Field Detail

• serialVersionUID

  private static final long serialVersionUID

  Use serialVersionUID for interoperability.

  See Also:

  Constant Field Values

• IMAGE_A

  public static final int IMAGE_A

  Display mode image A.

  See Also:

  Constant Field Values

• IMAGE_B

  public static final int IMAGE_B

  Display mode image B.

  See Also:

  Constant Field Values

• IMAGE_A_B

  public static final int IMAGE_A_B

  Display mode image A and B.

  See Also:

  Constant Field Values

• zoomMode

  protected int zoomMode

  DOCUMENT ME!

• absoluteLabel

  protected javax.swing.JLabel absoluteLabel

  Labels for the current absolute position:.

• absoluteLabelVals

  protected javax.swing.JLabel[] absoluteLabelVals

  Labels for the current absolute position values:.

• absolutePanel

  protected javax.swing.JPanel absolutePanel

  JPanel containing the absoulte position labels:.

• alphaBlend

  protected float alphaBlend

  Indicates the amount of blending when two images are loaded in the image frame.

• displayMode

  protected int displayMode

  Indicates which image is to be acted upon when two images are displayed.

• imageA

  protected ModelImage imageA

  Reference to the image A of this frame.

• imageB

  protected ModelImage imageB

  Reference to the image B of this frame.

• linkFrame

  protected ViewJFrameImage linkFrame

  Holds a reference (link) to another frame so that it be updated with this frame.

• linkTriFrame

  protected ViewJFrameTriImage linkTriFrame

  Holds a reference (link) to another frame so that it can be updated with this frame.

• defaultLUTa

  protected ModelLUT defaultLUTa

  Reference to LUT for image A and to the default LUT for image A.

• LUTa

  protected ModelLUT LUTa

  Reference to LUT for image A and to the default LUT for image A.

• defaultLUTb

  protected ModelLUT defaultLUTb

  Reference to LUT for image B and to the default LUT for image B.

• LUTb

  protected ModelLUT LUTb

  Reference to LUT for image B and to the default LUT for image B.

• progressBar

  protected ViewJProgressBar progressBar

  Reference to progress bar.

• scannerLPSLabel

  protected javax.swing.JLabel scannerLPSLabel

  Labels for the current scanner position:.

• scannerRASLabel

  protected javax.swing.JLabel scannerRASLabel

  Labels for the current scanner position:.

• scannerLPSLabelVals

  protected javax.swing.JLabel[] scannerLPSLabelVals

  Labels for the current scanner position values:.

• scannerRASLabelVals

  protected javax.swing.JLabel[] scannerRASLabelVals

  Labels for the current scanner position values:.

• scannerLPSPanel

  protected javax.swing.JPanel scannerLPSPanel

  JPanel containing the scanner position labels:.

• scannerRASPanel

  protected javax.swing.JPanel scannerRASPanel

  JPanel containing the scanner position labels:.

• tabbedPane

  protected javax.swing.JTabbedPane tabbedPane

  The main tabbed pane in the volume view frame.

• scannerTabbedPane

  protected javax.swing.JTabbedPane scannerTabbedPane

  The tabbed pane to hold teh LPS, RAS and absolution coordinate panels.

• userInterface

  protected ViewUserInterface userInterface

  Reference to the user interface.

• isClosing

  protected boolean isClosing

  Whether the frame's close() method is being called.

• blue

  private int blue

  Blue channel value of the paint color.

• enableCloseImageB

  private boolean enableCloseImageB

  Tells whether the ViewMenuBuilder should allow Close Image(B) after loading image B.

• newFrameCreated

  private boolean newFrameCreated

• green

  private int green

  Green channel value of the paint color.

• lastState

  private int lastState

  Save if last state was iconified or normal.

• opacity

  private float opacity

  Opacity value of the paint color.

• paintBitmap

  private java.util.BitSet paintBitmap

  Reference to the BitSet map used in painting the image.

• red

  private int red

  Red channel value of the paint color.

• voiSavedFileName

  private java.lang.String voiSavedFileName

  DOCUMENT ME!

• linkedScrolling

  protected boolean linkedScrolling

  Variable indicating if images of like dimensions should be scrolled simult.

