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;
}
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;
}