Surface/Contour/Point Dialog

This dialog has a collection of controls for more advanced modeling features: defining and manipulating surface numbers for contours; adjusting some properties of contours; giving sizes to individual points; and assigning names to surfaces, contours or points. There are also controls for the display of ghost contours from adjacent sections.

Surface controls

Each contour has its own surface number. The surface number can be used for subgrouping contours without having to create new objects. The surface number of the current contour is displayed in the Surface spin box. To the right of the spin box is the maximum surface number in the current object ("/ #"). You can go to the first contour in the next or previous surface by clicking the up or down arrows of the spin box. Non-existent surfaces are skipped when you move between surfaces. You can also go to the first contour of any surface by entering a number in the box and pressing Enter; the program will select the nearest available surface.

When the current object has a mesh with multiple surfaces but no contours, as can be produced wen saving an object from the Isosurface dialog, then the program keeps track of a current surface number within this object. In this case, the Surface spin box will show the current mesh surface and can be used to step between surfaces.

The Contour in surf Up and Down arrows can be used to step to the next and previous contours within the current surface.

The New button will start a new surface with the next free number and create an empty contour with that surface number.

The Ghost check box may be used during model editing to highlight the current contour, along with all other contours with the same surface number.

It is possible to have a label for each surface. The Label text box shows the label of the current surface; simply enter or change text in this box.

Contour controls

The Closed and Open radio buttons select between closed and open contours in an object defined as having closed contours. The default is a closed contour where the last point is connected to the first. An open contour will not be connected between the last and first points, thus allowing a partially cut surface to be represented by an object containing both closed and open contours. This setting has no effect for an object defined as having open or scattered point contours, so the buttons are disabled in that case.

If you have selected multiple contours, then changing the open/closed property for the current contour will also change all selected contours in closed contour objects. You will be asked to confirm that you want to change multiple contours. For example, you can use this function after selecting many contours with 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). There is also a hot key, Shift+O, for toggling the state of selected contours between open and closed, which has the same effect as pressing one of these radio buttons.

Two more features facilitate working with closed and open contours. First, when you start a new contour, it will inherit this property from the previously current contour, which is usually what you want. Second, when the current contour is open, triangles rather than circles are drawn at its endpoints, so that you can tell what kind of contour you have without looking at this dialog.

The Time Index spin box can be used to change the time index of contours in 4-dimensional datasets. The box shows the time index of the current contour, which can be incremented or decremented with the spin box arrows, or changed by typing in a new number followed by Enter. Contours with a non-zero time index display at only the relevant time; contours with a zero index display at all times. This box is active only when the Contours have time values check box is selected for the particular object in the Edit-Object-Type dialog.

It is possible to have a label for each contour. The Label text box shows the label of the current contour; simply enter or change text in this box.

Point controls

It is possible to assign a size for each point. Any point with an individual size will be displayed as a 3D sphere of this radius, even if the object type is not scattered points. The units are pixels in the image file, i.e., unbinned pixels if images are loaded in binned. Points without a size will still be displayed at the size specified for the object as a whole. You can change a size either by typing a number into the text box (followed by Enter) or by using the slider. If a point has no size, the text box displays the global point size for the object and "-Default".

If Set with mouse wheel is checked, then you can adjust the size of the current point with the scroll wheel when the mouse is in a Zap, XYZ, or Slicer window. This feature will work for points that already have some size. If a point does not have an individual size and the default size for the object is 0, then the wheel control is disabled. (This is to prevent inadvertent size changes while drawing ordinary planar contours.) To use the wheel control in this case, click the slider in this dialog to get some size, then go back to the Zap window and adjust with the wheel. The change in size for one click of the wheel varies with zoom for zooms between 1 and 4; to get the smallest increment, zoom up to 4 or higher.

Each individual point can also have its own label. The Label text box shows the label of the current point; simply enter or change text in this box.

Section ghost controls

These items may be used to control the ghost display mode, for showing items not on the current section in the Zap window. Use the spin box to control how far away items to be displayed can be from the current section. The distance set here works differently depending on the type of object. For closed contour objects and open contours that lie in a plane, the number simply corresponds to sections. For example, with a value of 3, contours will be displayed as ghosts from up to 3 sections away. With the special value of "Near", ghost contours will be displayed from the nearest section on which the object has contours.

For scattered point objects, the number set in the spinner is multiplied by the default diameter of the points (twice the radius set for the object in the Object Type dialog). Thus, this ghost display works in terms of "virtual sections" approximately the same thickness as the number of sections over which a point would display normally. For example, with a point radius of 4 and a distance of 1, a point will display normally up to 3 sections away from its central plane, and then display as a ghost for the next 8 sections. With the value of "Near", such points will display as ghosts from the 8 sections starting at the one with the nearest point in Z to the current section. Enter a large number in the spin box to display points from all Z levels. The ghost points will be displayed as they appear in their central planes, i.e., full-sized with a small cross in the center.

If the Up box is checked, then contours or points will be displayed as ghosts on following sections; the Down check box will display contours or points as ghosts on previous sections. The G hot key will toggle the combination selected by these boxes on and off.

If Lighter box is checked, the ghosts will be displayed in a lighter color, otherwise they will be drawn with a darker color. However, if items are being displayed from both directions (Up and Down both checked), the color of display is modified when Two shades is checked. In this case, the default is to show contours from lower and higher Z planes as darker and lighter, respectively, and the Lighter box reverses this scheme.

If the All closed/open objects box is checked, ghosts will be drawn for all objects with closed or planar open contours, instead of just for the current object. Similarly, if the All scattered objects box is checked, ghosts will be drawn for all objects with scattered points, instead of just for the current object.

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