% fixhydrarange - use acoustic range information from the ADV and PCADP to
% generate a range to boundary time series for the experiment
%
% function newrange = fixhydrarange(cdfsFile, cdfqFile, cdfsNewFile)
%
% cdfsFile = netCDF raw statistics data file containing ADV or PCADP data
% cdfqFile = the netCDF quality file
% cdfsNewFile = new copy of the netCDF raw statistics data file
% newrange = the new range time series as a cell array by beam
%
% First, some of the wild points are filtered out, then the user uses an
% interactive plot to drag the remainder back to a realistic value.
%
% (We have not yet found a reliable filter to automate this entirely, 
% if you find one that works on this data, please contact the author)
%

% Written by Marinna Martini
% for the USGS Woods Hole Field Center
% 8/11/04

% 1/12/06 
% -- add information to the quality file a difference between the before and after
% 9/16/04 change to always overwrite the output file

function newrange = fixhydrarange(cdfsFile, cdfqFile, cdfsNewFile)

prog_ver = 0.0;
newrange = [];

if exist('cdfsFile', 'var') ~=1,
    [inName, inPath, filterindex] = uigetfile('*s*.cdf', ...
        'Pick a netcdf file containing ADV or PCADP statistics data');
    if isequal(inName,0) | isequal(inName,0)
        disp('User pressed cancel')
        return
    end
    cdfsFile = fullfile(inPath, inName);
    disp(['User selected stats file ', cdfsFile])
end

if exist('cdfsNewFile', 'var') ~=1,
    [inPath, inName, inExt] = fileparts(cdfsFile);
    cdfsNewFile = fullfile(inPath, [inName,'a',inExt]);
    cdfsNewFile = inputdlg('Output file name needed','Output file',1,{cdfsNewFile})
    cdfsNewFile = char(cdfsNewFile);
    disp(['User selected output file ', cdfsFile])
end

if exist(cdfqFile,'file') ~=2, 
    [inName, inPath, filterindex] = uigetfile('*q.cdf', ...
        'Pick a netcdf file containing ADV or PCADP quality information');
    if isequal(inName,0) | isequal(inName,0)
        disp('User pressed cancel')
        return
    end
    cdfqFile = fullfile(inPath, inName);
    disp(['User selected quality file ', cdfqFile])
end
disp(['User selected ', cdfqFile])
cdfq = netcdf(cdfqFile,'write');
if isempty(cdfq),
    disp(['Unable to open ',cdfqFile]);
    return;
end

cdfs = netcdf(cdfsFile,'nowrite');
if isempty(cdfs),
    disp(sprintf('Could not open netCDF file %s',cdfsFile))
    close (cdfs)
    return
end    
% make sure this is a statistics ADV or PCADP data file
% get the variable names
if strcmp(cdfs.DESCRIPT(:),'Sontek ADV raw data statistics file'),
    nBeams = 1;
    rangevarnames = {'brange','vrange'};
elseif strcmp(cdfs.DESCRIPT(:),'Sontek PCADP raw data statistics file'),
    nBeams = cdfs.Nbeams(:);
    for iBeam = 1:nBeams, 
        rangevarnames{iBeam} = sprintf('MeanRange%d',iBeam); 
    end
else
    disp('File is not a Sontek ADV or PCADP raw data netCDF file containing statistics data (*s.cdf)')
    close (cdfs)
    return
end

% get the data, do the primary filtering
burstNum = cdfs{'burst'}(:);
for iBeam = 1:length(rangevarnames),
    range{iBeam} = cdfs{rangevarnames{iBeam}}(:);
    ecrange{iBeam} = ecorr(range{iBeam},0);  % suspend plots
    [x,y] = ydrag(burstNum, ecrange{iBeam});
    newrange{iBeam} = y;
end

close(cdfs);

% we're done, write a new file 
copyfile(cdfsFile, cdfsNewFile);
cdfsnew = netcdf(cdfsNewFile,'write');
for iBeam = 1:nBeams,
    cdfsnew{rangevarnames{iBeam}}(:) = newrange{iBeam};
end
data = cdfsnew.history(:);
data = sprintf('edited by %s %f; %s', mfilename, prog_ver, data);
cdfsnew.history = data;
close (cdfsnew)

% make the notes in the Quality file
cdfq = netcdf(cdfqFile,'write');
for iBeam = 1:length(rangevarnames),
    varname = sprintf('%s_%s',mfilename,rangevarnames{iBeam});
    cdfq{varname} = ncfloat('burst');
    cdfq{varname}(:) = range{iBeam}(:)-newrange{iBeam}(:);
end
close (cdfq)