CGAL users discussion list

["Jernej Barbic" <>]

Dear Greg,

My email below was in no way directed toward you. I merely stated that
the task at hand is not difficult, without referring to your C++
skills, or anyone's skills in particular. If you were offended, I
apologize.

I did not have to post my experience with CGAL in the first place (it
was a free volunteer contribution on my part), but I did so because
Dr. Alliez asked me to do it, and because I think CGAL is a very good
project. I will also give due credits to CGAL whenever I use CGAL in
my papers.

I am not obliged to provide any code to anybody, and I do not have any
more time to contribute to CGAL. Please direct any further code
requests to the CGAL team.

Regards,
Jernej Barbic

On Tue, Sep 2, 2008 at 5:13 PM, Greg Fokum 
<>
 wrote:
> I find your mail a bit rude !
>
> --- On Tue, 9/2/08, Jernej Barbic 
> <>
>  wrote:
>
> From: Jernej Barbic 
> <>
> Subject: Re: [cgal-discuss] my experience with CGAL
> To: 
> 
> Date: Tuesday, September 2, 2008, 1:43 PM
>
> Hi Greg,
>
> This should be very easy to do for any person proficient in C++. I
> looked into Complex_2_in_triangulation_3_file_writer.h and redirected
> the output to my memory buffer as opposed to an output stream.
>
> As per releasing my code: sorry, I don't have the time to clean my
> code and release it publicly (I am not a CGAL developer).
>
> Regards,
> Jernej
>
> On Tue, Sep 2, 2008 at 4:09 PM, Greg Fokum 
> <>
>  wrote:
>> hello there
>>
>> Saw your correspondence and struggles with CGAL. Could you please share
> your
>> code on how you got to obtain the vertices and faces of the triangulation
>> using Complex_2_in_triangulation_3_file_writer.h as suggested ?
>>
>> Regards
>>
>> GT
>>
>> --- On Tue, 9/2/08, Jernej Barbic 
>> <>
>>  wrote:
>>
>> From: Jernej Barbic 
>> <>
>> Subject: [cgal-discuss] my experience with CGAL
>> To: 
>> 
>> Date: Tuesday, September 2, 2008, 11:11 AM
>>
>> Dear CGAL,
>>
>> I am posting these two message by invitation of Dr. Pierre Alliez. I
>> attended the CGAL course at SIGGRAPH in LA, and then tried using CGAL
>> to do surface mesh generation. I then had an email discussion
>>  with
>> Pierre, relating my experience with CGAL. Also, please note that
>  (due
>> to other work) it might be difficult for me to keep up with the
>> follow-ups; however, I wanted to share my experience, so I wrote the
>> emails below. Best of luck to CGAL!
>>
>> Regards,
>> Jernej Barbic
>> Post-doc associate, Computer Science and Artificial Intelligence Lab,
>> Massachusetts Institute of Technology
>> http://people.csail.mit.edu/barbic/
>>
>> The first email message:
>> ===================
>>
>> Dear Pierre,
>>
>> I am a computer graphics post-doc at MIT, and I saw your presentation
>> in this year's SIGGRAPH class on CGAL in Los Angeles.
>>
>> I was impressed with the presentation and the capabilities of CGAL, so
>> I tried using it as a tool in my project. Specifically, I wanted to
>> use it to generate good quality triangulations of isosurfaces, as in
>> the "skull"
>>
>  example:
>>
> http://www.cgal.org/Manual/3.3/doc_html/cgal_manual/Surface_mesher/Chapter_main.html
>>
>> I managed to compile and run the "skull" example (under Mac OS
> X).
>> However, I then ran into a problem which will most likely seem quite
>> trivial to you: I was unable to adapt the example so that I could
>> actually capture the output. That is, CGAL will generate an output
>> mesh; I then wanted to convert this mesh to my own in-memory
>> representation. This representation would be very simple: a list of
>> vertices, each given as three double precision values, followed by a
>> list of faces (triangles), each a set of three integer indices into
>> the preceding table of vertices. I was ultimately unable to figure out
>> how to do this.
>>
>> I listened to your presentation at SIGGRAPH, and then read the CGAL
>> manual several times. I spent two days looking through
>  many CGAL
>> header files (about 8-10 hours of work total), following
>>  seemingly
>> endless templated (and cryptic at times) arguments, in an attempt to
>> find clues as per how to access vertices of triangulations, and how to
>> obtain the integer indices of the vertices of every face. For example,
>> I "chased" the definition of "Vertex", over many
> header
>> files,
>> following (many) typedefs and templates, and did not succeed in
>> finding a final answer.
>>
>> I program in C++ all the time, and am quite proficient with templates
>> and STL. I could not find a final answer - and got a bit frustrated
>> given how simple and trivial the task. If I was on the CGAL team, I am
>> pretty sure I could just ask somebody and get the answer very quickly,
>> but with the information available to me, things were difficult.
>>
>> Here is what I did figure out. One can
>  print out the vertices like this:
>>
>> for ( C2t3::Vertex_iterator v = c2t3.vertices_begin(); v !=
>> c2t3.vertices_end(); ++v)
>> {
>>     std::cout << "v
>>  " << v->point() <<
>> std::endl;
>>   }
>>
>> (but printing is not what I really wanted; it would be better if I
>> could store v->point() into a C array such as "double [3]")
>>
>> And one can traverse the faces (but unsure if these are tet mesh
>> cells, or surface mesh triangles, or surface mesh
>> triangles+edges+vertices) like this:
>>
>> int count = 0;
>> for(C2t3::Facet_iterator f = c2t3.facets_begin(); f != c2t3.facets_end();
>> f++)
>> {
>>    //printf("%d\n", f->second); // this I am guessing is
> the
>> dimensionality of the facet
>>    if (f->second == 3)
>>    {
>>      std::cout << f->first->vertex(0)->point()
>  <<
> "
>> ";
>>      std::cout << f->first->vertex(1)->point() <<
> "
>> ";
