[yt-users] Column density plot

Tue Nov 4 11:10:21 PST 2014

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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