Merge pull request #501 from aodn/2.5.38

2.5.38
aodn · Apr 19, 2018 · d8ad331 · d8ad331
2 parents a0eb1a5 + e29ac0d
commit d8ad331
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Showing 25 changed files with 86 additions and 103 deletions.
diff --git a/AutomaticQC/imosDensityInversionSetQC.m b/AutomaticQC/imosDensityInversionSetQC.m
@@ -75,6 +75,7 @@
 % read dataset QC parameters if exist and override previous parameters file
 currentQCtest = mfilename;
 threshold = readDatasetParameter(sample_data.toolbox_input_file, currentQCtest, 'threshold', 0.03); % default threshold value of 0.03kg/m3
+threshold = threshold(1); % fix for compatibility with previous version 2.5.37 and older that used to unnecessarily store an array of thresholds
 
 qcSet = str2double(readProperty('toolbox.qc_set'));
 rawFlag         = imosQCFlag('raw',         qcSet, 'flag');
@@ -142,8 +143,6 @@
 deltaUpBottom = [rhoPotI - rhoPotIp1; NaN];
 deltaBottomUp = [NaN; rhoPotIp1 - rhoPotI];
 
-threshold = ones(lenDataTested, 1) .* threshold;
-
 iDensInv = deltaUpBottom >= threshold | deltaBottomUp <= -threshold;
 
 flagsTested(iDensInv) = badFlag;

diff --git a/AutomaticQC/imosImpossibleDateQC.m b/AutomaticQC/imosImpossibleDateQC.m
@@ -103,10 +103,7 @@
     end
 
     if any(~iGoodTime)
-        disp(['Warning : ' num2str(sum(~iGoodTime)) ' points failed Impossible date QC test in file ' sample_data.toolbox_input_file]);
-    end
-    if all(~iGoodTime)
-        error('All points failed');
+        error([num2str(sum(~iGoodTime)) ' points failed Impossible date QC test in file ' sample_data.toolbox_input_file '. Try to re-play and fix this dataset when possible using the manufacturer''s software before processing it with the toolbox.']);
     end
 
     % write/update dataset QC parameters

diff --git a/FlowManager/exportManager.m b/FlowManager/exportManager.m
@@ -260,7 +260,9 @@ function exportQCPlots(sample_data, exportDir, mode, auto, progress)
 
         case 'profile'
             % profile specific plots
-            lineCastVar(sample_data, paramsName, true, true, exportDir);
+            for i=1:length(sample_data) % we only want one figure per profile for better readability
+                lineCastVar(sample_data(i), paramsName, true, true, exportDir);
+            end
 
     end
 catch e

diff --git a/GUI/mainWindow.m b/GUI/mainWindow.m
@@ -88,11 +88,12 @@ function mainWindow(windowTitle, sample_data, states, startState, selectionCallb
     sampleDataDescs{k} = genSampleDataDesc(sample_data{k});
 end
 
+backgroundPlotColor = [1 1 1]; % white
+
 % window figure
 fig = figure(...
     'Name',        windowTitle, ...
     'Visible',     'off',...
-    'Color',       [0.75 0.75 0.75],...
     'MenuBar',     'none',...
     'ToolBar',     'figure',...
     'Resize',      'on',...
@@ -165,9 +166,10 @@ function mainWindow(windowTitle, sample_data, states, startState, selectionCallb
 
 % main display
 mainPanel = uipanel(...
-    'Parent',     fig,...
-    'BorderType', 'none',...
-    'Tag',        'mainPanel');
+    'BackgroundColor',  backgroundPlotColor,...
+    'BorderType',       'none',...
+    'Parent',           fig,...
+    'Tag',              'mainPanel');
 
