Merge ctdac9 v2.m
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% MERGE_ctdac9.M
% DEC 97, JUL 98, 9/99
% John Ubante, SRW
% Input: none
% Look for: upused.txt, for pairing of ctd and ac9 files;
% LIST/list_ac9merge_ctd
% Output: $ctd$ac9.strip
% Assumptions: 1) This function called from directory with data,
% 2) The strip lists located in
% /home/scratch51/bbop/WORK/LIST/,
% 3) ac9file have just left sac9proc and begin with "m"
% 4) ac9files have 'core' name beginning with the
% first 'z'
% 4) ctdfiles are flat files that are already "stripped"
% 5) ctdfiles have 'core' name beginning withb the
% first 'X'
% Purpose: Merge ac9 and ctd datasets and create a strip-
% like file that contains the columns listed in
% [list_ac9merge_ctd; list_ac9merge_ac9]
% Calls: ctd2strip,merge_2files
% Maintain: {filename, columnarraylist, disp_text}
% Uses: PnB ac9 processing
% Example: merge_ctdac9
% Notes: Based on merge_merac9 as written for bbop ac9 processing
%Edited by Erik S. 6/7/2010 ' % % %' are altered areas
function merge_ctdac9(pb)
% initialize local variables
if findstr(computer,'PCWIN')
LIST='z:\links\WORK\LIST';
else
LIST = '/home/eriks/LIST/';
%LIST='/home/data241/bbop/RADIOMETRY/ARCHIVE_lcd/LIST/';
end
list_ctdac9=[];
list_ac9merge_ac9 = 'list_ac9merge_ac9';
HERE=pwd;
check=[];
% check for list files
cd ../.. % in $WORK/LIST
eval([ 'cd ' LIST ]);
[s,m]=unix([ 'ls ' list_ac9merge_ac9] );
if s
sprintf('Check your %s in %s.',list_ac9merge_ac9,LIST)
return
end
eval([ 'cd ' HERE ])
clear HERE
% copy strip lists HERE
% if not already HERE
[s,m]=unix([ 'ls ' list_ac9merge_ac9 ]);
if size(m,2)~=size(list_ac9merge_ac9,2)+1
eval([ '!cp ' LIST list_ac9merge_ac9 ' .' ]);
end
clear s m LIST
%load list file
name_list=list_load('upused.txt',[ 1:6 ],{'dum','dum','list_ac9bmdz', ...
'dum','dum','list_ctd'});
% $$$ % check for upused.txt in pwd
% $$$ [s,m]=unix('ls upused.txt');
% $$$ if isempty(m)
% $$$ msg=sprintf('Check your upused.txt.');
% $$$ disp(msg)
% $$$ return
% $$$ end
% $$$ clear s m
% $$$
% $$$ % load upused.txt
% $$$ fid=fopen('upused.txt','r');
% $$$ while fid~=-1
% $$$ check=fgetl(fid);
% $$$ if check~=-1,
% $$$ if(check(1) ~= '#')
% $$$ list_ctdac9=[list_ctdac9; check];
% $$$ end
% $$$ else
% $$$ break;
% $$$ end
% $$$ end
% $$$ clear fid check
% $$$
% $$$
% $$$ % parse ctd & ac9 names
% $$$ % into lists
% $$$ for i=1:size(list_ctdac9,1),
% $$$ list_ac9(i,:)=parse(list_ctdac9(i,:),3);
% $$$ list_ctd(i,:)=parse(list_ctdac9(i,:),6);
% $$$ end
% check to see if lists
% lengths are equal
if size(list_ctd,1)~=size(list_ac9bmdz,1)
error('You do not have 1 to 1 correspondence in your list_ctdac9.')
end
ifread=ones(size(list_ctd,1),2);
% check presence of ctd files
badfilectr=0;
for ifile=1:size(list_ctd,1)
[s,m]=unix(['ls ',list_ctd(ifile,:)]);
if s
badfilectr=badfilectr+1;
ifread(ifile,1)=0;
end
end
clear ifile
if badfilectr
list_ctd
msg=sprintf('%ifile missing ctd file(s).',badfilectr);
disp(msg)
warning('Your ctdlist includes a file not in pwd.')
end
clear s m badfilectr msg
% check presence of ac9 files
badfilectr=0;
for ifile=1:size(list_ac9bmdz,1)
[s,m]=unix(['ls ',list_ac9bmdz(ifile,:)]);
if s
badfilectr=badfilectr+1;
ifread(ifile,2)=0;
end
end
clear ifile
if badfilectr
list_ac9bmdz
msg=sprintf('%ifile missing ac9 file(s).',badfilectr);
disp(msg)
warning('Your ac9list includes a file not in pwd.')
