<div dir="ltr">here's the PR:<div><br></div><div><a href="https://bitbucket.org/yt_analysis/yt/pull-requests/2571/add-support-for-nyx-datasets-without/diff">https://bitbucket.org/yt_analysis/yt/pull-requests/2571/add-support-for-nyx-datasets-without/diff</a><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Apr 3, 2017 at 9:46 AM, Michael Zingale <span dir="ltr"><<a href="mailto:michael.zingale@stonybrook.edu" target="_blank">michael.zingale@stonybrook.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">it looks like a lot of that logic changed in the latest dev version of yt, but there is still an issue reading Nyx datasets without particles. I'll issue a PR to fix this on the dev version in a few minutes.</div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Mon, Apr 3, 2017 at 7:53 AM, Wolfram Schmidt <span dir="ltr"><<a href="mailto:wolfram.schmidt@uni-hamburg.de" target="_blank">wolfram.schmidt@uni-hamburg.<wbr>de</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<div bgcolor="#FFFFFF" text="#000000">
Hi,<br>
<br>
I encountered a problem when processing BoxLib (Nyx) data from pure
hydro simulations without particles, using an Anaconda installation
of yt.<br>
<br>
After loading a dataset with yt.load(), I get the following error
for ds.field_list:<br>
<pre><span class="m_8392733480149425423m_5777896458988137541ansired">------------------------------<wbr>------------------------------<wbr>---------------</span>
<span class="m_8392733480149425423m_5777896458988137541ansired">KeyError</span> Traceback (most recent call last)
<span class="m_8392733480149425423m_5777896458988137541ansigreen"><ipython-input-5-5aaf470c0415></span> in <span class="m_8392733480149425423m_5777896458988137541ansicyan"><module><span class="m_8392733480149425423m_5777896458988137541ansiblue">()</span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen">----> 1<span class="m_8392733480149425423m_5777896458988137541ansiyellow"> </span>ds<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>field_list<span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen">/sw/tools/anaconda3/4.1.1/gene<wbr>ric/lib/python3.5/site-package<wbr>s/yt/data_objects/static_<wbr>output.py</span> in <span class="m_8392733480149425423m_5777896458988137541ansicyan">field_list<span class="m_8392733480149425423m_5777896458988137541ansiblue">(self)</span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 459</span> <span class="m_8392733480149425423m_5777896458988137541ansiyellow">@</span>property<span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 460</span> <span class="m_8392733480149425423m_5777896458988137541ansigreen">def</span> field_list<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span>self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">:</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen">--> 461<span class="m_8392733480149425423m_5777896458988137541ansiyellow"> <span class="m_8392733480149425423m_5777896458988137541ansigreen">return</span> self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>index<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>field_list<span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 462</span> <span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 463</span> <span class="m_8392733480149425423m_5777896458988137541ansigreen">def</span> create_field_info<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span>self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">:</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen">/sw/tools/anaconda3/4.1.1/gene<wbr>ric/lib/python3.5/site-package<wbr>s/yt/data_objects/static_<wbr>output.py</span> in <span class="m_8392733480149425423m_5777896458988137541ansicyan">index<span class="m_8392733480149425423m_5777896458988137541ansiblue">(self)</span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 417</span> <span class="m_8392733480149425423m_5777896458988137541ansigreen">raise</span> RuntimeError<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span><span class="m_8392733480149425423m_5777896458988137541ansiblue">"You should not instantiate Dataset."</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 418</span> self._instantiated_index = self._index_class(
<span class="m_8392733480149425423m_5777896458988137541ansigreen">--> 419<span class="m_8392733480149425423m_5777896458988137541ansiyellow"> self, dataset_type=self.dataset_type<wbr>)
</span><span class="m_8392733480149425423m_5777896458988137541ansigreen"> 420</span> <span class="m_8392733480149425423m_5777896458988137541ansired"># Now we do things that we need an instantiated index for</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 421</span> <span class="m_8392733480149425423m_5777896458988137541ansired"># ...first off, we create our field_info now.</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen">/sw/tools/anaconda3/4.1.1/gene<wbr>ric/lib/python3.5/site-package<wbr>s/yt/frontends/boxlib/data_<wbr>structures.py</span> in <span class="m_8392733480149425423m_5777896458988137541ansicyan">__init__<span class="m_8392733480149425423m_5777896458988137541ansiblue">(self, ds, dataset_type)</span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 906</span> <span class="m_8392733480149425423m_5777896458988137541ansigreen">def</span> __init__<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span>self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">,</span> ds<span class="m_8392733480149425423m_5777896458988137541ansiyellow">,</span> dataset_type<span class="m_8392733480149425423m_5777896458988137541ansiyellow">=</span><span