CGAL error subtracting STL from a cube

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CGAL error subtracting STL from a cube

jon_bondy

Code that used to "work" (using a simpler STL) is now failing with this.  I am subtracting an STL from a cube.


Rendering Polygon Mesh using CGAL...

ERROR: CGAL error in CGAL_Nef_polyhedron3(): CGAL ERROR: assertion violation! Expr: e->incident_sface() != SFace_const_handle() File: /mxe/usr/x86_64-w64-mingw32.static.posix/include/CGAL/Nef_S2/SM_const_decorator.h Line: 329

Geometries in cache: 18



Any hints?


Jon


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Re: CGAL error subtracting STL from a cube

jon_bondy

I imagine that the STL was damaged.  After repairing it, the object is now appearing way off in the distance, so far away that I cannot even estimate how to bring it back to the origin.  Never had to deal with this before.

Grump.

On 10/26/2020 9:04 PM, jon wrote:

Code that used to "work" (using a simpler STL) is now failing with this.  I am subtracting an STL from a cube.


Rendering Polygon Mesh using CGAL...

ERROR: CGAL error in CGAL_Nef_polyhedron3(): CGAL ERROR: assertion violation! Expr: e->incident_sface() != SFace_const_handle() File: /mxe/usr/x86_64-w64-mingw32.static.posix/include/CGAL/Nef_S2/SM_const_decorator.h Line: 329

Geometries in cache: 18



Any hints?


Jon


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Re: CGAL error subtracting STL from a cube

cbernhardt
Can you post the code and the STL file?



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Re: CGAL error subtracting STL from a cube

cbernhardt
I received the two files you sent to me.  Here are some statistics for the
two files.

Jon-mesh-export-3 - MM Repair.stl
input=MESHMIXER-STL-BINARY-FORMAT
299660 Triangles
xmin=0.000 xmax=10.398 xrange=10.398
ymin=0.000 ymax=25.400 yrange=25.400
zmin=-0.000 zmax=16.921 zrange=16.921

Hollow Face 2.stl
input=solid OpenSCAD_Model ASCII format
xmin=1.696 xmax=80.000 xrange=78.304
ymin=-66.332 ymax=68.700 yrange=135.032
zmin=-178.294 zmax=11.098 zrange=189.392


In the picture below the  Jon-mesh-export-3 - MM Repair.stl mode is shown in
red and the Hollow Face 2.stl
model is in yellow.  You did not send me the OpenSCAD code so I don't know
how you are subtracting them from a cube.
Hope this helps.
Charles
<http://forum.openscad.org/file/t1309/jon_hollow.jpg>



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Re: CGAL error subtracting STL from a cube

jon_bondy

Charlie:

I sent you 3 emails, which bounced.  This is what was in them. I have also attached the OpenSCAD source code.


I have attached the test code and am sending two larger STLs using WeTransfer.  You will have to mess with the import() statement to aim it at the STL on your system.  The code is supposed to subtract two solid heads from each other, with one offset by 10 mm.  The result is supposed to be a thin facial surface, but what I see here is just the original STL file, probably as a result of the error.  I am also sending what I was expecting (but using a cartoon face).

The MM Repair STL is the one that is used by my code.  The Hollow Face 2 STL is just to show you what it is supposed to look like after the code runs.

I imagine that there is something about the complexity of the STL that is causing the problem.  Maybe you will see something that I have not.  Note that I have cleaned up this STL quite a few times using a variety of programs in order to remove pinholes and the like.

Thanks for your help!


This is the log from running that code:


Parsing design (AST generation)...
Compiling design (CSG Tree generation)...
Rendering Polygon Mesh using CGAL...

ERROR: CGAL error in CGALUtils::applyBinaryOperator difference: CGAL ERROR: assertion violation! Expr: itl != it->second.end() File: /mxe/usr/x86_64-w64-mingw32.static.posix/include/CGAL/Nef_3/SNC_external_structure.h Line: 1152

Geometries in cache: 7

Geometry cache size in bytes: 86304872

CGAL Polyhedrons in cache: 0

CGAL cache size in bytes: 0

Total rendering time: 0 hours, 23 minutes, 17 seconds

Top level object is a 3D object:

Simple: yes

Vertices: 149822

Halfedges: 898980

Edges: 449490

Halffacets: 599320

Facets: 299660

Volumes: 2

Rendering finished.

