From a3f831dc9eb213ae1082e57411955c6a8666c33c Mon Sep 17 00:00:00 2001
From: Dhanya Thattil <dhanya.thattil@psi.ch>
Date: Thu, 5 Jun 2025 00:38:27 +0200
Subject: [PATCH] efficiently read in one hyperslab read instead of multiple
 reads in a loop

---
 include/aare/Hdf5File.hpp | 10 ++++----
 src/Hdf5File.cpp          | 49 +++++++++++++++++----------------------
 2 files changed, 27 insertions(+), 32 deletions(-)

diff --git a/include/aare/Hdf5File.hpp b/include/aare/Hdf5File.hpp
index 0b7d306..0c5d643 100644
--- a/include/aare/Hdf5File.hpp
+++ b/include/aare/Hdf5File.hpp
@@ -38,8 +38,9 @@ struct H5Handles {
     offset[0] = static_cast<hsize_t>(frame_index);
   }
 
-  void get_data_into(size_t frame_index, std::byte *frame_buffer) {
+  void get_data_into(size_t frame_index, std::byte *frame_buffer, size_t n_frames = 1) {
     seek(frame_index);
+    count[0] = static_cast<hsize_t>(n_frames);
     //std::cout << "offset:" << offset << " count:" << count << std::endl;
     dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data());
     dataset.read(frame_buffer, datatype, *memspace, dataspace);
@@ -137,17 +138,18 @@ class Hdf5File : public FileInterface {
     /**
      * @brief read the frame at the given frame index into the image buffer
      * @param frame_number frame number to read
+     * @param n_frames number of frames to read (default is 1)
      * @param image_buf buffer to store the frame
      */
-    void get_frame_into(size_t frame_index, std::byte *frame_buffer,
-                        DetectorHeader *header = nullptr);
+    void get_frame_into(size_t frame_index, std::byte *frame_buffer, size_t n_frames = 1, DetectorHeader *header = nullptr);
     
     /**
      * @brief read the frame at the given frame index into the image buffer
      * @param frame_index frame number to read
+     * @param n_frames number of frames to read (default is 1)
      * @param frame_buffer buffer to store the frame
      */
-    void get_data_into(size_t frame_index, std::byte *frame_buffer);
+    void get_data_into(size_t frame_index, std::byte *frame_buffer, size_t n_frames = 1);
     
     /**
      * @brief read the header at the given frame index into the header buffer
diff --git a/src/Hdf5File.cpp b/src/Hdf5File.cpp
index a10341a..c829d51 100644
--- a/src/Hdf5File.cpp
+++ b/src/Hdf5File.cpp
@@ -27,30 +27,21 @@ Frame Hdf5File::read_frame(size_t frame_number) {
 }
 
 void Hdf5File::read_into(std::byte *image_buf, size_t n_frames) {
-    // TODO: implement this in a more efficient way
-
-    for (size_t i = 0; i < n_frames; i++) {
-        get_frame_into(m_current_frame++, image_buf);
-        image_buf += bytes_per_frame();
-    }
+    get_frame_into(m_current_frame++, image_buf, n_frames);
 }
 
 void Hdf5File::read_into(std::byte *image_buf) {
-    return get_frame_into(m_current_frame++, image_buf);
+    get_frame_into(m_current_frame++, image_buf);
 }
 
 void Hdf5File::read_into(std::byte *image_buf, DetectorHeader *header) {
 
-    return get_frame_into(m_current_frame++, image_buf, header);
+    get_frame_into(m_current_frame, image_buf, 1, header);
 }
 
 void Hdf5File::read_into(std::byte *image_buf, size_t n_frames,
                          DetectorHeader *header) {
-    for (size_t i = 0; i < n_frames; i++) {
-        get_frame_into(m_current_frame++, image_buf, header);
-        image_buf += bytes_per_frame();
-        header += n_modules();
-    }
+    get_frame_into(m_current_frame++, image_buf, n_frames, header);
 }
 
 size_t Hdf5File::bytes_per_frame() {
@@ -119,30 +110,25 @@ DetectorHeader Hdf5File::read_header(const std::filesystem::path &fname) {
 }
 
 
-Frame Hdf5File::get_frame(size_t frame_index) {
-    auto f = Frame(m_rows, m_cols, Dtype::from_bitdepth(m_master.bitdepth()));
-    std::byte *frame_buffer = f.data();
-    get_frame_into(frame_index, frame_buffer);
-    return f;
-}
 
-
-void Hdf5File::get_frame_into(size_t frame_index, std::byte *frame_buffer,
-                              DetectorHeader *header) {
-    if (frame_index >= m_master.frames_in_file()) {
+void Hdf5File::get_frame_into(size_t frame_index, std::byte *frame_buffer, size_t n_frames, DetectorHeader *header) {
+    if ((frame_index + n_frames - 1) >= m_master.frames_in_file()) {
         throw std::runtime_error(LOCATION + "Frame number out of range");
     }
     get_data_into(frame_index, frame_buffer);
+    m_current_frame += n_frames;
     if (header) {
-        for (size_t part_idx = 0; part_idx != m_master.n_modules(); ++part_idx) {
-            get_header_into(frame_index, part_idx, header);
-            header++;
+        for (size_t i = 0; i < n_frames; i++) {
+            for (size_t part_idx = 0; part_idx != m_master.n_modules(); ++part_idx) {
+                get_header_into(frame_index + i, part_idx, header);
+                header++;
+            }
         }
     }
 }
 
-void Hdf5File::get_data_into(size_t frame_index, std::byte *frame_buffer) {
-    m_data_file->get_data_into(frame_index, frame_buffer);
+void Hdf5File::get_data_into(size_t frame_index, std::byte *frame_buffer, size_t n_frames) {
+    m_data_file->get_data_into(frame_index, frame_buffer, n_frames);
 }
 
 void Hdf5File::get_header_into(size_t frame_index, int part_index, DetectorHeader *header) {
@@ -170,6 +156,13 @@ void Hdf5File::get_header_into(size_t frame_index, int part_index, DetectorHeade
     }
 }
 
+Frame Hdf5File::get_frame(size_t frame_index) {
+    auto f = Frame(m_rows, m_cols, Dtype::from_bitdepth(m_master.bitdepth()));
+    std::byte *frame_buffer = f.data();
+    get_frame_into(frame_index, frame_buffer);
+    return f;
+}
+
 std::vector<Frame> Hdf5File::read_n(size_t n_frames) {
     // TODO: implement this in a more efficient way
     std::vector<Frame> frames;