IMOS Toolbox v2.5.38 - 19 Apr 2018

Changes from v2.5.37:

• imosImpossibleDateQC does not allow for any impossible date any more. Instead it triggers an error to force fixing the file (either manually or via manufacturer software or via toolbox parser when possible). f7aba04
• aquatecParse updated so that bad timestamps and their corresponding measurements are discarded. f8053e0
• In checkMooringPlannedDepths.m fastScatter has been replaced by scatter. fastScatter is not critical there since there are not many points to scatter (equals to number of instrument whic is usually less than 100, not a big deal for scatter). In addition this solves some bugs due to complexity of fastScatter when facing unusual cases. 8bee230
• Fix timeDriftPP in the case of drift offset start and drift offset end are the same. In this case, while there is no correction for drift, there must be a correction for offset which wasnt performed previously. 3569651
• In profile mode, when exporting several datasets at once, each dataset will generate its own .png file as opposed to a single .png where all the datasets used to be plotted (difficult to read when lots of datasets). 4d7293b
• In profile mode, in the Tools menu, profile plots are only produced for the currently selected datasets. Not all datasets are plotted in the same figure any more for better readability. 43925c2
• Fix for imosDensityInversionSetQC and re-processing. 3de96bf
• Change main plotting area to have a white background for better readability of axis. Most axis have their color set to none so that it is transparent (same color as main plotting area - white) except for 2D axis like ADCP currents which color is set to light grey so that it doesnt conflict with a colorbar that can include the color white. In addition, when manually QCing the dragging rectangle and selected points are not white any more but black to be visible with a white background. 68ac5a9
• Diagnostic scatter plots of 2D variables now have the figure background set to white while the axis background is still light grey. b07adfd
• Increment version to 2.5.38 and update binaries accordingly. e29ac0d

IMOS Toolbox v2.5.37 - 22 Mar 2018

Changes from 2.5.36:

• Add comment about nature of Signature ADCP AltimeterQualityAST. 75a3f2d
• A new DEPTH variable is always created from a PRES, PRES_REL or DEPTH variable from the current instrument or a nearby one so when adding DEPTH to a datasets we may as well consider re-using the dimensions info and coordinates attribute from this PRES, PRES_REL or DEPTH variable rather than re-using those of the last variable present in the current file (sometimes not a good move). Also, write/update the dataset PP parameters before moving to the next sample_data was being done twice unnecessarily. 44f7087
• In Matlab r2012b, option to disable filling with fill values when creating a NetCDF variable is actually NOFILL, not NC_NOFILL. 9ca26ab
• Fix instrument_sample_interval and instrument_burst_duration global attributes in Wetlabs readECOraw parser for the case when only one sample is output for a burst. 0e6d8c6
• Fix bug in checkMooringPresDiffs when selecting topmost instrument on mooring. In addition, fixed erroneous legend. e94e8b5
• Add support to old SEACAT PROFILER serial number and pressure data. 1f4495e
• Fix scatterMooring2DVarAgainstDepth for cases when ADCP doesnt have any good DEPTH data and nominal_depth info is used instead. 503ac96
• SBE19Parse is now looking for bin size averaging information in the proc header. In profile mode, if not found will issue a warning with reference to the CTD processing procedure document. 82eecc2
• Diagnostic plots now include a white background for improved contrast/readability except for the ones that involves ADCP data where a colorbar might include the color white (in that case the background is set to light grey). cdb1c8a
• Increment version to 2.5.37 and update binaries accordingly. 0b0d6d0

IMOS Toolbox v2.5.36 - 6 Nov 2017

Changes from 2.5.35:

