Auto bt

Picks points for the downcast matrix for PRR/C-OPS/CERBERUS

function auto_bt(varargin)
%Erik Stassinos 2-26-2014
%to automate picking tops and bottoms of casts
%this is needed for the CERBERUS where multiple casts are done
%prrstrip(1,prr_lcd,'Master_FrameNumber','LuZDepth') example function call

%==populate list_prr
fid=fopen('list_prr.txt','r');
list_prr = [];
badfilectr =0;
tmpfile=fullfile(pwd,'goprrbt_tmp');
while fid,
  check=fgetl(fid);
  if check == -1, break, end
  list_prr=[list_prr; check];
end


%==check if files are present
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
%===end check if files are present


for i=1:size(list_prr,1)

prr_lcd=list_prr(i,:);
prr_strip=[prr_lcd '.strip'];
var_1 = varargin{1};
var_2 = varargin{2};

prrstrip(1,prr_lcd,var_1,var_2) %pull columnds to create two variable file
%prrstrip(1,prr_lcd,'FrameCount','LuZDepth')

[fileA,headA]=read_strip(prr_strip);
depth = fileA(:,2);
index = fileA(:,1); %time

%shallowest points on shallow depth
rowmn = find(fileA(:,2) == max(fileA(:,2)));%shallowest point--use this to start

%downcast deepest point
rowdcmx = find(fileA(:,2) == min(fileA(rowmn:end,2)));
rowmx = find(fileA(:,2) == min(fileA(:,2)));%deepest point

%==========visualize points=====================
plot(index,depth) %plot all the data
hold on
plot(index(rowmx:rowmn),depth(rowmx:rowmn),'g-.') %plot deepest to shallowest green
hold on
plot(index(rowmn:rowdcmx),depth(rowmn:rowdcmx),'r-.') %plot downcast only red
%=========end visualize=====================


%========creat bt file=====================
fid=fopen( 'bt.pts', 'w' ); %create bt.pts file
fprintf(fid,'castid	index	1mer_time	1depth\n');
bt_pts = [[rowmn(1);rowdcmx(1)], [index(rowmn(1));index(rowdcmx(1))],[sqrt((depth(rowmn(1)))^2);sqrt((depth(rowdcmx(1)))^2)]]; %assemble parameters for castid



%btpts is index, time, depth
%id is number of casts processed---- always going to be one per file at
%this time
bt_castname=[ prr_lcd(1:9),'dt','1']; %castdir is dt db for downcast top or bottom
fprintf(fid,'%s %1.7e %1.7e %1.7e \n',bt_castname,bt_pts(1,:)); %print castID matrix
fprintf(fid,'%s %1.7e %1.7e %1.7e \n',bt_castname,bt_pts(2,:));
fclose(fid);


eval(['!mv ' prr_lcd ' ' tmpfile])
unix(sprintf('sed ''-e /<sampled_parameters>/ r bt.pts'' -e//N %s > %s',tmpfile,prr_lcd))



% eval([ '!awk < ' prr_lcd ' > ' tmpfile...
% 	  ' ''$1=="<sampled_parameters>"{system("cat bt.pts")}{print $0}'''])
%     eval([ '!mv ' tmpfile ' ' prr_lcd ]);

end