Package gov.nih.mipav.model.algorithms.DiffusionTensorImaging

Class AlgorithmDTICreateListFile

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.DiffusionTensorImaging.AlgorithmDTICreateListFile

All Implemented Interfaces:

AlgorithmInterface, ActionListener, WindowListener, Runnable, EventListener

public class AlgorithmDTICreateListFile
extends AlgorithmBase
implements AlgorithmInterface

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	AlgorithmDTICreateListFile.InstanceNumberComparator	This inner class is used to sort the list by instance number
private class	AlgorithmDTICreateListFile.InstanceNumberVolComparator	This inner class is used to sort the list by instance number and vol. the vol is determined by the filename

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

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private int	avgVolIndex	Philips puts in one volume as the average of all the DWIs.
private String	bmatrixFileName	B Matrix file name
private String	bmtxtFilePath	This is the full path to the b matrix file
private ArrayList<Float>	bValuesArrayList	this is an array of b-values that for each volume
private float	coarseRate	registration option parameters
private float	coarseRateX	registration option parameters
private float	coarseRateY	registration option parameters
private float	coarseRateZ	registration option parameters
private int	cost	registration option parameters
private String	dicomB0VolumePath	path to dicom B0 for registration purposes
private String[]	dicomInfo	Array that holds the dicom tag info*
private float[][]	direction	this is the gradient matrix that is populated when reading the gradient file
private int	DOF	registration option parameters
private boolean	doGraph	registration option parameters
private boolean	doMultiThread	registration option parameters
private boolean	doSubsample	registration option parameters
private JTextField	dwiPathTextField	handle to dwi data textfield of main dialog
private boolean	fastMode	registration option parameters
private FileInfoPARREC	fileInfoPR	file info Par/Rec
private FileIO	fileIO	file IO
private FilePARREC	fileParRec	FileParRec handle
private float	fineRate	registration option parameters
private float	fineRateX	registration option parameters
private float	fineRateY	registration option parameters
private float	fineRateZ	registration option parameters
private FileInfoDicom	firstFileInfoDicom	first fileinfo dicom...used for list file info
private int	geSoftwareVersion	int telling software version if datset is GE
private String	gradientFilePath	This is the full path to the gradient file
private String	horizontalFOVString	horizontal FOV
private ModelImage	image4D	ModelImage of 4D par/rec dataset
private ViewImageFileFilter	imageFilter	This is the image filter needed to select the correct dicom images
private String	imageOrientationString	image orientation
private String	imageSlicesDirPath	path for imageSlicesDir
private int	interp	registration option parameters
private int	interp2	registration option parameters
private boolean	isDICOM	boolean indicating if we are dealing with dicom or par/rec
private boolean	isEDTI	boolean telling if dataset is eDTI
private boolean	isGE	boolean telling if datset is GE
private boolean	isInterleaved	boolean if dataset is interelaved
private boolean	isOldVersion	boolean identifying if par/rec datset is older than version 4.1
private boolean	isProcDirCreated	boolean if proc dir was created
private boolean	isSiemens	boolean telling if datset is SIEMENS
private String	listFileName	List file name
private ModelImage	matchImage	model images
private int	maxIterations	registration option parameters
private boolean	maxOfMinResol	registration option parameters
private int	nim	this is the number of gradient quantities that is obtained by reading first line of gradient file
private int	nimCounter	this counter is used for version 4 of Par/Rec...nim is calculated from gradient file
private String	nimString	t dim
private int	numMinima	registration option parameters
private int	numSlicesPerVolume	this is the number of image slices per volume
private String	numSlicesString	z dim
private ArrayList<String[]>	oldVersionGradientsAL	arraylist of gradients for version 4 of Par/Rec
private String	originalColumnsString	x dim
private String	originalRowsString	y dim
private JTextArea	outputTextArea	TextArea of main dialog for text output
private String	pathFileName	Path File name
private boolean	performRegistration	boolean for performing registration
private String	phaseEncodingString	phase encoding...hard coded to vertical
private String	prFileDir	par rec file dir
private String	prFileName	par rec file name
private String	rawImageFormatString	raw image format...hardcoded to float since we will be outputting par/rec slices in float format
private ModelImage	refImage	model images
private AlgorithmRegOAR3D	reg3	handle to AlgorithmRegOAR3D
private AlgorithmRegOAR35D	reg35	handle to AlgorithmRegOAR35D
private String	registeredDicomB0VolumePathParentFolder	registered B0 parent folder
private String	registeredStudyName	study name for registered data set
private int	registerTo	registration option parameters
private String	relativeImageSlicesDirPath	relative path for slices dir for outputting to path file
private ModelImage	resultImage	model images
private float	rotateBegin	registration option parameters
private float	rotateBeginX	registration option parameters
private float	rotateBeginY	registration option parameters
private float	rotateBeginZ	registration option parameters
private float	rotateEnd	registration option parameters
private float	rotateEndX	registration option parameters
private float	rotateEndY	registration option parameters
private float	rotateEndZ	registration option parameters
private TreeMap<Integer,TreeSet<String[]>>	seriesFileInfoTreeMap	This is an ordered map of series number and seriesFileInfoTreeSet
private TreeSet<String[]>	seriesFileInfoTreeSet	This is an ordered list of files per series number
private String	sliceGapString	slice gap String
private String	sliceThicknessString	sliec thickness
private String	studyName	This is the dir name of the study
private String	studyPath	This is the full path of the study
private boolean	success	flag indicating if method was successful
private int	tDim	tDim of 4d image
private int	totalImageSlices	total image slices
private int	totalNumVolumes	total num of volumes in study
private AlgorithmTransform	transform	handle to AlgorithmTransform
private ArrayList<String>	unsortedPathsArrayList	arraylist of unsorted path strings to image slices
private String	verticalFOVString	vertical FOV
private HashMap<String,String>	volParameters	vol parameters
private int	xDim	xDIm of 4d image
private int	xdimA	parameter for AlgorithmTransform
private float	xresA	parameter for AlgorithmTransform
private int	yDim	yDim of 4d image
private int	ydimA	parameter for AlgorithmTransform
private float	yresA	parameter for AlgorithmTransform
private int	zDim	zDim of 4d image
private int	zdimA	parameter for AlgorithmTransform
private float	zresA	parameter for AlgorithmTransform

