mirror of
https://github.com/slsdetectorgroup/aare.git
synced 2026-02-20 06:38:41 +01:00
7f3123d68f
- New aare:to_string/string_to similar to what we have in slsDetectorPackage - Added members period and exptime to RawMasterFile - Parsing exposure time and period for json and raw master file formats - Parsing of RawMasterFile from string stream to enable test without files Comments: - to_string is at the moment not a public header. Can make it later if needed. This gives us full freedom with the API - FileConfig should probably be deprecated need to look into it. Meanwhile removed python bindings and string conv
248 lines
10 KiB
C++
248 lines
10 KiB
C++
// SPDX-License-Identifier: MPL-2.0
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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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// Disable warnings for unused parameters, as we ignore some
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// in the __exit__ method
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#pragma GCC diagnostic push
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#pragma GCC diagnostic ignored "-Wunused-parameter"
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void define_file_io_bindings(py::module &m) {
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py::enum_<DetectorType>(m, "DetectorType")
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.value("Jungfrau", DetectorType::Jungfrau)
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.value("Eiger", DetectorType::Eiger)
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.value("Mythen3", DetectorType::Mythen3)
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.value("Moench", DetectorType::Moench)
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.value("Moench03", DetectorType::Moench03)
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.value("Moench03_old", DetectorType::Moench03_old)
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.value("ChipTestBoard", DetectorType::ChipTestBoard)
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.value("Unknown", DetectorType::Unknown);
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PYBIND11_NUMPY_DTYPE(DetectorHeader, frameNumber, expLength, packetNumber,
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bunchId, timestamp, modId, row, column, reserved,
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debug, roundRNumber, detType, version, packetMask);
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py::class_<File>(m, "File")
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.def(py::init([](const std::filesystem::path &fname) {
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return File(fname, "r", {});
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}))
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.def(py::init(
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[](const std::filesystem::path &fname, const std::string &mode) {
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return File(fname, mode, {});
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}))
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.def(py::init<const std::filesystem::path &, const std::string &,
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const FileConfig &>())
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.def("frame_number", py::overload_cast<>(&File::frame_number))
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.def("frame_number", py::overload_cast<size_t>(&File::frame_number))
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.def_property_readonly("bytes_per_frame", &File::bytes_per_frame)
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.def_property_readonly("pixels_per_frame", &File::pixels_per_frame)
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.def("seek", &File::seek)
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.def("tell", &File::tell)
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.def_property_readonly("total_frames", &File::total_frames)
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.def_property_readonly("rows", &File::rows)
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.def_property_readonly("cols", &File::cols)
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.def_property_readonly("bitdepth", &File::bitdepth)
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.def_property_readonly("bytes_per_pixel", &File::bytes_per_pixel)
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.def_property_readonly(
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"detector_type",
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[](File &self) { return self.detector_type(); })
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.def("read_frame",
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[](File &self) {
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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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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(
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reinterpret_cast<std::byte *>(image.mutable_data()));
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return image;
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})
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.def("read_frame",
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[](File &self, size_t frame_number) {
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self.seek(frame_number);
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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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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(
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reinterpret_cast<std::byte *>(image.mutable_data()));
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return image;
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})
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.def("read_n",
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[](File &self, size_t n_frames) {
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// adjust for actual frames left in the file
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n_frames =
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std::min(n_frames, self.total_frames() - self.tell());
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if (n_frames == 0) {
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throw std::runtime_error("No frames left in file");
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}
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std::vector<size_t> shape{n_frames, self.rows(), self.cols()};
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py::array image;
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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(
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reinterpret_cast<std::byte *>(image.mutable_data()),
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n_frames);
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return image;
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})
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.def("__enter__", [](File &self) { return &self; })
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.def("__exit__",
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[](File &self, const std::optional<pybind11::type> &exc_type,
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const std::optional<pybind11::object> &exc_value,
