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ctf_resample.m
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ctf_resample.m
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function ctf = ctf_resample(folder,newFreq)
% ctf_resample - Resamples a CTF .ds folder to a different sampling rate.
%
% ctf = ctf_resample(folder,newFreq)
%
% The function modifies two files in the .ds folder:
%
% *.meg4 - the raw data
% *.res4 - the data resource file (essentially a header).
%
% This function calls the matlab resample function. There is also a
% -resample option in the ctf software command, newDs, but it does not
% specify the sample rate in Hz.
%
% INPUTS: folder (optional - brings up a file selector if not specified):
% This is the .ds folder containing both the .meg4 and the .res4
% files
% NEWFREQ: Frequency (in Hz) that you want to pretend the data were sampled
% at. This can be lower or higher than the actual sampling
% frequency.
% RETURNS: 'ctf': the ctf data structure (without the raw data): contains the new
% parameters for sample_rate etc
%
% $Revision: 1.1 $ $Date: 2009-01-30 03:49:27 $
%
% Copyright (C) 2003 Alex Wade wade@ski.org
%
% This program 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 2
% of the License, or (at your option) any later version.
%
% This program 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 this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
% Modified: 05/2003, Alex Wade wade@ski.org
% - Wrote it
% Not tested with pretrigger points or averaged data sets.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%--------------------------------------------------------------
ver = '$Revision: 1.1 $';
fprintf('\nCTF_RESAMPLE [v %s]\n',ver(11:15)); tic;
% Populate the 'ctf' data structure
if exist('folder','var')
if(~isempty(folder))
ctf = ctf_read_meg4(folder,[],[],[0 0]); % Read in no actual data
else
ctf = ctf_read_meg4([],[],[],[0 0]); %
end
else
ctf = ctf_read_meg4([],[],[],[0 0]); %
end
if ~exist('COEFS','var'),
COEFS = false;
end
if ~exist('folder','var'),
if ~exist('ctf','var'),
ctf = ctf_folder;
else
ctf = ctf_folder([],ctf);
end
else
if ~exist('ctf','var'),
ctf = ctf_folder(folder);
else
ctf = ctf_folder(folder,ctf);
end
end
if ~isfield(ctf,'setup'),
ctf = ctf_read_res4(ctf.folder,1,COEFS);
end
% RESAMPLING GOES HERE...
% A typical ctf data structure looks like...
% folder: [1x97 char]
% res4: [1x1 struct]
% setup: [1x1 struct]
% sensor: [1x1 struct]
% meg4: [1x1 struct]
% data: [294000x275 double]
% The fields to change are:
% ctf.setup.sample_rate
% ctf.setup.number_samples
% ctf.setup.sample_sec
% ctf.setup.sample_msec
% ctf.setup.pretrigger_samples (if there were any)
% ctf.setup.run_description (to append the fact that we've resampled the
% data)
%
%
oldFreq = ctf.setup.sample_rate;
nChannels = ctf.setup.number_channels;
nPoints = ctf.setup.sample_rate * ctf.setup.duration_trial;
nTrials = ctf.setup.number_trials;
newNPoints = round(nPoints * newFreq / oldFreq); % This should match 'resample's idea of the new number of points
ctf.setup.sample_rate = newFreq;
ctf.setup.number_samples = newNPoints;
ctf.setup.sample_sec = (ctf.setup.sample_sec * oldFreq / newFreq);
ctf.setup.sample_msec = ctf.setup.sample_sec * 1000;
ctf.setup.pretrigger_samples = round(ctf.setup.pretrigger_samples * newFreq / oldFreq);
% When we write out the meg4 file, we will just skip the first 8 bytes (the
% header 'MEG41CP'+13? and then start fwriting (signed) 4-byte integers
% ('int32')
fidOld = fopen(ctf.meg4.file,'rb+','s'); % 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
fidNew = fopen([ctf.meg4.file,'.resamp'],'wb','s');
% ordering and 64 bit long data type.
