Field Detail

• serialVersionUID

  private static final long serialVersionUID

  Use serialVersionUID for interoperability.

  See Also:

  Constant Field Values

• ACTIVE_IMAGE_COLOR

  public static java.awt.Color ACTIVE_IMAGE_COLOR

  Color used in the rectangle indicating the image is active. Images which are not active will not have the recangle drawn.

• GEOMETRIC_ZOOM

  public static final int GEOMETRIC_ZOOM

  Used to indicte geometric zoom steps (2x, 4x, 8x, 16x ...).

  See Also:

  Constant Field Values

• LINEAR_ZOOM

  public static final int LINEAR_ZOOM

  Used to indicte linear zoom steps (2x, 3x, 4x, 5x ...).

  See Also:

  Constant Field Values

• checkerDialog

  public JDialogCheckerBoard checkerDialog

  Dialog used to set properties of the checkerboard display:(Image A displayed in alternating squares with Image B.

• growDialog

  public RegionGrowDialog growDialog

  Dialog used to control region growing of the paint tool.

• intensityDropper

  public float intensityDropper

  Used in paint to indicate intensity painted into the image.

• MAGR_HEIGHT

  public int MAGR_HEIGHT

  Default size of magnifier window = 120 pixels.

• MAGR_MAG

  public float MAGR_MAG

  Magnification value of magnifier window -- default = 4.0.

• MAGR_WIDTH

  public int MAGR_WIDTH

  default = 120 pixels.

• allActive

  protected boolean allActive

  Set to true when all contours of a VOI are active.

• alphaBlend

  protected float alphaBlend

  Value used to control the display when compositing two images. Usually = 1 - alphaPrime.

• alphaPrime

  protected float alphaPrime

  Value used to control the display when compositing two images. It is the amount of image A to display and is has a range of [0,1]

• rgbString

  protected java.lang.String rgbString

  String representing RGB components used in applied paint

• cleanImageBufferA

  protected int[] cleanImageBufferA

  Buffer used to store ARGB images of the image presently being displayed.

• cleanImageBufferB

  protected int[] cleanImageBufferB

  Buffer used to store ARGB images of the image presently being displayed.

• crosshairCursor

  protected java.awt.Cursor crosshairCursor

  Crosshair cursor that can be changed per user preference (in Mipav Options).

• cursorMode

  protected int cursorMode

  Used to describe the cursor mode.

• displayFuzzy

  protected boolean displayFuzzy

  DOCUMENT ME!

• drawVOIs

  protected boolean drawVOIs

  Flag used to prohibit VOI drawing.

• frame

  protected ViewJFrameBase frame

  Frame where the component image is displayed.

• frameControls

  protected ViewControlsImage frameControls

  Controls having color and opacity.

• fuzzyThreshold

  protected float fuzzyThreshold

  Region grow parameters fuzzyConnectedness is not used if fuzzyThreshold is less than 0. When fuzzyConnectedness is used, fuzzyThreshold ranges from 0 to 1.

• imageA

  protected ModelImage imageA

  Model for image A.

• imageActive

  protected ModelImage imageActive

  Active image.

• imageB

  protected ModelImage imageB

  Model for image B.

• imageBufferA

  protected float[] imageBufferA

  Buffer for image A, raw intensity.

• imageBufferActive

  protected float[] imageBufferActive

  Buffer for active image.

• imageBufferB

  protected float[] imageBufferB

  Buffer for image B, raw intensity.

• imageExtents

  protected int[] imageExtents

  The dimensionality of the image.

• imageStatList

  protected JDialogVOIStatistics imageStatList

  DOCUMENT ME!

• less

  protected float less

  DOCUMENT ME!

• lessB

  protected float lessB

  DOCUMENT ME!

• lessG

  protected float lessG

  DOCUMENT ME!

• lessR

  protected float lessR

  DOCUMENT ME!

• logMagDisplay

  protected boolean logMagDisplay

  Flag for displaying logMag.

• LUTa

  protected ModelLUT LUTa

  Lookup table for image A.

• LUTb

  protected ModelLUT LUTb

  Lookup table for image B.

• m_kPatientSlice

  protected PatientSlice m_kPatientSlice

  PatientSlice contains all the Patient Coordinate system view-specific data for rendering this component:.

• magSettings

  protected JDialogMagnificationControls magSettings

  Dialog used to control the magnification of the image.

• maxDistance

  protected float maxDistance

  DOCUMENT ME!

• maxExtents

  protected int[] maxExtents

  DOCUMENT ME!

• modifyFlag

  protected boolean modifyFlag

  Used to "lock" display when an algorithm is in the calculation process.

• more

  protected float more

  DOCUMENT ME!

• moreB

  protected float moreB

  DOCUMENT ME!

• moreG

  protected float moreG

  DOCUMENT ME!

• moreR

  protected float moreR

  DOCUMENT ME!

• mousePressIsShiftDown

  protected boolean mousePressIsShiftDown

  Keep track of state of shift for mouse Pressed events.

• nColumnCheckers

  protected int nColumnCheckers

  The number columns when two images are displayed in the checker board mode.

• nRowCheckers

  protected int nRowCheckers

  Checkerboard display parameters. The number of rows to display.

• onTop

  protected boolean onTop

  for the use of the user-notifier.

• orientation

  protected int orientation

  orientation of the slice, may be AXIAL, CORONAL, SAGITTAL, or UNKNOWN_ORIENT.

• paintBitmap

  protected java.util.BitSet paintBitmap

  Buffer used to indicate if the pixel location is painted (true) or unpainted (false).

• paintBitmapBU

  protected java.util.BitSet paintBitmapBU

  Backup of paint buffer for undo.

• paintBitmapSwitch

  protected boolean paintBitmapSwitch

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

• paintBrush

  protected java.util.BitSet paintBrush

  BitSet used for painting (brushes on/off).

• paintBrushDim

  protected java.awt.Dimension paintBrushDim

  Dimension of the paint.

• paintBrushDimPrevious

  protected java.awt.Dimension paintBrushDimPrevious

  DOCUMENT ME!

• paintBrushPrevious

  protected java.util.BitSet paintBrushPrevious

  DOCUMENT ME!

• paintBrushSize

  protected int paintBrushSize

  Paint brush size.

• paintImage

  protected java.awt.image.BufferedImage paintImage

  buffered image that is transparent to show the paintbrush cursor.

• paintImagePrevious

  protected java.awt.image.BufferedImage paintImagePrevious

  DOCUMENT ME!

• pixBuffer

  protected int[] pixBuffer

  The buffer used to store the ARGB image of the image presently being displayed.

• pixBufferB

  protected int[] pixBufferB

  Buffer used to store ARGB image of the windowed imageB.

• previousPaintBrush

  protected int previousPaintBrush

  The previous paint brush we were using when the user temporarily changes the paint brush size using keyboard shortcuts (by pressing 1, 2, 3, 4).

• RGBTA

  protected ModelRGB RGBTA

  DOCUMENT ME!

• RGBTB

  protected ModelRGB RGBTB

  DOCUMENT ME!

• saveValue

  protected float saveValue

  Used with commitMask(int imagesDone), to save the value.

• saveValueB

  protected float saveValueB

  DOCUMENT ME!

• saveValueG

  protected float saveValueG

  DOCUMENT ME!

• saveValueR

  protected float saveValueR

  DOCUMENT ME!

• saveX

  protected short saveX

  Used with commitMask(int imagesDone), to save positions.

• saveY

  protected short saveY

  Used with commitMask(int imagesDone), to save positions.

• saveZ

  protected short saveZ

  Used with commitMask(int imagesDone), to save positions.

• seedPaintBitmap

  protected java.util.BitSet seedPaintBitmap

  Buffer used to remember the area painted around the last seed point for region growing.

