[Paraview] Data formats and XDMF

[Lucas Clemente Vella]

Hi,

I need to write the output of a CFD code, attributes are cell centered
and my mesh looks like the picture attached: orthogonal edges, cells
are rectangular, but unstructured (leafs of a tree, not necessarily
octree).

I know how to work with HDF5, thus I prefer to write it in XDMF +
HDF5, but I could settle with any format that provides compression,
and I am able to write the tree once, and reuse it with different
attribute fields per time step (I know how to do it both from XDMF and
directly from HDF5).

So, is XDMF recommended, or should I use something else?

Also, in the picture, the bigger cell, can it be written as a
hexahedron, ignoring that one face actually interfaces with 4 other
cells, or should I describe it as a 9 face polyhedron, where there are
4 coplanar faces? The former is much easier, is there any difference
from visualization standpoint? Is it more "correct" to use a 9 face
polyhedron?

I have an idea on how to make a XDMF using only hexahedron, but not a
clue with polyhedra of variable number of faces. Could you please
assemble a sample XDMF depicting that mesh for me to use as base?

-- 
Lucas Clemente Vella
lve...@gmail.com
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Re: [Paraview] XDMF Set

[David E DeMarle]

I believe in this case the intent was to get the edge'th edge out of the
face'th face out of the cell'th cell.

So in your example we get four edges out.

cell 0's 0'th face's 0'th edge,
cell 0's 1'st face's 1'st edge,
cell 1's 2'nd face's 0'th edge,
and
cell 1's 3'rd face's 2'nd edge.
The ordering in each case is defined by VTK.

However, in the code (specifically vtkXdmfHeavyData.cxx:1507) it looks like
it does exactly as you say.
This appears to be a bug.

In the Xdmf3 version  we do it properly (see vtkXdmf3DataSet.cxx:2205).




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

On Fri, Apr 17, 2015 at 5:39 AM, Chris Richardson 
wrote:

>
> I would like to be able to specify data, or subsets of data in the XDMF
> format with Edge or Facet sets.
>
> According to the header file of XdmfSet.h:
>
> XdmfSet is a Class that handles sets of nodes,cells,faces, and edges
> on an XdmfGrid. They may be centered on the Node, Edge,
> Face, Cell. An XdmfSet can have from 1 to 3 DataItems. The last
> DataItem
> is always the "Ids" or the indexes into Nodes, Cells, etc. If
> SetType is
> "Face" or "Edge", the First DataItem defines the CellIds. If
> SetType is
> "Edge" second DataItem defines FaceIds
>
> I have two questions:
>
> 1) What is the purpose of the FaceIds for a set of Edges?
>
> From what I can tell, using ParaView, the three dataitems provide:
> global CellIDs, unused FaceIDs, cell-local EdgeIds
>
> e.g. in this case, the first DataItem "0 0 1 1" lists the cells,
>  the second DataItem "0 1 2 3" is ignored, and the third DataItem "0 1
> 0 2"
>  lists the cell-local Edges which have data attached?
>
>  
>   
>   0 0 1 1
>   
>   
>   0 1 2 3
>   
>   
>   0 1 0 2
>   
>   
>   
>   100 200 400 600
>   
>   
>   
>
> Is that correct?
>
> 2) How can I specify an Edge set in 2D? Nothing seems to work in this case,
>as ParaView complains that the cells have invalid Faces.
>
>
> --
> Chris Richardson
> BP Institute
> Madingley Road
> Cambridge CB3 0EZ
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[Paraview] Saving Stereo Files - Eye Separation Control

[Rinehart, Richard D. (GRC-VG00)[DB Consulting Group, Inc.]]

Greetings!
Is there a stereo file saving eye separation control for the binary Win 
version?  Poking around but seems as not with the prebuilt version.
-rich

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[Paraview] Update ImageData

[Dean, Kevin]

I have written a script that generates an ImageData and constantly changes
the Scalar values. With this script I would like to test how I can update
the visualization of this image within ParaView. Is there a way, or a file
I can compare/contrast to, in order to adjust a reader plugin to constantly
listen and publish data to the pipeline? Thanks.

