Re: [Paraview] Using Probe Filter To Get The Average Value Around A Point

[Moreland, Kenneth]

As far as I know, there is no way to get the probe filter to get all points 
within a radius as you describe. You may instead consider the Point Data to 
Cell Data Filter. That will for each cell take the values of all attached 
points and average them.

The point volume interpolator filter will create a grid (by default 100^3) and, 
in gaussian kernel mode, will “splat” a gaussian function onto the grid from 
every point. Another way to think of it is that a 3D gaussian function is 
convolved with a 3D function comprising an impulse function at every point in 
the mesh scaled by the field value (and then sampled on the grid).

-Ken

Sent from my iPad

> On Feb 6, 2018, at 8:21 PM, Jeremias Gonzalez <jgonzale...@ucmerced.edu> 
> wrote:
> 
> Thank you very much for your explanations and suggestions. Responses 
> interspersed below.
> 
>> On 2/5/2018 4:57 PM, Moreland, Kenneth wrote:
>> Jeremias,
>> When you set a radius and number of points in the probe filter, then the 
>> filter will randomly sample the volume within the defined sphere the number 
>> of times requested. The resulting values are the field values at those 
>> randomly sampled locations. >
>> An easy way to get an average of your samples is to run the result of the 
>> probe filter through the descriptive statistics filter. Look at the 
>> "Statistical Model" table and it will report the mean value for each field. 
>> (Note that if you are using ParaView 5.4 there is a bug, #17627, that shows 
>> the Statistical Model table wrong by default. You have to also change the 
>> Composite Data Set Index parameter in the Display part of the properties 
>> panel to select only the Derived Statistics block.)
>> A couple of caveats to this approach. First, because the sampling is random, 
>> don't expect the exact same answer every time you run it. Second, if one of 
>> the samples happens to lie outside of the mesh, that sample will be filled 
>> with 0's for all fields. That will throw off the average value.
> 
> Is there a probe setting that will simply grab all the points living in the 
> original mesh within the radius of the sphere I choose?
> 
>> That said, another approach you might want to take is to first filter the 
>> data in a way that blurs out the noise first. One way you can do that is to 
>> run the Point Volume Interpolator filter. Change the Kernel to something 
>> like Gaussian (the default Voronoi filter will not do the averaging that you 
>> want). Set the radius appropriately. You can then probe the resulting data 
>> set with a single value (radius 0) and immediate see the "averaged" result.
>> -Ken
> 
> I don't seem to be finding any information on what exactly the Gaussian 
> kernel does with the data, so how close is it to the plain averaging I would 
> like it to be doing?
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Re: [Paraview] Using Probe Filter To Get The Average Value Around A Point

[Moreland, Kenneth]

Jeremias,

When you set a radius and number of points in the probe filter, then the filter 
will randomly sample the volume within the defined sphere the number of times 
requested. The resulting values are the field values at those randomly sampled 
locations.

An easy way to get an average of your samples is to run the result of the probe 
filter through the descriptive statistics filter. Look at the "Statistical 
Model" table and it will report the mean value for each field. (Note that if 
you are using ParaView 5.4 there is a bug, #17627, that shows the Statistical 
Model table wrong by default. You have to also change the Composite Data Set 
Index parameter in the Display part of the properties panel to select only the 
Derived Statistics block.)

A couple of caveats to this approach. First, because the sampling is random, 
don't expect the exact same answer every time you run it. Second, if one of the 
samples happens to lie outside of the mesh, that sample will be filled with 0's 
for all fields. That will throw off the average value.

That said, another approach you might want to take is to first filter the data 
in a way that blurs out the noise first. One way you can do that is to run the 
Point Volume Interpolator filter. Change the Kernel to something like Gaussian 
(the default Voronoi filter will not do the averaging that you want). Set the 
radius appropriately. You can then probe the resulting data set with a single 
value (radius 0) and immediate see the "averaged" result.

-Ken


On 2/5/18, 5:27 PM, "ParaView on behalf of Jeremias Gonzalez" 
 wrote:

Hi, I'm trying to find a way to get the average value around a point in 
a mesh that I know to be noisy due to its coarseness. Currently, I am 
unable to understand determine the exact nature of the radius and number 
of point parameters from the documentation ( 

https://www.paraview.org/ParaView/Doc/Nightly/www/py-doc/paraview.simple.ProbeLocation.html
 
), but I am guessing from some third party posts that the radius enables 
one to find a point nearby to a desired point in a given region, and the 
number of points expands the amount captured. The problem I have past 
that, if those are correct understandings, is what to do with the probe 
once I have it. Looking at the resulting spreadsheet from using the 
probe location with a given radius and number of points each labelled 
from 0 to 99, for example, it seems that I may have to use another loop, 
after I introduce and use the probe, with code like

my_running_total=0

for y in range(0, 99):
my_running_total += 
mycalcprobepoint.GetPointData(y).GetArray('Result').GetValue(0)

my_running_total /= 100

that will take that batch of points collected by the probe and average 
all the values I want. Is this the correct interpretation, and a valid 
way to carry out this objective?
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Re: [Paraview] Save Animation option in ParaView 5.4.0 vs 5.3.0

[Moreland, Kenneth]

Mark,

One more thing to help until the num frames/time step comes back. If you want 
to use the sequence mode and get a time stamp that reflects the time in your 
time step, try using the Annotate Time Filter (as opposed to the Annotate Time 
Source) and attach it to your data. That should report the time of your data 
instead of the global ParaView time. (There is an exercise in the ParaView 
tutorial demonstrating this.)

-Ken

Sent from my iPad

On Jan 26, 2018, at 10:59 AM, David E DeMarle 
> wrote:

Hey Mark,

Looks like we took that out as part of the revamp described here:
https://gitlab.kitware.com/paraview/paraview/issues/15917

Specifically this merge request took out the "No. Frames" entry.
https://gitlab.kitware.com/paraview/paraview/merge_requests/896
because, at least at that time, apparently the control didn't do anything at 
all.

A 1 commit merge request that restores the widget and hooks it up to do what it 
apparently did at one time is
here. https://gitlab.kitware.com/paraview/paraview/merge_requests/2197

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Fri, Jan 26, 2018 at 10:17 AM, Van Moer, Mark W 
> wrote:
Hello,

In ParaView 5.3.0 and earlier, when Animation mode was Snap to TimeSteps, in 
the Save Animation dialog box there was an option for No. of Frames / timestep. 
This doesn't show up in the 5.4.0 dialog box. Was this just moved or was it 
removed completely?

My use case for this is a data set with 25 timesteps, each of which is on the 
order of either 5 minutes or 30 minutes apart in real world time. I'd render 30 
frames / timestep to get a 25 second movie to show each discrete timestep for 
one second. The video should show those discrete jumps in time and not use 
interpolation.

I can do the frame replication in BASH but it was handy to have that option.

Thanks,
Mark

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Re: [Paraview] Reading netCDF files Earth models

[Moreland, Kenneth]

Manochehr,

ParaView always renders in a Cartesian space. So if you want the lat/lon/depth 
values to look like a sphere, the coordinates have to be converted and you will 
loose the original values. I can see the point of your use case. It just never 
came up before. It seems reasonable to be able to save the original lat/lon 
values in a field, so I raised a bug for it.

https://gitlab.kitware.com/paraview/paraview/issues/17943

As far as getting the coordinates in a script, it is possible but not 
recommended. If you need to access field or coordinate values directly, it is 
usually best to do so in a programmable filter.

-Ken

Sent from my iPad

On Jan 18, 2018, at 7:06 AM, Manochehr Bahavar 
<man...@iris.washington.edu<mailto:man...@iris.washington.edu>> wrote:

Hi Aashish,

Thank you for your reply. That will be great if it gets looked into:) Going 
back and forth between coordinate systems may be a little confusing, but I will 
give it a try and see how it works out.


Could you also point me in the right direction for getting the latitude, 
longitude and depth arrays? As I mentioned in my reply to Ken (below), using 
Python, I go as far as getting the extents and bounds but cannot get the actual 
values.

Thank you again for your quick reply and useful suggestions.

Best,

—manoch



On Jan 17, 2018, at 10:29 PM, Aashish Chaudhary 
<aashish.chaudh...@kitware.com<mailto:aashish.chaudh...@kitware.com>> wrote:

Hi Manoch,

I think what you want is not possible right now but let us get back to you on 
it as something we might want to look into before we can say it for sure. One 
workaround would be you load the data (uncheck the sphere coordinate system), 
apply the filter, and then write the data back as NetCDF. It is not ideal by 
any means. You can also look into vtkSphericalTransform (if you want to convert 
data back to spherical coordinate system) but you will not get the exact shape 
of earth which is a ellipsoid (which I am not sure if you would be interested 
in anyways).

Hope this helps.

On Wed, Jan 17, 2018 at 7:12 PM Manochehr Bahavar 
<man...@iris.washington.edu<mailto:man...@iris.washington.edu>> wrote:
Ken,

Thanks for your reply. The problem with that approach is that all the features 
I am interested in make sense if they are plotted on a sphere (they approximate 
the Earth surface). So, there is no builtin solution for that?

One more question: How can I access the actual latitude, longitude and depth 
parameter values using Python. I can see their extent and bounds, but I can not 
see how I can access the individual values:

temp.GetBounds()
(0.0, 359.0, -89.0, 89.0, -2750.0, 50.0)
temp.GetDimensions()
(360, 179, 57)
temp.GetExtent()
(0, 359, 0, 178, 0, 56)
temp.GetCenter()
(179.5, 0.0, -1350.0)
temp.GetNumberOfPoints()
3673080L

Really appreciate your help

—manoch


On Jan 17, 2018, at 3:57 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:

Manochehr,

If you uncheck the “Spherical Coordiantes” option, then the longitude, 
latitude, and depth values will be preserved as x, y, and z coordinates. 
(Instead of translated to a sphere, the data will appear in a rectangle.)

-Ken


On 1/17/18, 4:34 PM, "ParaView on behalf of Manochehr Bahavar" 
<paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org> on behalf 
of man...@iris.washington.edu<mailto:man...@iris.washington.edu>> wrote:

   Hello,

   I am trying to see if I can visualize my netCDF Earth models (longitude, 
latitude,depth) using ParaView. I have been able to load the models, with the 
"Spherical Coordinates" option selected. However it appears that I now lose my 
coordinates and depth values and as a result to extract a subset, I have to use 
the depth index (not the actual depth value). Is there a way to preserve the 
latitude, longitude and depth values and work with ParaView using the actual 
values (not their index) directly?

   Thank you,

   —manoch
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Re: [Paraview] Reading netCDF files Earth models

[Moreland, Kenneth]

Manochehr,

If you uncheck the “Spherical Coordiantes” option, then the longitude, 
latitude, and depth values will be preserved as x, y, and z coordinates. 
(Instead of translated to a sphere, the data will appear in a rectangle.)

-Ken


On 1/17/18, 4:34 PM, "ParaView on behalf of Manochehr Bahavar" 
 wrote:

Hello,

I am trying to see if I can visualize my netCDF Earth models (longitude, 
latitude,depth) using ParaView. I have been able to load the models, with the 
"Spherical Coordinates" option selected. However it appears that I now lose my 
coordinates and depth values and as a result to extract a subset, I have to use 
the depth index (not the actual depth value). Is there a way to preserve the 
latitude, longitude and depth values and work with ParaView using the actual 
values (not their index) directly?

Thank you,

—manoch
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Re: [Paraview] ParaView 5.x not showing all objects available in Pipeline Browser

[Moreland, Kenneth]

Omid,

The only other thing I can think of is that there is something odd about the 
OpenGL driver/hardware on your system that for some reason is not supporting 
the coincident topology resolution in ParaView. ParaView changed its rendering 
system from OpenGL 1.3 to OpenGL 3.1 in version 5, the version that you report 
seeing the issue.

Once again, I recommend trying to run ParaView on a completely different 
computer if you can find access to one. You might also try updating the OpenGL 
drivers on your computer. Beyond that, I am out of ideas.

-Ken

From: Omid Mahabadi <omid.mahab...@geomechanica.com>
Date: Tuesday, January 16, 2018 at 7:58 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>
Cc: "paraview@paraview.org" <paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] ParaView 5.x not showing all objects 
available in Pipeline Browser

Hi Ken,
Thanks for your feedback and sorry for my late reply. Somehow I didn't get this 
message and only found your reply after searching in my mailbox.

I tried various values for the Z Shift, increasing it by one order of magnitude 
until reaching a value of 200, restarting in between changes. This didn't help.

I haven't really made any other changes in ParaView settings. I even restored 
to defaults a couple of times. I've been using Linux Mint 17 and have also 
experienced the same issue on Ubuntu 14.04 both 64 bit.

Thanks

Best regards,
Omid



On Wed, Jan 10, 2018 at 12:45 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Omid,

Even after applying the Threshold filter, I cannot replicate your problem. I’ve 
tried on both ParaView 5.2 and 5.4. Both work fine for me.

My settings are the default. “Resolve Coincident Topology” is set to “Shift 
z-buffer when rendering lines and points”. “Z Shift” is set to 0.002. (Polygon 
offset should not matter in this mode.) You could try increasing the Z Shift to 
fix the problem. Note that you have to restart ParaView in order for these 
options to take effect.

It is possible that there is some quirk with the rendering system on your 
computer that does not implement the topology resolution. Do you happen to have 
another computer on which you can try to run this? I also noted that if I turn 
on OSPRay rendering, I do get the missing line issue you describe. There might 
be other display/rendering parameters that cause issues. But the defaults 
should be fine, so unless you have done some tinkering you should be OK.

-Ken

From: Omid Mahabadi 
[mailto:omid.mahab...@geomechanica.com<mailto:omid.mahab...@geomechanica.com>]
Sent: Wednesday, January 10, 2018 9:21 AM
To: Moreland, Kenneth <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>
Cc: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] ParaView 5.x not showing all objects 
available in Pipeline Browser

Hi Ken,
Thanks for the detailed reply. I could not get anything out of the settings 
dialog as per your suggestion. Did you have a combination of those settings 
that might work for my files?
I can also see the image you sent; that's usually fine. However, I typically 
apply a Threshold filter to the _basic_ files (Scalar: alive; min: 0.1; max: 
1). In this case, the _basic_ object is always drawn in front of the 
_broken_joint_ object.
In addition, I visualize dozens of these files every day so Transforming every 
single object is a bit tedious.
Thank you,
Omid


On Mon, Jan 8, 2018 at 5:56 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Omid,

I am unable to replicate your issue in ParaView 5.4.1. When I loaded your data 
and showed the broken_joint data in wireframe, I was clearly able to see the 
lines of broken_joint over the polygons of basic. (See the attached image.)

The problem you are getting is likely caused by z-buffer fighting in the 
rendering. This happens when two objects are the exact same distance from the 
viewer, as I believe is the case in your data. Wanting to draw lines on top of 
polygons is common enough that there are some corrections to help the rendering 
determine what to draw in front. Perhaps by changing the settings on resolving 
coincident topology will resolve your issue. You can find them by opening the 
ParaView settings dialog (Edit → Settings), clicking on the Render View tab, 
and turning on the advanced options. The options you are looking for are 
“Resolve Coincident Topology,” “Polygon Offset Parameters”, and “Z Shift.”

Another, possibly easier, solution it to simply move the lines of the 
broken_joint data closer to the camera. Click the broken_joint object and add 
the Transform filter. Change the Translate parameter to 0, 0, 1 and apply. That 
should shift the wireframe forward enough to see it properly.

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Omid Mahabadi
Sent: Mon

Re: [Paraview] ParaView 5.x not showing all objects available in Pipeline Browser

[Moreland, Kenneth]

Omid,

Even after applying the Threshold filter, I cannot replicate your problem. I’ve 
tried on both ParaView 5.2 and 5.4. Both work fine for me.

My settings are the default. “Resolve Coincident Topology” is set to “Shift 
z-buffer when rendering lines and points”. “Z Shift” is set to 0.002. (Polygon 
offset should not matter in this mode.) You could try increasing the Z Shift to 
fix the problem. Note that you have to restart ParaView in order for these 
options to take effect.

It is possible that there is some quirk with the rendering system on your 
computer that does not implement the topology resolution. Do you happen to have 
another computer on which you can try to run this? I also noted that if I turn 
on OSPRay rendering, I do get the missing line issue you describe. There might 
be other display/rendering parameters that cause issues. But the defaults 
should be fine, so unless you have done some tinkering you should be OK.

-Ken

From: Omid Mahabadi [mailto:omid.mahab...@geomechanica.com]
Sent: Wednesday, January 10, 2018 9:21 AM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] ParaView 5.x not showing all objects 
available in Pipeline Browser

Hi Ken,
Thanks for the detailed reply. I could not get anything out of the settings 
dialog as per your suggestion. Did you have a combination of those settings 
that might work for my files?
I can also see the image you sent; that's usually fine. However, I typically 
apply a Threshold filter to the _basic_ files (Scalar: alive; min: 0.1; max: 
1). In this case, the _basic_ object is always drawn in front of the 
_broken_joint_ object.
In addition, I visualize dozens of these files every day so Transforming every 
single object is a bit tedious.
Thank you,
Omid


On Mon, Jan 8, 2018 at 5:56 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Omid,

I am unable to replicate your issue in ParaView 5.4.1. When I loaded your data 
and showed the broken_joint data in wireframe, I was clearly able to see the 
lines of broken_joint over the polygons of basic. (See the attached image.)

The problem you are getting is likely caused by z-buffer fighting in the 
rendering. This happens when two objects are the exact same distance from the 
viewer, as I believe is the case in your data. Wanting to draw lines on top of 
polygons is common enough that there are some corrections to help the rendering 
determine what to draw in front. Perhaps by changing the settings on resolving 
coincident topology will resolve your issue. You can find them by opening the 
ParaView settings dialog (Edit → Settings), clicking on the Render View tab, 
and turning on the advanced options. The options you are looking for are 
“Resolve Coincident Topology,” “Polygon Offset Parameters”, and “Z Shift.”

Another, possibly easier, solution it to simply move the lines of the 
broken_joint data closer to the camera. Click the broken_joint object and add 
the Transform filter. Change the Translate parameter to 0, 0, 1 and apply. That 
should shift the wireframe forward enough to see it properly.

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Omid Mahabadi
Sent: Monday, January 8, 2018 2:30 PM
To: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] ParaView 5.x not showing all objects available 
in Pipeline Browser

Hi,
I use ParaView to visualize data of our simulations using the Unstructured Grid 
data format. Up until ParaView 4.x everything worked fine: we typically 
visualize one set of data files as Surfaces and another as Wireframe. The 
Wireframe dataset refers to "fracture lines" in our simulations.
See below how the simulation looked like in PV version 4.x. You could clearly 
see the line around the boundaries of the model.

[Inline image 1]
However, in PV 5.x the lines are not fully visualized as if they're hidden 
below the other data object:

[Inline image 2]
I've tried a few versions of 5.x but they all behave similarly.
Does anyone know what might be going on here? Is this a bug / removed featured 
from the new version or should I do something different with 5.x? I've noticed 
that this issue does not happen consistently. I've seen the issue on both Linux 
Mint 17.3 (64 bit) and Ubuntu
I've attached two example VTU files. Please visualize the second file as 
Wireframe (_broken_joint). Below are two large VTU files.
https://www.dropbox.com/s/kzt4jq1wbwfua4j/out.zip?dl=0

Can someone else reproduce this issue?

I'd really hope to start using ParaView 5 since it finally has the long-missing 
Reload Files options!
Thank you,
Omid




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h

Re: [Paraview] Plot selection over time for threshold

[Moreland, Kenneth]

Jairaj,

I’m not sure what exactly you mean by “the threshold,” but there are many ways 
to plot the average of a threshold-selection of cells over time.

The most straightforward way is to open up the Find Data dialog box, select the 
cells you want to plot, and then create a Plot Selection Over Time filter. 
Specifically, here are steps that will do such a plot:


  1.  Open your data in ParaView. Apply.
  2.  Open the Find Data dialog box (Edit → Find Data or click the toolbar 
button on the top toolbar).
  3.  In the top row, set the left combo box to either “Cell(s)” or “Point(s)” 
depending on whether your data is cell or point data. In the longer combo box 
to the right, make sure that your data is selected.
  4.  In the second row, set the left combo box to the field you want to 
threshold on. Change the next combo box to say “is between”. This will create 
to text edit boxes where you enter the minimum and maximum values of your 
threshold range.
  5.  Click the “Run Selection Query” button. This will select all cells or 
points matching your threshold.
  6.  Click the “Plot Selection Over Time” at the bottom of the Find Data 
dialog box. This will create a filter in the pipeline browser.
  7.  Close the Find Data dialog box and click the Apply button.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Jairaj Mathur
Sent: Friday, January 5, 2018 4:53 PM
To: paraview 
Subject: [EXTERNAL] [Paraview] Plot selection over time for threshold

Dear all

How can I plot the average over time of only the threshold cells? It should 
only average the cells that are within the threshold.

Thanks a lot!

--
Jairaj Mathur,
Mechanical Engineering
Washington University in St Louis

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Re: [Paraview] Question about build paraview

[Moreland, Kenneth]

Actually I find the easiest way to do it is, assuming you have icc in your 
path, to set the CC and CXX environment variables on the command of the first 
run of cmake (or ccmake or cmake-gui, whichever one you are using). So the 
start of your build would be something like this:

mkdir paraview-build
cd paraview-build
CC=icc CXX=icc cmake ../paraview

That should ignore gcc. (Remember, you have to delete all of any build files 
you have created so far and start over. Once CMake picks a compiler, you cannot 
change it without starting over.)

-Ken

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Cory Quammen
Sent: Monday, January 8, 2018 7:23 AM
To: Yangguang Liao 
Cc: ParaView 
Subject: [EXTERNAL] Re: [Paraview] Question about build paraview

It's kind of a quirk of CMake, but once CMAKE_CXX_COMPILER is set by the 
initial CMake configuration, you can't change it. So what should you do?

The solution is to set an environment variable named CMAKE_CXX_COMPILER in your 
shell prior to running CMake for the first time. Set that variable to the path 
of version of gcc or icc you want to use, and that should do it. You may also 
need to set CMAKE_C_COMPILER as well.

HTH,
Cory

On Mon, Jan 8, 2018 at 12:17 AM, Yangguang Liao  wrote:
> Hi,
>
> Anyone has experience build paraview on TACC Maverick or other 
> clusters before? I need to build my own paraview. I use superbuild to build 
> paraview.
> but everytime it stop at the step of configure paraview due to GCC 
> version is lower than 4.6. Maverick does have GCC 4.9 and 5.4 
> installed and also have intel icc and icpc installed. When I try to 
> change CMAKE_CXX_COMPILER to high verion GCC it still detect GCC is 
> lower than 4.6. Even when I try to use icc to compile it still detects 
> GCC lower version error. No idea how to fix. I know I should probably 
> ask Maverick system admin. Just wonder if anybody happen to know this issue.
> Thanks.
>
> --
> Yangguang Liao
> PhD. student of Computer Science Department University of California, 
> Davis
>
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Re: [Paraview] [EXTERNAL] Error about reading .pvtk file

[Moreland, Kenneth]

Yangguang,

If the file size is not too big and you are using the Kitware build of 
ParaView, here are 2 other things you might want to check (although they seem 
less likely than what you already checked).

Corrupt files. Make sure the files did not get corrupted when you copied them 
to your local computer. Check that the file sizes are the same. Also, try 
running a hash function (like md5) at each location and make sure they are the 
same.

Bad filenames. Windows file systems are a bit more restrictive than Linux file 
systems when it comes to allowable characters. If you have a strange character 
in a filename, that might be enough to crash the program when it tries to open 
it.

If you can verify that the files are identical on both systems and all files 
have ordinary names, then I have no idea what the problem could be.

-Ken


From: ParaView  on behalf of Yangguang Liao 

Date: Wednesday, January 3, 2018 at 8:23 PM
To: Walter Scott 
Cc: "paraview@paraview.org" 
Subject: Re: [Paraview] [EXTERNAL] Error about reading .pvtk file

I tried kitware download and my own build. both get crash. and I use windows.

On Wed, Jan 3, 2018 at 6:53 PM, Scott, W Alan 
> wrote:
Is the ParaView a kitware download?  What OS?

Alan

From: Yangguang Liao [mailto:ygl...@ucdavis.edu]
Sent: Wednesday, January 3, 2018 7:52 PM
To: Scott, W Alan >
Cc: paraview@paraview.org
Subject: Re: [EXTERNAL] [Paraview] Error about reading .pvtk file

I don't think so. the test file is not big. and I check the memory usage of 
paraview on remote machine, it is only 500MB. and My local machine should have 
enough memory space.

On Wed, Jan 3, 2018 at 6:27 PM, Scott, W Alan 
> wrote:
Overflowing memory?  Try looking at the amount of memory you are using on the 
cluster, then again on your local computer.  View/ Memory Inspector.

Alan

From: ParaView 
[mailto:paraview-boun...@paraview.org] On 
Behalf Of Yangguang Liao
Sent: Wednesday, January 3, 2018 7:26 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Error about reading .pvtk file

Hi,

I am trying to read a pvtk file with data store in vtk file. when I read it on 
my own local computer, paraview will always crash. but when I read it by using 
paraview on remote supercomputer, it works. May I ask why? I used a MPI 
supported version in my local computer. did I miss something in my build?

--
Yangguang Liao
PhD. student of Computer Science Department
University of California, Davis



--
Yangguang Liao
PhD. student of Computer Science Department
University of California, Davis



--
Yangguang Liao
PhD. student of Computer Science Department
University of California, Davis
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Re: [Paraview] plot colors: function value -> RGB tuple

[Moreland, Kenneth]

You can achieve this by writing making a filter that creates a 3D vector field 
where each vector represents an RGB color. If writing out floating point 
values, the color channel values should be between 0 and 1. You can then render 
this 3D vector field directly as colors by turning off the “Map Scalars” 
display parameter. “Map Scalars” is an advanced option, so the easiest way to 
find it is to type “map” into the search bar at the top of the properties panel.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Nico Schlömer
Sent: Thursday, December 14, 2017 7:15 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] plot colors: function value -> RGB tuple

Hi everyone,

I need to plot complex-valued functions over various domains, and instead of 
splitting the values into real and imaginary part (or absolute value and 
angle), I would like to use a "2D colormap" approach as sometimes suggested for 
complex-valued functions (see, e.g., [1]).
As a lowkey approach of getting this into ParaView, I was wondering if it's 
possible to create a filter that takes a point value (or two), runs it through 
some specified (Python) code, and uses the returned RGB tuple for rendering the 
plot.

Any hints?

Cheers,
Nico

[1] https://github.com/BIDS/colormap/issues/6#issuecomment-220839685
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Re: [Paraview] curvilinear CF conventions

[Moreland, Kenneth]

David,

The ParaView netCDF/CF reader does support the coordinates specified in Section 
5.2. As the name of that section implies, this specification of coordinates 
applies explicitly to latitude and longitude coordinates. The rational, as far 
as I can tell, is that the direction of each coordinate is determined by the 
“units” parameter being either latitude or longitude. (At least, this is how 
the ParaView reader identifies each coordinate.) Even if we were to generalize 
to non-lat/lon coordinates, this specification provides no mechanism for 
applying the height field that you want to apply.

This limitation might seem weird, but you have to remember that the CF 
convention is designed for climate and forecast data and is therefore really 
geared toward geospatial coordinates. It is a testament to how well thought out 
the CF convention is that we are able to leverage it for so many different use 
cases, but sometimes you run into limitations of this nature.