• seedVal

  protected float seedVal

  Seed value to start the region grow.

• seedValB

  protected float seedValB

  DOCUMENT ME!

• seedValG

  protected float seedValG

  DOCUMENT ME!

• seedValR

  protected float seedValR

  DOCUMENT ME!

• sizeLimit

  protected int sizeLimit

  DOCUMENT ME!

• slice

  protected int slice

  DOCUMENT ME!

• stringOverride

  protected java.lang.String stringOverride

  String used to override the slice number in the lower left corner.

• time

  protected long time

  DOCUMENT ME!

• timeSlice

  protected int timeSlice

  DOCUMENT ME!

• toppedColor

  protected java.awt.Color toppedColor

  DOCUMENT ME!

• useVOI

  protected boolean useVOI

  This flag is used by the fuzzy connectedness to indicate that a VOI should be used to calculate certain values to initialize the process.

• variableThresholds

  protected boolean variableThresholds

  DOCUMENT ME!

• visRect

  protected java.awt.Rectangle visRect

  Visible rectangle to draw topped.

• winLevelSet

  protected boolean winLevelSet

  User invokes window and level adjustment with right mouse drag in DEFAULT mode.

• xPG

  protected short xPG

  X coord of seed point.

• yPG

  protected short yPG

  Y coord of seed point.

• zPG

  protected short zPG

  Z coord of seed point.

• cleanImageB

  private java.awt.Image cleanImageB

  DOCUMENT ME!

• intensityLabel

  private boolean intensityLabel

  If true then the x,y location and pixel/voxel intensity should be displayed (x,y: intensity).

• lastWinRegionSlice

  private int lastWinRegionSlice

  Last slice the image was at when win region was ON. its necessary because otherwise, a new cleanImageB would have to be created upon every repaint. should be initialized to a negative number

• m_kWinLevel

  protected WindowLevel m_kWinLevel

  window / level mouse control:.

• offscreenImage

  private java.awt.Image offscreenImage

  DOCUMENT ME!

• paintImageBuffer

  private int[] paintImageBuffer

  This image indicates which images have been painted.

• shiftDown

  private boolean shiftDown

  Flag used to indicate if the shift key is depressed. True indicates the shift key is depressed.

• showMagIntensity

  private boolean showMagIntensity

  Flag used to indicate that the intensity values of the image should be displayed in the magnified portion of the image. The intensity values can only be shown if the magnification is high enough to fit the text representation of the value in the magnified voxel/pixel.

• wasDragging

  private boolean wasDragging

  Boolean to determine if the mouse had been dragging before mouse release (for moving and setting active).

• windowedRegionSize

  private int windowedRegionSize

  The window region size of used when two images are displayed in the same frame. The size of the window indicates how much of image B is displayed.

• useRComp

  protected boolean useRComp

• useGComp

  protected boolean useGComp

• useBComp

  protected boolean useBComp

• zeroToOneLUTAdj

  private boolean zeroToOneLUTAdj

  flag indicating whether there is 0 to 1 LUT Adjustment *

• paintBuffer

  protected int[] paintBuffer

• gridColor

  protected java.awt.Color gridColor

  color of grid.

• gridLabelingOn

  protected boolean gridLabelingOn

  if number/lettering should be displayed for grid boxes.

• gridLabelOrientation

  protected boolean gridLabelOrientation

  boolean to determine the orientation: true is x-axis numbered false is x-axis lettered.

• gridOverlayOn

  protected boolean gridOverlayOn

  Flag to indicate if NEI grid overlay should be displayed.

• gridSpacingX

  protected float gridSpacingX

  spacing of the grid (horizontal) in terms of resolution.

• gridSpacingY

  protected float gridSpacingY

  spacing of the grid (vertical) in terms of resolution.

• overlayOn

  protected boolean overlayOn

  Flag to indicate if DICOM overlay should be displayed.

• voiManager

  protected VOIManager voiManager

• lastMouseEvent

  private long lastMouseEvent

• doCheckerboardAnimate

  private boolean doCheckerboardAnimate

• xSep

  private int xSep

• ySep

  private int ySep

• xMod

  int xMod

• yMod

  int yMod

• xStart

  int[] xStart

• yStart

  int[] yStart

• makingCheckerboard

  private boolean makingCheckerboard

• bandSpacing

  private int[] bandSpacing

• refPtsLocation

  private java.lang.String refPtsLocation

• eyeTrackerRecordingMode

  private int eyeTrackerRecordingMode

• SingleFrameEyetrackerMode

  public static int SingleFrameEyetrackerMode

• MultiFrameEyetrackerMode

  public static int MultiFrameEyetrackerMode

• PluginEyetrackerMode

  public static int PluginEyetrackerMode

• winLevel

  protected JDialogWinLevel winLevel

Constructor Detail

• ViewJComponentEditImage

  public ViewJComponentEditImage​(ViewJFrameBase _frame,
                                 ModelImage _imageA,
                                 ModelLUT _LUTa,
                                 float[] imgBufferA,
                                 ModelImage _imageB,
                                 ModelLUT _LUTb,
                                 float[] imgBufferB,
                                 int[] pixelBuffer,
                                 float zoom,
                                 int[] extents,
                                 boolean logMagDisplay,
                                 int _orientation)

  Constructor: ImageA and ImageB are expected to be of the same dimensionality !!

  Parameters:

  _frame - frame where image(s) will be displayed

  _imageA - Model of the image that will be displayed

  _LUTa - LUT used to display imageA

  imgBufferA - storage buffer used to display image A

  _imageB - Model of the image that will be displayed

  _LUTb - LUT used to display imageB

  imgBufferB - storage buffer used to display image B

  pixelBuffer - storage buffer used to build a displayable image

  zoom - initial magnification of image

  extents - initial display dimensions of the image

  logMagDisplay - display log magnitude of image

  _orientation - orientation of the image

Method Detail

• getScannerPositionLabels

  public static final java.lang.String[] getScannerPositionLabels​(ModelImage image,
                                                                  WildMagic.LibFoundation.Mathematics.Vector3f position)

  Gets position data to display in message bar - for DICOM and MINC images, gives patient position as well. The image's associated transformation must be FileInfoBase.TRANSFORM_SCANNER_ANATOMICAL, or the orientations must be set up correctly, or else the function returns null.

  Parameters:

  image - The image the point lies within.

  position - (x,y,z(slice)) position in FileCoordinates

  Returns:

  An array of strings that represent patient position.

• getRASScannerPositionLabels

  public static final java.lang.String[] getRASScannerPositionLabels​(ModelImage image,
                                                                     WildMagic.LibFoundation.Mathematics.Vector3f position)

  Gets position data to display in message bar - for DICOM and MINC images, gives patient position as well. The image's associated transformation must be FileInfoBase.TRANSFORM_SCANNER_ANATOMICAL, or the orientations must be set up correctly, or else the function returns null.

  Parameters:

  image - The image the point lies within.

  position - (x,y,z(slice)) position in FileCoordinates

  Returns:

  An array of strings that represent patient position.

• calcPaintedVolume

  public void calcPaintedVolume​(java.lang.String str)

  Calculates the volume of the painted voxels.

  Parameters:

  str - string in showRegionGrow #showRegionGrow(int, String)

• cine

  public void cine​(int ms)

  Loops through the images and displays them.

  Parameters:

  ms - how long to wait between each image

• commitMask

  public void commitMask​(int imagesDone,
                         boolean clearPaintMask,
                         boolean polarity,
                         boolean commitMasksAs4D)

  Replace intensities in the image using painted mask.

  Parameters:

  imagesDone - IMAGE_A, IMAGE_B, or BseedVOTH

  clearPaintMask - if true clear paint mask

  polarity - DOCUMENT ME!

