Mise en place d'un fichier de log

tsg_io/readBucketData.m

@@ -89,6 +89,10 @@ if fid ~= -1
       tsg.SSPS_WS_QC        = tsg.SSPS_WS_QC(iOrder);
     end
 
+    % Keep the name of the file for the log file
+    % ------------------------------------------
+    tsg.report.wsfile   = filename;
+    
     % Save the data in the application GUI
     % ------------------------------------
     setappdata( hTsgGUI, 'tsg_data', tsg );

tsg_io/readCoriolisData.m

-function [error] = readCoriolisData( hTsgGUI, filename)
+function [error] = readCoriolisData( hMainFig, filename)
 
 % Format :
 % 1,6 Date du profil ARGO : YYYY-MM-DD HH:MI:SS
@@ -33,7 +33,7 @@ if fid ~= -1
 
     % Get the tsg structure from application GUI
     % ------------------------------------------
-    tsg = getappdata( hTsgGUI, 'tsg_data');
+    tsg = getappdata( hMainFig, 'tsg_data');
     
     % Read the file
     % -------------
@@ -107,9 +107,14 @@ if fid ~= -1
       tsg.SSPS_EXT_TYPE      = tsg.SSPS_EXT_TYPE(iOrder,:);
       tsg.SSTP_EXT_TYPE      = tsg.SSTP_EXT_TYPE(iOrder,:);
     end
+        
+    % Keep the name of the file for the log file
+    % ------------------------------------------
+    tsg.report.extfile = filename;
+
     % Save the data in the application GUI
     % ------------------------------------
-    setappdata( hTsgGUI, 'tsg_data', tsg );
+    setappdata( hMainFig, 'tsg_data', tsg );
     
     % Clear the Workspace
     % -------------------

tsg_io/readTsgDataLabview.m

-function [error] = readTsgDataLabview( hTsgGUI, filename  )
+function [error] = readTsgDataLabview( hMainFig, filename  )
 % 
 % Fonction de lecture des fichiers TSG issus du programme
 % d'acquisition LabView XXX
@@ -6,7 +6,7 @@ function [error] = readTsgDataLabview( hTsgGUI, filename  )
 % [error] = rdtsglabview( Fichier )
 %
 % Input
-% hTsgGUI ............ Handel to the main user interface
+% hMainFig ............ Handel to the main user interface
 % filename ........... Data filename
 %
 % Output
@@ -33,7 +33,7 @@ function [error] = readTsgDataLabview( hTsgGUI, filename  )
 
 % Get the data from the application GUI
 % -------------------------------------
-tsg = getappdata( hTsgGUI, 'tsg_data');
+tsg = getappdata( hMainFig, 'tsg_data');
 
 % Display read file info on console
 % ---------------------------------
@@ -69,7 +69,7 @@ if fid ~= -1
 
     % Nombre de lignes du fichier
     % ---------------------------
-    nblig = length(sst);
+    nbrecords = length(sst);
 
     % decode tsg raw data
     % -------------------
@@ -110,12 +110,12 @@ if fid ~= -1
     
     % initialize and set <data>_FREQ to NaN
     % -------------------------------------
-    tsg.SSJT_FREQ = nan(nblig,1);
-    tsg.CNDC_FREQ = nan(nblig,1);
+    tsg.SSJT_FREQ = nan(nbrecords,1);
+    tsg.CNDC_FREQ = nan(nbrecords,1);
     
     % loop on all TsgRaw data
     % -----------------------
-    for i=1:nblig
+    for i=1:nbrecords
       
       % remove leading and trailing white space when string contain NaN
       % ---------------------------------------------------------------
@@ -139,7 +139,7 @@ if fid ~= -1
     % -------------------------------------------
     noNaN = find( strcmp( date, 'NaN') == 0 & strcmp( time, 'NaN') == 0 );
     
-    if~isempty( noNaN )
+    if ~isempty( noNaN )
 
       % Every variable are put in a structure
       % -------------------------------------
@@ -183,17 +183,22 @@ if fid ~= -1
         fileparts(filename);
       tsg.file.type = 'LABVIEW';
 
