Re: [Paraview] Average data from multiple nodes

2015-01-30 Thread Moreland, Kenneth
Alan,

Try selecting the points you want and then plot the selection over time. I 
think the current version of plot selection over time creates a series for the 
average value of the selection.

-Ken

Sent from my iPad so blame autocorrect.

On Jan 23, 2015, at 1:45 PM, Scott, W Alan 
wasc...@sandia.govmailto:wasc...@sandia.gov wrote:

I was wondering if there was a tool that could average values from multiple 
nodes and plot that over time.  For example, I would like to take a selection 
of nodes, average their velocities, and plot that vs. time.

Thanks for the help.

Alan



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Re: [Paraview] .cube files in pvbatch

2015-01-30 Thread Insley, Joseph A.
Success!  Thanks, Jean.

joe

On Jan 30, 2015, at 2:18 AM, Favre Jean jfa...@cscs.ch wrote:

 try this:
 
 bk2_cube = GaussianCubeReader( guiName=bk2.cube, 
 FileName='/sandbox/bk2.cube' )
 
 contour1 = Contour(Input=servermanager.OutputPort(bk2_cube, 1))
 -
 Jean/CSCS
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[Paraview] Memory use with Xdmf files

2015-01-30 Thread Michael Jackson
I have written an Xdmf file that uses the 3D CoRectMesh to display a
montage of 54 gray scale images. They are laid out in a 9x6 fashion. Each
Image is about 1292x968 pixels. We have run stitching algorithms on the
images to find their correct coordinates in XYZ space so that they will
form the montage correctly.

The raw amount of memory is 67,535,424 bytes. If that has to be as RGBA for
rendering then it is 270,141,696 bytes.

Then ParaView has to create a cell for each pixel and then some other
stuff. At one point ParaView spiked to 120GB of RAM and then fell back to
about 36GB of RAM. This seems a bit excessive to me. This is with ParaView
4.3.1 on a Windows 8.1 workstation. Am I doing something wrong? Just seems
like a lot of memory.

Are their alternate ways of writing the Xdmf file so that each image is a
single cell perhaps?

Thanks for any insights.

I can make the data set available to anyone who needs it.
_
Mike Jackson  mike.jack...@bluequartz.net
BlueQuartz Softwarewww.bluequartz.net
Principal Software Engineer  Dayton, Ohio
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Re: [Paraview] Gradient of 2D velocity field with paraview

2015-01-30 Thread Eleonora Piersanti
Thank you so much! It seems to really work! :)Just out of curiosity, what 
Extract surface filter does? Since velocity is approximated with quadratic 
elements, do I loose accouracy using Extract surface filter?  Kind 
regards,Eleonora


 Il Venerdì 30 Gennaio 2015 11:48, Andy Bauer andy.ba...@kitware.com ha 
scritto:
   

 It looks like the Gradient of Unstructured Data Set filter isn't working 
properly with quadratic triangles. Try using the Extract Surface filter before 
computing gradients to convert them into linear triangles.

If you want to get more familiar with using ParaView, the ParaView tutorial at 
http://www.paraview.org/Wiki/The_ParaView_Tutorial is a good place to start.

Regards,
Andy

On Fri, Jan 30, 2015 at 6:25 AM, Eleonora Piersanti 
eleonorapiersa...@yahoo.it wrote:

 Thank you for the answer.I think that the dimension of the .vtk file was too 
big. You can download the .vtk file from:
https://www.dropbox.com/s/o1wjo2brsaeu5ag/stability_realEigU_up0.vtk.tar.gz?dl=0

In which sense should I use the Slice filter? Sorry but I am quite new with 
paraview.Kind regards,Eleonora   Il Venerdì 30 Gennaio 2015 11:16, Eleonora 
Piersanti eleonorapiersa...@yahoo.it ha scritto:
   

 Thank you, for the answer.I attach the .vtk file. In which sense should I use 
the Slice filter? Sorry but I am quite new with paraview.Kind regards,Eleonora 

 Il Venerdì 30 Gennaio 2015 10:59, Andy Bauer andy.ba...@kitware.com ha 
scritto:
   

 Your description is a bit vague to diagnose the issue. Can you share your data 
set? I was able to use the Wavelet source, use the Slice filter and then use 
the Gradient of Unstructured Data Set without any issues. Can you see if that 
works for you?

Regards,
Andy

On Fri, Jan 30, 2015 at 5:26 AM, Eleonora Piersanti 
eleonorapiersa...@yahoo.it wrote:

Hi to everyone!I computed with finite elements a 2D velocity field. I plotted 
without any problem the velocity field with paraview. I would like to compute 
the gradient. 
I tried Filters-Gradient of Unstructured Data Set but without succes.Can you 
help me?Thanks, 
Nora

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Re: [Paraview] Average data from multiple nodes

2015-01-30 Thread Scott, W Alan
Ken,
I don't think that works.  Try the following:

can.exo.
select a few dozen points.  plot selection over time.  apply.
Notice that it only shows the first point.  Select multiple points.  (this now 
works).
You never get an average.

