function nc = defineSonarNcFile(outFileRoot, settings, ncdims, whichFlag);
%  called by procsonar_MM.m to create the netcdf files
%
% usage: nc = defineSonarNcFile(outFileRoot, settings, ncdims, whichFlag);
%  outFileRoot is the second argument to procsonarMM, ie. 'MVCOfantst'
%  settings containg parameters gleaned from th metadata.txt file, again an
%    argument to procsonarMM
%  ncdims defines the dimensions of the variables in the .nc files
%  whichFlag sayw whether to create the raw ('r') or processed format
%
% emontgomery from mmartini

nc = netcdf([outFileRoot,'.cdf'],'clobber');
%% Global attributes:
 
nc.CREATION_DATE = ncchar(' ');
nc.DATA_TYPE = ncchar('IMAGE');
nc.DATA_SUBTYPE = ncchar(' ');
nc.DATA_ORIGIN = ncchar('USGS/WHSC');
nc.EXPERIMENT = ncchar(' ');
nc.PROJECT = ncchar(' ');
nc.MOORING = ncchar(' ');
nc.DELTA_T = ncchar(' ');
nc.COMPOSITE = nclong(0);
nc.DATA_CMNT = ncchar(' ');
nc.POS_CONST = nclong(0);
nc.DEPTH_CONST = nclong(0);
nc.WATER_MASS = ncchar('?');
nc.DESCRIPT = ncchar(' ');
nc.DRIFTER = nclong(0);
nc.history = ncchar(' ');
nc.start_time = ncchar(' ');
nc.stop_time = ncchar(' ');
nc.latitude = ncfloat(999);
nc.longitude = ncfloat(999);
nc.magnetic_variation = ncfloat(0);
nc.water_depth = ncfloat(0);
nc.CREATION_DATE = ncchar(' ');
nc.INST_TYPE = ncchar(' ');

% do different things with creating the file depending on whether you're
% making a raw or processed file
  % set dimensions
if (strncmp(upper(whichFlag),'R',1))  %R here is raw or processed- NOT rotate
  nc('time') = 0; %unlimited dimension 
  nc('scan') = ncdims.nscans;
  nc('points') = ncdims.npoints;
   if strmatch(settings.SonartoAnimate,'azm')
    nc('rots')= ncdims.rots;
   end
else    % now do the processed
  if strmatch('fan',lower(settings.SonartoAnimate))  
    nc('time') = 0; %unlimited dimension
    nc('sweep')= ncdims.sweep;
    nc('x') = ncdims.x;
    nc('y') = ncdims.y;
  elseif strmatch('pen',lower(settings.SonartoAnimate))
    nc('time') = 0; %unlimited dimension
    nc('sweep')= ncdims.sweep;
    nc('x') = ncdims.npoints;
    nc('z') = ncdims.nscans;  
  elseif strmatch('azm', lower(settings.SonartoAnimate))
    nc('time') = 0; %unlimited dimension
    nc('rots')= ncdims.rots;
    nc('x') = ncdims.npoints;
    nc('z') = ncdims.nscans;  
  else
    nc('time') = 0; %unlimited dimension
    nc('sweep')= ncdims.sweep;
    nc('x') = ncdims.npoints;
    nc('z') = ncdims.nscans;       
  end
end
 
% global attributes
% write metadata
metaFields = fieldnames(settings);
for i = 1:length(metaFields)
   theField = metaFields{i};
   theFieldDef = getfield(settings,theField);
   nRows = size(theFieldDef,1);
   nCols = size(theFieldDef,2);
   temp = [];
   if ischar(theFieldDef)
      if nRows>1
         for ii = 1:nRows
            temp = [temp,' ',theFieldDef(ii,1:nCols)];
         end
         theFieldDef = temp;
      end
      eval(['nc.',theField,' = ncchar(theFieldDef);'])
   else
      eval(['nc.',theField,'= ncfloat(theFieldDef);'])
   end
end

% write additional metadata
    nc.CREATION_DATE = ncchar(datestr(now));