class="m_8392733480149425423m_5777896458988137541ansiblue">'nyx_native'</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">:</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 907</span> super<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span>NyxHierarchy<span class="m_8392733480149425423m_5777896458988137541ansiyellow">,</span> self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>__init__<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span>ds<span class="m_8392733480149425423m_5777896458988137541ansiyellow">,</span> dataset_type<span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen">--> 908<span class="m_8392733480149425423m_5777896458988137541ansiyellow"> </span>self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>_read_particle_header<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 909</span> <span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 910</span> <span class="m_8392733480149425423m_5777896458988137541ansigreen">def</span> _read_particle_header<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span>self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">:</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen">/sw/tools/anaconda3/4.1.1/gene<wbr>ric/lib/python3.5/site-package<wbr>s/yt/frontends/boxlib/data_<wbr>structures.py</span> in <span class="m_8392733480149425423m_5777896458988137541ansicyan">_read_particle_header<span class="m_8392733480149425423m_5777896458988137541ansiblue">(self)</span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 909</span> <span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 910</span> <span class="m_8392733480149425423m_5777896458988137541ansigreen">def</span> _read_particle_header<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span>self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">:</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen">--> 911<span class="m_8392733480149425423m_5777896458988137541ansiyellow"> <span class="m_8392733480149425423m_5777896458988137541ansigreen">if</span> <span class="m_8392733480149425423m_5777896458988137541ansigreen">not</span> self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>ds<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>parameters<span class="m_8392733480149425423m_5777896458988137541ansiyellow">[</span><span class="m_8392733480149425423m_5777896458988137541ansiblue">"particles"</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"><wbr>]</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">:</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 912</span> self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>pgrid_info <span class="m_8392733480149425423m_5777896458988137541ansiyellow">=</span> np<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>zeros<span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">(</span>self<span class="m_8392733480149425423m_5777896458988137541ansiyellow">.</span>num_grids<span class="m_8392733480149425423m_5777896458988137541ansiyellow">,</span> <span class="m_8392733480149425423m_5777896458988137541ansicyan">3</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">,</span> dtype<span class="m_8392733480149425423m_5777896458988137541ansiyellow">=</span><span class="m_8392733480149425423m_5777896458988137541ansiblue">'int64'</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow">)</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansigreen"> 913</span> <span class="m_8392733480149425423m_5777896458988137541ansigreen">return</span><span class="m_8392733480149425423m_5777896458988137541ansiyellow"></span>
<span class="m_8392733480149425423m_5777896458988137541ansired">KeyError</span>: 'particles'
</span></span></span></span></span></span></span></span></span></span></span></span></pre>
Same problem with slices. I am not sure what exactly causes the
error here, but since I can load datasets from cosmological
simulations with Nyx and process them without problems, I suppose
the problem outlined above is somehow related to the missing
particles.<br>
<br>
How can this be fixed?<br>
<br>
Best<span class="m_8392733480149425423HOEnZb"><font color="#888888"><br>
Wolfram<br>
<br>
</font></span></div>
<br></div></div>______________________________<wbr>_________________<br>
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<br></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div class="m_8392733480149425423gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div>Michael Zingale</div><div>Associate Professor</div><div><br></div><div>Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800</div><div><i>phone</i>: <a href="tel:(631)%20632-8225" value="+16316328225" target="_blank">631-632-8225</a></div><div><i>e-mail</i>: <a href="mailto:Michael.Zingale@stonybrook.edu" target="_blank">Michael.Zingale@stonybrook.edu</a></div><div><i>web</i>: <a href="http://www.astro.sunysb.edu/mzingale" target="_blank">http://www.astro.sunysb.edu/<wbr>mzingale</a></div><div>github: <a href="http://github.com/zingale" target="_blank">http://github.com/zingale</a></div><div><br></div></div></div></div>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div>Michael Zingale</div><div>Associate Professor</div><div><br></div><div>Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800</div><div><i>phone</i>: 631-632-8225</div><div><i>e-mail</i>: <a href="mailto:Michael.Zingale@stonybrook.edu" target="_blank">Michael.Zingale@stonybrook.edu</a></div><div><i>web</i>: <a href="http://www.astro.sunysb.edu/mzingale" target="_blank">http://www.astro.sunysb.edu/mzingale</a></div><div>github: <a href="http://github.com/zingale" target="_blank">http://github.com/zingale</a></div><div><br></div></div></div></div>
</div>