-Ken

From: David Deepwell [mailto:ddeepw...@uwaterloo.ca]
Sent: Monday, December 11, 2017 7:16 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: David Deepwell <ddeepw...@uwaterloo.ca>; paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] curvilinear CF conventions

Hi Ken,

So section 5.2 
(http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html#_two_dimensional_latitude_longitude_coordinate_variables)
 doesn’t apply for arbitrary coordinate variables? I would have thought that it 
would be general and not just for latitude and longitude.

I have used the warp by scalar before, but I would prefer it if Paraview simply 
understood the geometry immediately. I have also found another method to adjust 
the grid which is quite good. The calculator has a Coordinate Results option 
which creates the vector field of the grid.

Thanks,
David



On Dec 11, 2017, at 7:09 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:

David,

The way you are attempting to specify coordinates does not follow the CF 
convention. Your variables have a “coordinates” property that simply says “zc.” 
That is not sufficient in the CF convention to use that as a Z coordinate to 
add to the other independent coordinates. In fact, I cannot find any part of 
the CF convention (http://cfconventions.org/latest.html) that allows you to 
arbitrarily assign a Z coordinate to a 2D grid.

That said, accomplishing what you want is easy with ParaView. Just load your 
data like you are now (so it comes in as a flat rectilinear grid). Then run the 
“Warp By Scalar” filter and set the “Scalars” property to “zc”. That will apply 
the elevation to your data like you want.

-Ken

From: David Deepwell [mailto:ddeepw...@uwaterloo.ca]
Sent: Saturday, December 9, 2017 12:54 PM
To: Moreland, Kenneth <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>
Cc: David Deepwell <ddeepw...@uwaterloo.ca<mailto:ddeepw...@uwaterloo.ca>>; 
paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] curvilinear CF conventions

Hi Ken,

I’ve attached a file which I think satisfies the curvilinear CF conventions. 
The grid is 2 dimensional where the z coordinate (called zc) depends on the 
horizontal and vertical dimensions (x and z).

Cheers,
David




On Dec 9, 2017, at 11:34 AM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:

David,

The netCDF/CF reader should be able to read curvilinear coordinates. There is 
not enough information in your email to determine whether the issue is with the 
ParaView reader or an issue with the data file. It would be helpful if you 
could send us an example file so we can replicate your problem.

-Ken

Sent from my iPad

On Dec 9, 2017, at 9:12 AM, David Deepwell 
<ddeepw...@uwaterloo.ca<mailto:ddeepw...@uwaterloo.ca>> wrote:
Hi all,

I have a netcdf file that follows the CF conventions in curvilinear 
(structured) coordinates. Paraview however doesn’t recognize the auxiliary 
variable as the grid variable on which the rest of the fields should be plotted 
on. I’m not sure if this a bug with paraview misinterpreting the CF convention 
or if I just happen to have an attribute missing that Paraview is looking for.

Cheers,
David
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Re: [Paraview] curvilinear CF conventions

[Moreland, Kenneth]

David,

The way you are attempting to specify coordinates does not follow the CF 
convention. Your variables have a “coordinates” property that simply says “zc.” 
That is not sufficient in the CF convention to use that as a Z coordinate to 
add to the other independent coordinates. In fact, I cannot find any part of 
the CF convention (http://cfconventions.org/latest.html) that allows you to 
arbitrarily assign a Z coordinate to a 2D grid.

That said, accomplishing what you want is easy with ParaView. Just load your 
data like you are now (so it comes in as a flat rectilinear grid). Then run the 
“Warp By Scalar” filter and set the “Scalars” property to “zc”. That will apply 
the elevation to your data like you want.

-Ken

From: David Deepwell [mailto:ddeepw...@uwaterloo.ca]
Sent: Saturday, December 9, 2017 12:54 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: David Deepwell <ddeepw...@uwaterloo.ca>; paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] curvilinear CF conventions

Hi Ken,

I’ve attached a file which I think satisfies the curvilinear CF conventions. 
The grid is 2 dimensional where the z coordinate (called zc) depends on the 
horizontal and vertical dimensions (x and z).

Cheers,
David



On Dec 9, 2017, at 11:34 AM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:

David,

The netCDF/CF reader should be able to read curvilinear coordinates. There is 
not enough information in your email to determine whether the issue is with the 
ParaView reader or an issue with the data file. It would be helpful if you 
could send us an example file so we can replicate your problem.

-Ken

Sent from my iPad

On Dec 9, 2017, at 9:12 AM, David Deepwell 
<ddeepw...@uwaterloo.ca<mailto:ddeepw...@uwaterloo.ca>> wrote:
Hi all,

I have a netcdf file that follows the CF conventions in curvilinear 
(structured) coordinates. Paraview however doesn’t recognize the auxiliary 
variable as the grid variable on which the rest of the fields should be plotted 
on. I’m not sure if this a bug with paraview misinterpreting the CF convention 
or if I just happen to have an attribute missing that Paraview is looking for.

Cheers,
David
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Re: [Paraview] curvilinear CF conventions

[Moreland, Kenneth]

David,

The netCDF/CF reader should be able to read curvilinear coordinates. There is 
not enough information in your email to determine whether the issue is with the 
ParaView reader or an issue with the data file. It would be helpful if you 
could send us an example file so we can replicate your problem.

-Ken

Sent from my iPad

On Dec 9, 2017, at 9:12 AM, David Deepwell 
> wrote:


Hi all,

I have a netcdf file that follows the CF conventions in curvilinear 
(structured) coordinates. Paraview however doesn't recognize the auxiliary 
variable as the grid variable on which the rest of the fields should be plotted 
on. I'm not sure if this a bug with paraview misinterpreting the CF convention 
or if I just happen to have an attribute missing that Paraview is looking for.

Cheers,
David

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Re: [Paraview] Displaying volume outside of mesh as solid

[Moreland, Kenneth]

It looks like the email to the list at large is awaiting moderator approval for 
the attachment. In the meantime, here is the response without the referenced 
attachment.

-Ken

From: Moreland, Kenneth
Sent: Monday, November 27, 2017 10:05 AM
To: Quammen, Cory (External Contacts) <cory.quam...@kitware.com>; sergey 
<schar...@gmail.com>
Cc: ParaView <paraview@paraview.org>
Subject: Re: [Paraview] Displaying volume outside of mesh as solid

Sergey,

What Cory said is true that ParaView cannot directly render empty spaces. 
However, you might be able to get something close enough with the backface 
styling rendering controls. These controls let you render surfaces whose 
“outside” is facing you different than surfaces whose “inside” is facing you. 
They are an advanced property under “Display” in the properties panel. The 
easiest way to get to them is to type “backface” in the search box on the 
properties panel (as shown in the attached screenshot).

Try changing the “Backface Representation” to “Cull Frontface”. That tells 
ParaView to not render any part of the surface where the outside is facing to 
you. That should remove the outer surface in the front and instead show the 
inner surface that should be facing your hollow volume. The attached screenshot 
shows me using this to show a sphere clipped out of the center of a grid. You 
will note that you also see the back faces of the larger grids. That is 
inevitable. There is no way for ParaView to know the difference between the 
faces of your mesh that are on the interior hollow region and those that are on 
the external empty space.

(Note, that if “Cull Frontface” does not seem to show anything different, try 
“Cull Backface”. That might work if your surfaces are for some reason inward 
facing. That shouldn’t be the case, though, when ParaView is rendering the 
surface of a volume.)

I hope that helps.

-Ken


From: ParaView 
<paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>> on behalf 
of Cory Quammen <cory.quam...@kitware.com<mailto:cory.quam...@kitware.com>>
Date: Monday, November 27, 2017 at 9:18 AM
To: sergey <schar...@gmail.com<mailto:schar...@gmail.com>>
Cc: ParaView <paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] Re: [Paraview] Displaying volume outside of mesh as solid

There isn't anything in ParaView to view empty volumes. At some stage, the 
volume you are talking about needs to be represented by a grid or mesh for it 
to be visualized with ParaView. If you can generate a volumetric mesh outside 
of ParaView, then you could use all the visualization techniques in ParaView 
that apply to volume meshes. As a post-processing application, ParaView has 
essentially no built-in functions for generating volume meshes.

Hope that helps,
Cory

On Mon, Nov 20, 2017 at 7:42 PM, sergey 
<schar...@gmail.com<mailto:schar...@gmail.com>> wrote:
Hello,

I am looking for a way to display a volume that is not covered by mesh
(its located somewhere in the middle of mesh).

By default such volumes (without mesh) are shown as empty area, and
meshed area is shown as solid.

I need to reverse the solid and empty areas, so that non-meshed volume
is shown as solid, and meshed volume as empty.

Mesh is in 3D.

Is there a way to do this?

Thank you very much.

Best,

Sergey

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Re: [Paraview] Disable automatic mesh warping

[Moreland, Kenneth]

John,

Sam’s advice is sound, but I am curious where your data is coming from. 
ParaView usually does not automatically apply displacements by warping. The 
only exception I know of is the Exodus II reader, and in that case you can turn 
off the warping by unchecking the Apply Displacements checkbox.

Otherwise, it might be that the displacements are already applied in your data 
file. In which case Sam’s suggestion for undoing them with a negative warp 
should do the trick.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Samuel Key
Sent: Wednesday, November 22, 2017 7:25 AM
To: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] Disable automatic mesh warping


John--

Have tried the Warp filter with a scale of -1.0?

--Sam

On 11/22/2017 2:52 AM, John Mangeri wrote:
Hello,
I am working in a reduced unit system where the computed strain fields are 
around order 1. I could write postprocessors to rescale before visualization 
but that would increase my computational time.
Is there a way to turn off the automatic warping that ParaView performs on 
disp_k (k =x, y, z) fields?
I tried to use the WarpByVector filter with scale of 0.1 or smaller and that 
did not seem to work properly. I should mention I'm on version 5.0 (my favorite 
for a variety of reasons), so maybe the this WarpByVector issue is resolved in 
newer versions.
Thanks,
John




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Re: [Paraview] surface construction with holes

[Moreland, Kenneth]

Ufuk,

The short answer is, no. You cannot keep the Delaunay2D filter from filling 
holes.

The mathematical description of Delaunay triangulation fills in all the space 
in the convex hull of the points. The question about having the Delaunay 
triangulation keeping open space that is supposed to be empty comes up 
frequently on this list. However, generally identifying what should not be 
filled is not easy to describe, especially in a general sense. When you ask me 
about the “hole” in your data, I, as a human, can immediately identify what you 
mean. But can you describe it in such a way that it can be easily picked out by 
a computer? I cannot. And even if we did come up with something, there is a 
good chance it would fail for holes of other shapes.

That said, you might be able to resolve the problem by removing the triangles 
over the hole after you create the surface. I note that what you mean by a hole 
is a region where points are spread out, so we could start by removing big 
triangles. You can identify triangle size using the Mesh Quality filter. Add 
the Mesh Quality filter and change Triangle Quality Measure to Area. After you 
run that, use the threshold filter to remove all triangles with a “quality” 
(actually area) greater than 0.01.

That removes some of the triangles in the holes, but not all of them. You will 
also see that the remaining triangles are skinny ones that stretch across cords 
of the circular hole. So, we could also remove skinny triangles. Run the Mesh 
Quality filter again on the output, this time setting the Triangle Quality 
Measure to Radius Ratio. Then use the Threshold filter again to remove 
triangles greater than a value somewhere in the range of 5 to 15. You might 
notice at this point that it is getting difficult to specify values that work 
well around the holes along the sides. Low values start removing valid 
triangles on the sides. High values leave some of the holes covered. This is 
what I meant by it being difficult to describe the holes to a computer.

An alternate approach is to select the triangles over the wholes, invert the 
selection, and then extract the selection. You could also do that to the result 
of the procedure I just gave you.

One final note. You are using Delaunay 2D on a set of data that is 3D. I 
presume you are aware that Delaunay 2D is actually projecting all of your 
points onto a plane and finding a triangulation there. It is not finding a 
surface in 3D. The only way to find the true 3D surface (in ParaView) would be 
to do a Delaunay 3D and then extract the external faces.

-Ken


On 11/14/17, 5:11 AM, "ParaView on behalf of Ufuk Utku Turuncoglu (BE)" 
 
wrote:

Hi,

I am trying to create surface for a poly data (see attached figure). In 
this case, if i use Delaunay2D filter, it creates surface but it also 
fills the holes. So, i just wonder that is it possible to create surface 
for it without filling holes. You could also find a simple dataset as 
attachment.

Regards,

--ufuk



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Re: [Paraview] NaN values

[Moreland, Kenneth]

Doina,

I wasn’t trying to suggest removing all the NaN values by hand. I was saying 
that the file is being written incorrectly, and you need to change the way you 
are saving it. The simplest way should be to change the Matlab script that 
writes the file in the first place. I appreciate that the matrix you are 
storing the data in Matlab has to be dense, but why do you have to write every 
entry of the matrix into the file? Write a for loop over the dimensions of the 
matrix and conditionally write a number if it is not NaN.

If for whatever reason you cannot do that (maybe you are using someone else’s 
Matlab file writing script and don’t want to or can’t change it), then you 
could probably automatically remove all the NaN’s with a script after the fact. 
For example, you should be able to use sed to remove all instances of the 
string NaN from the file. (This, of course, runs the danger of removing a NaN 
from elsewhere in the file that you want.)

-Ken

From: "Doina Gumeniuc (224252 MAHS)" <224...@via.dk>
Date: Tuesday, November 14, 2017 at 12:42 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>, Mathieu Westphal 
<mathieu.westp...@kitware.com>, "paraview@paraview.org" <paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] NaN values


Hi!

Yes, I of course understand your point. There is a bit of a problem though: In 
reality, this file is much more bigger and deleting the NaNs by hand is not an 
option (also I am trying to make it all happen automatically). If I ask matlab 
to delete the zeros from my file, the shape of the matrix will change, so the 
only solution I found so far is to replace the zeros by NaNs in matlab, which 
gives me error in paraview, for the reason you, Moreland, explained.

So my question would be again, is it possible to replace it with anything else?

Thank you!

____
From: Moreland, Kenneth <kmo...@sandia.gov>
Sent: November 14, 2017 12:24:03 AM
To: Doina Gumeniuc (224252 MAHS); Mathieu Westphal; paraview@paraview.org
Subject: Re: [Paraview] NaN values


Doina,



vtk files support Nan’s in general. (I just tried it. It worked fine.) However, 
you are trying to introduce NaN’s in a list of integer connections, which is 
just wrong on many levels. However, I do not see why you need NaN at all. The 
LINES connectivity list allows you to vary the length of the line chain.



It looks like you can solve your problem by simply not writing out the NaN’s in 
the fill. In the example you sent us, I presume that you mean to have 4 line 
cells with 2, 3, 2, and 2 vertices, respectively. The following should be the 
correct representation of that:



LINES 4 13

2 0 1

3 1 2 3

2 3 4

2 4 5



-Ken





From: ParaView <paraview-boun...@paraview.org> on behalf of "Doina Gumeniuc 
(224252 MAHS)" <224...@via.dk>
Date: Monday, November 13, 2017 at 12:55 PM
To: Mathieu Westphal <mathieu.westp...@kitware.com>, "paraview@paraview.org" 
<paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] NaN values



Hi Mathieu,

Sadly I can not import the whole file, but here is an example:



LINES 4 13

2 0 1 NaN

3 1 2 3

2 3 4 NaN

2 4 5 NaN



I make the vtk file in matlab by extracting the information from a .dat file. 
Originally, instead of NaN there are zeros, but I just need blanks without 
changing the shape of the matrix, which is why I use NaN, but it gives me error 
in paraview.



I hope it explains what I mean. Thank you!



From: Mathieu Westphal <mathieu.westp...@kitware.com>
Sent: November 13, 2017 4:29:18 PM
To: Doina Gumeniuc (224252 MAHS)
Cc: paraview@paraview.org
Subject: Re: [Paraview] NaN values



Hi

Can you share your dataset ?

Thanks,


Mathieu Westphal



On Mon, Nov 13, 2017 at 4:10 PM, Doina Gumeniuc (224252 MAHS) 
<224...@via.dk<mailto:224...@via.dk>> wrote:

Hi Mathieu,



I am using a vtk poly data file, which when I load in paraview, it gives me 
error (paraview just stops working). I was thinking it is because of my NaN 
values.



From: Mathieu Westphal 
<mathieu.westp...@kitware.com<mailto:mathieu.westp...@kitware.com>>
Sent: November 13, 2017 2:53:19 PM
To: Doina Gumeniuc (224252 MAHS)
Cc: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: Re: [Paraview] NaN values



Hi

ParaView understand NaN correctly as blanks.

If you are reading a .csv file, the correct string that is interpreted as NaN 
is "nan" without the quotes.

Best,


Mathieu Westphal



On Mon, Nov 13, 2017 at 2:48 PM, Doina Gumeniuc (224252 MAHS) 
<224...@via.dk<mailto:224...@via.dk>> wrote:

Hi all,



I have a file with NaN values in almost every column and row. The integer 
numbers represent which points should be connected by lines, therefor I can not 
replace NaN with zeros because it will interpret it as Point with ID

Re: [Paraview] NaN values

[Moreland, Kenneth]

Doina,

vtk files support Nan’s in general. (I just tried it. It worked fine.) However, 
you are trying to introduce NaN’s in a list of integer connections, which is 
just wrong on many levels. However, I do not see why you need NaN at all. The 
LINES connectivity list allows you to vary the length of the line chain.

It looks like you can solve your problem by simply not writing out the NaN’s in 
the fill. In the example you sent us, I presume that you mean to have 4 line 
cells with 2, 3, 2, and 2 vertices, respectively. The following should be the 
correct representation of that:

LINES 4 13
2 0 1
3 1 2 3
2 3 4
2 4 5

-Ken


From: ParaView  on behalf of "Doina Gumeniuc 
(224252 MAHS)" <224...@via.dk>
Date: Monday, November 13, 2017 at 12:55 PM
To: Mathieu Westphal , "paraview@paraview.org" 

Subject: [EXTERNAL] Re: [Paraview] NaN values


Hi Mathieu,

Sadly I can not import the whole file, but here is an example:



LINES 4 13

2 0 1 NaN

3 1 2 3

2 3 4 NaN

2 4 5 NaN



I make the vtk file in matlab by extracting the information from a .dat file. 
Originally, instead of NaN there are zeros, but I just need blanks without 
changing the shape of the matrix, which is why I use NaN, but it gives me error 
in paraview.



I hope it explains what I mean. Thank you!


From: Mathieu Westphal 
Sent: November 13, 2017 4:29:18 PM
To: Doina Gumeniuc (224252 MAHS)
Cc: paraview@paraview.org
Subject: Re: [Paraview] NaN values

Hi
Can you share your dataset ?
Thanks,

Mathieu Westphal

On Mon, Nov 13, 2017 at 4:10 PM, Doina Gumeniuc (224252 MAHS) 
<224...@via.dk> wrote:

Hi Mathieu,



I am using a vtk poly data file, which when I load in paraview, it gives me 
error (paraview just stops working). I was thinking it is because of my NaN 
values.


From: Mathieu Westphal 
>
Sent: November 13, 2017 2:53:19 PM
To: Doina Gumeniuc (224252 MAHS)
Cc: paraview@paraview.org
Subject: Re: [Paraview] NaN values

Hi

ParaView understand NaN correctly as blanks.
If you are reading a .csv file, the correct string that is interpreted as NaN 
is "nan" without the quotes.
Best,

Mathieu Westphal

On Mon, Nov 13, 2017 at 2:48 PM, Doina Gumeniuc (224252 MAHS) 
<224...@via.dk> wrote:

Hi all,



I have a file with NaN values in almost every column and row. The integer 
numbers represent which points should be connected by lines, therefor I can not 
replace NaN with zeros because it will interpret it as Point with ID 0.

Is there any way I can replace this NaNs with something which paraview reads as 
blanks?

Thank you!

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Re: [Paraview] Create 4D Animation from sets of 3D Data

[Moreland, Kenneth]

It looks like the NRRD reader does not support time series. I wrote up a bug 
(https://gitlab.kitware.com/paraview/paraview/issues/17820), but in the mean 
time you could try a different image format. You could try either raw or tiff 
format.

-Ken

From: Joe Ping-Lin Hsiao [mailto:phs...@cs.unc.edu]
Sent: Monday, November 6, 2017 9:21 AM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: Quang Ha <qt...@cam.ac.uk>; DeMarle, David E. (External Contacts) 
<dave.dema...@kitware.com>; paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D Data

Hi Ken,

I I can load a bunch of .nrrd volume scans into ParaView as one unit. But when 
I play the animation, the animation only stays at the first volume and would 
not proceed.

The reason may be that the files do not have time step information. In the 
"information" tab, the "Time" table of my 4d stack is empty.

Is there an easy way to fix this? I used ImageJ to create those images.

-Joe

On Mon, Jul 28, 2014 at 5:02 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Image segmentation is not my specialty, but I don't think there is an easy 
answer. You might be able to use a level set method that starts with the mesh 
from the first image and constrains the topology to be the same, but that would 
probably create artifacts that compound over time.

-Ken

From: Quang Ha <qt...@cam.ac.uk<mailto:qt...@cam.ac.uk>>
Date: Monday, July 28, 2014 9:25 AM
To: Kenneth Moreland <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>, David E 
DeMarle <dave.dema...@kitware.com<mailto:dave.dema...@kitware.com>>

Cc: paraview-help <paraview-h...@sandia.gov<mailto:paraview-h...@sandia.gov>>, 
"paraview@paraview.org<mailto:paraview@paraview.org>" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D Data

Hi,

Thank you very much for your reply. It seems that I would have to deal with the 
input data once again.

Is there a way for the surface to be modified in such way that you have stated? 
Would you suggested starting to look at vtk/CGAL codes or something similar?

Best regards,
Quang
On 28/07/14 15:46, Moreland, Kenneth wrote:
Quang,

First before answering your question, let me alert you to an easier way to load 
your data into ParaView. First, name your files with numbers just before the 
extension (e.g. left_ventricle_00.stl, left_ventricle_01.stl, 
left_ventricle_02.stl, etc.). Then just load this file series as one unit (they 
will be grouped in the ParaView file browser) and ParaView will automatically 
animate them; no need to add them manually with the Animation View.

Now the bad news. I don't think the Temporal Interpolator is going to work with 
your data. The Temporal Interpolator needs a way to register where a point in 
one time step goes to in the next time step. It does this in a very simplistic 
way by assuming the topology is consistent across time steps. That is, each 
data set has the exact same triangles listed in the same order connected the 
same way but at different positions. The surface from your segmentation is 
surely not of this nature.

-Ken

From: Quang-Thinh Ha <qt...@cam.ac.uk<mailto:qt...@cam.ac.uk>>
Date: Friday, July 25, 2014 11:34 PM
To: David E DeMarle <dave.dema...@kitware.com<mailto:dave.dema...@kitware.com>>
Cc: paraview-help <paraview-h...@sandia.gov<mailto:paraview-h...@sandia.gov>>, 
"paraview@paraview.org<mailto:paraview@paraview.org>" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D Data


Hi,

Thanks for your reply.

1) The data sets are all in STL format.

2) I am not very sure about this. After using text editor to open the mesh file 
I can say that they are not... Is there anyway to change this?

Quang
On 26 Jul 2014 04:17, David E DeMarle 
<dave.dema...@kitware.com<mailto:dave.dema...@kitware.com>> wrote:
1) What file format are the 10 data sets in?
2) do all meshes have the same number of points and cells and do the come in 
the same order in every timstep? temporal interpolation requires a 1:1 
correspondence so that it knows what to interpolate between.


On Friday, July 25, 2014, Quang Ha <qt...@cam.ac.uk<mailto:qt...@cam.ac.uk>> 
wrote:
Hi,

I have a group of 10 data sets of the left ventricle at different cardiac 
phases. They have been 3D reconstructed using segmentation method. Now I am 
trying to use ParaView to see the dynamic changes over different cardiac phases.

I have been able to get to the View -> Animation mode and add each 3D data at 
different time, but they only show me a jump from one data to another, rather 
than 'deforming' into another. I

Re: [Paraview] [EXTERNAL] 2d decimation

[Moreland, Kenneth]

This is a total guess, but I would not be surprised if your slice is on a multi 
block data set that there are holes at the boundaries between blocks. I don't 
think there are any guarantees about the shape held after the decimation. 
Likewise if running MPI and the slice is distributed.

-Ken

Sent from my iPad

On Oct 13, 2017, at 12:06 PM, Scott, W Alan 
> wrote:

OK, thanks.  It was a fairly complex users state file.  Let me try to replicate 
on something that isn't a few thousand files.

Alan

From: Cory Quammen >
Date: Friday, October 13, 2017 at 12:04 PM
To: W Scott >
Cc: "paraview@paraview.org" 
>
Subject: Re: [Paraview] [EXTERNAL] 2d decimation

Alan,
I just tried it on a Slice through a Wavelet and it seemed to work okay. Can 
you list the steps you took to reproduce the holes?
Thanks,
Cory

On Fri, Oct 13, 2017 at 1:48 PM, Scott, W Alan 
> wrote:
Ping?

From: ParaView 
> on behalf 
of W Scott >
Date: Wednesday, October 11, 2017 at 12:08 PM
To: "paraview@paraview.org" 
>
Subject: [EXTERNAL] [Paraview] 2d decimation

I tried the decimation filter on a slice, and it ended up with huge holes.
Is this a fool's errand, or should we be able to decimate a slice and not have 
holes?  Do we need a new filter - decimate2d?

Alan



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--
Cory Quammen
Staff R Engineer
Kitware, Inc.
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Re: [Paraview] Saving as csv data

[Moreland, Kenneth]

Teng,

The issue is that your stress field data is associated with the cells and you 
are writing out the point data in your csv file. Thus, the stress data is not 
being written. There are two solutions, both with flaws:

Solution 1: When you get the dialog box labeled "Configure Writer 
(DataSetCSVWriter)" (after you choose a filename), change the option "Field 
Association" from "Points" to "Cells". If you do this option, you will only get 
the x, y, and z for the stress (labeled "stress:0", "stress:1", and 
"stress:2"). You will not get the x, y, z information for the placement of the 
points.

Solution 2: Before writing out the csv file, run the "Cell Data to Point Data" 
filter. Then write out the csv file with point data as you have been doing. You 
will get the x, y, and z for the stress (labeled "stress:0", "stress:1", and 
"stress:2") and you will also get the positional x, y, and z (labeled 
"Points:0", "Points:1", and "Points:2"). The problem with this solution is that 
it will alter the stress data slightly by averaging values of adjacent cells to 
points.

Also note that neither of these options will automatically write out the 
magnitude of the stress. To write out the stress magnitude, first run the 
"Calculator" filter to compute the magnitude of the stress vectors.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Li, Teng
Sent: Monday, October 9, 2017 11:17 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Saving as csv data

Hi all,

I have a question about saving vtk data in a csv file. Please find the 
following link for the vtk file:

https://drive.google.com/file/d/0B-Dmy2O1v21NbGlfTm9odlZpa2M/view?usp=sharinghttps://drive.google.com/file/d/0B-Dmy2O1v21NbGlfTm9odlZpa2M/view?usp=sharing

I expected to see 7 components in the csv file I saved: x, y, z, stress_x, 
stress_y, stress_z, stress_magnitude. However, in the csv file I saved, there 
are only three columns of data. Please find the csv file I saved:

https://drive.google.com/file/d/0B-Dmy2O1v21NeWZnejVqbHEzME0/view?usp=sharinghttps://drive.google.com/file/d/0B-Dmy2O1v21NeWZnejVqbHEzME0/view?usp=sharing

I saved the vtk file by first highlighting the vtk file in the pipeline, and 
then click save data. Then I used the default settings. Is there anything wrong 
in my saving process?