• absoluteXLabel

  protected javax.swing.JLabel absoluteXLabel

  voxel absolute goto components*

• absoluteYLabel

  protected javax.swing.JLabel absoluteYLabel

  voxel absolute goto components*

• absoluteZLabel

  protected javax.swing.JLabel absoluteZLabel

  voxel absolute goto components*

• absoluteXTextField

  protected javax.swing.JTextField absoluteXTextField

• absoluteYTextField

  protected javax.swing.JTextField absoluteYTextField

• absoluteZTextField

  protected javax.swing.JTextField absoluteZTextField

• absoluteGoToButton

  protected javax.swing.JButton absoluteGoToButton

• absoluteGoToPanel

  protected javax.swing.JPanel absoluteGoToPanel

• scannerLPS_RLLabel

  protected javax.swing.JLabel scannerLPS_RLLabel

  scanner lps goto components*

• scannerLPS_APLabel

  protected javax.swing.JLabel scannerLPS_APLabel

  scanner lps goto components*

• scannerLPS_ISLabel

  protected javax.swing.JLabel scannerLPS_ISLabel

  scanner lps goto components*

• scannerLPS_RLTextField

  protected javax.swing.JTextField scannerLPS_RLTextField

• scannerLPS_APTextField

  protected javax.swing.JTextField scannerLPS_APTextField

• scannerLPS_ISTextField

  protected javax.swing.JTextField scannerLPS_ISTextField

• scannerLPS_GoToButton

  protected javax.swing.JButton scannerLPS_GoToButton

• scannerLPS_GoToPanel

  protected javax.swing.JPanel scannerLPS_GoToPanel

• scannerRAS_RLLabel

  protected javax.swing.JLabel scannerRAS_RLLabel

  scanner ras goto components*

• scannerRAS_APLabel

  protected javax.swing.JLabel scannerRAS_APLabel

  scanner ras goto components*

• scannerRAS_ISLabel

  protected javax.swing.JLabel scannerRAS_ISLabel

  scanner ras goto components*

• scannerRAS_RLTextField

  protected javax.swing.JTextField scannerRAS_RLTextField

• scannerRAS_APTextField

  protected javax.swing.JTextField scannerRAS_APTextField

• scannerRAS_ISTextField

  protected javax.swing.JTextField scannerRAS_ISTextField

• scannerRAS_GoToButton

  protected javax.swing.JButton scannerRAS_GoToButton

• scannerRAS_GoToPanel

  protected javax.swing.JPanel scannerRAS_GoToPanel

• talXLabel

  protected javax.swing.JLabel talXLabel

  talairach goto components*

• talYLabel

  protected javax.swing.JLabel talYLabel

  talairach goto components*

• talZLabel

  protected javax.swing.JLabel talZLabel

  talairach goto components*

• talXTextField

  protected javax.swing.JTextField talXTextField

• talYTextField

  protected javax.swing.JTextField talYTextField

• talZTextField

  protected javax.swing.JTextField talZTextField

• talGoToButton

  protected javax.swing.JButton talGoToButton

• talGoToPanel

  protected javax.swing.JPanel talGoToPanel

Constructor Detail

• ViewJFrameBase

  public ViewJFrameBase​(ModelImage _imageA,
                        ModelImage _imageB)

  Makes an image frame.

  Parameters:

  _imageA - model image A

  _imageB - model image B

Method Detail

• actionPerformed

  public abstract void actionPerformed​(java.awt.event.ActionEvent event)

  Method to handle action events generated by the main UI when the current frame is selected. Implemented by specific frame classes.

  Specified by:

  actionPerformed in interface java.awt.event.ActionListener

  Parameters:

  event - the event from the UI

• getControls

  public abstract ViewControlsImage getControls()

  Gets the control widgets for the frame.

  Returns:

  the frame's image controls

• getImageA

  public abstract ModelImage getImageA()

  Accessor that returns the imageA.

  Returns:

  imageA

• getImageB

  public abstract ModelImage getImageB()

  Accessor that returns the imageB.

  Returns:

  imageB

• removeControls

  public abstract void removeControls()

  Removes the menu and controls of the main frame so that a new frame can load the main frame with the proper controls. Abstract and must be extended.

• setActiveImage

  public abstract void setActiveImage​(int active)

  Sets the active image (image that should be processed for drawing VOIs and applying algorithms.

  Parameters:

  active - IMAGE_A or IMAGE_B

• setAlphaBlend

  public abstract void setAlphaBlend​(int value)

  Sets the alpha blending parameter for two image display.

  Parameters:

  value - amount [0,100] that is the percentage of Image A to be displayed and (1-percentage) of Image B to be displayed

• setControls

  public abstract void setControls()

  Sets the menu and controls (i.e. toolbars) of the main frame! This puts only the menus and controls needed to controls the operations of this frame. Different image frames have different menu and controls.

• setEnabled

  public abstract void setEnabled​(boolean flag)

  Controls whether or not the images/VOIs of the frame can be modified.

  Overrides:

  setEnabled in class java.awt.Component

  Parameters:

  flag - if true the image/VOIs can be modified; if false image/VOIs can NOT be modified

• setImageB

  public abstract void setImageB​(ModelImage imageB)

  Accessor that sets the imageB.

  Parameters:

  imageB - The image to make image-B in this frame.

• setPaintBitmapSwitch

  public abstract void setPaintBitmapSwitch​(boolean flag)

  If true do not getMask on a setActiveImage command so as to keep the mask from the old active image.

  Parameters:

  flag - if true do not getMask on a setActiveImage command

• setRGBTA

  public abstract void setRGBTA​(ModelRGB RGBT)

  Set the RGB table for image A.

  Parameters:

  RGBT - the RGB table to use for image A

• setRGBTB

  public abstract void setRGBTB​(ModelRGB RGBT)

  Set the RGB table for image B.

  Parameters:

  RGBT - the RGB table to use for image B

• setTitle

  public abstract void setTitle()

  Sets the Title bar of the frame.

• updateImageExtents

  public abstract boolean updateImageExtents()

  The extents on this image have changed, so the extents need to be read in again and menus, panes and slide bars adjusted accordingly.

  Specified by:

  updateImageExtents in interface ViewImageUpdateInterface

  Returns:

  true if the update was successful, false otherwise

  See Also:

  ViewImageUpdateInterface

• about

  public void about​(int zSlice,
                    int tSlice)

  Makes an aboutDialog box that displays information about the image slice.

  Parameters:

  zSlice - index to slice in z-Plane about the specific image slice

  tSlice - index to slice in time about the specific image slice

• buildLabelPanel

  public void buildLabelPanel()

  The label panel of the x, y, z slider position.

