Re: [Paraview] can't do stereo animation output in batch mode
Any thoughts on this issue? Has anyone else successfully output stereo images from pvbatch? On Fri, Oct 30, 2015 at 3:38 PM, Ryan Abernathey <ryan.abernat...@gmail.com> wrote: > I am trying to output an animation using batch mode in stereo. I want to > output one set of images for the left eye and one for the right eye. In my > script, I tried to do this by setting view.StereoType = "Left" or "Right". > However, this doesn't work; both produce identical output. > > Can you give me some advice? Script is below. I am executing this with > pvbatch. > > > import os > paraview.simple._DisableFirstRenderCameraReset() > > state_dir = '/scratch/Paraview/hurricane/long_hourly_rotating/try4' > fname = 'filter_pre_render.pvsm' > st = 'left' > # or > # st = 'right' > > > servermanager.LoadState(os.path.join(state_dir, fname)) > outdir = > '/scratch/Paraview/hurricane/long_hourly_rotating/output/top_view/' + st > view = GetRenderView() > view.ViewSize = [1920, 1080] > view.StereoType = st.capitalize() > SetActiveView(view) > Render() > WriteAnimation(os.path.join(outdir, 'top_view_%s.png' % st)) > ___ 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 Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] segmentation fault with netCDF when loading state file
Yes, I can confirm that this state loads without crashing in 4.4. The fields are not actually accessible at the current timestep (appear with a "?"), but can be rewound to the beginning and restarted without crashing. On Tue, Oct 27, 2015 at 1:16 PM, Ryan Abernathey <ryan.abernat...@gmail.com> wrote: > David, > Thanks for your investigation. I will be able to try this tomorrow. The > original issue was with Paraview 4.3.1. We recently built the latest > master, so I will be able to confirm whether it was fixed in between. > Best, > Ryan > > > > On Tue, Oct 27, 2015 at 10:23 AM, David Lonie <david.lo...@kitware.com> > wrote: > >> Hi Ryan, >> >> I'm looking into this issue. >> >> I download the sample data you provided, and the state file loads and >> renders fine for me with the current (as of this morning) master branch of >> ParaView. What version of ParaView are you using? Can you test the latest >> master branch? It appears that whatever the bug was, it has been fixed. >> >> Dave >> >> On Wed, Oct 21, 2015 at 9:50 AM, Aashish Chaudhary < >> aashish.chaudh...@kitware.com> wrote: >> >>> Ryan, >>> >>> would it be possible for you to share a sample dataset? The NetCDF >>> reader has fails to read data in certain corner cases but without having >>> the data to reproduce the issue it is kind of little tricky to get to the >>> problem. >>> >>> - Aashish >>> >>> On Wed, Oct 21, 2015 at 9:44 AM, Ryan Abernathey < >>> ryan.abernat...@gmail.com> wrote: >>> >>>> Does anyone have any feedback on this issue? >>>> >>>> I have no idea how to debug or continue. I will have to abandon >>>> paraview for my project unless I can get some help somehow. >>>> >>>> Thanks, >>>> >>>> Ryan Abernathey >>>> Assistant Professor >>>> Columbia University, Department of Earth & Environmental Sciences >>>> Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics >>>> 205 C Oceanography >>>> 61 Route 9W - PO Box 1000 >>>> Palisades, NY 10964-8000 >>>> http://rabernat.github.io >>>> r...@ldeo.columbia.edu >>>> >>>> >>>> On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey < >>>> ryan.abernat...@gmail.com> wrote: >>>> >>>>> Hello, >>>>> >>>>> I am extremely frustrated and stuck on this problem. Any advice would >>>>> be appreciated. >>>>> >>>>> I am working with a dataset of 2400 sequentially numbered netCDF files >>>>> (generic & CF conventions). >>>>> >>>>> In a fresh pipeline, Paraview is able to recognizes these files as a >>>>> single source and load them correctly. I then create a standard pipeline >>>>> involving various filters (contour, etc., nothing funny) and save a state >>>>> file. >>>>> >>>>> When I attempt to load the state file, I get the following >>>>> segmentation fault. Further down you can see a ncdump of the offending >>>>> file. >>>>> >>>>> Would appreciate any advice on how to debug / overcome this issue. Is >>>>> it a bug? It sure feels like one... >>>>> >>>>> Best, >>>>> Ryan Abernathey >>>>> >>>>> >>>>> ERROR: In >>>>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx, >>>>> line 822 >>>>> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds >>>>> dimension bound >>>>> >>>>> >>>>> ERROR: In >>>>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, >>>>> line 784 >>>>> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm >>>>> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: >>>>> vtkInformation >>>>> (0x8141700) >>>>> Debug: Off >>>>> Modified Time: 05 >>>>> Reference Count: 1 >>>>> Registered Events: (none) >>>>> Request: REQUEST_DATA >>>>> FORWARD_DIRECTION: 0 >>>>> FROM_OUTPUT_PORT
