java.lang.Object
- gov.nih.mipav.view.ViewUserInterface

All Implemented Interfaces:

ScriptRecordingListener, CommandLineParser, java.awt.event.ActionListener, java.awt.event.KeyListener, java.awt.event.WindowListener, java.util.EventListener
```
public class ViewUserInterface
extends java.lang.Object
implements java.awt.event.ActionListener, java.awt.event.WindowListener, java.awt.event.KeyListener, ScriptRecordingListener, CommandLineParser
```
This class is the _glue_ keeps a record of the present structure of the application. It keeps a list of all the image frames presently being displayed and keeps a hash table of all the images (ModelImage) open in the application. In addition, this class keeps a reference to the main MIPAV frame and the message frame with much of the imaging results are output.

Version:

1.1 June 1, 2012

Author:

Justin Senseney, Matthew McAuliffe, Ph.D.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`ViewUserInterface.DicomQueryListener`
`private class`	`ViewUserInterface.ImageTransferHandler`	Handles drag and drop events to the main mipav gui.
`private class`	`ViewUserInterface.MemoryUsageUpdater`
`private class`	`ViewUserInterface.OpenFileInfo`	Stores file name and switch for multifile.

Field Summary

Fields
Modifier and Type	Field	Description
`protected java.util.Vector<javax.swing.JMenuBar>`	`aloneMenu`	Stores all stand-alone menus that have been created by the user.
`private javax.swing.JButton`	`btnGpuComp`	The button indicating that MIPAV is set to run OpenCL -- GPU based algorithms
`private javax.swing.JButton`	`btnMultiCore`	The button indicating that MIPAV is set to run in a threaded environment
`private TransMatrix`	`clippedMatrix`	Matrix for copy/paste actions in image's or between image's matrix edit panel.
`private java.util.Vector<java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>>`	`clippedScannerVectors`	DOCUMENT ME!
`private ViewVOIVector`	`clippedVOIs`	Vector to hold clipped VOIs (multiple).
`private java.lang.String`	`cmdLineArguments`	String holding the command line arguments for data provenance usage.
`private java.util.Vector<VOIBase>`	`copyVOIList`	Vector to hold clipped VOIs (multiple).
`private java.util.Vector<java.lang.String>`	`copyVOINameList`	Vector to hold VOI names (multiple).
`private DICOM_Receiver`	`DICOMcatcher`	Reference to the DICOM receiver that listens for DICOM formatted images sent by a DICOM server.
`private ViewJFrameDICOMQuery`	`DICOMQueryFrame`	DICOM query frame for sending and receiving DICOM images.
`private JDialogDataProvenance`	`dpDialog`	Dialog to display the mipav system data provenance
`private static java.io.File`	`exceptions`	Exception logging file
`private boolean`	`exitCmdLineOnError`	error handling for cmd line, if set to false will not exit on MipavUtil.displayError()
`private boolean`	`forceAlgorithmInPlace`	boolean to force the algorithm to replace the image rather than opening a new frame
`private java.awt.Dimension`	`frameLocation`	Location of new image frames.
`private java.util.Vector<java.awt.Frame>`	`imageFrameVector`	Stores array of images frames the first of which is the active image frame.
`private CustomHashtable<ModelImage>`	`imageHashtable`	A list of image models currently open in MIPAV.
`private ViewJFrameRegisteredImages`	`imgMonitorFrame`	Frame that monitors the registered images.
`private boolean`	`isAppFrameVisible`	Whether the mipav GUI should be shown; set by the -hide command line option.
`private boolean`	`isPlugInFrameVisible`	Whether a plugin standalone frame is visible
`private JarClassLoader`	`jarClassLoader`	Class/resource loader for plugins that are in jars
`private boolean`	`lastStackFlag`	Indicates the user's last choice of whether to open images as multi-file (stack) or single file in the file open dialog.
`private static java.lang.String`	`LOADING_STR`	String to use as the progress bar loading prefix.
`protected javax.swing.JFrame`	`mainFrame`	The main menu bar that runs MIPAV.
`private JDialogMemoryAllocation`	`mallocFrame`	Dialog that allows changes to the amount of heap requested of the system by the java Virtual Machine for MIPAV during java start.
`private ViewJFrameMemory`	`memoryFrame`	Dialog that displays the used and available memory.
`private javax.swing.JLabel`	`memoryUsageLabel`	The label showing the current memory usage of MIPAV.
`private ViewUserInterface.MemoryUsageUpdater`	`memoryUsageUpdater`	The periodic thread which updates the memory usage display once every second.
`protected ViewMenuBuilder`	`menuBuilder`	The object used to build and enable/select the menus.
`protected javax.swing.JTextField`	`messageField`	Message line at the bottom of the mainFrame.
`protected ViewJFrameMessage`	`messageFrame`	Message area for multi-line text output.
`private int`	`numTileSheets`	if user selects to open images as tiles, then this counter tells us how many tile sheets there are*
`private static java.lang.String`	`OPENING_STR`	String to use as the progress bar opening prefix.
`protected javax.swing.JMenuBar`	`openingMenuBar`	Initial menubar for MIPAV.
`private JDialogMipavOptions`	`optionsDialog`	Dialog that allows changes to the amount of heap requested of the system by the java Virtual Machine for MIPAV during java start.
`private static java.lang.String`	`outputDir`	This is the outputDir path that the user entered as a command line argument when running a script *
`private javax.swing.JMenu`	`pluginsMenu`	Stores the plugins menu so that it can be removed/updated when plugins are installed.
`private java.lang.String`	`progressBarPrefix`	The current progress bar prefix to use.
`private static boolean`	`providedOutputDir`	This boolean tells if the user has provided an ouputDir parameter as a command line argument when running a script
`private static boolean`	`providedUserDefaultDir`	This boolean tells if the user has provided an inputDir parameter as a command line argument when running a script
`private static JDialogShortcutEditor`	`shortcutEd`	Key shortcut editor dialog.
`private boolean`	`shortcutRecording`	Indicates whether the user is currently recording a new keyboard shortcut using the shortcut editor dialog.
`private ProvenanceHolder`	`systemDPHolder`	System DP holder (separate from images data provenance...this has everything).
`private static java.util.Vector<java.lang.String>`	`tempDirList`
`private static java.lang.String`	`userDefaultDir`	This is the inputDir path that the user entered as a command line argument when running a script *
`protected static ViewUserInterface`	`userInterfaceReference`	A reference to the only ViewUserInterface object in MIPAV.

Constructor Summary

Constructors
Modifier Constructor Description

protected ViewUserInterface()
Constructs main UI frame.

