Re: [Paraview] slicing a large VTK_POLYHEDRON

[Pierre Van Hauwaert]

Hi,

As requested I attached with that email a list of 8 segfaulting 
polyhedrons. It happens with a centre of (0,0,0) and an oZ normal.


Regards,

Pierre
On 01/04/2017 10:11 AM, Mathieu Westphal wrote:

Hi

It may be a different issue than the one i'm fixing. If you can share 
the segfaulting polyhedron, please do so i can take a look when i get 
back on this issue ( which my not be soon, feel free to find other 
solutions)


Regards,

Mathieu Westphal

On Tue, Jan 3, 2017 at 10:46 PM, Pierre Van Hauwaert 
> wrote:


Hi Mathieu and Thomas,

Thank you for the suggestions.

1) I tried the tetrahedralize filter on my data but I did not get
the results I was expecting. I have a polyhedron which is not
convex (https://postimg.org/image/9s3egl8rz/
) and the filter fill the
gap as you can see here (https://postimg.org/image/5u1nt6d2h/
) and it is not what I was
expecting. Indeed, the initial purpose of the slice was to
visualize the hole.

2) I tried this fix:
https://gitlab.kitware.com/vtk/vtk/merge_requests/2088

only modifying the 2 files (*Common/DataModel/vtkPolyhedron.cxx*


*Common/Core/vtkSetGet.h) *


And compile VTK alone. I used a python script (activating the
python VTK wrapping) to do the test with the vtkCutter function
but I ended having the same exact issue (segfault, no error
message) with only the polyhedron that have more than 1024 faces.
I am not sure I should get the same results if I manage to compile
paraview. When I will manage I will get back to you.

Thanks,

Pierre



On 03-01-17 16:51, Mathieu Westphal wrote:

Hi

Indeed, incorrect copy paste. thanks for pointing it out.

Mathieu Westphal

On Tue, Jan 3, 2017 at 4:46 PM, T.J. Corona
> wrote:

Hi Mathieu and Pierre,

Perhaps you meant to point to this “work in progress” branch?

https://gitlab.kitware.com/vtk/vtk/merge_requests/2088


Sincerely,
T.J.

Thomas J. Corona, Ph.D.
Kitware, Inc.
R Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4443 


On Jan 3, 2017, at 10:18 AM, Mathieu Westphal
> wrote:

Hello

for your information there is a bug in the slicing of
vtkPolyHedron that can cause a segfault.
It looks very much like your error. It has yet to be corrected.
https://gitlab.kitware.com/vtk/vtk/issues/16877


You can already test this "work in progress" branch to see
if this fixes your issue :
https://gitlab.kitware.com/vtk/vtk/merge_requests/2304


You could of course modify your data to tetrahedron with
tetrahedralize filter.

Regards,

Mathieu Westphal

On Tue, Jan 3, 2017 at 4:10 PM, Pierre Van Hauwaert
> wrote:

Hi,

I am using paraview to visualise my data. I generate my
data using a combination of the 2 following types
(http://www.vtk.org/doc/nightly/html/vtkCellType_8h_source.html)
VTK_VOXEL

=
11
VTK_POLYHEDRON = 42 I can visualize that data with
parview without a problem. But, because I ended up
having a segfault without any error message when slicing
(Z=0) the data. I decomposed my data in separate files
for each VTK_POLYHEDRON in order to investigate the problem.

I found out that only the polyhedrons with the largest
size were having the problem. The limit is somewhere
between the 2 files:
- poly-F1000-2395.vtu : working: 466 points, 928 faces
- poly-F1000-2987.vtu : segfault when slicing: 546
points, 1088 faces

So my guess is that there is a limit for the number of
points or the number of faces that can have the
polyhedron (1024 ?) if I want to be able to use the
slice function.

