I tried executing the example in http://doc.cgal.org/latest/Surface_mesh_skeletonization/index.html to get the skeleton of a surface mesh.
I tried using a mesh model of blood vessels with thin structures. However, no matter how refined my meshes are, parts of the skeletons seems to always be outside the mesh models.
In the sample code, there seems to be no parameters which I am able to play around with, so I am asking if there is anything i can do to make sure the skeleton stays within the mesh model.
I have tried to refined the meshes, till the program crashes. Thanks for any help provided. thanks!
I guess you have used the free function setting all parameters to their default. In case you want to tune the parameters you need to use the class Mean_curvature_flow_skeletonization.
It has 3 parameters that need to be fine tuned so that your skeleton lies within the mesh:
quality_speed_tradeoff
medially_centered_speed_tradeoff
is_medially_centered
Note that the polyhedron demo includes a plugin where you can try the effect of the different parameters.
If you can share the mesh with me, I can also have a look.
Related
I'm trying to use Polygonal Surface Reconstruction with building point cloud to create simplified building models.
I did first tests with this CGAL code example and got first promising results.
As an example, I used this point cloud with vertex normals correctly oriented and got the following result from PSR. Some faces are clearly inverted (dark faces with normals pointing inside the watertight mesh and therefore not visible).
I was wondering if there a way to fix this face orientation error. I've noticed orientation methods on Polygon mesh but I don't really know to apply them to the resulting PSR surface mesh. As far as logic is concerned making normal point outwards should not be too complicated I guess.
Thanks in advance for any help
You can use the function reverse_face_orientations in the Polygon mesh processing package.
Note that this package has several functions that can help you to correct/modify your mesh.
I am attempting to mesh a complicated design (~80,000 faces) for a microchannel heat sink, as pictured, and I would appreciate some advice. I have tried a range of different mesh controls (especially face sizing and body sizing), mesh settings and element sizes, and all have failed to produce a working mesh. The most common errors are shown in the linked picture, in particular the one regarding "The following surfaces cannot be meshed with acceptable quality. Try using a different element size or virtual topology." However, I have already reduced the element size to 2x10^-6 m, which takes two days to resolve before failure.
Unfortunately I cannot alter the geometry significantly, as it is imported from generation in SolidWORKS as either a STEP or an x.t file. As such, any advice for how I can successfully mesh the geometry for CFD analysis in FLUENT would be greatly appreciated.
I can provide more details or the geometry file itself if required.
Thanks in advance.
Meshing Attempt
Probably your cad design is not clean at all. But it is impossible to notice from this image. If you don't have control over the geometry source it is trouble. Because you might ask somebody else about check and fix something. First check you can do with your model it's trying to reduce the number of elements until the minimum possible value. Then if the mesh runs properly you can relay in the surfaces of your cad model. After that, you can refine the mesh, but the refining process is something that you have to do following some error criteria. If you are also the designer why not try to simplify a bit the geometry if you consider it is really hard to mesh? Meshing properly is a hard task, you should go step-by-step until you reach some solution. Also, you must not allow the preprocessor mesh automatically, without giving some criteria. Probably the first thing you have to answer even before apply any mesh is, what is your Reynolds number? And what is the most valuable result in which you can base the goodness of your discretization?
Thank you for your suggestions. In the end I solved the issue by importing the original mesh generated by COMSOL into SpaceClaim, then employing both the "Smooth" and "Reduce Faces" tools in tandem to simplify the geometry, before finally using SolidWORKS to turn the smoothed mesh into a solid body. This body retained many of the same features as the original, but was much less complex, having two orders of magnitude fewer faces. In turn, this permitted both meshing and heat transfer analysis in FLUENT.
I'm new to CGAL and I'm trying to cut a cube with an arbitrary surface mesh in 3d (no self intersections, not closed/no volume). The goal is to get a volume which consists of one "side" of the cut cube, closed by the part of the surface inside the cube.
The surface itself consists of unordered triangles which should have the same winding order (consistent normal directions) but have no neighborhood information and could contain same points multiple times for different triangles.
I tried to use the clip function, like:
CGAL::Polygon_mesh_processing::clip(cube,surface,true);
Which of course does not work because the surface is not closed (as far as I understood). But It shows the idea on how the operation should work.
Boolean operations (https://doc.cgal.org/latest/Polygon_mesh_processing/index.html#title14)) cannot be used for this as well since they are calculated on volumes and the surface has no volume.
I also thought about extending the outside of the surface so that it is closed. This, however, does not seem like a good approach.
Sadly, my research on similar problems was not successful.
I'm pretty sure that there is a nice way to do this in CGAL. Maybe someone with more experience in CGAL knows how to do this.
What would be the best approach for getting this volume?
Regards
EDIT:
By removing redundant points in my surface mesh I was able to get clip to work. Nevertheless, I do not always get the right side of the volume, even though the winding order should yield normals which point to the outside.
Is it necessary to calculate the normals and pass them as an extra parameter (see here) of the surface before the cut in order to always get the same "inner" side of the volume?
Also, the clip function seems to be quite slow. I have to do this cut for a very high number of cubes and different surfaces.
I use CGAL as header only lib and without GMP and MPFR, since it crashed my other application. How big is the speedup using these libraries and are there any other tricks which can be used to speedup computation, e.g. using parallelization?
I saw that CGAL uses Intel's TBB which. But in the header files which are included by the clipping algorithm CGAL_LINKED_WITH_TBB is not tested.
Thanks
It was a problem with the clipping mesh. Clipping could not be done properly. I increased it size and now it always intersects the volume.
I have a very fine mesh (STL) of some organic shapes (e.g., a bone) and would like to convert it to a few patches of NURBS, which will be much smoother with reasonable simplification.
