function nc = definerawsonarncfile(outFileRoot, settings, ncdims, whichFlag)
% definerawsonarncfile - Set up netcdf file for raw sonar data
%  nc = defineSonarNcFile(outFileRoot, settings, ncdims, whichFlag);
%
%  outFileRoot - name of output .cdf file
%  settings - parameters gleaned from the metadata.txt file,
%  ncdims - dimensions of the variables in the .nc files
%  whichFlag - no longer used (can omit the variable), used to have to be 'r'

% 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/WHCMSC');
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.DESCRIPTION = 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.CREATION_DATE = ncchar(' ');
nc.INST_TYPE = ncchar(' ');
nc.Conventions = ncchar('EPIC');
nc.platform_type=ncchar('tripod');

% set dimensions
nc('time') = 0; %unlimited dimension
nc('scan') = ncdims.nscans;
nc('points') = ncdims.npoints;
if strmatch(settings.SonartoAnimate,'azm')
    nc('rots')= ncdims.rots;
end

% write metadata into global attributes
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
% since we only have one instrument of each type we can do this- if we get
% more variety, this code will have to change
if strmatch(settings.SonartoAnimate,'azm') 
    sn='3937';
    type='rotating Imagenex Model 881A Digital profiling sonar';
elseif strmatch(settings.SonartoAnimate,'pen')
    sn='3937';
    type='Imagenex Model 881A Digital profiling sonar';
else
    sn='1751';
    type='Imagenex Model 881 Digital tilt adjusting imaging sonar';
end
nc.INST_TYPE(:)=type;
nc.serial_number=ncchar(sn);

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

% add coordinate variables in all data
nc{'time'} = nclong('time');
nc{'time'}.units = ncchar('EPIC Julian Day');
nc{'time'}.type = ncchar('EVEN');
nc{'time'}.epic_code = ncshort(624);

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

% 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'} = ncshort('scan') ;
    nc{'scan'}.units = ncchar('scan number');
    nc{'scan'}.type = ncchar('EVEN');
    
    nc{'points'} = ncshort('points') ;
    nc{'points'}.units = ncchar('number of points in each scan');
    nc{'points'}.type = ncchar('EVEN');
    
    nc{'rots'} = ncshort('rots') ;
    nc{'rots'}.units = ncchar('number of angles swept ');
    nc{'rots'}.type = ncchar('EVEN');
    
