mirror of
https://github.com/slsdetectorgroup/aare.git
synced 2025-06-20 02:57:13 +02:00
wip at fixing hdf5 master file
This commit is contained in:
@ -1,4 +1,5 @@
|
||||
#include "aare/Hdf5MasterFile.hpp"
|
||||
#include "aare/logger.hpp"
|
||||
#include <sstream>
|
||||
#include <iomanip>
|
||||
namespace aare {
|
||||
@ -62,32 +63,6 @@ const std::string &Hdf5FileNameComponents::base_name() const {
|
||||
const std::string &Hdf5FileNameComponents::ext() const { return m_ext; }
|
||||
int Hdf5FileNameComponents::file_index() const { return m_file_index; }
|
||||
|
||||
// "[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]"
|
||||
/*ScanParameters::ScanParameters(const std::string &par) {
|
||||
std::istringstream iss(par.substr(1, par.size() - 2));
|
||||
std::string line;
|
||||
while (std::getline(iss, line)) {
|
||||
if (line == "enabled") {
|
||||
m_enabled = true;
|
||||
} else if (line.find("dac") != std::string::npos) {
|
||||
m_dac = line.substr(4);
|
||||
} else if (line.find("start") != std::string::npos) {
|
||||
m_start = std::stoi(line.substr(6));
|
||||
} else if (line.find("stop") != std::string::npos) {
|
||||
m_stop = std::stoi(line.substr(5));
|
||||
} else if (line.find("step") != std::string::npos) {
|
||||
m_step = std::stoi(line.substr(5));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
int ScanParameters::start() const { return m_start; }
|
||||
int ScanParameters::stop() const { return m_stop; }
|
||||
void ScanParameters::increment_stop() { m_stop += 1; };
|
||||
//int ScanParameters::step() const { return m_step; }
|
||||
const std::string &ScanParameters::dac() const { return m_dac; }
|
||||
bool ScanParameters::enabled() const { return m_enabled; }
|
||||
*/
|
||||
Hdf5MasterFile::Hdf5MasterFile(const std::filesystem::path &fpath)
|
||||
: m_fnc(fpath) {
|
||||
if (!std::filesystem::exists(fpath)) {
|
||||
@ -131,18 +106,12 @@ size_t Hdf5MasterFile::total_frames_expected() const {
|
||||
return m_total_frames_expected;
|
||||
}
|
||||
|
||||
std::optional<size_t> Hdf5MasterFile::number_of_rows() const {
|
||||
return m_number_of_rows;
|
||||
}
|
||||
|
||||
xy Hdf5MasterFile::geometry() const { return m_geometry; }
|
||||
|
||||
size_t Hdf5MasterFile::n_modules() const {
|
||||
return m_geometry.row * m_geometry.col;
|
||||
}
|
||||
|
||||
std::optional<uint8_t> Hdf5MasterFile::quad() const { return m_quad; }
|
||||
|
||||
// optional values, these may or may not be present in the master file
|
||||
// and are therefore modeled as std::optional
|
||||
std::optional<size_t> Hdf5MasterFile::analog_samples() const {
|
||||
@ -156,13 +125,17 @@ std::optional<size_t> Hdf5MasterFile::transceiver_samples() const {
|
||||
return m_transceiver_samples;
|
||||
}
|
||||
|
||||
/*
|
||||
std::optional<size_t> Hdf5MasterFile::number_of_rows() const {
|
||||
return m_number_of_rows;
|
||||
}
|
||||
|
||||
std::optional<uint8_t> Hdf5MasterFile::quad() const { return m_quad; }
|
||||
|
||||
std::optional<ROI> Hdf5MasterFile::roi() const { return m_roi; }
|
||||
|
||||
ScanParameters Hdf5MasterFile::scan_parameters() const {
