Subsections


8 Control of map3d

This section describes all the means of controlling the function of map3d, at least all the ones we are willing to tell you about.

8.1 Control by surface

There is an ever growing number of parameters that the user can alter for displaying the surfaces in map3d. Some of the more important (and stable) include the following:

Visibility:
of points, mesh, potentials, vectors, etc, can all be controlled individually by using the appropriate function key (see Section 8.2.2),
Lead markings:
of the nodes in the geometry according to their node number, channel number, lead number or even value,
Scaling:
scaling of value to colour and to contour line values,
Landmarks:
appearance of the landmarks on the surface.

Since this level of control is provided for each surface, it is possible to have points showing on one surface, mesh on another, and rendered potential shading on a third, and so on.


8.1.1 Selecting which surface to control

To control the display of each surface, be that a surface in its own window or sharing a single window with other surfaces, a user must select that surface. Otherwise, display options will affect all the surfaces. There are two different multi-surface situations and each has its own method of selecting the surface:

Selecting surfaces for display controls
Multi-surface layout Selection method
One surface per window Mouse location establishes currently active window.
Several surfaces in one window Up/down arrows selects the surface. Hitting the up-arrow key after selecting the last surface selects all surface.

Note that in the surface window, the lock icons in the lower left corner indicate if parameter settings act on all surface (locks visible) or just single surfaces (locks invisible). Each lock controls a different aspect of map3d:

General Lock:
is represented by the yellow (or first) lock icon. When this lock is active, menu items and keyboard commands pertain to all surfaces. To turn this lock off and on use the up and down arrow keys.
Transformation Lock:
is represented by the red (or second) lock icon. When this lock is active, rotation and translation pertain to all surfaces. To turn this lock on and off, use the ``t'' key.
Frame Lock:
is represented by the blue (or third) lock icon. When this lock is active, frame advancing, retreating, and resetting pertain to all surfaces. To turn this lock on and off, use the ``f'' key or select from the menu under Frame Controls.

Note: in the case where all surfaces are in the same window, unlocking the general lock by means of the up or down arrow keys selects the single surface to display. However, when the general lock is active and either of the other locks is disabled, the active surface mesh appears in a different color (blue by default). This identifies the selected surface and all modifications apply to this surface. To select the desired surface use the (/) keys; ``('' selects the next surface and ``)'' selects the previous.

8.2 Mouse control, keyboard mapping, dials, and menus

Direct interactive control of map3d is by the keyboard and mouse. Many option are available via the menus controlled with the right mouse button, while others can be activated or toggled with single keystrokes. Variable (non-binary) adjustments usually occur through dialogues, or by repeating keystrokes. Below are tables of all the current control devices and their function. When the program launches, the user sets one or more windows which can be resized and moved at any time. When launching the program with the -b option, the resulting borderless sub-window(s) can still be moved and resized within a main window using the Alt-key together with the left and middle mouse buttons respectively.

8.2.1 Mouse control

The mouse can be used for different purposes depending on the current mode. This is especially important when picking is selected. To shift between modes requires simultaneous pressing of the various modifier keys, shift, control, alt. Figure 3 shows the various actions of the mouse buttons.

Figure 3: Mouse action for map3d. Picking makes intensive use of the mouse, as does moving objects in the surface window.
 
mouse action

8.2.1.1 In surface windows:

when the mouse is over a surface window, mouse buttons have the following actions:
Mouse Actions
Control Key Button Action
None Left rotation objects
  Middle scale objects (downwards increases size, upwards decreases size)
  Right activate pull-down menu
Cntrl Left pick a node (and if time series data is present, select the channel to display in the time series window)
  Middle no action
  Right no action
Shift Left translate objects
  Middle scale objects (rotates clipping planes if they are active - more info later)
  Right no action

8.2.1.2 In borderless windows:

when the mouse is over a surface within a borderless main window (-b option), the buttons have the following additional actions:
Mouse Actions
Control Key Button Action
Alt Left Move a single surface subwindow
  Middle Resize single surface subwindow (no indication of change until release of mouse button).
  Right no action

Note: if map3d does not respond as described in these tables, it could be that your window manager is grabbing the mouse/key combinations for its own purpose or maps the keys a little differently. This will require some setting changes for the window manager. To make such changes under IRIX, examine the .4Dwmrc file; in Linux there is usually a control panel or utility application to manage all window system interactions.


