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    <title>PFS-JIRA</title>
    <link>https://pfspipe.ipmu.jp/jira</link>
    <description>This file is an XML representation of an issue</description>
    <language>en-us</language>    <build-info>
        <version>8.3.4</version>
        <build-number>803005</build-number>
        <build-date>13-09-2019</build-date>
    </build-info>


<item>
            <title>[PIPE2D-411] reduceArc.py does not work with --config reduceExposure.doSubtractContinuum=True reduceExposure.doWriteCalexp=True</title>
                <link>https://pfspipe.ipmu.jp/jira/browse/PIPE2D-411</link>
                <project id="10002" key="PIPE2D">DRP 2-D Pipeline</project>
                    <description>&lt;p&gt;reduceArc.py seems to fail with the config parameters&lt;/p&gt;
 &lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt; --config reduceExposure.doSubtractContinuum=True reduceExposure.doWriteCalexp=True&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;

&lt;p&gt;Note that at the moment reduceArc passes without these config parameters specified,  but it creates psfArm file that is 0 bytes for the first visit id. If more values for visit id are passed, psfArm files that have non-zero size are created for the non-initial visits. This is described in comments of &lt;a href=&quot;https://pfspipe.ipmu.jp/jira/browse/PIPE2D-339&quot; title=&quot;Model arc line amplitudes&quot; class=&quot;issue-link&quot; data-issue-key=&quot;PIPE2D-339&quot;&gt;&lt;del&gt;PIPE2D-339&lt;/del&gt;&lt;/a&gt;. Perhaps fixing that issue will fix this one as well.&lt;/p&gt;

&lt;p&gt;With pfs_pipe2d 5.0-10-gff9a74e and checkout of tickets/&lt;a href=&quot;https://pfspipe.ipmu.jp/jira/browse/PIPE2D-404&quot; title=&quot;Support for raw exposures with W_PFDSGN not set&quot; class=&quot;issue-link&quot; data-issue-key=&quot;PIPE2D-404&quot;&gt;&lt;del&gt;PIPE2D-404&lt;/del&gt;&lt;/a&gt;, on tigress, this works :&lt;/p&gt;
&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;reduceArc.py /tigress/ncaplar/ReducedData/HgArFeb_2019 --calib /tigress/ncaplar/ReducedData/HgArFeb_2019/CALIB --rerun Apr25_2019_reduce_subtract/arc --id visit=11748..11753 -j 20&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;

&lt;p&gt;while this does not:&lt;/p&gt;
&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;
reduceArc.py /tigress/ncaplar/ReducedData/HgArFeb_2019 --calib /tigress/ncaplar/ReducedData/HgArFeb_2019/CALIB --rerun Apr25_2019_reduce_subtract/arc --id visit=11748..11753 -j 20 --config reduceExposure.doSubtractContinuum=True reduceExposure.doWriteCalexp=True &lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;</description>
                <environment></environment>
        <key id="13543">PIPE2D-411</key>
            <summary>reduceArc.py does not work with --config reduceExposure.doSubtractContinuum=True reduceExposure.doWriteCalexp=True</summary>
                <type id="1" iconUrl="https://pfspipe.ipmu.jp/jira/secure/viewavatar?size=xsmall&amp;avatarId=10503&amp;avatarType=issuetype">Bug</type>
                                            <priority id="10000" iconUrl="https://pfspipe.ipmu.jp/jira/images/icons/priorities/medium.svg">Normal</priority>
                        <status id="10002" iconUrl="https://pfspipe.ipmu.jp/jira/images/icons/statuses/generic.png" description="The issue is resolved, reviewed, and merged">Done</status>
                    <statusCategory id="3" key="done" colorName="green"/>
                                    <resolution id="10000">Done</resolution>
                                        <assignee username="price">price</assignee>
                                    <reporter username="ncaplar">ncaplar</reporter>
                        <labels>
                    </labels>
                <created>Fri, 26 Apr 2019 16:20:22 +0000</created>
                <updated>Wed, 1 May 2019 13:27:31 +0000</updated>
                            <resolved>Tue, 30 Apr 2019 14:42:13 +0000</resolved>
                                                                        <due></due>
                            <votes>0</votes>
                                    <watches>3</watches>
                                                                <comments>
                            <comment id="15371" author="price" created="Fri, 26 Apr 2019 19:26:36 +0000"  >&lt;p&gt;I believe I&apos;ve fixed this on branch &lt;tt&gt;tickets/&lt;a href=&quot;https://pfspipe.ipmu.jp/jira/browse/PIPE2D-411&quot; title=&quot;reduceArc.py does not work with --config reduceExposure.doSubtractContinuum=True reduceExposure.doWriteCalexp=True&quot; class=&quot;issue-link&quot; data-issue-key=&quot;PIPE2D-411&quot;&gt;&lt;del&gt;PIPE2D-411&lt;/del&gt;&lt;/a&gt;&lt;/tt&gt; of drp_stella. (There&apos;s also a tiny fix to pfs_pipe2d which is related but not necessary to fix it.)&lt;/p&gt;