|
||||
return m_scan_parameters;
|
||||
}
|
||||
*/
|
||||
|
||||
// std::optional<ROI> Hdf5MasterFile::roi() const { return m_roi; }
|
||||
|
||||
const std::string Hdf5MasterFile::metadata_group_name =
|
||||
"/entry/instrument/detector/";
|
||||
@ -202,59 +175,59 @@ void Hdf5MasterFile::parse_acquisition_metadata(
|
||||
H5::H5File file(fpath, H5F_ACC_RDONLY);
|
||||
|
||||
// Attribute - version
|
||||
double dVersion{0.0};
|
||||
{
|
||||
H5::Attribute attr = file.openAttribute("version");
|
||||
H5::DataType attr_type = attr.getDataType();
|
||||
double value{0.0};
|
||||
attr.read(attr_type, &value);
|
||||
attr.read(attr_type, &dVersion);
|
||||
std::ostringstream oss;
|
||||
oss << std::fixed << std::setprecision(1) << value;
|
||||
oss << std::fixed << std::setprecision(1) << dVersion;
|
||||
m_version = oss.str();
|
||||
// fmt::print("Version: {}\n", m_version);
|
||||
LOG(logDEBUG) << "Version: " << m_version;
|
||||
}
|
||||
|
||||
// Scalar Dataset
|
||||
// Detector Type
|
||||
m_type = StringTo<DetectorType>(h5_get_scalar_dataset<std::string>(
|
||||
file, std::string(metadata_group_name + "Detector Type")));
|
||||
// fmt::print("Detector Type: {}\n", (ToString(m_type)));
|
||||
LOG(logDEBUG) << "Detector Type: " << ToString(m_type);
|
||||
|
||||
// Timing Mode
|
||||
m_timing_mode = StringTo<TimingMode>(h5_get_scalar_dataset<std::string>(
|
||||
file, std::string(metadata_group_name + "Timing Mode")));
|
||||
// fmt::print("Timing Mode: {}\n", (ToString(m_timing_mode)));
|
||||
LOG(logDEBUG) << "Timing Mode: " << ToString(m_timing_mode);
|
||||
|
||||
// Geometry
|
||||
m_geometry.row = h5_get_scalar_dataset<int>(
|
||||
file, std::string(metadata_group_name + "Geometry in y axis"));
|
||||
m_geometry.col = h5_get_scalar_dataset<int>(
|
||||
file, std::string(metadata_group_name + "Geometry in x axis"));
|
||||
// fmt::print("Geometry: {}\n", m_geometry.to_string());
|
||||
LOG(logDEBUG) << "Geometry: " << m_geometry.to_string();
|
||||
|
||||
// Image Size
|
||||
m_image_size_in_bytes = h5_get_scalar_dataset<int>(
|
||||
file, std::string(metadata_group_name + "Image Size"));
|
||||
// fmt::print("Image size: {}\n", m_image_size_in_bytes);
|
||||
LOG(logDEBUG) << "Image size: {}\n" << m_image_size_in_bytes;
|
||||
|
||||
// Frames in File
|
||||
m_frames_in_file = h5_get_scalar_dataset<uint64_t>(
|
||||
file, std::string(metadata_group_name + "Frames in File"));
|
||||
// fmt::print("Frames in File: {}\n", m_frames_in_file);
|
||||
LOG(logDEBUG) << "Frames in File: " << m_frames_in_file;
|
||||
|
||||
// Pixels
|
||||
m_pixels_y = h5_get_scalar_dataset<int>(
|
||||
file,
|
||||
std::string(metadata_group_name + "Number of pixels in y axis"));
|
||||
// fmt::print("Pixels in y: {}\n", m_pixels_y);
|
||||
LOG(logDEBUG) << "Pixels in y: " << m_pixels_y;
|
||||
m_pixels_x = h5_get_scalar_dataset<int>(
|
||||
file,
|
||||
std::string(metadata_group_name + "Number of pixels in x axis"));
|
||||
// fmt::print("Pixels in x: {}\n", m_pixels_x);
|
||||
LOG(logDEBUG) << "Pixels in x: " << m_pixels_x;
|
||||
|
||||