Alan

From: Moreland, Kenneth
Sent: Friday, January 30, 2015 8:23 AM
To: Scott, W Alan
Cc: paraview@paraview.org
Subject: Re: [Paraview] Average data from multiple nodes

Alan,

Try selecting the points you want and then plot the selection over time. I 
think the current version of plot selection over time creates a series for the 
average value of the selection.
-Ken

Sent from my iPad so blame autocorrect.

On Jan 23, 2015, at 1:45 PM, Scott, W Alan 
wasc...@sandia.govmailto:wasc...@sandia.gov wrote:
I was wondering if there was a tool that could average values from multiple 
nodes and plot that over time.  For example, I would like to take a selection 
of nodes, average their velocities, and plot that vs. time.

Thanks for the help.

Alan



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Re: [Paraview] Average data from multiple nodes

2015-01-30 Thread Moreland, Kenneth
Huh. I'm thinking of the behavior described in bug 0014940. When you make a 
query selection, you get statistics like average. When you make a surface 
selection (which is essentially an id selection) you get that first point. When 
you make a frustum selection, you get an error.

I would report this as a bug. I expect the plot selection over time to be 
consistent over all types of selection. And I would want the behavior to be as 
described in bug 0014945.

-Ken

From: Scott, Walter Scott wasc...@sandia.govmailto:wasc...@sandia.gov
Date: Friday, January 30, 2015 at 11:04 AM
To: Kenneth Moreland kmo...@sandia.govmailto:kmo...@sandia.gov
Cc: paraview@paraview.orgmailto:paraview@paraview.org 
paraview@paraview.orgmailto:paraview@paraview.org
Subject: RE: [Paraview] Average data from multiple nodes

Ken,
I don't think that works.  Try the following:

can.exo.
select a few dozen points.  plot selection over time.  apply.
Notice that it only shows the first point.  Select multiple points.  (this now 
works).
You never get an average.

Alan

From: Moreland, Kenneth
Sent: Friday, January 30, 2015 8:23 AM
To: Scott, W Alan
Cc: paraview@paraview.orgmailto:paraview@paraview.org
Subject: Re: [Paraview] Average data from multiple nodes

Alan,

Try selecting the points you want and then plot the selection over time. I 
think the current version of plot selection over time creates a series for the 
average value of the selection.
-Ken

Sent from my iPad so blame autocorrect.

On Jan 23, 2015, at 1:45 PM, Scott, W Alan 
wasc...@sandia.govmailto:wasc...@sandia.gov wrote:
I was wondering if there was a tool that could average values from multiple 
nodes and plot that over time.  For example, I would like to take a selection 
of nodes, average their velocities, and plot that vs. time.

Thanks for the help.

Alan



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Re: [Paraview] ParaView Seg Faults when running Animation in a Programmable Filter

2015-01-30 Thread Omid Mahabadi
After a lot of debugging, it turns out the issue is with the SetCells
function of the vtk unstructured grid. Below are the bits of my
Programmable Filter code that are relevant to the seg fault:

output  = self.GetOutputDataObject(0)

cellArray   = vtk.vtkCellArray()
cellTypes   = []

# Create a polygon to display the selected points
polygon = vtk.vtkPolygon()
polygon.GetPoints().DeepCopy(pointArray)
polygon.GetPointIds().SetNumberOfIds(len(coordinates))
for i in range(len(coordinates)):
  polygon.GetPointIds().SetId(i, coordinates[i][0])

# Add the polygon to a list of Cells
cellArray.InsertNextCell(polygon)
cellTypes.append(vtk.VTK_POLYGON)

# Get the cell containing a given cell  add it to the cellArray
selectedCell  = input.GetCell(cellID)  
cellArray.InsertNextCell(selectedCell)
cellTypes.append(vtk.VTK_TETRA)

# SetCells of the output with only the selected analyzed cells
output.SetCells(cellTypes, cellArray)

The last line above seg faults on one of my computers but not on the
other one, both using Linux Mint 15 OS, and similar versions of
ParaView. Any thoughts?


On 15-01-28 07:27 PM, Omid Mahabadi wrote:
 Hi,
 I've been experiencing a very weird seg faults in various versions of
 ParaView (4.1.x, 4.2.0, 4.3.x) when running an animation (streaming
 over time) of my Programmable Filter. I'm not even sure this is a
 ParaView issue, but I'll still share my story in case someone has any
 insights that they can kindly share.

