Class LocalizerPoster
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);
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected javax.vecmath.Vector3d
protected javax.vecmath.Tuple3d
protected double[]
protected javax.vecmath.Vector3d
protected javax.vecmath.Vector3d
protected javax.vecmath.Point3d
protected javax.vecmath.Tuple3d
protected double[]
protected javax.vecmath.Matrix3d
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Method Summary
Modifier and TypeMethodDescriptionprotected static boolean
classifyCornersIntoEdgeCrossingZPlane
(javax.vecmath.Point3d startCorner, javax.vecmath.Point3d endCorner) protected void
protected Vector
drawLinesBetweenAnyPointsWhichIntersectPlaneWhereZIsZero
(javax.vecmath.Point3d[] corners) protected Vector
drawOutlineOnLocalizer
(Vector corners) protected Vector
drawOutlineOnLocalizer
(javax.vecmath.Point3d[] corners) static Rectangle
getBoundsOfContainedRectangle
(javax.vecmath.Point3d[] containedRectangle, javax.vecmath.Point3d[] wholeRectangle, 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[]
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 Vector
getIntersectionsOfCubeWithZPlane
(javax.vecmath.Point3d[] corners) final Vector
Get the shape on the localizer of a zero-thickness slice specified by the geometry of a 2D rectangle.abstract 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.final 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 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.
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Field Details
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localizerRow
protected javax.vecmath.Vector3d localizerRow -
localizerColumn
protected javax.vecmath.Vector3d localizerColumn -
localizerNormal
protected javax.vecmath.Vector3d localizerNormal -
localizerTLHC
protected javax.vecmath.Point3d localizerTLHC -
localizerVoxelSpacing
protected javax.vecmath.Tuple3d localizerVoxelSpacing -
localizerVoxelSpacingArray
protected double[] localizerVoxelSpacingArray -
localizerDimensions
protected javax.vecmath.Tuple3d localizerDimensions -
localizerDimensionsArray
protected double[] localizerDimensionsArray -
rotateIntoLocalizerSpace
protected javax.vecmath.Matrix3d rotateIntoLocalizerSpace
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Method Details
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validateDirectionCosines
public static void validateDirectionCosines(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column) throws IllegalArgumentException Check that the row and column vectors are unit vectors and are orthogonal.
- Parameters:
row
- the row direction cosinescolumn
- the column direction cosines- Throws:
IllegalArgumentException
- thrown if not
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validateDirectionCosines
public static void validateDirectionCosines(javax.vecmath.Vector3d row, javax.vecmath.Vector3d column, javax.vecmath.Vector3d normal) throws IllegalArgumentException Check that the row and column and slice direction vectors are unit vectors and are orthogonal.
- Parameters:
row
- the row direction cosinescolumn
- the column direction cosinesnormal
- the normal to the row and column plane (the slice direction)- Throws:
IllegalArgumentException
- thrown if not
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getCornersOfSourceRectangleInSourceSpace
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
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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 intervaldimensions
- 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
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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 intervalsliceThickness
- the slice thicknessdimensions
- 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
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getIntersectionOfRectanglesInXYPlane
public static javax.vecmath.Point3d[] getIntersectionOfRectanglesInXYPlane(javax.vecmath.Point3d[] rect1, javax.vecmath.Point3d[] rect2) -
getBoundsOfContainedRectangle
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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 transformedtlhc
- 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
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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 transformedtlhc
- 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
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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
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transformPointInLocalizerPlaneIntoImageSpace
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
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drawOutlineOnLocalizer
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drawOutlineOnLocalizer
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intersectLineBetweenTwoPointsWithPlaneWhereZIsZero
protected javax.vecmath.Point3d intersectLineBetweenTwoPointsWithPlaneWhereZIsZero(double[] a, double[] b) -
intersectLineBetweenTwoPointsWithPlaneWhereZIsZero
protected javax.vecmath.Point3d intersectLineBetweenTwoPointsWithPlaneWhereZIsZero(javax.vecmath.Point3d aP, javax.vecmath.Point3d bP) -
drawLinesBetweenAnyPointsWhichIntersectPlaneWhereZIsZero
protected Vector drawLinesBetweenAnyPointsWhichIntersectPlaneWhereZIsZero(javax.vecmath.Point3d[] corners) -
classifyCornersIntoEdgeCrossingZPlane
protected static boolean classifyCornersIntoEdgeCrossingZPlane(javax.vecmath.Point3d startCorner, javax.vecmath.Point3d endCorner) -
getIntersectionsOfCubeWithZPlane
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doCommonConstructorStuff
protected void doCommonConstructorStuff() -
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 systemcolumn
- the unit vector (direction cosine) of the row direction in the DICOM coordinate systemtlhc
- the position in the DICOM coordinate system of the center of the top left hand corner of the imagevoxelSpacing
- the row and column pixel spacing in mmdimensions
- the number of rows and columns
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setLocalizerGeometry
Established the geometry of the localizer image to be posted.
- Parameters:
geometry
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getOutlineOnLocalizerForThisGeometry
public abstract 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 systemcolumn
- the unit vector (direction cosine) of the row direction in the DICOM coordinate systemtlhc
- the position in the DICOM coordinate system of the center of the top left hand corner pixel of the slicevoxelSpacing
- the row and column and slice interval in mmsliceThickness
- the slice thickness in mmdimensions
- 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
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getOutlineOnLocalizerForThisGeometry
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
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getOutlineOnLocalizerForThisVolumeLocalization
public final 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
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