- /* TODO
-
-
- SliceType::RegionType sliceRegion = tmp->GetLargestPossibleRegion();
- SliceType::SizeType size = sliceRegion.GetSize();
- SliceType::SpacingType spacing = tmp->GetSpacing();
- SliceType::PointType origin = tmp->GetOrigin();
- SliceType::IndexType start = sliceRegion.GetIndex();
-
- SliceType::Pointer seedsObject = SliceType::New();
- seedsObject->SetRegions(sliceRegion);
- seedsObject->SetOrigin(origin);
- seedsObject->SetSpacing(spacing);
- seedsObject->Allocate();
- seedsObject->FillBuffer(0);
-
- SliceType::Pointer seedsBackground = SliceType::New();
- seedsBackground->SetRegions(sliceRegion);
- seedsBackground->SetOrigin(origin);
- seedsBackground->SetSpacing(spacing);
- seedsBackground->Allocate();
- seedsBackground->FillBuffer(0);
-
- typedef itk::ImageRegionIteratorWithIndex<SliceType> SliceIteratorType;
- SliceIteratorType itSliceMori(tmp, tmp->GetLargestPossibleRegion());
-
- int len = 0;
- int numO = 0;
- int numB = 0;
-
- itSliceMori.GoToBegin();
-
- while (!itSliceMori.IsAtEnd())
- {
- if (itSliceMori.Get() != 0)
- len++;
-
- typename TImage::PixelType vessVal = vess->GetPixel(itSliceMori.GetIndex());
- typename TImage::PixelType imgVal = data->GetPixel(itSliceMori.GetIndex());
- typename TImage::PixelType bw = tmp->GetPixel(itSliceMori.GetIndex());
-
- if (bw != 0 && vessVal > this->m_VessTh * this->m_vessMax / 100)
- {
- seedsObject->SetPixel(itSliceMori.GetIndex(), 1);
- numO++;
- }
-
- itSliceMori++;
- }
-
- if (len == 0)
- {
- std::cout << "Slice " << z << ": - brak pikseli zakwalifikowanych do drzewa" << std::endl;
- continue;
- }
-
- SliceIteratorType itSliceVess(vess, vess->GetLargestPossibleRegion());
- itSliceVess.GoToBegin();
-
- while (!itSliceVess.IsAtEnd())
- {
- if (itSliceVess.Get() < this->m_VessTh * this->m_vessMax / 100)
- {
- seedsBackground->SetPixel(itSliceVess.GetIndex(), 1);
- numB++;
- }
- itSliceVess++;
-
- }
-
- std::cout << "slice: " << z << "seeds obj: " << numO << " seeds bkg " << numB << std::endl;
- // przygotowania do Random Walkera
-
- typename TImage::PixelType *bufferImg = 0;
- typename TImage::PixelType *bufferSeedsObj = 0;
- typename TImage::PixelType *bufferSeedsBkg = 0;
-
- int dims[2], dims2[2], dims3[2];
- double spac[2], orig[2], spac2[2], orig2[2], spac3[2], orig3[2];
-
- image2buffer(bufferImg, dims, spac, orig, 2, data);
- image2buffer(bufferSeedsObj, dims2, spac2, orig2, 2, seedsObject);
- image2buffer(bufferSeedsBkg, dims3, spac3, orig3, 2, seedsBackground);
-
- // TO DO HERE
- int width = dims[0];
- int height = dims[1];
-
- PixelType *mask = new PixelType[width*height];
- double *probs = new double[2 * width*height];
-
- int i, j, no_seeds = 0;
-
- for (i = 0; i < width*height; i++)
-
- if (bufferSeedsObj[i] == 1 || bufferSeedsBkg[i] == 1)
- no_seeds++;
-
- int *seed_indexes = new int[no_seeds];
- int *seed_labels = new int[no_seeds];
-
- for (j = 0, i = 0; i < width*height; i++)
- {
- if (bufferSeedsObj[i] == 1)
- {
- seed_indexes[j] = i + 1;//=i+1 (i)
- seed_labels[j] = this->m_replaceValue;
- j++;
- }
- else if (bufferSeedsBkg[i] == 1)
- {
- seed_indexes[j] = i + 1;//=i+1 (i)
- seed_labels[j] = 0;
