[ITK] [ITK-users] How to make ITK-binaries NOT ignore kernel out of memory messages?

Dr. Roman Grothausmann grothausmann.roman at mh-hannover.de
Wed Jul 16 09:06:05 EDT 2014


Hi Matt,


Many thanks for Your reply. I'll check if ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 
prevents the problems. Although I'd be astonished if it does because 
BinaryMask3DMeshSource seems to use only one core anyway.

Thanks again for Your help
Roman

On 15/07/14 02:55, Matt McCormick wrote:
> Hi Roman,
>
> The CMake configuration variable:
>
>    ITK_COMPUTER_MEMORY_SIZE
>
> is only used to choose which unit tests to run, and has no effect on
> your program.
>
>
> It may be worth a try to run
>
>    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
>
> before starting your program on the server to see the effect.  It is
> possible that too many threads or being spawned or that the amount of
> memory consumed is scaling (poorly) with the number of threads used.
>
> Hope this helps,
> Matt
>
> On Mon, Jun 23, 2014 at 6:36 AM, Dr. Roman Grothausmann
> <grothausmann.roman at mh-hannover.de> wrote:
>> Dear Luis,
>>
>>
>> Many thanks for Your reply. It took me some time to reproduce the problem,
>> because Your test program works as expected on our server:
>>
>> ~$ ~/itk/simple/build_itk-4.5.1/memtest_01 1000
>> ITK Hello World !
>>
>> ~$ ~/itk/simple/build_itk-4.5.1/memtest_01 10000
>> /opt/itk-4.5.1/include/ITK-4.5/itkImportImageContainer.hxx:192:
>>
>> Failed to allocate memory for image.
>>
>> One program of mine for which the problem exists is below. The problem
>> occurs when BinaryMask3DMeshSource acquires more memory after running for
>> some minutes. The very strange thing to me is, that the program is killed by
>> the kernel as expected on my desktop PC:
>>
>> ~/itk/simple/build_itk4_pc3G48243/euler-characteristic_01 13-511_EAA_ot.mha
>> 255
>> component type is: unsigned_char
>> numDimensions: 3
>> component size: 1
>> pixel type (string): scalar
>> pixel type: 1
>> _________________________
>>
>> Executing ImageFileReader  done. Took 2.78 seconds.
>> Executing BinaryMask3DMeshSource Killed
>>
>>
>> The header of 13-511_EAA_ot.mha:
>>
>> ObjectType = Image
>> NDims = 3
>> BinaryData = True
>> BinaryDataByteOrderMSB = False
>> CompressedData = True
>> CompressedDataSize = 20474538
>> TransformMatrix = 1 0 0 0 1 0 0 0 1
>> Offset = 0 0 0
>> CenterOfRotation = 0 0 0
>> AnatomicalOrientation = RAI
>> ElementSpacing = 1 1 1
>> DimSize = 998 998 1034
>> ElementType = MET_UCHAR
>> ElementDataFile = LOCAL
>>
>>
>> However on the server it is not terminated when the RAM runs out, instead
>> many processes go nuts that had been mostly sleeping and finally the system
>> does not respond any more at all and a cold start is necessary. The
>> itk-4.5.1 is configured on the server with (see attached
>> CMakeCache_itk-4.5.1.txt):
>>
>> ITK_COMPUTER_MEMORY_SIZE  190
>>
>> The server has 256GB of RAM an no Swap enabled:
>>
>> free
>>               total       used       free     shared    buffers     cached
>> Mem:     264498496    1341020  263157476          0     285760     289120
>> -/+ buffers/cache:     766140  263732356
>> Swap:            0          0          0
>>
>>
>> Has 12x2 Intel(R) Xeon(R) CPUs:
>>
>> cat /proc/cpuinfo
>> processor       : 0
>> vendor_id       : GenuineIntel
>> cpu family      : 6
>> model           : 45
>> model name      : Intel(R) Xeon(R) CPU E5-2630L 0 @ 2.00GHz
>> stepping        : 7
>> microcode       : 0x710
>> cpu MHz         : 1200.000
>> cache size      : 15360 KB
>> physical id     : 0
>> siblings        : 12
>> core id         : 0
>> cpu cores       : 6
>> apicid          : 0
>> initial apicid  : 0
>> fpu             : yes
>> fpu_exception   : yes
>> cpuid level     : 13
>> wp              : yes
>> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
>> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
>> pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology
>> nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2
>> ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer
>> aes xsave avx lahf_lm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi
>> flexpriority ept vpid
>> bogomips        : 4000.56
>> clflush size    : 64
>> cache_alignment : 64
>> address sizes   : 46 bits physical, 48 bits virtual
>> power management:
>> .
