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http-equiv="Content-Type">
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<div class="moz-cite-prefix">Look in Google some presentations about
vtk to understand how vtk handle the different types of datasets
(Uniform Rectilinear Grids, Unstructured Grid...).<br>
Some filters in Paraview change the type of the dataset, this
implies sometimes some memory penalty.<br>
<br>
One way to see this phenomena is to create a Wavelet (Sources
menu), look the information panel (type: Uniform Rectilinear
Grid), type and memory.<br>
And then apply a CleanToGrid to generate a Unstructured Grid (so
we can move the points). <br>
<br>
<br>
Felipe<br>
<br>
<br>
<br>
Le 05/04/2013 19:36, Nikolaos Beratlis a écrit :<br>
</div>
<blockquote
cite="mid:CALdMxnxgoQQfFuQ2b75sPh-nyHWR1vUjQQTWe425so7N+LrL5A@mail.gmail.com"
type="cite">
<div dir="ltr">So I have done the following test. I have created a
xmf file of a grid in cylindrical coordinates "grid3d_cyl.xmf"
specified as Topology Type 3DSMesh and Geometry Type XYZ. That
is a full 3D array is written:
<div>
<br>
</div>
<div>
<div><?xml version="1.0" ?></div>
<div><!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []></div>
<div><Xdmf Version="2.2"></div>
<div><Domain></div>
<div><Grid GridType="Uniform"></div>
<div><Topology TopologyType="3DSMesh" Dimensions=" 30
70 40"/></div>
<div><Geometry GeometryType="XYZ"></div>
<div><DataItem Dimensions="84000 3" NumberType="Float"
Precision="4" Format="XML"></div>
</div>
<div>....</div>
<div>....</div>
<div>....</div>
<div>
<div></DataItem></div>
<div></Geometry></div>
<div></Grid></div>
<div></Domain></div>
<div></Xdmf></div>
</div>
<div><br>
</div>
<div style="">The grid is 30x70x40 and the file "grid3d_cyl.xmf"
is 15.8 MB large. When I read this into Paraview the
information windows shows it uses 0.98MB of memory.</div>
<div style=""><br>
</div>
<div style="">I then create a grid in cartesian coordinates
"grid3d_car" specified as Topology Type 3DRectMesh and
Geometry Type VXVYVZ. Here instead of the full 3D array I
write thee 1D arrays, one for each coordinates. The file looks
like:</div>
<div style=""><br>
</div>
<div style="">
<div><?xml version="1.0" ?></div>
<div><!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []></div>
<div><Xdmf Version="2.2"></div>
<div><Domain></div>
<div>
<Grid GridType="Uniform"></div>
<div><Topology TopologyType="3DRectMesh" Dimensions=" 30
70 40"/></div>
<div><Geometry GeometryType="VXVYVZ"></div>
<div><DataItem Dimensions=" 40" NumberType="Float"
Precision="4" Format="XML"></div>
<div> 0.0000 1.0000 2.0000 3.0000 4.0000 5.0000
6.0000 7.0000 8.0000 9.0000 10.0000 11.0000 12.0000
13.0000 14.0000 15.0000 16.0000 17.0000 18.0000
19.0000 20.0000 21.0000 22.0000 23.0000 24.0000
25.0000 26.0000 27.0000 28.0000 29.0000 30.0000
31.0000 32.0000 33.0000 34.0000 35.0000 36.0000
37.0000 38.0000 39.0000</div>
<div></DataItem></div>
<div><DataItem Dimensions=" 70" NumberType="Float"
Precision="4" Format="XML"></div>
<div> 0.0000 0.0911 0.1821 0.2732 0.3642 0.4553
0.5464 0.6374 0.7285 0.8195 0.9106 1.0017 1.0927
1.1838 1.2748 1.3659 1.4570 1.5480 1.6391
1.7302 1.8212 1.9123 2.0033 2.0944 2.1855 2.2765
2.3676 2.4586 2.5497 2.6408 2.7318 2.8229
2.9139 3.0050 3.0961 3.1871 3.2782 3.3692 3.4603
3.5514 3.6424 3.7335 3.8245 3.9156 4.0067
4.0977 4.1888 4.2799 4.3709 4.4620 4.5530 4.6441
4.7352 4.8262 4.9173 5.0083 5.0994 5.1905
5.2815 5.3726 5.4636 5.5547 5.6458 5.7368 5.8279
5.9189 6.0100 6.1011 6.1921 6.2832</div>
<div></DataItem></div>
<div><DataItem Dimensions=" 30" NumberType="Float"
Precision="4" Format="XML"></div>
<div> 1.0000 2.0000 3.0000 4.0000 5.0000 6.0000
7.0000 8.0000 9.0000 10.0000 11.0000 12.0000 13.0000
14.0000 15.0000 16.0000 17.0000 18.0000 19.0000
20.0000 21.0000 22.0000 23.0000 24.0000 25.0000
26.0000 27.0000 28.0000 29.0000 30.0000</div>
<div></DataItem></div>
<div></Geometry></div>
<div></Grid></div>
<div></Domain></div>
<div></Xdmf></div>
<div><br>
</div>
<div style="">The gris is still 30x70x40 but the file
"grid3d_car.xmf" is more compact, it is only 2.2 KB in size.
