Merge pull request #497 from aodn/2.5.37

2.5.37
aodn · Mar 22, 2018 · a0eb1a5 · a0eb1a5
2 parents 8d7823e + 0b0d6d0
commit a0eb1a5
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Showing 21 changed files with 164 additions and 106 deletions.
diff --git a/Graph/checkMooringPlannedDepths.m b/Graph/checkMooringPlannedDepths.m
@@ -72,7 +72,7 @@ function checkMooringPlannedDepths(sample_data, isQC, saveToFile, exportDir)
 timeVar = dataVar;
 isPlottable = false;
 
-backgroundColor = [0.85 0.85 0.85];
+backgroundColor = [1 1 1]; % white
 
 for i=1:lenSampleData
     %only look at instruments with pressure
@@ -184,6 +184,7 @@ function checkMooringPlannedDepths(sample_data, isQC, saveToFile, exportDir)
     'Name',             title, ...
     'NumberTitle',      'off', ...
     'Visible',          visible, ...
+    'Color',            backgroundColor, ...
     'OuterPosition',    monitorRect(iBigMonitor, :));
 
 hAxPress     = subplot(2,1,1,'Parent', hFigPress);
@@ -206,9 +207,10 @@ function checkMooringPlannedDepths(sample_data, isQC, saveToFile, exportDir)
 hold(hAxDepthDiff, 'on');
 grid(hAxDepthDiff, 'on');
 
-% set background to be grey
-set(hAxPress, 'Color', backgroundColor);
-set(hAxDepthDiff, 'Color', backgroundColor);
+% set axes background to be transparent (figure color shows
+% through)
+set(hAxPress, 'Color', 'none');
+set(hAxDepthDiff, 'Color', 'none');
 
 %color map
 lenMetaDepth = length(metaDepth);
@@ -222,7 +224,7 @@ function checkMooringPlannedDepths(sample_data, isQC, saveToFile, exportDir)
 cMap = flipud(cMap);
 
 % dummy entry for first entry in legend
-hLineVar(1) = plot(hAxPress, 0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color grey same as background (invisible)
+hLineVar(1) = plot(hAxPress, 0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color same as background (invisible in legend)
 
 %now plot the data:Have to do it one at a time to get the colors right..
 for i = 1:lenMetaDepth
@@ -272,7 +274,7 @@ function checkMooringPlannedDepths(sample_data, isQC, saveToFile, exportDir)
         'FontSize', fontSizeAx,...
         'xscale', xscale);
     posAx = get(hAxPress, 'Position');
-    set(hLegend, 'Units', 'Normalized', 'color', backgroundColor);
+    set(hLegend, 'Units', 'Normalized', 'Color', 'none');
 
     % for some reason this call brings everything back together while it
     % shouldn't have moved previously anyway...
@@ -355,7 +357,7 @@ function checkMooringPlannedDepths(sample_data, isQC, saveToFile, exportDir)
         fileName = strrep(fileName, '_PARAM_', '_DEPTH_vs_NOMINAL_DEPTH_'); % IMOS_[sub-facility_code]_[site_code]_FV01_[deployment_code]_[PLOT-TYPE]_[PARAM]_C-[creation_date].png
         fileName = strrep(fileName, '_PLOT-TYPE_', '_CHECK_');
 
-        fastSaveas(hFigPress, fullfile(exportDir, fileName));
+        fastSaveas(hFigPress, backgroundColor, fullfile(exportDir, fileName));
 
         close(hFigPress);
     end

diff --git a/Graph/checkMooringPresDiffs.m b/Graph/checkMooringPresDiffs.m
@@ -125,7 +125,7 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
 
 isPlottable = false;
 
-backgroundColor = [0.85 0.85 0.85];
+backgroundColor = [1 1 1]; % white
 
 %plot
 fileName = genIMOSFileName(sample_data{iCurrSam}, 'png');
@@ -135,14 +135,15 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
     'Name',             title, ...
     'NumberTitle',      'off', ...
     'Visible',          visible, ...
+    'Color',            backgroundColor, ...
     'OuterPosition',    monitorRect(iBigMonitor, :));
 