Thanks!

Best,
Teng


Teng Li

Master Candidate in Structures

Department of Civil and Environmental Engineering

University of Illinois at Urbana-Champaign

205 North Mathews Ave, Urbana, IL. 61801

Phone:(217)8196210, Email: teng...@illinois.edu




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Re: [Paraview] Averaging data in paraview

[Moreland, Kenneth]

I don’t think there is anything ready made that will do what you are 
describing. However, I think if your points are lined up along the x axis 
(assuming width=x), I think you can fake it by squishing the data to a line and 
telling ParaView to merge coincident points (clean the data). Try the following 
steps:


1.   Add the Transform filter. Change the Scale parameter to [0, 1, 1]. 
Apply.

2.   Add the Clean to Grid filter. Apply.

3.   Add the Plot Over Line filter. Apply.

Another alternative is to just create a scatterplot with the Y value on the 
bottom axis and the value on the right. (Turn off lines, turn on markers.) It’s 
different than showing the average, but it contains more information.

-Ken


From: ParaView  on behalf of JAIRAJ MATHUR 

Date: Thursday, September 14, 2017 at 2:30 PM
To: paraview 
Subject: [EXTERNAL] [Paraview] Averaging data in paraview

Hey all!

I have an unstructured grid type data(it is cell data, image attached below). I 
wish to do a plot in paraview such that I am averaging along the width, and 
plotting this averaged data along the length. In order to do that, what am I 
looking at here?
Essentially, I want a scatter plot of the average along width.

Thanks!

--
Jairaj Mathur,
Mechanical Engineering
Washington University in St Louis

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Re: [Paraview] Read files in different folders at the same time

[Moreland, Kenneth]

An easier but equally unsatisfactory solution is to do an “ln -s” command to 
create symbolic links in a common directory. It’s technically not a copy of the 
file and ParaView will pick them up as if they were the regular file.

-Ken


On 9/8/17, 5:31 AM, "ParaView on behalf of Utkarsh Ayachit" 
 wrote:

I am afraid that's not possible currently. A workaround is to create a
pvd file as follows:



  





  


Make sure that header matches the header in one of the vtu files.

Utkarsh

On Thu, Sep 7, 2017 at 7:04 PM, Ke Gao  wrote:
> Hi all,
>
> When I do the simulation, I restart the computation and as a result there
> are files generated in different folders but with sequential vtu file 
names.
> For example, in the first folder we have vtu files numbered from 0 to 100,
> and in the second folder we have vtu files from 101 to 200. I wonder if
> there is a convenient way to animate all these 200 files in one setup,
> without copy them into the same folder?
>
> Thanks.
>
> --
> 
..
> Ke Gao
>
> ___
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Re: [Paraview] [EXTERNAL] Is anyone using the Extra Headlight in ParaView?

[Moreland, Kenneth]

The use case Alan brings up is captured in bug 17236: 
https://gitlab.kitware.com/paraview/paraview/issues/17236. Until that bug is 
fixed, I would argue strenuously against disabling the headlight. The 
implementation of the bug fix may or may not require the headlight to stick 
around (depending on how it is implemented).

I don’t personally have any other use case for the headlight, but it is a 
convenient way to get a bright light shining directly on the view. It’s 
valuable to quickly illuminate an object where the shading has made the colors 
murky. Is there a compelling reason to get rid of it? It’s tucked away in an 
innocuous corner of the GUI.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Scott, W Alan
Sent: Thursday, August 17, 2017 11:16 AM
To: DeMarle, David E. (External Contacts) ; 
paraview@paraview.org
Subject: Re: [Paraview] [EXTERNAL] Is anyone using the Extra Headlight in 
ParaView?

No objection here.  Only thought I have is that the lights may be setup by 
default slightly differently for 2d and 3d.  We may want a “headlight” for 2d.


Alan

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of David E 
DeMarle
Sent: Thursday, August 17, 2017 7:35 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Is anyone using the Extra Headlight in ParaView?

By default, Paraview illuminates the scene with a 
vtkLightKit. You can 
however add an extra headlight. I am about to add a more general capability 
which lets you add any number and any kind of light, including the headlight. 
When I do that, the semi-hardcoded extra headlight becomes redundant. I would 
like to remove it to streamline both the code and the UI.
Are there any objections to me doing that?

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909
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Re: [Paraview] Dynamic colouring of the geometry in the animation of warped eigenmodes

[Moreland, Kenneth]

Juha,

As Cory said you can create a plugin to replicate this behavior, but I believe 
you can also get similar behavior through a collection of filters. Although 
this is a bit cumbersome, you can try the following steps:

1. Before applying the WarpByVector filter, add the Calculator filter to your 
data. Set the "Result Array Name" to "OriginalCoords" and the expression to 
simply "coords". This will capture the point coordinates before warping.
2. Apply WarpByVector to this calculator filter as you did before to the FEM 
data.
3. Apply another Calculator filter to the output of WarpByVector. This time, 
set the "Result Array Name" to "ActualDisplacement" and the expression to 
"coords-OriginalCoords". This will capture the actual displacement applied 
after the scale factor is used.
4. Color your data by the "ActualDispalcement" field.
5. Set up your animation of the "ScaleFactor" for the WarpByVector filter as 
you did before.

You should now see "dynamic" colors based on the magnitude of the actual 
displacement.

-Ken

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Cory Quammen
Sent: Monday, August 7, 2017 7:27 AM
To: Juha Kortelainen 
Cc: ParaView 
Subject: [EXTERNAL] Re: [Paraview] Dynamic colouring of the geometry in the 
animation of warped eigenmodes

On Sun, Aug 6, 2017 at 1:30 PM, Juha Kortelainen  
wrote:
> Hi all,
>
> I’m using the warp filter to visualise the computed eigenmodes of a 
> structure (computed using a FEM code). Animating the eigenmodes works 
> fine with the WarpByVector filter using the ScalarFactor as the 
> animation variable. In addition to animating the deformation of the 
> structure, I would like to apply colouring of the deformation vector 
> field on the geometry so that the colour would change dynamically 
> according to the magnitude of deformation during the animation. This 
> can be done with the Salome platform’s ParaViS modile (a modified 
> version of ParaView), which has an additional ScaleVector filter to do 
> the colouring trick. Can this dynamic colouring be done with standard 
> ParaView and if so, how is it done?

Yes, with some work. Take a look at this blog post for the general
idea: 
https://blog.kitware.com/easy-customization-of-the-paraview-python-programmable-filter-property-panel/

Basically, you can create XML plugins based on the Programmable Filter that 
feature some properties, such as a scale factor. The scale factor property 
should be exposed in the animation controls. Within your Programmable Filter 
script, you can perform the scaling of the vector with that scale factor 
property value. There are many examples of Python scripts for the Programmable 
Filter in Section 13.3 the ParaView Guide to get you started.

HTH,
Cory

>
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Re: [Paraview] Point data to 2d plane data

[Moreland, Kenneth]

Teng,

When you saved your data to a csv file, you lost all cell information. If you 
want to look at cells in your data, you will have to recreate them.

The easiest way to create cells is probably to use the Delaunay 2D filter. 
Note, however, that the cells created will not be the same as in your original 
vtk file.

If you want to keep your original cells, you will have to save them in a file 
that supports cell topology. One way to do that is when you save your csv file, 
also save a vtk file of the same data. Then, after you have run Matlab, load 
both the csv file and the vtk file. Do the TableToPoints on the csv data as 
before. Then use append attributes to copy the csv data to the vtk cell data.

-Ken

Sent from my iPad

On Jul 26, 2017, at 12:41 AM, Li, Teng 
> wrote:

Dear Paraview developers,

I have a question about how to convert point data (vtk file) to 2d plane data. 
Actually, originally, I was working with vtk file. Then I use the extract 
selection to select some cells in the original model. In order to process the 
data of the selected cells, I save the data as the csv file. Then I use Matlab 
to do some calculation on the data in the csv file. After that, I open the 
modified csv file by using Paraview directly. And now, I can only see this csv 
file in spreadsheet view. After searching some online information, I use 
TabletoPoint to convert the data to point data. However, I still want to view 
them as the 2d cell. So I use point interpolation to try to convert the points 
data to 2d plane cell data. However, It doesn't work.

So my question is, how to show the data value in the space between different 2d 
points data by using point interpolation? Or is there any way that I can 
process the 2d cell plane data without saving it as the csv file?

Best,
Teng Li


Teng Li

Master Candidate in Structures

Department of Civil and Environmental Engineering

University of Illinois at Urbana-Champaign

205 North Mathews Ave, Urbana, IL. 61801

Phone:(217)8196210, Email: teng...@illinois.edu



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[Paraview] **Deadline Extended** CFP: 3rd Annual Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization (ISAV 2017)

[Moreland, Kenneth]

Sorry for the spam, but ParaView/Catalyst users may be interested in this 
workshop.


Update: paper submission due date extended to 15 Aug 2017 23:59 AoE

ISAV 2017: In Situ Infrastructures for Enabling Extreme-Scale Analysis and 
Visualization

In cooperation with SIGHPC and held in conjunction with SC17: The International 
Conference on High Performance Computing, Networking, Storage and Analysis, 
Denver, Colorado, U.S.A.

ISAV 2017 - http://vis.lbl.gov/Events/ISAV-2017/

 Full-day 9:00 AM - 5:30 PM Sunday November 12th, 2017

Workshop Theme

The considerable interest in the HPC community regarding in situ analysis and 
visualization is  due to several factors. First is an I/O cost savings, where 
data is analyzed/visualized while  being generated, without first storing to a 
file system. Second is the potential for increased  accuracy, where fine 
temporal sampling of transient analysis might expose some complex behavior 
missed in coarse temporal sampling. Third is the ability to use all available 
resources, CPUs and accelerators, in the computation of analysis products.

The workshop brings together researchers, developers and practitioners from 
industry, academia, and government laboratories developing, applying, and 
deploying in situ methods in extreme-scale, high performance computing. The 
goal is to present research findings, lessons learned, and insights related to 
developing and applying in situ methods and infrastructure across a range of 
science and engineering applications in HPC environments; to discuss topics 
like opportunities presented by new architectures, existing infrastructure 
needs, requirements, and gaps, and experiences to foster and enable in situ 
analysis and visualization; to serve as a "center of gravity" for researchers, 
practitioners, and users/consumers of in situ methods and infrastructure in the 
HPC space.

Participation/Call for Papers and Oral Presentations

We invite two types of submissions to ISAV 2017: (1) short, 4-page papers that 
present research results, that identify opportunities or challenges, and that 
present case studies/best practices for in situ methods/infrastructure in the 
areas of data management, analysis and visualization; (2) lightning 
presentation submission, consisting of a 1- or 2-page submission, for a brief 
oral presentation at the workshop. 
Short papers will appear in the workshop proceedings and will be invited to 
give an oral presentation of 15 to 20 minutes; lightning round submissions that 
are invited to present at the workshop will have author names and titles 
included as part of the proceedings. Submissions of both types are welcome that 
fall within one or more areas of interest, as follows:

Areas of interest for ISAV, include, but are not limited to:

In situ infrastructures

   * Current Systems: production quality, research prototypes
   * Opportunities
   * Gaps

System resources, hardware, and emerging architectures

   * Enabling Hardware
   * Hardware and architectures that provide opportunities for in situ 
processing, such as burst buffers, staging computations on I/O nodes, sharing 
cores within a node for both simulation and in situ processing

Methods/algorithms/applications/Case studies

   * Best practices
   * Analysis: feature detection, statistical methods, temporal methods, 
geometric methods
   * Visualization: information visualization, scientific visualization, 
time-varying methods
   * Data reduction/compression
   * Examples/case studies of solving a specific science challenge with in 
situ methods/infrastructure.

Simulation

   * Integration: data modeling, software-engineering
   * Resilience: error detection, fault recovery
   * Workflows for supporting complex in situ processing pipelines

Requirements

   * Preserve important elements
   * Significantly reduce the data size
   * Flexibility for post-processing exploration


Review Process

All submissions will undergo a peer-review process consisting of three reviews 
by experts in the field, and evaluated according to relevance to the workshop 
theme, technical soundness, creativity, originality, and impactfulness of 
method/results. Lightning round submissions will be evaluated primarily for 
relevance to the workshop.

Submission Process

Authors are invited to submit papers of at most 4 pages in PDF format, 
excluding references, and lightning presentations of at most 2 pages in PDF 
format, excluding references. Papers must be submitted in PDF format (readable 
by Adobe Acrobat Reader 5.0 and higher) and formatted for 8.5" x 11" (U.S. 
Letter). Submissions are required in the ACM format 
(http://www.acm.org/sigs/publications/proceedings-templates) using the 
sample-sigconf template and submitted via EasyChair 
(https://easychair.org/conferences/?conf=isav17). No changes to the margins, 
spacing, or font sizes as specified by the 

Re: [Paraview] Dilation Operation ...

[Moreland, Kenneth]

Niklas,

My first question is, are the data actually being read in as a point data field 
or a cell data field? If you go to the Information panel, what does it say the 
data are?

I'm not at my computer to check this, but I believe that if you read data as a 
lon/lat projection, the mesh is most likely read as a 2D "image", and if so, 
that is rendered with the "slice" representation. If that's the case, can you 
try changing the representation to "surface"?

-Ken

Sent from my iPad

> On Jul 5, 2017, at 7:10 AM, Niklas Röber  wrote:
> 
> Dear All,
> 
> I have a very low resolution netCDF that I would like to visualize as cell 
> data using lon/lat projection. Reading the data using lon/lat projection, the 
> variables are represented as point data (image1). If the data is read in 
> spherical, the variables are represented as cell data (image2). Comparing 
> both, shows that some features are missing in the lon/lat projection, see for 
> example central America and Spain. Applying a PointDataToCellData filter to 
> the point data in lon/lat smoothes these features away completely (image3).
> Is there a possibility to visualize the data correctly, as shown with 
> spherical projection, but in lon/lat? Or can the point data somehow be 
> dilated so that central America and half of Europe are not "filtered" out?
> 
> Thanks for any help!
> Cheers, Niklas
> 
> 
> 
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Re: [Paraview] netcdf

[Moreland, Kenneth]

Rupert,

It has been multiple years since I really took a look at the CF convention, so 
I don’t remember the details of whether it supports varying coordinates across 
multiple dimensions or whether the ParaView reader supports that. If the 
ParaView reader is missing some corner of the CF convention, let us know and we 
can work on that.

In any case, you can displace a 2D or 3D image by a height value that is stored 
in a field by simply running the “Warp by Scalar” filter.

-Ken


From: Rupert Gladstone <rupertgladstone1...@gmail.com>
Date: Tuesday, May 16, 2017 at 12:31 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>
Cc: Aashish Chaudhary <aashish.chaudh...@kitware.com>, "paraview@paraview.org" 
<paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] netcdf

Hi all, thanks very much for your replies so far.  I must say I am finding the 
Paraview community very helpful.
Having considered my data further, I would be able to make a 1D coordinate 
variable for my x and y dimensions but not for my z dimension.  The ocean model 
uses a hybrid coordinate which can be transformed into depth, but the resulting 
depth coordinate will be spatially varying across my data set.  In other words 
my z coordinate variable will need to be a 3D variable.  From my understanding 
of COARDS and CF this is allowed.  But I think from your email that Paraview 
will not be able to associate this 3D z coordinate variable to another variable 
(e.g. ocean temperature) for the purposes of plotting.  At least, not using the 
Paraview CF interface.  Is that correct?
I don't currently have a handy netcdf file (I have a rather large one).  I 
could generate a smaller netcdf file to demonstrate the issue, but I am not 
sure it is needed here, as the problem is not that Paraview fails to read the 
file as expected, but rather than I am trying to clarify what I can reasonably 
expect from Paraview with its current functionality.
Do you have a suggestion for how to read in a (topologically) structured data 
set on a rectangular cartesian projection in which the the vertical coordinate 
variable varies across all three dimensions?  Should I ask Paraview to read it 
in as unstructured data?  I think I saw that Paraview offers some kind of 
interface for unstructured data in netcdf files.  Are the requirements of this 
documented somewhere?  Or do you still feel that I need to provide an example 
netcdf file for you to better understand the problem?
Thanks again for your help.
Regards,
Rupert



On Tue, May 16, 2017 at 6:36 AM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Rupert,

As Aashish said, it might be easier to diagnose the issue if you sent us a 
file. But if your file is not following the CF or COARDS convention, then the 
reader will simply interpret the arrays in the file as uniform grids with 
spacing of 1. This is not likely to conform with the coordinates you want.

The official documentation for the CF convention is maintained here: 
http://cfconventions.org/. In summary, you specify coordinates by using arrays 
of the same name as the dimension. So for example if you have a 3D array with 
dimensions named “Z”, “Y”, and “X”, then you also make a 1D variable named “X” 
on the “X” dimension that has the x coordinate for each grid point in the 
dimension. Likewise, you have a “Y” variable on the “Y” dimension for y 
coordinates and a “Z” variable on the “Z” dimension for the z coordinates.

Or, if you don’t want to mess with your file format, you can do as Sam 
suggested and transform the data once it is loaded into ParaView.

-Ken


From: ParaView 
<paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>> on behalf 
of Aashish Chaudhary 
<aashish.chaudh...@kitware.com<mailto:aashish.chaudh...@kitware.com>>
Date: Monday, May 15, 2017 at 9:08 AM
To: Rupert Gladstone 
<rupertgladstone1...@gmail.com<mailto:rupertgladstone1...@gmail.com>>, 
"paraview@paraview.org<mailto:paraview@paraview.org>" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] Re: [Paraview] netcdf

Rupert,

Would it be possible for you to send us a sample file and what the list of VARS 
you expect to see in the paraview?

Thanks,

On Mon, May 15, 2017 at 3:37 AM Rupert Gladstone 
<rupertgladstone1...@gmail.com<mailto:rupertgladstone1...@gmail.com>> wrote:

Hi, I have a question about netcdf formats.  I am developing a coupled ice 
sheet - ocean model.  Currently both models run in the same cartesian 
coordinate system.  The ice model outputs unstructured .vtu files, which 
paraview reads just fine.  The ocean model outputs structured netcdf files.  If 
I naively select the "generic and CF conventions" option when reading the ocean 
netcdf file then the data display ok, but not to scale.  It seems like the 
structured fields have been read in just fine, 

Re: [Paraview] netcdf

[Moreland, Kenneth]

Rupert,

As Aashish said, it might be easier to diagnose the issue if you sent us a 
file. But if your file is not following the CF or COARDS convention, then the 
reader will simply interpret the arrays in the file as uniform grids with 
spacing of 1. This is not likely to conform with the coordinates you want.

The official documentation for the CF convention is maintained here: 
http://cfconventions.org/. In summary, you specify coordinates by using arrays 
of the same name as the dimension. So for example if you have a 3D array with 
dimensions named “Z”, “Y”, and “X”, then you also make a 1D variable named “X” 
on the “X” dimension that has the x coordinate for each grid point in the 
dimension. Likewise, you have a “Y” variable on the “Y” dimension for y 
coordinates and a “Z” variable on the “Z” dimension for the z coordinates.

Or, if you don’t want to mess with your file format, you can do as Sam 
suggested and transform the data once it is loaded into ParaView.

-Ken


From: ParaView  on behalf of Aashish Chaudhary 

Date: Monday, May 15, 2017 at 9:08 AM
To: Rupert Gladstone , "paraview@paraview.org" 

Subject: [EXTERNAL] Re: [Paraview] netcdf

Rupert,

Would it be possible for you to send us a sample file and what the list of VARS 
you expect to see in the paraview?

Thanks,

On Mon, May 15, 2017 at 3:37 AM Rupert Gladstone 
> wrote:

Hi, I have a question about netcdf formats.  I am developing a coupled ice 
sheet - ocean model.  Currently both models run in the same cartesian 
coordinate system.  The ice model outputs unstructured .vtu files, which 
paraview reads just fine.  The ocean model outputs structured netcdf files.  If 
I naively select the "generic and CF conventions" option when reading the ocean 
netcdf file then the data display ok, but not to scale.  It seems like the 
structured fields have been read in just fine, but the coordinate variables 
have not.  I don't think the netcdf files are CF compliant.  I would like to be 
able to read in both .vtu files and netcdf files and display the data sets 
together on the same scale.

Do you know what I need to do to read in the netcdf coordinate vars correctly?  
I am hoping that I can simply insert a post-processing step to implement some 
minor manipulation to the ocean model output files so that Paraview can read 
them in to scale.  Is it simply a case of renaming the coordinate variables in 
the netcdf file such that they have the same names as the corresponding 
dimensions?  Note that this is not in general possible as some of the 
coordinate variables are two-dimensional variables (in the horizontal plane), 
though for most of the simulations we plan in the near future I can enforce 
that the coord vars will have a one to one correspondence to the dimension vars 
(i.e. I can enforce that coord vars are 1D).

Is the ordering of dimensions important?
Is the ordering of coordinate vars important?
Is the naming of dimensions important?
Is the naming of coord vars important?
Can Paraview cope with 2D coord vars?  If so, how does Paraview know which 
coordinate var applies to which var?
Thanks very much for your help.
Regards,
Rupert Gladstone
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Re: [Paraview] Visualization ternary saturation

[Moreland, Kenneth]

Aha! I figured out the issue. Yes, ParaView correctly shows floating point 
colors when in the Surface representation, but it does not work for the Slice 
representation. (I happened to be creating data on a Mandelbrot source.)

I raised a bug: https://gitlab.kitware.com/paraview/paraview/issues/17423

-Ken

From: Dan Lipsa [mailto:dan.li...@kitware.com]
Sent: Tuesday, May 9, 2017 7:59 AM
To: Quammen, Cory (External Contacts) <cory.quam...@kitware.com>
Cc: Moreland, Kenneth <kmo...@sandia.gov>; Waldon, Shawn (External Contacts) 
<shawn.wal...@kitware.com>; ParaView <paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] Visualization ternary saturation

Hi all,

Indeed, rather than supporting only 'unsigned char' for direct color mapping - 
using color mode VTK_COLOR_MODE_DEFAULT, all integer and floating point types 
can be used for direct color mapping using the color mode 
VTK_COLOR_MODE_DIRECT_SCALARS.
Integer type colors should be between 0-255 and floating point colors should be 
between 0-1.

Dan


On Mon, May 8, 2017 at 10:16 PM, Cory Quammen 
<cory.quam...@kitware.com<mailto:cory.quam...@kitware.com>> wrote:
> I tried it your way in ParaView 5.3.0, and it did not work correctly. Are
> you sure this is implemented in 5.3 and not a new feature in the upcoming
> 5.4?

Ken,

This was implemented some time ago. In 5.3.0, I could do the following:

* Add Sphere Source
* Add Programmable Filter with the Script set to

A = inputs[0].PointData['Normals'][:,0]
B = inputs[0].PointData['Normals'][:,1]
C = inputs[0].PointData['Normals'][:,2]
colors = numpy.empty((len(A),3), dtype='float')
colors[:,0] = A
colors[:,1] = B
colors[:,2] = C
output.PointData.append(colors, 'colors')

* Turn off Map Scalars

You could also skip this silly use of the Programmable Filter
altogether and color the Sphere source by 'Normals', then turn Map
Scalars off.

I believe the capability to treat floating-point arrays of 3-tuples
was added to VTK in commit

commit 00de9a942ff74e797fbe4cd8c67307c8065cdade
Author: Dan Lipsa <dan.li...@kitware.com<mailto:dan.li...@kitware.com>>
Date:   Thu Nov 20 13:35:35 2014 -0500

Add VTK_COLOR_MODE_DIRECT_SCALARS. See vtkScalarsToColors::MapScalars.

- Cory

> From: Shawn Waldon 
> [mailto:shawn.wal...@kitware.com<mailto:shawn.wal...@kitware.com>]
> Sent: Monday, May 8, 2017 12:11 PM
> To: Moreland, Kenneth <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>
> Cc: Thomas Oliveira 
> <thomas.olive...@gmail.com<mailto:thomas.olive...@gmail.com>>; ParaView
> <paraview@paraview.org<mailto:paraview@paraview.org>>
> Subject: [EXTERNAL] Re: [Paraview] Visualization ternary saturation
>
>
>
> Ken beat me to answering this one... I'll just add that if the data is
> floating point in the range [0, 1], you don't need to convert it to uint8 or
> multiply by 255.  Just creating a floating point vector will give the same
> result.  This is a more recent extension of the functionality: I know it
> works in 5.3 and master but I'm not sure how many versions back support it.
>
> A = inputs[0].CellData['A']
>
> B = inputs[0].CellData['B']
>
> C = inputs[0].CellData['C']
>
> colors = numpy.empty((len(A),3), dtype='float')
>
> colors[:,0] = A
>
> colors[:,1] = B
>
> colors[:,2] = C
>
> output.CellData.append(colors, 'colors')
>
>
> HTH,
>
> Shawn
>
>
>
> On Mon, May 8, 2017 at 1:56 PM, Moreland, Kenneth 
> <kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
>
> ParaView does not directly support ternary color maps, but if you create a
> field of colors (represented by three unsigned chars), then you can render
> those colors directly by turning off the Map Scalars option. You can create
> these colors with a Programmable Filter with a script like the following:
>
>
>
> A = inputs[0].CellData['A']
>
> B = inputs[0].CellData['B']
>
> C = inputs[0].CellData['C']
>
> colors = numpy.empty((len(A),3), dtype='uint8')
>
> colors[:,0] = A*255
>
> colors[:,1] = B*255
>
> colors[:,2] = C*255
>
> output.CellData.append(colors, 'colors')
>
>
>
> Once you apply that script, color by the new “colors” array and uncheck the
> box marked “Map Scalars” (it is an advanced option in the properties panel).
>
>
>
> -Ken
>
>
>
> From: ParaView 
> [mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] 
> On Behalf Of Thomas
> Oliveira
> Sent: Saturday, May 6, 2017 7:24 AM
> To: ParaView <paraview@paraview.org<mailto:paraview@paraview.org>>
> Subject: [EXTERNAL] [Paraview] Visualization ternary saturation
>
>
>
> Dear all,
>
> Given three cell arrays (A,B,C) representation saturations (A+B+C = 1 for
> every cell) is it p

Re: [Paraview] Visualization ternary saturation

[Moreland, Kenneth]

Shawn,

I tried it your way in ParaView 5.3.0, and it did not work correctly. Are you 
sure this is implemented in 5.3 and not a new feature in the upcoming 5.4?

