code cleanup

11 files changed, 288 insertions, 518 deletions

diff --git a/matlab/mex/astra_mex_algorithm_c.cpp b/matlab/mex/astra_mex_algorithm_c.cpp
index f719a6b..98cf8a4 100644
--- a/matlab/mex/astra_mex_algorithm_c.cpp
+++ b/matlab/mex/astra_mex_algorithm_c.cpp
@@ -78,26 +78,23 @@ void astra_mex_algorithm_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr
 	}
 
 	// turn MATLAB struct to an XML-based Config object
-	XMLDocument* xml = struct2XML("Algorithm", prhs[1]);
-	Config cfg;
-	cfg.self = xml->getRootNode();
+	Config* cfg = structToConfig("Algorithm", prhs[1]);
 
-	CAlgorithm* pAlg = CAlgorithmFactory::getSingleton().create(cfg.self->getAttribute("type"));
+	CAlgorithm* pAlg = CAlgorithmFactory::getSingleton().create(cfg->self->getAttribute("type"));
 	if (!pAlg) {
-		delete xml;
+		delete cfg;
 		mexErrMsgTxt("Unknown algorithm. \n");
 		return;
 	}
 
 	// create algorithm
-	if (!pAlg->initialize(cfg)) {
-		delete xml;
+	if (!pAlg->initialize(*cfg)) {
+		delete cfg;
 		delete pAlg;
 		mexErrMsgTxt("Algorithm not initialized. \n");
 		return;
 	}
-
-	delete xml;
+	delete cfg;
 
 	// store algorithm
 	int iIndex = CAlgorithmManager::getSingleton().store(pAlg);
@@ -322,7 +319,7 @@ void mexFunction(int nlhs, mxArray* plhs[],
 	// INPUT: Mode
 	string sMode = "";
 	if (1 <= nrhs) {
-		sMode = mex_util_get_string(prhs[0]);	
+		sMode = mexToString(prhs[0]);	
 	} else {
 		printHelp();
 		return;
diff --git a/matlab/mex/astra_mex_c.cpp b/matlab/mex/astra_mex_c.cpp
index 2989b7a..760bd51 100644
--- a/matlab/mex/astra_mex_c.cpp
+++ b/matlab/mex/astra_mex_c.cpp
@@ -122,7 +122,7 @@ void mexFunction(int nlhs, mxArray* plhs[],
 	// INPUT0: Mode
 	string sMode = "";
 	if (1 <= nrhs) {
-		sMode = mex_util_get_string(prhs[0]);	
+		sMode = mexToString(prhs[0]);	
 	} else {
 		printHelp();
 		return;
diff --git a/matlab/mex/astra_mex_data2d_c.cpp b/matlab/mex/astra_mex_data2d_c.cpp
index 03d3807..5f79e98 100644
--- a/matlab/mex/astra_mex_data2d_c.cpp
+++ b/matlab/mex/astra_mex_data2d_c.cpp
@@ -98,10 +98,10 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra
 		return;
 	}
 
-	string sDataType = mex_util_get_string(prhs[1]);	
+	string sDataType = mexToString(prhs[1]);	
 	CFloat32Data2D* pDataObject2D = NULL;
 
