<div dir="ltr"><div>Hi, helpful folks. Another issue I have been struggling with, which is similar to this thread<br><a href="http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-May/003652.html">http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2013-May/003652.html</a><br>
<br></div>I am working on some FLASH data with the current version of yt using MacOS 10.7.5. Using this exact same data set, I managed to create some nice phaseplots using spheres centered on the densest spot. However, I now want to make some plots for a much larger volume of scientific interest... <br>
Here is the code<br><br>from yt.mods import *<br>%matplotlib inline<br>import matplotlib.pyplot as plt<br>import numpy as np<br>pf = load("Strat_Box_hdf5_plt_cnt_0064")<br>pc = PlotCollection(pf, [0.5, 0.5, 0.5])<br>
plane = pf.h.region([0.5,0.5,0.5],[0.0,0.0,0.4],[1.0,1.0,0.6])<br>pc.save("plane_cnt_0064")<br><br>I then get the following error <br><pre><span class="">ValueError</span>: Data has no positive values, and therefore can not be log-scaled<br>
<br></pre><pre>Following the advice in the thread listed above, John Wise suggested <br>"For your "empty" plot, do you have any gas with densities between <br>1e-26 and 1e-27 g/cm^3 in this sphere? If there's no gas in this <br>
range, then CellVolume will be zero and will give you that error <br>message when it tries to take the log of CellVolume. If you want <br>to manually inspect the CellVolume field, you can print out the following variable
pc.plots[-1].data['CellVolume']
which will give you the CellVolume as a function of the x-variable<br>for the last plot you have added to your PlotCollection."<br><br></pre><pre>The writer did not respond in the next thread, so I'm not sure if <br>
this worked. But when I try it, I get the following:<br><span class="">KeyError</span> Traceback (most recent call last)
<span class=""><ipython-input-18-71f93f9e2cb6></span> in <span class=""><module><span class="">()</span>
<span class="">----> 1<span class=""> </span>pc</span><span class="">.</span></span>plots<span class="">[</span><span class="">-</span><span class="">1</span><span class="">]</span><span class="">.</span>data<span class="">[</span><span class="">"CellVolume"</span><span class="">]</span><span class=""></span>
<span class="">/Users/kde/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc</span> in <span class="">__getitem__<span class="">(self, key)</span>
<span class=""> 160</span> <span class=""># This raises a KeyError if it doesn't exist</span><span class=""></span><span class=""></span></span>
<span class=""> 161</span> <span class=""># This is because we explicitly want to add all fields</span><span class=""></span><span class=""></span>
<span class="">--> 162<span class=""> <span class="">return</span> </span>self</span><span class="">.</span>field_data<span class="">[</span>key<span class="">]</span><span class=""></span>
<span class=""> 163</span> <span class=""></span>
<span class=""> 164</span> <span class="">def</span> __setitem__<span class="">(</span>self<span class="">,</span> key<span class="">,</span> value<span class="">)</span><span class="">:</span><span class=""></span>
<span class="">KeyError</span>: 'CellVolume'<br><br></pre><pre>Even though CellVolume is explicitly listed in my list of derived fields...<br></pre><pre>Also, I did try the same command for Density rather than CellVolume,<br>
</pre><pre>and the numbers were in the e-24 g cm-3 range...in fact, all the numbers<br>were exactly the same. So I don't know if I've screwed up my data container<br>somehow, or if the density values really are too low?<br>
</pre><pre><br>any ideas?<br>thanks SO much<br>kathy<br></pre><br clear="all"><div><div><br>-- <br>Kathy DeGioia Eastwood, Ph.D.<br>Professor of Physics and Astronomy<br>Northern Arizona University<br>Flagstaff, AZ 86011-6010<br>
Ph: 928-523-7159 FX: 928-523-1371<br><a href="mailto:Kathy.Eastwood@nau.edu" target="_blank">Kathy.Eastwood@nau.edu</a><br>deliveries: 602 S. Humphreys St., Bldg 19 Rm 209
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