java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Dialog
      - javax.swing.JDialog
        
        gov.nih.mipav.view.dialogs.JDialogBase
        
        gov.nih.mipav.view.dialogs.JDialogScriptableBase
        
        gov.nih.mipav.view.dialogs.JDialogTreMethod
        
        gov.nih.mipav.view.dialogs.JDialogTreT1

All Implemented Interfaces:

AlgorithmInterface, ScriptableActionInterface, DialogDefaultsInterface, ActionDiscovery, AlgorithmTreParams, java.awt.event.ActionListener, java.awt.event.FocusListener, java.awt.event.ItemListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants
```
public class JDialogTreT1
extends JDialogTreMethod
implements AlgorithmInterface, ActionDiscovery, AlgorithmTreParams
```
See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`JDialogTreT1.FlipAngleChangeListener`
`private class`	`JDialogTreT1.ProcessChoiceListener`	This listener focuses on the TRE processing choice chosen.
`private class`	`JDialogTreT1.ScannerChoiceListener`	This listener focuses on the type of scanner used to acquire the images.

Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase
JDialogBase.CancelAction, JDialogBase.HelpAction, JDialogBase.OKAction

Nested classes/interfaces inherited from class javax.swing.JDialog
javax.swing.JDialog.AccessibleJDialog

Nested classes/interfaces inherited from class java.awt.Dialog
java.awt.Dialog.AccessibleAWTDialog, java.awt.Dialog.ModalExclusionType, java.awt.Dialog.ModalityType

Nested classes/interfaces inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type

Nested classes/interfaces inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Nested classes/interfaces inherited from interface gov.nih.mipav.view.dialogs.AlgorithmTreParams
AlgorithmTreParams.FieldStrength, AlgorithmTreParams.InversionType, AlgorithmTreParams.ScannerType, AlgorithmTreParams.Threshold

Field Summary

Fields
Modifier and Type	Field	Description
`private double`	`angleIncrement`
`private javax.swing.JComboBox`	`b1Field`
`private int`	`b1ImageIndex`
`private boolean`	`calculateM0`
`private boolean`	`calculateT1`	The list of possible maps that can be calculated
`private AlgorithmTreT1`	`cAlgo`
`private javax.swing.JTextField[]`	`convFAFieldAr`
`private javax.swing.JComboBox[]`	`convimageComboAr`
`private javax.swing.JTextField`	`convRepTime`
`private javax.swing.JPanel`	`convSpec`
`private static int`	`dialogWidthAdd`
`private int[]`	`direction`
`private javax.swing.JRadioButton`	`doConvTre`
`private javax.swing.JRadioButton`	`doHifiTre`
`private javax.swing.JRadioButton`	`doubleInvRadio`
`private double[]`	`estimates`
`private javax.swing.ButtonGroup`	`fieldStrengthGroup`
`private javax.swing.JTextField[]`	`flipAngleAr`
`private javax.swing.JPanel`	`hifiPanel`
`private javax.swing.JPanel`	`hifiSpec`
`private javax.swing.ButtonGroup`	`inversionGroup`
`private AlgorithmTreParams.InversionType`	`inversionType`
`private boolean`	`invertT1toR1`
`private javax.swing.JComboBox[]`	`irspgrCombo`
`private double[]`	`irspgrData`
`private double`	`irspgrFA`
`private javax.swing.JTextField`	`irspgrFAField`
`private javax.swing.JTextField[]`	`irspgrField`
`private javax.swing.JPanel`	`irspgrGeneralPanel`
`private int[]`	`irspgrImageIndex`
`private double`	`irspgrKy`
`private javax.swing.JTextField`	`irspgrNum`
`private javax.swing.JScrollPane`	`irspgrPanel`
`private double[]`	`irspgrTI`
`private double[]`	`irspgrTr`
`private double`	`irspgrTR`
`private javax.swing.JTextField`	`irspgrTRField`
`private javax.swing.JRadioButton`	`isGEButton`
`private javax.swing.JRadioButton`	`isSiemensButton`
`private javax.swing.JCheckBox`	`leastSquaresCheck`
`private double`	`maxAngle`
`private double`	`maxM0`
`private javax.swing.JTextField`	`maxM0Field`
`private double`	`maxT1`
`private javax.swing.JTextField`	`maxT1Field`
`private AlgorithmTreParams.FieldStrength`	`mriStrength`	The following GUI choices change algorithm operation using enums
`private int`	`Nsa`
`private int`	`Nti`
`private javax.swing.JTextField`	`numSlicesField`
`private boolean`	`performStraightTreT1`
`private boolean`	`performTreT1HIFI`
`private boolean`	`performTreT1withPreCalculatedB1Map`
`private double`	`pointScale`
`private double[]`	`residuals`
`private double`	`scale`
`private double`	`scaleIncrement`
`private AlgorithmTreParams.ScannerType`	`scannerType`
`private javax.swing.JCheckBox`	`showB1Check`
`private boolean`	`showB1Map`
`private javax.swing.JCheckBox`	`showM0Map`
`private javax.swing.JCheckBox`	`showR1Map`
`private javax.swing.JCheckBox`	`showT1Map`
`private javax.swing.JRadioButton`	`singleInvRadio`
`private javax.swing.JCheckBox`	`smoothB1Box`
`private boolean`	`smoothB1Field`
`private double[]`	`spgrData`
`private javax.swing.JComboBox[]`	`spgrImageComboBoxAr`
`private int[]`	`spgrImageIndex`
`private javax.swing.JTextField`	`spgrNumFA`
`private javax.swing.JScrollPane`	`spgrPanel`
`private javax.swing.JTextField`	`spgrRepTime`
`private javax.swing.JPanel`	`straightPanel`
`private javax.swing.JRadioButton`	`t15Radio`
`private javax.swing.JRadioButton`	`t30Radio`
`private javax.swing.JTabbedPane`	`tab`
`private static java.lang.String`	`title`
`private java.lang.String[]`	`titles`	The GUI list of images
`private double[]`	`treFA`
`private javax.swing.JScrollPane`	`treLong`
`private double`	`treTR`
`private boolean`	`uniformAngleSpacing`
`private javax.swing.JCheckBox`	`useB1Map`
`private boolean`	`useWeights`
`private java.lang.String[]`	`wList`	The ordered list of images that the algorithm is dependent on.