-	if (nrhs >= 4 && !(mex_is_scalar(prhs[3])|| mxIsDouble(prhs[3]) || mxIsLogical(prhs[3]) || mxIsSingle(prhs[3]) )) {
+	if (nrhs >= 4 && !(mexIsScalar(prhs[3])|| mxIsDouble(prhs[3]) || mxIsLogical(prhs[3]) || mxIsSingle(prhs[3]) )) {
 		mexErrMsgTxt("Data must be single, double or logical.");
 		return;
 	}
@@ -116,23 +116,20 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra
 		if (!mxIsStruct(prhs[2])) {
 			mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
 		}
-		XMLDocument* xml = struct2XML(string("VolumeGeometry"), prhs[2]);
-		if (!xml)
-			return;
-		Config cfg;
-		cfg.self = xml->getRootNode();
+		
+		Config* cfg = structToConfig("VolumeGeometry", prhs[2]);
 		CVolumeGeometry2D* pGeometry = new CVolumeGeometry2D();
-		if (!pGeometry->initialize(cfg)) {
+		if (!pGeometry->initialize(*cfg)) {
 			mexErrMsgTxt("Geometry class not initialized. \n");
-			delete xml;
+			delete cfg;
 			delete pGeometry;
 			return;
 		}
 		// If data is specified, check dimensions
-		if (nrhs >= 4 && !mex_is_scalar(prhs[3])) {
+		if (nrhs >= 4 && !mexIsScalar(prhs[3])) {
 			if (pGeometry->getGridColCount() != mxGetN(prhs[3]) || pGeometry->getGridRowCount() != mxGetM(prhs[3])) {
 				mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
-				delete xml;
+				delete cfg;
 				delete pGeometry;
 				return;
 			}
@@ -140,21 +137,18 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra
 		// Initialize data object
 		pDataObject2D = new CFloat32VolumeData2D(pGeometry);		
 		delete pGeometry;
-		delete xml;
+		delete cfg;
 	}
 	else if (sDataType == "-sino") {
 		// Read geometry
 		if (!mxIsStruct(prhs[2])) {
 			mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
 		}
-		XMLDocument* xml = struct2XML("ProjectionGeometry", prhs[2]);
-		if (!xml)
-			return;
-		Config cfg;
-		cfg.self = xml->getRootNode();
+		
+		Config* cfg = structToConfig("ProjectionGeometry", prhs[2]);
 		// FIXME: Change how the base class is created. (This is duplicated
 		// in 'change_geometry' and Projector2D.cpp.)
-		std::string type = cfg.self->getAttribute("type");
+		std::string type = cfg->self->getAttribute("type");
 		CProjectionGeometry2D* pGeometry;
 		if (type == "sparse_matrix") {
 			pGeometry = new CSparseMatrixProjectionGeometry2D();
@@ -168,25 +162,25 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra
 		} else {
 			pGeometry = new CParallelProjectionGeometry2D();	
 		}
-		if (!pGeometry->initialize(cfg)) {
+		if (!pGeometry->initialize(*cfg)) {
 			mexErrMsgTxt("Geometry class not initialized. \n");
 			delete pGeometry;
-			delete xml;
+			delete cfg;
 			return;
 		}
 		// If data is specified, check dimensions
-		if (nrhs >= 4 && !mex_is_scalar(prhs[3])) {
+		if (nrhs >= 4 && !mexIsScalar(prhs[3])) {
 			if (pGeometry->getDetectorCount() != mxGetN(prhs[3]) || pGeometry->getProjectionAngleCount() != mxGetM(prhs[3])) {
 				mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
 				delete pGeometry;
-				delete xml;
+				delete cfg;
 				return;
 			}
 		}
 		// Initialize data object
 		pDataObject2D = new CFloat32ProjectionData2D(pGeometry);
 		delete pGeometry;
-		delete xml;
+		delete cfg;
 	}
 	else {
 		mexErrMsgTxt("Invalid datatype.  Please specify '-vol' or '-sino'. \n");
@@ -210,7 +204,7 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra
 	// Store data
 	if (nrhs >= 4) {
 		// fill with scalar value
-		if (mex_is_scalar(prhs[3])) {
+		if (mexIsScalar(prhs[3])) {
 			float32 fValue = (float32)mxGetScalar(prhs[3]);
 			for (int i = 0; i < pDataObject2D->getSize(); ++i) {
 				pDataObject2D->getData()[i] = fValue;
@@ -294,7 +288,7 @@ void astra_mex_data2d_store(int nlhs, mxArray* plhs[], int nrhs, const mxArray*
 	}
 	int iDataID = (int)(mxGetScalar(prhs[1]));
 
-	if (!(mex_is_scalar(prhs[2]) || mxIsDouble(prhs[2]) || mxIsLogical(prhs[2]) || mxIsSingle(prhs[2]))) {
+	if (!(mexIsScalar(prhs[2]) || mxIsDouble(prhs[2]) || mxIsLogical(prhs[2]) || mxIsSingle(prhs[2]))) {
 		mexErrMsgTxt("Data must be single, double or logical.");
 		return;
 	}
@@ -312,7 +306,7 @@ void astra_mex_data2d_store(int nlhs, mxArray* plhs[], int nrhs, const mxArray*
 	
 	// step3: insert data
 	// fill with scalar value
-	if (mex_is_scalar(prhs[2])) {
+	if (mexIsScalar(prhs[2])) {
 		float32 fValue = (float32)mxGetScalar(prhs[2]);
 		for (int i = 0; i < pDataObject->getSize(); ++i) {
 			pDataObject->getData()[i] = fValue;
@@ -440,12 +434,10 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const
 		if (!mxIsStruct(prhs[2])) {
 			mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
 		}
-		XMLDocument* xml = struct2XML("ProjectionGeometry", prhs[2]);
-		Config cfg;
-		cfg.self = xml->getRootNode();
+		Config* cfg = structToConfig("ProjectionGeometry2D", prhs[2]);
 		// FIXME: Change how the base class is created. (This is duplicated
 		// in 'create' and Projector2D.cpp.)
-		std::string type = cfg.self->getAttribute("type");
+		std::string type = cfg->self->getAttribute("type");
 		CProjectionGeometry2D* pGeometry;
 		if (type == "sparse_matrix") {
 			pGeometry = new CSparseMatrixProjectionGeometry2D();
@@ -459,24 +451,24 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const
 		} else {
 			pGeometry = new CParallelProjectionGeometry2D();	
 		}
-		if (!pGeometry->initialize(cfg)) {
+		if (!pGeometry->initialize(*cfg)) {
 			mexErrMsgTxt("Geometry class not initialized. \n");
 			delete pGeometry;
-			delete xml;
+			delete cfg;
 			return;
 		}
 		// If data is specified, check dimensions
 		if (pGeometry->getDetectorCount() != pSinogram->getDetectorCount() || pGeometry->getProjectionAngleCount() != pSinogram->getAngleCount()) {
 			mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
 			delete pGeometry;
-			delete xml;
+			delete cfg;
 			return;
 		}
 
