woSource

Class ImgRegistration

java.lang.Object

woSource.ImgRegistration

All Implemented Interfaces:

ij.plugin.PlugIn

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

This is a front end to ImageRegistration(), where the latter has the GUI.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	autoSaveParams
ArrayDisplay	resultAD

Constructor Summary

Constructors

Constructor and Description
ImgRegistration()

Method Summary

Modifier and Type	Method and Description
void	destroy()
void	doreg(ij.ImagePlus firstset, ij.ImagePlus secondset)
void	doreg(ij.ImagePlus firstset, short[][][] firstimg, ij.ImagePlus secondset, short[][][] secimg)
void	doreg(ij.ImagePlus firstset, short[][][] firstimg, Rectangle3D firstCroppedRect, ij.ImagePlus secondset, short[][][] secimg, Rectangle3D secondCroppedRect)
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 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()
void	run(java.lang.String arg) This method is called when the plugin is loaded.
void	showAbout()

Methods inherited from class java.lang.Object

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

Field Detail

resultAD

public ArrayDisplay resultAD

autoSaveParams

public boolean autoSaveParams

Constructor Detail

ImgRegistration

public ImgRegistration()

Method Detail

showAbout

public void showAbout()

doreg

public void doreg(ij.ImagePlus firstset,
                  ij.ImagePlus secondset)

doreg

public void doreg(ij.ImagePlus firstset,
                  short[][][] firstimg,
                  ij.ImagePlus secondset,
                  short[][][] secimg)

doreg

public void doreg(ij.ImagePlus firstset,
                  short[][][] firstimg,
                  Rectangle3D firstCroppedRect,
                  ij.ImagePlus secondset,
                  short[][][] secimg,
                  Rectangle3D secondCroppedRect)

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

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()

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 coords in xyz order.

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)

destroy

public void destroy()