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Re: [Cleaver] NaN coordinates in generated tetrahedral mesh


Chronological Thread 
  • From: "Jonathan Bronson" <bronson@sci.utah.edu>
  • To: Johan Andruejol <johan.andruejol@kitware.com>
  • Cc: Julien Finet <julien.finet@kitware.com>, Joshua Levine <levinej@clemson.edu>, "cleaver@sci.utah.edu" <cleaver@sci.utah.edu>
  • Subject: Re: [Cleaver] NaN coordinates in generated tetrahedral mesh
  • Date: Wed, 19 Feb 2014 22:19:17 -0600
Hi Johan,

I'd be happy to look into what is going on with Cleaver and this dataset.
The web address for the data appears to have restricted access rights:

"Access Denied
You do not have the necessary permission on the specified resource(s).
Details: Invalid policy: no read access"

Please send me a personal email with instructions for accessing the data.

Thanks!
Jonathan

On Tue, 18 Feb 2014 16:00:06 -0500
Johan Andruejol <johan.andruejol@kitware.com> wrote:
Hi all,

Following Julien's e-mail, we dug even further and found some NaN
coordinates (again).
This time we made sure to reproduce the bug with Cleaver on the command
line :)

You can find the data we used here: http://packages.kitware.com/folder/246
The Label*.nrrd files are the files we generate from the BrokenVolume.nrrd.
We ran the following command line: "./cleaver -i label0.nrrd label1.nrrd
label2.nrrd label3.nrrd -o result".
The result.ply file is the result with the NaN coordinates we obtained with
the cleaver command line.

Do you know where this might come from ?


On Wed, Feb 5, 2014 at 2:22 PM, Jonathan Bronson <bronson@sci.utah.edu>wrote:

Hi Julien,

No worries at all. We're glad to hear that it's not an issue with Cleaver
itself.

Cheers,
Jonathan

On Feb 5, 2014, at 2:20 PM, Julien Finet <julien.finet@kitware.com> wrote:

Hi,

I had a chance to investigate a bit further and... false alarm. The error
was inside our wrapping of Cleaver.
I'm really sorry for the disturbance.

Regards,
Julien.



On Wed, Feb 5, 2014 at 12:18 PM, Jonathan Bronson <bronson@sci.utah.edu>wrote:

Hi Julien

I agree with Josh, we'd need the material volumes you're generating
with that label map in order to diagnose what's going on. Also, as
Josh mentioned I'm on travel, so please excuse any delays in response
this week.

Best,
Jonathan


On Tue, 4 Feb 2014 17:27:30 -0500
Joshua Levine <levinej@clemson.edu> wrote:

Hi Julien,

Jonathan is traveling for the moment, so our responses may be a little
delayed.

Could you clarify exactly how the NaN's are produced? Perhaps sending
us the exact data might be required.

I did the following with your code; which did not produce any NaNs:

(1) From the input, I took each material label (0, 17, 143, 209) and
created a binary image
(2) I then ran Cleaver with the 4 input files, this required running
with -p since there were cuts on the boundary.

In this default configuration, everything looks OK. I did receive a
couple of warnings stating "Failed to Project Triple BACK into 3D.
Using barycenter"

This is with version 1.5.4 of cleaver, freshly downloaded from the
website and built on OSX.

Josh

On Tue, Feb 4, 2014 at 8:34 AM, Julien Finet <julien.finet@kitware.com>
wrote:

Hi,

I am using Cleaver 1.5.4 and it works great. Very nice work!
However, with some data, I have NaN coordinates in the generated mesh.
Please see an example volume enclosed. I tried to make it as small as
possible.
There are 4 materials in that volume (0 is air). Let me know if you
want the
volume of each label.

Can you please let me know what can be done to fix that ?

Thanks a lot,
Julien.







--
Johan Andruejol
R&D Engineer, Kitware Inc.
http://www.kitware.com/
Phone: (919) 869-8860


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