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efficiently read in one hyperslab read instead of multiple reads in a loop
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maliakal_d 2025-06-05 00:38:27 +02:00
parent 76b8872fe6
commit a3f831dc9e
2 changed files with 27 additions and 32 deletions
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10
include/aare/Hdf5File.hpp
View File

@ -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

49
src/Hdf5File.cpp
View File

@ -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;