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
AlgorithmDTICreateListFile(String studyPath, String studyName, String dicomB0VolumePath, String gradientFilePath, String bmtxtFilePath, JTextArea outputTextArea, boolean isInterleaved, boolean performRegsitration, int cost, int DOF, int interp, int interp2, float rotateBeginX, float rotateEndX, float coarseRateX, float fineRateX, float rotateBeginY, float rotateEndY, float coarseRateY, float fineRateY, float rotateBeginZ, float rotateEndZ, float coarseRateZ, float fineRateZ, boolean maxOfMinResol, boolean doSubsample, boolean doMultiThread, boolean fastMode, int bracketBound, int maxIterations, int numMinima, JTextField dwiPathTextField)	constructor for dicom if registration is to be done first
AlgorithmDTICreateListFile(String fileName, String fileDir, String gradientFilePath, String bmtxtFilePath, JTextArea outputTextArea, boolean performRegsitration)	constructor for par/rec
AlgorithmDTICreateListFile(String studyPath, String studyName, String gradientFilePath, String bmtxtFilePath, JTextArea outputTextArea, boolean isInterleaved, boolean performRegsitration)	constructor for dicom
AlgorithmDTICreateListFile(String fileName, String fileDir, String gradientFilePath, String bmtxtFilePath, JTextArea outputTextArea, boolean performRegsitration, int cost, int DOF, int interp, int interp2, int registerTo, float rotateBegin, float rotateEnd, float coarseRate, float fineRate, boolean doSubsample, boolean doMultiThread, boolean fastMode, int bracketBound, int maxIterations, int numMinima, JTextField dwiPathTextField)	constructor for par/rec if registration is to be done first

