Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-17 Thread Krishnakumar Gopalakrishnan 
Hi,

Thanks a lot to everyone who offered valuable help on this.

Finally, I could get Paraview to plot the 1D set of .vtu files.  Turns out
that the default viewport is set to render, and the correct one to use is
the "plot" filter which sets up a new view pane.

Krishna




On Tue, 17 Mar 2020 at 01:56, Bruno Blais  wrote:

> I concur with Wolfgang.
> The same can be done with Paraview also. I have found that using the plot
> over line tool of paraview in 1D allows to obtain animation of 1D results
> in a very beautiful and user friendly fashion.
> There is a Python VTK library by the way which allows easy (relatively)
> opening of vtk file and conversion into numpy arrays. It can be pretty
> handy, although the documentation is poor.
>
> :)!
>
>
> On Monday, 16 March 2020 13:00:57 UTC-4, Wolfgang Bangerth wrote:
>>
>> On 3/16/20 9:37 AM, Krishnakumar Gopalakrishnan wrote:
>> >
>> > Are we all agreeing that sophisticated VisIT and Paraview cannot
>> produce
>> > simple 1D visualizations/animations?
>>
>> No, we definitely do not agree :-) Attached is a visualization of the
>> output
>> when replacing all occurrences of <2> by <1> in step-3, using visit. I'm
>> showing the solution in color, elevated by the value of the solution.
>>
>>
>> > If so, there must be anAssert()
>> > pre-condition check for the DataOut::write_vtk() and
>> DataOut::write_vtu()
>> > functions of the library which return an exception with "dimension not
>> > implemented" error.
>>
>> As others have pointed out, there are other reasons to output in these
>> file
>> formats that may not include visualization with Paraview only.
>>
>> Best
>>   W.
>>
>>
>> --
>> 
>> Wolfgang Bangerth  email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>> --
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> 
> .
>

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Bruno Blais 
I concur with Wolfgang.
The same can be done with Paraview also. I have found that using the plot 
over line tool of paraview in 1D allows to obtain animation of 1D results 
in a very beautiful and user friendly fashion.
There is a Python VTK library by the way which allows easy (relatively) 
opening of vtk file and conversion into numpy arrays. It can be pretty 
handy, although the documentation is poor.

:)!


On Monday, 16 March 2020 13:00:57 UTC-4, Wolfgang Bangerth wrote:
>
> On 3/16/20 9:37 AM, Krishnakumar Gopalakrishnan wrote: 
> > 
> > Are we all agreeing that sophisticated VisIT and Paraview cannot produce 
> > simple 1D visualizations/animations? 
>
> No, we definitely do not agree :-) Attached is a visualization of the 
> output 
> when replacing all occurrences of <2> by <1> in step-3, using visit. I'm 
> showing the solution in color, elevated by the value of the solution. 
>
>
> > If so, there must be anAssert() 
> > pre-condition check for the DataOut::write_vtk() and 
> DataOut::write_vtu() 
> > functions of the library which return an exception with "dimension not 
> > implemented" error. 
>
> As others have pointed out, there are other reasons to output in these 
> file 
> formats that may not include visualization with Paraview only. 
>
> Best 
>   W. 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Wolfgang Bangerth 

On 3/16/20 9:37 AM, Krishnakumar Gopalakrishnan wrote:


Are we all agreeing that sophisticated VisIT and Paraview cannot produce 
simple 1D visualizations/animations?


No, we definitely do not agree :-) Attached is a visualization of the output 
when replacing all occurrences of <2> by <1> in step-3, using visit. I'm 
showing the solution in color, elevated by the value of the solution.



If so, there must be anAssert() 
pre-condition check for the DataOut::write_vtk() and DataOut::write_vtu() 
functions of the library which return an exception with "dimension not 
implemented" error.


As others have pointed out, there are other reasons to output in these file 
formats that may not include visualization with Paraview only.


Best
 W.


