Merge branch 'feature/cpu-projectors' into 'master' (cb03ef44) · Commits · IP / elsa · GitLab

elsa/core/DataContainer.h

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		@@ -6,6 +6,7 @@
		#include "DataHandler.h"

		#include <memory>
		#include <type_traits>

		namespace elsa
		{
		@@ -107,6 +108,21 @@ namespace elsa
		/// return an element by n-dimensional coordinate as read-only (not bounds-checked!)
		const data_t& operator()(IndexVector_t coordinate) const;

		template <typename idx0_t, typename... idx_t,
		typename = std::enable_if_t<std::is_integral_v<idx0_t> && (... && std::is_integral_v<idx_t>)>>
		data_t& operator()(idx0_t idx0, idx_t... indices) {
		IndexVector_t coordinate(sizeof...(indices)+1);
		((coordinate<<idx0) , ... , indices);
		return operator()(coordinate);
		}

		template <typename idx0_t, typename... idx_t,
		typename = std::enable_if_t<std::is_integral_v<idx0_t> && (... && std::is_integral_v<idx_t>)>>
		const data_t& operator()(idx0_t idx0, idx_t... indices) const{
		IndexVector_t coordinate(sizeof...(indices)+1);
		((coordinate<<idx0) , ... , indices);
		return operator()(coordinate);
		}

		/// return the dot product of this signal with the one from container other
		data_t dot(const DataContainer<data_t>& other) const;

elsa/core/tests/test_DataContainer.cpp

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		@@ -140,14 +140,17 @@ SCENARIO("Element-wise access of DataContainers") {
		THEN("it works as expected when using indices/coordinates") {
		REQUIRE(dc[index] == 0.0_a);
		REQUIRE(dc(coord) == 0.0_a);
		REQUIRE(dc(17, 4) == 0.0_a);

		dc[index] = 2.2;
		REQUIRE(dc[index] == 2.2_a);
		REQUIRE(dc(coord) == 2.2_a);
		REQUIRE(dc(17, 4) == 2.2_a);

		dc(coord) = 3.3;
		REQUIRE(dc[index] == 3.3_a);
		REQUIRE(dc(coord) == 3.3_a);
		REQUIRE(dc(17, 4) == 3.3_a);
		}
		}
		}

elsa/projectors/CMakeLists.txt

+8 −2

Original line number	Diff line number	Diff line
		@@ -12,7 +12,10 @@ set(MODULE_HEADERS
		BoundingBox.h
		Intersection.h
		TraverseAABB.h
		BinaryMethod.h)
		TraverseAABBJosephsMethod.h
		BinaryMethod.h
		SiddonsMethod.h
		JosephsMethod.h)

		# list all the code files of the module
		set(MODULE_SOURCES
		@@ -20,7 +23,10 @@ set(MODULE_SOURCES
		BoundingBox.cpp
		Intersection.cpp
		TraverseAABB.cpp
		BinaryMethod.cpp)
		TraverseAABBJosephsMethod.cpp
		BinaryMethod.cpp
		SiddonsMethod.cpp
		JosephsMethod.cpp)


		# build the module library

elsa/projectors/JosephsMethod.cpp

0 → 100644

+202 −0

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		#include "JosephsMethod.h"
		#include "Timer.h"
		#include "TraverseAABBJosephsMethod.h"

		#include <stdexcept>

		namespace elsa
		{
		template <typename data_t>
		JosephsMethod<data_t>::JosephsMethod(const DataDescriptor& domainDescriptor, const DataDescriptor& rangeDescriptor,
		const std::vector<Geometry>& geometryList, Interpolation interpolation)
		: LinearOperator<data_t>(domainDescriptor, rangeDescriptor), _geometryList{geometryList},
		_boundingBox{domainDescriptor.getNumberOfCoefficientsPerDimension()}, _interpolation{interpolation}
		{
		auto dim = _domainDescriptor->getNumberOfDimensions();
		if (dim!=2 && dim != 3) {
		throw std::invalid_argument("JosephsMethod:only supporting 2d/3d operations");
		}

		if (dim != _rangeDescriptor->getNumberOfDimensions()) {
		throw std::invalid_argument("JosephsMethod: domain and range dimension need to match");
		}

		if (_geometryList.empty()) {
		throw std::invalid_argument("JosephsMethod: geometry list was empty");
		}
		}

		template <typename data_t>
		void JosephsMethod<data_t>::_apply(const DataContainer<data_t>& x, DataContainer<data_t>& Ax)
		{
		Timer<> timeguard("JosephsMethod", "apply");
		traverseVolume<false>(x, Ax);
		}

		template <typename data_t>
		void JosephsMethod<data_t>::_applyAdjoint(const DataContainer<data_t>& y, DataContainer<data_t>& Aty)
		{
		Timer<> timeguard("JosephsMethod", "applyAdjoint");
		traverseVolume<true>(y, Aty);
		}

		template <typename data_t>
		JosephsMethod<data_t>* JosephsMethod<data_t>::cloneImpl() const{
		return new JosephsMethod(_domainDescriptor, _rangeDescriptor, _geometryList);
		}

		template <typename data_t>
		bool JosephsMethod<data_t>::isEqual(const LinearOperator<data_t>& other) const
		{
		if (!LinearOperator<data_t>::isEqual(other))
		return false;

		auto otherJM = dynamic_cast<const JosephsMethod*>(&other);
		if (!otherJM)
		return false;

		if (_geometryList != otherJM->_geometryList \|\| _interpolation != otherJM->_interpolation)
		return false;

		return true;
		}

		template <typename data_t>
		template <bool adjoint>
		void JosephsMethod<data_t>::traverseVolume(const DataContainer<data_t>& vector, DataContainer<data_t>& result) const
		{
		if(adjoint) result = 0;

		const index_t sizeOfRange = _rangeDescriptor->getNumberOfCoefficients();
		const auto rangeDim = _rangeDescriptor->getNumberOfDimensions();

		// iterate over all rays
		#pragma omp parallel for
		for (index_t ir = 0; ir < sizeOfRange; ir++) {
		Ray ray = computeRayToDetector(ir,rangeDim);

		// --> setup traversal algorithm
		TraverseAABBJosephsMethod traverse(_boundingBox, ray);

		if(!adjoint) result[ir] = 0;

		// Make steps through the volume
		while (traverse.isInBoundingBox()) {

		IndexVector_t currentVoxel = traverse.getCurrentVoxel();
		float intersection = traverse.getIntersectionLength();

		// to avoid code duplicates for apply and applyAdjoint
		index_t from;
		index_t to;
		if (adjoint) {
		to = _domainDescriptor->getIndexFromCoordinate(currentVoxel);
		from = ir;
		} else {
		to = ir;
		from = _domainDescriptor->getIndexFromCoordinate(currentVoxel);
		}

		switch (_interpolation) {
		case Interpolation::LINEAR:
		LINEAR(vector, result, traverse.getFractionals(), adjoint, rangeDim,
		currentVoxel, intersection, from, to, traverse.getIgnoreDirection());
		break;
		case Interpolation::NN:
		if (adjoint) {
		#pragma omp atomic
		result[to] += intersection * vector[from];
		}
		else {
		result[to] += intersection * vector[from];
		}
		break;
		}

		// update Traverse
		traverse.updateTraverse();
		}
		}
		}

		template <typename data_t>
		typename JosephsMethod<data_t>::Ray JosephsMethod<data_t>::computeRayToDetector(index_t detectorIndex, index_t dimension) const
		{
		auto detectorCoord = _rangeDescriptor->getCoordinateFromIndex(detectorIndex);

		//center of detector pixel is 0.5 units away from the corresponding detector coordinates
		auto geometry = _geometryList.at(detectorCoord(dimension - 1));
		auto [ro, rd] = geometry.computeRayTo(detectorCoord.block(0, 0, dimension-1, 1).template cast<real_t>().array() + 0.5);

		return Ray(ro, rd);
		}

		template <typename data_t>
		void JosephsMethod<data_t>::LINEAR(const DataContainer<data_t>& vector, DataContainer<data_t>& result,
		const RealVector_t& fractionals, bool adjoint, int domainDim,
		const IndexVector_t& currentVoxel, float intersection, index_t from, index_t to,
		int mainDirection) const
		{
		float weight = intersection;
		IndexVector_t interpol = currentVoxel;

		//handle diagonal if 3D
		if(domainDim==3) {
		for (int i=0;i<domainDim;i++) {
		if(i != mainDirection) {
		weight *= fabs(fractionals(i));
		interpol(i) += (fractionals(i) < 0.0) ? -1 : 1;
		// mirror values at border if outside the volume
		if(interpol(i)<_boundingBox._min(i) \|\| interpol(i)>_boundingBox._max(i))
		interpol(i) = _boundingBox._min(i);
		else if(interpol(i) == _boundingBox._max(i))
		interpol(i) = _boundingBox._max(i)-1;
		}
		}
		if (adjoint) {
		#pragma omp atomic
		result(interpol) += weight * vector[from];
		} else {
		result[to] += weight * vector(interpol);
		}
		}

		// handle current voxel
		weight = intersection*(1-fractionals.array().abs()).prod()/(1-fabs(fractionals(mainDirection)));
		if (adjoint) {
		#pragma omp atomic
		result[to] += weight * vector[from];
		}
		else {
		result[to] += weight * vector[from];
		}

		// handle neighbors not along the main direction
		for (int i = 0; i < domainDim; i++) {
		if (i != mainDirection) {
		float weightn = weight * fabs(fractionals(i))/(1-fabs(fractionals(i)));
		interpol = currentVoxel;
		interpol(i) += (fractionals(i) < 0.0) ? -1 : 1;

		// mirror values at border if outside the volume
		if(interpol(i)<_boundingBox._min(i) \|\| interpol(i)>_boundingBox._max(i))
		interpol(i) = _boundingBox._min(i);
		else if(interpol(i) == _boundingBox._max(i))
		interpol(i) = _boundingBox._max(i)-1;

		if (adjoint) {
		#pragma omp atomic
		result(interpol) += weightn * vector[from];
		} else {
		result[to] += weightn * vector(interpol);
		}
		}
		}
		}

