detectors/aare
25
0
Fork 0
mirror of https://github.com/slsdetectorgroup/aare.git synced 2025-06-14 00:07:13 +02:00
Code Issues Actions Packages Releases Activity

Merge branch 'main' into developer

Browse Source
This commit is contained in:
Erik Fröjdh
2024-11-11 18:52:23 +01:00
committed by GitHub
parent 5f21759c8c d8d1f0c517
commit a0b6c4cc03
19 changed files with 233 additions and 8 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
src/RawFile.cpp
View File

@ -13,11 +13,13 @@ RawFile::RawFile(const std::filesystem::path &fname, const std::string &mode)
: m_master(fname) {
m_mode = mode;
if (mode == "r") {
n_subfiles = find_number_of_subfiles(); // f0,f1...fn
n_subfile_parts =
m_master.geometry().col * m_master.geometry().row; // d0,d1...dn
find_geometry();
update_geometry_with_roi();
open_subfiles();
} else {
throw std::runtime_error(LOCATION +
@ -41,11 +43,11 @@ void RawFile::read_into(std::byte *image_buf, size_t n_frames) {
}
}
void RawFile::read_into(std::byte *image_buf) {
return get_frame_into(m_current_frame++, image_buf);
};
void RawFile::read_into(std::byte *image_buf, DetectorHeader *header) {
return get_frame_into(m_current_frame++, image_buf, header);
@ -53,6 +55,7 @@ void RawFile::read_into(std::byte *image_buf, DetectorHeader *header) {
size_t RawFile::n_mod() const { return n_subfile_parts; }
size_t RawFile::bytes_per_frame() {
return m_rows * m_cols * m_master.bitdepth() / 8;
}
@ -88,6 +91,7 @@ void RawFile::open_subfiles() {
v[j] = new RawSubFile(m_master.data_fname(j, i),
m_master.detector_type(), pos.height,
pos.width, m_master.bitdepth());
}
subfiles.push_back(v);
}
@ -128,12 +132,14 @@ int RawFile::find_number_of_subfiles() {
fmt::print("Found: {} subfiles\n", n_files);
#endif
return n_files;
}
void RawFile::find_geometry() {
uint16_t r{};
uint16_t c{};
for (size_t i = 0; i < n_subfile_parts; i++) {
auto h = this->read_header(m_master.data_fname(i, 0));
r = std::max(r, h.row);
@ -145,6 +151,7 @@ void RawFile::find_geometry() {
g.width = m_master.pixels_x();
g.height = m_master.pixels_y();
m_module_pixel_0.push_back(g);
}
r++;
@ -154,6 +161,7 @@ void RawFile::find_geometry() {
m_cols = (c * m_master.pixels_x());
m_rows += static_cast<size_t>((r - 1) * cfg.module_gap_row);
#ifdef AARE_VERBOSE
fmt::print("\nRawFile::find_geometry()\n");
for (size_t i = 0; i < m_module_pixel_0.size(); i++) {
@ -227,6 +235,7 @@ void RawFile::update_geometry_with_roi() {
fmt::print("Updated image size: {}x{}\n\n", m_rows, m_cols);
fmt::print("\n");
#endif
}
Frame RawFile::get_frame(size_t frame_index) {
@ -236,18 +245,22 @@ Frame RawFile::get_frame(size_t frame_index) {
return f;
}
size_t RawFile::bytes_per_pixel() const {
return m_master.bitdepth() / 8;
}
void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, DetectorHeader *header) {
if (frame_index > total_frames()) {
throw std::runtime_error(LOCATION + "Frame number out of range");
}
std::vector<size_t> frame_numbers(n_subfile_parts);
std::vector<size_t> frame_indices(n_subfile_parts, frame_index);
// sync the frame numbers
if (n_subfile_parts != 1) {
for (size_t part_idx = 0; part_idx != n_subfile_parts; ++part_idx) {
auto subfile_id = frame_index / m_master.max_frames_per_file();
@ -302,6 +315,7 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
//TODO! should we read row by row?
// create a buffer large enough to hold a full module
auto bytes_per_part = m_master.pixels_y() * m_master.pixels_x() *
m_master.bitdepth() /
8; // TODO! replace with image_size_in_bytes
@ -331,6 +345,7 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
part_buffer + cur_row * pos.width *
m_master.bitdepth() / 8,
pos.width * m_master.bitdepth() / 8);
}
}
delete[] part_buffer;

