Add sketch for lut projector

elsa/core/DataContainer.cpp

@@ -8,6 +8,7 @@
 #include "PartitionDescriptor.h"
 #include "Error.h"
 #include "TypeCasts.hpp"
+#include "Assertions.h"
 
 #include <utility>
 
@@ -108,26 +109,53 @@ namespace elsa
     template <typename data_t>
     data_t& DataContainer<data_t>::operator[](index_t index)
     {
+        ELSA_VERIFY(index >= 0);
+        ELSA_VERIFY(index < getSize());
+
         return (*_dataHandler)[index];
     }
 
     template <typename data_t>
     const data_t& DataContainer<data_t>::operator[](index_t index) const
     {
+        ELSA_VERIFY(index >= 0);
+        ELSA_VERIFY(index < getSize());
+
         return static_cast<const DataHandler<data_t>&>(*_dataHandler)[index];
     }
 
+    template <typename data_t>
+    data_t DataContainer<data_t>::at(IndexVector_t coordinate) const
+    {
+        const auto arr = coordinate.array();
+        if ((arr < 0).any()
+            || (arr >= _dataDescriptor->getNumberOfCoefficientsPerDimension().array()).any()) {
+            return 0;
+        }
+
+        return (*this)[_dataDescriptor->getIndexFromCoordinate(std::move(coordinate))];
+    }
+
     template <typename data_t>
     data_t& DataContainer<data_t>::operator()(IndexVector_t coordinate)
     {
-        return (*_dataHandler)[_dataDescriptor->getIndexFromCoordinate(std::move(coordinate))];
+        const auto arr = coordinate.array();
+        const auto shape = _dataDescriptor->getNumberOfCoefficientsPerDimension().array();
+        ELSA_VERIFY((arr >= 0).all());
+        ELSA_VERIFY((arr < shape).all());
+
+        return (*this)[_dataDescriptor->getIndexFromCoordinate(std::move(coordinate))];
     }
 
     template <typename data_t>
     const data_t& DataContainer<data_t>::operator()(IndexVector_t coordinate) const
     {
-        return static_cast<const DataHandler<data_t>&>(
-            *_dataHandler)[_dataDescriptor->getIndexFromCoordinate(std::move(coordinate))];
+        const auto arr = coordinate.array();
+        const auto shape = _dataDescriptor->getNumberOfCoefficientsPerDimension().array();
+        ELSA_VERIFY((arr >= 0).all());
+        ELSA_VERIFY((arr < shape).all());
+
+        return (*this)[_dataDescriptor->getIndexFromCoordinate(coordinate)];
     }
 
     template <typename data_t>

elsa/core/DataContainer.h

@@ -177,6 +177,8 @@ namespace elsa
         /// return an element by n-dimensional coordinate as read-only (not bounds-checked!)
         const data_t& operator()(IndexVector_t coordinate) const;
 
+        data_t at(IndexVector_t coordinate) const;
+
         /// return an element by its coordinates (not bounds-checked!)
         template <typename idx0_t, typename... idx_t,
                   typename = std::enable_if_t<

elsa/projectors/Blobs.cpp

+#include "Blobs.h"
+
+namespace elsa
+{
+    template <typename data_t>
+    constexpr Blob<data_t>::Blob(data_t radius, SelfType_t<data_t> alpha, SelfType_t<data_t> order)
+        : radius_(radius), alpha_(alpha), order_(order)
+    {
+    }
+
+    template <typename data_t>
+    constexpr data_t Blob<data_t>::operator()(data_t s)
+    {
+        return blobs::blob_evaluate(s, radius_, alpha_, order_);
+    }
+
+    template <typename data_t>
+    constexpr data_t Blob<data_t>::radius() const
+    {
+        return radius_;
+    }
+
+    template <typename data_t>
+    constexpr data_t Blob<data_t>::alpha() const
+    {
+        return alpha_;
+    }
+
+    template <typename data_t>
+    constexpr data_t Blob<data_t>::order() const
+    {
+        return order_;
+    }
+    // ------------------------------------------
+    // explicit template instantiation
+    namespace blobs
+    {
+        template float blob_evaluate<float>(float, SelfType_t<float>, SelfType_t<float>,
+                                            SelfType_t<float>);
+        template double blob_evaluate<double>(double, SelfType_t<double>, SelfType_t<double>,
+                                              SelfType_t<double>);
+
+        template float blob_projected<float>(float, SelfType_t<float>, SelfType_t<float>,
+                                             SelfType_t<float>);
+        template double blob_projected<double>(double, SelfType_t<double>, SelfType_t<double>,
+                                               SelfType_t<double>);
+
+        template float blob_projected<float>(float);
+        template double blob_projected<double>(double);
+    } // namespace blobs
+    template class Blob<float>;
+    template class Blob<double>;
+} // namespace elsa