On 10/29/2020 4:57 PM, cbernhardt wrote:
I received the two files you sent to me.  Here are some statistics for the
two files.


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Hollow Face Test.scad (624 bytes) Download Attachment
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Re: CGAL error subtracting STL from a cube

cbernhardt
I tried your code and OpenSCAD chocked.  The first thing I noticed is that (I
assume) you are trying to get a 10mm thick face shell, but your model is
only 10 x 25 x 17.  I think OpenSCAD is not the program with which to
accomplish this.  I scaled up your model by a factor of 10, brought it into
Meshmixer, sliced off the back face, brought it into Blender and solidified
it 2mm.  Below is the result.  Not the answer you were looking for, but it
works
<http://forum.openscad.org/file/t1309/face.jpg>



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Re: CGAL error subtracting STL from a cube

jon_bondy
Thanks!

l understand that the STL is small, but I scale it up to the correct
side in the code.  I have about 20 different models that I derive from
that face STL in OpenSCAD, so getting it to work is important to me.  
That said, it may be impossible, for reasons I cannot understand.

Jon

On 10/30/2020 4:11 PM, cbernhardt wrote:

> I tried your code and OpenSCAD chocked.  The first thing I noticed is that (I
> assume) you are trying to get a 10mm thick face shell, but your model is
> only 10 x 25 x 17.  I think OpenSCAD is not the program with which to
> accomplish this.  I scaled up your model by a factor of 10, brought it into
> Meshmixer, sliced off the back face, brought it into Blender and solidified
> it 2mm.  Below is the result.  Not the answer you were looking for, but it
> works
> <http://forum.openscad.org/file/t1309/face.jpg>
>
>
>
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Re: CGAL error subtracting STL from a cube

rickan
This post was updated on .
I have some ideas. If you send me the stl file I'll see if they are relevant, and
see what I can do.



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Re: CGAL error subtracting STL from a cube

rickan
None of my ideas were relevant.

But I made two attempts to get what I think you want using different methods
and both look oddly fractured in preview and do not render with thin shells.
The surreal fractures in preview seem identical with both methods and
independent of thickness. I mean when I change the file the preview doesn't
change except for the thickness if I change that. The fractures do not
change. But they migrate and morph oddly as if not part of the model when
you alter the POV.

The errors from render are in the scad file.

I set it up to generate the shell using scale instead of translate and the
surreal fractures show up in preview even when the shell thickness is 50%.
However! It renders at that thickness! (It did not render at 25% and at
least one thinner value I tried, probably 5%.) I suppose you could do a
binary search for a thickness that is thinner than 50% which renders. This
has me thinking that the stl interferes with itself when the shell thickness
is too thin, i.e. one or more of the craggy features, e.g. in the beard
perforate the shell. That's just a hypothesis. Well, I'm pretty sure it
happens if the shell is thin enough, but I don't know why that would be a
problem.

I made a third attempt just to subtract the face from a cube and that
previews and renders fine. I would expect, from my limited experience, that
any difference or intersection with the stl would fail, not just a
difference or intersection of the stl with itself depending on the relative
scale.

I did do a 1% translation to avoid the pesky ~0 thickness membrane. Maybe
that's big enough to cause interference between the two surfaces. Maybe that
should be reduced to 0.1%. I kind of doubt that's the problem though.

HollowFaceRMK.scad <http://forum.openscad.org/file/t1112/HollowFaceRMK.scad>  

HollowFaceRMK.png <http://forum.openscad.org/file/t1112/HollowFaceRMK.png>  




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Re: CGAL error subtracting STL from a cube

nophead
I think you need to set convexity in the import statement to get it to preview correctly.

On Sat, 31 Oct 2020 at 03:20, rickan <[hidden email]> wrote:
None of my ideas were relevant.

But I made two attempts to get what I think you want using different methods
and both look oddly fractured in preview and do not render with thin shells.
The surreal fractures in preview seem identical with both methods and
independent of thickness. I mean when I change the file the preview doesn't
change except for the thickness if I change that. The fractures do not
change. But they migrate and morph oddly as if not part of the model when
you alter the POV.

