function [data, mri, sourcemodel] = nutmeg2fieldtrip(cfg, fileorstruct)

% NUTMEG2FIELDTRIP converts from NUTMEG either a sensor data structure

% ('nuts') to a valid FieldTrip 'raw' structure (plus 'sourcemodel' and

% 'mri' if available), OR a source structure ('beam') to a valid FieldTrip

% source structure.

%

% Use as

% [data, mri, sourcemodel] = nutmeg2fieldtrip(cfg, fileorstruct)

%

% Input:

% cfg

% .keepmri (required for either input): =1 calls ft_read_mri for 'mri' output; =0 not save out 'mri'

% .out (required for source input): 's' (pos_freq_time) or 'trial' (pos_rpt)

% fileorstruct: may be one of following:

% 1) *.mat file containing nuts sensor structure

% 2) nuts sensor structure

% 3) s*.mat file containing beam source structure

% 4) beam source structure (output from Nutmeg (beamforming_gui, tfbf, or tfZ)

% (only scalar not vector results supported at the moment)

%

% Output: depending on input, one of options

% 1) If nuts sensor structure input, then 'data' will be 'raw' and

% optionally 'sourcemodel' if Lp present, or 'mri' if individual MRI present

% 2) If beam source structure input, then 'data' will be 'source'

% (May be an array of source structures (source{1} etc))

% 'sourcemodel' and 'mri' may be output as well if present in beam structure

%

% See alo FT_DATATYPE_RAW, FT_DATATYPE_SOURCE, LORETA2FIELDTRIP, SPASS2FIELDTRIP,

% FIELDTRIP2SPSS

% Copyright (C) 2011, Johanna Zumer

%

% 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/>.

%

% $Id$

% these are used by the ft_preamble/ft_postamble function and scripts

ft_revision = '$Id$';

ft_nargin = nargin;

ft_nargout = nargout;

% do the general setup of the function

ft_defaults

ft_preamble init

ft_preamble debug

ft_preamble provenance

if ~isstruct(fileorstruct) && exist(fileorstruct,'file')

structin=load(fileorstruct);

elseif isstruct(fileorstruct)

structin=fileorstruct;

elseif ~isstruct(fileorstruct)

ft_error('please enter either a structure (beam or nuts) or filename containing either beam or nuts')

end

clear fileorstruct

if isfield(structin,'meg')

nutsorbeam=1;

elseif isfield(structin,'nuts')

structin=structin.nuts;

nutsorbeam=1;

elseif isfield(structin,'s')

nutsorbeam=2;

elseif isfield(structin,'sa')

structin=nut_beam_legacy_compatibility(structin);

nutsorbeam=2;

elseif isfield(structin,'beam')

structin=structin.beam;

if isfield(structin,'sa')

structin=nut_beam_legacy_compatibility(structin);

end

nutsorbeam=2;

else

ft_error('not sure of the input type. maybe you need to call nut_beam_legacy_compatibility?')

end

if cfg.keepmri

mri=ft_read_mri(structin.coreg.mripath);

if isfield(mri,'transform')

mri.transform=0.1*structin.coreg.meg2mri_tfm*mri.transform; % now .transform goes from MRI voxel to MEG cm, and matches .pos

else

% not yet sure what to do with lack of mri.transform

end

else

mri=[];

end

if isfield(structin,'voxels')

sourcemodel.pos=0.1*structin.voxels; % NM in CTF mm, FT in cm

sourcemodel.unit='cm';

sourcemodel.inside=1:size(structin.voxels,1);

sourcemodel.outside=[];

end

if isfield(structin,'Lp')

for kk=1:size(structin.Lp,3)

sourcemodel.leadfield{kk}=structin.Lp(:,:,kk);

end

end

if isfield(structin,'W')

sourcemodel.filter=structin.W;

end

if nutsorbeam==1

for kk=1:size(structin.meg.data,3)

raw.trial{kk}=structin.meg.data(:,:,kk)';

raw.time{kk}=0.001*structin.meg.latency';

end

raw.label=structin.meg.sensor_labels;

raw.grad.label=structin.meg.sensor_labels;

if isfield(structin.meg,'refSensorOrient')

raw.grad.coilori=[structin.meg.sensorOrient; structin.meg.refSensorOrient];

raw.grad.coilpos=[structin.meg.sensorCoord; structin.meg.refSensorCoord];

else

raw.grad.coilori=[structin.meg.sensorOrient];

raw.grad.coilpos=[structin.meg.sensorCoord];

end

if size(raw.grad.coilori,1)<2*size(structin.meg.data,2)

raw.grad.coilori=cat(1,raw.grad.coilori,raw.grad.coilori);