protected ViewUserInterface(boolean forceQuiet)
Constructs main UI frame.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`void`	`about()`	Creates simple dialog that describes basic info about MIPAV, with MIPAV as the title.
`void`	`about(java.lang.String title, java.lang.String filename)`	Creates a fairly simple plain-text viewing box.
`void`	`aboutDataProvenance()`	Displays the system data provenance using a simple dialog with table and jtextarea (for current selection).
`void`	`aboutJava()`	Creates simple dialog that describes basic info about the version of Java.
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Calls various methods based on the user's actions.
`boolean`	`addAloneMenu(javax.swing.JMenuBar menu)`	Adds a standalone menu to the user interface.
`private void`	`addPluginToMenu(java.lang.Class<?> plugin, java.lang.String pluginName, java.lang.String name, javax.swing.JMenu currentMenu, java.awt.event.ActionListener al, java.lang.String jarContainer)`
`static void`	`addToTempDirList(java.lang.String path)`
`void`	`buildAnonDirectoryDialog()`	Builds the anonymize directory dialog and displays it.
`JDialogDicomDir`	`buildDICOMDIRFrame()`	Builds the image tree dialog and displays it.
`ViewJFrameDICOMParser`	`buildDICOMFrame()`	Builds the image tree dialog and displays it.
`void`	`buildEditDICOMFrame()`	Builds the edit dicom tag interface.
`javax.swing.JMenuBar`	`buildMenu()`	Builds menus for the User Interface.
`ViewJFrameMessage`	`buildMessageFrame()`	Builds the message frame where user/program data can be displayed.
`javax.swing.JMenu`	`buildPlugInsMenu(java.awt.event.ActionListener al)`	Called by either userInterface (this) or by another actionlistener (ViewJFrameImage) to build the plugins menu bar.
`void`	`buildTreeDialog()`	Builds the image tree dialog and displays it.
`void`	`changeRecordingStatus(int recorderStatus)`	Alerts the listener to a change in whether the ScriptRecorder is currently recording a script.
`private void`	`checkHeapMaxAgainstPreferences()`	Test for VM memory sizes being the same as last run in preferences: displays a user-warning that the preferences & VM config files disagree and presents the JDialogMemoryAllocation dialog with "use preference" buttons to quicken the matching process.
`static void`	`checkPrefDirCommand(java.lang.String[] args, int initArg)`	If the preferences name command is about to be performed before an existing preferences directory command, this guarantees that the directory command will be executed first.
`void`	`cleanupAndExit()`
`void`	`clearAllDataText()`	Accessor to clear all of data frame.
`void`	`clearClippedVOIs()`	Deprecated.
`void`	`closeAllImages()`	this method closes all registered images
`void`	`copyClippedVOIs(ViewVOIVector copyList)`	Deprecated.
`void`	`copyVOIs(java.util.Vector<VOIBase> copyList)`
`static ViewUserInterface`	`create()`	This method should only be called once, and it should only be called by MipavMain to during the initialization of MIPAV.
`ModelImage`	`createBlankImage(FileInfoBase fileInfo)`	Creates a blank Image based on the information found in the fileInfo object and places it in a frame.
`ModelImage`	`createBlankImage(FileInfoBase fileInfo, boolean doDisplay, boolean allowRecording)`	Creates a blank Image based on the information found in the fileInfo object.
`ModelImage`	`createEmptyImage(FileInfoBase fileInfo)`	Creates a blank Image based on the information found in the default fileInfo object.
`private void`	`deleteItem(java.lang.String name, boolean deleteFrame, boolean runGC)`	Deletes the item specified by name.
`private void`	`deleteMenu(javax.swing.JMenu menu)`	Recursive deletion algorithm to delete JMenus which contain no JMenuItems exclusive of JMenus in any children.
`boolean`	`doExitCmdLineOnError()`	Tells whether or not to exit on an error when running from the command line
`boolean`	`doForceInPlace()`	Checks whether the dialog should force the algorithm to replace the image (no new frame)
`void`	`enableOutputWindow(boolean doShowFrame)`	Toggles the display of the Output window and updates all JFrameImages so that the menu checkbox will reflect the status of the output window.
`static java.lang.String`	`generateCmdUsageInfo()`	Generates automatic list of available commands.
`ViewJFrameImage`	`getActiveImageFrame()`	Accessor that returns the active image frame vector.
`java.lang.String`	`getAppTitle()`	Accessor to get the title of this application.
`TransMatrix`	`getClippedMatrix()`	Retrieves the clipped matrix for paste action.
`java.util.Vector<java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>>`	`getClippedScannerVectors()`	Deprecated.
`ViewVOIVector`	`getClippedVOIs()`	Deprecated.
`java.lang.String`	`getCmdLineArguments()`	Returns the Command line arguments (as one string, each separated by a space) .
`java.util.Vector<java.lang.String>`	`getCopyVOINames()`
`java.util.Vector<VOIBase>`	`getCopyVOIs()`
`java.lang.String`	`getDefaultDirectory()`	Accessor to get directory location of last file access.
`java.lang.String`	`getDefaultScriptDirectory()`	Accessor to get directory location of script files.
`DICOM_Receiver`	`getDICOMCatcher()`	Accessor to get the DICOM receiver.
`ViewJFrameDICOMQuery`	`getDICOMQueryFrame()`	Accessor to get the DICOM query frame.
`static java.util.Vector<java.lang.Class<ActionDiscovery>>`	`getDiscoverableActionList()`
`static java.util.Vector<java.lang.Class<ActionDiscovery>>`	`getDiscoverableActionList(java.lang.String baseDir)`
`static java.io.File`	`getExceptions()`
`ViewJFrameImage`	`getFrameContainingImage(ModelImage image)`	Accessor that returns the active image frame vector.
`java.util.Vector<java.awt.Frame>`	`getImageFrameVector()`	Accessor that returns frame vector.
`JarClassLoader`	`getJarClassLoader()`
`java.lang.String`	`getLastScript()`	Returns the last script file used from the preferences.
`boolean`	`getLastStackFlag()`	Gets the last checkbox entry for "multi-file" for opening images.
`javax.swing.JFrame`	`getMainFrame()`	Accessor that returns the main user interface frame.
`ViewMenuBuilder`	`getMenuBuilder()`	Returns the interface's menu builder.
`ViewJFrameMessage`	`getMessageFrame()`	Accessor that returns the message frame.
`java.lang.String`	`getMessageText()`	Accessor to get text of message field.
`java.awt.Dimension`	`getNewFrameLocation(int newImageXDim, int newImageYDim)`	Changes location of image when first displayed.
`java.awt.Dimension`	`getNewFrameYLocation()`	Changes vertical location of image when first displayed.
`static java.lang.String`	`getOutputDir()`
`java.lang.String`	`getProgressBarPrefix()`	Gets the string "Opening " or "Loading " based on what the progress bar should be displaying.
`ProvenanceHolder`	`getProvenanceHolder()`	Accessor for the mipav's data provenance .
`static ViewUserInterface`	`getReference()`	Get a reference to the ViewUserInterface object.
`int`	`getRegisteredFramedImagesNum()`	Return an num of images with frames(elements) from the image hashtable.
`ModelImage`	`getRegisteredImageByName(java.lang.String name)`	Return a registered image from the image hashtable based on the name of the image.
`java.util.Enumeration<java.lang.String>`	`getRegisteredImageNames()`	Return an enumeration of keys (image names) from the image hashtable.
`java.util.Enumeration<ModelImage>`	`getRegisteredImages()`	Return an enumeration of images (elements) from the image hashtable.
`int`	`getRegisteredImagesNum()`	Return an num of images (elements) from the image hashtable.
`static java.io.File`	`getSecondaryPluginsDir()`
`static java.lang.String`	`getUserDefaultDir()`
`void`	`imageRegistryMonitoring()`	Display image registry frame.
`void`	`imagesToFront()`	Brings all images and message frame to the front.
`protected javax.swing.JPanel`	`initCreateMemoryUsagePanel()`	Construct the panel which displays the current memory usage/limit and a garbage collection button.
`protected void`	`initCreateMessageBar()`	Create the panel containing components which show the application title initially, and will later be used to show image coordinates and intensities.
`protected javax.swing.JTextField`	`initCreateMessageField(java.lang.String title)`	Creates the message field for the main frame using the title given.
`protected javax.swing.JPanel`	`initCreateMultiCoreGpuIndicatorPanel()`	Construct the panel which displays whether the CPU and GPU could be utilized by algorithms based on the preferences settings by the user.
`protected void`	`initDicomReceiver()`	Starts the DICOM receiver if the flag in the preference file is `true`.
`void`	`initializeGui()`	Initializes the user interface.
`protected void`	`initMacintoshJDKversionCheck()`	Method checks to verify that when running on a Machintosh, the JDK version is at least 1�x2e;4.
`protected void`	`initPrefsFile()`	Set the preferences file to use (Preferences defaults to mipav.preferences).
`protected void`	`initPrefsTrim()`	Gets the TRIM_VOI, TRIM_MASK and TRIM_FLAG values from the preferences file, and if it cannot find them, it sets to some default value: TRIM_VOI will be 0.3, TRIM_MASK will be 0.0, and TRIM_FLAG will be true.
