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iCAPs/packages/spm12/external/mne/mne_ex_read_epochs.m
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mne_ex_read_epochs.m
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function [data,times,ch_names] = mne_ex_read_epochs(fname,event,eventname,tmin,tmax)
%
% Example of reading raw data
%
% [ data, times, ch_names ] = mne_ex_read_epochs(fname,event,eventname,tmin,tmax)
%
% Input :
%
% fname - The name of the input file
% event - The event
% eventname - Name of the event file
% tmin - Starting time in seconds
% tmax - Ending time in seconds
%
% Output :
%
% data - Array of structures corresponding to the epochs with fields:
%
% epoch the epoch, channel by channel
% event event #
% tmin starting time in the raw data file (initial skip omitted)
% tmax ending stime in the raw data file (initial skip omitted)
%
% times - The time points of the samples, in seconds
% ch_names - Names of the channels included
%
%
% NOTE 1: The purpose of this function is to demonstrate the raw data reading
% routines. You may need to modify this for your purposes
%
% NOTE 2: You need to run mne_process_raw once as
%
% mne_process_raw --raw <fname> --projoff
%
% to create the fif-format event file (or open the file in mne_browse_raw).
%
%
% Author : Matti Hamalainen, MGH Martinos Center
% License : BSD 3-clause
%
% Revision 1.7 2009/03/21 00:17:35 msh
% Added one missing semicolon.
%
% Revision 1.6 2009/03/12 17:59:06 msh
% Included channel names were not picked.
%
% Revision 1.5 2009/01/27 22:02:17 msh
% Added some more diagnostic output
%
% Revision 1.4 2009/01/27 21:55:44 msh
% Fixed error in reading a text event file with negative sample numbers.
% The conversion from time to event numbers was not correctly done.
%
% Revision 1.3 2009/01/12 20:30:16 msh
% Improved the comments
%
% Revision 1.2 2009/01/10 18:21:26 msh
% Added an option to specify the event file
% Changed the format of the output data
%
% Revision 1.1 2008/10/10 16:13:57 msh
% Added mne_ex_read_epochs. Fixed help text of mne_write_cov_file.m
%
%
%
% Fiddle with the arguments
%
me='MNE:mne_ex_read_epochs';
keep_comp = false;
dest_comp = 0;
pick_all = true;
if nargin ~= 5
error(me,'Incorrect number of arguments');
end
%
% Setup for reading the raw data
%
try
raw = fiff_setup_read_raw(fname);
catch
error(me,'%s',mne_omit_first_line(lasterr));
end
if pick_all
%
% Pick all
%
picks = 1:raw.info.nchan;
%
else
%
% Set up pick list: MEG + STI 014 - bad channels (modify to your needs)
%
include{1} = 'STI 014';
want_meg = true;
want_eeg = false;
want_stim = false;
%
%
picks = fiff_pick_types(raw.info,want_meg,want_eeg,want_stim,include,raw.info.bads);
end
ch_names = raw.info.ch_names(picks);
%
% Set up projection
%
if isempty(raw.info.projs)
fprintf(1,'No projector specified for these data\n');
raw.proj = [];
else
%
% Activate the projection items
%
for k = 1:length(raw.info.projs)
raw.info.projs(k).active = true;
end
fprintf(1,'%d projection items activated\n',length(raw.info.projs));
%
% Create the projector
%
[proj,nproj] = mne_make_projector_info(raw.info);
if nproj == 0
fprintf(1,'The projection vectors do not apply to these channels\n');
raw.proj = [];
else
fprintf(1,'Created an SSP operator (subspace dimension = %d)\n',nproj);
raw.proj = proj;
end
end
%
% Set up the CTF compensator
%
current_comp = mne_get_current_comp(raw.info);
if current_comp > 0
fprintf(1,'Current compensation grade : %d\n',current_comp);
end
if keep_comp
dest_comp = current_comp;
end
if current_comp ~= dest_comp
try
raw.comp = mne_make_compensator(raw.info,current_comp,dest_comp);
fprintf(1,'Appropriate compensator added to change to grade %d.\n',dest_comp);
catch
error(me,'%s',mne_omit_first_line(lasterr));
end
end
%
% Read the events
%
if isempty(eventname)
p = strfind(fname,'.fif');
if p > 1
eventname = sprintf('%s-eve.fif',fname(1:p-1));
else
error(me,'Raw file name does not end properly');
end
events = mne_read_events(eventname);
fprintf(1,'Events read from %s\n',eventname);
else
%
% Binary file
%
p = strfind(eventname,'-eve.fif');
if p > 1
try
events = mne_read_events(eventname);
catch
error(me,mne_omit_first_line(lasterr));
end
fprintf(1,'Binary event file %s read\n',eventname);
else
%
% Text file
%
try
events = load(eventname);
catch
error(me,mne_omit_first_line(lasterr));
end
if size(events,1) < 1
error(me,'No data in the event file');
end
%
% Convert time to samples if sample number is negative
%
for p = 1:size(events,1)
if events(p,1) < 0
events(p,1) = events(p,2)*raw.info.sfreq;
end
end
%
% Select the columns of interest (convert to integers)
%
events = int32(events(:,[1 3 4]));
%
% New format?
%
if events(1,2) == 0 && events(1,3) == 0
fprintf(1,'The text event file %s is in the new format\n',eventname);
if events(1,1) ~= raw.first_samp
error(me,'This new format event file is not compatible with the raw data');
end
else
fprintf(1,'The text event file %s is in the old format\n',eventname);
%
% Offset with first sample
%
events(:,1) = events(:,1) + raw.first_samp;
end
end
end
%
% Select the desired events
%
count = 0;
selected = [];
for p = 1:size(events,1)
if events(p,2) == 0 && events(p,3) == event
count = count + 1;
selected = [ selected p];
end
end
if count > 0
fprintf(1,'%d matching events found\n',count);
else
error(me,'No desired events found.');
end
for p = 1:count
%
% Read a data segment
%
event_samp = events(selected(p),1);
from = event_samp + tmin*raw.info.sfreq;
to = event_samp + tmax*raw.info.sfreq;
try
if p == 1
[ epoch ] = fiff_read_raw_segment(raw,from,to,picks);
times = double([(int32(from)-int32(event_samp)):(int32(to)-int32(event_samp))])/raw.info.sfreq;
else
[ epoch ] = fiff_read_raw_segment(raw,from,to,picks);
end
data(p).epoch = epoch;
data(p).event = event;
data(p).tmin = (double(from)-double(raw.first_samp))/raw.info.sfreq;
data(p).tmax = (double(to)-double(raw.first_samp))/raw.info.sfreq;
catch
fclose(raw.fid);
error(me,'%s',mne_omit_first_line(lasterr));
end
end
fprintf(1,'Read %d epochs, %d samples each.\n',count,length(data(1).epoch));
return;
end
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