function epname = mavs_avg(infile, outfile)
% function epname = mavs_avg(infile, outfile)
% calibrates MAVS data from the BASS variables from the average
% records of MIDAS data.
% epname is a cell array of the names of the variables created.
% infile is the name of a netcdf file of raw data, to which
%		calibration constants have been attached as attributes.
% outfile is the name of an EPIC compliant netcdf file containing
%		the variables listed in epname.
% Fran Hotchkiss 22 Jun 2000.
calcomment = '';

nc = netcdf(infile)%;
disp ('mavs_avg.m is running')%********************
if isempty(nc)
   [infile,inpath] = uigetfile('*.cdf','Choose input file');
   nc = netcdf(infile);
   if isempty(nc)
      disp (['Cannot open input file ' infile]);
      disp (['Execution ends.']);
      return;
   end
end

bass1 = nc{'bass_1'}(:);
bass2 = nc{'bass_2'}(:);
burst_per_avg = nc{'burst_per_avg'}(:);
bass_error1 = nc{'bass_error_1'}(:);
bass_error2 = nc{'bass_error_2'}(:);
mavsnum = nc{'bass_1'}.instrument_number(:);
mavszeros = [0 0 0 0];
ivar = nc{'bass_1'};

% Choose MAVS calibration routine zeros.
MAVS.axes = {{'All','A omitted','B omitted','C omitted',...
               'D omitted'},1};
MAVS.zeros={{'pre-deployment','post-deployment','provided'},2};
MAVS.zero_A = 0.;
MAVS.zero_B = 0.;
MAVS.zero_C = 0.;
MAVS.zero_D = 0.;
if running(batch)
   str = get(batch);
   eval(['MAVS.axes{2} = ' str ';']);      
   str = get(batch);
   eval(['MAVS.zeros{2} = ' str ';']);      
   str = get(batch);
   eval(['MAVS.zero_A = ' str ';']);      
   str = get(batch);
   eval(['MAVS.zero_B = ' str ';']);      
   str = get(batch);
   eval(['MAVS.zero_C = ' str ';']);      
   str = get(batch);
   eval(['MAVS.zero_D = ' str ';']);      
else
	B = MAVS;
   MAVS = guido(B,'Select MAVS calibration parameters');
	if isempty(MAVS)
      disp ('MAVS Parameter Menu must be completed. Execution ends.')
      close (nc)
 	  	return
   end
end
      
switch MAVS.zeros{2}
case 1
	mavszeros(1) = ivar.pre_zero_offset_A(1);
	mavszeros(2) = ivar.pre_zero_offset_B(1);
	mavszeros(3) = ivar.pre_zero_offset_C(1);
	mavszeros(4) = ivar.pre_zero_offset_D(1);
   calcomment = [calcomment 'Pre zeroes used. ']%;
case 2
	mavszeros(1) = ivar.post_zero_offset_A(1);
	mavszeros(2) = ivar.post_zero_offset_B(1);
	mavszeros(3) = ivar.post_zero_offset_C(1);
	mavszeros(4) = ivar.post_zero_offset_D(1);
   calcomment = [calcomment 'Post zeroes used. ']%;
otherwise
	mavszeros(1) = MAVS.zero_A;
	mavszeros(2) = MAVS.zero_B;
	mavszeros(3) = MAVS.zero_C;
	mavszeros(4) = MAVS.zero_D;
   calcomment = [calcomment 'User-provided zeroes. ']%;
end

switch MAVS.axes{2}
case 1
   [Ve, Vn, Vup, H, P, R, mavszeros] = mavs2earth(bass1, bass2, burst_per_avg,...
   	bass_error1, bass_error2, mavsnum, mavszeros, 0);
otherwise
   disp ('MAVS calibration with less than 4 axes not implemented.')
   close (nc)
   return
end

% Put data in normal units.
Ve = Ve/10;
Vn = Vn/10;
Vup = Vup/10;
P = P/100;
R = R/100;
% Now make speed and direction.
[vdir,vspd] = cart2pol(Vn,Ve);
ilow = find(vdir < 0)%;
vdir(ilow) =vdir(ilow) + 2*pi;
vdir = vdir .* 180 ./ pi;


epname = {'Ptch_1216','Roll_1217','Hdg_1215','u_1205','v_1206','CD_310','CS_300','w_1204'};
datname = {'P','R','H','Ve','Vn','vdir','vspd','Vup'};
vardesc = 'Ptch:Roll:Hdg:u:v:CD:CS:w';
nvarout = 8%;

% Make EPIC time from MIDAS raw data set time.
% Input data and base time for time.
ivar = nc{'time'};
rawdat = ivar(:);
yr = ivar.base_date(1);
mo = ivar.base_date(2);
da = ivar.base_date(3);
hr = ivar.base_date(4);
mi = ivar.base_date(5);
sc = ivar.base_date(6);
% Find decimal day numbers for base time and time data.
base = datenum(yr,mo,da,hr,mi,sc);
rtime = base + rawdat./86400;
% Call function to make EPIC time.
alltime = EP_Time(rtime);
time = alltime(:,1);
time2 = alltime(:,2);
stime = ep_datenum(alltime(1,:));
[n m] = size(alltime);
ltime = ep_datenum(alltime(n,:));

