Re: [Paraview] Bug report: ParaView 4.1.0 crashes in 'Edit-Find Data' dialog on MultiBlockDataSet

2014-02-06 Thread richard.gre...@onera.fr

Hello,

I confirm the crash.

But before the crash, I have this warning message at step 3 when I apply 
Statistics-K Means:


Warning: In 
/home/utkarsh/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/ParaViewCore/VTKExtensions/Default/vtkSciVizStatistics.cxx, 
line 444


vtkPSciVizKMeans (0x48c0560): Either TrainingFraction (0.1) is high 
enough to include all observations after rounding or the minimum 
number of observations required for training is at least the size of 
the entire input. Any assessment will not be able to detect overfitting.




Tested with PV 4.1.0 Linux 64 bits

Richard


Hi,

There is a bug in ParaView 4.1.0 (Windows  Linux) that is bothering me,
and I haven't found a report for it yet in the mailing list or in the bug
tracker. So here it comes:

It seems that the 'Find Data' dialog doesn't work very well
vtkMultiBlockDataSets that are filled with vtkTables. Running the query
makes ParaView segfault.

To reproduce:
1) Open ParaView
2) Choose from the 'Sources' menu 'Sphere', and click Apply.
3) Choose from the 'Filters' menu 'Statistics-K Means', and click Apply
4) Choose from the Edit menu 'Find Data'
5) Choose the 'Statistical Model' as the source.
6) Click 'Run Selection Query'
After that it crashes. On Linux there is a segmentation fault. Windows will
report that 'paraview.exe' has stopped working.


By the way, here is another weird phenomenon: After step number 3, you see
three views: The sphere in 3D, a spreadsheet view of the 'Statistical
Model', and a spreadsheet view of the 'Assessed Data'. Notice that when you
click on a row in the view of the 'Assessed Data', the row is selected and
highlighted (with a blue background color), while if you click on a row in
the view of the 'Statistical Model' the highlight appears for a moment but
then disappears quickly again. Somehow this doesn't feel right.

kind regards,
Wijnand


--
 Richard GRENON
 ONERA
 Departement d'Aerodynamique Appliquee - DAAP/ACI
 8 rue des Vertugadins
 92190 MEUDON - FRANCE
 phone : +33 1 46 73 42 17
 fax   : +33 1 46 73 41 46
 mailto:richard.gre...@onera.fr
 http://www.onera.fr

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

2014-02-06 Thread 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] Bug report: ParaView 4.1.0 crashes in 'Edit-Find Data' dialog on MultiBlockDataSet

2014-02-06 Thread Utkarsh Ayachit
I suspect this is related to this issue that arose on the mailing list
a few days ago (http://paraview.org/Bug/view.php?id=14556).

Utkarsh

On Thu, Feb 6, 2014 at 3:31 AM, richard.gre...@onera.fr
richard.gre...@onera.fr wrote:
 Hello,

 I confirm the crash.

 But before the crash, I have this warning message at step 3 when I apply
 Statistics-K Means:

 Warning: In
 /home/utkarsh/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/ParaViewCore/VTKExtensions/Default/vtkSciVizStatistics.cxx,
 line 444

 vtkPSciVizKMeans (0x48c0560): Either TrainingFraction (0.1) is high enough
 to include all observations after rounding or the minimum number of
 observations required for training is at least the size of the entire input.
 Any assessment will not be able to detect overfitting.


 Tested with PV 4.1.0 Linux 64 bits

 Richard


 Hi,

 There is a bug in ParaView 4.1.0 (Windows  Linux) that is bothering me,
 and I haven't found a report for it yet in the mailing list or in the bug
 tracker. So here it comes:

 It seems that the 'Find Data' dialog doesn't work very well
 vtkMultiBlockDataSets that are filled with vtkTables. Running the query
 makes ParaView segfault.

 To reproduce:
 1) Open ParaView
 2) Choose from the 'Sources' menu 'Sphere', and click Apply.
 3) Choose from the 'Filters' menu 'Statistics-K Means', and click Apply
 4) Choose from the Edit menu 'Find Data'
 5) Choose the 'Statistical Model' as the source.
 6) Click 'Run Selection Query'
 After that it crashes. On Linux there is a segmentation fault. Windows will
 report that 'paraview.exe' has stopped working.


