[Paraview] pv 3.8 segfaults on opening raw binary files
Mohammad Mirzadeh
mirzadeh at gmail.com
Thu May 17 20:44:45 EDT 2012
YESSSSSSSSS! Alright fixed the problem. This might help other folks having
the same problem:
http://public.kitware.com/pipermail/paraview/2007-October/006066.html
Since I know what big pain this is, email me if you needed assistance
getting your code working :D
On Thu, May 17, 2012 at 4:13 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>wrote:
> Thanks David. I have thoroughly looked through that file format document
> but with no luck. It the mean time, I have tried the xml format and while
> my ascii writer (both in legacy and xml versions) work, I'm hopeless when
> it comes to the binary version.
>
> It seems that (for xml binary) pv is confused (well, actually I'm also!).
> What exactly should the offset values be? Initially I thought they are
> simply the size of the DataArray you are writing, but then I loaded my
> ascii version and saved it as a binary file. Comparing the two, it seems pv
> adds another variable of sizeof(int). What exactly is this? I cannot find
> any hint in the file-format document or anywhere online!
>
> I can send my code again if someone is willing to take a look.
>
> Thanks
>
>
> On Thu, May 17, 2012 at 8:20 AM, David E DeMarle <dave.demarle at kitware.com
> > wrote:
>
>> Something is wrong with this binary file. Paraview opens up other
>> binary files just fine, but 3.8 and newer versions of paraview don't
>> open up this one.
>>
>> ParaView appears to failing near vtkDataSetSurfaceFilter.cxx:1097
>> where it is trying to process the cells.
>>
>> Try these to diagnose the specific problem:
>> * take a closer look at http://www.vtk.org/VTK/img/file-formats.pdf
>> * load this in a simple vtk program that loads and then renders the
>> data under a debugger
>> * change your writer to convert this binary file to the corresponding
>> ascii version.
>>
>> David E DeMarle
>> Kitware, Inc.
>> R&D Engineer
>> 21 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-881-4909
>>
>>
>> On Wed, May 16, 2012 at 2:49 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>
>> wrote:
>> > If it helps, here's the source code and attached is a sample binary
>> file:
>> >
>> > void QuadTree::writeBinaryVTK(string file_name, vtk_data_format format){
>> >
>> >
>> > CaslInt num_of_nodes, num_of_cells, num_of_leaf_cells;
>> >
>> > CaslInt node_of_cell[4];
>> >
>> > const QuadCell *cell = this -> get_cells();
>> >
>> > const QuadNode *node = this -> get_nodes();
>> >
>> > double x, y, z;
>> >
>> >
>> > CaslInt i_max, j_max;
>> >
>> > CaslInt i_min, j_min;
>> >
>> >
>> >
>> >
>> > num_of_cells = this -> number_of_cells();
>> >
>> > num_of_nodes = this -> number_of_nodes();
>> >
>> >
>> > ofstream binWriter(file_name.c_str(), ios::binary);
>> >
>> >
>> > binWriter << "# vtk DataFile Version 2.0 \n";
>> >
>> > binWriter << "Quadtree Mesh \n";
>> >
>> > binWriter << "BINARY \n";
>> >
>> > binWriter << "DATASET UNSTRUCTURED_GRID \n";
>> >
>> > binWriter << "POINTS " << number_of_nodes() << " double \n";
>> >
>> >
>> > for (CaslInt n=0; n<num_of_nodes; n++){
>> >
>> > x = this -> x_fr_i(node[n].i);
>> >
>> > y = this -> y_fr_j(node[n].j);
>> >
>> > z = 0.0;
>> >
>> >
>> > binWriter.write((char*)&x, sizeof(double));
