecmath.Tuple3d dimensions) Get the corners of a volume in the 3D coordinate space of that volume.
static javax.vecmath.Point3d[]	getCornersOfSourceRectangleInSourceSpace(GeometryOfSlice g) Get the corners of a slice in the 3D coordinate space of that slice.
static javax.vecmath.Point3d[]	getCornersOfSourceRectangleInSourceSpace(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column, javax.vecmath.Point3d originalTLHC, javax.vecmath.Tuple3d voxelSpacing, javax.vecmath.Tuple3d dimensions) Get the corners of a slice in the 3D coordinate space of that slice.
static javax.vecmath.Point3d[]	getIntersectionOfRectanglesInXYPlane(javax.vecmath.Point3d[] rect1, javax.vecmath.Point3d[] rect2)
protected java.util.Vector	getIntersectionsOfCubeWithZPlane(javax.vecmath.Point3d[] corners)
java.util.Vector	getOutlineOnLocalizerForThisGeometry(GeometryOfSlice geometry) Get the shape on the localizer of a zero-thickness slice specified by the geometry of a 2D rectangle.
abstract java.util.Vector	getOutlineOnLocalizerForThisGeometry(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column, javax.vecmath.Point3d tlhc, javax.vecmath.Tuple3d voxelSpacing, double sliceThickness, javax.vecmath.Tuple3d dimensions) Get the shapes on the localizer of the specified slice.
java.util.Vector	getOutlineOnLocalizerForThisVolumeLocalization(SpectroscopyVolumeLocalization spectroscopyVolumeLocalization) Get the shape on the localizer of one or more volume localization slabs.
protected javax.vecmath.Point3d	intersectLineBetweenTwoPointsWithPlaneWhereZIsZero(double[] a, double[] b)
protected javax.vecmath.Point3d	intersectLineBetweenTwoPointsWithPlaneWhereZIsZero(javax.vecmath.Point3d aP, javax.vecmath.Point3d bP)
void	setLocalizerGeometry(GeometryOfSlice geometry) Established the geometry of the localizer image to be posted.
void	setLocalizerGeometry(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column, javax.vecmath.Point3d tlhc, javax.vecmath.Tuple3d voxelSpacing, javax.vecmath.Tuple3d dimensions) Established the geometry of the localizer image to be posted.
protected javax.vecmath.Point3d	transformPointFromSourceSpaceIntoLocalizerSpace(javax.vecmath.Point3d point) Transform a point into the "viewport" defined by the localizer that we are an instance of.
static javax.vecmath.Point3d	transformPointFromSourceSpaceIntoSpecifiedSpace(javax.vecmath.Point3d point, javax.vecmath.Point3d tlhc, javax.vecmath.Vector3d row, javax.vecmath.Vector3d column) Transform a point into the "viewport" defined by an origin and row and column vectors in the same 3D space, by shifting the points to the origin (TLHC) and rotating.
protected java.awt.geom.Point2D.Double	transformPointInLocalizerPlaneIntoImageSpace(javax.vecmath.Point3d point) Project a point in localizer 3D space onto the plane of the localizer by ignoring the Z component, and return the X and Y coordinates as image-TLHC relative column and row offsets.
static javax.vecmath.Point3d[]	transformPointsFromSourceSpaceIntoSpecifiedSpace(javax.vecmath.Point3d[] points, javax.vecmath.Point3d tlhc, javax.vecmath.Vector3d row, javax.vecmath.Vector3d column) Transform a set of points into the "viewport" defined by an origin and row and column vectors in the same 3D space, by shifting the points to the origin (TLHC) and rotating.
static void	validateDirectionCosines(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column) Check that the row and column vectors are unit vectors and are orthogonal.
static void	validateDirectionCosines(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column, javax.vecmath.Vector3d normal) Check that the row and column and slice direction vectors are unit vectors and are orthogonal.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

localizerColumn

protected javax.vecmath.Vector3d localizerColumn

localizerDimensions

protected javax.vecmath.Tuple3d localizerDimensions

localizerDimensionsArray

protected double[] localizerDimensionsArray

localizerNormal

protected javax.vecmath.Vector3d localizerNormal

localizerRow

protected javax.vecmath.Vector3d localizerRow

localizerTLHC

protected javax.vecmath.Point3d localizerTLHC

localizerVoxelSpacing

protected javax.vecmath.Tuple3d localizerVoxelSpacing

localizerVoxelSpacingArray

protected double[] localizerVoxelSpacingArray

rotateIntoLocalizerSpace

protected javax.vecmath.Matrix3d rotateIntoLocalizerSpace

Method Detail

classifyCornersIntoEdgeCrossingZPlane

protected static boolean classifyCornersIntoEdgeCrossingZPlane(javax.vecmath.Point3d startCorner,
                                                               javax.vecmath.Point3d endCorner)

doCommonConstructorStuff

protected void doCommonConstructorStuff()

