[ITK] Error in itk::BinaryImageToLabelMapFilter for images with 1 row and N columns
Girish Mallya Udupi
indianzeppelin at gmail.com
Thu Jul 31 11:40:37 EDT 2014
1) Thanks for this. Will go through it.
2) If I am not wrong, the number of threads used by default is the number
of CPU cores in my machine? If so, it would be 4 in my case. As expected,
setting the number of threads to 1 fixes the issue, while the error is
thrown for values other than 1.
3) Sure. I went through that page and have performed the initial setup,
except the git push access, which I suppose I wouldn't need?
On Thu, Jul 31, 2014 at 3:50 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:
> 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 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
>>
>> ...
>
> [Message clipped]
--
Regards,
Girish
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