Work on rebasing to C++-11 and reorganization of Modules.

CMakeLists.txt

 # Add the c++11 flag 
 # TODO add compiler specific instructions
 include(CheckCXXCompilerFlag)
+CHECK_CXX_COMPILER_FLAG(-std=c++14 COMPILER_SUPPORTS_CXX14)
 CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-CHECK_CXX_COMPILER_FLAG(-std=c++0x COMPILER_SUPPORTS_CXX0X)
 
-if(COMPILER_SUPPORTS_CXX11)
+if(COMPILER_SUPPORTS_CXX14)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
+elseif(COMPILER_SUPPORTS_CXX11)
 	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-elseif(COMPILER_SUPPORTS_CXX0X)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
 else()
-	message(FATAL_ERROR "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support. Please use a different C++ compiler.")
+	message(FATAL_ERROR "The compiler ${CMAKE_CXX_COMPILER} has no C++11 or C++14 support. Please use a different C++ compiler.")
 endif()
 
 option( LEMMA_USE_OPENMP  "Use OpenMP in Lemma" OFF)
 ########################################################################
 # 
 include_directories(${CMAKE_INSTALL_PREFIX}/include)
-add_executable(Hello "${PROJECT_SOURCE_DIR}/src/test.cpp")
-target_link_libraries(Hello lemmacore)
-add_dependencies(Hello YAML-CPP)
+
+#add_executable(Hello "${PROJECT_SOURCE_DIR}/src/test.cpp")
+#target_link_libraries(Hello lemmacore)
+#add_dependencies(Hello YAML-CPP)
 
 
 # add a target to generate API documentation with Doxygen

LemmaCore/examples/CMakeLists.txt

 #FILE(GLOB  examples  "*.cpp")
 
-add_executable( datatem datatem.cpp )
-target_link_libraries(datatem "lemmacore")
+#add_executable( datatem datatem.cpp )
+#target_link_libraries(datatem "lemmacore")
 
-add_executable( wireantenna wireantenna.cpp )
-target_link_libraries(wireantenna "lemmacore")
+#add_executable( wireantenna wireantenna.cpp )
+#target_link_libraries(wireantenna "lemmacore")
 
-add_executable( DCIPElectrode  DCIPElectrode.cpp )
-target_link_libraries(DCIPElectrode "lemmacore")
+#add_executable( DCIPElectrode  DCIPElectrode.cpp )
+#target_link_libraries(DCIPElectrode "lemmacore")
 
-add_executable( digitalfiltercostrans  digitalfiltercostrans.cpp )
-target_link_libraries(digitalfiltercostrans "lemmacore")
+#add_executable( digitalfiltercostrans  digitalfiltercostrans.cpp )
+#target_link_libraries(digitalfiltercostrans "lemmacore")
 
-add_executable( dipolefreqsweep  dipolefreqsweep.cpp )
-target_link_libraries(dipolefreqsweep "lemmacore")
+#add_executable( dipolefreqsweep  dipolefreqsweep.cpp )
+#target_link_libraries(dipolefreqsweep "lemmacore")
 
-add_executable( dipolesource  dipolesource.cpp )
-target_link_libraries(dipolesource "lemmacore")
+#add_executable( dipolesource  dipolesource.cpp )
+#target_link_libraries(dipolesource "lemmacore")
 
-add_executable( edipole  edipole.cpp )
-target_link_libraries(edipole "lemmacore")
+#add_executable( edipole  edipole.cpp )
+#target_link_libraries(edipole "lemmacore")
 
-add_executable( emdipearth1d  emdipearth1d.cpp )
-target_link_libraries(emdipearth1d "lemmacore")
+#add_executable( emdipearth1d  emdipearth1d.cpp )
+#target_link_libraries(emdipearth1d "lemmacore")
 
-add_executable( femforward  femforward.cpp )
-target_link_libraries(femforward "lemmacore")
+#add_executable( femforward  femforward.cpp )
+#target_link_libraries(femforward "lemmacore")
 
 add_executable( filter  filter.cpp )
 target_link_libraries(filter "lemmacore")

LemmaCore/examples/DCIPElectrode.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      11/10/2014 12:31:01 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include "DCIPElectrode.h"
-#include "DCSurvey.h"
-
-using namespace Lemma;
-
-int main() {
-
-
-    //DCIPElectrode* Electrode1 = DCIPElectrode::New();
-    DCIPElectrode* Electrode2 = DCIPElectrode::New();
-    DCIPElectrode* Electrode3 = DCIPElectrode::New();
-    DCIPElectrode* Electrode4 = DCIPElectrode::New();
-    DCIPElectrode* Electrode5 = DCIPElectrode::New();
-    DCIPElectrode* Electrode6 = DCIPElectrode::New();
-    DCIPElectrode* Electrode7 = DCIPElectrode::New();
-    DCIPElectrode* Electrode8 = DCIPElectrode::New();
-    DCIPElectrode* Electrode9 = DCIPElectrode::New();
-
-        //Electrode1->SetLocation( Vector3r( 23.23, 18.1, -45 )  );
-        Electrode2->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-        Electrode3->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-        Electrode4->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-        Electrode4->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-        Electrode5->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-        Electrode6->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-        Electrode7->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-        Electrode8->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-        Electrode9->SetLocation( Vector3r( 13.23, 18.1, -25 ) );
-
-//:        std::cout << *Electrode1 << std::endl;
-//     std::ofstream ofstr("DCIPElectrode.yaml");
-//         ofstr << *Electrode1;
-//         ofstr.close();
-
-    /*
-    //std::ifstream ifstr("DCIPElectrode.yaml");
-    std::ifstream ifstr("test.yaml");
-    YAML::Node node = YAML::Load(ifstr);
-    DCIPElectrode* Ex = DCIPElectrode::DeSerialize(node);
-    std::cout << *Ex << std::endl;
-    */
-    //exit(1);
-
-    //std::cout << *Electrode << std::endl;
-    //std::cout << *Electrode2 << std::endl;
-
-    // Set up a Survey
-    DCSurvey* Survey = DCSurvey::New();
-        // Instead we should just put location in, and then survey acts as factory?
-        DCIPElectrode* Electrode1 = Survey->PoundElectrode( Vector3r( 13.23, 18.1, -25 ), "L0-E0" );
-        Survey->PoundElectrode( Electrode2 , "L0-E1" );
-        Survey->PoundElectrode( Electrode3 , "L0-E2" );
-        Survey->PoundElectrode( Electrode4 , "L0-E3" );
-        Survey->PoundElectrode( Electrode5 , "L0-E4" );
-        Survey->PoundElectrode( Electrode6 , "L0-E5" );
-        Survey->PoundElectrode( Electrode7 , "L0-E6" );
-        Survey->PoundElectrode( Electrode8 , "L0-E7" );
-        Survey->PoundElectrode( Electrode9 , "L0-E8" );
-
-        int J0 = Survey->AddInjection( Electrode1, Electrode2, 1.0 );
-            Survey->AddMeasurement(J0, Electrode3, Electrode4 );
-            Survey->AddMeasurement(J0, Electrode5, Electrode6 );
-            Survey->AddMeasurement(J0, Electrode6, Electrode7 );
-            Survey->AddMeasurement(J0, "L0-E7", "L0-E8" );
-
-        int J1 = Survey->AddInjection( Electrode2, Electrode3, 1.0 );
-            Survey->AddMeasurement(J1, Electrode3, Electrode4 );
-            Survey->AddMeasurement(J1, Electrode5, Electrode6 );
-            Survey->AddMeasurement(J1, Electrode6, Electrode7 );
-
-        int J2 = Survey->AddInjection( Electrode3, Electrode4, 1.0 );
-            Survey->AddMeasurement(J2, Electrode3, Electrode4 );
-            Survey->AddMeasurement(J2, Electrode5, Electrode6 );
-            Survey->AddMeasurement(J2, Electrode6, Electrode7 );
-
-        //Survey->AddMeasurement(L1, L2)
-        std::cout << *Survey << std::endl;
-
-        std::ofstream outstr("DC.yaml");
-            outstr << *Survey << std::endl;
-            outstr.close();
-
-        Survey->Delete();
-
-        //TODO recheck DeSerialize make sure we are filling in all the Tag vectors
-
-        std::ifstream ifstr2("DC.yaml");
-        YAML::Node node2 = YAML::Load(ifstr2);
-        DCSurvey* Survey2 = DCSurvey::DeSerialize(node2);
-
-        std::cout << "==============================================================\n";
-        std::cout << *Survey2 << std::endl;
-
-    return(EXIT_SUCCESS);
-
-}
-

LemmaCore/examples/datatem.cpp

-// ===========================================================================
-//
-//       Filename:
-//
-//    Description:
-//
-//        Version:  0.0
-//        Created:  03/02/2010 02:10:53 PM
-//       Revision:  none
-//       Compiler:  Tested with g++, icpc, and MSVC 2000
-//
-//         Author:  Trevor Irons (ti)
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//                  United States Geological Survey (USGS)
-//
-//          Email:  tirons@mines.edu, tirons@usgs.gov
-//
-//  This program is free software: you can redistribute it and/or modify
-//  it under the terms of the GNU General Public License as published by
-//  the Free Software Foundation, either version 3 of the License, or
-//  (at your option) any later version.
-//
-//  This program is distributed in the hope that it will be useful,
-//  but WITHOUT ANY WARRANTY; without even the implied warranty of
-//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-//  GNU General Public License for more details.
-//
-//  You should have received a copy of the GNU General Public License
-//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
-//
-// ===========================================================================
-
-#include "Lemma"
-using namespace Lemma;
-
-int main() {
-
-	DataTEM * tdata = DataTEM::New();
-	std::cout << *tdata << std::endl;
-	tdata->Zero();
-	tdata->Delete();
-
-}

LemmaCore/examples/dipolefreqsweep.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      01/29/2014 09:53:49 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include <iostream>
-#include <fstream>
-#include "dipolesource.h"
-#include "layeredearthem.h"
-#include "receiverpoints.h"
-#include "emearth1d.h"
-
-#ifdef LEMMAUSEOMP
-#include "omp.h"
-#endif
-
-// For testing purposes disable VTK and run scale.sh
-//#undef LEMMAUSEVTK
-//#undef KIHALEE_EM1D
-
-#ifdef LEMMAUSEVTK
-#include "vtkRenderer.h"
-#include "vtkRenderWindow.h"
-#include "vtkRenderWindowInteractor.h"
-#include "vtkDoubleArray.h"
-#include "vtkXYPlotActor.h"
-#include "vtkXYPlotWidget.h"
-#include "vtkProperty2D.h"
-#endif
-
-#include "timer.h"
-
-using namespace Lemma;
-
-int main() {
-
-    // Do calculation
-    jsw_timer timer;
-
-    DipoleSource *dipole = DipoleSource::New();
-    dipole->SetType(MAGNETICDIPOLE);
-        dipole->SetPolarisation(0., 0.0,  1.0);
-        //dipole->SetPolarisation(XPOLARISATION);
-        //dipole->SetPolarisation(YPOLARISATION);
-        //dipole->SetPolarisation(ZPOLARISATION);
-
-        //dipole->SetMoment(1);
-        //dipole->SetLocation(1,1,-.0100328);
-        dipole->SetLocation(0., 0., -0.001);
-        //dipole->SetLocation(-2.5,1.25,0);
-        int iif=10000;
-        dipole->SetNumberOfFrequencies(iif);
-        Real w0 = 10;
-        for (int iw=0; iw<iif; ++iw) {
-            dipole->SetFrequency(iw, w0);
-            w0 += 1523.;
-        }
-
-    VectorXcr sigma(8);
-    sigma << 0., 3e-4, 5e-4, 1e-2, .5, 5e-6, .03, .04;
-    VectorXr  thick(6);
-        thick << 10 , 10 , 10 , 10 , 10 , 10;
-
-    LayeredEarthEM *earth = LayeredEarthEM::New();
-        earth->SetNumberOfLayers(8);
-        earth->SetLayerConductivity(sigma);
-        earth->SetLayerThickness(thick);
-
-    ReceiverPoints *receivers = ReceiverPoints::New();
-        Vector3r loc;
-        receivers->SetNumberOfReceivers(1);
-        loc << 150, 175, -.01;
-        receivers->SetLocation(0, loc);
-
-    // EmEarth
-    EMEarth1D  *EmEarth = EMEarth1D::New();
-        EmEarth->AttachDipoleSource(dipole);
-        EmEarth->AttachLayeredEarthEM(earth);
-        EmEarth->AttachReceiverPoints(receivers);
-        //EmEarth->SetFieldsToCalculate(BOTH);
-        EmEarth->SetFieldsToCalculate(H);
-
-        //EmEarth->SetHankelTransformMethod(GAUSSIANQUADRATURE);
-        //EmEarth->SetHankelTransformMethod(DIGITALFILTERING);
-        //EmEarth->SetHankelTransformMethod(FHTKEY201);
-        EmEarth->SetHankelTransformMethod(QWEKEY);
-
-    timer.begin();
-    EmEarth->MakeCalc3();
-    //std::cout << "H\n" << receivers->GetHfield(0)
-    //          << "End of H" << std::endl;
-    Real  lemmaTime = timer.end();
-    //std::cout << receivers->GetHfield() << std::endl;
-    std::cout << lemmaTime << "\t";
-
-    #ifdef LEMMAUSEVTK
-    vtkDataObject *_dataObjectxr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
-                    0, iif, XCOMPONENT, dipole->GetFrequencies());
-
-    vtkDataObject *_dataObjectxi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
-                    0, iif, XCOMPONENT, dipole->GetFrequencies());
-
-    vtkDataObject *_dataObjectyr= receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
-                    0, iif, YCOMPONENT, dipole->GetFrequencies());
-
-    vtkDataObject *_dataObjectyi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
-                    0, iif, YCOMPONENT, dipole->GetFrequencies());
-
-    vtkDataObject *_dataObjectzr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
-                    0, iif, ZCOMPONENT, dipole->GetFrequencies());
-
-    vtkDataObject *_dataObjectzi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
-                    0, iif, ZCOMPONENT, dipole->GetFrequencies());
-    #endif
-
-
-//     //dipole->SetPolarisation(XPOLARISATION);
-//     //std::cout << "Fortran Calc" << std::endl;
-//     #ifdef KIHALEE_EM1D
-//     timer.begin();
-//     EmEarth->MakeCalc();
-//     Real fortranTime = timer.end();
-//     std::cout << fortranTime << "\t";
-//     std::cout << fortranTime/lemmaTime << std::endl;
-//     #endif
-
-//     #ifdef LEMMAUSEVTK
-//     vtkDataObject *_fdataObjectxr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
-//                     0, receivers->GetNumberOfReceivers(), XCOMPONENT, dipole->GetFrequencies());
-//
-//     vtkDataObject *_fdataObjectxi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
-//                     0, receivers->GetNumberOfReceivers(), XCOMPONENT, dipole->GetFrequencies());
-//
-//     vtkDataObject *_fdataObjectyr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
-//                     0, receivers->GetNumberOfReceivers(), YCOMPONENT, dipole->GetFrequencies());
-//
-//     vtkDataObject *_fdataObjectyi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
-//                     0, receivers->GetNumberOfReceivers(), YCOMPONENT, dipole->GetFrequencies());
-//
-//     vtkDataObject *_fdataObjectzr = receivers->GetVtkDataObjectFreq(HFIELDREAL, 0,
-//                     0, receivers->GetNumberOfReceivers(), ZCOMPONENT, dipole->GetFrequencies());
-//
-//     vtkDataObject *_fdataObjectzi = receivers->GetVtkDataObjectFreq(HFIELDIMAG, 0,
-//                     0, receivers->GetNumberOfReceivers(), ZCOMPONENT, dipole->GetFrequencies());
-//     #endif
-
-
-    #ifdef LEMMAUSEVTK
-    vtkRenderer *_ren = vtkRenderer::New();
-    vtkRenderWindow *_renwin = vtkRenderWindow::New();
-    _renwin->AddRenderer(_ren);
-
-    ///////////////////////////////////////////////
-    // X Component Plot
-    vtkXYPlotActor *_xplot = vtkXYPlotActor::New();
-    //vtkXYPlotWidget *_wplot = vtkXYPlotWidget::New();
-        // Add the datasets
-        _xplot->AddDataObjectInput( _dataObjectxr);
-        _xplot->AddDataObjectInput( _dataObjectxi);
-        //_xplot->AddDataObjectInput(_fdataObjectxr);
-        //_xplot->AddDataObjectInput(_fdataObjectxi);
-        _xplot->SetTitle("X field");
-        _xplot->SetXTitle("Depth");
-        _xplot->SetYTitle("E Field");
-        _xplot->SetXValuesToValue();
-        //_plot->SetXValuesToIndex();
-
-        // set which parts of the data object are to be used for which axis
-        _xplot->SetDataObjectXComponent(0,1);
-        _xplot->SetDataObjectYComponent(0,0);
-        _xplot->SetDataObjectXComponent(1,1);
-        _xplot->SetDataObjectYComponent(1,0);
-        _xplot->SetDataObjectXComponent(2,1);
-        _xplot->SetDataObjectYComponent(2,0);
-        _xplot->SetDataObjectXComponent(3,1);
-        _xplot->SetDataObjectYComponent(3,0);
-        _xplot->SetNumberOfXLabels(3);
-        _xplot->SetPlotColor(0,1,1,1);
-        _xplot->SetPlotColor(1,1,1,1);
-        _xplot->SetPlotColor(2,1,0,0);
-        _xplot->SetPlotColor(3,1,0,0);
-        _xplot->GetProperty()->SetLineWidth(2);
-        _xplot->GetProperty()->SetPointSize(4);
-
-        //  _plot->SetPlotPoints(0,0);
-        //  _plot->SetPlotPoints(1,0);
-        //  _plot->SetPlotPoints(2,0);
-        //  _plot->SetPlotPoints(3,0);
-
-        //  _plot->SetPlotLines(0,0);
-        //  _plot->SetPlotLines(1,0);
-        //  _plot->SetPlotLines(2,0);
-        //  _plot->SetPlotLines(3,0);
-
-        _xplot->PlotCurvePointsOff();
-        _xplot->PlotCurveLinesOff();
-        _xplot->GetPositionCoordinate()->SetValue(0.0, 0.67, 0);
-        _xplot->GetPosition2Coordinate()->SetValue(1.0, 0.33, 0);
-        //_plot->SetReverseYAxis(1); // Just flips axis, not data!
-
-    ///////////////////////////////////////////////
-    // Y Component Plot
-    vtkXYPlotActor *_yplot = vtkXYPlotActor::New();
-    //vtkXYPlotWidget *_wplot = vtkXYPlotWidget::New();
-        // Add the datasets
-        _yplot->AddDataObjectInput( _dataObjectyr);
-        _yplot->AddDataObjectInput( _dataObjectyi);
-        //_yplot->AddDataObjectInput(_fdataObjectyr);
-        //_yplot->AddDataObjectInput(_fdataObjectyi);
-        _yplot->SetTitle("Y field");
-        _yplot->SetXTitle("Depth");
-        _yplot->SetYTitle("E Field");
-        _yplot->SetXValuesToValue();
-        //_yplot->SetXValuesToIndex();
-
-        // set which parts of the data object are to be used for which axis
-        _yplot->SetDataObjectXComponent(0,1);
-        _yplot->SetDataObjectYComponent(0,0);
-        _yplot->SetDataObjectXComponent(1,1);
-        _yplot->SetDataObjectYComponent(1,0);
-        _yplot->SetDataObjectXComponent(2,1);
-        _yplot->SetDataObjectYComponent(2,0);
-        _yplot->SetDataObjectXComponent(3,1);
-        _yplot->SetDataObjectYComponent(3,0);
-        _yplot->SetNumberOfXLabels(3);
-        _yplot->SetPlotColor(0,1,1,1);
-        _yplot->SetPlotColor(1,1,1,1);
-        _yplot->SetPlotColor(2,1,0,0);
-        _yplot->SetPlotColor(3,1,0,0);
-        _yplot->GetProperty()->SetLineWidth(2);
-        _yplot->GetProperty()->SetPointSize(4);
-        _yplot->GetPositionCoordinate()->SetValue(0.00, 0.33, 0);
-        _yplot->GetPosition2Coordinate()->SetValue(1.0, 0.33, 0);
-
-        //  _plot->SetPlotPoints(0,0);
-        //  _plot->SetPlotPoints(1,0);
-        //  _plot->SetPlotPoints(2,0);
-        //  _plot->SetPlotPoints(3,0);
-
-        //  _plot->SetPlotLines(0,0);
-        //  _plot->SetPlotLines(1,0);
-        //  _plot->SetPlotLines(2,0);
-        //  _plot->SetPlotLines(3,0);
-
-        _yplot->PlotCurvePointsOff();
-        _yplot->PlotCurveLinesOff();
-        //_plot->SetReverseYAxis(1)
-
-    ///////////////////////////////////////////////
-    // Z Component Plot
-    vtkXYPlotActor *_zplot = vtkXYPlotActor::New();
-    //vtkXYPlotWidget *_wplot = vtkXYPlotWidget::New();
-        // Add the datasets
-        _zplot->AddDataObjectInput( _dataObjectzr);
-        _zplot->AddDataObjectInput( _dataObjectzi);
-        //_zplot->AddDataObjectInput(_fdataObjectzr);
-        //_zplot->AddDataObjectInput(_fdataObjectzi);
-        _zplot->SetTitle("Z field");
-        _zplot->SetXTitle("Depth");
-        _zplot->SetYTitle("E Field");
-        _zplot->SetXValuesToValue();
-        //_plot->SetXValuesToIndex();
-
-        // set which parts of the data object are to be used for which axis
-        _zplot->SetDataObjectXComponent(0,1);
-        _zplot->SetDataObjectYComponent(0,0);
-        _zplot->SetDataObjectXComponent(1,1);
-        _zplot->SetDataObjectYComponent(1,0);
-        _zplot->SetDataObjectXComponent(2,1);
-        _zplot->SetDataObjectYComponent(2,0);
-        _zplot->SetDataObjectXComponent(3,1);
-        _zplot->SetDataObjectYComponent(3,0);
-        _zplot->SetNumberOfXLabels(3);
-        _zplot->SetPlotColor(0,1,1,1);
-        _zplot->SetPlotColor(1,1,1,1);
-        _zplot->SetPlotColor(2,1,0,0);
-        _zplot->SetPlotColor(3,1,0,0);
-        _zplot->GetProperty()->SetLineWidth(2);
-        _zplot->GetProperty()->SetPointSize(4);
-        _zplot->GetPositionCoordinate()->SetValue(0.0, 0.0, 0);
-        _zplot->GetPosition2Coordinate()->SetValue(1.0, 0.33, 0);
-        //  _plot->SetPlotPoints(0,0);
-        //  _plot->SetPlotPoints(1,0);
-        //  _plot->SetPlotPoints(2,0);
-        //  _plot->SetPlotPoints(3,0);
-
-        //  _plot->SetPlotLines(0,0);
-        //  _plot->SetPlotLines(1,0);
-        //  _plot->SetPlotLines(2,0);
-        //  _plot->SetPlotLines(3,0);
-
-        _zplot->PlotCurvePointsOff();
-        _zplot->PlotCurveLinesOff();
-        //_plot->SetReverseYAxis(1)
-
-    _ren->AddActor2D(_xplot);
-    _ren->AddActor2D(_yplot);
-    _ren->AddActor2D(_zplot);
-
-    vtkRenderWindowInteractor *_iren = vtkRenderWindowInteractor::New();
-    _iren->SetRenderWindow(_renwin);
-    _iren->Initialize();
-    _renwin->Render();
-
-    //_wplot->SetXYPlotActor(_plot);
-    //_wplot->SetInteractor(_iren);
-    //_wplot->EnabledOn();
-
-    _iren->Start();
-
-    // TODO clean up you dirty whore
-//  _iren->Delete();
-//  _plot->Delete();
-//  _dataObject->Delete();
-//  _fieldData->Delete();
-//  _renwin->Delete();
-//  _ren->Delete();
-//  _xdatareal->Delete();
-//  _ydata->Delete();
-//  _depth->Delete();
-    #endif
-
-    EmEarth->Delete();
-    receivers->Delete();
-    earth->Delete();
-    dipole->Delete();
-
-    return 0;
-
-
-}

LemmaCore/examples/edipole.cpp

-// ===========================================================================
-//
-//       Filename:  utsnmrinversion1d.cpp
-//
-//        Created:  10/07/2010 08:57:04 AM
-//       Compiler:  Tested with g++, icpc, and MSVC 2010
-//
-//         Author:  Trevor Irons (ti)
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//                  United States Geological Survey (USGS)
-//
-//          Email:  tirons@mines.edu, tirons@usgs.gov
-//
-//  This program is free software: you can redistribute it and/or modify
-//  it under the terms of the GNU General Public License as published by
-//  the Free Software Foundation, either version 3 of the License, or
-//  (at your option) any later version.
-//
-//  This program is distributed in the hope that it will be useful,
-//  but WITHOUT ANY WARRANTY; without even the implied warranty of
-//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-//  GNU General Public License for more details.
-//
-//  You should have received a copy of the GNU General Public License
-//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
-//
-// ===========================================================================
-
-/**
-  @file
-  @author   Trevor Irons
-  @date     10/07/2010
-  @version   0.0
- **/
-
-#include "receiverpoints.h"
-#include "emearth1d.h"
-#include "dipolesource.h"
-
-using namespace Lemma;
-
-std::vector<Real>  readinpfile(const std::string& fname);
-
-int main(int argc, char** argv) {
-
-    std::cout <<
-    "\n"
-    << "ediple.exe Copyright (C) 2011 Broken Spoke Development, LLC\n\n"
-    << "This program is free software: you can redistribute it and/or modify\n"
-    << "it under the terms of the GNU General Public License as published by\n"
-    << "the Free Software Foundation, either version 3 of the License, or\n"
-    << "(at your option) any later version.\n\n"
-
-    << "This program is distributed in the hope that it will be useful,\n"
-    << "but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
-    << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n"
-    << "GNU General Public License for more details.\n\n"
-
-    << "You should have received a copy of the GNU General Public License\n"
-    << "along with this program.  If not, see <http://www.gnu.org/licenses/>.\n\n";
-
-    if (argc < 4) {
-        std::cout << "usage: edipole.exe  dipole.inp cond.inp points.inp \n";
-        exit(0);
-    }
-
-    std::vector<Real> Trans   = readinpfile(std::string(argv[1]));
-    std::vector<Real> CondMod = readinpfile(std::string(argv[2]));
-    std::vector<Real> Points  = readinpfile(std::string(argv[3]));
-
-    //////////////////////////////////////
-    // Define dipole source
-    DipoleSource* dipole = DipoleSource::New();
-        switch ( (int)(Trans[0]) ) {
-            case 0:
-                dipole->SetType(MAGNETICDIPOLE);
-                break;
-            case 1:
-                dipole->SetType(GROUNDEDELECTRICDIPOLE);
-                break;
-            default:
-                std::cerr << "Undefined dipole type, must be:\n"
-                     << "\t0 -> Magnetic\n"
-                     << "\t1 -> Grounded Electric\n";
-                exit(EXIT_FAILURE);
-        }
-
-        switch ( (int)(Trans[1]) ) {
-            case 0:
-                dipole->SetPolarisation(XPOLARISATION);
-                break;
-            case 1:
-                dipole->SetPolarisation(YPOLARISATION);
-                break;
-            case 2:
-                dipole->SetPolarisation(ZPOLARISATION);
-                break;
-            default:
-                std::cerr << "Undefined orientation, must be:\n"
-                          << "\t0 -> x\n"
-                          << "\t1 -> y\n"
-                          << "\t2 -> z\n";
-                exit(EXIT_FAILURE);
-        }
-        dipole->SetNumberOfFrequencies(1);
-        dipole->SetFrequency(0, Trans[2]);
-        dipole->SetLocation(Trans[3], Trans[4], Trans[5]);
-        dipole->SetMoment(Trans[6]);
-
-	// Receivers
- 	ReceiverPoints *receivers = ReceiverPoints::New();
-        int nx = (int)Points[0];
-        int ny = (int)Points[1];
-        int nz = (int)Points[2];
-        Real ox = Points[3];
-        Real oy = Points[4];
-        Real oz = Points[5];
-     	Vector3r loc;
-        VectorXr dx(nx-1); // TODO map the dx, dy, dz vectors
-        VectorXr dy(ny-1);
-        VectorXr dz(nz-1);
-        int ip = 6;
-        int ir = 0;
-        for ( ; ip <6+nx-1; ++ip) {
-            dx[ir] = Points[ip];
-            ++ir;
-        }
-        ir = 0;
-        for ( ; ip <6+ny-1+nx-1; ++ip) {
-            dy[ir] = Points[ip];
-            ++ir;
-        }
-        ir = 0;
-        for ( ; ip <6+nz-1+ny-1+nx-1; ++ip) {
-            dz[ir] = Points[ip];
-            ++ir;
-        }
- 		receivers->SetNumberOfReceivers(nx*ny*nz);
- 		ir = 0;
-        Real pz  = oz;
- 		for (int iz=0; iz<nz; ++iz) {
- 		    Real py    =  oy;
- 		    for (int iy=0; iy<ny; ++iy) {
- 		        Real px    =  ox;
- 		        for (int ix=0; ix<nx; ++ix) {
- 			        loc << px, py, pz;
- 			        receivers->SetLocation(ir, loc);
- 			        if (ix < nx-1) px += dx[ix];
- 			        ++ ir;
-     	        }
-                if (iy<ny-1) py += dy[iy];
-            }
-            if (iz<nz-1) pz += dz[iz];
-        }
-
-    ////////////////////////////////////
-    // Define model
-    LayeredEarthEM *earth = LayeredEarthEM::New();
-    VectorXcr sigma;
-    VectorXr  thick;
- 	earth->SetNumberOfLayers(CondMod[0]+1);
- 	sigma.resize(CondMod[0]+1); sigma(0) = 0; // airlayer
-    thick.resize(CondMod[0]-1);
-    int ilay=1;
-    for ( ; ilay/2<CondMod[0]-1; ilay+=2) {
-        sigma(ilay/2+1) =  1./CondMod[ilay];
-        thick(ilay/2) =  CondMod[ilay+1];
-    }
-    sigma(ilay/2+1) = 1./ CondMod[ilay];
-	earth->SetLayerConductivity(sigma);
-    if (thick.size() > 0) earth->SetLayerThickness(thick);
-
-	EMEarth1D  *EmEarth = EMEarth1D::New();
-		EmEarth->AttachDipoleSource(dipole);
-		EmEarth->AttachLayeredEarthEM(earth);
-		EmEarth->AttachReceiverPoints(receivers);
-		EmEarth->SetFieldsToCalculate(E);
-        EmEarth->MakeCalc3();
-
-    ////////////////////////////////////
-    // Report
- 	std::fstream hreal("efield.dat", std::ios::out);
-    hreal << *dipole << std::endl;
-    hreal << *earth << std::endl;
-    hreal << "Right hand coordinate system, z is positive down\n\n";
-    hreal << "x[m]\ty[m]\tz[m]\tRe(Ex) [V/m]\t Im(Ex) [V/m]\tRe(Ey) [V/m]\tIm(Ey) [V/m]\tRe(Ez) [V/m] Im(Ez) [V/m]\n";
-    hreal << "\\\\ ====================================================================================================\n";
-    hreal.precision(8);
-    int i=0;
-	for (int iz=0; iz<nz; ++iz) {
-	for (int iy=0; iy<ny; ++iy) {
-	for (int ix=0; ix<nx; ++ix) {
-        hreal << receivers->GetLocation(i).transpose() << "\t";
- 		hreal << std::real(receivers->GetEfield(0, i).transpose()[0]) << "\t";
- 		hreal << std::imag(receivers->GetEfield(0, i).transpose()[0]) << "\t";
- 		hreal << std::real(receivers->GetEfield(0, i).transpose()[1]) << "\t";
- 		hreal << std::imag(receivers->GetEfield(0, i).transpose()[1]) << "\t";
- 		hreal << std::real(receivers->GetEfield(0, i).transpose()[2]) << "\t";
- 		hreal << std::imag(receivers->GetEfield(0, i).transpose()[2]) << "\n";
-        ++i;
-    }
-    }
-    }
-    hreal.close();
-
-    // Clean up
-    EmEarth->Delete();
-    earth->Delete();
-    receivers->Delete();
-    dipole->Delete();
-}
-
-std::vector<Real>  readinpfile(const std::string& fname) {
-    std::string buf;
-    char dump[255];
-    std::vector<Real> vals;
-    std::fstream input(fname.c_str(), std::ios::in);
-    if (input.fail()) {
-        std::cerr << "Input file " << fname << " failed to open\n";
-        exit(EXIT_FAILURE);
-    }
-    while (input >> buf) {
-        if (buf.substr(0,2) == "//") {
-            input.getline(dump, 255);
-        } else {
-            vals.push_back( atof(buf.c_str() ));
-        }
-    }
-    return vals;
-}

LemmaCore/examples/emdipearth1d.cpp

-// ===========================================================================
-//
-//       Filename:  utemdipearth1d.cpp
-//
-//    Description:
-//
-//        Version:  0.0
-//        Created:  01/06/2010 04:27:56 PM
-//       Revision:  none
-//       Compiler:  g++ (c++)
-//
-//         Author:  Trevor Irons (ti)
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//                  United States Geological Survey (USGS)
-//
-//          Email:  tirons@mines.edu, tirons@usgs.gov
-//
-//  This program is free software: you can redistribute it and/or modify
-//  it under the terms of the GNU General Public License as published by
-//  the Free Software Foundation, either version 3 of the License, or
-//  (at your option) any later version.
-//
-//  This program is distributed in the hope that it will be useful,
-//  but WITHOUT ANY WARRANTY; without even the implied warranty of
-//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-//  GNU General Public License for more details.
-//
-//  You should have received a copy of the GNU General Public License
-//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
-//
-// ===========================================================================
-#include "emearth1d.h"
-#include "dipolesource.h"
-#include "layeredearthem.h"
-#include "receiverpoints.h"
-
-using namespace Lemma;
-
-int main() {
-
-	// Test with a single dipole
-	DipoleSource *dipole = DipoleSource::New();
-		dipole->SetType(GROUNDEDELECTRICDIPOLE);
-		dipole->SetPolarisation(XPOLARISATION);
-		dipole->SetNumberOfFrequencies(1);
-		dipole->SetMoment(1);
-		dipole->SetFrequency(0, 4400.1000);
-		//dipole->SetPhase(0);
-		//dipole->SetLocation( (VectorXr(3) << 49, 49, -1e-4).finished() );
-		dipole->SetLocation( 49, 49, -1e-4  );
-
-
-	// Define model
-	VectorXcr sigma(2);
-		sigma << 0., 1e-3;//, .1;//, .01, .001;
-	VectorXr  thick(1);
-		thick << 10;//, 10, 10;
-
-	LayeredEarthEM *earth = LayeredEarthEM::New();
-        earth->SetNumberOfLayers(2);
-		earth->SetLayerConductivity(sigma);
-		//earth->SetLayerThickness(thick);
-
-	// Receivers
-	ReceiverPoints *receivers = ReceiverPoints::New();
-		Vector3r loc;
-		//Real ox = -5.1456;
-		//Real oy =  2.2350;
-		Real ox =    50.;
-		Real oy =    20.;
-		Real depth = 18.10;
-		Real dz = 2.6;
-		int  nz = 1;
-
-		receivers->SetNumberOfReceivers(nz);
-		int ir = 0;
-		for (int iz=0; iz<nz; ++iz) {
-			loc << ox, oy, depth;
-			receivers->SetLocation(ir, loc);
-			depth += dz;
-			++ ir;
-		}
-	//receivers->SetLocation(1, ox, oy, depth);
-
-	EMEarth1D *EmEarth = EMEarth1D::New();
-        //EmEarth->SetHankelTransformMethod(DIGITALFILTERING);
-        EmEarth->SetFieldsToCalculate(BOTH); // Fortran needs this
-		EmEarth->AttachDipoleSource(dipole);
-		EmEarth->AttachLayeredEarthEM(earth);
-		EmEarth->AttachReceiverPoints(receivers);
-
-        //dipole->SetType(ELECTRICDIPOLE);
-//         receivers->SetNumberOfReceivers(1);
-//         //for
-// 	    receivers->SetLocation(0, ox, oy, depth);
-
-
-	std::cout << "C++\n";
-	EmEarth->MakeCalc3();
-	std::cout << receivers->GetEfield(0,0) << std::endl;
-	//std::cout << receivers->GetEfield(0) << std::endl;
-	//std::cout << receivers->GetHfield(1) << std::endl;
-	//std::cout << receivers->GetEfield(1) << std::endl;
-	receivers->ClearFields();
-
-    // swap tx rx posigion
-    receivers->SetLocation(0, dipole->GetLocation());
-    dipole->SetLocation(loc);
-	EmEarth->MakeCalc3();
-	std::cout << receivers->GetEfield(0,0) << std::endl;
-
-	receivers->ClearFields();
- #ifdef KIHALEE_EM1D
-// 	//std::cout << "\nFORTRAN\n";
- 	EmEarth->MakeCalc();
-// 	std::cout << receivers->GetHfield(0,0) << std::endl;
- 	std::cout << receivers->GetEfield(0,0) << std::endl;
- #endif
-
-    dipole->Delete();
-    EmEarth->Delete();
-    receivers->Delete();
-    earth->Delete();
-
-// 	try {
-//
-// 	}
-//
-// 	// Catch exceptions
-// 	catch (NullEarth) {
-// 			std::cout << "Earth model not set dummy\n";
-// 	}
-//
-// 	catch (NullReceivers) {
-// 			std::cout << "Receivers not set dummy\n";
-// 	}
-
-	//EmEarth->TestBess();
-
-}

LemmaCore/examples/femforward.cpp

-// ===========================================================================
-// 
-//       Filename:  utfemforward.cpp
-// 
-//    Description:  
-// 
-//        Version:  0.0
-//        Created:  01/15/2013 12:11:34 PM
-//       Revision:  none
-//       Compiler:  Tested with g++ 
-// 
-//         Author:  M. Andy Kass (MAK)
-//
-//   Organisation:  Broken Spoke Development, LLC
-//                  
-//
-//          Email:  mkass@numericalgeo.com
-// 
-//  This program is free software: you can redistribute it and/or modify
-//  it under the terms of the GNU General Public License as published by
-//  the Free Software Foundation, either version 3 of the License, or
-//  (at your option) any later version.
-//
-//  This program is distributed in the hope that it will be useful,
-//  but WITHOUT ANY WARRANTY; without even the implied warranty of
-//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-//  GNU General Public License for more details.
-//
-//  You should have received a copy of the GNU General Public License
-//  along with this program.  If not, see <http://www.gnu.org/licenses/>.
-//
-// ===========================================================================
-
-#include <time.h>
-#include "Lemma"
-#include "banner.h"
-
-using namespace Lemma;
-
-#ifdef LEMMAUSEVTK
-#include "matplot.h"
-using namespace matplot;
-#endif
-
-int main() {
-
-	clock_t launch = clock();
-
-	// Banner display
-	std::string name;
-	std::string version;
-	std::string usage;
-	name = "FEM Forward Modeller - 1D ";
-	version = "1.0alpha";
-	usage = "utfemforward [inputfile]";
-	banner(name,version,usage);
-
-	time_t curr = time(0);
-	std::cout << std::endl << "  Start time: " << ctime(&curr) << std::endl;
-
-	// Define some objects
-	DipoleSource* Trans = DipoleSource::New();
-	ReceiverPoints* Receivers = ReceiverPoints::New();
-	LayeredEarthEM* Earth = LayeredEarthEM::New();
-
-
-
-	// SINGLE SOUNDING
-
-	// Create new data object to receive forward model
-	DataFEM* modelledData = DataFEM::New();
-
-	// Create instrument object
-	InstrumentFem* theinstrument = InstrumentFem::New();	
-
-	// Set up EMEarthModel
-	Earth->SetNumberOfLayers(5);
-	Earth->SetLayerConductivity((VectorXcr(5) << 0.,1.e-4,1.e-2,
-		1.e-4,1.e-6).finished());
-	Earth->SetLayerThickness((VectorXr(3) << 20.,5.,50.).finished());
-	
-	// Set up transmitter
-	Real momtemp;
-	momtemp = 1;
-	Real freq;
-	freq = 391;
-	Trans->SetType(MAGNETICDIPOLE);
-	Trans->SetLocation(0,0,-1.e-3);
-	Trans->SetPolarisation(ZPOLARISATION);
-	// as a test
-	Trans->SetNumberOfFrequencies(1);
-	Trans->SetFrequency(0,freq);
-	Trans->SetMoment(momtemp);
-
-	// Set up receivers
-	Vector3r loc1;
-	Vector3r loc2;
-	Receivers->SetNumberOfReceivers(1);
-	loc1 << 9,0,-1.e-3;
-	Receivers->SetLocation(0,loc1);
-
-
-	// Attach to instrument
-	theinstrument->SetReceiverPoints(Receivers);
-	theinstrument->SetDipoleSource(Trans);
-	theinstrument->EMEarthModel(Earth);
-	theinstrument->SetOutputData(modelledData);
-
-	// Calculate
-	theinstrument->MakeCalculation();
-
-	// See what comes back...
-	std::cout << Receivers->GetHfield(0,0)(2) << std::endl;
-	
-	// Need to convert H field to ppm
-
-
-	theinstrument->Delete();
-	modelledData->Delete();
-
-	// MULTIPLE SOUNDING MODEL USING READ-IN DATA
-
-
-	InstrumentFem* theinstrument2 = InstrumentFem::New();
-	DataFEM* modelledData2 = DataFEM::New();
-
-	// Using the UBC data reader to read in the survey params
-	// this will be used for the multiple sounding testing
-	std::string datfile;
-	datfile = "126.obs";
-
-	DataReaderFemUBC* Reader = DataReaderFemUBC::New();
-	DataFEM* inpdata = DataFEM::New();
-	Reader->SetDataFEM(inpdata);
-	try {
-		Reader->ReadData(datfile,1);
-	} catch(std::exception& e) {
-		exit(EXIT_FAILURE);
-	}
-	std::cout << *inpdata << std::endl;
-	theinstrument2->SetOutputData(modelledData2);
-	theinstrument2->AlignWithData(inpdata);
-	// Now, how do I want to pass it an earth model for each sounding?
-	//
-	inpdata->Delete();
-
-
-
-
-	// Need to loop over transmitters
-	// The relative positions of the transmitter and receiver is fixed
-	// For testing, do some kind of random realisation of Earth model?
-//	int nObs;
-//	int nFreqs;
-//	nObs = inpdata->GetnObs();
-//	nFreqs = inpdata->GetnFreq();
-
-//	Trans->SetType(MAGNETICDIPOLE);
-//	Trans->SetLocation(0,0,-1e-3);
-
-//	Vector3r loc;
-//	Receivers->SetNumberOfReceivers(1);
-//	loc << 0,0,-1e-3;
-//	Receivers->SetLocation(0,loc);
-
-//	Earth->SetNumberOfLayers(5); //Including the two halfspaces
-//	Earth->SetLayerConductivity((VectorXcr(5) << 0.,1.e-4,1.e-2,
-//		1.e-4,1.e-6).finished());
-//	Earth->SetLayerThickness((VectorXr(3) << 20.,5.,50.).finished());
-
-//	for (int ii=0;ii<nObs;ii++) {
-//		for (int jj=0;jj<nFreqs;jj++) {
-//			Trans->SetMoment(inpdata->GetTxMom().coeff(jj));
-//			
-//		}
-//	}
-	
-	//This is a bunch of testing stuff
-	//theinstrument->AlignWithData(inpdata);
-	//theinstrument->MakeCalculation();
-	//inpdata->Delete();
-	//theinstrument->MakeCalculation();
-
-
-	theinstrument2->Delete();
-	Reader->Delete();
-	Earth->Delete();
-	Receivers->Delete();
-	Trans->Delete();
-
-	// Timey-wimey stuff
-	Real time;
-	clock_t done = clock();
-	time = (done-launch)/CLOCKS_PER_SEC;
-	std::cout << "  Execution time: " << time << " [CPU] seconds."
-		<< std::endl;
-
-	return EXIT_SUCCESS;
-}

