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STYLE: Change vector to point when possible #841

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5 changes: 5 additions & 0 deletions documentation/docs/rtk_3_migration_guide.md
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Expand Up @@ -43,3 +43,8 @@ Most users intuitively expect this for the backprojector matched to `rtk::CudaFo
## CUDA forward / ray-cast step size default

The CUDA forward projector and the CUDA ray-cast backprojector now use the minimum voxel spacing of the input volume as the ray step when StepSize is not set. The previous default value was 1.

## Positions now use `itk::Point` instead of `itk::Vector`

APIs that represent physical *positions* were changed from `itk::Vector<double,3>` to `itk::Point<double,3>`. This makes a clear distinction between points (locations) and vectors (directions or offsets).
Projection iterators (`rtkProjectionsRegionConstIteratorRayBased*`), Joseph forward/back projectors, ray-box filters, convex/quadric shapes, Ora geometry readers, Forbild phantom readers, and test/phantom helpers now expect `PointType` for positions (source, pixel, box corners, shape centers).
2 changes: 1 addition & 1 deletion examples/FirstReconstruction/FirstCudaReconstruction.cxx
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Expand Up @@ -54,7 +54,7 @@ main(int argc, char ** argv)
REIType::Pointer rei = REIType::New();
rei->SetDensity(2.);
rei->SetAngle(0.);
rei->SetCenter(itk::MakeVector(0., 0., 10.));
rei->SetCenter(itk::MakePoint(0., 0., 10.));
rei->SetAxis(itk::MakeVector(50., 50., 50.));
rei->SetGeometry(geometry);
rei->SetInput(constantImageSource->GetOutput());
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2 changes: 1 addition & 1 deletion examples/FirstReconstruction/FirstReconstruction.cxx
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Expand Up @@ -53,7 +53,7 @@ main(int argc, char ** argv)
REIType::Pointer rei = REIType::New();
rei->SetDensity(2.);
rei->SetAngle(0.);
rei->SetCenter(itk::MakeVector(0., 0., 10.));
rei->SetCenter(itk::MakePoint(0., 0., 10.));
rei->SetAxis(itk::MakeVector(50., 50., 50.));
rei->SetGeometry(geometry);
rei->SetInput(constantImageSource->GetOutput());
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2 changes: 1 addition & 1 deletion include/rtkConvexShape.h
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Expand Up @@ -57,7 +57,7 @@ class RTK_EXPORT ConvexShape : public itk::DataObject
/** Convenient type alias. */
static constexpr unsigned int Dimension = 3;
using ScalarType = double;
using PointType = itk::Vector<ScalarType, Dimension>;
using PointType = itk::Point<ScalarType, Dimension>;
using VectorType = itk::Vector<ScalarType, Dimension>;
using RotationMatrixType = itk::Matrix<ScalarType, Dimension, Dimension>;

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12 changes: 6 additions & 6 deletions include/rtkDrawBoxImageFilter.h
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Expand Up @@ -77,10 +77,10 @@ class ITK_TEMPLATE_EXPORT DrawBoxImageFilter : public DrawConvexImageFilter<TInp
SetBoxFromImage(const ImageBaseType * img, bool bWithExternalHalfPixelBorder = true);

/** Get/Set the box parameters. See rtk::BoxShape. */
itkGetMacro(BoxMin, VectorType);
itkSetMacro(BoxMin, VectorType);
itkGetMacro(BoxMax, VectorType);
itkSetMacro(BoxMax, VectorType);
itkGetMacro(BoxMin, PointType);
itkSetMacro(BoxMin, PointType);
itkGetMacro(BoxMax, PointType);
itkSetMacro(BoxMax, PointType);
itkGetMacro(Direction, RotationMatrixType);
itkSetMacro(Direction, RotationMatrixType);

Expand All @@ -96,8 +96,8 @@ class ITK_TEMPLATE_EXPORT DrawBoxImageFilter : public DrawConvexImageFilter<TInp
std::vector<VectorType> m_PlaneDirections;
std::vector<ScalarType> m_PlanePositions;

