function [MSL,Dstd,Dout] = rdsurface(rawdata,ADCP_offset,ensembles,progPath,DepthFile);

%function [MSL,Dstd,Dout] = rdsurface(rawdata,ADCP_offset,ensembles,progPath,DepthFile);

%This function will run the RDI surface program to obtain an approximate
%water depth.  If file names are not given, they will be requested.
%
%INPUTS:
%	rawdata = ADCP Binary data file
%	ADCP_offset = the height of the ADCP above the bottom in meters!
%						if not give will be pulled from netcdf file.
%	ensembles = the index number for the good ensembles,
%				  is likely to be different than the ensemble numbers in rawdata 	
%	progPath = the full path for the RDI surface program on your computer
%	DepthFile = the output depth data file name, this is created based on the 
%					rawdata file name if not given
%
%Outputs:
%	MSL = the mean sea level
%	Dstd = the standard of deviation of the depth which should 
%			 be an approximate tidal fluctuation
%	Dout = the surface depth at each ensemble as distinguished by 
%			 RDI's surface program

% Written by Jessica M. Cote
% for the U.S. Geological Survey
% Coastal and Marine Geology Program
% Woods Hole, MA
% http://woodshole.er.usgs.gov/
% Please report bugs to jcote@usgs.gov

%version 1.0
% update 03-Jan-2001 14:18:52 - need to account for place holders for missing ens numbers 
%     created by fixEns.m
% update 27-Dec-2000 15:29:06 - to read long and short ADCP data file names (ALR)
% updated 06-sep-2000 - to read long ADCP data file names
% updated 17-Feb-2000 14:32:50
% updated 02-Feb-2000 09:34:12
%	- if run with batch, will be prompted to look at depth limits unless
%	a depth is explicitly defined
%updated 10-Aug-1999 16:20:42


if nargin < 1, rawdata='';, end
if nargin < 2, ADCP_offset = '';, end
if nargin < 3, ensembles='';,end
if nargin < 4, progPath='';,end
if nargin < 5, DepthFile ='';, end

if isempty(rawdata), rawdata ='*';, end
if isempty(ADCP_offset), ADCP_offset = NaN;, end
if isempty(DepthFile), DepthFile = '*';, end

%where are we currently
s=pwd;

%Get binary ADCP data file
if any(rawdata == '*')
   [dataFile, dataPath] = uigetfile(rawdata, 'Select Binary ADCP File:');
   if ~any(dataFile), return, end
   if dataPath(end) ~= filesep, dataPath(end+1) = filesep; end
   rawdata = [dataPath dataFile];
else
   [dataPath, dataname, ext]=fileparts(rawdata);
   dataFile=[dataname ext];
end


%get the ADCP trasnducer offset out of *.cdf file
if isnan(ADCP_offset)
   [theFile, thePath] = uigetfile('*.cdf', 'Select Netcdf ADCP File to find ADCP offset:');
	if ~any(theFile), return, end
	if thePath(end) ~= filesep, thePath(end+1) = filesep; end
	cdfFile = [thePath theFile];
   f=netcdf(cdfFile);
   ADCP_offset=f{'D'}.xducer_offset_from_bottom(:);
   close(f)
end


%where is the program located
if isempty(progPath)
prompt={'In put Path:'};
title='Where is RDI surface program?';
lineNo=1;
DefAns={['drive' filesep 'folder' filesep]};
dlgresult=inputdlg(prompt,title,lineNo,DefAns);
   progPath=char(dlgresult{1});   
   
end

if progPath(end) ~= filesep, progPath(end+1) = filesep; end

   
%Create output file for depths
if any(DepthFile == '*')
   [thePath,theFile,ext] = fileparts(rawdata);
   if length(theFile) < 7
      DepthFile = fullfile(thePath, [theFile,'.dat']);
   else
      DepthFile = fullfile(thePath, [theFile(1:7) '.dat']);
   end
end

[Dpath, Dname, dext]=fileparts(DepthFile);
Dfile=([Dname dext]);

%SURFACE InFile OutFile [Ensembles Skip Bin1 LastBin]
% Copy the ADCP file to a the RDI directory.
if length(dataname) < 7
   surfFile = [dataname ext];
else
   surfFile = [dataname(1:7) ext];
end
cpfile = fullfile(progPath,surfFile)

if isunix
		eval(['!cp ' rawdata ' ' cpfile])
	elseif any(findstr(lower(computer), 'pcwin')) | isVMS
		eval(['!copy ' rawdata ' ' cpfile])
	elseif any(findstr(lower(computer), 'mac')) & ...
			exist('aduplicate') == 2
		feval('aduplicate', rawdata, cpfile)
	else
		fcopy(rawdata, cpfile)
      
   end
   
%this all has to happen in the same directory as the surface program
	try
		eval(['cd ' progPath])
	catch
   	prompt={'Correct Path:'};
		title='Path incorrect or missing end filesep?';
		lineNo=1;
		DefAns={progPath};
		dlgresult=inputdlg(prompt,title,lineNo,DefAns);
   	progPath=char(dlgresult{1});   
      if progPath(end) ~= filesep, progPath(end+1) = filesep; end
      eval(['cd ' progPath]);
   end
   
disp('Running RDI surface program')   
eval(['!surface ' surfFile ' ' Dfile])
delete(cpfile)

datfile = ([Dname '.out']);
datfile = mfriend(Dfile,datfile);
surfdat=load(datfile);

