[Paraview] python programmable source not parallel?
I have a python programmable source which mimics an already working C++ Reader. The Reader works in parallel and correctly gets the Update Extent assigning to each proc, a different sub-region of the whole. The Python prog. source works fine in serial mode. When run in parallel, *all* procs receive the same Update Extent equal to the Whole Extent, as if the Extent Translator ignores the parallelism. I get the following printed for the Update Extent: Process id: 0 (0, 63, 0, 31, 0, 24) Process id: 3 (0, 63, 0, 31, 0, 24) Process id: 2 (0, 63, 0, 31, 0, 24) Process id: 1 (0, 63, 0, 31, 0, 24) Have other been successful with Programmable Source running in parallel? My script is atached. Jean -- Swiss National Supercomputing Center ps = servermanager.sources.ProgrammableSource() ps.OutputDataSetType = 3 str1 = rg = self.GetRectilinearGridOutput()\ndims = [64, 32, 25]\nrg.SetWholeExtent(0, dims[0]-1, 0, dims[1]-1, 0, dims[2]-1) str2 = rg = self.GetRectilinearGridOutput()\nexts = rg.GetUpdateExtent()\nwhole = rg.GetWholeExtent()\ndims = [exts[1]-exts[0]+1, exts[3]-exts[2]+1, exts[5]-exts[4]+1]\nrg.SetExtent(exts)\nprint exts\nimport math\nphi = [0]\ntheta = [0]\nR = [.53]\nfor i in range(1,whole[1]+1):\n phi.append(i*2*math.pi/(whole[1]-1))\nfor i in range(1,whole[3]+1):\n theta.append(i*math.pi/(whole[3]-1))\nfor i in range(1,whole[5]+1):\n R.append(.53+i*(1.53-0.53)/(whole[5]-1))\nVTKphi = vtk.vtkFloatArray()\nVTKphi.SetNumberOfTuples(dims[0])\nVTKtheta = vtk.vtkFloatArray()\nVTKtheta.SetNumberOfTuples(dims[1])\nVTKR = vtk.vtkFloatArray()\nVTKR.SetNumberOfTuples(dims[2])\nfor i in range(exts[0], exts[1]+1):\n VTKphi.SetValue(i, phi[i])\nfor j in range(exts[2], exts[3]+1):\n VTKtheta.SetValue(j, theta[j])\nfor k in range(exts[4], exts[5]+1):\n VTKR.SetValue(k, R[k])\nrg.SetXCoordinates(VTKphi)\nrg.SetYCoordinates(VTKtheta)\nrg.SetZCoordinates(VTKR) ps.InformationScript = str1 ps.Script = str2 ps.UpdatePipeline() view = servermanager.GetRenderView() rep = servermanager.CreateRepresentation(ps, view) view.ResetCamera() view.StillRender() servermanager.ProxyManager().RegisterProxy(sources, mysource, ps) servermanager.ProxyManager().RegisterProxy(representations, mysource, rep) ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] particletracer
Martin I don't really know what to say. I tried myself using our installed version of ParaView 3.4 (linux) to 1) load a time dependent dataset 2) Add a temporal cache 3) Create a line source 4) Instantiate the ParticleTracer (don't use the Pathline filter - that is used to generate trails from particles that you create with the particle tracer). I got the input selection dialog box and all seemed normal. I do not use a Mac so I just don't know what could be wrong, but it seems unlikely that the mac version could work normally the rest of the time and only have this one dialog missing. Can you try another machine/platform. JB Hi again, thank you for fast answer John! I'm aware of the problem that my particle tracer doesnt have any seed source, but I have been working for quite awhile sloving this problem. I did as you said, created temporalcache and seed (point seed) but I cant connect the 2 with my particle tracer. I found your (John's) great powerpoint presentation on the web explaining everything there is to explain. Though I cant make it work!!! In one of the pictures in the presentation there are some boxes where you can choose which sources to use in the particle tracer (in object inspector - properties - source). I dont have that option in my program. Does someone know why (using v3.4.0 on a Mac)? About v3.4.0, isnt it the lastest version? Cant fint anything newer on paraview.org. Cheers, Martin Uppman Martin ERROR: In /Users/kitware/Berk/ParaView3/VTK/Filtering/vtkDemandDrivenPipeline.cxx, line 722 vtkCompositeDataPipeline (0x217c7fb0): Input port 1 of algorithm vtkTemporalStreamTracer(0x1e345e00) has 0 connections but is not optional. Input 0 should be a time dependent dataset. It is best to use a TemporalCache before the particle tracer to stop multiple updates for the same time step. Input 1 should be some seed points. Ensight - TemporalCache - ParticleTracer Some Other data eg.line/plane - the ignore pipeline time option is provided to get around some animation issues that used to plague paraview. You should not need it, but the correct way to use it, is set IgnorePipelineTime to true, then set an animation keyframe to animate TimeStep from 0-N - the particle tracer will then use the timestep to generate update times for the Ensight input, instead of usigin the GUI generated time. If you are using the particle tracer from prior to 3.4 then you should switch to a newer one as it is contiunually being improved. I will soon (months, not days) be checking in a lot of changes which enable it to handle dynamic meshes better. JB I've been looking for information on this and a found a thread which I think concerns the same problem. In that thread Berk made a patch to fix this problem. I also tried to ignore pipeline time, but this doent work. I'm working with .case files and I want to animate the blood flow in a human heart using particle tracers. I'm using a Mac with ParaView version 3.4.0. Thanks for looking into this. Cheers, Martin Uppman ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview -- John Biddiscombe,email:biddisco @ cscs.ch http://www.cscs.ch/ CSCS, Swiss National Supercomputing Centre | Tel: +41 (91) 610.82.07 Via Cantonale, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 -- John Biddiscombe,email:biddisco @ cscs.ch http://www.cscs.ch/ CSCS, Swiss National Supercomputing Centre | Tel: +41 (91) 610.82.07 Via Cantonale, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Set directory name on the reader
Hi, This is weird. I followed the same post as you, and it works for me, in the stable 3.4 and in the CVS 3.5 (nightly). As the vtkDICOMImageReader does not make use of DICOMDIR, but only dcm type files, are you this is not a problem in your dcm files? I think that they have to contains the information of slice indices. If they don't, the reader 'think' that there is only one file in the list... I will check your xml on my system. You didn't mention the CMake file: what about? regards, Jerome 2009/2/10 Biao She sheb...@gmail.com: Hi Utkarsh. I read your post at http://markmail.org/message/iswwagv2ejsybjhy#query:paraview%20dicom+page:2+mid:6ex4hkecehwma6t2+state:results I am currently trying to integrate a DICOM reader to Paraview. The first problem I met is how to pass a directory name to a paraview reader. You mentioned that I just committed a feature to CVS where if the UseDirectoryName / hint is present on the filename property, the directory name will be used instead of the file name in your post. I am wondering if this feature is avaliable in the latest stable verison of Paraview (3.4.0). I tried the XML code you provided in the latest stable version. It doesn't work for me. The vtkDICOMReader still only read one DICOM file. Here is my server side XML files: ServerManagerConfiguration ProxyGroup name=sources SourceProxy name=DICOMReader class=vtkDICOMImageReader label=DICOM reader Documentation short_help=Read DICOM files. long_help=Read DICOM files. The DICOM reader reads DICOM files. /Documentation StringVectorProperty name=Directory command=SetDirectory number_of_elements=1 FileListDomain name=files/ Hints UseDirectoryName / /Hints /StringVectorProperty !-- End PNGReader -- /SourceProxy /ProxyGroup /ServerManagerConfiguration Maybe I did thing in a wrong way? Thanks very much for your help! Aaron ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] python programmable source not parallel?
