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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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93
src/RawFile.cpp
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@ -1,9 +1,9 @@
#include "aare/RawFile.hpp"
#include "aare/algorithm.hpp"
#include "aare/PixelMap.hpp"
#include "aare/algorithm.hpp"
#include "aare/defs.hpp"
#include "aare/logger.hpp"
#include "aare/geo_helpers.hpp"
#include "aare/logger.hpp"
#include <fmt/format.h>
#include <nlohmann/json.hpp>
@ -17,8 +17,9 @@ RawFile::RawFile(const std::filesystem::path &fname, const std::string &mode)
m_mode = mode;
if (mode == "r") {
find_geometry();
if (m_master.roi()){
m_geometry = update_geometry_with_roi(m_geometry, m_master.roi().value());
if (m_master.roi()) {
m_geometry =
update_geometry_with_roi(m_geometry, m_master.roi().value());
}
open_subfiles();
} else {
@ -47,32 +48,31 @@ 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);
}
void RawFile::read_into(std::byte *image_buf, size_t n_frames, DetectorHeader *header) {
void RawFile::read_into(std::byte *image_buf, size_t n_frames,
DetectorHeader *header) {
// return get_frame_into(m_current_frame++, image_buf, header);
for (size_t i = 0; i < n_frames; i++) {
this->get_frame_into(m_current_frame++, image_buf, header);
image_buf += bytes_per_frame();
if(header)
header+=n_modules();
if (header)
header += n_modules();
}
}
size_t RawFile::n_modules() const { return m_master.n_modules(); }
size_t RawFile::bytes_per_frame() {
return m_geometry.pixels_x * m_geometry.pixels_y * m_master.bitdepth() / bits_per_byte;
return m_geometry.pixels_x * m_geometry.pixels_y * m_master.bitdepth() /
bits_per_byte;
}
size_t RawFile::pixels_per_frame() {
// return m_rows * m_cols;
size_t RawFile::pixels_per_frame() {
// return m_rows * m_cols;
return m_geometry.pixels_x * m_geometry.pixels_y;
}
@ -128,27 +128,25 @@ DetectorHeader RawFile::read_header(const std::filesystem::path &fname) {
return h;
}
RawMasterFile RawFile::master() const { return m_master; }
/**
* @brief Find the geometry of the detector by opening all the subfiles and
* reading the headers.
* reading the headers.
*/
void RawFile::find_geometry() {
//Hold the maximal row and column number found
//Later used for calculating the total number of rows and columns
// Hold the maximal row and column number found
// Later used for calculating the total number of rows and columns
uint16_t r{};
uint16_t c{};
for (size_t i = 0; i < n_modules(); i++) {
auto h = read_header(m_master.data_fname(i, 0));
r = std::max(r, h.row);
c = std::max(c, h.column);
// positions.push_back({h.row, h.column});
ModuleGeometry g;
g.origin_x = h.column * m_master.pixels_x();
g.origin_y = h.row * m_master.pixels_y();
@ -157,34 +155,30 @@ void RawFile::find_geometry() {
g.width = m_master.pixels_x();
g.height = m_master.pixels_y();
m_geometry.module_pixel_0.push_back(g);
}
r++;
c++;
m_geometry.pixels_y = (r * m_master.pixels_y());
m_geometry.pixels_x = (c * m_master.pixels_x());
m_geometry.pixels_x = (c * m_master.pixels_x());
m_geometry.modules_x = c;
m_geometry.modules_y = r;
m_geometry.pixels_y += static_cast<size_t>((r - 1) * cfg.module_gap_row);
}
Frame RawFile::get_frame(size_t frame_index) {
auto f = Frame(m_geometry.pixels_y, m_geometry.pixels_x, Dtype::from_bitdepth(m_master.bitdepth()));
auto f = Frame(m_geometry.pixels_y, m_geometry.pixels_x,
Dtype::from_bitdepth(m_master.bitdepth()));
std::byte *frame_buffer = f.data();
get_frame_into(frame_index, frame_buffer);
return f;
}
size_t RawFile::bytes_per_pixel() const { return m_master.bitdepth() / 8; }
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) {
void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
DetectorHeader *header) {
LOG(logDEBUG) << "RawFile::get_frame_into(" << frame_index << ")";
if (frame_index >= total_frames()) {
throw std::runtime_error(LOCATION + "Frame number out of range");
@ -192,12 +186,12 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
std::vector<size_t> frame_numbers(n_modules());
std::vector<size_t> frame_indices(n_modules(), frame_index);
// sync the frame numbers
if (n_modules() != 1) { //if we have more than one module
if (n_modules() != 1) { // if we have more than one module
for (size_t part_idx = 0; part_idx != n_modules(); ++part_idx) {
frame_numbers[part_idx] = m_subfiles[part_idx]->frame_number(frame_index);
frame_numbers[part_idx] =
m_subfiles[part_idx]->frame_number(frame_index);
}
// 1. if frame number vector is the same break
@ -218,7 +212,8 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
}
frame_numbers[min_frame_idx] =
m_subfiles[min_frame_idx]->frame_number(frame_indices[min_frame_idx]);
m_subfiles[min_frame_idx]->frame_number(
frame_indices[min_frame_idx]);
}
}
@ -226,15 +221,18 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
// get the part from each subfile and copy it to the frame
for (size_t part_idx = 0; part_idx != n_modules(); ++part_idx) {
auto corrected_idx = frame_indices[part_idx];
// This is where we start writing
auto offset = (m_geometry.module_pixel_0[part_idx].origin_y * m_geometry.pixels_x +
m_geometry.module_pixel_0[part_idx].origin_x)*m_master.bitdepth()/8;
if (m_geometry.module_pixel_0[part_idx].origin_x!=0)
throw std::runtime_error(LOCATION + " Implementation error. x pos not 0.");
//TODO! What if the files don't match?
// This is where we start writing
auto offset = (m_geometry.module_pixel_0[part_idx].origin_y *
m_geometry.pixels_x +
m_geometry.module_pixel_0[part_idx].origin_x) *
m_master.bitdepth() / 8;
if (m_geometry.module_pixel_0[part_idx].origin_x != 0)
throw std::runtime_error(LOCATION +
" Implementation error. x pos not 0.");
// TODO! What if the files don't match?
m_subfiles[part_idx]->seek(corrected_idx);
m_subfiles[part_idx]->read_into(frame_buffer + offset, header);
if (header)
@ -242,7 +240,7 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
}
} else {
//TODO! should we read row by row?
// 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() *
@ -260,7 +258,7 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
m_subfiles[part_idx]->seek(corrected_idx);
m_subfiles[part_idx]->read_into(part_buffer, header);
if(header)
if (header)
++header;
for (size_t cur_row = 0; cur_row < static_cast<size_t>(pos.height);
@ -271,15 +269,13 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
auto dest = (irow * this->m_geometry.pixels_x + icol);
dest = dest * m_master.bitdepth() / 8;
memcpy(frame_buffer + dest,
part_buffer + cur_row * pos.width *
m_master.bitdepth() / 8,
part_buffer +
cur_row * pos.width * m_master.bitdepth() / 8,
pos.width * m_master.bitdepth() / 8);
}
}
delete[] part_buffer;
}
}
std::vector<Frame> RawFile::read_n(size_t n_frames) {
@ -299,5 +295,4 @@ size_t RawFile::frame_number(size_t frame_index) {
return m_subfiles[0]->frame_number(frame_index);
}
} // namespace aare