[yt-users] gradient field in yt3

Thu Aug 13 13:29:57 PDT 2015

See:
https://bitbucket.org/yt_analysis/yt/pull-requests/1699/fix-issue-with-gradient-fields-of-unitless/diff

On Thu, Aug 13, 2015 at 2:52 PM, Yuan Li <bear0980 at gmail.com> wrote:

> Hi Nathan,
>
> I think you are probably right!
>
> The script is super short:
>
> import yt
> import numpy as numpy
> from yt import derived_field
> @derived_field(name="logP",units="")
> def _logP(field,data):
>     return numpy.log(numpy.array(data["gas","pressure"]))
> pf=yt.load("DD0060/data0060") #load your data
> pf.add_gradient_fields(("gas","logP"))
> print pf.derived_field_list
> dd=pf.all_data()
> a=dd["gas","logP_gradient_y"]
>
> I forgot how to make a PR...It has been a while. I should relearn it, but
> it might be easier for you to do this one :). Thank you!!
>
>
> Yuan
>
> On Thu, Aug 13, 2015 at 3:40 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>> So I *think* the parenthesis in the units are coming from this line:
>>
>>
>> https://bitbucket.org/yt_analysis/yt/src/603eab147248f1a165778c76208906201eb7baae/yt/fields/fluid_fields.py?at=yt#fluid_fields.py-218
>>
>> And I think this is happening because no one has tried to create a
>> gradient field for a unitless field. This is something we should be able to
>> do, but it's definitely a corner case.
>>
>> I don't have a script to run to test out any possible fixes, is there any
>> chance you could make a script that uses one of the public test datasets on
>> yt-project.org/data so I can reproduce your issue locally?
>>
>> Please also feel free to try fixing this yourself in your local copy of
>> yt so you can make a PR.  I think all we need to do is modify the line I
>> linked to so if "field_units" is an empty string, we drop the parenthesis
>> and just make the gradient field units "1/cm".
>>
>> On Thu, Aug 13, 2015 at 2:30 PM, Yuan Li <bear0980 at gmail.com> wrote:
>>
>>> Traceback (most recent call last):
>>>   File "logP.py", line 11, in <module>
>>>     a=dd["gas","logP_gradient_y"]
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 253, in __getitem__
>>>     self.get_data(f)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 751, in get_data
>>>     self._generate_fields(fields_to_generate)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 771, in _generate_fields
>>>     fd = self._generate_field(field)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 290, in _generate_field
>>>     tr = self._generate_fluid_field(field)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 308, in _generate_fluid_field
>>>     rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 318, in _generate_spatial_fluid
>>>     rv = self.ds.arr(np.empty(self.ires.size, dtype="float64"), units)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/yt_array.py", line
>>> 332, in __new__
>>>     units = Unit(input_units, registry=registry)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py",
>>> line 204, in __new__
>>>     unit_data = _get_unit_data_from_expr(unit_expr, registry.lut)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py",
>>> line 496, in _get_unit_data_from_expr
>>>     unit_data = _get_unit_data_from_expr(expr, unit_symbol_lut)
>>>   File
>>> "/Users/yuanli/source/yt3/yt-x86_64/src/yt-hg/yt/units/unit_object.py",
>>> line 504, in _get_unit_data_from_expr
>>>     "objects." % str(unit_expr))
>>> yt.units.unit_object.UnitParseError: Cannot parse for unit data from
>>> '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
>>>
>>> On Thu, Aug 13, 2015 at 3:28 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Thu, Aug 13, 2015 at 2:22 PM, Yuan Li <yuan at astro.columbia.edu>
>>>> wrote:
>>>>
>>>>> Hi all:
>>>>>
>>>>> I am having trouble creating a gradient field in yt3. What I want is
>>>>> the gradient of logP, where logP is defined as:
>>>>>
>>>>> @derived_field(name="logP",units="")
>>>>> def _logP(field,data):
>>>>>     return numpy.log(numpy.array(data["gas","pressure"]))
>>>>>
>>>>> Then I add the gradient field:
>>>>>
>>>>> pf.add_gradient_fields(("gas","logP"))
>>>>>
>>>>
>>>>> which seems to work and I can find it in pf.derived_field_list.
>>>>>
>>>>> But if I try to use it, I get this error message:
>>>>> yt.units.unit_object.UnitParseError: Cannot parse for unit data from
>>>>> '()'. Please supply an expression of only Unit, Symbol, Pow, and Mulobjects.
>>>>>
>>>>
>>>> Can you pastebin the full traceback?
>>>>
>>>>
>>>>>
>>>>> Is this because logP does not have a unit?
>>>>>
>>>>> Also, I had another unrelated question about the gradient fields:
>>>>> Can I add the gradient fields globally instead of to a specific
>>>>> dataset?
>>>>>
>>>>>
>>>> Not right now, no.
>>>>
>>>>
>>>>>
>>>>> Thanks!
>>>>> Yuan
>>>>>
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>>>>>
>>>>
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