srf_combine.m

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

function [nfile1, nfile2] = srf_Combine(hfile, hfile2, cbopt)
% SRF::Combine  - combines two SRFs into one
%
% FORMAT:   [csrf [, csmp]] = srf1.Combine(srf2, cbopt);
%
% Input fields:
%
%       srf2        surface to use to combine given SRF with
%       cbopt       struct with mandatory field
%       .type       one of
%                   'backtoback' - rotate one mesh 180 in XY plane
%                   'custom'     - build custom scene, see below
%                   'gapped'     - join contents with a gap
%                   'wholebrain' - simply join contents
%           and optional fields
%       .color1     1x4 double for .Color1 field in SRF options
%       .color2     1x4 double for .Color2 field in SRF options
%       .filename   store combined under new filename
%       .gap        1x1 double, mm to insert between two meshes
%                   (applied for all types accordingly, defaults:
%                   backtoback: 25, gapped: 100, outandin: 20,
%                   outintb: 25, patched: 25, spm2: 25, wholebrain: 0)
%       .linkedmtc  filename of linked MTC, set to empty if not given
%       .smp1       BVQXfile object representing the SMP for the first and
%       .smp2       the second Surface MaP object for the given SRFs
%       .transform  1x2 cell array with 4x4 double transformation matrices,
%                   needed for custom scenaries
%
% Output fields:
%
%       csrf        combined SRF
%       csmp        combined SMP (if given in cbopt)

% Version:  v0.7b
% Build:    7090215
% Date:     Sep-02 2007, 3:54 PM CEST
% Author:   Jochen Weber, Brain Innovation, B.V., Maastricht, NL
% URL/Info: http://wiki.brainvoyager.com/BVQXtools

% check arguments
if nargin < 3 || ...
    numel(hfile) ~= 1 || ...
    numel(hfile2) ~= 1 || ...
   ~isBVQXfile(hfile, 'srf') || ...
   ~isBVQXfile(hfile2, 'srf') || ...
   ~isstruct(cbopt) || ...
    numel(cbopt) ~= 1 || ...
   ~isfield(cbopt, 'type') || ...
   ~ischar(cbopt.type)
    error( ...
        'BVQXfile:BadArguments', ...
        'Invalid call to %s.', ...
        mfilename ...
    );
end
bc1 = bvqxfile_getcont(hfile.L);
bc2 = bvqxfile_getcont(hfile2.L);

% argument check
tavail = {'backtoback', 'custom', 'gapped', 'outandin', 'outintb', 'spm2', 'wholebrain'};
if ~any(strcmpi(cbopt.type, tavail))
    error( ...
        'BVQXtools:BadArgument', ...
        'Bad argument in call.' ...
    );
end
if isfield(cbopt, 'smp1') && ...
    isfield(cbopt, 'smp2') && ...
    numel(cbopt.smp1) == 1 && ...
    numel(cbopt.smp2) == 1 && ...
    isBVQXfile(cbopt.smp1, 'smp') && ...
    isBVQXfile(cbopt.smp2, 'smp')
    smpin = true;
    sbc1 = bvqxfile_getcont(cbopt.smp1.L);
    sbc2 = bvqxfile_getcont(cbopt.smp2.L);
    if sbc1.NrOfVertices ~= bc1.NrOfVertices || ...
        sbc2.NrOfVertices ~= bc2.NrOfVertices || ...
        numel(sbc1.Map) ~= numel(sbc2.Map)
        error( ...
            'BVQXfile:BadArgument', ...
            'NrOfVertices and NrOfMaps must match.' ...
        );
    end
    nfile2 = aft_CopyObject(cbopt.smp1);
    sfile2 = bvqxfile_getscont(nfile2.L);
    sfile2.F = '';
else
    smpin = false;
end
nfile1 = aft_CopyObject(hfile);
sfile1 = bvqxfile_getscont(nfile1.L);
sfile1.F = '';

% check some more things for custom type
cbtype = lower(cbopt.type);
if strcmp(cbtype, 'custom')
    if ~isfield(cbopt, 'transform') || ...
       ~iscell(cbopt.transform) || ...
        numel(cbopt.transform) ~= 2
        bvqxfile_clear(nfile1.L);
        bvqxfile_clear(nfile2.L);
        error( ...
            'BVQXtools:BadArgument', ...
            'Missing or bad transformation matrices for input SRF''s.' ...
        );
    end
    try
        if ~all(size(cbopt.transform{1}) == 4)
            srf_t1 = tfmatrix(cbopt.transform{1});
        else
            srf_t1 = cbopt.transform{1}(:,:,1);
        end
        if ~all(size(cbopt.transform{2}) == 4)
            srf_t2 = tfmatrix(cbopt.transform{2});
        else
            srf_t2 = cbopt.transform{2}(:,:,1);
        end
    catch
        bvqxfile_clear(nfile1.L);
        bvqxfile_clear(nfile2.L);
        error( ...
            'BVQXtools:BadArgument', ...
            'Bad transformation matrix for input SRF %d.', ...
            tc ...
        );
    end
end
if isfield(cbopt, 'color1') && ...
    isa(cbopt.color1, 'double') && ...
    numel(cbopt.color1) == 4 && ...
   ~any(isnan(cbopt.color1(:)) | isinf(cbopt.color1(:)) | ...
     cbopt.color1(:) < 0 | cbopt.color1(:) > 1)
    sfile1.C.ConvexColor = cbopt.color1(:)';
end
if isfield(cbopt, 'color2') && ...
    isa(cbopt.color2, 'double') && ...
    numel(cbopt.color2) == 4 && ...
   ~any(isnan(cbopt.color2(:)) | isinf(cbopt.color2(:) | ...
     cbopt.color2(:) < 0 | cbopt.color2(:) > 1))
    sfile1.C.ConcaveColor = cbopt.color2(:)';
end
if ~isfield(cbopt, 'gap') || ...
   ~isa(cbopt.gap, 'double') || ...
    numel(cbopt.gap) ~= 1 || ...
    isnan(cbopt.gap) || ...
    isinf(cbopt.gap) || ...
    cbopt.gap < -512 || ...
    cbopt.gap > 512
    cbopt.gap = [];
end
if isfield(cbopt, 'linkedmtc') && ...
    ischar(cbopt.linkedmtc) && ...
   ~isempty(cbopt.linkedmtc)
    sfile1.C.AutoLinkedMTC = cbopt.linkedmtc(:)';
end

