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

All Implemented Interfaces:

AlgorithmInterface, java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
java.lang.Thread.State, java.lang.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 java.lang.String`	`bmatrixFileName`	B Matrix file name
`private java.lang.String`	`bmtxtFilePath`	This is the full path to the b matrix file
`private java.util.ArrayList<java.lang.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 java.lang.String`	`dicomB0VolumePath`	path to dicom B0 for registration purposes
`private java.lang.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 javax.swing.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 java.lang.String`	`gradientFilePath`	This is the full path to the gradient file
`private java.lang.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 java.lang.String`	`imageOrientationString`	image orientation
`private java.lang.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 java.lang.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 java.lang.String`	`nimString`	t dim
`private int`	`numMinima`	registration option parameters
`private int`	`numSlicesPerVolume`	this is the number of image slices per volume
`private java.lang.String`	`numSlicesString`	z dim
`private java.util.ArrayList<java.lang.String[]>`	`oldVersionGradientsAL`	arraylist of gradients for version 4 of Par/Rec
`private java.lang.String`	`originalColumnsString`	x dim
`private java.lang.String`	`originalRowsString`	y dim
`private javax.swing.JTextArea`	`outputTextArea`	TextArea of main dialog for text output
`private java.lang.String`	`pathFileName`	Path File name
`private boolean`	`performRegistration`	boolean for performing registration
`private java.lang.String`	`phaseEncodingString`	phase encoding...hard coded to vertical
`private java.lang.String`	`prFileDir`	par rec file dir
`private java.lang.String`	`prFileName`	par rec file name
`private java.lang.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 java.lang.String`	`registeredDicomB0VolumePathParentFolder`	registered B0 parent folder
`private java.lang.String`	`registeredStudyName`	study name for registered data set
`private int`	`registerTo`	registration option parameters
`private java.lang.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 java.util.TreeMap<java.lang.Integer,java.util.TreeSet<java.lang.String[]>>`	`seriesFileInfoTreeMap`	This is an ordered map of series number and seriesFileInfoTreeSet
`private java.util.TreeSet<java.lang.String[]>`	`seriesFileInfoTreeSet`	This is an ordered list of files per series number
`private java.lang.String`	`sliceGapString`	slice gap String
`private java.lang.String`	`sliceThicknessString`	sliec thickness
`private java.lang.String`	`studyName`	This is the dir name of the study
`private java.lang.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 java.util.ArrayList<java.lang.String>`	`unsortedPathsArrayList`	arraylist of unsorted path strings to image slices
`private java.lang.String`	`verticalFOVString`	vertical FOV
`private java.util.HashMap<java.lang.String,java.lang.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(java.lang.String studyPath, java.lang.String studyName, java.lang.String dicomB0VolumePath, java.lang.String gradientFilePath, java.lang.String bmtxtFilePath, javax.swing.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, javax.swing.JTextField dwiPathTextField)	constructor for dicom if registration is to be done first
`AlgorithmDTICreateListFile(java.lang.String fileName, java.lang.String fileDir, java.lang.String gradientFilePath, java.lang.String bmtxtFilePath, javax.swing.JTextArea outputTextArea, boolean performRegsitration)`	constructor for par/rec
`AlgorithmDTICreateListFile(java.lang.String studyPath, java.lang.String studyName, java.lang.String gradientFilePath, java.lang.String bmtxtFilePath, javax.swing.JTextArea outputTextArea, boolean isInterleaved, boolean performRegsitration)`	constructor for dicom
AlgorithmDTICreateListFile(java.lang.String fileName, java.lang.String fileDir, java.lang.String gradientFilePath, java.lang.String bmtxtFilePath, javax.swing.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, javax.swing.JTextField dwiPathTextField)	constructor for par/rec if registration is to be done first

