[yt-users] phase objects in the modern era

[David Collins]

I was under the impression that these things used the values of take_log
that from FieldInfo, which is False for the velocity components.

Using Density instead of x-velocity still throws the same error.

d.


On Fri, Apr 26, 2013 at 5:11 PM, Geoffrey So <gsiisg at gmail.com> wrote:

> Could it also be trying to take log of negative values in the velocity?
>  If so changing x-velcity to another positive field would not end in error.
>
> From
> G.S.
>
>
> On Fri, Apr 26, 2013 at 4:06 PM, David Collins <dcollins4096 at gmail.com>wrote:
>
>> Hi, all--
>>
>> I'm running into problems making phase objects.  It looks like the error
>> is in the color bar, and is similar to other errors I get when trying to
>> use PlotCollections.  The hash I'm on is 34b95297062b.  I'm trying:
>>
>> pf = load(fname)
>> pc = PlotCollection(pf,'c')
>> phase=pc.add_phase_object(pf.h.all_data(),['CellMass',
>>     'x-velocity','CellVolume'],weight=None)
>>
>> min/max are as follows:
>> CellMass: [4.1e-12,1.5e-03] (30631133,)
>> x-velocity: [-7.2e+01,5.5e+01]
>> CellVolume: [1.45e-11,6.0e-08]
>>
>> Is there a more up-to-date manner to do this that doesn't use
>> PlotCollection? Or is there something obvious that I'm missing?
>>
>> It seems to be choking in plot_types.py/__init_colorbar
>>
>>     def __init_colorbar(self):
>>         temparray = np.ones((self.x_bins.size, self.y_bins.size))
>>         self.norm = matplotlib.colors.Normalize()
>>         self.image = self._axes.pcolormesh(self.x_bins, self.y_bins,
>>                                       temparray, shading='flat',
>>                                       norm=self.norm, cmap=self.cmap,
>>                                       rasterized=True)
>>         self.colorbar = self._figure.colorbar(self.image,
>>                                     extend='neither', shrink=0.95,
>>                                     format="%0.2e" )
>>
>> It looks like what's happening is figure.colorbar chokes on the fact that
>> temparray is "ones", so the spacing between elements is zero.  This is
>> outside of my yt knowledge, though.
>>
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "p14_phase_test.py", line 4, in <module>
>>
>> phase=pc.add_phase_object(pf.h.all_data(),['CellMass','x-velocity','CellVolume'])
>>   File
>> "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_collection.py",
>> line 1184, in add_phase_object
>>     figure=figure, axes=axes))
>>   File
>> "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py",
>> line 815, in __init__
>>     self.__init_colorbar()
>>   File
>> "/nics/b/home/collins/local_2013_03_12/src/yt-hg/yt/visualization/plot_types.py",
>> line 834, in __init_colorbar
>>     format="%0.2e" )
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/figure.py",
>> line 1387, in colorbar
>>     cb = cbar.colorbar_factory(cax, mappable, **kw)
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
>> line 1173, in colorbar_factory
>>     cb = Colorbar(cax, mappable, **kwargs)
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
>> line 854, in __init__
>>     ColorbarBase.__init__(self, ax, **kw)
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
>> line 298, in __init__
>>     self.draw_all()
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
>> line 323, in draw_all
>>     self._config_axes(X, Y)
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
>> line 409, in _config_axes
>>     self.update_ticks()
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
>> line 345, in update_ticks
>>     ticks, ticklabels, offset_string = self._ticker()
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
>> line 560, in _ticker
>>     ticks = self._locate(b)
>>   File
>> "/nics/b/home/collins/local_2013_03_12/lib/python2.7/site-packages/matplotlib/colorbar.py",
>> line 808, in _locate
>>     z = np.take(y, i0) + (xn-np.take(b,i0))*dy/db
>> FloatingPointError: invalid value encountered in divide
>>
>>
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