This is a feature rather than a bug. The programmable source sets the extent translator to be a vtkOnePieceExtentTranslator. To override this behavior, add the following to your RequestInformations script: from paraview import util self.GetExecutive().SetExtentTranslator(self.GetExecutive().GetOutputInformation(0), vtk.vtkExtentTranslator()) -berk On Tue, Feb 10, 2009 at 5:54 AM, Jean Favre jfa...@cscs.ch wrote: I have a python programmable source which mimics an already working C++ Reader. The Reader works in parallel and correctly gets the Update Extent assigning to each proc, a different sub-region of the whole. The Python prog. source works fine in serial mode. When run in parallel, *all* procs receive the same Update Extent equal to the Whole Extent, as if the Extent Translator ignores the parallelism. I get the following printed for the Update Extent: Process id: 0 (0, 63, 0, 31, 0, 24) Process id: 3 (0, 63, 0, 31, 0, 24) Process id: 2 (0, 63, 0, 31, 0, 24) Process id: 1 (0, 63, 0, 31, 0, 24) Have other been successful with Programmable Source running in parallel? My script is atached. Jean -- Swiss National Supercomputing Center ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] python programmable source not parallel?
Berk Geveci wrote: This is a feature rather than a bug. The programmable source sets the extent translator to be a vtkOnePieceExtentTranslator. To override this behavior, add the following to your RequestInformations script: The thought never crossed my mind this could be a bug, but it sure defied my understanding of parallelism. Made me doubt for a while. As per the motivation of the ParaView developpers to do that, besides providing an exercise for the more adventurous folks? N.B. I added the code in my Update Script, not in the RequestInformation Script as suggested, because it would cause the server to crash. (PV 3.4.0) Thanks for the tip. Jean ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] [ParaView3-Developer] Locking (MPI?) problems with ParaView 3.5
John, Here's my understanding of what may be happening: * pvclient has done a gather data information and is waiting to receive that data * pvserver0 has received this gather data request is asking all satellites to gather data * pvserver1 also received that gather data request but before is starts processing it, pv1 needs to pass on the message to it's child i.e process 3 (this is the fancy tree based message communication that we are now using. So now, instead of the root node sending the message to all processes one after the other, it uses a tree structure). * pvserver2 I believe is happily waiting for the next message. It already processed the gather data request, sent the response to the root (although root has not processed that response yet) and now is waiting for the next request. * pvserver3 is the rogue. It's stuck in Cancel, hence it won't receive any messages other send to it. This cancel was not done as a part of this gather data request but was done at the end of some previous request. Thus it's not yet able to receive the gather data request pvserver1 is trying to send, consequently freezing pvserver1. Of course, this is just one possible explanation. I've attached a patch. Can you please test if this overcomes the issue. If not, you may also want to try by connecting the Cancel out all together. That will at the least help us narrow down the problem. Utkarsh On Tue, Feb 10, 2009 at 2:56 AM, John Biddiscombe biddi...@cscs.ch wrote: I've been having problems with paraview 3.5 (CVS) since I started working on a parallel problem last week (which means it may have existed for some time, but I was doing other things). How to reproduce the problem Start pvserver on 4 (or more) nodes and pvclient on 1 Create Sources/wavelet ParaView hangs indefinitley without showing bounding box of cube. Reproducibility : not always (3 out of 4 times - for me). Sometimes paraview completes as usual, but shows other hanging symptoms later on. ParaView 3.4 does not have this problem. Something seems to have changed between 3.4 and 3.5 which is affecting the client server delivery of data. It appears to be an MPI related issue. I have attached the debugger to all pvserver nodes and the stack traces are shown below To summarize : pvserver 3 : Cancelled a request pvserver 2 : waiting in ReceiveDataInternal pvserver 1 : still in vtkMPICommunicatorSendDatachar pvserver 0 : still in vtkMPICommunicatorSendDatachar pvclient : trying to Receive It seems that one of the pvserver nodes has given up sending, or has nothing to send and the others are waiting without end. Notes 1: It took me time to go from one node to the other and attach gdb, so if I stopped one task - another might have been affected before it had its stack trace dumped. I'm not very expert at gdb. Notes 2: ParaView 3.4 seems to work flawlessly. Something is different in 3.5 Notes 3: I ran the b_eff_io ( https://fs.hlrs.de/projects/par/mpi//b_eff_io/ - NB. link unreliable) on 15 nodes and it completed without error and without any unusual behaviuor, so my instinct is that our hpmpi is working ok. Questions : 1) Has anyone else observed this behaviour? 