uff_readfile.m

toolbox of BVQX, This is the access between BV and matlab. It will help you to analysis data from BV

function imdata = uff_ReadFile(hfile, filename, numimages)
% UFF::ReadFile  - read a UFF specified file
%
% FORMAT:       imdata = uff.ReadFile(filename [, numimages])
%
% Input fields:
%
%       filename    filename of image data file
%       numimages   number of images to read from file
%
% Output fields:
%
%       imdata      image data (N-D array)

% Version:  v0.7b
% Build:    7090213
% Date:     Sep-02 2007, 1:50 PM CEST
% Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
% URL/Info: http://wiki.brainvoyager.com/BVQXtools

% argument check
if nargin < 2 || ...
    numel(hfile) ~= 1 || ...
   ~isBVQXfile(hfile, 'uff') || ...
   ~ischar(filename) || ...
    isempty(filename) || ...
    exist(filename(:)', 'file') ~= 2
    error( ...
        'BVQXfile:BadArgument', ...
        'Invalid call to %s or file not found.', ...
        mfilename ...
    );
end
ui = bvqxfile_getcont(hfile.L);
if nargin < 3 || ...
   ~isa(numimages, 'double') || ...
    numel(numimages) ~= 1 || ...
    isinf(numimages) || ...
    isnan(numimages) || ...
    numimages < 1
    numimages = Inf;
else
    numimages = fix(real(numimages));
end

% get shortcuts
sh = ui.SubHeaderSize;

% reject DICOM files
if ui.IsDICOM
    error( ...
        'BVQXfile:FileTypeNotSupported', ...
        'Please use a real DICOM reader.' ...
    );
end

% open file according to syntax
filename = filename(:)';
try
    if ui.IsBigEndian
        fid = fopen(filename, 'rb', 'ieee-be');
    else
        fid = fopen(filename, 'rb', 'ieee-le');
    end
    if fid < 1
        error('INVALID_FID');
    end
catch
    error( ...
        'BVQXfile:FileOpenError', ...
        'Error opening specified file.' ...
    );
end

% get file size
fseek(fid, 0, 1);
flen = ftell(fid);

% position IO pointer after header
fseek(fid, ui.HeaderSize, -1);

% element size
switch (ui.PixelFormat(1))
    case {1}
        rclass = '*uint8';
        rcsize = 1;
        imdata = uint8(0);
    case {2}
        rclass = '*uint16';
        rcsize = 2;
        imdata = uint16(0);
    case {3}
        rclass = '*uint32';
        rcsize = 4;
        imdata = uint32(0);
    case {4}
        rclass = '*single';
        rcsize = 4;
        imdata = single(0);
    otherwise
        error( ...
            'BVQXfile:InvalidValue', ...
            'Invalid PixelFormat value.' ...
        );
end

% slice size
noc = ui.NrOfCols;
nor = ui.NrOfRows;
sls = noc * nor * rcsize;
fdt = ui.FirstDimIsTime;

% if time dim is first, calculate size
if any([1, 2] == ui.SingleFuncType(1))
    tdim = floor((flen - ui.HeaderSize) / sls);
else
    tdim = 1;
end

% skip images ?
if ~isempty(ui.ImageIndex) && ...
    fix(ui.ImageIndex(1)) > 1 && ...
    fdt == 0
    for sc = 2:fix(ui.ImageIndex)
        try
            fseek(fid, sh + sls, 0);
        catch
            warning( ...
                'BVQXfile:FileReadError', ...
                'Error skipping slice images UFF file.' ...
            );
            return;
        end
    end
end

% read slices (time is not first)
if fdt == 0
    
    % estimate number of slices if needed
    if isinf(numimages)
        sm = 1 + ceil((flen - ui.HeaderSize) / (sh + sls));
    else
        sm = numimages;
    end
    
    % initialize imdata
    imdata(1:nor, 1:noc, 1:sm) = imdata(1);

    sc = 1;
    while numimages > 0
        try
            fseek(fid, sh, 0);
            imdata(:, :, sc) = fread(fid, [nor, noc], rclass);
            sc = sc + 1;
        catch
            warning( ...
                'BVQXfile:FileReadError', ...
                'Error reading slice %d in file.', ...
                sc ...
            );
            return;
        end
        if ~isinf(numimages)
            numimages = numimages - 1;
        end
        if (ftell(fid) + sh + sls) > flen
            break;
        end
    end
    
    % remove unneeded slices
    imdata(:, :, sc:end) = [];

% time is first
else

    % ignore sub header size!
    imdata = reshape(fread(fid, [tdim, nor * noc], rclass), ...
        [tdim, nor, noc]);
end