-Ken

From: Shawn Waldon [mailto:shawn.wal...@kitware.com]
Sent: Monday, May 8, 2017 12:11 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: Thomas Oliveira <thomas.olive...@gmail.com>; ParaView 
<paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] Visualization ternary saturation

Ken beat me to answering this one... I'll just add that if the data is floating 
point in the range [0, 1], you don't need to convert it to uint8 or multiply by 
255.  Just creating a floating point vector will give the same result.  This is 
a more recent extension of the functionality: I know it works in 5.3 and master 
but I'm not sure how many versions back support it.
A = inputs[0].CellData['A']
B = inputs[0].CellData['B']
C = inputs[0].CellData['C']
colors = numpy.empty((len(A),3), dtype='float')
colors[:,0] = A
colors[:,1] = B
colors[:,2] = C
output.CellData.append(colors, 'colors')

HTH,
Shawn

On Mon, May 8, 2017 at 1:56 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
ParaView does not directly support ternary color maps, but if you create a 
field of colors (represented by three unsigned chars), then you can render 
those colors directly by turning off the Map Scalars option. You can create 
these colors with a Programmable Filter with a script like the following:

A = inputs[0].CellData['A']
B = inputs[0].CellData['B']
C = inputs[0].CellData['C']
colors = numpy.empty((len(A),3), dtype='uint8')
colors[:,0] = A*255
colors[:,1] = B*255
colors[:,2] = C*255
output.CellData.append(colors, 'colors')

Once you apply that script, color by the new “colors” array and uncheck the box 
marked “Map Scalars” (it is an advanced option in the properties panel).

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Thomas Oliveira
Sent: Saturday, May 6, 2017 7:24 AM
To: ParaView <paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] [Paraview] Visualization ternary saturation

Dear all,
Given three cell arrays (A,B,C) representation saturations (A+B+C = 1 for every 
cell) is it possible to generate a ternary saturation image like the one 
attached (obtained in 
http://www.esss.com.br/Kraken/wp-content/uploads/2014/07/Ternary-Saturation.png)?
In the figure, A, B, C are saturations of water, oil and gas.
Best regards,
Thomas Oliveira

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Re: [Paraview] Visualization ternary saturation

[Moreland, Kenneth]

ParaView does not directly support ternary color maps, but if you create a 
field of colors (represented by three unsigned chars), then you can render 
those colors directly by turning off the Map Scalars option. You can create 
these colors with a Programmable Filter with a script like the following:

A = inputs[0].CellData['A']
B = inputs[0].CellData['B']
C = inputs[0].CellData['C']
colors = numpy.empty((len(A),3), dtype='uint8')
colors[:,0] = A*255
colors[:,1] = B*255
colors[:,2] = C*255
output.CellData.append(colors, 'colors')

Once you apply that script, color by the new “colors” array and uncheck the box 
marked “Map Scalars” (it is an advanced option in the properties panel).

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Thomas 
Oliveira
Sent: Saturday, May 6, 2017 7:24 AM
To: ParaView 
Subject: [EXTERNAL] [Paraview] Visualization ternary saturation

Dear all,
Given three cell arrays (A,B,C) representation saturations (A+B+C = 1 for every 
cell) is it possible to generate a ternary saturation image like the one 
attached (obtained in 
http://www.esss.com.br/Kraken/wp-content/uploads/2014/07/Ternary-Saturation.png)?
In the figure, A, B, C are saturations of water, oil and gas.
Best regards,
Thomas Oliveira
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Re: [Paraview] Programmable Filter - Multiple Inputs - Crash

[Moreland, Kenneth]

Gabriel,

I was using scalar data, but I just tried again with vectors of three 
components, and everything still worked fine.

Your data is not that large, so I doubt you are running out. It could be 
because you are setting point data to an array that is the wrong size. That is 
generally a pretty bad idea. I tried that, too, and it worked OK for me. But I 
imagine that there could be filters or other components that could crash with a 
buffer overrun.

My first suggestion would be trying the latest version of ParaView to see if 
that fixes the problem. If it doesn’t, then I would alter your script to make 
sure you never add a PointData field to an output when the size does not match 
the number of points.

-Ken

From: Gabriel Nahas [mailto:gabrielrezendena...@gmail.com]
Sent: Tuesday, April 25, 2017 8:58 AM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] Programmable Filter - Multiple Inputs - Crash

Ken,

Thank you very much for trying.

I am using version 4.3 of ParaView, but I also tried my code in the version 5.1 
and it is also crashing.

The first input data is a PointData vector with three components (x,y,z) and 
around 41,000 points. The second input are the normal vectors of my geometry 
that consist in around 12,000 points. To get the Normal Vectors, I used Extract 
Surface > Generate Surface Normals > Cell Data to Pointa Data.


[https://mailfoogae.appspot.com/t?sender=aZ2FicmllbHJlemVuZGVuYWhhc0BnbWFpbC5jb20%3D=zerocontent=60863486-e7b0-4ecd-8704-e5c1e32284a5]ᐧ

On 25 April 2017 at 16:48, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Gabriel,

I tried loading in your script into ParaView 5.3 and was unable to replicate 
your crash even when the number of points did not match or I used fields that 
did not exist. Are you using the most recent version of ParaView? If so, can 
you tell us more about your data?

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Gabriel Nahas
Sent: Tuesday, April 25, 2017 8:30 AM
To: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] Programmable Filter - Multiple Inputs - Crash

Dear all,

I am trying to use a programmable filter that takes two other filters from 
different blocks as inputs. When I get each data as input (and output) 
separately my filter works, but when I try with both filters as input and 
output at the same time it crashes. Does anyone know what might be the cause?

Here the short code of the script I am using that crashes.

a = inputs[0].PointData["a"]
b = inputs[1].PointData["b"]
output.PointData.append(a, "a")
output.PointData.append(b, "b")

PS: For information, I am trying doing a script that calculates wall shear 
stress. One of the input is the velocity gradient and the other one the normal 
vectors.

Best regards,

Gabriel Nahas
--

[photo]

Gabriel Nahas
Master Student at École Polytechnique
+33 6 38 28 29 92<tel:+33+6+38+28+29+92> | Skype: 
gabrielrezendenahas<https://webapp.wisestamp.com/>
[https://s3.amazonaws.com/images.wisestamp.com/icons_32/facebook.png]<http://www.facebook.com/gabriel.nahas.9>
 [https://s3.amazonaws.com/images.wisestamp.com/icons_32/linkedin.png] 
<http://in.linkedin.com/in/gabriel-nahas-2566b892>


[https://mailfoogae.appspot.com/t?sender=aZ2FicmllbHJlemVuZGVuYWhhc0BnbWFpbC5jb20%3D=zerocontent=9905502d-9c30-455a-8535-196b6961a18b]ᐧ



--

[photo]

Gabriel Nahas
Master Student at École Polytechnique
+33 6 38 28 29 92<tel:+33+6+38+28+29+92> | Skype: 
gabrielrezendenahas<https://webapp.wisestamp.com/>
[https://s3.amazonaws.com/images.wisestamp.com/icons_32/facebook.png]<http://www.facebook.com/gabriel.nahas.9>
 [https://s3.amazonaws.com/images.wisestamp.com/icons_32/linkedin.png] 
<http://in.linkedin.com/in/gabriel-nahas-2566b892>


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Re: [Paraview] Programmable Filter - Multiple Inputs - Crash

[Moreland, Kenneth]

Gabriel,

I tried loading in your script into ParaView 5.3 and was unable to replicate 
your crash even when the number of points did not match or I used fields that 
did not exist. Are you using the most recent version of ParaView? If so, can 
you tell us more about your data?

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Gabriel Nahas
Sent: Tuesday, April 25, 2017 8:30 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Programmable Filter - Multiple Inputs - Crash

Dear all,

I am trying to use a programmable filter that takes two other filters from 
different blocks as inputs. When I get each data as input (and output) 
separately my filter works, but when I try with both filters as input and 
output at the same time it crashes. Does anyone know what might be the cause?

Here the short code of the script I am using that crashes.

a = inputs[0].PointData["a"]
b = inputs[1].PointData["b"]
output.PointData.append(a, "a")
output.PointData.append(b, "b")

PS: For information, I am trying doing a script that calculates wall shear 
stress. One of the input is the velocity gradient and the other one the normal 
vectors.

Best regards,

Gabriel Nahas
--

[photo]

Gabriel Nahas
Master Student at École Polytechnique
+33 6 38 28 29 92 | Skype: 
gabrielrezendenahas
[https://s3.amazonaws.com/images.wisestamp.com/icons_32/facebook.png]
 [https://s3.amazonaws.com/images.wisestamp.com/icons_32/linkedin.png] 



[https://mailfoogae.appspot.com/t?sender=aZ2FicmllbHJlemVuZGVuYWhhc0BnbWFpbC5jb20%3D=zerocontent=9905502d-9c30-455a-8535-196b6961a18b]ᐧ
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Re: [Paraview] Integrating drag and lift over time

[Moreland, Kenneth]

Sanjeeb,

You could click File → Save Data and then save the result of the Integrate 
Variables filter as a CSV file. After the file dialog you get another dialog of 
options. Check the box marked "Write All Time Steps" and click OK. You should 
get a CSV file for every time step in your data.

-Ken

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of SanjeebPal
Sent: Friday, April 21, 2017 7:07 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Integrating drag and lift over time

Hello:

I have transient simulation results that I read into Paraview. I would like to 
calculate drag and lift at each time step. I have the normal and tangential 
wall stresses output at every time step. How do I accomplish this ?

For a given time step, I understand that I can use the sequence of filters

Extract Boundary surface -> Generate surface normals -> Multiply stress by area 
-> Multiply by normals -> Integrate Variables Filter

How do I get this drag and lift output written out at each time step ?

Regards,
Sanjeeb Pal
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Re: [Paraview] Difference in dataset for multiple variables

[Moreland, Kenneth]

The programmable filter just runs the Python script you give it. Use Python to 
iterate over all the fields in your dataset. Augmenting the example in the 
email you reference, use something like this to iterate over all the fields:

for field in inputs[0].PointData.keys():
data0 = inputs[0].PointData[field]
data1 = inputs[1].PointData[field]
output.PointData.append(data0-data1, field + '-diff')

-Ken


From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of John Haase
Sent: Friday, March 24, 2017 2:11 PM
To: ParaView 
Subject: [EXTERNAL] [Paraview] Difference in dataset for multiple variables

Hello Paraviewers,

I want to make sure my multivariable cyclic simulation has reached "steady 
state" so I am trying to match the corresponding timesteps and get the R^2 
error. To take the difference between the two datasets, I was thinking of 
following the method laid out here

http://paraview.markmail.org/search/?q=difference#query:difference+page:1+mid:lc6a4ss2j5hi37ps+state:results

and using the ProgrammableFilter to take the difference. That works great for a 
single variable. However, is there a way to take the difference of all the 
variables in the data set? Or do I just have to have a ProgrammableFilter for 
each variable?

Thank you for the advice

Regards,

John
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Re: [Paraview] How do you "see" FieldData

[Moreland, Kenneth]

The Exodus II file format has the concept of "global data." When this is read 
into ParaView/VTK, it gets placed into what vtkDataSet calls the "field data." 
Because of this, I tend to use the two interchangeably (and likewise so does 
the ParaView GUI). Personally, I prefer the term "global data" as it is more 
descriptive.

Arrays in global/field data can be whatever you want and whatever size you 
want. For example, someone might want to record the total volume of the data 
set. That could reasonably be stored in the global/field data. Another example 
might be that someone wants to record the time at which a particular event 
occurs. This could be stored in the global/field data as an array of marked 
time indices. As you can see, global/field data can mean pretty much whatever 
you want it to mean, so you can't do much with it unless you understand the 
semantics. Consequently, global/field data is mostly ignored by ParaView.

One thing that we have encountered with simulations at Sandia is that the 
simulation might track some global information, such as the mean of a field, 
and append that value to an array in the global data every time a timestep is 
written out. Thus, you end up with a global/field data array of length equal to 
the number of timesteps. The Plot Global Data Over Time filter addresses this 
use case and only this use case.

If you want to compute a value and then plot how that value changes over time, 
your best approach is to write that value out to a table and then use Plot 
Selection Over Time to plot the value.

-Ken

From: Scott, W Alan
Sent: Friday, March 24, 2017 12:17 PM
To: Moreland, Kenneth <kmo...@sandia.gov>; paraview@paraview.org
Subject: RE: [Paraview] How do you "see" FieldData

OK, looking at your reply, I think I have a fundamental misunderstanding, and 
have been mixing up terms.  What is a "global data" and "field data"?  What's 
the difference?

I think you are saying that if we have 43 timesteps (can.exo), any global 
arrays will have 43 entries (such as time or atmospheric pressure).  However, 
field data will have a single entry (such as Title)?  Below, you are setting - 
and resetting - the field data over and over again?

Alan

From: Moreland, Kenneth
Sent: Thursday, March 23, 2017 4:00 PM
To: Scott, W Alan <wasc...@sandia.gov<mailto:wasc...@sandia.gov>>; 
paraview@paraview.org<mailto:paraview@paraview.org>
Subject: RE: [Paraview] How do you "see" FieldData

I don't think Plot Global Variables Over Time works the way you think it does. 
This filter assumes that the global arrays contain a static array the same size 
as the number of time steps and then plots that with the time array on the x 
axis and the entries in this array in the y axis. If the size of the global 
variable does not equal the number of time steps, the view will show nothing.

I think you really want to use Plot Selection Over Time. That you can give a 
value and it will iterate the pipeline over time and compute the value for each 
time step. Unfortunately, it looks like the filter is broken for selections on 
field data. It works, however, on table data, so you can write the result as 
that.

I got what I think you want using the can data set. Here are the steps I used:

1. Load can.ex2. All variables. Apply.
2. Add the Programmable Filter. Set the output type to vtkTable (!) and use the 
following script:
disp_y = inputs[0].PointData["DISPL"][:,1]
mean_disp = mean(disp_y)
output.RowData.append(mean_disp, "MEAN_DISP")
3. Select the single row shown in the spreadsheet that pops up.
4. Add Plot Selection Over Time filter. Apply.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Scott, W Alan
Sent: Thursday, March 23, 2017 3:06 PM
To: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] How do you "see" FieldData

>From a user:




How do you "see" FieldData variables created in the ProgrammableFilter in the 
PlotGlobalVariablesOverTime filter?  I'm creating a FieldData variable in the 
ProgrammableFilter.  Now I'd like to plot it over time.  It isn't available as 
an option for me to plot, though.  I see other global variables, just not this 
one.



disp_y = inputs[0].PointData["displ_"][:,1]



mean_disp = mean(disp_y)



output.FieldData.append(mean_disp, "MEAN_DISP")





Am I doing something wrong here?

Thanks,

Alan


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Re: [Paraview] How do you "see" FieldData

[Moreland, Kenneth]

I don't think Plot Global Variables Over Time works the way you think it does. 
This filter assumes that the global arrays contain a static array the same size 
as the number of time steps and then plots that with the time array on the x 
axis and the entries in this array in the y axis. If the size of the global 
variable does not equal the number of time steps, the view will show nothing.

I think you really want to use Plot Selection Over Time. That you can give a 
value and it will iterate the pipeline over time and compute the value for each 
time step. Unfortunately, it looks like the filter is broken for selections on 
field data. It works, however, on table data, so you can write the result as 
that.

I got what I think you want using the can data set. Here are the steps I used:

1. Load can.ex2. All variables. Apply.
2. Add the Programmable Filter. Set the output type to vtkTable (!) and use the 
following script:
disp_y = inputs[0].PointData["DISPL"][:,1]
mean_disp = mean(disp_y)
output.RowData.append(mean_disp, "MEAN_DISP")
3. Select the single row shown in the spreadsheet that pops up.
4. Add Plot Selection Over Time filter. Apply.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Scott, W Alan
Sent: Thursday, March 23, 2017 3:06 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] How do you "see" FieldData

>From a user:




How do you "see" FieldData variables created in the ProgrammableFilter in the 
PlotGlobalVariablesOverTime filter?  I'm creating a FieldData variable in the 
ProgrammableFilter.  Now I'd like to plot it over time.  It isn't available as 
an option for me to plot, though.  I see other global variables, just not this 
one.



disp_y = inputs[0].PointData["displ_"][:,1]



mean_disp = mean(disp_y)



output.FieldData.append(mean_disp, "MEAN_DISP")





Am I doing something wrong here?

Thanks,

Alan


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Re: [Paraview] Scale time

[Moreland, Kenneth]

You can add the Temporal Shift Scale filter and set the Scale, in your case, to 
1000.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Scott, W Alan
Sent: Thursday, March 23, 2017 2:42 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Scale time

Is it possible to scale time, and then display this on the screen with the 
Annotate Time source?  For instance, assuming can.exo's time is in seconds, I 
would like to present time on screen in milliseconds.  Can.exo's first timestep 
is at 0.0001 seconds.  I want to display it as 0.1 milliseconds.

Alan


W. Alan Scott
ParaView Support Manager

SAIC
Sandia National Laboratories, MS 0822
Org 9326 - Building 880 A1-K
(505) 284-0932   FAX (505) 284-5619

The most exciting phrase to hear in science
is not "Eureka!" but "That's funny..."  -- Isaac Asimov
-

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Re: [Paraview] Field value question from a user

[Moreland, Kenneth]

Alan,

So in summary, yes it is possible to do this with the programmable filter. What 
you do is check the time to see if it equals the target time step. If so, save 
the array from the desired field in a global variable. Then on other time steps 
do the difference. 

You may have noticed I'm not giving you code. This is because I am too lazy to 
spend the hour or so getting it to work. 

-Ken

Sent from my iPad so blame autocorrect.

On Mar 10, 2017, at 12:15 PM, Utkarsh Ayachit  
wrote:

>> You could declare
>> a global variable, but are you guaranteed to get the same interpreter
>> instance each call? That’s a question for Utkarsh.
> 
> Yes, you are.
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Re: [Paraview] Field value question from a user

[Moreland, Kenneth]

This is complex but can be done with the time support in VTK’s pipeline. 
However, it requires the filter to hold state from one call of RequestData to 
the next. This is simple enough in C++, but I’m not sure how you do it in the 
Python interpreter (used by the programmable filter). You could declare a 
global variable, but are you guaranteed to get the same interpreter instance 
each call? That’s a question for Utkarsh.

-Ken


From: ParaView  on behalf of Walter Scott 

Date: Friday, March 10, 2017 at 1:16 PM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] Field value question from a user


Greetings,

Is there a way with the calculator or something similar in paraview to grab the 
field value at a particular time step, so that I could then subtract it off of 
the time varying field?



Thanks,



Alan


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Re: [Paraview] 答复: Help: How to convert a group of vtk data files at one time though ParaView

[Moreland, Kenneth]

(Responding back to the list.)

As I said, click on the “Save Data” toolbar button (or select File -> Save 
Data). This will give you an option to save the data from the vtk file as a csv 
file.

-Ken

From: 董 舒迪 <ganpla...@hotmail.com>
Date: Thursday, March 9, 2017 at 3:51 PM
To: "Moreland, Kenneth" <kmo...@sandia.gov>
Subject: [EXTERNAL] 答复: [Paraview] Help: How to convert a group of vtk data 
files at one time though ParaView


Hello Ken,



Really thank you for your reply.



Yes, my data files are written as a numeric series, and I notice that ParaView 
will load all of them when I press play button.

However, I have a confusion. I am not sure about the meaning of "write out", do 
you mean export?  I obtained those files from my colleague with another 
simulation software, this is why I want to convert (or export) those series 
data file with ParaView. I will try your method, and thank you for your kind 
reply.

Best regards,
Stan

________
发件人: Moreland, Kenneth <kmo...@sandia.gov>
发送时间: 2017年3月9日 20:08
收件人: 董 舒迪; paraview@paraview.org
主题: Re: [Paraview] Help: How to convert a group of vtk data files at one time 
though ParaView

Stan,

I don’t know if this functionality goes all the way back to version 4.1 (I only 
tried back to 4.3), but if you load your vtk data as a time series then you can 
similarly write them out as a time series of csv files.

Assuming that your vtk files are written as a numeric series (e.g. file001.vtk, 
file002.vtk, file003.vtk, …), ParaView will interpret that as a file series. 
When you click on the file series in the browser to open it, ParaView only 
actually reads in the first file. If you hit the play button, ParaView will 
load your files one by one as an animation over time.

If you have data in a time series like that, you can write out a series of csv 
files as a time series. Simply click on Save Data, specify a csv file name in 
the file browser, and then in the next dialog box check the box for “Write All 
Time Steps”. ParaView will then write out a series of numbered csv file, one 
per time step, which corresponds to each of your input files.

-Ken

From: ParaView <paraview-boun...@paraview.org> on behalf of 董 舒迪 
<ganpla...@hotmail.com>
Date: Thursday, March 9, 2017 at 1:09 PM
To: "paraview@paraview.org" <paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] Help: How to convert a group of vtk data files 
at one time though ParaView

Dear all,

I am currently use ParaView version 4.1, to analyse vtk data. I want to export 
a group of data file from vtk into csv. However, there are about 900 data file 
in that group, and I don't think I could export them one by one. Do you know is 
there any way I could select them all and export them together at one time?  I 
cannot find relevant information in guidebook of version 4.1, and I am 
wondering is this due to the limitation of the old version?

Many Thanks,
Stan

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Re: [Paraview] Help: How to convert a group of vtk data files at one time though ParaView

[Moreland, Kenneth]

Stan,

I don’t know if this functionality goes all the way back to version 4.1 (I only 
tried back to 4.3), but if you load your vtk data as a time series then you can 
similarly write them out as a time series of csv files.

Assuming that your vtk files are written as a numeric series (e.g. file001.vtk, 
file002.vtk, file003.vtk, …), ParaView will interpret that as a file series. 
When you click on the file series in the browser to open it, ParaView only 
actually reads in the first file. If you hit the play button, ParaView will 
load your files one by one as an animation over time.

If you have data in a time series like that, you can write out a series of csv 
files as a time series. Simply click on Save Data, specify a csv file name in 
the file browser, and then in the next dialog box check the box for “Write All 
Time Steps”. ParaView will then write out a series of numbered csv file, one 
per time step, which corresponds to each of your input files.

-Ken

From: ParaView  on behalf of 董 舒迪 

Date: Thursday, March 9, 2017 at 1:09 PM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] Help: How to convert a group of vtk data files 
at one time though ParaView

Dear all,

I am currently use ParaView version 4.1, to analyse vtk data. I want to export 
a group of data file from vtk into csv. However, there are about 900 data file 
in that group, and I don't think I could export them one by one. Do you know is 
there any way I could select them all and export them together at one time?  I 
cannot find relevant information in guidebook of version 4.1, and I am 
wondering is this due to the limitation of the old version?

Many Thanks,
Stan

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Re: [Paraview] CSV to PVTU

[Moreland, Kenneth]

Sorry, I might have mislead you a little bit before. What you actually need is 
the Glyph filter with Glyph Type set to 2D Glyph and then the secondary Glyph 
Type set to Vertex.

By default the glyph filter subsamples the data (to prevent occlusion when 
creating glyphs with size). Under Masking change the Glyph Mode to All Points, 
and you should get what you want.

Also, check the vtu files being generated by ParaView 4.0.1 carefully. I 
suspect one of them is very large and all the others are very small. I think 
the old version of ParaView is writing a bunch of vtu files with no points 
whereas new versions of ParaView are not writing out pointless empty vtu files.

-Ken

From: Faiz Abidi [mailto:fabid...@vt.edu]
Sent: Sunday, March 5, 2017 4:09 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: ParaView <paraview@paraview.org>; Rajamohan, Srijith <sriji...@vt.edu>; 
Nicholas Polys <npo...@vt.edu>; Ayat Mohammed <maaa...@vt.edu>
Subject: Re: [EXTERNAL] Re: [Paraview] CSV to PVTU

Btw, I am a bit confused that why after applying a "2D Glyph" filter and "Glyph 
Type" as "Vertex", the number of points decreases. For example, if after 
applying "TableToPoints" filter I have 1 cell and 100k points, I get  502 cells 
and 502 points after applying a "2D Glyph" filter. I was expecting the number 
of cells to increase but total number of points should have remained 100k, no?

I am not really sure if applying a 2D Glyph is the best solution in my case. I 
may go back to using 4.0.1 to convert this csv data into pvtu and then use the 
latest version to load it up.

On Fri, Mar 3, 2017 at 2:14 PM, Faiz Abidi 
<fabid...@vt.edu<mailto:fabid...@vt.edu>> wrote:
I see.

I did that because when I choose "Assign Cells Uniquely" as the "Boundary Mode" 
in the D3 filter, I was getting a warning like below:

Warning: In /home/faiz89/git/ParaView/VTK/Common/DataModel/vtkKdTree.cxx, line 
1887
vtkKdTree (0x2db5950): vtkKdTree::BuildMapForDuplicatePoints - invalid tolerance

But in spite of the warning, 8 vtu files get generated along with 1 pvtu file. 
So, maybe that warning can be ignored.

On Thu, Mar 2, 2017 at 6:42 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
I’m pretty sure if you select Duplicate Cells it will just copy all the points 
to all processes, so that is not a good option. The divide cells is also giving 
poor results on this front. I think you are better off using the 2D Glyph 
filter to break up the cell first.

-Ken

From: Faiz Abidi [mailto:fabid...@vt.edu<mailto:fabid...@vt.edu>]
Sent: Thursday, March 2, 2017 2:44 PM
To: Moreland, Kenneth <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>
Cc: ParaView <paraview@paraview.org<mailto:paraview@paraview.org>>; Rajamohan, 
Srijith <sriji...@vt.edu<mailto:sriji...@vt.edu>>; Nicholas Polys 
<npo...@vt.edu<mailto:npo...@vt.edu>>; Ayat Mohammed 
<maaa...@vt.edu<mailto:maaa...@vt.edu>>
Subject: Re: [EXTERNAL] Re: [Paraview] CSV to PVTU

Ohk, that makes more sense. I could get it to work as well but also had to 
check "Boundary Mode" as "Duplicate Cells" while applying the D3 filter.

Thanks Moreland!

On Thu, Mar 2, 2017 at 3:59 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Faiz,

I was able to replicate your problem. It looks like it is not an issue with D3 
but a change with how Table to Points creates data (or perhaps how data are 
written). It looks like Table to Points is creating one “cell” with a lot of 
points. This saves a little memory but ends up preventing D3 from dividing the 
points up.

The best solution is to add a “2D Glyph” filter after the Table to Points but 
before the D3 filter. Set the “Glyph Type” to “Vertex”. Then apply the D3 
filter to the output of the 2D Glyph filter.

-Ken

From: Faiz Abidi [mailto:fabid...@vt.edu<mailto:fabid...@vt.edu>]
Sent: Thursday, March 2, 2017 1:38 PM
To: Moreland, Kenneth <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>
Cc: ParaView <paraview@paraview.org<mailto:paraview@paraview.org>>; Rajamohan, 
Srijith <sriji...@vt.edu<mailto:sriji...@vt.edu>>; Nicholas Polys 
<npo...@vt.edu<mailto:npo...@vt.edu>>; Ayat Mohammed 
<maaa...@vt.edu<mailto:maaa...@vt.edu>>
Subject: [EXTERNAL] Re: [Paraview] CSV to PVTU

Hi Moreland,

Thanks for your reply.

I thought same except maybe not use the GUI since my data is big and takes 
forever to load up in Paraview.

Quick question/observation - using the GUI and 8 processes, and applying the 
Tables to Points filter + D3 and then trying to save files doesn't create 8 vtu 
files and 1 pvtu file as expected. Instead, what happens is that I get only 1 
pvtu file along with 1 vtu file instead. Clearly something wrong. This was done 
using v5.2.0.

Re: [Paraview] [EXTERNAL] Re: CSV to PVTU

[Moreland, Kenneth]

I’m pretty sure if you select Duplicate Cells it will just copy all the points 
to all processes, so that is not a good option. The divide cells is also giving 
poor results on this front. I think you are better off using the 2D Glyph 
filter to break up the cell first.