2) Has anyone changed anything in the mpi-commmunicator code which might have caused this behaviour 3) It's possible we have a network problem and this is causing the locking, but our logs do not show any errors - can we rule this out? 4) If anyone has answered yes to 1/2, do they know what's wrong and can they fix it? I welcome help as this is preventing me finishing my current project. JB Stack trace for pvserver 3 == #0 0x003dbd4afba9 in sched_yield () from /lib64/tls/libc.so.6 #1 0x002a9a725a97 in hpmp_yield () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #2 0x002a9a71f3b4 in hpmp_adv () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #3 0x002a9a757012 in hpmp_waitany () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #4 0x002a9a756cf0 in VMPI_Waitany () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #5 0x002a9a753a9e in VMPI_Wait () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #6 0x002a9a754520 in VMPI_Cancel () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #7 0x002a99e27045 in vtkMPICommunicator::Request::Cancel (this=0xacf740) at /users/biddisco/code/pv-meshless/VTK/Parallel/vtkMPICommunicator.cxx:973 #8 0x002a95639e36 in vtkPVProgressHandler::CleanupSatellites (this=0xae8dd0) at /users/biddisco/code/pv-meshless/Servers/Common/vtkPVProgressHandler.cxx:399 #9 0x002a95639c85 in vtkPVProgressHandler::CleanupPendingProgress (this=0xae8dd0) at /users/biddisco/code/pv-meshless/Servers/Common/vtkPVProgressHandler.cxx:337 #10 0x002a956061ce in vtkProcessModule::CleanupPendingProgress (this=0x590ee0) at /users/biddisco/code/pv-meshless/Servers/Common/vtkProcessModule.cxx:1267 #11 0x002a965b22f7 in vtkProcessModuleCommand (arlu=0x591d20, ob=0x590ee0,
Re: [Paraview] DICOM series reader for Paraview
Hi,
I use 3 files for the vtkDICOMImageReader plugin :
- One CMakeList.txt where you can find those lines:
# READERS PLUGIN --
# Use the ADD_PARAVIEW_PLUGIN macro to build a plugin
ADD_PARAVIEW_PLUGIN(
DICOMImageReader #--Name for the plugin
1.0#--Version string
SERVER_MANAGER_XML DICOMReader.xml #-- server manager xml
GUI_RESOURCE_FILES DICOMReaderGUI.xml
)
#--
You can also use this file for other ADD_PARAVIEW_PLUGIN command
- One DICOMReaderGUI.xml
- One DICOMReader.xml
Both latter are given.
Regarding the GDCMReader, I am sorry I could not help you. As I said,
I had never tried this lib in a Paraview framework. The best you can
do - well, the laziest in fact - is to ask the GDCM development team
to give a built-in paraview plugin.
Today, the vtkDICOMImageReader is sufficient for me, and what I give
here makes it works in ParaView 3.4 stable and nightly CVS 3.5, both
Windows (XP and Vista) and Linux (Fedora 9). This is true when the
plugin is loaded on the computer that built Paraview. Other problems
arise when deploying on 'pure-of-devel-stuff' systems.
I hope this will help.
Best regards,
Jerome
2009/2/9 Biao She sheb...@gmail.com:
Thanks for your help, Jerome.
I find the vtkGdcmReader files in the latest GDCM package. After I build
these files as a Paraview Plug-in and load it, I got this error message from
Paraview console:
ERROR: In
/usr/scratch/bshe/Paraview/ParaView-3.4.0/Servers/Common/vtkProcessModule.cxx,
line 1079
vtkProcessModule (0x8a7c2e0): Cannot create object of type vtkGdcmReader.
while processing
Message 0 = New
Argument 0 = string_value {vtkGdcmReader}
Argument 1 = id_value {84}
ERROR: In
/usr/scratch/bshe/Paraview/ParaView-3.4.0/Servers/Common/vtkProcessModule.cxx,
line 1080
vtkProcessModule (0x8a7c2e0): Aborting execution for debugging purposes.
I must do something wrong, but when I build the vtkGdcmReader, no error
message at all. Here is my CMakeLists file:
FIND_PACKAGE(ParaView REQUIRED)
INCLUDE(${PARAVIEW_USE_FILE})
FIND_PACKAGE (GDCM)
IF (GDCM_FOUND)
INCLUDE(${GDCM_USE_FILE})
ENDIF (GDCM_FOUND)
ADD_PARAVIEW_PLUGIN(vtkGDCMReader 1.0 SERVER_MANAGER_SOURCES
vtkGdcmReader.cxx)
ADD_PARAVIEW_PLUGIN(vtkGDCMReader 1.0 GUI_RESOURCE_FILES pqReader.xml)
ADD_PARAVIEW_PLUGIN(vtkGDCMReader 1.0 SERVER_MANAGER_XML reader.xml)
You also mentioned that you use vtkDICOMImageReader as your DICOM reader in
Paraview. It seems that I can only use the reader to read one DICOM image
file. How can I write the XML files for vtkDICOMImageReader to read a series
of DICOM files? Could you please email me your XML files for
vtkDICOMImageReader if possible? Thanks very much!
Aaron
On Fri, Feb 6, 2009 at 12:52 AM, Jérôme jerome.ve...@gmail.com wrote:
Hi,
if you intend to use a DICOM reader in Paraview, why not using
directly GDCM, instead of ITK? It contains a VTK Reader... If I am
right, you will just have to write the XML/CMake files that make the
reader available in Paraview.
In my case, I use the vtkDICOMImageReader, that is a very simple dcm
file series reader: just give the folder containing the files, and let
it read. If you need more functionalities, the GDCM reader will do the
trick.
You can find a later version of GDCM than the ITK integrated one, on
this website: http://www.creatis.insa-lyon.fr/Public/Gdcm/ . I cannot
help you more, as I had never use it for now.
Cheers,
Jerome
2009/2/6 Biao She sheb...@gmail.com:
Hi everyone.
I am wondering if anyone know how to integrate a ITK(GDCM) based DICOM
reader to Paraview?
My basic idea is:
1. Read DICOM series data through ITK(GDCM)
2. Export the data to a vtkImageImport class
3. Use the data in vtkImageImport as a source of Paraview
I have done the first two steps. But I am not sure how to do the third
one.
I have read something about how to write a Paraview Reader in the
Paraview
book. It is said that all the readers must derive from vtkAlgorithm or
one
of its subclass. Fortunately, vtkImageImport is one of its subclass. So,
I
guess it would be a good idea to choose vtkImageImport as a superclass
of my
reader. Am I right?