Method Summary

Modifier and Type	Method	Description
void	algorithmPerformed(AlgorithmBase algorithm)	Called after an algorithm this listener is registered to exits (maybe successfully, maybe not).
boolean	copyBMatrixFile()	This method copies the optional b matrix file that user provided, and copies it to proc dir and renames it to the correct naming syntax.
boolean	createBMatrixFileDICOM()	This method creates the b-matrix file.
boolean	createBMatrixFileParRec()	This method creates the B-Matrix file
boolean	createListFileDICOM()	This method creates the list file.
boolean	createListFileParRec()	This method creates the list file.
boolean	createPathFileDICOM()	This method creates the path file.
boolean	createPathFileForInterleavedDICOM()	This method creates the path file for interleaverd datasets
boolean	createPathFileParRec()	This method creates the path file
boolean	createProcDirAndImageSlicesDirParRec()	this method creates the proc dir in which the list file, path file, and b-matrix file go.
boolean	createProcDirDICOM()	this method creates the proc dir in which the list file, path file, and b-matrix file go.
boolean	createSubDirsInRegisteredDir(File dir)
boolean	deleteAllFiles(File dir)
void	finalize()	this method cleans up the proc dir if success is false and it sets the lists to null.
boolean	obtainBValuesDICOM()	This method obtains the b-values for each volume from either the public tag or the private tag.
boolean	obtainListFileDataParRec()	This method obtains list file data mostly from the 1st slice
boolean	parse(File file)	this method parses the study dir sort into lists using series number that is available in dicom tag. then based on the filename, get vol number (for example mipav_dicom_dti_series11_volume10005.dcm), and sort within lists using vol number and instance number that comes from dicom tag.
boolean	performRegistrationDICOM()	regsitration of DICOM DWI dataset
boolean	performRegistrationPARREC()	regsitration of PAR REC DWI dataset
boolean	readGradientFileDICOM()	This method reads in the gradient file gradient file can be in 2 differetn ways....for eDTI, there will be a number on first line followed by correct number of gradients if it is DTI, there will be no number and just 7 linies of gradients....this needs to be duplicated as many times as there are series.
boolean	readGradientFileParRec()	this method reads the gradient file
boolean	registerAndSaveVolumes(File dir)
void	runAlgorithm()	Actually runs the algorithm.
void	runAlgorithmDICOM()	run algorithm for dicom
void	runAlgorithmPARREC()	run algorithm for par/rec
boolean	setInitialInfo()	this method sets initial info about the study.
boolean	writeImageSlicesParRec()	This method writes out the image slices as raw float

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

actionPerformed, 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, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

