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Merge pull request #52 from slsdetectorgroup/feature/formatting-in-cmake

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add formatting as target in cmake
This commit is contained in:
Bechir Braham 2024-04-04 17:25:45 +02:00 committed by GitHub
commit 818ad608d9
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21 changed files with 320 additions and 401 deletions
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6
.github/workflows/format.yml vendored
View File

@ -11,9 +11,13 @@ jobs:
# find all examples in build/examples and run them
run: |
pwd
find -name "*.cpp" -not -path "./build/*" | xargs -I {} -n 1 -P 10 clang-format {} -Werror --dry-run -style='file:.clang-format'
mkdir build
cd build
cmake ..
cmake --build . --target=check-format

19
CMakeLists.txt
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@ -164,3 +164,22 @@ add_subdirectory(examples)
if(AARE_PYTHON_BINDINGS)
add_subdirectory(python)
endif()
# 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
)

111
core/include/aare/CircularFifo.hpp
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@ -14,29 +14,27 @@ template <class ItemType> class CircularFifo {
uint32_t fifo_size;
folly::ProducerConsumerQueue<ItemType> free_slots;
folly::ProducerConsumerQueue<ItemType> filled_slots;
public:
CircularFifo() : CircularFifo(100){};
CircularFifo(uint32_t size)
: fifo_size(size), free_slots(size+1), filled_slots(size+1) {
CircularFifo(uint32_t size) : fifo_size(size), free_slots(size + 1), filled_slots(size + 1) {
// TODO! how do we deal with alignment for writing? alignas???
// Do we give the user a chance to provide memory locations?
// Do we give the user a chance to provide memory locations?
// Templated allocator?
for (size_t i = 0; i < fifo_size; ++i) {
free_slots.write(ItemType{});
}
}
bool next(){
//TODO! avoid default constructing ItemType
ItemType it;
if(!filled_slots.read(it))
return false;
if(!free_slots.write(std::move(it)))
return false;
return true;
bool next() {
// TODO! avoid default constructing ItemType
ItemType it;
if (!filled_slots.read(it))
return false;
if (!free_slots.write(std::move(it)))
return false;
return true;
}
~CircularFifo() {}
@ -47,66 +45,53 @@ template <class ItemType> class CircularFifo {
auto numFreeSlots() const noexcept { return free_slots.sizeGuess(); }
auto isFull() const noexcept { return filled_slots.isFull(); }
ItemType pop_free() {
ItemType v;
while (!free_slots.read(v))
;
return std::move(v);
// return v;
}
bool try_pop_free(ItemType& v){
return free_slots.read(v);
}
ItemType pop_value(std::chrono::nanoseconds wait,
std::atomic<bool> &stopped) {
ItemType v;
while (!filled_slots.read(v) && !stopped) {
std::this_thread::sleep_for(wait);
ItemType pop_free() {
ItemType v;
while (!free_slots.read(v))
;
return std::move(v);
// return v;
}
return std::move(v);
}
ItemType pop_value() {
ItemType v;
while (!filled_slots.read(v))
;
return std::move(v);
}
bool try_pop_free(ItemType &v) { return free_slots.read(v); }
ItemType* frontPtr(){
return filled_slots.frontPtr();
}
ItemType pop_value(std::chrono::nanoseconds wait, std::atomic<bool> &stopped) {
ItemType v;
while (!filled_slots.read(v) && !stopped) {
std::this_thread::sleep_for(wait);
}
return std::move(v);
}
// TODO! Add function to move item from filled to free to be used
// with the frontPtr function
ItemType pop_value() {
ItemType v;
while (!filled_slots.read(v))
;
return std::move(v);
}
ItemType *frontPtr() { return filled_slots.frontPtr(); }
template <class... Args>
void push_value(Args&&... recordArgs) {
while (!filled_slots.write(std::forward<Args>(recordArgs)...))
;
}
// TODO! Add function to move item from filled to free to be used
// with the frontPtr function
template <class... Args>
bool try_push_value(Args&&... recordArgs) {
return filled_slots.write(std::forward<Args>(recordArgs)...);
template <class... Args> void push_value(Args &&...recordArgs) {
while (!filled_slots.write(std::forward<Args>(recordArgs)...))
;
}
}
template <class... Args> bool try_push_value(Args &&...recordArgs) {
return filled_slots.write(std::forward<Args>(recordArgs)...);
}
template <class... Args>
void push_free(Args&&... recordArgs) {
while (!free_slots.write(std::forward<Args>(recordArgs)...))
;
}
template <class... Args>
bool try_push_free(Args&&... recordArgs) {
return free_slots.write(std::forward<Args>(recordArgs)...);
}
template <class... Args> void push_free(Args &&...recordArgs) {
while (!free_slots.write(std::forward<Args>(recordArgs)...))
;
}
template <class... Args> bool try_push_free(Args &&...recordArgs) {
return free_slots.write(std::forward<Args>(recordArgs)...);
}
};
} // namespace aare

2
core/include/aare/DType.hpp
View File

@ -19,7 +19,7 @@ enum class endian {
};
class DType {
//TODO! support for non native endianess?
// TODO! support for non native endianess?
static_assert(sizeof(long) == sizeof(int64_t), "long should be 64bits");
public:

