at.mug.iqm.img.bundle.imagej

Class IqmImage_Stabilizer

java.lang.Object

at.mug.iqm.img.bundle.imagej.IqmImage_Stabilizer

All Implemented Interfaces:

ij.plugin.filter.PlugInFilter

public class IqmImage_Stabilizer
extends Object
implements ij.plugin.filter.PlugInFilter

This is an expanded version of the ImageJ Image_Stabilizer plugin by Kang Li in order to work within Iqm new process method added K. Li, "The image stabilizer plugin for ImageJ," http://www.cs.cmu.edu/~kangli/code/Image_Stabilizer.html This plugin stabilizes jittery image stacks using the Lucas-Kanade algorithm. It supports both grayscale and color images.

Changes

• added method public ImagePlus getStabilizedImage()
• added method public void processIqm(ImagePlus targetImPlus, ImagePlus sourceImPlus, int regMode, int pyrLevels, float tempUpCo, float maxIt, float errTol)

Since:

2010 05

Author:

Helmut Ahammer

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static int	AFFINE
(package private) double	alpha
(package private) ij.ImagePlus	imp
(package private) ij.plugin.frame.Editor	logEditor
(package private) boolean	logEnabled
(package private) int	maxIter
(package private) String	outputDir
(package private) boolean	outputNewStack
(package private) int	pyramidLevel
(package private) ij.ImageStack	stack
(package private) ij.ImageStack	stackOut
(package private) boolean	stackVirtual
(package private) double	tol
(package private) int	transform
(package private) static int	TRANSLATION

Fields inherited from interface ij.plugin.filter.PlugInFilter

CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, KEEP_THRESHOLD, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, PARALLELIZE_IMAGES, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

Constructors

Constructor and Description
IqmImage_Stabilizer()

Method Summary

Modifier and Type	Method and Description
(package private) void	combine(ij.process.ImageProcessor ipOut, ij.process.ImageProcessor ip)
(package private) float[]	dot(float[] p1, float[] p2)
(package private) double	dotSum(float[] p1, float[] p2)
(package private) float[]	dx(ij.process.ImageProcessor ip)
(package private) float[]	dy(ij.process.ImageProcessor ip)
(package private) double[][]	estimateAffine(double[][] wp, ij.process.ImageProcessor ip, ij.process.ImageProcessor ipRef, int maxIter, double tol)
(package private) double[][]	estimateAffine(ij.process.ImageProcessor ip, ij.process.ImageProcessor ipRef, ij.process.ImageProcessor[] ipPyramid, ij.process.ImageProcessor[] ipRefPyramid, int maxIter, double tol)
(package private) double[][]	estimateTranslation(double[][] wp, ij.process.ImageProcessor ip, ij.process.ImageProcessor ipRef, int maxIter, double tol)
(package private) double[][]	estimateTranslation(ij.process.ImageProcessor ip, ij.process.ImageProcessor ipRef, ij.process.ImageProcessor[] ipPyramid, ij.process.ImageProcessor[] ipRefPyramid, int maxIter, double tol)
(package private) void	gaussian(double[][] a, int[] index) Gaussian elimination (required by invert).
(package private) String	getBaseName(String fileName)
ij.ImagePlus	getStabilizedImage() This method gets the stabilized output from ImageJ.
(package private) int	getTransform(String name)
(package private) String	getTransformName(int xform)
(package private) void	gradient(ij.process.ImageProcessor ipOut, ij.process.ImageProcessor ip)
(package private) double[][]	invert(double[][] a) Matrix inversion with the Gaussian elimination scheme.
(package private) void	process(ij.process.ImageProcessor ipRef, int firstSlice, int lastSlice, int interval, int tick)
void	processIqm(ij.ImagePlus targetImPlus, ij.ImagePlus sourceImPlus, int regMode, int pyrLevels, float tempUpCo, float maxIt, float errTol) This method puts the Iqm parameters to the Image_Stabilizer plugin structure
(package private) double[]	prod(double[][] m, double[] v)
(package private) double[][]	prod(double[][] a, double[][] b)
(package private) void	resize(ij.process.ImageProcessor ipOut, ij.process.ImageProcessor ip)
(package private) double	rootMeanSquare(ij.process.ImageProcessor ip)
void	run(ij.process.ImageProcessor ip)
(package private) void	saveImage(ij.process.ImageProcessor ip, int slice)
int	setup(String arg, ij.ImagePlus imp)
(package private) boolean	showDialog(ij.process.ImageProcessor ip)
(package private) void	showProgress(double percent)
(package private) void	subtract(ij.process.ImageProcessor ipOut, ij.process.ImageProcessor ip)
(package private) void	warpAffine(ij.process.ImageProcessor ipOut, ij.process.ImageProcessor ip, double[][] wp)
(package private) void	warpColorAffine(ij.process.ImageProcessor ipOut, ij.process.ColorProcessor ip, double[][] wp)
(package private) void	warpColorTranslation(ij.process.ImageProcessor ipOut, ij.process.ColorProcessor ip, double[][] wp)
(package private) void	warpTranslation(ij.process.ImageProcessor ipOut, ij.process.ImageProcessor ip, double[][] wp)