LemmaCore/examples/filter.cpp

   @version   0.0
  **/
 
-#include "windowfilter.h"
+#include "WindowFilter.h"
 using namespace Lemma;
 
 int main() {
 
-    WindowFilter* Hamming = WindowFilter::New();
+    auto Hamming = WindowFilter::NewSP();
 
         Hamming->SetWindowType( HANNING );
         Hamming->SetSamplingInterval(1e-4);
     std::cout << Hamming->GetFilterCoefficients() //.transpose()
               << std::endl;
 
-    Hamming->Delete();
 
 }

LemmaCore/include/ASCIIParser.h

 
     // ====================  LIFECYCLE     =======================
 
-    /** @copybrief LemmaObject::New()
-     *  @copydetails LemmaObject::New()
-     */
-    static ASCIIParser* New();
-
-    /** @copybrief   LemmaObject::Delete()
-     *  @copydetails LemmaObject::Delete()
+    /**
+     *  Factory method for generating concrete class.
+     *  @return a std::shared_ptr of type ASCIIParser
      */
-    void Delete();
+    static std::shared_ptr< ASCIIParser >  NewSP();
 
     // ====================  OPERATORS     =======================
 

LemmaCore/include/CubicSplineInterpolator.h

     // ====================  LIFECYCLE     =======================
 
     /**
-     * @copybrief LemmaObject::New()
-     * @copydetails LemmaObject::New()
+     *  Factory method for generating concrete class.
+     *  @return a std::shared_ptr of type CubicSplineInterpolator
      */
-    static CubicSplineInterpolator* New();
+    static std::shared_ptr<CubicSplineInterpolator> NewSP();
 
-    /**
-     *  @copybrief   LemmaObject::Delete()
-     *  @copydetails LemmaObject::Delete()
-     */
-    void Delete();
 
     // ====================  OPERATORS     =======================
 
     /** Default protected constructor, use New */
     CubicSplineInterpolator (const std::string& name);
 
-    /** Default protected destructor, use Delete */
+    /** Default protected destructor, smart pointers auto delete */
     ~CubicSplineInterpolator ();
 
     /**

LemmaCore/include/DCIPElectrode.h

-/* 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      11/10/2014 10:53:34 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-
-#ifndef  DCIPELECTRODE_INC
-#define  DCIPELECTRODE_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    /**
-      \brief
-      \details
-     */
-    class DCIPElectrode : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const DCIPElectrode &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static DCIPElectrode* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        // ====================  ACCESS        =======================
-
-        /** Sets the physical location of the electrode
-         *  @param[in] loc is the location
-         */
-        void SetLocation(const Vector3r& loc);
-
-        /** Sets the tag (label) for the electrode
-         */
-        void SetLabel(const std::string& tag);
-
-        /** Sets the tag (label) for the electrode
-         */
-        std::string GetLabel( );
-
-        int GetNodeID() {return Node_ID;}
-        // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-        /**
-         *  Uses YAML to serialize this object.
-         *  @return a YAML::Node
-         */
-        YAML::Node Serialize() const;
-
-        /**
-         *   Constructs an object from a YAML::Node.
-         */
-        static DCIPElectrode* DeSerialize(const YAML::Node& node);
-#endif
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        DCIPElectrode (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-        DCIPElectrode (const YAML::Node& node);
-#endif
-
-        /** Default protected destructor, use Delete */
-        ~DCIPElectrode ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        /** The location of the electrode */
-        Vector3r Location;
-
-        /** Local Node_ID on a mesh */
-        int Node_ID;
-
-        /** String label for the electrode */
-        std::string Label;
-
-    }; // -----  end of class  DCIPElectrode  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef DCIPELECTRODE_INC  -----
-

LemmaCore/include/DCSurvey.h

-/* 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      10/08/2014 01:51:50 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#ifndef  DCSURVEY
-#define  DCSURVEY
-
-#include "LemmaObject.h"
-#include "DCIPElectrode.h"
-
-#ifdef HAVE_YAMLCPP
-#include "yaml-cpp/yaml.h"
-#endif
-
-#ifdef LEMMAUSEVTK
-#include <vtkDataSet.h>
-#endif
-
-namespace Lemma {
-
-    #define EINFINITY -9999
-
-    /**
-      \brief   Describes a DC survey.
-      \details This class aims to encapulate any type of DC survey.
-     */
-    class DCSurvey : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const DCSurvey &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static DCSurvey* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        /**
-         *   Adds new electrode to the survey.
-         *   @param[in] Electrode `Pounds' a new Electrode into place.
-         *   @return integer index to this electrode.
-         *   @note Single electrodes cannot be pulled once they are pounded. The reason for this is that
-         *         every index then would become invalid. Furthurmore these are stored in a std::vector and
-         *         removing arbitrary items is inefficient.
-         *   @see PullElectrodes
-         *   @param[in] label is an optional tag for electrode.
-         *   @param[in] nodeID is the optional node ID on a mesh
-         */
-        int PoundElectrode( DCIPElectrode* Electrode, const std::string& label = "NULL", const int& nodeID=-1 );
-
-        /** Alternative Factory method of setting electrodes. IN this manner all memoy management
-         *  is handled by DCSurvey.
-         *  @note there is no logic preventing one from pounding coincident electrodes. Don't do it.
-         *  @note Single electrodes cannot be pulled once they are pounded. The reason for this is that
-         *         every index then would become invalid. Furthurmore these are stored in a std::vector and
-         *         removing arbitrary items is inefficient.
-         *  @see PullElectrodes
-         *  @param[in] loc is the location of the electrode.
-         *  @param[in] label is an optional label for electrode.
-         *  @param[in] nodeID is the optional node ID on a mesh
-         */
-        DCIPElectrode* PoundElectrode( const Vector3r& loc, const std::string& label = "NULL", const int& nodeID=-1  );
-
-#ifdef LEMMAUSEVTK
-        DCIPElectrode* PoundElectrode( const int& nodeID, vtkDataSet* Mesh, const std::string& label = "NULL" );
-#endif
-
-        /**
-         *  Pulls all electrodes and removes connections.
-         */
-        void PullElectrodes();
-
-        /**
-         *   Adds an injection point.
-         *   @param[in] A is the positive current electrode
-         *   @param[in] B is the negative current electrode
-         *   @param[in] J is the current intensity
-         *   @see AddInjection(const int& iA, const int& iB, const Real& J)
-         *   @see AddInjection(const int& iA, const Real& J)
-         *   @see AddInjection(DCIPElectrode* A, const Real& J)
-         */
-        int AddInjection( DCIPElectrode* A, DCIPElectrode* B, const Real& J);
-
-        /**
-         *   Adds an injection point.
-         *   @param[in] A is the positive current electrode.
-         *   @param[in] J is the current intensity.
-         *   B,  the negative current electrode is taken to be infinity
-         *   @see AddInjection(const int& iA, const int& iB, const Real& J)
-         *   @see AddInjection(const int& iA, const Real& J)
-         *   @see AddInjection(DCIPElectrode* A, DCIPElectrode* B, const Real& J)
-         */
-        int AddInjection( DCIPElectrode* A, const Real& J );
-
-        /**
-         *   Adds an injection point.
-         *   @param[in] A is the positive current electrode index
-         *   @param[in] B is the negative current electrode index
-         *   @param[in] J is the current intensity
-         *   @see AddInjection(DCIPElectrode* A, DCIPElectrode* B, const Real& J)
-         *   @see AddInjection(DCIPElectrode* A, const Real& J)
-         *   @see AddInjection(const int& iA, const Real& J)
-         */
-        int AddInjection( const int& iA, const int& iB, const Real& J );
-
-        /**
-         *   Adds an injection point with the negative electrode at infinity.
-         *   @param[in] A is the positive current electrode index
-         *   @param[in] J is the current intensity
-         *   @see AddInjection(DCIPElectrode* A, DCIPElectrode* B, const Real& J)
-         *   @see AddInjection(DCIPElectrode* A, const Real& J)
-         *   @see AddInjection(const int& iA, const int& iB, const Real& J)
-         */
-        int AddInjection( const int& iA, const Real& J );
-
-        /** Adds a potential measurement via the electrode pair comparison \f$ M - N \f$.
-         *   @param[in] M is a pointer to the `positive' electrode
-         *   @param[in] N is a pointer to the `negative' electrode
-         *   @param[in] iJ is the current injection index to associate with this measurement
-         */
-        void AddMeasurement( const int& iJ, DCIPElectrode* M, DCIPElectrode* N );
-
-        /** Adds a potential measurement via the electrode pair comparison \f$ M - N \f$.
-         *   @param[in] M is the `positive' electrode string label name
-         *   @param[in] N is the `negative' electrode string label name
-         *   @param[in] iJ is the current injection index to associate with this measurement
-         *   @see AddMeasurement( const int& iJ, DCIPElectrode* M, DCIPElectrode* N )
-         */
-        void AddMeasurement( const int& ij, const std::string& M, const std::string& N);
-
-        /**
-         *  Used to probe for the index and current of an injection
-         *  @param[in] ij is the current injection indes
-         *  @param[out] ii is the node index
-         *  @param[out] jj is the current
-         */
-        void GetA( const int& ij, int& ii, Real& jj );
-
-        /**
-         *  Used to probe for the index and current of an injection
-         *  @param[in] ij is the current injection indes
-         *  @param[out] ii is the node index
-         *  @param[out] jj is the current
-         */
-        void GetB( const int& ij, int& ii, Real& jj );
-
-
-        // ====================  ACCESS        =======================
-
-        // ====================  INQUIRY       =======================
-
-        #ifdef HAVE_YAMLCPP
-        YAML::Node Serialize() const;
-        static DCSurvey* DeSerialize(const YAML::Node& node);
-        #endif
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        DCSurvey (const std::string& name);
-
-        #ifdef HAVE_YAMLCPP
-        /** Default protected constructor, use New */
-        DCSurvey (const YAML::Node& node);
-        #endif
-
-        /** Default protected destructor, use Delete */
-        ~DCSurvey ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        /** The electrodes */
-        std::vector<DCIPElectrode*>                Electrodes;
-
-        /** Tags for the electrodes, lines etc. Ordered with Electrodes std::vector */
-        std::vector<std::string>                   OrderedElectrodeLabels;
-
-        /** Map of tags for the electrodes, lines etc. */
-        std::map<std::string, std::pair<DCIPElectrode*, int> >      ElectrodeLabelMap;
-
-        /** The A Injection electrodes */
-        std::vector<int>     A_Electrodes;
-
-        /** The A Injection electrodes */
-        std::vector<int>     B_Electrodes;
-
-        /** The A Injection electrodes */
-        std::vector<Real>    J_Electrodes;
-
-        /** First Potential electrodes */
-        std::vector< std::vector<int> > M_Electrodes;
-
-        /** Second Potential electrodes */
-        std::vector< std::vector<int> > N_Electrodes;
-
-    }; // -----  end of class  DCSurvey  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef DCSURVEY  -----

LemmaCore/include/datareader.h → LemmaCore/include/DataReader.h

 #define  DATAREADER_H_INC
 
 #include "LemmaObject.h"
-#include "data.h"
+#include "Data.h"
 
 namespace Lemma {
 

LemmaCore/include/FHTKey.h

-/* 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      02/11/2014 03:33:08 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-
-#ifndef  FHTKEY_INC
-#define  FHTKEY_INC
-
-#include "hankeltransform.h"
-
-namespace Lemma {
-
-    /**
-      \brief   Impliments the fast Hankel transform as outlines by Key 2011
-      \details This filter uses 61, 121, or 201 filter points and supports both lagged and related
-                kernel arguments. This algorithm is a port of code carrying the following copyright and
-                restriction:
-                %------------------------------------------------------------------%
-                % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
-                % For more information, go to http://software.seg.org/2012/0003 .  %
-                % You must read and accept usage terms at:                         %
-                % http://software.seg.org/disclaimer.txt before use.               %
-                %------------------------------------------------------------------%
-     */
-    class FHTKey : public HankelTransform {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const FHTKey &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static FHTKey* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        Complex Zgauss(const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel);
-
-        /// Computes related kernels, if applicable, otherwise this is
-        /// just a dummy function.
-        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
-
-        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
-
-        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
-
-        // ====================  ACCESS        =======================
-
-        // ====================  INQUIRY       =======================
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        FHTKey (const std::string& name);
-
-        /** Default protected destructor, use Delete */
-        ~FHTKey ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        // Shared Filter Weights
-		static const Eigen::Matrix<Real, 201, 3>  WT201;
-
-        /// Holds answer, dimensions are NumConv, and NumberRelated.
-        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zans;
-
-    }; // -----  end of class  FHTKey  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef FHTKEY_INC  -----
-

LemmaCore/include/FHTKey101.h

-/* 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      02/11/2014 03:33:08 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-
-#ifndef  FHTKEY101_INC
-#define  FHTKEY101_INC
-
-#include "hankeltransform.h"
-
-namespace Lemma {
-
-    /**
-      \brief   Impliments the fast Hankel transform as outlines by Key 2011
-      \details This filter uses 51, 101, or 201 filter points and supports both lagged and related
-                kernel arguments. This algorithm is a port of code carrying the following copyright and
-                restriction:
-                %------------------------------------------------------------------%
-                % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
-                % For more information, go to http://software.seg.org/2012/0003 .  %
-                % You must read and accept usage terms at:                         %
-                % http://software.seg.org/disclaimer.txt before use.               %
-                %------------------------------------------------------------------%
-     */
-    class FHTKey101 : public HankelTransform {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const FHTKey101 &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static FHTKey101* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        Complex Zgauss(const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel);
-
-        /// Computes related kernels, if applicable, otherwise this is
-        /// just a dummy function.
-        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
-
-        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
-
-        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
-
-        // ====================  ACCESS        =======================
-
-        // ====================  INQUIRY       =======================
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        FHTKey101 (const std::string& name);
-
-        /** Default protected destructor, use Delete */
-        ~FHTKey101 ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        // Shared Filter Weights
-		static const Eigen::Matrix<Real, 101, 3>  WT101;
-
-        /// Holds answer, dimensions are NumConv, and NumberRelated.
-        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zans;
-
-    }; // -----  end of class  FHTKey101  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef FHTKEY101_INC  -----
-

LemmaCore/include/FHTKey51.h

-/* 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      02/11/2014 03:33:08 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-
-#ifndef  FHTKEY51_INC
-#define  FHTKEY51_INC
-
-#include "hankeltransform.h"
-
-namespace Lemma {
-
-    /**
-      \brief   Impliments the fast Hankel transform as outlines by Key 2011
-      \details This filter uses 51, 101, or 201 filter points and supports both lagged and related
-                kernel arguments. This algorithm is a port of code carrying the following copyright and
-                restriction:
-                %------------------------------------------------------------------%
-                % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
-                % For more information, go to http://software.seg.org/2012/0003 .  %
-                % You must read and accept usage terms at:                         %
-                % http://software.seg.org/disclaimer.txt before use.               %
-                %------------------------------------------------------------------%
-     */
-    class FHTKey51 : public HankelTransform {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const FHTKey51 &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static FHTKey51* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        Complex Zgauss(const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel);
-
-        /// Computes related kernels, if applicable, otherwise this is
-        /// just a dummy function.
-        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
-
-        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
-
-        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
-
-        // ====================  ACCESS        =======================
-
-        // ====================  INQUIRY       =======================
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        FHTKey51 (const std::string& name);
-
-        /** Default protected destructor, use Delete */
-        ~FHTKey51 ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        // Shared Filter Weights
-		static const Eigen::Matrix<Real, 51, 3>  WT51;
-
-        /// Holds answer, dimensions are NumConv, and NumberRelated.
-        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zans;
-
-    }; // -----  end of class  FHTKey51  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef FHTKEY51_INC  -----
-

LemmaCore/include/GridReader.h

 #define  GRIDREADER_INC
 
 #include "LemmaObject.h"
-#include "grid.h"
+#include "Grid.h"
 
 namespace Lemma {
 
 
             virtual void ReadASCIIGridFile( const std::string& name )=0;
 
-            virtual Grid* GetGrid( )=0;
+            virtual std::shared_ptr< Grid > GetGrid( )=0;
 
             // ====================  ACCESS        =======================
 

LemmaCore/include/GroundedElectricDipole.h

-/* 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      01/29/2014 06:59:39 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-
-#ifndef  GROUNDEDELECTRICDIPOLE_INC
-#define  GROUNDEDELECTRICDIPOLE_INC
-
-#include "dipolesource.h"
-
-namespace Lemma {
-
-    /**
-      \brief   Grounded electric dipole
-      \details Used to model an idealised grounded electrid dipole of arbitrary
-               polarisation.
-     */
-    class GroundedElectricDipole : public DipoleSource {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const GroundedElectricDipole &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static GroundedElectricDipole* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        // ====================  ACCESS        =======================
-
-        // ====================  INQUIRY       =======================
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        GroundedElectricDipole (const std::string& name);
-
-        /** Default protected destructor, use Delete */
-        ~GroundedElectricDipole ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-    }; // -----  end of class  GroundedElectricDipole  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef GROUNDEDELECTRICDIPOLE_INC  -----
-

LemmaCore/include/layeredearth.h → LemmaCore/include/LayeredEarth.h

 #ifndef __LAYEREDEARTH_H
 #define __LAYEREDEARTH_H
 
-#include "earthmodel.h"
+#include "EarthModel.h"
 
 namespace Lemma {
 

LemmaCore/include/LayeredEarthEMReader.h

-/* 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      09/27/2013 01:44:36 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2013, XRI Geophysics, LLC
- * @copyright Copyright (c) 2013, Trevor Irons
- */
-
-#ifndef  LAYEREDEARTHEMREADER_INC
-#define  LAYEREDEARTHEMREADER_INC
-
-#include "LemmaObject.h"
-#include "ASCIIParser.h"
-#include "layeredearthem.h"
-
-namespace Lemma {
-
-    /**
-      \brief
-      \details
-     */
-    class LayeredEarthEMReader : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const LayeredEarthEMReader &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static LayeredEarthEMReader* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        /** Reads ASCII input file. The format is as follows
-@code
-4           // Number of NON-AIR layers
-200   10    // resistivity, thickness layer 1 [Ohm-m] [m]
-20    10    // resistivity, thickness layer 2 [Ohm-m] [m]
-1120  10    // resistivity, thickness layer 3 [Ohm-m] [m]
-200         // resistivity of bottom layer [Ohm-m]
-@endcode
-         * @param[in] name is the filename
-         */
-        void ReadASCIIInputFile( const std::string& name );
-
-        // ====================  ACCESS        =======================
-
-        /** @return the pointer address of the LayeredEarthEM
-         */
-        LayeredEarthEM* GetLayeredEarth();
-
-        // ====================  INQUIRY       =======================
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        LayeredEarthEMReader (const std::string& name);
-
-        /** Default protected destructor, use Delete */
-        ~LayeredEarthEMReader ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        LayeredEarthEM*         LayEarth;
-
-    }; // -----  end of class  LayeredEarthEMReader  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef LAYEREDEARTHEMREADER_INC  -----

LemmaCore/include/LemmaObject.h

 /**
   @file
   @author   Trevor Irons
-  @date     06/25/2009
-  @version  $Id: LemmaObject.h 199 2014-12-29 19:25:20Z tirons $
+  @date     06-13-2016
  **/
 
 #ifndef __LEMMAOBJECT_H
 #include "yaml-cpp/yaml.h"
 #endif
 
+#include <memory>
+
 namespace Lemma {
 
-// ==========================================================================
-//        Class:  LemmaObject
-/** \brief    Abstract class providing simple reference counting and memory
-  *           management.
-  * \details  Since objects can be members of other objects, and may be
-  *           of multiple objects it becomes useful to count the number of
-  *           Classes an object is a member of. Objects cannot be deleted that
-  *           contain references to other objects.
+/** \brief    Abstract class providing common interface for Lemma Objects.
+  * \details  Lemma objects can be members of other Lemma, and may be members
+  *           of multiple objects. Since updates should be atomic, and objects
+  *           can be large, it becomes useful to count the number of
+  *           Classes an object is a member of.
+  *           Before C++-11, this was done internally in Lemma, with the inclusion of
+  *           more sophisticated smart pointers, this logic has been offloaded to the
+  *           standard. All Lemma objects should be created as C++-11 Smart pointers, using
+  *           the supplied New method. Calls to Delete are no longer necessary or available.
   */
-// ==========================================================================
-
-/** Base class for all of Lemma. Reference counted object provides simple
- * reference counting. This allows for much easier maintainance of shared
- * objects among classes.
- */
 class LemmaObject {
 
     /** Recursively prints information about this object
     friend YAML::Emitter& operator << (YAML::Emitter& out, const LemmaObject &ob) ;
     #endif
 
-    friend class DeleteObjectWithReferences;
+    friend class LemmaObjectDeleter;
 
     public:
 
-        // Needed because some derived classes have Eigen vectors as members,
+        // ====================  LIFECYCLE     ==============================
+        //virtual std::shared_ptr<LemmaObject> NewSP() const = 0;
+
+        // Needed because many derived classes have Eigen vectors as members,
         // causing alignment issues when vectorisation is enabled.
         EIGEN_MAKE_ALIGNED_OPERATOR_NEW
 
 
         // ====================  OPERATIONS    ==============================
 
-        /**
-         * Deletes this objects self reference. If there are no remaining
-         * references, Release is called freeing all memory. Otherwise Release
-         * is called if/when the last reference is removed.
-         */
-        virtual void Delete()=0;
-
-        /** Attaches this object to another object */
-        void AttachTo(LemmaObject *);
-
-        /** Detaches this object from another object */
-        void DetachFrom(LemmaObject *);
-
         // ====================  ACCESS        ==============================
 
         // ====================  INQUIRY       ==============================
 
-        /** Returns the number of objects attached to this. */
-        unsigned int GetNumberOfReferences();
-
-        /** Returns address(s) to class(es) of which this is a member
-         */
-        std::vector<LemmaObject*> GetReferences();
-
-        /** Returns name of this model */
-        std::string GetName();
+        /** Returns the name of the class, similiar to Python's type */
+        std::string GetName() const;
 
         #ifdef HAVE_YAMLCPP
         /**
          *        two families in to a LemmaInternalClass without serializing and perhaps this class for
          *        all external classes that might need to be serialized.
          */
-        virtual YAML::Node Serialize() const{
+        virtual YAML::Node Serialize() const {
             return YAML::Node();
         };
         #endif
         LemmaObject (const YAML::Node& node);
         #endif
 
-        // ====================  DATA MEMBERS  ==============================
         /** Protected default destructor. This is an abstract class and
          *  cannot be instantiated.
          */
-        virtual ~LemmaObject ();
+        virtual ~LemmaObject();
 
-        /**
-         *  Releases all memory back to the heap. Just calls the protected
-         *  destructor at the derived class level.
-         */
-        virtual void Release()=0;
-
-        // ====================  OPERATIONS    ==============================
+    private:
 
         // ====================  DATA MEMBERS  ==============================
 
-        /** Number of other classes claiming this as a member. */
-        unsigned int NumberOfReferences;
-
-        /** List of the addresses of the other classes referencing this as a
-         * member
-         */
-        std::vector<LemmaObject *> RefPtrList;
-
         /** Stores an ASCII string representation of the class name */
         std::string Name;
 
 }; // -----  end of class  LemmaObject  -----
 
+class LemmaObjectDeleter
+{
+    public:
+        void operator()(LemmaObject* p) { delete p; }
+};
+
     /////////////////////////////////////////////////////////////////
     // BOILERPLATE MACROS
     #define DESERIALIZECHECK( node, Object ) { \
     /////////////////////////////////////////////////////////////////
     // Error Classes
 
-    /** Error called when ReferenceCounting breaks. If an object is
-     * deleted that has refences still, this is thrown.
-     */
-    class DeleteObjectWithReferences : public std::runtime_error {
-
-        public:
-
-            /** Call this method internally when an object is deleted with
-             * references.
-             */
-            DeleteObjectWithReferences(LemmaObject *ptr);
-
-            /** @deprecated this error may be thrown, but the error message is much
-            * less insightful than
-            * DeleteObjectWithReferences(LemmaObject* ptr).
-            */
-            DeleteObjectWithReferences( );
-    };
-
-
     /** Error called when DeSerializing breaks. If the node type is not the expected one
      *  this error is thown.
      */

LemmaCore/include/MagneticDipole.h

-/* 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      09/25/2013 08:20:14 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2013, XRI Geophysics, LLC
- * @copyright Copyright (c) 2013, Trevor Irons
- */
-
-#ifndef  MAGNETICDIPOLE_INC
-#define  MAGNETICDIPOLE_INC
-
-#include "dipolesource.h"
-
-namespace Lemma {
-
-/**
-  @class
-  \brief   Magnetic Dipole
-  \details Used to model an idealised magnetic dipole of arbitrary
-           polarisation.
- */
-class MagneticDipole : public DipoleSource {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const MagneticDipole &ob);
-
-    public:
-
-    // ====================  LIFECYCLE     =======================
-
-    /**
-     * @copybrief LemmaObject::New()
-     * @copydetails LemmaObject::New()
-     */
-    static MagneticDipole* New();
-
-    /**
-     *  @copybrief   LemmaObject::Delete()
-     *  @copydetails LemmaObject::Delete()
-     */
-    void Delete();
-
-    // ====================  OPERATORS     =======================
-
-    // ====================  OPERATIONS    =======================
-
-    // ====================  ACCESS        =======================
-
-    // ====================  INQUIRY       =======================
-
-    protected:
-
-    // ====================  LIFECYCLE     =======================
-
-    /** Default protected constructor, use New */
-    MagneticDipole (const std::string& name);
-
-    /** Default protected destructor, use Delete */
-    ~MagneticDipole ();
-
-    /**
-     *  @copybrief   LemmaObject::Release()
-     *  @copydetails LemmaObject::Release()
-     */
-    void Release();
-
-    private:
-
-    // ====================  DATA MEMBERS  =========================
-
-    KernelEM1DManager*          Kernels;
-
-}; // -----  end of class  MagneticDipole  -----
-
-} // namespace Lemma
-
-#endif   // ----- #ifndef MAGNETICDIPOLE_INC  -----

LemmaCore/include/ParticleSwarmOptimizer.h

-/* 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      01/27/2015 01:50:59 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2015, XRI Geophysics, LLC
- * @copyright Copyright (c) 2015, Trevor Irons
- */
-
-#ifndef  PARTICLESWARMOPTIMIZER_INC
-#define  PARTICLESWARMOPTIMIZER_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-struct Particle{
-    Real       fitness;
-    VectorXr   best;
-};
-
-/**
-  \brief
-  \details
- */
-class ParticleSwarmOptimizer : public LemmaObject {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const ParticleSwarmOptimizer &ob);
-
-    public:
-
-    // ====================  LIFECYCLE     =======================
-
-    /**
-     * @copybrief LemmaObject::New()
-     * @copydetails LemmaObject::New()
-     */
-    static ParticleSwarmOptimizer* New();
-
-    /**
-     *  @copybrief   LemmaObject::Delete()
-     *  @copydetails LemmaObject::Delete()
-     */
-    void Delete();
-
-    // ====================  OPERATORS     =======================
-
-    // ====================  OPERATIONS    =======================
-
-    // ====================  ACCESS        =======================
-
-    // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-    /**
-     *  Uses YAML to serialize this object.
-     *  @return a YAML::Node
-     */
-    YAML::Node Serialize() const;
-
-    /**
-     *   Constructs an object from a YAML::Node.
-     */
-    static ParticleSwarmOptimizer* DeSerialize(const YAML::Node& node);
-#endif
-
-    protected:
-
-    // ====================  LIFECYCLE     =======================
-
-    /** Default protected constructor, use New */
-    ParticleSwarmOptimizer (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-    /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-    ParticleSwarmOptimizer (const YAML::Node& node);
-#endif
-
-    /** Default protected destructor, use Delete */
-    ~ParticleSwarmOptimizer ();
-
-    /**
-     *  @copybrief   LemmaObject::Release()
-     *  @copydetails LemmaObject::Release()
-     */
-    void Release();
-
-    private:
-
-    // ====================  DATA MEMBERS  =========================
-
-}; // -----  end of class  ParticleSwarmOptimizer  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef PARTICLESWARMOPTIMIZER_INC  -----
-

LemmaCore/include/PolygonalWireAntenna.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     05/18/2010
-  @version  $Id: PolygonalWireAntenna.h 211 2015-02-27 05:43:26Z tirons $
- **/
-
-#include "WireAntenna.h"
-
-#ifndef  POLYGONALWIREANTENNA_INC
-#define  POLYGONALWIREANTENNA_INC
-
-namespace Lemma {
-
-    // ===================================================================
-    //        Class:  PolygonalWireAntenna
-    /// \brief   Class representing polygonal wire antennae.
-    /// \details For EM calculations, dipoles representing this loop are
-    ///    created dynamically, depending on receiver location.
-    /// @todo enforce minimum dipole moment.
-    // ===================================================================
-    class PolygonalWireAntenna : public WireAntenna {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const PolygonalWireAntenna &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /**
-             * Declares all memory and returns a new instance.
-             */
-            static PolygonalWireAntenna* New();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-            /// Makes a deep copy of this antenna with all connections except
-            /// the dipole approximation.
-            PolygonalWireAntenna* Clone();
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /// Approximates with ungrounded electrical dipoles, such that
-            /// minDipoleRatio is satisfied.
-            virtual void ApproximateWithElectricDipoles(const Vector3r &rp);
-
-            /** Sets the minimum ratio for dipole moments to be used to
-             * approximate the loop. A smaller ratio yields a more accurate
-             * result, but is more expensive. Default is (1/5).
-             */
-            void SetMinDipoleRatio(const Real& ratio);
-
-            /** Sets the minimum moment for dipole moments to be used to
-             * approximate the loop.
-             */
-            void SetMinDipoleMoment(const Real& m);
-
-            /** Sets the minimum moment for dipole moments to be used to
-             * approximate the loop.
-             */
-            void SetMaxDipoleMoment(const Real& m);
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-            #ifdef HAVE_YAMLCPP
-            /**
-             *  Uses YAML to serialize this object.
-             *  @return a YAML::Node
-             */
-            YAML::Node Serialize() const;
-
-            /**
-             *   Constructs an object from a YAML::Node.
-             */
-            static PolygonalWireAntenna* DeSerialize(const YAML::Node& node);
-            #endif
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            PolygonalWireAntenna (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-            /// Default protected constructor.
-            PolygonalWireAntenna (const YAML::Node& node);
-#endif
-
-            /// Default protected constructor.
-            ~PolygonalWireAntenna ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  DATA MEMBERS  =======================
-
-            /// minimum ratio of dipole moment to distance to receiver point
-            Real minDipoleRatio;
-
-            /// Maximum dipole moment allowed
-            Real minDipoleMoment;
-
-            /// Maximum dipole moment allowed
-            Real maxDipoleMoment;
-
-            /// appends
-            void PushXYZDipoles(const Vector3r &step, const Vector3r &cp,
-                            const Vector3r &dir,
-                            std::vector<DipoleSource*> &Dipoles) ;
-
-            /// corrects for overstep
-            void CorrectOverstepXYZDipoles(const Vector3r &step,
-                            const Vector3r &cp,
-                            const Vector3r &dir,
-                            std::vector<DipoleSource*> &Dipoles );
-
-            // ====================  OPERATIONS    =======================
-
-
-            /// Returns the nearest point on a line segment to another point.
-            /// if the point is not on the line-segment, return the
-            /// nearest end-point
-            /// @param[in] p0, p1 define the line segement
-            /// @param[in] rp is a point in space. The function returns the
-            /// closest point on the line to this point.
-            /// @return The point (Lemma::Vector3r) on the line defined by p0,
-            /// and p1, closest to rp
-            Vector3r ClosestPointOnLine(const Vector3r &p0, const Vector3r &p1,
-                            const Vector3r &rp);
-
-            /// Interpolates dipoles along line segment defined by p0 and p1.
-            void InterpolateLineSegment(const Vector3r &p0, const Vector3r &p1,
-                            const Vector3r &rp);
-
-
-            /// List of the dipoles
-            //std::vector<DipoleSource*>           Dipoles;
-
-            /// Points that define this loop
-            //Vector3Xr                            Points;
-
-        private:
-
-            Vector3r                               rRepeat;
-
-    }; // -----  end of class  PolygonalWireAntenna  -----
-
-}       // -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef POLYGONALWIREANTENNA_INC  -----

LemmaCore/include/QWEKey.h

-/* 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      02/12/2014 10:20:18 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#ifndef  QWEKEY_INC
-#define  QWEKEY_INC
-
-#include	"hankeltransform.h"
-#include    <Eigen/Eigenvalues>
-#ifdef HAVEBOOSTSPECIALFUNCTIONS
-#include "boost/math/special_functions.hpp"
-#include "boost/math/special_functions/bessel.hpp"
-#endif
-
-namespace Lemma {
-
-    /** breakpoint to use in division of domain, based on zeros of bessel function or
-        regular nPi spacing.
-     */
-    enum sZeroType{J0, J1, NPI};
-
-    /**
-      \brief  Port of Key's quadrature with extrapolation Hankel transform algorithm.
-      \details Details of the algorithm can be found in Key2011. This code is a port
-               of the published algorithm, which contains the following notice:
-        %------------------------------------------------------------------%
-        % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
-        % For more information, go to http://software.seg.org/2012/0003 .  %
-        % You must read and accept usage terms at:                         %
-        % http://software.seg.org/disclaimer.txt before use.               %
-        %------------------------------------------------------------------%
-     */
-    class QWEKey : public HankelTransform {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const QWEKey &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static QWEKey* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        void TestPrivate(const int& N);
-
-        // ====================  OPERATIONS    =======================
-
-
-        Complex Zgauss(const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel);
-
-        /// Computes related kernels, if applicable, otherwise this is
-        /// just a dummy function.
-        void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
-
-        void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
-
-        void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
-
-        // ====================  ACCESS        =======================
-
-        // ====================  INQUIRY       =======================
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        QWEKey (const std::string& name);
-
-        /** Default protected destructor, use Delete */
-        ~QWEKey ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        /** Calculates Gauss quadrature weights of order N on the interval -1,1
-            Algorithm from p 129 in:
-            Trefethen, L. N., 2000, Spectral methods in MATLAB: Society for
-            Industrial and Applied Mathematics (SIAM), volume 10 of Software,
-            Environments, and Tools.
-        */
-        void GaussQuadWeights(const int& N);
-
-        /** Returns the quadrature intervals and Bessel function weights used for the
-            QWE method.
-
-         */
-        void BesselWeights( const sZeroType& sType);
-
-        /**  Computes an infinite integral using the partial sum of quadrature terms
-             accelerated by sequence extrapolation using the Shanks transformation
-             implemented with Wynn's epsilon algorithm.
-         */
-        void QWE(const Real& rho);
-
-        /** Calls the underlying kernel functions evaluated as necessary
-         */
-        void getEyKernel(const int& i, const int& idx, const Real& rho);
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        /** Relative tolerance, default is 1e-6 */
-        Real    RelTol;
-
-        /** Absolute tolerance, default is 1e-24 */
-        Real    AbsTol;
-
-        /** Quadrature order, higher is more accurate but more expensive. Eefault is 9 */
-        int     nQuad;
-
-        /** in QWE partial integrals before Shanks recurive algorithm. Defaults to 1  */
-        int nDelay;
-
-        /** Maximum number of intervals to integrate over . Defaults to 40  */
-        int nIntervalsMax;
-
-        /** Weighing of gaussian quadrature points */
-        VectorXr GaussWeights;
-
-        /** Abscissa locations of quadrature points */
-        VectorXr GaussAbscissa;
-
-        /** Breakpoints for dividing up the global integral */
-        VectorXr xInt;
-
-        /** All quadrature points between all breakpoints */
-        VectorXr Bx;
-
-        /** J0 weights */
-        VectorXr BJ0;
-
-        /** J1 weights */
-        VectorXr BJ1;
-
-        /** array of lambda arguments */
-        VectorXr Lambda;
-
-        /** array of lambda arguments */
-        VectorXr Intervals;
-
-        MatrixXcr TS;
-        VectorXi  Tn;
-        MatrixXcr Textrap;
-        MatrixXr  TrelErr;
-        MatrixXr  TabsErr;
-
-        /** Container to hold bessel arguments */
-        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic > Zwork;
-
-        /** Container to hold bessel arguments */
-        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic > Zans;
-
-        /** Manager for related kernels to evaluate */
-        KernelEM1DManager* KernelManager;
-
-    }; // -----  end of class  QWEKey  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef QWEKEY_INC  -----
-
-

LemmaCore/include/rectilineargrid.h → LemmaCore/include/RectilinearGrid.h

 #ifndef  RECTILINEARGRID_INC
 #define  RECTILINEARGRID_INC
 
-#include "grid.h"
+#include "Grid.h"
 
 namespace Lemma {
 
 
             // ====================  LIFECYCLE     =======================
 
-            /** Returns a pointer to a new object of type RectilinearGrid.
-             * It allocates all necessary memory.
-             */
-            static RectilinearGrid* New();
-
             /**
-             *  @copybrief   LemmaObject::Delete()
-             *  @copydetails LemmaObject::Delete()
+             *  Factory method for generating concrete class.
+             *  @return a std::shared_ptr of type RectilinearGrid
              */
-            void Delete();
+            static std::shared_ptr<RectilinearGrid> NewSP();
 
             // ====================  OPERATORS     =======================
 
             /// Default protected constructor.
             ~RectilinearGrid ();
 
-            /**
-             *  @copybrief   LemmaObject::Release()
-             *  @copydetails LemmaObject::Release()
-             */
-            void Release();
-
             // ====================  DATA MEMBERS  =========================
 
             /// Number of cells in the x dimension

LemmaCore/include/RectilinearGridReader.h

 #define  RECTILINEARGRIDREADER_INC
 
 #include "GridReader.h"
-#include "rectilineargrid.h"
+#include "RectilinearGrid.h"
 #include "ASCIIParser.h"
 
 namespace Lemma {
             // ====================  LIFECYCLE     =======================
 
             /**
-             * @copybrief LemmaObject::New()
-             * @copydetails LemmaObject::New()
+             *  Factory method for generating concrete class.
+             *  @return a std::shared_ptr of type RectilinearGridReader
              */
-            static RectilinearGridReader* New();
-
-            /**
-             *  @copybrief   LemmaObject::Delete()
-             *  @copydetails LemmaObject::Delete()
-             */
-            void Delete();
+            static std::shared_ptr< RectilinearGridReader > NewSP();
 
             // ====================  OPERATORS     =======================
 
              * Accessor method for the underlying RectilinearGrid class constructed
              * from the input file.
              */
-            RectilinearGrid* GetGrid();
+            std::shared_ptr<Grid> GetGrid();
 
             // ====================  INQUIRY       =======================
 
             /** Default protected constructor, use Delete */
             ~RectilinearGridReader ();
 
-            /**
-             *  @copybrief   LemmaObject::Release()
-             *  @copydetails LemmaObject::Release()
-             */
-            void Release();
-
         private:
 
             // ====================  DATA MEMBERS  =========================
 
             /** Object holding constructed Grid */
-            RectilinearGrid* Grid;
+            std::shared_ptr<RectilinearGrid> rGrid;
 
             /** Performs actual file parsing */
-            ASCIIParser* Parser;
+            std::shared_ptr<ASCIIParser> Parser;
 
     }; // -----  end of class  RectilinearGridReader  -----
 

LemmaCore/include/RectilinearGridVTKExporter.h

 #ifdef  LEMMAUSEVTK
 
 #include "LemmaObject.h"
-#include "rectilineargrid.h"
+#include "RectilinearGrid.h"
 
+#include <vtkSmartPointer.h>
 #include "vtkXMLRectilinearGridWriter.h"
 #include "vtkRectilinearGrid.h"
 #include "vtkDoubleArray.h"
     static RectilinearGridVTKExporter* New();
 
     /**
-     *  @copybrief   LemmaObject::Delete()
-     *  @copydetails LemmaObject::Delete()
+     *  Factory method for generating concrete class.
+     *  @return a std::shared_ptr of type RectilinearGridVTKExporter
      */
-    void Delete();
+    static std::shared_ptr< RectilinearGridVTKExporter > NewSP();
 
     // ====================  OPERATORS     =======================
 
     /**
      * Sets the Grid to be exported
      */
-    void SetGrid(RectilinearGrid* Grid);
+    void SetGrid( std::shared_ptr<RectilinearGrid> Grid);
 
     // ====================  INQUIRY       =======================
 
     /**
      *  @return Returns a pointer to a vtkRectilinearGrid containing same information as the Lemma Grid.
      */
-    vtkRectilinearGrid*  GetVTKGrid();
+    vtkSmartPointer<vtkRectilinearGrid>  GetVTKGrid();
 
     /**
      *  Writes the exported VTKGrid out to a .vtr XML file
     /** Default protected destructor, use Delete */
     ~RectilinearGridVTKExporter ();
 
-    /**
-     *  @copybrief   LemmaObject::Release()
-     *  @copydetails LemmaObject::Release()
-     */
-    void Release();
-
     private:
 
     void BuildVTKRectilinearGrid();
     // ====================  DATA MEMBERS  =========================
 
     /** The Grid to convert from */
-    RectilinearGrid*    Grid;
+    std::shared_ptr<RectilinearGrid>    Grid;
 
     /** The Grid to convert to */
-    vtkRectilinearGrid*    VTKGrid;
+    vtkSmartPointer<vtkRectilinearGrid> VTKGrid;
 
 }; // -----  end of class  RectilinearGridVTKExporter  -----
 

LemmaCore/include/TEMInductiveReceiver.h

-/* 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      10/08/2014 03:17:52 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-
-#ifndef  TEMINDUCTIVERECEIVER_INC
-#define  TEMINDUCTIVERECEIVER_INC
-
-#include "TEMReceiver.h"
-
-namespace Lemma {
-
-    /**
-      \brief   Derived class of TEMReceiver.
-      \details An inductive receiver, measures dB/dt
-     */
-    class TEMInductiveReceiver : public TEMReceiver {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const TEMInductiveReceiver &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static TEMInductiveReceiver* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        // ====================  ACCESS        =======================
-
-        // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-        /**
-         *  Uses YAML to serialize this object.
-         *  @return a YAML::Node
-         */
-        YAML::Node Serialize() const;
-
-        /**
-         *   Constructs an object from a YAML::Node.
-         */
-        static TEMInductiveReceiver* DeSerialize(const YAML::Node& node);
-#endif
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        TEMInductiveReceiver (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-        /** Default protected constructor, use New */
-        TEMInductiveReceiver (const YAML::Node& node);
-#endif
-
-        /** Default protected destructor, use Delete */
-        ~TEMInductiveReceiver ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-    }; // -----  end of class  TEMInductiveReceiver  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TEMINDUCTIVERECEIVER_INC  -----
-
-