Re: [Paraview] slicing a large VTK_POLYHEDRON

[Mathieu Westphal]

Hi

It may be a different issue than the one i'm fixing. If you can share the
segfaulting polyhedron, please do so i can take a look when i get back on
this issue ( which my not be soon, feel free to find other solutions)

Regards,

Mathieu Westphal

On Tue, Jan 3, 2017 at 10:46 PM, Pierre Van Hauwaert <
pie...@rtech-engineering.nl> wrote:

> Hi Mathieu and Thomas,
>
> Thank you for the suggestions.
>
> 1) I tried the tetrahedralize filter on my data but I did not get the
> results I was expecting. I have a polyhedron which is not convex (
> https://postimg.org/image/9s3egl8rz/) and the filter fill the gap as you
> can see here (https://postimg.org/image/5u1nt6d2h/) and it is not what I
> was expecting. Indeed, the initial purpose of the slice was to visualize
> the hole.
> 2) I tried this fix: https://gitlab.kitware.com/vtk
> /vtk/merge_requests/2088
> only modifying the 2 files (*Common/DataModel/vtkPolyhedron.cxx *
> 
>  *Common/Core/vtkSetGet.h)  *
> 
> And compile VTK alone. I used a python script (activating the python VTK
> wrapping) to do the test with the vtkCutter function but I ended having the
> same exact issue (segfault, no error message) with only the polyhedron that
> have more than 1024 faces. I am not sure I should get the same results if I
> manage to compile paraview. When I will manage I will get back to you.
>
> Thanks,
>
> Pierre
>
>
>
> On 03-01-17 16:51, Mathieu Westphal wrote:
>
> Hi
>
> Indeed, incorrect copy paste. thanks for pointing it out.
>
> Mathieu Westphal
>
> On Tue, Jan 3, 2017 at 4:46 PM, T.J. Corona  wrote:
>
>> Hi Mathieu and Pierre,
>>
>> Perhaps you meant to point to this “work in progress” branch?
>>
>> https://gitlab.kitware.com/vtk/vtk/merge_requests/2088
>>
>> Sincerely,
>> T.J.
>>
>> Thomas J. Corona, Ph.D.
>> Kitware, Inc.
>> R Engineer
>> 21 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-881-4443 <%28518%29%20881-4443>
>>
>> On Jan 3, 2017, at 10:18 AM, Mathieu Westphal <
>> mathieu.westp...@kitware.com> wrote:
>>
>> Hello
>>
>> for your information there is a bug in the slicing of vtkPolyHedron that
>> can cause a segfault.
>> It looks very much like your error. It has yet to be corrected.
>> https://gitlab.kitware.com/vtk/vtk/issues/16877
>>
>> You can already test this "work in progress" branch to see if this fixes
>> your issue  :
>> https://gitlab.kitware.com/vtk/vtk/merge_requests/2304
>>
>> You could of course modify your data to tetrahedron with tetrahedralize
>> filter.
>>
>> Regards,
>>
>> Mathieu Westphal
>>
>> On Tue, Jan 3, 2017 at 4:10 PM, Pierre Van Hauwaert <
>> pie...@rtech-engineering.nl> wrote:
>>
>>> Hi,
>>>
>>> I am using paraview to visualise my data. I generate my data using a
>>> combination of the 2 following types (
>>> 
>>> http://www.vtk.org/doc/nightly/html/vtkCellType_8h_source.html)
>>> VTK_VOXEL
>>> 
>>> = 11
>>> VTK_POLYHEDRON = 42 I can visualize that data with parview without a
>>> problem. But, because I ended up having a segfault without any error
>>> message when slicing (Z=0) the data. I decomposed my data in separate files
>>> for each VTK_POLYHEDRON in order to investigate the problem.
>>>
>>> I found out that only the polyhedrons with the largest size were having
>>> the problem. The limit is somewhere between the 2 files:
>>> - poly-F1000-2395.vtu : working: 466 points, 928 faces
>>> - poly-F1000-2987.vtu : segfault when slicing: 546 points, 1088 faces
>>>
>>> So my guess is that there is a limit for the number of points or the
>>> number of faces that can have the polyhedron (1024 ?) if I want to be able
>>> to use the slice function.
>>>
>>> My questions are :
>>> 1) Is there actually a limitation in Paraview (VTK?) regarding the
>>> number of faces or the number of the point that the slice function can
>>> handle for a polyhedron ?
>>> 2) If there is this limitation, is there an option to remove it in
>>> Paraview ? (specific version, compilation option, etc)
>>> 3) If there is this limitation, is there any work around that exist so I
>>> am able to slice my data ? For example a different format ?
>>>
>>>
>>> I attached the data to be able to back up my statement:
>>>
>>> poly-F1000-*.vtu : files describing a polyhedron each:
>>> poly-F1000.pvd : load all those files
>>>
>>> Biggest file for which the slicing works (size, name):
>>> 34K poly-F1000-2395.vtu
>>>
>>> The 8 biggest files triggering the crash when doing a slice: (size, name)
>>> 38K poly-F1000-2987.vtu
>>> 39K poly-F1000-2983.vtu
>>> 39K poly-F1000-2935.vtu
>>> 39K poly-F1000-2988.vtu
>>> 39K poly-F1000-2931.vtu
>>> 40K 

