Re: [Paraview] Fluid Flow Simulation in ParaView

[Armin Wehrfritz]

Hi Rohit,

I had a look at your data file and I don't understand where your problem 
is. I can visualize the X and Y component of velocity and get seemingly 
correct results (i.e. X and Y have negative and positive values). The 
magnitude of the velocity vector is as expected everywhere positive.


Also the Glyph filter produces reasonable results with the default 
settings (e.g. the arrows can be colored by X or Y component with 
positive and negative values or by magnitude with only positive values).


So my question would be: What exactly do you want to visualize?

-Armin












On 04/06/2015 03:29 PM, Rohit Narurkar wrote:

Hello!

I tried applying the "Glyph" filter, but still the negative values
aren't being considered. It considers only the magnitude.

Can somebody please explain in detail how I should go about this? Please
have a look at the .vtk file I have attached above, I am stuck at this
point.

Thank you

On Thu, Mar 19, 2015 at 9:13 PM, Samuel Key mailto:samuel...@bresnan.net>> wrote:

Rohit,

Assuming that the x-component of VecVelocity has negative values,
then from the selection [Magnitude|x|y|z] pick x and then only
VecVelocity_x will be displayed.

On the other hand, if "vector plots" are your goal, use PV's Glyph
filter.

Sam


On 3/19/2015 5:49 AM, Rohit Narurkar wrote:

Is there no simple feature or option that considers negative
values as well?

On Wed, Mar 18, 2015 at 5:50 PM, Utkarsh Ayachit
mailto:utkarsh.ayac...@kitware.com>>
wrote:

Try applying the "Glyph" filter or using the "Surface LIC"
plugin[1]

[1]
http://www.paraview.org/Wiki/ParaView/Line_Integral_Convolution

Utkarsh

On Tue, Mar 17, 2015 at 8:37 AM, Rohit Narurkar
mailto:rohitnarur...@gmail.com>> wrote:
> Hello
>
> I wish to simulate fluid flow using ParaView. I have 1000
.vtk files for the
> 1000 time steps.
> I have attached along with this mail one of the .vtk files.
When I open this
> collection in ParaView, and change the 'coloring' to the
velocity name I
> have given i.e. "VecVelocity" as you can see in the sample
.vtk file. There
> is another option to its right which offers 'magnitude',
'x', 'y' and 'z'.
> But there are some points with negative velocities and
ParaView is only
> considering the magnitude (hence positive). I wish to
display even the
> negative values. How do I do that?
>
> Any help would be great!
>
> Thank you!
>
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Re: [Paraview] to be sure about used hardware ...

[Armin Wehrfritz]

I cannot directly answer your question, but there has been some 
discussion about slow volume rendering previously. Search the archive 
for a thread called "Hardware suggestions for volume rendering".


A quick summary:
The performance depends on the type of dataset you have, i.e. structured 
grids (even up to 70M grid points) will render decently fast on a single 
Nvidia Quadro K2100M GPU, but unstructured grids are very slow already 
for much smaller grids.


You can test this by using the wavelet source, which gives you a 
arability sized structured dataset.


-Armin



On 05/11/2015 04:15 PM, Ufuk Utku Turuncoglu (BE) wrote:

Hi All,

My question could be very basic but how to be sure that Paraview uses
installed graphics card (in my case Nvidia K2000)? Do i need to install
Paraview from source (using Nvidia drivers) to use the full capability
of underlying hardware? I am asking because volume rendering seems
little bit slow when i try to use binary Paraview installation after
installing driver of the graphics card. I just want to be sure about it.

Regards,

--ufuk
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Re: [Paraview] to be sure about used hardware ...

[Armin Wehrfritz]

Can you post the output of the following commands:
1) paraview --version
2) glxinfo | grep OpenGL

Concerning different dataset types and volume rendering:
Are you sure that your dataset is recognized by ParaView as a structured 
dataset? For instance, some simulation software packages produce always 
unstructured dataset (e.g. OpenFOAM), even if you setup a completely 
uniform grid.
Also some filter in ParaView produce unstructured grids (e.g. threshold 
filter) no matter what the input type is.


The grid type is easy to check from the Information panel in ParaView.

-Armin



On 05/12/2015 05:24 PM, Utkarsh Ayachit wrote:

That's weird. What version of ParaView are you using on your Debian 8?

On Tue, May 12, 2015 at 6:49 AM, Ufuk Utku Turuncoglu (BE)
 wrote:

Hi,

I checked "Volume Rendering Mode" but i could not see it in my case. It is
exist in my local laptop (Mac OS) but it is not in ParaView installed under
Debian 8.0. I think that after selecting representation type to Volume, it
must show up in the Properties menu. Right?

--ufuk


On 11/05/15 17:47, Utkarsh Ayachit wrote:


Is out of box ParaView binary
could use full capability of hardware or not?


ParaVIew binaries don't ship with any OpenGL implementation. It uses
whatever OpenGL drivers setup on the machine it's being run. So long
as your environment is setup properly, ParaView will indeed use the
hardware available. However, not all rendering techniques in ParaView
will use the graphics card  -- as Armin alluded to. Your dataset seems
like small enough that volume rendering should be pretty
instantaneous. What is the "Volume Rendering Mode" on the Properties
panel set to? It should be "Smart" by default -- that will ensure that
the graphics card is used, if possible.

Utkarsh




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Re: [Paraview] to be sure about used hardware ...

[Armin Wehrfritz]

On 05/12/2015 09:58 PM, u.utku.turunco...@be.itu.edu.tr wrote:

Okay. That makes sense because i have a Threshold filter in my
visualisation pipeline. If i use wavelet source then i could see the
"Volume Rendering Mode" and it is set as "Smart". So, using Threshold
filter might also reduce the performance of the volume rendering. Right?
Yes, the performance is severely impaired when you apply the threshold 
filer to a structured dataset, since it produces an unstructured dataset.
To my understand you don't get a true volume rendering for unstructured 
dataset, but maybe somebody who knows more about the details can comment 
on this.


However, since you have already a structured dataset to begin with, you 
should be able to get a decent performance. As I said, I can render a 
64M structured dataset (i.e. a 400x400x400 wavelet source) instantly on 
my laptop. So your 8M dataset should be no problem, just don't use the 
threshold filter.


If you want to work only on a subset of your dataset, you can use the 
"Extract Subset" filter, which outputs a structured dataset again.
Otherwise you can achieve similar effects as with the threshold filter 
by adjusting the transfer function/color scale for the volume rendering.


-Armin






Can you post the output of the following commands:
1) paraview --version
2) glxinfo | grep OpenGL

Concerning different dataset types and volume rendering:
Are you sure that your dataset is recognized by ParaView as a structured
dataset? For instance, some simulation software packages produce always
unstructured dataset (e.g. OpenFOAM), even if you setup a completely
uniform grid.
Also some filter in ParaView produce unstructured grids (e.g. threshold
filter) no matter what the input type is.

The grid type is easy to check from the Information panel in ParaView.

-Armin



On 05/12/2015 05:24 PM, Utkarsh Ayachit wrote:

That's weird. What version of ParaView are you using on your Debian 8?

On Tue, May 12, 2015 at 6:49 AM, Ufuk Utku Turuncoglu (BE)
 wrote:

Hi,

I checked "Volume Rendering Mode" but i could not see it in my case. It
is
exist in my local laptop (Mac OS) but it is not in ParaView installed
under
Debian 8.0. I think that after selecting representation type to Volume,
it
must show up in the Properties menu. Right?

--ufuk


On 11/05/15 17:47, Utkarsh Ayachit wrote:


Is out of box ParaView binary
could use full capability of hardware or not?


ParaVIew binaries don't ship with any OpenGL implementation. It uses
whatever OpenGL drivers setup on the machine it's being run. So long
as your environment is setup properly, ParaView will indeed use the
hardware available. However, not all rendering techniques in ParaView
will use the graphics card  -- as Armin alluded to. Your dataset seems
like small enough that volume rendering should be pretty
instantaneous. What is the "Volume Rendering Mode" on the Properties
panel set to? It should be "Smart" by default -- that will ensure that
the graphics card is used, if possible.

Utkarsh








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Re: [Paraview] xdmf: orders of Origin DXDYDZ arrays in Origin_DXDYDZ

[Armin Wehrfritz]

I encountered the same issue and you can find from the ParaView and XDMF
mailinglist-archives some explanations concerning this topic (search for
"Odd behavior of XDMF files with 3DCORECTMesh").


Concerning the different structured grid types:
3DCoRectMesh (aka vtkImageData):
Axis are perpendicular and spacing is constant (i.e. you only have to
set the mesh dimensions (nx, ny, nz), mesh origin (x0, y0, z0) and cell
dimensions (dx, dy, dz))

3DRectMesh (aka vtkRectilinearGrid):
Axis are perpendicular (i.e. you have to specify the nodes coordinates
along the three axes)

3DSMesh (aka vtkStructuredGrid):
Curvilinear (i.e. you have to specify the coordinates for all mesh nodes)

-Armin




On 05/19/2015 05:08 PM, Liang Wang wrote:

In the first place, I do not understand the difference between
3DRectMesh and 3DCoRectMesh.

I picked the following coordinate for testing:

Nz,Ny,Nx = [80, 90, 100] z0,y0,x0 = [-3.,-2.,-1.] lz,ly,lx =
[Nz*3,Ny*2,Nx] dz,dy,dx = [lz/(Nz-1), ly/(Ny-1), lx/(Nx-1)]

I found I have to use the following lines in the xdmf to get the
correct grid to be shown in Paraview for 3DRectMesh and 3DCoRectMesh,
respectively:

  

-1 -2 -3  1 2 3 

  

-3 -2 -1  3 2 1 

Note that, the Dimensions for Topology in both cases are in zyx
order, while the Origin/DxDyDz arrays have different orders in the
two cases:

3DRectMesh requires Origin=[x0,y0,z0], DX=[dx,dy,dz], i.e., xyz
order 3DCoRectMesh requires Origin=[z0,y0,x0], DX=[dz,dy,dx], i.e.,
zyx order.

Am I writing the correct xdmf codes? How would you specify these
data? Thanks.


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Re: [Paraview] paraview for a "new" application

[Armin Wehrfritz]

Hi Paul,

as you and Dan already stated, the HDF5 format is a very good choice to 
write out large datasets.


I usually write the HDF5 files directly from my simulation codes and 
generate a XDMF file afterwards.
The actual XDMF file contains just the meta data in XML format [1] and 
this can be tailored to your application/dataset (I use python with h5py 
and xml.etree to do this).
Hence, my simulation codes (written in C++) only depend on the HDF5 
libraries.


Eventually, this will enable you to store your data in a robust, 
flexible and portable file format.


For more complex setups I would also consider using the VTK libraries to 
handle the data IO as Dan suggested.


-Armin

[1] http://www.xdmf.org/index.php/XDMF_Model_and_Format




On 06/07/2015 10:40 PM, Dan Lipsa wrote:

You are right, ParaView does not read hdf5 directly but rather hdf5
based formats (hdf5 + additional info):  both netcdf and xdmf have readers.
You can get a list of all readers supported by your ParaView
installation using Help in ParaView. Additional readers can be enabled with
compile time options.

You can write Xdmf data using vtkXdmfWriter or vtkXdm3Writer (you'll
have to link with the VTK library). These writers have tests which is a
good way to see an example of how to use the class. You can also take a
look at the VTK XML based formats: vtkXMLPolyDataWriter,
vtkXMLImageDataWriter, vtkXMLUnstructuredGridWriter/Reader. Probably you
could write data with a library that comes with that format and then
read it with ParaView.

Do you need parallel writing/reading?

Dan




On Sun, Jun 7, 2015 at 4:26 AM Paul Anton Letnes mailto:p...@letnes.com>> wrote:

Hi Dan!

I’m familiar with the HDF5 library and documentation, but thanks
anyway for the link.

I don’t see how I can have ParaView read and understand HDF5 files.
That is, there are several readers (e.g. H5Nimrod) that use HDF5 as
the underlying format, but I don’t see how to get paraview to
understand which arrays are coordinates (nodes?), which are results,
etc. for my application.

Perhaps I should stress again that I have limited experience with
ParaView, and since the supported file formats and possibilities
seem endless, I have trouble getting an overview of sensible choices.

My preference for hdf5 is partly due to other software in my
organization supporting this format, and my own familiarity with it.

Paul

 > On 7. jun. 2015, at 04.07, Dan Lipsa mailto:dan.li...@kitware.com>> wrote:
 >
 > Hi Paul,
 > Indeed #2 makes sense, especially if you want to change the
in-house format. To write the file (from the simulation) it seems to
me you should checkout
 >
 > https://www.hdfgroup.org/HDF5/doc/fortran/index.html
 >
 > I don't see why ParaView would be used in that process. Am I
missing something?
 > Dan
 >
 >
 >
 > On Sat, Jun 6, 2015 at 8:04 AM Paul Anton Letnes mailto:p...@letnes.com>> wrote:
 > Hi, fellow paraviewers!
 >
 > I’ve spent some time playing with tutorials and user manuals, and
so far I’m impressed with what paraview can do.
 >
 > I am working on a specialized structural engineering program
that, mainly, performs simulations of pipes with circular cross
sections. Each pipe is split into nodes and 1D elements, and results
are reported at points (or, less commonly, elements) along the pipe.
 >
 > Some results are reported once per cross section; e.g, the
tension in the pipe has a single value for the entire cross section.
Other results, e.g. plastic strain, is reported for a number of
points along the circumference of the pipe (say, 5-50 points), for
each of the cross sections. The results can be either “snapshots” or
time series.
 >
 > After what I’ve seen from the paraview documentation, possible
approaches include:
 > 1. Create a paraview plugin to read our current in-house file format.
 > 2. Directly write output files in an already supported format.
 > 3. Write pvpython scripts that perform the conversion on the fly.
 >
 > Approach 1 is probably a lot of work and the file format is not
of interest to anyone else (optimally, I’d like to replace it), so
this seems less attractive. Approach 3 is probably less
user-friendly for our users.
 >
 > The second approach seems sensible, but the paraview
documentation does not give many examples of how to do this.
Optimally, I’d like to write a hdf5-based format (xdmf? netcdf? raw
hdf5?) directly from Fortran, but I haven’t found documentation on
how to do this. Using hdf5 seems attractive as it’s so widely
supported by e.g. matlab, python, and other postprocessing tools
used in the industry. Getting a single results database would
simplify a lot of workflows!
 >
 > What would you guys do?
 >
 > Cheers
 > Paul
 > 

Re: [Paraview] Xdmf Sample Files

[Armin Wehrfritz]

I posted some XDMF examples earlier on the mailing-list, see e.g. the 
attachments in these two mails:

http://public.kitware.com/pipermail/paraview/2015-March/033566.html
http://public.kitware.com/pipermail/paraview/2015-March/033568.html

-Armin


On 06/06/2015 04:42 PM, Chris Richardson wrote:

This is implemented in FEniCS (www.fenicsproject.org). I can post an example 
output, if that is useful...

On 6 Jun 2015 13:40, Teo Ioannis  wrote:


I would like to use the xdmf file format combined with hdf5 in order to output 
results of a finite element simulation with multiple timesteps. Can anyone 
supply any sample files for doing so? Is there a tutorial or a starting point 
to look? Thank you very much in advance.

Theofilos Manitaras

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Re: [Paraview] Probe location in a script

[Armin Wehrfritz]

Here is a little script that shows you how to read and write dataset in 
ParaView using a simple for loop.


Hope this helps.

-Armin




On 07/02/2015 05:47 PM, mctoli...@netcourrier.com wrote:

Thanks for the tip. I actually already used tracing in order to find the
command:
 Probelocation.ProbeType.Center = [10.0,20.0,30.0]

But the problem is that I don't know how to access to the data (rho, vx,
vy...) at that location in the python script

And since tracing does not capture "Save data", I don't even know how to
write the data in a file

Cheers,
Mc Fly




Date : 02/07/2015 15:55:04 CEST

Hi McFly,

The Python Tracing facility in ParaView is perfect for this kind of
task. It records a trace of your actions in the ParaView GUI to a Python
script that you can modify a bit to process a bunch of files. To turn on
tracing, choose the Tools -> Start Trace menu item.

More info on tracing is available in the ParaView User Guide [1] under
section 1.6.2.

Best regards,
Cory

[1] http://www.paraview.org/paraview-guide/

On Thu, Jul 2, 2015 at 9:39 AM, mailto:mctoli...@netcourrier.com>> wrote:

__

Hi everybody,

I am a new Paraview user. I am trying to extract points from a bunch
of vtu files. It is pretty easily done with "probe location". But
since I have a lot of files, I would like to automatize the process
(with a macro or a python script).

Could someone maybe show me how it's done?

My best guess is that I should have the following in a python script:
Probelocation.ProbeType.Center = [10.0,20.0,30.0]
assuming I want to probe at x=10, y=20, z=30. But then, I don't
really know how to retrieve the variables values at that location.