end

raw.grad.coilpos=reshape(permute(raw.grad.coilpos,[1 3 2]),size(raw.grad.coilpos,1)*size(raw.grad.coilpos,3),size(raw.grad.coilpos,2));

if isfield(structin.meg,'chanmixMtx')

raw.grad.tra=structin.meg.chanmixMtx{1};

else

raw.grad.tra=zeros(size(structin.meg.data,2),2*size(structin.meg.data,2)+size(structin.meg.refSensorCoord,1));

raw.grad.tra(:,1:size(structin.meg.data,2))=eye(size(structin.meg.data,2));

raw.grad.tra(:,size(structin.meg.data,2)+1:2*size(structin.meg.data,2))=eye(size(structin.meg.data,2));

raw.grad.tra(:,2*size(structin.meg.data,2)+1:end)=structin.meg.Gcoef;

ft_warning('FIXME: should Gcoef be added regardless of structin.meg.grad_order?')

end

if structin.meg.grad_order==0

raw.grad.balance.current='none';

elseif structin.meg.grad_order==1

raw.grad.balance.current='G1BR';

elseif structin.meg.grad_order==2

raw.grad.balance.current='G2BR';

elseif structin.meg.grad_order==3

raw.grad.balance.current='G3BR';

end

raw.headmodel.o = structin.meg.lsc; % note this may include reference channels. may need to do str_match of lsc_sensor_labels with sensor_labels?

data=raw;

clear raw

elseif nutsorbeam==2

cfg.ftsource='old'; % 'old' way of source structure in FT

tmp.pos=0.1*structin.voxels; % NM in CTF mm, FT in cm

tmp.inside=1:size(structin.voxels,1);

tmp.outside=[];

if strcmp(cfg.out,'s')

if isfield(structin,'bands')

tmp.freq=mean(structin.bands'); % center of each band.

end

if isfield(structin,'timepts')

tmp.time=0.001*structin.timepts'; % NM in ms, FT in s

end

if strcmp(cfg.ftsource,'old')

% must have separate outputs per freq band

if size(structin.s{1},4)==1

for ii=1:size(structin.s,2)

for jj=1:size(structin.s{1},3)

source{ii,jj}=tmp;

source{ii,jj}.freq=source{ii,jj}.freq(jj);

for vv=1:size(structin.s{ii},1)

source{ii,jj}.avg(vv).pow=structin.s{ii}(vv,:,jj);

end

end

end

elseif size(structin.s{1},4)>1

for ii=1:size(structin.s,2)

source{ii}=tmp;

for kk=1:size(structin.s{ii},4)

for vv=1:size(structin.s{ii},1)

source{ii}.avg(vv).mom(kk,:)=structin.s{ii}(vv,:,1,kk);

end

end

end

end

elseif strcmp(cfg.ftsource,'new')

if size(structin.s{1},2)>1 && size(structin.s{1},3)>1

tmp.powdimord='pos_freq_time'; % FIXME is this valid dimord?

elseif size(structin.s{1},3)>1

tmp.powdimord='pos_freq';

elseif size(structin.s{1},4)>1

tmp.powdimord='pos_ori_time';

elseif size(structin.s{1},2)>1

tmp.powdimord='pos_time';

else

tmp.powdimord='pos';

end

if size(structin.s{1},2)>1

if size(structin.s{1},4)==1

for ii=1:size(structin.s,2)

source{ii}=tmp;

source{ii}.pow=squeeze(permute(structin.s{ii},[1 3 2]));

end

elseif size(structin.s{1},4)==1

for ii=1:size(structin.s,2)

source{ii}=tmp;

source{ii}.pow=squeeze(permute(structin.s{ii},[1 4 3 2]));

end

end

end

end

elseif strcmp(cfg.out,'trial')

if isfield(structin,'trial') % from tfZ keeptrials='yes'

for ii=1:size(structin.trial,2)

source{ii}=tmp;

if strcmp(cfg.ftsource,'old')

for jj=1:size(structin.trial{ii},2)

source{ii}.trial(jj).pow=structin.trial{ii}(:,jj);

end

elseif strcmp(cfg.ftsource,'new')

source{ii}.powdimord='pos_rpt'; % FIXME is this a valid field?

source{ii}.pow=structin.trial{ii};

end

end

end

else

ft_error('not a valid cfg.out specified');

end

data=source;

clear source

end

% do the general cleanup and bookkeeping at the end of the function

ft_postamble debug

ft_postamble provenance

% save the output cfg in all three output data structures

ft_postamble history data

ft_postamble history mri

ft_postamble history sourcemodel