• commitMask

  public void commitMask​(int imagesDone,
                         boolean clearPaintMask,
                         boolean polarity,
                         java.util.Vector<java.lang.Integer> intensityLockVector,
                         boolean commitMasksAs4D)

  Replace intensities in the image using painted mask.

  Parameters:

  imagesDone - IMAGE_A, IMAGE_B, or BseedVOTH

  clearPaintMask - if true clear paint mask

  polarity - DOCUMENT ME!

  intensityLockVector - Vector containing Integers values which are indexed to the locked intensity values in the image

• commitMask

  public void commitMask​(ModelImage affectedImage,
                         boolean clearPaintMask,
                         boolean polarity,
                         java.util.Vector<java.lang.Integer> intensityLockVector,
                         boolean showProgressBar,
                         boolean commitMasksAs4D)

  Replace intensities in the image using painted mask.

  Parameters:

  affectedImage - IMAGE_A, IMAGE_B, or BseedVOTH

  clearPaintMask - if true clear paint mask

  polarity - DOCUMENT ME!

  intensityLockVector - Vector containing Integers values which are indexed to the locked intensity values in the image

  showProgressBar - if true, shows the progress bar for this algorithm

• commitMask

  public void commitMask​(int imagesDone,
                         boolean clearPaintMask,
                         boolean polarity,
                         java.util.Vector<java.lang.Integer> intensityLockVector,
                         boolean showProgressBar,
                         boolean commitMasksAs4D)

  Replace intensities in the image using painted mask.

  Parameters:

  imagesDone - IMAGE_A, IMAGE_B, or BseedVOTH

  clearPaintMask - if true clear paint mask

  polarity - DOCUMENT ME!

  intensityLockVector - Vector containing Integers values which are indexed to the locked intensity values in the image

  showProgressBar - if true, shows the progress bar for this algorithm

• commitPaintToUbyteMask

  public java.lang.String commitPaintToUbyteMask()

  Creates a new ubyte image from the paint mask.

  Returns:

  the name of the new ubyte image

• commitPaintToMask

  public java.lang.String commitPaintToMask()

  Creates a new short image from the paint mask.

  Returns:

  the name of the new short image

• dispose

  public void dispose​(boolean flag)

  Sets all variables to null, disposes, and garbage collects.

  Overrides:

  dispose in class ViewJComponentBase

  Parameters:

  flag - if true garbage collector should be called.

• disposeLocal

  public void disposeLocal​(boolean flag)

  Deprecated.

  Old method that does not match up with signature from VJCBase.
  Sets all variables to null, disposes, and garbage collects. Old method that does not match up with signature from VJCBase.

  Parameters:

  flag - if true garbage collector should be called.

• drawGradicules

  public void drawGradicules​(java.awt.Graphics g,
                             float xRes,
                             float yRes)

  Draws the gradicules (the half-image lines which demarcate lengths in the image).

  Parameters:

  g - The graphics object which will do the painting.

  xRes - The resolutions in the x-direction.

  yRes - The resolutions in the y-direction.

• drawStringBW

  public final void drawStringBW​(java.lang.String str,
                                 java.awt.Graphics g,
                                 int x,
                                 int y)

  Draws a white character on a black surround.

  Parameters:

  str - string to be displayed

  g - graphics contexts (where to draw the string)

  x - x coordinate of where the string is to be drawn

  y - y coordinate of where the string is to be drawn

• eraseAllPaint

  public void eraseAllPaint​(boolean onlyCurrent)

  Erases all paint.

  Parameters:

  onlyCurrent - DOCUMENT ME!

• getActiveImage

  public ModelImage getActiveImage()

  Returns the active image.

  Specified by:

  getActiveImage in interface PaintGrowListener

  Returns:

  active image

• getActiveImageBuffer

  public float[] getActiveImageBuffer()

  Returns the active image buffer.

  Returns:

  active image buffer

• getActiveImageSliceBuffer

  public float[] getActiveImageSliceBuffer()

  Returns the active image buffer for this slice.

  Returns:

  active image buffer for this slice

• getActiveLUT

  public ModelLUT getActiveLUT()

  Returns the active image.

  Returns:

  active image

• getActiveRGB

  public ModelRGB getActiveRGB()

  Returns the active image.

  Returns:

  active image

• getAlphaBlend

  public float getAlphaBlend()

  Returns float alphaBlend. The value used to blend two images displayed in the same frame.

  Returns:

  alphaBlend

• getCursorMode

  public int getCursorMode()

  Returns the VOI mode.

  Returns:

  drawing mode for the VOI tools (i.e. ELLIPSE, LINE ...)

• getFrame

  public ViewJFrameBase getFrame()

  Returns the frame.

  Returns:

  frame

• getImageA

  public ModelImage getImageA()

  Returns the imageA.

  Returns:

  imageA

• getImageB

  public ModelImage getImageB()

  Returns the imageB.

  Returns:

  imageB

• getImageBufferA

  public float[] getImageBufferA()

  Gets imageA's image buffer of intensities.

  Returns:

  float[] imageA's intensity buffer

• getImageBufferB

  public float[] getImageBufferB()

  Gets imageB's image buffer of intensities.

  Returns:

  float[] imageB's intensity buffer

• getIntensityDropper

  public float getIntensityDropper()

  Gets the intensityDropper intensity.

  Returns:

  the intensity dropper

• getLUTa

  public ModelLUT getLUTa()

  Returns the model lut for the imageA.

  Returns:

  the model LUT for imageA

• getLUTb

  public ModelLUT getLUTb()

  Returns the model lut for the imageB.

  Returns:

  the model LUT for imageB

• getModifyFlag

  public boolean getModifyFlag()

  DOCUMENT ME!

  Returns:

  boolean

• getNumPoints

  public int getNumPoints()

  Finds the number of points in the active VOI contour.

  Returns:

  the number of points in the selected VOI

• getnVOI

  public int getnVOI()

  Returns the number of VOIs in the active image.

  Returns:

  int number of VOIs

• getOpacity

  public float getOpacity()

  Returns float opacity.

  Returns:

  opacity

• getOrientation

  public int getOrientation()

  Returns the image's orientation.

  Returns:

  image orientation

• getPaintBitmap

  public java.util.BitSet getPaintBitmap()

  Returns BitSet paintBitmap.

  Returns:

  paintBitmap

• getPaintBuffer

  public int[] getPaintBuffer()

  Gets the paint buffer.

  Returns:

  int[] paint buffer

• getPaintMask

  public java.util.BitSet getPaintMask()

  Gets the paint mask.

  Returns:

  the current paint mask

• getPixBuffer

  public int[] getPixBuffer()

  Gets the buffer used to store ARGB images of the image presently being displayed.

  Returns:

  int[] buffer of ARGB image A

• getPixBufferB

  public int[] getPixBufferB()

  Gets the buffer used to store ARGB images of the image presently being displayed.

  Returns:

  int[] buffer of ARGB image A

• getRGBTA

  public ModelRGB getRGBTA()

  Returns the ModelRGB RGBTA for imageA.

  Returns:

  RGBTA for imageA

• getRGBTB

  public ModelRGB getRGBTB()

  Returns the ModelRGB for imageB.

  Returns:

  RGBTB for imageB

• getShowMagIntensityEnabled

  public boolean getShowMagIntensityEnabled​(int width,
                                            int height,
                                            float mag)

  Determines whether to enable the showIntensity checkbox for magnification box.

  Returns:

  whether to enable showIntensity checkbox

• getSlice

  public int getSlice()

  Returns the slice of the image.

  Specified by:

  getSlice in interface ScreenCoordinateListener

  Returns:

  the slice

• getTimeSlice

  public int getTimeSlice()

  Gets the time slice of the image.

