[Insight-users] Image filtering and feature detection-
Dan Mueller
dan.muel at gmail.com
Mon Aug 16 11:54:08 EDT 2010
Hi Lars,
Glad that you worked it out.
Cheers, Dan
On 16 August 2010 17:19, Lars Friedrich Lars <lars-friedrich at gmx.net> wrote:
> 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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