-      % Save the data in the application GUI
-      % ------------------------------------
-      setappdata( hTsgGUI, 'tsg_data', tsg );
-
       % Clear the Workspace
       % -------------------
       clear date time lat lon sst sss cond condRaw sog cog
-    end
-
+      
+      % Perform somme automatic tests
+      % -----------------------------
+      automaticQC( hMainFig )
+      
+      % Keep somme information for the log file
+      % ---------------------------------------
+      tsg.report.tsgfile  = filename;
+      tsg.report.nodate   = nbrecords - length(noNaN); 
 
-    if ~isempty( noNaN )
+      % Save the data in the application GUI
+      % ------------------------------------
+      setappdata( hMainFig, 'tsg_data', tsg );
 
       % Close the file
       % --------------

tsg_io/readTsgDataNetCDF.m

-function [error] = readTsgDataNetCDF( hTsgGUI, filename)
+function [error] = readTsgDataNetCDF( hMainFig, filename)
 % Function to read the TSG data. Should be a NetCDF file
 % GOSUD data format TSG V1.4
 %
 % Input
 % -----
-% hTsgGUI ............ Handel to the main user interface
+% hMainFig ............ Handel to the main user interface
 % filename ........... Data filename
 %
 % Output
@@ -21,7 +21,7 @@ function [error] = readTsgDataNetCDF( hTsgGUI, filename)
 
 % Get the data from the application GUI
 % -------------------------------------
-tsg = getappdata( hTsgGUI, 'tsg_data');
+tsg = getappdata( hMainFig, 'tsg_data');
 
 % Display read file info on console
 % ---------------------------------
@@ -106,10 +106,17 @@ for i=1:length(variables)
   end
 end
 
+% Perform somme automatic tests
+% -----------------------------
+automaticQC( hMainFig )
+
+% Keep somme information for the log file
+% ---------------------------------------
+tsg.report.tsgfile = filename;
+
 % Save the data in the application GUI
 % ------------------------------------
-setappdata( hTsgGUI, 'tsg_data', tsg );
-
+setappdata( hMainFig, 'tsg_data', tsg );
 
 % Close the file
 % --------------

tsg_io/readTsgDataTxt.m

-function [error] = readTsgDataTxt( hTsgGUI, filename)
+function [error] = readTsgDataTxt( hMainFig, filename)
 % Function to read the TSG data. Should be a NetCDF file
 %
 % Input
 % -----
-% hTsgGUI ............ Handle to the main user interface
+% hMainFig ............ Handle to the main user interface
 % filename ........... Data filename
 %
 % Output
@@ -18,7 +18,7 @@ function [error] = readTsgDataTxt( hTsgGUI, filename)
 
 % Get the data from the application GUI
 % -------------------------------------
-tsg = getappdata( hTsgGUI, 'tsg_data');
+tsg = getappdata( hMainFig, 'tsg_data');
 
 % Display read file info on console
 % ---------------------------------
@@ -48,8 +48,8 @@ tsgData = fscanf(fid, '%d/%d/%d %d:%d:%d %f %f %f %f %d %f %f', [13 Inf])';
 
 % Every variable are put in a structure
 % -------------------------------------
-tsg.DAYD       = datenum(tsgData(:,3), tsgData(:,2),tsgData(:,1), ...
-  tsgData(:,4),tsgData(:,5),tsgData(:,6));
+tsg.DAYD = datenum(tsgData(:,3), tsgData(:,2),tsgData(:,1), ...
+                   tsgData(:,4),tsgData(:,5),tsgData(:,6));
 
 % save original date
 % ------------------
@@ -73,12 +73,20 @@ tsg.file.type = 'ASCII';
 
 % Save the data in the application GUI
 % ------------------------------------
-setappdata( hTsgGUI, 'tsg_data', tsg );
+setappdata( hMainFig, 'tsg_data', tsg );
 
