function ncp = do_fan_rots(settings, fname, img_nums)
% do_fan_rots - Processes Imagenex fan sonar data from the raw netCDF file.
%   this program applies a constant rotation to the fan sonar data to
%   orient it relative to North.  Will process one or more samples
%
% usage:  ncp = do_fan_rots(settings, '8369fan331_raw.cdf', [1:10])
%   where:  settings is the structure containing metafields
%           fname is the netcdf file containing the raw data.  The
%                     rootname will be used to create the name of the
%                     processed file
%           img_nums is the array of image indices to process
%                     can use [1 10 25] or [132:181],
%                     default is to process all
%              ** nb: if you choose discontinuous elements, they will be
%                     put into sequential elements in the output file, so
%                     the timebase is likely to be irregular.
%           ncp is the processed output netcdf object
%
% USGS Woods Hole Field Center
% emontgomery@usgs.gov
%
% Dependencies:
%   USGS NetCDF Toolbox (C. Denham)
%   -dap enabled mexnc doesn't work! ==> mexnc_win_2006a\mexnc.mexw32 works
%   procfan.m (E. Montgomery)
%   definefanprocnc.m  (E. Montgomery)
%
% 3/25/08 at CRS request, splitting procsonar into two parts: 1) make the
%         raw.cdf file and 2) apply rotations and what-have-you
%
close all
more off

% get the current SVN version- the value is automatically obtained in svn
% is the file's svn.keywords is set to "Revision"
rev_info= 'SVN $Revision$';

% Check that the metadata contains required fields.
reqFields = {'SonartoAnimate','fanadcp_off','adcp3val'};
for f = 1:length(reqFields)
    if ~isfield(settings,reqFields{f})
        disp(['The field ''',reqFields{f},''' is not specified in settings'])
        missingFields(f) = 1;
    else
        missingFields(f) = 0;
    end
end
%If a required field is missing, ask the user for it.
if any(missingFields)
    disp('Required fields missing from the metadata');
    % Default settings for Eurostrat first deployment 2002-2003
    settings.SonartoAnimate = 'fan';
    settings.fanadcp_off = 0;
    settings.adcp3val = 0;
    settings.sweeps = 1;
    settings.dxy = 0.02;    % Key setting...determines image resolution at cost of
    % speed (reasonable range 0.02 to 0.005)
end
clear reqFields missingFields

clear FanTime
Fanidx = 1;

save settings settings;
% open existing cdf file of raw fan data
if exist(fname, 'file') ~= 2 || isempty(fname)
    disp('The raw cdf file name entered does not exist, please choose another.')
    [fname,PathName,FilterIndex] = uigetfile('*');
    fname=[PathName fname];
end

ncr=netcdf(fname);
% set up output file name
if isfield(settings,'onameRoot')
    ofproc=[settings.onameRoot '_proc.cdf'];
else
    uidx=strfind(fname,'_');
    outFileRoot=fname(1:uidx-1);
    ofproc=[outFileRoot '_proc.cdf'];
end
% decide how big the resulting matrices need to be
if isfield(settings,'dxy')
    x=[-ncr.Range(:):settings.dxy(:):ncr.Range(:)];
else
    x=[-ncr.Range(:):ncr.dxy(:):ncr.Range(:)];
end

dim_nc.x=length(x);
dim_nc.y=length(x);
% let a settings.sweeps superceede what's in the raw file, or compensate if
% there isn't one in the raw file.
if (isfield(settings,'sweeps'))
  dim_nc.sweep=settings.sweeps;
else
  dim_nc.sweep=ncr.sweeps(:);
  settings.sweeps=ncr.sweeps(:);
end
if isempty(dim_nc.sweep)
    tmpsw= input('how many sweeps were made per sample? ');
   dim_nc.sweep=tmpsw;
   settings.sweeps=dim_nc.sweep;
end

% instantiate the output ncfile
ncp = definefanprocnc(ofproc, settings, dim_nc);

% if we ended up with sweep and sweeps attributes delete sweep
tmp=att(ncp,'sweep');
if ~isempty(tmp)
    ncp.sweep=[];
end
clear tmp
% copy attributes from raw file
rawAtts=ncnames(att(ncr));
for ik=1:length(rawAtts)
    eval(['ncp.' char(rawAtts(ik)) '= ncr.' char(rawAtts(ik)) '(:);'])
end
% if there's information in settings, replace the ncp attributes
% with the values in settings
nn=fieldnames(settings);
for ik = 1:length(nn)
    eval(['ncp.' nn{ik} '(:)=settings.' nn{ik} ';'])
end
% since StepSize is wrong in header, add degreesPerStep here
ncp.DegPerStep=ncr.StepSize(:);
ncp.DegPerStep(:)= ncr{'headangle'}(5)-ncr{'headangle'}(4);
%reset creation date to now
ncp.CREATION_DATE = ncchar(datestr(now));