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogTreMethod
guiBuilder, hardCheckBox, hardNoiseThreshold, lowerLeftCorner, lowerRightCorner, noCheckBox, noiseScale, smartCheckBox, SUCCESS, thresholdMethod, totalThreshold, upperLeftCorner, upperRightCorner

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase
displayInNewFrame, isComplete, scriptParameters

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogBase
applyButton, bar, cancelButton, cancelFlag, closeButton, HELP, helpButton, mainDialogPanel, NEW, OKButton, parentFrame, progressBar, REPLACE, runInSeparateThread, runningScriptFlag, runQuiet, serif12, serif12B, voiManager

Fields inherited from class javax.swing.JDialog
accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Dialog
DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Constructor Summary

Constructors
Constructor	Description
`JDialogTreT1()`	Blank constructor needed for dynamic instantiation.
`JDialogTreT1(java.awt.Frame theParentFrame, ModelImage im)`	Construct the TRE dialog.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`
`void`	`algorithmPerformed(AlgorithmBase algorithm)`	Called after an algorithm this listener is registered to exits (maybe successfully, maybe not).
`private void`	`buildConventionalTabs()`	This method builds the conventional tabs based on possibly pre-defined values.
`protected javax.swing.JPanel`	`buildConventionalTreT1Panel()`
`protected javax.swing.JPanel`	`buildHIFIPanel()`
`private void`	`buildHIFITabs()`
`protected javax.swing.JScrollPane`	`buildIRSPGRPanel()`
`private javax.swing.JPanel`	`buildIRSPGRPanelGEInner()`
`private javax.swing.JPanel`	`buildIRSPGRPanelSiemensInner()`
`protected javax.swing.JScrollPane`	`buildSPGRPanel()`
`private javax.swing.JPanel`	`buildSPGRPanelInner()`
`protected javax.swing.JPanel`	`buildTreT1HIFISpecificsPanel()`
`private javax.swing.JPanel`	`buildTreT1HIFISpecificsPanelInner()`
`protected javax.swing.JScrollPane`	`buildTreT1LongPanel()`
`private javax.swing.JPanel`	`buildTreT1LongPanelInner()`
`protected javax.swing.JPanel`	`buildTreT1SpecificsPanel()`
`private javax.swing.JPanel`	`buildTreT1SpecificsPanelInner()`
`protected void`	`callAlgorithm()`	Starts the algorithm.
`ParameterTable`	`createInputParameters()`	Returns a table listing the input parameters of this algorithm (which should match up with the scripting parameters used in `setGUIFromParams()`).
`ParameterTable`	`createOutputParameters()`	Returns a table listing the output parameters of this algorithm (usually just labels used to obtain output image names later).
`protected void`	`displayTotalDialog()`
`protected void`	`doPostAlgorithmActions()`	Store the result image in the script runner's image table now that the action execution is finished.
`ActionMetadata`	`getActionMetadata()`	Return meta-information about this discoverable action for categorization and labeling purposes.
`java.lang.String`	`getOutputImageName(java.lang.String imageParamName)`	Returns the name of an image output by this algorithm, the image returned depends on the parameter label given (which can be used to retrieve the image object from the image registry).
`private void`	`initParams()`
`boolean`	`isActionComplete()`	Returns whether the action has successfully completed its execution.
`private void`	`run()`
`private void`	`setDialogWidthAdd()`	Specifies an addendum to the preferred size of the dialog equal to the length of the longest image.
`protected void`	`setGUIFromParams()`	Set the dialog GUI using the script parameters while running this algorithm as part of a script.
`private void`	`setProcessConvUI()`
`private void`	`setProcessHifiUI()`
`private java.lang.String`	`setUI(boolean process)`	Sets UI variables for either saving between processing steps or later reuse.
`protected void`	`storeParamsFromGUI()`	Record the parameters just used to run this algorithm in a script.
`private boolean`	`validateUI()`

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogTreMethod
buildHardThresholdPanel, buildNoThresholdPanel, buildSmartThresholdPanel, buildThresholdPanel, setHardThresholdUI, setSmartThresholdUI

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase
getDialogActionString, insertScriptLine, isComplete, scriptRun, setComplete

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogBase
buildApplyButton, buildButtons, buildCancelButton, buildCancelButton, buildCloseButton, buildHelpButton, buildImageComboBox, buildOKButton, buildOKButton, buildOKCancelButtons, buildTitledBorder, buildTitledBorder, createLabel, createProgressBar, createProgressBar, createTextField, focusGained, focusLost, getDialogName, isCancelled, isQuietRunning, isRunInSeparateThread, isScriptRunning, itemStateChanged, loadDefaults, loadDefaults, makeImageName, makeString, openNewFrame, saveDefaults, saveDefaults, setLeftHandSystem, setQuietRunning, setScriptRunning, setSeparateThread, setVisible, setVisible, setVisibleMenuBar, setVisibleStandard, setVOIManager, setWCSystem, testParameter, testParameterMin, updateFFTFileInfo, updateFileInfo, updateFileInfoOtherModality, updateFileInfoStatic, updateFileInfoStatic, updateFileTypeInfo, updateFileTypeInfo, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class javax.swing.JDialog
addImpl, createRootPane, dialogInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Dialog
addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, show, toBack

Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, toFront

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setMixingCutoutShape, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface gov.nih.mipav.view.dialogs.ActionDiscovery
scriptRun

