java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.DiffusionTensorImaging.AlgorithmDWI2DTI

All Implemented Interfaces:

AlgorithmInterface, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmDWI2DTI
extends AlgorithmBase
implements AlgorithmInterface
```
Algorithm calculates a Diffusion Tensor Image from a series of Diffusion Weighted Images. See: Introduction to Diffusion Tensor Imaging, by Susumu Mori

Nested Class Summary
- 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 AlgorithmBrainSurfaceExtractor`	`alg`	handle to BSE Algorithm *
`private java.util.HashMap<java.lang.String,float[]>`	`m_3dbufferMap_float`
`private java.util.HashMap<java.lang.String,int[]>`	`m_3dbufferMap_int`
`private java.util.HashMap<java.lang.String,float[]>`	`m_4dbufferMap_float`
`private java.util.HashMap<java.lang.String,int[]>`	`m_4dbufferMap_int`
`private java.lang.String[][]`	`m_aakDWIList`	List of file names for the Diffusion Weighted Images, from the .path file.
`private int[]`	`m_aiMatrixEntries`	keeps track of unique entries in the BMatrix
`private boolean`	`m_bDisplayB0`	Whether to just display the B0 weighted image and return, or to do a full calculation:
`private boolean`	`m_bUseDTIParameters`	When true, use the ModelImage DTI parameters.
`private float`	`m_fMeanNoise`	The mean noise value:
`private int`	`m_iBOrig`	Number of different entries in the BMatrix:
`private int`	`m_iDimX`	X Dimension of the input images:
`private int`	`m_iDimY`	Y Dimension of the input images:
`private int`	`m_iSlices`	Number of slices in the input images:
`private int`	`m_iWeights`	Number of images in the weighted series:
`private ViewJFrameImage`	`m_kB0Frame`	ViewJFrameImage for displaying the B0 weighted image:
`private ModelImage`	`m_kB0Image`	B0 weighted image:
`private WildMagic.LibFoundation.Mathematics.GMatrixd`	`m_kBMatrix`	General matrix storing BMatrix values.
`private ModelImage`	`m_kDTI`	Output DTI Image:
`private ModelImage`	`m_kDWIImage`	DWI Image 4D series of weighted diffusion images
`private ModelImage`	`m_kMaskImage`	Mask Image for masking brain regions during tensor calculation:
`private java.lang.String`	`m_kRawImageFormat`	Format of the raw data: (float, int, dicom, etc.)

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
`AlgorithmDWI2DTI(ModelImage kMaskImage, boolean bDisplayB0, int iSlices, int iDimX, int iDimY, int iBOrig, int iWeights, float fMeanNoise, java.lang.String[][] aakDWIList, int[] aiMatrixEntries, WildMagic.LibFoundation.Mathematics.GMatrixd kBMatrix, java.lang.String kRawFormat)`	Create a new AlgorithmDWI2DTI
`AlgorithmDWI2DTI(ModelImage kDWIImage, ModelImage maskImage)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	Called after an algorithm this listener is registered to exits (maybe successfully, maybe not).
`void`	`calculateDTI(int start, int end, float[] dtiData, float[][][] weightData, Jama.Matrix B, Jama.Matrix H)`
`void`	`calculateDTIVoxel(float[] dtiData, float[][] dwiData, float[][][] weightData, int x, int y, int z, Jama.Matrix B)`
`void`	`calculateDTIVoxel2(float[] dtiData, float[][] dwiData, float[][][] weightData, int x, int y, int z, Jama.Matrix H, int volumeSize)`
`Jama.Matrix`	`calculateMatrix(Jama.Matrix m)`
`private void`	`createDWI()`
`float[]`	`createDWIImage()`	Second step in processing the diffusion weighted images.
`private void`	`createMaskImage()`	Create the mask image.
`private float[][][]`	`createTensorWeights()`	Creates the weighted data for the tensor calculation from the diffusion weighted images.
`void`	`deleteImages()`
`void`	`disposeLocal()`
`ModelImage`	`getDTI()`	Return the DTI Image.
`ModelImage`	`getDWI()`
`private float[]`	`readDicomWeight(int iSlice, int iWeight)`	Get the slice data for the image with the given slice and weight.
`private float`	`readFloat(byte[] abData, int iIndex)`	Translates the byte[] into float values at the given indes iIndex.
`private float[]`	`readFloatWeight(int iSlice, int iWeight)`	Get the slice data for the image with the given slice and weight.
`private int`	`readInteger(byte[] abData, int iIndex)`	Translates the byte[] into integer values at the given indes iIndex.
`private float[]`	`readIntegerWeight(int iSlice, int iWeight)`	Get the slice data for the image with the given slice and weight.
`private float[]`	`readSliceWeight(int iSlice, int iWeight)`	Get the slice data for the image with the given slice and weight.
`void`	`runAlgorithm()`	Calculate the DTI image.
