CASA User Testing Meeting Minutes - 2015-08-04, 09:00 Socorro / 11:00 Charlottesville

Post-meeting minutes notes appended in blue text.

Agenda

Participants

Present: Mark R., Crystal, Anand, Drew, Steve

Apologies: Juergen, Amanda

Locations

https://staff.nrao.edu/cal/RoomListing.htm

• Socorro: AOC-317; IP: 146.88.6.8
• Charlottesville: Room 331; IP: 192.33.117.19

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Minutes (Main Points Only)

Status

• 4.4.0 has been released for all supported platforms.
• 4.5 feature freeze was scheduled for August 3rd 2015. Test/stable/monthly packages are being produced.
  • The same general-purpose CASA launcher script has now been deployed at CV, SOC and GB. Details are on the appropriate drop-down menu of the public CASA pages at http://casa.nrao.edu
    • For anyone using test machines zuul01, 03 and 04 are running RHEL6, zuul02 is running RHEL5. REMEMBER: Use /usr/bin/casa on these machines to make sure that you are running the new test/stable packages (there are RPM installations on these).
• 4.3.1 VLA Pipeline version released (RHEL links posted, OS X packages available, links to be posted pending testing approval). Question raised: At what point will the Pipeline major release number catch up with the rest of CASA? 4.3.1 is not currently supported on OS X 10.9 or 10.10 (for example). It is known that Dirk Muders is doing some teting with a 4.4-based version.

• Planned 4.5 release timeline:
  • Aug 3: Feature Freeze (all new features are now in the codebase and ready for test)
  • Aug 14: Code Freeze (Bug fixes etc are expected to be in the trunk at this point, we should have all regressions passing as well)
  • Aug 17: Release Branch Created
    • Feature tests complete: obviously detected issues will need to be fixed and retested, but everything should have been at least had one look
  • Aug 17-31:
    • Identified defects are being fixed, documentation generated
    • All commits require authorization
    • First round of GUI testing
  • Aug 31: First release candidate available for random user testing
    • Final spot check of GUIs
  • Sept 9: Release Target

Number of CASA Jira tickets with "Ready To Test"/"Under Test" status (including EA, EU, JAO, Software-only tickets, but excluding Pipeline) prior to review: 83.

Number of CASA Jira tickets with "Ready To Test"/"Under Test" status (including EA, EU, JAO, Software-only tickets) following review/meeting: 71/72.

Testing Tracking

• New ticket assignments.
• The "nag list", "input required" items
• Major test coverage areas for 4.5 testing
  • • tclean testing to be handled as a short-term project all of its own. Strategy was agreed upon for ALMA between Jeff & Crystal. VLA similar?
      • Dedicated parent tickets with systematic subtasks specifically to track tclean testing efforts have been set up: CAS-7664 and CAS-7669. The main questions to be addressed will be: (1) Does the user interface work as expected? and (2) Does it actually do the right thing?
      • An ALMA Pipeline testing package intended purely for internal NRAO testing use only has been put together that makes use of tclean. It is expected that the Pipeline people in Europe will be comparing manual and the new basic automatic imaging. The PA Pipeline people will be performing the "deep dive" testing (e.g. terms:2 at B3, etc.).
      • For the 4.5 CASA release, it is anticipated that one or two CASA Guides will be produced that essentially outline "This is how you do it with the old clean, and here is the tclean equivalent."
      • It will be necessary to ensure that the clean regression tests are shown to work with tclean (modulo any appropriate tweaking).
      • Crystal et al. have access on lustre to a CASA 4.5 test/stable package containing tclean that she was to begin testing from June 29th. The overall aim is to at least ensure that it works well enough for ~5 or 6 of the most common-use cases.
      • Crystal reported that there were previously three different implementations of the Clark clean algorithm in CASA, and due to contrasting results when attempting to clean mosaics and single fields, two of these have now been linked in for tclean (old Clark -> "clark2" in tclean (suitable for single field); Clark -> "clark" in tclean (suitable for mosaics)). Using the inappropriate one appears to generate deep negative holes in images, and it is suspected that the two implementations were over-optimized for specific cases. Steve also noted that tclean seems to exhibit problems with restarts (e.g. first run with a mask, then second without).
    • Parallelization is also expected to feature more prominently in CASA 4.5. It would be good if this could be relied upon to help speed up flagdata, although our most immediate concern is that it is not responsible for additional breakage (particularly if any such breakage makes it more difficult to test/debug any tclean issues).
      • For a limited group: HPC work (e.g. number of open files, etc.). The Pipeline group are also involved in testing this. This probably does not need a lot of additional dedicated science user testing yet, beyond routinely trying to use split2, day-to-day MSTransform-type work, etc. Amanda had been looking into testing routine split2, cvel2 and other MS_Transform-related issues.
    • Ephemeris handling?
    • Weight column (including weight column -> initialized weight spectrum). See CAS-4469. Testers to work with George. Steve was to look into this.
  • Other matters previously arising
    • It had previously been decided that a wiki page would be created for the NA Imaging Team to collect together a list of common use cases to be tested. Socorro staff were then to review the list, and add any VLA-specific entries for which they also see a need. Juergen was to provide a copy of his old plotms testing automation targets to use as a starting point.
    • Mark R. really needs to get going on the tools documentation again soon. The documentation on the imager (in particular) is just plain wrong in places.