The errors from render are in the scad file.

I set it up to generate the shell using scale instead of translate and the
surreal fractures show up in preview even when the shell thickness is 50%.
However! It renders at that thickness! (It did not render at 25% and at
least one thinner value I tried, probably 5%.) I suppose you could do a
binary search for a thickness that is thinner than 50% which renders. This
has me thinking that the stl interferes with itself when the shell thickness
is too thin, i.e. one or more of the craggy features, e.g. in the beard
perforate the shell. That's just a hypothesis. Well, I'm pretty sure it
happens if the shell is thin enough, but I don't know why that would be a
problem.

I made a third attempt just to subtract the face from a cube and that
previews and renders fine. I would expect, from my limited experience, that
any difference or intersection with the stl would fail, not just a
difference or intersection of the stl with itself depending on the relative
scale.

I did do a 1% translation to avoid the pesky ~0 thickness membrane. Maybe
that's big enough to cause interference between the two surfaces. Maybe that
should be reduced to 0.1%. I kind of doubt that's the problem though.

HollowFaceRMK.scad <http://forum.openscad.org/file/t1112/HollowFaceRMK.scad

HollowFaceRMK.png <http://forum.openscad.org/file/t1112/HollowFaceRMK.png




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Re: CGAL error subtracting STL from a cube

jon_bondy

nophead:

Thanks for the suggestion.  A convexity of 1000 does not fix the CGAL error.  The STL in question is a 3D scan of my face, and I have a large beard.  Perhaps convexity needs to be 10,000.  Who knows.

Jon

On 10/31/2020 4:29 AM, nop head wrote:
I think you need to set convexity in the import statement to get it to preview correctly.

On Sat, 31 Oct 2020 at 03:20, rickan <[hidden email]> wrote:
None of my ideas were relevant.

But I made two attempts to get what I think you want using different methods
and both look oddly fractured in preview and do not render with thin shells.
The surreal fractures in preview seem identical with both methods and
independent of thickness. I mean when I change the file the preview doesn't
change except for the thickness if I change that. The fractures do not
change. But they migrate and morph oddly as if not part of the model when
you alter the POV.

The errors from render are in the scad file.

I set it up to generate the shell using scale instead of translate and the
surreal fractures show up in preview even when the shell thickness is 50%.
However! It renders at that thickness! (It did not render at 25% and at
least one thinner value I tried, probably 5%.) I suppose you could do a
binary search for a thickness that is thinner than 50% which renders. This
has me thinking that the stl interferes with itself when the shell thickness
is too thin, i.e. one or more of the craggy features, e.g. in the beard
perforate the shell. That's just a hypothesis. Well, I'm pretty sure it
happens if the shell is thin enough, but I don't know why that would be a
problem.

I made a third attempt just to subtract the face from a cube and that
previews and renders fine. I would expect, from my limited experience, that
any difference or intersection with the stl would fail, not just a
difference or intersection of the stl with itself depending on the relative
scale.

I did do a 1% translation to avoid the pesky ~0 thickness membrane. Maybe
that's big enough to cause interference between the two surfaces. Maybe that
should be reduced to 0.1%. I kind of doubt that's the problem though.

HollowFaceRMK.scad <http://forum.openscad.org/file/t1112/HollowFaceRMK.scad

HollowFaceRMK.png <http://forum.openscad.org/file/t1112/HollowFaceRMK.png




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Re: CGAL error subtracting STL from a cube

adrianv
The convexity argument is only used for displaying in preview.  It has
NOTHING to do with CGAL errors which are from render.  If you're getting
CGAL errors it means CGAL thinks your geometry is not a manifold or is
somehow malformed, so the only fix is going to be to change the geometry.  


jon_bondy wrote

> nophead:
>
> Thanks for the suggestion.  A convexity of 1000 does not fix the CGAL
> error.  The STL in question is a 3D scan of my face, and I have a large
> beard.  Perhaps convexity needs to be 10,000.  Who knows.
>
> Jon
>
> On 10/31/2020 4:29 AM, nop head wrote:
>> I think you need to set convexity in the import statement to get it to
>> preview correctly.
>>
>> On Sat, 31 Oct 2020 at 03:20, rickan &lt;