`float[]`	`solve(Jama.Matrix y, Jama.Matrix m)`

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, 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
  - m_kMaskImage
```
private ModelImage m_kMaskImage
```
    Mask Image for masking brain regions during tensor calculation:
  - m_kDWIImage
```
private ModelImage m_kDWIImage
```
    DWI Image 4D series of weighted diffusion images
  - m_kB0Image
```
private ModelImage m_kB0Image
```
    B0 weighted image:
  - m_kB0Frame
```
private ViewJFrameImage m_kB0Frame
```
    ViewJFrameImage for displaying the B0 weighted image:
  - m_bDisplayB0
```
private boolean m_bDisplayB0
```
    Whether to just display the B0 weighted image and return, or to do a full calculation:
  - m_iSlices
```
private final int m_iSlices
```
    Number of slices in the input images:
  - m_iDimX
```
private final int m_iDimX
```
    X Dimension of the input images:
  - m_iDimY
```
private final int m_iDimY
```
    Y Dimension of the input images:
  - m_iBOrig
```
private final int m_iBOrig
```
    Number of different entries in the BMatrix:
  - m_iWeights
```
private final int m_iWeights
```
    Number of images in the weighted series:
  - m_fMeanNoise
```
private float m_fMeanNoise
```
    The mean noise value:
  - m_kBMatrix
```
private WildMagic.LibFoundation.Mathematics.GMatrixd m_kBMatrix
```
    General matrix storing BMatrix values.
  - m_aakDWIList
```
private java.lang.String[][] m_aakDWIList
```
    List of file names for the Diffusion Weighted Images, from the .path file.
  - m_aiMatrixEntries
```
private int[] m_aiMatrixEntries
```
    keeps track of unique entries in the BMatrix
  - m_kRawImageFormat
```
private java.lang.String m_kRawImageFormat
```
    Format of the raw data: (float, int, dicom, etc.)
  - m_kDTI
```
private ModelImage m_kDTI
```
    Output DTI Image:
  - m_bUseDTIParameters
```
private boolean m_bUseDTIParameters
```
    When true, use the ModelImage DTI parameters.
  - alg
```
private AlgorithmBrainSurfaceExtractor alg
```
    handle to BSE Algorithm *
  - m_3dbufferMap_float
```
private final java.util.HashMap<java.lang.String,float[]> m_3dbufferMap_float
```
  - m_4dbufferMap_float
```
private final java.util.HashMap<java.lang.String,float[]> m_4dbufferMap_float
```
  - m_3dbufferMap_int
```
private final java.util.HashMap<java.lang.String,int[]> m_3dbufferMap_int
```
  - m_4dbufferMap_int
```
private final java.util.HashMap<java.lang.String,int[]> m_4dbufferMap_int
```
- Constructor Detail
  - AlgorithmDWI2DTI
```
public AlgorithmDWI2DTI(ModelImage kMaskImage,
                        boolean bDisplayB0,
                        int iSlices,
                        int iDimX,
                        int iDimY,
                        int iBOrig,
                        int iWeights,
                        float fMeanNoise,
                        java.lang.String[][] aakDWIList,
                        int[] aiMatrixEntries,
                        WildMagic.LibFoundation.Mathematics.GMatrixd kBMatrix,
                        java.lang.String kRawFormat)
```
    Create a new AlgorithmDWI2DTI
    
    Parameters:
    
    kMaskImage - mask image masking non-brain regions, if null it is calculated.
    
    bDisplayB0 - when true open and display the B0 weighted image and return.
    
    iSlices - number of slices in the raw data.
    
    iDimX - x-dimensions of the raw data.
    
    iDimY - y-dimensions of the raw data.
    
    iBOrig - number of different entries in the BMatrix.
    
    iWeights - number of weighted series.
    
    fMeanNoise - mean noise value.
    
    aakDWIList - list of file names in the weighted series.
    
    repidx -
    
    kBMatrix - BMatrix values.
    
    kRawFormat - format string for the raw data.
  - AlgorithmDWI2DTI
```
public AlgorithmDWI2DTI(ModelImage kDWIImage,
                        ModelImage maskImage)
```
- Method Detail
  - algorithmPerformed
```
public void algorithmPerformed(AlgorithmBase algorithm)
```
    Description copied from interface: AlgorithmInterface
    
    Called after an algorithm this listener is registered to exits (maybe successfully, maybe not). If the algorithm is run in a separate thread, this call will be made within that thread. If not, this call will be made from that same, shared thread.
    
    Specified by:
    
    algorithmPerformed in interface AlgorithmInterface
    
    Parameters:
    
    algorithm - the algorithm which has just completed
  - calculateDTI
```
public void calculateDTI(int start,
                         int end,
                         float[] dtiData,
                         float[][][] weightData,
                         Jama.Matrix B,
                         Jama.Matrix H)
```
  - calculateDTIVoxel
```
public void calculateDTIVoxel(float[] dtiData,
                              float[][] dwiData,
                              float[][][] weightData,
                              int x,
                              int y,
                              int z,
                              Jama.Matrix B)
```
  - calculateDTIVoxel2
```
public void calculateDTIVoxel2(float[] dtiData,
                               float[][] dwiData,
                               float[][][] weightData,
                               int x,
                               int y,
                               int z,
                               Jama.Matrix H,
                               int volumeSize)
```
  - calculateMatrix
```
public Jama.Matrix calculateMatrix(Jama.Matrix m)
```
  - createDWIImage
```
public float[] createDWIImage()
```
    Second step in processing the diffusion weighted images. This function is called once the brain extractor is complete. The brain image is transformed into a mask image, which is passed to this function. The mask image limits where the tensor calculations are performed. The tensor is calculated, then the eigen vectors and functional anisotropy images. The DialogDTIColorDisplay is then launched.
