Merge pull request #353 from aodn/2.5.10

2.5.10
aodn · May 30, 2016 · e98338d · e98338d
2 parents bcf31e5 + 1c10a87
commit e98338d
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Showing 79 changed files with 418 additions and 361 deletions.
diff --git a/AutomaticQC/imosImpossibleDepthQC.m b/AutomaticQC/imosImpossibleDepthQC.m
@@ -100,9 +100,8 @@
 depthInfos = {'DEPTH', 'PRES_REL', 'PRES'};
 if ~any(strcmpi(paramName, depthInfos)), return; end
 
-% get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
-% If no value is set then default mode is 'timeSeries'
-mode = lower(readProperty('toolbox.mode'));
+% get the toolbox execution mode
+mode = readProperty('toolbox.mode');
 
 switch mode
     case 'profile'
@@ -198,7 +197,7 @@
             end
         end
 
-    otherwise % 'timeSeries'
+    case 'timeSeries'
         % this test doesn't apply on dimensions
         if ~strcmp(type, 'variables'), return; end
 

diff --git a/AutomaticQC/imosInOutWaterQC.m b/AutomaticQC/imosInOutWaterQC.m
@@ -92,9 +92,8 @@
 end
 time = sample_data.(tTime){iTime}.data;
 
-% get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
-% If no value is set then default mode is 'timeSeries'
-mode = lower(readProperty('toolbox.mode'));
+% get the toolbox execution mode
+mode = readProperty('toolbox.mode');
 
 switch mode
     case 'profile'
@@ -110,7 +109,7 @@
             error(['TIME value ' datestr(time, 'yyyy-mm-dd HH:MM:SS') ' is greater than time_deployment_end ' datestr(time_out_water, 'yyyy-mm-dd HH:MM:SS') ' => Check ddb station time values against data file time values!']);
         end
 
-    otherwise % 'timeSeries'
+    case 'timeSeries'
         qcSet     = str2double(readProperty('toolbox.qc_set'));
         rawFlag   = imosQCFlag('raw', qcSet, 'flag');
         failFlag  = imosQCFlag('bad', qcSet, 'flag');

diff --git a/AutomaticQC/imosRegionalRangeQC.m b/AutomaticQC/imosRegionalRangeQC.m
@@ -87,7 +87,6 @@
 %     site = sample_data.meta.site_name; % source = ddb
 %     if strcmpi(site, 'UNKNOWN'), site = sample_data.site_code; end % source = global_attributes file
 site = sample_data.site_code;
-site = imosSites(site);
 
 % test if site information exists
 if isempty(site)
@@ -121,11 +120,11 @@
     end
 
     % read values from imosRegionalRangeQC properties file
-    [regionalMin, regionalMax, isSite] = getImosRegionalRange(site.name, paramName);
+    [regionalMin, regionalMax, isSite] = getImosRegionalRange(site, paramName);
 
     if ~isSite
         fprintf('%s\n', ['Warning : ' 'File imosRegionalRangeQC.txt is not documented '...
-        'for site ' site.name]);
+        'for site ' site]);
     else
         if ~isnan(regionalMin)
             % get the flag values with which we flag good and out of range data

diff --git a/AutomaticQC/imosVerticalVelocityQC.m b/AutomaticQC/imosVerticalVelocityQC.m
@@ -73,7 +73,7 @@
 % get all necessary dimensions and variables id in sample_data struct
 idWcur = 0;
 paramName = sample_data.(type){k}.name;
-if strcmpi(paramName, 'WCUR'), idWcur = k; end
+if strncmpi(paramName, 'WCUR', 4), idWcur = k; end
 
 % check if the data is compatible with the QC algorithm
 idMandatory = idWcur;

diff --git a/FlowManager/autoIMOSToolbox.m b/FlowManager/autoIMOSToolbox.m
@@ -65,27 +65,16 @@ function autoIMOSToolbox(toolboxVersion, fieldTrip, dataDir, ppChain, qcChain, e
 %
 narginchk(1, 6);
 
-% get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
-% If no value is set then default mode is 'timeSeries'
-mode = lower(readProperty('toolbox.mode'));
+% get the toolbox execution mode.
+mode = readProperty('toolbox.mode');
 