  Returns:

  the current time slice

• getVOIHandler

  public VOIHandlerInterface getVOIHandler()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• isCheckerboarded

  public boolean isCheckerboarded()

  Tells whether or not the image is being displayed in checkerboard mode.

  Returns:

  boolean

• loadImageFile

  private java.awt.image.BufferedImage loadImageFile​(java.lang.String imageName)
                                              throws java.io.IOException

  Reads in an image icon from either the set of mipav icons or the user's $HOME/mipav/brushes/ directory.

  Parameters:

  imageName - The

  Returns:

  Throws:

  java.io.IOException

• loadPaintBrush

  public void loadPaintBrush​(java.lang.String paintName,
                             boolean isQuick)

  Loads built-in (.gif) or custom (.png) paint brushes based on the last-used paint brush in preferences.

  Parameters:

  paintName - the name of the brush to load

  isQuick - DOCUMENT ME!

• mouseClicked

  public void mouseClicked​(java.awt.event.MouseEvent mouseEvent)

  A mouse event. When the mouse is clicked in the image, several different things may happen. If a Volume of Interest (VOI) is selected and the click count is 2, a VOI dialog should pop up. If the click count is 1 and the mouse is in an VOI, it should select the VOI. In all other cases, a click within the image but not in an VOI should deselect all VOIs.

  Specified by:

  mouseClicked in interface java.awt.event.MouseListener

  Parameters:

  mouseEvent - event that triggers function; contains click count

• mouseDragged

  public void mouseDragged​(java.awt.event.MouseEvent mouseEvent)

  A mouse event. Drags a VOI real time by calling a series of translations and draws. Once the mouse is released, the positions are reset permenantly. Also rubberbands points if the cursor indicates it by calling rubberbandVOI.

  Specified by:

  mouseDragged in interface java.awt.event.MouseMotionListener

  Parameters:

  mouseEvent - event that triggered function

• mouseEntered

  public void mouseEntered​(java.awt.event.MouseEvent mouseEvent)

  Store the lastMouse position.

  Specified by:

  mouseEntered in interface java.awt.event.MouseListener

  Parameters:

  mouseEvent - event

• mouseExited

  public void mouseExited​(java.awt.event.MouseEvent mouseEvent)

  Resets the level set stack.

  Specified by:

  mouseExited in interface java.awt.event.MouseListener

  Parameters:

  mouseEvent - event that triggered function

• mouseMoved

  public void mouseMoved​(java.awt.event.MouseEvent mouseEvent)

  A mouse event. If the mode is level set, draws level sets as user moves mouse. Otherwise, changes the cursor depending on where the mouse is in relation to the VOI.

  Specified by:

  mouseMoved in interface java.awt.event.MouseMotionListener

  Parameters:

  mouseEvent - event that triggered the function

• setFullScreenModeLocation

  public void setFullScreenModeLocation​(java.lang.String _location)

• mousePressed

  public void mousePressed​(java.awt.event.MouseEvent mouseEvent)

  A mouse event. Sets the mode of the program depending on the cursor mode. If the mode is move, activates the contour or line and enables the delete button.

  Specified by:

  mousePressed in interface java.awt.event.MouseListener

  Parameters:

  mouseEvent - event that triggered function

• mouseReleased

  public void mouseReleased​(java.awt.event.MouseEvent mouseEvent)

  A mouse event. This function sets up and draws the VOI according to the mode.

  Specified by:

  mouseReleased in interface java.awt.event.MouseListener

  Parameters:

  mouseEvent - event that triggered function

• mouseWheelMoved

  public void mouseWheelMoved​(java.awt.event.MouseWheelEvent mouseWheelEvent)

  ************************************************************************ ************************** Mouse Wheel Events *************************.************************************************************************

  Specified by:

  mouseWheelMoved in interface java.awt.event.MouseWheelListener

  Parameters:

  mouseWheelEvent - DOCUMENT ME!

• restartCheckerboardAnimateThread

  public void restartCheckerboardAnimateThread()

• openUDLUTandTransferFunct

  public void openUDLUTandTransferFunct()

  Open the user defined LUT table and transfer function.

• getRGBPaintComponents

  public java.lang.String getRGBPaintComponents()

• setRGBPaintComponents

  public void setRGBPaintComponents​(java.lang.String rgb)

• paintComponent

  public void paintComponent​(java.awt.Graphics graphics)

  Paints the image and calls drawSelf for all VOIs.

  Overrides:

  paintComponent in class ViewJComponentBase

  Parameters:

  graphics - graphics

• setDrawVOIs

  public void setDrawVOIs​(boolean drawVOIs)

• paintComponentForPrinter

  public void paintComponentForPrinter​(int tx,
                                       int ty,
                                       java.awt.Graphics g)

  Paints the image and calls drawSelf for all VOIs and also resizes the image if it is too big for printer.

  Parameters:

  tx - x translation

  ty - y translation

  g - graphics

• paintMagComponent

  public void paintMagComponent​(java.awt.Graphics2D graphics2d)

  Paints a magnified window over the image centered about the cursor.

  Parameters:

  graphics2d - graphics component

• quickSwitchBrush

  public void quickSwitchBrush()

  Backups up ( and swaps if not null) the current and previously used paintBrush.

• regionGrow

  public void regionGrow​(java.lang.String str)

  Grows a region based on a starting supplied. A voxel is added to the the paintBitmap mask if its intensity is between previously supplied bounds.

  Specified by:

  regionGrow in interface PaintGrowListener

  Parameters:

  str - the string to prepend to message containing region growth statistics

• regionGrow

  public void regionGrow​(short x,
                         short y,
                         short z,
                         float value,
                         java.lang.String str,
                         boolean click)

  Grows a region based on a starting supplied. A voxel is added to the the paintBitmap mask if its intensity is between the the bounds which are also supplied. Used on black and white images.

  when click false, adds points in the newly grown region which weren't in the old one remove points which were in the old region but aren't in the new one (and which weren't in the region painted before the last click), otherwise, the regions are simply added into the new set.

  Parameters:

  x - x coordinate of the seed point

  y - y coordinate of the seed point

  z - z coordinate of the seed point

  value - Intensity value at the seed point

  str - String to start line with

  click - whether this region grow was initiated by a click on the image

• regionGrow

  public void regionGrow​(short x,
                         short y,
                         short z,
                         float value,
                         ModelImage image,
                         java.lang.String leadString,
                         boolean click)

  Grows a region based on a starting supplied. A voxel is added to the the paintBitmap mask if its intensity is between the the bounds which are also supplied. Used for black and white images.

  When click is false, adds points in the newly grown region which weren't in the old one remove points which were in the old region but aren't in the new one (and which weren't in the region painted before the last click), otherwise, the regions are simply added into the new set.

  Parameters:

  x - x coordinate of the seed point

  y - y coordinate of the seed point

  z - z coordinate of the seed point

  value - Intensity value at the seed point

  image - the image to perform the region grow in

  leadString - the string to append to the region grow output

  click - whether this region grow was initiated by a click on the image

• regionGrow

  public void regionGrow​(short x,
                         short y,
                         short z,
                         float valueR,
                         float valueG,
                         float valueB,
                         java.lang.String str,
                         boolean click)

  Grows a region based on a starting supplied. A voxel is added to the the paintBitmap mask if its intensity is between the the bounds which are also supplied. Used on color images.

  when click false, adds points in the newly grown region which weren't in the old one remove points which were in the old region but aren't in the new one (and which weren't in the region painted before the last click), otherwise, the regions are simply added into the new set.

