mrg_AQD_dat_to_mat

 Reads .dat files from the Aquadopp
 Outputs a structured array containing the data.
   TODO:
       Add compass correction (have as input)
       Add pressure correction (also as input)
       Allow header items as input (currently hard-coded below)
       Allow side-lobe depth correction as an input (also hard-coded
       below)
       Optimise / speed up!
       Deal with testing for equidistances
   V2 DP 4/7/2012
       - Removed all reference to the 'arbitary' percentage of the water
       column cut-off (which is totally bollocks).  The correct number is
       always cos(deg2rad(angle_of_the_beam)) - which for Nortek equipment
       happens to be approx 90%
       - Added 'header_items' as input (assumes 19 as the default if not supplied).

0001 function [AQDdat_mat_out] = mrg_AQD_dat_to_mat(filename, n_header_items)
0002 % Reads .dat files from the Aquadopp
0003 % Outputs a structured array containing the data.
0004 %   TODO:
0005 %       Add compass correction (have as input)
0006 %       Add pressure correction (also as input)
0007 %       Allow header items as input (currently hard-coded below)
0008 %       Allow side-lobe depth correction as an input (also hard-coded
0009 %       below)
0010 %       Optimise / speed up!
0011 %       Deal with testing for equidistances
0012 %   V2 DP 4/7/2012
0013 %       - Removed all reference to the 'arbitary' percentage of the water
0014 %       column cut-off (which is totally bollocks).  The correct number is
0015 %       always cos(deg2rad(angle_of_the_beam)) - which for Nortek equipment
0016 %       happens to be approx 90%
0017 %       - Added 'header_items' as input (assumes 19 as the default if not supplied).
0018 
0019 %% Check input variables
0020 
0021 % Check that the supplied file exists
0022 if ~exist(filename, 'file')
0023     error(['The filename you passed to ' mfilename ' does not exists, or is not accessible by MATLAB']);
0024 end
0025 
0026 % The number of header items (find this in the AquaDopp .hdr file).
0027 if ~exist('n_header_items', 'var')
0028     n_header_items = 19;
0029     warning('mrg:DefaultValue', ['The function ' mfilename ' is assuming you have 19 header items']);
0030 end
0031 
0032 %% Try to open a file connection
0033 fid = fopen(filename, 'r');
0034 % Check that the file was opened
0035 if fid == -1
0036     error(['MATLAB was unable to open the file supplied to ' mfilename]);
0037 end
0038 
0039 %% Check compass correction input
0040 
0041 
0042 %% Check pressure correction input
0043 
0044 
0045 %% Get started
0046 
0047 AQDdat_mat = [];
0048 AQDdat_raw_meta = {};
0049 
0050 % Setup some counters and internal variables
0051 text_line_no = 1;
0052 meta_dim = 1;
0053 
0054 % Read a line of text.  The first line should be a header
0055 text_line = fgetl(fid);
0056 
0057 while text_line ~= -1 % i.e. Until the end of the file
0058     header = textscan(text_line, '%d %d %d %d %d %d %s %s %f %f %f %f %f %f %f %f %f %f %f');
0059     % Is a floating point number the best way to read this?
0060     if length(header) ~= n_header_items
0061         error(['The header on line ', num2str(text_line_no), ' did not have ', num2str(n_header_items), ' items.  This is probably an error.']);
0062     else
0063         % Write the header to the meta object
0064         AQDdat_raw_meta(meta_dim,:) = header;
0065         % Now we need to read the actual profile data...
0066         % First, lets figure out how many lines to read...
0067         nread = header{n_header_items};
0068         % n_read should be the last object in the header
0069         % i.e. it should be the number of bins and therefore the number of
0070         % lines to read
0071         data_line_no = 1; % Set (or re-set) a new line counter...
0072         while data_line_no <= nread
0073             text_line = fgetl(fid);
0074             text_line_no = text_line_no+1; % Increment the whole-file line counter
0075             data_line = textscan(text_line, '%f');
0076             AQDdat_mat(meta_dim,data_line_no,:) = data_line{1};
0077             data_line_no = data_line_no + 1; % Increment the local data_line counter
0078         end
0079        
0080         text_line = fgetl(fid); % Get a new line to feed back into the while loop test
0081         text_line_no = text_line_no+1; % Increment the whole-file line counter
0082         meta_dim = meta_dim+1; % and increment the meta_dim counter
0083     end
0084 end
0085 
0086 fclose(fid);
0087 
0088 %% Converting to MATLAB datetime and finding duplicates
0089 datevector = cell2mat(AQDdat_raw_meta(:,[3,1,2,4,5,6]));
0090 datetime = datenum(double(datevector));
0091 % Looking for double ups in datetimes...
0092 % This is probably caused by the wavebursts (profiles can't be taken while
0093 % the wavebursts are underway)
0094 % The ASCII output function of AquaPro seems to just duplicate the next 'good' profile to fill the gap.
0095 % e.g. if 1715 is missing, there will be two (identical) readings for 1730.
0096 [~, m, ~] = unique(datetime, 'last');
0097 
0098 % Dropping double ups before processing...
0099 datetime = datetime(m);
0100 datevector = datevector(m,:);
0101 
0102 AQDdat_mat = AQDdat_mat(m,:,:);
0103 AQDdat_raw_meta = AQDdat_raw_meta(m,:,:);
0104 
0105 %% Generating output
0106 % Ideally this would be dymanic i.e. read from the .hdr file.  Oh well.
0107 AQDdat_mat_out = struct(...
0108     'datetime', datetime, ...
0109     'datevector', datevector, ...
0110     'error_code', {AQDdat_raw_meta(:,7)}, ...
0111     'status_code', {AQDdat_raw_meta(:,8)}, ...
0112     'batt_volt_v', cell2mat(AQDdat_raw_meta(:,9)), ...
0113     'heading_deg', cell2mat(AQDdat_raw_meta(:,11)), ...
0114     'pitch_deg', cell2mat(AQDdat_raw_meta(:,12)), ...
0115     'roll_deg', cell2mat(AQDdat_raw_meta(:,13)), ...
0116     'pressure_dbar', cell2mat(AQDdat_raw_meta(:,14)), ...
0117     'temp_degC', cell2mat(AQDdat_raw_meta(:,15))...
0118     );
0119 % Appending the profile data from above...
0120 AQDdat_mat_out.profile = AQDdat_mat;
0121 
0122 end