 % use normalized units
 set(fig,              'Units', 'normalized');
@@ -304,7 +306,7 @@ function mainWindow(windowTitle, sample_data, states, startState, selectionCallb
         set(hToolsDiagram2DCommonVarDepthNonQC, 'callBack', {@displayDiagramMooringVar,    false,  false, 'DEPTH'});
         set(hToolsDiagram2DCommonVarDepthQC,    'callBack', {@displayDiagramMooringVar,    true,   false, 'DEPTH'});
     case 'profile'
-        hToolsLineCastVar             = uimenu(hToolsMenu,        'label', '1D variable vs DEPTH profile line plot');
+        hToolsLineCastVar             = uimenu(hToolsMenu,        'label', '1D variable vs DEPTH selected profile line plot');
         hToolsLineCastVarNonQC        = uimenu(hToolsLineCastVar, 'label', 'all data');
         hToolsLineCastVarQC           = uimenu(hToolsLineCastVar, 'label', 'only good and non QC''d data');
 
@@ -648,29 +650,33 @@ function disableZoomAndPan(source, ev)
 
     function displayLineCastVar(source, ev, isQC)
         %DISPLAYLINECASTVAR Opens a new window where all the
-        % variables collected by the CTD cast are line-plotted in a profile plot.
+        % variables collected by the currently selected CTD cast are line-plotted in a profile plot.
         %
 
+        % only currently selected profile for better readability
+        iSampleMenu = get(sampleMenu, 'Value');
+        sam = sample_data(iSampleMenu);
+
         % get all params names
-        lenSampleData = length(sample_data);
+        lenSampleData = length(sam);
         paramsName = {};
         for i=1:lenSampleData
-            lenParamsSample = length(sample_data{i}.variables);
+            lenParamsSample = length(sam{i}.variables);
             for j=1:lenParamsSample
-                isParamQC = any(sample_data{i}.variables{j}.flags == 1) || any(sample_data{i}.variables{j}.flags == 2);
+                isParamQC = any(sam{i}.variables{j}.flags == 1) || any(sam{i}.variables{j}.flags == 2);
                 if i==1 && j==1
-                    paramsName{1} = sample_data{1}.variables{1}.name;
+                    paramsName{1} = sam{1}.variables{1}.name;
                 else
-                    sameParam = strcmpi(paramsName, sample_data{i}.variables{j}.name);
+                    sameParam = strcmpi(paramsName, sam{i}.variables{j}.name);
                     if ~any(sameParam)
-                        paramsName{end+1} = sample_data{i}.variables{j}.name;
+                        paramsName{end+1} = sam{i}.variables{j}.name;
                     end
                 end
                 % get rid of non QC'd params if only interested in QC
                 if isQC && ~isParamQC; paramsName(end) = []; end
             end
         end
-        lineCastVar(sample_data, paramsName, isQC, false, '');
+        lineCastVar(sam, paramsName, isQC, false, '');
     end
 
     function displayScatterMooringVar(source, ev, isQC, is1D)

diff --git a/Graph/DepthProfile/graphDepthProfileGeneric.m b/Graph/DepthProfile/graphDepthProfileGeneric.m
@@ -94,8 +94,8 @@
     end
 end
 
-% set background to be grey
-set(ax, 'Color', [0.85 0.85 0.85])
+% set background to be transparent (same as figure background)
+set(ax, 'Color', 'none')
 
 labels = {var.name, 'DEPTH'};
 

diff --git a/Graph/DepthProfile/highlightDepthProfileGeneric.m b/Graph/DepthProfile/highlightDepthProfileGeneric.m
@@ -82,6 +82,6 @@
         'Parent',          gca, ...
         'LineStyle',       'none', ...
         'Marker',          'o', ...
-        'MarkerEdgeColor', 'white', ...
-        'MarkerFaceColor', 'white');
+        'MarkerEdgeColor', 'black', ...
+        'MarkerFaceColor', 'black');
 end
diff --git a/Graph/TimeSeries/graphTimeSeriesGeneric.m b/Graph/TimeSeries/graphTimeSeriesGeneric.m
@@ -84,8 +84,8 @@
     end
 end
 
-% set background to be grey
-set(ax, 'Color', [0.85 0.85 0.85])
+% set background to be transparent (same as background color)
+set(ax, 'Color', 'none')
 
 if strncmp(var.name, 'DEPTH', 4) || strncmp(var.name, 'PRES', 4) || strncmp(var.name, 'PRES_REL', 8)
     set(ax, 'YDir', 'reverse');

diff --git a/Graph/TimeSeries/graphTimeSeriesTimeDepth.m b/Graph/TimeSeries/graphTimeSeriesTimeDepth.m
@@ -91,8 +91,8 @@
 if length(cbLabel) > 20, cbLabel = [cbLabel(1:17) '...']; end
 set(get(cb, 'YLabel'), 'String', cbLabel, 'Interpreter', 'none');
 
