Isotropic remeshing failed with is_valid_polygon_mesh()

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Isotropic remeshing failed with is_valid_polygon_mesh()

yyhu
Hi,

I was trying to use CGAL::Polygon_mesh_processing::isotropic_remeshing() to remesh a CGAL::Surface_mesh. However, I got the following error message:

========== Error message begins. ==========

terminate called after throwing an instance of 'CGAL::Assertion_exception'
  what():  CGAL ERROR: assertion violation!
Expr: is_valid_polygon_mesh(mesh_)
File: /home/yaoyu/Libraries/cgal/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/internal/Isotropic_remeshing/remesh_impl.h
Line: 1037

========== Error message ends. ==========

I was trying the code listed at https://doc.cgal.org/latest/Polygon_mesh_processing/Polygon_mesh_processing_2isotropic_remeshing_example_8cpp-example.html and I enclosed the source file. I am not sure about the reason why CGAL thinks the Surface_mesh is not a valid polygon mesh.

The input mesh is in PLY format and you could find the file at https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing

One thing that might be interesting is that if I use the CGAL Polyhedron Demo program to load and do the isotropic remeshing, no errors are encountered. 

Any comments are appreciated.

Thank you!

Yaoyu

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Fwd: Isotropic remeshing failed with is_valid_polygon_mesh()

yyhu
Sorry for the duplicated messages. 

I did not specify my CGAL version in the last email. `git status` tells me that I am using CGAL 5.0.2.

Thanks!

---------- Forwarded message ---------
From: Yaoyu Hu <[hidden email]>
Date: Sun, Sep 6, 2020 at 12:47 AM
Subject: Isotropic remeshing failed with is_valid_polygon_mesh()
To: <[hidden email]>


Hi,

I was trying to use CGAL::Polygon_mesh_processing::isotropic_remeshing() to remesh a CGAL::Surface_mesh. However, I got the following error message:

========== Error message begins. ==========

terminate called after throwing an instance of 'CGAL::Assertion_exception'
  what():  CGAL ERROR: assertion violation!
Expr: is_valid_polygon_mesh(mesh_)
File: /home/yaoyu/Libraries/cgal/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/internal/Isotropic_remeshing/remesh_impl.h
Line: 1037

========== Error message ends. ==========

I was trying the code listed at https://doc.cgal.org/latest/Polygon_mesh_processing/Polygon_mesh_processing_2isotropic_remeshing_example_8cpp-example.html and I enclosed the source file. I am not sure about the reason why CGAL thinks the Surface_mesh is not a valid polygon mesh.

The input mesh is in PLY format and you could find the file at https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing

One thing that might be interesting is that if I use the CGAL Polyhedron Demo program to load and do the isotropic remeshing, no errors are encountered. 

Any comments are appreciated.

Thank you!

Yaoyu

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Re: Isotropic remeshing failed with is_valid_polygon_mesh()

Sebastien Loriot (GeometryFactory)
In reply to this post by yyhu
Could you check the value returned by
CGAL::is_valid_polygon_mesh(my_mesh) called on your mesh before calling
the CGAL function? It might be that the input is not a valid polygon
mesh (non-manifold vertices for example).

Thanks,

Sebastien.



On 9/6/20 6:47 AM, Yaoyu Hu ([hidden email] via cgal-discuss
Mailing List) wrote:

> Hi,
>
> I was trying to use CGAL::Polygon_mesh_processing::isotropic_remeshing()
> to remesh a CGAL::Surface_mesh. However, I got the following error message:
>
> ========== Error message begins. ==========
>
> terminate called after throwing an instance of 'CGAL::Assertion_exception'
>    what():  CGAL ERROR: assertion violation!
> Expr: is_valid_polygon_mesh(mesh_)
> File:
> /home/yaoyu/Libraries/cgal/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/internal/Isotropic_remeshing/remesh_impl.h
> Line: 1037
>
> ========== Error message ends. ==========
>
> I was trying the code listed at
> https://doc.cgal.org/latest/Polygon_mesh_processing/Polygon_mesh_processing_2isotropic_remeshing_example_8cpp-example.html 
> and I enclosed the source file. I am not sure about the reason why CGAL
> thinks the Surface_mesh is not a valid polygon mesh.
>
> The input mesh is in PLY format and you could find the file at
> https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing
>
> One thing that might be interesting is that if I use the CGAL Polyhedron
> Demo program to load and do the isotropic remeshing, no errors are
> encountered.
>
> Any comments are appreciated.
>
> Thank you!
>
> Yaoyu
>
> --
> You are currently subscribed to cgal-discuss.
> To unsubscribe or access the archives, go to
> https://sympa.inria.fr/sympa/info/cgal-discuss
>

