[yt-users] Column density plot

Stephanie Tonnesen stonnes at gmail.com
Tue Nov 4 13:37:08 PST 2014


I want the cylindrical_r bins to be in linear space.  When I do just the
first line, I still get everything in log space.  When I include
"logs=logs" in the profile call, it crashes.

alld = ds.all_data()
gal = alld.cut_region("obj['density'] > 1.01e-28")
logs = {('index', 'cylindrical_r'): False}
#logs = {('gas', 'cell_mass'): False}
profile = yt.create_profile(gal,
                            [('index', 'cylindrical_r')],          # the
bin field
                            [('gas', 'cell_mass')],  # profile field
                            weight_field=None, n_bins=17,logs=logs)
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

---------------------------------------------------------------------------KeyError
                                 Traceback (most recent call
last)<ipython-input-23-a4ffd8615abf> in <module>()      6
               [('index', 'cylindrical_r')],          # the bin field
    7                             [('gas', 'cell_mass')],  # profile
field----> 8                             weight_field=None,
n_bins=17,logs=logs)      9 coldens =
profile["gas","cell_mass"]/1.6733e-24     10 coldens[0] =
coldens[0]/(3.14159*profile.x[0]*profile.x[0])
/Users/stephanietonnesen/yt-x86_64/src/yt-hg/yt/data_objects/profiles.pyc
in create_profile(data_source, bin_fields, fields, n_bins, extrema,
logs, units, weight_field, accumulation, fractional)   1326
     for f in bin_fields]   1327     else:-> 1328         logs =
[logs[bin_field[-1]] for bin_field in bin_fields]   1329     if
extrema is None:   1330         ex =
[data_source.quantities["Extrema"](f, non_zero=l)
KeyError: 'cylindrical_r'



--
Dr. Stephanie Tonnesen
Alvin E. Nashman Postdoctoral Fellow
Carnegie Observatories, Pasadena, CA
stonnes at gmail.com

On Tue, Nov 4, 2014 at 1:31 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

>
>
> 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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>>>>>>>>
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