Merge pull request #457 from aodn/2.5.29

2.5.29
aodn · Jul 12, 2017 · 0db75fe · 0db75fe
2 parents 4efea08 + 7fd08a6
commit 0db75fe
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Showing 23 changed files with 303 additions and 200 deletions.
diff --git a/AutomaticQC/imosImpossibleDepthQC.m b/AutomaticQC/imosImpossibleDepthQC.m
@@ -311,7 +311,7 @@
         % possibleMin shouldn't be above the surface (~global range value)
         % possibleMax cannot be below the site depth
         possibleMin = max(possibleMin, imosParameters('DEPTH', 'valid_min')); % value from global range
-        possibleMax = min(possibleMax, siteNominalDepth + 20*siteNominalDepth/100); % we allow +20% to the nominal site depth
+        possibleMax = min(possibleMax, siteNominalDepth + zNominalMargin); % we allow the same flexibility for nominal site depth as for instrument nominal_depth
 
         if any(strcmpi(paramName, {'PRES', 'PRES_REL'}))
             if ~isempty(sample_data.geospatial_lat_min) && ~isempty(sample_data.geospatial_lat_max)

diff --git a/Graph/DepthProfile/graphDepthProfileGeneric.m b/Graph/DepthProfile/graphDepthProfileGeneric.m
@@ -1,4 +1,4 @@
-function [h labels] = graphDepthProfileGeneric( ax, sample_data, var )
+function [h, labels] = graphDepthProfileGeneric( ax, sample_data, var )
 %GRAPHDEPTHPROFILEGENERIC Plots the given variable (x axis) against depth 
 % (y axis).
 %
@@ -92,9 +92,10 @@
 
 % for global/regional range display
 mWh = findobj('Tag', 'mainWindow');
-sMh = findobj('Tag', 'samplePopUpMenu');
-iSample = get(sMh, 'Value');
 climatologyRange = get(mWh, 'UserData');
+
+iSample = find(arrayfun(@(x) strcmp(x.dataSet, sample_data.toolbox_input_file), climatologyRange));
+
 if ~isempty(climatologyRange)
     if isfield(climatologyRange, ['rangeMin' var.name])
         xLim = get(ax, 'XLim');

diff --git a/Graph/TimeSeries/graphTimeSeriesGeneric.m b/Graph/TimeSeries/graphTimeSeriesGeneric.m
@@ -1,4 +1,4 @@
-function [h labels] = graphTimeSeriesGeneric( ax, sample_data, var, color, xTickProp )
+function [h, labels] = graphTimeSeriesGeneric( ax, sample_data, var, color, xTickProp )
 %GRAPHTIMESERIESGENERIC Plots the given variable as normal, single dimensional, 
 % time series data. If the data are multi-dimensional, multiple lines will be
 % plotted and returned.
@@ -66,9 +66,10 @@
 
 % for global/regional range and in/out water display
 mWh = findobj('Tag', 'mainWindow');
-sMh = findobj('Tag', 'samplePopUpMenu');
-iSample = get(sMh, 'Value');
 qcParam = get(mWh, 'UserData');
+
+iSample = find(arrayfun(@(x) strcmp(x.dataSet, sample_data.toolbox_input_file), qcParam));
+
 if ~isempty(qcParam)
     if isfield(qcParam, ['rangeMin' var.name])
         hold(ax, 'on');

diff --git a/Graph/XvY/graphXvYGeneric.m b/Graph/XvY/graphXvYGeneric.m
@@ -58,9 +58,10 @@
 
 % for global/regional range display
 mWh = findobj('Tag', 'mainWindow');
-sMh = findobj('Tag', 'samplePopUpMenu');
-iSample = get(sMh, 'Value');
 climatologyRange = get(mWh, 'UserData');
+
+iSample = find(arrayfun(@(x) strcmp(x.dataSet, sample_data.toolbox_input_file), climatologyRange));
+
 if ~isempty(climatologyRange)
     if isfield(climatologyRange, ['rangeMin' sample_data.variables{vars(1)}.name])
         xLim = get(ax, 'XLim');

diff --git a/Graph/graphDepthProfile.m b/Graph/graphDepthProfile.m
@@ -109,6 +109,7 @@
     depth = sample_data.dimensions{depth};
   end
 
+  yLimits = [NaN, NaN];
   for k = 1:length(vars)
 
     name = sample_data.variables{vars(k)}.name;
@@ -164,7 +165,11 @@
         curData = sample_data.variables{vars(k)}.data;
         curDepth = depth.data;
         curFlag = sample_data.variables{vars(k)}.flags;
-        iGood = (curFlag == goodFlag) | (curFlag == pGoodFlag) | (curFlag == rawFlag);
+
+        iGood = curDepth >= 0;
+        if strcmpi(mode, 'timeSeries')
+            iGood = (curFlag == goodFlag) | (curFlag == pGoodFlag) | (curFlag == rawFlag);
+        end
 
