Merlin/python/pyMerlin.cpp

/* This file is part of Lemma, a geophysical modelling and inversion API.
 * More information is available at http://lemmasoftware.org
 */

/* This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/.
 */

/**
 * @file
 * @date      22/04/19 14:06:32
 * @version   $Id$
 * @author    Trevor Irons (ti)
 * @email     Trevor.Irons@utah.edu
 * @copyright Copyright (c) 2019, University of Utah
 * @copyright Copyright (c) 2019, Lemma Software, LLC
 */

#include <pybind11/pybind11.h>
#include <pybind11/iostream.h>
#include <pybind11/stl.h>
#include <pybind11/complex.h>
#include <pybind11/eigen.h>
#include "Merlin"

namespace py = pybind11;

PYBIND11_MODULE(Merlin, m) {

    py::add_ostream_redirect(m, "ostream_redirect");

    m.doc() = "Python binding of Lemma::Merlin, additional details can be found at https://lemmasoftware.org";

    py::class_<Lemma::KernelV0, std::shared_ptr<Lemma::KernelV0> > KernelV0(m, "KernelV0");

        // lifecycle
        KernelV0.def(py::init(&Lemma::KernelV0::NewSP))
            .def_static("DeSerialize", py::overload_cast<const std::string&>(&Lemma::KernelV0::DeSerialize),
            "Construct object from yaml representation")

            // print
            .def("Serialize", &Lemma::KernelV0::Print, "YAML representation of the class")
            .def("__repr__", &Lemma::KernelV0::Print)

            // modifiers
            .def("PushCoil", &Lemma::KernelV0::PushCoil, "Adds a coil to the sNMR instrument")
            .def("SetLayeredEarthEM", &Lemma::KernelV0::SetLayeredEarthEM, "Sets the EM model used in kernel calculation")
            .def("SetIntegrationSize", &Lemma::KernelV0::SetIntegrationSize, "Sets the size of the volume to integrate the kernel")
            .def("SetIntegrationOrigin", &Lemma::KernelV0::SetIntegrationOrigin, "Sets the origin of the integration volume")
            .def("SetPulseCurrent", &Lemma::KernelV0::SetPulseCurrent, "Sets the current of the pulses")
            .def("SetTemperature", &Lemma::KernelV0::SetTemperature, "Sets the temperature, in K")
            .def("SetTolerance", &Lemma::KernelV0::SetTolerance, "Sets the tolerance used in octree splitting")
            .def("SetMinLevel", &Lemma::KernelV0::SetMinLevel, "Sets the minimum leaf level used in octree splitting")
            .def("SetMaxLevel", &Lemma::KernelV0::SetMaxLevel, "Sets the maximum leaf level used in octree splitting")
            .def("SetPulseDuration", &Lemma::KernelV0::SetPulseDuration, "Sets the duration of the pulse")
            .def("SetDepthLayerInterfaces", &Lemma::KernelV0::SetDepthLayerInterfaces, "Sets the layer depth interfaces")
            .def("SetHankelTransformType", &Lemma::KernelV0::SetHankelTransformType, "Sets the Hankel transform type")

            // accessors
            .def("GetName", &Lemma::KernelV0::GetName, "Returns the name of the class")
            .def("GetSigmaModel", &Lemma::KernelV0::GetSigmaModel, "Returns the conductivity model")
            .def("GetKernel", &Lemma::KernelV0::GetKernel, "Returns the imaging kernel in matrix form")
            .def("GetTolerance", &Lemma::KernelV0::GetTolerance, "Returns the tolerance which was used to construct the kernel")
            .def("GetInterfaces", &Lemma::KernelV0::GetInterfaces, "Returns the layer interfaces")
            .def("GetPulseCurrent", &Lemma::KernelV0::GetPulseCurrent, "Returns the pulse current")
            .def("GetPulseDuration", &Lemma::KernelV0::GetPulseDuration, "Returns the length of the pulse moment")

            // operations
            .def("CalculateK0", &Lemma::KernelV0::CalculateK0, "Calculates an intial amplitude kernel")

            //.def("AlignWithAkvoDataset", &Lemma::KernelV0::AlignWithAkvoDataset, "Aligns the kernel parameters with a dataset")
            .def("AlignWithAkvoDataset", py::overload_cast< const std::string& >(&Lemma::KernelV0::AlignWithAkvoDataset), "Aligns Kernel pulse with specified dataset file")