-% set background to be grey
-set(ax, 'Color', [0.75 0.75 0.75])
+% set background to be light grey (colorbar can include white color)
+set(ax, 'Color', [0.85 0.85 0.85])
 
 labels = {time.name, depth.name};
 

diff --git a/Graph/TimeSeries/graphTimeSeriesTimeFrequency.m b/Graph/TimeSeries/graphTimeSeriesTimeFrequency.m
@@ -86,8 +86,8 @@
 if length(cbLabel) > 20, cbLabel = [cbLabel(1:17) '...']; end
 set(get(cb, 'YLabel'), 'String', cbLabel, 'Interpreter', 'none');
 
-% set background to be grey
-set(ax, 'Color', [0.75 0.75 0.75])
+% set background to be light grey (colorbar can include white color)
+set(ax, 'Color', [0.85 0.85 0.85])
 
 labels = {time.name, freq.name};
 

diff --git a/Graph/TimeSeries/graphTimeSeriesTimeFrequencyDirection.m b/Graph/TimeSeries/graphTimeSeriesTimeFrequencyDirection.m
@@ -199,8 +199,8 @@
 if length(cbLabel) > 20, cbLabel = [cbLabel(1:17) '...']; end
 set(get(cb, 'YLabel'), 'String', cbLabel, 'Interpreter', 'none');
 
-% set background to be grey
-set(ax, 'Color', [0.75 0.75 0.75])
+% set background to be light grey (colorbar can include white color)
+set(ax, 'Color', [0.85 0.85 0.85])
 
 labels = {};
 

diff --git a/Graph/TimeSeries/highlightTimeSeriesGeneric.m b/Graph/TimeSeries/highlightTimeSeriesGeneric.m
@@ -78,6 +78,6 @@
         'Parent',          gca, ...
         'LineStyle',       'none', ...
         'Marker',          'o', ...
-        'MarkerEdgeColor', 'white', ...
-        'MarkerFaceColor', 'white');
+        'MarkerEdgeColor', 'black', ...
+        'MarkerFaceColor', 'black');
 end
diff --git a/Graph/TimeSeries/highlightTimeSeriesTimeDepth.m b/Graph/TimeSeries/highlightTimeSeriesTimeDepth.m
@@ -81,7 +81,7 @@
         'Parent',          gca, ...
         'LineStyle',       'none', ...
         'Marker',          'o', ...
-        'MarkerEdgeColor', 'white', ...
-        'MarkerFaceColor', 'white', ...
+        'MarkerEdgeColor', 'black', ...
+        'MarkerFaceColor', 'black', ...
         'MarkerSize',      3);
 end
diff --git a/Graph/TimeSeries/highlightTimeSeriesTimeFrequencyDirection.m b/Graph/TimeSeries/highlightTimeSeriesTimeFrequencyDirection.m
@@ -70,7 +70,7 @@
         'Parent',          gca, ...
         'LineStyle',       'none', ...
         'Marker',          'o', ...
-        'MarkerEdgeColor', 'white', ...
-        'MarkerFaceColor', 'white', ...
+        'MarkerEdgeColor', 'black', ...
+        'MarkerFaceColor', 'black', ...
         'MarkerSize',      3);
 end
diff --git a/Graph/TimeSeries/selectTimeSeriesGeneric.m b/Graph/TimeSeries/selectTimeSeriesGeneric.m
@@ -107,7 +107,7 @@ function buttonDown(source,ev)
     rect = rectangle(...
       'Parent',    gca,...
       'Position',  rectPos,...
-      'EdgeColor', [1 1 1],...
+      'EdgeColor', 'black',...
       'LineStyle', '--',...
       'LineWidth', 0.25);
 

diff --git a/Graph/Transect/graphTransectGeneric.m b/Graph/Transect/graphTransectGeneric.m
@@ -60,7 +60,7 @@
 if length(cbLabel) > 20, cbLabel = [cbLabel(1:17) '...']; end
 set(get(cb, 'YLabel'), 'String', cbLabel, 'Interpreter', 'none');
 
