https://wiki-pnb.eri.ucsb.edu/index.php?action=history&feed=atom&title=Auto_bt 2026-04-08T00:15:31Z Revision history for this page on the wiki MediaWiki 1.34.0 https://wiki-pnb.eri.ucsb.edu/index.php?title=Auto_bt&diff=744&oldid=prev 2014-04-10T21:27:03Z

<p>Created page with &quot;Picks points for the downcast matrix for PRR/C-OPS/CERBERUS &lt;pre&gt; function auto_bt(varargin) %Erik Stassinos 2-26-2014 %to automate picking tops and bottoms of casts %this ...&quot;</p> <p><b>New page</b></p><div>Picks points for the downcast matrix for PRR/C-OPS/CERBERUS<br /> <br /> &lt;pre&gt;<br /> <br /> <br /> function auto_bt(varargin)<br /> %Erik Stassinos 2-26-2014<br /> %to automate picking tops and bottoms of casts<br /> %this is needed for the CERBERUS where multiple casts are done<br /> %prrstrip(1,prr_lcd,'Master_FrameNumber','LuZDepth') example function call<br /> <br /> %==populate list_prr<br /> fid=fopen('list_prr.txt','r');<br /> list_prr = [];<br /> badfilectr =0;<br /> tmpfile=fullfile(pwd,'goprrbt_tmp');<br /> while fid,<br /> check=fgetl(fid);<br /> if check == -1, break, end<br /> list_prr=[list_prr; check];<br /> end<br /> <br /> <br /> %==check if files are present<br /> for i=1:size(list_prr,1)<br /> [s,m]=unix(['ls ',list_prr(i,:)]);<br /> if s<br /> badfilectr=badfilectr+1;<br /> end<br /> end<br /> clear i<br /> if badfilectr<br /> if badfilectr==1<br /> msg=sprintf('%i missing prr file.',badfilectr);<br /> disp(msg)<br /> error('Your prrlist includes a file not in pwd.')<br /> else<br /> msg=sprintf('%i missing prr files.',badfilectr);<br /> disp(msg)<br /> error('Your prrlist includes files not in pwd.')<br /> end<br /> end<br /> clear s m badfilectr msg<br /> %===end check if files are present<br /> <br /> <br /> for i=1:size(list_prr,1)<br /> <br /> prr_lcd=list_prr(i,:);<br /> prr_strip=[prr_lcd '.strip'];<br /> var_1 = varargin{1};<br /> var_2 = varargin{2};<br /> <br /> prrstrip(1,prr_lcd,var_1,var_2) %pull columnds to create two variable file<br /> %prrstrip(1,prr_lcd,'FrameCount','LuZDepth')<br /> <br /> [fileA,headA]=read_strip(prr_strip);<br /> depth = fileA(:,2);<br /> index = fileA(:,1); %time<br /> <br /> %shallowest points on shallow depth<br /> rowmn = find(fileA(:,2) == max(fileA(:,2)));%shallowest point--use this to start<br /> <br /> %downcast deepest point<br /> rowdcmx = find(fileA(:,2) == min(fileA(rowmn:end,2)));<br /> rowmx = find(fileA(:,2) == min(fileA(:,2)));%deepest point<br /> <br /> %==========visualize points=====================<br /> plot(index,depth) %plot all the data<br /> hold on<br /> plot(index(rowmx:rowmn),depth(rowmx:rowmn),'g-.') %plot deepest to shallowest green<br /> hold on<br /> plot(index(rowmn:rowdcmx),depth(rowmn:rowdcmx),'r-.') %plot downcast only red<br /> %=========end visualize=====================<br /> <br /> <br /> %========creat bt file=====================<br /> fid=fopen( 'bt.pts', 'w' ); %create bt.pts file<br /> fprintf(fid,'castid index 1mer_time 1depth\n');<br /> 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<br /> <br /> <br /> <br /> %btpts is index, time, depth<br /> %id is number of casts processed---- always going to be one per file at<br /> %this time<br /> bt_castname=[ prr_lcd(1:9),'dt','1']; %castdir is dt db for downcast top or bottom<br /> fprintf(fid,'%s %1.7e %1.7e %1.7e \n',bt_castname,bt_pts(1,:)); %print castID matrix<br /> fprintf(fid,'%s %1.7e %1.7e %1.7e \n',bt_castname,bt_pts(2,:));<br /> fclose(fid);<br /> <br /> <br /> eval(['!mv ' prr_lcd ' ' tmpfile])<br /> unix(sprintf('sed ''-e /&lt;sampled_parameters&gt;/ r bt.pts'' -e//N %s &gt; %s',tmpfile,prr_lcd))<br /> <br /> <br /> <br /> % eval([ '!awk &lt; ' prr_lcd ' &gt; ' tmpfile...<br /> % ' ''$1==&quot;&lt;sampled_parameters&gt;&quot;{system(&quot;cat bt.pts&quot;)}{print $0}'''])<br /> % eval([ '!mv ' tmpfile ' ' prr_lcd ]);<br /> <br /> end<br /> <br /> &lt;/pre&gt;</div>

Eriks