--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan 
Confusingly, there are two versions of MayaVi.  MayaVi 1 and MayaVi2.  They
didn't have a brew cask, so I didn't look at it so far.  I also don't want
to learn yet another full-blown python library commands just for a one-off
visualization exercise.  I really like Praveen's solution, but again
gnuplot is yet another plotting language that I need to learn.

Can matplotlib import .vtk files and produce time-step animations?  What an
irony that 1D visualisation is harder than 2D (for non-technical reasons)
:).

Regards,
Krishna

On Mon, 16 Mar 2020 at 16:30, Bruno Turcksin 
wrote:

> Krishna,
>
> I am not an expert on visualization but I know mayavi (
> https://docs.enthought.com/mayavi/mayavi/) can read vtk and vtu. This is
> more geared towards python users though. If you think that the
> documentation is lacking, feel free to open a pull request ;-)
>
> Best,
>
> Bruno
> On 3/16/20 12:14 PM, Krishnakumar Gopalakrishnan wrote:
>
> Hi Bruno,
>
> Thanks for this information.
>
> I am genuinely curious to know about these other programs that are capable
> of reading .vtk and .vtu files.  Everyone says that these files are so
> standard, and claim that there are a lot of tools that can read them.   I
> could not find really find any general purpose visualisation software
> outside of VisIT and Paraview that reads these files.  There are also
> couple of medical simulation visualizers/toolkits that again come out of
> kitware stables.  For an open-source framework like the VTK with a business
> -riendly BSD license, it is rather surprising that no other company or
> university has built a competing product.
>
>
>
> * Some people also use vtk to transfer data between programs. *
>
> What could be examples of such work flow, especially in a 1D context?  For
> all practical purposes, 1D .vtu/.vtk files seem useless.  At least could we
> have a warning/note block of text in the write_vtu() and write_vtk() pages
> of the documentation that 1D visualisation using .vtk is a non-starter?  I
> have seen many such notes calling for the readers' attention.  I spent
> nearly two days under the belief that a 1D simulation shoud just be a walk
> in the park for the two vtk-based heavyweights.
>
>
> Regards,
> Krishna
>
>
>
>
> On Mon, 16 Mar 2020 at 15:51, Bruno Turcksin 
> wrote:
>
>> Krishna,
>>
>> VisIt and Paraview are just two of many visualization software that can
>> read .vtk and .vtu files. Some people also use vtk to transfer data between
>> programs. Why should we restrict the output because two visualization tools
>> don't support 1D?
>>
>> Best,
>>
>> Bruno
>>
>> On Monday, March 16, 2020 at 11:37:57 AM UTC-4, Krishnakumar
>> Gopalakrishnan wrote:
>>>
>>> Hi Praveen,
>>>
>>> Thank you.  That really helps. I shall definitely check it out and
>>> report back.  I just have standard Q1 linear elements in a unit (0,1)
>>> domain, solving a standard 1D diffusion problem.
>>>
>>> Are we all agreeing that sophisticated VisIT and Paraview cannot produce
>>> simple 1D visualizations/animations? If so, there must be an Assert() 
>>> pre-condition
>>> check for the DataOut::write_vtk() and DataOut::write_vtu() functions
>>> of the library which return an exception with "dimension not implemented"
>>> error.
>>>
>>> Regards,
>>> Krishna
>>>
>>>
>>>
>>> On Mon, 16 Mar 2020 at 15:31, Praveen C  wrote:
>>>
 I have a 1d example here

 https://bitbucket.org/cpraveen/deal_ii/src/master/dg/1d_scalar_legendre/

 The blank lines in the output file denote different elements. It is not
 necessary to sort if you use gnuplot to plot it. gnuplot makes one curve
 for the solution in each element. If the FE space is continuous, you will
 get a plot which is globally continuous.

 Best
 praveen

 On 16-Mar-2020, at 8:50 PM, Krishnakumar Gopalakrishnan <
 krish...@vt.edu> wrote:

 Hi Praveen,

 Thanks for your reply. Yes, I had success with gnuplot, but the
 following were the difficulties.

