Remove small component

Beginner Questions
1

I intend to remove from sitk::Image the smallest component from it (in the first stage). For that, I wrote:

BOOL CMyDoc::Segement(sitk::Image& img)
{
		sitk::Image imgTemp(img);
		int64_t nMaxLabel = 0, nMaxSize = 0;
		sitk::Image cc = sitk::SLIC(imgTemp);
		sitk::LabelIntensityStatisticsImageFilter statistics;
		statistics.Execute(cc, imgTemp);
		std::vector<int64_t>::iterator it;
		std::vector<int64_t> labels = statistics.GetLabels();
		for (it = labels.begin(); it != labels.end(); ++it)
		{
			if (nMaxLabel < statistics.GetPhysicalSize(*it))
			{
				nMaxLabel = *it;
				nMaxSize = statistics.GetPhysicalSize(*it);
			}
		}

		CArray<long, long> arr;
		for (it = labels.begin(); it != labels.end(); ++it)
		{
			if (statistics.GetPhysicalSize(*it) > nMaxSize * 0.5)
				arr.Add(*it);
		}

My question is, how can use it arr object to remove the points from the resulting image ? What kind of filter should I use ?

I have read about this filter:https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1MaskNegatedImageFilter.html, but I don’t know how to use it in this case … I mean, what mask image should I provide ? https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1MaskNegatedImageFilter.html#ad5c71726224210803c9233e5ed8473d0

Might be a trivial question, but for me is not. Thank you for your patience and your time.

Flaviu.

2

Relabel filter reorders the labels and removes the small ones. Would that work for you?

1 Like
3

Good point, I will try it.

I have tried myself something:

	std::vector<unsigned int> size = imgTemp.GetSize();
	int64_t* p = imgTemp.GetBufferAsInt64();
	unsigned int nCount = size[0] * size[1] * size[2];
	for (unsigned int i = 0; i < nCount; ++i)
	{
		TRACE("%d===%I64d\n", i, p[i]);
	}

but this is no fit with statistics.GetLabels() method:

sitk::ERROR: The image is of type: 16-bit signed integer but the GetBuffer access method requires type: 64-bit signed integer!

… hmm … what could I plugin the data ?

4

@dzenanz, seem to work sitk::RelabelComponent filter … :slight_smile: the resulting image are not very sharp, but it is a step forward.

5

I have used sitk::RelabelComponent with pretty well results. But I noticed that if I denoise the image before applying this filter I got an error. Here is the code:

	sitk::Image imgTemp(imgOrg);
	sitk::Image curvature = sitk::CurvatureFlow(imgTemp, 0.125, 5);
	imgOuput = sitk::RelabelComponent(curvature, 200);

and the error is: sitk::ERROR: Pixel type: 64-bit float is not supported in 3D byclass itk::simple::RelabelComponentImageFilter

If I didn’t apply sitk::CurvatureFlow I have no problem … how can I overcome this error ?

Thanks much.
Flaviu.

6

@blowekamp @zivy?

7

It makes no sense to run diffusion on a labeled image and then “relabel” it. I can’t help here.

9

“run diffusion on a labeled image” imgOrg is not labeled image. Here is the functional code:

imgOut = sitk::CurvatureFlow(imgOrg, 0.022, 1);

And here is the code with the error:

sitk::Image curvature = sitk::CurvatureFlow(imgOrg, 0.022, 1);
imgOut = sitk::RelabelComponent(curvature, 200);

The fact is that another filter is run without any problem:

sitk::Image curvature = sitk::CurvatureFlow(imgOrg, 0.022, 1);
imgOut = sitk::ConnectedThreshold(curvature, list, 1400, 2600);
10

I guess I have found a workaround for CurvatureFlow / RelabelComponent issue, and I am listing here for anyone who meet the same problem:

sitk::Image curvature = sitk::CurvatureFlow(imgOrg, 0.022, 1);
sitk::Image imgCast = sitk::Cast(curvature, imgOrg.GetPixelID());
imgOut = sitk::RelabelComponent(imgCast, 200);

Please correct me if I did something wrong.

Flaviu.

1 Like