Model View Object Edit

This dialog box contains many controls for changing how individual objects are displayed, as well as some features governing the overall model display. The top sections contains some general controls and the bottom section shows one out of several available panels with more specialized controls.

Several hot keys are active only when this dialog is open because they depend on the object selected for editing here. They are listed in the "Drawing Type and Clipping Plane Operations" section of Model View Keyboard Commands.
Line color
Fill color
Material
Points
Lines
Values
Clip
Move
Subsets
Mesh draw
Meshing

General Controls

Select the current object with the Object spin box or the slider.

The Edit Each/All/On's/Group option menu allows one to edit just the current object, all objects at once, just the objects that are currently turned On, or objects belonging to a group selected in the Object List window. Features that can be edited in tandem for many objects include: point size, line width, material properties, drawing data type (contours or mesh) and style, and meshing parameters. Line color can also be changed in tandem if a separate check box is selected. When On's is selected, and the current object is not On, then it will not be changed, but a nearby object that was changed will be made the current one so that the dialog can reflect your change. Similar behavior occurs when Group is selected and the current object is not a member of the group defined in the Object List window. For a feature that cannot be edited in multiple objects, this setting has no effect - the current object is the only one changed.

The name of each object can be edited using the text edit box.

The Synchronize with current model object checkbox allows you to keep the object being edited here the same as the current object in 3dmod (it appears only after starting the program as 3dmod). When this is checked, changing the selection here will change the current object in the 3dmod Information window, and vice versa; otherwise the two objects are independent.

The numbered check boxes allow one to conveniently turn selected objects on and off. When an object is turned on, it becomes the current object. Only 48 checkboxes will be displayed here; if you have more objects, use the Edit - Object List menu entry to bring up a complete Object List window.

The Draw option selects which type of data to draw. You can select to draw contour data or mesh data. There is also an entry to turn drawing Off, and an entry to turn the drawing back On without having to select contour or mesh type. The latter is useful when you want to turn all items back on after turning them off.

The Style option selects the drawing style. You can select between drawing points, lines, filled or filled outline.

To select which parameter group is displayed in the panel in the lower right part of the window, use the mouse to select one of the entries in the list box in the lower left. The controls in each group are listed below.

Line color

Use the Red, Green, and Blue sliders to adjust the line color of the current object. This also sets the fill color unless a separate color is selected in the Fill Color panel. The Transparency slider selects object transparency. Transparency is only an approximation and can easily generate artifacts. To minimize these artifacts, the back face of the object will not be displayed unless the Light Both Sides button is selected in the Material panel. Try it both ways to see which looks best.

By default, color changes will be applied to only one object in one model. Check Change multiple objects to modify more than one object at a time. The setting of the Edit combo box and the Edit radio buttons in the Model Edit window will then control which objects are changed together with the current object.

Fill color

Use the sliders to adjust the fill color of the current object. Select Use fill color to have this color used instead of the line color whenever the object is being displayed as filled. Select Use for spheres to have the fill color used just for display of spheres. This would allow you to have a surface of one color studded with spheres of another color at selected points.

Material

The Ambient slider adjusts ambient, or non-directional, light hitting the object. The Diffuse slider adjusts light hitting the object from the light source, which then diffuses in a direction-dependent way. The Shininess and Specularity sliders together adjust the shininess or highlights of the object.

Select Light Both Sides to have the object lit on both its outside and inside surfaces. If you just want to have the inside surface show up less dark than it does by default, try increasing the Ambient value and decreasing the Diffuse value to compensate.

Points

This panel controls the rendering of spheres that are displayed at individual points. The sphere radius can be incremented, decremented, or typed into the spin box. Note that setting the radius non-zero will cause points to be displayed at each point, even for open and closed contour objects. The quality of the spheres is controlled by the two quality spin boxes, one to set the quality for the particular object, and one to set the overall minimum quality for all objects. The display quality for an object is the maximum of its own quality setting and the global setting (range 1 - 4). The global setting can also be controlled by the G and Shift+G hot keys.

Lines

This panel has controls that affect the drawing of lines in the model view window, as well as some other object properties that you might want to change for multiple objects at once.