if smpin
    for mc = 1:numel(sbc1.Map)
        sfile2.C.Map(mc).SMPData = [sbc1.Map(mc).SMPData; sbc2.Map(mc).SMPData];
    end
    sfile2.C.NrOfVertices = size(sfile2.C.Map(1).SMPData, 1);
    bvqxfile_setscont(nfile2.L, sfile2);
end

% get coordinates, etc.
srf_p1 = bc1.VertexCoordinate;
srf_n1 = bc1.VertexNormal;
srf_np1 = size(srf_p1, 1);
srf_nt1 = size(bc1.TriangleVertex, 1);
srf_p2 = bc2.VertexCoordinate;
srf_n2 = bc2.VertexNormal;
srf_np2 = size(srf_p2, 1);
srf_nt2 = size(bc2.TriangleVertex, 1);

% summary
srf_np = srf_np1 + srf_np2;
srf_nt = srf_nt1 + srf_nt2;

% wholebrain is special (zero) gap case
if strcmp(cbtype, 'wholebrain')
    if isempty(cbopt.gap), cbopt.gap = 0; end
    cbtype = 'gapped';
end

% for new center
cpos = (bc1.MeshCenter + bc2.MeshCenter) / 2;

% which type
switch cbtype, case {'backtoback'}

    if isempty(cbopt.gap)
        cbopt.gap = 25;
    end
    srf_p1(:, 2) = srf_p1(:, 2) - min(srf_p1(:, 2)) + cbopt.gap / 2;
    srf_p2(:, 2) = srf_p2(:, 2) - min(srf_p2(:, 2)) + cbopt.gap / 2;
    srf_p2(:, 1:2) = -srf_p2(:, 1:2);
    srf_n2(:, 1:2) = -srf_n2(:, 1:2);
    cpos = [256, 128, 128];

case {'custom'}
    
    % prepare points and normals matrices
    srf_p1(:, 4) = 1;
    srf_p2(:, 4) = 1;
    
    % apply transformation matrices to points and normals
    srf_p1 = (srf_t1 * srf_p1')';
    srf_n1 = (srf_t1(1:3, 1:3) * srf_n1')';
    srf_p2 = (srf_t2 * srf_p2')';
    srf_n2 = (srf_t2(1:3, 1:3) * srf_n2')';
    
    % remove fourth coordinate again
    srf_p1(:, 4) = [];
    srf_p2(:, 4) = [];

case {'gapped'}
    
    if isempty(cbopt.gap)
        cbopt.gap = 100;
    end
    srf_p1(:, 3) = srf_p1(:, 3) - cbopt.gap / 2;
    srf_p2(:, 3) = srf_p2(:, 3) + cbopt.gap / 2;
    
end

% build neighbors and triangle strip lists
neigh = [bc1.Neighbors; bc2.Neighbors];
for nc = (srf_np1 + 1):srf_np
    neigh{nc, 2} = neigh{nc, 2} + srf_np1;
end
trist = bc2.TriangleStripSequence;
rtrist = (trist > 0);
trist(rtrist) = trist(rtrist) + srf_np1;

% set fields correctly
sfile1.C.NrOfVertices = srf_np;
sfile1.C.NrOfTriangles = srf_nt;
sfile1.C.VertexCoordinate = [srf_p1; srf_p2];
sfile1.C.VertexNormal = [srf_n1; srf_n2];
sfile1.C.MeshCenter = cpos;
sfile1.C.VertexColor = [bc1.VertexColor; bc2.VertexColor];
sfile1.C.Neighbors = neigh;
sfile1.C.TriangleVertex = [bc1.TriangleVertex; (bc2.TriangleVertex + srf_np1)];
sfile1.C.TriangleStripSequence = [bc1.TriangleStripSequence; trist];
sfile1.C.NrOfTriangleStrips = numel(sfile1.C.TriangleStripSequence);
bvqxfile_setscont(nfile1.L, sfile1);

% write output?
if isfield(cbopt, 'filename') && ...
    ischar(cbopt.filename) && ...
   ~isempty(cbopt.filename)
    try
        aft_SaveAs(nfile1, cbopt.filename);
        if smpin && ...
            numel(cbopt.filename) > 4 && ...
            strcmpi(cbopt.filename(end-3:end), '.srf')
            aft_SaveAs(nfile2, [cbopt.filename(1:end-4) '.smp']);
        end
    catch
        warning( ...
            'BVQXfile:ErrorWritingFile', ...
            'Couldn''t write new SRF/SMP file: ''%s''.', ...
            cbopt.filename ...
        );
    end
end