 %pressure plot
 hAxPress = subplot(2,1,1,'Parent', hFigPressDiff);
 set(hAxPress, 'YDir', 'reverse')
 set(get(hAxPress, 'XLabel'), 'String', 'Time');
 set(get(hAxPress, 'YLabel'), 'String', [presRelCode ' (' varUnit ')'], 'Interpreter', 'none');
-set(get(hAxPress, 'Title'), 'String', [varTitle '( ' varUnit ')'], 'Interpreter', 'none');
+set(get(hAxPress, 'Title'), 'String', [varTitle ' (' varUnit ')'], 'Interpreter', 'none');
 set(hAxPress, 'XTick', (xMin:(xMax-xMin)/4:xMax));
 set(hAxPress, 'XLim', [xMin, xMax]);
 hold(hAxPress, 'on');
@@ -152,16 +153,13 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
 set(get(hAxPressDiff, 'XLabel'), 'String', 'Time');
 set(get(hAxPressDiff, 'YLabel'), 'String', ['Pressure differences (' varUnit ')'], 'Interpreter', 'none');
 set(get(hAxPressDiff, 'Title'), 'String', ...
-    ['Pressure differences in ' varUnit ' (minus respective median over 1st quarter) between ' instrumentDesc{iCurrSam} ' (in black above) and 4 (max) nearest neighbours'] , 'Interpreter', 'none');
+    ['Pressure differences in ' varUnit ' (minus respective median over 1st quarter) between ' instrumentDesc{iCurrSam} ' (in black above) and 4 (when possible) nearest neighbours'] , 'Interpreter', 'none');
 set(hAxPressDiff, 'XTick', (xMin:(xMax-xMin)/4:xMax));
 set(hAxPressDiff, 'XLim', [xMin, xMax]);
 hold(hAxPressDiff, 'on');
 
 linkaxes([hAxPressDiff,hAxPress],'x')
 
-%zero line
-line([xMin, xMax], [0, 0], 'Color', 'black');
-
 %now plot the data of interest:
 iCurrTime = getVar(sample_data{iCurrSam}.dimensions, 'TIME');
 curSamTime = sample_data{iCurrSam}.dimensions{iCurrTime}.data;
@@ -197,14 +195,17 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
     nOthers = nOthersMax;
 end
 
+% put iOthers back in metaDepth order
+iOthers = sort(iOthers);
+
 %color map
-% no need to reverse the colorbar since instruments are plotted from
-% nearest (blue) to farthest (yellow)
+% we reverse the colormap since we want close to bottom == blue while close
+% to surface == yellow.
 try
     defaultColormapFh = str2func(readProperty('visualQC.defaultColormap'));
-    cMap = colormap(hAxPress, defaultColormapFh(nOthers));
+    cMap = flipud(colormap(hAxPress, defaultColormapFh(nOthers)));
 catch e
-    cMap = colormap(hAxPress, parula(nOthers));
+    cMap = flipud(colormap(hAxPress, parula(nOthers)));
 end
 % current sample is black
 cMap(iOthers == iCurrSam, :) = [0, 0, 0];
@@ -268,9 +269,10 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
             'LineStyle', '-', ...
             'Parent',    hAxPressDiff);
 
-        % set background to be grey
-        set(hAxPress, 'Color', backgroundColor)
-        set(hAxPressDiff, 'Color', backgroundColor)
+        % set axes background to be transparent (figure color shows
+        % through)
+        set(hAxPress, 'Color', 'none')
+        set(hAxPressDiff, 'Color', 'none')
     end
 end
 
@@ -289,14 +291,7 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
     'Layer',        'top');
 
 if isPlottable
-    iOthersLogical = false(max(iOthers), 1);
-    iOthersLogical(iOthers) = true;
-    iNan = isnan(hLineVar);
-    if any(iNan)
-        hLineVar(iNan) = [];
-        instrumentDesc(iNan) = [];
-        iOthersLogical(iNan) = [];
-    end
+    instrumentDesc = instrumentDesc(iOthers);
 
     datetick(hAxPressDiff, 'x', 'dd-mm-yy HH:MM:SS', 'keepticks');
     datetick(hAxPress, 'x', 'dd-mm-yy HH:MM:SS', 'keepticks');
@@ -315,14 +310,14 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
         xscale = 0.75;
     end
     hYBuffer = 1.1 * (2*(fontSizeAx + fontSizeLb));
-    hLegend = legendflex(hAxPress, instrumentDesc(iOthersLogical),...
+    hLegend = legendflex(hAxPress, instrumentDesc,...
         'anchor', [6 2], ...
         'buffer', [0 -hYBuffer], ...
         'ncol', nCols,...
         'FontSize', fontSizeAx,...
         'xscale', xscale);
     posAx = get(hAxPress, 'Position');
-    set(hLegend, 'Units', 'Normalized', 'color', backgroundColor);
+    set(hLegend, 'Units', 'Normalized', 'Color', 'none');
 
