mirror of
https://github.com/slsdetectorgroup/aare.git
synced 2026-02-21 06:28:41 +01:00
AliceMazzoleni99
218f31ce60
Reading multiple ROI's for aare - read_frame, read_n etc throws for multiple ROIs - new functions read_ROIs, read_n_ROIs - read_roi_into (used for python bindings - to not copy) all these functions use get_frame or get_frame_into where one passes the roi_index ## Refactoring: - each roi keeps track of its subfiles that one has to open e.g. subfiles can be opened several times - refactored class DetectorGeometry - keep track of the updated module geometries in new class ROIGeometry. - ModuleGeometry updates based on ROI ## ROIGeometry: - stores number of modules overlapping with ROI and its indices - size of ROI Note: only tested size of the resulting frames not the actual values --------- Co-authored-by: Erik Fröjdh <erik.frojdh@psi.ch> Co-authored-by: Erik Fröjdh <erik.frojdh@gmail.com>
498 lines
18 KiB
C++
498 lines
18 KiB
C++
// SPDX-License-Identifier: MPL-2.0
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#include "aare/RawFile.hpp"
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#include "aare/DetectorGeometry.hpp"
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#include "aare/PixelMap.hpp"
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#include "aare/ROIGeometry.hpp"
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#include "aare/algorithm.hpp"
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#include "aare/defs.hpp"
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#include "aare/logger.hpp"
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#include <fmt/format.h>
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#include <nlohmann/json.hpp>
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using json = nlohmann::json;
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namespace aare {
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RawFile::RawFile(const std::filesystem::path &fname, const std::string &mode)
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: m_master(fname),
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m_geometry(m_master.geometry(), m_master.pixels_x(), m_master.pixels_y(),
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m_master.udp_interfaces_per_module(), m_master.quad()) {
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m_mode = mode;
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m_subfiles.resize(m_master.rois().has_value() ? m_master.rois()->size()
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: 1);
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if (mode == "r") {
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if (m_master.rois().has_value()) {
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m_ROI_geometries.reserve(m_master.rois()->size());
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// iterate over all ROIS
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size_t roi_index = 0;
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const auto rois = m_master.rois().value();
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for (const auto &roi : rois) {
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m_ROI_geometries.push_back(ROIGeometry(roi, m_geometry));
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// open subfiles
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open_subfiles(roi_index);
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++roi_index;
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}
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} else {
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// no ROI use full detector
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m_ROI_geometries.reserve(1);
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m_ROI_geometries.push_back(ROIGeometry(m_geometry));
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open_subfiles(0);
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}
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} else {
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throw std::runtime_error(LOCATION +
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" Unsupported mode. Can only read RawFiles.");
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}
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}
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Frame RawFile::read_roi(const size_t roi_index) {
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if (!m_master.rois()) {
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throw std::runtime_error(LOCATION +
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"No ROIs defined in the master file.");
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}
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if (roi_index >= m_ROI_geometries.size()) {
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throw std::runtime_error(LOCATION + "ROI index out of range.");
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}
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return get_frame(m_current_frame++, roi_index);
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}
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std::vector<Frame> RawFile::read_rois() {
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if (!m_master.rois()) {
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throw std::runtime_error(LOCATION +
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"No ROIs defined in the master file.");
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}
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const size_t num_rois = m_ROI_geometries.size();
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std::vector<Frame> frames;
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frames.reserve(num_rois);
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for (size_t roi_idx = 0; roi_idx < num_rois; ++roi_idx) {
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frames.push_back(get_frame(m_current_frame, roi_idx));
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}
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++m_current_frame;
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return frames;
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}
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Frame RawFile::read_frame() {
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(LOCATION +
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"Multiple ROIs defined in the master file. "
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"Use read_ROIs() instead.");
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}
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return get_frame(m_current_frame++);
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}
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Frame RawFile::read_frame(size_t frame_number) {
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(
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LOCATION + "Multiple ROIs defined in the master file. "
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"Use read_ROIs(const size_t frame_number) instead.");
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}
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seek(frame_number);
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return read_frame();
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}
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void RawFile::read_into(std::byte *image_buf, size_t n_frames) {
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// TODO: implement this in a more efficient way
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(LOCATION +
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"Cannot use read_into for multiple ROIs.");
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}
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for (size_t i = 0; i < n_frames; i++) {
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this->get_frame_into(m_current_frame++, image_buf);
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image_buf += bytes_per_frame();
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}
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}
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void RawFile::read_into(std::byte *image_buf) {
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(LOCATION +
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"Cannot use read_into for multiple ROIs. Use "
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"read_roi_into() for a single ROI instead.");
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}
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return get_frame_into(m_current_frame++, image_buf);
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}
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void RawFile::read_roi_into(std::byte *image_buf, const size_t roi_index,
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const size_t frame_number, DetectorHeader *header) {
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if (!m_master.rois().has_value()) {
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throw std::runtime_error(LOCATION +
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"No ROIs defined in the master file.");
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}
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if (roi_index >= num_rois()) {
