function theMeta = aqa2mat(theMeta, verbose)
% AQA2MAT use Aquatec toolbox to prepare data for aqa2cdf
%
% theMeta.input_directory = 'E:\PV_2007\842_B3_geoprobe\8427abss\datafiles'; % where the .aqa files are
% verbose = set to 1 for diagnostic output
%
% This m-file uses Aquatec's ReadAquascat1000, which will bomb if any of
% the *.aqa data files are not complete.  Short data files can occur during
% the download process, so it is recommended that they be weeded out before
% running this m-file.

% 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))

% have to deal with the Aquatec idiosyncracies

% ## directory with .aqa and .aqf files (required)
if ~isfield(theMeta,'input_directory') || isempty(theMeta.input_directory) || ...
        isempty(dir(fullfile(theMeta.input_directory,'*.aqa'))),
    theMeta.input_directory = uigetdir(pwd,'Where are the .aqa files?');
    if ~theMeta.input_directory, theMeta.input_directory= []; return; end
end

% get a *.aqa file name, needed to make ReadAquascat work right
% we are first after the information
filesInDir = dir(fullfile(theMeta.input_directory,'*.aqa'));
if exist([filesInDir(1).name '.mat'],'file')
    delete([filesInDir(1).name '.mat'])
end
[fpath, fname] = fileparts(filesInDir(1).name);
ReadAquaScat1000(fullfile(theMeta.input_directory,fname),'STRUCT');

% STRUCT gives instrument info
load(fullfile(theMeta.input_directory,[filesInDir(1).name '.mat']))
theMeta.ABSSmodel = BurstInfo.IntsrumentType; % yes, it is spelled wrong
theMeta.ABSSSerialNumber = BurstInfo.SerialNumber;
theMeta.ABSSBoardVersion = BurstInfo.BoardVersion;

% gives other data...
ReadAquaScat1000(fullfile(theMeta.input_directory,fname));
load(fullfile(theMeta.input_directory,[filesInDir(1).name '.mat']))

theMeta.AbsTransducerName = AbsTransducerName; 
theMeta.frequency = AbsTxFrequency; % shape ntransducers x 1
theMeta.AbsTxPulseLength = AbsTxPulseLength; % shape ntransducers x 1
theMeta.BurstDuration = AbsProfileRate; % shape ntransducers x 1
theMeta.PingRate = PingRate;
theMeta.NumPings = NumPings;
theMeta.AbsAverage = AbsAverage; % shape ntransducers x 1
theMeta.AbsBinLengthMM = AbsBinLengthMM; % shape ntransducers x 1
theMeta.AbsBinRange = AbsBinRange; % shape nbins x ntransducers
theMeta.AbsNumBins = AbsNumBins; % shape ntransducers x 1
theMeta.AbsNumProfiles = AbsNumProfiles; % shape ntransducers x 1
theMeta.AbsProfileRate = AbsProfileRate; % shape ntransducers x 1
theMeta.AbsStartingGain = AbsStartingGain; % shape ntransducers x 1
% take this directly from the shape of the data
theMeta.nBins = size(AbsData,1); %number of bins
theMeta.nProfiles = size(AbsData,2); %number of profiles
theMeta.nXducers = size(AbsData,3); %number of xducers

if verbose, disp(theMeta); end

if ~isfield(theMeta, 'metaFileName'), 
    theMeta.metaFileName = fullfile(theMeta.output_directory,[theMeta.outFileRoot 'Meta']);
end
disp(sprintf('saving metadata to %s',theMeta.metaFileName))
save(theMeta.metaFileName,'theMeta')

disp('Commencing extraction to .mat files')
% now extract all the data files
filesSorted = sortrows({filesInDir.name}');
NumFiles = size(filesSorted,1);

disp(sprintf('There are %d .aqa files to process', NumFiles))

for ifile = 1:NumFiles
    fname = fullfile(theMeta.input_directory,filesSorted{ifile});      %assumes .AQA
    ReadAquaScat1000(regexprep (fname, '.aqa' ,'','ignorecase'));
end