     % for some reason this call brings everything back together while it
     % shouldn't have moved previously anyway...
@@ -332,7 +327,7 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
         fileName = strrep(fileName, '_PARAM_', ['_', varName, '_']); % IMOS_[sub-facility_code]_[site_code]_FV01_[deployment_code]_[PLOT-TYPE]_[PARAM]_C-[creation_date].png
         fileName = strrep(fileName, '_PLOT-TYPE_', '_LINE_');
 
-        fastSaveas(hFigPressDiff, fullfile(exportDir, fileName));
+        fastSaveas(hFigPressDiff, backgroundColor, fullfile(exportDir, fileName));
 
         close(hFigPressDiff);
     end

diff --git a/Graph/diagramMooring1DVarAgainstOther.m b/Graph/diagramMooring1DVarAgainstOther.m
@@ -1,6 +1,6 @@
 function diagramMooring1DVarAgainstOther(sample_data, varName, yAxisVarName, isQC, saveToFile, exportDir)
 %DIAGRAMMOORING1DVARAGAINSTOTHER Opens a new window where the selected 1D
-% variable collected by all the intruments on the mooring are plotted in a digram plot.
+% variable collected by all the intruments on the mooring are plotted in a diagram plot.
 %
 % Inputs:
 %   sample_data - cell array of structs containing the entire data set and dimension data.
@@ -169,7 +169,7 @@ function diagramMooring1DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
     end
 end
 
-backgroundColor = [0.85 0.85 0.85];
+backgroundColor = [1 1 1]; % white
 
 if any(isPlottable)
     % collect visualQC config
@@ -210,6 +210,7 @@ function diagramMooring1DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
                     'Name',             title, ...
                     'NumberTitle',      'off', ...
                     'Visible',          visible, ...
+                    'Color',            backgroundColor, ...
                     'OuterPosition',    monitorRect(iBigMonitor, :));
 
                 hAxMooringVar = axes('Parent',   hFigMooringVar);
@@ -224,7 +225,7 @@ function diagramMooring1DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
                 hold(hAxMooringVar, 'on');
 
                 % dummy entry for first entry in legend
-                hScatterVar(1) = plot(0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color grey same as background (invisible)
+                hScatterVar(1) = plot(0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color same as background (invisible in legend)
 
                 % set data cursor mode custom display
                 dcm_obj = datacursormode(hFigMooringVar);
@@ -349,8 +350,9 @@ function diagramMooring1DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
                     'YGrid',        'on', ...
                     'Layer',        'top');
 
-                % set background to be grey
-                set(hAxMooringVar, 'Color', backgroundColor)
+                % set axes background to be transparent (figure color shows
+                % through)
+                set(hAxMooringVar, 'Color', 'none')
             end
 
             if strcmpi(yAxisVarName, 'DEPTH')
@@ -418,7 +420,7 @@ function diagramMooring1DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
             end
         end
         posAx = get(hAxMooringVar, 'Position');
-        set(hLegend, 'Units', 'Normalized', 'color', backgroundColor);
+        set(hLegend, 'Units', 'Normalized', 'Color', 'none');
         posLh = get(hLegend, 'Position');
         if posLh(2) < 0
             set(hLegend, 'Position',[posLh(1), abs(posLh(2)), posLh(3), posLh(4)]);
@@ -440,7 +442,7 @@ function diagramMooring1DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
         fileName = strrep(fileName, '_PARAM_', ['_' varName '_vs_' yAxisVarName '_']); % IMOS_[sub-facility_code]_[site_code]_FV01_[deployment_code]_[PLOT-TYPE]_[PARAM]_vs_[OTHER-PARAM]_C-[creation_date].png
         fileName = strrep(fileName, '_PLOT-TYPE_', '_DIAGRAM_');
 
-        fastSaveas(hFigMooringVar, fullfile(exportDir, fileName));
+        fastSaveas(hFigMooringVar, backgroundColor, fullfile(exportDir, fileName));
 
         close(hFigMooringVar);
     end

diff --git a/Graph/diagramMooring2DVarAgainstOther.m b/Graph/diagramMooring2DVarAgainstOther.m
@@ -225,7 +225,7 @@ function diagramMooring2DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
     end
 end
 
-backgroundColor = [0.85 0.85 0.85];
+backgroundColor = [1 1 1]; % white
 
 if any(isPlottable)
     % collect visualQC config
@@ -280,6 +280,7 @@ function diagramMooring2DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
                     'Name',             title, ...
                     'NumberTitle',      'off', ...
                     'Visible',          visible, ...
+                    'Color',            backgroundColor, ...
                     'OuterPosition',    monitorRect(iBigMonitor, :));
 
                 hAxMooringVar = axes('Parent', hFigMooringVar);
@@ -294,7 +295,7 @@ function diagramMooring2DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
                 hold(hAxMooringVar, 'on');
 