LemmaCore/include/TEMReceiver.h

-/* 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      10/08/2014 02:36:47 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#ifndef  TEMRECEIVER_INC
-#define  TEMRECEIVER_INC
-
-#include "receiverpoints.h"
-
-//#include <boost/random.hpp>
-//#include <boost/random/normal_distribution.hpp>
-#include <random>
-
-namespace Lemma {
-
-#ifdef HAVE_YAMLCPP
-#include "yaml-cpp/yaml.h"
-#endif
-
-
-/**
-  \brief
-  \details
- */
-class TEMReceiver : public ReceiverPoints {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const TEMReceiver &ob);
-
-    public:
-
-    // ====================  LIFECYCLE     =======================
-
-    /**
-     * @copybrief LemmaObject::New()
-     * @copydetails LemmaObject::New()
-     */
-    static TEMReceiver* New();
-
-    /**
-     *   @return a deep copy of this
-     */
-    TEMReceiver* Clone();
-
-    /**
-     *  @copybrief   LemmaObject::Delete()
-     *  @copydetails LemmaObject::Delete()
-     */
-    void Delete();
-
-    // ====================  OPERATORS     =======================
-
-    // ====================  OPERATIONS    =======================
-
-    /**
-     * Uses the standard deviations provided to provide an instance
-     * of the expected noise. A realisation of the noise.
-     */
-    VectorXr SampleNoise();
-
-    // ====================  ACCESS        =======================
-
-    /**
-     *    Sets the gate integration windows
-     */
-    void SetWindows(const VectorXr& centres, const VectorXr& widths, const TIMEUNITS& Units);
-
-    /**
-     *   Sets the moment of the receiver. Defaults to 1 for normalized response.
-     */
-    void SetMoment( const Real&  moment);
-
-    /**
-     *  Sets std deviation values for noise channels.
-     *  @param[in] noise must be of the same length as the number of windows.
-     */
-    void SetNoiseSTD( const VectorXr& noise );
-
-    /**
-     *  Gets std deviation values for noise channels.
-     *  @return noise std dev.
-     */
-    VectorXr GetNoiseSTD(  );
-
-    /**
-     *  @param[in] refTime sets the reference time, defaults to 0
-     */
-    void SetReferenceTime( const Real& refTime, const TIMEUNITS& units );
-
-    /**
-     *  What field component to return
-     */
-    void SetComponent ( const FIELDCOMPONENT& COMP );
-
-    /**
-     *   @param[in] loc is the location of the dipole receiver
-     */
-    void SetRxLocation ( const Vector3r& loc );
-
-    // ====================  INQUIRY       =======================
-
-     #ifdef HAVE_YAMLCPP
-	/**
-     *  Uses YAML to serialize this object.
-     *  @return a YAML::Node
-     */
-    YAML::Node Serialize() const;
-
-    /**
-     *   Constructs an object from a YAML::Node.
-     */
-    static TEMReceiver* DeSerialize(const YAML::Node& node);
-     #endif
-
-    /**
-     * @return centre point of gates in sec
-     */
-    VectorXr GetWindowCentres();
-
-    /**
-     * @return width of gates in sec
-     */
-    VectorXr GetWindowWidths();
-
-    /**
-     *  @return the reference time
-     */
-    Real    GetReferenceTime();
-    protected:
-
-    // ====================  LIFECYCLE     =======================
-
-    /** Default protected constructor, use New */
-    TEMReceiver (const std::string& name);
-
-     #ifdef HAVE_YAMLCPP
-    /** Default protected de-serializing constructor, use factory DeSerialize */
-    TEMReceiver (const YAML::Node& node);
-    #endif
-
-    /** Default protected destructor, use Delete */
-    ~TEMReceiver ();
-
-    /**
-     *  @copybrief   LemmaObject::Release()
-     *  @copydetails LemmaObject::Release()
-     */
-    void Release();
-
-    private:
-
-    // ====================  DATA MEMBERS  =========================
-
-    Real            moment;
-    Real            referenceTime;
-    Vector3r        nHat;
-    FIELDCOMPONENT  component;
-
-    VectorXr        windowCentres;
-    VectorXr        windowWidths;
-    VectorXr        noiseSTD;
-    //Vector3r        location;
-
-}; // -----  end of class  TEMReceiver  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TEMRECEIVER_INC  -----
-

LemmaCore/include/TEMSurvey.h

-/* 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      10/08/2014 01:51:50 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#ifndef  TEMSURVEY_INC
-#define  TEMSURVEY_INC
-
-#include "LemmaObject.h"
-#include "TEMSurveyLine.h"
-#include "TEMSurveyData.h"
-
-#include "layeredearthem.h"
-
-#ifdef HAVE_YAMLCPP
-#include "yaml-cpp/yaml.h"
-#endif
-
-namespace Lemma {
-
-
-    /**
-      \brief   Describes a TEM survey.
-      \details This class aims to encapulate any type of TEM survey.
-     */
-    class TEMSurvey : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const TEMSurvey &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static TEMSurvey* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        /**  @param[in] idx the index to return
-         *   @return the SurveyLine with index idx
-         */
-        TEMSurveyLine* operator( ) ( const int& idx ) const ;
-
-        /**  @param[in] iline the line index to return
-         *   @param[in] irec the line index to return
-         *   @return the SurveyLine with index iline, irec
-         */
-        TEMSurveyLineRecord* operator( ) ( const int& iline, const int& irec ) const;
-
-        // ====================  OPERATIONS    =======================
-
-        /**
-         *  @param[in] nlines sets the number of lines (TEMSurveyLine) in the survey. A line is any kind of
-         *             related set of measurements. In Airborne EM, this is a flight line, but
-         *             the idea extends to ground based profile lines.
-         */
-        void SetNumberOfLines( const int& nlines );
-
-        /**
-         *  Most basic form of forward modelling. Uses input model for ALL TEMSurveyLines and
-         *  TEMSurveyLineRecords (atomic). Most useful in the
-         *  case that there is only 1 line and 1 record. But even in that case it can be called directly from
-         *  the record. This method will likely be replaced  soon.
-         */
-        TEMSurveyData* ForwardModel(LayeredEarthEM* model, bool additiveNoise=false);
-
-        // ====================  ACCESS        =======================
-
-        /**
-         *   @return pointer to requested TEMSurveyLine
-         */
-        TEMSurveyLine*  GetLine(const unsigned int& iline);
-
-        // ====================  INQUIRY       =======================
-
-        #ifdef HAVE_YAMLCPP
-        YAML::Node Serialize() const;
-        static TEMSurvey* DeSerialize(const YAML::Node& node);
-        #endif
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        TEMSurvey (const std::string& name);
-
-        #ifdef HAVE_YAMLCPP
-        /** Default protected constructor, use New */
-        TEMSurvey (const YAML::Node& node);
-        #endif
-
-        /** Default protected destructor, use Delete */
-        ~TEMSurvey ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        std::vector<TEMSurveyLine*>     Lines;
-
-    }; // -----  end of class  TEMSurvey  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TEMSURVEY_INC  -----

LemmaCore/include/TEMSurveyData.h

-/* 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      03/03/2015 09:54:25
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2015, XRI Geophysics, LLC
- * @copyright Copyright (c) 2015, Trevor Irons
- */
-
-#ifndef  TEMSURVEYDATA_INC
-#define  TEMSURVEYDATA_INC
-
-#include "LemmaObject.h"
-#include "TEMSurveyLineData.h"
-
-namespace Lemma {
-
-    /**
-      \brief    Holds data from a TEMSurvey.
-      \details  Any form of TEMSurvey may be represented here. The
-                majority of the specification can be found in the associated
-                TEMSurvey. The TEMSurveyData object is intended to be lightweight.
-     */
-    class TEMSurveyData : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const TEMSurveyData &ob);
-
-        friend class TEMSurvey;
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static TEMSurveyData* New();
-
-        /**
-         *  @return a deep copy of this, this is acomplished through Serialize
-         *          and DeSerialize methods.
-         */
-        TEMSurveyData* Clone();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        /** Surveys can be added or subtracted from each other, throws a
-         *  pointer that will need to be managed (Deleted)
-         */
-        TEMSurveyData* operator+(const TEMSurveyData& Survey);
-
-        /** Surveys can be added or subtracted from each other, throws a
-         *  pointer that will need to be managed (Deleted).
-         */
-        TEMSurveyData* operator-(const TEMSurveyData& Survey);
-
-        /** Surveys can be added or subtracted from each other
-         */
-        void operator+=(const TEMSurveyData& Survey);
-
-        /** Surveys can be added or subtracted from each other
-         */
-        void operator-=(const TEMSurveyData& Survey);
-
-
-        /**  @param[in] idx the index to return
-         *   @return the SurveyLine with index idx
-         */
-        TEMSurveyLineData* operator( ) ( const int& idx ) const;
-
-        /**  @param[in] iline the line index to return
-         *   @param[in] irec the line index to return
-         *   @return the SurveyLine with index iline, irec
-         */
-        TEMSurveyLineRecordData* operator( ) ( const int& iline, const int& irec ) const;
-
-
-        // ====================  OPERATIONS    =======================
-
-        /** Sets the number of lines
-         */
-        void SetNumberOfLines( const int& nlines );
-
-        // ====================  ACCESS        =======================
-
-        /** @return the number of lines in the data
-         */
-        int GetNumberOfLines() const;
-
-        /**
-         *   @return pointer to line
-         */
-        TEMSurveyLineData* GetLine(const int& iline) const;
-
-        // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-        /**
-         *  Uses YAML to serialize this object.
-         *  @return a YAML::Node
-         */
-        YAML::Node Serialize() const;
-
-        /**
-         *   Constructs an object from a YAML::Node.
-         */
-        static TEMSurveyData* DeSerialize(const YAML::Node& node);
-#endif
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        TEMSurveyData (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-        TEMSurveyData (const YAML::Node& node);
-#endif
-
-        /** Default protected destructor, use Delete */
-        ~TEMSurveyData ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        std::vector<TEMSurveyLineData*>  LineData;
-
-    }; // -----  end of class  TEMSurveyData  -----
-
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TEMSURVEYDATA_INC  -----

LemmaCore/include/TEMSurveyLine.h

-/* 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      10/10/2014 11:14:39 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#ifndef  TEMSURVEYLINE_INC
-#define  TEMSURVEYLINE_INC
-
-#include "LemmaObject.h"
-#include "TEMSurveyLineRecord.h"
-#include "TEMSurveyLineData.h"
-
-namespace Lemma {
-
-    /**
-      \brief    Represents a TEM survey line.
-      \details  This class is managed by TEMSurvey. You cannot create a TEMSurvey line directly
-                this should be done through a TEMSurvey.
-                @todo neeed to impliment a BaseClass besides LemmaObject without pure virtual Delete.
-     */
-    class TEMSurveyLine : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const TEMSurveyLine &ob);
-
-        friend class TEMSurvey;
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        // ====================  ACCESS        =======================
-
-        /**
-            @return returns pointer to a specific record along the line
-         */
-        TEMSurveyLineRecord*  GetRecord(const unsigned int& irec);
-
-        /**
-            @param[in] nrec is the number of records along the line
-         */
-        void SetNumberOfRecords( const int& nrec );
-
-        // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-        /**
-         *  Uses YAML to serialize this object.
-         *  @return a YAML::Node
-         */
-        YAML::Node Serialize() const;
-
-        /**
-         *   Constructs an object from a YAML::Node.
-         */
-        static TEMSurveyLine* DeSerialize(const YAML::Node& node);
-#endif
-
-        protected:
-
-        TEMSurveyLineData* ForwardModel(LayeredEarthEM* model, bool additiveNoise = false);
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        TEMSurveyLine (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-        TEMSurveyLine (const YAML::Node& node);
-#endif
-
-        /** Default protected destructor, use Delete */
-        ~TEMSurveyLine ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        /**
-         *   Delete should not be called...
-         */
-        void Delete();
-
-        // ====================  DATA MEMBERS  =========================
-
-        std::vector<TEMSurveyLineRecord*>     Records;
-
-    }; // -----  end of class  TEMSurveyLine  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TEMSURVEYLINE_INC  -----

LemmaCore/include/TEMSurveyLineData.h

-/* 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      03/03/2015 10:16:47
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2015, XRI Geophysics, LLC
- * @copyright Copyright (c) 2015, Trevor Irons
- */
-
-#ifndef  TEMSURVEYLINEDATA_INC
-#define  TEMSURVEYLINEDATA_INC
-
-#include "LemmaObject.h"
-#include "TEMSurveyLineRecordData.h"
-
-namespace Lemma {
-
-/**
-  \brief   Holds Data for a TEM survey line
-  \details An entire flight line worth of data is stored here.
- */
-class TEMSurveyLineData : public LemmaObject {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const TEMSurveyLineData &ob);
-
-    //friend class TEMSurveyData;
-    friend class TEMSurveyLine;
-
-    public:
-
-    // ====================  LIFECYCLE     =======================
-
-    /**
-     * @copybrief LemmaObject::New()
-     * @copydetails LemmaObject::New()
-     */
-    static TEMSurveyLineData* New();
-
-    /**
-     *  @return a deep copy of this, this is acomplished through Serialize
-     *          and DeSerialize methods.
-     */
-    TEMSurveyLineData* Clone();
-
-    /**
-     *  @copybrief   LemmaObject::Delete()
-     *  @copydetails LemmaObject::Delete()
-     */
-    void Delete();
-
-    // ====================  OPERATORS     =======================
-
-    /** Survey lines can be added or subtracted from each other
-     */
-    TEMSurveyLineData* operator+(const TEMSurveyLineData& Survey);
-
-    /** Survey lines can be added or subtracted from each other
-     */
-    TEMSurveyLineData* operator-(const TEMSurveyLineData& Survey);
-
-    /** Survey lines can be added or subtracted from each other
-     */
-    void operator+=(const TEMSurveyLineData& Survey);
-
-    /** Survey lines can be added or subtracted from each other
-     */
-    void operator-=(const TEMSurveyLineData& Survey);
-
-    /**  @param[in] ir the index to return
-     *   @return the SurveyLineRecord with index ir
-     */
-    TEMSurveyLineRecordData* operator( ) ( const int& ir ) const ;
-
-    // ====================  OPERATIONS    =======================
-
-    // ====================  ACCESS        =======================
-
-    /**
-     *    @return pointer to specified record
-     */
-    TEMSurveyLineRecordData*  GetRecord(const int& ir) const ;
-
-    /**
-     * @return the number of records
-     */
-    int GetNumberOfRecords() const;
-
-    // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-    /**
-     *  Uses YAML to serialize this object.
-     *  @return a YAML::Node
-     */
-    YAML::Node Serialize() const;
-
-    /**
-     *   Constructs an object from a YAML::Node.
-     */
-    static TEMSurveyLineData* DeSerialize(const YAML::Node& node);
-#endif
-
-    protected:
-
-    // ====================  LIFECYCLE     =======================
-
-    /** Default protected constructor, use New */
-    TEMSurveyLineData (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-    /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-    TEMSurveyLineData (const YAML::Node& node);
-#endif
-
-    /** Default protected destructor, use Delete */
-    ~TEMSurveyLineData ();
-
-    /**
-     *  @copybrief   LemmaObject::Release()
-     *  @copydetails LemmaObject::Release()
-     */
-    void Release();
-
-    private:
-
-    // ====================  DATA MEMBERS  =========================
-
-    std::vector<TEMSurveyLineRecordData*>   RecordData;
-
-}; // -----  end of class  TEMSurveyLineData  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TEMSURVEYLINEDATA_INC  -----
-

LemmaCore/include/TEMSurveyLineRecord.h

-/* 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      10/10/2014 12:15:03 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#ifndef  TEMSURVEYLINERECORD_INC
-#define  TEMSURVEYLINERECORD_INC
-
-#include "LemmaObject.h"
-#include "TEMReceiver.h"
-#include "TEMTransmitter.h"
-#include "TEMSurveyLineRecordData.h"
-#include "instrumenttem.h"
-
-namespace Lemma {
-
-    /**
-      \brief    Class holding everything necessary to create a TEM record.
-      \details  A TEM record represents the nexus of a transmitter with
-                receiver(s) and pulse moment(s). Therefore a record can contain
-                multiple sounding curves.
-     */
-    class TEMSurveyLineRecord : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const TEMSurveyLineRecord &ob);
-
-        friend class TEMSurveyLine;
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        /**
-         *  Perfoms forward modelling given model.
-         *  @param[in] model is the earth model responsible for the response
-         *  @param[in] additiveNoise is whether or not to add noise to the response, defaults to false
-         *  @return the modelled data.
-         */
-        TEMSurveyLineRecordData* ForwardModel(LayeredEarthEM* model, bool additiveNoise=false);
-
-        /**
-         *  @param[in] nseq is the number of pulse sequences
-         */
-        void SetNumberOfPulseSequences( const int& nseq );
-
-        /**
-         *  @return the number of pulse sequences
-         */
-        int GetNumberOfPulseSequences();
-
-        /**
-         *  Sets the PulseSequence and Receiver pair used to model a *SINGLE* response curve.
-         *  @param[in] Seq is the Pulse Sequence
-         *  @param[in] Rx is the receiver for that pulse sequence
-         */
-        void SetTransmitterReceiverPair( const int& ii, TEMTransmitter* Seq, TEMReceiver* Rx );
-
-        // ====================  ACCESS        =======================
-
-        /**
-         *  @return a pointer to the specified receiver
-         */
-        TEMReceiver*   GetReceiver(const int& irec);
-
-        // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-        /**
-         *  Uses YAML to serialize this object.
-         *  @return a YAML::Node
-         */
-        YAML::Node Serialize() const;
-
-        /**
-         *   Constructs an object from a YAML::Node.
-         */
-        static TEMSurveyLineRecord* DeSerialize(const YAML::Node& node);
-#endif
-
-        protected:
-
-
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        TEMSurveyLineRecord (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-        TEMSurveyLineRecord (const YAML::Node& node);
-#endif
-
-        /** Default protected destructor, use Delete */
-        ~TEMSurveyLineRecord ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        /**
-         *   Delete is private, this class is managed through TEMSurvey
-         */
-        void Delete();
-
-        // ====================  DATA MEMBERS  =========================
-
-        int     numberOfPulseSequences;
-
-        std::vector<TEMTransmitter*>    Transmitters;
-        std::vector<TEMReceiver*>       Receivers;
-
-    }; // -----  end of class  TEMSurveyLineRecord  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TEMSURVEYLINERECORD_INC  -----

LemmaCore/include/TEMSurveyLineRecordData.h

-/* 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      03/03/2015 10:29:01
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2015, XRI Geophysics, LLC
- * @copyright Copyright (c) 2015, Trevor Irons
- */
-#ifndef  TEMSURVEYLINERECORDDATA_INC
-#define  TEMSURVEYLINERECORDDATA_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    /**
-      \brief
-      \details
-     */
-    class TEMSurveyLineRecordData : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const TEMSurveyLineRecordData &ob);
-
-        friend class TEMSurveyLineRecord;
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static TEMSurveyLineRecordData* New();
-
-
-        /** Provides deep copy
-         */
-        TEMSurveyLineRecordData* Clone();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        /**
-         * Records can be added
-         */
-        TEMSurveyLineRecordData* operator + (const TEMSurveyLineRecordData&);
-
-        /**
-         * Records can be subtracted
-         */
-        TEMSurveyLineRecordData* operator - (const TEMSurveyLineRecordData&);
-
-        /**
-         * Records can be added in place
-         */
-        void operator += (const TEMSurveyLineRecordData&);
-
-        /**
-         * Records can be subtracted in place
-         */
-        void operator -= (const TEMSurveyLineRecordData&);
-
-        // ====================  OPERATIONS    =======================
-
-        // ====================  ACCESS        =======================
-
-        /** @return a VectorXr of the merged data (all moments)
-         * @todo TODO this is actually a copy? is this intended?
-         */
-        VectorXr GetCombinedData();
-
-        /** @return a VectorXr of the combined gate centres alligned with
-         *          GetCombinedData();
-         */
-        VectorXr GetCombinedGateCentres();
-        // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-        /**
-         *  Uses YAML to serialize this object.
-         *  @return a YAML::Node
-         */
-        YAML::Node Serialize() const;
-
-        /**
-         *   Constructs an object from a YAML::Node.
-         */
-        static TEMSurveyLineRecordData* DeSerialize(const YAML::Node& node);
-#endif
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        TEMSurveyLineRecordData (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-        TEMSurveyLineRecordData (const YAML::Node& node);
-#endif
-
-        /** Default protected destructor, use Delete */
-        ~TEMSurveyLineRecordData ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-        std::vector<VectorXr>           DataSeries;
-
-        std::vector<VectorXr>           GateCentres;
-
-    }; // -----  end of class  TEMSurveyLineRecordData  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TEMSURVEYLINERECORDDATA_INC  -----

LemmaCore/include/TEMTransmitter.h

-/* 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      09/29/2014 11:43:17 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#ifndef  TEMTRANSMITTER_INC
-#define  TEMTRANSMITTER_INC
-
-#include "PolygonalWireAntenna.h"
-
-#ifdef HAVE_YAMLCPP
-#include "yaml-cpp/yaml.h"
-#endif
-
-namespace Lemma {
-
-/**
-  \brief   Describes a TEM pulse sequence
-  \details Flexible class desribing a pulse sequence used by
-           a TEM instruement. Can be used by Airborne or Ground
-           instruments.
- */
-class TEMTransmitter : public PolygonalWireAntenna {
-
-    friend std::ostream &operator<<(std::ostream &stream, const TEMTransmitter &ob);
-
-    public:
-
-    // ====================  LIFECYCLE     =======================
-
-    /**
-     * @copybrief LemmaObject::New()
-     * @copydetails LemmaObject::New()
-     */
-    static TEMTransmitter* New();
-
-    /**
-     *  Performs a deep copy of this and returns pointer
-     */
-    TEMTransmitter* Clone();
-
-    /**
-     *  @copybrief   LemmaObject::Delete()
-     *  @copydetails LemmaObject::Delete()
-     */
-    void Delete();
-
-    // ====================  OPERATORS     =======================
-
-    // ====================  OPERATIONS    =======================
-
-    // ====================  ACCESS        =======================
-
-    /** Sets the repetition frequency
-     */
-    void SetRepFrequency(const Real& fr, const FREQUENCYUNITS& units);
-
-    void SetWaveform( const VectorXr& times, const VectorXr& amps, const TIMEUNITS& units );
-
-    /**
-     *  @return the waveform times in seconds
-     */
-    VectorXr GetWfmTimes();
-
-    /** @return the waveform current in amps
-     */
-    VectorXr GetWfmAmps();
-
-    // ====================  INQUIRY       =======================
-
-#ifdef HAVE_YAMLCPP
-    YAML::Node Serialize() const;
-    static TEMTransmitter* DeSerialize(const YAML::Node& node);
-#endif
-
-    protected:
-
-    // ====================  LIFECYCLE     =======================
-
-    /** Default protected constructor, use New */
-    TEMTransmitter (const std::string& name);
-
-#ifdef HAVE_YAMLCPP
-    /** Default protected constructor, use New */
-    TEMTransmitter (const YAML::Node& node);
-#endif
-
-    /** Default protected destructor, use Delete */
-    ~TEMTransmitter ();
-
-    /**
-     *  @copybrief   LemmaObject::Release()
-     *  @copydetails LemmaObject::Release()
-     */
-    void Release();
-
-    private:
-
-    // ====================  DATA MEMBERS  =========================
-
-    Real                    repFreq;
-    FREQUENCYUNITS          repFreqUnits;
-    VectorXr                wfmTimes;
-    VectorXr                wfmAmps;
-
-}; // -----  end of class  TEMTransmitter  -----
-
-} // namespace Lemma
-
-#endif   // ----- #ifndef TEMTRANSMITTER_INC  -----
-

LemmaCore/include/UngroundedElectricDipole.h

-/* 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      01/29/2014 08:52:43 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-
-#ifndef  UNGROUNDEDELECTRICDIPOLE_INC
-#define  UNGROUNDEDELECTRICDIPOLE_INC
-
-#include "dipolesource.h"
-
-namespace Lemma {
-
-    /**
-      \brief  Ungrounded electric dipole
-      \details Used to model an idealised ungrounded electric dipole. Used primarily in integrating
-                around current sources.
-     */
-    class UngroundedElectricDipole : public DipoleSource {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const UngroundedElectricDipole &ob);
-
-        public:
-
-        // ====================  LIFECYCLE     =======================
-
-        /**
-         * @copybrief LemmaObject::New()
-         * @copydetails LemmaObject::New()
-         */
-        static UngroundedElectricDipole* New();
-
-        /**
-         *  @copybrief   LemmaObject::Delete()
-         *  @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        // ====================  ACCESS        =======================
-
-        // ====================  INQUIRY       =======================
-
-        protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /** Default protected constructor, use New */
-        UngroundedElectricDipole (const std::string& name);
-
-        /** Default protected destructor, use Delete */
-        ~UngroundedElectricDipole ();
-
-        /**
-         *  @copybrief   LemmaObject::Release()
-         *  @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        private:
-
-        // ====================  DATA MEMBERS  =========================
-
-    }; // -----  end of class  UngroundedElectricDipole  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef UNGROUNDEDELECTRICDIPOLE_INC  -----
-

LemmaCore/include/windowfilter.h → LemmaCore/include/WindowFilter.h

 
 #ifndef  WINDOWFILTER_INC
 #define  WINDOWFILTER_INC
-#include "filter.h"
+#include "Filter.h"
 
 namespace Lemma {
     /** Types of filter window that are supported.
 
             // ====================  LIFECYCLE     =======================
 
-            /**
-             * Returns a pointer to a new object of type WindowFilter.
-             * It allocates all necessary memory.
-             */
-            static WindowFilter* New();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
+           /**
+            *  Factory method for generating concrete class.
+            *  @return a std::shared_ptr of type WindowFilter
+            */
+            static std::shared_ptr< WindowFilter > NewSP();
 
             // ====================  OPERATORS     =======================
 
             /// Default protected constructor.
             ~WindowFilter ();
 
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
             // ====================  DATA MEMBERS  =========================
 
             /// Width of the window

LemmaCore/include/WireAntenna.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     12/16/2009
-  @version  $Id: WireAntenna.h 201 2015-01-03 00:07:47Z tirons $
- **/
-
-#ifndef __WIREANTENNA_H
-#define __WIREANTENNA_H
-
-#include "LemmaObject.h"
-#include "dipolesource.h"
-
-#ifdef LEMMAUSEVTK
-#include "vtkActor.h"
-#endif
-
-namespace Lemma {
-
-
-    // ===================================================================
-    /**      Class:  WireAntenna
-      * \brief   Class representing a wire antennae.
-      * \details This is an abstract class.
-	  */
-    // ===================================================================
-    class WireAntenna : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-            const WireAntenna &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /**
-             * Initialises antenna to contain no points, with no current
-             * and no frequency. NumberOfTurns set to 1
-             */
-            static WireAntenna* New();
-
-            /**
-             * Provides deep copy
-             */
-            virtual WireAntenna* Clone();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /**
-              * Approximates with evenly spaced electric dipoles around loop
-              * @param[in] delta is the spacing between moments
-			  */
-            virtual void ApproximateWithElectricDipoles(const Real &delta);
-
-            // ====================  ACCESS        =======================
-
-			/**
-              * Sets the number of turns in the loop, default is 1
-              * @param[in] nturns is the number of turns of the loop.
-			  */
-            void SetNumberOfTurns(const int &nturns);
-
-            /**
-              * Sets the number of points in the loop
-			  */
-            void SetNumberOfPoints(const int &np);
-
-			/**
-              * Sets a corner point of the loop. Counting starts at 0. It
-              * is not required to have the loop be closed right now, but
-              * its a good idea.
-			  */
-            void SetPoint(const int &p, const Vector3r &pos);
-
-            /**
-              * Sets a corner point of the loop. Counting starts at 0. It
-              * is not required to have the loop be closed right now, but
-              * its a good idea.
-			  */
-            void SetPoint(const int &p, const Real&x, const Real& y, const Real& z);
-
-            /** Sets the frequency of the current in the loop, default is 0
-			  * @param[in] ifreq is the frequency number to set
-              * @param[in] freq is the frequency (Hz) of the current
-			  */
-            void SetFrequency(const int& ifreq, const Real &freq);
-			/**
-              * Sets the number of frequencies.
-              * @param[in] nfreq is the number of frequencies that will be
-              * computed.
-			  */
-            void SetNumberOfFrequencies(const int& nfreq);
-
-			/**
-              * Sets the current in the loop, default is 0
-              * @param[in] amp is the current in the loop, in Amperes
-			  */
-            void SetCurrent(const Real &amp);
-
-            // ====================  INQUIRY       =======================
-
-            #ifdef HAVE_YAMLCPP
-            /**
-             *  Uses YAML to serialize this object.
-             *  @return a YAML::Node
-             */
-            YAML::Node Serialize() const;
-
-            /**
-             *   Constructs an object from a YAML::Node.
-             */
-            static WireAntenna* DeSerialize(const YAML::Node& node);
-            #endif
-
-			/**
-              * Returns the number of turns
-              * @return the number of turns of the loop.
-			  */
-            int GetNumberOfTurns( );
-
-            /**
-             * Returns all of the points
-             */
-            Vector3Xr GetPoints();
-
-            /**
-             * Returns all of the points in a general matrix, useful for python wrapper
-             */
-            MatrixXr GetPointsMat();
-
-			/**
-              * Returns the frequency in the loop.
-              * @return is the frequency in the loop in Hz
-			  */
-            Real GetFrequency(const int& ifreq);
-
-
-			/**
-              * Returns the current in the loop.
-              * @return is the Current
-			  */
-            Real GetCurrent( );
-
-
-			/**
-              * Returns pointer to a dipole source
-			  */
-            DipoleSource* GetDipoleSource(const int &dip);
-
-			/**
-              * returns number of dipoles used to approximate this
-              * loop
-			  */
-            int GetNumberOfDipoles();
-
-			/**
-              * @return the number of frequencies of this wire loop.
-			  */
-            int GetNumberOfFrequencies();
-
-            #ifdef LEMMAUSEVTK
-            /** Returns an actor that can be placed into a vtk scene easily
-              * Note that this function throws a pointer, it is the
-              * receivers job to manage this memory!
-			  */
-            vtkActor* GetVtkActor(const int &idip);
-            #endif
-
-            /** Returns true or false if loop is horizontally planar
-             */
-            bool IsHorizontallyPlanar();
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-			/**
-              * Default protected constructor.
-			  */
-            WireAntenna (const std::string &name);
-
-#ifdef HAVE_YAMLCPP
-        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-            WireAntenna (const YAML::Node& node);
-#endif
-
-			/**
-              * Default protected destructor.
-			  */
-            ~WireAntenna ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  DATA MEMBERS  =======================
-
-			/**
-              * Number of points that define the loop
-			  */
-            int NumberOfPoints;
-
-			/**
-              * Current in antennae (Amps)
-			  */
-            Real Current;
-
-			/**
-              * Number of turns
-			  */
-            int NumberOfTurns;
-
-			/**
-              * List of the dipoles
-			  */
-            std::vector<DipoleSource*>           Dipoles;
-
-			/**
-              * Points that define this loop
-			  */
-            Vector3Xr                            Points;
-
-			/**
-              * Frequencies of the loop.
-			  */
-            VectorXr                             Freqs;
-
-        private:
-
-    }; // -----  end of class  WireAntenna  -----
-
-}
-#endif // __WIREANTENNA_H

LemmaCore/include/emearth1d.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     12/02/2009
-  @version  $Id: emearth1d.h 266 2015-04-01 03:24:00Z tirons $
- **/
-
-#ifndef __EMEARTH1D_H
-#define __EMEARTH1D_H
-
-#include "dipolesource.h"
-#include "layeredearthem.h"
-#include "receiverpoints.h"
-#include "WireAntenna.h"
-#include "PolygonalWireAntenna.h"
-#include "kernelem1dspec.h"
-#include "kernelem1dmanager.h"
-#include "hankeltransformgaussianquadrature.h"
-#include "hankeltransformhankel2.h"
-#include "FHTKey.h"
-#include "FHTKey51.h"
-#include "FHTKey101.h"
-#include "QWEKey.h"
-#include "CubicSplineInterpolator.h"
-
-#ifdef HAVEBOOSTPROGRESS
-#include "boost/progress.hpp"
-#endif
-
-namespace Lemma {
-
-    // =======================================================================
-    //        Class:  EmEarth1D
-    /// \brief  Implimentation of 1D EM solution.
-    /// \details  We've done a lot of different things.
-    // =======================================================================
-    class EMEarth1D : public LemmaObject {
-
-		friend std::ostream &operator<<(std::ostream &stream,
-			const EMEarth1D &ob);
-
-        public:
-
-            //friend class KernelEm1D;
-
-            // ====================  LIFECYCLE     ===========================
-
-            /**
-             *  Returns pointer to new EMEarth1D. Location is
-             *  initialized to (0,0,0) type and polarization are
-             *  initialized  to nonworking values that will throw
-             *  exceptions if used.
-             */
-            static EMEarth1D* New();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-            /** stream debugging info to std::out
-             */
-            void Query();
-
-            #ifdef HAVE_YAMLCPP
-            /** YAML Serializing method
-             */
-            YAML::Node Serialize() const;
-
-            //static EMEarth1D* DeSerialize(const YAML::Node& node);
-            #endif
-
-            // ====================  OPERATORS     ===========================
-
-            // ====================  OPERATIONS    ===========================
-
-            /// Calculates the field(s) due to an ungrounded dipole source
-            /// Calls FORTRAN library em1d (em1dnew.for)
-#ifdef COMPILE_FORTRAN
-            void MakeCalc();
-#endif
-
-            /** C++ wrapper for em1dnew.for, serial */
-            void MakeCalc3();
-
-            /** Calculates the field(s) due to a wire antennae */
-            void CalculateWireAntennaFields(bool progressbar=false);
-
-            // ====================  ACCESS        ===========================
-
-            /** Attaches an antennae */
-            void AttachWireAntenna(WireAntenna *antennae);
-
-            /** Attaches a dipole for calculation */
-            void AttachDipoleSource(DipoleSource *dipole);
-
-            /** Attaches a layered earth model for calculation */
-            void AttachLayeredEarthEM(LayeredEarthEM *Earth);
-
-            /** Attaches a set of receiver points for calculation */
-            void AttachReceiverPoints(ReceiverPoints *Receivers);
-
-            /** Sets the fields that are calcultated, E,H or BOTH */
-            void SetFieldsToCalculate(const FIELDCALCULATIONS &calc);
-
-            /** Sets the method to use to evaluate the Hankel integral,
-             */
-            void SetHankelTransformMethod(const HANKELTRANSFORMTYPE &type);
-
-            // ====================  INQUIRY       ===========================
-
-        protected:
-
-            // ====================  LIFECYCLE     ===========================
-
-            /** Default protected constructor. */
-            EMEarth1D (const std::string& name);
-
-            #ifdef HAVE_YAMLCPP
-            /** Default protected constructor. */
-			EMEarth1D (const YAML::Node& node);
-            #endif
-
-            /** Default protected constructor. */
-            ~EMEarth1D ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  OPERATIONS    ===========================
-
-            /** Used internally, this is the innermost loop of the MakeCalc3,
-             *  and CalculateWireAntennaField routines.
-             */
-            void SolveSingleTxRxPair(const int &irec,
-                    HankelTransform *Hankel,
-                    const Real &wavef, const int &ifreq,
-                    DipoleSource *tDipole);
-
-            /** Used internally, this is the innermost loop of the MakeCalc3,
-             *  and CalculateWireAntennaField routines.
-             */
-            void SolveLaggedTxRxPair(const int &irec, Hankel2* Hankel,
-                    const Real &wavef, const int &ifreq,
-                    PolygonalWireAntenna* antenna);
-
-            /** Removes all connections */
-            void DetachAll();
-
-            // ====================  DATA MEMBERS  ===========================
-
-            /** Computes field due to dipole */
-            DipoleSource*        Dipole;
-
-            /** Earth model (Cole-cole) */
-            LayeredEarthEM*      Earth;
-
-            /** Receiver points */
-            ReceiverPoints*      Receivers;
-
-            /** Wire antennae tx */
-            WireAntenna*         Antenna;
-
-            /** What fields are wanted */
-            FIELDCALCULATIONS    FieldsToCalculate;
-
-            /** The type of Hankel transform to use, default to digital
-             *  filtering
-             */
-            HANKELTRANSFORMTYPE  HankelType;
-
-            /** Counter for number of caclulations made
-             */
-            int icalcinner;
-
-            /** Counter for number of caclulations made
-             */
-            int icalc;
-
-    }; // -----  end of class  EMEarth1D  -----
-
-    /////////////////////////////////////////
-    // Exception classes
-
-    /** If a Receivers Class is NULL valued, throw this.
-     */
-    class NullReceivers : public std::runtime_error {
-            /** Thrown when Receivers pointer is NULL
-             */
-            public: NullReceivers();
-    };
-
-    /** If an Antenna is NULL valued, throw this error.
-     */
-    class NullAntenna : public std::runtime_error {
-            /** Thrown when an antenna pointer is NULL
-             */
-            public: NullAntenna();
-    };
-
-    /** If an Instrument is NULL valued, throw this error.
-     */
-    class NullInstrument : public std::runtime_error {
-            /** thrown when an instrument pointer is NULL.
-             *  @param[in] ptr is a pointer to the class throwing the exception.
-             */
-            public: NullInstrument(LemmaObject* ptr);
-    };
-
-    /** If a dipole source is specified, but a method calling a wire antenna is
-     * called, throw this.
-     */
-    class DipoleSourceSpecifiedForWireAntennaCalc : public std::runtime_error {
-            /** Thrown when a dipole source is specified when a wire antenna is
-             * expected
-             */
-            public: DipoleSourceSpecifiedForWireAntennaCalc();
-    };
-
-} // Namespace Lemma
-
-#endif // __EMEARTH1D_H

LemmaCore/include/emearth3d.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     10/28/2010
-  @version  $Id: emearth3d.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-
-#ifndef  EMEARTH3D_INC
-#define  EMEARTH3D_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-
-    // ===================================================================
-    //  Class:  EMEarth3D
-    /**
-      @class
-      \brief   Impliments a 3D EM solution to a general conductivity
-               structure.
-      \details Calculations are made on a rectilinear grid. General 3D
-               conductivity is supported, but not magnetic permeability.
-     */
-    // ===================================================================
-    class EMEarth3D : public LemmaObject {
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Returns a pointer to a new object of type EMEarth3D.
-             * It allocates all necessary memory.
-             */
-            static EMEarth3D* New();
-
-            /** Deletes this object. Delete also disconnects any
-             * attachments to this object.
-             */
-            void Delete();
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            EMEarth3D (const std::string& name);
-
-            /// Default protected constructor.
-            ~EMEarth3D ();
-
-            /// Frees all memory
-            void Release();
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-    }; // -----  end of class  EMEarth3D  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef EMEARTH3D_INC  -----

LemmaCore/include/gaussianquadrature.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     10/07/2010
-  @version  $Id: gaussianquadrature.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef __gaussianquadrature_h
-#define __gaussianquadrature_h
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-
-	// ===================================================================
-	//        Class:  gaussianquadrature
-	/// \brief Numerical integration via Legendre-Gauss Quadrature.
-	/// \details Returns integration result, weights, and abscissae.  This
-	/// script computes the Legendre-Gauss nodes and weights on an interval
-	/// [a,b] with truncation order N.  This class is heavily derived from
-	/// lgwt.m by Greg von Winckel (2/25/2004).
-	// ===================================================================
-	class gaussianquadrature {
-
-		public:
-
-			friend std::ostream &operator<<(std::ostream &stream,
-						const gaussianquadrature &ob);
-
-			// ====================  LIFECYCLE     =======================
-
-			static gaussianquadrature* New();
-
-			void Delete();
-
-			// ====================  OPERATORS     =======================
-
-			// ====================  OPERATIONS    =======================
-			/// Perform Gaussian Quadrature Integration
-			void Integrate();
-
-			/// Calculate abscissae and weights
-			void CalcAW();
-
-			// ====================  ACCESS        =======================
-			/// Set number of points and limits
-			void SetFreqs(const int& nfreq, const Real& a, const Real& b);
-
-			/// Eigen Vector of function values to be integrated over
-			void SetFunc(const VectorXr& fx);
-
-			// ====================  INQUIRY       =======================
-			/// Returns Eigen Vector of Abscissae
-			VectorXr GetAbscissae();
-
-			/// Returns Eigen Vector of Weights
-			VectorXr GetWeights();
-
-			/// Returns integration result
-			Real GetResult();
-
-
-		protected:
-
-			// ====================  LIFECYCLE     =======================
-
-			/// Default protected constructor.
-			gaussianquadrature ();
-
-			/// Default protected constructor.
-			~gaussianquadrature ();
-
-
-
-			// ====================  DATA MEMBERS  =========================
-			/// Interval
-			Real dx;
-
-			/// Machine precision
-			Real machineeps;
-
-			/// Bookkeeping variable
-			int N;
-
-			/// Bookkeeping variable
-			int N1;
-
-			/// Bookkeeping variable
-			int N2;
-
-			/// Lower bound
-			Real a;
-
-			/// Upper bound
-			Real b;
-
-			/// Placeholder vector
-			VectorXr ytemp;
-
-			/// Abscissae
-			VectorXr xu;
-
-			/// Intermediate Abscissae vector
-			VectorXr y;
-
-			/// Intermediate Abscissae vector
-			VectorXr y0;
-
-			/// Legendre-Gauss Vandermonde Matrix
-			MatrixXr L;
-
-			/// Derivative of LGVM
-			VectorXr Lp;
-
-			/// Intermediate Matrix
-			VectorXr Ltemp;
-
-			/// Weights Vector
-			VectorXr wgq;
-
-			///Function to integrate
-			VectorXr funcx;
-
-			/// Integration result
-			Real intres;
-
-		private:
-
-	}; // -----  end of class  gaussianquadrature  -----
-} // end of namespace Lemma
-#endif // __gaussianquadrature_h
-