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throw std::runtime_error(LOCATION + "ROI index out of range.");
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}
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return get_frame_into(frame_number, image_buf, roi_index, header);
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}
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void RawFile::read_into(std::byte *image_buf, DetectorHeader *header) {
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(LOCATION +
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"Cannot use read_into for multiple ROIs. Use "
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"read_roi_into() for a single ROI instead.");
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}
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return get_frame_into(m_current_frame++, image_buf, 0, header);
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}
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void RawFile::read_into(std::byte *image_buf, size_t n_frames,
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DetectorHeader *header) {
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// return get_frame_into(m_current_frame++, image_buf, header);
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(
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LOCATION +
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"Cannot use read_into for multiple ROIs."); // TODO: maybe pass
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// roi_index so one can
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// use read_into for a
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// specific ROI
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}
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for (size_t i = 0; i < n_frames; i++) {
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this->get_frame_into(m_current_frame++, image_buf, 0, header);
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image_buf += bytes_per_frame();
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if (header)
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header += m_ROI_geometries[0].num_modules_in_roi();
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}
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}
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size_t RawFile::bytes_per_frame() {
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(
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LOCATION + "Pass the desired roi_index to bytes_per_frame to get "
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"bytes_per_frame for the specific ROI. ");
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}
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return bytes_per_frame(0);
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}
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size_t RawFile::bytes_per_frame(const size_t roi_index) {
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return m_ROI_geometries.at(roi_index).pixels_x() *
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m_ROI_geometries.at(roi_index).pixels_y() * m_master.bitdepth() /
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bits_per_byte;
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}
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size_t RawFile::pixels_per_frame() {
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(
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LOCATION + "Pass the desired roi_index to pixels_per_frame to get "
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"pixels_per_frame for the specific ROI. ");
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}
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return pixels_per_frame(0);
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}
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size_t RawFile::pixels_per_frame(const size_t roi_index) {
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return m_ROI_geometries.at(roi_index).pixels_x() *
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m_ROI_geometries.at(roi_index).pixels_y();
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}
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DetectorType RawFile::detector_type() const { return m_master.detector_type(); }
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void RawFile::seek(size_t frame_index) {
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// check if the frame number is greater than the total frames
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// if frame_number == total_frames, then the next read will throw an
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// error
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if (frame_index > total_frames()) {
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throw std::runtime_error(
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fmt::format("frame number {} is greater than total frames {}",
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frame_index, total_frames()));
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}
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m_current_frame = frame_index;
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}
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size_t RawFile::tell() { return m_current_frame; }
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size_t RawFile::total_frames() const { return m_master.frames_in_file(); }
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size_t RawFile::rows() const {
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(LOCATION +
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"Pass the desired roi_index to rows to get "
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"rows for the specific ROI. ");
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}
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return rows(0);
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}
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size_t RawFile::rows(const size_t roi_index) const {
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return m_ROI_geometries.at(roi_index).pixels_y();
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}
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size_t RawFile::cols() const {
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if (m_master.rois().has_value() && m_master.rois()->size() > 1) {
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throw std::runtime_error(LOCATION +
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"Pass the desired roi_index to cols to get "
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"cols for the specific ROI. ");
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}
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return cols(0);
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}
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size_t RawFile::cols(const size_t roi_index) const {
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return m_ROI_geometries.at(roi_index).pixels_x();
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}
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size_t RawFile::bitdepth() const { return m_master.bitdepth(); }
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xy RawFile::geometry() const {
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return xy{static_cast<uint32_t>(m_geometry.modules_y()),
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static_cast<uint32_t>(m_geometry.modules_x())};
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}
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size_t RawFile::n_modules() const { return m_geometry.n_modules(); };
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size_t RawFile::num_rois() const {
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if (m_master.rois().has_value()) {
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return m_master.rois()->size();
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} else {
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return 0;
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}
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};
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const ROIGeometry &RawFile::roi_geometries(size_t roi_index) const {
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return m_ROI_geometries[roi_index];
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}
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std::vector<size_t> RawFile::n_modules_in_roi() const {
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std::vector<size_t> results(m_ROI_geometries.size());
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std::transform(
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m_ROI_geometries.begin(), m_ROI_geometries.end(), results.begin(),
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[](const ROIGeometry &roi) { return roi.num_modules_in_roi(); });
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return results;
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};
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void RawFile::open_subfiles(const size_t roi_index) {
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if (m_mode == "r") {
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m_subfiles[roi_index].reserve(
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m_ROI_geometries[roi_index].num_modules_in_roi());
