works for hdf5, needs refactoring

include/aare/Hdf5File.hpp

@@ -8,6 +8,66 @@
 
 namespace aare {
 
+struct H5Handles {
+  std::string file_name{};
+  std::string dataset_name{};
+  H5::H5File file;
+  H5::DataSet dataset;
+  H5::DataSpace dataspace;
+  H5::DataType datatype;
+  std::unique_ptr<H5::DataSpace> memspace{nullptr};
+  std::vector<hsize_t>dims;
+  std::vector<hsize_t> count;
+  std::vector<hsize_t> offset;
+
+  H5Handles(const std::string& fname, const std::string& dname, int rank):
+    file_name(fname),
+    dataset_name(dname),
+    file(fname, H5F_ACC_RDONLY),
+    dataset(file.openDataSet(dname)),
+    dataspace(dataset.getSpace()),
+    datatype(dataset.getDataType())
+  {
+    if (dataspace.getSimpleExtentNdims() != rank) {
+      throw std::runtime_error(LOCATION + "Expected rank of " + dname + " dataset to be 1. Got " + std::to_string(rank));
+    }
+    dims.resize(rank);
+    dataspace.getSimpleExtentDims(dims.data(), nullptr);
+
+    // to slice 1 frame with hyperslab    
+    count.push_back(1);
+    offset.push_back(0);
+
+    // header datasets
+    if (rank == 1) {
+      memspace = std::make_unique<H5::DataSpace>(H5S_SCALAR);
+    } 
+    // data dataset
+    else {
+      hsize_t dimsm[2] = {dims[1], dims[2]};
+      memspace = std::make_unique<H5::DataSpace>(2, dimsm);
+      count.push_back(dims[1]);
+      count.push_back(dims[2]);
+      offset.push_back(0);
+      offset.push_back(0);
+    }
+  };
+
+  void seek(size_t frame_index) {
+    if (frame_index >= dims[0]) {
+        throw std::runtime_error(LOCATION + "Invalid frame number");
+    }
+    offset[0] = static_cast<hsize_t>(frame_index);
+  };
+
+  void get_frame_into(size_t frame_index, std::byte *frame_buffer) {
+    seek(frame_index);
+    dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data());
+    dataset.read(frame_buffer, datatype, *memspace, dataspace);
+  };
+
+};
+
 /**
  * @brief Class to read .h5 files. The class will parse the master file
  * to find the correct geometry for the frames.
@@ -21,11 +81,6 @@ class Hdf5File : public FileInterface {
     size_t m_total_frames{};
     size_t m_rows{};
     size_t m_cols{};
-    H5::DataType m_datatype{};
-
-    std::unique_ptr<H5::H5File> file{nullptr};
-    std::unique_ptr<H5::DataSet> dataset{nullptr};
-    std::unique_ptr<H5::DataSpace> dataspace{nullptr};
 
   public:
     /**
@@ -71,10 +126,23 @@ class Hdf5File : 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 read the frame at the given frame index into the image buffer
+     * @param frame_index frame number to read
+     * @param frame_buffer buffer to store the frame
+     */
+    void get_data_into(size_t frame_index, std::byte *frame_buffer);
+    
+    /**
+     * @brief read the header at the given frame index into the header buffer
+     * @param frame_index frame number to read
+     * @param header buffer to store the header
+     */
+    void get_header_into(size_t frame_index, DetectorHeader *header);
+    
     /**
      * @brief get the frame at the given frame index
      * @param frame_number frame number to read
@@ -90,7 +158,13 @@ class Hdf5File : public FileInterface {
     static DetectorHeader read_header(const std::filesystem::path &fname);
 
     static const std::string metadata_group_name;
-    void open_file();
+    static const std::vector<std::string> header_dataset_names;
+
+    std::unique_ptr<H5Handles> m_data_file{nullptr};
+    std::vector<std::unique_ptr<H5Handles>> m_header_files;
+
+    void open_data_file();
+    void open_header_files();
 };
 
 } // namespace aare