>> .
>> .
>>
>>
>> The server runs a Debian Wheezy (7.2):
>> uname -a
>> Linux img1-serv 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
>>
>> My desktop PC has the same Debian (also same update state):
>> uname -a
>> Linux pc3G48243 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
>>
>> free
>>               total       used       free     shared    buffers     cached
>> Mem:       8180356    1185364    6994992          0      23348     216084
>> -/+ buffers/cache:     945932    7234424
>> Swap:            0          0          0
>>
>>
>> and 4 AMD FX(tm)-4100 Quad-Core Processors:
>>
>> cat /proc/cpuinfo
>> processor       : 0
>> vendor_id       : AuthenticAMD
>> cpu family      : 21
>> model           : 1
>> model name      : AMD FX(tm)-4100 Quad-Core Processor
>> stepping        : 2
>> microcode       : 0x6000626
>> cpu MHz         : 1400.000
>> cache size      : 2048 KB
>> physical id     : 0
>> siblings        : 4
>> core id         : 0
>> cpu cores       : 2
>> apicid          : 16
>> initial apicid  : 0
>> fpu             : yes
>> fpu_exception   : yes
>> cpuid level     : 13
>> wp              : yes
>> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
>> cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
>> pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc extd_apicid
>> aperfmperf pni pclmulqdq monitor ssse3 cx16 sse4_1 sse4_2 popcnt aes xsave
>> avx lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse
>> 3dnowprefetch osvw ibs xop skinit wdt lwp fma4 nodeid_msr topoext
>> perfctr_core arat cpb hw_pstate npt lbrv svm_lock nrip_save tsc_scale
>> vmcb_clean flushbyasid decodeassists pausefilter pfthreshold
>> bogomips        : 7233.41
>> TLB size        : 1536 4K pages
>> clflush size    : 64
>> cache_alignment : 64
>> address sizes   : 48 bits physical, 48 bits virtual
>> power management: ts ttp tm 100mhzsteps hwpstate [9]
>>
>>
>> Knowing now, that itk checks for available RAM, the only sources for this
>> problem I can think of would be an odd configuration of ITK itself or its
>> use in programs compiled on the server, or some configuration differences in
>> the (Debian) system, or some hardware problem.
>>
>> Do You have any idea what it could be?
>> Or do You have any suggestions how I should go on searching for the cause?
>>
>>
>> Any help or hints are very much appriciated.
>> Many thanks for Your help again!
>>
>> Roman
>>
>>
>> _____________________________________________
>>
>>
>>
>> ////program to calculate the Euler characteristic of a binary image
>> converted to itkQuadEdgeMesh
>> ////THEREFORE does NOT take filled regions into account only covering
>> surfaces!