• imosVerticalSpikeQC is to be used in profile mode only. Fix added to leave out of the test any data with flag bad and probably bad. 7facc17
• Update getPresRelForGSW so that presName content is now provided via separate zName and zComment variables. dfacb54
• Added new QC test for profile data inspired from the density inversion test from Argo. ee83f35
• Right click on a graph can now be used for manual QC. It differs from the left click in that instead of highlighting what is included in the box, it highlights what is outside the box. 0ec9dd3
• Need to close resultset and statement objects used by JDBCDDB.java just like the connection at the end. 46ed41f
• Update parsers for Signature Nortek ADCP to support SRS files: * Update readAD2CPBinary to Nortek Signature Integration manual 2017. 223a933
  • Add support to new data records such as: Burst Altimiter Raw, DVL Bottom Track, Altimiter, Avg Altimiter Raw.
  • Beam coordinate system information is being parsed.
  • Similar data records (same type, same config) are being grouped together in the same dataset across programmed modes.
  • Added following diagnostic parameters: AmbiguityVel, TransmitEnergy, NominalCorrelation, Error.
  • Add support to velocity in BEAM coordinates.
  • Add support to Altimeter LE and AST parameters.
  • Update support of .mat files so that result is consistent with .ad2cp files. Support Alt_Average and Alt_Burst programmed modes.
  • Generate as many datasets/NetCDF files as there is different programmed modes.
  • Add burst metadata in global attributes.
• Increment version to 2.5.36 and update binaries accordingly. bbd4580

IMOS Toolbox v2.5.35 - 11 Oct 2017

Changes from 2.5.34:

• Fix case in rinkoDoPP when depth (positive down) is <= -5m. 03f4a8d
• Fix diagnostic 1D line plots when a dataset doesnot have the relevant variable while it exists in other datasets. 9778996
• Fix checkMooringPresDiffs for the case when a dataset does not have a single good data for a variable while the variable exist in other datasets. 7073a70
• Fix imosSalinityFromPTQC for the case when PRES or PRES_REL has failed but DEPTH has been inferred from neighbouring sensors and is good. de517ea
• Fix depthPP for the case where there is only one nearby pressure sensor and it is below the other instrument. 8636669
• Increment version to v2.5.35 and update binaries accordingly. 3d541ad

IMOS Toolbox v2.5.34 - 5 Oct 2017

Changes from 2.5.33:

• Fix in rinkoDoPP and getPresRelForGSW for when the only vertical information available is nominal depth. 2cfc524
• Fix typo that bugs when reading voltage from workhorse and last value of the channel data is NaN. b2b9950
• Fix case in getPresRelForGSW.m and rinkoDoPP.m for when TEMP is not available in the dataset. What we need access to, is the main dimension of the dataset. f65bbdf
• Wetlabs ECO and BB9 parsers now assume that the instrument is collecting data in burst. bd71ac8
• Revert addition of warning message for 2D diagnostic plots. 1D variable can get caught there unwillingly. b06405c
• Fix battery voltage computed value for long ranger RDI ADCPs + added comment about nature of voltage measurement. 63fd574
• Increment version to 2.5.34 and update binaries accordingly. af41045

IMOS Toolbox v2.5.33 - 21 Sep 2017

Changes from 2.5.32:

• Updated software licensing to GPLv3. 0feae8a
• Re-arrange TEOS10 files in a TEOS10 directory. 2ba56a1
• Revert changes on readWQMraw.m from v2.5.32. O2 is provided in ml/l following Weiss calculation. 67247c5
• More detailed warning message has been added when a deployment has all the values of a parameter flagged bad so that the toolbox is not trying to plot diagnostic plots for them. 901187f
• Added support to battery voltage from RDI workhorse ADCPs to be output in NetCDF files. 252be57
• Frequency profiles timeseries have their plots adjusted along X axis so that it aligns with 1D timeseries plots, just like Depth profiles timeseries. 38fdcb9
• Fix selection for manual QC in DepthProfile and XvY graphing modes. Especially when also displaying extra instrument. 80f31f2
• Reword entries for diagnostic plots in Tools menu. Add a new entry to produce 1D var / DEPTH diagram plots. 9519c83
• Add a new entry in Tools menu to produce 2D var / DEPTH diagram plots 17f87ee
• Fix empty figure that pops-up when batch processing a deployment. e94c0f4
• checkMooringPlannedDepths has been added to the default diagnostic plots produced when exporting NetCDFs. In batch mode it considers the first quarter of the deployment for its analysis. fcfb83b
• Increment version to 2.5.33 and update binaries accordingly. 164bb52