 		// If ok, change geometry
 		pSinogram->changeGeometry(pGeometry);
 		delete pGeometry;
-		delete xml;
+		delete cfg;
 
 		return;
 	}
@@ -490,27 +482,25 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const
 		if (!mxIsStruct(prhs[2])) {
 			mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
 		}
-		XMLDocument* xml = struct2XML(string("VolumeGeometry"), prhs[2]);
-		Config cfg;
-		cfg.self = xml->getRootNode();
+		Config* cfg = structToConfig("VolumeGeometry2D", prhs[2]);
 		CVolumeGeometry2D* pGeometry = new CVolumeGeometry2D();
-		if (!pGeometry->initialize(cfg)) {
+		if (!pGeometry->initialize(*cfg)) {
 			mexErrMsgTxt("Geometry class not initialized. \n");
-			delete xml;
+			delete cfg;
 			delete pGeometry;
 			return;
 		}
 		// If data is specified, check dimensions
 		if (pGeometry->getGridColCount() != pVolume->getWidth() || pGeometry->getGridRowCount() != pVolume->getHeight()) {
 			mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
-			delete xml;
+			delete cfg;
 			delete pGeometry;
 			return;
 		}
 
 		// If ok, change geometry
 		pVolume->changeGeometry(pGeometry);
-		delete xml;
+		delete cfg;
 		delete pGeometry;
 
 	}
@@ -639,7 +629,7 @@ void mexFunction(int nlhs, mxArray* plhs[],
 	// INPUT0: Mode
 	string sMode = "";
 	if (1 <= nrhs) {
-		sMode = mex_util_get_string(prhs[0]);	
+		sMode = mexToString(prhs[0]);	
 	} else {
 		printHelp();
 		return;
diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp
index 64c013d..0a3f85d 100644
--- a/matlab/mex/astra_mex_data3d_c.cpp
+++ b/matlab/mex/astra_mex_data3d_c.cpp
@@ -83,7 +83,7 @@ void astra_mex_data3d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra
 		return;
 	}
 
-	const string sDataType = mex_util_get_string(prhs[1]);
+	const string sDataType = mexToString(prhs[1]);
 
 	// step2: Allocate data
 	CFloat32Data3DMemory* pDataObject3D =
@@ -152,7 +152,7 @@ void astra_mex_data3d_link(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray*
 		return;
 	}
 
-	string sDataType = mex_util_get_string(prhs[1]);
+	string sDataType = mexToString(prhs[1]);
 
 	// step2: Allocate data
 	CFloat32Data3DMemory* pDataObject3D =
@@ -365,7 +365,7 @@ void mexFunction(int nlhs, mxArray* plhs[],
 	// INPUT: Mode
 	string sMode = "";
 	if (1 <= nrhs) {
-		sMode = mex_util_get_string(prhs[0]);	
+		sMode = mexToString(prhs[0]);	
 	} else {
 		printHelp();
 		return;
diff --git a/matlab/mex/astra_mex_matrix_c.cpp b/matlab/mex/astra_mex_matrix_c.cpp
index 016566a..01ad08b 100644
--- a/matlab/mex/astra_mex_matrix_c.cpp
+++ b/matlab/mex/astra_mex_matrix_c.cpp
@@ -406,7 +406,7 @@ void mexFunction(int nlhs, mxArray* plhs[],
 	// INPUT0: Mode
 	string sMode = "";
 	if (1 <= nrhs) {
-		sMode = mex_util_get_string(prhs[0]);	
+		sMode = mexToString(prhs[0]);	
 	} else {
 		printHelp();
 		return;
diff --git a/matlab/mex/astra_mex_projector3d_c.cpp b/matlab/mex/astra_mex_projector3d_c.cpp
index b2f6b02..5381cf6 100644
--- a/matlab/mex/astra_mex_projector3d_c.cpp
+++ b/matlab/mex/astra_mex_projector3d_c.cpp
@@ -65,16 +65,16 @@ void astra_mex_projector3d_create(int nlhs, mxArray* plhs[], int nrhs, const mxA
 	}
 
 	// turn MATLAB struct to an XML-based Config object
-	XMLDocument* xml = struct2XML("Projector3D", prhs[1]);
-	Config cfg;
-	cfg.self = xml->getRootNode();
+	Config* cfg = structToConfig("Projector3D", prhs[1]);
 
 	// create algorithm
-	CProjector3D* pProj = CProjector3DFactory::getSingleton().create(cfg);
+	CProjector3D* pProj = CProjector3DFactory::getSingleton().create(*cfg);
 	if (pProj == NULL) {
+		delete cfg;
 		mexErrMsgTxt("Error creating Projector3D. \n");
 		return;
 	}
+	delete cfg;
 