>> ////if fillings should be accounted use instead a vtk program taking 3D
>> cells into account
>>
>>
>>
>> #include <itkImageFileReader.h>
>> //#include <itkImage.h>
>> #include <itkBinaryMask3DMeshSource.h> //itk marching cubes (mc) very slow
>> and resource hungry :-(
>> #include <itkQuadEdgeMeshTopologyChecker.h>
>> #include <itkQuadEdgeMeshBoundaryEdgesMeshFunction.h>
>>
>>
>>
>> #include "itkFilterWatcher2.h"
>>
>>
>>
>>
>> void dispatch_cT(itk::ImageIOBase::IOPixelType,
>> itk::ImageIOBase::IOComponentType, size_t, int, char **);
>>
>> template<typename InputComponentType>
>> void dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t, int, char
>> **);
>>
>> template<typename InputComponentType, typename InputPixelType>
>> void dispatch_D(size_t, int, char **);
>>
>> template<typename InputComponentType, typename InputPixelType, size_t
>> Dimension>
>> int DoIt(int, char *argv[]);
>>
>>
>>
>>
>>
>> template<typename InputComponentType, typename InputPixelType, size_t
>> Dimension>
>> int DoIt(int argc, char *argv[]){
>>
>>    typedef InputPixelType  OutputPixelType;
>>
>>    typedef itk::Image<InputPixelType, Dimension>  InputImageType;
>>    typedef itk::Image<OutputPixelType, Dimension>  OutputImageType;
>>
>>
>>    typedef itk::ImageFileReader<InputImageType> ReaderType;
>>    typename ReaderType::Pointer reader = ReaderType::New();
>>
>>    reader->SetFileName(argv[1]);
>>    FilterWatcher watcherI(reader, "reading");
>>    watcherI.QuietOn();
>>    watcherI.ReportTimeOn();
>>    try
>>      {
>>        reader->Update();
>>      }
>>    catch (itk::ExceptionObject &ex)
>>      {
>>        if (!strcmp(ex.GetDescription(), "Filter does not have progress.")){
>>        std::cerr << ex.GetDescription() << std::endl;
>>        return EXIT_FAILURE;
>>        }
>>      }
>>
>>
>>    typedef double        CoordType;
>>
>>    //typedef itk::Mesh<CoordType> MeshType;
>>    typedef itk::QuadEdgeMesh<CoordType, Dimension> InputMeshType;
>>
>>    const InputPixelType isoValue= static_cast<InputPixelType>(atof(argv[2]));
>>
>>    typedef itk::BinaryMask3DMeshSource<InputImageType, InputMeshType>
>> MeshSourceType;
>>    typename MeshSourceType::Pointer meshSource = MeshSourceType::New();
>>
>>    meshSource->SetInput(reader->GetOutput());
>>    meshSource->SetObjectValue(isoValue);
>>
>>    FilterWatcher watcher(meshSource, "BinaryMask3DMeshSource");
>>    watcher.QuietOn();
>>    watcher.ReportTimeOn();
>>    try
>>      {
>>        meshSource->Update();
>>      }
>>    catch (itk::ExceptionObject &ex)
>>      {
>>        if (!strcmp(ex.GetDescription(), "Filter does not have progress.")){
>>          std::cerr << ex.GetDescription() << std::endl;
>>          return EXIT_FAILURE;
>>        }
>>      }
>>
>>
>>    std::cout << "Nodes = " << meshSource->GetNumberOfNodes() << std::endl;
>>    std::cout << "Cells = " << meshSource->GetNumberOfCells() << std::endl;
>>
>>    typename InputMeshType::Pointer mesh= meshSource->GetOutput();
>>
>>    //// check if meshSource can be represented as an itkQuadEdgeMesh
>>    //// if BinaryMask3DMeshSource caps boundary surfaces this check is not
>> necessary!
