[yt-users] Column density plot

[Stephanie Tonnesen]

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?

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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