end
clear s m badfilectr msg
% loop through pairs
for i=find(all(ifread')),
ctd_file=list_ctd(i,:);
ac9_lcd=list_ac9bmdz(i,:);
% create output name
location1=find(ctd_file=='X');
output=ctd_file(location1(1):location1(1)+7);
output=[output '.' ctd_file(size(ctd_file,2))];
location1=find(ac9_lcd=='z');
location2=find(ac9_lcd=='.');
output=[output '.' ac9_lcd(location1+2:location2-1) '.'];
output=[output ac9_lcd(size(ac9_lcd,2)) '.strip']
clear location1 location2
% strip em
ctd_base=ctd_file(1:8)
pb
ctd2strip_v2(pb,ctd_base)% % %------------------------------------ mofified to have no ctd_head return ctd_head =
% % fid=fopen('ctd_head','w');%
% % for j=1:size(ctd_head,1),
% % fprintf(fid,'%s\n',ctd_head(j,:)');%
% % end
%fclose(fid);
eval([ '!cat ctd_head_n > ' ctd_file '.strip']);
eval([ '!cat ' ctd_file ' >> ' ctd_file '.strip']);
% %eval([ '!cat ctd_head > ' ctd_file '.strip']);
% %eval([ '!cat ' ctd_file ' >> ' ctd_file '.strip']);
%eval('!\rm ctd_head' );
ctd_strip=[ctd_file '.strip']
ac9_strip=[ac9_lcd '.strip'];
%eval([ '!bbopstrip -f ' list_ac9merge_ac9 ' ' ac9_lcd ' ' ac9_strip ])
%ac9_lcd
E_BBstrip(pb,ac9_lcd,list_ac9merge_ac9);
ac9_strip = strcat(ac9_lcd,'.strip');%
% call merge_2files
msg=sprintf('Merging %s and %s into %s.',ctd_file,ac9_lcd,output);
disp(msg)%
[data,header]=merge_2files(ctd_strip,ac9_strip);
% write merged stripfile to disk
fid=fopen('merging_header.temp','w');
for j=1:size(header,1)
fprintf(fid,'%3s\n',header(j,:)');
end
fclose(fid);
save merging_data.temp data -ascii
eval([ '!cat merging_header.temp merging_data.temp > ' output ]);
eval('!\rm merging_header.temp merging_data.temp');
%clear output fid header data j
% rm strip files
% eval([ '!rm ' ctd_strip ' ' ac9_strip ])
end % end for loop
clear i ctd2strip_v2 ac9_strip
% rm strip list files
% $$$ eval([ '!rm ' list_ac9merge_ac9 ' ' list_ac9merge_mer ]);
% MERGE_2FILES.M
% NOV 97
% John Ubante
% Input: [mer,ac9]:string
% Output: [headAB:char array,fileAB:{200x(N1+N2-1)}]
% Assumptions: errorflag=(-9.9e+35); depth will be the second column of mer
% data and the first column of ac9 data
% Purpose: to paste 2 strip-version files together using binned depths
% as index; to place errorflag values at depths that don't exist
% if there is an error with inputted files, program will return
% to keyboard
% Calls: read_strip, unique
% Uses: 97 ac9 processing, esp. called from merge_merac9.m
%
% Example: [data,header]=merge_2files('mer.strip','ac9.strip')
% NOTES: in script, "fileA" refers to SECOND parameter and "fileB"
% refers to FIRST parameter;
function [fileAB,headAB]=merge_2files(ctd,ac9);
% declare local variables
errorflag=-9.9e+35;
depthrange=[1:220]; % note that the 0m depth line is still added
fileAB=[];
headAB=['#filename ',ctd,' ',ac9];
% load stripped files
%eval(['[fileA,headA]=read_strip(ac9);'])
%eval(['[fileB,headB]=read_strip(ctd);'])
eval(['[fileA,headA]=hdrload(ac9);']);
eval(['[fileB,headB]=hdrload(ctd);']);
clear ctd ac9
%add depth column in 2 for ctd, will take out at the end
fileB=[fileB(:,1) fileB(:,3) fileB(:,2:size(fileB,2))];
%zerodepth=fileB(1,:);
% remove lines with
% errorflag for depth
indA=find(fileA(:,1)==errorflag);
fileA(indA,:)=[];
indB=find(fileB(:,2)==errorflag);
fileB(indB,:)=[];
clear indA indB
% ensure depths are
% positive values
fileA(:,1)=abs(fileA(:,1));
fileB(:,2)=abs(fileB(:,2));
% ensure depths are
% integral values
for i=1:size(fileB,1)
if fileB(i,2)~=round(fileB(i,2))
%fileB(i,2)
%round(fileB(i,2))
error('Depth is not integral in first parameter. Try again.')
