Merge pull request #510 from aodn/2.5.39

2.5.39

FlowManager/displayManager.m

@@ -112,7 +112,7 @@ function displayManager(windowTitle, sample_data, callbacks)
   mainWindow(windowTitle, sample_data, states, 3, @stateSelectCallback);
 
   function state = stateSelectCallback(event,...
-    panel, updateCallback, state, sample_data, graphType, setIdx, vars, extraSetIdx)
+    panel, updateCallback, state, sample_data, graphType, setIdx, vars, extraSetIdx, isFlagVisible)
   %STATESELECTCALLBACK Called when the user interacts with the main 
   % window, by changing the state, the selected data set, the selected
   % variables or the selected graph type.
@@ -127,6 +127,7 @@ function displayManager(windowTitle, sample_data, callbacks)
   %   setIdx         - currently selected sample_data struct (index)
   %   vars           - currently selected variables (indices).
   %   extraSetIdx    - currently selected extra sample_data struct (index)
+  %   isFlagVisible  - currently selected visibility of flags (boolean)
   %
   % Outputs:
   %   state          - If a state change was forced, tells the main window
@@ -335,12 +336,14 @@ function qcDataCallback()
 
         [graphs, lines, vars] = graphFunc(panel, sample_data{setIdx}, vars, extra_sample_data);
 
-        if isempty(flagFunc)
-          warning(['Cannot display QC flags using ' graphType ...
-                   '. Try a different graph type.']);
-          return;
-        else
-          flags = flagFunc( panel, graphs, sample_data{setIdx}, vars);
+        if isFlagVisible
+            if isempty(flagFunc)
+                warning(['Cannot display QC flags using ' graphType ...
+                    '. Try a different graph type.']);
+                return;
+            else
+                flags = flagFunc( panel, graphs, sample_data{setIdx}, vars);
+            end
         end
 
       catch e
@@ -477,8 +480,10 @@ function dataSelectCallback(ax, type, range)
               updateCallback(sample_data{setIdx});
 
               % update graph
-              if ~isempty(flags), delete(flags(flags ~= 0)); end
-              flags = flagFunc(panel, graphs, sample_data{setIdx}, vars);
+              if isFlagVisible
+                  if ~isempty(flags), delete(flags(flags ~= 0)); end
+                  flags = flagFunc(panel, graphs, sample_data{setIdx}, vars);
+              end
 
               % write/update manual QC file for this dataset
               mqcFile = [sample_data{setIdx}.toolbox_input_file, '.mqc'];

GUI/mainWindow.m

@@ -127,7 +127,7 @@ function mainWindow(windowTitle, sample_data, states, startState, selectionCallb
 % extra instrument check box
 extraSampleCb = uicontrol(...
     'Style',    'checkbox',...
-    'String',   'Graph extra instrument (black)',...
+    'String',   'Graph extra instrument good data only (black)',...
     'Value',    0,...
     'Tag',      'extraSampleCheckBox');
 
@@ -139,6 +139,20 @@ function mainWindow(windowTitle, sample_data, states, startState, selectionCallb
     'Enable', 'off',...
     'Tag',    'extraSamplePopUpMenu');
 
+% flag visibility check box
+visiFlagCb = uicontrol(...
+    'Style',    'checkbox',...
+    'String',   'Show data flag if any',...
+    'Value',    1,...
+    'Tag',      'visiFlagCheckBox');
+
+% bad data visibility check box
+visiBadCb = uicontrol(...
+    'Style',    'checkbox',...
+    'String',   'Hide bad data',...
+    'Value',    0,...
+    'Tag',      'visiBadCheckBox');
+
 % side panel
 sidePanel = uipanel(...
     'Parent',     fig,...
@@ -181,6 +195,8 @@ function mainWindow(windowTitle, sample_data, states, startState, selectionCallb
 set(graphMenu,        'Units', 'normalized');
 set(extraSampleCb,    'Units', 'normalized');
 set(extraSampleMenu,  'Units', 'normalized');
+set(visiFlagCb,       'Units', 'normalized');
+set(visiBadCb,        'Units', 'normalized');
 set(stateButtons,     'Units', 'normalized');
 
 % set window position
@@ -198,12 +214,14 @@ function mainWindow(windowTitle, sample_data, states, startState, selectionCallb
 set(fig, 'Units', 'normalized');
 
