[vtk-developers] Re: [vtkusers] Problem with using vtkArrayCalculator to extract fields for vtkImageFFT Processing

[Randall Hand]

Done... Bug #2234

http://www.vtk.org/Bug/bug.php?op=show&bugid=2234&pos=2

On 9/14/05, Mathieu Malaterre <mathieu.malaterre at kitware.com> wrote:
> 
> Ok this is a bug:
> 
> i ========== End of Data Statistics ===============
> ==30679==
> ==30679== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 9 from 4)
> ==30679==
> ==30679== 1 errors in context 1 of 1:
> ==30679== Invalid read of size 8
> ==30679== at 0x12A4B8F5: void
> vtkImageFFTExecute<double>(vtkImageFFT*, vtkImageData*, int*, double*,
> vtkImageData*, int*, double*, int) (vtkImageFFT.cxx:137)
> ==30679== by 0x12A4A645: vtkImageFFT::ThreadedExecute(vtkImageData*,
> vtkImageData*, int*, int) (vtkImageFFT.cxx:203)
> ==30679== by 0x1353AEA2:
> vtkThreadedImageAlgorithm::ThreadedRequestData(vtkInformation*,
> vtkInformationVector**, vtkInformationVector*, vtkImageData***,
> vtkImageData**, int*, int) (vtkThreadedImageAlgorithm.cxx:327)
> ==30679== by 0x1353AA8E:
> vtkThreadedImageAlgorithmThreadedExecute(void*)
> (vtkThreadedImageAlgorithm.cxx:200)
> ==30679== by 0x13BA30F9: start_thread (in /lib64/tls/libpthread-2.3.5.so<http://2.3.5.so>
> )
> ==30679== by 0x1561AA62: clone (in /lib64/tls/libc-2.3.5.so<http://2.3.5.so>
> )
> ==30679== Address 0x19992030 is 0 bytes after a block of size 16777216
> alloc'd
> ==30679== at 0x11B1A8E2: operator new[](unsigned long) (in
> /usr/lib64/valgrind/vgpreload_memcheck.so)
> ==30679== by 0x1380B136: vtkDataArrayTemplate<double>::Allocate(long
> long, long long) (vtkDataArrayTemplate.txx:99)
> ==30679== by 0x1380BF2E:
> vtkDataArrayTemplate<double>::SetNumberOfValues(long long)
> (vtkDataArrayTemplate.txx:536)
> ==30679== by 0x1380B409:
> vtkDataArrayTemplate<double>::SetNumberOfTuples(long long)
> (vtkDataArrayTemplate.txx:330)
> ==30679== by 0x12154566:
> vtkArrayCalculator::RequestData(vtkInformation*, vtkInformationVector**,
> vtkInformationVector*) (vtkArrayCalculator.cxx:279)
> ==30679== by 0x1341A5AA:
> vtkDataSetAlgorithm::ProcessRequest(vtkInformation*,
> vtkInformationVector**, vtkInformationVector*)
> (vtkDataSetAlgorithm.cxx:175)==30679== by 0x1342CBC9:
> vtkExecutive::CallAlgorithm(vtkInformation*, int,
> vtkInformationVector**, vtkInformationVector*) (vtkExecutive.cxx:679)
> ==30679== by 0x13427AF7:
> vtkDemandDrivenPipeline::ExecuteData(vtkInformation*,
> vtkInformationVector**, vtkInformationVector*)
> (vtkDemandDrivenPipeline.cxx:464)
> ==30679== by 0x1342732B:
> vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, int,
> vtkInformationVector**, vtkInformationVector*)
> (vtkDemandDrivenPipeline.cxx:244)
> ==30679== by 0x1352487E:
> vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, int,
> vtkInformationVector**, vtkInformationVector*)
> (vtkStreamingDemandDrivenPipeline.cxx:144)
> ==30679== by 0x13427927: vtkDemandDrivenPipeline::UpdateData(int)
> (vtkDemandDrivenPipeline.cxx:406)
> ==30679== by 0x13524A04:
> vtkStreamingDemandDrivenPipeline::Update(int)
> (vtkStreamingDemandDrivenPipeline.cxx:190)
> 
> 
> Could you open a bug in the bugtracker(*) for this. Add your program as
> an attachment.
> 
> Thanks
> Mathieu
> (*) http://vtk.org/Bug
> 
> 
> 
> Randall Hand wrote:
> > Ok, I posted this once before, but here it is again with some more
> > information.
> >
> > I've written a piece of code to create a synthetic dataset. It's a
> > 128^3 dataset, each point with a 3-component double value consisting of
> > (sin(x), junk, morejunk). I extract just the first component, and do an
> > FFT. You'll find the code at the end of this message, along with my
> > "PrintStatistics" function attached.
> >
> > You'll see from the #if/#endif blocks that there's two possible ways to
> > do it. The first is with a vtkArrayCalculator, where I set a very
> > trivial function to simply copy out the one value. The other way is
> > with a vtkImageExtractComponents. When doing it with the
> > vtkArrayCalculator, the filter seems to work just fine but then the FFT
> > yields values like :
> > p Array [0]: vtkDoubleArray "result", 2,097,152 points, 8 bytes
> > per point
