Homec4science
Diffusion iCAPs public version 2 (master) Browse

iCAPs_v2/packages/spm12/external/mne/fiff_setup_read_raw.m
e5f5005bb2efmaster

Last Change
Raw File

fiff_setup_read_raw.m
View Options

function [data] = fiff_setup_read_raw(fname,allow_maxshield)
%
% [data] = fiff_setup_read_raw(fname,allow_maxshield)
%
% Read information about raw data file
%
% fname Name of the file to read
% allow_maxshield Accept unprocessed MaxShield data
%
%
% Author : Matti Hamalainen, MGH Martinos Center
% License : BSD 3-clause
%
% Revision 1.12 2009/03/30 11:37:37 msh
% Added copying of measurement info blocks from the original like in mne_browse_raw
%
% Revision 1.11 2008/09/30 17:22:39 msh
% Added possibility to load unprocessed MaxShield data
%
% Revision 1.10 2008/06/16 20:26:03 msh
% Added some semicolons to avoid unncessary output.
%
% Revision 1.9 2008/06/16 19:48:32 msh
% Added some comments
%
% Revision 1.8 2008/06/16 19:46:30 msh
% Fixed handling of initial skip so that the result is compatible with the event files
%
% Revision 1.7 2007/06/08 14:44:16 msh
% Fixed problem appearing with multiple skips in a data file
%
% Revision 1.6 2006/05/03 18:53:05 msh
% Approaching Matlab 6.5 backward compatibility
%
% Revision 1.5 2006/04/23 15:29:40 msh
% Added MGH to the copyright
%
% Revision 1.4 2006/04/21 16:17:48 msh
% Added handling of CTF compensation
%
% Revision 1.3 2006/04/21 14:23:16 msh
% Further improvements in raw data reading
%
% Revision 1.2 2006/04/21 11:33:18 msh
% Added raw segment reading routines
%
% 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_setup_read_raw';
if nargin ~= 1 && nargin ~= 2
error(me,'Incorrect number of arguments');
end
if nargin == 1
allow_maxshield = false;
end
%
% Open the file
%
%fprintf(1,'Opening raw data file %s...\n',fname);
[ fid, tree ] = fiff_open(fname);
%
% Read the measurement info
%
[ info, meas ] = fiff_read_meas_info(fid,tree);
%
% Locate the data of interest
%
raw = fiff_dir_tree_find(meas,FIFF.FIFFB_RAW_DATA);
if isempty(raw)
raw = fiff_dir_tree_find(meas,FIFF.FIFFB_CONTINUOUS_DATA);
end
%
% Special handling of data recorded with Internal Active Shielding
%
raw = fiff_dir_tree_find(meas,FIFF.FIFFB_RAW_DATA);
if isempty(raw)
raw = fiff_dir_tree_find(meas,FIFF.FIFFB_CONTINUOUS_DATA);
end
if isempty(raw) && allow_maxshield
raw = fiff_dir_tree_find(meas,FIFF.FIFFB_SMSH_RAW_DATA);
if ~isempty(raw)
disp([10 '--------' 10 ...
'WARNING: This file contains raw Internal Active Shielding data. It may be distorted.' 10 ...
'Elekta recommends it be run through MaxFilter to produce reliable results.' 10 ...
'Consider closing the file and running MaxFilter on the data.' 10 ...
'--------' 10]);
end
end
if isempty(raw)
error(me,'No raw data in file');
end
%
% Set up the output structure
%
info.filename = fname;
data.fid = fid;
data.info = info;
data.first_samp = 0;
data.last_samp = 0;
%
% Process the directory
%
dir = raw.dir;
nent = raw.nent;
nchan = info.nchan;
first = 1;
first_samp = 0;
first_skip = 0;
%
% Get first sample tag if it is there
%
if dir(first).kind == FIFF.FIFF_FIRST_SAMPLE
tag = fiff_read_tag(fid,dir(first).pos);
first_samp = tag.data;
first = first + 1;
end
%
% Omit initial skip
%
if dir(first).kind == FIFF.FIFF_DATA_SKIP
%
% This first skip can be applied only after we know the buffer size
%
tag = fiff_read_tag(fid,dir(first).pos);
first_skip = tag.data;
first = first + 1;
end
%
% Get first sample tag if it is there
%
if dir(first).kind == FIFF.FIFF_FIRST_SAMPLE
tag = fiff_read_tag(fid,dir(first).pos);
first_samp = first_samp + tag.data;
first = first + 1;
end
data.first_samp = first_samp;
%
% Go through the remaining tags in the directory
%
rawdir = struct('ent',{},'first',{},'last',{},'nsamp',{});
nskip = 0;
ndir = 0;
for k = first:nent
ent = dir(k);
if ent.kind == FIFF.FIFF_DATA_SKIP
tag = fiff_read_tag(fid,ent.pos);
nskip = tag.data;
elseif ent.kind == FIFF.FIFF_DATA_BUFFER
%
% Figure out the number of samples in this buffer
%
switch ent.type
case FIFF.FIFFT_DAU_PACK16
nsamp = ent.size/(2*nchan);
case FIFF.FIFFT_SHORT
nsamp = ent.size/(2*nchan);
case FIFF.FIFFT_FLOAT
nsamp = ent.size/(4*nchan);
case FIFF.FIFFT_INT
nsamp = ent.size/(4*nchan);
otherwise
fclose(fid);
error(me,'Cannot handle data buffers of type %d',ent.type);
end
%
% Do we have an initial skip pending?
%
if first_skip > 0
first_samp = first_samp + nsamp*first_skip;
data.first_samp = first_samp;
first_skip = 0;
end
%
% Do we have a skip pending?
%
if nskip > 0
ndir = ndir+1;
rawdir(ndir).ent = [];
rawdir(ndir).first = first_samp;
rawdir(ndir).last = first_samp + nskip*nsamp - 1;
rawdir(ndir).nsamp = nskip*nsamp;
first_samp = first_samp + nskip*nsamp;
nskip = 0;
end
%
% Add a data buffer
%
ndir = ndir+1;
rawdir(ndir).ent = ent;
rawdir(ndir).first = first_samp;
rawdir(ndir).last = first_samp + nsamp - 1;
rawdir(ndir).nsamp = nsamp;
first_samp = first_samp + nsamp;
end
end
data.last_samp = first_samp - 1;
%
% Add the calibration factors
%
cals = zeros(1,data.info.nchan);
for k = 1:data.info.nchan
cals(k) = data.info.chs(k).range*data.info.chs(k).cal;
end
%
data.cals = cals;
data.rawdir = rawdir;
data.proj = [];
data.comp = [];
%
fprintf(1,'\tRange : %d ... %d = %9.3f ... %9.3f secs\n',...
data.first_samp,data.last_samp,...
double(data.first_samp)/data.info.sfreq,...
double(data.last_samp)/data.info.sfreq);
%fprintf(1,'Ready.\n');
fclose(data.fid);
data.fid = -1;
return;
function [tag] = find_tag(node,findkind)
for p = 1:node.nent
kind = node.dir(p).kind;
pos = node.dir(p).pos;
if kind == findkind
tag = fiff_read_tag(fid,pos);
return;
end
end
tag = [];
return
end
end
c4science · Help