 % set widget positions
-set(sidePanel,          'Position', posUi2(fig, 100, 100, 11:100,  1:10,  0));
-set(mainPanel,          'Position', posUi2(fig, 100, 100, 11:100, 11:100, 0));
+set(sidePanel,          'Position', posUi2(fig, 100, 100, 16:100,  1:10,  0));
+set(mainPanel,          'Position', posUi2(fig, 100, 100, 16:100, 11:100, 0));
 set(sampleMenu,         'Position', posUi2(fig, 100, 100,  1:5,    1:75,  0));
 set(graphMenu,          'Position', posUi2(fig, 100, 100,  1:5,   76:100, 0));
 set(extraSampleMenu,    'Position', posUi2(fig, 100, 100,  6:10,   1:75,  0));
 set(extraSampleCb,      'Position', posUi2(fig, 100, 100,  6:10,  76:100, 0));
+set(visiFlagCb,         'Position', posUi2(fig, 100, 100, 11:15,  76:100, 0));
+set(visiBadCb,          'Position', posUi2(fig, 100, 100, 11:15,  51:75,  0));
 
 % varPanel and butPanel are positioned relative to sidePanel
 set(butPanel, 'Position', posUi2(sidePanel, 10, 1, 1:5,  1, 0));
@@ -221,6 +239,8 @@ function mainWindow(windowTitle, sample_data, states, startState, selectionCallb
 set(graphMenu,          'Callback', @graphMenuCallback);
 set(extraSampleCb,      'Callback', @sampleMenuCallback);
 set(extraSampleMenu,    'Callback', @sampleMenuCallback);
+set(visiFlagCb,         'Callback', @sampleMenuCallback);
+set(visiBadCb,          'Callback', @sampleMenuCallback);
 set(stateButtons,       'Callback', @stateButtonCallback);
 
 set(fig, 'Visible', 'on');
@@ -342,6 +362,8 @@ function selectionChange(event)
             extraSam.meta.index = 0;
         end
 
+        isFlagVisible = get(visiFlagCb, 'value');
+
         % clear main panel
         children = get(mainPanel, 'Children');
         delete(children);
@@ -362,7 +384,8 @@ function selectionChange(event)
             graph, ...              % currently selected graph type (string).
             sam.meta.index, ...     % currently selected sample_data struct (index)
             vars, ...               % currently selected variables (indices).
-            extraSam.meta.index);   % currently selected extra sample_data struct (index)
+            extraSam.meta.index, ...% currently selected extra sample_data struct (index)
+            isFlagVisible);         % currently selected visibility of flags (boolean)
 
         % set data cursor mode custom display
         dcm_obj = datacursormode(fig);

Graph/DepthProfile/flagDepthProfileGeneric.m

@@ -43,7 +43,16 @@
 if ~isnumeric(var),        error('var must be numeric');          end
 
 qcSet = str2double(readProperty('toolbox.qc_set'));
-rawFlag = imosQCFlag('raw', qcSet, 'flag');
+noDisplayFlag = imosQCFlag('raw', qcSet, 'flag'); % raw flags are not displayed by default
+
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we add bad flags to the list of flags not to be displayed
+    noDisplayFlag = [noDisplayFlag, ...
+        imosQCFlag('probablyBad', qcSet, 'flag'), ...
+        imosQCFlag('bad', qcSet, 'flag')];
+end
 
 % get the toolbox execution mode
 mode = readProperty('toolbox.mode');
@@ -76,9 +85,9 @@
 % get a list of the different flag types to be graphed
 flagTypes = unique(fl);
 
-% don't display raw data flags
-iRawFlag = (flagTypes == rawFlag);
-if any(iRawFlag), flagTypes(iRawFlag) = []; end
+% don't display specific flags
+iNoDisplayFlag = ismember(flagTypes, noDisplayFlag);
+if any(iNoDisplayFlag), flagTypes(iNoDisplayFlag) = []; end
 
 lenFlag = length(flagTypes);
 

Graph/DepthProfile/graphDepthProfileGeneric.m

@@ -58,6 +58,20 @@
 
 var  = sample_data.variables{var};
 
