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create_vtu.m
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create_vtu.m
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function [fname_number,fname_vtk]=create_vtu(path,name,X_yin,Y_yin,Z_yin,X_yang,Y_yang,Z_yang,Fields,time)
start_dir = pwd;
cd(path);%.inv_par
%==========================================================================
% 1) Take the surface of the 2 grids, patch together and triangulate
%==========================================================================
X_yin_s = X_yin(:,:,end);
Y_yin_s = Y_yin(:,:,end);
Z_yin_s = Z_yin(:,:,end);
X_yang_s = X_yang(:,:,end);
Y_yang_s = Y_yang(:,:,end);
Z_yang_s = Z_yang(:,:,end);
R_yin_s = sqrt(X_yin_s.^2 + Y_yin_s.^2 + Z_yin_s.^2);
Th_yin_s = atan2(sqrt(X_yin_s.^2 + Y_yin_s.^2),Z_yin_s);
Ph_yin_s = atan2(Y_yin_s,X_yin_s);
R_yang_s = sqrt(X_yang_s.^2 + Y_yang_s.^2 + Z_yang_s.^2);
Th_yang_s = atan2(sqrt(X_yang_s.^2 + Y_yang_s.^2),Z_yang_s);
Ph_yang_s = atan2(Y_yang_s,X_yang_s);
% Cut off the corners from grid #1, which seems to do #2 as well (PJT):
theta12 = acos(sin(Th_yin_s).*sin(Ph_yin_s)); % theta coords of grid 1 in coord system of grid 2
ind_corner = find( (theta12>pi/4 & Ph_yin_s>pi/2) | (theta12<3*pi/4 & Ph_yin_s<-pi/2 ) );
% Form indices of remaining
ind = 1:numel(Ph_yin_s);
ind([ind_corner])=[];
%ind([ind_corner1 ind_corner2])=[];
% Create an array with unique r, theta & phi values
numberYin = ones(size(R_yin_s));
numberYin(find(R_yin_s==R_yin_s)) = find(R_yin_s==R_yin_s);
numberYang = ones(size(R_yang_s));
numberYang(find(R_yang_s==R_yang_s)) = find(R_yang_s==R_yang_s)+ max(numberYin(:));
%Closed Yin grid, w/o corners and completely closed
R_s = [R_yin_s(ind), ]';
Th_s = [Th_yin_s(ind) ]';
Ph_s = [Ph_yin_s(ind), ]';
NumYin = [numberYin(ind)]';
% x,y,z coordinates of complete grid:
X_s = [X_yin_s(ind) -X_yin_s(ind)];
Y_s = [Y_yin_s(ind) Z_yin_s(ind)];
Z_s = [Z_yin_s(ind) Y_yin_s(ind)];
NumYang = [NumYin + max(numberYin(:)) ];
Number = [NumYin(:); NumYang(:) ]';
% remove redundant coordinates
tri = convhulln([X_s(:), Y_s(:),Z_s(:)]); % simple way to grid it
triYingYang = Number(tri);
X_s = [X_yin_s(:); X_yang_s(:)];
Y_s = [Y_yin_s(:); Y_yang_s(:)];
Z_s = [Z_yin_s(:); Z_yang_s(:)];
%==========================================================================
% triYingYang now contains the numbers of all triangles
%==========================================================================
%==========================================================================
% 2) Create a 3D grid with tetrahedron elements
%==========================================================================
% Number all gridpoints we have
NUMBER_1 = ones(size(X_yin));
NUMBER_2 = ones(size(X_yang));
NUMBER_1(find(NUMBER_1)) = find(NUMBER_1);
NUMBER_2(find(NUMBER_2)) = find(NUMBER_2) + max(NUMBER_1(:));
% Make a loop over all levels
ElementNumbers = [];
for iz=1:size(X_yang,3)-1
num_upper1 = NUMBER_1(:,:,iz+1);
num_upper2 = NUMBER_2(:,:,iz+1);
num_upper = [num_upper1(:); num_upper2(:)];
num_lower1 = NUMBER_1(:,:,iz);
num_lower2 = NUMBER_2(:,:,iz);
num_lower = [num_lower1(:); num_lower2(:)];
ElementNumbers = [ElementNumbers; num_upper(triYingYang), num_lower(triYingYang)];
end
%--------------------------------------------------------------------------
% Convert data into correct vector format
%--------------------------------------------------------------------------
Points = zeros(max(NUMBER_2(:)),3);
Points(NUMBER_1(:),1) = X_yin(:);
Points(NUMBER_2(:),1) = X_yang(:);
Points(NUMBER_1(:),2) = Y_yin(:);
Points(NUMBER_2(:),2) = Y_yang(:);
Points(NUMBER_1(:),3) = Z_yin(:);
Points(NUMBER_2(:),3) = Z_yang(:);
Radius = sqrt(sum(Points.^2,2));
Field_Names=fieldnames(Fields);
for k=1:length(Field_Names)
Field_yin=Fields.(Field_Names{k})(:,1:length(X_yin(1,:,1)),:);
Field_yang=Fields.(Field_Names{k})(:,length(X_yin(1,:,1))+1:2*length(X_yin(1,:,1)),:);
eval(strcat(Field_Names{k},'=zeros(max(NUMBER_2(:)),1);'));
eval(strcat(Field_Names{k},'(NUMBER_1(:))=Field_yin(:);'));
eval(strcat(Field_Names{k},'(NUMBER_2(:))=Field_yang(:);'));
end
%==========================================================================
% 3) Write VTK file (unstructured mesh)
%==========================================================================
ElementNumbers = ElementNumbers-1; % VTK is zero-based
%==========================================================================
% Definitions and innitialization
sizeof_Float32 = 4;
sizeof_Float64 = 4;
sizeof_UInt32 = 4;
sizeof_UInt8 = 1;
Offset = 0; % Initial offset
%--------------------------------------------------------------------------
% Write the header for a structured grid:
%--------------------------------------------------------------------------
fname_number =num2str(1000000+time)
fname_vtk = [name,'_',fname_number,'.vtu'];
fid = fopen(fname_vtk,'w','b'); % note the 'b': not doing BigEndian does not work with MATLAB!
