[Paraview] Pasting multiple .csv inputs together
All, Say I have a .csv file containing x, y and z output from a simulation, and a second .csv file with the same number of rows that contains just a single column containing something such as pressure. Is there a Paraview equivalent of the unix 'paste' command that will do a column bind? Some way to turn something that might look like: geom.csv: x,y,z -1,-1,0 0,0,1.2 ... press.csv: pres 1.23 3.45 ... into: x,y,z,pres -1,-1,0,1.23 0,0,1.2,3.45 ... Or some way to amend a set of points from TableToPoints with a loaded .csv? Obviously the assumption is that the information in the additional file is in the same order as the loaded geometry. -David Ortley ___ 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: https://paraview.org/mailman/listinfo/paraview
[Paraview] Complex filters for structured meshes
Hello,
I work with a CFD code that uses a structured mesh. We frequently want to
do math operations that require each cell to have knowledge of its
neighbors. Things such as a calculating the max of a certain variable, or
a gradient in a given direction.
I'm not sure the best way to accomplish this. I have a code snippet for
use in the programmable filter that I use (copied below), but its behavior
is similar to the calculator in that it works on individual cells without
knowledge of cell neighbors.
Can somebody A) critique my skeleton code below to let me know if I could
write it better and B) help me with figuring out a method (any method) that
has visibility of neighbor cells?
Thanks
-David Ortley
# Programmable filter snippet:
pdi=self.GetInput()
pdo=self.GetOutput()
numCells = pdi.GetNumberOfCells()
cells = pdi.GetCellData()
# Some array already in the calc results that I'm going to reason on
# say it's pressure or energy or something
orig_array = cells.GetArray("orig_array")
# Storing
new_array = vtk.vtkDoubleArray()
new_array.SetName("new_array")
for i in range(numCells):
# do some work
blah = pkovpr.GetValue(i) * 1.23456789
# store as new val in array
new_array.InsertNextValue(blah)
# Add the array I just created to the output so Paraview can do stuff with
it
pdo.GetCellData().AddArray(betaMax)
___
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] Change request for Lights Dialog box
All, When one clicks the 'Edit' button for the Lights section in the Properties tab, the default behavior when [Enter] is pressed, is to reset all of the settings. As an example, if I were to change the Key light's Elevation, then hit [Enter], the value gets reset. This has bitten me more than once when I've made a handful of changes, and then accidentally hit [Enter] just to have all of my changes reset. It would be nice to have behavior consistent with the other Paraview dialog boxes. This is on OS X (El Capitan). I don't know if this is the behavior on Windows/Linux/other... -David Ortley ___ 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] Slice filter to Image
All, Is there a way to make an image out of a slice? I want to take a slice of a 3D hydro (cell data) and turn it into an image of just the slice, without the extra information such as the background, perspective, etc... I'm specifically going to be doing this in a python script that I run with pvbatch --mpi. If there isn't a quick way, but someone can point me to some examples that can help me get where I'm trying to go, that would be great as well. Thanks. -David Ortley ___ 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] Parallel unfriendly filters?
Just an update. Kenneth, I think I understand the logic of what you're saying. I have a large calculation that I'm working on this week that will require some visualization. I'll update this thread with my progress as I get the chance. -David Ortley On Tue, Feb 9, 2016 at 7:04 AM, Dan Lipsa <dan.li...@kitware.com> wrote: > >> >> Cell Data to Point Data is the only way I know of to activate the contour >> filter for silo files. The results are stored in cell arrays, which >> apparently don't activate the contour filter. I stumbled upon using Cell >> Data to Point Data by accident, so if there's a better way to do this, I'm >> open to it. >> > > I see. I would go with Ken's suggestions, then. I would also create a new > array called 'vtkGhostType' from 'avtGhostZones'. You could do that > instead of thresholding out the ghost zones. VTK knows about vtkGhostType > name. I think you could leave those in as they should not be rendered. > > You can create the new array from avtGhostZone using the Calculator filter. > > Dan > > ___ 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] Parallel unfriendly filters?
Kenneth: The ghost zones are the contents of the ghost zones stored from the calculation. They overlap into the hydro from neighboring processors (the silo library stores a block per processor the way we're using it in our code.) If I leave them in there, I get artifacts. I'm actually thresholding out a variable called 'avtGhostZones', which the silo libraries call the stored ghost zone values. Dan: Cell Data to Point Data is the only way I know of to activate the contour filter for silo files. The results are stored in cell arrays, which apparently don't activate the contour filter. I stumbled upon using Cell Data to Point Data by accident, so if there's a better way to do this, I'm open to it. Thanks. -David Ortley On Mon, Feb 8, 2016 at 1:35 PM, Moreland, Kenneth <kmo...@sandia.gov> wrote: > Have you tried doing the threshold last (after the contour) rather than > first? Generally, ParaView relies on ghost zones (cells) to avoid artifacts > across process boundaries. > > -Ken > > > From: ParaView <paraview-boun...@paraview.org> on behalf of David Ortley < > djort...@gmail.com> > Date: Monday, February 8, 2016 at 1:14 PM > To: "paraview@paraview.org" <paraview@paraview.org> > Subject: [EXTERNAL] [Paraview] Parallel unfriendly filters? > > I'm running Paraview in client/server mode with the server running on an > HPC platform across multiple nodes. > > My input is a multi-block silo file that contains ghost zone information. > The way I do a seamless contour when visualizing on my workstation is to do > the following: > > Load the silo file > -> Threshold out the ghost zones (threshold filter) > -> Merge the blocks > -> Cell data to point data > -> Contour > > This works well enough when on a single machine. But when visualizing > client/server with the server running across multiple nodes, there appear > seams on the contours. > > Is this an expected behavior given my setup? Are any of the filters that > I listed above (Threshold, Merge Blocks, Cell data to point data, and > Contour) not fully implemented in parallel yet? > > nb - I've not spent a lot of time trying to debug the problem, so I don't > know if the problem exists when a server is running on a single node only. > It looks like something that is happening at node boundaries, but I could > be wrong and it could be a per/processor thing. > > Thanks. > > -David Ortley > ___ 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] Parallel unfriendly filters?