• canCloseImageBAfterLoad

  public boolean canCloseImageBAfterLoad()

  Returns whether or not the close image B option should appear after loading.

  Returns:

  whether the "Close image B" option should appear after image B is loaded

• newFrameBeenCreated

  public boolean newFrameBeenCreated()

• close

  public void close()

  Closes both image A and image B (if it exists). It ensures the images are un-registered from the main-frame then removes any display listeners.

• close

  public void close​(boolean closeAll)

  Closes both image A and image B (if it exists). It ensures the images are un-registered from the main-frame then removes any display listeners.

• closeImageB

  public void closeImageB()

  Removes image B from the frame and resets image A to be the active frame for all image controls. Ensures the image is removed, disconnected from the frame and un-registered. Also informs the garbage-collector to release any held memory.

• componentHidden

  public void componentHidden​(java.awt.event.ComponentEvent event)

  Does nothing.

  Specified by:

  componentHidden in interface java.awt.event.ComponentListener

  Parameters:

  event - the component event

• componentMoved

  public void componentMoved​(java.awt.event.ComponentEvent event)

  Does nothing.

  Specified by:

  componentMoved in interface java.awt.event.ComponentListener

  Parameters:

  event - the component event

• componentResized

  public void componentResized​(java.awt.event.ComponentEvent event)

  Does nothing.

  Specified by:

  componentResized in interface java.awt.event.ComponentListener

  Parameters:

  event - the component event

• componentShown

  public void componentShown​(java.awt.event.ComponentEvent event)

  Does nothing.

  Specified by:

  componentShown in interface java.awt.event.ComponentListener

  Parameters:

  event - the component event

• getAlphaBlend

  public float getAlphaBlend()

  Returns a default alphaBlend value for blending of two images.

  Returns:

  a default alphaBlend value

• getDisplayMode

  public int getDisplayMode()

  Accessor that returns displayMode.

  Returns:

  displayMode

• getImageNameA

  public java.lang.String getImageNameA()

  Accessor that returns the title of image A.

  Returns:

  frame title for Image A

• getImageNameB

  public java.lang.String getImageNameB()

  Accessor that returns the title of image B.

  Returns:

  frame title for Image B

• getLastState

  public int getLastState()

  getLastState.

  Returns:

  lastState Should be either Frame.NORMAL or Frame.ICONIFIED

• getLUTa

  public ModelLUT getLUTa()

  Accessor that returns LUTa.

  Returns:

  LUTa

• getLUTb

  public ModelLUT getLUTb()

  Accessor that returns LUTb.

  Returns:

  LUTb

• getDefaultLUTa

  public ModelLUT getDefaultLUTa()

  Accessor that returns the default LUTa for the frame.

  Returns:

  defaultLUTa

• getDefaultLUTb

  public ModelLUT getDefaultLUTb()

  Accessor that returns the default LUTb for the frame.

  Returns:

  defaultLUTb

• getRGBTA

  public ModelRGB getRGBTA()

  Get the RGB table for image A.

  Returns:

  null (may be overridden by inheriting classes)

• getRGBTB

  public ModelRGB getRGBTB()

  Get the RGB table for image B.

  Returns:

  null (may be overridden by inheriting classes)

• getTriImg

  public ViewJFrameTriImage getTriImg()

  Get the ViewJFrameTriImage reference.

  Returns:

  linkTriFrame ViewJFrameTriImage.

• getUserInterface

  public ViewUserInterface getUserInterface()

  Accessor that returns the user interface.

  Returns:

  the user interface

• loadAllVOIs

  public void loadAllVOIs​(boolean quietMode)

  This method loads all VOIs to the active image from the default VOI directory for that image.

  Parameters:

  quietMode - if true indicates that warnings should not be displayed.

• loadAllVOIsFrom

  public void loadAllVOIsFrom​(java.lang.String voiDir,
                              boolean quietMode)

  This method loads all VOIs to the active image from a given directory.

  Parameters:

  voiDir - the directory to load voi's from

  quietMode - if true indicates that warnings should not be displayed.

• loadImage

  public boolean loadImage​(java.lang.Object obj,
                           ViewJComponentEditImage compImage,
                           boolean stackFlag,
                           boolean doOrigins,
                           boolean doOrients,
                           double defaultValue,
                           double defaultRed,
                           double defaultGreen,
                           double defaultBlue,
                           boolean isQuiet)

  Loads an image into imageB slot of frame. Matches the imageB resolutions and dimensions to imageA, and can optionally match the images' origins and orientations.

  Parameters:

  obj - an object which is either a ModelImage to be loaded into the modelimage (as say, imageB, imported from another frame) or a File to be read in via FileIO.readImage(...)

  compImage - image component where image is set so that it can be displayed.

  stackFlag - flag indicating multi file

  doOrigins - when calling MatchImages to match resolutions and dimensions, should origins be matched too?

  doOrients - when calling MatchImages to match resolutions and dimensions, should orientations be matched too?

  Returns:

  true if the load was successful, false otherwise

  See Also:

  JDialogLoadImage

• matchImages

  private void matchImages​(ModelImage imageA,
                           ModelImage imageB,
                           boolean doOrigins,
                           boolean doOrients,
                           double defaultValue,
                           double defaultRed,
                           double defaultGreen,
                           double defaultBlue)

• loadLUT

  public void loadLUT​(boolean loadAll,
                      boolean quietMode)

  This method loads the LUT for the active image. If the image is not a color image then both the functions and the LUT data are loaded. If this is a color image, then only the functions are loaded.