Thanks a lot,
Mc Fly

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 import the simple module from the paraview
from paraview.simple import *
 disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()

# Generate some dummy dataset and write them to files
for i in range(10):
data = Wavelet()
data.WholeExtent = [-10, 10, -10, 10, -10, 10]
data.Center = [i, i, i]
SaveData('./wavelet_%01i.xmf' % (i), proxy=data)

# Clean-up
Delete(data)
del data


# Read the dataset from the files and probe them
for i in range(10):
reader = XDMFReader(FileNames=['./wavelet_%01i.xmf' % (i)])
reader.PointArrayStatus = ['RTData']

# create a new 'Probe Location'
probeFilter = ProbeLocation(Input=reader, ProbeType='Fixed Radius Point Source')

# init the 'Fixed Radius Point Source' selected for 'ProbeType'
probeFilter.ProbeType.Center = [i, i, i]
probeFilter.ProbeType.NumberOfPoints = 1
probeFilter.ProbeType.Radius = 0.0
probeFilter.UpdatePipeline()
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Re: [Paraview] Probe location in a script

[Armin Wehrfritz]

I typically use VTK directly when I want to access the raw data from 
python/numpy.  See the series of Blog post by Berk Geveci for more 
information on that: http://kitware.com/blog/home/post/709


In ParaView, to my understanding, you first have to get the data from 
the backend to the frontend with "servermanager.Fetch".  I attached a 
modified version of the script that shows you how to do this in a 
quick-and-dirty way.  See more here: 
http://www.paraview.org/Wiki/ParaView/Python_Scripting


If there is a better way to get access to the raw data, I would be 
really happy to learn how to do this.


Best regards,
Armin





On 07/03/2015 11:21 AM, mctoli...@netcourrier.com wrote:

Thanks for the script, but how can I now access the data that were found
by ProbeLocation? How can I put them in a variable, print them on the
screen?

Cheers,
Mc Fly




 Message d'origine ----
De : "Armin Wehrfritz" 
À : paraview@paraview.org
Objet : Re: [Paraview] Probe location in a script
Date : 02/07/2015 17:07:42 CEST

Here is a little script that shows you how to read and write dataset in
ParaView using a simple for loop.

Hope this helps.

-Armin




On 07/02/2015 05:47 PM, mctoli...@netcourrier.com wrote:
 > Thanks for the tip. I actually already used tracing in order to find the
 > command:
 > Probelocation.ProbeType.Center = [10.0,20.0,30.0]
 >
 > But the problem is that I don't know how to access to the data (rho, vx,
 > vy...) at that location in the python script
 >
 > And since tracing does not capture "Save data", I don't even know how to
 > write the data in a file
 >
 > Cheers,
 > Mc Fly
 >
 >
 >
 >
 > Date : 02/07/2015 15:55:04 CEST
 >
 > Hi McFly,
 >
 > The Python Tracing facility in ParaView is perfect for this kind of
 > task. It records a trace of your actions in the ParaView GUI to a Python
 > script that you can modify a bit to process a bunch of files. To turn on
 > tracing, choose the Tools -> Start Trace menu item.
 >
 > More info on tracing is available in the ParaView User Guide [1] under
 > section 1.6.2.
 >
 > Best regards,
 > Cory
 >
 > [1] http://www.paraview.org/paraview-guide/
 >
 > On Thu, Jul 2, 2015 at 9:39 AM,  <mailto:mctoli...@netcourrier.com>> wrote:
 >
 > __
 >
 > Hi everybody,
 >
 > I am a new Paraview user. I am trying to extract points from a bunch
 > of vtu files. It is pretty easily done with "probe location". But
 > since I have a lot of files, I would like to automatize the process
 > (with a macro or a python script).
 >
 > Could someone maybe show me how it's done?
 >
 > My best guess is that I should have the following in a python script:
 > Probelocation.ProbeType.Center = [10.0,20.0,30.0]
 > assuming I want to probe at x=10, y=20, z=30. But then, I don't
 > really know how to retrieve the variables values at that location.
 >
 > Thanks a lot,
 > Mc Fly
 >
 > ___
 > Powered by www.kitware.com <http://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
 >
 >
 >
 >
 > --
 > Cory Quammen
 > R&D Engineer
 > Kitware, Inc.
 >
 >
 > ___
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 >
 > 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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Re: [Paraview] Box clipping is very slow and wasteful!

[Armin Wehrfritz]

This indicates that ParaView is not selecting a subset of your current 
dataset, but creates a new one.  Things like that happen, when you have 
a structured dataset and apply e.g. the threshold or clipping filter. 
By this, you do not only duplicate a part of the orignal data, you also 
create a unstructured dataset which uses significantly more memory than 
a structured dataset.


So, which kind of dataset do you have?

If you have a structured grid (e.g. vtkImageData, vtkRectilinearGrid, 
vtkStructuredGrid) then you could use the "Extract Subset" instead of 
the clipping filter.


-Armin





On 07/06/2015 03:47 PM, Dinu Patirniche wrote:

Hi everybody,

I'm new to this forum, and I am not entirely sure if this is the right
place to post this question, so please direct me to the right corner if
that should be the case.

Ok - to the technical bit now: I am using paraview 4.3.1 to load a 2gb
vtk dataset. One the volume is loaded, I see a memory increase of about
7gb. Now, as a very first thing, I want to clip the volume, to about a
10th (with the box option selected from the clip menu). Now, I set up
the box from which I want to extract the volume - but the entire rest of
physical memory (about 5gb) gets eaten up plus another 32gb swap space.
By than, paraview gets killed and I have to start all over again. So why
is it that selecting a small range out of a 7gb volume ends up taking
least 37gbs of memory?

Thanks.
Dinu.



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Re: [Paraview] Axes Grid bug with 2D surfaces

[Armin Wehrfritz]

Wow! Thanks for the very quick response!

Indeed the suggested workaround fixes this issue, there were just too
many options already in the basic settings that I didn't find the right
one to adjust this from the advanced settings.


Also, now that I started to play with this, I would have two suggestions
for improving the otherwise very nice Axes Grid:

1) Adjusting the font, color, etc. for all axes together in one step.
Currently I have to change e.g. the color 6 times, which is quite
tedious if I just quickly want to adjust the color of the axes.

2) Changing the origin of the "Axes Grid". In the old "Cube Axes" this
was easily done by adjusting the "Custom bounds".


Thanks for the great effort you are putting into developing ParaView!

Best regards,
Armin




On 09/16/2015 06:40 PM, Utkarsh Ayachit wrote:

There's a workaround: uncheck "Label Unique Edges Only" in the "Edit
 Axes Grid" dialog. It's an advanced property, so you'll need to
search for it or use the "gear" button in the  dialog. You can futher
customize the sides to label using "Axes to Label". State file
attached.


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Re: [Paraview] Axes Grid bug with 2D surfaces

[Armin Wehrfritz]

OK, I see. Thanks a lot for the clarification.

-Armin



On 09/18/2015 04:48 PM, Utkarsh Ayachit wrote:

That's indeed not supported. As mentioned in the blog post [1], the
Axes Grid is intended for the entire scene, and not for a specific
dataset. Certain implementation choices (esp for supporting parallel
rendering with distributed data) require that the axes bounds are
always greater or equal to all the data being rendered in the scene.


[1] http://www.kitware.com/blog/home/post/871

On Thu, Sep 17, 2015 at 12:32 PM, Armin Wehrfritz  wrote:

2) Changing the origin of the "Axes Grid". In the old "Cube Axes"
this was easily done by adjusting the "Custom bounds".



You should be able to use the "Data Transform" group of properties
for a similar effect.



I tried this, but couldn't get the desired result. I attached an
screenshot and state file to show what I'm after (using the old Cube axes).

The "Data Transform" changes the labels but doesn't shift the axes.

-Armin

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Re: [Paraview] Correctly Parallel Processing of OpenFoam results using pvserver

[Armin Wehrfritz]

As it was mentioned already, there are two independently developed
OpenFOAM reader for ParaView.

ParaView comes with its own built-in OpenFOAM reader (vtkOpenFOAMReader,
using the file extension .foam), and OpenFOAM has and alternative reader
(PV4FoamReader, using the file extension .OpenFOAM). OpenFOAM comes with
a little wrapper script called paraFoam, which creates/deletes a dummy
file with the respective extension and opens that file with ParaView.
Try "paraFoam -builtin" to use ParaView's built-in reader, or just
create a .foam file and open it with ParaView.

I generally use ParaView's built-in reader ("feels" faster and can read
decomposed cases :)) and hence I can use always the latest ParaView
version. But just to mention, if you have a heavy dataset also the
latest ParaView version won't be miraculously faster. Quite often the
biggest bottleneck is the disk IO. Also, OpenFOAM data is always
unstructured, which is slow in any case, no matter which reader or
version you use.

If you work a lot with OpenFOAM "zones" or "sets", one reader or the
other may be better suited. I rarely encounter any missing functionality
in ParaView's built-in reader, meaning you can visualise the usual flow
and Lagrangian fields. Just give it a try you can easily switch.

-Armin



On 10/02/2015 03:27 PM, Leonard Cassady wrote:

Hi,

   I didn't realize that there are 2 different extensions for OpenFOAM
projects.  I also didn't realize that Paraview had a native OpenFoam
reader.  What functionality (normally supplied by OpenFOAM paraFoam ) is
lost when using Paraview without starting with paraFoam?  I'm asking
because I've heard that ParaView 4.4 is extremely fast and would like to
test it out with OpenFoam files but not paraFoam.

Thanks

On Thu, Oct 1, 2015 at 7:44 PM, mailto:ronald.fow...@stfc.ac.uk>> wrote:

Hi,
It is simple to create a .foam file; just do "touch xxx.foam" in the
working directory. Then point ParaView at that file and it will use
the builtin openFoam reader which should offer the
reconstructed/decomposed option. The empty file just tells ParaView
which reader to use based on the extension.
Ron



From: ParaView [paraview-boun...@paraview.org
] on behalf of Leonard Cassady
[le...@intuitivemachines.com ]
Sent: 30 September 2015 21:50
To: David E DeMarle
Cc: paraview@paraview.org 
Subject: Re: [Paraview] Correctly Parallel Processing of OpenFoam
results using pvserver

David,

I do not have a chooser for "case type".  I found a web page
that shows the "case type" chooser.  They were opening a .foam
file.  I have .OpenFOAM case.

Should I consider converting the foam to VTK?



On Wed, Sep 30, 2015 at 2:59 PM, David E DeMarle
mailto:dave.dema...@kitware.com>>> wrote:
Looping the list back in to the thread.

Look on the properties panel when you open the file and before you
hit "Apply" look for a chooser for "Case Type". The default is
"Reconstructed Case" so change it to "Decomposed Case".


David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909 >

On Wed, Sep 30, 2015 at 3:51 PM, Leonard Cassady
mailto:le...@intuitivemachines.com>>> wrote:
Dave,

I don't know how to switch to decomposed type.

Thanks,


On Wed, Sep 30, 2015 at 2:47 PM, David E DeMarle
mailto:dave.dema...@kitware.com>>> wrote:
As I recall, reconstructed means that the root node does all the
work. Switch to decomposed type in the reader and let us know how it
works then.

thanks



David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909 >

On Wed, Sep 30, 2015 at 3:35 PM, Leonard Cassady
mailto:le...@intuitivemachines.com>>> wrote:
I'm attempting to use pvserver to accelerate the post-processing of
my openfoam solution. I have a 48 core machine. I have correctly
installed and compiled a parallel copy of paraview 4.1.0 with
OpenFOAM 2.4.x. If I open a simple .obj file I can see that
different parts of the surface are rendered using different
processors. I can also see that the memory is shared among the
parallel processes.

When I open a reconstructed openFOAM solution with 20 million cells
with paraview connected to 40 process pvserver, the image seems to
be rendered (or processed) with only 1 processor. Is there a step
that I'm missing to parallelize th

[Paraview] rpath error when compiling ParaView 5.0

[Armin Wehrfritz]

Hi,

I'm building ParaView (version 5.0 RC1) for openSUSE Tumbleweed (using
gcc 5.2.1) and get an error related to rpath (see below). I cannot say
much more about this, since don't really understand what's going wrong here.

Does anybody have some hints how to solve this?

Please let me know if you need more information.

Cheers,
Armin






...
-- Installing: 
/home/abuild/rpmbuild/BUILDROOT/paraview50-5.0.0-1.1.x86_64/opt/paraview/5.0/include/paraview-5.0/vtkSIUnstructuredGridVolumeRepresentationProxy.h
-- Installing: 
/home/abuild/rpmbuild/BUILDROOT/paraview50-5.0.0-1.1.x86_64/opt/paraview/5.0/include/paraview-5.0/vtkPVServerImplementationRenderingModule.h
-- Installing: 
/home/abuild/rpmbuild/BUILDROOT/paraview50-5.0.0-1.1.x86_64/opt/paraview/5.0/lib/cmake/paraview-5.0/Modules/vtkUtilitiesProcessXML.cmake
-- Installing: 
/home/abuild/rpmbuild/BUILDROOT/paraview50-5.0.0-1.1.x86_64/opt/paraview/5.0/bin/vtkkwProcessXML-pv5.0
CMake Error at Utilities/ProcessXML/cmake_install.cmake:49 (file):
  file RPATH_CHANGE could not write new RPATH:

$ORIGIN/../lib/paraview-5.0

  to the file:


/home/abuild/rpmbuild/BUILDROOT/paraview50-5.0.0-1.1.x86_64/opt/paraview/5.0/bin/vtkkwProcessXML-pv5.0

  The current RUNPATH is:


/home/abuild/rpmbuild/BUILD/ParaView-v5.0.0-RC1-source/build-paraview50/lib:/usr/lib64/mpi/gcc/openmpi/lib64

  which does not contain:

/home/abuild/rpmbuild/BUILD/ParaView-v5.0.0-RC1-source/build-paraview50/lib:

  as was expected.
Call Stack (most recent call first):
  VTK/cmake_install.cmake:221 (include)
  cmake_install.cmake:117 (include)
...


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Re: [Paraview] rpath error when compiling ParaView 5.0

[Armin Wehrfritz]

Thanks for your reply!

On 12/07/2015 06:38 PM, Ben Boeckel wrote:

On Sat, Dec 05, 2015 at 20:53:49 +0200, Armin Wehrfritz wrote:

I'm building ParaView (version 5.0 RC1) for openSUSE Tumbleweed (using
gcc 5.2.1) and get an error related to rpath (see below). I cannot say
much more about this, since don't really understand what's going wrong here.

Does anybody have some hints how to solve this?


Are you giving any rpath-related settings to CMake? What is the
configure line?

No, not that I would be aware of. Here my configure line:

cmake \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX:PATH=/opt/paraview/5.0 \
-DCMAKE_CXX_COMPILER:STRING='mpicxx' \
-DCMAKE_C_COMPILER:STRING='mpicc' \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DBUILD_DOCUMENTATION:BOOL=ON \
-DBUILD_EXAMPLES:BOOL=ON \
-DBUILD_TESTING:BOOL=OFF \
-DPARAVIEW_BUILD_QT_GUI:BOOL=ON \
-DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=ON \
-DPARAVIEW_ENABLE_PYTHON:BOOL=ON \
-DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \
-DPARAVIEW_USE_MPI:BOOL=ON \
-DVTK_WRAP_PYTHON:BOOL=ON \
-DVTK_WRAP_PYTHON_SIP:BOOL=ON \
-DVTK_OPENGL_HAS_OSMESA:BOOL=OFF \
-DVTK_USE_SYSTEM_EXPAT:BOOL=ON \
-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON \
-DVTK_USE_SYSTEM_JPEG:BOOL=ON \
-DVTK_USE_SYSTEM_PNG:BOOL=ON \
-DVTK_USE_SYSTEM_TIFF:BOOL=ON \
-DVTK_USE_SYSTEM_ZLIB:BOOL=ON \
-DVTK_USE_SYSTEM_ZOPE:BOOL=ON \
-DVTK_USE_SYSTEM_TWISTED:BOOL=ON \
../


Please let me know if you need more information.


What version of CMake are you using?

I'm using CMake 3.3.2.

I can send the CMakeCache.txt file if that helps to track this down.

-Armin

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Re: [Paraview] rpath error when compiling ParaView 5.0

[Armin Wehrfritz]

Hi,

as a follow up, I found that the error is related to this option:
 PARAVIEW_INSTALL_DEVELOPMENT_FILES

For some reason I had it switched on and by switching it off, I can
avoid the rpath error. Though I don't know why.

I should probably note that for older build environments (cmake 3.0.2/
gcc 4.8.3) this error does not appear.

-Armin





On 12/12/2015 08:11 PM, Armin Wehrfritz wrote:

Thanks for your reply!

On 12/07/2015 06:38 PM, Ben Boeckel wrote:

On Sat, Dec 05, 2015 at 20:53:49 +0200, Armin Wehrfritz wrote:

I'm building ParaView (version 5.0 RC1) for openSUSE Tumbleweed (using
gcc 5.2.1) and get an error related to rpath (see below). I cannot say
much more about this, since don't really understand what's going
wrong here.

Does anybody have some hints how to solve this?


Are you giving any rpath-related settings to CMake? What is the
configure line?

