Ac9bt.m

% AC9BT
% FEB 98,FEB 99
% Stephen Wolfe
% Input:	none
% Look for:	list_ac9
% 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 ac9 processing, ref: ac9.ins
% Example:  	ac9bt
% 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.

a=1;
clf;
list_ac9=[];
ac9_files=[];
not_ac9_files=[];
tmpfile=fullfile(pwd,'goac9bt_tmp')                                              % check for list_ac9 in pwd
[s,m]=unix('ls list_ac9');

if isempty(m)
 msg=sprintf('Check your list_ac9.');
 disp(msg)
 return
end
clear s m
						% load list_ac9
fid=fopen('list_ac9','r');
while fid,
  check=fgetl(fid);
  if check == -1, break, end
  list_ac9=[list_ac9; check];
end
list_ac9;
clear fid check
						% check presence of ac9 files
badfilectr=0;
for i=1:size(list_ac9,1)
 [s,m]=unix(['ls ',list_ac9(i,:)]);
 if s
  badfilectr=badfilectr+1;
 end
end
clear i
if badfilectr
 if badfilectr==1
  msg=sprintf('%i missing ac9 file.',badfilectr);
  disp(msg)
  error('Your ac9list includes a file not in pwd.')
 else
  msg=sprintf('%i missing ac9 files.',badfilectr);
  disp(msg)
  error('Your ac9list includes files not in pwd.')
 end
end
clear s m badfilectr msg
						% loop through 
for i=1:size(list_ac9,1)
  ac9_lcd=list_ac9(i,:); %changes directory in and out
						% strip em
  ac9_strip=[ac9_lcd '.strip'];
 % cd ..
 
  %eval(['E_BBstrip -sz 1mer_time 1depth', ac9_lcd ' ' ac9_strip]); %modified from BBopstrip to E_BBstrip removed ! -sz
  E_BBstrip(a,ac9_lcd,'1mer_time','1depth')
  ac9_strip;
 
  %cd .. 
  
  [fileA,headA]=read_strip(ac9_strip);
  pwd;
  %eval(['!rm ''ac9_strip']);
  %cd ..
  [bt_pts]=bt_ac9(fileA);

  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('ac9bt: increase size of castdir.');
    %end
    dd=[];
    idir=[];
    dd=diff(bt_pts(:,3));
    dd=[dd; 0];
    id=1;
    %cd('pb218')
   %------------------------------------------have to change
    
    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=[ ac9_lcd(1:9),castdir1(i,:),num2str(id) ];
      fprintf(fid,'%s %1.7e %1.7e %1.7e \n',bt_castname,bt_pts(i,:));
      bt_castname=[ ac9_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);
   % cd .. %-------------------------------------------------------have to change
   
    %do this by calling a script that takes care of the awk and archive
  %changed this 
    eval([ '!awk < ' ac9_lcd ' > ' tmpfile...
	  ' ''$1=="<sampled_parameters>"{system("cat bt.pts")}{print $0}''']);
    eval([ '!mv ' tmpfile ' ' ac9_lcd ]);
    
    %archive
    %cruisename=eval(['echo ' ac9_lcd ' | cut -b 3-6'])
    cruisename=ac9_lcd(3:6);
   % mkdir(strcat(pwd,'/ARCHIVE/'))
    archive=[ pwd '/ARCHIVE/' ];
    %archive=[ '/home/data92/bbop/ARCHIVE/' ];
    %cp $lcd_file /home/data92/bbop/ARCHIVE/$cruisename/ac9
    %eval(['!cp ' ac9_lcd ' ' archive cruisename '/ac9']);
    %echo $lcd_file has been archived to /home/data92/bbop/ARCHIVE/$cruisename/ac9
    eval(['!echo ' ac9_lcd ' has been archived to ' archive cruisename '/ac9']);

    ac9_files=[ac9_files; ac9_lcd];
  else
    not_ac9_files=[not_ac9_files; ac9_lcd];
  end
      
  %cleanup
  %clear ac9_lcd bt_pts fileA headA ac9_strip;
  %eval('!rm bt.pts');
end
%cd ..
ac9_files
not_ac9_files