24
core/include/aare/Frame.hpp
View File

@ -4,7 +4,6 @@
#include <cstddef>
#include <cstdint>
#include <memory>
#include <vector>
#include <sys/types.h>
#include <vector>
@ -27,15 +26,13 @@ class Frame {
Frame(std::byte *fp, ssize_t rows, ssize_t cols, ssize_t m_bitdepth);
std::byte *get(int row, int col);
//TODO! can we, or even want to remove the template?
template <typename T>
void set(int row, int col, T data) {
assert(sizeof(T) == m_bitdepth/8);
// TODO! can we, or even want to remove the template?
template <typename T> void set(int row, int col, T data) {
assert(sizeof(T) == m_bitdepth / 8);
if (row < 0 || row >= m_rows || col < 0 || col >= m_cols) {
throw std::out_of_range("Invalid row or column index");
}
std::memcpy(m_data+(row*m_cols + col)*(m_bitdepth/8), &data, m_bitdepth/8);
std::memcpy(m_data + (row * m_cols + col) * (m_bitdepth / 8), &data, m_bitdepth / 8);
}
ssize_t rows() const { return m_rows; }
@ -43,7 +40,7 @@ class Frame {
ssize_t bitdepth() const { return m_bitdepth; }
ssize_t size() const { return m_rows * m_cols * m_bitdepth / 8; }
std::byte *data() const { return m_data; }
Frame &operator=(Frame &other) {
m_rows = other.rows();
m_cols = other.cols();
@ -62,20 +59,15 @@ class Frame {
other.m_rows = other.m_cols = other.m_bitdepth = 0;
}
template <typename T>
NDView<T> view() {
template <typename T> NDView<T> view() {
std::vector<ssize_t> shape = {m_rows, m_cols};
T* data = reinterpret_cast<T *>(m_data);
T *data = reinterpret_cast<T *>(m_data);
return NDView<T>(data, shape);
}
template <typename T>
NDArray<T> image() {
return NDArray<T>(this->view<T>());
}
template <typename T> NDArray<T> image() { return NDArray<T>(this->view<T>()); }
~Frame() { delete[] m_data; }
};
} // namespace aare

