function [dat,vals,vstr]=extract_hab(fname)
% extract_hab: code that will extract inst_heights info from a .xls
%
% xls is based on the mooring log with inst. heights added
% outputs a usable structure for applying to existing netcdf files
% as part of the water_depth correction process.  Called by
% do_adj_tripod_dep.m
%
% usage [dat, dnums, dstrs]=extract_hab('test_mbay_senshab.xls');
%   expects the name of an excel file as input
%   outputs:  dat is a structure containing these fields:
%             tripod_id, habname, hab, sn- 
%             the last 3 are cell arrays
%             dnums are the numeric elements returned by xlsread
%             dstrs are the string elements returned by xlsread
%
% this can only run on PC because xlsread doesn't work well on linux.
% HAVE TO make column 1 & _sn columns 'text' and any with _cmab 'numeric'
%
%emontgomery 11/17/08
%
% Program written in Matlab v7.4.0336 (2007a)
% Program updated in Matlab 7.2.0.232 (R2006a)
% Program ran on PC with Windows XP Professional OS.
%
% "Although this program has been used by the USGS, no warranty,
% expressed or implied, is made by the USGS or the United States
% Government as to the accuracy and functioning of the program
% and related program material nor shall the fact of distribution
% constitute any such warranty, and no responsibility is assumed
% by the USGS in connection therewith."


if ~ispc
    disp ('this can only run on a PC due to xlsread- sorry!')
    return
else
    if ~exist(fname,'file')
    disp ('file name entered does not exist, please choose another')
        [fname, pathname, filterindex] = uigetfile('*.xls','Open a xls file with heights above bottom');
    end        
    [vals, vstr, vraw]=xlsread(fname);

    % often there are more labels than data, so usr length(vals) as limit
    [rws,cols]=size(vals);

    % look at the title line and find the columns with _cmab and _sn
    xx=strfind(vstr(1,1:cols),'_sn');
    k=1;
    for kk=1:length(xx)
        tf=isempty(xx{kk});
        if tf==0
            snloc(k)=kk;
            k=k+1;
        end
    end
    clear xx;
    k=1;
    xx=strfind(vstr(1,1:cols),'_cmab');
    for kk=1:length(xx)
        tf=isempty(xx{kk});
        if tf==0
            habloc(k)=kk;
            k=k+1;
        end
    end
    clear xx tf kk k;
    tmpsn={'?'};

    % make sure we don't run into trouble with lengths later
    if length(habloc) > length(snloc)
        ff=[habloc;habloc];
        ff(2,1:length(snloc))=snloc;
        snloc=ff(2,:);
    end
    % loop through the rows to collect each instrumnet's height and sn into a
    %  structure- row 1 has the titles, and the rest have content, thus start
    %  the loop at 2 and put things into jj-1
    kntr=1;
    for jj=2:rws
        % there are still some fields where content may be in an unexpected
        % place, height should be in vals, but will be nan if missing
        idx=find(~isnan(vals(jj-1,habloc)));
        if isempty(idx)
            disp(['no inst. heights for tripod ' char(vstr(jj))])
            kntr=kntr+1;
        else
            locs=find(habloc(idx)>16);   %get beyond the header info section
            % now put the bits we need into the structure
            if strcmp(vstr(jj,1),'') %check whether mooring ID is numeric
                dat(jj-kntr).tripodid=cellstr(num2str(vals(jj-1,1)));
            else
                dat(jj-kntr).tripodid=vstr(jj,1);
            end
            dat(jj-kntr).habname=vstr(1,habloc(idx(locs)));
            dat(jj-kntr).hab=vals(jj-1,habloc(idx(locs)));
            % _sn files should all be text in the input .xls file
            for tt=1:length(locs)
                if ~isnan(vals(jj-kntr,snloc(idx(locs(tt)))))
                    tmpsn(tt)=cellstr(num2str(vals(jj-1,snloc(idx(locs(tt))))));
                elseif strcmp(vstr(jj,snloc(idx(locs(tt)))),'')
                    tmpsn(tt)=cellstr('0');
                else
                    tmpsn(tt)=cellstr(vstr(jj,snloc(idx(locs(tt)))));
                end
            end

            dat(jj-kntr).sn=tmpsn;
            clear idx locs tmpsn
            disp ([num2str(jj) ' records processed'])
        end     %if isempty idx
    end
    disp(['finished parsing ' fname])
end