% Get mooring log parameters.
if running(batch)
	str = get(batch);
   eval(['epicat.experiment = ' str ';']);      
	str = get(batch);
   eval(['epicat.project = ' str ';']);      
	str = get(batch);
   eval(['epicat.comment = ' str ';']);      
	str = get(batch);
   eval(['epicat.MAVS_pod_depth = ' str ';']);      
else
	epicat.experiment = 'ECOHAB';
	epicat.project = 'WHFC';
	epicat.comment = 'Boston BASS MIDAS';
	epicat.MAVS_pod_depth = 2.9;
	e = epicat;
   epicat = guido(e,'Input mooring log parameters.');
end


% Open output cdf
outc = netcdf(outfile,'noclobber')%;
if isempty(outc)
   [outfile,outpath] = uiputfile('*.nc','Choose output file');
   outc = netcdf(outfile,'noclobber');
   if isempty(outc)
      disp (['Cannot open output file ' outfile]);
      disp (['Data will be parked in temporary.nc']);
      outc = netcdf('temporary.nc','clobber');
   end
end

% Copy global attributes from ep_standard.nc to output cdf.
eps = netcdf('ep_standard.nc')%;
if isempty(eps)
   [epsfile,epspath] = uigetfile('*.nc','Choose epic standard file');
   eps = netcdf(epsfile);
   if isempty(eps)
      try
         mkep_standard;
			eps = netcdf('ep_standard.nc')%;
      catch
	      disp (['Cannot open epic standard file ' epsfile]);
   	   disp (['Execution ends.']);
      	ncclose;
         return;
      end
   end
end
disp ('ep_standard.nc is open')%*****************
stdatts = att(eps);
for i = 1, length(stdatts);
   copy(stdatts(i),outc);
end

%% Modify Global attributes:
 
outc.DATA_ORIGIN = nc.data_source(:);
outc.EXPERIMENT = epicat.experiment;
outc.PROJECT = epicat.project;
outc.MOORING = nc.mooring_number(:);
outc.DELTA_T = ncchar(num2str(nc.average_interval(1)));
outc.DATA_CMNT = epicat.comment;
outc.WATER_DEPTH = nc.water_depth(1);
outc.DESCRIPT = nc.comment(:);
outc.FILL_FLAG = nclong(0);
outc.VAR_FILL = ncfloat(NaN);
history =['Calibrated using mavs_avg.m. ' calcomment ':' nc.history(:)]%; 
disp (['history is ' history]) %********************
outc.history = history;
outc.start_time = datestr(stime,0);
outc.stop_time = datestr(ltime,0);
outc.latitude = dms2deg(nc.lat_ddmmss(:));
outc.longitude = -dms2deg(nc.lon_ddmmss(:));
outc.water_depth = nc.water_depth(1);
outc.CREATION_DATE = ncchar(datestr(now,0));
outc.INST_TYPE = nc.instrument_type(:);
outc.instrument_number = nc.instrument_number(:);
outc.magnetic_variation = nc.magnetic_variation(1);
outc.VAR_DESC = ncchar(vardesc);
outc.MAVS_zero_offset_A = mavszeros(1);
outc.MAVS_zero_offset_B = mavszeros(2);
outc.MAVS_zero_offset_C = mavszeros(3);
outc.MAVS_zero_offset_D = mavszeros(4);

%% Dimensions:
outc('time') = 0;
outc('depth') = 1;
outc('lon') = 1;
outc('lat') = 1;
 
 %% Variables and attributes:
copy(eps{'time'},outc,0,1);
copy(eps{'time2'},outc,0,1);
copy(eps{'depth'},outc,0,1);
copy(eps{'lon'},outc,0,1);
copy(eps{'lat'},outc,0,1);

for i = 1: nvarout;
   ivar = eps{epname{i}}%;
   disp (['Writing attributes for variable ' epname{i}])%*******
   if ~isempty(ivar)
      copy(ivar,outc,0,1);
   else
      display (['Variable ' epname{i} ' not found in ep_standard.nc. Execution ends.'])
      ncclose 
      return
   end
   ivar = nc{'bass_1'};
	ovar = outc{epname{i}};
	ovar.sensor_type = ivar.instrument_type(:);
	ovar.sensor_depth = ncfloat(epicat.MAVS_pod_depth);
	ovar.serial_number = ivar.instrument_number(:);
	eval (['ovar.minimum = ncfloat(min(' datname{i} '));']);
   eval (['ovar.maximum = ncfloat(max(' datname{i} '));']);
end
close (eps)
disp ('ep_standard.nc is closed')%******************************
endef(outc)

n=length(time)%;
outc{'time'}(1:n) = time;
outc{'time2'}(1:n) = time2;
outc{'lat'}(1) = nc{'lat'}(1);
outc{'lon'}(1) = nc{'lon'}(1);
outc{'depth'}(1) = epicat.MAVS_pod_depth;
for i = 1:nvarout
	ovar = outc{epname{i}}%;
   eval (['ovar(1:n) = ' datname{i} ';' ]);
end
close (nc)%;
close (outc)%;