int runGrAnisDiff(unsigned char* imgIn, int r, int c, int z, int iter, int timeStep, int comductance)
{
//pixel types
typedef unsigned char InputPixelType;
typedef float OutputPixelType;
typedef itk::Image< InputPixelType, 3 > InputImageType;
typedef itk::Image< OutputPixelType, 3 > OutputImageType;
//create an ITK image from the input image
OutputImageType::Pointer im;
im = OutputImageType::New();
OutputImageType::PointType origin;
origin[0] = 0.;
origin[1] = 0.;
origin[2] = 0.;
im->SetOrigin( origin );
OutputImageType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
start[2] = 0; // first index on Z
OutputImageType::SizeType size;
size[0] = c; // size along X
size[1] = r; // size along Y
size[2] = z; // size along Z
OutputImageType::RegionType region;
region.SetSize( size );
region.SetIndex( start );
// double spacing[3];
//spacing[0] = 1; //spacing along x
//spacing[1] = 1; //spacing along y
//spacing[2] = sampl_ratio; //spacing along z
im->SetRegions( region );
//im->SetSpacing(spacing);
im->Allocate();
im->FillBuffer(0);
im->Update();
//copy the input image into the ITK image
typedef itk::ImageRegionIteratorWithIndex< OutputImageType > IteratorType;
IteratorType iterator1(im,im->GetRequestedRegion());
for(int i=0; i<r*c*z; i++)
{
iterator1.Set((float)imgIn[i]);
++iterator1;
}
//apply gradient anisotropic diffusion
typedef itk::GradientAnisotropicDiffusionImageFilter< OutputImageType, OutputImageType > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( im );
filter->SetNumberOfIterations( iter );
filter->SetTimeStep( timeStep );
filter->SetConductanceParameter( comductance );
try
{
filter->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << err << std::endl;
return 0;
}
typedef itk::RescaleIntensityImageFilter< OutputImageType, InputImageType > RescaleFilterType;
RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
rescaler->SetOutputMinimum( 0 );
rescaler->SetOutputMaximum( 255 );
rescaler->SetInput( filter->GetOutput() );
rescaler->Update();
//overwrite the input image for now in order to save space
typedef itk::ImageRegionIteratorWithIndex< InputImageType > IteratorType2;
IteratorType2 iterator2(rescaler->GetOutput(),rescaler->GetOutput()->GetRequestedRegion());
for(int i=0; i<r*c*z; i++)
{
imgIn[i] = iterator2.Get();
++iterator2;
}
return 1;
}
void IntrinsicFeatureCalculator::GetDistanceToSurfaceMeasures(vtkSmartPointer<vtkTable> table, std::vector< ftk::Object::Point > surfacePoints)
{
typedef itk::Image< IPixelT, 3 > InputImageType;
typedef itk::Image< LPixelT, 3 > OutputImageType;
typedef itk::DanielssonDistanceMapImageFilter< OutputImageType, OutputImageType > DanielssonFilterType;
typedef itk::RescaleIntensityImageFilter< OutputImageType, OutputImageType > RescalerType;
typedef itk::ImageFileReader< InputImageType > ReaderType;
typedef itk::ImageFileWriter< InputImageType > InputWriterType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
typedef itk::LineIterator< OutputImageType > LineIteratorType;
vtkSmartPointer<vtkDoubleArray> column = vtkSmartPointer<vtkDoubleArray>::New();
column->SetName( "Dist_To_Surface" );
column->SetNumberOfValues( table->GetNumberOfRows() );
table->AddColumn(column);
OutputImageType::Pointer im;
im = OutputImageType::New();
OutputImageType::PointType origin;
origin[0] = 0;
origin[1] = 0;
origin[2] = 0;
im->SetOrigin( origin );
OutputImageType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
start[2] = 0; // first index on Z
OutputImageType::Pointer temp_image = labelImage->GetItkPtr< LPixelT >(0,0);
itk::Size<3> im_size = temp_image->GetBufferedRegion().GetSize();
im_size[2] = 1;
InputImageType::RegionType region;
region.SetSize( im_size );
region.SetIndex( start );
im->SetRegions( region );
im->Allocate();
im->FillBuffer(0);
im->Update();
//copy the input image into the ITK image
for(int p = 1; p < (int)surfacePoints.size(); ++p)
{
itk::Index<3> indx,indy;
indx[0] = surfacePoints[p-1].x;
indx[1] = surfacePoints[p-1].y;
indx[2] = 0;
indy[0] = surfacePoints[p].x;
indy[1] = surfacePoints[p].y;
indy[2] = 0;
LineIteratorType it( im, indx, indy );
//it.GoToBegin();
//while(!it.IsAtEnd())
for(it.GoToBegin(); !it.IsAtEnd(); ++it)
{
it.Set(255);
}
}
DanielssonFilterType::Pointer danielssonFilter = DanielssonFilterType::New();
WriterType::Pointer writer = WriterType::New();
danielssonFilter->SetInput( im );
writer->SetFileName( "DistanceMap.tif" );
danielssonFilter->InputIsBinaryOn();
danielssonFilter->Update();
OutputImageType::Pointer distMap = danielssonFilter->GetOutput();
writer->SetInput( distMap );
writer->Update();
for(int row=0; row<(int)table->GetNumberOfRows(); ++row)
{
OutputImageType::IndexType indx;
indx[0] = table->GetValue(row, 1).ToInt();
indx[1] = table->GetValue(row, 2).ToInt();
indx[2] = 0;
int dist = distMap->GetPixel(indx);
table->SetValueByName(row, "Dist_To_Surface", vtkVariant(dist));
}
}