% set up how many images to process
if nargin == 3
    nimg_nums=img_nums;
else
    nimg_nums=[1:1:length(ncr{'time'})];
end
% do the right number of time elements
ncp{'time'}(1:length(nimg_nums))=ncr{'time'}(nimg_nums);
ncp{'time2'}(1:length(nimg_nums))=ncr{'time2'}(nimg_nums);
% put the outputs into processed netcdf file
for kj=1:settings.sweeps
    ncp{'sweep'}(kj)=kj;
end

for jj=(nimg_nums(1):nimg_nums(end))
    % process the images and put into output netcdf file
       [Xplot,Yplot, thi, ri, Zs, rot]=procfan(ncr,jj,'polar', settings);
    % and put what's returned in the output file and object
    if Fanidx==1
        ncp{'x'}(1:length(Xplot))=Xplot;
        ncp{'y'}(1:length(Yplot))=Yplot;
     end
    % Zs is float- needs to be multiplied by 10000 to store as short
    for kk=1:settings.sweeps
        tmp1=floor(Zs(kk,:,:)*10000);
        %have to force it to uint16 since sonar_image is nc_short
        tmp1=uint16(tmp1);          
        ncp{'sonar_image'}(Fanidx,kk,1:length(Xplot),1:length(Yplot))=squeeze(tmp1);
        clear tmp1
    end
    Fanidx=Fanidx+1;
end
ncp{'sonar_image'}.scale_factor(:)=10000;

% this is the last we need ncr...
close(ncr);

% add to history & make some notes to the netcdf file
hist = ncp.history(:);
hist_new = ['Sonar processed with ' ,mfilename, ', ', rev_info, ', using Matlab ' ,...
    version, '; ',hist];
ncp.history = hist_new;

ncp.NOTE =['radial data interpolated onto x-y grid to make image;',...
    'image rotated so that +y (up) is N'];
ncp.NOTE1 = ['To view images in Matlab type the following at the command ',...
    'prompt:  nc=netdcf(''sonarxxx.nc'');',...
    'imagesc(nc{''x''}(:),nc{''y''}(:),squeeze(nc{''sonar_image''}(n,p,:,:)));',...
    'set(gca,''ydir'',''normal''); **where n & p are the time and sweep indexes'];
       % the rotation of the image is comprised of fanadcp_off, adcp3val and
        % magnetic_variation, but that angle isn't captured in the attributes
        ncp.image_rotation_degrees=rot;
% this is where the data is saved
%  writing to netCDF doesn't work, but you get a .mat file for each fan and
%  Pencil run
if strcmpi(settings.SonartoAnimate,'fan'),
   t_all= ncp{'time'}(:)+ncp{'time2'}(:)./86400000;
    ncp.start_time = datestr(gregorian(t_all(1)));
    ncp.stop_time = datestr(gregorian(t_all(end)));
    % if time data is evenly spaced
    if length(t_all) > 1 & isempty(find(diff(diff(t_all))) ~= 0) 
        ncp.DELTA_T = [num2str(gmean(diff(t_all))*24*60),' sec'];
        % time and time2 are EVEN by default
    else
        ncp{'time'}.type(:)='UNEVEN';
        ncp{'time2'}.type(:)='UNEVEN';
        ncp.DELTA_T = ['? sec'];
    end
    % close the writeable version
    close(ncp);
    ncclose;
    % re-open it read-only to return to matlab
    eval(['ncp=netcdf(''' ofproc ''');'])
end

% ---------------- Subfunction: readSonarMeta.m ------------------------- %
function userMeta = readSonarMeta(metaFile);
[atts, defs] = textread(metaFile,'%s %63c','commentstyle','shell');
defs = cellstr(defs);
for i = 1:length(atts)
    theAtt = atts{i}(:)';
    theDef = defs{i}(:)';
    % deblank removes trailing whitespace
    theAtt = deblank(theAtt);
    theDef = deblank(theDef);
    % check for and replace spaces in
    % the attributes with underscores
    f1 = find(isspace(theAtt));
    f2 = strfind(theAtt,'-');
    f = union(f1,f2);
    if ~isempty(f)
        theAtt(f) = '_';
    end
    % attribute definitions read in as characters; convert to
    % numbers where appropriate
    theDefNum = str2double(theDef);
    if ~isnan(theDefNum)
        theDef = theDefNum;
    end
    eval(['userMeta.',theAtt,'= theDef;'])
end