PFS-JIRA

PFS-JIRA https://pfspipe.ipmu.jp/jira This file is an XML representation of an issue en-us

8.3.4

803005

13-09-2019

[PIPE2D-100] Please address code review issues with PIPE2D-48 https://pfspipe.ipmu.jp/jira/browse/PIPE2D-100 DRP 2-D Pipeline PIPE2D-100

Please address code review issues with PIPE2D-48

Story Major Done Done aritter aritter Wed, 12 Oct 2016 03:23:45 +0000 Thu, 22 Jun 2017 21:30:56 +0000 Thu, 22 Jun 2017 21:30:56 +0000 0 1 These are the original comments in <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-48" title="Change extraction tasks to read FiberTrace parameters from disk" class="issue-link" data-issue-key="PIPE2D-48"><del>PIPE2D-48</del></a>: <div class="panel" style="border-width: 1px;"><div class="panelContent"> <ol> <li>Please remove personal entries from .gitignore</li> <li>There should be no config overrides in runPipeline</li> <li>Please move runPipeline to examples</li> <li>Please put all white-space only changes into a separate commit, and label it appropriately</li> <li>Check that the memory is contiguous for all the data in a given fibre. If you need to transpose, please add a note to <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-35" title="Read & write 2-D outputs according to the data model " class="issue-link" data-issue-key="PIPE2D-35"><del>PIPE2D-35</del></a></li> <li>Please don't comment out templates; remove them</li> <li>Remove all cout << statements; use logging (including tracing as appropriate)</li> <li>remove all python print statements to use log</li> <li>How many info logs should become debug?</li> <li>Please remove all if False blocks. If they are possibly useful control them with variables (probably set by LsstDebug)</li> <li>There's no need to specify the wavelength files on the command line.</li> <li>Please factor the I/O into separate functions, and don't read it for every exposure</li> <li>Use "not success" not "success == False"</li> <li>What do comments like "THIS DOESN'T WORK" mean?</li> <li>Please remove all commented out code</li> <li>Use np.empty((N, M)) not np.array(shape=(N, M))</li> <li>Explain shape for wLenTemp</li> <li>Use k += 1 not k = k + 1</li> <li>Use # not """ ... """ for comments</li> <li>Things like getAllFluxes() should not need to make a copy if you get the column/row major right</li> <li>Split Spectra.py tests into separate tests if you might not want to run them (and then use a skip decorator)</li> </ol> </div></div> 1. Please remove personal entries from .gitignore: done 2. There should be no config overrides in runPipeline: already happened 3. Please move runPipeline to examples already happened 4. Please put all white-space only changes into a separate commit, and label it appropriately: filed ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-166" title="Remove all remaining trailing spaces" class="issue-link" data-issue-key="PIPE2D-166"><del>PIPE2D-166</del></a> and put white-space change commits there 5. Check that the memory is contiguous for all the data in a given fibre. If you need to transpose, please add a note to <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-35" title="Read & write 2-D outputs according to the data model " class="issue-link" data-issue-key="PIPE2D-35"><del>PIPE2D-35</del></a>: I checked all class variables in <tt>FiberTrace</tt> and <tt>Spectrum</tt> visually if the storage order makes sense and could not find any problems 6. Please don't comment out templates; remove them I filed ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-167" title="Remove all commented out code" class="issue-link" data-issue-key="PIPE2D-167"><del>PIPE2D-167</del></a> and moved commits which remove commented out lines there 7. Remove all <tt>cout <<</tt> statements; use logging (including tracing as appropriate): I filed ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-165" title="Replace {{cout <<}} and {{print}} with appropriate LSST log messages" class="issue-link" data-issue-key="PIPE2D-165"><del>PIPE2D-165</del></a> and moved commits there 8. remove all python print statements to use log: included in ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-165" title="Replace {{cout <<}} and {{print}} with appropriate LSST log messages" class="issue-link" data-issue-key="PIPE2D-165"><del>PIPE2D-165</del></a> 9. How many info logs should become debug?: included in ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-165" title="Replace {{cout <<}} and {{print}} with appropriate LSST log messages" class="issue-link" data-issue-key="PIPE2D-165"><del>PIPE2D-165</del></a> 10. Please remove all if False blocks. If they are possibly useful control them with variables (probably set by LsstDebug): 11. There's no need to specify the wavelength files on the command line. already happened 12. Please factor the I/O into separate functions, and don't read it for every exposure Filed ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-182" title="Please factor the I/O in reduceArc(RefSpec)Task into separate functions" class="issue-link" data-issue-key="PIPE2D-182"><del>PIPE2D-182</del></a>. 13. Use "not success" not "success == False" Done as part of this ticket. 14. What do comments like "THIS DOESN'T WORK" mean? "THIS DOESN'T WORK" was a leftover from a previous code change. It concerned the values of the private class variable <tt>_iTrace</tt> in the C++ classes <tt>FiberTrace</tt> and <tt>Spectrum</tt>. Setting the value for the <tt>Spectrum</tt> is being taken care of in <tt>ExtractSpectraTask</tt>. I removed all the lines which set <tt>iTrace</tt> for the spectra (commit "reduceArcTask: check iTrace for correct values"). Currently the trace IDs have to be set for the FiberTraceSet via <tt>assignITrace</tt> after tracing the FiberTraces. I filed ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-180" title="include assignITrace in findAndTraceApertures" class="issue-link" data-issue-key="PIPE2D-180"><del>PIPE2D-180</del></a> to include <tt>assignITrace</tt> in <tt>findAndTraceApertures</tt>. 15. Please remove all commented out code I filed ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-167" title="Remove all commented out code" class="issue-link" data-issue-key="PIPE2D-167"><del>PIPE2D-167</del></a> to remove all commented out code from all source files 16. Use np.empty((N, M)) not np.array(shape=(N, M)) I filed ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-173" title="Use np.empty((N, M)) not np.ndarray(shape=(N, M))" class="issue-link" data-issue-key="PIPE2D-173"><del>PIPE2D-173</del></a> to replace all appearances of <tt>np.array</tt> with <tt>np.empty</tt> 17. Explain shape for wLenTemp Changed setting of wLenTemp to <tt>wLenTemp = wavelengths[np.where(traceIds == traceId)]</tt> which should be much clearer 18. Use k += 1 not k = k + 1 Done 19. Use # not """ ... """ for comments Filed ticket <a href="https://pfspipe.ipmu.jp/jira/browse/PIPE2D-169" title="Use # not """ ... """ for comments" class="issue-link" data-issue-key="PIPE2D-169"><del>PIPE2D-169</del></a> 20. Things like getAllFluxes() should not need to make a copy if you get the column/row major right They need to in this case to create an array of the shape nFiberx x nCCDRows. The FiberTraces and Spectra are still only as long as they appear on the CCD. This is hidden from the end user as they are persisted with the height of nCCDRows. It would be a lot of work to change this... 21. Split Spectra.py tests into separate tests if you might not want to run them (and then use a skip decorator) Removed all <tt>if True:</tt> statements merged into master Relates PIPE2D-166 PIPE2D-167 PIPE2D-168 PIPE2D-169 PIPE2D-172 PIPE2D-165 PIPE2D-173 Development Rank 0|ii00uv: Reviewers rhl Sprint 2014-16 Story Points 1.0