Re: [Paraview] Volumes of Interest

2010-02-18 Thread Jean M. Favre
Natalie Happenhofer wrote:
> Another topic - selecting volumes of interest: I can do that for one file, 
> and it works well. But is it really necessary to repeat this procedure for 
> every file I open in Paraview? Is it possible to select a volume of interest 
> and for every file I open afterward, just this VoI is displayed?
>
>   
I would suggest doing this in Python in order to avoid reading the full
resolution dataset by default. When opening a file, paraview forces you
to click Apply before you can do anything else (such as creating an
Extract Subset filter). Thus, the data reader uses
UPDATE_EXTENT=WHOLE_EXTENT and you may run out of memory before being
able to subset the grid.

if instead, you instantiate your reader, do not execute it, do not
create a representation for it, then create an Extract Subset with the
VOI you desire, and then execute the whole thing, you will end-up
passing the VOI extents upstream directly to the reader, and your reader
will only execute once with the correct extents.

Use the python shell and the followin example:

reader = XMLImageDataReader( FileName= '/path/to/data/foo.vti'] )
reader.PointArrayStatus = ['data1']

ExtractSubset1 = ExtractSubset()

ExtractSubset1.VOI = [2000, 2255, 2000, 2255, 2000, 2255]

DataRepresentation2 = Show(ExtractSubset1)

Render()

Jean--
Swiss National Supercomputing Center
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[Paraview] vtkHyperOctree

2010-02-17 Thread Jean M. Favre
Folks

I am evaluating the possibilities of using the HyperOctree to support an
astro-physics code. First question: Can we set a threshold to switch the
GeometryFilter to a bounding box mode when loading an hyperoctree? By
default the surface-mode is always ON and for an octree beyond 8 levels
of refinement, things are getting heavy.

Second question: I don't see what method should be used for
parallelizing the construction of the octree. Could one use  tags such a
mixture of UPDATE_RESOLUTION and UPDATE_PIECE_NUMBER  to divide up the
load? Are filters downstream ready to propagate the meta-data requests
for octrees? The example of the HyperOctree Fractal does a depth-first
construction. I suppose breadth-first is also possible since the
HyperOctreeCursor enables navigation in both direction. Simulation codes
actually use space-filling curves (e.g. Hilbert curves or others) and in
terms of reading back the data, this could one efficient way to access
data from disk, where each server follows a segment of the Hilbert
curve.  I just don't know if anyone has ever done parallel octree builds
in ParaView and if this is feasible?

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Jean
Swiss National Supercomputing Center
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Re: [Paraview] Cannot find SaveData for python scripting

2010-02-16 Thread Jean M. Favre
Fabian Wein wrote:
> Hi,
>
> I searched and googled but could not find the python call for SaveData().
>   
All the writers can be found under... servermanager.writers

dir(servermanager.writers)

['AnimationSceneImageWriter', 'CSVWriter', 'DataSetCSVWriter',
'DataSetWriter', 'EnSightWriter', 'ExodusIIWriter', 'MetaImageWriter',
'PDataSetWriter', 'PNGWriter', 'PPLYWriter', 'PSTLWriter',
'XMLDataSetWriterBase', 'XMLHierarchicalBoxDataWriter',
'XMLHyperOctreeWriter', 'XMLImageDataWriter', 'XMLMultiBlockDataWriter',
'XMLPImageDataWriter', 'XMLPPolyDataWriter',
'XMLPRectilinearGridWriter', 'XMLPStructuredGridWriter',
'XMLPUnstructuredGridWriter', 'XMLPVAnimationWriter', 'XMLPVDWriter',
'XMLPolyDataWriter', 'XMLRectilinearGridWriter',
'XMLStructuredGridWriter', 'XMLUnstructuredGridWriter', 'XdmfWriter',
'XdmfWriter2',..]