VectorType m_BoxMin{ 0. };
VectorType m_BoxMax{ 0. };
PointType m_BoxMin{ 0. };
PointType m_BoxMax{ 0. };
RotationMatrixType m_Direction;
};

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24 changes: 10 additions & 14 deletions include/rtkFourDSARTConeBeamReconstructionFilter.hxx
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Expand Up @@ -236,20 +236,16 @@ FourDSARTConeBeamReconstructionFilter<VolumeSeriesType, ProjectionStackType>::Ge

// Create the m_RayBoxFiltersectionImageFilter
m_RayBoxFilter->SetGeometry(this->GetGeometry());
itk::Vector<double, 3> Corner1, Corner2;

Corner1[0] = this->GetInput(0)->GetOrigin()[0];
Corner1[1] = this->GetInput(0)->GetOrigin()[1];
Corner1[2] = this->GetInput(0)->GetOrigin()[2];
Corner2[0] = this->GetInput(0)->GetOrigin()[0] +
this->GetInput(0)->GetLargestPossibleRegion().GetSize()[0] * this->GetInput(0)->GetSpacing()[0];
Corner2[1] = this->GetInput(0)->GetOrigin()[1] +
this->GetInput(0)->GetLargestPossibleRegion().GetSize()[1] * this->GetInput(0)->GetSpacing()[1];
Corner2[2] = this->GetInput(0)->GetOrigin()[2] +
this->GetInput(0)->GetLargestPossibleRegion().GetSize()[2] * this->GetInput(0)->GetSpacing()[2];

m_RayBoxFilter->SetBoxMin(Corner1);
m_RayBoxFilter->SetBoxMax(Corner2);
itk::Point<double, 3> corner1, corner2;
for (unsigned int i = 0; i < 3; ++i)
{
corner1[i] = this->GetInput(0)->GetOrigin()[i];
corner2[i] = this->GetInput(0)->GetOrigin()[i] +
this->GetInput(0)->GetLargestPossibleRegion().GetSize()[i] * this->GetInput(0)->GetSpacing()[i];
}

m_RayBoxFilter->SetBoxMin(corner1);
m_RayBoxFilter->SetBoxMax(corner2);

m_RayBoxFilter->UpdateOutputInformation();
m_ExtractFilter->UpdateOutputInformation();
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22 changes: 10 additions & 12 deletions include/rtkIterativeFDKConeBeamReconstructionFilter.hxx
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Expand Up @@ -97,18 +97,16 @@ IterativeFDKConeBeamReconstructionFilter<TInputImage, TOutputImage, TFFTPrecisio
m_ConstantProjectionStackSource->SetConstant(0);

// Set box for the m_RayBoxFiltersectionImageFilter
itk::Vector<double, 3> Corner1, Corner2;
Corner1[0] = this->GetInput(0)->GetOrigin()[0];
Corner1[1] = this->GetInput(0)->GetOrigin()[1];
Corner1[2] = this->GetInput(0)->GetOrigin()[2];
Corner2[0] = this->GetInput(0)->GetOrigin()[0] +
this->GetInput(0)->GetLargestPossibleRegion().GetSize()[0] * this->GetInput(0)->GetSpacing()[0];
Corner2[1] = this->GetInput(0)->GetOrigin()[1] +
this->GetInput(0)->GetLargestPossibleRegion().GetSize()[1] * this->GetInput(0)->GetSpacing()[1];
Corner2[2] = this->GetInput(0)->GetOrigin()[2] +
this->GetInput(0)->GetLargestPossibleRegion().GetSize()[2] * this->GetInput(0)->GetSpacing()[2];
m_RayBoxFilter->SetBoxMin(Corner1);
m_RayBoxFilter->SetBoxMax(Corner2);
itk::Point<double, 3> corner1, corner2;
for (unsigned int i = 0; i < 3; ++i)
{
corner1[i] = this->GetInput(0)->GetOrigin()[i];
corner2[i] = this->GetInput(0)->GetOrigin()[i] +
this->GetInput(0)->GetLargestPossibleRegion().GetSize()[i] * this->GetInput(0)->GetSpacing()[i];
}

m_RayBoxFilter->SetBoxMin(corner1);
m_RayBoxFilter->SetBoxMax(corner2);

