[Paraview] IMPORTANT-Particles+HPC

Mon Mar 23 14:13:22 EDT 2015

ParaView does not do anything special about the grains. It does not even understand the concept of "grain."

You can ask ParaView to find all cells with a grain ID, for example 3732. You, as a human, can then look at those cells, understand that collectively they are a grain, and examine its neighbors.

-Ken

From: <Zhang>, Ying <yingz at ufl.edu<mailto:yingz at ufl.edu>>
Date: Monday, March 23, 2015 at 11:44 AM
To: Kenneth Moreland <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "Chiu,Steven" <s.chiu at ufl.edu<mailto:s.chiu at ufl.edu>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>, "Sahi,Catherine A" <csahi at ufl.edu<mailto:csahi at ufl.edu>>
Subject: [EXTERNAL] Re: IMPORTANT-Particles+HPC

Hi Ken,

I am a little puzzled. For Steven’s VTI file, each cluster/grain has a unique ID, for example: 3732, 3240, 4955, etc. When Paraview visualize this file, how does it place one grain next to each other, or how does it determine one grain is adjacent to another? Is there any algorithm in paraview that defines adjacency? (I work in Research Computing center at UF and try to help Steven to run his program, so not really familiar with this work.)

Thanks,

Ying

On Mar 23, 2015, at 1:21 PM, Moreland, Kenneth <kmorel at sandia.gov<mailto:kmorel at sandia.gov>> wrote:

That clarifies things, but I'm not sure how much I can help you.

First, you just asked how ParaView will interpret this file. ParaView will read this as an "image" that is a regular 2D grid of data. It will show the data pretty much the same as the image below. (The colors will be different, but the meaning will be the same.)

If you want to look at a single grain at a time, you can do that fairly easily with what is available in ParaView. You can either use the Threshold filter to extract a grain with a particular ID. Better yet, you can use the Find Data feature to select all "cells" that belong to a particular grain. That will help you locate a grain in the image, where you can zoom in and manually peek at neighboring grains.

Beyond that, you might need to design your own analysis algorithms. At this point, I'm not sure what you want to see. From an image processing point of view, your data is already classified since there is a unique identifier for each grain. You could write a custom operation to identify all neighbors of all grains, but I'm not sure what you do with it after that.

-Ken

From: <Chiu>, Steven <s.chiu at ufl.edu<mailto:s.chiu at ufl.edu>>
Date: Monday, March 23, 2015 at 10:23 AM
To: "Zhang,Ying" <yingz at ufl.edu<mailto:yingz at ufl.edu>>, Kenneth Moreland <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>, "Sahi,Catherine A" <csahi at ufl.edu<mailto:csahi at ufl.edu>>
Subject: [EXTERNAL] IMPORTANT-Particles+HPC

Hello all,

Sorry for the delayed response. We were at the TMS conference the past week.

> Steven, could you explain to Ken about your image and the information you are trying to find?

Ken, we are in the Material Science and Engineering field.
These files come from Dream3d and SPPARKS simulations.

What do you mean by a "grain"?  Is that some roundish feature in the image?

<b&w.png>
An individual grain is define as 1 of the objects seen in the picture of above showing a 2-D face of our microstructure.

What does it mean for two grains to be neighbors?  Does it mean they are touching?
-neighboring grains are grains that are adjacent to each other in the picture above.

From the vti file stand point:
1 grain is comprised of 1 set of unique contiguous spins as see below. <Screen Shot 2015-03-16 at 1.12.43 PM.png>

Link to dump.#.vti file in google drive:
https://drive.google.com/folderview?id=0B-JhfuaY4N27fndFQXpYOEtHN0NzTWoyN2Q4cUtvY1BFV21lWHZoSFV3bnlwMUVzc2l6VHM&usp=sharing

That they are within some certain distance of each other?
I'm not sure what you mean. When we make the structures in dream3d, there is an option for spacing.
<Screen Shot 2015-03-23 at 12.10.43 PM.png>

That they are not being obscured by some other grain?
This will be on a 2-D scale so it will be like the image as seen previously. However, our microstructures are 3-D and we manually take a slice through it using paraview.

Additionally,

How would paraview interpret /read this vti?

Contact me if you need anything.
Best,
Steven.

________________________________
From: Zhang,Ying
Sent: Monday, March 16, 2015 12:08 PM
To: Moreland, Kenneth
Cc: paraview at paraview.org<mailto:paraview at paraview.org>; Chiu,Steven
Subject: Re: [Paraview] Algorithm to find grain neighbors

Sorry that I forgot to Cc Steven.

> On Mar 16, 2015, at 11:18 AM, Zhang,Ying <yingz at UFL.EDU<mailto:yingz at UFL.EDU>> wrote:
>
> Hi Ken,
>
> I work in Research Computing at University of Florida and have a user (Cc'ed) who is using Paraview to visualize his grain image on our computing systems.
>
> Steven, could you explain to Ken about your image and the information you are trying to find?
>
> Thanks,
>
> Ying
>
>> On Mar 16, 2015, at 11:05 AM, Moreland, Kenneth <kmorel at sandia.gov<mailto:kmorel at sandia.gov>> wrote:
>>
>> I don't really understand the question, but the answer is probably no.
>>
>>
>> What do you mean by a "grain"? Is that some roundish feature in the image?
>> And what does it mean for two grains to be neighbors? Does it mean they
>> are touching? That they are within some certain distance of each other?
>> That they are not being obscured by some other grain?
>>
>> Assuming I've guessed closed in any of these aspects, I don't think
>> ParaView comes with any filters that perform that action.
>>
>> -Ken
>>
>> On 3/13/15, 3:21 PM, "Zhang,Ying" <yingz at ufl.edu<mailto:yingz at ufl.edu>> wrote:
>>
>>> Dear Paraview developers,
>>>
>>> I sent a question a while ago and probably didn¹t get to the list. But
>>> here is my question again:
>>>
>>> I have a grain image in vti format and use Paraview to visualize the
>>> grains. In Paraview I use Representation/Surface along with xml template
>>> for coloring to display the grain image based on the vti file. I would
>>> like to know if there is a way to find out the number of neighbors each
>>> grain has. I wonder if paraview has a such tool to give this information.
>>>
>>> Thank you!
>>>
>>> Ying Zhang
>>>
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com<http://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
>>
>

<b&w.png><Screen Shot 2015-03-16 at 1.12.43 PM.png><Screen Shot 2015-03-23 at 12.10.43 PM.png>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/paraview/attachments/20150323/6529aa94/attachment.html>