> richard@

>  
> &gt; &lt;mailto:

> richard@

> &gt;> wrote:
>>
>>     None of my ideas were relevant.
>>
>>     But I made two attempts to get what I think you want using
>>     different methods
>>     and both look oddly fractured in preview and do not render with
>>     thin shells.
>>     The surreal fractures in preview seem identical with both methods and
>>     independent of thickness. I mean when I change the file the
>>     preview doesn't
>>     change except for the thickness if I change that. The fractures do
>> not
>>     change. But they migrate and morph oddly as if not part of the
>>     model when
>>     you alter the POV.
>>
>>     The errors from render are in the scad file.
>>
>>     I set it up to generate the shell using scale instead of translate
>>     and the
>>     surreal fractures show up in preview even when the shell thickness
>>     is 50%.
>>     However! It renders at that thickness! (It did not render at 25%
>>     and at
>>     least one thinner value I tried, probably 5%.) I suppose you could
>>     do a
>>     binary search for a thickness that is thinner than 50% which
>>     renders. This
>>     has me thinking that the stl interferes with itself when the shell
>>     thickness
>>     is too thin, i.e. one or more of the craggy features, e.g. in the
>>     beard
>>     perforate the shell. That's just a hypothesis. Well, I'm pretty
>>     sure it
>>     happens if the shell is thin enough, but I don't know why that
>>     would be a
>>     problem.
>>
>>     I made a third attempt just to subtract the face from a cube and that
>>     previews and renders fine. I would expect, from my limited
>>     experience, that
>>     any difference or intersection with the stl would fail, not just a
>>     difference or intersection of the stl with itself depending on the
>>     relative
>>     scale.
>>
>>     I did do a 1% translation to avoid the pesky ~0 thickness
>>     membrane. Maybe
>>     that's big enough to cause interference between the two surfaces.
>>     Maybe that
>>     should be reduced to 0.1%. I kind of doubt that's the problem though.
>>
>>     HollowFaceRMK.scad
>>     &lt;http://forum.openscad.org/file/t1112/HollowFaceRMK.scad
> &gt;     &lt;http://forum.openscad.org/file/t1112/HollowFaceRMK.scad&gt;>
>>
>>     HollowFaceRMK.png
>>     &lt;http://forum.openscad.org/file/t1112/HollowFaceRMK.png
> &gt;     &lt;http://forum.openscad.org/file/t1112/HollowFaceRMK.png&gt;>
>>
>>
>>
>>
>>     --
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Re: CGAL error subtracting STL from a cube

rickan
In reply to this post by nophead
Yes!

Setting convexity to 2 removes nearly all the fractures. Setting it higher
seems to remove them all but makes preview extremely laggy on my computer.

Without the distraction of the fractures the holes in the shell become
obvious.

In the attached image of the stl model subtracted from the cube with
viewport settings

$vpt = [-1.97, -9.31, 0.42]; $vpr = 90.00, 0.00, 90.00]; $vpd = 2.30;

There is what looks like a separate blob. It is not separate, however, it is
a hook in the stl which becomes an empty loop in the subtraction. Maybe that
is part of the problem.

HollowFaceIsland.png
<http://forum.openscad.org/file/t1112/HollowFaceIsland.png>  

Maybe there are other nearly invisible features, e.g., long extremely thin
spikes, which are causing problems also.



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Re: CGAL error subtracting STL from a cube

cacb
In reply to this post by adrianv
On 2020-10-31 13:37, adrianv wrote:
> The convexity argument is only used for displaying in preview.  It has
> NOTHING to do with CGAL errors which are from render.  If you're
> getting
> CGAL errors it means CGAL thinks your geometry is not a manifold or is
> somehow malformed, so the only fix is going to be to change the
> geometry.

Indeed, the convexity parameter has nothing at all to do with geometric
calculations. In my opinion that parameter should not even exist, but
that's another story.

Where is the STL that you are struggling with?

Carsten Arnholm

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Re: CGAL error subtracting STL from a cube

jon_bondy
Thanks, everyone, for helping out.

