[yt-users] cutting plane not working or changed

Nathan Goldbaum nathan12343 at gmail.com
Wed Mar 15 11:42:36 PDT 2017

Ah, apologies for not checking how yt behaves on a stable release. I'm able
to reproduce the behavior you're seeing on yt 3.3.5. It looks like this
behavior doesn't manifest itself on the yt branch, so it looks like some
changes we've made have "fixed" this since we branched off for yt 3.4 last
summer. I suspect this has something to do with the pixelizers being
rewritten to use compositing but I'd need to check in detail with hg bisect
to be sure.

Can you try testing out the development version of yt? You should be able
to build yt from source by uninstalling your current version of yt, cloning
the repository, checking out the "yt" branch, and running "python setup.py
develop". See this page for more details:


Is the new behavior (wtihout the NaNs) what you expect?

I might try to backport this to the stable branch, but given that a lot of
code has changed in the pixelizers it might be difficult to backport just
this fix. Would you be ok with running on the development branch for now?
I'd ideally like to get yt 3.4.0 out the door by this summer.

On Wed, Mar 15, 2017 at 1:00 PM, Slavin, Jonathan <jslavin at cfa.harvard.edu>

> ​Hi Nathan,
> I finally got around to testing your code on LodegIt that uses the
> IsolatedGalaxy data.  I ran it as is except I added some plotting
> statements (using matplotlib) at the end.  I again do get the problem of
> NaNs:
> ​In [2]: run slice_prob_test.py
> Parsing Hierarchy : 100%|██████████████████| 173/173 [00:00<00:00,
> 23359.45it/s]
> /export/slavin/python/anaconda/lib/python2.7/site-
> packages/yt/visualization/fixed_resolution.py:546: RuntimeWarning:
> invalid value encountered in divide
>   bounds).transpose()
> (nan g/cm**3, nan g/cm**3)
> True
> ​Where the (nan g/cm**3... line is from the print(image.max()...
> statement.  Also np.any(np.isnan(image)) returns True.  The image that is
> produced is shown in the attached png file.
> The RuntimeWarning is apparently associated with this statement:
> ​buff = pixelize_off_axis_cartesian(
>                                self.data_source['x'],
> self.data_source['y'],   self.data_source['z'],
>                                self.data_source['px'],
>  self.data_source['py'],
>                                self.data_source['pdx'],
> self.data_source['pdy'], self.data_source['pdz'],
>                                self.data_source.center,
> self.data_source._inv_mat, indices,
>                                self.data_source[item],
>                                self.buff_size[0], self.buff_size[1],
>                                bounds).transpose()
> ​which is in the __getitem__ method of ​the ObliqueFixedResolutionBuffer
> class.  That's about all I could tell you at this point.
> The package versions I'm using are yt 3.3.5, python 2.7.12, matplotlib
> 2.0.0 (running on Linux CentOS 6.8 if that matters).
> ​Regards,
> Jon​
> On Fri, Mar 10, 2017 at 4:05 PM, <yt-users-request at lists.spacepope.org>
> wrote:
>> Date: Fri, 10 Mar 2017 12:14:55 -0800
>> From: Nathan Goldbaum <nathan12343 at gmail.com>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] cutting plane not working or changed behavior
>> Message-ID:
>>         <CAJXewOmWwY1CU4nrafG5_=GrAScGBnq=VMNxxh3s0OUzDzaGVw at mail.
>> gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>> Hi Jonathan,
>> I'm not able to reproduce the behavior you're seeing with a test dataset
>> (e.g. see http://paste.yt-project.org/show/7080/, this uses a dataset
>> from
>> yt-project.org/data).
>> Is there any chance you can share a dataset that triggers this?
>> Alternatively, can you reproduce this using one of the test datasets on
>> yt-project.org/data?
>> The yt curldrop might be useful to share a dataset that triggers the issue
>> you're seeing, see docs.hub.yt. If you're not comfortable sharing the
>> dataset publicly, feel free to share it with me off-list.
>> -Nathan
> --
> ________________________________________________________
> Jonathan D. Slavin                 Harvard-Smithsonian CfA
> jslavin at cfa.harvard.edu       60 Garden Street, MS 83
> phone: (617) 496-7981       Cambridge, MA 02138-1516
> cell: (781) 363-0035             USA
> ________________________________________________________
> _______________________________________________
> yt-users mailing list
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> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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