vmr_update.m

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

function hfile = vmr_Update(hfile, F, S, V)
% VMR::Update  - called after subsasgn for VMRs

% Version:  v0.7b
% Build:    7083012
% Date:     Aug-30 2007, 12:29 PM CEST
% Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
% URL/Info: http://wiki.brainvoyager.com/BVQXtools

% persistent config
persistent bvqxfile_vmrconfig;
if isempty(bvqxfile_vmrconfig)
    bvqxfile_vmrconfig = struct;

    bvqxfile_vmrconfig.fields = cell(1,4);
    bvqxfile_vmrconfig.fields{1} = ...
        {'FileVersion', 'NrOfCrossCorrLags', ...
         'DimX', 'DimY', 'DimZ', 'VMR8bit', 'VMRData', ...
         'VMRData16', 'OffsetX', 'OffsetY', 'OffsetZ', 'FramingCube'};
    bvqxfile_vmrconfig.fields{2} = ...
        {'FileVersion', 'DimX', 'DimY', 'DimZ', 'VMR8bit', 'VMRData', ...
         'VMRData16', 'OffsetX', 'OffsetY', 'OffsetZ', 'FramingCube'};
    bvqxfile_vmrconfig.fields{3} = ...
        {'FileVersion', 'DimX', 'DimY', 'DimZ', 'VMR8bit', 'VMRData', ...
         'VMRData16', 'OffsetX', 'OffsetY', 'OffsetZ', 'FramingCube', ...
         'PosInfoVerified', 'CoordinateSystem', ...
         'Slice1CenterX', 'Slice1CenterY', 'Slice1CenterZ', ...
         'SliceNCenterX', 'SliceNCenterY', 'SliceNCenterZ', ...
         'RowDirX', 'RowDirY', 'RowDirZ', 'ColDirX', 'ColDirY', 'ColDirZ', ...
         'NRows', 'NCols', 'FoVRows', 'FoVCols', ...
         'SliceThickness', 'GapThickness', 'NrOfPastSpatialTransformations', ...
         'Convention', 'VoxResX', 'VoxResY', 'VoxResZ', ...
         'VoxResInTalairach', 'VoxResVerified', ...
         'MinOriginalValue', 'MeanOriginalValue', 'MaxOriginalValue'};
    bvqxfile_vmrconfig.fields{4} = ...
        {'FileVersion', 'DimX', 'DimY', 'DimZ', 'VMR8bit', 'VMRData', ...
         'OffsetX', 'OffsetY', 'OffsetZ', 'FramingCube', ...
         'PosInfoVerified', 'CoordinateSystem', ...
         'Slice1CenterX', 'Slice1CenterY', 'Slice1CenterZ', ...
         'SliceNCenterX', 'SliceNCenterY', 'SliceNCenterZ', ...
         'RowDirX', 'RowDirY', 'RowDirZ', 'ColDirX', 'ColDirY', 'ColDirZ', ...
         'NRows', 'NCols', 'FoVRows', 'FoVCols', ...
         'SliceThickness', 'GapThickness', 'NrOfPastSpatialTransformations', ...
         'Convention', 'VoxResX', 'VoxResY', 'VoxResZ', ...
         'VoxResInTalairach', 'VoxResVerified', ...
         'MinOriginalValue', 'MeanOriginalValue', 'MaxOriginalValue'};

    bvqxfile_vmrconfig.defaults = struct( ...
        'NrOfCrossCorrLags',  0, ...
        'OffsetX',            0, ...
        'OffsetY',            0, ...
        'OffsetZ',            0, ...
        'VMR8bit',            true, ...
        'FramingCube',        '!256 * (1 + double((max(max(@DimX, @DimY), @DimZ) > 256)))!', ...
        'PosInfoVerified',    0, ...
        'CoordinateSystem',   0, ...
        'Slice1CenterX',      0, ...
        'Slice1CenterY',      0, ...
        'Slice1CenterZ',      '!- @DimZ/2!', ...
        'SliceNCenterX',      0, ...
        'SliceNCenterY',      0, ...
        'SliceNCenterZ',      '!@DimZ/2!', ...
        'RowDirX',            1, ...
        'RowDirY',            0, ...
        'RowDirZ',            0, ...
        'ColDirX',            0, ...
        'ColDirY',            1, ...
        'ColDirZ',            0, ...
        'NRows',              '!@DimX!', ...
        'NCols',              '!@DimY!', ...
        'FoVRows',            '!@DimX!', ...
        'FoVCols',            '!@DimY!', ...
        'SliceThickness',     1, ...
        'GapThickness',       0, ...
        'NrOfPastSpatialTransformations', cell2struct(cell(0, 0, 5), ...
            {'NameOfSpatialTransformation', ...
             'TypeOfSpatialTransformation', ...
             'SourceFileOfSpatialTransformation', ...
             'NrOfSpatialTransformationValues', ...
             'TransformationValues'}, 3), ...
        'Convention',         1, ...
        'VoxResX',            1, ...
        'VoxResY',            1, ...
        'VoxResZ',            1, ...
        'VoxResInTalairach',  0, ...
        'VoxResVerified',     0, ...
        'MinOriginalValue',   0, ...
        'MeanOriginalValue',127, ...
        'MaxOriginalValue', 255);
    