1. Weirdly, the x-axis co-ordinates of the mesh are not sorted in a
particular order (they appear rather randomly, arranged in  groups of 2
rows with blank lines between them).
2. The time-animation is not easy to visualize.  Paraview has a
nice animation player for such sets of .vtu files.

 Is there some trick to visualize time-series of 1D spatial data?


 Regards,
 Krishna


 --
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Bruno Turcksin 

Krishna,

I am not an expert on visualization but I know mayavi 
(https://docs.enthought.com/mayavi/mayavi/) can read vtk and vtu. This 
is more geared towards python users though. If you think that the 
documentation is lacking, feel free to open a pull request ;-)


Best,

Bruno

On 3/16/20 12:14 PM, Krishnakumar Gopalakrishnan wrote:

Hi Bruno,

Thanks for this information.

I am genuinely curious to know about these other programs that are 
capable of reading .vtk and .vtu files.  Everyone says that these 
files are so standard, and claim that there are a lot of tools that 
can read them.   I could not find really find any general purpose 
visualisation software outside of VisIT and Paraview that reads these 
files.  There are also couple of medical simulation 
visualizers/toolkits that again come out of kitware stables.  For an 
open-source framework like the VTK with a business -riendly BSD 
license, it is rather surprising that no other company or university 
has built a competing product.



/Some people also use vtk to transfer data between programs.
/
/
/
What could be examples of such work flow, especially in a 1D context?  
For all practical purposes, 1D .vtu/.vtk files seem useless.  At least 
could we have a warning/note block of text in the write_vtu() and 
write_vtk() pages of the documentation that 1D visualisation using 
.vtk is a non-starter?  I have seen many such notes calling for the 
readers' attention.  I spent nearly two days under the belief that a 
1D simulation shoud just be a walk in the park for the two vtk-based 
heavyweights.



Regards,
Krishna




On Mon, 16 Mar 2020 at 15:51, Bruno Turcksin > wrote:


Krishna,

VisIt and Paraview are just two of many visualization software
that can read .vtk and .vtu files. Some people also use vtk to
transfer data between programs. Why should we restrict the output
because two visualization tools don't support 1D?

Best,

Bruno

On Monday, March 16, 2020 at 11:37:57 AM UTC-4, Krishnakumar
Gopalakrishnan wrote:

Hi Praveen,

Thank you.  That really helps. I shall definitely check it out
and report back.  I just have standard Q1 linear elements in a
unit (0,1) domain, solving a standard 1D diffusion problem.

Are we all agreeing that sophisticated VisIT and Paraview
cannot produce simple 1D visualizations/animations? If so,
there must be anAssert() pre-condition check for the
DataOut::write_vtk() and DataOut::write_vtu() functions of the
library which return an exception with "dimension not
implemented" error.

Regards,
Krishna



On Mon, 16 Mar 2020 at 15:31, Praveen C
mailto:prav...@tifrbng.res.in>> wrote:

I have a 1d example here


https://bitbucket.org/cpraveen/deal_ii/src/master/dg/1d_scalar_legendre/

The blank lines in the output file denote different
elements. It is not necessary to sort if you use gnuplot
to plot it. gnuplot makes one curve for the solution in
each element. If the FE space is continuous, you will get
a plot which is globally continuous.

Best
praveen


On 16-Mar-2020, at 8:50 PM, Krishnakumar Gopalakrishnan
mailto:krish...@vt.edu>> wrote:

Hi Praveen,

Thanks for your reply. Yes, I had success with gnuplot,
but the following were the difficulties.

 1. Weirdly, the x-axis co-ordinates of the mesh are not
sorted in a particular order (they appear rather
randomly, arranged in  groups of 2 rows with blank
lines between them).
 2. The time-animation is not easy to visualize. 
Paraview has a nice animation player for such sets of
.vtu files.

