<div dir="ltr">Hillary & Pengfei,<div><br></div><div>I'm going to hopefully add to this discussion. I've been working for a little bit on some improvements to the fitting procedure, primarily because I've been interested in being able to fit spectra with specified uncertainties and a significant amount of noise. </div>
<div><br></div><div>Although down the line my (quite extensive) modifications to the fitting procedure may be problematic to merge with the main repo, I would be very interested in obtaining a new test case to try out my version on. Even though my modifications were in the context of noisy spectra, they still may perform well in dealing with the strange results you are seeing.</div>
<div><br></div><div>I may or may not be of help here, but if you don't mind sending your absorption spectra over to me to test it out I would appreciate it. The turnaround time on this may be long, but I should be able to get to play around with it soon and let you know what happens.</div>
<div><br></div><div>If things go well, I'll point you to my fork where you can obtain the modifications I've made.</div><div><br></div><div><br></div><div><br></div><div>Andrew E.</div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Wed, Mar 5, 2014 at 10:30 AM, Hilary Egan <span dir="ltr"><<a href="mailto:hilaryye@gmail.com" target="_blank">hilaryye@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Pengfei,<div><br></div><div>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. </div>
<div><br></div><div>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. </div>
<div><br></div><div>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.</div>
<span class="HOEnZb"><font color="#888888">
<div><br></div><div>-Hilary</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Mar 4, 2014 at 11:32 PM, Pengfei Chen <span dir="ltr"><<a href="mailto:madcpf@gmail.com" target="_blank">madcpf@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Hilary,<div><br></div><div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">
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. </div>
<div style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br></div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">Thank you very much for your effort in fixing this! Please tell me if you need any test data from me.</div>
<span><font color="#888888">
</font></span></div><span><font color="#888888"><div style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br></div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">Pengfei</div>
</font></span></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Fri, Feb 14, 2014 at 3:30 PM, Pengfei Chen <span dir="ltr"><<a href="mailto:madcpf@gmail.com" target="_blank">madcpf@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Hilary,<div><br></div><div>Thank you! I'm looking forward to it.</div><span><font color="#888888"><div><br></div><div>Pengfei</div></font></span></div><div><div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Feb 13, 2014 at 7:32 PM, Hilary Egan <span dir="ltr"><<a href="mailto:hilaryye@gmail.com" target="_blank">hilaryye@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Pengfei,<div><br></div><div>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.</div>
<div><br></div><div>-Hilary</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Thu, Feb 13, 2014 at 8:04 PM, Pengfei Chen <span dir="ltr"><<a href="mailto:madcpf@gmail.com" target="_blank">madcpf@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Hi all,</span><div>
<font face="arial, sans-serif"><br>
</font><div style="font-family:arial,sans-serif;font-size:13px">I've used the<br><br>yt.analysis_modules.absorption_spectrum.absorption_spectrum_fit<br>
<br>script to fit an Lya absorption spectrum generated by yt.</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">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:</div>
<div style="font-family:arial,sans-serif;font-size:13px"><div><div><br></div><div>HI_parameters = {'name':'HI',</div><div> 'f': [.4164],</div><div> 'Gamma':[6.265E8],</div>
<div> 'wavelength':[1215.67],</div><div> 'numLines':1,</div><div> 'maxN': 1E22, 'minN':1E11,</div><div><div> 'maxb': 300, 'minb':1,</div>
<div> 'maxz': 5, 'minz':0,</div></div><div> 'init_b':40,</div><div> 'init_N':1E14}</div></div></div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">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. </div>
<div style="font-family:arial,sans-serif;font-size:13px"><div><br></div></div><div style="font-family:arial,sans-serif;font-size:13px">Please tell me if you need any datasets.</div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">Thank you!</div></div><span><font color="#888888"><div style="font-family:arial,sans-serif;font-size:13px">Pengfei</div></font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div style="font-family:arial;font-size:small">Graduate Student </div><div style="font-family:arial;font-size:small">Columbia University</div>
<div style="font-family:arial;font-size:small">Department of Astronomy</div></div>
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