Re: [Paraview] Function JOIN of XDMF in Paraview

[Gallagher, Timothy P]

The thing that jumps out at me is missing the Dimensions tag on the function 
itself. For instance, we create our grids as:



grid.h5:/Domain_1/x
grid.h5:/Domain_1/y
grid.h5:/Domain_1/z



We also use a comma between the JOIN, not a semicolon -- not sure if that 
matters or not.


If you change your JOIN to look like:




  EvolvingSquare_01.h5:Coordinates

  EvolvingSquare_02.h5:Coordinates




does that fix the problem?


Tim


From: ParaView  on behalf of dl...@cornell.edu 

Sent: Monday, September 19, 2016 10:20 PM
To: paraview@paraview.org
Subject: [Paraview] Function JOIN of XDMF in Paraview


Hi,

I am now working on a project which needs the use of JOIN function in xdmf to 
concatenate the data from multiple h5 files and visualize those files in 
Paraview. I have created a small trial to test this JOIN function. I create two 
h5 files, each of which contains two points of a unit square. For each point, I 
assign a value to it as its attribute. Then I write one xdmf file, which uses 
function JOIN to concatenate the dataset from two h5 files. But when I load my 
xdmf file into Paraview, Paraview just crashes directly.  This is the xdmf file 
I have written:





http://www.w3.org/2001/XInclude; Version="2.97">

  



  



  EvolvingSquare_01.h5:Coordinates

 EvolvingSquare_02.h5:Coordinates



  

  

  



  EvolvingSquare_01.h5:Attributes

  EvolvingSquare_02.h5:Attributes



  



  





To avoid the problem of h5 file itself, I have also written two separate xdmf 
files for each h5 file and load each xdmf file separately into Paraview. I can 
successfully load these two h5 files separately into Paraview, so the problem 
might no be my h5 files. Can anyone help me with this problem? Are there any 
mistakes of my ways of using JOIN function in xdmf?

Thanks


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Re: [Paraview] Function JOIN of XDMF in Paraview

[Gallagher, Timothy P]

Maybe to be more clear (because there are some differences in the grid 
definition in some other places), here is what our full grid definition looks 
like:


   



/grid.h5:/Domain_1/x
/grid.h5:/Domain_1/y
/grid.h5:/Domain_1/z






The first difference is the 2DSMesh in yours instead of the 3DSMesh in mine. 
But we also use Dimensions in the Topology tag (instead of the 
NumberOfElements). We also interleave our coordinates (that's what the comma 
does) instead of appending the arrays (that's what the semicolon does) in the 
JOIN.


I would skip the attribute for now and focus on getting the format correct for 
the coordinates, and then look at the attribute. We also use the JOIN to create 
velocity vectors from individual arrays and it follows the same format as the 
grid coordinates.


Tim


From: Gallagher, Timothy P
Sent: Monday, September 19, 2016 10:41 PM
To: dl...@cornell.edu; paraview@paraview.org
Subject: Re: [Paraview] Function JOIN of XDMF in Paraview


The thing that jumps out at me is missing the Dimensions tag on the function 
itself. For instance, we create our grids as:



grid.h5:/Domain_1/x
grid.h5:/Domain_1/y
grid.h5:/Domain_1/z



We also use a comma between the JOIN, not a semicolon -- not sure if that 
matters or not.


If you change your JOIN to look like:




  EvolvingSquare_01.h5:Coordinates

  EvolvingSquare_02.h5:Coordinates




does that fix the problem?


Tim


From: ParaView  on behalf of dl...@cornell.edu 

Sent: Monday, September 19, 2016 10:20 PM
To: paraview@paraview.org
Subject: [Paraview] Function JOIN of XDMF in Paraview


Hi，

I am now working on a project which needs the use of JOIN function in xdmf to 
concatenate the data from multiple h5 files and visualize those files in 
Paraview. I have created a small trial to test this JOIN function. I create two 
h5 files, each of which contains two points of a unit square. For each point, I 
assign a value to it as its attribute. Then I write one xdmf file, which uses 
function JOIN to concatenate the dataset from two h5 files. But when I load my 
xdmf file into Paraview, Paraview just crashes directly.  This is the xdmf file 
I have written:





http://www.w3.org/2001/XInclude; Version="2.97">

  



  



  EvolvingSquare_01.h5:Coordinates

 EvolvingSquare_02.h5:Coordinates



  

  

  



  EvolvingSquare_01.h5:Attributes

  EvolvingSquare_02.h5:Attributes



  



  





To avoid the problem of h5 file itself, I have also written two separate xdmf 
files for each h5 file and load each xdmf file separately into Paraview. I can 
successfully load these two h5 files separately into Paraview, so the problem 
might no be my h5 files. Can anyone help me with this problem? Are there any 
mistakes of my ways of using JOIN function in xdmf?