Re: [Paraview] slicing a large VTK_POLYHEDRON

[Pierre Van Hauwaert]

Hi Mathieu and Thomas,

Thank you for the suggestions.

1) I tried the tetrahedralize filter on my data but I did not get the 
results I was expecting. I have a polyhedron which is not convex 
(https://postimg.org/image/9s3egl8rz/) and the filter fill the gap as 
you can see here (https://postimg.org/image/5u1nt6d2h/) and it is not 
what I was expecting. Indeed, the initial purpose of the slice was to 
visualize the hole.


2) I tried this fix: 
https://gitlab.kitware.com/vtk/vtk/merge_requests/2088 

only modifying the 2 files (*Common/DataModel/vtkPolyhedron.cxx* 
 
*Common/Core/vtkSetGet.h) * 

And compile VTK alone. I used a python script (activating the python VTK 
wrapping) to do the test with the vtkCutter function but I ended having 
the same exact issue (segfault, no error message) with only the 
polyhedron that have more than 1024 faces. I am not sure I should get 
the same results if I manage to compile paraview. When I will manage I 
will get back to you.


Thanks,

Pierre


On 03-01-17 16:51, Mathieu Westphal wrote:

Hi

Indeed, incorrect copy paste. thanks for pointing it out.

Mathieu Westphal

On Tue, Jan 3, 2017 at 4:46 PM, T.J. Corona > wrote:


Hi Mathieu and Pierre,

Perhaps you meant to point to this “work in progress” branch?

https://gitlab.kitware.com/vtk/vtk/merge_requests/2088


Sincerely,
T.J.

Thomas J. Corona, Ph.D.
Kitware, Inc.
R Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4443 


On Jan 3, 2017, at 10:18 AM, Mathieu Westphal
> wrote:

Hello

for your information there is a bug in the slicing of
vtkPolyHedron that can cause a segfault.
It looks very much like your error. It has yet to be corrected.
https://gitlab.kitware.com/vtk/vtk/issues/16877


You can already test this "work in progress" branch to see if
this fixes your issue  :
https://gitlab.kitware.com/vtk/vtk/merge_requests/2304


You could of course modify your data to tetrahedron with
tetrahedralize filter.

Regards,

Mathieu Westphal

On Tue, Jan 3, 2017 at 4:10 PM, Pierre Van Hauwaert
> wrote:

Hi,

I am using paraview to visualise my data. I generate my data
using a combination of the 2 following types
(http://www.vtk.org/doc/nightly/html/vtkCellType_8h_source.html
)
VTK_VOXEL

=
11
VTK_POLYHEDRON = 42 I can visualize that data with parview
without a problem. But, because I ended up having a segfault
without any error message when slicing (Z=0) the data. I
decomposed my data in separate files for each VTK_POLYHEDRON
in order to investigate the problem.

I found out that only the polyhedrons with the largest size
were having the problem. The limit is somewhere between the 2
files:
- poly-F1000-2395.vtu : working: 466 points, 928 faces
- poly-F1000-2987.vtu : segfault when slicing: 546 points,
1088 faces

So my guess is that there is a limit for the number of points
or the number of faces that can have the polyhedron (1024 ?)
if I want to be able to use the slice function.

