[ITK] Error in itk::BinaryImageToLabelMapFilter for images with 1 row and N columns

[Girish Mallya Udupi]

Great! I've gotten started on this. Thanks for your input.


On Thu, Jul 31, 2014 at 4:53 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Awesome! Thanks for taking the effort to contribute!
>
> That is very interesting that the problem relates to the number of threads!
>
> You will need push access to Gerrit, so that you can push your patch to
> gerrit for review.
>
> The next step is to create a topic, and work locally to add you code as an
> ITK test. This will involve modifying the CMakeLists[1] file and creating a
> new cxx say called itkBinaryIMageToLabelMapFilterTest2.cxx something like
> [2].
>
> Hope that get you started,
> Brad
>
> [1]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/test/CMakeLists.txt
> [2]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/LabelMap/test/itkBinaryImageToLabelMapFilterTest.cxx
>
>
> On Jul 31, 2014, at 11:40 AM, Girish Mallya Udupi <
> indianzeppelin at gmail.com> wrote:
>
> 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
>
>
>


-- 
Regards,
Girish
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