If I choose vtkImageImport as a superclass, to make my reader works
properly, which methods should be implemented in my reader?
The last question is: How do I read the path to DICOM files from
Paraview
Client GUI and pass it to my reader? For example, the DICOM data is
stored
in /usr/DATA/ directory, how can I pass this value to my reader?
Thanks very much for your help!
Aaron
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ServerManagerConfiguration
ProxyGroup name=sources
!--
Re: [Paraview] [ParaView3-Developer] Locking (MPI?) problems with ParaView 3.5
Sweet. I've committed the patch to CVS. On Tue, Feb 10, 2009 at 10:45 AM, John Biddiscombe biddi...@cscs.ch wrote: Utkarsh Looks good. 10 out of 10 successes with the patch applied (using 5 to 10 pvserver nodes) - I'll try with more later when the rest of the machine is free. Thanks yet again for your help. If the problem comes back in another flavour I'll be sure to let you know. JB John, Here's my understanding of what may be happening: * pvclient has done a gather data information and is waiting to receive that data * pvserver0 has received this gather data request is asking all satellites to gather data * pvserver1 also received that gather data request but before is starts processing it, pv1 needs to pass on the message to it's child i.e process 3 (this is the fancy tree based message communication that we are now using. So now, instead of the root node sending the message to all processes one after the other, it uses a tree structure). * pvserver2 I believe is happily waiting for the next message. It already processed the gather data request, sent the response to the root (although root has not processed that response yet) and now is waiting for the next request. * pvserver3 is the rogue. It's stuck in Cancel, hence it won't receive any messages other send to it. This cancel was not done as a part of this gather data request but was done at the end of some previous request. Thus it's not yet able to receive the gather data request pvserver1 is trying to send, consequently freezing pvserver1. Of course, this is just one possible explanation. I've attached a patch. Can you please test if this overcomes the issue. If not, you may also want to try by connecting the Cancel out all together. That will at the least help us narrow down the problem. Utkarsh On Tue, Feb 10, 2009 at 2:56 AM, John Biddiscombe biddi...@cscs.ch wrote: I've been having problems with paraview 3.5 (CVS) since I started working on a parallel problem last week (which means it may have existed for some time, but I was doing other things). How to reproduce the problem Start pvserver on 4 (or more) nodes and pvclient on 1 Create Sources/wavelet ParaView hangs indefinitley without showing bounding box of cube. Reproducibility : not always (3 out of 4 times - for me). Sometimes paraview completes as usual, but shows other hanging symptoms later on. ParaView 3.4 does not have this problem. Something seems to have changed between 3.4 and 3.5 which is affecting the client server delivery of data. It appears to be an MPI related issue. I have attached the debugger to all pvserver nodes and the stack traces are shown below To summarize : pvserver 3 : Cancelled a request pvserver 2 : waiting in ReceiveDataInternal pvserver 1 : still in vtkMPICommunicatorSendDatachar pvserver 0 : still in vtkMPICommunicatorSendDatachar pvclient : trying to Receive It seems that one of the pvserver nodes has given up sending, or has nothing to send and the others are waiting without end. Notes 1: It took me time to go from one node to the other and attach gdb, so if I stopped one task - another might have been affected before it had its stack trace dumped. I'm not very expert at gdb. Notes 2: ParaView 3.4 seems to work flawlessly. Something is different in 3.5 Notes 3: I ran the b_eff_io ( https://fs.hlrs.de/projects/par/mpi//b_eff_io/ - NB. link unreliable) on 15 nodes and it completed without error and without any unusual behaviuor, so my instinct is that our hpmpi is working ok. Questions : 1) Has anyone else observed this behaviour? 2) Has anyone changed anything in the mpi-commmunicator code which might have caused this behaviour 3) It's possible we have a network problem and this is causing the locking, but our logs do not show any errors - can we rule this out? 4) If anyone has answered yes to 1/2, do they know what's wrong and can they fix it? I welcome help as this is preventing me finishing my current project. JB Stack trace for pvserver 3 == #0 0x003dbd4afba9 in sched_yield () from /lib64/tls/libc.so.6 #1 0x002a9a725a97 in hpmp_yield () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #2 0x002a9a71f3b4 in hpmp_adv () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #3 0x002a9a757012 in hpmp_waitany () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #4 0x002a9a756cf0 in VMPI_Waitany () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #5 0x002a9a753a9e in VMPI_Wait () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #6 0x002a9a754520 in VMPI_Cancel () from /opt/hpmpi/lib/linux_amd64/libmpi.so.1 #7 0x002a99e27045 in vtkMPICommunicator::Request::Cancel (this=0xacf740) at /users/biddisco/code/pv-meshless/VTK/Parallel/vtkMPICommunicator.cxx:973 #8 0x002a95639e36 in vtkPVProgressHandler::CleanupSatellites (this=0xae8dd0) at
Re: [Paraview] python programmable source not parallel?
