Merge pull request #381 from aodn/2.5.18

2.5.18
aodn · Oct 27, 2016 · 65452f9 · 65452f9
2 parents b97e0f9 + 27d2ae2
commit 65452f9
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Showing 11 changed files with 109 additions and 36 deletions.
diff --git a/IMOS/imosParameters.txt b/IMOS/imosParameters.txt
@@ -50,7 +50,7 @@ DIR,                 0, from_direction,
 DIR_MAG,             0, from_direction,                                                                           degree,        clockwise,     magnetic north,                    E, 999999.0, 0.0,      360.0,    float
 DIRECTION,           0, direction_of_the_profile,                                                                 ,              ,              ,                                  ,  ,         ,         ,         char
 DIRT,                0, to_direction,                                                                             degree,        clockwise,     true north,                        E, 999999.0, 0.0,      360.0,    float
-DIST_ALONG_BEAMS,    0, distance_from_sensor_along_beams,                                                         m,             up,            sensor,                            Z, 999999.0, -12000.0, 12000.0,  float
+DIST_ALONG_BEAMS,    0, distance_from_sensor_along_beams,                                                         m,             ,              sensor,                            Z, 999999.0, -12000.0, 12000.0,  float
 DOX1,                1, mole_concentration_of_dissolved_molecular_oxygen_in_sea_water,                            umol l-1,      ,              ,                                  O, 999999.0, 0.0,      900000.0, float
 DOX2,                1, moles_of_oxygen_per_unit_mass_in_sea_water,                                               umol kg-1,     ,              ,                                  O, 999999.0, 0.0,      880000.0, float
 DOXS,                1, fractional_saturation_of_oxygen_in_sea_water,                                             percent,       ,              ,                                  O, 999999.0, ,         ,         float

diff --git a/NetCDF/template/dist_along_beams_attributes.txt b/NetCDF/template/dist_along_beams_attributes.txt
@@ -1,7 +1,7 @@
 S, standard_name             = [mat imosParameters('DIST_ALONG_BEAMS', 'standard_name')]
 S, long_name                 = distance_from_sensor_along_beams
 S, units                     = [mat imosParameters('DIST_ALONG_BEAMS', 'uom')]
-S, axis                      = Z
+S, axis                      = 
 S, positive                  = [mat imosParameters('DIST_ALONG_BEAMS', 'positive')]
 S, reference_datum           = [mat imosParameters('DIST_ALONG_BEAMS', 'reference_datum')]
 N, valid_min                 = [mat imosParameters('DIST_ALONG_BEAMS', 'valid_min')]

diff --git a/Preprocessing/CTDDepthBinPP.m b/Preprocessing/CTDDepthBinPP.m
@@ -87,7 +87,10 @@
        zend = zbin(2:end);
 
        z = (zstart + zend)/2; % depth of the actual centre of each bin
-       curSam.dimensions{iDepth}.data = z(:);
+
+       curSam.dimensions{iDepth}.data = z(:); % update dimension and global attribute values
+       curSam.geospatial_vertical_min = min(z(:));
+       curSam.geospatial_vertical_max = max(z(:));
 
        [Z, ZSTART] = meshgrid(depth, zstart);
        [~, ZEND] = meshgrid(depth, zend);

diff --git a/Preprocessing/adcpBinMappingPP.m b/Preprocessing/adcpBinMappingPP.m
@@ -148,9 +148,10 @@
     % impacted parameter
     isBinMapApplied = false;
     for j=1:length(sample_data{k}.variables)
-        if any(sample_data{k}.variables{j}.dimensions == distAlongBeamsIdx) ... % only process variables that are function of DIST_ALONG_BEAMS
+        if any(sample_data{k}.variables{j}.dimensions == distAlongBeamsIdx) % only process variables that are function of DIST_ALONG_BEAMS
 
-            beamNumber = sample_data{k}.variables{j}.name(end);
+            % only process variables that are in beam coordinates
+            beamNumber = sample_data{k}.variables{j}.long_name(end);
             switch beamNumber
                 case '1'
                     nonMappedHeightAboveSensor = nonMappedHeightAboveSensorBeam1;
@@ -187,23 +188,26 @@
 %                 mappedData(i,iLastGoodBin) = interp1(nonMappedHeightAboveSensor(i,:), nonMappedData(i,:), mappedHeightAboveSensor(i,iLastGoodBin), 'spline');
             end
 
-            binMappingComment = ['adcpBinMappingPP.m: data in beam coordinates originally referenced to DISTANCE_ALONG_BEAMS ' ...
+            binMappingComment = ['adcpBinMappingPP.m: data in beam coordinates originally referenced to DIST_ALONG_BEAMS ' ...
                 'has been vertically bin-mapped to HEIGHT_ABOVE_SENSOR using tilt information.'];
 