My questions are :
1) Is there actually a limitation in Paraview (VTK?)
regarding the number of faces or the number of the point that
the slice function can handle for a polyhedron ?
2) If there is this limitation, is there an option to remove
it in Paraview ? (specific version, compilation option, etc)
3) If there is this limitation, is there any work around that
exist so I am able to slice my data ? For example a different
format ?


I attached the data to be able to back up my statement:

poly-F1000-*.vtu : files describing a polyhedron each:
poly-F1000.pvd : load all those files

Biggest file for which the slicing works (size, name):
34K poly-F1000-2395.vtu

The 8 biggest files triggering the crash when doing a slice:
(size, name)
38K poly-F1000-2987.vtu
39K 

Re: [Paraview] slicing a large VTK_POLYHEDRON

[T.J. Corona]

Hi Mathieu and Pierre,

Perhaps you meant to point to this “work in progress” branch?

https://gitlab.kitware.com/vtk/vtk/merge_requests/2088

Sincerely,
T.J.

Thomas J. Corona, Ph.D.
Kitware, Inc.
R Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4443

> On Jan 3, 2017, at 10:18 AM, Mathieu Westphal  
> wrote:
> 
> Hello
> 
> for your information there is a bug in the slicing of vtkPolyHedron that can 
> cause a segfault.
> It looks very much like your error. It has yet to be corrected.
> https://gitlab.kitware.com/vtk/vtk/issues/16877 
> 
> 
> You can already test this "work in progress" branch to see if this fixes your 
> issue  :
> https://gitlab.kitware.com/vtk/vtk/merge_requests/2304 
> 
> 
> You could of course modify your data to tetrahedron with tetrahedralize 
> filter.
> 
> Regards,
> 
> Mathieu Westphal
> 
> On Tue, Jan 3, 2017 at 4:10 PM, Pierre Van Hauwaert 
> > wrote:
> Hi,
> 
> I am using paraview to visualise my data. I generate my data using a 
> combination of the 2 following types ( 
> http://www.vtk.org/doc/nightly/html/vtkCellType_8h_source.html
>  )
> VTK_VOXEL 
> 
>   = 11
> VTK_POLYHEDRON = 42
> I can visualize that data with parview without a problem. But, because I 
> ended up having a segfault without any error message when slicing (Z=0) the 
> data. I decomposed my data in separate files for each VTK_POLYHEDRON in order 
> to investigate the problem.
> 
> I found out that only the polyhedrons with the largest size were having the 
> problem. The limit is somewhere between the 2 files:
> - poly-F1000-2395.vtu : working: 466 points, 928 faces 
> - poly-F1000-2987.vtu : segfault when slicing: 546 points, 1088 faces 
> 
> So my guess is that there is a limit for the number of points or the number 
> of faces that can have the polyhedron (1024 ?) if I want to be able to use 
> the slice function.
> 
> My questions are : 
> 1) Is there actually a limitation in Paraview (VTK?) regarding the number of 
> faces or the number of the point that the slice function can handle for a 
> polyhedron ?
> 2) If there is this limitation, is there an option to remove it in Paraview ? 
> (specific version, compilation option, etc)   
> 3) If there is this limitation, is there any work around that exist so I am 
> able to slice my data ? For example a different format ?
> 
> 
> I attached the data to be able to back up my statement:
> 
> poly-F1000-*.vtu : files describing a polyhedron each:  
> poly-F1000.pvd : load all those files
> 
> Biggest file for which the slicing works (size, name):
> 34K poly-F1000-2395.vtu
> 
> The 8 biggest files triggering the crash when doing a slice: (size, name)
> 38K poly-F1000-2987.vtu
> 39K poly-F1000-2983.vtu
> 39K poly-F1000-2935.vtu
> 39K poly-F1000-2988.vtu
> 39K poly-F1000-2931.vtu
> 40K poly-F1000-2937.vtu
> 40K poly-F1000-2981.vtu
> 40K poly-F1000-2930.vtu
> fail.pvd: load those 8 files
> 
> the other files can be sliced without any issues
> 
> 
> Thanks,  
> 
> Pierre 
> 
> -- 
> R.Tech Engineering B.V. 
> Eekholt 42 - 1112 XH Diemen - the Netherlands 
> Tel: +31 (0) 2 04 95 02 22 
> 
> ___
> Powered by www.kitware.com 
> 
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html 
> 
> 
> Please keep messages on-topic and check the ParaView Wiki at: 
> http://paraview.org/Wiki/ParaView 
> 
> Search the list archives at: http://markmail.org/search/?q=ParaView 
> 
> 
> Follow this link to subscribe/unsubscribe:
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> 
> 
> 
> ___
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
> 
> Please keep messages on-topic and check the ParaView Wiki at: 
> http://paraview.org/Wiki/ParaView
> 
> Search the list archives at: http://markmail.org/search/?q=ParaView
> 
> Follow this link to subscribe/unsubscribe:
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Search the 

