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https://github.com/slsdetectorgroup/aare.git
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Taking v1 as the first release (#92)
- file reading - decoding master file
This commit is contained in:
Erik Fröjdh
328
src/RawMasterFile.cpp
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328
src/RawMasterFile.cpp
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#include "aare/RawMasterFile.hpp"
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#include <sstream>
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namespace aare {
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RawFileNameComponents::RawFileNameComponents(
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const std::filesystem::path &fname) {
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m_base_path = fname.parent_path();
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m_base_name = fname.stem();
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m_ext = fname.extension();
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if (m_ext != ".json" && m_ext != ".raw") {
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throw std::runtime_error(LOCATION +
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"Unsupported file type. (only .json or .raw)");
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}
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// parse file index
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try {
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auto pos = m_base_name.rfind('_');
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m_file_index = std::stoi(m_base_name.substr(pos + 1));
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} catch (const std::invalid_argument &e) {
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throw std::runtime_error(LOCATION + "Could not parse file index");
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}
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// remove master from base name
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auto pos = m_base_name.find("_master_");
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if (pos != std::string::npos) {
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m_base_name.erase(pos);
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} else {
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throw std::runtime_error(LOCATION +
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"Could not find _master_ in file name");
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}
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}
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std::filesystem::path RawFileNameComponents::master_fname() const {
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return m_base_path /
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fmt::format("{}_master_{}{}", m_base_name, m_file_index, m_ext);
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}
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std::filesystem::path RawFileNameComponents::data_fname(size_t mod_id,
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size_t file_id) const {
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return m_base_path / fmt::format("{}_d{}_f{}_{}.raw", m_base_name, mod_id,
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file_id, m_file_index);
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}
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const std::filesystem::path &RawFileNameComponents::base_path() const {
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return m_base_path;
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}
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const std::string &RawFileNameComponents::base_name() const {
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return m_base_name;
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}
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const std::string &RawFileNameComponents::ext() const { return m_ext; }
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int RawFileNameComponents::file_index() const { return m_file_index; }
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// "[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]"
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ScanParameters::ScanParameters(const std::string& par){
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std::istringstream iss(par.substr(1, par.size()-2));
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std::string line;
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while(std::getline(iss, line)){
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if(line == "enabled"){
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m_enabled = true;
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}else if(line.find("dac") != std::string::npos){
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m_dac = line.substr(4);
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}else if(line.find("start") != std::string::npos){
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m_start = std::stoi(line.substr(6));
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}else if(line.find("stop") != std::string::npos){
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m_stop = std::stoi(line.substr(5));
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}else if(line.find("step") != std::string::npos){
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m_step = std::stoi(line.substr(5));
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}
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}
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}
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int ScanParameters::start() const { return m_start; }
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int ScanParameters::stop() const { return m_stop; }
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int ScanParameters::step() const { return m_step; }
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const std::string &ScanParameters::dac() const { return m_dac; }
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bool ScanParameters::enabled() const { return m_enabled; }
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RawMasterFile::RawMasterFile(const std::filesystem::path &fpath)
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: m_fnc(fpath) {
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if (!std::filesystem::exists(fpath)) {
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throw std::runtime_error(LOCATION + " File does not exist");
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}
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if (m_fnc.ext() == ".json") {
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parse_json(fpath);
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} else if (m_fnc.ext() == ".raw") {
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parse_raw(fpath);
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} else {
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throw std::runtime_error(LOCATION + "Unsupported file type");
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}
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}
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std::filesystem::path RawMasterFile::data_fname(size_t mod_id,
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size_t file_id) const {
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return m_fnc.data_fname(mod_id, file_id);
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}
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const std::string &RawMasterFile::version() const { return m_version; }
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const DetectorType &RawMasterFile::detector_type() const { return m_type; }
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const TimingMode &RawMasterFile::timing_mode() const { return m_timing_mode; }
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size_t RawMasterFile::image_size_in_bytes() const {
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return m_image_size_in_bytes;
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}
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size_t RawMasterFile::frames_in_file() const { return m_frames_in_file; }
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size_t RawMasterFile::pixels_y() const { return m_pixels_y; }
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size_t RawMasterFile::pixels_x() const { return m_pixels_x; }
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size_t RawMasterFile::max_frames_per_file() const {
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return m_max_frames_per_file;
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}
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size_t RawMasterFile::bitdepth() const { return m_bitdepth; }
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size_t RawMasterFile::frame_padding() const { return m_frame_padding; }
