Added to wrapper for WireAntenna including serialize

Modules/FDEM1D/CMakeLists.txt

@@ -29,6 +29,11 @@ if (LEMMA_ENABLE_TESTING)
 	add_subdirectory(testing)
 endif()
 
+# Python Bindings
+if (LEMMA_PYTHON3_BINDINGS)
+	add_subdirectory(python)
+endif()
+
 # Install
 install ( TARGETS fdem1d DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
 install ( FILES include/FDEM1D  DESTINATION ${CMAKE_INSTALL_PREFIX}/include/Lemma ) 

Modules/FDEM1D/include/PolygonalWireAntenna.h

@@ -67,6 +67,14 @@ namespace Lemma {
              */
             static std::shared_ptr<PolygonalWireAntenna> 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<PolygonalWireAntenna> DeSerialize( const std::string& node ) {
+                return PolygonalWireAntenna::DeSerialize(YAML::Load(node));
+            }
+
             // ====================  OPERATORS     =======================
 
             // ====================  OPERATIONS    =======================

Modules/FDEM1D/include/WireAntenna.h

@@ -69,6 +69,14 @@ namespace Lemma {
              */
             static std::shared_ptr<WireAntenna> 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<WireAntenna> DeSerialize( const std::string& node ) {
+                return WireAntenna::DeSerialize(YAML::Load(node));
+            }
+
             // ====================  OPERATORS     =======================
 
             // ====================  OPERATIONS    =======================

Modules/FDEM1D/python/CMakeLists.txt

@@ -0,0 +1,5 @@
+add_library(pyFDEM1D MODULE pyFDEM1D.cpp)
+target_link_libraries(pyFDEM1D PRIVATE pybind11::module lemmacore fdem1d )
+set_target_properties(pyFDEM1D PROPERTIES PREFIX "${PYTHON_MODULE_PREFIX}"
+                                       SUFFIX "${PYTHON_MODULE_EXTENSION}")
+

Modules/FDEM1D/python/pyFDEM1D.cpp

@@ -0,0 +1,108 @@
+/* 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 "FDEM1D"
+
+namespace py = pybind11;
+
+PYBIND11_MODULE(pyFDEM1D, m) {
+
+    py::add_ostream_redirect(m, "ostream_redirect");
+
+    m.doc() = "Python binding of Lemma::FDEM1D, additional details can be found at https://lemmasoftware.org";
+
+
+    py::class_<Lemma::WireAntenna, std::shared_ptr<Lemma::WireAntenna> > WireAntenna(m, "WireAntenna"); //, py::dynamic_attr());
+
+        // lifecycle
+        WireAntenna.def(py::init(&Lemma::WireAntenna::NewSP))
+
+        // print
+        .def("__repr__", &Lemma::WireAntenna::Print)
+        .def("Serialize", &Lemma::WireAntenna::Print, "YAML representation of the class")
+        .def_static("DeSerialize", py::overload_cast<const std::string&>(&Lemma::WireAntenna::DeSerialize), "Construct object from yaml representation")
+
+        // modifiers
+        .def("SetNumberOfPoints", &Lemma::WireAntenna::SetNumberOfPoints, "Sets the number of points comprising the antenna")
+        .def("SetPoint", py::overload_cast<const int&, const Lemma::Real&, const Lemma::Real&, const Lemma::Real&>(&Lemma::WireAntenna::SetPoint), "Sets a point in the antenna")
+        .def("SetPoint", py::overload_cast<const int&, const Lemma::Vector3r&>(&Lemma::WireAntenna::SetPoint), "Sets a point in the antenna")
+        .def("SetNumberOfTurns", &Lemma::WireAntenna::SetNumberOfTurns, "Sets the number of turns of the antenna")
+        .def("SetNumberOfFrequencies", &Lemma::WireAntenna::SetNumberOfFrequencies, "Sets the number of frequencies of the transmitter")
+        .def("SetFrequency", &Lemma::WireAntenna::SetFrequency, "Sets a single frequency of the transmitter")
+        .def("SetCurrent", &Lemma::WireAntenna::SetCurrent, "Sets the current of the transmitter in amps")
+
+        // accessors
+        .def("GetCurrent", &Lemma::WireAntenna::GetCurrent, "Returns the current of the transmitter in amps")
+        .def("GetPoints", &Lemma::WireAntenna::GetPoints, "Returns the points defining the transmitter")
+        .def("GetNumberOfDipoles", &Lemma::WireAntenna::GetNumberOfDipoles, "Returns the number of dipoles defining the transmitter")
+        .def("GetNumberOfFrequencies", &Lemma::WireAntenna::GetNumberOfFrequencies, "Returns the number of frequencies for the transmitter")
+        .def("IsHorizontallyPlanar", &Lemma::WireAntenna::IsHorizontallyPlanar, "Returns true if the transmitter is flat")
+        .def("GetName", &Lemma::WireAntenna::GetName, "Returns the class name of the object")
+
+        // operations
+        .def("ApproximateWithElectricDipoles", &Lemma::WireAntenna::ApproximateWithElectricDipoles, "Approximates loop with electric dipoles")
+
+    ;
+
+    py::class_<Lemma::PolygonalWireAntenna, std::shared_ptr<Lemma::PolygonalWireAntenna> > PolygonalWireAntenna(m, "PolygonalWireAntenna", WireAntenna); //, py::dynamic_attr())
+
+        // lifecycle
+        PolygonalWireAntenna.def(py::init(&Lemma::PolygonalWireAntenna::NewSP))
+
+        // 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")
+
+        // modifiers
+        //.def("SetNumberOfPoints", &Lemma::WireAntenna::SetNumberOfPoints, "Sets the number of points comprising the antenna")
+
+        // operations
+        .def("ApproximateWithElectricDipoles", &Lemma::PolygonalWireAntenna::ApproximateWithElectricDipoles, "Approximates loop with series of electric dipoles around loop")
+
+    ;
+
+}
+
+
+/*
+BOOST_PYTHON_MODULE(pyLemmaCore)
+{
+    Py_Initialize();
+    np::initialize();
+
+ 	bp::class_<Lemma::PolygonalWireAntenna, boost::noncopyable> ("PolygonalWireAntenna", boost::python::no_init)
+
+        // print
+        .def(boost::python::self_ns::str(bp::self))
+
+        // Lifecycle
+        .def("__init__", boost::python::make_constructor(&Lemma::PolygonalWireAntenna::NewSP))
+        //.def("Serialize", &Lemma::PolygonalWireAntenna::Serialize)
+        //.def("DeSerialize", &Lemma::PolygonalWireAntenna::DeSerialize)
+
+        // Accessors
+    ;
+}
+*/