No, not that I would be aware of. Here my configure line:

cmake \
 -DCMAKE_BUILD_TYPE=Release \
 -DCMAKE_INSTALL_PREFIX:PATH=/opt/paraview/5.0 \
 -DCMAKE_CXX_COMPILER:STRING='mpicxx' \
 -DCMAKE_C_COMPILER:STRING='mpicc' \
 -DBUILD_SHARED_LIBS:BOOL=ON \
 -DBUILD_DOCUMENTATION:BOOL=ON \
 -DBUILD_EXAMPLES:BOOL=ON \
 -DBUILD_TESTING:BOOL=OFF \
 -DPARAVIEW_BUILD_QT_GUI:BOOL=ON \
 -DPARAVIEW_BUILD_PLUGIN_SLACTools:BOOL=ON \
 -DPARAVIEW_ENABLE_PYTHON:BOOL=ON \
 -DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON \
 -DPARAVIEW_USE_MPI:BOOL=ON \
 -DVTK_WRAP_PYTHON:BOOL=ON \
 -DVTK_WRAP_PYTHON_SIP:BOOL=ON \
 -DVTK_OPENGL_HAS_OSMESA:BOOL=OFF \
 -DVTK_USE_SYSTEM_EXPAT:BOOL=ON \
 -DVTK_USE_SYSTEM_FREETYPE:BOOL=ON \
 -DVTK_USE_SYSTEM_JPEG:BOOL=ON \
 -DVTK_USE_SYSTEM_PNG:BOOL=ON \
 -DVTK_USE_SYSTEM_TIFF:BOOL=ON \
 -DVTK_USE_SYSTEM_ZLIB:BOOL=ON \
 -DVTK_USE_SYSTEM_ZOPE:BOOL=ON \
 -DVTK_USE_SYSTEM_TWISTED:BOOL=ON \
 ../


Please let me know if you need more information.


What version of CMake are you using?

I'm using CMake 3.3.2.

I can send the CMakeCache.txt file if that helps to track this down.

-Armin


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Re: [Paraview] ANN: ParaView 5.0.0 is available for download

[Armin Wehrfritz]

Kazuyoshi,

maybe you could try the "Anaconda" python distribution [1]?

I have been using it now for a couple of years and I can just recommend 
it. I'm using it under a 64bit Linux, but it's available for a wide 
range of operating systems, including 64bit Windows.


PyQt and NumPy are available in the Anaconda distribution.


-Armin

[1] https://www.continuum.io/downloads





On 01/14/2016 02:16 AM, Kazuyoshi Furutaka wrote:

Dear list and Kitware foks,

Congratulation for the new release!

Do you have any plan of making a 32-bit Windows binary available?

I want it just because Python(x,y) is only for 32 bit;
I wrote some ParaView Python macros (with GUIs using PyQt) for my
colleagues who are using windows and are non-expert Python user,
and I recommended them to use Python(x,y) as a backend...
(are there any recommended Python distributions which include e.g.
PyQt and NumPy?)

Thanks in advance,

Kazuyoshi
--
Kazuyoshi Furutaka
furutaka _dot_ kazuyoshi _at_ jaea _dot_ go _dot_ jp
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Re: [Paraview] SWKey: Help with VTK XML-Formatted "Writer" Routine.

[Armin Wehrfritz]

On this wiki page you find information on how polyhedrons are stored in
unstructured XML files (search the page for vtkXMLUnstructuredGrid):
http://www.vtk.org/Wiki/VTK/Polyhedron_Support

Hope it helps.

-Armin



On 02/17/2016 09:59 PM, Samuel Key wrote:

My simulation software has a functioning VTK XML-formatted, "ascii"
output routine. To facilitate datum set transfers, I want to add
arbitrary, m-vertex polyhedral finite elements to the simulation
software's existing Writer (VTK_POLYHEDRON = 42).

Originally, I used the VTK File Formats Version 4.2 to construct the
program's Writer. It is not clear to me what the XML structures should
contain with respect to the polyhedral finite elements.

Three files are attached: (1) *.inp is an input snippet for a polyhedral
finite element used by the simulation software, (2) *.png is a ParaView
screenshot display for this polyhedron read in from an EnSight-formatted
file, and (3) *.vtu is a ParaView 'Save Data' output file for this
polyhedral finite element.

Referring to the *.vtu file, I am having difficulty relating the
simulation software's and  EnSight's corresponding input description to
the ParaView output description, particularly, "connectivity" and "faces."

Do you have any advice on how I should proceed?

Note: The simulation software does not require the polygon faces to be
planar, nor the polyhedron volume to be convex. The simulation software
computes proper mean quadrature gradient/divergence operators for
non-planar facets and a restricted form of polyhedral star-convexity.

Thanks in advance for the indicating how I should continue,

Samuel Key
FMA Development, LLC
1005 39th Ave NE
Great Falls, Montana 59404
USA




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Re: [Paraview] Export scene creates images without actual object

[Armin Wehrfritz]

IIRC there was problem with "Export Scene" and the new OpenGL2 backend.
This has been discussed on the mailing-list several times, see e.g.:
https://www.mail-archive.com/paraview@paraview.org/msg25912.html

Hope this helps!

-Armin




On 04/19/2016 10:53 AM, Schlottke-Lakemper, Michael wrote:

Hi folks,

When I connect with PV5 (self-compiled from source) running on OS X to a
pvserver on a remote Linux machine, I have problems using the “Export
scene” feature. Whenever I try to save the current scene e.g. as PDF or
EPS, the visualization object (in this case a 2D unstructured dataset)
flickers on and off for 2-3 times and then stays hidden. When I look at
the generated PDF/EPS, indeed, the object is not there either. I can
make it reappear in PV if I hide-unhide the object in the pipeline
browser, but of course this does not help with the exported file.
Strangely enough, the color bar is not affected, i.e., in the exported
PDF/EPS file I end up with a lonely color bar on an otherwise empty grey
background.

Any idea what I have to do to be able to again create EPS/PDF files?

Thanks a lot in advance

Michael


--
Michael Schlottke-Lakemper

Chair of Fluid Mechanics and Institute of Aerodynamics
RWTH Aachen University
Wüllnerstraße 5a
52062 Aachen
Germany

Phone: +49 (241) 80 95188
Fax: +49 (241) 80 92257
Mail: m.schlottke-lakem...@aia.rwth-aachen.de

Web: http://www.aia.rwth-aachen.de



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Re: [Paraview] Export scene creates images without actual object

[Armin Wehrfritz]

Thanks for the hint! We are using the legacy OpenGL backend
client-side. Server-side I don't know since it was pre-installed on
the system I'm using. Is there a way for me to check how the pvserver
was compiled or is it only dependent on the client anyways?

I don't know how to check for the OpenGL backend on the server. Neither
do I know if that would effect the "export scene" feature.
Where is the rendering done, server-side or client-side?

If you know that your client is compiled with the old OpenGL backend,
you could enforce the rendering on the client and see if that works. To
do that you have to adjust the remote rendering threshold in the settings.

-Armin
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Re: [Paraview] Change default color mapping

[Armin Wehrfritz]

There are there buttons at the bottom of the Color Map Editor panel that
let you save or load the default settings.

-Armin





On 04/25/2016 08:34 PM, Alex Lindsay wrote:

Is there a way to change the default color mapping? The default is cool
to warm, but I prefer blue to red rainbow. I saw in the manual
directions for customizing properties, sources, filter, etc, but I think
I need a little more help
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Re: [Paraview] Direct URL to official binaries

[Armin Wehrfritz]

Right next to the download button is a small button which will give you 
the direct link.


Cheers,
Armin




On 04/28/2016 04:25 PM, Tabrez Ali wrote:

I want to download ParaView directly on a machine remotely using
wget/curl but I cannot find a direct working link to the official
binaries available through http://www.paraview.org/download/

Any ideas?

Thanks in advance.

Tabrez
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Re: [Paraview] Paraview compile download timeout

[Armin Wehrfritz]

As a workaround, you could disabled the testing
(-DBUILD_TESTING:BOOL=OFF).

-Armin





On 05/10/2016 04:13 PM, Daniel Zuidinga wrote:

there are still problems?

Am 10.05.2016 um 11:14 schrieb Mathieu Westphal:

We are experiencing timeout with midas currently.
Please recompile, it should work.



Mathieu Westphal

On Tue, May 10, 2016 at 10:56 AM, Daniel Zuidinga mailto:i...@seoaachen.de>> wrote:

Hello,

when compiling paraview I get the error:


http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=534871355b0e4de0d6b727c8ed317027&algorithm=MD5
("Timeout was reached")

http://www.paraview.org/files/ExternalData/MD5/534871355b0e4de0d6b727c8ed317027
("HTTP response code said error")

any ideas?


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Re: [Paraview] tikz/tex export for paraview contour plots

[Armin Wehrfritz]

Hi Richard,



We created a small python tool, that essentially embeds the figure
created in paraview into a tikz picture and adds axes. However, we
still need to manually specify the the extent of the plot in that
script which is tedious.

This is slightly off-topic, but I have been using a similar approach
(tikz/tex + png images) to include plots from python/matplotlib in my
LaTeX documents. For this I can just recommend the matplotlib2tikz
package [1].

Using VTK/ParaView, I have had some attempts to set the render window
size and camera in python scripts, but could not yet figure out how
to extract the information on the data/viewport extend.



a) Did anyone encounter the same issue and is willing to share a
script or so?

My VTK and ParaView scripts are based on information I gathered from two
mailing list discussions, see [2,3]. My scripts are probably not much of
help, but I can dig them out if you are interested.



b) If not, is there a way to extract the Viewport extent in a python
 script so that we can directly set them in the script?

That's the missing piece in the puzzle I couldn't quite figure out yet,
but I would also be interested in this. The code in discussion [2] has
some examples on coordinate transforms in VTK, but I didn't have the
time to look deeper into this.


Cheers,
Armin


[1] https://github.com/nschloe/matplotlib2tikz
[2] http://www.vtk.org/pipermail/vtk-developers/2005-November/019314.html
[3]
http://paraview.paraview.narkive.com/8hsmkC4u/python-paraview-simple-zoom-to-data

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Re: [Paraview] Slow with just 1M cells

[Armin Wehrfritz]

Hi Michele and Ken,

I'm also dealing with dataset that contain polyhedral cells. More
precisely my grids are generated using a "cutcell" approach where an
initially fully hexahedral mesh is refined in the main region of
interest. While most cells will be again hexahedral after the
refinement, the cells on the coarse side of the interface are of general
polyhderal shape. I assume Michele has a very similar approach, though
my data stem from CFD simulation using OpenFOAM.

The OpenFOAM reader in ParaView has an option to decompose polyhedral
cells into standard shapes (mostly pyramids in my case). For instance,
my original dataset has about 10.9M hexahedral and 147k polyhedral
cells. When reading the dataset in ParaView and decomposing the
polyhedral cells, I get in total 12.7M cells, i.e. approximately 1.7M
more than in the original dataset due to the decomposition.
Applying the tetrahedralize filter to the original dataset leads to
67.4M cells and the memory usage more than doubles. (The numbers are
listed below.)

I also experience a slowdown when I do not decompose the polyhedral
cells for the usual post-processing/visualization tasks.
However, I should note that for instance volume rendering of my dataset
with decomposed polyhedral cells is still painfully slow using ParaView
5.0.1 on my laptop (Intel i7-4800MQ 2.70GHz/ NVIDIA Quadro K2100M).
ParaView appears to spend the most of the time with something called
"OpenGLProjectedTetrahedraMapper".

I'm not sure which readers, other than the OpenFOAM reader, support the
decomposition of polyhedral cells, but the approach should work for any
unstructured dataset. So it might be worth considering to implement this
on a more general level, rather than in a specific reader.

Best regards,
Armin



Statistics
==

OpenFOAM reader
Decompose polyhedra: On

Cells: 12.7M
Points: 11.4M
Memory: 1100 MB

OpenFOAM reader
Decompose polyhedra: Off

Cells: 11M
Points: 11.3M
Memory: 1800 MB

OpenFOAM reader
Decompose polyhedra: Off
Tetrahedralize filter

Cells: 67.4M
Points: 11.3M
Memory: 3400 MB





On 05/25/2016 09:05 PM, Moreland, Kenneth wrote:

Michele,

I took a look at the data you sent me. I experienced many of the
issues you brought up.

After taking a closer look at the data, I realized that many of the
cells in your data are of the general polyhedral type. Unlike the
standard cell shapes like tetrahedron and hexahedron, polyhedral
shapes are general polyhedra formed by specifying the face polygons.
They allow you to specify any flat faceted shape, but computing basic
operations on them such as interpolations, derivatives, and location
finding is very expensive. This is why operations like streamlines
are going so slowly.

If the cells are represented as standard shapes, things go much
faster. For example, if you tetrahedralize the data, streamlines
takes well under 10 seconds. That gets the operations to about the
range where your nameless commercial product is running. I suspect,
but cannot verify, that this other visualization package is probably
downgrading the cells to something like hexahedra, which makes it run
faster.

I don’t recommend running the tetrahedralization filter all the time
on your data. It is also slow and really bloats the data. If you
could write out an alternate form of the data that wrote hexahedra
instead of polyhedra, I suspect things would run much faster. You
would probably have a problem with faces not being aligned, though.

One final note, although the clip filter is taking a long time, I
found the slice filter to be much faster. Generally, when dealing
with large data, you should favor slice over clip. It’s much faster,
uses much less memory, and usually gives you the same information.

-Ken

On 5/21/16, 9:47 AM, "Moreland, Kenneth"  wrote:


Michele,

Taking over a minute to process a data set with 1 million cells
does seem like an unreasonably long time, even for a moderately
powered PC. Perhaps something odd is happening here. Can you
describe in more detail what your data look like and what you are
doing with them?

-Ken

On 5/20/16, 11:55 AM, "ParaView on behalf of Michele Battistoni"
 wrote:


Paraview is awesome for lots of functionalities, however I find
it extremely slow in processing data with any filter type, or in
changing timestep as soon as the model size is around one million
cells or above. I have experience with a commercial tool which on
the same model and pc is 100x faster. Let's say a second vs. a
min!

Is there any specific settings for ram of parallelization among
cores?

Thanks Michele

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[Paraview] Transparent background in python scripts

[Armin Wehrfritz]

Hi!

How can I save screenshots with a transparent (alpha channel based)
background from a python script?

Currently, I'm using this command to save screenshots:

SaveScreenshot('image.png', magnification=3, view=renderView)

But this does not write the alpha channel information.


Using "File/ Save Screenshot" in the Paraview GUI, the screenshots
have the alpha channel information saved correctly when I setting "Edit/
Settings/ General/ Transparent Background".

I'm using ParaView 5.0.1 on a 64bit Linux workstation with the latest
Nvidia driver (367.27).


-Armin
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Re: [Paraview] Transparent background in python scripts

[Armin Wehrfritz]

Thanks, I would really appreciate this feature. 
I'm looking forward to 5.2 then. :)


-Armin 



On Wed Jun 22 23:42:11 2016 GMT+0300, Utkarsh Ayachit wrote:
> Currently, it's not exposed to Python. It's on the TODO list to get
> that fixed for 5.2.
> 
> On Mon, Jun 20, 2016 at 12:03 PM, Armin Wehrfritz  wrote:
> > Hi!
> >
> > How can I save screenshots with a transparent (alpha channel based)
> > background from a python script?
> >
> > Currently, I'm using this command to save screenshots:
> >>
> >> SaveScreenshot('image.png', magnification=3, view=renderView)
> >
> > But this does not write the alpha channel information.
> >
> >
> > Using "File/ Save Screenshot" in the Paraview GUI, the screenshots
> > have the alpha channel information saved correctly when I setting "Edit/
> > Settings/ General/ Transparent Background".
> >
> > I'm using ParaView 5.0.1 on a 64bit Linux workstation with the latest
> > Nvidia driver (367.27).
> >
> >
> > -Armin
> > ___
> > Powered by www.kitware.com
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> > http://paraview.org/Wiki/ParaView
> >
> > Search the list archives at: http://markmail.org/search/?q=ParaView
> >
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Re: [Paraview] VTK XML Unstructured Grid format

[Armin Wehrfritz]

Hi Chris,

a unstructured grid (without polyhedral cells) is described by three arrays:
1) connectivity: An array storing the point ids of the unique points of
 all cells.
2) offsets: An array indicating the end position of each cell in the
connectivity array.
3) types: An array storing the types of each cell.

Regarding your example, from the "types" and "offsets" arrays you can
deduct that you have 4 cells of type "12", i.e. hexahedrons (see [1]).
Now, the offsets array tells you that the first 8 numbers in the
connectivity array are the point ids for the first cell, second number
tells you that the point ids from 9 to 16 are for the second cell and so on.
The line breaks in the connectivity array have no meaning.

HTH,
Armin

[1] 
https://gitlab.kitware.com/vtk/vtk/blob/master/Common/DataModel/vtkCellType.h






On 08/24/2016 07:50 PM, Christopher Neal wrote:

Hi All,



Does anyone have a link to an example or documentation describing how
one can interpret a *.vtu file that is XML ascii? I’m looking at a file
that was written for a 2x2x1 group of cells i.e. 4 hexahedral cells, and
the connectivity looks like:







  0 6 8 2 1 7

  9 3 2 8 10 4

  3 9 11 5 6 12

  14 8 7 13 15 9

  8 14 16 10 9 15

  17 11





  8 16 24 32





  12 12 12 12



  


I can’t seem to understand the connectivity info that is displayed. I
would image there should be 8 entries per line for a hexahedral cell.


Any material on this would be greatly appreciated.

Thank you,

Chris Neal



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Re: [Paraview] [Non-DoD Source] Questions about XMF - 3DCoRectMesh

[Armin Wehrfritz]

This is apparently a "very very old bug" [1] and pops up every now and
then on this mailing-list. There was apparently a plan to fix this back
in 2009 [2], but I'm doubtful that this was done.

