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Write_VTK_XML.m
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Write_VTK_XML.m
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%Write_VTK_XML
%
% writes the grid into a VTK-XML file
%
disp(['Creating VTK files'])
%clear;
%$load test
%fname = 'test';
% Create the names
VTK_Grid = ['Grid',fname(1:end-4)];
VTK_Poly = ['Poly',fname(1:end-4)];
nnode = 0;
NumNodes = zeros(size(X));
for iz=1:size(X,3)
for ix=1:size(X,2)
for iy=1:size(X,1)
NumNodes(iy,ix,iz) = nnode;
nnode=nnode+1;
end
end
end
num_nodes = prod(size(X));
%==========================================================================
% Prepare the data for writing to VTK file
%==========================================================================
nel = nel_x*nel_y*nel_z;
nnel = 8;
%Points = zeros(nel*nnel,3);
num_el = 1;
Cells = zeros(nel,nnel+1);
Vx_vec = zeros(nel*8,1);
for iel_x=1:nel_x;
for iel_y=1:nel_y;
for iel_z=1:nel_z;
% Retrieve indices
ind_local = sub2ind(size(X),...
[iel_x iel_x+1 iel_x+1 iel_x iel_x iel_x+1 iel_x+1 iel_x ],...
[iel_y iel_y iel_y+1 iel_y+1 iel_y iel_y iel_y+1 iel_y+1],...
[iel_z iel_z iel_z iel_z iel_z+1 iel_z+1 iel_z+1 iel_z+1]);
%Points( ((num_el-1)*nnel+1):num_el*nnel,1) = X(ind_local);
%Points( ((num_el-1)*nnel+1):num_el*nnel,2) = Y(ind_local);
%Points( ((num_el-1)*nnel+1):num_el*nnel,3) = Z(ind_local);
%Cells(num_el,:) = [8, [((num_el-1)*nnel+1):num_el*nnel]-1 ];
Cells(num_el,:) = [8, NumNodes(ind_local)];
% Store velocity
%Velocity_vec( ((num_el-1)*nnel+1):num_el*nnel,1) = Vx(ind_local);
%Velocity_vec( ((num_el-1)*nnel+1):num_el*nnel,2) = Vy(ind_local);
%Velocity_vec( ((num_el-1)*nnel+1):num_el*nnel,3) = Vz(ind_local);
% Density, Viscosity
%Density_vec(((num_el-1)*nnel+1):num_el*nnel,1) = Rho(iel_x,iel_y,iel_z);
%Viscosity_vec(((num_el-1)*nnel+1):num_el*nnel,1) = Mu(iel_x,iel_y,iel_z);
Density_vec( num_el,1) = Rho(iel_x,iel_y,iel_z);
Viscosity_vec( num_el,1) = Mu(iel_x,iel_y,iel_z);
num_el = num_el+1;
end
end
end
Velocity_Vec = [];
Velocity_Vec(:,1) = Vx(:);
Velocity_Vec(:,2) = Vy(:);
Velocity_Vec(:,3) = Vz(:);
Points = [];
Points(:,1) = X(:);
Points(:,2) = Y(:);
Points(:,3) = Z(:);
%nel = 1;
%==========================================================================
% End of preparing the data
%==========================================================================
%==========================================================================
%
% START WRITING VTU FILE
%
%==========================================================================
% header
fid = fopen([VTK_Grid,'.vtu'],'w');
fprintf(fid,'<?xml version="1.0"?> \n');
%fprintf(fid,'<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" compressor="vtkZLibDataCompressor">\n');
fprintf(fid,'<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" >\n');
fprintf(fid,' <UnstructuredGrid> \n');
fprintf(fid,' <Piece NumberOfPoints="%i" NumberOfCells="%i" >\n',num_nodes, nel);
% Point-wise data==========================================================
fprintf(fid,' <PointData Vectors="Velocity" Scalars="Vx">\n');
fprintf(fid,' <DataArray type="Float32" Name="Velocity" NumberOfComponents="3" format="ascii"> \n');
fprintf(fid,' ');
offset = nnel;
for i=1:num_nodes
for k=1:3
fprintf(fid,' %g',Velocity_Vec(i,k));
end
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' <DataArray type="Float32" Name="Vx" format="ascii"> \n');
fprintf(fid,' ');
offset = nnel;
for i=1:num_nodes
fprintf(fid,' %g',Velocity_Vec(i,1));
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' <DataArray type="Float32" Name="Vy" format="ascii"> \n');
fprintf(fid,' ');
offset = nnel;
for i=1:num_nodes
fprintf(fid,' %g',Velocity_Vec(i,2));
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' <DataArray type="Float32" Name="Vz" format="ascii"> \n');
fprintf(fid,' ');
offset = nnel;
for i=1:num_nodes
fprintf(fid,' %g',Velocity_Vec(i,3));
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' </PointData>\n');
%==========================================================================
% Cell-wise data===========================================================
fprintf(fid,' <CellData Scalar="Density">\n');
fprintf(fid,' <DataArray type="Float32" Name="Density" format="ascii"> \n');
fprintf(fid,' ');
offset = nnel;
for i=1:nel
fprintf(fid,' %g',Density_vec(i));
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' <DataArray type="Float32" Name="Viscosity" format="ascii"> \n');
fprintf(fid,' ');
offset = nnel;
for i=1:nel
fprintf(fid,' %g',Viscosity_vec(i));
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' </CellData>\n');
%==========================================================================
% Nodal coordinates =======================================================
fprintf(fid,' <Points>\n');