>> >
>> > binWriter.write((char*)&y, sizeof(double));
>> >
>> > binWriter.write((char*)&z, sizeof(double));
>> >
>> > }
>> >
>> >
>> > num_of_leaf_cells = 0;
>> >
>> > for (CaslInt n=0; n<num_of_cells; n++){
>> >
>> > if ( cell[n].is_leaf() ) num_of_leaf_cells++;
>> >
>> > }
>> >
>> > binWriter << "\n";
>> >
>> > binWriter << "CELLS " << num_of_leaf_cells << " " <<
>> 5*num_of_leaf_cells
>> > << "\n";
>> >
>> >
>> > for (CaslInt n=0; n<num_of_cells; n++){
>> >
>> > if ( cell[n].is_leaf() ){
>> >
>> > i_min = cell[n].imin;
>> >
>> > j_min = cell[n].jmin;
>> >
>> > i_max = cell[n].imax();
>> >
>> > j_max = cell[n].jmax();
>> >
>> >
>> >
>> > node_of_cell[0] = this ->
>> get_node_by_coordinates(i_min,j_min);
>> >
>> > node_of_cell[1] = this ->
>> get_node_by_coordinates(i_max,j_min);
>> >
>> > node_of_cell[2] = this ->
>> get_node_by_coordinates(i_max,j_max);
>> >
>> > node_of_cell[3] = this ->
>> get_node_by_coordinates(i_min,j_max);
>> >
>> >
>> > int num_of_childs = 4;
>> >
>> > binWriter.write((char*)&num_of_childs, sizeof(int));
>> >
>> > binWriter.write((char*)&node_of_cell[0], sizeof(int)*4);
>> >
>> > }
>> >
>> > }
>> >
>> > binWriter << "\n";
>> >
>> > binWriter << "CELL_TYPES " << num_of_leaf_cells << "\n";
>> >
>> >
>> > int cell_type = 9;
>> >
>> > for (CaslInt n=0; n<num_of_leaf_cells; n++)
>> > binWriter.write((char*)&cell_type, sizeof(int));
>> >
>> >
>> > binWriter << "\n";
>> >
>> >
>> > switch (format){
>> >
>> > case POINT_DATA:{
>> >
>> > binWriter << "POINT_DATA " << num_of_nodes << "\n";
>> >
>> > break;
>> >
>> > }
>> >
>> >
>> > case CELL_DATA:{
>> >
>> > binWriter << "CELL_DATA " << num_of_cells << "\n";
>> >
>> > break;
>> >
>> > }
>> >
>> >
>> > }
>> >
>> > binWriter.close();
>> >
>> > }
>> >
>> > void QuadTree::writeBinaryVTK(ArrayV<double> &F, string data_name,
>> string
>> > file_name){
>> >
>> >
>> > ofstream binWriter(file_name.c_str(), ios::app | ios::binary);
>> >
>> >
>> > binWriter << "SCALARS " << data_name << " double \n";
>> >
>> > binWriter << "LOOKUP_TABLE default \n";
>> >
>> >
>> > double *pF = (double*)F;
>> >
>> > binWriter.write((char*)pF, sizeof(double)*F.size());
>> >
>> >
>> > binWriter.close();
>> >
>> > }
>> >
>> >
>> >
>> >
>> > On Tue, May 15, 2012 at 2:25 PM, Mohammad Mirzadeh <mirzadeh at gmail.com>
>> > wrote:
>> >>
>> >> Hi guys,
>> >>
>> >> I have a problem getting pv open my binary file. It basically segfaults
>> >> and terminates without any information. When I run in gdb I get:
>> >>
>> >> ERROR: In /build/buildd/paraview-3.8.1/VTK/IO/vtkDataReader.cxx, line
>> 1910
>> >> vtkUnstructuredGridReader (0x19f6890): Unsupported data type: 1
>> >>
>> >> Program received signal SIGBUS, Bus error.
>> >> 0x00007fffeaeb6597 in
>> >> vtkDataSetSurfaceFilter::UnstructuredGridExecute(vtkDataSet*,
>> vtkPolyData*)
>> >> ()
>> >> from /usr/lib/paraview/libvtkGraphics.so.pv3.8
>> >>
>> >> Program terminated with signal SIGBUS, Bus error.
>> >>
>> >> Is there something wrong with my data file? I could send a sample file
>> if
>> >> needed. I basically followed
>> http://www.vtk.org/VTK/img/file-formats.pdf to
>> >> write the binary format.
>> >>
>> >
>> >
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>>
>
>
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