 My Programmable Filter code works fine for the Current time step,
 regardless at which time step I run it (i.e., hit the Apply button of
 the Programmable Filter). However, when I hit the Play button to loop
 over time steps (which appends some information to a CSV file),
 ParaView seg faults after reaching the /3rd time step/. The filter has
 been working for some time and this started to happen all of a sudden,
 without any system update.

 It may be related to a weird combination of hardware, software, and
 drivers. My script works fine on a desktop computer I have but it seg
 faults on my main workstation, which has an AMD/ATI Radeon R9 280x GPU
 running on Linux Mint 15, 64-bit. When I completely removed the AMD
 drivers, it still seg faulted but after reaching the /6th time step/
 after the current one. Then, I launched an Ubuntu 14.04 LTS 64-bit,
 live on a USB flash drive. The script in Programmable Filter worked
 perfectly fine. As a result, I installed the OS, but it acted up
 exactly as the Linux Mint installation.

 The input files are massive vtk unstructured grids (about 800 MB
 each). I created smaller files, but unfortunately I couldn't reproduce
 the error. But I'm fairly sure that the files are not corrupted. As
 such, I can't send out the files that cause the issue. I also
 monitored the memory usage using free -h command while Playing. Here's
 the output for the -/+ buffers/cache line:

  total   used   free
 -/+ buffers/cache:   7.2G   8.4G (Opening the .vtu files)
 -/+ buffers/cache:   7.2G   8.4G
 -/+ buffers/cache:   7.4G   8.2G
 -/+ buffers/cache:   7.6G   8.0G
 -/+ buffers/cache:   7.6G   8.0G
 -/+ buffers/cache:   7.6G   8.0G
 -/+ buffers/cache:   7.9G   7.7G
 -/+ buffers/cache:   8.3G   7.4G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.6G   7.0G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.6G   7.0G
 -/+ buffers/cache:   8.9G   6.7G
 -/+ buffers/cache:   9.1G   6.5G
 -/+ buffers/cache:   9.3G   6.3G
 -/+ buffers/cache:   9.4G   6.2G (Seg faults here)
 -/+ buffers/cache:   7.0G   8.6G

 As you can see, my system still had a lot of free memory when the seg
 fault happened and I haven't done anything explicitly to limit memory
 usage by a single process.

 Looking at syslog, this is the error message for the seg fault:

 kernel: [77995.911073] paraview[22483]: segfault at 7f3c8e0398ac
 ip 7f3a47ebe169 sp 7fff9106ab50 error 4 in
 fglrx_dri.so[7f3a479e9000+21e9000]


 Am I missing something here? Is there any other debugging steps I
 should take? Any insights or help will be hugely appreciated.

 Thank you,
 Omid



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-- 
Omid Mahabadi, 

Re: [Paraview] particle surface based on position

2015-01-30 Thread timcfagan .
I can generate surfaces but it seems none of them are based on particle
positions. Anyone know if this is part of paraview functionality?

On Wed, Jan 28, 2015 at 3:55 PM, timcfagan . timcfa...@gmail.com wrote:

 Is there a way for paraview to generate a surface based on point positions?

 Viewing particle data as a surface, it just shows the points. One way I
 have generated a surface is to use a contour by mass on nodal points. But
 this is a bit iffy as changing the mass threshold will add or remove parts
 of the surface.

 Attached is an image for both of these. The contour looks okay, but
 probably isn't the right way to go about it...

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

2015-01-30 Thread Martin Huarte Espinosa
Thanks Armin.

Martin.

On Thu, Jan 29, 2015 at 9:43 AM, Armin Wehrfritz dkxl...@gmail.com wrote:

 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 dkxl...@gmail.com
 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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 http://paraview.org/Wiki/ParaView

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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/




-- 

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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[Paraview] Gradient of 2D velocity field with paraview

2015-01-30 Thread Eleonora Piersanti
Hi to everyone!I computed with finite elements a 2D velocity field. I plotted 
without any problem the velocity field with paraview. I would like to compute 
the gradient. 
I tried Filters-Gradient of Unstructured Data Set but without succes.Can you 
help me?Thanks, 
Nora


 

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Re: [Paraview] .cube files in pvbatch

2015-01-30 Thread Favre Jean
try this:

bk2_cube = GaussianCubeReader( guiName=bk2.cube, FileName='/sandbox/bk2.cube' 
)

contour1 = Contour(Input=servermanager.OutputPort(bk2_cube, 1))
-
Jean/CSCS
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Re: [Paraview] Gradient of 2D velocity field with paraview