  Parameters:

  x - x coordinate of the seed point

  y - y coordinate of the seed point

  z - z coordinate of the seed point

  valueR - Red intensity value at the seed point

  valueG - Green intensity value at the seed point

  valueB - Blue intensity value at the seed point

  str - String to start line with

  click - whether this region grow was initiated by a click on the image

• regionGrow

  public void regionGrow​(short x,
                         short y,
                         short z,
                         float valueR,
                         float valueG,
                         float valueB,
                         ModelImage image,
                         java.lang.String leadString,
                         boolean click)

  Grows a region based on a starting supplied. A voxel is added to the the paintBitmap mask if its intensity is between the the bounds which are also supplied. Used for color images.

  When click is false, adds points in the newly grown region which weren't in the old one remove points which were in the old region but aren't in the new one (and which weren't in the region painted before the last click), otherwise, the regions are simply added into the new set.

  Parameters:

  x - x coordinate of the seed point

  y - y coordinate of the seed point

  z - z coordinate of the seed point

  valueR - Red value at the seed point

  valueG - Green value at the seed point

  valueB - Blue value at the seed point

  image - the image to perform the region grow in

  leadString - the string to append to the region grow output

  click - whether this region grow was initiated by a click on the image

• regionGrowColor

  public void regionGrowColor​(java.lang.String str)

  Grows a region based on a starting supplied. A voxel is added to the the paintBitmap mask if its intensity is between previously supplied bounds.

  Parameters:

  str - the string to prepend to message containing region growth statistics

• rememberPaintBrushSize

  public void rememberPaintBrushSize()

  Remembers the current paint brush size so that it can be reset later.

• resetLUTs

  public void resetLUTs()

  Resets the LUTs.

• resetPaintBrushSize

  public void resetPaintBrushSize()

  Resets the paint brush size to the remembered value.

• 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

• readLUTandTFunctFrom

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

  This method reads a LUT and Transfer function from a file diretory specified.

  Parameters:

  filename - filename of LUT

  dirName - directory of LUT

• saveUDLUT

  public void saveUDLUT()

  Save user defined LUT table.

• setActiveImage

  public void setActiveImage​(int active)

  Sets the active image for drawing VOIs.

  Parameters:

  active - IMAGE_A or IMAGE_B

• setAlphaBlend

  public void setAlphaBlend​(int value)

  Sets the alpha blending of parameter for two image displaying.

  Parameters:

  value - amount [0,100] that is the percentage of Image A to be displayed

• setBuffers

  public void setBuffers​(float[] imgBufferA,
                         float[] imgBufferB,
                         int[] pixBuff,
                         int[] pixBuffB)

  The frame in which the image(s) is displayed, allocates the memory and uses this method to pass the references to the buffers.

  Parameters:

  imgBufferA - storage buffer used to display image A

  imgBufferB - storage buffer used to display image B

  pixBuff - storage buffer used to build a displayable image

  pixBuffB - storage buffer used to build a displayable imageB for the window

• setCheckerboard

  public void setCheckerboard​(int rowCheckers,
                              int columnCheckers)

  Sets the image to display in "Checkerboard" mode with the given numbers of rows and columns.

  Parameters:

  rowCheckers - int # of rows

  columnCheckers - int # of columns

• setCrosshairCursor

  public void setCrosshairCursor​(java.awt.Cursor curs)

  Changes the Crosshair cursor to be either the default crosshair or a pre-existing gif.

  Parameters:

  curs - the new crosshair cursor

• setCursorMode

  public void setCursorMode​(int mode)

  Switches modes based on the variable mode. Sets voiHandler.getRubberband() activity and the cursor.

  Parameters:

  mode - the integer mode

• setDisplayFuzzy

  public void setDisplayFuzzy​(boolean val)

  Sets whether a fuzzy image is displayed.

  Specified by:

  setDisplayFuzzy in interface PaintGrowListener

  Parameters:

  val - whether to show the fuzzy connectedness image

• setEnabled

  public void setEnabled​(boolean flag)

  Enables or disables the component for modification.

  Overrides:

  setEnabled in class javax.swing.JComponent

  Parameters:

  flag - true = modify, and false = locked

• setFrameControls

  public void setFrameControls​(ViewControlsImage controls)

  Sets the frameControls.

  Parameters:

  controls - the controls with color and opacity information

• setFuzzyThreshold

  public void setFuzzyThreshold​(float val)

  Sets whether fuzzy connectedness is used and the fuzzy threshold.

  Specified by:

  setFuzzyThreshold in interface PaintGrowListener

  Parameters:

  val - the fuzzy connectedness threshold value

• setGrowDialog

  public void setGrowDialog​(RegionGrowDialog dialog)

  Sets the RegionGrowDialog for this class (usually used to set it to null).

  Specified by:

  setGrowDialog in interface PaintGrowListener

  Parameters:

  dialog - the paint grow dialog

• setHasThreshold1

  public void setHasThreshold1​(boolean hasThreshold1)

  Sets the hasThreshold1 for setPaintBuffers.

  Parameters:

  hasThreshold1 - whether the paint buffer has a threshold1

• setHasThreshold2

  public void setHasThreshold2​(boolean hasThreshold2)

  Sets the hasThreshold2 for setPaintBuffers.

  Parameters:

  hasThreshold2 - whether the paint buffer has a threshold2

• setHighlightColor

  public void setHighlightColor​(java.awt.Color c)

  Changes the color used to highlight the currently on-top image.

  Parameters:

  c - the new color to use.

• setImageA

  public void setImageA​(ModelImage image)

  Sets component's ImageA. assumes dimensionality same as image B's for now.

  Parameters:

  image - imageA

• setImageB

  public void setImageB​(ModelImage image)

  Sets component's ImageB. !!!!!! assumes dimensionality same as image A's for now will fix soon.

  Parameters:

  image - imageB

• setImageBufferB

  public void setImageBufferB​(float[] buffer)

  Sets component's ImageB buffer.

  Parameters:

  buffer - image buffer to put in the buffer for Image B

• setImageColocalize

  public void setImageColocalize​(ModelImage imageColocalize)

  Sets the colocalize image.

  Parameters:

  imageColocalize - the colocalization image

• setImageExtents

  public void setImageExtents​(int[] imageExtents)

  DOCUMENT ME!

  Parameters:

  imageExtents - int[]

• setIntensityDropper

  public void setIntensityDropper​(float intensityDropper)

  Sets the intensityDropper intensity.

  Parameters:

  intensityDropper - the dropper intensity

• setLess

  public void setLess​(float val)

  Sets less for regionGrow.

  Specified by:

  setLess in interface PaintGrowListener

  Parameters:

  val - lower region grow delta

• setLessB

  public void setLessB​(float val)

  Sets lessB for regionGrow.

  Parameters:

  val - lower region grow delta

• setLessG

  public void setLessG​(float val)

  Sets lessG for regionGrow.

  Parameters:

  val - lower region grow delta

• setLessR

  public void setLessR​(float val)

  Sets lessR for regionGrow.

  Parameters:

  val - lower region grow delta

• setLogMagDisplay

  public void setLogMagDisplay​(boolean flag)

  Sets the log magnitude display flag.

  Parameters:

  flag - if true display log of the Magnitude of the complex image

• setLUTa

  public void setLUTa​(ModelLUT LUT)

  accessor that sets the model LUT for the imageA.

  Parameters:

  LUT - the model LUT

• setLUTb

  public void setLUTb​(ModelLUT LUT)

  Sets the model LUTb for the imageB.

  Parameters:

  LUT - the model LUT

• setMaxDistance

  public void setMaxDistance​(int val)

  Sets maxDistance for regionGrow.

  Specified by:

  setMaxDistance in interface PaintGrowListener

  Parameters:

  val - the maximum region grow distance

• setModifyFlag

  public void setModifyFlag​(boolean flag)

  DOCUMENT ME!

  Parameters:

  flag - DOCUMENT ME!

• setMore

  public void setMore​(float val)

  Sets more for regionGrow.