-Ken

From: Faiz Abidi [mailto:fabid...@vt.edu]
Sent: Thursday, March 2, 2017 2:44 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: ParaView <paraview@paraview.org>; Rajamohan, Srijith <sriji...@vt.edu>; 
Nicholas Polys <npo...@vt.edu>; Ayat Mohammed <maaa...@vt.edu>
Subject: Re: [EXTERNAL] Re: [Paraview] CSV to PVTU

Ohk, that makes more sense. I could get it to work as well but also had to 
check "Boundary Mode" as "Duplicate Cells" while applying the D3 filter.

Thanks Moreland!

On Thu, Mar 2, 2017 at 3:59 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Faiz,

I was able to replicate your problem. It looks like it is not an issue with D3 
but a change with how Table to Points creates data (or perhaps how data are 
written). It looks like Table to Points is creating one “cell” with a lot of 
points. This saves a little memory but ends up preventing D3 from dividing the 
points up.

The best solution is to add a “2D Glyph” filter after the Table to Points but 
before the D3 filter. Set the “Glyph Type” to “Vertex”. Then apply the D3 
filter to the output of the 2D Glyph filter.

-Ken

From: Faiz Abidi [mailto:fabid...@vt.edu<mailto:fabid...@vt.edu>]
Sent: Thursday, March 2, 2017 1:38 PM
To: Moreland, Kenneth <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>
Cc: ParaView <paraview@paraview.org<mailto:paraview@paraview.org>>; Rajamohan, 
Srijith <sriji...@vt.edu<mailto:sriji...@vt.edu>>; Nicholas Polys 
<npo...@vt.edu<mailto:npo...@vt.edu>>; Ayat Mohammed 
<maaa...@vt.edu<mailto:maaa...@vt.edu>>
Subject: [EXTERNAL] Re: [Paraview] CSV to PVTU

Hi Moreland,

Thanks for your reply.

I thought same except maybe not use the GUI since my data is big and takes 
forever to load up in Paraview.

Quick question/observation - using the GUI and 8 processes, and applying the 
Tables to Points filter + D3 and then trying to save files doesn't create 8 vtu 
files and 1 pvtu file as expected. Instead, what happens is that I get only 1 
pvtu file along with 1 vtu file instead. Clearly something wrong. This was done 
using v5.2.0.

I tried the same thing using v4.0.1 (yes, old but it works!) and I got 8 vtu 
files and 1 pvtu file as expected.

Do you think this is a bug with 5.2.0? Or do I need to do something different 
with 5.2.0? Any pointers appreciated!

On Wed, Mar 1, 2017 at 4:15 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
You can use ParaView itself to read in the csv file, convert it to an 
unstructured grid (Table to Points filter), redistributed on your 8 parallel 
processors (D3 filter) and then write out a pvtu file.

Offhand I cannot think of an easier way.

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Faiz Abidi
Sent: Wednesday, March 1, 2017 2:03 PM
To: ParaView <paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] [Paraview] CSV to PVTU

Hi again community!

Looking for suggestions - what would be a decently fast way to convert a huge 
CSV file into PVTU files?

What I want to do - load this huge file in a CAVE like environment, and use 8 
parallel processors.
--
Faiz Abidi | Master's Student at Virginia Tech | 
www.faizabidi.com<http://www.faizabidi.com> | 
+1-540-998-6636<tel:(540)%20998-6636>



--
Faiz Abidi | Master's Student at Virginia Tech | 
www.faizabidi.com<http://www.faizabidi.com> | 
+1-540-998-6636<tel:(540)%20998-6636>



--
Faiz Abidi | Master's Student at Virginia Tech | 
www.faizabidi.com<http://www.faizabidi.com> | +1-540-998-6636
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Re: [Paraview] [EXTERNAL] Re: CSV to PVTU

[Moreland, Kenneth]

Faiz,

I was able to replicate your problem. It looks like it is not an issue with D3 
but a change with how Table to Points creates data (or perhaps how data are 
written). It looks like Table to Points is creating one “cell” with a lot of 
points. This saves a little memory but ends up preventing D3 from dividing the 
points up.

The best solution is to add a “2D Glyph” filter after the Table to Points but 
before the D3 filter. Set the “Glyph Type” to “Vertex”. Then apply the D3 
filter to the output of the 2D Glyph filter.

-Ken

From: Faiz Abidi [mailto:fabid...@vt.edu]
Sent: Thursday, March 2, 2017 1:38 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: ParaView <paraview@paraview.org>; Rajamohan, Srijith <sriji...@vt.edu>; 
Nicholas Polys <npo...@vt.edu>; Ayat Mohammed <maaa...@vt.edu>
Subject: [EXTERNAL] Re: [Paraview] CSV to PVTU

Hi Moreland,

Thanks for your reply.

I thought same except maybe not use the GUI since my data is big and takes 
forever to load up in Paraview.

Quick question/observation - using the GUI and 8 processes, and applying the 
Tables to Points filter + D3 and then trying to save files doesn't create 8 vtu 
files and 1 pvtu file as expected. Instead, what happens is that I get only 1 
pvtu file along with 1 vtu file instead. Clearly something wrong. This was done 
using v5.2.0.

I tried the same thing using v4.0.1 (yes, old but it works!) and I got 8 vtu 
files and 1 pvtu file as expected.

Do you think this is a bug with 5.2.0? Or do I need to do something different 
with 5.2.0? Any pointers appreciated!

On Wed, Mar 1, 2017 at 4:15 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
You can use ParaView itself to read in the csv file, convert it to an 
unstructured grid (Table to Points filter), redistributed on your 8 parallel 
processors (D3 filter) and then write out a pvtu file.

Offhand I cannot think of an easier way.

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Faiz Abidi
Sent: Wednesday, March 1, 2017 2:03 PM
To: ParaView <paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] [Paraview] CSV to PVTU

Hi again community!

Looking for suggestions - what would be a decently fast way to convert a huge 
CSV file into PVTU files?

What I want to do - load this huge file in a CAVE like environment, and use 8 
parallel processors.
--
Faiz Abidi | Master's Student at Virginia Tech | 
www.faizabidi.com<http://www.faizabidi.com> | 
+1-540-998-6636<tel:(540)%20998-6636>



--
Faiz Abidi | Master's Student at Virginia Tech | 
www.faizabidi.com<http://www.faizabidi.com> | +1-540-998-6636
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Re: [Paraview] [Non-DoD Source] Re: CSV to PVTU (UNCLASSIFIED)

[Moreland, Kenneth]

My description just involves using ParaView to convert a CSV file to a PVTU 
file using its GUI. I don't know what if any idiosyncrasies are involved if 
using a CAVE. I've never used one with ParaView. I'll let someone else answer 
that part.

-Ken

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Su, Simon M 
CIV USARMY RDECOM ARL (US)
Sent: Wednesday, March 1, 2017 2:18 PM
To: Faiz Abidi <fabid...@vt.edu>; ParaView <paraview@paraview.org>
Subject: [EXTERNAL] Re: [Paraview] [Non-DoD Source] Re: CSV to PVTU 
(UNCLASSIFIED)

CLASSIFICATION: UNCLASSIFIED

Hello,

>> What I want to do - load this huge file in a CAVE like environment, 
>> and use
>> 8 parallel processors.

if you don't mind, can you elaborate a little on the process you are using to 
do that (running in the CAVE like environment)?

thanks
-simon

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Moreland, 
Kenneth
Sent: Wednesday, March 01, 2017 4:15 PM
To: Faiz Abidi <fabid...@vt.edu>; ParaView <paraview@paraview.org>
Subject: [Non-DoD Source] Re: [Paraview] CSV to PVTU

All active links contained in this email were disabled. Please verify the 
identity of the sender, and confirm the authenticity of all links contained 
within the message prior to copying and pasting the address to a Web browser.







You can use ParaView itself to read in the csv file, convert it to an 
unstructured grid (Table to Points filter), redistributed on your 8 parallel 
processors (D3 filter) and then write out a pvtu file.



Offhand I cannot think of an easier way.



-Ken



From: ParaView [Caution-mailto:paraview-boun...@paraview.org]On Behalf Of Faiz 
Abidi
Sent: Wednesday, March 1, 2017 2:03 PM
To: ParaView <paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] CSV to PVTU



Hi again community!



Looking for suggestions - what would be a decently fast way to convert a huge 
CSV file into PVTU files?



What I want to do - load this huge file in a CAVE like environment, and use 8 
parallel processors.
-- 

Faiz Abidi | Master's Student at Virginia Tech | Caution-www.faizabidi.com < 
Caution-http://www.faizabidi.com >  | +1-540-998-6636


CLASSIFICATION: UNCLASSIFIED
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Re: [Paraview] CSV to PVTU

[Moreland, Kenneth]

You can use ParaView itself to read in the csv file, convert it to an 
unstructured grid (Table to Points filter), redistributed on your 8 parallel 
processors (D3 filter) and then write out a pvtu file.

Offhand I cannot think of an easier way.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Faiz Abidi
Sent: Wednesday, March 1, 2017 2:03 PM
To: ParaView 
Subject: [EXTERNAL] [Paraview] CSV to PVTU

Hi again community!

Looking for suggestions - what would be a decently fast way to convert a huge 
CSV file into PVTU files?

What I want to do - load this huge file in a CAVE like environment, and use 8 
parallel processors.
--
Faiz Abidi | Master's Student at Virginia Tech | 
www.faizabidi.com | +1-540-998-6636
___
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Re: [Paraview] 2d image tiling problem

[Moreland, Kenneth]

I cannot think of any existing reader with a format that is similar to what you 
describe. That said, the VTK/ParaView data structures could hold such a thing 
no problem. It might be your best bet is to create a reader (or programmable 
source) that reads in the metafile.

-Ken


From: ParaView  on behalf of Walter Scott 

Date: Tuesday, February 28, 2017 at 12:57 PM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] 2d image tiling problem

Hi guys,
I have a user that wants to visualize very large images (i.e., terrabyte size 
images).  These images are composed of tiles or subimages, which are offset in 
the main image according to a metafile.  Does Kitware have any tools for 
visualizing and manipulating large images?

Thanks,

Alan

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Re: [Paraview] Paraview crashes with netCDF

[Moreland, Kenneth]

Adam,

Was able to replicate your problem. It looks like there are minor issues with 
both gdalwarp and ParaView that together are causing the crash.

The first problem is that gdalwarp is not writing the units attribute correctly 
when outputting the coordinates in feet. Instead, the units are set to an empty 
string. This seems wrong. The attribute should be set to “ft” or “feet”. When 
you use gdalwarp to write units of meters, it correctly writes this attribute 
as “m”. This is probably a bug, but it shouldn’t cause ParaView to crash.

So you probably already see where this is going. NetCDF attributes of empty 
strings are odd, and the ParaView reader probably has never encountered one 
before. Lo and behold in this case the reader tries to pull a pointer out of an 
empty std::string, and std::string throws an exception.

I’ve raised a bug for ParaView 
(https://gitlab.kitware.com/paraview/paraview/issues/17173) and will look into 
fixing this. I’ll leave it up to you whether you want to contact the GDAL 
developers about the issue with gdalwarp.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Adam 
Dershowitz
Sent: Monday, February 13, 2017 9:20 AM
To: ParaView@paraview.org
Subject: [EXTERNAL] Re: [Paraview] Paraview crashes with netCDF

I found a bit more information.  When pareview crashes, here is part of the 
crash log:

Application Specific Information:
terminating with uncaught exception of type std::out_of_range: basic_string
abort() called

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib 0x7fffcb43add6 __pthread_kill + 
10
1   libsystem_pthread.dylib  0x7fffcb526787 pthread_kill + 90
2   libsystem_c.dylib   0x7fffcb3a0420 abort + 129
3   libc++abi.dylib   0x7fffc9efb85a abort_message + 266
4   libc++abi.dylib   0x7fffc9f20c37 
default_terminate_handler() + 243
5   libobjc.A.dylib 0x7fffcaa2af33 _objc_terminate() + 124
6   libc++abi.dylib   0x7fffc9f1dd69 std::__terminate(void 
(*)()) + 8
7   libc++abi.dylib   0x7fffc9f1d9f2 __cxa_rethrow + 99
8   QtCore 0x00010db17d2d 
QEventLoop::exec(QFlags) + 845
9   QtCore 0x00010db1ad97 
QCoreApplication::exec() + 199
10  org.paraview.ParaView 0x00010b083fd2 main + 386
11  libdyld.dylib   0x7fffcb30c255 start + 1

Any idea why that happens with one feet, but not meters in an otherwise 
identical file?

-- Adam


From: Dershowitz Adam 
>
Date: Tuesday, February 7, 2017 at 11:58 AM
To: "ParaView@paraview.org" 
>
Subject: Paraview crashes with netCDF

I have a geotiff file that I want to view in Paraview.  But, Paraview seems to 
not show the correct offset (0,0 instead of respected the offset).  The work 
around I have been trying is to warp it to the correct location using gdalwarp 
and to export it as a netCDF.  Then Paraview should be able to show it 
correctly.
But, I have run into a crash.
If I do this:
gdalwarp  -t_srs EPSG:3652 -of netCDF test.tiff test_ft.nc

then I try to open test.nc in Paraview immediately crashes.

While, instead if do this:

gdalwarp  -t_srs EPSG:3651 -of netCDF test.tiff test_m.nc

then it opens fine.  The difference between these two files is that EPSG 3652 
uses feet (which is better for me, for this particular project) while 3651 uses 
meters.  Both appear to be valid NetCDF files.  I’ve tried both readers “CAM 
NetCDF (Unstructured)” and “NetCDF files generic and CF conventions” with the 
same results.

I’m running Paraview 5.2.0 64-bit on Mac OS 10.12.3.  But, I have seen 
identical results on an older Mac with a prior OS.  I had also tried an older 
version of Paraview with the same result.

Any ideas why this consistently crashes Paraview, or what to do about it?  
Using netCDF was already a work around, and I willing to try others to view 
these files.  The offset and scale are important because I then need to put in 
other data that is in the correct location and units.

The files are too big for me to send to the mailing list, so I have not posted 
them.

Thanks,

-- Adam

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Re: [Paraview] First trial file does not work-help!

[Moreland, Kenneth]

I'm not sure I understand what you are asking. I think you want to show the two 
blocks with different representations (outline and surface, respectively). If 
you take a look at the Multi-block Inspector (View → Multi-block Inspector) you 
can find controls to add different display properties to different blocks. 
Unfortunately, you are not able to set different representations on different 
blocks. Here is a way around the problem though:

1. Add the Outline filter to the reader (Filters → Alphabetical → Outline). You 
will now see geometry, gauss points, and outlines around both.
2. Select the reader in the pipeline browser, go to the Multi-block Inspector, 
right click on the block for geometry, and select Hide Block.
3. Select the Outline filter in the pipeline browser, go to the Multi-block 
Inspector, right click on the block for gauss points, and select Hide Block.

-Ken

-Original Message-
From: Emrah Ersan Erdogan [mailto:emrahersanerdo...@gmail.com] 
Sent: Friday, February 3, 2017 3:02 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] First trial file does not work-help!

Thanks, that works very well. Since I just learn at the moment I prefer to work 
on text editor. I guess when I integrate it to my FE solver in c++, it will be 
ok from now on.

The only thing is that I think it is not possible to make one show the outline 
(geometry) and the other gaussian points at the same time in paraview.

Do you know any way to do it? Because otherwise I will be forced to work on 
separate files unfortunately.

Best

Ersan



> On 3 Feb 2017, at 18:57, Moreland, Kenneth <kmo...@sandia.gov> wrote:
> 
> Trust me, you are not the first person to be burned by smart quotes. 
> (Viva la vim?)
> 
> I suggest putting each piece in its own vtu file and then create a vtm file 
> that points to the two of them. Here is a simple example of the contents of a 
> vtm file:
> 
>  byte_order="LittleEndian" header_type="UInt64">  
>
>
>
>
>  
> 
> 
> 
> -Ken
> 
> 
> On 2/3/17, 6:37 AM, "Emrah Ersan Erdogan" <emrahersanerdo...@gmail.com> wrote:
> 
>You are a life-saver, literally. That would not have occurred to me for a 
> long time believe me.
> 
>As a final step, in the first piece I want to create only the geometry and 
> in the second piece some points (these are gauss points actually) and with 
> some data.
>The problem is, paraview does not see “strain” when it is defined as given 
> below. However, if I swap the point dataset to the first piece it works: on 
> the wrong points of course.
>And second, it is apparently not possible to show the geometry and point 
> values at the same time. Do you think I need to define two separate files and 
> "light them up" separately on main paraview screen?
> 
>Thank you a lot again. I think this will conclude my problem entirely.
> 
>Ersan
> 
>
>
>   
>  
> 
> format="ascii">
>   0.00 0.00 0.00 1.00 0.00 0.00 1.00 1.00 0.00 0.00 1.00 0.00
>
> 
> 
>
>   0 1 2 3
>
>
>   4
>
>
>   9
>
> 
> 
> 
> 
> 
>  
>  
> 
> format="ascii">
>   0.25 0.25 0.00 0.75 0.25 0.00 0.75 0.75 0.00 0.25 0.75 0.00
>
> 
> 
>
>
>
>   
>
>
> 
> 
> format="ascii">
>   2.0 3.0 0.0
>   3.0 2.0 0.0
>   0.0 0.0 0.0
> 
>   1.0 2.0 0.0
>   2.0 1.0 0.0
>   0.0 0.0 0.0
> 
>   5.0 4.0 0.0
>   4.0 1.0 0.0
>   0.0 0.0 0.0
> 
>   3.0 6.0 0.0
>   6.0 7.0 0.0
>   0.0 0.0 0.0
>
> 
> 
> 
>  
>   
>
> 
>> On 3 Feb 2017, at 01:24, Moreland, Kenneth <kmo...@sandia.gov> wrote:
>> 
>> Did you type this in a text editor? The first thing I notice is that many of 
>> the quotes are the fancy open/close characters. Many text editors use a 
>> “smart quotes” feature that replaces the straight quote to a 

Re: [Paraview] First trial file does not work-help!

[Moreland, Kenneth]

Trust me, you are not the first person to be burned by smart quotes. (Viva la 
vim?)

I suggest putting each piece in its own vtu file and then create a vtm file 
that points to the two of them. Here is a simple example of the contents of a 
vtm file:


  




  



-Ken


On 2/3/17, 6:37 AM, "Emrah Ersan Erdogan" <emrahersanerdo...@gmail.com> wrote:

You are a life-saver, literally. That would not have occurred to me for a 
long time believe me.

As a final step, in the first piece I want to create only the geometry and 
in the second piece some points (these are gauss points actually) and with some 
data.
The problem is, paraview does not see “strain” when it is defined as given 
below. However, if I swap the point dataset to the first piece it works: on the 
wrong points of course.
And second, it is apparently not possible to show the geometry and point 
values at the same time. Do you think I need to define two separate files and 
"light them up" separately on main paraview screen?

Thank you a lot again. I think this will conclude my problem entirely.

Ersan



   
  
 

   0.00 0.00 0.00 1.00 0.00 0.00 1.00 1.00 0.00 0.00 1.00 0.00

 
 

   0 1 2 3


   4


   9

 
 
 
 
 
  
  
 

   0.25 0.25 0.00 0.75 0.25 0.00 0.75 0.75 0.00 0.25 0.75 0.00

 
 



   


 
 

   2.0 3.0 0.0
   3.0 2.0 0.0
   0.0 0.0 0.0

   1.0 2.0 0.0
   2.0 1.0 0.0
   0.0 0.0 0.0

   5.0 4.0 0.0
   4.0 1.0 0.0
   0.0 0.0 0.0

   3.0 6.0 0.0
   6.0 7.0 0.0
   0.0 0.0 0.0

 
 
 
  
   


> On 3 Feb 2017, at 01:24, Moreland, Kenneth <kmo...@sandia.gov> wrote:
> 
> Did you type this in a text editor? The first thing I notice is that many 
of the quotes are the fancy open/close characters. Many text editors use a 
“smart quotes” feature that replaces the straight quote to a bent open or 
closed quote. The VTK reader only accepts the straight quotes (ASCII character 
34).
> 
> -Ken
> 
> 
> On 2/2/17, 5:58 PM, "ParaView on behalf of Emrah Ersan Erdogan" 
<paraview-boun...@paraview.org on behalf of emrahersanerdo...@gmail.com> wrote:
> 
>Hi,
> 
>I am a new user of paraview and try to understand .vtu file format. 
>Just as a simple test I wanted to create two pieces one solely defines 
4 points and a cell with no attributes, hence forming geometry only. And the 
second piece defines only points with point attributes.
> 
>However, it seems I am doing something(s) wrong since paraview reader 
does not recognize the information. It would be great if somebody tells me what 
I am doing wrong. Afterwards I can take it off by myself I guess.
> 
>Thanks a bunch!
> 
>Ersan
> 
> 
>
>
>
>   2.0 2.0 3.0 1.0
>
> 
> 
> 
>  
>   
>
> 
>___
>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: 
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> 
>Search the list archives at: http://markmail.org/search/?q=ParaView
> 
>Follow this link to subscribe/unsubscribe:
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> 
> 



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Re: [Paraview] First trial file does not work-help!

[Moreland, Kenneth]

Did you type this in a text editor? The first thing I notice is that many of 
the quotes are the fancy open/close characters. Many text editors use a “smart 
quotes” feature that replaces the straight quote to a bent open or closed 
quote. The VTK reader only accepts the straight quotes (ASCII character 34).

-Ken


On 2/2/17, 5:58 PM, "ParaView on behalf of Emrah Ersan Erdogan" 
 wrote:

Hi,

I am a new user of paraview and try to understand .vtu file format. 
Just as a simple test I wanted to create two pieces one solely defines 4 
points and a cell with no attributes, hence forming geometry only. And the 
second piece defines only points with point attributes.

However, it seems I am doing something(s) wrong since paraview reader does 
not recognize the information. It would be great if somebody tells me what I am 
doing wrong. Afterwards I can take it off by myself I guess.

Thanks a bunch!

Ersan





   2.0 2.0 3.0 1.0

 
 
 
  
   


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Re: [Paraview] Point cloud to structured mesh

[Moreland, Kenneth]

The most direct approach is probably to use the Gaussian Resampling filter.

Another approach is to run the Delaunay 3D filter and then run the resample to 
image filter.

-Ken

From: ParaView  on behalf of Walter Scott 

Date: Monday, January 30, 2017 at 4:19 PM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] Point cloud to structured mesh

Is it possible to convert a point cloud to a structured mesh or an image stack 
in ParaView?

Thanks,

Alan


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Re: [Paraview] Generate IDs

[Moreland, Kenneth]

Daniel,

As you have discovered, trying to “connect” data sets in this way after the 
clip filter is applied is problematic because it changes the locations of 
points and the structure of cells. It makes the grids no longer isomorphic or 
sub-isomorphic.

I would suggest one of two approaches. The first approach would be to combine 
all the data arrays into one data set before doing any of the extractions, 
thresholds, or clips. If all your arrays are on data sets with the exact same 
grid structure, then you can use the append attributes filter to combine the 
arrays of all these data sets into a single data set. Then the arrays will 
simply be available from the output of the clip.

If that approach will not work for some reason, a second approach is to use the 
resample with dataset filter. You can use this to sample the other data sets 
onto the clipped data set, which I think in the end gives you the effect you 
are looking for.

-Ken


From: ParaView  on behalf of Daniel Frisch 

Date: Tuesday, January 31, 2017 at 1:20 AM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] Generate IDs

Hello, I want to

- open an unstructured grid,
- view a sub-volume using the Threshold filter that selects a certain material
- apply some Clip filters to remove unwanted parts
- select everything I am seeing now
- and create an "Extract Selection" filter that can be used for other vtk files 
containing the same unstructured grid but other data arrays.

But the "GenerateIDs" filter removes the material array from the dataset so I 
can't apply the Threshold filter anymore. I see the "Extract Selection" works 
only with the current IDs anyway that are different from the original cell IDs 
due to the Clip filters.

How can I have a filter that extracts a certain set of cells that I define and 
apply it to other .vtk files?

Thank you very much in advance,
Daniel
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Re: [Paraview] Gradient between cell data

[Moreland, Kenneth]

Christoph,

To my knowledge, there is no direct way to do this. If your data are in an 
ImageData or some other type of structured grid, it should be fairly 
straightforward to use a programmable filter to build a new grid with one fewer 
point in each dimension and then copy the cell data of this original mesh to 
the point data of the new mesh. You can then do finite differences on the 
points of the new mesh and get the result you are looking for.

-Ken

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Christoph 
Grüninger
Sent: Thursday, January 26, 2017 6:09 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Gradient between cell data

Dear ParaView!

I have a simulation computed with a finite volume method which outputs pressure 
as cell data. The pressure gradient is related to the velocity (Darcy's law). 
Is it possible to calculate the gradient as a finite difference between the 
cell centers of adjacent cells?
The result would be located between the cells, not sure whether this works at 
all.

Converting cell data to point data and using the gradient filter is not what I 
want.

Bye
Christoph
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Re: [Paraview] Display all time steps on the same window

[Moreland, Kenneth]

Try applying the “Group Time Steps” filter (introduced in ParaView 5.2).

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Júlio 
Hoffimann
Sent: Wednesday, January 18, 2017 12:00 PM
To: paraview 
Subject: [EXTERNAL] [Paraview] Display all time steps on the same window

Hi,

I am struggling with a very simple task in ParaView. I have 500 time steps that 
represent an object moving in space. I would like to display all the positions 
of the object (thus, the trajectory) in a single window.

I have a set of 500 *.vtu files and a pvd collection that I can successfully 
load into ParaView to play with the time. How to display all time steps in the 
window, or alternatively, how to merge all these *.vtu files into a single 
unstructured mesh?

-Júlio
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Re: [Paraview] exodusII reader & writer in parallel

[Moreland, Kenneth]

Hmm. That’s disappointing. Although I’ve heard of files missing fields on 
element blocks because no blocks with that field is local, I guess having no 
data on a process is not something simulations typically experience.

I agree with modifying the reader then. I would not mess around with the third 
party code over this.

-Ken

From: Andy Bauer [mailto:andy.ba...@kitware.com]
Sent: Friday, January 13, 2017 2:03 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] exodusII reader & writer in parallel

It's looking like there could be a decent amount of hacking in the ExodusII 
code to get the writer to work properly for this (as well as the reader to read 
it back in without issues). The main issue appears to be that NetCDF doesn't 
allow creating a dimension of 0 length/size. Thus the stuff in 
VTK/ThirdParty/exodusII/vtkexodusII would need to be changed.
Both the reader and writer make the assumption that if the num_nodes dimension 
exists that there are points to be read in.
At this point I'm thinking it's better to modify the reader than the writer...

On Fri, Jan 13, 2017 at 2:59 PM, Andy Bauer 
<andy.ba...@kitware.com<mailto:andy.ba...@kitware.com>> wrote:
Hi Ken,
Thanks for the input.
There is an explicit check in the writer to see if there are any points before 
writing out point data. I took that check out and am hitting a NetCDF error 
that the "num_nodes" dimension isn't specified. It will probably take a bit of 
investigating to fix this but at least you've helped me go down the correct 
path.
Thanks,
Andy

On Fri, Jan 13, 2017 at 2:44 PM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Andy,

That sounds like a bug in our Exodus writer to me. I’m not positive, but I’m 
pretty sure that you can specify in Exodus point and cell arrays if no grid 
points or cells exist. The writer is probably making a shortcut and skipping 
that if there is no actual data.