>>      std::cout << f->first->vertex(2)->point();
>>      std::cout << std::endl;
>>      count++;
>>    }
>> }
>>
>> However, here I don't know what to do with
>>  f->first->vertex to pull
>> out the global integer index of that vertex. As you can see, I figured
>> out how to convert the vertex to its 3D location (3 coordinates); but
>> getting the global integer index would be much better. Also, I am not
>> sure if this method will give me the triangle faces of the surface
>> mesh, or will it give me the entire tet mesh. And if I run it on the
>> (unmodified, as shipped with CGAL) skull example, I get many 4-tuples
>> (I assume tets from the output tetrahedralization) that look ok, but
>> at the end there are several that have
>  three zero entries and one
>> entry equalling 1. So if those are tets, unsure what they mean.
>>
>> I think CGAL is great: it really implements many useful algorithms and
>> the ability to have exact arithmetic is very good. Based on my
>> experience, may I add a suggestion: right now, the manual talks a lot
>> about templates and about computational geometry algorithms, which
>>  is
>> all good. Templates certainly make CGAL more powerful. However, at
>> times the manual reads like the art of templatization was the main
>> point of CGAL; there is a lot of template lingo. This will be good for
>> somebody who is much into templates, but might be difficult to read
>> for other people. I would add even more concrete examples: whenever
>> you present some generic datastructure or algorithm (such as the
>> kernel, for example), consider giving concrete examples of templated
>>
>  arguments that one can pass to those datastructures or algorithms. And
>> as per triangulations, it would be good to have a manual page listing
>> the methods available to vertex iterators, face iterators, cell
>> iterators; the difference between face, facet, cell; and more
>> documentation on input and output.
>>
>> Thank you for creating CGAL, and for your help,
>> Jernej Barbic
>>
>> The second email message:
>> ======================
>>
>>>>dear
>>  Jernej,
>>>>
>>>>thanks for your positive feedback, that's very useful and
>> encouraging.
>>>>
>>>>as I am still on holidays, the short answer can be found in file
>> Complex_2_in_triangulation_3_file_writer.h
>>>>
>>>>I invite you to post your detailed email to the CGAL discuss list,
> so
>> that all developers see the trend (more and more people
>  start using that
>> surface
>> mesh generator, that's good to know).
>>>>
>>>>thanks again for your time,
>>>>
>>>>Pierre
>>
>> Hi Pierre,
>>
>> Thank you very much for the pointer to
>> Complex_2_in_triangulation_3_file_writer.h. I was able to
>> "reverse-engineer" that file and now the mesher works fine for
> me. I
>> already meshed several isosurfaces. The mesher is very good. I am not
>> aware of any other mesher that can achieve similar results.
>>
>> One minor issue that I noticed is that there is sometimes a spot on
>> the output mesh
>>  where for some reason the vertex density is
>> unnecessarily high. If there is such a spot, there is always exactly
>> one. It's not a big deal, but it does require either removing it
>> manually, or running several runs, guessing parameters until it
>> disappears. The location
>  of this spot might be related to the location
>> of the center of the bounding sphere (user-supplied parameter), and to
>> how deep that center is inside the volume enclosed by the isosurface.
>> But not 100% sure.
>>
>> Also, documentation says that the sphere center must be inside the
>> volume enclosed by the isosurface - but I noticed that the mesher
>> produces a plausible result even if it is not. And, I am not
>> completely sure if the bounding sphere has to cover the entire volume
>> where the grayscale image is defined, or only the output isosurface.
>> Also, I don't exactly understand the difference between the
> "distance
>> bound" and "radius bound" (inputs to the
>>  mesher); I read it
>> several
>> times in the manual and from that text I don't see the difference (and
>> I know they must be different, or else you would not have two separate
>>
>  parameters).
>>
>> FYI: I am combining your surface mesher with "tetgen" to
> generate
>> volumetric tet meshes (I do so since I am assuming that your mesher
>> doesn't generate a (quality) tet mesh, only a quality surface mesh). I
>> am getting very good quality meshes using this process.
>>
>> Again, my suggestion to CGAL would be to boost the documentation. Much
>> of the documentation talks about "concepts" and how these
> concepts
>> are
>> implemented in "models". This is interesting on its own,
> however, it
>> might be hard for a CGAL novice to parse this. For example, I'd try to
>> lookup "Vertex", expecting to see a concrete class, and a list
> of
>> methods that can be used with this class. Instead, there would be lots
>> of typedefs and talk about how this is a model of
>>  some concept and how
>> it has to implement certain things. And then I'd wonder why
>  those
>> typedefs are the way they are, and what alternative choices would be
>> and where I would look up those. And whether the class that I am
>> looking at (Vertex) is an actual class that I can use, or is it just
>> an abstract concept for me to implement (or partially implement), etc.
>> All this is just my 5 cents of course, take my criticism lightly. I
>> realize templatization has big benefits.
>>
>> As per posting to the CGAL discussion list, please go ahead and post
>> my previous email, in my name (it is easier for me if you post it,
>> than if I post it). You can also post this email if you wish.
>>
>> Thank you for your help.
>> Jernej Barbic
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