  Specified by:

  setMore in interface PaintGrowListener

  Parameters:

  val - upper region grow delta

• setMoreB

  public void setMoreB​(float val)

  Sets moreB for regionGrow.

  Parameters:

  val - upper region grow delta

• setMoreG

  public void setMoreG​(float val)

  Sets moreG for regionGrow.

  Parameters:

  val - upper region grow delta

• setMoreR

  public void setMoreR​(float val)

  Sets moreR for regionGrow.

  Parameters:

  val - upper region grow delta

• setPaintBitmapSwitch

  public void setPaintBitmapSwitch​(boolean paintBitmapSwitch)

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

  Parameters:

  paintBitmapSwitch - if true do not getMask on a setActiveImage command

• setPaintBrushSize

  public void setPaintBrushSize​(int paintBrushSize)

  Switches modes based on the variable mode. Sets the number of pixels to be drawn when painting.

  Parameters:

  paintBrushSize - the integer mode

• setPaintMask

  public void setPaintMask​(java.util.BitSet mask)

  Sets the paint mask.

  Parameters:

  mask - the new paint mask

• setPixelInformationAtLocation

  public void setPixelInformationAtLocation​(int xS,
                                            int yS,
                                            boolean isControlDown)

  Prints ModelImage information at the mouse location.

  Parameters:

  xS - mouse x location

  yS - mouse y location

• isCheckerboardAnimate

  public boolean isCheckerboardAnimate()

• setCheckerboardAnimate

  public void setCheckerboardAnimate​(boolean doCheckerboardAnimate)

• isMakingCheckerboard

  public boolean isMakingCheckerboard()

• setMakingCheckerboard

  public void setMakingCheckerboard​(boolean makingCheckerboard)

• getCleanImageBufferB

  public int[] getCleanImageBufferB()

• getMaxExtents

  public int[] getMaxExtents()

• getxSep

  public int getxSep()

• setxSep

  public void setxSep​(int xSep)

• getySep

  public int getySep()

• setySep

  public void setySep​(int ySep)

• setRegionGrowVars

  public void setRegionGrowVars​(short x,
                                short y,
                                short z,
                                float val)

  Sets the variables used to remember the point where the last region grow was started from.

  Parameters:

  x - x coordinate

  y - y coordinate

  z - z coordinate

  val - intensity at the point (x,y,z)

• setRGBTA

  public void setRGBTA​(ModelRGB RGBT)

  Sets the RGB table for ARGB image A.

  Parameters:

  RGBT - RGB table

• setRGBTB

  public void setRGBTB​(ModelRGB RGBT)

  Sets the RGB table for ARGB image B.

  Parameters:

  RGBT - RGB table

• setShowMagIntensity

  public void setShowMagIntensity​(boolean flag)

  Sets whether to show intensity in mag. box

  Parameters:

  flag - whether to show intensity in mag. box

• setShowSliceNum

  public void setShowSliceNum​(boolean flag)

  Sets whether the slice number will be shown in the lower left hand corner of the image.

  Parameters:

  flag - whether to display the slice number

• setSizeLimit

  public void setSizeLimit​(int val)

  Sets sizeLimit for regionGrow.

  Specified by:

  setSizeLimit in interface PaintGrowListener

  Parameters:

  val - the maximum region grow size

• setSlice

  public void setSlice​(int _slice)

  Sets the slice of the image.

  Parameters:

  _slice - image slice to be displayed

• setStringOverride

  public void setStringOverride​(java.lang.String str)

  Sets the string painted on the lower left.

  Parameters:

  str - str that is painted on the lower left of image

• setThresholdColors

  public void setThresholdColors​(boolean useRedThreshold,
                                 boolean useGreenThreshold,
                                 boolean useBlueThreshold)

  Sets the booleans for using thresholds in setColorPaintBuffers.

  Parameters:

  useRedThreshold - whether to threshold the red paint buffer

  useGreenThreshold - whether to threshold the green paint buffer

  useBlueThreshold - whether to threshold the blue paint buffer

• setThresholds

  public void setThresholds​(float threshold1,
                            float threshold2)

  Sets the thresholds.

  Parameters:

  threshold1 - the first threshold

  threshold2 - the second threshold

• setTimeSlice

  public void setTimeSlice​(int _slice)

  Sets the time slice of the image.

  Parameters:

  _slice - the time slice to be displayed

• setUseVOI

  public void setUseVOI​(boolean val)

  Sets whether a selected VOI is used to calculate the initial variance.

  Specified by:

  setUseVOI in interface PaintGrowListener

  Parameters:

  val - whether to use the selected VOI to get the initial variance for the fuzzy regionGrow

• setVariableThresholds

  public void setVariableThresholds​(boolean variableThresholds)

  If true varies thresholds with region growth.

  Parameters:

  variableThresholds - boolean

• show

  public boolean show​(int tSlice,
                      int zSlice,
                      boolean forceShow)

  For generating the display of 1 or 2 images.

  Parameters:

  tSlice - t (time) slice to show

  zSlice - z slice to show

  forceShow - forces this method to import image and recalculate java image

  Returns:

  boolean to indicate if the show was successful

• show

  public boolean show​(int tSlice,
                      int zSlice,
                      ModelLUT _LUTa,
                      ModelLUT _LUTb,
                      boolean forceShow)

  Shows the image and the VOI(s).

  Parameters:

  tSlice - t (time) slice to show

  zSlice - z slice to show

  _LUTa - LUTa - to change to new LUT for imageA else null

  _LUTb - LUTb - to change to new LUT for imageB else null

  forceShow - forces this method to import image and recalculate java image

  Returns:

  boolean to indicate if the show was successful

• show

  public boolean show​(int tSlice,
                      int zSlice,
                      ModelLUT _LUTa,
                      ModelLUT _LUTb,
                      boolean forceShow,
                      int interpMode)

  Shows the image and the VOI(s).

  Parameters:

  tSlice - t (time) slice to show

  zSlice - z slice to show

  _LUTa - LUTa - to change to new LUT for imageA else null

  _LUTb - LUTb - to change to new LUT for imageB else null

  forceShow - forces this method to import image and recalculate java image

  interpMode - image interpolation method (Nearest or Smooth)

  Returns:

  boolean to indicate if the show was successful

• showBlank

  public boolean showBlank()

  Resets the buffer to 0s and displays a blank image.

  Returns:

  boolean to indicate that the show was successful

• showRegionInfo

  public void showRegionInfo​(int count,
                             java.lang.String leadString)

  Display statistics about the grown region.

  Specified by:

  showRegionInfo in interface PaintGrowListener

  Parameters:

  count - Number of pixels (voxels)

  leadString - the string to prepend to message containing region growth statistics

• showRegionInfo

  public void showRegionInfo​(int count,
                             float[] total,
                             float[] mean,
                             float[] stdDev,
                             java.lang.String leadString)

  Display statistics about the grown region.

  Parameters:

  count - Number of pixels (voxels)

  total - Sum of pixel intensities

  mean - Average pixel intensity

  stdDev - Standard deviation of pixel intensities

  leadString - the string to prepend to message containing region growth statistics

• showRegionInfo

  public void showRegionInfo​(int count,
                             double[] total,
                             double[] mean,
                             double[] stdDev,
                             java.lang.String leadString)

  Display statistics about the grown region.

  Parameters:

  count - Number of pixels (voxels)

  total - Sum of pixel intensities

  mean - Average pixel intensity

  stdDev - Standard deviation of pixel intensities

  leadString - the string to prepend to message containing region growth statistics

• showStatisticsCalculator

  public void showStatisticsCalculator()

  Opens a JDialogStatistics to allow computation ofROI statistics.

• undoLastPaint

  public void undoLastPaint()

  Undoes the last paint.