8.2.2 Keyboard controls

Each key of the regular keyboard, the function keys, and the keypad may be mapped to some function of the map3d. Some keyboard keys serve as toggles to change between a mode being on or off, e.g., ``n'' toggles the display of node markings. Others cycle through a set of choices, e.g., ``m'' runs through a series of display options for the mesh. A list of the keyboard keys and their functions is shown in table 1 and table 2 describes the action for each of the function and arrow keys, and table 3 the actions of the keypad keys. The keys affect action only in the Geometry Window unless otherwise specified.


Table 1: Keyboard controls for Geometry Window in map. When control contains both lower and upper cases of a letter, one cycles through a parameter in one direction and the other in the reverse direction. Note that when clipping is active, the screen information disappears.
Regular keyboard
a/A-key Switch colour tables
c-key Toggle contour draw
d-key Toggle depth cueing
f-key Toggle frame lock (also in Time signal window)
i-key Toggle ``direction'' (invert) of color table
l-key Toggle use of lighting
m/M-key Step through mesh/node drawing options
n-key Toggle display of node labels (some node marking must be selected)
p-key Toggle information in time signal (pick) window (also in Time Signal Window)
q-key Quit or destroy a sub-window - Legend Window and Time Signal Window only (Escape quits the whole program)
r-key Reset to startup conditions
R-key Reset shading model (to wireframe rendering)
s/S-key Cycle through the various surface data draw options
t-key Toggle transformation lock
x-key Draw axis
Escape Quit the program, if pressed in a Geometry Window, or Destroys a Time Signal Window if pressed there.
+/- key Increases/Decreases size of of currently-selected object (see Section 8.4.3)
(/) key Changes which susrface inside a window will be affected when the general lock is on but the transform or frame lock is off (see Section 8.1.1)
Clipping Controls
<-key Toggle front clipping plane
>-key Toggle rear clipping plane
[/]-key Move front clipping plane in (initially) +z/-z direction respectively
{/}-key Move rear clipping plane in (initially) +z/-z direction respectively
,-key Lock/Unlock clipping plane rotation with object rotation (when unlocked, shift-Middle-click rotates clipping planes)
.-key Lock/Unlock clipping planes from each other. When active, clipping planes move together



Table 2: Control of map3d via the arrow keys
Arrow Keys
Left Arrow Key Retreat by current frame step (Also in Time Signal Window)
Right Arrow Key Advance by current frame step (Also in Time Signal Window)
Up Arrow key Select next surface
Down Arrow Key Select previous surface



Table 3: Keypad controls in map3d - have NUM-Lock off for these to work properly. Again, based on how you have your keys mapped, you might have to use the non-keypad keys, but something should work for you for each key.
Keypad Keys
Ctrl-Keypad Left-arrow Y-axis rotate, CW (left) Ctrl-Keypad Right-arraow Y-axis rotate, CCW (right)
Ctrl-Keypad Up-arrow X-axis rotate, CCW (down) Ctrl-Keypad Down-arrow X-axis rotate, CW (up)
Ctrl-Keypad Home Z-axis rotate, CCW Ctrl-Keypad PgUp Z-axis rotate, CW
Ctrl-Keypad End Zoom down Ctrl-Keypad PgDn Zoom up
Alt-Keypad Left-Arrow -X-translation (left) Alt-Keypad Right-Arrow +X-translation (right)
Alt-Keypad Down-Arrow -Y-translation (down) Alt-Keypad Up-Arrow +Y-translation (up)
Alt-Keypad Home -Z-translation (away) Alt-Keypad PgUp +Z-translation (towards)
Plus/Minus key Increase/Decrease size of currently-selected object. (see Section 8.4.3)



8.2.3 Menu layout

Access to the menus is by means of the right mouse button, as per the usual OpenGL convention. Below is a series of tables of the menu layout for map3d's Geometry Window.


