Merge pull request #448 from aodn/2.5.28

2.5.28

AutomaticQC/imosSalinityFromPTQC.m

@@ -1,7 +1,8 @@
 function [data, flags, paramsLog] = imosSalinityFromPTQC ( sample_data, data, k, type, auto )
-%IMOSSALINITYFROMPTQC Flags salinity data which is flagged in pressure/depth and temperature.
+%IMOSSALINITYFROMPTQC Flags salinity data which is flagged in pressure/depth, conductivity
+% and temperature.
 %
-% Looks for highest flags from pressure/depth and temperature variables and give
+% Looks for highest flags from pressure/depth, conductivity and temperature variables and give
 % them to salinity
 %
 % Inputs:
@@ -105,9 +106,9 @@
     % initialise all flags to non QC'd
     flags = ones(lenData, 1, 'int8')*rawFlag;
 
-    % we look for flags from pressure and temperature data to give them
+    % we look for flags from pressure, conductivity and temperature data to give them
     % to salinity as well
-    paramNames = {'DEPTH', 'PRES_REL', 'PRES', 'TEMP'};
+    paramNames = {'DEPTH', 'PRES_REL', 'PRES', 'TEMP', 'CNDC'};
 
     for i=1:length(sample_data.(type))
         % let's handle the case we have multiple same param distinguished by "_1",

IMOS/finaliseData.m

@@ -217,20 +217,21 @@
 end
 
 function sam = forceMonotonic(sam, mode)
-  % We make sure that DEPTH/TIME coordinate variables appear
-  % ordered and that there is no redundant value.
+  % We make sure that TIME coordinate variable appears
+  % ordered monotically and that there is no redundant value.
   switch mode
-      case 'profile'
-          if strcmpi(sam.dimensions{1}.name, 'MAXZ'), return; end % this case produces non compliant files anyway
-
-          dimensionName = 'DEPTH'; % so far we only produce downcasts to be compliant
-          sortMode = 'ascend';
-          sortModeStr = 'increasingly';
-
       case 'timeSeries'
           dimensionName = 'TIME';
           sortMode = 'ascend';
           sortModeStr = 'increasingly';
+
+      otherwise
+          % we do nothing, profile data should already be ordered 
+          % monotically either because pre-processing Tim Ingleton's 
+          % protocol was followed using SeaBird software or because
+          % CTDDepthBinPP is being used in the toolbox for non binned 
+          % profiles.
+          return;
 
   end
   iDim = getVar(sam.dimensions, dimensionName);

Parser/readXR620.m

@@ -247,10 +247,10 @@
                       data.(vars{k}) = data.(vars{k})/10;
 
                       %Temperature (Celsius degree)
-                  case {'Temp', 'temp02'}, name = 'TEMP';
+                  case {'Temp', 'temp02', 'temp12'}, name = 'TEMP';
 
                       %Pressure (dBar)
-                  case {'Pres', 'pres20'}, name = 'PRES';
+                  case {'Pres', 'pres20', 'pres21'}, name = 'PRES';
 
                       %Relative Pressure (dBar)
                   case {'pres08'}, name = 'PRES_REL';
@@ -514,7 +514,7 @@
                       data.(fields{k}) = data.(fields{k})/10;
 
                       %Temperature (Celsius degree)
-                  case {'Temp', 'temp02'}, name = 'TEMP';
+                  case {'Temp', 'temp02', 'temp12'}, name = 'TEMP';
 
                       %Pressure (dBar)
                   case {'Pres', 'pres08'}, name = 'PRES';
@@ -881,7 +881,11 @@
       if isempty(strfind(data.Date{1}, '-'))
           data.time = datenum(data.Date, 'yyyy/mmm/dd') + datenum(data.Time, 'HH:MM:SS.FFF') - datenum('00:00:00', 'HH:MM:SS');
       else
-          data.time = datenum(data.Date, 'dd-mmm-yyyy') + datenum(data.Time, 'HH:MM:SS.FFF') - datenum('00:00:00', 'HH:MM:SS');
+          % Ruskin version number <= 1.12 date format 'dd-mmm-yyyy'
+          % Ruskin version number 1.13 date format 'yyyy-mm-dd'
+          % can either do some simple date format test or see if datenum
+          % can figure it out
+          data.time = datenum(data.Date) + datenum(data.Time, 'HH:MM:SS.FFF') - datenum('00:00:00', 'HH:MM:SS');
       end
   end
 

Preprocessing/depthPP.m

@@ -68,12 +68,13 @@
 
 % get the toolbox execution mode
 mode = readProperty('toolbox.mode');
+
+depthVarType = 'variables';
+isProfile = false;
 switch mode
     case 'profile'
         depthVarType = 'dimensions';
-
-    otherwise
-        depthVarType = 'variables';
+        isProfile = true;
 
 end
 
@@ -160,7 +161,7 @@
     useItsOwnPresRel(iCurSam) = readDatasetParameter(sample_data{iCurSam}.toolbox_input_file, currentPProutine, 'useItsOwnPresRel', useItsOwnPresRel(iCurSam));
 
     % look for nearest instruments with depth or pressure information
-    if isSensorHeight || isSensorTargetDepth
+    if ~isProfile && (isSensorHeight || isSensorTargetDepth)
         % let's see if part of a mooring with pressure data from other
         % sensors
         for iOtherSam = 1:nDatasets
@@ -309,10 +310,12 @@
             secondNearestInst(iCurSam) = readDatasetParameter(sample_data{iCurSam}.toolbox_input_file, currentPProutine, 'secondNearestInst', secondNearestInst(iCurSam));
         end
     else
-        fprintf('%s\n', ['Warning : ' sample_data{iCurSam}.toolbox_input_file ...
-            ' please document either instrument_nominal_height or instrument_nominal_depth '...
-            'global attributes so that an actual depth can be '...
-            'computed from other pressure sensors in the mooring']);
+        if ~isProfile
+            fprintf('%s\n', ['Warning : ' sample_data{iCurSam}.toolbox_input_file ...
+                ' please document either instrument_nominal_height or instrument_nominal_depth '...
+                'global attributes so that an actual depth can be '...
+                'computed from other pressure sensors in the mooring']);
+        end
         continue;
     end
 end
@@ -353,7 +356,7 @@
     end
 end
 
-if ~auto
+if ~auto && ~isProfile
     f = figure(...
         'Name',        'Depth Computation',...
         'Visible',     'off',...

imosToolbox.m

@@ -74,7 +74,7 @@ function imosToolbox(auto, varargin)
 end
 
 % Set current toolbox version
-toolboxVersion = ['2.5.27 - ' computer];
+toolboxVersion = ['2.5.28 - ' computer];
 
 switch auto  
   case 'auto',    autoIMOSToolbox(toolboxVersion, varargin{:});