123
core/include/aare/NDArray.hpp
View File

@ -22,31 +22,24 @@ namespace aare {
template <typename T, ssize_t Ndim = 2> class NDArray {
public:
NDArray()
: shape_(), strides_(c_strides<Ndim>(shape_)), size_(0),
data_(nullptr){};
NDArray() : shape_(), strides_(c_strides<Ndim>(shape_)), size_(0), data_(nullptr){};
explicit NDArray(std::array<ssize_t, Ndim> shape)
: shape_(shape), strides_(c_strides<Ndim>(shape_)),
size_(std::accumulate(shape_.begin(), shape_.end(), 1,
std::multiplies<ssize_t>())),
data_(new T[size_]){};
size_(std::accumulate(shape_.begin(), shape_.end(), 1, std::multiplies<ssize_t>())), data_(new T[size_]){};
NDArray(std::array<ssize_t, Ndim> shape, T value) : NDArray(shape) {
this->operator=(value);
}
NDArray(std::array<ssize_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*/
NDArray(NDView<T, Ndim> span):NDArray(span.shape()){
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)
: shape_(other.shape_), strides_(c_strides<Ndim>(shape_)),
size_(other.size_), data_(nullptr) {
: shape_(other.shape_), strides_(c_strides<Ndim>(shape_)), size_(other.size_), data_(nullptr) {
data_ = other.data_;
other.reset();
// fmt::print("NDArray(NDArray &&other)\n");
@ -54,20 +47,17 @@ template <typename T, ssize_t Ndim = 2> class NDArray {
// Copy constructor
NDArray(const NDArray &other)
: shape_(other.shape_), strides_(c_strides<Ndim>(shape_)),
size_(other.size_), data_(new T[size_]) {
: 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_;
}
~NDArray() { delete[] data_; }
auto begin() { return data_; }
auto end() { return data_ + size_; }
using value_type = T;
using value_type = T;
NDArray &operator=(NDArray &&other); // Move assign
NDArray &operator=(const NDArray &other); // Copy assign
@ -80,8 +70,7 @@ template <typename T, ssize_t Ndim = 2> class NDArray {
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) {
template <typename V> NDArray &operator/=(const NDArray<V, Ndim> &other) {
// check shape
if (shape_ == other.shape()) {
for (int i = 0; i < size_; ++i) {
@ -118,21 +107,15 @@ template <typename T, ssize_t Ndim = 2> class NDArray {
NDArray &operator++(); // pre inc
template <typename... Ix>
typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type
operator()(Ix... index) {
template <typename... Ix> typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type operator()(Ix... index) {
return data_[element_offset(strides_, index...)];
}
template <typename... Ix>
typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type
operator()(Ix... index) const{
template <typename... Ix> typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type operator()(Ix... index) const {
return data_[element_offset(strides_, index...)];
}
template <typename... Ix>
typename std::enable_if<sizeof...(Ix) == Ndim, T>::type value(Ix... index) {
template <typename... Ix> typename std::enable_if<sizeof...(Ix) == Ndim, T>::type value(Ix... index) {
return data_[element_offset(strides_, index...)];
}
@ -142,7 +125,7 @@ template <typename T, ssize_t Ndim = 2> class NDArray {
T *data() { return data_; }
std::byte *buffer() { return reinterpret_cast<std::byte *>(data_); }
ssize_t size() const { return size_; }
size_t total_bytes() const {return size_*sizeof(T);}
size_t total_bytes() const { return size_ * sizeof(T); }
std::array<ssize_t, Ndim> shape() const noexcept { return shape_; }
ssize_t shape(ssize_t i) const noexcept { return shape_[i]; }
std::array<ssize_t, Ndim> strides() const noexcept { return strides_; }
@ -175,8 +158,7 @@ template <typename T, ssize_t Ndim = 2> class NDArray {
};
// Move assign
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(NDArray<T, Ndim> &&other) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(NDArray<T, Ndim> &&other) {
if (this != &other) {
delete[] data_;
data_ = other.data_;
@ -188,15 +170,12 @@ NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(NDArray<T, Ndim> &&other) {
return *this;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> NDArray<T, Ndim>::operator+(const NDArray &other) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator+(const NDArray &other) {
NDArray result(*this);
result += other;
return result;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &
NDArray<T, Ndim>::operator+=(const NDArray<T, Ndim> &other) {
template <typename T, ssize_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) {
@ -208,16 +187,13 @@ NDArray<T, Ndim>::operator+=(const NDArray<T, Ndim> &other) {
}
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> NDArray<T, Ndim>::operator-(const NDArray &other) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator-(const NDArray &other) {
NDArray result{*this};
result -= other;
return result;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &
NDArray<T, Ndim>::operator-=(const NDArray<T, Ndim> &other) {
template <typename T, ssize_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) {
@ -228,16 +204,13 @@ NDArray<T, Ndim>::operator-=(const NDArray<T, Ndim> &other) {
throw(std::runtime_error("Shape of ImageDatas must match"));
}
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const NDArray &other) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const NDArray &other) {
NDArray result = *this;
result *= other;
return result;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &
NDArray<T, Ndim>::operator*=(const NDArray<T, Ndim> &other) {
template <typename T, ssize_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) {
@ -249,15 +222,13 @@ NDArray<T, Ndim>::operator*=(const NDArray<T, Ndim> &other) {
}
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> NDArray<T, Ndim>::operator/(const NDArray &other) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator/(const NDArray &other) {
NDArray result = *this;
result /= other;
return result;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &NDArray<T, Ndim>::operator&=(const T &mask) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator&=(const T &mask) {
for (auto it = begin(); it != end(); ++it)
*it &= mask;
return *this;
@ -278,8 +249,7 @@ NDArray<T, Ndim> &NDArray<T, Ndim>::operator&=(const T &mask) {
// }
// }
template <typename T, ssize_t Ndim>
NDArray<bool, Ndim> NDArray<T, Ndim>::operator>(const NDArray &other) {
template <typename T, ssize_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) {
@ -291,9 +261,7 @@ NDArray<bool, Ndim> NDArray<T, Ndim>::operator>(const NDArray &other) {
}
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &
NDArray<T, Ndim>::operator=(const NDArray<T, Ndim> &other) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(const NDArray<T, Ndim> &other) {
if (this != &other) {
delete[] data_;
shape_ = other.shape_;
@ -305,8 +273,7 @@ NDArray<T, Ndim>::operator=(const NDArray<T, Ndim> &other) {
return *this;
}
template <typename T, ssize_t Ndim>
bool NDArray<T, Ndim>::operator==(const NDArray<T, Ndim> &other) const {
template <typename T, ssize_t Ndim> bool NDArray<T, Ndim>::operator==(const NDArray<T, Ndim> &other) const {
if (shape_ != other.shape_)
return false;
@ -317,68 +284,57 @@ bool NDArray<T, Ndim>::operator==(const NDArray<T, Ndim> &other) const {
return true;
}
template <typename T, ssize_t Ndim>
bool NDArray<T, Ndim>::operator!=(const NDArray<T, Ndim> &other) const {
template <typename T, ssize_t Ndim> bool NDArray<T, Ndim>::operator!=(const NDArray<T, Ndim> &other) const {
return !((*this) == other);
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &NDArray<T, Ndim>::operator++() {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator++() {
for (int i = 0; i < size_; ++i)
data_[i] += 1;
return *this;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator=(const T &value) {
std::fill_n(data_, size_, value);
return *this;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &NDArray<T, Ndim>::operator+=(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator+=(const T &value) {
for (int i = 0; i < size_; ++i)
data_[i] += value;
return *this;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> NDArray<T, Ndim>::operator+(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator+(const T &value) {
NDArray result = *this;
result += value;
return result;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &NDArray<T, Ndim>::operator-=(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator-=(const T &value) {
for (int i = 0; i < size_; ++i)
data_[i] -= value;
return *this;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> NDArray<T, Ndim>::operator-(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator-(const T &value) {
NDArray result = *this;
result -= value;
return result;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &NDArray<T, Ndim>::operator/=(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator/=(const T &value) {
for (int i = 0; i < size_; ++i)
data_[i] /= value;
return *this;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> NDArray<T, Ndim>::operator/(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator/(const T &value) {
NDArray result = *this;
result /= value;
return result;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> &NDArray<T, Ndim>::operator*=(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> &NDArray<T, Ndim>::operator*=(const T &value) {
for (int i = 0; i < size_; ++i)
data_[i] *= value;
return *this;
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const T &value) {
template <typename T, ssize_t Ndim> NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const T &value) {
NDArray result = *this;
result *= value;
return result;
@ -408,8 +364,7 @@ template <typename T, ssize_t Ndim> void NDArray<T, Ndim>::Print_some() {
}
}
template <typename T, ssize_t Ndim>
void save(NDArray<T, Ndim> &img, std::string pathname) {
template <typename T, ssize_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));
@ -417,8 +372,7 @@ void save(NDArray<T, Ndim> &img, std::string pathname) {
}
template <typename T, ssize_t Ndim>
NDArray<T, Ndim> load(const std::string &pathname,
std::array<ssize_t, Ndim> shape) {
NDArray<T, Ndim> load(const std::string &pathname, std::array<ssize_t, Ndim> shape) {
NDArray<T, Ndim> img{shape};
std::ifstream f;
f.open(pathname, std::ios::binary);
@ -427,5 +381,4 @@ NDArray<T, Ndim> load(const std::string &pathname,
return img;
}
} // namespace aare