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

Field Details

studyName

private String studyName

This is the dir name of the study.*

studyPath

private String studyPath

This is the full path of the study.*

prFileName

private String prFileName

par rec file name

prFileDir

private String prFileDir

par rec file dir

gradientFilePath

private String gradientFilePath

This is the full path to the gradient file.*

bmtxtFilePath

private String bmtxtFilePath

This is the full path to the b matrix file.*

isInterleaved

private boolean isInterleaved

boolean if dataset is interelaved

outputTextArea

private JTextArea outputTextArea

TextArea of main dialog for text output.*

dwiPathTextField

private JTextField dwiPathTextField

handle to dwi data textfield of main dialog

seriesFileInfoTreeMap

private TreeMap<Integer,TreeSet<String[]>> seriesFileInfoTreeMap

This is an ordered map of series number and seriesFileInfoTreeSet.*

seriesFileInfoTreeSet

private TreeSet<String[]> seriesFileInfoTreeSet

This is an ordered list of files per series number.*

isDICOM

private boolean isDICOM

boolean indicating if we are dealing with dicom or par/rec

listFileName

private String listFileName

List file name

bmatrixFileName

private String bmatrixFileName

B Matrix file name

pathFileName

private String pathFileName

Path File name

success

private boolean success

flag indicating if method was successful.*

totalImageSlices

private int totalImageSlices

total image slices.*

totalNumVolumes

private int totalNumVolumes

total num of volumes in study.*

isEDTI

private boolean isEDTI

boolean telling if dataset is eDTI.*

isGE

private boolean isGE

boolean telling if datset is GE.*

isSiemens

private boolean isSiemens

boolean telling if datset is SIEMENS.*

firstFileInfoDicom

private FileInfoDicom firstFileInfoDicom

first fileinfo dicom...used for list file info.*

geSoftwareVersion

private int geSoftwareVersion

int telling software version if datset is GE.*

imageFilter

private ViewImageFileFilter imageFilter

This is the image filter needed to select the correct dicom images.*

dicomInfo

private String[] dicomInfo

Array that holds the dicom tag info*

isProcDirCreated

private boolean isProcDirCreated

boolean if proc dir was created.*

numSlicesPerVolume

private int numSlicesPerVolume

this is the number of image slices per volume.*

nim

private int nim

this is the number of gradient quantities that is obtained by reading first line of gradient file.*

direction

private float[][] direction

this is the gradient matrix that is populated when reading the gradient file.*

bValuesArrayList

private ArrayList<Float> bValuesArrayList

this is an array of b-values that for each volume.*

fileParRec

private FilePARREC fileParRec

FileParRec handle

fileInfoPR

private FileInfoPARREC fileInfoPR

file info Par/Rec

image4D

private ModelImage image4D

ModelImage of 4D par/rec dataset

originalColumnsString

private String originalColumnsString

x dim

originalRowsString

private String originalRowsString

y dim

numSlicesString

private String numSlicesString

z dim

nimString

private String nimString

t dim

phaseEncodingString

private String phaseEncodingString

phase encoding...hard coded to vertical

horizontalFOVString

private String horizontalFOVString

horizontal FOV

verticalFOVString

private String verticalFOVString

vertical FOV

sliceGapString

private String sliceGapString

slice gap String

sliceThicknessString

private String sliceThicknessString

sliec thickness

imageOrientationString

private String imageOrientationString

image orientation

volParameters

private HashMap<String,String> volParameters

vol parameters

avgVolIndex

private int avgVolIndex

Philips puts in one volume as the average of all the DWIs. This volume will have a non-zero B value and 0 in the gradients Once we find this volume, exclude it.... this int represents which volume index to exclude

isOldVersion

private boolean isOldVersion

boolean identifying if par/rec datset is older than version 4.1

oldVersionGradientsAL

private ArrayList<String[]> oldVersionGradientsAL

arraylist of gradients for version 4 of Par/Rec

nimCounter

private int nimCounter

this counter is used for version 4 of Par/Rec...nim is calculated from gradient file

imageSlicesDirPath

private String imageSlicesDirPath

path for imageSlicesDir

relativeImageSlicesDirPath

private String relativeImageSlicesDirPath

relative path for slices dir for outputting to path file

rawImageFormatString

private String rawImageFormatString

raw image format...hardcoded to float since we will be outputting par/rec slices in float format

