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Paraview .vtr files in binary

Dear all,
I am trying to write my output files in vtr format and the following gives me a correct output file in ASCII.

Code:

#include <iostream>

#include <fstream>

#include <cmath>



// Function to calculate phi = sin(x) * cos(y)

double phi(double x, double y) {

    return sin(x) * cos(y);

}



int main() {

    int n = 10; // Size of the mesh (10x10)

    double step = 1.0 / (n - 1); // Step size

    

    std::ofstream outfile("output.vtr");

    

    // Writing the header

    outfile << "<?xml version=\"1.0\"?>\n";

    outfile << "<VTKFile type=\"RectilinearGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n";

    outfile << "<RectilinearGrid WholeExtent=\"0 " << n-1 << " 0 " << n-1 << " 0 0\">\n";

    outfile << "<Piece Extent=\"0 " << n-1 << " 0 " << n-1 << " 0 0\">\n";

    // Writing the scalar data (phi)

    outfile << "<PointData>\n";

    outfile << "<DataArray type=\"Float64\" Name=\"phi\" NumberOfComponents=\"1\" format=\"ascii\">\n";

    for (int j = 0; j < n; ++j) {

        for (int i = 0; i < n; ++i) {

            double x = i * step;

            double y = j * step;

            outfile << phi(x, y) << " ";

        }

    }

    outfile << "\n</DataArray>\n";

    outfile << "</PointData>\n";

    // Writing the coordinates

    outfile << "<Coordinates>\n";

    outfile << "<DataArray type=\"Float64\" Name=\"X_COORDINATES\" NumberOfComponents=\"1\" format=\"ascii\">\n";

    for (int i = 0; i < n; ++i) {

        outfile << i * step << " ";

    }

    outfile << "\n</DataArray>\n";

    outfile << "<DataArray type=\"Float64\" Name=\"Y_COORDINATES\" NumberOfComponents=\"1\" format=\"ascii\">\n";

    for (int j = 0; j < n; ++j) {

        outfile << j * step << " ";

    }

    outfile << "\n</DataArray>\n";  

    outfile << "<DataArray type=\"Float64\" Name=\"Z_COORDINATES\" NumberOfComponents=\"1\" format=\"ascii\">\n";

    outfile << "0.0 \n";

    outfile << "</DataArray>\n";

    outfile << "</Coordinates>\n";

    

    // Closing tags

    outfile << "</Piece>\n";

    outfile << "</RectilinearGrid>\n";

    outfile << "</VTKFile>\n";

    

    outfile.close();

    

    std::cout << "Output file generated: output.vtr\n";

    

    return 0;

}

To get output file in BINARY, I tried the following:

Code:

#include <iostream>

#include <fstream>

#include <cmath>



// Function to calculate phi = sin(x) * cos(y)

double phi(double x, double y) {

    return sin(x) * cos(y);

}



int main() {

    int n = 10; // Size of the mesh (10x10)

    double step = 1.0 / (n - 1); // Step size

    

    std::ofstream outfile("output.vtr");

    

    double A[n][n];

    double xx[n];

    double yy[n];

    

    for (int j = 0; j < n; ++j) {

        for (int i = 0; i < n; ++i) {

            double x = i * step;

            double y = j * step;

            //outfile << phi(x, y) << " ";

            A[i][j]= phi(x, y);

        }

    }

    

    for (int i = 0; i < n; ++i) {

        xx[i] =i * step;

    }

    

    for (int j = 0; j < n; ++j) {

        yy[j] =j * step;

    }

    

    // Writing the header

    outfile << "<?xml version=\"1.0\"?>\n";

    outfile << "<VTKFile type=\"RectilinearGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n";

    outfile << "<RectilinearGrid WholeExtent=\"0 " << n-1 << " 0 " << n-1 << " 0 0\">\n";

    outfile << "<Piece Extent=\"0 " << n-1 << " 0 " << n-1 << " 0 0\">\n";

    // Writing the scalar data (phi)

    outfile << "<PointData>\n";

    outfile << "<DataArray type=\"Int64\" Name=\"phi\" NumberOfComponents=\"1\" format=\"binary\">\n";

    for (int j = 0; j < n; ++j) {

        for (int i = 0; i < n; ++i) {

            outfile.write(reinterpret_cast<const char*>(&A[i][j]), sizeof(double));

        }

    }

    outfile << "\n</DataArray>\n";

    outfile << "</PointData>\n";

    // Writing the coordinates

    outfile << "<Coordinates>\n";

    outfile << "<DataArray type=\"Int64\" Name=\"X_COORDINATES\" NumberOfComponents=\"1\" format=\"binary\">\n";

    for (int i = 0; i < n; ++i) {

        outfile.write(reinterpret_cast<const char*>(&xx[i]), sizeof(double));