As per the motivation of the ParaView developpers to do that, besides providing an exercise for the more adventurous folks? This was left from the days when charts expected rectilinear grid input. Consider the case where you are applying a programmable filter to an unstructured grid which computed a histogram. In that case, you don't want to produce a portion of the output in each process but rather produce the whole output and accumulate the result somehow. Since we now use tables for charts, that can probably go away. I will think a bit more before I remove it. -berk On Tue, Feb 10, 2009 at 9:31 AM, Jean Favre jfa...@cscs.ch wrote: Berk Geveci wrote: This is a feature rather than a bug. The programmable source sets the extent translator to be a vtkOnePieceExtentTranslator. To override this behavior, add the following to your RequestInformations script: The thought never crossed my mind this could be a bug, but it sure defied my understanding of parallelism. Made me doubt for a while. As per the motivation of the ParaView developpers to do that, besides providing an exercise for the more adventurous folks? N.B. I added the code in my Update Script, not in the RequestInformation Script as suggested, because it would cause the server to crash. (PV 3.4.0) Thanks for the tip. Jean ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] compiling without VTK
Is there anyway to build paraview using an existing VTK installation instead of having to have another copy of VTK inside paraview? -- Thanks, David ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] compiling without VTK
David Is there anyway to build paraview using an existing VTK installation instead of having to have another copy of VTK inside paraview? Possible to do, but your life is too short to make it worthwhile. Instead, Build paraview as per usual, and stop using vtk on its own! Simply point your projects to /my/path/to/paraview/build/VTK and they will pick up the VTK config from there. JB ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Visualizing histogram
John, Thanks a lot for your help. I have re-used part of your code to create a Multi-block to table filter. (Basically exactly the same as your probeIntegration but without the integration step). The problem I have now is in creating a histogram which has the Block Id (String - first column of data in my vtkTable) on the x axis and the data on the y axis. It seems that the histogram plotting capability in ParaView can not handle String Ids instead of numbers. - Has anyone implemented such capability ? - What is the best way to access the vtkTable object through Python directly (to then possibly use some python plotting facility)? - Is it possible to create an image (Jpg, png etc..) from Python of an XY plot or a Bar Chart ? Jacques PAPPER Applied CFD Team Leader Tel: +44 (0) 1234 324677 --- This email contains information that is private and confidential and is intended only for the addressee. If you are not the intended recipient please delete it and notify us immediately by e-mailing the sender. Note: All email sent to or from this address may be accessed by someone other than the recipient, for system management and security reasons. Aircraft Research Association Ltd. Registered in England, Registration No 503668 Registered Office: Manton Lane, Bedford MK41 7PF England VAT No GB 196351245 ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Visualizing histogram
The new charts in vtk/guisupport/qt/chart have support for strings and numbers on the axes. The old charts only support numbers. We're currently integrating the new charts into paraview. Then, you'll be able to view the vtkTable. The chart views in vtk/guisupport/qt can be displayed using python. There are some tests you can use as an example (I can't remember where they are at the moment). I'm not sure how well that will work in paraview though. It may have to be done stand-alone. Mark Richardson - Original Message - From: Jacques Papper jpap...@ara.co.uk To: John Biddiscombe biddi...@cscs.ch, paraview paraview@paraview.org Sent: Tuesday, February 10, 2009 9:30:29 AM GMT -07:00 US/Canada Mountain Subject: [Paraview] Visualizing histogram John, Thanks a lot for your help. I have re-used part of your code to create a Multi-block to table filter. (Basically exactly the same as your probeIntegration but without the integration step). The problem I have now is in creating a histogram which has the Block Id (String - first column of data in my vtkTable) on the x axis and the data on the y axis. It seems that the histogram plotting capability in ParaView can not handle String Ids instead of numbers. - Has anyone implemented such capability ? - What is the best way to access the vtkTable object through Python directly (to then possibly use some python plotting facility)? - Is it possible to create an image (Jpg, png etc..) from Python of an XY plot or a Bar Chart ? Jacques PAPPER Applied CFD Team Leader Tel: +44 (0) 1234 324677 --- This email contains information that is private and confidential and is intended only for the addressee. If you are not the intended recipient please delete it and notify us immediately by e-mailing the sender. Note: All email sent to or from this address may be accessed by someone other than the recipient, for system management and security reasons. Aircraft Research Association Ltd. Registered in England, Registration No 503668 Registered Office: Manton Lane, Bedford MK41 7PF England VAT No GB 196351245 ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] DICOM series reader for Paraview
Thanks very much, Jerome.
The vtkDICOMReader works right now. The problem was in my xml file for
server manager.
Again, thanks very much. I am really appreciate your help!
Aaron
On Tue, Feb 10, 2009 at 7:49 AM, Jérôme jerome.ve...@gmail.com wrote:
Hi,
I use 3 files for the vtkDICOMImageReader plugin :
- One CMakeList.txt where you can find those lines:
# READERS PLUGIN --
# Use the ADD_PARAVIEW_PLUGIN macro to build a plugin
ADD_PARAVIEW_PLUGIN(
DICOMImageReader #--Name for the plugin
1.0#--Version string
SERVER_MANAGER_XML DICOMReader.xml #-- server manager xml
GUI_RESOURCE_FILES DICOMReaderGUI.xml
)
#--
You can also use this file for other ADD_PARAVIEW_PLUGIN command
- One DICOMReaderGUI.xml
- One DICOMReader.xml
Both latter are given.
Regarding the GDCMReader, I am sorry I could not help you. As I said,
I had never tried this lib in a Paraview framework. The best you can
do - well, the laziest in fact - is to ask the GDCM development team
to give a built-in paraview plugin.
Today, the vtkDICOMImageReader is sufficient for me, and what I give
here makes it works in ParaView 3.4 stable and nightly CVS 3.5, both
Windows (XP and Vista) and Linux (Fedora 9). This is true when the
plugin is loaded on the computer that built Paraview. Other problems
arise when deploying on 'pure-of-devel-stuff' systems.
I hope this will help.
Best regards,
Jerome
2009/2/9 Biao She sheb...@gmail.com:
Thanks for your help, Jerome.
I find the vtkGdcmReader files in the latest GDCM package. After I build
these files as a Paraview Plug-in and load it, I got this error message
from
Paraview console:
ERROR: In
/usr/scratch/bshe/Paraview/ParaView-3.4.0/Servers/Common/vtkProcessModule.cxx,
line 1079
vtkProcessModule (0x8a7c2e0): Cannot create object of type
vtkGdcmReader.
while processing
Message 0 = New
Argument 0 = string_value {vtkGdcmReader}
Argument 1 = id_value {84}
ERROR: In
/usr/scratch/bshe/Paraview/ParaView-3.4.0/Servers/Common/vtkProcessModule.cxx,
line 1080
vtkProcessModule (0x8a7c2e0): Aborting execution for debugging purposes.
I must do something wrong, but when I build the vtkGdcmReader, no error
message at all. Here is my CMakeLists file:
FIND_PACKAGE(ParaView REQUIRED)
INCLUDE(${PARAVIEW_USE_FILE})
FIND_PACKAGE (GDCM)
IF (GDCM_FOUND)
INCLUDE(${GDCM_USE_FILE})
ENDIF (GDCM_FOUND)
ADD_PARAVIEW_PLUGIN(vtkGDCMReader 1.0 SERVER_MANAGER_SOURCES
vtkGdcmReader.cxx)
ADD_PARAVIEW_PLUGIN(vtkGDCMReader 1.0 GUI_RESOURCE_FILES pqReader.xml)
ADD_PARAVIEW_PLUGIN(vtkGDCMReader 1.0 SERVER_MANAGER_XML reader.xml)
You also mentioned that you use vtkDICOMImageReader as your DICOM reader
in
Paraview. It seems that I can only use the reader to read one DICOM image
file. How can I write the XML files for vtkDICOMImageReader to read a
series
of DICOM files? Could you please email me your XML files for
vtkDICOMImageReader if possible? Thanks very much!