        ;
//
//     py::class_<Lemma::PolygonalWireAntenna, std::shared_ptr<Lemma::PolygonalWireAntenna> > PolygonalWireAntenna(m,
//             "PolygonalWireAntenna", KernelV0);
//
//         // lifecycle
//         PolygonalWireAntenna.def(py::init(&Lemma::PolygonalWireAntenna::NewSP))
//         .def_static("DeSerialize", py::overload_cast<const std::string&>(&Lemma::PolygonalWireAntenna::DeSerialize),
//             "Construct object from yaml representation")
//
//         // print
//         .def("__repr__", &Lemma::PolygonalWireAntenna::Print)
//         .def("Serialize", &Lemma::PolygonalWireAntenna::Print, "YAML representation of the class")
//
//         // accessors
//         .def("GetName", &Lemma::PolygonalWireAntenna::GetName, "Returns the name of the class")
//
//         // operations
//         .def("ApproximateWithElectricDipoles", &Lemma::PolygonalWireAntenna::ApproximateWithElectricDipoles,
//             "Approximates loop with series of electric dipoles around loop")
//
//         // modifiers
//         .def("SetMinDipoleRatio", &Lemma::PolygonalWireAntenna::SetMinDipoleRatio,
//             "Sets the minimum dipole ratio use, smaller values increase precision")
//         .def("SetMinDipoleMoment", &Lemma::PolygonalWireAntenna::SetMinDipoleMoment,
//             "Sets the minimum dipole moment which will be used, smaller values increase precision and computational time")
//         .def("SetMaxDipoleMoment", &Lemma::PolygonalWireAntenna::SetMaxDipoleMoment,
//             "Sets the maximum dipole moment which will be used, smaller values increase precision and computational time")
//     ;
//
//     py::class_<Lemma::DipoleSource, std::shared_ptr<Lemma::DipoleSource> > DipoleSource(m, "DipoleSource");
//
//         // lifecycle
//         DipoleSource.def(py::init(&Lemma::DipoleSource::NewSP))
//         .def_static("DeSerialize", py::overload_cast<const std::string&>(&Lemma::DipoleSource::DeSerialize),
//             "Construct object from yaml representation")
//
//         // print
//         .def("Serialize", &Lemma::DipoleSource::Print, "YAML representation of the class")
//         .def("__repr__", &Lemma::DipoleSource::Print)
//
//         // accessors
//         .def("GetName", &Lemma::DipoleSource::GetName, "Returns the name of the class")
//         .def("GetNumberOfFrequencies", &Lemma::DipoleSource::GetNumberOfFrequencies,
//                 "Returns the number of frequencies")
//         .def("GetFrequencies", &Lemma::DipoleSource::GetFrequencies, "Returns an array of frequencies")
//         .def("GetFrequency", &Lemma::DipoleSource::GetFrequency, "Returns the frequency of the argument index")
//         .def("GetAngularFrequency", &Lemma::DipoleSource::GetAngularFrequency,
//             "Returns the angular frequency of the argument index")
//         .def("GetPhase", &Lemma::DipoleSource::GetPhase, "Returns the phase of the dipole")
//         .def("GetMoment", &Lemma::DipoleSource::GetMoment, "Returns the moment of the dipole")
//         .def("GetLocation", py::overload_cast< >(&Lemma::DipoleSource::GetLocation), "Returns the location of the dipole")
//         .def("GetPolarisation", &Lemma::DipoleSource::GetPolarisation, "Returns the polarisation of the dipole")
//
//         // modifiers
//         .def("SetLocation", py::overload_cast<const Lemma::Vector3r&> (&Lemma::DipoleSource::SetLocation),
//             "Sets the location of the dipole")
//         .def("SetPolarisation", py::overload_cast<const Lemma::Vector3r&> (&Lemma::DipoleSource::SetPolarisation),
//             "Sets the polarisation of the dipole")
//         .def("SetType", &Lemma::DipoleSource::SetType, "Sets the type")
//         .def("SetMoment", &Lemma::DipoleSource::SetMoment, "Sets the moment of the dipole")
//         .def("SetPhase", &Lemma::DipoleSource::SetPhase, "Sets the phase of the dipole")
//         .def("SetNumberOfFrequencies", &Lemma::DipoleSource::SetNumberOfFrequencies,
//             "Sets the number of frequencies to calculate for the dipole")
//         .def("SetFrequency", &Lemma::DipoleSource::SetFrequency,
//             "Sets a single frequency, first argument is index, second argument is frequency")
//         .def("SetFrequencies", &Lemma::DipoleSource::SetFrequencies,
//             "Sets all frequencies, argument is numpy array of frequencies")
//         ;
//