         [nSamples, nBins] = size(curData);
         if strcmpi(mode, 'timeSeries') && nBins > 1
@@ -173,7 +178,7 @@
             curDepth = repmat(curDepth, 1, nBins) - repmat(sample_data.dimensions{iVertDim}.data', nSamples, 1);
         end
 
-        yLimits = [floor(min(curDepth(iGood))*10)/10, ceil(max(curDepth(iGood))*10)/10];
+        yLimits = [min(floor(min(curDepth(iGood))*10)/10, yLimits(1)), max(ceil(max(curDepth(iGood))*10)/10, yLimits(2))];
         xLimits = [floor(min(curData(iGood))*10)/10,  ceil(max(curData(iGood))*10)/10];
 
         %check for my surface soak flags - and set xLimits to flag range

diff --git a/IMOS/imosParameters.txt b/IMOS/imosParameters.txt
diff --git a/NetCDF/template/global_attributes_profile.txt b/NetCDF/template/global_attributes_profile.txt
@@ -1,7 +1,7 @@
 % what
 S, project                      = Integrated Marine Observing System (IMOS)
 S, Conventions                  = CF-1.6,IMOS-1.4
-S, standard_name_vocabulary     = NetCDF Climate and Forecast (CF) Metadata Convention Standard Name Table 27
+S, standard_name_vocabulary     = NetCDF Climate and Forecast (CF) Metadata Convention Standard Name Table 45
 S, title                        = 
 S, institution                  = 
 D, date_created                 = [mat now_utc]

diff --git a/NetCDF/template/global_attributes_timeSeries.txt b/NetCDF/template/global_attributes_timeSeries.txt
@@ -1,7 +1,7 @@
 % what
 S, project                      = Integrated Marine Observing System (IMOS)
 S, Conventions                  = CF-1.6,IMOS-1.4
-S, standard_name_vocabulary     = NetCDF Climate and Forecast (CF) Metadata Convention Standard Name Table 27
+S, standard_name_vocabulary     = NetCDF Climate and Forecast (CF) Metadata Convention Standard Name Table 45
 S, title                        = 
 S, institution                  = 
 D, date_created                 = [mat now_utc]

diff --git a/NetCDF/template/spct_attributes.txt b/NetCDF/template/spct_attributes.txt
@@ -21,5 +21,5 @@ N, accuracy                  =
 N, precision                 = 
 N, resolution                = 
 S, cell_methods              = 
-S, flag_values               = 0 1 3 9
+S, flag_values               = [mat char(uint8([0 1 3 9]))]
 S, flag_meanings             = Pressure Velocity Acoustic_Surface_Tracking Unknown
diff --git a/Parser/awacParse.m b/Parser/awacParse.m
@@ -421,7 +421,7 @@
     'HEADING_MAG',  1,       waveData.Heading; ...
     'PITCH',        1,       waveData.Pitch; ...
     'ROLL',         1,       waveData.Roll; ...
-    'SSWV_MAG',     [1 3 4], waveData.fullSpectrum; ... % sea_surface_wave_magnetic_directional_variance_spectral_density
+    'SSWV_MAG',     [1 3 4], waveData.fullSpectrum; ... % sea_surface_wave_directional_variance_spectral_density
     'SPCT',         1,       waveData.SpectraType % awac_spectra_calculation_method
     };
 clear waveData;

diff --git a/Parser/convertECOrawVar.m b/Parser/convertECOrawVar.m
@@ -118,6 +118,7 @@
 
     case 'CDOM' %ppb
         name = 'CDOM';
+        comment = 'Expressed as equivalent mass fraction (ppb) of quinine sulfate dihydrate.';
         data = (sample - columnsInfo.offset)*columnsInfo.scale;
         calibration(1).formula = 'value_engineering_units = (counts - calibration_dark_count) x calibration_scale_factor';
         calibration(1).dark_count = columnsInfo.offset;

diff --git a/Parser/readWQMdat.m b/Parser/readWQMdat.m
@@ -379,7 +379,7 @@ case upper('DO(mg/l)') % DOX1_3
               cndc = sample_data.variables{cndc};
               % conductivity is in S/m and gsw_C3515 in mS/cm
               crat = 10*cndc.data ./ gsw_C3515;
-
+              psal = struct;
               psal.data = gsw_SP_from_R(crat, temp.data, pres.data);
           end
 