 	// store projector
 	int iIndex = CProjector3DManager::getSingleton().store(pProj);
@@ -397,7 +397,7 @@ void mexFunction(int nlhs, mxArray* plhs[],
 	// INPUT: Mode
 	string sMode = "";
 	if (1 <= nrhs) {
-		sMode = mex_util_get_string(prhs[0]);	
+		sMode = mexToString(prhs[0]);	
 	} else {
 		printHelp();
 		return;
diff --git a/matlab/mex/astra_mex_projector_c.cpp b/matlab/mex/astra_mex_projector_c.cpp
index 4793020..58cd953 100644
--- a/matlab/mex/astra_mex_projector_c.cpp
+++ b/matlab/mex/astra_mex_projector_c.cpp
@@ -74,19 +74,16 @@ void astra_mex_projector_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr
 
 
 	// turn MATLAB struct to an XML-based Config object
-	XMLDocument* xml = struct2XML("Projector2D", prhs[1]);
-	Config cfg;
-	cfg.self = xml->getRootNode();
+	Config* cfg = structToConfig("Projector2D", prhs[1]);
 
 	// create algorithm
-	CProjector2D* pProj = CProjector2DFactory::getSingleton().create(cfg);
+	CProjector2D* pProj = CProjector2DFactory::getSingleton().create(*cfg);
 	if (pProj == NULL) {
-		delete xml;
+		delete cfg;
 		mexErrMsgTxt("Error creating projector. \n");
 		return;
 	}
-
-	delete xml;
+	delete cfg;
 
 	// store projector
 	iIndex = CProjector2DManager::getSingleton().store(pProj);
@@ -473,7 +470,7 @@ void mexFunction(int nlhs, mxArray* plhs[],
 	// INPUT: Mode
 	string sMode = "";
 	if (1 <= nrhs) {
-		sMode = mex_util_get_string(prhs[0]);	
+		sMode = mexToString(prhs[0]);	
 	} else {
 		printHelp();
 		return;
diff --git a/matlab/mex/mexCopyDataHelpFunctions.cpp b/matlab/mex/mexCopyDataHelpFunctions.cpp
index 6dfd4a6..80fb834 100644
--- a/matlab/mex/mexCopyDataHelpFunctions.cpp
+++ b/matlab/mex/mexCopyDataHelpFunctions.cpp
@@ -263,7 +263,7 @@ copyMexToCFloat32Array(const mxArray * const in,
 #pragma omp parallel
 	{
 		// fill with scalar value
-		if (mex_is_scalar(in)) {
+		if (mexIsScalar(in)) {
 			astra::float32 fValue = 0.f;
 			if (!mxIsEmpty(in)) {
 				fValue = (astra::float32)mxGetScalar(in);
diff --git a/matlab/mex/mexDataManagerHelpFunctions.cpp b/matlab/mex/mexDataManagerHelpFunctions.cpp
index f9d971c..d482428 100644
--- a/matlab/mex/mexDataManagerHelpFunctions.cpp
+++ b/matlab/mex/mexDataManagerHelpFunctions.cpp
@@ -105,7 +105,7 @@ checkID(const astra::int32 & id, astra::CFloat32Data3DMemory *& pDataObj)
 bool
 checkDataType(const mxArray * const in)
 {
-	return (mex_is_scalar(in) || mxIsDouble(in) || mxIsSingle(in) || mxIsLogical(in));
+	return (mexIsScalar(in) || mxIsDouble(in) || mxIsSingle(in) || mxIsLogical(in));
 }
 
 //-----------------------------------------------------------------------------------------
@@ -213,7 +213,7 @@ allocateDataObject(const std::string & sDataType,
 	bool bUnshare = true;
 	if (unshare)
 	{
-		if (!mex_is_scalar(unshare))
+		if (!mexIsScalar(unshare))
 		{
 			mexErrMsgTxt("Argument 5 (read-only) must be scalar");
 			return NULL;
@@ -225,7 +225,7 @@ allocateDataObject(const std::string & sDataType,
 	mwIndex iZ = 0;
 	if (zIndex)
 	{
-		if (!mex_is_scalar(zIndex))
+		if (!mexIsScalar(zIndex))
 		{
 			mexErrMsgTxt("Argument 6 (Z) must be scalar");
 			return NULL;
@@ -237,25 +237,19 @@ allocateDataObject(const std::string & sDataType,
 	if (sDataType == "-vol")
 	{
 		// Read geometry
-		astra::XMLDocument* xml = struct2XML("VolumeGeometry", geometry);
-		if (!xml) {
-			return NULL;
-		}
-		astra::Config cfg;
-		cfg.self = xml->getRootNode();
-
+		astra::Config* cfg = structToConfig("VolumeGeometry3D", geometry);
 		astra::CVolumeGeometry3D* pGeometry = new astra::CVolumeGeometry3D();
-		if (!pGeometry->initialize(cfg))
+		if (!pGeometry->initialize(*cfg))
 		{
 			mexErrMsgTxt("Geometry class not initialized. \n");
 			delete pGeometry;
-			delete xml;
+			delete cfg;
 			return NULL;
 		}
-		delete xml;
+		delete cfg;
 