-% set background to be grey
-set(ax, 'Color', [0.85 0.85 0.85])
+% set background to be transparent (same as background color)
+set(ax, 'Color', 'none')
 
 labels = {'LATITUDE', 'LONGITUDE'};
diff --git a/Graph/XvY/graphXvYGeneric.m b/Graph/XvY/graphXvYGeneric.m
@@ -66,7 +66,7 @@
     end
 end
 
-% set background to be grey
-set(ax, 'Color', [0.85 0.85 0.85])
+% set background to be transparent (same as background color)
+set(ax, 'Color', 'none')
 
 labels = {sample_data.variables{vars(1)}.name, sample_data.variables{vars(2)}.name};
diff --git a/Graph/checkMooringPlannedDepths.m b/Graph/checkMooringPlannedDepths.m
@@ -313,39 +313,12 @@ function checkMooringPlannedDepths(sample_data, isQC, saveToFile, exportDir)
 for i = 1:lenMetaDepth
     avgDep(i) = median(dataVar(i, ~iNaN(i, :)));
 
-    if fastScatter
-        % for performance, we use plot (1 single handle object
-        % returned) rather than scatter (as many handles returned as
-        % points to plot). We plot as many subsets of the total amount
-        % of points as we want colors to be displayed. This is
-        % performed by the function plotclr.
-
-        % !!! The result is such that the overlapping of points is dictated by
-        % the order of the colors to be plotted and not by the X axis order (from
-        % first to last) of the total points given. We choose an ordering from
-        % centre to both ends of colorbar in order to keep extreme colors visible
-        % though.
-
-        plotclr(hAxDepthDiff, ...
-            metaDepth(i), ...
-            avgDep(i) - metaDepth(i), ...
-            metaDepth(i), ...
-            'o', ...
-            [min(metaDepth) max(metaDepth)], ...
-            'Color', cMap(i, :), ...
-            'MarkerFaceColor', cMap(i, :), ...
-            'MarkerSize',  2.5);
-    else
-        % faster than scatter, but legend requires adjusting
-        fastScatterMesh(hAxDepthDiff, ...
-            metaDepth(i), ...
-            avgDep(i) - metaDepth(i), ...
-            metaDepth(i), ...
-            [min(metaDepth) max(metaDepth)], ...
-            'Marker',      'o', ...
-            'FaceColor', cMap(i, :), ...
-            'MarkerSize',  2.5);
-    end
+    scatter(hAxDepthDiff, ...
+        metaDepth(i), ...
+        avgDep(i) - metaDepth(i), ...
+        [], ...
+        cMap(i, :), ...
+        'filled');
 end
 
 instrumentDesc(1) = [];

diff --git a/Graph/pcolorMooring2DVar.m b/Graph/pcolorMooring2DVar.m
@@ -92,7 +92,8 @@ function pcolorMooring2DVar(sample_data, varName, isQC, saveToFile, exportDir)
 
 initiateFigure = true;
 
-backgroundColor = [0.85 0.85 0.85]; % light grey to allow for colorbar with white
+backgroundFigure = [1 1 1]; % white
+backgroundAxis = [0.85 0.85 0.85]; % light grey to allow for colorbar with white
 
 for i=1:lenSampleData
     % instrument description
@@ -146,7 +147,7 @@ function pcolorMooring2DVar(sample_data, varName, isQC, saveToFile, exportDir)
                 'Name',             title, ...
                 'NumberTitle',      'off', ...
                 'Visible',          visible, ...
-                'Color',            backgroundColor, ...
+                'Color',            backgroundFigure, ...
                 'OuterPosition',    monitorRect(iBigMonitor, :));
 
             hAxMooringVar = axes('Parent',   hFigMooringVar);
@@ -227,9 +228,8 @@ function pcolorMooring2DVar(sample_data, varName, isQC, saveToFile, exportDir)
 
             set(get(hCBar, 'Title'), 'String', [varName ' (' varUnit ')'], 'Interpreter', 'none');
 
