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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>
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<item>
            <title>[PIPE2D-856] bootstrapDetectorMap fails with recent SuNSS m data</title>
                <link>https://pfspipe.ipmu.jp/jira/browse/PIPE2D-856</link>
                <project id="10002" key="PIPE2D">DRP 2-D Pipeline</project>
                    <description>&lt;p&gt;A recent problem occurred when trying to process SuNSS &lt;tt&gt;m&lt;/tt&gt;-band data. Details below.&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;
root INFO: Running: /tigress/hassans/software/drp_stella/bin/bootstrapDetectorMap.py /projects/HSC/PFS/Subaru/ --calib /projects/HSC/PFS/Subaru&lt;span class=&quot;code-comment&quot;&gt;//CALIB-SuNSS-2021-06-16 --rerun hassan/mband5 --flatId visit=63050 arm=m --arcId visit=63106 arm=m -c isr.doDark=False
&lt;/span&gt;WARNING: You are using OpenBLAS with multiple threads (40), but have not
specified the number of threads using one of the OpenBLAS environment variables:
OPENBLAS_NUM_THREADS, GOTO_NUM_THREADS, OMP_NUM_THREADS.
This may indicate that you are unintentionally using multiple threads, which may
cause problems. WE HAVE THEREFORE DISABLED OpenBLAS THREADING. If you know
what you are doing and want threads enabled implicitly, set the environment
variable LSST_ALLOW_IMPLICIT_THREADS.
bootstrap.isr INFO: Performing ISR on sensor {&lt;span class=&quot;code-quote&quot;&gt;&apos;visit&apos;&lt;/span&gt;: 63050, &lt;span class=&quot;code-quote&quot;&gt;&apos;arm&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;m&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;dateObs&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;2021-06-11&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;site&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;S&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;category&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;A&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;spectrograph&apos;&lt;/span&gt;: 1, &lt;span class=&quot;code-quote&quot;&gt;&apos;field&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;SEEING_TEST&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;ccd&apos;&lt;/span&gt;: 1, &lt;span class=&quot;code-quote&quot;&gt;&apos;filter&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;m&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;expTime&apos;&lt;/span&gt;: 8.0, &lt;span class=&quot;code-quote&quot;&gt;&apos;dataType&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;DOMEFLAT&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;taiObs&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;2021-06-11T20:30:55.814&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;pfsDesignId&apos;&lt;/span&gt;: 3735928559, &lt;span class=&quot;code-quote&quot;&gt;&apos;slitOffset&apos;&lt;/span&gt;: 0.0}
bootstrap.isr INFO: Converting exposure to floating point values
bootstrap.isr INFO: Assembling CCD from amplifiers
bootstrap.isr INFO: Applying bias correction.
bootstrap.isr INFO: Masking defects.
bootstrap.isr INFO: Masking NAN value pixels.
bootstrap.isr INFO: Widening saturation trails.
bootstrap.isr INFO: Interpolating masked pixels.
bootstrap.isr WARN: No rough magnitude zero point set &lt;span class=&quot;code-keyword&quot;&gt;for&lt;/span&gt; filter m
bootstrap.isr INFO: Setting rough magnitude zero point: 30.257725
bootstrap.profiles WARN: Failed to identify 221 fiberIds: [6, 9, 12, 15, 18, 21, 24, 27, 30, 32, 35, 38, 41, 49, 52, 55, 58, 61, 63, 66, 69, 72, 75, 78, 81, 84, 87, 90, 95, 98, 101, 104, 107, 110, 113, 116, 119, 122, 127, 130, 133, 141, 144, 147, 150, 153, 159, 182, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 208, 210, 212, 215, 217, 219, 221, 223, 225, 227, 231, 233, 235, 240, 242, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 266, 268, 270, 275, 278, 281, 284, 287, 290, 293, 296, 299, 302, 304, 306, 308, 311, 313, 338, 341, 344, 347, 349, 351, 354, 357, 360, 363, 366, 369, 372, 375, 378, 381, 385, 387, 389, 391, 393, 395, 397, 399, 401, 403, 406, 408, 410, 413, 415, 417, 419, 421, 423, 425, 429, 431, 433, 436, 438, 440, 443, 445, 447, 449, 451, 453, 457, 459, 461, 464, 466, 468, 474, 477, 479, 482, 485, 488, 491, 494, 497, 500, 502, 504, 506, 508, 510, 512, 514, 518, 520, 522, 525, 527, 529, 532, 535, 537, 540, 543, 546, 549, 552, 555, 558, 563, 565, 567, 570, 572, 574, 576, 579, 582, 585, 587, 589, 592, 595, 598, 601, 604, 612, 615, 618, 621, 623, 625, 627, 630, 632, 634, 636, 639, 642, 645, 647, 649]
bootstrap.profiles INFO: Profiled 254 fibers