                 % dummy entry for first entry in legend
-                hScatterVar(1) = plot(0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color grey same as background (invisible)
+                hScatterVar(1) = plot(0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color same as background (invisible in legend)
 
                 % set data cursor mode custom display
                 dcm_obj = datacursormode(hFigMooringVar);
@@ -445,8 +446,9 @@ function diagramMooring2DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
                     'YGrid',        'on', ...
                     'Layer',        'top');
 
-                % set background to be grey
-                set(hAxMooringVar, 'Color', backgroundColor)
+                % set axes background to be transparent (figure color shows
+                % through)
+                set(hAxMooringVar, 'Color', 'none')
             end
 
             if strcmpi(yAxisVarName, 'DEPTH')
@@ -509,7 +511,7 @@ function diagramMooring2DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
         end
     end
     posAx = get(hAxMooringVar, 'Position');
-    set(hLegend, 'Units', 'Normalized', 'color', backgroundColor)
+    set(hLegend, 'Units', 'Normalized', 'Color', 'none')
     posLh = get(hLegend, 'Position');
     if posLh(2) < 0
         set(hLegend, 'Position',[posLh(1), abs(posLh(2)), posLh(3), posLh(4)]);
@@ -524,7 +526,7 @@ function diagramMooring2DVarAgainstOther(sample_data, varName, yAxisVarName, isQ
         fileName = strrep(fileName, '_PARAM_', ['_' varName '_vs_' yAxisVarName '_']); % IMOS_[sub-facility_code]_[site_code]_FV01_[deployment_code]_[PLOT-TYPE]_[PARAM]_vs_[OTHER-PARAM]_C-[creation_date].png
         fileName = strrep(fileName, '_PLOT-TYPE_', '_DIAGRAM_');
 
-        fastSaveas(hFigMooringVar, fullfile(exportDir, fileName));
+        fastSaveas(hFigMooringVar, backgroundColor, fullfile(exportDir, fileName));
 
         close(hFigMooringVar);
     end

diff --git a/Graph/lineCastVar.m b/Graph/lineCastVar.m
@@ -57,7 +57,7 @@ function lineCastVar(sample_data, varNames, isQC, saveToFile, exportDir)
 
 initiateFigure = true;
 
-backgroundColor = [0.85 0.85 0.85];
+backgroundColor = [1 1 1]; % white
 
 lenVarNames = length(varNames);
 for k=1:lenVarNames
@@ -122,6 +122,7 @@ function lineCastVar(sample_data, varNames, isQC, saveToFile, exportDir)
                     'Name',             title, ...
                     'NumberTitle',      'off', ...
                     'Visible',          visible, ...
+                    'Color',            backgroundColor, ...
                     'OuterPosition',    monitorRect(iBigMonitor, :));
 
                 initiateFigure = false;
@@ -147,7 +148,7 @@ function lineCastVar(sample_data, varNames, isQC, saveToFile, exportDir)
                 hold(hAxCastVar, 'on');
 
                 % dummy entry for first entry in legend
-                hLineVar(1) = plot(0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color grey same as background (invisible)
+                hLineVar(1) = plot(0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color same as background (invisible in legend)
 
                 cMap = colormap(hAxCastVar, parula(lenSampleData));
                 cMap = flipud(cMap);
@@ -265,8 +266,9 @@ function lineCastVar(sample_data, varNames, isQC, saveToFile, exportDir)
                 'YGrid',        'on', ...
                 'Layer',        'top');
 
-            % set background to be grey
-            set(hAxCastVar, 'Color', backgroundColor)
+            % set axes background to be transparent (figure color shows
+            % through)
+            set(hAxCastVar, 'Color', 'none')
         end
     end
 
@@ -297,7 +299,7 @@ function lineCastVar(sample_data, varNames, isQC, saveToFile, exportDir)
 if saveToFile
     fileName = strrep(fileName, '_PLOT-TYPE_', '_LINE_'); % IMOS_[sub-facility_code]_[platform_code]_FV01_[time_coverage_start]_[PLOT-TYPE]_C-[creation_date].png
 
-    fastSaveas(hFigCastVar, fullfile(exportDir, fileName));
+    fastSaveas(hFigCastVar, backgroundColor, fullfile(exportDir, fileName));
 
     close(hFigCastVar);
 end