Graphical User Interface

The main JIV window is composed of one or more ``panels'' -- columns of interface elements separated by vertical lines. Each panel has a title indicating its content and type. There are two kinds of panels:

combined data volume panel

Has a title of the form ``vol_name1 <-> vol_name2'', and displays a combined view of two 3D data volumes.

individual data volume panel

Has a title of the form ``vol_name'', and displays a single 3D data volume.

The two data volumes that are displayed together in a combined volume panel are always displayed in their individual panels as well.

JIV allows its main window to be resized at will (using the techniques specific to your platform and windowing environment). However, if the window is too small (especially if it's too narrow for the number of displayed panels) some interface components may overlap in a confusing way, or even become completely obscured.

Common panel features

Each panel is composed of four visible main elements, aligned in a vertical column; from top to bottom, they are:

1. ``Transverse'' 2D slice viewport ($Z = const$).
2. ``Sagittal'' 2D slice viewport ($X = const$).
3. ``Coronal'' 2D slice viewport ($Y = const$).
4. Panel controls area.

The $x, y, z$ axes and their positive direction are (respectively): left to right, posterior to anterior, and inferior to superior of the head. Besides the (always visible) controls area at the bottom of the panel, additional controls are available through a panel-specific pop-up menu.

Slice viewport

Inside a 2D slice viewport, the following mouse actions are available:

primary-mouse-button

Moves the cursor to a new position in slice's plane. Can also drag the cursor around.

secondary-mouse-button

Combined with a vertical mouse movement, moves the cursor along the axis orthogonal to slice's plane (i.e. changes the displayed slice). The cursor displacement is proportional to the relative vertical mouse drag movement. This operation can also be performed using keyboard commands (see below).

Shift or Ctrl + primary-mouse-button

Moves the field of view (i.e. does a pan) by following the mouse drag movement.

Shift or Ctrl + secondary-mouse-button

Combined with a vertical mouse movement, changes the zoom/scaling factor. The change in the scaled image dimensions is proportional to the relative vertical mouse drag movement.

double-click primary-mouse-button

Marks the current cursor position as the origin (first point) for the in-slice distance measurement. Also, it enables the distance measurement mode, if necessary.

double-click secondary-mouse-button

Disables the distance measurement mode.

The meaning of ``primary'' and ``secondary'' mouse buttons is provided by the Java implementation used to run JIV, and is platform-dependent -- e.g. on a Unix/X-Windows platform, with the common right-handed mouse configuration, primary is the left button, and secondary is either of the middle or right mouse buttons. On all platforms, the secondary button can be emulated by pressing the Meta or Alt key together with the primary button.

The following keys can be used for changing the displayed slice - that is, moving the cursor along the coordinate axis orthogonal to slice's plane by an amount of 1mm (one voxel):

• Right($\rightarrow$), Up($\uparrow$), or + : positive increment (next slice).
• Left($\leftarrow$), Down($\downarrow$), or - : negative increment (previous slice).

The in-slice distance measurement feature interactively displays the world-coordinates distance between the origin (``marked point'') and the current cursor position. The value is always given in real world units (mm). The measurement origin is preserved across slice changes, same as the current in-slice cursor position is. The following keys can also be used for controlling this measurement feature:

• d : same as double-click primary-mouse-button (see above).
• c : same as double-click secondary-mouse-button (see above).

The image scaling (i.e. zoom-up/down) is done using nearest-neighbour interpolation: pixels are replicated (for enlargements) or skipped (for reductions) as needed.

When the viewport dimensions change (as a consequence of the main window being resized), JIV will adjust the field of view such that it's not less than the previous field of view, while at the same time using as much of possible of the new viewport area.

Controls area

The controls area of each panel has, at the top, a group of three text fields that display the current $X,Y,Z$ coordinates of the cursor in that panel. These fields also allow editing (text input) - the usual text editing commands of your platform should work. If a value out of range is given, the field will revert to its previous (valid) value. The coordinates displayed (and read in) are voxel or world coordinates, depending on the current panel setting.

Any horizontal sliders present in this area are implemented using platform-specific scrollbars, thus their behaviour in response to mouse (and maybe keyboard) actions should be similar to the other scrollbars on your computer platform (and/or windowing system).

Pop-up menu

The mouse and/or keyboard command that brings up the pop-up menu is the usual one for triggering context-sensitive (pop-up) menus on your particular computer platform -- e.g. on Unix and on Microsoft Windows, it's usually the right (second or third) mouse button.

The following menu actions are available in all panels:

• Coordinates type [choice] : Changes the type of coordinates that are displayed, and read in, in the controls area at the bottom.
• Sync all cursors [toggle] : If on, the cursor positions in all panels will be kept the same. When changing this control from off to on, all cursors will be set to the cursor position of the first panel (from the left).
• Help [menu]: Provides access to the JIV version and copyright info (the About command), and to this help document (the Help command). If JIV is running as an applet in a web browser, the online help file should be opened in a new browser window¹. The online help is not available if JIV is running as a standalone application.
• Quit : Closes the JIV window and exists the application. However, when running JIV using a web browser or an appletviewer, this action is probably not enough; in order to completely dispose of this running copy of the JIV applet you may have to move out of the HTML document that launched it, or maybe even close that browser frame/window. To make things worse, some web browsers don't release the (possibly large amount of) memory formerly used by the applet unless you completely shutdown the browser!

Individual volume panel features

The 8-bit intensity values in the data volume are displayed in the viewports using a user-controlled colormap. This is composed of a certain color-coding scheme (in between adjustable lower and upper limits), an ``under'' color (below the lower color-coding limit) and an ``over'' color (above the upper color-coding limit).

Controls area

To the left of the three coordinate fields, there's a read-only text field displaying the voxel (intensity) value at the cursor position.

Below the coordinate text fields, there are controls for the lower color-coding limit (left text display/entry field and lower slider) and for the upper color-coding limit (right text display/entry field and upper slider). The lower limit can never be higher than the upper limit.

The values displayed (or read in) by the voxel intensity and lower/upper color-coding limit text fields can be a fractional ones (in the range 0.0-1.0) or byte values (in the range 0-255), depending on how this instance of JIV was configured.

The current colormap is displayed as a color bar at the very bottom of the panel.

Pop-up menu

The following menu actions are available in the individual volume panels only:

• Color coding [choice] : Changes the color-coding scheme.
• "Under" color [choice] : Changes the ``under'' color ((default) means the same color as the one at color-coding's lower limit).
• "Over" color [choice] : Changes the ``over'' color ((default) means the same color as the one at color-coding's upper limit).
• Tie colormap sliders [toggle] : If on, the two color-coding limits behave like being connected together by a solid rod -- adjusting one value implies changing the other one such that their difference (``distance'') remains the same.

Combined volume panel features

The coloring of each of the two data volumes is the one from the individual volume panel representing that data volume. If a data volume (i.e. a volume alias) is displayed by more individual volume panels, then the left-most such panel is used as the coloring source for that data volume.

Currently, the only method available for combining (``compositing'') the two data volumes is blended: the color of each pixel of the combined image is given by

$$color\_in\_volume\_1 \times ( 1 - \beta ) + color\_in\_volume\_2 \times \beta$$

where $\beta$ is the blend factor: a fractional value in the range 0.0-1.0 (this compositing is done in RGB color space).

Controls area

Below the coordinate text fields, there is a blend factor ($\beta$) slider, surrounded by two text display/entry fields: the left one for $1 - \beta$, and the right one for $\beta$. In other words, these two text fields contain the weighting factors for the two combined data volumes.