// Max Frames per File
|
||||
m_max_frames_per_file = h5_get_scalar_dataset<int>(
|
||||
file, std::string(metadata_group_name + "Maximum frames per file"));
|
||||
// fmt::print("Max frames per File: {}\n", m_max_frames_per_file);
|
||||
LOG(logDEBUG) << "Max frames per File: " << m_max_frames_per_file;
|
||||
|
||||
// Bit Depth
|
||||
// Not all detectors write the bitdepth but in case
|
||||
@ -266,27 +239,26 @@ void Hdf5MasterFile::parse_acquisition_metadata(
|
||||
} catch (H5::FileIException &e) {
|
||||
m_bitdepth = 16;
|
||||
}
|
||||
// fmt::print("Bit Depth: {}\n", m_bitdepth);
|
||||
LOG(logDEBUG) << "Bit Depth: " << m_bitdepth;
|
||||
H5Eset_auto(H5E_DEFAULT, reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
stderr);
|
||||
|
||||
// Total Frames
|
||||
m_total_frames_expected = h5_get_scalar_dataset<uint64_t>(
|
||||
file, std::string(metadata_group_name + "Total Frames"));
|
||||
// fmt::print("Total Frames: {}\n", m_total_frames_expected);
|
||||
LOG(logDEBUG) << "Total Frames: " << m_total_frames_expected;
|
||||
|
||||
// Frame Padding
|
||||
m_frame_padding = h5_get_scalar_dataset<int>(
|
||||
file, std::string(metadata_group_name + "Frame Padding"));
|
||||
// fmt::print("Frame Padding: {}\n", m_frame_padding);
|
||||
LOG(logDEBUG) << "Frame Padding: " << m_frame_padding;
|
||||
|
||||
// Frame Discard Policy
|
||||
m_frame_discard_policy =
|
||||
StringTo<FrameDiscardPolicy>(h5_get_scalar_dataset<std::string>(
|
||||
file,
|
||||
std::string(metadata_group_name + "Frame Discard Policy")));
|
||||
// fmt::print("Frame Discard Policy: {}\n",
|
||||
// (ToString(m_frame_discard_policy)));
|
||||
LOG(logDEBUG) << "Frame Discard Policy: " << ToString(m_frame_discard_policy);
|
||||
|
||||
// Number of rows
|
||||
// Not all detectors write the Number of rows but in case
|
||||
@ -297,7 +269,7 @@ void Hdf5MasterFile::parse_acquisition_metadata(
|
||||
} catch (H5::FileIException &e) {
|
||||
// keep the optional empty
|
||||
}
|
||||
// fmt::print("Number of rows: {}\n", m_number_of_rows);
|
||||
LOG(logDEBUG) << "Number of rows: " << m_number_of_rows;
|
||||
H5Eset_auto(H5E_DEFAULT, reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
stderr);
|
||||
|
||||
@ -313,7 +285,7 @@ void Hdf5MasterFile::parse_acquisition_metadata(
|
||||
// to try to decode analog samples (Old Moench03)
|
||||
m_analog_flag = 1;
|
||||
}
|
||||
// fmt::print("Analog Flag: {}\n", m_analog_flag);
|
||||
LOG(logDEBUG) << "Analog Flag: " << m_analog_flag;
|
||||
H5Eset_auto(H5E_DEFAULT, reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
stderr);
|
||||
|
||||
@ -331,7 +303,7 @@ void Hdf5MasterFile::parse_acquisition_metadata(
|
||||
}
|
||||
H5Eset_auto(H5E_DEFAULT, reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
stderr);
|
||||
// fmt::print("Analog Samples: {}\n", m_analog_samples);
|
||||
LOG(logDEBUG) << "Analog Samples: " << m_analog_samples;
|
||||
//-----------------------------------------------------------------
|
||||
|
||||
// Quad
|
||||
@ -342,23 +314,23 @@ void Hdf5MasterFile::parse_acquisition_metadata(
|
||||
} catch (H5::FileIException &e) {
