[Paraview] Writing a Paraview Reader - Only part of the data available
Dan Lipsa
dan.lipsa at kitware.com
Wed Aug 26 12:16:06 EDT 2015
James,
Great. I am glad you found the problem.
You set scalar data by
1. create and fill a vtkDataArray
2. dataset->GetPointData()->SetScalars(vtkDataArray*)
On Wed, Aug 26, 2015 at 10:49 AM, James Furness <pcxjf1 at nottingham.ac.uk>
wrote:
> Thanks Dan,
>
> I found the problem whilst cleaning up the code to send you a copy. Funny
> how that happens…
>
> It turned out to be an old
>
> int extent[6] = {0, 1, 0, 1, 0, 1};
> outInfo->Set
> (vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT(), extent, 6);
>
> call in RequestInformation( … ) that was wrongly setting the extent to
> [0,1,0,1,0,1].
>
> Fixing that seemed to fix the problem of only 8 points showing up.
>
> I’ve been looking now at using the vtkRectilinearGrid class, I’ve set the
> X, Y and Z coordinates using the respective
> SetXCoordinates (vtkDataArray *) methods. But I can’t work out from the
> documentation how to enter my scalar data into this grid for use within
> paraview.
>
> Can you offer any advice on this? Or better point me to an example to
> learn from?
>
> Many thanks,
> James
>
> On 25 Aug 2015, at 15:39, Dan Lipsa <dan.lipsa at kitware.com> wrote:
>
> 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
>> and may contain confidential information. If you have received this
>> message in error, please send it back to me, and immediately delete it.
>>
>> 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
>> computer system, you are advised to perform your own checks. Email
>> communications with the University of Nottingham may be monitored as
>> permitted by UK legislation.
>>
>>
>
>
>
> This message and any attachment are intended solely for the addressee
> and may contain confidential information. If you have received this
> message in error, please send it back to me, and immediately delete it.
>
> 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
> computer system, you are advised to perform your own checks. Email
> communications with the University of Nottingham may be monitored as
> permitted by UK legislation.
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
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>
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