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we replace values flagged as bad by NaN before plotting
+    qcSet = str2double(readProperty('toolbox.qc_set'));
+    rawFlag      = imosQCFlag('raw',          qcSet, 'flag');
+    goodFlag     = imosQCFlag('good',         qcSet, 'flag');
+    probGoodFlag = imosQCFlag('probablyGood', qcSet, 'flag');
+
+    iGood = ismember(var.flags, [rawFlag, goodFlag, probGoodFlag]);
+
+    var.data(~iGood) = NaN;
+end
+
 switch mode
     case 'profile'
         h            = line(var.data(:, 1), depth.data(:, 1), 'Parent', ax, 'LineStyle', '-', 'Color', color); % downcast

Graph/TimeSeries/flagTimeSeriesGeneric.m

@@ -43,7 +43,16 @@
 if ~isnumeric(var),        error('var must be numeric');          end
 
 qcSet = str2double(readProperty('toolbox.qc_set'));
-rawFlag = imosQCFlag('raw', qcSet, 'flag');
+noDisplayFlag = imosQCFlag('raw', qcSet, 'flag'); % raw flags are not displayed by default
+
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we add bad flags to the list of flags not to be displayed
+    noDisplayFlag = [noDisplayFlag, ...
+        imosQCFlag('probablyBad', qcSet, 'flag'), ...
+        imosQCFlag('bad', qcSet, 'flag')];
+end
 
 iTimeDim = getVar(sample_data.dimensions, 'TIME');
 time = sample_data.dimensions{iTimeDim};
@@ -55,9 +64,9 @@
 % get a list of the different flag types to be graphed
 flagTypes = unique(fl);
 
-% don't display raw data flags
-iRawFlag = (flagTypes == rawFlag);
-if any(iRawFlag), flagTypes(iRawFlag) = []; end
+% don't display specific flags
+iNoDisplayFlag = ismember(flagTypes, noDisplayFlag);
+if any(iNoDisplayFlag), flagTypes(iNoDisplayFlag) = []; end
 
 lenFlag = length(flagTypes);
 

Graph/TimeSeries/flagTimeSeriesTimeDepth.m

@@ -42,7 +42,16 @@
 if ~isnumeric(var),        error('var must be numeric');          end
 
 qcSet = str2double(readProperty('toolbox.qc_set'));
-rawFlag = imosQCFlag('raw', qcSet, 'flag');
+noDisplayFlag = imosQCFlag('raw', qcSet, 'flag'); % raw flags are not displayed by default
+
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we add bad flags to the list of flags not to be displayed
+    noDisplayFlag = [noDisplayFlag, ...
+        imosQCFlag('probablyBad', qcSet, 'flag'), ...
+        imosQCFlag('bad', qcSet, 'flag')];
+end
 
 iTimeDim = getVar(sample_data.dimensions, 'TIME');
 depth = sample_data.variables{var}.dimensions(2);
@@ -55,9 +64,9 @@
 % get a list of the different flag types to be graphed
 flagTypes = unique(fl);
 
-% don't display raw data flags
-iRawFlag = (flagTypes == rawFlag);
-if any(iRawFlag), flagTypes(iRawFlag) = []; end
+% don't display specific flags
+iNoDisplayFlag = ismember(flagTypes, noDisplayFlag);
+if any(iNoDisplayFlag), flagTypes(iNoDisplayFlag) = []; end
 
 lenFlag = length(flagTypes);
 

Graph/TimeSeries/flagTimeSeriesTimeFrequency.m

@@ -42,7 +42,16 @@
 if ~isnumeric(var),        error('var must be numeric');          end
 
 qcSet = str2double(readProperty('toolbox.qc_set'));
-rawFlag = imosQCFlag('raw', qcSet, 'flag');
+noDisplayFlag = imosQCFlag('raw', qcSet, 'flag'); % raw flags are not displayed by default
+
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we add bad flags to the list of flags not to be displayed
+    noDisplayFlag = [noDisplayFlag, ...
+        imosQCFlag('probablyBad', qcSet, 'flag'), ...
+        imosQCFlag('bad', qcSet, 'flag')];
+end
 
 iTimeDim = getVar(sample_data.dimensions, 'TIME');
 freq  = sample_data.variables{var}.dimensions(2);
@@ -55,9 +64,9 @@
 % get a list of the different flag types to be graphed
 flagTypes = unique(fl);
 