// Initial internal connections
m_DisplacedDetectorFilter->SetInput(this->GetInput(1));
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11 changes: 6 additions & 5 deletions include/rtkJosephBackProjectionImageFilter.hxx
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Expand Up @@ -109,8 +109,8 @@ JosephBackProjectionImageFilter<TInputImage,
itIn = InputRegionIterator::New(this->GetInput(1), buffReg, geometry, volPPToIndex);

// Create intersection functions, one for each possible main direction
auto box = BoxShape::New();
typename BoxShape::VectorType boxMin, boxMax;
auto box = BoxShape::New();
typename BoxShape::PointType boxMin, boxMax;
for (unsigned int i = 0; i < Dimension; i++)
{
boxMin[i] = this->GetOutput()->GetRequestedRegion().GetIndex()[i];
Expand All @@ -127,11 +127,12 @@ JosephBackProjectionImageFilter<TInputImage,
double superiorClip = 1. - m_InferiorClip;

// Go over each pixel of the projection
typename BoxShape::VectorType stepMM, np, fp;
typename BoxShape::VectorType stepMM;
typename BoxShape::PointType np, fp;
for (unsigned int pix = 0; pix < buffReg.GetNumberOfPixels(); pix++, itIn->Next())
{
typename InputRegionIterator::PointType pixelPosition = itIn->GetPixelPosition();
typename InputRegionIterator::PointType dirVox = -itIn->GetSourceToPixel();
typename InputRegionIterator::PointType pixelPosition = itIn->GetPixelPosition();
typename InputRegionIterator::VectorType dirVox = -itIn->GetSourceToPixel();

// Select main direction
unsigned int mainDir = 0;
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7 changes: 4 additions & 3 deletions include/rtkJosephForwardAttenuatedProjectionImageFilter.h
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Expand Up @@ -189,6 +189,7 @@ class ITK_TEMPLATE_EXPORT ProjectedValueAccumulationAttenuated
{
public:
using VectorType = itk::Vector<double, 3>;
using PointType = itk::Point<double, 3>;

ProjectedValueAccumulationAttenuated() = default;
~ProjectedValueAccumulationAttenuated() = default;
Expand All @@ -210,10 +211,10 @@ class ITK_TEMPLATE_EXPORT ProjectedValueAccumulationAttenuated
TOutput & output,
const TOutput & rayCastValue,
const VectorType & /*stepInMM*/,
const VectorType & itkNotUsed(source),
const PointType & itkNotUsed(source),
const VectorType & itkNotUsed(sourceToPixel),
const VectorType & itkNotUsed(nearestPoint),
const VectorType & itkNotUsed(farthestPoint))
const PointType & itkNotUsed(nearestPoint),
const PointType & itkNotUsed(farthestPoint))
{
output = input + rayCastValue;
m_Attenuation[threadId] = 0;
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7 changes: 4 additions & 3 deletions include/rtkJosephForwardProjectionImageFilter.h
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Expand Up @@ -115,6 +115,7 @@ class ITK_TEMPLATE_EXPORT ProjectedValueAccumulation
{
public:
using VectorType = itk::Vector<double, 3>;
using PointType = itk::Point<double, 3>;

ProjectedValueAccumulation() = default;
~ProjectedValueAccumulation() = default;
Expand All @@ -135,10 +136,10 @@ class ITK_TEMPLATE_EXPORT ProjectedValueAccumulation
TOutput & output,
const TOutput & rayCastValue,
const VectorType & stepInMM,
const VectorType & itkNotUsed(source),
const PointType & itkNotUsed(source),
const VectorType & itkNotUsed(sourceToPixel),
const VectorType & itkNotUsed(nearestPoint),
const VectorType & itkNotUsed(farthestPoint)) const
const PointType & itkNotUsed(nearestPoint),
const PointType & itkNotUsed(farthestPoint)) const
{
output = input + rayCastValue * stepInMM.GetNorm();
}
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14 changes: 8 additions & 6 deletions include/rtkJosephForwardProjectionImageFilter.hxx
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Expand Up @@ -221,8 +221,8 @@ JosephForwardProjectionImageFilter<TInputImage,
}