 % Clear the Workspace
 % -------------------
 clear tsgdata
 
+% Perform somme automatic tests
+% -----------------------------
+automaticQC( hMainFig );
+
+% Keep somme information for the log file
+% ---------------------------------------
+tsg.report.tsgfile = filename;
+
 % Close the file
 % --------------
 fclose( fid );

tsg_io/readTsgDataXML.m

-function [error] = readTsgDataXML( hTsgGUI, filename)
+function [error] = readTsgDataXML( hMainFig, filename)
 % Function to read the TSG data XML file
 %
 % Input
 % -----
-% hTsgGUI ............ Handel to the main user interface
+% hMainFig ............ Handel to the main user interface
 % filename ........... Data filename
 %
 % Output
@@ -18,7 +18,7 @@ function [error] = readTsgDataXML( hTsgGUI, filename)
 
 % Get the data from the application GUI
 % -------------------------------------
-tsg = getappdata( hTsgGUI, 'tsg_data');
+tsg = getappdata( hMainFig, 'tsg_data');
 
 % Display read file info on console
 % ---------------------------------
@@ -173,7 +173,7 @@ end
 %
 %     % Save the data in the application GUI
 %     % ------------------------------------
-%     setappdata( hTsgGUI, 'tsg_data', tsg );
+%     setappdata( hMainFig, 'tsg_data', tsg );
     
     % Clear the Workspace
     % -------------------
@@ -182,7 +182,15 @@ end
     % Close the file
     % --------------
     fclose( fid );
+   
+    % Perform somme automatic tests
+    % -----------------------------
+    automaticQC( hMainFig )
     
+    % Keep somme information for the log file
+    % ---------------------------------------
+    tsg.report.tsgfile = filename;
+
     % Display time to read file on console
     % ------------------------------------
     t = toc; fprintf('...done (%6.2f sec).\n\n',t);