&lt;p&gt;&lt;a href=&quot;https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=ncaplar&quot; class=&quot;user-hover&quot; rel=&quot;ncaplar&quot;&gt;ncaplar&lt;/a&gt;, please let me know if this fixes it for you.&lt;/p&gt;</comment>
                            <comment id="15378" author="ncaplar" created="Fri, 26 Apr 2019 21:07:18 +0000"  >&lt;p&gt;&lt;a href=&quot;https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=price&quot; class=&quot;user-hover&quot; rel=&quot;price&quot;&gt;price&lt;/a&gt; Good news - this fixes the problem raised in &lt;a href=&quot;https://pfspipe.ipmu.jp/jira/browse/PIPE2D-339&quot; title=&quot;Model arc line amplitudes&quot; class=&quot;issue-link&quot; data-issue-key=&quot;PIPE2D-339&quot;&gt;&lt;del&gt;PIPE2D-339&lt;/del&gt;&lt;/a&gt;, (first visit psfArm has 0 bytes). Bad news - it does not seem to fix problem raised in this ticket, i.e., the problem when one tries to run reduceArc with &lt;/p&gt;
&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;reduceExposure.doSubtractContinuum=True &lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;

&lt;p&gt;I have place the output which ends with reduceArc FATAL at &lt;a href=&quot;https://gist.github.com/nevencaplar/6b618c5360ac84f1c3751d2969f1b1ea&quot; class=&quot;external-link&quot; rel=&quot;nofollow&quot;&gt;https://gist.github.com/nevencaplar/6b618c5360ac84f1c3751d2969f1b1ea&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;NOTE: I only did checkout of drp_stella, and left pfs_pipe2d at ticket/404&lt;/p&gt;</comment>
                            <comment id="15383" author="price" created="Sat, 27 Apr 2019 01:40:15 +0000"  >&lt;p&gt;I can&apos;t reproduce this with the simulated data, so it seems to be peculiar to the LAM data. The error seems to be due to a bad wavelength solution, and because this is before we do a fit on the arc, I&apos;m suspicious of the detectorMap. Which detectorMap are you using?&lt;br/&gt;
I see two in your calibs directory, but according to the calib registry the only one active is &lt;tt&gt;pfsDetectorMap-011748-r1.fits&lt;/tt&gt;, and that one is indeed non-monotonic. That looks like it was put together from LAM data, but it&apos;s not clear to me how it was made. Perhaps it was over-fit or there weren&apos;t a lot of lines, leading to non-monotonicity at the ends? Do you have the log from its creation?&lt;/p&gt;

&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;
&amp;gt;&amp;gt;&amp;gt; &lt;span class=&quot;code-keyword&quot;&gt;import&lt;/span&gt; numpy as np
&amp;gt;&amp;gt;&amp;gt; &lt;span class=&quot;code-keyword&quot;&gt;import&lt;/span&gt; pfs.drp.stella
&amp;gt;&amp;gt;&amp;gt; detMap = pfs.drp.stella.DetectorMap.readFits(&lt;span class=&quot;code-quote&quot;&gt;&quot;DETECTORMAP/pfsDetectorMap-011748-r1.fits&quot;&lt;/span&gt;)
&amp;gt;&amp;gt;&amp;gt; [np.all(ww[1:] - ww[:-1] &amp;gt; 0) or np.all(ww[1:] - ww[:-1] &amp;lt; 0) &lt;span class=&quot;code-keyword&quot;&gt;for&lt;/span&gt; ww in detMap.wavelength]
[True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True]
&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;</comment>
                            <comment id="15391" author="ncaplar" created="Sat, 27 Apr 2019 18:02:21 +0000"  >&lt;p&gt;I am not surprised that there are differences between simulated and LAM data &lt;img class=&quot;emoticon&quot; src=&quot;https://pfspipe.ipmu.jp/jira/images/icons/emoticons/smile.png&quot; height=&quot;16&quot; width=&quot;16&quot; align=&quot;absmiddle&quot; alt=&quot;&quot; border=&quot;0&quot;/&gt;&lt;/p&gt;