 % validate and save field trip
 if nargin > 1
     if isnumeric(fieldTrip), error('field trip must be a string'); end
-    switch mode
-        case 'profile'
-            writeProperty('startDialog.fieldTrip.profile', fieldTrip);
-        otherwise
-            writeProperty('startDialog.fieldTrip.timeSeries', fieldTrip);
-    end
+    writeProperty(['startDialog.fieldTrip.' mode], fieldTrip);
 else
     try
-        switch mode
-            case 'profile'
-                fieldTrip = readProperty('startDialog.fieldTrip.profile');
-            otherwise
-                fieldTrip = readProperty('startDialog.fieldTrip.timeSeries');
-        end
+        fieldTrip = readProperty(['startDialog.fieldTrip.' mode]);
     catch e
     end
 end
@@ -95,20 +84,10 @@ function autoIMOSToolbox(toolboxVersion, fieldTrip, dataDir, ppChain, qcChain, e
     if ~ischar(dataDir),       error('dataDir must be a string');    end
     if ~exist(dataDir, 'dir'), error('dataDir must be a directory'); end
 
-    switch mode
-        case 'profile'
-            writeProperty('startDialog.dataDir.profile', dataDir);
-        otherwise
-            writeProperty('startDialog.dataDir.timeSeries', dataDir);
-    end
+    writeProperty(['startDialog.dataDir.' mode], dataDir);
 else
     try
-        switch mode
-            case 'profile'
-                dataDir = readProperty('startDialog.dataDir.profile');
-            otherwise
-                dataDir = readProperty('startDialog.dataDir.timeSeries');
-        end
+        dataDir = readProperty(['startDialog.dataDir.' mode]);
     catch e
     end
 end
@@ -134,12 +113,7 @@ function autoIMOSToolbox(toolboxVersion, fieldTrip, dataDir, ppChain, qcChain, e
         ppChainStr = '';
     end
 
-    switch mode
-        case 'profile'
-            writeProperty('preprocessManager.preprocessChain.profile', ppChainStr);
-        otherwise
-            writeProperty('preprocessManager.preprocessChain.timeSeries', ppChainStr);
-    end
+    writeProperty(['preprocessManager.preprocessChain.' mode], ppChainStr);
 end
 
 % validate and save qc chain
@@ -163,12 +137,7 @@ function autoIMOSToolbox(toolboxVersion, fieldTrip, dataDir, ppChain, qcChain, e
         qcChainStr = '';
     end
 
-    switch mode
-        case 'profile'
-            writeProperty('autoQCManager.autoQCChain.profile', qcChainStr);
-        otherwise
-            writeProperty('autoQCManager.autoQCChain.timeSeries', qcChainStr);
-    end
+    writeProperty(['autoQCManager.autoQCChain.' mode], qcChainStr);
 end
 
 % validate and save export dir
@@ -189,15 +158,11 @@ function autoIMOSToolbox(toolboxVersion, fieldTrip, dataDir, ppChain, qcChain, e
 [~, sourceFolder] = fileparts(dataDir);
 fprintf('%s\n', ['Processing field trip ' fieldTrip ' from folder ' sourceFolder]);
 
-% get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
-% If no value is set then default mode is 'timeSeries'
-mode = lower(readProperty('toolbox.mode'));
-
 % get infos from current field trip
 switch mode
     case 'profile'
         [~, deps, sits, dataDir] = getCTDs(true);
-    otherwise
+    case 'timeSeries'
         [~, deps, sits, dataDir] = getDeployments(true);
 end
 

diff --git a/FlowManager/autoQCManager.m b/FlowManager/autoQCManager.m
@@ -75,7 +75,7 @@
 
   % get last filter chain if there is one
   try
-      % get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
+      % get the toolbox execution mode
       mode = readProperty('toolbox.mode');
       qcChain = textscan(readProperty(['autoQCManager.autoQCChain.' mode]), '%s');
       qcChain = qcChain{1};
@@ -227,8 +227,7 @@
   qcRoutines = listAutoQCRoutines();
   qcChain    = {};
 
-  % get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
-  % If no value is set then default mode is 'timeSeries'
+  % get the toolbox execution mode
   mode = readProperty('toolbox.mode');
 
   % get default filter chain if there is one

diff --git a/FlowManager/displayManager.m b/FlowManager/displayManager.m
@@ -115,9 +115,8 @@ function displayManager(windowTitle, sample_data, callbacks)
   qcSet      = str2double(readProperty('toolbox.qc_set'));
   badFlag    = imosQCFlag('bad', qcSet, 'flag');
 
-  % get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
-  % If no value is set then default mode is 'timeSeries'
-  mode = lower(readProperty('toolbox.mode'));
+  % get the toolbox execution mode
+  mode = readProperty('toolbox.mode');
 