Modules/LemmaCore/CMakeLists.txt

@@ -46,7 +46,6 @@ endif()
 # Python Bindings
 if (LEMMA_PYTHON3_BINDINGS)
 	add_subdirectory(python)
-	#pybind11_add_module(Lemma pyLemmaCore.cpp)
 endif()
 
 # Install

Modules/LemmaCore/include/ASCIIParser.h

@@ -169,4 +169,4 @@ class ASCIIParser : public LemmaObject {
 #endif   // ----- #ifndef ASCIIPARSER_INC  -----
 
 /* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp syntax=cpp.doxygen: */
+/* vim: set filetype=cpp syntax=cpp.doxygen */

Modules/LemmaCore/include/LemmaObject.h

@@ -111,6 +111,12 @@ class LemmaObject {
 
         // ====================  ACCESS        ==============================
 
+        virtual std::string Print() {
+            YAML::Emitter out;
+            out << this->Serialize();
+            return out.c_str();
+        }
+
         // ====================  INQUIRY       ==============================
 
         /** Returns the name of the underlying class; Run-time type information (RTTI). This approach

Modules/LemmaCore/include/RectilinearGrid.h

@@ -72,12 +72,6 @@ namespace Lemma {
             virtual YAML::Node Serialize() const;
 
             /**
-             *  Uses YAML to serialize this object.
-             *  @return a YAML::Node
-             */
-            virtual std::string Print() const;
-
-            /**
              *  Factory method for generating concrete class.
              *  @return a std::shared_ptr of type RectilinearGrid
              */

Modules/LemmaCore/python/CMakeLists.txt

@@ -1,6 +1,3 @@
-# include directories
-#include_directories(${CMAKE_CURRENT_SOURCE_DIR}/python)
-
 # create the lib
 #add_subdirectory( ${CMAKE_CURRENT_SOURCE_DIR} )
 #pybind11_add_module(pyLemmaCore pyLemmaCore.cpp)
@@ -10,17 +7,3 @@ target_link_libraries(pyLemmaCore PRIVATE pybind11::module lemmacore )
 set_target_properties(pyLemmaCore PROPERTIES PREFIX "${PYTHON_MODULE_PREFIX}"
                                          SUFFIX "${PYTHON_MODULE_EXTENSION}")
 