Methods inherited from class java.lang.Object

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

Field Detail

TRANSLATION

static final int TRANSLATION

See Also:

Constant Field Values

AFFINE

static final int AFFINE

See Also:

Constant Field Values

imp

ij.ImagePlus imp

stack

ij.ImageStack stack

stackOut

ij.ImageStack stackOut

outputDir

String outputDir

stackVirtual

boolean stackVirtual

outputNewStack

boolean outputNewStack

transform

int transform

pyramidLevel

int pyramidLevel

maxIter

int maxIter

tol

double tol

alpha

double alpha

logEnabled

boolean logEnabled

logEditor

ij.plugin.frame.Editor logEditor

Constructor Detail

IqmImage_Stabilizer

public IqmImage_Stabilizer()

Method Detail

setup

public int setup(String arg,
                 ij.ImagePlus imp)

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

run

public void run(ij.process.ImageProcessor ip)

Specified by:

run in interface ij.plugin.filter.PlugInFilter

getTransform

int getTransform(String name)

getTransformName

String getTransformName(int xform)

showDialog

boolean showDialog(ij.process.ImageProcessor ip)

showProgress

void showProgress(double percent)

getStabilizedImage

public ij.ImagePlus getStabilizedImage()

This method gets the stabilized output from ImageJ.

Returns:

ImagePlus

Since:

2010 05

processIqm

public void processIqm(ij.ImagePlus targetImPlus,
                       ij.ImagePlus sourceImPlus,
                       int regMode,
                       int pyrLevels,
                       float tempUpCo,
                       float maxIt,
                       float errTol)

This method puts the Iqm parameters to the Image_Stabilizer plugin structure

Parameters:

targetImPlus -

sourceImPlus -

regMode -

pyrLevels -

tempUpCo -

maxIt -

errTol -

Since:

2010 05

process

void process(ij.process.ImageProcessor ipRef,
             int firstSlice,
             int lastSlice,
             int interval,
             int tick)

saveImage

void saveImage(ij.process.ImageProcessor ip,
               int slice)

getBaseName

String getBaseName(String fileName)

estimateAffine

double[][] estimateAffine(ij.process.ImageProcessor ip,
                          ij.process.ImageProcessor ipRef,
                          ij.process.ImageProcessor[] ipPyramid,
                          ij.process.ImageProcessor[] ipRefPyramid,
                          int maxIter,
                          double tol)

estimateAffine

double[][] estimateAffine(double[][] wp,
                          ij.process.ImageProcessor ip,
                          ij.process.ImageProcessor ipRef,
                          int maxIter,
                          double tol)

estimateTranslation

double[][] estimateTranslation(ij.process.ImageProcessor ip,
                               ij.process.ImageProcessor ipRef,
                               ij.process.ImageProcessor[] ipPyramid,
                               ij.process.ImageProcessor[] ipRefPyramid,
                               int maxIter,
                               double tol)

estimateTranslation

double[][] estimateTranslation(double[][] wp,
                               ij.process.ImageProcessor ip,
                               ij.process.ImageProcessor ipRef,
                               int maxIter,
                               double tol)

gradient

void gradient(ij.process.ImageProcessor ipOut,
              ij.process.ImageProcessor ip)

resize

void resize(ij.process.ImageProcessor ipOut,
            ij.process.ImageProcessor ip)

prod

double[] prod(double[][] m,
              double[] v)

prod

double[][] prod(double[][] a,
                double[][] b)

dx

float[] dx(ij.process.ImageProcessor ip)

dy

float[] dy(ij.process.ImageProcessor ip)

dot

float[] dot(float[] p1,
            float[] p2)

dotSum

double dotSum(float[] p1,
              float[] p2)

gaussian

void gaussian(double[][] a,
              int[] index)

Gaussian elimination (required by invert). This Java program is part of the book, "An Introduction to Computational Physics, 2nd Edition," written by Tao Pang and published by Cambridge University Press on January 19, 2006.

invert

double[][] invert(double[][] a)

Matrix inversion with the Gaussian elimination scheme. This Java program is part of the book, "An Introduction to Computational Physics, 2nd Edition," written by Tao Pang and published by Cambridge University Press on January 19, 2006.

rootMeanSquare

double rootMeanSquare(ij.process.ImageProcessor ip)

combine

void combine(ij.process.ImageProcessor ipOut,
             ij.process.ImageProcessor ip)

subtract

void subtract(ij.process.ImageProcessor ipOut,
              ij.process.ImageProcessor ip)

warpAffine

void warpAffine(ij.process.ImageProcessor ipOut,
                ij.process.ImageProcessor ip,
                double[][] wp)

warpColorAffine

void warpColorAffine(ij.process.ImageProcessor ipOut,
                     ij.process.ColorProcessor ip,
                     double[][] wp)

warpTranslation

void warpTranslation(ij.process.ImageProcessor ipOut,
                     ij.process.ImageProcessor ip,
                     double[][] wp)

warpColorTranslation

void warpColorTranslation(ij.process.ImageProcessor ipOut,
                          ij.process.ColorProcessor ip,
                          double[][] wp)