unsortedPathsArrayList

private ArrayList<String> unsortedPathsArrayList

arraylist of unsorted path strings to image slices

xDim

private int xDim

xDIm of 4d image

yDim

private int yDim

yDim of 4d image

zDim

private int zDim

zDim of 4d image

tDim

private int tDim

tDim of 4d image

performRegistration

private boolean performRegistration

boolean for performing registration

reg35

private AlgorithmRegOAR35D reg35

handle to AlgorithmRegOAR35D

reg3

private AlgorithmRegOAR3D reg3

handle to AlgorithmRegOAR3D

cost

private int cost

registration option parameters

DOF

private int DOF

registration option parameters

interp

private int interp

registration option parameters

interp2

private int interp2

registration option parameters

registerTo

private int registerTo

registration option parameters

maxIterations

private int maxIterations

registration option parameters

numMinima

private int numMinima

registration option parameters

rotateBegin

private float rotateBegin

registration option parameters

rotateEnd

private float rotateEnd

registration option parameters

coarseRate

private float coarseRate

registration option parameters

fineRate

private float fineRate

registration option parameters

rotateBeginX

private float rotateBeginX

registration option parameters

rotateEndX

private float rotateEndX

registration option parameters

coarseRateX

private float coarseRateX

registration option parameters

fineRateX

private float fineRateX

registration option parameters

rotateBeginY

private float rotateBeginY

registration option parameters

rotateEndY

private float rotateEndY

registration option parameters

coarseRateY

private float coarseRateY

registration option parameters

fineRateY

private float fineRateY

registration option parameters

rotateBeginZ

private float rotateBeginZ

registration option parameters

rotateEndZ

private float rotateEndZ

registration option parameters

coarseRateZ

private float coarseRateZ

registration option parameters

fineRateZ

private float fineRateZ

registration option parameters

doGraph

private boolean doGraph

registration option parameters

doSubsample

private boolean doSubsample

registration option parameters

doMultiThread

private boolean doMultiThread

registration option parameters

fastMode

private boolean fastMode

registration option parameters

maxOfMinResol

private boolean maxOfMinResol

registration option parameters

dicomB0VolumePath

private String dicomB0VolumePath

path to dicom B0 for registration purposes

refImage

private ModelImage refImage

model images

matchImage

private ModelImage matchImage

model images

resultImage

private ModelImage resultImage

model images

fileIO

private FileIO fileIO

file IO

registeredStudyName

private String registeredStudyName

study name for registered data set

transform

private AlgorithmTransform transform

handle to AlgorithmTransform

xdimA

private int xdimA

parameter for AlgorithmTransform

ydimA

private int ydimA

parameter for AlgorithmTransform

zdimA

private int zdimA

parameter for AlgorithmTransform

xresA

private float xresA

parameter for AlgorithmTransform

yresA

private float yresA

parameter for AlgorithmTransform

zresA

private float zresA

parameter for AlgorithmTransform

registeredDicomB0VolumePathParentFolder

private String registeredDicomB0VolumePathParentFolder

registered B0 parent folder

Constructor Details

AlgorithmDTICreateListFile

public AlgorithmDTICreateListFile(String studyPath,
 String studyName,
 String gradientFilePath,
 String bmtxtFilePath,
 JTextArea outputTextArea,
 boolean isInterleaved,
 boolean performRegsitration)

constructor for dicom

Parameters:

studyPath -

studyName -

gradientFilePath -

bmtxtFilePath -

outputTextArea -

AlgorithmDTICreateListFile

public AlgorithmDTICreateListFile(String studyPath,
 String studyName,
 String dicomB0VolumePath,
 String gradientFilePath,
 String bmtxtFilePath,
 JTextArea outputTextArea,
 boolean isInterleaved,
 boolean performRegsitration,
 int cost,
 int DOF,
 int interp,
 int interp2,
 float rotateBeginX,
 float rotateEndX,
 float coarseRateX,
 float fineRateX,
 float rotateBeginY,
 float rotateEndY,
 float coarseRateY,
 float fineRateY,
 float rotateBeginZ,
 float rotateEndZ,
 float coarseRateZ,
 float fineRateZ,
 boolean maxOfMinResol,
 boolean doSubsample,
 boolean doMultiThread,
 boolean fastMode,
 int bracketBound,
 int maxIterations,
 int numMinima,
 JTextField dwiPathTextField)

constructor for dicom if registration is to be done first

Parameters:

studyPath -

studyName -

gradientFilePath -

bmtxtFilePath -

outputTextArea -

AlgorithmDTICreateListFile

public AlgorithmDTICreateListFile(String fileName,
 String fileDir,
 String gradientFilePath,
 String bmtxtFilePath,
 JTextArea outputTextArea,
 boolean performRegsitration)