14
core/include/aare/NDView.hpp
View File

@ -4,17 +4,16 @@
#include <cassert>
#include <cstdint>
#include <numeric>
#include <vector>
#include <stdexcept>
#include <vector>
namespace aare {
template <ssize_t Ndim> using Shape = std::array<ssize_t, Ndim>;
//TODO! fix mismatch between signed and unsigned
template <ssize_t Ndim>
Shape<Ndim> make_shape(const std::vector<size_t>& shape){
if(shape.size() != Ndim)
// TODO! fix mismatch between signed and unsigned
template <ssize_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());
@ -44,11 +43,11 @@ template <ssize_t Ndim> std::array<ssize_t, Ndim> make_array(const std::vector<s
return arr;
}
template <typename T, ssize_t Ndim=2> class NDView {
template <typename T, ssize_t Ndim = 2> class NDView {
public:
NDView(){};
NDView(T* buffer, std::array<ssize_t, Ndim> shape) {
NDView(T *buffer, std::array<ssize_t, Ndim> shape) {
buffer_ = buffer;
strides_ = c_strides<Ndim>(shape);
shape_ = shape;
@ -60,7 +59,6 @@ template <typename T, ssize_t Ndim=2> class NDView {
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<ssize_t>());
}
template <typename... Ix> typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type operator()(Ix... index) {

231
core/include/aare/ProducerConsumerQueue.hpp
View File

@ -31,158 +31,151 @@
#include <type_traits>
#include <utility>
constexpr std::size_t hardware_destructive_interference_size = 128;
constexpr std::size_t hardware_destructive_interference_size = 128;
namespace folly {
/*
* ProducerConsumerQueue is a one producer and one consumer queue
* without locks.
*/
template <class T>
struct ProducerConsumerQueue {
typedef T value_type;
template <class T> struct ProducerConsumerQueue {
typedef T value_type;
ProducerConsumerQueue(const ProducerConsumerQueue&) = delete;
ProducerConsumerQueue& operator=(const ProducerConsumerQueue&) = delete;
ProducerConsumerQueue(const ProducerConsumerQueue &) = delete;
ProducerConsumerQueue &operator=(const ProducerConsumerQueue &) = delete;
// size must be >= 2.
//
// Also, note that the number of usable slots in the queue at any
// given time is actually (size-1), so if you start with an empty queue,
// isFull() will return true after size-1 insertions.
explicit ProducerConsumerQueue(uint32_t size)
: size_(size),
records_(static_cast<T*>(std::malloc(sizeof(T) * size))),
readIndex_(0),
writeIndex_(0) {
assert(size >= 2);
if (!records_) {
throw std::bad_alloc();
}
}
~ProducerConsumerQueue() {
// We need to destruct anything that may still exist in our queue.
// (No real synchronization needed at destructor time: only one
// thread can be doing this.)
if (!std::is_trivially_destructible<T>::value) {
size_t readIndex = readIndex_;
size_t endIndex = writeIndex_;
while (readIndex != endIndex) {
records_[readIndex].~T();
if (++readIndex == size_) {
readIndex = 0;
// size must be >= 2.
//
// Also, note that the number of usable slots in the queue at any
// given time is actually (size-1), so if you start with an empty queue,
// isFull() will return true after size-1 insertions.
explicit ProducerConsumerQueue(uint32_t size)
: size_(size), records_(static_cast<T *>(std::malloc(sizeof(T) * size))), readIndex_(0), writeIndex_(0) {
assert(size >= 2);
if (!records_) {
throw std::bad_alloc();
}
}
}
std::free(records_);
}
~ProducerConsumerQueue() {
// We need to destruct anything that may still exist in our queue.
// (No real synchronization needed at destructor time: only one
// thread can be doing this.)
if (!std::is_trivially_destructible<T>::value) {
size_t readIndex = readIndex_;
size_t endIndex = writeIndex_;
while (readIndex != endIndex) {
records_[readIndex].~T();
if (++readIndex == size_) {
readIndex = 0;
}
}
}
template <class... Args>
bool write(Args&&... recordArgs) {
auto const currentWrite = writeIndex_.load(std::memory_order_relaxed);
auto nextRecord = currentWrite + 1;
if (nextRecord == size_) {
nextRecord = 0;
}
if (nextRecord != readIndex_.load(std::memory_order_acquire)) {
new (&records_[currentWrite]) T(std::forward<Args>(recordArgs)...);
writeIndex_.store(nextRecord, std::memory_order_release);
return true;
std::free(records_);
}
// queue is full
return false;
}
template <class... Args> bool write(Args &&...recordArgs) {
auto const currentWrite = writeIndex_.load(std::memory_order_relaxed);
auto nextRecord = currentWrite + 1;
if (nextRecord == size_) {
nextRecord = 0;
}
if (nextRecord != readIndex_.load(std::memory_order_acquire)) {
new (&records_[currentWrite]) T(std::forward<Args>(recordArgs)...);
writeIndex_.store(nextRecord, std::memory_order_release);
return true;
}
// move (or copy) the value at the front of the queue to given variable
bool read(T& record) {
auto const currentRead = readIndex_.load(std::memory_order_relaxed);