-% don't display raw data flags
-iRawFlag = (flagTypes == rawFlag);
-if any(iRawFlag), flagTypes(iRawFlag) = []; end
+% don't display specific flags
+iNoDisplayFlag = ismember(flagTypes, noDisplayFlag);
+if any(iNoDisplayFlag), flagTypes(iNoDisplayFlag) = []; end
 
 lenFlag = length(flagTypes);
 

Graph/TimeSeries/flagTimeSeriesTimeFrequencyDirection.m

@@ -41,7 +41,16 @@
 if ~isnumeric(var),        error('var must be numeric');          end
 
 qcSet = str2double(readProperty('toolbox.qc_set'));
-rawFlag = imosQCFlag('raw', qcSet, 'flag');
+noDisplayFlag = imosQCFlag('raw', qcSet, 'flag'); % raw flags are not displayed by default
+
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we add bad flags to the list of flags not to be displayed
+    noDisplayFlag = [noDisplayFlag, ...
+        imosQCFlag('probablyBad', qcSet, 'flag'), ...
+        imosQCFlag('bad', qcSet, 'flag')];
+end
 
 freq = sample_data.variables{var}.dimensions(2);
 dir  = sample_data.variables{var}.dimensions(3);
@@ -67,9 +76,9 @@
 % get a list of the different flag types to be graphed
 flagTypes = unique(sswvFlags);
 
-% don't display raw data flags
-iRawFlag = (flagTypes == rawFlag);
-if any(iRawFlag), flagTypes(iRawFlag) = []; end
+% don't display specific flags
+iNoDisplayFlag = ismember(flagTypes, noDisplayFlag);
+if any(iNoDisplayFlag), flagTypes(iNoDisplayFlag) = []; end
 
 lenFlag = length(flagTypes);
 

Graph/TimeSeries/graphTimeSeriesGeneric.m

@@ -49,6 +49,20 @@
 
 if ischar(var.data), var.data = str2num(var.data); end % we assume data is an array of one single character
 
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we replace values flagged as bad by NaN before plotting
+    qcSet = str2double(readProperty('toolbox.qc_set'));
+    rawFlag      = imosQCFlag('raw',          qcSet, 'flag');
+    goodFlag     = imosQCFlag('good',         qcSet, 'flag');
+    probGoodFlag = imosQCFlag('probablyGood', qcSet, 'flag');
+
+    iGood = ismember(var.flags, [rawFlag, goodFlag, probGoodFlag]);
+
+    var.data(~iGood) = NaN;
+end
+
 h    = line(time.data, var.data, 'Parent', ax, 'Color', color);
 set(ax, 'Tag', 'axis1D');
 

Graph/TimeSeries/graphTimeSeriesTimeDepth.m

@@ -50,6 +50,20 @@
 depth = sample_data.dimensions{depth};
 var   = sample_data.variables {var};
 
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we replace values flagged as bad by NaN before plotting
+    qcSet = str2double(readProperty('toolbox.qc_set'));
+    rawFlag      = imosQCFlag('raw',          qcSet, 'flag');
+    goodFlag     = imosQCFlag('good',         qcSet, 'flag');
+    probGoodFlag = imosQCFlag('probablyGood', qcSet, 'flag');
+
+    iGood = ismember(var.flags, [rawFlag, goodFlag, probGoodFlag]);
+
+    var.data(~iGood) = NaN;
+end
+
 xPcolor = time.data;
 yPcolor = depth.data;
 

Graph/TimeSeries/graphTimeSeriesTimeFrequency.m

@@ -50,6 +50,20 @@
 freq = sample_data.dimensions{freq};
 var  = sample_data.variables {var};
 
+visiBadCbh = findobj('Tag', 'visiBadCheckBox');
+isBadHidden = get(visiBadCbh, 'value');
+if isBadHidden
+    % we replace values flagged as bad by NaN before plotting
+    qcSet = str2double(readProperty('toolbox.qc_set'));
+    rawFlag      = imosQCFlag('raw',          qcSet, 'flag');
+    goodFlag     = imosQCFlag('good',         qcSet, 'flag');
+    probGoodFlag = imosQCFlag('probablyGood', qcSet, 'flag');
+
+    iGood = ismember(var.flags, [rawFlag, goodFlag, probGoodFlag]);
+
+    var.data(~iGood) = NaN;
+end
+
 xPcolor = time.data;
 yPcolor = freq.data;