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https://github.com/slsdetectorgroup/aare.git
synced 2025-06-11 06:47:14 +02:00
WIP
This commit is contained in:
froejdh_e
@ -78,11 +78,15 @@ base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/ci/aare_test_da
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# # cols = 1024-roi.xmin
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# # sf = RawSubFile(base / raw, DetectorType.Jungfrau, rows, cols, 16)
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from aare import RawFile
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base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/Jungfrau10/Jungfrau_DoubleModule_1UDP_ROI/SideBySide/')
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fname = base / Path('241019_JF_12keV_Si_FF_GaAs_FF_7p88mmFilter_PedestalStart_ZPos_5.5_master_0.json')
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from aare import RawFile, File
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base = Path('/mnt/sls_det_storage/matterhorn_data/aare_test_data/Jungfrau10/Jungfrau_DoubleModule_1UDP_ROI/')
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fname = base / Path('SideBySide/241019_JF_12keV_Si_FF_GaAs_FF_7p88mmFilter_PedestalStart_ZPos_5.5_master_0.json')
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# fname = Path(base / 'jungfrau/jungfrau_single_master_0.json')
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# fname = base / 'Stacked/241024_JF10_m450_m367_KnifeEdge_TestBesom_9keV_750umFilter_PedestalStart_ZPos_-6_master_0.json'
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f = RawFile(fname)
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h,img = f.read_frame()
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print(f'{h["frameNumber"]}')
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@ -169,39 +169,7 @@ void define_file_io_bindings(py::module &m) {
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});
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py::class_<RawMasterFile>(m, "RawMasterFile")
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.def(py::init<const std::filesystem::path &>())
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.def("data_fname", &RawMasterFile::data_fname)
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.def_property_readonly("version", &RawMasterFile::version)
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.def_property_readonly("detector_type", &RawMasterFile::detector_type)
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.def_property_readonly("timing_mode", &RawMasterFile::timing_mode)
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.def_property_readonly("image_size_in_bytes",
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&RawMasterFile::image_size_in_bytes)
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.def_property_readonly("frames_in_file", &RawMasterFile::frames_in_file)
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.def_property_readonly("pixels_y", &RawMasterFile::pixels_y)
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.def_property_readonly("pixels_x", &RawMasterFile::pixels_x)
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.def_property_readonly("max_frames_per_file",
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&RawMasterFile::max_frames_per_file)
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.def_property_readonly("bitdepth", &RawMasterFile::bitdepth)
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.def_property_readonly("frame_padding", &RawMasterFile::frame_padding)
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.def_property_readonly("frame_discard_policy",
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&RawMasterFile::frame_discard_policy)
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.def_property_readonly("total_frames_expected",
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&RawMasterFile::total_frames_expected)
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.def_property_readonly("geometry", &RawMasterFile::geometry)
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.def_property_readonly("analog_samples", &RawMasterFile::analog_samples)
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.def_property_readonly("digital_samples",
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&RawMasterFile::digital_samples)
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.def_property_readonly("transceiver_samples",
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&RawMasterFile::transceiver_samples)
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.def_property_readonly("number_of_rows", &RawMasterFile::number_of_rows)
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.def_property_readonly("quad", &RawMasterFile::quad)
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.def_property_readonly("scan_parameters",
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&RawMasterFile::scan_parameters)
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.def_property_readonly("roi", &RawMasterFile::roi);
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py::class_<ScanParameters>(m, "ScanParameters")
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.def(py::init<const std::string &>())
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.def(py::init<const ScanParameters &>())
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@ -221,39 +189,15 @@ void define_file_io_bindings(py::module &m) {
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.def_readwrite("ymax", &ROI::ymax)
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.def("__str__", [](const ROI& self){
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return fmt::format("ROI: xmin: {} xmax: {} ymin: {} ymax: {}", self.xmin, self.xmax, self.ymin, self.ymax);
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})
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.def("__repr__", [](const ROI& self){
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return fmt::format("<ROI: xmin: {} xmax: {} ymin: {} ymax: {}>", self.xmin, self.xmax, self.ymin, self.ymax);
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})
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.def("__iter__", [](const ROI &self) {
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return py::make_iterator(&self.xmin, &self.ymax+1);
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});
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py::class_<RawFile>(m, "RawFile")
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.def(py::init<const std::filesystem::path &>())
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.def("read_frame",
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[](RawFile &self) {
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size_t image_size = self.bytes_per_frame();
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const uint8_t item_size = self.bytes_per_pixel();
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py::array image;
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std::vector<ssize_t> shape;
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shape.reserve(2);
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shape.push_back(self.rows());
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shape.push_back(self.cols());
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//return headers from all subfiles
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py::array_t<DetectorHeader> header(self.n_mod());
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if (item_size == 1) {
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image = py::array_t<uint8_t>(shape);
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} else if (item_size == 2) {
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image = py::array_t<uint16_t>(shape);
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} else if (item_size == 4) {
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image = py::array_t<uint32_t>(shape);
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}
