% Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions 

%

%=========================================================================

%

%  Copyright (c) 2008 Thomas Yeo and Mert Sabuncu

%  All rights reserved.

%

%Redistribution and use in source and binary forms, with or without

%modification, are permitted provided that the following conditions are met:

%

%    * Redistributions of source code must retain the above copyright notice,

%      this list of conditions and the following disclaimer.

%

%    * Redistributions in binary form must reproduce the above copyright notice,

%      this list of conditions and the following disclaimer in the documentation

%      and/or other materials provided with the distribution.

%

%    * Neither the names of the copyright holders nor the names of future

%      contributors may be used to endorse or promote products derived from this

%      software without specific prior written permission.

%

%THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND

%ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED

%WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

%DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR

%ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES

%(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;

%LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON

%ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

%(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS

%SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.    

%

%=========================================================================

function write_annotation(filename, vertices, label, ct)



% write_annotation(filename, vertices, label, ct)

%

% Only writes version 2...

%

% vertices expected to be simply from 0 to number of vertices - 1;

% label is the vector of annotation

%

% ct is a struct

% ct.numEntries = number of Entries

% ct.orig_tab = name of original ct

% ct.struct_names = list of structure names (e.g. central sulcus and so on)

% ct.table = n x 5 matrix. 1st column is r, 2nd column is g, 3rd column

% is b, 4th column is flag, 5th column is resultant integer values

% calculated from r + g*2^8 + b*2^16 + flag*2^24. flag expected to be all 0



fp = fopen(filename, 'w', 'b');



% first write vertices and label



count = fwrite(fp, int32(length(label)), 'int');

if(count~=1)

   error('write_annotation: Writing #vertices/labels not successful!!');

end



temp = zeros(length(label)*2,1);

temp(1:2:end) = vertices;

temp(2:2:end) = label;

temp = int32(temp);



count = fwrite(fp, int32(temp), 'int');

if(count~=length(temp))

   error('write_annotation: Writing labels/vertices not successful!!');

end



%Write that ct exists

count = fwrite(fp, int32(1), 'int');

if(count~=1)

   error('write_annotation: Unable to write flag that ct exists!!');

end



%write version number

count = fwrite(fp, int32(-2), 'int');

if(count~=1)

    error('write_annotation: Unable to write version number!!');

end



%write number of entries

count = fwrite(fp, int32(ct.numEntries), 'int');

if(count~=1)

    error('write_annotation: Unable to write number of entries in ct!!');

end



%write original table

orig_tab = [ct.orig_tab char(0)];

count = fwrite(fp, int32(length(orig_tab)), 'int');

if(count~=1)

    error('write_annotation: Unable to write length of ct source!!');

end



count = fwrite(fp, orig_tab, 'char');

if(count~=length(orig_tab))

    error('write_annotation: Unable to write orig_tab!!');

end



%write number of entries

count = fwrite(fp, int32(ct.numEntries), 'int');

if(count~=1)

    error('write_annotation: Unable to write number of entries in ct!!');

end



%write ct

for i = 1:ct.numEntries

    count = fwrite(fp, int32(i-1), 'int');

    if(count~=1)

        error('write_annotation: Unable to write structure number!!');

    end

    

    structure_name = [ct.struct_names{i} char(0)];

    count = fwrite(fp, int32(length(structure_name)), 'int');

    if(count~=1)

        error('write_annotation: Unable to write length of structure name!!');

    end

    count = fwrite(fp, structure_name, 'char');

    if(count~=length(structure_name))

        error('write_annotation: Unable to write structure name!!');

    end

    

    count = fwrite(fp, int32(ct.table(i, 1)), 'int');

    if(count~=1)

       error('write_annotation: Unable to write red color'); 

    end

    

    count = fwrite(fp, int32(ct.table(i, 2)), 'int');

    if(count~=1)

       error('write_annotation: Unable to write blue color'); 

    end

    

    count = fwrite(fp, int32(ct.table(i, 3)), 'int');

    if(count~=1)

       error('write_annotation: Unable to write green color'); 

    end

    

    count = fwrite(fp, int32(ct.table(i, 4)), 'int');

    if(count~=1)

       error('write_annotation: Unable to write padded color'); 

    end 

    

end



fclose(fp);