Table 4: The overall menu structure of the Geometry Window
Overview of Geometry Window menus
Surface Data display features of the scalar data displayed on the mesh
Scaling links between data values and color
Mesh display features of the mesh
Contours number or spacing and display features of the contours
Picking selecting times signals, mesh information, or other direct interactions with the display via the mouse
Node marking marking of the nodes
Graphics general display features such as lighting, clipping, and depth cueing
Landmarks features for toggling and displaying landmarks
Frame Controls modifying frame controls
Window Attributes features of the windows such as color and text labels
.



Table 5: Submenus to control the display of scalar data on the mesh.
Surface Display Menus
Color    
  Rainbow use rainbow color map to render scalar values on the mesh
  Green to red use green to red color map
  White to Black use black and white color map
  Invert invert the sense of any color map, e.g., black becomes white and white becomes black
Render style    
  None Turn Shading off
  Flat colour each mesh element in a constant color according to the mean value of scalar data over the vertices
  Gouraud shade each polygon using linear interpolation
  Banded draw the regions between contour lines as bands of constant color
Toggle surface display toggle display of the scalar data on the mesh (without changing other settings)



Table 6: Menu for scaling, the mapping from data value to color for rendering.
Scaling Menus
Scaling... opens up the scaling dialog. (see Section 8.5.3)
Range    
  Local scale based on the local extrema for each surface and time instant
  Global over all frames in one surface scale based on the extrema over the full times series
  Global over all surfaces in one frame scale based on the extrema over each surface for the local time instant
  Global over all surfaces and frames scale based on the extrema over all surfaces and all time instants
  Scaling over groups in one frame scale based on the extrema over each surface in specified group for the local time instant
  Scaling over groups in all frames scale based on the extrema over each surface in a specified group for all time instants
  Slave Scaling over one frame scale based on the extrema over each surface's master surface (set with -sl in command line) for one time instant
  Slave Scaling over all frames scale based on the extrema over each surface's master surface (set with -sl in command line) for all time instants
  Command-line specified range scale based on the extrema set in -ph/-pl options
Function    
  Linear linear mapping between value and color
  Logarithmic color changes as log(value)
  Exponential color changes as exp(value)
  Lab standard color reflects lab standard
  Lab 13 standard color reflects lab 13 standard
Mapping    
  True use true extrema
  Symmetric about zero take largest of absolute values of extrema to determine scaling
  Separate about zero scale positive and negative portions of the scale independently
Grouping    
  Move to group # Select a group to place the current surface (make sure the general (yellow) lock is off, or all surfaces will be placed in that group)



Table 7: Submenus for the Mesh Display menu
Mesh render menu
Files... Opens the Map3d Files Dialog (see Section 8.5.1)
Render as    
  None Do not render the mesh
  Elements render filled surfaces for all elements
  Connectivity render connectivity mesh
  Elements and connectivity rendered front facing triangles as elements and back facing as connectivity
  Points render points
  Points and connectivity render both points and connectivity
Use +/- to select Using +/- will change interactively the size of some feature.
    Use this menu to select which feature to change the size of. (see Section 8.4.3)
  Large Font Size Change the largest font size (This is the title for the Colormap and Geometry windows)
  Medium Font Size Change the medium font size (This is all text not small or large)
  Small Font Size Change the small font size (This is the size for the node marks, the axis labels in the Time Signal Window, and the Contour Labels in the ColorMap Window)
  Contour Size Change the contour width
  Line/Point Size Change the width of Lines/Points in the mesh
  Node Marks (all) Size Change the width of node marks
  Node Marks (extrema) Size  
  Node Marks (time signal) Size  
  Node Marks (leads) Size  
  Change in translation Change how fast the keyboard translation happens
  Change in scaling Change how fast the keyboard scaling happens
  Change in rotation Change how fast the keyboard rotation happens
Line/point size set the size of the mesh's points and lines
Color set the color of the mesh
Secondary Mesh Color set color of active mesh when multiple surfaces are in same window
Show Legend Window display mesh's legend window
Hide Legend Window turn off display of mesh's legend window
Reload Geometry reload file associated with this geometry
Reload Data reload file associated with this geometry's surface data
Reload Both Geometry and Data reload files associated with this geometryand its data