[1] http://public.kitware.com/pipermail/paraview/2014-September/032263.html
[2] http://public.kitware.com/pipermail/paraview/2009-May/012278.html

-Armin






On 09/09/2016 05:15 PM, Burns, Andrew J CTR USARMY RDECOM ARL (US) wrote:

We noticed this also, I believe the plan is to remove the flipping of dimension 
ordering. However, I am unsure on when that will occur.

Andrew Burns
Software Engineer | Leidos
Phone: 410-306-0409
ARL DSRC
andrew.j.burns35@mail.mil

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Lúcio Corrêa
Sent: Friday, September 09, 2016 9:29 AM
To: paraview@paraview.org
Subject: [Non-DoD Source] [Paraview] Questions about XMF - 3DCoRectMesh

Hi everbody,

I have a stupid question about the XMF - 3DCoRectMesh...

I tried to build an "extruded rectangle" using this function (I attached the 
files).

I asked for a 6 by 16 by 46 elements as you can see in the XMF file...

 
 
   
 -0.60
 -1.60
 -4.60

but when I open in Paraview (4.3.1 and 5.1.2) I found a 46 by 16 by 6 
elements...

I tried also to look in: VTK/ThirdParty/xdmf3/vtkxdmf3/XdmfRegularGrid.cpp, but I didn't 
found the reason to Paraview "change" the X axis by the Z axis.

Someone found the same thing? Or, where I made a mistake?

Regards,


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Re: [Paraview] Combination of polygonal-data and unstructured grid?

[Armin Wehrfritz]

Hi Stefan,

If I understand your problem correctly, then you are looking for
polyhedral cells (i.e. N face cells, where each face is a M edge
polygon). Polyhedral cells are commonly used in Computational Fluid
Dynamics codes, as e.g. OpenFOAM, and VTK/ParaView support them already
for quite some time (i.e. since around 2010), see [1] for more details.


My problem is now i have a set of complex shaped volumes (dual-grid
data) which cannot be found in the list of cell types for
unstructured grid data. Therefore i use the polygonal data and color
each cell with one color. Of course for further analysis (e.g.
integration of the cell volumes, volume gradient and so on) i need a
way to give a set of (closed surface) poly-data elements a kind
connection to form a volume to handle them together.

In which file format do you store your data?

For example, the unstructured VTK XML format [2] has support for
polyhedral cells. An alternative would be the XDMF file format [3] to
which I recently added polyhedral cell support [4,5]. Please note that
the latest release versions of VTK (7.0) or ParaView (5.1) don't support
the polyhedral cells in XDMF yet, but the nightly builds and the
upcoming releases (i.e. VTK 7.1 and ParaView 5.2) will have this feature.

Cheers,
Armin


[1] http://www.vtk.org/Wiki/VTK/Polyhedron_Support
[2] http://www.vtk.org/Wiki/VTK_XML_Formats
[3] http://www.xdmf.org
[4] 
https://gitlab.kitware.com/xdmf/xdmf/commit/0a9fbd0590dff8a677c86754169cd2ccd72fe4b1
[5] 
https://gitlab.kitware.com/vtk/vtk/commit/802c9b61de28e560c2659d2af76660bbb49c68be



--
Armin Wehrfritz, Dipl.-Ing. (M.Sc.)
Aalto University, School of Engineering
Department of Mechanical Engineering
PO Box 14300
FI-00076 Aalto, Finland
+358 50 4340607
armin.wehrfr...@aalto.fi
https://people.aalto.fi/armin_wehrfritz
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Re: [Paraview] Combination of polygonal-data and unstructured grid?

[Armin Wehrfritz]

Hi Stefan,

IIRC there is a .vtu file containing polyhderal cells in the VTK DATA
repository.

Otherwise, I attached a .xmf and a .vtu file containing each containing
identical data, i.e. 2 hexahedral and 2 polyhderal cell.
Please note that the white-space in these files has no meaning, and that
for the .xmf file you need a recent ParaView nightly build.

Best regards,
Armin





On 09/27/2016 07:42 AM, Stefan Melber wrote:

Hi Armin,

sounds thats the thing i searched for! Will check it out today and see
if it does the job. Is there a demo-xml file around with such polyhedral
cells?

Best regards and thank you,

  Stefan



Hi Stefan,

If I understand your problem correctly, then you are looking for
polyhedral cells (i.e. N face cells, where each face is a M edge
polygon). Polyhedral cells are commonly used in Computational Fluid
Dynamics codes, as e.g. OpenFOAM, and VTK/ParaView support them already
for quite some time (i.e. since around 2010), see [1] for more details.


My problem is now i have a set of complex shaped volumes (dual-grid
data) which cannot be found in the list of cell types for
unstructured grid data. Therefore i use the polygonal data and color
each cell with one color. Of course for further analysis (e.g.
integration of the cell volumes, volume gradient and so on) i need a
way to give a set of (closed surface) poly-data elements a kind
connection to form a volume to handle them together.

In which file format do you store your data?

For example, the unstructured VTK XML format [2] has support for
polyhedral cells. An alternative would be the XDMF file format [3] to
which I recently added polyhedral cell support [4,5]. Please note that
the latest release versions of VTK (7.0) or ParaView (5.1) don't support
the polyhedral cells in XDMF yet, but the nightly builds and the
upcoming releases (i.e. VTK 7.1 and ParaView 5.2) will have this feature.

Cheers,
Armin


[1] http://www.vtk.org/Wiki/VTK/Polyhedron_Support
[2] http://www.vtk.org/Wiki/VTK_XML_Formats
[3] http://www.xdmf.org
[4]
https://gitlab.kitware.com/xdmf/xdmf/commit/0a9fbd0590dff8a677c86754169cd2ccd72fe4b1

[5]
https://gitlab.kitware.com/vtk/vtk/commit/802c9b61de28e560c2659d2af76660bbb49c68be







polyhedron.vtu
Description: model/vnd.vtu


polyhedron.xmf
Description: audio/xmf
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Re: [Paraview] slice as background image?

[Armin Wehrfritz]

The "Camera parallel projection" is an advanced property and hence
hidden. You can find it by using the search or by toggling the advanced
properties (i.e. the small button with the wheel beside the search box).

-Armin




On 10/03/2016 05:27 PM, Zenker, Dr. Matthias wrote:

Hi Cory,

that was what I looked for!
Just for the records, I didn't find the "Camera parallel projection" checkbox 
under the properties of the transform filter, but I got the desired effect by changing 
the camera interaction mode on the toolbar of the graphics window from 3d to 2D (ParaView 
5.1.2 under Linux).

Thank you!

Matthias

Von: Cory Quammen [cory.quam...@kitware.com]
Gesendet: Montag, 3. Oktober 2016 14:52
An: Zenker, Dr. Matthias
Cc: paraview@paraview.org
Betreff: Re: [Paraview] slice as background image?

Matthias,

You could change the camera from using perspective projection to parallel projection, 
then translate the plane to be being the streamlines. Check the "Camera Parallel 
Projection" checkbox under the View properties panel. As long as your view direction 
is orthogonal to the slice plane, the streamlines will appear in the correct position 
relative to the slice plane after you translate one or the other.

HTH,
Cory

On Mon, Oct 3, 2016 at 4:36 AM, Zenker, Dr. Matthias 
mailto:matthias.zen...@erbe-med.com>> wrote:
Hi,

from a 3D dataset, I need to view a slice and streamlines from a line source 
lying in the slice plane. The problem is that the slice and the streamlines are 
overlapping, and part of the streamlines are covered by the slice. I cannot 
change the origins of slice or streamlines in order to move them slightly 
forward or backward, because that would make me lose details of what I want to 
see. When I use the transform filter to translate the slice, I get a mismatch 
due to the perspective rendering.
What I would like to do is just to put the slice in the background and the 
streamlines in the foreground. Is there a way to do that apart from saving the 
slice as image and use that as background image?

Thank you for a helpful hint,

Matthias


Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: 
Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137

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--
Cory Quammen
Staff R&D Engineer
Kitware, Inc.


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Please keep m

Re: [Paraview] Legend for superposed contour plots

[Armin Wehrfritz]

OK, I see what you want to do... quite tricky. Would it be an option to
plot the contour lines with matplotlib, i.e. pass the x,y coordinates to
a python view? This way you would get the legend very easily in exactly
the way you want it.
For more information on how to do the plotting with matplotlib in
ParaView see these two blog posts:
https://blog.kitware.com/matplotlib-view-coming-in-paraview-4-1/
https://blog.kitware.com/paraview-python-view-is-now-more-versatile/

Otherwise I'm afraid I have no simple solution for your problem.

-Armin





On 10/03/2016 07:36 PM, Zenker, Dr. Matthias wrote:

Hi Armin,

thank you for your answer. I am aware that I can adjust color scales.
My problem is that I don't get a legend at all in the first place. I
have several variants of a contour plot superposed, using solid
colors for each variant. I could of course add an empty contour plot,
switch the coloring to e.g. potential and fiddle around with the
color map. But that is not what I would like to have. But I would
like to have a legend similar to the legend of the "plot over line"
where I don't have a color map, but just colored line patterns with
their respective meaning, like

[blue line here]  Variant 1
[red line here] Variant 2
[green line here]  Variant 3

How can I generate such a legend?

Thank you,

Matthias
____
Von: Armin Wehrfritz [dkxl...@gmail.com]
Gesendet: Montag, 3. Oktober 2016 17:20
An: Zenker, Dr. Matthias; paraview@paraview.org
Betreff: Re: [Paraview] Legend for superposed contour plots

Hi,

I'm not sure if I understand completely what you try to do, but probably
it's already enough if you use a discrete color legend and set the
number of values to the number of contours. (See the attached screenshot
and state file.)

Otherwise, the color legend can be adjusted in arbitrary ways using
python. For an example, have a look at the attached python
script. Note that the script is very specific for one of my cases, but
demonstrates how one can arbitrarily adjust color scales.

HTH,
Armin




On 10/03/2016 05:41 PM, Zenker, Dr. Matthias wrote:

Hi,

I want to superpose different contour plots, each one having one
contour line. They are color coded, i.e. I use the solid color and
assign one color to each of the lines. Now I would like to have a
legend for the resulting plot. Is there a way to build a customized
legend, or a possibility to have a legened similar to what I get when
I superpose several "plot over line" curves?

Thank you,
Matthias


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Re: [Paraview] bug report: xdmf AttributeType handling error

[Armin Wehrfritz]

Hi Chenz,

without commenting further on your problem, could you tell which Xdmf
version you are using. ParaView comes currently with two Xdmf
implementations called "Xdmf" and "Xdmf3". Which one did you use for
reading/writing your dataset?

-Armin



On 10/11/2016 07:32 PM, Chen Zhang wrote:

Hi,

I recently noticed a strange error in xdmf reading. If a multi-demension array 
(e.g. 32x32x32x24 ) is exported to Xdmf format by paraview, it will generate 
something like this:


  test.h5:/Block_0_t00/Cell/resistance_slip
 

Although the original data is a 24 length vector for each cell, Paraview is 
only interpolating it as a simple scalar, thus break the data structure. This 
error can not be resolved by manually switching AttributeType to “Matrix”, 
which indicates the “Matrix” type of support is somehow missing at the moment.

I am currently running the Paraview 5.2.0-RC1 on a MacBook pro (mid 2012) 
running macOS Sierra.

cheers,
Chenz



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Re: [Paraview] ParaView 5.2 Release Candidate 3 available for download

[Armin Wehrfritz]

Hi,

I tested 5.2 RC3 and encountered an issue when reading OpenFOAM cases.

The problem only occurs when the OpenFOAM data (i.e. the mesh or fields)
are written in binary format. I setup two test cases that are otherwise
identical, where for the one the data is in ascii and the other one in
binary format.
With ParaView 5.1.2 I can read both cases without any error, but with
ParaView 5.2 RC3 the cases for which the data is in binary format leads
to an error (see below for the exact error message).

The case is taken directly from the official OpenFOAM 4.x tutorials, and
here is a link to the case files that can be directly used for debugging:
https://www.dropbox.com/s/l0cb8vd6pjkb1zz/debug_PV_OF.tar.gz?dl=0

All tests were done with the ParaView binaries distributed by Kitware.

Let me know if you need more information or if I can help debugging this
further.

Cheers,
Armin




ERROR: In 
/home/buildslave/dashboards/buildbot/paraview-pvbinsdash-linux-shared-release_opengl2_qt4_superbuild/source-paraview/VTK/IO/Geometry/vtkOpenFOAMReader.cxx,
 line 5147
vtkOpenFOAMReaderPrivate (0x4896cf0): Error reading line 1277 of 
/home/arminw/tmp/debug_PV_OF/pitzDaily_binary/constant/polyMesh/points: 
Expected punctuation token ')', found �


ERROR: In 
/home/buildslave/dashboards/buildbot/paraview-pvbinsdash-linux-shared-release_opengl2_qt4_superbuild/source-paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
 line 784
vtkPVCompositeDataPipeline (0x48ba200): Algorithm vtkPOpenFOAMReader(0x488a610) 
returned failure for request: vtkInformation (0x47af0c0)
  Debug: Off
  Modified Time: 224666
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA
  FROM_OUTPUT_PORT: 0
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0

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Re: [Paraview] ParaView 5.2 Release Candidate 3 available for download

[Armin Wehrfritz]

Thanks for the quick response and fix of this issue!

I will test it once there is a ParaView version (RC or release) that has
the fix.

-Armin



On 11/04/2016 07:05 PM, David Lonie wrote:

On Fri, Nov 4, 2016 at 10:18 AM, Armin Wehrfritz mailto:dkxl...@gmail.com>> wrote:

Hi,

I tested 5.2 RC3 and encountered an issue when reading OpenFOAM cases.

The problem only occurs when the OpenFOAM data (i.e. the mesh or fields)
are written in binary format. I setup two test cases that are otherwise
identical, where for the one the data is in ascii and the other one in
binary format.
With ParaView 5.1.2 I can read both cases without any error, but with
ParaView 5.2 RC3 the cases for which the data is in binary format leads
to an error (see below for the exact error message).

The case is taken directly from the official OpenFOAM 4.x tutorials, and
here is a link to the case files that can be directly used for
debugging:
https://www.dropbox.com/s/l0cb8vd6pjkb1zz/debug_PV_OF.tar.gz?dl=0
<https://www.dropbox.com/s/l0cb8vd6pjkb1zz/debug_PV_OF.tar.gz?dl=0>

All tests were done with the ParaView binaries distributed by Kitware.

Let me know if you need more information or if I can help debugging this
further.


Thanks for the bug report! I have a patch for this here:

https://gitlab.kitware.com/vtk/vtk/merge_requests/2147

This should be able to make it into the upcoming release.

Dave

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Re: [Paraview] Compilation error under Linux with MPI and Python

[Armin Wehrfritz]

The problem actually occurs only for openmpi versions > 1.6, I 
successfully compiled now ParaView under openSUSE 12.3 (openmpi 1.6).


I also found a quick-and-dirty, workaround for openmpi 1.7.2 by manually 
adding libdl to the libraries in CMakeCache.txt:

MPI_CXX_LIBRARIES:STRING=/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so;/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so;/usr/lib64/libdl.so
MPI_C_LIBRARIES:STRING=/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so;/usr/lib64/libdl.so


Maybe a ParaView developer can add libdl to the linking targets for 
mpi4py to fix the problem properly.


-Armin


On 02/06/2014 05:02 AM, Orion Poplawski wrote:

On 02/05/2014 01:14 PM, Armin Wehrfritz wrote:

Hi,

I get this error when compiling Paraview 4.1.0 under Linux x64:


[  230s] CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o: In function
`OPENMPI_dlopen_libmpi':
[  230s] MPI.c:(.text+0x6eb1): undefined reference to `dlopen'
[  230s] MPI.c:(.text+0x6ecd): undefined reference to `dlopen'
[  230s] MPI.c:(.text+0x6ee3): undefined reference to `dlopen'
[  230s] MPI.c:(.text+0x6ef9): undefined reference to `dlopen'
[  230s] CMakeFiles[  4%] /mpi4py.MPI.dir/src/MPI.c.o: In function
`__pyx_pf_6mpi4py_3MPI_16Init':
[  230s] MPI.c:(.text+0x1349b): undefined reference to `dlopen'
[  230s] CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o:MPI.c:(.text+0x135bd):
more undefined references to `dlopen' follow
[  230s] collect2: error: ld returned 1 exit status
[  230s] make[2]: *** [lib/site-packages/mpi4py/MPI.so] Error 1
[  230s] make[1]: ***
[ThirdParty/mpi4py/vtkmpi4py/CMakeFiles/mpi4py.MPI.dir/all] Error 2
[  230s] make[1]: *** Waiting for unfinished jobs


The error seems related to newer versions of openmpi in combination with
and Python.
When compiling under openSUSE 12.2 (openmpi 1.5.4) everything works
fine, but under openSUSE 12.3 (openmpi 1.6) and openSUSE 13.1 (openmpi
1.7.2) the compilation fails.

Apparently, in newer versions of openmpi, the wrapper doesn't add '-ldl'
anymore to the linker flags.
See also here:
https://svn.open-mpi.org/trac/ompi/ticket/3103

I'm not sure if this should be fixed in openmpi or paraview, but I would
appreciate any hint on how to fix it.

Best regards,
Armin


It needs to be fixed in paraview - it bundles mpi4py, and mpi4py uses
dlopen(), so mpi4py needs to be linked to -ldl.  Not sure the
appropriate way to fix that in paraview though.