-            % we create the HEIGHT_ABOVE_SENSOR dimension if needed
             if ~heightAboveSensorIdx
-                sample_data{k}.dimensions{end+1}            = sample_data{k}.dimensions{distAlongBeamsIdx};
-                sample_data{k}.dimensions{end}.name         = 'HEIGHT_ABOVE_SENSOR';
-                sample_data{k}.dimensions{end}.long_name    = 'height_above_sensor';
-                sample_data{k}.dimensions{end}.axis         = 'Z';
-                sample_data{k}.dimensions{end}.positive     = 'up';
-                sample_data{k}.dimensions{end}.comment      = ['Data has been vertically bin-mapped using tilt information so that the cells ' ...
+                % we create the HEIGHT_ABOVE_SENSOR dimension if needed
+                sample_data{k}.dimensions{end+1}             = sample_data{k}.dimensions{distAlongBeamsIdx};
+
+                % attributes units, reference_datum, valid_min/max and _FillValue are the same as with DIST_ALONG_BEAMS, the rest differs
+                sample_data{k}.dimensions{end}.name            = 'HEIGHT_ABOVE_SENSOR';
+                sample_data{k}.dimensions{end}.long_name       = 'height_above_sensor';
+                sample_data{k}.dimensions{end}.standard_name   = imosParameters('HEIGHT_ABOVE_SENSOR', 'standard_name');
+                sample_data{k}.dimensions{end}.axis            = 'Z';
+                sample_data{k}.dimensions{end}.positive        = imosParameters('HEIGHT_ABOVE_SENSOR', 'positive');
+                sample_data{k}.dimensions{end}.comment         = ['Data has been vertically bin-mapped using tilt information so that the cells ' ...
                     'have consistant heights above sensor in time.'];
 
                 heightAboveSensorIdx = getVar(sample_data{k}.dimensions, 'HEIGHT_ABOVE_SENSOR');
             end
 
-            % we re-assign the parameter to this dimension
+            % we re-assign the parameter to the HEIGHT_ABOVE_SENSOR dimension
             sample_data{k}.variables{j}.dimensions(sample_data{k}.variables{j}.dimensions == distAlongBeamsIdx) = heightAboveSensorIdx;
 
             sample_data{k}.variables{j}.data = mappedData;
@@ -220,6 +224,29 @@
     end
 
     if isBinMapApplied
+        % let's look for remaining variables assigned to DIST_ALONG_BEAMS,
+        % if none we can remove this dimension (RDI for example)
+        isDistAlongBeamsUsed = false;
+        for j=1:length(sample_data{k}.variables)
+            if any(sample_data{k}.variables{j}.dimensions == distAlongBeamsIdx)
+                isDistAlongBeamsUsed = true;
+                break;
+            end
+        end
+        if ~isDistAlongBeamsUsed
+            if length(sample_data{k}.dimensions) > distAlongBeamsIdx
+                for j=1:length(sample_data{k}.variables)
+                    dimToUpdate = sample_data{k}.variables{j}.dimensions > distAlongBeamsIdx;
+                    if any(dimToUpdate)
+                        sample_data{k}.variables{j}.dimensions(dimToUpdate) = sample_data{k}.variables{j}.dimensions(dimToUpdate) - 1;
+                    end
+                end
+            end
+            sample_data{k}.dimensions(distAlongBeamsIdx) = [];
+
+            binMappingComment = [binMappingComment ' DIST_ALONG_BEAMS is not used by any variable left and has been removed.'];
+        end
+
         history = sample_data{k}.history;
         if isempty(history)
             sample_data{k}.history = sprintf('%s - %s', datestr(now_utc, readProperty('exportNetCDF.dateFormat')), binMappingComment);

diff --git a/Preprocessing/adcpNortekVelocityBeam2EnuPP.m b/Preprocessing/adcpNortekVelocityBeam2EnuPP.m
@@ -171,6 +171,29 @@
         end
     end
 
+    % let's look for remaining variables assigned to DIST_ALONG_BEAMS,
+    % if none we can remove this dimension
+    isDistAlongBeamsUsed = false;
+    for j=1:length(sample_data{k}.variables)
+        if any(sample_data{k}.variables{j}.dimensions == distAlongBeamsIdx)
+            isDistAlongBeamsUsed = true;
+            break;
+        end
+    end
+    if ~isDistAlongBeamsUsed
+        if length(sample_data{k}.dimensions) > distAlongBeamsIdx
+            for j=1:length(sample_data{k}.variables)
+                dimToUpdate = sample_data{k}.variables{j}.dimensions > distAlongBeamsIdx;
+                if any(dimToUpdate)
+                    sample_data{k}.variables{j}.dimensions(dimToUpdate) = sample_data{k}.variables{j}.dimensions(dimToUpdate) - 1;
+                end
+            end
+        end
+        sample_data{k}.dimensions(distAlongBeamsIdx) = [];
+
+        Beam2EnuComment = [Beam2EnuComment ' DIST_ALONG_BEAMS is not used by any variable left and has been removed.'];
+    end
+
     if ~isfield(sample_data{k}, 'history')
         sample_data{k}.history = sprintf('%s - %s', datestr(now_utc, readProperty('exportNetCDF.dateFormat')), Beam2EnuComment);
     else