Table 8: Menus for contour spacing/number.
Contour Menus
Number of Contours    
  value selection of 5-50 contours
  Command line spacing use the value of contour spacing in the -cs option of the command line
Draw style    
  Dashed line for negative values draw positive contours in solid, negative in broken lines
  Solid lines for all contours draw all contours in solid lines
Line size set the line thickness
Toggle contours toggle display of contours without changing settings



Table 9: Pick mode menus. Picking is based on a mode (selectable in this menu), and is done with CTRL-left mouse button unless otherwise specified.
Picking Menus
Time Signal (new window mode) create a new time signal window with each pick of a node
Time Signal (refresh window mode) update the last time signal window with each pick of a node
Display node info mode Picking will cause certain node information to be dumped to the console.
Display triangle info mode Picking will cause information about the triangle you click in to be dumped to the console. It may be easier to pick triangles with clipping planes on.
Triangle construction/deletion Normal picking (ctrl-clicking on nodes) will select points to form a triangle (triangulate). Clicking the first two nodes in this fashion will display the selected nodes, and then a line between the two. When the third is clicked, a new triangle is displayed and added to the geometry.
  CTRL-middle clicking selects a triangle (and not nodes) to be deleted. Again, it may be easier to pick triangles with clipping planes on.
Flip triangle mode Will change the order of drawing the triangle's points. This will cause front-facing triangles to become back-facing and vice-versa.
Edit node mode Will allow you to pick a point and translate it with the keyboard transform controls (see Section 8.2.2, keypad controls)
Edit landmark point mode Will allow you to pick a landmark point and translate it with the keyboard transform controls (see Section 8.2.2, keypad controls)
Delete node mode Will remove from the geometry any node that you pick and any triangles associated with it.
Size of picking aperture select the size of the region around the mouse pointer that will register a ``hit'' when picking; larger values will make it easier to pick an object but also easier to hit multiple objects.
Show Time Signal Window info Toggles display modes in time series window. When there is no info, the graph takes up more room in the window. This is equivalent to pressing 'p' in a geometry window or selecting the toggle display mode option of a time series window's menu.
Show all pick windows Causes all Time Series (Pick) Windows associated with this geometry to become visible.
Hide all pick windows Causes all Time Series (Pick) Windows associated with this geometry to become hidden.



Table 10: Menus for marking nodes in the display. If all surfaces are currently displayed, any of these settings will affect all surfaces based on the rules in locks section (see Section 8.4.3). If we have a single or current) surface only, then change only that surface.
Node Marking Menus
All   Make all the nodes in this (or all) surface(s)
  Sphere mark each node with a sphere
  Node # mark each node with the node number in the geometry
  Channel # mark each node with the associated data channel number
  Data value mark each node with the associated data value
  Color set the color for marking all nodes
  Size set the size of all node markings
  Clear all marks remove all node marking settings
Extrema   Make all the nodes that are the extrema
  Sphere mark each extrema with a sphere
  Node # mark each extrema with the node number in the geometry
  Channel # mark each extrema with the associated data channel number
  Data value mark each extrema with the associated data value
  Size set the size of all extrema markings
  Clear all marks remove all extrema marking settings
Time signal   Make all the nodes that identify the location of time signals shown in the display
  Sphere mark each times signal location with a sphere
  Node # mark each times signal location with the node number in the geometry
  Channel # mark each times signal location with the associated data channel number
  Data value mark each times signal location with the associated data value
  Color set the color for marking all times signal locations
  Size set the size of all time signal markings
  Clear all marks remove all time signal marking settings
Lead links   Make all the nodes that identify the features from leadlinks file (see Section 6.4) shown in the display
  Sphere mark each lead location with a sphere
  Node # mark each lead location with the node number in the geometry
  Channel # mark each lead location with the associated data channel number
  Data value mark each lead location with the associated data value
  Lead labels mark each lead with the label from the leadlinks file.
  Color set the color for marking all lead locations
  Size set the size of all lead markings
  Clear all marks remove all lead marking settings



