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#include "../lua/data.h"
#include "../lua/functions.h"
#include "pyfunctions.h"
#include <pybind11/pybind11.h>
#include <pybind11/operators.h>
#include <iostream>
namespace py = pybind11;
PYBIND11_MODULE(aoflagger, m) {
m.doc() = "AOFlagger module for detection of radio-frequency interference";
py::enum_<enum aoflagger::TelescopeId>(m, "TelescopeId")
.value("Generic", aoflagger::TelescopeId::GENERIC_TELESCOPE)
.value("AARTFAAC", aoflagger::TelescopeId::AARTFAAC_TELESCOPE)
.value("Arecibo", aoflagger::TelescopeId::ARECIBO_TELESCOPE)
.value("Bighorns", aoflagger::TelescopeId::BIGHORNS_TELESCOPE)
.value("JVLA", aoflagger::TelescopeId::JVLA_TELESCOPE)
.value("LOFAR", aoflagger::TelescopeId::LOFAR_TELESCOPE)
.value("MWA", aoflagger::TelescopeId::MWA_TELESCOPE)
.value("Parkes", aoflagger::TelescopeId::PARKES_TELESCOPE)
.value("WSRT", aoflagger::TelescopeId::WSRT_TELESCOPE);
py::class_<aoflagger::ImageSet>(
m, "ImageSet",
"A set of time-frequency 'images' which together contain data for one \n"
"correlated baseline or dish. \n"
"The class either holds 1, 2, 4 or 8 images. These images have time on "
"the \n"
"x-axis (most rapidly changing index) and frequency on the y-axis. The \n"
"cells specify flux levels, which do not need to have been calibrated. \n"
"\n"
"If the set contains only one image, it specifies amplitudes of a single "
"\n"
"polarization. If it contains two images, it specifies the real and "
"imaginary \n"
"parts of a single polarization. With four images, it contains the real "
"\n"
"and imaginary values of two polarizations (ordered real pol A, imag pol "
"A, \n"
"real pol B, imag pol B). With eight images, it contains complex values "
"for \n"
"four correlated polarizations (ordered real pol A, imag pol A, real pol "
"B, \n"
"... etc). \n"
"\n"
"This class wraps the C++ class aoflagger::ImageSet.\n")
.def("width", &aoflagger::ImageSet::Width,
"Get width (number of time steps) of images")
.def("height", &aoflagger::ImageSet::Height,
"Get height (number of frequency channels) of images")
.def("image_count", &aoflagger::ImageSet::ImageCount,
"Get number of images, see class description for details")
.def("horizontal_stride", &aoflagger::ImageSet::HorizontalStride)
.def("set", &aoflagger::ImageSet::Set,
"Set all samples to the specified value")
.def("get_image_buffer", aoflagger_python::GetImageBuffer,
"Get access to one of the image sets stored in this object. \n"
"Returns a numpy double array of ntimes x nchannels.")
.def("set_image_buffer", aoflagger_python::SetImageBuffer,
"Replace the data of one of the image sets. This function expects\n"
"a numpy double array of ntimes x nchannels.")
.def("resize_without_reallocation",
&aoflagger::ImageSet::ResizeWithoutReallocation);
py::class_<aoflagger::FlagMask>(
m, "FlagMask",
"A two-dimensional flag mask.\n\n"
"The flag mask specifies which values in an ImageSet are flagged.\n"
"A value true means a value is flagged, i.e., contains RFI and should\n"
"not be used in further data processing (calibration, imaging, etc.).\n"
"A flag denotes that all the value at that time-frequency position "
"should\n"
"be ignored for all polarizations.\n"
"\n"
"If polarization-specific flags are needed, one could run the flagger "
"on\n"
"each polarization individually. However, note that some algorithms, "
"like\n"
"the morphological scale-invariant rank operator (SIR operator), work "
"best\n"
"when seeing the flags from all polarizations.\n"
"\n"
"This class wraps the C++ class aoflagger::FlagMask.")
.def("width", &aoflagger::FlagMask::Width,
"Get width (number of time steps) of flag mask")
.def("height", &aoflagger::FlagMask::Height,
"Get height (number of frequency channels) of flag mask")
.def("horizontal_stride", &aoflagger::FlagMask::HorizontalStride)
.def("get_buffer", aoflagger_python::GetBuffer,
"Returns the flag mask as a bool numpy array with dimensions ntimes "
"x nchannels.")
.def("set_buffer", aoflagger_python::SetBuffer,
"Sets the flag mask from a bool numpy array with dimensions ntimes "
"x nchannels.");
py::class_<aoflagger::Strategy>(
m, "Strategy",
"Holds a flagging strategy.\n\n"
"Telescope-specific flagging strategies can be created with \n"
"AOFlagger.make_strategy(), or "
"can be loaded from disk with AOFlagger.load_strategy(). Strategies\n"
"can not be changed with this interface. A user can create strategies\n"
"with the @c rfigui tool that is part of the aoflagger package.")
.def("run", aoflagger_python::Run1)
.def("run", aoflagger_python::Run2);
py::class_<aoflagger::QualityStatistics>(m, "QualityStatistics")
.def(py::self += py::self)
.def("collect_statistics",
&aoflagger::QualityStatistics::CollectStatistics)
.def("write_statistics", &aoflagger::QualityStatistics::WriteStatistics);
py::class_<aoflagger::AOFlagger>(
m, "AOFlagger",
"Main class that gives access to the aoflagger functions.")
.def(py::init<>())
.def("make_image_set", aoflagger_python::MakeImageSet1,
py::return_value_policy::move)
.def("make_image_set", aoflagger_python::MakeImageSet2,
py::return_value_policy::move)
.def("make_image_set", aoflagger_python::MakeImageSet3,
py::return_value_policy::move)
.def("make_image_set", aoflagger_python::MakeImageSet4,
py::return_value_policy::move)
.def("make_flag_mask", aoflagger_python::MakeFlagMask1,
py::return_value_policy::move)
.def("make_flag_mask", aoflagger_python::MakeFlagMask2,
py::return_value_policy::move)
.def("find_strategy_file", aoflagger_python::FindStrategyFile1)
.def("find_strategy_file", aoflagger_python::FindStrategyFile2)
.def("load_strategy_file", aoflagger_python::LoadStrategyFile,
py::return_value_policy::move)
.def("make_quality_statistics", aoflagger_python::MakeQualityStatistics1,
py::return_value_policy::move)
.def("make_quality_statistics", aoflagger_python::MakeQualityStatistics2,
py::return_value_policy::move)
.def_static("get_version_string", &aoflagger::AOFlagger::GetVersionString)
.def_static("get_version_date", &aoflagger::AOFlagger::GetVersionDate);
}
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