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Re: Isotropic remeshing failed with is_valid_polygon_mesh()

yyhu
Hi Sebastien,

Thank you for your reply. I tried to use CGAL::is_valid_polygon_mesh(), it indeed returns false. However, I do not know how to visualize the content in the CGAL::Verbose_ostream, then I manually stepped into the source code. I found that the check fails inside is_valid_halfedge_graph() which is defined in cgal/BGL/include/CGAL/boost/graph/helpers.h . The actual place that triggers the failure is the following code section

========== Code section begins. ==========

for(vertex_descriptor vbegin : vertices(g))
  {
    // Pointer integrity.
    if(halfedge(vbegin, g) != boost::graph_traits<Graph>::null_halfedge())
      valid = (target(halfedge(vbegin, g), g) == vbegin);
    else
      valid = false;

    if(!valid)
    {
      verr << "vertex " << v << " halfedge incident to vertex is the null halfedge." << std::endl;
      verr << "Halfedge Graph Structure is NOT VALID." << std::endl;
      return false;
    }

.....other codes..........
}

========== Code section ends. ==========

The v value is 12718 for this particular mesh. (mesh link: https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing )

The input mesh, as I provided in the previous email and as the above link, is a resulting mesh from the advancing front surface reconstruction of CGAL (I wrote another separate piece of code to do that). The reconstructed mesh was saved to the file system with CGAL::write_ply() function. This mesh can be processed by the Polyhedron Demo program which performs isotropic remeshing without any warnings or errors. 

What should I do to make the mesh a valid polygon mesh? Is there a way to fix this situation? I tried to remove the self-intersection facets by first using CGAL::Polygon_mesh_processing::self_intersections() and then CGAL::Euler::remove_face(). Additionally, I tried CGAL::Polygon_mesh_processing::duplicate_non_manifold_vertices(). No intersections and no non-manifold vertices are found. But the mesh is still not valid.

I may try to look into the vertex 12718 ( if using 0-based indexing, it is 12717 I suppose ) and try to figure out what makes this vertex so special.

Hoping to get more insights into the problem from your help.

Regards,

Yaoyu

On Mon, Sep 7, 2020 at 12:50 AM "Sebastien Loriot (GeometryFactory)" <[hidden email]> wrote:
Could you check the value returned by
CGAL::is_valid_polygon_mesh(my_mesh) called on your mesh before calling
the CGAL function? It might be that the input is not a valid polygon
mesh (non-manifold vertices for example).

Thanks,

Sebastien.



On 9/6/20 6:47 AM, Yaoyu Hu ([hidden email] via cgal-discuss
Mailing List) wrote:
> Hi,
>
> I was trying to use CGAL::Polygon_mesh_processing::isotropic_remeshing()
> to remesh a CGAL::Surface_mesh. However, I got the following error message:
>
> ========== Error message begins. ==========
>
> terminate called after throwing an instance of 'CGAL::Assertion_exception'
>    what():  CGAL ERROR: assertion violation!
> Expr: is_valid_polygon_mesh(mesh_)
> File:
> /home/yaoyu/Libraries/cgal/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/internal/Isotropic_remeshing/remesh_impl.h
> Line: 1037
>
> ========== Error message ends. ==========
>
> I was trying the code listed at
> https://doc.cgal.org/latest/Polygon_mesh_processing/Polygon_mesh_processing_2isotropic_remeshing_example_8cpp-example.html
> and I enclosed the source file. I am not sure about the reason why CGAL
> thinks the Surface_mesh is not a valid polygon mesh.
>
> The input mesh is in PLY format and you could find the file at
> https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing
>
> One thing that might be interesting is that if I use the CGAL Polyhedron
> Demo program to load and do the isotropic remeshing, no errors are
> encountered.
>
> Any comments are appreciated.
>
> Thank you!
>
> Yaoyu
>
> --
> You are currently subscribed to cgal-discuss.
> To unsubscribe or access the archives, go to
> https://sympa.inria.fr/sympa/info/cgal-discuss
>

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Re: Isotropic remeshing failed with is_valid_polygon_mesh()

Sebastien Loriot (GeometryFactory)
I opened your file in the demo and did not see any issue.
The issue you mentioned that is detected by the code indicates that you
have isolated vertices (i.e. vertices with no edge/face attached).

If you have such an error for a mesh that is the output of the CGAL
advancing front algorithm, then this is a bug. If this is the case,
could you please try to come up with an example and a point cloud
showing the issue so that we can reproduce it and fix it?