Is there some trick to visualize time-series of 1D
spatial data?


Regards,
Krishna


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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan 
Hi Bruno,

Thanks for this information.

I am genuinely curious to know about these other programs that are capable
of reading .vtk and .vtu files.  Everyone says that these files are so
standard, and claim that there are a lot of tools that can read them.   I
could not find really find any general purpose visualisation software
outside of VisIT and Paraview that reads these files.  There are also
couple of medical simulation visualizers/toolkits that again come out of
kitware stables.  For an open-source framework like the VTK with a business
-riendly BSD license, it is rather surprising that no other company or
university has built a competing product.



* Some people also use vtk to transfer data between programs. *

What could be examples of such work flow, especially in a 1D context?  For
all practical purposes, 1D .vtu/.vtk files seem useless.  At least could we
have a warning/note block of text in the write_vtu() and write_vtk() pages
of the documentation that 1D visualisation using .vtk is a non-starter?  I
have seen many such notes calling for the readers' attention.  I spent
nearly two days under the belief that a 1D simulation shoud just be a walk
in the park for the two vtk-based heavyweights.


Regards,
Krishna




On Mon, 16 Mar 2020 at 15:51, Bruno Turcksin 
wrote:

> Krishna,
>
> VisIt and Paraview are just two of many visualization software that can
> read .vtk and .vtu files. Some people also use vtk to transfer data between
> programs. Why should we restrict the output because two visualization tools
> don't support 1D?
>
> Best,
>
> Bruno
>
> On Monday, March 16, 2020 at 11:37:57 AM UTC-4, Krishnakumar
> Gopalakrishnan wrote:
>>
>> Hi Praveen,
>>
>> Thank you.  That really helps. I shall definitely check it out and report
>> back.  I just have standard Q1 linear elements in a unit (0,1) domain,
>> solving a standard 1D diffusion problem.
>>
>> Are we all agreeing that sophisticated VisIT and Paraview cannot produce
>> simple 1D visualizations/animations? If so, there must be an Assert() 
>> pre-condition
>> check for the DataOut::write_vtk() and DataOut::write_vtu() functions of
>> the library which return an exception with "dimension not implemented"
>> error.
>>
>> Regards,
>> Krishna
>>
>>
>>
>> On Mon, 16 Mar 2020 at 15:31, Praveen C  wrote:
>>
>>> I have a 1d example here
>>>
>>> https://bitbucket.org/cpraveen/deal_ii/src/master/dg/1d_scalar_legendre/
>>>
>>> The blank lines in the output file denote different elements. It is not
>>> necessary to sort if you use gnuplot to plot it. gnuplot makes one curve
>>> for the solution in each element. If the FE space is continuous, you will
>>> get a plot which is globally continuous.
>>>
>>> Best
>>> praveen
>>>
>>> On 16-Mar-2020, at 8:50 PM, Krishnakumar Gopalakrishnan 
>>> wrote:
>>>
>>> Hi Praveen,
>>>
>>> Thanks for your reply. Yes, I had success with gnuplot, but the
>>> following were the difficulties.
>>>
>>>1. Weirdly, the x-axis co-ordinates of the mesh are not sorted in a
>>>particular order (they appear rather randomly, arranged in  groups of 2
>>>rows with blank lines between them).
>>>2. The time-animation is not easy to visualize.  Paraview has a nice
>>>animation player for such sets of .vtu files.
>>>
>>> Is there some trick to visualize time-series of 1D spatial data?
>>>
>>>
>>> Regards,
>>> Krishna
>>>
>>>
>>> --
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> 
> .
>

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Bruno Turcksin 
Krishna,

VisIt and Paraview are just two of many visualization software that can 
read .vtk and .vtu files. Some people also use vtk to transfer data between 
programs. Why should we restrict the output because two visualization tools 
don't support 1D?