fprintf(fid,'<?xml version="1.0"?> \n');
fprintf(fid,'<VTKFile type="UnstructuredGrid" version="0.1" byte_order="BigEndian" >\n');
fprintf(fid,' <UnstructuredGrid>\n');
fprintf(fid,' <Piece NumberOfPoints="%i" NumberOfCells="%i">\n', int32(size(Points,1)), int32(size(ElementNumbers,1)));
%--------------------------------------------------------------------------
% Add point-wise data
%--------------------------------------------------------------------------
fprintf(fid,' <PointData Scalars="T" Vectors="Velocity" >\n');
% TEMPERATURE -----------
for k=1:length(Field_Names)
fprintf(fid,strcat(' <DataArray type="Float32" Name="',Field_Names{k},'" format="appended" offset="%i">\n'), int32(Offset));
eval(strcat('Offset = Offset + length(',Field_Names{k},'(:))*sizeof_Float32 + 1*sizeof_UInt32;'));
fprintf(fid,' </DataArray>\n');
end
% -----------------------
fprintf(fid,' </PointData>\n');
%--------------------------------------------------------------------------
% Add coordinates of structured grid
%--------------------------------------------------------------------------
fprintf(fid,' <Points>\n');
fprintf(fid,' <DataArray type="Float32" Name="Array" NumberOfComponents="3" format="appended" offset="%i" >\n',int32(Offset));
Offset = Offset + length(Points(:))*sizeof_Float32 + 1*sizeof_UInt32;
fprintf(fid,' </DataArray>\n');
fprintf(fid,' </Points>\n');
%--------------------------------------------------------------------------
% Add CELLS data
%--------------------------------------------------------------------------
fprintf(fid,' <Cells>\n');
% Connectivity -----------
fprintf(fid,' <DataArray type="Int32" Name="connectivity" format="appended" offset="%i">\n',int32(Offset));
Offset = Offset + length(ElementNumbers(:))*sizeof_UInt32 + 1*sizeof_UInt32;
fprintf(fid,' </DataArray>\n');
% Offsets -----------
offsets = cumsum(ones(size(ElementNumbers,1),1)*6);
fprintf(fid,' <DataArray type="Int32" Name="offsets" format="appended" offset="%i">\n',int32(Offset));
Offset = Offset + length(offsets(:))*sizeof_UInt32 + 1*sizeof_UInt32;
fprintf(fid,' </DataArray>\n');
% types -----------
types = ones(size(ElementNumbers,1),1)*13;
fprintf(fid,' <DataArray type="UInt8" Name="types" format="appended" offset="%i">\n',int32(Offset));
Offset = Offset + length(types(:))*sizeof_UInt8 + 1*sizeof_UInt32;
fprintf(fid,' </DataArray>\n');
fprintf(fid,' </Cells>\n');
% -----------------------
fprintf(fid,' </Piece>\n');
fprintf(fid,' </UnstructuredGrid>\n');
%--------------------------------------------------------------------------
% Append binary data in raw format: the order in which data arrays are
% added should be the same as how they are defined above
fprintf(fid,' <AppendedData encoding="raw"> \n');
fprintf(fid,'_');
% Add Temperature in binary format
for k=1:length(Field_Names)
eval(strcat('Field=',Field_Names{k},';'));
fwrite(fid,uint32(length(Field(:))*sizeof_Float32),'uint32');
fwrite(fid,single(Field(:)).' , 'float32');
end
% Add Coordinates in binary format
fwrite(fid,uint32(length(Points(:))*sizeof_Float32),'uint32');
fwrite(fid,single(Points).' , 'float32');
% Add Element connectivity in binary format
fwrite(fid,uint32(length(ElementNumbers(:))*sizeof_UInt32),'uint32');
fwrite(fid,uint32(ElementNumbers).' , 'int32');
% Add offsets array in binary format
fwrite(fid,uint32(length(offsets(:))*sizeof_UInt32),'uint32');
fwrite(fid,uint32(offsets).' , 'int32');
% Add types array in binary format
fwrite(fid,uint32(length(types(:))*sizeof_UInt32),'uint32');
fwrite(fid,uint8(types).' , 'int8');
fprintf(fid,' </AppendedData> \n');
fprintf(fid,'</VTKFile>\n');
fclose(fid);
disp(['Created Binary YinYang XML-VTK output file ',fname_vtk])
cd(start_dir); % Change back to original directory