// Create intersection functions, one for each possible main direction
auto box = BoxShape::New();
typename BoxShape::VectorType boxMin, boxMax;
auto box = BoxShape::New();
typename BoxShape::PointType boxMin, boxMax;
for (unsigned int i = 0; i < Dimension; i++)
{
boxMin[i] = this->GetInput(1)->GetBufferedRegion().GetIndex()[i];
Expand All @@ -239,11 +239,13 @@ JosephForwardProjectionImageFilter<TInputImage,
double superiorClip = 1. - m_InferiorClip;

// Go over each pixel of the projection
typename BoxShape::VectorType stepMM, np, fp;
typename BoxShape::VectorType stepMM;
typename InputRegionIterator::PointType np, fp;
for (unsigned int pix = 0; pix < outputRegionForThread.GetNumberOfPixels(); pix++, itIn->Next(), ++itOut)
{
typename InputRegionIterator::PointType pixelPosition = itIn->GetPixelPosition();
typename InputRegionIterator::PointType dirVox = -itIn->GetSourceToPixel();
stepMM.Fill(0.);
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@axel-grc axel-grc Dec 19, 2025

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This seems to fix the failing test that occurred because of pixelPosition that was corrected to stepMM line 422

typename InputRegionIterator::PointType pixelPosition = itIn->GetPixelPosition();
typename InputRegionIterator::VectorType dirVox = -itIn->GetSourceToPixel();

// Select main direction
unsigned int mainDir = 0;
Expand Down Expand Up @@ -417,7 +419,7 @@ JosephForwardProjectionImageFilter<TInputImage,
}
else
m_ProjectedValueAccumulation(
threadId, itIn->Get(), itOut.Value(), {}, pixelPosition, pixelPosition, dirVox, pixelPosition, pixelPosition);
threadId, itIn->Get(), itOut.Value(), {}, stepMM, pixelPosition, dirVox, pixelPosition, pixelPosition);
}
delete itIn;
}
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18 changes: 10 additions & 8 deletions include/rtkMaskCollimationImageFilter.hxx
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Expand Up @@ -73,26 +73,28 @@ MaskCollimationImageFilter<TInputImage, TOutputImage>::DynamicThreadedGenerateDa
for (unsigned int pix = 0; pix < npixperslice; pix++, itIn->Next(), ++itOut)
{
using PointType = typename InputRegionIterator::PointType;
PointType source = itIn->GetSourcePosition();
double sourceNorm = source.GetNorm();
PointType pixel = itIn->GetPixelPosition();
using VectorType = typename InputRegionIterator::VectorType;

PointType pixelToSource(source - pixel);
PointType sourceDir = source / sourceNorm;
VectorType source = itIn->GetSourcePosition().GetVectorFromOrigin();
double sourceNorm = source.GetNorm();
VectorType pixel = itIn->GetPixelPosition().GetVectorFromOrigin();

VectorType pixelToSource(source - pixel);
VectorType sourceDir = source / sourceNorm;

// Get the 3D position of the ray and the main plane
// (at 0,0,0 and orthogonal to source to center)
const double mag = sourceNorm / (pixelToSource * sourceDir);
PointType intersection = source - mag * pixelToSource;
VectorType intersection = source - mag * pixelToSource;

// The first coordinate on the plane is measured along the detector
// orthogonal to the plane defined by the detector source direction
// and the secon detector vector
PointType v;
VectorType v;
v[0] = this->GetGeometry()->GetRotationMatrix(iProj)[m_RotationAxisIndex][0];
v[1] = this->GetGeometry()->GetRotationMatrix(iProj)[m_RotationAxisIndex][1];
v[2] = this->GetGeometry()->GetRotationMatrix(iProj)[m_RotationAxisIndex][2];
PointType u = CrossProduct(v, sourceDir);
VectorType u = CrossProduct(v, sourceDir);
u /= u.GetNorm();
double ucoord = u * intersection;

