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
<br>an attachment.<br><br>Thanks<br>Mathieu<br>(*) <a href="http://vtk.org/Bug">http://vtk.org/Bug</a><br><br><br><br>Randall Hand wrote:<br>> Ok, I posted this once before, but here it is again with some more<br>> 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,
<br>> but on more complex datasets I seem to get results that are a little off<br>> from the expected result. I don't know if the cause of all this is<br>> related, but I'm chasing down what I can.<br>><br>> 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>
> This is the private VTK discussion list.<br>> Please keep messages on-topic. Check the FAQ at: <a href="http://www.vtk.org/Wiki/VTK_FAQ">http://www.vtk.org/Wiki/VTK_FAQ</a><br>> Follow this link to subscribe/unsubscribe:
<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>