The STL is huge (>10MB) so I am sending it to individuals who
volunteer.  I will send a copy to Carsten; if anyone else is curious,
please let me know

Jon

On 10/31/2020 8:52 AM, [hidden email] wrote:

> On 2020-10-31 13:37, adrianv wrote:
>> The convexity argument is only used for displaying in preview.  It has
>> NOTHING to do with CGAL errors which are from render.  If you're getting
>> CGAL errors it means CGAL thinks your geometry is not a manifold or is
>> somehow malformed, so the only fix is going to be to change the
>> geometry.
>
> Indeed, the convexity parameter has nothing at all to do with
> geometric calculations. In my opinion that parameter should not even
> exist, but that's another story.
>
> Where is the STL that you are struggling with?
>
> Carsten Arnholm
>
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Re: CGAL error subtracting STL from a cube

cacb
On 31.10.2020 15:13, jon wrote:
> Thanks, everyone, for helping out.
>
> The STL is huge (>10MB) so I am sending it to individuals who
> volunteer.  I will send a copy to Carsten; if anyone else is curious,
> please let me know

I got your file, thanks.

I ran it through polyfix which reported a number of issues (see below),
and saved it in AMF format, as that is supported in OpenSCAD since
2019.05. I then ran it through your .scad code using OpenSCAD version
2020.10.11.nightly (git b416aa2) under Ubuntu.

However, it failed:
ERROR: CGAL error in CGAL_Nef_polyhedron3(): CGAL ERROR: assertion
violation! Expr: e->incident_sface() != SFace_const_handle() File:
/usr/include/CGAL/Nef_S2/SM_const_decorator.h Line: 329, location unknown


So instead I ran your STL through polyfix again and saved it as OBJ, as
that is much more compact than AMF (but OBJ is not supported in OpenSCAD):


$ polyfix "Jon-mesh-export-3 - MM Repair.stl" -out=Jon_Face_polyfix.obj

Parameters:
   input_file = Jon-mesh-export-3 - MM Repair.stl
          out = Jon_Face_polyfix.obj


polyhedron 0 ================= volume=1992, dtol=0.01, atol=1e-06,
maxiter=10
iteration 0: vertices=898980 faces=299660

              warning: nonmanifold edges: uc(1)=898980
              merged 749167 vertices
              removed 12 collapsed or zero area faces
              removed 7 duplicate faces
              removed 2 nonmanifold faces
              total changes=749188
              warning: nonmanifold edges: uc(1)=5 uc(3)=4 uc(4)=1

iteration 1: vertices=149813 faces=299639
              warning: nonmanifold edges: uc(1)=5 uc(3)=4 uc(4)=1
              split 3 faces
              removed 1 duplicate face
              removed 3 nonmanifold faces
              removed 6 zero area faces
              total changes=13
              warning: nonmanifold edges: uc(4)=1

iteration 2: vertices=149813 faces=299634
              warning: nonmanifold edges: uc(4)=1
              removed 1 unused vertex
              total changes=1
              warning: nonmanifold edges: uc(4)=1

iteration 3: vertices=149812 faces=299634
              warning: nonmanifold edges: uc(4)=1
              total changes=0
              warning: nonmanifold edges: uc(4)=1

Summary:
              polyhedron 0: vertices=149812 faces=299634 : warning:
nonmanifold edges: uc(4)=1

Writing: Jon_Face_polyfix_1.obj

... polyfix finished, time used: 0d 00h 02m 36s


The summary says the result contains one edge with use-count=4, so it is
not perfectly repaired, but it might still work in AngelCAD. I wrote a
few lines of code to make the hollow face, but dropped the cube as it
did not seem to intersect with the Face (?).

See attached image of result.

If you allow I will upload the AngelCAD code and the resulting STL (26.1
MB) to a github gist, so you can be viewed and you can download it. Is
that ok?

Regards
Carsten Arnholm

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Re: CGAL error subtracting STL from a cube

cacb
> On 31.10.2020 15:13, jon wrote:
>> Thanks, everyone, for helping out.

The script and files are here:
https://github.com/arnholm/hollow_face

You can get the file in 2 ways

Method 1: Go to the page above and find the green button that says
"Code" and select the "Download Zip" to get all files, including the STL
and OBJ files.

Method 2: Clone the repository using git to get all files.

$ git clone https://github.com/arnholm/hollow_face

Carsten Arnholm

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