//     py::class_<Lemma::LayeredEarthEM, std::shared_ptr<Lemma::LayeredEarthEM> >
//         LayeredEarthEM(m, "LayeredEarthEM");
//
//         // lifecycle
//         LayeredEarthEM.def(py::init(&Lemma::LayeredEarthEM::NewSP))
//         .def_static("DeSerialize", py::overload_cast<const std::string&>
//             (&Lemma::LayeredEarthEM::DeSerialize),"Construct object from yaml representation")
//
//         // print
//         .def("Serialize", &Lemma::LayeredEarthEM::Print, "YAML representation of the class")
//         .def("__repr__", &Lemma::LayeredEarthEM::Print)
//
//         // accessors
//         .def("GetName", &Lemma::LayeredEarthEM::GetName, "Returns the name of the class")
//
//         .def("GetLayerConductivity", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerConductivity),
//             "Returns the conductivity of all layers")
//         .def("GetLayerConductivity1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerConductivity),
//             "Returns the conductivity of the specified layer")
//
//         .def("GetLayerSusceptibility", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerSusceptibility),
//             "Returns the susceptibility of all layers")
//         .def("GetLayerSusceptibility1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerSusceptibility),
//             "Returns the susceptibilty of the specified layer")
//         .def("GetLayerLowFreqSusceptibility", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerLowFreqSusceptibility),
//             "Returns the low frequqncy permitivity of all layers")
//         .def("GetLayerLowFreqSusceptibility1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerLowFreqSusceptibility),
//             "Returns the low frequency permitivity of the specified layer")
//         .def("GetLayerHighFreqSusceptibility", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerHighFreqSusceptibility),
//             "Returns the low frequency permitivity of all layers")
//         .def("GetLayerHighFreqSusceptibility1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerHighFreqSusceptibility),
//             "Returns the low frequency permitivity of the specified layer")
//         .def("GetLayerTauSusceptibility", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerTauSusceptibility),
//             "Returns the tau permitivity of all layers")
//         .def("GetLayerTauSusceptibility1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerTauSusceptibility),
//             "Returns the tau permitivity of the specified layer")
//         .def("GetLayerBreathSusceptibility", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerBreathSusceptibility),
//             "Returns the breth permitivity of all layers")
//         .def("GetLayerBreathSusceptibility1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerBreathSusceptibility),
//             "Returns the breath permitivity of the specified layer")
//
//         .def("GetLayerPermitivity", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerPermitivity),
//             "Returns the permitivity of all layers")
//         .def("GetLayerPermitivity1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerPermitivity),
//             "Returns the permitivity of the specified layer")
//         .def("GetLayerLowFreqPermitivity", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerLowFreqPermitivity),
//             "Returns the low frequqncy permitivity of all layers")
//         .def("GetLayerLowFreqPermitivity1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerLowFreqPermitivity),
//             "Returns the low frequency permitivity of the specified layer")
//         .def("GetLayerHighFreqPermitivity", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerHighFreqPermitivity),
//             "Returns the low frequency permitivity of all layers")
//         .def("GetLayerHighFreqPermitivity1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerHighFreqPermitivity),
//             "Returns the low frequency permitivity of the specified layer")
//         .def("GetLayerTauPermitivity", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerTauPermitivity),
//             "Returns the tau permitivity of all layers")
//         .def("GetLayerTauPermitivity1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerTauPermitivity),
//             "Returns the tau permitivity of the specified layer")