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Andy Bauer
Sent: Friday, January 13, 2017 12:00 PM
To: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] exodusII reader & writer in parallel

Hi,
I'm trying out the ExodusII writer in parallel and had some questions about how 
it should work in general when there isn't any data on process 0. Currently 
what happens in ParaView is that a file for each process is written out but the 
file corresponding to process 0 doesn't have any grid information or field data 
(an example is attached). When I read this back into ParaView using the 
built-in server (i.e. in serial) the ExodusII reader gets the proper points and 
cells but no field data is read in.
So my question is this, does the ExodusII file format allow specifying point 
and cell arrays in a file if no grid points or cells exist?
I'm tempted to fix this issue by modifying the reader to properly pass the 
field data information to process 0 from another one that has data but wanted 
to get the community's thoughts on this before I go through the implementation. 
The alternative would be to modify the writer to include point and cell data 
information and that's probably a better solution, assuming that the ExodusII 
format allows for that.
Thanks,
Andy
ps. Attached is a sample set of ExodusII files that doesn't have any data on 
parallel.ex2.4.0 in case someone wants to play around with it.


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Re: [Paraview] exodusII reader & writer in parallel

[Moreland, Kenneth]

Andy,

That sounds like a bug in our Exodus writer to me. I’m not positive, but I’m 
pretty sure that you can specify in Exodus point and cell arrays if no grid 
points or cells exist. The writer is probably making a shortcut and skipping 
that if there is no actual data.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Andy Bauer
Sent: Friday, January 13, 2017 12:00 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] exodusII reader & writer in parallel

Hi,
I'm trying out the ExodusII writer in parallel and had some questions about how 
it should work in general when there isn't any data on process 0. Currently 
what happens in ParaView is that a file for each process is written out but the 
file corresponding to process 0 doesn't have any grid information or field data 
(an example is attached). When I read this back into ParaView using the 
built-in server (i.e. in serial) the ExodusII reader gets the proper points and 
cells but no field data is read in.
So my question is this, does the ExodusII file format allow specifying point 
and cell arrays in a file if no grid points or cells exist?
I'm tempted to fix this issue by modifying the reader to properly pass the 
field data information to process 0 from another one that has data but wanted 
to get the community's thoughts on this before I go through the implementation. 
The alternative would be to modify the writer to include point and cell data 
information and that's probably a better solution, assuming that the ExodusII 
format allows for that.
Thanks,
Andy
ps. Attached is a sample set of ExodusII files that doesn't have any data on 
parallel.ex2.4.0 in case someone wants to play around with it.
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Re: [Paraview] [EXTERNAL] Decode a vtu file

[Moreland, Kenneth]

Documentation for vtu file format (and several other standard VTK formats) is 
here:

http://www.vtk.org/VTK/img/file-formats.pdf

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Andi Hartarto
Sent: Thursday, January 12, 2017 7:54 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Decode a vtu file

Hello all,

Can I please have guidance/help in decoding a vtu file?

My file is a


  

  
  
  


  
  

  
  



  

  
  
  (data long list)

The file can be found in this link:
https://drive.google.com/open?id=0BzmZiSDoM7l3U2poYWNTbUhBWVU

I don't understand how to decode a vtk file and couldn't find anything in 
google. I've tried using some scripts in python for base64 but it didn't work..

The reason why I need to decode this is because somehow this vtk file which 
load in paraview perfectly becomes a 2d file in another software "MOOSE" .. So 
I think somehow in the encoded data is telling the other software "only display 
the 2D intersection of blocks". But I want a 3D cube not a 2D surface. If 
someone knows about this please tell me .

Thank you,
Andi
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Re: [Paraview] Paraview Vtu to Exodus. Single block, multi element?

[Moreland, Kenneth]

Andi,

I am having a really hard time trying to understand what it is you are asking. 
I’m not sure what it means to “make object id = tetrahedrarank.”

I am going to make another guess at what it is you really want to do. You have 
data (from an Exodus file) that has a single block. One of the cell arrays is 
named tetrahedrarank. All the values of tetrahedrarank are either 1 or 2. You 
want to have a data set that has two blocks. One block has all cells with 
tetrahedrarank = 1. The other block has all cells with tetrahedrarank = 2. The 
following are the instructions to do that.

1. After loading the Exodus data, run the “Merge Blocks” filter.
2. Run a “Threshold” filter on the merged blocks. Set the “Scalars” property to 
TetrahedraRank. Set both “Minimum” and “Maximum” to 1.
3. Select the Merge Blocks filter in the Pipeline Browser again and add a 
second “Threshold” filter. On this second Threshold filter set the “Scalars” 
property to TetrahedraRank and set both “Minimum” and “Maximum” to 2.
4. Select both Threshold filters in the pipeline browser and add the “Group 
Datasets” filter. That will give you a data set with two blocks corresponding 
to the cells with TetrahedraRank 1 or 2.

-Ken

From: Andi Hartarto [mailto:andi3...@gmail.com]
Sent: Tuesday, January 10, 2017 6:26 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] Paraview Vtu to Exodus. Single block, multi 
element?

Ken,

From your email, I did filters > alphabetical> calculator> properties> 
attribute mode from point to cell data > result array name to dummy > 
expression to 0 > apply > save data as exodus file > open saved exodus file. I 
still don't see the 2 element data fields?

I hope i didn't misunderstand anything or misphrase... The main idea is that as 
shown in kenneth1.png, i need my element blocks to be of 2 arrays not just 1. I 
can see its unnamed block id:5 but I want it to be following my tetrahedral 
rank which is 1 and 2. In kenneth2. There is a clear distinction of colors 
because i use my tetrahedral rank to color it. I don't know how to make my 
block id = tetrahedra rank.

so my problem is actually:
How do i make object id = tetrahedrarank > hopefully this makes 2 data arrays 
in element blocks.

Thank you,
Andi

On 10 January 2017 at 03:32, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Andi,

You said you need an output with multiple blocks, but your last comment, “I 
need 1 block data set with 2 or more element data inside it,” suggests that 
what you really need is to add a second field of data.

Try using the calculator to add that second field. Set the attribute mode to 
“Cell Data”, the “Result Array Name” to “Dummy”, and the Expression to 0. Now 
when you write that out to an Exodus file you should have two element data 
fields: the original tetrahedral rank and the Dummy field you created.

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Andi Hartarto
Sent: Sunday, January 8, 2017 4:58 PM
To: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] Paraview Vtu to Exodus. Single block, multi 
element?

Hi all, i need help please.

Introduction:
My problem is that I need to convert a vtu file into an exodus formatted file 
that reads several element block data.
When I load my data in vtu, all i see is a white cubic block.
This block has 2 data arrays named tetrahedra rank and tetrahedra number. When 
I change my coloring to tetrahedra rank, I can see 2 colors red and blue 
coloring my block.

I want to save the vtu file into an exodus format file and load it to another 
software but the other software only shows me the output of colors if there are 
several element blocks.
 In my case, the vtu file converted to exodus has only 1 element block.
In paraview, I can go properties, add the variables of tetrahedra rank and then 
change coloring then i see what i want to see.
But in the software I am supposed to load the data, I can't do that.
Im supposed to make my exodus data into 2 or more element blocks and then load 
it in that software which makes the software goes "ok so there are various data 
! lets color it".

I don't know what should i do to change my vtu file with cell data of 
tetrahedra rank clearly showing the 2 data sets into 2 element blocks.
I have tried to use edit> find data> extract selection > repeat for the next > 
group the data.
I get a multi block data set. It didn't work. I need 1 block data set with 2 or 
more element data inside it.

Please help,
Andi

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Re: [Paraview] [EXTERNAL] How to load different data files for multiple pvservers

[Moreland, Kenneth]

I recommend writing out your data as .pvtp instead .vtk files. The file formats 
are similar, but pvtp supports reading and writing in parallel. Both formats 
are documented here:

http://www.vtk.org/VTK/img/file-formats.pdf

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of ???
Sent: Tuesday, January 10, 2017 4:41 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] How to load different data files for multiple 
pvservers



Hello,

I'm using ParaView for parallel visualization. My dataset is polydata, it is 
not "parallel aware". However, using the D3 filter, as the ParaView User's 
Guide says, is too expensive, which slow down the whole process significantly. 
As my data is  generated in parallel, I want to assign these data files to  
multiple pvservers. For example, I have a dataset contains four files: 
file0.vtk, file1.vtk, file2.vtk and file3.vtk. Note that they are not temporal 
file series, but each represent a different area of the simulation domain. And, 
I start four pvservers by mpirun -np 4 ./pvserver. I can connect to the 
pvserver using paraview GUI on my PC, but I don't how to distribute the four 
files to each pvserver. I tried to select the four files using the Ctrl key and 
hit Apply, but it seems that they are all assigned to the process 0. Is there 
any way I can distribute the data files to each pvserver using the paraview GUI?

Thanks a lot!
-Zhang

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Re: [Paraview] get name of source in pipeline gui

[Moreland, Kenneth]

I think the only way to get the name of the active source (or any source for 
that matter) is to search for it in the values of the dictionary returned by 
GetSources(). If you look at this dictionary, it has a set of keys that are a 
pair consisting of the name in the pipeline browser and a unique id string (in 
case two items in the pipeline browser have the same name). This rather obtuse 
expression should return the string of the name of the active source in the 
pipeline browser:

list(GetSources().keys())[list(GetSources().values()).index(GetActiveSource())][0]

Maybe someone knows of another Python binding I am not familiar with, but this 
should at least solve your problem.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Bob Flandard
Sent: Sunday, January 8, 2017 4:37 AM
To: paraview 
Subject: [EXTERNAL] [Paraview] get name of source in pipeline gui

Hi,
How to get the name of the active source in the pipeline? (the gui name)
gas=GetActiveSource()
Then what?
I've spent an hour or more on this.
Thanks, Bob
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Re: [Paraview] Paraview Vtu to Exodus. Single block, multi element?

[Moreland, Kenneth]

Andi,

You said you need an output with multiple blocks, but your last comment, “I 
need 1 block data set with 2 or more element data inside it,” suggests that 
what you really need is to add a second field of data.

Try using the calculator to add that second field. Set the attribute mode to 
“Cell Data”, the “Result Array Name” to “Dummy”, and the Expression to 0. Now 
when you write that out to an Exodus file you should have two element data 
fields: the original tetrahedral rank and the Dummy field you created.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Andi Hartarto
Sent: Sunday, January 8, 2017 4:58 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Paraview Vtu to Exodus. Single block, multi 
element?

Hi all, i need help please.

Introduction:
My problem is that I need to convert a vtu file into an exodus formatted file 
that reads several element block data.
When I load my data in vtu, all i see is a white cubic block.
This block has 2 data arrays named tetrahedra rank and tetrahedra number. When 
I change my coloring to tetrahedra rank, I can see 2 colors red and blue 
coloring my block.

I want to save the vtu file into an exodus format file and load it to another 
software but the other software only shows me the output of colors if there are 
several element blocks.
 In my case, the vtu file converted to exodus has only 1 element block.
In paraview, I can go properties, add the variables of tetrahedra rank and then 
change coloring then i see what i want to see.
But in the software I am supposed to load the data, I can't do that.
Im supposed to make my exodus data into 2 or more element blocks and then load 
it in that software which makes the software goes "ok so there are various data 
! lets color it".

I don't know what should i do to change my vtu file with cell data of 
tetrahedra rank clearly showing the 2 data sets into 2 element blocks.
I have tried to use edit> find data> extract selection > repeat for the next > 
group the data.
I get a multi block data set. It didn't work. I need 1 block data set with 2 or 
more element data inside it.

Please help,
Andi
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Re: [Paraview] Thanks for your help!

[Moreland, Kenneth]

I am out this week, so I am not following this thread closely, but it's not 
clear from the description of your hardware that you are ever going to get an 
improvement from parallel rendering.

You said you have 8 cores. Are these 8 cores in the same machine? If so, I 
don't think running in parallel will help with your rendering. Probably all 8 
instances of MPI are rendering with the same GPU, which means all the rendering 
instructions from the parallel job fight with each other to get queued up on 
the same GPU, which will make the overall rendering slower, not faster.

Somewhere in the thread I thought I read that you have 2 GPUs. Unless you have 
set up something special, one of them is probably being ignored. Even if you go 
through the pain of managing to set up a parallel ParaView to use both GPUs, I 
doubt you will get much if any speed up. The parallel rendering, which was 
designed for cluster computing, has an overhead; buffers are read back, pixels 
are transferred, and blending operations are performed. You are unlikely to 
gain much of that back with only 2 GPUs.

-Ken

Sent from my iPad so blame autocorrect.

On Dec 27, 2016, at 12:36 PM, Chuck Atkins 
> wrote:


In my case, the dataset consists only of random numbers and it's in a single 
partition. I will try to generate a dataset in parallel in a few days and 
render it as you told me.

5M point's is actually a pretty small dataset that should be easy to handle 
from a rendering standpoint, i.e. you should be fine handling it on a single 
node.  Most of your time is likely spent in I/O and data conversion rather than 
rendering.  How are you getting your data into ParaView, i.e. what file format 
are you using?  There is likely a better way that my address most of the 
performance issues you are having and remove the need for parallel rendering 
entirely.

Just for some context, I generated 5M random points in a 100x100x100 cube with 
a single field data assigned to each point.
CSV File:

  *   File size: 177M
  *   Read file: 29 sec
  *   Convert to points: 0.1 sec

VTK XML (binary encoding of data arrays):

  *   File Size: 130M
  *   Read File: 1.4 sec.

In both cases, once the file is read, the first frame render time with the 
basic on-board Intel graphics card on my laptop is only 0.15 sec with the 
subsequent frame render times being 0.04 sec.  You can see from this that the 
bulk of the time is spent in file I/O and data conversion, especialy with using 
something like CSV.  This was with ParaView 5.2.  With 4.4, the I/O times are 
the same but the first-frame render time is much slower: 0.6 sec.  Still much 
closer to a usable frame rate. than 100 sec.

- Chuck
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Re: [Paraview] [EXTERNAL] Time Synchronization for Case and Geometry Sequences

[Moreland, Kenneth]

I may have told you the wrong parameters. Try using 0.005 for the temporal 
shift rather than -0.005.

-Ken

On 12/1/16, 3:10 PM, "Huangrui Mo" <huangrui...@uwaterloo.ca> wrote:

Hello Ken,

Thank you for the provided solution, however, it seems like the solution 
does not work well: using the Paraview 5.2.0
(I just downloaded the latest version, and realizing that there is a 
modification on showing the max counter of time steps),
after applying the method you provided, it artificially works for the 
first 9 counts, but when you input "10", then you would realize that
the mismatch is still there :D

I have found the following weired situation:

1) The time values in field.case, field.pvd, geo_stl.pvd are all exactly 
the same and are all in ASCII format.
2) When paraview read in the field.pvd or geo_stl.pvd, it will change 
the floating point values slightly, however, it maintains consistence
if they are ".pvd" files. Therefore, it correctly synchronizes these two 
data sets.
3) When paraview read in the field.case, the floating point 
representation of the time values are changed slightly and are not 
consistently with ".pvd" files.
However, in this mixed case, the "0" value is the same, so paraview 
merges field.case and geo_stl.pvd for time "0", and reduces the total 
number of cases
from 11 + 11 to 21. (sorry for previous miscalculation of the counter, 
it's 11 rather than 10 for each data set.)

Is it because when reading Ensight format, paraview choose single 
precision, but using double  precision for .pvd file? Is there a way to 
fix this problem, since
the time values are all in ASCII format.

    Thanks,
Huangrui

On 2016-12-01 03:35 PM, Moreland, Kenneth wrote:
> Huangrui,
>
> I found a work around that I think does what you want. After you load in 
your two data sets, right click on one of them in the Pipeline Browser and 
check on the “Ignore Time” option. This will tell ParaView to ignore the time 
in that data set, so will only visit the time steps in the other data set.
>
> Actually, this _almost_ works. There is in fact a problem (at least with 
the example data sets you sent us). The imprecision is not uniform. Sometimes 
the time for field.case is ahead, other times the time for geo_stl.pvd is 
ahead. So, when you play through the time steps, sometimes the data for which 
you are ignoring time are skipped because the time is first just before one 
step and then just after another.
>
> To fix this problem, you can use the Temporal Shift Scale filter to 
adjust the time of one of the data sets to subtract a bit to ensure that every 
time hits in between time steps. Here is specifically what I did with the test 
data that you sent to fix the problem.
>
> 1. Load in the field.case and geo_stl.pvd files. Apply both.
> 2. Add the Temporal Shift Scale filter to geo_stl.pvd. Set the Pre Shift 
to -0.005. Apply.
> 3. Right click on TemporalShiftScale1 in the pipeline browser and select 
“Ignore Time”
>
> Now when you hit play you should get the right amount of time steps with 
the data you expect loaded.
>
> -Ken
>
> On 12/1/16, 1:58 PM, "Huangrui Mo" <huangrui...@uwaterloo.ca> wrote:
>
>  Hello Alan and Ken,
>  
>  Thank you very much for your prompt response of my question.
>  
>  After testing your suggestions, I found both the Real Time Mode and
>  Sequence Mode can correctly synchronize the
>  two data sets with mixed formats, if a correct number of steps is 
given.
>  However, both of the above two methods
>  share a common subproblem: they give artificial time steps that are
>  different with the "true" time moments contained in
>  the case (or pvd) files, when a annotated time filter is used, even 
the
>  specified number of steps matches the true number of case files.
>  
>  Regarding the Snap to Timesteps mode and the numerical imprecision of
>  the different times problem raised by Ken, I provided an example
>  data set attached in this email. This data set contains the simulated
>  flow field of three airfoils running on a fixed Cartesian background 
grid.
>  Since the Cartesian grid is fixed, therefore, using Ensight format 
for
>  the field data has the advantage to avoid outputting the grid
>  coordinates in each
>  time step but only the physical quantities. To facilitate the 
testing, I
>  solved this problem exactly twice, the only difference is that one 
uses
>  Ensigh

Re: [Paraview] [EXTERNAL] Time Synchronization for Case and Geometry Sequences

[Moreland, Kenneth]

Huangrui,

I found a work around that I think does what you want. After you load in your 
two data sets, right click on one of them in the Pipeline Browser and check on 
the “Ignore Time” option. This will tell ParaView to ignore the time in that 
data set, so will only visit the time steps in the other data set.

Actually, this _almost_ works. There is in fact a problem (at least with the 
example data sets you sent us). The imprecision is not uniform. Sometimes the 
time for field.case is ahead, other times the time for geo_stl.pvd is ahead. 
So, when you play through the time steps, sometimes the data for which you are 
ignoring time are skipped because the time is first just before one step and 
then just after another.

To fix this problem, you can use the Temporal Shift Scale filter to adjust the 
time of one of the data sets to subtract a bit to ensure that every time hits 
in between time steps. Here is specifically what I did with the test data that 
you sent to fix the problem.

1. Load in the field.case and geo_stl.pvd files. Apply both.
2. Add the Temporal Shift Scale filter to geo_stl.pvd. Set the Pre Shift to 
-0.005. Apply.
3. Right click on TemporalShiftScale1 in the pipeline browser and select 
“Ignore Time”

Now when you hit play you should get the right amount of time steps with the 
data you expect loaded.

-Ken

On 12/1/16, 1:58 PM, "Huangrui Mo" <huangrui...@uwaterloo.ca> wrote:

Hello Alan and Ken,

Thank you very much for your prompt response of my question.

After testing your suggestions, I found both the Real Time Mode and 
Sequence Mode can correctly synchronize the
two data sets with mixed formats, if a correct number of steps is given. 
However, both of the above two methods
share a common subproblem: they give artificial time steps that are 
different with the "true" time moments contained in
the case (or pvd) files, when a annotated time filter is used, even the 
specified number of steps matches the true number of case files.

Regarding the Snap to Timesteps mode and the numerical imprecision of 
the different times problem raised by Ken, I provided an example
data set attached in this email. This data set contains the simulated 
flow field of three airfoils running on a fixed Cartesian background grid.
Since the Cartesian grid is fixed, therefore, using Ensight format for 
the field data has the advantage to avoid outputting the grid 
coordinates in each
time step but only the physical quantities. To facilitate the testing, I 
solved this problem exactly twice, the only difference is that one uses 
Ensight for field data
and VTK for geometry, the other uses both VTK. Each data sets has 10 
time sequences, and the time steps in each data sets are all the same.

When loading the mixed data sets, the field.case + geo_stl.pvd gives 20 
sequences, and the field.pvd + geo_stl.pvd  gives 10 synchronized sequences.

Due to the artificial times steps in the Real Time Mode and Sequence 
Mod, is there a way to synchronize the mixed case in the Snap to 
Timesteps mode?

Thanks a lot,
Huangrui



    On 2016-12-01 01:54 PM, Moreland, Kenneth wrote:
> Actually, I think Sequence mode is more appropriate than Real Time mode 
in this case, but I too think that is the answer.
>
> To explain more what (we think) is going on: When you load data with time 
in ParaView, it goes to a Snap to Timesteps mode where it will visit each 
unique timestep once regardless of how far apart they are. Thus, ParaView is 
treating the numerical imprecision of the different times as unique time steps. 
If you switch to Sequence or Real Time mode, ParaView uses its own time units 
and will provide an even temporal spacing.
>
> There is more information about the different animation modes in the 
ParaView tutorial.
>
> -Ken
>
> Sent from my iPad so blame autocorrect.
>
>> On Dec 1, 2016, at 11:35 AM, Scott, W Alan <wasc...@sandia.gov> wrote:
>>
>> Not sure if this is the correct answer, but try view/ animation View.  
Then, change the Mode to Real Time.  Enter your start time and end time, and 
number of time steps of interest (i.e., 500).
>>
>> Is that what you are looking for?
>>
>> alan
>>
>> -Original Message-
>> From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of 
Huangrui Mo
>> Sent: Thursday, December 1, 2016 9:54 AM
>> To: paraview@paraview.org
>> Subject: [EXTERNAL] [Paraview] Time Synchronization for Case and 
Geometry Sequences
>>
>> Dear Paraview Developer,
>>
>> May you please help me with the following issue:
>>
>> Suppose when a solver 

Re: [Paraview] [EXTERNAL] Time Synchronization for Case and Geometry Sequences

[Moreland, Kenneth]

Actually, I think Sequence mode is more appropriate than Real Time mode in this 
case, but I too think that is the answer. 

To explain more what (we think) is going on: When you load data with time in 
ParaView, it goes to a Snap to Timesteps mode where it will visit each unique 
timestep once regardless of how far apart they are. Thus, ParaView is treating 
the numerical imprecision of the different times as unique time steps. If you 
switch to Sequence or Real Time mode, ParaView uses its own time units and will 
provide an even temporal spacing. 

There is more information about the different animation modes in the ParaView 
tutorial. 

-Ken

Sent from my iPad so blame autocorrect.

> On Dec 1, 2016, at 11:35 AM, Scott, W Alan  wrote:
> 
> Not sure if this is the correct answer, but try view/ animation View.  Then, 
> change the Mode to Real Time.  Enter your start time and end time, and number 
> of time steps of interest (i.e., 500).
> 
> Is that what you are looking for?
> 
> alan
> 
> -Original Message-
> From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Huangrui Mo
> Sent: Thursday, December 1, 2016 9:54 AM
> To: paraview@paraview.org
> Subject: [EXTERNAL] [Paraview] Time Synchronization for Case and Geometry 
> Sequences
> 
> Dear Paraview Developer,
> 
> May you please help me with the following issue:
> 
> Suppose when a solver writes data out, the field data is written in Ensight 
> format, and the time sequence is streamed in "ensight.case".
> Meanwhile, the geometry data is written in VTK format, and the time sequence 
> is streamed in "paraview.pvd".
> At last, let's assume the number of time sequences is 500.
> 
> Then, when loading into paraview, it does not synchronize the cases in a 
> perfect sense and would show up with 1000 cases. When animating, there is a 
> slight mismatch in time for the field data and geometry data. 
> However, if I use the VTK format for both the field and geometry data, then 
> paraview does a great job to synchronize the data sets.
> 
> Therefore, my question would be that is it possible to handle time 
> synchronization even for different formats?
> 
> Thank you very much for your time and help, Huangrui
> 
> --
> *
> Huangrui Mo, PhD Candidate
> Fluid Mechanics
> Department of Mechanical & Mechatronics Engineering University of Waterloo 
> Waterloo, Ontario N2L 3G1, Canada
> E-mail: huangrui...@uwaterloo.ca
> *
> 
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Re: [Paraview] Need urgent help: Edit Color Bar: How to revert to default

[Moreland, Kenneth]

Marc,

Sorry for the low response on this question. Your question came in right as 
Thanksgiving holiday weekend started in the US.

If you scroll down to the bottom of the Color Map Editor you will see a row of 
buttons on the bottom. The leftmost of these buttons is a circle of two arrows. 
If you press that button, the current color map will be restored to ParaView 
defaults. Then you should press the button that is two over with the same icon 
as save data (a folder with a green arrow pointing down into it). When you 
click that button, the current color map becomes the default color map.

If you are still having trouble, you should be able to get around the problem 
by simply deleting your ParaView configuration files, which will restore all of 
ParaView settings to their defaults. The location of these configuration files 
is documented here:

http://www.paraview.org/Wiki/ParaView_Settings_Files

-Ken

From: ParaView  on behalf of Herbalife Ottawa 

Date: Wednesday, November 23, 2016 at 8:35 PM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] Need urgent help: Edit Color Bar: How to revert 
to default

Hello Fellow Members,

I was playing with the Paraview Color bar editor and I messed up the Color 
Scale bar. I just kept clicking and new points were created and I kept moving 
them here and there. Initially, the color space was set to 'diverging', and the 
initial color bar was ranging from red to navy blue color.

I was doing all this under the assumption that the "Make default" button at the 
bottom will set everything to default again. But it doesn't work.

I even uninstalled Paraview and reinstalled again, but the changes I made 
remain.

Can any one please tell me how to get rid of this and revert back to my 
original red to blue scale. I tried reading how to edit the bar but I couldn't 
revert back to the original colors. Some what close but not original.

Please help.

Thanks!
Marc
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Re: [Paraview] Need node numbers and element node connectivity

[Moreland, Kenneth]

Chaitanya,

If I understand your question correctly, you should be able to solve your 
problem by running the Generate Ids filter before writing out the CSV file.

-Ken


From: ParaView  on behalf of Chaitanya Raj Goyal 

Date: Thursday, November 24, 2016 at 6:44 PM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] Need node numbers and element node connectivity

Dear All,

I run a FEM simulation in FEniCS to obtain two output files. One is of .vtu 
format and the other is of .xdmf format.

However, because I do parallel processing, in the former case, I actually 
obtain different .vtu files for different processors, a single .pvtu file and  
a single .pvd file. In the latter case, I obtain a single .xdmf and a .h5 file.

Both simulations are 2D, and if you open the spreadsheet format in Paraview, 
you see something like this:

[cid:image001.png@01D248D2.926E9B60]
​
I need to do some post processing on the solution vectors 'u' and 'v'. You may 
also refer to them as 'ux' and 'uy' OR "f_18_1" and "f_18_2". Therefore, I need 
to import it in MATLAB. To do that, in ParaView, I first go to menu >> save 
data >> save file in CSV format for all points. The csv file I am looking at 
gives me 6 columns - Coordinate X, Y, Z, Solution ux, uy, uz. Here Z and uz are 
zero vectors. How can I also get the node number for the given node 
coordinates, and how can I get the elemental nodal connectivity? Any help is 
greatly appreciated!