Table 11: Graphics menus. These control general graphic rendering options.
Graphics Menus
Light source   select the source for the lighting model
  From above light shines from above the surface
  None no lighting (turn lighting off)
Toggle clipping   toggles particular clipping plane options
  Front plane toggles front clipping plane
  Back plane toggles rear clipping plane
  Locking planes together makes planes translate together
  Locking planes with object rotate surface with the planes or rotate surface through the planes
Toggle Depth cue   apply/disable depth cueing (fog)



Table 12: Landmark menus. These control landmark display options.
Landmarks Menus
Coronary/Catheter   toggle and select color for coronary/catheter
  Toggle Coronary toggle coronary artery
  Toggle Catheter toggle catheter display
  Wireframe Coronary show coronary artery as wireframe and pt. numbers
  Coronary Color select coronary color
  Catheter Color select catheter color
Points   toggle and select color for point landmarks
  Toggle temporary occlusions toggle temporary occlusion display
  Toggle permanent occlusions (stich) toggle stitch display
  Toggle stimulation site toggle stim display
  Toggle recording site (lead) toggle lead display
  Occlus Color select occlus color
  Stitch Color select stitch color
  Stim Color select stim color
  Lead Color select lead color
  Toggle All Points turn on/off point landmarks
Planes   toggle and select color for plane landmarks
  Toggle Plane toggle plane display
  Toggle Plane Transparency make plane transparent or opaque
  Plane Color select plane color
Points   toggle and select color for point landmarks
  Toggle rod toggle rod display
  Toggle recording needle toggle recneedle display
  Toggle pace needle toggle pace needle display
  Toggle fiber (lead) toggle fiber display
  Toggle cannula (lead) toggle cannula display
  Rod Color select rod color
  Recneedle Color select recneedle color
  Paceneedle Color select paceneedle color
  Fiber Color select fiber color
  Cannula Color select cannula color
  Toggle All Rods turn on/off rod-type landmarks
Toggle All Landmarks turn all landmarks on/off



Table 13: Controls for the attributes of the map3d windows.
Frame Control Menus
Lock Frames toggle whether frames operations affect one surface or all surfaces
Set Frame Interval    
  value select between 1 and 90 for frame animation step
  Command Line Interval use the value of interval specified in the -i option of the command line
Reset Frames to 0   positions the surface at the first position in time
Align meshes to this frame num   Positions all surfaces' frames to the current surface. What 'current surface' means will vary based on the status of the locks (see Section 8.1.1)



Table 14: Controls for the attributes of the map3d windows.
Window Attributes Menus
Save... Opens Save Dialog (see Section 8.5.2)
Screen info   select the text written to the screen
  Turn screen info on  
  Turn screen info off  
  show/hide lock icons toggle lock display
  Show Legend Window Turns on Colormap window
  Hide Legend Window Turns off Colormap window
Color   select window colors with the separate color selector
  Background select background color for the window
  Foreground select foreground color for the window
Size   select some size options
  value set window to specified resolution
Axes   select options for axes
  Axes Color Select axes color
  Axes Placement select whether axes displayed per window or mesh
  Toggle Axes turn on/off axes
Toggle Transformation Lock   toggle whether surfaces transform together or independently


Following are the controls for the menus of the Time Signal Window, Legend Window, and Main Window, respectively.


Table 15: Controls for the attributes of the Time Signal Window.
Time Signal Window Controls
Axes Color Select Axes Color
Graph Color Color of data graph
Toggle Display Mode Shows values and graph or show larger graph



Table 16: Controls for the attributes of the Legend window.
Legend Window Controls
Orientation   Layout of information in Legend Window
  Vertical  
  Horizontal  
Number of Tick Marks   select number of ticks to appear on bar
  2,4,8 Either 2,4,8 ticks. These will not be colored as they do not directly correspond to contour values.
  Match Contours Match number of contours in corresponding geometry



Table 17: Controls for the Legend Window Menu
Main Window Controls
Set Background Color Select bg Color
Set Foreground Color Select color of Main Window Text
Show Info Whether or not to show text info in the Main Window
Quit Map3D Quit Map3D
.



