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@gmail.com

On Mon, Nov 3, 2014 at 9:45 PM, Suoqing JI <suoqing@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@gmail.com> wrote:

On Mon, Nov 3, 2014 at 5:29 PM, Suoqing JI <suoqing@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@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@gmail.com

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