When I read it into Paraview the information windows shows
it uses only 0.003MB. So far so good, I end up saving space
both on the hard drive and in memory.</div>
<div style=""><br>
</div>
<div style="">I then convert the cartesian grid to cylindrical
coordinates using the CleantoGrid Filter and also a
programmable Filter:</div>
<div style=""><br>
</div>
<div style="">
<p style="margin:0px">pdi = self.GetInput()</p>
<p style="margin:0px">pdo = self.GetOutput()</p>
<p style="margin:0px">newPoints = vtk.vtkPoints()</p>
<p style="margin:0px">numPoints = pdi.GetNumberOfPoints()</p>
<p style="margin:0px">for i in range(0, numPoints):</p>
<p style="margin:0px"> coord = pdi.GetPoint(i)</p>
<p style="margin:0px"> x, y, z = coord[:3]</p>
<p style="margin:0px"> r = x * cos(y)</p>
<p style="margin:0px"> t = x * sin(y)</p>
<p style="margin:0px"> newPoints.InsertPoint(i, r, t, z)</p>
<p style="margin:0px">pdo.SetPoints(newPoints)</p>
<p style="margin:0px"><br>
</p>
<p style="margin:0px">The information window in Paraview
shows that The CleanToGrid Filter uses 7.2 MB and the
ProgrammableFilter another 7.1MB so in total the cartesian
to cylindrical conversion uses 14.3 MB. That's a huge
memory penalty. Here's a summary:</p>
<p style="margin:0px"><br>
</p>
<p style="margin:0px">File Size
Memory</p>
<p style="margin:0px">grid3d_cyl.xmf 15.8MB 0.98MB</p>
</div>
</div>
<div style="">grid3d_car.xmf 2.2KB 0.003MB</div>
<div style="">CleanToGrid - 7.2MB</div>
<div style="">Programmable - 7.1MB</div>
<div style=""><br>
</div>
<div style="">Since both grids contain the exact same coordinate
information I would expect the approach of converting the grid
from cartesian to cylindrical to not take more than 0.98MB of
memory, instead it takes 14.3MB. Does it make any sense? Am I
doing sth wrong? Can I avoid the memory penalty?</div>
<div style=""><br>
</div>
<div style="">Thank you,</div>
<div style=""><br>
</div>
<div style="">Nikos</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Fri, Apr 5, 2013 at 3:48 AM, Felipe
Bordeu <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:felipe.bordeu@ec-nantes.fr" target="_blank">felipe.bordeu@ec-nantes.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>By "pipelines", I think you want to say "filters". I
do not know how to delete intermediary results. <br>
One way is to apply a filter and then save the result
("File"-> "Save Data"). So you can open it later
without the deed to recreate the hole pipeline.<br>
<br>
Felipe<br>
<br>
Le 04/04/2013 19:51, Nikolaos Beratlis a écrit :<br>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Felipe,
<div><br>
</div>
<div>When I try this script to transform from
cartesian to cylindrical coordinates after I
have applied the CleantoGrid Filter:</div>
<div><br>
</div>
<div>
<div
style="font-family:arial,sans-serif;font-size:13px">
<div style="margin:0px">pdi = self.GetInput()</div>
<div style="margin:0px">pdo = self.GetOutput()</div>
<div style="margin:0px">newPoints =
vtk.vtkPoints()</div>
<div style="margin:0px">numPoints =
pdi.GetNumberOfPoints()</div>
<div style="margin:0px">for i in range(0,
numPoints):</div>
<div style="margin:0px">coord =
pdi.GetPoint(i)</div>
<div style="margin:0px">x, y, z = coord[:3]</div>
<div style="margin:0px">r = x * cos(y)</div>
<div style="margin:0px"> t = x * sin(y)</div>
<div style="margin:0px">newPoints.InsertPoint(i,
r, t, z)</div>
<div style="margin:0px">pdo.SetPoints(newPoints)</div>
</div>
<div
style="font-family:arial,sans-serif;font-size:13px;margin:0px">pdo.GetPointData().AddArray(pdi.GetPointData().GetArray(0))</div>
<div
style="font-family:arial,sans-serif;font-size:13px;margin:0px">pdo.GetPointData().AddArray(pdi.GetPointData().GetArray(1))</div>
<div
style="font-family:arial,sans-serif;font-size:13px;margin:0px">pdo.GetPointData().AddArray(pdi.GetPointData().GetArray(2))</div>
