[vtkusers] vtkDataArray: Memory allocation problem
michiel mentink
michael.mentink at st-hughs.ox.ac.uk
Wed Jan 27 10:51:51 EST 2010
Would this example help? Constructing a .vtk volume manually.
http://www.cmake.org/Wiki/VTK/Examples/IterateImageData
Michael
On Wed, Jan 27, 2010 at 10:33 AM, Malsoaz James <jmalsoaz at yahoo.fr> wrote:
> I need the ITK images data to do some processes. Thus, I use ITK to read
> the Dicom series. Then, I need to build "manually" the vtkVolume in order to
> display it.
>
> --- En date de : *Mer 27.1.10, michiel mentink <
> michael.mentink at st-hughs.ox.ac.uk>* a écrit :
>
>
> De: michiel mentink <michael.mentink at st-hughs.ox.ac.uk>
>
> Objet: Re: [vtkusers] vtkDataArray: Memory allocation problem
> À: "Malsoaz James" <jmalsoaz at yahoo.fr>
> Cc: "Bill Lorensen" <bill.lorensen at gmail.com>, vtkusers at vtk.org
> Date: Mercredi 27 Janvier 2010, 9h34
>
>
>
> 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<http://mc/compose?to=jmalsoaz@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<http://mc/compose?to=bill.lorensen@gmail.com>
>> >* a écrit :
>>
>>
>> De: Bill Lorensen <bill.lorensen at gmail.com<http://mc/compose?to=bill.lorensen@gmail.com>
>> >
>> Objet: Re: [vtkusers] vtkDataArray: Memory allocation problem
>> À: "Malsoaz James" <jmalsoaz at yahoo.fr<http://mc/compose?to=jmalsoaz@yahoo.fr>
>> >
>> Cc: vtkusers at vtk.org <http://mc/compose?to=vtkusers@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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>
>
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