Done... Bug #2234<br>

<br>

<a href="http://www.vtk.org/Bug/bug.php?op=show&bugid=2234&pos=2">http://www.vtk.org/Bug/bug.php?op=show&bugid=2234&pos=2</a><br><br><div><span class="gmail_quote">On 9/14/05, <b class="gmail_sendername">

Mathieu Malaterre</b> <<a href="mailto:mathieu.malaterre@kitware.com">mathieu.malaterre@kitware.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">

Ok this is a bug:<br><br>i ========== End of Data Statistics ===============<br>==30679==<br>==30679== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 9 from 4)<br>==30679==<br>==30679== 1 errors in context 1 of 1:<br>

==30679== Invalid read of size 8<br>==30679==    at 0x12A4B8F5: void<br>vtkImageFFTExecute<double>(vtkImageFFT*, vtkImageData*, int*, double*,<br>vtkImageData*, int*, double*, int) (vtkImageFFT.cxx:137)<br>==30679==    by 0x12A4A645: vtkImageFFT::ThreadedExecute(vtkImageData*,

<br>vtkImageData*, int*, int) (vtkImageFFT.cxx:203)<br>==30679==    by 0x1353AEA2:<br>vtkThreadedImageAlgorithm::ThreadedRequestData(vtkInformation*,<br>vtkInformationVector**, vtkInformationVector*, vtkImageData***,<br>vtkImageData**, int*, int) (

vtkThreadedImageAlgorithm.cxx:327)<br>==30679==    by 0x1353AA8E:<br>vtkThreadedImageAlgorithmThreadedExecute(void*)<br>(vtkThreadedImageAlgorithm.cxx:200)<br>==30679==    by 0x13BA30F9: start_thread (in /lib64/tls/libpthread-

<a href="http://2.3.5.so">2.3.5.so</a>)<br>==30679==    by 0x1561AA62: clone (in /lib64/tls/libc-<a href="http://2.3.5.so">2.3.5.so</a>)<br>==30679==  Address 0x19992030 is 0 bytes after a block of size 16777216<br>alloc'd

<br>==30679==    at 0x11B1A8E2: operator new[](unsigned long) (in<br>/usr/lib64/valgrind/vgpreload_memcheck.so)<br>==30679==    by 0x1380B136: vtkDataArrayTemplate<double>::Allocate(long<br>long, long long) (vtkDataArrayTemplate.txx

:99)<br>==30679==    by 0x1380BF2E:<br>vtkDataArrayTemplate<double>::SetNumberOfValues(long long)<br>(vtkDataArrayTemplate.txx:536)<br>==30679==    by 0x1380B409:<br>vtkDataArrayTemplate<double>::SetNumberOfTuples(long long)

<br>(vtkDataArrayTemplate.txx:330)<br>==30679==    by 0x12154566:<br>vtkArrayCalculator::RequestData(vtkInformation*, vtkInformationVector**,<br>vtkInformationVector*) (vtkArrayCalculator.cxx:279)<br>==30679==    by 0x1341A5AA:

<br>vtkDataSetAlgorithm::ProcessRequest(vtkInformation*,<br>vtkInformationVector**, vtkInformationVector*)<br>(vtkDataSetAlgorithm.cxx:175)==30679==    by 0x1342CBC9:<br>vtkExecutive::CallAlgorithm(vtkInformation*, int,<br>

vtkInformationVector**, vtkInformationVector*) (vtkExecutive.cxx:679)<br>==30679==    by 0x13427AF7:<br>vtkDemandDrivenPipeline::ExecuteData(vtkInformation*,<br>vtkInformationVector**, vtkInformationVector*)<br>(vtkDemandDrivenPipeline.cxx

:464)<br>==30679==    by 0x1342732B:<br>vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, int,<br>vtkInformationVector**, vtkInformationVector*)<br>(vtkDemandDrivenPipeline.cxx:244)<br>==30679==    by 0x1352487E:<br>

vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, int,<br>vtkInformationVector**, vtkInformationVector*)<br>(vtkStreamingDemandDrivenPipeline.cxx:144)<br>==30679==    by 0x13427927: vtkDemandDrivenPipeline::UpdateData(int)

<br>(vtkDemandDrivenPipeline.cxx:406)<br>==30679==    by 0x13524A04:<br>vtkStreamingDemandDrivenPipeline::Update(int)<br>(vtkStreamingDemandDrivenPipeline.cxx:190)<br><br><br>Could you open a bug in the bugtracker(*) for this. Add your program as

an attachment. Thanks Mathieu (*) <a href="http://vtk.org/Bug">http://vtk.org/Bug</a> Randall Hand wrote: > Ok, I posted this once before, but here it is again with some more > information.

