[yt-users] Column density plot

Nathan Goldbaum nathan12343 at gmail.com
Tue Nov 4 12:32:44 PST 2014


On Tue, Nov 4, 2014 at 12:26 PM, Stephanie Tonnesen <stonnes at gmail.com>
wrote:

> Okay, I've got that, but does that mean that I can't set something in the
> parenthesis to force the bins to be in linear space?  and I need to do the
> take_log setting earlier in the code?
>

You can, you would need to have something like:

logs = {('gas', 'cell_mass'): False}

profile = yt.create_profile(gal,
                            [('index', 'cylindrical_r')],          # the
bin field
                            [('gas', 'cell_mass')],  # profile field
                            weight_field=None, logs=logs)


>
> Thanks,
> Stephanie
>
> --
> Dr. Stephanie Tonnesen
> Alvin E. Nashman Postdoctoral Fellow
> Carnegie Observatories, Pasadena, CA
> stonnes at gmail.com
>
> On Tue, Nov 4, 2014 at 11:10 AM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Tue, Nov 4, 2014 at 10:59 AM, Stephanie Tonnesen <stonnes at gmail.com>
>> wrote:
>>
>>> Thank you both!  I ended up generally following Suoqing's method, but
>>> tried to use create_profile.  I want my radial spacing to be linear, and
>>> when I look at the help page:
>>>
>>> http://yt-project.org/docs/dev/reference/api/generated/yt.data_objects.profiles.create_profile.html#yt.data_objects.profiles.create_profile
>>>
>>> I read that I should set logs=False
>>>
>>> So I type in:
>>>
>>> profile = yt.create_profile(gal,
>>>                             [('index', 'cylindrical_r')],          # the
>>> bin field
>>>                             [('gas', 'cell_mass')],  # profile field
>>>                             weight_field=None, logs=False)
>>>
>>> and yt does not like that.  Nor does it like take_log or log_space.  Can
>>> someone tell me what I should be setting there?
>>>
>>>
>> In this case, logs is a dictionary that maps field names to logging
>> selection.  From the docstrings for create_profile:
>>
>> logs : dict of boolean values
>>
>>         Whether or not to log the bin_fields for the profiles.
>>
>>         The keys correspond to the field names. Defaults to the take_log
>>
>>         attribute of the field.
>>
>>
>>> Thanks again!
>>>
>>> Stephanie
>>>
>>> --
>>> Dr. Stephanie Tonnesen
>>> Alvin E. Nashman Postdoctoral Fellow
>>> Carnegie Observatories, Pasadena, CA
>>> stonnes at gmail.com
>>>
>>> On Mon, Nov 3, 2014 at 9:45 PM, Suoqing JI <suoqing at physics.ucsb.edu>
>>> wrote:
>>>
>>>> Hi Stephanie,
>>>>
>>>> profile.add_fields(‘cell_mass’, weight=None)
>>>>>
>>>>
>>>> Sorry I’ve missed the later part of my old script — after getting the
>>>> profile[‘cell_mass’] it should be divided by the unit surface area. The
>>>> following is the full code and it has been tested with AMR data:
>>>>
>>>> profile = BinnedProfile1D(mydisk, Nbin, 'cylindrical_r', rmin, rmax,
>>>> log_space=True, lazy_reader=True, end_collect=False)
>>>> profile.add_fields('cell_mass', weight=None)
>>>>
>>>> R = profile['cylindrical_r’]
>>>> Sigma = profile[‘cell_mass']
>>>>
>>>> R_edge = np.logspace(np.log10(rmin), np.log10(rmax), num=Nbin+1)
>>>> for i in range(0, Nbin): Sigma[i] = Sigma[i] / (np.pi*(R_edge[i+1]**2 -
>>>> R_edge[i]**2.))
>>>>
>>>> And Nathan’s approach which takes the advantage of image buffer should
>>>> also work.
>>>>
>>>> Best wishes,
>>>> --
>>>> Suoqing JI
>>>> Ph.D Student
>>>> Department of Physics
>>>> University of California, Santa Barbara
>>>> CA 93106, USA
>>>>
>>>> On Nov 3, 2014, at 8:40 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>>>> wrote:
>>>>
>>>>
>>>>
>>>> On Mon, Nov 3, 2014 at 5:29 PM, Suoqing JI <suoqing at physics.ucsb.edu>
>>>> wrote:
>>>>
>>>>> Hi Stephanie,
>>>>>
>>>>> Maybe you could specify a disk, use BinnedProfile1D to create bins
>>>>> along cylindrical radial ('cylindrical_r'), and do
>>>>>
>>>>> profile.add_fields(‘cell_mass’, weight=None)
>>>>>
>>>>> then you could plot profile[‘cell_mass’] vs. profile['cylindrical_r’]
>>>>> and get the 1-D plot the surface density.
>>>>>
>>>>
>>>> This will be a profile of the gas mass as a function of radius, but
>>>> it's not quite a surface density profile.  That said, for an unweighted
>>>> projection, I think it's the same up to a constant scaling factor.
>>>>
>>>>
>>>>>
>>>>> Best wishes,
>>>>> --
>>>>> Suoqing JI
>>>>> Ph.D Student
>>>>> Department of Physics
>>>>> University of California, Santa Barbara
>>>>> CA 93106, USA
>>>>>
>>>>> On Nov 3, 2014, at 5:17 PM, Stephanie Tonnesen <stonnes at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hi yt-users,
>>>>>
>>>>> I would like to make a 1D plot of column density vs radius for a disk
>>>>> (to compare with observations).  I can make a projectionplot, but want
>>>>> something a bit more simple to look at.  I am using yt3.0.1--is there a
>>>>> nice way to to this?
>>>>>
>>>>>
>>>> The key is to use the numpy.digitize and numpy.bincount functions to
>>>> find the histogram of the surface density as a function of radius.  Here's
>>>> an example:
>>>>
>>>> http://nbviewer.ipython.org/gist/ngoldbaum/af8e7f317efe8f115e8b
>>>>
>>>> This is a simplified version of what I've done for a project I'm
>>>> working on right now, which involves making a ton of radial plots of
>>>> projected quantities:
>>>>
>>>>
>>>> https://bitbucket.org/ngoldbaum/galaxy_analysis/src/910f5a7e278247a36f25d62bdc478a7b5a7fe8ce/galanyl/galaxy_analyzer.py?at=default#cl-338
>>>>
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Stephanie
>>>>>
>>>>> --
>>>>> Dr. Stephanie Tonnesen
>>>>> Alvin E. Nashman Postdoctoral Fellow
>>>>> Carnegie Observatories, Pasadena, CA
>>>>> stonnes at gmail.com
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