- Field Detail
  - title
```
private static java.lang.String title
```
  - dialogWidthAdd
```
private static int dialogWidthAdd
```
  - treTR
```
private double treTR
```
  - irspgrTR
```
private double irspgrTR
```
  - irspgrKy
```
private double irspgrKy
```
  - irspgrFA
```
private double irspgrFA
```
  - maxT1
```
private double maxT1
```
  - maxM0
```
private double maxM0
```
  - treFA
```
private double[] treFA
```
  - irspgrTr
```
private double[] irspgrTr
```
  - irspgrTI
```
private double[] irspgrTI
```
  - spgrData
```
private double[] spgrData
```
  - irspgrData
```
private double[] irspgrData
```
  - scale
```
private double scale
```
  - pointScale
```
private double pointScale
```
  - scaleIncrement
```
private double scaleIncrement
```
  - estimates
```
private double[] estimates
```
  - residuals
```
private double[] residuals
```
  - direction
```
private int[] direction
```
  - spgrImageIndex
```
private int[] spgrImageIndex
```
  - irspgrImageIndex
```
private int[] irspgrImageIndex
```
  - b1ImageIndex
```
private int b1ImageIndex
```
  - angleIncrement
```
private double angleIncrement
```
  - Nsa
```
private int Nsa
```
  - Nti
```
private int Nti
```
  - maxAngle
```
private double maxAngle
```
  - smoothB1Field
```
private boolean smoothB1Field
```
  - mriStrength
```
private AlgorithmTreParams.FieldStrength mriStrength
```
    The following GUI choices change algorithm operation using enums
  - scannerType
```
private AlgorithmTreParams.ScannerType scannerType
```
  - inversionType
```
private AlgorithmTreParams.InversionType inversionType
```
  - calculateT1
```
private boolean calculateT1
```
    The list of possible maps that can be calculated
  - showB1Map
```
private boolean showB1Map
```
  - calculateM0
```
private boolean calculateM0
```
  - invertT1toR1
```
private boolean invertT1toR1
```
  - useWeights
```
private boolean useWeights
```
  - uniformAngleSpacing
```
private boolean uniformAngleSpacing
```
  - wList
```
private java.lang.String[] wList
```
    The ordered list of images that the algorithm is dependent on.
  - titles
```
private java.lang.String[] titles
```
    The GUI list of images
  - cAlgo
```
private AlgorithmTreT1 cAlgo
```
  - doConvTre
```
private javax.swing.JRadioButton doConvTre
```
  - doHifiTre
```
private javax.swing.JRadioButton doHifiTre
```
  - hifiPanel
```
private javax.swing.JPanel hifiPanel
```
  - straightPanel
```
private javax.swing.JPanel straightPanel
```
  - spgrPanel
```
private javax.swing.JScrollPane spgrPanel
```
  - convSpec
```
private javax.swing.JPanel convSpec
```
  - hifiSpec
```
private javax.swing.JPanel hifiSpec
```
  - treLong
```
private javax.swing.JScrollPane treLong
```
  - spgrImageComboBoxAr
```
private javax.swing.JComboBox[] spgrImageComboBoxAr