end

% argument check
if nargin < 2 || ...
   ~all(isBVQXfile(hfile(:), 'vmr')) || ...
   ~ischar(F) || ...
    isempty(F)
    error( ...
        'BVQXfile:BadArgument', ...
        'Invalid call to %s.', ...
        mfilename ...
    );
end
if nargin < 3 || ...
   ~isstruct(S)
    S = struct;
    S.type = '.';
    S.subs = F;
end
if nargin < 4
    V = [];
end

% get content
bc = bvqxfile_getcont(hfile.L);

% linearize
F = makelabel(F(:)');

% F valid
if ~isfield(bc, F)
    error( ...
        'BVQXfile:InvalidProperty', ...
        'Cannot find property ''%s'' for type VMR.', ...
        F ...
    );
end

% what field has changed
switch (lower(F))

    % reframing
    case {'dimx', 'dimy', 'dimz'}

        % which target type
        if bc.VMR8bit
            is8bit = true;
        else
            is8bit = false;
        end

        % get destination and current data size
        dsize = [bc.DimX, bc.DimY, bc.DimZ];
        csize = size(bc.VMRData);

        % changes ?
        if any(dsize ~= csize)

            % dim1
            if dsize(1) < csize(1)
                srange1 = round(0.5 + (csize(1) - dsize(1)) / 2);
                srange1(2) = srange1 + dsize(1) - 1;
                trange1 = [1, dsize(1)];
            elseif dsize(1) > csize(1)
                srange1 = [1, csize(1)];
                trange1 = round(0.5 + (dsize(1) - csize(1)) / 2);
                trange1(2) = trange1 + csize(1) - 1;
            else
                srange1 = [1, csize(1)];
                trange1 = srange1;
            end

            % dim2
            if dsize(2) < csize(2)
                srange2 = round(0.5 + (csize(2) - dsize(2)) / 2);
                srange2(2) = srange2 + dsize(2) - 1;
                trange2 = [1, dsize(2)];
            elseif dsize(2) > csize(2)
                srange2 = [1,csize(2)];
                trange2 = round(0.5 + (dsize(2) - csize(2)) / 2);
                trange2(2) = trange2 + csize(2) - 1;
            else
                srange2 = [1, csize(2)];
                trange2 = srange2;
            end

            % dim3
            if dsize(3) < csize(3)
                srange3 = round(0.5 + (csize(3) - dsize(3)) / 2);
                srange3(2) = srange3 + dsize(3) - 1;
                trange3 = [1, dsize(3)];
            elseif dsize(3) > csize(3)
                srange3 = [1,csize(3)];
                trange3 = round(0.5 + (dsize(3) - csize(3)) / 2);
                trange3(2) = trange3 + csize(3) - 1;
            else
                srange3 = [1, csize(3)];
                trange3 = srange3;
            end

            % get source data
            VMRsrc = bc.VMRData( ...
                srange1(1):srange1(2), ...
                srange2(1):srange2(2), ...
                srange3(1):srange3(2));

            % create target data
            if is8bit
                bc.VMRData = uint8(0);
            else
                bc.VMRData = uint16(0);
            end
            bc.VMRData(1:dsize(1), 1:dsize(2), 1:dsize(3)) = 0;

            % put source in target
            bc.VMRData( ...
                trange1(1):trange1(2), ...
                trange2(1):trange2(2), ...
                trange3(1):trange3(2)) = VMRsrc;
        end


    % changing file version
    case {'fileversion'}

        % get wanted version
        reqv = bc.FileVersion;

        % check version
        if isempty(reqv) || ...
           ~isa(reqv, 'double') || ...
            isnan(reqv(1)) || ...
            isinf(reqv(1)) || ...
            fix(reqv(1)) ~= reqv(1) || ...
            reqv(1) < 0 || ...
            reqv(1) > 3

            % give warning if required
            warning( ...
                'BVQXfile:InvalidPropertyValue', ...
                'Invalid FileVersion value given.' ...
            );