Jean--
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[Paraview] GetDataInformation() troubles

2010-02-08 Thread Jean M. Favre

I am having troubles with a reader plugin which works well under 3.6.2
but is missing some DataInformation under the CVS version. Specifically,
my reader produces a hierarchy of multi-blocks, so some data fields are
only stored on some datasets, and PV3.6.2 correctly associates them and
displays them as "partial".

in PV3.6.2, printing my reader.GetDataInformation().DataInformation,
each *and all* fields is displayed, and correctly marked with "IsPartial".

in PV3.7, the "partial" fields are missing, although they are read and
stuffed in memory, and consequently, I cannot used them in Display
Properties.

Did I miss some new developments which causes this side-effect?

Jean
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Re: [Paraview] Problems writing an .vtu file

2010-01-28 Thread Jean M. Favre
s.habbinga wrote:
> Hello everybody,
>
> I've been trying to write a c++ function to convert my data into .vtu
> files. Unfortunately, paraview isn't able to read my .vtu files. I get
> the following error-message:
>
>
>   

there is a typographic error in your file.

Replace the line
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[Paraview] Array Calculator missing blocks in a hierarchical multi-block dataset

2009-10-19 Thread Jean M. Favre

I have a MB dataset of 4 objects, each block being itself a multi-block
dataset. The first MB is a composite object of vtkStructuredGrids, while
the last 3 are again multi-blocks, each one a composite of
vtkStructuredGrids. This is not AMR, just a complex geometry, cleanly
separated into functional objects.

Well, ArrayCalculator does not handle that well. It produces the same
hierarchy, but most objects have empty data fields, except for the first
 MB (at the lowest level), of the last MB at the first level.

Is it possible that the traversal of a multi-composite object does not
quite fully visit all leaf objects? Yet, if I slice the multi-composite
object, I get the correct multi-composite slices. So, is there something
particular to the ArrayCalculator?

Jean--
Swiss National Supercomputing Center

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[Paraview] XMLPUnstructuredGridWriter arguments

2009-10-19 Thread Jean M. Favre
Dear all

I am porting some code python code from 3.4 to 3.6 and cvs

The following code, which works fine in 3.4 raises an error in the more
recent versions.

writer = sm.writers.XMLPUnstructuredGridWriter()
writer.NumberOfPieces = 4

Attribute NumberOfPieces does not exist...

Any fix possible?

TIA
Jean--
Swiss National Supercomputing Center

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[Paraview] IntegrateAttributes gives different results when run in parallel?

2009-09-29 Thread Jean M. Favre

I could not find any test for IntegrateAttributes, and I am questioning
the output generated when run in parallel, on a 2D surface mesh.
Although the area computed is equal to the area computed by the serial
builtin paraview, some other variables (but not all) show large
differences in integrated values. The results depend on the number of
processors used as well.

I have tested with some physical data which we have validated and the
serial integrations are correct. The parallel runs are not.

I have also tested with some simple Wavelet data, and by using a D3
before the integration filter, insuring that cells were assigned uniquely.

My questions are: How are the results of IntegrateAttributes validated?
Is there a test somewhere? What about parallel runs?

Thanks for any tips.

Jean--
Swiss National Supercomputing Center

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Re: [Paraview] forcing server to do all computations/rendering; unrelated, rendering vertices as pixels

2009-09-28 Thread Jean M. Favre
Christine Corbett Moran wrote:
> Hi,
> 
> I have two questions I am hoping someone can give me some insight on.
> 
> 1. How to force the server to do all computations and rendering?
> After playing around with the ParaView server settings, I haven't yet
> been able to force the server to do all computations and rendering,
> only sending images to the client. I want to do this for testing
> purposes. Is there a way to do this easily?


under Edit->Settings->Render View->Server

set the Remote Render Threshold to 0 and the servers will do all
rendering. An easy way to check is that during interactive rendering, if
you enable "interactive Subsample Rate", you will see fat pixels
rendered. That is the image composited server-side, then sub-sampled,
and sent over to the client for display.