LemmaCore/include/hankeltransform.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     01/28/2010
-  @version  $Id: hankeltransform.h 270 2015-08-24 15:45:41Z tirons $
- **/
-
-#ifndef __hankeltransform_h
-#define __hankeltransform_h
-
-#include "LemmaObject.h"
-#include "kernelem1dbase.h"
-#include "kernelem1dspec.h"
-#include "kernelem1dmanager.h"
-
-namespace Lemma {
-
-        // ===================================================================
-        //        Class:  HankelTransform
-        /// \brief  Pure abstract class for hankel transforms
-        /// \details
-        // ===================================================================
-        class HankelTransform : public LemmaObject {
-
-            public:
-
-                /// Prints out basic info about the class
-                friend std::ostream &operator<<(std::ostream &stream,
-                        const HankelTransform &ob);
-
-                // ====================  LIFECYCLE     =======================
-
-                //static HankelTransform* New();
-
-                //void Delete();
-
-                // ====================  OPERATORS     =======================
-
-                // ====================  OPERATIONS    =======================
-
-                /// @todo this is actually a deprecated function. Only Chave
-                ///   uses this.
-                /// Performs numerical integration using Gaussian quadrature
-                /// ikk:   type of kernel depending on source and receiver couple
-                /// imode: a switch for TE(0) and TM(1) mode
-                /// itype: order of Bessel function
-                /// rho is argument to integral
-                /// wavef is the propogation constant of free space
-                /// = omega * sqrt( EP*AMU )  amu = 4 pi e-7  ep = 8.85e-12
-                virtual Complex Zgauss(const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel)=0;
-
-                /// Computes related kernels, if applicable, otherwise this is
-                /// just a dummy function.
-                virtual void ComputeRelated(const Real& rho, KernelEm1DBase* Kernel);
-
-                virtual void ComputeRelated(const Real& rho, std::vector< KernelEm1DBase* > KernelVec);
-
-                virtual void ComputeRelated(const Real& rho, KernelEM1DManager* KernelManager);
-
-                // ====================  ACCESS        =======================
-
-                // ====================  INQUIRY       =======================
-
-                // ====================  DATA MEMBERS  =======================
-
-            protected:
-
-                // ====================  LIFECYCLE     =======================
-
-                /// Default protected constructor.
-                HankelTransform (const std::string &name);
-
-                /// Default protected constructor.
-                ~HankelTransform ();
-
-            private:
-
-    }; // -----  end of class  HankelTransform  -----
-
-}
-
-#endif // __hankeltransform_h

LemmaCore/include/hankeltransformgaussianquadrature.h

-/* 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
-  @author   Trevor Irons
-  @date     01/02/2010
-  @version  $Id: hankeltransformgaussianquadrature.h 199 2014-12-29 19:25:20Z tirons $
- **/
-
-#ifndef  _HANKELTRANSFORMGAUSSIANQUADRATURE_h_INC
-#define  _HANKELTRANSFORMGAUSSIANQUADRATURE_h_INC
-
-#include "hankeltransform.h"
-#include "kernelem1dbase.h"
-
-#ifdef HAVEBOOSTCYLBESSEL
-#include "boost/math/special_functions.hpp"
-#endif
-
-namespace Lemma {
-
-
-	// =======================================================================
-	//        Class:  HankelTransformGaussianQuadrature
-	/// \brief  Calculates hankel transform using gaussian quadrature.
-	/// \details  Accurate but slow, this is a port of Alan Chave's public domain
-    /// fortran code
-	// =======================================================================
-	class HankelTransformGaussianQuadrature : public HankelTransform {
-
-		friend std::ostream &operator<<(std::ostream &stream,
-				const HankelTransformGaussianQuadrature &ob);
-
-		public:
-
-			// ====================  LIFECYCLE     ===========================
-
-            /**
-             *  Returns pointer to new HankelTransformGaussianQuadrature.
-             *  Location is
-             *  initialized to (0,0,0) type and polarization are
-             *  initialized  to nonworking values that will throw
-             *  exceptions if used.
-             */
-			static HankelTransformGaussianQuadrature* New();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-			// ====================  OPERATORS     ===========================
-
-			// ====================  OPERATIONS    ===========================
-
-			/// Performs numerical integration using Gaussian quadrature
-			/// ikk:   type of kernel depending on source and receiver couple
-			/// imode: a switch for TE(0) and TM(1) mode
-			/// itype: order of Bessel function
-			/// rho is argument to integral
-			/// wavef is the propogation constant of free space
-			/// = omega * sqrt( EP*AMU )  amu = 4 pi e-7  ep = 8.85e-12
-            //template <EMMODE T>
-			Complex Zgauss(const int &ikk, const EMMODE &imode,
-							const int &itype, const Real &rho,
-							const Real &wavef, KernelEm1DBase *Kernel);
-
-			// ====================  ACCESS        ============================
-
-			// ====================  INQUIRY       ============================
-
-			// ====================  DATA MEMBERS  ============================
-
-		protected:
-
-			// ====================  LIFECYCLE     ============================
-
-			/// Default protected constructor.
-			HankelTransformGaussianQuadrature (const std::string &name);
-
-            /// Default protected constructor.
-			~HankelTransformGaussianQuadrature ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-			// ====================  OPERATIONS    ============================
-
-			/// Modified by Yoonho Song to branch cut, June, 1996
-			/// Separate Gaussian quarature integral by two interval
-			/// first:  integal from 0 to wavenumber of free space
-			/// second: integral from wavenunmber of free space to infinity
-			///         for large arguments, it uses continued fraction also
-			/// It is recommended to use nl = 1 to 6, nu =7
-			/// PERFORMS AUTOMATIC CALCULATION OF BESSEL TRANSFORM TO SPECIFIED
-			/// RELATIVportisheadE AND ABSOLUTE ERROR
-			///
-			/// ARGUMENT LIST:
-			///
-			/// BESR,BESI-REAL AND IMAGINARY PARTS RETURNED BY BESAUX
-			/// iorder-ORDER OF THE BESSEL FUNCTION
-			/// NL-LOWER LIMIT FOR GAUSS ORDER TO START COMPUTATION
-			/// NU-UPPER LIMIT FOR GAUSS ORDER
-			/// NU,NL=1,...7 SELECTS 3,7,15,31,63,127,AND 255 POINT GAUSS
-			/// QUADRATURE BETWEEN THE ZERO CROSSINGS OF THE BESSEL FUNCTION
-			/// R-ARGUMENT OF THE BESSEL FUNCTION
-			/// RERR,AERR-RELATIVE AND ABSOLUTE ERROR FOR TERMINATION
-			/// BESAUX TERMINATES WHEN INCREASING THE GAUSS ORDER DOES NOT
-			/// CHANGE THE RESULT BY MORE THAN RERR OR WHEN THE ABSOLUTE ERROR
-			/// IS LESS THAN AERR OR WHEN A GAUSS ORDER OF NU IS REACHED.
-			/// NPCS-NUMBER OF PIECES INTO WHICH EACH PARTIAL INTEGRAND
-			/// IS DIVIDED,
-			/// ORDINARILY SET TO ONE. FOR VERY SMALL VALUES OF R WHERE
-			/// THE KERNEL FUNCTION IS APPRECIABLE ONLY OVER THE FIRST FEW
-			/// LOOPS OF THE BESSEL FUNCTION, NPCS MAY BE INCREASED TO ACHIEVE
-			/// REASONABLE ACCURACY.
-			/// NEW  IF NEW=1, THE INTEGRANDS ARE COMPUTED AND SAVED AT EACH
-			/// GAUSS
-			/// ORDER. IF NEW=2, PREVIOUSLY COMPUTED INTEGRANDS ARE USED. NOTE
-			/// THAT ORDER,R, AND NPCS MUST NOT BE CHANGED WHEN SETTING NEW=2.
-			/// IERR-ERROR PARAMETER
-			/// IERR=0--NORMAL RETURN
-			/// IERR=1--RESULT NOT ACCURATE TO RERR DUE TO TOO LOW A GAUSS
-			///  ORDER OR CONVERGENCE NOT ACHIEVED IN BESTRX
-            //template <EMMODE T>
-			void Besautn(Real &besr, Real &besi, const int &iorder,
-							const int &nl, const int &nu, const Real &rho,
-							const Real &rerr, const Real &aerr,
-							const int &npcs, int &inew, const Real &aorb,
-							KernelEm1DBase *Kernel);
-
-			/// COMPUTES BESSEL TRANSFORM OF SPECIFIED ORDER DEFINED AS
-			/// INTEGRAL(FUNCT(X)*J-SUB-ORDER(X*R)*DX) FROM X=0 TO INFINITY
-			/// COMPUTATION IS ACHIEVED BY INTEGRATION BETWEEN THE ASYMPTOTIC
-			/// ZERO CROSSINGS OF THE BESSEL FUNCTION USING GAUSS QUADRATURE.
-			/// THE RESULTING SERIES OF PARTIAL INTEGRANDS IS SUMMED BY
-			/// CALCULATING THE PADE APPROXIMANTS TO SPEED UP CONVERGENCE.
-			/// ARGUMENT LIST:
-			/// BESR,BESI  REAL AND IMAGINARY PARTS RETURNED BY BESTRN
-			/// iorder  ORDER OF THE BESSEL FUNCTIONC  NG  NUMBER OF GAUSS
-			/// POINTS TO USE IN THE QUADRATURE ROUTINE.
-			/// NG=1 THROUGH 7 SELECTS 3,7,15,31,63,126,AND 255 TERMS.
-			///   R     ARGUMENT OF THE BESSEL FUNCTION
-			///   RERR,AERR  SPECIFIED RELATIVE AND ABSOLUTE ERROR FOR THE
-			///           CALCULATION.  THE INTEGRATION
-			///  TERMINATES WHEN AN ADDITIONAL TERM DOES NOT CHANGE THE
-			///  RESULT BY MORE THAN RERR*RESULT+AERR
-			///  NPCS  NUMBER OF PIECES INTO WHICH EACH PARTIAL I
-			///        NTEGRAND IS DIVIDED,
-			///        ORDINARILY SET TO ONE. FOR VERY SMALL VALUES OF RANGE
-			///        WHERE THE KERNEL FUNCTION IS APPRECIABLE ONLY OVER THE
-			///        FIRST FEW LOOPS OF THE BESSEL FUNCTION, NPCS MAY BE
-			///        INCREASED TO ACHIEVE REASONABLE ACCURACY. NOTE THAT
-			///        NPCS AFFECTS ONLY THE PADE
-			///        SUM PORTION OF THE INTEGRATION, OVER X(NSUM) TO INFINITY.
-			/// XSUM  VECTOR OF VALUES OF THE KERNEL ARGUMENT OF FUNCT FOR WHICH
-			/// EXPLICIT CALCULATION OF THE INTEGRAL IS DESIRED, SO THAT THE
-			/// INTEGRAL OVER 0 TO XSUM(NSUM) IS ADDED TO THE INTEGRAL OVER
-			/// XSUM(NSUM) TO INFINITY WITH THE PADE METHOD INVOKED ONLY FOR
-			/// THE LATTER. THIS ALLOWS THE PADE SUMMATION METHOD TO BE
-			/// OVERRIDDEN AND SOME TYPES OF SINGULARITIES TO BE HANDLED.
-			/// NSUM  NUMBER OF VALUES IN XSUM, MAY BE ZERO.
-			/// NEW   DETERMINES METHOD OF KERNEL CALCULATION
-			/// NEW=0 MEANS  CALCULATE BUT DO NOT SAVE INTEGRANDS
-			/// NEW=1 MEANS CALCULATE KERNEL BY CALLING FUNCT-SAVE KERNEL
-			///       TIMES BESSEL FUNCTION
-			/// NEW=2 MEANS USE SAVED KERNELS TIMES BESSEL FUNCTIONS IN
-			///       COMMON /BESINT/. NOTE THAT ORDER,R,NPCS,XSUM, AND
-			///       NSUM MAY NOT BE CHANGED WHEN SETTING NEW=2.
-			/// IERR  ERROR PARAMETER
-			///       0 NORMAL RETURN-INTEGRAL CONVERGED
-			///       1 MEANS NO CONVERGENCE AFTER NSTOP TERMS IN THE PADE SUM
-			///
-			/// SUBROUTINES REQUIRED:
-			/// BESQUD,PADECF,CF,ZEROJ,DOT,JBESS
-			///  A.CHAVE IGPP/UCSD
-			/// NTERM IS MAXIMUM NUMBER OF BESSEL FUNCTION LOOPS STORED IF
-			/// NEW.NE.0
-			/// NSTOP IS MAXIMUM Number of Pade terms
-            //template <EMMODE T>
- 			void Bestrn( Real &BESR, Real &BESI, const int &iorder,
- 					const int &NG, const Real &R,
- 					const Real &RERR, const Real &AERR, const int &npcs,
- 					VectorXi &XSUM, int &NSUM, int &NEW,
- 					int &IERR, int &NCNTRL, const Real &AORB,
-					KernelEm1DBase *Kernel);
-
-			/// CALCULATES THE INTEGRAL OF F(X)*J-SUB-N(X*R) OVER THE
-			/// INTERVAL A TO B AT A SPECIFIED GAUSS ORDER THE RESULT IS
-			/// OBTAINED USING A SEQUENCE OF 1, 3, 7, 15, 31, 63, 127, AND 255
-			/// POINT INTERLACING GAUSS FORMULAE SO THAT NO INTEGRAND
-			/// EVALUATIONS ARE WASTED. THE KERNEL FUNCTIONS MAY BE
-			/// SAVED SO THAT BESSEL TRANSFORMS OF SIMILAR KERNELS ARE COMPUTED
-			/// WITHOUT NEW EVALUATION OF THE KERNEL.  DETAILS ON THE FORMULAE
-			/// ARE GIVEN IN 'THE OPTIMUM ADDITION OF POINTS TO QUADRATURE
-			/// FORMULAE' BY T.N.L. PATTERSON, MATHS.COMP. 22,847-856 (1968).
-			/// GAUSS WEIGHTS TAKEN FROM COMM. A.C.M. 16,694-699 (1973)
-			/// ARGUMENT LIST:
-			/// A      LOWER LIMIT OF INTEGRATION
-			/// B      UPPER LIMIT OF INTEGRATION
-			/// BESR,BESI RETURNED INTEGRAL VALUE REAL AND IMAGINARY PARTS
-			/// NG NUMBER OF POINTS IN THE GAUSS FORMULA.  NG=1,...7
-			///        SELECTS 3,7,15,31,63,127,AND 255 POINT QUADRATURE.
-			///  NEW SELECTS METHOD OF KERNEL EVALUATION
-			///    NEW=0 CALCULATES KERNELS BY CALLING F - NOTHING SAVED
-			///    NEW=1 CALCULATES KERNELS BY CALLING F AND SAVES KERNEL TIMES
-			///           BESSEL FUNCTION IN COMMON /BESINT/
-			///    NEW=2 USES SAVED KERNEL TIMES BESSEL FUNCTIONS IN
-			///           COMMON /BESINT/
-			/// iorder ORDER OF THE BESSEL FUNCTION
-			/// R    ARGUMENT OF THE BESSEL FUNCTION
-			/// F     F(X) IS THE EXTERNAL INTEGRAND SUBROUTINE
-			/// A.CHAVE IGPP/UCSDC
-			/// MAXIMUM NUMBER OF BESSEL FUNCTION LOOPS THAT CAN BE SAVED
-            //template <EMMODE T>
-			void Besqud(const Real &A, const Real &B, Real &BESR, Real &BESI,
-							const int &NG, const int &NEW, const int &iorder,
-							const Real &R, KernelEm1DBase *Kernel);
-
-			/// COMPUTES SUM(S(I)),I=1,...N BY COMPUTATION OF PADE APPROXIMANT
-			/// USING CONTINUED FRACTION EXPANSION.  FUNCTION IS DESIGNED TO BE
-			/// CALLED SEQUENTIALLY AS N IS INCREMENTED FROM 1 TO ITS FINAL
-			/// VALUE.  THE NTH CONTINUED FRACTION COEFFICIENT IS CALCULATED AND
-			/// STORED AND THE NTH CONVERGENT RETURNED.  IT IS UP TO THE USER TO
-			/// STOP THE CALCULATION WHEN THE DESIRED ACCURACY IS ACHIEVED.
-			/// ALGORITHM FROM HANGGI ET AL., Z.NATURFORSCH. 33A,402-417 (1977)
-			/// IN THEIR NOTATION, VECTORS CFCOR,CFCOI ARE LOWER CASE D,
-			/// VECTORS DR, DI ARE UPPER CASE D, VECTORS XR,XI ARE X, AND
-			/// VECTORS SR,SI ARE S
-			/// A.CHAVE IGPP/UCSD
-			void Padecf(Real &SUMR, Real &SUMI, const int &N);
-
-			/// EVALUATES A COMPLEX CONTINUED FRACTION BY RECURSIVE DIVISION
-			/// STARTING AT THE BOTTOM, AS USED BY PADECF
-			/// RESR,RESI ARE REAL AND IMAGINARY PARTS RETURNED
-			/// CFCOR,CFCOI ARE REAL AND IMAGINARY VECTORS OF CONTINUED FRACTION
-			/// COEFFICIENTS
-			void CF(        Real& RESR, Real &RESI,
-							Eigen::Matrix<Real, 100, 1> &CFCOR,
-							Eigen::Matrix<Real, 100, 1> &CFCOI,
-							const int &N);
-
-
-			/// COMPUTES ZERO OF BESSEL FUNCTION OF THE FIRST KIND FROM
-			/// MCMAHON'S ASYMPTOTIC EXPANSION
-			/// NZERO-NUMBER OF THE ZERO
-			/// iorder-ORDER OF THE BESSEL FUNCTION (0 OR 1)
-			Real ZeroJ(const int &ZERO, const int &IORDER);
-
-			/// COMPUTES BESSEL FUNCTION OF ORDER "ORDER" AND ARGUMENT X BY
-			/// CALLING NBS ROUTINES J0X AND J1X (REAL*8 BUT APPROXIMATELY
-			/// REAL*4 ACCURACY).
-			/// FOR MORE ACCURACY JBESS COULD BE CHANGED TO CALL, FOR EXAMPLE,
-			/// THE IMSL ROUTINES MMBSJ0,MMBSJ1 << SEE C// BELOW >>
-			Real Jbess(const Real &X, const int &IORDER);
-
-			/// COMPUTES DOT PRODUCT OF TWO D.P. VECTORS WITH NONUNIT
-			/// INCREMENTING ALLOWED. REPLACEMENT FOR BLAS SUBROUTINE SDOT.
-			/// Currently does no checking, kind of stupid.
-			/// The fortran version will wrap around if (inc*N) > X1.size()
-			/// but not in a nice way.
-			Real _dot(const int&N,
-				const Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> &X1,
-							const int &INC1,
-				const Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> &X2,
-				const int &INC2);
-
-			// ====================  DATA MEMBERS  ============================
-
-            static const Real PI2;
-			static const Real X01P;
-			static const Real XMAX;
-			static const Real XSMALL;
-			static const Real J0_X01;
-			static const Real J0_X02;
-			static const Real J0_X11;
-			static const Real J0_X12;
-			static const Real FUDGE;
-			static const Real FUDGEX;
-			static const Real TWOPI1;
-			static const Real TWOPI2;
-			static const Real RTPI2;
-			static const Real XMIN;
-			static const Real J1_X01;
-			static const Real J1_X02;
-			static const Real J1_X11;
-			static const Real J1_X12;
-
-			/// Highest gauss order used, Was NG
-			int HighestGaussOrder;
-
-			/// Total number of partial integrals on last call, was NI
-			int NumberPartialIntegrals;
-
-			/// Total number of function calls, was NF
-			int NumberFunctionEvals;
-
-			int          np;
-			int          nps;
-
-            /////////////////////////////////////////////////////////////
-			// Eigen members
-
-            // Shared constant values
-			static const VectorXr  WT;
-			static const VectorXr  WA;
-
-			Eigen::Matrix<int,  100, 1>    Nk;
-			//Eigen::Matrix<Real, 255, 100>  karg;
-			//Eigen::Matrix<Real, 510, 100>  kern;
-			Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic>  karg;
-			Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic>  kern;
-
-			// Was Besval COMMON block
-			Eigen::Matrix<Real, 100, 1> Xr;
-			Eigen::Matrix<Real, 100, 1> Xi;
-			Eigen::Matrix<Real, 100, 1> Dr;
-			Eigen::Matrix<Real, 100, 1> Di;
-			Eigen::Matrix<Real, 100, 1> Sr;
-			Eigen::Matrix<Real, 100, 1> Si;
-			Eigen::Matrix<Real, 100, 1> Cfcor;
-			Eigen::Matrix<Real, 100, 1> Cfcoi;
-
-		private:
-
-	}; // -----  end of class  HankelTransformGaussianQuadrature  -----
-
-    //////////////////////////////////////////////////////////////
-    // Exception Classes
-
-    /** If the lower integration limit is greater than the upper limit, throw this
-     * error.
-     */
-    class LowerGaussLimitGreaterThanUpperGaussLimit :
-        public std::runtime_error {
-        /** Thrown when the LowerGaussLimit is greater than the upper limit.
-         */
-        public: LowerGaussLimitGreaterThanUpperGaussLimit();
-    };
-
-}	   // -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef _HANKELTRANSFORMGAUSSIANQUADRATURE_h_INC  -----

LemmaCore/include/hankeltransformhankel2.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     06/26/2009
-  @version  $Id: hankeltransformhankel2.h 201 2015-01-03 00:07:47Z tirons $
- **/
-
-#ifndef __HANKEL2_H
-#define __HANKEL2_H
-
-#include "hankeltransform.h"
-#include "kernelem1dbase.h"
-#include "kernelem1dspec.h"
-#include "CubicSplineInterpolator.h"
-
-namespace Lemma {
-
-// ==========================================================================
-//        Class:  Hankel2
-/** \brief   Computes the Hankel transform of orders 0 and 1 using lagged
-             and related convolutions.
-    \details A rewrite of work by Anderson who wrote a FORTRAN program
-             that he released while working at the USGS.
-             The  transform evaluates an integral of the form:
-             \f[ \int_0^\infty K(\lambda) J_I (\lambda r) ~ d \lambda
-             \f]
-             Where \f$ K(\lambda) \f$ is some kernel function. The value
-             \f$ J_I \f$ is the Bessel function of order
-             \f$I, I \in \{0,1\} \f$
-             The kernel function is unique for each source and is computed
-             in the class CalculateKernel. The value \f$r\f$ is the radial
-             distance away from the centre of the grid \f$ r=\sqrt{x^2 + y^2} \f$
-             The Hankel transform is useful as it allows a double fourier
-             transform to be written as a single integral:
-             \f[ \mathop {\int \!\!\! \int}_{\!\!\!\!\!-\infty}^{\,\,\infty}
-             F(k_x^2 + k_y^2)
-                 e^{\imath (k_x x + k_y y)} dk_x \, dk_y = 2 \pi
-                 \int_0^\infty K(\lambda) J_I (\lambda r) ~ d \lambda
-             \f]
-             This can only be done where there is radial symmetry. Hence
-             its application to 1D solutions here.
- */
-// ==========================================================================
-
-class Hankel2 : public HankelTransform {
-
-    friend std::ostream &operator<<(std::ostream &stream, const Hankel2 &ob);
-
-    public:
-
-        // ====================  LIFECYCLE     ==============================
-        /**
-         *  Returns pointer to new Hankel2. Location is
-         *  initialized to (0,0,0) type and polarization are
-         *  initialized  to nonworking values that will throw
-         *  exceptions if used.
-         */
-        static Hankel2 *New();
-
-        /**
-         * @copybrief LemmaObject::Delete()
-         * @copydetails LemmaObject::Delete()
-         */
-        void Delete();
-
-        // ====================  OPERATORS     ==============================
-
-        // ====================  OPERATIONS    ==============================
-
-        /// Sets the number of convolutions
-        void SetNumConv(const int &i);
-
-        /// Computes the hankel transform with arguments
-        /// @param rho [input] rho is the hankel transform argument
-        /// @param ntol [input] ntol is
-        /// @param tol [input] tol is
-        void Compute(const Real &rho, const int& ntol, const Real &tol);
-
-        /// Computes the related
-        void ComputeRelated(const Real &rho, KernelEm1DBase* Kernel);
-
-        /// Computes the related
-        void ComputeRelated(const Real &rho,  std::vector< KernelEm1DBase* > KernelVec);
-
-        /// Computes the related
-        void ComputeRelated(const Real &rho,  KernelEM1DManager* Manager);
-
-        /// Computes the related and lagged convolutions
-        void ComputeLaggedRelated(const Real &rho, const int& nlag,  KernelEM1DManager* Manager);
-
-        // ====================  ACCESS        ==============================
-
-        /// Returns the answer
-        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>  GetAnswer();
-
-        /// Returns the arguments for lagged convolutions
-        VectorXr GetArg() {return Arg;};
-
-        /// Returns the value of Abscissa stepping
-        Real GetABSER( ) { return ABSER; };
-
-        /// Sets the lagged kernel index so that the proper value is returned
-        void SetLaggedArg(const Real& rho);
-
-
-        // ====================  INQUIRY       ==============================
-
-        /// Calculates Hankel Transform using filtering.
-        /// ikk:   type of kernel depending on source and receiver couple
-        /// imode: a switch for TE(0) and TM(1) mode
-        /// itype: order of Bessel function
-        /// rho is argument to integral
-        /// wavef is the propogation constant of free space
-        /// = omega * sqrt( EP*AMU )  amu = 4 pi e-7  ep = 8.85e-12
-        Complex Zgauss(const int &ikk, const EMMODE &imode,
-                        const int &itype, const Real &rho,
-                        const Real &wavef, KernelEm1DBase *Kernel);
-
-    protected:
-
-        // ====================  LIFECYCLE     ==============================
-
-        /** A rewrite of Anderson's Pseudo-subroutine. */
-        inline void StoreRetreive(const int &idx, const int &lag,
-                        Complex &Zsum, const int &irel, Complex &C, const Real& rho0) {
-
-            int look = idx+lag;
-    		int	iq = look/801;
-    		int	ir = look%801;
-    		int iroll = iq*800;
-
-    		if(this->Key[ir] <= iroll) {
-			    this->Key[ir] = iroll + ir;
- 	    		++this->NumFun;
-                Manager->ComputeReflectionCoeffs(this->Lambda, idx, rho0);
- 			    for (unsigned int ir2=0; ir2<this->kernelVec.size(); ++ir2) {
- 			        this->Zwork(ir, ir2) = this->kernelVec[ir2]->RelBesselArg(this->Lambda);
- 			    }
-		    }
-
-		    C = this->Zwork(ir, irel) * this->FilterWeights(this->BesselOrder, idx);
-		    Zsum += C;
-		    return;
-	    }
-
-        /// Default protected constructor
-        Hankel2(const std::string& name);
-
-        /// Default protected destructor
-        ~Hankel2();
-
-        /**
-         * @copybrief LemmaObject::Release()
-         * @copydetails LemmaObject::Release()
-         */
-        void Release();
-
-        // ====================  OPERATIONS    ==============================
-
-        void DeleteSplines();
-
-        // ====================  DATA MEMBERS  ==============================
-
-        /// The hankel transform wavenumber embedded in the integral
-        Real Lambda;
-
-        /// Number of times a kernel was evaluated
-        int NumFun;
-
-        /// Number of lagged convolutions
-        /// must be greater or equal to 1
-        /// It is set automatically in the @see Compute function so
-        /// that  \f$ \rho \exp\left( -.1*(\mathtt{NumConv} -1) \right) \f$
-        /// does not underflow the exponent range
-        int NumConv;
-
-        /// Number of related kernels
-        int NumRel;
-
-        /** Bessel transform order to use */
-        int BesselOrder;
-
-        /** Lag argument */
-        int iLag;
-
-        /* Should results be cached? Useful for repeated calculations of few receiver points */
-        // turned out to have only marginal benefits in best case, and awful consequences in many
-        //bool cacheResults;
-
-        /** Related Kernel Manager */
-        KernelEM1DManager*          Manager;
-
-        /// Used as base for filter abscissa generation
-        static const Real ABSCISSA;
-
-        /// Also used in abscissa generation \f$ ABSE = \exp{.1} \f$
-        static const Real ABSE;
-
-        /// Also used in abscissa generation \f$ ABSER = 1 / \exp{.1} \f$
-        static const Real ABSER;
-
-        /// Counter for calculated
-        int icount;
-
-        /// Kernel Calculator
-        std::vector <KernelEm1DBase*> kernelVec;
-
-        /// Spines for lagged convolutions (real part)
-        std::vector <CubicSplineInterpolator*> splineVecReal;
-
-        /// Spines for lagged convolutions (imaginary part)
-        std::vector <CubicSplineInterpolator*> splineVecImag;
-
-        /// Key used internally
-        Eigen::Matrix<int, 801, 1> Key;
-        //int  Key[801];
-        //Eigen::Matrix<int, Eigen::Dynamic, 1> Key;
-
-        /// Filter weight coefficients. Set for either \f$J_0\f$ or \f$J_1\f$
-        /// internally by protected function SetFilterWeights.
-        /// Fixed sized will yield better performance. (not necessarily)
-        //Eigen::Matrix<Real, 801, 1> FilterWeights;
-        static const Eigen::Matrix<Real, 2, 801> FilterWeights;
-        //static const Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> FilterWeights;
-
-        /// Zwork from Anderson
-        Eigen::Matrix<Complex, 801, Eigen::Dynamic> Zwork;
-        //Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zwork;
-
-        /// Holds answer, dimensions are NumConv, and NumberRelated.
-        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> Zans;
-
-        /// Holds the arguments for lagged convolutions
-        VectorXr Arg;
-
-}; // -----  end of class  HankelTransform  -----
-
-}
-
-#endif // __HANKEL2_h

LemmaCore/include/instrumentfem.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   M. Andy Kass
-  @date     01/14/2013
-  @version  $Id$
- **/
-
-#ifndef __INSTRUMENTFEM_H
-#define __INSTRUMENTFEM_H
-
-#include "instrument.h"
-#include "emearth1d.h"
-#include "WireAntenna.h"
-#include "PolygonalWireAntenna.h"
-#include "receiverpoints.h"
-#include "dipolesource.h"
-#include "layeredearthem.h"
-#include "datafem.h"
-
-namespace Lemma {
-
-// ===================================================================
-//        Class:  InstrumentFem
-/// \brief
-/// \details
-// ===================================================================
-	class InstrumentFem : public Instrument {
-		friend std::ostream &operator<<(std::ostream &stream,
-			const InstrumentFem &ob);
-
-
-	public:
-
-	// ====================  LIFECYCLE     =======================
-
-		static InstrumentFem* New();
-
-		void Delete();
-
-	// ====================  OPERATORS     =======================
-
-	// ====================  OPERATIONS    =======================
-
-		/// Make the forward model calculation
-		void MakeCalculation();
-
-		/// Forward model from a vector of inputs
-		void ForwardModelProfile();
-
-	// ====================  ACCESS        =======================
-	//
-		/// Set layered earth model
-		void EMEarthModel(LayeredEarthEM* Earth);
-
-		/// Set dipole source
-		void SetDipoleSource(DipoleSource* dipolesource);
-
-		/// Set Field Points
-		void SetReceiverPoints(ReceiverPoints* receiver);
-
-		/// Copy parameters from data object
-		void AlignWithData(DataFEM* inpdata);
-
-		/// Set a data object for output
-		void SetOutputData(DataFEM* outputdata);
-
-
-
-	// ====================  INQUIRY       =======================
-
-
-	protected:
-
-	// ====================  LIFECYCLE     =======================
-
-		/// Default protected constructor.
-		InstrumentFem (const std::string &name);
-
-		/// Default protected constructor.
-		~InstrumentFem ();
-
-		void Release();
-
-	// ====================  DATA MEMBERS  =========================
-
-	LayeredEarthEM* EarthModel;
-
-	DipoleSource* Dipole;
-
-	ReceiverPoints* Receiver;
-
-	DataFEM* InputData;
-
-	DataFEM* OutputData;
-
-	/// Vector of dipole sources - may be superceded by boost
-	std::vector<DipoleSource*> Transmitters;
-
-	/// Vector of receivers - may be superceded by boost
-	/// not necessary--one set of receivers for all dipoles,
-	/// except the number of frequencies is built into the receiver
-	std::vector<ReceiverPoints*> Receivers;
-
-	/// Vector of Earth Models - may be superceded by boost
-	//std::vector<LayeredEarthEM*> EarthModels;
-
-	/// Number of frequencies
-	int nFreq;
-
-	/// Number of observation locations
-	int nObs;
-
-	/// Array of frequencies
-	VectorXr freq;
-
-	/// Position vector, with z as height above the ground surface (pos)
-	Vector3Xr xyz;
-
-	/// Array of Tx orientations (x,y,z) for each freq
-	Eigen::Matrix<ORIENTATION,Eigen::Dynamic,1> TxOrientation;
-
-	/// Array of Rx orientations (x,y,z) for each freq
-	Eigen::Matrix<ORIENTATION,Eigen::Dynamic,1> RxOrientation;
-
-	/// Transmitter moments, one for each frequency
-	VectorXr TxMom;
-
-	/// Tx/Rx Separation in local, right hand system with x aligned with flight
-	Vector3Xr TxRxSep;
-
-	/// Scale factor as described in EM1DFM manual
-	VectorXr ScaleFac;
-
-	private:
-
-}; // -----  end of class  InstrumentFem  -----
-} // end of namespace Lemma
-#endif

LemmaCore/include/instrumenttem.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   M. Andy Kass
-  @date     02/10/2011
-  @version  $Id: instrumenttem.h 201 2015-01-03 00:07:47Z tirons $
- **/
-
-#ifndef __INSTRUMENTTEM_H
-#define __INSTRUMENTTEM_H
-
-#include "instrument.h"
-#include "emearth1d.h"
-#include "WireAntenna.h"
-#include "PolygonalWireAntenna.h"
-#include "receiverpoints.h"
-#include "dipolesource.h"
-#include "layeredearthem.h"
-#include "digitalfiltercostrans.h"
-#include "digitalfiltersintrans.h"
-#include "temintegrationkernel.h"
-#include "CubicSplineInterpolator.h"
-
-namespace Lemma {
-
-enum ReceiverType { INDUCTIVE, MAGNETOMETER, ELECTRIC };
-
-// ===================================================================
-//        Class:  InstrumentTem
-/// \brief  TEM Instrument Class
-/// \details Provides utility to forward model TEM data in Lemma.
-// ===================================================================
-class InstrumentTem : public Instrument {
-
-	friend std::ostream &operator<<(std::ostream &stream,
-		const InstrumentTem &ob);
-
-	public:
-
-	// ====================  LIFECYCLE     =======================
-
-		static InstrumentTem* New();
-
-		void Delete();
-
-	// ====================  OPERATORS     =======================
-
-	// ====================  OPERATIONS    =======================
-
-		/// Perform the forward model calculation
-		void MakeDirectCalculation( const HANKELTRANSFORMTYPE& hType );
-
-        /** Perform the forward model calculation, use lagged convolutions to
-         *  speed up the calculations
-         */
-		void MakeLaggedCalculation( const HANKELTRANSFORMTYPE& hType );
-
-	// ====================  ACCESS        =======================
-
-		/** Sets pulse parameters as a linearly segmented graph, so
-         *  for example a triangle wave needs three points in Amps and
-         *  times, a trapazoidal needs for. The pulse is assumed (defaults) to be
-         *  bipolar, only the positive polarity should be specified.
-         *  @param[in] Amp is the waveform current in Amps
-         *  @param[in] times are the abscissa values of the waveform
-         *  @param[in] bipolar specifies whether or not the pulse is bipolar
-         */
-		void SetPulse( const VectorXr& Amp, const VectorXr& times, bool bipolar=true );
-
-		/// Sets layered earth model
-		void EMEarthModel(LayeredEarthEM* Earth);
-
-		/// Sets transmitter parameters
-		void SetTransmitLoop(WireAntenna *antennae);
-
-		/// Sets dipole source parameters
-		void SetDipoleSource(DipoleSource* dipolesource);
-
-		/// Sets receiver points and parameters
-		void SetReceiver(ReceiverPoints* Receivers);
-
-        /** Sets the type of receiver/measurement
-         */
-        void SetReceiverType( const ReceiverType& rtype  );
-
-		/// Return calculated data
-		MatrixXr GetMeasurements();
-
-		/**
-            Set time gates, assumes gates widths are delta (instantaneous)
-            @param[in] times gate centres units are in seconds
-         */
-
-		void SetTimes(const VectorXr &times);
-
-        /** Sets time gates centres and widths, both in seconds. The window is assumed to be
-         *  a simple boxcar. Simpson's rule is used to integrate the response
-         * @param[in] times gate centres units are in seconds
-         * @param[in] widths gate widths units are in seconds
-         */
-        void SetTimeGates(const VectorXr &centres, const VectorXr& widths);
-
-		/// Get number of times
-		int GetNumberOfTimes();
-
-        /** Sets reference time for time gate to pulse time offset.
-         */
-        void SetReferenceTime(const Real& RefTime);
-
-		/// Attach EMEarth1D
-		//void AttachEMEarth1D(EMEarth1D *EMEarth);
-
-	// ====================  INQUIRY       =======================
-
-
-
-	protected:
-
-	// ====================  LIFECYCLE     =======================
-
-		/// Default protected constructor.
-		InstrumentTem (const std::string &name);
-
-		/// Default protected constructor.
-		~InstrumentTem ();
-
-		void Release();
-
-    // ====================  OPERATIONS    =======================
-
-        /**
-         *  Converts impulse B response (step db/dt) into inductive db/dt
-         *  response for general waveform.
-         */
-        void FoldAndConvolve( CubicSplineInterpolator* Spline );
-
-        /** Convolves the transmitter waveform(s), takes the impulse response
-            and uses simpson's rule to evaluate the integral.
-            @param[in] Spline is the Cubic Spline object representing the solution.
-            @param[in] t is the evaluation time.
-         */
-        Real ConvolveWaveform( CubicSplineInterpolator* Spline, const Real& t );
-
-        /** Subtracts previous waveform(s) from current impulse response, and re-splines.
-         */
-        void SubtractPrevious( CubicSplineInterpolator* Spline );
-
-
-	// ====================  DATA MEMBERS  =========================
-
-		//EMEarth1D* EmEarth;
-
-		WireAntenna* Antenna;
-
-		ReceiverPoints* Receiver;
-
-		LayeredEarthEM* EarthMod;
-
-		DipoleSource* Dipole;
-
-        bool     bipolarWaveform;
-
-        /** Number of previous pules to model */
-        int      NPreviousPulse;
-
-        /** Reference time (relative to pulse abscissa) for time gates */
-        Real     RefTime;
-
-        /** Pulse period, if bimodal 1/2 repitition period */
-        Real     PulseT;
-
-        /** Transmitter repitition frequency */
-        Real     TxFreq;
-
-        /** Receiver type */
-        ReceiverType  RType;
-
-        MatrixXr ModelledData;
-
-        /** Centre of time gate */
-		VectorXr TimeGates;
-
-        /** Width of time gates */
-        VectorXr GateWidths;
-
-        /** Pulse waveform */
-        VectorXr Waveform;
-
-        /** Current Amplitude of pulse */
-        VectorXr  TxAmp;
-
-        /** Current -delta of pulse */
-        VectorXr  TxDelta;
-
-        /** Current derivative of pulse */
-        VectorXr  TxDiff;
-
-        /** times associated with TxAmp segments */
-        VectorXr  TxAbs;
-
-	private:
-
-}; // -----  end of class  InstrumentTem  -----
-
-} // End of namespace Lemma
-
-#endif // __TEMINSTRUMENT_H
-

LemmaCore/include/integrationkernel.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     02/07/2011
-  @version  $Id: integrationkernel.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  INTEGRATIONKERNEL_INC
-#define  INTEGRATIONKERNEL_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    // ===================================================================
-    //  Class:  IntegrationKernel
-    /**
-      @class
-      \brief    Abstract class that computes arguments for numerical
-                integrators.
-      \details  Needs to provide Argument function, as well as be able to
-                set necessary integration parameters.
-     */
-    // ===================================================================
-    template <typename T>
-    class IntegrationKernel : public LemmaObject {
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /** Returns the argument of a function at a given argument. Also
-             *  capable or returning related function values.
-             */
-            //template <typename T>
-            virtual T Argument(const Real& x, const int& iRelated)=0;
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-            virtual int GetNumRel()=0;
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            IntegrationKernel (const std::string& name);
-
-            /// Default protected constructor.
-            ~IntegrationKernel ();
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-    }; // -----  end of class  IntegrationKernel  -----
-
-    template <typename T>
-    IntegrationKernel<T>::IntegrationKernel(const std::string& name) :
-        LemmaObject(name) {
-    }
-
-    template<typename T>
-    IntegrationKernel<T>::~IntegrationKernel( ) {
-    }
-
-//     template <typename T>
-//     T IntegrationKernel<T>::Argument(const Real& x, const int& iRelated) {
-//         return 11.;
-//     }
-//
-//     template <typename T>
-//     int IntegrationKernel<T>::GetNumRel( ) {
-//         return 0;
-//     }
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef INTEGRATIONKERNEL_INC  -----

LemmaCore/include/integrator.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     02/07/2011
-  @version  $Id: integrator.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  INTEGRATOR_INC
-#define  INTEGRATOR_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    // ===================================================================
-    //  Class:  Integrator
-    /**
-      @class
-      \brief
-      \details
-     */
-    // ===================================================================
-    class Integrator : public LemmaObject {
-
-        /// Prints out basic info about the class
-        friend std::ostream &operator<<(std::ostream &stream,
-                        const Integrator &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            Integrator (const std::string& name);
-
-            /// Default protected constructor.
-            ~Integrator ();
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-    }; // -----  end of class  Integrator  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef INTEGRATOR_INC  -----
-

LemmaCore/include/inversesolver.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     07/14/2010
-  @version  $Id: inversesolver.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  INVERSESOLVER_H_INC
-#define  INVERSESOLVER_H_INC
-
-#include "LemmaObject.h"
-#include "data.h"
-#include "instrument.h"
-#include "octreegrid.h"
-
-namespace Lemma {
-
-
-    // ===================================================================
-    //  Class:  InverseSolver
-    /**
-      @class  InverseSolver
-      \brief   Abstract class for inverse problem solver.
-      \details General solution of inverse problems.
-     */
-    // ===================================================================
-    class InverseSolver : public LemmaObject {
-
-        friend  std::ostream &operator<<(std::ostream &stream,
-                const InverseSolver &ob);
-
-        friend class OctreeGrid;
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            // ====================  ACCESS        =======================
-
-            /** @brief Sets the obsered data, any instance of Data.
-             *  @details This may either be field data, or forward modelled
-             *  data.
-             *  @param[in] ObsData a pointer to the observed data class.
-             */
-            void SetObservedData(Data* ObsData);
-
-            /** @brief Sets the instument that is used to create the data.
-             *  @details This is used for all forward modelling.
-             *  @param[in] inst is a pointer to the instrument class.
-             */
-            void SetInstrument(Instrument* inst);
-
-            /** @brief Returns the predicted data.
-             *  @return a pointer to the predicted data.
-             */
-            Data* GetPredictedData();
-
-            // ====================  INQUIRY       =======================
-
-            /** Returns the number of iterations it took to converge to a
-             *  solution.
-             */
-            virtual int NumberOfIterations()=0;
-
-            /** Returns true if the inversion converged successfully.
-             */
-            virtual bool Success()=0;
-
-            /** Returns a vector of \f$ \phi_M \f$
-             */
-            virtual VectorXr GetPhiMVector()=0;
-
-            /** Returns a vector of \f$ \phi_D \f$
-             */
-            virtual VectorXr GetPhiDVector()=0;
-
-        protected:
-
-            // ====================  OPERATIONS    =======================
-
-            /// Used as a callback function from iterating mesh.
-            virtual void FillInG(const Vector3r& pos, const Vector3r& step)=0;
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            InverseSolver (const std::string &name);
-
-            /// Default protected constructor.
-            ~InverseSolver ();
-
-            // ====================  DATA MEMBERS  =========================
-
-            /// The Observed Data
-            Data* ObservedData;
-
-            /// The Predicted Data
-            Data* PredictedData;
-
-            /// Instrument that makes the data
-            Instrument*            ModelInstrument;
-
-        private:
-
-    }; // -----  end of class  InverseSolver  -----
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef INVERSESOLVER_H_INC  -----

