Appendix D - Guide to point cloud and polygon mesh editing in Geomagic Qualify®

Note: Many actions are not reversible in Geomagic Qualify ®, or only until the next action has been completed. Take care to save your data often and with altered filenames! Note: instructions here refer to version 8.0 of Geomagic®. Other version may require slightly different command inputs.

Transferring data from Geomagic® to Rhinoceros® and back. Both Geomagic® and Rhinoceros® use program-specific file types. Neither program can reliably import the other program's specific files. Therefore, data must be saved in formats that can be read by both programs, for which standardized file types are advisable. Point clouds can be saved as IGES files (*.igs), while polygon meshes are best saved as binary Stereolithography files (*.stl).

Creating polygon meshes from point clouds

1. Load the point cloud file. Acceptable formats are e.g. *.obj and *.igs
2. Choose a selection tool ('Edit-->Selection Tools-->) and select erroneous points.
3. Delete selected points by pressing [Del]. Unmark the selection by pressing [Ctrl]+[C].
4. Select the wrapping tool ('Points-->Wrap') and choose the 'Surface' wrap type.
5. Check the 'advanced options' box and set the meshing quality to maximum.
6. Click 'OK'

Removing artifacts from and smoothing a polygon mesh. Smoothing via the 'smooth' command cleans up the surface in one work step. Less aggressive are 'Remove Noise' and 'Remove Spikes'. They allow the user to control the degree of smoothing, and 'Remove Noise' also has options to show the deviation between the original and the smoothed version.

Smoothing a polygon mesh:

1. Select 'Polygons-->Smooth'.
2. Click 'OK'.

Removing spikes: This tool works well for little pyramidal shapes on the surface caused by points that lie slightly outwards or inwards of the plane of the neighboring points.

1. Select 'Polygons-->Remove Spikes'.
2. Set the slider to the desired degree of smoothness.
3. Click 'Apply'.
4. Check the result. Repeat 2. and 3. until satisfied, then click 'OK'.

Removing noise:

1. Select 'Polygons-->Remove Noise'.
2. Set parameters as desired.
3. In order to see deviations, mark 'Show Deviations'. Set colors and values as required.
4. Click 'Apply'. If marked, the deviations are now shown as color changes according to the options chosen.
5. Repeat 2. to 4. until satisfied, then click 'OK'.

Reducing the polygon number in a mesh

The shape of the bone is preserved better if the reduction is done in small steps. Thus, reducing to 80% several times is better than going down to 20% in one instance.

1. Select 'Polygons-->Decimate'.
2. Set either the target number of polygons or the target percentage desired.
3. Mark 'Fix Boundaries' to preserve the extreme points and edges of the object. If this option is not selected, edges will be smoothed over.
4. Click 'Apply'.
5. Check the result. When satisfied, click 'OK'.

Removing artifacts on a polygon mesh

Removing artifacts and other erroneous triangles will leave holes in the object. They can be filled using the 'Fill Holes' tool.

1. Choose a selection tool ('Edit-->Selection Tools-->)
2. Choose the proper selection mode ('Edit-->....). Selecting 'Backface mode' allows selecting both triangle fronts and backs, deselecting it allows selecting polygons from the outside only. 'Select visible only' selects visible triangles only, while 'Select through' selects any triangle that is in the direct line of projection, whether it is visible or hidden by other polygons.

CAUTION - It is easy to accidentally delete triangles on the reverse side of the model when using 'Select Through'

3. Select erroneous triangles. Holding down [CTRL] while clicking removes triangles from the selection.
4. Press [DEL].

Erroneous triangles can also be removed while using the 'Fill Holes' tool (see there). Especially useful is the option removing floating data.

Filling holes: Note that it is usually advisable to first clean up a polygon mesh and then fill the holes. This is faster, as many small holes will be filled automatically by the 'Smooth', 'Remove Spikes' and 'Remove Noise' commands.

1. Start the 'Fill Holes' mode ('Polygons-->Fill Holes')
2. Select the appropriate mode:

'Fill' fills holes completely. Select the appropriate options and click on the boundary of a hole to fill it.

'Fill partial' allows defining a stretch of boundary along which the hole will be filled. The rest of the hole stays open. Click on the boundary in two places, then click that part of the boundary were the fill should take place.

