WIP

include/aare/Dtype.hpp

@@ -0,0 +1,83 @@
+#pragma once
+#include <cstdint>
+#include <map>
+#include <string>
+#include <typeinfo>
+
+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<T>::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<int>(m_type)]); }
+    std::string numpy_descr() const { return std::string(1, NUMPY_FORMAT_DSC[static_cast<int>(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

include/aare/Frame.hpp

@@ -0,0 +1,76 @@
+#pragma once
+#include "aare/Dtype.hpp"
+#include "aare/NDArray.hpp"
+#include "aare/defs.hpp"
+
+#include <cstddef>
+#include <cstdint>
+#include <memory>
+#include <vector>
+
+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 <typename T> 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 <typename T> 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 <typename T> NDView<T, 2> view() {
+        std::array<int64_t, 2> shape = {static_cast<int64_t>(m_rows), static_cast<int64_t>(m_cols)};
+        T *data = reinterpret_cast<T *>(m_data);
+        return NDView<T, 2>(data, shape);
+    }
+
+    template <typename T> NDArray<T> image() { return NDArray<T>(this->view<T>()); }
+};
+
+} // namespace aare

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 <algorithm>
+#include <array>
+#include <cmath>
+#include <fmt/format.h>
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <numeric>
+
+namespace aare {
+
+template <typename T, int64_t Ndim = 2> class NDArray {
+  public:
+    NDArray() : shape_(), strides_(c_strides<Ndim>(shape_)), data_(nullptr){};
+
+    explicit NDArray(std::array<int64_t, Ndim> shape)
+        : shape_(shape), strides_(c_strides<Ndim>(shape_)),
+          size_(std::accumulate(shape_.begin(), shape_.end(), 1, std::multiplies<>())), data_(new T[size_]){};
+
+    NDArray(std::array<int64_t, Ndim> 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<T, Ndim> span) : NDArray(span.shape()) {
+        std::copy(span.begin(), span.end(), begin());
+        // fmt::print("NDArray(NDView<T, Ndim> span)\n");
+    }
+
+    // Move constructor
+    NDArray(NDArray &&other) noexcept
+        : shape_(other.shape_), strides_(c_strides<Ndim>(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<Ndim>(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 <typename V> NDArray &operator/=(const NDArray<V, Ndim> &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<bool, Ndim> 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 <typename... Ix> std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) {
+        return data_[element_offset(strides_, index...)];
+    }
+
+    template <typename... Ix> std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) const {
+        return data_[element_offset(strides_, index...)];
+    }
+
+    template <typename... Ix> std::enable_if_t<sizeof...(Ix) == Ndim, 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<std::byte *>(data_); }
+    uint64_t size() const { return size_; }
+    size_t total_bytes() const { return size_ * sizeof(T); }
+    std::array<int64_t, Ndim> shape() const noexcept { return shape_; }
+    int64_t shape(int64_t i) const noexcept { return shape_[i]; }
+    std::array<int64_t, Ndim> strides() const noexcept { return strides_; }
+    size_t bitdepth() const noexcept { return sizeof(T) * 8; }
+    std::array<int64_t, Ndim> byte_strides() const noexcept {
+        auto byte_strides = strides_;
+        for (auto &val : byte_strides)
+            val *= sizeof(T);
+        return byte_strides;
+        // return strides_;
+    }
+
+    NDView<T, Ndim> span() const { return NDView<T, Ndim>{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<int64_t, Ndim> shape_;
+    std::array<int64_t, Ndim> strides_;
+    uint64_t size_{};
+    T *data_;
+};
+
+// Move assign
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(NDArray<T, Ndim> &&other) noexcept {
+    if (this != &other) {
+        delete[] data_;
+        data_ = other.data_;
+        shape_ = other.shape_;
+        size_ = other.size_;
+        strides_ = other.strides_;
+        other.reset();
+    }
+    return *this;
+}
+
+template <typename T, int64_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator+(const NDArray &other) {
+    NDArray result(*this);
+    result += other;
+    return result;
+}