IMOS Toolbox v2.5.32 - 29 Aug 2017

Changes from 2.5.31:

• Oxygen calculations are removed from parsers to be performed by a dedicated pre-processing routine using GibbsSeaWater toolbox. This new oxygenPP routine has ben added to the list of default PP routines that needs to be performed in the toolboxProperties.txt config file: this will likely create a conflict with your cloned copy see this example on how to resolve. A unit test has been added to check oxygen calculations. This unit test is ran before trying to compile a binary. This change moves all the oxygen calcs from the instrument read routines to a oxygen pre-processor. Also test for checking the output from the pre-processing against Sea-Bird calculation. dc1a63b
• In convertSBEcnvVar.m, SBE oxsol and oxsat are different from the actual o2 reading from the instrument. These parameters are not read any more. Also fix bug on supporting voltage outputs with non word characters in their label. 967bed0
• Improved SBE cnv model string regexp. A unit test has been added and is ran before trying to compile. dfb00c6
• In magneticDeclinationPP, improve IF conditions for when a user is prompted to manually enter missing depth, latitude and longitude. efa5a58
• TIME flags are now taken into account for graphing timeSeries so that X axis is auto set to good/probablyGood/nonQC data only. 4152f11
• Fix timeDriftPP to be able to run without DDB. c87276e
• rearrange files in Seawater directory so that gsw_ files are stored in the same hierarchy as what TEOS-10 provides. 9c3454b
• Updated GSW toolbox from v3.05 to v3.06. 87aa02a
• Handle alternate wap format (AWAC wave ASCII file format) with only 15 column. Add support to more wave variables in historical 31 column format. CF standard name sea_surface_wave_zero_upcrossing_period has been replaced by sea_surface_wave_mean_period in v45 of CF stnadrad name table so that IMOS parameter code VAVT can be replaced by WPMH. ad46cbd
• New function Parser/addAWACWaveToSample.m created so that can be used by other parsers than awacParse.m. 1f73834
• Fix makeNetCDFCompliant for case when DDB field Sensors.Parameter is empty. a6161b1
• Refactor database query interface. Select between DDB and CSV database interface at DDB/executeQuery 859b584
• Fix JDBCDDB.java so that last column of a table is retrieved. Updated ddb.jar accordingly. 4daebca
• Get rid of any call to old Seawater toolbox EOS-80. The new Gibbs-SeaWater toolbox TEOS-10 is now exclusively used. 06ffea2
• Update list of required files for the reading of Nortek wave data. 54d32a6
• Capture directional/compass offset from Nortek .whr wave file. a96fa0b
• Improved depthPP for the case when only one P sensor is available. Before, the same displacement seen on the nearest P sensor from its nominal depth was applied to the current sensor. Now we take into account the site nominal depth in order to locate the current sensor. The current limitation is that the tidal amplitude is flattenned (the actual site depth varies with time != site nominal depth). efd7e97
• Added new parser for .tid files produced by SBE26. a6defb0
• Increment version to 2.5.32 and update binaries accordingly. 8c46f5f

IMOS Toolbox v2.5.31 - 25 Jul 2017

Changes from 2.5.30:

