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    Metadata details:
    filename: getCTFBalanceCoefs.m
    path of file: ./repos/spm/external/ctf
    
    the code of the file until where you have to start completion: function [alphaMEG,MEGindex,MEGbalanceindex,alphaGref,Grefindex,Gbalanceindex]=...
  getCTFBalanceCoefs(ds,balanceType,unit);

%  Reads balance coefficients for SQUID data in phi0's, and converts to coefficients
%  for data in physical units.

%  Input : ds : (1) ds structure from readCTFds
%           balanceType : 'NONE'  : No balancing
%                          'G1BR'  : 1st order balancing
%                          'G2BR'  : 2nd order balancing
%                          'G3BR'  : 3rd order balancing
%                          'G3AR'  : 3rd order balancing + adaptive
%                  If only MEG balance table is requested, size(balanceType)=[1 5]
%                  If Gref balance table is requested also, size(balanceType)=[2 4]
%          unit:  Type of units.  Option: 'fT','T','phi0','int'.
%                 If unit is not entered, of unit=[], the default is unit='fT'.

%  Outputs : 
%     alphaMEG,MEGindex,MEGbalanceindex : MEG balancing coefficients for data in fT or T.
%            Suppose data array returned by getTrial2 has size(data)=[npt nchan].
%            nMEG = number of MEG channels in the data set.   
%            MEG channels have sensorTypeIndex==5.
%            
%            MEGindex = list of MEG channels referred to the channel numbering in
%                       the complete dataset (i.e. it is not referred to only the list of
%                       SQUID sensors).
%            by looking for sensors with ds.res4.senres.sensorTypeIndex==5
%                      size(MEGindex)=[1 nMEG]
%                      MEG data = data(:,MEGindex)

%            MEGbalanceindex = list of reference channels for MEG balancing.   
%                size(MEGbalanceindex)=[1 nRef]
%                Reference data for MEG balancing = data(:,MEGbalanceindex)

%            alphaMEG = balance coefficients.  size(alphaMEG)=[nRef nMEG]
%
%            Balancing MEG data : 
%              - Start with data AFTER converting to physical units.
%                (I.e. SQUID data must be in fT or T.)
%              - balanced_data(:,MEGindex)=data(:,MEGindex)-data(:,MEGbalanceindex)*alphaMEG

%            If user specifies balanceType=[], ' ' or 'none', then getCTFBalanceCoefs returns 
%            alphaMEG=zeros(0,nMEG), MEGindex=list of MEG sensor channels,  
%            MEGbalanceindex=[], alphaGref=zeros(0,nGef), Grefindex=list of Gref channels
%            and Gbalanceindex=[];

%   alphaGref,Grefindex,Gbalanceindex : Reference-gradiometer balancing coeficients.
%            These output arrays are optional.  If the calling statement includes
%            them, then this program extracts a table of balance coefficients for
%            the reference gradiometers from the G1BR table in the coefficient files.
%               nGref = no. of reference gradiometers channels in the data set
%                       (sensorTypeIndex=1)
%               Grefindex = list of reference channels.   size(Grefindex)=[1 nGref]
%                           Gradient reference data = data(:,Grefindex)
%               Gbalanceindex = list of channels for balancing reference 
%                                 gradiometers.  size(Gbalanceindex)=[1 nGbalcoef]
%               Balancing reference data = data(:,Gbalanceindex)

%               alph
    
function [betaMEG,MEGindex,Refindex,betaGref,Grefindex,Gbalanceindex]=...
  getRawCTFBalanceCoefs(ds,balanceType);

%  getRawCTFBalanceCoefs.  Extracts raw-data (i.e. integer data) gradiometer balancing
%                          coefficients from structure array ds.res4.scrr (ds is produced
%                          by readCTFds).