6
src/RawMasterFile.cpp
View File

@ -8,8 +8,6 @@ RawFileNameComponents::RawFileNameComponents(
m_base_name = fname.stem();
m_ext = fname.extension();
AARE_ASSERT(false);
if (m_ext != ".json" && m_ext != ".raw") {
throw std::runtime_error(LOCATION +
"Unsupported file type. (only .json or .raw)");
@ -145,8 +143,10 @@ ScanParameters RawMasterFile::scan_parameters() const {
return m_scan_parameters;
}
std::optional<ROI> RawMasterFile::roi() const { return m_roi; }
void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
std::ifstream ifs(fpath);
json j;
@ -244,6 +244,7 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
// not a scan
}
try{
ROI tmp_roi;
auto obj = j.at("Receiver Roi");
@ -276,6 +277,7 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
// Update detector type for Moench
// TODO! How does this work with old .raw master files?
#ifdef AARE_VERBOSE

91
src/SubFile.cpp Normal file
View File

@ -0,0 +1,91 @@
#include "aare/SubFile.hpp"
#include "aare/PixelMap.hpp"
#include <cstring> // memcpy
#include <fmt/core.h>
#include <iostream>
namespace aare {
SubFile::SubFile(const std::filesystem::path &fname, DetectorType detector, size_t rows, size_t cols, size_t bitdepth,
const std::string &mode)
: m_bitdepth(bitdepth), m_fname(fname), m_rows(rows), m_cols(cols), m_mode(mode), m_detector_type(detector) {
if (m_detector_type == DetectorType::Moench03_old) {
pixel_map = GenerateMoench03PixelMap();
}
if (std::filesystem::exists(fname)) {
n_frames = std::filesystem::file_size(fname) / (sizeof(DetectorHeader) + rows * cols * bitdepth / 8);
} else {
n_frames = 0;
}
if (mode == "r") {
fp = fopen(m_fname.string().c_str(), "rb");
} else {
throw std::runtime_error(LOCATION + "Unsupported mode. Can only read RawFiles.");
}
if (fp == nullptr) {
throw std::runtime_error(LOCATION + fmt::format("Could not open file {}", m_fname.string()));
}
#ifdef AARE_VERBOSE
fmt::print("Opened file: {} with {} frames\n", m_fname.string(), n_frames);
fmt::print("m_rows: {}, m_cols: {}, m_bitdepth: {}\n", m_rows, m_cols, m_bitdepth);
#endif
}
size_t SubFile::get_part(std::byte *buffer, size_t frame_index) {
if (frame_index >= n_frames) {
throw std::runtime_error("Frame number out of range");
}
fseek(fp, sizeof(DetectorHeader) + (sizeof(DetectorHeader) + bytes_per_part()) * frame_index, // NOLINT
SEEK_SET);
if (pixel_map){
// read into a temporary buffer and then copy the data to the buffer
// in the correct order
auto part_buffer = new std::byte[bytes_per_part()];
auto wc = fread(part_buffer, bytes_per_part(), 1, fp);
auto *data = reinterpret_cast<uint16_t *>(buffer);
auto *part_data = reinterpret_cast<uint16_t *>(part_buffer);
for (size_t i = 0; i < pixels_per_part(); i++) {
data[i] = part_data[(*pixel_map)(i)];
}
delete[] part_buffer;
return wc;
}else{
// read directly into the buffer
return fread(buffer, this->bytes_per_part(), 1, this->fp);
}
}
size_t SubFile::write_part(std::byte *buffer, DetectorHeader header, size_t frame_index) {
if (frame_index > n_frames) {
throw std::runtime_error("Frame number out of range");
}
fseek(fp, static_cast<int64_t>((sizeof(DetectorHeader) + bytes_per_part()) * frame_index), SEEK_SET);
auto wc = fwrite(reinterpret_cast<char *>(&header), sizeof(header), 1, fp);
wc += fwrite(buffer, bytes_per_part(), 1, fp);
return wc;
}
size_t SubFile::frame_number(size_t frame_index) {
DetectorHeader h{};
fseek(fp, (sizeof(DetectorHeader) + bytes_per_part()) * frame_index, SEEK_SET); // NOLINT
size_t const rc = fread(reinterpret_cast<char *>(&h), sizeof(h), 1, fp);
if (rc != 1)
throw std::runtime_error(LOCATION + "Could not read header from file");
return h.frameNumber;
}
SubFile::~SubFile() {
if (fp) {
fclose(fp);
}
}
} // namespace aare

2
src/defs.cpp
View File

@ -1,6 +1,7 @@
#include "aare/defs.hpp"
#include <stdexcept>
#include <string>
#include <fmt/core.h>
namespace aare {
@ -12,6 +13,7 @@ void assert_failed(const std::string &msg)
}
/**
* @brief Convert a DetectorType to a string
* @param type DetectorType