>>
>>    typedef itk::QuadEdgeMeshTopologyChecker<InputMeshType> TQEchecker;
>>    typename TQEchecker::Pointer QEchecker = TQEchecker::New();
>>    QEchecker->SetMesh(mesh);
>>    std::cerr << "Executing
>> QuadEdgeMeshTopologyChecker->ValidateEulerCharacteristic()";
>>    if(!QEchecker->ValidateEulerCharacteristic()){
>>      std::cerr << "Not a valid QuadEdgeMesh! Aborting." << std::endl;
>>      return EXIT_FAILURE;
>>    }
>>    std::cerr << " done." << std::endl;
>>
>>    //// calc Euler characteristics \xi
>>    //// For closed smooth manifolds, the Euler characteristic coincides with
>> the Euler number:
>> http://en.wikipedia.org/wiki/Euler_characteristic#Relations_to_other_invariants
>>    //// general formula see:
>> http://en.wikipedia.org/wiki/Genus_%28mathematics%29#Orientable_surface
>>    ////
>>    ////
>>    ////
>>    //// good QuadEdge explanation:
>> http://www.cs.cmu.edu/afs/andrew/scs/cs/15-463/2001/pub/src/a2/quadedge.html
>>    /// from itkQuadEdgeMeshTopologyChecker.hxx
>>
>>    typedef itk::QuadEdgeMeshBoundaryEdgesMeshFunction<InputMeshType>
>> BoundaryEdges;
>>
>>    typename BoundaryEdges::Pointer boundaryEdges = BoundaryEdges::New();
>>
>>    // Number of USED points
>>    typedef typename InputMeshType::PointIdentifier
>> PointIdentifier;
>>    std::cerr << "ComputeNumberOfPoints";
>>    PointIdentifier numPoints = mesh->ComputeNumberOfPoints();
>>    std::cerr << " done." << std::endl;
>>    // Number of USED edges
>>    typedef typename InputMeshType::CellIdentifier
>> CellIdentifier;
>>    std::cerr << "ComputeNumberOfEdges";
>>    CellIdentifier numEdges  = mesh->ComputeNumberOfEdges();
>>    std::cerr << " done." << std::endl;
>>    // Number of USED faces
>>    std::cerr << "ComputeNumberOfFaces";
>>    CellIdentifier numFaces  = mesh->ComputeNumberOfFaces();
>>    std::cerr << " done." << std::endl;
>>    // Number of Boundaries
>>    std::cerr << "ComputeNumberOfBoundaryEdges";
>>    typename BoundaryEdges::OutputType
>>      listOfBoundaries = boundaryEdges->Evaluate((*mesh));
>>    std::cerr << " done." << std::endl;
>>    CellIdentifier numBounds = listOfBoundaries->size();
>>    delete listOfBoundaries;
>>
>>    /**
>>     * Number of points
>>     *
>>     * There are two methods to get the number of points.
>>     * 1. itk::QuadEdgeMesh::ComputeNumberOfPoints()
>>     * 2. itk::Mesh::GetNumberOfPoints()
>>     *
>>     * As an itk::QuadEdgeMesh is an itk::Mesh by inheritance, the user
>>     * can use both. 1. will returned the number of points actually
>>     * used by at least one edge, while 2. will give you the number
>>     * of points in the container. Number of unused points can be found
>>     * by making the difference between the two values.
>>     */
>>    if(mesh->GetNumberOfPoints() != numPoints){
>>      std::cerr << "There are isolated vertices! Aborting." << std::endl;
>>      return EXIT_FAILURE;
>>    }
>>
>>    // The euler formula states:
>>    // numFaces - numEdges + numPoints == 2 - 2 * genus - numBounds == \xi
>>    // hence 2 * genus= 2 - numBounds - numFaces + numEdges - numPoints must
>> be an oddeven number.
