[vtk-developers] Re: [vtkusers] Problem with using vtkArrayCalculator to extract fields for vtkImageFFT Processing
Mathieu Malaterre
mathieu.malaterre at kitware.com
Wed Sep 14 13:51:56 EDT 2005
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)
==30679== by 0x1561AA62: clone (in /lib64/tls/libc-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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