```
  - flipAngleAr
```
private javax.swing.JTextField[] flipAngleAr
```
  - spgrRepTime
```
private javax.swing.JTextField spgrRepTime
```
  - spgrNumFA
```
private javax.swing.JTextField spgrNumFA
```
  - irspgrNum
```
private javax.swing.JTextField irspgrNum
```
  - isGEButton
```
private javax.swing.JRadioButton isGEButton
```
  - isSiemensButton
```
private javax.swing.JRadioButton isSiemensButton
```
  - irspgrTRField
```
private javax.swing.JTextField irspgrTRField
```
  - irspgrFAField
```
private javax.swing.JTextField irspgrFAField
```
  - numSlicesField
```
private javax.swing.JTextField numSlicesField
```
  - doubleInvRadio
```
private javax.swing.JRadioButton doubleInvRadio
```
  - singleInvRadio
```
private javax.swing.JRadioButton singleInvRadio
```
  - t15Radio
```
private javax.swing.JRadioButton t15Radio
```
  - t30Radio
```
private javax.swing.JRadioButton t30Radio
```
  - smoothB1Box
```
private javax.swing.JCheckBox smoothB1Box
```
  - irspgrCombo
```
private javax.swing.JComboBox[] irspgrCombo
```
  - irspgrField
```
private javax.swing.JTextField[] irspgrField
```
  - inversionGroup
```
private javax.swing.ButtonGroup inversionGroup
```
  - fieldStrengthGroup
```
private javax.swing.ButtonGroup fieldStrengthGroup
```
  - leastSquaresCheck
```
private javax.swing.JCheckBox leastSquaresCheck
```
  - convRepTime
```
private javax.swing.JTextField convRepTime
```
  - convFAFieldAr
```
private javax.swing.JTextField[] convFAFieldAr
```
  - convimageComboAr
```
private javax.swing.JComboBox[] convimageComboAr
```
  - b1Field
```
private javax.swing.JComboBox b1Field
```
  - maxT1Field
```
private javax.swing.JTextField maxT1Field
```
  - maxM0Field
```
private javax.swing.JTextField maxM0Field
```
  - showT1Map
```
private javax.swing.JCheckBox showT1Map
```
  - showM0Map
```
private javax.swing.JCheckBox showM0Map
```
  - showR1Map
```
private javax.swing.JCheckBox showR1Map
```
  - showB1Check
```
private javax.swing.JCheckBox showB1Check
```
  - tab
```
private javax.swing.JTabbedPane tab
```
  - irspgrGeneralPanel
```
private javax.swing.JPanel irspgrGeneralPanel
```
  - irspgrPanel
```
private javax.swing.JScrollPane irspgrPanel
```
  - performTreT1withPreCalculatedB1Map
```
private boolean performTreT1withPreCalculatedB1Map
```
  - performStraightTreT1
```
private boolean performStraightTreT1
```
  - performTreT1HIFI
```
private boolean performTreT1HIFI
```
  - useB1Map
```
private javax.swing.JCheckBox useB1Map
```
- Constructor Detail
  - JDialogTreT1
```
public JDialogTreT1()
```
    Blank constructor needed for dynamic instantiation.
  - JDialogTreT1
```
public JDialogTreT1(java.awt.Frame theParentFrame,
                    ModelImage im)
```
    Construct the TRE dialog.
    