>>
>>    typedef ::itk::OffsetValueType    OffsetValueType;
>>
>>    OffsetValueType xi=
>>      + OffsetValueType(numFaces)
>>      - OffsetValueType(numEdges)
>>      + OffsetValueType(numPoints);
>>
>>    std::cout << "The Euler characteristic Xi is: " << xi << std::endl;
>>
>>    OffsetValueType twiceGenus=
>>      + OffsetValueType(2) - OffsetValueType(numBounds)
>>      - xi;
>>
>>    std::cout << "The genus is: " << twiceGenus/OffsetValueType(2) <<
>> std::endl;
>>
>>    return EXIT_SUCCESS;
>>
>> }
>>
>>
>> void dispatch_cT(itk::ImageIOBase::IOComponentType componentType,
>> itk::ImageIOBase::IOPixelType pixelType, size_t dimensionType, int argc,
>> char *argv[]){
>>
>>
>> //http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#a8dc783055a0af6f0a5a26cb080feb178
>>    //http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00107
>>    //IOComponentType: UNKNOWNCOMPONENTTYPE, UCHAR, CHAR, USHORT, SHORT, UINT,
>> INT, ULONG, LONG, FLOAT, DOUBLE
>>
>>    switch (componentType){
>>    case itk::ImageIOBase::UCHAR:{
>>      typedef unsigned char InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::CHAR:{
>>      typedef char InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::USHORT:{
>>      typedef unsigned short InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::SHORT:{
>>      typedef short InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::UINT:{
>>      typedef unsigned int InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    case itk::ImageIOBase::INT:{
>>      typedef int InputComponentType;
>>      dispatch_pT<InputComponentType>(pixelType, dimensionType, argc, argv);
>>    }
>>      break;
>>    // case itk::ImageIOBase::ULONG:{
>>    //   typedef unsigned long InputComponentType;
>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::LONG:{
>>    //   typedef long InputComponentType;
>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::FLOAT:{
>>    //   typedef float InputComponentType;
>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::DOUBLE:{
>>    //   typedef double InputComponentType;
>>    //   dispatch_pT<InputComponentType>(pixelType, dimensionType, argc,
>> argv);
>>    // }
>>    // break;
>>    case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
>>    default:
>>      std::cout << "unknown component type" << std::endl;
>>      break;
>>    }//switch
>> }
>>
>> template<typename InputComponentType>
>> void dispatch_pT(itk::ImageIOBase::IOPixelType pixelType, size_t
>> dimensionType, int argc, char *argv[]){
>>
>>
>> //http://www.itk.org/Doxygen45/html/classitk_1_1ImageIOBase.html#abd189f096c2a1b3ea559bc3e4849f658
>>      //http://www.itk.org/Doxygen45/html/itkImageIOBase_8h_source.html#l00099
>>      //IOPixelType:: UNKNOWNPIXELTYPE, SCALAR, RGB, RGBA, OFFSET, VECTOR,
>> POINT, COVARIANTVECTOR, SYMMETRICSECONDRANKTENSOR, DIFFUSIONTENSOR3D,
>> COMPLEX, FIXEDARRAY, MATRIX
>>
>>    switch (pixelType){
>>    case itk::ImageIOBase::SCALAR:{
>>      typedef InputComponentType InputPixelType;
>>      //typedef itk::SCALARPixel<InputComponentType> InputPixelType;
>>      dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>> argv);
>>    }
>>      break;
>>    // case itk::ImageIOBase::RGB:{
>>    //   typedef itk::RGBPixel<InputComponentType> InputPixelType;
>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::RGBA:{
>>    //   typedef itk::RGBAPixel<InputComponentType> InputPixelType;
>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    // case itk::ImageIOBase::VECTOR:{
>>    //   //typedef itk::VECTORPixel<InputComponentType> InputPixelType; //does
>> not work!