Jean--
Swiss National Supercomputing Center

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[Paraview] Parallel Reading and Extent Translator

2009-09-10 Thread Jean M. Favre
Back in March 2009, I answered a question by another user
(http://www.paraview.org/pipermail/paraview/2009-March/011303.html),
asking how to override the default splitting of data chunks. By default,
structured volumes are split among all 3 main directions. My answer,
validated with version 3.4, was to tell the Extent Translator to use an
alternate SplitMode, like this:

vtkStreamingDemandDrivenPipeline *exec =
static_cast(this->GetExecutive());
exec->GetExtentTranslator(outInfo)->SetSplitModeToXSlab();

I have verified today that the solution works well, producing the
required split, either as X, Y or Z slabs.

My problem is that I cannot reproduce this in version 3.6.1. When the
same data reader source code is compiled against version 3.6, my request
to SetSplitModeTo?Slab() are ignored all the times. I am using the same
grid resolution and the same number of processes. What works in version
3.4 cannot be reproduced in version 3.6.

Has anyone seen this too?

If anyone wonders, it does matter greatly. Reading HDF5 hyperslabs can
be 10 times faster in one direction or the other. That is what I need to
support.

Jean--
Swiss National Supercomputing Center.

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Re: [Paraview] [PV-3.6.1] Problem compiling with Python in linux x86_64

2009-09-01 Thread Jean M. Favre
Renato Elias wrote:
> 
> Moreover, how can I force the make process to be more verbose?


make VERBOSE=1

:-)
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Re: [Paraview] Loading a Plugin from a Python-Script in 3.6.1

2009-08-31 Thread Jean M. Favre
Bernhard Gschaider wrote:
> Hi!
> 
> I'm trying to update a pvpython-script from 3.4 to 3.6.1
> 
> Amongst other things it should load a Plugin. The plugin loads
> perfectly over the GUI, but when I try to do it from the script it
> fails with this message:
> 
>   File 
> "/home/bgschaid/Development/OpenFOAM/Python/PyFoam/PyFoam/Paraview/ServermanagerWrapper.py",
>  line 41, in __init__
> servermanager.LoadPlugin(path.join(p,plug1))
>   File 
> "/home/openfoam/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linux64Gcc/Utilities/VTKPythonWrapping/paraview/servermanager.py",
>  line 2094, in LoadPlugin
> if not parser.Parse(f.read()):
> TypeError: function takes exactly 2 arguments (1 given)


the error message indicates that the second argument is missing. Please
try again using the following syntax:

LoadPlugin("yourlibname.so", ns=globals())

this is documented in the source code of
Utilities/VTKPythonWrapping/paraview/simple.py

def LoadPlugin(filename, ns=None):
"""Loads a ParaView plugin and updates this module with new constructors
if any. If you loaded the simple module with from paraview.simple
import *,
make sure to pass globals() as the second arguments:
LoadPlugin("myplugin", globals())
Otherwise, the new functions will not appear in the global namespace."""


Jean--
Swiss National Supercomputing Center
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Re: [Paraview] animation + python

2009-08-28 Thread Jean M. Favre
Stephane PLOIX wrote:
> Hi,
> 
> At the end of the python scripting wiki page 
> (http://paraview.org/Wiki/ParaView/Python_Scripting), you give an example 
> on how to create an animation via python.
> 
> However, this animation is not visible in the Animation View, and I did 
> not find how to save the images to create a film. 


> *How to dump the animation to images with the scene.Play method? 

the answer lies in the source code of servermanager.py

Add these 5 lines to your code:

writer = servermanager.vtkSMAnimationSceneImageWriter()
writer.SetFileName("/tmp/foo.jpg")
writer.SetFrameRate(1)
writer.SetAnimationScene(scene.SMProxy)
writer.Save()

Jean--
Swiss National Supercomputing Center
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Re: [Paraview] Integrate Variables not updating?

2009-08-27 Thread Jean M. Favre
Berk Geveci wrote:
> By any chance, is the filter visible on any views? If its visibility
> is turned off everywhere, it will not execute (by design).

good catch. The filter was not visible. Once made visible, it updates
correctly.

the reason I did not make it visible is essentially because using a
spreadsheet view for a dataset with a single point is a big waste of
real estate. The "showing" label which allows selection of an active
source is by default the size of the longest string name from the full
list of sources, and does not resize when I select
"IntegrateAttriutes1". Since I have some very long names in the
filenames, I end up with a spreadsheet which has a minimal width of over
1200 pixels, no matter where I put it. Wasting too much screen space. I
was limiting myself to looking at the Information tab in the Object
Inspector.