drawLinesBetweenAnyPointsWhichIntersectPlaneWhereZIsZero

protected java.util.Vector drawLinesBetweenAnyPointsWhichIntersectPlaneWhereZIsZero(javax.vecmath.Point3d[] corners)

drawOutlineOnLocalizer

protected java.util.Vector drawOutlineOnLocalizer(javax.vecmath.Point3d[] corners)

drawOutlineOnLocalizer

protected java.util.Vector drawOutlineOnLocalizer(java.util.Vector corners)

getBoundsOfContainedRectangle

public static java.awt.Rectangle getBoundsOfContainedRectangle(javax.vecmath.Point3d[] containedRectangle,
                                                               javax.vecmath.Point3d[] wholeRectangle,
                                                               java.awt.Rectangle boundsOfWholeRectangle)

getCornersOfSourceCubeInSourceSpace

public static javax.vecmath.Point3d[] getCornersOfSourceCubeInSourceSpace(javax.vecmath.Vector3d row,
                                                                          javax.vecmath.Vector3d column,
                                                                          javax.vecmath.Point3d originalTLHC,
                                                                          javax.vecmath.Tuple3d voxelSpacing,
                                                                          double sliceThickness,
                                                                          javax.vecmath.Tuple3d dimensions)

Get the corners of a volume in the 3D coordinate space of that volume.

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+

originalTLHC - 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 the slice interval

sliceThickness - the slice thickness

dimensions - the row and column dimensions and number of frames for the third dimension

Returns:

an array of eight points that are the tlhcT, trhcT, brhcT, blhcT, tlhcB, trhcB, brhcB, blhcB of the volume

getCornersOfSourceRectangleInSourceSpace

public static javax.vecmath.Point3d[] getCornersOfSourceRectangleInSourceSpace(GeometryOfSlice g)

Get the corners of a slice in the 3D coordinate space of that slice.

Parameters:

g - the geometry of a slice

Returns:

an array of four points that are the tlhc,trhc, brhc, blhc of the slice

getCornersOfSourceRectangleInSourceSpace

public static javax.vecmath.Point3d[] getCornersOfSourceRectangleInSourceSpace(javax.vecmath.Vector3d row,
                                                                               javax.vecmath.Vector3d column,
                                                                               javax.vecmath.Point3d originalTLHC,
                                                                               javax.vecmath.Tuple3d voxelSpacing,
                                                                               javax.vecmath.Tuple3d dimensions)

Get the corners of a slice in the 3D coordinate space of that slice.

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+

originalTLHC - 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 the slice interval

dimensions - the row and column dimensions and 1 for the third dimension

Returns:

an array of four points that are the tlhc,trhc, brhc, blhc of the slice

getIntersectionOfRectanglesInXYPlane

public static javax.vecmath.Point3d[] getIntersectionOfRectanglesInXYPlane(javax.vecmath.Point3d[] rect1,
                                                                           javax.vecmath.Point3d[] rect2)

getIntersectionsOfCubeWithZPlane

protected java.util.Vector getIntersectionsOfCubeWithZPlane(javax.vecmath.Point3d[] corners)

getOutlineOnLocalizerForThisGeometry

public final java.util.Vector getOutlineOnLocalizerForThisGeometry(GeometryOfSlice geometry)

Get the shape on the localizer of a zero-thickness slice specified by the geometry of a 2D rectangle.

Parameters:

geometry -

Returns:

vector of shapes java.awt.Shape to be drawn in the localizer row and column coordinates

getOutlineOnLocalizerForThisGeometry

public abstract java.util.Vector getOutlineOnLocalizerForThisGeometry(javax.vecmath.Vector3d row,
                                                                      javax.vecmath.Vector3d column,
                                                                      javax.vecmath.Point3d tlhc,
                                                                      javax.vecmath.Tuple3d voxelSpacing,
                                                                      double sliceThickness,
                                                                      javax.vecmath.Tuple3d dimensions)

Get the shapes on the localizer of the specified slice.

Parameters:

row - the unit vector (direction cosine) of the row direction in the DICOM coordinate system

column - the unit vector (direction cosine) of the row direction in the DICOM coordinate system

tlhc - the position in the DICOM coordinate system of the center of the top left hand corner pixel of the slice

voxelSpacing - the row and column and slice interval in mm

sliceThickness - the slice thickness in mm

dimensions - the number of rows and columns and slices

Returns:

vector of shapes java.awt.Shape to be drawn in the localizer row and column coordinates

getOutlineOnLocalizerForThisVolumeLocalization

public final java.util.Vector getOutlineOnLocalizerForThisVolumeLocalization(SpectroscopyVolumeLocalization spectroscopyVolumeLocalization)

Get the shape on the localizer of one or more volume localization slabs.