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const std::optional<pybind11::object> &traceback) {
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// self.close();
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})
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.def("__iter__", [](File &self) { return &self; })
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.def("__next__", [](File &self) {
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try {
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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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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(
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reinterpret_cast<std::byte *>(image.mutable_data()));
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return image;
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} catch (std::runtime_error &e) {
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throw py::stop_iteration();
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}
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});
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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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.def_property_readonly("enabled", &ScanParameters::enabled)
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.def_property_readonly("dac", &ScanParameters::dac)
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.def_property_readonly("start", &ScanParameters::start)
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.def_property_readonly("stop", &ScanParameters::stop)
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.def_property_readonly("step", &ScanParameters::step);
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py::class_<ROI>(m, "ROI")
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.def(py::init<>())
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.def(py::init<ssize_t, ssize_t, ssize_t, ssize_t>(), py::arg("xmin"),
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py::arg("xmax"), py::arg("ymin"), py::arg("ymax"))
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.def_readwrite("xmin", &ROI::xmin)
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.def_readwrite("xmax", &ROI::xmax)
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.def_readwrite("ymin", &ROI::ymin)
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.def_readwrite("ymax", &ROI::ymax)
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.def("__str__",
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[](const ROI &self) {
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return fmt::format("ROI: xmin: {} xmax: {} ymin: {} ymax: {}",
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self.xmin, self.xmax, self.ymin, self.ymax);
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})
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.def("__repr__",
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[](const ROI &self) {
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return fmt::format(
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"<ROI: xmin: {} xmax: {} ymin: {} ymax: {}>", self.xmin,
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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); // NOLINT
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});
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#pragma GCC diagnostic pop
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// py::class_<ClusterHeader>(m, "ClusterHeader")
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// .def(py::init<>())
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// .def_readwrite("frame_number", &ClusterHeader::frame_number)
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// .def_readwrite("n_clusters", &ClusterHeader::n_clusters)
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// .def("__repr__", [](const ClusterHeader &a) { return "<ClusterHeader:
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// " + a.to_string() + ">"; });
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// py::class_<ClusterV2_>(m, "ClusterV2_")
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// .def(py::init<>())
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// .def_readwrite("x", &ClusterV2_::x)
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// .def_readwrite("y", &ClusterV2_::y)
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// .def_readwrite("data", &ClusterV2_::data)
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// .def("__repr__", [](const ClusterV2_ &a) { return "<ClusterV2_: " +
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// a.to_string(false) + ">"; });
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// py::class_<ClusterV2>(m, "ClusterV2")
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// .def(py::init<>())
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// .def_readwrite("cluster", &ClusterV2::cluster)
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// .def_readwrite("frame_number", &ClusterV2::frame_number)
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// .def("__repr__", [](const ClusterV2 &a) { return "<ClusterV2: " +
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// a.to_string() + ">"; });
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// py::class_<ClusterFileV2>(m, "ClusterFileV2")
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// .def(py::init<const std::filesystem::path &, const std::string &>())
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// .def("read", py::overload_cast<>(&ClusterFileV2::read))
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// .def("read", py::overload_cast<int>(&ClusterFileV2::read))
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// .def("frame_number", &ClusterFileV2::frame_number)
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// .def("write", py::overload_cast<std::vector<ClusterV2> const
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// &>(&ClusterFileV2::write))
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// .def("close", &ClusterFileV2::close);
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// m.def("to_clustV2", [](std::vector<DynamicCluster> &clusters, const int
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// frame_number) {
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// std::vector<ClusterV2> clusters_;
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// for (auto &c : clusters) {
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// ClusterV2 cluster;
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// cluster.cluster.x = c.x;
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// cluster.cluster.y = c.y;
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// int i=0;
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// for(auto &d : cluster.cluster.data) {
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// d=c.get<double>(i++);
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// }
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// cluster.frame_number = frame_number;
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// clusters_.push_back(cluster);
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// }
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// return clusters_;
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// });
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}
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