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Re: [Paraview] Compilation error under Linux with MPI and Python

[Armin Wehrfritz]

Yes, the patch addresses the problem. Just finished the compilation for 
openmpi 1.7.2 and everything seems fine (i.e. no errors occurred).


Thanks!

-Armin


On 02/10/2014 04:54 PM, Utkarsh Ayachit wrote:

Does the attached patch address the problem?  We may need to duplicate
the code for each of the modules.

On Thu, Feb 6, 2014 at 5:11 AM, Armin Wehrfritz  wrote:

The problem actually occurs only for openmpi versions > 1.6, I successfully
compiled now ParaView under openSUSE 12.3 (openmpi 1.6).

I also found a quick-and-dirty, workaround for openmpi 1.7.2 by manually
adding libdl to the libraries in CMakeCache.txt:



MPI_CXX_LIBRARIES:STRING=/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so;/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so;/usr/lib64/libdl.so

MPI_C_LIBRARIES:STRING=/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so;/usr/lib64/libdl.so



Maybe a ParaView developer can add libdl to the linking targets for mpi4py
to fix the problem properly.

-Armin



On 02/06/2014 05:02 AM, Orion Poplawski wrote:


On 02/05/2014 01:14 PM, Armin Wehrfritz wrote:


Hi,

I get this error when compiling Paraview 4.1.0 under Linux x64:


[  230s] CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o: In function
`OPENMPI_dlopen_libmpi':
[  230s] MPI.c:(.text+0x6eb1): undefined reference to `dlopen'
[  230s] MPI.c:(.text+0x6ecd): undefined reference to `dlopen'
[  230s] MPI.c:(.text+0x6ee3): undefined reference to `dlopen'
[  230s] MPI.c:(.text+0x6ef9): undefined reference to `dlopen'
[  230s] CMakeFiles[  4%] /mpi4py.MPI.dir/src/MPI.c.o: In function
`__pyx_pf_6mpi4py_3MPI_16Init':
[  230s] MPI.c:(.text+0x1349b): undefined reference to `dlopen'
[  230s] CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o:MPI.c:(.text+0x135bd):
more undefined references to `dlopen' follow
[  230s] collect2: error: ld returned 1 exit status
[  230s] make[2]: *** [lib/site-packages/mpi4py/MPI.so] Error 1
[  230s] make[1]: ***
[ThirdParty/mpi4py/vtkmpi4py/CMakeFiles/mpi4py.MPI.dir/all] Error 2
[  230s] make[1]: *** Waiting for unfinished jobs



The error seems related to newer versions of openmpi in combination with
and Python.
When compiling under openSUSE 12.2 (openmpi 1.5.4) everything works
fine, but under openSUSE 12.3 (openmpi 1.6) and openSUSE 13.1 (openmpi
1.7.2) the compilation fails.

Apparently, in newer versions of openmpi, the wrapper doesn't add '-ldl'
anymore to the linker flags.
See also here:
https://svn.open-mpi.org/trac/ompi/ticket/3103

I'm not sure if this should be fixed in openmpi or paraview, but I would
appreciate any hint on how to fix it.

Best regards,
Armin



It needs to be fixed in paraview - it bundles mpi4py, and mpi4py uses
dlopen(), so mpi4py needs to be linked to -ldl.  Not sure the
appropriate way to fix that in paraview though.




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Re: [Paraview] Is Paraview the right program?

[Armin Wehrfritz]

Hi,

ParaView offers you a lot of visualisation and data handling options, so 
yes definitely the right choice. :)


Concerning the file format:
The VTK data-structures are well suited for such kind of data, however I 
personally find the learning curve of VTK rather steep. Meaning, it 
might be quite difficult to get started with this task.


An alternative is to used a HDF5/XDMF file format. I got a simple HDF5 
writer rather quickly implemented, there are good tutorials on the web, 
and I generate the XDMF file in a post-processing step with a python 
script. (ParaView supports XDMF files very well.)

Oh and yes, you can read HDF5 files conveniently with Matlab and Python too.

In any case both options, HDF5/XDMF or VTK, are better than plain 
ascii-files. ;)


Regards,
Armin

P.S.: Which language do you write the FEM program in?



On 03/25/2014 11:33 AM, Marco Nawijn wrote:

Hello Florian,

Yes! Paraview is definitely a good choice. I would also recommend to use
VTK for managing some of the FEM related datastructures. In particular,
I would recommend to use one or more of the grid/cell classes. This also
provides
you automatically with different export formats (see for example the
vtkXMLUnstructuredGridWriter).

Regards,

Marco







On Tue, Mar 25, 2014 at 12:42 AM, Florian Schmidt mailto:fsli...@web.de>> wrote:

Hello,

I want to write my own FEM program. And now I am looking for a
visualization and post-processing tool.

What do you think: is paraview a good choice?


Is there an ascii-fileformat you would recommend to use as output
from the FEM program and as input for paraview?

Thanks,
Florian
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Re: [Paraview] paraview & HDF5/XDMF: how to control memory usage?

[Armin Wehrfritz]

Hello,

I know it's a bit off-topic, but since the next generation xdmf 
reader/write was mentioned in here:


Will the new XDMF reader have a "Reload"/"Refresh" functionality?

I'm currently using a workaround suggested by Sebastien [1], which works 
fine.

The topic has also been discussed here [2], with no outcome I believe.

Cheers,
Armin Wehrfritz

[1] http://www.paraview.org/pipermail/paraview/2013-June/028596.html
[2] http://www.paraview.org/pipermail/paraview/2014-January/030299.html


On 06/10/2014 10:36 PM, Jason Fleming wrote:

Hello

I would also like to that it is great to hear that a next generation
XDMF reader is in the works for Paraview. I've used XDMF files very
successfully with Paraview; both manually generated XML to go with
NetCDF4 as well as HDF5/XML files generated using the XDMF2 API.

The only rough spot I've had with the existing Paraview XDMF reader is
that it seems to use more and more memory when generating a time series
animation. If the dataset is large enough, the Paraview process will
eventually run out of memory. I have an unchanging unstructured mesh
with nodally centered data and a temporal collection with one XML file
and one heavy data file containing all time steps.

I can provide a link to full size data files if that helps the
development/test process.

Cheers
Jason


On Tue, Jun 10, 2014 at 3:05 AM, Favre Jean mailto:jfa...@cscs.ch>> wrote:


Allow me to add my 2 cents to this thread, since Dave talks about a
new generation xdmf reader/writer in the making.

I too use a series of files for each timestep ( one XMF file and one
HDF5 file per step), since I have discovered that creating temporal
collections does not work correctly if the grid resolution changes
over the timesteps. I have a multi-resolution simulation. The grid
starts at low res., then the resolution steadily increases. Using a
temporal collection in XDMF, the grid resolution of the first grid
in the temporal collection is used throughout the full time series.
I see my data is read correctly, but is truncated by the lowest
resolution bounds.

I hope this gets fixed with the new reader.
TIA.

-
Jean/CSCS
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Re: [Paraview] Multiple Domains with XDMF

[Armin Wehrfritz]

I faced some weeks ago essentially the same problem. I can just 
recommend you to write separate files for each grid  (if somehow 
possible), it will save you a lot of trouble in many perspectives.


-Armin

P.S.: With ParaView state files you can still "load" several files, i.e. 
grids, at the same time - a very handy feature. ;)





On 06/25/2014 08:20 PM, Truman Ellis wrote:

I essentially have two grids with different solution variables defined
on each one. I am using the XDMF format to output the data. When I
create a spatial collection of the two grids, the solution variables
show up as "partial" data in Paraview. Say solution variable u lives on
grid 1 while f lives on grid 2. If I color by u, grid 2 shows up as some
solid color that doesn't go away unless I turn off the block that
corresponds to grid 2. And vice versa for f.

I read that XDMF supports multiple domains, which sounded like it might
be the right solution for this problem. But when I load such a mesh into
Paraview, it only picks up on the last defined domain. It seems like
having different solution variables on different grids is a common
problem, so I'm wondering if anyone has a cleaner solution than
selectively turning on and off the blocks corresponding to the solution
variable I am currently considering.
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[Paraview] Odd behavior of XDMF files with 3DCORECTMesh

[Armin Wehrfritz]

Hi,

I lately started to write my data in HDF5/XDMF files. This works so far
very well for unstructured data using TopologyType="Mixed" and Polygon
cells, but I have some trouble with structured grids.

I attached a very simple VTK file, which is correctly visualized in
ParaView. More precisely, the DIMENSIONS keyword specifies the
dimensions in X Y Z direction and the SPACING and POINT_DATA keywords
are specified accordingly.

Opening the VTK file in ParaView and exporting the data as XDMF leads to
an XDMF file with dimensions and the spacing is in reverse order (Z Y
X), where seemingly the data is written in the same order as in the VTK
file.
Is this intended or a bug?
Just to note, the data from the ParaView-created XDMF and the original
VTK file are displayed consistently.

When I however manually converter the VTK to a XDMF file with
dimensions, spacing and data specified as in the VTK file, I get a
completely wrong representation in ParaView.
Seemingly, in the "Topology" element the "Dimensions" keyword specifies
the dimensions in Z Y X direction, which I thing is rather odd.
The whole thing gets then completely messed up when specifying the data.

Am I doing something wrong when manually creating the XDMF file or is
this a bug?

Best regards,
Armin



--
Armin Wehrfritz, Dipl.-Ing. (M.Sc.)
Aalto University, School of Engineering
Department of Energy Technology
PO Box 14300
FI-00076 Aalto, Finland
# vtk DataFile Version 2.0
testing
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 3 4 1
ORIGIN 0.0 0.0 0.0
SPACING 0.5 0.5 1.0
POINT_DATA 12
SCALARS test_scalar float
LOOKUP_TABLE default
0.0
1.0
2.0
1.0
2.0
3.0
2.0
3.0
4.0
3.0
4.0
5.0
VECTORS test_vector float
0.0 0.0 0.0
1.0 1.0 1.0
2.0 2.0 2.0
1.0 1.0 1.0
2.0 2.0 2.0
3.0 3.0 3.0
2.0 2.0 2.0
3.0 3.0 3.0
4.0 4.0 4.0
3.0 3.0 3.0
4.0 4.0 4.0
5.0 5.0 5.0


test_manual.xmf
Description: audio/xmf


test_paraview.xmf
Description: audio/xmf
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Re: [Paraview] Odd behavior of XDMF files with 3DCORECTMesh

[Armin Wehrfritz]

Thanks for your reply!

I'm not quite sure if that is really the problem, but it could be related.
I still think there is something wrong in the XDMF class itself.

I did some quick conversion tests for the the different mesh types using
the example data from vtk.org/VTKData.git <http://vtk.org/VTKData.git>:

VTKData/Data/SampleStructGrid.vtk:
 DATASET STRUCTURED_GRID
 DIMENSIONS 20 30 40
=>  


VTKData/Data/RectGrid2.vtk:
 DATASET RECTILINEAR_GRID
 DIMENSIONS 47 33 11
=>  


VTKData/Data/matrix.vtk
 DATASET STRUCTURED_POINTS
 DIMENSIONS 10 5 1
=>  


In all cases, the XDMF class reads and writes the dimensions in the
"wrong" way, i.e. ZYX instead of XYZ. Also the data arrays are
read/written in ZYX order.

The most important part for me to notice was that "ORIGIN_DXDYDZ"
(*CoRectMesh) actually specifies the spacing in ZYX and not as the
name suggests in XYZ.
Whereas the data items in "VXVYVZ" ( *RectMesh) specify the XYZ
data.
In my opinion this is kind of a bit messy, but probably not really a bug.

In my specific case, I have HDF5 files with data-arrays in XYZ order, 
i.e. z is

iterated over the fastest, then y, and x is iterated over the slowest.
After some trial and error I managed to create a valid .xmf file and read
my data correctly into paraview, though the coordinate axes are still kind
of wrong (ZYX instead of XYZ).
Important to notice here was that the "Dimensions" in the Topology section
need to match the data-structure in the HDF5 file.

Thanks for your help!

-Armin



On 09/25/2014 01:00 AM, David E DeMarle wrote:
> I think this is a very very old bug.
>
> For some reason, *RECTMesh (vtkRectilinearGrid) has been ijk instead of
> kji for as long as I can remember.
>
> *SMesh (vtkStructuredGrid) and *CoRectMesh (vtkImageData) are normal on
> the other hand.
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909 
>
> On Sat, Sep 20, 2014 at 7:38 AM, Armin Wehrfritz <mailto:dkxl...@gmail.com>

> <mailto:dkxl...@gmail.com <mailto:dkxl...@gmail.com>>> wrote:
>
> Hi,
>
> I lately started to write my data in HDF5/XDMF files. This works 
so far
> very well for unstructured data using TopologyType="Mixed" and 
Polygon

> cells, but I have some trouble with structured grids.
>
> I attached a very simple VTK file, which is correctly visualized in
> ParaView. More precisely, the DIMENSIONS keyword specifies the
> dimensions in X Y Z direction and the SPACING and POINT_DATA keywords
> are specified accordingly.
>
> Opening the VTK file in ParaView and exporting the data as XDMF 
leads to

> an XDMF file with dimensions and the spacing is in reverse order (Z Y
> X), where seemingly the data is written in the same order as in 
the VTK

> file.
> Is this intended or a bug?
> Just to note, the data from the ParaView-created XDMF and the 
original

> VTK file are displayed consistently.
>
> When I however manually converter the VTK to a XDMF file with
> dimensions, spacing and data specified as in the VTK file, I get a
> completely wrong representation in ParaView.
> Seemingly, in the "Topology" element the "Dimensions" keyword 
specifies

> the dimensions in Z Y X direction, which I thing is rather odd.
>     The whole thing gets then completely messed up when specifying 
the data.

>
> Am I doing something wrong when manually creating the XDMF file or is
> this a bug?
>
> Best regards,
> Armin
>
>
>
> --
> Armin Wehrfritz, Dipl.-Ing. (M.Sc.)
> Aalto University, School of Engineering
> Department of Energy Technology
> PO Box 14300
> FI-00076 Aalto, Finland
>
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>
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Re: [Paraview] Animating over MultiBlock data set

[Armin Wehrfritz]

Do I understand it correctly that you have always a uniform geometry, 
just the data changes in time?


Are you using something like this:


Well, I attached a small xdmf file that shows how to animate in time 
(assuming a constant geometry). Hope it is of help.


-Armin



On 10/08/2014 07:26 PM, Michael Jackson wrote:

I am writing an Xdmf file with 75 "Grids" where each grid represents a
time step from a simulation. When I read it into ParaView it shows 75
Blocks. I can load each one at a time and I get the expected output.
What is the magic to animating over a multi-block data set. Each block
has the same exact set of Data arrays.

Ideas?
_
Mike JacksonBlueQuartz Software
Help: drea...@bluequartz.net 
Web|Download http://dream3d.bluequartz.net



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circAvg2.xmf
Description: audio/xmf
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Re: [Paraview] Animating over MultiBlock data set

[Armin Wehrfritz]

In that case you have to at least put the Geometry section inside the 
temporal grid.


I attached a xdmf file that shows how it should look then (the file 
works for changing Geometry and Topology).


If you can post the relevant part of your xdmf file, it would probably 
be easier see what is going wrong.


-Armin




On 10/08/2014 09:14 PM, Michael Jackson wrote:

The Topology stays the same for every time step (There are Vertex Points). The 
actual position of the points move in time (The Geometry changes).


Mike Jackson.

On Oct 8, 2014, at 1:18 PM, Armin Wehrfritz  wrote:


Do I understand it correctly that you have always a uniform geometry, just the 
data changes in time?

Are you using something like this:


Well, I attached a small xdmf file that shows how to animate in time (assuming 
a constant geometry). Hope it is of help.

-Armin



On 10/08/2014 07:26 PM, Michael Jackson wrote:

I am writing an Xdmf file with 75 "Grids" where each grid represents a
time step from a simulation. When I read it into ParaView it shows 75
Blocks. I can load each one at a time and I get the expected output.
What is the magic to animating over a multi-block data set. Each block
has the same exact set of Data arrays.

Ideas?
_
Mike JacksonBlueQuartz Software
Help: drea...@bluequartz.net <mailto:drea...@bluequartz.net>
Web|Download http://dream3d.bluequartz.net



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surfaces.runTime_xzPlane2.xmf
Description: audio/xmf
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Re: [Paraview] PV 4.2.0 Color legend disappearing

[Armin Wehrfritz]

I have experienced it too, but cannot reproduce it!

For me it happened so far only in a client-server setup. When I grab the 
surface (HDF5/XDMF files; 2D unstructured cells) and rotate or move it, 
the legend comes back, but will disappear as soon as I release the 
surface again.
When copying the very same data to my local machine and visualizing it 
in a local ParaView session, everything works fine.


Very odd indeed!

My workstation:
openSUSE 13.1
ParaView 4.2.0
Intel Core i7-4800QM QC Processor
NVIDIA Quadro K2100M Graphics Card

-Armin



On 10/30/2014 01:26 AM, Scott, W Alan wrote:

In ParaView 4.2.0, I have found a few cases where the color legend
disappears, and I can’t get it back.  Has anyone else seen this, and
found a way to replicate it?  Mind passing the voodoo on how to
replicate this bug?
Thanks,
Alan


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Re: [Paraview] [EXTERNAL] Re: PV 4.2.0 Color legend disappearing

[Armin Wehrfritz]

OK, I'm still not yet able to reproduce this bug, but at least I was 
able to write out some state files.