LemmaCore/include/inversesolvertem1d.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   M. Andy Kass
-  @date     03/23/2011
-  @version  $Id: inversesolvertem1d.h 201 2015-01-03 00:07:47Z tirons $
- **/
-
-#ifndef _INVERSESOLVERTEM1D__H
-#define _INVERSESOLVERTEM1D__H
-
-#include "inversesolver.h"
-#include "layeredearthem.h"
-#include "WireAntenna.h"
-#include "dipolesource.h"
-#include "receiverpoints.h"
-#include "instrumenttem.h"
-#include "cg.h"
-
-namespace Lemma {
-	// ===================================================================
-	//        Class:  InverseSolverTEM1D
-	/// \brief  Inversion for 1D TEM data
-	/// \details
-	// ===================================================================
-	class InverseSolverTEM1D : public InverseSolver {
-
-		friend std::ostream &operator<<(std::ostream &stream,
-			const InverseSolverTEM1D &ob);
-
-		public:
-
-		// ====================  LIFECYCLE     =======================
-
-		static InverseSolverTEM1D* New();
-
-		void Delete();
-
-		// ====================  OPERATORS     =======================
-
-		// ====================  OPERATIONS    =======================
-
-		/// Perform the inverse calculation
-		void Calculate();
-
-		// ====================  ACCESS        =======================
-
-		/// Attach starting model
-		void AttachStartMod(LayeredEarthEM* inpstartmod);
-
-		/// Attach recovered model
-		void AttachRecMod(LayeredEarthEM* inprecmod);
-
-		/// Attach wire antenna source
-		void AttachWireAntenna(WireAntenna* inpwireantenna);
-
-		/// Attach dipole source
-		void AttachDipoleSource(DipoleSource* inpdipsource);
-
-		/// Attach receiver points
-		void AttachReceiver(ReceiverPoints* inpreceiver);
-
-		/// Set the time gates
-		void SetTimes(VectorXr &inptimes);
-
-		/// Show forward modelled data
-		void ShowSoln();
-
-		/// Write recovered model to file
-		void WriteSoln(const std::string &filename);
-
-		/// Set free parameter indices: layer, conductivity
-		void SetFreeParams(const VectorXi &layers, const VectorXi &cond);
-
-		/// Attach measured data for misfit comparison
-		void AttachMeasuredData(const MatrixXr &data);
-
-		// ====================  INQUIRY       =======================
-		/// Report number of iterations
-		int NumberOfIterations();
-
-		/// Report success/failure
-		bool Success();
-
-		/// Return phi m vector
-		VectorXr GetPhiMVector();
-
-		/// Return phi d vector
-		VectorXr GetPhiDVector();
-
-
-		protected:
-
-		/// Some crap trevor uses
-		void FillInG(const Vector3r& pos, const Vector3r& step);
-
-		/// Calculate Jacobian
-		MatrixXr CalcJac(LayeredEarthEM* m0);
-
-		// ====================  LIFECYCLE     =======================
-
-		/// Default protected constructor.
-		InverseSolverTEM1D (const std::string &name);
-
-		/// Default protected constructor.
-		~InverseSolverTEM1D ();
-
-        void Release();
-
-		// ====================  DATA MEMBERS  =========================
-
-		WireAntenna* Antenna;
-
-		DipoleSource* Dipole;
-
-		ReceiverPoints* Receiver;
-
-		LayeredEarthEM* StartingMod;
-
-		LayeredEarthEM* RecoveredMod;
-
-		InstrumentTem *InstrumentFor;
-
-		MatrixXr MeasuredData;
-
-		VectorXr Times;
-
-		/// Vector of indices for which layer conductivities are solved for
-		VectorXi SCondIndex;
-
-		/// Vecor of indices for which layer thicknesses are solved for
-		VectorXi SThickIndex;
-
-		/// Temporary vector for returning linearised step
-		VectorXr RecModStep;
-
-		private:
-
-}; // -----  end of class  InverseSolverTEM1D  -----
-} // End of namespace Lemma
-#endif // _INVERSESOLVERTEM1D__H

LemmaCore/include/kernel.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     01/29/2010
-  @version  $Id: kernel.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef __kernel_h
-#define __kernel_h
-
-#ifdef LEMMAUSEVTK
-#include "vtkImplicitFunction.h"
-#endif
-
-#include "LemmaObject.h"
-#include "receivercubes.h"
-
-namespace Lemma {
-
-        // ==================================================================
-        //        Class:  Kernel
-        /// \brief Pure abstract class for some kind of kernel function.
-        /// \details Provides a consistent interface to kernel functions.
-        // ==================================================================
-        class Kernel : public LemmaObject {
-
-            /// Prints out basic info about the class
-            friend std::ostream &operator<<(std::ostream &stream,
-                        const Kernel &ob);
-
-            public:
-
-                // ====================  LIFECYCLE     ======================
-
-                //static Kernel* New();
-
-                virtual void Delete()=0;
-
-                // ====================  OPERATORS     ======================
-
-                // ====================  OPERATIONS    ======================
-
-                // ====================  ACCESS        ======================
-
-                // ====================  INQUIRY       ======================
-
-                virtual VectorXcr ComputeSensitivity()=0;
-
-                #ifdef LEMMAUSEVTK
-                virtual VectorXcr ComputeSensitivity(vtkImplicitFunction* Impl)=0;
-                #endif
-
-                /** computes sensitivity for same value */
-                virtual VectorXcr ComputeSensitivity(const Real& fval)=0;
-
-                /** Computes sensitivity for array of values */
-                virtual VectorXcr ComputeSensitivity(const VectorXr& fval)=0;
-
-                virtual void SetFieldCubes(ReceiverCubes* pts)=0;
-
-                // ====================  DATA MEMBERS  ======================
-
-            protected:
-
-                // ====================  LIFECYCLE     ======================
-
-                /// Default protected constructor.
-                Kernel (const std::string& name);
-
-                /// Default protected constructor.
-                ~Kernel ();
-
-        private:
-
-    }; // -----  end of class  Kernel  -----
-
-}
-
-#endif // __kernel_h

LemmaCore/include/kernelem1dbase.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-
-  @author   Trevor Irons
-  @date     05/18/2012
-  @version  $Id: kernelem1dbase.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  KERNELEM1DBASE_INC
-#define  KERNELEM1DBASE_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    // Transverse electric or magnetic mode
-    enum EMMODE {TM, TE, NONE};
-
-    // ===================================================================
-    //  Class:  KernelEm1DBase
-    /**
-      @class
-      \brief   Pure virtual base class of KernelEm1D
-      \details Defines interface for HankelTransform classes
-     */
-    // ===================================================================
-    class KernelEm1DBase : public LemmaObject {
-
-        friend class KernelEM1DManager;
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /** Returns the Complex bessel argument to be evaluated for a given
-			 * lambda value
-             */
-            virtual Complex BesselArg(const Real& lambda)=0;
-
-            /** Returns the complex bessel argument. Same as above, but does not
-             *  call reflection coefficient calculation in KernelEM1DReflBase.
-             *  @param[in] lambda is the hankel wave value.
-             */
-            virtual Complex RelBesselArg(const Real& lambda)=0;
-
-            // ====================  ACCESS        =======================
-            virtual void SetIk(const int& ik)=0;
-
-            virtual void SetMode(const EMMODE& mode)=0;
-
-            int GetManagerIndex() {
-                return this->managerIdx;
-            }
-
-            // ====================  INQUIRY       =======================
-            virtual int GetNumRel()=0;
-
-            virtual int GetBesselOrder()=0;
-
-            virtual Complex GetZm()=0;
-
-            virtual Complex GetYm()=0;
-
-            virtual Complex GetZs()=0;
-
-            virtual Complex GetKs()=0;
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            KernelEm1DBase (const std::string& name) : LemmaObject(name)
-            {
-            }
-
-            /// Default protected constructor.
-            ~KernelEm1DBase () {
-                if (this->NumberOfReferences > 0)
-                    throw DeleteObjectWithReferences( this );
-            }
-
-            void Release() {
-                delete this;
-            }
-
-            // ====================  OPERATIONS    =======================
-
-
-            // ====================  DATA MEMBERS  =========================
-
-            /** Where does this kernel live on the vector managed by the manager */
-            int  managerIdx;
-
-        private:
-
-    }; // -----  end of class  KernelEm1DBase  -----
-
-} // namespace Lemma
-
-#endif   // ----- #ifndef KERNELEM1DBASE_INC  -----

LemmaCore/include/kernelem1dmanager.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     06/26/2012
-  @version   0.0
- **/
-
-#ifndef  KERNELEM1DMANAGER_INC
-#define  KERNELEM1DMANAGER_INC
-
-//#include "dipolesource.h"
-//#include "kernelem1dreflbase.h"
-#include "kernelem1dbase.h"
-#include "kernelem1dspec.h"
-
-namespace Lemma {
-
-    class DipoleSource;
-    class KernelEM1DReflBase;
-
-    // ===================================================================
-    //  Class:  KernelEM1DManager
-    /**
-      @class
-      \brief
-      \details
-     */
-    // ===================================================================
-    class KernelEM1DManager : public LemmaObject {
-
-        public:
-
-            friend std::ostream &operator<<(std::ostream &stream,
-                        const KernelEM1DManager &ob);
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Returns a pointer to a new object of type KernelEM1DManager.
-             * It allocates all necessary memory.
-             */
-            static KernelEM1DManager* New();
-
-            /** Deletes this object. Delete also disconnects any
-             * attachments to this object.
-             */
-            void Delete();
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-            int AddKernel( );
-            /*
-            {
-
-                KernelEm1DSpec<Mode, Ikernel, Isource, Irecv>* NewKern =
-                    KernelEm1DSpec<Mode, Ikernel, Isource, Irecv>::New();
-                KernelVec.push_back( NewKern );
-                NewKern->managerIdx = KernelVec.size()-1;
-                switch (Mode) {
-                    case TE:
-                        if (TEReflBase == NULL) {
-                            TEReflBase = KernelEM1DReflSpec<TE, Isource, Irecv>::New();
-                            TEReflBase->Initialise(Earth);
-                            TEReflBase->SetUpSource(Dipole, ifreq);
-                            TEReflBase->SetUpReceiver( rx_z );
-                        }
-                        NewKern->SetReflBase(TEReflBase);
-                        break;
-                    case TM:
-                        if (TMReflBase == NULL) {
-                            TMReflBase = KernelEM1DReflSpec<TM, Isource, Irecv>::New();
-                            TMReflBase->Initialise(Earth);
-                            TMReflBase->SetUpSource(Dipole, ifreq);
-                            TMReflBase->SetUpReceiver( rx_z );
-                        }
-                        NewKern->SetReflBase(TMReflBase);
-                        break;
-                }
-                return static_cast<int>(KernelVec.size()-1);
-            }
-            */
-
-            void ResetSource(const int& ifreq);
-
-            /** For use in related Kernel calculations. This function calles
-             * ComputeReflectionCoeffs on TEReflBase and TMReflBase, if they
-             * exist. After this has been called, KernelEM1DBase::RelBesselArg() may be safely
-             * called. This method stores solutions of the same idx. rho0 is the intial lambda argument
-             */
-            void ComputeReflectionCoeffs(const Real& lambda, const int& idx, const Real& rho0);
-
-            /** Clears the vector of kernels */
-            void ClearVec() {
-                for (unsigned int ik=0; ik<this->KernelVec.size(); ++ik) {
-                    this->KernelVec[ik]->Delete();
-                }
-                KernelVec.clear();
-            }
-
-            // ====================  ACCESS        =======================
-
-            /** Sets the LayeredEarthEM class that will be used by the kernels.
-             */
-            void SetEarth( LayeredEarthEM*   Earth);
-
-            /** Sets the source of the kernels */
-            void SetDipoleSource( DipoleSource*   Dipole, const int& ifreq, const Real& rx_zin);
-
-            /** Returns pointer to specified kernel indice. Indices are assigned in the same
-                order as they are created by AddKernel.
-             */
-            KernelEm1DBase*    GetKernel(const unsigned int& ik);
-
-            /** Returns pointer to connected dipole.
-             */
-            DipoleSource*    GetDipole( );
-
-            inline std::vector<KernelEm1DBase*>  GetSTLVector() {
-                return KernelVec;
-            }
-
-            // ====================  INQUIRY       =======================
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Default protected constructor. */
-            KernelEM1DManager (const std::string& name);
-
-            /** Default protected constructor. */
-            ~KernelEM1DManager ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  DATA MEMBERS  =========================
-
-            /** List of KernelEm1D instances */
-            std::vector<KernelEm1DBase*>           KernelVec;
-
-            /** Reflection base used for TE mode */
-            KernelEM1DReflBase*                    TEReflBase;
-
-            /** Reflection base used for TM mode */
-            KernelEM1DReflBase*                    TMReflBase;
-
-            /** EmEarth Class */
-            LayeredEarthEM*                        Earth;
-
-            /** EM dipole souce */
-            DipoleSource*                          Dipole;
-
-            /** Frequency index for the sources */
-            int                                    ifreq;
-
-            /** Receiver height */
-            Real                                   rx_z;
-
-        private:
-
-    }; // -----  end of class  KernelEM1DManager  -----
-
-    // template methods
-    template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    int KernelEM1DManager::AddKernel( ) {
-
-        KernelEm1DSpec<Mode, Ikernel, Isource, Irecv>* NewKern =
-                    KernelEm1DSpec<Mode, Ikernel, Isource, Irecv>::New();
-        KernelVec.push_back( NewKern );
-        NewKern->managerIdx = KernelVec.size()-1;
-        switch (Mode) {
-            case TE:
-                if (TEReflBase == NULL) {
-                    TEReflBase = KernelEM1DReflSpec<TE, Isource, Irecv>::New();
-                    TEReflBase->Initialise(Earth);
-                    TEReflBase->SetUpSource(Dipole, ifreq);
-                    TEReflBase->SetUpReceiver( rx_z );
-                }
-                NewKern->SetReflBase(TEReflBase);
-                break;
-            case TM:
-                if (TMReflBase == NULL) {
-                    TMReflBase = KernelEM1DReflSpec<TM, Isource, Irecv>::New();
-                    TMReflBase->Initialise(Earth);
-                    TMReflBase->SetUpSource(Dipole, ifreq);
-                    TMReflBase->SetUpReceiver( rx_z );
-                }
-                NewKern->SetReflBase(TMReflBase);
-                break;
-        }
-        return static_cast<int>(KernelVec.size()-1);
-     }
-
-
-//     /** Clears the vector of kernels */
-//     void ClearVec() {
-//         for (unsigned int ik=0; ik<this->KernelVec.size(); ++ik) {
-//             this->KernelVec[ik]->Delete();
-//         }
-//         KernelVec.clear();
-//     }
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef KERNELEM1DMANAGER_INC  -----

LemmaCore/include/kernelem1dreflbase.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     05/18/2012
-  @version  $Id: kernelem1dreflbase.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  KERNELEM1DREFLBASE_INC
-#define  KERNELEM1DREFLBASE_INC
-
-#include "dipolesource.h"
-#include "kernelem1dbase.h"
-#include "layeredearthem.h"
-//#include "kernelem1dspec.h"
-
-namespace Lemma {
-
-    //class DipoleSource;
-
-    enum DIPOLE_LOCATION { INAIR, INGROUND };
-
-    // forward declaration for friend
-    template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    class KernelEm1DSpec;
-
-
-    // ===================================================================
-    //  Class:  KernelEM1DReflBase
-    /**
-      @class
-      \brief   Abstract class defining EM1DRefl class.
-      \details Derived classes are template specialized for optimal performance.
-     */
-    // ===================================================================
-    class KernelEM1DReflBase : public LemmaObject {
-
-        template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-        friend class KernelEm1DSpec;
-        friend class KernelEM1DManager;
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            void Initialise(LayeredEarthEM* EarthIn) {
-
-                nlay = EarthIn->GetNumberOfLayers();
-                zh = VectorXcr::Zero(nlay);
-                yh = VectorXcr::Zero(nlay);
-                u = VectorXcr::Zero(nlay);
-                cf = VectorXcr::Zero(nlay);    // nlay -1 (lay 0 empty)
-                rtu = VectorXcr::Zero(nlay);   // nlay -1 Interfaces only
-                rtd = VectorXcr::Zero(nlay);   // nlay -1 Interfaces only
-                kk = VectorXcr::Zero(nlay);
-                Zyu = VectorXcr::Zero(nlay);
-                Zyd = VectorXcr::Zero(nlay);
-                Zyi = VectorXcr::Zero(nlay);
-                th = VectorXcr::Zero(nlay);
-
-                // Don't attach Earth, because this is performance critical.
-                // Everying is internal, it's OK relax Frankie
-                //if (Earth != NULL) {
-                //    Earth->DetachFrom(this);
-                //    Earth = NULL;
-                //}
-                //EarthIn->AttachTo(this);
-                Earth = EarthIn;
-
-                LayerThickness.resize(nlay);
-                for (int ilay=0; ilay<nlay; ++ilay) {
-                    LayerThickness(ilay) =  Earth->GetLayerThickness(ilay);
-                }
-
-                LayerDepth.resize(nlay);
-                for (int ilay=0; ilay<nlay; ++ilay) {
-                    LayerDepth(ilay) =  Earth->GetLayerDepth(ilay);
-                }
-
-            }
-
-            void SetUpSource(DipoleSource *Dipole, const int &ifreq) {
-
-                zh(0) = Complex(0, Dipole->GetAngularFrequency(ifreq)*MU0);
-                yh(0) = Complex(0, Dipole->GetAngularFrequency(ifreq)*EPSILON0);
-                kk(0) = -zh(0) * yh(0);
-
-                Earth->EvaluateColeColeModel(Dipole->GetAngularFrequency(ifreq));
-
-                for (int ilay=1; ilay<Earth->GetNumberOfLayers(); ++ilay) {
-                    zh(ilay) = zh(0) * Earth->GetLayerSusceptibility(ilay);
-                    yh(ilay) = Earth->GetLayerConductivity(ilay) +
-                            yh(0)*Earth->GetLayerPermitivity(ilay);
-                    kk(ilay)   = -zh(ilay)*yh(ilay);
-                }
-
-                tx_z = Dipole->GetLocation(2);
-                lays = 0;
-                Real Depth(0);
-                for (int ilay=1; ilay<nlay; ++ilay) {
-                    if (tx_z > Depth) {
-                        lays = ilay;
-                    }
-                    Depth += LayerThickness(ilay);
-                }
-            }
-
-            void SetUpReceiver(const Real &rz) {
-                rx_z = rz;
-                Real Depth(0.);
-                layr = 0;
-                for (int ilay=1; ilay<Earth->GetNumberOfLayers(); ++ilay) {
-                    if (rx_z > Depth) {
-                        layr = ilay;
-                    }
-                    Depth += LayerThickness(ilay);
-                }
-            }
-
-            // ====================  ACCESS        =======================
-            Complex GetYm() {
-                return yh(layr);
-            }
-
-            Complex GetZm() {
-                return zh(layr);
-            }
-
-            Complex GetZs() {
-                return zh(lays);
-            }
-
-            Complex GetKs() {
-                return kk(lays);
-            }
-
-            // ====================  INQUIRY       =======================
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            KernelEM1DReflBase (const std::string& name) : LemmaObject(name)
-            {
-            }
-
-            /// Default protected constructor.
-            ~KernelEM1DReflBase () {
-                if (this->NumberOfReferences > 0)
-                    throw DeleteObjectWithReferences( this );
-            }
-
-            void Release() {
-                delete this;
-            }
-
-            // ====================  OPERATIONS    =======================
-
-            /** Computes reflection coefficients. Depending on the
-             * specialisation, this will either be TM or TE mode.
-             */
-            virtual void ComputeReflectionCoeffs(const Real& lambda)=0;
-
-            /** Precomputes expensive calculations that are reused by insances
-             * of KernelEM1DSpec in the calculation of Related potentials.
-             */
-            virtual void PreComputePotentialTerms()=0;
-
-            // ====================  DATA MEMBERS  =========================
-
-			/// Bessel order, only 0 or 1 supported
-			int id; // Needs to be dim nRel, or separate
-
-            /// Layer the source is in
-			int lays;
-
-			/// Layer the receiver is in
-			int layr;
-
-			/// Number of Layers
-			int nlay;
-
-            /// Number of Related kernels to be computed
-            int nRelated;
-
-            /// Used in related kernel precompute calls
-            int relIud;
-
-			/// Receiver z position
-			Real rx_z;
-
-			/// Transmitter z position
-			Real tx_z;
-
-            /// bessel arg squared
-            Real rams;
-
-            /** Related part of con term */
-            Complex  relCon;
-
-            Complex  relenukadz;
-
-            Complex  relexp_pbs1;
-
-            Complex  relexp_pbs2;
-
-            Complex  rel_a;
-
-			/// TM or TE mode
-			EMMODE mode;
-
-            /// Pointer to layered earth
-            LayeredEarthEM *Earth;
-
-			Complex       uk;
-			Complex       um;
-			VectorXcr     cf;  // nlay
-			VectorXcr      u;  // nlay
-			VectorXcr     yh;  // nlay
-			VectorXcr     zh;  // nlay
-			VectorXcr     kk;  // nlay
-			VectorXcr    Zyu;  //(nlay); //Zyu.setZero();
-			VectorXcr    Zyd;  //(nlay); //Zyd.setZero();
-			VectorXcr    Zyi;  //(nlay); //Zyi.setZero();
-			VectorXcr     th;  //(nlay);
-			VectorXr     LayerThickness;
-			VectorXr     LayerDepth;
-
-			/// Reflection/Transmission coeffients for upgoing waves in a
-			/// layered earth model
-			VectorXcr    rtu;
-
-			/// Reflection/Transmission coeffients for downgoing waves in
-			/// a layered earth model
-			VectorXcr    rtd;
-
-        private:
-
-    }; // -----  end of class  KernelEM1DReflBase  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef KERNELEM1DREFLBASE_INC  -----

LemmaCore/include/kernelem1dreflspec.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     05/18/2012
-  @version  $Id: kernelem1dreflspec.h 123 2014-02-05 23:47:20Z tirons $
- **/
-
-#ifndef  KERNELEM1DREFLSPEC_INC
-#define  KERNELEM1DREFLSPEC_INC
-
-#include "dipolesource.h"
-#include "kernelem1dreflbase.h"
-#include "layeredearthem.h"
-
-// #include<unordered_map> // for caching results
-
-namespace Lemma {
-
-    // forward declare
-    //struct cache;
-    // Simple container to hold reflection results
-    struct  cache {
-        Real                       rho0;
-        Real                       lambda[805];
-        Real                       rams[805];
-        Complex                    uk[805];
-        Complex                    um[805];
-        Real                       zh0i[805];
-        VectorXcr                  Rtd[805];
-        VectorXcr                  Rtu[805];
-        VectorXcr                  u[805];
-        VectorXcr                  cf[805];
-        VectorXcr                  kk[805];
-        const Real                 epsilon;
-        //bool                       nc;
-        cache( ) : epsilon (std::numeric_limits<Real>::epsilon() ) { // TODO reset to precision of Real
-            //Rtd = VectorXcr::Zero(805);
-            //Rtu = VectorXcr::Zero(805);
-        }
-    };
-
-    // forward declaration for friend
-    template<EMMODE Mode, int Ikernel, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    class KernelEm1DSpec;
-
-    // ===================================================================
-    //  Class:  KernelEM1DReflSpec
-    /**
-      @class
-      \brief   Specialized version of KernelEM1DReflBase
-      \details Through use of template specialisations, this KernelEm1D
-               class delivers much better performance.
-     */
-    // ===================================================================
-    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    class KernelEM1DReflSpec : public KernelEM1DReflBase {
-
-        public:
-
-            template<EMMODE Mode2, int Ikernel2, DIPOLE_LOCATION Isource2, DIPOLE_LOCATION Irecv2>
-            friend class KernelEm1DSpec;
-            friend class KernelEM1DManager;
-
-            // ====================  LIFECYCLE     =======================
-
-            static KernelEM1DReflSpec* New() {
-                KernelEM1DReflSpec<Mode, Isource, Irecv>*  Obj =
-                    new KernelEM1DReflSpec<Mode, Isource, Irecv>("KernelEM1DReflSpec<>");
-                Obj->AttachTo(Obj);
-                return Obj;
-            }
-
-            void Delete() {
-                this->DetachFrom(this);
-            }
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            KernelEM1DReflSpec (const std::string& name) : KernelEM1DReflBase(name)
-            {
-            }
-
-            /// Default protected constructor.
-            ~KernelEM1DReflSpec () {
-                if (this->NumberOfReferences > 0)
-                    throw DeleteObjectWithReferences( this );
-            }
-
-            void Release() {
-                delete this;
-            }
-
-            // ====================  OPERATIONS    =======================
-
-            /** Computes reflection coefficients. Depending on the
-             * specialisation, this will either be TM or TE mode.
-             */
-            void ComputeReflectionCoeffs(const Real &lambda);
-
-            /* Computes reflection coefficients. Depending on the
-             * specialisation, this will either be TM or TE mode. This method
-             * stores previous results in a struct. For a given index, and
-             * lambda, the result will be the same. Turned out to be of limited utility.
-             */
-            //void ComputeReflectionCoeffs(const Real &lambda, const int& idx);
-
-            /** Precomputes expensive calculations that are reused by insances
-             * of KernelEM1DSpec in the calculation of Related potentials. This
-             * method is specialised based on template parameters
-             */
-            void PreComputePotentialTerms();
-
-            /*
-             * Sets the cache in CACHE to use. Somewhat expensive, avoid calling in tight loops
-             */
-            //void SetTCache(const Real& rho0);
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-            //** Storage container for reused results */
-            //static std::unordered_map<Real, cache> CACHE;
-
-            //** Currenly used cache */
-            //cache* tcache;
-            //#pragma omp threadprivate(tcache)
-
-    }; // -----  end of class  KernelEM1DReflSpec  -----
-
-    //template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    //std::unordered_map<Real, cache> KernelEM1DReflSpec<Mode, Isource, Irecv>::CACHE;
-
-    //template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    //cache*  KernelEM1DReflSpec<Mode, Isource, Irecv>::tcache;
-
-    ///////////////////////////////////////////////
-    // Declarations of specialisations
-
-    template<>
-    void KernelEM1DReflSpec<TM, INAIR, INAIR>::ComputeReflectionCoeffs(const Real& lambda);
-
-    template<>
-    void KernelEM1DReflSpec<TE, INAIR, INAIR>::ComputeReflectionCoeffs(const Real& lambda);
-
-    template<>
-    void KernelEM1DReflSpec<TM, INAIR, INGROUND>::ComputeReflectionCoeffs(const Real& lambda);
-
-    template<>
-    void KernelEM1DReflSpec<TE, INAIR, INGROUND>::ComputeReflectionCoeffs(const Real& lambda);
-
-    template<>
-    void KernelEM1DReflSpec<TM, INAIR, INAIR>::PreComputePotentialTerms( );
-
-    template<>
-    void KernelEM1DReflSpec<TE, INAIR, INAIR>::PreComputePotentialTerms( );
-
-    template<>
-    void KernelEM1DReflSpec<TM, INAIR, INGROUND>::PreComputePotentialTerms( );
-
-    template<>
-    void KernelEM1DReflSpec<TE, INAIR, INGROUND>::PreComputePotentialTerms( );
-
-    ///////////////////////////////////////////////
-    // Default mode definitions
-
-/*
-    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    void KernelEM1DReflSpec<Mode, Isource, Irecv>::SetTCache(const Real& rho0) {
-       #ifdef LEMMAUSEOMP
-        #pragma omp critical
-        #endif
-        {
-        this->tcache = &this->CACHE[rho0];
-        }
-    }
-*/
-
-/*
-    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    void KernelEM1DReflSpec<Mode, Isource, Irecv>::ComputeReflectionCoeffs(const Real& lambda, const int& idx) {
-
-        if ( (std::abs(this->tcache->lambda[idx]-lambda) <= this->tcache->epsilon) &&
-            this->tcache->u[idx].size() > 0  && std::abs(this->kk(0) - this->tcache->kk[idx](0)) <= this->tcache->epsilon ) {
-            //std::cout << "USING CACHED RESULTS !!!!!!" << std::endl;
-            // load all the values we need
-            this->u   = this->tcache->u[idx];
-            this->rams = this->tcache->rams[idx];
-            this->cf = this->tcache->cf[idx];
-            //this->kk = this->tcache->kk[idx];
-            this->uk = this->tcache->uk[idx];
-            this->um = this->tcache->um[idx];
-            this->rtd = this->tcache->Rtd[idx];
-            this->rtu = this->tcache->Rtu[idx];
-
-        } else { // else do the work
-        }
-
-        ComputeReflectionCoeffs(lambda);
-
-        //#pragma omp critical
-        //{
-        //std::cout << idx << "\t" << lambda << "\t" << rtd.transpose() << std::endl;
-        //}
-        // store the results
-        this->tcache->u[idx]      = this->u;
-        this->tcache->cf[idx]     = this->cf;
-        this->tcache->kk[idx]     = this->kk;
-        this->tcache->uk[idx]     = this->uk;
-        this->tcache->um[idx]     = this->um;
-        this->tcache->Rtd[idx]    = this->rtd;
-        this->tcache->Rtu[idx]    = this->rtu;
-        this->tcache->zh0i[idx]    = std::imag(this->zh[0]);
-        this->tcache->lambda[idx] = lambda;
-        this->tcache->rams[idx]   = rams;
-
-        }
-
-        return;
-    }
-*/
-
-    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    void KernelEM1DReflSpec<Mode, Isource, Irecv>::ComputeReflectionCoeffs(const Real& lambda) {
-        static bool called = false;
-        if (!called) {
-            std::cout << "unspecialised Reflection function KernelEM1DReflSpec<"
-                      << Mode << ", " << Isource << ", "
-                      << Irecv << " >::ComputeReflectionCoeffs( const Real& lambda ) --> SLOW PERFORMANCE EXPECTED\n";
-            called = true;
-        }
-
-        rams = lambda*lambda;
-        //////////////////////////////////////////
-        // Compute TEM stuff
-
-        // This call to sqrt takes ~ 15% of execution time
-        u  = (rams-kk.array()).sqrt();
-        uk = u(lays);
-        um = u(layr);
-
-        switch (Mode) {
-
-            // TM mode
-            case (TM):
-                Zyu(1) = -u(0)/yh(0);
-                Zyi    =  u.array() / yh.array();
-                break;
-
-            // TE mode
-            case (TE):
-                Zyu(1) = -u(0)/zh(0);
-                Zyi    =  u.array() / zh.array();
-                break;
-
-            default:
-                throw 11; //IllegalMode(this);
-        }
-
-        Zyd.tail<1>() = Zyi.tail<1>();
-
-        for (int ilay=1; ilay<nlay-1; ++ilay) {
-            cf(ilay) =
-                std::exp(-(Real)(2.)*u(ilay)*LayerThickness(ilay));
-            th(ilay) = ((Real)(1.)-cf(ilay)) / ((Real)(1.)+cf(ilay));
-        }
-
-        // Can't use blocks, b/c recursive
-        for (int N=1; N<lays; ++N){
-            Zyu(N+1)=Zyi(N)*(Zyu(N)-Zyi(N)*th(N)) /
-                            (Zyi(N)-Zyu(N)*th(N)) ;
-        }
-
-        int ne = nlay-2;
-        for (int N=ne; N >=lays+1; --N) {
-            Zyd(N) = Zyi(N)*(Zyd(N+1)+Zyi(N)*th(N)) /
-                            (Zyi(N)+Zyd(N+1)*th(N)) ;
-        }
-
-        rtd(nlay-1) = 0;
-
-        if (layr < lays) {
-            // Receiver above source layer
-            int ls = layr;
-            if (ls == 0) {
-                ls = layr+1;
-            }
-            for (int N=ls; N<=lays; ++N) {
-                rtu(N)= (Zyi(N)+Zyu(N)) /
-                        (Zyi(N)-Zyu(N)) ;
-            }
-            if (lays < nlay-1) {
-                rtd(lays) = (Zyi(lays)-Zyd(lays+1)) /
-                            (Zyi(lays)+Zyd(lays+1)) ;
-            }
-        } else {
-            // RECEIVER IN OR BELOW THE SOURCE LAYER
-            if (lays == layr) {  // Rx In source Layer
-                if (layr == 0) {
-                    rtd(0) = (Zyu(1)+Zyd(1)) /
-                             (Zyu(1)-Zyd(1)) ;
-                } else if (layr == nlay-1) {
-                    rtu(nlay-1) = (Zyi(nlay-1)+Zyu(nlay-1)) /
-                                  (Zyi(nlay-1)-Zyu(nlay-1)) ;
-                } else {
-                    rtu(layr) = (Zyi(layr)+Zyu(layr)) /
-                                (Zyi(layr)-Zyu(layr)) ;
-                    rtd(layr) = (Zyi(layr)-Zyd(layr+1)) /
-                                (Zyi(layr)+Zyd(layr+1)) ;
-                }
-            } else { // receiver below source layer
-                if (lays == 0) {
-                    rtd(0) = (Zyu(1)+Zyd(1)) /
-                             (Zyu(1)-Zyd(1)) ;
-                } else {
-                    rtu(lays) = (Zyi(lays)+Zyu(lays)) /
-                                (Zyi(lays)-Zyu(lays)) ;
-                }
-                int le = layr;
-                if (le == nlay-1) --le;
-                int ls = lays;
-                if (lays == 0   ) ++ls;
-
-                // TODO use blocks to vectorize maybe?
-                // This works but gives same to slightly worse
-                // performance as loop.
-//                 int nn = le-ls+1;
-//                 rtd.segment(ls, nn) =
-//                      (Zyi.segment(ls  , nn).array() -
-//                       Zyd.segment(ls+1, nn).array()).array() /
-//                      (Zyi.segment(ls  , nn).array() +
-//                       Zyd.segment(ls+1, nn).array()).array() ;
-                for (int N=ls; N<=le; ++N) {
-                    rtd(N) = (Zyi(N)-Zyd(N+1)) /
-                             (Zyi(N)+Zyd(N+1)) ;
-                }
-            }
-        } // End in or below source layer
-        return;
-    }
-
-    template<EMMODE Mode, DIPOLE_LOCATION Isource, DIPOLE_LOCATION Irecv>
-    void KernelEM1DReflSpec<Mode, Isource, Irecv>::PreComputePotentialTerms( ) {
-        static bool called = false;
-        if (!called) {
-            std::cerr << "unspecialised function KernelEM1DReflSpec<"
-                      << Mode << ", " << Isource << ", "
-                      << Irecv << " >::PreComputePotentialTerms\n";
-            called = true;
-        }
-    }
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef KERNELEM1DREFLSPEC_INC  -----

LemmaCore/include/layeredearthem.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     06/24/2009
-  @version   0.0
- **/
-
-#ifndef __LAYEREDEARTHEM_H
-#define __LAYEREDEARTHEM_H
-
-#include "layeredearth.h"
-#include <iomanip>
-
-namespace Lemma {
-
-    // =======================================================================
-    //        Class:  LayeredEarthEM
-    /// \brief  1D layered earth. Attributes include all aspects of
-    /// Cole-Cole model.
-    /// \details   Primarily used for EM calculations.
-    // =======================================================================
-    class LayeredEarthEM : public LayeredEarth {
-
-        public:
-
-            // ====================    FRIENDS     ===========================
-
-            /** Recursively streams information about this class */
-            friend std::ostream &operator<<(std::ostream &stream,
-                        const LayeredEarthEM &ob);
-
-            // ====================  LIFECYCLE     ===========================
-
-            /**
-             *  Public constructor. Creates a new instance of the class and
-             *  assigns a reference to the thrown pointer.
-             */
-            static LayeredEarthEM* New();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-            #ifdef HAVE_YAMLCPP
-            /** YAML Serializing method
-             */
-            YAML::Node Serialize() const;
-
-
-            //static LayeredEarthEM* DeSerialize(const YAML::Node& node);
-            #endif
-
-            /** @return a deep copy
-             */
-			LayeredEarthEM* Clone();
-
-            // ====================  OPERATORS     ===========================
-
-            // ====================  OPERATIONS    ===========================
-
-            /** Evaluates the cole-cole model for suceptability and
-             * permeability.
-             * @param[in] omega is the frequency in Hz
-             */
-            void EvaluateColeColeModel(const Real& omega);
-
-            // ====================  ACCESS        ===========================
-
-            /** Sets the number of layers and resizes all model parameters to
-             *  be the correct size, finally initialises all values to free
-             *  space.
-             *  @param[in] nlay is the number of layers
-             */
-            virtual void SetNumberOfLayers(const int& nlay);
-
-            /** Sets Complex Conductivity of the layers
-             *  @param[in] sigma is a vector of the conducivity of the layers
-             */
-            void SetLayerConductivity(const VectorXcr &sigma);
-
-            /** Sets Complex Conductivity of a single layer
-             *  @param[in] sigma is  the conducivity of the layer
-             *  @param[in] ilay is  the layer index
-             */
-            void SetLayerConductivity(const int& ilay, const Complex &sigma);
-
-            /* Sets Complex resitivity of the layers
-             *  @param[in] ohm is a vector of the resistivity of the layers
-                Singularity at 0 resistivity in air. Need to reformaulat things a bit
-             */
-            //void SetLayerResistivity(const VectorXcr &ohm);
-
-            /** Sets the thickness of the layers
-             *  @param[in] thick is a vector of the thicknesses of the layers.
-             *  Must be two less than the total number of Layers as the top and
-             *  bottom layers are assumed infinite.
-             */
-            void SetLayerThickness(const VectorXr &thick);
-
-            /** Sets the High frequency susceptibility
-             */
-            void SetLayerHighFreqSusceptibility(const VectorXr& sushi);
-
-            /** Sets the Low frequency susceptibility
-             */
-            void SetLayerLowFreqSusceptibility(const VectorXr& sushi);
-
-            /** Sets the Layer breath susceptibility
-             */
-            void SetLayerBreathSusceptibility(const VectorXr& susbr);
-
-            /** Sets the Layer tau susceptibility
-             */
-            void SetLayerTauSusceptibility(const VectorXr& susta);
-
-            /** Sets the High frequency permitivity
-             */
-            void SetLayerHighFreqPermitivity(const VectorXr& sushi);
-
-            /** Sets the Low frequency permitivity
-             */
-            void SetLayerLowFreqPermitivity(const VectorXr& sushi);
-
-            /** Sets the Layer breath permitivity
-             */
-            void SetLayerBreathPermitivity(const VectorXr& oerbr);
-
-            /** Sets the Layer breath permitivity
-             */
-            void SetLayerTauPermitivity(const VectorXr& oerbr);
-
-            // ====================  INQUIRY       ===========================
-
-            /** Returns the thickness of a layer
-                @return a VectorXcr of the layer conductivities.
-             */
-            VectorXcr GetLayerConductivity( );
-
-            /** Returns the conductivity of a layer
-             *  @param[in] ilay is the layer indice of interest
-             *  @return the complex valued conductivity of the layer of
-             *  interest.
-             */
-            Complex GetLayerConductivity(const int &ilay);
-
-            /** Returns the susceptibility of a layer
-             *  @param[in] ilay is the layer indice of interest.
-             *  @return a Complex value of the electrical susceptibility of the
-             *  probes layer.
-             */
-            Complex GetLayerSusceptibility(const int &ilay);
-
-            /** Returns the Susceptibility of Cole-Cole model
-             *  @return a VectorXcr of the suceptibilities of the model.
-             */
-            VectorXcr GetLayerSusceptibility( );
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            Real GetLayerLowFreqSusceptibility(const int &ilay);
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            VectorXr GetLayerLowFreqSusceptibility( );
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            Real GetLayerHighFreqSusceptibility(const int &ilay);
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            VectorXr GetLayerHighFreqSusceptibility( );
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            Real GetLayerTauSusceptibility(const int &ilay);
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            VectorXr GetLayerTauSusceptibility( );
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            Real GetLayerBreathSusceptibility(const int &ilay);
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            VectorXr GetLayerBreathSusceptibility( );
-
-            /** Returns the Relative Permitivity of the cole cole model
-             */
-            VectorXcr GetLayerPermitivity( );
-
-            /** Returns the conductivity of a layer
-             *  @param[in] ilay is the layer indice of interest.
-             *  @return a Complex value of the electrical permitivity of the
-             *  probed layer.
-             */
-            Complex GetLayerPermitivity(const int &ilay);
-
-            /** Low Freq permivitity
-             */
-            VectorXr  GetLayerLowFreqPermitivity( );
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            Real GetLayerLowFreqPermitivity(const int &ilay);
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            Real GetLayerHighFreqPermitivity(const int &ilay);
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            VectorXr GetLayerHighFreqPermitivity( );
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            Real GetLayerTauPermitivity(const int &ilay);
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            VectorXr GetLayerTauPermitivity( );
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            Real GetLayerBreathPermitivity(const int &ilay);
-
-            /** Returns the low freq susceptibility of a layer
-             */
-            VectorXr GetLayerBreathPermitivity( );
-
-        protected:
-
-            // ====================  LIFECYCLE     ===========================
-
-            /** Default protected constructor. */
-            LayeredEarthEM (const std::string &name);
-
-            #ifdef HAVE_YAMLCPP
-            /** Default protected constructor. */
-			LayeredEarthEM (const YAML::Node& node);
-            #endif
-
-            /** Default protected constructor. */
-            ~LayeredEarthEM ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  DATA MEMBERS  ===========================
-
-            /** Vector of layer Conductivity */
-            VectorXcr         LayerConductivity;
-
-            /** Vector of layer Susceptibility (chi)
-             *  This is calculated using the Cole-Cole model
-             *  \f[ sus(i) = sush(i)
-             *   + \frac{(susl(i)-sush(i))}  {(1+(jw * sustau(i))^{susalp(i)})} \f]
-             */
-            VectorXcr         LayerSusceptibility;
-
-            /** Vector of low frequency susceptibility, for use in Cole-Cole
-              model */
-            VectorXr          LayerLowFreqSusceptibility;
-
-            /** Vector of high frequency susceptibility, for use in Cole-Cole
-             model */
-            VectorXr          LayerHighFreqSusceptibility;
-
-            /** Vector of relaxation time constants, for use in Cole-Cole model
-             */
-            VectorXr          LayerTauSusceptibility;
-
-            /** Vector relaxation breath, for use in Cole-Cole model
-             */
-            VectorXr          LayerBreathSusceptibility;
-
-            /** Vector of Layer Permitivity (epsilon)
-             *  Calculated using the Cole-Cole model
-             *  \f[ epr(i) = eprh(i)
-             *     + \frac{ (eprl(i)-eprh(i))}  { (1+(jw*eprtau(i))^{epralp(i)})} \f]
-             */
-            VectorXcr         LayerPermitivity;
-
-            /** Low frequency permitivity for each layer */
-            VectorXr          LayerLowFreqPermitivity;
-
-            /** High frequency permitivity for each layer */
-            VectorXr          LayerHighFreqPermitivity;
-
-            /** Decay time constant for each layer */
-            VectorXr          LayerTauPermitivity;
-
-            /** Relaxation breath for each layer */
-            VectorXr          LayerBreathPermitivity;
-
-    }; // -----  end of class  LayeredEarthEM  -----
-
-
-} // namespace Lemma
-
-#endif // __LAYEREDEARTHEM_H