• updatePaint

  public void updatePaint​(java.util.BitSet region,
                          boolean backup,
                          boolean isGrower)

  Causes the image to update its paint bit mask and redisplay itself.

  Specified by:

  updatePaint in interface PaintGrowListener

  Parameters:

  region - new paint region bit set

  backup - whether to save the previous paint mask to allow the update to be un-done

  isGrower - whether this paint listener is the one that did the region grow

• updatePaintBrushCursor

  public void updatePaintBrushCursor()

  Updates the Paint Cursor's BufferedImage with the correct color/opacity.

• useHighlight

  public void useHighlight​(boolean hilite)

  Sets this component to paint the "on top" high-light. It is not required to use the coloured rectangle to high-light the on-top component, but the component is not aware of its position in the user-interface, and thus, that the user-interface controls point to it.

  Parameters:

  hilite - true will set this component to paint the 'on-top' high-light the next time it is redrawn. false, of course, will not let the component paint the coloured rectangle when repainted.

• isHighlight

  public boolean isHighlight()

• draw3DVOIs

  protected void draw3DVOIs​(java.awt.Graphics offscreenGraphics2d,
                            boolean bBlend)

• finalize

  protected void finalize()
                   throws java.lang.Throwable

  Calls dispose to dump this instance.

  Overrides:

  finalize in class ViewJComponentBase

  Throws:

  java.lang.Throwable - DOCUMENT ME!

• getBrushSize

  protected int getBrushSize()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• getHBrushSize

  protected int getHBrushSize()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• getZoomMagnitudeX

  protected float getZoomMagnitudeX​(boolean reverse)

  DOCUMENT ME!

  Parameters:

  reverse - DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• getZoomMagnitudeY

  protected float getZoomMagnitudeY​(boolean reverse)

  DOCUMENT ME!

  Parameters:

  reverse - DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• mousePressedPaint

  protected void mousePressedPaint​(java.awt.event.MouseEvent mouseEvent)

  When a mousePressed event is triggered and the mode is DROPPER_PAINT, ERASER_PAINT, PAINT_VOI, or MAG_REGION this function is called. It is shared with the derived classes.

  Parameters:

  mouseEvent - the mouseEvent that triggered this function call.

• createImg

  public boolean createImg​(int slice)

  Creates the Java image to be displayed from the model image. Makes it from the appropriate slice.

  Parameters:

  slice - Slice of image to create java image from.

  Returns:

  Flag indicating success or failure.

• createImg

  public boolean createImg​(int timeSlice,
                           int slice)

  Creates the Java image to be displayed from the model image. Makes it from the appropriate slice.

  Parameters:

  slice - Slice of image to create java image from.

  Returns:

  Flag indicating success or failure.

• performPaint

  protected void performPaint​(java.awt.event.MouseEvent event)

  DOCUMENT ME!

  Parameters:

  event - DOCUMENT ME!

• performPaint

  protected void performPaint​(java.awt.event.MouseEvent mouseEvent,
                              boolean erase)

  This method will set or clear the paint bitmap as the user paints on-screen.

  Parameters:

  mouseEvent - MouseEvent the mouseEvent associated with this paint action

  erase - boolean if true, paintBitmap is cleared (erased), otherwise paintBitmap is set (painted)

• processDefaultMouseDrag

  protected void processDefaultMouseDrag​(java.awt.event.MouseEvent mouseEvent,
                                         int xS,
                                         int yS)

  processDefaultMouseDrag performs the mouseDrag operations when in DEFAULT mode. The default operation when the right mouse button is held down is the window-level image adjustment, and setting the ModelImage information at the pixel location. This function in shared with the deried classes.

  Parameters:

  mouseEvent - the mouse event

  xS - the mouse x location on screen

  yS - the mouse y location on screen

• adjustOpacityFor000Color

  private void adjustOpacityFor000Color()

  >>>>>>> .r533 The purpose of this method is to examine both LUTs to determine if they are zero-based, that is, if they map values of zero to the color R=0, G=0, B=0. If the LUT does, in fact, do this, then this method ensures that those pixels are completely transparent so that no blending takes place for those pixels.

• backupPaintBitmap

  private void backupPaintBitmap()

  Backs up the paintBitmap into the paintBitmapBU variable.

• cleanBuffer

  private void cleanBuffer​(int buffer)

  DOCUMENT ME!

  Parameters:

  buffer - DOCUMENT ME!

• drawImageText

  private void drawImageText​(java.awt.Graphics2D offscreenGraphics2d)

  Draws text onto the image, such as the slice number.

  Parameters:

  offscreenGraphics2d - Graphics2D graphics context to draw in

• getZoomMagnitude

  private float getZoomMagnitude​(float zoom,
                                 boolean reverse)

  Returns the magnitude zoom depending on the zoom mode.

  Parameters:

  zoom - the zoom factor (x or y)

  reverse - for reverse zoom

  Returns:

  the calculated zoom factor

• makeCheckerboard

  private void makeCheckerboard()

  Sets the number of checkers in a row and a column.

• loopBandSpacing

  public void loopBandSpacing()

• loopBandSpacingReverse

  public void loopBandSpacingReverse()

• getBandSpacing

  public int[] getBandSpacing()

• setBandSpacing

  public void setBandSpacing​(int[] bandSpacing)

• getxStart

  public int[] getxStart()

• getyStart

  public int[] getyStart()

• getyMod

  public int getyMod()

• getxMod

  public int getxMod()

• repaintImageIntensityLabelFast

  private void repaintImageIntensityLabelFast​(java.awt.Graphics2D graphics2d)

  Repaints the image intensity label.

  Parameters:

  graphics2d - Graphics2D the graphics context to draw in

• repaintPaintBrushCursorFast

  private void repaintPaintBrushCursorFast​(java.awt.Graphics2D graphics2d)

  Repaints the paint brush cursor without repainting the entire image.

  Parameters:

  graphics2d - Graphics2D the graphics context to draw in

• resetLUT

  public void resetLUT​(ModelLUT LUT,
                       ModelImage image)

  DOCUMENT ME!

  Parameters:

  LUT - DOCUMENT ME!

  image - DOCUMENT ME!

• resetRGB

  private void resetRGB​(ModelRGB RGBT)

  DOCUMENT ME!

  Parameters:

  RGBT - DOCUMENT ME!

• setZeroToOneLUTAdj

  public void setZeroToOneLUTAdj​(boolean zeroToOneLUTAdj)

  Parameters:

  zeroToOneLUTAdj -

• isZeroToOneLUTAdj

  public boolean isZeroToOneLUTAdj()

  Returns:

• fileToScreen

  public WildMagic.LibFoundation.Mathematics.Vector3f fileToScreen​(WildMagic.LibFoundation.Mathematics.Vector3f kFile)

• patientToScreen

  public WildMagic.LibFoundation.Mathematics.Vector3f patientToScreen​(WildMagic.LibFoundation.Mathematics.Vector3f kPt)

• screenToFile

  public boolean screenToFile​(int iX,
                              int iY,
                              int iZ,
                              WildMagic.LibFoundation.Mathematics.Vector3f kVolumePt)

• screenToFile

  public boolean screenToFile​(WildMagic.LibFoundation.Mathematics.Vector3f kScreen,
                              WildMagic.LibFoundation.Mathematics.Vector3f kFile)

• screenToFile

  public WildMagic.LibFoundation.Mathematics.Vector3f screenToFile​(WildMagic.LibFoundation.Mathematics.Vector3f kScreen)

• upSlice

  public WildMagic.LibFoundation.Mathematics.Vector3f upSlice()

  Increments the current slice in local coordinates and returns the new position in the view-independent file coordinates.

  Returns:

• downSlice

  public WildMagic.LibFoundation.Mathematics.Vector3f downSlice()

  Decrements the current slice in local coordinates and returns the new position in the view-independent file coordinates.

