function E = m_cmpl(Flag)
% M_CMPL - Compile eqpac files. 
% Reads files in ep1 and ep2, compiles them, and creates derived products
%
% M_CMPL Reads all the files created by Bob Herlein's programs in directories ep1 and eo2
% After reading the nescessary files, It calculates derived products from them and 
% writes the correct headers
%
% Use As: E = m_cmpl;
%         E = m_cmpl(EditFlag);
%
% Inputs: EditFlag can equal 0 or 1
%         1: (default) edit for outliers in pressure, salinity, and temperature
%           If bad data is found the entire row is marked bad.
%         0: Do not edit for outliers
%
% Ouputs: E = Structure with the following fields
%             id: m id# (ex. 'm1')
%             dat: matrix of data, refer to M_INI for column names
%
% Requires: READOASIS

% Brian Schlining
% 29 Jan 1999

if ~nargin
   EditFlag = 1;
end


%=======================================
% Loop through ep1 and ep 2 directories
%=======================================
for m = 1:3
   
   %=================================
   % Set path based on computer type
   %=================================
   switch computer
   case 'PCWIN'
      PathS = ['\\tsunami.shore.mbari.org\oasis\m' num2str(ep) '\'];
      PathCfg = ['\\tsunami.shore.mbari.org\oasis\cfg\m'
   otherwise
      PathS      = ['/hosts/tsunami/oasis/m' num2str(ep) '/'];
   end
   
   %=================================================================
   % Combine the noon and 12:30 files. Most of the work is done here
   % using the subfunction COALLATE.
   %=================================================================
   mx = coallate(PathS);   
   
   %=============================================================
   % Locate important variables in epx to simplify the equations
   % If modifications are made to COALLATE these may have to be
   % changes
   %=============================================================
   Pressure     = repmat(epx(:,2),1,7);
   Lu_2m        = epx(:,13:19);  % Actually Lu(1.5m) but rounded for naming purposes, can't use decimals in variable names
   Lu_20m       = epx(:,28:34);
   Ed_20m       = epx(:,21:26);
   Lu490_0m     = epx(:,15);
   Lu555_0m     = epx(:,17);
   Lu490_20m    = epx(:,30);
   Lu555_20m    = epx(:,32);
   Lu443_0m     = epx(:,14);
   Lu443_20m    = epx(:,29);
   Lu683_0m     = epx(:,19);
   Lu683_20m    = epx(:,34);
   Ed_0m        = epx(:,6:11);
   
   % Edit for outliers. This assumes pressure is in column 2, Salinity in column
   if EditFlag
      epx = editep(epx);
   end
   
   %=================================================
   % Calculate Derived products from measured values
   %=================================================
   % Calculate ELw
   % ELw = Ed(0m+) = a*Lu(1.5m) + b
   % Where Lu comes from the OCR100 at 1.5m depth
   [r c]        = size(epx);
   Es           = c + 1;
   Ee           = c + 7;
   aLw          = [0.5574 0.5588 0.5632 0.5778 0.6005 0.6713 0.5904];
   bLw          = [0.014 0.012 0.003 0.003 0.002 0.001 0.001];
   for i = 1:7
      epx(:,Es+i-1) = aLw(i).*Lu_2m(:,i) + bLw(i); % Get these coef
   end
   
   % Calculate LLw
   % LLw = Lu(0m+) = 0.544*exp(((ln(Lu(20m))-ln(Lu(1.5m))/(depth-1.5))*-1.5)+ln(Lu(1.5m)))
   % This is calculated from a linear extrapolation of the 20m and 1.5m Lu data.
   [r c]        = size(epx);
   Ls           = c + 1;
   Le           = c + 7;
   epx(:,Ls:Le) = 0.544*exp((((log(Lu_20m)-log(Lu_2m))./(Pressure-1.5))*-1.5)+log(Lu_2m));
   
   % Calculate KLw
   % Klw = 0.544*(0.98*Ed(0m+))/Ed(20m)*Lu(20m)
   % KLw is Lu(om+) calculated by bakc-propagating the 20m Lu data, using K values at each wavelength
   [r c]        = size(epx);
   Ks           = c + 1;
   Ke           = c + 6;
   epx(:,Ks:Ke) = 0.544*(0.98.*Ed_0m)./Ed_20m.*Lu_20m(:,1:6);
   
