Package gov.nih.mipav.model.algorithms

Class AlgorithmASM

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.AlgorithmASM

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmASM
extends AlgorithmBase
implements java.awt.event.ActionListener

Author:

William Gandler This is a port of active shape model code from MATLAB to Java. The license is given below: Copyright (c) 2010, Dirk-Jan Kroon All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	AlgorithmASM.AppData
class	AlgorithmASM.ASMData
class	AlgorithmASM.FileMATLAB
class	AlgorithmASM.LandData
class	AlgorithmASM.Options
class	AlgorithmASM.P
class	AlgorithmASM.PData
class	AlgorithmASM.SData
class	AlgorithmASM.TData

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	fatalError
private java.lang.String	fileDir
private VOI	initialVOI
private ModelImage	Itest
private int[][]	Lines
private javax.swing.JButton	OKButton
private AlgorithmASM.P	p
private javax.swing.JDialog	pauseDialog
private boolean	pressedOK
private ViewJFrameImage	testFrame
private double[][]	Vertices

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AlgorithmASM()

Method Summary

Modifier and Type	Method	Description
void	actionPerformed(java.awt.event.ActionEvent event)	Calls various methods depending on the action.
void	ASM_2D_example()
private void	ASM_align_data_inverse2D(double[][] pos, AlgorithmASM.TData tform)
private void	ASM_align_data2D(double[][] Vertices, AlgorithmASM.TData tform)
private void	ASM_ApplyModel2D(ModelImage Itest, AlgorithmASM.TData tform, AlgorithmASM.SData ShapeData, AlgorithmASM.AppData[] AppearanceData, AlgorithmASM.Options options)
private double[][]	ASM_GetContourNormals2D(double[][] V, int[][] L)
private void	ASM_getProfileAndDerivatives2D(ModelImage I, double[][] P, double[][] N, int k, double[][] gtc, double[][] dgtc)
private void	ASM_MakeAppearanceModel2D(AlgorithmASM.ASMData[] TrainingData, AlgorithmASM.Options options, AlgorithmASM.AppData[] AppearanceData)
private void	ASM_MakeShapeModel2D(AlgorithmASM.ASMData[] TrainingData, AlgorithmASM.SData ShapeData)
private void	createPauseDialog(java.awt.event.ActionListener al)
void	finalize()	Prepares this class for destruction.
private void	linspace_multi(double[] d1, double[] d2, int n, double[][] X)
private void	LoadDataSetNiceContour(java.lang.String fileName, int nBetween, boolean verbose)
private void	PCA(double[][] x, double[] Evalues, double[][] Evectors, double[] x_mean)
void	runAlgorithm()	Starts the algorithm.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

fileDir

private java.lang.String fileDir

fatalError

private boolean fatalError

p

private AlgorithmASM.P p

Vertices

private double[][] Vertices

Lines

private int[][] Lines

pauseDialog

private javax.swing.JDialog pauseDialog

Itest

private ModelImage Itest

initialVOI

private VOI initialVOI

OKButton

private javax.swing.JButton OKButton

pressedOK

private boolean pressedOK

testFrame

private ViewJFrameImage testFrame

Constructor Detail

AlgorithmASM

public AlgorithmASM()

Method Detail

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

ASM_2D_example

public void ASM_2D_example()

ASM_ApplyModel2D

private void ASM_ApplyModel2D(ModelImage Itest,
                              AlgorithmASM.TData tform,
                              AlgorithmASM.SData ShapeData,
                              AlgorithmASM.AppData[] AppearanceData,
                              AlgorithmASM.Options options)

createPauseDialog

private void createPauseDialog(java.awt.event.ActionListener al)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent event)

Calls various methods depending on the action.

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Overrides:

actionPerformed in class AlgorithmBase

Parameters:

event - event that triggered function

ASM_align_data_inverse2D

private void ASM_align_data_inverse2D(double[][] pos,
                                      AlgorithmASM.TData tform)

ASM_MakeAppearanceModel2D

private void ASM_MakeAppearanceModel2D(AlgorithmASM.ASMData[] TrainingData,
                                       AlgorithmASM.Options options,
                                       AlgorithmASM.AppData[] AppearanceData)

ASM_getProfileAndDerivatives2D

private void ASM_getProfileAndDerivatives2D(ModelImage I,
                                            double[][] P,
                                            double[][] N,
                                            int k,
                                            double[][] gtc,
                                            double[][] dgtc)

linspace_multi

private void linspace_multi(double[] d1,
                            double[] d2,
                            int n,
                            double[][] X)

ASM_GetContourNormals2D

private double[][] ASM_GetContourNormals2D(double[][] V,
                                           int[][] L)

ASM_MakeShapeModel2D

private void ASM_MakeShapeModel2D(AlgorithmASM.ASMData[] TrainingData,
                                  AlgorithmASM.SData ShapeData)

PCA

private void PCA(double[][] x,
                 double[] Evalues,
                 double[][] Evectors,
                 double[] x_mean)

ASM_align_data2D

private void ASM_align_data2D(double[][] Vertices,
                              AlgorithmASM.TData tform)

LoadDataSetNiceContour

private void LoadDataSetNiceContour(java.lang.String fileName,
                                    int nBetween,
                                    boolean verbose)

runAlgorithm

public void runAlgorithm()

Starts the algorithm.

Specified by:

runAlgorithm in class AlgorithmBase