//         .def("GetLayerBreathPermitivity", py::overload_cast<>(&Lemma::LayeredEarthEM::GetLayerBreathPermitivity),
//             "Returns the breth permitivity of all layers")
//         .def("GetLayerBreathPermitivity1", py::overload_cast<const int&>(&Lemma::LayeredEarthEM::GetLayerBreathPermitivity),
//             "Returns the breath permitivity of the specified layer")
//
//
//         // modifiers
//         .def("SetNumberOfLayers", &Lemma::LayeredEarthEM::SetNumberOfLayers,
//             "Sets the number of layers in the model")
//         .def("SetLayerConductivity", py::overload_cast< const Lemma::VectorXcr& >(&Lemma::LayeredEarthEM::SetLayerConductivity),
//             "Sets the conductivity of the layers, the input is a complex array of conductivity")
//         .def("SetLayerConductivity1", py::overload_cast< const int&, const Lemma::Complex& >(&Lemma::LayeredEarthEM::SetLayerConductivity),
//             "Sets the conductivity of a single layer, the first input is the layer index, and the secondinput is a complex conductivity")
//         .def("SetLayerThickness", &Lemma::LayeredEarthEM::SetLayerThickness,
//             "Sets the thickness of layers, excluding the air and bottom which are infinite")
//
//         .def("SetLayerHighFreqSusceptibility", &Lemma::LayeredEarthEM::SetLayerHighFreqSusceptibility,
//             "Sets the high frequency susceptibility for Cole-COle model")
//         .def("SetLayerLowFreqSusceptibility", &Lemma::LayeredEarthEM::SetLayerLowFreqSusceptibility,
//             "Sets the low frequency susceptibility for Cole-COle model")
//         .def("SetLayerBreathSusceptibility", &Lemma::LayeredEarthEM::SetLayerBreathSusceptibility,
//             "Sets thesusceptibility breath for Cole-COle model")
//
//         .def("SetLayerHighFreqPermitivity", &Lemma::LayeredEarthEM::SetLayerHighFreqPermitivity,
//             "Sets the high frequency permitivity for Cole-COle model")
//         .def("SetLayerLowFreqPermitivity", &Lemma::LayeredEarthEM::SetLayerLowFreqPermitivity,
//             "Sets the low frequency permitivity for Cole-COle model")
//         .def("SetLayerBreathPermitivity", &Lemma::LayeredEarthEM::SetLayerBreathPermitivity,
//             "Sets the permitivity breath for Cole-COle model")
//
//
//         // methods
//         .def("EvaluateColeColeModel", &Lemma::LayeredEarthEM::EvaluateColeColeModel,
//             "Calculates complex resistivity based on cole-cole parameters")
//         ;
//
//     py::class_<Lemma::EMEarth1D, std::shared_ptr<Lemma::EMEarth1D> >
//         EMEarth1D(m, "EMEarth1D");
//
//         // lifecycle
//         EMEarth1D.def(py::init(&Lemma::EMEarth1D::NewSP))
//         //.def_static("DeSerialize", py::overload_cast<const std::string&>
//         //    (&Lemma::EMEarth1D::DeSerialize),"Construct object from yaml representation")
//
//         // print
//         .def("Serialize", &Lemma::EMEarth1D::Print, "YAML representation of the class")
//         .def("__repr__", &Lemma::EMEarth1D::Print)
//
//         // accessors
//         .def("GetName", &Lemma::EMEarth1D::GetName, "Returns the name of the class")
//         .def("GetFieldPoints", &Lemma::EMEarth1D::GetFieldPoints, "Returns the FieldPoint class")
//
//         // modifiers
//         .def("AttachWireAntenna", &Lemma::EMEarth1D::AttachWireAntenna,
//             "Sets the wire antenna to use for calculations")
//         .def("AttachDipoleSOurce", &Lemma::EMEarth1D::AttachDipoleSource,
//             "Sets a DipoleSource to use for calculations")
//         .def("AttachFieldPoints", &Lemma::EMEarth1D::AttachFieldPoints,
//             "Sets the FieldPoints to use for calculations")
//         .def("AttachLayeredEarthEM", &Lemma::EMEarth1D::AttachLayeredEarthEM,
//             "Sets the LayeredEarthEM to use for calculations")
//
//         .def("SetFieldToCalculate", &Lemma::EMEarth1D::SetFieldsToCalculate,
//             "Sets which fields to calculate")
//         .def("SetHankelTransformMethod", &Lemma::EMEarth1D::SetHankelTransformMethod,
//             "Sets which Hankel transform to use")
//         .def("SetTxRxMode", &Lemma::EMEarth1D::SetTxRxMode,
//             "Sets the TxRx mode flag")
//
//         //methods
// #ifdef KIHALEE_EM1D
//         .def("MakeCalc", &Lemma::EMEarth1D::MakeCalc, "Calls KiHa Lee's EM1D FORTRAN77 code")
// #endif
//
//         .def("MakeCalc3", &Lemma::EMEarth1D::MakeCalc3, "Native Lemma EM calculation")