diff --git a/Parser/workhorseParse.m b/Parser/workhorseParse.m
@@ -501,26 +501,26 @@
           'LATITUDE',       [],         NaN; ...
           'LONGITUDE',      [],         NaN; ...
           'NOMINAL_DEPTH',  [],         NaN; ...
-          'WSSH',           1,          waveData.param.Hs; ...   % sea_surface_wave_spectral_significant_height
-          'WPPE',           1,          waveData.param.Tp; ...   % sea_surface_wave_period_at_variance_spectral_density_maximum
-          ['WPDI' magExt],  1,          waveData.param.Dp; ...   % sea_surface_wave_from_direction_at_variance_spectral_density_maximum
-          'WWSH',           1,          waveData.param.Hs_W; ... % sea_surface_wind_wave_significant_height
-          'WWPP',           1,          waveData.param.Tp_W; ... % sea_surface_peak_wind_sea_wave_period
-          ['WWPD' magExt],  1,          waveData.param.Dp_W; ... % sea_surface_peak_wind_sea_wave_from_direction
-          'SWSH',           1,          waveData.param.Hs_S; ... % sea_surface_swell_wave_significant_height
-          'SWPP',           1,          waveData.param.Tp_S; ... % sea_surface_peak_swell_wave_period
-          ['SWPD' magExt],  1,          waveData.param.Dp_S; ... % sea_surface_peak_swell_wave_from_direction
+          'WSSH',           1,          waveData.param.Hs; ...   % Significant Wave Height Hs = 4 sqrt(M0)
+          'WPPE',           1,          waveData.param.Tp; ...   % Peak Wave Period (seconds) - period associated with the largest peak in the power spectrum
+          ['WPDI' magExt],  1,          waveData.param.Dp; ...   % Peak Wave Direction (degrees) - peak direction at the peak period
+          'WWSH',           1,          waveData.param.Hs_W; ... % Significant Wave Height in the sea region of the power spectrum
+          'WWPP',           1,          waveData.param.Tp_W; ... % Peak Sea Wave Period (seconds) - period associated with the largest peak in the sea region of the power spectrum
+          ['WWPD' magExt],  1,          waveData.param.Dp_W; ... % Peak Sea Wave Direction (degrees) - peak sea direction at the peak period in the sea region
+          'SWSH',           1,          waveData.param.Hs_S; ... % Significant Wave Height in the swell region of the power spectrum
+          'SWPP',           1,          waveData.param.Tp_S; ... % Peak Swell Wave Period (seconds) - period associated with the largest peak in the swell region of the power spectrum
+          ['SWPD' magExt],  1,          waveData.param.Dp_S; ... % Peak Swell Wave Direction (degrees) - peak swell direction at the peak period in the swell region
           % ht is in mm
           'DEPTH',          1,          waveData.param.ht/1000; ...
-          'WMXH',           1,          waveData.param.Hmax; ...  % sea_surface_wave_maximum_height
-          'WMPP',           1,          waveData.param.Tmax; ...  % sea_surface_wave_maximum_zero_crossing_period
-          'WHTH',           1,          waveData.param.Hth; ...   % sea_surface_wave_significant_height_of_highest_one_third
-          'WPTH',           1,          waveData.param.Tth; ...   % sea_surface_wave_period_of_highest_one_third
-          'WMSH',           1,          waveData.param.Hmn; ...   % sea_surface_wave_zero_crossing_mean_height
-          'WPMH',           1,          waveData.param.Tmn; ...   % sea_surface_wave_zero_crossing_period
-          'WHTE',           1,          waveData.param.Hte; ...   % sea_surface_wave_significant_height_of_highest_one_tenth
-          'WPTE',           1,          waveData.param.Tte; ...   % sea_surface_wave_period_of_highest_one_tenth
-          ['VDIR' magExt],  1,          waveData.param.Dmn; ...   % sea_surface_wave_from_direction
+          'WMXH',           1,          waveData.param.Hmax; ...  % Maximum wave height (meters) as determined by Zero-Crossing analysis of the surface track time series
+          'WMPP',           1,          waveData.param.Tmax; ...  % Maximum Peak Wave Period (seconds) as determined by Zero-Crossing analysis of the surface track time series
+          'WHTH',           1,          waveData.param.Hth; ...   % Significant wave height of the largest 1/3 of the waves in the field as determined by Zero-Crossing analysis of the surface track time series
+          'WPTH',           1,          waveData.param.Tth; ...   % The period associated with the peak wave height of the largest 1/3 of the waves in the field as determined by Zero-Crossing analysis of the surface track time series
+          'WMSH',           1,          waveData.param.Hmn; ...   % The mean significant wave height of the waves in the field as determined by Zero-Crossing analysis of the surface track time series
+          'WPMH',           1,          waveData.param.Tmn; ...   % The period associated with the mean significant wave height of the waves in the field as determined by Zero-Crossing analysis of the surface track time series
+          'WHTE',           1,          waveData.param.Hte; ...   % Significant wave height of the largest 1/10 of the waves in the field as determined by Zero-Crossing analysis of the surface track time series
+          'WPTE',           1,          waveData.param.Tte; ...   % The period associated with the peak wave height of the largest 1/10 of the waves in the field as determined by Zero-Crossing analysis of the surface track time series
+          ['VDIR' magExt],  1,          waveData.param.Dmn; ...   % Mean Peak Wave Direction
           % Vspec is in mm/sqrt(Hz)
           'VDEV',           [1 2],      (waveData.Vspec.data/1000).^2; ... % sea_surface_wave_variance_spectral_density_from_velocity
           'VDEP',           [1 2],      (waveData.Pspec.data/1000).^2; ... % sea_surface_wave_variance_spectral_density_from_pressure

