woSource

Class DoseReader

java.lang.Object

woSource.DoseReader

All Implemented Interfaces:

ij.plugin.PlugIn

Direct Known Subclasses:

DoseCalc

public class DoseReader
extends java.lang.Object
implements ij.plugin.PlugIn

Field Summary

Fields

Modifier and Type	Field and Description
int	Depth
float[]	doseDepths
float	doseGridScalingFactor
float[]	doseHeights
protected Point3D	doseImgTopLeft
protected Point3D	doseImgXdir
protected Point3D	doseImgYdir
protected Point3D	doseImgZdir
Rectangle3D	doseRect
float[][][]	doseValues
float[]	doseWidths
protected double[]	fittedCoeffs
int	Height
java.lang.String	Label
float	mmPerPixelX
float	mmPerPixelY
int	rOrder
float	sliceThickness
int	thetaOrder
boolean	wasDicom
int	Width

Constructor Summary

Constructors

Constructor and Description
DoseReader()
DoseReader(java.lang.String arg)

Method Summary

Modifier and Type	Method and Description
void	avgToCenter()
Rectangle3D	convDose2CTscannerCoords(java.util.Properties[] CTprops, Point3D imgTLFmm, Rectangle3D roi, float[] CTdepthCoords, float[] CTwidthCoords, float[] CTheightCoords) returns the shifts needed to align the dose field to the image set, and // sets doseDepths, widths, heights [mm] and other parameters read from dicom header // WO 10/12/2012 modified to use dose data as 3D dicom image.
void	cropDoseField(int doffset, int woffset, int hoffset, int newdepth, int newwidth, int newheight)
void	fitDoseCoeffs() fit the 3D dose field to a spherical harmonic like series, probably intended to help create synthetic dose- response image set for testing and validation
void	flipDepth()
void	flipHeight()
void	flipWidth()
boolean	Read(java.lang.String arg)
void	run(java.lang.String arg) This method is called when the plugin is loaded.
void	showAbout()
void	smoothDoseValues(int rOrder, int thetaOrder)
java.lang.String	toString()
boolean	Write()

Methods inherited from class java.lang.Object

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

Field Detail

Label

public java.lang.String Label

Width

public int Width

Height

public int Height

Depth

public int Depth

doseDepths

public float[] doseDepths

doseWidths

public float[] doseWidths

doseHeights

public float[] doseHeights

doseValues

public float[][][] doseValues

doseGridScalingFactor

public float doseGridScalingFactor

doseRect

public Rectangle3D doseRect

mmPerPixelX

public float mmPerPixelX

mmPerPixelY

public float mmPerPixelY

sliceThickness

public float sliceThickness

fittedCoeffs

protected double[] fittedCoeffs

rOrder

public int rOrder

thetaOrder

public int thetaOrder

wasDicom

public boolean wasDicom

doseImgTopLeft

protected Point3D doseImgTopLeft

doseImgXdir

protected Point3D doseImgXdir

doseImgYdir

protected Point3D doseImgYdir

doseImgZdir

protected Point3D doseImgZdir

Constructor Detail

DoseReader

public DoseReader(java.lang.String arg)

DoseReader

public DoseReader()

Method Detail

run

public void run(java.lang.String arg)

Description copied from interface: ij.plugin.PlugIn

This method is called when the plugin is loaded. 'arg', which may be blank, is the argument specified for this plugin in IJ_Props.txt.

Specified by:

run in interface ij.plugin.PlugIn

showAbout

public void showAbout()

avgToCenter

public void avgToCenter()

cropDoseField

public void cropDoseField(int doffset,
                          int woffset,
                          int hoffset,
                          int newdepth,
                          int newwidth,
                          int newheight)

convDose2CTscannerCoords

public Rectangle3D convDose2CTscannerCoords(java.util.Properties[] CTprops,
                                            Point3D imgTLFmm,
                                            Rectangle3D roi,
                                            float[] CTdepthCoords,
                                            float[] CTwidthCoords,
                                            float[] CTheightCoords)

returns the shifts needed to align the dose field to the image set, and // sets doseDepths, widths, heights [mm] and other parameters read from dicom header // WO 10/12/2012 modified to use dose data as 3D dicom image. // UF Pinnacle conventions are origin = bottom-left corner of first CT image, while for dose Dicom // standard the Dicom header has origin = top-left corner of first slice, while the CT dicom is in // mm w.r.t. the scanner center. But it turns out that we do not need to worry about any of that // as for lungPt_000 and lungPt_017 the dose matrix Top-left-front is in scanner mm coords already, // so just need to invert the stack in depth direction to align with scanner coords. Note that you // also need to later sub-sample the dose field to match the different-sized CT image voxels (done // in DoseVsIntensity()

Returns:

Rectangle3D where x,y,z are the pixel indices of the TLF corner of the dose field, and width,height,depth are the pixel dimensions of the dose field

flipDepth

public void flipDepth()

flipWidth

public void flipWidth()

flipHeight

public void flipHeight()

Read

public boolean Read(java.lang.String arg)
             throws java.io.IOException

Throws:

java.io.IOException

Write

public boolean Write()

fitDoseCoeffs

public void fitDoseCoeffs()

fit the 3D dose field to a spherical harmonic like series, probably intended to help create synthetic dose- response image set for testing and validation

smoothDoseValues

public void smoothDoseValues(int rOrder,
                             int thetaOrder)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object