[Paraview] Writing a Paraview Reader - Only part of the data available
Dan Lipsa
dan.lipsa at kitware.com
Tue Aug 25 10:39:14 EDT 2015
Hi James,
I was used to the old style and it kind of made sense with the problem you
are seeing, but you are right, setDimensions does not seem to be the
problem.
Is it any way I can get the code and a sample data so that I can run it
through a debugger. I cannot see anything else in the code.
Dan
On Tue, Aug 25, 2015 at 9:20 AM, James Furness <pcxjf1 at nottingham.ac.uk>
wrote:
> Thanks for your advice, however it hasn’t quite solved my problem.
>
> You are missing image->SetDimensions() - that may be a reason why your
> scalar does not have all values.
>
>
> The documentation marks vtkImageData::SetDimensions( ... ) as
> depreciated, and instead vtkImageData::SetExtent( ... ) should be used. It
> remarks that SetDimension is equivalent to SetExtent(0, i-1, 0, j-1, 0,
> k-1).
>
> (( doc page -
> http://www.vtk.org/doc/nightly/html/classvtkImageData.html#a42bc5faee908c50407e9d9ec97f74238
> ))
>
> Regardless, I tried using SetDimensions in this way, and resulted in some
> nasty set-fault crashes. Whilst now 64 elements were found correctly, all
> passed the first 8 were memory junk. When I use SetExtent( … ) the
> information print on the image object happily reports dimensions of 4, 4, 4
> as expected. So it seems this is set by SetExtent( … ).
>
> vtkRectilinear grid is like an image data with variable extents and warped
> grid.
>
>
> I’ll look into this class. It’s possible that I am mangling this reader by
> trying to shoehorn my problem into an inappropriate class at the moment.
> Thanks for pointing this out.
>
> Many thanks,
> James
>
> On 24 Aug 2015, at 15:31, Dan Lipsa <dan.lipsa at kitware.com> wrote:
>
> James,
> You are missing image->SetDimensions() - that may be a reason why your
> scalar does not have all values.
>
> vtkRectilinear grid is like an image data with variable extents and warped
> grid.
>
>
> On Fri, Aug 21, 2015 at 6:55 AM, James Furness <pcxjf1 at nottingham.ac.uk>
> wrote:
>
>> 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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> This message and any attachment are intended solely for the addressee
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>
> Please do not use, copy or disclose the information contained in this
> message or in any attachment. Any views or opinions expressed by the
> author of this email do not necessarily reflect the views of the
> University of Nottingham.
>
> This message has been checked for viruses but the contents of an
> attachment may still contain software viruses which could damage your
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> communications with the University of Nottingham may be monitored as
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