&lt;p&gt;I have placed the whole script at &lt;a href=&quot;https://gist.github.com/nevencaplar/6a01956f33bcc5e249c57f674f8ee67d&quot; class=&quot;external-link&quot; rel=&quot;nofollow&quot;&gt;https://gist.github.com/nevencaplar/6a01956f33bcc5e249c57f674f8ee67d&lt;/a&gt;. I should have done immediately.  As you can see inside that I am using &lt;/p&gt;
&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;ingestCalibs.py $TARGET --calib $TARGET/CALIB --validity 1800 \
		$OBS_PFS_DIR/pfs/camera/detectorMap-sim-1-r.fits --mode=copy --config clobber=True || exit 1&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;
&lt;p&gt; I was under the impression that that is what we were supposed do use that as a starting point? I believe that &lt;a href=&quot;https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=naoki.yasuda&quot; class=&quot;user-hover&quot; rel=&quot;naoki.yasuda&quot;&gt;naoki.yasuda&lt;/a&gt; is also using detectorMap-sim-1-r?&lt;/p&gt;

&lt;p&gt;Final note, as this is a script modified from integration_test, there is a line inside with &lt;/p&gt;
&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;rm -rf $TARGET&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;
&lt;p&gt; which means that if you just use it out of the box, you will have to use recreate everything from scratch, which might not be something that you wish to do.&lt;/p&gt;

&lt;p&gt;I do not have any extra files which are not in the directory ( /tigress/ncaplar/ReducedData/HgArFeb_2019/) which is specified in the gist from the previous comment (&lt;a href=&quot;https://gist.github.com/nevencaplar/6b618c5360ac84f1c3751d2969f1b1ea&quot; class=&quot;external-link&quot; rel=&quot;nofollow&quot;&gt;https://gist.github.com/nevencaplar/6b618c5360ac84f1c3751d2969f1b1ea&lt;/a&gt;).&lt;/p&gt;</comment>
                            <comment id="15400" author="price" created="Mon, 29 Apr 2019 18:50:17 +0000"  >&lt;p&gt;Ah, &lt;tt&gt;obs_pfs/pfs/camera/detectorMap-sim-1-r.fits&lt;/tt&gt; is bad. I hadn&apos;t remembered that it was there when I discovered it had problems. The detector maps on master in drp_stella_data are better. I&apos;ll try them out and see how they do in this case.&lt;/p&gt;</comment>
                            <comment id="15401" author="price" created="Mon, 29 Apr 2019 19:04:20 +0000"  >&lt;p&gt;I copied &lt;tt&gt;/tigress/ncaplar/ReducedData/HgArFeb_2019/CALIB&lt;/tt&gt;, deleted the detectorMap files and entries in the &lt;tt&gt;calibRegistry.sqlite3&lt;/tt&gt; and then:&lt;/p&gt;

&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;
pprice@tiger2-sumire:/tigress/pprice/pipe2d-411 $ ingestCalibs.py /tigress/ncaplar/ReducedData/HgArFeb_2019 --calib CALIB ../drp_stella_data/raw/detectorMap-sim-*.fits --validity 1000 --mode=copy
pprice@tiger2-sumire:/tigress/pprice/pipe2d-411 $ reduceArc.py /tigress/ncaplar/ReducedData/HgArFeb_2019 --calib CALIB --output out --id visit=11748..11753 -j 8 --config reduceExposure.doSubtractContinuum=True reduceExposure.doWriteCalexp=True
&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;

&lt;p&gt;And that worked just fine. I&apos;ll copy the good detector maps over, and we should be good to go.&lt;/p&gt;</comment>
                            <comment id="15404" author="price" created="Mon, 29 Apr 2019 19:12:59 +0000"  >&lt;p&gt;OK, &lt;a href=&quot;https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=ncaplar&quot; class=&quot;user-hover&quot; rel=&quot;ncaplar&quot;&gt;ncaplar&lt;/a&gt;, this is ready for review, please.&lt;/p&gt;

&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;
price@MacBook:~/pfs/obs_pfs/pfs/camera (tickets/PIPE2D-411=) $ cd ~/pfs/obs_pfs/price@MacBook:~/pfs/obs_pfs (tickets/PIPE2D-411=) $ git sub
commit a1553397b7684c97ec8e525ec6463d75d7163587 (HEAD -&amp;gt; tickets/PIPE2D-411, origin/tickets/PIPE2D-411)
Author: Paul Price &amp;lt;price@astro.princeton.edu&amp;gt;
Date:   Mon Apr 29 15:07:25 2019 -0400

    replace bad detectorMap with better ones
    
    The pfs/camera/detectorMap-sim-1-r.fits file comes from when I
    was over-fitting the wavelength solution, and it has
    non-monotonic wavelength solutions that &lt;span class=&quot;code-keyword&quot;&gt;break&lt;/span&gt; continuum
    subtraction in reduceArc (reduceExposure.doSubtractContinuum=True).
    