    % we want head angle for sure
    nc{'headangle'} = ncfloat('time','rots','scan');
    nc{'headangle'}.long_name = ncchar('angle of transducer head during scan');
    nc{'headangle'}.units = ncchar('degrees relative to head orientation');
    nc{'headangle'}.valid_range = ncfloat([-180 180]);
    nc{'headangle'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'headangle'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'headangle'}.serial_number = ncchar(sn);
    nc{'headangle'}.sensor_type = ncchar(type);
    nc{'headangle'}.height_depth_units = ncchar('m');
    nc{'headangle'}.FillValue_ = ncfloat(1e35);
    nc{'headangle'}.NOTE1 = ncchar('headangle is computed from head_pos');
    % we want az angle for sure
    nc{'azangle'} = ncshort('time','rots');
    nc{'azangle'}.long_name = ncchar('rotation angle of transducer during scan');
    nc{'azangle'}.units = ncchar('degrees relative to transducer 0');
    nc{'azangle'}.valid_range = ncshort([0 180]);
    nc{'azangle'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'azangle'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'azangle'}.height_depth_units = ncchar('m');
    nc{'azangle'}.serial_number = nc.serial_number(:);
    nc{'azangle'}.sensor_type = nc.INST_TYPE(:)'
    nc{'azangle'}.FillValue_ = ncshort(-32767);
    nc{'azangle'}.NOTE1 = ncchar('azangle is only possible for .R## files');
    % now profile_range  (only for azimuth)
    nc{'profile_range'} = ncshort('time','rots','scan');
    nc{'profile_range'}.long_name = ncchar('first value above threshold');
    nc{'profile_range'}.units = ncchar('cm');
    nc{'profile_range'}.valid_range = ncfloat([0 1500]);
    nc{'profile_rangee'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'profile_range'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'profile_range'}.serial_number = nc.serial_number(:);
    nc{'profile_range'}.sensor_type = nc.INST_TYPE(:)
    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'} = ncshort('time','rots','points','scan');
    nc{'raw_image'}.long_name = ncchar('sonar return echo intensity');
    nc{'raw_image'}.units = ncchar('counts');
    nc{'raw_image'}.valid_range = ncshort([0 127]);
    nc{'raw_image'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'raw_image'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'raw_image'}.serial_number = nc.serial_number(:);
    nc{'raw_image'}.sensor_type = nc.INST_TYPE(:);
    nc{'raw_image'}.height_depth_units = ncchar('m');
    nc{'raw_image'}.FillValue_ = ncshort(-32767);
    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       % for fan and pencil
    nc{'scan'} = ncshort('scan') ;
    nc{'scan'}.units = ncchar('scan number');
    nc{'scan'}.type = ncchar('EVEN');
    %
    nc{'points'} = ncshort('points') ;
    nc{'points'}.units = ncchar('number of points');
    nc{'points'}.type = ncchar('EVEN');
    % we want head angle for sure
    nc{'headangle'} = ncfloat('scan');
    nc{'headangle'}.long_name = ncchar('angle of transducer head during scan');
    nc{'headangle'}.units = ncchar('degrees relative to head orientation');
    nc{'headangle'}.valid_range = ncfloat([-180 180]);
    nc{'headangle'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'headangle'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'headangle'}.height_depth_units = ncchar('m');
    nc{'headangle'}.serial_number = nc.serial_number(:);
    nc{'headangle'}.sensor_type = nc.INST_TYPE(:);
    nc{'headangle'}.FillValue_ = ncfloat(1e35);
    nc{'headangle'}.NOTE1 = ncchar('headangle is computed from head_pos');
    % now profile_range
    nc{'profile_range'} = ncshort('time','scan');
    nc{'profile_range'}.long_name = ncchar('first value above threshold');
    nc{'profile_range'}.units = ncchar('cm');
    nc{'profile_range'}.valid_range = ncshort([0 2048]);
    nc{'profile_range'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'profile_range'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'profile_range'}.height_depth_units = ncchar('m');
    nc{'profile_range'}.serial_number = nc.serial_number(:);
    nc{'profile_range'}.sensor_type = nc.INST_TYPE(:);
    nc{'profile_range'}.FillValue_ = ncshort(-32767);
    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'} = ncshort('time','scan');
    nc{'head_pos'}.long_name = ncchar('Head position during scan');
    nc{'head_pos'}.units = ncchar('numeric location');
    nc{'head_pos'}.valid_range = ncshort([0 5000]);
    nc{'head_pos'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'head_pos'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'head_pos'}.height_depth_units = ncchar('m');
    nc{'head_pos'}.serial_number = nc.serial_number(:);
    nc{'head_pos'}.sensor_type = nc.INST_TYPE(:);
    nc{'head_pos'}.FillValue_ = ncshort(-32767);
    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 a matrix of the image data
    nc{'raw_image'} = ncshort('time','points','scan');
    nc{'raw_image'}.long_name = ncchar('sonar return echo intensity');
    nc{'raw_image'}.units = ncchar('?');
    nc{'raw_image'}.valid_range = ncshort([0 252]);
    nc{'raw_image'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'raw_image'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'raw_image'}.sensor_type = nc.INST_TYPE(:);
    nc{'raw_image'}.height_depth_units = ncchar('m');
    nc{'raw_image'}.serial_number = nc.serial_number(:);
    nc{'raw_image'}.sensor_type = nc.INST_TYPE(:);
    nc{'raw_image'}.FillValue_ = ncshort(-32767);
    nc{'raw_image'}.scale_factor = ncshort(1);
    nc{'raw_image'}.NOTE1 = ncchar('raw image is matrix of return amplitudes as returned by logger');
    % now NDataBytes
    nc{'nDataBytes'} = ncshort('scan');
    nc{'nDataBytes'}.long_name = ncchar('number of data bytes/scan');
    nc{'nDataBytes'}.units = ncchar('count');
    nc{'nDataBytes'}.valid_range = ncshort([0 550]);
    nc{'nDataBytes'}.initial_sensor_height = ncfloat(nc.Height(:));
    nc{'nDataBytes'}.sensor_depth = ncfloat(nc.WATER_DEPTH(:)-nc.Height(:));
    nc{'nDataBytes'}.height_depth_units = ncchar('m');
    nc{'nDataBytes'}.serial_number = nc.serial_number(:);
    nc{'nDataBytes'}.sensor_type = nc.INST_TYPE(:);
    nc{'nDataBytes'}.FillValue_ = ncshort(-32767);
    nc{'nDataBytes'}.NOTE1 = ncchar('nDataBytes is returned in each scan header: combined into a vector');
    nc{'nDataBytes'}.NOTE2 = ncchar('var_name matches Imagenex doc');
    %
    nc.VAR_DESC = ncchar('points:scans:head_pos:Headangle:nDataBytes:profile_range:raw_image');
end