function grad = yokogawa2grad_new(hdr)

% YOKOGAWA2GRAD_NEW converts the position and weights of all coils that
% compromise a gradiometer system into a structure that can be used
% by FieldTrip. This implementation uses the new "yokogawa_meg_reader"
% toolbox.
%
% See also FT_READ_HEADER, CTF2GRAD, BTI2GRAD, FIF2GRAD, YOKOGAWA2GRAD

% Copyright (C) 2005-2012, Robert Oostenveld
% Copyright (C) 2010, Tilmann Sander-Thoemmes
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
%    FieldTrip is free software: you can redistribute it and/or modify
%    it under the terms of the GNU General Public License as published by
%    the Free Software Foundation, either version 3 of the License, or
%    (at your option) any later version.
%
%    FieldTrip is distributed in the hope that it will be useful,
%    but WITHOUT ANY WARRANTY; without even the implied warranty of
%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%    GNU General Public License for more details.
%
%    You should have received a copy of the GNU General Public License
%    along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$

% The following line is only a safety measure: No function of the toolbox
% is actually called in this routine.
if ~ft_hastoolbox('yokogawa_meg_reader')
    ft_error('cannot determine whether Yokogawa toolbox is present');
end

if isfield(hdr, 'label')
  label = hdr.label; % keep for later use
end

if isfield(hdr, 'orig')
  hdr = hdr.orig; % use the original header, not the FieldTrip header
end

% The "channel_info.channel(i)" structure contains the details of coils.
% For the sepcifications, see Yokogawa MEG Reader Toolbox 1.5 specifications.pdf.
% type, type of sensor
% data.x (in m, inner coil)
% data.y (in m, inner coil)
% data.z (in m, inner coil)
% data.size (in m, coil diameter)

% for gradiometers
% data.baseline (in m)

% for axial gradiometers and magnetometers
% data.zdir orientation of inner coil (theta in deg: angle to z-axis)
% data.xdir orientation of inner coil (phi in deg: angle to x-axis)

% for planar gradiometers
% Note, that Yokogawa planar gradiometers contain two coils perpendicular to
% the sphere, i.e. the planar gradiometers normal is the spheres tangential.
% Therefore the definition of an inner coil makes sense here in contrast to
% planar gradiometers from Neuromag, where the gradiometer normal is radial.
% data.zdir1 orientation of inner coil (theta in deg: angle to z-axis)
% data.xdir1 orientation of inner coil (phi in deg: angle to x-axis)
% data.zdir2 baseline orientation from inner coil (theta in deg: angle to z-axis)
% data.xdir2 baseline orientation from inner coil (phi in deg: angle to x-axis)

%
% The code below is not written for speed or elegance, but for readability.
%

% shorten names
ch_info = hdr.channel_info.channel;
type = [ch_info.type];
handles    = definehandles;


%% get all axial grads, planar grads, and magnetometers.
%% reference channels without position information are excluded.
%grad_ind = [1:hdr.channel_count];
%isgrad   = (type==handles.AxialGradioMeter | type==handles.PlannerGradioMeter |  ...
%    type==handles.MagnetoMeter);
%isref = (type==handles.RefferenceAxialGradioMeter | type==handles.RefferencePlannerGradioMeter |  ...
%    type==handles.RefferenceMagnetoMeter);
%for i = 1: hdr.channel_count
%    if isref(i) &&  sum( ch_info( i ).data.x^2 + ch_info( i ).data.y^2 + ch_info( i ).data.z^2 ) > 0.0, isgrad(i) = 1; end
%end


% get all axial grads, planar grads, and magnetometers.
% All reference channels are excluded even if some of them have position information.
grad_ind = [1:hdr.channel_count];
isgrad   = (type==handles.AxialGradioMeter | type==handles.PlannerGradioMeter | type==handles.MagnetoMeter);

grad_ind = grad_ind(isgrad);
grad_nr = size(grad_ind,2);

grad = [];
grad.coilpos   = zeros(2*grad_nr,3);
grad.coilori   = zeros(2*grad_nr,3);

% define gradiometer and magnetometer
for i = 1:grad_nr
  ch_ind = grad_ind(i);
  grad.coilpos(i,1) =  ch_info(ch_ind).data.x*100; % cm
  grad.coilpos(i,2) =  ch_info(ch_ind).data.y*100; % cm
  grad.coilpos(i,3) =  ch_info(ch_ind).data.z*100; % cm
  grad.chanpos = grad.coilpos(1:grad_nr,:);

  if ch_info(ch_ind).type==handles.AxialGradioMeter || ch_info(ch_ind).type==handles.RefferenceAxialGradioMeter
      baseline = ch_info(ch_ind).data.baseline;

      ori_1st = [ch_info(ch_ind).data.zdir ch_info(ch_ind).data.xdir ];
      % polar to x,y,z coordinates
      ori_1st = ...
      [sin(ori_1st(:,1)/180*pi).*cos(ori_1st(:,2)/180*pi) ...
      sin(ori_1st(:,1)/180*pi).*sin(ori_1st(:,2)/180*pi) ...
      cos(ori_1st(:,1)/180*pi)];

      grad.coilori(i,:) = ori_1st;

      grad.coilpos(i+grad_nr,:) = [grad.coilpos(i,:)+ori_1st*baseline*100];
      grad.coilori(i+grad_nr,:) = -ori_1st;
  elseif ch_info(ch_ind).type==handles.PlannerGradioMeter || ch_info(ch_ind).type==handles.RefferencePlannerGradioMeter
      baseline = ch_info(ch_ind).data.baseline;