  Parameters:

  loadAll - boolean indicating that both lut and transfer functions should be loaded. If false, then only transfer functions are loaded.

  quietMode - if true indicates that warnings should not be displayed.

• loadLUTandTransferFunctionFrom

  public void loadLUTandTransferFunctionFrom​(boolean loadAll,
                                             java.lang.String filename,
                                             java.lang.String dirName,
                                             boolean quietMode)

  This method loads the LUT for the active image. If the image is not a color image then both the functions and the LUT data are loaded. If this is a color image, then only the functions are loaded.

  Parameters:

  loadAll - boolean indicating that both lut and transfer functions should be loaded. If false, then only transfer functions are loaded.

  filename - filename to save LUT as

  dirName - directory to save LUT to

  quietMode - if true indicates that warnings should not be displayed.

• loadLUTandTransferFunctionFrom

  public static void loadLUTandTransferFunctionFrom​(ModelImage image,
                                                    ModelStorageBase lut,
                                                    boolean loadAll,
                                                    java.lang.String filename,
                                                    java.lang.String dirName,
                                                    boolean quietMode)

  Reads the input LUT (ModelLUT or ModelRGB) from file.

  Parameters:

  image -

  lut -

  loadAll -

  filename -

  dirName -

  quietMode -

• openVOI

  public boolean openVOI​(boolean quietMode,
                         boolean doLabels)

  This method opens an existing VOI.

  Parameters:

  quietMode - if true indicates that warnings should not be displayed.

  doLabels - DOCUMENT ME!

  Returns:

  whether a VOI was successfully opened (ie - the dialog wasn't cancelled)

• openVOI

  public VOI[] openVOI​(ModelImage image,
                       boolean quietMode)

  This method opens an existing VOI.

  Parameters:

  image - image where VOI(s) are to registered

  quietMode - if true indicates that warnings should not be displayed.

  Returns:

  the VOI(s)

• pickImageFile

  public java.io.File pickImageFile()

  Brings up a FileChooser to pick a file.

  Returns:

  File the File the chooser picks.

• save

  public void save​(FileWriteOptions options,
                   int filterType)

  Creates save dialog so that the image can be saved // This should be moved to imageModel.save();

  Parameters:

  options - File-write options.

  filterType - only used if >= 0

• save

  public void save​(ModelImage img,
                   FileWriteOptions options,
                   int filterType)

  Creates save dialog so that the image can be saved // This should be moved to imageModel.save();

  Parameters:

  img - DOCUMENT ME!

  options - DOCUMENT ME!

  filterType - only used if value >= 0

• save

  public void save​(ModelImage img,
                   FileWriteOptions options,
                   int filterType,
                   boolean operateQuiet)

  Creates save dialog so that the image can be saved // This should be moved to imageModel.save();

  Parameters:

  img - DOCUMENT ME!

  options - DOCUMENT ME!

  filterType - only used if value >= 0

  operateQuiet - informs the FileIO to not notify user of errors or interrogate for more information.

• saveAllVOIs

  public void saveAllVOIs()

  This method saves all VOIs for the active image to the default VOI directory for that image.

• saveAllVOIsTo

  public void saveAllVOIsTo​(java.lang.String voiDir)

  This method saves all VOIs for the active image to a given directory.

  Parameters:

  voiDir - directory that contains VOIs for this image.

• saveLabels

  public void saveLabels​(boolean saveAll)

  DOCUMENT ME!

  Parameters:

  saveAll - DOCUMENT ME!

• saveLUT

  public void saveLUT​(boolean saveAll)

  This method saves the LUT for the active image. If the image is not a color image then both the functions and the LUT data are saved. If this is a color image, then only the functions are saved.

  Parameters:

  saveAll - - boolean indicating that both lut and transfer functions should be saved. If false, then only transfer functions are saved.

• saveLUTAs

  public void saveLUTAs​(boolean saveAll,
                        java.lang.String filename,
                        java.lang.String dirName)

  This method saves the LUT for the active image. If the image is not a color image then both the functions and the LUT data are saved. If this is a color image, then only the functions are saved.

  Parameters:

  saveAll - boolean indicating that both lut and transfer functions should be saved. If false, then only transfer functions are saved.

  If either filename or directory is null, then the user will be prompted for a filename.

  filename - filename to save LUT as

  dirName - directory to save LUT to

• saveLUTAs

  public static void saveLUTAs​(ModelImage image,
                               ModelStorageBase lut,
                               boolean saveAll)

  Saves the LUT associated with the input image (either a ModelLUT or ModelRGB).

  Parameters:

  image -

  lut -

  saveAll -

• saveLUTandTransferFunction

  public void saveLUTandTransferFunction​(java.lang.String filename,
                                         java.lang.String dirName)

  This method saves the LUT for the active image. If the image is not a color image then both the functions and the LUT data are saved. If this is a color image, then only the functions are saved.

  Parameters:

  filename - filename to save LUT as

  dirName - directory to save LUT to

• saveLUTandTransferFunction

  public static void saveLUTandTransferFunction​(ModelImage image,
                                                ModelLUT lut,
                                                java.lang.String filename,
                                                java.lang.String dirName)

  Saves the ModelLUT and transfer function.