if (currentRead == writeIndex_.load(std::memory_order_acquire)) {
// queue is empty
return false;
// queue is full
return false;
}
auto nextRecord = currentRead + 1;
if (nextRecord == size_) {
nextRecord = 0;
// move (or copy) the value at the front of the queue to given variable
bool read(T &record) {
auto const currentRead = readIndex_.load(std::memory_order_relaxed);
if (currentRead == writeIndex_.load(std::memory_order_acquire)) {
// queue is empty
return false;
}
auto nextRecord = currentRead + 1;
if (nextRecord == size_) {
nextRecord = 0;
}
record = std::move(records_[currentRead]);
records_[currentRead].~T();
readIndex_.store(nextRecord, std::memory_order_release);
return true;
}
record = std::move(records_[currentRead]);
records_[currentRead].~T();
readIndex_.store(nextRecord, std::memory_order_release);
return true;
}
// pointer to the value at the front of the queue (for use in-place) or
// nullptr if empty.
T* frontPtr() {
auto const currentRead = readIndex_.load(std::memory_order_relaxed);
if (currentRead == writeIndex_.load(std::memory_order_acquire)) {
// queue is empty
return nullptr;
// pointer to the value at the front of the queue (for use in-place) or
// nullptr if empty.
T *frontPtr() {
auto const currentRead = readIndex_.load(std::memory_order_relaxed);
if (currentRead == writeIndex_.load(std::memory_order_acquire)) {
// queue is empty
return nullptr;
}
return &records_[currentRead];
}
return &records_[currentRead];
}
// queue must not be empty
void popFront() {
auto const currentRead = readIndex_.load(std::memory_order_relaxed);
assert(currentRead != writeIndex_.load(std::memory_order_acquire));
// queue must not be empty
void popFront() {
auto const currentRead = readIndex_.load(std::memory_order_relaxed);
assert(currentRead != writeIndex_.load(std::memory_order_acquire));
auto nextRecord = currentRead + 1;
if (nextRecord == size_) {
nextRecord = 0;
auto nextRecord = currentRead + 1;
if (nextRecord == size_) {
nextRecord = 0;
}
records_[currentRead].~T();
readIndex_.store(nextRecord, std::memory_order_release);
}
records_[currentRead].~T();
readIndex_.store(nextRecord, std::memory_order_release);
}
bool isEmpty() const {
return readIndex_.load(std::memory_order_acquire) ==
writeIndex_.load(std::memory_order_acquire);
}
bool isFull() const {
auto nextRecord = writeIndex_.load(std::memory_order_acquire) + 1;
if (nextRecord == size_) {
nextRecord = 0;
bool isEmpty() const {
return readIndex_.load(std::memory_order_acquire) == writeIndex_.load(std::memory_order_acquire);
}
if (nextRecord != readIndex_.load(std::memory_order_acquire)) {
return false;
bool isFull() const {
auto nextRecord = writeIndex_.load(std::memory_order_acquire) + 1;
if (nextRecord == size_) {
nextRecord = 0;
}
if (nextRecord != readIndex_.load(std::memory_order_acquire)) {
return false;
}
// queue is full
return true;
}
// queue is full
return true;
}
// * If called by consumer, then true size may be more (because producer may
// be adding items concurrently).
// * If called by producer, then true size may be less (because consumer may
// be removing items concurrently).
// * It is undefined to call this from any other thread.
size_t sizeGuess() const {
int ret = writeIndex_.load(std::memory_order_acquire) -
readIndex_.load(std::memory_order_acquire);
if (ret < 0) {
ret += size_;
// * If called by consumer, then true size may be more (because producer may
// be adding items concurrently).
// * If called by producer, then true size may be less (because consumer may
// be removing items concurrently).
// * It is undefined to call this from any other thread.
size_t sizeGuess() const {
int ret = writeIndex_.load(std::memory_order_acquire) - readIndex_.load(std::memory_order_acquire);
if (ret < 0) {
ret += size_;
}
return ret;
}
return ret;
}
// maximum number of items in the queue.
size_t capacity() const { return size_ - 1; }
// maximum number of items in the queue.
size_t capacity() const { return size_ - 1; }
private:
using AtomicIndex = std::atomic<unsigned int>;
private:
using AtomicIndex = std::atomic<unsigned int>;
char pad0_[hardware_destructive_interference_size];
const uint32_t size_;
T* const records_;
char pad0_[hardware_destructive_interference_size];
const uint32_t size_;
T *const records_;
alignas(hardware_destructive_interference_size) AtomicIndex readIndex_;
alignas(hardware_destructive_interference_size) AtomicIndex writeIndex_;
alignas(hardware_destructive_interference_size) AtomicIndex readIndex_;
alignas(hardware_destructive_interference_size) AtomicIndex writeIndex_;
char pad1_[hardware_destructive_interference_size - sizeof(AtomicIndex)];
char pad1_[hardware_destructive_interference_size - sizeof(AtomicIndex)];
};
} // namespace folly