bootstrap FATAL: Failed on dataId={&lt;span class=&quot;code-quote&quot;&gt;&apos;visit&apos;&lt;/span&gt;: 63050, &lt;span class=&quot;code-quote&quot;&gt;&apos;arm&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;m&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;dateObs&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;2021-06-11&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;site&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;S&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;category&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;A&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;spectrograph&apos;&lt;/span&gt;: 1, &lt;span class=&quot;code-quote&quot;&gt;&apos;field&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;SEEING_TEST&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;ccd&apos;&lt;/span&gt;: 1, &lt;span class=&quot;code-quote&quot;&gt;&apos;filter&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;m&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;expTime&apos;&lt;/span&gt;: 8.0, &lt;span class=&quot;code-quote&quot;&gt;&apos;dataType&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;DOMEFLAT&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;taiObs&apos;&lt;/span&gt;: &lt;span class=&quot;code-quote&quot;&gt;&apos;2021-06-11T20:30:55.814&apos;&lt;/span&gt;, &lt;span class=&quot;code-quote&quot;&gt;&apos;pfsDesignId&apos;&lt;/span&gt;: 3735928559, &lt;span class=&quot;code-quote&quot;&gt;&apos;slitOffset&apos;&lt;/span&gt;: 0.0}: RuntimeError: Mismatch between number of traces (254) and number of fibers (251)
Traceback (most recent call last):
  File &lt;span class=&quot;code-quote&quot;&gt;&quot;/tigress/HSC/PFS/stack/20190925/stack/miniconda3-4.5.12-1172c30/Linux64/pipe_base/18.1.0/python/lsst/pipe/base/cmdLineTask.py&quot;&lt;/span&gt;, line 388, in __call__
    result = self.runTask(task, dataRef, kwargs)
  File &lt;span class=&quot;code-quote&quot;&gt;&quot;/tigress/HSC/PFS/stack/20190925/stack/miniconda3-4.5.12-1172c30/Linux64/pipe_base/18.1.0/python/lsst/pipe/base/cmdLineTask.py&quot;&lt;/span&gt;, line 447, in runTask
    &lt;span class=&quot;code-keyword&quot;&gt;return&lt;/span&gt; task.runDataRef(dataRef, **kwargs)
  File &lt;span class=&quot;code-quote&quot;&gt;&quot;/tigress/hassans/software/drp_stella/python/pfs/drp/stella/bootstrap.py&quot;&lt;/span&gt;, line 131, in runDataRef
    traces = self.traceFibers(flatRef, flatConfig)
  File &lt;span class=&quot;code-quote&quot;&gt;&quot;/tigress/hassans/software/drp_stella/python/pfs/drp/stella/bootstrap.py&quot;&lt;/span&gt;, line 172, in traceFibers
    (len(traces), len(indices)))
RuntimeError: Mismatch between number of traces (254) and number of fibers (251)
&lt;/pre&gt;
&lt;/div&gt;&lt;/div&gt;</description>
                <environment></environment>
        <key id="16889">PIPE2D-856</key>
            <summary>bootstrapDetectorMap fails with recent SuNSS m data</summary>
                <type id="1" iconUrl="https://pfspipe.ipmu.jp/jira/secure/viewavatar?size=xsmall&amp;avatarId=10503&amp;avatarType=issuetype">Bug</type>
                                            <priority id="1" iconUrl="https://pfspipe.ipmu.jp/jira/images/icons/priorities/blocker.svg">Blocker</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="hassan">hassan</reporter>
                        <labels>
                            <label>SuNSS</label>
                    </labels>
                <created>Thu, 17 Jun 2021 16:52:37 +0000</created>
                <updated>Thu, 17 Jun 2021 20:35:13 +0000</updated>
                            <resolved>Thu, 17 Jun 2021 20:35:13 +0000</resolved>
                                                                        <due></due>
                            <votes>0</votes>
                                    <watches>2</watches>
                                                                <comments>
                            <comment id="21508" author="rhl" created="Thu, 17 Jun 2021 18:54:17 +0000"  >&lt;p&gt;My guess is that bootstrap hasn&apos;t been run since we labelled the three broken fibres in SuNSS (251 is the number of illuminated fibres; &#160;there are 254 in the pfsConfig)&lt;/p&gt;</comment>
                            <comment id="21509" author="price" created="Thu, 17 Jun 2021 19:08:47 +0000"  >&lt;p&gt;As &lt;a href=&quot;https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=rhl&quot; class=&quot;user-hover&quot; rel=&quot;rhl&quot;&gt;rhl&lt;/a&gt; suspected, the problem was that we&apos;re finding traces for broken fibers.&lt;/p&gt;

&lt;p&gt;The fix requires &lt;a href=&quot;https://pfspipe.ipmu.jp/jira/browse/PIPE2D-770&quot; title=&quot;Support sub-selection of pfsConfig&quot; class=&quot;issue-link&quot; data-issue-key=&quot;PIPE2D-770&quot;&gt;&lt;del&gt;PIPE2D-770&lt;/del&gt;&lt;/a&gt; and &lt;a href=&quot;https://pfspipe.ipmu.jp/jira/browse/PIPE2D-762&quot; title=&quot;pfsConfig.selectFiber returns a transposed array with an extra dimension&quot; class=&quot;issue-link&quot; data-issue-key=&quot;PIPE2D-762&quot;&gt;&lt;del&gt;PIPE2D-762&lt;/del&gt;&lt;/a&gt;.&lt;/p&gt;</comment>
                            <comment id="21518" author="hassan" created="Thu, 17 Jun 2021 20:18:16 +0000"  >&lt;p&gt;&lt;tt&gt;bootstrapDetectorMap&lt;/tt&gt; runs to completion with these fixes.&lt;/p&gt;</comment>
                            <comment id="21519" author="hassan" created="Thu, 17 Jun 2021 20:18:52 +0000"  >&lt;p&gt;Updates made in pull request look fine to me.&lt;/p&gt;</comment>
                            <comment id="21520" author="price" created="Thu, 17 Jun 2021 20:35:13 +0000"  >&lt;p&gt;Merged.&lt;/p&gt;</comment>
                    </comments>
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