• Any Other Business:
  • BDF flagging has been shown to be problematic. Fixes are being put in by Michel, but it is an ongoing issue. See PRTSIR-6800. Mark R. has now created a CASA placeholder "Blocker" tracking ticket (CAS-7773) to ensure that this gets sufficient attention prior to the 4.5 public release.
    

PART 1: Items to be Covered During Meetings (as time permits)

"Ready To Test" Items Pending Tester Assignment

Selected items only covered

• CAS-7589 (Jun 2015): ImageFitter segfaults with empty estimates file. 4.5 item. Tester: DA (ticket currently with Anand)
• CAS-7620 (Jun 2015): ImageProfileFitter segfaults for a small channel range. 4.5 item. Tester: DA (ticket currently with Anand)
• CAS-7621 (Jun 2015): Residual image not correct when fitting a single change of an image cube with a 2D fit. 4.5 item. Tester: DA (ticket passed to Anand)
• CAS-7717 (Jul 2015): txt file created by the spectral viewer has wrong units. 4.5 item. Tester: TBA (ticket passed to Anand)
• CAS-4277 (Jul 2015): plotms creates incomplete png file. RTT Tester: TBD
• CAS-4277 (Jul 2015): plotms creates incomplete png file. 4.4(!) item. Tester: Anand
• CAS-7319 (Jul 2015): MSMD additions. 4.5 item. RTT Tester: Stewart Williams

• CAS-3080 (Jul 2015): flagmanager mode='save' -- default behavior should not destroy existing flagversion. 4.5 item. RTT Tester: TBD. This item proved controversial, because although the requested behavior is consistent with normal practices at the VLA, it will cause problems whenever re-running ALL of the ALMA reduction scripts, which were written under the assumption of the previous behavior.
• CAS-7286 (Jul 2015): Deploy CalibratingTVI within MSTransform framework. 4.5 item. RTT. Tester: Amanda
• CAS-7315 (Jul 2015): Migrate phase shifting code to TVI. 4.5 item. Subtask of CAS-4864. MSTransform issue. RTT. Ticket currently with Mark R. Tester: Amanda
• CAS-7505 (Jul 2015): Decouple visCube and flagCube MSTransformBuffer. 4.5 item. Subtask of CAS-4864. MSTransform issue. RTT. Ticket currently with Mark R. Tester: Amanda
• CAS-7301 (Jul 2015): Enforce geocentric ephemerides in radial velocity correction. 4.5 item. RTT. Ticket currently with Mark R. Tester: Todd
• CAS-7110 (Jul 2015): Virtual image concat along spectral axis (similar to mms). 4.5 item. RTT. Blocker Tester: TBD. This would require a large testing effort. Moreover, it is not very clear from the ticket what the use cases are for this, what needs to be run, and what the test plan should be. We suspect that this should probably be tested by the HPC group. Ticket pinged for more details.

