prt_cleanup.m

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

function hfile = prt_CleanUp(hfile, varargin)
% PRT::CleanUp  - clean up protocols
%
% FORMAT:       [prt] = prt.CleanUp([fullclean]);
%
% Input fields:
%
%       fullclean   if given and true, perform full cleanup
%
% Output fields:
%
%       prt         altered PRT

% Version:  v0.7b
% Build:    7090213
% Date:     Sep-02 2007, 1:08 PM CET
% Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
% URL/Info: http://wiki.brainvoyager.com/BVQXtools

% argument check
if nargin < 1 || ...
    numel(hfile) ~= 1 || ...
   ~isBVQXfile(hfile, 'prt')
    error( ...
        'BVQXfile:BadArgument', ...
        'Invalid call to %s.', ...
        mfilename ...
    );
end
bc = bvqxfile_getcont(hfile.L);
if nargin > 1 && ...
   (isa(varargin{1}, 'double') || islogical(varargin{1})) && ...
   ~isempty(varargin{1}) && ...
    varargin{1}(1)
    fullclean = true;
else
    fullclean = false;
end

% get settings
ncon = numel(bc.Cond);
if ~isempty(bc.ResolutionOfTime) && ...
    lower(bc.ResolutionOfTime(1)) == 'm'
    tresms = 1;
    tresvol = 0;
else
    tresms = 0;
    tresvol = 1;
end

% loop over number of conditions
lastend = 0;
for cc = ncon:-1:1

    % get condition, update last end
    c = bc.Cond(cc);
    bc.Cond(cc).NrOfOnOffsets = size(c.OnOffsets, 1);

    % skip empty conditions
    if isempty(c.OnOffsets)
        if fullclean
            bc.Cond(cc) = [];
        end
        continue;
    end

    % update last index and set changed flag
    lastend = max(lastend, max(c.OnOffsets(:, 2)));

    % loop over onsets, starting at the end
    for oc = c.NrOfOnOffsets:-1:2

        % check intervals
        if (c.OnOffsets(oc - 1, 2) + 1) >= c.OnOffsets(oc, 1)

            % give warning ?
            if (c.OnOffsets(oc - 1, 2) + tresvol) > c.OnOffsets(oc, 1)
                warning( ...
                    'BVQXfile:ProtocolWarning', ...
                    'Overlapping stimulus durations in same condition.' ...
                );
            end

            % concatenate epochs
            c.OnOffsets(oc, 1) = c.OnOffsets(oc - 1, 1);
            c.OnOffsets(oc - 1, :) = [];
        end
    end

    % put back
    c.NrOfOnOffsets = size(c.OnOffsets, 1);
    bc.Cond(cc) = c;
end

% update number of conditions
if fullclean
    ncon = numel(bc.Cond);
    bc.NrOfConditions = ncon;
end

% that's it ?
if ~fullclean || ...
    ncon < 1
    return;
end

% get old conditions
ocond = bc.Cond;
oc1 = ocond(1);

% otherwise create a new protocol and copy initial settings
nbc = BVQXfile(0, 'newcont', 'prt');
nbc.FileVersion        = bc.FileVersion;
nbc.ResolutionOfTime   = bc.ResolutionOfTime;
nbc.Experiment         = bc.Experiment;
nbc.BackgroundColor    = bc.BackgroundColor;
nbc.TextColor          = bc.TextColor;
nbc.TimeCourseColor    = bc.TimeCourseColor;
nbc.TimeCourseThick    = bc.TimeCourseThick;
nbc.ReferenceFuncColor = bc.ReferenceFuncColor;
nbc.ReferenceFuncThick = bc.ReferenceFuncThick;
nbc.Cond               = oCond;
nbc.Cond(:) = [];

% get combined list and matrix of on/offsets
iact = uint8(0);
iact(1:ncon, 1:lastend) = iact(1);
for cc = 1:ncon
    c = ocond(cc);
    onum = c.NrOfOnOffsets;
    for oc = 1:onum
        iact(cc,(c.OnOffsets(oc,1)+tresms):(c.OnOffsets(oc,2))) = uint8(1);
    end
end
numc = sum(iact);

% resting condition ?
rest = (numc == 0);
if any(rest)