> > p Magnitude Range: 0.0000 1482912.5793
> > p Component 0 Range: -1048575.9848 1048575.8760
> > p Component 1 Range: -1048572.9243 1048579.0968
> > With a simple sin wave, the result should be almost purely imaginary, so
> > the Component 0 range should be almost 0 to 0.
> >
> > When I switch to using the vtkImageExtractComponents, the results look
> > better:
> > p Array [0]: vtkDoubleArray "image", 2,097,152 points, 8 bytes per
> > point
> > p Magnitude Range: 0.0000 1048576.0091
> > p Component 0 Range: -0.0557 0.0011
> > p Component 1 Range: -1048576.0089 1048576.0091
> >
> >
> > Unfortunately, when working with the vtkImageExtractComponents filter, I
> > lose the other two fields if I had planned on using them for coloring or
> > something. Also, my results aren't quite what I expected. Much better,
> > but on more complex datasets I seem to get results that are a little off
> > from the expected result. I don't know if the cause of all this is
> > related, but I'm chasing down what I can.
> >
> > So, any ideas?
> >
> > ----- Code starts here -------
> > #include <stdio.h>
> > #include <string.h>
> > #include <stdlib.h>
> > #include <unistd.h>
> > #include "stat.h"
> > #include <sys/types.h>
> > #include <sys/stat.h>
> > #include <sys/mman.h>
> > #include <fcntl.h>
> > #include <vtkObject.h>
> > #include "vtkImageData.h"
> > #include "vtkPointData.h"
> > #include <vtkDataArray.h>
> > #include <vtkUnsignedCharArray.h>
> > #include <vtkDoubleArray.h>
> > #include <vtkImageData.h>
> > #include <vtkImageFFT.h>
> > #include <vtkArrayCalculator.h>
> > #include <vtkImageExtractComponents.h>
> >
> > int main (int argc, char *argv[])
> > {
> > double *data;
> > int xdim, ydim, zdim;
> > double kx;
> > int x,y,z;
> > long index;
> > xdim = 128;
> > ydim = 128;
> > zdim = 128;
> >
> > if ((data = (double*)malloc(sizeof(double)*xdim*ydim*zdim*3)) == NULL) {
> > perror("Unable to allocate memory!\n\t");
> > return -1;
> > }
> >
> > printf("Constructing sin(kx * x) dataset...\n");
> > kx = 2.0 * 3.1415926 / (double)xdim;
> > for(x=0; x<xdim; x++) {
> > for(y=0; y<ydim; y++) {
> > for(z=0; z<zdim; z++) {
> > index = z + (y*zdim) + (x * ydim * zdim);
> > data[(index*3)+0] = sin(kx * (double)x);
> > data[(index*3)+1] = cos(kx * (double)x);
> > data[(index*3)+2] = tan(kx * (double)x);
> > }
> > }
> > }
> >
> > vtkDoubleArray *ucPointer = vtkDoubleArray::New();
> > ucPointer->SetNumberOfComponents(3);
> > ucPointer->SetArray(data, xdim*ydim*zdim*3, 1);
> > ucPointer->SetName("image");
> >
> > vtkImageData *image = vtkImageData::New();
> > image->Initialize();
> > image->SetDimensions(xdim, ydim, zdim);
> > image->SetExtent(1, xdim, 1, ydim, 1, zdim);
> > image->SetScalarTypeToDouble();
> > image->SetNumberOfScalarComponents(3);
> > image->GetPointData()->SetScalars(ucPointer);
> > PrintStatistics(image);
> > printf("Extracting Velocity X-Component...\n");
> >
> > #if 0
> > vtkArrayCalculator *extract = vtkArrayCalculator::New();
> > extract->SetInput(image);
> > extract->SetResultArrayName("result");
> > extract->AddScalarVariable("x", "image", 0);
> > extract->SetFunction("(x*1.0)+0.0");
> > extract->ReplaceInvalidValuesOff();
> > extract->Update();
> > extract->GetOutput()->GetPointData()->RemoveArray("image");
> > extract->GetOutput()->GetPointData()->SetActiveScalars("result");
> > #else
> > vtkImageExtractComponents *extract = vtkImageExtractComponents::New();
> > extract->SetInput(image);
> > extract->SetComponents(0);
> > extract->Update();
> > #endif
> > PrintStatistics(extract->GetOutput());
> >
> > printf("Computing FFT...\n");
> > vtkImageFFT *fft = vtkImageFFT::New();
> > fft->SetInput(extract->GetOutput());
> > fft->Update();
> > PrintStatistics(fft->GetOutput());
> >
> > }
> >
> >
> > --
> > Randall Hand
> > Visualization Scientist,
> > ERDC-MSRC Vicksburg, MS
> > Homepage: http://www.yeraze.com
> >
> >
> > ------------------------------------------------------------------------
> >
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> 
> 


-- 
Randall Hand
Visualization Scientist, 
ERDC-MSRC Vicksburg, MS
Homepage: http://www.yeraze.com
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