[Insight-users] Generating coocurence feature maps for 2D images

[Zachary Pincus]

I think that the glcm calculations are inherently expensive: they 
require several passes through a 2D histogram in order to calculate 
various features.

I don't know of any particular shortcuts around this. My suggestion 
would be to run a profiler on the code to see what the slow parts are. 
(Is it scanning across the image? Iterating through the histogram? 
Actually computing the features?) Once you know the slow parts, you can 
try to speed them up.

For example, you could modify the texture coefficient calculator class 
to only calculate the single texture value you require, if that value 
needs fewer passes through the histogram than the calculator currently 
takes. Or modifying the code to use a sparse frequency container for 
the histogram might be a good idea.

Anyhow, you're basically in optimization-land at this point, so all the 
general advice applies. I don't know of any particularly better way to 
compute the GLCM values specifically.

You might also think about down-sampling your images first. Do you 
really need texture calculated at *every* pixel? Would interpolation 
work instead? If not, then there can be some savings there. It's worth 
thinking about alternate solutions.

Zach



On Mar 3, 2005, at 11:09 PM, Sachin Jambawalikar wrote:

> Hi  Zach,
> thanks  for your prompt reply.
> I made the necessary changes you asked for. But still the  Glcm takes
> about  360 second
>  for one slice with  the radius of neighboorhood 12. I was wondering
> if you  know of a faster implementation of glcm or have come across
> some references  for fast glcm matrix computation, I had implemented a
>  C code for (without using the itk library) glcm maps computation
> which  computed   glcm maps for window 5x5  and histogram bins 256 in
> about  780 second ,so I feel that the glcm computation with  your
> class  is slightly faster
> or round about the same ( for your class  I am using radius 12 ie
> window of 25x25). Is there any scope  for improving the speed .
>
> I'm trying to compute slice by slice glcm feature maps for a 3D
> volume.And my volumes are 512x512x50 so it would take me like 5 hours
> for a volume.
>
> this is the   out put and the changed code:
>           Probe Tag    Starts    Stops           Time
>           Slice glcm           1            1           360.968
> computed0thslice
>           Probe Tag    Starts    Stops           Time
>           Slice glcm           1            1           364.125
> computed1thslice
>           Probe Tag    Starts    Stops           Time
>           Slice glcm           1            1           370.906
> computed2thslice
>           Probe Tag    Starts    Stops           Time
>           Slice glcm           1            1           371.359
> computed3thslice
>
>
>
>
> ComputeNeighboorhoodConvolution(ImagePointer2D inimage)
> 	{
> 	
> //typedef  PixelType short;
>
> 	 itk::TimeProbesCollectorBase collector;
>
> typedef itk::Image<double,2> InternalPixelType;
> InternalPixelType::Pointer output = InternalPixelType::New();
> typedef itk::ImageRegionIterator< InternalPixelType>        
> Iterator2DType;
>
> output->SetRegions(inimage->GetRequestedRegion());
> output->Allocate();
> output->FillBuffer(0.0);
>
> ImageType2D::Pointer BBOut = ImageType2D::New();
> BBOut=inimage;
>
> NeighborhoodIteratorType::RadiusType radius;
> 	
>
> itk::NeighborhoodInnerProduct<ImageType2D> innerProduct;
> 	radius.Fill(12);
> 	typedef itk::NeighborhoodAlgorithm::ImageBoundaryFacesCalculator<
> ImageType2D > FaceCalculatorType;
> 	FaceCalculatorType faceCalculator;
> 	FaceCalculatorType::FaceListType faceList;
> 	faceList = faceCalculator(inimage, output->GetRequestedRegion(),
> 		radius);
> 	FaceCalculatorType::FaceListType::iterator fit;
>
> 	Iterator2DType out;
>   NeighborhoodIteratorType it;
> 	typedef itk::Statistics::ScalarImageTextureCalculator<ImageType2D>
> ScalarImageTextureCalculatorType;
> ScalarImageTextureCalculatorType::Pointer
> texturecal=ScalarImageTextureCalculatorType::New();
> typedef itk::RegionOfInterestImageFilter< ImageType2D,ImageType2D >
> ROIFilterType;
>
> typedef VectorContainer<unsigned char, double>      FeatureValueVector;
> typedef typename FeatureValueVector::Pointer        
> FeatureValueVectorPointer;
> double result=0.0;
>
> ROIFilterType::Pointer roifilter=ROIFilterType::New();
>  	roifilter->SetInput(inimage);
> 			fit=faceList.begin();
> 		it = NeighborhoodIteratorType( radius,inimage, *fit );
> 		out = Iterator2DType( output, *fit );
>    collector.Start("Slice glcm");
>  texturecal->SetNumberOfBinsPerAxis(16);	
> 	 for (it.GoToBegin(), out.GoToBegin(); ! it.IsAtEnd(); ++it, ++out)
> 			{
> 		
>    	BBOut->SetRequestedRegion(it.GetBoundingBoxAsImageRegion());
> 	     texturecal->SetInput(BBOut);
> 			  texturecal->Compute();
> 		 	FeatureValueVectorPointer tmp= texturecal->GetFeatureMeans();
> 				result=static_cast<double>(tmp->GetElement(0));
> 				out.Set(result);
> 			}
> 	
> 		collector.Stop("Slice glcm");
> 		collector.Report();
>
> 		
> 	return inimage;
> 	}
>
>
>
>
> Regards
> --Sachin
>