Propose to Close Items

• TBA

Items Overdue for Status Updates (i.e. the "Nag List")

• CAS-7318 (Feb): 4.5 item (former 4.4 item). Verify unpolarized calibrator mode for linear basis (ALMA). Under Test. Tester: Steve. Ticket pinged. Steve and George to nag each other about this one. Ticket pinged repeatedly.
• CAS-7109 (Mar 2015): Linear full mosaics. Available in stable now. Under Test. 4.5 item (former 4.4 item. Testing started, Input requested from developer. Fix put in by Kumar for problem found. Tester: Steve. Ticket pinged.
• CAS-4983 (Mar 2015): frequencies in gain tables derived using combine='spw' are incorrect. 4.5 item (formerly 4.4). Available in stable now. Under Test. Tester: was Claire, now Crystal. Some duplication with CAS-7097 (assigned to Claire). Claire reports: "Have tested gaincal with solving for individual spws, looks OK, labels for delays now match complex gain, at least in plotcal plots (used to be edge frequency instead of center frequency). Still have to test with averaged spws." Crystal had felt that Claire's testing so far was already almost sufficient. While the remaining testing should be done before the release, it is probably less urgent than other issues right now. Ticket pinged.
• CAS-1390 (Aug 2014): ImageRegrid required for Complex images. Under Test in 4.5 item (was 4.4). Tester: Preshanth. Ticket pinged.
• CAS-7560 (Jul 2015): Include Prolate Spheroidal in AW-Projection. Under Test in 4.5. Tester: Preshanth Ticket pinged.
• CAS-7314 (Mar 2015): Add capability to average across fields. Officially Under Test already, but needs the VI/VB2 version of PlotMS to test, so this would be an advance assignment. Intended science use case for this: Different observations of the same field source might carry different field IDs. May also have mosaicking applications. 4.5 item (was 4.4). Tester: Steve. Ticket pinged repeatedly.
• CAS-7227 (May 2015): better reporting of tabular spectral axes. 4.5 item. Under Test. Tester: Remy. Ticket pinged repeatedly.
• CAS-6421 (Jul 2015): modify casapy launching script to drop into the python interpreter. Under Test in 4.4 public release or later. Done? Tester: Todd
• CAS-7501 (Jul 2015): Allow users to specify callib filename in plotms GUI. 4.5 item. ARTT Tester: Drew B.
• CAS-3953 (May 2015): Subtraction / Fixing of outlier fields in clean. Subtask of CAS-6622. Ready to test in tclean via interactive viewer. VLA item. Tester: Steve.
• CAS-7699 (Jul 2015): plotms transform=True produces an incorrect x-axis scale when avgchannel is also set (even to 1). RTT Tester: Mark L. (and Amanda). High priority testing item! Mark L. will try to look at this as soon as he can, but is currently filling in for Felix's archive duties as well.
• CAS-6951 (Oct): 4.5 item now. mstransform creates a 4-polarization DATA column for single-polarization ALMA WVR data, and a 1-polarization DATA column for four-polarization ALMA data. Fix already included in current new-style test/stable packages newer than 4.2.23. Under Test. Tester: Todd.
• CAS-7731 (Jul): 4.5 item. plotms iterator plotfile name should not include the '&' character (nor spaces). Under Test. Tester: Todd.
• CAS-6980 (Jul): 4.5 item. SPLIT fails when channel averaging if files not in pwd. Under Test. Close to resolved? Tester: Anita.
• CAS-4852 (Jul): 4.5 item. exportuvfits writes wrong field table information when multisource=False. Under Test. Tester: Dirk P.
• CAS-7765 (Jul): 4.5 item. mpv fails in mode "length" for pa='90deg' and pa='270deg'. Under Test. Tester: Dirk P.
• CAS-6980 (Jul): 4.5 item. Baseline-based types unflag data on apply. Under Test. Blocker. Tester: Crystal
• CAS-7741 (Jul): 4.5 item. flagdata shadow flagging fails for sources in ICRS, APP or TOPO. Under Test. Tester: Crystal
• CAS-6130 (Jul): 4.5 item. Parametrized tables in cal library. Under Test. Blocker. Tester: Steve
• CAS-7718 (Jul): 4.5 item. setjy to use 'Perley-Butler 2013' as default standard. Under Test. Tester: Juergen
• CAS-7584 (Jul): 4.5 item. no random number seed in ia.addnoise() ?. Under Test. Tester: Peter Teuben
• CAS-7698 (Jul): 4.5 item. imregrid won't regrid these two images. Under Test. Tester: Remy
• CAS-5524 (Jul): 4.5 item. import uvfits should do make consistent when getting visibilities in STOKES form. Under Test. Tester: Kumar
• CAS-6215 (Jul): 4.5 item. data averaging in flagdata. Under Test. Tester: Emmanuel(?)
• CAS-7382 (Jul): 4.5 item. cvel and mstransform radial velocity correction needs correction. Under Test. Tester: Dirk P.
• CAS-7753 (Jul): 4.5 item. plotbandpass misnamed plots if multiple scans are present in caltable. Under Test. Tester: Stewart W.
• CAS-2077 (Jul): 4.5 item. Plotting flagged data in plotms. Fixed in 4.1? Under Test. Tester: Juergen
• CAS-7737 (Jul): 4.5 item. plotms Error during cache loading. Under Test. Blocker. Tester: Brian K.