</div>
<div
style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:13px;margin:0px">it
creates two more pipelines, one for CleantoGrid
and one for Programmable Filter. Both pipelines
are linked to the original pipeline and both
pipelines require the same memory as the
original pipeline. Is there a way to to delete
the previous two pipelines (original with
cartesian coordinates and cleantoGrid) so that I
only use one memory amount and not three?</div>
<div
style="font-family:arial,sans-serif;font-size:13px;margin:0px"><br>
</div>
<div
style="font-family:arial,sans-serif;font-size:13px;margin:0px">Nikos</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote"> On Wed, Apr 3, 2013 at
12:05 PM, Felipe Bordeu <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:felipe.bordeu@ec-nantes.fr"
target="_blank">felipe.bordeu@ec-nantes.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>you need to copy the point data: add
this line to the end of your script:<br>
<br>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">pdo.GetPointData().AddArray(pdi.GetPointData().GetArray(0))</p>
<br>
this will work only for one field, you can
put this line inside a loop to add all the
pointdata.<br>
<br>
Felipe<br>
<br>
Le 03/04/2013 17:59, Nikolaos Beratlis a
écrit :<br>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">I did and it shows me
the transformed grid, but the
ProgrammableFilter doesn't contain
the variable var. I cannot plot
contours. Should I change the
script?</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote"> On Wed,
Apr 3, 2013 at 11:48 AM, Felipe
Bordeu <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:felipe.bordeu@ec-nantes.fr"
target="_blank">felipe.bordeu@ec-nantes.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF"
text="#000000">
<div>You must apply the
programmablefilter to the
cleantoGrid not to the
var3d.xmf. <br>
<br>
look at the screenshot.<br>
<br>
Felipe<br>
<br>
<img
src="cid:part4.06000205.07090906@ec-nantes.fr"
alt=""><br>
<br>
Le 03/04/2013 17:43,
Nikolaos Beratlis a écrit :<br>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Hi
Felipe,
<div><br>
</div>
<div>I applied the
CleanToGrid Filter
first and then
applied the
following script:</div>
<div>
<p
style="margin:0px"><br>
</p>
<p
style="margin:0px">pdi
= self.GetInput()</p>
<p
style="margin:0px">pdo
= self.GetOutput()</p>
<p
style="margin:0px">newPoints
= vtk.vtkPoints()</p>
<p
style="margin:0px">numPoints
=
pdi.GetNumberOfPoints()</p>
<p
style="margin:0px">for
i in range(0,
numPoints):</p>
<p
style="margin:0px">
coord =
pdi.GetPoint(i)</p>
<p
style="margin:0px">
x, y, z =
coord[:3]</p>
<p
style="margin:0px">
r = x * <span
style="background-color:rgb(243,243,243)"><font
color="#ff0000">cos</font></span>(y)</p>
<p
style="margin:0px">
t = x * <font
color="#ff0000">sin</font>(y)</p>
<p
style="margin:0px">
newPoints.InsertPoint(i,
r, t, z)</p>
<p
style="margin:0px">pdo.SetPoints(newPoints)</p>
</div>
<div><br>
</div>
<div>Notice
the indentation and
also the change of
the cos(y) and
sin(y) assignments. </div>
<div><br>
</div>
<div>but I got this
error:</div>
<br>
Traceback (most recent
call last):<br>
<br>
File "<string>",
line 26, in
<module><br>
<br>
File "<string>",
line 12, in
RequestData<br>
<br>
AttributeError:
SetPoints
<div>
<p
style="margin:0px">
</p>
</div>
<div><br>
</div>
<div>What am I doing
wrong?</div>
</div>
<div class="gmail_extra"><br>
<br>
<div
class="gmail_quote">On
Wed, Apr 3, 2013 at
11:13 AM, Felipe
Bordeu <span
dir="ltr"><<a
moz-do-not-send="true"
href="mailto:felipe.bordeu@ec-nantes.fr" target="_blank">felipe.bordeu@ec-nantes.fr</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0 0
0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
bgcolor="#FFFFFF"
text="#000000">
<div>apply a