 		// If data is specified, check dimensions
-		if (data && !mex_is_scalar(data))
+		if (data && !mexIsScalar(data))
 		{
 			if (! (zIndex
 					? checkDataSize(data, pGeometry, iZ)
@@ -288,16 +282,10 @@ allocateDataObject(const std::string & sDataType,
 	else if (sDataType == "-sino" || sDataType == "-proj3d" || sDataType == "-sinocone")
 	{
 		// Read geometry
-		astra::XMLDocument* xml = struct2XML("ProjectionGeometry", geometry);
-		if (!xml) {
-			return NULL;
-		}
-		astra::Config cfg;
-		cfg.self = xml->getRootNode();
-
+		astra::Config* cfg = structToConfig("ProjectionGeometry3D", geometry);
 		// FIXME: Change how the base class is created. (This is duplicated
 		// in Projector3D.cpp.)
-		std::string type = cfg.self->getAttribute("type");
+		std::string type = cfg->self->getAttribute("type");
 		astra::CProjectionGeometry3D* pGeometry = 0;
 		if (type == "parallel3d") {
 			pGeometry = new astra::CParallelProjectionGeometry3D();
@@ -312,16 +300,16 @@ allocateDataObject(const std::string & sDataType,
 			return NULL;
 		}
 
-		if (!pGeometry->initialize(cfg)) {
+		if (!pGeometry->initialize(*cfg)) {
 			mexErrMsgTxt("Geometry class not initialized. \n");
 			delete pGeometry;
-			delete xml;
+			delete cfg;
 			return NULL;
 		}
-		delete xml;
+		delete cfg;
 
 		// If data is specified, check dimensions
-		if (data && !mex_is_scalar(data))
+		if (data && !mexIsScalar(data))
 		{
 			if (! (zIndex
 					? checkDataSize(data, pGeometry, iZ)
diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp
index c25123a..c0ac711 100644
--- a/matlab/mex/mexHelpFunctions.cpp
+++ b/matlab/mex/mexHelpFunctions.cpp
@@ -38,307 +38,154 @@ $Id$
 #include <boost/algorithm/string/split.hpp>
 #include <boost/algorithm/string/classification.hpp>
 
-#include "astra/SparseMatrixProjectionGeometry2D.h"
-#include "astra/FanFlatVecProjectionGeometry2D.h"
-#include "astra/AstraObjectManager.h"
-
 using namespace std;
 using namespace astra;
 
 
 //-----------------------------------------------------------------------------------------
 // get string from matlab 
-std::string mex_util_get_string(const mxArray* pInput)
+string mexToString(const mxArray* pInput)
 {
-	if (!mxIsChar(pInput)) {
-		return "";
+	// is string?
+	if (mxIsChar(pInput)) {
+		mwSize iLength = mxGetNumberOfElements(pInput) + 1;
+		char* buf = new char[iLength]; 
+		mxGetString(pInput, buf, iLength);
+		std::string res = std::string(buf);
+		delete[] buf;
+		return res;
 	}
-	mwSize iLength = mxGetNumberOfElements(pInput) + 1;
-	char* buf = new char[iLength]; 
-	mxGetString(pInput, buf, iLength);
-	std::string res = std::string(buf);
-	delete[] buf;
-	return res;
+
+	// is scalar?
+	if (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1) {
+		return boost::lexical_cast<string>(mxGetScalar(pInput));
+	}
+
+	return "";
 }
 
 //-----------------------------------------------------------------------------------------
-// is option
-bool isOption(std::list<std::string> lOptions, std::string sOption) 
+// return true if the argument is a scalar
+bool mexIsScalar(const mxArray* pInput)
 {
-	return std::find(lOptions.begin(), lOptions.end(), sOption) != lOptions.end();
+	return (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1);
 }
 
 //-----------------------------------------------------------------------------------------
-// turn a matlab struct into a c++ map
-std::map<std::string, mxArray*> parseStruct(const mxArray* pInput) 
+void get3DMatrixDims(const mxArray* x, mwSize *dims)
 {
-	std::map<std::string, mxArray*> res;
-
-	// check type
-	if (!mxIsStruct(pInput)) {
-      mexErrMsgTxt("Input must be a struct.");
-	  return res;
+	const mwSize* mdims = mxGetDimensions(x);
+	mwSize dimCount = mxGetNumberOfDimensions(x);
+	if (dimCount == 1) {
+		dims[0] = mdims[0];
+		dims[1] = 1;
+		dims[2] = 1;
+	} else if (dimCount == 2) {
+		dims[0] = mdims[0];
+		dims[1] = mdims[1];
+		dims[2] = 1;
+	} else if (dimCount == 3) {
+		dims[0] = mdims[0];
+		dims[1] = mdims[1];
+		dims[2] = mdims[2];
+	} else {
+		dims[0] = 0;
+		dims[1] = 0;
+		dims[2] = 0;
 	}
+} 
+
+
+
+
 
-	// get field names
-	int nfields = mxGetNumberOfFields(pInput);
-	for (int i = 0; i < nfields; i++) {
-		std::string sFieldName = std::string(mxGetFieldNameByNumber(pInput, i));
-		res[sFieldName] = mxGetFieldByNumber(pInput,0,i);
-	}
-	return res;
-}
 
