Merge pull request #406 from aodn/2.5.23

2.5.23

FlowManager/autoQCManager.m

@@ -126,8 +126,8 @@
       end
   end
 
-  % we reset QC flags to 0
   for k = 1:length(sample_data)
+      % reset QC flags to 0
       type{1} = 'dimensions';
       type{2} = 'variables';
       for m = 1:length(type)
@@ -136,6 +136,9 @@
               sample_data{k}.(type{m}){l}.flags(:) = 0;
           end
       end
+
+      % reset QC results
+      sample_data{k}.meta.QCres = {};
   end
 
   % run each data set through the chain

Graph/TimeSeries/graphTimeSeriesGeneric.m

@@ -89,32 +89,6 @@
     end
 end
 
-% Set axis position so that 1D data and 2D data vertically matches on X axis
-mainPanel = findobj('Tag', 'mainPanel');
-last_pos_with_colorbar = get(mainPanel, 'UserData');
-if isempty(last_pos_with_colorbar) % this is to avoid too many calls to colorbar()
-    cb = colorbar();
-    set(get(cb, 'YLabel'), 'String', 'TEST');
-    pos_with_colorbar = get(ax, 'Position');
-    last_pos_with_colorbar = pos_with_colorbar;
-    colorbar(cb, 'off');
-    set(mainPanel, 'UserData', last_pos_with_colorbar);
-else
-    pos_with_colorbar = get(ax, 'Position');
-
-    if pos_with_colorbar(1) == last_pos_with_colorbar(1)
-        pos_with_colorbar(3) = last_pos_with_colorbar(3);
-    else
-        cb = colorbar();
-        set(get(cb, 'YLabel'), 'String', 'TEST');
-        pos_with_colorbar = get(ax, 'Position');
-        last_pos_with_colorbar = pos_with_colorbar;
-        colorbar(cb, 'off');
-        set(mainPanel, 'UserData', last_pos_with_colorbar);
-    end
-end
-set(ax, 'Position', pos_with_colorbar);
-
 % set background to be grey
 set(ax, 'Color', [0.75 0.75 0.75])
 

Graph/TimeSeries/graphTimeSeriesTimeDepth.m

@@ -70,9 +70,15 @@
 % xPcolor = [time.data(1:end-1) - diff(time.data)/2; time.data(end) - (time.data(end)-time.data(end-1))/2];
 % yPcolor = [depth.data(1:end-1) - diff(depth.data)/2; depth.data(end) - (depth.data(end)-depth.data(end-1))/2];
 
+posWithoutCb = get(ax, 'Position');
+
 h = pcolor(ax, double(xPcolor), double(yPcolor), double(var.data'));
 set(h, 'FaceColor', 'flat', 'EdgeColor', 'none');
-cb = colorbar();
+cb = colorbar('peer', ax);
+
+% reset position to what it was without the colorbar so that it aligns with
+% 1D datasets
+set(ax, 'Position', posWithoutCb);
 
 % Attach the context menu to colorbar
 hMenu = setTimeSerieColorbarContextMenu(var);

Graph/TimeSeries/graphTimeSeriesTimeFrequency.m

@@ -72,7 +72,7 @@
 
 h = pcolor(ax, double(xPcolor), double(yPcolor), double(var.data'));
 set(h, 'FaceColor', 'flat', 'EdgeColor', 'none');
-cb = colorbar();
+cb = colorbar('peer',ax);
 
 % Attach the context menu to colorbar
 hMenu = setTimeSerieColorbarContextMenu(var);

Graph/TimeSeries/graphTimeSeriesTimeFrequencyDirection.m

@@ -200,7 +200,7 @@
     'Position'  , posUi2(mainPanel, 50, 1, 50, 1, 0), ...
     'String'    ,'Time cursor');
 
-cb = colorbar();
+cb = colorbar('peer',ax);
 
 % Attach the context menu to colorbar
 hMenu = setTimeSerieColorbarContextMenu(myVar);