As mentioned before, I only see this happening in a client/server mode, 
i.e. running pvserver on a remote machine.


Three state files are attached, simply visualizing 2D cut-plane data:
1. colorLegBug_OK.pvsm:
   Everything is still working fine and color legend appears as
   expected.
2. colorLegBug_Fail_0.pvsm:
   Switched the color array (from 'Z' to 'SourcePV') -> color legend
   disappears for 'SourcePV', but still is present when switching back
   to 'Z'
3. colorLegBug_Fail_1.pvsm:
   After some more switching of color arrays, the color legend
   disappears for all quantities.

Hope this gives some clues to track down this bug.

Thanks,
Armin




On 10/31/2014 01:34 AM, Scott, W Alan wrote:

Yep, that's the bug.   I have seen it local server.  Anyone else have any ideas 
how to replicate it?  If anyone does see it, mind writing a state file and 
sending to me?  It's a long shot, but maybe that will help us figure out what 
is going on.

Thanks,

Alan

-Original Message-
From: Armin Wehrfritz [mailto:dkxl...@gmail.com]
Sent: Thursday, October 30, 2014 6:25 AM
To: Scott, W Alan; paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] PV 4.2.0 Color legend disappearing

I have experienced it too, but cannot reproduce it!

For me it happened so far only in a client-server setup. When I grab the 
surface (HDF5/XDMF files; 2D unstructured cells) and rotate or move it, the 
legend comes back, but will disappear as soon as I release the surface again.
When copying the very same data to my local machine and visualizing it in a 
local ParaView session, everything works fine.

Very odd indeed!

My workstation:
openSUSE 13.1
ParaView 4.2.0
Intel Core i7-4800QM QC Processor
NVIDIA Quadro K2100M Graphics Card

-Armin



On 10/30/2014 01:26 AM, Scott, W Alan wrote:

In ParaView 4.2.0, I have found a few cases where the color legend
disappears, and I can't get it back.  Has anyone else seen this, and
found a way to replicate it?  Mind passing the voodoo on how to
replicate this bug?
Thanks,
Alan


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Description: application/gzip
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Re: [Paraview] Display velocity in paraview

[Armin Wehrfritz]

This should be fairly straight forward once you have a reader for your 
data. Hence the first questions that comes up:

In which file format is the data stored?

ParaView has a large selection of readers for all kinds of file formats, 
ranging from simple text files (i.e. CSV files) to advanced HPC file 
formats like XDMF. See here:

http://www.paraview.org/Wiki/ParaView/Users_Guide/List_of_readers

I personally prefer writing my data in XDMF/HDF5 files, for which 
ParaView has a very good reader.


For custom, but still simple, file formats also the "Python Programmable 
Filter" might be an option. Google will give you several examples for that.


-Armin




On 11/19/2014 07:07 AM, Rohit Narurkar wrote:

Dear all,

I have a 400x400 lattice grid, where each lattice has a velocity u and v
in the x and y direction respectively. I wish to display this in
paraview, which filters should I use? and how do I proceed?

Thank you,
Rohit Narurkar


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Re: [Paraview] scalarbar visibility issue in client/server mode

[Armin Wehrfritz]

This issue has been already reported/discussed here on the mailing list 
and we are in the process of tracking it down.

Search the mailing-list archive for "PV 4.2.0 Color legend disappearing".

-Armin





On 11/20/2014 06:28 PM, Luc Bordier wrote:

Hello,

I am using paraview 4.2.0 in client / server mode and i am facing
problem of visibility of colorbars.

After i proceeded my different filters (slice, streamlines,...), my
colobars are disappearing from the rendering view.
What is strange is that if i am interacting the view, the colorbars are
shown again. And when i get still, they disappeared again.
Then the only way to show scalarbars is to interact the view.
I made this observation with :

linux server (RHEL 5.8), linux client on same host
linux server (RHEL 5.8), windows client (win 7)

Is it a known issue ? any drawbacks ?

Thank you


--
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DCNS Research/SIREHNA
Responsable d'études et de recherche (MSH)
1, rue de la Noë, BP 42105, F44321 NANTES CEDEX 3
Tél : 02 51 86 02 93



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Re: [Paraview] XDMF Bug (Hard-coded drive letter C:)

[Armin Wehrfritz]

This sounds strange.
Though, I cannot reproduce this bug under Linux (ParaView 4.2.0, 
openSUSE 13.1 64bit).


However, I noticed that the XDMF file written by ParaView contains the 
absolute path to the HDF5 file, which makes the file not really "portable".


Probably this could be solved by using relative paths in the XDMF file?

There is actually an ancient bug-report concerning that topic:
http://public.kitware.com/Bug/view.php?id=4433

-Armin





On 12/01/2014 04:32 AM, Ken Sheldon wrote:

It appears ParaView uses the wrong drive letter when writing or reading
HDF5 files via XDMF.

Steps to reproduce:

Start ParaView (I am using Version 4.2.0 64 Bit for Windows 7 64-bit)

 From the menu, select  Sources --> Plane

Set X Resolution 10

Set Y Resolution 10

Apply

File --> Save Data

   File format Xdmf data file

   File name D:\SAMPLE.XMF

Open the XMF file in a text editor.

Bug 1: The file refers to D:/SAMPLE.h5 .   However, there is no such
file.  The HDF5 file is C:\SAMPLE.H5.

Bug 2: Reset the ParaView session and open the file D:\SAMPLE.XMF.
Apply. The data loads properly, although the XMF file refers to
D:/SAMPLE.h5, which does not exist.

Bug 2.1: Reset the ParaView session. Move the file SAMPLE.H5 to D:\
(The directory referenced in D:\SAMPLE.XMF) In Paraview, select File -->
Open SAMPLE.XMF.  Apply.

The program displays the Output Messages window with the following error
message:

ERROR: In
C:\DBD\pvs-x64\paraview\src\paraview\VTK\IO\Xdmf2\vtkXdmfReader.cxx,
line 409

vtkXdmfReader (0EA5E7E0): Failed to read data.

ERROR: In
C:\DBD\pvs-x64\paraview\src\paraview\VTK\Common\ExecutionModel\vtkExecutive.cxx,
line 783

vtkPVCompositeDataPipeline (0DBCCA70): Algorithm
vtkFileSeriesReader(0DBCC5C0) returned failure for request:
vtkInformation (0C4FE530)

   Debug: Off

   Modified Time: 673302

   Reference Count: 1

   Registered Events: (none)

   Request: REQUEST_DATA

   ALGORITHM_AFTER_FORWARD: 1

   FORWARD_DIRECTION: 0

   FROM_OUTPUT_PORT: 0



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Re: [Paraview] Enabling parallel projection

[Armin Wehrfritz]

The switch is very well hidden... too well in my opinion.

In the properties panel, you have to toggle the advanced properties (the 
gear button), the parallel projection checkbox will appear then at the 
bottom of the panel.


-Armin



On 12/05/2014 10:58 AM, Florian Lindner wrote:

Hello,

in recent paraview 4.2.0 I am unable to find how to enable the parallel
projection. The wiki is outdated.

Thanks,
Florian

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Re: [Paraview] Enabling parallel projection

[Armin Wehrfritz]

Cool, didn't realize that the search also find advanced settings. :)

Is there a way to set parallel project as default?

Up to 4.1 this could be done in Edit->View Settings->General, but that 
option somehow got lost in 4.2 (or at least I couldn't find it by using 
the search in Edit->Settings).


-Armin


On 12/05/2014 05:07 PM, Sebastien Jourdain wrote:

You can also just search what you are looking for in the search box of
the property panel.
If so, you could have found it without toggling the advanced option and
just by typing "par" in that search box.

Hope that help to find other hidden/advanced options.

Seb

On Fri, Dec 5, 2014 at 4:02 AM, Armin Wehrfritz mailto:dkxl...@gmail.com>> wrote:

The switch is very well hidden... too well in my opinion.

In the properties panel, you have to toggle the advanced properties
(the gear button), the parallel projection checkbox will appear then
at the bottom of the panel.

-Armin




On 12/05/2014 10:58 AM, Florian Lindner wrote:

Hello,

in recent paraview 4.2.0 I am unable to find how to enable the
parallel
projection. The wiki is outdated.

Thanks,
Florian

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Re: [Paraview] [EXTERNAL] Re: Enabling parallel projection

[Armin Wehrfritz]

Thanks a lot for the hints, I got my defaults properly set now!

One has to get used to the new search/settings/defaults thing, but it 
works really nicely after all.


I probably should have read the blog posts before I switched to ParaView 
4.2. :)


-Armin




On 12/07/2014 06:40 PM, Utkarsh Ayachit wrote:

For more details, refer to these blog posts: [1] and [2].

Utkarsh

[1] http://www.kitware.com/blog/home/post/702
[2] http://www.kitware.com/blog/home/post/672


On Fri, Dec 5, 2014 at 8:08 PM, Scott, W Alan  wrote:

I had forgotten, but just got reminded by Utkarsh.  ParaView 4.2 has a really 
sweet feature - you can save any state in the Properties Panel as default.  You 
go it by group.

With regards to parallel projection, Properties Panel/ Advanced/ Camera Parallel 
Projection on.  You will notice this is under the sub header (or whatever you call it) of 
"View (Render View)" .  On the right side of this button (which allows Render 
View to be minimized/ maximized), are two buttons.  One is restore default settings, one 
is save settings as default.  Click on save settings as default.

Alan

p.s. - Utkarsh, I just tested this functionality and it worked just fine.

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Armin 
Wehrfritz
Sent: Friday, December 05, 2014 9:25 AM
To: Sebastien Jourdain
Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] Enabling parallel projection

Cool, didn't realize that the search also find advanced settings. :)

Is there a way to set parallel project as default?

Up to 4.1 this could be done in Edit->View Settings->General, but that option 
somehow got lost in 4.2 (or at least I couldn't find it by using the search in 
Edit->Settings).

-Armin


On 12/05/2014 05:07 PM, Sebastien Jourdain wrote:

You can also just search what you are looking for in the search box of
the property panel.
If so, you could have found it without toggling the advanced option
and just by typing "par" in that search box.

Hope that help to find other hidden/advanced options.

Seb

On Fri, Dec 5, 2014 at 4:02 AM, Armin Wehrfritz mailto:dkxl...@gmail.com>> wrote:

 The switch is very well hidden... too well in my opinion.

 In the properties panel, you have to toggle the advanced properties
 (the gear button), the parallel projection checkbox will appear then
 at the bottom of the panel.

 -Armin




 On 12/05/2014 10:58 AM, Florian Lindner wrote:

 Hello,

 in recent paraview 4.2.0 I am unable to find how to enable the
 parallel
 projection. The wiki is outdated.

 Thanks,
 Florian

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Re: [Paraview] How to plot data from a specific point over time?

[Armin Wehrfritz]

Have you tried the "Plot Selection Over Time" filter?
It's in "Filter->Data Analysis". You can select cell or point data.

-Armin



On 01/21/2015 06:35 PM, Pedro Ceccon Thurler wrote:

Hey guys!
I'm in trouble trying to make some plots in paraview.
For my analysis, it's important to plot data from a specific point over
time.
I'm trying some filters, but I'm not succeeding. Do you have some tips
or advices? Thank you for your attention.

Pedro Ceccon Thurler

Bolsista CNPq - Laboratório de Simulação de Sistemas de Construção Naval
Departamento de Engenharia Naval e Oceânica - UFRJ
Cel: (21) 9 8234-9794


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Re: [Paraview] Fwd: Visualization in ParaView/VisIt

[Armin Wehrfritz]

For such kind of data I typically write a custom made XDMF [1] file. 
XDMF is basically a XML wrapper that contains the description of the 
HDF5 data file.
What comes in handy in your cases, is that you have the heavy data 
already in a HDF5 file.


I typically write the XDMF file with a hand crafted python script since 
I typically deal with data sets from various source.
However, there is also a XDMF library [2,3], which should provide some 
convenient advantages.


The XDMF file format is very well supported by ParaView, or VisIt for 
that matter.


I attached 2 XDMF files, so you get an idea what I'm talking of (the 
HDF5 data files are missing though).


-Armin

[1] http://www.xdmf.org/index.php/Main_Page
[2] http://www.xdmf.org/index.php/Get_Xdmf
[3] http://www.xdmf.org/index.php/Write_Xdmf



On 01/28/2015 09:52 PM, Martín Huarte E wrote:

Dear Paraview community: Good day. I need assistance on visualizing a
matlab file? Any tips will be greatly appreciated. Thanks.


Details:
I need to visualize temperature distribution in a volume.  The volume is
a wedge-like slice of a hollow cylinder (shown in the attached schematic).

The calculations are made in MATLAB.  The three-dimensional matrices of
the solution (T) and the node-coordinates (X, Y and Z) are saved in a
HDF5 file.

So far, I have not been able to make ParaView to visualize the result in
the actual geometry. They get the length, width and height of the volume
and simply build a cuboid out of them.

Thanks

My best, Martín
__
/Martín Huarte-Espinosa, Ph.D./
/Computational Physicist  - //High Performance Computing Specialist/
/linkedin.com/pub/martin-huarte-espinosa/59/6b7/13a
/





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ex1.xmf
Description: audio/xmf


ex2.xmf
Description: audio/xmf
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Re: [Paraview] Fwd: Visualization in ParaView/VisIt

[Armin Wehrfritz]

I just stumbled across this interesting blog:
http://berkgeveci.github.io/2015/01/08/h5py-writer-reader/

If you have some kind of python knowledge, especially the "HDF5Reader" 
part should be very interesting for you.

For this you don't even need the XDMF files.

-Armin



On 01/28/2015 10:55 PM, Martin Huarte Espinosa wrote:

Dear Armin and Dave: thanks for your replies. I will try.

Martin.

On Wed, Jan 28, 2015 at 2:30 PM, Armin Wehrfritz mailto:dkxl...@gmail.com>> wrote:

For such kind of data I typically write a custom made XDMF [1] file.
XDMF is basically a XML wrapper that contains the description of the
HDF5 data file.
What comes in handy in your cases, is that you have the heavy data
already in a HDF5 file.

I typically write the XDMF file with a hand crafted python script
since I typically deal with data sets from various source.
However, there is also a XDMF library [2,3], which should provide
some convenient advantages.

The XDMF file format is very well supported by ParaView, or VisIt
for that matter.

I attached 2 XDMF files, so you get an idea what I'm talking of (the
HDF5 data files are missing though).

-Armin

[1] http://www.xdmf.org/index.php/__Main_Page
<http://www.xdmf.org/index.php/Main_Page>
[2] http://www.xdmf.org/index.php/__Get_Xdmf
<http://www.xdmf.org/index.php/Get_Xdmf>
[3] http://www.xdmf.org/index.php/__Write_Xdmf
<http://www.xdmf.org/index.php/Write_Xdmf>



On 01/28/2015 09:52 PM, Martín Huarte E wrote:

Dear Paraview community: Good day. I need assistance on
visualizing a
matlab file? Any tips will be greatly appreciated. Thanks.


Details:
I need to visualize temperature distribution in a volume.  The
volume is
a wedge-like slice of a hollow cylinder (shown in the attached
schematic).

The calculations are made in MATLAB.  The three-dimensional
matrices of
the solution (T) and the node-coordinates (X, Y and Z) are saved
in a
HDF5 file.

So far, I have not been able to make ParaView to visualize the
result in
the actual geometry. They get the length, width and height of
the volume
and simply build a cuboid out of them.

Thanks

My best, Martín
__
/Martín Huarte-Espinosa, Ph.D./
/Computational Physicist  - //High Performance Computing Specialist/
/linkedin.com/pub/martin-__huarte-espinosa/59/6b7/13a
<http://linkedin.com/pub/martin-huarte-espinosa/59/6b7/13a>
<http://linkedin.com/pub/__martin-huarte-espinosa/59/6b7/__13a
<http://linkedin.com/pub/martin-huarte-espinosa/59/6b7/13a>>/





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--

My best, Martín
__
/Martín Huarte-Espinosa, Ph.D./
/Computational Physicist  - //High Performance Computing Specialist/
/linkedin.com/pub/martin-huarte-espinosa/59/6b7/13a
<http://linkedin.com/pub/martin-huarte-espinosa/59/6b7/13a>/

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Re: [Paraview] visualizing xdmf/hdf5 files in parallel

[Armin Wehrfritz]

There has been a similar discussion half a year ago:
http://public.kitware.com/pipermail/paraview/2014-June/031350.html

I believe this is still investigated/ under development.

-Armin




On 02/04/2015 01:56 AM, Inanc Senocak wrote:

Hi Everybody,

We have a parallel structured Cartesian grid flow solver. We output our
solution file using xdmf/hdf5 format. File sizes are large (56 GB) so we
need to render the flow solution in parallel.

We are able to use VisIT to load and render the solution files
(xdmf/hdf5) efficiently. But we haven't had luck with Paraview. We use
version 4.3. Basically as we are loading the files, pvserver consumes
all the memory per node (64TB) and then it crashes. We are able to use
pvserver to render (in parallel) smaller simulation files (xdmf/hdf5)
without any issues.

We have tried several options building pvserver but it did not make any
difference in rendering large files. Maybe there is a bug in the way our
simulation code writes xdmf/hdf5 files.

Does anyone have a large xdmf/hdf5 simulation file that we can download
to verify our paraview installation and its parallel rendering performance?

