CERBbt E

% AC9BT
% FEB 98,FEB 99
% Stephen Wolfe
% Input:	none
% Look for:	list_prr
% Output: 	z*.lcd.?, z*.lcd.strip
% Assumptions:	fixed for either single casts or yo-yo's. Have to
%               pick something for at least 1 profile of each yo-yo
%               for the profile numbers to work correctly. Can't tell
%               if you skip a down-up pair.
%		
% Purpose:	pick tops and bottoms 
%		
% Calls:	bt_ac9
% Maintain: 	{filename, columnarraylist, disp_text}
% Uses:     	perfect for prr processing, ref: prr.ins
% Example:  	prrbt
% Notes:        This will run on NT if the call to bbopstrip is
%               commented out and the files are already stripped
%               Should label direction in castid table as well as
%               profile number. Work from left to right. If you
%               choose not to save points for a profile, you can
%               repick them and choose save and then go on.
% TO DO:        The archive scheme does not work due to changes in
%               naming convention. Doesn't create the log directory
%               if it's not there either.
%Erik Stassinos Apr 2013
clf;
list_prr=[];
prr_files=[];
not_prr_files=[];
tmpfile=fullfile(pwd,'goprrbt_tmp');
                                                % check for list_prr in pwd
[s,m]=unix('ls list_prr');
if isempty(m)
 msg=sprintf('Check your list_prr.');
 disp(msg)
 return
end
clear s m
						% load list_prr
fid=fopen('list_prr.txt','r');
while fid,
  check=fgetl(fid);
  if check == -1, break, end
  list_prr=[list_prr; check];
end
list_prr;
clear fid check
						% check presence of prr files
badfilectr=0;
for i=1:size(list_prr,1)
 [s,m]=unix(['ls ',list_prr(i,:)]);
 if s
  badfilectr=badfilectr+1;
 end
end
clear i
if badfilectr
 if badfilectr==1
  msg=sprintf('%i missing prr file.',badfilectr);
  disp(msg)
  error('Your prrlist includes a file not in pwd.')
 else
  msg=sprintf('%i missing prr files.',badfilectr);
  disp(msg)
  error('Your prrlist includes files not in pwd.')
 end
end
clear s m badfilectr msg
						% loop through 
for i=1:size(list_prr,1)
  prr_lcd=list_prr(i,:);
						% strip em
  prr_strip=[prr_lcd '.strip'];
  %eval(['!sbtprr_mob ',prr_lcd])
  %eval(['!bbopstrip -sz  1mer_time 1depth ' prr_lcd ' 'prr_strip]);
  %prrstrip(1,prr_lcd,'1mer_time','depth_ed') %changed 9-18-2012
  %prrstrip(1,prr_lcd,'1mer_time','1Depth') %need to change to accomodate screwed up LCD conversion 12-3-12
 % prrstrip(1,prr_lcd,'1mer_time','1Depth')
   prrstrip(1,prr_lcd,'Master_FrameNumber','LuZDepth')
  [fileA,headA]=read_strip(prr_strip);
  %eval(['!rm ''prr_strip']);
  
  [bt_pts]=bt_ac9(fileA);
  bt_pts

  if ~isempty(bt_pts),
    %create header, castid matrix
    %castid  index   1mer_time       1depth
    %zub11008adt1     7.5000000e+01   2.1710000e+04   2.0443990e+02
    %zub11008adb1     1.2810000e+03   3.7655000e+05   1.3007170e+00 
    %castdir={ 'dt','db','ub','ut' };
    %castdir=[castdir castdir castdir castdir]; %  good for 4 yoyo's
    %if size(bt_pts,1)>size(castdir,2),
    %  error('prrbt: increase size of castdir.');
    %end
    dd=[];
    idir=[];
    dd=diff(bt_pts(:,3));
    dd=[dd; 0];
    id=1;
    fid=fopen( 'bt.pts', 'w' );
    fprintf(fid,'castid	index	1mer_time	1depth\n');
    for i=1:2:size(bt_pts,1),
      if dd(i)>0,
	if idir==1,
	  id=id+1;
	end
	idir=1;
	castdir1(i:i+1,:)=['dt'; 'db'];
      else
	idir=2;
	castdir1(i:i+1,:)=['ub'; 'ut'];
      end
      bt_castname=[ prr_lcd(1:9),castdir1(i,:),num2str(id) ];
      fprintf(fid,'%s %1.7e %1.7e %1.7e \n',bt_castname,bt_pts(i,:));
      bt_castname=[ prr_lcd(1:9),castdir1(i+1,:),num2str(id) ];
      fprintf(fid,'%s %1.7e %1.7e %1.7e \n',bt_castname,bt_pts(i+1,:));
      if idir==2,
	id=id+1;
      end
    end
    fclose(fid);
    
    %do this by calling a script that takes care of the awk and archive
    eval([ '!awk < ' prr_lcd ' > ' tmpfile...
	  ' ''$1=="<sampled_parameters>"{system("cat bt.pts")}{print $0}'''])
    eval([ '!mv ' tmpfile ' ' prr_lcd ]);

    %archive
    %cruisename=eval(['echo ' prr_lcd ' | cut -b 3-6'])
    %cruisename=prr_lcd(3:6);
    %%cruisename=prr_lcd(11:17); commented 9-18-2012
    %archive=[ pwd '/ARCHIVE/' ];
    %=>archive=[ '/home/data92/bbop/ARCHIVE/' ];
    %cp $lcd_file /home/data92/bbop/ARCHIVE/$cruisename/prr
   % eval(['!cp ' prr_lcd ' ' archive cruisename '/prr']);
    %echo $lcd_file has been archived to /home/data92/bbop/ARCHIVE/$cruisename/prr
    %=>eval(['!echo ' prr_lcd ' has been archived to 'archive cruisename '/prr']);

    prr_files=[prr_files; prr_lcd];
  else
    not_prr_files=[not_prr_files; prr_lcd];
  end
      
  %cleanup
  %clear prr_lcd bt_pts fileA headA prr_strip;

  %eval('!rm bt.pts');
end
prr_files
not_prr_files