tsg_io/saveReport.m

+function error = saveReport( hMainFig )
+%
+% Input
+% -----
+% hMainFig ............ Handel to the main user interface
+%
+% Output
+% ------
+% error .............. 1: OK ; -1 : an error occured
+
+error = -1;
+
+% Get the data from the application GUI
+% -------------------------------------
+tsg = getappdata( hMainFig, 'tsg_data');
+
+nPara = 3;
+PARA  = ['SSPS'; 'SSJT'; 'SSTP'];
+
+% Get NO_CONTROL and INTERPOLATED_VALUE codes
+% -------------------------------------------
+MISSING_VALUE      = get(tsg.qc.hash, 'MISSING_VALUE', 'code');
+NO_CONTROL         = get(tsg.qc.hash, 'NO_CONTROL', 'code');
+GOOD               = get(tsg.qc.hash, 'GOOD', 'code');
+PROBABLY_GOOD      = get(tsg.qc.hash, 'PROBABLY_GOOD', 'code');
+BAD                = get(tsg.qc.hash, 'BAD', 'code');
+PROBABLY_BAD       = get(tsg.qc.hash, 'PROBABLY_BAD', 'code');
+VALUE_CHANGED      = get(tsg.qc.hash, 'VALUE_CHANGED', 'code');
+HARBOUR            = get(tsg.qc.hash, 'HARBOUR', 'code');
+INTERPOLATED_VALUE = get(tsg.qc.hash, 'INTERPOLATED_VALUE', 'code');
+
+% Get the prefix of the TSG filename
+% Delete the path
+% ----------------------------------
+[token, remain]  = strtok(tsg.report.tsgfile, filesep);
+while ~isempty( remain )
+  [token, remain]  = strtok(remain, filesep);
+end
+[token, remain]  = strtok(token, '.');
+
+% Open the dialog box to choose the Directory and name of the file
+% ----------------------------------------------------------------
+[FileName, PathName, FilterIndex] = ...
+  uiputfile('*.log','Save the log file', [token '.log'] );
+
+if FileName ~= 0
+  
+  % Open the file
+  % -------------
+  fid = fopen( [PathName FileName], 'w' );
+  
+  if fid ~= -1
+    
+    % Write the date and time when the file is saved
+    % ----------------------------------------------
+    fprintf( fid, '\t\t\t\t TSGQC REPORT \n');
+
+    fprintf( fid, '\t\t\t %s \n\n', datestr( fix(clock), 0));
+    
+    % Write the name of the files used during the session
+    % ---------------------------------------------------
+    fprintf( fid, 'TSG file : %s\n\n', tsg.report.tsgfile);
+    if ~isempty( tsg.report.wsfile )
+      fprintf( fid, 'Water sample file : %s\n\n', tsg.report.wsfile);
+    else
+      fprintf( fid, 'No water sample file used during this session\n\n');
+    end
+    if ~isempty( tsg.report.wsfile )
+      fprintf( fid, 'External file : %s\n\n', tsg.report.extfile);
+    else
+      fprintf( fid, 'No external sample file used during this session\n\n');
+    end
+    
+    % Position interpolation
+    % ----------------------
+    ind = find( tsg.POSITION_QC == INTERPOLATED_VALUE );
+    fprintf( fid, '%d records have interpolated position\n\n', length( ind ));
+    
+    % No date
+    % -------
+    fprintf( fid, ...
+      '%d records have been deleted because they have no date\n\n',...
+      tsg.report.nodate);
+    
+    % Records deleted because date is not increasing
+    % -------------------------------------------------
+    fprintf( fid, ...
+      '%d records deleted  because its date is not increasing\n\n',...
+      tsg.report.nodate);
+    
+    % Records calibrated ?
+    % --------------------
+    for ipar = 1 : nPara
+
+      para = PARA(ipar,:);
+
+      fprintf( fid, '\n****************** %s PARAMETER **************\n\n', para);
+
+      noNaN = find( isnan( tsg.([para '_CAL']) == 0));
+
+      if ~isempty( tsg.(para) )
+
+        % --------------------
+        % Test for calibration
+        % --------------------
+        if ~isempty( tsg.([para '_CAL'])) & isempty( noNaN )
+          fprintf( fid, 'Time series calibrated\n');
+          fprintf( fid, '\t\tUsed oefficients: \n' );
+
+          % Peculiar case. No calibration coefficient for SSPS but for
+          % conductivity
+          % ----------------------------------------------------------
+          para_old = '';
+          if strcmp( para, 'SSPS' )
+            para_old = para;
+            para = 'CNDC';
+          end
+          fprintf( fid, '\t\tSlope  : %f\n', tsg.([para '_LINCOEF'])(1));
+          fprintf( fid, '\t\tOffset : %f\n\n', tsg.([para '_LINCOEF'])(2));
+          if ~isempty( para_old )
+            para= para_old;
+          end
+
+        else
+
+          fprintf( fid, 'Time series not calibrated \n\n' );
+        end    % if ~isempty( tsg.([para '_CAL'])) & isempty( noNaN )
+
+        % ---------------
+        % Validation code
+        % ---------------
+        
+        % get list of keys from hashtable tsg.qc.hash, defined inside
+        % tsg_initialisation.m
+        % -----------------------------------------------------------
+        qc_list = get(tsg.qc.hash);
+
+        % iterate (loop) on each key store inside hastable
+        % ------------------------------------------------
+        for i=1:numel(qc_list)
+
+          % get key and some values in hashtable
+          % ------------------------------------
+          key   = qc_list{i};
+          code = get(tsg.qc.hash, key, 'code');
+
+          % find number of sample flag with this QC code
+          % --------------------------------------------
+          ind = find(tsg.([para '_QC']) == code);
+
+          fprintf( fid, '%07d %s code \n', length( ind ), key );
+
+        end
+
+        % --------------------------------------------
+        % Number of record corrected versus calibrated
+        % --------------------------------------------
+%         ind = find( tsg.([para '_QC']) == VALUE_CHANGED );
+%         if ~isempty( ind )
+%           ind = find( tsg.([para '_ADJUSTED_ERROR']) );
+%           if ~isempty( ind )
+%             printf( fid, '%d records have been adjusted\n\n', length( ind ));
+%           end
+%         end
+        
+        % ----------------------
+        % Number of Water sample
+        % ----------------------
+          
+        
+        % -------------------------------
+        % Number of External Water sample
+        % -------------------------------
+
+      else
+
+        fprintf( fid, 'no time series \n\n' );
+      end      % ~isempty( tsg.para )
+    end        % for ipar
+
+
+  else
+
+    error = -1;
+
+  end       % if fid
+end         % if FileName
+

tsg_util/automaticQC.m

@@ -16,6 +16,8 @@ function [] = automaticQC( hMainFig )
 % --------------------------------------
 tsg  = getappdata( hMainFig, 'tsg_data');
 
