[vtkusers] vtkDataArray: Memory allocation problem

[michiel mentink]

I'm curious, why don't you use the dicomseriesreader? Shown below here is an
example to create a metaImage volume,
but writing a VTK volume should be nearly identical:

int main(int argc, char *argv[])
{
  if(argc != 3)
    {
    vtkstd::cout << "Required arguments: Folder containing .dcm files and
also name of OutputFile" << vtkstd::endl;
    }
  vtkstd::string folder = argv[1];
  vtkstd::string outputFile = argv[2];

  // Read all the DICOM files in the specified directory.
  vtkSmartPointer<vtkDICOMImageReader> reader =
vtkSmartPointer<vtkDICOMImageReader>::New();
  reader->SetDirectoryName(folder.c_str());
  reader->Update();

  vtkImageData* imagedata = reader->GetOutput();
  vtkSmartPointer<vtkMetaImageWriter> metaImageWriter =
vtkSmartPointer<vtkMetaImageWriter>::New();
  metaImageWriter->SetInput(imagedata);
  metaImageWriter->SetFileName(outputFile.c_str());
  metaImageWriter->Update();

  return 0;
} Michael

On Wed, Jan 27, 2010 at 8:21 AM, Malsoaz James <jmalsoaz at yahoo.fr> wrote:

>  Thanks for the answer. I guess I need to add some explanation to my
> application.
>
> I'm reading a Dicom series using ITK to build a 3D vtk volume. This part is
> working well whatever the number of slices. I have no problem for the
> allocation with vtkIntArray.
> Here is the code for this part:
>
> scalars=vtkIntArray::New();
> scalars->SetNumberOfValues(nbPixelX*nbPixelY*nbPixelZ);
>
> std::vector <ImageType::Pointer>::iterator iterator;
> iterator = SlicesList.begin();
>
> for (unsigned int lz=0;lz<numberOfSlice;lz++)
>     {
>         itk::ImageRegionConstIterator<ImageType>  inputIt(*iterator,
> (*iterator)->GetLargestPossibleRegion());
>         inputIt.GoToBegin();
>         int currentvalue;
>         while( !inputIt.IsAtEnd() )
>         {
>             lurrentvalue = inputIt.Get();
>             m_scalars->SetValue(offset,currentvalue);
>             offset++;
>             ++inputIt;
>         iterator++;
>     }
>
>  As I said, this is working and I have been able to allocate X*Y*Z elements
> in my vtkIntArray.
>
> Then, I'm working with ITK to do some process with ITK (threshold, opening,
> closing, labeling, ...). At the end, I have the boundaries of some objects
> in my slices.
> In order to display these boundaries on the vtkVolume, I'm building a new
> 3D volume with only the boundaries. Further to this, I'm displaying the
> boundaries on the raw volume using Texture. The error of allocation appears
> here and only when the number of slices in my volume is important (more than
> 300 slices). Here is the code I'm using:
>
> vtkIntArray* scalars = vtkIntArray::New();
> scalars->SetNumberOfValues(nbPixelX*nbPixelY*nbPixelZ);
> for (points in my boundaries)
> {
>  scalars->SetValue(offset,1);
>  }
>  Note that the error appears at the first "SetValue". I have been trying to
> fill the new volume with 0 using "InsertTuple1(offset, 0)". Thus, I'm able
> to see where the allocation is crashing. It seems to be around the 33 555
> 448th elements. I can't explain why.
>
> I hope this has clarify my problem.
> Best
> James
>
> --- En date de : *Mar 26.1.10, Bill Lorensen <bill.lorensen at gmail.com>* a
> écrit :
>
>
> De: Bill Lorensen <bill.lorensen at gmail.com>
> Objet: Re: [vtkusers] vtkDataArray: Memory allocation problem
> À: "Malsoaz James" <jmalsoaz at yahoo.fr>
> Cc: vtkusers at vtk.org
> Date: Mardi 26 Janvier 2010, 16h10
>
>
> Are there other filters involved in the processing? What does your vtk
> pipeline look like?
>
> On Tue, Jan 26, 2010 at 10:59 AM, Malsoaz James <jmalsoaz at yahoo.fr<http://mc/compose?to=jmalsoaz@yahoo.fr>
> > wrote:
>
>> Hello,
>>
>> First of all, I would like to expose the context of my problem. I'm
>> working on an application which is in charge of loading/building a 3D volume
>> from Dicom files. The building of the 3D volume is working perfectly using a
>> vtkIntArray and setScalars().
>>
>>
>> Unfortunately, later in the software, I need to rebuild a new 3D volume
>> using one more time vtkIntArray with the same size but I got an error like:
>> vtkIntArray: Unable to allocate X elements of size 4. Although I have enough
>> memory (I have 3Go of RAM), I'm doing exactly the same thing as the first
>> build and the charge on Windows for the application is always under 1Go. My
>> application is working with small volume (ie 150 slices) and I got this
>> allocation error with big volume (ie more than 300 slices).
>> For information, the images have a size of 512*512.
>>
>> Do you know what is the origin of the problem? How can I solve this ?
>>
>>
>> Best
>> James
>>
>>
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>
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