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7 changes: 4 additions & 3 deletions include/rtkMaximumIntensityProjectionImageFilter.h
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Expand Up @@ -78,6 +78,7 @@ class ITK_TEMPLATE_EXPORT MaximumIntensityProjectedValueAccumulation
{
public:
using VectorType = itk::Vector<double, 3>;
using PointType = itk::Point<double, 3>;

bool
operator!=(const MaximumIntensityProjectedValueAccumulation &) const
Expand All @@ -96,10 +97,10 @@ class ITK_TEMPLATE_EXPORT MaximumIntensityProjectedValueAccumulation
TOutput & output,
const TOutput & rayCastValue,
const VectorType & stepInMM,
const VectorType & itkNotUsed(source),
const PointType & itkNotUsed(source),
const VectorType & itkNotUsed(sourceToPixel),
const VectorType & itkNotUsed(nearestPoint),
const VectorType & itkNotUsed(farthestPoint)) const
const PointType & itkNotUsed(nearestPoint),
const PointType & itkNotUsed(farthestPoint)) const
{
TOutput tmp = static_cast<TOutput>(input);
if (tmp < rayCastValue)
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9 changes: 5 additions & 4 deletions include/rtkProjectionsRegionConstIteratorRayBased.h
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Expand Up @@ -65,7 +65,8 @@ class ITK_TEMPLATE_EXPORT ProjectionsRegionConstIteratorRayBased : public itk::I
/** Types inherited from the Superclass */
using OffsetValueType = typename Superclass::OffsetValueType;
using RegionType = typename Superclass::RegionType;
using PointType = typename itk::Vector<double, 3>;
using VectorType = typename itk::Vector<double, 3>;
using PointType = typename itk::Point<double, 3>;
using IndexValueType = typename Superclass::IndexValueType;

using MatrixType = itk::Matrix<double, 3, 4>;
Expand Down Expand Up @@ -130,15 +131,15 @@ class ITK_TEMPLATE_EXPORT ProjectionsRegionConstIteratorRayBased : public itk::I
{
return this->m_PixelPosition;
}
const PointType &
const VectorType &
GetSourceToPixel()
{
return this->m_SourceToPixel;
}

/** Computes and returns a unit vector pointing from the source to the
* current pixel, i.e., GetSourceToPixel()/||GetSourceToPixel()||. */
const PointType
const VectorType
GetDirection()
{
return m_SourceToPixel / m_SourceToPixel.GetNorm();
Expand All @@ -158,7 +159,7 @@ class ITK_TEMPLATE_EXPORT ProjectionsRegionConstIteratorRayBased : public itk::I
MatrixType m_PostMultiplyMatrix;
PointType m_SourcePosition;
PointType m_PixelPosition;
PointType m_SourceToPixel;
VectorType m_SourceToPixel;
};
} // namespace rtk

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3 changes: 2 additions & 1 deletion include/rtkProjectionsRegionConstIteratorRayBasedWithCylindricalPanel.h
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Expand Up @@ -50,7 +50,8 @@ class ITK_TEMPLATE_EXPORT ProjectionsRegionConstIteratorRayBasedWithCylindricalP
using MatrixType = typename Superclass::MatrixType;
using IndexValueType = typename Superclass::IndexValueType;

using PointType = typename itk::Vector<double, 3>;
using PointType = typename itk::Point<double, 3>;
using VectorType = typename itk::Vector<double, 3>;
using HomogeneousMatrixType = itk::Matrix<double, 4, 4>;

/** Constructor establishes an iterator to walk a particular image and a
Expand Down
4 changes: 3 additions & 1 deletion include/rtkProjectionsRegionConstIteratorRayBasedWithCylindricalPanel.hxx
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Expand Up @@ -49,7 +49,9 @@ ProjectionsRegionConstIteratorRayBasedWithCylindricalPanel<TImage>::NewProjectio
// Set source position in volume indices
// GetSourcePosition() returns coordinates in mm. Multiplying by
// volPPToIndex gives the corresponding volume index
this->m_SourcePosition = this->m_PostMultiplyMatrix * this->m_Geometry->GetSourcePosition(iProj);
VectorType sourcePos = this->m_PostMultiplyMatrix * this->m_Geometry->GetSourcePosition(iProj);
for (unsigned int i = 0; i < this->GetImageDimension(); ++i)
this->m_SourcePosition[i] = sourcePos[i];

// Compute matrix to transform projection index to position on a flat panel
// if the panel were flat, before accounting for the curvature
Expand Down
3 changes: 2 additions & 1 deletion include/rtkProjectionsRegionConstIteratorRayBasedWithFlatPanel.h
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Expand Up @@ -47,7 +47,8 @@ class ITK_TEMPLATE_EXPORT ProjectionsRegionConstIteratorRayBasedWithFlatPanel
/** Types inherited from the Superclass */
using OffsetValueType = typename Superclass::OffsetValueType;
using RegionType = typename Superclass::RegionType;
using PointType = typename itk::Vector<double, 3>;
using PointType = typename itk::Point<double, 3>;
using VectorType = typename itk::Vector<double, 3>;
using MatrixType = typename Superclass::MatrixType;
using HomogeneousMatrixType = itk::Matrix<double, 4, 4>;

Expand Down
4 changes: 3 additions & 1 deletion include/rtkProjectionsRegionConstIteratorRayBasedWithFlatPanel.hxx
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Expand Up @@ -42,7 +42,9 @@ ProjectionsRegionConstIteratorRayBasedWithFlatPanel<TImage>::NewProjection()
// Set source position in volume indices
// GetSourcePosition() returns coordinates in mm. Multiplying by
// volPPToIndex gives the corresponding volume index
this->m_SourcePosition = this->m_PostMultiplyMatrix * this->m_Geometry->GetSourcePosition(this->m_PositionIndex[2]);
VectorType transformed = this->m_PostMultiplyMatrix * this->m_Geometry->GetSourcePosition(this->m_PositionIndex[2]);
for (unsigned int i = 0; i < this->GetImageDimension(); ++i)
this->m_SourcePosition[i] = transformed[i];

// Compute matrix to transform projection index to volume index
// IndexToPhysicalPointMatrix maps the 2D index of a projection's pixel to its 2D position on the detector (in mm)
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10 changes: 6 additions & 4 deletions src/rtkBoxShape.cxx
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Expand Up @@ -145,17 +145,19 @@ BoxShape ::SetBoxFromImage(const ImageBaseType * img, bool bWithExternalHalfPixe
itkGenericExceptionMacro(<< "BoxShape and image dimensions must agree");

// BoxShape corner 1
m_BoxMin = img->GetOrigin().GetVectorFromOrigin();
m_BoxMin = img->GetOrigin();
if (bWithExternalHalfPixelBorder)
m_BoxMin -= img->GetDirection() * img->GetSpacing() * 0.5;

// BoxShape corner 2
VectorType max;
for (unsigned int i = 0; i < Dimension; i++)
if (bWithExternalHalfPixelBorder)
m_BoxMax[i] = img->GetSpacing()[i] * img->GetLargestPossibleRegion().GetSize()[i];
max[i] = img->GetSpacing()[i] * img->GetLargestPossibleRegion().GetSize()[i];
else
m_BoxMax[i] = img->GetSpacing()[i] * (img->GetLargestPossibleRegion().GetSize()[i] - 1);
m_BoxMax = m_BoxMin + img->GetDirection() * m_BoxMax;
max[i] = img->GetSpacing()[i] * (img->GetLargestPossibleRegion().GetSize()[i] - 1);
max = img->GetDirection() * max;
m_BoxMax = m_BoxMin + max;

SetDirection(img->GetDirection());
}
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