CleanToGrid
filter before
the python
programmable
filter and
this is a
corrected
version of
your script:<br>
<br>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">pdi
=
self.GetInput()</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">pdo
=
self.GetOutput()</p>
<div>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">newPoints
=
vtk.vtkPoints()</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">numPoints
=
pdi.GetNumberOfPoints()</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">for
i in range(0,
numPoints):</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
coord =
pdi.GetPoint(i)</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
x, y, z =
coord[:3]</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
r = x * sin(y)</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
t = x * cos(y)</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">
newPoints.InsertPoint(i,
r, t, z)</p>
<p
style="margin-top:0px;margin-bottom:0px;margin-left:0px;margin-right:0px;text-indent:0px">pdo.SetPoints(newPoints)</p>
<br>
<br>
</div>
Felipe<br>
<br>
Le 03/04/2013
04:55,
Nikolaos
Beratlis a
écrit :<br>
</div>
<blockquote
type="cite">
<div>
<div>
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
I am reading
the following
xmf file
(attached as
var3d.xmf)
into Paraview:
<div><br>
</div>
<div>
<div><?xml
version="1.0"
?></div>
<div><!DOCTYPE
Xdmf SYSTEM
"Xdmf.dtd"
[]></div>
<div><Xdmf
Version="2.2"></div>
<div><Domain></div>
<div><Grid
GridType="Uniform"></div>
<div><Topology
TopologyType="3DRectMesh"
Dimensions="
2 4
3"/></div>
<div><Geometry
GeometryType="VXVYVZ"></div>
<div><DataItem
Dimensions="
3"
NumberType="Float"
Precision="4"
Format="XML"></div>
<div> 0.0000
1.0000
2.0000</div>
<div></DataItem></div>
<div><DataItem
Dimensions="
4"
NumberType="Float"
Precision="4"
Format="XML"></div>
<div> 0.0000
<a
moz-do-not-send="true"
href="tel:2.0944%20%C2%A0%204.1888" value="+12094441888" target="_blank">2.0944
4.1888</a>
6.2832</div>
<div></DataItem></div>
<div><DataItem
Dimensions="
2"
NumberType="Float"
Precision="4"
Format="XML"></div>
<div> 1.0000
2.0000</div>
<div></DataItem></div>
<div></Geometry></div>
<div>
<Attribute
Name="var"
AttributeType="Scalar"
Center="Node"></div>
<div><DataItem
Dimensions="24"
NumberType="Float"
Precision="4"
Format="XML"></div>
<div>0 1 2 3 4
5 6 7 8 9 10
11 12 13 14 15
16 17 18 19 20
21 22 23</div>
<div></DataItem></div>
<div></Attribute></div>
<div></Grid></div>
<div></Domain></div>
<div></Xdmf></div>
<div><br>
</div>
<div> The grid
is a 3D
orthogonal
grid read in
cartesian
coordinates
(see attached
image showing
grid and
contours of
variable). I
then want to
transform the
grid from
cartesian to
cylindrical
coordinates. I
tried using
the following
Python script:</div>
<div><br>
</div>
<div>
<p
style="margin:0px">pdi
=
self.GetPolyDataInput()</p>
<p
style="margin:0px">pdo
=
self.GetPolyDataOutput()</p>
<p
style="margin:0px">newPoints
=
vtk.vtkPoints()</p>
<p
style="margin:0px">numPoints
=
pdi.GetNumberOfPoints()</p>
<p
style="margin:0px">for
i in range(0,
numPoints):</p>
<p
style="margin:0px">
coord =
pdi.GetPoint(i)</p>
<p
style="margin:0px">
x, y, z =
coord[:3]</p>
<p
style="margin:0px">
r = x * sin(y)</p>
<p
style="margin:0px">
t = x * cos(y)</p>
<p
style="margin:0px">
newPoints.InsertPoint(i,
r, t, z)</p>
<p
style="margin:0px">pdo.SetPoints(newPoints)</p>
<p
style="margin:0px"><br>
</p>
<p
style="margin:0px">with
Output Data
Set Type
chosen to be
the Same as
Input, but I
get this
error:</p>
<p
style="margin:0px"><br>
</p>
Traceback
(most recent
call last):<br>
File
"<string>",
line 26, in
<module><br>
File
"<string>",
line 12, in
RequestData<br>
AttributeError:
'NoneType'
object has no
attribute
'SetPoints'</div>
</div>
<div><br>
</div>
<div>I have no
experience
with Python
scripting.