Kevin E. Dean

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Re: [Paraview] Question about programmable data source

[David E DeMarle]

You have to provide the whole extent in the request information pass.

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

On Wed, May 13, 2015 at 1:19 PM, Wu, James  wrote:

> I add a programmable data source using vtkImageData. The following is the
> script.
> There is nothing displayed after click "Apply". I am new user to paraview.
> Can any point me what's wrong with the script?
>
> Thanks,
> James
>
> dim = 10
> pdo = self.GetImageDataOutput()
> pdo.SetDimensions(dim, dim, dim)
> pdo.SetOrigin(0, 0, 0)
> pdo.SetSpacing(1, 1, 1)
> pdo.SetExtent(0, dim - 1, 0, dim - 1, 0, dim - 1)
> pdo.AllocateScalars(vtk.VTK_FLOAT, 1)
>
> for x in range(0, dim):
> for y in range(0, dim):
> for z in range(0, dim):
> pdo.SetScalarComponentFromFloat(x, y, z, 0, 0.2)
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[Paraview] Question about programmable data source

[Wu, James]

I add a programmable data source using vtkImageData. The following is the 
script.
There is nothing displayed after click "Apply". I am new user to paraview. Can 
any point me what's wrong with the script?

Thanks,
James

dim = 10
pdo = self.GetImageDataOutput()
pdo.SetDimensions(dim, dim, dim)
pdo.SetOrigin(0, 0, 0)
pdo.SetSpacing(1, 1, 1)
pdo.SetExtent(0, dim - 1, 0, dim - 1, 0, dim - 1)
pdo.AllocateScalars(vtk.VTK_FLOAT, 1)

for x in range(0, dim):
for y in range(0, dim):
for z in range(0, dim):
pdo.SetScalarComponentFromFloat(x, y, z, 0, 0.2)
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Re: [Paraview] ERROR WITH FIND DATA UTILITY

[Utkarsh Ayachit]

Ah, good catch! Mind reporting a bug. For now, you can use the
Calculator filter to rename the array to not include the "[", "]".

Utkarsh



On Wed, May 13, 2015 at 6:26 AM, Gaspare Argento
 wrote:
> Hello everybody,
>
> I've a problem using the "Find Data" function in Paraview. When I
> select a data that has in his name a parenthesis I get the following
> error:
>
> Example for the quantity: Absolute_Pressure_[mbar]
> __
> Error: Failed to evaluate Expression '(Absolute_Pressure_[mbar] >
> 5000) & (Absolute_Pressure_[mbar] < 5005)'. The following exception
> stack should provide additional developer specific information. This
> typically implies a malformed expression. Verify that the expression
> is valid.
>
>
> Traceback (most recent call last):
>
> File "", line 8, in 
>
> File "", line 5, in vtkPythonExtractSelection_RequestData
>
> File "C:\Program Files (x86)\ParaView
> 4.3.1\lib\paraview-4.3\site-packages\paraview\extract_selection.py",
> line 74, in execute
>
> maskArray = calculator.compute(inputs, query, ns=elocals)
>
> File "C:\Program Files (x86)\ParaView
> 4.3.1\lib\paraview-4.3\site-packages\paraview\calculator.py", line 74,
> in compute
>
> retVal = eval(expression, globals(), mylocals)
>
> File "", line 1, in 
>
> NameError: name 'Absolute_Pressure_' is not defined
> __
>
> As you can see in the last line of the error message, Paraview searchs
> for a quantity name that is different from the correct one, because it
> is truncated: "Absolute_Pressure_" without "[mbar]"
>
> Any tips?
>
> Gaspare
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Re: [Paraview] Glyph filter instead of legacy glyph filter

[Utkarsh Ayachit]

> Is there a way that I can use the newer “Glyph” filter in my visualization
> and remove the constant vectors perpendicular to the y-axis?

You can use the "Vectors" drop-down box to choose which vectors to use
for orienting the glyph. You can use "Scale Mode" to control how to
scale the glyph.