Re: [Paraview] segmentation fault with netCDF when loading state file
David, Thanks for your investigation. I will be able to try this tomorrow. The original issue was with Paraview 4.3.1. We recently built the latest master, so I will be able to confirm whether it was fixed in between. Best, Ryan On Tue, Oct 27, 2015 at 10:23 AM, David Lonie <david.lo...@kitware.com> wrote: > Hi Ryan, > > I'm looking into this issue. > > I download the sample data you provided, and the state file loads and > renders fine for me with the current (as of this morning) master branch of > ParaView. What version of ParaView are you using? Can you test the latest > master branch? It appears that whatever the bug was, it has been fixed. > > Dave > > On Wed, Oct 21, 2015 at 9:50 AM, Aashish Chaudhary < > aashish.chaudh...@kitware.com> wrote: > >> Ryan, >> >> would it be possible for you to share a sample dataset? The NetCDF reader >> has fails to read data in certain corner cases but without having the data >> to reproduce the issue it is kind of little tricky to get to the problem. >> >> - Aashish >> >> On Wed, Oct 21, 2015 at 9:44 AM, Ryan Abernathey < >> ryan.abernat...@gmail.com> wrote: >> >>> Does anyone have any feedback on this issue? >>> >>> I have no idea how to debug or continue. I will have to abandon paraview >>> for my project unless I can get some help somehow. >>> >>> Thanks, >>> >>> Ryan Abernathey >>> Assistant Professor >>> Columbia University, Department of Earth & Environmental Sciences >>> Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics >>> 205 C Oceanography >>> 61 Route 9W - PO Box 1000 >>> Palisades, NY 10964-8000 >>> http://rabernat.github.io >>> r...@ldeo.columbia.edu >>> >>> >>> On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey < >>> ryan.abernat...@gmail.com> wrote: >>> >>>> Hello, >>>> >>>> I am extremely frustrated and stuck on this problem. Any advice would >>>> be appreciated. >>>> >>>> I am working with a dataset of 2400 sequentially numbered netCDF files >>>> (generic & CF conventions). >>>> >>>> In a fresh pipeline, Paraview is able to recognizes these files as a >>>> single source and load them correctly. I then create a standard pipeline >>>> involving various filters (contour, etc., nothing funny) and save a state >>>> file. >>>> >>>> When I attempt to load the state file, I get the following segmentation >>>> fault. Further down you can see a ncdump of the offending file. >>>> >>>> Would appreciate any advice on how to debug / overcome this issue. Is >>>> it a bug? It sure feels like one... >>>> >>>> Best, >>>> Ryan Abernathey >>>> >>>> >>>> ERROR: In >>>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx, >>>> line 822 >>>> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds >>>> dimension bound >>>> >>>> >>>> ERROR: In >>>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, >>>> line 784 >>>> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm >>>> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation >>>> (0x8141700) >>>> Debug: Off >>>> Modified Time: 05 >>>> Reference Count: 1 >>>> Registered Events: (none) >>>> Request: REQUEST_DATA >>>> FORWARD_DIRECTION: 0 >>>> FROM_OUTPUT_PORT: 0 >>>> ALGORITHM_AFTER_FORWARD: 1 >>>> >>>> >>>> >>>> >>>> ERROR: In >>>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, >>>> line 784 >>>> vtkCompositeDataPipeline (0x744fde0): Algorithm >>>> vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation >>>> (0x5737250) >>>> Debug: Off >>>> Modified Time: 43 >>>> Reference Count: 1 >>>> Registered Events: (none) >>>> Request: REQUEST_DATA_OBJECT >>>> FORWARD_DIRECTION: 0 >>>> FROM_OUTPUT_PORT: 0 >>>> A
Re: [Paraview] segmentation fault with netCDF when loading state file
Does anyone have any feedback on this issue?
I have no idea how to debug or continue. I will have to abandon paraview
for my project unless I can get some help somehow.