+MISSING_VALUE      = get(tsg.qc.hash, 'MISSING_VALUE', 'code');
+
 % ************************** TEST 1 ***********************************
 %
 % Detect records with date and time at NaN.
@@ -28,9 +30,13 @@ tsg  = getappdata( hMainFig, 'tsg_data');
 % Delete the records with inversion
 % 
 % Find negative differences between successive dates
-difDate = diff( tsg.DAYD );
-ind = find( difDate < 0 ) + 1;
+nbBadDate = 0;
+difDate   = diff( tsg.DAYD );
+ind       = find( difDate < 0 ) + 1;
 while ~isempty( ind )
+  
+  nbBadDate = nbBadDate + length( nbBadDate );
+  
   if ~isempty( tsg.DAYD );      tsg.DAYD(ind)      = []; end;
   if ~isempty( tsg.DATE );      tsg.DATE(ind, :)   = []; end;
   if ~isempty( tsg.LATX );      tsg.LATX(ind)      = []; end;
@@ -48,8 +54,27 @@ while ~isempty( ind )
 
   difDate = diff( tsg.DAYD );
   ind = find( difDate < 0 ) + 1;
+end
+
+% Keep the number of data not in increasing date
+% ----------------------------------------------
+tsg.report.sortdate =  nbBadDate;
 
+% NO_VALUE code
+% -------------
+ind = find( isnan(tsg.SSPS) == 1);
+if ~isempty( ind )
+  tsg.SSPS_QC(ind) = MISSING_VALUE;
 end
+ind = find( isnan(tsg.SSJT) == 1);
+if ~isempty( ind )
+  tsg.SSJT_QC(ind) = MISSING_VALUE;
+end
+ind = find( isnan(tsg.SSTP) == 1);
+if ~isempty( ind )
+  tsg.SSTP_QC(ind) = MISSING_VALUE;
+end
+
 
 % ************************** TEST 3 ***********************************
 %
@@ -71,6 +96,20 @@ if ~isempty( ind )
   tsg.SSPS_QC(ind) = castByteQC( badCode, ind );
 end
 
+% Set salinity QC to BAD for SSTP > 40
+% -----------------------------------
+ind = find(tsg.SSTP > 40);
+if ~isempty( ind )
+  tsg.SSTP_QC(ind) = castByteQC( badCode, ind );
+end
+
+% Set salinity QC to BAD for STP < -3
+% -----------------------------------
+ind = find(tsg.SSTP < -3);
+if ~isempty( ind )
+  tsg.SSTP_QC(ind) = castByteQC( badCode, ind );
+end
+
 % Save the data in the application GUI
 % ------------------------------------
 setappdata( hMainFig, 'tsg_data', tsg );

tsg_util/plot_Correction.m

@@ -90,20 +90,20 @@ end
 % Plot SSPS, with no code, on axe3
 % --------------------------------
 plot_Tsg( hMainFig, hPlotAxes, 3, tsg.DAYD, tsg.([PARA '_ADJUSTED']), [],...
-            [PARA '_ADJUSTED'],'r','none','*',1);
+            [PARA '_ADJUSTED'],'r','none','*',2);
           
 plot_Tsg( hMainFig, hPlotAxes, 3, tsg.DAYD, tsg.(PARA),...
-          [],PARA,'k','none','*',1);
+          [],PARA,'k','none','*',2);
 
 % Plot TSG_ADJUSTED + ERROR on axe 3
 % -----------------------------------
 if iERR ~= 0
   plot_Tsg( hMainFig, hPlotAxes, 3, tsg.DAYD(iVC(iERR)),...
           tsg.([PARA '_ADJUSTED'])(iVC(iERR)) + tsg.([PARA '_ADJUSTED_ERROR'])(iVC(iERR)),...
-          [], [PARA '_ADJUSTED'],'g','none','*',1);
+          [], [PARA '_ADJUSTED'],'g','none','*',2);
   plot_Tsg( hMainFig, hPlotAxes, 3, tsg.DAYD(iVC(iERR)),...
           tsg.([PARA '_ADJUSTED'])(iVC(iERR)) - tsg.([PARA '_ADJUSTED_ERROR'])(iVC(iERR)),...
-          [], [PARA '_ADJUSTED'],'g','none','*',1);
+          [], [PARA '_ADJUSTED'],'g','none','*',2);
 end
 
