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added CtbRawFile

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This commit is contained in:
Erik Fröjdh
2024-11-05 14:36:18 +01:00
parent b8a4498379
commit 80a39415de
24 changed files with 687 additions and 262 deletions
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155
python/src/file.hpp
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@ -1,32 +1,63 @@
#include "aare/Frame.hpp"
#include "aare/File.hpp"
#include "aare/CtbRawFile.hpp"
#include "aare/File.hpp"
#include "aare/Frame.hpp"
#include "aare/defs.hpp"
// #include "aare/fClusterFileV2.hpp"
#include <cstdint>
#include <filesystem>
#include <pybind11/numpy.h>
#include <pybind11/iostream.h>
#include <pybind11/numpy.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <pybind11/stl/filesystem.h>
#include <string>
namespace py = pybind11;
using namespace::aare;
using namespace ::aare;
void define_file_io_bindings(py::module &m) {
PYBIND11_NUMPY_DTYPE(DetectorHeader, frameNumber, expLength, packetNumber,
bunchId, timestamp, modId, row, column, reserved,
debug, roundRNumber, detType, version, packetMask);
py::class_<CtbRawFile>(m, "CtbRawFile")
.def(py::init<const std::filesystem::path &>());
.def(py::init<const std::filesystem::path &>())
.def("read_frame",
[](CtbRawFile &self) {
size_t image_size = self.image_size_in_bytes();
py::array image;
std::vector<ssize_t> shape;
shape.reserve(2);
shape.push_back(1);
shape.push_back(image_size);
py::array_t<DetectorHeader> header(1);
// always read bytes
image = py::array_t<uint8_t>(shape);
self.read_into(
reinterpret_cast<std::byte *>(image.mutable_data()),
header.mutable_data());
return py::make_tuple(header, image);
})
.def("seek", &CtbRawFile::seek)
.def("tell", &CtbRawFile::tell);
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(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)
@ -38,44 +69,48 @@ void define_file_io_bindings(py::module &m) {
.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_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;
@ -91,7 +126,8 @@ void define_file_io_bindings(py::module &m) {
} else if (item_size == 4) {
image = py::array_t<uint32_t>(shape);
}
self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()), n_frames);
self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
n_frames);
return image;
});
@ -107,37 +143,44 @@ void define_file_io_bindings(py::module &m) {
.def_readwrite("dtype", &FileConfig::dtype)
.def("__eq__", &FileConfig::operator==)
.def("__ne__", &FileConfig::operator!=)
.def("__repr__", [](const FileConfig &a) { return "<FileConfig: " + a.to_string() + ">"; });
.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() + ">"; });
// .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) + ">"; });
// .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() + ">"; });
// .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("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) {
// m.def("to_clustV2", [](std::vector<Cluster> &clusters, const int
// frame_number) {
// std::vector<ClusterV2> clusters_;
// for (auto &c : clusters) {
// ClusterV2 cluster;