  Parameters:

  image -

  lut -

  filename -

  dirName -

• saveVOI

  public void saveVOI​(boolean saveAllContours)

  This method saves a selected VOI - should this be in VOI structure ??!!!

  Parameters:

  saveAllContours - if true all contours are saved

• saveVOIAs

  public java.lang.String saveVOIAs()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• saveVOIAs

  public void saveVOIAs​(boolean saveAllContours)

  This method allows the user to choose how to save the VOI.

  Parameters:

  saveAllContours - if true all contours are saved

• saveVOIIntensities

  public void saveVOIIntensities()

  Save intensities in VOI to a text file of format x,y,z,intensity on each line if not color or complex. If color use format x,y,z,a,r,g,b on each line and if complex use format x,y,z,real,imaginary on each line.

• saveVOIIntensitiesTo

  public void saveVOIIntensitiesTo​(java.lang.String voiIntensitiesDir)

  Save intensities in VOI to a text file of format x,y,z,intensity on each line if not color or complex. If color use format x,y,z,a,r,g,b on each line and if complex use format x,y,z,real,imaginary on each line.

• setEnableCloseImageBAfterLoad

  public void setEnableCloseImageBAfterLoad​(boolean enable)

  Sets whether the close image B option should appear after loading.

  Parameters:

  enable - whether the "Close image B" option should appear after image B is loaded

• setImageA

  public void setImageA​(ModelImage image)

  Accessor that sets the imageA.

  Parameters:

  image - The image to make image-A in this frame.

• setLastState

  public void setLastState​(int state)

  setLastState.

  Parameters:

  state - Should be either Frame.NORMAL or Frame.ICONIFIED

• setLinkedFrame

  public void setLinkedFrame​(ViewJFrameImage linkFrame)

  Accessor that sets the link Frame.

  Parameters:

  linkFrame - set frame to link to.

• setLinkedTriFrame

  public void setLinkedTriFrame​(ViewJFrameTriImage linkTriFrame)

  Accessor that sets the link Frame.

  Parameters:

  linkTriFrame - set frame to link to.

• setLUTa

  public void setLUTa​(ModelLUT lut)

  Accessor that sets LUTa.

  Parameters:

  lut - DOCUMENT ME!

• setLUTb

  public void setLUTb​(ModelLUT lut)

  Accessor that sets LUTb.

  Parameters:

  lut - DOCUMENT ME!

• setLUTs

  public void setLUTs​(ModelLUT _LUTa,
                      ModelLUT _LUTb)

  Sets LUTa and LUTb.

  Parameters:

  _LUTa - DOCUMENT ME!

  _LUTb - DOCUMENT ME!

• setMessageText

  public final void setMessageText​(java.lang.String str)

  Accessor to set the text of the main frame's text field.

  Parameters:

  str - string to be display in the main frame's text field

• setOpacityInfo

  public void setOpacityInfo​(float _OPACITY,
                             float _alphaBlend)

  Sets RGB Information.

  Parameters:

  _OPACITY - DOCUMENT ME!

  _alphaBlend - DOCUMENT ME!

• setpaintBitmap

  public void setpaintBitmap​(java.util.BitSet _paintBitmap)

  Sets the paint Bitmap.

  Parameters:

  _paintBitmap - DOCUMENT ME!

• stateChanged

  public void stateChanged​(javax.swing.event.ChangeEvent event)

  Does nothing.

  Specified by:

  stateChanged in interface javax.swing.event.ChangeListener

  Parameters:

  event - the change event

• windowActivated

  public void windowActivated​(java.awt.event.WindowEvent event)

  Tells the UI that this frame is the currently active one.

  Specified by:

  windowActivated in interface java.awt.event.WindowListener

  Parameters:

  event - the window event

• windowClosed

  public void windowClosed​(java.awt.event.WindowEvent event)

  Does nothing.

  Specified by:

  windowClosed in interface java.awt.event.WindowListener

  Parameters:

  event - the window event

• windowClosing

  public void windowClosing​(java.awt.event.WindowEvent event)

  Cleans up the frame before closing.

  Specified by:

  windowClosing in interface java.awt.event.WindowListener

  Parameters:

  event - the window event that triggered this method

• windowDeactivated

  public void windowDeactivated​(java.awt.event.WindowEvent event)

  Does nothing.

  Specified by:

  windowDeactivated in interface java.awt.event.WindowListener

  Parameters:

  event - the window event

• windowDeiconified

  public void windowDeiconified​(java.awt.event.WindowEvent event)

  Does nothing.

  Specified by:

  windowDeiconified in interface java.awt.event.WindowListener

  Parameters:

  event - the window event

• windowIconified

  public void windowIconified​(java.awt.event.WindowEvent event)

  Does nothing.

  Specified by:

  windowIconified in interface java.awt.event.WindowListener

  Parameters:

  event - the window event

• windowOpened

  public void windowOpened​(java.awt.event.WindowEvent event)

  Does nothing.

  Specified by:

  windowOpened in interface java.awt.event.WindowListener

  Parameters:

  event - the window event

• finalize

  protected void finalize()
                   throws java.lang.Throwable

  Cleans memory.

  Overrides:

  finalize in class java.lang.Object

  Throws:

  java.lang.Throwable - the Exception raised by this method

• makeString

  protected java.lang.String makeString​(float number,
                                        int decPts)

  Makes a string of a float with a specific number of decimal points.

