measureDrift.m

function drift = measureDrift(pathDir, fileIndex);

startFileIndex = fileIndex(1); % Which file in the directory list do we start with?
endFileIndex   = fileIndex(2); % Which file in the directory list do we end with?

% Open a series of files, channel by channel
chNum        = 38;
freqSampling = 19530 ;
samplesPerChunk = chNum*freqSampling*30;
badChannels = 4;

%% Define Filters
% LFP filter
% orderButter     = 2;
% ftype           = 'bandpass';
% freqLow         = 0.5;
% freqHigh        = 100;
% Wn              = [2*freqLow/freqSampling 2*freqHigh/freqSampling];
% [z, p, k]       = butter(orderButter,Wn,ftype);
% [sos,g]         = zp2sos(z,p,k);
% bandPassFilter  = dfilt.df2sos(sos,g);
% [b_LFP,a_LFP]   = sos2tf(sos,g);
% 
% % Spike filter
% orderButter  = 4;
% ftype        = 'high';
% freqLow      = 300;
% Wn           = [2*freqLow/freqSampling];
% 
% [z, p, k]    = butter(orderButter,Wn,ftype);
% [sos,g]      = zp2sos(z,p,k);
% bandPassFilter = dfilt.df2sos(sos,g);
% [b,a]          = sos2tf(sos,g);

%% Map Electrodes
% 
% IntanToNeuralynx = [32 30 31 28 29 26 27 24 25 22 23 21 20 19 18 17 11  9  7  5  3  1  2  4  6  8 10 12 13 14 15 16]; %First channel (as in the files) from SGL to the Probes
% %AndrewTo32x1     = [17 16 18 15 19 14 20 13 21 12 22 11 23 10 24  9 25  8 26  7 27  6 28  5 29  4 30  3 31  2 32  1]; % Electrode numbering in Probes to my reference (1 at top, 16 bottom)
% Buz32ToIntan     = [1 8 2 7 3 6 4 5 9 16 10 15 11 14 12 13 17 24 18 23 19 22 20 21 25 32 26 31 27 30 28 29]; % Electrode numbering in Probes to my reference (1 at top, 16 bottom)
% 
% 
% for i=1:32,
%     IntanToBuz32(i) = find (IntanToNeuralynx == Buz32ToIntan(i));
%     InverseIntanToBuz32 (find (IntanToNeuralynx == Buz32ToIntan(i))) = i;
% end
% 

%% Reading

%pathDir    = '/Lab/Silicon/ANM144443/110811/';
d          = dir([pathDir '*DG*']);
fileList   = cell(length(d),1);
for i = 1:length(d);
    fileList{i}=d(i).name;
end
%startFileIndex = 1; % Which file in the directory list do we start with?
%endFileIndex   = 266; % Which file in the directory list do we end with?

%% Create initial timestamp
% Timestamps are uint32, starting with the hour/minute/second of the first
% file processed
% timestamp of the first timepoint in the first file
% timestamps are initialized based on the modification time of each .bin
% file. If the recordings finish and end less than 1 second apart,
% timestamps may overlap, breaking the code.

initialtime=datevec(d(startFileIndex).date)
initialtime=uint32((initialtime(4)*60*60+initialtime(5)*60+initialtime(6))*freqSampling) % convert first file timestamp to uint32 stamp
spkdata=[]

for fnum = startFileIndex:endFileIndex%1:length(d);
    tic
    fid = fopen([pathDir fileList{fnum}],'r');


    % Read data from file, minute by minute
    fileChunks = ceil(d(fnum).bytes/(samplesPerChunk*2));  % How many reads of the file do we do?

    for i = 1:fileChunks 
        display(['Reading ' d(fnum).name ' / Chunk ' num2str(i)])
        fid      = fopen([pathDir fileList{fnum}],'r');
        fileTime = datevec(d(fnum).date);
        fileTime = uint32((fileTime(4)*60*60+fileTime(5)*60+fileTime(6))*freqSampling); % convert file timestamp to uint32 stamp

        % set readpoint of file
        startPointer = (i-1)*(samplesPerChunk)*2;     
        fileStatus   = fseek(fid,startPointer,-1);  

        if startPointer + (samplesPerChunk)*2 < d(fnum).bytes;
            matrixRaw = fread(fid,samplesPerChunk,'uint16'); % Read a full chunk
        else
        matrixRaw = fread(fid,samplesPerChunk,'uint16'); % Read till file end
        end
        
    end

    st=fclose('all');

    matrixVol=double(10*(matrixRaw-(sign(matrixRaw-2^15)+1)*2^15)/2^16); % Convert to doubles and scale voltage
    clear matrixRaw
    ch=reshape(matrixVol,chNum,size(matrixVol,1)/chNum)';
    clear matrixVol
    
    %drift.frameTriggers{fnum} = ch(:,34);
    %drift.fileTime{fnum} = fileTime;
    
    drift{fnum}.first = find(ch(:,34) > 4.5,1,'first');
    drift{fnum}.last = find(ch(:,34) > 4.5,1,'last');
    
    
end