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator+=(const NDArray<T, Ndim> &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 <typename T, int64_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator-(const NDArray &other) {
+    NDArray result{*this};
+    result -= other;
+    return result;
+}
+
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator-=(const NDArray<T, Ndim> &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 <typename T, int64_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const NDArray &other) {
+    NDArray result = *this;
+    result *= other;
+    return result;
+}
+
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator*=(const NDArray<T, Ndim> &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 <typename T, int64_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator/(const NDArray &other) {
+    NDArray result = *this;
+    result /= other;
+    return result;
+}
+
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator&=(const T &mask) {
+    for (auto it = begin(); it != end(); ++it)
+        *it &= mask;
+    return *this;
+}
+
+// template <typename T, int64_t Ndim>
+// NDArray<T, Ndim>& NDArray<T, Ndim>::operator/=(const NDArray<T, Ndim>&
+// 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 <typename T, int64_t Ndim> NDArray<bool, Ndim> NDArray<T, Ndim>::operator>(const NDArray &other) {
+    if (shape_ == other.shape_) {
+        NDArray<bool> 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 <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(const NDArray<T, Ndim> &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 <typename T, int64_t Ndim> bool NDArray<T, Ndim>::operator==(const NDArray<T, Ndim> &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 <typename T, int64_t Ndim> bool NDArray<T, Ndim>::operator!=(const NDArray<T, Ndim> &other) const {
+    return !((*this) == other);
+}
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator++() {
+    for (uint32_t i = 0; i < size_; ++i)
+        data_[i] += 1;
+    return *this;
+}
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(const T &value) {
+    std::fill_n(data_, size_, value);
+    return *this;
+}
+
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator+=(const T &value) {
+    for (uint32_t i = 0; i < size_; ++i)
+        data_[i] += value;
+    return *this;
+}
+
+template <typename T, int64_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator+(const T &value) {
+    NDArray result = *this;
+    result += value;
+    return result;
+}
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator-=(const T &value) {
+    for (uint32_t i = 0; i < size_; ++i)
+        data_[i] -= value;
+    return *this;
+}
+template <typename T, int64_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator-(const T &value) {
+    NDArray result = *this;
+    result -= value;
+    return result;
+}
+
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator/=(const T &value) {
+    for (uint32_t i = 0; i < size_; ++i)
+        data_[i] /= value;
+    return *this;
+}
+template <typename T, int64_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator/(const T &value) {
+    NDArray result = *this;
+    result /= value;
+    return result;
+}
+template <typename T, int64_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator*=(const T &value) {
+    for (uint32_t i = 0; i < size_; ++i)
+        data_[i] *= value;
+    return *this;
+}
+template <typename T, int64_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const T &value) {
+    NDArray result = *this;
+    result *= value;
+    return result;
+}
+template <typename T, int64_t Ndim> void NDArray<T, Ndim>::Print() {
+    if (shape_[0] < 20 && shape_[1] < 20)
+        Print_all();
+    else
+        Print_some();
+}
+template <typename T, int64_t Ndim> void NDArray<T, Ndim>::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 <typename T, int64_t Ndim> void NDArray<T, Ndim>::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 <typename T, int64_t Ndim> void save(NDArray<T, Ndim> &img, std::string &pathname) {
+    std::ofstream f;
+    f.open(pathname, std::ios::binary);
+    f.write(img.buffer(), img.size() * sizeof(T));
+    f.close();
+}
+
+template <typename T, int64_t Ndim>
+NDArray<T, Ndim> load(const std::string &pathname, std::array<int64_t, Ndim> shape) {
+    NDArray<T, Ndim> 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