constructor for par/rec

AlgorithmDTICreateListFile

public AlgorithmDTICreateListFile(String fileName,
 String fileDir,
 String gradientFilePath,
 String bmtxtFilePath,
 JTextArea outputTextArea,
 boolean performRegsitration,
 int cost,
 int DOF,
 int interp,
 int interp2,
 int registerTo,
 float rotateBegin,
 float rotateEnd,
 float coarseRate,
 float fineRate,
 boolean doSubsample,
 boolean doMultiThread,
 boolean fastMode,
 int bracketBound,
 int maxIterations,
 int numMinima,
 JTextField dwiPathTextField)

constructor for par/rec if registration is to be done first

Method Details

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

performRegistrationPARREC

public boolean performRegistrationPARREC()

regsitration of PAR REC DWI dataset

performRegistrationDICOM

public boolean performRegistrationDICOM()

regsitration of DICOM DWI dataset

registerAndSaveVolumes

public boolean registerAndSaveVolumes(File dir)

createSubDirsInRegisteredDir

public boolean createSubDirsInRegisteredDir(File dir)

deleteAllFiles

public boolean deleteAllFiles(File dir)

runAlgorithmDICOM

public void runAlgorithmDICOM()

run algorithm for dicom

runAlgorithmPARREC

public void runAlgorithmPARREC()

run algorithm for par/rec

setInitialInfo

public boolean setInitialInfo()

this method sets initial info about the study.

Returns:

boolean success

parse

public boolean parse(File file)
              throws IOException,
OutOfMemoryError

this method parses the study dir sort into lists using series number that is available in dicom tag. then based on the filename, get vol number (for example mipav_dicom_dti_series11_volume10005.dcm), and sort within lists using vol number and instance number that comes from dicom tag.

Parameters:

file -

Returns:

boolean success

Throws:

IOException

OutOfMemoryError

createProcDirDICOM

public boolean createProcDirDICOM()

this method creates the proc dir in which the list file, path file, and b-matrix file go.

Returns:

boolean success

createPathFileForInterleavedDICOM

public boolean createPathFileForInterleavedDICOM()

This method creates the path file for interleaverd datasets

Returns:

boolean success

createPathFileDICOM

public boolean createPathFileDICOM()

This method creates the path file.

Returns:

boolean success

createListFileDICOM

public boolean createListFileDICOM()

This method creates the list file.

Returns:

boolean success

readGradientFileDICOM

public boolean readGradientFileDICOM()

This method reads in the gradient file gradient file can be in 2 differetn ways....for eDTI, there will be a number on first line followed by correct number of gradients if it is DTI, there will be no number and just 7 linies of gradients....this needs to be duplicated as many times as there are series.

Returns:

boolean success

obtainBValuesDICOM

public boolean obtainBValuesDICOM()

This method obtains the b-values for each volume from either the public tag or the private tag.

Returns:

boolean success

createBMatrixFileDICOM

public boolean createBMatrixFileDICOM()

This method creates the b-matrix file.

Returns:

boolean success

obtainListFileDataParRec

public boolean obtainListFileDataParRec()

This method obtains list file data mostly from the 1st slice

Returns:

readGradientFileParRec

public boolean readGradientFileParRec()

this method reads the gradient file

Returns:

createProcDirAndImageSlicesDirParRec

public boolean createProcDirAndImageSlicesDirParRec()

this method creates the proc dir in which the list file, path file, and b-matrix file go.

Returns:

boolean success

createListFileParRec

public boolean createListFileParRec()

This method creates the list file.

Returns:

boolean success

createBMatrixFileParRec

public boolean createBMatrixFileParRec()

This method creates the B-Matrix file

Returns:

writeImageSlicesParRec

public boolean writeImageSlicesParRec()

This method writes out the image slices as raw float

Returns:

createPathFileParRec

public boolean createPathFileParRec()

This method creates the path file

Returns:

finalize

public void finalize()

this method cleans up the proc dir if success is false and it sets the lists to null.

Overrides:

finalize in class AlgorithmBase

copyBMatrixFile

public boolean copyBMatrixFile()

This method copies the optional b matrix file that user provided, and copies it to proc dir and renames it to the correct naming syntax.

Returns:

boolean

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