[yt-users] Column density plot

Tue Nov 4 12:26:20 PST 2014

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?

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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