include/aare/NDView.hpp

@@ -0,0 +1,159 @@
+#pragma once
+#include <algorithm>
+#include <array>
+#include <cassert>
+#include <cstdint>
+#include <functional>
+#include <iomanip>
+#include <iostream>
+#include <numeric>
+#include <stdexcept>
+#include <vector>
+namespace aare {
+
+template <int64_t Ndim> using Shape = std::array<int64_t, Ndim>;
+
+// TODO! fix mismatch between signed and unsigned
+template <int64_t Ndim> Shape<Ndim> make_shape(const std::vector<size_t> &shape) {
+    if (shape.size() != Ndim)
+        throw std::runtime_error("Shape size mismatch");
+    Shape<Ndim> arr;
+    std::copy_n(shape.begin(), Ndim, arr.begin());
+    return arr;
+}
+
+template <int64_t Dim = 0, typename Strides> int64_t element_offset(const Strides & /*unused*/) { return 0; }
+
+template <int64_t Dim = 0, typename Strides, typename... Ix>
+int64_t element_offset(const Strides &strides, int64_t i, Ix... index) {
+    return i * strides[Dim] + element_offset<Dim + 1>(strides, index...);
+}
+
+template <int64_t Ndim> std::array<int64_t, Ndim> c_strides(const std::array<int64_t, Ndim> &shape) {
+    std::array<int64_t, Ndim> 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 <int64_t Ndim> std::array<int64_t, Ndim> make_array(const std::vector<int64_t> &vec) {
+    assert(vec.size() == Ndim);
+    std::array<int64_t, Ndim> arr{};
+    std::copy_n(vec.begin(), Ndim, arr.begin());
+    return arr;
+}
+
+template <typename T, int64_t Ndim = 2> class NDView {
+  public:
+    NDView() = default;
+    ~NDView() = default;
+    NDView(const NDView &) = default;
+    NDView(NDView &&) = default;
+
+    NDView(T *buffer, std::array<int64_t, Ndim> shape)
+        : buffer_(buffer), strides_(c_strides<Ndim>(shape)), shape_(shape),
+          size_(std::accumulate(std::begin(shape), std::end(shape), 1, std::multiplies<>())) {}
+
+    // NDView(T *buffer, const std::vector<int64_t> &shape)
+    //     : buffer_(buffer), strides_(c_strides<Ndim>(make_array<Ndim>(shape))), shape_(make_array<Ndim>(shape)),
+    //       size_(std::accumulate(std::begin(shape), std::end(shape), 1, std::multiplies<>())) {}
+
+    template <typename... Ix> std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) {
+        return buffer_[element_offset(strides_, index...)];
+    }
+
+    template <typename... Ix> std::enable_if_t<sizeof...(Ix) == Ndim, 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<int64_t, Ndim> 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<T>()); }
+    NDView &operator-=(const T val) { return elemenwise(val, std::minus<T>()); }
+    NDView &operator*=(const T val) { return elemenwise(val, std::multiplies<T>()); }
+    NDView &operator/=(const T val) { return elemenwise(val, std::divides<T>()); }
+
+    NDView &operator/=(const NDView &other) { return elemenwise(other, std::divides<T>()); }
+
+    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<int64_t, Ndim> strides_{};
+    std::array<int64_t, Ndim> shape_{};
+    uint64_t size_{};
+
+    template <class BinaryOperation> NDView &elemenwise(T val, BinaryOperation op) {
+        for (uint64_t i = 0; i != size_; ++i) {
+            buffer_[i] = op(buffer_[i], val);
+        }
+        return *this;
+    }
+    template <class BinaryOperation> 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 <typename T, int64_t Ndim> void NDView<T, Ndim>::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

include/aare/defs.hpp

@@ -0,0 +1,156 @@
+#pragma once
+
+#include "aare/Dtype.hpp"
+// #include "aare/utils/logger.hpp"
+
+#include <array>
+#include <stdexcept>
+
+#include <cassert>
+#include <cstdint>
+#include <cstring>
+#include <string>
+#include <string_view>
+#include <variant>
+#include <vector>
+
+/**
+ * @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 <typename T> T get(int idx) {
+        (sizeof(T) == dt.bytes()) ? 0 : throw std::invalid_argument("[ERROR] Type size mismatch");
+        return *reinterpret_cast<T *>(m_data + idx * dt.bytes());
+    }
+    template <typename T> 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 <typename T> 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<T *>(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<uint8_t, 64> 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 <typename T> 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<uint32_t>;
+
+using dynamic_shape = std::vector<int64_t>;
+
+enum class DetectorType { Jungfrau, Eiger, Mythen3, Moench, ChipTestBoard, Unknown };
+
+enum class TimingMode { Auto, Trigger };
+
+template <class T> T StringTo(const std::string &arg) { return T(arg); }
+
+template <class T> 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<uint16_t, uint32_t>;
+
+} // namespace aare