//         .def("CalculateWireAntennaFields", &Lemma::EMEarth1D::CalculateWireAntennaFields,
//             "Native Lemma calculation of a wire antenna")
//         ;
//
//     py::class_<Lemma::FieldPoints, std::shared_ptr<Lemma::FieldPoints> >
//         FieldPoints(m, "FieldPoints");
//
//         // lifecycle
//         FieldPoints.def(py::init(&Lemma::FieldPoints::NewSP))
//         .def_static("DeSerialize", py::overload_cast<const std::string&>
//             (&Lemma::FieldPoints::DeSerialize),"Construct object from yaml representation")
//
//         // print
//         .def("Serialize", &Lemma::FieldPoints::Print, "YAML representation of the class")
//         .def("__repr__", &Lemma::FieldPoints::Print)
//
//         // modifiers
//         .def("SetNumberOfPoints", &Lemma::FieldPoints::SetNumberOfPoints,
//             "Sets the number of locations to make calculations on.")
//         .def("SetLocation", py::overload_cast< const int&, const Lemma::Vector3r& >
//             (&Lemma::FieldPoints::SetLocation), "Sets the location of the index-specified point." )
//         .def("SetLocation", py::overload_cast< const int&,
//                     const Lemma::Real&, const Lemma::Real&, const Lemma::Real& >
//             (&Lemma::FieldPoints::SetLocation),
//             "Sets the location of the index-specified point with the three coordinates")
//
//         // accessors
//         .def("GetNumberOfPoints", &Lemma::FieldPoints::GetNumberOfPoints,
//             "Returns the number of locations to make calculations on.")
//         .def("GetLocations", &Lemma::FieldPoints::GetLocations,
//             "Returns the locations which calculations are made on.")
//         .def("GetLocationsMat", &Lemma::FieldPoints::GetLocationsMat,
//             "Returns a matrix of the locations which calculations are made on.")
//         .def("GetLocation", &Lemma::FieldPoints::GetLocation,
//             "Returns the location of the specified index.")
//         .def("GetLocationX", &Lemma::FieldPoints::GetLocationX,
//             "Returns the northing (x) location of the specified index.")
//         .def("GetLocationY", &Lemma::FieldPoints::GetLocationY,
//             "Returns the easting (y) location of the specified index.")
//         .def("GetLocationZ", &Lemma::FieldPoints::GetLocationZ,
//             "Returns the altitude/depth (z) location of the specified index.")
//         .def("GetEfield", py::overload_cast<  > (&Lemma::FieldPoints::GetEfield),
//             "Returns the electric field for all frequencies.")
//         .def("GetEfield", py::overload_cast< const int& > (&Lemma::FieldPoints::GetEfield),
//             "Returns the electric field for the specified frequency index.")
//         .def("GetEfield", py::overload_cast< const int&, const int& > (&Lemma::FieldPoints::GetEfield),
//             "Returns the electric field for the specified frequency and location index.")
//         .def("GetEfieldMat", &Lemma::FieldPoints::GetEfieldMat,
//             "Returns the electric field for the specified frequency.")
//         .def("GetHfield", py::overload_cast<  > (&Lemma::FieldPoints::GetHfield),
//             "Returns the H field for all frequencies.")
//         .def("GetHfield", py::overload_cast< const int& > (&Lemma::FieldPoints::GetHfield),
//             "Returns the H field for the specified frequency index.")
//         .def("GetHfield", py::overload_cast< const int&, const int& > (&Lemma::FieldPoints::GetHfield),
//             "Returns the H field for the specified frequency and location index.")
//         //.def("GetBfield", py::overload_cast< const int&, const int& > (&Lemma::FieldPoints::GetBfield),
//         //    "Returns the magnetic (B) field for the specified frequency and location index.")
//         .def("GetHfieldMat", &Lemma::FieldPoints::GetHfieldMat,
//             "Returns the H field for the specified frequency.")
//         .def("GetMask", &Lemma::FieldPoints::MaskPoint, "Return the mask boolean value for the specified index")
//
//         // methods
//         .def("ClearFields", &Lemma::FieldPoints::ClearFields, "Clears calculated fields")
//         .def("MaskPoint", &Lemma::FieldPoints::MaskPoint, "Masks the index resulting in no calculation")
//         .def("UnMaskPoint", &Lemma::FieldPoints::UnMaskPoint, "Unmasks the index resulting in a calculation")
//
//         ;
}