`protected void`	`initSetMainFrameDefaults(java.awt.LayoutManager prefLayout, boolean resize)`	Sets the layout of the Main Frame with the given, preferred layout manager; makes the main frame resizable as given; makes this class a window-listener; sets the default operation to do nothing on close; and the icon is set.
`protected void`	`initSetTitles(java.lang.String mainFrameTitle, java.lang.String appTitle)`	Sets the titles for for the main frame and the application using the strings given.
`protected void`	`initUsingPreferences()`	Performs a variety of start-up operations based on user-preferences; First, it tries to read from the preferences file; if it cannot, it sets the user directory.
`boolean`	`isAppFrameVisible()`	Accessor to check whether the application frame visible or not.
`boolean`	`isImageHashtableEmpty()`	Indicates if the image hashtable is empty.
`boolean`	`isImageRegistered(java.lang.String imageName)`	Indicates if the image name is found in the hashtable.
`boolean`	`isPlugInFrameVisible()`	Accessor to see if a stand-alone plugin frame is visible (not app frame)
`static boolean`	`isProvidedOutputDir()`	This is the getter for providedOutputDir providedOutputDir: This boolean tells if the user has provided an ouputDir parameter as a command line argument when running a script
`static boolean`	`isProvidedUserDefaultDir()`
`boolean`	`isShorcutRecording()`	Determines if the UserInterface is currently recording an action command as a shortcut.
`void`	`keyPressed(java.awt.event.KeyEvent e)`	Pass the key event to the selected image frame (if one exists).
`void`	`keyReleased(java.awt.event.KeyEvent e)`	Pass the key event to the selected image frame (if one exists).
`void`	`keyTyped(java.awt.event.KeyEvent e)`	Pass the key event to the selected image frame (if one exists).
`private void`	`loadMouseDrivers()`
`void`	`memoryAllocation()`	Display memory allocation frame (request more from the JVM on next JVM-start).
`void`	`memoryFrame()`	Display memory usage frame.
`void`	`openImageFrame()`	This method opens an image and puts it into a frame.
`void`	`openImageFrame(java.lang.String imageFile)`	Open an image and put it into a new frame, given the image file name.
`void`	`openImageFrame(java.lang.String imageFile, boolean multiFile)`	Open an image or images and put it into a new frame, given the image file name.
`void`	`openImageFrame(java.lang.String imageFileName, java.lang.String imageFileDir)`	Open an image and put it into a new frame, given the image file name.
`void`	`openJSONImageFrames()`
`void`	`openLastImage(int index)`	Attempts to open an image from the quicklist.
`void`	`options()`	Display Options dialog for all mipav options (including image specific options) to allow user to adjust display in one place.
`int`	`parseArguments(java.lang.String[] args, int initArg)`	Required by the CommandLineParser interface.
`static int`	`parseStaticArguments(java.lang.String[] args, int initArg)`	Required by the CommandLineParser interface.
`static void`	`printUsageAndExit()`	Displays command line help information on usage of all commands and then exits.
`static void`	`printUsageAndExit(Argument c)`	Displays command line help information on usage to standard out and then into an informational dialog box then exits the MIPAV application.
`void`	`regFrame(java.awt.Frame frame)`	Method that registers an image frame by putting it in the image frame vector and does NOT loads controls.
`void`	`registerFrame(java.awt.Frame frame)`	Method that registers an image frame by adding it to the vector and loads controls.
`java.lang.String`	`registerImage(ModelImage image)`	Register image model by adding it to the image hashtable.
`java.lang.String`	`registerImage(java.lang.String key, ModelImage image)`	Register image model by adding it to the image hashtable.
`boolean`	`removeAloneMenu(javax.swing.JMenuBar menu)`	Removes the stand-alone menu from the user interface.
`protected void`	`runCmdLine(java.lang.String scriptFile, java.util.Vector<ViewUserInterface.OpenFileInfo> imageList, java.util.Vector<java.util.Vector<java.lang.String>> voiList)`	This method is used when running MIPAV from the command line.
`void`	`setActiveFrame(java.awt.Frame frame)`	Method sets the parameter frame to top and active.
`void`	`setAppFrameVisible(boolean isVisible)`	Tells the application to show the MIPAV UI or suppress it (progress bars, image frames, etc).
`void`	`setClippedMatrix(TransMatrix tMat)`	Sets the clipped matrix for copy/paste actions.
`void`	`setControls()`	Sets the menu for the main frame.
`void`	`setDataText(java.lang.String str)`	Accessor to set text of data FRAME.
`void`	`setDefaultDirectory(java.lang.String defaultDirectory)`	Sets directory location of last file access.
`void`	`setDefaultScriptDirectory(java.lang.String dir)`	Sets directory location of the script files.
`void`	`setDICOMCatcher(DICOM_Receiver rcv)`	Accessor to set the DICOM receiver.
`void`	`setDICOMQueryFrame(ViewJFrameDICOMQuery frame)`	Accessor to set the DICOM query frame.
`void`	`setExitCmdLineOnError(boolean doExit)`	Sets MIPAV to exit (true) or not (false) on an error when running from the command line
`void`	`setForceInPlace(boolean doForce)`	Sets the dialogs to only replace the image (no new frame)
`void`	`setGlobalDataText(java.lang.String str)`	Accessor to set text of global data FRAME.
`void`	`setJarClassLoader(JarClassLoader jarClassLoader)`
`void`	`setLastScript(java.lang.String script)`	Sets last used script files in preferences.
`void`	`setLastStackFlag(boolean lastStackFlag)`	Sets the last value for opened multi-files (or single).
`void`	`setLoad(boolean doLoad)`	Tells the progress bar to say "Loading" rather than "Opening" for images being loaded if true.
`private void`	`setMenuActionListeners(java.awt.Component comp, java.awt.event.ActionListener frame)`
`void`	`setMessageText(java.lang.String str)`	Accessor to set text of message field.
`static void`	`setOutputDir(java.lang.String outputDir)`
`void`	`setPlugInFrameVisible(boolean isVisible)`	Tells the UI that a standalone plugin frame is visible
`static void`	`setProvidedOutputDir(boolean providedOutputDir)`
`static void`	`setProvidedUserDefaultDir(boolean providedUserDefaultDir)`
`static void`	`setSecondaryPluginsDir(java.io.File secondaryPluginsDir)`
`void`	`setShortcutRecording(boolean doRecord)`	Sets the UI to either be/not be recording action command.
`void`	`setTitle(java.lang.String str)`	Gets the application title from the preference file and prepends to the string passed into the method and displays the resultant string in the title of the main frame.
`static void`	`setUserDefaultDir(java.lang.String userDefaultDir)`
`void`	`setUseVOIName(boolean useName)`	Sets the Preference to use VOI Names instead of labels, then updates all frames to reflect this change with their VOIs.
`void`	`setVisible(boolean visible)`	Change whether the GUI should be visible.
`void`	`showLicense()`	Displays the MIPAV Software Transfer Agreement in a JDialogText window.
`void`	`showLicense(java.lang.String title, java.lang.String filename)`	Displays the MIPAV Software Transfer Agreement in a JDialogText window.
`void`	`showShortcutEditor(boolean doUpdate)`	Opens a dialog for viewing/modifying shortcuts.
`void`	`showSplashGraphics()`	Shows the MIPAV splash screen for a few seconds, or until the user clicks it.
`void`	`unregisterFrame(java.awt.Frame frame)`	Method that unregisters an image frame by removing it from the image frame vector.
`void`	`unregisterFrame(java.awt.Frame frame, boolean closeAll)`	Method that unregisters an image frame by removing it from the image frame vector.
`void`	`unRegisterImage(ModelImage image)`	Unregister image model by removing it from the image hashtable.
`void`	`unRegisterImage(java.lang.String imageKey)`	Unregister image model by removing it from the image hashtable given the key to the hashtable.
`void`	`updateGpuUsage()`	This method updates the "whether algorithms will use the GPU" when the relevant button has been pushed in either the preferences pane.
`void`	`updateMemoryUsage()`	This method is a callback method.
`void`	`updateMultiCoreUsage()`	This method updates the "whether multi-core should be used" button when the relevant button has been pushed in either the preferences pane.
`void`	`updateScript(java.lang.String newScriptText)`	Do nothing - required by ScriptRecordingListener interface.
`void`	`windowActivated(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`windowClosed(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`windowClosing(java.awt.event.WindowEvent event)`	Confirms if the user really wants to exit, then closes the application.
`void`	`windowDeactivated(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`windowDeiconified(java.awt.event.WindowEvent event)`	Deiconify only the other frames who's last state was normal (ie- restore other frames to their lastState).
`void`	`windowIconified(java.awt.event.WindowEvent event)`	Iconify all other frames associateed with MIPAV.
`void`	`windowOpened(java.awt.event.WindowEvent event)`	Do nothing.
`void`	`writeDataProvenance()`	Writes Mipav's data provenance to the default location.