Jean
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Re: [Paraview] Integrate Variables not updating?

2009-08-27 Thread Jean M. Favre
Berk Geveci wrote:
> Do you know if the filter executes at all? I am wondering if the bug
> is because the client is not pulling the results or because the filter
> is not executing.


the filter is not executing at all. I have set up an animation of my
threshold. The Timer log shows no activity from vtkIntegrateAtttributes,
and when I do an explicit call to UpdatePipeline() in the python shell,
it takes a long time to return the result, which I believe means it is
not simply pulling the result from the server, but the server actually
goes ahead and does the full work.

N.B. I haven't tried with "simple" data. My data is a full AMR hierarchy
of blocks. And I run in parallel.

Jean

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[Paraview] Integrate Variables not updating?

2009-08-26 Thread Jean M. Favre

I am running a parallel pipeline, using IntegrateVariables to calculate
mass, volume, and other quantities in a region.

I find that when the region is changed (e.g. a threshold of an
iso-clip), IntegrateVariables does not update and recalculates.

Going to the Python shell and forcing an UpdatePipeline each time I
change the threshold is enough to get the correct value. Shouldn't this
update be automatic? I use paraview cvs version.

TIA
Jean
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[Paraview] XY Plots single precision

2009-08-26 Thread Jean M. Favre

Am I guessing right that XY Plots do not support double precision
numbers? I have CSV tables of numbers in the range e+48 e+49. the
paraview Spreadsheet view works fine, but the XY plot is empty. Too bad
I have to export the data and do the final visualization with another tool.

Jean
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[Paraview] tiled display with gaps?

2009-08-25 Thread Jean M. Favre

I am having a problem running paraview-3.6 and paraview-CVS on a tiled
display. There are large gaps (several 100s) of pixels between each
tile, no matter what the -tmx and -tmy options are set to.

ParaView 3.4 and EqualizerGraphics 0.9 work perfectly well on the same
cluster and tiled display setup, with no gaps between rows and columns.

Has some setting gotten lost in version 3.6 and above?

Jean

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[Paraview] load plugin in pvpython/pvbatch (CVS)

2009-08-19 Thread Jean M. Favre

I've got plugins working fine with paraview, but I cannot load them with
pvpython (pv3.7 CVS). Loading them without globals() gives no errors,
but they ain't visible. Loading them with globals() gives this error:

>>> LoadPlugin("MySMPlugin.so", remote='False', ns=globals())
Traceback (most recent call last):
  File "", line 1, in 
  File
"/local/apps/ParaView3Build/Utilities/VTKPythonWrapping/paraview/simple.py",
line 530, in LoadPlugin
servermanager.LoadPlugin(filename, remote)
  File
"/local/apps/ParaView3Build/Utilities/VTKPythonWrapping/paraview/servermanager.py",
line 2083, in LoadPlugin
plinfo = plm.LoadPlugin(filename, connection.ID, serverURI, remote)
TypeError: function takes exactly 1 argument (4 given)


looking at the source code of simple.py, it seems like globals() is
required, but should not be the second argument, but the third argument.
 is this a copy-and-paste error from LoadXML()?

def LoadPlugin(filename, remote=True, ns=None):
"""Loads a ParaView plugin and updates this module with new
constructors if any. If you loaded the simple module with from
paraview.simple import *, make sure to pass globals() as the second
arguments: LoadPlugin("myplugin", globals()) Otherwise, the new
functions will not appear in the global namespace."""

thanks for any tip

Jean
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Re: [Paraview] Rendering bug in ParaView-CVS

2009-08-14 Thread Jean M. Favre
Michael Wild wrote:
> True, but you could write a small utility which directly operates on
> your output data and scales it there

scaling data while reading it only gets you that far, until what you are
looking for are not just Colorful Visualization, but quantitative data
analysis.