The 2D Line Width slider changes the line width used when drawing the model in image display windows in 3dmod.
The 3D Line Width slider changes the line width used to draw draw the objects in the model view window.
The Anti-alias rendering check box selects anti-alias rendering for lines. Lines will look smoother with this option on; however, some artifacts may be noticed.
The Thicken current contour check box can be used to highlight the current contour by drawing it thicker than other contours. This will have an effect only for objects whose drawing style is Lines. This feature is most useful when using the third mouse button to select contours.
The Open object type check box is enabled when the object type is closed or open, and can be used to switch objects between open and closed. If the Edit combo box is set to All or On's, then changing this setting for the current object will affect all open and closed contour objects, or all that are turned on.
The New contour at new Z check box is enabled for open contour objects and controls whether a new contour is started automatically when drawing on a new section in the Zap window. If the Edit combo box is set to All or On's, then changing this setting for the current object will affect all open contour objects, or all that are turned on.

Values

This panel controls the display of values that have been stored in the model in one of two ways. Some programs will now store values for each contour or point using the fine-grained storage capabilities. The sda program stored surface density values in the mesh as the magnitude of the surface normals. The radio buttons at the top allow you to select whether to Show stored values or to Show normal magnitudes.

The Black and White sliders adjust the contrast range of the displayed values. The intensity ramp can be inverted by setting the Black slider higher than the White one.

By default, the values will be shown as an intensity modulation of the object's color. Use the False color checkbox to display the values in false color instead. Alternatively, the Fixed color checkbox can be used to keep the color constant instead of modulating it with the stored values.

The Turn off Low and High buttons can be used to turn off the drawing of contours or points whose stored values fall below the lower of the Black and White levels or above the higher of the two levels, respectively. This feature does not work for mesh displays. If you do not want to view values in false color, you can used the Fixed color option to distinguish clearly between items below and above the low threshold (otherwise, items just above the threshold will be too dark to see).

Note that once the drawing of stored values is turned on, it is applied to model features drawn in the image display windows, if any.

Clip

These controls allow you to set up clipping planes for an individual object as well as global clipping planes that will be applied to all objects. The position and orientation of a plane is adjusted by holding down the Ctrl key and doing the same operations that would ordinarily move or rotate the model.

The controls at the top of the panel affect the behavior of the program rather than applying to the current object. Select Show current plane to have the current plane drawn as a semi-transparent plane so that you can see its position better. When you switch planes or objects, you will see the new current plane, if any. Use the Object and Global radio buttons to select whether to adjust global planes or planes for the current object.

The remaining controls affect stored properties of the global clipping planes, or the current object and its clipping planes. If you want the current object to be clipped only by its own planes and not by any global planes, turn on Skip global planes. The Plane # spin box allows you to select the current plane, the one that is adjusted by the remaining controls. Use Clipping plane ON to toggle the current clipping plane on or off. The Plane # spin box always allows you to select one plane past the highest one that has already been defined, so you can add another plane just by selecting the next available number and turning the plane on.

The Reset X, Y, Z buttons move the plane back to its default location through the middle of the object or model and orient it perpendicular to the X, Y or Z axis. The Invert button inverts the direction of the clipping plane. Turn on Adjust all planes to operate on all of the object or global planes at once; these operations include moving, rotating, and turning on or off. This option is useful if you have set up several planes to enclose a box and want to shift or rotate the box as a unit.

Once the current plane is turned on, hold down the Ctrl key to move and rotate the plane instead of the model. Use the left mouse button or the arrow keys to move the plane, and the middle mouse button or the keypad keys to rotate the plane.

Up to 6 clipping planes may be defined for each object, as well as 6 global planes. However, the OpenGL implementation on your machine limits the total number of planes that can be applied to an object. There are guaranteed to be at least 6 but probably are only 6. If this limit comes into play, object planes count first toward the limit.

Move

This panel allows one to view orthogonal faces of the model. Each column of buttons will move by 90 degree rotations about one of the three axes. The Center on Object button will center the display on the current object.

Subsets

This panel allows one to view the current object, Surface or contour of the model, if one is selected, or just the current point in a scattered point object. Current Surface Only or Current Contour Only will show only the current Surface or contour in the current object. Surface & Other Objects or Contour & Other Objects will show the current Surface or contour in the current object, plus all other objects that are turned on. Point & Other Objects is available only when the current object type is scattered points and will show only the current point in the current object, along with all other objects that are turned on.

Mesh draw

This panel has some options to control how the meshed surface is displayed.

You can display a surface with separation between the inner and outer sides by setting Surface thickness non-zero. A pair of meshes will then be drawn separated by this thickness, one lit from the inside and one from the outside. The two meshes are created equidistant from the original mesh. For example, if you want the surface to pass through both edges of a membrane, model the middle of the membrane and adjust the thickness to the membrane thickness in pixels.