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

- Field Detail
  - userInterfaceReference
```
protected static ViewUserInterface userInterfaceReference
```
    A reference to the only ViewUserInterface object in MIPAV.
    
    See Also:
    
    ViewUserInterface(), getReference()
  - OPENING_STR
```
private static final java.lang.String OPENING_STR
```
    String to use as the progress bar opening prefix.
    
    See Also:
    
    Constant Field Values
  - LOADING_STR
```
private static final java.lang.String LOADING_STR
```
    String to use as the progress bar loading prefix.
    
    See Also:
    
    Constant Field Values
  - shortcutEd
```
private static JDialogShortcutEditor shortcutEd
```
    Key shortcut editor dialog.
  - providedUserDefaultDir
```
private static boolean providedUserDefaultDir
```
    This boolean tells if the user has provided an inputDir parameter as a command line argument when running a script
  - userDefaultDir
```
private static java.lang.String userDefaultDir
```
    This is the inputDir path that the user entered as a command line argument when running a script *
  - providedOutputDir
```
private static boolean providedOutputDir
```
    This boolean tells if the user has provided an ouputDir parameter as a command line argument when running a script
  - outputDir
```
private static java.lang.String outputDir
```
    This is the outputDir path that the user entered as a command line argument when running a script *
  - mainFrame
```
protected javax.swing.JFrame mainFrame
```
    The main menu bar that runs MIPAV.
  - menuBuilder
```
protected ViewMenuBuilder menuBuilder
```
    The object used to build and enable/select the menus.
  - messageField
```
protected javax.swing.JTextField messageField
```
    Message line at the bottom of the mainFrame.
  - messageFrame
```
protected ViewJFrameMessage messageFrame
```
    Message area for multi-line text output. The message area has the ability to save/copy/paste the data to a file or clip board. This frame contains the Global Data, Data, Logging and Debug text areas. The Global and Debug text areas are common to all images (i.e. there is only one). The Data and logging window are unique and associated to their respect image.
  - openingMenuBar
```
protected javax.swing.JMenuBar openingMenuBar
```
    Initial menubar for MIPAV.
  - clippedMatrix
```
private TransMatrix clippedMatrix
```
    Matrix for copy/paste actions in image's or between image's matrix edit panel.
  - clippedScannerVectors
```
private final java.util.Vector<java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>> clippedScannerVectors
```
    DOCUMENT ME!
  - clippedVOIs
```
private final ViewVOIVector clippedVOIs
```
    Vector to hold clipped VOIs (multiple).
  - copyVOIList
```
private java.util.Vector<VOIBase> copyVOIList
```
    Vector to hold clipped VOIs (multiple).
  - copyVOINameList
```
private final java.util.Vector<java.lang.String> copyVOINameList
```
    Vector to hold VOI names (multiple).
  - jarClassLoader
```
private JarClassLoader jarClassLoader
```
    Class/resource loader for plugins that are in jars
  - cmdLineArguments
```
private java.lang.String cmdLineArguments
```
    String holding the command line arguments for data provenance usage.
  - DICOMcatcher
```
private DICOM_Receiver DICOMcatcher
```
    Reference to the DICOM receiver that listens for DICOM formatted images sent by a DICOM server.
  - DICOMQueryFrame
```
private ViewJFrameDICOMQuery DICOMQueryFrame
```
    DICOM query frame for sending and receiving DICOM images.
  - frameLocation
```
private final java.awt.Dimension frameLocation
```
    Location of new image frames. This location is updated with each additional image opened.
    
    See Also:
    
    #getNewFrameLocation()
  - imageFrameVector
```
private final java.util.Vector<java.awt.Frame> imageFrameVector
```
    Stores array of images frames the first of which is the active image frame.
  - imageHashtable
```
private final CustomHashtable<ModelImage> imageHashtable
```
    A list of image models currently open in MIPAV.
  - imgMonitorFrame
```
private ViewJFrameRegisteredImages imgMonitorFrame
```
    Frame that monitors the registered images.
  - isAppFrameVisible
```
private boolean isAppFrameVisible
```
    Whether the mipav GUI should be shown; set by the -hide command line option.
  - isPlugInFrameVisible
```
private boolean isPlugInFrameVisible
```
    Whether a plugin standalone frame is visible
  - lastStackFlag
```
private boolean lastStackFlag
```
    Indicates the user's last choice of whether to open images as multi-file (stack) or single file in the file open dialog.
  - mallocFrame
```
private JDialogMemoryAllocation mallocFrame
```
    Dialog that allows changes to the amount of heap requested of the system by the java Virtual Machine for MIPAV during java start.
  - memoryFrame
```
private ViewJFrameMemory memoryFrame
```
    Dialog that displays the used and available memory.
  - dpDialog
```
private JDialogDataProvenance dpDialog
```
    Dialog to display the mipav system data provenance
  - memoryUsageLabel
```
private javax.swing.JLabel memoryUsageLabel
```
    The label showing the current memory usage of MIPAV.
  - btnMultiCore
```
private javax.swing.JButton btnMultiCore
```
    The button indicating that MIPAV is set to run in a threaded environment
  - btnGpuComp
```
private javax.swing.JButton btnGpuComp
```
    The button indicating that MIPAV is set to run OpenCL -- GPU based algorithms
  - memoryUsageUpdater
```
private ViewUserInterface.MemoryUsageUpdater memoryUsageUpdater
```
    The periodic thread which updates the memory usage display once every second.
    
    See Also:
    
    updateMemoryUsage()
  - optionsDialog
```
private JDialogMipavOptions optionsDialog
```
    Dialog that allows changes to the amount of heap requested of the system by the java Virtual Machine for MIPAV during java start.
  - pluginsMenu
```
private javax.swing.JMenu pluginsMenu
```
    Stores the plugins menu so that it can be removed/updated when plugins are installed.
  - aloneMenu
```
protected java.util.Vector<javax.swing.JMenuBar> aloneMenu
```
    Stores all stand-alone menus that have been created by the user.
  - progressBarPrefix
```
private java.lang.String progressBarPrefix
```
    The current progress bar prefix to use.
  - shortcutRecording
```
private boolean shortcutRecording
```
    Indicates whether the user is currently recording a new keyboard shortcut using the shortcut editor dialog.
  - systemDPHolder
```
private ProvenanceHolder systemDPHolder
```
    System DP holder (separate from images data provenance...this has everything).
  - forceAlgorithmInPlace
```
private boolean forceAlgorithmInPlace
```
    boolean to force the algorithm to replace the image rather than opening a new frame
  - exitCmdLineOnError
```
private boolean exitCmdLineOnError
```
    error handling for cmd line, if set to false will not exit on MipavUtil.displayError()
  - numTileSheets
```
private int numTileSheets
```
    if user selects to open images as tiles, then this counter tells us how many tile sheets there are*
  - exceptions
```
private static java.io.File exceptions
```
    Exception logging file
  - tempDirList
```
private static java.util.Vector<java.lang.String> tempDirList
```
- Constructor Detail
  - ViewUserInterface
```
protected ViewUserInterface()
```
    Constructs main UI frame. Accesses the .preferences file to set up variables. Sets up DICOM hashtable for reading in DICOM files and starts the catcher, if appropriate. This method cannot be called directly. To use this constructor, you must call createReference. This class is a singleton, which means that only one type of this class is allowed to be instantiated in a single VM.
  - ViewUserInterface
```
protected ViewUserInterface(boolean forceQuiet)
```
    Constructs main UI frame. Accesses the .preferences file to set up variables. Sets up DICOM hashtable for reading in DICOM files and starts the catcher, if appropriate. This method cannot be called directly. To use this constructor, you must call createReference. This class is a singleton, which means that only one type of this class is allowed to be instantiated in a single VM.
    
    Parameters:
    
    forceQuiet - Mipav will not display any error, warning, or info messages. If a error displays MIPAV will exit.
- Method Detail
  - create
```
public static ViewUserInterface create()
```
    This method should only be called once, and it should only be called by MipavMain to during the initialization of MIPAV.
    
    Returns:
    
    ViewUserInterface
  - getReference
```
public static ViewUserInterface getReference()
```
    Get a reference to the ViewUserInterface object.
    
    Returns:
    
    ViewUserInterface
  - about
```
public void about()
```
    Creates simple dialog that describes basic info about MIPAV, with MIPAV as the title.
  - about
```
public void about(java.lang.String title,
                  java.lang.String filename)
```
    Creates a fairly simple plain-text viewing box.
    
    Parameters:
    
    title - the title for the about frame.
    
    filename - the filename of the about file to display.
  - aboutDataProvenance
```
public void aboutDataProvenance()
```
    Displays the system data provenance using a simple dialog with table and jtextarea (for current selection).
    .
  - aboutJava
```
public void aboutJava()
```
    Creates simple dialog that describes basic info about the version of Java.
  - addAloneMenu
```
public boolean addAloneMenu(javax.swing.JMenuBar menu)
```
    Adds a standalone menu to the user interface.
    
    Parameters:
    
    menu - the standalone JMenu
    
    Returns:
    
    whether addition to the vector was successful
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Calls various methods based on the user's actions.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Parameters:
    
    event - Event that triggered this function.
  - createEmptyImage
```
public ModelImage createEmptyImage(FileInfoBase fileInfo)
```
    Creates a blank Image based on the information found in the default fileInfo object.
    
    Parameters:
    
    fileInfo - This object contains the enough image information to build a ModelImage with nothing inside (eg. blank image).
    
    image - Created blank image.
  - copyClippedVOIs
```
@Deprecated
public void copyClippedVOIs(ViewVOIVector copyList)
```
    Deprecated.
    
    Copies into the VOI clipboard.
    
    Parameters:
    
    voi - VOI
  - copyVOIs
```
public void copyVOIs(java.util.Vector<VOIBase> copyList)
```
  - buildAnonDirectoryDialog
```
public void buildAnonDirectoryDialog()
```
    Builds the anonymize directory dialog and displays it.
  - buildDICOMFrame
```
public ViewJFrameDICOMParser buildDICOMFrame()
```
    Builds the image tree dialog and displays it.
  - buildEditDICOMFrame
```
public void buildEditDICOMFrame()
```
    Builds the edit dicom tag interface.
  - buildDICOMDIRFrame
```
public JDialogDicomDir buildDICOMDIRFrame()
```
    Builds the image tree dialog and displays it.
  - buildMenu
```
public javax.swing.JMenuBar buildMenu()
```
    Builds menus for the User Interface.
  - buildMessageFrame
```
public ViewJFrameMessage buildMessageFrame()
```
    Builds the message frame where user/program data can be displayed.
  - buildPlugInsMenu
```
public javax.swing.JMenu buildPlugInsMenu(java.awt.event.ActionListener al)
```
    Called by either userInterface (this) or by another actionlistener (ViewJFrameImage) to build the plugins menu bar.
    
