[ITK] Error in itk::BinaryImageToLabelMapFilter for images with 1 row and N columns
Girish Mallya Udupi
indianzeppelin at gmail.com
Thu Jul 31 10:34:13 EDT 2014
Thanks for your reply, Brad!
1) No, the OtsuThreshold isn't required. It's there just to create a binary
input image which is required by BinaryImageToLabelMapFilter. I did as you
said (writing out the resulting binary image, loading it and then providing
it as input), and the error is still there.
2) Yes, it fails with all images which are 1 x N (rows x cols), except when
N = 1 (i.e., it works fine with 1 x 1 images). I am not sure how to create
an image procedurally, but I created a simple 1 x 10 image in MATLAB and
saved it as bmp, jpg and tiff. The test case produces the error for all
three.
Also, there is no error if the image is N x 1.
Basically, the following shorter piece of code can reproduce the error.
// start code
typedef itk::Image< unsigned char, 2 > ScalarImageType;
typedef itk::ImageFileReader< ScalarImageType > ReaderType;
typedef itk::BinaryImageToLabelMapFilter< ScalarImageType >
BinaryImageToLabelMapFilterType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName("test_bw.jpg");
try {
reader->Update();
}
catch ( itk::ExceptionObject & err ) {
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
}
BinaryImageToLabelMapFilterType::Pointer binarytoLabelmapFilter =
BinaryImageToLabelMapFilterType::New();
binarytoLabelmapFilter->SetInput(reader->GetOutput());
try {
binarytoLabelmapFilter->Update();
}
catch ( itk::ExceptionObject & err ) {
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
}
// end code
Let me know if there is anything else I could try.
On Thu, Jul 31, 2014 at 2:34 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:
> Hello,
>
> Thank you for reporting this. This looks like it may be a bug inside ITK.
> However it would be good to make this a little more reproducible to aid in
> debugging.
>
> 1) Is the OtsuThreshold required? If you write out the results of the otsu
> to a file, then just loaded them in this test case will it still have the
> error?
> 2) I don't have your data which causes this failure. How big is it? Does
> it fail with all data this shape? Could you change this test case to have a
> hard coded image? One that is procedurally created?
>
> Thanks again for reporting this issue.
>
> Brad
>
>
>
>
>
>
>
> On Jul 31, 2014, at 5:35 AM, Girish Mallya Udupi <indianzeppelin at gmail.com>
> wrote:
>
> Hi all,
>
> I am new to both C++ and ITK, and have been fiddling with test code for
> learning purposes.
>
> The following is a simple piece of code to read in a grayscale image,
> threshold it to get a binary image, and get a label map out of it. I use MS
> VS2010 and ITK v4.5.1.
>
> typedef itk::Image< unsigned char, 2 > ScalarImageType;
> typedef itk::ImageFileWriter< ScalarImageType > WriterType;typedef itk::ImageFileReader< ScalarImageType > ReaderType;
> typedef itk::OtsuThresholdImageFilter< ScalarImageType, ScalarImageType > OtsuThresholdImageFilterType;typedef itk::BinaryImageToLabelMapFilter< ScalarImageType > BinaryImageToLabelMapFilterType;
> // read a grayscale imageReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName("test_grey.jpg");try{
> reader->Update();}catch( itk::ExceptionObject &err ){
> std::cerr << "ExceptionObject caught !" << std::endl;
> std::cerr << err << std::endl;
> return(FALSE);}
> // threshold the grayscale imageOtsuThresholdImageFilterType::Pointer otsuThresImgFilter = OtsuThresholdImageFilterType::New();
> otsuThresImgFilter->SetInput(reader->GetOutput());
> otsuThresImgFilter->SetInsideValue(255);
> otsuThresImgFilter->SetOutsideValue(0);try{
> otsuThresImgFilter->Update();}catch( itk::ExceptionObject &err ){
> std::cerr << "ExceptionObject caught !" << std::endl;
> std::cerr << err << std::endl;
> return(FALSE);}
> // get a label map from the binary imageBinaryImageToLabelMapFilterType::Pointer binarytoLabelmapFilter = BinaryImageToLabelMapFilterType::New();
> binarytoLabelmapFilter->SetInput(otsuThresImgFilter->GetOutput());try{
> binarytoLabelmapFilter->Update();}catch( itk::ExceptionObject &err ){
> std::cerr << "ExceptionObject caught !" << std::endl;
> std::cerr << err << std::endl;
> return(FALSE);}
>
>
> This works fine for all images, except those which have only 1 row and N
> columns (interestingly, 1 x 1 images go through fine).