Aaron
On Fri, Feb 6, 2009 at 12:52 AM, Jérôme jerome.ve...@gmail.com wrote:
Hi,
if you intend to use a DICOM reader in Paraview, why not using
directly GDCM, instead of ITK? It contains a VTK Reader... If I am
right, you will just have to write the XML/CMake files that make the
reader available in Paraview.
In my case, I use the vtkDICOMImageReader, that is a very simple dcm
file series reader: just give the folder containing the files, and let
it read. If you need more functionalities, the GDCM reader will do the
trick.
You can find a later version of GDCM than the ITK integrated one, on
this website: http://www.creatis.insa-lyon.fr/Public/Gdcm/ . I cannot
help you more, as I had never use it for now.
Cheers,
Jerome
2009/2/6 Biao She sheb...@gmail.com:
Hi everyone.
I am wondering if anyone know how to integrate a ITK(GDCM) based DICOM
reader to Paraview?
My basic idea is:
1. Read DICOM series data through ITK(GDCM)
2. Export the data to a vtkImageImport class
3. Use the data in vtkImageImport as a source of Paraview
I have done the first two steps. But I am not sure how to do the third
one.
I have read something about how to write a Paraview Reader in the
Paraview
book. It is said that all the readers must derive from vtkAlgorithm or
one
of its subclass. Fortunately, vtkImageImport is one of its subclass.
So,
I
guess it would be a good idea to choose vtkImageImport as a superclass
of my
reader. Am I right?
If I choose vtkImageImport as a superclass, to make my reader works
properly, which methods should be implemented in my reader?
The last question is: How do I read the path to DICOM files from
Paraview
Client GUI and pass it to my reader? For example, the DICOM data is
stored
in
Re: [Paraview] Losing data when clip multi-block
Eric, I think we dealt with this problem since 3.4. I can't reproduce the problem with your first set of instructions on cvs head. Do you mind trying the cvs version? -berk On Fri, Feb 6, 2009 at 2:57 PM, Eric E. Monson emon...@cs.duke.edu wrote: Hey Alan, Are you seeing both the point and cell Ids arrays? When I do this I end up with only the cell Ids array -- the points one is missing. Here's another one that loses a data array consistently: Create a Point Source (100 pts, 10 radius) Apply Elevation filter to points Create a Sphere Source Apply Curvature filter to sphere Select Elevation then Curvature Group Clip Gauss_Curvature is missing in Clip Information (only see Elevation Normals) (or, after deleting clip and group filters) Select Curvature then Elevation Group Clip Elevation is missing in Clip Information (only see Gauss_Curvature Normals) Any luck with that one? (I'd just like to hear that someone can reproduce the problem before I file a bug report...) Thanks, -Eric On Feb 6, 2009, at 1:47 PM, Scott, W Alan wrote: Eric, I was trying to replicate this bug, and cannot. Please give me detailed instructions on how to replicate it, and I will put it in the bug tracker. Better yet would be you putting it in the bug tracker. I tried: ParaView CVS trunk from late January, XP, non client/server. Source/Box Source/Wavelet (Highlight Box) Filters/ Generate Ids (Highlight GenerateId and Wavelet) Filters/ Group Datasets Clip I then see the Ids points data as follows: Ids (partial) alan -Original Message- From: paraview-boun...@paraview.org [mailto:paraview-boun...@paraview.org] On Behalf Of Eric E. Monson Sent: Friday, February 06, 2009 7:09 AM To: ParaView List Subject: Re: [Paraview] Losing data when clip multi-block Hey Utkarsh, No, I've never seen the clip lose data on one dataset by itself. The other interesting thing is that I can't always get this data loss to happen if the data was generated as part of a source from the Sources menu. It's much more likely to disappear when the data was generated by a filter or brought in by a reader. For example, if you generate a Box and a Wavelet source, grouping and clipping them won't lose any data, but if you run Generate IDs on one of them, then select GenerateIds1 second before grouping, then clip, the Ids point data disappears... Thanks, -Eric On Feb 6, 2009, at 7:37 AM, Utkarsh Ayachit wrote: Eric, Does the loss of arrays happen even if you clip the orginal dataset by itself (without grouping it using the group filter)? Utkarsh On Wed, Feb 4, 2009 at 3:53 PM, Eric E. Monson emon...@cs.duke.edu wrote: Hello, I'm creating a multi-block data set using the group filter and then clipping it. The results of the clip are always missing one of the scalars associated with the second data set that I highlighted before applying the group filter. This only seems to happen if one of the data sets has multiple scalars or vectors associated with it -- if they each only have one, nothing is lost in the clip. (ParaView 3.4 and CVS, OS X 10.5.6 and Windows XP 32-bit, no MPI) I originally saw this with my own data, but I am able to easily replicate this by creating two point sources. I apply the Elevation filter to the first. Then, to the second I apply Brownian Vectors, plus a Calculator that computes the magnitude of those vectors. If I highlight Elevation and then Calculator, then Group and Clip, I lose the vector magnitude scalar at the Clip stage. If I highlight the Calculator and then the Elevation, then Group and Clip, I lose the elevation scalar. Please let me know if anyone has any ideas about where this could be coming from. Thanks a lot, -Eric -- Eric E Monson Duke Visualization Technology Group ___ ParaView mailing list ParaView@paraview.org http://www.paraview.org/mailman/listinfo/paraview ___ ParaView mailing list ParaView@paraview.org http://www.paraview.org/mailman/listinfo/paraview ___ ParaView mailing list ParaView@paraview.org http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] particletracer
