[Insight-users] Image filtering and feature detection-

[Lars Friedrich Lars]

Hello Dan,

thank you for the quick reply. This was the source code:


#include <stdlib.h>

#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
#include <itkImage.h>
#include <itkWhiteTopHatImageFilter.h>
#include <itkBinaryBallStructuringElement.h>

int main(int argc, char *argv[])
{
  typedef itk::Image<unsigned char, 2> ImageType;
  typedef itk::ImageFileReader<ImageType> ReaderType;
  typedef itk::ImageFileWriter<ImageType> WriterType;
  typedef itk::BinaryBallStructuringElement<unsigned char, 2> KernelType;
  typedef itk::WhiteTopHatImageFilter<ImageType, ImageType, KernelType> FilterType;

  ReaderType::Pointer r = ReaderType::New();
  r->SetFileName(argv[1]);
  try
  {
    r->Update();
  }
  catch (itk::ExceptionObject &e)
  {
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
  }

  ImageType::Pointer image = r->GetOutput();
  KernelType kernel;
  kernel.SetRadius(20);
  FilterType::Pointer filter = FilterType::New();
  filter->SetKernel(kernel);
  filter->SetInput(image);
  try
  {
    filter->Update();
  }
  catch (itk::ExceptionObject &e)
  {
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
  }

  WriterType::Pointer w = WriterType::New();
  w->SetFileName(argv[2]);
  w->SetInput(filter->GetOutput());
  try
  {
    w->Update();
  }
  catch (itk::ExceptionObject &e)
  {
    std::cerr << e << std::endl;
    return EXIT_FAILURE;
  }

  return EXIT_SUCCESS;
}


I have ITK 3.16 here, so I do not have the FlatStructuringElement (without review). Maybe that's the problem?

THANK YOU!

lars



-------- Original-Nachricht --------
> Datum: Mon, 16 Aug 2010 16:49:22 +0200
> Von: Dan Mueller <dan.muel at gmail.com>
> An: Lars Friedrich Lars <lars-friedrich at gmx.net>
> CC: ryanleesmith at gmail.com, insight-users at itk.org
> Betreff: Re: [Insight-users] Image filtering and feature detection-

> Hi Lars,
> 
> I used my ITK-based scripting program called "SharpImage"
>     http://www.insight-journal.org/browse/publication/161
> 
> with the following commands
>     Open "D:/Temp/wd3Yt.jpg#F2"
>     MorphologicalOpen Kernel=itkFlatStructuringElement.Ball(itkSize(5,5))
>     BinaryPixelMath Input1="wd3Yt.jpg"
> Input2="wd3Yt_MorphologicalOpen.jpg" Operation="Sub"
>     BinaryThreshold Lower=35 Upper=255
> 
> I'm not sure why your pipeline did not work. Can you please post your
> source code?
> 
> HTH
> 
> Cheers, Dan
> 
> On 16 August 2010 16:37, Lars Friedrich Lars <lars-friedrich at gmx.net>
> wrote:
> > Hello Dan,
> >
> > I also tried the WhiteTopHat-filter on the image. I used a
> BinaryBallStructuringElement-kernel with varying radius (1,3,5,6,10,20). However, I
> never got an output image that was that 'clean' as the one that you sent on the
> mailing list (wd3Yt_WhiteTopHat.jpg).
> > Could you please tell me which kernel or possibly which exact pipeline
> did you use to produce this output? I face a comparable problem and would be
> interest in your pipeline.
> > Thank you very much!!
> >
> > regards,
> > lars
> >
> > p.s.: I attached the produced output with radius = 5.
> >
> > -------- Original-Nachricht --------
> >> Datum: Mon, 16 Aug 2010 06:22:12 +0200
> >> Von: Dan Mueller <dan.muel at gmail.com>
> >> An: Ryan Smith <ryanleesmith at gmail.com>
> >> CC: insight-users at itk.org
> >> Betreff: Re: [Insight-users] Image filtering and feature detection-
> >
> >> Hi Ryan,
> >>
> >> You might consider using the "white top hat" operation to remove the
> >> background:
> >>     WhiteTopHat = I - Dilate( Erode(I) )
> >> where I is the image, Erode is morphological erosion, and Dilate is
> >> morphological dilation.
> >>
> >> You can find an implementation of this operation in:
> >>     Code/BasicFilters/itkWhiteTopHatImageFilter.h
> >>
> >> Once the background is removed, a simple global intensity threshold
> >> should suffice to segment the spots. The following filters may be
> >> helpful for that task:
> >>     Code/BasicFilters/itkBinaryThresholdImageFilter.h
> >>     Code/Algorithms/itkOtsuThresholdImageFilter.h
> >>     Code/Review/itkKappaSigmaThresholdImageFilter.h
> >>
> >> HTH
> >>
> >> Cheers, Dan
> >>
> >> On 15 August 2010 23:04, Ryan Smith <ryanleesmith at gmail.com> wrote:
> >> > Hi-
> >> > I am attempting to remove the background and detect features in the
> >> > following image:
> >> > http://i.imgur.com/wd3Yt.jpg
> >> >
> >> > I have a series of images in which the white circular spots travel
> and
> >> the
> >> > white vertical stripes remain stationary.  I would like to apply
> some
> >> simple
> >> > background subtraction to remove the white stripes then autodetect
> the
> >> > intensity maxima associated with the circular features.
> >> >
> >> > A brief search provided the following results which address similar
> >> problems
> >> > using itkConnectedComponentFilter.  Is this what I want after my
> >> background
> >> > is subtracted?  Any example code on how to get the location and
> sizes
> >> of the
> >> > components? Thanks in advance-
> >> >
> >> > -Ryan

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