Commit d47f7aaa authored by Robert Maynard's avatar Robert Maynard

Add an ImageMedian filter

parent c68919fc
......@@ -42,6 +42,7 @@ set(headers
Gradient.h
Histogram.h
ImageConnectivity.h
ImageMedian.h
Lagrangian.h
LagrangianStructures.h
Mask.h
......@@ -107,6 +108,7 @@ set(header_template_sources
Gradient.hxx
Histogram.hxx
ImageConnectivity.hxx
ImageMedian.hxx
Lagrangian.hxx
LagrangianStructures.hxx
Mask.hxx
......
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#ifndef vtk_m_filter_ImageMedian_h
#define vtk_m_filter_ImageMedian_h
#include <vtkm/filter/FilterCell.h>
/// \brief Median algorithm for general image blur
///
/// The ImageMedian filter finds the median value for each pixel in an image.
/// Currently the algorithm has the following restrictions.
/// - Only supports a neighborhood of 5x5x1 or 3x3x1
///
/// This means that volumes are basically treated as an image stack
/// along the z axis
///
/// Default output field name is 'median'
namespace vtkm
{
namespace filter
{
class ImageMedian : public vtkm::filter::FilterField<ImageMedian>
{
int Neighborhood = 1;
public:
using SupportedTypes = vtkm::TypeListTagScalarAll;
VTKM_CONT ImageMedian();
VTKM_CONT void Perform3x3() { this->Neighborhood = 1; };
VTKM_CONT void Perform5x5() { this->Neighborhood = 2; };
template <typename T, typename StorageType, typename DerivedPolicy>
VTKM_CONT vtkm::cont::DataSet DoExecute(const vtkm::cont::DataSet& input,
const vtkm::cont::ArrayHandle<T, StorageType>& field,
const vtkm::filter::FieldMetadata& fieldMetadata,
const vtkm::filter::PolicyBase<DerivedPolicy>&);
};
}
} // namespace vtkm::filter
#include <vtkm/filter/ImageMedian.hxx>
#endif //vtk_m_filter_ImageMedian_h
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#ifndef vtk_m_filter_ImageMedian_hxx
#define vtk_m_filter_ImageMedian_hxx
#include <vtkm/Swap.h>
namespace vtkm
{
namespace worklet
{
// An implementation of the quickselect/Hoare's selection algorithm to find medians
// inplace, generally fairly fast for reasonable sized data.
//
template <typename T>
VTKM_EXEC inline T find_median(T* values, std::size_t mid, std::size_t size)
{
std::size_t begin = 0;
std::size_t end = size - 1;
while (begin < end)
{
T x = values[mid];
std::size_t i = begin;
std::size_t j = end;
do
{
for (; values[i] < x; i++)
{
}
for (; x < values[j]; j--)
{
}
if (i <= j)
{
vtkm::Swap(values[i], values[j]);
i++;
j--;
}
} while (i <= j);
begin = (j < mid) ? i : begin;
end = (mid < i) ? j : end;
}
return values[mid];
}
struct ImageMedian : public vtkm::worklet::WorkletPointNeighborhood
{
int Neighborhood;
ImageMedian(int neighborhoodSize)
: Neighborhood(neighborhoodSize)
{
}
using ControlSignature = void(CellSetIn, FieldInNeighborhood, FieldOut);
using ExecutionSignature = void(_2, _3);
template <typename InNeighborhoodT, typename T>
VTKM_EXEC void operator()(const InNeighborhoodT& input, T& out) const
{
vtkm::Vec<T, 25> values;
int index = 0;
for (int x = -this->Neighborhood; x <= this->Neighborhood; ++x)
{
for (int y = -this->Neighborhood; y <= this->Neighborhood; ++y)
{
values[index++] = input.Get(x, y, 0);
}
}
std::size_t len =
static_cast<std::size_t>((this->Neighborhood * 2 + 1) * (this->Neighborhood * 2 + 1));
std::size_t mid = len / 2;