Other Items Currently "Under Test"

TBA

Single Dish (to be skipped during the meeting)

• See SD ticket list below

Input Required

* CAS-5730 (Jul): plotms does not plot negative amplitudes as negative values. Currently Input Required (in the form of a sample dataset) from Neil P. * CAS-7697 (Jul): imstat(axes[0,1]) does not compute min/max correct if all data masked in a channel. Currently Input Required from Peter Teuben.

• CAS-4469 (Jun+ 2013): Split with channel averaging is creating spurious spectral features and weight is wrong when there has been channel flagging. Subtask of CAS-5245. 4.5 item. Critical item. was "Under Test". Extensive comments provided by George and Justo. Currently "Input Required" from Crystal.
• CAS-5583: Frequency in exportuvfits output. Currently with Brian K., who is liaising with the user in question.
• CAS-5806 Mathematical prediction of post-gridding single dish beam. Formerly a 4.3+ Blocker, now "Critical". "Input Required?* Developer has done some modelling, but... ? This is a "blocker of a different kind..." High priority (blocking further development). Currently Input Required from Kana. Crystal and Kumar had been in discussion, but this ticket has been quiet since (effectively) December. 4.5+ item now. Proposal made to close this as "Incomplete". Request for any objections posted.
• CAS-4735 (Nov): imsmooth needs additional option for single dish use. Subtask of CAS-5844 (above). Input Required again. Tester: Tsuyoshi. Critical item. Code committed to trunk. 4.3 item. Some testing done, mostly works as intended. Input Required from Crystal for some remaining changes. Any remaining future work will have to be for 4.5(+). Feedback provided. Set back to "Scheduled".
• CAS-6124: imfit subtasks:
  • CAS-4538: migrate imfit input estimates from file to input parameters. Input Required (was "On Hold"). Subtask of CAS-6124. Ticket passed to Juergen, pending a CSSC discussion of what needs to be done and a scheduling of the work. Pushed back to 4.5. Ticket pinged. Juergen: More thought about imfit still needed by Science.
• CAS-4748 (Dec 2012): Polarization selection does not select SIGMA. Input Required. Passed to Jeff for prioritization. Sanjay thinks it's a low-priority item. Version 4.5+.
• CAS-5886 (Dec 2013): bizarre clean boxes for large images. Awaiting input from one developer to another. Version 4.5+.
• CAS-2825 Support for Lissajous mapping. Pushed back to 4.5+. Input from Tsuyoshi needed, but he is not able to provide it yet.
• CAS-5162 (Sep 2013): Improvements in flagging documentation and examples. Input Required from Science (via Jeff). This ticket has been left untouched since May 2013... Version 4.5+.
• CAS-6794 clean is very slow handling this simple, small ACA mosaic. Input Required from Juergen. Kumar commented on this.