Graph/graphTimeSeries.m

@@ -1,4 +1,4 @@
-function [graphs lines vars] = graphTimeSeries( parent, sample_data, vars )
+function [graphs, lines, vars] = graphTimeSeries( parent, sample_data, vars )
 %GRAPHTIMESERIES Graphs the given data in a time series style using subplots.
 %
 % Graphs the selected variables from the given data set. Each variable is
@@ -186,20 +186,46 @@
     col = col(mod(vars(k),length(col))+1,:);
 
     % plot the variable
-    [lines(k,:) labels] = plotFunc(graphs(k), sample_data, k, col, xTickProp);
+    [lines(k,:), labels] = plotFunc(graphs(k), sample_data, k, col, xTickProp);
 
     if ~isempty(labels)
         % set x labels and ticks
         xlabel(graphs(k), labels{1});
 
         % set y label and ticks
-        try      uom = [' (' imosParameters(labels{2}, 'uom') ')'];
+        try      uom = ['(' imosParameters(labels{2}, 'uom') ')'];
         catch e, uom = '';
         end
-        yLabel = strrep([labels{2} uom], '_', ' ');
-        if length(yLabel) > 20, yLabel = [yLabel(1:17) '...']; end
+
+        % decide where to cut the Y label to display it on 1 or 2 lines 
+        % depending on the number of words obtained from the variable name
+        yLabel = regexp(labels{2}, '\_', 'split');
+        if numel(yLabel) < 4
+            nthWordToCut = min(2, numel(yLabel));
+        elseif numel(yLabel) < 6
+            nthWordToCut = 3;
+        else
+            nthWordToCut = 4;
+        end
+        yLabel = {strjoin(yLabel(1:nthWordToCut),     ' '), ...
+                  strjoin(yLabel(nthWordToCut+1:end), ' ')};
+        yLabel = yLabel(~cellfun(@isempty, yLabel));
+
+        yLabel{end+1} = strrep(uom, '_', ' ');
+        iLength = 12; % arbitrary string cutoff length
+        %iLong = strlength(yLabel) > iLength; % only R2016b onwards
+        iLong = cellfun(@length, yLabel) > iLength;
+        yLabel(iLong) = cellfun(@(x) [x(1:iLength) '...'], yLabel(iLong), 'UniformOutput', false);
         ylabel(graphs(k), yLabel);
     end
   end
-
+
+    function str = strjoin(strCell, sep)
+        %STRJOIN Join strings in a cell array.
+        % http://stackoverflow.com/questions/5292437/how-can-i-concatenate-strings-in-a-cell-array-with-spaces-between-them-in-matlab
+        % R2012b onwards
+        nCells = numel(strCell);
+        strCell(1:nCells-1) = strcat(strCell(1:nCells-1), {sep});
+        str = [strCell{:}];
+    end
 end

IMOS/finaliseData.m

@@ -96,6 +96,10 @@
       end
   end
 
+  % CF requires DEPTH/TIME coordinate variables must be monotonic (strictly increasing 
+  % or decreasing)
+  sam = forceMonotonic(sam, mode);
+
   % add empty QC flags for all variables
   for k = 1:length(sam.variables)
 
@@ -181,27 +185,27 @@
   % set the time coverage period from the data
   switch mode
       case 'profile'
-          time = getVar(sam.variables, 'TIME');
-          if time ~= 0
+          iTime = getVar(sam.variables, 'TIME');
+          if iTime ~= 0
               if isempty(sam.time_coverage_start),
-                  sam.time_coverage_start = sam.variables{time}.data(1);
+                  sam.time_coverage_start = sam.variables{iTime}.data(1);
               end
               if isempty(sam.time_coverage_end),
-                  sam.time_coverage_end   = sam.variables{time}.data(end);
+                  sam.time_coverage_end   = sam.variables{iTime}.data(end);
               end
           else
               if isempty(sam.time_coverage_start), sam.time_coverage_start = []; end
               if isempty(sam.time_coverage_end),   sam.time_coverage_end   = []; end
           end
 