 //-----------------------------------------------------------------------------------------
-// turn a c++ map into a matlab struct
-mxArray* buildStruct(std::map<std::string, mxArray*> mInput) 
+// turn an std vector<float32> object to an mxArray
+mxArray* vectorToMxArray(std::vector<astra::float32> mInput)
 {
-	mwSize dims[2] = {1, 1};
-	mxArray* res = mxCreateStructArray(2,dims,0,0);
-	
-	for (std::map<std::string, mxArray*>::iterator it = mInput.begin(); it != mInput.end(); it++) {
-		mxAddField(res, (*it).first.c_str());
-		mxSetField(res, 0, (*it).first.c_str(), (*it).second);
+	mxArray* res = mxCreateDoubleMatrix(1, mInput.size(), mxREAL);
+	double* pdData = mxGetPr(res);
+	for (unsigned int i = 0; i < mInput.size(); i++) {
+		pdData[i] = mInput[i];
 	}
 	return res;
 }
 
 //-----------------------------------------------------------------------------------------
-// parse projection geometry data
-astra::CProjectionGeometry2D* parseProjectionGeometryStruct(const mxArray* prhs)
+// turn a vector<vector<float32>> object to an mxArray
+mxArray* vector2DToMxArray(std::vector<std::vector<astra::float32> > mInput)
 {
-	// parse struct	
-	std::map<string, mxArray*> mStruct = parseStruct(prhs);
-
-	// create projection geometry object
-	string type = mex_util_get_string(mStruct["type"]);
-	if (type == "parallel") {
-
-		// detector_width
-		float32 fDetWidth = 1.0f;
-		mxArray* tmp = mStruct["detector_width"];
-		if (tmp != NULL) {
-			fDetWidth = (float32)(mxGetScalar(tmp));
-		}
-
-		// detector_count
-		int iDetCount = 100;
-		tmp = mStruct["detector_count"];
-		if (tmp != NULL) {
-			iDetCount = (int)(mxGetScalar(tmp));
-		}
-
-		// angles
-		float32* pfAngles;
-		int iAngleCount;
-		tmp = mStruct["projection_angles"];
-		if (tmp != NULL) {
-			double* angleValues = mxGetPr(tmp);
-			iAngleCount = mxGetN(tmp) * mxGetM(tmp);
-			pfAngles = new float32[iAngleCount];
-			for (int i = 0; i < iAngleCount; i++) {
-				pfAngles[i] = angleValues[i];
-			}
-		} else {
-			mexErrMsgTxt("'angles' not specified, error.");
-			return NULL;
-		}
-
-		// create projection geometry
-		return new astra::CParallelProjectionGeometry2D(iAngleCount,	// number of projections
-														iDetCount,		// number of detectors
-														fDetWidth,		// width of the detectors
-														pfAngles);		// angles array
-	} 
-	
-	else if (type == "fanflat") {
-
-		// detector_width
-		float32 fDetWidth = 1.0f;
-		mxArray* tmp = mStruct["detector_width"];
-		if (tmp != NULL) {
-			fDetWidth = (float32)(mxGetScalar(tmp));
-		}
-
-		// detector_count
-		int iDetCount = 100;
-		tmp = mStruct["detector_count"];
-		if (tmp != NULL) {
-			iDetCount = (int)(mxGetScalar(tmp));
-		}
-
-		// angles
-		float32* pfAngles;
-		int iAngleCount;
-		tmp = mStruct["projection_angles"];
-		if (tmp != NULL) {
-			double* angleValues = mxGetPr(tmp);
-			iAngleCount = mxGetN(tmp) * mxGetM(tmp);
-			pfAngles = new float32[iAngleCount];
-			for (int i = 0; i < iAngleCount; i++) {
-				pfAngles[i] = angleValues[i];
-			}
-		} else {
-			mexErrMsgTxt("'angles' not specified, error.");
-			return NULL;
-		}
-
-		// origin_source_dist
-		int iDistOriginSource = 100;
-		tmp = mStruct["origin_source_dist"];
-		if (tmp != NULL) {
-			iDistOriginSource = (int)(mxGetScalar(tmp));
-		}
+	unsigned int sizex = mInput.size();
+	if (sizex == 0) return mxCreateString("empty");
+	unsigned int sizey = mInput[0].size();
 
-		// origin_det_dist
-		int iDistOriginDet = 100;
-		tmp = mStruct["origin_det_dist"];
-		if (tmp != NULL) {
-			iDistOriginDet = (int)(mxGetScalar(tmp));
+	mxArray* res = mxCreateDoubleMatrix(sizex, sizey, mxREAL);
+	double* pdData = mxGetPr(res);
+	for (unsigned int i = 0; i < sizex; i++) {
+		for (unsigned int j = 0; j < sizey && j < mInput[i].size(); j++) {
+			pdData[j*sizex+i] = mInput[i][j];
 		}
-
-		// create projection geometry
-		return new astra::CFanFlatProjectionGeometry2D(iAngleCount,			// number of projections
-													   iDetCount,			// number of detectors
-													   fDetWidth,			// width of the detectors
-													   pfAngles,			// angles array
-													   iDistOriginSource,	// distance origin source
-													   iDistOriginDet);		// distance origin detector
-	}
-
-	else {
-		mexPrintf("Only parallel and fanflat projection geometry implemented.");
-		return NULL;
 	}
+	return res;
 }
 