 end

tsg_util/plot_Interpolation.m

@@ -20,13 +20,13 @@ switch nPlot
     if ~isempty( tsg.LATX ) && ~isempty( tsg.SSPS)
 
       ind = find( isnan(tsg.LATX) == 1 | isnan(tsg.LONX) == 1);
-      if ~isempty( tsg.ssps_smooth )
+      if ~isempty( ind )
         plot_Tsg( hMainFig, hPlotAxes, 1, tsg.DAYD(ind), tsg.SSPS(ind), [],...
           'SSPS_NOPOS','b','none','*',2);
       end
 
       ind = find( isnan(tsg.LATX) == 0 | isnan(tsg.LONX) == 0);
-      if ~isempty( tsg.SSPS )
+      if ~isempty( ind )
         plot_Tsg( hMainFig, hPlotAxes, 1, tsg.DAYD(ind), tsg.SSPS(ind), [],...
           'SSPS','k','none','*',2);
       end

tsg_util/tsg_initialisation.m

@@ -58,10 +58,19 @@ tsg.file.type    = [];
 % -------------------------------------------------------------------------
 %%              Smooth TSG time serie fields
 % -------------------------------------------------------------------------
-tsg.ssps_smooth      = [];
-tsg.ssps_smooth.nval = [];
-tsg.SSTP_smooth      = [];
-tsg.SSTP_smooth.nval = [];
+% tsg.ssps_smooth      = [];
+% tsg.ssps_smooth.nval = [];
+% tsg.SSTP_smooth      = [];
+% tsg.SSTP_smooth.nval = [];
+
+% -------------------------------------------------------------------------
+%%              Variable used for the report
+% -------------------------------------------------------------------------
+tsg.report.tsgfile  = '';  % Name of the TSG file
+tsg.report.wsfile   = '';  % Name of the Water sample file
+tsg.report.extfile  = '';  % Name of the External sample file
+tsg.report.nodate   =  0;  % Records eliminated because they have no date
+tsg.report.sortdate =  0;  % Records eliminated because date is not increasing
 
 % -------------------------------------------------------------------------
 %%              Structure used to merge WS and EXT sample

tsgqc_GUI.m

@@ -365,6 +365,16 @@ hHeaderPushtool  = uipushtool(...   % Open headerForm button
   'Enable', 'off',...
   'ClickedCallback', @HeaderMenuCallback);
 
+hReportPushtool  = uipushtool(...   % Open Report saving button
+  'Parent',hToolbar,...
+  'TooltipString','Save a report',...
+  'CData',iconRead(...
+  [DEFAULT_PATH_FILE 'tsg_icon' filesep 'reporticon.mat']),...
+  'HandleVisibility','on', ...
+  'Tag','PUSHTOOL_REPORT',...
+  'Enable', 'off',...
+  'ClickedCallback', @ReportMenuCallback);
+
 %% Dynamic text area
 %   -----------------------------------------------------------------------
 %  Dynamic text area that displays the loaded filename, date, position and
@@ -1083,10 +1093,6 @@ end
           tsg_initialisation(hMainFig);
           errTsg = readTsgDataLabview( hMainFig, fullFileName );
 
-          if errTsg > 0           % Reading is OK
-            automaticQC( hMainFig );
-          end
-
         case 5                      % Read bucket file *.btl
           if ~isempty( tsg.SSPS )
             errSpl = readBucketData(     hMainFig, fullFileName );
@@ -2598,6 +2604,18 @@ end
 
   end
 
+%% ReportMenuCallback
+% -------------------------------------------------------------------
+% Callback function run when the Report tool bar item is selected
+% -------------------------------------------------------------------
+  function ReportMenuCallback(hObject, eventdata)
+
+    % call report function
+    % --------------------
+    saveReport(hMainFig);
+
+  end
+
 %% SaveMenuCallback
 % -------------------------------------------------------------------
 % Callback function run when the Save menu item is selected