rdi2cdf.m

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data(fld)=fread(fid,1,'ushort');
if verbose, disp(sprintf('Depth cell size %d cm',data(fld))); end
% this attribute is tagged to the depth variable
fld=fld+1;
% blanking distance (WF)
data(fld)=fread(fid,1,'ushort');
if verbose, disp(sprintf('Blank after xmit distance %d cm',data(fld))); end
% this attribute is tagged to the depth variable
fld=fld+1;
% Profiling mode (WM)
data(fld)=fread(fid,1,'uchar');
if verbose, disp(sprintf('Profiling mode %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','profiling_mode','LONG',1,data(fld));
%cdf.profiling_mode = nclong(data(fld));
fld=fld+1;

%Predicted Accuracy given in PLAN and entered by user
mexcdf('ATTPUT',cdf,'GLOBAL','pred_accuracy','FLOAT',1,pred_accuracy);

% Minimum correlation threshold (WC)
data(fld)=fread(fid,1,'uchar');
if verbose, disp(sprintf('Valid range for correlation %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','valid_correlation_range','LONG',2,[data(fld) 255]);
%cdf.valid_correlation_range = nclong([data(fld) 0]);
fld=fld+1;

% number of code repetitions
data(fld)=fread(fid,1,'uchar');
if verbose, disp(sprintf('Code repetitions %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','code_repetitions','LONG',1,data(fld));
%cdf.code_repetitions = nclong(data(fld));
fld=fld+1;

% Minimum percent good to output data (WG)
data(fld)=fread(fid,1,'uchar');
if verbose, disp(sprintf('Minimum and maximum percent good for output %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','minmax_percent_good','LONG',2,[data(fld) 100]);
%cdf.minmax_percent_good = nclong([data(fld) 0]);
fld=fld+1;

% Error velocity threshold (WE)
data(fld)=fread(fid,1,'ushort');
if verbose, disp(sprintf('Minimum and Maximum Error Velocity values permitted %d mm/s',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','error_velocity_threshold','LONG',1,data(fld));
%cdf.minmax_error_velocity = nclong([data(fld) 0]);
fld=fld+1;

% time between ping groups (TP)
data(fld)=fread(fid,1,'uchar');
fld=fld+1;
data(fld)=fread(fid,1,'uchar');
fld=fld+1;
data(fld)=fread(fid,1,'uchar');
tp=[data(fld-2),data(fld-1),data(fld)];  %added by JMC
TP = str2num(sprintf('%d.%d',(tp(1)*60 + tp(2)),tp(3)));

if verbose, disp(['Time between ping groups ' TP]); end
mexcdf('ATTPUT',cdf,'GLOBAL','time_between_ping_groups','FLOAT',1,...
	TP);
%cdf.time_between_ping_groups = ncfloat(TP);

fld=fld+1;
% coordinate transformation (EX)
data(fld)=fread(fid,1,'uchar');
if verbose, 
	disp(sprintf('Coordinate Transformation = %d',data(fld))); 
	%b=dec2bin(data(fld));
   %b=zeros(1,8); %dec2bin(data(fld));
   b=dec2bin(data(fld),8);
   %b(9-length(dec2bin(data(fld))):8)=dec2bin(data(fld));
   %b=char(b);
	transform=bin2dec(b(4:5));
	if transform == 0, 
		disp('	Data stored coordinates = Beam'); 
      mexcdf('ATTPUT',cdf,'GLOBAL','transform','CHAR',4,'BEAM');
      %cdf.transform = 'BEAM';
	end
	if transform == 1, 
		disp('	Data stored coordinates = Instrument'); 
      mexcdf('ATTPUT',cdf,'GLOBAL','transform','CHAR',4,'INST');
      %cdf.transform = 'INST';
	end
	if transform == 2, 
		disp('	Data stored coordinates = Ship'); 
      mexcdf('ATTPUT',cdf,'GLOBAL','transform','CHAR',4,'SHIP');
      %cdf.transform = 'SHIP';
	end
	if transform == 3, 
		disp('	Data stored coordinates = Earth'); 
      mexcdf('ATTPUT',cdf,'GLOBAL','transform','CHAR',5,'EARTH');
      %cdf.transform = 'EARTH';
	end
%	if b(6) == '1', disp('	Tilts used in transformation'); end
%	if b(7) == '1', disp('	3-beam solution used, this ensemble'); end
end
fld=fld+1;
% Heading Alignment (EA)
data(fld)=fread(fid,1,'int16');
if verbose, disp(sprintf('Heading alignment %d',data(fld)./100)); end
hdg_alignment = data(fld)./100;

fld=fld+1;
% Heading Bias (EB)
data(fld)=fread(fid,1,'int16');
if verbose, disp(sprintf('Heading Bias: %d deg',data(fld)./100)); end
hdg_bias = data(fld)./100;

fld=fld+1;
% Sensor source (EZ)
data(fld)=fread(fid,1,'uchar');
if verbose,
	disp(sprintf('Sensor Source = %d',data(fld))); 
	%b=(data(fld));
   b=zeros(1,8); %dec2bin(data(fld));
   b(9-length(dec2bin(data(fld))):8)=dec2bin(data(fld));
   b=char(b);
	if b(2) == '1',
		buf='Sound speed computed from ED, ES & ET';
		disp(['  ',buf]); 
		mcnote(cdf,'GLOBAL',buf,notenum);	
		notenum=notenum+1;
	end
	if b(3) == '1', 
		buf = 'ED taken from depth sensor';
		disp(['  ',buf]); 
		mcnote(cdf,'GLOBAL',buf,notenum);	
		notenum=notenum+1;
	end	
	if b(4) == '1', 
		buf = 'EH taken from xducer heading sensor';
		disp(['  ',buf]); 
		mcnote(cdf,'GLOBAL',buf,notenum);	
		notenum=notenum+1;
	end	
	if b(5) == '1', 
		buf = 'EP taken from xducer pitch sensor';	
		disp(['  ',buf]); 
		mcnote(cdf,'GLOBAL',buf,notenum);	
		notenum=notenum+1;
	end	
	if b(6) == '1', 
		buf = 'ER taken from xducer roll sensor';	
		disp(['  ',buf]); 
		mcnote(cdf,'GLOBAL',buf,notenum);	
		notenum=notenum+1;
	end	
	if b(7) == '1', 
		buf = 'ES derived from conductivity sensor';	
		disp(['  ',buf]); 
		mcnote(cdf,'GLOBAL',buf,notenum);	
		notenum=notenum+1;
	end	
	if b(8) == '1', 
		buf = 'ET taken from temperature sensor';
		disp(['  ',buf]); 
		mcnote(cdf,'GLOBAL',buf,notenum);	
		notenum=notenum+1;
	end	
end
fld=fld+1;
% Sensors available
data(fld)=fread(fid,1,'uchar');
if verbose,
	disp(sprintf('Sensor Availability = %d',data(fld))); 
	%b=dec2bin(data(fld));
   b=zeros(1,8); %dec2bin(data(fld));
   b(9-length(dec2bin(data(fld))):8)=dec2bin(data(fld));
   b=char(b);
	if b(3) == '1', disp('	depth sensor'); 
		mcnote(cdf,'GLOBAL','depth sensor available',notenum);	
		notenum=notenum+1;
	end	
	if b(4) == '1', disp('	heading sensor');  
		mcnote(cdf,'GLOBAL','depth sensor available',notenum);	
		notenum=notenum+1;
	end	
	if b(5) == '1', disp('	pitch sensor');  
		mcnote(cdf,'GLOBAL','pitch sensor available',notenum);	
		notenum=notenum+1;
	end	
	if b(6) == '1', disp('	roll sensor');  
		mcnote(cdf,'GLOBAL','roll sensor available',notenum);	
		notenum=notenum+1;
	end	
	if b(7) == '1', disp('	conductivity sensor');  
		mcnote(cdf,'GLOBAL','conductivity sensor available',notenum);	
		notenum=notenum+1;
	end	
	if b(8) == '1', disp('	temperature sensor');  
		mcnote(cdf,'GLOBAL','temperature sensor available',notenum);	
		notenum=notenum+1;
	end	
end
fld=fld+1;
% Bin 1 distance
data(fld)=fread(fid,1,'ushort');
if verbose, disp(sprintf('Distance to center of bin 1: %d cm',data(fld))); end
% this is saved with the depth variable
fld=fld+1;
% xmit pulse length
data(fld)=fread(fid,1,'ushort');
if verbose, disp(sprintf('Transmit pulse length %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','transmit_pulse_length','LONG',1,data(fld));
%cdf.transmit_pulse_length = nclong(data(fld));
mcnote(cdf,'GLOBAL','transmit_pulse_length units are cm',notenum);	
notenum=notenum+1;
fld=fld+1;
% starting depth cell
data(fld)=fread(fid,1,'uchar');
if verbose, disp(sprintf('Starting water layer %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','starting_water_layer','LONG',1,data(fld));
%cdf.starting_water_layer = nclong(data(fld));
fld=fld+1;
% ending depth cell
data(fld)=fread(fid,1,'uchar');
if verbose, disp(sprintf('Ending water layer %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','ending_water_layer','LONG',1,data(fld));
%cdf.ending_water_layer = nclong(data(fld));
fld=fld+1;
% false target reject threshold
data(fld)=fread(fid,1,'uchar');
if verbose, disp(sprintf('False target reject range values %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','false_target_reject_values','LONG',2,[data(fld) 255]);
%cdf.false_target_reject_values = nclong([data(fld) 0]);
fld=fld+1;
% spare
data(fld)=fread(fid,1,'uchar');
fld=fld+1;
% transmit lag distance
data(fld)=fread(fid,1,'ushort');
if verbose, disp(sprintf('Transmit lag distance %d',data(fld))); end
mexcdf('ATTPUT',cdf,'GLOBAL','transmit_lag_distance','LONG',1,data(fld));
%cdf.transmit_lag_distance = nclong(data(fld));
mexcdf('ATTPUT',cdf,'GLOBAL','ADCP_serial_number','LONG',1,ADCP_serial_number);
%cdf.ADCP_serial_number = nclong(ADCP_serial_number);

% save the rest of the data for later
fleader = data;
disp('-----------')
%
% ------ Set up the variables -----
%

% determine the number of ensembles from the file size
%	and number of bytes per ensemble
% there is an 8260 byte leader in every file
LEADERSIZE = 0; % original size 8260;
% the checksum at the end of every ensemble record is two bytes
CHECKSUMSIZE = 2;
fseek(fid,0,1);	% go to end of file
infilesize = ftell(fid)
nens = ceil((infilesize-LEADERSIZE)/(nbytes+CHECKSUMSIZE));
disp(sprintf('%d ensembles estimated from file size',nens))

% dimensions
ensid=mexcdf('DIMDEF',cdf,'ensemble','NC_UNLIMITED');
%cdf('ensemble') = 0; 	% the record dimension
binid=mexcdf('DIMDEF',cdf,'bin',nbins);
%cdf('bin') = nbins;

% variables
% 
mexcdf('VARDEF',cdf,'D','FLOAT',1,[binid]);
%cdf{'D'} = ncfloat('bin');
mexcdf('ATTPUT',cdf,'D','units','CHAR',1,'m');
%cdf{'D'}.units = 'm';
mexcdf('ATTPUT',cdf,'D','long_name','CHAR',9,'DEPTH (m)');
%cdf{'D'}.long_name = 'DEPTH (m)';
mexcdf('ATTPUT',cdf,'D','_FillValue','FLOAT',1,1e35);
% note, netcdf will not handle leading _
%cdf{'D'}.FillValue = ncfloat(1e35);
mexcdf('ATTPUT',cdf,'D','epic_code','LONG',1,3);
%cdf{'D'}.epic_code = nclong(3);


bin1=fleader(26)/100;
mexcdf('ATTPUT',cdf,'D','center_first_bin','FLOAT',1,bin1);
%cdf{'D'}.center_first_bin = ncfloat(fleader(26)/100);

blank=fleader(12)/100;
mexcdf('ATTPUT',cdf,'D','blanking_distance','FLOAT',1,blank);
%cdf{'D'}.blanking_distance = ncfloat(fleader(12)/100);

binsize=fleader(11)/100;
mexcdf('ATTPUT',cdf,'D','bin_size','FLOAT',1,binsize);
%cdf{'D'}.bin_size = ncfloat(fleader(11)/100);

bincnt=nbins;
mexcdf('ATTPUT',cdf,'D','bin_count','LONG',1,nbins);
%cdf{'D'}.bin_count = nclong(nbins);
water_depth = 0;
mexcdf('ATTPUT',cdf,'D','water_depth','FLOAT',1,water_depth);
%cdf{'D'}.water_depth = ncfloat(water_depth);
%xducer_offset = 0;
mexcdf('ATTPUT',cdf,'D','xducer_offset_from_bottom','FLOAT',1,xducer_offset);
%cdf{'D'}.xducer_offset_from_bottom = ncfloat(xducer_offset);

switch orientation  %Added 10-Jan-2003
case 'up'
    mcnote(cdf,'D','bin depths are relative to the seabed',notenum);
    notenum=notenum+1;
    % compute bin locations
    depths = bin1:binsize:(((bincnt-1)*binsize)+bin1);
    % adjust for ADCP position and save depths for later
    depths = depths+xducer_offset;
case 'down'
     mcnote(cdf,'D','bin depths are relative to the transducer head',notenum);
     notenum=notenum;
    % compute bin locations
    depths = bin1:binsize:(((bincnt-1)*binsize)+bin1);
    depths = depths * -1;
end

mexcdf('VARDEF',cdf,'TIM','DOUBLE',1,0);
%cdf{'TIM'} = ncdouble('ensemble');
mexcdf('ATTPUT',cdf,'TIM','units','CHAR',12,'decimal days');
%cdf{'TIM'}.units = 'decimal days';
mexcdf('ATTPUT',cdf,'TIM','long_name','CHAR',11,'JULIAN DAYS');
%cdf{'TIM'}.long_name = 'JULIAN DAYS';
mexcdf('ATTPUT',cdf,'TIM','_FillValue','DOUBLE',1,1e35);
%cdf{'TIM'}.FillValue = 1e35;
mexcdf('ATTPUT',cdf,'TIM','epic_code','LONG',1,627);
%cdf{'TIM'}.epic_code = nclong(627);
mexcdf('ATTPUT',cdf,'TIM','valid_min','LONG',1,0);
%cdf{'TIM'}.valid_min = nclong(0);
mexcdf('ATTPUT',cdf,'TIM','slow_by','LONG',1,slow_by);
mcnote(cdf,'TIM','amount of time the ADCP clock was "slow_by" is in seconds',notenum);	
notenum=notenum+1;


mexcdf('VARDEF',cdf,'Rec','LONG',1,0);
%cdf{'Rec'} = nclong('ensemble');
mexcdf('ATTPUT',cdf,'Rec','units','CHAR',6,'counts');
%cdf{'Rec'}.units = 'counts';
mexcdf('ATTPUT',cdf,'Rec','long_name','CHAR',7,'Records');
%cdf{'Rec'}.long_name = 'Records';
mexcdf('ATTPUT',cdf,'Rec','_FillValue','LONG',1,1e35);
%cdf{'Rec'}.FillValue = nclong(1e35);
mexcdf('ATTPUT',cdf,'Rec','epic_code','LONG',1,1207);
%cdf{'Rec'}.epic_code = nclong(1207);
mexcdf('ATTPUT',cdf,'Rec','valid_min','LONG',1,0);
%cdf{'Rec'}.valid_min = nclong(0);
%
mexcdf('VARDEF',cdf,'sv','LONG',1,0);
%cdf{'sv'} = nclong('ensemble');
mexcdf('ATTPUT',cdf,'sv','units','CHAR',5,'m s-1');
%cdf{'sv'}.units = 'm s-1';
mexcdf('ATTPUT',cdf,'sv','long_name','CHAR',20,'sound velocity (m/s)');
%cdf{'sv'}.long_name = 'sound velocity (m/s)';
mexcdf('ATTPUT',cdf,'sv','_FillValue','LONG',1,1e35);
%cdf{'sv'}.FillValue = nclong(1e35);
mexcdf('ATTPUT',cdf,'sv','epic_code','LONG',1,80);
%cdf{'sv'}.epic_code = nclong(80);
mexcdf('ATTPUT',cdf,'sv','valid_range','LONG',2,[1400 1600]);
%cdf{'sv'}.valid_range = nclong([1400 1600]);
%
for i=1:nbeams,
	varname = [VARNAMES(VELOCITY,:),int2str(i)];
   mexcdf('VARDEF',cdf,varname,'FLOAT',2,[0 1]);
   %eval(['cdf{''',varname,'''} = ncfloat(''ensemble'',''bin'');'])
	mexcdf('ATTPUT',cdf,varname,'units','CHAR',6,'mm s-1');
   %eval(['cdf{''',varname,'''}.units = ''mm s-1'';'])
	if ~transform,	% this EPIC code is for BEAM coordinates only
		buf=sprintf('Beam %1i velocity, mm/s',i);
		mexcdf('ATTPUT',cdf,varname,'long_name','CHAR',length(buf),buf);
		%eval(['cdf{''',varname,'''}.long_name = buf;'])
      mexcdf('ATTPUT',cdf,varname,'epic_code','LONG',1,1279+i);