function trimprofile(inFile,bins2keep,trimFile)

% function trimprofile(inFile,trimFile,bins2keep)
% or
% function trimprofile(settings)
% where
%   settings.inFile = the cdf input file to trim
%   settings.trimFile = the cdf trimmed output file
%       if not provided, file will be written appended with 'T'
%   settings.bins2keep = [M N] for M:N bins to preserve
%       may also be uncontiguous indeces [ 1 3 5 9 11];
%       keeping only two bins? then use
%       settings.bins2keep.bin1
%       settings.bins2keep.bin2
%
% this code expects EPIC convention files where trimming is done 
% based on the 'depth' dimension
% this code expects depth to be the first or second dimension in a variable

%%% START USGS BOILERPLATE -------------%
% Use of this program is described in:
%
% Acoustic Doppler Current Profiler Data Processing System Manual
% Jessica M. Côté, Frances A. Hotchkiss, Marinna Martini, Charles R. Denham
% Revisions by: Andrée L. Ramsey, Stephen Ruane
% U.S. Geological Survey Open File Report 00-458
% Check for later versions of this Open-File, it is a living document.
%
% Program written in Matlab v7.1.0 SP3
% 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."
%
%%% END USGS BOILERPLATE --------------

% written by Marinna Martini 27 Jun 08

% get the current SVN version- the value is automatically obtained in svn
% is the file's svn.keywords which is set to "Revision"
rev_info = 'SVN $Revision: $';
disp(sprintf('%s %s running',mfilename,rev_info))

if nargin==1 && isstruct(inFile),
    settings = inFile;
    if isfield(settings,'inFile'), inFile = settings.inFile;
    else inFile = ''; end
    if isfield(settings,'trimFile'), trimFile = settings.trimFile;
    else trimFile = ''; end
    if isfield(settings,'bins2keep'), bins2keep = settings.bins2keep;
    else bins2keep = []; end
end

if isempty(inFile)
    [theFile, thePath] = uigetfile('*.cdf', 'Select ABSS netcdf File to trim:');
    if isempty(inFile), return, end
    inFile = fullfile(thePath, theFile);
end

% make sure it's EPIC, or some other thing we expect
cdfin = netcdf(inFile);
if isempty(cdfin), 
    disp(sprintf('unable to open %s',inFile))
    return
end
% TODO check for EPIC convention

dimnames = ncnames(dim(cdfin));
dimflag = 0;
for idim = 1:length(dimnames),
    if strcmp(dimnames(idim),'depth'), dimflag = 1; end
end
if dimflag, 
    if length(dim(cdfin,'depth')) == 1,
        disp('There is only one depth bin in this data, there is nothing to trim')
        close(cdfin); return
    end
else
    disp('Depth dimension required for this m-file to work')
    close(cdfin); return
end

if isempty(trimFile)
    [thePath, theFile, theExt] = fileparts(inFile);
    trimFile = fullfile(thePath, [theFile,'T',theExt]);
end

if isstruct(bins2keep),
    bins2keep = [bins2keep.bin1 bins2keep.bin2];
elseif length(bins2keep) == 2,
    bins2keep = bins2keep(1):bins2keep(2);
end

depths = cdfin{'depth'}(:);
disp(sprintf('Original depths from %d at %f m to %d at %f m',...
    1,depths(1),length(depths),depths(end)))
if find(bins2keep < 0), 
    disp('some bins to keep are < zero, aborting')
    close(cdfin); return
end
if find(bins2keep > length(depths)), 
    disp(sprintf('Some bins to keep are > the number of bins (%d), aborting',...
        length(depths)))
    close(cdfin); return
end
newdepths = depths(bins2keep);
disp(sprintf('Keeping bins %d to %d',bins2keep(1),bins2keep(end)))
disp(sprintf('From depths, bin index, or cell %g to %g',...
    newdepths(1),depths(end)))

disp(sprintf('Copying %s to %s',inFile,trimFile));
copyfile(inFile,trimFile);