LemmaCore/include/modelreader.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   M. Andy Kass
-  @date     02/18/2011
-  @version  $Id: modelreader.h 201 2015-01-03 00:07:47Z tirons $
- **/
-
-#ifndef __MODELREADER_H
-#define __MODELREADER_H
-
-#include "LemmaObject.h"
-#include "layeredearthem.h"
-#include "PolygonalWireAntenna.h"
-#include "receiverpoints.h"
-
-namespace Lemma {
-
-// ===================================================================
-//        Class:  ModelReader
-/// \brief Model and instrument reader for forward modelling.
-/// \details This is an abstract class.
-// ===================================================================
-class ModelReader : public LemmaObject {
-
-	friend std::ostream &operator<<(std::ostream &stream,
-		const ModelReader &ob);
-
-	public:
-
-		// ====================  LIFECYCLE     =======================
-
-		static ModelReader* New();
-
-		void Delete();
-
-		// ====================  OPERATORS     =======================
-
-		// ====================  OPERATIONS    =======================
-
-		// ====================  ACCESS        =======================
-
-		// ====================  INQUIRY       =======================
-
-
-
-	protected:
-
-		// ====================  LIFECYCLE     =======================
-
-		/// Default protected constructor.
-		ModelReader (const std::string &name);
-
-		/// Default protected constructor.
-		~ModelReader ();
-        /**
-        * @copybrief LemmaObject::Release()
-        * @copydetails LemmaObject::Release()
-        */
-		void Release();
-		// ====================  DATA MEMBERS  =========================
-
-	private:
-
-}; // -----  end of class  ModelReader  -----
-} // end of namespace lemma
-#endif // __MODELREADER_H
-

LemmaCore/include/modelreaderfem1d.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   M. Andy Kass
-  @date     01/03/2013
-  @version  $Id$
- **/
-
-#ifndef __MODELREADERFEM1D_H
-#define __MODELREADERFEM1D_H
-
-#include "modelreader.h"
-
-namespace Lemma {
-
-
-// ===================================================================
-//        Class:  ModelReaderFem1D
-/// \brief
-/// \details
-// ===================================================================
-	class ModelReaderFem1D : public ModelReader {
-
-		friend std::ostream &operator<<(std::ostream &stream,
-			const ModelReaderFem1D &ob);
-
-	public:
-
-	// ====================  LIFECYCLE     =======================
-
-	static ModelReaderFem1D* New();
-
-	void Delete();
-
-	// ====================  OPERATORS     =======================
-
-	// ====================  OPERATIONS    =======================
-
-	// ====================  ACCESS        =======================
-
-	// ====================  INQUIRY       =======================
-
-
-
-	protected:
-
-	// ====================  LIFECYCLE     =======================
-
-	/// Default protected constructor.
-	ModelReaderFem1D (const std::string &name);
-
-	/// Default protected constructor.
-	~ModelReaderFem1D ();
-
-	void Release();
-
-	// ====================  DATA MEMBERS  =========================
-
-	private:
-
-}; // -----  end of class  ModelReaderFem1D  -----
-} // end of namespace Lemma
-#endif // __MODELREADERFEM1D_H

LemmaCore/include/modelreadertem1d.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   M. Andy Kass
-  @date     02/19/2011
-  @version  $Id: modelreadertem1d.h 87 2013-09-05 22:44:05Z tirons $
- **/
-
-#ifndef __MODELREADERTEM1D_H
-#define __MODELREADERTEM1D_H
-
-#include "modelreader.h"
-
-namespace Lemma {
-
-// ===================================================================
-//        Class:  ModelReaderTem1D
-/// \brief Model reader class for forward modelling 1D TEM data
-/// \details This is a mostly abstract class.
-// ===================================================================
-class ModelReaderTem1D : public ModelReader {
-
-	friend std::ostream &operator<<(std::ostream &stream,
-		const ModelReaderTem1D &ob);
-
-	public:
-
-		// ====================  LIFECYCLE     =======================
-
-		static ModelReaderTem1D* New();
-
-		void Delete();
-
-		// ====================  OPERATORS     =======================
-
-		// ====================  OPERATIONS    =======================
-
-		//void ReadParameters(/* Pass file name */);
-
-		// ====================  ACCESS        =======================
-
-		// ====================  INQUIRY       =======================
-
-
-	protected:
-
-		// ====================  LIFECYCLE     =======================
-
-		/// Default protected constructor.
-		ModelReaderTem1D (const std::string &name);
-
-		/// Default protected constructor.
-		~ModelReaderTem1D ();
-
-		void Release();
-
-		/// Read in the Earth Model file and attach
-		//void ReadModel();
-
-		/// Read in the instrument parameters and attach
-		//void ReadInstrument();
-
-		/// Read in the waveform file (future)
-		//void ReadWaveform();
-
-		// ====================  DATA MEMBERS  =========================
-
-		//std::string modelfile;
-
-		//std::string instrumentfile;
-
-		//std::string waveformfile;
-
-	private:
-
-}; // -----  end of class  ModelReaderTem1D  -----
-} // end of namespace lemma
-#endif // __MODELREADERTEM1D_H

LemmaCore/include/modelreadertem1dubc.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   M. Andy Kass
-  @date     02/19/2011
-  @version  $Id: modelreadertem1dubc.h 87 2013-09-05 22:44:05Z tirons $
- **/
-
-#ifndef __MODELREADERTEM1DUBC_H
-#define __MODELREADERTEM1DUBC_H
-
-#include "modelreadertem1d.h"
-
-namespace Lemma {
-
-// ===================================================================
-//        Class:  ModelReaderTem1DUBC
-/// \brief Model reader class for forward modelling 1D TEM data
-/// \details Reads UBC 1D TEM forward model format
-// ===================================================================
-class ModelReaderTem1DUBC : public ModelReaderTem1D {
-
-	friend std::ostream &operator<<(std::ostream &stream,
-		const ModelReaderTem1DUBC &ob);
-
-	public:
-
-		// ====================  LIFECYCLE     =======================
-
-		static ModelReaderTem1DUBC* New();
-
-		void Delete();
-
-		// ====================  OPERATORS     =======================
-
-		// ====================  OPERATIONS    =======================
-
-		void ReadParameters(const std::string &params);
-
-		// ====================  ACCESS        =======================
-
-		/// Attaches a LayeredEarthEM object
-		void SetEMEarth1D(LayeredEarthEM* earth);
-
-		/// Attaches a WireAntenna object
-		void SetTransmitter(WireAntenna *antennae);
-
-		/// Attaches a ReceiverPoints object
-		void SetReceiver(ReceiverPoints* receiver);
-
-		VectorXr GetTimes();
-
-		// ====================  INQUIRY       =======================
-
-
-	protected:
-
-		// ====================  LIFECYCLE     =======================
-
-		/// Default protected constructor.
-		ModelReaderTem1DUBC (const std::string &name);
-
-		/// Default protected constructor.
-		~ModelReaderTem1DUBC ();
-
-		void Release();
-
-		/// Read in the Earth Model file and attach
-		void ReadModel();
-
-		/// Read in the instrument parameters and attach
-		void ReadInstrument();
-
-		/// Read in the waveform file (future)
-		void ReadWaveform();
-
-		// ====================  DATA MEMBERS  =========================
-
-		std::string modelfile;
-
-		std::string instrumentfile;
-
-		std::string waveformfile;
-
-		WireAntenna* Trans;
-
-		ReceiverPoints* Receivers;
-
-		LayeredEarthEM* EarthMod;
-
-		/// Simulated noise flag
-		bool addednoise;
-
-		/// Simulated noise percentage
-		Real noisepercent;
-
-		/// Baseline threshold percentage
-		Real noisethresh;
-
-		/// Seed for random number generator
-		Real noiseseed;
-
-		VectorXr receivermoment;
-
-		VectorXr modtimes;
-
-	private:
-
-}; // -----  end of class  ModelReaderTem1DUBC  -----
-} // end of namespace lemma
-#endif // __MODELREADERTEM1DUBC_H

LemmaCore/include/octreegrid.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     03/19/2010
-  @version  $Id: octreegrid.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  OCTREEGRID_INC
-#define  OCTREEGRID_INC
-
-// This class depends on VTK!
-
-#ifdef  LEMMAUSEVTK
-#include "grid.h"
-#include "vtkHyperOctree.h"        // In Filtering
-#include "vtkHyperOctreeCursor.h"
-#include "vtkHyperOctreeSampleFunction.h"
-#include "vtkImplicitFunction.h"
-#include "vtkCell.h"
-#include "vtkGenericCell.h"
-
-#ifdef  LEMMA_SINGLE_PRECISION
-#include "vtkFloatArray.h"
-#else      // -----  not LEMMA_SINGLE_PRECISION  -----
-#include "vtkDoubleArray.h"
-#endif     // -----  not LEMMA_SINGLE_PRECISION  -----
-
-#include "kernel.h"
-#include "receiverpoints.h"
-#include "receivercubes.h"
-#include "layeredearth.h"
-//#include "layeredearthnmr.h"
-#include "inversesolver.h"
-
-//#include "FastDelegate.h"
-//#include "FastDelegateBind.h"
-
-namespace Lemma {
-
-    // forward declaration
-    class InverseSolver ;
-
-    // ===================================================================
-    //        Class:  OctreeGrid
-    /** An Octree class, builds off VtkHyperOctree so this class can
-        only be used when compiled with VTK libs.
-        An Octree is a heirarchial 3D mesh with rectangular cells containing
-        either 0 or 8 children.
-     */
-    // ===================================================================
-    class OctreeGrid : public Grid {
-
-        friend class InverseSolver;
-        //friend class SNMRInversion1D;        // From Merlin Module
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const OctreeGrid &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /**
-             * new grid octreee
-             */
-            static OctreeGrid* New();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-            // ====================  OPERATORS     =======================
-
-
-            // ====================  ACCESS        =======================
-
-            /** Sets the kernel function to be used to make the mesh.
-             *  @param[in] kern is a kernel that is used to generate a mesh.
-             */
-            void SetKernel(Kernel* kern);
-
-            /// Sets a 1D model associated with this kernel.
-            /// @param[in] model1d is a pointer to a LayeredEarth model that
-            /// will be used to pre-subdivide leaves that overlap several
-            /// layers.
-            void SetLayeredEarth(LayeredEarth* model1d);
-
-            /** Sets the size of the mesh
-                @param[in] size is the size of the mesh. The mesh must start at
-                [0,0,0] and goes to [sizex, sizey, sizez].
-             */
-            void SetSize(const Vector3r& size);
-
-            /** Sets the origin of the mesh
-                @param[in] origin is the origin of the mesh.
-             */
-            void SetOrigin(const Vector3r& origin);
-
-            /** Sets the minimum depth to model. This must be greater than 0.
-                @param[in] depth is the new minimum depth.
-             */
-            void SetMinimumDepth(const Real& depth);
-
-            /** Fills in the leaf data with the kernel sensitivity
-             */
-            void FillMeshWithKernel();
-
-            /** Fills in the leaf data with the kernel sensitivity
-             */
-            void FillMeshWithKernel(vtkImplicitFunction* Impl);
-
-            /** Sets the size of the mesh
-             */
-            void SetSize(const Real &x, const Real &y, const Real &z);
-
-            /** Generates mesh to specified tolerance.
-             *  @param[in] tol is the kernel tolerance.
-             */
-            void GenerateMesh(const Real &tol);
-
-
-            /** Generates a mesh to specified tolerance, but initially splits
-             *  based on implicit function.
-             *  @param[in] tol is the kernel tolerance.
-             *  @param[in] Impl is the implicit dataset used for initial
-             *  subdivision
-             *  @param[in] impltol is the tolerance for the initial model based
-             *  subdividing.
-             */
-            void GenerateMesh(const Real& tol, vtkImplicitFunction* Impl,
-                              const Real& impltol);
-
-            /** Generates an Octree mesh using a pre-sampled input Octree Dataset.
-                Speeds up repeated kernel calculations when the underlying model in
-                the above ImplicitFunction needs to be called often or is complex.
-             */
-            void GenerateMesh(const Real& tol, vtkImplicitFunction* Impl,
-                    vtkHyperOctreeSampleFunction* OctSamp);
-
-            /** Evaluates the kernel on the mesh. In some cases this is the same thing
-                as generate mesh, but if more that one calculation are needed on a
-                mesh you can use this method. It interfaces with the kernels by
-                calling
-             */
-            Complex EvaluateKernelOnMesh();
-
-            /** Returns a receiver cube class that represents the same Geometry as the
-                HyperOctree. This is useful as it can be passed directly to em1dearth,
-                and currently, an Octree cannot. But this requires storage of all the
-                cell volumes and locations. In the future, you should be able to pass
-                around this class just like a ReceiverCubes.
-             */
-            void ReceiverCubeRepresentation();
-
-            /** Returns the receiver cube class. */
-            ReceiverCubes* GetReceiverCubes();
-
-            /** returns the kernel sum from generation */
-            Complex GetKernelSum();
-
-            /** Accessor to underlying vtkClass.
-             *  @return a vtkHyperOctree that can be used for visualization.
-             */
-            vtkHyperOctree* GetVtkHyperOctree( );
-
-            /** Traverse the data structure and call a function at each leaf
-             */
-            void TraverseAndCall(InverseSolver* Inverse);
-
-            /** Traverse the data structure and call a function at each leaf
-             */
-            void TraverseAndCall( vtkImplicitFunction* Impl );
-
-            /**
-             */
-            void TraverseLeaves(vtkImplicitFunction* Impl);
-
-            /**
-             */
-            void FollowExistingTree(vtkHyperOctree* Leader, vtkHyperOctreeCursor* LeaderCursor,
-                    vtkImplicitFunction* Impl);
-
-            // ====================  OPERATIONS    =======================
-
-            /** Binds any derived member function of a derived class of
-                LayeredEarth to SampleScalarFromLayeredEarthFD. This function is then
-                used to sample the Octree mesh for that parameter. The member function
-                needs to be of the type GetLayerXXX(const int Layer& lay).
-                @param[in] earth is a pointer to a derived class of LayeredEarth
-                @param[in] fcnptr is a function pointer to a member function. It
-                should be called like &LayeredEarthNMR::GetLayerPorosity
-                @param[in] name is a std::string identifier.
-             */
-            template <class Derived>
-            void SampleScalarFromLayeredEarth(LayeredEarth* earth,
-                    Real (Derived::*fcnptr)(const int& id), const std::string &name) {
-                std::cerr << "In octreegrid.h SampleScalrFromLayeredEarth FastDelegate method was "
-                         << "removed, need to fix with move semantics or function pointer." << std::endl;
-                exit(3);
-                //TODO fix SampleScalar below, as call to SampleScalarFromLayeredEarthFD is
-                //     removed there.
-/*
-                SampleScalarFromLayeredEarthFD.bind(static_cast<Derived*>(earth), fcnptr);
-                GetLayerInt.bind(earth, &LayeredEarth::GetLayerAtThisDepth);
-                // TODO, don't use KernelArray, instead create new Array, and set it
-                // in there. Then delete?
-                this->KernelArray->SetName(name.c_str());
-                this->KernelArray->SetNumberOfTuples(Octree->GetNumberOfLeaves());
-                SampleScalar();
-                this->Octree->GetLeafData()->SetScalars( KernelArray );
-                this->Octree->GetLeafData()->AddArray( KernelArray );
-*/
-            }
-
-            /** Sends cursor to root
-             */
-            void CursorToRoot();
-
-            // ====================  INQUIRY       =======================
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Default protected constructor. */
-            OctreeGrid (const std::string &name);
-
-            /** Default protected constructor. */
-            ~OctreeGrid ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  OPERATIONS    =======================
-
-            /** Used internally. The leaf data is saved and then set as the vtk leaf
-             *  data.
-             */
-            void SetLeafDataFromGridCreation();
-
-            /** Return position of leaf, returns centre location
-             */
-            void GetPosition( Real* p );
-
-            /* Used to fill leaf data with a scalar value from a layered earth
-             *  model
-             */
-            //fastdelegate::FastDelegate1< const int&, Real > SampleScalarFromLayeredEarthFD;
-
-            /* Used to get the Layer of delagated model.
-             */
-            //fastdelegate::FastDelegate1< const Real&, int >  GetLayerInt;
-
-            /** Recursively determines the mesh to use
-             */
-            void EvaluateKids( );
-
-            /** Recursively determines the mesh to use
-                @param[in] kval is the current leaf kernel value
-                           which may be reused in analysis.
-             */
-            void EvaluateKids( Complex kval );
-
-            /** Same as above, but uses an implict function.
-             */
-            void EvaluateKids (vtkImplicitFunction* Impl);
-
-            /** Same as above, but lets function value be passed directly
-             */
-            void EvaluateKids (const Real& fval, vtkImplicitFunction* Impl);
-
-            /** Same as above but is passed a static fval to reuse. Useful when underlying model is smooth
-             */
-            void EvaluateKidsStatic(const Real& fval);
-
-            /** Same as above, but lets function value be passed directly
-             */
-            void SampleFunction(vtkImplicitFunction* Impl);
-
-            /** Recursively determines the mesh to use
-             */
-            void FillGrid( );
-
-            /** Recursively determines the mesh to use
-             */
-            void FillGrid(vtkImplicitFunction* Impl);
-
-            /** Used internally to build a receiver cube representation
-             */
-            void AssembleReceiverCubes( );
-
-            /** Samples a scalar from a LayeredEarth object. Used internally and calls
-             *  SampleScalarFromLayeredEarthFD, which can be set using
-             *  SampleScalarFromLayeredEarth.
-             */
-            void SampleScalar();
-
-
-
-            // Returns ReceiverPoints for the Octree.
-            //void ComputeFieldOnOctree( WireAntenna* loop );
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-            Vector3r                Size;
-            Vector3r                Origin;
-            Vector3r                step;
-            Vector3r                cpos;
-
-            int                     level;
-            int                     maxlevel;
-            int                     index;
-            int                     counter;
-
-            Real                    cvol;
-            Real                    tvol;
-            Real                    tol;
-            Complex                 KernelSum;
-
-            Eigen::Matrix<Real, 8, 3> Posadd;
-
-            std::vector<Real>       leafdata;
-            std::vector<vtkIdType>  leafids;
-
-            Kernel                 *SenseKernel;
-            ReceiverCubes          *Cubes;
-            LayeredEarth           *Model1D;
-
-            vtkHyperOctree               *Octree;
-            vtkHyperOctreeCursor         *Cursor;
-            vtkHyperOctreeSampleFunction *OctSamp;
-
-            #ifdef  LEMMA_SINGLE_PRECISION
-            vtkFloatArray          *KernelArray;
-            #else      // -----  not LEMMA_SINGLE_PRECISION  -----
-            vtkDoubleArray         *KernelArray;
-            #endif     // -----  not LEMMA_SINGLE_PRECISION  -----
-            vtkDataArray           *SampleArray;
-
-    }; // -----  end of class  OctreeGrid  -----
-
-}       // -----  end of Lemma  name  -----
-
-#endif     // -----  not LEMMAUSEVTK  -----
-#endif   // ----- #ifndef OCTREEGRID_INC  -----

LemmaCore/include/pulse.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     02/05/2010
-  @version  $Id: pulse.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  _PULSE_H_INC
-#define  _PULSE_H_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    // =======================================================================
-    //        Class:  Pulse
-    /// \brief Pure abstract class defining interace to some sort of pulse.
-    /// \details
-    // =======================================================================
-    class Pulse : public LemmaObject {
-
-        public:
-
-            /** Recursively prints information about this object
-             */
-            friend std::ostream &operator<<(std::ostream &stream,
-                    const Pulse &ob);
-
-            // ====================  LIFECYCLE     ===========================
-
-            // ====================  OPERATORS     ===========================
-
-            // ====================  OPERATIONS    ===========================
-
-            // ====================  ACCESS        ===========================
-
-            // ====================  INQUIRY       ===========================
-
-            // ====================  DATA MEMBERS  ===========================
-
-        protected:
-
-            // ====================  LIFECYCLE     ===========================
-
-            /// Default protected constructor.
-            Pulse (const std::string &name);
-
-            /// Default protected constructor.
-            ~Pulse ();
-
-    }; // -----  end of class  Pulse  -----
-
-}       // -----  end of Lemma  name  -----
-
-
-#endif   // ----- #ifndef _PULSE_H_INC  -----

LemmaCore/include/quasinewtonbfgs.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     08/09/2010
-  @version  $Id: quasinewtonbfgs.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  QUASINEWTONBFGS_INC
-#define  QUASINEWTONBFGS_INC
-
-#include "inversesolver.h"
-
-namespace Lemma {
-
-
-    // ===================================================================
-    //  Class:  QuasiNewtonBFGS
-    /**
-      @class  QuasiNewtonBFGS
-      \brief  Implimentation of a quasi-newton BFGS solver applied to
-              inverse problems.
-      \details Based of the algorithm described in Nocedal and Wright book.
-     */
-    // ===================================================================
-    class QuasiNewtonBFGS : public InverseSolver {
-
-        friend  std::ostream &operator<<(std::ostream &stream,
-                const QuasiNewtonBFGS &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Returns a pointer to a new object of type QuasiNewtonBFGS.
-             * It allocates all necessary memory.
-             */
-            static QuasiNewtonBFGS* New();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-            /** @copybrief InverseSolver::NumberOfIterations()
-             *  @copydetails InverseSolver::NumberOfIterations()
-             */
-            int NumberOfIterations();
-
-            /** @copybrief InverseSolver::Success()
-             *  @copydetails InverseSolver::Success()
-             */
-            bool Success();
-
-            /** @copybrief InverseSolver::GetPhiMVector()
-             *  @copydetails InverseSolver::GetPhiMVector()
-             */
-            VectorXr GetPhiMVector();
-
-            /** @copybrief InverseSolver::GetPhiDVector()
-             *  @copydetails InverseSolver::GetPhiDVector()
-             */
-            VectorXr GetPhiDVector();
-
-            /// TODO remove this, test
-            void PrintNorm();
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            QuasiNewtonBFGS (const std::string& cname);
-
-            /// Default protected constructor.
-            ~QuasiNewtonBFGS ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  OPERATIONS    =======================
-
-            /// Just a filler
-            void FillInG(const Vector3r& pos, const Vector3r& step);
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-    }; // -----  end of class  QuasiNewtonBFGS  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef QUASINEWTONBFGS_INC  -----

LemmaCore/include/receivercubes.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     06/17/2010
-  @version  $Id: receivercubes.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  RECEIVERCUBES_INC
-#define  RECEIVERCUBES_INC
-
-#include "receiverpoints.h"
-
-namespace Lemma {
-
-
-    // ===================================================================
-    //        Class:  ReceiverCubes
-    /** This class builds on Reciver points, but supports a cube around
-     * each point. It is a direct descendent and may be used wherever
-     * ReceiverPoints is used
-     */
-    // ===================================================================
-    class ReceiverCubes : public ReceiverPoints {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const ReceiverCubes &ob);
-
-        friend class EmDipEarth1D;
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /**
-             *  Returns pointer to new DipoleSource. Location is
-             *  initialized to (0,0,0) type and polarization are
-             *  initialized  to nonworking values that will throw
-             *  exceptions if used.
-             */
-            static ReceiverCubes* New();
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /** Sets the number of reciver cubes.
-             *  This method also resizes all the dynamic vectors in the class
-             *  to support this size.
-             *  @param[in] nrec is the number of cubes in the class.
-             */
-            void SetNumberOfReceivers(const int &nrec);
-
-            /** Sets the length of the x dimension of a single cube.
-             * @param[in] i is the cube number.
-             * @param[in] lx is the length of this cube, in this dimension.
-             */
-            void SetLengthX(const int &i, const Real &lx);
-
-            /** Sets the length of the y dimension of a single cube.
-             * @param[in] i is the cube number.
-             * @param[in] ly is the length of this cube, in this dimension.
-             */
-            void SetLengthY(const int &i, const Real &ly);
-
-            /** Sets the length of the z dimension of a single cube.
-             * @param[in] i is the cube number.
-             * @param[in] lz is the length of this cube, in this dimension.
-             */
-            void SetLengthZ(const int &i, const Real &lz);
-
-            /** Sets the lengths of all three dimensions of a single cube.
-             * @param[in] i is the cube number.
-             * @param[in] lx is the length of this cube, in this dimension.
-             * @param[in] ly is the length of this cube, in this dimension.
-             * @param[in] lz is the length of this cube, in this dimension.
-             */
-            void SetLength(const int &i, const Real& lx, const Real& ly,
-                            const Real &lz);
-
-            /** Sets the length of the x dimension of a single cube.
-             * @param[in] i is the cube number.
-             * @param[in] V is a vector of lenths.
-             */
-            void SetLength(const int &i, const Vector3r &V);
-
-
-            /** Gets the x dimension of cube i
-              * @param[in] i is the cube in quesion
-              * @return The legth of the x dimension of cube i
-              */
-            Real GetLengthX(const int &i);
-
-            /** Gets the y dimension of cube i
-              * @param[in] i is the cube in quesion
-              * @return The length of the y dimension of cube i
-              */
-            Real GetLengthY(const int &i);
-
-            /** Gets the z dimension of cube i
-              * @param[in] i is the cube in quesion
-              * @return The length of the z dimension of cube i
-              */
-            Real GetLengthZ(const int &i);
-
-            /** Gets the z dimension of cube i
-              * @param[in] i is the cube in quesion
-              * @return A vector of the lengths of the cube
-              */
-            Vector3r GetLength(const int& i);
-
-            /** Returns the volume of a cube
-              * @param[in] i is the cube of interest
-              * @return is the volume
-              */
-            Real GetVolume(const int&i);
-
-            /** Returns the volume of all the receiver cubes.
-              */
-            Real GetVolumeSum();
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-            // Returns the volume of a cube.
-            //Real GetCubeVolume(const int&i);
-            //VectorXr GetCubeVolumes();
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            ReceiverCubes (const std::string &name);
-
-            /// Default protected constructor.
-            ~ReceiverCubes ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  DATA MEMBERS  =========================
-
-            /// Dimension of each cube stored here, first indice is x, second y, and
-            /// third z
-            Vector3Xr Lengths;
-
-        private:
-
-    }; // -----  end of class  ReceiverCubes  -----
-
-}       // -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef RECEIVERCUBES_INC  -----

LemmaCore/include/receiverpoints.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     12/02/2009
-  @version  $Id: receiverpoints.h 199 2014-12-29 19:25:20Z tirons $
- **/
-
-#ifndef __RECEIVERPOINTS_H
-#define __RECEIVERPOINTS_H
-
-#ifdef LEMMAUSEVTK
-#include "vtkPointData.h"
-#include "vtkFieldData.h"
-#include "vtkGlyph3D.h"
-#include "vtkArrowSource.h"
-#include "vtkActor.h"
-#include "vtkPolyDataMapper.h"
-#include "vtkPoints.h"
-#include "vtkPolyData.h"
-#include "vtkDoubleArray.h"
-#include "vtkDataObject.h"
-#endif
-
-#include "LemmaObject.h"
-#include "dipolesource.h"
-
-#ifdef HAVE_YAMLCPP
-#include "yaml-cpp/yaml.h"
-#endif
-
-namespace Lemma {
-
-    // =======================================================================
-    //        Class:  ReceiverPoints
-    /// \brief  Points in the subsurface to make EM calculations,
-    ///  more general than the grids.
-    // =======================================================================
-    class ReceiverPoints : public LemmaObject {
-
-        public:
-
-            // ====================    FRIENDS     ===========================
-
-            /** Stream operator printing out information about this class.
-             */
-            friend std::ostream &operator<<(std::ostream &stream,
-                        const ReceiverPoints &ob);
-
-            friend class EMEarth1D;
-            friend class DipoleSource;
-
-            // ====================  LIFECYCLE     ===========================
-
-            /**
-             *  Returns pointer to new DipoleSource. Location is
-             *  initialized to (0,0,0) type and polarization are
-             *  initialized  to nonworking values that will throw
-             *  exceptions if used.
-             */
-            static ReceiverPoints* New();
-
-
-            /**
-             * @copybrief LemmaObject::Delete()
-             * @copydetails LemmaObject::Delete()
-             */
-            void Delete();
-
-            // ====================  OPERATORS     ===========================
-
-            // ====================  OPERATIONS    ===========================
-
-            // ====================  ACCESS        ===========================
-
-            /// Sets the number of receivers
-            virtual void SetNumberOfReceivers(const int &nrec);
-
-            /// Returns the location of a single receiver as an Eigen Vector
-            void SetLocation(const int& nrec, const Vector3r& loc);
-
-            /// Returns the location of a single receiver as an Eigen Vector
-            void SetLocation(const int& nrec, const Real& xp, const Real& yp,
-                            const Real& zp);
-
-            // ====================  INQUIRY       ===========================
-
-            /// Returns the number of receiverpoints.
-            int GetNumberOfReceivers();
-
-            /// Returns all the receiver locations as a 3 X matrix
-            Vector3Xr GetLocations();
-
-            /// Returns all the receiver locations as a general matrix, useful for python wrapper
-            MatrixXr GetLocationsMat();
-
-            /// Returns the E field for all locations
-            /// nfreq is the freqency desired
-            Vector3Xcr GetEfield(const int &nfreq);
-
-            /// Returns the E field for all locations
-            /// nfreq is the freqency desired, cast to general dynamic matrix, for python interoperability
-            MatrixXcr GetEfieldMat(const int &nfreq);
-
-            /// Returns the H field for all locations
-            /// nfreq is the freqency desired, cast to general dynamic matrix, for python interoperability
-            MatrixXcr GetHfieldMat(const int &nfreq);
-
-            /// Returns the H field for all locations
-            /// nfreq is the freqency desired
-            Vector3Xcr GetHfield(const int &nfreq);
-
-            /// Returns all of the computed H fields. Every frequency
-            std::vector<Vector3Xcr> GetHfield( );
-
-            /// Returns all of the computed E fields. Every frequency
-            std::vector<Vector3Xcr> GetEfield( );
-
-            /// Returns the E field of a single receiver as an Eigen Vector
-            /// nfreq is the freqency desired
-            Vector3cr GetEfield(const int &nfreq, const int& loc);
-
-            /// Returns the H field of a single receiver as an Eigen Vector
-            /// nfreq is the freqency desired
-            Vector3cr GetHfield(const int &nfreq, const int& loc);
-
-            /// Returns the B field of a single receiver as an Eigen Vector
-            /// nfreq is the freqency desired
-            Vector3cr GetBfield(const int &nfreq, const int& loc);
-
-            #ifdef LEMMAUSEVTK
-            /// Returns vtk Glyph actor that can be placed into scenes
-            vtkActor* GetVtkGlyphActor(const FIELDTYPE &ftype,
-                const Real& clip, const Real &scale,
-                const int &nfreq);
-
-            /// Returns a vtk Data Object that can easily be plotted
-            vtkDataObject * GetVtkDataObject(const FIELDTYPE &ftype,
-                const int& nbin,
-                const int& start, const int& end,
-                const FIELDCOMPONENT& fcomp,
-                const SPATIALCOORDINANT& scord);
-
-            /// Returns a vtk Data Object that can easily be plotted
-            vtkDataObject * GetVtkDataObjectFreq(const FIELDTYPE &ftype,
-                const int& nrec,
-                const int& fstart, const int& fend,
-                const FIELDCOMPONENT& fcomp,
-                const VectorXr& Freqs);
-            #endif
-
-            /// Returns the location of a single receiver as an Eigen Vector
-            Vector3r GetLocation(const int& loc);
-
-            /// Returns the x component of the location
-            Real GetLocationX(const int& loc);
-
-            /// Returns the y component of the location
-            Real GetLocationY(const int& loc);
-
-            /// Returns the z component of the location
-            Real GetLocationZ(const int& loc);
-
-            /// Resets fields
-            void ClearFields();
-
-            /// Sets the mask variable to true for this point.
-            void MaskPoint(const int& i);
-
-            /// Turns the mask off for this point.
-            void UnMaskPoint(const int& i);
-
-            /// Removes making on all points
-            void UnMaskAllPoints();
-
-            /// Returns the mask for this point
-            int GetMask(const int& i);
-
-            #ifdef HAVE_YAMLCPP
-        	/**
-             *  Uses YAML to serialize this object.
-             *  @return a YAML::Node
-             */
-            YAML::Node Serialize() const;
-
-            /**
-             *   Constructs an object from a YAML::Node.
-             */
-            static ReceiverPoints* DeSerialize(const YAML::Node& node);
-            #endif
-
-        protected:
-
-            // ====================  LIFECYCLE     ===========================
-
-            /// Default protected constructor.
-            ReceiverPoints (const std::string& name);
-
-            #ifdef HAVE_YAMLCPP
-            /// Default protected constructor.
-            ReceiverPoints (const YAML::Node& node);
-            #endif
-
-            /// Default protected constructor.
-            ~ReceiverPoints ();
-
-            /**
-             * @copybrief LemmaObject::Release()
-             * @copydetails LemmaObject::Release()
-             */
-            void Release();
-
-            // ====================  OPERATIONS    ===========================
-
-            /// Sets the number of H bins. These bins are often frequencies.
-            void SetNumberOfBinsH(const int& nbins);
-
-            /// Sets the number of E bins. These bins are often frequencies.
-            void SetNumberOfBinsE(const int& nbins);
-
-            /** Internal function that resizes the EField data structure */
-            void ResizeEField();
-
-            /** Internal function that resizes the HField data structure */
-            void ResizeHField();
-
-            /// Sets the value of the E field
-            void SetEfield(const int &nfreq, const int& loc,
-                const Complex &ex, const Complex &ey, const Complex &ez);
-
-            /// Sets the value of the H field
-            void SetHfield(const int &nfreq, const int& loc,
-                const Complex &hx, const Complex &hy, const Complex &hz);
-
-            /// Appends the value of the E field. This method is not
-            /// thread safe.
-            void AppendEfield(const int&nfreq, const int& loc,
-                const Complex &ex, const Complex &ey, const Complex &ez);
-
-            /// Appends the value of the H field. This method is not
-            /// thread safe.
-            void AppendHfield(const int &nfreq, const int& loc,
-                const Complex &hx, const Complex &hy, const Complex &hz);
-
-            // ====================  DATA MEMBERS  ===========================
-
-            /// Number of receivers
-            int                         NumberOfReceivers;
-
-            /// Number of fields
-            int                         NumberOfBinsE;
-
-            /// Number of fields
-            int                         NumberOfBinsH;
-
-            /// Used to mask this point so no computation is made at
-            /// this point.
-            VectorXi                    Mask;
-
-            /// Locations of receivers
-            Vector3Xr                   Locations;
-
-        private:
-
-            // NOTE, these are not serialized in output!
-
-            /// Electric field at receiver locations
-            std::vector<Vector3Xcr>     Efield;
-
-            /// H field at receiver locations
-            std::vector<Vector3Xcr>     Hfield;
-
-    }; // -----  end of class  ReceiverPoints  -----
-}
-
-#endif // __RECEIVERPOINTS

LemmaCore/include/sintransintegrationkernel.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     02/08/2011
-  @version  $Id: sintransintegrationkernel.h 87 2013-09-05 22:44:05Z tirons $
- **/
-
-#ifndef  SINTRANSINTEGRATIONKERNEL_INC
-#define  SINTRANSINTEGRATIONKERNEL_INC
-
-#include "integrationkernel.h"
-
-namespace Lemma {
-
-    // ===================================================================
-    //  Class:  SinTransIntegrationKernel
-    /**
-      @class
-      \brief    Integration kernel for testing sinine transform.
-      \details  Evaluates sinine at the argument, using lagged convolution.
-                all of these kernels have exact solutions.
-     */
-    // ===================================================================
-    class SinTransIntegrationKernel : public IntegrationKernel<Real> {
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Returns a pointer to a new object of type SinTransIntegrationKernel.
-             * It allocates all necessary memory.
-             */
-            static SinTransIntegrationKernel* New();
-
-            /** Deletes this object. Delete also disconnects any
-             * attachments to this object.
-             */
-            void Delete();
-
-            // ====================  OPERATORS     =======================
-
-            Real Argument(const Real&x, const int& iRelated);
-
-            int GetNumRel();
-
-            /// Sets the value 'A' used in test cases
-            void SetA(const Real& A);
-
-            /** Sets the integral to evaluate (1, 2, 3)
-             */
-            void SetIntegral(const int& i);
-
-            /** Returns the analytical answer at A and B */
-            Real GetAnalytical(const Real& B);
-            // ====================  OPERATIONS    =======================
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Deletes this object. Delete also disconnects any
-             * attachments to this object.
-             */
-            void Release();
-
-            /// Default protected constructor.
-            SinTransIntegrationKernel (const std::string& name);
-
-            /// Default protected constructor.
-            ~SinTransIntegrationKernel ();
-
-            // ====================  DATA MEMBERS  =========================
-
-            /** Value used in test cases  */
-            Real A;
-
-            /** Test integral to evaluate */
-            int Integral;
-
-        private:
-
-    }; // -----  end of class  SinTransIntegrationKernel  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef SINTRANSINTEGRATIONKERNEL_INC  -----

LemmaCore/include/temintegrationkernel.h

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   M. Andy Kass
-  @date     02/10/2011
-  @version  $Id: temintegrationkernel.h 190 2014-10-16 23:02:09Z tirons $
- **/
-
-#ifndef __TEMINTEGRATIONKERNEL_H
-#define __TEMINTEGRATIONKERNEL_H
-
-#include "integrationkernel.h"
-#include "emearth1d.h"
-
-namespace Lemma {
-
-
-// ===================================================================
-//        Class:  TemIntegrationKernel
-/// \brief  Integration kernel for calculation of TEM data
-/// \details Calculates the integration kernel for the sine transform
-// ===================================================================
-
-class TemIntegrationKernel : public IntegrationKernel<Real>{
-
-	//friend std::ostream &operator<<(std::ostream &stream,
-	//	const TemIntegrationKernel &ob);
-
-	public:
-
-	// ====================  LIFECYCLE     =======================
-
-		static TemIntegrationKernel* New();
-
-		void Delete();
-
-	// ====================  OPERATORS     =======================
-
-	// ====================  OPERATIONS    =======================
-
-	// ====================  ACCESS        =======================
-
-		/// Calculates the integration argument.  Passed a frequency.
-		Real Argument(const Real&x, const int& iRelated);
-
-		int GetNumRel();
-
-		/// Attach EMEarth1D object to TemIntegrationKernel
-		void SetEMEarth1D(EMEarth1D* earth);
-
-		/// Attach Transmitter object
-		void SetTransmitter(WireAntenna *antennae);
-
-		/// Attach Dipole object
-		void SetDipole(DipoleSource* dipolesource);
-
-		/// Attach Receiver object
-		void SetReceiver(ReceiverPoints *receiver);
-
-        /**
-         *   @param[in] comp is the component to integrate
-         */
-        void SetComponent(const FIELDCOMPONENT& comp);
-	// ====================  INQUIRY       =======================
-
-
-
-	protected:
-
-	// ====================  LIFECYCLE     =======================
-
-		/// Default protected constructor.
-		TemIntegrationKernel (const std::string& name);
-
-		/// Default protected constructor.
-		~TemIntegrationKernel ();
-
-		void Release();
-
-	// ====================  DATA MEMBERS  =========================
-
-        FIELDCOMPONENT  component;
-
-		EMEarth1D* EmEarthInt;
-
-		WireAntenna* Trans;
-
-		DipoleSource* DipoleS;
-
-		ReceiverPoints* Receivers;
-
-	private:
-
-}; // -----  end of class  TemIntegrationKernel  -----
-
-} // End of namespace Lemma
-
-#endif // __TEMINTEGRATIONKERNEL_H

LemmaCore/src/ASCIIParser.cpp

 
     //--------------------------------------------------------------------------------------
     //       Class:  ASCIIParser
-    //      Method:  New()
-    // Description:  public constructor
+    //      Method:  NewSP()
+    // Description:  public smart pointer factory constructor
     //--------------------------------------------------------------------------------------
-    ASCIIParser* ASCIIParser::New() {
-        ASCIIParser*  Obj = new ASCIIParser("ASCIIParser");
-        Obj->AttachTo(Obj);
-        return Obj;
+    std::shared_ptr< ASCIIParser > ASCIIParser::NewSP() {
+        std::shared_ptr<ASCIIParser> sp(new  ASCIIParser("ASCIIParser"), LemmaObjectDeleter() );
+        return sp;
     }
 
     //--------------------------------------------------------------------------------------
 
     //--------------------------------------------------------------------------------------
     //       Class:  ASCIIParser
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void ASCIIParser::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
     //      Method:  Release
     // Description:  destructor (protected)
     //--------------------------------------------------------------------------------------

LemmaCore/src/CMakeLists.txt

 set (SOURCE 
 	${SOURCE}
-	${CMAKE_CURRENT_SOURCE_DIR}/AEMSurvey.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/AEMSurveyReader.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/ASCIIParser.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/helper.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/banner.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/costransintegrationkernel.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/ASCIIParser.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/CubicSplineInterpolator.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/data.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/datafem.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/datareader.cpp
-#	${CMAKE_CURRENT_SOURCE_DIR}/datareaderfem.cpp
-#	${CMAKE_CURRENT_SOURCE_DIR}/datareaderfemubc.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/datareadertem.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/datatem.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/DCIPElectrode.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/DCSurvey.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/digitalfiltercostrans.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/digitalfilterintegrator.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/digitalfiltersintrans.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/dipolesource.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/earthmodel.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/emearth1d.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/emearth3d.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/FHTKey101.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/FHTKey51.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/FHTKey.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/filter.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/gaussianquadrature.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/grid.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/GroundedElectricDipole.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/hankeltransform.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/hankeltransformgaussianquadrature.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/hankeltransformhankel2.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/helper.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/instrument.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/instrumentfem.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/instrumenttem.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/integrator.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/inversesolver.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/inversesolvertem1d.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/kernel.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/kernelem1dmanager.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/kernelem1dreflspec.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/kernelem1dspec.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/layeredearth.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/layeredearthem.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/LayeredEarthEMReader.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/lemma.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/Data.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/DataReader.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/EarthModel.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/Instrument.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/LayeredEarth.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/LemmaObject.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/MagneticDipole.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/modelreader.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/modelreaderfem1d.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/modelreadertem1d.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/modelreadertem1dubc.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/octreegrid.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/ParticleSwarmOptimizer.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/PolygonalWireAntenna.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/pulse.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/quasinewtonbfgs.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/QWEKey.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/receivercubes.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/receiverpoints.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/rectilineargrid.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/Grid.cpp       
+	${CMAKE_CURRENT_SOURCE_DIR}/RectilinearGrid.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/RectilinearGridReader.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/RectilinearGridVTKExporter.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/sintransintegrationkernel.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMInductiveReceiver.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/temintegrationkernel.cpp
-#	${CMAKE_CURRENT_SOURCE_DIR}/integrationkernel.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMReceiver.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMSurvey.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMSurveyData.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMSurveyLine.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMSurveyLineData.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMSurveyLineRecord.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMSurveyLineRecordData.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/TEMTransmitter.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/UngroundedElectricDipole.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/windowfilter.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/WireAntenna.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/Filter.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/WindowFilter.cpp
 	PARENT_SCOPE
 )
-
-