Thanks,
Ryan Abernathey
Assistant Professor
Columbia University, Department of Earth & Environmental Sciences
Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics
205 C Oceanography
61 Route 9W - PO Box 1000
Palisades, NY 10964-8000
http://rabernat.github.io
r...@ldeo.columbia.edu
On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey <ryan.abernat...@gmail.com>
wrote:
> Hello,
>
> I am extremely frustrated and stuck on this problem. Any advice would be
> appreciated.
>
> I am working with a dataset of 2400 sequentially numbered netCDF files
> (generic & CF conventions).
>
> In a fresh pipeline, Paraview is able to recognizes these files as a
> single source and load them correctly. I then create a standard pipeline
> involving various filters (contour, etc., nothing funny) and save a state
> file.
>
> When I attempt to load the state file, I get the following segmentation
> fault. Further down you can see a ncdump of the offending file.
>
> Would appreciate any advice on how to debug / overcome this issue. Is it a
> bug? It sure feels like one...
>
> Best,
> Ryan Abernathey
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
> line 822
> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
> dimension bound
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
> line 784
> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
> (0x8141700)
> Debug: Off
> Modified Time: 05
> Reference Count: 1
> Registered Events: (none)
> Request: REQUEST_DATA
> FORWARD_DIRECTION: 0
> FROM_OUTPUT_PORT: 0
> ALGORITHM_AFTER_FORWARD: 1
>
>
>
>
> ERROR: In
> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
> line 784
> vtkCompositeDataPipeline (0x744fde0): Algorithm
> vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
> (0x5737250)
> Debug: Off
> Modified Time: 43
> Reference Count: 1
> Registered Events: (none)
> Request: REQUEST_DATA_OBJECT
> FORWARD_DIRECTION: 0
> FROM_OUTPUT_PORT: 0
> ALGORITHM_AFTER_FORWARD: 1
>
>
>
>
> Segmentation fault (core dumped)
>
>
>
>
>
>
> $ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
> netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
> dimensions:
> x = 512 ;
> y = 512 ;
> z = 64 ;
> time = UNLIMITED ; // (1 currently)
> variables:
> float x(x) ;
> x:units = "m" ;
> float y(y) ;
> y:units = "m" ;
> float z(z) ;
> z:units = "m" ;
> z:long_name = "height" ;
> float time(time) ;
> time:units = "d" ;
> time:long_name = "time" ;
> float p(z) ;
> p:units = "mb" ;
> p:long_name = "pressure" ;
> float zi(z) ;
> zi:units = "m" ;
> zi:long_name = "intfc_ht" ;
> float U(time, z, y, x) ;
> U:long_name = "X Wind
> Component" ;
> U:units = "m/s " ;
> float V(time, z, y, x) ;
> V:long_name = "Y Wind
> Component" ;
> V:units = "m/s " ;
> float W(time, z, y, x) ;
> W:long_name = "Z Wind
> Component" ;
> W:units = "m/s " ;
> float PP(time, z, y, x) ;
> PP:long_name = "Pressure
> Perturbation " ;
> PP:units = "Pa" ;
> float QRAD(time, z, y, x) ;
> QRAD:long_name = "Radiative heating
> rate " ;
> QRAD:units = "K/day " ;
> float TABS(time, z, y, x) ;
> TABS:long_name = "Absolute
> Temperature" ;
> TABS:units
[Paraview] segmentation fault with netCDF when loading state file
Hello,
I am extremely frustrated and stuck on this problem. Any advice would be
appreciated.
I am working with a dataset of 2400 sequentially numbered netCDF files
(generic & CF conventions).
In a fresh pipeline, Paraview is able to recognizes these files as a single
source and load them correctly. I then create a standard pipeline involving
various filters (contour, etc., nothing funny) and save a state file.
When I attempt to load the state file, I get the following segmentation
fault. Further down you can see a ncdump of the offending file.
Would appreciate any advice on how to debug / overcome this issue. Is it a
bug? It sure feels like one...
