LabelImagePointer DeriveForegroundLabelImage(const ImagePointer I, const int threshold)
{   itk::ImageLinearConstIteratorWithIndex<ImageType> originitr(I, I->GetRequestedRegion());
    originitr.SetDirection(2);
    originitr.GoToBegin();
    ImageType::SizeType originsize = I->GetLargestPossibleRegion().GetSize();

    LabelImagePointer pBinaryImage = LabelImageType::New();
    LabelImageType::SizeType size;
    size[0] = originsize[0];
    size[1] = originsize[1];
    size[2] = originsize[2];
    LabelImageType::IndexType idx;
    idx.Fill(0);
    LabelImageType::RegionType region;
    region.SetSize(size);
    region.SetIndex(idx);
    pBinaryImage->SetRegions(region);
    pBinaryImage->Allocate();
    pBinaryImage->FillBuffer(0);
    itk::ImageLinearIteratorWithIndex<LabelImageType> 
                        binaryitr(pBinaryImage, pBinaryImage->GetRequestedRegion());
    binaryitr.SetDirection(2);
    binaryitr.GoToBegin();

    while( !originitr.IsAtEnd() && !binaryitr.IsAtEnd())
    {
        while(!originitr.IsAtEndOfLine()){
            if (originitr.Get() > threshold){
                binaryitr.Set(1);
            }
            ++originitr;
            ++binaryitr;
        }
        originitr.NextLine();
        binaryitr.NextLine();
    }
    
    return pBinaryImage;
}
Example #2
0
vtkSmartPointer<vtkPolyData> getVTKPolyDataPrecise(LabelImageType::Pointer label)
{
	LabelIteratorType liter = LabelIteratorType(label,label->GetLargestPossibleRegion());
	liter.GoToBegin();

	//find the maximum number of cells
	unsigned short max1 = 0;
	for(liter.GoToBegin();!liter.IsAtEnd();++liter)
		max1 = MAX(max1,liter.Get());

	//find all the cubes in which cells lie
	cubecoord* carray = new cubecoord[max1+1];
	for(int counter=0; counter<=max1; counter++)
	{
		carray[counter].sx=60000; carray[counter].sy=60000;carray[counter].sz=60000;
		carray[counter].ex=0;carray[counter].ey=0;carray[counter].ez=0;
	}

	typedef itk::ImageRegionConstIteratorWithIndex<LabelImageType> ConstLabelIteratorWithIndex;
	ConstLabelIteratorWithIndex cliter = ConstLabelIteratorWithIndex(label,label->GetLargestPossibleRegion());
	InputImageType::IndexType index;
	for(cliter.GoToBegin();!cliter.IsAtEnd();++cliter)
	{
		int cur = cliter.Get();
		if(cur!=0)
		{
			index = cliter.GetIndex();
			carray[cur].sx= MIN(index[0],carray[cur].sx);
			carray[cur].sy= MIN(index[1],carray[cur].sy);
			carray[cur].sz= MIN(index[2],carray[cur].sz);
			carray[cur].ex= MAX(index[0],carray[cur].ex);
			carray[cur].ey= MAX(index[1],carray[cur].ey);
			carray[cur].ez= MAX(index[2],carray[cur].ez);
		}
	}

	//find the largest image size we need
	unsigned short wx=0,wy=0,wz=0;
	for(int counter=1; counter<=max1; counter++)
	{
		wx = MAX(carray[counter].ex-carray[counter].sx+1,wx);
		wy = MAX(carray[counter].ey-carray[counter].sy+1,wy);
		wz = MAX(carray[counter].ez-carray[counter].sz+1,wz);
	}
	// accommodate padding
	wx = wx+2;wy = wy +2; wz = wz+2;
	printf("wx wy wz %u %u %u\n",wx,wy,wz);
	// create a tiny image of maximum size


	//appendfilter->UserManagedInputsOn();
	//appendfilter->SetNumberOfInputs(max1);
	vtkSmartPointer<vtkAppendPolyData> appendfilter = vtkSmartPointer<vtkAppendPolyData>::New();

