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iCAPs_v2/packages/spm12/external/mne/fiff_read_meas_info.m
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fiff_read_meas_info.m
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function [info,meas] = fiff_read_meas_info(source,tree)
%
% [info,meas] = fiff_read_meas_info(source,tree)
%
% Read the measurement info
%
% If tree is specified, source is assumed to be an open file id,
% otherwise a the name of the file to read. If tree is missing, the
% meas output argument should not be specified.
%
%
% Author : Matti Hamalainen, MGH Martinos Center
% License : BSD 3-clause
%
%
% Revision 1.14 2009/03/31 01:12:30 msh
% Improved ID handling
%
% Revision 1.13 2008/04/16 22:24:57 msh
% Added megacq parameters to the measurement info
%
% Revision 1.12 2008/03/13 19:18:06 msh
% Read and write FIFF_MEAS_DATE from/to FIFFB_MEAS_INFO as appropriate
%
% Revision 1.11 2007/11/13 10:55:32 msh
% Specify the second argument to all calls to the exist function
%
% Revision 1.10 2006/09/24 18:52:43 msh
% Added FIFFV_REF_MEG_CH to fiff_define_constants.
% Added coord_frame field to dig point structure.
%
% Revision 1.9 2006/09/08 19:27:13 msh
% Added KIT coil type to mne_load_coil_def
% Allow reading of measurement info by specifying just a file name.
%
% Revision 1.8 2006/04/23 15:29:40 msh
% Added MGH to the copyright
%
% Revision 1.7 2006/04/18 20:44:46 msh
% Added reading of forward solution.
% Use length instead of size when appropriate
%
% Revision 1.6 2006/04/14 15:49:49 msh
% Improved the channel selection code and added ch_names to measurement info.
%
% Revision 1.5 2006/04/13 23:09:46 msh
% Further streamlining of the coordinate transformations.
%
% Revision 1.4 2006/04/13 22:37:03 msh
% Added head_head_trans field to info.
%
% Revision 1.3 2006/04/13 17:05:45 msh
% Added reading of bad channels to fiff_read_meas_info.m
% Added mne_pick_channels_cov.m
%
% Revision 1.2 2006/04/12 10:29:02 msh
% Made evoked data writing compatible with the structures returned in reading.
%
% Revision 1.1 2006/04/10 23:26:54 msh
% Added fiff reading routines
%
%
global FIFF;
if isempty(FIFF)
FIFF = fiff_define_constants();
end
me='MNE:fiff_read_meas_info';
if nargin ~= 2 && nargin ~= 1
error(me,'Incorrect number of arguments');
end
if nargin == 1 && nargout == 2
error(me,'meas output argument is not allowed with file name specified');
end
if nargin == 1
[ fid, tree ] = fiff_open(source);
open_here = true;
else
fid = source;
open_here = false;
end
%
% Find the desired blocks
%
meas = fiff_dir_tree_find(tree,FIFF.FIFFB_MEAS);
if length(meas) == 0
if open_here
fclose(fid);
end
error(me,'Could not find measurement data');
end
%
meas_info = fiff_dir_tree_find(meas,FIFF.FIFFB_MEAS_INFO);
if length(meas_info) == 0
if open_here
fclose(fid);
end
error(me,'Could not find measurement info');
end
%
% Read measurement info
%
dev_head_t=[];
ctf_head_t=[];
meas_date=[];
p = 0;
for k = 1:meas_info.nent
kind = meas_info.dir(k).kind;
pos = meas_info.dir(k).pos;
switch kind
case FIFF.FIFF_NCHAN
tag = fiff_read_tag(fid,pos);
nchan = tag.data;
case FIFF.FIFF_SFREQ
tag = fiff_read_tag(fid,pos);
sfreq = tag.data;
case FIFF.FIFF_CH_INFO
p = p+1;
tag = fiff_read_tag(fid,pos);
chs(p) = tag.data;
case FIFF.FIFF_LOWPASS
tag = fiff_read_tag(fid,pos);
lowpass = tag.data;
case FIFF.FIFF_HIGHPASS
tag = fiff_read_tag(fid,pos);
highpass = tag.data;
case FIFF.FIFF_MEAS_DATE
tag = fiff_read_tag(fid,pos);
meas_date = tag.data;
case FIFF.FIFF_COORD_TRANS
tag = fiff_read_tag(fid,pos);
cand = tag.data;
if cand.from == FIFF.FIFFV_COORD_DEVICE && ...
cand.to == FIFF.FIFFV_COORD_HEAD
dev_head_t = cand;
elseif cand.from == FIFF.FIFFV_MNE_COORD_CTF_HEAD && ...
cand.to == FIFF.FIFFV_COORD_HEAD
ctf_head_t = cand;
elseif cand.from == FIFF.FIFFV_COORD_HEAD && ...