    
    Parameters:
    
    kMaskImage - mask image representing the brain.
  - deleteImages
```
public void deleteImages()
```
  - disposeLocal
```
public void disposeLocal()
```
  - getDTI
```
public ModelImage getDTI()
```
    Return the DTI Image.
    
    Returns:
    
    the DTI Image.
  - getDWI
```
public ModelImage getDWI()
```
  - runAlgorithm
```
public void runAlgorithm()
```
    Calculate the DTI image. If the mask image is null, calculate the mask image first.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - solve
```
public float[] solve(Jama.Matrix y,
                     Jama.Matrix m)
```
  - createDWI
```
private void createDWI()
```
  - createMaskImage
```
private void createMaskImage()
```
    Create the mask image. Create an image with the B0 weighted data, if one has not already been created. Next use the JDialogBrainSurfaceExtractor to extract only the brain regions.
  - createTensorWeights
```
private float[][][] createTensorWeights()
```
    Creates the weighted data for the tensor calculation from the diffusion weighted images.
    
    Returns:
    
    float[][][] containing the weights used in the tensor calculation.
  - readDicomWeight
```
private float[] readDicomWeight(int iSlice,
                                int iWeight)
```
    Get the slice data for the image with the given slice and weight.
    
    Parameters:
    
    iSlice - slice to read.
    
    iWeight - weight to read.
    
    Returns:
    
    float[] containing the data.
  - readFloat
```
private float readFloat(byte[] abData,
                        int iIndex)
```
    Translates the byte[] into float values at the given indes iIndex.
    
    Parameters:
    
    abData - byte[] containing float values.
    
    iIndex - index into the array to get the float from.
    
    Returns:
    
    float value representing 4 bytes starting at abData[iIndex*4].
  - readFloatWeight
```
private float[] readFloatWeight(int iSlice,
                                int iWeight)
```
    Get the slice data for the image with the given slice and weight. For 3d and 4d non-multifile images, the whole buffer is read in and stored...then slice data is extracted from that buffer
    
    Parameters:
    
    iSlice - slice to read.
    
    iWeight - weight to read.
    
    Returns:
    
    float[] containing the data.
  - readInteger
```
private int readInteger(byte[] abData,
                        int iIndex)
```
    Translates the byte[] into integer values at the given indes iIndex.
    
    Parameters:
    
    abData - byte[] containing integer values.
    
    iIndex - index into the array to get the float from.
    
    Returns:
    
    integer value representing 4 bytes starting at abData[iIndex*4].
  - readIntegerWeight
```
private float[] readIntegerWeight(int iSlice,
                                  int iWeight)
```
    Get the slice data for the image with the given slice and weight. For 3d and 4d non-multifile images, the whole buffer is read in and stored...then slice data is extracted from that buffer
    
    Parameters:
    
    iSlice - slice to read.
    
    iWeight - weight to read.
    
    Returns:
    
    float[] containing the data.
  - readSliceWeight
```
private float[] readSliceWeight(int iSlice,
                                int iWeight)
```
    Get the slice data for the image with the given slice and weight.
    
    Parameters:
    
    iSlice - slice to read.
    
    iWeight - weight to read.
    
    Returns:
    
    float[] containing the data.

Class AlgorithmDWI2DTI

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

m_kMaskImage

m_kDWIImage

m_kB0Image

m_kB0Frame

m_bDisplayB0

m_iSlices

m_iDimX

m_iDimY

m_iBOrig

m_iWeights

m_fMeanNoise

m_kBMatrix

m_aakDWIList

m_aiMatrixEntries

m_kRawImageFormat

m_kDTI

m_bUseDTIParameters

alg

m_3dbufferMap_float

m_4dbufferMap_float

m_3dbufferMap_int

m_4dbufferMap_int

Constructor Detail

AlgorithmDWI2DTI

AlgorithmDWI2DTI

Method Detail

algorithmPerformed

calculateDTI

calculateDTIVoxel

calculateDTIVoxel2

calculateMatrix

createDWIImage

deleteImages

disposeLocal

getDTI

getDWI

runAlgorithm

solve

createDWI

createMaskImage

createTensorWeights

readDicomWeight

readFloat

readFloatWeight

readInteger

readIntegerWeight

readSliceWeight