Best,
Ryan Abernathey
ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
line 822
vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
dimension bound
ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
line 784
vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
(0x8141700)
Debug: Off
Modified Time: 05
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
FORWARD_DIRECTION: 0
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1
ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
line 784
vtkCompositeDataPipeline (0x744fde0): Algorithm
vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
(0x5737250)
Debug: Off
Modified Time: 43
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA_OBJECT
FORWARD_DIRECTION: 0
FROM_OUTPUT_PORT: 0
ALGORITHM_AFTER_FORWARD: 1
Segmentation fault (core dumped)
$ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
dimensions:
x = 512 ;
y = 512 ;
z = 64 ;
time = UNLIMITED ; // (1 currently)
variables:
float x(x) ;
x:units = "m" ;
float y(y) ;
y:units = "m" ;
float z(z) ;
z:units = "m" ;
z:long_name = "height" ;
float time(time) ;
time:units = "d" ;
time:long_name = "time" ;
float p(z) ;
p:units = "mb" ;
p:long_name = "pressure" ;
float zi(z) ;
zi:units = "m" ;
zi:long_name = "intfc_ht" ;
float U(time, z, y, x) ;
U:long_name = "X Wind
Component" ;
U:units = "m/s " ;
float V(time, z, y, x) ;
V:long_name = "Y Wind
Component" ;
V:units = "m/s " ;
float W(time, z, y, x) ;
W:long_name = "Z Wind
Component" ;
W:units = "m/s " ;
float PP(time, z, y, x) ;
PP:long_name = "Pressure
Perturbation " ;
PP:units = "Pa" ;
float QRAD(time, z, y, x) ;
QRAD:long_name = "Radiative heating
rate " ;
QRAD:units = "K/day " ;
float TABS(time, z, y, x) ;
TABS:long_name = "Absolute
Temperature" ;
TABS:units = "K " ;
float QV(time, z, y, x) ;
QV:long_name = "Water
Vapor "
;
QV:units = "g/kg " ;
float QN(time, z, y, x) ;
QN:long_name = "Non-precipitating Condensate
(Water+Ice)" ;
QN:units = "g/kg " ;
float QP(time, z, y, x) ;
QP:long_name = "Precipitating Water
(Rain+Snow) " ;
QP:units = "g/kg " ;
float LQRAD(time, z, y, x) ;
LQRAD:long_name = "LW Radiative heating
rate " ;
LQRAD:units = "K/day " ;
float SQRAD(time, z, y, x) ;
SQRAD:long_name = "SW Radiative heating
rate " ;
SQRAD:units = "K/day " ;
}
___
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
Search the list archives at: http://markmail.org/search/?q=ParaView
Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview
[Paraview] colormap nan opacity
Hi, I use paraview to render ocean model data. My datasets are usually rectilinear grids, cell data and / or point data. Frequently I want to mask points that are below the level of topography, so I usually set those points to NaN when preparing my data for paraview. I do a lot of volume rendering, so I am very familiar with the opacity mapping options within the colormap editor. The colormap editor allows you to choose your NaN color, but this dialog doesn't include an alpha / opacity option. Would that be difficult to add? It would really help me. Instead, what I have to do is use a clip filter to mask the NaNs, which ends up turning my rectilinear grid data into unstructure grid data, with significant performance and memory impacts. If NaNs could be made transparent at the level of the color map editor, it would make my pipeline much more efficient. Is this a feature that might be supported in future releases? Thanks, Ryan Abernathey ___ 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 Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
[Paraview] animate parameter for python programmable filter
Hi,
I would like to animate a parameter with a python programmable filter using
keyframes. In this simple example, I just want to rescale a scalar variable
by a constant factor (alpha). But I want to animate this factor. Here is my
filter:
from paraview.vtk import dataset_adapter as DA
self.SetParameter('alpha', 0.1)
pdi = self.GetInputDataObject(0,0)
pdo = self.GetOutputDataObject(0)
pdo.CopyAttributes(pdi)
d = alpha * inputs[0].PointData['temperature']
arr = DA.numpyTovtkDataArray(d, 'temperature_scaled')
pdo.GetPointData().AddArray(arr)
This script works, but I can't set alpha using keyframes. It just doesn't
show up in the animation view.
Perhaps I have understood what the whole SetParameter framework does.
What is the point of setting these parameters if they can't be modified
from outside the filter?
Thanks in advance for your help.
