[Insight-users] Image filtering and feature detection-
Lars Friedrich Lars
lars-friedrich at gmx.net
Mon Aug 16 11:19:34 EDT 2010
Hi Dan,
uups, I forgot the
kernel.CreateStructuringElement();
source line!!!
Sorry for my noise!!
regards,
lars
-------- Original-Nachricht --------
> Datum: Mon, 16 Aug 2010 16:57:35 +0200
> Von: "Lars Friedrich Lars" <lars-friedrich at gmx.net>
> An: Dan Mueller <dan.muel at gmail.com>
> CC: insight-users at itk.org, ryanleesmith at gmail.com
> Betreff: Re: [Insight-users] Image filtering and feature detection-
> 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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