I have similar problems, on the other side of the number spectrum, with
astro-physics data. 10^50 numbers. We're now taking better advantage of
ParaView to calculate volumes, fluxes, etc. The units have better be
right, and it's easier to look at data in true scale.

I vote for no-scaling to get immediate feedback on quantitative data
analysis.

my 2 cents

Jean--
Swiss National Supercomputing Center
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Re: [Paraview] Mimicking the 'set view plane direction' GUI buttons in Python script

2009-07-09 Thread Jean M. Favre
Adriano Gagliardi wrote:

> //===
> 
> Is it possible Render() calls ResetCamera()? 
> 
> ===

You may look at the source code in
/Utilities/VTKPythonWrapping/paraview/simple.py

def Render(view=None):
"""Renders the given view (default value is active view)"""
if not view:
view = active_objects.view
view.StillRender()
if _funcs_internals.first_render:
view.ResetCamera()
view.StillRender()
_funcs_internals.first_render = False
return view


So, it would seem that if a first rendering has not been done, then yes,
it calls ResetCamera. Try doing a Render call before setting your
camera, and then follow your usual procedure

Jean--
Swiss National Supercomputing Center
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Re: [Paraview] Block names for multi-block data set

2009-07-06 Thread Jean M. Favre
Adriano Gagliardi wrote:
> I've written a reader that takes a mesh file, stores zones within it as a
> vtkUnstructuredGrid and then stores them all in a vtkMultiBlockDataSet. When
> I go to extract blocks after reading the mesh in, I am faced with a list of
> each block number all called vtkUnstructuredGrid. Is it possible to assign
> names to each of the blocks within the reader? I can't seem to find any
> function to do so in the respective vtk class lists.


I believe you need this line:


volumes->GetMetaData(grid_number)->Set(vtkCompositeDataSet::NAME(),
"grid-name");
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Re: [Paraview] 2D plotting in paraview3.6

2009-06-19 Thread Jean M. Favre
Paul Edwards wrote:
> In the "Display" tab in the "Object Inspector", change the "X Axis Data" to
> "Use Data Array" and select "Points(0)".

Exactly as Paul said. Well done.

but there is a caveat. It assumes the numbering of vertices along the
profile is in increasing order. It works well with the NACA dataset in
VTKData/EnSight because the mesh is curvilinear structured.

It is much more difficult to get when the profile is the intersection of
a plane with the 3D surface of an airfoil (typically unstructured), and
the numbering of vertices is all but monotonously increasing. Yet
harder, if the profile is the intersection of a 3D multi-block airfoil
surface.

Jean --
Swiss National Supercomputing Center.
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Re: [Paraview] Syntax Change setting Representations ColorArrayName Property

2009-06-18 Thread Jean M. Favre
Tobias Froebel wrote:
> Hello,
> 
> I'm encountering a problem with paraview-cvs and paraview-3.6. The
> following example from the servermanager documentation worked fine for
> me in paraview 3.4
> 


Please read Berk's very nice email on May 25, subject: "ParaView Python
users please read"

Many changes have gone in, and the scripting is now much nicer and user
friendly. You must change your syntax though. It is all nicely
documented here:

http://paraview.org/Wiki/ParaView/Python_Scripting

your new script should be:

from paraview.simple import *
sm=servermanager
sm.Connect()

cone=sm.sources.Cone()
elev=sm.filters.Elevation(Input=cone)

view=sm.CreateRenderView()
rep=sm.CreateRepresentation(elev,view)

lt=sm.rendering.PVLookupTable()
rep.LookupTable=lt
rep.ColorAttributeType='POINT_DATA'
rep.ColorArrayName='Elevation'
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[Paraview] FieldData

2009-06-02 Thread Jean M. Favre

Can someone refresh my memory about FieldData?

I have a dataset with PointData and FieldData. The FieldData contains
multiple scalar arrays. Each array has a different number of tuples.

ParaView (3.6) reads them without complaining. The Object Inspector
shows the correct bounds ([min, max]), meaning the arrays were read to
the end. So far so good.