Best,

Bruno

On Monday, March 16, 2020 at 11:37:57 AM UTC-4, Krishnakumar Gopalakrishnan 
wrote:
>
> Hi Praveen,
>
> Thank you.  That really helps. I shall definitely check it out and report 
> back.  I just have standard Q1 linear elements in a unit (0,1) domain, 
> solving a standard 1D diffusion problem.
>
> Are we all agreeing that sophisticated VisIT and Paraview cannot produce 
> simple 1D visualizations/animations? If so, there must be an Assert() 
> pre-condition 
> check for the DataOut::write_vtk() and DataOut::write_vtu() functions of 
> the library which return an exception with "dimension not implemented" 
> error.  
>
> Regards,
> Krishna
>
>
>
> On Mon, 16 Mar 2020 at 15:31, Praveen C  wrote:
>
>> I have a 1d example here
>>
>> https://bitbucket.org/cpraveen/deal_ii/src/master/dg/1d_scalar_legendre/
>>
>> The blank lines in the output file denote different elements. It is not 
>> necessary to sort if you use gnuplot to plot it. gnuplot makes one curve 
>> for the solution in each element. If the FE space is continuous, you will 
>> get a plot which is globally continuous.
>>
>> Best
>> praveen
>>
>> On 16-Mar-2020, at 8:50 PM, Krishnakumar Gopalakrishnan  
>> wrote:
>>
>> Hi Praveen,
>>
>> Thanks for your reply. Yes, I had success with gnuplot, but the following 
>> were the difficulties.
>>
>>1. Weirdly, the x-axis co-ordinates of the mesh are not sorted in a 
>>particular order (they appear rather randomly, arranged in  groups of 2 
>>rows with blank lines between them).
>>2. The time-animation is not easy to visualize.  Paraview has a nice 
>>animation player for such sets of .vtu files.
>>
>> Is there some trick to visualize time-series of 1D spatial data?
>>
>>
>> Regards,
>> Krishna
>>
>>
>>

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan 
Hi Praveen,

Thank you.  That really helps. I shall definitely check it out and report
back.  I just have standard Q1 linear elements in a unit (0,1) domain,
solving a standard 1D diffusion problem.

Are we all agreeing that sophisticated VisIT and Paraview cannot produce
simple 1D visualizations/animations? If so, there must be an Assert()
pre-condition
check for the DataOut::write_vtk() and DataOut::write_vtu() functions of
the library which return an exception with "dimension not implemented"
error.

Regards,
Krishna



On Mon, 16 Mar 2020 at 15:31, Praveen C  wrote:

> I have a 1d example here
>
> https://bitbucket.org/cpraveen/deal_ii/src/master/dg/1d_scalar_legendre/
>
> The blank lines in the output file denote different elements. It is not
> necessary to sort if you use gnuplot to plot it. gnuplot makes one curve
> for the solution in each element. If the FE space is continuous, you will
> get a plot which is globally continuous.
>
> Best
> praveen
>
> On 16-Mar-2020, at 8:50 PM, Krishnakumar Gopalakrishnan 
> wrote:
>
> Hi Praveen,
>
> Thanks for your reply. Yes, I had success with gnuplot, but the following
> were the difficulties.
>
>1. Weirdly, the x-axis co-ordinates of the mesh are not sorted in a
>particular order (they appear rather randomly, arranged in  groups of 2
>rows with blank lines between them).
>2. The time-animation is not easy to visualize.  Paraview has a nice
>animation player for such sets of .vtu files.
>
> Is there some trick to visualize time-series of 1D spatial data?
>
>
> Regards,
> Krishna
>
>
>

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan 
Hi Praveen,

Thanks for your reply. Yes, I had success with gnuplot, but the following
were the difficulties.

   1. Weirdly, the x-axis co-ordinates of the mesh are not sorted in a
   particular order (they appear rather randomly, arranged in  groups of 2
   rows with blank lines between them).
   2. The time-animation is not easy to visualize.  Paraview has a nice
   animation player for such sets of .vtu files.

Is there some trick to visualize time-series of 1D spatial data?