            % set better value and go on
            reqv = 3;
            bc.FileVersion = reqv;
        end

        % get good field list
        goodf = bvqxfile_vmrconfig.fields{reqv + 1};
        deffc = bvqxfile_vmrconfig.defaults;

        % iterate over existing fields and remove all superfluous first
        hasf = fieldnames(bc);
        for fc = 1:length(hasf)
            if ~any(strcmp(hasf{fc}, goodf))
                bc = rmfield(bc, hasf{fc});
            end
        end

        % iterate over goodf and add default for any missing
        for fc = 1:length(goodf)
            if ~any(strcmp(goodf{fc}, hasf))
                goodv = deffc.(goodf{fc});
                if ischar(goodv) && ...
                   ~isempty(goodv) && ...
                    goodv(1) == '!' && ...
                    goodv(end) == '!' && ...
                    any(goodv == '@')
                    try
                        eval(['goodv=' ...
                            strrep(goodv(2:end-1), '@', 'bc.') ...
                            ';']);
                    catch
                        warning( ...
                            'BVQXfile:EvaluationError', ...
                            'Error evaluating default value for %s: %s.', ...
                            goodf{fc}, deffc.(goodf{fc}) ...
                        );
                        goodv = [];
                    end
                end
                bc.(goodf{fc}) = goodv;
            end
        end


    % set to 8 bit (max intensity 223)
    case {'vmr8bit'}

        % get target state
        tt = bc.VMR8bit;
        if isempty(tt)
            tt = false;
        elseif ~isnumeric(tt)
            tt = true;
        elseif tt(1)
            tt = true;
        else
            tt = false;
        end

        % only check type for 8bit (other is checked in VMRData handler)
        if tt && ...
           ~isa(bc.VMRData, 'uint8')

            % set and find maxval
            maxval = 223;
            curmax = double(max(bc.VMRData(:)));

            % only reset if greater than possible values!
            if curmax > 255

                % recalculate intensities
                bc.VMRData = uint8(round( ...
                    double(bc.VMRData) * (maxval/curmax)));

            % else just adapt datatype
            elseif ~isa(bc.VMRData, 'uint8')

                % set datatype
                bc.VMRData = uint8(bc.VMRData);
            end
        end

        % if ~tt and ~uint16
        if ~tt && ...
           ~isa(bc.VMRData, 'uint16')

            % set datatype
            bc.VMRData = uint16(bc.VMRData);
        end


    % new data set (either partial or complete!)
    case {'vmrdata'}

        % get current datatype
        if bc.VMR8bit
            is8bit = true;
            maxval = uint8(255);
        else
            is8bit = false;
            maxval = uint16(4095);
        end

        % check type
        checkcont = false;
        if is8bit
            if ~isa(bc.VMRData, 'uint8')
                checkcont = true;
            end
        else
            if ~isa(bc.VMRData, 'uint16')
                checkcont = true;
            end
        end

        % if type must be converted
        if checkcont

            % check numeric content
            if ~isnumeric(bc.VMRData)

                % give warning
                warning( ...
                    'BVQXfile:InvalidDataType', ...
                    'Invalid datatype for VMRData property.' ...
                );

                % and fill with type according zeros
                csize = [bc.DimX, bc.DimY, bc.DimZ];
                if is8bit
                    bc.VMRData = uint8(0);
                else
                    bc.VMRData = uint16(0);
                end
                bc.VMRData(1:csize(1), 1:csize(2), 1:csize(3)) = 0;
            else

                % replace NaN's and Inf's
                bc.VMRData(isnan(bc.VMRData)) = 0;
                bc.VMRData(isinf(bc.VMRData)) = maxval;

                % get min and max val
                curmin = double(min(bc.VMRData(:)));
                if curmin > 0
                    curmin = 0;
                end
                curmax = double(max(bc.VMRData(:)));

                % reframe intensities
                if is8bit
                    if curmax > 255
                        maxval = uint8(223);
                    end
                    bc.VMRData = uint8(round( ...
                        (double(bc.VMRData) - curmin) / ...
                        (curmax + eps - curmin) * double(maxval)));
                else
                    bc.VMRData = uint16(round( ...
                        (double(bc.VMRData) - curmin) / ...
                        (curmax + eps - curmin) * double(maxval)));
                end
            end
        end

        % get source and current data size
        ssize = [bc.DimX, bc.DimY, bc.DimZ];
        csize = size(bc.VMRData);

        % changes ?
        if any(ssize ~= csize)
            bc.DimX = csize(1);
            bc.DimY = csize(2);
            bc.DimZ = csize(3);
        end    
end

% update contents
bvqxfile_setcont(hfile.L, bc);