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auto module_indices =
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m_ROI_geometries[roi_index].module_indices_in_roi();
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for (const size_t i :
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m_ROI_geometries[roi_index].module_indices_in_roi()) {
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const auto pos = m_geometry.get_module_geometries(i);
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m_subfiles[roi_index].emplace_back(std::make_unique<RawSubFile>(
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m_master.data_fname(i, 0), m_master.detector_type(), pos.height,
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pos.width, m_master.bitdepth(), pos.row_index, pos.col_index));
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}
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} else {
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throw std::runtime_error(LOCATION +
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"Unsupported mode. Can only read RawFiles.");
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}
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}
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DetectorHeader RawFile::read_header(const std::filesystem::path &fname) {
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DetectorHeader h{};
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FILE *fp = fopen(fname.string().c_str(), "r");
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if (!fp)
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throw std::runtime_error(
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fmt::format("Could not open: {} for reading", fname.string()));
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size_t const rc = fread(reinterpret_cast<char *>(&h), sizeof(h), 1, fp);
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if (rc != 1)
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throw std::runtime_error(LOCATION + "Could not read header from file");
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if (fclose(fp)) {
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throw std::runtime_error(LOCATION + "Could not close file");
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}
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return h;
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}
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RawMasterFile RawFile::master() const { return m_master; }
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Frame RawFile::get_frame(size_t frame_index, const size_t roi_index) {
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auto f = Frame(m_ROI_geometries[roi_index].pixels_y(),
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m_ROI_geometries[roi_index].pixels_x(),
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Dtype::from_bitdepth(m_master.bitdepth()));
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std::byte *frame_buffer = f.data();
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get_frame_into(frame_index, frame_buffer, roi_index);
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return f;
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}
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size_t RawFile::bytes_per_pixel() const { return m_master.bitdepth() / 8; }
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void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
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const size_t roi_index, DetectorHeader *header) {
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LOG(logDEBUG) << "RawFile::get_frame_into(" << frame_index << ")";
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if (frame_index >= total_frames()) {
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throw std::runtime_error(LOCATION + "Frame number out of range");
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}
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std::vector<size_t> frame_numbers(
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m_ROI_geometries[roi_index].num_modules_in_roi());
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std::vector<size_t> frame_indices(
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m_ROI_geometries[roi_index].num_modules_in_roi(), frame_index);
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// sync the frame numbers
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if (m_ROI_geometries[roi_index].num_modules_in_roi() !=
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1) { // if we have more than one module
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for (size_t part_idx = 0;
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part_idx != m_ROI_geometries[roi_index].num_modules_in_roi();
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++part_idx) {
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frame_numbers[part_idx] =
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m_subfiles[roi_index][part_idx]->frame_number(frame_index);
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}
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// 1. if frame number vector is the same break
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while (!all_equal(frame_numbers)) {
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// 2. find the index of the minimum frame number,
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auto min_frame_idx = std::distance(
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frame_numbers.begin(),
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std::min_element(frame_numbers.begin(), frame_numbers.end()));
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// 3. increase its index and update its respective frame
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// number
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frame_indices[min_frame_idx]++;
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// 4. if we can't increase its index => throw error
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if (frame_indices[min_frame_idx] >= total_frames()) {
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throw std::runtime_error(LOCATION +
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"Frame number out of range");
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}
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frame_numbers[min_frame_idx] =
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m_subfiles[roi_index][min_frame_idx]->frame_number(
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frame_indices[min_frame_idx]);
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}
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}
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if (m_master.geometry().col == 1) {
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// get the part from each subfile and copy it to the frame
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for (size_t part_idx = 0;
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part_idx != m_ROI_geometries[roi_index].num_modules_in_roi();
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++part_idx) {
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auto corrected_idx = frame_indices[part_idx];
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// This is where we start writing
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auto offset =
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(m_geometry
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.get_module_geometries(
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m_ROI_geometries[roi_index].module_indices_in_roi(
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part_idx))
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.origin_y *
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m_ROI_geometries[roi_index].pixels_x() +
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m_geometry
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.get_module_geometries(
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m_ROI_geometries[roi_index].module_indices_in_roi(
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part_idx))
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.origin_x) *
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m_master.bitdepth() / 8;
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if (m_geometry
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.get_module_geometries(
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m_ROI_geometries[roi_index].module_indices_in_roi(
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part_idx))
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.origin_x != 0)
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throw std::runtime_error(
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LOCATION +
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" Implementation error. x pos not 0."); // TODO:
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// origin
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// can still
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// change if
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// roi
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// changes
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// TODO! What if the files don't match?
