[yt-users] Column density plot
Stephanie Tonnesen
stonnes at gmail.com
Tue Nov 4 17:05:22 PST 2014
Definitely will! Must wait a couple hrs until little one asleep. Will let
you know when done
On Tuesday, November 4, 2014, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> I've updated the pull request I created earlier for John Regan's issue to
> include a fix for this, since they're related:
> https://bitbucket.org/yt_analysis/yt/pull-request/1292/ensure-profiled-data-are-in-the-correct/diff
>
> Would you mind giving it a test drive?
>
> On Tue, Nov 4, 2014 at 1:39 PM, Nathan Goldbaum <nathan12343 at gmail.com
> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>
>>
>>
>> On Tue, Nov 4, 2014 at 1:37 PM, Stephanie Tonnesen <stonnes at gmail.com
>> <javascript:_e(%7B%7D,'cvml','stonnes at gmail.com');>> wrote:
>>
>>> 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'
>>>
>>>
>> This looks like a bug. Can you file an issue? It would be great if you
>> included a script exhibiting the behavior that makes use of one of the
>> public datasets on yt-project.org/data
>>
>>
>>>
>>> --
>>> Dr. Stephanie Tonnesen
>>> Alvin E. Nashman Postdoctoral Fellow
>>> Carnegie Observatories, Pasadena, CA
>>> stonnes at gmail.com <javascript:_e(%7B%7D,'cvml','stonnes at gmail.com');>
>>>
>>> On Tue, Nov 4, 2014 at 1:31 PM, Nathan Goldbaum <nathan12343 at gmail.com
>>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>>>
>>>>
>>>>
>>>> On Tue, Nov 4, 2014 at 1:29 PM, Stephanie Tonnesen <stonnes at gmail.com
>>>> <javascript:_e(%7B%7D,'cvml','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 <javascript:_e(%7B%7D,'cvml','stonnes at gmail.com');>
>>>>>
>>>>> On Tue, Nov 4, 2014 at 12:32 PM, Nathan Goldbaum <
>>>>> nathan12343 at gmail.com
>>>>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Nov 4, 2014 at 12:26 PM, Stephanie Tonnesen <
>>>>>> stonnes at gmail.com <javascript:_e(%7B%7D,'cvml','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
>>>>>>> <javascript:_e(%7B%7D,'cvml','stonnes at gmail.com');>
>>>>>>>
>>>>>>> On Tue, Nov 4, 2014 at 11:10 AM, Nathan Goldbaum <
>>>>>>> nathan12343 at gmail.com
>>>>>>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Nov 4, 2014 at 10:59 AM, Stephanie Tonnesen <
>>>>>>>> stonnes at gmail.com
>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>> <javascript:_e(%7B%7D,'cvml','stonnes at gmail.com');>
>>>>>>>>>
>>>>>>>>> On Mon, Nov 3, 2014 at 9:45 PM, Suoqing JI <
>>>>>>>>> suoqing at physics.ucsb.edu
>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Nov 3, 2014 at 5:29 PM, Suoqing JI <
>>>>>>>>>> suoqing at physics.ucsb.edu
>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','stonnes at gmail.com');>
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>
--
--
Dr. Stephanie Tonnesen
Alvin E. Nashman Postdoctoral Fellow
Carnegie Observatories, Pasadena, CA
stonnes at gmail.com
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