8.3 Controlling the time signal window

There are two ways to create a time signal window:

  1. Specify a -at xmin xmin ymin ymax on the command line (optionally with a -t trace-lead-number to specify the channel to use).
  2. Using picking to select a lead to show in the time signal window, when the current pick mode is time signal new-window mode or time signal refresh mode. Note that subsequent time signal picking can be set to either a) update the last time signal window to the new data channel or b) add yet another time signal window.

The format of the scalar display is fairly simple , with a vertical bar moving along the time axis as the frame number is advanced. map3d derives the time axis label from the frame numbers of the signal relative to the time series data file, not relative to the subset of frame read in, i.e., if frames (or pot file numbers) 10-20 are read in with an increment of 2, then frame number will begin at 10, and go through 12, 14, 16, 18 and end at 20 rather then beginning at 0 or 1 and going to 10 (the number of frames of data actually read).


8.3.1 Adjusting the frame marker

In order to facilitate rapid movement through large datasets, the user can control the frame number being displayed by interacting with the scalar window itself. If the user moves the cursor to the scalar window and pushes the left mouse button, the vertical time bar will jump to the nearest sample to the cursor location. The user can then hold the left button down and slide the time marker left and right and set a desired frame. Once the mouse button is released,map3d updates the map display. The left and right arrow keys also shift the frame marker back and forth. The only other command allowed when the cursor is within the scalar window is the ``q''-key, to shut down just the scalar window, the ``f'' key, to toggle the frame lock, or the ``p'' key, to toggle the display mode. Any other attempt at input will not be accepted.


8.4 Color/Size Selection

It is frequently necessary to control color and size of elements of the map3d display and this, we have selection subwindows that appear as necessary and disappear upon selection. While the Color and Size Picker leave much to be desired aesthetically, they improve on past versions, and have slightly more functionality.

8.4.1 Color Picker

Figure 4: Color Picker.
 
Color Picker

The Color Picker shows a number of colors to select from. There are only a limited number of colors so that the color selection can be easily reproduced on subsequent runs. When you open up the Color Picker, the current (original) color will be in a small box on the bottom left, whereas the box next to it will show the color that was most recently selected. There is a new ``Preview'' button which will change the color and let you see what it would do, but will also allow you to push the ``Cancel'' button and return to the original color, shown in the bottom left.

8.4.2 Size Picker

Figure 5: Size Picker.
 
Size Picker

The Size Picker shows 10 sizes to select from, currently (to change later) represented by the size of boxes, where the width of the box represents the selectable size. When you open up the Size Picker, the current (original) size will be represented in a box on the bottom left, whereas the box next to it will show the size that was most recently selected. There is a new ``Preview'' button which will change the size and let you see what it would do, but will also allow you to push the ``Cancel'' button and return to the original size, shown in the bottom left.


8.4.3 Interactive Size Control

Rather than having to open the Size Picker over and over, map3d provides a few options that can be changed by a single keystroke. To do this, open the menu in the Geometry Window and select ``Mesh->Use +/- to select'' and then select a feature you wish to dynamically adjust. Then press + or - to adjust the size. However, most of these only have 10 possible sizes.


8.5 Interactive GUIs - File Selection, File Saving, and Scaling Options

This version of map3d adds new GUI support. The most noticeable new addition is the ``map3d Files'' window, allows you to interactively select filenames, data windows, etc. The others are for saving files, and for quick scaling changes.


8.5.1 Files Window

Figure 6: Files Dialog for map3d.
 
Files Dialog

The ``map3d Files'' window can be accessed by the ``Mesh->Files...'' menu entry. This window displays one row for each surface, where each row shows the surface number, the window the surface appears in, the geometry filename, the geometry number, the data filename, the start frame number, the end frame number, a graph of the RMS curve, and a button to show other files. Most of these columns can be modified at any time. If you click on the ``New Surface'' button, an empty row will pop up, allowing you to add a surface from scratch.

