[ITK] Error in itk::BinaryImageToLabelMapFilter for images with 1 row and N columns
Bradley Lowekamp
blowekamp at mail.nih.gov
Thu Jul 31 10:50:19 EDT 2014
OK,
That is great progress in narrowing down the bug.
1) Here is a little snipped where two images are manually created:
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageIntensity/test/itkMaskImageFilterTest.cxx#L45-L91
2) How many threads are you using for this algorithm? The BinaryImageToLabelMapFilter has a "SetNumberOfThreads" method inherited from the ProcessObject class. Try setting this value to 1, and see if the issue is there... try other values too.
http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#ae5ccbe3a8c5687b4a82d3638b9e49409
3) Are you interested in learning how to use git to contribute this test to facilitate fixing this bug?
http://www.itk.org/Wiki/ITK/Git/Develop
Brad
On Jul 31, 2014, at 10:34 AM, Girish Mallya Udupi <indianzeppelin at gmail.com> wrote:
> 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 image
>> ReaderType::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 image
>> OtsuThresholdImageFilterType::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 image
>> BinaryImageToLabelMapFilterType::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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