  % add coordinate variables in all data 
    nc{'time'} = nclong('time');
    nc{'time'}.FORTRAN_format = ncchar('F10.2');
    nc{'time'}.units = ncchar('True Julian Day');
    nc{'time'}.type = ncchar('EVEN');
    nc{'time'}.epic_code = ncint(624);

    nc{'time2'} = nclong('time') ;
    nc{'time2'}.FORTRAN_format = ncchar('F10.2');
    nc{'time2'}.units = ncchar('msec since 0:00 GMT');
    nc{'time2'}.type = ncchar('EVEN');
    nc{'time2'}.epic_code = ncint(624);

   % now do the raw vs processed fork, within which are fan and pencil
   % splits
   if (strncmp(upper(whichFlag),'R',1)) 
       %fan and pencil can be treated the same here, but not azimuth.
       % add the rest of the coordinate vars as appropriate    
     if strmatch('azm',lower(settings.SonartoAnimate))
       nc{'scan'} = ncint('scan') ;
       nc{'scan'}.FORTRAN_format = ncchar('F10.2');
       nc{'scan'}.units = ncchar('scan number in the radial sweep');
       nc{'scan'}.type = ncchar('EVEN');

       nc{'points'} = ncint('points') ;
       nc{'points'}.FORTRAN_format = ncchar('F10.2');
       nc{'points'}.units = ncchar('number of points in each scan');
       nc{'points'}.type = ncchar('EVEN');

       nc{'rots'} = ncint('rots') ;
       nc{'rots'}.FORTRAN_format = ncchar('F10.2');
       nc{'rots'}.units = ncchar('number of angles swept ');
       nc{'rots'}.type = ncchar('EVEN');

       % we want head angle for sure
       nc{'headangle'} = ncfloat('time','rots','points');
       nc{'headangle'}.long_name = ncchar('angle of xducer head during scan');
       nc{'headangle'}.units = ncchar('degrees relative to head orientation');
       nc{'headangle'}.valid_range = ncfloat([-180 180]);
       nc{'headangle'}.FORTRAN_format = ncchar('F10.2');
       nc{'headangle'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'headangle'}.note1 = ncchar('headangle is computed from head_pos');
        % we want head angle for sure
       nc{'azangle'} = ncint('time','rots');
       nc{'azangle'}.long_name = ncchar('rotatio nangle of xducer head during scan');
       nc{'azangle'}.units = ncchar('degrees relative to xducer 0');
       nc{'azangle'}.valid_range = ncfloat([0 180]);
       nc{'azangle'}.FORTRAN_format = ncchar('F10.2');
       nc{'azangle'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'azangle'}.note1 = ncchar('azangle is only possible for .R## files');   
      % now profile_range
       nc{'profile_range'} = ncint('time','rots','points');
       nc{'profile_range'}.long_name = ncchar('first value above threshold');
       nc{'profile_range'}.units = ncchar('cm');
       nc{'profile_range'}.valid_range = ncfloat([0 5000]);
       nc{'profile_range'}.FORTRAN_format = ncchar('F10.2');
       nc{'profile_range'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'profile_range'}.note1 = ncchar('profile_range is returned in each scan header: combined into a vector');
       nc{'profile_range'}.note2 = ncchar('var_name matches Imagenex doc');
       % now a matrix of the image data 
       nc{'raw_image'} = ncint('time','rots','points','scan');
       nc{'raw_image'}.long_name = ncchar('sonar return echo intensity');
       nc{'raw_image'}.units = ncchar('?');
       nc{'raw_image'}.valid_range = ncfloat([0 252]);
       nc{'raw_image'}.sensor_type = nc.INST_TYPE(:);
       nc{'raw_image'}.FORTRAN_format = ncchar('F10.2');
       nc{'raw_image'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'raw_image'}.scale_factor = ncint(1);
       nc{'raw_image'}.note1 = ncchar('raw image is matrix of amplitudes as returned by logger');

       nc.VAR_DESC = ncchar('points:scans:rots:Headangle:azangle:profile_range:raw_image');
     else
       nc{'scan'} = ncint('scan') ;
       nc{'scan'}.FORTRAN_format = ncchar('F10.2');
       nc{'scan'}.units = ncchar('scan number in the radial sweep');
       nc{'scan'}.type = ncchar('EVEN');

       nc{'points'} = ncint('points') ;
       nc{'points'}.FORTRAN_format = ncchar('F10.2');
       nc{'points'}.units = ncchar('number of points in each scan');
       nc{'points'}.type = ncchar('EVEN');

