[yt-users] Column density plot
Nathan Goldbaum
nathan12343 at gmail.com
Wed Nov 5 14:24:03 PST 2014
On Tue, Nov 4, 2014 at 9:16 PM, Stephanie Tonnesen <stonnes at gmail.com>
wrote:
> Dear Nathan,
>
> Looks great! Thanks so much!
>
> So once it is officially commited, I should be able to just type hg update
> and it will update? What folder do I need to be in for that to happen (it
> keeps on saying no .hg file is not in the folder).
>
The PR has been merged. You should be able to get the update by doing "yt
update" at the command line.
If you want to do it manually, you'll need to "hg pull" before you "hg
update". "yt update" is just automating the hg workflow.
>
>
> -Stephanie
>
> --
> Dr. Stephanie Tonnesen
> Alvin E. Nashman Postdoctoral Fellow
> Carnegie Observatories, Pasadena, CA
> stonnes at gmail.com
>
> On Tue, Nov 4, 2014 at 5:05 PM, Stephanie Tonnesen <stonnes at gmail.com>
> wrote:
>
>> 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>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Tue, Nov 4, 2014 at 1:37 PM, Stephanie Tonnesen <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
>>>>>
>>>>> 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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>>>
>>
>> --
>> --
>> Dr. Stephanie Tonnesen
>> Alvin E. Nashman Postdoctoral Fellow
>> Carnegie Observatories, Pasadena, CA
>> stonnes at gmail.com
>>
>>
>
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