% do100X process LISST 100X data using Sequoia's mfile
%
% function do100X(inFile, zscFile, ringFile, settings, [samplerange]);
% inFile = binary or ascii LISST data file
% zscFile = background file to use (this from your calibration)
% ringFile = ring area (detector calibration) file (this from the factory)
% settings = a structure with metadata
% settings.expYear = 2006; %the year the experiment started
% settings.LISSTtype = 'A';  %type  A (5-500 micrions), 
%                                   B (1.2-250 microns),
%                                   C (2.5-500 microns),
%                                   F
% settings.volconv = 45733; % for LISST 1172
% settings.navg = 1;    % number of samples to average together
% settings.pscale = 0.01;  % pscale is the pressure scale from the INI file, HK4Scale
% settings.poffset = 0;  %poffset is the pressure offset from the INI file, HK4Off
% settings.raux % raux converts counts to volts for aux channel (from the INI file)
% samplerange = [1 Inf]; % for all or a set range
%
% this uses mfile from Sequoia, set up as a function rather than in
% interactive script

% Assumptions
% Header size is 80 bytes in settling experiments

% written by Marinna Martini 22 July 2008

% TODO need to differentiate between settling experiments and time series
% at the moment, treat all data as simple time series
% could use a utility to extract part of an experiment as the background
% calibration

function [lisst, settings] = do100X(inFile, zscFile, ringFile, settings, samplerange)

% get the current SVN version- the value is automatically obtained in svn
% is the file's svn.keywords which is set to "Revision"
rev_info = 'SVN $Revision$';
disp(sprintf('%s %s running',mfilename,rev_info))

Settling = 0;

% get the data file
if exist('inFile','var') ~=1,
    FilterSpec(1,:) = {'*.DAT','*.DAT binary LISST data file'};  
    [fname, pathname] = uigetfile(FilterSpec, 'Pick a LISST data file');
    if isequal(fname,0) || isequal(pathname,0)
        disp('User pressed cancel')
        return
    end
    inFile = fullfile(pathname, fname);
    disp(['User selected data file ', inFile])
    if fname(1) == 'S',
        disp('This is a settling experiment')
        Settling = 1;
    end
end
settings.inFile = inFile;
settings.Settling = Settling;

% get the background scatter calibration file
if exist('zscFile','var') ~=1,
    FilterSpec(1,:) = {'*.asc','*.asc ASCII LISST background file'};
    FilterSpec(2,:) = {'*.DAT','*.DAT binary LISST background file'};  
    [fname, pathname] = uigetfile(FilterSpec, 'Pick a LISST background scatter file');
    if isequal(fname,0) || isequal(pathname,0)
        disp('User pressed cancel')
        return
    end
    zscFile = fullfile(pathname, fname);
    disp(['User selected background file ', zscFile])
end
% is it Binary or ASCII?
[inPath, inName, inExt] = fileparts(zscFile);
if strcmp(inExt,'.asc')   
    % ASCII cal files have only 32 data points
    zsclab = load(zscFile);
else
    zsclab = tt2mat(zscFile,nVariables);
    % a binary file could be anything, including part of an experiment
    zsclab = mean(zsclab); 
end
settings.zscFile = zscFile;
settings.zsclab = zsclab;

% get the ring area file
if exist('ringFile','var') ~=1,
    [fname, pathname] = uigetfile('*.asc', 'Pick a ring area (detector calibration) file');
    if isequal(fname,0) || isequal(pathname,0)
        disp('User pressed cancel')
        return
    end
    ringFile = fullfile(pathname, fname);
    disp(['User selected ring area file ', ringFile])
end
settings.ringFile = ringFile;

% make sure all the metadata is here
if exist('settings','var') ~=1,
    settings = [];
end
if isfield(settings, 'expYear'),
    expYear = settings.expYear;
else
    d = gregoria(julian(datevec(now)));
    expYear = inputdlg('Is this the year of the start of the time series?',...
        'Input the year',1,{sprintf('%d',d(1))});
    expYear = str2double(char(expYear));
    settings.expYear = expYear;
end
disp(sprintf('The year of the experiment is %d',expYear))

% what LISST is it?
LISSTtypes = {'A','B','C','F'};
LISSTtype = [];
if isfield(settings, 'LISSTtype'),
    settings.LISSTtype = lower(settings.LISSTtype);
else
    [n,v] = listdlg('PromptString','Select type of instrument:',...
        'SelectionMode','single','ListString',LISSTtypes);
    if ~v,
        disp('LISST type is required information')
        return
    end
    LISSTtype = lower(LISSTtypes{n});
    settings.LISSTtype = LISSTtype;
end
disp(sprintf('The LISST type is %s',settings.LISSTtype))
% now convert to a number
for itype = 1:length(LISSTtypes),
    if strcmpi(settings.LISSTtype, LISSTtypes{itype}), LISSTtype = itype; end
end
if isempty(LISSTtype),
    disp([settings.LISSTtype ' not found'])
    return;
end

if isfield(settings, 'navg'),
    navg = settings.navg;
else navg = 1;
    settings.navg = navg;
end
disp(sprintf('%d samples will be averaged',navg))
if isfield(settings, 'pscale'),
    pscale = settings.pscale;
else pscale = 0.01;
    disp('Pscale not given')
end
disp(sprintf('Pscale is %f',pscale))
if isfield(settings, 'poffset'),
    poffset = settings.poffset;
else poffset = 0;
    disp('Poffset not given')
end
disp(sprintf('Poffset is %f',poffset))
if isfield(settings, 'raux'),
    raux = settings.raux;
else raux = 5/4095;
    disp('Aux. input conversion not given')
end
disp(sprintf('Aux. input conversion is %f',raux))
if isfield(settings, 'volconv'),
    volconv = settings.volconv;
else volconv = 1;
    disp('volconv input conversion not given')
end
disp(sprintf('volconv conversion is %f',volconv))

% samplerange = [1 Inf]; % for all or a set range
if ~exist('samplerange','var'),
    samplerange = [1 Inf];
end
if isinf(samplerange(2)), samplerange(2) = -1; end

fid = fopen(fullfile(pwd,'nliafunc.log'),'w');
disp(['Writing error messages to ',fullfile(pwd,'nliafunc.log')])
disp('Sequoia''s nlia function will take some time to process without update messages')
disp('please be patient')
[vd,tau,dias32,scat,mzsc, press,temp,aux,bvolt, Lref, beam_c, vdate] = ...
    nlia_func(inFile,zscFile,ringFile,samplerange(1),samplerange(2),...
    navg,volconv,LISSTtype, pscale, poffset, raux, fid);

fclose(fid);

lisst.vd = vd;
lisst.tau = tau;
lisst.dias32 = dias32;
lisst.scat = scat;
lisst.mzsc = mzsc;
lisst.press = press;
lisst.temp = temp;
lisst.aux1 = aux;
lisst.batt = bvolt;
lisst.laserref = Lref;
lisst.beamc = beam_c;

% compute the time stamps in julian and MATLAB
dayone = datenum([expYear,1,1,0,0,0]);
yearday = floor(vdate(:,1)./100);
hour =  rem(vdate(:,1),100);
min = floor(vdate(:,2)./100);
sec =  rem(vdate(:,2),100);
tm = dayone+yearday+hour./24+min./(24*60)+sec./(24*3600);
tj = julian(datevec(tm));
lisst.tj = tj;
lisst.tm = tm;

return