 By the way, here is another weird phenomenon: After step number 3, you see
 three views: The sphere in 3D, a spreadsheet view of the 'Statistical
 Model', and a spreadsheet view of the 'Assessed Data'. Notice that when you
 click on a row in the view of the 'Assessed Data', the row is selected and
 highlighted (with a blue background color), while if you click on a row in
 the view of the 'Statistical Model' the highlight appears for a moment but
 then disappears quickly again. Somehow this doesn't feel right.

 kind regards,
 Wijnand


 --
  Richard GRENON
  ONERA
  Departement d'Aerodynamique Appliquee - DAAP/ACI
  8 rue des Vertugadins
  92190 MEUDON - FRANCE
  phone : +33 1 46 73 42 17
  fax   : +33 1 46 73 41 46
  mailto:richard.gre...@onera.fr
  http://www.onera.fr


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Re: [Paraview] Revisiting aliasing effect

2014-02-06 Thread Lisa Avila
Hello Den,

This actually has nothing to do with NVIDIA antialiasing and probably
everything to do with the step size used on the mapper. Most likely the
issue is related to the automatic trade-off of quality to ensure
performance (depending on the mapper being used it will increase step size,
decrease the size of the generated image, and/or decrease the volume size
in order to meet the desired update rate). So either you are not seeing the
final image (which should fill in with better quality than the
interactive image) or for some reason the image is taking so long that the
mapper thinks that's the best it can do within its allocated time slice. Do
you see a change in image quality when you stop rotating? Are you having
performance issue while rotating?

Lisa


On Thu, Jan 30, 2014 at 2:45 AM, Den Fairol den.fai...@infovalley.net.mywrote:

 Hi,



 I'm a little confused regarding the inconsistent behavior of ParaView
 (v4.x), specifically the quality of its volume rendering representation.
 The Smart/GPU renderer for Windows version is slightly inferior to its
 RayCast renderer counterpart whereas for the Unix/Linux version, it is kind
 of like something you'd expect from a 'B' horror movie (see attachment for
 Smart/GPU-based rendered images). It is mentioned here:
 http://www.paraview.org/pipermail/paraview/2011-June/022062.html 
 http://www.paraview.org/pipermail/paraview/2010-June/017961.html that
 anti-aliasing (AA) is disabled by default. Then how could the Windows
 (Windows 7, NVIDIA Quadro 600 + driver v320.xx) version persist to appear
 so smooth despite setting NVIDIA's Control Panel AA handling to 'Off'?
 Conversely, changing the same option in Linux (Ubuntu 12.04, NVIDIA Quadro
 K5000 + driver v304.xx/v319.xx/v331.xx) to 'Override-application' adds
 nothing to the quality. As of now, RayCasting is may not be a viable
 solution since it induces substantial latency overhead.



 Regards,

 Den



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[Paraview] Class for animating camera view

2014-02-06 Thread Ganesh Vijayakumar
Dear All,

 Please find attached a class I created for animating camera views. It
takes a set of pvcc camera files generated using Paraview and spline
interpolates between them. I have an example case with a box source. Let me
know if this wiki worthy material.. and I'll put it there.

btw.. Thanks to all you guys who make Paraview so easy to use for
us...never thought I'll be submitting python scripts on a cluster to make
movies to analyse data for my Ph.D!

ganesh
import xml.etree.ElementTree as ET
from numpy import *
from scipy import interpolate

class animateParaviewCamera:
timeList = empty(0)
positionSplrep = []
viewUpSplrep = []
parallelScaleSplrep = 0
position = empty((2,3))
viewUp = empty((2,3))
parallelScale = empty(2)

def __init__(self,t, f):
self.timeList = t
fileNames = f
#self.timeList = arange(0.3,0.8,0.005)
#fileNames = ['camera1.pvcc','camera2.pvcc','camera3.pvcc','camera4.pvcc']
nPositions = len(fileNames)
interpTime = linspace(self.timeList[0],self.timeList[-1],nPositions)
print interpTime

self.position = empty((nPositions,3))
self.viewUp = empty((nPositions,3))
self.parallelScale = empty(nPositions)

