com.pixelmed.geometry

Class GeometryOfVolume

java.lang.Object

com.pixelmed.geometry.GeometryOfVolume

Direct Known Subclasses:

GeometryOfVolumeFromAttributeList

public class GeometryOfVolume
extends java.lang.Object

A class to describe the spatial geometry of an entire volume of contiguous cross-sectional image slices.

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 and Description
protected boolean	areParallel
protected int	C
protected GeometryOfSlice[]	frames
protected boolean	isVolume
protected int	N
protected int	R

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	GeometryOfVolume()
	GeometryOfVolume(GeometryOfSlice[] frames)

Method Summary

Modifier and Type	Method and Description
boolean	areAllSlicesParallel() Are all the frames in the set of frames parallel ?
void	checkAndSetVolumeSampledRegularlyAlongFrameDimension() Check if the set of frames regularly sampled along the frame dimension.
int	findClosestSliceInSamePlane(GeometryOfSlice otherSlice) Find the slice in the our geometry that is closest to the supplied slice geometry.
protected void	findMaxComponents(double[] rowArray, double[] columnArray, double[] normalArray)
java.lang.String	getColumnOrientation(int frame) Get the letter representation of the orientation of the columns of this slice.
java.lang.String	getColumnOrientation(int frame, boolean quadruped) Get the letter representation of the orientation of the columns of this slice.
double[]	getDistanceAlongNormalFromOrigin() Given the present geometry, determine the distances along the normal to the plane of the slices of the TLHC of each slice from the origin of the coordinate space (0,0,0).
GeometryOfSlice	getGeometryOfSlice(int frame) Get the geometry of the selected slice.
GeometryOfSlice[]	getGeometryOfSlices() Get the geometry of the slices.
int	getNumberOfSlices() Get the number of slices.
java.lang.String	getRowOrientation(int frame) Get the letter representation of the orientation of the rows of this slice.
java.lang.String	getRowOrientation(int frame, boolean quadruped) Get the letter representation of the orientation of the rows of this slice.
boolean	hasFrameInformation() Is the geometry of each frame available?
boolean	isVolumeSampledRegularlyAlongFrameDimension() Is the set of frames regularly sampled along the frame dimension?
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 volume coordinates (column and row and frame 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 volume coordinates (column and row and frame offset).
void	lookupImageCoordinate(double[] location, double column, double row, int frame) Given the present geometry, look up the location of a point specified in image coordinates (column and row and frame 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, int frame) Given the present geometry, look up the location of a point specified in image coordinates (column and row and frame offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
double[]	lookupImageCoordinate(double column, double row, int frame) Given the present geometry, look up the location of a point specified in image coordinates (column and row and frame offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
double[]	lookupImageCoordinate(int column, int row, int frame) Given the present geometry, look up the location of a point specified in image coordinates (column and row and frame offset) and return the x,y and z coordinates of the point in the DICOM 3D coordinate space.
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

areParallel

protected boolean areParallel

C

protected int C

frames

protected GeometryOfSlice[] frames

isVolume

protected boolean isVolume

N

protected int N

R

protected int R

Constructor Detail

GeometryOfVolume

protected GeometryOfVolume()

GeometryOfVolume

public GeometryOfVolume(GeometryOfSlice[] frames)

Method Detail

areAllSlicesParallel

public final boolean areAllSlicesParallel()

Are all the frames in the set of frames parallel ?

Returns:

true if all frames have the same orientation

checkAndSetVolumeSampledRegularlyAlongFrameDimension

public final void checkAndSetVolumeSampledRegularlyAlongFrameDimension()

Check if the set of frames regularly sampled along the frame dimension.

Method is public only to make it accessible from constructors in other packages.

findClosestSliceInSamePlane

public final int findClosestSliceInSamePlane(GeometryOfSlice otherSlice)

Find the slice in the our geometry that is closest to the supplied slice geometry.

Specifically, the shortest distance along the normal to the plane of the common orientation is chosen.

Parameters:

otherSlice - the geometry of the slice to match

Returns:

the index of the closest frame in this volume (numbered from 0), or -1 if something goes wrong

findMaxComponents

protected final void findMaxComponents(double[] rowArray,
                                       double[] columnArray,
                                       double[] normalArray)

getColumnOrientation

public final java.lang.String getColumnOrientation(int frame)

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.

Parameters:

frame - the offset along the frames from first frame, zero being no offset

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

getColumnOrientation

public final java.lang.String getColumnOrientation(int frame,
                                                   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:

frame - the offset along the frames from first frame, zero being no offset

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

getDistanceAlongNormalFromOrigin

public final double[] getDistanceAlongNormalFromOrigin()

Given the present geometry, determine the distances along the normal to the plane of the slices of the TLHC of each slice from the origin of the coordinate space (0,0,0).

Returns:

an array of the distances of the TLHCs from the origin along the normal axis

getGeometryOfSlice

public final GeometryOfSlice getGeometryOfSlice(int frame)

Get the geometry of the selected slice.

Parameters:

frame - the offset along the frames from first frame, zero being no offset

Returns:

the geometry of the selected slice

getGeometryOfSlices

public final GeometryOfSlice[] getGeometryOfSlices()

Get the geometry of the slices.

Returns:

an array of the geometry of the slices

getNumberOfSlices

public final int getNumberOfSlices()

Get the number of slices.

Returns:

the number of slices

getRowOrientation

public final java.lang.String getRowOrientation(int frame)

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.

Parameters:

frame - the offset along the frames from first frame, zero being no offset

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

getRowOrientation

public final java.lang.String getRowOrientation(int frame,
                                                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:

frame - the offset along the frames from first frame, zero being no offset

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

hasFrameInformation

public final boolean hasFrameInformation()

Is the geometry of each frame available?

Returns:

true if per-slice geometry of each frame is available

isVolumeSampledRegularlyAlongFrameDimension

public final boolean isVolumeSampledRegularlyAlongFrameDimension()

Is the set of frames regularly sampled along the frame dimension?

Returns:

true if same spacing between centers of frames and position monotonically increasing

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 volume coordinates (column and row and frame offset).

Parameters:

location - the x, y and z location in 3D space

Returns:

the column and row and frame offsets from the top left hand corner of the volume (or NaN if not a regularly sampled volume)

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 volume coordinates (column and row and frame offset).

Parameters:

offsets - an array in which to return the column and row and frame offsets from the top left hand corner of the volume (or NaN if not a regularly sampled volume)

location - the x, y and z location in 3D space

lookupImageCoordinate

public final void lookupImageCoordinate(double[] location,
                                        double column,
                                        double row,
                                        int frame)

Given the present geometry, look up the location of a point specified in image coordinates (column and row and frame 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

frame - the offset along the frames from first frame, zero being no offset

lookupImageCoordinate

public final void lookupImageCoordinate(double[] location,
                                        int column,
                                        int row,
                                        int frame)

Given the present geometry, look up the location of a point specified in image coordinates (column and row and frame 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

frame - the offset along the frames from first frame, zero being no offset

lookupImageCoordinate

public final double[] lookupImageCoordinate(double column,
                                            double row,
                                            int frame)

Given the present geometry, look up the location of a point specified in image coordinates (column and row and frame 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

frame - the offset along the frames from first frame, zero being no offset

Returns:

the x, y and z location in 3D space

lookupImageCoordinate

public final double[] lookupImageCoordinate(int column,
                                            int row,
                                            int frame)

Given the present geometry, look up the location of a point specified in image coordinates (column and row and frame 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

frame - the offset along the frames from first frame, zero being no offset

Returns:

the x, y and z location in 3D space

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