-Ryan
___
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://public.kitware.com/mailman/listinfo/paraview
[Paraview] ParticleTracer particle lifetime
Hello, I am continuing my ongoing quest to do something like this http://earth.nullschool.net/#current/wind/isobaric/1000hPa/orthographic=267.73,5.54,350 or this http://www.youtube.com/watch?v=xusdWPuWAoU in Paraview using ***time dependent velocity vectors***. While the LIC plugin is very cool, it does something different. I followed the previous suggestion and tried to use the streamline filter: http://paraview.org/Wiki/ParaView/Custom_Filters Unfortunately that is not quite right either. The problem with the streamline filter is that it treats each timestep as completely independent and regenerates the streamlines whenever the velocity field changes. (This is the correct behavior: streamlines are defined by the *instantaneous* flow.) What we see in those videos are truly particle trajectories. In particular: - particles are seeded randomly (in space and time) - they leave a decaying trail (sometimes called a streaklet) - the particles disappear after a short lifetime This is the combination of ingredients I need to reproduce in paraview. The best candidate is clearly the ParticleTracer filter. However, I have hit a serious problem: it doesn't appear that this filter is able to make the particles die after a temporal lifetime. Compare the v 3.3 documentation http://paraview.org/OnlineHelpCurrent/ParticleTracer.html with the current documentation http://paraview.org/Wiki/ParaView/Users_Guide/List_of_filters#ParticleTracer In the old version, there was an option called Termination Time that is missing from the new version. Without such an option, the particles will never disappear, the domain will get more and more crowded, and the computational expense will grow with time. Let me know if you have any suggestions or if you know how to re-enable this Termination Time option. Thanks a lot, Ryan ___ 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 particle lifetime
Berk, That might be the correct interpretation for the first video, which I think uses a steady (i.e. not time-dependent) flow field. For steady flows, streamlines, streaklines, and trajectories are all identical. But if you look at the second video, I think you can see that they are plotting Lagrangian trajectories. My velocity data is time-dependent, so I think I need the trajectories. -Ryan On Tue, Jan 14, 2014 at 2:47 PM, Berk Geveci berk.gev...@kitware.comwrote: Hi Ryan, When I look at these movies carefully, it looks like they are using streaklines that are seeded for a short burst. It looks like they pick a number of seeds each time step and start a streakline from each and keep them active for a few time steps. Then those streaklines seem to be killed eventually. It also appears as if they are playing with transparency depending on the age of the streakline. Am I right? -berk On Tue, Jan 14, 2014 at 2:20 PM, Ryan Abernathey ryan.abernat...@gmail.com wrote: Hello, I am continuing my ongoing quest to do something like this http://earth.nullschool.net/#current/wind/isobaric/1000hPa/orthographic=267.73,5.54,350 or this http://www.youtube.com/watch?v=xusdWPuWAoU in Paraview using ***time dependent velocity vectors***. While the LIC plugin is very cool, it does something different. I followed the previous suggestion and tried to use the streamline filter: http://paraview.org/Wiki/ParaView/Custom_Filters Unfortunately that is not quite right either. The problem with the streamline filter is that it treats each timestep as completely independent and regenerates the streamlines whenever the velocity field changes. (This is the correct behavior: streamlines are defined by the *instantaneous* flow.) What we see in those videos are truly particle trajectories. In particular: - particles are seeded randomly (in space and time) - they leave a decaying trail (sometimes called a streaklet) - the particles disappear after a short lifetime This is the combination of ingredients I need to reproduce in paraview. The best candidate is clearly the ParticleTracer filter. However, I have hit a serious problem: it doesn't appear that this filter is able to make the particles die after a temporal lifetime. Compare the v 3.3 documentation http://paraview.org/OnlineHelpCurrent/ParticleTracer.html with the current documentation http://paraview.org/Wiki/ParaView/Users_Guide/List_of_filters#ParticleTracer In the old version, there was an option called Termination Time that is missing from the new version. Without such an option, the particles will never disappear, the domain will get more and more crowded, and the computational expense will grow with time. Let me know if you have any suggestions or if you know how to re-enable this Termination Time option. Thanks a lot, Ryan ___ 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] ParticleTracer particle lifetime