cand.to == FIFF.FIFFV_COORD_DEVICE
dev_head_t = fiff_invert_transform(cand);
end
end
end
%
% Check that we have everything we need
%
if ~exist('nchan','var')
if open_here
fclose(fid);
end
error(me,'Number of channels in not defined');
end
if ~exist('sfreq','var')
if open_here
fclose(fid);
end
error(me,'Sampling frequency is not defined');
end
if ~exist('chs','var')
if open_here
fclose(fid);
end
error(me,'Channel information not defined');
end
if length(chs) ~= nchan
if open_here
fclose(fid);
end
error(me,'Incorrect number of channel definitions found');
end
if isempty(dev_head_t) || isempty(ctf_head_t)
hpi_result = fiff_dir_tree_find(meas_info,FIFF.FIFFB_HPI_RESULT);
if length(hpi_result) == 1
for k = 1:hpi_result.nent
kind = hpi_result.dir(k).kind;
pos = hpi_result.dir(k).pos;
if kind == FIFF.FIFF_COORD_TRANS
tag = fiff_read_tag(fid,pos);
cand = tag.data;
if cand.from == FIFF.FIFFV_COORD_DEVICE && ...
cand.to == FIFF.FIFFV_COORD_HEAD
dev_head_t = cand;
elseif cand.from == FIFF.FIFFV_MNE_COORD_CTF_HEAD && ...
cand.to == FIFF.FIFFV_COORD_HEAD
ctf_head_t = cand;
end
end
end
end
end
%
% Locate the Polhemus data
%
isotrak = fiff_dir_tree_find(meas_info,FIFF.FIFFB_ISOTRAK);
dig=struct('kind',{},'ident',{},'r',{},'coord_frame',{});
coord_frame = FIFF.FIFFV_COORD_HEAD;
if length(isotrak) == 1
p = 0;
for k = 1:isotrak.nent
kind = isotrak.dir(k).kind;
pos = isotrak.dir(k).pos;
if kind == FIFF.FIFF_DIG_POINT
p = p + 1;
tag = fiff_read_tag(fid,pos);
dig(p) = tag.data;
else
if kind == FIFF.FIFF_MNE_COORD_FRAME
tag = fiff_read_tag(fid,pos);
coord_frame = tag.data;
elseif kind == FIFF.FIFF_COORD_TRANS
tag = fiff_read_tag(fid,pos);
dig_trans = tag.data;
end
end
end
end
for k = 1:length(dig)
dig(k).coord_frame = coord_frame;
end
if exist('dig_trans','var')
if (dig_trans.from ~= coord_frame && dig_trans.to ~= coord_frame)
clear('dig_trans');
end
end
%
% Locate the acquisition information
%
acqpars = fiff_dir_tree_find(meas_info,FIFF.FIFFB_DACQ_PARS);
acq_pars = [];
acq_stim = [];
if length(acqpars) == 1
for k = 1:acqpars.nent
kind = acqpars.dir(k).kind;
pos = acqpars.dir(k).pos;
if kind == FIFF.FIFF_DACQ_PARS
tag = fiff_read_tag(fid,pos);
acq_pars = tag.data;
else if kind == FIFF.FIFF_DACQ_STIM
tag = fiff_read_tag(fid,pos);
acq_stim = tag.data;
end
end
end
end
%
% Load the SSP data
%
projs = fiff_read_proj(fid,meas_info);
%
% Load the CTF compensation data
%
comps = fiff_read_ctf_comp(fid,meas_info,chs);
%
% Load the bad channel list
%
bads = fiff_read_bad_channels(fid,meas_info);
%
% Put the data together
%
if ~isempty(tree.id)
info.file_id = tree.id;
else
info.file_id = [];
end
%
% Make the most appropriate selection for the measurement id
%
if isempty(meas_info.parent_id)
if isempty(meas_info.id)
if isempty(meas.id)
if isempty(meas.parent_id)
info.meas_id = info.file_id;
else
info.meas_id = meas.parent_id;
end
else
info.meas_id = meas.id;
end
else
info.meas_id = meas_info.id;
end
else
info.meas_id = meas_info.parent_id;
end
if isempty(meas_date)
info.meas_date = [ info.meas_id.secs info.meas_id.usecs ];
else
info.meas_date = meas_date;
end
info.nchan = nchan;
info.sfreq = sfreq;
if exist('highpass','var')
info.highpass = highpass;
else
info.highpass = 0;
end
if exist('lowpass','var')
info.lowpass = lowpass;
else
info.lowpass = info.sfreq/2.0;
end
%
% Add the channel information and make a list of channel names
% for convenience
%
info.chs = chs;
for c = 1:info.nchan
info.ch_names{c} = info.chs(c).ch_name;
end
%
% Add the coordinate transformations
%
info.dev_head_t = dev_head_t;
info.ctf_head_t = ctf_head_t;
if ~isempty(info.dev_head_t) && ~isempty(info.ctf_head_t)
info.dev_ctf_t = info.dev_head_t;
info.dev_ctf_t.to = info.ctf_head_t.from;
info.dev_ctf_t.trans = inv(ctf_head_t.trans)*info.dev_ctf_t.trans;
else
info.dev_ctf_t = [];
end
%
% All kinds of auxliary stuff
%
info.dig = dig;
if exist('dig_trans','var')
info.dig_trans = dig_trans;
end
info.bads = bads;
info.projs = projs;
info.comps = comps;
info.acq_pars = acq_pars;
info.acq_stim = acq_stim;
if open_here
fclose(fid);
end
return;
function [tag] = find_tag(node,findkind)
for p = 1:node.nent
if node.dir(p).kind == findkind
tag = fiff_read_tag(fid,node.dir(p).pos);
return;
end
end
tag = [];
end
end
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