% find the depth dependent variables
theVar = ncnames(var(cdfin)); % variable names
v2trim = zeros(size(theVar)); % flags
for ivar = 1:length(theVar),
    %disp(theVar{ivar})
    theDim = ncnames(dim(cdfin{theVar{ivar}}));
    for idim = 1:length(theDim),
        %disp(theDim{idim})
        if strcmp(theDim{idim},'depth'),
            disp(sprintf('%s has a depth dimension and will be trimmed',theVar{ivar}));
            v2trim(ivar) = 1;
        end
    end
end

% open the new file
cdfT=netcdf(trimFile,'clobber');
if isempty(cdfT), return, end;

%  Duplication of NetCDF objects via "copy":
%        copy(f, myNetCDF) copies netcdf f into myNetCDF.
%        copy(d, f) copies dimension d into netcdf f.
%        copy(a, f) copies attribute a into netcdf f.
%        copy(a, v) copies attribute a into variable v.
%        copy(v, f, copyData, copyAttributes) copies variable v into
%           netcdf f, as directed by the flags (defaults = 0).
%        copy(v, myVariable, copyData, copyAttributes) copies the
%           contents of variable v into variable myVariable, as
%           directed by the flags (defaults = 0).

% copy global attributes
gattobj = att(cdfin);
for iatt = 1: length(gattobj),
    copy(gattobj(iatt), cdfT);
end
% copy dimensions
dimobj = dim(cdfin);
theDim = ncnames(dim(cdfin));
for idim = 1:length(theDim),
    if strcmp(theDim(idim),'depth'),
        disp(sprintf('Found depth, defining new dimension to length %d',...
            length(newdepths)))
        cdfT('depth') = length(newdepths);
    else
        copy(dimobj(idim), cdfT);
    end
end
depidx = 0;
latidx = 0;
lonidx = 0;
timidx = 0;
odimidx = 0; iodim = 0;
tic;
burstflag = 0;
% copy the data, resized appropriately, this is not pretty!
for ivar = 1:length(theVar),
    burstdim = 0;
    disp(sprintf('copying %s',theVar{ivar}))
    if v2trim(ivar),
        copy(cdfin{theVar{ivar}},cdfT,0,1) % copy attributes only
        % check the chapes of things by checking the first dimension
        % this assumes EPIC conventionality
        theDim = ncnames(dim(cdfin{theVar{ivar}}));
        ndims = length(theDim);
        % now, where is depth and time and are there an extra dimensions
        for idim = 1:ndims,
            switch theDim{idim},
                case 'depth', depidx = idim; % could be || profile || bin || cell
                case 'lat', latidx = idim;
                case 'lon', lonidx = idim;
                case 'time', timidx = idim; % could be || burst || ens
                otherwise, iodim = iodim + 1;
                    % this might be sample, 
                    odimidx(iodim) = idim;
            end
            if strcmp(theDim{idim},'profile') || strcmp(theDim{idim},'sample'),
                disp('variable contains burst data')
                burstdim = idim;
                burstflag = 1;
            end
        end
        switch ndims,
            case 1, % probably depth as the ordinate dimension
                cdfT{theVar{ivar}}(:) = cdfin{theVar{ivar}}(bins2keep);
            case 2, % probably time and depth, though this would be unusual
                if depidx == 1, 
                    cdfT{theVar{ivar}}(:,:) = cdfin{theVar{ivar}}(bins2keep,:);
                elseif depidx == 2, 
                    cdfT{theVar{ivar}}(:,:) = cdfin{theVar{ivar}}(:,bins2keep);  
                end
            case 3, % probably time, depth and something else but not lat & lon
                if ~burstdim, % who knows...
                    if depidx == 1,
                        cdfT{theVar{ivar}}(:,:,:) = cdfin{theVar{ivar}}(bins2keep,:,:);
                    elseif depidx == 2,
                        cdfT{theVar{ivar}}(:,:,:) = cdfin{theVar{ivar}}(:,bins2keep,:);
                    elseif depidx == 3,