%move some stuff around
%if ~isequal(Dpath,progPath)
	if isunix
		eval(['!mv ' Dfile ' ' DepthFile])
	elseif any(findstr(lower(computer), 'pcwin')) | isVMS
		eval(['!move ' Dfile ' ' DepthFile])
	elseif any(findstr(lower(computer), 'mac')) & ...
			exist('aduplicate') == 2
      feval('aduplicate', Dfile, DepthFile)
      delete(Dfile)
	else
		fcopy(Dfile,DepthFile)
      delete(Dfile)
   end
%end

%go back to where we were before
cd(s)

%these are 2 ways of finding the good data,
%the first is by the data quality given by rdi
[m,n] = size(surfdat);
qual = surfdat(:,7) > 2;
Dall = surfdat(:,6);

%if the records are not numbered sequentially or 
% the first ensemble in the raw data record does not start with 1 there
% will be problems.  Also problems when the fill values have been
% added to the rawcdf file for missing ensemble numbers
%To remedy this:
datrec = surfdat(:,1);

%First, check and fill missing ens if necessary
dr=diff(datrec);
ii=length(datrec);
if max(dr)>1
   iFill=find(dr>1);
   missEns=datrec(iFill)+1;
   
   [m,n]=size(surfdat);  %size of original file
   l=length(missEns); %number of missing ensembles
   newEns=1:m+l;  %number of original ens plus missing ens
   newTemp=ones(m+l,n)*nan;  %set size of new file 
 
   good_count=1;
   miss_count=1;
   
   for k=1:l+m
      % loop to fill in missing data columns
      if miss_count <= l % only do while we have records
         if newEns(k)==missEns(miss_count)  
           % newTemp(:,k)=fillV;
            newTemp(k,1)=newEns(k); % added to give ensemble number at head of column
            miss_count=miss_count+1;    
         end
      end
      % loop to fill in good data columns
      if good_count <= ii % only do while we have records
         if newEns(k)==datrec(good_count)
            newTemp(k,:)=surfdat(good_count,:);
            good_count=good_count+1; 
         end  
      end
   end
   
   surfdat = newTemp;
   qual = surfdat(:,7) > 2;
   Dall = surfdat(:,6);
   datrec = surfdat(:,1);
   
end %(if loop, filling in missing ens numbers)

%Now check to see what ens number the data starts and ends on
if ~isempty(ensembles)
	ens1 = find(datrec == ensembles(1));
	ens2 = find(datrec == ensembles(end));
else
   ens1 = datrec(1);
   ens2 = length(datrec);
end

idgood = ens1(1):ens2(end);
  
%Use just the depths for the ensembles we consider to be good
if ~isempty(idgood)
   qual = qual(idgood);
   Dall = Dall(idgood);
end

%need to preserve the depth in the same length variable for output
%However, also need the depth variable to operate on
Dout = Dall.*qual;
Dm = Dall(qual);

Davg=mean(Dm);
Dmin=min(Dm);
Dmax=max(Dm);
Dstd=std(Dm);
disp(['RDI surface program found the following depth constraints in meters: min = '...
   num2str(Dmin) ' max = ' num2str(Dmax) ' Mean = ' num2str(Davg)])
%are we really getting only the good data?
p=figure;, plot(Dm,'r.'), hold

%Depth_constraints.Are_these_depths_reasonable={'radiobutton',0}
%Depth_constraints.Minimum_depth_in_meters={num2str(Dmin)};
%Depth_constraints.Maximum_depth={num2str(Dmax)};
%Depth_constraints=uigetinfo(Depth_constraints);

prompt={'Minimum depth in meters:',...
   'Maximum depth in meters:','Are these depths reasonable?'};
title='Check surface program output';
lineNo=1;
DefAns={num2str(Dmin),num2str(Dmax),'N'};
dlgresult=inputdlg(prompt,title,lineNo,DefAns);
   
if ~isequal(Dmin,str2num(dlgresult{1})) | ~isequal(Dmax,str2num(dlgresult{2})) 
   Dmin=str2num(dlgresult{1});
   Dmax=str2num(dlgresult{2});
	idgood=find(Dm >= Dmin & Dm <= Dmax);
	clf, plot(Dm(idgood),'r.');,hold;
   
elseif upper(char(dlgresult{3}))=='N';       
      prompt={'Minimum depth allowed:',...
   'Maximum depth allowed:'};
   title='Input valid range for depth';
   lineNo=1;
   DefAns={num2str(Dmin),num2str(Dmax)};
   dlgresult=inputdlg(prompt,title,lineNo,DefAns);
   
   Dmin=str2num(dlgresult{1});
   Dmax=str2num(dlgresult{2});
	idgood=find(Dm >= Dmin & Dm <= Dmax);
   clf, plot(Dm(idgood),'r.');
else
   Dmin=str2num(dlgresult{1});
   Dmax=str2num(dlgresult{2});
   idgood=find(Dm >= Dmin & Dm <= Dmax);
end

if exist('idgood')
   Davg=mean(Dm(idgood));
	Dstd=std(Dm(idgood));
	Dm=Dm(idgood);
	disp(['User modified depth constraints in meters: min = '...
   	num2str(Dmin) ' max = ' num2str(Dmax) ' Mean = ' num2str(Davg)])
end

MSL=Davg+ADCP_offset;
disp(['ADCP measured ' num2str(MSL) ' m from surface to the seabed (mean sea level)']);
disp(['The tidal range is approximately ' num2str(Dstd) ' m']);
disp([' '])

pause(3)
close(p);