		// ------------------------------------------
		// explicit template instantiation
		template class JosephsMethod<float>;
		template class JosephsMethod<double>;

		} // namespace elsa

elsa/projectors/JosephsMethod.h

0 → 100644

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		#pragma once

		#include "LinearOperator.h"
		#include "Geometry.h"
		#include "BoundingBox.h"

		#include <vector>
		#include <utility>

		#include <Eigen/Geometry>

		namespace elsa
		{
		/**
		* \brief Operator representing the discretized X-ray transform in 2d/3d using Joseph's method.
		*
		* \author Christoph Hahn - initial implementation
		* \author Maximilian Hornung - modularization
		* \author Nikola Dinev - fixes
		*
		* \tparam data_t data type for the domain and range of the operator, defaulting to real_t
		*
		* The volume is traversed along the rays as specified by the Geometry. For interior voxels
		* the sampling point is located in the middle of the two planes orthogonal to the main
		* direction of the ray. For boundary voxels the sampling point is located at the center of the
		* ray intersection with the voxel.
		*
		* The geometry is represented as a list of projection matrices (see class Geometry), one for each
		* acquisition pose.
		*
		* Two modes of interpolation are available:
		* NN (NearestNeighbours) takes the value of the pixel/voxel containing the point
		* LINEAR performs linear interpolation for the nearest 2 pixels (in 2D)
		* or the nearest 4 voxels (in 3D).
		*
		* Forward projection is accomplished using apply(), backward projection using applyAdjoint().
		* This projector is matched.
		*/
		template <typename data_t = real_t>
		class JosephsMethod : public LinearOperator<data_t> {
		public:
		/// Available interpolation modes
		enum class Interpolation { NN, LINEAR };

		/**
		* \brief Constructor for Joseph's traversal method.
		*
		* \param[in] domainDescriptor describing the domain of the operator (the volume)
		* \param[in] rangeDescriptor describing the range of the operator (the sinogram)
		* \param[in] geometryList vector containing the geometries for the acquisition poses
		*
		* The domain is expected to be 2 or 3 dimensional (volSizeX, volSizeY, [volSizeZ]),
		* the range is expected to be matching the domain (detSizeX, [detSizeY], acqPoses).
		*/
		JosephsMethod(const DataDescriptor& domainDescriptor, const DataDescriptor& rangeDescriptor,
		const std::vector<Geometry>& geometryList, Interpolation interpolation = Interpolation::LINEAR);

		/// default destructor
		~JosephsMethod() = default;

		protected:
		/// apply the binary method (i.e. forward projection)
		void _apply(const DataContainer<data_t>& x, DataContainer<data_t>& Ax) override;

		/// apply the adjoint of the binary method (i.e. backward projection)
		void _applyAdjoint(const DataContainer<data_t>& y, DataContainer<data_t>& Aty) override;

		/// implement the polymorphic clone operation
		JosephsMethod<data_t>* cloneImpl() const override;

		/// implement the polymorphic comparison operation
		bool isEqual(const LinearOperator<data_t>& other) const override;

		private:
		/// the bounding box of the volume
		BoundingBox _boundingBox;

		/// the geometry list
		std::vector<Geometry> _geometryList;

		/// the interpolation mode
		Interpolation _interpolation;

		/// the traversal routine (for both apply/applyAdjoint)
		template <bool adjoint>
		void traverseVolume(const DataContainer<data_t>& vector, DataContainer<data_t>& result) const;

		/// convenience typedef for ray
		using Ray = Eigen::ParametrizedLine<real_t, Eigen::Dynamic>;

		/**
		* \brief computes the ray to the middle of the detector element
		*
		* \param[in] detectorIndex the index of the detector element
		* \param[in] dimension the dimension of the detector (1 or 2)
		*
		* \returns the ray
		*/
		Ray computeRayToDetector(index_t detectorIndex, index_t dimension) const;


		/**
		* \brief Linear interpolation, works in any dimension
		*
		* \param vector the input DataContainer
		* \param result DataContainer for results
		* \param fractionals the fractional numbers used in the interpolation
		* \param adjoint true for backward projection, false for forward
		* \param domainDim number of dimensions
		* \param currentVoxel coordinates of voxel for interpolation
		* \param intersection weighting for the interpolated values depending on the incidence angle
		* \param from index of the current vector position
		* \param to index of the current result position
		*/
		void LINEAR(const DataContainer<data_t>& vector, DataContainer<data_t>& result, const RealVector_t& fractionals, bool adjoint,
		int domainDim, const IndexVector_t& currentVoxel, float intersection, index_t from, index_t to, int mainDirection) const;

		/// lift from base class
		using LinearOperator<data_t>::_domainDescriptor;
		using LinearOperator<data_t>::_rangeDescriptor;
		};
		} // namespace elsa

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