-            % set axes background to be transparent (figure color shows
-            % through)
-            set(hAxMooringVar, 'Color', 'none')
+            % set axes background
+            set(hAxMooringVar, 'Color', backgroundAxis)
         end
     end
 end
@@ -247,7 +247,7 @@ function pcolorMooring2DVar(sample_data, varName, isQC, saveToFile, exportDir)
         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_', '_PCOLOR_');
 
-        fastSaveas(hFigMooringVar, backgroundColor, fullfile(exportDir, fileName));
+        fastSaveas(hFigMooringVar, backgroundFigure, fullfile(exportDir, fileName));
 
         close(hFigMooringVar);
     end

diff --git a/Graph/scatterMooring2DVarAgainstDepth.m b/Graph/scatterMooring2DVarAgainstDepth.m
@@ -170,7 +170,8 @@ function scatterMooring2DVarAgainstDepth(sample_data, varName, isQC, saveToFile,
     end
 end
 
-backgroundColor = [0.85 0.85 0.85]; % light grey to allow for colorbar with white
+backgroundFigure = [1 1 1]; % white
+backgroundAxis = [0.85 0.85 0.85]; % light grey to allow for colorbar with white
 
 if any(isPlottable)
     % collect visualQC config
@@ -246,7 +247,7 @@ function scatterMooring2DVarAgainstDepth(sample_data, varName, isQC, saveToFile,
                     'Name',             title, ...
                     'NumberTitle',      'off', ...
                     'Visible',          visible, ...
-                    'Color',            backgroundColor, ...
+                    'Color',            backgroundFigure, ...
                     'OuterPosition',    monitorRect(iBigMonitor, :));
 
                 hAxMooringVar = axes('Parent', hFigMooringVar);
@@ -260,7 +261,7 @@ function scatterMooring2DVarAgainstDepth(sample_data, varName, isQC, saveToFile,
                 hold(hAxMooringVar, 'on');
 
                 % dummy entry for first entry in legend
-                hScatterVar(1) = plot(0, 0, 'Color', backgroundColor, 'Visible', 'off'); % color same as background (invisible in legend)
+                hScatterVar(1) = plot(0, 0, 'Color', backgroundAxis, 'Visible', 'off'); % color same as background (invisible in legend)
 
                 % set data cursor mode custom display
                 dcm_obj = datacursormode(hFigMooringVar);
@@ -403,9 +404,8 @@ function scatterMooring2DVarAgainstDepth(sample_data, varName, isQC, saveToFile,
                     'YGrid',        'on', ...
                     'Layer',        'top');
 
-                % set axes background to be transparent (figure color shows
-                % through)
-                set(hAxMooringVar, 'Color', 'none')
+                % set axes background
+                set(hAxMooringVar, 'Color', backgroundAxis)
             end
 
             % we plot the instrument nominal depth
@@ -468,7 +468,7 @@ function scatterMooring2DVarAgainstDepth(sample_data, varName, isQC, saveToFile,
         end
     end
     posAx = get(hAxMooringVar, 'Position');
-    set(hLegend, 'Units', 'Normalized', 'Color', 'none')
+    set(hLegend, 'Units', 'Normalized', 'Color', backgroundAxis)
     posLh = get(hLegend, 'Position');
     if posLh(2) < 0
         set(hLegend, 'Position',[posLh(1), abs(posLh(2)), posLh(3), posLh(4)]);
@@ -477,13 +477,11 @@ function scatterMooring2DVarAgainstDepth(sample_data, varName, isQC, saveToFile,
         set(hAxMooringVar, 'Position',[posAx(1), posAx(2)+abs(posLh(2)), posAx(3), posAx(4)-abs(posLh(2))]);
     end
 
-    %     set(hLegend, 'Box', 'off', 'Color', 'none');
-
     if saveToFile
         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_', '_SCATTER_');
 
-        fastSaveas(hFigMooringVar, backgroundColor, fullfile(exportDir, fileName));
+        fastSaveas(hFigMooringVar, backgroundFigure, fullfile(exportDir, fileName));
 
         close(hFigMooringVar);
     end