• In the main window, any 1D parameter of the selected instrument is now always plotted with a blue coloured line. Alternating random colours for different parameters of the same instrument was not justified. 4fdeed8
• Updated fastSaveAs to force GUI to update itself before saving to file. For example on Linux the colorbar might be missing otherwise. 6688ee5
• Updated background of axis in main window and other diagnostic figures with a lighter grey for 1D plots in order to improve readability. 25c66ca
• Cleanup mainWindow.m code and indent it properly. 37af98e
• Modified main window GUI to be able to graph an extra instrument (black) on top of the currently graphed one (blue). This works in timeSeries or profile mode for TimeSeries and XvY graph types on 1D variables, and for DepthProfile graph type for both 1D and 2D variables. 1d6fbdc
• Make sure auto zoom on graph(s) other than current one takes into account extra sample data if extra sample is selected. 2a4be73
• Graph type XvY can support nD variables with n>=1. X and Y just need to have matching number of dimensions. 8cb2dc4
• Replaced "Save Graph" button by "Save Figure" button from uitoolbar. Rearranged state buttons in a uipanel and filled a bit of unused space. 8837d2e
• Fix variableOffsetPP for the case when global attributes instrument_nominal_depth and / or time_deployment_start exist but set to empty. 3238a6e
• Fix error message in scatterMooring1DVarAgainstDepth and scatterMooring2DVarAgainstDepth when instrument_nominal_depth is not documented. 0a102e1
• Modify variableOffsetPP.m so that not only scalar values are accepted but also any Matlab statement, including the sam data structure representing the currently selected instrument. 3a23fbc
• Increment version to v2.5.31 and update binaries accordingly. 7d123b5
• Remi was born the 22nd of July :-)
  

IMOS Toolbox v2.5.30 - 18 Jul 2017

Changes from 2.5.29:

• Fix bug when trying to manually flag velocity data from single point current metres. 330d7ea
• It is now possible to load more instruments (for example load instruments from two moorings at once) from the deployment database using the Import button. 1a0cf0d
• revert initial commit that introduced screenCapture. ca1020c
• Now using hgexport function in order to print figure to file. Figure size is set to full screen size of bigger screen (make sure we fit the legend) except on Linux where it is set to a static dimension because of some Linuxes not able to distinct several screens. 53f3997
• Increment version to v2.5.30 and update binaries accordingly. 3d01a96

IMOS Toolbox v2.5.29 - 12 Jul 2017

Changes from 2.5.28:

• Fix unintialized struct in readWQMdata when density needs to be computed to get DOX2 and there is conductivity but no salinity. psal was previous used as type real, but when returning from gsw_SP_from_R you are trying to create a struct. 86f7e67
• variableOffsetPP can now store specific offsets/scales in .ppp files for re-processing. variableOffsetPP.txt file is not used at all anymore. An extra column shows (when possible) the differences with the nearest instrument on the mooring (offset). 6401445
• In depthPP, when reset parameters via GUI, the pp file is not deleted anymore, instead the fields in the structure belonging to depthPP routine are deleted. Labels on button for resetting to default or last saved mappins have been updated for clarity. aefa41f
• Fix readDatasetParameter to output the default value given in input when the parameter needed to be retrieved doesnt exist. b14d543
• Fix typo in writeDatasetParameter for the handling of .ppp files. f528c80
• Update CF standard name from v27 to v45. 6877694 /!\ When doing a git pull, this is likely to produce a conflict with your NetCDF/template/global_attribute_timeSeries.txt and NetCDF/template/global_attribute_profile.txt files/!\ See example on how to solve a conflict with git.
• Change returning imosToolbox('version') logic so that we dont bother setting paths. If user is only calling imosToolbox to get the version string don't bother setting paths etc. 6ca99bc
• Fix flag_values variable attribute values for SPCT IMOS paramter in NetCDF/template/spct_attributes.txt. 67e6c99
• Fix GUI error about qcParam in graphTimeSeriesGeneric, graphDepthProfileGeneric and graphXvYGeneric when two distinct datasets come from the same file name. be90f10
• Updated imosImpossibleDepthQC to consider adding zNominalMargin (default value is 15m) to the site_nominal_depth as a possible maximum depth rather than adding 20% of the site_nominal_depth. This is to be able to deal with shallow sites that can face large tides (ex. DARWIN). 924d048
• Fix change introduced in v2.5.25 on graphDepthProfile. In profile mode, any data with depth >=0 should be displayed. In timeSeries mode, the Y limits are chosen (biggest range based on good data only) so that they can be applied consistently across graphs. bdce59c
• Increment version to v2.5.29 and update binaries accordingly. 7fd08a6