jksbxread.m

function x = jksbxread(fname,k,N,varargin)

% img = sbxread(fname,k,N,varargin)
%
% Reads from frame k to k+N-1 in file fname
% 
% fname - the file name (e.g., 'xx0_000_001')
% k     - the index of the first frame to be read.  The first index is 0.
% N     - the number of consecutive frames to read starting with k.
%
% If N>1 it returns a 4D array of size = [#pmt rows cols N] 
% If N=1 it returns a 3D array of size = [#pmt rows cols]
%
% #pmts is the number of pmt channels being sampled (1 or 2)
% rows is the number of lines in the image
% cols is the number of pixels in each line
%
%
% The function also creates a global 'info' variable with additional
% informationi about the file

% sbxread not working, not reading anything... 02/23/16 info.fid NOT
% defined, even though there was info_loaded defined.


% global info_loaded info
global info

load(fname);
    
if(exist([fname ,'.align'])) % aligned?
    info.aligned = load([fname ,'.align'],'-mat');
else
    info.aligned = [];
end   
    
% info_loaded = fname;
    
if(~isfield(info,'sz'))
    sz = [512 796];
end
    
if(info.scanmode==0)
    info.recordsPerBuffer = info.recordsPerBuffer*2;
end
    
switch info.channels
    case 1
        info.nchan = 2;      % both PMT0 & 1
        factor = 1;
    case 2
        info.nchan = 1;      % PMT 0
        factor = 2;
    case 3
        info.nchan = 1;      % PMT 1
        factor = 2;
end
    
info.fid = fopen([fname '.sbx']);
d = dir([fname '.sbx']);
info.nsamples = (info.sz(2) * info.recordsPerBuffer * 2 * info.nchan);   % bytes per record 
%Edit Patrick: to maintain compatibility with new version

if isfield(info,'scanbox_version') && info.scanbox_version >= 2
    info.max_idx =  d.bytes/info.recordsPerBuffer/info.sz(2)*factor/4 - 1;
    info.nsamples = (info.sz(2) * info.recordsPerBuffer * 2 * info.nchan);   % bytes per record 
else
    info.max_idx =  d.bytes/info.bytesPerBuffer*factor - 1;
end

try
    fseek(info.fid,k*info.nsamples,'bof');
    x = fread(info.fid,info.nsamples/2 * N,'uint16=>uint16');
    x = reshape(x,[info.nchan info.sz(2) info.recordsPerBuffer  N]);
catch
    error('Cannot read frame.  Index range likely outside of bounds.');
end

x = intmax('uint16')-permute(x,[1 3 2 4]);
fclose(info.fid);
end