Can you tell us exactly (detailed, step-by-step) what you are doing? That dialog works fine for me (running OS X 10.5). -berk On Tue, Feb 10, 2009 at 4:10 AM, Martin Uppman f0...@student.lth.se wrote: Hi again, thank you for fast answer John! I'm aware of the problem that my particle tracer doesnt have any seed source, but I have been working for quite awhile sloving this problem. I did as you said, created temporalcache and seed (point seed) but I cant connect the 2 with my particle tracer. I found your (John's) great powerpoint presentation on the web explaining everything there is to explain. Though I cant make it work!!! In one of the pictures in the presentation there are some boxes where you can choose which sources to use in the particle tracer (in object inspector - properties - source). I dont have that option in my program. Does someone know why (using v3.4.0 on a Mac)? About v3.4.0, isnt it the lastest version? Cant fint anything newer on paraview.org. Cheers, Martin Uppman Martin ERROR: In /Users/kitware/Berk/ParaView3/VTK/Filtering/vtkDemandDrivenPipeline.cxx, line 722 vtkCompositeDataPipeline (0x217c7fb0): Input port 1 of algorithm vtkTemporalStreamTracer(0x1e345e00) has 0 connections but is not optional. Input 0 should be a time dependent dataset. It is best to use a TemporalCache before the particle tracer to stop multiple updates for the same time step. Input 1 should be some seed points. Ensight - TemporalCache - ParticleTracer Some Other data eg.line/plane - the ignore pipeline time option is provided to get around some animation issues that used to plague paraview. You should not need it, but the correct way to use it, is set IgnorePipelineTime to true, then set an animation keyframe to animate TimeStep from 0-N - the particle tracer will then use the timestep to generate update times for the Ensight input, instead of usigin the GUI generated time. If you are using the particle tracer from prior to 3.4 then you should switch to a newer one as it is contiunually being improved. I will soon (months, not days) be checking in a lot of changes which enable it to handle dynamic meshes better. JB I've been looking for information on this and a found a thread which I think concerns the same problem. In that thread Berk made a patch to fix this problem. I also tried to ignore pipeline time, but this doent work. I'm working with .case files and I want to animate the blood flow in a human heart using particle tracers. I'm using a Mac with ParaView version 3.4.0. Thanks for looking into this. Cheers, Martin Uppman ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview -- John Biddiscombe,email:biddisco @ cscs.ch http://www.cscs.ch/ CSCS, Swiss National Supercomputing Centre | Tel: +41 (91) 610.82.07 Via Cantonale, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Creating ImageData w/Programmable Source
Nope -- I have no idea how to do that. Could you give me some guidance? I really appreciate it, -Eric On Feb 10, 2009, at 12:50 PM, Berk Geveci wrote: Did you set the whole extent in the RequestInformation script? -berk On Fri, Feb 6, 2009 at 11:28 AM, Eric E. Monson emon...@cs.duke.edu wrote: Hello, I'm having trouble creating vtkImageData with the Python Programmable Source. The PolyData Helix example works fine for me, but when I try to create ImageData it seems to build the data structure within Python (i.e. I can print the characteristics of the ImageData and it looks fine in the Output Messages), but no data shows in the Information tab or the 3d render view. Here's the simplest case of the things I've tried (after selecting vtkImageData from the combo box): pdo = self.GetImageDataOutput() pdo.SetDimensions(10,10,10) pdo.SetOrigin(0,0,0) pdo.SetSpacing(1,1,1) print pdo I can add scalars to it, or create a new vtkImageData and then shallow or deep copy that over to the output, and those things look like they're working fine at the print statement, but they don't seem to help get the data to really show up in the pipeline. I hope someone can just point out something I'm forgetting to do... (PV 3.4 CVS, OS X 10.5.6 WinXP) Thanks, -Eric -- Eric E Monson Duke Visualization Technology Group ___ ParaView mailing list ParaView@paraview.org http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Creating ImageData w/Programmable Source
It should be something like: from paraview import util util.SetOutputWholeExtent(self, [0, 10, 0, 10, 0, 10]) Make sure that you are putting this in the RequestInformation script. I think in the future, we should have a widget with six entry boxes... -berk On Tue, Feb 10, 2009 at 2:31 PM, Eric E. Monson emon...@cs.duke.edu wrote: Nope -- I have no idea how to do that. Could you give me some guidance? I really appreciate it, -Eric On Feb 10, 2009, at 12:50 PM, Berk Geveci wrote: Did you set the whole extent in the RequestInformation script? -berk On Fri, Feb 6, 2009 at 11:28 AM, Eric E. Monson emon...@cs.duke.edu wrote: Hello, I'm having trouble creating vtkImageData with the Python Programmable Source. The PolyData Helix example works fine for me, but when I try to create ImageData it seems to build the data structure within Python (i.e. I can print the characteristics of the ImageData and it looks fine in the Output Messages), but no data shows in the Information tab or the 3d render view. Here's the simplest case of the things I've tried (after selecting vtkImageData from the combo box): pdo = self.GetImageDataOutput() pdo.SetDimensions(10,10,10) pdo.SetOrigin(0,0,0) pdo.SetSpacing(1,1,1) print pdo I can add scalars to it, or create a new vtkImageData and then shallow or deep copy that over to the output, and those things look like they're working fine at the print statement, but they don't seem to help get the data to really show up in the pipeline. I hope someone can just point out something I'm forgetting to do... (PV 3.4 CVS, OS X 10.5.6 WinXP) Thanks, -Eric -- Eric E Monson Duke Visualization Technology Group ___ ParaView mailing list ParaView@paraview.org http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Creating ImageData w/Programmable Source
That works great -- thanks! Now that you pointed me in the right direction, I can see how both WholeExtent and UpdateExtent were [0, -1, 0, -1, 0, -1] in the output with my original script. Maybe it should have been obvious, but I didn't know enough to look for that. It also seems to work fine if I set these in the main script: pdo.SetWholeExtent(0,9,0,9,0,9) pdo.SetUpdateExtentToWholeExtent() Thanks again, -Eric On Feb 10, 2009, at 3:13 PM, Berk Geveci wrote: It should be something like: from paraview import util util.SetOutputWholeExtent(self, [0, 10, 0, 10, 0, 10]) Make sure that you are putting this in the RequestInformation script. I think in the future, we should have a widget with six entry boxes... -berk On Tue, Feb 10, 2009 at 2:31 PM, Eric E. Monson emon...@cs.duke.edu wrote: Nope -- I have no idea how to do that. Could you give me some guidance? I really appreciate it, -Eric On Feb 10, 2009, at 12:50 PM, Berk Geveci wrote: Did you set the whole extent in the RequestInformation script? -berk On Fri, Feb 6, 2009 at 11:28 AM, Eric E. Monson emon...