In the meantime you can also try the function remove_isolated_vertices()

https://doc.cgal.org/latest/Polygon_mesh_processing/group__PMP__repairing__grp.html#ga91c02ef57e638faf2622eae93e7a25e2

Thanks,

Sebastien.


On 9/7/20 6:54 PM, Yaoyu Hu ([hidden email] via cgal-discuss
Mailing List) wrote:

> Hi Sebastien,
>
> Thank you for your reply. I tried to use CGAL::is_valid_polygon_mesh(),
> it indeed returns false. However, I do not know how to visualize the
> content in the CGAL::Verbose_ostream, then I manually stepped into the
> source code. I found that the check fails
> inside is_valid_halfedge_graph() which is defined in
> cgal/BGL/include/CGAL/boost/graph/helpers.h . The actual place that
> triggers the failure is the following code section
>
> ========== Code section begins. ==========
>
> for(vertex_descriptor vbegin : vertices(g))
>    {
>      // Pointer integrity.
>      if(halfedge(vbegin, g) != boost::graph_traits<Graph>::null_halfedge())
>        valid = (target(halfedge(vbegin, g), g) == vbegin);
>      else
>        valid = false;
>
>      if(!valid)
>      {
>        verr << "vertex " << v << " halfedge incident to vertex is the
> null halfedge." << std::endl;
>        verr << "Halfedge Graph Structure is NOT VALID." << std::endl;
>        return false;
>      }
>
> .....other codes..........
> }
>
> ========== Code section ends. ==========
>
> The v value is 12718 for this particular mesh. (mesh link:
> https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing 
> )
>
> The input mesh, as I provided in the previous email and as the above
> link, is a resulting mesh from the advancing front surface
> reconstruction of CGAL (I wrote another separate piece of code to do
> that). The reconstructed mesh was saved to the file system
> with CGAL::write_ply() function. This mesh can be processed by the
> Polyhedron Demo program which performs isotropic remeshing without any
> warnings or errors.
>
> What should I do to make the mesh a valid polygon mesh? Is there a way
> to fix this situation? I tried to remove the self-intersection facets by
> first using CGAL::Polygon_mesh_processing::self_intersections() and then
> CGAL::Euler::remove_face(). Additionally, I
> tried CGAL::Polygon_mesh_processing::duplicate_non_manifold_vertices().
> No intersections and no non-manifold vertices are found. But the mesh is
> still not valid.
>
> I may try to look into the vertex 12718 ( if using 0-based indexing, it
> is 12717 I suppose ) and try to figure out what makes this vertex so
> special.
>
> Hoping to get more insights into the problem from your help.
>
> Regards,
>
> Yaoyu
>
> On Mon, Sep 7, 2020 at 12:50 AM "Sebastien Loriot (GeometryFactory)"
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>     Could you check the value returned by
>     CGAL::is_valid_polygon_mesh(my_mesh) called on your mesh before calling
>     the CGAL function? It might be that the input is not a valid polygon
>     mesh (non-manifold vertices for example).
>
>     Thanks,
>
>     Sebastien.
>
>
>
>     On 9/6/20 6:47 AM, Yaoyu Hu ([hidden email]
>     <mailto:[hidden email]> via cgal-discuss
>     Mailing List) wrote:
>      > Hi,
>      >
>      > I was trying to
>     use CGAL::Polygon_mesh_processing::isotropic_remeshing()
>      > to remesh a CGAL::Surface_mesh. However, I got the following
>     error message:
>      >
>      > ========== Error message begins. ==========
>      >
>      > terminate called after throwing an instance of
>     'CGAL::Assertion_exception'
>      >    what():  CGAL ERROR: assertion violation!
>      > Expr: is_valid_polygon_mesh(mesh_)
>      > File:
>      >
>     /home/yaoyu/Libraries/cgal/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/internal/Isotropic_remeshing/remesh_impl.h
>      > Line: 1037
>      >
>      > ========== Error message ends. ==========
>      >
>      > I was trying the code listed at
>      >
>     https://doc.cgal.org/latest/Polygon_mesh_processing/Polygon_mesh_processing_2isotropic_remeshing_example_8cpp-example.html
>
>      > and I enclosed the source file. I am not sure about the reason
>     why CGAL
>      > thinks the Surface_mesh is not a valid polygon mesh.
>      >
>      > The input mesh is in PLY format and you could find the file at
>      >
>     https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing
>      >
>      > One thing that might be interesting is that if I use the CGAL
>     Polyhedron
>      > Demo program to load and do the isotropic remeshing, no errors are
>      > encountered.
>      >
>      > Any comments are appreciated.
>      >
>      > Thank you!
>      >
>      > Yaoyu
>      >
>      > --
>      > You are currently subscribed to cgal-discuss.
>      > To unsubscribe or access the archives, go to
>      > https://sympa.inria.fr/sympa/info/cgal-discuss
>      >
>
>     --
>     You are currently subscribed to cgal-discuss.
>     To unsubscribe or access the archives, go to
>     https://sympa.inria.fr/sympa/info/cgal-discuss
>
>
>
> --
> You are currently subscribed to cgal-discuss.
> To unsubscribe or access the archives, go to
> https://sympa.inria.fr/sympa/info/cgal-discuss
>