If you have any other tips/experiences regarding parallel rendering of
large xdmf/hdf5 files, please let me know.

Thank you!

Inanc


--
Inanc Senocak
Associate Professor
Mechanical & Biomedical Engineering
Boise State University
1910 University Dr.
Boise, ID 83725-2085
phone: (208) 426-4066
fax: (208) 426-4800
e-mail: seno...@boisestate.edu 
website: http://coen.boisestate.edu/senocak


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Re: [Paraview] CPack issue with hdf5/libhdf5.settings

[Armin Wehrfritz]

Hi Christoph,

How are you building the packages?

I'm building packages for paraview 4.2.0 and 4.3.1 on the "openSUSE 
Build Service". If you want to compile ParaView with specific options 
you can copy my spec file and start from there:

https://build.opensuse.org/package/view_file/home:dkxls:cfd/paraview43/paraview43.spec

If it is nothing too exotic I can also enable your options for the 
packages. You can install them easily from here:

http://software.opensuse.org/package/paraview43


-Armin



Disclaimer: I'm not a ParaView developer, just a regular user. The 
packages above are neither supported by Kitware nor openSUSE and are 
just intended to ease the installation on the openSUSE workstations in 
our research group.




On 02/10/2015 06:57 AM, Christoph Grüninger wrote:

Hi ParaView devs,
I tried to build a openSuse RPM for ParaView 4.3.1 but I get the
following error. I guess it is related to ParaView's CPack scripts:


[ 6390s] Checking for unpackaged file(s): /usr/lib/rpm/check-files
/home/abuild/rpmbuild/BUILDROOT/paraview-4.3.1-30.1.x86_64
[ 6390s] error: Installed (but unpackaged) file(s) found:
[ 6390s]/usr/share/cmake/hdf5/libhdf5.settings
[ 6390s]
[ 6390s]
[ 6390s] RPM build errors:
[ 6390s] Installed (but unpackaged) file(s) found:
[ 6390s]/usr/share/cmake/hdf5/libhdf5.settings
[ 6391s] ### WATCHDOG MARKER START ###

Sorry for not providing a patch.

Bye
Christoph


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Re: [Paraview] Loading whole time series in ParaView at once

[Armin Wehrfritz]

Hi,

I cannot directly answer your question, but I have a few remarks/questions:

Which reader are you using for your OpenFOAM cases?

There are two OpenFOAM readers for ParaView, a) the built-in reader in
ParaView (file ending .foam) and b) the reader supplied with OpenFOAM
(file ending .OpenFOAM).

For my cases the built-in reader works much faster/efficient than the
one from OpenFOAM (but that may very well be cases specific).
With the ParaView built-in reader you also have the option to cache the
mesh in memory.

If you use the OpenFOAM command "paraFoam" you will by default use the
reader that comes with OpenFOAM. To use the built-in reader from
ParaView use "paraFoam -builtin".
Alternatively just create a file with either ending (.foam or .OpenFOAM)
to switch between the readers.


-Armin





On 02/13/2015 01:03 PM, j.dub...@centrum.cz wrote:

Hi, I'm currently struggling with one problem in ParaView, where I
didn't find any solution up to now.

My problem looks like this: I have a transient OpenFOAM simulation
and want to do postprocessing of my results. This itself is not a big
problem. I can load the data and switch between the timesteps and it
works. The problem is, that it works terribly slowly. As far as I
understand it, the way how this work is, that with every switching
from one step to the other Paraview has to load the results and the
mesh every time.

What I would prefere much more would be the option to let ParaView
load all the time steps at once. Of course this would need much more
 resources, but exactly with the resources I'm not really limited
(having a huge cluster with ~500 nodes).

Therefore loading the whole time series and having the possibility to
switch between the timesteps quickly without having to load the
mesh/data all the time would be a great improvement for me.

Is there any way how this could be done, or is it something that
ParaView has not really been designed for? For example ine Ensight I
 do have this option and it makes the work with the transient results
 much better.

Many thanks in advance for any help or advice on this issue.

Regards

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Re: [Paraview] Loading whole time series in ParaView at once

[Armin Wehrfritz]

thanks  for your reply. I'm using the ParaView builtin reader. I
always do "touch xxx.foam" in my OpenFOAM folder and after this I
just start the paraview binary.

But actually I'm not sure if this is the problem of the reader or
ParaView itself. We have the same problem when loading other data
formats too. Paraview always loads the time steps one by one. This is
quite annoying if you're switching from one step to the other.


I agree, the "loading of a whole time series" issue is a ParaView
limitation/feature and most likely not reader specific.



However I didn't try the option you've mention. How can I tell
ParaView to cache at least the mesh in memory?

For the built-in ParaView reader, the default is to cache the mesh.
There is a checkbox in the properties panel.


Cheers,
Armin
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Re: [Paraview] Ep_g from region in paraview

[Armin Wehrfritz]

A couple of weeks back has been a similar discussion, see more here:
http://public.kitware.com/pipermail/paraview/2015-January/033104.html

-Armin



On 02/23/2015 02:54 PM, David Fiorillo wrote:

Dears,

Anyone could suggest how to plot average Ep_g over time over a region of
interest in the paraview?

Imagem inline 1

Best regards,

David



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Re: [Paraview] Import of XDMF/HDF5:Cell centered attribute of 2D Rectangular grid

[Armin Wehrfritz]

Hi all!

Thanks a lot Tim for the clarifications on the XDMF/HDF5 data format!

You are right, without proper bug reports the potential problems won't 
be fixed. So, I probably should have reported the not working XDMF files 
with screenshots, but I just figured that I might do something wrong and 
got it working otherwise. :)



There where two important things that I learned step by step about 
VTK/XDMF/HDF5:


1. The 2D grids (e.g. 2DRectMesh) allow only two-component vectors, kind 
of logic, but I also did that mistake.


2. Paraview reads the dimensions, origin and spacing for uniform 
rectangular meshes (i.e. 2DCoRectMesh and 3DCoRectMesh) in ZYX order as 
opposed to XYZ. The underlying reason is probably the C memory layout, 
as Tim already explained (more details can also be found here [1]).
However, this behavior is not always consistent in all XDMF readers. For 
example, the 1D coordinate arrays for a 3DRectMesh (using VXVYVZ) have 
to be listed in X, Y, Z order, while the dimensions are specified in ZYX 
order (see my earlier mail for an example).

In all cases, the data arrays have to be in reveres (i.e. ZYX) order.

Now, when I started to read and write XDMF/HDF5 files, I also had to 
experiment quite a bit and I believe the major reason why I didn't get 
the 2D grids working was related to the memory layout.


Nowadays, I use XDMF/HDF5 files for almost everything. It's just to easy 
to have a quick look at the data in ParaView, and one can read them 
otherwise very nicely with python (using vtk or h5py directly). Though, 
I haven't looked into the more advanced stuff like hyperslabs and the 
like yet.


Attached is one more example of a 3DCoRectMesh, which essentially is a 
2D surface (has however three-component vectors).



-Armin


[1] http://www.visitusers.org/index.php?title=Memory_access




On 03/07/2015 01:24 AM, Tim Gallagher wrote:> Don't forget to reply to 
the list --


Without seeing errors or images of what was wrong about it, there isn't
much we can do to help. The file I sent does work and PV reads it just
fine. The coordinate axes in this case is Y-Z, but ultimately those are
just names since it's 2D right? It doesn't matter if I call it X-Y, Y-Z,
or X-Z so long as I have 2 orthogonal coordinates.

The axes are specified in reverse order when you list them the way it is
done there. So the first dataitem is always Z, the second is always Y
and the third, if you have one, is always X. This also comes up when you
specify the multi-dimensional data items in the attribute section
because you have to remember it uses C memory layout (row major), which
is different from the Fortran layout (column major).

We use XDMF for massive multiblock structured simulations and we store
our coordinates in hdf5 files in full 3D arrays (so what something like
the meshgrid function returns in Matlab/Numpy) and I've put an example
at the end of my email here. In this case, we have a grid which in
Fortran would have coordinates X(I,J,K) where I = 1, 83; J = 1, 83; K =
1, 4. Note that the indexing is flipped when we specify it in the XDMF
file. It is also flipped from what one would expect coming from Fortran
when you look at the h5dump (after the XDMF example). Our strategy is to
specify our grid points as an array of vectors and we create that array
of vectors using the JOIN function.

The XDMF documentation isn't always as helpful as I'd like sometimes. It
took a lot of trial and error on our part to get this working (and it's
made more complicated because we use hyperslabs a lot to only display
portions of our data). The PV release binaries are also not helpful in
understanding the problems sometimes -- very often, it will just
segfault or crash with a glibc double-linked list error or something.
Building PV yourself with debug options may help if you are really stuck.

But what you seem to be trying to do is fully supported and you just
need to keep working at it to understand why it doesn't work. And if you
are having problems, posting images of what it looks like when you
import the data would really help if the issue is just that it doesn't
seem to be what you think it should be.

Tim

 
 
 
 &gridpath;/grid.h5:/Domain_1/x
 &gridpath;/grid.h5:/Domain_1/y
 &gridpath;/grid.h5:/Domain_1/z
 
 
 
 
 &outputpath;/RESTS/REST_0.h5:/FlowData/temperature

GROUP "/" {
GROUP "Domain_1" {
   DATASET "x" {
  DATATYPE  H5T_IEEE_F64LE
  DATASPACE  SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) }
   }
   DATASET "y" {
  DATATYPE  H5T_IEEE_F64LE
  DATASPACE  SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) }
   }
   DATASET "z" {
  DATATYPE  H5T_IEEE_F64LE
  DATASPACE  SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) }
   

Re: [Paraview] Temporal collection problem

[Armin Wehrfritz]

At a first glance I don't see anything wrong with the XDMF file, but if 
you could upload the HDF5 file somewhere and post the link, it would be 
easier to figure out whats going wrong.


It would already help to see the structure of the HDF5 file, essentially 
the output of this:



h5dump -H filename.h5 > filename.h5dump


-Armin



On 03/13/2015 01:34 PM, Gottfried Necker wrote:

Hello,

I'm pretty new to ParaView. I'm trying to visualize a short sequence (2 time
steps) using a Xdmf file with a temporal collection. When I open the file in
ParaView 4.3.1 (binary for Linux x64 from paraview.org) I can see the first
time step and display a variable using the threshold filter. Using the
"Current Time Controls" I can go to the second time step, but the display does
not change. On the information tab I can see that ParaView recognizes the 2
time steps, but when I change the time using the controls the "Current  data
time" stays at the first time step.

When I open the same file in ParaView 4.2.0 I can switch between the two time
steps as expected and everything seems to work fine for this simple case. And
of course the displayed image looks as expected.

I've attached the XML file to this mail. If anybody is interested to try this,
I can provide the HDF5 files too.

Is there something wrong with the file(s)?

Thanks

Gottfried



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Re: [Paraview] Fetching data from xdmf temporal collection

[Armin Wehrfritz]

I'm not quite sure what the problem here is.
However, I think this is nothing XDMF specific, but rather a general 
question on how to access the raw data in ParaView at a certain time level.

Am I correct with this Jean-Michel?

I attached a script that simply loads a xdmf file, steps though all 
time-steps, renders the data and prints the min/max values of the 
selected field.


There are probably better ways to do this though.
Generally, I prefer to use VTK directly for such kind of tasks, 
especially with the new VTK dataset adapter [1].


-Armin


[1] http://www.kitware.com/blog/home/post/709



On 03/18/2015 04:19 PM, Jean-Michel wrote:

Hi Ken,

Thank you very much for offering your help.
Attached is the xmf file from which I'm trying to extract the data. I did
delete a fair amount of lines from it to keep only the first 10 time steps -
hope it won't affect anything.

Jean-Michel

-Message d'origine-
De : Ken Sheldon [mailto:kshel...@slb.com]
Envoyé : mercredi 18 mars 2015 14:55
À : paraview@paraview.org
Cc : jm.lu...@gantha.com
Objet : RE: [Paraview] Fetching data from xdmf temporal collection

Jean-Michel
I find the reader is very sensitive to input errors. The diagnostic messages
are not always sufficient to identify mistakes in the XDMF file. I spent
some time getting this to work for some our data.  If you would like send me
a copy of your XDMF (not the HDF5), or at least the first few timesteps of
it, I would be happy to take a look.
Ken

Date: Tue, 17 Mar 2015 17:46:08 +0100
From: "Jean-Michel" 
To: 
Subject: [Paraview] Fetching data from xdmf temporal collection
Message-ID: <001b01d060d1$df435e70$9dca1b50$@lu...@gantha.com>
Content-Type: text/plain; charset="utf-8"

Dear all,

I am trying to fetch data out of a xdmf/h5 file.

My xdmf file is a temporal collection and the xdmf reader recognizes the
time steps (index/values in the information block).

I would like to access the point data for each time steps. However, I seem
to only get one time step when fetching the point data from the multi-block
dataset and I don't know how to iterate over the different time steps.

Hope somebody can help. Thank you very much,

Jean-Michel


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#!/usr/bin/env python

"""
"""

from paraview.simple import *

fileName = 'testfile.xmf'
fieldName = 'Pressure'

# create a new 'XDMF Reader'
reader = XDMFReader(FileNames=[fileName])
reader.PointArrayStatus = [fieldName]

# Mark the reader as visible
Show()

# Get the active view and set the view size
view = GetActiveView()

# Scan time steps and get the number of time steps
reader.UpdatePipelineInformation()
nTimeSteps = len(reader.TimestepValues)
print 'Number of time steps = ', nTimeSteps

# Step through the time steps
for stepI in range(nTimeSteps):
# Get the stepI-th time value
timeValue = reader.TimestepValues[stepI]
print 'Time step = ', stepI, ', Time value = ', timeValue

# Set the view time to timeValue
view.ViewTime = timeValue

#reader.UpdatePipeline()
ra = reader.PointData[fieldName].GetRange()
print fieldName, 'min/max = ', ra[0], '/', ra[1]

# Render
Render()
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Re: [Paraview] Hardware suggestions for volume rendering

[Armin Wehrfritz]

Hey Kevin and Aashish,

I found this discussion rather interesting, especially since I'm 
basically facing the same problem as Kevin.


In almost all cases, we are dealing here with large unstructured grids 
(e.g. 12M cells) and the volume rendering is performance is extremely 
bad, not to say unusable, for these cases.


I only tested it with ParaView 4.3.1 and older versions, i.e. with the 
old OpenGL algorithms, but the performance is barely influenced by the 
actual volume renderer (i.e. GPU vs. CPU based).


For an unstructured grid the volume rendering seems to be CPU limited in 
any case, at least my CPU is at 100% for quite some time and the GPU 
load is negligible. ParaView's status bar indicates that it's busy with

"OpenGLProjectedTetrahedraMapper".

This can be easily reproduced with the wavelet source (with e.g. 125k 
points) and tessellation filter.


So far I have resorted to resampling the data onto a structured grid. 
This has the clear drawback that a structured grid with the same 
resolution has about 70M grid points compared to the 12M points of the 
unstructured grid.
The volume rendering performance of a 70M unstructured grid is however 
already decent with the old OpenGL algorithms.


So is there a way to improve the rendering of unstructured grids to 
avoid the resampling?


Best regards,
Armin




On 03/24/2015 04:48 PM, Aashish Chaudhary wrote:

Hey Kevin,



On Fri, Mar 20, 2015 at 2:33 PM, Kevin Lau mailto:kevin.d@gmail.com>> wrote:

Dear Aashish,

Thanks for your reply.

(1)

We tried testing it with 2 different data sets of simulation data,
one medium sized and one very large:

Medium
Cells: 1309489
Points: 247984
Memory [MB]: 119.179
Geometry [MB]: 8.201

Very Large
Cells: 51937191
Points: 11019274
Memory [MB]: 4709.731
Geometry [MB]: 776.237

These datasets are unstructured grids (tetrahedral meshes) read into
ParaView using the Phasta data reader.

I see. Most of the performance improvements we have achieved is with GPU
RayCast Volume mapper (uses image data). If you can sample your data
into a strucuted grid then you will be able to use the new mapper.

Thanks,

(2)

The OS used was Ubuntu

(3)

The graphics card was a NVIDIA Quatro K6000 running the NVIDIA
drivers from the Ubuntu Repos (v 331.113)

(4)

We configured ParaView using the default CMake options, changing
VTK_RENDERING_BACKEND=OpenGL2 and disabling all the plug-ins. These
tests were run in serial, as building with MPI was throwing errors.

(5)

We expected that the OpenGL2 version of ParaView would be able to
volume render faster than the standard OpenGL version. However the
reported frame rates were the same in both builds when clicking and
dragging (~2 FPS).

This is a problem because we're mainly interested in visualising our
data and having users able to rotate the model and interact with it.
At these frame rates the response is a bit sluggish.

Also I've done serial test using an OpenGL2 build on Windows using
an old GeForce 8800 with the same medium sized data. On this machine
the frame rate was similar at around ~1.5 FPS.

(6)

ParaView was built by checking out the master from git. Sadly I'm
not on that test machine now, so I can't check the SHA

Many thanks for your help again.

Kevin


On 20 March 2015 at 10:33, Aashish Chaudhary
mailto:aashish.chaudh...@kitware.com>> wrote:

Hey Kevin,

On Thu, Mar 19, 2015 at 5:33 PM, Kevin Lau
mailto:kevin.d@gmail.com>> wrote:

Dear Aashish,

Thanks for your reply, I've now managed to build ParaView
from the Master branch with VTK_RENDERING_BACKEND set to
OpenGL2 and I have noticed a visible difference in the
rendering.