  Parameters:

  number - number to be converted to a string

  decPts - the number of decimal points

  Returns:

  string representation of the number

• setAbsPositionLabels

  protected void setAbsPositionLabels​(WildMagic.LibFoundation.Mathematics.Vector3f position)

  Sets the Absolute position label.

  Parameters:

  position - DOCUMENT ME!

• setScannerPosition

  protected void setScannerPosition​(WildMagic.LibFoundation.Mathematics.Vector3f position)

  Sets the Scanner position label.

  Parameters:

  position - DOCUMENT ME!

• handleZoomPopupMenu

  protected void handleZoomPopupMenu​(java.awt.Component component,
                                     java.awt.event.MouseEvent event)

  DOCUMENT ME!

  Parameters:

  component - DOCUMENT ME!

  event - DOCUMENT ME!

• handleMaskPopupMenu

  public static void handleMaskPopupMenu​(java.awt.Component component,
                                         java.awt.event.MouseEvent event)

  Handles the popup menu for the Quick Mask buttons

  Parameters:

  component - DOCUMENT ME!

  event - DOCUMENT ME!

• handlePaintToMaskPopupMenu

  protected void handlePaintToMaskPopupMenu​(java.awt.Component component,
                                            java.awt.event.MouseEvent event)

  Handles the pop-up menu for Paint to Mask buttons (inside/outside)

  Parameters:

  component - DOCUMENT ME!

  event - DOCUMENT ME!

• initExtents

  protected static int[] initExtents​(ModelImage img)

  Get the extents of an image. (don't know why this is really needed...)

  Parameters:

  img - the image

  Returns:

  the image's extents

• initImageBuffer

  protected static float[] initImageBuffer​(int[] extents,
                                           boolean isColor,
                                           int imageType)

  Create the intensity buffer for an image.

  Parameters:

  extents - the extents of the image

  isColor - whether the image is in color

  Returns:

  a buffer which is big enough to contain the image intensity data

• initNumSlices

  protected static int[] initNumSlices​(ModelImage img)

  Get the total number of time slices and volume slices.

  Parameters:

  img - the image to get the slices of

  Returns:

  an array containing the number of volume slices (in the first element) and the number of time slices in the image (in the second element)

• initPixelBuffer

  protected static int[] initPixelBuffer​(int[] extents)

  Create the pixel buffer for an image.

  Parameters:

  extents - the extents of the image

  Returns:

  a buffer which is big enough to contain the image pixel data

• initResFactor

  protected static float[] initResFactor​(float[] imgResols,
                                         int[] imgUnits)

  Get the resolution correction needed for non-isotropic images.

  Parameters:

  imgResols - the image resolution

  imgUnits - the image units of measure

  Returns:

  the resolution correction factor in the x (the first element) and y (the second element) dimensions

• initResolutions

  protected static float[] initResolutions​(ModelImage img)

  DOCUMENT ME!

  Parameters:

  img - DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• initSlicePositions

  protected static int[] initSlicePositions​(ModelImage img)

  Get the initial time and volume slice positions.

  Parameters:

  img - the image to get the slice positions of

  Returns:

  an array containing the slice in the volume (in the first element) and the time slice (in the second element)

• initUnits

  protected static int[] initUnits​(ModelImage img)

  DOCUMENT ME!

  Parameters:

  img - DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• initLUT

  public static ModelLUT initLUT​(ModelImage img)
                          throws java.lang.OutOfMemoryError

  Creates and initializes the LUT for an image.

  Parameters:

  img - the image to create a LUT for

  Returns:

  a LUT for the image img (null if a color image)

  Throws:

  java.lang.OutOfMemoryError - if enough memory cannot be allocated for this method

• initRGB

  public static ModelRGB initRGB​(ModelImage img)
                          throws java.lang.OutOfMemoryError

  Creates and initializes the ModelRGB for an image.

  Parameters:

  img - the image to create a ModelRGB for

  Returns:

  a ModelRGB for the image img (null if NOT a color image)

  Throws:

  java.lang.OutOfMemoryError - if enough memory cannot be allocated for this method

• initZoom

  protected static float initZoom​(ModelImage img,
                                  float xResFactor,
                                  float yResFactor,
                                  int screenX,
                                  int screenY)

  Initializes the zoom variables for an image.

  Parameters:

  img - the image to use to initialize the zoom

  xResFactor - correction factor in the x direction for images that are do not have isotropic voxels

  yResFactor - correction factor in the x direction for images that are do not have isotropic voxels

  Returns:

  the initial zoom to use for this image

• findFilter

  private javax.swing.filechooser.FileFilter findFilter​(javax.swing.JFileChooser chooser,
                                                        int filterType)

  Finds the FileFilter that matches the file type.

  Parameters:

  chooser - JFileChooser

  filterType - int the file filter type

  Returns:

  FileFilter the filter that matches the filter type.

• isImageResampleable

  private boolean isImageResampleable​(ModelImage image)

  Returns whether an image can be resampled to match imageA for loading into the imageB slot of the frame.

  Parameters:

  image - the image to check

  Returns:

  true if the image is either 3D or 4D (but not if the 4th dim differs)

• isResampleNeeded

  private boolean isResampleNeeded​(ModelImage image)

  Returns whether a image should be resampled to match the extents and resolutions of imageA.

