From b1b020ad60ee41ade1efbb82a39ad67afae25319 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Erik=20Fr=C3=B6jdh?= Date: Fri, 25 Oct 2024 10:23:34 +0200 Subject: [PATCH 01/87] WIP --- CMakeLists.txt | 255 ++++++++++++++++++++++++++ README.md | 13 ++ cmake/helpers.cmake | 6 + include/aare/Dtype.hpp | 83 +++++++++ include/aare/Frame.hpp | 76 ++++++++ include/aare/NDArray.hpp | 380 +++++++++++++++++++++++++++++++++++++++ include/aare/NDView.hpp | 159 ++++++++++++++++ include/aare/defs.hpp | 156 ++++++++++++++++ src/CMakeLists.txt | 33 ++++ src/Dtype.cpp | 191 ++++++++++++++++++++ src/Dtype.test.cpp | 54 ++++++ src/Frame.cpp | 110 ++++++++++++ src/Frame.test.cpp | 152 ++++++++++++++++ src/NDArray.test.cpp | 377 ++++++++++++++++++++++++++++++++++++++ src/NDView.test.cpp | 193 ++++++++++++++++++++ src/defs.cpp | 65 +++++++ src/defs.test.cpp | 42 +++++ tests/CMakeLists.txt | 44 +++++ tests/test.cpp | 21 +++ tests/test_config.hpp.in | 7 + 20 files changed, 2417 insertions(+) create mode 100644 CMakeLists.txt create mode 100644 cmake/helpers.cmake create mode 100644 include/aare/Dtype.hpp create mode 100644 include/aare/Frame.hpp create mode 100644 include/aare/NDArray.hpp create mode 100644 include/aare/NDView.hpp create mode 100644 include/aare/defs.hpp create mode 100644 src/CMakeLists.txt create mode 100644 src/Dtype.cpp create mode 100644 src/Dtype.test.cpp create mode 100644 src/Frame.cpp create mode 100644 src/Frame.test.cpp create mode 100644 src/NDArray.test.cpp create mode 100644 src/NDView.test.cpp create mode 100644 src/defs.cpp create mode 100644 src/defs.test.cpp create mode 100644 tests/CMakeLists.txt create mode 100644 tests/test.cpp create mode 100644 tests/test_config.hpp.in diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 0000000..f169113 --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,255 @@ +cmake_minimum_required(VERSION 3.12) + +set(CMAKE_CXX_STANDARD 17) #TODO! Global or per target? +set(CMAKE_CXX_STANDARD_REQUIRED ON) +set(CMAKE_CXX_EXTENSIONS OFF) + +project(aare + VERSION 0.1 + DESCRIPTION "Data processing library for PSI detectors" + HOMEPAGE_URL "https://github.com/slsdetectorgroup/aare" + LANGUAGES C CXX +) + +cmake_policy(SET CMP0135 NEW) +cmake_policy(SET CMP0079 NEW) + +include(GNUInstallDirs) +include(FetchContent) + +#Set default build type if none was specified +include(cmake/helpers.cmake) +default_build_type("Release") + +option(AARE_USE_WARNINGS "Enable warnings" ON) +option(AARE_PYTHON_BINDINGS "Build python bindings" ON) +option(AARE_TESTS "Build tests" ON) +option(AARE_EXAMPLES "Build examples" ON) +option(AARE_IN_GITHUB_ACTIONS "Running in Github Actions" OFF) + +option(AARE_FETCH_FMT "Use FetchContent to download fmt" ON) +option(AARE_FETCH_PYBIND11 "Use FetchContent to download pybind11" ON) +option(AARE_FETCH_CATCH "Use FetchContent to download catch2" ON) +option(AARE_FETCH_JSON "Use FetchContent to download nlohmann::json" ON) +option(AARE_FETCH_ZMQ "Use FetchContent to download libzmq" ON) +option(ENABLE_DRAFTS "Enable zmq drafts (depends on gnutls or nss)" OFF) + + +#Convenience option to use system libraries +option(AARE_SYSTEM_LIBRARIES "Use system libraries" OFF) +if(AARE_SYSTEM_LIBRARIES) + message(STATUS "Build using system libraries") + set(AARE_FETCH_FMT OFF CACHE BOOL "Disabled FetchContent for FMT" FORCE) + set(AARE_FETCH_PYBIND11 OFF CACHE BOOL "Disabled FetchContent for pybind11" FORCE) + set(AARE_FETCH_CATCH OFF CACHE BOOL "Disabled FetchContent for catch2" FORCE) + set(AARE_FETCH_JSON OFF CACHE BOOL "Disabled FetchContent for nlohmann::json" FORCE) + set(AARE_FETCH_ZMQ OFF CACHE BOOL "Disabled FetchContent for libzmq" FORCE) + +endif() + + +set(CMAKE_EXPORT_COMPILE_COMMANDS ON) + +if(AARE_FETCH_ZMQ) + + FetchContent_Declare( + libzmq + GIT_REPOSITORY https://github.com/zeromq/libzmq.git + GIT_TAG v4.3.4 + ) + # TODO! Verify that this is what we want to do in aare + # Using GetProperties and Populate to be able to exclude zmq + # from install (not possible with FetchContent_MakeAvailable(libzmq)) + FetchContent_GetProperties(libzmq) + if(NOT libzmq_POPULATED) + FetchContent_Populate(libzmq) + add_subdirectory(${libzmq_SOURCE_DIR} ${libzmq_BINARY_DIR} EXCLUDE_FROM_ALL) + endif() + +else() + find_package(ZeroMQ 4 REQUIRED) +endif() + + +if (AARE_FETCH_FMT) + set(FMT_TEST OFF CACHE INTERNAL "disabling fmt tests") + FetchContent_Declare( + fmt + GIT_REPOSITORY https://github.com/fmtlib/fmt.git + GIT_TAG 10.2.1 + GIT_PROGRESS TRUE + USES_TERMINAL_DOWNLOAD TRUE + ) + FetchContent_MakeAvailable(fmt) + set_property(TARGET fmt PROPERTY POSITION_INDEPENDENT_CODE ON) +else() + find_package(fmt 6 REQUIRED) +endif() + + +add_library(aare_compiler_flags INTERFACE) +target_compile_features(aare_compiler_flags INTERFACE cxx_std_17) + +################# +# MSVC specific # +################# +if(MSVC) +add_compile_definitions(AARE_MSVC) +if(CMAKE_BUILD_TYPE STREQUAL "Release") + message(STATUS "Release build") + target_compile_options(aare_compiler_flags INTERFACE /O2) +else() + message(STATUS "Debug build") + target_compile_options( + aare_compiler_flags + INTERFACE + /Od + /Zi + /MDd + /D_ITERATOR_DEBUG_LEVEL=2 + ) + target_link_options( + aare_compiler_flags + INTERFACE + /DEBUG:FULL + ) +endif() +target_compile_options( + aare_compiler_flags + INTERFACE + /w # disable warnings +) + + +else() +###################### +# GCC/Clang specific # +###################### + +if(CMAKE_BUILD_TYPE STREQUAL "Release") + message(STATUS "Release build") + target_compile_options(aare_compiler_flags INTERFACE -O3) +else() + message(STATUS "Debug build") + target_compile_options( + aare_compiler_flags + INTERFACE + -Og + -ggdb3 + # -D_GLIBCXX_DEBUG # causes errors with boost + -D_GLIBCXX_DEBUG_PEDANTIC + ) + + if (NOT AARE_PYTHON_BINDINGS) + target_compile_options( + aare_compiler_flags + INTERFACE + -fdiagnostics-parseable-fixits + # -fdiagnostics-generate-patch + -fdiagnostics-show-template-tree + -fsanitize=address,undefined,pointer-compare + -fno-sanitize-recover + # -D_FORTIFY_SOURCE=2 # not needed for debug builds + # -fstack-protector # cause errors wih folly? (ProducerConsumerQueue.hpp) + -fno-omit-frame-pointer + ) + + target_link_libraries( + aare_compiler_flags + INTERFACE + -fdiagnostics-parseable-fixits + # -fdiagnostics-generate-patch + -fdiagnostics-show-template-tree + -fsanitize=address,undefined,pointer-compare + -fno-sanitize-recover + # -D_FORTIFY_SOURCE=2 + -fno-omit-frame-pointer + ) + endif() + +endif() + +if(AARE_USE_WARNINGS) + target_compile_options( + aare_compiler_flags + INTERFACE + -Wall + -Wextra + -pedantic + -Wshadow + -Wnon-virtual-dtor + -Woverloaded-virtual + -Wdouble-promotion + -Wformat=2 + -Wredundant-decls + -Wvla + -Wdouble-promotion + -Werror=return-type #important can cause segfault in optimzed builds + ) +endif() + + + +endif() #GCC/Clang specific + + + + + + + + +if(AARE_TESTS) + enable_testing() + add_subdirectory(tests) +endif() + +add_subdirectory(src) + + +#Overall target to link to when using the library +add_library(aare INTERFACE) +target_link_libraries(aare INTERFACE aare_core aare_compiler_flags) +target_include_directories(aare INTERFACE + $ + $ +) + +# add_subdirectory(examples) + + + + +# custom target to run check formatting with clang-format +add_custom_target( + check-format + COMMAND find \( -name "*.cpp" -o -name "*.hpp" \) -not -path "./build/*" | xargs -I {} -n 1 -P 10 bash -c "clang-format -Werror -style=\"file:.clang-format\" {} | diff {} -" + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} + COMMENT "Checking code formatting with clang-format" + VERBATIM + +) + +add_custom_target( + format-files + COMMAND find \( -name "*.cpp" -o -name "*.hpp" \) -not -path "./build/*" | xargs -I {} -n 1 -P 10 bash -c "clang-format -i -style=\"file:.clang-format\" {}" + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} + COMMENT "Formatting with clang-format" + VERBATIM +) + +if (AARE_IN_GITHUB_ACTIONS) + message(STATUS "Running in Github Actions") + set(CLANG_TIDY_COMMAND "clang-tidy-17") +else() + set(CLANG_TIDY_COMMAND "clang-tidy") +endif() + +add_custom_target( + clang-tidy + COMMAND find \( -path "./src/*" -a -not -path "./src/python/*" -a \( -name "*.cpp" -not -name "*.test.cpp"\) \) -not -name "CircularFifo.hpp" -not -name "ProducerConsumerQueue.hpp" -not -name "VariableSizeClusterFinder.hpp" | xargs -I {} -n 1 -P 10 bash -c "${CLANG_TIDY_COMMAND} --config-file=.clang-tidy -p build {}" + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} + COMMENT "linting with clang-tidy" + VERBATIM +) + diff --git a/README.md b/README.md index b7ee44c..765e4c5 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,15 @@ # aare Data analysis library for PSI hybrid detectors + + + +## Project structure + +include/aare - public headers + + +## Open questions + +- How many sub libraries? +- Where to place test data? This data is also needed for github actions... +- What to return to numpy? Our NDArray or a numpy ndarray? Lifetime? \ No newline at end of file diff --git a/cmake/helpers.cmake b/cmake/helpers.cmake new file mode 100644 index 0000000..2a6dfb7 --- /dev/null +++ b/cmake/helpers.cmake @@ -0,0 +1,6 @@ +function(default_build_type val) +if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) + message(STATUS "No build type selected, default to Release") + set(CMAKE_BUILD_TYPE ${val} CACHE STRING "Build type (default ${val})" FORCE) +endif() +endfunction() diff --git a/include/aare/Dtype.hpp