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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> 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<http://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.
_______________________________________________
Powered by www.kitware.com
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