None of the changes you make will take effect until you click on the ``Apply'' button. If you click on the ``Close'' button, the window will close, but if you open it again, it will look exactly as when you closed it.

Column description
Surf Number of the surface
Win# Number of the window that contains this surface. You can change this number to move the surface to any open window, or to a new window (by selecting the last number from the drop-down menu.
Geom File Name of the geometry file of this surface. You may change the geom file by clicking on the ... button and finding the file you want in the file picking window that will appear. You may reload the current geometry by selecting the ``Mesh->Reload Geometry'' menu entry.
Geom# Number of surface within the geometry file (see Section 6.1.3). If there is more than one surface in the geometry file, you may select which one you want from the drop-down menu. If you change the geometry file, this menu will be updated.
Time Series File Name of the data file of this surface. You may change the data file by clicking on the ... button and finding the file you want in the file picking window that will appear. You may reload the current geometry by selecting the ``Mesh->Reload Data'' menu entry.
Start Frame Start reading data at this frame. You can also left-click in the graph section and drag to select the correct frame and this number will be updated.
End Frame Finish reading data at this frame. You can also middle-click in the graph section and drag to select the correct frame and this number will be updated.
Graph Graph of the root-mean-square deviation of each node for each time instance. You can left- or middle-click in this graph to select your data window, (and the number in start frame or end frame will update).
Other Files This button will pop open another window in which you can view/modify the channels, leadlinks, or landmarks file to use with this surface.

Figure 7: Other Files Dialog for map3d - Select Channels, Leadlinks, and Landmarks files
 
Other Files Dialog

Also note that this window allows you to run map3d without any arguments. If you do so, or if map3d3d determines that none of the geometry files were valid, the files window will pop up with an empty row waiting for input. If you try to close this window without any input, map3d will treat is as though you were exiting the program.

Figure 8: Empty Files Dialog. map3d will start up this way if you run without arguments.
 
Empty Files Dialog


8.5.2 Saving Files

Figure 9: Saving Dialog.
 
Save Dialog

The ``Save...'' Window will display if you select ``Window Attributes->Save...'' from the menu. The first section is to save geometry files, and the second is for images.

In the Geometry section it displays each surface number with its current geometry filename. Next to each there is a check box. If that check box is checked when you click one of the save buttons, then that surface will be one of the ones that is saved. If the second check box (labelled Transform?) is checked, then map3d will save the geometry will be saved with the current transformations (translations and rotations) applied.

Make sure to modify the filename or the current filename will be replaced (if you click on ... you can browse for a filename). If the filename ends in the extension .fac, it will save filename.fac and filename.pts. If the filename ends in .geom, it will save the file in the CVRTI binary file format (see Section 6.1.3). If Transforms is selected and there is a landmarks file, then a filename.lmark.

Clicking on the ``Save in 1 geom file'' button will save all of the geometry into 1 CVRTI binary file (see Section 6.1.3), choosing the filename of the first entry, which must have a .geom extension. Clicking ``Save individually'' will save each in its own filename. There is currently a known bug with saving .geom files under Windows and reading them back in again.

In the image section, select a filename (you can click on ... to browse for a filename) and click save. The filename may have the extension .ppm, ,png, or .jpg to save in one of those formats. The image that will save is approximately the space that all open map3d windows cover. There is currently a known bug that on X-based systems, images will not save if your default color depth is not 24 bits.


8.5.3 Scaling Options

Figure 10: The three tabs of the Scaling Dialog.
 