elsa/projectors/Blobs.h

+#pragma once
+
+#include "elsaDefines.h"
+
+namespace elsa
+{
+    template <class T>
+    struct SelfType {
+        using type = T;
+    };
+
+    template <class T>
+    using SelfType_t = typename SelfType<T>::type;
+
+    namespace blobs
+    {
+        template <typename data_t>
+        constexpr data_t blob_evaluate(data_t r, SelfType_t<data_t> a, SelfType_t<data_t> alpha,
+                                       SelfType_t<data_t> m)
+        {
+            const auto w = static_cast<data_t>(1) - std::pow(r / a, static_cast<data_t>(2));
+            if (w >= 0) {
+                const data_t Im1 = std::cyl_bessel_i(m, alpha);
+                const data_t arg = std::sqrt(w);
+                const data_t Im2 = std::cyl_bessel_i(m, alpha * arg);
+
+                return Im2 / Im1 * std::pow(arg, m);
+            }
+            return 0;
+        }
+
+        /// @brief Compute line integral of blob through a straight line
+        /// @param distance distance of blob center to straight line, in literature often referred
+        /// to as `r`
+        /// @param radius radius of blob, often referred to as `a`
+        /// @param alpha smoothness factor of blob
+        /// @param order order of Bessel function, often referred to as `m`
+        /// Ref:
+        /// https://github.com/I2PC/xmipp/blob/3d4cc3f430cbc99a337635edbd95ebbcef33fc44/src/xmipp/libraries/data/blobs.cpp#L91A
+        /// Distance-Driven Projection and Backprojection for Spherically Symmetric Basis Functions
+        /// in CT - Levakhina
+        /// Spherically symmetric volume elements as basis functions for image reconstructions in
+        /// computed laminography - P. Trampert
+        /// Semi-Discrete Iteration Methods in X-Ray Tomography - Jonas Vogelgesang
+        template <typename data_t>
+        constexpr data_t blob_projected(data_t s, SelfType_t<data_t> a, SelfType_t<data_t> alpha,
+                                        SelfType_t<data_t> m)
+        {
+            // Equation derived in Lewitt 1990
+            const data_t w = static_cast<data_t>(1) - ((s * s) / (a * a));
+
+            // If `w` is close to zero or negative, `s` > `a`, and therefore just return 0
+            if (w > 1e-10) {
+                const data_t root = std::sqrt(w);
+
+                // First three terms of equation
+                const data_t q1 = a / std::cyl_bessel_i(m, alpha);
+                const data_t q2 = std::sqrt(2 * pi<data_t> / alpha);
+                const data_t q3 = std::pow(root, m + static_cast<data_t>(0.5));
+
+                const data_t q4 = std::cyl_bessel_i(m + static_cast<data_t>(0.5), alpha * root);
+
+                return q1 * q2 * q3 * q4;
+            }
+            return 0;
+        }
+
+        template <typename data_t>
+        constexpr data_t blob_projected(data_t s)
+        {
+            return blob_projected(s, 2.f, 10.83f, 2);
+        }
+    } // namespace blobs
+
+    template <typename data_t>
+    class Blob
+    {
+    public:
+        constexpr Blob(data_t radius, SelfType_t<data_t> alpha, SelfType_t<data_t> order);
+
+        constexpr data_t operator()(data_t s);
+
+        constexpr data_t radius() const;
+
+        constexpr data_t alpha() const;
+
+        constexpr data_t order() const;
+
+    private:
+        data_t radius_;
+        data_t alpha_;
+        data_t order_;
+    };
+
+    template <typename data_t>
+    class ProjectedBlob
+    {
+    public:
+        constexpr ProjectedBlob(data_t radius, SelfType_t<data_t> alpha, SelfType_t<data_t> order)
+            : radius_(radius), alpha_(alpha), order_(order)
+        {
+        }
+
+        constexpr data_t operator()(data_t s)
+        {
+            return blobs::blob_projected(s, radius_, alpha_, order_);
+        }
+#
+        data_t radius() const { return radius_; }
+
+        data_t alpha() const { return alpha_; }
+
+        data_t order() const { return order_; }
+
+    private:
+        data_t radius_;
+        data_t alpha_;
+        data_t order_;
+    };
+
+} // namespace elsa