       case 'timeSeries'
-          time = getVar(sam.dimensions, 'TIME');
-          if time ~= 0
+          iTime = getVar(sam.dimensions, 'TIME');
+          if iTime ~= 0
               if isempty(sam.time_coverage_start),
-                  sam.time_coverage_start = sam.dimensions{time}.data(1);
+                  sam.time_coverage_start = sam.dimensions{iTime}.data(1);
               end
               if isempty(sam.time_coverage_end),
-                  sam.time_coverage_end   = sam.dimensions{time}.data(end);
+                  sam.time_coverage_end   = sam.dimensions{iTime}.data(end);
               end
           else
               if isempty(sam.time_coverage_start), sam.time_coverage_start = []; end
@@ -210,4 +214,87 @@
 
   end
 
+end
+
+function sam = forceMonotonic(sam, mode)
+  % We make sure that DEPTH/TIME coordinate variables appear
+  % ordered 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';
+
+  end
+  iDim = getVar(sam.dimensions, dimensionName);
+
+  fixStr = ['Try to re-play and fix this dataset when possible using the ' ...
+      'manufacturer''s software before processing it with the toolbox.'];
+  currentDateStr = datestr(now_utc, readProperty('exportNetCDF.dateFormat'));
+
+  [sam.dimensions{iDim}.data, iSort] = sort(sam.dimensions{iDim}.data, sortMode);
+  if any(iSort ~= (1:length(sam.dimensions{iDim}.data))')
+      % We need to sort variables that are functions of this
+      % dimension accordingly
+      for k = 1:length(sam.variables)
+          iFunOfDim = sam.variables{k}.dimensions == iDim;
+          if any(iFunOfDim)
+              sam.variables{k}.data = sam.variables{k}.data(iSort,:); % data(iSort,:) works because we know that the sorted dimension is the first one!
+          end
+      end
+
+      sortedStr = [dimensionName ' values (and their corresponding measurements) had ' ...
+          'to be sorted ' sortModeStr];
+      disp(['Info : ' sortedStr ' in ' sam.toolbox_input_file '. ' fixStr]);
+      if isfield(sam.dimensions{iDim}, 'comment')
+          sam.dimensions{iDim}.comment = [sam.dimensions{iDim}.comment ' ' sortedStr '.'];
+      else
+          sam.dimensions{iDim}.comment = [sortedStr '.'];
+      end
+      if isfield(sam, 'history')
+          sam.history = sprintf('%s\n%s - %s', sam.history, currentDateStr, [sortedStr '.']);
+      else
+          sam.history = sprintf('%s - %s', currentDateStr, [sortedStr '.']);
+      end
+  end
+
+  iRedundantDim = [(diff(sam.dimensions{iDim}.data) == 0); false];
+  if any(iRedundantDim)
+      sam.dimensions{iDim}.data(iRedundantDim) = []; % removing first duplicate values
+
+      % We need to remove duplicates for variables that are functions of this
+      % dimension accordingly
+      for k = 1:length(sam.variables)
+          iFunOfDim = sam.variables{k}.dimensions == iDim;
+          if any(iFunOfDim)
+              extraDims = size(sam.variables{k}.data);
+              extraDims(iFunOfDim) = 1;
+              sam.variables{k}.data(repmat(iRedundantDim, extraDims)) = [];
+              extraDims(iFunOfDim) = length(sam.dimensions{iDim}.data);
+              sam.variables{k}.data = reshape(sam.variables{k}.data, extraDims);
+          end
+      end
+
+      redundantStr = [num2str(sum(iRedundantDim)) ' ' dimensionName ' first duplicate values ' ...
+          '(and their corresponding measurements) had to be discarded'];
+      disp(['Info : ' redundantStr ' in ' sam.toolbox_input_file '. ' fixStr]);
+      if isfield(sam.dimensions{iDim}, 'comment')
+          sam.dimensions{iDim}.comment = [sam.dimensions{iDim}.comment ' ' redundantStr '.'];
+      else
+          sam.dimensions{iDim}.comment = [redundantStr '.'];
+      end
+      if isfield(sam, 'history')
+          sam.history = sprintf('%s\n%s - %s', sam.history, currentDateStr, [redundantStr '.']);
+      else
+          sam.history = sprintf('%s - %s', currentDateStr, [redundantStr '.']);
+      end
+  end
+
 end