  Returns:

• getGridColor

  public java.awt.Color getGridColor()

  get the color of the grid.

  Returns:

  Color grid color

• getGridLabeling

  public boolean getGridLabeling()

  Whether or not labels should be drawn on the grid overlay.

  Returns:

  boolean

• getGridLabelOrientation

  public boolean getGridLabelOrientation()

  DOCUMENT ME!

  Returns:

  DOCUMENT ME!

• getGridOverlay

  public boolean getGridOverlay()

  returns whether grid overlay is being displayed.

  Returns:

  boolean is grid overlay on?

• getGridSpacingX

  public float getGridSpacingX()

  returns the grid spacing in terms of resolution.

  Returns:

  float grid spacing

• getGridSpacingY

  public float getGridSpacingY()

  returns the grid spacing in terms of resolution.

  Returns:

  float grid spacing

• setGridColor

  public void setGridColor​(java.awt.Color color)

  set the color of the grid.

  Parameters:

  color - Color

• setGridLabelingOn

  public void setGridLabelingOn​(boolean doLabel)

  Tells the grid overlay (if on) to show abc/123 labeling.

  Parameters:

  doLabel - boolean

• setGridLabelOrientation

  public void setGridLabelOrientation​(boolean or)

  Sets the axis orientation of abc and 123 labeling of the grid overlay.

  Parameters:

  or - boolean true = x-axis numbered, false = x-axis lettered

• setGridOverlay

  public void setGridOverlay​(boolean flag)

  Sets whether or not to show the NEI grid overlay.

  Parameters:

  flag - boolean show grid overlay (or not!)

• setGridSpacingX

  public void setGridSpacingX​(float spacing)

  sets the grid spacing (horizontal) in terms of resolution.

  Parameters:

  spacing - float new grid spacing

• setGridSpacingY

  public void setGridSpacingY​(float spacing)

  sets the grid spacing (horizontal) in terms of resolution.

  Parameters:

  spacing - float new grid spacing

• getVOIManager

  public VOIManager getVOIManager()

• setVOIManager

  public void setVOIManager​(VOIManager kManager)

• getOverlayOn

  public boolean getOverlayOn()

  Returns if image/dicom overlay should be shown.

  Returns:

  boolean is the overlay shown

• setOverlay

  public void setOverlay​(boolean flag)

  Sets whether or not to show the overlay.

  Parameters:

  flag - boolean that tells whether or not to show the overlay

• showGridOverlay

  protected void showGridOverlay​(java.awt.Graphics g)

  Draws a grid on top of the image according to the gridSpacingX and gridSpacingY.

  Parameters:

  g - Graphics the graphics used to draw

• showOverlay

  public void showOverlay​(java.awt.Graphics g)

  Displays Image overlays (DICOM or image attributes).

  Parameters:

  g - Graphics object used to paint and display the strings.

• buildOverlayStrings

  private java.lang.String buildOverlayStrings​(FileInfoBase inf,
                                               java.lang.String name,
                                               java.lang.String attribString)

  Builds the overlay Strings from the tag's value. Concatenates the output strings from the tags and ensures that any properly read-in string has usable (if empty) values.

  Parameters:

  inf - The FileInfo with DICOM tags to display.

  name - DOCUMENT ME!

  attribString - Key of tag to display.

  Returns:

  null when value is not a String or when the tag does not exist.

• fileToScreenVOI

  public WildMagic.LibFoundation.Mathematics.Vector3f fileToScreenVOI​(WildMagic.LibFoundation.Mathematics.Vector3f kFile)

  Description copied from interface: ScreenCoordinateListener
  Converts image file X,Y,Z coordinates into local screen coordinates.

  Specified by:

  fileToScreenVOI in interface ScreenCoordinateListener

  Parameters:

  kFile - image file coordinates.

  Returns:

  local screen coordinates.

• patientToScreenVOI

  public WildMagic.LibFoundation.Mathematics.Vector3f patientToScreenVOI​(WildMagic.LibFoundation.Mathematics.Vector3f kPt)

  Description copied from interface: ScreenCoordinateListener
  Converts local patient coordinate view (Axial, Coronal, Sagittal) of the image into the screen coordinates.

  Specified by:

  patientToScreenVOI in interface ScreenCoordinateListener

  Parameters:

  kPt - local patient (Axial, Coronal, Sagittal) coordinates.

  Returns:

  screen coordinate representation of the input point.

• screenToFileVOI

  public boolean screenToFileVOI​(int iX,
                                 int iY,
                                 int iZ,
                                 WildMagic.LibFoundation.Mathematics.Vector3f kVolumePt)

  Description copied from interface: ScreenCoordinateListener
  Converts local screen coordinates, usually from a MouseEvent, into image file coordinates.

  Specified by:

  screenToFileVOI in interface ScreenCoordinateListener

  Parameters:

  iX - input X position in local screen coordinates.

  iY - input Y position in local screen coordinates.

  iZ - input slice position in the local image orientation, or z=0 for 2D images.

  kVolumePt - image file coordinates return value.

  Returns:

  returns true if the screen coordinate is clipped (is outside the displayed image space).

• screenToFileVOI

  public WildMagic.LibFoundation.Mathematics.Vector3f screenToFileVOI​(WildMagic.LibFoundation.Mathematics.Vector3f kScreen)

  Description copied from interface: ScreenCoordinateListener
  Converts local screen coordinates, usually from a MouseEvent, into image file coordinates.

  Specified by:

  screenToFileVOI in interface ScreenCoordinateListener

  Parameters:

  kScreen - input X,Y,Z position in local screen coordinates, where z = local image slice or 0 for 2D images.

  Returns:

  image file coordinates.

• screenToFileVOI

  public boolean screenToFileVOI​(WildMagic.LibFoundation.Mathematics.Vector3f kScreen,
                                 WildMagic.LibFoundation.Mathematics.Vector3f kFile)

  Description copied from interface: ScreenCoordinateListener
  Converts local screen coordinates, usually from a MouseEvent, into image file coordinates.

  Specified by:

  screenToFileVOI in interface ScreenCoordinateListener

  Parameters:

  kScreen - input X,Y,Z position in local screen coordinates, where z = local image slice or 0 for 2D images.

  kFile - image file coordinates return value.

  Returns:

  true if the screen coordinate is clipped (is outside the displayed image space).

• setCenter

  public void setCenter​(WildMagic.LibFoundation.Mathematics.Vector3f center)

  Description copied from interface: ScreenCoordinateListener
  Sets the currently displayed image slice.

  Specified by:

  setCenter in interface ScreenCoordinateListener

• getImageTimeStamp

  private java.lang.String getImageTimeStamp()

  Get the system timestamp.

  Returns:

• getTime

  private java.lang.String getTime()

  Get the system timestamp.

  Returns:

• setEyetrackerRecordingMode

  public void setEyetrackerRecordingMode​(int modeType)

  Set the eye tracking recording mode type

  Parameters:

  modeType -

• setEyetrackerRecordMode

  public void setEyetrackerRecordMode​(int modeType)

• recordZoom

  public void recordZoom​(boolean zoomIn)

• recordPanning

  public void recordPanning()

• recordLineMeasure

  private void recordLineMeasure()

• setImageSlice

  public void setImageSlice​(int slice)

  Set the image slice number, and recording the action as slider changes on single eye tracker viewer.

  Parameters:

  slice -

• setWindLevel

  public void setWindLevel​(int window,
                           int level)

  Set the window level value from the eye tracker

  Parameters:

  window -

  level -

• ctMode

  public void ctMode​(int preset1,
                     int preset2)

  Sets mode to CT and sets range to CT presets.

  Parameters:

  preset1 - first CT preset

  preset2 - second CT preset