LemmaCore/src/CubicSplineInterpolator.cpp

 
     //--------------------------------------------------------------------------------------
     //       Class:  CubicSplineInterpolator
-    //      Method:  New()
+    //      Method:  NewSP()
     // Description:  public constructor
     //--------------------------------------------------------------------------------------
-    CubicSplineInterpolator* CubicSplineInterpolator::New() {
-        CubicSplineInterpolator*  Obj = new CubicSplineInterpolator("CubicSplineInterpolator");
-        Obj->AttachTo(Obj);
-        return Obj;
+    std::shared_ptr<CubicSplineInterpolator> CubicSplineInterpolator::NewSP() {
+        std::shared_ptr<CubicSplineInterpolator> sp(new  CubicSplineInterpolator("CubicSplineInterpolator"), LemmaObjectDeleter() );
+        return sp;
     }
 
     //--------------------------------------------------------------------------------------
 
     //--------------------------------------------------------------------------------------
     //       Class:  CubicSplineInterpolator
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void CubicSplineInterpolator::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
     //      Method:  Release
     // Description:  destructor (protected)
     //--------------------------------------------------------------------------------------

LemmaCore/src/DCIPElectrode.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      11/10/2014 10:53:53 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include "DCIPElectrode.h"
-
-namespace Lemma {
-
-
-
-    // ====================  FRIEND METHODS  =====================
-#ifdef HAVE_YAMLCPP
-    std::ostream &operator << (std::ostream &stream, const DCIPElectrode &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulate thingy
-        return stream;
-    }
-#else
-    std::ostream &operator<<(std::ostream &stream, const DCIPElectrode& ob) {
-        stream << *(LemmaObject*)(&ob);
-        return stream;
-    }
-#endif
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  DCIPElectrode
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    DCIPElectrode::DCIPElectrode (const std::string& name) : LemmaObject(name), Node_ID(-1), Label(std::string("None")) {
-
-    }  // -----  end of method DCIPElectrode::DCIPElectrode  (constructor)  -----
-
-#ifdef HAVE_YAMLCPP
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  DCIPElectrode
-    // Description:  DeSerializing constructor (protected)
-    //--------------------------------------------------------------------------------------
-    DCIPElectrode::DCIPElectrode (const YAML::Node& node) : LemmaObject(node) {
-        if (node.Tag() != this->Name) {
-            throw std::runtime_error("In DCIPElectrode(node), node is of wrong type");
-        }
-        this->Location = node["Location"].as<Vector3r>();
-        this->Node_ID = node["Node_ID"].as<int>();
-        this->Label = node["Label"].as<std::string>();
-    }  // -----  end of method DCIPElectrode::DCIPElectrode  (constructor)  -----
-#endif
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    DCIPElectrode* DCIPElectrode::New() {
-        DCIPElectrode*  Obj = new DCIPElectrode("DCIPElectrode");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  ~DCIPElectrode
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    DCIPElectrode::~DCIPElectrode () {
-
-    }  // -----  end of method DCIPElectrode::~DCIPElectrode  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void DCIPElectrode::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void DCIPElectrode::Release() {
-        delete this;
-    }
-
-
-#ifdef HAVE_YAMLCPP
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  Serialize
-    //--------------------------------------------------------------------------------------
-    YAML::Node  DCIPElectrode::Serialize (  ) const {
-        YAML::Node node = LemmaObject::Serialize();
-        node.SetTag( this->Name );
-        // FILL IN CLASS SPECIFICS HERE
-        node["Location"] = Location;
-        node["Node_ID"] = Node_ID;
-        node["Label"] = Label;
-        return node;
-    }		// -----  end of method DCIPElectrode::Serialize  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  DeSerialize
-    //--------------------------------------------------------------------------------------
-    DCIPElectrode* DCIPElectrode::DeSerialize ( const YAML::Node& node  ) {
-        DCIPElectrode* Object = new DCIPElectrode(node);
-        Object->AttachTo(Object);
-        DESERIALIZECHECK( node, Object )
-        return Object ;
-    }		// -----  end of method DCIPElectrode::DeSerialize  -----
-#endif
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  SetLocation
-    //--------------------------------------------------------------------------------------
-    void DCIPElectrode::SetLocation ( const Vector3r& loc ) {
-        Location = loc;
-        return ;
-    }		// -----  end of method DCIPElectrode::SetLocation  -----
-
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  SetTag
-    //--------------------------------------------------------------------------------------
-    void DCIPElectrode::SetLabel ( const std::string& inLabel  ) {
-        Label = inLabel;
-        return ;
-    }		// -----  end of method DCIPElectrode::SetTag  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCIPElectrode
-    //      Method:  get_Label
-    //--------------------------------------------------------------------------------------
-    std::string DCIPElectrode::GetLabel (  ) {
-        return Label;
-    }		// -----  end of method DCIPElectrode::get_Label  -----
-
-
-}		// -----  end of Lemma  name  -----
-

LemmaCore/src/DCSurvey.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      10/08/2014 01:52:04 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include	"DCSurvey.h"
-
-namespace Lemma {
-
-
-    // ====================  FRIEND METHODS  =====================
-
-    #ifdef HAVE_YAMLCPP
-    std::ostream &operator << (std::ostream &stream, const DCSurvey &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- a direct stream should encapsulate object
-        return stream;
-    }
-    #else
-    std::ostream &operator<<(std::ostream &stream, const DCSurvey &ob) {
-        stream << *(LemmaObject*)(&ob);
-        return stream;
-    }
-    #endif
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  DCSurvey
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    DCSurvey::DCSurvey (const std::string& name) : LemmaObject(name) {
-
-    }  // -----  end of method DCSurvey::DCSurvey  (constructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  DCSurvey
-    // Description:  DeSerializing constructor (protected)
-    //--------------------------------------------------------------------------------------
-    #ifdef HAVE_YAMLCPP
-    DCSurvey::DCSurvey (const YAML::Node& node) : LemmaObject(node) {
-
-        if (node.Tag() != "DCSurvey") {
-            throw std::runtime_error("DCSurvey->DeSerialize cannot deserialize non-DCSurvey");
-        }
-
-        std::map<YAML::Node, int>  eMap;
-        for(YAML::const_iterator it=node["Electrodes"].begin(); it!=node["Electrodes"].end(); ++it) {
-            std::string e = it->first.as<std::string>();
-            Electrodes.push_back( DCIPElectrode::DeSerialize( node["Electrodes"][e] ) );
-            Electrodes[Electrodes.size()-1]->AttachTo(this);
-            eMap[ node["Electrodes"][Electrodes.size()-1] ] = Electrodes.size() -1 ;
-            OrderedElectrodeLabels.push_back(e);
-            ElectrodeLabelMap[e] = std::pair<DCIPElectrode*, int>(Electrodes[Electrodes.size()-1], Electrodes.size()-1);
-        }
-
-        //std::cout << "J-0\n" << node["Injections"]["J-0"] << std::endl;
-        int ij = 0 ;
-        for(YAML::const_iterator it=node["Injections"].begin(); it!=node["Injections"].end(); ++it) {
-
-            //std::cout << "it->first" << it->first << std::endl;
-
-            A_Electrodes.push_back( ElectrodeLabelMap[ it->second["A"]["Label"].as<std::string>() ].second );
-            B_Electrodes.push_back( ElectrodeLabelMap[ it->second["B"]["Label"].as<std::string>() ].second );
-            J_Electrodes.push_back( it->second["J"].as<Real>() );
-            //std::string Jstr = it->first.as<std::string>(); // J-1
-
-            M_Electrodes.push_back( std::vector<int>() );
-            N_Electrodes.push_back( std::vector<int>() );
-
-            for (int ii=0; ii<it->second["Measurements"]["Number"].as<int>(); ++ii) {
-                std::string Mstr = std::string("V-") + to_string(ii);
-                //std::cout << "measurements" << it->second["Measurements"][Mstr]["M"]["Label"] << std::endl;
-                M_Electrodes[ij].push_back( ElectrodeLabelMap[ it->second["Measurements"][Mstr]["M"]["Label"].as<std::string>() ].second );
-                N_Electrodes[ij].push_back( ElectrodeLabelMap[ it->second["Measurements"][Mstr]["N"]["Label"].as<std::string>() ].second );
-            }
-            ++ ij;
-        }
-
-    }  // -----  end of method DCSurvey::DCSurvey  (constructor)  -----
-    #endif
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    DCSurvey* DCSurvey::New() {
-        DCSurvey*  Obj = new DCSurvey("DCSurvey");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  ~DCSurvey
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    DCSurvey::~DCSurvey () {
-
-    }  // -----  end of method DCSurvey::~DCSurvey  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void DCSurvey::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void DCSurvey::Release() {
-        this->PullElectrodes();
-        delete this;
-    }
-
-    #ifdef HAVE_YAMLCPP
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  Serialize
-    //--------------------------------------------------------------------------------------
-    YAML::Node  DCSurvey::Serialize (  ) const {
-        YAML::Node node = LemmaObject::Serialize();
-        node.SetTag( this->Name );
-        node["NumberOfElectrodes"] = Electrodes.size();
-
-        // All the electrodes
-        for (std::map<std::string, std::pair<DCIPElectrode*, int> >::const_iterator it  = ElectrodeLabelMap.begin();
-                                                                                    it != ElectrodeLabelMap.end(); ++it) {
-            node["Electrodes"][ it->first ] = it->second.first->Serialize();
-        }
-
-        // Injections and Measurements
-        for (unsigned int ic=0; ic<A_Electrodes.size(); ++ic) {
-            std::string strLab = std::string("J-") + to_string(ic);
-            node["Injections"][strLab]["A"] = node["Electrodes"][ OrderedElectrodeLabels[ A_Electrodes[ic] ] ];
-            node["Injections"][strLab]["B"] = node["Electrodes"][ OrderedElectrodeLabels[ B_Electrodes[ic] ] ];
-            node["Injections"][strLab]["J"] = J_Electrodes[ic];
-            node["Injections"][strLab]["Measurements"]["Number"] = M_Electrodes[ic].size();
-            for (unsigned int iv=0; iv<M_Electrodes[ic].size(); ++iv) {
-                node["Injections"][strLab]["Measurements"][std::string("V-") + to_string(iv)]["M"] =
-                    node["Electrodes"][ OrderedElectrodeLabels[M_Electrodes[ic][iv]] ];
-                node["Injections"][strLab]["Measurements"][std::string("V-") + to_string(iv)]["N"] =
-                    node["Electrodes"][ OrderedElectrodeLabels[N_Electrodes[ic][iv]] ];
-            }
-        }
-
-        return node;
-    }		// -----  end of method DCSurvey::Serialize  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  DeSerialize
-    //--------------------------------------------------------------------------------------
-    DCSurvey* DCSurvey::DeSerialize ( const YAML::Node& node  ) {
-        DCSurvey* Object = new DCSurvey(node);
-        Object->AttachTo(Object);
-        DESERIALIZECHECK( node, Object )
-        return Object ;
-    }		// -----  end of method DCSurvey::DeSerialize  -----
-    #endif
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  PoundElectrode
-    //--------------------------------------------------------------------------------------
-    int DCSurvey::PoundElectrode ( DCIPElectrode* Electrode, const std::string& tag, const int&nodeID ) {
-        Electrodes.push_back(Electrode);
-        if (tag != "NULL") {
-            OrderedElectrodeLabels.push_back(tag);
-            //ElectrodeTagMap[tag] = Electrode;
-            ElectrodeLabelMap[tag] = std::pair<DCIPElectrode*, int> (Electrode, Electrodes.size()-1);
-            Electrode->SetLabel(tag);
-        } else {
-            OrderedElectrodeLabels.push_back( std::string("E") + to_string(Electrodes.size()-1) );
-            //ElectrodeTagMap[std::string("E") + to_string(Electrodes.size()-1)] = Electrode;
-            ElectrodeLabelMap[std::string("E") + to_string(Electrodes.size()-1)] =
-                std::pair<DCIPElectrode*, int>(Electrode, Electrodes.size()-1);
-            Electrode->SetLabel( std::string("E") + to_string(Electrodes.size()-1) );
-        }
-        Electrode->AttachTo(this);
-        return  static_cast<int>( Electrodes.size() ) ;
-    }		// -----  end of method DCSurvey::PoundElectrode  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  PoundElectrode
-    //--------------------------------------------------------------------------------------
-    DCIPElectrode* DCSurvey::PoundElectrode ( const Vector3r& loc, const std::string& tag, const int& nodeID ) {
-        DCIPElectrode* Electrode = DCIPElectrode::New();
-            Electrode->SetLocation( loc );
-        Electrodes.push_back(Electrode);
-        if (tag != "NULL") {
-            OrderedElectrodeLabels.push_back(tag);
-            ElectrodeLabelMap[tag] = std::pair<DCIPElectrode*, int> (Electrode, Electrodes.size()-1);
-            Electrode->SetLabel(tag);
-        } else {
-            OrderedElectrodeLabels.push_back( std::string("E") + to_string(Electrodes.size()-1) );
-            ElectrodeLabelMap[std::string("E") + to_string(Electrodes.size()-1)] =
-                std::pair<DCIPElectrode*, int>(Electrode, Electrodes.size()-1);
-            Electrode->SetLabel( std::string("E") + to_string(Electrodes.size()-1) );
-        }
-        Electrode->AttachTo(this);
-        return  Electrode;
-    }		// -----  end of method DCSurvey::PoundElectrode  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  PoundElectrode
-    //--------------------------------------------------------------------------------------
-#ifdef LEMMAUSEVTK
-    DCIPElectrode* DCSurvey::PoundElectrode( const int& nodeID, vtkDataSet* Mesh, const std::string& tag ) {
-        DCIPElectrode* Electrode = DCIPElectrode::New();
-        double* loc = Mesh->GetPoint(nodeID);
-        Electrode->SetLocation( Vector3r(loc[0], loc[1], loc[2]) );
-        Electrodes.push_back(Electrode);
-        if (tag != "NULL") {
-            OrderedElectrodeLabels.push_back(tag);
-            ElectrodeLabelMap[tag] = std::pair<DCIPElectrode*, int> (Electrode, Electrodes.size()-1);
-            Electrode->SetLabel(tag);
-        } else {
-            OrderedElectrodeLabels.push_back( std::string("E") + to_string(Electrodes.size()-1) );
-            ElectrodeLabelMap[std::string("E") + to_string(Electrodes.size()-1)] =
-                std::pair<DCIPElectrode*, int>(Electrode, Electrodes.size()-1);
-            Electrode->SetLabel( std::string("E") + to_string(Electrodes.size()-1) );
-        }
-        Electrode->AttachTo(this);
-        return Electrode;
-    }		// -----  end of method DCSurvey::PoundElectrode  -----
-#endif
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  PullElectrodes
-    //--------------------------------------------------------------------------------------
-    void DCSurvey::PullElectrodes (  ) {
-        for (std::vector<DCIPElectrode*>::iterator it = Electrodes.begin() ; it != Electrodes.end(); ++it) {
-            (*it)->DetachFrom(this);
-        }
-        Electrodes.clear();
-        OrderedElectrodeLabels.clear();
-        ElectrodeLabelMap.clear();
-        A_Electrodes.clear();
-        B_Electrodes.clear();
-        M_Electrodes.clear();
-        N_Electrodes.clear();
-
-        return ;
-    }		// -----  end of method DCSurvey::PullElectrodes  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  AddInjection
-    //--------------------------------------------------------------------------------------
-    int DCSurvey::AddInjection ( DCIPElectrode* A, DCIPElectrode* B, const Real& J ) {
-        bool fA = false;
-        bool fB = false;
-        for (unsigned int i=0; i<Electrodes.size(); ++i) {
-            if (Electrodes[i] == A) {
-                A_Electrodes.push_back(i);
-                M_Electrodes.push_back( std::vector<int>() );
-                N_Electrodes.push_back( std::vector<int>() );
-                fA = true;
-            }
-            if (Electrodes[i] == B) {
-                B_Electrodes.push_back(i);
-                fB = true;
-            }
-            if (fA == true && fB == true) break;
-        }
-        if (!fA) {
-            throw std::runtime_error( "Injection point A not found" );
-        }
-        if (!fB) {
-            throw std::runtime_error( "Injection point B not found" );
-        }
-        J_Electrodes.push_back(J);
-        return A_Electrodes.size()-1; // we want index
-    }		// -----  end of method DCSurvey::AddInjection  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  AddMeasurement
-    //--------------------------------------------------------------------------------------
-    void DCSurvey::AddMeasurement ( const int& iJ, DCIPElectrode* M, DCIPElectrode* N  ) {
-        bool fM = false;
-        bool fN = false;
-        for (unsigned int i=0; i<Electrodes.size(); ++i) {
-            if (Electrodes[i] == M) {
-                M_Electrodes[iJ].push_back(i);
-                fM = true;
-            }
-            if (Electrodes[i] == N) {
-                N_Electrodes[iJ].push_back(i);
-                fN = true;
-            }
-            if (fM == true && fN == true) break;
-        }
-        if (!fM) {
-            throw std::runtime_error( "Injection point M not found" );
-        }
-        if (!fN) {
-            throw std::runtime_error( "Injection point N not found" );
-        }
-        return ;
-    }		// -----  end of method DCSurvey::AddMeasurement  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  AddMeasurement
-    //--------------------------------------------------------------------------------------
-
-    void DCSurvey::AddMeasurement ( const int& iJ, const std::string& M, const std::string& N ) {
-
-        std::pair<DCIPElectrode*, int> Mp = ElectrodeLabelMap[M];
-        std::pair<DCIPElectrode*, int> Np = ElectrodeLabelMap[N];
-
-        if (Mp.first == NULL) {
-            throw std::runtime_error( "Injection point M not found" );
-        }
-        if (Np.first == NULL) {
-            throw std::runtime_error( "Injection point N not found" );
-        }
-
-        M_Electrodes[iJ].push_back( Mp.second );
-        N_Electrodes[iJ].push_back( Np.second );
-
-        return ;
-    }		// -----  end of method DCSurvey::AddMeasurement  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  GetA
-    //--------------------------------------------------------------------------------------
-    void DCSurvey::GetA (const int& iA, int& iB, Real& J ) {
-        iB = Electrodes[A_Electrodes[iA]]->GetNodeID();
-        J = J_Electrodes[iA];
-        return ;
-    }		// -----  end of method DCSurvey::GetA  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  DCSurvey
-    //      Method:  GetB
-    //--------------------------------------------------------------------------------------
-    void DCSurvey::GetB (const int& iA, int& iB, Real& J ) {
-        iB = Electrodes[B_Electrodes[iA]]->GetNodeID();
-        J = -J_Electrodes[iA];
-        return ;
-    }		// -----  end of method DCSurvey::GetA  -----
-
-
-}		// -----  end of Lemma  name  -----
-

LemmaCore/src/data.cpp → LemmaCore/src/Data.cpp

   @version  $Id: data.cpp 193 2014-11-10 23:51:41Z tirons $
  **/
 
-#include "data.h"
+#include "Data.h"
 
 namespace Lemma {
 

LemmaCore/src/datareader.cpp → LemmaCore/src/DataReader.cpp

   @version  $Id: datareader.cpp 193 2014-11-10 23:51:41Z tirons $
  **/
 
-#include "datareader.h"
+#include "DataReader.h"
 
 namespace Lemma {
 

LemmaCore/src/earthmodel.cpp → LemmaCore/src/EarthModel.cpp

   @version  $Id: earthmodel.cpp 210 2015-02-25 02:57:03Z tirons $
  **/
 
-#include "earthmodel.h"
+#include "EarthModel.h"
 
 namespace Lemma {
 
 
     YAML::Node EarthModel::Serialize() const {
         YAML::Node node = LemmaObject::Serialize();
-        node.SetTag( this->Name );
+        node.SetTag( this->GetName() );
         node["BField"] = BField;
         node["BInc"] = BInc;
         node["BDec"] = BDec;

LemmaCore/src/FHTKey.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      02/11/2014 03:42:53 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include "FHTKey.h"
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator<<(std::ostream &stream, const FHTKey &ob) {
-
-        stream << *(HankelTransform*)(&ob);
-
-        return stream;
-    }
-
-
-    // ====================  STATIC CONST MEMBERS     ============
-
-    const Eigen::Matrix<Real, 201, 3>  FHTKey::WT201 =
-        ( Eigen::Matrix<Real, 201, 3>()   <<
-        // Base                   J0                      J1
-          4.1185887075357082e-06, 1.5020099209519960e-03, 4.7827871332506182e-10
-        , 4.6623077830484039e-06,-1.0381698214761684e-02,-2.9784175503440788e-09
-        , 5.2778064058937756e-06, 3.6840860097595164e-02, 9.7723832770897220e-09
-        , 5.9745606155328603e-06,-8.9903380392274704e-02,-2.2382340996085809e-08
-        , 6.7632974390298035e-06, 1.7082286536833860e-01, 4.0446774329470848e-08
-        , 7.6561600412698171e-06,-2.7115749656836280e-01,-6.1734815854553919e-08
-        , 8.6668946776271221e-06, 3.7649328091859574e-01, 8.3293912185608189e-08
-        , 9.8110623273521872e-06,-4.7220778569122657e-01,-1.0249453502284080e-07
-        , 1.1106278265924788e-05, 5.4778211089647089e-01, 1.1780779749909977e-07
-        , 1.2572483264760042e-05,-5.9823516853035097e-01,-1.2870061460834850e-07
-        , 1.4232250593579901e-05, 6.2345791612185331e-01, 1.3559243438349901e-07
-        , 1.6111133551969887e-05,-6.2650436648257724e-01,-1.3921010821521872e-07
-        , 1.8238058880617237e-05, 6.1197225351173345e-01, 1.4065745722769670e-07
-        , 2.0645772109076137e-05,-5.8470173866140451e-01,-1.4074881908375281e-07
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-        , 8.8337984088275090e-01, 8.9193635262987042e-02, 4.1225008900614292e-02
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-        , 1.5867051413382505e+04, 9.8453630538596172e-07,-1.0690622166177854e-04
-        , 1.7961754025908867e+04,-8.6148574493190796e-07, 9.3468580362568137e-05
-        , 2.0332990628312182e+04, 7.5206242699701732e-07,-8.1551328581234316e-05
-        , 2.3017268096126892e+04,-6.5460810334682633e-07, 7.0964174631531072e-05
-        , 2.6055912791858576e+04, 5.6764451596029765e-07,-6.1539592468666665e-05
-        , 2.9495706813754354e+04,-4.8985884555184997e-07, 5.3130609116145443e-05
-        , 3.3389608239508460e+04, 4.2009674106879252e-07,-4.5609105983126460e-05
-        , 3.7797566453568354e+04,-3.5736212641225517e-07, 3.8864648584181207e-05
-        , 4.2787445110585410e+04, 3.0082215969939671e-07,-3.2803856352344075e-05
-        , 4.8436066944688770e+04,-2.4981510481639669e-07, 2.7350296775876261e-05
-        , 5.4830396510166145e+04, 2.0385823466866512e-07,-2.2444816150805301e-05
-        , 6.2068879062685897e+04,-1.6265189071584773e-07, 1.8046076281584239e-05
-        , 7.0262956194088882e+04, 1.2607416700611311e-07,-1.4130826937491561e-05
-        , 7.9538781555028458e+04,-9.4158417913450858e-08, 1.0693106849359383e-05
-        , 9.0039163080228551e+04, 6.7043911217063425e-08,-7.7412053314530284e-06
-        , 1.0192576161830177e+05,-4.4891090827293947e-08, 5.2910576443698300e-06
-        , 1.1538157981559623e+05, 2.7761325666544702e-08,-3.3552268362550323e-06
-        , 1.3061377957221285e+05,-1.5480404355710375e-08, 1.9282956206367452e-06
-        , 1.4785687144693290e+05, 7.5327300141098751e-09,-9.7253712572058755e-07
-        , 1.6737632511421290e+05,-3.0524770418657847e-09, 4.1100807632959352e-07
-        , 1.8947265645880660e+05, 9.5877856096830783e-10,-1.3553176263207053e-07
-        , 2.1448605423174356e+05,-2.0575286298055636e-10, 3.0748587523233524e-08
-        , 2.4280161749832361e+05, 2.2414416956474645e-11,-3.5668195345476294e-09 ).finished();
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  FHTKey
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    FHTKey::FHTKey (const std::string& name) : HankelTransform(name) {
-
-    }  // -----  end of method FHTKey::FHTKey  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    FHTKey* FHTKey::New() {
-        FHTKey*  Obj = new FHTKey("FHTKey");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  ~FHTKey
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    FHTKey::~FHTKey () {
-
-    }  // -----  end of method FHTKey::~FHTKey  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void FHTKey::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void FHTKey::Release() {
-        delete this;
-    }
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  Zgauss
-    //--------------------------------------------------------------------------------------
-    Complex FHTKey::Zgauss ( const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel ) {
- 		return Zans(0, Kernel->GetManagerIndex());
-    }		// -----  end of method FHTKey::ComputeRelated  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
-        return ;
-    }		// -----  end of method FHTKey::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
-        return ;
-    }		// -----  end of method FHTKey::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManager ) {
-
-        //kernelVec = KernelManager->GetSTLVector();
-        int nrel = (int)(KernelManager->GetSTLVector().size());
-        Eigen::Matrix<Complex, 201, Eigen::Dynamic > Zwork;
-        // TODO, if we want to allow lagged, then 1 below should be nlag
-        Zans= Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
-        Zwork.resize(201, nrel);
-        VectorXr lambda = WT201.col(0).array()/rho;
-        int NumFun = 0;
-        int idx = 0;
-
-        // Get Kernel values
-        for (int ir=0; ir<lambda.size(); ++ir) {
-            // irelated loop
-            ++NumFun;
-            KernelManager->ComputeReflectionCoeffs(lambda(ir), idx, rho);
-            for (int ir2=0; ir2<nrel; ++ir2) {
-                // Zwork* needed due to sign convention of filter weights
- 			    Zwork(ir, ir2) = std::conj(KernelManager->GetSTLVector()[ir2]->RelBesselArg(lambda(ir)));
-            }
-
-        }
-
-        // We diverge slightly from Key here, each kernel is evaluated seperately, whereby instead
-        // they prefer to sum them. The reason is that all those terms have been removed from the kernels
-        // in the interests of making them as generic and reusable as possible. This approach requires slightly
-        // more multiplies, but the same number of kernel evaluations, which is the expensive part.
-        // Inner product and scale
-        for (int ir2=0; ir2<nrel; ++ir2) {
-            Zans(0, ir2) = Zwork.col(ir2).dot(WT201.col(KernelManager->GetSTLVector()[ir2]->GetBesselOrder() + 1))/rho;
-        }
-
-        return ;
-    }		// -----  end of method FHTKey::ComputeRelated  -----
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/FHTKey101.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      02/11/2014 03:42:53 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include "FHTKey101.h"
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator<<(std::ostream &stream, const FHTKey101 &ob) {
-
-        stream << *(HankelTransform*)(&ob);
-
-        return stream;
-    }
-
-
-    // ====================  STATIC CONST MEMBERS     ============
-
-    const Eigen::Matrix<Real, 101, 3>  FHTKey101::WT101 =
-        ( Eigen::Matrix<Real, 101, 3>()   <<
-       // Base                   J0                      J1
-       5.5308437014783363e-04,   5.1818808036862153e-02,   4.1746363961646286e-06,
-       6.4259236035555788e-04,  -2.9258492652779172e-01,  -2.5993370843637242e-05,
-       7.4658580837667996e-04,   8.7289913080159265e-01,   9.2506838353721647e-05,
-       8.6740895730700251e-04,  -1.8525183961240297e+00,  -2.4318740269846489e-04,
-       1.0077854290485113e-03,   3.2096055660873608e+00,   5.2276050788732404e-04,
-       1.1708796207911744e-03,  -4.9248158048315069e+00,  -9.5803859755432658e-04,
-       1.3603680375478939e-03,   7.0219167445719828e+00,   1.5308357107396591e-03,
-       1.5805221687362171e-03,  -9.4781099645811544e+00,  -2.1584605764249656e-03,
-       1.8363047770289071e-03,   1.2098564895534539e+01,   2.7161344302423967e-03,
-       2.1334817700377098e-03,  -1.4476661837664896e+01,  -3.0845361397036195e-03,
-       2.4787521766663585e-03,   1.6146079632847474e+01,   3.2133980102756368e-03,
-       2.8798991580882430e-03,  -1.6810370923047440e+01,  -3.1305779240645847e-03,
-       3.3459654574712720e-03,   1.6506202923977266e+01,   2.9239120736637542e-03,
-       3.8874572434761303e-03,  -1.5534747212675301e+01,  -2.6680602560576316e-03,
-       4.5165809426126703e-03,   1.4267433361428399e+01,   2.4131379039476304e-03,
-       5.2475183991813838e-03,  -1.2939053370802849e+01,  -2.1549566068119440e-03,
-       6.0967465655156379e-03,   1.1628520257389562e+01,   1.9058200916563901e-03,
-       7.0834089290521185e-03,  -1.0325503688577493e+01,  -1.6533122444456158e-03,
-       8.2297470490200302e-03,   9.0574401975545840e+00,   1.4391633836110848e-03,
-       9.5616019305435132e-03,  -7.8759096646654951e+00,  -1.2363666069459527e-03,
-       1.1108996538242306e-02,   6.8446506699312666e+00,   1.0907227256323094e-03,
-       1.2906812580479873e-02,  -5.9542991234257840e+00,  -9.2712769282234358e-04,
-       1.4995576820477703e-02,   5.1830565431894602e+00,   8.2888526218099687e-04,
-       1.7422374639493515e-02,  -4.4805481279340267e+00,  -6.7675613963809832e-04,
-       2.0241911445804391e-02,   3.8608298760715378e+00,   6.3558641899842260e-04,
-       2.3517745856009110e-02,  -3.3125736597743227e+00,  -4.8591507683128695e-04,
-       2.7323722447292573e-02,   2.8648088091590589e+00,   5.1892328126100203e-04,
-       3.1745636378067953e-02,  -2.4710577422247479e+00,  -3.3190335155472070e-04,
-       3.6883167401240015e-02,   2.1450315408533416e+00,   4.6189809360776176e-04,
-       4.2852126867040180e-02,  -1.8334353019592327e+00,  -1.8326476919948130e-04,
-       4.9787068367863944e-02,   1.5850020809005190e+00,   4.7669939315323097e-04,
-       5.7844320874838456e-02,  -1.3468969891769780e+00,  -1.7380345519175726e-05,
-       6.7205512739749784e-02,   1.1802299801807625e+00,   5.9009214750893949e-04,
-       7.8081666001153169e-02,  -9.9988174688478793e-01,   2.1645139320505843e-04,
-       9.0717953289412512e-02,   8.8503813256539254e-01,   8.5203135609860704e-04,
-       1.0539922456186433e-01,  -7.3165077099639619e-01,   5.9560990889710838e-04,
-       1.2245642825298191e-01,   6.5909386165012596e-01,   1.3651107378683781e-03,
-       1.4227407158651359e-01,  -5.3038429622108840e-01,   1.2606987195022564e-03,
-       1.6529888822158656e-01,   5.0119791866928076e-01,   2.3131990435032663e-03,
-       1.9204990862075413e-01,  -3.8269840749371159e-01,   2.4572002938857678e-03,
-       2.2313016014842982e-01,   3.8622329595139565e-01,   4.0408430887840449e-03,
-       2.5924026064589156e-01,  -2.6413330193320073e-01,   4.6278078809669602e-03,
-       3.0119421191220208e-01,   3.0353632730294311e-01,   7.1437051276295131e-03,
-       3.4993774911115533e-01,  -1.7255655176111537e-01,   8.5723466849983495e-03,
-       4.0656965974059917e-01,   2.5119774955173280e-01,   1.2684763573137947e-02,
-       4.7236655274101469e-01,  -9.8536724013140092e-02,   1.5643387012124067e-02,
-       5.4881163609402650e-01,   2.1755876398162183e-01,   2.2480928663078600e-02,
-       6.3762815162177333e-01,  -3.4268716744688760e-02,   2.8124131719595692e-02,
-       7.4081822068171788e-01,   1.9925218957836366e-01,   3.9373999883133115e-02,
-       8.6070797642505781e-01,   1.8319735495994052e-02,   4.9445586323210833e-02,
-       1.0000000000000000e+00,   1.8963099219918259e-01,   6.7326587032714463e-02,
-       1.1618342427282831e+00,   5.7228135568732394e-02,   8.3541701874077570e-02,
-       1.3498588075760032e+00,   1.7266316834158107e-01,   1.0961776964853986e-01,
-       1.5683121854901687e+00,   6.8141322181604499e-02,   1.3118216481048459e-01,
-       1.8221188003905089e+00,   1.2468074033081850e-01,   1.6144181878027153e-01,
-       2.1170000166126748e+00,   2.1678852838804014e-02,   1.7704476632134886e-01,
-       2.4596031111569494e+00,   1.1114005126278175e-02,   1.9032654055463888e-01,
-       2.8576511180631639e+00,  -1.0424806190544497e-01,   1.6333927603825021e-01,
-       3.3201169227365472e+00,  -1.6473681128667569e-01,   1.1034442879456068e-01,
-       3.8574255306969740e+00,  -2.3603153458714107e-01,  -1.1282682226217962e-02,
-       4.4816890703380645e+00,  -2.2093965064386309e-01,  -1.4579378661401318e-01,
-       5.2069798271798486e+00,  -7.5633542915308175e-02,  -2.7560051939484942e-01,
-       6.0496474644129448e+00,   1.3358180223826097e-01,  -2.3333751023296440e-01,
-       7.0286875805892928e+00,   3.3949946683489907e-01,  -5.9615109981928909e-03,
-       8.1661699125676499e+00,   1.2815187347111337e-01,   3.2380356528743487e-01,
-       9.4877358363585262e+00,  -2.2988301163130145e-01,   2.1970582679149839e-01,
-       1.1023176380641601e+01,  -3.3425750283830036e-01,  -2.8302631898505476e-01,
-       1.2807103782663029e+01,   4.4350537603751145e-01,  -2.2706962776315812e-01,
-       1.4879731724872830e+01,  -8.8943820418669634e-02,   4.7351258711649669e-01,
-       1.7287781840567639e+01,  -1.8646079800862164e-01,  -3.5417866045339608e-01,
-       2.0085536923187668e+01,   2.4494657419883456e-01,   1.6582378621661517e-01,
-       2.3336064580942711e+01,  -2.0169045144304532e-01,  -5.1221107687420810e-02,
-       2.7112638920657883e+01,   1.4661206655803793e-01,   3.5484710794282063e-03,
-       3.1500392308747923e+01,  -1.0564640256629308e-01,   1.1614894738175324e-02,
-       3.6598234443677974e+01,   7.8487036158411266e-02,  -1.4776256489774963e-02,
-       4.2521082000062783e+01,  -6.0533748554794195e-02,   1.4194293010344678e-02,
-       4.9402449105530167e+01,   4.8243702864613026e-02,  -1.2609914713728791e-02,
-       5.7397457045446188e+01,  -3.9347085461672239e-02,   1.0854082569077052e-02,
-       6.6686331040925154e+01,   3.2489421068688185e-02,  -9.2082270347668624e-03,
-       7.7478462925260828e+01,  -2.6982535264609676e-02,   7.7880648968821110e-03,
-       9.0017131300521811e+01,   2.2530196869950080e-02,  -6.6089268276601255e-03,
-       1.0458498557711414e+02,  -1.8947601435977172e-02,   5.6159700146012417e-03,
-       1.2151041751873485e+02,   1.6017457455233256e-02,  -4.7432063636330263e-03,
-       1.4117496392147686e+02,  -1.3519422964231352e-02,   3.9609893136500528e-03,
-       1.6402190729990167e+02,   1.1318328695851308e-02,  -3.2753768787828126e-03,
-       1.9056626845862999e+02,  -9.3839154851987506e-03,   2.6945716306237466e-03,
-       2.2140641620418697e+02,   7.7256174599644543e-03,  -2.2042319512562145e-03,
-       2.5723755590577474e+02,  -6.3199190181430056e-03,   1.7733135127602079e-03,
-       2.9886740096706029e+02,   5.0986473606509210e-03,  -1.3773733375919272e-03,
-       3.4723438047873447e+02,  -3.9929354358609528e-03,   1.0137885881408651e-03,
-       4.0342879349273511e+02,   2.9783618569305080e-03,  -6.9751488719640639e-04,
-       4.6871738678241655e+02,  -2.0802747552777045e-03,   4.4545125438205673e-04,
-       5.4457191012592898e+02,   1.3429398653973710e-03,  -2.6373575275283686e-04,
-       6.3270229281225352e+02,  -7.9345560431147465e-04,   1.4519595835116970e-04,
-       7.3509518924197266e+02,   4.2530878973518046e-04,  -7.4640168948626184e-05,
-       8.5405876252615155e+02,  -2.0457624610548748e-04,   3.5826939350044606e-05,
-       9.9227471560502534e+02,   8.6750842046621606e-05,  -1.5854604622793124e-05,
-       1.1528587427833875e+03,  -3.1406113278782205e-05,   6.2412989356183992e-06,
-       1.3394307643944169e+03,   9.1385289919391839e-06,  -2.0349222128793154e-06,
-       1.5561965278371533e+03,  -1.8949818224609619e-06,   4.8072849734177625e-07,
-       1.8080424144560632e+03,   2.0794387557779629e-07,  -6.0462736574031818e-08).finished();
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  FHTKey101
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    FHTKey101::FHTKey101 (const std::string& name) : HankelTransform(name) {
-
-    }  // -----  end of method FHTKey101::FHTKey101  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    FHTKey101* FHTKey101::New() {
-        FHTKey101*  Obj = new FHTKey101("FHTKey101");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  ~FHTKey101
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    FHTKey101::~FHTKey101 () {
-
-    }  // -----  end of method FHTKey101::~FHTKey101  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void FHTKey101::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void FHTKey101::Release() {
-        delete this;
-    }
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  Zgauss
-    //--------------------------------------------------------------------------------------
-    Complex FHTKey101::Zgauss ( const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel ) {
- 		return Zans(0, Kernel->GetManagerIndex());
-    }		// -----  end of method FHTKey101::ComputeRelated  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey101::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
-        return ;
-    }		// -----  end of method FHTKey101::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey101::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
-        return ;
-    }		// -----  end of method FHTKey101::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey101
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey101::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManager ) {
-
-        //kernelVec = KernelManager->GetSTLVector();
-        int nrel = (int)(KernelManager->GetSTLVector().size());
-        Eigen::Matrix<Complex, 101, Eigen::Dynamic > Zwork;
-        // TODO, if we want to allow lagged, then 1 below should be nlag
-        Zans= Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
-        Zwork.resize(101, nrel);
-        VectorXr lambda = WT101.col(0).array()/rho;
-        int NumFun = 0;
-        int idx = 0;
-
-        // Get Kernel values
-        for (int ir=0; ir<lambda.size(); ++ir) {
-            // irelated loop
-            ++NumFun;
-            KernelManager->ComputeReflectionCoeffs(lambda(ir), idx, rho);
-            for (int ir2=0; ir2<nrel; ++ir2) {
-                // Zwork* needed due to sign convention of filter weights
- 			    Zwork(ir, ir2) = std::conj(KernelManager->GetSTLVector()[ir2]->RelBesselArg(lambda(ir)));
-            }
-
-        }
-
-        // We diverge slightly from Key here, each kernel is evaluated seperately, whereby instead
-        // they prefer to sum them. The reason is that all those terms have been removed from the kernels
-        // in the interests of making them as generic and reusable as possible. This approach requires slightly
-        // more multiplies, but the same number of kernel evaluations, which is the expensive part.
-        // Inner product and scale
-        for (int ir2=0; ir2<nrel; ++ir2) {
-            Zans(0, ir2) = Zwork.col(ir2).dot(WT101.col(KernelManager->GetSTLVector()[ir2]->GetBesselOrder() + 1))/rho;
-        }
-
-        return ;
-    }		// -----  end of method FHTKey101::ComputeRelated  -----
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/FHTKey51.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      02/11/2014 03:42:53 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include "FHTKey51.h"
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator<<(std::ostream &stream, const FHTKey51 &ob) {
-
-        stream << *(HankelTransform*)(&ob);
-
-        return stream;
-    }
-
-
-    // ====================  STATIC CONST MEMBERS     ============
-
-    const Eigen::Matrix<Real, 51, 3>  FHTKey51::WT51 =
-        ( Eigen::Matrix<Real, 51, 3>()   <<
-        // Base                   J0                      J1
-           4.9915939069102170e-03,   6.5314496156480717e-02,   3.8409924166118657e-05,
-           6.1703482511978082e-03,  -2.2265895125268051e-01,  -9.4382633059055269e-05,
-           7.6274629409160176e-03,   4.2794928430042073e-01,   1.6377612356675232e-04,
-           9.4286721829279947e-03,  -5.8890658905204007e-01,  -1.7853487610334151e-04,
-           1.1655233178024955e-02,   6.7897324897038758e-01,   1.9759569268356316e-04,
-           1.4407591843112350e-02,  -6.8296549495756353e-01,  -1.2796247718553291e-04,
-           1.7809914185937643e-02,   6.4702210424566342e-01,   1.3163370416771999e-04,
-           2.2015687754376449e-02,  -5.6843090153083187e-01,   1.7066927559149181e-05,
-           2.7214645856121149e-02,   4.9960500362966542e-01,   4.1368007808198310e-05,
-           3.3641326918204623e-02,  -4.0923517268678855e-01,   2.3582259002758631e-04,
-           4.1585655121173182e-02,   3.5487831784012780e-01,  -1.9929745662753875e-05,
-           5.1406019627642255e-02,  -2.7408257835871558e-01,   5.8196110748926486e-04,
-           6.3545442443014022e-02,   2.4668368971888163e-01,   1.1164151202379049e-05,
-           7.8551564282309541e-02,  -1.7348161774657314e-01,   1.2053942009238238e-03,
-           9.7101350057185065e-02,   1.7509173908347012e-01,   2.8328713800714110e-04,
-           1.2003162851145673e-01,  -1.0007796678766585e-01,   2.4375075610646724e-03,
-           1.4837684372696586e-01,   1.3297302593795621e-01,   1.1709289200267103e-03,
-           1.8341572156771246e-01,  -4.3822390117083297e-02,   5.0080095645252103e-03,
-           2.2672895630607542e-01,   1.1415804492335258e-01,   3.5856849047131551e-03,
-           2.8027051982381157e-01,   4.2584271963990363e-03,   1.0536604059335859e-02,
-           3.4645581033005746e-01,   1.1496183925974515e-01,   9.6674718436839564e-03,
-           4.2827061721265969e-01,   5.1313336759457658e-02,   2.2583365267100426e-02,
-           5.2940581770869455e-01,   1.3312389010285514e-01,   2.4201911801947001e-02,
-           6.5442388190885858e-01,   1.0111673764393908e-01,   4.8602551164692191e-02,
-           8.0896469756649991e-01,   1.6331446488042209e-01,   5.6856974938076565e-02,
-           1.0000000000000000e+00,   1.4704406144951229e-01,   1.0202078096072606e-01,
-           1.2361478850785035e+00,   1.8341391219815678e-01,   1.2202639829343022e-01,
-           1.5280615937840571e+00,   1.5073655145087875e-01,   1.9561985197118459e-01,
-           1.8889101074258496e+00,   1.2356364992866918e-01,   2.1570853920674185e-01,
-           2.3349722343978727e+00,   1.1529465836107913e-02,   2.8552388758852060e-01,
-           2.8863709892679585e+00,  -1.2852626053530605e-01,   2.0559964796530625e-01,
-           3.5679813939355345e+00,  -2.9874216118407571e-01,   1.1666011451374350e-01,
-           4.4105526541128617e+00,  -3.1330553036684633e-01,  -2.3636714743601936e-01,
-           5.4520953354089947e+00,  -3.2332453606385231e-02,  -3.4036030266164258e-01,
-           6.7395961181122024e+00,   4.2056051544727674e-01,  -1.9475364255836261e-01,
-           8.3311374876876929e+00,   1.3883637369942961e-01,   5.7608115965662166e-01,
-           1.0298517985703377e+01,  -5.0223684329542873e-01,  -2.1471464584834585e-01,
-           1.2730491227470161e+01,   3.7996073748731690e-01,  -1.2611070492338947e-01,
-           1.5736769806847677e+01,  -1.7984404170109178e-01,   2.0019703515125831e-01,
-           1.9452974714702009e+01,   7.0557286965350657e-02,  -1.6147664664730754e-01,
-           2.4046753552064487e+01,  -2.7522277139686569e-02,   1.1398023016900673e-01,
-           2.9725343546388515e+01,   1.1909130661901874e-02,  -7.9924455203352035e-02,
-           3.6744920558100112e+01,  -5.8977428045126450e-03,   5.7024556382799692e-02,
-           4.5422155835273074e+01,   3.2648420034561555e-03,  -4.1006636508593382e-02,
-           5.6148501871478999e+01,  -1.9304039780209286e-03,   2.9192063091319696e-02,
-           6.9407851838755207e+01,   1.1594138315987755e-03,  -2.0089573135329029e-02,
-           8.5798369258319340e+01,  -6.7050941490060716e-04,   1.2965400526524978e-02,
-           1.0605947270185592e+02,   3.5089803807606258e-04,  -7.5154910983038946e-03,
-           1.3110519287294045e+02,  -1.5287051174029577e-04,   3.6269079130258285e-03,
-           1.6206540689269471e+02,   4.8238483411813232e-05,  -1.2668720233377250e-03,
-           2.0033680997479166e+02,  -8.0433917146487977e-06,   2.3403502580547994e-04).finished();
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  FHTKey51
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    FHTKey51::FHTKey51 (const std::string& name) : HankelTransform(name) {
-
-    }  // -----  end of method FHTKey51::FHTKey51  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    FHTKey51* FHTKey51::New() {
-        FHTKey51*  Obj = new FHTKey51("FHTKey51");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  ~FHTKey51
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    FHTKey51::~FHTKey51 () {
-
-    }  // -----  end of method FHTKey51::~FHTKey51  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void FHTKey51::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void FHTKey51::Release() {
-        delete this;
-    }
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  Zgauss
-    //--------------------------------------------------------------------------------------
-    Complex FHTKey51::Zgauss ( const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel ) {
- 		return Zans(0, Kernel->GetManagerIndex());
-    }		// -----  end of method FHTKey51::ComputeRelated  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey51::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
-        return ;
-    }		// -----  end of method FHTKey51::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey51::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
-        return ;
-    }		// -----  end of method FHTKey51::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  FHTKey51
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void FHTKey51::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManager ) {
-
-        //kernelVec = KernelManager->GetSTLVector();
-        int nrel = (int)(KernelManager->GetSTLVector().size());
-        Eigen::Matrix<Complex, 51, Eigen::Dynamic > Zwork;
-        // TODO, if we want to allow lagged, then 1 below should be nlag
-        Zans= Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
-        Zwork.resize(51, nrel);
-        VectorXr lambda = WT51.col(0).array()/rho;
-        int NumFun = 0;
-        int idx = 0;
-
-        // Get Kernel values
-        for (int ir=0; ir<lambda.size(); ++ir) {
-            // irelated loop
-            ++NumFun;
-            KernelManager->ComputeReflectionCoeffs(lambda(ir), idx, rho);
-            for (int ir2=0; ir2<nrel; ++ir2) {
-                // Zwork* needed due to sign convention of filter weights
- 			    Zwork(ir, ir2) = std::conj(KernelManager->GetSTLVector()[ir2]->RelBesselArg(lambda(ir)));
-            }
-
-        }
-
-        // We diverge slightly from Key here, each kernel is evaluated seperately, whereby instead
-        // they prefer to sum them. The reason is that all those terms have been removed from the kernels
-        // in the interests of making them as generic and reusable as possible. This approach requires slightly
-        // more multiplies, but the same number of kernel evaluations, which is the expensive part.
-        // Inner product and scale
-        for (int ir2=0; ir2<nrel; ++ir2) {
-            Zans(0, ir2) = Zwork.col(ir2).dot(WT51.col(KernelManager->GetSTLVector()[ir2]->GetBesselOrder() + 1))/rho;
-        }
-
-        return ;
-    }		// -----  end of method FHTKey51::ComputeRelated  -----
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/filter.cpp → LemmaCore/src/Filter.cpp

