<div dir="ltr">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.<div><br></div><div>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:</div><div><br></div><div><a href="http://yt-project.org/docs/dev/installing.html#installing-yt-using-pip-or-from-source">http://yt-project.org/docs/dev/installing.html#installing-yt-using-pip-or-from-source</a><br></div><div><br></div><div>Is the new behavior (wtihout the NaNs) what you expect?</div><div><br></div><div>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.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 15, 2017 at 1:00 PM, Slavin, Jonathan <span dir="ltr"><<a href="mailto:jslavin@cfa.harvard.edu" target="_blank">jslavin@cfa.harvard.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Hi Nathan,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">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:</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">In [2]: run slice_prob_test.py</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Parsing Hierarchy : 100%|██████████████████| 173/173 [00:00<00:00, 23359.45it/s]</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">/export/slavin/python/<wbr>anaconda/lib/python2.7/site-<wbr>packages/yt/visualization/<wbr>fixed_resolution.py:546: RuntimeWarning: invalid value encountered in divide</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> bounds).transpose()</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">(nan g/cm**3, nan g/cm**3)</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">True</div><div><br></div><div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">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.</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">The RuntimeWarning is apparently associated with this statement:</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">buff = pixelize_off_axis_cartesian(</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> self.data_source['x'], self.data_source['y'], self.data_source['z'],</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> self.data_source['px'], self.data_source['py'],</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> self.data_source['pdx'], self.data_source['pdy'], self.data_source['pdz'],</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> self.data_source.center, self.data_source._inv_mat, indices,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> self.data_source[item],</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> self.buff_size[0], self.buff_size[1],</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> bounds).transpose()</div><div><br></div><div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">which is in the __getitem__ method of the ObliqueFixedResolutionBuffer class. That's about all I could tell you at this point. </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">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).</div><br></div><div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Regards,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Jon</div><br></div><br></div><span class=""><br><div class="gmail_quote">On Fri, Mar 10, 2017 at 4:05 PM, <span dir="ltr"><<a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.<wbr>spacepope.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div id="m_-888897076803494013gmail-:hr" class="m_-888897076803494013gmail-a3s m_-888897076803494013gmail-aXjCH m_-888897076803494013gmail-m15aba0a525517a43">Date: Fri, 10 Mar 2017 12:14:55 -0800<br>
From: Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] cutting plane not working or changed behavior<br>
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<br>
Hi Jonathan,<br>
<br>
I'm not able to reproduce the behavior you're seeing with a test dataset<br>
(e.g. see <a href="http://paste.yt-project.org/show/7080/" rel="noreferrer" target="_blank">http://paste.yt-project.org/sh<wbr>ow/7080/</a>, this uses a dataset from<br>
<a href="http://yt-project.org/data" rel="noreferrer" target="_blank">yt-project.org/data</a>).<br>
<br>
Is there any chance you can share a dataset that triggers this?<br>
Alternatively, can you reproduce this using one of the test datasets on<br>
<a href="http://yt-project.org/data" rel="noreferrer" target="_blank">yt-project.org/data</a>?<br>
<br>
The yt curldrop might be useful to share a dataset that triggers the issue<br>
you're seeing, see <a href="http://docs.hub.yt" rel="noreferrer" target="_blank">docs.hub.yt</a>. If you're not comfortable sharing the<br>
dataset publicly, feel free to share it with me off-list.<br>
<br>
-Nathan</div></blockquote></div><br><br><br clear="all"><div><br></div></span><span class="">-- <br><div class="m_-888897076803494013gmail_signature"><div dir="ltr"><div><div dir="ltr">______________________________<wbr>__________________________<br>Jonathan D. Slavin Harvard-Smithsonian CfA<br><a href="mailto:jslavin@cfa.harvard.edu" target="_blank">jslavin@cfa.harvard.edu</a> 60 Garden Street, MS 83<br>phone: <a href="tel:(617)%20496-7981" value="+16174967981" target="_blank">(617) 496-7981</a> Cambridge, MA 02138-1516<br>cell: <a href="tel:(781)%20363-0035" value="+17813630035" target="_blank">(781) 363-0035</a> USA<br>______________________________<wbr>__________________________<br><br></div></div></div></div>
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