   % define the user options, and create the main window
   states = {'Import', 'Metadata', 'Raw data', 'QC data', 'QC stats', 'Reset manual QC' ...
@@ -240,7 +239,7 @@ function rawDataCallback()
       switch mode
           case 'profile'
               nVar = length(sample_data{setIdx}.variables) - 5;
-          otherwise
+          case 'timeSeries'
               nVar = length(sample_data{setIdx}.variables) - 3;
       end
       vars(vars > nVar) = [];

diff --git a/FlowManager/exportManager.m b/FlowManager/exportManager.m
@@ -75,9 +75,8 @@ function exportManager(dataSets, levelNames, output, auto)
     otherwise,     error(['unknown output type: ' output]);
   end
 
-  % get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
-  % If no value is set then default mode is 'timeSeries'
-  mode = lower(readProperty('toolbox.mode'));
+  % get the toolbox execution mode
+  mode = readProperty('toolbox.mode');
 
   setNames = {};
   for k = 1:numSets
@@ -246,38 +245,39 @@ function exportQCPlots(sample_data, exportDir, mode, auto, progress)
 
 paramsName = unique(paramsName);
 
-if strcmpi(mode, 'timeseries')
-    % we get rid of specific parameters
-    notNeededParams = {'TIMESERIES', 'PROFILE', 'TRAJECTORY', 'LATITUDE', 'LONGITUDE', 'NOMINAL_DEPTH'};
-    for i=1:length(notNeededParams)
-        iNotNeeded = strcmpi(paramsName, notNeededParams{i});
-        paramsName(iNotNeeded) = [];
-    end
-
-    % timeseries specific plots
-    nParams = length(paramsName);
-    for i=1:nParams
-        if ~auto
-            waitbar(i / nParams, progress, ['Exporting ' paramsName{i} ' plots']);
+switch mode
+    case 'timeSeries'
+        % we get rid of specific parameters
+        notNeededParams = {'TIMESERIES', 'PROFILE', 'TRAJECTORY', 'LATITUDE', 'LONGITUDE', 'NOMINAL_DEPTH'};
+        for i=1:length(notNeededParams)
+            iNotNeeded = strcmpi(paramsName, notNeededParams{i});
+            paramsName(iNotNeeded) = [];
         end
+
+        % timeseries specific plots
+        nParams = length(paramsName);
+        for i=1:nParams
+            if ~auto
+                waitbar(i / nParams, progress, ['Exporting ' paramsName{i} ' plots']);
+            end
+            try
+                lineMooring1DVar(sample_data, paramsName{i}, true, true, exportDir);
+                scatterMooring1DVarAgainstDepth(sample_data, paramsName{i}, true, true, exportDir);
+                scatterMooring2DVarAgainstDepth(sample_data, paramsName{i}, true, true, exportDir);
+                %pcolorMooring2DVar(sample_data, paramsName{i}, true, true, exportDir);
+            catch e
+                errorString = getErrorString(e);
+                fprintf('%s\n',   ['Error says : ' errorString]);
+            end
+        end
+    case 'profile'
+        % profile specific plots
         try
-            lineMooring1DVar(sample_data, paramsName{i}, true, true, exportDir);
-            scatterMooring1DVarAgainstDepth(sample_data, paramsName{i}, true, true, exportDir);
-            scatterMooring2DVarAgainstDepth(sample_data, paramsName{i}, true, true, exportDir);
-            %pcolorMooring2DVar(sample_data, paramsName{i}, true, true, exportDir);
+            lineCastVar(sample_data, paramsName, true, true, exportDir);
         catch e
             errorString = getErrorString(e);
             fprintf('%s\n',   ['Error says : ' errorString]);
         end
-    end
-else
-    % profile specific plots
-    try
-        lineCastVar(sample_data, paramsName, true, true, exportDir);
-    catch e
-        errorString = getErrorString(e);
-        fprintf('%s\n',   ['Error says : ' errorString]);
-    end
 end
 
 

diff --git a/FlowManager/flowManager.m b/FlowManager/flowManager.m
@@ -43,9 +43,8 @@ function flowManager(toolboxVersion)
 
   lastAutoQCSetIdx = 0;
 
-  % get the toolbox execution mode. Values can be 'timeSeries' and 'profile'. 
-  % If no value is set then default mode is 'timeSeries'
-  mode = lower(readProperty('toolbox.mode'));
+  % get the toolbox execution mode
+  mode = readProperty('toolbox.mode');
 
   % import data
   nonUTCRawData = importManager(toolboxVersion);