   @version  $Id: filter.cpp 193 2014-11-10 23:51:41Z tirons $
  **/
 
-#include "filter.h"
+#include "Filter.h"
 
 namespace Lemma {
 

LemmaCore/src/grid.cpp → LemmaCore/src/Grid.cpp

   @version  $Id: grid.cpp 193 2014-11-10 23:51:41Z tirons $
  **/
 
-#include "grid.h"
+#include "Grid.h"
 
 namespace Lemma {
 

LemmaCore/src/GroundedElectricDipole.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      01/29/2014 07:05:13 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include "GroundedElectricDipole.h"
-
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator<<(std::ostream &stream, const GroundedElectricDipole &ob) {
-
-        stream << *(DipoleSource*)(&ob);
-
-        return stream;
-    }
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  GroundedElectricDipole
-    //      Method:  GroundedElectricDipole
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    GroundedElectricDipole::GroundedElectricDipole (const std::string& name) : DipoleSource(name) {
-
-    }  // -----  end of method GroundedElectricDipole::GroundedElectricDipole  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  GroundedElectricDipole
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    GroundedElectricDipole* GroundedElectricDipole::New() {
-        GroundedElectricDipole*  Obj = new GroundedElectricDipole("GroundedElectricDipole");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  GroundedElectricDipole
-    //      Method:  ~GroundedElectricDipole
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    GroundedElectricDipole::~GroundedElectricDipole () {
-
-    }  // -----  end of method GroundedElectricDipole::~GroundedElectricDipole  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  GroundedElectricDipole
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void GroundedElectricDipole::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  GroundedElectricDipole
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void GroundedElectricDipole::Release() {
-        delete this;
-    }
-
-}		// -----  end of Lemma  name  -----
-

LemmaCore/src/instrument.cpp → LemmaCore/src/Instrument.cpp

   @version  $Id: instrument.cpp 193 2014-11-10 23:51:41Z tirons $
  **/
 
-#include "instrument.h"
+#include "Instrument.h"
 
 namespace Lemma {
 

LemmaCore/src/layeredearth.cpp → LemmaCore/src/LayeredEarth.cpp

   @version  $Id: layeredearth.cpp 210 2015-02-25 02:57:03Z tirons $
  **/
 
-#include "layeredearth.h"
+#include "LayeredEarth.h"
 
 namespace Lemma {
 
 
 
 	LayeredEarth::~LayeredEarth() {
-		if (NumberOfReferences != 0) {
-			throw DeleteObjectWithReferences(this);
-		}
 	}
 
     #ifdef HAVE_YAMLCPP
         node["NumberOfLayers"] = NumberOfLayers;
         node["NumberOfInterfaces"] = NumberOfInterfaces;
         node["LayerThickness"] = LayerThickness;
-        node.SetTag( Name );
+        node.SetTag( this->GetName() );
         return node;
     }
     #endif

LemmaCore/src/LayeredEarthEMReader.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      09/27/2013 01:44:46 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2013, XRI Geophysics, LLC
- * @copyright Copyright (c) 2013, Trevor Irons
- */
-
-#include "LayeredEarthEMReader.h"
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator<<(std::ostream &stream, const LayeredEarthEMReader &ob) {
-
-        stream << *(LemmaObject*)(&ob);
-
-        return stream;
-    }
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  LayeredEarthEMReader
-    //      Method:  LayeredEarthEMReader
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    LayeredEarthEMReader::LayeredEarthEMReader (const std::string& name) : LemmaObject(name),
-        LayEarth(NULL) {
-
-    }  // -----  end of method LayeredEarthEMReader::LayeredEarthEMReader  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  LayeredEarthEMReader
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    LayeredEarthEMReader* LayeredEarthEMReader::New() {
-        LayeredEarthEMReader*  Obj = new LayeredEarthEMReader("LayeredEarthEMReader");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  LayeredEarthEMReader
-    //      Method:  ~LayeredEarthEMReader
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    LayeredEarthEMReader::~LayeredEarthEMReader () {
-        if (LayEarth) LayEarth->Delete();
-    }  // -----  end of method LayeredEarthEMReader::~LayeredEarthEMReader  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  LayeredEarthEMReader
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void LayeredEarthEMReader::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  LayeredEarthEMReader
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void LayeredEarthEMReader::Release() {
-        delete this;
-    }
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  LayeredEarthEMReader
-    //      Method:  GetLayeredEarth
-    //--------------------------------------------------------------------------------------
-    LayeredEarthEM* LayeredEarthEMReader::GetLayeredEarth (  ) {
-        return LayEarth;
-    }		// -----  end of method LayeredEarthEMReader::GetLayeredEarth  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  LayeredEarthEMReader
-    //      Method:  ReadASCIIInputFile
-    //--------------------------------------------------------------------------------------
-    void LayeredEarthEMReader::ReadASCIIInputFile ( const std::string& name ) {
-        if (LayEarth) LayEarth->Delete();
-        ASCIIParser* Parser = ASCIIParser::New();
-        LayEarth = LayeredEarthEM::New();
-
-        Parser->SetCommentString("//");
-        Parser->Open(name);
-
-        int nlay = Parser->ReadInts( 1 )[0]; // non-air layers
-            LayEarth->SetNumberOfLayers(nlay+1);
-
-        VectorXcr sigma = VectorXcr::Zero(nlay+1);
-        VectorXr  thick(nlay-1);
-        for (int ilay=1; ilay<nlay; ++ilay) {
-            std::vector<Real> rval = Parser->ReadReals(2);
-            sigma(ilay) =  1./rval[0];
-            thick(ilay-1) =  rval[1]; //CondMod[ilay+1];
-        }
-        sigma(nlay) = 1./Parser->ReadReals(1)[0];
-        LayEarth->SetLayerConductivity(sigma);
-        if (thick.size() > 0) LayEarth->SetLayerThickness(thick);
-        Parser->Delete();
-        return ;
-    }		// -----  end of method LayeredEarthEMReader::ReadASCIIInputFile  -----
-
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/LemmaObject.cpp

 
 namespace Lemma {
 
-    std::ostream &operator << (std::ostream &stream,
+    std::ostream &operator<<(std::ostream &stream,
                 const LemmaObject &ob) {
       stream << "Class name= " << ob.Name  << "\n";
       return stream;
 
     // Destructor
     LemmaObject::~LemmaObject() {
-        std::cout << "~LemmaObject()" << std::endl;
     }
 
     // ====================  OPERATIONS    ==============================

LemmaCore/src/MagneticDipole.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      09/25/2013 08:20:14 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2013, XRI Geophysics, LLC
- * @copyright Copyright (c) 2013, Trevor Irons
- */
-
-#include "MagneticDipole.h"
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator<<(std::ostream &stream, const MagneticDipole &ob) {
-
-        stream << *(DipoleSource*)(&ob);
-
-        return stream;
-    }
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  MagneticDipole
-    //      Method:  MagneticDipole
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    MagneticDipole::MagneticDipole (const std::string& name) : DipoleSource(name) {
-
-    }  // -----  end of method MagneticDipole::MagneticDipole  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  MagneticDipole
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    MagneticDipole* MagneticDipole::New() {
-        MagneticDipole*  Obj = new MagneticDipole("MagneticDipole");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  MagneticDipole
-    //      Method:  ~MagneticDipole
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    MagneticDipole::~MagneticDipole () {
-
-    }  // -----  end of method MagneticDipole::~MagneticDipole  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  MagneticDipole
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void MagneticDipole::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  MagneticDipole
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void MagneticDipole::Release() {
-        delete this;
-    }
-
-} // namespace Lemma

LemmaCore/src/ParticleSwarmOptimizer.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      01/27/2015 01:59:03 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2015, XRI Geophysics, LLC
- * @copyright Copyright (c) 2015, Trevor Irons
- */
-
-#include "ParticleSwarmOptimizer.h"
-
-namespace Lemma {
-
-
-
-    // ====================  FRIEND METHODS  =====================
-#ifdef HAVE_YAMLCPP
-    std::ostream &operator << (std::ostream &stream, const ParticleSwarmOptimizer &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-#else
-    std::ostream &operator<<(std::ostream &stream, const ParticleSwarmOptimizer& ob) {
-        stream << *(LemmaObject*)(&ob);
-        return stream;
-    }
-#endif
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ParticleSwarmOptimizer
-    //      Method:  ParticleSwarmOptimizer
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    ParticleSwarmOptimizer::ParticleSwarmOptimizer (const std::string& name) : LemmaObject(name) {
-
-    }  // -----  end of method ParticleSwarmOptimizer::ParticleSwarmOptimizer  (constructor)  -----
-
-#ifdef HAVE_YAMLCPP
-    //--------------------------------------------------------------------------------------
-    //       Class:  ParticleSwarmOptimizer
-    //      Method:  ParticleSwarmOptimizer
-    // Description:  DeSerializing constructor (protected)
-    //--------------------------------------------------------------------------------------
-    ParticleSwarmOptimizer::ParticleSwarmOptimizer (const YAML::Node& node) : LemmaObject(node) {
-
-    }  // -----  end of method ParticleSwarmOptimizer::ParticleSwarmOptimizer  (constructor)  -----
-#endif
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ParticleSwarmOptimizer
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    ParticleSwarmOptimizer* ParticleSwarmOptimizer::New() {
-        ParticleSwarmOptimizer*  Obj = new ParticleSwarmOptimizer("ParticleSwarmOptimizer");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ParticleSwarmOptimizer
-    //      Method:  ~ParticleSwarmOptimizer
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    ParticleSwarmOptimizer::~ParticleSwarmOptimizer () {
-
-    }  // -----  end of method ParticleSwarmOptimizer::~ParticleSwarmOptimizer  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ParticleSwarmOptimizer
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void ParticleSwarmOptimizer::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ParticleSwarmOptimizer
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void ParticleSwarmOptimizer::Release() {
-        delete this;
-    }
-
-
-#ifdef HAVE_YAMLCPP
-    //--------------------------------------------------------------------------------------
-    //       Class:  ParticleSwarmOptimizer
-    //      Method:  Serialize
-    //--------------------------------------------------------------------------------------
-    YAML::Node  ParticleSwarmOptimizer::Serialize (  ) const {
-        YAML::Node node = LemmaObject::Serialize();;
-        node.SetTag( this->Name );
-        // FILL IN CLASS SPECIFICS HERE
-        return node;
-    }		// -----  end of method ParticleSwarmOptimizer::Serialize  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ParticleSwarmOptimizer
-    //      Method:  DeSerialize
-    //--------------------------------------------------------------------------------------
-    ParticleSwarmOptimizer* ParticleSwarmOptimizer::DeSerialize ( const YAML::Node& node  ) {
-        ParticleSwarmOptimizer* Object = new ParticleSwarmOptimizer(node);
-        Object->AttachTo(Object);
-        DESERIALIZECHECK( node, Object )
-            return Object ;
-    }		// -----  end of method ParticleSwarmOptimizer::DeSerialize  -----
-#endif
-
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/PolygonalWireAntenna.cpp

-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* 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
-  @author   Trevor Irons
-  @date     05/18/2010
-  @version  $Id: PolygonalWireAntenna.cpp 211 2015-02-27 05:43:26Z tirons $
- **/
-
-#include "PolygonalWireAntenna.h"
-
-namespace Lemma {
-
-#ifdef HAVE_YAMLCPP
-    std::ostream &operator << (std::ostream &stream, const PolygonalWireAntenna &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-#else
-	std::ostream &operator<<(std::ostream &stream,
-				const PolygonalWireAntenna &ob) {
-
-		stream << *(WireAntenna*)(&ob);
-		//stream << "Current: " << ob.Current << " [A]\n";
-		//stream << "Frequencies: " << ob.Freqs.transpose() << " [Hz]\n";
-		//stream << "Number of points " << ob.NumberOfPoints << "\n";
-		//stream << "Points:\n" << ob.Points.transpose() << "\n";
-		//stream << "Dipoles used to approximate " << ob.Dipoles.size();
-		return stream;
-	}
-#endif
-	// ====================  LIFECYCLE     =======================
-
-	PolygonalWireAntenna::PolygonalWireAntenna(const std::string& name)
-		: WireAntenna(name), minDipoleRatio(.15),
-   		minDipoleMoment(1e-6), maxDipoleMoment(1e1), rRepeat(1e10,1e10,1e10) {
-		Points.setZero();
-        //rRepeat.setOnes();
-	}
-
-#ifdef HAVE_YAMLCPP
-    PolygonalWireAntenna::PolygonalWireAntenna(const YAML::Node& node)
-		: WireAntenna(node) {
-// minDipoleRatio(.15),
-// minDipoleMoment(1e-4),
-// maxDipoleMoment(1e-0)
-        minDipoleRatio   = node["minDipoleRatio"].as<Real>();
-        maxDipoleMoment  = node["maxDipoleMoment"].as<Real>();
-        minDipoleMoment  = node["minDipoleMoment"].as<Real>();
-	}
-#endif
-
-	PolygonalWireAntenna::~PolygonalWireAntenna() {
-        if (this->NumberOfReferences != 0)
-            throw DeleteObjectWithReferences( this );
-		// Taken care of in parent
-        //for (unsigned int id=0; id<Dipoles.size(); ++id) {
-		//	Dipoles[id]->Delete();
-		//}
-		//Dipoles.clear();
-	}
-
-	PolygonalWireAntenna* PolygonalWireAntenna::New() {
-		PolygonalWireAntenna* Obj = new
-            PolygonalWireAntenna("PolygonalWireAntenna");
-        Obj->AttachTo(Obj);
-        return Obj;
-	}
-
-	PolygonalWireAntenna* PolygonalWireAntenna::Clone() {
-		PolygonalWireAntenna* copy = PolygonalWireAntenna::New();
-		//copy->AttachTo(copy); // NO! Attached above!
-        copy->minDipoleRatio = this->minDipoleRatio;
-		copy->minDipoleMoment = this->minDipoleMoment;
-		copy->maxDipoleMoment = this->maxDipoleMoment;
-		copy->NumberOfPoints = this->NumberOfPoints;
-		copy->Freqs = this->Freqs;
-		copy->Current = this->Current;
-		copy->NumberOfTurns = this->NumberOfTurns;
-		copy->Points = this->Points;
-		//copy->Dipoles = this->Dipoles; // no, disaster
-		return copy;
-	}
-
-	void PolygonalWireAntenna::Delete() {
-		this->DetachFrom(this);
-	}
-
-    void PolygonalWireAntenna::Release() {
-		delete this;
-	}
-
-    void PolygonalWireAntenna::SetMinDipoleRatio (const Real& ratio) {
-        minDipoleRatio = ratio;
-    }
-
-    void PolygonalWireAntenna::SetMinDipoleMoment (const Real& m) {
-        minDipoleMoment = m;
-    }
-
-    void PolygonalWireAntenna::SetMaxDipoleMoment (const Real& m) {
-        maxDipoleMoment = m;
-    }
-
-	// ====================  OPERATIONS    =======================
-
-	void PolygonalWireAntenna::ApproximateWithElectricDipoles(const Vector3r &rp) {
-        // Only resplit if necessary. Save a few cycles if repeated
-        if ( (rRepeat-rp).norm() > 1e-16 ) {
-		    for (unsigned int id=0; id<Dipoles.size(); ++id) {
-			    Dipoles[id]->Delete();
-		    }
-		    Dipoles.clear();
-
-		    // loop over all segments
-		    for (int iseg=0; iseg<NumberOfPoints-1; ++iseg) {
-			    InterpolateLineSegment(Points.col(iseg), Points.col(iseg+1), rp);
-		    }
-            rRepeat = rp;
-
-        } else {
-            for (unsigned int id=0; id<Dipoles.size(); ++id) {
-                Dipoles[id]->SetFrequencies(Freqs);
-            }
-        }
-	}
-
-	Vector3r PolygonalWireAntenna::ClosestPointOnLine(const Vector3r &p1,
-					const Vector3r &p2, const Vector3r &tp) {
-
-		Vector3r v1 = p2 - p1;
-		Vector3r v2 = p1 - tp;
-		Vector3r v3 = p1 - p2;
-		Vector3r v4 = p2 - tp;
-
-		Real dot1 = v2.dot(v1);
-		Real dot2 = v1.dot(v1);
-		Real dot3 = v4.dot(v3);
-		Real dot4 = v3.dot(v3);
-		Real t1 = -1.*dot1/dot2;
-		Real t2 = -1.*dot3/dot4;
-
-		Vector3r pos =  p1+v1*t1 ;
-
-		// check if on line
-		//	else give back the closest end point
-		if ( t1>=0 && t2>=0. ) {
-			return pos;
-		} else if (t1<0) {
-			return p1;
-		} else {
-			return p2;
-		}
-	}
-
-	void PolygonalWireAntenna::PushXYZDipoles(const Vector3r &step,
-				    const Vector3r &cp, const Vector3r &dir,
-					std::vector<DipoleSource*> &xDipoles) {
-
-		Real scale = (Real)(NumberOfTurns)*Current;
-
-        DipoleSource *tx = DipoleSource::New();
-		    tx->SetLocation(cp);
-		    tx->SetType(UNGROUNDEDELECTRICDIPOLE);
-			tx->SetPolarisation(dir);
-			tx->SetFrequencies(Freqs);
-			tx->SetMoment(scale*step.norm());
-			xDipoles.push_back(tx);
-	}
-
-	void PolygonalWireAntenna::CorrectOverstepXYZDipoles(const Vector3r &step,
-				    const Vector3r &cp,	const Vector3r &dir,
-					std::vector<DipoleSource*> &xDipoles ) {
-
-		Real scale = (Real)(NumberOfTurns)*Current;
-
-		// X oriented dipoles
-		if (step.norm() > minDipoleMoment) {
-			xDipoles[xDipoles.size()-1]->SetLocation(cp);
-			xDipoles[xDipoles.size()-1]->SetMoment(scale*step.norm());
-		}
-	}
-
-	void PolygonalWireAntenna::InterpolateLineSegment(const Vector3r &p1,
-					const Vector3r &p2, const Vector3r & tp) {
-
-
-		Vector3r phat = (p1-p2).array() / (p1-p2).norm();
-		Vector3r c    = this->ClosestPointOnLine(p1, p2, tp);
-		Real dtp = (tp-c).norm();    // distance to point at c
-		Real dc1 = (p1-c).norm();    // distance to c from p1
-		Real dc2 = (p2-c).norm();    // distance to c from p1
-
-        // unit vector
-		Vector3r cdir = (p2-p1).array() / (p2-p1).norm();
-
-		///////////////////
-		// dipoles for this segment
-		std::vector<DipoleSource*>           xDipoles;
-
-		// go towards p1
-		if ( ((c-p1).array().abs() > minDipoleMoment).any() ) {
-
-			// cp = current pos, lp = last pos
-			Vector3r cp = c + phat*(dtp*minDipoleRatio)*.5;
-			Vector3r lp = c;
- 			Real dist = (cp-p1).norm();
- 			Real dist_old = dist+1.;
-
-			// check that we didn't run past the end, or that we aren't starting at
-			// the end, or that initial step runs over!
-			Vector3r dir = (p1-cp).array() / (p1-cp).norm();   // direction of movement
-			Vector3r step = phat*(dtp*minDipoleRatio);
- 			Vector3r stepold = Vector3r::Zero();
-
-			// (dir-phat) just shows if we are stepping towards or away  from p1
-			while (dist < dist_old && (dir-phat).norm() < 1e-8) {
-
-				PushXYZDipoles(step, cp, cdir, xDipoles);
-
-				// Make 1/2 of previous step, 1/2 of this step, store this step
-				stepold  = step;
-				step     = phat*( (cp-tp).norm()*minDipoleRatio );
-			    while ( (step.array().abs() > maxDipoleMoment).any() ) {
-				    step *= .5;
-			    }
-				lp       = cp;
-				cp      += .5*stepold + .5*step;
-				dist     = (cp-p1).norm();
-				dir      = (p1-cp).array() / (p1-cp).norm();
-			}
-
-			// cp now points to end last of dipole moments
-			cp -= .5*step;
-
-			// Fix last dipole position, so that entire wire is represented,
-			// and no more
-			Real distLastSeg = (c - cp).norm();
-
-			if (distLastSeg + minDipoleMoment < dc1) {
-				// case 1: understep, add dipole
-				step  = (p1-cp).array();
-				cp   += .5*step;
-				PushXYZDipoles(step, cp, cdir, xDipoles);
-			} else if (distLastSeg > dc1 + minDipoleMoment) {
-				// case 2: overstep, reposition dipole and size
-				step  = (p1 - (lp-.5*stepold));
-				cp =  (lp-.5*stepold) + (.5*step);
-				CorrectOverstepXYZDipoles(step, cp, cdir, xDipoles);
-			}
-			// else case 0: nearly 'perfect' fit do nothing
-		}
-
-		// go towards p2
-		if ( ( (c-p2).array().abs() > minDipoleMoment).any() ) {
-
- 			// cp = current pos, lp = last pos
- 			Vector3r step = -phat*(dtp*minDipoleRatio);
-			while ( (step.array().abs() > maxDipoleMoment).any() ) {
-				step *= .5;
-			}
-
- 			Vector3r cp = c + step*.5;
- 			Vector3r lp = c;
-  			Real dist = (p2-cp).norm();
-  			Real dist_old = dist+1e3;
-
-			// check that we didn't run past the end, or that we aren't starting at
-			// the end, or that initial step runs over!
-			Vector3r dir = (p2-cp).array() / (p2-cp).norm();   // direction of movement
-
- 			Vector3r stepold = Vector3r::Zero();
-
- 			// (dir-phat) just shows if we are stepping towards or away  from p1
- 			while (dist < dist_old && (dir+phat).norm() < 1e-8) {
-
- 				PushXYZDipoles(step, cp, cdir, xDipoles);
-
-				// Make 1/2 of previous step, 1/2 of this step, store this step
-				stepold  = step;
-				step     = -phat*( (cp-tp).norm()*minDipoleRatio );
-			    while ( (step.array().abs() > maxDipoleMoment).any() ) {
-				    step *= .5;
-			    }
-				lp       = cp;
-				cp      += .5*stepold + .5*step;
-				dist     = (cp-p2).norm();
-				dir      = (p2-cp).array() / (p2-cp).norm();
-			}
-
-			// cp now points to end last of dipole moments
-			cp -= .5*step;
-
-			// Fix last dipole position, so that entire wire is represented,
-			// and no more
-			Real distLastSeg = (c - cp).norm();
-			if (distLastSeg + minDipoleMoment < dc2) {
-				// case 1: understep, add dipole
-				step  = (p2-cp).array();
-				cp   += .5*step;
-				PushXYZDipoles(step, cp, cdir, xDipoles);
-
-			} else if (distLastSeg > dc2 + minDipoleMoment) {
-
-				// case 2: overstep, reposition dipole and size
-				step  = (p2 - (lp-.5*stepold));
-				cp =  (lp-.5*stepold) + (.5*step);
-				CorrectOverstepXYZDipoles(step, cp, cdir, xDipoles);
-
-			}
-			// else case 0: nearly 'perfect' fit do nothing
-		}
-		Dipoles.insert(Dipoles.end(), xDipoles.begin(), xDipoles.end());
-	}
-
-    #ifdef HAVE_YAMLCPP
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  PolygonalWireAntenna
-    //      Method:  Serialize
-    //--------------------------------------------------------------------------------------
-    YAML::Node PolygonalWireAntenna::Serialize (  ) const {
-        YAML::Node node = WireAntenna::Serialize();
-        node.SetTag( this->Name );
-        node["minDipoleRatio"]  = minDipoleRatio;
-        node["maxDipoleMoment"] = maxDipoleMoment;
-        node["minDipoleMoment"] = minDipoleMoment;
-        return node;
-    }		// -----  end of method PolygonalWireAntenna::Serialize  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  WireAntenna
-    //      Method:  DeSerialize
-    //--------------------------------------------------------------------------------------
-    PolygonalWireAntenna* PolygonalWireAntenna::DeSerialize ( const YAML::Node& node ) {
-        PolygonalWireAntenna* Object = new PolygonalWireAntenna(node);
-        Object->AttachTo(Object);
-        DESERIALIZECHECK( node, Object )
-        return Object ;
-    }		// -----  end of method WireAntenna::DeSerialize  -----
-
-    #endif
-
-}

LemmaCore/src/QWEKey.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/.
- */
-
-/*      Original code is port of algorithm published by Key2011
-        %------------------------------------------------------------------%
-        % Copyright (c) 2012 by the Society of Exploration Geophysicists.  %
-        % For more information, go to http://software.seg.org/2012/0003 .  %
-        % You must read and accept usage terms at:                         %
-        % http://software.seg.org/disclaimer.txt before use.               %
-        %------------------------------------------------------------------%
-*/
-
-/**
- * @file
- * @date      02/12/2014 10:28:15 AM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, XRI Geophysics, LLC
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include "QWEKey.h"
-
-//#include <Eigen/Eigenvalues>
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator<<(std::ostream &stream, const QWEKey &ob) {
-
-        stream << *(HankelTransform*)(&ob);
-
-        return stream;
-    }
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  QWEKey
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    //
-    QWEKey::QWEKey (const std::string& name) : HankelTransform(name), RelTol(1e-12), AbsTol(1e-32), nQuad(61), nDelay(1),
-    //QWEKey::QWEKey (const std::string& name) : HankelTransform(name), RelTol(1e-38), AbsTol(1e-48), nQuad(39), nDelay(5),
-        nIntervalsMax(40) {
-        BesselWeights( J0 ); // TODO experiment with zero weight (J0, J1) options, should be static one time method
-    }  // -----  end of method QWEKey::QWEKey  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  New()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    QWEKey* QWEKey::New() {
-        QWEKey*  Obj = new QWEKey("QWEKey");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  ~QWEKey
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    QWEKey::~QWEKey () {
-
-    }  // -----  end of method QWEKey::~QWEKey  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  Delete
-    // Description:  public destructor
-    //--------------------------------------------------------------------------------------
-    void QWEKey::Delete() {
-        this->DetachFrom(this);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void QWEKey::Release() {
-        delete this;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  Zgauss
-    //--------------------------------------------------------------------------------------
-    Complex QWEKey::Zgauss ( const int &ikk, const EMMODE &imode,
-                            const int &itype, const Real &rho,
-                            const Real &wavef, KernelEm1DBase *Kernel ) {
-        return Textrap(Kernel->GetManagerIndex(), Tn(Kernel->GetManagerIndex())) ;
-    }		// -----  end of method QWEKey::Zgauss  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void QWEKey::ComputeRelated ( const Real& rho, KernelEm1DBase* Kernel ) {
-        return ;
-    }		// -----  end of method QWEKey::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void QWEKey::ComputeRelated ( const Real& rho, std::vector< KernelEm1DBase* > KernelVec ) {
-        return ;
-    }		// -----  end of method QWEKey::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  ComputeRelated
-    //--------------------------------------------------------------------------------------
-    void QWEKey::ComputeRelated ( const Real& rho, KernelEM1DManager* KernelManagerIn ) {
-        KernelManager = KernelManagerIn;  // OK becauase this is internal and we know what we are doing
-
-        Lambda = Bx.array()/rho;
-        Intervals = xInt.array()/rho;
-        int nrel = (int)(KernelManager->GetSTLVector().size());
-        Zans = Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
-        QWE(rho);
-        return ;
-    }		// -----  end of method QWEKey::ComputeRelated  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  GaussQuadWeights
-    //--------------------------------------------------------------------------------------
-    void QWEKey::GaussQuadWeights(const int& N) {
-        std::cerr<<"QWEKey needs work to remove Boost, etc." << std::endl;
-        // Below works with older Eigen, need to find problem
-//         VectorXr Nv = VectorXr::LinSpaced(N-1, 1, N-1);
-//         VectorXr beta  = 0.5 / (1.-(2.*Nv.array()).pow(-2)).sqrt();
-//         MatrixXr T = MatrixXr::Zero(N,N);
-//         //std::cerr << "Eigen ERROR BELOW, QWEKey.cpp  QWEKey::GaussQuadWeights, COMMENTED OUT ";
-//         T.bottomLeftCorner(N-1, N-1) = beta.asDiagonal();
-//         Eigen::SelfAdjointEigenSolver<MatrixXr> eig( T.selfadjointView< Eigen::Lower >() ); // PROBLEM LINE
-//             GaussAbscissa = eig.eigenvalues();
-//             GaussWeights = 2.*eig.eigenvectors().row(0).array().pow(2);
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  BesselWeights
-    //--------------------------------------------------------------------------------------
-    void QWEKey::BesselWeights ( const sZeroType& sType ) {
-    #ifdef HAVEBOOSTSPECIALFUNCTIONS
-        GaussQuadWeights(nQuad); // TODO should this be moved out of initializer?
-        std::vector<Real> bz;
-        xInt = VectorXr(nIntervalsMax+1);
-        xInt(0) = 1e-20;
-        switch (sType) {
-            case J0:
-                boost::math::cyl_bessel_j_zero(0.0, 1, nIntervalsMax, std::back_inserter(bz));
-                xInt.tail(nIntervalsMax) = VectorXr::Map(&bz[0], nIntervalsMax);
-                break;
-            case J1:
-                boost::math::cyl_bessel_j_zero(1.0, 1, nIntervalsMax, std::back_inserter(bz));
-                xInt.tail(nIntervalsMax) = VectorXr::Map(&bz[0], nIntervalsMax);
-                break;
-            case NPI:
-                xInt << 1e-20, VectorXr::LinSpaced(nIntervalsMax, 1, nIntervalsMax).array() * PI;
-                break;
-        }
-        VectorXr dx = ( xInt.tail(nIntervalsMax) - xInt.head(nIntervalsMax) ).array() / 2.;
-        //  x = GaussAbscissa
-        //        dx in every row        GaussWeights+1 rows, cols = n
-        //     dx[0] dx[1] ... dx[N]       Gw[0]  Gw[0]  ... ndX
-        //     dx[0] dx[1] ... dx[N]       Gw[1]
-        MatrixXr Bxm = (dx.transpose().replicate(GaussAbscissa.size(), 1)).eval().array() *
-                 ((GaussAbscissa.replicate(1, dx.size()).array() + 1.));
-        Bxm.array() += xInt.head(Bxm.cols()).transpose().replicate( Bxm.rows(), 1 ).array();
-        Bx =  VectorXr::Map( &Bxm(0,0), Bxm.size() );
-        BJ0 = VectorXr(Bx.size());
-        BJ1 = VectorXr(Bx.size());
-        int iw = 0;
-        for (int ii=0; ii<Bx.size(); ++ii) {
-            BJ0(ii) = boost::math::cyl_bessel_j(0, Bx(ii)) * GaussWeights(iw);
-            BJ1(ii) = boost::math::cyl_bessel_j(1, Bx(ii)) * GaussWeights(iw);
-            ++iw;
-            if (iw == GaussWeights.size()) iw = 0;
-        }
-        return ;
-    # else
-        std::cerr  << "QWEKey requires Boost functionalility that is missing\n";
-    #endif
-    }		// -----  end of method QWEKey::BesselWeights  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  QWE
-    //--------------------------------------------------------------------------------------
-    void QWEKey::QWE ( const Real& rho ) {
-
-        // TODO, is -1 needed here?
-        int nTerms = nIntervalsMax - nDelay;// - 1;
-        int nrel = (int)(KernelManager->GetSTLVector().size());
-
-        // TODO GREMLINS LIVE IN HERE
-        MatrixXcr prev = Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(1, nrel);
-        for (int i=0; i<nDelay; ++i) {
-            getEyKernel(i, 0, rho);
-            prev += Zans;
-        }
-
-        // Some of these are complex
-        TS      = MatrixXcr::Zero(nrel, nTerms);
-        Tn      = VectorXi::Zero(nrel);
-        Textrap = MatrixXcr::Zero(nrel, nTerms);
-        TrelErr = MatrixXr::Zero(nrel, nTerms);
-        TabsErr = MatrixXr::Zero(nrel, nTerms);
-        VectorXi Converged = VectorXi::Zero(nrel);
-
-        // is nTerms right, 1 array shifting
-        for (int i=nDelay; i<nTerms; ++i) {
-
-            int n = i-nDelay;
-            getEyKernel(i, 0, rho);
-
-            for (int j=0; j<nrel; ++j) {
-
-                if (!Converged(j)) { //continue;
-
-                    Tn(j) = n;                            // order of the expansion
-                    TS(j,n+1) = TS(j, n) + Zans(0, j);    // working array for transformation
-
-                    /* Compute the Shanks transform using the Epsilon algorithm:
-                        Structured after Weniger (1989, p26) */
-                    /* TI - some kind ob bug here, shanks extrapolation doesn't buy much for TEM at least */
-                    Complex aux2(0);
-                    for (int k=n+1; k>0; --k) {
-                        Complex aux1 = aux2;
-                        aux2 = TS(j,k-1);
-                        Complex ddff = TS(j,k) - aux2;
-                        if (std::abs(ddff) < std::numeric_limits<Real>::min() ) {
-                            TS(j,k-1) = std::numeric_limits<Real>::max() ;
-                        } else {
-                            TS(j,k-1) = aux1 + 1./ddff;
-                        }
-
-                    }
-
-                    // The extrapolated result plus the prev integration term:
-                    Textrap(j,n) = TS(j, (n-1)%2)+prev(0, j);
-                    //Textrap(j,n) = TS(j, n%2 + 1)+prev(0, j);
-
-                    // Step 3: Analyze for convergence:
-                    if (n > 1) {
-                        TabsErr(j,n) = std::abs( Textrap(j, n) - Textrap(j, n-1));
-                        TrelErr(j,n) = TabsErr(j, n) / std::abs(Textrap(j, n)) ;
-                        Converged(j) = TrelErr(j,n) < RelTol + AbsTol/std::abs(Textrap(j,n));
-                    }
-                }
-            }
-            if ( Converged.all() == 1 ) break;
-        }
-
-        // Trim up results
-        // Clean up the T structure arrays? We can't really do this
-        // because they are fixed size, maybe see how they are used and
-        // init to zero. If they are only summed we are OK.
-        /*
-        for (int j = 0; j<nrel; ++j) {:nKernels
-            n = Tn(j);
-            T(j).extrap = T(j).extrap(1:n);
-            T(j).relErr = T(j).relErr(1:n);
-            T(j).absErr = T(j).absErr(1:n);
-        }
-        */
-        return ;
-    }		// -----  end of method QWEKey::QWE  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  QWEKey
-    //      Method:  getEyKernel
-    //--------------------------------------------------------------------------------------
-    void QWEKey::getEyKernel ( const int& i, const int& idx, const Real& rho ) {
-        int bidx = i*nQuad;
-        int nrel = (int)(KernelManager->GetSTLVector().size());
-        Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic > Zwork =
-            Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic>::Zero(nQuad, nrel);
-        for (int ik=0; ik<nQuad; ++ik) {
-            KernelManager->ComputeReflectionCoeffs( Lambda(bidx+ik), idx, rho );
-            for (int ir2=0; ir2<nrel; ++ir2) {
-                // Zwork* needed due to sign convention (e^-jwt) of FT in filter weights
- 			    Zwork(ik, ir2) =    std::conj(KernelManager->GetSTLVector()[ir2]->RelBesselArg(Lambda(bidx+ik)));
- 			}
-        }
-
-        Real bma  = (Intervals(i+1)-Intervals(i))/2;
-        for (int ir2=0; ir2<nrel; ++ir2) {
-            if (KernelManager->GetSTLVector()[ir2]->GetBesselOrder() == 0) {
-                Zans(0, ir2) = bma * Zwork.col(ir2).dot( BJ0.segment(bidx, nQuad) ); // / rho;
-            } else {
-                Zans(0, ir2) = bma * Zwork.col(ir2).dot( BJ1.segment(bidx, nQuad) ); // / rho;
-            }
-        }
-        // fcount += nQuad
-        return ;
-    }		// -----  end of method QWEKey::getEyKernel  -----
-
-    void QWEKey::TestPrivate(const int& N) {
-
-        //GaussQuadWeights(N);
-        //std::cout << "abscissa\n" << GaussAbscissa << std::endl;
-        //std::cout << "weights\n" << GaussWeights << std::endl;
-        BesselWeights( J1 );
-        //BesselZeros(0, N);
-        std::cout << std::scientific;
-        std::cout << "BJ0" << BJ0 << std::endl;
-        std::cout << "BJ1" << BJ1 << std::endl;
-        //std::cout << "Bess Zero\n" << xInt << std::endl;
-
-    }
-
-}		// -----  end of Lemma  name  -----
-

LemmaCore/src/rectilineargrid.cpp → LemmaCore/src/RectilinearGrid.cpp

   @version  $Id: rectilineargrid.cpp 193 2014-11-10 23:51:41Z tirons $
  **/
 
-#include "rectilineargrid.h"
+#include "RectilinearGrid.h"
 
 namespace Lemma {
 
 
     }
 
-    RectilinearGrid* RectilinearGrid::New() {
-        RectilinearGrid*  Obj = new RectilinearGrid("RectilinearGrid");
-        Obj->AttachTo(Obj);
-        return Obj;
-    }
-
-    void RectilinearGrid::Delete() {
-        this->DetachFrom(this);
-    }
-
-    void RectilinearGrid::Release() {
-        delete this;
+    std::shared_ptr< RectilinearGrid > RectilinearGrid::NewSP() {
+        std::shared_ptr<RectilinearGrid> sp(new  RectilinearGrid("RectilinearGrid"), LemmaObjectDeleter() );
+        return sp;
     }
 
     // ====================  OPERATIONS    =======================