What am I
doing wrong?</div>
<div><br>
</div>
<div>Thank
you,</div>
<div><br>
</div>
<div>Nikos</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
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<span><font
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</font></span></blockquote>
<span><font
color="#888888">
<br>
<br>
<pre cols="72">--
Felipe Bordeu Weldt
Ingénieur de Recherche
-------------------------------------
Tél. : <a moz-do-not-send="true" href="tel:33%20%280%292%2040%2037%2016" value="+13302403716" target="_blank">33 (0)2 40 37 16</a> 57
Fax. : <a moz-do-not-send="true" href="tel:33%20%280%292%2040%2074%2074" value="+13302407474" target="_blank">33 (0)2 40 74 74</a> 06
<a moz-do-not-send="true" href="mailto:Felipe.Bordeu@ec-nantes.fr" target="_blank">Felipe.Bordeu@ec-nantes.fr</a>
Institut GeM - UMR CNRS 6183
École Centrale Nantes
1 Rue de La Noë, 44321 Nantes, FRANCE
-------------------------------------</pre>
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Felipe Bordeu Weldt
Ingénieur de Recherche
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Tél. : <a moz-do-not-send="true" href="tel:33%20%280%292%2040%2037%2016" value="+13302403716" target="_blank">33 (0)2 40 37 16</a> 57
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<a moz-do-not-send="true" href="mailto:Felipe.Bordeu@ec-nantes.fr" target="_blank">Felipe.Bordeu@ec-nantes.fr</a>
Institut GeM - UMR CNRS 6183
École Centrale Nantes
1 Rue de La Noë, 44321 Nantes, FRANCE
-------------------------------------</pre>
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<pre cols="72">--
Felipe Bordeu Weldt
Ingénieur de Recherche
-------------------------------------
Tél. : <a moz-do-not-send="true" href="tel:33%20%280%292%2040%2037%2016" value="+13302403716" target="_blank">33 (0)2 40 37 16</a> 57
Fax. : <a moz-do-not-send="true" href="tel:33%20%280%292%2040%2074%2074" value="+13302407474" target="_blank">33 (0)2 40 74 74</a> 06
<a moz-do-not-send="true" href="mailto:Felipe.Bordeu@ec-nantes.fr" target="_blank">Felipe.Bordeu@ec-nantes.fr</a>
Institut GeM - UMR CNRS 6183
École Centrale Nantes
1 Rue de La Noë, 44321 Nantes, FRANCE
-------------------------------------</pre>
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<pre cols="72">--
Felipe Bordeu Weldt
Ingénieur de Recherche
-------------------------------------
Tél. : <a moz-do-not-send="true" href="tel:33%20%280%292%2040%2037%2016" value="+13302403716" target="_blank">33 (0)2 40 37 16</a> 57
Fax. : <a moz-do-not-send="true" href="tel:33%20%280%292%2040%2074%2074" value="+13302407474" target="_blank">33 (0)2 40 74 74</a> 06
<a moz-do-not-send="true" href="mailto:Felipe.Bordeu@ec-nantes.fr" target="_blank">Felipe.Bordeu@ec-nantes.fr</a>
Institut GeM - UMR CNRS 6183
École Centrale Nantes
1 Rue de La Noë, 44321 Nantes, FRANCE
-------------------------------------</pre>
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_______________________________________________<br>
Powered by <a moz-do-not-send="true"
href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
<br>
Visit other Kitware open-source projects at <a
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href="http://www.kitware.com/opensource/opensource.html"
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Please keep messages on-topic and check the ParaView Wiki
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<pre class="moz-signature" cols="72">--
Felipe Bordeu Weldt
Ingénieur de Recherche
-------------------------------------
Tél. : 33 (0)2 40 37 16 57
Fax. : 33 (0)2 40 74 74 06
<a class="moz-txt-link-abbreviated" href="mailto:Felipe.Bordeu@ec-nantes.fr">Felipe.Bordeu@ec-nantes.fr</a>
Institut GeM - UMR CNRS 6183
École Centrale Nantes
1 Rue de La Noë, 44321 Nantes, FRANCE
-------------------------------------</pre>
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