Thanks in advance!
Chaitanya
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Re: [Paraview] how to compute the averaged value of variable on the whole domain?

[Moreland, Kenneth]

Fande,

I think you may be looking for the “Integrate Variables” filter.

-Ken


From: ParaView  on behalf of Fande Kong 

Date: Sunday, November 27, 2016 at 3:17 PM
To: ParaView 
Subject: [EXTERNAL] [Paraview] how to compute the averaged value of variable on 
the whole domain?

Hi ALL,

There is question. I have a pressure variable named p defined on the whole 
domain. How can calculate a averaged value for p? I think mathematically we 
should integrate p on the whole domain, then and divide by the volume of the 
domain.

Thanks so much.


Fande,
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Re: [Paraview] RAW (binary) file import issues

[Moreland, Kenneth]

Although we have certainly run into issues with communicating large messages, 
I’m not sure this is the issue with MPI-I/O. File sizes and linear offsets use 
a type MPI_Offset, which according to the specification should be large enough 
to hold the size of any file supported by the file system. Although it is true 
that creating the 3D subarray uses 32-bit indices, those are for each of the 
separate dimensions, and 2000 falls well below that limit.

Besides, it looks like that error happens when checking an ifstream object, so 
it looks like the reader is bypassing the MPI-I/O path anyway.

I would follow Berk’s suggesting of looking into the filesystem before diving 
into the guts of MPI-I/O.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Burlen Loring
Sent: Tuesday, November 22, 2016 12:55 PM
To: Geveci, Berk (External Contact) ; Keyes S.D. 

Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] RAW (binary) file import issues

I've hit that before. the RAW reader uses MPI-I/O, and MPI uses signed int 
everywhere in its API, so there are limits that you end up hitting. For 
instance to partition the data among processors one must give MPI-I/O the 
starting offset of the data in the file as a signed int, and that is limited to 
2^31.

Burlen
On 11/22/2016 11:20 AM, Berk Geveci wrote:
Hmmm that happens to be around 4 GB which makes me wonder if there is a limit 
somewhere in that reader... Any chance you can try this on a Linux machine?

On Thu, Nov 17, 2016 at 10:30 AM, Keyes S.D. 
> wrote:
Dear all,

I am encountering issues when trying to import large 8 bit RAW volumes to 
Paraview 5.1.2 (64 bit).

The file I wish to import has xyz dimensions of 2000x2000x1920 voxels (Unsigned 
char), 7.5GB.  I am running a machine with 192 GB RAM and 12 CPU cores.

I can import up to a 2000x2000x1000 crop of this file, but I encounter the 
following message when I attempt larger z dimensions:

ERROR: In C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx, 
line 592

vtkPVImageReader (07767F90): Initialize: Could not open file 
\\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw


I cannot find an obvious memory ceiling within the paraview settings - any 
ideas as to whether there is some effective upper limit to import file size?

Sam

Samuel D Keyes, MEng, PhD
New Frontiers Fellow
Bioengineering / μVIS Centre for Computed Tomography
University of Southampton
E: 
s.d.ke...@soton.ac.ukredir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBpAGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMALgB1AGsA=mailto%3aS.D.Keyes%40soton.ac.uk>
T: 07898720248
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Re: [Paraview] [EXTERNAL] animating particle pathlines

[Moreland, Kenneth]

(Replying back to the ParaView mailing list so others can benefit from the 
conversation or fill in my knowledge gaps.)

I admit that I have found the Temporal Particles To Pathlines filter sometimes 
temperamental. I have to guess what might be going wrong. Here are some 
possibilities:


· The filter draws lines of data as points move around over time. No 
lines will be drawn unless you hit that play button.

· The filter needs to have consistent ids to know how to attach points 
from one time step to another.

· The filter has a mask points feature that by default tracks only 1 
out of every 100 points. You might need to lower that (possibly down to 1) to 
make things visible.

· The filter has a max step distance option that will ignore 
connections of particles that move more than a certain distance between time 
steps. By default, that distance is 1 unit in every direction. If you have data 
that covers a large space, it might be the particles are moving too far to be 
tracked. You might need to bump that up.

· The filter relies on time metadata in its input dataset to track when 
time advances. If this metadata is not there, you will probably get some errors 
in the output message window (with one about DATA_TIME_STEPS), and you will get 
no output data.

Without seeing your data, I don’t think I can narrow down the problem any 
further.

-Ken

From: "David I. Robinson" <d.robin...@hrwallingford.com>
Date: Tuesday, November 15, 2016 at 2:32 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>
Subject: RE: [EXTERNAL] [Paraview] animating particle pathlines

Hi Ken,

Do you know how to make that work?  I’ve have wrestled with that filter 
endlessly with no success.  I just get a blank screen, or it crashes.

Dave

From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Monday, November 14, 2016 10:30 PM
To: David I. Robinson
Cc: paraview@paraview.org
Subject: Re: [EXTERNAL] [Paraview] animating particle pathlines

That sounds like a job for the "Temporal Particles To Pathlines" filter.
-Ken

Sent from my iPad so blame autocorrect.

On Nov 14, 2016, at 10:54 AM, David I. Robinson 
<d.robin...@hrwallingford.com<mailto:d.robin...@hrwallingford.com>> wrote:
Hello,

I’m trying to visualise lagrangian particle pathlines.  I have run an openFoam 
simulation with particle tracking and would like to view the paths that the 
particles take.  I have read lots of discussion of this on the internet, but 
without much success.  I can load the data in Paraview and assign glyphs, but I 
can’t visualise the pathlines taken by the particles.

I am cautious that Paraview might have some functionality for interpolating 
particle tracking from the eulerian data.  I might end-up visualising this 
approximation, rather than the lagrangian data calculated on a 
timestep-by-timestep basis by openFoam.  (Although an ability to do either or 
both would be useful!)

So far, my best luck seems to have come from masking my data and then using the 
particlepath filter, using the un-masked data as my input and the masked data 
as a seed.  This is OK, but requires me to incrementally increase the finished 
time to observe the particle paths.

Can you offer any help?


Dr David Robinson
Engineer, Coastal Structures

E: d.robin...@hrwallingford.com<mailto:d.robin...@hrwallingford.com>
T: +44 (0)1491 822397
<http://www.hrwallingford.com/banner.html>

[R Wallingford Logo]

HR Wallingford
Howbery Park, Wallingford, Oxfordshire OX10 8BA, United Kingdom
T: +44 (0)1491 835381 F: +44 (0)1491 832233
www.hrwallingford.com

[R Wallingford Secondary Logo]





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Re: [Paraview] [EXTERNAL] animating particle pathlines

[Moreland, Kenneth]

That sounds like a job for the "Temporal Particles To Pathlines" filter.

-Ken

Sent from my iPad so blame autocorrect.

On Nov 14, 2016, at 10:54 AM, David I. Robinson 
> wrote:

Hello,

I'm trying to visualise lagrangian particle pathlines.  I have run an openFoam 
simulation with particle tracking and would like to view the paths that the 
particles take.  I have read lots of discussion of this on the internet, but 
without much success.  I can load the data in Paraview and assign glyphs, but I 
can't visualise the pathlines taken by the particles.

I am cautious that Paraview might have some functionality for interpolating 
particle tracking from the eulerian data.  I might end-up visualising this 
approximation, rather than the lagrangian data calculated on a 
timestep-by-timestep basis by openFoam.  (Although an ability to do either or 
both would be useful!)

So far, my best luck seems to have come from masking my data and then using the 
particlepath filter, using the un-masked data as my input and the masked data 
as a seed.  This is OK, but requires me to incrementally increase the finished 
time to observe the particle paths.

Can you offer any help?


Dr David Robinson
Engineer, Coastal Structures

E: d.robin...@hrwallingford.com
T: +44 (0)1491 822397


[HR Wallingford Logo]

HR Wallingford
Howbery Park, Wallingford, Oxfordshire OX10 8BA, United Kingdom
T: +44 (0)1491 835381 F: +44 (0)1491 832233
www.hrwallingford.com

[HR Wallingford Secondary Logo]





HR Wallingford and its subsidiaries uses faxes and emails for confidential and 
legally privileged business communications. They do not of themselves create 
legal commitments. Disclosure to parties other than addressees requires our 
specific consent. We are not liable for unauthorised disclosures nor reliance 
upon them.
If you have received this message in error please advise us immediately and 
destroy all copies of it.

HR Wallingford Limited
Howbery Park, Wallingford, Oxfordshire, OX10 8BA, United Kingdom
Registered in England No. 02562099



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Re: [Paraview] Volume Rendering "Brightness"

[Moreland, Kenneth]

It looks like this is an old message that has been stuck waiting for a 
moderator to release it, but in case you are still interested in the answer 
here goes.

There used to be a parameter in the color map named Scalar Opacity Unit 
Distance (or something like that) that could be used to uniformly control how 
opaque the opacity parameter is interpreted. However, it looks like that option 
was removed from the GUI quite a while ago (probably because no one understood 
it). The effect would be a perceived change in the brightness of the volume.

You can still get around it through the Python interface though. I used that to 
create the following pair of macros. To load them in ParaView, go to the Macros 
-> Add New Macro menu item and load in each file. You can then increase and 
decrease the brightness of a volume rendering by hitting the two macro buttons.

Sorry for the delay.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Evan Kao
Sent: Thursday, January 21, 2016 3:02 PM
To: ParaView 
Subject: [EXTERNAL] [Paraview] Volume Rendering "Brightness"

Hello all,
This may be a silly question, but is there a way to increase the brightness of 
a volume rendering?  For instance, in the image below, the render on the right 
is brighter than the render on the left:

[Inline image 1]
The difference is that the image on the right is just two volume 
representations of the same object.  Is there a smarter way to increase the 
brightness?
Thanks,
Evan Kao


Increase Volume Render Brightness.py
Description: Increase Volume Render Brightness.py


Decrease Volume Render Brightness.py
Description: Decrease Volume Render Brightness.py
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Re: [Paraview] Electric field plot

[Moreland, Kenneth]

Chara,

If you look in the Properties panel in the Display section under the heading “X 
Axis Parameters,” there is a combo box named “X Array Name.” Change the value 
of that box from arc_length to Points_Y.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Chara Kitsaki
Sent: Saturday, December 5, 2015 1:49 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Electric field plot

Hi,

I would like to create a plot of the electric field vs y_coordinate. I created 
a .sif file (attached) which computes the electric field using the ElmerFEM 
software and I exported all the results into a .vtu file (attached).
All I have done is to use the filter PlotOverLine but what I get as a plot is 
the electric field vs the arc_length.

Thanks in advance,

Chara

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Re: [Paraview] delta between times

[Moreland, Kenneth]

This sounds exactly like a question that was posted to this list a few days ago:

http://markmail.org/thread/zxtz6p32prxu76h3

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Scott, W Alan
Sent: Thursday, November 3, 2016 2:48 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] delta between times

>From a user:


If I have a time series with positions (It's a set of csv files, one time step 
per file, each file has the same set of points), is there a method of computing 
the delta position from the current time to the next time and using that as a 
glyph vector?


Thanks,
Alan
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Re: [Paraview] Data structure type

[Moreland, Kenneth]

Chris,

Ultimately to represent your data in the way you describe, you will need to 
store it in an unstructured grid. Even though your data are regular in the X 
and Y directions, the structured data types will insist on connecting the 
points of the cells, which you explicitly stated that you do not want. The 
unstructured grid does not have this restriction. Although it can (and usually 
does) share points across cells, it does not have to.

-Ken

From: ParaView  on behalf of Christian Gabriel 

Date: Friday, October 28, 2016 at 6:06 AM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] Re: [Paraview] Data structure type

Thanks Dave, I’ll take a closer look.
I think I’m still a little confused about cell based data versus node based 
data at the top and bottom of the cell ….

I found this which was generated with Paraview, so I know it can be done ☺

[id:image001.jpg@01D230F1.D9A2EA70]




From: David E DeMarle [mailto:dave.dema...@kitware.com]
Sent: October-28-16 7:32 AM
To: Christian Gabriel
Cc: paraview@paraview.org
Subject: Re: [Paraview] Data structure type


Try vtkStructuredGrid and the Cell Data to Point Data filter.

hth

On Oct 27, 2016 9:30 PM, "Christian Gabriel" 
> wrote:
Good day.

I’m looking into Paraview for 3D visualisation of modelling results from an 
integrated surface water/groundwater model.

The model domain is discretized as a uniform rectilinear grid; calculations are 
performed for the grid centroids.
However, the vertical extent of a grid cell is described by a top and bottom 
elevation, constant over the cell.
This results in a staggered arrangement of cells (kinda like Lego blocks) in 
cross-section view:

[cid:image002.png@01D23143.6D01A580]

NOT:

[cid:image003.jpg@01D23143.6D01A580]



I’m wondering what data type/structure I would use for this kind of data?

Also, is there an easy way/filter in Paraview to re-project/interpolate the 
centre based (const) elevation data to the corners/nodes of the uniform 
rectilinear “horizontal” grid, which would allow for a display as shown on the 
right (instead of staggered)?

Thanks a lot,

Chris


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Re: [Paraview] [EXTERNAL] RE: [EXT] Re: Any way to select nodes that are inside a volume

[Moreland, Kenneth]

OK, I think I misinterpreted your question. I thought you were asking how to 
extract the truss part out of a blob of elements. I guess you are asking to 
clip one set of elements (the truss) with another set of elements (the blob).

I don’t think there is any way of clipping the truss by a surface. I believe 
there is an algorithm in VTK to do it, but it is very fragile and often fails. 
It is better to start with the blob as solid elements and intersect the two.

Unfortunately, I do not think there is a filter to intersect two data sets. 
(Perhaps someone else can point one out.) However, you should be able to get 
close with the following steps. First, run the Resample With Dataset filter 
with the blob set as “Input” and the truss set as “Source”. This filter will 
add a field named vtkValidPointMask. Second, run the Clip filter on the output 
of Resample With Dataset. Set Clip Type to Scalar, the Scalars to 
vtkValidPointMask, and the Value to something more than 1.

-Ken


From: Dennis Conklin <dennis_conk...@goodyear.com>
Date: Tuesday, October 25, 2016 at 8:05 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>, "Paraview (paraview@paraview.org)" 
<paraview@paraview.org>
Subject: RE: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that 
are inside a volume

Ken,

I might be a little dense here, but I missed the part where I clip the truss 
elements by the surface of the solid before writing them out.

Dennis

From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Monday, October 24, 2016 5:33 PM
To: Dennis Conklin <dennis_conk...@goodyear.com>; Paraview 
(paraview@paraview.org) <paraview@paraview.org>
Subject: Re: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that 
are inside a volume

So the “Extract Block” filter should do the trick. Extract the blocks with the 
truss elements and write that out to a mesh file.

-Ken


From: Dennis Conklin 
<dennis_conk...@goodyear.com<mailto:dennis_conk...@goodyear.com>>
Date: Monday, October 24, 2016 at 4:33 PM
To: "Moreland, Kenneth" <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>, 
"Paraview (paraview@paraview.org<mailto:paraview@paraview.org>)" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: RE: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that 
are inside a volume

Ken,

Actually, I want to get just the truss elements that are embedded in the hex 
elements and write them out to a mesh file.  I’ve been playing in Patran, but I 
still end up with some trusses sticking out of the solid.

So, not rendering, I want to make a new element block which is clipped by the 
surface of the solid mesh.   So any truss element with a node outside the 
surface should be excluded when I write out the trimmed truss mesh.

I hope this is a little clearer.

Thanks for looking at this
Dennis

From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Monday, October 24, 2016 4:28 PM
To: Dennis Conklin 
<dennis_conk...@goodyear.com<mailto:dennis_conk...@goodyear.com>>; Paraview 
(paraview@paraview.org<mailto:paraview@paraview.org>) 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: Re: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that 
are inside a volume

Having the data in multiblock format is good. It is pretty easy to turn blocks 
on and off.

The easiest way to turn of the visibility of a block is to right click it in 
the 3D view and selected “Hide Block” from the pop-up menu.

For somewhat more sophisticated controls, use the Multi-block Inspector. From 
the menu bar, select View -> Multi-block Inspector. The Multi-block Inspector 
by default is placed underneath the Properties panel. The Multi-block Inspector 
allows you to quickly select blocks as well as turn their visibility on and 
off. (It’s also the only way to make visible blocks that are hidden with the 
pop-up menu.)

Note that both of these techniques only change what data is being rendered. If 
for some reason you need to extract the rebar blocks so that they can be 
independently proceed by filters, you can use the Extract Block filter.

-Ken


From: Dennis Conklin 
<dennis_conk...@goodyear.com<mailto:dennis_conk...@goodyear.com>>
Date: Monday, October 24, 2016 at 7:47 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>, 
"Paraview (paraview@paraview.org<mailto:paraview@paraview.org>)" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that are 
inside a volume

Ken,

Yes it is a multiblock dataset and the rebar blocks are different than the hex 
blocks.

Dennis

From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Friday, October 21, 2016 10:56 PM
To: Dennis Conklin 
<dennis_conk...@goodyear.com<mailto:dennis_conk...@

Re: [Paraview] [EXTERNAL] RE: [EXT] Re: Any way to select nodes that are inside a volume

[Moreland, Kenneth]

So the “Extract Block” filter should do the trick. Extract the blocks with the 
truss elements and write that out to a mesh file.

-Ken


From: Dennis Conklin <dennis_conk...@goodyear.com>
Date: Monday, October 24, 2016 at 4:33 PM
To: "Moreland, Kenneth" <kmo...@sandia.gov>, "Paraview (paraview@paraview.org)" 
<paraview@paraview.org>
Subject: RE: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that 
are inside a volume

Ken,

Actually, I want to get just the truss elements that are embedded in the hex 
elements and write them out to a mesh file.  I’ve been playing in Patran, but I 
still end up with some trusses sticking out of the solid.

So, not rendering, I want to make a new element block which is clipped by the 
surface of the solid mesh.   So any truss element with a node outside the 
surface should be excluded when I write out the trimmed truss mesh.

I hope this is a little clearer.

Thanks for looking at this
Dennis

From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Monday, October 24, 2016 4:28 PM
To: Dennis Conklin <dennis_conk...@goodyear.com>; Paraview 
(paraview@paraview.org) <paraview@paraview.org>
Subject: Re: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that 
are inside a volume

Having the data in multiblock format is good. It is pretty easy to turn blocks 
on and off.

The easiest way to turn of the visibility of a block is to right click it in 
the 3D view and selected “Hide Block” from the pop-up menu.

For somewhat more sophisticated controls, use the Multi-block Inspector. From 
the menu bar, select View -> Multi-block Inspector. The Multi-block Inspector 
by default is placed underneath the Properties panel. The Multi-block Inspector 
allows you to quickly select blocks as well as turn their visibility on and 
off. (It’s also the only way to make visible blocks that are hidden with the 
pop-up menu.)

Note that both of these techniques only change what data is being rendered. If 
for some reason you need to extract the rebar blocks so that they can be 
independently proceed by filters, you can use the Extract Block filter.

-Ken


From: Dennis Conklin 
<dennis_conk...@goodyear.com<mailto:dennis_conk...@goodyear.com>>
Date: Monday, October 24, 2016 at 7:47 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>, 
"Paraview (paraview@paraview.org<mailto:paraview@paraview.org>)" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that are 
inside a volume

Ken,

Yes it is a multiblock dataset and the rebar blocks are different than the hex 
blocks.

Dennis

From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Friday, October 21, 2016 10:56 PM
To: Dennis Conklin 
<dennis_conk...@goodyear.com<mailto:dennis_conk...@goodyear.com>>; Paraview 
(paraview@paraview.org<mailto:paraview@paraview.org>) 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXT] Re: [Paraview] Any way to select nodes that are inside a volume

Is there any feature of your data that distinguishes the rebar from the larger 
blob? Do you have a multiblock data with one or more blocks containing only 
rebar? Do you have field data that might be unique to the rebar such as 
material type or density?

-Ken

From: ParaView 
<paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>> on behalf 
of Dennis Conklin 
<dennis_conk...@goodyear.com<mailto:dennis_conk...@goodyear.com>>
Date: Friday, October 21, 2016 at 2:47 PM
To: "Paraview (paraview@paraview.org<mailto:paraview@paraview.org>)" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] [Paraview] Any way to select nodes that are inside a volume

All,

I have a solid blob of elements.   Then I have a large cloud of embedded rebars 
that is much bigger than the solid blob.   I only want rebars that are inside 
the blob.Is there anyway to select only the rebar (truss element) nodes 
that are inside the solid blob.   Like if I extract surfaces from the blob, is 
there any any way to clip the nodes using those surfaces.   I have gotten close 
using clips, but I just can’t get them perfectly arranged to do what I need.

Are there any plug-ins out there or something?  Any ideas?

Thanks

Dennis
___
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Re: [Paraview] [EXTERNAL] RE: [EXT] Re: Any way to select nodes that are inside a volume

[Moreland, Kenneth]

Having the data in multiblock format is good. It is pretty easy to turn blocks 
on and off.

The easiest way to turn of the visibility of a block is to right click it in 
the 3D view and selected “Hide Block” from the pop-up menu.

For somewhat more sophisticated controls, use the Multi-block Inspector. From 
the menu bar, select View -> Multi-block Inspector. The Multi-block Inspector 
by default is placed underneath the Properties panel. The Multi-block Inspector 
allows you to quickly select blocks as well as turn their visibility on and 
off. (It’s also the only way to make visible blocks that are hidden with the 
pop-up menu.)

Note that both of these techniques only change what data is being rendered. If 
for some reason you need to extract the rebar blocks so that they can be 
independently proceed by filters, you can use the Extract Block filter.

-Ken


From: Dennis Conklin <dennis_conk...@goodyear.com>
Date: Monday, October 24, 2016 at 7:47 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>, "Paraview (paraview@paraview.org)" 
<paraview@paraview.org>
Subject: [EXTERNAL] RE: [EXT] Re: [Paraview] Any way to select nodes that are 
inside a volume

Ken,

Yes it is a multiblock dataset and the rebar blocks are different than the hex 
blocks.

Dennis

From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Friday, October 21, 2016 10:56 PM
To: Dennis Conklin <dennis_conk...@goodyear.com>; Paraview 
(paraview@paraview.org) <paraview@paraview.org>
Subject: [EXT] Re: [Paraview] Any way to select nodes that are inside a volume

Is there any feature of your data that distinguishes the rebar from the larger 
blob? Do you have a multiblock data with one or more blocks containing only 
rebar? Do you have field data that might be unique to the rebar such as 
material type or density?

-Ken

From: ParaView 
<paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>> on behalf 
of Dennis Conklin 
<dennis_conk...@goodyear.com<mailto:dennis_conk...@goodyear.com>>
Date: Friday, October 21, 2016 at 2:47 PM
To: "Paraview (paraview@paraview.org<mailto:paraview@paraview.org>)" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] [Paraview] Any way to select nodes that are inside a volume

All,

I have a solid blob of elements.   Then I have a large cloud of embedded rebars 
that is much bigger than the solid blob.   I only want rebars that are inside 
the blob.Is there anyway to select only the rebar (truss element) nodes 
that are inside the solid blob.   Like if I extract surfaces from the blob, is 
there any any way to clip the nodes using those surfaces.   I have gotten close 
using clips, but I just can’t get them perfectly arranged to do what I need.

Are there any plug-ins out there or something?  Any ideas?

Thanks

Dennis
___
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: 
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Re: [Paraview] Any way to select nodes that are inside a volume

[Moreland, Kenneth]

Is there any feature of your data that distinguishes the rebar from the larger 
blob? Do you have a multiblock data with one or more blocks containing only 
rebar? Do you have field data that might be unique to the rebar such as 
material type or density?

-Ken

From: ParaView  on behalf of Dennis Conklin 

Date: Friday, October 21, 2016 at 2:47 PM
To: "Paraview (paraview@paraview.org)" 
Subject: [EXTERNAL] [Paraview] Any way to select nodes that are inside a volume

All,

I have a solid blob of elements.   Then I have a large cloud of embedded rebars 
that is much bigger than the solid blob.   I only want rebars that are inside 
the blob.Is there anyway to select only the rebar (truss element) nodes 
that are inside the solid blob.   Like if I extract surfaces from the blob, is 
there any any way to clip the nodes using those surfaces.   I have gotten close 
using clips, but I just can’t get them perfectly arranged to do what I need.

Are there any plug-ins out there or something?  Any ideas?

Thanks

Dennis
___
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] Gradient filter: boundary effects

[Moreland, Kenneth]

As far as VTK/ParaView are concerned, lines and triangles are just different 
types of cells. The filters treat each cell uniformly. That is, the gradient 
filter is treating triangles and lines the same and mixing the results together 
in the same way as if the data contained triangles and quadrilaterals.

In many ways, the problem is that the mesh and boundary cells are not properly 
distinguished in the data. The lines in the data are really a “face set” or 
“edge set” that has different properties that the interior triangle cells (in 
addition to the difference in dimentionality). Although this is not 
specifically supported in VTK’s data structures, we typically manage it by 
creating a multiblock data set with the interior and boundary cells in 
different blocks.

However, although I don’t think the gradient filter’s treatment of the data is 
fundamentally wrong, I cannot think of a viable use case for computing 
gradients over cells of different dimensionality. So it would probably be a 
reasonable feature request to ask that the gradient filter only average 
gradients from cells of the highest dimension. That said, I don’t think it 
would be correct to change the behavior of cell data to point data as that is 
used for plenty of use cases other than gradients.

-Ken

From: "Zenker, Dr. Matthias" <matthias.zen...@erbe-med.com>
Date: Tuesday, September 27, 2016 at 11:43 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>
Cc: "'paraview@paraview.org'" <paraview@paraview.org>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi again,

I have examined my mesh (which you can find in the attachment) with Salome and 
gmsh – there are no flat faces at the boundaries. But there are line elements! 
So I am relieved as far as my worried questions in the last mail are concerned 
– mesher and the FEM solver are doing their work as they should.
But IMO it makes no sense to compute the derivatives over the line elements and 
average it with the derivatives over the face elements. Is it possible that 
this is exactly what happens in the gradient filter (and in the 
computederivative + celldatatopointdata filters)? If so, why? And can that be 
switched off, as IMO it should?
Or, to put it differently: Apparently ParaView does not make a difference 
between a line and a face. Why is this so? Shouldn’t it do that?

Thanks for a clarification,

Matthias


Von: Zenker, Dr. Matthias
Gesendet: Dienstag, 27. September 2016 17:00
An: 'Moreland, Kenneth'
Cc: paraview@paraview.org
Betreff: AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

thank you for pointing this out! I was not aware that boundary lines are also 
inifinitely flat cells. This seems true for all boundaries, also the internal 
boundaries between the two faces.
The question for me is now: Is this normal, or does that mean that the whole 
FEM simulation is corrupt? Should I have a mesh that does not have those line 
cells? The mesh has been calculated by the Salome mesher, which uses netgen. 
The boundaries were declared as groups. The mesh has then been exported as unv, 
imported by Elmer which has done the FEM calculations, and saved the results as 
vtu. If those line cells represent a problem, where in this chain do I have to 
look for the mistake?