<br>><br>> I've written a piece of code to create a synthetic dataset.  It's a<br>> 128^3 dataset, each point with a 3-component double value consisting of<br>> (sin(x), junk, morejunk).  I extract just the first component, and do an

<br>> FFT.  You'll find the code at the end of this message, along with my<br>> "PrintStatistics" function attached.<br>><br>> You'll see from the #if/#endif blocks that there's two possible ways to<br>

> do it.  The first is with a vtkArrayCalculator, where I set a very<br>> trivial function to simply copy out the one value.  The other way is<br>> with a vtkImageExtractComponents.  When doing it with the<br>> vtkArrayCalculator, the filter seems to work just fine but then the FFT

<br>> yields values like :<br>> p       Array [0]: vtkDoubleArray "result", 2,097,152 points, 8 bytes<br>> per point<br>>

p                      

Magnitude

Range:        0.0000  1482912.5793<br>>

p                      

Component 0

Range:      -1048575.9848  

1048575.8760<br>>

p                      

Component 1

Range:      -1048572.9243  

1048579.0968<br>> With a simple sin wave, the result should be almost purely imaginary, so<br>> the Component 0 range should be almost 0 to 0.<br>><br>> When I switch to using the vtkImageExtractComponents, the results look

<br>> better:<br>> p       Array [0]: vtkDoubleArray "image", 2,097,152 points, 8 bytes per<br>> point<br>>

p                      

Magnitude

Range:        0.0000  1048576.0091<br>>

p                      

Component 0 Range:      -0.0557 0.0011<br>>

p                      

Component 1

Range:      -1048576.0089  

1048576.0091<br>><br>><br>> Unfortunately, when working with the vtkImageExtractComponents filter, I<br>> lose the other two fields if I had planned on using them for coloring or<br>> 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?

<br>><br>> ----- Code starts here -------<br>> #include <stdio.h><br>> #include <string.h><br>> #include <stdlib.h><br>> #include <unistd.h><br>> #include "stat.h"<br>

> #include <sys/types.h><br>> #include <sys/stat.h><br>> #include <sys/mman.h><br>> #include <fcntl.h><br>> #include <vtkObject.h><br>> #include "vtkImageData.h"<br>

> #include "vtkPointData.h"<br>> #include <vtkDataArray.h><br>> #include <vtkUnsignedCharArray.h><br>> #include <vtkDoubleArray.h><br>> #include <vtkImageData.h><br>> #include <

vtkImageFFT.h><br>> #include <vtkArrayCalculator.h><br>> #include <vtkImageExtractComponents.h><br>><br>> int main (int argc, char *argv[])<br>> {<br>>     double *data;<br>>     int xdim, ydim, zdim;

<br>>     double kx;<br>>     int x,y,z;<br>>     long index;<br>>     xdim = 128;<br>>     ydim = 128;<br>>     zdim = 128;<br>><br>>     if ((data = (double*)malloc(sizeof(double)*xdim*ydim*zdim*3)) == NULL) {

<br>>         perror("Unable to allocate memory!\n\t");<br>>         return -1;<br>>     }<br>><br>>     printf("Constructing sin(kx * x) dataset...\n");<br>>     kx = 2.0 * 3.1415926

 / (double)xdim;<br>>     for(x=0; x<xdim; x++) {<br>>         for(y=0; y<ydim; y++) {<br>>             for(z=0; z<zdim; z++) {<br>>                

index = z + (y*zdim) + (x * ydim * zdim);<br>>                

data[(index*3)+0] = sin(kx * (double)x);<br>>                

data[(index*3)+1] = cos(kx * (double)x);<br>>                

data[(index*3)+2] = tan(kx * (double)x);<br>>             }<br>>         }<br>>     }<br>><br>>     vtkDoubleArray *ucPointer = vtkDoubleArray::New();<br>>     ucPointer->SetNumberOfComponents(3);<br>

>     ucPointer->SetArray(data, xdim*ydim*zdim*3, 1);<br>>     ucPointer->SetName("image");<br>><br>>     vtkImageData *image = vtkImageData::New();<br>>     image->Initialize();<br>>     image->SetDimensions(xdim, ydim, zdim);

<br>>     image->SetExtent(1, xdim, 1, ydim, 1, zdim);<br>>     image->SetScalarTypeToDouble();<br>>     image->SetNumberOfScalarComponents(3);<br>>     image->GetPointData()->SetScalars(ucPointer);

<br>>     PrintStatistics(image);<br>>     printf("Extracting Velocity X-Component...\n");<br>><br>> #if 0<br>>     vtkArrayCalculator *extract = vtkArrayCalculator::New();<br>>     extract->SetInput(image);

<br>>     extract->SetResultArrayName("result");<br>>     extract->AddScalarVariable("x", "image", 0);<br>>     extract->SetFunction("(x*1.0)+0.0");<br>>     extract->ReplaceInvalidValuesOff();

<br>>     extract->Update();<br>>     extract->GetOutput()->GetPointData()->RemoveArray("image");<br>>     extract->GetOutput()->GetPointData()->SetActiveScalars("result");

<br>> #else<br>>     vtkImageExtractComponents *extract = vtkImageExtractComponents::New();<br>>     extract->SetInput(image);<br>>     extract->SetComponents(0);<br>>     extract->Update();<br>> #endif

<br>>     PrintStatistics(extract->GetOutput());<br>><br>>     printf("Computing FFT...\n");<br>>     vtkImageFFT *fft = vtkImageFFT::New();<br>>     fft->SetInput(extract->GetOutput());<br>

>     fft->Update();<br>>     PrintStatistics(fft->GetOutput());<br>><br>> }<br>><br>><br>> --<br>> Randall Hand<br>> Visualization Scientist,<br>> ERDC-MSRC Vicksburg, MS<br>> Homepage: 

<a href="http://www.yeraze.com">http://www.yeraze.com</a><br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>

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<br>> <a href="http://www.vtk.org/mailman/listinfo/vtkusers">http://www.vtk.org/mailman/listinfo/vtkusers</a><br><br></blockquote></div><br><br clear="all"><br>-- <br>Randall Hand<br>Visualization Scientist, <br>ERDC-MSRC Vicksburg, MS

<br>Homepage: <a href="http://www.yeraze.com">http://www.yeraze.com</a>