    }

    outfile << "\n</DataArray>\n";

    outfile << "<DataArray type=\"Int64\" Name=\"Y_COORDINATES\" NumberOfComponents=\"1\" format=\"binary\">\n";

    for (int j = 0; j < n; ++j) {

        outfile.write(reinterpret_cast<const char*>(&yy[j]), sizeof(double));

    }

    outfile << "\n</DataArray>\n";  

    outfile << "<DataArray type=\"Int64\" Name=\"Z_COORDINATES\" NumberOfComponents=\"1\" format=\"binary\">\n";

    double z =0.0;

    outfile.write(reinterpret_cast<const char*>(&z), sizeof(double));

    //outfile << "0.0 \n";

    outfile << "\n</DataArray>\n";

    outfile << "</Coordinates>\n";

    

    // Closing tags

    outfile << "</Piece>\n";

    outfile << "</RectilinearGrid>\n";

    outfile << "</VTKFile>\n";

    

    outfile.close();

    

    std::cout << "Output file generated: output.vtr\n";

    

    return 0;

}

The generated output is not correctly read by Paraview. It gives me the following error.

ERROR: In /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/IO/XMLParser/vtkXMLParser.cxx, line 379
vtkXMLDataParser (0x1659c570): Error parsing XML in stream at line 7, column 0, byte index 255: not well-formed (invalid token)

ERROR: In /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/IO/XML/vtkXMLReader.cxx, line 521
vtkXMLRectilinearGridReader (0x17dda5a0): Error parsing input file. ReadXMLInformation aborting.

I am using a Ubuntu system; byte_order is LittleEndian and using g++ compiler. Paraview version is 5.10.1.

Can anyone help me fix this. A similar example for writing binary vtr files using c++ will also help.

Successfully ported to legacy VTK. But xml vtk binary is still unaccomplished

Hi all,
I have successfully implemented the output file writing in binary using the legacy vtk format. For this, I had to use byte swap to BigEndian. The code is as follows.

Code:



#include <iostream>

#include <fstream>

#include <cmath>



template <typename T>

void SwapEnd(T& var)

{

  char* varArray = reinterpret_cast<char*>(&var);

  for(long i = 0; i < static_cast<long>(sizeof(var)/2); i++)

    std::swap(varArray[sizeof(var) - 1 - i],varArray[i]);

}



int main()

{

    int n = 10; // Size of the mesh (10x10)

    double step = 1.0 / (n - 1); // Step size



    double A[n][n];

    double xx[n];

    double yy[n];

    

    for (int j = 0; j < n; j++) {

        for (int i = 0; i < n; i++) {

            double x = i * step;

            double y = j * step;

            A[i][j]= sin(x) * cos(y);

        }

    }

    

    for (int i = 0; i < n; i++) {

        xx[i] =i * step;

    }

    

    for (int j = 0; j < n; j++) {

        yy[j] =j * step;

    }



  std::ofstream vtkstream;

  vtkstream.open("outputBinary.vtk", std::ios::out | std::ios::binary);

  if (vtkstream) {

    vtkstream<<"# vtk DataFile Version 2.0"<<"\n";

    vtkstream<<"Phi=sin(x)"<<"\n";

    vtkstream<<"BINARY"<<"\n";

    vtkstream<<"DATASET RECTILINEAR_GRID"<<std::endl;

    vtkstream<<"DIMENSIONS " << n << " " << n << " 1"<<std::endl;

    vtkstream<<"X_COORDINATES " << n << " double"<<std::endl;

    //for (int i = 0; i < n; i++) {

    for (unsigned int i = 0; i < n; i++) {

        SwapEnd(xx[i]);

        vtkstream.write((char*)&xx[i], sizeof(double));

        //vtkstream<< xx[i] << " ";

    }

    vtkstream<<"\nY_COORDINATES " << n << " double"<<std::endl;

    //for (int j = 0; j < n; j++) {

    for (unsigned int j = 0; j < n; j++) {

        SwapEnd(yy[j]);

        vtkstream.write((char*)&yy[j], sizeof(double));

        //vtkstream<< yy[j] << " ";

    }

    vtkstream<<"\nZ_COORDINATES " << 1 << " double"<<std::endl;

    double zz = 0.0;

    SwapEnd(zz);

    vtkstream.write((char*)&zz, sizeof(double));

    //vtkstream<< "0.0" << "\n";

    vtkstream<<"POINT_DATA " << n*n << std::endl;

    vtkstream<<"SCALARS " << "Phi " << " double 1" <<std::endl;

    vtkstream<<"LOOKUP_TABLE default" <<std::endl;

    for (int j = 0; j < n; j++) {

        for (int i = 0; i < n; i++) {

            SwapEnd(A[i][j]);

            vtkstream.write((char*)&A[i][j], sizeof(double));

        }

    }

    vtkstream.close();

  } 

  

  else {

    std::cout<<"ERROR"<<std::endl;

  }

  return 0;

}

I desperately want to convert this to XML VTK in binary. Specifically, I wish to understand the following.