2015-01-30 Thread Eleonora Piersanti
 Thank you for the answer.I think that the dimension of the .vtk file was too 
big. You can download the .vtk file from:
https://www.dropbox.com/s/o1wjo2brsaeu5ag/stability_realEigU_up0.vtk.tar.gz?dl=0

In which sense should I use the Slice filter? Sorry but I am quite new with 
paraview.Kind regards,Eleonora   Il Venerdì 30 Gennaio 2015 11:16, Eleonora 
Piersanti eleonorapiersa...@yahoo.it ha scritto:
   

 Thank you, for the answer.I attach the .vtk file. In which sense should I use 
the Slice filter? Sorry but I am quite new with paraview.Kind regards,Eleonora 

 Il Venerdì 30 Gennaio 2015 10:59, Andy Bauer andy.ba...@kitware.com ha 
scritto:
   

 Your description is a bit vague to diagnose the issue. Can you share your data 
set? I was able to use the Wavelet source, use the Slice filter and then use 
the Gradient of Unstructured Data Set without any issues. Can you see if that 
works for you?

Regards,
Andy

On Fri, Jan 30, 2015 at 5:26 AM, Eleonora Piersanti 
eleonorapiersa...@yahoo.it wrote:

Hi to everyone!I computed with finite elements a 2D velocity field. I plotted 
without any problem the velocity field with paraview. I would like to compute 
the gradient. 
I tried Filters-Gradient of Unstructured Data Set but without succes.Can you 
help me?Thanks, 
Nora

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Re: [Paraview] Gradient of 2D velocity field with paraview

2015-01-30 Thread Andy Bauer
It looks like the Gradient of Unstructured Data Set filter isn't working
properly with quadratic triangles. Try using the Extract Surface filter
before computing gradients to convert them into linear triangles.

If you want to get more familiar with using ParaView, the ParaView tutorial
at http://www.paraview.org/Wiki/The_ParaView_Tutorial is a good place to
start.

Regards,
Andy

On Fri, Jan 30, 2015 at 6:25 AM, Eleonora Piersanti 
eleonorapiersa...@yahoo.it wrote:

 Thank you for the answer.
 I think that the dimension of the .vtk file was too big. You can download
 the .vtk file from:


 https://www.dropbox.com/s/o1wjo2brsaeu5ag/stability_realEigU_up0.vtk.tar.gz?dl=0

 In which sense should I use the Slice filter? Sorry but I am quite new
 with paraview.
 Kind regards,
 Eleonora

Il Venerdì 30 Gennaio 2015 11:16, Eleonora Piersanti 
 eleonorapiersa...@yahoo.it ha scritto:


 Thank you, for the answer.
 I attach the .vtk file. In which sense should I use the Slice filter?
 Sorry but I am quite new with paraview.
 Kind regards,
 Eleonora


   Il Venerdì 30 Gennaio 2015 10:59, Andy Bauer andy.ba...@kitware.com
 ha scritto:


 Your description is a bit vague to diagnose the issue. Can you share your
 data set? I was able to use the Wavelet source, use the Slice filter and
 then use the Gradient of Unstructured Data Set without any issues. Can you
 see if that works for you?

 Regards,
 Andy

 On Fri, Jan 30, 2015 at 5:26 AM, Eleonora Piersanti 
 eleonorapiersa...@yahoo.it wrote:

 Hi to everyone!
 I computed with finite elements a 2D velocity field. I plotted without any
 problem the velocity field with paraview. I would like to compute the
 gradient.
 I tried Filters-Gradient of Unstructured Data Set but without succes.
 Can you help me?
 Thanks,
 Nora

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Re: [Paraview] Gradient of 2D velocity field with paraview

2015-01-30 Thread Andy Bauer
Your description is a bit vague to diagnose the issue. Can you share your
data set? I was able to use the Wavelet source, use the Slice filter and
then use the Gradient of Unstructured Data Set without any issues. Can you
see if that works for you?

Regards,
Andy

On Fri, Jan 30, 2015 at 5:26 AM, Eleonora Piersanti 
eleonorapiersa...@yahoo.it wrote:

 Hi to everyone!
 I computed with finite elements a 2D velocity field. I plotted without any
 problem the velocity field with paraview. I would like to compute the
 gradient.
 I tried Filters-Gradient of Unstructured Data Set but without succes.
 Can you help me?
 Thanks,
 Nora

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 Visit other Kitware open-source projects at
 http://www.kitware.com/opensource/opensource.html

 Please keep messages on-topic and check the ParaView Wiki at:
 http://paraview.org/Wiki/ParaView

 Search the list archives at: http://markmail.org/search/?q=ParaView

 Follow this link to subscribe/unsubscribe:
 http://public.kitware.com/mailman/listinfo/paraview


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