elsa/projectors/CMakeLists.txt

@@ -5,10 +5,12 @@ set(MODULE_HEADERS
     TraverseAABB.h
     TraverseAABBJosephsMethod.h
     SliceTraversal.h
+    LutProjector.h
     BinaryMethod.h
     SiddonsMethod.h
     JosephsMethod.h
     SubsetSampler.h
+    Blobs.h
 )
 
 # list all the code files of the module
@@ -18,10 +20,12 @@ set(MODULE_SOURCES
     TraverseAABB.cpp
     TraverseAABBJosephsMethod.cpp
     SliceTraversal.cpp
+    LutProjector.cpp
     BinaryMethod.cpp
     SiddonsMethod.cpp
     JosephsMethod.cpp
     SubsetSampler.cpp
+    Blobs.cpp
 )
 
 list(APPEND MODULE_PUBLIC_DEPS elsa_core elsa_logging)
@@ -44,5 +48,5 @@ if(ELSA_BUILD_PYTHON_BINDINGS)
         ${PROJECT_SOURCE_DIR}/tools/bindings_generation/hints/${ELSA_MODULE_NAME}_hints.cpp ${MODULE_SOURCES}
     )
 endif()
- 
+
 write_module_config(${ELSA_MODULE_NAME} DEPENDENCIES elsa_core elsa_logging)

elsa/projectors/LutProjector.cpp

+#include "LutProjector.h"
+#include "Timer.h"
+#include "SliceTraversal.h"
+#include "Assertions.h"
+
+namespace elsa
+{
+    template <typename data_t>
+    BlobProjector<data_t>::BlobProjector(data_t radius, data_t alpha, data_t order,
+                                         const VolumeDescriptor& domainDescriptor,
+                                         const DetectorDescriptor& rangeDescriptor)
+        : LutProjector<data_t, BlobProjector<data_t>>(domainDescriptor, rangeDescriptor),
+          lut_(radius, alpha, order)
+    {
+        // sanity checks
+        auto dim = domainDescriptor.getNumberOfDimensions();
+        if (dim < 2 || dim > 3) {
+            throw InvalidArgumentError("BlobProjector: only supporting 2d/3d operations");
+        }
+
+        if (dim != rangeDescriptor.getNumberOfDimensions()) {
+            throw InvalidArgumentError("BlobProjector: domain and range dimension need to match");
+        }
+
+        if (_detectorDescriptor.getNumberOfGeometryPoses() == 0) {
+            throw InvalidArgumentError("BlobProjector: rangeDescriptor without any geometry");
+        }
+    }
+
+    template <typename data_t>
+    BlobProjector<data_t>::BlobProjector(const VolumeDescriptor& domainDescriptor,
+                                         const DetectorDescriptor& rangeDescriptor)
+        : BlobProjector(2, 10.83, 2, domainDescriptor, rangeDescriptor)
+    {
+    }
+
+    // ------------------------------------------
+    // explicit template instantiation
+    template class BlobProjector<float>;
+    template class BlobProjector<double>;
+} // namespace elsa

