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formatted main branch

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mazzol_a
2025-06-10 16:09:06 +02:00
parent efd2338f54
commit f9751902a2
87 changed files with 1710 additions and 1639 deletions
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65
src/RawSubFile.cpp
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@ -1,36 +1,30 @@
#include "aare/RawSubFile.hpp"
#include "aare/PixelMap.hpp"
#include "aare/algorithm.hpp"
#include "aare/utils/ifstream_helpers.hpp"
#include "aare/logger.hpp"
#include "aare/utils/ifstream_helpers.hpp"
#include <cstring> // memcpy
#include <fmt/core.h>
#include <iostream>
#include <regex>
namespace aare {
RawSubFile::RawSubFile(const std::filesystem::path &fname,
DetectorType detector, size_t rows, size_t cols,
size_t bitdepth, uint32_t pos_row, uint32_t pos_col)
: m_detector_type(detector), m_bitdepth(bitdepth),
m_rows(rows), m_cols(cols),
m_bytes_per_frame((m_bitdepth / 8) * m_rows * m_cols), m_pos_row(pos_row),
m_pos_col(pos_col) {
: m_detector_type(detector), m_bitdepth(bitdepth), m_rows(rows),
m_cols(cols), m_bytes_per_frame((m_bitdepth / 8) * m_rows * m_cols),
m_pos_row(pos_row), m_pos_col(pos_col) {
LOG(logDEBUG) << "RawSubFile::RawSubFile()";
LOG(logDEBUG) << "RawSubFile::RawSubFile()";
if (m_detector_type == DetectorType::Moench03_old) {
m_pixel_map = GenerateMoench03PixelMap();
} else if (m_detector_type == DetectorType::Eiger && m_pos_row % 2 == 0) {
m_pixel_map = GenerateEigerFlipRowsPixelMap();
}
parse_fname(fname);
scan_files();
open_file(m_current_file_index); // open the first file
@ -51,7 +45,8 @@ void RawSubFile::seek(size_t frame_index) {
auto frame_offset = (file_index)
? frame_index - m_last_frame_in_file[file_index - 1]
: frame_index;
auto byte_offset = frame_offset * (m_bytes_per_frame + sizeof(DetectorHeader));
auto byte_offset =
frame_offset * (m_bytes_per_frame + sizeof(DetectorHeader));
m_file.seekg(byte_offset);
}
@ -69,7 +64,7 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
m_file.seekg(sizeof(DetectorHeader), std::ios::cur);
}
if (m_file.fail()){
if (m_file.fail()) {
throw std::runtime_error(LOCATION + ifstream_error_msg(m_file));
}
@ -78,14 +73,15 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
// read into a temporary buffer and then copy the data to the buffer
// in the correct order
// TODO! add 4 bit support
if(m_bitdepth == 8){
if (m_bitdepth == 8) {
read_with_map<uint8_t>(image_buf);
}else if (m_bitdepth == 16) {
} else if (m_bitdepth == 16) {
read_with_map<uint16_t>(image_buf);
} else if (m_bitdepth == 32) {
read_with_map<uint32_t>(image_buf);
}else{
throw std::runtime_error("Unsupported bitdepth for read with pixel map");
} else {
throw std::runtime_error(
"Unsupported bitdepth for read with pixel map");
}
} else {
@ -93,11 +89,11 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
m_file.read(reinterpret_cast<char *>(image_buf), bytes_per_frame());
}
if (m_file.fail()){
if (m_file.fail()) {
throw std::runtime_error(LOCATION + ifstream_error_msg(m_file));
}
++ m_current_frame_index;
++m_current_frame_index;
if (m_current_frame_index >= m_last_frame_in_file[m_current_file_index] &&
(m_current_frame_index < m_total_frames)) {
++m_current_file_index;
@ -105,7 +101,8 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
}
}
void RawSubFile::read_into(std::byte *image_buf, size_t n_frames, DetectorHeader *header) {
void RawSubFile::read_into(std::byte *image_buf, size_t n_frames,
DetectorHeader *header) {
for (size_t i = 0; i < n_frames; i++) {
read_into(image_buf, header);
image_buf += bytes_per_frame();
@ -115,10 +112,7 @@ void RawSubFile::read_into(std::byte *image_buf, size_t n_frames, DetectorHeader
}
}
template <typename T>
void RawSubFile::read_with_map(std::byte *image_buf) {
template <typename T> void RawSubFile::read_with_map(std::byte *image_buf) {
auto part_buffer = new std::byte[bytes_per_frame()];
m_file.read(reinterpret_cast<char *>(part_buffer), bytes_per_frame());
auto *data = reinterpret_cast<T *>(image_buf);
@ -157,14 +151,17 @@ void RawSubFile::parse_fname(const std::filesystem::path &fname) {
std::smatch match;
if (std::regex_match(m_base_name, match, pattern)) {
m_offset = std::stoi(match[4].str()); // find the first file index in case of a truncated series
m_base_name = match[1].str() + match[2].str() + match[3].str() + "{}" + match[5].str();
m_offset = std::stoi(match[4].str()); // find the first file index in
// case of a truncated series
m_base_name = match[1].str() + match[2].str() + match[3].str() + "{}" +
match[5].str();
LOG(logDEBUG) << "Base name: " << m_base_name;
LOG(logDEBUG) << "Offset: " << m_offset;
LOG(logDEBUG) << "Path: " << m_path.string();
} else {
throw std::runtime_error(
LOCATION + fmt::format("Could not parse file name {}", fname.string()));
LOCATION +
fmt::format("Could not parse file name {}", fname.string()));
}
}
@ -175,12 +172,13 @@ std::filesystem::path RawSubFile::fpath(size_t file_index) const {
void RawSubFile::open_file(size_t file_index) {
m_file.close();
auto fname = fpath(file_index+m_offset);
auto fname = fpath(file_index + m_offset);
LOG(logDEBUG) << "RawSubFile::open_file(): " << fname.string();
m_file.open(fname, std::ios::binary);
if (!m_file.is_open()) {
throw std::runtime_error(
LOCATION + fmt::format("Could not open file {}", fpath(file_index).string()));
LOCATION +
fmt::format("Could not open file {}", fpath(file_index).string()));
}
m_current_file_index = file_index;
}
@ -190,20 +188,21 @@ void RawSubFile::scan_files() {
// find how many files we have and the number of frames in each file
m_last_frame_in_file.clear();
size_t file_index = m_offset;
while (std::filesystem::exists(fpath(file_index))) {
auto n_frames = std::filesystem::file_size(fpath(file_index)) /
(m_bytes_per_frame + sizeof(DetectorHeader));
m_last_frame_in_file.push_back(n_frames);
LOG(logDEBUG) << "Found: " << n_frames << " frames in file: " << fpath(file_index).string();
LOG(logDEBUG) << "Found: " << n_frames
<< " frames in file: " << fpath(file_index).string();
++file_index;
}
// find where we need to open the next file and total number of frames
m_last_frame_in_file = cumsum(m_last_frame_in_file);
if(m_last_frame_in_file.empty()){
if (m_last_frame_in_file.empty()) {
m_total_frames = 0;
}else{
} else {
m_total_frames = m_last_frame_in_file.back();
}
}