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fmt::print("item_size: {} rows: {} cols: {}\n", item_size, self.rows(), self.cols());
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self.read_into(
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reinterpret_cast<std::byte *>(image.mutable_data()),
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header.mutable_data());
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return py::make_tuple(header, image);
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});
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py::class_<RawSubFile>(m, "RawSubFile")
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.def(py::init<const std::filesystem::path &, DetectorType, size_t,
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@ -1,5 +1,7 @@
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//Files with bindings to the different classes
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#include "file.hpp"
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#include "raw_file.hpp"
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#include "raw_master_file.hpp"
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#include "var_cluster.hpp"
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#include "pixel_map.hpp"
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#include "pedestal.hpp"
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@ -13,6 +15,8 @@ namespace py = pybind11;
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PYBIND11_MODULE(_aare, m) {
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define_file_io_bindings(m);
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define_raw_file_io_bindings(m);
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define_raw_master_file_bindings(m);
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define_var_cluster_finder_bindings(m);
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define_pixel_map_bindings(m);
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define_pedestal_bindings<double>(m, "Pedestal");
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93
python/src/raw_file.hpp
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93
python/src/raw_file.hpp
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@ -0,0 +1,93 @@
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#include "aare/CtbRawFile.hpp"
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#include "aare/File.hpp"
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#include "aare/Frame.hpp"
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#include "aare/RawFile.hpp"
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#include "aare/RawMasterFile.hpp"
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#include "aare/RawSubFile.hpp"
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#include "aare/defs.hpp"
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// #include "aare/fClusterFileV2.hpp"
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#include <cstdint>
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#include <filesystem>
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#include <pybind11/iostream.h>
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#include <pybind11/numpy.h>
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#include <pybind11/pybind11.h>
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#include <pybind11/stl.h>
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#include <pybind11/stl/filesystem.h>
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#include <string>
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namespace py = pybind11;
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using namespace ::aare;
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void define_raw_file_io_bindings(py::module &m) {
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py::class_<RawFile>(m, "RawFile")
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.def(py::init<const std::filesystem::path &>())
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.def("read_frame", [](RawFile &self) {
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size_t image_size = self.bytes_per_frame();
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py::array image;
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std::vector<ssize_t> shape;
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shape.reserve(2);
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shape.push_back(self.rows());
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shape.push_back(self.cols());
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// return headers from all subfiles
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py::array_t<DetectorHeader> header(self.n_mod());
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const uint8_t item_size = self.bytes_per_pixel();
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if (item_size == 1) {
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image = py::array_t<uint8_t>(shape);
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} else if (item_size == 2) {
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image = py::array_t<uint16_t>(shape);
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} else if (item_size == 4) {
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image = py::array_t<uint32_t>(shape);
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}
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self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
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header.mutable_data());
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return py::make_tuple(header, image);
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})
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.def("read_n", [](RawFile &self, size_t n_frames) {
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py::array image;
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std::vector<ssize_t> shape;
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shape.reserve(3);
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shape.push_back(n_frames);
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shape.push_back(self.rows());
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shape.push_back(self.cols());
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// return headers from all subfiles
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py::array_t<DetectorHeader> header({self.n_mod(),n_frames});
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const uint8_t item_size = self.bytes_per_pixel();
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if (item_size == 1) {
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image = py::array_t<uint8_t>(shape);
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} else if (item_size == 2) {
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image = py::array_t<uint16_t>(shape);
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} else if (item_size == 4) {
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image = py::array_t<uint32_t>(shape);
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}
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self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),n_frames,
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header.mutable_data());
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return py::make_tuple(header, image);
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})
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.def("frame_number", &RawFile::frame_number)
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.def_property_readonly("bytes_per_frame", &RawFile::bytes_per_frame)
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.def_property_readonly("pixels_per_frame", &RawFile::pixels_per_frame)
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.def_property_readonly("bytes_per_pixel", &RawFile::bytes_per_pixel)
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.def("seek", &RawFile::seek, R"(
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Seek to a specific frame number.