elsa/projectors/LutProjector.h

+#pragma once
+
+#include "elsaDefines.h"
+#include "Timer.h"
+#include "Luts.hpp"
+#include "SliceTraversal.h"
+#include "LinearOperator.h"
+#include "VolumeDescriptor.h"
+#include "DetectorDescriptor.h"
+#include "DataContainer.h"
+#include "BoundingBox.h"
+#include "Logger.h"
+#include "Blobs.h"
+
+namespace elsa
+{
+    template <typename data_t, typename Derived>
+    class LutProjector : public LinearOperator<data_t>
+    {
+    public:
+        LutProjector(const VolumeDescriptor& domainDescriptor,
+                     const DetectorDescriptor& rangeDescriptor)
+            : LinearOperator<data_t>(domainDescriptor, rangeDescriptor),
+              _boundingBox{domainDescriptor.getNumberOfCoefficientsPerDimension()},
+              _detectorDescriptor(static_cast<DetectorDescriptor&>(*_rangeDescriptor)),
+              _volumeDescriptor(static_cast<VolumeDescriptor&>(*_domainDescriptor))
+        {
+            // sanity checks
+            auto dim = _domainDescriptor->getNumberOfDimensions();
+            if (dim < 2 || dim > 3) {
+                throw InvalidArgumentError("LutProjector: only supporting 2d/3d operations");
+            }
+
+            if (dim != _rangeDescriptor->getNumberOfDimensions()) {
+                throw InvalidArgumentError(
+                    "LutProjector: domain and range dimension need to match");
+            }
+
+            if (_detectorDescriptor.getNumberOfGeometryPoses() == 0) {
+                throw InvalidArgumentError("LutProjector: rangeDescriptor without any geometry");
+            }
+        }
+
+        /// default destructor
+        ~LutProjector() override = default;
+
+        Derived& self() { return static_cast<Derived&>(*this); }
+
+        const Derived& self() const { return static_cast<const Derived&>(*this); }
+
+    protected:
+        /// apply the binary method (i.e. forward projection)
+        void applyImpl(const DataContainer<data_t>& x, DataContainer<data_t>& Ax) const override
+        {
+            Timer t("LutProjector", "apply");
+
+            // Be sure to zero out the result
+            Ax = 0;
+
+            const auto sizeRange = Ax.getSize();
+            const auto volume_shape = x.getDataDescriptor().getNumberOfCoefficientsPerDimension();
+
+            // Loop over all the poses, and for each pose loop over all detector pixels
+#pragma omp parallel for
+            for (index_t rangeIndex = 0; rangeIndex < sizeRange; ++rangeIndex) {
+                // --> get the current ray to the detector center
+                auto ray = _detectorDescriptor.computeRayFromDetectorCoord(rangeIndex);
+
+                index_t leadingdir = 0;
+                ray.direction().array().cwiseAbs().maxCoeff(&leadingdir);
+
+                auto& rangeVal = Ax[rangeIndex];
+
+                // Expand bounding box as rays have larger support now
+                auto aabb = _boundingBox;
+                aabb._min.array() -= support;
+                aabb._min[leadingdir] += support;
+
+                aabb._max.array() += support;
+                aabb._max[leadingdir] -= support;
+
+                // --> setup traversal algorithm
+                SliceTraversal traversal(aabb, ray);
+
+                for (const auto [curPos, curVoxel, t] : traversal) {
+                    for (auto neighbour :
+                         neighbours_in_slice(curVoxel, support, leadingdir, lower, upper)) {
+                        // Correct position, such that the distance is still correct
+                        auto correctedPos = neighbour.template cast<real_t>().array() + 0.5;
+
+                    const auto distance = ray.distance(curPos);
+                    const auto weight = self().weight(distance);
+                    rangeVal += weight * x.at(curVoxel);
+                }
+            }
+        }
+
+        /// apply the adjoint of the binary method (i.e. backward projection)
+        void applyAdjointImpl(const DataContainer<data_t>& y,
+                              DataContainer<data_t>& Aty) const override
+        {
+            Timer t("LutProjector", "apply");
+
+            const auto sizeRange = y.getSize();
+            Aty = 0;
+
+            const auto shape = _domainDescriptor->getNumberOfCoefficientsPerDimension();
+
+#pragma omp parallel for
+            // Loop over all the poses, and for each pose loop over all detector pixels
+            for (index_t rangeIndex = 0; rangeIndex < sizeRange; ++rangeIndex) {