Yes, that sounds very sensible! Of course, the difficult part (for me, a relative noob) is to actually implement those steps in terms of a Paraview pipeline. Or would you recommend creating a new custom filter? Unfortunately experimentation has been difficult because of the slowness / instability of the ParticleTracer filter. Even with a very modest number of particles (~10), I experience crippling delays when advancing timesteps. Perhaps pre-generating the trajectories is the answer. Thanks a lot for your suggestions. -Ryan On Tue, Jan 14, 2014 at 3:32 PM, Berk Geveci berk.gev...@kitware.comwrote: I got it. I think that the correct way of doing this would be: 1. Seed particles 2. Integrate 1 time step 3. Kill particles that are older that threshold 4. Connect particles to generate streaklets 5. If time step % n == 0, update seed source randomly 6. Go to 1 if time step left Does this make sense? -berk On Tue, Jan 14, 2014 at 3:17 PM, Ryan Abernathey ryan.abernat...@gmail.com wrote: Berk, That might be the correct interpretation for the first video, which I think uses a steady (i.e. not time-dependent) flow field. For steady flows, streamlines, streaklines, and trajectories are all identical. But if you look at the second video, I think you can see that they are plotting Lagrangian trajectories. My velocity data is time-dependent, so I think I need the trajectories. -Ryan On Tue, Jan 14, 2014 at 2:47 PM, Berk Geveci berk.gev...@kitware.com wrote: Hi Ryan, When I look at these movies carefully, it looks like they are using streaklines that are seeded for a short burst. It looks like they pick a number of seeds each time step and start a streakline from each and keep them active for a few time steps. Then those streaklines seem to be killed eventually. It also appears as if they are playing with transparency depending on the age of the streakline. Am I right? -berk On Tue, Jan 14, 2014 at 2:20 PM, Ryan Abernathey ryan.abernat...@gmail.com wrote: Hello, I am continuing my ongoing quest to do something like this http://earth.nullschool.net/#current/wind/isobaric/1000hPa/orthographic=267.73,5.54,350 or this http://www.youtube.com/watch?v=xusdWPuWAoU in Paraview using ***time dependent velocity vectors***. While the LIC plugin is very cool, it does something different. I followed the previous suggestion and tried to use the streamline filter: http://paraview.org/Wiki/ParaView/Custom_Filters Unfortunately that is not quite right either. The problem with the streamline filter is that it treats each timestep as completely independent and regenerates the streamlines whenever the velocity field changes. (This is the correct behavior: streamlines are defined by the *instantaneous* flow.) What we see in those videos are truly particle trajectories. In particular: - particles are seeded randomly (in space and time) - they leave a decaying trail (sometimes called a streaklet) - the particles disappear after a short lifetime This is the combination of ingredients I need to reproduce in paraview. The best candidate is clearly the ParticleTracer filter. However, I have hit a serious problem: it doesn't appear that this filter is able to make the particles die after a temporal lifetime. Compare the v 3.3 documentation http://paraview.org/OnlineHelpCurrent/ParticleTracer.html with the current documentation http://paraview.org/Wiki/ParaView/Users_Guide/List_of_filters#ParticleTracer In the old version, there was an option called Termination Time that is missing from the new version. Without such an option, the particles will never disappear, the domain will get more and more crowded, and the computational expense will grow with time. Let me know if you have any suggestions or if you know how to re-enable this Termination Time option. Thanks a lot, Ryan ___ 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
[Paraview] how do I do this?
I have vector velocity data from a CFD simulation, and I would like to visualize the flow like this: http://earth.nullschool.net/#current/wind/isobaric/1000hPa/orthographic=267.73,5.54,350 Is there any way I can do this with paraview? Thanks, Ryan ___ 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] Building Paraview against Enthought Canopy Python on Mac OS 10.8.5
Dear Paraview Community, This is mostly just a description of my experience successfully building Paraview. However there is one outstanding issue involving RPATH (described at the end) that I would greatly appreciate some advice on. I use what is probably an increasingly popular platform for scientific computing: Mac OS plus the excellent Enthought Canopy python environment. Canopy greatly simplifies the installation of numpy / scipy and related packages and is free for academic use. Canopy creates a standalone python installation on Mac OS, completely replacing the system python. The problem is that the paraview binary distribution for Mac OS links against the standard system python, meaning that I cannot load scipy modules from within the paraview python shell, or in pvpython. To fix this, I decided to build a new paraview from source linking against the Canopy python. For the most part, the build was very straightforward following the wiki instructions http://paraview.org/Wiki/ParaView:Build_And_Install I installed cmake 2.8.8 from source and QT 4.8.5 