Setting Fine Grain Properties

This window is used to set display properties at a finer level than is ordinarily allowed. Properties such as color and line width can be set for individual points within a contour, for individual contours, or for specific surfaces.

The radio buttons at the top are used to select whether properties are being shown and controlled for the current Point, Contour, or Surface. For the current item, the various controls show the existing display properties of that item. For each property, there appears the letter D if the property has a default value, or S if the property has been set.

The fine grain changes operate somewhat differently for points than for contours and surfaces. For points, when a property is set for one point, its value applies to all following points in the contour until the change in property is ended, or until a different value is set for a later point. Thus, when a property has a non-default value for the current point, an End button is enabled to allow you to end the sequence of changes at that point. In addition, a Clear button is enabled, which will allow you to reset that property to the default for the whole contiguous sequence of points that have the property set. There are two exceptions to this pattern: Gap to next point applies only to the single point at which it is set, so that one can create an opening in a contour. The Mesh Connection # also applies only to a single point.

For contours and surfaces, all changes apply only to a single contour or surface. Thus, once a property has been set, the Clear button is enabled to allow you to restore the default value, while the End button has no function.

Once you have set a property, the Last button is enabled so that you can conveniently apply the same change to other items, for example points in a corresponding position on another contour.

The Go to Next Change button near the top can be used to step forward to the next item where a change occurs. When point properties are being displayed, this will move the current point to the point where the next change occurs (which can be the end of a change or the beginning of a new one). With contour properties displayed, the program will move to the next contour with a nondefault property; and with surface properties displayed, it will move to the first contour of the next surface with changes.

If the rubberband is on in the Zap window and positioned over the current contour, then pressing a Set button will apply the property change to all the points and line segments within the rubberband. This feature should make it easy to change several properties in tandem, and to apply similar changes on successive sections. If any of the included points already has this property set, then those changes will be cleared out first, as if the Clear button were pressed for every point in the range. Unfortunately, this feature will not work on both the start and end of a contour if the rubberband spans the endpoints of the contour.

Most property changes will show up immediately in the image or model view windows. However, properties that affect a mesh display will have an effect only after being incorporated into the mesh, and you will not see any change in the display of the mesh until the model is saved, remeshed with Imodmesh, and reloaded. Changes in surface properties are a potential exception to this rule. Ordinarily, Imodmesh encodes surface information into the mesh just like the lower levels of information. However, if surfaces are meshed separately with the -S option to Imodmesh, then surface properties are not encoded in the mesh. Instead, they are applied during model display, because in this case each mesh can be identified by surface number. As a result, surface properties can be changed dynamically and visualized immediately.

A final general note before descriptions of individual properties: the ability to make these fine grained changes in the model represents a big change in the potential content of IMOD models. Many programs outside of 3dmod will ignore, discard, or garble this information until they are modified to handle it properly. Even some operations within 3dmod will not deal with the fine grained data correctly, notably sorting of points and use of the line tracker.