aare/python/src/file.hpp

#include "aare/Frame.hpp"
#include "aare/File.hpp"
#include "aare/CtbRawFile.hpp"
#include "aare/defs.hpp"
// #include "aare/fClusterFileV2.hpp"

#include <cstdint>
#include <filesystem>
#include <pybind11/numpy.h>
#include <pybind11/iostream.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <pybind11/stl/filesystem.h>
#include <string>

namespace py = pybind11;
using namespace::aare;

void define_file_io_bindings(py::module &m) {

    py::class_<CtbRawFile>(m, "CtbRawFile")
        .def(py::init<const std::filesystem::path &>());
        

    py::class_<File>(m, "File")
        .def(py::init([](const std::filesystem::path &fname) { return File(fname, "r", {}); }))
        .def(
            py::init([](const std::filesystem::path &fname, const std::string &mode) { return File(fname, mode, {}); }))
        .def(py::init<const std::filesystem::path &, const std::string &, const FileConfig &>())

        .def("frame_number", &File::frame_number)
        .def_property_readonly("bytes_per_frame", &File::bytes_per_frame)
        .def_property_readonly("pixels_per_frame", &File::pixels_per_frame)
        .def("seek", &File::seek)
        .def("tell", &File::tell)
        .def_property_readonly("total_frames", &File::total_frames)
        .def_property_readonly("rows", &File::rows)
        .def_property_readonly("cols", &File::cols)
        .def_property_readonly("bitdepth", &File::bitdepth)
        .def_property_readonly("bytes_per_pixel", &File::bytes_per_pixel)
        .def_property_readonly("detector_type", [](File &self){
            return ToString(self.detector_type());
        })
        .def("read_frame", [](File &self) {
            const uint8_t item_size = self.bytes_per_pixel();
            py::array image;
            std::vector<ssize_t> shape;
            shape.reserve(2);
            shape.push_back(self.rows());
            shape.push_back(self.cols());
            if (item_size == 1) {
                image = py::array_t<uint8_t>(shape);
            } else if (item_size == 2) {
                image = py::array_t<uint16_t>(shape);
            } else if (item_size == 4) {
                image = py::array_t<uint32_t>(shape);
            }
            self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()));
            return image;
        })
        .def("read_frame", [](File &self, size_t frame_number) {
            self.seek(frame_number);
            const uint8_t item_size = self.bytes_per_pixel();
            py::array image;
            std::vector<ssize_t> shape;
            shape.reserve(2);
            shape.push_back(self.rows());
            shape.push_back(self.cols());
            if (item_size == 1) {
                image = py::array_t<uint8_t>(shape);
            } else if (item_size == 2) {
                image = py::array_t<uint16_t>(shape);
            } else if (item_size == 4) {
                image = py::array_t<uint32_t>(shape);
            }
            self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()));
            return image;
        })
        .def("read_n", [](File &self, size_t n_frames) {
            const uint8_t item_size = self.bytes_per_pixel();
            py::array image;
            std::vector<ssize_t> shape;
            shape.reserve(3);
            shape.push_back(n_frames);
            shape.push_back(self.rows());
            shape.push_back(self.cols());
            if (item_size == 1) {
                image = py::array_t<uint8_t>(shape);
            } else if (item_size == 2) {
                image = py::array_t<uint16_t>(shape);
            } else if (item_size == 4) {
                image = py::array_t<uint32_t>(shape);
            }
            self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()), n_frames);
            return image;
        });

    py::class_<FileConfig>(m, "FileConfig")
        .def(py::init<>())
        .def_readwrite("rows", &FileConfig::rows)
        .def_readwrite("cols", &FileConfig::cols)
        .def_readwrite("version", &FileConfig::version)
        .def_readwrite("geometry", &FileConfig::geometry)
        .def_readwrite("detector_type", &FileConfig::detector_type)
        .def_readwrite("max_frames_per_file", &FileConfig::max_frames_per_file)
        .def_readwrite("total_frames", &FileConfig::total_frames)
        .def_readwrite("dtype", &FileConfig::dtype)
        .def("__eq__", &FileConfig::operator==)
        .def("__ne__", &FileConfig::operator!=)
        .def("__repr__", [](const FileConfig &a) { return "<FileConfig: " + a.to_string() + ">"; });

    // py::class_<ClusterHeader>(m, "ClusterHeader")
    //     .def(py::init<>())
    //     .def_readwrite("frame_number", &ClusterHeader::frame_number)
    //     .def_readwrite("n_clusters", &ClusterHeader::n_clusters)
    //     .def("__repr__", [](const ClusterHeader &a) { return "<ClusterHeader: " + a.to_string() + ">"; });

    // py::class_<ClusterV2_>(m, "ClusterV2_")
    //     .def(py::init<>())
    //     .def_readwrite("x", &ClusterV2_::x)
    //     .def_readwrite("y", &ClusterV2_::y)
    //     .def_readwrite("data", &ClusterV2_::data)
    //     .def("__repr__", [](const ClusterV2_ &a) { return "<ClusterV2_: " + a.to_string(false) + ">"; });

    // py::class_<ClusterV2>(m, "ClusterV2")
    //     .def(py::init<>())
    //     .def_readwrite("cluster", &ClusterV2::cluster)
    //     .def_readwrite("frame_number", &ClusterV2::frame_number)
    //     .def("__repr__", [](const ClusterV2 &a) { return "<ClusterV2: " + a.to_string() + ">"; });

    // py::class_<ClusterFileV2>(m, "ClusterFileV2")
    //     .def(py::init<const std::filesystem::path &, const std::string &>())
    //     .def("read", py::overload_cast<>(&ClusterFileV2::read))
    //     .def("read", py::overload_cast<int>(&ClusterFileV2::read))
    //     .def("frame_number", &ClusterFileV2::frame_number)
    //     .def("write", py::overload_cast<std::vector<ClusterV2> const &>(&ClusterFileV2::write))
        
    //     .def("close", &ClusterFileV2::close);

    // m.def("to_clustV2", [](std::vector<Cluster> &clusters, const int frame_number) {
    //     std::vector<ClusterV2> clusters_;
    //     for (auto &c : clusters) {
    //         ClusterV2 cluster;
    //         cluster.cluster.x = c.x;
    //         cluster.cluster.y = c.y;
    //         int i=0;
    //         for(auto &d : cluster.cluster.data) {
    //             d=c.get<double>(i++);
    //         }
    //         cluster.frame_number = frame_number;
    //         clusters_.push_back(cluster);
    //     }
    //     return clusters_;
    // });
}