Parameters:

spectroscopyVolumeLocalization -

Returns:

vector of shapes java.awt.Shape to be drawn in the localizer row and column coordinates

intersectLineBetweenTwoPointsWithPlaneWhereZIsZero

protected javax.vecmath.Point3d intersectLineBetweenTwoPointsWithPlaneWhereZIsZero(double[] a,
                                                                                   double[] b)

intersectLineBetweenTwoPointsWithPlaneWhereZIsZero

protected javax.vecmath.Point3d intersectLineBetweenTwoPointsWithPlaneWhereZIsZero(javax.vecmath.Point3d aP,
                                                                                   javax.vecmath.Point3d bP)

setLocalizerGeometry

public void setLocalizerGeometry(GeometryOfSlice geometry)

Established the geometry of the localizer image to be posted.

Parameters:

geometry -

setLocalizerGeometry

public void setLocalizerGeometry(javax.vecmath.Vector3d row,
                                 javax.vecmath.Vector3d column,
                                 javax.vecmath.Point3d tlhc,
                                 javax.vecmath.Tuple3d voxelSpacing,
                                 javax.vecmath.Tuple3d dimensions)

Established the geometry of the localizer image to be posted.

Parameters:

row - the unit vector (direction cosine) of the row direction in the DICOM coordinate system

column - the unit vector (direction cosine) of the row direction in the DICOM coordinate system

tlhc - the position in the DICOM coordinate system of the center of the top left hand corner of the image

voxelSpacing - the row and column pixel spacing in mm

dimensions - the number of rows and columns

transformPointFromSourceSpaceIntoLocalizerSpace

protected javax.vecmath.Point3d transformPointFromSourceSpaceIntoLocalizerSpace(javax.vecmath.Point3d point)

Transform a point into the "viewport" defined by the localizer that we are an instance of.

Parameters:

point - a 3D point to be transformed

Returns:

a new, transformed point

transformPointFromSourceSpaceIntoSpecifiedSpace

public static javax.vecmath.Point3d transformPointFromSourceSpaceIntoSpecifiedSpace(javax.vecmath.Point3d point,
                                                                                    javax.vecmath.Point3d tlhc,
                                                                                    javax.vecmath.Vector3d row,
                                                                                    javax.vecmath.Vector3d column)

Transform a point into the "viewport" defined by an origin and row and column vectors in the same 3D space, by shifting the points to the origin (TLHC) and rotating.

Parameters:

point - a 3D point to be transformed

tlhc - the position of the top left hand corner of the slice as a point (X, Y and Z) LPH+

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+

Returns:

a new, transformed point

transformPointInLocalizerPlaneIntoImageSpace

protected java.awt.geom.Point2D.Double transformPointInLocalizerPlaneIntoImageSpace(javax.vecmath.Point3d point)

Project a point in localizer 3D space onto the plane of the localizer by ignoring the Z component, and return the X and Y coordinates as image-TLHC relative column and row offsets.

Will return sub-pixel values ranging from 0.5 to 0.5 less than the maximum dimensions of the image, which allows points at the very edges of the rendered image to be drawn (e.g. a column of 0.5 will draw at the extreme left and a column of 255.5 will draw at the extreme right of a 256 pixel wide image (whereas 256.0 will not, though 0.0 will).

Parameters:

point - the point in 3D localizer space, the Z coordinate of which is ignored

Returns:

an array of 2 values in which the column, then the row location on the image is returned

transformPointsFromSourceSpaceIntoSpecifiedSpace

public static javax.vecmath.Point3d[] transformPointsFromSourceSpaceIntoSpecifiedSpace(javax.vecmath.Point3d[] points,
                                                                                       javax.vecmath.Point3d tlhc,
                                                                                       javax.vecmath.Vector3d row,
                                                                                       javax.vecmath.Vector3d column)

Transform a set of points into the "viewport" defined by an origin and row and column vectors in the same 3D space, by shifting the points to the origin (TLHC) and rotating.

Parameters:

points - an array of 3D points to be transformed

tlhc - the position of the top left hand corner of the slice as a point (X, Y and Z) LPH+

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+

Returns:

a new array of transformed points

validateDirectionCosines

public static void validateDirectionCosines(javax.vecmath.Vector3d row,
                                            javax.vecmath.Vector3d column)
                                     throws java.lang.IllegalArgumentException

Check that the row and column vectors are unit vectors and are orthogonal.

Parameters:

row - the row direction cosines

column - the column direction cosines

Throws:

java.lang.IllegalArgumentException - thrown if not

validateDirectionCosines

public static void validateDirectionCosines(javax.vecmath.Vector3d row,
                                            javax.vecmath.Vector3d column,
                                            javax.vecmath.Vector3d normal)
                                     throws java.lang.IllegalArgumentException

Check that the row and column and slice direction vectors are unit vectors and are orthogonal.

Parameters:

row - the row direction cosines

column - the column direction cosines

normal - the normal to the row and column plane (the slice direction)

Throws:

java.lang.IllegalArgumentException - thrown if not