[yt-users] Fitting an absorption spectrum

[Pengfei Chen]

Hi Hilary,

Thank you very much for your comments! I'm interested in looking into this
problem. Could you please give me some suggestions about what I need to do?

Thanks,
Pengfei



On Wed, Mar 5, 2014 at 7:30 AM, Hilary Egan <hilaryye at gmail.com> wrote:

> Hi Pengfei,
>
> I'm glad at least some of my fixes worked! I'm not sure whats going on
> with your b-value distributions. I've performed the same analysis for my
> absorption spectra and I dont see anything like the peaks at ~40 km/s that
> you do (see attached). At the high end, I do see a very slight excess of
> absorbers at the high end, but again nothing like what you're showing.
>
> This leads me to the conclusion that the fitting process works well for
> spectra generated like mine, but behaves somewhat poorly for yours. Having
> looked briefly at one example lightray of yours (offlist) I can definitely
> see that yours looks qualitatively different than mine and has a lot more
> lines and those lines are much narrower, although having little idea what
> exactly you're looking at I can't really extrapolate beyond that.
>
> Going forward I can relatively quickly add something that throws away
> lines with these parameters as they're clearly unphysical; however, I'm
> somewhat uncomfortable doing that as its probably an indication of a larger
> problem for a certain class of spectra. I wish I could guarantee that I
> could look at this and completely fix it for you, but I really don't have
> more time to devote to this project at the moment. If you're interested in
> helping look at it I'd be more than happy to point you in the right
> direction and we can chat offlist/in the irc. Otherwise I'll update the
> pull request to just remove those lines, and heavily comment it so any
> future user can remove/play around with it if they're unsatisfied with this
> stop-gap measure.
>
> -Hilary
>
>
> On Tue, Mar 4, 2014 at 11:32 PM, Pengfei Chen <madcpf at gmail.com> wrote:
>
>> Hi Hilary,
>>
>> Thank you very much for your update and I'm sorry for the late reply.
>> I've tested the new code with two datasets. The results are attached. The
>> abnormal peaks in the statistics of N have disappeared, and the abnormal
>> peaks for b are much lower now, but still visible.
>>
>> Thank you very much for your effort in fixing this! Please tell me if you
>> need any test data from me.
>>
>> Pengfei
>>
>>
>> On Fri, Feb 14, 2014 at 3:30 PM, Pengfei Chen <madcpf at gmail.com> wrote:
>>
>>> Hi Hilary,
>>>
>>> Thank you! I'm looking forward to it.
>>>
>>> Pengfei
>>>
>>>
>>> On Thu, Feb 13, 2014 at 7:32 PM, Hilary Egan <hilaryye at gmail.com> wrote:
>>>
>>>> Hi Pengfei,
>>>>
>>>> I have a fix for this issue that just needs a little more testing! I'll
>>>> push it shortly and reply to this message when it's been accepted.
>>>>
>>>> -Hilary
>>>>
>>>>
>>>> On Thu, Feb 13, 2014 at 8:04 PM, Pengfei Chen <madcpf at gmail.com> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I've used the
>>>>>
>>>>> yt.analysis_modules.absorption_spectrum.absorption_spectrum_fit
>>>>>
>>>>> script to fit an Lya absorption spectrum generated by yt.
>>>>>
>>>>> But there are some abnormal peaks when I did statistics of line width
>>>>> b and column density N. Two figures are attached. I've tried with different
>>>>> redshifts and all of them had peaks in b-distribution at init_b (which is
>>>>> 40km/s here) and maxb(which is 300km/s here). For the N-distribution I got
>>>>> peaks around 10^12 cm^-2 at every redshift. The parameters I used were:
>>>>>
>>>>> HI_parameters = {'name':'HI',
>>>>>                  'f': [.4164],
>>>>>                  'Gamma':[6.265E8],
>>>>>                  'wavelength':[1215.67],
>>>>>                  'numLines':1,
>>>>>                  'maxN': 1E22, 'minN':1E11,
>>>>>                  'maxb': 300, 'minb':1,
>>>>>                  'maxz': 5, 'minz':0,
>>>>>                  'init_b':40,
>>>>>                  'init_N':1E14}
>>>>>
>>>>> Could someone please tell me how to solve this? All the analysis were
>>>>> done with the latest development version of yt and I made no changes to the
>>>>> source code.
>>>>>
>>>>> Please tell me if you need any datasets.
>>>>>
>>>>> Thank you!
>>>>> Pengfei
>>>>>
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>>>>>
>>>>>
>>>>
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