if (fidOld<0)
error('Could not open meg4 file for reading - does it exist?');
end
if (fidNew<0)
fclose(fidOld);
error('Could not open new meg4 file for writing - check file permissions');
end
disp('Copying header');
header=fread(fidOld,8,'char'); % Start writing at the 9th byte (first 8 are the header)
cnt=fwrite(fidNew,header,'char');
if (cnt~=8)
fclose(fidOld);
fclose(fidNew);
error('Failed to write to the new meg4 file.');
end
% Loop over trials and channels
disp('Resampling...');
h=waitbar(0,'Resampling');
% Resample will work on the columns of a data matrix. But it runs out of
% memory if we try to process the whole thing at once. So we will do it
% channel by channel at the same time that we write it out...
for thisTrial = 1:nTrials
for thisChannel = 1:nChannels
% Do resampling on raw data from disk - not stuff stored in
% ctf.data. Avoids any messing around with channel gains...
origData = fread(fidOld,nPoints,'int32');
% Using the default matlab resamp params.
newDataVector = round((resample(double(origData),newFreq,oldFreq)));
cnt = fwrite(fidNew,newDataVector,'int32');
if (cnt ~= newNPoints) % Check for write success
disp(cnt);
disp(newNPoints);
fclose(fidNew);
error('Failed to write all the data - check to see if the disk is full and whether you have the correct permissions');
end
waitbar(thisChannel/nChannels);
end
end
close(h); % Close the progress bar
% Close the files
fclose(fidOld);
fclose(fidNew);
fprintf('\nDone meg4\n');
% Finished writing the raw data....
% Now create a new .res4 file.
fidOld = fopen(ctf.res4.file,'rb','ieee-be.l64');
fidNew = fopen([ctf.res4.file,'.resamp'],'wb','ieee-be.l64');
if fidOld < 0, error('cannot open original.res4 file'); end
if fidNew < 0
fclose(fidOld);
error('Cannot open temp.res4 file');
end
% Copy the first set of data from the file
buff = fread(fidOld,1288,'uint8');
cnt = fwrite(fidNew,buff,'uint8');
if (cnt ~= length(buff))
fclose(fidOld);
fclose(fidNew);
error('Failed to write to the new res4 file.');
end
%---NUMBER OF SAMPLES
dummy = fread(fidOld,1,'int32');
cnt = fwrite(fidNew,ctf.setup.number_samples,'int32');
% Only check writing once
if (cnt~=1)
fclose(fidOld);
fclose(fidNew);
error('Failed to write to the new res4 file.');
end
%---SAMPLE RATE
% Copy next 4 bytes
buff = fread(fidOld,4,'uint8');
cnt = fwrite(fidNew,buff,'uint8');
if (cnt ~= length(buff))
fclose(fidOld);
fclose(fidNew);
error('Failed to write to the new res4 file.');
end
dummy = fread(fidOld,1,'double');
cnt = fwrite(fidNew,ctf.setup.sample_rate,'double');
if (cnt ~= 1)
fclose(fidOld);
fclose(fidNew);
error('Failed to write to the new res4 file.');
end
% copy next 16 bytes
buff = fread(fidOld,16,'uint8');
cnt = fwrite(fidNew,buff,'uint8');
if (cnt ~= length(buff))
fclose(fidOld);
fclose(fidNew);
error('Failed to write to the new res4 file.');
end
%---PRETRIGGER POINTS
cnt = fwrite(fidNew,ctf.setup.pretrigger_samples,'int32');
if (cnt ~= 1)
fclose(fidOld);
fclose(fidNew);
error('Failed to write to the new res4 file.');
end
dummy = fread(fidOld,1,'int32');
buff = fread(fidOld,inf,'uint8');
cnt = fwrite(fidNew,buff,'uint8');
if (cnt ~= length(buff))
fclose(fidOld);
fclose(fidNew);
error('Failed to write to the new res4 file.');
end
fclose(fidOld);
fclose(fidNew);
return