I'm running Paraview in client/server mode with the server running on an HPC platform across multiple nodes. My input is a multi-block silo file that contains ghost zone information. The way I do a seamless contour when visualizing on my workstation is to do the following: Load the silo file -> Threshold out the ghost zones (threshold filter) -> Merge the blocks -> Cell data to point data -> Contour This works well enough when on a single machine. But when visualizing client/server with the server running across multiple nodes, there appear seams on the contours. Is this an expected behavior given my setup? Are any of the filters that I listed above (Threshold, Merge Blocks, Cell data to point data, and Contour) not fully implemented in parallel yet? nb - I've not spent a lot of time trying to debug the problem, so I don't know if the problem exists when a server is running on a single node only. It looks like something that is happening at node boundaries, but I could be wrong and it could be a per/processor thing. Thanks. -David Ortley ___ 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] Bug in 4.2 and above
All, I've found a problem in Paraview that seems to be in every version from 4.2 to current (4.4) which involves the selecting and exporting of points as .csv files. This problem doesn't appear in version 4.1, and I don't recall it appearing in versions prior, but I've not tested that fully. I've also only tested the problem out with moderate sized data sets (around 10k or more points) and only on a Mac Pro (with 64 Gigs of Ram). To test the problem, I used the following R script will create a file named 'break.csv' (though this seems to be a problem with any large set of points) : #!/usr/bin/env Rscript # cols x,y,z are position # col r is radius, col n is an index number df=data.frame(x=rnorm(1),y=rnorm(1),z=rnorm(1),n=seq(1)) df$r=sqrt(df$x**2 + df$y**2 + df$z**2) write.csv(df, 'break.csv', row.names=F, quote=F) Load the file in Paraview, then add 'Table To Points', assigning X,Y and Z appropriately. Enable the 'Table To Points' filter in the 3D view and use the 'Select points through (g)' button on the 3D view to select about half of the points. In the Spreadsheet view, make sure the 'TableToPoints*' filter is selected and click the 'Show only selected elements'. With the Spreadsheet view still active: File -> Export Scene... and save the file as a .CSV. If you load the newly saved .CSV file and apply 'Table To Points' to Points:0, Points:1 and Points:2, the data is a mess (you may have to reset your view to see some of the mess.) Is anybody else able to reproduce this? If so, is there already an open ticket somewhere, or does a bug report need to be written? -David Ortley. ___ 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] Smooth seams in SILO files
Utkarsh: Thanks. That did the trick. I had to add a 'Threshold' filter in the mix to remove the ghost cells, which were confusing the 'Merge Blocks' filter. I've actually been staring at those boundary lines for over a year and a half and I've very glad to finally have them gone Again, thank you very much. -David Ortley On Wed, Feb 25, 2015 at 7:26 AM, Utkarsh Ayachit utkarsh.ayac...@kitware.com wrote: Try applying Merge Blocks and before applying the CellDatatoPointData. ParaView indeed treats each block separately. When you do Merge Blocks, it will merge all the blocks into a single unstructured grid. This will make it possible to get a more reliable CellDataToPointData conversion across the block seams and hence avoid the seams on contouring. Utkarsh On Tue, Feb 24, 2015 at 6:13 PM, David Ortley djort...@gmail.com wrote: Hello all, We have a CFD code that generates silo files using the silo library. For each dump in the simulation, there are multiple files per dump (one file per processor) and a single master file. When we use Visit to visualize a contour, the contours look good. When using Paraview (any version), there exist obvious seams at the file boundaries. To visualize in Paraview, we use the 'CellDatatoPointData' filter followed by the 'Contour' filter. I'm currently trying to track down if either Visit is magically healing over a bug in our implementation, or if the problem lies with Paraview somehow...or with how I'm trying to generate the contour (via the 'CellDatatoPointData' filter.) It almost looks like Paraview is treating the edge of each file as if it were an open boundary regardless of whether it is buttressed up against another file. Thanks for any help in this. -David Ortley ___ 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 ___ 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] Smooth seams in SILO files
Hello all, We have a CFD code that generates silo files using the silo library. For each dump in the simulation, there are multiple files per dump (one file per processor) and a single master file. When we use Visit to visualize a contour, the contours look good. When using Paraview (any version), there exist obvious seams at the file boundaries. To visualize in Paraview, we use the 'CellDatatoPointData' filter followed by the 'Contour' filter. I'm currently trying to track down if either Visit is magically healing over a bug in our implementation, or if the problem lies with Paraview somehow...or with how I'm trying to generate the contour (via the 'CellDatatoPointData' filter.) It almost looks like Paraview is treating the edge of each file as if it were an open boundary regardless of whether it is buttressed up against another file. Thanks for any help in this. -David Ortley ___ 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