 //-----------------------------------------------------------------------------------------
-// parse reconstruction geometry data
-astra::CVolumeGeometry2D* parseVolumeGeometryStruct(const mxArray* prhs)
+// turn a boost::any object to an mxArray
+mxArray* anyToMxArray(boost::any _any) 
 {
-	// parse struct	
-	std::map<string, mxArray*> mStruct = parseStruct(prhs);
-
-	std::map<string, mxArray*> mOptions = parseStruct(mStruct["option"]);
-
-	// GridColCount
-	int iWindowColCount = 128;
-	mxArray* tmp = mStruct["GridColCount"];
-	if (tmp != NULL) {
-		iWindowColCount = (int)(mxGetScalar(tmp));
-	} 
-
-	// GridRowCount
-	int iWindowRowCount = 128;
-	tmp = mStruct["GridRowCount"];
-	if (tmp != NULL) {
-		iWindowRowCount = (int)(mxGetScalar(tmp));
+	if (_any.type() == typeid(std::string)) {
+		std::string str = boost::any_cast<std::string>(_any);
+		return mxCreateString(str.c_str());     
 	}
-
-	// WindowMinX
-	float32 fWindowMinX = - iWindowColCount / 2;
-	tmp = mOptions["WindowMinX"];
-	if (tmp != NULL) {
-		fWindowMinX = (float32)(mxGetScalar(tmp));
-	} 
-
-	// WindowMaxX
-	float32 fWindowMaxX = iWindowColCount / 2;
-	tmp = mOptions["WindowMaxX"];
-	if (tmp != NULL) {
-		fWindowMaxX = (float32)(mxGetScalar(tmp));
-	} 
-
-	// WindowMinY
-	float32 fWindowMinY = - iWindowRowCount / 2;
-	tmp = mOptions["WindowMinY"];
-	if (tmp != NULL) {
-		fWindowMinY = (float32)(mxGetScalar(tmp));
-	} 
-
-	// WindowMaxX
-	float32 fWindowMaxY = iWindowRowCount / 2;
-	tmp = mOptions["WindowMaxY"];
-	if (tmp != NULL) {
-		fWindowMaxY = (float32)(mxGetScalar(tmp));
-	} 
-	
-	// create and return reconstruction geometry
-	return new astra::CVolumeGeometry2D(iWindowColCount, iWindowRowCount, 
-										fWindowMinX, fWindowMinY, 
-										fWindowMaxX, fWindowMaxY);
+	if (_any.type() == typeid(int)) {
+		return mxCreateDoubleScalar(boost::any_cast<int>(_any));
+	}
+	if (_any.type() == typeid(float32)) {
+		return mxCreateDoubleScalar(boost::any_cast<float32>(_any));
+	}
+	if (_any.type() == typeid(std::vector<astra::float32>)) {
+		return vectorToMxArray(boost::any_cast<std::vector<float32> >(_any));
+	}
+	if (_any.type() == typeid(std::vector<std::vector<astra::float32> >)) {
+		return vector2DToMxArray(boost::any_cast<std::vector<std::vector<float32> > >(_any));
+	}
+	return NULL;
 }
 
 
-//-----------------------------------------------------------------------------------------
-string matlab2string(const mxArray* pField)
-{
-	// is string?
-	if (mxIsChar(pField)) {
-		return mex_util_get_string(pField);
-	}
 
-	// is scalar?
-	if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) {
-		return boost::lexical_cast<string>(mxGetScalar(pField));
-	}
 
-	return "";
-}
+
+
+
+
 
 //-----------------------------------------------------------------------------------------
-// Options struct to xml node
-bool readOptions(XMLNode* node, const mxArray* pOptionStruct)
+// turn a MATLAB struct into a Config object
+Config* structToConfig(string rootname, const mxArray* pStruct)
 {
-	// loop all fields
-	int nfields = mxGetNumberOfFields(pOptionStruct);
-	for (int i = 0; i < nfields; i++) {
-		std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i));
-		const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i);
+	if (!mxIsStruct(pStruct)) {
+		mexErrMsgTxt("Input must be a struct.");
+		return NULL;
+	}
 
-		if (node->hasOption(sFieldName)) {
-			mexErrMsgTxt("Duplicate option");
-			return false;
-		}
-	
-		// string or scalar
-		if (mxIsChar(pField) || mex_is_scalar(pField)) {
-			string sValue = matlab2string(pField);
-			node->addOption(sFieldName, sValue);
-		} else
-		// numerical array
-		if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) {
-			if (!mxIsDouble(pField)) {
-				mexErrMsgTxt("Numeric input must be double.");
-				return false;
-			}
+	// create the document
+	Config* cfg = new Config();
+	cfg->initialize(rootname);
 