63
core/include/aare/VariableSizeClusterFinder.hpp
View File

@ -5,7 +5,6 @@
#include <unordered_map>
#include <vector>
#include "aare/NDArray.hpp"
const int MAX_CLUSTER_SIZE = 200;
@ -23,9 +22,9 @@ template <typename T> class ClusterFinder {
// std::vector<int16_t> rows{};
// std::vector<int16_t> cols{};
int16_t rows[MAX_CLUSTER_SIZE]={0};
int16_t cols[MAX_CLUSTER_SIZE]={0};
double enes[MAX_CLUSTER_SIZE]={0};
int16_t rows[MAX_CLUSTER_SIZE] = {0};
int16_t cols[MAX_CLUSTER_SIZE] = {0};
double enes[MAX_CLUSTER_SIZE] = {0};
};
private:
@ -39,11 +38,11 @@ template <typename T> class ClusterFinder {
bool use_noise_map = false;
int peripheralThresholdFactor_ = 5;
int current_label;
const std::array<int, 4> di{{0, -1, -1, -1}}; // row ### 8-neighbour by scaning from left to right
const std::array<int, 4> dj{{-1, -1, 0, 1}}; // col ### 8-neighbour by scaning from top to bottom
const std::array<int, 4> di{{0, -1, -1, -1}}; // row ### 8-neighbour by scaning from left to right
const std::array<int, 4> dj{{-1, -1, 0, 1}}; // col ### 8-neighbour by scaning from top to bottom
const std::array<int, 8> di_{{0, 0, -1, 1, -1, 1, -1, 1}}; // row
const std::array<int, 8> dj_{{-1, 1, 0, 0, 1, -1, -1, 1}}; // col
std::map<int, int> child; // heirachy: key: child; val: parent
const std::array<int, 8> dj_{{-1, 1, 0, 0, 1, -1, -1, 1}}; // col
std::map<int, int> child; // heirachy: key: child; val: parent
std::unordered_map<int, Hit> h_size;
std::vector<Hit> hits;
// std::vector<std::vector<int16_t>> row
@ -51,14 +50,16 @@ template <typename T> class ClusterFinder {
public:
ClusterFinder(image_shape shape, T threshold)
: shape_(shape), labeled_(shape, 0), peripheral_labeled_(shape, 0), binary_(shape),
threshold_(threshold) {
: shape_(shape), labeled_(shape, 0), peripheral_labeled_(shape, 0), binary_(shape), threshold_(threshold) {
hits.reserve(2000);
}
NDArray<int, 2> labeled() { return labeled_; }
void set_noiseMap(NDView<T, 2> noise_map) { noiseMap = noise_map; use_noise_map = true; }
void set_noiseMap(NDView<T, 2> noise_map) {
noiseMap = noise_map;
use_noise_map = true;
}
void set_peripheralThresholdFactor(int factor) { peripheralThresholdFactor_ = factor; }
void find_clusters(NDView<T, 2> img);
void find_clusters_X(NDView<T, 2> img);
@ -81,8 +82,8 @@ template <typename T> class ClusterFinder {
fmt::print("{} -> {}\n", it->first, it->second);
}
}
size_t total_clusters() const{
//TODO! fix for stealing
size_t total_clusters() const {
// TODO! fix for stealing
return hits.size();
}
@ -103,8 +104,8 @@ template <typename T> class ClusterFinder {
auto old = it->second;
it->second = to;
add_link(old, to);
}else{
//found value is smaller than what we want to link
} else {
// found value is smaller than what we want to link
add_link(to, it->second);
}
}
@ -117,7 +118,7 @@ template <typename T> int ClusterFinder<T>::check_neighbours(int i, int j) {
for (int k = 0; k < 4; ++k) {
const auto row = i + di[k];
const auto col = j + dj[k];
if (row >= 0 && col >= 0 && row<shape_[0] && col < shape_[1]) {
if (row >= 0 && col >= 0 && row < shape_[0] && col < shape_[1]) {
auto tmp = labeled_.value(i + di[k], j + dj[k]);
if (tmp != 0)
neighbour_labels.push_back(tmp);
@ -139,8 +140,7 @@ template <typename T> int ClusterFinder<T>::check_neighbours(int i, int j) {
auto next = current + 1;
add_link(*current, *next);
}
return neighbour_labels.back(); //already sorted
return neighbour_labels.back(); // already sorted
}
}
@ -162,7 +162,7 @@ template <typename T> void ClusterFinder<T>::find_clusters_X(NDView<T, 2> img) {
for (int i = 0; i < shape_[0]; ++i) {
for (int j = 0; j < shape_[1]; ++j) {
if (use_noise_map)
threshold_ = 5*noiseMap(i, j);
threshold_ = 5 * noiseMap(i, j);
if (original_(i, j) > threshold_) {
// printf("========== Cluster index: %d\n", clusterIndex);
rec_FillHit(clusterIndex, i, j);
@ -178,7 +178,7 @@ template <typename T> void ClusterFinder<T>::find_clusters_X(NDView<T, 2> img) {
template <typename T> void ClusterFinder<T>::rec_FillHit(int clusterIndex, int i, int j) {
// printf("original_(%d, %d)=%f\n", i, j, original_(i,j));
// printf("h_size[%d].size=%d\n", clusterIndex, h_size[clusterIndex].size);
if (h_size[clusterIndex].size < MAX_CLUSTER_SIZE){
if (h_size[clusterIndex].size < MAX_CLUSTER_SIZE) {
h_size[clusterIndex].rows[h_size[clusterIndex].size] = i;
h_size[clusterIndex].cols[h_size[clusterIndex].size] = j;
h_size[clusterIndex].enes[h_size[clusterIndex].size] = original_(i, j);
@ -197,11 +197,10 @@ template <typename T> void ClusterFinder<T>::rec_FillHit(int clusterIndex, int i
const auto col = j + dj_[k];
if (row >= 0 && col >= 0 && row < shape_[0] && col < shape_[1]) {
if (use_noise_map)
threshold_ = peripheralThresholdFactor_*noiseMap(row, col);
if (original_(row, col) > threshold_){
threshold_ = peripheralThresholdFactor_ * noiseMap(row, col);
if (original_(row, col) > threshold_) {
rec_FillHit(clusterIndex, row, col);
}
else{
} else {
// if (h_size[clusterIndex].size < MAX_CLUSTER_SIZE){
// h_size[clusterIndex].size += 1;
// h_size[clusterIndex].rows[h_size[clusterIndex].size] = row;
@ -229,7 +228,7 @@ template <typename T> void ClusterFinder<T>::first_pass() {
for (int i = 0; i < original_.size(); ++i) {
if (use_noise_map)
threshold_ = 5*noiseMap(i);
threshold_ = 5 * noiseMap(i);
binary_(i) = (original_(i) > threshold_);
}
@ -258,8 +257,8 @@ template <typename T> void ClusterFinder<T>::second_pass() {
while (it != child.end()) {
current_label = it->second;
it = child.find(current_label);
//do this once before doing the second pass?
//all values point to the final one...
// do this once before doing the second pass?
// all values point to the final one...
}
labeled_(i) = current_label;
}
@ -280,14 +279,13 @@ template <typename T> void ClusterFinder<T>::store_clusters() {
// (j-1 >= 0 and labeled_(i, j-1) != 0) or
// (i+1 < shape_[0] and labeled_(i+1, j) != 0) or
// (j+1 < shape_[1] and labeled_(i, j+1) != 0)
){
) {
Hit &record = h_size[labeled_(i, j)];
if (record.size < MAX_CLUSTER_SIZE){
if (record.size < MAX_CLUSTER_SIZE) {
record.rows[record.size] = i;
record.cols[record.size] = j;
record.enes[record.size] = original_(i, j);
}
else{
} else {
continue;
}
record.size += 1;
@ -301,10 +299,9 @@ template <typename T> void ClusterFinder<T>::store_clusters() {
}
}
}
for (const auto &h : h_size)
hits.push_back(h.second);
}
} // namespace aare

