[yt-users] Column density plot

Nathan Goldbaum nathan12343 at gmail.com
Tue Nov 4 13:31:44 PST 2014


On Tue, Nov 4, 2014 at 1:29 PM, Stephanie Tonnesen <stonnes at gmail.com>
wrote:

> Okay, I think I must be missing something because right now I am still
> getting log-spaced bins:
>
> alld = ds.all_data()
> gal = alld.cut_region("obj['density'] > 1.01e-28")
> logs = {('index', 'cylindrical_r'): False}
> logs = {('gas', 'cell_mass'): False}
>

Do you want both of these to be linearly spaced?  Right now you're
overwriting the first one when you redeclare "logs".


> profile = yt.create_profile(gal,
>                             [('index', 'cylindrical_r')],          # the
> bin field
>                             [('gas', 'cell_mass')],  # profile field
>                             weight_field=None, n_bins=17)
>

Did you forget to pass logs in here?


> coldens = profile["gas","cell_mass"]/1.6733e-24
> coldens[0] = coldens[0]/(3.14159*profile.x[0]*profile.x[0])
> i = 1
> while i < len(coldens):
>     coldens[i] = coldens[i]/((3.14159*profile.x[i]*profile.x[i]) -
> (3.14159*profile.x[i-1]*profile.x[i-1]))
>     i = i+1
> mp.plot(profile.x/3.086e21,coldens)
> mp.show()
> print profile.x
>
> [  2.59949407e+20   3.49922639e+20   4.71037249e+20   6.34071835e+20
>    8.53535665e+20   1.14895993e+21   1.54663592e+21   2.08195484e+21
>    2.80255739e+21   3.77257363e+21   5.07833019e+21   6.83603292e+21
>    9.20210863e+21   1.23871263e+22   1.66745367e+22   2.24458981e+22
>    3.02148330e+22] cm
>
>
>
> --
> Dr. Stephanie Tonnesen
> Alvin E. Nashman Postdoctoral Fellow
> Carnegie Observatories, Pasadena, CA
> stonnes at gmail.com
>
> On Tue, Nov 4, 2014 at 12:32 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
>>
>>
>> On Tue, Nov 4, 2014 at 12:26 PM, Stephanie Tonnesen <stonnes at gmail.com>
>> wrote:
>>
>>> 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?
>>>
>>
>> You can, you would need to have something like:
>>
>> logs = {('gas', 'cell_mass'): False}
>>
>> profile = yt.create_profile(gal,
>>                             [('index', 'cylindrical_r')],          # the
>> bin field
>>                             [('gas', 'cell_mass')],  # profile field
>>                             weight_field=None, logs=logs)
>>
>>
>>>
>>> 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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