https://pfspipe.ipmu.jp/jira This file is an XML representation of an issue en-us 8.3.4 803005 13-09-2019 https://pfspipe.ipmu.jp/jira/browse/PIPE2D-345 DRP 2-D Pipeline <p>Provide a method for estimating the line intensities for 1D spectra.</p> <p>The code should provide a single value for each line, based on the integrated flux about the line centroid as opposed to the line peak value. This way, the effect of line broadening is removed.</p> <p>The code for estimating these line intensities may already be available in the 2D DRP software. This needs to be checked.</p> PIPE2D-345

Provide a method for determining line intensities

Story Normal Done Done price hassan Thu, 7 Feb 2019 21:32:48 +0000 Mon, 28 Oct 2019 18:46:03 +0000 Sat, 26 Oct 2019 19:04:54 +0000 6.0 0 5 <p>You'll probably want to rewrite this in python if the C++ code doesn't just work. We'll need to handle blends at some point &#8211; remember that we know the wavelengths (very?) well.</p> <p>I have not started on this ticket yet, but do you mean there is an existing code in C++?</p> <p>One simple question is whether this method would use LSF or not.</p> <p> </p> <p>There is C++ code, but it dates from Andreas and I don't think it's easy to extend.  It fits a Gaussian, which is good enough for isolated lines but probably/possibly not for blends.</p> <p>I have a python implementation of finding and fitting lines as part of <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-319" title="Make line identification robust against wavelength shifts" class="issue-link" data-issue-key="PIPE2D-319"><del>PIPE2D-319</del></a>.</p> <p>I'm sorry for the delayed response but I have looked at Paul's implementation and it looks good enough.</p> <p>Should we merge this tickets to <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-319" class="external-link" rel="nofollow">PIPE2D-319</a>?</p> <p>I have basically copied Paul's code to python/pfs/drp/stella/SpectrumContinued.py.</p> <p><a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=naoki.yasuda" class="user-hover" rel="naoki.yasuda">naoki.yasuda</a> can you add your updates to the ticket branch for this ticket please? <tt>tickets/<a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-345" title="Provide a method for determining line intensities" class="issue-link" data-issue-key="PIPE2D-345"><del>PIPE2D-345</del></a></tt>.</p> <p><a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=naoki.yasuda" class="user-hover" rel="naoki.yasuda">naoki.yasuda</a> could you create a pull request so that Paul and I can review the code before it is merged to master? Thanks.</p> <p>I suggest extending the new <a href="https://github.com/Subaru-PFS/drp_stella/blob/master/python/pfs/drp/stella/findLines.py" class="external-link" rel="nofollow"><tt>FindLinesTask</tt></a> to return the intensities in addition to the centroids.</p> <p>Following 2D DRP tech telecon 2019-10-14: re-assigned to <a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=price" class="user-hover" rel="price">price</a> . Suggested algorithm makes use of gaussians, which may not be adequate for broadened arc lines. However, if the broadened arc lines are limited (<a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=ncaplar" class="user-hover" rel="ncaplar">ncaplar</a> feels that there should not be more than 5 of such lines) we could remove those lines from the modelling process.</p> <p>I have put a proposed implementation in <tt>u/price/<a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-345" title="Provide a method for determining line intensities" class="issue-link" data-issue-key="PIPE2D-345"><del>PIPE2D-345</del></a></tt> of drp_stella (<a href="https://github.com/Subaru-PFS/drp_stella/pull/84" class="external-link" rel="nofollow">GitHub PR</a>). It's currently on a <tt>u</tt> branch to avoid contaminating the original proposal.</p> <p><a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=naoki.yasuda" class="user-hover" rel="naoki.yasuda">naoki.yasuda</a>, would you please have a look and let me know if this does not meet your needs?</p> <p>There are changes made as part of <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-391" title="Generate fiberTraces from odd/even flats" class="issue-link" data-issue-key="PIPE2D-391"><del>PIPE2D-391</del></a> that move the line fitting into C++ for speed. This will cause some conflicts with the work done here, but should be straightforward to resolve.</p> <p>Thank you. I have reviewed the changes of the code. I think it is fine and very useful for my task. One thing I'm not sure but not so important is that in a function <tt>FindLinesTask.convolve()</tt> there is a line</p> <div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent"> <pre class="code-java"> grow = <span class="code-object">int</span>(self.config.width + 0.5) </pre> </div></div> <p>Why <tt>width</tt> is used instead of <tt>halfSize</tt>?</p> <p>We don't want to grow the masked pixels by the kernel size, because pixels at the edge of the kernel have only a tiny contribution to the convolved value. For the LSST image convolutions, we grow by a single pixel, but maybe that's not ideal, so I've made this configurable.</p> <p>I put your work onto <tt>u/yasuda/<a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-345" title="Provide a method for determining line intensities" class="issue-link" data-issue-key="PIPE2D-345"><del>PIPE2D-345</del></a></tt> and moved my work from <tt>u/price/<a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-345" title="Provide a method for determining line intensities" class="issue-link" data-issue-key="PIPE2D-345"><del>PIPE2D-345</del></a></tt> onto the formal ticket branch, <tt>tickets/<a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-345" title="Provide a method for determining line intensities" class="issue-link" data-issue-key="PIPE2D-345"><del>PIPE2D-345</del></a></tt>.</p> <p><a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=naoki.yasuda" class="user-hover" rel="naoki.yasuda">naoki.yasuda</a>, are you too busy to do a code review, or should I ask someone else?</p> <p>What is the official procedure of code review? In the previous comment, I meant I have reviewed and the code looks fine. Is this not enough?</p> <p>Ah, I thought perhaps you had only considered the idea, and not the actual code. I'll go ahead and merge. Thanks!</p> <p>Merged to master, and tagged 5.1.4.</p> Blocks PIPE2D-339 Relates PIPE2D-319 Development Rank 0|02qpt6:508yl03z09 Reviewers naoki.yasuda Sprint 2DDRP-2019 C 2DDRP-2019 D 2DDRP-2019 E 2DDRP-2019 F 2DDRP-2019 G 2DDRP-2019 H Story Points 4.0