Scaling Dialog

This dialog is pretty much a duplicate of the Scaling Menu in the Geometry menu, but in dialog form for convenience sake. Click on the tab at the top of the scaling type you wish to change (Range, Function, or Mapping), and click on the check box of the feature you wish to select, and map3d will update. (see Section 8.2.3, scaling menu)


8.6 Picking mode

By ``picking'' we mean selecting some piece of the display in the current window using the mouse (with buttons). map3d currently supports selection of nodes or triangles with different actions, all of which either return some information, affect the display, or even alter the geometry of the display. In version 5.4, the choices are limited to node information, triangle information, time signal displays, triangulation, triangle deletion, and triangle flipping. Note that picking is successful and the desired results occur only when there is one (no more, no less) hit. To aid in getting the one hit, you may adjust the picking aperture or activate the clipping planes. In any picking mode where your geometry is modified, you might want to save your geometry (see Section 8.5.2). To control picking, use the top-level ``Picking'' menu. See Table 9 for the available options.

8.6.1 Time Signal (new window mode)

This mode opens up a new window and provides information about the node/channel. It tells the node number, channel number, the associated surface, the current frame number, and the value of the scalar data at the current time instance. In addition, it shows a graph of the scalar data associated with that node over time.

8.6.2 Time Signal (refresh window mode)

This mode provides the same information and graph as the new window mode, but displays the information in the most-recently created window (and creates one if one doesn't exist).

8.6.3 Node Information

This mode outputs information of the selected node to the console: Surface number, frame number, node number, channel number, current data value, and the X,Y,Z coordinates of the point (as read by the geometry file).

8.6.4 Triangle Information

This mode outputs information of the selected triangle to the console: Surface number, triangle number, and the numbers and X,Y,Z coordinates of the 3 triangle points (as read by the geometry file).


8.6.5 Triangle Construction (Triangulating) and Deletion

In this mode, the left mouse is used to select the nodes that you wish connected into a triangle. Note that each time you select a valid point a change is made to the geometry. The first valid point you will see a new point on the mesh. The second will be similar except there will be a line connecting the two points, and the third time will add the completed triangle to the geometry

Pushing CTRL-middle mouse button selects a triangle and kills it, removing it from the list.

8.6.6 Triangle flipping

Often it is necessary to know the orientation of the triangles in the geometry. While this can be computed, there remains a 180-degree ambiguity as to which way the normal points. To resolve this, triangles nodes should be ordered in a counterclockwise direction as viewed from the ``outside'' of the surface to which the triangle belongs. This convention is used by OpenGL to decide which triangles to show in ``hide backfacing triangles'' mode. Unfortunately, it is not always possible when constructing geometric models to tell which way the triangle is to be viewed--this is still something humans do better than computers--and so we often need to edit a geometric model so that the triangles are 'flipped' the right way. Hence, the ``Flip triangle'' option in the ``Picking'' menu.

8.6.7 Edit node

If your surface isn't perfect, you can edit the positions of the nodes. Select this pick mode in the Picking menu, and pick a node. A mark will appear on the node that you pick. Then use the keyboard transformation controls to translate a node (see Section 8.2.2, keypad controls). Note that keyboard rotation won't work in this mode.

8.6.8 Edit landmark point

If your landmarks aren't perfect, you can edit their positions. Select this pick mode in the Picking menu, and pick a landmark point. A mark will appear on the point that you pick. Then use the keyboard transformation controls to translate it (see Section 8.2.2, keypad controls). Note that keyboard rotation won't work in this mode.

8.6.9 Delete node

In this mode, any node you pick and any triangle that connects with it will be removed from the geometry.


8.7 Control of landmark display

There are some lighting and colour controls for the display of landmarks that are useful to know about. Table 12 describes all the specific menus mentioned here.

Coronary/Catheter:
these are controls to adjust color and visibility of the vessel type landmark, the ones we use for arteries and also for catheters. You can also switch from a rendered version of this landmark type to a wire mesh that is labeled according to segment numbers--a debugging tool when the vessels are not going where you expect.
Points:
there are a range of point types in the landmark suite and this option allows you to control them turn them off and on, adjust color, etc.
Planes:
for the plane landmark, you can set color, but also the transparency level of the plane. Default is transparent and this usually works best.
Rods:
as with points, there are different rod type landmarks and with this menu you can control their visibility and color.
Toggle all landmarks:
this is the master switch and toggling it turns all the landmarks from on to off or vice versa.

Rob Macleod 2004-04-08