[yt-users] phase objects in the modern era

[Geoffrey So]

I think another way of doing similar things is using BinnedProfile2D, or if
the dataset is small matplotlib has a histogram2d which I sometimes use.

From
G.S.


On Fri, Apr 26, 2013 at 4:15 PM, David Collins <dcollins4096 at gmail.com>wrote:

> 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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