@cs.duke.edu wrote: Hello, I'm having trouble creating vtkImageData with the Python Programmable Source. The PolyData Helix example works fine for me, but when I try to create ImageData it seems to build the data structure within Python (i.e. I can print the characteristics of the ImageData and it looks fine in the Output Messages), but no data shows in the Information tab or the 3d render view. Here's the simplest case of the things I've tried (after selecting vtkImageData from the combo box): pdo = self.GetImageDataOutput() pdo.SetDimensions(10,10,10) pdo.SetOrigin(0,0,0) pdo.SetSpacing(1,1,1) print pdo I can add scalars to it, or create a new vtkImageData and then shallow or deep copy that over to the output, and those things look like they're working fine at the print statement, but they don't seem to help get the data to really show up in the pipeline. I hope someone can just point out something I'm forgetting to do... (PV 3.4 CVS, OS X 10.5.6 WinXP) Thanks, -Eric -- Eric E Monson Duke Visualization Technology Group ___ ParaView mailing list ParaView@paraview.org http://www.paraview.org/mailman/listinfo/paraview ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Losing data when clip multi-block
Thanks a lot, Alan. This was driving me nuts that nobody could reproduce it! :) For now I wish I could predict which variable was going to be lost so I could at least create a sacrificial array that could disappear and leave my real data intact. I also wish I knew the difference in Berk's build that won't reproduce my first example since I still see the data loss on today's CVS. I'm trying an MPI build in case there would be a difference in how multi- block data sets are handled, but I know that's probably grasping at straws... Anyway, thanks for filing the bug and I'll take a look at it later to see if I can add anything. Talk to you later, -Eric On Feb 10, 2009, at 3:33 PM, Scott, W Alan wrote: Eric, Sorry for taking time to get back to you - I wanted to verify with the developers that this isn't expected behavior. You have correctly found a bug. I wrote this up as bug number 8494 in the Kitware bug tracker. I used your very simple, excellent Point and Sphere source example listed below. If I missed anything, please feel free to modify the bug appropriately. Alan -Original Message- From: Berk Geveci [mailto:berk.gev...@kitware.com] Sent: Tuesday, February 10, 2009 10:59 AM To: Eric E. Monson Cc: Scott, W Alan; ParaView List Subject: Re: [Paraview] Losing data when clip multi-block Eric, I think we dealt with this problem since 3.4. I can't reproduce the problem with your first set of instructions on cvs head. Do you mind trying the cvs version? -berk On Fri, Feb 6, 2009 at 2:57 PM, Eric E. Monson emon...@cs.duke.edu wrote: Hey Alan, Are you seeing both the point and cell Ids arrays? When I do this I end up with only the cell Ids array -- the points one is missing. Here's another one that loses a data array consistently: Create a Point Source (100 pts, 10 radius) Apply Elevation filter to points Create a Sphere Source Apply Curvature filter to sphere Select Elevation then Curvature Group Clip Gauss_Curvature is missing in Clip Information (only see Elevation Normals) (or, after deleting clip and group filters) Select Curvature then Elevation Group Clip Elevation is missing in Clip Information (only see Gauss_Curvature Normals) Any luck with that one? (I'd just like to hear that someone can reproduce the problem before I file a bug report...) Thanks, -Eric On Feb 6, 2009, at 1:47 PM, Scott, W Alan wrote: Eric, I was trying to replicate this bug, and cannot. Please give me detailed instructions on how to replicate it, and I will put it in the bug tracker. Better yet would be you putting it in the bug tracker. I tried: ParaView CVS trunk from late January, XP, non client/server. Source/Box Source/Wavelet (Highlight Box) Filters/ Generate Ids (Highlight GenerateId and Wavelet) Filters/ Group Datasets Clip I then see the Ids points data as follows: Ids (partial) alan -Original Message- From: paraview-boun...@paraview.org [mailto:paraview-boun...@paraview.org] On Behalf Of Eric E. Monson Sent: Friday, February 06, 2009 7:09 AM To: ParaView List Subject: Re: [Paraview] Losing data when clip multi-block Hey Utkarsh, No, I've never seen the clip lose data on one dataset by itself. The other interesting thing is that I can't always get this data loss to happen if the data was generated as part of a source from the Sources menu. It's much more likely to disappear when the data was generated by a filter or brought in by a reader. For example, if you generate a Box and a Wavelet source, grouping and clipping them won't lose any data, but if you run Generate IDs on one of them, then select GenerateIds1 second before grouping, then clip, the Ids point data disappears... Thanks, -Eric On Feb 6, 2009, at 7:37 AM, Utkarsh Ayachit wrote: Eric, Does the loss of arrays happen even if you clip the orginal dataset by itself (without grouping it using the group filter)? Utkarsh On Wed, Feb 4, 2009 at 3:53 PM, Eric E. Monson emon...@cs.duke.edu wrote: Hello, I'm creating a multi-block data set using the group filter and then clipping it. The results of the clip are always missing one of the scalars associated with the second data set that I highlighted before applying the group filter. This only seems to happen if one of the data sets has multiple scalars or vectors associated with it -- if they each only have one, nothing is lost in the clip. (ParaView 3.4 and CVS, OS X 10.5.6 and Windows XP 32-bit, no MPI) I originally saw this with my own data, but I am able to easily replicate this by creating two point sources. I apply the Elevation filter to the first. Then, to the second I apply Brownian Vectors, plus a Calculator that computes the magnitude of those vectors. If I highlight Elevation and then Calculator, then Group and Clip, I lose the vector magnitude scalar at the Clip stage. If I highlight the Calculator and then the Elevation, then Group and Clip, I lose the elevation scalar.
[Paraview] How to change the default mapper for 3d volume rendering?
Thanks to this mailing list, I know how to make Paraview read the DICOM files right now. However, the volume rendering speed is not satisfactory. I am wondering if I want to use vtkOpenGLVolumeTextureMapper3d for the volume rendering, how should I change paraview's code? Moreover, if I want to use my own GPU-based volume rendering algorithm in Paraview, how should I do it? Or is that possible? Thanks very much! Aaron ___ Powered by www.kitware.com 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 Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