fprintf(fid,' <DataArray type="Float32" NumberOfComponents="3" format="ascii">\n');
%fprintf(fid,' <DataArray type="Float32" NumberOfComponents="3" format="appended" offset="0">\n');
fprintf(fid,' ');
for ipoint=1:num_nodes
for k=1:3
fprintf(fid,' %g',Points(ipoint,k));
end
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' </Points> \n');
%==========================================================================
% describe the cells=======================================================
fprintf(fid,' <Cells> \n');
fprintf(fid,' <DataArray type="Int32" Name="connectivity" format="ascii"> \n');
fprintf(fid,' ');
for iel=1:nel
for inode=2:nnel+1
fprintf(fid,' %i',Cells(iel,inode));
end
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' <DataArray type="Int32" Name="offsets" format="ascii"> \n');
fprintf(fid,' ');
offset = nnel;
for iel=1:nel
fprintf(fid,' %i',offset);
offset = offset+nnel;
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' <DataArray type="UInt8" Name="types" format="ascii"> \n');
fprintf(fid,' ');
types = 12;
for iel=1:nel
fprintf(fid,' %i',types);
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' </Cells> \n');
%==========================================================================
fprintf(fid,' </Piece>\n');
fprintf(fid,' </UnstructuredGrid> \n');
fprintf(fid,'</VTKFile>\n');
fclose(fid);
%==========================================================================
%
% FINISHED WRITING VTU FILE
%
%==========================================================================
%==========================================================================
%
% START WRITING VTP FILE
%
%==========================================================================
% header
fid = fopen([VTK_Poly,'.vtp'],'w');
fprintf(fid,'<?xml version="1.0"?> \n');
fprintf(fid,'<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" >\n');
fprintf(fid,' <PolyData> \n');
fprintf(fid,' <Piece NumberOfPoints="%i" NumberOfVerts="%i" NumberOfLines="%i" \n',size(PassiveParticles,1), 0 ,0);
fprintf(fid,' NumberOfStrips="%i" NumberOfPolys="%i"> \n',0,size(TRI,1));
% Point-wise data==========================================================
fprintf(fid,' <PointData>\n');
fprintf(fid,' </PointData>\n');
%==========================================================================
% Cell-wise data===========================================================
fprintf(fid,' <CellData>\n');
fprintf(fid,' </CellData>\n');
%==========================================================================
% Nodal coordinates =======================================================
fprintf(fid,' <Points>\n');
fprintf(fid,' <DataArray type="Float32" NumberOfComponents="3" format="ascii">\n');
fprintf(fid,' ');
for ipoint=1:size(PassiveParticles,1)
for k=1:3
fprintf(fid,' %g',PassiveParticles(ipoint,k));
end
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' </Points> \n');
%==========================================================================
% Polys =======================================================
fprintf(fid,' <Polys>\n');
% Connectivity
fprintf(fid,' <DataArray type="Int32" Name="connectivity" format="ascii">\n');
fprintf(fid,' ');
for itri=1:size(TRI,1)
for k=1:3
fprintf(fid,' %i',TRI(itri,k)-1);
end
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' <DataArray type="Int32" Name="offsets" format="ascii">\n');
fprintf(fid,' ');
offset = 3;
for itri=1:size(TRI,1)
fprintf(fid,' %i',offset);
offset = offset+3;
end
fprintf(fid,'\n');
fprintf(fid,' </DataArray> \n');
fprintf(fid,' </Polys> \n');
%==========================================================================
fprintf(fid,' </Piece>\n');
fprintf(fid,' </PolyData> \n');
fprintf(fid,'</VTKFile>\n');
fclose(fid);
%==========================================================================
%
% FINISHED WRITING VTP FILE
%
%==========================================================================
disp(['Finished writing VTK files: ', [VTK_Grid,'.vtu'],' and ' [VTK_Poly,'.vtp']])
% Write the Poly file in binary form
% Write points
fid = fopen([fname,'VTK_Poly.vtk'],'w','b'); % note the 'b' for big endian!
fprintf(fid,'# vtk DataFile Version 3.0 \n'); % VTK format
fprintf(fid,'Passive tracer surface \n');
fprintf(fid,'BINARY \n');
fprintf(fid,'DATASET POLYDATA\n');
% Write points
PassiveParticles = single(full(PassiveParticles)); % ensure that it has correct dataformat
fprintf(fid,'POINTS %i float \n',size(PassiveParticles,1)); % # of points
fwrite(fid,PassiveParticles.','single'); % Write binary data
% Write triangle-edgepoints
Data_TRI = [ones(size(TRI,1),1,'int32')*3, int32(TRI-1)]; % should be integer*32
fprintf(fid,'\nTRIANGLE_STRIPS %i %i \n',size(TRI,1),size(TRI,1)*4 ); % description of triangles
fwrite(fid,Data_TRI.','int') % Write Binary data
fclose(fid)