/**************/
			ExportFilterType::Pointer itkexporter = ExportFilterType::New();
			
			vtkSmartPointer<vtkImageImport> vtkimporter = vtkSmartPointer<vtkImageImport>::New();
			ConnectPipelines(itkexporter,(vtkImageImport *)vtkimporter);
			vtkSmartPointer<vtkMarchingCubes> contourf = vtkSmartPointer<vtkMarchingCubes>::New();
			contourf->SetInputData(vtkimporter->GetOutput());
			contourf->SetValue(0,127);
			contourf->ComputeNormalsOff();
			contourf->ComputeScalarsOff();
			contourf->ComputeGradientsOff();
			vtkSmartPointer<vtkSmoothPolyDataFilter> smoothf = vtkSmartPointer<vtkSmoothPolyDataFilter>::New();
			smoothf->SetInputData(contourf->GetOutput());
			smoothf->SetRelaxationFactor(0.3);
			smoothf->SetNumberOfIterations(20);

			vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
			transform->PostMultiply();
	
			transform->Identity();
			vtkSmartPointer<vtkTransformPolyDataFilter> tf = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
			tf->SetTransform(transform);
			tf->SetInputData(smoothf->GetOutput());
		
/******************/



InputImageType::Pointer t = getEmpty(wx,wy,wz);
	for(int counter=1; counter<=max1; counter++)
	{

		
			
			//printf("Maximum tiny image size I need is [%d %d %d]\n",wx,wy,wz);

			if(carray[counter].sx > 59999)
				continue;
			printf("Working..\n");
	//		scanf("%*d");
			InputImageType::SizeType size;
			InputImageType::RegionType region;
			index.Fill(1);

			region.SetIndex(index);
			region.SetSize(size);


			LabelImageType::SizeType lsize;
			LabelImageType::IndexType lindex;
			LabelImageType::RegionType lregion;

			itkexporter->SetInput(t);

			
			
		

			t->FillBuffer(0);
			lsize[0] = carray[counter].ex-carray[counter].sx+1;
			lsize[1] = carray[counter].ey-carray[counter].sy+1;
			lsize[2] = carray[counter].ez-carray[counter].sz+1;

			lindex[0] = carray[counter].sx;
			lindex[1] = carray[counter].sy;
			lindex[2] = carray[counter].sz;

			lregion.SetIndex(lindex);
			lregion.SetSize(lsize);
			LabelIteratorType localiter = LabelIteratorType(label,lregion);

			size = lsize;
			region.SetSize(size);
			IteratorType iter = IteratorType(t,region);
			for(localiter.GoToBegin(),iter.GoToBegin();!localiter.IsAtEnd();++localiter,++iter)
			{
				if(localiter.Get()==counter)
				{
					iter.Set(255);
				}
			}
			t->Modified();
			vtkimporter->Modified();

			transform->Identity();	
			transform->Translate(carray[counter].sx-1,carray[counter].sy-1,carray[counter].sz-1);
			tf->SetTransform(transform);
			tf->Update();
		vtkSmartPointer<vtkPolyData> pol=vtkSmartPointer<vtkPolyData>::New();
		pol->DeepCopy(tf->GetOutput());
	//	tf->GetOutput()->Print(std::cout);
		
		appendfilter->AddInputData(pol);
		//appendfilter->Update();
	
		//appendfilter->SetInputByNumber(counter-1,tf->GetOutput());
	//	appendfilter->Update();
	//	appendfilter->GetOutput()->Print(std::cout);
		//if(counter>500)
		//	break;
		printf("Completed %d/%d\r",counter,max1);
	//	scanf("%*d");
	}

	appendfilter->Update();
	vtkSmartPointer<vtkDecimatePro> decimate = vtkSmartPointer<vtkDecimatePro>::New();
	decimate->SetInputData(appendfilter->GetOutput());
	decimate->SetTargetReduction(0.1);
	//decimate->SetNumberOfDivisions(32,32,32);
	printf("Decimating the contours...");
	decimate->Update();
	printf("Done\n");
	printf("Smoothing the contours after decimation...");
	vtkSmartPointer<vtkSmoothPolyDataFilter> smoothfinal = vtkSmartPointer<vtkSmoothPolyDataFilter>::New();
	smoothfinal->SetRelaxationFactor(0.2);
	smoothfinal->SetInputData(decimate->GetOutput());
	smoothfinal->SetNumberOfIterations(0);
	smoothfinal->Update();
	printf("Done\n");
	delete [] carray;
	vtkSmartPointer<vtkPolyData> out = smoothfinal->GetOutput();
	return out;
}