Re: [Paraview] slicing a large VTK_POLYHEDRON

[Mathieu Westphal]

Hello

for your information there is a bug in the slicing of vtkPolyHedron that
can cause a segfault.
It looks very much like your error. It has yet to be corrected.
https://gitlab.kitware.com/vtk/vtk/issues/16877

You can already test this "work in progress" branch to see if this fixes
your issue  :
https://gitlab.kitware.com/vtk/vtk/merge_requests/2304

You could of course modify your data to tetrahedron with tetrahedralize
filter.

Regards,

Mathieu Westphal

On Tue, Jan 3, 2017 at 4:10 PM, Pierre Van Hauwaert <
pie...@rtech-engineering.nl> wrote:

> Hi,
>
> I am using paraview to visualise my data. I generate my data using a
> combination of the 2 following types (
> 
> http://www.vtk.org/doc/nightly/html/vtkCellType_8h_source.html)
> VTK_VOXEL
> 
> = 11
> VTK_POLYHEDRON = 42 I can visualize that data with parview without a
> problem. But, because I ended up having a segfault without any error
> message when slicing (Z=0) the data. I decomposed my data in separate files
> for each VTK_POLYHEDRON in order to investigate the problem.
>
> I found out that only the polyhedrons with the largest size were having
> the problem. The limit is somewhere between the 2 files:
> - poly-F1000-2395.vtu : working: 466 points, 928 faces
> - poly-F1000-2987.vtu : segfault when slicing: 546 points, 1088 faces
>
> So my guess is that there is a limit for the number of points or the
> number of faces that can have the polyhedron (1024 ?) if I want to be able
> to use the slice function.
>
> My questions are :
> 1) Is there actually a limitation in Paraview (VTK?) regarding the number
> of faces or the number of the point that the slice function can handle for
> a polyhedron ?
> 2) If there is this limitation, is there an option to remove it in
> Paraview ? (specific version, compilation option, etc)
> 3) If there is this limitation, is there any work around that exist so I
> am able to slice my data ? For example a different format ?
>
>
> I attached the data to be able to back up my statement:
>
> poly-F1000-*.vtu : files describing a polyhedron each:
> poly-F1000.pvd : load all those files
>
> Biggest file for which the slicing works (size, name):
> 34K poly-F1000-2395.vtu
>
> The 8 biggest files triggering the crash when doing a slice: (size, name)
> 38K poly-F1000-2987.vtu
> 39K poly-F1000-2983.vtu
> 39K poly-F1000-2935.vtu
> 39K poly-F1000-2988.vtu
> 39K poly-F1000-2931.vtu
> 40K poly-F1000-2937.vtu
> 40K poly-F1000-2981.vtu
> 40K poly-F1000-2930.vtu
> fail.pvd: load those 8 files
>
> the other files can be sliced without any issues
>
>
> Thanks,
>
> Pierre
>
> --
> R.Tech Engineering B.V.
> Eekholt 42 - 1112 XH Diemen - the Netherlands
> Tel: +31 (0) 2 04 95 02 22
>
> ___
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
___
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Please keep messages on-topic and check the ParaView Wiki at: 
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Search the list archives at: http://markmail.org/search/?q=ParaView

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