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)")
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.def("tell", &RawFile::tell)
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.def_property_readonly("total_frames", &RawFile::total_frames)
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.def_property_readonly("rows", &RawFile::rows)
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.def_property_readonly("cols", &RawFile::cols)
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.def_property_readonly("bitdepth", &RawFile::bitdepth)
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.def_property_readonly("geometry", &RawFile::geometry)
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.def_property_readonly("n_mod", &RawFile::n_mod)
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.def_property_readonly("detector_type", &RawFile::detector_type)
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.def_property_readonly("master", &RawFile::master);
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}
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58
python/src/raw_master_file.hpp
Normal file
58
python/src/raw_master_file.hpp
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@ -0,0 +1,58 @@
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#include "aare/CtbRawFile.hpp"
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#include "aare/File.hpp"
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#include "aare/Frame.hpp"
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#include "aare/RawFile.hpp"
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#include "aare/RawMasterFile.hpp"
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#include "aare/RawSubFile.hpp"
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#include "aare/defs.hpp"
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// #include "aare/fClusterFileV2.hpp"
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#include <cstdint>
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#include <filesystem>
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#include <pybind11/iostream.h>
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#include <pybind11/numpy.h>
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#include <pybind11/pybind11.h>
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#include <pybind11/stl.h>
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#include <pybind11/stl/filesystem.h>
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#include <string>
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namespace py = pybind11;
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using namespace ::aare;
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void define_raw_master_file_bindings(py::module &m) {
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py::class_<RawMasterFile>(m, "RawMasterFile")
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.def(py::init<const std::filesystem::path &>())
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.def("data_fname", &RawMasterFile::data_fname)
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.def_property_readonly("version", &RawMasterFile::version)
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.def_property_readonly("detector_type", &RawMasterFile::detector_type)
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.def_property_readonly("timing_mode", &RawMasterFile::timing_mode)
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.def_property_readonly("image_size_in_bytes",
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&RawMasterFile::image_size_in_bytes)
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.def_property_readonly("frames_in_file", &RawMasterFile::frames_in_file)
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.def_property_readonly("pixels_y", &RawMasterFile::pixels_y)
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.def_property_readonly("pixels_x", &RawMasterFile::pixels_x)
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.def_property_readonly("max_frames_per_file",
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&RawMasterFile::max_frames_per_file)
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.def_property_readonly("bitdepth", &RawMasterFile::bitdepth)
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.def_property_readonly("frame_padding", &RawMasterFile::frame_padding)
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.def_property_readonly("frame_discard_policy",
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&RawMasterFile::frame_discard_policy)
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.def_property_readonly("total_frames_expected",
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&RawMasterFile::total_frames_expected)
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.def_property_readonly("geometry", &RawMasterFile::geometry)
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.def_property_readonly("analog_samples", &RawMasterFile::analog_samples)
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.def_property_readonly("digital_samples",
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&RawMasterFile::digital_samples)
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.def_property_readonly("transceiver_samples",
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&RawMasterFile::transceiver_samples)
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.def_property_readonly("number_of_rows", &RawMasterFile::number_of_rows)
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.def_property_readonly("quad", &RawMasterFile::quad)
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.def_property_readonly("scan_parameters",
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&RawMasterFile::scan_parameters)
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.def_property_readonly("roi", &RawMasterFile::roi);
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}
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