    Parameters:
    
    theParentFrame - Parent frame.
    
    im - Source image.
- Method Detail
  - initParams
```
private void initParams()
```
  - 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
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Overrides:
    
    actionPerformed in class JDialogBase
  - buildHIFIPanel
```
protected javax.swing.JPanel buildHIFIPanel()
```
  - buildConventionalTreT1Panel
```
protected javax.swing.JPanel buildConventionalTreT1Panel()
```
  - buildSPGRPanel
```
protected javax.swing.JScrollPane buildSPGRPanel()
```
  - buildSPGRPanelInner
```
private javax.swing.JPanel buildSPGRPanelInner()
```
  - buildIRSPGRPanel
```
protected javax.swing.JScrollPane buildIRSPGRPanel()
```
  - buildIRSPGRPanelGEInner
```
private javax.swing.JPanel buildIRSPGRPanelGEInner()
```
  - buildIRSPGRPanelSiemensInner
```
private javax.swing.JPanel buildIRSPGRPanelSiemensInner()
```
  - buildTreT1LongPanel
```
protected javax.swing.JScrollPane buildTreT1LongPanel()
```
  - buildTreT1LongPanelInner
```
private javax.swing.JPanel buildTreT1LongPanelInner()
```
  - buildTreT1SpecificsPanel
```
protected javax.swing.JPanel buildTreT1SpecificsPanel()
```
  - buildTreT1SpecificsPanelInner
```
private javax.swing.JPanel buildTreT1SpecificsPanelInner()
```
  - buildTreT1HIFISpecificsPanel
```
protected javax.swing.JPanel buildTreT1HIFISpecificsPanel()
```
  - buildTreT1HIFISpecificsPanelInner
```
private javax.swing.JPanel buildTreT1HIFISpecificsPanelInner()
```
  - callAlgorithm
```
protected void callAlgorithm()
```
    Description copied from class: JDialogScriptableBase
    
    Starts the algorithm. Already exists in most algorithm dialogs. Should be called during scripted execution and regular operation.
    
    Specified by:
    
    callAlgorithm in class JDialogScriptableBase
  - displayTotalDialog
```
protected void displayTotalDialog()
```
  - setDialogWidthAdd
```
private void setDialogWidthAdd()
```
    Specifies an addendum to the preferred size of the dialog equal to the length of the longest image.
  - doPostAlgorithmActions
```
protected void doPostAlgorithmActions()
```
    Store the result image in the script runner's image table now that the action execution is finished.
    
    Overrides:
    
    doPostAlgorithmActions in class JDialogScriptableBase
  - setGUIFromParams
```
protected void setGUIFromParams()
```
    Description copied from class: JDialogScriptableBase
    
    Set the dialog GUI using the script parameters while running this algorithm as part of a script.
    
    Specified by:
    
    setGUIFromParams in class JDialogScriptableBase
  - storeParamsFromGUI
```
protected void storeParamsFromGUI()
                           throws ParserException
```
    Description copied from class: JDialogScriptableBase
    
    Record the parameters just used to run this algorithm in a script.
    
