[Insight-users] Image filtering and feature detection-
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Mon Aug 16 11:57:50 EDT 2010
Le 16 août 10 à 17:54, Dan Mueller a écrit :
> 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();
Hi,
That's a very common mistake - I hope that it will be fixed in ITK v4,
for example by deprecating BallStructuringElement in favor of
FlatStructuringElement, which does not suffer that problem.
Regards,
Gaëtan
>>
>> 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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>>
>> --
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>>
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> Visit other Kitware open-source projects at
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--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr
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