[yt-users] profile object / data container question
Britton Smith
brittonsmith at gmail.com
Wed Aug 31 08:39:20 PDT 2016
HI Molly,
I have identified the source of this bug and will be issuing a pull request
to fix it momentarily. Sorry for the inconvenience.
Britton
On Mon, Aug 29, 2016 at 7:56 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:
> A workaround that seems to work for me is to manually copy over the
> missing field_info data:
>
> https://paste.yt-project.org/show/6792/
>
> Keep in mind that you need to do it like I did, `profile =
> prof_ds.profile`, and then work with that profile object from then on,
> because `prof_ds.profile` is a property that doesn't cache its own result,
> so every time you access it you get back a new profile object.
>
> On Mon, Aug 29, 2016 at 1:41 PM, Molly Peeples <molly at stsci.edu> wrote:
>
>> Hey Nathan,
>>
>> So currently there’s no way to save the profile and read it in later with
>> this working? (The profile takes approximately forever to generate, so
>> iterating on plotting while not in iPython is currently a p.i.t.a.)
>>
>> —Molly
>>
>>
>> On August 29, 2016 at 2:37:56 PM, Nathan Goldbaum (nathan12343 at gmail.com)
>> wrote:
>>
>> Hi Molly,
>>
>> I think this is a bug in yt - the issue is that the field_info associated
>> with the original profile object is not being saved to the profile dataset.
>>
>> I've filed this issue here:
>>
>> https://bitbucket.org/yt_analysis/yt/issues/1267
>>
>> For now, you should be able to create a PhasePlot using the profile
>> object you created from the original dataset:
>>
>> nhT_prof_new = yt.create_profile(sph, [('gas',
>> 'H_number_density'),('gas','temperature')], fields='cell_mass',
>>
>> extrema=extrema,fractional=True, n_bins=6)
>> plot = yt.PhasePlot.from_profile(nht_prof_new)
>>
>> -Nathan
>>
>> On Mon, Aug 29, 2016 at 12:45 PM, Molly Peeples <molly at stsci.edu> wrote:
>>
>>> Hi folks,
>>>
>>> I’m trying to construct and save a 2d profile container to make a phase
>>> plot. Here’s what I have:
>>>
>>> nhT_prof_new = yt.create_profile(sph, [('gas',
>>> 'H_number_density'),('gas','temperature')], fields='cell_mass',
>>> extrema=extrema,fractional=True, n_bins=6)
>>>
>>> nhT_prof_new.save_as_dataset()
>>>
>>> prof_ds = yt.load("snap_047_z000p000_Profile2D.h5")
>>>
>>> (just using a small number of bins for now to play with…)
>>>
>>> In [115]: prof_ds.data["temperature"]
>>>
>>> ...: prof_ds.data["H_number_density"]
>>>
>>> ...: prof_ds.data["cell_mass"]
>>>
>>> ...:
>>>
>>> Out[115]:
>>>
>>> YTArray([[ 0.01685665, 0.0405085 , 0.03575519, 0.03091732,
>>> 0.02552936,
>>>
>>> 0.0230379 ],
>>>
>>> [ 0.03770747, 0.05441198, 0.04859202, 0.03285325, 0.02385346,
>>>
>>> 0.04674817],
>>>
>>> [ 0.03022001, 0.05150457, 0.03591368, 0.01974481, 0.01052408,
>>>
>>> 0.00331175],
>>>
>>> [ 0.04278126, 0.01889035, 0.0177686 , 0.01644028, 0.01598129,
>>>
>>> 0.00578262],
>>>
>>> [ 0.05010083, 0.06573628, 0.04247398, 0.03914208, 0. ,
>>>
>>> 0. ],
>>>
>>> [ 0. , 0.11691224, 0. , 0. , 0. ,
>>>
>>> 0. ]]) dimensionless
>>>
>>> but when I try to create a PhasePlot:
>>>
>>> In [116]: p = yt.PhasePlot(prof_ds.data, "H_number_density",
>>> "temperature","cell_mass",weight_field=None)
>>>
>>> ...:
>>>
>>> ------------------------------------------------------------
>>> ---------------
>>>
>>> KeyError Traceback (most recent call
>>> last)
>>>
>>> <ipython-input-116-37b81d75b563> in <module>()
>>>
>>> ----> 1 p = yt.PhasePlot(prof_ds.data,"H_number_density",
>>> "temperature","cell_mass",weight_field=None)
>>>
>>>
>>> /Users/molly/anaconda2/envs/astroconda/lib/python2.7/site-pa
>>> ckages/yt/visualization/profile_plotter.pyc in __init__(self,
>>> data_source, x_field, y_field, z_fields, weight_field, x_bins, y_bins,
>>> accumulation, fractional, fontsize, figure_size)
>>>
>>> 756
>>>
>>> 757 type(self)._initialize_instance(self, data_source,
>>> profile, fontsize,
>>>
>>> --> 758 figure_size)
>>>
>>> 759
>>>
>>> 760 @classmethod
>>>
>>>
>>> /Users/molly/anaconda2/envs/astroconda/lib/python2.7/site-pa
>>> ckages/yt/visualization/profile_plotter.pyc in _initialize_instance(cls,
>>> obj, data_source, profile, fontsize, figure_size)
>>>
>>> 773 obj.profile = profile
>>>
>>> 774 super(PhasePlot, obj).__init__(data_source, figure_size,
>>> fontsize)
>>>
>>> --> 775 obj._setup_plots()
>>>
>>> 776 obj._initfinished = True
>>>
>>> 777 return obj
>>>
>>>
>>> /Users/molly/anaconda2/envs/astroconda/lib/python2.7/site-pa
>>> ckages/yt/visualization/profile_plotter.pyc in _setup_plots(self)
>>>
>>> 854 cax = self.plots[f].cax
>>>
>>> 855
>>>
>>> --> 856 x_scale, y_scale, z_scale = self._get_field_log(f,
>>> self.profile)
>>>
>>> 857 x_title, y_title, z_title = self._get_field_title(f,
>>> self.profile)
>>>
>>> 858
>>>
>>>
>>> /Users/molly/anaconda2/envs/astroconda/lib/python2.7/site-pa
>>> ckages/yt/visualization/profile_plotter.pyc in _get_field_log(self,
>>> field_z, profile)
>>>
>>> 813
>>>
>>> 814 def _get_field_log(self, field_z, profile):
>>>
>>> --> 815 zfi = profile.field_info[field_z]
>>>
>>> 816 if self.x_log is None:
>>>
>>> 817 x_log = profile.x_log
>>>
>>>
>>> KeyError: ('data', 'cell_mass')
>>>
>>>
>>>
>>>
>>> Suggestions?
>>> —Molly
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
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