Merge pull request #135 from KrisThielemans/cpp_fixes

C++ helper fixes (setting version to 0.7.2)

Author: KrisThielemans

cpp/CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.12.0) # older would work, but could give warnings on policy CMP0074
-project(petsird VERSION 0.7.1)
+project(petsird VERSION 0.7.2)
 
 set(CMAKE_CXX_STANDARD 17)
 
@@ -15,16 +15,5 @@ if(CCACHE_PROGRAM)
   message(STATUS "ccache found, so we will use it.")
 endif()
 
-add_executable(petsird_generator petsird_generator.cpp)
-target_link_libraries(petsird_generator petsird_generated)
-target_include_directories(petsird_generator PRIVATE "${PROJECT_SOURCE_DIR}/helpers/include")
-# needed for generated PETSIRD files
-target_include_directories(petsird_generator PRIVATE "${PROJECT_SOURCE_DIR}/")
-
-add_executable(petsird_analysis petsird_analysis.cpp)
-target_link_libraries(petsird_analysis petsird_generated)
-target_include_directories(petsird_analysis PRIVATE "${PROJECT_SOURCE_DIR}/helpers/include")
-# needed for generated PETSIRD files
-target_include_directories(petsird_analysis PRIVATE "${PROJECT_SOURCE_DIR}/")
-
 add_subdirectory(generated)
+add_subdirectory(helpers)

cpp/helpers/CMakeLists.txt

@@ -0,0 +1,12 @@
+
+add_executable(petsird_generator petsird_generator.cpp)
+target_link_libraries(petsird_generator petsird_generated)
+target_include_directories(petsird_generator PRIVATE "${PROJECT_SOURCE_DIR}/helpers/include")
+# needed for generated PETSIRD files
+target_include_directories(petsird_generator PRIVATE "${PROJECT_SOURCE_DIR}/")
+
+add_executable(petsird_analysis petsird_analysis.cpp)
+target_link_libraries(petsird_analysis petsird_generated)
+target_include_directories(petsird_analysis PRIVATE "${PROJECT_SOURCE_DIR}/helpers/include")
+# needed for generated PETSIRD files
+target_include_directories(petsird_analysis PRIVATE "${PROJECT_SOURCE_DIR}/")

cpp/petsird_helpers.h cpp/helpers/include/petsird_helpers.hcpp/petsird_helpers.h renamed to cpp/helpers/include/petsird_helpers.h

@@ -3,6 +3,8 @@
 
   SPDX-License-Identifier: Apache-2.0
 */
+#ifndef __petsird_helpers_h__
+#define __petsird_helpers_h__
 
 #include "generated/types.h"
 #include <array>
@@ -138,3 +140,5 @@ get_detection_efficiency(const ScannerInformation& scanner, const TypeOfModulePa
 }
 
 } // namespace petsird_helpers
+
+#endif

cpp/helpers/include/petsird_helpers/create.h

@@ -4,6 +4,9 @@
   SPDX-License-Identifier: Apache-2.0
 */
 
+#ifndef __petsird_helpers_create_h__
+#define __petsird_helpers_create_h__
+
 #include "generated/types.h"
 #include <array>
 
@@ -12,8 +15,6 @@ namespace petsird_helpers
 namespace create
 {
 
-using namespace petsird;
-
 //! Helper function to create a std::vector<T>
 /*! This function is added to have a 1D analogue construct_2D_nested_vector() */
 template <typename T>
@@ -76,3 +77,4 @@ initialize_scanner_information_dimensions(petsird::ScannerInformation& scanner,
 
 } // namespace create
 } // namespace petsird_helpers
+#endif

cpp/helpers/include/petsird_helpers/geometry.h

@@ -1,9 +1,18 @@
+/*
+  Copyright (C) 2024, 2025 University College London
+
+  SPDX-License-Identifier: Apache-2.0
+*/
+#ifndef __petsird_helpers_geometry_h__
+#define __petsird_helpers_geometry_h__
+
 #include <xtensor/xarray.hpp>
 #include <xtensor/xview.hpp>
 #include <xtensor/xio.hpp>
 #include <xtensor-blas/xlinalg.hpp>
 #include <vector>
 #include "generated/types.h"
+#include "petsird_helpers.h"
 
 namespace petsird_helpers
 {
@@ -12,40 +21,40 @@ namespace geometry
 
 //! Convert RigidTransformation to 4x4 matrix
 inline xt::xarray<float>
-transform_to_mat44(const RigidTransformation& transform)
+transform_to_mat44(const petsird::RigidTransformation& transform)
 {
   xt::xarray<float> bottom_row = { { 0.0f, 0.0f, 0.0f, 1.0f } };
   return xt::concatenate(xt::xtuple(transform.matrix, bottom_row), 0);
 }
 
 //! Convert 4x4 matrix to RigidTransformation
-inline RigidTransformation
+inline petsird::RigidTransformation
 mat44_to_transform(const xt::xarray<float>& mat)
 {
-  RigidTransformation transform;
+  petsird::RigidTransformation transform;
   transform.matrix = xt::view(mat, xt::range(0, 3), xt::all());
   return transform;
 }
 
 //! Convert Coordinate to homogeneous vector
 inline xt::xarray<float>
-coordinate_to_homogeneous(const Coordinate& coord)
+coordinate_to_homogeneous(const petsird::Coordinate& coord)
 {
   return xt::concatenate(xt::xtuple(coord.c, xt::xarray<float>{ 1.0f }), 0);
 }
 