for i in range(nPositions):
tree = ET.parse(fileNames[i])
root = tree.getroot()
for child in root[0]:
if child.attrib['name'] == 'CameraPosition':
for subChild in child:
self.position[i,int(subChild.attrib['index'])] = float(subChild.attrib['value'])
if child.attrib['name'] == 'CameraViewUp':
for subChild in child:
self.viewUp[i,int(subChild.attrib['index'])] = float(subChild.attrib['value'])
if child.attrib['name'] == 'CameraParallelScale':
self.parallelScale[i] = float(child[0].attrib['value'])

print self.position

for i in range(3):
self.positionSplrep.append(interpolate.splrep(interpTime, self.position[:,i],k=1))
self.viewUpSplrep.append(interpolate.splrep(interpTime, self.viewUp[:,i],k=1))
self.parallelScaleSplrep = interpolate.splrep(interpTime, self.parallelScale)


def cameraPosition(self,t):
if(t  self.timeList[0]):
return self.position[0].tolist()
elif(t  self.timeList[-1]):
return [interpolate.splev(t,self.positionSplrep[0]), interpolate.splev(t,self.positionSplrep[1]), interpolate.splev(t,self.positionSplrep[2])]
else:
return self.position[-1].tolist()

def cameraViewUp(self,t):
if(t  self.timeList[0]):
return self.viewUp[0].tolist()
elif(t  self.timeList[-1]):
return [interpolate.splev(t,self.viewUpSplrep[0]), interpolate.splev(t,self.viewUpSplrep[1]), interpolate.splev(t,self.viewUpSplrep[2])]
else:
return self.viewUp[-1].tolist()

def cameraParallelScale(self,t):
if(t  self.timeList[0]):
return self.parallelScale[0]
elif(t  self.timeList[-1]):
return interpolate.splev(t,self.parallelScaleSplrep)
else:
return self.parallelScale[0]

if __name__ == __main__:
timeList = arange(0.3,0.8,0.005)
fileNames = ['camera1.pvcc','camera2.pvcc','camera3.pvcc','camera4.pvcc']
a = animateParaviewCamera(array([0.4,0.6]),fileNames)
for i in range(size(timeList)):
print a.cameraPosition(timeList[i])

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[Paraview] Two Machines - Each one with one monitor - Mirrored and different angles of the same data

2014-02-06 Thread Léo Pessanha
Hi,

Working with | Windows 7 - 64bit  | in both machines


I am a paraview user, i work with oil leak data

My next task is to do the following:

I have two machines and each one controls a monitor.

The monitors are disposed in a way that a L shape is created(one is in the
floor)

I want to see the same thing in both machines but i want to be able to
change the angle like on cave.pvx parameters

LowerLeft=-1 -1 -2
LowerRight=1 -1 -2
UpperRight=1  1 -2

but in different machines.

The angle that i wanna change is the inicial one.  Something like in the
front monitor i am looking the data from the front and in the other monitor
i am looking the data from the top

How am i supposed to do that?

The things that i already know how to do:

Having ONLY ONE machine with 2 monitors changing the angles of each monitor
on a .pvx file

Connect to a server and have the front view for everyone with a master
controlling the angles for everyone or each one controlling the own angle

If it gets hard to explain i can try to explain better

Sorry for the bad english

Att,
Leonardo Pessanha
Rio de Janeiro, Brazil
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[Paraview] qsqlquery compilation error

2014-02-06 Thread mathieu . westphal
Hello

I'm trying to compile a fresh version of paraview with the following setup

module load gnu-devel/4.4.6
module load cmake/2.8.11.2_gcc-4.4.6
module load qt/4.8.3_gcc-4.4.6
module load python/2.7.5_gcc-4.4.6

export CFLAGS= -pthread $CFLAGS
export CXXFLAGS=$CFLAGS
export LDFLAGS= -lpthread $LDFLAGS

cmake
-DCMAKE_INSTALL_PREFIX:PATH=/applis/site/stow/gcc_4.4.6/paraview_git
-DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=ON -DBUILD_TESTING:BOOL=OFF
-DPARAVIEW_BUILD_QT_GUI:BOOL=ON -Wno-dev ../../ParaView

make
[ 93%] Compiling Qt help project EyeDomeLightingView.qhp
Building up file structure...
QSqlQuery::value: not positioned on a valid record
Cannot register namespace EyeDomeLightingView.org!
make[2]: ***
[Plugins/EyeDomeLighting/ParaViewPlugin/doc/EyeDomeLightingView.qch]
Error 255
make[1]: ***

[Plugins/EyeDomeLighting/ParaViewPlugin/CMakeFiles/EyeDomeLightingView.dir/all]
Error 2
make: *** [all] Error 2



Any idea ?

Thanks

Mathieu

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Re: [Paraview] Generate Programmable Sources with Timesteps

2014-02-06 Thread Magician
Hi Utkarsh,


Great! Almost the code works.

Maybe the last variable 'req_timesteps[0]' is wrong, isn't it?
My code is working with 'req_time'.


Then I have one question.
What does the function SetOutputTimesteps() of RequestInformation means?
I tested to remove the block, but the source still works as before.


Magician


On Feb 5, 2014, at 5:19, Utkarsh Ayachit utkarsh.ayac...@kitware.com wrote:

 Magician,
 
 I've updated the Wiki. The API has changed since ParaView 4.0. It's no
 longer DATA_TIME_STEPS/UPDATE_TIME_STEPS, it has been replaced by
 DATA_TIME_STEP/UPDATE_TIME_STEP.
 
 Utkarsh
 
 On Thu, Nov 28, 2013 at 4:59 PM, Magician f_magic...@mac.com wrote:
 Any ideas?
 
 I'd like to generate moving object with the Programmable Source,
 but there are not enough informations on the Web to do it.
 
 
 Magician
 
 
 Begin forwarded message:
 
 From: Magician f_magic...@mac.com
 Subject: Generate Programmable Sources with Timesteps
 Date: November 27, 2013 at 6:50:54 GMT+9
 To: ParaView paraview@paraview.org
 
 Hi all,
 
 
 I'm trying to generate programmable sources with timesteps.
 The URL may describe how to do them:
 http://www.paraview.org/Wiki/Here_are_some_more_examples_of_simple_ParaView_3_python_filters.#Producing_Data_with_Timesteps_.28Source.29
 
 But when I try the code, I got an error as below:
 Traceback (most recent call last):
 File string, line 19, in module
 File string, line 14, in RequestData
 File string, line 5, in GetUpdateTimesteps
 AttributeError: UPDATE_TIME_STEPS
 
 I have Mac OS 10.9 and ParaView 4.0.1.
 The attached pvsm file is what I coded. # just copied the sample code
 
 How can I run it exactly?
 
 
 Magician
 
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Re: [Paraview] Get Values of CSV sources with Programmable Filter

2014-02-06 Thread Magician
Hi Berk,


Thanks for your reply.

Hmmm...
My purpose is extracting CSVs to vtkImageData with the Programmable Filter.
And the CSVs don't have headers, so it's not so good idea for me to get values 
per columns.
If possible, I want to get the values as 2D numpy.array directly as 
numpy.loadtxt().


Magician


On Feb 6, 2014, at 0:03, Berk Geveci berk.gev...@kitware.com wrote:

 If one of the inputs to the programmable filter is a table, you can
 values (columns) from it with something like:
 
 inputs[0].RowData['array_name']
 
 This will give a (n,1) numpy array where n == number of rows.
 
 Best,
 -berk
 
 On Wed, Feb 5, 2014 at 9:29 AM, Magician f_magic...@mac.com wrote:
 Hi Utkarsh,
 
 
 I already checked it, but there are no information about getting all values
 of VTKTable with NumPy.
 Now I'm using for-loops and the GetValue(i, j) function, but it's not smart.
 Do you have any other information?
 
 
 Magician
 
 
 On Feb 5, 2014, at 4:05, Utkarsh Ayachit utkarsh.ayac...@kitware.com wrote:
 
 Here's some text that describes how to go back and forth between NumPy
 and VTK arrays 
 :http://www.paraview.org/Wiki/ParaView/Users_Guide/Python_Programmable_Filter#Mixing_VTK_and_NumPy_APIs
 
 Utkarsh
 
 On Fri, Jan 31, 2014 at 10:30 PM, Magician f_magic...@mac.com wrote:
 Hi all,
 
 
 I'm using PV 4.1.0 and trying to get values of CSV sources with 
 Programmable Filter.
 It's better to get them as numpy.array.
 How can I code it?
 
 
 Magician
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Re: [Paraview] Generate Programmable Sources with Timesteps

2014-02-06 Thread Utkarsh Ayachit
 Maybe the last variable 'req_timesteps[0]' is wrong, isn't it?
 My code is working with 'req_time'.

That's correct. I fixed it the Wiki.

 Then I have one question.
 What does the function SetOutputTimesteps() of RequestInformation means?
 I tested to remove the block, but the source still works as before.


SetOutputTimesteps tells the pipeline what timesteps this source
produces. VTK will not call RequestData() on a filter when time value
requested changes unless the filter said it was time-dependent.

Utkarsh
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Re: [Paraview] [EXTERNAL] Segmentation fault; core dumped

2014-02-06 Thread Scott, W Alan
Paul,
Please keep this dialog on the paraview list.

I am sorry, I don't know what is going.  Maybe someone else on the list does.

Alan

From: Paul, Immanuvel [mailto:p.immanu...@imperial.ac.uk]
Sent: Thursday, February 06, 2014 7:39 AM
To: Scott, W Alan
Subject: RE: [EXTERNAL] [Paraview] Segmentation fault; core dumped

Hi Alan,

Thank you so much for your kind response.

If I start Paraview from root, I get this warning while Paraview is starting. 
Could this be a problem?

The warning I get in my terminal is below:
(process:3218): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Did not receive a reply. Possible causes include: the remote application did 
not send a reply, the message bus security policy blocked the reply, the reply 
timeout expired, or the network connection was broken.
Qt: Session management error: None of the authentication protocols specified 
are supported

Could you please help me in this regard?

Looking forward to your response.

Thanks.

Best Regards,
Immanuvel Paul.

From: Scott, W Alan [wasc...@sandia.gov]
Sent: 05 February 2014 17:14
To: Paul, Immanuvel
Subject: RE: [EXTERNAL] [Paraview] Segmentation fault; core dumped
Sorry Paul - I don't know.  the only other thing that I can think of is that 
you have a bad video driver.  Did your Linux machine do an update?  Can you try 
on another Linux machine?

Alan

From: Paul, Immanuvel [mailto:p.immanu...@imperial.ac.uk]
Sent: Wednesday, February 05, 2014 6:34 AM
To: Scott, W Alan
Subject: RE: [EXTERNAL] [Paraview] Segmentation fault; core dumped

Hi Alan,

When I run Paraview, I get these initial warnings in my screen, which 
eventually leads to crashing of the program.

QVariantMap DBusMenuExporterDBus::getProperties(int, const QStringList) const: 
Condition failed: action
QVariantMap DBusMenuExporterDBus::getProperties(int, const QStringList) const: 
Condition failed: action
QVariantMap DBusMenuExporterDBus::getProperties(int, const QStringList) const: 
Condition failed: action
QVariantMap DBusMenuExporterDBus::getProperties(int, const QStringList) const: 
Condition failed: action
Segmentation fault (core dumped)

However, if I start paraview without specifying any input file, it doesn't show 
these.

Can you help me?

Looking forward to your response.

Thanks.

Best Regards,
Immanuvel Paul.

From: Scott, W Alan [wasc...@sandia.gov]
Sent: 04 February 2014 17:26
To: Paul, Immanuvel; paraview@paraview.orgmailto:paraview@paraview.org
Subject: RE: [EXTERNAL] [Paraview] Segmentation fault; core dumped
Paul,

Try removing the state configuration files.  I have seen this happen when they 
become corrupt.  These file's locations are documented here: 
http://www.paraview.org/Wiki/ParaView_Settings_Files.  Just delete all of these 
files - ParaView will automatically generate new ones.

Alan

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Paul, 
Immanuvel
Sent: Tuesday, February 04, 2014 4:51 AM
To: paraview@paraview.orgmailto:paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Segmentation fault; core dumped

Hi,

I am new to paraview.. I have VTK6.0 in my Linux machine.

Paraview was working well till yesterday. Even I have used 'plot over a line' 
option many times earlier. But, when I tried to plot over a line yesterday, it 
crashed. The error showed in my terminal was : Segmentation Fault, Core dumped. 
The problem continues to exist. Could you please help me?


Best Regards,
Immanuvel Paul.
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