Select Draw mesh on images to have mesh lines drawn on the images in Zap and Slicer windows. This is the only way to see the mesh lines in an isosurface object. For drawn objects, such lines will ordinarily fall on the regular contour lines in the Zap window, so they would be useful only to see the lines of a paired mesh display with a surface thickness set. In the Slicer, the entire mesh is drawn in 3D and lines will show up at any angle, particularly if the model thickness selected to be be drawn there is increased. Color changes introduced with the Fine Grained dialog or by painting an isosurface will be reproduced in the drawn lines, but other fine-grained changes in the mesh (transparency, 3D width, or general values) will not. Note that complex meshes, especially painted isosurfaces, may take significant time to drawn in the Slicer, since repeated drawing is not accelerated with vertex buffers as it is in Model View.

Meshing

This panel allows the current object to be meshed if it is an open or closed object. The various controls correspond to options in Imodmesh; see that man page for more details. If the object has been meshed before, the parameters for that meshing will be used to set these controls. In addition, any parameters set through Imodmesh but not appearing here, such as X or Y limits or lists of Z values to not cap to, will still be applied when remeshing through this interface. If you changing the meshing parameters for more than one object (i.e., with an Edit option of with editing of multiple models enabled), then an object will be changed only if the particular parameter change is relevant for that kind of object or appropriate given the other parameters set for that object.

The controls are:

Skip: Connect contours across sections with no contours (-s option). By default, connections are made only between adjacent sections. If sections have been either completely skipped or completely modeled for this object, then this option alone is enough to mesh the object. If some sections are partially modeled, the Passes option is needed as well.
Tube: Make a tubular (cylindrical) mesh around open contours (-t option).
Low res: Make a low resolution mesh separate from the regular one and keep the regular mesh (-l option). Once a low resolution mesh has been made, the only way to delete is to run Imodmesh with the -l and -e options.
Surface: Use Surface numbers for connections; only connect contours in the same Surface (-S option).
Cap: Normally, cap all unconnected ends of the object (-C option). When Tube is selected, this checkbox controls whether the ends of tubes are capped (-E option).
Dome cap: When Tube is selected, you can use this option to get hemispherical caps on the ends of tubes (-H option). It is not necessary to turn on Cap also.
Passes: Number of passes for connecting contours farther apart in Z (-P option). If sections have been completely skipped when modeling, it is best to use the Skip option to get across them. If Passes is also needed to connect across partially modelled sections, using the Skip option as well will allow a smaller number of passes, which will help prevent spurious connections.
Diam: Diameter for tube meshing (-d option). If the value is 0, the 3D line width will be used; for -1 or negative numbers between 0 and -1, the sphere size will be used; for -2 or negative numbers less than -1, the symbol size will be used.
Tol: Tolerance for point reduction; points will be removed if they are within this distance of the remaining lines (-R option). A separate value is maintained for regular and low resolution meshing.
Z inc: Increment in Z at which to mesh contours (-i option). A separate value is maintained for regular and low resolution meshing.
Flat crit: Criterion Z extent of contours; if any contours vary by more than this amount in Z, then each Surface will be analyzed for the orientation of its contours and the tilted contours will be meshed (-F option). A value of 0 disables the analysis.
Z: Starting and ending Z of range over which to mesh, numbered from 1 (-z option, except that is numbered from 0). Enter a single number to mesh a single pair of planes, as long as the Z increment is 1; e.g., "23" will mesh sections 23 and 24.

Pressing Mesh One will start the meshing on the current object on a separate thread, so you can continue using the program before the mesh is done. When the mesh is done, the drawing of the object will be switched to Mesh and Fill if appropriate. The resolution mode will be switched to match the resolution of the mesh just computed. Note that the hot key Ctrl+R is used to switch between resolutions.

Pressing Mesh All will mesh all closed and open contour objects in the model. The meshing parameters used for each object will be the ones defined for that object, if it has been meshed before, or it will be the default parameters that you would see in this panel if you switched to that object. The parameters visible for the current object are not necessarily the defaults for the other objects.

The ^ and v buttons are enabled when there is an entry for a Z range in the Z: box. They allow you to step up or down by 1 in Z and remesh the current object. This is particularly useful for finding contours that are meshing incorrectly when the mesh looks like it has a problem. Every pair of planes is considered independently, so for this purpose there is no need to mesh at more than one Z at a time. Changing the drawing type to "Mesh" - "Lines" will help for visualizing the connections, and it can also be useful to set the Z scale much higher temporarily so that it is easier to distinguish the two planes. See the Fine Grain Dialog help page for details on how to set connection numbers to solve some problems.

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