                        cdfT{theVar{ivar}}(:,:,:) = cdfin{theVar{ivar}}(:,:,bins2keep);
                    end
                else % this is burst, and must take it in chunks so as not to run out of memory
                    nprofiles = length(cdfin(theDim{burstdim}));
                    for iprofile = 1:nprofiles,
                        if depidx == 1,
                            if burstdim == 2,
                                cdfT{theVar{ivar}}(:,iprofile,:) = cdfin{theVar{ivar}}(bins2keep,iprofile,:);
                            else
                                cdfT{theVar{ivar}}(:,:,iprofile) = cdfin{theVar{ivar}}(bins2keep,:,iprofile);
                            end
                        elseif depidx == 2,
                            if burstdim == 1,  % unlikely, but while I'm at it might as well...
                                cdfT{theVar{ivar}}(iprofile,:,:) = cdfin{theVar{ivar}}(iprofile,bins2keep,:);
                            else
                                cdfT{theVar{ivar}}(:,:,iprofile) = cdfin{theVar{ivar}}(:,bins2keep,iprofile);
                            end
                        elseif depidx == 3,
                            if burstdim == 1,  % unlikely, but while I'm at it might as well...
                                cdfT{theVar{ivar}}(iprofile,:,:) = cdfin{theVar{ivar}}(iprofile,:,bins2keep);
                            else
                                cdfT{theVar{ivar}}(:,iprofile,:) = cdfin{theVar{ivar}}(:,iprofile,bins2keep);
                            end
                        end
                        %Update the user with the code's progress
                        if mod(iprofile,100)==0
                            fprintf('Finished writing profile %d of %d; %6.2f minutes elapsed\n',iprofile,nprofiles,toc/60)
                        end
                    end
                end
            case 4, % probably time, depth, lat, lon
                if depidx == 1, 
                    cdfT{theVar{ivar}}(:,:,:,:) = cdfin{theVar{ivar}}(bins2keep,:,:,:);
                elseif depidx == 2, 
                    cdfT{theVar{ivar}}(:,:,:,:) = cdfin{theVar{ivar}}(:,bins2keep,:,:);  
                elseif depidx == 3, 
                    cdfT{theVar{ivar}}(:,:,:,:) = cdfin{theVar{ivar}}(:,:,bins2keep,:);  
                elseif depidx == 4, 
                    cdfT{theVar{ivar}}(:,:,:,:) = cdfin{theVar{ivar}}(:,:,:,bins2keep);  
                end
            case 5, % probably time, depth, lat, lon and something else
                if depidx == 1, 
                    cdfT{theVar{ivar}}(:,:,:,:,:) = cdfin{theVar{ivar}}(bins2keep,:,:,:,:);
                elseif depidx == 2, 
                    cdfT{theVar{ivar}}(:,:,:,:,:) = cdfin{theVar{ivar}}(:,bins2keep,:,:,:);  
                elseif depidx == 3, 
                    cdfT{theVar{ivar}}(:,:,:,:,:) = cdfin{theVar{ivar}}(:,:,bins2keep,:,:);  
                elseif depidx == 4, 
                    cdfT{theVar{ivar}}(:,:,:,:,:) = cdfin{theVar{ivar}}(:,:,:,bins2keep,:);  
                elseif depidx == 5, 
                    cdfT{theVar{ivar}}(:,:,:,:,:) = cdfin{theVar{ivar}}(:,:,:,:,bins2keep);  
                end
            otherwise,
                disp('This variable has depth with more than 5 dimensions, you will have to modify the code')
        end         
    else
        copy(cdfin{theVar{ivar}},cdfT,1,1) % copy all, no trimming
    end
end

% disp(sprintf('Data is from bin 1 at %7.2f to last bin at %7.2f meters',...
%     cdf{'depth'}(1),cdf{'depth'}(end)))
% 
% % add minimums and maximums
% TODO - this currently bombs due to outo f memry on burst files.
if ~burstflag,
    add_minmaxvalues(cdfT);
end

close(cdfin)
close(cdfT)

%Done
% hist = cdf.history(:);
% cdf.history = sprintf('Bins trimmed by %s %s;\n%s',...
%     mfilename,rev_info,hist);