Class GeometryOfVolume
- Direct Known Subclasses:
GeometryOfVolumeFromAttributeList
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.
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
protected int
protected GeometryOfSlice[]
protected boolean
protected int
protected int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionfinal boolean
Are all the frames in the set of frames parallel ?final void
Check if the set of frames regularly sampled along the frame dimension.final int
findClosestSliceInSamePlane
(GeometryOfSlice otherSlice) Find the slice in the our geometry that is closest to the supplied slice geometry.protected final void
findMaxComponents
(double[] rowArray, double[] columnArray, double[] normalArray) final String
getColumnOrientation
(int frame) Get the letter representation of the orientation of the columns of this slice.final String
getColumnOrientation
(int frame, boolean quadruped) Get the letter representation of the orientation of the columns of this slice.final double[]
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).final GeometryOfSlice
getGeometryOfSlice
(int frame) Get the geometry of the selected slice.final GeometryOfSlice[]
Get the geometry of the slices.final int
Get the number of slices.final String
getRowOrientation
(int frame) Get the letter representation of the orientation of the rows of this slice.final String
getRowOrientation
(int frame, boolean quadruped) Get the letter representation of the orientation of the rows of this slice.final boolean
Is the geometry of each frame available?final boolean
Is the set of frames regularly sampled along the frame dimension?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).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).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.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.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.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.final String
toString()
Get a human-readable rendering of the geometry.
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Field Details
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frames
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R
protected int R -
C
protected int C -
N
protected int N -
areParallel
protected boolean areParallel -
isVolume
protected boolean isVolume
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Constructor Details
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GeometryOfVolume
protected GeometryOfVolume() -
GeometryOfVolume
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Method Details
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getNumberOfSlices
public final int getNumberOfSlices()Get the number of slices.
- Returns:
- the number of slices
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getGeometryOfSlices
Get the geometry of the slices.
- Returns:
- an array of the geometry of the slices
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getGeometryOfSlice
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
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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 offsetrow
- the offset along the row from the top left hand corner, zero being no offsetframe
- the offset along the frames from first frame, zero being no offset- Returns:
- the x, y and z location in 3D space
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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 spacecolumn
- the offset along the column from the top left hand corner, zero being no offsetrow
- the offset along the row from the top left hand corner, zero being no offsetframe
- the offset along the frames from first frame, zero being no offset
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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 offsetrow
- the offset along the row from the top left hand corner, zero being no offsetframe
- the offset along the frames from first frame, zero being no offset- Returns:
- the x, y and z location in 3D space
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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 spacecolumn
- the offset along the column from the top left hand corner, zero being no offsetrow
- the offset along the row from the top left hand corner, zero being no offsetframe
- the offset along the frames from first frame, zero being no offset
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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)
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findMaxComponents
protected final void findMaxComponents(double[] rowArray, double[] columnArray, double[] normalArray) -
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
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findClosestSliceInSamePlane
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
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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
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areAllSlicesParallel
public final boolean areAllSlicesParallel()Are all the frames in the set of frames parallel ?
- Returns:
- true if all frames have the same orientation
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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
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hasFrameInformation
public final boolean hasFrameInformation()Is the geometry of each frame available?
- Returns:
- true if per-slice geometry of each frame is available
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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.
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toString
Get a human-readable rendering of the geometry.
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getRowOrientation
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 offsetquadruped
- 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
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getColumnOrientation
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 offsetquadruped
- 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
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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.
- 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
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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.
- 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
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