    Parameters:
    
    al - the listener that wants to know about actions on the plugins menu
    
    Returns:
    
    the new plugin menu
  - addPluginToMenu
```
private void addPluginToMenu(java.lang.Class<?> plugin,
                             java.lang.String pluginName,
                             java.lang.String name,
                             javax.swing.JMenu currentMenu,
                             java.awt.event.ActionListener al,
                             java.lang.String jarContainer)
```
  - deleteMenu
```
private void deleteMenu(javax.swing.JMenu menu)
```
    Recursive deletion algorithm to delete JMenus which contain no JMenuItems exclusive of JMenus in any children.
    
    Parameters:
    
    menu - The menu to run through deletion
  - loadMouseDrivers
```
private void loadMouseDrivers()
```
  - buildTreeDialog
```
public void buildTreeDialog()
```
    Builds the image tree dialog and displays it.
  - changeRecordingStatus
```
public void changeRecordingStatus(int recorderStatus)
```
    Alerts the listener to a change in whether the ScriptRecorder is currently recording a script..*
    
    Specified by:
    
    changeRecordingStatus in interface ScriptRecordingListener
    
    Parameters:
    
    recorderStatus - DOCUMENT ME!
  - clearAllDataText
```
public final void clearAllDataText()
```
    Accessor to clear all of data frame.
  - clearClippedVOIs
```
@Deprecated
public void clearClippedVOIs()
```
    Deprecated.
    
    DOCUMENT ME!
  - createBlankImage
```
public ModelImage createBlankImage(FileInfoBase fileInfo)
```
    Creates a blank Image based on the information found in the fileInfo object and places it in a frame.
    
    Parameters:
    
    fileInfo - This object contains the enough image information to build a ModelImage with nothing inside (eg. blank image).
  - createBlankImage
```
public ModelImage createBlankImage(FileInfoBase fileInfo,
                                   boolean doDisplay,
                                   boolean allowRecording)
```
    Creates a blank Image based on the information found in the fileInfo object.
    
    Parameters:
    
    fileInfo - This object contains the enough image information to build a ModelImage with nothing inside (eg. blank image).
    
    doDisplay -
    
    allowRecording -
  - enableOutputWindow
```
public void enableOutputWindow(boolean doShowFrame)
```
    Toggles the display of the Output window and updates all JFrameImages so that the menu checkbox will reflect the status of the output window.
    
    Parameters:
    
    doShowFrame - Whether the output window should be shown.
  - getActiveImageFrame
```
public ViewJFrameImage getActiveImageFrame()
```
    Accessor that returns the active image frame vector. If the top frame is not an image frame, then the frame vector is iterated until an image frame is found. If none is found then null is returned.
    
    Returns:
    
    The vector that has a list of frames visible in the GUI.
  - getAppTitle
```
public java.lang.String getAppTitle()
```
    Accessor to get the title of this application.
    
    Returns:
    
    The title of this application.
  - getClippedMatrix
```
public TransMatrix getClippedMatrix()
```
    Retrieves the clipped matrix for paste action.
    
    Returns:
    
    clippedMatrix
  - getClippedScannerVectors
```
@Deprecated
public java.util.Vector<java.util.Vector<WildMagic.LibFoundation.Mathematics.Vector3f>> getClippedScannerVectors()
```
    Deprecated.
    
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getClippedVOIs
```
@Deprecated
public ViewVOIVector getClippedVOIs()
```
    Deprecated.
    
    Returns the VOIs copied into the clip board. For copying and pasting VOIs between images.
    
    Returns:
    
    Vector
  - getCopyVOIs
```
public java.util.Vector<VOIBase> getCopyVOIs()
```
  - getCopyVOINames
```
public java.util.Vector<java.lang.String> getCopyVOINames()
```
  - getCmdLineArguments
```
public java.lang.String getCmdLineArguments()
```
    Returns the Command line arguments (as one string, each separated by a space) .@return command line arguments concatenated with spaces
    
    Returns:
    
    DOCUMENT ME!
  - getDefaultDirectory
```
public java.lang.String getDefaultDirectory()
```
    Accessor to get directory location of last file access.
    
    Returns:
    
    The last file directory
  - getDefaultScriptDirectory
```
public java.lang.String getDefaultScriptDirectory()
```
    Accessor to get directory location of script files.
    
    Returns:
    
    The script file directory
  - getDICOMCatcher
```
public DICOM_Receiver getDICOMCatcher()
```
    Accessor to get the DICOM receiver.
    
    Returns:
    
    the DICOM receiver
  - getDICOMQueryFrame
```
public ViewJFrameDICOMQuery getDICOMQueryFrame()
```
    Accessor to get the DICOM query frame.
    
    Returns:
    
    The DICOM query frame.
  - getFrameContainingImage
```
public ViewJFrameImage getFrameContainingImage(ModelImage image)
```
    Accessor that returns the active image frame vector. If the top frame is not an image frame, then the frame vector is iterated until an image frame is found. If none is found then null is returned.
    
    Parameters:
    
    image - the image to find the frame for.
    
    Returns:
    
    The vector that has a list of frames visible in the GUI.
  - getImageFrameVector
```
public java.util.Vector<java.awt.Frame> getImageFrameVector()
```
    Accessor that returns frame vector.
    
    Returns:
    
    The vector that has a list of frames visible in the GUI.
  - getJarClassLoader
```
public JarClassLoader getJarClassLoader()
```
  - getLastScript
```
public java.lang.String getLastScript()
```
    Returns the last script file used from the preferences.
    
    Returns:
    
    LastScript
  - getLastStackFlag
```
public boolean getLastStackFlag()
```
    Gets the last checkbox entry for "multi-file" for opening images.
    
    Returns:
    
    boolean
  - getMainFrame
```
public javax.swing.JFrame getMainFrame()
```
    Accessor that returns the main user interface frame.
    
    Returns:
    
    The main user interface frame.
  - getMenuBuilder
```
public ViewMenuBuilder getMenuBuilder()
```
    Returns the interface's menu builder.
  - getMessageFrame
```
public ViewJFrameMessage getMessageFrame()
```
    Accessor that returns the message frame.
    
    Returns:
    
    The message frame.
  - getMessageText
```
public java.lang.String getMessageText()
```
    Accessor to get text of message field.
  - getNewFrameLocation
```
public java.awt.Dimension getNewFrameLocation(int newImageXDim,
                                              int newImageYDim)
```
    Changes location of image when first displayed.
    
    Returns:
    
    The new location.
  - getNewFrameYLocation
```
public java.awt.Dimension getNewFrameYLocation()
```
    Changes vertical location of image when first displayed.
    
    Returns:
    
    The new location.
  - getProgressBarPrefix
```
public java.lang.String getProgressBarPrefix()
```
    Gets the string "Opening " or "Loading " based on what the progress bar should be displaying.
    
    Returns:
    
    String OPENING_STR or LOADING_STR
  - getProvenanceHolder
```
public ProvenanceHolder getProvenanceHolder()
```
    Accessor for the mipav's data provenance .@return mipav's data provenance holder
    
    Returns:
    
    DOCUMENT ME!
  - getRegisteredFramedImagesNum
```
public int getRegisteredFramedImagesNum()
```
    Return an num of images with frames(elements) from the image hashtable.
    
    Returns:
    
    images number
    
    See Also:
    
    CustomHashtable
  - getRegisteredImageByName
```
public ModelImage getRegisteredImageByName(java.lang.String name)
```
    Return a registered image from the image hashtable based on the name of the image. This works as long as the image was registered and the name is unique.
    
    Parameters:
    
    name - The name of the image to be retrieved.
    
    Returns:
    
    the ImageModel associated with this name.
    
    Throws:
    
    java.lang.IllegalArgumentException - if the name is not in the image hastable.
    
    See Also:
    
    CustomHashtable
  - getRegisteredImageNames
```
public java.util.Enumeration<java.lang.String> getRegisteredImageNames()
```
    Return an enumeration of keys (image names) from the image hashtable.
    
    Returns:
    
    An Enumeration containing the keys (image names).
    
    See Also:
    
    CustomHashtable
  - getRegisteredImages
```
public java.util.Enumeration<ModelImage> getRegisteredImages()
```
    Return an enumeration of images (elements) from the image hashtable.
    
    Returns:
    
    An Enumeration containing the elements (images).
    