    % get rest on/offsets
    ron  = 1 + find(diff(rest) > 0);
    roff = 1 + find(diff(rest) < 0);
    if isempty(roff)
        roff = length(rest);
    end
    if isempty(ron) || ...
         ron(1) > roff(1)
         ron = [1, ron];
    end
    if roff(end) < ron(end)
        roff(end + 1) = length(rest);
    end
    numrest = length(ron);
    if numrest ~= length(roff)
        error( ...
            'BVQXfile:InternalError', ...
            'Mishap when figuring out rest phases.' ...
        );
    end
    ronoff = zeros(numrest, 2);
    for rc = 1:numrest
        ronoff(cc, :) = [ron, roff - tresvol];
    end

    % add rest to new file (first condition)
    disp(sprintf(' -> adding ''Rest'' condition with %d onsets', numrest));
    oc1.ConditionName = 'Rest';
    oc1.NrOfOnOffsets = size(ronoff, 1);
    oc1.OnOffsets = ronoff;
    oc1.Color = [32, 32, 32];
    nbc.Cond(end + 1) = oc1;
else

    % add rest with no onsets
    disp(' -> adding ''Rest'' condition with 0 onsets');
    oc1.ConditionName = 'Rest';
    oc1.NrOfOnOffsets = 0;
    oc1.OnOffsets = zeros(0, 2);
    oc1.Color = [32, 32, 32];
    nbc.Cond(end + 1) = oc1;
end
clear rest;

% find overlap between one .. ncon conditions
for cc = 1:max(numc)

    % scan conditions
    for scc = 1:ncon

        % find where numc == cc and condition(scc) is on
        ciact = diff([false, (numc == cc & (iact(scc, :) > 0)), false]);
        ciaon = find(ciact > 0) - tresms;
        ciaoff = find(ciact < 0) - 1;

        % check length
        if length(ciaon) ~= length(ciaoff)
            error( ...
                'BVQXfile:InternalError', ...
                'Error finding non-interaction periods.' ...
            );
        end

        % do nothing on emtpy array
        if isempty(ciaon)
            continue;
        end

        % no interaction
        if cc == 1

            % put into new file
            disp(sprintf(' -> keeping condition ''%s'' with %d onset(s)', ...
                deblank(ocond(scc).ConditionName{1}), length(ciaon)));
            nfile = prt_AddCond(nfile, ...
                deblank(ocond(scc).ConditionName{1}), ...
                [ciaon(:), ciaoff(:)], ...
                ocond(scc).Color);
            iact(cc, (numc == cc & (iact(scc, :) > 0))) = false;
            continue;
        end

        % repeat until interactions of level cc with condition(scc) OK
        while ~isempty(ciaon)

            % get "on" conditions on first onset
            oncon = find(iact(:, ciaon(1) + tresms) > 0);
            if length(oncon) ~= cc
                error( ...
                    'BVQXfile:InternalError', ...
                    'Error looking up interaction conditions.' ...
                );
            end

            % find phases where sum == cc and sum(oncon) == cc !
            siact = diff([false, (numc == cc & sum(iact(oncon(:)', :)) == cc), false]);
            siaon = find(siact > 0) - tresms;
            siaoff = find(siact < 0) - 1;

            % check length
            if length(siaon) ~= length(siaoff) || ...
                isempty(siaon)
                error( ...
                    'BVQXfile:InternalError', ...
                    'Error finding interaction periods.' ...
                );
            end

            % building new name
            newname = cell(1, numel(oncon));
            newcol = zeros(1, 3);
            for sscc = oncon(:)'
                newname{sscc} = deblank(ocond(sscc).ConditionName{1});
                newcol = newcol + ocond(sscc).Color;
            end
            newname = sprintf('Interaction (%s)', ...
                gluetostring(newname, ' & '));
            newcol = round(newcol / cc);

            % put into new file
            disp(sprintf(' -> building interaction ''%s'' with %d onset(s)', ...
                newname, length(siaon)));
            oc1.Name = newname;
            oc1.NrOfOnOffsets = numel(siaon);
            oc1.OnOffsets = [siaon(:), siaoff(:)];
            oc1.Color = newcol;
            nbc.Cond(end + 1) = oc1;

            % remove from array
            for soc = 1:length(siaon)
                iact(oncon(:)', siaon(soc)+tresms:siaoff(soc)) = false;
            end

            % do find again to get loop right
            numc = sum(iact);
            ciact = diff([false, (numc == cc & (iact(scc, :) > 0)), false]);
            ciaon = find(ciact > 0) - tresms;
            ciaoff = find(ciact < 0) - 1;

            % check length
            if length(ciaon) ~= length(ciaoff)
                error( ...
                    'BVQXfile:InternalError', ...
                    'Error finding non-interaction periods.' ...
                );
            end
        end
    end
end

% overwrite old with new content
bvqxfile_setcont(hfile.L, nbc);