    These detectorMaps (red and blue) were generated from the
    simulator, and I&apos;ve found they are much more reliable than
    the old one.

 pfs/camera/detectorMap-sim-1-r.fits | Bin 80205120 -&amp;gt; 0 bytes
 pfs/camera/detectorMap-sim-b1.fits  | Bin 0 -&amp;gt; 1465920 bytes
 pfs/camera/detectorMap-sim-r1.fits  | Bin 0 -&amp;gt; 1431360 bytes
 3 files changed, 0 insertions(+), 0 deletions(-)



price@MacBook:~/pfs/drp_stella (tickets/PIPE2D-411 %=) $ git sub
commit 149a73f1b06165d0d899ca7f085817c067775933 (HEAD -&amp;gt; tickets/PIPE2D-411, origin/tickets/PIPE2D-411)
Author: Paul Price &amp;lt;price@astro.princeton.edu&amp;gt;
Date:   Fri Apr 26 15:22:07 2019 -0400

    SpectrumSet: fix writeFits when used through the butler
    
    The butler gives us a temporary filename that we&apos;re supposed to
    write to, and then it moves it to the correct place. We were
    writing to the correct place, and then the empty temporary file
    was being written over the top. Instead, write to the filename
    we&apos;re given.

 python/pfs/drp/stella/SpectrumSetContinued.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)
&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;</comment>
                            <comment id="15405" author="ncaplar" created="Mon, 29 Apr 2019 23:15:15 +0000"  >&lt;p&gt;1. I have placed outputs of the pipeline for all 4 datasets in the Figure.&lt;/p&gt;

&lt;p&gt;2. I ran the whole pipeline again for HgAr data for which I want to run reduceArc.py with &lt;/p&gt;
&lt;div class=&quot;code panel&quot; style=&quot;border-width: 1px;&quot;&gt;&lt;div class=&quot;codeContent panelContent&quot;&gt;
&lt;pre class=&quot;code-java&quot;&gt;reduceExposure.doSubtractContinuum=True&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;
&lt;p&gt; I had to run again because I inadvertently deleted detectorMap tables when messing up with {{calibRegistry.sqlite3 }}.&lt;/p&gt;

&lt;p&gt;With the new fix I still get errors - final output at &lt;a href=&quot;https://gist.github.com/nevencaplar/22769c0b049aef709f3d177f2925252a&quot; class=&quot;external-link&quot; rel=&quot;nofollow&quot;&gt;https://gist.github.com/nevencaplar/22769c0b049aef709f3d177f2925252a&lt;/a&gt;.&lt;br/&gt;
 &lt;span class=&quot;nobr&quot;&gt;&lt;a href=&quot;https://pfspipe.ipmu.jp/jira/secure/attachment/11936/11936_pfs_Apr30_HgAr_Feb+copy.sh&quot; title=&quot;pfs_Apr30_HgAr_Feb copy.sh attached to PIPE2D-411&quot;&gt;pfs_Apr30_HgAr_Feb copy.sh&lt;sup&gt;&lt;img class=&quot;rendericon&quot; src=&quot;https://pfspipe.ipmu.jp/jira/images/icons/link_attachment_7.gif&quot; height=&quot;7&quot; width=&quot;7&quot; align=&quot;absmiddle&quot; alt=&quot;&quot; border=&quot;0&quot;/&gt;&lt;/sup&gt;&lt;/a&gt;&lt;/span&gt; . I have also attached the whole script that I have used (pfs_Apr30_HgAr_Feb copy.sh). &lt;/p&gt;

&lt;p&gt;The only difference is that ran without flat fielding as that takes long time. I would not expect that this creates a problem? I will let pipeline with flat-fielding run over night and report if that passes.&lt;/p&gt;</comment>
                            <comment id="15408" author="ncaplar" created="Tue, 30 Apr 2019 14:42:01 +0000"  >&lt;p&gt;The code passes. The problem are to be captured in the new ticket.&lt;/p&gt;</comment>
                            <comment id="15409" author="price" created="Tue, 30 Apr 2019 14:48:51 +0000"  >&lt;p&gt;Thanks Neven!&lt;/p&gt;

&lt;p&gt;Everything&apos;s merged to master.&lt;/p&gt;</comment>
                    </comments>
                    <attachments>
                            <attachment id="11932" name="HgArFeb.png" size="178556" author="ncaplar" created="Mon, 29 Apr 2019 23:04:24 +0000"/>
                            <attachment id="11933" name="KrFeb.png" size="104867" author="ncaplar" created="Mon, 29 Apr 2019 23:04:24 +0000"/>
                            <attachment id="11934" name="NeonApr.png" size="113204" author="ncaplar" created="Mon, 29 Apr 2019 23:04:25 +0000"/>
                            <attachment id="11935" name="NeonFeb.png" size="136671" author="ncaplar" created="Mon, 29 Apr 2019 23:04:24 +0000"/>
                            <attachment id="11936" name="pfs_Apr30_HgAr_Feb copy.sh" size="5122" author="ncaplar" created="Mon, 29 Apr 2019 23:10:07 +0000"/>
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