woSource

Class ImageRegistration

java.lang.Object

woSource.ImageRegistration

Direct Known Subclasses:

HistoMR_registration, ImageRegistrationPS

public class ImageRegistration
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	alreadySavedParams
boolean	autoSaveParams
static int	D
static int	H
boolean	matchXYscales
ArrayDisplay	transformedAD
protected boolean	viewTransformedImage
static int	W
boolean	wasReadIn

Constructor Summary

Constructors

Constructor and Description
ImageRegistration()
ImageRegistration(short[][][] refImg, java.util.Properties[] Props1, Rectangle3D refRoi, ij.io.FileInfo reffileinfo, short[][][] defImg, java.util.Properties[] Props2, Rectangle3D defRoi, ij.io.FileInfo deffileinfo)
ImageRegistration(short[][][] refImg, java.util.Properties[] Props1, Rectangle3D refRoi, short[][][] defImg, java.util.Properties[] Props2, Rectangle3D defRoi)
ImageRegistration(short[][][] refImg, java.util.Properties[] Props1, short[][][] defImg, java.util.Properties[] Props2)
ImageRegistration(short[][] ref2dImg, java.util.Properties prop1, short[][] def2dImg, java.util.Properties prop2)

Method Summary

Modifier and Type	Method and Description
float	CalcCorr(float[] curValues)
float	CalcNCCC()
float	CalcNMI()
void	Copy(ImageRegistration A)
void	finishReg(java.util.Properties[] props) WO 9/13/10 when done want to clear all the windows and the gui, but save the deformed floating images as an open window that the function that called this can continue to use.
float[]	getAmoebaCurValues()
float[]	getCurValues()
float	getDrot()
float	getDscale()
float	getHrot()
float	getHscale()
float[]	getInvTransformedPtCoords_px(float d, float w, float h)
float[]	getInvTransformedPtCoords_px(int d, int w, int h) inverse-transform the voxel dwh into the deformed coord system and return the sub-voxel coords dwh.
float[]	getTransformedPtCoords_mm(float d, float w, float h)
float[]	getTransformedPtCoords_mm(int d, int w, int h) transform the voxel dwh into the deformed coord system and return the mm scanner coords in xyz order.
float[]	getTransformedPtCoords_px(float d, float w, float h)
float[]	getTransformedPtCoords_px(int d, int w, int h) transform the voxel dwh into the deformed coord system and return the sub-voxel coords dwh.
float	getWrot()
float	getWscale()
float	getXshift()
float	getYshift()
float	getZshift()
float[]	putAmoebaCurValues(float[] shiftedVals)
boolean	read()
void	run(ArrayColorDisplay sumAd2D)
void	run(ArrayColorDisplay3D sumAd)
void	run(ArrayColorDisplay3D sumAd, ArrayColorDisplay sumAd2D)
void	setRegDisplay()
void	showAbout()
protected void	spaceWindowsOnScreen()
java.lang.String	toString()
void	updateRegDisplay(java.lang.String displayType)
void	write()
void	writeDefImgTrans() WO 5/13/09 want to stick the dicom headers from the refImages onto the defImgTrans data this is working for MRI T1 data at least.

Methods inherited from class java.lang.Object

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

Field Detail

D

public static final int D

See Also:

Constant Field Values

W

public static final int W

See Also:

Constant Field Values

H

public static final int H

See Also:

Constant Field Values

wasReadIn

public boolean wasReadIn

transformedAD

public ArrayDisplay transformedAD

viewTransformedImage

protected boolean viewTransformedImage

matchXYscales

public boolean matchXYscales

autoSaveParams

public boolean autoSaveParams

alreadySavedParams

protected boolean alreadySavedParams

Constructor Detail

ImageRegistration

public ImageRegistration()

ImageRegistration

public ImageRegistration(short[][] ref2dImg,
                         java.util.Properties prop1,
                         short[][] def2dImg,
                         java.util.Properties prop2)

ImageRegistration

public ImageRegistration(short[][][] refImg,
                         java.util.Properties[] Props1,
                         short[][][] defImg,
                         java.util.Properties[] Props2)