-#target_include_directories( lemmacore PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/../include" )
-
-#add_library(pyLemmaCore SHARED ${CMAKE_CURRENT_SOURCE_DIR}/pyLemmaCore.cpp)
-
-# link
-#target_link_libraries(pyLemmaCore lemmacore)
-
-# Copy the __init__.py file
-#configure_file(__init__.py ${CMAKE_CURRENT_BINARY_DIR}/__init__.py COPYONLY)
-
-# Suppress prefix "lib" because Python does not allow this prefix
-#set_target_properties(pyLemmaCore PROPERTIES PREFIX "")
-
-#install(TARGETS pyLemmaCore __init__.py DESTINATION "${PYTHON_INSTALL_PATH}")

Modules/LemmaCore/python/pyLemmaCore.cpp

@@ -37,7 +37,7 @@ PYBIND11_MODULE(pyLemmaCore, m) {
 
         // print
         .def("__repr__", &Lemma::RectilinearGrid::Print)
-        .def("Serialize", &Lemma::RectilinearGrid::Print)
+        .def("Serialize", &Lemma::RectilinearGrid::Print, "YAML representation of the class")
 
         // accessors
         .def("GetName", &Lemma::RectilinearGrid::GetName, "Returns the name of the class")
@@ -51,9 +51,37 @@ PYBIND11_MODULE(pyLemmaCore, m) {
         .def("GetDy", &Lemma::RectilinearGrid::GetDy, "Returns the grid spacing in the y direction")
         .def("GetDz", &Lemma::RectilinearGrid::GetDz, "Returns the grid spacing in the z direction")
 
+        // modifiers
         .def("SetDimensions", &Lemma::RectilinearGrid::SetDimensions, "Sets the number of cells in x, y, and z")
         .def("SetOffset", &Lemma::RectilinearGrid::SetOffset, "Sets the origin offset in x, y, and z")
         .def("SetSpacing", &Lemma::RectilinearGrid::SetSpacing, "Sets the grid spacing in x, y, and z");
+
+    py::class_<Lemma::ASCIIParser, std::shared_ptr<Lemma::ASCIIParser> >(m, "ASCIIParser")
+
+        // lifecycle
+        .def(py::init(&Lemma::ASCIIParser::NewSP))
+
+        // print
+        .def("__repr__", &Lemma::ASCIIParser::Print)
+        .def("Serialize", &Lemma::ASCIIParser::Print, "YAML representation of the class")
+
+        // accessors
+        .def("GetName", &Lemma::ASCIIParser::GetName, "Returns the name of the class")
+        .def("GetFileLocation", &Lemma::ASCIIParser::GetFileLocation, "Returns the current file location")
+
+        // modifiers
+        .def("SetCommentString", &Lemma::ASCIIParser::SetCommentString, "Sets the comment string after which all text is ignored")
+        .def("SetBufferSize", &Lemma::ASCIIParser::SetBufferSize, "Sets the buffer size")
+
+        // methods
+        .def("Open", &Lemma::ASCIIParser::Open, "Opens file specified by argument")
+        .def("Close", &Lemma::ASCIIParser::Close, "Closes current file object")
+        .def("ReadReals", &Lemma::ASCIIParser::ReadReals, "Returns vector of nr reals")
+        .def("ReadInts", &Lemma::ASCIIParser::ReadInts, "Returns vector of ni ints")
+        .def("ReadStrings", &Lemma::ASCIIParser::ReadStrings, "Returns vector of ns strings")
+        .def("JumpToLocation", &Lemma::ASCIIParser::JumpToLocation, "File object jumps to specified location")
+
+    ;
 }
 
 
@@ -74,10 +102,6 @@ BOOST_PYTHON_MODULE(pyLemmaCore)
         //.def("DeSerialize", &Lemma::RectilinearGrid::DeSerialize)
 
         // Accessors
-
-
-
     ;
-
 }
 */

Modules/LemmaCore/src/EarthModel.cpp

@@ -31,6 +31,7 @@ namespace Lemma {
         BDec = node["BDec"].as<double>();
         BMag = node["BMag"].as<double>();
         BField = node["BField"].as<Vector3r>();
+	    SetMagneticFieldIncDecMag(BInc, BDec, BMag, TESLA);
     }
 
 

Modules/LemmaCore/src/RectilinearGrid.cpp

@@ -69,13 +69,6 @@ namespace Lemma {
         return node;
     }
 
-    std::string RectilinearGrid::Print() const {
-        YAML::Emitter out;
-        out << this->Serialize();
-        return out.c_str();
-    }
-
-
     //--------------------------------------------------------------------------------------
     //       Class:  RectilinearGrid
     //      Method:  DeSerialize