diff --git a/Preprocessing/salinityPP.m b/Preprocessing/salinityPP.m
@@ -97,6 +97,9 @@
 
   cndc = sam.variables{cndcIdx}.data;
   temp = sam.variables{tempIdx}.data;
+
+  % pressure information used for Salinity computation is from the
+  % PRES or PRES_REL variables in priority
   if isPresVar
       if presRelIdx > 0
           presRel = sam.variables{presRelIdx}.data;
@@ -109,28 +112,36 @@
           presName = 'PRES substracting a constant value 10.1325 dbar for nominal atmospheric pressure';
       end
   else
+      % when no pressure variable exists, we use depth information either 
+      % from the DEPTH variable or from the instrument_nominal_depth 
+      % global attribute
       if depthIdx > 0
+          % with depth data
           depth = sam.(depthType){depthIdx}.data;
-          if ~isempty(sam.geospatial_lat_min) && ~isempty(sam.geospatial_lat_max)
-              % compute depth with Gibbs-SeaWater toolbox
-              % relative_pressure ~= gsw_p_from_z(-depth, latitude)
-              if sam.geospatial_lat_min == sam.geospatial_lat_max
-                  presRel = gsw_p_from_z(-depth, sam.geospatial_lat_min);
-              else
-                  meanLat = sam.geospatial_lat_min + ...
-                      (sam.geospatial_lat_max - sam.geospatial_lat_min)/2;
-                  presRel = gsw_p_from_z(-depth, meanLat);
-              end
-              presName = 'DEPTH';
+          presName = 'DEPTH';
+      else
+          % with nominal depth information
+          depth = sam.instrument_nominal_depth*ones(size(temp));
+          presName = 'instrument_nominal_depth';
+      end
+
+      % pressure information needed for Salinity computation is either
+      % retrieved from gsw_p_from_z when latitude is available or by 
+      % simply assuming 1dbar ~= 1m
+      if ~isempty(sam.geospatial_lat_min) && ~isempty(sam.geospatial_lat_max)
+          % compute depth with Gibbs-SeaWater toolbox
+          % relative_pressure ~= gsw_p_from_z(-depth, latitude)
+          if sam.geospatial_lat_min == sam.geospatial_lat_max
+              presRel = gsw_p_from_z(-depth, sam.geospatial_lat_min);
           else
-              % without latitude information, we assume 1dbar ~= 1m
-              presRel = depth;
-              presName = 'DEPTH (assuming 1 m ~ 1 dbar)';
+              meanLat = sam.geospatial_lat_min + ...
+                  (sam.geospatial_lat_max - sam.geospatial_lat_min)/2;
+              presRel = gsw_p_from_z(-depth, meanLat);
           end
-
       else
-          presRel = sam.instrument_nominal_depth*ones(size(temp));
-          presName = 'instrument_nominal_depth (assuming 1 m ~ 1 dbar)';
+          % without latitude information, we assume 1dbar ~= 1m
+          presRel = depth;
+          presName = [presName ' (assuming 1 m ~ 1 dbar)'];
       end
   end
 

diff --git a/Util/fastSaveas.m b/Util/fastSaveas.m
@@ -2,14 +2,23 @@ function fastSaveas( hFig, hPanel, fileDestination )
 %FASTSAVEAS is a faster alternative to saveas. 
 % It is used to save diagnostic plots when exporting netCDF files.
 
-drawnow;
-
 % preserve the color scheme
 set(hFig, 'InvertHardcopy', 'off');
 
+drawnow;
+
 % force figure full screen
-frame_h = get(handle(hFig), 'JavaFrame');
-set(frame_h, 'Maximized', 1);
+try
+    warning('off', 'MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
+    frame_h = get(handle(hFig), 'JavaFrame');
+    set(frame_h, 'Maximized', 1);
+catch
+    disp(['Warning : JavaFrame feature not supported. Figure is going full ' ...
+        'screen using normalised units which does not give best results.']);
+    oldUnits = get(hFig, 'Units');
+    set(hFig, 'Units', 'norm', 'Pos', [0, 0, 1, 1]);
+    set(hFig, 'Units', oldUnits);
+end
 
 % screencapture creates an image of what is really displayed on
 % screen.

diff --git a/imosToolbox.m b/imosToolbox.m
@@ -73,7 +73,7 @@ function imosToolbox(auto, varargin)
 end
 
 % Set current toolbox version
-toolboxVersion = ['2.5.17 - ' computer];
+toolboxVersion = ['2.5.18 - ' computer];
 
 switch auto  
   case 'auto', autoIMOSToolbox(toolboxVersion, varargin{:});

diff --git a/imosToolbox_Linux64.bin b/imosToolbox_Linux64.bin
diff --git a/imosToolbox_Win32.exe b/imosToolbox_Win32.exe
diff --git a/imosToolbox_Win64.exe b/imosToolbox_Win64.exe