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

All Methods Instance Methods Concrete Methods
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

Class AlgorithmASM

Nested Class Summary

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

Field Summary

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

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

fileDir

fatalError

p

Vertices

Lines

pauseDialog

Itest

initialVOI

OKButton

pressedOK

testFrame

Constructor Detail

AlgorithmASM

Method Detail

finalize

ASM_2D_example

ASM_ApplyModel2D

createPauseDialog

actionPerformed

ASM_align_data_inverse2D

ASM_MakeAppearanceModel2D

ASM_getProfileAndDerivatives2D

linspace_multi

ASM_GetContourNormals2D

ASM_MakeShapeModel2D

PCA

ASM_align_data2D

LoadDataSetNiceContour

runAlgorithm