out = find_median(&values[0], mid, len);
}
};
}
namespace filter
{
VTKM_CONT ImageMedian::ImageMedian()
{
this->SetOutputFieldName("median");
}
template <typename T, typename StorageType, typename DerivedPolicy>
inline VTKM_CONT vtkm::cont::DataSet ImageMedian::DoExecute(
const vtkm::cont::DataSet& input,
const vtkm::cont::ArrayHandle<T, StorageType>& field,
const vtkm::filter::FieldMetadata& fieldMetadata,
const vtkm::filter::PolicyBase<DerivedPolicy>& policy)
{
if (!fieldMetadata.IsPointField())
{
throw vtkm::cont::ErrorBadValue("Active field for ImageMedian must be a point field.");
}
const vtkm::cont::DynamicCellSet& cells = input.GetCellSet();
vtkm::cont::ArrayHandle<T> result;
if (this->Neighborhood == 1 || this->Neighborhood == 2)
{
this->Invoke(worklet::ImageMedian{ this->Neighborhood },
vtkm::filter::ApplyPolicyCellSetStructured(cells, policy),
field,
result);
}
else
{
throw vtkm::cont::ErrorBadValue("ImageMedian only support a 3x3 or 5x5 stencil.");
}
std::string name = this->GetOutputFieldName();
if (name.empty())
{
name = fieldMetadata.GetName();
}
return CreateResult(input, fieldMetadata.AsField(name, result));
}
}
}
#endif
......@@ -34,6 +34,7 @@ set(unit_tests
UnitTestGhostCellRemove.cxx
UnitTestHistogramFilter.cxx
UnitTestImageConnectivityFilter.cxx
UnitTestImageMedianFilter.cxx
UnitTestLagrangianFilter.cxx
UnitTestLagrangianStructuresFilter.cxx
UnitTestMaskFilter.cxx
......
//============================================================================
// Copyright (c) Kitware, Inc.
// All rights reserved.
// See LICENSE.txt for details.
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notice for more information.
//============================================================================
#include <vtkm/cont/testing/MakeTestDataSet.h>
#include <vtkm/cont/testing/Testing.h>
#include <vtkm/filter/ImageMedian.h>
namespace
{
void TestImageMedian()
{
std::cout << "Testing Image Median Filter on 3D structured data" << std::endl;
vtkm::cont::testing::MakeTestDataSet testDataSet;
vtkm::cont::DataSet dataSet = testDataSet.Make3DUniformDataSet2();
vtkm::filter::ImageMedian median;
median.Perform3x3();
median.SetActiveField("pointvar");
auto result = median.Execute(dataSet);
VTKM_TEST_ASSERT(result.HasPointField("median"), "Field missing.");
vtkm::cont::ArrayHandle<vtkm::Float32> resultArrayHandle;
result.GetPointField("median").GetData().CopyTo(resultArrayHandle);
auto cells = result.GetCellSet().Cast<vtkm::cont::CellSetStructured<3>>();
auto pdims = cells.GetPointDimensions();
//verified by hand
{
auto portal = resultArrayHandle.GetPortalConstControl();
std::cout << "spot to verify x = 1, y = 1, z = 0 is: ";
vtkm::Float32 temp = portal.Get(1 + pdims[0]);
std::cout << temp << std::endl << std::endl;
VTKM_TEST_ASSERT(test_equal(temp, 2), "incorrect median value");
std::cout << "spot to verify x = 1, y = 1, z = 2 is: ";
temp = portal.Get(1 + pdims[0] + (pdims[1] * pdims[0] * 2));
std::cout << temp << std::endl << std::endl;
VTKM_TEST_ASSERT(test_equal(temp, 2.82843), "incorrect median value");
}
}
}
int UnitTestImageMedianFilter(int argc, char* argv[])
{
return vtkm::cont::testing::Testing::Run(TestImageMedian, argc, argv);
}
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