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m_subfiles[roi_index][part_idx]->seek(corrected_idx);
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m_subfiles[roi_index][part_idx]->read_into(frame_buffer + offset,
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header);
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if (header)
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++header;
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}
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} else {
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// TODO! should we read row by row?
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// create a buffer large enough to hold a full module
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auto bytes_per_part =
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m_master.pixels_y() * m_master.pixels_x() * m_master.bitdepth() /
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8; // TODO! replace with image_size_in_bytes // TODO
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// shouldnt it only be the module size? - check
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auto *part_buffer = new std::byte[bytes_per_part];
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// TODO! if we have many submodules we should reorder them on
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// the module level
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for (size_t part_idx = 0;
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part_idx != m_ROI_geometries[roi_index].num_modules_in_roi();
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++part_idx) {
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auto pos = m_geometry.get_module_geometries(
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m_ROI_geometries[roi_index].module_indices_in_roi(part_idx));
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auto corrected_idx = frame_indices[part_idx];
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m_subfiles[roi_index][part_idx]->seek(corrected_idx);
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m_subfiles[roi_index][part_idx]->read_into(part_buffer, header);
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if (header)
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++header;
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for (size_t cur_row = 0; cur_row < static_cast<size_t>(pos.height);
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cur_row++) {
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auto irow = (pos.origin_y + cur_row);
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auto icol = pos.origin_x;
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auto dest =
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(irow * m_ROI_geometries[roi_index].pixels_x() + icol);
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dest = dest * m_master.bitdepth() / 8;
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memcpy(frame_buffer + dest,
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part_buffer +
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cur_row * pos.width * m_master.bitdepth() / 8,
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pos.width * m_master.bitdepth() / 8);
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}
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}
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delete[] part_buffer;
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}
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}
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std::vector<Frame> RawFile::read_n(size_t n_frames) {
|
|
// TODO: implement this in a more efficient way
|
|
if (num_rois() > 1) {
|
|
throw std::runtime_error(LOCATION +
|
|
"Multiple ROIs defined in the master "
|
|
"file. Use "
|
|
"read_num_rois for a specific ROI or use "
|
|
"read_ROIs to read one frame after "
|
|
"the other.");
|
|
}
|
|
|
|
std::vector<Frame> frames;
|
|
frames.reserve(n_frames);
|
|
for (size_t i = 0; i < n_frames; i++) {
|
|
frames.push_back(this->get_frame(m_current_frame));
|
|
m_current_frame++;
|
|
}
|
|
return frames;
|
|
}
|
|
|
|
std::vector<Frame> RawFile::read_n_with_roi(const size_t n_frames,
|
|
const size_t roi_index) {
|
|
if (roi_index >= num_rois()) {
|
|
throw std::runtime_error(LOCATION + "ROI index out of range.");
|
|
}
|
|
|
|
std::vector<Frame> frames;
|
|
frames.reserve(n_frames);
|
|
for (size_t i = 0; i < n_frames; i++) {
|
|
frames.push_back(this->get_frame(m_current_frame, roi_index));
|
|
m_current_frame++;
|
|
}
|
|
return frames;
|
|
}
|
|
|
|
size_t RawFile::frame_number(size_t frame_index) {
|
|
if (frame_index >= m_master.frames_in_file()) {
|
|
throw std::runtime_error(LOCATION + " Frame number out of range");
|
|
}
|
|
return m_subfiles[0][0]->frame_number(frame_index);
|
|
}
|
|
|
|
} // namespace aare
|