diff --git a/Preprocessing/depthPP.m b/Preprocessing/depthPP.m
@@ -366,8 +366,8 @@
         'NumberTitle', 'off');
 
     cancelButton       = uicontrol('Style', 'pushbutton', 'String', 'Cancel');
-    resetParamsButton  = uicontrol('Style', 'pushbutton', 'String', 'Reset parameters, restart from depthPP.txt');
-    resetMappingButton = uicontrol('Style', 'pushbutton', 'String', 'Reset to current default mapping');
+    resetParamsButton  = uicontrol('Style', 'pushbutton', 'String', 'Reset to default mapping (delete last saved)');
+    resetMappingButton = uicontrol('Style', 'pushbutton', 'String', 'Reset to last performed mapping (saved) if any');
     confirmButton      = uicontrol('Style', 'pushbutton', 'String', 'Ok');
 
     descSamUic           = nan(nDatasets, 1);
@@ -907,10 +907,24 @@ function resetParamsCallback(source,ev)
         %RESETPARAMSCALLBACK Reset dataset specific parameters re-start
         %from depthPP.txt parameters
         %
+        fieldsToBeDeleted = {'same_family', 'include', 'exclude', ...
+            'useItsOwnDepth', 'useItsOwnPres', 'useItsOwnPresRel', ...
+            'firstNearestInst', 'secondNearestInst'};
         for j = 1:nDatasets
+            ppp = struct([]);
             pppFile = [sample_data{j}.toolbox_input_file '.ppp'];
             if exist(pppFile, 'file')
-                delete(pppFile);
+                load(pppFile, '-mat', 'ppp')
+            end
+            if ~isempty(ppp)
+                if isfield(ppp, currentPProutine)
+                    for l = 1:length(fieldsToBeDeleted)
+                        if isfield(ppp.(currentPProutine), fieldsToBeDeleted{l})
+                            ppp.(currentPProutine) = rmfield(ppp.(currentPProutine), fieldsToBeDeleted{l});
+                        end
+                    end
+                end
+                save(pppFile, 'ppp');
             end
         end
         reset = true;

diff --git a/Preprocessing/magneticDeclinationPP.m b/Preprocessing/magneticDeclinationPP.m
@@ -156,13 +156,13 @@
                       % we make sure values fall within [0; 360[
                       data = make0To360(data);
 
-                  case 'VCUR_MAG' % magnetic_northward_sea_water_velocity (m s-1)
+                  case 'VCUR_MAG' % northward_sea_water_velocity (m s-1) referenced to magnetic north
                       data = vcur_mag*cos(geomagDeclin(i) * pi/180) - ucur_mag*sin(geomagDeclin(i) * pi/180);
 
-                  case 'UCUR_MAG' % magnetic_eastward_sea_water_velocity (m s-1)
+                  case 'UCUR_MAG' % eastward_sea_water_velocity (m s-1) referenced to magnetic north
                       data = vcur_mag*sin(geomagDeclin(i) * pi/180) + ucur_mag*cos(geomagDeclin(i) * pi/180);
 
-                  case 'SSWV_MAG' % sea_surface_wave_magnetic_directional_variance_spectral_density (m2 s deg-1)
+                  case 'SSWV_MAG' % sea_surface_wave_directional_variance_spectral_density (m2 s deg-1) referenced to magnetic north
                       % data stays "the same" but we modify the dimension
                       % from DIR_MAG to DIR
                       iDim = sample_data{iMagDataSet(i)}.variables{j}.dimensions(end);