>
> So, for 1 x N images, the program crashes in release mode. In debug mode,
> I get the "vector subscript out of range" error. Stepping through the code,
> I found that the crash happens on the line
> *binarytoLabelmapFilter->Update();* of my code.
>
> Call stack:
>
> msvcr100d.dll!_CrtDbgBreak() Line 85 C
> msvcr100d.dll!_VCrtDbgReportW(int nRptType, const wchar_t * szFile, int nLine, const wchar_t * szModule, const wchar_t * szFormat, char * arglist) Line 502 C
> msvcr100d.dll!_CrtDbgReportWV(int nRptType, const wchar_t * szFile, int nLine, const wchar_t * szModule, const wchar_t * szFormat, char * arglist) Line 241 + 0x1d bytes C++
> msvcr100d.dll!_CrtDbgReportW(int nRptType, const wchar_t * szFile, int nLine, const wchar_t * szModule, const wchar_t * szFormat, ...) Line 258 + 0x1d bytes C++
> msvcp100d.dll!std::_Debug_message(const wchar_t * message, const wchar_t * file, unsigned int line) Line 13 + 0x16 bytes C++HelloWorld.exe!std::vector<std::vector<itk::BinaryImageToLabelMapFilter<itk::Image<unsigned char,2>,itk::LabelMap<itk::LabelObject<unsigned long,2> > >::runLength,std::allocator<itk::BinaryImageToLabelMapFilter<itk::Image<unsigned char,2>,itk::LabelMap<itk::LabelObject<unsigned long,2> > >::runLength> >,std::allocator<std::vector<itk::BinaryImageToLabelMapFilter<itk::Image<unsigned char,2>,itk::LabelMap<itk::LabelObject<unsigned long,2> > >::runLength,std::allocator<itk::BinaryImageToLabelMapFilter<itk::Image<unsigned char,2>,itk::LabelMap<itk::LabelObject<unsigned long,2> > >::runLength> > > >::operator[](unsigned int _Pos) Line 932 + 0x17 bytes C++HelloWorld.exe!itk::BinaryImageToLabelMapFilter<itk::Image<unsigned char,2>,itk::LabelMap<itk::LabelObject<unsigned long,2> > >::ThreadedGenerateData(const itk::ImageRegion<2> & outputRegionForThread, unsigned int threadId) Line 190 + 0x1c bytes C++HelloWorld.exe!itk::ImageSource<itk::LabelMap<itk::LabelObject<unsigned long,2> > >::ThreaderCallback(void * arg) Line 295 + 0x25 bytes C++HelloWorld.exe!itk::MultiThreader::SingleMethodProxy(void * arg) Line 375 + 0xe bytes C++
> msvcr100d.dll!_callthreadstartex() Line 314 + 0xf bytes C
> msvcr100d.dll!_threadstartex(void * ptd) Line 297 C
> kernel32.dll!773f338a() [Frames below may be incorrect and/or missing, no symbols loaded for kernel32.dll]
> ntdll.dll!77a49f72()
> ntdll.dll!77a49f45()
>
> Being a novice, I am not sure if it is an issue in ITK or if it is due to
> something I am doing wrong.
>
>
>
> --
> Regards,
> Girish
> _______________________________________________
> Community mailing list
> Community at itk.org
> http://public.kitware.com/mailman/listinfo/community
>
>
>
--
Regards,
Girish
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