Skip to content

ENH: Replace SmallHoleFiller with pct::HoleFillingImageFilter #60

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
axel-grc wants to merge 3 commits into
base: main
Choose a base branch
from
Open

ENH: Replace SmallHoleFiller with pct::HoleFillingImageFilter #60

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
60dcdb0
STYLE: Rename SmallHoleFiller to pctHoleFillingImageFilter
axel-grc Oct 23, 2025
fc45319
ENH: Adapt pctHoleFillingImageFilter to inherits from itkImageToImage…
axel-grc Oct 23, 2025
fda0792
ENH: Add test for pct::HoleFillingImageFilter
axel-grc Oct 22, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 5 additions & 6 deletions applications/pctbackprojectionbinning/pctbackprojectionbinning.cxx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
#include <rtkThreeDCircularProjectionGeometryXMLFile.h>

#include "pctProtonPairsToBackProjection.h"
#include "SmallHoleFiller.h"
#include "pctHoleFillingImageFilter.h"

#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
Expand Down Expand Up @@ -124,17 +124,16 @@ main(int argc, char * argv[])

TRY_AND_EXIT_ON_ITK_EXCEPTION(projection->Update());

SmallHoleFiller<OutputImageType> filler;
auto holeFilter = pct::HoleFillingImageFilter<OutputImageType>::New();
if (args_info.fill_flag)
{
filler.SetImage(projection->GetOutput());
filler.SetHolePixel(0.);
filler.Fill();
holeFilter->SetInput(projection->GetOutput());
TRY_AND_EXIT_ON_ITK_EXCEPTION(holeFilter->Update());
}

auto cii = itk::ChangeInformationImageFilter<OutputImageType>::New();
if (args_info.fill_flag)
cii->SetInput(filler.GetOutput());
cii->SetInput(holeFilter->GetOutput());
else
cii->SetInput(projection->GetOutput());
cii->ChangeOriginOn();
Expand Down
11 changes: 5 additions & 6 deletions applications/pctbinning/pctbinning.cxx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
#include <rtkConstantImageSource.h>

#include "pctProtonPairsToDistanceDrivenProjection.h"
#include "SmallHoleFiller.h"
#include "pctHoleFillingImageFilter.h"

#include <itkImageFileWriter.h>
#include <itkRegularExpressionSeriesFileNames.h>
Expand Down Expand Up @@ -87,17 +87,16 @@ main(int argc, char * argv[])

TRY_AND_EXIT_ON_ITK_EXCEPTION(projection->Update());

SmallHoleFiller<OutputImageType> filler;
auto holeFilter = pct::HoleFillingImageFilter<OutputImageType>::New();
if (args_info.fill_flag)
{
filler.SetImage(projection->GetOutput());
filler.SetHolePixel(0.);
filler.Fill();
holeFilter->SetInput(projection->GetOutput());
TRY_AND_EXIT_ON_ITK_EXCEPTION(holeFilter->Update());
}

auto cii = itk::ChangeInformationImageFilter<OutputImageType>::New();
if (args_info.fill_flag)
cii->SetInput(filler.GetOutput());
cii->SetInput(holeFilter->GetOutput());
else
cii->SetInput(projection->GetOutput());
cii->ChangeOriginOn();
Expand Down
54 changes: 0 additions & 54 deletions include/SmallHoleFiller.h
View file
Open in desktop

This file was deleted.

172 changes: 0 additions & 172 deletions include/SmallHoleFiller.hxx
View file
Open in desktop

This file was deleted.

63 changes: 63 additions & 0 deletions include/pctHoleFillingImageFilter.h
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
#ifndef __pctHoleFillingImageFilter_h
#define __pctHoleFillingImageFilter_h

#include <itkImageToImageFilter.h>
#include <itkSmartPointer.h>
#include <itkNumericTraits.h>

namespace pct
{
/**
*
* A simple iterative hole filling filter. A pixel equal to the HolePixel is
* considered a hole. On each iteration, every hole pixel is replaced by the
* average of its non-hole neighbors in a radius=1 neighborhood (center
* excluded). Iterations repeat until no hole pixels remain or MaxIterations
* is reached or an iteration makes no progress.
*
* This filter reproduces the behavior of the project's SmallHoleFiller
* helper. For the original reference see:
* https://www.insight-journal.org/browse/publication/835/
*/

template <typename TInputImage, typename TOutputImage = TInputImage>
class HoleFillingImageFilter : public itk::ImageToImageFilter<TInputImage, TOutputImage>
{
public:
using Self = HoleFillingImageFilter;
using Superclass = itk::ImageToImageFilter<TInputImage, TOutputImage>;
using Pointer = itk::SmartPointer<Self>;
using ConstPointer = itk::SmartPointer<const Self>;

itkNewMacro(Self);
itkTypeMacro(HoleFillingImageFilter, ImageToImageFilter);

using InputImageType = TInputImage;
using OutputImageType = TOutputImage;
using PixelType = typename OutputImageType::PixelType;

itkSetMacro(HolePixelValue, PixelType);
itkGetConstMacro(HolePixelValue, PixelType);
itkSetMacro(MaximumNumberOfIterations, unsigned int);
itkGetConstMacro(MaximumNumberOfIterations, unsigned int);

protected:
HoleFillingImageFilter() = default;
~HoleFillingImageFilter() override = default;

void
GenerateData() override;

private:
ITK_DISALLOW_COPY_AND_MOVE(HoleFillingImageFilter);
PixelType m_HolePixelValue = itk::NumericTraits<PixelType>::Zero;
unsigned int m_MaximumNumberOfIterations = 20;
};

} // namespace pct

#ifndef ITK_MANUAL_INSTANTIATION
# include "pctHoleFillingImageFilter.hxx"
#endif

#endif
Loading
Loading