       % we want head angle for sure
       nc{'headangle'} = ncfloat('time','scan');
       nc{'headangle'}.long_name = ncchar('angle of xducer head during scan');
       nc{'headangle'}.units = ncchar('degrees relative to head orientation');
       nc{'headangle'}.valid_range = ncfloat([-180 180]);
       nc{'headangle'}.FORTRAN_format = ncchar('F10.2');
       nc{'headangle'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'headangle'}.note1 = ncchar('headangle is computed from head_pos');
      % now profile_range
       nc{'profile_range'} = ncfloat('time','scan');
       nc{'profile_range'}.long_name = ncchar('first value above threshold');
       nc{'profile_range'}.units = ncchar('cm');
       nc{'profile_range'}.valid_range = ncfloat([0 5000]);
       nc{'profile_range'}.FORTRAN_format = ncchar('F10.2');
       nc{'profile_range'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'profile_range'}.note1 = ncchar('profile_range is returned in each scan header: combined into a vector');
       nc{'profile_range'}.note2 = ncchar('var_name matches Imagenex doc');
       % now head position
       nc{'head_pos'} = ncfloat('time','scan');
       nc{'head_pos'}.long_name = ncchar('Head position during scan');
       nc{'head_pos'}.units = ncchar('numeric location');
       nc{'head_pos'}.valid_range = ncfloat([0 5000]);
       nc{'head_pos'}.FORTRAN_format = ncchar('F10.2');
       nc{'head_pos'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'head_pos'}.note1 = ncchar('head_pos is returned in each scan header: combined into a vector');
       nc{'head_pos'}.note2 = ncchar('var_name matches Imagenex doc');
       nc{'head_pos'}.note2 = ncchar('angle=deg/step*(head_pos-1400)');
       % now NDataBytes
       nc{'nDataBytes'} = ncfloat('time','scan');
       nc{'nDataBytes'}.long_name = ncchar('number of data bytes/scan');
       nc{'nDataBytes'}.units = ncchar('number');
       nc{'nDataBytes'}.valid_range = ncfloat([0 5000]);
       nc{'nDataBytes'}.FORTRAN_format = ncchar('F10.2');
       nc{'nDataBytes'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'nDataBytes'}.note1 = ncchar('nDataBytes is returned in each scan header: combined into a vector');
       nc{'nDataBytes'}.note2 = ncchar('var_name matches Imagenex doc');
      % now a matrix of the image data 
       nc{'raw_image'} = ncfloat('time','points','scan');
       nc{'raw_image'}.long_name = ncchar('sonar return echo intensity');
       nc{'raw_image'}.units = ncchar('?');
       nc{'raw_image'}.valid_range = ncfloat([0 252]);
       nc{'raw_image'}.sensor_type = nc.INST_TYPE(:);
       nc{'raw_image'}.FORTRAN_format = ncchar('F10.2');
       nc{'raw_image'}.FillValue_ = ncfloat(settings.FillVal);
       nc{'raw_image'}.scale_factor = ncint(1);
       nc{'raw_image'}.note1 = ncchar('raw image is matrix of return amplitudes as returned by logger');

       nc.VAR_DESC = ncchar('points:scans:head_pos:Headangle:nDataBytes:profile_range:raw_image');
     end
   else    % now do processed data files 
      %fan and pencil have different contents and variable names
      if strmatch('fan',lower(settings.SonartoAnimate)) 
          nc{'x'} = ncfloat('x') ;
          nc{'x'}.FORTRAN_format = ncchar('F10.2');
          nc{'x'}.long_name = ncchar('interpolated horizontal distance from sonar');
          nc{'x'}.valid_range = ncfloat([-5 5]);
          nc{'x'}.units = ncchar('m');
          nc{'x'}.type = ncchar('EVEN');

          nc{'y'} = ncfloat('y') ;
          nc{'y'}.FORTRAN_format = ncchar('F10.2');
          nc{'y'}.long_name = ncchar('interpolated horizontal distance from sonar');
          nc{'y'}.valid_range = ncfloat([-5 5]);
          nc{'y'}.units = ncchar('m');
          nc{'y'}.type = ncchar('EVEN');
          