Matthias

Von: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Gesendet: Dienstag, 27. September 2016 16:41
An: Zenker, Dr. Matthias
Cc: paraview@paraview.org<mailto:paraview@paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

As I suspected, your data has some boundary elements that are throwing off the 
gradient calculation. The data you sent me has line cells around the boarder of 
the data. The easiest way to see these line cells is to go to the Properties 
panel and change the “Line Width” parameter to something large. (Attached is an 
image that shows the boundary cells by setting the line width to 20.)

So in the example you gave, the gradient is computed correctly in the 
triangles, but the finite differences computation for the line cells can only 
compute the gradient in the direction of the line. Thus, there is no y 
component for the gradient in these line cells. Because the line cells share 
the points of the triangles along the bottom, the gradient average becomes 
incorrect.

-Ken


From: "Zenker, Dr. Matthias" 
<matthias.zen...@erbe-med.com<mailto:matthias.zen...@erbe-med.com>>
Date: Tuesday, September 27, 2016 at 9:51 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>
Cc: "paraview@paraview.org<mailto:paraview@paraview.org>" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

if you want to have a look – here is a simple test file. At  the bottom side, 
there are 4 adjacent cells having grad(y)~7900 from computede

Re: [Paraview] Gradient filter: boundary effects

[Moreland, Kenneth]

Matthias,

If values are being pulled from 7900 units down to 5300 units, there must be 
some neighbor with lower values. Why that is happening for you I cannot say 
without looking at your data. Perhaps on the boundary there are some malformed 
or 2D cells with invalid gradients.

-Ken


From: "Zenker, Dr. Matthias" <matthias.zen...@erbe-med.com>
Date: Tuesday, September 27, 2016 at 9:06 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>
Cc: "paraview@paraview.org" <paraview@paraview.org>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Ken,

what I don’t understand is that the cell gradients are correct, but their 
average at the border is not. (Example: All cell gradients adjacent to one node 
at the border have approx. 7900 units in y direction, the node has approx. 5300)
So it seems I cannot determine the gradient in the postprocessing step, but 
have to calculate it in the FEM solver (where I do get correct results now – I 
didn’t initially, which was the reason why I tried it with ParaView).

Thank you anyway, I have learned new bits of ParaView again (which is great 
software BTW)!

Have a nice holiday (if I interpret your autoreply correctly)!

Matthias

Von: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:36
An: Zenker, Dr. Matthias; paraview@paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

You could run the results through the point to cell filter, but that would give 
you the same answer as the gradient of unstructured dataset filter with the 
faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" 
<matthias.zen...@erbe-med.com<mailto:matthias.zen...@erbe-med.com>>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>, 
"paraview@paraview.org<mailto:paraview@paraview.org>" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and 
a plane given the potential…
The compute derivatives filter does not give me the problem at the boundary 
indeed. Instead it gives a value per cell, not per node, which does not look 
nice.
Is there a friendly filter or switch which would give me the smoothed surface 
representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview@paraview.org<mailto:paraview@paraview.org>
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly 
unexpected that there could be differences at the boundaries. However, the 
algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local 
gradient in each cell at each of the cell’s points. Then for every point it 
averages the gradient from all incident cells at that point. (If you have the 
Faster Approximation option on, then the filter only computes one gradient per 
cell in the center and averages those. Faster, but more artifacts, particularly 
at the edges.)

If this averaging is causing you an issue, you might try the Compute 
Derivatives filter. This does a wholly local operation within each cell, so you 
should not see any artifacts (unless the field itself has artifacts at the 
boundaries).

-Ken


From: ParaView 
<paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>> on behalf 
of "Zenker, Dr. Matthias" 
<matthias.zen...@erbe-med.com<mailto:matthias.zen...@erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview@paraview.org<mailto:paraview@paraview.org>" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects 
which are IMO unphysical. For the nodes on the outer boundary of my domain, the 
gradient magnitude is smaller than I would expect. The behavior is like the 
filter tries to use the adjacent nodes to calculate the gradient, and since 
there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug – is there a fix or workaround?

Thanks,

Matthias


Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: 
Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137


Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: 
Christian O. Erbe, Reiner Thede Registergericht: Stuttgart

Re: [Paraview] Gradient filter: boundary effects

[Moreland, Kenneth]

You could run the results through the point to cell filter, but that would give 
you the same answer as the gradient of unstructured dataset filter with the 
faster approximation option on.

-Ken

From: "Zenker, Dr. Matthias" <matthias.zen...@erbe-med.com>
Date: Tuesday, September 27, 2016 at 8:28 AM
To: "Moreland, Kenneth" <kmo...@sandia.gov>, "paraview@paraview.org" 
<paraview@paraview.org>
Subject: [EXTERNAL] AW: [Paraview] Gradient filter: boundary effects

Hi Kenneth,

thank you for the quick answer!
So it seems not that trivial to calculate an electrical field between a rod and 
a plane given the potential…
The compute derivatives filter does not give me the problem at the boundary 
indeed. Instead it gives a value per cell, not per node, which does not look 
nice.
Is there a friendly filter or switch which would give me the smoothed surface 
representation back?

Thanks,

Matthias


Von: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Gesendet: Dienstag, 27. September 2016 14:14
An: Zenker, Dr. Matthias; paraview@paraview.org
Betreff: Re: [Paraview] Gradient filter: boundary effects

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly 
unexpected that there could be differences at the boundaries. However, the 
algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local 
gradient in each cell at each of the cell’s points. Then for every point it 
averages the gradient from all incident cells at that point. (If you have the 
Faster Approximation option on, then the filter only computes one gradient per 
cell in the center and averages those. Faster, but more artifacts, particularly 
at the edges.)

If this averaging is causing you an issue, you might try the Compute 
Derivatives filter. This does a wholly local operation within each cell, so you 
should not see any artifacts (unless the field itself has artifacts at the 
boundaries).

-Ken


From: ParaView 
<paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>> on behalf 
of "Zenker, Dr. Matthias" 
<matthias.zen...@erbe-med.com<mailto:matthias.zen...@erbe-med.com>>
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview@paraview.org<mailto:paraview@paraview.org>" 
<paraview@paraview.org<mailto:paraview@paraview.org>>
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects 
which are IMO unphysical. For the nodes on the outer boundary of my domain, the 
gradient magnitude is smaller than I would expect. The behavior is like the 
filter tries to use the adjacent nodes to calculate the gradient, and since 
there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug – is there a fix or workaround?

Thanks,

Matthias


Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: 
Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137


Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: 
Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
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Re: [Paraview] Gradient filter: boundary effects

[Moreland, Kenneth]

Matthias,

The gradient is estimated with finite differences. Thus, it is not wholly 
unexpected that there could be differences at the boundaries. However, the 
algorithm does not assume zero for adjacent cells at the boundaries.

The way the unstructured gradient filter works is that it computes the local 
gradient in each cell at each of the cell’s points. Then for every point it 
averages the gradient from all incident cells at that point. (If you have the 
Faster Approximation option on, then the filter only computes one gradient per 
cell in the center and averages those. Faster, but more artifacts, particularly 
at the edges.)

If this averaging is causing you an issue, you might try the Compute 
Derivatives filter. This does a wholly local operation within each cell, so you 
should not see any artifacts (unless the field itself has artifacts at the 
boundaries).

-Ken


From: ParaView  on behalf of "Zenker, Dr. 
Matthias" 
Date: Tuesday, September 27, 2016 at 5:45 AM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] Gradient filter: boundary effects

Hi,

when I use the gradient filter (unstructured dataset), I observe edge effects 
which are IMO unphysical. For the nodes on the outer boundary of my domain, the 
gradient magnitude is smaller than I would expect. The behavior is like the 
filter tries to use the adjacent nodes to calculate the gradient, and since 
there are none  outside the domain, it assumes zero and finds a lower result.
If so, I would consider this a bug – is there a fix or workaround?

Thanks,

Matthias


Erbe Elektromedizin GmbH Firmensitz: 72072 Tuebingen Geschaeftsfuehrer: 
Christian O. Erbe, Reiner Thede Registergericht: Stuttgart HRB 380137
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Re: [Paraview] Precise location of contours on boundaries

[Moreland, Kenneth]

Saideep,

This may or may not be what you are asking for, but you should be able to get 
the exact location of the contour on the boundaries by first extracting the 
boundary and then running the contours on the boundary. This will give you the 
contours on the boundary only.

How you get the boundary depends on the type of data you have. Based on the 
question and the image you provided, I am assuming that you are talking about 
contours on 2D data. If your 2D data is poly data, you can get the boundary by 
running the “Feature Edges” filter and turning on the “Boundary Edges” option 
(while turning off all the rest). If you have some other 2D data (such as an 
image), you can first convert it to poly data with the “Extract Surface” filter 
and then follow the previous step of using the “Feature Edges” filter. Then 
just run the contour filter on the result of the feature edges and that will 
give you the exact position of the contours on the boundaries. You can then 
open up a spreadsheet view to view the exact locations of those contours.

-Ken

From: ParaView  on behalf of Saideep Pavuluri 

Date: Friday, September 9, 2016 at 11:28 AM
To: "paraview@paraview.org" 
Subject: [EXTERNAL] [Paraview] Precise location of contours on boundaries

Hi guys;

Is there a way to know the precise location of a contour on the boundaries (as 
shown in picture)? I use the  traditional tool “ruler”, however when I have too 
many points to measure (as in the figure) by hand it gets complicated.

I tried using the integrate variables(selecting the contour) however, the block 
numbering isn’t consistent and I particularly want values only at the 
boundaries. I am dealing with meniscus and it has a specific curvature based on 
flow.

Any advice here.

Thanks;
Saideep
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Re: [Paraview] Data handling in ParaView

[Moreland, Kenneth]

Stefan,

The idea of identifying each "cell" by a scalar value should work just fine and 
be scalable.

However, I do not understand what the issue is that the n-th cell's last point 
is connected to the n+1-th cell's first point. If there is no connection. I 
honestly do not see anything wrong with the pictures you posted except that in 
d4.png it looks like the lines of some "cells" are drawn on top of other lines. 
But that is exactly what I would expect if the cells are adjacent to each 
other, which I would also expect.

The only advice I can think of is to define the scalar values on the triangles 
(what ParaView calls cells) instead of the points. This will generally be more 
robust.

-Ken

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Stefan Melber
Sent: Thursday, September 1, 2016 4:01 AM
To: paraview 
Subject: [EXTERNAL] [Paraview] Data handling in ParaView

Hi,


i have (maybe) a simple problem: For the visualization of the so called 
dual-cells of an unstructured grid i use currently the block-structured 
vtu-format. The data thereby consists of many complex cells which are itself 
consists of a number of triangles - see the picture d1 attached. 
Therefore i have to write out EVERY cell in another vtu-file and group them 
with am vtm-file together. This way works well with a small number of cells 
(~1000 - as for the picture) however the aim is to go up to
100e6 cells. Depending on the numbers i got from 1000 cells this process will 
take ~70 days!

The bottleneck is clearly the huge number of files i have to write (and read in 
ParaView). So are there ideas to have another representation in only one file 
for such kind of data?

I did some experiments writing all cells in one vtk(vtu)-file and give them 
scalar values depending on the cell number. But then, the n-th cell (its last 
point) is connected to the n+1 (its first point) and so on. 
Looks ugly if the n-th cell is not a direct neighbor to the n+1 cell - and that 
can be the case in my data. And - cutting then the resulting stuff in ParaView 
i did not get the cutting pictures (like d4) i like to have ...

Best regards and hoping for some nice ideas,


 Stefan






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Re: [Paraview] Opacity mapping and image texture in ParaView 5.1.2

[Moreland, Kenneth]

Venke,

That definitely looks like a bug, and I was able to replicate the behavior. 
Thanks for reporting it. I added the issue to the bug tracker 
(https://gitlab.kitware.com/paraview/paraview/issues/16853).

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of 
postgu...@web.de
Sent: Tuesday, August 23, 2016 6:44 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Opacity mapping and image texture in ParaView 
5.1.2

Hello

I have an issue regarding the "enable opacity mapping for surfaces" (in the 
Color Map Editor) if the ParaView session contains another object that has an 
image loaded as texture. The problem occurs in ParaView 5.1.2 but not in 
earlier versions (tested with 5.0.1. and 4.3.1). I am working on Windows 64bit.

If I want to enable the opacity mapping for surfaces everything works as 
expected as long as I have no texture image. The behaviour is very strange: if 
I load a texture image in another object, this seems to be set to the 
background with the transparent volume cutting a window to see this image. I 
will include snapshots because I think that my explanation may not be very 
clear. With no opacity mapping enabled I can see the volume and the plane with 
the image as expected.

Should I do anything differently in the new ParaView to achieve a transparent 
volume along with the image texture object or is this "just" a bug? Thank you 
very much and best regards
Venke


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Re: [Paraview] Merging two datasets

[Moreland, Kenneth]

Does the Append Attributes filter do what you want? That combines the fields of 
the two data sets into one. 

-Ken

Sent from my iPad so blame autocorrect.

> On Aug 15, 2016, at 6:31 PM, Salazar De Troya, Miguel 
>  wrote:
> 
> Hello,
> 
> I have two data sets that share the same mesh and are both cell data. I want 
> to put them together in a single dataset so I can extract a selection of 
> cells given a criteria from one of the original datasets and then apply a 
> filter to the other dataset. I tried doing GroupDataSet, but it doesn’t 
> correctly plot one of the datasets. In the selection of the coloring I can 
> see “partial” next to the original dataset’s name. How can we do this?
> 
> Thanks
> Miguel
> 
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Re: [Paraview] Private pipeline

[Moreland, Kenneth]

Wow! Thousands of objects in your pipeline browser? You must have some scripts 
to generate all those objects (or spend hours each time setting up your 
pipelines).

There is no way in to get the pipeline browser to group sections of the 
pipeline or show subsections of it. It is conceivable to create your own 
version of a pipeline browser that showed subsets of the pipeline like you want 
and put that in your own plugin, but it would be a fairly difficult programming 
project.

You might consider simpler alternatives. Rather than create thousands of 
objects in your pipeline browser, perhaps you can create custom filters that 
encapsulate (and hide) lots of filters inside it. Implementing filters in 
VTK/ParaView using several other filters internally is pretty common. It is 
much easier to create a plugin with a custom filter than to make a plugin with 
a custom pipeline browser. You could also consider using the Custom Filter 
feature (http://www.paraview.org/Wiki/ParaView/Custom_Filters). It allows you 
to create a metafilter from a collection of other filters in the ParaView GUI. 
It is easier than making a plugin, but has more limited functionality.

-Ken

From: Шагит Зиганшин [mailto:ziganshinsha...@hotmail.com]
Sent: Monday, August 15, 2016 9:38 AM
To: Moreland, Kenneth <kmo...@sandia.gov>; paraview@paraview.org
Subject: [EXTERNAL] RE: [Paraview] Private pipeline

If I'm working in multiple layouts my pipeline browser becomes a list of 
thousands of loosely coupled objects. I wish each layout had own “custom“ 
pipeline browser, is it possible to make it as part of plug-in?

Shagit Ziganshin

From: Moreland, Kenneth<mailto:kmo...@sandia.gov>
Sent: Monday, August 15, 2016 6:18 PM
To: Шагит Зиганшин<mailto:ziganshinsha...@hotmail.com>; 
paraview@paraview.org<mailto:paraview@paraview.org>
Subject: RE: [Paraview] Private pipeline


I am not sure I totally understand by a “private pipeline,” but I think you 
mean that you have a pipeline that you set up in ParaView over and over again 
and you would like to add a button or something to ParaView to automatically 
create this pipeline with one click.



The short answer is, yes. There are many ways to customize ParaView. The 
easiest way is to add a macro based on a Python script. There are a pair of 
exercises in The ParaView Tutorial 
(http://www.paraview.org/Wiki/The_ParaView_Tutorial) that demonstrate how to do 
this.



-Ken



From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of ? 

Sent: Monday, August 15, 2016 7:28 AM
To: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] Private pipeline



Hello,

I am looking for a way how to implement a private pipeline for a particular 
layout. is it possible to do this as part of third-party plug-in?



Thank you

Shagit Ziganshin
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Re: [Paraview] Private pipeline

[Moreland, Kenneth]

I am not sure I totally understand by a “private pipeline,” but I think you 
mean that you have a pipeline that you set up in ParaView over and over again 
and you would like to add a button or something to ParaView to automatically 
create this pipeline with one click.

The short answer is, yes. There are many ways to customize ParaView. The 
easiest way is to add a macro based on a Python script. There are a pair of 
exercises in The ParaView Tutorial 
(http://www.paraview.org/Wiki/The_ParaView_Tutorial) that demonstrate how to do 
this.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of ? 

Sent: Monday, August 15, 2016 7:28 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Private pipeline

Hello,
I am looking for a way how to implement a private pipeline for a particular 
layout. is it possible to do this as part of third-party plug-in?

Thank you
Shagit Ziganshin
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Re: [Paraview] Slicing a sphere based on longitudes and latitudes

[Moreland, Kenneth]

Lester,

Once again, this problem can be solved with some basic geometry. Basically you 
want to slice by a plane that goes through the origin (0, 0, 0) and the two 
points defined by the 2 lat/lon coordiantes. Finding the plane that goes 
through 3 non-collinear points is straightforward (in Cartesian space).

The first step would be to convert your two lat/lon points to Cartesian 
coordinate (X,Y,Z).

Once you have that, you can define the slice plane by an origin point (0, 0, 0 
works just fine) and a normal (perpendicular) vector. The normal can be 
computed by taking the cross product of the vectors going from the origin to 
these two points. Just plug that into the normal for the slice plane and you 
are good to go.

If you need more information on finding the plane defined by three points, 
there are many resources on the web to do so. Here is one descriptive video I 
found with a simple Google search: https://www.youtube.com/watch?v=0qYJfKG-3l8. 
There are many others. Most of these instructions find the plane equation, but 
the plane equation is constructed with the point and normal, which are all you 
need in ParaView.

-Ken

-Original Message-
From: Lester Anderson [mailto:arctica1...@gmail.com] 
Sent: Tuesday, August 9, 2016 1:39 AM
To: Moreland, Kenneth <kmo...@sandia.gov>
Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] Slicing a sphere based on longitudes and 
latitudes

Hi Ken,

Thanks for the info, that all worked fine. Sorry bit of a late response.

On a similar theme, is it easy to make a great circle slice (with the origin at 
000) that plots through two long-lat points? I'm guessing that this scenario 
would be a rotation about x, y and z ?

Thanks
Lester
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Re: [Paraview] Slicing a sphere based on longitudes and latitudes

[Moreland, Kenneth]

Lester,

This is pretty straightforward problem in geometry. As I give you the answer, I 
am assuming that your sphere is centered at the origin (as you said), the axis 
that runs through the north/south pole is along the Z axis, and the prime 
meridian (0 degrees longitude) is in the positive X direction.

Making a slice along latitude is simply a slice by a plane parallel to the x-y 
plane offset by the Cartesian location of the latitude coordinate. The 
parameters of the latitude slice plane are:

Origin: [0, 0, sin lat]
Normal: [0, 0, 1]

Note here that "lat" is the latitude measured in degrees with positive values 
for north and negative values for south.

A slice along longitude can be thought of as the X-Z plane rotated about the Z 
axis by longitude degrees. You can do that by setting the X and Y of the normal 
of this plane to the sin and cos, respectively, of the longitude angle.

Origin: [0, 0, 0]
Normal: [sin lon, cos lon, 0]

Here "lon" is the longitude measured in degrees with positive values for west 
and negative values for east.

You should note that this longitude slice plane will give you a full circle, 
which technically gives you both the longitude you asked for plus the longitude 
180 degrees away. If you just want the semicircle for a single longitude line, 
you can clip away the half you do not want. You can do this with the clip 
filter (NOT the slice filter) with the plane set as:

Origin: [0, 0, 0]
Normal: [cos lon, -sin lon, 0]

As you do this calculations, be careful about degrees/radians conversions. 
Longitude/latitude is classically given in degrees and minutes whereas lots of 
computer trigonometry functions (including those in ParaView) perform sin and 
cos with radians. Also, if your sphere is oriented differently than I 
described, you will have to make corrections to these functions.

-Ken

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Lester 
Anderson
Sent: Friday, August 5, 2016 7:29 AM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Slicing a sphere based on longitudes and 
latitudes

Hello,

Quick query, but is there an easy way to slice a spherical Earth model based on 
longitude and latitude while keeping the origin at the centre?

What I am looking to do is slice along a fixed longitude or latitude, e.g.

Longitude slice at 150 degrees; Latitude slice at -30 degrees.

Based on the use of a Great circle definition with the origin at 0,0,0. The 
data are stored based on the Earth radii. The reference frame (XYZ) orients 
with the axes  Z (+/- 90), X( 0,180) and Y(-90,90)
- overlaying a coastline vector goes in the right place.

I can see where the values have to be entered using the origin/normal but not 
entirely sure about the formula to use. Hopefully someone can give a quick 
pointer on this?

Thanks
Lester
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Re: [Paraview] Convert structured exodus to voxel data

[Moreland, Kenneth]

Alan,

For reasons I am sure you are aware of, you cannot in general directly convert 
the points and cells of an unstructured grid like an Exodus mesh to a regular 
grid of voxels, and there is no such filter.

The easiest way to make this conversion is to run the Resample To Image filter. 
This will (potentially) reinterpret the data which could have side effects even 
if the sample grid matches the original Exodus grid (like interpolating cell 
data to point data).

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Scott, W Alan
Sent: Monday, July 25, 2016 1:31 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] Convert structured exodus to voxel data

>From a user - is this even possible?




How do you use paraview to convert an exodus mesh (with hex8 elements) into 
voxels and export as a VTK file?  Can I control the number of voxels in each 
dimension? The mesh is of uniform size in each direction and I need the number 
of voxels to be a factor of 8.




Thanks,

Alan
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Re: [Paraview] Probe Location

[Moreland, Kenneth]

If you know the point id, you can select exactly that with the Find Data 
dialog. You can then plot that selection over time. 

-Ken

Sent from my iPad so blame autocorrect.

> On Jul 3, 2016, at 8:11 AM, B O  wrote:
> 
> Dear Paraview developers
> 
> I intended to plot a quantity on a certain point with exact coordinates over 
> the time. To do so, I assumed that I should firstly use ‘’Select Points On 
> ‘’option. Then, I should use the “Plot Selection Over Time” tool.
> However, according to the fact that the chosen point is in the cross section 
> of my mesh and Paraview only allows me to choose the points on the mesh 
> element boundaries, I was not able to choose the exact point. As a result, I 
> had to use the “Probe Location” tool in order to be able to choose the exact 
> point. Nevertheless, I could not plot the desired quantity over the time (For 
> example, if I have 1 time steps, I am able to see the desired quantity in 
> each time step but it is time consuming to manually plot the raw data). I 
> would be so pleased if you could guide me how I can plot this quantity over 
> the time appropriately at the desired point.
> 
> Best regards
> Omid
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Re: [Paraview] [EXTERNAL] Symbol WinMain missing when compiling with Visual Studio

[Moreland, Kenneth]

Visual Studio 2013
CMake 3.5.2
Qt 4.8.6

-Ken

On 7/1/16, 7:25 AM, "Ben Boeckel"  wrote:

On Thu, Jun 30, 2016 at 19:20:58 +, Scott, W Alan wrote:
> Try building without Ninja?  If that also fails, I could try a build
> of my own.  Haven't done so in 6 months, but it seems to work.
> 
> By the way, what version of Visual Studio?

Also relevant: version of CMake and Qt.

--Ben


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Re: [Paraview] Animating trajectories of points

[Moreland, Kenneth]

Janessa,

Whether or not you need a separate file for each time step depends on how time 
is represented in the file format. For csv files, the only way to represent 
time is through a sequence of files, so you will always need those 150,000 
(unless you create your own reader or filter that adds a time-based convention 
to the file).

Most of the simplest text-based file formats I can think of also use a separate 
file for each time step (such as legacy VTK, XML-based VTK, PVD). I’m pretty 
sure XDMF (http://www.xdmf.org/) can support your data over all time steps in a 
single file, but you would have to write it out using the HDF5 library. The 
Exodus II file format can also support your data (as long as the number of 
points remains constant), but it also requires using an associated library.

-Ken

From: Janessa Tran [mailto:janessasocialme...@gmail.com]
Sent: Wednesday, June 29, 2016 7:24 PM
To: Moreland, Kenneth <kmo...@sandia.gov>
Subject: [EXTERNAL] Re: [Paraview] Animating trajectories of points

Thank you for your assistance, Ken. I was able to get it to run. An issue I see 
is that my animation requires 150,000 files. Is there a way to combine the data 
into a single file and run an animation over time?

Thank you,
Janessa

On Wed, Jun 29, 2016 at 9:44 AM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
(Responding back to paraview list.)

That is odd behavior. Can you take a look at the csv files in a text editor? It 
looks like maybe all the data got appended to output1.csv, and the rest of the 
files are empty.

-Ken

From: Janessa Tran 
[mailto:janessasocialme...@gmail.com<mailto:janessasocialme...@gmail.com>]
Sent: Wednesday, June 29, 2016 10:04 AM
To: Moreland, Kenneth <kmo...@sandia.gov<mailto:kmo...@sandia.gov>>
Subject: [EXTERNAL] Re: [Paraview] Animating trajectories of points

Hi Ken,

Thank you for your response. I managed to upload the sequence of files. They 
are named in the numeric fashion you mentioned (output1.csv, output2.csv, 
output3.csv, etc). When I add a filter "Table to Points" on the spreadsheet, I 
get the results in the image I attached to the email. What I am trying to do is 
to get an animation of the trajectory of the points, such that I can see the 
points being plotted over time.

Currently when I click play, everything goes blank. If you look at the second 
attached image, you will see the time is 13 of 15 at the top of the screen. 
How can I fix this so I can get the animation of the points over time?

Thank you very much in advance!

On Wed, Jun 29, 2016 at 8:22 AM, Moreland, Kenneth 
<kmo...@sandia.gov<mailto:kmo...@sandia.gov>> wrote:
Janessa,

ParaView should be able to read in a series of csv files as a time series. I 
just verified that when I have a sequence of csv files, ParaView treats it as a 
time series and plays through them.

For whatever reason, the image you originally attached to the email did not 
come through to me, so I cannot see exactly what you are doing. One problem 
could be that the names of the csv files have to follow a numbering convention 
so that ParaView knows to treat them as a sequence. Simply having them with 
sequential number names should do the trick (e.g. points1.csv, points2.csv, 
points3.csv, etc.). If ParaView understands the numbering convention, then the 
files should be grouped together in the file browser.

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org<mailto:paraview-boun...@paraview.org>] On 
Behalf Of Janessa Tran
Sent: Tuesday, June 28, 2016 10:45 PM
To: paraview@paraview.org<mailto:paraview@paraview.org>
Subject: [EXTERNAL] [Paraview] Animating trajectories of points

Hi,

This is my first time using ParaView and I am trying to get an animation of a 
trajectory of points. I have the data stored in separate csv files (one file 
for each time step). When I upload the data into ParaView, it is all grouped 
together and I can do it all at once. I am able to use the filter Table to 
Points to see the outcome of all the points together. What i am looking to do, 
however, is to animate a trajectory of the points over time.

Do you know how I should approach doing this? I assumed that i would be able to 
click "play" and it would work once I uploaded the data, however, this does not 
seem to be doing anything.

Thank you very much in advance!

This is what I have so far:

[Image removed by sender. Inline image 1]

- Janessa


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