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IMOS Toolbox v2.6.11 - 20 April 2021
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@ocehugo ocehugo released this 20 Apr 06:38
· 89 commits to master since this release
v2.6.11
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DO NOT USE THIS RELEASE - see notes in v2.6.13.

Release 2.6.11 is the Q2 & Q3 release of the IMOS Toolbox.

The release contains an overhauled handling of RDI workhorse ADCP data, updates to ADCP quality control, new magnetic declination tables, some bug fixes, and internal improvements.

Changes to RDI data ingestion:

The RDI workhorse parser is now using more information included in the binary file and with a reduced peak memory usage. We also added support for Beam coordinates to ENU coordinates in the parser and through a new PreProcessing step. See the wiki page for more details and the +Teledyne and +Workhorse packages for some of the related changes.

071783b feat(PP): RDI TeledyneADCP rotation conversions
eca2e8c feat(PP): RDI support and refact BinMappingPP
b2db280 feat(parser): Workhorse parse overhaul
495c601 review(Parser): fix typo in help
5f67b98 feat(rename): rename workhorseParse testfile
aeb6523 fix(adcpBinMappingPP): allow downward adcp
2543330 fix:(adcpWorkhorseVelocityBeam2EnuPP): comments
dd47547 fix(readWorkhorseEnsembles): compatibility revert
7a9a1fd fix(readWorkhorseEnsembles): remove typo
41de5f8 fix(readWorkhorseEnsembles): turn on memory saving

New optional ADCP QC tests:

  1. imosSurfaceDetectionByDepthSetQC - for simple surface detection in both upward/downward cases.
    02658c7 feat(QC): adcp surface detection by Depth

  2. imosEchoIntensitySetQC - for customisable behaviour in echo intensity markings. The test may be configured to be equivalent to the fish detection algorithm.
    9bafc2a feat(QC): a customisable echoIntensity QC test

In particular, imosEchoIntensitySetQC intend to deprecate the various attempts of Echo Intensity filtering scattered in the codebase and provide an easy way to customise its behaviour in the User Interface. Both tests are optional and in the evaluation phase. Other tests are likely to be deprecated in the future.

Behaviour Changes:

  1. imosErrorVelocitySetQC now uses deviations from the mean to classify ADCP error velocity estimates.
    7aa8513 BREAKING CHANGES(QC): ErrorVelocity adcp markings

  2. imosEchoIntensityVelocitySetQC now inspect fewer bins and support downward-looking ADCPs.
    ff061aa BREAKING CHANGES(qc): EchoIntensityVelocity

Miscellaneous changes:

  1. Draft support for [adcpThreshold] (https://github.com/aodn/imos-toolbox/blob/master/Graph/adcpThresholds.m) graphics.
    4f29ab8 feat(graph): improve timeSeries default axis plots
    c29c97c feat(graph): adcp Threshold visualisation diags
  2. Draft support for RDI bin averaging.
    4cd1e31 feat(processing): rdi adcp bin averaging
  3. Faster adcpBinMappingPP.
    eca2e8c feat(PP): RDI support and refact BinMappingPP
  4. Update magnetic parameters/Geomag to IGRF13 to support data collected beyond 2020+.
    e7c7477 fix: geomag for 2020+ with new IGRF13 tables
  5. Restore the ability to run the VerticalSpikeQC test.
    4a6f70b fix(QC): fix call signature matching
  6. Allow overwriting DEPTH estimates in depthPP.
    15d5eb9 fix(PP): allow overwriting of depth variable

New internal features:

97d1146 feat(IMOS): schema evaluation for PP/QC
fc362f0 feat(IMOS): metadata extraction queries
d994c7f feat(IMOS): adcp utilities
cccffc8 feat(IMOS): detect variables with given dimensions
bad34c6 feat(Util): disp that shows where the call came
28baf98 feat(Util): allow update config files
5e28104 feat(genSampleDataDesc): support missing fields
14a0030 feat(IMOS): New IMOS utility functions
6a4fce9 feat(Util): mem usage and double/cell comparisons
a19ef3b feat(Util): allow file extension filtering
7428351 feat(Util): only persist values in deployed case
a27c18c feat(IMOS): upgrades to the IMOS package
6866b9d feat(Util): improvements to errormsg/swarning
9efcff9 feat(test): update sites/instruments tables
a80159a feat(test): adcp single ping test
245d526 feat(qc): include EchoRangeSetQC tests

Other miscelaneous fixes and cleanups:

c3f1e61 hotfix: include compatible binaries
b531528 feat(Util): remove wrapTo360 dependency
990e09e fix(build): rm test files from binaries
b00323a fix(QC): support skip of invalid datasets
ddb6841 fix(QC): fix warning msgs
f5c6102 fix(Util): simplify genSampleDataDesc for tests
7c26add fix(imosEchoRangeSetQC): enu detection & clean
21bb738 fix: rm surfacedetectionsetQC old code
4f11f09 fix(genSampleDataDesc): remove license body
0ff821e fix(readMappings): close file id before error
d78fc69 fix(errormsg): put line error in single line
10de06b fix(Util): isinside support to diff. cells lens
b2f8708 fix(Util): only move files if their name differs
f49a895 cleanup: remove geomag tmp files
d967874 cleanup: remove rdiBeam2Earth.m deadcode
a6f948d fix(IMOS): add missing cf standard name
94e3f26 fix: avoid loading non-binary files in tests
3a60b58 fix(Util): missing semicolon in readMappings.
8217ace fix(Util): workaround to failing docstring tests
9fb7e36 fix(TestUtils): file report in checkDocstrings

We acknowledge some early code efforts provided by CSIRO and others in this release.

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