%  Date : 24 OCt 2006
%  Author : Harold Wilson

%  Inputs : ds   : Structure returned by readCTFds.
%           balanceType : 'NONE'  : No balancing
%                          'G1BR'  : 1st order balancing
%                          'G2BR'  : 2nd order balancing
%                          'G3BR'  : 3rd order balancing
%                          'G3AR'  : 3rd order balancing + adaptive
%                  If only MEG balance table is requested, size(balanceType)=[1 4]
%                  If Gref balance table is requested also, size(balanceType)=[2 4]
%           If balancing 'NONE' is specified, getRawCTFBalanceCoefs returns lists MEGindex and
%           Grefindex, and sets Refindex=[], Gbalanceindex=[].
%           The reference gradiometers have only G1BR balancing coefficients.

%  Outputs : 
%     betaMEG,MEGindex,Refindex : MEG balancing coefficients.
%            Suppose data array returned by getCTFdata has size(data)=[npt nchan].
%            nMEG = number of MEG channels in the data set.   
%            MEG channels have sensorTypeIndex==5.
%            
%            MEGindex = list of MEG channels in the data set.  It is assembled
%            by looking for sensors with ds.res4.senres.sensorTypeIndex==5
%                      size(MEGindex)=[1 nMEG]
%                      MEG data = data(:,MEGindex)

%            Refindex = list of reference channels for MEG balancing.   
%                size(Refindex)=[1 nRef]
%                Reference data = data(:,Refindex)

%            betaMEG = balance coefficients.  size(betaMEG)=[nRef nMEG]
%
%            Balancing MEG data : 
%              - Start with data BEFORE converting to physical units.
%                (I.e. SQUID data must be in phi0's or raw integers.)
%              - balanced_data(:,MEGindex)=data(:,MEGindex)-data(:,Refindex)*betaMEG

%            If user specifies balanceType=[] or ' ', then getRawCTFBalanceCoefs returns 
%            betaMEG=zeros(1,nMEG),Refindex=3 and nRef=1;


%   betaGref,Grefindex,Gbalanceindex : Reference-gradiometer balancing coeficients.
%            These output arrays are optional.  If the calling statement includes
%            them, then this program extracts a table of balance coefficients for
%            the reference gradiometers from the G1BR table in the coefficient files.
%               nGref = no. of reference gradiometers channels in the data set
%                       (sensorTypeIndex=1)
%               Grefindex = list of reference channels.   size(Grefindex)=[1 nGref]
%                           Gradient reference data = data(:,Grefindex)
%               Gbalanceindex = list of channels for balancing reference 
%                                 gradiometers.  size(Gbalanceindex)=[1 nGbalcoef]
%               Balancing reference data = data(:,Gbalanceindex)

%               betaGref = balance coefficients for ref. grads.  
%                          size(betaGref)=[nGbalcoef nGref]
%
%               Balancing ref. gradiometer data : 
%              balanced_data(:,Grefindex)=data(:,Grefindex)-data(:,Gbalanceindex)*betaGref

%  No function calls.
missingMEGMessage=0;
missingGrefMessage=0;
balanceOptions=strvcat('NONE','G1BR','G2BR','G3BR', 'G3AR');
balanceOptionsEnds = [size(balanceOptions, 1), 2]; % Which options are available for MEGs and Grefs.
common_mode_only=0;

Brefindex=[];  %  Index list of reference magnetometers in the data arrays
Grefindex=[];  %  Index list of reference gradiometers in the data arrays
MEGindex=[];   %  Index list of MEG sensors in the data arrays
Gbalanceindex=[]; % Index list of sensors used as references to balance the reference
%                   gradiometers 
Refindex=[];   %  Index list of sensors used to balance the MEG sensors 
betaMEG=[];
betaGref=[];

% Check that the inputs are sensible.
if nargin<2
  fprintf(['\ngetRawCTFBalanceCoefs: Only %d input arguments?  ',...
      'Must specify at least ds and balance.\n\n'],nargin);
  return
elseif ~isstruct(ds) | isempty(ds) | ~ischar(balanceType) | isempty(balanceType)
  fprintf('\ngetRawCTFBalanceCoefs: Wrong argument types or sizes.\n\n');
  whos ds balanceType
  return
elseif ~isfield(ds,'res4')
  fprintf('\ngetRawCTFBalanceCoefs: Field res4 is missing from structure ds.\n\n');
  ds
  return
end