1. format ="binary"
This involves base64 encoding. But I am not able to understand how to do this in c++ for an array of double.

2. format="appended"
< AppendedData encoding="raw">
_NNNNData
</AppendedData>

Here I am not understanding how to specify NNNN.

Experts, please help me with this.

Working code in c++ to generate xml vtk files in appended raw binary

After lots and lots of effort, I found out how to write in binary.

Some reverse engineering helped me. We can load ascii files in paraview and use file>save data to generate binary files.

I am sharing the code below.

Code:

#include <iostream>

#include <fstream>

#include <cmath>



int main() {

    int n = 10; // Size of the mesh (10x10)

    double step = 1.0 / (n - 1); // Step size

    

    double A[n][n];

    double xx[n];

    double yy[n];

    

    for (int i = 0; i < n; i++) {

        xx[i] =i * step;

    }

    

    for (int j = 0; j < n; j++) {

        yy[j] =j * step;

    }

    

    double zz =0.0;



    for (int j = 0; j < n; j++) {

        for (int i = 0; i < n; i++) {

            A[i][j]= sin(xx[i]) * cos(yy[j]);

        }

    }



    // Size of each array

    int N1 = n*n*sizeof(double); // size of A in bytes

    int N2 = n*sizeof(double);   // size of xx in bytes

    int N3 = n*sizeof(double);   // size of yy in bytes

    int N4 = 1*sizeof(double);   // size of zz in bytes



    // Offsets

    int offset1 = 0;

    int offset2 = offset1 + sizeof(double) + N1;

    int offset3 = offset2 + sizeof(double) + N2;

    int offset4 = offset3 + sizeof(double) + N3;

    

    std::ofstream outfile("output_binaryAppended.vtr", std::ios::out | std::ios::binary);

     

    if (outfile) {

        // Writing the header

        outfile << "<?xml version=\"1.0\"?>\n";

        outfile << "<VTKFile type=\"RectilinearGrid\" version=\"1.0\" header_type=\"UInt64\" byte_order=\"LittleEndian\">\n";

        outfile << "<RectilinearGrid WholeExtent=\"0 " << n-1 << " 0 " << n-1 << " 0 0\">\n";

        outfile << "<Piece Extent=\"0 " << n-1 << " 0 " << n-1 << " 0 0\">\n";

        // Writing the scalar data (phi)

        outfile << "<PointData>\n";

        outfile << "<DataArray type=\"Float64\" Name=\"phi\" format=\"appended\" offset=\"" << offset1 <<"\">\n";

        outfile << "</DataArray>\n";

        outfile << "</PointData>\n";

        // Writing the coordinates

        outfile << "<Coordinates>\n";

        outfile << "<DataArray type=\"Float64\" Name=\"X_COORDINATES\" format=\"appended\" offset=\"" << offset2 <<"\">\n";

        outfile << "</DataArray>\n";

        outfile << "<DataArray type=\"Float64\" Name=\"Y_COORDINATES\" format=\"appended\" offset=\"" << offset3 <<"\">\n";

        outfile << "</DataArray>\n"; 

        outfile << "<DataArray type=\"Float64\" Name=\"Z_COORDINATES\" format=\"appended\" offset=\"" << offset4 <<"\">\n";

        outfile << "</DataArray>\n";

        outfile << "</Coordinates>\n";

        // Closing tags

        outfile << "</Piece>\n";

        outfile << "</RectilinearGrid>\n";

        // Appended Data

        outfile << "<AppendedData encoding=\"raw\">\n";

        outfile << "_";

        outfile.write((char*)&N1, sizeof(double));

        for (int j = 0; j < n; j++) {

            for (int i = 0; i < n; i++) {

                outfile.write((char*)&A[i][j], sizeof(double));

            }

        }

        outfile.write((char*)&N2, sizeof(double));

        for (int i = 0; i < n; i++) {

            outfile.write((char*)&xx[i], sizeof(double));

        }

        outfile.write((char*)&N3, sizeof(double));

        for (int j = 0; j < n; j++) {

            outfile.write((char*)&yy[j], sizeof(double));

        }

        outfile.write((char*)&N4, sizeof(double));

        outfile.write((char*)&zz, sizeof(double));

        

        outfile << "\n</AppendedData>\n";

        // Final closing tags

        outfile << "</VTKFile>\n";

        outfile.close();

    } 

  

    else {

        std::cout<<"ERROR"<<std::endl;

    }

    

    std::cout << "Output file generated: output_binaryAppended.vtr\n";



    return 0;

}

Hope this helps someone some day!!!