Merge branch 'main' into developer

include/aare/NDArray.hpp

@@ -342,6 +342,7 @@ template <typename T, int64_t Ndim> void NDArray<T, Ndim>::Print() {
         Print_some();
 }
 
+
 template <typename T, int64_t Ndim>
 std::ostream& operator <<(std::ostream& os, const NDArray<T, Ndim>& arr){
     for (auto row = 0; row < arr.shape(0); ++row) {
@@ -354,6 +355,7 @@ std::ostream& operator <<(std::ostream& os, const NDArray<T, Ndim>& arr){
     return os;
 }
 
+
 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) {

include/aare/NDView.hpp

@@ -156,6 +156,7 @@ template <typename T, int64_t Ndim> void NDView<T, Ndim>::print_all() const {
     }
 }
 
+
 template <typename T, int64_t Ndim>
 std::ostream& operator <<(std::ostream& os, const NDView<T, Ndim>& arr){
     for (auto row = 0; row < arr.shape(0); ++row) {
@@ -168,4 +169,5 @@ std::ostream& operator <<(std::ostream& os, const NDView<T, Ndim>& arr){
     return os;
 }
 
+
 } // namespace aare

include/aare/RawFile.hpp

@@ -5,6 +5,7 @@
 #include "aare/NDArray.hpp" //for pixel map
 #include "aare/RawSubFile.hpp"
 
+
 #include <optional>
 
 namespace aare {
@@ -62,6 +63,7 @@ class RawFile : public FileInterface {
     //TODO! do we need to adapt the API? 
     void read_into(std::byte *image_buf, DetectorHeader *header);
 
+
     size_t frame_number(size_t frame_index) override;
     size_t bytes_per_frame() override;
     size_t pixels_per_frame() override;
@@ -75,6 +77,7 @@ class RawFile : public FileInterface {
     xy geometry();
     size_t n_mod() const;
 
+
     DetectorType detector_type() const override;
 
   private:
@@ -91,8 +94,10 @@ class RawFile : public FileInterface {
      * @param frame_number frame number to read
      * @param image_buf buffer to store the frame
      */
+
     void get_frame_into(size_t frame_index, std::byte *frame_buffer, DetectorHeader *header = nullptr);
 
+
     /**
      * @brief get the frame at the given frame index
      * @param frame_number frame number to read
@@ -111,6 +116,7 @@ class RawFile : public FileInterface {
 
     void update_geometry_with_roi();
     int find_number_of_subfiles();
+
     void open_subfiles();
     void find_geometry();
 };

include/aare/RawMasterFile.hpp

@@ -58,6 +58,7 @@ class ScanParameters {
     bool enabled() const;
 };
 
+
 struct ROI{
   size_t xmin{};
   size_t xmax{};
@@ -107,6 +108,7 @@ class RawMasterFile {
 
     std::optional<ROI> m_roi;
 
+
   public:
     RawMasterFile(const std::filesystem::path &fpath);
 
@@ -133,8 +135,10 @@ class RawMasterFile {
     std::optional<size_t> number_of_rows() const;
     std::optional<uint8_t> quad() const;
 
+
     std::optional<ROI> roi() const;
 
+
     ScanParameters scan_parameters() const;
 
   private:

include/aare/SubFile.hpp

@@ -0,0 +1,80 @@
+#pragma once
+#include "aare/Frame.hpp"
+#include "aare/defs.hpp"
+
+#include <cstdint>
+#include <filesystem>
+#include <map>
+#include <optional>
+
+
+namespace aare {
+
+/**
+ * @brief Class to read a subfile from a RawFile
+ */
+class SubFile {
+  public:
+    size_t write_part(std::byte *buffer, DetectorHeader header, size_t frame_index);
+    /**
+     * @brief SubFile constructor
+     * @param fname path to the subfile
+     * @param detector detector type
+     * @param rows number of rows in the subfile
+     * @param cols number of columns in the subfile
+     * @param bitdepth bitdepth of the subfile
+     * @throws std::invalid_argument if the detector,type pair is not supported
+     */
+    SubFile(const std::filesystem::path &fname, DetectorType detector, size_t rows, size_t cols, size_t bitdepth,
+            const std::string &mode = "r");
+
+    /**
+     * @brief read the subfile into a buffer
+     * @param buffer pointer to the buffer to read the data into
+     * @return number of bytes read
+     */
+    size_t read_impl_normal(std::byte *buffer);
+
+    /**
+     * @brief read the subfile into a buffer with the bytes flipped
+     * @param buffer pointer to the buffer to read the data into
+     * @return number of bytes read
+     */
+    template <typename DataType> size_t read_impl_flip(std::byte *buffer);
+
+    /**
+     * @brief read the subfile into a buffer with the bytes reordered
+     * @param buffer pointer to the buffer to read the data into
+     * @return number of bytes read
+     */
+    template <typename DataType> size_t read_impl_reorder(std::byte *buffer);
+
+    /**
+     * @brief read the subfile into a buffer with the bytes reordered and flipped
+     * @param buffer pointer to the buffer to read the data into
+     * @param frame_number frame number to read
+     * @return number of bytes read
+     */
+    size_t get_part(std::byte *buffer, size_t frame_index);
+    size_t frame_number(size_t frame_index);
+
+    // TODO: define the inlines as variables and assign them in constructor
+    inline size_t bytes_per_part() const { return (m_bitdepth / 8) * m_rows * m_cols; }
+    inline size_t pixels_per_part() const { return m_rows * m_cols; }
+
+    ~SubFile();
+
+  protected:
+    FILE *fp = nullptr;
+    size_t m_bitdepth;
+    std::filesystem::path m_fname;
+    size_t m_rows{};
+    size_t m_cols{};
+    std::string m_mode;
+    size_t n_frames{};
+    int m_sub_file_index_{};
+    DetectorType m_detector_type;
+    std::optional<NDArray<ssize_t, 2>> pixel_map;
+};
+
+} // namespace aare

include/aare/defs.hpp

@@ -15,10 +15,6 @@
 #include <vector>
 
 
-
-
-
-
 /**
  * @brief LOCATION macro to get the current location in the code
  */
@@ -27,6 +23,7 @@
         ":" + std::string(__func__) + ":"
 
 
+
 #ifdef AARE_CUSTOM_ASSERT
 #define AARE_ASSERT(expr)\
     if (expr)\
@@ -43,6 +40,7 @@ namespace aare {
 
 void assert_failed(const std::string &msg);
 
+
 class Cluster {
   public:
     int cluster_sizeX;
@@ -192,6 +190,7 @@ struct ModuleGeometry{
     int width{};
 };
 
+
 using dynamic_shape = std::vector<int64_t>;
 
 //TODO! Can we uniform enums between the libraries?