Trouble comes with the Spreadsheet view. I expected to see a column of a
different size for each array when choosing the FieldData attribute.
Instead, the column displays are all truncated to the size of the first
array.

Same with "Plot Data". The length of the X axis gets truncated to the
number of tuples of the first array.

Any hints will be appreciated.
TIA

Jean -
Swiss National Supercomputing Center





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Re: [Paraview] 2D Glyph Circle

2009-04-21 Thread Jean M. Favre
Sreejith Kuttanikkad wrote:
> Dear Paraview,
> 
> When I select the 2D Glyph Circle option in Paraview 3.4.0, the glyphs look
> more like an octagon than a circle. I could not find an option to increase
> the number of sides or resolution so that it looks like circle. How can I do
> that,  like for instance, in sphere glyph there is an option to change theta
> resolution in the properties tab.
> 


You cannot change it, unless you modify the source code. It is
hard-coded to generate 8 points.

Look in ./VTK/Graphics/vtkGlyphSource2D.cxx

vtkGlyphSource2D::CreateCircle()

Jean --
Swiss National Supercomputing Center
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Re: [Paraview] Bug in Slice representation or in my XML ?

2009-04-20 Thread Jean M. Favre
Jérôme wrote:
> Dear list,
> Please find attached an XML that will expose vtkImageGaussianSource and
> vtkImageMagnitude to ParaView
> First of all, vtkImageGaussianSource behaves like it does not produce any
> data :
>- Add a Gaussian Source to the pipeline,
>- Apply
>- Then go to the information panel of the object inspector : No data
> arrays !!

This behavior can be traced back to the fact that the vtkDataArray
allocated in VTK/Filtering/vtkImageData.cxx does not name the array.
ParaView needs all data fields to be named. Adding this single line of
code makes wit work.


scalars->SetName("scalars");


For the rest of your comments concerning slicing and information, I
cannot reproduce any of the symptoms you mentioned. Slice representation
works fine and the Extents are not touched AFAIK.

Jean --
Swiss National Supercomputing Center
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Re: [Paraview] adding axes via python scripting

2009-04-09 Thread Jean M. Favre
Michael Müller wrote:
> I just tried to add the CubeAxesRepresentation via python scripting using 
> Paraview 3.4. Within the script I read some VTK-file, get its cell data, add 
> a color legend and save the screenshot as png-file. It looks like the 
> following:
> 
> 

try the following:

reader = sm.sources.LegacyVTKFileReader(FileNames=fname)
axes = sm.rendering.CubeAxesRepresentation(Input=reader)


Jean--
Swiss National Supercomputing Center
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[Paraview] libvtkPVServerManager.so: undefined reference

2009-04-08 Thread Jean M. Favre

when compiling paraview CVS with the option -DPARAVIEW_BUILD_QT_GUI=OFF
, I have the following problem since yesterday.

Linking CXX executable ../../bin/vtkSMExtractDocumentation
../../bin/libvtkPVServerManager.so: undefined reference to
`vtkSMChartTableRepresentationProxy::GetNumberOfSeries()'
../../bin/libvtkPVServerManager.so: undefined reference to
`vtkSMChartTableRepresentationProxy::GetSeriesName(int)'

any clue?

thanks in advance
Jean
CSCS
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Re: [Paraview] A general quesiton

2009-04-07 Thread Jean M. Favre
Battalgazi YILDIRIM wrote:
> Hi,
> 
> I have just begun with python scripting in Paraview. I agree that I should
> use servermanager to communicate to Paraview Engine.
> 
> But problem is  (at least for me) how will I add my own source (or reader)
> in servermanager.source.  is there any place or book I can look how I can
> create  new reader ( servermanager.sources.MyReader())?

Consult the following link to learn how to make a plugin reader. Once
compiled -- assuming you already have PYTHON enabled in your paraview
build -- your own reader will automatically be active as
servermanager.sources.MyReader

http://paraview.org/Wiki/Plugin_HowTo

Running pvpython for example, you may type the command
servermanager.LoadPlugin("/path/to/your-plugin/libMyReader*.so") and
your plugin will be loaded.

Jean
Swiss National Supercomputing Centre
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