          nc{'sweep'} = ncint('sweep') ;
          nc{'sweep'}.FORTRAN_format = ncchar('I4');
          nc{'sweep'}.long_name = ncchar('integer sweep number');
          nc{'sweep'}.valid_range = ncfloat([1 12]);
          nc{'sweep'}.units = ncchar('none ');
          nc{'sweep'}.type = ncchar('EVEN');
         % a scale factor is applied to the variable 'sonar_image' in order to store
          % the image data as an integer rather than a float.
           nc{'sonar_image'} = ncfloat('time','sweep','x','y');
           nc{'sonar_image'}.long_name = ncchar('Imagenex Sonar Image');
           nc{'sonar_image'}.units = ncchar('?');
           nc{'sonar_image'}.valid_range = ncfloat([0 log10(256)*1000]);
           nc{'sonar_image'}.sensor_type = nc.INST_TYPE(:);
           nc{'sonar_image'}.FORTRAN_format = ncchar('F10.2');
           nc{'sonar_image'}.FillValue_ = settings.FillVal;
           nc{'sonar_image'}.scale_factor = ncfloat(1000);
           % adding the notes below makes a ncdim error occur, so
           % commenting out for now
           % nc('sonar_image').note1 = ncchar('made polar and rotated so +y is North');
           % nc('sonar_image').note2 = ncchar('the interpolated onto an x-y grid');
           nc.VAR_DESC=ncchar('x:y:sweep:sonar_image');
      elseif strmatch('pen',lower(settings.SonartoAnimate))            % pencil
          %horizontal scale for sonar_image
          nc{'x'} = ncfloat('x') ;
          nc{'x'}.FORTRAN_format = ncchar('F10.2');
          nc{'x'}.long_name = ncchar('interpolated horizontal distance from sonar');
          nc{'x'}.valid_range = ncfloat([-5 5]);
          nc{'x'}.units = ncchar('m');
          nc{'x'}.type = ncchar('EVEN');
          %vertical scale for sonar_image
          nc{'z'} = ncfloat('z') ;
          nc{'z'}.FORTRAN_format = ncchar('F10.2');
          nc{'z'}.long_name = ncchar('interpolated vertical distance from sonar');
          nc{'z'}.valid_range = ncfloat([-5 0]);
          nc{'z'}.units = ncchar('m');
          nc{'z'}.type = ncchar('EVEN');
          % now allow the sweeps
          nc{'sweep'} = ncint('sweep') ;
          nc{'sweep'}.FORTRAN_format = ncchar('I4');
          nc{'sweep'}.long_name = ncchar('integer sweep number');
          nc{'sweep'}.valid_range = ncfloat([1 12]);
          nc{'sweep'}.units = ncchar('none ');
          nc{'sweep'}.type = ncchar('EVEN');
          