    See Also:
    
    CustomHashtable
  - getRegisteredImagesNum
```
public int getRegisteredImagesNum()
```
    Return an num of images (elements) from the image hashtable.
    
    Returns:
    
    images number
    
    See Also:
    
    CustomHashtable
  - imageRegistryMonitoring
```
public void imageRegistryMonitoring()
```
    Display image registry frame.
  - imagesToFront
```
public void imagesToFront()
```
    Brings all images and message frame to the front.
  - initializeGui
```
public void initializeGui()
```
    Initializes the user interface. Starts by reading out some starting options out of the preferences file; setting up the main frame; building the message frame and setting the message frame into the preferences; building the menu; setting controls; initialising the DICOM dictionary; setting up the message field that is used in the main frame; setting the application titles; and showing the main frame.
    Recommendations for how to most easily perform modifications to the initialisation procedure are included with the individual method comments, although in most cases, it suffices to simply over-ride an individual method.
    
    See Also:
    
    initPrefsFile(), initUsingPreferences(), initSetMainFrameDefaults(java.awt.LayoutManager, boolean), buildMessageFrame(), buildMenu(), setControls(), initCreateMessageField(String), initSetTitles(String, String)
  - isAppFrameVisible
```
public boolean isAppFrameVisible()
```
    Accessor to check whether the application frame visible or not.
    
    Returns:
    
    isAppFrameVisible application frame visibility flag
  - isImageHashtableEmpty
```
public boolean isImageHashtableEmpty()
```
    Indicates if the image hashtable is empty.
    
    Returns:
    
    A boolean showing state of hashtable.
    
    See Also:
    
    CustomHashtable
  - isImageRegistered
```
public boolean isImageRegistered(java.lang.String imageName)
```
    Indicates if the image name is found in the hashtable.
    
    Parameters:
    
    imageName - the image name (key).
    
    Returns:
    
    A boolean indicating that image name.
    
    See Also:
    
    CustomHashtable
  - isPlugInFrameVisible
```
public boolean isPlugInFrameVisible()
```
    Accessor to see if a stand-alone plugin frame is visible (not app frame)
    
    Returns:
  - isShorcutRecording
```
public boolean isShorcutRecording()
```
    Determines if the UserInterface is currently recording an action command as a shortcut.
    
    Returns:
    
    boolean is it recording
  - setAppFrameVisible
```
public void setAppFrameVisible(boolean isVisible)
```
    Tells the application to show the MIPAV UI or suppress it (progress bars, image frames, etc).
    
    Parameters:
    
    isVisible - Set to false to hide the MIPAV UI.
  - setPlugInFrameVisible
```
public void setPlugInFrameVisible(boolean isVisible)
```
    Tells the UI that a standalone plugin frame is visible
    
    Parameters:
    
    isVisible - is the plugin frame visible
  - keyPressed
```
public void keyPressed(java.awt.event.KeyEvent e)
```
    Pass the key event to the selected image frame (if one exists). If not, check the shortcut table and attempt to handle it here.
    
    Specified by:
    
    keyPressed in interface java.awt.event.KeyListener
    
    Parameters:
    
    e - a key event generated by the user
  - keyReleased
```
public void keyReleased(java.awt.event.KeyEvent e)
```
    Pass the key event to the selected image frame (if one exists).
    
    Specified by:
    
    keyReleased in interface java.awt.event.KeyListener
    
    Parameters:
    
    e - a key event generated by the user
  - keyTyped
```
public void keyTyped(java.awt.event.KeyEvent e)
```
    Pass the key event to the selected image frame (if one exists).
    
    Specified by:
    
    keyTyped in interface java.awt.event.KeyListener
    
    Parameters:
    
    e - a key event generated by the user
  - memoryAllocation
```
public void memoryAllocation()
```
    Display memory allocation frame (request more from the JVM on next JVM-start).
  - memoryFrame
```
public void memoryFrame()
```
    Display memory usage frame.
  - closeAllImages
```
public void closeAllImages()
```
    this method closes all registered images
  - deleteItem
```
private void deleteItem(java.lang.String name,
                        boolean deleteFrame,
                        boolean runGC)
```
    Deletes the item specified by name. If false, only the model image is deleted
    
    Parameters:
    
    name - the object to delete
    
    deleteFrame - whether the frame should be deleted along with the image
    
    runGC - whether to run application-wide garbage collector once item is deleted
  - openJSONImageFrames
```
public void openJSONImageFrames()
```
  - openImageFrame
```
public void openImageFrame()
```
    This method opens an image and puts it into a frame.
  - openImageFrame
```
public void openImageFrame(java.lang.String imageFile)
```
    Open an image and put it into a new frame, given the image file name.
    
    Parameters:
    
    imageFile - the image file name with the path.
  - openImageFrame
```
public void openImageFrame(java.lang.String imageFileName,
                           java.lang.String imageFileDir)
```
    Open an image and put it into a new frame, given the image file name.
    
    Parameters:
    
    imageFileName - the file name, without the path
    
    imageFileDir - the directory where the file is
  - openImageFrame
```
public void openImageFrame(java.lang.String imageFile,
                           boolean multiFile)
```
    Open an image or images and put it into a new frame, given the image file name.
    
    Parameters:
    
    imageFile - the image file name with the path.
    
    multiFile - If true, the image is composed of image slices each in their own file.
  - openLastImage
```
public void openLastImage(int index)
```
    Attempts to open an image from the quicklist.
    
    Parameters:
    
    index - int index of image on quicklist
  - options
```
public void options()
```
    Display Options dialog for all mipav options (including image specific options) to allow user to adjust display in one place.
  - parseArguments
```
public int parseArguments(java.lang.String[] args,
                          int initArg)
```
    Required by the CommandLineParser interface. Processes MIPAV command line arguments that require MIPAV to have already been initialized. Returns the next argument to be processed (finished if returns args.length)
    
    Specified by:
    
    parseArguments in interface CommandLineParser
    
    Parameters:
    
    args - command arguments
    
    Returns:
    
    the location of the next command to be processed, if equal to args.length, then no further processing is necessary
  - regFrame
```
public void regFrame(java.awt.Frame frame)
```
    Method that registers an image frame by putting it in the image frame vector and does NOT loads controls.
    
    Parameters:
    
    frame - Frame to be registered with this the main UI.
  - registerFrame
```
public void registerFrame(java.awt.Frame frame)
```
    Method that registers an image frame by adding it to the vector and loads controls.
    
    Parameters:
    
    frame - Frame to be registered with this the main UI. The zero element frame is the active image. Any new image registered is made the active window.
  - setMenuActionListeners
```
private void setMenuActionListeners(java.awt.Component comp,
                                    java.awt.event.ActionListener frame)
```
  - registerImage
```
public java.lang.String registerImage(ModelImage image)
```
    Register image model by adding it to the image hashtable. Use the image name as the key. If the name is not unique then the CustomHashtable will attempt to make it unique. The image name will be reset with the new name. Classes calling this method need to check the returned key (image name) from this method.
    
    Parameters:
    
    image - Image to be registered.
    
    Returns:
    
    the String value of the key (image name)
    
    See Also:
    
    CustomHashtable
  - registerImage
```
public java.lang.String registerImage(java.lang.String key,
                                      ModelImage image)
```
    Register image model by adding it to the image hashtable. Use the String provided as the key. If the key is not unique then the CustomHashtable will attempt to make it unique. The actual key used will be returned.
    
    Parameters:
    
    key - the desired image key
    
    image - Image to be registered.
    
    Returns:
    
    the actual image key used (unique)
    
    See Also:
    
    CustomHashtable
  - removeAloneMenu
```
public boolean removeAloneMenu(javax.swing.JMenuBar menu)
```
    Removes the stand-alone menu from the user interface.
    
    Parameters:
    
    menu - the menu to be removed.
  - setActiveFrame
```
public void setActiveFrame(java.awt.Frame frame)
```
    Method sets the parameter frame to top and active.
    
    Parameters:
    
    frame - Frame to be set active (i.e. to the top of the list).
  - setClippedMatrix
```
public void setClippedMatrix(TransMatrix tMat)
```
    Sets the clipped matrix for copy/paste actions.
    
    Parameters:
    
    tMat - transmatrix for copy/paste
  - setControls
```
public void setControls()
```
    Sets the menu for the main frame.
  - setDataText
```
public final void setDataText(java.lang.String str)
```
    Accessor to set text of data FRAME.
    
    Parameters:
    
    str - String to be displayed in text panel.
  - setDefaultDirectory
```
public void setDefaultDirectory(java.lang.String defaultDirectory)
```
    Sets directory location of last file access.
    
    Parameters:
    
    defaultDirectory - Directory to set it to.
  - setDefaultScriptDirectory
```
public void setDefaultScriptDirectory(java.lang.String dir)
```
    Sets directory location of the script files.
    