   % Calculate K, attenuation coeeficeints
   % From p10750 in Morelm 1988
   % K = (ln(0.98*Ed(0m+)/Ed(20m))/Depth
   [r c]        = size(epx);
   ks           = c + 1;
   ke           = c + 6;
   epx(:,ks:ke) = (log(0.98*Ed_0m./Ed_20m))./Pressure(:,1:6);
   
   % Calculated Morel Chl
   % Chl = ((K490 - 0.0217)/0.0690)^(1/0.702)
   % This is a rearrangement of eqn(9) in Morel 1988, using the coeff in table 2 
   [r c]     = size(epx);
   Cs        = c + 1;
   epx(:,Cs) = ((epx(:,ks+2) - 0.0217)/0.0690).^(1/0.702);
   BAD = find(epx(:,Cs) < 0);
   if ~isempty(BAD)
      epx(BAD,Cs) = NaN;
   end
   
   
   % Add OC2V2 Chl
   % chl = a_oc2_c(LU_490,LU_555)
   [r c]      = size(epx);
   C0         = c + 1;
   C20        = c + 2;
   epx(:,C0)  = a_oc2_c(Lu490_0m,Lu555_0m);
   epx(:,C20) = a_oc2_c(Lu490_20m,Lu555_20m);
   
   % Calculate Lu443/Lu555 Chl
   % Chl(0m) = 0.7469*(Lu443(0m)/Lu555(0m))^-1.2797;
   % Chl(20m) = 1.0498*(Lu443(20m)/Lu555(20m))^-1.0948
   [r c]       = size(epx);
   Cx0         = c + 1;
   Cx20        = c + 2;
   epx(:,Cx0)  = 0.7469*(Lu443_0m./Lu555_0m).^-1.2797;
   BAD = find(epx(:,Cx0) < 0);
   if ~isempty(BAD)
      epx(BAD,Cx0) = NaN;
   end
   
   epx(:,Cx20) = 1.0498*(Lu443_20m./Lu555_20m).^-1.0948;
   BAD = find(epx(:,Cx20) < 0);
   if ~isempty(BAD)
      epx(BAD,Cx20) = NaN;
   end
   
   % Add Fouling Ratio = (Lu490/Lu555)
   [r c]      = size(epx);
   F0         = c + 1;
   F20        = c + 2;
   epx(:,F0)  = Lu683_0m./Lu555_0m;
   epx(:,F20) = Lu683_20m./Lu555_20m;
    
   % Add CZCS Chl: log10(C) = 0.053 + 1.71*log10(Lw550/Lw443)
   [r c] = size(epx);
   Cz    = c + 1;
   epx(:,Cz) = 10.^(0.053 + 1.71*log10(epx(:,47)./epx(:,44)));

   E(ep).id  = ['ep' num2str(ep)];
   E(ep).dat = epx;
   
   
end

%======================================================================================
%======================================================================================
% subfunctions
%======================================================================================
%======================================================================================

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% COALLATE - Reads the files in the mx directories
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function Dat = coallate(PathS)
Dat = readoasis(PathS);


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% EDITEP
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function epx = editep(epx);
i = find(epx(:,2) > 30 | epx(:,2) < 10);
if ~isempty(i)
   epx(i,6:end) = NaN;
end

i = find(epx(:,5) > 38 | epx(:,5) < 32);
if ~isempty(i)
   epx(i,6:end) = NaN;
end

i = find(epx(:,4) > 35 | epx(:,4) < 15);
if ~isempty(i)
   epx(i,6:end) = NaN;
end

i = find(isinf(epx));
if ~isempty(i)
   epx(i) = NaN;
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% READMCP
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [x10, x30] = readmcp(FileName)
x   = readeqpac_(FileName);
x   = sortrows(x,[2 1]);
i   = min(find(x(:,2) == 30));
x10 = x(1:(i - 1),:);
x30 = x(i:end,:);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% READEQPAC_
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function X = readeqpac_(FileLoc, NumOfDays)
fid = fopen(FileLoc,'r');
OK  = 1;
while OK		 						    	% Trash the header
   S = fgetl(fid);
   if ~strcmp(S(1),'#')
      break
   end
end
i = 1;
while ~feof(fid)					     	% Read the data
   XS     = fgetl(fid);			    	% Get a line from the file
   X(i,:) = sscanf(XS,'%f')';		   % Read the data from the line
   i      = i + 1;
end
fclose(fid);
X = unique(X,'rows');               % Remove duplicate rows