from the dmg ( http://qt-project.org/downloads) I did not install ffmpeg or mesa. Then I downloaded the Paraview v4.0.1 source. FYI, my Canopy version is 1.1.0 64-bit. I had to use several custom settings in ccmake. Of course, PARAVIEW_ENABLE_PYTHON = On I had to point ccmake at the canopy python enviroment. This took some figuring out. With canopy, your python executable is $HOME/Library/Enthought/Canopy_64bit/User/bin/python Naturally I thought to use the following settings PYTHON_EXECUTABLE=$HOME/Library/Enthought/Canopy_64bit/User/bin/python PYTHON_INCLUDE_DIR=$HOME/Library/Enthought/Canopy_64bit/User/include PYTHON_LIBRARY=$HOME/Library/Enthought/Canopy_64bit/User/Python However, this caused ccmake to give an error, complaining about a missing patchlevel.h file in the python include directory. I poked around and found a different version of the includes inside the Canopy app. The settings that ended up working were PYTHON_INCLUDE_DIR=/Applications/Canopy.app/appdata/canopy-1.1.0.1371.macosx-x86_64/Canopy.app/Contents/include/python2.7/ PYTHON_LIBRARY=/Applications/Canopy.app/appdata/canopy-1.1.0.1371.macosx-x86_64/Canopy.app/Contents/lib/libpython2.7.dylib After this ccmake was able to finish successfully. Then I built and installed (make make install) with no errors. The only issue I have now is that paraview binaries link to python using RPATH. Compare the original paraview binary: $ otool -L /Applications/paraview_original.app/Contents/bin/pvpython ... /System/Library/Frameworks/Python.framework/Versions/2.7/Python (compatibility version 2.7.0, current version 2.7.1) ... with my new paraview binary $ otool -L /Applications/paraview.app/Contents/bin/pvpython ... @rpath/Python (compatibility version 2.7.0, current version 2.7.0) ... The problem is that the linker cannot find the python libraries at runtime using rpath. $ Applications/paraview.app/Contents/MacOS/paraview dyld: Library not loaded: @rpath/Python Referenced from: /Applications/paraview.app/Contents/MacOS/paraview Reason: image not found Trace/BPT trap: 5 However, if I pass the library path using DYLD_LIBRARY_PATH, it works fine. $ DYLD_LIBRARY_PATH=/Users/rpa/Library/Enthought/Canopy_64bit/User /Applications/paraview.app/Contents/MacOS/paraview The documentation on ccmake and RPATH is quite overwhelming for a novice like me. I am content to use my DYLD_LIBRARY_PATH hack, but if anyone knows how to overcome this issue, my build would be flawless. In any case, I hope this message will be useful for anyone else interested in using paraview with a canopy-based python. Best, Ryan Abernathey ___ 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] VTK error in server mode
Hello, I have been running paraview in client server mode. I recently decided to upgrade my setup for version 3.14 to the latest version. My client version is now 3.98.1 64-bit on Mac OS 10.7.5. It works fine. On the server, I build paraview from source with MPI support following the online instructions. I updated my git repository, which apparently gave me version 3.98.1-112-g9dd3ee9. Is this correct? Is this a stable version? I don't understand the subtleties of git. The build goes fine, and I am able to run pvserver and connect to it from my client as usual. The problem arises when I try to read in a VTK file. This file worked absolutely fine on the server in version 3.14. It also works fine on my local machine in 3.98.1. However, when I try to load it on the server in version 3.98.1-112-g9dd3ee9, I get this error: ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/ParaViewCore/ClientServerCore/Core/vtkPVArrayInformation.cxx, line 721 vtkPVArrayInformation (0x11ca92270): Error parsing range of component. In the information tab, the data range shows as THETA: double [1e+299,-1e+299] To me this looks like an error in endianness or something like that. (For reference, the vtk file is online here: http://www-pord.ucsd.edu/~rpa/THETA.00.vtr) I don't understand this error. I fear that I am using some sort of unstable development branch, but I don't know how to check out / build a different version. Any advice you have would be greatly appreciated. -Ryan Abernathey ___ 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] [EXTERNAL] Animation Resolution Problem
Thanks for your suggestions. I wasn't able to get any of them to work in 3.14.1, so I just upgraded. Now everything works fine! Many thanks. -Ryan On Wed, Nov 28, 2012 at 12:41 PM, Scott, W Alan wasc...@sandia.gov wrote: I think this was a known bug that was fixed. I looked in the bug tracker, and couldn’t find it. Try removing your configuration files – I believe this can cause your problem. ** ** If that doesn’t fix it, I just tried remote and local server, making the animation larger and smaller than my window, on Linux. All succeeded . This is with the newest, latest, greatest, bestest version of paraView – 3.98.0. RC3 is currently on the web site. ** ** Alan ** ** *From:* paraview-boun...@paraview.org [mailto: paraview-boun...