22
core/include/aare/ZmqSocket.hpp
View File

@ -1,10 +1,9 @@
#pragma once
#include <array>
#include <cstdint>
#include <map>
#include <string>
#include <cstdint>
// Socket to receive data from a ZMQ publisher
// needs to be in sync with the main library (or maybe better use the versioning in the header)
@ -12,7 +11,7 @@
// forward declare zmq_msg_t to avoid including zmq.h in the header
class zmq_msg_t;
namespace aare{
namespace aare {
/** zmq header structure (from slsDetectorPackage)*/
struct zmqHeader {
@ -65,24 +64,23 @@ struct zmqHeader {
std::array<int, 4> rx_roi{};
};
class ZmqSocket{
class ZmqSocket {
void *m_context{nullptr};
void *m_socket{nullptr};
std::string m_endpoint;
int m_zmq_hwm{1000};
int m_timeout_ms{1000};
constexpr static size_t m_max_header_size = 1024;
char* m_header_buffer = new char[m_max_header_size];
char *m_header_buffer = new char[m_max_header_size];
bool decode_header(zmqHeader &h);
public:
ZmqSocket(const std::string& endpoint);
public:
ZmqSocket(const std::string &endpoint);
~ZmqSocket();
ZmqSocket(const ZmqSocket&) = delete;
ZmqSocket operator=(const ZmqSocket&) = delete;
ZmqSocket(ZmqSocket&&) = delete;
ZmqSocket(const ZmqSocket &) = delete;
ZmqSocket operator=(const ZmqSocket &) = delete;
ZmqSocket(ZmqSocket &&) = delete;
void connect();
void disconnect();
@ -90,8 +88,6 @@ public:
void set_timeout_ms(int n);
int receive(zmqHeader &header, std::byte *data);
};
} // namespace aare

32
core/include/aare/defs.hpp
View File

@ -1,15 +1,15 @@
#pragma once
#include <array>
#include <vector>
#include <sys/types.h>
#include <string_view>
#include <string>
#include <stdexcept>
#include <fmt/format.h>
#include <stdexcept>
#include <string>
#include <string_view>
#include <sys/types.h>
#include <variant>
#include <vector>
namespace aare{
namespace aare {
typedef struct {
uint64_t frameNumber;
@ -26,7 +26,7 @@ typedef struct {
uint8_t detType;
uint8_t version;
uint8_t packetMask[64];
}__attribute__((packed)) sls_detector_header;
} __attribute__((packed)) sls_detector_header;
struct xy {
int row;
@ -36,29 +36,21 @@ struct xy {
// using image_shape = std::array<ssize_t, 2>;
using dynamic_shape = std::vector<ssize_t>;
enum class DetectorType { Jungfrau, Eiger, Mythen3, Moench,ChipTestBoard };
enum class DetectorType { Jungfrau, Eiger, Mythen3, Moench, ChipTestBoard };
enum class TimingMode {Auto, Trigger};
enum class TimingMode { Auto, Trigger };
template<class T>
T StringTo(std::string sv){
return T(sv);
}
template <class T> T StringTo(std::string sv) { return T(sv); }
template<class T>
std::string toString(T sv){
return T(sv);
}
template <class T> std::string toString(T sv) { return T(sv); }
template <> DetectorType StringTo(std::string);
template <> std::string toString(DetectorType type);
template <> TimingMode StringTo(std::string);
using DataTypeVariants = std::variant<uint16_t, uint32_t>;
struct RawFileConfig {
int module_gap_row{};
int module_gap_col{};
@ -72,6 +64,4 @@ struct RawFileConfig {
}
};
} // namespace aare

9
file_io/include/aare/File.hpp
View File

@ -1,7 +1,7 @@
#pragma once
#include "aare/FileInterface.hpp"
namespace aare{
namespace aare {
class File {
private:
FileInterface *file_impl;
@ -12,8 +12,8 @@ class File {
// - w writing (overwrites existing file)
// - a appending (appends to existing file)
// TODO! do we need to support w+, r+ and a+?
File(std::filesystem::path fname, std::string mode,FileConfig cfg = {});
void write(Frame& frame);
File(std::filesystem::path fname, std::string mode, FileConfig cfg = {});
void write(Frame &frame);
Frame read();
Frame iread(size_t frame_number);
std::vector<Frame> read(size_t n_frames);
@ -27,10 +27,9 @@ class File {
size_t total_frames() const;
ssize_t rows() const;
ssize_t cols() const;
ssize_t bitdepth() const;
ssize_t bitdepth() const;
File(File &&other);
~File();
};

4
file_io/include/aare/FileFactory.hpp
View File

@ -4,7 +4,7 @@
#include "aare/utils/logger.hpp"
#include <filesystem>
namespace aare{
namespace aare {
class FileFactory {
// Class that will be used to create FileInterface objects
@ -17,7 +17,7 @@ class FileFactory {
// virtual int deleteFile() = 0;
static FileInterface *load_file(std::filesystem::path p, std::string mode, FileConfig cfg = {}) {
if ((mode == "r" or mode == "a") and not std::filesystem::exists(p)) {
throw std::runtime_error(LOCATION+"File does not exist");
throw std::runtime_error(LOCATION + "File does not exist");
}
auto factory = get_factory(p);

4
file_io/include/aare/FileInterface.hpp
View File

@ -1,7 +1,7 @@
#pragma once
#include "aare/DType.hpp"
#include "aare/Frame.hpp"
#include "aare/defs.hpp"
#include "aare/DType.hpp"
#include "aare/utils/logger.hpp"
#include <filesystem>
#include <vector>
@ -96,4 +96,4 @@ class FileInterface {
ssize_t m_bitdepth{};
};
}
} // namespace aare