  Parameters:

  image - the image to check against imageA

  Returns:

  true if a resampling of the image is required

• loadResampledImage

  private void loadResampledImage​(ModelImage image)

  Resamples an image and loads it into the imageB slot. This image should already be matched against imageA.

  Parameters:

  image - the image to resample and load as imageB

• reorderAfni

  private boolean reorderAfni​(ModelImage image,
                              int[] axisA,
                              int[] axisB)

  Reorders the AFNI image based on the axis orientations. B0 to A1 indicates changing x to y; B0 to A2 indicates a change from x to z.

  Parameters:

  image - Image to reorder.

  axisA - axis indices orientation of reordered image

  axisB - axis indices orientation of original image

  Returns:

  true if the reordering of the Afni file is successful, false otherwise

• setImageBAfni

  private int setImageBAfni​(ModelImage imageA,
                            ModelImage image)

  Sets image B to an AFNI image, performing the appropriate transformations.

  Parameters:

  imageA - Image A.

  image - AFNI image to set to image A.

  Returns:

  -1 if failure; 0 if no tranformation needed; and 1 if transformation and set successful.

• transformACPC

  private void transformACPC​(ModelImage image,
                             float[] imgBuffer,
                             TransMatrix xfrm,
                             float iXres,
                             float iYres,
                             float iZres,
                             int iXdim,
                             int iYdim,
                             int iZdim,
                             int iTdim,
                             int planeGap,
                             int[] gapArray,
                             boolean doNN,
                             float oXres,
                             float oYres,
                             float oZres,
                             int oXdim,
                             int oYdim,
                             int oZdim)

  This routine is designed to transform AFNI functional images which have already been transformed to match AFNI original images to match AFNI +acpc images.

  AFNI:Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages by Robert W. Cox states:

  "In some applications, gaps are present between the functional slices. For example, some investigators using sagittal functional images do not collect data that spans the longitudinal fissure, but instead leave a 3-5 mm gap there. The auxiliary program abut can provide zero-filled images to fill in the gaps, and can resample the nonzero slices to a finer mesh if needed(e.g., to fill a 2 mm gap in a series of 4 mm functional slices). Resampling in the slice select direction between contiguous input slices can be done using nearest- neighbor, linear, or cubic interpolation, at the user's discretion. Interpolation is not done across the boundaries between the gap-filling zero images and the nonzero user-supplied images; that is, interpolation is only done inside spatially contiguous blocks of actual input data."

  A second special consideration exists in the interpolation of functional data. The MCW AFNI - User Manual states: "In this version of AFNI, the threshold data (e.g., correlation coefficient) is always resampled using the nearest neighbor method. This is because thresholding with an interpolated nonlinear statistic is a somewhat dubious procedure." At another point the manual states: "Threshold data in functional datasets is always resampled using the nearest neighbor mode. This is becasue it is somewhat unreasonable to interpolate a nonlinear statistic (such as correlation coefficient) between voxels, and then to interpret this statistic using probabilistic models that assume independence."

  Thus, the intensity data is interpolated with trilinear interpolation and the threshold data is interpolated with nearest neighbor interpolation.

  Parameters:

  image - image being created

  imgBuffer - source image array

  xfrm - transformation matrix to be applied

  iXres - input x resolution

  iYres - input y resolution

  iZres - input z resolution

  iXdim - input x dimesnion

  iYdim - input y dimension

  iZdim - input z dimension

  iTdim - input t dimension

  planeGap - -1 if no zero filled gaps, 0 for x axis gaps, 1 for y axis, 2 for z axis

  gapArray - array of coordinates at which the zero filled planes occur

  doNN - true if functional, false if anatomical

  oXres - output x resolution

  oYres - output y resolution

  oZres - output z resolution

  oXdim - output x dimension

  oYdim - output y dimension

  oZdim - output z dimension

• transformAFNI

  private void transformAFNI​(ModelImage image,
                             float[] imgBuffer,
                             float iXres,
                             float iYres,
                             float iZres,
                             int iXdim,
                             int iYdim,
                             int iZdim,
                             int iTdim,
                             float ilowXmm,
                             float ilowYmm,
                             float ilowZmm,
                             float ihighXmm,
                             float ihighYmm,
                             float ihighZmm,
                             int planeGap,
                             int[] gapArray,
                             boolean doNN,
                             float oXres,
                             float oYres,
                             float oZres,
                             int oXdim,
                             int oYdim,
                             int oZdim,
                             float olowXmm,
                             float olowYmm,
                             float olowZmm,
                             float ohighXmm,
                             float ohighYmm,
                             float ohighZmm)

  This routine is designed to transform AFNI functional images and AFNI 3D + time anatomical images to match AFNI original 3D anatomical images. Here the 3 axes of the 2 images are parallel and the spatial orientation of the 2 sets of axes are identical.

  AFNI:Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages by Robert W. Cox states:

  "In some applications, gaps are present between the functional slices. For example, some investigators using sagittal functional images do not collect data that spans the longitudinal fissure, but instead leave a 3-5 mm gap there. The auxiliary program abut can provide zero-filled images to fill in the gaps, and can resample the nonzero slices to a finer mesh if needed(e.g., to fill a 2 mm gap in a series of 4 mm functional slices). Resampling in the slice select direction between contiguous input slices can be done using nearest- neighbor, linear, or cubic interpolation, at the user's discretion. Interpolation is not done across the boundaries between the gap-filling zero images and the nonzero user-supplied images; that is, interpolation is only done inside spatially contiguous blocks of actual input data."

  A second special consideration exists in the interpolation of functional data. The MCW AFNI - User Manual states: "In this version of AFNI, the threshold data (e.g., correlation coefficient) is always resampled using the nearest neighbor method. This is because thresholding with an interpolated nonlinear statistic is a somewhat dubious procedure."

  At another point the manual states: "Threshold data in functional datasets is always resampled using the nearest neighbor mode. This is becasue it is somewhat unreasonable to interpolate a nonlinear statistic (such as correlation coefficient) between voxels, and then to interpret this statistic using probabilistic models that assume independence."

  Thus, the intensity data is interpolated with trilinear interpolation and the threshold data is interpolated with nearest neighbor interpolation.

  Parameters:

  image - image being created

  imgBuffer - source image array

  iXres - input x resolution

  iYres - input y resolution

  iZres - input z resolution

  iXdim - input x dimesnion

  iYdim - input y dimension

  iZdim - input z dimension

  iTdim - input t dimension

  ilowXmm - lowest valid input x location in space in millimeters

  ilowYmm - lowest valid input y location in space in millimeters

  ilowZmm - lowest valid input z location in space in millimeters

  ihighXmm - highest valid input x location in space in millimeters

  ihighYmm - highest valid input y location in space in millimeters

  ihighZmm - highest valid input z location in space in millimeters

  planeGap - -1 if no zero filled gaps, 0 for x axis gaps, 1 for y axis, 2 for z axis

  gapArray - array of coordinates at which the zero filled planes occur

  doNN - true if functional, false if anatomical

  oXres - output x resolution

  oYres - output y resolution

  oZres - output z resolution

  oXdim - output x dimension

  oYdim - output y dimension

  oZdim - output z dimension

  olowXmm - lowest valid output x location in space in millimeters

  olowYmm - lowest valid output y location in space in millimeters

  olowZmm - lowest valid output z location in space in millimeters

  ohighXmm - highest valid output x location in space in millimeters

  ohighYmm - highest valid output y location in space in millimeters

  ohighZmm - highest valid output z location in space in millimeters

• transformTalairach

  private void transformTalairach​(ModelImage image,
                                  float[] imgBuffer,
                                  TransMatrix xfrm,
                                  float iXres,
                                  float iYres,
                                  float iZres,
                                  int iXdim,
                                  int iYdim,
                                  int iZdim,
                                  int iTdim,
                                  int planeGap,
                                  int[] gapArray,
                                  boolean doNN,
                                  float oXres,
                                  float oYres,
                                  float oZres,
                                  int oXdim,
                                  int oYdim,
                                  int oZdim,
                                  int botX,
                                  int botY,
                                  int botZ,
                                  int topX,
                                  int topY,
                                  int topZ)

  This routine is designed to transform AFNI functional images which have already been transformed to match AFNI original images to match AFNI +tlrc images.

  AFNI:Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages by Robert W. Cox states:

  "In some applications, gaps are present between the functional slices. For example, some investigators using sagittal functional images do not collect data that spans the longitudinal fissure, but instead leave a 3-5 mm gap there. The auxiliary program abut can provide zero-filled images to fill in the gaps, and can resample the nonzero slices to a finer mesh if needed(e.g., to fill a 2 mm gap in a series of 4 mm functional slices). Resampling in the slice select direction between contiguous input slices can be done using nearest- neighbor, linear, or cubic interpolation, at the user's discretion. Interpolation is not done across the boundaries between the gap-filling zero images and the nonzero user-supplied images; that is, interpolation is only done inside spatially contiguous blocks of actual input data."

  A second special consideration exists in the interpolation of functional data. The MCW AFNI - User Manual states: "In this version of AFNI, the threshold data (e.g., correlation coefficient) is always resampled using the nearest neighbor method. This is because thresholding with an interpolated nonlinear statistic is a somewhat dubious procedure." At another point the manual states: "Threshold data in functional datasets is always resampled using the nearest neighbor mode. This is becasue it is somewhat unreasonable to interpolate a nonlinear statistic (such as correlation coefficient) between voxels, and then to interpret this statistic using probabilistic models that assume independence."

  Thus, the intensity data is interpolated with trilinear interpolation and the threshold data is interpolated with nearest neighbor interpolation.

  Parameters:

  image - image being created

  imgBuffer - source image array

  xfrm - transformation matrix to be applied

  iXres - input x resolution

  iYres - input y resolution

  iZres - input z resolution

  iXdim - input x dimesnion

  iYdim - input y dimension

  iZdim - input z dimension

  iTdim - input t dimension

  planeGap - -1 if no zero filled gaps, 0 for x axis gaps, 1 for y axis, 2 for z axis

  gapArray - array of coordinates at which the zero filled planes occur

  doNN - true if functional, false if anatomical

  oXres - output x resolution

  oYres - output y resolution

  oZres - output z resolution

  oXdim - output x dimension

  oYdim - output y dimension

  oZdim - output z dimension

  botX - lowest x output value in this 1 of the 12 Talairach regions

  botY - lowest y output value in this 1 of the 12 Talairach regions

  botZ - lowest z output value in this 1 of the 12 Talairach regions

  topX - highest x output value in this 1 of the 12 Talairach regions

  topY - highest y output value in this 1 of the 12 Talairach regions

  topZ - highest z output value in this 1 of the 12 Talairach regions