Process COPS

function process_COPS(pb)
%created by Erik Stassinos 6-11-2013
%This is the global script which calls all COPS processing scripts


% % %=============
% check if files have already been generated
starttime = tic;

ml = fopen('mpblist_prr.txt');
 if ml ~= -1
     disp('most processing has already been started')
     disp('remove all files other than P*.lcd files to restart')
     disp('this will be changed to adapt to processing steps already implemented')
     yorn = input('Do you want to remove files and start over? y or n ','s')
     yn = lower(yorn)
     if strncmp(yn,'n',1) == 1
         fclose(ml);
        return
     end
     if strncmp(yn,'y',1) == 1
        delete a*
        delete A*
        delete b*
        delete r*
        delete t*
        delete m*
        delete K*
        delete l*
        pause(3)
     end

 end

prrfile('p') %changed from P list 6/24/2013
movefile('plist_prr.txt','list_prr.txt') %changed from P list 6/24/2013
%=========================
% % %CPSbt_E
%=========================
num =1;
%domath('bsakrmP101216B.lcd.1','r','1Lu412','1Ed412',0,'rrs412')


prrfile('p'); %creates list of prr files "P" %changed from P list 6/24/2013
%changed back to lowercase p list 9-18-2013

prlist = fopen('plist_prr.txt');%changed from P list 6/24/2013
                                 %changed back to lowercase p list
                                 %9-18-2013



%=========first math sequence
while ~feof(prlist)
newl(num,:) = fgets(prlist);
num = num +1;
end
frewind(prlist)
    for i = 1:num -1
    filename = newl(i,:);
    %domath(filename,'s','LuZDepth',0,0.486,'depth_Lu') %changed 6-24-13
    domath (filename,'s','LuZDepth',0,0.4,'depth_ed')
    end
    
    
    
cpsfile('mpb')
mlist = fopen('mpblist_prr.txt');

num =1;
%==============radQC sequence
%compares data to limits specified in Copsrqclist.txt
    while ~feof(mlist)
    newl2(num,:) = fgets(mlist);
    num = num +1;
    end
    %disp('Copy rqclist.txtfrom a previous processing example and update to this folder')
    %disp('Press return to continue')
    %pause
    for i = 1:num -1
        filename = newl2(i,:);
        %path = '/home/data65/pb/REPROCESS_2010/PRR/rqclist.txt';
         path = '/home/oceancolor/Plumes_and_Blooms/workspace/eriks/C-OPS/Copsrqclist.txt';
         COPSradQC(filename,path);
    end

cpsfile('rqcm')
rlist = fopen('rqclist_prr.txt');
num =1;
%============doKQ sequence
    while ~feof(rlist)
    newl3(num,:) = fgets(rlist);
    num = num +1;
    end   
    for i = 1:num -1
        infile = newl3(i,:);
        infile = strtrim(infile);
        CPSdoKQ(infile,'m','EdZ412',10,0.005,0.02) %-m 2Es412 10 0.005 0.02
    end

cpsfile('Krqc')
Klist = fopen('Krqlist_prr.txt');
num =1;
%============angQ sequence
    while ~feof(Klist)
    newl4(num,:) = fgets(Klist);
    num = num +1;
    end   
    for i = 1:num -1
        infile = newl4(i,:);
        infile = strtrim(infile);
        CPSangQ(infile,'EdZPitch','EdZRoll','EdZ443','LuZ443'); %hard coded range is 10 deg, flag is "2" changed 12-3-12
        %keyboard
        CPSangQ(strcat('an',infile),'EdZPitch','Ed0Roll','EdZ443','LuZ443');
    end    
cpsfile('anKr');

movefile('anKlist_prr.txt','list_prr.txt')


% 
% 
 pause(5)

%=======split cast and binning
%prr_split %takes list_prr.txt %==========replaced with split file

splist = fopen('list_prr.txt');
num =1;
while ~feof(splist)
    newlA(num,:) = fgets(splist);
    num = num +1;
end  
    for i = 1:num -1
        infile = newlA(i,:);
        infile = strtrim(infile);
        prr_split_file(infile);

    end


list_file = 'slist.txt';
bincolnum =2; %COPS depth column
 
%%%%prr_binner(list_file,bincolnum)
% % %prr_bincheat(list_file,bincolnum);

% % %cpsfile('banK');
% % %banlist = fopen('banlist_prr.txt'); %binned list

banlist = fopen('slist.txt');

num =1;

    while ~feof(banlist)
        var = strtrim(fgets(banlist));
    newl5(num,:) = var;% fgets(banlist)
    num = num +1;
    end   
    for i = 1:num -1
        infile = newl5(i,:);
        infile = strtrim(infile);
        %doKQ(infile,'m','2Es412',10,0.005,0.02) %-m 2Es412 10 0.005 0.02
 %========bscalc sequence   
 COPSbscalcloop(infile) %calls bscalc

   end

%%movefile('banlist_prr.txt','list_prr.txt')

cpsfile('bsanK')
%bsmlist = fopen('list_prr.txt'); %binned list
bsmlist = fopen('bsalist_prr.txt'); %binned list
num =1;
%==========mathloop squence
    while ~feof(bsmlist)
    newl6(num,:) = fgets(bsmlist);
    num = num +1;
    end  

    for i = 1:num -1
        infile = newl6(i,:);
        infile = strtrim(infile);
        %mathloop('bsbanKrqcmP101216E.lcd.1')
        COPSmathloop(infile)

    end


cpsfile('mbs')
movefile('mbslist_prr.txt','list_prr.txt')

 mblist = fopen('list_prr.txt'); %binned list
 num =1;
 
     while ~feof(mblist)
     newl7(num,:) = fgets(mblist);
     num = num +1;
     end   
     for i = 1:num -1
        infi = newl7(i,:);
        infi = strtrim(infi);
        %kcloop('mbsbanKrqcmP101216E.lcd.1')
        COPSkcloop(infi) %used to be bbopkc

     end
     
     mkdir final
     movefile('kcmbs*',[pwd,'/final'])
% % % % % % % % % % % 
elapsed = toc(starttime)

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