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Re: Isotropic remeshing failed with is_valid_polygon_mesh()

yyhu
Hi Sebastien,

You are very helpful!

I tried to use CGAL::Polygon_mesh_processing::remove_isolated_vertices() and it worked. There are 4 isolated points removed by the remove_isolated_vertices() function. Then the downstream isotropic remeshing works without any problem. 

As suggested by you, I am sharing the point cloud and sample code to do the advancing front surface reconstruction with CGAL. You could find the point cloud at
and the source code as the attachment.

I tested the sample code on my machine with CGAL 5.0.2, the reconstructed mesh will have 4 isolated points that get removed by remove_isolated_vertices(). Please note that, the advancing front surface reconstruction takes hundreds of seconds with the Debug build but only a couple of tens seconds if executed in the Release build. I am not sure if the efficiency difference indicating any other issues.

Hope this helps to identify any potential issues in the reconstruction.

Regards,

Yaoyu


On Tue, Sep 8, 2020 at 12:52 AM "Sebastien Loriot (GeometryFactory)" <[hidden email]> wrote:
I opened your file in the demo and did not see any issue.
The issue you mentioned that is detected by the code indicates that you
have isolated vertices (i.e. vertices with no edge/face attached).

If you have such an error for a mesh that is the output of the CGAL
advancing front algorithm, then this is a bug. If this is the case,
could you please try to come up with an example and a point cloud
showing the issue so that we can reproduce it and fix it?

In the meantime you can also try the function remove_isolated_vertices()

https://doc.cgal.org/latest/Polygon_mesh_processing/group__PMP__repairing__grp.html#ga91c02ef57e638faf2622eae93e7a25e2

Thanks,

Sebastien.