b/include/aare/Dtype.hpp new file mode 100644 index 0000000..7e1e62a --- /dev/null +++ b/include/aare/Dtype.hpp @@ -0,0 +1,83 @@ +#pragma once +#include +#include +#include +#include + +namespace aare { + +// The format descriptor is a single character that specifies the type of the data +// - python documentation: https://docs.python.org/3/c-api/arg.html#numbers +// - py::format_descriptor::format() (in pybind11) does not return the same format as +// written in python.org documentation. +// - numpy also doesn't use the same format. and also numpy associates the format +// with variable bitdepth types. (e.g. long is int64 on linux64 and int32 on win64) +// https://numpy.org/doc/stable/reference/arrays.scalars.html +// +// github issue discussing this: +// https://github.com/pybind/pybind11/issues/1908#issuecomment-658358767 +// +// [IN LINUX] the difference is for int64 (long) and uint64 (unsigned long). The format +// descriptor is 'q' and 'Q' respectively and in the documentation it is 'l' and 'k'. + +// in practice numpy doesn't seem to care when reading buffer info: the library +// interprets 'q' or 'l' as int64 and 'Q' or 'L' as uint64. +// for this reason we decided to use the same format descriptor as pybind to avoid +// any further discrepancies. + +// in the following order: +// int8, uint8, int16, uint16, int32, uint32, int64, uint64, float, double +const char DTYPE_FORMAT_DSC[] = {'b', 'B', 'h', 'H', 'i', 'I', 'q', 'Q', 'f', 'd'}; + +// on linux64 & apple +const char NUMPY_FORMAT_DSC[] = {'b', 'B', 'h', 'H', 'i', 'I', 'l', 'L', 'f', 'd'}; +/** + * @brief enum class to define the endianess of the system + */ +enum class endian { +#ifdef _WIN32 + little = 0, + big = 1, + native = little +#else + little = __ORDER_LITTLE_ENDIAN__, + big = __ORDER_BIG_ENDIAN__, + native = __BYTE_ORDER__ +#endif +}; + +/** + * @brief class to define the data type of the pixels + * @note only native endianess is supported + */ +class Dtype { + public: + enum TypeIndex { INT8, UINT8, INT16, UINT16, INT32, UINT32, INT64, UINT64, FLOAT, DOUBLE, ERROR, NONE }; + + uint8_t bitdepth() const; + size_t bytes() const; + std::string format_descr() const { return std::string(1, DTYPE_FORMAT_DSC[static_cast(m_type)]); } + std::string numpy_descr() const { return std::string(1, NUMPY_FORMAT_DSC[static_cast(m_type)]); } + + explicit Dtype(const std::type_info &t); + explicit Dtype(std::string_view sv); + static Dtype from_bitdepth(uint8_t bitdepth); + + // not explicit to allow conversions form enum to DType + Dtype(Dtype::TypeIndex ti); // NOLINT + + bool operator==(const Dtype &other) const noexcept; + bool operator!=(const Dtype &other) const noexcept; + bool operator==(const std::type_info &t) const; + bool operator!=(const std::type_info &t) const; + + // bool operator==(DType::TypeIndex ti) const; + // bool operator!=(DType::TypeIndex ti) const; + std::string to_string() const; + void set_type(Dtype::TypeIndex ti) { m_type = ti; } + + private: + TypeIndex m_type{TypeIndex::ERROR}; +}; + +} // namespace aare \ No newline at end of file diff --git a/include/aare/Frame.hpp b/include/aare/Frame.hpp new file mode 100644 index 0000000..88e4ab2 --- /dev/null +++ b/include/aare/Frame.hpp @@ -0,0 +1,76 @@ +#pragma once +#include "aare/Dtype.hpp" +#include "aare/NDArray.hpp" +#include "aare/defs.hpp" + +#include +#include +#include +#include + +namespace aare { + +/** + * @brief Frame class to represent a single frame of data + * model class + * should be able to work with streams coming from files or network + */ +class Frame { + uint32_t m_rows; + uint32_t m_cols; + Dtype m_dtype; + std::byte *m_data; + + public: + Frame(uint32_t rows, uint32_t cols, Dtype dtype); + Frame(const std::byte *bytes, uint32_t rows, uint32_t cols, Dtype dtype); + ~Frame() noexcept; + + // disable copy and assignment + Frame &operator=(const Frame &other)=delete; + Frame(const Frame &other)=delete; + + // enable move + Frame &operator=(Frame &&other) noexcept; + Frame(Frame &&other) noexcept; + + // explicit copy + Frame copy() const; + + uint32_t rows() const; + uint32_t cols() const; + size_t bitdepth() const; + Dtype dtype() const; + uint64_t size() const; + size_t bytes() const; + std::byte *data() const; + + std::byte *get(uint32_t row, uint32_t col); + + // TODO! can we, or even want to remove the template? + template void set(uint32_t row, uint32_t col, T data) { + assert(sizeof(T) == m_dtype.bytes()); + if (row >= m_rows || col >= m_cols) { + throw std::out_of_range("Invalid row or column index"); + } + std::memcpy(m_data + (row * m_cols + col) * m_dtype.bytes(), &data, m_dtype.bytes()); + } + template T get_t(uint32_t row, uint32_t col) { + assert(sizeof(T) == m_dtype.bytes()); + if (row >= m_rows || col >= m_cols) { + throw std::out_of_range("Invalid row or column index"); + } + T data; + std::memcpy(&data, m_data + (row * m_cols + col) * m_dtype.bytes(), m_dtype.bytes()); + return data; + } + template NDView view() { + std::array shape = {static_cast(m_rows), static_cast(m_cols)}; + T *data = reinterpret_cast(m_data); + return NDView(data, shape); + } + + template NDArray image() { return NDArray(this->view()); } +}; + +} // namespace aare \ No newline at end of file diff --git a/include/aare/NDArray.hpp b/include/aare/NDArray.hpp new file mode 100644 index 0000000..0a54091 --- /dev/null +++ b/include/aare/NDArray.hpp @@ -0,0 +1,380 @@ +#pragma once +/* +Container holding image data, or a time series of image data in contigious +memory. + + +TODO! Add expression templates for operators + +*/ +#include "aare/NDView.hpp" + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace aare { + +template class NDArray { + public: + NDArray() : shape_(), strides_(c_strides(shape_)), data_(nullptr){}; + + explicit NDArray(std::array shape) + : shape_(shape), strides_(c_strides(shape_)), + size_(std::accumulate(shape_.begin(), shape_.end(), 1, std::multiplies<>())), data_(new T[size_]){}; + + NDArray(std::array shape, T value) : NDArray(shape) { this->operator=(value); } + + /* When constructing from a NDView we need to copy the data since + NDArray expect to own its data, and span is just a view*/ + explicit NDArray(NDView span) : NDArray(span.shape()) { + std::copy(span.begin(), span.end(), begin()); + // fmt::print("NDArray(NDView span)\n"); + } + + // Move constructor + NDArray(NDArray &&other) noexcept + : shape_(other.shape_), strides_(c_strides(shape_)), size_(other.size_), data_(other.data_) { + + other.reset(); + // fmt::print("NDArray(NDArray &&other)\n"); + } + + // Copy constructor + NDArray(const NDArray &other) + : shape_(other.shape_), strides_(c_strides(shape_)), size_(other.size_), data_(new T[size_]) { + std::copy(other.data_, other.data_ + size_, data_); + // fmt::print("NDArray(const NDArray &other)\n"); + } + + ~NDArray() { delete[] data_; } + + auto begin() { return data_; } + auto end() { return data_ + size_; } + + using value_type = T; + + NDArray &operator=(NDArray &&other) noexcept; // Move assign + NDArray &operator=(const NDArray &other); // Copy assign + + NDArray operator+(const NDArray &other); + NDArray &operator+=(const NDArray &other); + NDArray operator-(const NDArray &other); + NDArray &operator-=(const NDArray &other); + NDArray operator*(const NDArray &other); + NDArray &operator*=(const NDArray &other); + NDArray operator/(const NDArray &other); + // NDArray& operator/=(const NDArray& other); + template NDArray &operator/=(const NDArray &other) { + // check shape + if (shape_ == other.shape()) { + for (uint32_t i = 0; i < size_; ++i) { + data_[i] /= other(i); + } + return *this; + } + throw(std::runtime_error("Shape of NDArray must match")); + } + + NDArray operator>(const NDArray &other); + + bool operator==(const NDArray &other) const; + bool operator!=(const NDArray &other) const; + + NDArray &operator=(const T & /*value*/); + NDArray &operator+=(const T & /*value*/); + NDArray operator+(const T & /*value*/); + NDArray &operator-=(const T & /*value*/); + NDArray operator-(const T & /*value*/); + NDArray &operator*=(const T & /*value*/); + NDArray operator*(const T & /*value*/); + NDArray &operator/=(const T & /*value*/); + NDArray operator/(const T & /*value*/); + + NDArray &operator&=(const T & /*mask*/); + + void sqrt() { + for (int i = 0; i < size_; ++i) { + data_[i] = std::sqrt(data_[i]); + } + } + + NDArray &operator++(); // pre inc + + template std::enable_if_t operator()(Ix... index) { + return data_[element_offset(strides_, index...)]; + } + + template std::enable_if_t operator()(Ix... index) const { + return data_[element_offset(strides_, index...)]; + } + + template std::enable_if_t value(Ix... index) { + return data_[element_offset(strides_, index...)]; + } + + T &operator()(int i) { return data_[i]; } + const T &operator()(int i) const { return data_[i]; } + + T *data() { return data_; } + std::byte *buffer() { return reinterpret_cast(data_); } + uint64_t size() const { return size_; } + size_t total_bytes() const { return size_ * sizeof(T); } + std::array shape() const noexcept { return shape_; } + int64_t shape(int64_t i) const noexcept { return shape_[i]; } + std::array strides() const noexcept { return strides_; } + size_t bitdepth() const noexcept { return sizeof(T) * 8; } + std::array byte_strides() const noexcept { + auto byte_strides = strides_; + for (auto &val : byte_strides) + val *= sizeof(T); + return byte_strides; + // return strides_; + } + + NDView span() const { return NDView{data_, shape_}; } + + void Print(); + void Print_all(); + void Print_some(); + + void reset() { + data_ = nullptr; + size_ = 0; + std::fill(shape_.begin(), shape_.end(), 0); + std::fill(strides_.begin(), strides_.end(), 0); + } + + private: + std::array shape_; + std::array strides_; + uint64_t size_{}; + T *data_; +}; + +// Move assign +template NDArray &NDArray::operator=(NDArray &&other) noexcept { + if (this != &other) { + delete[] data_; + data_ = other.data_; + shape_ = other.shape_; + size_ = other.size_; + strides_ = other.strides_; + other.reset(); + } + return *this; +} + +template NDArray NDArray::operator+(const NDArray &other) { + NDArray result(*this); + result += other; + return result; +} +template NDArray &NDArray::operator+=(const NDArray &other) { + // check shape + if (shape_ == other.shape_) { + for (uint32_t i = 0; i < size_; ++i) { + data_[i] += other.data_[i]; + } + return *this; + } + throw(std::runtime_error("Shape of ImageDatas must match")); +} + +template NDArray NDArray::operator-(const NDArray &other) { + NDArray result{*this}; + result -= other; + return result; +} + +template NDArray &NDArray::operator-=(const NDArray &other) { + // check shape + if (shape_ == other.shape_) { + for (uint32_t i = 0; i < size_; ++i) { + data_[i] -= other.data_[i]; + } + return *this; + } + throw(std::runtime_error("Shape of ImageDatas must match")); +} +template NDArray NDArray::operator*(const NDArray &other) { + NDArray result = *this; + result *= other; + return result; +} + +template NDArray &NDArray::operator*=(const NDArray &other) { + // check shape + if (shape_ == other.shape_) { + for (uint32_t i = 0; i < size_; ++i) { + data_[i] *= other.data_[i]; + } + return *this; + } + throw(std::runtime_error("Shape of ImageDatas must match")); +} + +template NDArray NDArray::operator/(const NDArray &other) { + NDArray result = *this; + result /= other; + return result; +} + +template NDArray &NDArray::operator&=(const T &mask) { + for (auto it = begin(); it != end(); ++it) + *it &= mask; + return *this; +} + +// template +// NDArray& NDArray::operator/=(const NDArray& +// other) +// { +// //check shape +// if (shape_ == other.shape_) { +// for (int i = 0; i < size_; ++i) { +// data_[i] /= other.data_[i]; +// } +// return *this; +// } else { +// throw(std::runtime_error("Shape of ImageDatas must match")); +// } +// } + +template NDArray NDArray::operator>(const NDArray &other) { + if (shape_ == other.shape_) { + NDArray result{shape_}; + for (int i = 0; i < size_; ++i) { + result(i) = (data_[i] > other.data_[i]); + } + return result; + } + throw(std::runtime_error("Shape of ImageDatas must match")); +} + +template NDArray &NDArray::operator=(const NDArray &other) { + if (this != &other) { + delete[] data_; + shape_ = other.shape_; + strides_ = other.strides_; + size_ = other.size_; + data_ = new T[size_]; + std::copy(other.data_, other.data_ + size_, data_); + } + return *this; +} + +template bool NDArray::operator==(const NDArray &other) const { + if (shape_ != other.shape_) + return false; + + for (uint32_t i = 0; i != size_; ++i) + if (data_[i] != other.data_[i]) + return false; + + return true; +} + +template bool NDArray::operator!=(const NDArray &other) const { + return !((*this) == other); +} +template NDArray &NDArray::operator++() { + for (uint32_t i = 0; i < size_; ++i) + data_[i] += 1; + return *this; +} +template NDArray &NDArray::operator=(const T &value) { + std::fill_n(data_, size_, value); + return *this; +} + +template NDArray &NDArray::operator+=(const T &value) { + for (uint32_t i = 0; i < size_; ++i) + data_[i] += value; + return *this; +} + +template NDArray NDArray::operator+(const T &value) { + NDArray result = *this; + result += value; + return result; +} +template NDArray &NDArray::operator-=(const T &value) { + for (uint32_t i = 0; i < size_; ++i) + data_[i] -= value; + return *this; +} +template NDArray NDArray::operator-(const T &value) { + NDArray result = *this; + result -= value; + return result; +} + +template NDArray &NDArray::operator/=(const T &value) { + for (uint32_t i = 0; i < size_; ++i) + data_[i] /= value; + return *this; +} +template NDArray NDArray::operator/(const T &value) { + NDArray result = *this; + result /= value; + return result; +} +template NDArray &NDArray::operator*=(const T &value) { + for (uint32_t i = 0; i < size_; ++i) + data_[i] *= value; + return *this; +} +template NDArray NDArray::operator*(const T &value) { + NDArray result = *this; + result *= value; + return result; +} +template void NDArray::Print() { + if (shape_[0] < 20 && shape_[1] < 20) + Print_all(); + else + Print_some(); +} +template void NDArray::Print_all() { + for (auto row = 0; row < shape_[0]; ++row) { + for (auto col = 0; col < shape_[1]; ++col) { + std::cout << std::setw(3); + std::cout << (*this)(row, col) << " "; + } + std::cout << "\n"; + } +} +template void NDArray::Print_some() { + for (auto row = 0; row < 5; ++row) { + for (auto col = 0; col < 5; ++col) { + std::cout << std::setw(7); + std::cout << (*this)(row, col) << " "; + } + std::cout << "\n"; + } +} + +template void save(NDArray &img, std::string &pathname) { + std::ofstream f; + f.open(pathname, std::ios::binary); + f.write(img.buffer(), img.size() * sizeof(T)); + f.close(); +} + +template +NDArray load(const std::string &pathname, std::array shape) { + NDArray img{shape}; + std::ifstream f; + f.open(pathname, std::ios::binary); + f.read(img.buffer(), img.size() * sizeof(T)); + f.close(); + return img; +} + +} // namespace aare \ No newline at end of file diff --git a/include/aare/NDView.hpp b/include/aare/NDView.hpp new file mode 100644 index 0000000..8a73038 --- /dev/null +++ b/include/aare/NDView.hpp @@ -0,0 +1,159 @@ +#pragma once +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +namespace aare { + +template using Shape = std::array; + +// TODO! fix mismatch between signed and unsigned +template Shape make_shape(const std::vector &shape) { + if (shape.size() != Ndim) + throw std::runtime_error("Shape size mismatch"); + Shape arr; + std::copy_n(shape.begin(), Ndim, arr.begin()); + return arr; +} + +template int64_t element_offset(const Strides & /*unused*/) { return 0; } + +template +int64_t element_offset(const Strides &strides, int64_t i, Ix... index) { + return i * strides[Dim] + element_offset(strides, index...); +} + +template std::array c_strides(const std::array &shape) { + std::array strides{}; + std::fill(strides.begin(), strides.end(), 1); + for (int64_t i = Ndim - 1; i > 0; --i) { + strides[i - 1] = strides[i] * shape[i]; + } + return strides; +} + +template std::array make_array(const std::vector &vec) { + assert(vec.size() == Ndim); + std::array arr{}; + std::copy_n(vec.begin(), Ndim, arr.begin()); + return arr; +} + +template class NDView { + public: + NDView() = default; + ~NDView() = default; + NDView(const NDView &) = default; + NDView(NDView &&) = default; + + NDView(T *buffer, std::array shape) + : buffer_(buffer), strides_(c_strides(shape)), shape_(shape), + size_(std::accumulate(std::begin(shape), std::end(shape), 1, std::multiplies<>())) {} + + // NDView(T *buffer, const std::vector &shape) + // : buffer_(buffer), strides_(c_strides(make_array(shape))), shape_(make_array(shape)), + // size_(std::accumulate(std::begin(shape), std::end(shape), 1, std::multiplies<>())) {} + + template std::enable_if_t operator()(Ix... index) { + return buffer_[element_offset(strides_, index...)]; + } + + template std::enable_if_t operator()(Ix... index) const { + return buffer_[element_offset(strides_, index...)]; + } + + uint64_t size() const { return size_; } + size_t total_bytes() const { return size_ * sizeof(T); } + std::array strides() const noexcept { return strides_; } + + T *begin() { return buffer_; } + T *end() { return buffer_ + size_; } + T &operator()(int64_t i) const { return buffer_[i]; } + T &operator[](int64_t i) const { return buffer_[i]; } + + bool operator==(const NDView &other) const { + if (size_ != other.size_) + return false; + for (uint64_t i = 0; i != size_; ++i) { + if (buffer_[i] != other.buffer_[i]) + return false; + } + return true; + } + + NDView &operator+=(const T val) { return elemenwise(val, std::plus()); } + NDView &operator-=(const T val) { return elemenwise(val, std::minus()); } + NDView &operator*=(const T val) { return elemenwise(val, std::multiplies()); } + NDView &operator/=(const T val) { return elemenwise(val, std::divides()); } + + NDView &operator/=(const NDView &other) { return elemenwise(other, std::divides()); } + + NDView &operator=(const T val) { + for (auto it = begin(); it != end(); ++it) + *it = val; + return *this; + } + + NDView &operator=(const NDView &other) { + if (this == &other) + return *this; + shape_ = other.shape_; + strides_ = other.strides_; + size_ = other.size_; + buffer_ = other.buffer_; + return *this; + } + + NDView &operator=(NDView &&other) noexcept { + if (this == &other) + return *this; + shape_ = std::move(other.shape_); + strides_ = std::move(other.strides_); + size_ = other.size_; + buffer_ = other.buffer_; + other.buffer_ = nullptr; + return *this; + } + + auto &shape() { return shape_; } + auto shape(int64_t i) const { return shape_[i]; } + + T *data() { return buffer_; } + void print_all() const; + + private: + T *buffer_{nullptr}; + std::array strides_{}; + std::array shape_{}; + uint64_t size_{}; + + template NDView &elemenwise(T val, BinaryOperation op) { + for (uint64_t i = 0; i != size_; ++i) { + buffer_[i] = op(buffer_[i], val); + } + return *this; + } + template NDView &elemenwise(const NDView &other, BinaryOperation op) { + for (uint64_t i = 0; i != size_; ++i) { + buffer_[i] = op(buffer_[i], other.buffer_[i]); + } + return *this; + } +}; +template void NDView::print_all() const { + for (auto row = 0; row < shape_[0]; ++row) { + for (auto col = 0; col < shape_[1]; ++col) { + std::cout << std::setw(3); + std::cout << (*this)(row, col) << " "; + } + std::cout << "\n"; + } +} + +} // namespace aare \ No newline at end of file diff --git a/include/aare/defs.hpp b/include/aare/defs.hpp new file mode 100644 index 0000000..1db17f2 --- /dev/null +++ b/include/aare/defs.hpp @@ -0,0 +1,156 @@ +#pragma once + +#include "aare/Dtype.hpp" +// #include "aare/utils/logger.hpp" + +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +/** + * @brief LOCATION macro to get the current location in the code + */ +#define LOCATION std::string(__FILE__) + std::string(":") + std::to_string(__LINE__) + ":" + std::string(__func__) + ":" + + +namespace aare { + +class Cluster { + public: + int cluster_sizeX; + int cluster_sizeY; + int16_t x; + int16_t y; + Dtype dt; + + private: + std::byte *m_data; + + public: + Cluster(int cluster_sizeX_, int cluster_sizeY_, Dtype dt_ = Dtype(typeid(int32_t))) + : cluster_sizeX(cluster_sizeX_), cluster_sizeY(cluster_sizeY_), dt(dt_) { + m_data = new std::byte[cluster_sizeX * cluster_sizeY * dt.bytes()]{}; + } + Cluster() : Cluster(3, 3) {} + Cluster(const Cluster &other) : Cluster(other.cluster_sizeX, other.cluster_sizeY, other.dt) { + if (this == &other) + return; + x = other.x; + y = other.y; + memcpy(m_data, other.m_data, other.bytes()); + } + Cluster &operator=(const Cluster &other) { + if (this == &other) + return *this; + this->~Cluster(); + new (this) Cluster(other); + return *this; + } + Cluster(Cluster &&other) noexcept + : cluster_sizeX(other.cluster_sizeX), cluster_sizeY(other.cluster_sizeY), x(other.x), y(other.y), dt(other.dt), + m_data(other.m_data) { + other.m_data = nullptr; + other.dt = Dtype(Dtype::TypeIndex::ERROR); + } + ~Cluster() { delete[] m_data; } + template T get(int idx) { + (sizeof(T) == dt.bytes()) ? 0 : throw std::invalid_argument("[ERROR] Type size mismatch"); + return *reinterpret_cast(m_data + idx * dt.bytes()); + } + template auto set(int idx, T val) { + (sizeof(T) == dt.bytes()) ? 0 : throw std::invalid_argument("[ERROR] Type size mismatch"); + return memcpy(m_data + idx * dt.bytes(), &val, (size_t)dt.bytes()); + } + // auto x() const { return x; } + // auto y() const { return y; } + // auto x(int16_t x_) { return x = x_; } + // auto y(int16_t y_) { return y = y_; } + + template std::string to_string() const { + (sizeof(T) == dt.bytes()) ? 0 : throw std::invalid_argument("[ERROR] Type size mismatch"); + std::string s = "x: " + std::to_string(x) + " y: " + std::to_string(y) + "\nm_data: ["; + for (int i = 0; i < cluster_sizeX * cluster_sizeY; i++) { + s += std::to_string(*reinterpret_cast(m_data + i * dt.bytes())) + " "; + } + s += "]"; + return s; + } + /** + * @brief size of the cluster in bytes when saved to a file + */ + size_t size() const { return cluster_sizeX * cluster_sizeY ; } + size_t bytes() const { return cluster_sizeX * cluster_sizeY * dt.bytes(); } + auto begin() const { return m_data; } + auto end() const { return m_data + cluster_sizeX * cluster_sizeY * dt.bytes(); } + std::byte *data() { return m_data; } +}; + +/** + * @brief header contained in parts of frames + */ +struct sls_detector_header { + uint64_t frameNumber; + uint32_t expLength; + uint32_t packetNumber; + uint64_t bunchId; + uint64_t timestamp; + uint16_t modId; + uint16_t row; + uint16_t column; + uint16_t reserved; + uint32_t debug; + uint16_t roundRNumber; + uint8_t detType; + uint8_t version; + std::array packetMask; + std::string to_string() { + std::string packetMaskStr = "["; + for (auto &i : packetMask) { + packetMaskStr += std::to_string(i) + ", "; + } + packetMaskStr += "]"; + + return "frameNumber: " + std::to_string(frameNumber) + "\n" + "expLength: " + std::to_string(expLength) + "\n" + + "packetNumber: " + std::to_string(packetNumber) + "\n" + "bunchId: " + std::to_string(bunchId) + "\n" + + "timestamp: " + std::to_string(timestamp) + "\n" + "modId: " + std::to_string(modId) + "\n" + + "row: " + std::to_string(row) + "\n" + "column: " + std::to_string(column) + "\n" + + "reserved: " + std::to_string(reserved) + "\n" + "debug: " + std::to_string(debug) + "\n" + + "roundRNumber: " + std::to_string(roundRNumber) + "\n" + "detType: " + std::to_string(detType) + "\n" + + "version: " + std::to_string(version) + "\n" + "packetMask: " + packetMaskStr + "\n"; + } +}; + +template struct t_xy { + T row; + T col; + bool operator==(const t_xy &other) const { return row == other.row && col == other.col; } + bool operator!=(const t_xy &other) const { return !(*this == other); } + std::string to_string() const { return "{ x: " + std::to_string(row) + " y: " + std::to_string(col) + " }"; } +}; +using xy = t_xy; + +using dynamic_shape = std::vector; + +enum class DetectorType { Jungfrau, Eiger, Mythen3, Moench, ChipTestBoard, Unknown }; + +enum class TimingMode { Auto, Trigger }; + +template T StringTo(const std::string &arg) { return T(arg); } + +template std::string toString(T arg) { return T(arg); } + +template <> DetectorType StringTo(const std::string & /*name*/); +template <> std::string toString(DetectorType arg); + +template <> TimingMode StringTo(const std::string & /*mode*/); + +using DataTypeVariants = std::variant; + +} // namespace aare \ No newline at end of file diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt new file mode 100644 index 0000000..e14b87e --- /dev/null +++ b/src/CMakeLists.txt @@ -0,0 +1,33 @@ + + +set(SourceFiles + ${CMAKE_CURRENT_SOURCE_DIR}/defs.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/Dtype.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/Frame.cpp +) + + +add_library(aare_core STATIC ${SourceFiles}) +target_include_directories(aare_core PUBLIC ${CMAKE_SOURCE_DIR}/include) +target_link_libraries(aare_core PUBLIC fmt::fmt PRIVATE aare_compiler_flags ) + +if (AARE_PYTHON_BINDINGS) +set_property(TARGET aare_core PROPERTY POSITION_INDEPENDENT_CODE ON) +endif() + +if(AARE_TESTS) + set(TestSources + ${CMAKE_CURRENT_SOURCE_DIR}/defs.test.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/Dtype.test.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/Frame.test.cpp + # ${CMAKE_CURRENT_SOURCE_DIR}/test/ProducerConsumerQueue.test.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/NDArray.test.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/NDView.test.cpp + # ${CMAKE_CURRENT_SOURCE_DIR}/test/CircularFifo.test.cpp + # ${CMAKE_CURRENT_SOURCE_DIR}/test/wrappers.test.cpp + # ${CMAKE_CURRENT_SOURCE_DIR}/test/Transforms.test.cpp + + ) + target_sources(tests PRIVATE ${TestSources} ) + target_link_libraries(tests PRIVATE aare_core) +endif() \ No newline at end of file diff --git a/src/Dtype.cpp b/src/Dtype.cpp new file mode 100644 index 0000000..565d509 --- /dev/null +++ b/src/Dtype.cpp @@ -0,0 +1,191 @@ + +#include "aare/Dtype.hpp" +#include "aare/defs.hpp" + +#include + +namespace aare { + +/** + * @brief Construct a DType object from a type_info object + * @param t type_info object + * @throw runtime_error if the type is not supported + * @note supported types are: int8_t, uint8_t, int16_t, uint16_t, int32_t, uint32_t, int64_t, uint64_t, float, double + * @note the type_info object is obtained using typeid (e.g. typeid(int)) + */ +Dtype::Dtype(const std::type_info &t) { + if (t == typeid(int8_t)) + m_type = TypeIndex::INT8; + else if (t == typeid(uint8_t)) + m_type = TypeIndex::UINT8; + else if (t == typeid(int16_t)) + m_type = TypeIndex::INT16; + else if (t == typeid(uint16_t)) + m_type = TypeIndex::UINT16; + else if (t == typeid(int32_t)) + m_type = TypeIndex::INT32; + else if (t == typeid(uint32_t)) + m_type = TypeIndex::UINT32; + else if (t == typeid(int64_t)) // NOLINT + m_type = TypeIndex::INT64; + else if (t == typeid(uint64_t)) + m_type = TypeIndex::UINT64; + else if (t == typeid(float)) + m_type = TypeIndex::FLOAT; + else if (t == typeid(double)) + m_type = TypeIndex::DOUBLE; + else + throw std::runtime_error("Could not construct data type. Type not supported."); +} + +/** + * @brief Get the bitdepth of the data type + * @return bitdepth + */ +uint8_t Dtype::bitdepth() const { + switch (m_type) { + case TypeIndex::INT8: + case TypeIndex::UINT8: + return 8; + case TypeIndex::INT16: + case TypeIndex::UINT16: + return 16; + case TypeIndex::INT32: + case TypeIndex::UINT32: + return 32; + case TypeIndex::INT64: + case TypeIndex::UINT64: + return 64; + case TypeIndex::FLOAT: + return 32; + case TypeIndex::DOUBLE: + return 64; + case TypeIndex::NONE: + return 0; + default: + throw std::runtime_error(LOCATION + "Could not get bitdepth. Type not supported."); + } +} + +/** + * @brief Get the number of bytes of the data type + */ +size_t Dtype::bytes() const { return bitdepth() / 8; } + +/** + * @brief Construct a DType object from a TypeIndex + * @param ti TypeIndex + * + */ +Dtype::Dtype(Dtype::TypeIndex ti) : m_type(ti) {} + +/** + * @brief Construct a DType object from a string + * @param sv string_view + * @throw runtime_error if the type is not supported + * @note example strings: ""); pos != std::string_view::npos) { + const auto endianess = [](const char c) { + if (c == '<') + return endian::little; + return endian::big; + }(sv[pos]); + if (endianess != endian::native) { + throw std::runtime_error("Non native endianess not supported"); + } + } + + // we are done with the endianess so we can remove the prefix + sv.remove_prefix(std::min(sv.find_first_not_of("<>"), sv.size())); + + if (sv == "i1") + m_type = TypeIndex::INT8; + else if (sv == "u1") + m_type = TypeIndex::UINT8; + else if (sv == "i2") + m_type = TypeIndex::INT16; + else if (sv == "u2") + m_type = TypeIndex::UINT16; + else if (sv == "i4") + m_type = TypeIndex::INT32; + else if (sv == "u4") + m_type = TypeIndex::UINT32; + else if (sv == "i8") + m_type = TypeIndex::INT64; + else if (sv == "u8") + m_type = TypeIndex::UINT64; + else if (sv == "f4") + m_type = TypeIndex::FLOAT; + else if (sv == "f8") + m_type = TypeIndex::DOUBLE; + else + throw std::runtime_error("Cannot construct data type from string."); +} + +Dtype Dtype::from_bitdepth(uint8_t bitdepth) { + switch (bitdepth) { + case 8: + return Dtype(TypeIndex::UINT8); + case 16: + return Dtype(TypeIndex::UINT16); + case 32: + return Dtype(TypeIndex::UINT32); + case 64: + return Dtype(TypeIndex::UINT64); + default: + throw std::runtime_error("Could not construct data type from bitdepth."); + } +} +/** + * @brief Get the string representation of the data type + * @return string representation + */ +std::string Dtype::to_string() const { + + char ec{}; + if (endian::native == endian::little) + ec = '<'; + else + ec = '>'; + + switch (m_type) { + case TypeIndex::INT8: + return fmt::format("{}i1", ec); + case TypeIndex::UINT8: + return fmt::format("{}u1", ec); + case TypeIndex::INT16: + return fmt::format("{}i2", ec); + case TypeIndex::UINT16: + return fmt::format("{}u2", ec); + case TypeIndex::INT32: + return fmt::format("{}i4", ec); + case TypeIndex::UINT32: + return fmt::format("{}u4", ec); + case TypeIndex::INT64: + return fmt::format("{}i8", ec); + case TypeIndex::UINT64: + return fmt::format("{}u8", ec); + case TypeIndex::FLOAT: + return "f4"; + case TypeIndex::DOUBLE: + return "f8"; + case TypeIndex::ERROR: + throw std::runtime_error("Could not get string representation. Type not supported."); + case TypeIndex::NONE: + throw std::runtime_error("Could not get string representation. Type not supported."); + } + return {}; +} + +bool Dtype::operator==(const Dtype &other) const noexcept { return m_type == other.m_type; } +bool Dtype::operator!=(const Dtype &other) const noexcept { return !(*this == other); } + +bool Dtype::operator==(const std::type_info &t) const { return Dtype(t) == *this; } +bool Dtype::operator!=(const std::type_info &t) const { return Dtype(t) != *this; } + +} // namespace aare diff --git a/src/Dtype.test.cpp b/src/Dtype.test.cpp new file mode 100644 index 0000000..b252267 --- /dev/null +++ b/src/Dtype.test.cpp @@ -0,0 +1,54 @@ + + +#include "aare/Dtype.hpp" +#include + +using aare::Dtype; +using aare::endian; + +TEST_CASE("Construct from typeid") { + REQUIRE(Dtype(typeid(int)) == typeid(int)); + REQUIRE(Dtype(typeid(int)) != typeid(double)); +} + +TEST_CASE("Construct from string") { + if (endian::native == endian::little) { + REQUIRE(Dtype("i1") == typeid(int8_t)); + REQUIRE(Dtype(">u1") == typeid(uint8_t)); + REQUIRE(Dtype(">i2") == typeid(int16_t)); + REQUIRE(Dtype(">u2") == typeid(uint16_t)); + REQUIRE(Dtype(">i4") == typeid(int)); + REQUIRE(Dtype(">u4") == typeid(unsigned)); + REQUIRE(Dtype(">i4") == typeid(int32_t)); + // REQUIRE(Dtype(">i8") == typeid(long)); + REQUIRE(Dtype(">i8") == typeid(int64_t)); + REQUIRE(Dtype(">u4") == typeid(uint32_t)); + REQUIRE(Dtype(">u8") == typeid(uint64_t)); + REQUIRE(Dtype("f4") == typeid(float)); + REQUIRE(Dtype("f8") == typeid(double)); + } +} + +TEST_CASE("Construct from string with endianess") { + // TODO! handle big endian system in test! + REQUIRE(Dtype("i4") == typeid(int32_t)); +} + +TEST_CASE("Convert to string") { REQUIRE(Dtype(typeid(int)).to_string() == " +#include +#include +#include + +namespace aare { + +/** + * @brief Construct a new Frame + * @param bytes pointer to the data to be copied into the frame + * @param rows number of rows + * @param cols number of columns + * @param bitdepth bitdepth of the pixels + */ +Frame::Frame(const std::byte *bytes, uint32_t rows, uint32_t cols, Dtype dtype) + : m_rows(rows), m_cols(cols), m_dtype(dtype), m_data(new std::byte[rows * cols * m_dtype.bytes()]) { + + std::memcpy(m_data, bytes, rows * cols * m_dtype.bytes()); +} + +/** + * @brief Construct a new Frame + * @param rows number of rows + * @param cols number of columns + * @param bitdepth bitdepth of the pixels + * @note the data is initialized to zero + */ +Frame::Frame(uint32_t rows, uint32_t cols, Dtype dtype) + : m_rows(rows), m_cols(cols), m_dtype(dtype), m_data(new std::byte[rows * cols * dtype.bytes()]) { + + std::memset(m_data, 0, rows * cols * dtype.bytes()); +} + +uint32_t Frame::rows() const { return m_rows; } +uint32_t Frame::cols() const { return m_cols; } +size_t Frame::bitdepth() const { return m_dtype.bitdepth(); } +Dtype Frame::dtype() const { return m_dtype; } +uint64_t Frame::size() const { return m_rows * m_cols; } +size_t Frame::bytes() const { return m_rows * m_cols * m_dtype.bytes(); } +std::byte *Frame::data() const { return m_data; } + +/** + * @brief Get the pointer to the pixel at the given row and column + * @param row row index + * @param col column index + * @return pointer to the pixel + * @note the user should cast the pointer to the appropriate type + */ +std::byte *Frame::get(uint32_t row, uint32_t col) { + if ((row >= m_rows) || (col >= m_cols)) { + std::cerr << "Invalid row or column index" << '\n'; + return nullptr; + } + return m_data + (row * m_cols + col) * (m_dtype.bytes()); +} + +// Frame &Frame::operator=(const Frame &other) { +// if (this == &other) { +// return *this; +// } +// m_rows = other.rows(); +// m_cols = other.cols(); +// m_dtype = other.dtype(); +// m_data = new std::byte[m_rows * m_cols * m_dtype.bytes()]; +// if (m_data == nullptr) { +// throw std::bad_alloc(); +// } +// std::memcpy(m_data, other.m_data, m_rows * m_cols * m_dtype.bytes()); +// return *this; +// } +Frame &Frame::operator=(Frame &&other) noexcept { + if (this == &other) { + return *this; + } + m_rows = other.rows(); + m_cols = other.cols(); + m_dtype = other.dtype(); + if (m_data != nullptr) { + delete[] m_data; + } + m_data = other.m_data; + other.m_data = nullptr; + other.m_rows = other.m_cols = 0; + other.m_dtype = Dtype(Dtype::TypeIndex::ERROR); + return *this; +} +Frame::Frame(Frame &&other) noexcept + : m_rows(other.rows()), m_cols(other.cols()), m_dtype(other.dtype()), m_data(other.m_data) { + + other.m_data = nullptr; + other.m_rows = other.m_cols = 0; + other.m_dtype = Dtype(Dtype::TypeIndex::ERROR); +} +// Frame::Frame(const Frame &other) +// : m_rows(other.rows()), m_cols(other.cols()), m_dtype(other.dtype()), +// m_data(new std::byte[m_rows * m_cols * m_dtype.bytes()]) { + +// std::memcpy(m_data, other.m_data, m_rows * m_cols * m_dtype.bytes()); +// } + +Frame Frame::copy() const { + Frame frame(m_rows, m_cols, m_dtype); + std::memcpy(frame.m_data, m_data, m_rows * m_cols * m_dtype.bytes()); + return frame; +} + +Frame::~Frame() noexcept { delete[] m_data; } +} // namespace aare diff --git a/src/Frame.test.cpp b/src/Frame.test.cpp new file mode 100644 index 0000000..e8ce5d2 --- /dev/null +++ b/src/Frame.test.cpp @@ -0,0 +1,152 @@ +#include "aare/Frame.hpp" +#include "aare/Dtype.hpp" +#include + +using namespace aare; + +TEST_CASE("Construct a frame") { + size_t rows = 10; + size_t cols = 10; + size_t bitdepth = 8; + + Frame frame(rows, cols, Dtype::from_bitdepth(bitdepth)); + + REQUIRE(frame.rows() == rows); + REQUIRE(frame.cols() == cols); + REQUIRE(frame.bitdepth() == bitdepth); + REQUIRE(frame.bytes() == rows * cols * bitdepth / 8); + + // data should be initialized to 0 + for (size_t i = 0; i < rows; i++) { + for (size_t j = 0; j < cols; j++) { + uint8_t *data = (uint8_t *)frame.get(i, j); + REQUIRE(data != nullptr); + REQUIRE(*data == 0); + } + } +} + +TEST_CASE("Set a value in a 8 bit frame") { + size_t rows = 10; + size_t cols = 10; + size_t bitdepth = 8; + + Frame frame(rows, cols, Dtype::from_bitdepth(bitdepth)); + + // set a value + uint8_t value = 255; + frame.set(5, 7, value); + + // only the value we did set should be non-zero + for (size_t i = 0; i < rows; i++) { + for (size_t j = 0; j < cols; j++) { + uint8_t *data = (uint8_t *)frame.get(i, j); + REQUIRE(data != nullptr); + if (i == 5 && j == 7) { + REQUIRE(*data == value); + } else { + REQUIRE(*data == 0); + } + } + } +} + +TEST_CASE("Set a value in a 64 bit frame") { + size_t rows = 10; + size_t cols = 10; + size_t bitdepth = 64; + + Frame frame(rows, cols, Dtype::from_bitdepth(bitdepth)); + + // set a value + uint64_t value = 255; + frame.set(5, 7, value); + + // only the value we did set should be non-zero + for (size_t i = 0; i < rows; i++) { + for (size_t j = 0; j < cols; j++) { + uint64_t *data = (uint64_t *)frame.get(i, j); + REQUIRE(data != nullptr); + if (i == 5 && j == 7) { + REQUIRE(*data == value); + } else { + REQUIRE(*data == 0); + } + } + } +} + +TEST_CASE("Move construct a frame") { + size_t rows = 10; + size_t cols = 10; + size_t bitdepth = 8; + + Frame frame(rows, cols, Dtype::from_bitdepth(bitdepth)); + std::byte *data = frame.data(); + + Frame frame2(std::move(frame)); + + // state of the moved from object + REQUIRE(frame.rows() == 0); + REQUIRE(frame.cols() == 