Beginning of python wrapper for Merlin

CMakeLists.txt

@@ -34,6 +34,11 @@ if (LEMMA_ENABLE_TESTING)
 	add_subdirectory(testing)
 endif()
 
+# Python Bindings
+if (LEMMA_PYTHON3_BINDINGS)
+	add_subdirectory(python)
+endif()
+
 # Install
 install ( TARGETS merlin DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
 install ( FILES include/Merlin  DESTINATION ${CMAKE_INSTALL_PREFIX}/include/Lemma ) 

examples/KernelV0.cpp

@@ -58,7 +58,7 @@ int main(int argc, char** argv) {
 
         Kern->SetIntegrationSize( (Vector3r() << 200,200,200).finished() );
         Kern->SetIntegrationOrigin( (Vector3r() << 0,0,0).finished() );
-        Kern->SetTolerance( 1e-11 ); // 1e-12
+        Kern->SetTolerance( 1e-12 ); // 1e-12
 
         auto AkvoDataNode = YAML::LoadFile(argv[4]);
         Kern->AlignWithAkvoDataset( AkvoDataNode );

include/KernelV0.h

@@ -35,8 +35,8 @@
 #include "vtkHyperTree.h"
 #include "vtkHyperTree.h"
 #include "vtkHyperTreeGrid.h"
-#include "vtkHyperTreeCursor.h"
 #include "vtkXMLHyperTreeGridWriter.h"
+#include "vtkHyperTreeCursor.h"  // not in VTK 8.90
 //#include "vtkHyperTreeGridLevelEntry.h" VTK 9
 #include "vtkDoubleArray.h"
 #endif
@@ -129,6 +129,14 @@ namespace Lemma {
          */
         static std::shared_ptr<KernelV0> DeSerialize(const YAML::Node& node);
 
+        /**
+         *   Constructs an object from a string representation of a YAML::Node. This is primarily
+         *   used in Python wrapping
+         */
+        static std::shared_ptr<KernelV0> DeSerialize( const std::string& node ) {
+            return KernelV0::DeSerialize(YAML::Load(node));
+        }
+
         // ====================  OPERATORS     =======================
 
         // ====================  OPERATIONS    =======================

python/CMakeLists.txt

@@ -0,0 +1,14 @@
+
+add_library(pyMerlin MODULE pyMerlin.cpp)
+target_link_libraries(pyMerlin PRIVATE pybind11::module lemmacore fdem1d merlin )
+set_target_properties(pyMerlin PROPERTIES PREFIX "${PYTHON_MODULE_PREFIX}"
+                                       SUFFIX "${PYTHON_MODULE_EXTENSION}"
+                                                      OUTPUT_NAME "Merlin"
+)
+
+install(TARGETS pyMerlin
+	COMPONENT python
+	RUNTIME DESTINATION "${CMAKE_INSTALL_PREFIX}/pyLemma/pyLemma/"
+	LIBRARY DESTINATION "${CMAKE_INSTALL_PREFIX}/pyLemma/pyLemma/"
+	ARCHIVE DESTINATION "${CMAKE_INSTALL_PREFIX}/pyLemma/pyLemma/"
+)

python/pyMerlin.cpp

@@ -0,0 +1,342 @@
+/* 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/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("SetPulseDuration", &Lemma::KernelV0::SetPulseDuration, "Sets the duration of the pulse")
+            .def("SetDepthLayerInteraces", &Lemma::KernelV0::SetDepthLayerInterfaces, "Sets the layer depth interfaces")
+
+            // 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")
+
+
+
+        ;
+//
+//     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")
+//
+//         ;
+}
+
+

src/KernelV0.cpp

@@ -49,6 +49,8 @@ namespace Lemma {
     //--------------------------------------------------------------------------------------
     KernelV0::KernelV0 (const YAML::Node& node, const ctor_key& key) : MerlinObject(node, key) {
 
+        std::cout << "DESERIALIZING" << std::endl;
+
         //node["PulseType"] = "FID";
         Larmor = node["Larmor"].as<Real>();
         Temperature = node["Temperature"].as<Real>();
@@ -60,13 +62,15 @@ namespace Lemma {
         Origin = node["IntegrationOrigin"].as<Vector3r>();
 
         if (node["AlignWithAkvoData"]) {
+            std::cout << "About to align" << std::endl;
             // Match pulse info with dataset
-            AlignWithAkvoDataset( YAML::LoadFile( node["AlignWithAkvoData"].as<std::string>()));
+            AlignWithAkvoDataset( YAML::LoadFile( node["AlignWithAkvoData"].as<std::string>()) );
         } else {
             // Read Pulse info direct from Kernel file
             PulseI = node["PulseI"].as<VectorXr>();
             Taup = node["Taup"].as<Real>();
         }
+        std::cout << "Aligned!!!" << std::endl;
 
         if (node["SigmaModel"]) {
             if (node["SigmaModel"].Tag() == "LayeredEarthEM") {
@@ -81,6 +85,7 @@ namespace Lemma {
                 if ( coil.second.Tag() == "PolygonalWireAntenna" ) {
                     TxRx[ coil.first.as<std::string>() ] = PolygonalWireAntenna::DeSerialize( coil.second );
                 } else {
+                    std::cout << "Reading in coil file " << std::endl;
                     TxRx[ coil.first.as<std::string>() ] =
                         PolygonalWireAntenna::DeSerialize( YAML::LoadFile(coil.second.as<std::string>()) );
                 }
@@ -191,8 +196,14 @@ namespace Lemma {
     //--------------------------------------------------------------------------------------
     void KernelV0::CalculateK0 (const std::vector< std::string>& Tx,
                                 const std::vector<std::string >& Rx, bool vtkOutput ) {
+
+        std::cout << "Calculating Kernel" << std::endl;
+        std::cout << *this << std::endl;
+
         // Set up
         Larmor = SigmaModel->GetMagneticFieldMagnitude()*GAMMA; // in rad  2246.*2.*PI;
+        std::cout << std::endl;
+        std::cout << "Calculated Larmor Frequency " << Larmor / (2.*PI)  << std::endl;
 
         // All EM calculations will share same field points
         cpoints = FieldPoints::NewSP();