On 9/7/20 6:54 PM, Yaoyu Hu ([hidden email] via cgal-discuss
Mailing List) wrote:
> Hi Sebastien,
>
> Thank you for your reply. I tried to use CGAL::is_valid_polygon_mesh(),
> it indeed returns false. However, I do not know how to visualize the
> content in the CGAL::Verbose_ostream, then I manually stepped into the
> source code. I found that the check fails
> inside is_valid_halfedge_graph() which is defined in
> cgal/BGL/include/CGAL/boost/graph/helpers.h . The actual place that
> triggers the failure is the following code section
>
> ========== Code section begins. ==========
>
> for(vertex_descriptor vbegin : vertices(g))
>    {
>      // Pointer integrity.
>      if(halfedge(vbegin, g) != boost::graph_traits<Graph>::null_halfedge())
>        valid = (target(halfedge(vbegin, g), g) == vbegin);
>      else
>        valid = false;
>
>      if(!valid)
>      {
>        verr << "vertex " << v << " halfedge incident to vertex is the
> null halfedge." << std::endl;
>        verr << "Halfedge Graph Structure is NOT VALID." << std::endl;
>        return false;
>      }
>
> .....other codes..........
> }
>
> ========== Code section ends. ==========
>
> The v value is 12718 for this particular mesh. (mesh link:
> https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing
> )
>
> The input mesh, as I provided in the previous email and as the above
> link, is a resulting mesh from the advancing front surface
> reconstruction of CGAL (I wrote another separate piece of code to do
> that). The reconstructed mesh was saved to the file system
> with CGAL::write_ply() function. This mesh can be processed by the
> Polyhedron Demo program which performs isotropic remeshing without any
> warnings or errors.
>
> What should I do to make the mesh a valid polygon mesh? Is there a way
> to fix this situation? I tried to remove the self-intersection facets by
> first using CGAL::Polygon_mesh_processing::self_intersections() and then
> CGAL::Euler::remove_face(). Additionally, I
> tried CGAL::Polygon_mesh_processing::duplicate_non_manifold_vertices().
> No intersections and no non-manifold vertices are found. But the mesh is
> still not valid.
>
> I may try to look into the vertex 12718 ( if using 0-based indexing, it
> is 12717 I suppose ) and try to figure out what makes this vertex so
> special.
>
> Hoping to get more insights into the problem from your help.
>
> Regards,
>
> Yaoyu
>
> On Mon, Sep 7, 2020 at 12:50 AM "Sebastien Loriot (GeometryFactory)"
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>     Could you check the value returned by
>     CGAL::is_valid_polygon_mesh(my_mesh) called on your mesh before calling
>     the CGAL function? It might be that the input is not a valid polygon
>     mesh (non-manifold vertices for example).
>
>     Thanks,
>
>     Sebastien.
>
>
>
>     On 9/6/20 6:47 AM, Yaoyu Hu ([hidden email]
>     <mailto:[hidden email]> via cgal-discuss
>     Mailing List) wrote:
>      > Hi,
>      >
>      > I was trying to
>     use CGAL::Polygon_mesh_processing::isotropic_remeshing()
>      > to remesh a CGAL::Surface_mesh. However, I got the following
>     error message:
>      >
>      > ========== Error message begins. ==========
>      >
>      > terminate called after throwing an instance of
>     'CGAL::Assertion_exception'
>      >    what():  CGAL ERROR: assertion violation!
>      > Expr: is_valid_polygon_mesh(mesh_)
>      > File:
>      >
>     /home/yaoyu/Libraries/cgal/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/internal/Isotropic_remeshing/remesh_impl.h
>      > Line: 1037
>      >
>      > ========== Error message ends. ==========
>      >
>      > I was trying the code listed at
>      >
>     https://doc.cgal.org/latest/Polygon_mesh_processing/Polygon_mesh_processing_2isotropic_remeshing_example_8cpp-example.html
>
>      > and I enclosed the source file. I am not sure about the reason
>     why CGAL
>      > thinks the Surface_mesh is not a valid polygon mesh.
>      >
>      > The input mesh is in PLY format and you could find the file at
>      >
>     https://drive.google.com/file/d/1Z9AMfRnbkJGmDuUOc7ZAdMAvbhhhx_Vn/view?usp=sharing
>      >
>      > One thing that might be interesting is that if I use the CGAL
>     Polyhedron
>      > Demo program to load and do the isotropic remeshing, no errors are
>      > encountered.
>      >
>      > Any comments are appreciated.
>      >
>      > Thank you!
>      >
>      > Yaoyu
>      >
>      > --
>      > You are currently subscribed to cgal-discuss.
>      > To unsubscribe or access the archives, go to
>      > https://sympa.inria.fr/sympa/info/cgal-discuss
>      >
>
>     --
>     You are currently subscribed to cgal-discuss.
>     To unsubscribe or access the archives, go to
>     https://sympa.inria.fr/sympa/info/cgal-discuss
>
>
>
> --
> You are currently subscribed to cgal-discuss.
> To unsubscribe or access the archives, go to
> https://sympa.inria.fr/sympa/info/cgal-discuss
>

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ReconstructionTest.cpp (8K) Download Attachment
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Re: Isotropic remeshing failed with is_valid_polygon_mesh()

andreas.fabri

Hello Yaoyu Hu,

Can you give us the points you used for Advancing Front Surface Reconstruction
as well as the parameters of your call, preferably on  gist.github.com

Best,

Andreas

On 9/8/2020 8:16 PM, Yaoyu Hu ([hidden email] via cgal-discuss Mailing List) wrote:
If you have such an error for a mesh that is the output of the CGAL
advancing front algorithm, then this is a bug. If this is the case,
could you please try to come up with an example and a point cloud
showing the issue so that we can reproduce it and fix it?
-- 
Andreas Fabri, PhD
Chief Officer, GeometryFactory
Editor, The CGAL Project

phone: +33.492.954.912    skype: andreas.fabri

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Re: Isotropic remeshing failed with is_valid_polygon_mesh()

yyhu
Hi Andreas, 

I created a public gist. The link is here


There are the sample code, point cloud, and a short ReadMe describing the gist.

Best,

Yaoyu

On Wed, Sep 9, 2020 at 3:47 AM Andreas Fabri <[hidden email]> wrote:

Hello Yaoyu Hu,

Can you give us the points you used for Advancing Front Surface Reconstruction
as well as the parameters of your call, preferably on  gist.github.com

Best,

Andreas

On 9/8/2020 8:16 PM, Yaoyu Hu ([hidden email] via cgal-discuss Mailing List) wrote:
If you have such an error for a mesh that is the output of the CGAL
advancing front algorithm, then this is a bug. If this is the case,
could you please try to come up with an example and a point cloud
showing the issue so that we can reproduce it and fix it?
-- 
Andreas Fabri, PhD
Chief Officer, GeometryFactory
Editor, The CGAL Project

phone: +33.492.954.912    skype: andreas.fabri

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