ISI_read.m

function [ISIdata] = ISI_read(prmts)
% ISI_READ  Load ISI data
% Load trials from binary file generated by LabView IOS application.
%
% Notes on use:
%  If function reports an Out of Memory error, try enabling pixel binning
%  to reduce memory usage when the function runs.
%

% Changelog:
%  03/01/11 Modified from Pablo's code, engineered to match the output of
%           ISI_recordframes_piezo.vi. All data formats should be in 
%           little-endian. Linux may not read 8 byte spacers correctly.
%           Also converts int16 data to single, instead of double. MP
%  02/02/12 Modified to allow pixel binning during file read. PMK
%  02/10/12 Fixed reading files on Linux. PMK
%  03/26/12 Fixed reading files with non-integer trial durations. PMK
%

% Open file
ISIdata = [];
sFilepath = fullfile(prmts.path2dir, prmts.name);
fid = fopen(sFilepath);
if fid == -1
    error(['Failed to open ' sFilepath]);
    return
end

% Get file size
fseek(fid, 0, 'eof');
nFileSize = ftell(fid);

% Return file position indicator to start of file
fseek(fid, 0, 'bof');

% Get file headers
thestarttime = fread(fid,4,'int32');
size_x = fread(fid, 1, 'int16');
size_y = fread(fid, 1, 'int16');
frame_rate = fread(fid,1,'int16');
bin_duration = fread(fid,1,'int16');

% Read trial duration
nsec = fread(fid,1,'uint16');
bit_depth1 = fread(fid,1,'int16');
fpos = ftell(fid);
ntrials = fread(fid,1,'int32');
%nFramesPerTrial = nsec*(frame_rate/bin_duration);
bin_duration_sec = bin_duration / frame_rate;
if ~isempty(prmts.Trials2Use)
    trial_range = sprintf('[%d %d]', prmts.Trials2Use(1), prmts.Trials2Use(end));
else
    trial_range = sprintf('[0 %d]', ntrials);
end

% Estimate frames/trial from file filesize and known header sizes
nFrameSize = size_x * size_y * 2; % bytes
nHeaderSize = 20 + (ntrials * 47); % each trial has headers of 47 bytes
nFramesPerTrial = int32((nFileSize-nHeaderSize) / nFrameSize / ntrials);

% Print file into to prompt
fprintf('\nFilename:\t\t%s\nTrials:\t\t\t%d\nFrame Rate:\t\t%d frames/s\nBin Duration:\t%d frames / %.2f s\nFrame Size:\t\t%dx%d px\nFrames/trial:\t%d\nBit Depth:\t\t%d\nTrial Duration:\t%d s\nTrials Used:\t%s\n',...
    prmts.name, ntrials, frame_rate, bin_duration, bin_duration_sec, size_x,size_y,nFramesPerTrial,bit_depth1,nsec,trial_range);

% Check that frames/trial estimate is consistent with header information
% Note: These numbers WILL deviate if the trial duration is non-integer.
%       In these cases, we will issue a warning to prompt.
if nFramesPerTrial ~= [nsec*(frame_rate/bin_duration)]
    disp(sprintf('Warning: Frames/trial estimated from filesize (%.0f) is different from that retrieved from file headers (%d)', nFramesPerTrial, nsec*(frame_rate/bin_duration)))
end

if ~prmts.DoLoad
    return
end

fseek(fid, 25-4, 0);

hFig = findobj('Tag', 'ISIanalysisGUI_fig'); % ensure function can stil be run w/o GUI
hWait = waitbar(0,'Loading frames...', 'visible', 'off');
if ~isempty(hFig)
    centerfig(hWait, hFig);
end
set(hWait, 'visible', 'on')

try % may fail with Out of Memory error if file is large
    ISIdata.frameStack = cell(ntrials,(nsec*(frame_rate/bin_duration)));
catch mExcep
    warndlg('Failed to load datafile. This file may be too large. Although all analysis methods require the entire file to be loaded into memory, you may still process this file with any of the available plug-in scripts.');
    close(hWait)
    return
end

size(ISIdata.frameStack);
for k = 1:ntrials
    % Read trial header
    intcheck = fread(fid,1,'int32');        % should be -9999
    if intcheck ~= -9999
        warning('intcheck does not return -9999 in ISI_read.m. Entering debugging mode.')
        keyboard
    end
    trial = fread(fid,1,'uint32');          % trial #, starting with 0
    stimnum = fread(fid,1,'int32');
    if isunix
        trial_times = fread(fid,24,'signed char');   % On Windows, specifying 'char' works, but not on Linux
    else
        trial_times = fread(fid,24,'char');   % On Windows, specifying 'char' works
    end
    fseek(fid, 25, 0);
    fseek(fid, -8, 0); % back up by 4 int16 because not writing array size, like earlier version.

    %for m = 1:((1/bin_duration_sec)*nsec)
    for m = 1:nFramesPerTrial
        mFrame = single([]);
        mFrame = single(fread(fid, [size_x size_y], prmts.precision));

        % Bin pixels
        if isfield(prmts, 'imgBin')
            if prod(prmts.imgBin) > 1
                mFrame = downsamp2d(mFrame, prmts.imgBin);
            end
        end
        
        % Assign 
        ISIdata.frameStack{k,m} = single([]);
        ISIdata.frameStack{k,m} = mFrame;
    end
    if ishandle(hWait)
        waitbar(k/ntrials, hWait)
    else
        error('File read aborted.');
    end
end

% Check that we have read the correct number of frames by verifying that
% we are at the end-of-file.
if nFileSize ~= ftell(fid)
    disp('Warning: Not all file data was read!')
end

close(hWait)
fclose(fid);

% Store parameters relevant for further analysis
ISIdata.ntrials = ntrials;
ISIdata.nsec = nsec;
ISIdata.frame_rate = frame_rate;
ISIdata.bin_duration = bin_duration;
ISIdata.nFramesPerTrial = nFramesPerTrial;

% Frame size
ISIdata.frameSizeYX = [size_y size_x];
if isfield(prmts, 'imgBin')
    if prod(prmts.imgBin) > 1
        ISIdata.frameSizeYX = ISIdata.frameSizeYX ./ prmts.imgBin;
    end
end

ISIdata.nPreStimFrames = (frame_rate./bin_duration) * prmts.preStimDurSec;
ISIdata.nStimFrames = (frame_rate./bin_duration) * prmts.stimDurSec;
ISIdata.nPostStimFrames = nFramesPerTrial - (ISIdata.nPreStimFrames + ISIdata.nStimFrames);

return