0); + REQUIRE(frame.dtype() == Dtype(Dtype::TypeIndex::ERROR)); + REQUIRE(frame.data() == nullptr); + + // state of the moved to object + REQUIRE(frame2.rows() == rows); + REQUIRE(frame2.cols() == cols); + REQUIRE(frame2.bitdepth() == bitdepth); + REQUIRE(frame2.bytes() == rows * cols * bitdepth / 8); + REQUIRE(frame2.data() == data); +} + +TEST_CASE("Move assign a frame") { + size_t rows = 10; + size_t cols = 10; + size_t bitdepth = 8; + + Frame frame(rows, cols, Dtype::from_bitdepth(bitdepth)); + std::byte *data = frame.data(); + + Frame frame2(5, 5, Dtype::from_bitdepth(16)); + + frame2 = std::move(frame); + + // state of the moved from object + REQUIRE(frame.rows() == 0); + REQUIRE(frame.cols() == 0); + REQUIRE(frame.dtype() == Dtype(Dtype::TypeIndex::ERROR)); + REQUIRE(frame.data() == nullptr); + + // state of the moved to object + REQUIRE(frame2.rows() == rows); + REQUIRE(frame2.cols() == cols); + REQUIRE(frame2.bitdepth() == bitdepth); + REQUIRE(frame2.bytes() == rows * cols * bitdepth / 8); + REQUIRE(frame2.data() == data); +} + +TEST_CASE("test explicit copy constructor") { + size_t rows = 10; + size_t cols = 10; + size_t bitdepth = 8; + + Frame frame(rows, cols, Dtype::from_bitdepth(bitdepth)); + std::byte *data = frame.data(); + + Frame frame2 = frame.copy(); + + // state of the original object + REQUIRE(frame.rows() == rows); + REQUIRE(frame.cols() == cols); + REQUIRE(frame.bitdepth() == bitdepth); + REQUIRE(frame.bytes() == rows * cols * bitdepth / 8); + REQUIRE(frame.data() == data); + + // state of the copied object + REQUIRE(frame2.rows() == rows); + REQUIRE(frame2.cols() == cols); + REQUIRE(frame2.bitdepth() == bitdepth); + REQUIRE(frame2.bytes() == rows * cols * bitdepth / 8); + REQUIRE(frame2.data() != data); +} \ No newline at end of file diff --git a/src/NDArray.test.cpp b/src/NDArray.test.cpp new file mode 100644 index 0000000..97aafa0 --- /dev/null +++ b/src/NDArray.test.cpp @@ -0,0 +1,377 @@ +#include "aare/NDArray.hpp" +#include +#include + +using aare::NDArray; +using aare::NDView; +using aare::Shape; + +TEST_CASE("Initial size is zero if no size is specified") { + NDArray a; + REQUIRE(a.size() == 0); + REQUIRE(a.shape() == Shape<2>{0, 0}); +} + +TEST_CASE("Construct from a DataSpan") { + std::vector some_data(9, 42); + NDView view(some_data.data(), Shape<2>{3, 3}); + + NDArray image(view); + + REQUIRE(image.shape() == view.shape()); + REQUIRE(image.size() == view.size()); + REQUIRE(image.data() != view.data()); + + for (uint32_t i = 0; i < image.size(); ++i) { + REQUIRE(image(i) == view(i)); + } + + // Changing the image doesn't change the view + image = 43; + for (uint32_t i = 0; i < image.size(); ++i) { + REQUIRE(image(i) != view(i)); + } +} + +TEST_CASE("1D image") { + std::array shape{{20}}; + NDArray img(shape, 3); + REQUIRE(img.size() == 20); + REQUIRE(img(5) == 3); +} + +TEST_CASE("Accessing a const object") { + const NDArray img({3, 4, 5}, 0); + REQUIRE(img(1, 1, 1) == 0); + REQUIRE(img.size() == 3 * 4 * 5); + REQUIRE(img.shape() == Shape<3>{3, 4, 5}); + REQUIRE(img.shape(0) == 3); + REQUIRE(img.shape(1) == 4); + REQUIRE(img.shape(2) == 5); +} + +TEST_CASE("Indexing of a 2D image") { + std::array shape{{3, 7}}; + NDArray img(shape, 5); + for (uint32_t i = 0; i != img.size(); ++i) { + REQUIRE(img(i) == 5); + } + + for (uint32_t i = 0; i != img.size(); ++i) { + img(i) = i; + } + REQUIRE(img(0, 0) == 0); + REQUIRE(img(0, 1) == 1); + REQUIRE(img(1, 0) == 7); +} + +TEST_CASE("Indexing of a 3D image") { + NDArray img{{{3, 4, 2}}, 5.0f}; + for (uint32_t i = 0; i != img.size(); ++i) { + REQUIRE(img(i) == 5.0f); + } + + // Double check general properties + REQUIRE(img.size() == 3 * 4 * 2); + + for (uint32_t i = 0; i != img.size(); ++i) { + img(i) = float(i); + } + REQUIRE(img(0, 0, 0) == 0); + REQUIRE(img(0, 0, 1) == 1); + REQUIRE(img(0, 1, 1) == 3); + REQUIRE(img(1, 2, 0) == 12); + REQUIRE(img(2, 3, 1) == 23); +} + +TEST_CASE("Divide double by int") { + NDArray a{{5}, 5}; + NDArray b{{5}, 5}; + a /= b; + for (auto it : a) { + REQUIRE(it == 1.0); + } +} + +TEST_CASE("Elementwise multiplication of 3D image") { + std::array shape{3, 4, 2}; + NDArray a{shape}; + NDArray b{shape}; + for (uint32_t i = 0; i != a.size(); ++i) { + a(i) = i; + b(i) = i; + } + auto c = a * b; + REQUIRE(c(0, 0, 0) == 0 * 0); + REQUIRE(c(0, 0, 1) == 1 * 1); + REQUIRE(c(0, 1, 1) == 3 * 3); + REQUIRE(c(1, 2, 0) == 12 * 12); + REQUIRE(c(2, 3, 1) == 23 * 23); +} + +TEST_CASE("Compare two images") { + NDArray a; + NDArray b; + CHECK((a == b)); + + a = NDArray{{5, 10}, 0}; + CHECK((a != b)); + + b = NDArray{{5, 10}, 0}; + CHECK((a == b)); + + b(3, 3) = 7; + CHECK((a != b)); +} + +TEST_CASE("Size and shape matches") { + int64_t w = 15; + int64_t h = 75; + std::array shape{w, h}; + NDArray a{shape}; + REQUIRE(a.size() == static_cast(w * h)); + REQUIRE(a.shape() == shape); +} + +TEST_CASE("Initial value matches for all elements") { + double v = 4.35; + NDArray a{{5, 5}, v}; + for (uint32_t i = 0; i < a.size(); ++i) { + REQUIRE(a(i) == v); + } +} + +TEST_CASE("Data layout of 3D image, fast index last") { + NDArray a{{3, 3, 3}, 0}; + REQUIRE(a.size() == 27); + int *ptr = a.data(); + + for (int i = 0; i < 9; ++i) { + *ptr++ = 10 + i; + REQUIRE(a(0, 0, i) == 10 + i); + REQUIRE(a(i) == 10 + i); + } +} + +TEST_CASE("Bitwise and on data") { + + NDArray a({3}, 0); + uint16_t mask = 0x3FF; + a(0) = 16684; + a(1) = 33068; + a(2) = 52608; + + a &= mask; + + REQUIRE(a(0) == 300); + REQUIRE(a(1) == 300); + REQUIRE(a(2) == 384); +} + +// TEST_CASE("Benchmarks") +// { +// NDArray img; +// std::array shape{ 512, 1024 }; +// BENCHMARK("Allocate 500k double image") +// { +// NDArrayim{ shape }; +// } +// BENCHMARK("Allocate 500k double image with initial value") +// { +// NDArrayim{ shape, 3.14 }; +// } + +// NDArray a{ shape, 1.2 }; +// NDArray b{ shape, 53. }; +// auto c = a + b; +// c = a * b; +// BENCHMARK("Multiply two images") +// { +// c = a * b; +// } +// BENCHMARK("Divide two images") +// { +// c = a / b; +// } +// BENCHMARK("Add two images") +// { +// c = a + b; +// } +// BENCHMARK("Subtract two images") +// { +// c = a - b; +// } +// } + +TEST_CASE("Elementwise operatios on images") { + std::array shape{5, 5}; + double a_val = 3.0; + double b_val = 8.0; + + SECTION("Add two images") { + NDArray A(shape, a_val); + NDArray B(shape, b_val); + + auto C = A + B; + + // Value of C matches + for (uint32_t i = 0; i < C.size(); ++i) { + REQUIRE(C(i) == a_val + b_val); + } + + // Value of A is not changed + for (uint32_t i = 0; i < A.size(); ++i) { + REQUIRE(A(i) == a_val); + } + + // Value of B is not changed + for (uint32_t i = 0; i < B.size(); ++i) { + REQUIRE(B(i) == b_val); + } + + // A, B and C referes to different data + REQUIRE(A.data() != B.data()); + REQUIRE(B.data() != C.data()); + } + SECTION("Subtract two images") { + NDArray A(shape, a_val); + NDArray B(shape, b_val); + auto C = A - B; + + // Value of C matches + for (uint32_t i = 0; i < C.size(); ++i) { + REQUIRE(C(i) == a_val - b_val); + } + + // Value of A is not changed + for (uint32_t i = 0; i < A.size(); ++i) { + REQUIRE(A(i) == a_val); + } + + // Value of B is not changed + for (uint32_t i = 0; i < B.size(); ++i) { + REQUIRE(B(i) == b_val); + } + + // A, B and C referes to different data + REQUIRE(A.data() != B.data()); + REQUIRE(B.data() != C.data()); + } + SECTION("Multiply two images") { + NDArray A(shape, a_val); + NDArray B(shape, b_val); + auto C = A * B; + + // Value of C matches + for (uint32_t i = 0; i < C.size(); ++i) { + REQUIRE(C(i) == a_val * b_val); + } + + // Value of A is not changed + for (uint32_t i = 0; i < A.size(); ++i) { + REQUIRE(A(i) == a_val); + } + + // Value of B is not changed + for (uint32_t i = 0; i < B.size(); ++i) { + REQUIRE(B(i) == b_val); + } + + // A, B and C referes to different data + REQUIRE(A.data() != B.data()); + REQUIRE(B.data() != C.data()); + } + SECTION("Divide two images") { + NDArray A(shape, a_val); + NDArray B(shape, b_val); + auto C = A / B; + + // Value of C matches + for (uint32_t i = 0; i < C.size(); ++i) { + REQUIRE(C(i) == a_val / b_val); + } + + // Value of A is not changed + for (uint32_t i = 0; i < A.size(); ++i) { + REQUIRE(A(i) == a_val); + } + + // Value of B is not changed + for (uint32_t i = 0; i < B.size(); ++i) { + REQUIRE(B(i) == b_val); + } + + // A, B and C referes to different data + REQUIRE(A.data() != B.data()); + REQUIRE(B.data() != C.data()); + } + + SECTION("subtract scalar") { + NDArray A(shape, a_val); + NDArray B(shape, b_val); + double v = 1.0; + auto C = A - v; + REQUIRE(C.data() != A.data()); + + // Value of C matches + for (uint32_t i = 0; i < C.size(); ++i) { + REQUIRE(C(i) == a_val - v); + } + + // Value of A is not changed + for (uint32_t i = 0; i < A.size(); ++i) { + REQUIRE(A(i) == a_val); + } + } + SECTION("add scalar") { + NDArray A(shape, a_val); + NDArray B(shape, b_val); + double v = 1.0; + auto C = A + v; + REQUIRE(C.data() != A.data()); + + // Value of C matches + for (uint32_t i = 0; i < C.size(); ++i) { + REQUIRE(C(i) == a_val + v); + } + + // Value of A is not changed + for (uint32_t i = 0; i < A.size(); ++i) { + REQUIRE(A(i) == a_val); + } + } + SECTION("divide with scalar") { + NDArray A(shape, a_val); + NDArray B(shape, b_val); + double v = 3.7; + auto C = A / v; + REQUIRE(C.data() != A.data()); + + // Value of C matches + for (uint32_t i = 0; i < C.size(); ++i) { + REQUIRE(C(i) == a_val / v); + } + + // Value of A is not changed + for (uint32_t i = 0; i < A.size(); ++i) { + REQUIRE(A(i) == a_val); + } + } + SECTION("multiply with scalar") { + NDArray A(shape, a_val); + NDArray B(shape, b_val); + double v = 3.7; + auto C = A / v; + REQUIRE(C.data() != A.data()); + + // Value of C matches + for (uint32_t i = 0; i < C.size(); ++i) { + REQUIRE(C(i) == a_val / v); + } + + // Value of A is not changed + for (uint32_t i = 0; i < A.size(); ++i) { + REQUIRE(A(i) == a_val); + } + } +} \ No newline at end of file diff --git a/src/NDView.test.cpp b/src/NDView.test.cpp new file mode 100644 index 0000000..3070de6 --- /dev/null +++ b/src/NDView.test.cpp @@ -0,0 +1,193 @@ +#include "aare/NDView.hpp" +#include + +#include +#include + +using aare::NDView; +using aare::Shape; + +TEST_CASE("Element reference 1D") { + std::vector vec; + for (int i = 0; i != 10; ++i) { + vec.push_back(i); + } + NDView data(vec.data(), Shape<1>{10}); + REQUIRE(vec.size() == static_cast(data.size())); + for (int i = 0; i != 10; ++i) { + REQUIRE(data(i) == vec[i]); + REQUIRE(data[i] == vec[i]); + } +} + +TEST_CASE("Element reference 2D") { + std::vector vec; + for (int i = 0; i != 12; ++i) { + vec.push_back(i); + } + + NDView data(vec.data(), Shape<2>{3, 4}); + REQUIRE(vec.size() == static_cast(data.size())); + int i = 0; + for (int row = 0; row != 3; ++row) { + for (int col = 0; col != 4; ++col) { + REQUIRE(data(row, col) == i); + REQUIRE(data[i] == vec[i]); + ++i; + } + } +} + +TEST_CASE("Element reference 3D") { + std::vector vec; + for (int i = 0; i != 24; ++i) { + vec.push_back(i); + } + NDView data(vec.data(), Shape<3>{2, 3, 4}); + REQUIRE(vec.size() == static_cast(data.size())); + int i = 0; + for (int frame = 0; frame != 2; ++frame) { + for (int row = 0; row != 3; ++row) { + for (int col = 0; col != 4; ++col) { + REQUIRE(data(frame, row, col) == i); + REQUIRE(data[i] == vec[i]); + ++i; + } + } + } +} + +TEST_CASE("Plus and miuns with single value") { + std::vector vec; + for (int i = 0; i != 12; ++i) { + vec.push_back(i); + } + NDView data(vec.data(), Shape<2>{3, 4}); + data += 5; + int i = 0; + for (int row = 0; row != 3; ++row) { + for (int col = 0; col != 4; ++col) { + REQUIRE(data(row, col) == i + 5); + ++i; + } + } + data -= 3; + i = 0; + for (int row = 0; row != 3; ++row) { + for (int col = 0; col != 4; ++col) { + REQUIRE(data(row, col) == i + 2); + ++i; + } + } +} + +TEST_CASE("Multiply and divide with single value") { + std::vector vec; + for (int i = 0; i != 12; ++i) { + vec.push_back(i); + } + NDView data(vec.data(), Shape<2>{3, 4}); + data *= 5; + int i = 0; + for (int row = 0; row != 3; ++row) { + for (int col = 0; col != 4; ++col) { + REQUIRE(data(row, col) == i * 5); + ++i; + } + } + data /= 3; + i = 0; + for (int row = 0; row != 3; ++row) { + for (int col = 0; col != 4; ++col) { + REQUIRE(data(row, col) == (i * 5) / 3); + ++i; + } + } +} + +TEST_CASE("elementwise assign") { + std::vector vec(25); + NDView data(vec.data(), Shape<2>{5, 5}); + + data = 3; + for (auto it : data) { + REQUIRE(it == 3); + } +} + +TEST_CASE("iterators") { + std::vector vec; + for (int i = 0; i != 12; ++i) { + vec.push_back(i); + } + NDView data(vec.data(), Shape<1>{12}); + int i = 0; + for (const auto item : data) { + REQUIRE(item == vec[i]); + ++i; + } + REQUIRE(i == 12); + + for (auto ptr = data.begin(); ptr != data.end(); ++ptr) { + *ptr += 1; + } + for (auto &item : data) { + ++item; + } + + i = 0; + for (const auto item : data) { + REQUIRE(item == i + 2); + ++i; + } +} + +// TEST_CASE("shape from vector") { +// std::vector vec; +// for (int i = 0; i != 12; ++i) { +// vec.push_back(i); +// } +// std::vector shape{3, 4}; +// NDView data(vec.data(), shape); +// } + +TEST_CASE("divide with another span") { + std::vector vec0{9, 12, 3}; + std::vector vec1{3, 2, 1}; + std::vector result{3, 6, 3}; + + NDView data0(vec0.data(), Shape<1>{static_cast(vec0.size())}); + NDView data1(vec1.data(), Shape<1>{static_cast(vec1.size())}); + + data0 /= data1; + + for (size_t i = 0; i != vec0.size(); ++i) { + REQUIRE(data0[i] == result[i]); + } +} + +TEST_CASE("Retrieve shape") { + std::vector vec; + for (int i = 0; i != 12; ++i) { + vec.push_back(i); + } + NDView data(vec.data(), Shape<2>{3, 4}); + REQUIRE(data.shape()[0] == 3); + REQUIRE(data.shape()[1] == 4); +} + +TEST_CASE("compare two views") { + std::vector vec1; + for (int i = 0; i != 12; ++i) { + vec1.push_back(i); + } + NDView view1(vec1.data(), Shape<2>{3, 4}); + + std::vector vec2; + for (int i = 0; i != 12; ++i) { + vec2.push_back(i); + } + NDView view2(vec2.data(), Shape<2>{3, 4}); + + REQUIRE((view1 == view2)); +} \ No newline at end of file diff --git a/src/defs.cpp b/src/defs.cpp new file mode 100644 index 0000000..f3cf9d9 --- /dev/null +++ b/src/defs.cpp @@ -0,0 +1,65 @@ +#include "aare/defs.hpp" +#include +#include + +namespace aare { + +/** + * @brief Convert a DetectorType to a string + * @param type DetectorType + * @return string representation of the DetectorType + */ +template <> std::string toString(DetectorType arg) { + switch (arg) { + case DetectorType::Jungfrau: + return "Jungfrau"; + case DetectorType::Eiger: + return "Eiger"; + case DetectorType::Mythen3: + return "Mythen3"; + case DetectorType::Moench: + return "Moench"; + case DetectorType::ChipTestBoard: + return "ChipTestBoard"; + default: + return "Unknown"; + } +} + +/** + * @brief Convert a string to a DetectorType + * @param name string representation of the DetectorType + * @return DetectorType + * @throw runtime_error if the string does not match any DetectorType + */ +template <> DetectorType StringTo(const std::string &arg) { + if (arg == "Jungfrau") + return DetectorType::Jungfrau; + if (arg == "Eiger") + return DetectorType::Eiger; + if (arg == "Mythen3") + return DetectorType::Mythen3; + if (arg == "Moench") + return DetectorType::Moench; + if (arg == "ChipTestBoard") + return DetectorType::ChipTestBoard; + throw std::runtime_error("Could not decode dector from: \"" + arg + "\""); +} + +/** + * @brief Convert a string to a TimingMode + * @param mode string representation of the TimingMode + * @return TimingMode + * @throw runtime_error if the string does not match any TimingMode + */ +template <> TimingMode StringTo(const std::string &arg) { + if (arg == "auto") + return TimingMode::Auto; + if (arg == "trigger") + return TimingMode::Trigger; + throw std::runtime_error("Could not decode timing mode from: \"" + arg + "\""); +} + +// template <> TimingMode StringTo(std::string mode); + +} // namespace aare \ No newline at end of file diff --git a/src/defs.test.cpp b/src/defs.test.cpp new file mode 100644 index 0000000..7475fe6 --- /dev/null +++ b/src/defs.test.cpp @@ -0,0 +1,42 @@ +#include "aare/defs.hpp" +// #include "aare/utils/floats.hpp" + +#include +#include +TEST_CASE("Enum to string conversion") { + // By the way I don't think the enum string conversions should be in the defs.hpp file + // but let's use this to show a test + REQUIRE(toString(aare::DetectorType::Jungfrau) == "Jungfrau"); +} + +TEST_CASE("Cluster creation") { + aare::Cluster c(13, 15); + REQUIRE(c.cluster_sizeX == 13); + REQUIRE(c.cluster_sizeY == 15); + REQUIRE(c.dt == aare::Dtype(typeid(int32_t))); + REQUIRE(c.data() != nullptr); + + aare::Cluster c2(c); + REQUIRE(c2.cluster_sizeX == 13); + REQUIRE(c2.cluster_sizeY == 15); + REQUIRE(c2.dt == aare::Dtype(typeid(int32_t))); + REQUIRE(c2.data() != nullptr); +} + +// TEST_CASE("cluster set and get data") { + +// aare::Cluster c2(33, 44, aare::Dtype(typeid(double))); +// REQUIRE(c2.cluster_sizeX == 33); +// REQUIRE(c2.cluster_sizeY == 44); +// REQUIRE(c2.dt == aare::Dtype::DOUBLE); +// double v = 3.14; +// c2.set(0, v); +// double v2 = c2.get(0); +// REQUIRE(aare::compare_floats(v, v2)); + +// c2.set(33 * 44 - 1, 123.11); +// double v3 = c2.get(33 * 44 - 1); +// REQUIRE(aare::compare_floats(123.11, v3)); + +// REQUIRE_THROWS_AS(c2.set(0, 1), std::invalid_argument); // set int to double +// } \ No newline at end of file diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt new file mode 100644 index 0000000..bea9e32 --- /dev/null +++ b/tests/CMakeLists.txt @@ -0,0 +1,44 @@ + +if (AARE_FETCH_CATCH) + FetchContent_Declare( + Catch2 + GIT_SHALLOW TRUE + GIT_REPOSITORY https://github.com/catchorg/Catch2.git + GIT_TAG v3.5.3 + ) + FetchContent_MakeAvailable(Catch2) +else() + find_package(Catch2 3 REQUIRED) +endif() + + +list(APPEND CMAKE_MODULE_PATH ${Catch2_SOURCE_DIR}/extras) + +add_executable(tests test.cpp) +target_link_libraries(tests PRIVATE Catch2::Catch2WithMain) + +set_target_properties(tests PROPERTIES + RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR} + OUTPUT_NAME run_tests +) + +include(CTest) +include(Catch) +catch_discover_tests(tests) + +set(TestSources + ${CMAKE_CURRENT_SOURCE_DIR}/test.cpp + ) +target_sources(tests PRIVATE ${TestSources} ) + +#Work around to remove, this is not the way to do it =) +# target_include_directories(tests PRIVATE ${CMAKE_SOURCE_DIR}/include/common) +target_link_libraries(tests PRIVATE aare_core aare_compiler_flags) + + + +#configure a header to pass test file paths +get_filename_component(TEST_FILE_PATH ${PROJECT_SOURCE_DIR}/data ABSOLUTE) +configure_file(test_config.hpp.in test_config.hpp) +target_include_directories(tests PRIVATE ${CMAKE_CURRENT_BINARY_DIR}) + diff --git a/tests/test.cpp b/tests/test.cpp new file mode 100644 index 0000000..1a76f0a --- /dev/null +++ b/tests/test.cpp @@ -0,0 +1,21 @@ +#include "test_config.hpp" +#include +#include +#include +#include + +TEST_CASE("Test suite can find data assets") { + auto fpath = test_data_path() / "numpy" / "test_numpy_file.npy"; + REQUIRE(std::filesystem::exists(fpath)); +} + +TEST_CASE("Test suite can open data assets") { + auto fpath = test_data_path() / "numpy" / "test_numpy_file.npy"; + auto f = std::ifstream(fpath, std::ios::binary); + REQUIRE(f.is_open()); +} + +TEST_CASE("Test float32 and char8") { + REQUIRE(sizeof(float) == 4); + REQUIRE(CHAR_BIT == 8); +} \ No newline at end of file diff --git a/tests/test_config.hpp.in b/tests/test_config.hpp.in new file mode 100644 index 0000000..7669d49 --- /dev/null +++ b/tests/test_config.hpp.in @@ -0,0 +1,7 @@ +#pragma once +#include + +static constexpr auto test_data_path_str = "@TEST_FILE_PATH@"; +inline auto test_data_path() { + return std::filesystem::path(test_data_path_str); +} \ No newline at end of file From 54dd88f0704f80a9addc26e77e64ed2efceeb393 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Erik=20Fr=C3=B6jdh?