    Parameters:
    
    dir - Directory to set the script directory to.
  - setDICOMCatcher
```
public void setDICOMCatcher(DICOM_Receiver rcv)
```
    Accessor to set the DICOM receiver.
    
    Parameters:
    
    rcv - the DICOM receiver
  - setDICOMQueryFrame
```
public void setDICOMQueryFrame(ViewJFrameDICOMQuery frame)
```
    Accessor to set the DICOM query frame.
    
    Parameters:
    
    frame - The DICOM query frame.
  - setExitCmdLineOnError
```
public void setExitCmdLineOnError(boolean doExit)
```
    Sets MIPAV to exit (true) or not (false) on an error when running from the command line
    
    Parameters:
    
    doExit -
  - doExitCmdLineOnError
```
public boolean doExitCmdLineOnError()
```
    Tells whether or not to exit on an error when running from the command line
    
    Returns:
    
    boolean whether to exit
  - doForceInPlace
```
public boolean doForceInPlace()
```
    Checks whether the dialog should force the algorithm to replace the image (no new frame)
    
    Returns:
    
    if only algorithm image replacement is allowed
  - setForceInPlace
```
public void setForceInPlace(boolean doForce)
```
    Sets the dialogs to only replace the image (no new frame)
    
    Parameters:
    
    doForce - do force the dialog to replace the image (in-place)
  - setGlobalDataText
```
public final void setGlobalDataText(java.lang.String str)
```
    Accessor to set text of global data FRAME.
    
    Parameters:
    
    str - String to be displayed in text panel.
  - setJarClassLoader
```
public void setJarClassLoader(JarClassLoader jarClassLoader)
```
  - setLastScript
```
public void setLastScript(java.lang.String script)
```
    Sets last used script files in preferences.
    
    Parameters:
    
    script - Script to set the LastScript to.
  - setLastStackFlag
```
public void setLastStackFlag(boolean lastStackFlag)
```
    Sets the last value for opened multi-files (or single).
    
    Parameters:
    
    lastStackFlag - boolean
  - setLoad
```
public void setLoad(boolean doLoad)
```
    Tells the progress bar to say "Loading" rather than "Opening" for images being loaded if true.
    
    Parameters:
    
    doLoad - boolean do set progress bar to load
  - setMessageText
```
public void setMessageText(java.lang.String str)
```
    Accessor to set text of message field.
    
    Parameters:
    
    str - String to be displayed in text field.
  - setShortcutRecording
```
public void setShortcutRecording(boolean doRecord)
```
    Sets the UI to either be/not be recording action command.
    
    Parameters:
    
    doRecord - boolean true = is recording, false = not
  - setTitle
```
public void setTitle(java.lang.String str)
```
    Gets the application title from the preference file and prepends to the string passed into the method and displays the resultant string in the title of the main frame.
    
    Parameters:
    
    str - the application title
  - setUseVOIName
```
public void setUseVOIName(boolean useName)
```
    Sets the Preference to use VOI Names instead of labels, then updates all frames to reflect this change with their VOIs.
    
    Parameters:
    
    useName - boolean show name instead of label
  - setVisible
```
public void setVisible(boolean visible)
```
    Change whether the GUI should be visible. The order is strage because we want the main frame to be first on the taskbar, but also focused when the windows show up.
    
    Parameters:
    
    visible - whether the message and main frames should be shown on the screen
  - showLicense
```
public void showLicense()
```
    Displays the MIPAV Software Transfer Agreement in a JDialogText window.
    The "license.html" file is read (using the GetPath class) and displayed as HTML with a JDialogText. If the file is not found, or there is a problem opening it, a notation is made in the Preferences.debug window and is otherwise ignored. A warning box is displayed when the license dialog cannot be created (and throws a NullPointerException). Finally, the main frame does not record this item in its list of windows, so many instances of this window may be made.
  - showLicense
```
public void showLicense(java.lang.String title,
                        java.lang.String filename)
```
    Displays the MIPAV Software Transfer Agreement in a JDialogText window.
    The "license.html" file is read (using the GetPath class) and displayed as HTML with a JDialogText. If the file is not found, or there is a problem opening it, a notation is made in the Preferences.debug window and is otherwise ignored. A warning box is displayed when the license dialog cannot be created (and throws a NullPointerException). Finally, the main frame does not record this item in its list of windows, so many instances of this window may be made.
    
    Parameters:
    
    title - The title of the frame
    
    filename - the name of the license file.
  - showShortcutEditor
```
public void showShortcutEditor(boolean doUpdate)
```
    Opens a dialog for viewing/modifying shortcuts.
    
    Parameters:
    
    doUpdate - whether to update the shortcut table
  - showSplashGraphics
```
public void showSplashGraphics()
```
    Shows the MIPAV splash screen for a few seconds, or until the user clicks it.
  - unregisterFrame
```
public void unregisterFrame(java.awt.Frame frame)
```
    Method that unregisters an image frame by removing it from the image frame vector.
    
    Parameters:
    
    frame - Frame to be unregistered with this the main UI.
  - unregisterFrame
```
public void unregisterFrame(java.awt.Frame frame,
                            boolean closeAll)
```
    Method that unregisters an image frame by removing it from the image frame vector.
    
    Parameters:
    
    frame - Frame to be unregistered with this the main UI.
  - unRegisterImage
```
public void unRegisterImage(ModelImage image)
```
    Unregister image model by removing it from the image hashtable. Assume that the imageName is the key to the image. Display an error if the image key is not found.
    
    Parameters:
    
    image - Image to be unregistered.
    
    Throws:
    
    java.lang.IllegalArgumentException - if image is null
  - unRegisterImage
```
public void unRegisterImage(java.lang.String imageKey)
```
    Unregister image model by removing it from the image hashtable given the key to the hashtable. Display an error if the image key is not found.
    
    Parameters:
    
    imageKey - The key to the image to be unregistered (a string).
    
    Throws:
    
    java.lang.IllegalArgumentException - if imageKey is null
  - updateMemoryUsage
```
public void updateMemoryUsage()
```
    This method is a callback method. The purpose is to update the memory usage readout every one second. A separate thread calls this method every one second.
  - updateMultiCoreUsage
```
public void updateMultiCoreUsage()
```
    This method updates the "whether multi-core should be used" button when the relevant button has been pushed in either the preferences pane.
  - updateGpuUsage
```
public void updateGpuUsage()
```
    This method updates the "whether algorithms will use the GPU" when the relevant button has been pushed in either the preferences pane.
  - updateScript
```
public void updateScript(java.lang.String newScriptText)
```
    Do nothing - required by ScriptRecordingListener interface.
    
    Specified by:
    
    updateScript in interface ScriptRecordingListener
    
    Parameters:
    
    newScriptText - Ignored.
  - windowActivated
```
public void windowActivated(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowActivated in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event.
  - windowClosed
```
public void windowClosed(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowClosed in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event.
  - windowClosing
```
public void windowClosing(java.awt.event.WindowEvent event)
```
    Confirms if the user really wants to exit, then closes the application.
    
    Specified by:
    