        % horizontal distance- use with elev and max_ret   
        % may only need one of these but keeping all for now
          nc{'hdst'} = ncfloat('time','sweep','x') ;
          nc{'hdst'}.FORTRAN_format = ncchar('F10.2');
          nc{'hdst'}.long_name = ncchar('horizontal distance from below sonar head-interpolated ');
          nc{'hdst'}.valid_range = ncfloat([-5 5]);
          nc{'hdst'}.units = ncchar('m');
          nc{'hdst'}.type = ncchar('EVEN');
          nc{'hdst'}.FillValue_ = ncfloat(settings.FillVal);
         % height (or elevation) of max return 
           nc{'elev'} = ncfloat('time','sweep','x');
           nc{'elev'}.long_name = ncchar('Distance to strongest pencil return (seafloor) -interpolated');
           nc{'elev'}.units = ncchar('m');
           nc{'elev'}.valid_range = ncfloat([-5 0]);
           nc{'elev'}.FORTRAN_format = ncchar('F10.2');
           nc{'elev'}.FillValue_ = ncfloat(settings.FillVal);
         %value of the max return the height in elev
         % anything with the potential to have fillvalue has to be ncfloat
           nc{'max_ret'} = ncfloat('time','sweep','x');
           nc{'max_ret'}.long_name = ncchar('value of highest return of Pencil Beam scans- interpolated');
           nc{'max_ret'}.units = ncchar('');
           nc{'max_ret'}.valid_range = ncfloat([0 255]);
           nc{'max_ret'}.sensor_type = nc.INST_TYPE(:);
           nc{'max_ret'}.FORTRAN_format = ncchar('F10.2');
           nc{'max_ret'}.FillValue_ = settings.FillVal;
           nc{'max_ret'}.scale_factor = ncint(1);
           % for the shaped image showing max_ret and elev
           nc{'sonar_image'} = ncfloat('time','sweep','x','z');
           nc{'sonar_image'}.long_name = ncchar('Imagenex Sonar Image');
           nc{'sonar_image'}.units = ncchar('?');
           nc{'sonar_image'}.valid_range = ncfloat([0 256]);
           nc{'sonar_image'}.sensor_type = nc.INST_TYPE(:);
           nc{'sonar_image'}.FORTRAN_format = ncchar('F10.2');
           nc{'sonar_image'}.FillValue_ = settings.FillVal;
           nc{'sonar_image'}.scale_factor = ncint(1000);
      % found in slant range coords, then trig done to compensate
          nc{'rdst'} = ncfloat('time','x') ;
          nc{'rdst'}.FORTRAN_format = ncchar('F10.2');
          nc{'rdst'}.long_name = ncchar('horizontal distance from below middle of sonar head -raw');
          nc{'rdst'}.valid_range = ncfloat([-5 5]);
          nc{'rdst'}.units = ncchar('m');
          nc{'rdst'}.type = ncchar('EVEN');
          nc{'rdst'}.FillValue_ = ncfloat(settings.FillVal);
       % height of max return 
           nc{'relev'} = ncfloat('time','x');
           nc{'relev'}.long_name = ncchar('vertical Distance to seafloor -raw');
           nc{'relev'}.units = ncchar('m');
           nc{'relev'}.valid_range = ncfloat([0 settings.max_range]);
           nc{'relev'}.FORTRAN_format = ncchar('F10.2');
           nc{'relev'}.FillValue_ = settings.FillVal;
             nc.VAR_DESC=ncchar('x:z:hdst:elev:max_ret:sonar_image'); 
      elseif strmatch('azm',lower(settings.SonartoAnimate)) 
          nc{'x'} = ncfloat('x') ;
          nc{'x'}.FORTRAN_format = ncchar('F10.2');
          nc{'x'}.long_name = ncchar('interpolated horizontal distance from sonar');
          nc{'x'}.valid_range = ncfloat([-5 5]);
          nc{'x'}.units = ncchar('m');
          nc{'x'}.type = ncchar('EVEN');

          nc{'y'} = ncfloat('y') ;
          nc{'y'}.FORTRAN_format = ncchar('F10.2');
          nc{'y'}.long_name = ncchar('interpolated horizontal distance from sonar');
          nc{'y'}.valid_range = ncfloat([-5 5]);
          nc{'y'}.units = ncchar('m');
          nc{'y'}.type = ncchar('EVEN');
          
          nc{'rot_ang'} = ncint('rot_angle') ;
          nc{'rot_ang'}.FORTRAN_format = ncchar('I4');
          nc{'rot_ang'}.long_name = ncchar('integer sweep number');
          nc{'rot_ang'}.valid_range = ncfloat([1 180]);
          nc{'rot_ang'}.units = ncchar('none ');
          nc{'rot_ang'}.type = ncchar('EVEN');
          
         % a scale factor is applied to the variable 'sonar_image' in order to store
          % the image data as an integer rather than a float.
           nc{'sonar_image'} = ncfloat('time','rot_angle','x','y');
           nc{'sonar_image'}.long_name = ncchar('Imagenex Sonar Image');
           nc{'sonar_image'}.units = ncchar('?');
           nc{'sonar_image'}.valid_range = ncfloat([0 log10(256)*1000]);
           nc{'sonar_image'}.sensor_type = nc.INST_TYPE(:);
           nc{'sonar_image'}.FORTRAN_format = ncchar('F10.2');
           nc{'sonar_image'}.FillValue_ = settings.FillVal;
           nc{'sonar_image'}.scale_factor = ncint(1000);
           % adding the notes below makes a ncdim error occur, so
           % commenting out for now
           % nc('sonar_image').note1 = ncchar('made polar and rotated so +y is North');
           % nc('sonar_image').note2 = ncchar('the interpolated onto an x-y grid');
           nc.VAR_DESC=ncchar('x:y:rot_ang:sonar_image');
      else
          disp('does not match existing categories - not processing')
          exit
      end  
end