= Date: Fri, 25 Oct 2024 13:54:36 +0200 Subject: [PATCH 02/87] added documentation --- CMakeLists.txt | 9 +- cmake/FindSphinx.cmake | 11 + docs/CMakeLists.txt | 58 + docs/Doxyfile.in | 2482 ++++++++++++++++++++++++++++++++++++++++ docs/conf.py.in | 66 ++ docs/src/Dtype.rst | 5 + docs/src/Frame.rst | 5 + docs/src/NDArray.rst | 5 + docs/src/NDView.rst | 5 + docs/src/index.rst | 15 + docs/static/extra.css | 4 + 11 files changed, 2664 insertions(+), 1 deletion(-) create mode 100644 cmake/FindSphinx.cmake create mode 100644 docs/CMakeLists.txt create mode 100644 docs/Doxyfile.in create mode 100644 docs/conf.py.in create mode 100644 docs/src/Dtype.rst create mode 100644 docs/src/Frame.rst create mode 100644 docs/src/NDArray.rst create mode 100644 docs/src/NDView.rst create mode 100644 docs/src/index.rst create mode 100644 docs/static/extra.css diff --git a/CMakeLists.txt b/CMakeLists.txt index f169113..db6501c 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -21,11 +21,16 @@ include(FetchContent) include(cmake/helpers.cmake) default_build_type("Release") + + +set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH}) + option(AARE_USE_WARNINGS "Enable warnings" ON) option(AARE_PYTHON_BINDINGS "Build python bindings" ON) option(AARE_TESTS "Build tests" ON) option(AARE_EXAMPLES "Build examples" ON) option(AARE_IN_GITHUB_ACTIONS "Running in Github Actions" OFF) +option(AARE_DOCS "Build documentation" OFF) option(AARE_FETCH_FMT "Use FetchContent to download fmt" ON) option(AARE_FETCH_PYBIND11 "Use FetchContent to download pybind11" ON) @@ -217,7 +222,9 @@ target_include_directories(aare INTERFACE # add_subdirectory(examples) - +if(AARE_DOCS) + add_subdirectory(docs) +endif() # custom target to run check formatting with clang-format diff --git a/cmake/FindSphinx.cmake b/cmake/FindSphinx.cmake new file mode 100644 index 0000000..f42276f --- /dev/null +++ b/cmake/FindSphinx.cmake @@ -0,0 +1,11 @@ +#Look for an executable called sphinx-build +find_program(SPHINX_EXECUTABLE + NAMES sphinx-build sphinx-build-3.6 + DOC "Path to sphinx-build executable") + +include(FindPackageHandleStandardArgs) + +#Handle standard arguments to find_package like REQUIRED and QUIET +find_package_handle_standard_args(Sphinx + "Failed to find sphinx-build executable" + SPHINX_EXECUTABLE) \ No newline at end of file diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt new file mode 100644 index 0000000..45aa42a --- /dev/null +++ b/docs/CMakeLists.txt @@ -0,0 +1,58 @@ +find_package(Doxygen REQUIRED) +find_package(Sphinx REQUIRED) + +#Doxygen +set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in) +set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile) +configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY) + +#Sphinx +set(SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/src) +set(SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR}) + +set(SPHINX_SOURCE_FILES + src/index.rst + src/NDArray.rst + src/NDView.rst + src/Frame.rst + src/Dtype.rst +) + +foreach(filename ${SPHINX_SOURCE_FILES}) +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${filename} + "${SPHINX_BUILD}/${filename}") +endforeach(filename ${SPHINX_SOURCE_FILES}) + +configure_file( + "${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in" + "${SPHINX_BUILD}/conf.py" + @ONLY +) + + +configure_file( + "${CMAKE_CURRENT_SOURCE_DIR}/static/extra.css" + "${SPHINX_BUILD}/static/css/extra.css" + @ONLY +) + +add_custom_target( + docs + COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT} + COMMAND ${SPHINX_EXECUTABLE} -a -b html + -Dbreathe_projects.aare=${CMAKE_CURRENT_BINARY_DIR}/xml + -c "${SPHINX_BUILD}" + ${SPHINX_BUILD}/src + ${SPHINX_BUILD}/html + COMMENT "Generating documentation with Sphinx" +) + +add_custom_target( + rst + COMMAND ${SPHINX_EXECUTABLE} -a -b html + -Dbreathe_projects.aare=${CMAKE_CURRENT_BINARY_DIR}/xml + -c "${SPHINX_BUILD}" + ${SPHINX_BUILD}/src + ${SPHINX_BUILD}/html + COMMENT "Generating documentation with Sphinx" +) \ No newline at end of file diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in new file mode 100644 index 0000000..1ce53c0 --- /dev/null +++ b/docs/Doxyfile.in @@ -0,0 +1,2482 @@ +# Doxyfile 1.8.14 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See +# https://www.gnu.org/software/libiconv/ for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = @CMAKE_PROJECT_NAME@ + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. This +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = @PROJECT_VERSION@ + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = @CMAKE_CURRENT_BINARY_DIR@ + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines (in the resulting output). You can put ^^ in the value part of an +# alias to insert a newline as if a physical newline was in the original file. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: +# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: +# Fortran. In the later case the parser tries to guess whether the code is fixed +# or free formatted code, this is the default for Fortran type files), VHDL. For +# instance to make doxygen treat .inc files as Fortran files (default is PHP), +# and .f files as C (default is Fortran), use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up +# to that level are automatically included in the table of contents, even if +# they do not have an id attribute. +# Note: This feature currently applies only to Markdown headings. +# Minimum value: 0, maximum value: 99, default value: 0. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +TOC_INCLUDE_HEADINGS = 0 + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = NO + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO, these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. +# The default value is: NO. + +WARN_AS_ERROR = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING +# Note: If this tag is empty the current directory is searched. + +INPUT = @PROJECT_SOURCE_DIR@ + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: https://www.gnu.org/software/libiconv/) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, +# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.java \ + *.ii \ + *.ixx \ + *.ipp \ + *.i++ \ + *.inl \ + *.idl \ + *.ddl \ + *.odl \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.cs \ + *.d \ + *.php \ + *.php4 \ + *.php5 \ + *.phtml \ + *.inc \ + *.m \ + *.markdown \ + *.md \ + *.mm \ + *.dox \ + *.py \ + *.pyw \ + *.f90 \ + *.f95 \ + *.f03 \ + *.f08 \ + *.f \ + *.for \ + *.tcl \ + *.vhd \ + *.vhdl \ + *.ucf \ + *.qsf + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = */docs/* */tests/* */python/* */manual */slsDetectorServers/* */libs/* */integrationTests *README* */slsDetectorGui/* */ctbGui/* */slsDetectorCalibration/* *TobiSchluter* + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see https://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = NO + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# https://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to YES can help to show when doxygen was last run and thus if the +# documentation is up to date. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = NO + +# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML +# documentation will contain a main index with vertical navigation menus that +# are dynamically created via Javascript. If disabled, the navigation index will +# consists of multiple levels of tabs that are statically embedded in every HTML +# page. Disable this option to support browsers that do not have Javascript, +# like the Qt help browser. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_MENUS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: https://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See https://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://doc.qt.io/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://doc.qt.io/qt-4.8/qthelpproject.html#virtual-folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://doc.qt.io/qt-4.8/qthelpproject.html#custom-filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://doc.qt.io/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANSPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# https://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = NO + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from https://www.mathjax.org before deployment. +# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/ + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /