Cleaning up the code

Documentation/Doxyfile.in

@@ -27,6 +27,8 @@ DOXYFILE_ENCODING      = UTF-8
 
 PROJECT_NAME           = Lemma
 
+# Copies main logo so that the html and latex can find it
+PROJECT_LOGO           = @CMAKE_CURRENT_SOURCE_DIR@/Documentation/lemma.png
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number.
 # This could be handy for archiving the generated documentation or
@@ -588,7 +590,7 @@ USE_MATHJAX = YES
 #INPUT                  = @CMAKE_CURRENT_SOURCE_DIR@/LemmaCore/include @CMAKE_CURRENT_SOURCE_DIR@/Modules/FEM4EllipticPDE.git/include
 INPUT   = @CMAKE_CURRENT_SOURCE_DIR@/Modules/*/include
 INPUT  += @CMAKE_CURRENT_SOURCE_DIR@/Modules/
-INPUT  += @CMAKE_CURRENT_SOURCE_DIR@/Documentation/dox
+INPUT  += @CMAKE_CURRENT_SOURCE_DIR@/Documentation/
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is

LemmaCore/CMakeLists.txt

@@ -1,47 +0,0 @@
-include_directories(${CMAKE_INSTALL_PREFIX}/include)
-
-add_subdirectory("src")
-
-#option (SHARED_LEMMA_LIB off)
-#
-#if (SHARED_LEMMA_LIB)
-#	add_library( lemmacore SHARED ${SOURCE} )  
-#else()
-#	add_library( lemmacore STATIC ${SOURCE} )  
-#endif()
-add_library( lemmacore ${SOURCE} )  
-
-set_target_properties(lemmacore PROPERTIES 
-	VERSION  "${LEMMA_VERSION}"
-	SOVERSION "${LEMMA_VERSION_MAJOR}.${LEMMA_VERSION_MINOR}"
-	PROJECT_LABEL "Lemma ${LABEL_SUFFIX}"
-)
-
-# Linking
-add_dependencies(lemmacore YAML-CPP)
-if (LEMMA_TINYXML_SUPPORT)
-	add_dependencies(lemmacore TINYXML2)
-endif()
-if (LEMMA_MATIO_SUPPORT)
-	add_dependencies(lemmacore MATIO)
-endif()
-
-if ( LEMMA_VTK6_SUPPORT OR LEMMA_VTK7_SUPPORT ) 
-	target_link_libraries(lemmacore ${VTK_LIBRARIES})
-	target_link_libraries(lemmacore "matplot")
-endif()
-
-target_link_libraries(lemmacore "yaml-cpp")
-
-# Testing
-if (LEMMA_ENABLE_TESTING)
-	add_subdirectory(testing)
-endif()
-
-# Install
-install ( TARGETS lemmacore DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
-
-option( LEMMA_BUILD_EXAMPLES "Compile example Lemma applications" OFF )
-if (LEMMA_BUILD_EXAMPLES)
-	add_subdirectory(examples)
-endif()

LemmaCore/examples/CMakeLists.txt

@@ -1,33 +0,0 @@
-#FILE(GLOB  examples  "*.cpp")
-
-#add_executable( datatem datatem.cpp )
-#target_link_libraries(datatem "lemmacore")
-
-#add_executable( wireantenna wireantenna.cpp )
-#target_link_libraries(wireantenna "lemmacore")
-
-#add_executable( DCIPElectrode  DCIPElectrode.cpp )
-#target_link_libraries(DCIPElectrode "lemmacore")
-
-#add_executable( digitalfiltercostrans  digitalfiltercostrans.cpp )
-#target_link_libraries(digitalfiltercostrans "lemmacore")
-
-#add_executable( dipolefreqsweep  dipolefreqsweep.cpp )
-#target_link_libraries(dipolefreqsweep "lemmacore")
-
-#add_executable( dipolesource  dipolesource.cpp )
-#target_link_libraries(dipolesource "lemmacore")
-
-#add_executable( edipole  edipole.cpp )
-#target_link_libraries(edipole "lemmacore")
-
-#add_executable( emdipearth1d  emdipearth1d.cpp )
-#target_link_libraries(emdipearth1d "lemmacore")
-
-#add_executable( femforward  femforward.cpp )
-#target_link_libraries(femforward "lemmacore")
-
-add_executable( filter  filter.cpp )
-target_link_libraries(filter "lemmacore")
-
-

LemmaCore/examples/filter.cpp

@@ -1,52 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  utfilter.cpp
-//
-//        Created:  07/20/2010 10:12:07 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/>.
-//
-// ===========================================================================
-
-/**
-  @author   Trevor Irons
-  @date     07/20/2010
-  @version   0.0
- **/
-
-#include "WindowFilter.h"
-using namespace Lemma;
-
-int main() {
-
-    auto Hamming = WindowFilter::NewSP();
-
-        Hamming->SetWindowType( HANNING );
-        Hamming->SetSamplingInterval(1e-4);
-        Hamming->SetBandwidth(300);
-        Hamming->SetNumberOfSamples(1./1e-4);
-
-    std::cout << Hamming->GetFilterCoefficients() //.transpose()
-              << std::endl;
-
-
-}

LemmaCore/examples/utORS.cpp

@@ -1,342 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  utdipolesource.cpp
-//
-//    Description:
-//
-//        Version:  0.0
-//        Created:  12/02/2009 11:57:14 AM
-//       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 <iostream>
-#include <fstream>
-
-#include "dipolesource.h"
-#include "layeredearth.h"
-#include "receiverpoints.h"
-#include "emearth1d.h"
-#include "WireAntenna.h"
-#include "PolygonalWireAntenna.h"
-
-#if  LEMMAUSEVTK
-#include "vtkRenderer.h"
-#include "vtkRenderWindow.h"
-#include "vtkRenderWindowInteractor.h"
-#include "vtkRenderLargeImage.h"
-#include "vtkPNGWriter.h"
-#include "vtkRectilinearGrid.h"
-#include "vtkXMLRectilinearGridWriter.h"
-#include "vtkDoubleArray.h"
-#include "vtkFieldData.h"
-#include "vtkCellData.h"
-#endif     // -----  not LEMMA_USE_VTK  -----
-
-// For testing purposes disable VTK and run scale.sh
-//#undef LEMMAUSEVTK
-
-#include "timer.h"
-
-using namespace Lemma;
-
-double randDouble(double low, double high) {
-	//srand(time(0));
-	double temp;
-	/* swap low & high around if the user makes no sense */
-	if (low > high)	{
-	temp = low;
-	low = high;
-	high = temp;
-	}
-	/* calculate the random number & return it */
-	temp = (rand() / (static_cast<double>(RAND_MAX) + 1.0))
-	* (high - low) + low;
-	return temp;
-}
-
-
-int main() {
-
-	// Keep track of time
-	jsw_timer timer;
-
-
-	srand(time(0));
-
-	PolygonalWireAntenna *pa = PolygonalWireAntenna::New();
-	pa->SetNumberOfFrequencies(1);
-	pa->SetFrequency(0, 540000);
-    Real Depth  =   370;  // nominal depth
-    Real Width  = 0.14;  // transmitter height
-    Real Height = 0.70;//  .14;  //.014;  // transmitter width
-
-
-	pa->SetNumberOfPoints(5);
-    /*
-    pa->SetPoint(0, Vector3r(       0,       0, Depth));
-	pa->SetPoint(1, Vector3r(       0,       0, Depth+Height));
-	pa->SetPoint(2, Vector3r(       0,   Width, Depth+Height));
-	pa->SetPoint(3, Vector3r(       0,   Width, Depth));
-	pa->SetPoint(4, Vector3r(       0,       0, Depth));
-    */
-
-    pa->SetPoint(0, Vector3r(   -Width/2., -Height/2., Depth));
-	pa->SetPoint(1, Vector3r(    Width/2., -Height/2., Depth));
-	pa->SetPoint(2, Vector3r(    Width/2.,  Height/2., Depth));
-	pa->SetPoint(3, Vector3r(   -Width/2.,  Height/2., Depth));
-	pa->SetPoint(4, Vector3r(   -Width/2., -Height/2., Depth));
-
-	pa->SetCurrent(1.);
-    pa->SetNumberOfTurns(6);
-	//Vector3r rp = Vector3r::Random(3);
-	//rp << 150., 10, 0.;
-	//rp << -27.1456, 15.2350, -1e-3;
-	//rp << randDouble(-35,35), randDouble(-35,35), randDouble(-35,35);
-	//rp << 3.22806, -13.1548, 14.9695;
-	//rp.setRandom(3);
-	//std::cout <<  "rp " << rp.transpose() << std::endl;
-	//pa->ApproximateWithElectricDipoles(rp);
-
-
-	// Define model
-    Real Sigma = 1.0/20. ; // .05;
-	VectorXcr sigma(2);
-		sigma << Complex(0.,0), Complex(Sigma,0);
-	VectorXr  thick(1);
-		thick << 10;
-	LayeredEarthEM *earth = LayeredEarthEM::New();
-		earth->SetNumberOfLayers(2);
-		earth->SetLayerConductivity(sigma);
-		//earth->SetLayerThickness(thick);
-
-	// Receivers
-	ReceiverPoints *receivers = ReceiverPoints::New();
-		Vector3r loc;
-		Real ox    =    -5.*Width - .003373;
-		Real oy    =    -3.*Height - .003373;
-		Real oz    =    Depth - Height/2. - .003373;
-		int nx     =   120; // 60;
-		int ny     =   180; //  50;
-		int nz     =   100; // 40;
-		Real hx    =    11.*Width/nx;
-		Real hy    =     7.*Height/ny;
-		Real hz    =     1.*Height/nz;
-
-        receivers->SetNumberOfReceivers(nx*ny*nz);
-		int ir = 0;
-		for (int iz=0; iz<nz; ++iz) {
-		for (int iy=0; iy<ny; ++iy) {
-		for (int ix=0; ix<nx; ++ix) {
-			loc << ox+ix*hx, oy+iy*hy, oz+iz*hz;
-			receivers->SetLocation(ir, loc);
-			++ ir;
-		}
-        }
-        }
-
-	// EmEarth
-	EMEarth1D  *EmEarth = EMEarth1D::New();
-		//EmEarth->AttachWireAntenna(wire);
-		EmEarth->AttachWireAntenna(pa);
-		EmEarth->AttachLayeredEarthEM(earth);
-		EmEarth->AttachReceiverPoints(receivers);
-		EmEarth->SetFieldsToCalculate(E);
-        //EmEarth->SetHankelTransformMethod(GAUSSIANQUADRATURE);
-        EmEarth->SetHankelTransformMethod(ANDERSON801);
-
-	// Do calculation
-	timer.begin();
-	EmEarth->CalculateWireAntennaFields();
-	Real paTime = timer.end();
-	std::cout << "Polygonal wire antennae time: " << paTime << "\n";
-
-	//EmEarth->AttachWireAntenna(wire);
-	//timer.begin();
-	//EmEarth->CalculateWireAntennaFields();
-	//Real waTime = timer.end();
-	//std::cout << "Fixed wire antennae time: " << waTime << "\n";
-/*
-	depth = depth2;
-	std::fstream real("reale_lay.dat", std::ios::out);
-	std::fstream imag("image_lay.dat", std::ios::out);
-	for (int iz=0; iz<nz; ++iz) {
-		Vector3cr temp = receivers->GetEfield(0,iz);
-		real << ox << "\t" << oy << "\t" << depth << "\t"
-				<< temp(0).real() << "\t" << temp(1).real()
-				<< "\t" << temp(2).real() << std::endl;
-		imag << ox << "\t" << oy << "\t" << depth << "\t"
-				<< std::imag(temp(0)) << "\t" << std::imag(temp(1))
-				<< "\t" << std::imag(temp(2)) << std::endl;
-		depth += dx;
-	}
-	real.close();
-	imag.close();
-*/
-
-	//wire->Delete();
-#if  LEMMAUSEVTK
-
-    // Set Coordinates
-    vtkDoubleArray *xCoords = vtkDoubleArray::New();
-    xCoords->InsertNextValue(ox-hx/2.);
-    double xm1 = ox-hx/2.;
-    for (int ix=0; ix<nx; ix++) {
-        xCoords->InsertNextValue(xm1 + hx);
-        xm1 += hx;
-    }
-
-    vtkDoubleArray *yCoords = vtkDoubleArray::New();
-    yCoords->InsertNextValue(oy-hy/2.);
-    double ym1 = oy-hy/2.;
-    for (int iy=0; iy<ny; iy++) {
-        yCoords->InsertNextValue(ym1 + hy);
-        ym1 += hy;
-    }
-
-    vtkDoubleArray *zCoords = vtkDoubleArray::New();
-    zCoords->InsertNextValue(oz-hz/2.);
-    double zm1 = oz-hz/2.;
-    for (int iz=0; iz<nz; iz++) {
-        zCoords->InsertNextValue(zm1 + hz);
-        zm1 += hz;
-    }
-
-    vtkDoubleArray *EReal = vtkDoubleArray::New();
-    vtkDoubleArray *EImag = vtkDoubleArray::New();
-    vtkDoubleArray *Watts = vtkDoubleArray::New();
-    EReal->SetNumberOfComponents(3);
-    EImag->SetNumberOfComponents(3);
-    Watts->SetNumberOfComponents(1);
-
-    ir = 0;
-    Real WattsTotal(0);
-    Real WattsInterior(0);
-    for (int iz=0; iz<nz; ++iz) {
-    for (int iy=0; iy<ny; ++iy) {
-    for (int ix=0; ix<nx; ++ix) {
-        //sigmaArray->InsertTuple1(i,  sigma[ix][iy][iz] );
-		Vector3cr E = receivers->GetEfield(0, ir);
-        EReal-> InsertTuple3(ir, real(E(0)), real(E(1)), real(E(2)));
-        EImag-> InsertTuple3(ir, imag(E(0)), imag(E(1)), imag(E(2)));
-        //std::cout << std::abs(ox+ix*hx) << "\t"  <<  Width/2. << endl; // && std::abs(oy+iy*hy) > Height/2. ) { // && std::abs(oz+iz*hz - Depth) > Width/2. ) {
-        //if ( std::abs( ox+ix*hx ) < Width/2. && std::abs(oy+iy*hy) < Height/2. && std::abs(oz+iz*hz - Depth) < Width/2. ) {
-        if ( std::sqrt( std::pow(ox+ix*hx,2)  + std::pow(oz+iz*hz - Depth, 2) ) < .085 && std::abs(oy+iy*hy) < Height/2. ) {
-            Watts-> InsertTuple1(ir,  1e-20 );
-            WattsInterior += .5*  (( pow((std::abs(E(0)) + std::abs(E(1)) + std::abs(E(2))), 2)*Sigma)*hx*hy*hz );
-        } else {
-            Watts-> InsertTuple1(ir, .5* (pow( (std::abs(E(0)) + std::abs(E(1)) + std::abs(E(2))), 2)*Sigma)*hx*hy*hz );
-            //Watts-> InsertTuple1(ir,  1e-20 );
-            WattsTotal += .5*  (( pow((std::abs(E(0)) + std::abs(E(1)) + std::abs(E(2))), 2)*Sigma)*hx*hy*hz );
-        }
-		++ ir;
-    }
-    }
-    }
-    std::cout << "Total Power: " << Sigma << "\t" << WattsTotal << "\t" << WattsInterior << endl;
-
-    EReal->SetName("E_real");
-    EImag->SetName("E_imag");
-    Watts->SetName("Power");
-
-    vtkRectilinearGrid *rgrid = vtkRectilinearGrid::New();
-        rgrid->SetDimensions(nx+1,ny+1,nz+1);
-        rgrid->SetXCoordinates(xCoords);
-        rgrid->SetYCoordinates(yCoords);
-        rgrid->SetZCoordinates(zCoords);
-
-        rgrid->GetCellData()->AddArray(EReal);
-        rgrid->GetCellData()->AddArray(EImag);
-        rgrid->GetCellData()->AddArray(Watts);
-        //rgrid->Update();
-
-    vtkXMLRectilinearGridWriter *gridWrite = vtkXMLRectilinearGridWriter::New();
-        gridWrite->SetInputData(rgrid);
-        gridWrite->SetFileName("ors.vtr");
-        gridWrite->Write();
-        //gridWrite->Update();
-
-#endif
-	EmEarth->Delete();
-	receivers->Delete();
-	earth->Delete();
-
-#if  LEMMAUSEVTKX
-	// Create the usual rendering stuff.
-	vtkRenderer           *renderer = vtkRenderer::New();
-	vtkRenderWindow         *renWin = vtkRenderWindow::New();
-	vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
-
-	std::cout << "wire antennae approximating " << std::endl;
-	loc << 0, .5*Width, Depth+.5*Height;
-	pa->ApproximateWithElectricDipoles(loc);
-    std::cout <<  "Wire approximated with " << pa->GetNumberOfDipoles() << std::endl;
-
-    vtkActor **pdipActors = new vtkActor*[pa->GetNumberOfDipoles()];
-	for (int id=0; id<pa->GetNumberOfDipoles(); ++id) {
-		pdipActors[id] = pa->GetVtkActor(id);
-		renderer->AddActor(pdipActors[id]);
-	}
-
-    /*
-    vtkActor **dipActors = new vtkActor*[wire->GetNumberOfDipoles()];
-	for (int id=0; id<wire->GetNumberOfDipoles(); ++id) {
-		dipActors[id] = wire->GetVtkActor(id);
-		renderer->AddActor(dipActors[id]);
-	}
-    */
-
-	renderer->SetBackground(1,1,1);
-
-	// Render the window
-	renWin->AddRenderer(renderer);
-	renWin->SetWindowName("Wire antennae");
-
-	iren->SetRenderWindow(renWin);
-	iren->Initialize();
-	iren->Start();
-	iren->Render();
-
-    #if 0
-	cout << "Enter File name?: ";
-	std::string pngName;
-	std::cin >> pngName;
-	vtkPNGWriter *pngwrite = vtkPNGWriter::New();
-	vtkRenderLargeImage *renlarge = vtkRenderLargeImage::New();
-	renlarge->SetInput(renderer);
-	renlarge->SetMagnification(2);
-	pngwrite->SetInputConnection(renlarge->GetOutputPort());
-	pngName.append(".png");
-	pngwrite->SetFileName(pngName.c_str());
-	pngwrite->Write();
-    #endif
-
-#endif     // -----  not LEMMA_USE_VTK  -----
-
-
-	//std::cout << *pa << std::endl;
-	//pa->Delete();
-
-	return 0;
-}

LemmaCore/examples/utQWEKey.cpp

@@ -1,34 +0,0 @@
-/* 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 01:01:29 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 "QWEKey.h"
-using namespace Lemma;
-
-int main() {
-
-    // TODO chech
-
-    QWEKey* QWE = QWEKey::New();
-    QWE->TestPrivate( 5 );
-    QWE->Delete();
-
-    return 0;
-}
-
-

LemmaCore/examples/utSerialize.cpp

@@ -1,86 +0,0 @@
-/* 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 01:31:26 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 "Lemma"
-
-using namespace Lemma;
-
-#ifdef  HAVE_YAMLCPP
-#include "yaml-cpp/yaml.h"
-
-int main() {
-
-    std::ofstream ofstr("output.yaml");
-    //ofstr << "%YAML 1.2\n" << "---\n";
-    //ofstr << "LEMMA_CLASSES:\n";
-
-    // This works for individual classes or even groups of unrelated classes. But
-    // How should references work? One option would be to hack YAML and allow for references
-    // across 'Docs'. This is maybe undesireable, as then it's not valid YAML anymore.
-    // OR we could have some other kind of IDENTIFIER that could be used and Connections could be
-    // made AFTER the whole file is processed?
-
-    // Alternative is each class is written to it's own file. And then implicit on the Serialize function, the file tags are written
-    // into the YAML instead of the pointer. Alternatively, tags could do this too.
-
-    // Or file could be saved as pointer.yaml
-
-    // *
-    // * Or a file contains all the subclasses it point to. So that it's self-enclosed. This is nice as it's quite
-    // * flexible. The only downwside is possible repeat of classes. Basically if the API is careful though, only 1
-    // * instance will need to be serialized.
-    // *
-
-
-    TEMTransmitter* Seq = TEMTransmitter::New();
-        Seq->SetRepFrequency( 20, KHZ );
-        VectorXr Times (18);
-        VectorXr Amps (18);
-        Times << 0.0, 0.03051, 0.10267, 0.19408, 0.19889, 0.21332, 0.74249, 1.3775, 1.83452, 2.52245, \
-                3.191132, 3.9031135, 4.0, 4.00484486, 4.123904, 4.200182, 4.20732, 4.212946;
-        Amps << 0.0, 14.71872, 62.34372, 114.84372, 117.84372, 118.96872, 118.96872, 118.96872, 118.96872,\
-                118.59372, 119.34372, 120.0, 120.0, 117.94176, 47.60364, 0.8905848, 0.1203888, 0.0;
-        Seq->SetWaveform(Times, Amps, MILLISEC);
-    // OK dump to disk
-    ofstr << *Seq ;
-    ofstr.close();
-    Seq->Delete();
-
-
-    // OK now load
-    std::ifstream ifstr("output.yaml");
-    std::vector<YAML::Node> nodes = YAML::LoadAll(ifstr);
-
-    TEMTransmitter* Seq2 = TEMTransmitter::DeSerialize( nodes[0] );
-    std::cout << "Loaded\n" << *Seq2;
-    Seq2->Delete();
-    ifstr.close();
-
-    //YAML::Node nodes = YAML::LoadFile("output.yaml");
-    //std::cout << nodes[0] << std::endl;
-    //std::cout << nodes[1] << std::endl;
-
-    exit(EXIT_SUCCESS);
-}
-
-#else
-int main() {
-
-}
-#endif

LemmaCore/examples/utSkyTEM.cpp

@@ -1,31 +0,0 @@
-/* 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      02/27/2015 11:02:43 AM
- * @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
- */
-
-// SkyTEM forward modelling programme
-
-#include "TEMSurvey.h"
-
-int main() {
-
-    std::cout << "SkyTEM modelling\n";
-
-
-
-}
-

LemmaCore/examples/utTEMSurvey.cpp

@@ -1,197 +0,0 @@
-/* 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      10/06/2014 10:37:30 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 "Lemma"
-using namespace Lemma;
-
-int main() {
-
-    // Each pulse sequence functions as an autonomous transmitter. A record may contain multiple transmitters (moments).
-    // There is some small overhead for wire loop locations, but generality is retained doing this, as well as monitoring of
-    // slight changes in geometry for both pulses.
-    TEMTransmitter* TxHM = TEMTransmitter::New();
-        TxHM->SetRepFrequency( 20, KHZ );
-        VectorXr Times (18);
-        VectorXr Amps (18);
-        Times << 0.0, 0.03051, 0.10267, 0.19408, 0.19889, 0.21332, 0.74249, 1.3775, 1.83452, 2.52245, \
-                3.191132, 3.9031135, 4.0, 4.00484486, 4.123904, 4.200182, 4.20732, 4.212946;
-        Amps << 0.0, 14.71872, 62.34372, 114.84372, 117.84372, 118.96872, 118.96872, 118.96872, 118.96872,\
-                118.59372, 119.34372, 120.0, 120.0, 117.94176, 47.60364, 0.8905848, 0.1203888, 0.0;
-        TxHM->SetWaveform( Times, Amps, MILLISEC );
-        // Define wire loop
-        TxHM->SetNumberOfPoints(8);
-        TxHM->SetPoint(0, Vector3r( -16.10,    2.13,  -34));
-        TxHM->SetPoint(1, Vector3r(  -7.51,   10.72,  -34));
-        TxHM->SetPoint(2, Vector3r(   7.51,   10.72,  -34));
-        TxHM->SetPoint(3, Vector3r(  14.92,    3.31,  -34));
-        TxHM->SetPoint(4, Vector3r(  14.92,   -3.31,  -34));
-        TxHM->SetPoint(5, Vector3r(   7.51,  -10.72,  -34));
-        TxHM->SetPoint(6, Vector3r(  -7.51,  -10.72,  -34));
-        TxHM->SetPoint(7, Vector3r( -16.10,   -2.13,  -34));
-        TxHM->SetNumberOfTurns(8);
-
-    // Each Transmitter needs its own `Receiver(s)', the only difference may be the time gates, but that's OK.
-    //     It's a minor amount of overhead for greatly improved genearality. As sometimes different gates are
-    //     masked.
-    TEMInductiveReceiver* RxHM = TEMInductiveReceiver::New();
-        RxHM->SetComponent( ZCOMPONENT );      // What about Overloaded to take (X), (X,Y), or (X,Y,Z) or what about tilt?
-        RxHM->SetMoment( 1 );                  // Normalized
-        RxHM->SetReferenceTime( 4., MILLISEC );
-        RxHM->SetRxLocation( (Vector3r() << -16.80, 0, -36.00).finished() );
-
-        // Gate Centres  ms
-        VectorXr centres (37);
-        centres << 7.15000000e-04,   2.21500000e-03,   4.21500000e-03,   6.21500000e-03,
-                   8.21500000e-03,   1.02150000e-02,   1.22150000e-02,   1.47150000e-02,
-                   1.82150000e-02,   2.27150000e-02,   2.82150000e-02,   3.52150000e-02,
-                   4.42150000e-02,   5.57150000e-02,   7.02150000e-02,   8.82150000e-02,
-                   1.10715000e-01,   1.38715000e-01,   1.74215000e-01,   2.19715000e-01,
-                   2.76715000e-01,   3.48715000e-01,   4.39715000e-01,   5.53715000e-01,
-                   6.97715000e-01,   8.79215000e-01,   1.10771500e+00,   1.39621500e+00,
-                   1.76021500e+00,   2.21871500e+00,   2.79671500e+00,   3.52571500e+00,
-                   4.44471500e+00,   5.60321500e+00,   7.06321500e+00,   8.90421500e+00,
-                   1.10667200e+01;
-        //centres.array() += 4.;
-
-        // Gate Widths  ms
-        VectorXr widths (37);
-        widths <<   4.30000000e-04,   1.43000000e-03,   3.43000000e-03,   5.43000000e-03,
-                    7.43000000e-03,   9.43000000e-03,   1.14300000e-02,   1.34300000e-02,
-                    1.64300000e-02,   2.04300000e-02,   2.54300000e-02,   3.14300000e-02,
-                    3.94300000e-02,   4.94300000e-02,   6.24300000e-02,   7.84300000e-02,
-                    9.84300000e-02,   1.23430000e-01,   1.54430000e-01,   1.94430000e-01,
-                    2.45430000e-01,   3.08430000e-01,   3.89430000e-01,   4.90430000e-01,
-                    6.17430000e-01,   7.78430000e-01,   9.80430000e-01,   1.23543000e+00,
-                    1.55743000e+00,   1.96343000e+00,   2.47443000e+00,   3.11943000e+00,
-                    3.93243000e+00,   4.95743000e+00,   6.24943000e+00,   7.87743000e+00,
-                    9.93143000e+00;
-
-        RxHM->SetWindows(centres, widths, MILLISEC);
-
-    TEMTransmitter* TxLM = TEMTransmitter::New();
-        TxLM->SetRepFrequency( 20, KHZ );
-        VectorXr TimesLM (18);
-        VectorXr AmpsLM (18);
-
-        TimesLM << -8.00000E-004, -7.86965E-004, -7.66493E-004, -7.23688E-004,
-                   -6.39938E-004, -5.16174E-004, -3.93340E-004, -2.63993E-004,
-                   -1.43952E-004, -7.15990E-006, -2.50712E-006,  0.00000E+000,
-                    2.19597E-007,  1.47193E-006,  3.34398E-006,  4.68669E-006,
-                    5.96484E-006,  7.04934E-006;
-        TimesLM.array() = TimesLM.array() + 8e-4;  // Valgrind Hack += yields error. Correct for SkyTEM convention
-
-
-        AmpsLM <<  0.00000E+000,  3.67188E-002,  6.17188E-002,  1.17969E-001,
-                   2.14844E-001,  3.28906E-001,	 4.75781E-001,  6.30469E-001,
-                   7.82031E-001,  9.92969E-001,	 1.00000E+000,  1.00000E+000,
-                   9.63459E-001,  6.01030E-001,  2.29652E-001,  8.64702E-002,
-                   2.53196E-002,  0.00000E+000;
-        AmpsLM.array() = AmpsLM.array() * 8.;   // Also correct for SkyTEM convention in .geo file
-
-        TxLM->SetWaveform( TimesLM, AmpsLM, SEC );
-        // Define wire loop
-        TxLM->SetNumberOfPoints(8);
-        TxLM->SetPoint(0, Vector3r( -16.10,    2.13,  -34));
-        TxLM->SetPoint(1, Vector3r(  -7.51,   10.72,  -34));
-        TxLM->SetPoint(2, Vector3r(   7.51,   10.72,  -34));
-        TxLM->SetPoint(3, Vector3r(  14.92,    3.31,  -34));
-        TxLM->SetPoint(4, Vector3r(  14.92,   -3.31,  -34));
-        TxLM->SetPoint(5, Vector3r(   7.51,  -10.72,  -34));
-        TxLM->SetPoint(6, Vector3r(  -7.51,  -10.72,  -34));
-        TxLM->SetPoint(7, Vector3r( -16.10,   -2.13,  -34));
-        TxLM->SetNumberOfTurns(8);
-
-
-    TEMInductiveReceiver* RxLM = TEMInductiveReceiver::New();
-        RxLM->SetComponent( ZCOMPONENT );      // What about Overloaded to take (X), (X,Y), or (X,Y,Z) or what about tilt?
-        RxLM->SetMoment( 1 );                  // Normalized
-        RxLM->SetReferenceTime( 8e-4, SEC );
-        RxLM->SetRxLocation( (Vector3r() << -16.80, 0, -36.00).finished() );
-
-        // Gate Centres  ms
-        VectorXr centresLM (26);
-            centresLM << 7.150000E-07, 2.215000E-06, 4.215000E-06, 6.215000E-06, 8.215000E-06,
-                         1.021500E-05, 1.221500E-05, 1.471500E-05, 1.821500E-05, 2.271500E-05,
-                         2.821500E-05, 3.521500E-05, 4.421500E-05, 5.571500E-05, 7.021500E-05,
-                         8.821500E-05, 1.107150E-04, 1.387150E-04, 1.742150E-04, 2.197150E-04,
-                         2.767150E-04, 3.487150E-04, 4.397150E-04, 5.537150E-04, 6.977150E-04,
-                         8.792150E-04;
-
-        VectorXr widthsLM (26);
-            widthsLM << 5.700000E-07, 1.570000E-06, 1.570000E-06, 1.570000E-06, 1.570000E-06,
-                        1.570000E-06, 1.570000E-06, 2.570000E-06, 3.570000E-06, 4.570000E-06,
-                        5.570000E-06, 7.570000E-06, 9.570000E-06, 1.257000E-05, 1.557000E-05,
-                        1.957000E-05, 2.457000E-05, 3.057000E-05, 3.957000E-05, 5.057000E-05,
-                        6.257000E-05, 8.057000E-05, 1.005700E-04, 1.265700E-04, 1.605700E-04,
-                        2.015700E-04;
-
-        RxLM->SetWindows(centresLM, widthsLM, SEC);
-
-
-
-    // Specifies survey, this is the Glue Class, the top of the structure, etc.
-    TEMSurvey* Survey = TEMSurvey::New();
-        Survey->SetNumberOfLines(1);  // Flight lines or
-                                      // Internally each line is a class? But that's sort of hidden to the
-                                      // end user. Having each line seperate is nice for constrained inversion, where
-                                      // each line is a nice thing to deal with.
-        Survey->GetLine(0)->SetNumberOfRecords(1);    // Each Record then contains everything needed for modelling response curve(s)
-        Survey->GetLine(0)->GetRecord(0)->SetNumberOfPulseSequences( 1 );
-        Survey->GetLine(0)->GetRecord(0)->SetTransmitterReceiverPair( 0, TxHM, RxHM );
-        //Survey->GetLine(0)->GetRecord(0)->SetTransmitterReceiverPair( 1, TxHM, RxHM );
-
-
-    LayeredEarthEM* Earth = LayeredEarthEM::New();
-        Earth->SetNumberOfLayers(31);
-        Earth->SetLayerThickness( (VectorXr(29) <<  5.00E+00,  5.40E+00,
-             5.80E+00, 6.30E+00, 6.80E+00, 7.30E+00, 7.80E+00, 8.50E+00,
-             9.10E+00, 9.80E+00, 1.06E+01, 1.14E+01, 1.23E+01, 1.33E+01,
-             1.43E+01, 1.54E+01, 1.66E+01, 1.79E+01, 1.93E+01, 2.08E+01,
-             2.25E+01, 2.42E+01, 2.61E+01, 2.81E+01, 3.03E+01, 3.27E+01,
-             3.52E+01, 3.80E+01, 4.10E+01).finished() );
-
-        VectorXcr rho = ( (VectorXcr(31) << 0, 1.54E+01, 4.21E+01,
-            9.25E+01, 1.26E+02, 1.17E+02, 7.57E+01, 3.21E+01, 1.40E+01, 1.96E+01,
-            2.67E+01, 2.56E+01, 2.00E+01, 1.86E+01, 2.31E+01, 2.97E+01, 3.50E+01,
-            3.79E+01, 3.75E+01, 3.32E+01, 2.52E+01, 1.57E+01, 8.38E+00, 5.38E+00,
-            5.49E+00, 6.34E+00, 7.07E+00, 7.81E+00, 8.67E+00, 9.59E+00, 1.05E+01
-        ).finished() ); // 200 Ohm-m half space
-
-        Earth->SetLayerConductivity( 1./rho.array() );
-        // ALL SET UP
-        std::cout << *Survey << std::endl;
-
-        // OK do your thinc
-        //DataTEM* data =
-        Survey->ForwardModel( Earth );
-
-
-    // Clean up
-
-
-
-//     //Survey->Delete();
-//     Earth->Delete();
-//
-//     TxHM->Delete();
-//     RxHM->Delete();
-//     TxLM->Delete();
-//     RxLM->Delete();
-
-}

LemmaCore/examples/utXMLParse.cpp

@@ -1,168 +0,0 @@
-/* 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      04/03/2014 01:08:28 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 "Lemma"
-#ifdef TINYXMLSUPPORT
-#include "tinyxml2.h"
-
-#include <ctime>
-using namespace tinyxml2;
-using namespace Lemma;
-
-void ParseTEM( XMLElement* element );
-
-template <typename T>
-std::vector<T> ReadLine( const int& nr, const std::string& line ) ;
-
-int main(int argc, char **argv) {
-
-    if ( argc > 1 ) {
-		XMLDocument* doc = new XMLDocument();
-		clock_t startTime = clock();
-		doc->LoadFile( argv[1] );
-		clock_t loadTime = clock();
-		int errorID = doc->ErrorID();
-
-        // Get some info
-        //static const char* xml = "<element/>";
-        //doc->Parse( xml );
-        //XMLNode* titleElement = doc->FirstChild(); //Element()->FirstChildElement( "PLAY" )->FirstChildElement( "TITLE" );
-        XMLElement* titleElement = doc->FirstChildElement( ); //->FirstChildElement( "TITLE" );
-        //const char* title = titleElement->Value(); //GetText();
-        const char* title = titleElement->Value(); //GetText();
-
-        printf( "Test file '%s' loaded. ErrorID=%d\n", argv[1], errorID );
-        printf( "Name of FirstChildElement: %s\n", title );
-
-        if (strcmp ( titleElement->Value(), "NGXFile" ) != 0) {
-            std::cout <<"NGX file was not detected!" << std::endl;
-            exit(EXIT_FAILURE);
-        } else {
-            //std::cout <<
-            //titleElement->FirstAttribute() ;//"type");// << std::endl;;
-            if (strcmp(  titleElement->FindAttribute("type")->Value(),"tem") == 0) {
-                // Parse TEM file
-                ParseTEM( titleElement );
-            } else {
-                std::cout << "No parser for NGX filetype " << titleElement->FindAttribute("type")->Value() << std::endl;
-                std::cout << "YOU should write one!\n";
-                exit(EXIT_FAILURE);
-            }
-
-        }
-
-		delete doc; doc = 0;
-
-        clock_t deleteTime = clock();
-		if ( !errorID ) {
-			printf( "========================================================\n");
-			printf( "Load time=%u\n",   (unsigned)(loadTime - startTime) );
-			printf( "Delete time=%u\n", (unsigned)(deleteTime - loadTime) );
-			printf( "Total time=%u\n",  (unsigned)(deleteTime - startTime) );
-		}
-
-
-		exit(0);
-	} else {
-        std::cout << "Enter NGX.x file to parse\n";
-    }
-}
-
-void ParseTEM( XMLElement* element ) {
-
-    std::cout << "This is a NGX.t file" << std::endl;
-
-
-    if (strcmp( element->FindAttribute("version")->Value(),"0.1") == 0) {
-        std::cout << "Version 0.1 detected" << std::endl;
-    } else {
-        std::cout << "Unsupported NGX.t version" << std::endl;
-    }
-
-    // system description
-    std::cout << "System description" << std::endl;
-    std::cout << element->FirstChildElement("system")->FirstChildElement("name")->GetText() << std::endl;
-    XMLElement* system = element->FirstChildElement("system");
-        int ntx = atoi(system->FirstChildElement("transmitters")->FindAttribute("num")->Value());
-        std::cout << "numTx = " << ntx << std::endl;
-        // OK Parse Transmitter(s)
-        XMLElement* tx = system->FirstChildElement("transmitters")->FirstChildElement("transmitter");
-        //    std::cout << "Tx id = " << tx->FindAttribute("id")->Value() << std::endl;
-        //std::cout << tx->FirstChildElement("loop.coordinates")->FindAttribute("npoint")->Value();//->FirstChildElement("northingPoints")->Value() << std::endl;
-        //std::cout << tx->FirstChildElement("loop.coordinates")->FirstChildElement("northing.points")->GetText();//->FirstChildElement("northingPoints")->Value() << std::endl;
-        for (int it=0; it<ntx; ++it) {
-            std::cout << "\nTransmitter " << it << std::endl;
-            if (it > 0) tx = tx->NextSiblingElement();
-            int npoints = atoi(tx->FirstChildElement("loop.coordinates")->FindAttribute("npoint")->Value());
-
-            std::cout << "points= " << npoints; // tx->FirstChildElement("loop.coordinates")->FindAttribute("npoint")->Value();//->FirstChildElement("northingPoints")->Value() << std::endl;
-            std::vector<Real> LP = ReadLine<Real>( npoints, std::string(tx->FirstChildElement("loop.coordinates")->FirstChildElement("northing.points")->GetText()) );
-            for (int ii=0; ii<npoints; ++ii) std::cout << "\t"<< LP[ii] ;
-            //std::cout << tx->FirstChildElement("loop.coordinates")->FirstChildElement("northing.points")->GetText();//->FirstChildElement("northingPoints")->Value() << std::endl;
-            //std::cout << tx->FirstChildElement("loop.coordinates")->FirstChildElement("easting.points")->GetText();//->FirstChildElement("northingPoints")->Value() << std::endl;
-        }
-    std::cout << "\nEND system description\n";
-
-}
-
-
-template <typename T>
-std::vector<T> ReadLine( const int& nr, const std::string& line ) {
-
-    std::vector<T>   lineData;
-    std::stringstream  lineStream(line);
-
-    T value;
-    while(lineStream >> value) {
-        lineData.push_back(value);
-    }
-    return lineData;
-}
-#else
-
-int main() {
-    std::cout << "you have to compile lemma with external tinyxml library to use this" << std::endl;
-}
-
-#endif
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  ReadInts
-    //--------------------------------------------------------------------------------------
-//     std::vector<int> ReadInts ( const int& nr ) {
-//         std::string buf;
-//         char *dump = new char[BufferSize];
-//         std::vector<int> vals(0);
-//         while (input >> buf) {
-//             if (buf.substr(0, CommentString.size()) == CommentString) {
-//                 input.getline(dump, BufferSize);
-//             } else {
-//                 vals.push_back( atoi(buf.c_str() ));
-//             }
-//             if (static_cast<int>(vals.size()) == nr) {
-//                 delete [] dump;
-//                 return vals;
-//             }
-//
-//         }
-//         delete [] dump;
-//         return vals;
-//     }		// -----  end of method ASCIIParser::ReadInts  -----
-

LemmaCore/examples/utYAMLconfig.cpp

@@ -1,67 +0,0 @@
-#ifdef HAVE_YAMLCPP
-
-#include "yaml-cpp/yaml.h"
-#include "yaml-cpp/eventhandler.h"
-#include <fstream>
-#include <iostream>
-#include <vector>
-
-struct Params {
-	bool hasFile;
-	std::string fileName;
-};
-
-Params ParseArgs(int argc, char **argv) {
-	Params p;
-
-	std::vector<std::string> args(argv + 1, argv + argc);
-
-	return p;
-}
-
-class NullEventHandler: public YAML::EventHandler
-{
-public:
-	virtual void OnDocumentStart(const YAML::Mark&) {}
-	virtual void OnDocumentEnd() {}
-
-	virtual void OnNull(const YAML::Mark&, YAML::anchor_t) {}
-	virtual void OnAlias(const YAML::Mark&, YAML::anchor_t) {}
-	virtual void OnScalar(const YAML::Mark&, const std::string&, YAML::anchor_t, const std::string&) {}
-
-	virtual void OnSequenceStart(const YAML::Mark&, const std::string&, YAML::anchor_t) {}
-	virtual void OnSequenceEnd() {}
-
-	virtual void OnMapStart(const YAML::Mark&, const std::string&, YAML::anchor_t) {}
-	virtual void OnMapEnd() {}
-};
-
-void parse(std::istream& input)
-{
-	try {
-		YAML::Node doc = YAML::Load(input);
-		std::cout << doc << "\n";
-	} catch(const YAML::Exception& e) {
-		std::cerr << e.what() << "\n";
-	}
-}
-
-int main(int argc, char **argv)
-{
-	Params p = ParseArgs(argc, argv);
-
-	if(argc > 1) {
-		std::ifstream fin;
-		fin.open(argv[1]);
-		parse(fin);
-	} else {
-		parse(std::cin);
-	}
-
-	return 0;
-}
-#else
-int main() {
-}
-#endif
-

LemmaCore/examples/utgaussquad.cpp

@@ -1,84 +0,0 @@
-// ===========================================================================
-// 
-//       Filename:  utqaussquad.cpp
-// 
-//    Description:  Test for gaussian quadrature algorithm
-// 
-//        Version:  0.0
-//        Created:  10/05/2010 08:54:26 AM
-//       Revision:  none
-//       Compiler:  Tested with g++
-// 
-//         Author:  M. Andy Kass (MAK)
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//                  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 "Lemma"
-using namespace Lemma;
-using namespace std;
-
-#ifdef LEMMAUSEVTK
-#include "matplot.h"
-using namespace matplot;
-#endif
-
-int main() {
-
-	int N = 600;
-	int upb = 5;
-	int lowb = -1;
-	VectorXr func(N);
-	VectorXr wx(N);
-	Real integrationres,actres;
-
-	gaussianquadrature *lgqw = gaussianquadrature::New();
-	lgqw->SetFreqs(N,upb,lowb);
-	lgqw->CalcAW();
-
-	wx=lgqw->GetAbscissae();
-	func=cos(wx.array());
-//	for (int ii=0;ii<N;++ii) {
-//		cout << wx(ii) << "  " << func(ii) << endl;
-//	}
-
-	lgqw->SetFunc(func);
-	lgqw->Integrate();
-	integrationres=lgqw->GetResult();
-
-	actres = -sin((Real)upb)+sin((Real)lowb);
-	
-	cout << "Gaussian Quadrature Result: " << integrationres << endl;
-	cout << "Actual Result: " << actres << endl;
-	
-		
-	//Plot things
-	#ifdef LEMMAUSEVTK
-	double colour1[3] = {0.0,0.0,1.0};
-
-	Plot2D_VTK p1("X", "Y", 800,600);
-	p1.plot(wx,func,colour1,".-");
-	p1.show();
-
-	#endif
-
-	return EXIT_SUCCESS;
-}
-

LemmaCore/examples/utgmrprint.cpp

@@ -1,258 +0,0 @@
-// ===========================================================================
-//   This file is distributed with Lemma,
-//
-//       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
- **/
-
-#ifdef LEMMAUSEVTK
-#include "vtkRenderer.h"
-#include "vtkRenderWindow.h"
-#include "vtkRenderWindowInteractor.h"
-#include "vtkPNGWriter.h"
-#include "vtkRenderLargeImage.h"
-#endif
-
-#include "receiverpoints.h"
-#include "emearth1d.h"
-#include "PolygonalWireAntenna.h"
-
-using namespace Lemma;
-
-std::vector<Real>  readinpfile(const std::string& fname);
-
-int main(int argc, char** argv) {
-
-    std::cout <<
-    "\n"
-    << "hantenna - a programme for computing the h field from polygonal wire\n"
-    << "loop sources \n\n"
-    << "The following copyrights apply to this application:\n"
-    << "Copyright (C) 2009, 2010, 2011, 2012 Colorado School of Mines\n"
-    << "Copyright (C) 2009, 2010, 2011, 2012 Trevor Irons\n"
-    << "Copyright (C) 2011 Broken Spoke Development, LLC\n\n"
-    << "hantenna was built using Lemma (Lemma is an Electromagnetics Modelling API)\n"
-    << "More information may be found at https://lemmasoftware.org\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: hantenna.exe  trans.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 transmitter
-    PolygonalWireAntenna* trans = PolygonalWireAntenna::New();
-        trans->SetNumberOfPoints((int)(Trans[0]));
-        int ip=1;
-        for ( ; ip<=(int)(Trans[0])*2; ip+=2) {
-            trans->SetPoint(ip/2, Vector3r (Trans[ip], Trans[ip+1], -1e-3));
-        }
- 	    trans->SetNumberOfFrequencies(1);
- 	    trans->SetFrequency(0, Trans[ip]);
-        trans->SetCurrent(Trans[ip+1]);
-
-	// 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);
-        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->AttachWireAntenna(trans);
-		EmEarth->AttachLayeredEarthEM(earth);
-		EmEarth->AttachReceiverPoints(receivers);
-		EmEarth->SetFieldsToCalculate(H);
-        EmEarth->CalculateWireAntennaFields();
-
-    #ifdef LEMMAUSEVTK
-	vtkRenderer           *renderer = vtkRenderer::New();
-	vtkRenderWindow         *renWin = vtkRenderWindow::New();
-	vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
-    trans->ApproximateWithElectricDipoles( (VectorXr (3) << 0,0,0).finished() );
-	vtkActor **dipActors = new vtkActor*[trans->GetNumberOfDipoles()];
-	for (int id=0; id<trans->GetNumberOfDipoles(); ++id) {
-		dipActors[id] = trans->GetVtkActor(id);
-		renderer->AddActor(dipActors[id]);
-	}
-    vtkActor *hfield  = receivers->GetVtkGlyphActor (HFIELDREAL, 3, 1e2, 0);
- 	vtkActor *hfieldi = receivers->GetVtkGlyphActor (HFIELDIMAG, 3, 1e2, 0);
-    hfieldi->GetProperty()->SetColor(1,0,1);
- 	hfield->GetProperty()->SetColor(0,1,0);
- 	renderer->AddActor(hfield);
- 	renderer->AddActor(hfieldi);
-	renderer->SetBackground(0,0,0);
-	// Render the window
-	renWin->AddRenderer(renderer);
-	iren->SetRenderWindow(renWin);
-	iren->Initialize();
-	iren->Start();
-	iren->Render();
-	cout << "Enter File name?: ";
-	std::string pngName;
-	std::cin >> pngName;
-	vtkPNGWriter *pngwrite = vtkPNGWriter::New();
-	vtkRenderLargeImage *renlarge = vtkRenderLargeImage::New();
-	renlarge->SetInput(renderer);
-	renlarge->SetMagnification(2);
-	pngwrite->SetInputConnection(renlarge->GetOutputPort());
-	pngName.append(".png");
-	pngwrite->SetFileName(pngName.c_str());
-	pngwrite->Write();
-	iren->Delete();
-	renWin->Delete();
-	renderer->Delete();
-    #endif
-
-    ////////////////////////////////////
-    // Report
- 	std::fstream hreal("hfield.dat", std::ios::out);
-    hreal << *trans << std::endl;
-    hreal << *earth << std::endl;
-    hreal << "Right hand coordinate system, z is positive down\n";
-    hreal << "x[m]\ty[m]\tz[m]\tHx[A/m]\tHy[A/m]\tHz[A/m]\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->GetHfield(0, i).transpose()[0]) << "\t";
- 		hreal << std::imag(receivers->GetHfield(0, i).transpose()[0]) << "\t";
- 		hreal << std::real(receivers->GetHfield(0, i).transpose()[1]) << "\t";
- 		hreal << std::imag(receivers->GetHfield(0, i).transpose()[1]) << "\t";
- 		hreal << std::real(receivers->GetHfield(0, i).transpose()[2]) << "\t";
- 		hreal << std::imag(receivers->GetHfield(0, i).transpose()[2]) << "\n";
-        ++i;
-    }
-    }
-    }
-    hreal.close();
-
-    // Clean up
-    EmEarth->Delete();
-    earth->Delete();
-    receivers->Delete();
-    trans->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/uthankel2.cpp

@@ -1,93 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  uthankel2.cpp
-//
-//    Description:
-//
-//        Version:  0.0
-//        Created:  05/14/2010 10:26:59 AM
-//       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 "hankeltransformhankel2.h"
-#include "hankeltransformgaussianquadrature.h"
-#include "kernelem1d.h"
-#include "layeredearthem.h"
-
-using namespace Lemma;
-
-int main() {
-
-	// Define model
-	LayeredEarthEM *Earth = LayeredEarthEM::New();
-		VectorXcr sigma(3);
-		sigma << 0., .1, 0.01;
-		VectorXr  thick(1);
-		thick << 10;
-		Earth->SetNumberOfLayers(3);
-		Earth->SetLayerConductivity(sigma);
-		Earth->SetLayerThickness(thick);
-
-	// Source
-	// Test with a single dipole
-	DipoleSource *dipole = DipoleSource::New();
-		dipole->SetMoment(2);
-		dipole->SetType(MAGNETICDIPOLE);
-		dipole->SetPolarisation(ZPOLARISATION);
-		dipole->SetLocation(0,0,0);
-		dipole->SetNumberOfFrequencies(1);
-		dipole->SetFrequency(0,1000);
-		dipole->SetPhase(0);
-
-	KernelEm1D *Kernel = KernelEm1D::New();
-		Kernel->Initialise(Earth);
-		Kernel->SetUpSource(dipole, 0);
-		Kernel->SetUpReceiver(-0.4);
-    //std::vector< KernelEm1DBase* > KernelVec;
-    //    KernelVec.push_back( )
-
-	std::cout.precision(10);
-
-	Hankel2 *dig = Hankel2::New();
-//         dig->ComputeRelated(.23 , Kernel);
-//  		std::cout << "  dig->Zgauss "
-//  				  << dig->Zgauss(0, TE, 0, 100.,
-//  								  1000.*std::sqrt(MU0*EPSILON0), Kernel)
-//  			      << std::endl;
-
-// 	HankelTransformGaussianQuadrature *gauss =
-// 			HankelTransformGaussianQuadrature::New();
-// 		std::cout << "gauss->Zgauss "
-// 				  << gauss->Zgauss(0, TE, 0, 100.,
-// 								  1000.*std::sqrt(MU0*EPSILON0), Kernel)
-// 			      << std::endl;
-
-	Earth->Delete();
-	dig->Delete();
-	//gauss->Delete();
-    dipole->Delete();
-	Kernel->Delete();
-	return EXIT_SUCCESS;
-}

LemmaCore/examples/uthantenna.cpp

@@ -1,257 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  hantenna.cpp
-//
-//        Created:  10/07/2010 08:57:04 AM
-//       Modified:  14 Aug 2012
-//       Compiler:  Tested with g++, icpc, and MSVC 2010
-//
-//         Author:  Trevor Irons (ti)
-//
-//       Copyright (C) 2011    Broken Spoke Development, LLC
-//       Copyright (C) 2012    Trevor Irons
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//
-//          Email:  tirons@mines.edu
-//
-//  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  $Revision: 208 $
-  $Id$
- **/
-
-#include "receiverpoints.h"
-#include "emearth1d.h"
-#include "PolygonalWireAntenna.h"
-#ifdef LEMMAUSEOMP
-#include "omp.h"
-#endif
-
-#include "timer.h"
-
-using namespace Lemma;
-
-std::vector<Real>  readinpfile(const std::string& fname);
-
-std::vector<std::string>  readinpfile2(const std::string& fname);
-
-int main(int argc, char** argv) {
-
-    std::cout <<
-    "\n"
-    << "hantenna- $Date: 2015-01-26 10:11:24 -0700 (Mon, 26 Jan 2015) $ $Revision: 208 $\n\n"
-    << "hantenna is a programme for computing the h field from polygonal wire\n"
-    << "loop sources \n\n"
-    << "hantenna was built using Lemma (Lemma is an Electromagnetics Modelling API)\n"
-    << "Lemma is Free and Open Source Software (FOSS) and is released under\n"
-    << "the MPL, it is covered by the following copyrights:\n"
-    << "Copyright (C) 2009, 2010, 2011, 2012      Colorado School of Mines\n"
-    << "Copyright (C) 2009, 2010, 2011, 2012      Trevor P. Irons\n"
-    << "Copyright (C) 2011, 2012                  M. Andy Kass\n\n"
-    << "More information may be found at: https://lemmasoftware.org\n"
-    << "                                  info@lemmasoftware.org\n\n"
-    << "=====================================================================\n"
-    << "This programme is part of Lemma, a geophysical modelling and inversion API \n"
-    << "This Source Code Form is subject to the terms of the Mozilla Public\n"
-    << "License, v. 2.0. If a copy of the MPL was not distributed with this\n"
-    << "file, You can obtain one at http://mozilla.org/MPL/2.0/. \n"
-    << "=====================================================================\n\n\n";
-
-    if (argc < 5) {
-        std::cout << "usage: hantenna.exe  trans.inp cond.inp points.inp config.inp \n";
-        exit(0);
-    }
-
-    #ifdef LEMMAUSEOMP
-    std::cout << "OpenMP is using " << omp_get_max_threads() << " threads" << std::endl;
-    #endif
-
-    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]));
-    std::vector<std::string> config  = readinpfile2(std::string(argv[4]));
-
-    //////////////////////////////////////
-    // Define transmitter
-    PolygonalWireAntenna* trans = PolygonalWireAntenna::New();
-        trans->SetNumberOfPoints((int)(Trans[0]));
-        int ip=1;
-        for ( ; ip<=(int)(Trans[0])*2; ip+=2) {
-            trans->SetPoint(ip/2, Vector3r (Trans[ip], Trans[ip+1], -1e-3));
-        }
- 	    trans->SetNumberOfFrequencies(1);
- 	    trans->SetFrequency(0, Trans[ip]);
-        trans->SetCurrent(Trans[ip+1]);
-        trans->SetMinDipoleRatio(atof(config[1].c_str()));
-        trans->SetMinDipoleMoment(atof(config[2].c_str()));
-        trans->SetMaxDipoleMoment(atof(config[3].c_str()));
-
-	// 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);
-        VectorXr dy(ny-1);
-        VectorXr dz(nz-1);
-        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->AttachWireAntenna(trans);
-		EmEarth->AttachLayeredEarthEM(earth);
-		EmEarth->AttachReceiverPoints(receivers);
-		EmEarth->SetFieldsToCalculate(H);
-        EmEarth->SetHankelTransformMethod(string2Enum<HANKELTRANSFORMTYPE>(config[0]));
-        EmEarth->SetHankelTransformMethod(FHTKEY201);
-
-	// Keep track of time
-	jsw_timer timer;
-  	timer.begin();
-    clock_t launch = clock();
-    EmEarth->CalculateWireAntennaFields(true);    // true=status bar
-	Real paTime = timer.end();
-
-    std::cout << "\n\n===========================================\ncalc. real time: " << paTime/60. << "\t[m]\n";
-
-    std::cout << "calc. user time: " <<  (clock()-launch)/CLOCKS_PER_SEC/60.   << "\t[CPU m]"
-		 << std::endl;
-
-    ////////////////////////////////////
-    // Report
- 	std::fstream hrep("hfield.yaml", std::ios::out);
-    std::fstream hreal("hfield.dat", std::ios::out);
-
-    hrep << *EmEarth << std::endl;
-    hrep.close();
-    //hreal << *trans << std::endl;
-    //hreal << *earth << std::endl;
-
-    hreal << "// Right hand coordinate system, z is positive down\n";
-    hreal << "// x[m]\ty[m]\tz[m]\tHx[A/m]\tHy[A/m]\tHz[A/m]\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 << receivers->GetHfield(0, i).transpose() << "\n";
-        ++i;
-    }
-    }
-    }
-    hreal.close();
-    // Clean up
-    EmEarth->Delete();
-    earth->Delete();
-    receivers->Delete();
-    trans->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;
-}
-
-std::vector<std::string>  readinpfile2(const std::string& fname) {
-    std::string buf;
-    char dump[255];
-    std::vector<std::string> 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( std::string(buf.c_str() ));
-        }
-    }
-    return vals;
-}

LemmaCore/examples/utlogbarriercg.cpp

@@ -1,218 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  utlogbarriercg.cpp
-//
-//        Created:  12/29/2010 09:40:23 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     12/29/2010
-  @version   0.0
- **/
-
-#include "LemmaObject.h"
-//#include "logbarriercg.h"
-//#include "datasnmr.h"
-#include <ctime>
-
-#ifdef HAVEBOOSTRANDOM
-#include <boost/random.hpp>
-#include <boost/random/normal_distribution.hpp>
-#endif
-
-using namespace std;
-using namespace Lemma;
-
-MatrixXr BuildG(const Real& T2, const Real& Larmor, const Real& T,
-        const Real& dt, const VectorXr& nT2Bins, const Real& scale);
-
-MatrixXr BuildGw(const Real& T2, const Real& Larmor, const Real& T,
-        const Real& dt, const VectorXr& nT2Bins, const Real& scale,
-        const VectorXr& freqs);
-
-/// test driver program for log-barrier optimization algorithm
-int main() {
-    return 0;
-}
-
-#ifdef AA
-    // Parameters
-    Real T2(.200);
-    Real Larmor(2000); // Hz
-    Real wL = 2.*PI * Larmor;
-    Real T(.6);
-    Real dt(1e-4);
-    int  nT2(20);
-    Real T2Low(.020);
-    Real T2Hi(.220);
-
-    // T2 bins
-    VectorXr T2Bins = VectorXr::LinSpaced(nT2, T2Low, T2Hi);
-
-    // Build true model
-    VectorXr m = VectorXr::Zero(T2Bins.size());
-    //m[4]  = .15;
-    //m[5]  = .15;
-    //m[6]  = .15;
-    m[7]  = .15;
-    m[8]  = .15;
-    m[11] = .15;
-    m[12] = .15;
-    m[13] = .15;
-    m[14] = .15;
-
-    // Build G
-    srand ( std::time(NULL) );
-    Real scale = 1e-4*std::abs(VectorXr::Random(1)[0]);
-    MatrixXr G = BuildG(T2, wL, T, dt, T2Bins, scale);
-
-    #ifdef HAVEBOOSTRANDOM
-    Real mean = 0;
-    Real variance = scale*.05*(.5+.15);
-    boost::mt19937 randgen(static_cast<unsigned int> (std::time(0)));
-    boost::normal_distribution<Real> noise(mean, variance);
-    boost::variate_generator<boost::mt19937, boost::normal_distribution<Real> > nD(randgen, noise);
-    VectorXr noisy = G*m;
-//     for (int i=0; i < noisy.size(); ++i) {
-//        noisy(i) += nD();
-//     }
-    #else
-    VectorXr d = G * m;
-    VectorXr noisy = d.array();// + .05*( .5 + .15 ) *Eigen::ArrayXd::Random(d.size());
-    #endif
-
-    // Clean Data, and 10% random noise data
-    VectorXr RefMod = VectorXr::Zero(m.size());
-
-    // todo let alpha's be set.
-    Real alpha_s  =  .0;
-    Real alpha_t2 = 1.0;
-    Eigen::SparseMatrix<Real> Wd (G.rows(), G.rows());
-    Eigen::SparseMatrix<Real> Wm (G.cols(), G.cols());
-
-    /////////////////
-    // Model objective function
-    int ii = 0;
-    for (int iT2=0; iT2<nT2; ++iT2) {
-        Wm.coeffRef(ii, ii) += alpha_s - alpha_t2;
-        if (iT2 < nT2-1) {
-            Wm.coeffRef(ii, ii+1) += alpha_t2;
-        }
-        ++ii;
-    }
-    Wm.finalize();
-    std::fstream  WmOut( "wmMatrix.dat" , std::ios::out);
-    WmOut << Wm << std::endl;
-    WmOut.close();
-
-    // Data objective function
-    /// @todo add measure of suspected std dev to this.
-    for (int id=0; id<G.rows(); ++id) {
-        Wd.coeffRef(id, id) = 1.; // 1/sigma(i);
-    }
-    Wd.finalize();
-
-    // invert time-domain sinusoid exponent
-    //LogBarrierCG(G, RefMod, noisy, (Real)0., (Real)1e5, nT2, Wd, Wm, scale*1e1);
-    return EXIT_SUCCESS;
-
-//     #if 0
-//     // invert FD
-//     Eigen::FFT<Real> fft;
-//     fft.SetFlag(fft.HalfSpectrum);
-//     VectorXcr dw;
-//     fft.fwd(dw, noisy);
-//
-//     // Compute freqs Hz
-//     VectorXr freqs = DataSNMR::GetNMRSampledFrequencies(T/dt, dt);
-//     Real df = freqs[1];
-//     Real window = 300; // Hz
-//     int iL = (int)(Larmor/df);
-//     MatrixXr Gw = BuildGw(T2, wL, T, dt, T2Bins, scale, freqs.segment(iL-window/2, window));
-//
-//     VectorXr dwu = VectorXr::Zero(2.*window);
-//     dwu.head(window) = dw.segment(iL-window/2, window).real();
-//     dwu.tail(window) = dw.segment(iL-window/2, window).imag();
-//
-//     Eigen::DynamicSparseMatrix<Real> Wdw (Gw.rows(), Gw.rows());
-//     for (int id=0; id<Gw.rows(); ++id) {
-//         Wdw.coeffRef(id, id) = 1.; // 1/sigma(i);
-//     }
-//     Wdw.finalize();
-//     std::cout << "psize " << (Gw*RefMod).size() << std::endl;
-//     VectorXr dw2 = Gw*m;
-//     //std::cout << dw2 << std::endl;
-//     std::cout << "Gw " << Gw.rows() << "\t" << Gw.cols() << std::endl;
-//     std::cout << "dwu " << dwu.size() << std::endl;
-//     //RefMod.array() += .1;
-//     VectorXr mod = LogBarrierCG(Gw, RefMod, dwu, 0., 3., nT2, Wdw, Wm,scale*1e5);
-//     //VectorXr mod = LogBarrierCG(Gw, dwu, 0., 1e5);
-//
-//     std::fstream Gws("gw.out", std::ios::out);
-//     Gws << Gw << std::endl;
-//     Gws.close();
-//     #endif
-}
-
-#endif
-
-MatrixXr BuildG(const Real& T2, const Real& wL, const Real& T,
-            const Real& dt, const VectorXr& T2Bins, const Real& scale) {
-    std::cout << "scale " << scale << std::endl;
-    int nt = T/dt;
-    int nT2 = T2Bins.size();
-    MatrixXr G = MatrixXr::Zero(nt,nT2);
-    for (int iT2=0; iT2<nT2; ++iT2) {
-        Real t=0;
-        for (int it=0; it<nt; ++it) {
-            G(it, iT2) = scale * exp(-t/T2Bins(iT2)) * sin(wL * t);
-            t += dt;
-        }
-    }
-    return G;
-}
-
-
-MatrixXr BuildGw(const Real& T2, const Real& wL, const Real& T,
-            const Real& dt, const VectorXr& T2Bins, const Real& scale,
-            const VectorXr &freqs) {
-    VectorXr omegas = freqs.array() * 2.*PI;
-    std::cout << "scale " << scale << std::endl;
-    int nT2 = T2Bins.size();
-    MatrixXr Gw = MatrixXr::Zero(2*freqs.size(), nT2);
-    int nW = freqs.size();
-    Real sc = 1./dt;
-    for (int iT2=0; iT2<nT2; ++iT2) {
-        for (int iw=0; iw<freqs.size(); ++iw) {
-            Real a = 1./T2Bins(iT2);
-            Complex T = wL / ( wL*wL + (a+Complex(0, omegas[iw]))*(a+Complex(0,omegas[iw])) ) ;
-            Gw(iw, iT2)     = sc * scale * std::real(T);
-            Gw(iw+nW, iT2) = sc * scale * std::imag(T);
-        }
-    }
-    return Gw;
-}

LemmaCore/examples/utpolygonalantenna.cpp

@@ -1,67 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  utpolygonalantennae.cpp
-//
-//    Description:  Unit test of PolygonalAntenna
-//
-//        Version:  0.0
-//        Created:  05/26/2010 04:30:56 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() {
-
-    PolygonalWireAntenna *pa = PolygonalWireAntenna::New();
-        pa->SetNumberOfPoints(5);
-        pa->SetPoint(0, Vector3r(  0,  0, -1e-3));
-        pa->SetPoint(1, Vector3r( 10,  0, -1e-3));
-        pa->SetPoint(2, Vector3r( 10, 10, -1e-3));
-        pa->SetPoint(3, Vector3r(  0, 10, -1e-3));
-        pa->SetPoint(4, Vector3r(  0,  0, -1e-3));
-        pa->SetNumberOfFrequencies(1);
-        pa->SetFrequency(0,1000.);
-        pa->SetCurrent(10.);
-        pa->SetNumberOfTurns(1);
-
-    Vector3r pos;
-    pos << 23,23,23;
-    pa->ApproximateWithElectricDipoles(pos);
-    std::cout << "pos "<< pos.transpose() << "  ndipoles="
-              << pa->GetNumberOfDipoles() << std::endl;
-    pos << 2,2,2;
-    pa->ApproximateWithElectricDipoles(pos);
-    std::cout << "pos "<< pos.transpose() << "  ndipoles="
-              << pa->GetNumberOfDipoles() << std::endl;
-    pos << 1,1,1;
-    pa->ApproximateWithElectricDipoles(pos);
-    std::cout << "pos "<< pos.transpose() << "  ndipoles="
-              << pa->GetNumberOfDipoles() << std::endl;
-
-    pa->Delete();
-}

LemmaCore/examples/utreadfemubc.cpp

@@ -1,68 +0,0 @@
-// ===========================================================================
-// 
-//       Filename:  utreadfemubc.cpp
-// 
-//    Description:  
-// 
-//        Version:  0.0
-//        Created:  01/03/2013 02:47:24 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 "Lemma"
-
-using namespace Lemma;
-
-#ifdef LEMMAUSEVTK
-#include "matplot.h"
-using namespace matplot;
-#endif
-
-int main() {
-
-	std::string datfile;
-
-	datfile = "126.obs";
-	
-	DataReaderFemUBC* Reader = DataReaderFemUBC::New();
-	DataFEM* thedata = DataFEM::New();
-
-	Reader->SetDataFEM(thedata);
-
-	try {
-	Reader->ReadData(datfile,1);
-	} catch(std::exception& e) {
-		exit(EXIT_FAILURE);
-	}
-
-	std::cout << *Reader << std::endl;
-	std::cout << *thedata << std::endl;
-
-
-	thedata->Delete();
-	Reader->Delete();
-
-	return EXIT_SUCCESS;
-}

LemmaCore/examples/utsandbox.cpp

@@ -1,54 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  utsandbox.cpp
-//
-//        Created:  07/29/2010 10:34:23 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 test sandbox helm1rameters
-  @author   Trevor Irons
-  @date     07/29/2010
-  @version   0.0
- **/
-
-#include "Lemma"
-
-using namespace Lemma;
-
-int main() {
-
-    PolygonalWireAntenna *helm1 = PolygonalWireAntenna::New();
-	helm1->SetNumberOfFrequencies(1);
-	helm1->SetFrequency(0, 1000);
-	helm1->SetNumberOfPoints(5);
-	helm1->SetPoint(0, Vector3r(   0,   0, 0));
-	helm1->SetPoint(1, Vector3r(   0,   0, 0));
-	helm1->SetPoint(2, Vector3r(   0,   0, 0));
-	helm1->SetPoint(3, Vector3r(   0,   0, 0));
-	helm1->SetPoint(4, Vector3r(   0,   0, 0));
-	helm1->SetCurrent(1.);
-    helm1->Delete();
-}

LemmaCore/examples/uttemforward.cpp

@@ -1,199 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  uttemforward.cpp
-//
-//    Description:  TEM Forward Modeller
-//
-//        Version:  0.0
-//        Created:  02/10/2011 03:32:18 PM
-//       Revision:  none
-//       Compiler:  Tested with g++, icpc, and MSVC 2000
-//
-//         Author:  M. Andy Kass (MAK)
-//
-//		Copyright:  2011 Trevor Irons and M. Andy Kass
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//                  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(int argv, char** argc) {
-
-	// Just for timing
-	clock_t launch =clock();
-
-	// Banner display
-	std::string name;
-	std::string version;
-	std::string usage;
-	name = "TEM Forward Modeller - 1D";
-	version = "1.0beta";
-	usage = "temforward1d [inputfile]";
-	banner(name,version,usage);
-    if ( argv < 2 ) {
-        std::cout << "No input file specified, should be of format\n";
-        std::cout <<
-"origparabk.obsy        ! Observations-style file.\n\
-origpara.con           ! Starting model.\n\
-100                    ! Number of Hankel kernel evaluations.\n\
-100 1. 1.0E+10         ! Number of Fourier kernel evaluations, & min & max freq.\n\
-N                      ! Is noise to be added?\n\
-5.  1.0E-08  30        ! Noise to be added: percentage, threshold, seed.\n\
-" << std::endl;
-
-        exit(0);
-    }
-
-	time_t curr=time(0);
-	std::cout << std::endl;
-	std::cout << "  Start time: " << ctime(&curr) << std::endl;
-
-	// Define objects
-	PolygonalWireAntenna* Trans = PolygonalWireAntenna::New();
-//     PolygonalWireAntenna* pa = PolygonalWireAntenna::New();
-//         pa->SetNumberOfPoints(5);
-// 	    pa->SetPoint(0, Vector3r(   0,   0, -30.001));
-// 	    pa->SetPoint(1, Vector3r(   0,  20, -35.001));
-// 	    pa->SetPoint(2, Vector3r(  20 , 20, -35.001));
-// 	    pa->SetPoint(3, Vector3r(  20,   0, -30.001));
-// 	    pa->SetPoint(4, Vector3r(   0,   0, -30.001));
-// 	    pa->SetCurrent(100.);
-//         pa->SetNumberOfTurns(1);
-
-
-	//DipoleSource* Trans = DipoleSource::New();
-	ReceiverPoints *Receivers = ReceiverPoints::New();
-	LayeredEarthEM *Earth = LayeredEarthEM::New();
-	VectorXr maintimes;
-
-    /////////////////////////////////////
-	// Using model reader
-	ModelReaderTem1DUBC* Reader = ModelReaderTem1DUBC::New();
-	    Reader->SetEMEarth1D(Earth);
-	    Reader->SetTransmitter(Trans);
-	    Reader->SetReceiver(Receivers);
-	    Reader->ReadParameters( argc[1] );
-	    maintimes = Reader->GetTimes();
-
-	// Attach it to instrumentTEM
-	InstrumentTem *instrument = InstrumentTem::New();
-	    instrument->EMEarthModel(Earth);
-	    instrument->SetTransmitLoop(Trans);
-	    //instrument->SetTransmitLoop(pa);
-	    //instrument->SetDipoleSource(Trans);
-	    instrument->SetReceiver(Receivers);
-
-
-
-        // TODO need to input these
-        VectorXr widths = VectorXr::Ones(maintimes.size()); // * 1e-5;
-        /*
-        widths.segment(0,5).array()  *= 5e-6;
-        widths.segment(5,5).array()  *= 1e-5;
-        widths.segment(10,5).array() *= 5e-5;
-        widths.segment(15,5).array() *= 2e-4;
-        widths.segment(20,5).array() *= 4e-4;
-        //widths.segment(25,5).array() *= 4e-4;
-        */
-        /*
-        widths << .48,4.,8.,8.,8.,8.,8.,12.,12.,12.,16.,16.,16.,20.,24.,24.,28.,32.,32.,36.,40.,44.,52.,
-  				56.,64.,68.,76.,88.,96.,104.,120.,132.,144.,160.,180.,200.,220.,248.,272.,304.,336.,376.,
-  				416.,464.,516.,572.,636.,708.,784.,872.,968.,1076.,1196.,1328.,1476.,1640.,1824.,2024.,
-  				2248.,2500. ;
-        */
-        widths *= 1e-6;
-        std::cout << widths.transpose() << std::endl;
-
-        instrument->SetReferenceTime(.025);
-        //instrument->SetReferenceTime(.025);
-	    instrument->SetTimeGates(maintimes, widths);
-
-        //instrument->SetReceiverType(MAGNETOMETER);
-        instrument->SetReceiverType(INDUCTIVE);
-        // Set the pulse
-        VectorXr Amp(4); Amp << 0,1,1,0;
-        VectorXr Times(4); Times << 0., .0005, .02497, .025;
-
-        //VectorXr Amp(4); Amp << 0,1,1,0;
-        //VectorXr Times(4); Times << -0.025, -0.0245, -0.00003, 0.0;
-        //instrument->SetPulse(Amp, Times);
-
-        //VectorXr Amp(3); Amp << 0,1,0;
-        //VectorXr Times(3); Times << 0, .015, .030;
-        //instrument->SetPulse(Amp, Times);
-
-        //VectorXr Amp(3); Amp << 0,1,0;
-        //VectorXr Times(3); Times << 0, .01, .020;
-        instrument->SetPulse(Amp, Times);
-
-    std::cout << *Earth << "\n" << *Trans << "\n" << *Receivers << std::endl;
-
-	// Perform the forward model
-	//instrument->MakeDirectCalculation( FHTKEY201  );
-	//instrument->MakeLaggedCalculation( ANDERSON801 );
-	//instrument->MakeLaggedCalculation( QWEKEY );
-	//instrument->MakeLaggedCalculation( CHAVE );
-	instrument->MakeLaggedCalculation( FHTKEY201 );
-	//instrument->MakeLaggedCalculation( FHTKEY101 );
-
-    int nlag = instrument->GetMeasurements().rows();
-	// Output results to screen
-	for (int ii=0; ii<nlag; ii++) {
-		std::cout<<"  "<<instrument->GetMeasurements()(ii,0)<<"  "<<instrument->GetMeasurements()(ii,1)<<std::endl;
-	}
-
-	// Output results to file
-	std::ofstream outfile1;
-	outfile1.open("solution.out");
-    //outfile1 << "//timegate [ms]\t dB/dt [nT/s]" << std::endl;
-    outfile1 << "//timegate [s]\t dB/dt [T/s]" << std::endl;
-	for (int ii=0; ii<nlag; ii++) {
-		//outfile1 << 1e3*instrument->GetMeasurements()(ii,0)<< "\t" << (MU0*1e9)*instrument->GetMeasurements()(ii,1)<<std::endl;
-		outfile1 << instrument->GetMeasurements()(ii,0)<< "\t" << MU0*instrument->GetMeasurements()(ii,1) << std::endl;
-		//outfile1 << instrument->GetMeasurements()(ii,0)<< "\t" << instrument->GetMeasurements()(ii,1)<<std::endl;
-	}
-	outfile1.close();
-
-
-	// Timing stuff
-	std::cout << "  Time for execution: " <<  (clock()-launch)/CLOCKS_PER_SEC   << " [CPU] seconds."
-		 << std::endl;
-
-
-	instrument->Delete();
-	Trans->Delete();
-	Earth->Delete();
-	Receivers->Delete();
-	Reader->Delete();
-
-	return EXIT_SUCCESS;
-}
-
-

LemmaCore/examples/utteminv1d.cpp

@@ -1,131 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  utteminv1d.cpp
-//
-//    Description:  Invert for the difference in water table
-//
-//        Version:  0.0
-//        Created:  03/23/2011 02:07:19 PM
-//       Revision:  none
-//       Compiler:  Tested with g++, icpc, and MSVC 2000
-//
-//         Author:  M. Andy Kass (MAK)
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//                  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 "Lemma"
-#include "banner.h"
-
-using namespace Lemma;
-
-int main () {
-
-	VectorXr maintimes;
-	int ntimes;
-
-	//Banner
-	std::string name;
-	std::string version;
-	std::string usage;
-	name = "TEM Inversion - 1D";
-	version = "1.0beta";
-	usage = "teminv1d [inputfile]";
-	banner(name,version,usage);
-
-	PolygonalWireAntenna* Trans = PolygonalWireAntenna::New();
-	ReceiverPoints* Receivers = ReceiverPoints::New();
-	LayeredEarthEM* StartingMod = LayeredEarthEM::New();
-	//LayeredEarthEM* RecoveredMod = LayeredEarthEM::New();
-	InverseSolverTEM1D* Inverse = InverseSolverTEM1D::New();
-
-
-	Trans->SetNumberOfPoints(5);
-    Trans->SetPoint(0, Vector3r(   0,   0, -1e-3));
-    Trans->SetPoint(1, Vector3r( 100,   0, -1e-3));
-    Trans->SetPoint(2, Vector3r( 100, 100, -1e-3));
-    Trans->SetPoint(3, Vector3r(   0, 100, -1e-3));
-    Trans->SetPoint(4, Vector3r(   0,   0, -1e-3));
-	Trans->SetCurrent(1);
-	Trans->SetNumberOfTurns(1);
-    Trans->SetMinDipoleRatio(1/2.);
-
-	Vector3r loc;
-	Real ox = 50.;
-	Real oy = 50.;
-	Real depth = -1.e-3;
-	Receivers->SetNumberOfReceivers(1);
-	loc << ox,oy,depth;
-	Receivers->SetLocation(0,loc);
-
-	StartingMod->SetNumberOfLayers(22);
-	StartingMod->SetLayerConductivity( (VectorXcr(22) << 0.,1.e-3,
-		1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,
-		1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3,1.e-3).finished() );
-	StartingMod->SetLayerThickness((VectorXr(20)<<4,4,4,4,4,4,4,4,4,4,4,4,4,
-		4,4,4,4,4,4,4).finished());
-	//EM-47 gate times
-	ntimes = 30;
-	maintimes.resize(ntimes);
-	maintimes << 36.,45.25,57.,72.25,92.,117.,148.,186.5,234.,290.,
-		352.5,427.5,525.,647.5,802.5,1002.5,1257.5,1582.5,1997.5,2525.,
-		3197.5,4055.,5147.5,6542.5,8322.5,10592.,13490.,17187.,21902.,
-		27915.;
-	maintimes = maintimes.array() /1000000;
-
-	Inverse->AttachStartMod(StartingMod);
-	Inverse->AttachWireAntenna(Trans);
-	Inverse->AttachReceiver(Receivers);
-	Inverse->SetTimes(maintimes);
-	LayeredEarthEM* RecoveredMod = StartingMod->Clone();
-	Inverse->AttachRecMod(RecoveredMod);
-
-	//Read input data - temp for SEG!
-	/// TODO write a TEM data reader class.  and a functional TEM data class
-	std::fstream infile("rotateddat.dat",std::ios::in);
-	if (infile.fail()) {
-		std::cout << "Shit!" << std::endl;
-	}
-	MatrixXr rotinpdata;
-	rotinpdata.resize(30,1);
-	for (int ii=0;ii<30;ii++) {
-		infile >> rotinpdata(ii);
-	}
-	infile.close();
-
-
-	Inverse->AttachMeasuredData(rotinpdata);
-	//Inverse->SetFreeParams( (VectorXi(2)<<0,1).finished(),
-	//	(VectorXi(3)<<1,2,3).finished());
-
-	std::cout << *Inverse << std::endl;
-
-	Inverse->Calculate();
-	//Inverse->ShowSoln();
-	//Inverse->WriteSoln("temp.dat");
-
-	Inverse->Delete();
-	RecoveredMod->Delete();
-	StartingMod->Delete();
-	Receivers->Delete();
-	Trans->Delete();
-
-	return EXIT_SUCCESS;
-}

LemmaCore/examples/uttemreader.cpp

@@ -1,84 +0,0 @@
-// ===========================================================================
-// 
-//       Filename:  uttemreader.cpp
-// 
-//    Description:  
-// 
-//        Version:  0.0
-//        Created:  02/19/2011 12:30:59 PM
-//       Revision:  none
-//       Compiler:  Tested with g++, icpc, and MSVC 2000 
-// 
-//         Author:  M. Andy Kass (MAK)
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//                  Broken Spoke Brewery, 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 "Lemma"
-
-using namespace Lemma;
-
-
-int main() {
-
-	/*
-	ModelReaderTem1DUBC* Reader = ModelReaderTem1DUBC::New();
-	PolygonalWireAntenna* Trans = PolygonalWireAntenna::New();
-	ReceiverPoints *Receivers = ReceiverPoints::New();
-	LayeredEarthEM *Earth = LayeredEarthEM::New();
-	Reader->SetEMEarth1D(Earth);
-	Reader->SetTransmitter(Trans);
-	Reader->SetReceiver(Receivers);
-	Reader->ReadParameters("em1dtmfwd.in");
-
-	Reader->Delete();
-	Earth->Delete();
-	Receivers->Delete();
-	Trans->Delete();
-	*/
-
-	int rnObs;
-	int rnGates;
-	std::string inputfile;
-	MatrixXr somedata;
-	Vector3Xr somepositions;
-
-	DataTEM* TheData = DataTEM::New();
-	DataReaderTem* Reader = DataReaderTem::New();
-
-	inputfile = "temreadertest.txt";
-
-	Reader->SetDataTEM(TheData);
-	Reader->ReadData(inputfile);
-
-	rnObs = TheData->GetnObs();
-	rnGates = TheData->GetnGates();
-	somedata = TheData->GetData();
-	somepositions = TheData->GetPositions();
-
-	std::cout << rnObs << " " << rnGates << std::endl;
-	std::cout << somedata << std::endl;
-	std::cout << somepositions << std::endl;
-
-	Reader->Delete();
-	TheData->Delete();
-
-	return EXIT_SUCCESS;
-}

LemmaCore/examples/uttemsandbox.cpp

@@ -1,207 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  uttemsandbox.cpp
-//
-//        Created:  09/29/2010 07:38:26 AM
-//       Compiler:  Tested with g++, icpc, and MSVC 2010
-//
-//         Author:  Trevor Irons (ti), M. Andy Kass
-//
-//
-//   Organisation:  Colorado School of Mines (CSM)
-//                  United States Geological Survey (USGS)
-//					Broken Spoke Development, LLC
-//
-//          Email:  tirons@mines.edu, tirons@usgs.gov
-//					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/>.
-//
-// ===========================================================================
-
-/**
-  @file
-  @author   Trevor Irons
-  @date     09/29/2010
-  @version   0.0
- **/
-
-#include "Lemma"
-using namespace Lemma;
-
-#ifdef LEMMAUSEVTK
-#include "matplot.h"
-using namespace matplot;
-#endif
-
-int main() {
-
-
-    int nfreq  =    6000;  // Number of frequencies
-
-	// Specify receiver times
-	int ntimes	=	30;
-	VectorXr times(ntimes);
-	times <<
-	36.0, 45.25, 57.0, 72.25, 92.0,
-	117.0, 148.0, 186.5, 234.0, 290.0,
-	352.5, 427.5, 525.0, 647.5, 802.5,
-	1002.5, 1257.5, 1582.5, 1997.5, 2525.0,
-	3197.5, 4055.0, 5147.5, 6542.5, 8322.5,
-	10592.0, 13490.0, 17187.0, 21902.0, 27915.0;
-
-	times = times.array()*1.0e-6;
-
-	//CALCULATE ABSCISSA
-	//define bounds
-
-	gaussianquadrature *lgqw = gaussianquadrature::New();
-
-	Real lowb;
-	Real upb;
-	lowb = 1.0;
-	upb = 6000000.0;
-	lgqw->SetFreqs(nfreq,upb,lowb);
-	lgqw->CalcAW();
-
-	VectorXr xu(nfreq);
-	xu=lgqw->GetAbscissae();
-	DipoleSource* Trans=DipoleSource::New();
-	Trans->SetType(MAGNETICDIPOLE);
-	Trans->SetPolarisation(ZPOLARISATION);
-	Trans->SetLocation(0.0,0.0,-1e-4);
-
-
-    // Specify Transmitter
-    //PolygonalWireAntenna* Trans  = PolygonalWireAntenna::New();
-    //Trans->SetNumberOfPoints(5);
-    //Trans->SetPoint(0, Vector3r(   0,   0, -1e-3));
-    //Trans->SetPoint(1, Vector3r( 100,   0, -1e-3));
-    //Trans->SetPoint(2, Vector3r( 100, 100, -1e-3));
-    //Trans->SetPoint(3, Vector3r(   0, 100, -1e-3));
-    //Trans->SetPoint(4, Vector3r(   0,   0, -1e-3));
-    Trans->SetNumberOfFrequencies(nfreq);
-    VectorXr  f(nfreq);
-    for (int ifreq=0; ifreq<nfreq; ++ifreq) {
-    //    Trans->SetFrequency(ifreq, 1e-3 + dfreq*(Real)(ifreq));
-		Trans->SetFrequency(ifreq,xu(ifreq));
-        f(ifreq) = xu(ifreq);
-    }
-	//cout << Trans->GetFrequencies();
-    //Trans->SetCurrent(1);
-    //Trans->SetNumberOfTurns(1);
-
-    // Earth properties, top layer is air layer 0 conductivity is fine
-    LayeredEarthEM *Earth = LayeredEarthEM::New();
-        Earth->SetNumberOfLayers(4);
-        Earth->SetLayerConductivity( (VectorXcr(4) << 0.,1.e-6,1.e-2,1.e-6 ).finished() );
-        Earth->SetLayerThickness( (VectorXr(2) << 50, 20).finished() );
-
-    // Receivers, just 1 in the centre for now
-   	ReceiverPoints *Receivers = ReceiverPoints::New();
-		Vector3r loc;
-		Real ox     =    50.;
-		Real oy     =    50.;
-		Real depth  =  -1e-2;
-		Receivers->SetNumberOfReceivers(1);
-		loc << ox, oy, depth;
-		Receivers->SetLocation(0, loc);
-
-	// EmEarth
-	EMEarth1D  *EmEarth = EMEarth1D::New();
-		//EmEarth->AttachWireAntenna(Trans);
-		EmEarth->AttachDipoleSource(Trans);
-		EmEarth->AttachLayeredEarthEM(Earth);
-		EmEarth->AttachReceiverPoints(Receivers);
-		EmEarth->SetFieldsToCalculate(H);
-        // slower but may be more accurate, depending on frequencies
-        EmEarth->SetHankelTransformMethod(CHAVE);
-        //EmEarth->SetHankelTransformMethod(DIGITALFILTERING);
-
-    // Do calculation
-   	//EmEarth->CalculateWireAntennaFields();
-	//EmEarth->MakeCalc();
-	EmEarth->MakeCalc3();
-
-    // Grab Z component
-    // A little painful, I'll try to clean up the API
-    VectorXcr Hw(nfreq);
-    VectorXr  e(nfreq);
-    Hw(0) = 0.; // DC component
-    for (int ifreq=0; ifreq<nfreq; ++ifreq) {
-        Hw(ifreq) = (Receivers->GetHfield(ifreq, 0))(2);
-        e(ifreq) = ifreq;
-    }
-
-    VectorXr Ht(ntimes);                   // Time domain H field
-
-	//Sine transform
-	VectorXr func(nfreq);
-	for (int ii=0;ii<ntimes;++ii) {
-		func = (Hw.imag().array()*((f.array()*times(ii)).sin()));
-		lgqw->SetFunc(func);
-		lgqw->Integrate();
-		Ht(ii)=lgqw->GetResult();
-	}
-	Ht = Ht.array()*(-2.0/PI);
-
-	std::ofstream myfile1;
-	myfile1.open("solution.txt");
-	for (int ii=0;ii<ntimes;++ii) {
-		myfile1 << times(ii) << "   " << Ht(ii) << std::endl;
-	}
-	myfile1.close();
-
-	std::ofstream myfile2;
-	myfile2.open("freq_domain.txt");
-	for (int ii=0;ii<nfreq;++ii) {
-		myfile2 << f(ii) << "  " << Hw(ii).real() << "  " << Hw(ii).imag()
-			<< std::endl;
-	}
-	myfile2.close();
-
-    //std::cout << Ht << std::endl;
-    //std::cout << Hw.real() << std::endl;
-
-    // Quick and dirty plot
-    #ifdef  LEMMAUSEVTK
-    double colour1[3] = {0.0,0.0,1.0};
-    double colour2[3] = {1.0,0.0,0.0};
-
-    Plot2D_VTK p1("Hz", "Re(Hw)", 800, 600);
-    p1.plot(f, Hw.real().eval(), colour1, ".-");
-    p1.show();
-
-    Plot2D_VTK p2("Hz", "Im(Hw)", 800, 600);
-    p2.plot(f, Hw.imag().eval(), colour2, ".-");
-    p2.show();
-
-    Plot2D_VTK p3("Time (seconds)", "Ht", 800, 600);
-    p3.plot(times, Ht, colour2, ".-");
-    p3.show();
-
-	//Plot2D_VTK p4("index", "frequency",800,600);
-	//p4.plot(e,f,colour1,".-");
-	//p4.show();
-
-    #endif
-
-    // Clean up
-    Trans->Delete();
-    Earth->Delete();
-    Receivers->Delete();
-    EmEarth->Delete();
-
-    return EXIT_SUCCESS;
-}

LemmaCore/examples/wireantenna.cpp

@@ -1,319 +0,0 @@
-// ===========================================================================
-//
-//       Filename:  utdipolesource.cpp
-//
-//    Description:
-//
-//        Version:  0.0
-//        Created:  12/02/2009 11:57:14 AM
-//       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 <iostream>
-#include <fstream>
-
-#include "dipolesource.h"
-#include "layeredearth.h"
-#include "receiverpoints.h"
-#include "emearth1d.h"
-#include "WireAntenna.h"
-#include "PolygonalWireAntenna.h"
-
-#if  LEMMAUSEVTK
-#include "vtkRenderer.h"
-#include "vtkRenderWindow.h"
-#include "vtkRenderWindowInteractor.h"
-#include "vtkRenderLargeImage.h"
-#include "vtkPNGWriter.h"
-#endif     // -----  not LEMMA_USE_VTK  -----
-
-// For testing purposes disable VTK and run scale.sh
-//#undef LEMMAUSEVTK
-
-#include "timer.h"
-
-using namespace Lemma;
-
-double randDouble(double low, double high) {
-	//srand(time(0));
-	double temp;
-	/* swap low & high around if the user makes no sense */
-	if (low > high)	{
-	temp = low;
-	low = high;
-	high = temp;
-	}
-	/* calculate the random number & return it */
-	temp = (rand() / (static_cast<double>(RAND_MAX) + 1.0))
-	* (high - low) + low;
-	return temp;
-}
-
-
-int main() {
-
-	// Keep track of time
-	jsw_timer timer;
-
-
-	srand(time(0));
-
-	PolygonalWireAntenna *pa = PolygonalWireAntenna::New();
-	pa->SetNumberOfFrequencies(1);
-	pa->SetFrequency(0, 1000);
-	pa->SetNumberOfPoints(5);
-	pa->SetPoint(0, Vector3r(   0,   0, -.001));
-	pa->SetPoint(1, Vector3r( 100,   0, -.001));
-	pa->SetPoint(2, Vector3r( 100, 100, -.001));
-	pa->SetPoint(3, Vector3r(   0, 100, -.001));
-	pa->SetPoint(4, Vector3r(   0,   0, -.001));
-	pa->SetCurrent(1.);
-    pa->SetNumberOfTurns(1);
-	//Vector3r rp = Vector3r::Random(3);
-	//rp << 150., 10, 0.;
-	//rp << -27.1456, 15.2350, -1e-3;
-	//rp << randDouble(-35,35), randDouble(-35,35), randDouble(-35,35);
-	//rp << 3.22806, -13.1548, 14.9695;
-	//rp.setRandom(3);
-	//std::cout <<  "rp " << rp.transpose() << std::endl;
-	//pa->ApproximateWithElectricDipoles(rp);
-
-	WireAntenna *wire = WireAntenna::New();
-		wire->SetNumberOfPoints(5);
-		wire->SetPoint(0, Vector3r(   0,   0, -1e-3));
-		wire->SetPoint(1, Vector3r( 10,   0, -1e-3));
-		wire->SetPoint(2, Vector3r( 10, 10, -1e-3));
-		wire->SetPoint(3, Vector3r(   0, 10, -1e-3));
-		wire->SetPoint(4, Vector3r(   0,   0, -1e-3));
-		// TODO change wire antennae to use my class
-		//wire->SetNumberOfFrequencies(1);
-		wire->SetCurrent(1.);
-		wire->SetNumberOfFrequencies(1);
-		wire->SetFrequency(0, 1000);
-        wire->SetNumberOfTurns(1);
-		//wire->ApproximateWithElectricDipoles(5);
-
-	// Define model
-	VectorXcr sigma(2);
-		sigma << Complex(0.,0), Complex(.1,0);
-	VectorXr  thick(1);
-		thick << 10;
-	LayeredEarthEM *earth = LayeredEarthEM::New();
-		earth->SetNumberOfLayers(2);
-		earth->SetLayerConductivity(sigma);
-		//earth->SetLayerThickness(thick);
-
-	// Receivers
-	ReceiverPoints *receivers = ReceiverPoints::New();
-		Vector3r loc;
-		Real ox    =    50.561 ;
-		Real oy    =   105.235 ;
-		Real depth =    -3.75e1;
-		Real depth2 =   depth;
-		Real dx    =    1.;
-		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 += dx;
-			++ ir;
-		}
-
-	// EmEarth
-	EMEarth1D  *EmEarth = EMEarth1D::New();
-		//EmEarth->AttachWireAntenna(wire);
-		EmEarth->AttachWireAntenna(pa);
-		EmEarth->AttachLayeredEarthEM(earth);
-		EmEarth->AttachReceiverPoints(receivers);
-		EmEarth->SetFieldsToCalculate(H);
-        //EmEarth->SetHankelTransformMethod(GAUSSIANQUADRATURE);
-
-	// Do calculation
-	timer.begin();
-	EmEarth->CalculateWireAntennaFields();
-	Real paTime = timer.end();
-	std::cout << "Polygonal wire antennae time: " << paTime << "\n";
-
-	//EmEarth->AttachWireAntenna(wire);
-	//timer.begin();
-	//EmEarth->CalculateWireAntennaFields();
-	//Real waTime = timer.end();
-	//std::cout << "Fixed wire antennae time: " << waTime << "\n";
-
-	depth = depth2;
-	std::fstream real("reale_lay.dat", std::ios::out);
-	std::fstream imag("image_lay.dat", std::ios::out);
-	std::fstream hreal("real_lay.dat", std::ios::out);
-	std::fstream himag("imag_lay.dat", std::ios::out);
-	for (int iz=0; iz<nz; ++iz) {
-		Vector3cr temp = receivers->GetEfield(0,iz);
-		real << ox << "\t" << oy << "\t" << depth << "\t"
-				<< temp(0).real() << "\t" << temp(1).real()
-				<< "\t" << temp(2).real() << std::endl;
-		imag << ox << "\t" << oy << "\t" << depth << "\t"
-				<< std::imag(temp(0)) << "\t" << std::imag(temp(1))
-				<< "\t" << std::imag(temp(2)) << std::endl;
-		temp = receivers->GetHfield(0, iz);
-		hreal << ox << "\t" << oy << "\t" << depth << "\t"
-				<< std::real(temp(0)) << "\t" << std::real(temp(1))
-				<< "\t" << std::real(temp(2)) << std::endl;
-		himag << ox << "\t" << oy << "\t" << depth << "\t"
-				<< std::imag(temp(0)) << "\t" << std::imag(temp(1))
-				<< "\t" << std::imag(temp(2)) << std::endl;
-		depth += dx;
-	}
-	real.close();
-	imag.close();
-	hreal.close();
-	himag.close();
-	EmEarth->Delete();
-	receivers->Delete();
-	earth->Delete();
-	//wire->Delete();
-
-#if  LEMMAUSEVTK
-	// Create the usual rendering stuff.
-	vtkRenderer           *renderer = vtkRenderer::New();
-	vtkRenderWindow         *renWin = vtkRenderWindow::New();
-	vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
-
-	// Line of tx
-	vtkLineSource       *vline = vtkLineSource::New();
-	vtkTubeFilter       *vTube = vtkTubeFilter::New();
- 	vtkPolyDataMapper   *vMapper = vtkPolyDataMapper::New();
-	vtkActor             *vActor = vtkActor::New();
-	vline->SetPoint1(0,0,0);
-	vline->SetPoint2(10,0,0);
-
-	vTube->SetInputConnection(vline->GetOutputPort());
-	vTube->SetRadius(.2);
-	vTube->SetNumberOfSides(6);
-	vMapper->SetInputConnection(vTube->GetOutputPort());
-	vActor->SetMapper(vMapper);
-	vActor->GetProperty()->SetColor(0.0, .0, 1.0);
-	vActor->GetProperty()->SetOpacity(.15);
-	renderer->AddActor(vActor);
-
-	vtkLineSource       *vline2 = vtkLineSource::New();
-	vtkTubeFilter       *vTube2 = vtkTubeFilter::New();
- 	vtkPolyDataMapper   *vMapper2 = vtkPolyDataMapper::New();
-	vtkActor             *vActor2 = vtkActor::New();
-	vline2->SetPoint1(10,0,0);
-	vline2->SetPoint2(10,10,0);
-
-	vTube2->SetInputConnection(vline2->GetOutputPort());
-	vTube2->SetRadius(.2);
-	vTube2->SetNumberOfSides(6);
-	vMapper2->SetInputConnection(vTube2->GetOutputPort());
-	vActor2->SetMapper(vMapper2);
-	vActor2->GetProperty()->SetColor(0.0, .0, 1.0);
-	vActor2->GetProperty()->SetOpacity(.15);
-	renderer->AddActor(vActor2);
-
-	vtkLineSource       *vline3 = vtkLineSource::New();
-	vtkTubeFilter       *vTube3 = vtkTubeFilter::New();
- 	vtkPolyDataMapper   *vMapper3 = vtkPolyDataMapper::New();
-	vtkActor             *vActor3 = vtkActor::New();
-	vline3->SetPoint1(10,10,0);
-	vline3->SetPoint2(0,10,0);
-
-	vTube3->SetInputConnection(vline3->GetOutputPort());
-	vTube3->SetRadius(.2);
-	vTube3->SetNumberOfSides(6);
-	vMapper3->SetInputConnection(vTube3->GetOutputPort());
-	vActor3->SetMapper(vMapper3);
-	vActor3->GetProperty()->SetColor(0.0, .0, 1.0);
-	vActor3->GetProperty()->SetOpacity(.15);
-	renderer->AddActor(vActor3);
-
-	vtkLineSource       *vline4 = vtkLineSource::New();
-	vtkTubeFilter       *vTube4 = vtkTubeFilter::New();
- 	vtkPolyDataMapper   *vMapper4 = vtkPolyDataMapper::New();
-	vtkActor             *vActor4 = vtkActor::New();
-	vline4->SetPoint1(0,10,0);
-	vline4->SetPoint2(0,0,0);
-
-	vTube4->SetInputConnection(vline4->GetOutputPort());
-	vTube4->SetRadius(.2);
-	vTube4->SetNumberOfSides(6);
-	vMapper4->SetInputConnection(vTube4->GetOutputPort());
-	vActor4->SetMapper(vMapper4);
-	vActor4->GetProperty()->SetColor(0.0, .0, 1.0);
-	vActor4->GetProperty()->SetOpacity(.15);
-	renderer->AddActor(vActor4);
-
-    loc << 50, 50, -1e-3;
-	pa->ApproximateWithElectricDipoles(loc);
-
-    vtkActor **pdipActors = new vtkActor*[pa->GetNumberOfDipoles()];
-    std::cout <<  "Wire approximated with " << pa->GetNumberOfDipoles() << std::endl;
-	for (int id=0; id<pa->GetNumberOfDipoles(); ++id) {
-		pdipActors[id] = pa->GetVtkActor(id);
-		renderer->AddActor(pdipActors[id]);
-	}
-
-    /*
-    vtkActor **dipActors = new vtkActor*[wire->GetNumberOfDipoles()];
-	for (int id=0; id<wire->GetNumberOfDipoles(); ++id) {
-		dipActors[id] = wire->GetVtkActor(id);
-		renderer->AddActor(dipActors[id]);
-	}
-    */
-
-	renderer->SetBackground(1,1,1);
-
-	// Render the window
-	renWin->AddRenderer(renderer);
-	renWin->SetWindowName("Wire antennae");
-
-	iren->SetRenderWindow(renWin);
-	iren->Initialize();
-	iren->Start();
-	iren->Render();
-
-    #if 0
-	cout << "Enter File name?: ";
-	std::string pngName;
-	std::cin >> pngName;
-	vtkPNGWriter *pngwrite = vtkPNGWriter::New();
-	vtkRenderLargeImage *renlarge = vtkRenderLargeImage::New();
-	renlarge->SetInput(renderer);
-	renlarge->SetMagnification(2);
-	pngwrite->SetInputConnection(renlarge->GetOutputPort());
-	pngName.append(".png");
-	pngwrite->SetFileName(pngName.c_str());
-	pngwrite->Write();
-    #endif
-
-#endif     // -----  not LEMMA_USE_VTK  -----
-
-
-	//std::cout << *pa << std::endl;
-	//pa->Delete();
-
-	return 0;
-}

LemmaCore/include/ASCIIParser.h

@@ -1,161 +0,0 @@
-/* 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      09/23/2013 02:31:24 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2013, Trevor Irons
- */
-
-#ifndef  ASCIIPARSER_INC
-#define  ASCIIPARSER_INC
-
-#include "LemmaObject.h"
-#include <fstream>
-
-namespace Lemma {
-
-/**
- * \ingroup LemmaCore
- * \brief   Provides ASCII input file parsing
- * \details Able to accomodate various inputs and comment styles
- */
-class ASCIIParser : public LemmaObject {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const ASCIIParser &ob);
-
-    public:
-
-    // ====================  LIFECYCLE     =======================
-
-    /**
-     *  Factory method for generating concrete class.
-     *  @return a std::shared_ptr of type ASCIIParser
-     */
-    static std::shared_ptr< ASCIIParser >  NewSP();
-
-    /**
-     *  Constructs an object from a YAML serialization
-     *  @return a std::shared_ptr of type ASCIIParser
-     */
-    static std::shared_ptr< ASCIIParser >  DeSerialize( const YAML::Node& node );
-
-    /**
-     *  Uses YAML to serialize this object.
-     *  @return a YAML::Node
-     */
-    YAML::Node Serialize() const;
-
-    // ====================  OPERATORS     =======================
-
-    // ====================  OPERATIONS    =======================
-
-    /** Opens the file up for reading. Throws an exception if something bad happens.
-        @param[in] fname is the filename to be parsed.
-     */
-    void Open (const std::string& fname);
-
-
-    /** Closes the file. Throws an exception if something bad happens.
-     */
-    void Close ( );
-
-    /** Reads a series of Reals.
-     *  @param[in] nr is the number of reals to read. Enter -1 for the entire file
-     *  @todo throw exception if no file is open
-     */
-    std::vector<Real> ReadReals( const int& nr);
-
-    /** Reads a series of Reals.
-     *  @param[in] nr is the number of ints to read. Enter -1 for the entire file
-     *  @todo throw exception if no file is open
-     */
-    std::vector<int> ReadInts( const int& nr);
-
-    /** Reads a series of space delimited strings
-     *  @param[in] nr is the number of strings to read. Enter -1 for the entire file
-     *  @todo throw exception if no file is open
-     */
-    std::vector< std::string > ReadStrings( const int& nr);
-
-    /**
-     * @param[in] loc is the point in the file to jump to. Uses seekg
-     */
-    void JumpToLocation(const int& loc);
-
-    // ====================  ACCESS        =======================
-
-    /** Sets the comment identifier key.
-     * @param[in] key is a string identifying comments. All text after the key will be
-     *  ignored by the parser. Default is //
-     */
-    void SetCommentString( const std::string& key );
-
-    /** Sets the buffer size. This affects the maximum number of column in a line. Defaults
-     *  is 255.
-     *  @param[in] BufferSize is the size of the buffer to use
-     */
-    void SetBufferSize( const int& BufferSize);
-
-    /**
-     * @return the current position in the file, as reported by istream::tellg
-     */
-    int GetFileLocation();
-
-    /** Returns the name of the underlying class, similiar to Python's type */
-    virtual inline std::string GetName() const {
-        return CName;
-    }
-
-    // ====================  INQUIRY       =======================
-
-    protected:
-
-    // ====================  LIFECYCLE     =======================
-
-    /** Default protected constructor, use New */
-    ASCIIParser ( );
-
-    /** Constructor using YAML::Node */
-    ASCIIParser ( const YAML::Node& node );
-
-    /** Default protected destructor, use Delete */
-    ~ASCIIParser ();
-
-    /**
-     *  @copybrief   LemmaObject::Release()
-     *  @copydetails LemmaObject::Release()
-     */
-    void Release();
-
-    private:
-
-    // ====================  DATA MEMBERS  =========================
-
-    /** ASCII string representation of the class name */
-    static constexpr auto CName = "ASCIIParser";
-
-    /** c++ style file IO */
-    std::fstream input;
-
-    /** comment string, defaults to c++ style // */
-    std::string  CommentString;
-
-    /** Buffer size, max line width supported, defaults to 255 */
-    int BufferSize;
-
-}; // -----  end of class  ASCIIParser  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef ASCIIPARSER_INC  -----

LemmaCore/include/CubicSplineInterpolator.h

@@ -1,195 +0,0 @@
-/* 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  CUBICSPLINEINTERPOLATOR_INC
-#define  CUBICSPLINEINTERPOLATOR_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-// Simple struct to hold spline terms
-struct SplineSet{
-    VectorXr a;
-    VectorXr b;
-    VectorXr c;
-    VectorXr d;
-    VectorXr x;
-
-    SplineSet( ) {
-    }
-
-    SplineSet(const int&n) {
-        a = VectorXr::Zero(n+1);
-        b = VectorXr::Zero(n);
-        c = VectorXr::Zero(n+1);
-        d = VectorXr::Zero(n);
-        x = VectorXr::Zero(n+1);
-    }
-};
-
-/**
- * \ingroup LemmaCore
- * \brief   Real 1D Natural cubic spline interpolator.
- * \details Splines are fit between knots \f$j\f$ according to the forulae
- *          \f[ S_j(x) =  a_j + b_j(x - x_j) + c_j(x-x_j)^2 + d_j(x-x_y)^3  \f]
- *          The spline must satisfy the following conditions
- *           \f{eqnarray} {
- *               S_i(x_i) & = & y_i = S_{i-1}(x_i), i = 1,..., n-1 \\
- *               S'_i(x_i) & = &  S'_{i-1}(x_i), i = 1,..., n-1 \\
- *               S''_i(x_i) & = & S''_{i-1}(x_i), i = 1,..., n-1 \\
- *               S''_0(x_0) & = & S''_{n-1}(x_n) = 0
- *           \f}
- */
-class CubicSplineInterpolator : public LemmaObject {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const CubicSplineInterpolator &ob);
-
-    public:
-
-    // ====================  LIFECYCLE     =======================
-
-    /**
-     *  Factory method for generating concrete class.
-     *  @return a std::shared_ptr of type CubicSplineInterpolator
-     */
-    static std::shared_ptr<CubicSplineInterpolator> NewSP();
-
-    /**
-     *  Uses YAML to serialize this object.
-     *  @return a YAML::Node
-     */
-    YAML::Node Serialize() const;
-
-    /**
-     *   Constructs an object from a YAML::Node.
-     */
-    static std::shared_ptr< CubicSplineInterpolator > DeSerialize(const YAML::Node& node);
-
-    // ====================  OPERATORS     =======================
-
-    // ====================  OPERATIONS    =======================
-
-    /** Sets the knots to use for interpolation.
-        @param[in] x are the absissa values
-        @param[in] y are the ordinate values
-     */
-    void SetKnots(const VectorXr& x, const VectorXr& y);
-
-    /** Resets the knots to use for interpolation, when abscissa values haven't changed.
-        @param[in] y are the ordinate values
-     */
-    void ResetKnotOrdinate( const VectorXr& y );
-
-    /** Interpolate a monotonically increasing ordered set.
-        @param[in] x are the interpolation abscissa points
-        @return the ordinate values at x
-     */
-    VectorXr InterpolateOrderedSet(const VectorXr& x);
-
-    /** integrates the spline from x0 to x1. Uses composite Simpson's rule and n is the number of segments
-     *  @param[in] x0 is left argument
-     *  @param[in] x1 is right argument
-     *  @param[in] n is the number of points, must be even
-     */
-    Real Integrate(const Real& x0, const Real& x1, const int& n);
-
-    /** integrates using cubic spline values. Taken from AMRIRA P223F project code Leroi, which in turn was based on
-        This is a modification of the FUNCTION PPVALU in the book
-        "A PRACTICAL GUIDE TO SPLINES"  by C. DE BOOR
-     */
-    Real Integrate(const Real& x0, const Real& x1);
-
-    /** @returns the know abscissa values
-     */
-    VectorXr GetKnotAbscissa();
-
-    /** @returns the know abscissa values
-     */
-    VectorXr GetKnotOrdinate();
-
-    /** Interpolation at a single point.
-        @param[in] x is the interpolation abscissa point
-        @param[in] i is an optional index to start searching at. Defaults to zero
-        @return the ordinate value at x
-     */
-    Real Interpolate(const Real& x, int& i);
-
-    /** Interpolation at a single point.
-        @param[in] x is the interpolation abscissa point
-        @return the ordinate value at x
-     */
-    Real Interpolate(const Real& x);
-
-    // ====================  ACCESS        =======================
-
-    // ====================  INQUIRY       =======================
-
-    /** Returns the name of the underlying class, similiar to Python's type */
-    virtual inline std::string GetName() const {
-        return CName;
-    }
-
-    protected:
-
-    // ====================  LIFECYCLE     =======================
-
-    /** Default protected constructor, use New */
-    CubicSplineInterpolator ( );
-
-    /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-    CubicSplineInterpolator (const YAML::Node& node);
-
-    /** Default protected destructor, smart pointers auto delete */
-    ~CubicSplineInterpolator ();
-
-    /**
-     *  @copybrief   LemmaObject::Release()
-     *  @copydetails LemmaObject::Release()
-     */
-    void Release();
-
-    // ====================  OPERATIONS    =======================
-
-    /** Finds the interval of knots in spline to use for integration.
-     */
-    int Interval(const Real& x);
-
-    private:
-
-    /** ASCII string representation of the class name */
-    static constexpr auto CName = "CubicSplineInterpolator";
-
-    SplineSet Spline;
-
-    int ilo;
-
-    int mflag;
-
-    // ====================  DATA MEMBERS  =========================
-
-}; // -----  end of class  CubicSplineInterpolator  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef CUBICSPLINEINTERPOLATOR_INC  -----
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/include/Data.h

@@ -1,94 +0,0 @@
-/* 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     03/01/2010
-  @version  $Id: data.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  _DATA_H_INC
-#define  _DATA_H_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    // ===================================================================
-    //        Class:  Data
-    /**
-     *  \ingroup LemmaCore
-     *  \brief Abstract class for data from an instrument
-     *  \details Currently provides no functionality, but this will likely
-     *          change in the near future.
-     */
-    // ===================================================================
-    class Data : public LemmaObject {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const Data &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Copies the *structure* of this class to a new object and
-             * returns a pointer to this object. Memory management is
-             * the responsibility of the receiver!. The data values are
-             * not copied.
-             */
-            virtual Data* Clone()=0;
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /** Clears all data arrays and containers
-             */
-            virtual void Zero()=0;
-
-            /** Data2 needs to be compatible with the calling class. Data2 will
-             * be cast into the calling class type. Most of the time this
-             * cast will not perform anything, as Data2 *is* the same type
-             * as the calling class.
-             */
-            virtual Real Norm(Data* Data2)=0;
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return CName;
-            }
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Default protected constructor. */
-            Data (  );
-
-            /** Default protected constructor. */
-            ~Data ();
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-            /** ASCII string representation of the class name */
-            static constexpr auto CName = "Data";
-
-    }; // -----  end of class  Data  -----
-
-}       // -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef _DATA_H_INC  -----
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/include/DataReader.h

@@ -1,75 +0,0 @@
-/* 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     03/01/2010
-  @version  $Id: datareader.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  DATAREADER_H_INC
-#define  DATAREADER_H_INC
-
-#include "LemmaObject.h"
-#include "Data.h"
-
-namespace Lemma {
-
-// ===================================================================
-//        Class:  DataReader
-/// \ingroup LemmaCore
-/// \brief  Abstract class whose derived members read data files and
-/// converts them to Data Classes
-/// \details
-// ===================================================================
-class DataReader : public LemmaObject {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const DataReader &ob);
-
-    public:
-
-        // ====================  LIFECYCLE     =======================
-
-        // ====================  OPERATORS     =======================
-
-        // ====================  OPERATIONS    =======================
-
-        // ====================  ACCESS        =======================
-        virtual Data* GetData()=0;
-
-        // ====================  INQUIRY       =======================
-        /** Returns the name of the underlying class, similiar to Python's type */
-        virtual inline std::string GetName() const {
-            return CName;
-        }
-
-    protected:
-
-        // ====================  LIFECYCLE     =======================
-
-        /// Default protected constructor.
-        DataReader ( );
-
-        /// Default protected constructor.
-        ~DataReader ( );
-
-        // ====================  DATA MEMBERS  =========================
-
-    private:
-
-        /** ASCII string representation of the class name */
-        static constexpr auto CName = "DataReader";
-
-}; // -----  end of class  DataReader  -----
-
-}       // -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef DATAREADER_H_INC  -----
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/include/EarthModel.h

@@ -1,149 +0,0 @@
-/* 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     03/23/2010
-  @version  $Id: earthmodel.h 198 2014-12-27 06:14:05Z tirons $
- **/
-
-#ifndef  EARTHMODEL_INC
-#define  EARTHMODEL_INC
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    // ===================================================================
-    //        Class:  EarthModel
-    /// \ingroup LemmaGroup
-    /// \brief abstract class for Earth models
-    /// \details
-    // ===================================================================
-    class EarthModel : public LemmaObject {
-
-        // ====================    FRIENDS     ===========================
-        friend std::ostream &operator<<(std::ostream &stream,
-                        const EarthModel &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-            /** YAML Serializing method
-             */
-            YAML::Node Serialize() const;
-            //static LayeredEarth* DeSerialize(const YAML::Node& node);
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            // ====================  ACCESS        =======================
-
-            /** Sets the earth's magnetic field, in Tesla
-                @param[in] bfield contains the x,y, and z components of
-                the field. EarthModel::Inc, EarthModel::Dec, and
-                EarthModel::BMag are computed:
-                \f{eqnarray*}{ \mathrm{Inc} = &
-                \cos^{-1}( \mathbf{B} \cdot \hat{\mathbf{z}} / B )
-                \\ \mathrm{Dec} =& \cos^{-1}
-                         (\mathbf{B} \cdot \hat{\mathbf{x}} / B )
-                   \\           \mathrm{Mag} =& \Vert \mathbf{B} \Vert  \f}
-               @param[in] unit specifies the units of bfield.
-              */
-            void SetMagneticFieldComponents(const Vector3r &bfield,
-                            const MAGUNITS &unit);
-
-            /// Sets the magnetic field using inclination, declination,
-            /// and magnitude, units of Tesla
-            /// @param[in] inc is the field's inclination
-            /// @param[in] dec is the field's declination
-            /// @param[in] Mag is the field's magnitude
-            /// @param[in] unit specifies the the units used.
-            /// The components are set according to
-            /// \f{eqnarray*} { B_x =& B \cos(inc (\pi/180)) \cos(dec (\pi/180))
-            ///            \\   B_y =& B \cos(inc (\pi/180)) \sin(dec (\pi/180))
-            ///            \\   B_z =& B \sin(inc (\pi/180))
-            /// \f}
-            void SetMagneticFieldIncDecMag(const Real& inc, const Real&dec,
-                            const Real& Mag, const MAGUNITS &unit);
-
-            // ====================  INQUIRY       =======================
-
-            /// Gets the magnetic field of the earth, in T
-            Vector3r GetMagneticField( );
-
-            /// Gets the magnetic field of the earth, in T
-            Vector3r GetMagneticFieldInGauss(  );
-
-            /// Gets the magnetic field unit vector of the earth
-            Vector3r GetMagneticFieldUnitVector( );
-
-            /// Returns the magnitude of the magnetic field \f$ \Vert
-            /// \mathbf{B}_0 \Vert \f$
-            Real GetMagneticFieldMagnitude();
-
-            /// Returns the magnitude of the magnetic field \f$ \Vert
-            /// \mathbf{B}_0 \Vert \f$ in Gauss units
-            Real GetMagneticFieldMagnitudeInGauss( );
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return this->CName;
-            }
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            EarthModel ( );
-
-            /** Deserialize constructor */
-            EarthModel (const YAML::Node& node);
-
-            /// Default protected constructor.
-            ~EarthModel ();
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-            /** ASCII string representation of the class name */
-            static constexpr auto CName = "EarthModel";
-
-            /// Magnetic field, in units of nT
-            Vector3r          BField;
-
-            /// Magnetic field unit vector \f$  \hat{\mathbf{B}_0} \f$
-            Vector3r          BFieldUnit;
-
-            /// Inclination of the magnetic field
-            Real              BInc;
-
-            /// Declination of the magnetic field
-            Real              BDec;
-
-            /// Declination of the magnetic field
-            Real              BMag;
-
-    }; // -----  end of class  EarthModel  -----
-
-    //////////////////////////////////////////////////////////////
-    // Error Classes
-
-    /** If the Earth class is NULL valued, throw this
-     */
-    class NullEarth : public std::runtime_error {
-            /** Thrown when an Earth pointer is NULL
-             */
-            public: NullEarth ();
-    };
-
-}       // -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef EARTHMODEL_INC  -----

LemmaCore/include/Filter.h

@@ -1,71 +0,0 @@
-/* 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     07/20/2010
-  @version  $Id: filter.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-
-    // ===================================================================
-    //  Class:  Filter
-    /**
-      @class  Filter
-      \ingroup LemmaCore
-      \brief  Abstract class for filtering.
-      \details Derived classes include fourier domain and time domain filters.
-     */
-    // ===================================================================
-
-    class Filter : public LemmaObject {
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return this->CName;
-            }
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            Filter ( );
-
-            /// Default protected constructor.
-            ~Filter ();
-
-            // ====================  DATA MEMBERS  =========================
-
-        private:
-
-            /** ASCII string representation of the class name */
-            static constexpr auto CName = "Filter";
-
-    }; // -----  end of class  Filter  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/include/Grid.h

@@ -1,78 +0,0 @@
-/* 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     10/25/2009
-  @version  $Id: grid.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef __GRID_H
-#define __GRID_H
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-// ===============================================================================
-//        Class:  Grid
-/// \ingroup LemmaCore
-/// \brief Abstract base class for grids.
-/// \details Grids define values in space, they may either be an integral part
-/// of models, or simply the output of a forward modelling procedure.
-// ===============================================================================
-
-class Grid : public LemmaObject {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const Grid &ob);
-
-    public:
-
-        // ====================  LIFECYCLE     ===================================
-
-        YAML::Node Serialize() const;
-
-        // ====================  OPERATORS     ===================================
-
-        // ====================  OPERATIONS    ===================================
-
-        // ====================  ACCESS        ===================================
-
-        // ====================  INQUIRY       ===================================
-
-        /** Returns the name of the underlying class, similiar to Python's type */
-        virtual inline std::string GetName() const {
-            return this->CName;
-        }
-
-    protected:
-
-        // ====================  LIFECYCLE     ===================================
-
-        /** Protected DeDerializing constructor, use factory DeSerialize  method on non abstract classes*/
-        Grid (const YAML::Node& node);
-
-        /// Default protected constructor.
-        Grid ( );
-
-        /// Default protected constructor.
-        ~Grid ();
-
-        // ====================  DATA MEMBERS  ===================================
-
-    private:
-
-        /** ASCII string representation of the class name */
-        static constexpr auto CName = "Grid";
-
-}; // -----  end of class  Grid  -----
-
-} // namespace Lemma
-
-#endif // __GRID_H
-

LemmaCore/include/GridReader.h

@@ -1,84 +0,0 @@
-/* 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
-  @date      09/23/2013 11:25:11 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  GRIDREADER_INC
-#define  GRIDREADER_INC
-
-#include "LemmaObject.h"
-#include "Grid.h"
-
-namespace Lemma {
-
-    /**
-      @class
-      \ingroup LemmaCore
-      \brief   Abstract class for grid readers.
-      \details Provides a consistent interface for reading grid files in Lemma.
-     */
-    class GridReader : public LemmaObject {
-
-        friend std::ostream &operator << (std::ostream &stream, const GridReader &ob) {
-            stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-            return stream;
-        }
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            virtual void ReadASCIIGridFile( const std::string& name )=0;
-
-            virtual std::shared_ptr< Grid > GetGrid( )=0;
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return this->CName;
-            }
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Default protected constructor, use New */
-            GridReader ( ) : LemmaObject( ) {
-            }
-
-            /** Default protected constructor, use Delete */
-            ~GridReader () {
-            }
-
-        private:
-
-            /** ASCII string representation of the class name */
-            static constexpr auto CName = "GridReader";
-
-            // ====================  DATA MEMBERS  =========================
-
-    }; // -----  end of class  GridReader  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef GRIDREADER_INC  -----

LemmaCore/include/Instrument.h

@@ -1,71 +0,0 @@
-/* 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: instrument.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef __INSTRUMENT_H
-#define __INSTRUMENT_H
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-	// =======================================================================
-	//        Class:  Instrument
-    /// \ingroup LemmaCore
-	/// \brief    Abstract class for instruments
-	/// \details
-	// =======================================================================
-	class Instrument : public LemmaObject {
-
-		friend std::ostream &operator<<(std::ostream &stream,
-			const Instrument &ob);
-
-		public:
-
-			// ====================  LIFECYCLE     ===========================
-
-			// ====================  OPERATORS     ===========================
-
-			// ====================  OPERATIONS    ===========================
-            //virtual void ForwardModelOnOctreeMesh()=0;
-
-			// ====================  ACCESS        ===========================
-
-			// ====================  INQUIRY       ===========================
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return this->CName;
-            }
-
-			// ====================  DATA MEMBERS  ===========================
-
-		protected:
-
-			// ====================  LIFECYCLE     ===========================
-
-			/// Default protected constructor.
-			Instrument ( );
-
-			/// Default protected constructor.
-			~Instrument ();
-
-		private:
-
-            /** ASCII string representation of the class name */
-            static constexpr auto CName = "Instrument";
-
-	}; // -----  end of class  Instrument  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif // __INSTRUMENT_H

LemmaCore/include/LayeredEarth.h

@@ -1,174 +0,0 @@
-/* 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 __LAYEREDEARTH_H
-#define __LAYEREDEARTH_H
-
-#include "EarthModel.h"
-
-namespace Lemma {
-
-	const int MAXLAYERS	= 10;
-
-	// =======================================================================
-	//        Class:  LayeredEarth
-    /// \ingroup LemmaCore
-	/// \brief Abstract 1D layered earth.
-	// =======================================================================
-	class LayeredEarth : public EarthModel {
-
-        friend class LayeredEarthEM;
-
-		public:
-
-			// ====================    FRIENDS     ===========================
-			/** Recursively prints out information about this class
-             */
-            friend std::ostream &operator<<(std::ostream &stream,
-						const LayeredEarth &ob);
-
-			// ====================  LIFECYCLE     ===========================
-
-			// ====================  OPERATORS     ===========================
-
-			// ====================  OPERATIONS    ===========================
-
-			// ====================  ACCESS        ===========================
-
-			/** Sets the number of layers and resizes all model parameters to
-			 *  be the correct size, finally initialises all values to free
-			 *  space.
-             */
-			virtual void SetNumberOfLayers(const int& nlay)=0;
-
-			/** Sets the thickness of the layers
-             */
-			void SetLayerThickness(const VectorXr &thick);
-
-			// ====================  INQUIRY       ===========================
-
-			/** Returns the number of layers in the model */
-			int GetNumberOfLayers( );
-
-			/** Returns the number of layers in the model, excluding the air
-			 * layer
-             */
-			int GetNumberOfNonAirLayers( );
-
-			/** Returns the layer that a depth is in.
-			 * @param[in] depth is the depth you desire to know the layer of
-			 * @return the indice of the layer that depth is in.
-             */
-			int GetLayerAtThisDepth(const Real& depth);
-
-			/** Returns the thickness of a layer
-             *  @param[in] lay is the layer indice
-             *  @return the thickness of a layer
-             */
-			Real GetLayerThickness(const int & lay);
-
-			/** Returns the depth of the bottom interface of a layer
-             *  @param[in] lay is the layer indice
-             *  @return the depth of the bottom interface of a layer
-             */
-			Real GetLayerDepth(const int & lay);
-
-            /** YAML Serializing method
-             */
-            YAML::Node Serialize() const;
-            //static LayeredEarth* DeSerialize(const YAML::Node& node);
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return this->CName;
-            }
-
-		protected:
-
-			// ====================  LIFECYCLE     ===========================
-
-			/** Default protected constructor. */
-			LayeredEarth ( );
-
-            /** Default protected constructor. */
-			LayeredEarth (const YAML::Node& node);
-
-			/** Default protected constructor. */
-			~LayeredEarth ();
-
-			// ====================  DATA MEMBERS  ===========================
-
-        private:
-            /** ASCII string representation of the class name */
-            static constexpr auto CName = "LayeredEarth";
-
-			/** Number of layers in the model, including the air layer,
-			 * and counting from 0
-             */
-			int               NumberOfLayers;
-
-			/** Number of interfaces in the model. Equal to NumberOfLayers - 1
-			 */
-            int               NumberOfInterfaces;
-
-			/** Vector of layer thicknesses */
-			VectorXr          LayerThickness;
-
-	}; // -----  end of class  LayeredEarth  -----
-
-
-    ///////////////////////////////////////////////////////////////////
-    // Error classes
-
-    /** If a model with less than two layers is specified, throw error. Not set up
-     * for whole space solutions.
-     */
-    class EarthModelWithLessThanTwoLayers : public std::runtime_error {
-        public:
-            EarthModelWithLessThanTwoLayers( );
-    };
-
-    /** If a solver has a max number of layers, and this is exceeded, throw this
-     * error.
-     */
-    class EarthModelWithMoreThanMaxLayers : public std::runtime_error {
-        public:
-            /** Thrown when an Earth model with more than the maximum number of
-             *  Layers is given
-             */
-            EarthModelWithMoreThanMaxLayers( );
-    };
-
-    /** If the model parameters have different lengths than the earth model, throw
-     * this error.
-     */
-    class EarthModelParametersDoNotMatchNumberOfLayers : public std::runtime_error {
-        public:
-            /** Thrown when the parameters do not match the number of Layers
-             */
-            EarthModelParametersDoNotMatchNumberOfLayers ( );
-    };
-
-    /** If a request if made for a non-valid earth model parameter, throw this
-     * error.
-     */
-    class RequestForNonValidEarthModelParameter : public std::runtime_error {
-        public:
-            /** Thrown when a request is made for a non-valid earth parameter
-             */
-            RequestForNonValidEarthModelParameter ( );
-    };
-
-} // namespace Lemma
-
-#endif // __LAYEREDEARTH_H

LemmaCore/include/LemmaCore

@@ -1,40 +0,0 @@
-/* This file is part of Lemma, a geophysical modelling and inversion API */
-
-/* Copyright (C) 2009-2013 Trevor Irons <trevorirons@gmail.com> */
-
-/* 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
-  @version  $Id$
- **/
-
-// Convenience include all of LemmaCore
-#ifndef  LEMMAINCLUDE_INC
-#define  LEMMAINCLUDE_INC
-#include "ASCIIParser.h"
-#include "CubicSplineInterpolator.h"
-//#include "Data.h"
-//#include "DataReader.h"
-//#include "EarthModel.h"
-//#include "Filter.h"
-//#include "Grid.h"
-//#include "GridReader.h"
-//#include "Instrument.h"
-//#include "LayeredEarth.h"
-//#include "LemmaObject.h"
-#include "RectilinearGrid.h"
-#include "RectilinearGridReader.h"
-#include "RectilinearGridVTKExporter.h"
-#include "WindowFilter.h"
-// helpers and utilities
-#include "banner.h"
-#include "helper.h"
-#include "timer.h"
-#endif   // ----- #ifndef LEMMAINCLUDE_INC  -----
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/include/LemmaObject.h

@@ -1,168 +0,0 @@
-/* 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     06-13-2016
- **/
-
-#ifndef __LEMMAOBJECT_H
-#define __LEMMAOBJECT_H
-
-#include "helper.h"
-#include "lemma.h"
-#include "yaml-cpp/yaml.h"
-
-#include <chrono>
-#include <memory>
-
-namespace Lemma {
-
-/**
-  * \ingroup  LemmaCore
-  * \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.
-  */
-class LemmaObject {
-
-    /**
-     *  Streams class information as YAML::Node
-     */
-    friend YAML::Emitter& operator << (YAML::Emitter& out, const LemmaObject &ob) ;
-
-    friend class LemmaObjectDeleter;
-
-    public:
-
-        // ====================  LIFECYCLE     ==============================
-
-        // Needed because many derived classes have Eigen vectors as members,
-        // causing alignment issues when vectorisation is enabled.
-        EIGEN_MAKE_ALIGNED_OPERATOR_NEW
-
-        // ====================  OPERATORS     ==============================
-
-        // ====================  OPERATIONS    ==============================
-
-        // ====================  ACCESS        ==============================
-
-        // ====================  INQUIRY       ==============================
-
-        /** Returns the name of the underlying class; Run-time type information (RTTI). This approach
-            Was chosen over typeid due to name mangling among various compilers, and the need for consistency
-            in Serialized objects.
-         */
-        virtual inline std::string GetName() const {
-            return this->CName;
-        }
-
-        /**
-         *  Uses YAML to serialize this object.
-         *  @return a YAML::Node
-         *  FOR NOT LemmaObject does not write out any YAML info,
-         *      in the future the reference count could be logged? But the utility
-         *      of that is minimal.
-         *  @note Not every Lemma class needs to be Serializable, for instance HankelTransform
-         *        classes will never need to be Serialized. There may be a need to differentiate these
-         *        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 {
-            YAML::Node node = YAML::Node();
-            node.SetTag( GetName() );
-            std::time_t now = std::chrono::system_clock::to_time_t( std::chrono::system_clock::now() );
-            node["Serialized"] = std::ctime(&now);
-            return node;
-        };
-
-    protected:
-
-        // ====================  LIFECYCLE     ==============================
-
-        /** Protected default constructor. This is an abstract class and
-         *  cannot be instantiated.
-         */
-        LemmaObject ( );
-
-        /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-        LemmaObject (const YAML::Node& node);
-
-        /** Protected default destructor. This is an abstract class and
-         *  cannot be instantiated. Virtual is necessary so that if base class destructor is
-         *  called, we get the right behaviour.
-         */
-        virtual ~LemmaObject();
-
-    private:
-
-        // ====================  DATA MEMBERS  ==============================
-
-        /** ASCII string representation of the class name */
-        static constexpr auto CName = "LemmaObject";
-
-}; // -----  end of class  LemmaObject  -----
-
-class LemmaObjectDeleter
-{
-    public:
-        void operator()(LemmaObject* p) { delete p; }
-};
-
-    /////////////////////////////////////////////////////////////////
-    // Error Classes
-
-    /** Error called when DeSerializing breaks. If the node type is not the expected one
-     *  this error is thown.
-     */
-    class DeSerializeTypeMismatch : public std::runtime_error {
-        public:
-            DeSerializeTypeMismatch(const std::string& expected, const std::string& got);
-
-    };
-
-    /** If an assignment is made that is out of bounts, throw this.
-     */
-    class AssignmentOutOfBounds : public std::runtime_error {
-        public:
-            /** Throw when an assignment is out of bounds.
-             *  @param[in] ptr is a pointer to the class throwing the exception.
-             */
-            AssignmentOutOfBounds(LemmaObject *ptr);
-    };
-
-    /** If a pointer to a class is requested, but it is NULL valued, throw this
-     */
-    class RequestToReturnNullPointer : public std::runtime_error {
-        public:
-            /** Thrown when the pointer is NULL
-             *  @param[in] ptr is a pointer to the class throwing the exception.
-             */
-            RequestToReturnNullPointer(LemmaObject *ptr);
-    };
-
-    /** If an error in opening a .mat file is encountered, throw this.
-     */
-    class MatFileCannotBeOpened : public std::runtime_error {
-        /** thown when a mat file fails to be opened.
-         */
-            public: MatFileCannotBeOpened();
-    };
-
-	/** Generic file I/O error. */
-	class GenericFileIOError : public std::runtime_error {
-			public: GenericFileIOError(LemmaObject *ptr, const std::string &filename);
-	};
-
-}
-#endif // __LEMMAOBJECT_H

LemmaCore/include/RectilinearGrid.h

@@ -1,216 +0,0 @@
-/* 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: rectilineargrid.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  RECTILINEARGRID_INC
-#define  RECTILINEARGRID_INC
-
-#include "Grid.h"
-
-namespace Lemma {
-
-    // ===================================================================
-    //  Class:  RectilinearGrid
-    /**
-      @class
-      \ingroup LemmaCore
-      \brief   Impliments a rectilinear grid.
-      \details A rectilinear grid can vary regularily in space but must be
-               constant variation across each dimension. In this way three
-               vectors can define the entire grid, and each cell is right
-               aligned with all its neighbours.
-     */
-    // ===================================================================
-    class RectilinearGrid : public Grid {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-			const RectilinearGrid &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /**
-             *  Factory method for generating concrete class.
-             *  @return a std::shared_ptr of type RectilinearGrid
-             */
-            static std::shared_ptr<RectilinearGrid> NewSP();
-
-
-            /**
-             *  Uses YAML to serialize this object.
-             *  @return a YAML::Node
-             */
-            YAML::Node Serialize() const;
-
-            /**
-             *   Constructs an object from a YAML::Node.
-             */
-            static std::shared_ptr< RectilinearGrid > DeSerialize(const YAML::Node& node);
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /**
-             *  Sets the dimensions in x, y and z
-             *  @param[in] nx is the number of cells in x
-             *  @param[in] ny is the number of cells in y
-             *  @param[in] nz is the number of cells in z
-             */
-            void SetDimensions (const int &nx, const int &ny, const int &nz);
-
-            /**
-             *  Sets the offset in x, y and z. This sets the corner position of the top SW corner.
-             *  @param[in] ox is the number of cells in x
-             *  @param[in] oy is the number of cells in y
-             *  @param[in] oz is the number of cells in z
-             */
-            void SetOffset (const Real &ox, const Real &oy, const Real &oz);
-
-            /**
-             *  Sets the spacing in x, y and z
-             *  @param[in] dx is a Vector of cell spacing in x, must be same
-             *  size ad nx
-             *  @param[in] dy is a Vector of cell spacing in x, must be same
-             *  size ad ny
-             *  @param[in] dz is a Vector of cell spacing in x, must be same
-             *  size ad nz
-             */
-            void SetSpacing (const VectorXr &dx, const VectorXr &dy,
-                const VectorXr &dz);
-
-
-            // ====================  ACCESS        =======================
-
-            /** Returns the number of cells in x
-             *  @return number of cells in x
-             */
-            int GetNx();
-
-            /** Returns the number of cells in y
-             *  @return number of cells in y
-             */
-            int GetNy();
-
-            /** Returns the number of cells in z
-             *  @return number of cells in z
-             */
-            int GetNz();
-
-            /** Returns the offset of cells in x
-             *  @return offset of cells in x
-             */
-            Real GetOx();
-
-            /** Returns the number of cells in y
-             *  @return number of cells in y
-             */
-            Real GetOy();
-
-            /** Returns the offset of cells in z
-             *  @return offset of cells in z
-             */
-            Real GetOz();
-
-            /** Returns Spacing Vector
-             *  @return dx
-             */
-            VectorXr GetDx();
-
-            /** Returns a spacing
-             *  @return dx[ix]
-             */
-            Real GetDx(const int& ix);
-
-            /** Returns Spacing Vector
-             *  @return dy
-             */
-            VectorXr GetDy();
-
-            /** Returns a spacing
-             *  @return dy[iy]
-             */
-            Real GetDy(const int& iy);
-
-            /** Returns Spacing Vector
-             *  @return dz
-             */
-            VectorXr GetDz();
-
-            /** Returns Spacing Vector
-             *  @return dz[iz]
-             */
-            Real GetDz(const int& iz);
-
-            // ====================  INQUIRY       =======================
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return this->CName;
-            }
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Default protected constructor. */
-            RectilinearGrid ( );
-
-            /** Protected DeDerializing constructor, use factory DeSerialize  method*/
-            RectilinearGrid (const YAML::Node& node);
-
-            /** Default protected constructor. */
-            ~RectilinearGrid ();
-
-            // ====================  DATA MEMBERS  =========================
-
-            /// Number of cells in the x dimension
-            int nx;
-
-            /// Number of cells in the y dimension
-            int ny;
-
-            /// Number of cells in the z dimension
-            int nz;
-
-            /// Grid offset in x dimension
-            Real ox;
-
-            /// Grid offset in y dimension
-            Real oy;
-
-            /// Grid offset in z dimension
-            Real oz;
-
-            /// Cell spacing in the x dimension
-            VectorXr dx;
-
-            /// Cell spacing in the y dimension
-            VectorXr dy;
-
-            /// Cell spacing in the z dimension
-            VectorXr dz;
-
-        private:
-
-            /** ASCII string representation of the class name */
-            static constexpr auto CName = "RectilinearGrid";
-
-    }; // -----  end of class  RectilinearGrid  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef RECTILINEARGRID_INC  -----
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/include/RectilinearGridReader.h

@@ -1,110 +0,0 @@
-/* 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
-  @date      09/23/2013 11:05:11 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  RECTILINEARGRIDREADER_INC
-#define  RECTILINEARGRIDREADER_INC
-
-#include "GridReader.h"
-#include "RectilinearGrid.h"
-#include "ASCIIParser.h"
-
-namespace Lemma {
-
-    /**
-      @class
-      \ingroup LemmaCore
-      \brief   Base Class for rectilinear grid reader data files
-      \details
-     \todo this set of classes is deprecated, use serialize methods!
-     */
-    class RectilinearGridReader : public GridReader {
-
-        friend std::ostream &operator<<(std::ostream &stream,
-                const RectilinearGridReader &ob);
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-            /**
-             *  Factory method for generating concrete class.
-             *  @return a std::shared_ptr of type RectilinearGridReader
-             */
-            static std::shared_ptr< RectilinearGridReader > NewSP();
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /**
-            Reads a .mod file, a simple representation of the grid. These files
-            have the following format:
-            @verbatim
-            nx ny nz  // number of cells in x, y, and z
-            ox oy oz  // grid offset of top SW corner
-
-            hx[0] hx[1] ... hx[nx-1]  // grid cell spacing in x, from 0 to nx-1
-            hy[0] hy[1] ... hy[ny-1]  // grid cell spacing in y, from 0 to ny-1
-            hz[0] hz[1] ... hz[nz-1]  // grid cell spacing in z, from 0 to nz-1
-
-            // c++ style (//) comments are allowed anywhere, c-style are not
-            @endverbatim
-            */
-            void ReadASCIIGridFile( const std::string& name );
-
-            // ====================  ACCESS        =======================
-            /**
-             * Accessor method for the underlying RectilinearGrid class constructed
-             * from the input file.
-             */
-            std::shared_ptr<Grid> GetGrid();
-
-            // ====================  INQUIRY       =======================
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return this->CName;
-            }
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /** Default protected constructor, use New */
-            RectilinearGridReader ( );
-
-            /** Default protected constructor, use Delete */
-            ~RectilinearGridReader ();
-
-        private:
-
-            // ====================  DATA MEMBERS  =========================
-
-            /** ASCII string representation of the class name */
-            static constexpr auto CName = "RectilinearGridReader";
-
-            /** Object holding constructed Grid */
-            std::shared_ptr<RectilinearGrid> rGrid;
-
-            /** Performs actual file parsing */
-            std::shared_ptr<ASCIIParser> Parser;
-
-    }; // -----  end of class  RectilinearGridReader  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef RECTILINEARGRIDREADER_INC  -----

LemmaCore/include/RectilinearGridVTKExporter.h

@@ -1,124 +0,0 @@
-/* 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 08:20:01 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  RECTILINEARGRIDVTKEXPORTER_INC
-#define  RECTILINEARGRIDVTKEXPORTER_INC
-
-#ifdef  LEMMAUSEVTK
-
-#include "LemmaObject.h"
-#include "RectilinearGrid.h"
-
-#include <vtkSmartPointer.h>
-#include "vtkXMLRectilinearGridWriter.h"
-#include "vtkRectilinearGrid.h"
-#include "vtkDoubleArray.h"
-#include "vtkFieldData.h"
-#include "vtkCellData.h"
-
-namespace Lemma {
-
-/**
-  \ingroup LemmaCore
-  \brief   Exports a LemmaRectilinearGrid into a VTKRectilinearGrid.
-  \details Results can then be dumped to a VTK file or used directly.
- */
-class RectilinearGridVTKExporter : public LemmaObject {
-
-    friend std::ostream &operator<<(std::ostream &stream,
-            const RectilinearGridVTKExporter &ob);
-
-    public:
-
-    // ====================  LIFECYCLE     =======================
-
-    /**
-     * @copybrief LemmaObject::New()
-     * @copydetails LemmaObject::New()
-     */
-    static RectilinearGridVTKExporter* New();
-
-    /**
-     *  Factory method for generating concrete class.
-     *  @return a std::shared_ptr of type RectilinearGridVTKExporter
-     */
-    static std::shared_ptr< RectilinearGridVTKExporter > NewSP();
-
-    // ====================  OPERATORS     =======================
-
-    // ====================  OPERATIONS    =======================
-
-    // ====================  ACCESS        =======================
-    /**
-     * Sets the Grid to be exported
-     */
-    void SetGrid( std::shared_ptr<RectilinearGrid> Grid);
-
-    // ====================  INQUIRY       =======================
-
-    /**
-     *  @return Returns a pointer to a vtkRectilinearGrid containing same information as the Lemma Grid.
-     */
-    vtkSmartPointer<vtkRectilinearGrid>  GetVTKGrid();
-
-    /**
-     *  Writes the exported VTKGrid out to a .vtr XML file
-     *  @param[in] name is the filename to write to. The .vtr extension will be added
-     */
-    void WriteVTKGrid( const std::string& name );
-
-    /** Returns the name of the underlying class, similiar to Python's type */
-    virtual inline std::string GetName() const {
-        return this->CName;
-    }
-
-    protected:
-
-    // ====================  LIFECYCLE     =======================
-
-    /** Default protected constructor, use New */
-    RectilinearGridVTKExporter ( );
-
-    /** Default protected destructor, use Delete */
-    ~RectilinearGridVTKExporter ();
-
-    private:
-
-    /** ASCII string representation of the class name */
-    static constexpr auto CName = "RectilinearGridVTKExporter";
-
-    void BuildVTKRectilinearGrid();
-
-    // ====================  DATA MEMBERS  =========================
-
-    /** The Grid to convert from */
-    std::shared_ptr<RectilinearGrid>    Grid;
-
-    /** The Grid to convert to */
-    vtkSmartPointer<vtkRectilinearGrid> VTKGrid;
-
-}; // -----  end of class  RectilinearGridVTKExporter  -----
-
-}		// -----  end of Lemma  name  -----
-
-#endif     // -----  not LEMMAUSEVTK  -----
-
-#endif   // ----- #ifndef RECTILINEARGRIDVTKEXPORTER_INC  -----
-

LemmaCore/include/WindowFilter.h

@@ -1,127 +0,0 @@
-/* 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     07/20/2010
-  @version  $Id: windowfilter.h 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#ifndef  WINDOWFILTER_INC
-#define  WINDOWFILTER_INC
-#include "Filter.h"
-
-namespace Lemma {
-    /** Types of filter window that are supported.
-     */
-    enum WINDOWTYPE { HAMMING, /*!< A hamming window */
-                      HANNING, /*!< A hanning window */
-                      RECTANGULAR /*!< Rectangular window */
-                    };
-
-    // ===================================================================
-    //  Class:  WindowFilter
-    /**
-      @class   WindowFilter
-      \ingroup LemmaCore
-      \brief   Fourier domain window filter.
-      \details Current types are Hamming and Hanning. Others to be added.
-     */
-    // ===================================================================
-    class WindowFilter : public Filter {
-
-        public:
-
-            // ====================  LIFECYCLE     =======================
-
-           /**
-            *  Factory method for generating concrete class.
-            *  @return a std::shared_ptr of type WindowFilter
-            */
-            static std::shared_ptr< WindowFilter > NewSP();
-
-            // ====================  OPERATORS     =======================
-
-            // ====================  OPERATIONS    =======================
-
-            /// Sets the bandwith of the window.
-            /// @param[in] width Bandwidth in Hz
-            void SetBandwidth(const Real& width);
-
-            /// Sets the sampling rate of an input time domain signal.
-            /// @param[in] dt is the sampling rate, in seconds.
-            void SetSamplingInterval(const Real& dt);
-
-            /// Specifies the length of the time series to apply filter to.
-            void SetNumberOfSamples(const int& nt);
-
-            /// Sets the type of window to compute.
-            void SetWindowType(const WINDOWTYPE& type);
-
-            /** Returns the number of frequency bins for whole data record.
-             *  this is different then the length of the filter. This is
-             *  simply the length of the real to complex FFT, or
-             *  Nw = Nt%2 ? (Nt-1)/2+1 : (Nt)/2+1;
-             *  @return the number of frequency bins.
-             */
-            int GetNumberOfFrequencyBins();
-
-            // ====================  ACCESS        =======================
-
-            // ====================  INQUIRY       =======================
-
-            /// Returns a Vector of the filter coefficients.
-            VectorXr GetFilterCoefficients( );
-
-            /** Returns the name of the underlying class, similiar to Python's type */
-            virtual inline std::string GetName() const {
-                return this->CName;
-            }
-
-        protected:
-
-            // ====================  LIFECYCLE     =======================
-
-            /// Default protected constructor.
-            WindowFilter ( );
-
-            /// Default protected constructor.
-            ~WindowFilter ( );
-
-            // ====================  DATA MEMBERS  =========================
-
-            /// Width of the window
-            int         Width;
-
-            /// Length of time series
-            int         Nt;
-
-            /// Length of the frequency series representation
-            int         Nw;
-
-            /// Sampling rate of a time domain signal
-            Real        SamplingRate;
-
-            /// Bandwith of filter
-            Real        Bandwidth;
-
-            /// The filter coefficients
-            VectorXr    Coefficients;
-
-            /// The type of filter to use
-            WINDOWTYPE  Type;
-
-        private:
-
-        /** ASCII string representation of the class name */
-        static constexpr auto CName = "WindowFilter";
-
-    }; // -----  end of class  WindowFilter  -----
-
-}       // -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef WINDOWFILTER_INC  -----

LemmaCore/include/banner.h

@@ -1,24 +0,0 @@
-/* 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     05/03/2010
-  @version  $Id: banner.h 87 2013-09-05 22:44:05Z tirons $
- **/
-
-#ifndef __BANNER_H
-#define __BANNER_H
-#include <iostream>
-#include <ostream>
-void banner(const std::string &name, const std::string &version,
-		const std::string &usage);
-#endif
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/include/helper.h

@@ -1,288 +0,0 @@
-/* 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      10/02/2014 02:49:55 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
- */
-
-#pragma once
-
-#ifndef  HELPER_INC
-#define  HELPER_INC
-
-#include "lemma.h"
-#include "yaml-cpp/yaml.h"
-
-namespace Lemma {
-
-/** \addtogroup LemmaCore
- * @{
- */
-
-    /**
-     *  Convenience function for string conversion
-     *  @param[in] t input value to be converted to string
-     *  @return string representation of input value
-     */
-    template <class T>
-    inline std::string to_string (const T& t) {
-        std::stringstream ss;
-        ss << t;
-        return ss.str();
-    }
-
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const FREQUENCYUNITS& Units);
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const TIMEUNITS& Units);
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const MAGUNITS& Units);
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const TEMPUNITS& Units);
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const FEMCOILORIENTATION& Units);
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const ORIENTATION& Units);
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const FIELDCOMPONENT& Comp);
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const HANKELTRANSFORMTYPE& Htype);
-    /// convert enums to string saves repeated code useful for YAML serializing
-    std::string enum2String(const FIELDCALCULATIONS& Htype);
-
-    // other way around is a template, where template argument lets us know
-    // which specialisation to use.
-    template <typename T>
-    T string2Enum( const std::string& str );
-
-    // Handy little class that indents a stream.
-    // Based on solution provided here, todo may need to add to some managing class which keeps
-    // track of nesting levels? But perhaps not. A Lemma class will contain pointers to other Lemma
-    // classes. But those are not specifically listed out.
-    // http://stackoverflow.com/questions/9599807/how-to-add-indention-to-the-stream-operator
-    class IndentingOStreambuf : public std::streambuf {
-        std::streambuf*     myDest;
-        bool                myIsAtStartOfLine;
-        std::string         myIndent;
-        std::ostream*       myOwner;
-    protected:
-        virtual int         overflow( int ch )
-        {
-            if ( myIsAtStartOfLine && ch != '\n' ) {
-                myDest->sputn( myIndent.data(), myIndent.size() );
-            }
-            myIsAtStartOfLine = ch == '\n';
-            return myDest->sputc( ch );
-        }
-    public:
-        explicit            IndentingOStreambuf(
-                                std::streambuf* dest, int indent = 4 )
-            : myDest( dest )
-            , myIsAtStartOfLine( true )
-            , myIndent( indent, ' ' )
-            , myOwner( NULL )
-        {
-        }
-        explicit            IndentingOStreambuf(
-                                std::ostream& dest, int indent = 4 )
-            : myDest( dest.rdbuf() )
-            , myIsAtStartOfLine( true )
-            , myIndent( indent, ' ' )
-            , myOwner( &dest )
-        {
-            myOwner->rdbuf( this );
-        }
-        virtual             ~IndentingOStreambuf()
-        {
-            if ( myOwner != NULL ) {
-                myOwner->rdbuf( myDest );
-            }
-        }
-    };
-
-/** @}*/
-
-} // end namespace Lemma
-
-///////////////////////////////////////////////////////
-// YAML Serializing helper functions. Can we move this into helper.h
-namespace YAML {
-
-template<>
-struct convert<Lemma::Complex> {
-  static Node encode(const Lemma::Complex& rhs) {
-    Node node;
-    node["real"] = rhs.real();
-    node["imag"] = rhs.imag();
-
-    // No labels
-    //node.push_back(rhs.real());
-    //node.push_back(rhs.imag());
-
-    node.SetTag( "Complex" ); // too verbose?
-    return node;
-  }
-
-  static bool decode(const Node& node, Lemma::Complex& rhs) {
-    // Disabled due to overly verbose output. Just believe...
-    if( node.Tag() != "Complex" ) {
-        return false;
-    }
-    rhs = Lemma::Complex( node["real"].as<Lemma::Real>(), node["imag"].as<Lemma::Real>()  );
-    // no label style
-    //rhs = Lemma::Complex( node[0].as<Lemma::Real>(), node[1].as<Lemma::Real>()  );
-    return true;
-  }
-
-};
-
-template<>
-struct convert<Lemma::Vector3Xr> {
-  static Node encode(const Lemma::Vector3Xr& rhs) {
-    Node node;
-    node["size"] = rhs.cols();
-    //node["rows"] = rhs.rows(); // == 3
-    for (int ic=0; ic<rhs.cols(); ++ic) {
-        node[ic].push_back( rhs(0, ic) );
-        node[ic].push_back( rhs(1, ic) );
-        node[ic].push_back( rhs(2, ic) );
-    }
-    node.SetTag( "Vector3Xr" );
-    return node;
-  }
-
-  static bool decode(const Node& node, Lemma::Vector3Xr& rhs) {
-    if( node.Tag() != "Vector3Xr" ) {
-        return false;
-    }
-    rhs.resize( Eigen::NoChange, node["size"].as<int>() );
-    for (unsigned int ic=0; ic<node.size(); ++ic) {
-        int ir=0;
-        for(YAML::const_iterator it=node[ic].begin();it!=node[ic].end();++it) {
-            rhs(ir, ic) = it->as<Lemma::Real>();
-            ++ir;
-        }
-    }
-    return true;
-  }
-};
-
-template<>
-struct convert<Lemma::VectorXr> {
-  static Node encode(const Lemma::VectorXr& rhs) {
-    Node node;
-    node["size"] = rhs.size();
-    for (int ic=0; ic<rhs.size(); ++ic) {
-        node["data"].push_back( rhs(ic) );
-    }
-    node.SetTag( "VectorXr" );
-    return node;
-  }
-
-  static bool decode(const Node& node, Lemma::VectorXr& rhs) {
-    if( node.Tag() != "VectorXr" ) {
-        return false;
-    }
-    rhs.resize( node["size"].as<int>() );
-    int ir=0;
-    for(YAML::const_iterator it=node["data"].begin(); it!=node["data"].end(); ++it) {
-        rhs(ir) = it->as<Lemma::Real>();
-        ++ir;
-    }
-    return true;
-  }
-};
-
-template<>
-struct convert<Lemma::VectorXcr> {
-  static Node encode(const Lemma::VectorXcr& rhs) {
-    Node node;
-    node["size"] = rhs.size();
-    for (int ic=0; ic<rhs.size(); ++ic) {
-        node["data"].push_back( rhs(ic) );
-    }
-    node.SetTag( "VectorXcr" );
-    return node;
-  }
-
-  static bool decode(const Node& node, Lemma::VectorXcr& rhs) {
-    if( node.Tag() != "VectorXcr" ) {
-        return false;
-    }
-    rhs.resize( node["size"].as<int>() );
-    int ir=0;
-    for(YAML::const_iterator it=node["data"].begin(); it!=node["data"].end(); ++it) {
-        rhs(ir) = it->as<Lemma::Complex>();
-        ++ir;
-    }
-    return true;
-  }
-};
-
-
-template<>
-struct convert<Lemma::VectorXi> {
-  static Node encode(const Lemma::VectorXi& rhs) {
-    Node node;
-    node["size"] = rhs.size();
-    for (int ic=0; ic<rhs.size(); ++ic) {
-        node["data"].push_back( rhs(ic) );
-    }
-    node.SetTag( "VectorXi" );
-    return node;
-  }
-
-  static bool decode(const Node& node, Lemma::VectorXi& rhs) {
-    if( node.Tag() != "VectorXi" ) {
-        return false;
-    }
-    rhs.resize( node["size"].as<int>() );
-    int ir=0;
-    for(YAML::const_iterator it=node["data"].begin(); it!=node["data"].end(); ++it) {
-        rhs(ir) = it->as<int>();
-        ++ir;
-    }
-    return true;
-  }
-};
-
-template<>
-struct convert<Lemma::Vector3r> {
-  static Node encode(const Lemma::Vector3r& rhs) {
-    Node node;
-    for (int ic=0; ic<rhs.size(); ++ic) {
-        node[0].push_back( rhs(ic) );
-    }
-    node.SetTag( "Vector3r" );
-    return node;
-  }
-
-  static bool decode(const Node& node, Lemma::Vector3r& rhs) {
-    if( node.Tag() != "Vector3r" ) {
-        return false;
-    }
-    int ir=0;
-    for(YAML::const_iterator it=node[0].begin(); it!=node[0].end(); ++it) {
-        rhs(ir) = it->as<Lemma::Real>();
-        ++ir;
-    }
-    return true;
-  }
-};
-
-}
-
-#endif   // ----- #ifndef HELPER_INC  -----
-

LemmaCore/include/lemma.h

@@ -1,333 +0,0 @@
-/* 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     06/19/2009 09:12:20 AM  The Birth of Lemma!
-  @version  $Id: lemma.h 203 2015-01-09 21:19:04Z tirons $
- **/
-
-/** \mainpage Lemma is an ElectroMagnetics Modelling API
-    \image html lemma.png
-
-    \authors Trevor Irons and M. Andrew Kass and others
-
-    Lemma is a recursive acronym that stands for <B>L</B>emma is an
-    <B>E</B>lectro<B>M</B>agnetics <B>M</B>odelling <B>A</B>PI.
-    Lemma is a cross-platform library delivering an expressive API that
-    can be used to easily create versatile programs.
-    We are building a powerful, flexible,
-    expresive framework that allows for the straightforward creation of
-    geophysical EM applications. Lemma is not itself a program, instead
-    it is a collection of building blocks to make applications.
-    We chose this name because:
-
-    - In mathematics a Lemma is a proven proposition which is used as a
-    stepping stone to a larger result rather than as a statement in-and-of
-    itself.
-    - In addition to the electromagnetic modelling, some other facilities are
-    provided such as numerical optimization and inversion capabilities. These
-    tools are also considered stepping stones to final products.
-
-    We feel that this is a partucularily approprate name, as Lemma's
-    API can be leveraged create powerful applications such as forward
-    modelling and inverting frequency and time-domain
-    surveys of arbitrary survey design, SNMR surveys, CSAMT and more.
-
-    \section Motivation
-    Why another Geophysical EM project? For starters, there
-    aren't that many quality open source packages out there. Those that do
-    exist are generally specialized to perform a single task and extending
-    them is a major undertaking. Lemma's approach is much different, by
-    providing a set of general tools users can easily assemble applications
-    that suite their needs.
-
-    While most geophysical EM modeling packages are concerned with forward
-    modeling <B>DATA</B> between specific transmitters and receivers located
-    on the surface of the earth; Lemma is fundamentally concerned with
-    modelling <B>FIELDS</B> due to sources, the field values can be calculated
-    everywhere within the domain. This allows for solving multiphysics EM
-    problems. Tradional EM data may be forward modelled using the Lemma::Instrument
-    classes.
-
-    \section Capabilities Capabilities
-    In the long term, we have many goals for this software project. Due to its
-    design, Lemma can be built upon and extended easily. The initial aim is to
-    provide flexible 1D and 3D EM modelling in the time and frequency domains.
-    The project is still in beta, but we have made a lot of progress already.
-    We will release our first non-beta release as soon as the following are
-    supported.
-
-    \subsection FDM Frequency-domain forward modelling
-    Lemma was initially called EMMODFD: Electromagnetic Modelling in the Frequency
-    Domain. As such this is the most mature area of Lemma.
-
-    \par 1D
-    Frequency domain solutions to electrical and magnetic dipoles can be computed
-    quasi-analytically in 1D. Calculations can be made in or above the layered
-    media, and complex electrical conductivity and magnetic susceptibility are
-    supported according to the Cole-Cole model. Sources may be embdedded in the
-    media or in the resisitive air layer. Lemma can also can compute fields due
-    to arbitrarily shaped ungrounded wire loops, topography of the loops is also
-    supported. Two separate approaches to solving the Hankel transform, one
-    based on Anderson's digitial filtering technique, and another based on Gaussian
-    quadrature.
-
-    \par 3D
-    A fast 3D solver that can modify the 1D results based
-    on arbitrary electrical conductivity model is nearing completion.
-
-    \par future work
-    We are also planning on supporting grounded wires in the near future.
-
-    \subsection TDM Time-domain forward modelling
-	A 1D time-domain solution has been implemented that utilises both a
-	dipole source as well as a wire loop.  Currently, only one receiver is
-	modelled at a time, but will be generalised.  In addition, utilities
-	to read in data files for modelling have been implemented.
-    We would like to offer 3D time domain support, but this will not be
-    provided before our first stable release.
-
-    \subsection DataFormats Data Formats
-    The EM community is plagued with myriad data formats. Often each equiptment
-    manufacturer provides their own data format and interoperability is a
-    constant struggle. We are working on a flexible data format based on the XML
-    format that can be adapted to many types of data. The template for this
-    format will be publically released and we hope it catches on in the community.
-    At the least, it will provide a mechanism to compare datasets and datatypes
-    within Lemma.
-
-    \section Modules Modules
-    Due to Lemma's design, it is easy to extend the platform. In some cases this
-    extension results in adding functionality that is not directly related to
-    ElectroMagnetics. The following modules utilise parts of Lemma to provide
-    their functionality.
-
-    \subsection Merlin Merlin.
-    This module provides nuclear magnetic resonance functionality.
-
-
-    \section Tutorials
-        - \ref Tutorial - Basic intruduction to Lemma, including aquiring and
-          compiling the code, class structure, and building your own
-          applications.
-        - \ref Extending Tutorial on how to extend Lemma.
-
-
-    \section Development Development and design
-    Ths package is primarily being developed by the Center for Gravity,
-    Electrical, and Magnetic Studies (CGEM) at the Colorado School of Mines (CSM), the United
-    States Geological Survey (USGS), and Broken Spoke Development, LLC. It draws on work by
-    many others including Ki Ha Lee, and Walt Anderson. All new work and
-    interfaces are written entirely in C++. Several small external projects are
-    included, which are written in standard C, and FORTRAN 77. We adapt a
-    modern, test driven, object oriented, C++ framework.
-
-    \section Legalities
-
-    \subsection Copyrights
-    The following copyrights apply to the source.
-    Most of the code was developed either by Trevor
-    Copyright (C) 2008-2010 Trevor Irons <tirons@mines.edu> or
-    M. Andrew Kass Copyright (C) 2010 <mkass@numericalgeo.com>.
-
-    The 1D EM solver was derived (but updated heavily) from a fortran
-    programme written by Ki Ha Lee in 1984. We have communicated with Ki Ha,
-    and he assured us that this code is in the public domian.
-
-    A Gaussian quadrature hankel transform originally written by Alan Chave was
-    ported to C++. This code is in the public domain, and was published in Geophysics.
-
-    A digital filtering approach to the Hankel transform written by Walt
-    Anderson was also rewritten for Lemma. The origional fortran code is also in
-    the public domain. Using this Hankel transform works
-    arround the copyright issue mentioned above, but may not produce accurate
-    results for high frequencies.
-
-    Please note that Ki Ha Lee and Walt Anderson had no part in this work, and
-    the above should not be interpreted as any sort of endorsement by those
-    parties.
-
-    \subsection License
-
-    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/.
-
-    \section Contributing Suggestions and contributions
-        We welcome contributions and suggestions. Feel free to email the development
-        team at info@lemmasoftware.org.
-        Under the terms of the MPL, if you modify a Lemma file, you are obligated to
-        share those contributions back with the community.
-
-    \section Useful Useful links
-        - Home page https://lemmasoftware.org
-        - SVN repository https://svn.lemmasoftware.org
-        - Broken Spoke Develpment http://numericalgeo.com
-        - CGEM at the Coloroado School of Mines http://geophysics.mines.edu/cgem/
-**/
-
-#pragma once
-
-#ifndef __LEMMA_H
-#define __LEMMA_H
-
-    // Include some basic stuff that will always be needed
-    #include <iostream>
-    #include <iomanip>
-    #include <complex>
-    #include <fstream>
-    #include <string>
-    #include <vector>
-    #include <stdexcept>
-    #include <sstream>
-
-    #include <Eigen/Core>
-    #include <cstddef>
-    #include <Eigen/StdVector>
-    #include <Eigen/Sparse>
-    #include <unsupported/Eigen/FFT>
-    //#include <unsupported/Eigen/SparseExtra>
-    #include <Eigen/Geometry>
-
-    /** \brief The only namespace used by Lemma
-     *
-     *  \details The rational behind this namespace is that built-in
-     *  types should be used wherever possible, but not
-     *  not built-in names. This allows for code that is better
-     *  enacsulated and easier to modify. The typedefs and constants
-     *  specified here are defined so that
-     *  precision/inplimentation can easily be changed.
-     *  All floating precision types should be typedefed in this file
-     *  and should not be used natively within any code.
-     *  Lemma uses
-     *  the Eigen Matrix/Vector/Linear Algebra library.
-     *  <http://eigen.tuxfamily.org> and a lot of the namespece typedefs
-     *  are specifying Eigen types.
-     */
-    namespace Lemma {
-
-        /// Real defines precision for the whole API, default is double
-#ifdef  LEMMA_SINGLE_PRECISION
-        typedef float Real;
-#else      // -----      LEMMA_SINGLE_PRECISION  -----
-        typedef double Real;
-#endif     // -----  not LEMMA_SINGLE_PRECISION  -----
-
-        /// Complex version of Real.
-        typedef std::complex<Real> Complex;
-
-        /// A 3 component Eigen vector of Reals
-        typedef Eigen::Matrix<Real, 3, 1> Vector3r;
-
-        /// A 3 X Dynamic Component Eigen matrix of Reals
-        typedef Eigen::Matrix<Real, 3, Eigen::Dynamic> Vector3Xr;
-
-        /// Variable length Eigen vector of Reals
-        typedef Eigen::Matrix<Real, Eigen::Dynamic, 1> VectorXr;
-
-        /// Variable length Eigen vector of integers (int)
-        typedef Eigen::Matrix<int, Eigen::Dynamic, 1> VectorXi;
-
-        /// Variable length Eigen vector of Complexes
-        typedef Eigen::Matrix<Complex, Eigen::Dynamic, 1> VectorXcr;
-
-        /// A 3 Component Eigen vector of Complexes
-        typedef Eigen::Matrix<Complex, 3, 1> Vector3cr;
-
-        /// A 3 X Dynamic Component Eigen matrix of Complexes
-        typedef Eigen::Matrix<Complex, 3, Eigen::Dynamic> Vector3Xcr;
-
-        /// Variable length Eigen Matrix of Reals
-        typedef Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> MatrixXr;
-
-        /// Variable length Eigen Matrix of ints
-        typedef Eigen::Matrix<int, Eigen::Dynamic, Eigen::Dynamic> MatrixXi;
-
-        /// Variable length Eigen vector of Complexes
-        typedef Eigen::Matrix<Complex, Eigen::Dynamic, Eigen::Dynamic> MatrixXcr;
-
-        ////////////////////////////////////////
-        // Constants used across the programmes
-
-        /// Restating the obvious, this is pi
-        const Real PI = 4.0*atan(1.0);
-
-        /// Permitivity of Free Space
-        //const Real EPSILON0 = 8.854187817e-12;
-        const Real EPSILON0 = 8.854187817e-12;
-
-        /// Permeability of free space
-        const Real MU0 = 4.*PI*1e-7;
-
-        /// 1/4 of \f$ \pi\f$
-        const Real QPI = .25/PI;
-
-        /// Some functions will convert units from SI (standard) to Gauss
-        /// This is because NMR calculations are much more natural in Gauss
-        enum MAGUNITS  {TESLA, NANOTESLA, GAUSS};
-
-        /// Unit of temperature entered
-        enum TEMPUNITS {CELCIUS, KELVIN};
-
-        /// Unit of time entered
-        enum TIMEUNITS {SEC, MILLISEC, MICROSEC, NANOSEC, PICOSEC};
-
-        /// Unit of time entered
-        enum FREQUENCYUNITS {HZ, KHZ, MHZ, GHZ};
-
-		/// FEM coil relative orientations
-		enum FEMCOILORIENTATION {COAXIAL, COPLANAR};
-
-		/// General orientation relative to coordinate system
-		enum ORIENTATION {X, Y, Z, NX, NY, NZ};
-
-        /// Type of field
-        enum FIELDTYPE         {HFIELDREAL, HFIELDIMAG, EFIELDREAL, EFIELDIMAG};
-
-        /// Compenent of vector field
-        enum FIELDCOMPONENT    {XCOMPONENT=0, YCOMPONENT=1, ZCOMPONENT=2};
-
-        /// Spatial component of vector
-        enum SPATIALCOORDINANT  {XCOORD=0, YCOORD=1, ZCOORD=2};
-
-        /** Evaluation method for Hankel integrals.
-         *  ANDERSON801     Walt Anderson's 801 point filter
-         *  CHAVE           Alan Chave's gaussian quadrature integration method
-         *  FHTKEY201       Key's 201 point filter
-         *  FHTKEY201       Key's 101 point filter
-         *  FHTKEY51        Key's 51 point filter
-         *  QWEKEY          Key's Gaussian quadrature integration method
-         */
-        enum HANKELTRANSFORMTYPE { ANDERSON801, CHAVE, FHTKEY201, FHTKEY101, FHTKEY51, QWEKEY };
-
-        /** Enum is OK because these are the only physically possible sources.
-         @param NOSOURCETYPE is default.
-         @param ELECTRICDIPOLE is an electric dipole
-         @param MAGNETICDIPOLE is a magnetic dipole
-        */
-        enum DipoleSourceType {NOSOURCETYPE, GROUNDEDELECTRICDIPOLE, UNGROUNDEDELECTRICDIPOLE, MAGNETICDIPOLE};
-
-        /// Only three polarizations are supported. They may be summed to
-        /// approximate others
-        /// @param NOPOLARISATION is uninitialized, default value
-        /// @param XPOLARISATION is a dipole oriented in the x direction
-        /// @param YPOLARISATION is a dipole oriented in the y direction
-        /// @param ZPOLARISATION is a dipole oriented in the z direction
-        enum DipoleSourcePolarisation {NOPOLARISATION, XPOLARISATION,
-            YPOLARISATION,  ZPOLARISATION};
-
-        /// The polarity may be either negative or positinve
-        enum DipoleSourcePolarity {NEGATIVE, POSITIVE};
-
-        /** The fields to make calculations on
-        */
-        enum FIELDCALCULATIONS {E, H, BOTH};
-
-    }
-
-#endif // __Lemma_H

LemmaCore/include/timer.h

@@ -1,82 +0,0 @@
-/* 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     01/27/2010
-  @version  $Id: timer.h 87 2013-09-05 22:44:05Z tirons $
- **/
-
-#ifndef  TIMER_H_INC
-#define  TIMER_H_INC
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#ifdef LEMMAUSEOMP
-#include "omp.h"
-#endif
-
-#include "lemma.h"
-
-namespace Lemma {
-
-/** \brief Simple timer class.
-  * \details Can be used either with multithreaded applications, using
-  * OpenMP defined functions, or using system wall time. System wall time
-  * is not good for parallel programs as it reports cpu core execution time.
-  */
-class jsw_timer {
-
-    public:
-
-        /**
-          * Constructor that automatically starts the timer.
-          */
-        jsw_timer(): start ( std::clock() ), elapsed ( 0.0 ) {
-
-        }
-
-        /** begins the timer.
-          */
-        void begin() {
-            #ifdef LEMMAUSEOMP
-            start =  omp_get_wtime();
-            #else
-            start = std::clock();
-            #endif
-            elapsed = 0.0;
-        }
-
-        /** Ends the timer.
-          * @return the time that the stopwatch ended at.
-          */
-        Real end() {
-
-            #ifdef LEMMAUSEOMP
-            elapsed = static_cast<Real> (omp_get_wtime()) - start;
-            return elapsed;
-            #else
-            elapsed = static_cast<Real> ( std::clock() ) - start;
-            return elapsed /= CLOCKS_PER_SEC;
-            #endif
-
-        }
-
-        /**
-          * @return the elapsed time between start and end.
-          */
-        Real last() const { return elapsed; }
-
-    private:
-        std::clock_t start;
-        Real    elapsed;
-};
-
-}       // -----  end of Lemma  name  -----
-
-#endif   // ----- #ifndef TIMER_H_INC  -----

LemmaCore/src/ASCIIParser.cpp

@@ -1,238 +0,0 @@
-/* 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      09/23/2013 02:33:41 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2013, Trevor Irons
- */
-
-#include "ASCIIParser.h"
-
-namespace Lemma {
-
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator << (std::ostream &stream, const ASCIIParser &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  ASCIIParser
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    ASCIIParser::ASCIIParser ( ) : LemmaObject( ),
-            CommentString("//"), BufferSize(255) {
-
-    }  // -----  end of method ASCIIParser::ASCIIParser  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  NewSP()
-    // Description:  public smart pointer factory constructor
-    //--------------------------------------------------------------------------------------
-    std::shared_ptr< ASCIIParser > ASCIIParser::NewSP() {
-        std::shared_ptr<ASCIIParser> sp(new  ASCIIParser( ), LemmaObjectDeleter() );
-        return sp;
-        //return  std::make_shared<ASCIIParser>();
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  Serialize
-    //--------------------------------------------------------------------------------------
-    YAML::Node  ASCIIParser::Serialize (  ) const {
-        YAML::Node node = LemmaObject::Serialize();;
-        node.SetTag( GetName() );
-        node["CommentString"] = CommentString;
-        node["BufferSize"] = BufferSize;
-        return node;
-    }		// -----  end of method ASCIIParser::Serialize  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  DeSerialize
-    //--------------------------------------------------------------------------------------
-    std::shared_ptr<ASCIIParser> ASCIIParser::DeSerialize ( const YAML::Node& node  ) {
-        if (node.Tag() != "ASCIIParser") {
-            throw  DeSerializeTypeMismatch( "ASCIIParser", node.Tag());
-        }
-        std::shared_ptr<ASCIIParser> Object(new  ASCIIParser(node), LemmaObjectDeleter() );
-        return Object ;
-    }		// -----  end of method ASCIIParser::DeSerialize  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  ~ASCIIParser
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    ASCIIParser::~ASCIIParser () {
-
-    }  // -----  end of method ASCIIParser::~ASCIIParser  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  ASCIIParser
-    // Description:  DeSerializing constructor (protected)
-    //--------------------------------------------------------------------------------------
-    ASCIIParser::ASCIIParser (const YAML::Node& node) : LemmaObject(node) {
-        this->CommentString = node["CommentString"].as<std::string>();
-        this->BufferSize = node["BufferSize"].as<int>();
-    }  // -----  end of method ASCIIParser::ASCIIParser  (constructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void ASCIIParser::Release() {
-        delete this;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  Open
-    //--------------------------------------------------------------------------------------
-    void ASCIIParser::Open ( const std::string& fname ) {
-        input.open(fname.c_str(), std::ios::in);
-        if (input.fail()) {
-           throw  GenericFileIOError(this, fname);
-        }
-        return ;
-    }		// -----  end of method ASCIIParser::Open  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  Close
-    //--------------------------------------------------------------------------------------
-    void ASCIIParser::Close (  ) {
-        input.close();
-        return ;
-    }		// -----  end of method ASCIIParser::Close  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  ReadReals
-    //--------------------------------------------------------------------------------------
-    std::vector<Real> ASCIIParser::ReadReals ( const int& nr ) {
-        std::string buf;
-        char *dump = new char[BufferSize];
-        std::vector<Real> vals(0);
-        while (input >> buf) {
-            if (buf.substr(0, CommentString.size()) == CommentString) {
-                input.getline(dump, BufferSize);
-            } else {
-                vals.push_back( atof(buf.c_str() ));
-            }
-            if (static_cast<int>(vals.size()) == nr) {
-                delete [] dump;
-                return vals;
-            }
-        }
-        delete [] dump;
-        return vals;
-    }		// -----  end of method ASCIIParser::ReadReals  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  ReadInts
-    //--------------------------------------------------------------------------------------
-    std::vector<int> ASCIIParser::ReadInts ( const int& nr ) {
-        std::string buf;
-        char *dump = new char[BufferSize];
-        std::vector<int> vals(0);
-        while (input >> buf) {
-            if (buf.substr(0, CommentString.size()) == CommentString) {
-                input.getline(dump, BufferSize);
-            } else {
-                vals.push_back( atoi(buf.c_str() ));
-            }
-            if (static_cast<int>(vals.size()) == nr) {
-                delete [] dump;
-                return vals;
-            }
-
-        }
-        delete [] dump;
-        return vals;
-    }		// -----  end of method ASCIIParser::ReadInts  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  ReadStings
-    //--------------------------------------------------------------------------------------
-    std::vector<std::string> ASCIIParser::ReadStrings ( const int& nr ) {
-        std::string buf;
-        char *dump = new char[BufferSize];
-        std::vector<std::string> vals(0);
-        while (input >> buf) {
-            if (buf.substr(0, CommentString.size()) == CommentString) {
-                input.getline(dump, BufferSize);
-            } else {
-                vals.push_back( buf );
-            }
-            if (static_cast<int>(vals.size()) == nr) {
-                delete [] dump;
-                return vals;
-            }
-
-        }
-        delete [] dump;
-        return vals;
-    }		// -----  end of method ASCIIParser::ReadInts  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  SetCommentString
-    //--------------------------------------------------------------------------------------
-    void ASCIIParser::SetCommentString ( const std::string& key ) {
-        CommentString = key;
-    }		// -----  end of method ASCIIParser::SetCommentString  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  SetBufferSize
-    //--------------------------------------------------------------------------------------
-    void ASCIIParser::SetBufferSize ( const int& size ) {
-        BufferSize = size;
-    }		// -----  end of method ASCIIParser::SetCommentString  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  GetFileLocation
-    //--------------------------------------------------------------------------------------
-    int ASCIIParser::GetFileLocation (  ) {
-        return input.tellg();
-    }		// -----  end of method ASCIIParser::GetFileLocation  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  ASCIIParser
-    //      Method:  JumpToLocation
-    //--------------------------------------------------------------------------------------
-    void ASCIIParser::JumpToLocation ( const int& loc ) {
-        input.seekg( loc );
-        return ;
-    }		// -----  end of method ASCIIParser::JumpToLocation  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-

LemmaCore/src/CMakeLists.txt

@@ -1,20 +0,0 @@
-set (SOURCE 
-	${SOURCE}
-	${CMAKE_CURRENT_SOURCE_DIR}/helper.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/banner.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/ASCIIParser.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/CubicSplineInterpolator.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}/Grid.cpp       
-	${CMAKE_CURRENT_SOURCE_DIR}/RectilinearGrid.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/RectilinearGridReader.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/RectilinearGridVTKExporter.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/Filter.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/WindowFilter.cpp
-	PARENT_SCOPE
-)

LemmaCore/src/CubicSplineInterpolator.cpp

@@ -1,355 +0,0 @@
-/* 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      02/07/2014 12:50:52 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     Trevor.Irons@xri-geo.com
- * @copyright Copyright (c) 2014, Trevor Irons
- */
-
-#include "CubicSplineInterpolator.h"
-
-#include<iostream>
-#include<fstream>
-#include<vector>
-#include<algorithm>
-#include<cmath>
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator << (std::ostream &stream, const CubicSplineInterpolator &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  CubicSplineInterpolator
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    CubicSplineInterpolator::CubicSplineInterpolator ( ) : LemmaObject( ) {
-
-    }  // -----  end of method CubicSplineInterpolator::CubicSplineInterpolator  (constructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  CubicSplineInterpolator
-    // Description:  DeSerializing constructor (protected)
-    //--------------------------------------------------------------------------------------
-    CubicSplineInterpolator::CubicSplineInterpolator (const YAML::Node& node) : LemmaObject(node) {
-    }  // -----  end of method CubicSplineInterpolator::CubicSplineInterpolator  (constructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  NewSP()
-    // Description:  public constructor
-    //--------------------------------------------------------------------------------------
-    std::shared_ptr<CubicSplineInterpolator> CubicSplineInterpolator::NewSP() {
-        std::shared_ptr<CubicSplineInterpolator> sp(new  CubicSplineInterpolator( ), LemmaObjectDeleter() );
-        return sp;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  Serialize
-    //--------------------------------------------------------------------------------------
-    YAML::Node  CubicSplineInterpolator::Serialize (  ) const {
-        YAML::Node node = LemmaObject::Serialize();;
-        node.SetTag( GetName() );
-        // FILL IN CLASS SPECIFICS HERE
-        return node;
-    }		// -----  end of method CubicSplineInterpolator::Serialize  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  DeSerialize
-    //--------------------------------------------------------------------------------------
-    std::shared_ptr<CubicSplineInterpolator> CubicSplineInterpolator::DeSerialize ( const YAML::Node& node  ) {
-        if (node.Tag() != "CubicSplineInterpolator") {
-            throw  DeSerializeTypeMismatch( "CubicSplineInterpolator", node.Tag());
-        }
-        std::shared_ptr<CubicSplineInterpolator> Object(new  CubicSplineInterpolator(node), LemmaObjectDeleter() );
-        return Object ;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  ~CubicSplineInterpolator
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    CubicSplineInterpolator::~CubicSplineInterpolator () {
-
-    }  // -----  end of method CubicSplineInterpolator::~CubicSplineInterpolator  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  Release
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    void CubicSplineInterpolator::Release() {
-        delete this;
-    }
-
-    // ====================  OPERATIONS    =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  SetKnots
-    //--------------------------------------------------------------------------------------
-    void CubicSplineInterpolator::SetKnots ( const VectorXr& x, const VectorXr& y ) {
-
-        int n = x.size()-1;
-
-        Spline = SplineSet(n);
-
-        Spline.a = y;
-        Spline.x = x;
-        VectorXr h = VectorXr::Zero(n);
-        for(int i=0; i<n; ++i)
-            h(i) = Spline.x(i+1)-Spline.x(i);
-
-        VectorXr alpha(n-1);
-        for(int i=1; i<n-1; ++i)
-            alpha(i) =  3.*(Spline.a[i+1]-Spline.a[i])/h[i] - 3.*(Spline.a[i]-Spline.a[i-1])/h[i-1] ;
-
-        VectorXr l = VectorXr::Zero(n+1);
-        VectorXr mu  = VectorXr::Zero(n+1);
-        VectorXr z = VectorXr::Zero(n+1);
-        l[0] = 1;
-        mu[0] = 0;
-        z[0] = 0;
-
-        for(int i = 1; i < n-1; ++i) {
-            l[i] = 2 *(Spline.x[i+1]-Spline.x[i-1])-h[i-1]*mu[i-1];
-            mu[i] = h[i]/l[i];
-            z[i] = (alpha[i]-h[i-1]*z[i-1])/l[i];
-        }
-        l[n] = 1;
-        z[n] = 0;
-
-        for(int j = n-1; j >= 0; --j) {
-            Spline.c[j] = z[j] - mu[j] * Spline.c[j+1];
-            Spline.b[j] = (Spline.a[j+1]-Spline.a[j])/h[j]-h[j]*(Spline.c[j+1]+2*Spline.c[j])/3;
-            Spline.d[j] = (Spline.c[j+1]-Spline.c[j])/3/h[j];
-        }
-        // On OSX, this causes a strange bug 'sometimes', alignment?
-        //Spline.c = Spline.c.head(n);
-
-        return;
-    }		// -----  end of method CubicSplineInterpolator::SetKnots  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterplator
-    //      Method:  ResetKnotOrdinate
-    //--------------------------------------------------------------------------------------
-    void CubicSplineInterpolator::ResetKnotOrdinate ( const VectorXr& y ) {
-        VectorXr x = Spline.x;
-        SetKnots(x, y);
-        return ;
-    }		// -----  end of method CubicSplineInterplator::ResetKnotOrdinate  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  InterpolateOrderedSet
-    //--------------------------------------------------------------------------------------
-    VectorXr CubicSplineInterpolator::InterpolateOrderedSet ( const VectorXr& x ) {
-        VectorXr y = VectorXr::Zero(x.size());
-        int ii = 0;
-        for (int iy=0; iy<y.size(); ++iy) {
-            y[iy] = Interpolate(x[iy], ii);
-        }
-        return y;
-    }		// -----  end of method CubicSplineInterpolator::InterpolateOrderedSet  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  Interpolate
-    //--------------------------------------------------------------------------------------
-    Real CubicSplineInterpolator::Interpolate ( const Real& x, int& i) {
-        // O(n) search, could do bisection, but if these are sorted, then this is quick
-        while(Spline.x[i] < x && i<Spline.x.size()) {
-            ++i;
-        }
-        --i;
-
-        //if ( x > Spline.x[i] ) {
-        //    throw std::runtime_error("CubicSplineInterpolator::Interpolate ATTEMPT TO INTERPOLATE PAST LAST KNOT");
-        //}
-
-        return Spline.a[i] + Spline.b[i]*(x-Spline.x[i]) + Spline.c[i]*((x-Spline.x[i])*(x-Spline.x[i])) +
-               Spline.d[i]*((x-Spline.x[i])*(x-Spline.x[i])*(x-Spline.x[i]) );
-    }		// -----  end of method CubicSplineInterpolator::Interpolate  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  Interpolate
-    //--------------------------------------------------------------------------------------
-    Real CubicSplineInterpolator::Interpolate ( const Real& x ) {
-        int ii(0);
-        return Interpolate(x, ii);
-    }
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  Integrate
-    //--------------------------------------------------------------------------------------
-    Real CubicSplineInterpolator::Integrate ( const Real& x0, const Real& x1, const int& n ) {
-
-        assert(n > 0);
-        // force n to be even?
-        //n += (n % 2);
-
-        Real S = Interpolate(x0) + Interpolate(x1);
-        Real h = (x1 - x0) / Real(n);
-
-        int ik = 0;
-        for (int i=1; i<n; i+=2) {
-            S += 4. * Interpolate(x0 + (Real)(i)*h, ik);
-        }
-
-        ik = 0;
-        for (int i=2; i<n-1; i+=2) {
-            S += 2. * Interpolate(x0 + (Real)(i)*h, ik);
-        }
-
-        return  S * h / 3.;
-    }
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  Integrate
-    //--------------------------------------------------------------------------------------
-    Real CubicSplineInterpolator::Integrate ( const Real& x0, const Real& x1 ) {
-
-
-        int i0 = Interval(x0);
-        int i1 = Interval(x1);
-
-        Real h0 = x0 - Spline.x(i0);
-        if (mflag == -1) h0 = 0;
-        Real h1 = x1 - Spline.x(i1);
-
-        Real cubint = (((Spline.d(i1)*h1/4.0 + Spline.c(i1) )*h1/3.0 +
-                         Spline.b(i1) )*h1/2.0 + Spline.a(i1) )*h1
-                    - (((Spline.d(i0)*h0/4.0 + Spline.c(i0) )*h0/3.0 +
-                         Spline.b(i0) )*h0/2.0 + Spline.a(i0) )*h0;
-
-        // Include integrals over intervening intervals.
-        if (i1 > i0) {
-            for (int i=i0; i<i1-1; ++i) {
-                Real h = Spline.x(i+1) - Spline.x(i);
-                cubint +=  (((Spline.d(i)*h/4.0 + Spline.c(i) )*h/3.0 +
-                              Spline.b(i))*h/2.0 + Spline.a(i) )*h;
-            }
-        }
-        return cubint;
-    }		// -----  end of method CubicSplineInterpolator::Integrate  -----
-
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  Interval
-    //--------------------------------------------------------------------------------------
-    int CubicSplineInterpolator::Interval ( const Real& x ) {
-
-        std::cerr << "ENTERING CubicSplineInterpolator::Inverval. Known bugs here"  << std::endl;
-        int nx = Spline.x.size() - 2; // TODO check if this is correct or just -1
-        // when x not in range
-        if (x <= Spline.x(0) || nx <= 1 ) {
-            mflag = -1;
-            return 1;
-        }
-
-        if (x >= Spline.x(nx)) {
-            mflag = 1;
-            return nx;
-        }
-
-        mflag = 0;
-        if (ilo >= nx) ilo = nx-1;
-        int ihi = ilo+1;
-
-        // if x is already in the interval
-        if ( x<Spline.x(ihi) && x >= Spline.x(ilo) ) {
-            //std::cout << "TRIVIAL INTERVAL " << Spline.x(ilo) << "\t" << x << "\t" << Spline.x(ihi) << std::endl;
-            return ilo;
-        }
-
-        if (x <= Spline.x(ilo)) { // decrease ilo to capture
-            int istep = 1;
-            for (int ix=1; ix<nx; ++ix) {
-                ihi = ilo;
-                ilo = ihi - istep;
-                ilo = std::max(1, ilo);
-                if (x >= Spline.x(ilo) || ilo == 1) break;
-                istep *= 2;
-            }
-        } else if (x >= Spline.x(ihi)) { // increase ihi to capture
-            int istep = 1;
-            for (int ix=1; ix<nx; ++ix) {
-                ilo = ihi;
-                ihi = ilo + istep;
-                ihi = std::min(ihi, nx);
-                if (x <= Spline.x(ihi) || ihi == nx) break;
-                istep *= 2;
-            }
-        }
-
-        // Now Spline.x(ilo) <= x < Spline.x(ihi) --> Narrow the interval.
-        //std::cout << "WIDE INTERVAL " << Spline.x(ilo) << "\t" << x << "\t" << Spline.x(ihi) << std::endl;
-        for (int ix=1; ix<nx; ++ix) {
-            int middle = (ilo+ihi) / 2;
-            if (middle == ilo) break;
-            if (x < Spline.x(middle)) {
-                ihi = middle;
-            } else {
-                ilo = middle;
-            }
-        }
-        assert ( Spline.x(ilo) < x && x < Spline.x(ihi) );
-        return ilo;
-    }		// -----  end of method CubicSplineInterpolator::Inverval  -----
-
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterplator
-    //      Method:  GetAbscissa
-    //--------------------------------------------------------------------------------------
-    VectorXr CubicSplineInterpolator::GetKnotAbscissa (  ) {
-        return Spline.x;
-    }		// -----  end of method CubicSplineInterplator::get_GetAbscissa  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  CubicSplineInterpolator
-    //      Method:  GetKnotOrdinate
-    //--------------------------------------------------------------------------------------
-    VectorXr CubicSplineInterpolator::GetKnotOrdinate (  ) {
-        return Spline.a;
-    }		// -----  end of method CubicSplineInterpolator::GetKnotOrdinate  -----
-
-
-}		// -----  end of Lemma  name  -----
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/src/Data.cpp

@@ -1,30 +0,0 @@
-/* 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     03/01/2010
-  @version  $Id: data.cpp 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#include "Data.h"
-
-namespace Lemma {
-
-    std::ostream &operator << (std::ostream &stream, const Data &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-	Data::Data(  ) : LemmaObject( ) {
-	}
-
-
-	Data::~Data() {
-	}
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/DataReader.cpp

@@ -1,29 +0,0 @@
-/* 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     03/01/2010
-  @version  $Id: datareader.cpp 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#include "DataReader.h"
-
-namespace Lemma {
-
-    std::ostream &operator << (std::ostream &stream, const DataReader &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-	DataReader::DataReader( ) : LemmaObject( ) {
-	}
-
-	DataReader::~DataReader() {
-	}
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/EarthModel.cpp

@@ -1,129 +0,0 @@
-/* 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     03/23/2010
-  @version  $Id: earthmodel.cpp 210 2015-02-25 02:57:03Z tirons $
- **/
-
-#include "EarthModel.h"
-
-namespace Lemma {
-
-    std::ostream &operator << (std::ostream &stream, const EarthModel &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-	// ====================  LIFECYCLE     =======================
-
-	EarthModel::EarthModel() : LemmaObject( ),
-        BField(0,0,0), BFieldUnit(0,0,0), BInc(0), BDec(0), BMag(0) {
-	}
-
-    EarthModel::EarthModel(const YAML::Node& node) : LemmaObject(node) {
-        BInc = node["BInc"].as<double>();
-        BDec = node["BDec"].as<double>();
-        BMag = node["BMag"].as<double>();
-        BField = node["BField"].as<Vector3r>();
-    }
-
-
-    YAML::Node EarthModel::Serialize() const {
-        YAML::Node node = LemmaObject::Serialize();
-        node.SetTag( this->GetName() );
-        node["BField"] = BField;
-        node["BInc"] = BInc;
-        node["BDec"] = BDec;
-        node["BMag"] = BMag;
-        return node;
-    }
-
-	EarthModel::~EarthModel() {
-	}
-
- 	// ====================  ACCESS        ===================================
-	void EarthModel::SetMagneticFieldComponents(const Vector3r &bfield,
-					const MAGUNITS &unit) {
-
- 		this->BField = bfield;
-
-		switch (unit) {
-			case TESLA:
-				break;
-			case NANOTESLA:
-				BField *= 1e-9;
-				break;
-		  	case GAUSS:
-				BField *= 1e-4;
-				break;
-			default:
-				throw "MAGUNITS UNDEFINED\n";
-		}
-
-		BMag = bfield.norm(  );
-	    BInc = std::acos (bfield.dot(Vector3r(0,0,1)) / BMag) ;
-	    BDec = std::acos (bfield.dot(Vector3r(1,0,0)) / BMag) ;
-		BFieldUnit = BField.array() / BMag;
- 	}
-
-	void EarthModel::SetMagneticFieldIncDecMag(const Real &inc,
-			const Real &dec, const Real &mag, const MAGUNITS &unit) {
-		BMag = mag;
-		BInc = inc;
-		BDec = dec;
-
-		switch (unit) {
-			case TESLA:
-				break;
-			case NANOTESLA:
-				BMag *= 1e-9;
-				break;
-		  	case GAUSS:
-				BMag *= 1e-4;
-				break;
-			default:
-				throw "MAGUNITS UNDEFINED\n";
-		}
-
-		BField(0) = BMag * cos(BInc*(PI/180.)) * cos(BDec*(PI/180.));
-		BField(1) = BMag * cos(BInc*(PI/180.)) * sin(BDec*(PI/180.));
-		BField(2) = BMag * sin(BInc*(PI/180.))  ;
-		BFieldUnit = BField.array() / BMag;
-	}
-
-	// ====================  INQUIRY       =======================
-
-	Vector3r EarthModel::GetMagneticField( ) {
-		return this->BField;
-	}
-
-    Vector3r EarthModel::GetMagneticFieldInGauss( ) {
-		return this->BField*1e4;
-	}
-
-	Vector3r EarthModel::GetMagneticFieldUnitVector() {
-		return this->BFieldUnit;
-	}
-
-	Real  EarthModel::GetMagneticFieldMagnitude() {
-		return this->BMag;
-	}
-
-	Real  EarthModel::GetMagneticFieldMagnitudeInGauss() {
-		return this->BMag*1e4;
-	}
-
-    ////////////////////////////////////////////////////////
-    // Error Classes
-
-    NullEarth::NullEarth() :
-        runtime_error( "NULL VALUED LAYERED EARTH MODEL") {}
-
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/Filter.cpp

@@ -1,22 +0,0 @@
-/* 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     07/20/2010
-  @version  $Id: filter.cpp 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#include "Filter.h"
-
-namespace Lemma {
-
-    Filter::Filter( ) : LemmaObject( ) { }
-
-    Filter::~Filter( ) { }
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/Grid.cpp

@@ -1,43 +0,0 @@
-/* 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     10/25/2009
-  @version  $Id: grid.cpp 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#include "Grid.h"
-
-namespace Lemma {
-
-    std::ostream &operator << (std::ostream &stream, const Grid &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-    // ====================  LIFECYCLE     ===================================
-
-	Grid::Grid( ) : LemmaObject( ) {
-	}
-
-    Grid::Grid( const YAML::Node& node ) : LemmaObject(node) {
-
-    }
-
-	Grid::~Grid  ( ) {
-	}
-
-    YAML::Node Grid::Serialize() const {
-
-        YAML::Node node = LemmaObject::Serialize();
-        node.SetTag( this->GetName() );
-        return node;
-
-    }
-
-}

LemmaCore/src/Instrument.cpp

@@ -1,29 +0,0 @@
-/* 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: instrument.cpp 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#include "Instrument.h"
-
-namespace Lemma {
-
-    std::ostream &operator << (std::ostream &stream, const Instrument &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-	Instrument::Instrument( ) : LemmaObject() {
-	}
-
-	Instrument::~Instrument() {
-	}
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/LayeredEarth.cpp

@@ -1,130 +0,0 @@
-/* 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  $Id: layeredearth.cpp 210 2015-02-25 02:57:03Z tirons $
- **/
-
-#include "LayeredEarth.h"
-
-namespace Lemma {
-
-	// ====================    FRIENDS     ======================
-
-    std::ostream &operator << (std::ostream &stream, const LayeredEarth &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-	// ====================  LIFECYCLE     ===================================
-
-	LayeredEarth::LayeredEarth( ) : EarthModel( ),
-		NumberOfLayers(0), 	NumberOfInterfaces(0) {
-	}
-
-
-
-	LayeredEarth::~LayeredEarth() {
-	}
-
-    LayeredEarth::LayeredEarth(const YAML::Node& node) : EarthModel(node)
-    {
-        NumberOfLayers = node["NumberOfLayers"].as<int>();
-        NumberOfInterfaces = node["NumberOfInterfaces"].as<int>();
-        LayerThickness = node["LayerThickness"].as<VectorXr>();
-	}
-
-    YAML::Node LayeredEarth::Serialize() const {
-        YAML::Node node = EarthModel::Serialize();
-        node["NumberOfLayers"] = NumberOfLayers;
-        node["NumberOfInterfaces"] = NumberOfInterfaces;
-        node["LayerThickness"] = LayerThickness;
-        node.SetTag( this->GetName() );
-        return node;
-    }
-
-	// ====================  OPERATIONS    ===================================
-
-	// ====================  ACCESS        ===================================
-
-	void LayeredEarth::SetLayerThickness(const VectorXr &thick) {
-		if (thick.size() != this->NumberOfLayers - 2)
-			throw EarthModelParametersDoNotMatchNumberOfLayers( );
-		LayerThickness = thick;
-	}
-
-	// ====================  INQUIRY       ===================================
-
-	int LayeredEarth::GetNumberOfLayers () {
-		return this->NumberOfLayers;
-	}
-
-	int LayeredEarth::GetNumberOfNonAirLayers () {
-		return this->NumberOfLayers - 1;
-	}
-
-	Real LayeredEarth::GetLayerThickness(const int &ilay) {
-		// Take into account infinite top and bottom layers
-		// estimate infinity by 1000 m
-		if (ilay < 0 || ilay > NumberOfLayers - 1) {
-			throw RequestForNonValidEarthModelParameter( );
-		} else if (ilay == 0) {
-			return 1000.;
-		} else if (ilay == NumberOfLayers - 1) {
-			return 1000.;
-		} else {
-			return this->LayerThickness(ilay-1);
-		}
-	}
-
-	Real LayeredEarth::GetLayerDepth(const int &ilay) {
-
-		Real depth = 0;
-
-
-		if (ilay == 0) {
-			return depth;
-		} else {
-			for (int i=1; i<=ilay; ++i) {
-				depth += GetLayerThickness(i);
-			}
-		}
-		return depth;
-	}
-
-	int LayeredEarth::GetLayerAtThisDepth(const Real& depth) {
-
-		if (depth <= 0 || NumberOfLayers < 2) {
-			return 0;
-		}
-
-		Real laydep = 0;
-		for (int ilay=0; ilay<NumberOfLayers-2; ++ilay) {
-			laydep += LayerThickness[ilay];
-			if (laydep >= depth) { return ilay+1; }
-		}
-
-		return NumberOfLayers-1;
-	}
-
-    EarthModelWithLessThanTwoLayers::EarthModelWithLessThanTwoLayers() :
-        runtime_error( "EARTH MODEL WITH LESS THAN TWO LAYERS") { }
-
-    EarthModelWithMoreThanMaxLayers::EarthModelWithMoreThanMaxLayers() :
-        runtime_error( "EARTH MODEL WITH MORE THAN MAX LAYERS") { }
-
-    EarthModelParametersDoNotMatchNumberOfLayers::
-        EarthModelParametersDoNotMatchNumberOfLayers( ) :
-        runtime_error( "EARTH MODEL PARAMETERS DO NOT MATCH NUMBER OF LAYERS")
-        {}
-
-    RequestForNonValidEarthModelParameter::
-        RequestForNonValidEarthModelParameter() :
-        runtime_error( "REQUEST FOR NON VALID EARTH MODEL PARAMETER") {}
-}

LemmaCore/src/LemmaObject.cpp

@@ -1,86 +0,0 @@
-/* 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     06/25/2009
-  @version  $Id: LemmaObject.cpp 266 2015-04-01 03:24:00Z tirons $
- **/
-
-#include "LemmaObject.h"
-
-namespace Lemma {
-
-    YAML::Emitter& operator << (YAML::Emitter& out, const LemmaObject& ob) {
-        out << YAML::BeginMap;
-        out << YAML::Key <<"Class Name"    << YAML::Value << ob.GetName();
-        return out;
-    }
-
-    // ====================  LIFECYCLE     ==============================
-
-    // Constructor
-    LemmaObject::LemmaObject(  ) {
-
-    }
-
-    LemmaObject::LemmaObject(const YAML::Node &node) {
-
-    }
-
-    // Destructor
-    LemmaObject::~LemmaObject() {
-    }
-
-    // ====================  OPERATIONS    ==============================
-
-    // ====================  INQUIRY       ==============================
-
-    // ====================  ACCESS        ==============================
-
-    // ====================  ACCESS        ==============================
-
-    // ====================  OPERATORS     ==============================
-
-    //////////////////////////////////////////////////////////////////////
-    //////////////////////////////////////////////////////////////////////
-
-    DeSerializeTypeMismatch::DeSerializeTypeMismatch(const std::string& expected, const std::string& got) :
-        runtime_error("DESERIALIZE TYPE MISMATCH") {
-            std::cerr << "Expected " << expected << " got " << got << std::endl;
-        }
-
-    RequestToReturnNullPointer::
-        RequestToReturnNullPointer(LemmaObject *ptr) :
-        runtime_error("REQUEST TO RETURN NULL POINTER"){
-            std::cerr << "Thrown by instance of "
-                      << ptr->GetName() << std::endl;
-        }
-
-    MatFileCannotBeOpened::
-        MatFileCannotBeOpened() :
-        runtime_error("MATFILE CANNOT BE OPENED"){}
-
-    AssignmentOutOfBounds::
-        AssignmentOutOfBounds(LemmaObject *ptr) :
-        runtime_error("ASSIGNMENT OUT OF BOUNDS"){
-            std::cerr << "Thrown by instance of "
-                      << ptr->GetName() << std::endl;
-       }
-
-	GenericFileIOError::
-		GenericFileIOError(LemmaObject *ptr, const std::string &filename) : runtime_error("FILE I/O ERROR"){
-			std::cerr << std::endl;
-			std::cerr << "FILE I/O ERROR" << std::endl;
-			std::cerr << std::endl;
-			std::cerr << "Thrown by instance of "
-				<< ptr->GetName() << std::endl;
-			std::cerr << "  while trying to access " << filename << std::endl;
-			std::cerr << std::endl;
-		}
-
-} // end of namespace Lemma

LemmaCore/src/RectilinearGrid.cpp

@@ -1,215 +0,0 @@
-/* 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: rectilineargrid.cpp 193 2014-11-10 23:51:41Z tirons $
- **/
-
-#include "RectilinearGrid.h"
-
-namespace Lemma {
-
-    std::ostream &operator << (std::ostream &stream, const RectilinearGrid &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-    // ====================  LIFECYCLE     =======================
-
-    RectilinearGrid::RectilinearGrid( ) : Grid( ), nx(0), ny(0), nz(0) {
-
-    }
-
-    RectilinearGrid::RectilinearGrid( const YAML::Node& node ) : Grid(node) {
-
-        nx = node["nx"].as<int>( );
-        ny = node["ny"].as<int>( );
-        nz = node["nz"].as<int>( );
-
-        ox = node["ox"].as<Real>( );
-        oy = node["oy"].as<Real>( );
-        oz = node["oz"].as<Real>( );
-
-        dx = node["dx"].as< VectorXr >();
-        dy = node["dy"].as< VectorXr >();
-        dz = node["dz"].as< VectorXr >();
-
-    }
-
-    RectilinearGrid::~RectilinearGrid() {
-
-    }
-
-    std::shared_ptr< RectilinearGrid > RectilinearGrid::NewSP() {
-        std::shared_ptr<RectilinearGrid> sp(new  RectilinearGrid( ), LemmaObjectDeleter() );
-        return sp;
-    }
-
-    YAML::Node RectilinearGrid::Serialize() const {
-        YAML::Node node = Grid::Serialize();
-
-        node["nx"] = nx;
-        node["ny"] = ny;
-        node["nz"] = nz;
-
-        node["ox"] = ox;
-        node["oy"] = oy;
-        node["oz"] = oz;
-
-        node["dx"] = dx;
-        node["dy"] = dy;
-        node["dz"] = dz;
-
-        node.SetTag( this->GetName() );
-        return node;
-    }
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  DeSerialize
-    //--------------------------------------------------------------------------------------
-    std::shared_ptr<RectilinearGrid> RectilinearGrid::DeSerialize ( const YAML::Node& node  ) {
-        if (node.Tag() != "RectilinearGrid") {
-            throw  DeSerializeTypeMismatch( "RectilinearGrid", node.Tag());
-        }
-        std::shared_ptr<RectilinearGrid> Object(new  RectilinearGrid(node), LemmaObjectDeleter() );
-        return Object ;
-    }
-
-
-    // ====================  OPERATIONS    =======================
-
-    void RectilinearGrid::SetDimensions (const int &inx, const int &iny,
-            const int &inz) {
-        dx.resize(inx);
-        dy.resize(iny);
-        dz.resize(inz);
-        nx = inx;
-        ny = iny;
-        nz = inz;
-    }
-
-
-    void RectilinearGrid::SetOffset (const Real& iox, const Real& ioy, const Real& ioz) {
-        ox = iox;
-        oy = ioy;
-        oz = ioz;
-    }
-
-    void RectilinearGrid::SetSpacing (const VectorXr &idx, const VectorXr &idy,
-                const VectorXr &idz) {
-        nx = idx.size();
-        ny = idy.size();
-        nz = idz.size();
-        dx = idx;
-        dy = idy;
-        dz = idz;
-    }
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetNx
-    //--------------------------------------------------------------------------------------
-    int RectilinearGrid::GetNx (  ) {
-        return nx;
-    }		// -----  end of method RectilinearGrid::GetNx  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetNy
-    //--------------------------------------------------------------------------------------
-    int RectilinearGrid::GetNy (  ) {
-        return ny;
-    }		// -----  end of method RectilinearGrid::GetNy  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetNz
-    //--------------------------------------------------------------------------------------
-    int RectilinearGrid::GetNz (  ) {
-        return nz;
-    }		// -----  end of method RectilinearGrid::GetNz  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetOx
-    //--------------------------------------------------------------------------------------
-    Real RectilinearGrid::GetOx (  ) {
-        return ox;
-    }		// -----  end of method RectilinearGrid::GetOx  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetOy
-    //--------------------------------------------------------------------------------------
-    Real RectilinearGrid::GetOy (  ) {
-        return oy;
-    }		// -----  end of method RectilinearGrid::GetOy  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetOz
-    //--------------------------------------------------------------------------------------
-    Real RectilinearGrid::GetOz (  ) {
-        return oz;
-    }		// -----  end of method RectilinearGrid::GetOz  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetDx
-    //--------------------------------------------------------------------------------------
-    VectorXr RectilinearGrid::GetDx (  ) {
-        return dx;
-    }		// -----  end of method RectilinearGrid::GetDx  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetDx
-    //--------------------------------------------------------------------------------------
-    Real RectilinearGrid::GetDx ( const int& ix  ) {
-        return dx[ix];
-    }		// -----  end of method RectilinearGrid::GetDx  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetDy
-    //--------------------------------------------------------------------------------------
-    VectorXr RectilinearGrid::GetDy (  ) {
-        return dy;
-    }		// -----  end of method RectilinearGrid::GetDy  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetDy
-    //--------------------------------------------------------------------------------------
-    Real RectilinearGrid::GetDy ( const int& iy  ) {
-        return dy[iy];
-    }		// -----  end of method RectilinearGrid::GetDy  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetDz
-    //--------------------------------------------------------------------------------------
-    VectorXr RectilinearGrid::GetDz (  ) {
-        return dz;
-    }		// -----  end of method RectilinearGrid::GetDz  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGrid
-    //      Method:  GetDz
-    //--------------------------------------------------------------------------------------
-    Real RectilinearGrid::GetDz ( const int& iz  ) {
-        return dz[iz];
-    }		// -----  end of method RectilinearGrid::GetDz  -----
-
-}		// -----  end of Lemma  name  -----
-
-/* vim: set tabstop=4 expandtab: */
-/* vim: set filetype=cpp: */

LemmaCore/src/RectilinearGridReader.cpp

@@ -1,113 +0,0 @@
-/* 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
-  @date      09/23/2013 11:05:48 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 "RectilinearGridReader.h"
-
-namespace Lemma {
-
-    // ====================  FRIEND METHODS  =====================
-
-    std::ostream &operator << (std::ostream &stream, const RectilinearGridReader &ob) {
-        stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-        return stream;
-    }
-
-    // ====================  LIFECYCLE     =======================
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGridReader
-    //      Method:  RectilinearGridReader
-    // Description:  constructor (protected)
-    //--------------------------------------------------------------------------------------
-    RectilinearGridReader::RectilinearGridReader ( ) : GridReader( ),
-        rGrid( nullptr ), Parser( nullptr ) {
-
-    }  // -----  end of method RectilinearGridReader::RectilinearGridReader  (constructor)  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGridReader
-    //      Method:  NewSP()
-    // Description:  constructor
-    //--------------------------------------------------------------------------------------
-    std::shared_ptr< RectilinearGridReader > RectilinearGridReader::NewSP() {
-        std::shared_ptr<RectilinearGridReader> sp(new  RectilinearGridReader( ), LemmaObjectDeleter() );
-        return sp;
-    }
-
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGridReader
-    //      Method:  ~RectilinearGridReader
-    // Description:  destructor (protected)
-    //--------------------------------------------------------------------------------------
-    RectilinearGridReader::~RectilinearGridReader () {
-    }  // -----  end of method RectilinearGridReader::~RectilinearGridReader  (destructor)  -----
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGridReader
-    //      Method:  ReadASCIIGridFile
-    //--------------------------------------------------------------------------------------
-    void RectilinearGridReader::ReadASCIIGridFile ( const std::string& name  ) {
-
-        rGrid = RectilinearGrid::NewSP();
-        Parser = ASCIIParser::NewSP();
-
-        Parser->SetCommentString("//");
-
-        Parser->Open(name);
-
-        std::vector<int> vals = Parser->ReadInts(3);
-        rGrid->SetDimensions(vals[0], vals[1], vals[2]);
-
-        std::vector<Real> rvals = Parser->ReadReals(3);
-        rGrid->SetOffset(rvals[0], rvals[1], rvals[2]);
-        rvals.clear();
-
-        rvals = Parser->ReadReals( vals[0] );
-        VectorXr temp = VectorXr::Map(&rvals[0], vals[0]);
-        VectorXr hx = temp;
-
-        rvals.clear();
-        rvals = Parser->ReadReals( vals[1] );
-        VectorXr hy = VectorXr::Map(&rvals[0], vals[1]);
-
-        rvals.clear();
-        rvals = Parser->ReadReals( vals[2] );
-        VectorXr hz = VectorXr::Map(&rvals[0], vals[2]);
-
-        rGrid->SetSpacing(hx, hy, hz);
-
-        // Read in model(s)/data? Where should this be done?
-        Parser->Close();
-
-        return;
-
-    }		// -----  end of method RectilinearGridReader::ReadSCIIGridFile  -----
-
-
-    //--------------------------------------------------------------------------------------
-    //       Class:  RectilinearGridReader
-    //      Method:  GetGrid
-    //--------------------------------------------------------------------------------------
-    std::shared_ptr<Grid> RectilinearGridReader::GetGrid (  ) {
-        return std::static_pointer_cast<Grid> (rGrid);
-    }		// -----  end of method RectilinearGridReader::GetGrid  -----
-
-
-}		// -----  end of Lemma  name  -----

LemmaCore/src/RectilinearGridVTKExporter.cpp

@@ -1,147 +0,0 @@
-/* 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, Trevor Irons
- */
-
-#if  LEMMAUSEVTK
-
-#include "RectilinearGridVTKExporter.h"
-
-namespace Lemma {
-
-// ====================  FRIEND METHODS  =====================
-
-std::ostream &operator << (std::ostream &stream, const RectilinearGridVTKExporter &ob) {
-    stream << ob.Serialize()  << "\n---\n"; // End of doc --- as a direct stream should encapulste thingy
-    return stream;
-}
-
-
-// ====================  LIFECYCLE     =======================
-
-//--------------------------------------------------------------------------------------
-//       Class:  RectilinearGridVTKExporter
-//      Method:  RectilinearGridVTKExporter
-// Description:  constructor (protected)
-//--------------------------------------------------------------------------------------
-RectilinearGridVTKExporter::RectilinearGridVTKExporter ( ) : LemmaObject( ), Grid(nullptr), VTKGrid(nullptr) {
-
-}  // -----  end of method RectilinearGridVTKExporter::RectilinearGridVTKExporter  (constructor)  -----
-
-
-//--------------------------------------------------------------------------------------
-//       Class:  RectilinearGridVTKExporter
-//      Method:  NewSP()
-// Description:  public constructor
-//--------------------------------------------------------------------------------------
-std::shared_ptr< RectilinearGridVTKExporter > RectilinearGridVTKExporter::NewSP() {
-    std::shared_ptr<RectilinearGridVTKExporter> sp(new  RectilinearGridVTKExporter( ), LemmaObjectDeleter() );
-    return sp;
-}
-
-
-
-//--------------------------------------------------------------------------------------
-//       Class:  RectilinearGridVTKExporter
-//      Method:  ~RectilinearGridVTKExporter
-// Description:  destructor (protected)
-//--------------------------------------------------------------------------------------
-RectilinearGridVTKExporter::~RectilinearGridVTKExporter () {
-}  // -----  end of method RectilinearGridVTKExporter::~RectilinearGridVTKExporter  (destructor)  -----
-
-//--------------------------------------------------------------------------------------
-//       Class:  RectilinearGridVTKExporter
-//      Method:  SetGrid
-//--------------------------------------------------------------------------------------
-void RectilinearGridVTKExporter::SetGrid ( std::shared_ptr<RectilinearGrid> GridIn ) {
-    Grid = GridIn;
-    // I see no harm in just doing this now.
-    BuildVTKRectilinearGrid();
-    return ;
-}		// -----  end of method RectilinearGridVTKExporter::SetGrid  -----
-
-//--------------------------------------------------------------------------------------
-//       Class:  RectilinearGridVTKExporter
-//      Method:  GetVTKRectilinearGrid
-//--------------------------------------------------------------------------------------
-vtkSmartPointer<vtkRectilinearGrid> RectilinearGridVTKExporter::GetVTKGrid (  ) {
-    return VTKGrid;
-}		// -----  end of method RectilinearGridVTKExporter::GetVTKRectilinearGrid  -----
-
-//--------------------------------------------------------------------------------------
-//       Class:  RectilinearGridVTKExporter
-//      Method:  WriteVTKGrid
-//--------------------------------------------------------------------------------------
-void RectilinearGridVTKExporter::WriteVTKGrid ( const std::string& fname  ) {
-    vtkXMLRectilinearGridWriter *gridWrite = vtkXMLRectilinearGridWriter::New();
-        gridWrite->SetInputData(VTKGrid);
-        gridWrite->SetFileName( (fname+std::string(".vtr")).c_str() );
-        gridWrite->Update();
-        gridWrite->Write();
-        gridWrite->Delete();
-    return ;
-}		// -----  end of method RectilinearGridVTKExporter::WriteVTKGrid  -----
-
-//--------------------------------------------------------------------------------------
-//       Class:  RectilinearGridVTKExporter
-//      Method:  BuildVTKRectilinearGrid
-//--------------------------------------------------------------------------------------
-void RectilinearGridVTKExporter::BuildVTKRectilinearGrid (  ) {
-
-    // Set Coordinate>s
-    vtkDoubleArray *xCoords = vtkDoubleArray::New();
-    xCoords->InsertNextValue(Grid->GetOx()-Grid->GetDx(0)/2.);
-    double xm1 = Grid->GetOx() - Grid->GetDx(0)/2.;
-    for (int ix=0; ix<Grid->GetNx(); ix++) {
-        xCoords->InsertNextValue(xm1 + Grid->GetDx(ix));
-        xm1 += Grid->GetDx(ix);
-    }
-
-    vtkDoubleArray *yCoords = vtkDoubleArray::New();
-    yCoords->InsertNextValue(Grid->GetOy()-Grid->GetDy(0)/2.);
-    double ym1 = Grid->GetOy()-Grid->GetDy(0)/2.;
-    for (int iy=0; iy<Grid->GetNy(); iy++) {
-        yCoords->InsertNextValue(ym1 + Grid->GetDy(iy));
-        ym1 += Grid->GetDy(iy);
-    }
-
-    vtkDoubleArray *zCoords = vtkDoubleArray::New();
-    zCoords->InsertNextValue(Grid->GetOz()-Grid->GetDz(0)/2.);
-    double zm1 = Grid->GetOz()-Grid->GetDz(0)/2.;
-    for (int iz=0; iz<Grid->GetNz(); iz++) {
-        zCoords->InsertNextValue(zm1 + Grid->GetDz(iz));
-        zm1 += Grid->GetDz(iz);
-    }
-
-    VTKGrid = vtkSmartPointer<vtkRectilinearGrid>::New();
-        VTKGrid->SetDimensions(Grid->GetNx()+1, Grid->GetNy()+1, Grid->GetNz()+1);
-        VTKGrid->SetXCoordinates(xCoords);
-        VTKGrid->SetYCoordinates(yCoords);
-        VTKGrid->SetZCoordinates(zCoords);
-
-    // Clean up
-    xCoords->Delete();
-    yCoords->Delete();
-    zCoords->Delete();
-
-    return ;
-}		// -----  end of method RectilinearGridVTKExporter::BuildVTKRectilinearGrid  -----
-
-
-
-}		// -----  end of Lemma  name  -----
-
-#endif     // -----  not LEMMAUSEVTK  -----

LemmaCore/src/WindowFilter.cpp

@@ -1,83 +0,0 @@
-/* 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     07/20/2010
-  @version  $Id: windowfilter.cpp 87 2013-09-05 22:44:05Z tirons $
- **/
-
-#include "WindowFilter.h"
-
-namespace Lemma {
-
-    // ====================  LIFECYCLE     =======================
-
-    WindowFilter::WindowFilter( ) : Filter( ),
-        Width(0), SamplingRate(0), Bandwidth(0), Coefficients(),
-        Type(RECTANGULAR) {}
-
-    std::shared_ptr< WindowFilter > WindowFilter::NewSP() {
-        std::shared_ptr<WindowFilter> sp(new  WindowFilter( ), LemmaObjectDeleter() );
-        return sp;
-    }
-
-    WindowFilter::~WindowFilter() {
-    }
-
-
-    // ====================  OPERATIONS    =======================
-
-    void WindowFilter::SetWindowType(const WINDOWTYPE &type) {
-        Type = type;
-    }
-
-    void WindowFilter::SetBandwidth(const Real& width) {
-        Bandwidth = width;
-    }
-
-    void WindowFilter::SetSamplingInterval(const Real& rate) {
-        SamplingRate = rate;
-    }
-
-    int WindowFilter::GetNumberOfFrequencyBins() {
-        return this->Nw;
-    }
-
-    void WindowFilter::SetNumberOfSamples(const int& nt) {
-        Nt = nt;
-        Nw = Nt%2 ? (Nt-1)/2+1 : (Nt)/2+1;  // odd , even
-    }
-
-    VectorXr WindowFilter::GetFilterCoefficients() {
-        Real  Nyquist = .5/SamplingRate;
-        std::cout << "Window nyquist " << Nyquist << std::endl;
-        std::cout << "Window Nw  " << Nw << std::endl;
-        Real  df      = (Nyquist)/((Real)(Nw)); // df Hz per bin
-        Width         = Bandwidth/df;
-        Coefficients.resize(Width);
-        switch (Type) {
-            case HAMMING:
-           	    for (int n=0; n<Width; ++n) {
-		            Coefficients(n) = 0.5 * (1.- std::cos( (2.*PI*(Real)(n)) /
-                                       ((Real)(Width)-1.) ) );
-	            }
-                break;
-            case HANNING:
-	            for (int n=0; n<Width; ++n) {
-		            Coefficients(n) = 0.54 - 0.46 *
-                                std::cos( (2.*PI*(Real)(n)) /
-                                    ((Real)(Width)-1.) ) ;
-	            }
-                break;
-            case RECTANGULAR:
-                Coefficients.setOnes();
-                break;
-        }
-        return Coefficients;
-    }
-}		// -----  end of Lemma  name  -----

LemmaCore/src/banner.cpp

@@ -1,36 +0,0 @@
-/* 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     05/03/2010
-  @version  $Id: banner.cpp 87 2013-09-05 22:44:05Z tirons $
- **/
-
-#include "banner.h"
-
-///Prints banner information to the screen
-void banner(const std::string &name, const std::string &version,
-		const std::string &usage) {
-
-	std::cout << std::endl;
-	std::cout << "  " << name.c_str() << version.c_str() << std::endl;
-	std::cout << std::endl;
-	std::cout << "  A program built from Lemma v 1.0b" << std::endl;
-	std::cout << "  Usage: " << usage.c_str() << std::endl;
-	std::cout << std::endl;
-	std::cout << "  Developed jointly by the Center for Gravity, " <<
-		"Electrical, and Magnetic" <<std::endl;
-	std::cout << "   Studies (CGEM), the United States Geologic " <<
-		"Survey (USGS), and Broken" << std::endl;
-	std::cout << "   Spoke Development, LLC." <<std::endl;
-	std::cout << std::endl;
-	std::cout << "  (C) Copyright 2010, Trevor Irons and M. Andy Kass.  " <<
-		"Some rights reserved." << std::endl;
-	std::cout << "  Please see license for details." << std::endl;
-	std::cout << std::endl;
-}

LemmaCore/src/helper.cpp

@@ -1,201 +0,0 @@
-/* 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      10/02/2014 03:21:07 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 "helper.h"
-
-namespace Lemma {
-
-std::string enum2String(const FREQUENCYUNITS& FreqUnits) {
-    std::string t;
-    switch (FreqUnits) {
-        case HZ:
-            t = std::string("HZ");
-            break;
-        case KHZ:
-            t = std::string("KHZ");
-            break;
-        case MHZ:
-            t = std::string("MHZ");
-            break;
-        case GHZ:
-            t = std::string("GHZ");
-            break;
-    }
-    return t;
-}
-
-std::string enum2String(const TIMEUNITS& Units) {
-    std::string t;
-    switch (Units) {
-        case SEC:
-            t = std::string("SEC");
-            break;
-        case MILLISEC:
-            t = std::string("MILLISEC");
-            break;
-        case MICROSEC:
-            t = std::string("MICROSEC");
-            break;
-        case NANOSEC:
-            t = std::string("NANOSEC");
-            break;
-        case PICOSEC:
-            t = std::string("PICOSEC");
-            break;
-    }
-    return t;
-}
-
-
-std::string enum2String(const MAGUNITS& Units) {
-    std::string t;
-    switch (Units) {
-        case TESLA:
-            t = std::string("TESLA");
-            break;
-        case NANOTESLA:
-            t = std::string("NANOTESLA");
-            break;
-        case GAUSS:
-            t = std::string("GAUSS");
-            break;
-    }
-    return t;
-}
-
-std::string enum2String(const FIELDCALCULATIONS& Field) {
-    std::string t;
-    switch (Field) {
-        case E:
-            t = std::string("E");
-            break;
-        case H:
-            t = std::string("H");
-            break;
-        case BOTH:
-            t = std::string("BOTH");
-            break;
-    }
-    return t;
-}
-
-
-std::string enum2String(const TEMPUNITS& Units) {
-    std::string t;
-    switch (Units) {
-        case CELCIUS:
-            t = std::string("CELCIUS");
-            break;
-        case KELVIN:
-            t = std::string("KELVIN");
-            break;
-    }
-    return t;
-}
-
-std::string enum2String(const FIELDCOMPONENT& Comp) {
-    std::string t;
-    switch (Comp) {
-        case XCOMPONENT:
-            t = std::string("XCOMPONENT");
-            break;
-        case YCOMPONENT:
-            t = std::string("YCOMPONENT");
-            break;
-        case ZCOMPONENT:
-            t = std::string("ZCOMPONENT");
-            break;
-    }
-    return t;
-}
-
-std::string enum2String(const HANKELTRANSFORMTYPE& Type) {
-    std::string t;
-    switch (Type) {
-        case ANDERSON801:
-            t = std::string("ANDERSON801");
-            break;
-        case CHAVE:
-            t = std::string("CHAVE");
-            break;
-        case QWEKEY:
-            t = std::string("QWEKEY");
-            break;
-        case FHTKEY201:
-            t = std::string("FHTKEY201");
-            break;
-        case FHTKEY101:
-            t = std::string("FHTKEY101");
-            break;
-        case FHTKEY51:
-            t = std::string("FHTKEY51");
-            break;
-    }
-    return t;
-}
-
-template<>
-FREQUENCYUNITS string2Enum<FREQUENCYUNITS>( const std::string& str ) {
-    if       (str ==  "HZ") return   HZ;
-    else if  (str == "KHZ") return  KHZ;
-    else if  (str == "MHZ") return  MHZ;
-    else if  (str == "GHZ") return  GHZ;
-    else {
-        throw std::runtime_error("string not recognized as FREUENCYUNIT");
-    }
-}
-
-template<>
-HANKELTRANSFORMTYPE string2Enum<HANKELTRANSFORMTYPE>( const std::string& str ) {
-    if       (str ==  "ANDERSON801") return   ANDERSON801;
-    else if  (str == "CHAVE") return  CHAVE;
-    else if  (str == "QWEKEY") return  QWEKEY;
-    else if  (str == "FHTKEY201") return  FHTKEY201;
-    else if  (str == "FHTKEY51") return  FHTKEY51;
-    else if  (str == "FHTKEY101") return  FHTKEY101;
-    else {
-        throw std::runtime_error("string not recognized as HANKELTRANSFORMTYPE");
-    }
-}
-
-
-template<>
-TIMEUNITS string2Enum<TIMEUNITS>( const std::string& str ) {
-    if       (str == "SEC")      return      SEC;
-    else if  (str == "MILLISEC") return MILLISEC;
-    else if  (str == "MICROSEC") return MICROSEC;
-    else if  (str == "NANOSEC")  return  NANOSEC;
-    else if  (str == "PICOSEC")  return  PICOSEC;
-    else {
-        throw std::runtime_error("string not recognized as TIMEUNIT");
-    }
-}
-
-template<>
-FIELDCOMPONENT string2Enum<FIELDCOMPONENT>( const std::string& str) {
-    if       (str == "XCOMPONENT")      return XCOMPONENT;
-    else if  (str == "YCOMPONENT")      return YCOMPONENT;
-    else if  (str == "ZCOMPONENT")      return ZCOMPONENT;
-    else {
-        throw std::runtime_error("string not recognized as FieldComponent");
-    }
-}
-
-}		// -----  end of Lemma  name  -----
-

LemmaCore/testing/CMakeLists.txt

@@ -1,11 +0,0 @@
-#add_executable(testOne testOne.cpp)
-#add_executable(testTwo testTwo.cpp)
-#add_test( testLemmaCoreOne testOne )
-#add_test( testLemmaCoreTwo testTwo )
-
-CXXTEST_ADD_TEST(unittest_GetNameCheck GetNameCheck.cc ${CMAKE_CURRENT_SOURCE_DIR}/GetNameCheck.h)
-target_link_libraries(unittest_GetNameCheck "lemmacore")
-
-CXXTEST_ADD_TEST(unittest_SerializeCheck SerializeCheck.cc ${CMAKE_CURRENT_SOURCE_DIR}/SerializeCheck.h)
-target_link_libraries(unittest_SerializeCheck "lemmacore")
- 

LemmaCore/testing/GetNameCheck.h

@@ -1,69 +0,0 @@
-/* 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      06/16/2016 09:12:46 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     tirons@egi.utah.edu
- * @copyright Copyright (c) 2016, University of Utah
- * @copyright Copyright (c) 2016, Trevor Irons & Lemma Software, LLC
- */
-
-#include <cxxtest/TestSuite.h>
-#include <LemmaCore>
-
-using namespace Lemma;
-
-class MyTestSuite : public CxxTest::TestSuite
-{
-    public:
-
-    void testASCIIParser( void )
-    {
-        auto Obj = ASCIIParser::NewSP();
-        TS_ASSERT_EQUALS( Obj->GetName(), std::string("ASCIIParser") );
-    }
-
-    void testCubicSplineInterpolator(void)
-    {
-        auto Obj = CubicSplineInterpolator::NewSP();
-        TS_ASSERT_EQUALS( Obj->GetName(), std::string("CubicSplineInterpolator") );
-    }
-
-    void testRectilinearGrid( void )
-    {
-        auto Obj = RectilinearGrid::NewSP();
-        TS_ASSERT_EQUALS( Obj->GetName(), std::string("RectilinearGrid") );
-    }
-
-    void testRectilinearGridReader( void )
-    {
-        auto Obj = RectilinearGridReader::NewSP();
-        TS_ASSERT_EQUALS( Obj->GetName(), std::string("RectilinearGridReader") );
-    }
-
-// INCLUDE GUARDS DON'T WORK WITH CXXTEST, NEED TO MOVE VTK TESTS OUT
-// #ifdef LEMMAUSEVTK
-//     void testRectilinearGridVTKExporter( void )
-//     {
-//         auto Obj = RectilinearGridVTKExporter::NewSP();
-//         TS_ASSERT_EQUALS( Obj->GetName(), std::string("RectilinearGridVTKExporter") );
-//     }
-// #endif
-
-    void testWindowFilter( void )
-    {
-        auto Obj = WindowFilter::NewSP();
-        TS_ASSERT_EQUALS( Obj->GetName(), std::string("WindowFilter") );
-    }
-
-};
-

LemmaCore/testing/SerializeCheck.h

@@ -1,75 +0,0 @@
-/* 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      06/16/2016 09:12:46 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     tirons@egi.utah.edu
- * @copyright Copyright (c) 2016, University of Utah
- * @copyright Copyright (c) 2016, Trevor Irons & Lemma Software, LLC
- */
-
-#include <cxxtest/TestSuite.h>
-#include <LemmaCore>
-
-using namespace Lemma;
-
-class MyTestSuite : public CxxTest::TestSuite
-{
-    public:
-
-    void testASCIIParser( void )
-    {
-        auto Obj = ASCIIParser::NewSP();
-        YAML::Node node = Obj->Serialize();
-        auto Obj2 = ASCIIParser::DeSerialize(node);
-        TS_ASSERT_EQUALS( Obj->GetName(), Obj2->GetName() );
-    }
-
-
-    void testCubicSplineInterpolator(void)
-    {
-        auto Obj = CubicSplineInterpolator::NewSP();
-        YAML::Node node = Obj->Serialize();
-        auto Obj2 = CubicSplineInterpolator::DeSerialize(node);
-        TS_ASSERT_EQUALS( Obj->GetName(), Obj2->GetName() );
-    }
-
-    void testRectilinearGrid( void )
-    {
-        auto Obj = RectilinearGrid::NewSP();
-        YAML::Node node = Obj->Serialize();
-        auto Obj2 = RectilinearGrid::DeSerialize(node);
-        TS_ASSERT_EQUALS( Obj->GetName(), Obj2->GetName() );
-    }
-
-// /*
-//     void testRectilinearGridReader( void )
-//     {
-//         auto Obj = RectilinearGridReader::NewSP();
-//         TS_ASSERT_EQUALS( Obj->GetName(), std::string("RectilinearGridReader") );
-//     }
-//
-//     void testRectilinearGridVTKExporter( void )
-//     {
-//         auto Obj = RectilinearGridVTKExporter::NewSP();
-//         TS_ASSERT_EQUALS( Obj->GetName(), std::string("RectilinearGridVTKExporter") );
-//     }
-//
-//     void testWindowFilter( void )
-//     {
-//         auto Obj = WindowFilter::NewSP();
-//         TS_ASSERT_EQUALS( Obj->GetName(), std::string("WindowFilter") );
-//     }
-// */
-
-};
-

LemmaCore/testing/testOne.cpp

@@ -1,23 +0,0 @@
-/* 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      06/14/2016 09:30:38 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     tirons@egi.utah.edu
- * @copyright Copyright (c) 2016, University of Utah
- * @copyright Copyright (c) 2016, Trevor Irons & Lemma Software, LLC
- */
-
-int main() {
-    return 0;
-}
-

LemmaCore/testing/testTwo.cpp

@@ -1,23 +0,0 @@
-/* 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      06/14/2016 09:43:43 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     tirons@egi.utah.edu
- * @copyright Copyright (c) 2016, University of Utah
- * @copyright Copyright (c) 2016, Trevor Irons & Lemma Software, LLC
- */
-
-int main() {
-    return 0;
-}
-

LemmaCore/include/LemmaCore.h → Modules/FDEM1D/FDEM1D.dox

@@ -10,7 +10,6 @@
 /**
  * @file
  * @date      09/15/2016 04:28:16 PM
- * @version   $Id$
  * @author    Trevor Irons (ti)
  * @email     tirons@egi.utah.edu
  * @copyright Copyright (c) 2016, University of Utah
@@ -18,8 +17,8 @@
  */
 
 /**
-    \defgroup LemmaCore LemmaCore
-    @brief    LemmaCore provides the general framework and skeleton for applications.
-    @details  This module is the glue holding Lemma together.
+    \defgroup FDEM1D FDEM1D
+    @brief    FDEM1D provides 1D frequency-domain EM capabilities.
+    @details  FDEM1D provides classes and methods for 1D EM calculations.
 */
 

Modules/FDEM1D/README

@@ -1 +0,0 @@
-Frequency Domain EM in 1D

Modules/LemmaCore/include/lemma.h

@@ -20,11 +20,10 @@
     <B>E</B>lectro<B>M</B>agnetics <B>M</B>odelling <B>A</B>PI.
     Lemma is a cross-platform library delivering an expressive API that
     can be used to easily create versatile programs.
-    We are building a powerful, flexible,
-    expresive framework that allows for the straightforward creation of
-    geophysical EM applications. Lemma is not itself a program, instead
-    it is a collection of building blocks to make applications.
-    We chose this name because:
+    We are building a powerful, flexible, expresive framework that allows
+    for the straightforward creation of geophysical EM applications.
+    Lemma is not itself a program, instead it is a collection of building
+    blocks to make applications. We chose this name because:
 
     - In mathematics a Lemma is a proven proposition which is used as a
     stepping stone to a larger result rather than as a statement in-and-of
@@ -46,14 +45,6 @@
     providing a set of general tools users can easily assemble applications
     that suite their needs.
 
-    While most geophysical EM modeling packages are concerned with forward
-    modeling <B>DATA</B> between specific transmitters and receivers located
-    on the surface of the earth; Lemma is fundamentally concerned with
-    modelling <B>FIELDS</B> due to sources, the field values can be calculated
-    everywhere within the domain. This allows for solving multiphysics EM
-    problems. Tradional EM data may be forward modelled using the Lemma::Instrument
-    classes.
-
     \section Capabilities Capabilities
     In the long term, we have many goals for this software project. Due to its
     design, Lemma can be built upon and extended easily. The initial aim is to
@@ -107,10 +98,6 @@
     ElectroMagnetics. The following modules utilise parts of Lemma to provide
     their functionality.
 
-    \subsection Merlin Merlin.
-    This module provides nuclear magnetic resonance functionality.
-
-
     \section Tutorials
         - \ref Tutorial - Basic intruduction to Lemma, including aquiring and
           compiling the code, class structure, and building your own
@@ -119,34 +106,35 @@
 
 
     \section Development Development and design
-    Ths package is primarily being developed by the Center for Gravity,
-    Electrical, and Magnetic Studies (CGEM) at the Colorado School of Mines (CSM), the United
-    States Geological Survey (USGS), and Broken Spoke Development, LLC. It draws on work by
-    many others including Ki Ha Lee, and Walt Anderson. All new work and
+    Ths package was initially developed by the Center for Gravity, Electrical, and
+    Magnetic Studies (CGEM) at the Colorado School of Mines (CSM), the United
+    States Geological Survey (USGS), and Broken Spoke Development, LLC. Where it drew
+    on work by many others including Ki Ha Lee, and Walt Anderson. All new work and
     interfaces are written entirely in C++. Several small external projects are
     included, which are written in standard C, and FORTRAN 77. We adapt a
     modern, test driven, object oriented, C++ framework.
+    More recent development has been undertaken at the University of Utah through the Energy
+    and Geoscience Institute.
 
     \section Legalities
 
     \subsection Copyrights
     The following copyrights apply to the source.
     Most of the code was developed either by Trevor
-    Copyright (C) 2008-2010 Trevor Irons <tirons@mines.edu> or
-    M. Andrew Kass Copyright (C) 2010 <mkass@numericalgeo.com>.
+    Copyright (C) 2008-2010 Trevor Irons <trevor.irons@lemmasoftware.org> or
+    M. Andrew Kass Copyright (C) 2010 <mkass@usgs.gov>.
 
-    The 1D EM solver was derived (but updated heavily) from a fortran
+    The 1D EM solver was derived (but updated heavily) from a Fortran
     programme written by Ki Ha Lee in 1984. We have communicated with Ki Ha,
     and he assured us that this code is in the public domian.
 
     A Gaussian quadrature hankel transform originally written by Alan Chave was
-    ported to C++. This code is in the public domain, and was published in Geophysics.
+    ported to C++. This code is in the public domain, and the source code was
+    published in Geophysics.
 
     A digital filtering approach to the Hankel transform written by Walt
-    Anderson was also rewritten for Lemma. The origional fortran code is also in
-    the public domain. Using this Hankel transform works
-    arround the copyright issue mentioned above, but may not produce accurate
-    results for high frequencies.
+    Anderson was also rewritten for Lemma. The original Fortran code is also in
+    the public domain.
 
     Please note that Ki Ha Lee and Walt Anderson had no part in this work, and
     the above should not be interpreted as any sort of endorsement by those
@@ -166,9 +154,10 @@
 
     \section Useful Useful links
         - Home page https://lemmasoftware.org
-        - SVN repository https://svn.lemmasoftware.org
+        - Git repository https://git.lemmasoftware.org
         - Broken Spoke Develpment http://numericalgeo.com
         - CGEM at the Coloroado School of Mines http://geophysics.mines.edu/cgem/
+        - EGI at the Eniversity of Utah http://egi.utah.edu/
 **/
 
 #pragma once

Modules/LemmaCore/src/CMakeLists.txt

@@ -1,7 +1,6 @@
 set (SOURCE 
 	${SOURCE}
 	${CMAKE_CURRENT_SOURCE_DIR}/helper.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/banner.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/ASCIIParser.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/CubicSplineInterpolator.cpp
 	${CMAKE_CURRENT_SOURCE_DIR}/Data.cpp

include/LemmaConfig.h.in

@@ -1,26 +0,0 @@
-/* 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      01/15/2016 09:52:10 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     tirons@egi.utah.edu
- * @copyright Copyright (c) 2016, University of Utah
- * @copyright Copyright (c) 2016, Trevor Irons & Lemma Software, LLC
- */
-
-// the configured options and settings for Tutorial
-#define LEMMA_VERSION_MAJOR @LEMMA_VERSION_MAJOR@
-#define LEMMA_VERSION_MINOR @LEMMA_VERSION_MINOR@
-#define LEMMA_VERSION_PATCH @LEMMA_VERSION_PATCH@
-//#define LEMMA_VERSION @LEMMA_VERSION@
-
-

include/modules.h

@@ -1,24 +0,0 @@
-/* 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     11/26/2010
-  @version  $Id: modules.h 87 2013-09-05 22:44:05Z tirons $
- **/
-
-/**
-      \defgroup Merlin Merlin
-      @brief    Merlin is a nuclear magnetic resonance module.
-      @details  Much of Merlin focuses on surface, or earth's field NMR (SNMR)
-       but many of the algorithms may be extended to general NMR.
-
-     \defgroup Wavelet Wavelet
-      @brief    A wavlet transfer module.
-      @details  Provides multidimensional wavelet transforms and solver routines.
- */
-

src/myTestSuite.h

@@ -1,33 +0,0 @@
-/* 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      06/14/2016 10:06:34 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     tirons@egi.utah.edu
- * @copyright Copyright (c) 2016, University of Utah
- * @copyright Copyright (c) 2016, Trevor Irons & Lemma Software, LLC
- */
-
-// MyTestSuite.h
-#include <cxxtest/TestSuite.h>
-
-class MyTestSuite : public CxxTest::TestSuite
-{
-    public:
-    void testAddition( void )
-    {
-        TS_ASSERT( 1 + 1 > 1 );
-        TS_ASSERT( 3 - 1 > 1 );
-        TS_ASSERT_EQUALS( 1 + 1, 2 );
-    }
-};
-

src/test.cpp

@@ -1,29 +0,0 @@
-/* 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      01/15/2016 09:54:13 PM
- * @version   $Id$
- * @author    Trevor Irons (ti)
- * @email     tirons@egi.utah.edu
- * @copyright Copyright (c) 2016, University of Utah
- * @copyright Copyright (c) 2016, Trevor Irons & Lemma Software, LLC
- */
-
-#include <iostream>
-#include "LemmaConfig.h"
-#include "lemma.h"
-
-using namespace Lemma;
-
-int main() {
-    std::cout << "Hello Lemma " << LEMMA_VERSION_MAJOR << "\t" << LEMMA_VERSION_MINOR << std::endl;
-}
-

test

@@ -1 +0,0 @@
-Here is a test