Thanks


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[Paraview] Function JOIN of XDMF in Paraview

[dl826]

Hi，
I am now working on a project which needs the use of JOIN function in xdmf to 
concatenate the data from multiple h5 files and visualize those files in 
Paraview. I have created a small trial to test this JOIN function. I create two 
h5 files, each of which contains two points of a unit square. For each point, I 
assign a value to it as its attribute. Then I write one xdmf file, which uses 
function JOIN to concatenate the dataset from two h5 files. But when I load my 
xdmf file into Paraview, Paraview just crashes directly.  This is the xdmf file 
I have written:


http://www.w3.org/2001/XInclude; Version="2.97">
  

  

  EvolvingSquare_01.h5:Coordinates
  EvolvingSquare_02.h5:Coordinates 

  
   
  
   
  EvolvingSquare_01.h5:Attributes
  EvolvingSquare_02.h5:Attributes

  

  


To avoid the problem of h5 file itself, I have also written two separate xdmf 
files for each h5 file and load each xdmf file separately into Paraview. I can 
successfully load these two h5 files separately into Paraview, so the problem 
might no be my h5 files. Can anyone help me with this problem? Are there any 
mistakes of my ways of using JOIN function in xdmf? 
Thanks

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Re: [Paraview] How to merge .vtk files to visualize the result in Paraview

[Ethan Hereth]

Furthermore, if you end up opening them all individually in paraview, you
can select all of the input files in Pipeline Browser and then run the
Group Datasets filter on them. This is a poor man's solution I think, but
in a pinch it works well.

Cheers!

Ethan Alan

On Mon, Sep 19, 2016 at 2:32 PM Christopher Neal 
wrote:

> Hey Brennen,
>
> I’m not an expert at Paraview’s IO system, but I believe that individual
> .vtk files would have to be opened individually i.e. Paraview cannot stitch
> the .vtk files together.  If you want to be able to open a single file and
> have the data for each processor’s output file be shown in one coherent
> data set, then I think you should look into the parallel xml file format
> that Paraview uses.
>
> A PDF of VTK file formats (XML format is on page 11 of the document):
> http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf
>
>
> There is probably a better way to do this, but this is what I would do.
> 1.) Write a paraview python script to first convert all of the .vtk files
> to the newer xml format.  See:
> http://stackoverflow.com/questions/26158599/how-to-convert-vtk-legacy-files-to-vtu-format
>
> You will have to use the correct writer to write the
> proper XML file format for your data set type – See page 12 of that
> file-formats pdf that I posted above to see what types exist for the
> datasets
>
> 2.) Let’s assume your data is unstructured. You will now have data for
> each sub-domain written to a bunch of .vtu files. One .vtu file per
> processor, just like the .vtk files.  You can stitch all of these files
> together by using the parallel file format that VTK supports ( see page 16
> of that pdf ). You just need to write out a .pvtu file that essentially
> just has a list containing the name of every .vtu file.
>
> 3.) Paraview should be able to open this new .pvtu file and display all of
> the data for all of the sub-domains.
>
> Again, your xml file type might be .vti, .vtp, etc. depending on the data
> type that is being written to the .vtk files, structured, image, poly, etc.
>
> Hope this helps. If anyone has a more straightforward solution please
> share it.
>
> Best regards,
>
> Chris Neal
>
>
>
>
>
> *From: *ParaView  on behalf of Brennen
> Taylor 
> *Date: *Monday, September 19, 2016 at 12:13 AM
> *To: *
> *Subject: *[Paraview] How to merge .vtk files to visualize the result in
> Paraview
>
>
>
> Dear All,
>
>
>
> I am using Paraview in order to visualize the result produced by parallel
> program.
>
> Each processor currently outputs its own .vtk files , which corresponsd to
> the value of the fields in the domain.
>
>
>
> I would like to know if there is a way of merging these .vtk files into
> one .vtk file so that I can visualize using Paraview.
>
>
>
>
>
>
>
> Thanks in advance !!
>
>
>
> Best ,
>
>
>
> Brennen
>
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Re: [Paraview] How to merge .vtk files to visualize the result in Paraview

[Christopher Neal]

Hey Brennen,

I’m not an expert at Paraview’s IO system, but I believe that individual .vtk 
files would have to be opened individually i.e. Paraview cannot stitch the .vtk 
files together.  If you want to be able to open a single file and have the data 
for each processor’s output file be shown in one coherent data set, then I 
think you should look into the parallel xml file format that Paraview uses.

A PDF of VTK file formats (XML format is on page 11 of the document): 
http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf


There is probably a better way to do this, but this is what I would do.
1.) Write a paraview python script to first convert all of the .vtk files to 
the newer xml format.  See: 
http://stackoverflow.com/questions/26158599/how-to-convert-vtk-legacy-files-to-vtu-format

    You will have to use the correct writer to write the proper XML 
file format for your data set type – See page 12 of that file-formats pdf that 
I posted above to see what types exist for the datasets

2.) Let’s assume your data is unstructured. You will now have data for each 
sub-domain written to a bunch of .vtu files. One .vtu file per processor, just 
like the .vtk files.  You can stitch all of these files together by using the 
parallel file format that VTK supports ( see page 16 of that pdf ). You just 
need to write out a .pvtu file that essentially just has a list containing the 
name of every .vtu file.

3.) Paraview should be able to open this new .pvtu file and display all of the 
data for all of the sub-domains.

Again, your xml file type might be .vti, .vtp, etc. depending on the data type 
that is being written to the .vtk files, structured, image, poly, etc.

Hope this helps. If anyone has a more straightforward solution please share it.


Best regards,

Chris Neal

 

 

From: ParaView  on behalf of Brennen Taylor 

Date: Monday, September 19, 2016 at 12:13 AM
To: 
Subject: [Paraview] How to merge .vtk files to visualize the result in Paraview

 

Dear All,

 

I am using Paraview in order to visualize the result produced by parallel 
program. 

Each processor currently outputs its own .vtk files , which corresponsd to the 
value of the fields in the domain.

 

I would like to know if there is a way of merging these .vtk files into one 
.vtk file so that I can visualize using Paraview.

 

 

 

Thanks in advance !!

 

Best ,

 

Brennen

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