- j++;
- }
- }
-
- call_walker(mask, probs, bufferImg, height, width, seed_indexes, no_seeds, seed_labels, 2, this->m_beta);
-
- delete[] bufferSeedsObj;
- delete[] bufferSeedsBkg;
- delete[] seed_indexes;
- delete[] seed_labels;
-
- SliceType::Pointer img2 = buffer2image(mask, dims, spac, orig, 2);
-
- SliceType::PixelType *probs_img = new PixelType[width*height];
- for (i = 0; i < width*height; i++)
- probs_img[i] = floor(255 * probs[i]);
-
- SliceType::Pointer img3 = buffer2image(probs_img, dims, spac, orig, 2);
-
- typedef itk::MaximumImageFilter<SliceType> MaxFilterType;
- MaxFilterType::Pointer maxFilter = MaxFilterType::New();
- maxFilter->SetInput(0, img2);
- maxFilter->SetInput(1, next);
- maxFilter->Update();
-
- SliceType::Pointer sth = maxFilter->GetOutput();
- ImageAlgorithm::Copy(sth.GetPointer(), binaryTree[z + 1].GetPointer(), sth->GetRequestedRegion(), binaryTree[z + 1]->GetRequestedRegion());
-
- delete[] probs;
- */
- }
-}
-
-// -------------------------------------------------------------------------
-template< class _TImage, class _TLabels, class _TScalarImage >
-template< class _TBinaryTree, class _TData3D, class _TFusion >
-void
-_GoUp(
- _TBinaryTree& binaryTree,
- const _TData3D& data3D,
- const _TFusion& fusion,
- int numSlices
- )
-{
+ itk::ImageRegionConstIterator< _TSliceBinary > tIt( tmp, region );
+ itk::ImageRegionConstIterator< _TSliceFusion > vIt( vess, region );
+ itk::ImageRegionIterator< _TSliceBinary > sIt( seeds, region );
+ tIt.GoToBegin( );
+ vIt.GoToBegin( );
+ sIt.GoToBegin( );
+ int len = 0;
+ int numO = 0;
+ int numB = 0;
+ for( ; !tIt.IsAtEnd( ); ++tIt, ++vIt, ++sIt )
+ {
+ if( tIt.Get( ) != 0 )
+ {
+ len++;
+ if( vIt.Get( ) > this->m_VesselnessValue )
+ {
+ sIt.Set( 1 );
+ numO++;
+
+ } // fi
+
+ } // fi
+
+ if( vIt.Get( ) < this->m_VesselnessValue )
+ {
+ sIt.Set( 2 );
+ numB++;
+
+ } // fi
+
+ } // rof
+
+ if( len == 0 )
+ continue;
+
+ // Random walker function
+ typedef fpa::Functors::Dijkstra::Image::Gaussian< _TSliceData3D, _TSliceScalar > _TFunction;
+ typename _TFunction::Pointer edge = _TFunction::New( );
+ edge->SetBeta( this->m_Beta );
+ edge->SetEpsilon( this->m_Epsilon );
+ edge->TreatAsWeightOff( );
+
+ // Real random walker
+ typedef fpa::Common::RandomWalker< _TSliceData3D, _TSliceBinary, _TSliceScalar > _TRandomWalker;
+ typename _TRandomWalker::Pointer rw = _TRandomWalker::New( );
+ rw->SetInput( data );
+ rw->SetInputLabels( seeds );
+ rw->SetEdgeFunction( edge );
+
+ // Extract label
+ typedef itk::BinaryThresholdImageFilter< _TSliceBinary, _TSliceBinary > _TExtract;
+ typename _TExtract::Pointer extract = _TExtract::New( );
+ extract->SetInput( rw->GetOutput( ) );
+ extract->SetInsideValue( 1 );
+ extract->SetOutsideValue( 0 );
+ extract->SetLowerThreshold( 1 );
+ extract->SetUpperThreshold( 1 );
+
+ // Keep maximum
+ typedef itk::MaximumImageFilter< _TSliceBinary > _TMax;
+ typename _TMax::Pointer max = _TMax::New();
+ max->SetInput( 0, extract->GetOutput( ) );
+ max->SetInput( 1, next );
+ max->Update( );
+ binaryTree[ z + o ] = max->GetOutput( );
+ binaryTree[ z + o ]->DisconnectPipeline( );
+
+ } // elihw