      ori_1st = [ch_info(ch_ind).data.zdir1 ch_info(ch_ind).data.xdir1 ];
      % polar to x,y,z coordinates
      ori_1st = ...
      [sin(ori_1st(:,1)/180*pi).*cos(ori_1st(:,2)/180*pi) ...
      sin(ori_1st(:,1)/180*pi).*sin(ori_1st(:,2)/180*pi) ...
      cos(ori_1st(:,1)/180*pi)];

      grad.coilori(i,:) = ori_1st;

      ori_1st_to_2nd   = [ch_info(ch_ind).data.zdir2 ch_info(ch_ind).data.xdir2 ];
      % polar to x,y,z coordinates
      ori_1st_to_2nd = ...
      [sin(ori_1st_to_2nd(:,1)/180*pi).*cos(ori_1st_to_2nd(:,2)/180*pi) ...
      sin(ori_1st_to_2nd(:,1)/180*pi).*sin(ori_1st_to_2nd(:,2)/180*pi) ...
      cos(ori_1st_to_2nd(:,1)/180*pi)];

      grad.coilpos(i+grad_nr,:) = [grad.coilpos(i,:)+ori_1st_to_2nd*baseline*100];
      grad.coilori(i+grad_nr,:) = -ori_1st;
  else % magnetometer
      ori_1st = [ch_info(ch_ind).data.zdir ch_info(ch_ind).data.xdir ];
      % polar to x,y,z coordinates
      ori_1st = ...
      [sin(ori_1st(:,1)/180*pi).*cos(ori_1st(:,2)/180*pi) ...
      sin(ori_1st(:,1)/180*pi).*sin(ori_1st(:,2)/180*pi) ...
      cos(ori_1st(:,1)/180*pi)];

      grad.coilori(i,:) = ori_1st;

      grad.coilpos(i+grad_nr,:) = [0 0 0];
      grad.coilori(i+grad_nr,:) = [0 0 0];
  end

  grad.chanori = grad.coilori(1:grad_nr,:);

end

% Define the pair of 1st and 2nd coils for each gradiometer
grad.tra = repmat(diag(ones(1,grad_nr),0),1,2);

% for mangetometers change tra as there is no second coil
for i = 1:grad_nr
  ch_ind = grad_ind(i);
  if ch_info(ch_ind).type==handles.MagnetoMeter
    grad.tra(i,grad_nr+i) = 0;
  end
end

% the gradiometer labels should be consistent with the channel labels in
% read_yokogawa_header, the predefined list of channel names in ft_senslabel
% and with ft_channelselection:
% but it is ONLY consistent with read_yokogawa_header as NO FIXED relation
% between channel index and type of channel exists for Yokogawa systems.
% Therefore all have individual label sequences: Support in ft_senslabel
% is only partial.
if ~isempty(label)
    grad.label = label(grad_ind)';
else
    % this is only backup, if something goes wrong above.
    label = cell(grad_nr,1);
    for i=1:length(label)
    label{i,1} = sprintf('AG%03d', i);
    end
    grad.label = label;
end
grad.unit = 'cm';


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% this defines some usefull constants
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function handles = definehandles
handles.output = [];
handles.sqd_load_flag = false;
handles.mri_load_flag = false;
handles.NullChannel         = 0;
handles.MagnetoMeter        = 1;
handles.AxialGradioMeter    = 2;
handles.PlannerGradioMeter  = 3;
handles.RefferenceChannelMark = hex2dec('0100');
handles.RefferenceMagnetoMeter       = bitor( handles.RefferenceChannelMark, handles.MagnetoMeter );
handles.RefferenceAxialGradioMeter   = bitor( handles.RefferenceChannelMark, handles.AxialGradioMeter );
handles.RefferencePlannerGradioMeter = bitor( handles.RefferenceChannelMark, handles.PlannerGradioMeter );
handles.TriggerChannel      = -1;
handles.EegChannel          = -2;
handles.EcgChannel          = -3;
handles.EtcChannel          = -4;
handles.NonMegChannelNameLength = 32;
handles.DefaultMagnetometerSize       = (4.0/1000.0);       % Square of 4.0mm in length
handles.DefaultAxialGradioMeterSize   = (15.5/1000.0);      % Circle of 15.5mm in diameter
handles.DefaultPlannerGradioMeterSize = (12.0/1000.0);      % Square of 12.0mm in length
handles.AcqTypeContinuousRaw = 1;
handles.AcqTypeEvokedAve     = 2;
handles.AcqTypeEvokedRaw     = 3;
handles.sqd = [];
handles.sqd.selected_start  = [];
handles.sqd.selected_end    = [];
handles.sqd.axialgradiometer_ch_no      = [];
handles.sqd.axialgradiometer_ch_info    = [];
handles.sqd.axialgradiometer_data       = [];
handles.sqd.plannergradiometer_ch_no    = [];
handles.sqd.plannergradiometer_ch_info  = [];
handles.sqd.plannergradiometer_data     = [];
handles.sqd.nullchannel_ch_no   = [];
handles.sqd.nullchannel_data    = [];
handles.sqd.selected_time       = [];
handles.sqd.sample_rate         = [];
handles.sqd.sample_count        = [];
handles.sqd.pretrigger_length   = [];
handles.sqd.matching_info   = [];
handles.sqd.source_info     = [];
handles.sqd.mri_info        = [];
handles.mri                 = [];