Regards,
Krishna




On Mon, 16 Mar 2020 at 15:16, Praveen C  wrote:

> For 1d, you can save data in gnuplot format
>
>
> https://www.dealii.org/current/doxygen/deal.II/classDataOutInterface.html#a85407e870a68179ebe62410d9efc153f
>
> and use gnuplot to visualize it.
>
> Best
> praveen
>
> On 16-Mar-2020, at 8:33 PM, Krishnakumar Gopalakrishnan 
> wrote:
>
> Same as before -- have you actually tried this? Because I think they do
> just fine with 1d solutions!
>
>
>- Yes. Nothing shows up on the viewport. I thought it might be because
>I have just a 1D mesh.  Then looking at Paraview's official
>tutorial/documentation, the very first sentence of Chapter 1 Introduction
>says  *"ParaView is an open-source application for visualizing two-
>and three- dimensional data sets."*
>
> This raises doubts in one's head that 1D meshes are not supported. This is
> why I posted my question here. I haven't still been able to visualize my 1D
> simulation results.
>
> Regards,
> Krishna
>
>
>

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Praveen C 
For 1d, you can save data in gnuplot format

https://www.dealii.org/current/doxygen/deal.II/classDataOutInterface.html#a85407e870a68179ebe62410d9efc153f

and use gnuplot to visualize it.

Best
praveen

> On 16-Mar-2020, at 8:33 PM, Krishnakumar Gopalakrishnan  
> wrote:
> 
> Same as before -- have you actually tried this? Because I think they do just 
> fine with 1d solutions!
> 
> Yes. Nothing shows up on the viewport. I thought it might be because I have 
> just a 1D mesh.  Then looking at Paraview's official tutorial/documentation, 
> the very first sentence of Chapter 1 Introduction says  "ParaView is an 
> open-source application for visualizing two- and three- dimensional data 
> sets."
> This raises doubts in one's head that 1D meshes are not supported. This is 
> why I posted my question here. I haven't still been able to visualize my 1D 
> simulation results.
> 
> Regards,
> Krishna

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-16 Thread Krishnakumar Gopalakrishnan 
Same as before -- have you actually tried this? Because I think they do
just fine with 1d solutions!


   - Yes. Nothing shows up on the viewport. I thought it might be because I
   have just a 1D mesh.  Then looking at Paraview's official
   tutorial/documentation, the very first sentence of Chapter 1 Introduction
   says  *"ParaView is an open-source application for visualizing two- and
   three- dimensional data sets."*

This raises doubts in one's head that 1D meshes are not supported. This is
why I posted my question here. I haven't still been able to visualize my 1D
simulation results.

Regards,
Krishna


On Mon, 16 Mar 2020 at 00:22, Wolfgang Bangerth 
wrote:

> On 3/15/20 1:50 PM, Krishnakumar Gopalakrishnan wrote:
> >
> > It looks like both paraview and VTK can only visualise 2D/3D meshes?
> What's
> > the best way to visualise 1D outputs?
>
> Same as before -- have you actually tried this? Because I think they do
> just
> fine with 1d solutions!
>
> Best
>   W.
>
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
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> .
>

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Re: [deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-15 Thread Wolfgang Bangerth 

On 3/15/20 1:50 PM, Krishnakumar Gopalakrishnan wrote:


It looks like both paraview and VTK can only visualise 2D/3D meshes? What's 
the best way to visualise 1D outputs?


Same as before -- have you actually tried this? Because I think they do just 
fine with 1d solutions!


Best
 W.


--

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   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] How to visualise the simulation output in vtk format on a one dimensional mesh?

2020-03-15 Thread Krishnakumar Gopalakrishnan 
Using deal.ii, I got the results of a time-dependent 1D diffusion equation 
written to disk as a set of .vtu files (one per time-step).

It looks like both paraview and VTK can only visualise 2D/3D meshes? What's 
the best way to visualise 1D outputs?

Regards,
Krishna


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