end
end
for i=1:size(fileA,1)
if fileA(i,1)~=round(fileA(i,1))
fileA(i,1);
error('Depth is not integral in second parameter. Try again.')
end
end
clear i
% remove depths outside of
% depthrange
indA=find(fileA(:,1)<min(depthrange));
fileA(indA,:)=[];
indA=find(fileA(:,1)>max(depthrange));
fileA(indA,:)=[];
indB=find(fileB(:,2)<min(depthrange));
fileB(indB,:)=[];
indB=find(fileB(:,2)>max(depthrange));
fileB(indB,:)=[];
clear indA indB
% ensure depths are unique
if size(unique(fileA(:,1)),1)~=size(fileA,1)
error('Depth is not unique in second parameter. Try again.')
end
if size(unique(fileB(:,2)),1)~=size(fileB,1)
error('Depth is not unique in first parameter. Try again.')
end
% ensure depths are monotonic
if sort(fileA(:,1))~=fileA(:,1)
error('Depth is not monotonic in second parameter. Try again.')
keyboard
end
if sort(fileB(:,2))~=fileB(:,2)
error('Depth is not monotonic in first parameter. Try again.')
keyboard
end
% $$$ % join using depths
% $$$ for i=depthrange
% $$$ % fill in depth with errorflag if
% $$$ % missing
% $$$ if size(fileB,1)<i
% $$$ fileB=[fileB;errorflag,i,ones(1,size(fileB,2)-2)*errorflag];
% $$$ elseif fileB(i,2)~=i
% $$$ fileB=[fileB(1:i,:);errorflag,i,ones(1,size(fileB,2)-2)*errorflag;fileB(i:size(fileB,1),:)];
% $$$ end
% $$$ if size(fileA,1)<i
% $$$ fileA=[fileA;i,ones(1,size(fileA,2)-1)*errorflag];
% $$$ elseif fileA(i,1)~=i
% $$$ fileA=[fileA(1:i,:);i,ones(1,size(fileA,2)-1)*errorflag;fileA(i:size(fileA,1),:)];
% $$$ end
% $$$ % do IT
% $$$ fileAB(i,:)=[fileB(i,:),fileA(i,2:size(fileA,2))];
% $$$
% $$$ end % end for
% join using depths,
% replaces section above
emask=ones(size(depthrange,2),size(fileB,2))*errorflag;
irow=find(fileB(:,2) >= depthrange(1,1) & fileB(:,2) <= ...
depthrange(end));
if(isempty(irow));
error('No data in depthrange 1')
end
for i = 1:size(irow,1);
emask(fileB(irow(i,1),2),:) = fileB(irow(i,1),:);
end
fileB=emask;
clear emask irow
emask=ones(size(depthrange,2),size(fileA,2))*errorflag;
irow=find(fileA(:,1) > depthrange(1,1) & fileA(:,1) <= ...
depthrange(size(depthrange,2)));
if(isempty(irow));
error('No data in depthrange 2')
end
for i = 1:size(irow,1);
emask(fileA(irow(i,1),1),:) = fileA(irow(i,1),:);
end
fileA=emask;
%leaves out bin_1.0_depth
fileAB=[fileB,fileA(:,2:size(fileA,2))];
% $$$ % add 0m depth
% $$$ zerodepth(1,size(fileB,2)+1:size(fileB,2)+size(fileA,2)-1)=errorflag;
% $$$ fileAB=[zerodepth; fileAB];
% $$$ clear fileA fileB i depthrange errorflag zerodepth
%remove extra depth channel
%in col 2
fileAB(:,2)=[];
headAB=char(headAB,headB(2:size(headB,1),:),headA(3:size(headA,1),:));
clear headA headB
% $$$ % force headers' width = width
% $$$ width=size(headA(1,:),2)+size(headB(1,:),2);
% $$$ headA(:,width)=' ';
% $$$ headB(:,width)=' ';
% $$$ headAB(1,width)=' ';
% $$$ % combine headers
% $$$ headAB=[headAB;headB(2:size(headB,1),:);headA(3:size(headA,1),:)];
% $$$ clear width headA headB
return