    windowClosing in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - Event that triggered this function.
  - cleanupAndExit
```
public void cleanupAndExit()
```
  - windowDeactivated
```
public void windowDeactivated(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowDeactivated in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event.
  - windowDeiconified
```
public void windowDeiconified(java.awt.event.WindowEvent event)
```
    Deiconify only the other frames who's last state was normal (ie- restore other frames to their lastState).
    
    Specified by:
    
    windowDeiconified in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the deiconify window event.
  - windowIconified
```
public void windowIconified(java.awt.event.WindowEvent event)
```
    Iconify all other frames associateed with MIPAV.
    
    Specified by:
    
    windowIconified in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the iconify window event.
  - windowOpened
```
public void windowOpened(java.awt.event.WindowEvent event)
```
    Do nothing.
    
    Specified by:
    
    windowOpened in interface java.awt.event.WindowListener
    
    Parameters:
    
    event - the window event.
  - writeDataProvenance
```
public void writeDataProvenance()
```
    Writes Mipav's data provenance to the default location.
    .
  - initCreateMemoryUsagePanel
```
protected javax.swing.JPanel initCreateMemoryUsagePanel()
```
    Construct the panel which displays the current memory usage/limit and a garbage collection button.
    
    Returns:
    
    the memory usage panel
  - initCreateMultiCoreGpuIndicatorPanel
```
protected javax.swing.JPanel initCreateMultiCoreGpuIndicatorPanel()
```
    Construct the panel which displays whether the CPU and GPU could be utilized by algorithms based on the preferences settings by the user.
    
    Returns:
    
    the memory usage panel
  - initCreateMessageBar
```
protected void initCreateMessageBar()
```
    Create the panel containing components which show the application title initially, and will later be used to show image coordinates and intensities.
  - initCreateMessageField
```
protected javax.swing.JTextField initCreateMessageField(java.lang.String title)
```
    Creates the message field for the main frame using the title given. For other applications, extend this method to call the super method with the appropriate title.
    
    Parameters:
    
    title - the string use in the newly-created message field.
    
    Returns:
    
    the message field (displays coordinate info when an image is opened)
  - initDicomReceiver
```
protected void initDicomReceiver()
```
    Starts the DICOM receiver if the flag in the preference file is true.
  - initMacintoshJDKversionCheck
```
protected void initMacintoshJDKversionCheck()
```
    Method checks to verify that when running on a Machintosh, the JDK version is at least 1�x2e;4. It sets the start up file "Info.plist" to use java1.4 if it can. The check for these routines is System.getProperty("os.name").indexOf("Mac"), and we simply return doing nothing if the property for os.name is something different. If the os.name does not contain "Mac", and the Info.plist file is found,
    "Info.plist" file to hold its startup arguments, so we need that file anyway. All exceptions caught here are not propogated.
  - initPrefsFile
```
protected void initPrefsFile()
```
    Set the preferences file to use (Preferences defaults to mipav.preferences).
  - initPrefsTrim
```
protected void initPrefsTrim()
```
    Gets the TRIM_VOI, TRIM_MASK and TRIM_FLAG values from the preferences file, and if it cannot find them, it sets to some default value: TRIM_VOI will be 0.3, TRIM_MASK will be 0.0, and TRIM_FLAG will be true.
    Over-ride this method if these defaults are unnacceptable.
  - initSetMainFrameDefaults
```
protected void initSetMainFrameDefaults(java.awt.LayoutManager prefLayout,
                                        boolean resize)
```
    Sets the layout of the Main Frame with the given, preferred layout manager; makes the main frame resizable as given; makes this class a window-listener; sets the default operation to do nothing on close; and the icon is set. The image icon is set by the preferences.
    Over-riding classes can alter the preferred layout most easily by over-riding this method, but calling this method with a different layout and desired size-setting. To change the default close-operation with an over-riding class, call this super method, then set the default close operation, rather than creating a custom re-implemention of this method.
    
    Parameters:
    
    prefLayout - A layout manager to handle the main frame.
    
    resize - Whether to allow resizing of the main frame.
    
    See Also:
    
    JFrame.setDefaultCloseOperation(int), Preferences.getIconName()
  - initSetTitles
```
protected void initSetTitles(java.lang.String mainFrameTitle,
                             java.lang.String appTitle)
```
    Sets the titles for for the main frame and the application using the strings given. For other applications, extend this method to call the super method with the appropriate title.
    
    Parameters:
    
    mainFrameTitle - The string to use as the title for the main frame.
    
    appTitle - The string to put in the main frame's bottom status field.
  - initUsingPreferences
```
protected void initUsingPreferences()
```
    Performs a variety of start-up operations based on user-preferences; First, it tries to read from the preferences file; if it cannot, it sets the user directory. It then follows from the preferences file:
    
    splash screen
    
    checks the VM heap size max
    
    sets the default directory
    
    debug output
    
    sets the TRIM
    
    Over-riding classes should not over-ride this method unless one of these intermediate operations is not desired or more operations are needed. To modify the defaults used in creating a preferences file, over-ride one of the called methods.
    See Also:
    
    setDefaultDirectory(String), showSplashGraphics(), checkHeapMaxAgainstPreferences(), Preferences.print(), initPrefsTrim()
  - runCmdLine
```
protected void runCmdLine(java.lang.String scriptFile,
                          java.util.Vector<ViewUserInterface.OpenFileInfo> imageList,
                          java.util.Vector<java.util.Vector<java.lang.String>> voiList)
```
    This method is used when running MIPAV from the command line.
    
    Parameters:
    
    scriptFile - The script to run.
    
    imageList - A list of OpenImageFile objects to use in the script.
    
    voiList - A list of VOIs to put into the various images.
    
    See Also:
    
    printUsageAndExit()
  - checkHeapMaxAgainstPreferences
```
private void checkHeapMaxAgainstPreferences()
```
    Test for VM memory sizes being the same as last run in preferences: displays a user-warning that the preferences & VM config files disagree and presents the JDialogMemoryAllocation dialog with "use preference" buttons to quicken the matching process.
    Note, this method does not throw any NullPointerExceptions.
  - printUsageAndExit
```
public static void printUsageAndExit()
```
    Displays command line help information on usage of all commands and then exits.
  - printUsageAndExit
```
public static void printUsageAndExit(Argument c)
```
    Displays command line help information on usage to standard out and then into an informational dialog box then exits the MIPAV application. Help display just shows the different options, display help, load image, load script, load VOI, and hide menu bar, as well as examples of use.
  - generateCmdUsageInfo
```
public static java.lang.String generateCmdUsageInfo()
```
    Generates automatic list of available commands.
  - isProvidedOutputDir
```
public static boolean isProvidedOutputDir()
```
    This is the getter for providedOutputDir providedOutputDir: This boolean tells if the user has provided an ouputDir parameter as a command line argument when running a script
    
    Returns:
  - isProvidedUserDefaultDir
```
public static boolean isProvidedUserDefaultDir()
```
  - getDiscoverableActionList
```
public static java.util.Vector<java.lang.Class<ActionDiscovery>> getDiscoverableActionList()
```
  - getDiscoverableActionList
```
public static java.util.Vector<java.lang.Class<ActionDiscovery>> getDiscoverableActionList(java.lang.String baseDir)
```
  - getExceptions
```
public static java.io.File getExceptions()
```
    Returns:
    
    the exceptions
  - getOutputDir
```
public static java.lang.String getOutputDir()
```
  - getSecondaryPluginsDir
```
public static java.io.File getSecondaryPluginsDir()
```
  - getUserDefaultDir
```
public static java.lang.String getUserDefaultDir()
```
  - setProvidedOutputDir
```
public static void setProvidedOutputDir(boolean providedOutputDir)
```
  - setProvidedUserDefaultDir
```
public static void setProvidedUserDefaultDir(boolean providedUserDefaultDir)
```
  - setOutputDir
```
public static void setOutputDir(java.lang.String outputDir)
```
  - setSecondaryPluginsDir
```
public static void setSecondaryPluginsDir(java.io.File secondaryPluginsDir)
```
  - setUserDefaultDir
```
public static void setUserDefaultDir(java.lang.String userDefaultDir)
```
  - parseStaticArguments
```
public static int parseStaticArguments(java.lang.String[] args,
                                       int initArg)
```
    Required by the CommandLineParser interface. Processes MIPAV command line arguments that DO NOT require MIPAV to have already been initialized. In cases like the plugins directory, it is specifically required that MIPAV has not been initialized yet. Returns the next argument to be processed (finished if returns args.length)
  - checkPrefDirCommand
```
public static void checkPrefDirCommand(java.lang.String[] args,
                                       int initArg)
```
    If the preferences name command is about to be performed before an existing preferences directory command, this guarantees that the directory command will be executed first.
  - addToTempDirList
```
public static void addToTempDirList(java.lang.String path)
```

Modifier	Constructor	Description
`protected`	`ViewUserInterface()`	Constructs main UI frame.
`protected`	`ViewUserInterface(boolean forceQuiet)`	Constructs main UI frame.

Class ViewUserInterface

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

userInterfaceReference

OPENING_STR

LOADING_STR

shortcutEd

providedUserDefaultDir

userDefaultDir

providedOutputDir

outputDir

mainFrame

menuBuilder

messageField

messageFrame

openingMenuBar

clippedMatrix

clippedScannerVectors

clippedVOIs

copyVOIList

copyVOINameList

jarClassLoader

cmdLineArguments

DICOMcatcher

DICOMQueryFrame

frameLocation

imageFrameVector

imageHashtable

imgMonitorFrame

isAppFrameVisible

isPlugInFrameVisible

lastStackFlag

mallocFrame

memoryFrame

dpDialog

memoryUsageLabel

btnMultiCore

btnGpuComp

memoryUsageUpdater

optionsDialog

pluginsMenu

aloneMenu

progressBarPrefix

shortcutRecording

systemDPHolder

forceAlgorithmInPlace

exitCmdLineOnError

numTileSheets

exceptions

tempDirList

Constructor Detail

ViewUserInterface

ViewUserInterface

Method Detail

create

getReference

about

about

aboutDataProvenance

aboutJava

addAloneMenu

actionPerformed

createEmptyImage

copyClippedVOIs

copyVOIs

buildAnonDirectoryDialog

buildDICOMFrame

buildEditDICOMFrame

buildDICOMDIRFrame

buildMenu

buildMessageFrame

buildPlugInsMenu

addPluginToMenu

deleteMenu

loadMouseDrivers

buildTreeDialog