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https://github.com/slsdetectorgroup/aare.git
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WIP
This commit is contained in:
Erik Fröjdh
126
python/src/file.hpp
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126
python/src/file.hpp
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@ -0,0 +1,126 @@
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#include "aare/Frame.hpp"
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#include "aare/File.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/numpy.h>
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#include <pybind11/iostream.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_file_io_bindings(py::module &m) {
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py::class_<xy>(m, "xy")
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.def(py::init<>())
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.def(py::init<uint32_t, uint32_t>())
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.def_readwrite("row", &xy::row)
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.def_readwrite("col", &xy::col)
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.def("__eq__", &xy::operator==)
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.def("__ne__", &xy::operator!=)
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.def("__repr__",
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[](const xy &a) { return "<xy: row=" + std::to_string(a.row) + ", col=" + std::to_string(a.col) + ">"; });
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py::class_<File>(m, "File")
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.def(py::init([](const std::filesystem::path &fname) { return File(fname, "r", {}); }))
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.def(
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py::init([](const std::filesystem::path &fname, const std::string &mode) { return File(fname, mode, {}); }))
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.def(py::init<const std::filesystem::path &, const std::string &, const FileConfig &>())
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// .def("read", py::overload_cast<>(&File::read))
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// .def("read", py::overload_cast<size_t>(&File::read))
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.def("iread", py::overload_cast<size_t>(&File::iread),py::call_guard<py::gil_scoped_release>())
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.def("frame_number", &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("detector_type", &File::detector_type)
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.def_property_readonly("geometry", &File::geometry,
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py::call_guard<py::scoped_ostream_redirect, py::scoped_estream_redirect>())
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// .def("set_total_frames", &File::set_total_frames)
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.def("read_frame", [](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(reinterpret_cast<std::byte *>(image.mutable_data()));
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return image;
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});
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py::class_<FileConfig>(m, "FileConfig")
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.def(py::init<>())
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.def_readwrite("rows", &FileConfig::rows)
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.def_readwrite("cols", &FileConfig::cols)
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.def_readwrite("version", &FileConfig::version)
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.def_readwrite("geometry", &FileConfig::geometry)
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.def_readwrite("detector_type", &FileConfig::detector_type)
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.def_readwrite("max_frames_per_file", &FileConfig::max_frames_per_file)
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.def_readwrite("total_frames", &FileConfig::total_frames)
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.def_readwrite("dtype", &FileConfig::dtype)
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.def("__eq__", &FileConfig::operator==)
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.def("__ne__", &FileConfig::operator!=)
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.def("__repr__", [](const FileConfig &a) { return "<FileConfig: " + a.to_string() + ">"; });
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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: " + 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_: " + 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: " + 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 &>(&ClusterFileV2::write))
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// .def("close", &ClusterFileV2::close);
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// m.def("to_clustV2", [](std::vector<Cluster> &clusters, const int 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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@ -1,9 +1,14 @@
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#include "file.hpp"
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#include <pybind11/pybind11.h>
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#include <pybind11/stl.h>
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namespace py = pybind11;
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PYBIND11_MODULE(_aare, m) {
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define_file_io_bindings(m);
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}
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115
python/src/np_helper.hpp
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115
python/src/np_helper.hpp
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#pragma once
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#include <iostream>
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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 "aare/Frame.hpp"
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#include "aare/NDArray.hpp"
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namespace py = pybind11;
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// Pass image data back to python as a numpy array
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// template <typename T, ssize_t Ndim>
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// py::array return_image_data(pl::ImageData<T, Ndim> *image) {
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// py::capsule free_when_done(image, [](void *f) {
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// pl::ImageData<T, Ndim> *foo =
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// reinterpret_cast<pl::ImageData<T, Ndim> *>(f);
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// delete foo;
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// });
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// return py::array_t<T>(
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// image->shape(), // shape
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// image->byte_strides(), // C-style contiguous strides for double
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// image->data(), // the data pointer
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// free_when_done); // numpy array references this parent
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// }
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// template <typename T> py::array return_vector(std::vector<T> *vec) {
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// py::capsule free_when_done(vec, [](void *f) {
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// std::vector<T> *foo = reinterpret_cast<std::vector<T> *>(f);
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// delete foo;
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// });
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// return py::array_t<T>({vec->size()}, // shape
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// {sizeof(T)}, // C-style contiguous strides for double
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// vec->data(), // the data pointer
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// free_when_done); // numpy array references this parent
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// }
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// template <typename Reader> py::array do_read(Reader &r, size_t n_frames) {
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// py::array image;
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// if (n_frames == 0)
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// n_frames = r.total_frames();
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// std::array<ssize_t, 3> shape{static_cast<ssize_t>(n_frames), r.rows(),
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// r.cols()};
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// const uint8_t item_size = r.bytes_per_pixel();
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// if (item_size == 1) {
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// image = py::array_t<uint8_t, py::array::c_style | py::array::forcecast>(
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// shape);
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// } else if (item_size == 2) {
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// image =
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// py::array_t<uint16_t, py::array::c_style | py::array::forcecast>(
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// shape);
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// } else if (item_size == 4) {
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// image =
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// py::array_t<uint32_t, py::array::c_style | py::array::forcecast>(
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// shape);
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// }
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// r.read_into(reinterpret_cast<std::byte *>(image.mutable_data()), n_frames);
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// return image;
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// }
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py::array return_frame(pl::Frame *ptr) {
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py::capsule free_when_done(ptr, [](void *f) {
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pl::Frame *foo = reinterpret_cast<pl::Frame *>(f);
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delete foo;
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});
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const uint8_t item_size = ptr->bytes_per_pixel();
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std::vector<ssize_t> shape;
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for (auto val : ptr->shape())
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if (val > 1)
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shape.push_back(val);
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std::vector<ssize_t> strides;
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if (shape.size() == 1)
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strides.push_back(item_size);
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else if (shape.size() == 2) {
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strides.push_back(item_size * shape[1]);
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strides.push_back(item_size);
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}
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if (item_size == 1)
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return py::array_t<uint8_t>(
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shape, strides,
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reinterpret_cast<uint8_t *>(ptr->data()), free_when_done);
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else if (item_size == 2)
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return py::array_t<uint16_t>(shape, strides,
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reinterpret_cast<uint16_t *>(ptr->data()),
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free_when_done);
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else if (item_size == 4)
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return py::array_t<uint32_t>(shape, strides,
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reinterpret_cast<uint32_t *>(ptr->data()),
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free_when_done);
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return {};
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}
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// todo rewrite generic
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template <class T, int Flags> auto get_shape_3d(py::array_t<T, Flags> arr) {
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return pl::Shape<3>{arr.shape(0), arr.shape(1), arr.shape(2)};
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}
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template <class T, int Flags> auto make_span_3d(py::array_t<T, Flags> arr) {
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return pl::DataSpan<T, 3>(arr.mutable_data(), get_shape_3d<T, Flags>(arr));
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}
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template <class T, int Flags> auto get_shape_2d(py::array_t<T, Flags> arr) {
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return pl::Shape<2>{arr.shape(0), arr.shape(1)};
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}
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template <class T, int Flags> auto make_span_2d(py::array_t<T, Flags> arr) {
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return pl::DataSpan<T, 2>(arr.mutable_data(), get_shape_2d<T, Flags>(arr));
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}
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