Other Blockers

• CAS-7583 listobs failure on CASA 4.4. prerelease. Currently Scheduled". Ticket with Juergen
• CAS-6688 Turn on new vi/vb within imager and test. Was a 4.4 item, but now Unscheduled. Currently with Jim. Some scope modification suggested for this ticket.

General questions raised about callib expectations for 4.5. Implementation in PlotMS? (See Drew's ticket, above). Scratchless operation? Mark R. has asked George about this on CAS-7096

• CAS-7502 Create a C++ parser for the callib file. Currently Scheduled". Ticket with George M.
• CAS-7407 CalibratingVi2 Improvements. Currently Scheduled". Ticket with George M.
• CAS-7287 Deploy Calibration-aware MSTransformManager in solve context. Subtask of CAS-7096. Currently Scheduled". Ticket with George M.
• CAS-5617. CalLibrary Improvements. Currently Scheduled". Ticket with George M.
  • CAS-3517 Improve remapping interface. (Duplicate and subtask)
  • CAS-5618 Add method to limit range in interpolation. CalLibrary issue. Subtask of CAS-5617. Currently Scheduled". Ticket with George M.
  • CAS-3494 Handle uncalibrate-able spws better. CalLibrary issue. Subtask of CAS-5617. Currently Scheduled". Ticket with George M.

• Viewer registration tickets:
  • CAS-6560 contour image does not unzoom when master coordinate image is re-registered. Subtask of CAS-6604. Viewer issue. Currently Unscheduled.
  • CAS-6720 2 panels don't register. Viewer issue. Currently Unscheduled.
• tclean parent tickets (see also below):
  • CAS-7664 tclean science user testing: Continuum (MFS)
  • CAS-7669 tclean science user testing: Cubes

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PART 2: Items Listed for Informational Purposes (note that these will not normally be specifically discussed during the meeting unless someone raises them)

tclean

• tclean testing (for info only: to be skipped during the meeting: will be handled by the Imaging Group)
  • CAS-5048 (May 2015): Clarify when peak residual calcs use/ignore masks, and use consistent thresholding rules. Older ticket, now ready to be tested using new tClean in 4.5. Tester: TBD (was Emmanuel, back in the 4.1 cycle). Ticket with Urvashi
  • CAS-3729 (May 2015): clean to write out only those images that are necessary for a given run. Subtask of CAS-4640. Tester: TBD. Ticket with Urvashi
  • CAS-3290 (May 2015): Logging : clean logging for cube cleaning needs improvement. Subtask of CAS-6615. Tester: TBD. Ticket with Urvashi
  • CAS-4133 (May 2015): clean inline docs for masks and new region format... Subtask of CAS-6617. Tester: TBD (Brian Kent, who has history with this ticket? Or DA?). Ticket with Urvashi
  • CAS-1623 (May 2015): CLEAN should have option to continue from previous CLEAN state. Subtask of CAS-4640. Tester: TBD. Ticket with Urvashi
  • CAS-2673 (May 2015): The 'cyclefactor' parameter in the clean task. Subtask of CAS-6622. Tester: TBD (Is this really user testable? Maybe not...). Ticket with Urvashi
  • CAS-7292 (July 2015): clean spw parameter cannot stride >1 channel. 4.5 item. Under Test. Tester: Crystal (or other member of imaging team).