Checkout Chapter 5, Section 5.7.8 for the ParaView Guide [1] for more details:

Utkarsh

[1] http://www.paraview.org/paraview-guide/
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[Paraview] Glyph filter instead of legacy glyph filter

[Ramirez, Emilio (eramirez)]

I am currently visualizing MFIX unstructured grid data in Paraview.

I am trying to visualize the vector fields. After applying the 
"CellDataToPointData" I then apply the "Glyph" filter. This results in vector 
fields inside the reactor the way I want to visualize, but it also includes 
constant vectors perpendicular to the y axis and flow along the tube (reactor) 
wall.

Using the "LegacyGlyph" instead of the "Glyph" filter results in the correct 
visualization but the vectors change size throughout the visualization.

Is there a way that I can use the newer "Glyph" filter in my visualization and 
remove the constant vectors perpendicular to the y-axis?

Looking forward to a reply,

Emilio Ramirez
erami...@utk.edu
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[Paraview] Troubles with exporting selection labels from current ParaView render view

[Nenad Vujicic]

Hello everyone,

It has been a long time ParaView sources worked excellent with my
patches and the plugin (3D exporter). However, I'm having troubles
with the latest version (v4.3.1) to export labels which are shown over
selected points (both per point and per cell). This was my approach
which worked with v4.0.1 (100% sure) and v4.2 (I think, but, I'm not
definitely sure):

1. I traverse all visible pipeline sources and for all their
representations in currently active view do next,
2. For every representation, I check if it is DataLabelRepresentation
and if it is I save PointLabelVisibility, PointFieldDataArrayName, etc
properties ..
3. From other representations, I get vtkLODActor for which I bind my
labels properties,
4. In exporting code, I get current view, traverse its actors and
export them, however, there is one problem now. Let me give an
example:

- If I have Sphere on which I applied Elevation filter and
selected several points with turned on labels (with e.g. Elevation
selected as array),

- Strange 1: I don't have anymore instance in
DataLabelRepresentation for Elevation pipeline source (btw, during
this traversing I get only one actor),
- Strange 2: When I traverse vtkRenderer's actors, I get 2 actors
(sphere mesh and actor with selected points), but, I'm unable to
connect selection label properties (which are tied with Elevation
pipeline source actor - sphere mesh) and mesh with selected points /
cells.

Q1: How to identify actor from vtkRenderer which contains selection
points / cells and get selection properties from this actor or

Q2: How to identify actor from pqPipeline source on which are selected
points and how from appropriate representations to get actor which
contains selected points / cells?

Thanks everyone for possible answers!

Nenad.
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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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[Paraview] ERROR WITH FIND DATA UTILITY

[Gaspare Argento]

Hello everybody,

I've a problem using the "Find Data" function in Paraview. When I
select a data that has in his name a parenthesis I get the following
error:

Example for the quantity: Absolute_Pressure_[mbar]
__
Error: Failed to evaluate Expression '(Absolute_Pressure_[mbar] >
5000) & (Absolute_Pressure_[mbar] < 5005)'. The following exception
stack should provide additional developer specific information. This
typically implies a malformed expression. Verify that the expression
is valid.


Traceback (most recent call last):

File "", line 8, in 

File "", line 5, in vtkPythonExtractSelection_RequestData

File "C:\Program Files (x86)\ParaView
4.3.1\lib\paraview-4.3\site-packages\paraview\extract_selection.py",
line 74, in execute

maskArray = calculator.compute(inputs, query, ns=elocals)

File "C:\Program Files (x86)\ParaView
4.3.1\lib\paraview-4.3\site-packages\paraview\calculator.py", line 74,
in compute

retVal = eval(expression, globals(), mylocals)

File "", line 1, in 

NameError: name 'Absolute_Pressure_' is not defined
__

As you can see in the last line of the error message, Paraview searchs
for a quantity name that is different from the correct one, because it
is truncated: "Absolute_Pressure_" without "[mbar]"

Any tips?

Gaspare
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