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const FrameDiscardPolicy &RawMasterFile::frame_discard_policy() const {
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return m_frame_discard_policy;
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}
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size_t RawMasterFile::total_frames_expected() const {
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return m_total_frames_expected;
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}
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std::optional<size_t> RawMasterFile::number_of_rows() const {
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return m_number_of_rows;
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}
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xy RawMasterFile::geometry() const { return m_geometry; }
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std::optional<uint8_t> RawMasterFile::quad() const { return m_quad; }
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// optional values, these may or may not be present in the master file
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// and are therefore modeled as std::optional
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std::optional<size_t> RawMasterFile::analog_samples() const {
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return m_analog_samples;
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}
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std::optional<size_t> RawMasterFile::digital_samples() const {
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return m_digital_samples;
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}
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std::optional<size_t> RawMasterFile::transceiver_samples() const {
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return m_transceiver_samples;
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}
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ScanParameters RawMasterFile::scan_parameters() const {
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return m_scan_parameters;
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}
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void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
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std::ifstream ifs(fpath);
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json j;
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ifs >> j;
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double v = j["Version"];
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m_version = fmt::format("{:.1f}", v);
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m_type = StringTo<DetectorType>(j["Detector Type"].get<std::string>());
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m_timing_mode = StringTo<TimingMode>(j["Timing Mode"].get<std::string>());
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m_geometry = {j["Geometry"]["y"], j["Geometry"]["x"]};
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m_image_size_in_bytes = j["Image Size in bytes"];
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m_frames_in_file = j["Frames in File"];
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m_pixels_y = j["Pixels"]["y"];
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m_pixels_x = j["Pixels"]["x"];
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m_max_frames_per_file = j["Max Frames Per File"];
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// Not all detectors write the bitdepth but in case
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// its not there it is 16
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try {
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m_bitdepth = j.at("Dynamic Range");
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} catch (const json::out_of_range &e) {
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m_bitdepth = 16;
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}
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m_total_frames_expected = j["Total Frames"];
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m_frame_padding = j["Frame Padding"];
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m_frame_discard_policy = StringTo<FrameDiscardPolicy>(
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j["Frame Discard Policy"].get<std::string>());
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try {
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m_number_of_rows = j.at("Number of rows");
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} catch (const json::out_of_range &e) {
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// keep the optional empty
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}
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// ----------------------------------------------------------------
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// Special treatment of analog flag because of Moench03
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try{
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m_analog_flag = j.at("Analog Flag");
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}catch (const json::out_of_range &e) {
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// if it doesn't work still set it to one
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// to try to decode analog samples (Old Moench03)
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m_analog_flag = 1;
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}
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try {
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if (m_analog_flag) {
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m_analog_samples = j.at("Analog Samples");
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}
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} catch (const json::out_of_range &e) {
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// keep the optional empty
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// and set analog flag to 0
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m_analog_flag = 0;
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}
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//-----------------------------------------------------------------
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try {
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m_quad = j.at("Quad");
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} catch (const json::out_of_range &e) {
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// keep the optional empty
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}
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// try{
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// std::string adc_mask = j.at("ADC Mask");
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// m_adc_mask = std::stoul(adc_mask, nullptr, 16);
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// }catch (const json::out_of_range &e) {
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// m_adc_mask = 0;
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// }
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try {
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int digital_flag = j.at("Digital Flag");
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if (digital_flag) {
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m_digital_samples = j.at("Digital Samples");
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}
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} catch (const json::out_of_range &e) {
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// keep the optional empty
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}
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try{
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m_transceiver_flag = j.at("Transceiver Flag");
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if(m_transceiver_flag){
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m_transceiver_samples = j.at("Transceiver Samples");
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}
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}catch (const json::out_of_range &e) {
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// keep the optional empty
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}
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try{
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std::string scan_parameters = j.at("Scan Parameters");
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m_scan_parameters = ScanParameters(scan_parameters);
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}catch (const json::out_of_range &e) {
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// not a scan
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}
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// Update detector type for Moench
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// TODO! How does this work with old .raw master files?