Unable to Test Items

• CAS-4758 (Sep): 4.4 item. fluxscale fails if one of the reference fields is flagged. Previously "Under Test" (r31121+) in current (new-style) stable. Tester: Claire. No testing progress on this since October. Claire had been trying to find a suitable dataset for testing. Steve thought that this should actually be fairly easy to test and that Claire and/or he may have been able to test this one. Ticket with Brian Kent. Ticket pinged. Place On Hold, pending test data availability. No recent updates.
• CAS-5379 - Subtle inconsistencies with other programs in Galactic Coordinates (Adam and Harvey). In a nutshell, shifts of ~0.2" are seen when taking data into other packages (e.g. DS9, IDL which both seem to agree with each other). It is unclear yet if this is an incorrect implementation in one or more packages, or possibly just a precision error. This is a subtle issue, and was pushed back. Ticket stalled. Needs to be looked at by someone with lots of time. To be left as-is for now. This needs significant work, including new science papers on how to actually define the Galactic coordinate system? Needs casacore discussion; this can be part of that. Passed to Jeff for now. Pushed back to some indefinite future release. Unscheduled.
• CAS-4636 (Oct 2012): Elevation dependent opacity application w/ Tsys. Still awaiting input from Science. Had been "On Hold" since August, awaiting data. Previously switched to "Input Required" and passed to Crystal for comment. Bumped back to 4.4+. Work on this is Unscheduled until further notice (more than a year, now).
• CAS-3532 (Sep): Incorporation of Alma Primary Beam in Mosaic. Currently Unscheduled. Tester was Scott S., but ticket passed to Crystal for input. Some test imaging done. Ticket with developer.

Upcoming Ready to (Re)Test Items

Not Yet Assigned To Testers

• TBA

Single Dish

See below "assigned" SD list.

Already Assigned To Testers

• CAS-4592: plotms on 10.7 issues. Previously half fixed due to Qt updates. Shown to till be an issue under 10.10. Currently Unscheduled. Tester: was Nathan, to be Juergen. Exported plots all look OK, even if the plots in the GUI appear corrupted. Juergen to discuss prioritization with Jeff?
• CAS-5893 (May): Now a 4.5 item. Add the ability to write a spectral profile to an ASCII file in the ia tool. Was "Under Test" in 4.3. Now Scheduled. Tester: Assigned to Juergen for testing and a possible CSSC discussion. Might also need a task adding for this, but this will be 4.5 work. Recent testing done, passed back to developer for 4.5+ work.
• CAS-5127 (May): Document ia toolkit methods. Status Scheduled. Mark should start working on this again... Most of Juergen's prioritized list of 26 items had been done. Dates to be added his future documentation updates. Ongoing. ia.regrid docs will require more work. Still needs code commits. Mark to restart work on this under Linux soon.

Single Dish

• CAS-7513: (Jul 2015): Suppress generation of unfitted rows of baseline tables in tsdbaseline. Ready To Test. Ticket passed to Erik for reassignment/testing.
• CAS-7591: (Aug 2015): sdimaging should support intent selection. Ready To Test. Ticket passed to Erik for reassignment/testing.

• CAS-7735: (Jul 2015): MS transition: support on-the-fly averaging in sdms tool. Subtask of CAS-6988. Under Test. Mostly looks good, but may need a bit more work. Tester: Patricio.
• CAS-7598: (Jul 2015): beam size definition fails for data without REST_FREQUENCY. 4.5 item. Ready To Test. Ticket currently with Erik for reassignment/testing. Ticket pinged.
• CAS-6572: (Aug 2014): A new baseline task that handles baseline table. Was Under Test in 4.4. Now 4.5. Mostly done. Ticket with Kana. Some duplication with CAS-5855). Ticket pinged.

-- MarkRawlings - 2015-07-31