[Paraview] Writing a Paraview Reader - Only part of the data available

[James Furness]

Hello,

I have a program that will produce an output either in csv, or a binary format (which I have written and can alter). 

The data points are constructed by taking 3 vectors, and stepping at set intervals along these vectors to construct a 3D set of data. Ultimately there shouldn’t be a restriction on the three vectors, so the data may not be in a rectilinear array. But I’m leaving this for now and assuming the data is constructed from 3 orthogonal Axis aligned vectors to create a rectilinear structured grid. When I have a better grasp of preview readers I’ll update the reader to account for this. I guess it would require an unstructured data type to handle non-orthogonal grids?

Also, the user is free to select what data they save from the program. This could be many fields, both vector and scalar quantities. What has been selected is stored in a header to the file, and known on reading. For my toy example I save only one scalar quantity.

I’ve been trying to write a reader for paraview to import the binary files output. The csv format works ok, but the files can become large and it is a pain to have to construct the vector quantities from 3 scalars in each case, I want to avoid the user having to do this work. Another reason for writing a custom reader is to include additional information into the binary file for visualisation (e.g. the position of atoms, not a field quantity).

With that background and reasoning I have managed to follow the documentation enough to read a basic test file, get the origin and point spacing, and read a single scalar quantity into a vtkDataArray owned by a vtkImageData object. Paraview picks this up seemingly correctly, with one flaw:

It only takes 2 elements from each dimension, 0 and 1 displaying 8 elements in total. I am confident it has read the other values correctly as the Information tab reports “X extent 0 to 3” “X range: -1 to 1” (as expected) and similar for the other dimensions. If I view the data in spreadsheet layout the 8 values it has seem correct, but the others are missing.

The code I am using in the reader’s RequestData(  ) function is added below.

Does anyone know why this may be happening and how to fix it? Also, any advice on how I should structure the reader to handle the non-orthogonal data?

Thanks for your time, and thank you for such a stellar program. The results paraview produces for this data is brilliant, hence my want to make it convenient for our users!

Regards,
James Furness


CODE for RequestData( ) Method:
———————————————————————

int LondonReader::RequestData(
        vtkInformation*,
        vtkInformationVector**,
        vtkInformationVector *outputVector)
{
    vtkWarningMacro("Requesting the data!");


    ifstream finp;
    finp.open(this->FileName, ios::in | ios::binary);

    if (finp.is_open()) {
        cerr << "File is open without problem!" << endl;
    }   else    {
        cerr << "File failed to open :(" << endl;
        return 0;
    }

    // size of real numbers may not be 8. Check for this from file header
    int realSize;
    finp.read((char*)&realSize, sizeof(int));
    if(realSize != 8)   {
        cerr << "Not implimented yet!" << endl;
        return 0;
    }

    // number of data fields
    int nFields;
    finp.read((char*)&nFields, sizeof(int));

    vtkImageData* image = vtkImageData::GetData(outputVector);

    // Read the dimensions of the grid and set the extent accordingly
    int gridDim[3];
    finp.read((char*)&gridDim, 3*sizeof(int));
    int extent[6] = {0, gridDim[0]-1, 0, gridDim[1]-1, 0, gridDim[2]-1};
    image->SetExtent(extent);


    // Read the field names from the file
    std::vector<std::string> fields;
    std::string strBuf;
    for (int i = 0; i < nFields; i++)   {
        std::getline( finp, strBuf, '\0');
        fields.push_back(strBuf);
        cerr << "Printing Fields (" << i << "): " << fields[i] << endl;
    }

    // setup image for only one field for test case
    image->AllocateScalars(VTK_FLOAT, 1);
    vtkDataArray* scalars = image->GetPointData()->GetScalars();

    // currently there is only one field 'rho'
    scalars->SetName(fields[3].c_str());

    double x, y, z, rho;
    double oX, oY, oZ;      //origin coordinates
    double sX, sY, sZ;      //spacing of points

    for (vtkIdType itx = 0; itx < gridDim[0]; itx++)    {
        for (vtkIdType ity = 0; ity < gridDim[1]; ity++)    {
            for (vtkIdType itz = 0; itz < gridDim[2]; itz++)    {
                finp.read((char*)&x, realSize);
                finp.read((char*)&y, realSize);
                finp.read((char*)&z, realSize);
                finp.read((char*)&rho, realSize);

                // Find and set the origin and spacing
                if (itx == 0 && ity == 0 && itz == 0)   {
                    image->SetOrigin(x, y, z);
                    oX = x; oY = y; oZ = z;
                }   else if (itx == 1 && ity == 0 && itz == 0)  {
                    sX = x - oX;
                }   else if (itx == 0 && ity == 1 && itz == 0)  {
                    sY = y - oY;
                }   else if (itx == 0 && ity == 0 && itz == 1)  {
                    sZ = z - oZ;
                }
                //check correct read.
                cerr << x << "," << y << "," << z << "," << rho << ", at " << itx*(gridDim[1]*gridDim[2]) + ity*gridDim[2] + itz << endl;

                //add value
                scalars->SetTuple1(itx*gridDim[1]*gridDim[2] + ity*gridDim[2] + itz,
                        rho);
            }
        }
    }

    image->SetSpacing(sX, sY, sZ);

    image->Print(cerr);

    return 1;
}





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