updateFC.m

function [] = updateFC(SurveyName,DataFiles,DataFileSuffix)

% Usage: [] = updateFC(SurveyName,DataFiles,DataFileSuffix);
% Runs dnff for all data files *.bin in Survey/data for which there are
% binary data (*.bin) and system parameter files (*.sp) 
% in Survey/data and Survey/SP respectively.  Uses the list of available
% run files stored in cell array DataFiles.  Optional argument DataFileSuffix 
% can be used to change data file names from default *.bin to some other
% suffix (e.g., *.dbn, to run dnff on decimated files).  If second argument
% (DataFiles) is missing this generates the file list (i.e., DataFiles)
% by calling listFromXML
%
%  WARNINGS: 
%
%   --> IT WILL TAKE A FEW MINUTES FOR  dnff to RUN, 
%        ESPECIALLY FOR A LARGE NUMBER OF FILES
%

if nargin == 0
   Survey = startUpSurvey;
else
   Survey = startUpSurvey(SurveyName);
end

binDir = getenv('MTbin');
getOS;
if nargin < 2 
   XMLdir = Survey.metadata;
   DataFiles = listFromXML(XMLdir);
   DataFileSuffix = 'bin';
elseif nargin == 2
   DataFileSuffix = 'bin';
end

currentDir = pwd;
eval(['cd ''' Survey.home ''''])
nProc = 0;
dnffRunFile = ['tmp' filesep 'dnff.cfg'];
logFile =  ['tmp' filesep 'dnff_' date '.log'];
nFiles = length(DataFiles);
for k = 1:nFiles
   [pathstr,runID] = fileparts(DataFiles{k}.fileName);
   %runID = DataFiles{k}.Name;

   FCfile = [Survey.FC runID '.f5' ];
   FC = (exist(FCfile,'file')==2);

   dataFile = [Survey.data runID '.' DataFileSuffix ];
   DATA = (exist(dataFile,'file')==2);

   spFileRun = [Survey.SP runID '.sp'];
   spFileSite = [Survey.SP runID(1:end-1) '.sp'];
   SP = (exist(spFileSite,'file') > 0 | exist(spFileRun,'file') > 0);

   if ~FC & (SP & DATA)
      nProc = nProc+1;
      if nProc == 1
         fid = fopen(dnffRunFile,'w');
      else 
         fprintf(fid,'%s\n','y');
      end
      binFile = [ runID '.' DataFileSuffix ];
      fprintf(fid,'%s\n',binFile);
   end
end
if nProc > 0
   disp('Updating FC files...');
   fprintf(fid,'%s\n','n');
   fclose(fid);
   [status,output] = system([cmd binDir 'dnff -B < ' dnffRunFile '> ' logFile ' &']);
   disp(output);
else
   display('No FC files to compute')
end