ArrayManager.m

function [] = ArrayManager(SurveyName,maxSites,HZ)

% Usage: [] = ArrayManager(SurveyName,maxSites,HZ)
%
%  SurveyName gives the path (relative to MTdata, which should be set
%     as an environment variable before calling) of the specfic survey 
%     being processed (e.g., "Yellowstone").  This is the directory 
%     which contains subdirectories data, XML, original, MT, FC, tmp, etc.
%     If not specified, you get to choose the directory.
%  maxSites is an optional variable that is passed to dataTimes; 
%     this is used to control how many sites are
%  HZ is an optional variable that defines the default options files
%     in dataTimes / ComputeTF

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

if nargin <= 1
   maxSites = Inf;
end

if nargin <= 2
   HZ = 1;
end

dataHome = Survey.home;
setenv('dataHome',dataHome);

if ~exist(Survey.tmp,'dir'); mkdir(Survey.tmp); end
if ~exist(Survey.SP, 'dir'); mkdir(Survey.SP); end
if ~exist(Survey.FC, 'dir'); mkdir(Survey.FC); end
if ~exist(Survey.MT, 'dir'); mkdir(Survey.MT); end
if ~exist(Survey.MMT,'dir'); mkdir(Survey.MMT); end
if ~exist(Survey.data,'dir'); mkdir(Survey.data); end

XMLdir = Survey.metadata;
DataFiles = listFromXML(XMLdir,'update');
nFiles = length(DataFiles);

updateSP(SurveyName,DataFiles);
updateFC(SurveyName,DataFiles);

for k = 1:nFiles
   DataFiles{k}.surveyName = SurveyName;
end

[NIMSinfo] = mkNIMSinfo(SurveyName,DataFiles);

[Sites] = uniqueSites(DataFiles);

eval(['cd ''' dataHome '''' 'data']);
%  tUnits gives initial units for time axis for TSplot
%  choices are 'Seconds','Hours','Minutes','Days'
tUnits = 'Hours';
%  nTunits is number of Hours (more generally, tUnits) to plot on one page
nTunits = 24;
%  decFac is decimation factor to apply to time series before plotting
decFac = 1;
plotStart = plotSetup(tUnits,nTunits,decFac);
dataTimes(DataFiles,NIMSinfo,Sites,plotStart,maxSites,HZ);