'Create bridges' creates strips of polygons between two selected edges. Click on one edge for the bridge start, then on another for the bridge end.
'Delete' allows removing triangles based on various selection options. Checking the 'floating data' box allows removing triangles that have no connection to the external surface.
'Move' allows changing the shape of a bridge created in 'Create Bridge' mode.
Click the place where you want to apply the change, click and drag the arrow into the correct direction and set the shape and extension of the shape. Click 'Next' to confirm a move and start a new one.
3. Decide whether you want to use curvature based or flat filling. Check or uncheck the corresponding box accordingly. Flat filling creates a surface as planar as possible, while curvature based filling attempts to keep the tangency of the hole closing surface as constant as possible.
4. If satisfied with the fillings, click 'OK'. Otherwise, discard them by clicking 'Cancel'.

Sectioning polygon meshes. Cuts can be executed in two ways: with a plane or along a curve. The former option is not very useful if the resulting sections are used in kinetic modeling, as large gaps will appear when sections with straight cut-offs rotate versus each other. A curve allows creation of saddle-shaped cuts, so that rotary joints are almost gap-free.

Using curves, there are two options: to create closed objects (bodies) or open objects (surfaces). Creating closed bodies usually results in small gaps between neighboring objects and is more work intensive. Creating open objects is faster, but carries a high risk of artifacts at the edges if the openings are closed using the 'Fill Holes' function. The higher the resolution of the file is, the weaker the artifacts will be.

Using curves as cutting object to create closed section object:

1. The import the STL file.
2. Rotate it so that the view axis is parallel to the intended cut.
3. Select 'Polygon-->Section by Curve'.
4. Draw a curve from control points by clicking on the model. It is important to imagine how the two sections-to-be will be positioned after having rotated versus each other in kinetic modeling and place the curve accordingly. A circular arc would be ideal, but it is not easy to draw one given the tools offered by Geomagic®. [Ctrl-Z] removes the last point. This curve can NOT be saved!
5. Click 'Create' to see a preview of the curve on the model
6. Click 'Intersect Extrusion. This extrudes the curve to the depth given in the 'Profile Curve --> Depth' field. Usually, Geomagic® suggests a sufficient depth, lower depths will not penetrate the model fully.
7. Mark 'Delete Selection' and 'Fill Intersection'.
8. 'Reverse Selection' allows changing the part to be deleted and the part to be kept.
9. Click 'OK'

Now, one part has been cut away from the rest of the model along the extruded curve. It is advisable to rename and save it (right-click the part in the model manager window and choose the appropriate option). In order to create the contacting part, proceed as follows:

1. Into the same file, import the STL with the 'File-->Import' command.
2. In the model manager, select both the section created before and the complete part (hold 'Ctrl' to select both while clicking).
3. Rotate the viewport so that the cutting surface is parallel to the view axis.
4. Deselect the finished section by holding down 'Ctrl' and clicking the part again. It is now shown in ghosted view mode.
5. Select 'Polygon-->Section by Curve'.
6. Draw a curve along the cut line. Try to follow the boundary of the already created part as exactly as possible.
7. Click 'Intersect Extrusion. This extrudes the curve to the depth given in the 'Profile Curve --> Depth' field. Usually, Geomagic® suggests a sufficient depth, lower depths will not penetrate the full model.
8. Mark 'Delete Selection' and 'Fill Intersection'.
9. 'Reverse Selection' allows changing the part to be deleted and the part to be kept.
10. Click 'OK'

Now, the next part has been created. Depending on how close the two cutting curves correlate, there will be a small gap or overlap between the parts.

Using curves as cutting object to create open section object:

1. Import the STL file
2. Rotate it so that the view axis is parallel to the intended cut.
3. Select 'Polygon-->Section by Curve'.
4. Draw a curve from control points by clicking on the model. It is important to imagine how the two sections-to-be will be positioned after having rotated versus each other in kinetic modeling and place the curve accordingly. A circular arc would be ideal, but it is not easy to draw one in the fashion offered by Geomagic®. [Ctrl-Z] removes the last point. This curve can NOT be saved!
5. Click 'Create' to see a preview of the curve on the model
6. Click 'Intersect Extrusion. This extrudes the curve to the depth given in the 'Profile Curve --> Depth' field. Usually, Geomagic® suggests a sufficient depth, lower depths will not penetrate the full model.
7. Unmark 'Delete Selection'
8. Click 'OK'

Now the object has been split along the curve. Each part can be separately selected, e.g. with the lasso selection tool, and turned into a separate object ('Edit-->Selection to Object...'). In order to fill the holes, use the 'Polygons-->Fill Holes' function. Use 'Flat fill' and 'Create bridges' to build flat fills for both sides that correspond to each other.

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