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).
`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(java.io.File dir)`
`boolean`	`deleteAllFiles(java.io.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(java.io.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(java.io.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, 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
- studyName
```
private java.lang.String studyName
```
  This is the dir name of the study.*
- studyPath
```
private java.lang.String studyPath
```
  This is the full path of the study.*
- prFileName
```
private java.lang.String prFileName
```
  par rec file name
- prFileDir
```
private java.lang.String prFileDir
```
  par rec file dir
- gradientFilePath
```
private java.lang.String gradientFilePath
```
  This is the full path to the gradient file.*
- bmtxtFilePath
```
private java.lang.String bmtxtFilePath
```
  This is the full path to the b matrix file.*
- isInterleaved
```
private boolean isInterleaved
```
  boolean if dataset is interelaved
- outputTextArea
```
private javax.swing.JTextArea outputTextArea
```
  TextArea of main dialog for text output.*
- dwiPathTextField
```
private javax.swing.JTextField dwiPathTextField
```
  handle to dwi data textfield of main dialog
- seriesFileInfoTreeMap
```
private java.util.TreeMap<java.lang.Integer,java.util.TreeSet<java.lang.String[]>> seriesFileInfoTreeMap
```
  This is an ordered map of series number and seriesFileInfoTreeSet.*
- seriesFileInfoTreeSet
```
private java.util.TreeSet<java.lang.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 java.lang.String listFileName
```
  List file name
- bmatrixFileName
```
private java.lang.String bmatrixFileName
```
  B Matrix file name
- pathFileName
```
private java.lang.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 java.lang.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 java.util.ArrayList<java.lang.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 java.lang.String originalColumnsString
```
  x dim
- originalRowsString
```
private java.lang.String originalRowsString
```
  y dim
- numSlicesString
```
private java.lang.String numSlicesString
```
  z dim
- nimString
```
private java.lang.String nimString
```
  t dim
- phaseEncodingString
```
private java.lang.String phaseEncodingString
```
  phase encoding...hard coded to vertical
- horizontalFOVString
```
private java.lang.String horizontalFOVString
```
  horizontal FOV
- verticalFOVString
```
private java.lang.String verticalFOVString
```
  vertical FOV
- sliceGapString
```
private java.lang.String sliceGapString
```
  slice gap String
- sliceThicknessString
```
private java.lang.String sliceThicknessString
```
  sliec thickness
- imageOrientationString
```
private java.lang.String imageOrientationString
```
  image orientation
- volParameters
```
private java.util.HashMap<java.lang.String,java.lang.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 java.util.ArrayList<java.lang.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 java.lang.String imageSlicesDirPath
```
  path for imageSlicesDir
- relativeImageSlicesDirPath
```
private java.lang.String relativeImageSlicesDirPath
```
  relative path for slices dir for outputting to path file
- rawImageFormatString
```
private java.lang.String rawImageFormatString
```
  raw image format...hardcoded to float since we will be outputting par/rec slices in float format
- unsortedPathsArrayList
```
private java.util.ArrayList<java.lang.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 java.lang.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 java.lang.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 java.lang.String registeredDicomB0VolumePathParentFolder
```
  registered B0 parent folder

Constructor Detail

AlgorithmDTICreateListFile

public AlgorithmDTICreateListFile(java.lang.String studyPath,
                                  java.lang.String studyName,
                                  java.lang.String gradientFilePath,
                                  java.lang.String bmtxtFilePath,
                                  javax.swing.JTextArea outputTextArea,
                                  boolean isInterleaved,
                                  boolean performRegsitration)

constructor for dicom

Parameters:: studyPath -; studyName -; gradientFilePath -; bmtxtFilePath -; outputTextArea -

AlgorithmDTICreateListFile

public AlgorithmDTICreateListFile(java.lang.String studyPath,
                                  java.lang.String studyName,
                                  java.lang.String dicomB0VolumePath,
                                  java.lang.String gradientFilePath,
                                  java.lang.String bmtxtFilePath,
                                  javax.swing.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,
                                  javax.swing.JTextField dwiPathTextField)

constructor for dicom if registration is to be done first

Parameters:: studyPath -; studyName -; gradientFilePath -; bmtxtFilePath -; outputTextArea -

AlgorithmDTICreateListFile

public AlgorithmDTICreateListFile(java.lang.String fileName,
                                  java.lang.String fileDir,
                                  java.lang.String gradientFilePath,
                                  java.lang.String bmtxtFilePath,
                                  javax.swing.JTextArea outputTextArea,
                                  boolean performRegsitration)

constructor for par/rec

AlgorithmDTICreateListFile

public AlgorithmDTICreateListFile(java.lang.String fileName,
                                  java.lang.String fileDir,
                                  java.lang.String gradientFilePath,
                                  java.lang.String bmtxtFilePath,
                                  javax.swing.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,
                                  javax.swing.JTextField dwiPathTextField)

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

Method Detail
- 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(java.io.File dir)
```
- createSubDirsInRegisteredDir
```
public boolean createSubDirsInRegisteredDir(java.io.File dir)
```
- deleteAllFiles
```
public boolean deleteAllFiles(java.io.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(java.io.File file)
              throws java.io.IOException,
                     java.lang.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:
  
  java.io.IOException
  
  java.lang.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

Class AlgorithmDTICreateListFile

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

studyName

studyPath

prFileName

prFileDir

gradientFilePath

bmtxtFilePath

isInterleaved

outputTextArea

dwiPathTextField

seriesFileInfoTreeMap

seriesFileInfoTreeSet

isDICOM

listFileName

bmatrixFileName

pathFileName

success

totalImageSlices

totalNumVolumes

isEDTI

isGE

isSiemens

firstFileInfoDicom

geSoftwareVersion

imageFilter

dicomInfo

isProcDirCreated

numSlicesPerVolume

nim

direction

bValuesArrayList

fileParRec

fileInfoPR

image4D

originalColumnsString

originalRowsString

numSlicesString

nimString

phaseEncodingString

horizontalFOVString

verticalFOVString

sliceGapString

sliceThicknessString

imageOrientationString

volParameters

avgVolIndex

isOldVersion

oldVersionGradientsAL

nimCounter

imageSlicesDirPath

relativeImageSlicesDirPath

rawImageFormatString

unsortedPathsArrayList

xDim

yDim

zDim

tDim

performRegistration

reg35

reg3

cost

DOF

interp

interp2

registerTo

maxIterations

numMinima

rotateBegin

rotateEnd