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, or to a selected group of contours rather than a contiguous set of them. 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.
If the Change all selected contours checkbox is turned on, then changes will be applied to all currently selected contours. This feature is enabled only when contour properties are being controlled. You can use Ctrl and the first mouse button to select multiple contours in the Zap window, where they will be drawn extra-thick. You can also select multiple contours using Ctrl and the right mouse button in the Model View window (to see the selected contours there, turn on Thicken current contour in the Lines panel of the Edit-Objects dialog). In both cases, moving the mouse while holding down Ctrl and the relevant button will select contours crossed by the mouse. All properties except connection numbers can be changed in tandem for the selected contours.
The Draw dashed lines at gaps checkbox lets you see where you have inserted gaps in contours. This is especially useful for seeing line segments on the ends of open-type contours in closed contour objects. Such segments are added so that the whole contour will not cross itself or any other contours that it is meshed with.
The Draw mesh connections checkbox allows you to visualize the mesh connections that have been defined for individual points (see below). At each point with a mesh connection, a square will be drawn in the Zap window; the size of the square is the assigned mesh connection number plus 4.
The Go to Next Change button 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, surface properties are not encoded in the mesh if the object has multiple meshes with different surface numbers. 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. There are three ways to get such meshes: 1) meshing surfaces separately with the -S option to Imodmesh or the Surface option in the "Meshing" panel of the Model View Edit Objects dialog, 2) saving an isosurface object into multiple meshes with surface numbers using the Sort & Save button in the Isosurface dialog, or 3) splitting a single mesh saved from the Isosurface dialog into surfaces with Imodsortsurf. Note that in the latter two cases, the mesh has no corresponding contours, and the only way to select a surface in it is to right-click in the Model View window or to use the Surface/Contour/Point dialog.
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.
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