I can do this manually with Solidworks ScanTo3D function, but it is not scriptable. It's a pain when I need to do hundreds of them.
Would there be a way to automate it, e.g., with some open source libraries available? I am perfectly fine with quite some loss in accuracy. I use mainly Python, but I don't mind if it is in other languages and I can work my way around it.
Note that one thing I'd like to avoid is to convert an STL of 10,000 triangles to a NURBS with 10,000 patches. I'd like to automatically (programmatically, could be with some parameter tunings) divide the mesh into a few patches and then fit it. Again, I'm perfect fine with quite some loss in accuracy.
Converting an arbitrary mesh to nurbs is not easy in general. What is a good nurbs surface for a given mesh depends on the use case. Do you want to manually edit the nurbs surface afterwards? Should symmetric structures or other features be recognized and represented correctly in the nurbs body? Is it important to keep the volume of the body? Are there boundary lines that should not be simplified as they change the appearance or angles that must be kept?
If you just want to smooth the mesh or reduce the amount of vertices there are easier ways like mesh reduction and mesh smoothing.
If you require your output to be nurbs there are different methods leading to different topologies and approximations like indicated above. A commonly used method for object simplification is to register the mesh to some handmade prototype and then perform some smaller changes to shape the specific instance. If there are for example several classes of shapes like bones, hearts, livers etc. it might be possible to model a prototype nurbs body for each class once which defines the average appearance and topology of that organ. Each instance of a class can then be converted to a nurbs by fitting the prototype to that instance. As the topology is fixed the optimization problem is reduced to the problem where we need to find the control points that approximate the mesh with the smallest error.Disadvantage of this method is that you have to create a prototype for each class. The advantage is that the topology will be nice and easily editable.
Another approach would be to first smooth the mesh and reduce the polygon count (there are libraries available for mesh reduction) and then simply converting each triangle/ quad to a nurbs patch (like the Rhino MeshToNurb Command). This method should be easier to implement but the resulting nurbs body could have an ugly topology.
If one of this methods is applicable really depends on what you want to do with your transformed data.
Background
I'm working on a project where a user gets scanned by a Kinect (v2). The result will be a generated 3D model which is suitable for use in games.
The scanning aspect is going quite well, and I've generated some good user models.
Example:
Note: This is just an early test model. It still needs to be cleaned up, and the stance needs to change to properly read skeletal data.
Problem
The problem I'm currently facing is that I'm unsure how to place skeletal data inside the generated 3D model. I can't seem to find a program that will let me insert the skeleton in the 3D model programmatically. I'd like to do this either via a program that I can control programmatically, or adjust the 3D model file in such a way that skeletal data gets included within the file.
What have I tried
I've been looking around for similar questions on Google and StackOverflow, but they usually refer to either motion capture or skeletal animation. I know Maya has the option to insert skeletons in 3D models, but as far as I could find that is always done by hand. Maybe there is a more technical term for the problem I'm trying to solve, but I don't know it.
I do have a train of thought on how to achieve the skeleton insertion. I imagine it to go like this:
Scan the user and generate a 3D model with Kinect;
1.2. Clean user model, getting rid of any deformations or unnecessary information. Close holes that are left in the clean up process.
Scan user skeletal data using the Kinect.
2.2. Extract the skeleton data.
2.3. Get joint locations and store as xyz-coordinates for 3D space. Store bone length and directions.
Read 3D skeleton data in a program that can create skeletons.
Save the new model with inserted skeleton.
Question
Can anyone recommend (I know, this is perhaps "opinion based") a program to read the skeletal data and insert it in to a 3D model? Is it possible to utilize Maya for this purpose?
Thanks in advance.
Note: I opted to post the question here and not on Graphics Design Stack Exchange (or other Stack Exchange sites) because I feel it's more coding related, and perhaps more useful for people who will search here in the future. Apologies if it's posted on the wrong site.
A tricky part of your question is what you mean by "inserting the skeleton". Typically bone data is very separate from your geometry, and stored in different places in your scene graph (with the bone data being hierarchical in nature).
There are file formats you can export to where you might establish some association between your geometry and skeleton, but that's very format-specific as to how you associate the two together (ex: FBX vs. Collada).
Probably the closest thing to "inserting" or, more appropriately, "attaching" a skeleton to a mesh is skinning. There you compute weight assignments, basically determining how much each bone influences a given vertex in your mesh.
This is a tough part to get right (both programmatically and artistically), and depending on your quality needs, is often a semi-automatic solution at best for the highest quality needs (commercial games, films, etc.) with artists laboring over tweaking the resulting weight assignments and/or skeleton.
There are algorithms that get pretty sophisticated in determining these weight assignments ranging from simple heuristics like just assigning weights based on nearest line distance (very crude, and will often fall apart near tricky areas like the pelvis or shoulder) or ones that actually consider the mesh as a solid volume (using voxels or tetrahedral representations) to try to assign weights. Example: http://blog.wolfire.com/2009/11/volumetric-heat-diffusion-skinning/
However, you might be able to get decent results using an algorithm like delta mush which allows you to get a bit sloppy with weight assignments but still get reasonably smooth deformations.
Now if you want to do this externally, pretty much any 3D animation software will do, including free ones like Blender. However, skinning and character animation in general is something that tends to take quite a bit of artistic skill and a lot of patience, so it's worth noting that it's not quite as easy as it might seem to make characters leap and dance and crouch and run and still look good even when you have a skeleton in advance. That weight association from skeleton to geometry is the toughest part. It's often the result of many hours of artists laboring over the deformations to get them to look right in a wide range of poses.