21
file_io/include/aare/NumpyFile.hpp
View File

@ -1,19 +1,19 @@
#pragma once
#include "aare/DType.hpp"
#include "aare/FileInterface.hpp"
#include "aare/NumpyHelpers.hpp"
#include "aare/DType.hpp"
#include "aare/defs.hpp"
#include <filesystem>
#include <iostream>
#include <numeric>
#include <filesystem>
namespace aare{
namespace aare {
class NumpyFile : public FileInterface {
FILE *fp = nullptr;
size_t initial_header_len = 0;
size_t current_frame{};
std::filesystem::path m_fname;
std::filesystem::path m_fname;
uint32_t header_len{};
uint8_t header_len_size{};
ssize_t header_size{};
@ -26,9 +26,7 @@ class NumpyFile : public FileInterface {
Frame get_frame(size_t frame_number);
public:
NumpyFile(const std::filesystem::path& fname);
NumpyFile(const std::filesystem::path &fname);
NumpyFile(FileConfig, NumpyHeader);
void write(Frame &frame) override;
Frame read() override { return get_frame(this->current_frame++); }
@ -48,11 +46,10 @@ class NumpyFile : public FileInterface {
DType dtype() const { return m_header.dtype; }
std::vector<size_t> shape() const { return m_header.shape; }
//load the full numpy file into a NDArray
template<typename T, size_t NDim>
NDArray<T,NDim> load(){
NDArray<T,NDim> arr(make_shape<NDim>(m_header.shape));
// load the full numpy file into a NDArray
template <typename T, size_t NDim> NDArray<T, NDim> load() {
NDArray<T, NDim> arr(make_shape<NDim>(m_header.shape));
fseek(fp, header_size, SEEK_SET);
fread(arr.data(), sizeof(T), arr.size(), fp);
return arr;

7
file_io/include/aare/NumpyFileFactory.hpp
View File

@ -14,10 +14,9 @@ class NumpyFileFactory : public FileFactory {
public:
NumpyFileFactory(std::filesystem::path fpath);
void parse_metadata(FileInterface *_file) override{/*TODO! remove after refactor*/};
NumpyFile* load_file_read() override;
NumpyFile* load_file_write(FileConfig) override;
void parse_fname(FileInterface*)override{};
NumpyFile *load_file_read() override;
NumpyFile *load_file_write(FileConfig) override;
void parse_fname(FileInterface *) override{};
};
} // namespace aare

7
file_io/include/aare/NumpyHelpers.hpp
View File

@ -21,7 +21,7 @@ using shape_t = std::vector<size_t>;
struct NumpyHeader {
DType dtype{aare::DType::ERROR};
bool fortran_order{false};
shape_t shape{};
shape_t shape{};
std::string to_string() const;
};
@ -51,9 +51,8 @@ template <typename T, size_t N> bool in_array(T val, const std::array<T, N> &arr
bool is_digits(const std::string &str);
aare::DType parse_descr(std::string typestring);
size_t write_header(std::filesystem::path fname, const NumpyHeader &header) ;
size_t write_header(std::ostream &out, const NumpyHeader &header) ;
size_t write_header(std::filesystem::path fname, const NumpyHeader &header);
size_t write_header(std::ostream &out, const NumpyHeader &header);
} // namespace NumpyHelpers
} // namespace aare

13
file_io/include/aare/RawFile.hpp
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@ -9,10 +9,9 @@ namespace aare {
class RawFile : public FileInterface {
using config = RawFileConfig;
public:
std::filesystem::path m_fname; //TO be made private!
std::filesystem::path m_fname; // TO be made private!
void write(Frame &frame) override{};
Frame read() override { return get_frame(this->current_frame++); };
std::vector<Frame> read(size_t n_frames) override;
@ -27,10 +26,10 @@ class RawFile : public FileInterface {
size_t pixels() override { return m_rows * m_cols; }
// goto frame number
void seek(size_t frame_number) override{ this->current_frame = frame_number; };
void seek(size_t frame_number) override { this->current_frame = frame_number; };
// return the position of the file pointer (in number of frames)
size_t tell() override{ return this->current_frame; };
size_t tell() override { return this->current_frame; };
size_t n_subfiles;
size_t n_subfile_parts;
@ -66,8 +65,8 @@ class RawFile : public FileInterface {
size_t total_frames() const override { return m_total_frames; }
ssize_t rows() const override { return m_rows; }
ssize_t cols() const override{ return m_cols; }
ssize_t bitdepth() const override{ return m_bitdepth; }
ssize_t cols() const override { return m_cols; }
ssize_t bitdepth() const override { return m_bitdepth; }
private:
size_t current_frame{};
@ -75,4 +74,4 @@ class RawFile : public FileInterface {
Frame get_frame(size_t frame_number);
};
}
} // namespace aare

5
file_io/include/aare/RawFileFactory.hpp
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@ -10,10 +10,9 @@ class RawFileFactory : public FileFactory {
void parse_raw_metadata(RawFile *file);
public:
RawFileFactory(std::filesystem::path fpath);
RawFile *load_file_read() override;
RawFile *load_file_write(FileConfig) override{return new RawFile();};
RawFile *load_file_write(FileConfig) override { return new RawFile(); };
void parse_metadata(FileInterface *) override;
void parse_fname(FileInterface *) override;
void open_subfiles(FileInterface *);
@ -21,4 +20,4 @@ class RawFileFactory : public FileFactory {
void find_geometry(FileInterface *);
};
}
} // namespace aare

2
include/aare/aare.hpp
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@ -1 +1 @@
//This is the top level header to include and what most users will use
// This is the top level header to include and what most users will use

2
utils/include/aare/utils/logger.hpp
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@ -115,7 +115,7 @@ template <typename... Strings> void error(const Strings... s) { internal::logger
extern void set_streams(std::streambuf *out, std::streambuf *err);
extern void set_streams(std::streambuf *out);
extern void set_verbosity(LOGGING_LEVEL level);
extern void set_output_file(std::string filename);
extern void set_output_file(std::string filename);
extern Logger &get_logger_instance();
} // namespace logger