+                // --> get the current ray to the detector center (from reference to
+                // DetectorDescriptor)
+                auto ray = _detectorDescriptor.computeRayFromDetectorCoord(rangeIndex);
+
+                index_t leadingdir = 0;
+                ray.direction().array().cwiseAbs().maxCoeff(&leadingdir);
+
+                // Expand bounding box as rays have larger support now
+                auto aabb = _boundingBox;
+                aabb._min.array() -= support;
+                aabb._min[leadingdir] += support;
+
+                aabb._max.array() += support;
+                aabb._max[leadingdir] -= support;
+
+                // --> setup traversal algorithm
+                SliceTraversal traversal(aabb, ray);
+
+                const auto val = y[rangeIndex];
+
+                for (const auto [curPos, curVoxel, t] : traversal) {
+                    for (auto neighbour :
+                         neighbours_in_slice(curVoxel, support, leadingdir, lower, upper)) {
+                        // Correct position, such that the distance is still correct
+                        auto correctedPos = neighbour.template cast<real_t>().array() + 0.5;
+
+                        const auto distance = ray.distance(correctedPos);
+                        const auto weight = self().weight(distance);
+#pragma omp atomic
+                        Aty(neighbour) += weight * val;
+                    }
+                }
+            }
+        }
+
+        /// implement the polymorphic clone operation
+        LutProjector<data_t, Derived>* cloneImpl() const override
+        {
+            return new LutProjector(_volumeDescriptor, _detectorDescriptor);
+        }
+
+        /// implement the polymorphic comparison operation
+        bool isEqual(const LinearOperator<data_t>& other) const override
+        {
+            if (!LinearOperator<data_t>::isEqual(other))
+                return false;
+
+            auto otherOp = downcast_safe<LutProjector>(&other);
+            return static_cast<bool>(otherOp);
+        }
+
+    private:
+        /// the bounding box of the volume
+        BoundingBox _boundingBox;
+
+        /// Lift from base class
+        using LinearOperator<data_t>::_domainDescriptor;
+
+        /// Lift from base class
+        using LinearOperator<data_t>::_rangeDescriptor;
+
+    protected:
+        /// Reference to DetectorDescriptor stored in LinearOperator
+        DetectorDescriptor& _detectorDescriptor;
+
+        /// Reference to VolumeDescriptor stored in LinearOperator
+        VolumeDescriptor& _volumeDescriptor;
+    };
+
+    template <typename data_t = real_t>
+    class BlobProjector : public LutProjector<data_t, BlobProjector<data_t>>
+    {
+    public:
+        BlobProjector(data_t radius, data_t alpha, data_t order,
+                      const VolumeDescriptor& domainDescriptor,
+                      const DetectorDescriptor& rangeDescriptor);
+
+        BlobProjector(const VolumeDescriptor& domainDescriptor,
+                      const DetectorDescriptor& rangeDescriptor);
+
+        data_t weight(data_t distance) const { return lut_(distance); }
+
+        /// implement the polymorphic clone operation
+        BlobProjector<data_t>* cloneImpl() const override
+        {
+            return new BlobProjector(_volumeDescriptor, _detectorDescriptor);
+        }
+
+        /// implement the polymorphic comparison operation
+        bool isEqual(const LinearOperator<data_t>& other) const override
+        {
+            if (!Base::isEqual(other))
+                return false;
+
+            auto otherOp = downcast_safe<BlobProjector>(&other);
+            return static_cast<bool>(otherOp);
+        }
+
+    private:
+        ProjectedBlobLut<data_t, 100> lut_;
+
+        using Base = LutProjector<data_t, BlobProjector<data_t>>;
+        using Base::_detectorDescriptor;
+        using Base::_volumeDescriptor;
+    };
+} // namespace elsa

elsa/projectors/Luts.hpp

+#pragma once
+
+#include "Blobs.h"
+#include "Logger.h"
+
+#include <array>
+
+namespace elsa
+{
+    namespace detail
+    {
+        template <typename data_t, index_t N>
+        constexpr std::array<data_t, N> blob_lut(ProjectedBlob<data_t> blob)
+        {
+            std::array<data_t, N> lut;
+
+            auto t = static_cast<data_t>(0);
+            const auto step = blob.radius() / N;
+
+            for (std::size_t i = 0; i < N; ++i) {
+                lut[i] = blob(t);
+                t += step;
+            }
+
+            return lut;