    Specified by:
    
    storeParamsFromGUI in class JDialogScriptableBase
    
    Throws:
    
    ParserException - If there is a problem creating/recording the new parameters.
  - buildConventionalTabs
```
private void buildConventionalTabs()
```
    This method builds the conventional tabs based on possibly pre-defined values. Each method places these tabs in containers to allow for nice display.
  - buildHIFITabs
```
private void buildHIFITabs()
```
  - run
```
private void run()
```
  - setProcessConvUI
```
private void setProcessConvUI()
```
  - setProcessHifiUI
```
private void setProcessHifiUI()
```
  - setUI
```
private java.lang.String setUI(boolean process)
```
    Sets UI variables for either saving between processing steps or later reuse. When process is true, null values cause an issue to be returned, when process is false (indicating UI variables are just being transferred between processing steps), no action is taken for null values
    
    Parameters:
    
    process -
    
    Returns:
  - validateUI
```
private boolean validateUI()
```
  - createInputParameters
```
public ParameterTable createInputParameters()
```
    Returns a table listing the input parameters of this algorithm (which should match up with the scripting parameters used in setGUIFromParams()).
    
    Specified by:
    
    createInputParameters in interface ActionDiscovery
    
    Returns:
    
    A parameter table listing the inputs of this algorithm.
  - createOutputParameters
```
public ParameterTable createOutputParameters()
```
    Returns a table listing the output parameters of this algorithm (usually just labels used to obtain output image names later).
    
    Specified by:
    
    createOutputParameters in interface ActionDiscovery
    
    Returns:
    
    A parameter table listing the outputs of this algorithm.
  - getActionMetadata
```
public ActionMetadata getActionMetadata()
```
    Return meta-information about this discoverable action for categorization and labeling purposes.
    
    Specified by:
    
    getActionMetadata in interface ActionDiscovery
    
    Returns:
    
    Metadata for this action.
  - getOutputImageName
```
public java.lang.String getOutputImageName(java.lang.String imageParamName)
```
    Returns the name of an image output by this algorithm, the image returned depends on the parameter label given (which can be used to retrieve the image object from the image registry).
    
    Specified by:
    
    getOutputImageName in interface ActionDiscovery
    
    Parameters:
    
    imageParamName - The output image parameter label for which to get the image name.
    
    Returns:
    
    The image name of the requested output image parameter label.
  - isActionComplete
```
public boolean isActionComplete()
```
    Returns whether the action has successfully completed its execution.
    
    Specified by:
    
    isActionComplete in interface ActionDiscovery
    
    Returns:
    
    True, if the action is complete. False, if the action failed or is still running.

Class JDialogTreT1

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.view.dialogs.JDialogBase

Nested classes/interfaces inherited from class javax.swing.JDialog

Nested classes/interfaces inherited from class java.awt.Dialog

Nested classes/interfaces inherited from class java.awt.Window

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Nested classes/interfaces inherited from interface gov.nih.mipav.view.dialogs.AlgorithmTreParams

Field Summary

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogTreMethod

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase

Fields inherited from class gov.nih.mipav.view.dialogs.JDialogBase

Fields inherited from class javax.swing.JDialog

Fields inherited from class java.awt.Dialog

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface javax.swing.WindowConstants

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogTreMethod

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogScriptableBase

Methods inherited from class gov.nih.mipav.view.dialogs.JDialogBase

Methods inherited from class javax.swing.JDialog

Methods inherited from class java.awt.Dialog

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Methods inherited from interface gov.nih.mipav.view.dialogs.ActionDiscovery

Field Detail

title

dialogWidthAdd

treTR

irspgrTR

irspgrKy

irspgrFA

maxT1

maxM0

treFA

irspgrTr

irspgrTI

spgrData

irspgrData

scale

pointScale

scaleIncrement

estimates

residuals

direction

spgrImageIndex

irspgrImageIndex

b1ImageIndex

angleIncrement

Nsa

Nti

maxAngle

smoothB1Field

mriStrength

scannerType

inversionType

calculateT1

showB1Map

calculateM0

invertT1toR1

useWeights

uniformAngleSpacing

wList

titles

cAlgo

doConvTre

doHifiTre

hifiPanel

straightPanel

spgrPanel

convSpec

hifiSpec

treLong

spgrImageComboBoxAr

flipAngleAr