However comparison of the rendering performance in the
interactive mode of builds with the standard OpenGL backend
vs the OpenGL2 backend, both show similar frame rates.


Depending on the card and features you are using you may not see
a huge bump in performance. On some systems we have seen 300
times performance improvements and on others there were close
specially when you have VSync on. Said that, can you provide
more infromation on

1) Data size
2) OS
3) Graphics card
4) Features you have enabled?
5) You expectation and problem
6) What SHA of ParaView you are using?

Are there other build options that I'm missing? Should I be
building the VTK libraries themselves?


Just make sure that you built from a clean state other than that
you should be good.
Thanks,


Many thanks,

Kevin


On 3 March 2015 at 14:53, Aashish Chaudhary
mailto:aashish.chaudh...@kitware.com>> 

Re: [Paraview] Fetching data from xdmf temporal collection

[Armin Wehrfritz]

Hi Jean-Michel,

just to mention, I don't think VTK is significantly more efficient than 
ParaView. In practice you shouldn't feel a difference, since all the 
heavy data handling is anyways done by VTK.


Anyway, I attached a script that shows you how to read XDMF data, step 
through the time steps, wrap the data for numpy and print out some basic 
infos.


Regarding the GetOutput() method, to get data object from the XDMF 
reader you have to use the GetOutputDataObject(0) method.
But I don't know the difference between the two of them, and this also 
may depends on your VTK version, I'm using 6.2.


-Armin







On 03/23/2015 03:15 PM, Jean-Michel wrote:

Armin,

you said you would rather use vtk directly to access raw data in xdmf
files. I tried to follow your advice, but I struggle with the
vtkXdmfReader. Basically, here is what I do:

import vtk

reader = vtk.vtkXdmfReader()

reader.SetFileName(myfile)

reader.ReadAllScalarsOn()

reader.Update()

However, I don't know how to access the data inside reader once this is
done. The GetOutput() method doesn't seem to work. Do you know what I am
missing here ? If not, I'll try and move the discussion over at the
vtk-users list.

Thank you for your help.

Jean-Michel




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logiciel antivirus Avast.
www.avast.com 


#!/usr/bin/env python

"""
"""

import vtk
from vtk.numpy_interface import dataset_adapter as dsa
from vtk.numpy_interface import algorithms as alg
import numpy as np

fileName = './data/surfaces.runTime_xzPlane.xmf'
reader = vtk.vtkXdmfReader()
reader.SetFileName(fileName)

# Scan time steps and get the number of time steps
reader.UpdateInformation()
exe = reader.GetExecutive()
outInfo = exe.GetOutputInformation(0)
timeStepsKey = vtk.vtkStreamingDemandDrivenPipeline.TIME_STEPS()
nTimeSteps = outInfo.Length(timeStepsKey)
print 'Number of time steps = ', nTimeSteps

pd2cd = vtk.vtkPointDataToCellData()
pd2cd.SetInputConnection(reader.GetOutputPort())
pd2cd.PassPointDataOn()

# Step through the time steps
for stepI in range(nTimeSteps):
# Get the stepI-th time value and set the reader time
timeValue = outInfo.Get(timeStepsKey, stepI)
print '\nTime step = ', stepI, ', Time value = ', timeValue
exe.SetUpdateTimeStep(0, timeValue)
reader.Modified()

# Read the data
pd2cd.Update()

data = dsa.WrapDataObject(pd2cd.GetOutput())

print "Point data arrays", data.PointData.keys()
print "Cell data arrays", data.CellData.keys()

pts = data.GetPoints()

# Point data
Z = data.PointData['Z']
print "Z min/max = %f/%f" % (Z.min(), Z.max())

# Cell data (gradient and strain require cell data)
gradZ = alg.gradient(data.CellData['Z'])
strain = alg.strain(data.CellData['U'])
print "grad(Z) min/max = %f/%f" % (gradZ.min(), gradZ.max())
print "Strain min/max = %f/%f" % (strain.min(), strain.max())
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Re: [Paraview] Segfault reading polyhedral cells xdmf3 file

[Armin Wehrfritz]

Hi Alessandro,

I just tested the .xmf file on my Linux work-station using the ParaView
5.2 binaries from the Kitware webpage and everything works as expected.

Also, reading the .vtu file and saving the data as xdmf works correctly
on my machine.

I don't have a Windows PC and have never tested this functionality
anywhere else than under Linux. However, IIRC, the implementation of the
polyhedral cell support doesn't have any operating system specific code.
Just to note though, you need to use the Xdmf3 reader/writer in ParaView
for xdmf files with polyhedral cells.

Can you check that the .xmf file you generated from the .vtu file has
the same topology information as the original .xmf file?

Cheers,
Armin







On 11/29/2016 06:09 PM, Alessandro De Maio wrote:

Dear All,
 I would like to use xdmf file format for exporting polyhedral mesh
results from a CFD code to be opened with Paraview. If I'm not wrong
Paraview 5.2.0 should be able to read/write such kind o files.

Just to understand the format of the xmf file, I've been trying to open
a very easy example taken from the post by Armin Wehrfritz (Tue Sep 27
09:03:00 EDT 2016) in this mailing list (the title of the post was
"Combination of polygonal-data and unstructured grid") named
polyhedron.xmf (that I put in attach to this post). But using Paraview
5.2.0 (Windows 64bit) binary, it gives segmentation fault immediately
after the "Apply" button click.

I've tried also to read the vtu version of the same geometry
(polyhedron.vtu taken from the same post of Armin and in attach) and to
save it from Paraview in xdmf3 file format. Once I try to re-read the
xmf generated file, the behaviour is the same and Paraview crashes.

Has anyone of you experience with xdmf polyhedral files in Paraview?

Thank you in advance for any suggestion

Alessandro De Maio


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Re: [Paraview] Fwd: Segfault reading polyhedral cells xdmf3 file

[Armin Wehrfritz]

In attach you can find the output of the saving of the polyhedron.vtu
(saved.xmf and saved.h5) from the Windows machine.

OK, I tested the "saved.xmf" file and I can open it on my Linux machine
without issues. Also, I compared the files generated on windows and
linux machines, and the topology data is the same for both of them. The
datatype in the h5 file is different (H5T_STD_I32LE for the file from
the Windows machine vs. H5T_STD_I64LE for the file from the Linux
machine). The end of line in the xmf file is different, but I don't
think either one of them should cause an issue.


I've tried also to repeat the procedure (reading of your xmf file) on a
Linux workstation and the behaviour is different: it seems that
randomically the crash happens again (once on about ten tries) and
sometimes it seems that the topology has a connectivity error (see the
image in attachment), while for the most of the times it seems to do the
right job.

As said, on my Linux machine it works consistently.


I've tried also another case, a little bit heavier: a polyhedral mesh
read from the vtu in attach (cube.vtu) and saved with the Xdmf3 writer.
Trying to re-read the xmf version of this geometry always  produces a
crash also on the Linux machine.

I can confirm that the xmf file produce from the cube.vtu (using the
Xdmf3 writer in ParaView 5.2) leads consistently to seg fault.
However, even though the .vtu file works correctly, I'm not entirely
sure if this is xmf specific problem. To be more precise, the
implementation of polyhedral cells requires the face polygons to be
planar (see http://www.vtk.org/Wiki/VTK/Polyhedron_Support). The example
file you send has a whole lot of faces that are not planar.

I extracted a single cell with several non-planar faces from your
example and saved it as .xmf file (attached). I can read this particular
file without issues on my Linux machine, whereas the original data file
leads to a seg fault. One reason why the cube.vtu file works and the
respective .xmf doesn't, could be related to the different approaches
polyhedral cells are stored in vtu and xdmf files, but debugging this
would require quite a bit of work...

Maybe somebody else has an idea here.

-Armin


non_planar_faces.xmf
Description: audio/xmf


non_planar_faces.h5
Description: Binary data
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Re: [Paraview] Fwd: Segfault reading polyhedral cells xdmf3 file

[Armin Wehrfritz]

To follow up on this issue, I have done some more testing. From the link
below you can find two datasets with polyhedral cells, where one is
working just fine and the other one is crashing consistently when
opening it in ParaView 5.2.
The XDMF files are created form the respective .vtu files with ParaView
5.2 (Kitware binaries, Linux 64bit) using the Xdmf3 writer.

The strange thing is that the dataset leading to the seg fault is a
subset of the dataset that just works fine.

Here the link:
https://drive.google.com/file/d/0B5CHY8CFeTf2V09NVUhTRkpYSE0/view?usp=sharing

Alessandro, can you test these files and report back which ones are
working on your PC?

Thanks,
Armin







On 11/30/2016 08:19 PM, Alessandro De Maio wrote:

You're right: the polyhedral cells of the cube.vtu example do not
guarantee the planarity of faces, but this is a typical case of a
polyhedral mesh automatically generated starting from a tetrahedral one
(this example has been built using the Ansys-Fluent converter) and I
think it's quite a usual situation.
But I'm not sure this could generate a segfault as the problem could be
in the algorythms applied by Paraview after the reading of the file that
could consider this hypothesis (as you remarked), while the VTK
topological description of a polyhedral cell doesn't seem to need it,
and the reading phase should only build the data structure compliant
with VTK data representation, as actually happens for vtu file format.
But this is only my opinion and of course it could be wrong as I don't
have a deep knowledge of all the involved procedures.
My idea is that the problem could be due to a memory error, as it's only
unfrequent with a small case (by the way the one cell mesh you attached
can be read also on the windows machine although with a randomic
connectivity error as the one I showed in the image attached to the
previous message) but very frequent with a quite bigger case as the cube.
Is it possible to use something like valgrind to check for memory errors
in Paraview ?

On Wed, Nov 30, 2016 at 6:35 PM, Armin Wehrfritz mailto:dkxl...@gmail.com>> wrote:

In attach you can find the output of the saving of the
polyhedron.vtu
(saved.xmf and saved.h5) from the Windows machine.

OK, I tested the "saved.xmf" file and I can open it on my Linux machine
without issues. Also, I compared the files generated on windows and
linux machines, and the topology data is the same for both of them. The
datatype in the h5 file is different (H5T_STD_I32LE for the file from
the Windows machine vs. H5T_STD_I64LE for the file from the Linux
machine). The end of line in the xmf file is different, but I don't
think either one of them should cause an issue.

I've tried also to repeat the procedure (reading of your xmf
file) on a
Linux workstation and the behaviour is different: it seems that
randomically the crash happens again (once on about ten tries) and
sometimes it seems that the topology has a connectivity error
(see the
image in attachment), while for the most of the times it seems
to do the
right job.

As said, on my Linux machine it works consistently.

I've tried also another case, a little bit heavier: a polyhedral
mesh
read from the vtu in attach (cube.vtu) and saved with the Xdmf3
writer.
Trying to re-read the xmf version of this geometry always
produces a
crash also on the Linux machine.

I can confirm that the xmf file produce from the cube.vtu (using the
Xdmf3 writer in ParaView 5.2) leads consistently to seg fault.
However, even though the .vtu file works correctly, I'm not entirely
sure if this is xmf specific problem. To be more precise, the
implementation of polyhedral cells requires the face polygons to be
planar (see http://www.vtk.org/Wiki/VTK/Polyhedron_Support
<http://www.vtk.org/Wiki/VTK/Polyhedron_Support>). The example
file you send has a whole lot of faces that are not planar.

I extracted a single cell with several non-planar faces from your
example and saved it as .xmf file (attached). I can read this particular
file without issues on my Linux machine, whereas the original data file
leads to a seg fault. One reason why the cube.vtu file works and the
respective .xmf doesn't, could be related to the different approaches
polyhedral cells are stored in vtu and xdmf files, but debugging this
would require quite a bit of work...

Maybe somebody else has an idea here.

-Armin




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Re: [Paraview] [Non-DoD Source] XDMF makes paraview crash with JOIN

[Armin Wehrfritz]

Hi Frederic,

have you been able to make progress on this issue?

I apparently ran into the same problem, which is quite frustrating since
there is currently no way to concatenate more than 10 data items, despite
having to independent implementations of the xdmf reader!

I filed two bug reports for these issues in ParaView (not sure though if
this is an ParaView/VTK or XDMF issue):
https://gitlab.kitware.com/paraview/paraview/issues/17516
https://gitlab.kitware.com/paraview/paraview/issues/17517

Please feel free to add more information or test cases to these bug reports
as well.

@Andrew: I have never seen the "$0|$1" syntax in any xdmf documentation.
When was this added and shouldn't this be mentioned in the xdmf wiki (
http://www.xdmf.org/index.php/XDMF_Model_and_Format#Function)?

Cheers,
Armin



On Tue, Feb 14, 2017 at 12:41 AM, Burns, Andrew J CTR USARMY RDECOM ARL
(US)  wrote:

> In Xdmf3's reader, the assignment of variables occurs in
> XdmfArray::populateItem. The evaluation of the function occurs in
> XdmfFunction "|" denotes XdmfFunction::chunk (effectively concatenate).
> From there it should be a bunch of XdmfArray::insert calls.
>
> Xdmf3's source in Paraview is under Paraview/VTK/ThirdParty/xdmf3.
>
> Andrew Burns
> Software Engineer | Parsons
> Phone: 410-306-0409
> ARL DSRC
> andrew.j.burns35@mail.mil
>
> -Original Message-
> From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of
> Frederic Perez
> Sent: Saturday, February 11, 2017 6:03 PM
> To: paraview@paraview.org
> Subject: Re: [Paraview] [Non-DoD Source] XDMF makes paraview crash with
> JOIN
>
> All active links contained in this email were disabled.  Please verify the
> identity of the sender, and confirm the authenticity of all links contained
> within the message prior to copying and pasting the address to a Web
> browser.
>
>
>
>
> 
>
> Hi,
>
> I have been looking closely into this problem in the past few days, and I
> have never been able to make the Xdmf3 reader to JOIN any HDF5 data.
> Neither with the JOIN() syntax nor with the "$0|$1" one. At least to
> populate an Attribute's DataItem. The Xdmf2 reader works until 10 elements
> are joined.
>
> To go further in this investigation, could someone point me to the source
> code of the Xdmf3 reader, specifically where the "joining"
> takes place?
>
> Cheers
> Fred
>
>
> 2017-02-08 23:24 GMT+01:00 Frederic Perez :
> > I must have done something wrong in my previous attempt with Xdmf3,
> > because it no longer crashes. Note that it works even without your
> > suggestion, as the JOIN() syntax works.
> >
> > Now the problem is that, when I click "Apply", I get the following error:
> > "Failed to locate selected scalars. Will use image scalars by default
> > No scalar values found for texture input!"
> >
> > Note that the same exact file works with Xdmf instead of Xdmf3.
> >
> > Fred
> >
> >
> > 2017-02-08 22:54 GMT+01:00 Burns, Andrew J CTR USARMY RDECOM ARL (US)
> > :
> >> I think that is because Xdmf3 uses different syntax for concatenation.
> Try using Function="$0|$1|$2|$3|$4|$5|$6|$7|$8|$9" with the Xdmf3 reader.
> >>
> >> -Andrew Burns
> >>
> >> -Original Message-
> >> From: Frederic Perez [Caution-mailto:fredericper...@gmail.com]
> >> Sent: Wednesday, February 08, 2017 4:50 PM
> >> To: Burns, Andrew J CTR USARMY RDECOM ARL (US)
> >> 
> >> Cc: paraview@paraview.org
> >> Subject: Re: [Non-DoD Source] [Paraview] XDMF makes paraview crash
> >> with JOIN
> >>
> >> I tried both, but Xdmf3 makes ParaView crash even earlier (directly
> after opening the file) while Xdmf2 makes it crash upon "Apply".
> >>
> >> Fred
> >>
> >> 2017-02-08 22:28 GMT+01:00 Burns, Andrew J CTR USARMY RDECOM ARL (US)
> >> :
> >>> Are you using the Xdmf2 or Xdmf3 reader?
> >>>
> >>> Andrew Burns
> >>> Software Engineer | Parsons
> >>> Phone: 410-306-0409
> >>> ARL DSRC
> >>> andrew.j.burns35@mail.mil
> >>>
> >>> -Original Message-
> >>> From: ParaView [Caution-mailto:paraview-boun...@paraview.org] On
> >>> Behalf Of Frederic Perez
> >>> Sent: Wednesday, February 08, 2017 3:39 PM
> >>> To: paraview@paraview.org
> >>> Subject: [Non-DoD Source] [Paraview] XDMF makes paraview crash with
> >>> JOIN
> >>>
> >>> All active links contained in this email were disabled.  Please verify
> the identity of the sender, and confirm the authenticity of all links
> contained within the message prior to copying and pasting the address to a
> Web browser.
> >>>
> >>>
> >>>
> >>>
> >>> 
> >>>
> >>> Hi all,
> >>>
> >>> I have successfully used the JOIN Function for the XDMF reader to
> concatenate the data from several HDF5 files.
> >>>
> >>> 
> >>> 
> >>> 
> >>>  >>> TopologyType="2DCoRectMesh" Dimensions="21 10"/>
> >>>  GeometryType="ORIGIN_DXDY">
> >>>  >>> Dimensions="2">0.0 0.0
> >>>  >>> Dimensions="2">0.3 0.06
> >>> 
> >>> 
> >>>  >>> Function="JOIN($0,$1,$2,$3,$4,$5