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#ifdef AARE_VERBOSE
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fmt::print("Detecting Moench03: m_pixels_y: {}, m_analog_samples: {}\n",
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m_pixels_y, m_analog_samples.value_or(0));
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#endif
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if (m_type == DetectorType::Moench && !m_analog_samples &&
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m_pixels_y == 400) {
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m_type = DetectorType::Moench03;
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} else if (m_type == DetectorType::Moench && m_pixels_y == 400 &&
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m_analog_samples == 5000) {
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m_type = DetectorType::Moench03_old;
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}
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}
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void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
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std::ifstream ifs(fpath);
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for (std::string line; std::getline(ifs, line);) {
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if (line == "#Frame Header")
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break;
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auto pos = line.find(':');
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auto key_pos = pos;
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while (key_pos != std::string::npos && std::isspace(line[--key_pos]))
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;
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if (key_pos != std::string::npos) {
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auto key = line.substr(0, key_pos + 1);
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auto value = line.substr(pos + 2);
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// do the actual parsing
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if (key == "Version") {
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m_version = value;
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} else if (key == "TimeStamp") {
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} else if (key == "Detector Type") {
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m_type = StringTo<DetectorType>(value);
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} else if (key == "Timing Mode") {
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m_timing_mode = StringTo<TimingMode>(value);
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} else if (key == "Image Size") {
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m_image_size_in_bytes = std::stoi(value);
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} else if (key == "Frame Padding") {
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m_frame_padding = std::stoi(value);
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// } else if (key == "Frame Discard Policy"){
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// m_frame_discard_policy =
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// StringTo<FrameDiscardPolicy>(value);
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// } else if (key == "Number of rows"){
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// m_number_of_rows = std::stoi(value);
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} else if (key == "Analog Flag") {
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m_analog_flag = std::stoi(value);
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} else if (key == "Digital Flag") {
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m_digital_flag = std::stoi(value);
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} else if (key == "Analog Samples") {
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if (m_analog_flag == 1) {
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m_analog_samples = std::stoi(value);
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}
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} else if (key == "Digital Samples") {
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if (m_digital_flag == 1) {
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m_digital_samples = std::stoi(value);
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}
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} else if (key == "Frames in File") {
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m_frames_in_file = std::stoi(value);
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// } else if (key == "ADC Mask") {
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// m_adc_mask = std::stoi(value, nullptr, 16);
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} else if (key == "Pixels") {
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// Total number of pixels cannot be found yet looking at
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// submodule
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pos = value.find(',');
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m_pixels_x = std::stoi(value.substr(1, pos));
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m_pixels_y = std::stoi(value.substr(pos + 1));
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} else if (key == "Total Frames") {
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m_total_frames_expected = std::stoi(value);
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} else if (key == "Dynamic Range") {
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m_bitdepth = std::stoi(value);
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} else if (key == "Quad") {
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m_quad = std::stoi(value);
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} else if (key == "Max Frames Per File") {
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m_max_frames_per_file = std::stoi(value);
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} else if (key == "Geometry") {
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pos = value.find(',');
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m_geometry = {
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static_cast<uint32_t>(std::stoi(value.substr(1, pos))),
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static_cast<uint32_t>(std::stoi(value.substr(pos + 1)))};
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}
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}
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}
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}
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} // namespace aare
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