function settings = fillABSSmsk(settings)
% fillABSSmask - automate filling the mask of an netCDF data file
%
%function theMaskFile = fillABSSmsk(settings);
%
%Scans a raw netCDF data file and marks the mask file to 
%meet the good data criteria standards set by the following:
%
%Where:
%		settings.theDataFile= the raw ABSS data file in netcdf
%		settings.theMaskFile= Mask file created
%			If no mask is given you will be asked to create one.
%	
%	the pre-recorded values set prior to deployment.
%       settings.var(1).name = 'theVar'
%		settings.var(1).limits = [min max] 
%       ...
%       settings.var(n).name = 'theNextVar'
%		settings.var(n).limits = [min max] 
%


%%% START USGS BOILERPLATE -------------%
% Use of this program is described in:
%
% Acoustic Doppler Current Profiler Data Processing System Manual 
% Jessica M. Côté, Frances A. Hotchkiss, Marinna Martini, Charles R. Denham
% Revisions by: Andrée L. Ramsey, Stephen Ruane
% U.S. Geological Survey Open File Report 00-458 
% Check for later versions of this Open-File, it is a living document.
%
% Program written in Matlab v7.1.0 SP3
% Program updated in Matlab 7.2.0.232 (R2006a)
% Program ran on PC with Windows XP Professional OS.
%
% "Although this program has been used by the USGS, no warranty, 
% expressed or implied, is made by the USGS or the United States 
% Government as to the accuracy and functioning of the program 
% and related program material nor shall the fact of distribution 
% constitute any such warranty, and no responsibility is assumed 
% by the USGS in connection therewith."
%
%%% END USGS BOILERPLATE --------------

 

% 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
%
%Sub-programs
%	ncmkmask.m
%	premask.m-5/21/99 need the version of premask.m edited by JMC

% changed 5 jun 2008 MM - make it generic.
% version 1.0
% updated 14-mar-2008 MM - allow masking in earth case, don't get hung up on
% percent good
% updated 13-Oct-1999 16:43:41
% modified 17-Feb-2004 by ALR - if waves software has turned the Echo
% Intensiy off, fillmask will set the echo intensity to [50 255] to process
% the data.

% get the current SVN version- the value is automatically obtained in svn
% is the file's svn.keywords which is set to "Revision"
rev_info = 'SVN $Revision: $';
disp(sprintf('%s %s running',mfilename,rev_info))

if ~exist('settings','var'), settings = []; end

if ~isfield(settings,'theDataFile'), settings.theDataFile = ''; end
if ~isfield(settings,'theMaskFile'), settings.theMaskFile = ''; end

if isempty(settings.theDataFile)
   [theFile, thePath] = uigetfile('*.cdf', 'Select ADCP Data File');
   if ~any(theFile), return, end
   settings.theDataFile = fullfile(thePath, theFile);
   cd(thePath)
end

if isempty(settings.theMaskFile)
   [theFile, thePath] = uigetfile('*.msk', 'Select ADCP Mask File');
   
   %Check to see if there is a mask file, if not ask to create
   if ~any(theFile) 
      prompt={'Do you want to create a mask file now?'};
   title='Mask File Not Found';
   lineNo=1;
   DefAns={'Yes'};
   dlgresult=inputdlg(prompt,title,lineNo,DefAns);
   if strcmp(dlgresult{1},'Yes');
      [p, outFile] = fileparts(settings.theDataFile);
		settings.theMaskFile = [outFile '.msk'];
      %ncmkmask(settings.theDataFile,settings.theMaskFile);
      mkadcpmask(settings.theDataFile,settings.theMaskFile);
      disp(['The Mask file ' settings.theMaskFile ' was created'])
      else 
         disp('You must create a mask file to run fillmsk function')
         return, end
   end
   if thePath(end) ~= filesep, thePath(end+1) = filesep; end
   settings.theMaskFile = [thePath theFile];
end

f = netcdf(settings.theDataFile, 'write'); % Open the file.
if isempty(f), return, end 


if nargin < 3
        
	%Just autonan the velocities
% 	for ii=1:4;
%   		v=autonan(f{['vel' int2str(ii)]},1);
%   		eval(['vd' num2str(ii) '=v(:);'])
% 	end

	%check to make sure that the autonan worked
	check=length(isnan(vd1));
	if isempty(check)
   	disp(['error executing autonan function'])
	end


	%Get the max and min of the velocities of the four beams 
	%to set some criteria for masking
	disp(['Pulling out the needed Global attributes from the Data file'])
	disp(['This information sets the criteria for masking'])
	vlim=ones(4,2);
	[ii,jj]=size(vlim);
	for i=1:ii;
	   eval(['vlim(i,1)=min(min(vd' int2str(i) '));'])
	   eval(['vlim(i,jj)=max(max(vd' int2str(i) '));'])
	end
	vmin=min(min(vlim))/10; %in cm/sec for premask
	vmax=max(max(vlim))/10;
	settings.velR=[vmin vmax];

	%Undo autonan the velocities
	for ii=1:4;
	  v=autonan(f{['vel' int2str(ii)]},0);
	  eval(['vd' num2str(ii) '=v(:);'])
	end


    Pgd=f.minmax_percent_good(:);
    if strcmpi(f.transform(:),'BEAM'),
        if isequal(Pgd(1),0)
            Pgd = [25 Pgd(2)];
        end
    else % SHIP, INST, EARTH right now don't do anything different
        if isequal(Pgd(1),0)
            Pgd = [25 Pgd(2)];
        end
    end
    
	echI=f.false_target_reject_values(:);
    if isequal(echI(1),255)
        echI = [50 255]
        disp('Echo Intensity was turned off by Waves software.')
        disp('Values of 50 to 255 were set by the ADCP Toolbox to process file.')
      %Add in history comment
        %thecomment = sprintf('%s\n','Echo Intensity was turned off by Waves software. Values of 50 to 255 were set by the ADCP Toolbox.');
       % history(settings.theMaskFile,thecomment);
    end
	errV=f.minmax_error_velocity(:);
	corT=f.valid_correlation_range(:);
   
end %if nargin<3;  
 
close(f)

%Let's run premask based on these criteria
%premask(settings.theDataFile, settings.theMaskFile, vel, cor, agc, good)
premask(settings.theDataFile,settings.theMaskFile,settings.velR,corT,echI,Pgd);

%ncclose

disp(['The mask is filled '])