ImageRegistration

public ImageRegistration(short[][][] refImg,
                         java.util.Properties[] Props1,
                         Rectangle3D refRoi,
                         short[][][] defImg,
                         java.util.Properties[] Props2,
                         Rectangle3D defRoi)

ImageRegistration

public ImageRegistration(short[][][] refImg,
                         java.util.Properties[] Props1,
                         Rectangle3D refRoi,
                         ij.io.FileInfo reffileinfo,
                         short[][][] defImg,
                         java.util.Properties[] Props2,
                         Rectangle3D defRoi,
                         ij.io.FileInfo deffileinfo)

Method Detail

showAbout

public void showAbout()

run

public void run(ArrayColorDisplay sumAd2D)

run

public void run(ArrayColorDisplay3D sumAd)

run

public void run(ArrayColorDisplay3D sumAd,
                ArrayColorDisplay sumAd2D)

spaceWindowsOnScreen

protected void spaceWindowsOnScreen()

getTransformedPtCoords_px

public float[] getTransformedPtCoords_px(int d,
                                         int w,
                                         int h)

transform the voxel dwh into the deformed coord system and return the sub-voxel coords dwh. If you want the closest voxel use mathI.round(returned_dwh)

Parameters:

d,w,h - voxel coords to be transformed according to already computed registration parameters

getTransformedPtCoords_px

public float[] getTransformedPtCoords_px(float d,
                                         float w,
                                         float h)

getTransformedPtCoords_mm

public float[] getTransformedPtCoords_mm(int d,
                                         int w,
                                         int h)

transform the voxel dwh into the deformed coord system and return the mm scanner coords in xyz order.
If you want the mm with respect to the top left corner, then need to subtract off the top left corner scanner coords. You need to do this TLC subtraction to get the dhw pixel coords.

Parameters:

d,w,h - voxel coords to be transformed according to already computed registration parameters

getTransformedPtCoords_mm

public float[] getTransformedPtCoords_mm(float d,
                                         float w,
                                         float h)

getInvTransformedPtCoords_px

public float[] getInvTransformedPtCoords_px(int d,
                                            int w,
                                            int h)

inverse-transform the voxel dwh into the deformed coord system and return the sub-voxel coords dwh. If you want the closest voxel use MathI.round(returned_dwh)

Parameters:

d,w,h - voxel coords to be transformed according to already computed registration parameters

getInvTransformedPtCoords_px

public float[] getInvTransformedPtCoords_px(float d,
                                            float w,
                                            float h)

finishReg

public void finishReg(java.util.Properties[] props)

WO 9/13/10 when done want to clear all the windows and the gui, but save the deformed floating images as an open window that the function that called this can continue to use.

setRegDisplay

public void setRegDisplay()

updateRegDisplay

public void updateRegDisplay(java.lang.String displayType)

getAmoebaCurValues

public float[] getAmoebaCurValues()

putAmoebaCurValues

public float[] putAmoebaCurValues(float[] shiftedVals)

getCurValues

public float[] getCurValues()

getXshift

public float getXshift()

getYshift

public float getYshift()

getZshift

public float getZshift()

getWrot

public float getWrot()

getHrot

public float getHrot()

getDrot

public float getDrot()

getDscale

public float getDscale()

getWscale

public float getWscale()

getHscale

public float getHscale()

CalcCorr

public float CalcCorr(float[] curValues)

CalcNCCC

public float CalcNCCC()

CalcNMI

public float CalcNMI()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Copy

public void Copy(ImageRegistration A)

write

public void write()

read

public boolean read()

writeDefImgTrans

public void writeDefImgTrans()

WO 5/13/09 want to stick the dicom headers from the refImages onto the defImgTrans data this is working for MRI T1 data at least.
WO current error that slice 8 image is shifted to the right by about 20 pixels -- 5/18/09 this was because the length of the dicom header can vary from slice to slice. I was forcing all the headers to be of length 2846. The code now reads in the header length from the "Pixel Data:" header field independently for each slice.