>>    //   typedef itk::VariableLengthVector<InputComponentType> InputPixelType;
>>    //   dispatch_D<InputComponentType, InputPixelType>(dimensionType, argc,
>> argv);
>>    // }
>>    //   break;
>>    case itk::ImageIOBase::UNKNOWNPIXELTYPE:
>>    default:
>>      std::cout << "unknown pixel type" << std::endl;
>>      break;
>>    }//switch
>> }
>>
>>
>> template<typename InputComponentType, typename InputPixelType>
>> void dispatch_D(size_t dimensionType, int argc, char *argv[]){
>>    switch (dimensionType){
>>    // case 1:
>>    //   DoIt<InputComponentType, InputPixelType, 1>(argc, argv);
>>    //   break;
>>    // case 2:
>>    //   DoIt<InputComponentType, InputPixelType, 2>(argc, argv);
>>    //   break;
>>    case 3:
>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>      break;
>>    case 4:
>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>      break;
>>    case 5:
>>      DoIt<InputComponentType, InputPixelType, 3>(argc, argv);
>>      break;
>>    default:
>>      std::cout << "Images of dimension " << dimensionType << " are not
>> supported!" << std::endl;
>>      break;
>>    }
>> }
>>
>>
>>
>> ////from
>> http://itk-users.7.n7.nabble.com/Pad-image-with-0-but-keep-its-type-what-ever-it-is-td27442.html
>> //namespace itk{
>>    // Description:
>>    // Get the PixelType and ComponentType from fileName
>>
>> void GetImageType (std::string fileName,
>>      itk::ImageIOBase::IOPixelType &pixelType,
>>      itk::ImageIOBase::IOComponentType &componentType,
>>      size_t &dimensionType
>>      //ImageIOBase::IODimensionType &dimensionType
>>      ){
>>      typedef itk::Image<unsigned char, 3> ImageType;
>>      itk::ImageFileReader<ImageType>::Pointer imageReader=
>> itk::ImageFileReader<ImageType>::New();
>>      imageReader->SetFileName(fileName.c_str());
>>      imageReader->UpdateOutputInformation();
>>
>>      pixelType = imageReader->GetImageIO()->GetPixelType();
>>      componentType = imageReader->GetImageIO()->GetComponentType();
>>      dimensionType= imageReader->GetImageIO()->GetNumberOfDimensions();
>>
>>      //std::cerr << "Pixel Type is " <<
>> imageReader->GetImageIO()->GetComponentTypeAsString(pixelType) << std::endl;
>>      std::cerr << "component type is: " <<
>> imageReader->GetImageIO()->GetComponentTypeAsString(componentType) <<
>> std::endl;
>>      std::cerr << "numDimensions: " << dimensionType << std::endl;
>>      std::cerr << "component size: " <<
>> imageReader->GetImageIO()->GetComponentSize() << std::endl;
>>      std::cerr << "pixel type (string): " <<
>> imageReader->GetImageIO()->GetPixelTypeAsString(imageReader->GetImageIO()->GetPixelType())
>> << std::endl;
>>      std::cerr << "pixel type: " << pixelType << std::endl <<
>> "_________________________"  << std::endl << std::endl;
>>
>>
>>      }
>>
>>
>>
>> int main(int argc, char *argv[]){
>>      if ( argc != 3 )
>>          {
>>          std::cerr << "Missing Parameters: "
>>                    << argv[0]
>>                    << " Input_Image"
>>                    << " isoValue"
>>                    << std::endl;
>>
>>          return EXIT_FAILURE;
>>          }
>>
>>      std::string ifn = argv[1];
>>      // std::string ofn = argv[2];
>>      // int compress= atoi(argv[3]);
>>
>>      itk::ImageIOBase::IOPixelType pixelType;
>>      typename itk::ImageIOBase::IOComponentType componentType;
>>      //itk::ImageIOBase::IOComponentType componentType1;
>>      //itk::ImageIOBase::IODimensionType dimensionType1;
>>      size_t dimensionType;
>>
>>
>>      try
>>          {
>>          GetImageType(argv[1], pixelType, componentType, dimensionType);
>>
>>          dispatch_cT(componentType, pixelType, dimensionType, argc, argv);
>>          }//try
>>      catch( itk::ExceptionObject &excep)
>>          {
>>          std::cerr << argv[0] << ": exception caught !" << std::endl;
>>          std::cerr << excep << std::endl;
>>          return EXIT_FAILURE;
>>          }
>>
>>      return EXIT_SUCCESS;
>>
>>      }
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 08/06/14 15:51, Luis Ibanez wrote:
>>>
>>>
>>> Roman,
>>>
>>>
>>> Could you please share with the list an example
>>> of a program where you are observing this behavior ?