@paraview.org] *On Behalf Of *Ryan Abernathey *Sent:* Wednesday, November 28, 2012 12:55 PM *To:* paraview *Subject:* [EXTERNAL] [Paraview] Animation Resolution Problem ** ** Hello, ** ** I would like to export an animation (sequence of pngs) with a specific size. This seems straightforward to do using the Animation Settings Dialog. I enter my desired geometry where it says Resolution (pixels), specifically 640 x 720. Once the animation begins saving, however, the output png files do not have anything close to this resolution, and instead are 2758 × 1348, an unusably large size. As far as I can tell, the aspect ratio of the true output resolution is determined by the current view window, but the dimensions are rescaled to be much larger. The resolution I specify in the Animation Settings Dialog apparently has no affect whatsoever. ** ** I would appreciate any suggestion you have about how to overcome this problem. ** ** I am using Paraview 3.14.1, 64-bit, QT version 4.6.4. on Mac OS 10.7.5 ** ** Best Regards, Ryan Abernathey ___ 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] Animation Resolution Problem
Hello, I would like to export an animation (sequence of pngs) with a specific size. This seems straightforward to do using the Animation Settings Dialog. I enter my desired geometry where it says Resolution (pixels), specifically 640 x 720. Once the animation begins saving, however, the output png files do not have anything close to this resolution, and instead are 2758 × 1348, an unusably large size. As far as I can tell, the aspect ratio of the true output resolution is determined by the current view window, but the dimensions are rescaled to be much larger. The resolution I specify in the Animation Settings Dialog apparently has no affect whatsoever. I would appreciate any suggestion you have about how to overcome this problem. I am using Paraview 3.14.1, 64-bit, QT version 4.6.4. on Mac OS 10.7.5 Best Regards, Ryan Abernathey ___ 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] Client-Server Handshake failed
Hello, I am trying to establish a connection between my workstation (Mac OS 10.7.4, Paraview via binary installer version 3.14.1 64-bit) and a remote server. On the server side, I built an mpi-enabled paraview from scratch, following the instructions on the wiki, but using the intel compiler (2012.0.032) and the SGI MPI library (mpi-sgi/mpt.2.04.10789). This was no small task, but as far as I can tell, the build was completely successful. The server version is 3.14.1-1217-g611f58e. The essence of the problem is a Client/server version hash mismatch error, which paraview suggests is due to mismatched versions. However, my client and server versions the same. Below is a detailed description of the problem. I have invested a lot of time in this so far and now very frustrated to be stuck. I sincerely appreciate any help you can offer. Best Regards, Ryan Abernathey DETAILS The server nodes are behind a front-end node, so I have to use ssh tunneling. Following the wiki instructions ( http://paraview.org/Wiki/Reverse_connection_and_port_forwarding#A_Forward_Connection_Over_an_ssh_Tunnel) I am able to establish an ssh tunnel for a forward connection. I have verified that the client on my local host is able to open a connection to the server. The steps I take are: 1) Run an interactive PBS job to to get a compute node. 2) Knowing the host name of the compute node, I establish an ssh tunnel from my workstation like this: [LOCAL_WORKSTATION]$ ssh -v -L 1:COMPUTE_NODE:2 FRONT_END_HOST -N 3) Then I start the paraview server on the host [COMPUTE_NODE]$ mpiexec pvserver --server-port=2 4) Finally, I connect to the server from my workstation using the paraview client GUI. The settings are Server Type: Client / Server; Host: localhost; Port: 1. Since I used a verbose SSH tunnel, I can verify that the tunnel is working: debug1: Connection to port 1 forwarding to COMPUTE_NODE port 2 requested. debug1: channel 2: new [direct-tcpip] debug1: channel 2: free: direct-tcpip: listening port 1 for r211i0n0 port 2, connect from 127.0.0.1 port 58973, nchannels 3 (I have to admit that I don't understand what the last line means.) This is where the errors start. On the server side, I see: Waiting for client... Connection URL: cs://COMPUTE_NODE:2 Accepting connection(s): COMPUTE_NODE:2 ERROR: In /u/rpaberna/paraview/src/ParaView/VTK/Parallel/Core/vtkSocketCommunicator.cxx, line 506 vtkSocketCommunicator (0x1b2d2d0): Client/server version hash mismatch. On the client side, I see: ERROR: In /Source/ParaView/release/ParaView/VTK/Parallel/vtkSocketCommunicator.cxx, line 615 vtkSocketCommunicator (0x115f85830): Client/server version hash mismatch. ERROR: In /Source/ParaView/release/ParaView/ParaViewCore/ClientServerCore/vtkTCPNetworkAccessManager.cxx, line 321 vtkTCPNetworkAccessManager (0x10c655f20): Failed to connect to localhost:1. Client-Server Handshake failed. Please verify that the client and server versions are compatible with each other ERROR: In /Source/ParaView/release/ParaView/ParaViewCore/ServerManager/vtkSMSessionClient.cxx, line 257 vtkSMSessionClient (0x11650da80): Some error in socket processing. The connection fails. ___ 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