|
||||
// keep the optional empty
|
||||
}
|
||||
// fmt::print("Quad: {}\n", m_quad);
|
||||
LOG(logDEBUG) << "Quad: " << m_quad;
|
||||
H5Eset_auto(H5E_DEFAULT, reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
stderr);
|
||||
|
||||
// ADC Mask
|
||||
// H5::Exception::dontPrint();
|
||||
// try {
|
||||
// m_adc_mask = h5_get_scalar_dataset<int>(
|
||||
// file, std::string(metadata_group_name + "ADC
|
||||
// Mask"));
|
||||
// } catch (H5::FileIException &e) {
|
||||
// m_adc_mask = 0;
|
||||
// }
|
||||
// fmt::print("ADC Mask: {}\n", m_adc_mask);
|
||||
// H5Eset_auto(H5E_DEFAULT,
|
||||
// reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
// stderr);
|
||||
H5::Exception::dontPrint();
|
||||
try {
|
||||
m_adc_mask = h5_get_scalar_dataset<int>(
|
||||
file, std::string(metadata_group_name + "ADC
|
||||
Mask"));
|
||||
} catch (H5::FileIException &e) {
|
||||
m_adc_mask = 0;
|
||||
}
|
||||
LOG(logDEBUG) << "ADC Mask: " << m_adc_mask;
|
||||
H5Eset_auto(H5E_DEFAULT, reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
stderr);
|
||||
|
||||
|
||||
// Digital Flag, Digital Samples
|
||||
H5::Exception::dontPrint();
|
||||
@ -372,8 +344,8 @@ void Hdf5MasterFile::parse_acquisition_metadata(
|
||||
} catch (H5::FileIException &e) {
|
||||
// keep the optional empty
|
||||
}
|
||||
// fmt::print("Digital Flag: {}\n", m_digital_flag);
|
||||
// fmt::print("Digital Samples: {}\n", m_digital_samples);
|
||||
LOG(logDEBUG) << "Digital Flag: " << m_digital_flag;
|
||||
LOG(logDEBUG) << "Digital Samples: " << m_digital_samples;
|
||||
H5Eset_auto(H5E_DEFAULT, reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
stderr);
|
||||
|
||||
@ -390,23 +362,23 @@ void Hdf5MasterFile::parse_acquisition_metadata(
|
||||
} catch (H5::FileIException &e) {
|
||||
// keep the optional empty
|
||||
}
|
||||
// fmt::print("Transceiver Flag: {}\n", m_transceiver_flag);
|
||||
// fmt::print("Transceiver Samples: {}\n",
|
||||
// m_transceiver_samples);
|
||||
LOG(logDEBUG) << "Transceiver Flag: " << m_transceiver_flag;
|
||||
LOG(logDEBUG) << "Transceiver Samples: ",m_transceiver_samples;
|
||||
H5Eset_auto(H5E_DEFAULT, reinterpret_cast<H5E_auto2_t>(H5Eprint2),
|
||||
stderr);
|
||||
|
||||
// scan parameters
|
||||
/*try{
|
||||
std::string scan_parameters = j.at("Scan Parameters");
|
||||
try {
|
||||
std::string scan_parameters = h5_get_scalar_dataset<std::string>(
|
||||
file, std::string(metadata_group_name + "Scan Parameters"));
|
||||
m_scan_parameters = ScanParameters(scan_parameters);
|
||||
if(v<7.21){
|
||||
m_scan_parameters.increment_stop(); //adjust for
|
||||
endpoint being included
|
||||
}
|
||||
}catch (const json::out_of_range &e) {
|
||||
// not a scan
|
||||
if (dVersion < 7.21){
|
||||
m_scan_parameters.increment_stop(); //adjust for endpoint being included
|
||||
}
|
||||
} catch (H5::FileIException &e) {
|
||||
// keep the optional empty
|
||||
}
|
||||
LOG(logDEBUG) << "Scan Parameters: " << ToString(m_scan_parameters);
|
||||
|
||||
try{
|
||||
ROI tmp_roi;
|
||||
|
||||
Reference in New Issue
Block a user