>>>
>>> In particular, we would like to see if this is occurring with
>>> Image filters, or rather with other types of ITK objects.
>>>
>>>
>>>
>>> The itk::Image does listen to the (potential) memory allocation messages
>>> (that is, the bad_alloc exception).
>>>
>>>
>>>
>>> The itk::Image class uses a helper class to store the pixel data.
>>>
>>>
>>>
>>> This helper is the:
>>>
>>> itk::ImportImageContainer
>>>
>>>
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkImportImageContainer.h
>>>
>>>
>>>
>>>
>>> and its memory allocation is typically done in the AllocateElements()
>>> function
>>> in line:
>>>
>>>
>>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkImportImageContainer.hxx#L173
>>>
>>> the code looks like
>>>
>>>     TElement *data;
>>>
>>>     try
>>>       {
>>>       if ( UseDefaultConstructor )
>>>         {
>>>         data = new TElement[size](); //POD types initialized to 0, others
>>> use
>>> default constructor.
>>>         }
>>>       else
>>>         {
>>>         data = new TElement[size]; //Faster but uninitialized
>>>         }
>>>       }
>>>     catch ( ... )
>>>       {
>>>       data = ITK_NULLPTR;
>>>       }
>>>     if ( !data )
>>>       {
>>>       // We cannot construct an error string here because we may be out
>>>       // of memory.  Do not use the exception macro.
>>>       throw MemoryAllocationError(__FILE__, __LINE__,
>>>                                   "Failed to allocate memory for image.",
>>>                                   ITK_LOCATION);
>>>       }
>>>     return data;
>>>
>>>
>>>
>>> As you can see, the case of exceptions is managed in that function.
>>>
>>>
>>> Here is an example of a test program demonstrating that ITK image
>>> will throw exceptions when allocating memory beyond limits.
>>>
>>>
>>> #include "itkImage.h"
>>> #include <iostream>
>>>
>>> int main(int argc, char * argv[] )
>>> {
>>>     if( argc < 2 )
>>>       {
>>>       std::cerr << "Missing arguments" << std::endl;
>>>       return 1;
>>>       }
>>>
>>>     typedef itk::Image< unsigned short, 3 > ImageType;
>>>
>>>     ImageType::Pointer image = ImageType::New();
>>>
>>>     ImageType::RegionType region;
>>>     ImageType::SizeType size;
>>>
>>>     size_t side = atoi( argv[1] );
>>>
>>>     size[0] = side;
>>>     size[1] = side;
>>>     size[2] = side;
>>>
>>>     region.SetSize( size );
>>>
>>>     image->SetRegions( region );
>>>
>>>     try
>>>       {
>>>       image->Allocate();
>>>       }
>>>     catch( std::exception & excp )
>>>       {
>>>       std::cerr << excp.what() << std::endl;
>>>       return 1;
>>>       }
>>>
>>>     std::cout << "ITK Hello World !" << std::endl;
>>>
>>>     return 0;
>>> }
>>>
>>>
>>> and what happens when executing in an Ubuntu Linux machine with 32GB or
>>> RAM
>>>
>>>
>>> $ ./HelloWorld  1000
>>> ITK Hello World !
>>>
>>>
>>> $ ./HelloWorld  1000000
>>>
>>> /home/ibanez/src/ITK/Modules/Core/Common/include/itkImportImageContainer.hxx:199:
>>> Failed to allocate memory for image.
>>>
>>>
>>>
>>>
>>> Please share with the list a minimal example of the problem you are
>>> observing,
>>> and in this way we will be able to help track the issue.
>>>
>>>
>>>      Thanks
>>>
>>>
>>>          Luis
>>>
>>>
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-9574
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users


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