 //! Convert homogeneous vector to Coordinate
-inline Coordinate
+inline petsird::Coordinate
 homogeneous_to_coordinate(const xt::xarray<float>& hom_coord)
 {
-  Coordinate coord;
+  petsird::Coordinate coord;
   coord.c = xt::view(hom_coord, xt::range(0, 3));
   return coord;
 }
 
 //! Multiply a list of transformations
-inline RigidTransformation
-mult_transforms(const std::vector<RigidTransformation>& transforms)
+inline petsird::RigidTransformation
+mult_transforms(const std::vector<petsird::RigidTransformation>& transforms)
 {
   xt::xarray<float> mat = xt::eye<float>(4);
   for (auto it = transforms.rbegin(); it != transforms.rend(); ++it)
@@ -56,18 +65,18 @@ mult_transforms(const std::vector<RigidTransformation>& transforms)
 }
 
 //! Apply transformations to a coordinate
-inline Coordinate
-mult_transforms_coord(const std::vector<RigidTransformation>& transforms, const Coordinate& coord)
+inline petsird::Coordinate
+mult_transforms_coord(const std::vector<petsird::RigidTransformation>& transforms, const petsird::Coordinate& coord)
 {
   xt::xarray<float> hom = xt::linalg::dot(transform_to_mat44(mult_transforms(transforms)), coordinate_to_homogeneous(coord));
   return homogeneous_to_coordinate(hom);
 }
 
 //! Transform a BoxShape
-inline BoxShape
-transform_BoxShape(const RigidTransformation& transform, const BoxShape& box_shape)
+inline petsird::BoxShape
+transform_BoxShape(const petsird::RigidTransformation& transform, const petsird::BoxShape& box_shape)
 {
-  BoxShape new_box;
+  petsird::BoxShape new_box;
   for (size_t i = 0; i < box_shape.corners.size(); ++i)
     {
       new_box.corners[i] = mult_transforms_coord({ transform }, box_shape.corners[i]);
@@ -76,9 +85,9 @@ transform_BoxShape(const RigidTransformation& transform, const BoxShape& box_sha
 }
 
 //! find the BoxShape corresponding to a ExpandedDetectionBin
-inline BoxShape
-get_detecting_box(const ScannerInformation& scanner, const TypeOfModule& type_of_module,
-                  const ExpandedDetectionBin& expanded_detection_bin)
+inline petsird::BoxShape
+get_detecting_box(const petsird::ScannerInformation& scanner, const petsird::TypeOfModule& type_of_module,
+                  const petsird::ExpandedDetectionBin& expanded_detection_bin)
 {
   const auto& rep_module = scanner.scanner_geometry.replicated_modules[type_of_module];
   const auto& det_els = rep_module.object.detecting_elements;
@@ -88,11 +97,13 @@ get_detecting_box(const ScannerInformation& scanner, const TypeOfModule& type_of
 }
 
 //! find the BoxShape corresponding to a DetectionBin
-inline BoxShape
-get_detecting_box(const ScannerInformation& scanner, const TypeOfModule& type_of_module, const DetectionBin& detection_bin)
+inline petsird::BoxShape
+get_detecting_box(const petsird::ScannerInformation& scanner, const petsird::TypeOfModule& type_of_module,
+                  const petsird::DetectionBin& detection_bin)
 {
   return get_detecting_box(scanner, type_of_module, expand_detection_bin(scanner, type_of_module, detection_bin));
 }
 
 } // namespace geometry
 } // namespace petsird_helpers
+#endif

cpp/petsird_analysis.cpp cpp/helpers/petsird_analysis.cppcpp/petsird_analysis.cpp renamed to cpp/helpers/petsird_analysis.cpp

@@ -185,7 +185,7 @@ main(int argc, char const* argv[])
                             << "energy_index=" << expanded_detection_bin0.energy_index
                             << "), ExpandedDetectionBin(module=" << expanded_detection_bin1.module_index << ", "
                             << "el=" << expanded_detection_bin1.element_index << ", "
-                            << "energy_index=" << expanded_detection_bin0.energy_index << ")]\n";
+                            << "energy_index=" << expanded_detection_bin1.energy_index << ")]\n";
                   std::cout << "    efficiency:"
                             << petsird_helpers::get_detection_efficiency(header.scanner, type_of_module_pair, event) << "\n";
                 }

cpp/petsird_generator.cpp cpp/helpers/petsird_generator.cppcpp/petsird_generator.cpp renamed to cpp/helpers/petsird_generator.cpp

@@ -27,7 +27,7 @@ set shell := ['bash', '-ceuo', 'pipefail']
 
 @run-cpp: build-cpp
     #!/usr/bin/env bash
-    cd cpp/build
+    cd cpp/build/helpers
     ./petsird_generator testdata.petsird
     ./petsird_analysis testdata.petsird
     rm -f testdata.petsird

justfile

@@ -23,7 +23,7 @@ function buildToolbox (outdir)
 
     opts.ToolboxName = "PETSIRD";
 
-    opts.ToolboxVersion = "0.7.1";
+    opts.ToolboxVersion = "0.7.2";
     opts.OutputFile = fullfile(outdir, sprintf("petsird-%s.mltbx", opts.ToolboxVersion));
 
     opts.Description = "Positron Emission Tomography Standardization Initiative Raw Data (PETSIRD) toolbox for MATLAB";