[yt-users] Column density plot

Suoqing JI suoqing at physics.ucsb.edu
Mon Nov 3 21:45:46 PST 2014


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 <mailto: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 <mailto: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 <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 <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 <mailto:stonnes at gmail.com>
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