-			XMLNode* listbase = node->addChildNode("Option");
-			listbase->addAttribute("key", sFieldName);
-			listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField));
-			double* pdValues = mxGetPr(pField);
-			int index = 0;
-			for (unsigned int row = 0; row < mxGetM(pField); row++) {
-				for (unsigned int col = 0; col < mxGetN(pField); col++) {
-					XMLNode* item = listbase->addChildNode("ListItem");
-					item->addAttribute("index", index);
-					item->addAttribute("value", pdValues[col*mxGetM(pField)+row]);
-					index++;
-					delete item;
-				}
-			}
-			delete listbase;
-		} else {
-			mexErrMsgTxt("Unsupported option type");
-			return false;
-		}
+	// read the struct
+	bool ret = structToXMLNode(cfg->self, pStruct);
+	if (!ret) {
+		delete cfg;
+		mexErrMsgTxt("Error parsing struct.");
+		return NULL;		
 	}
-	return true;
+	return cfg;
 }
 
 //-----------------------------------------------------------------------------------------
-// struct to xml node
-bool readStruct(XMLNode* root, const mxArray* pStruct)
+bool structToXMLNode(XMLNode* node, const mxArray* pStruct) 
 {
 	// loop all fields
 	int nfields = mxGetNumberOfFields(pStruct);
@@ -350,27 +197,27 @@ bool readStruct(XMLNode* root, const mxArray* pStruct)
 
 		// string
 		if (mxIsChar(pField)) {
-			string sValue = matlab2string(pField);
+			string sValue = mexToString(pField);
 			if (sFieldName == "type") {
-				root->addAttribute("type", sValue);
+				node->addAttribute("type", sValue);
 			} else {
-				delete root->addChildNode(sFieldName, sValue);
+				delete node->addChildNode(sFieldName, sValue);
 			}
 		}
 
 		// scalar
-		if (mex_is_scalar(pField)) {
-			string sValue = matlab2string(pField);
-			delete root->addChildNode(sFieldName, sValue);
+		else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) {
+			string sValue = mexToString(pField);
+			delete node->addChildNode(sFieldName, sValue);
 		}
 
 		// numerical array
-		if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) {
+		else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) {
 			if (!mxIsDouble(pField)) {
 				mexErrMsgTxt("Numeric input must be double.");
 				return false;
 			}
-			XMLNode* listbase = root->addChildNode(sFieldName);
+			XMLNode* listbase = node->addChildNode(sFieldName);
 			listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField));
 			double* pdValues = mxGetPr(pField);
 			int index = 0;
@@ -386,16 +233,15 @@ bool readStruct(XMLNode* root, const mxArray* pStruct)
 			delete listbase;
 		}
 
-
 		// not castable to a single string
-		if (mxIsStruct(pField)) {
+		else if (mxIsStruct(pField)) {
 			if (sFieldName == "options" || sFieldName == "option" || sFieldName == "Options" || sFieldName == "Option") {
-				bool ret = readOptions(root, pField);
+				bool ret = optionsToXMLNode(node, pField);
 				if (!ret)
 					return false;
 			} else {
-				XMLNode* newNode = root->addChildNode(sFieldName);
-				bool ret = readStruct(newNode, pField);
+				XMLNode* newNode = node->addChildNode(sFieldName);
+				bool ret = structToXMLNode(newNode, pField);
 				delete newNode;
 				if (!ret)
 					return false;
@@ -406,93 +252,74 @@ bool readStruct(XMLNode* root, const mxArray* pStruct)
 
 	return true;
 }
-
 //-----------------------------------------------------------------------------------------
-// turn a MATLAB struct into an XML Document
-XMLDocument* struct2XML(string rootname, const mxArray* pStruct)
+// Options struct to xml node
+bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct)
 {
-	if (!mxIsStruct(pStruct)) {
-      mexErrMsgTxt("Input must be a struct.");
-	  return NULL;
-	}
-
-	// create the document
-	XMLDocument* doc = XMLDocument::createDocument(rootname);
-	XMLNode* rootnode = doc->getRootNode();
-
-	// read the struct
-	bool ret = readStruct(rootnode, pStruct);
-	delete rootnode;
-
-	if (!ret) {
-		delete doc;
-		doc = 0;
-	}
-
-	return doc;
-}
-
-
-
+	// loop all fields
+	int nfields = mxGetNumberOfFields(pOptionStruct);
+	for (int i = 0; i < nfields; i++) {
+		std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i));
+		const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i);
 
+		if (node->hasOption(sFieldName)) {
+			mexErrMsgTxt("Duplicate option");
+			return false;
+		}
+	
+		// string or scalar
+		if (mxIsChar(pField) || mexIsScalar(pField)) {
+			string sValue = mexToString(pField);
+			node->addOption(sFieldName, sValue);
+		}
+		// numerical array
+		else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) {
+			if (!mxIsDouble(pField)) {
+				mexErrMsgTxt("Numeric input must be double.");
+				return false;
+			}
 
-//-----------------------------------------------------------------------------------------
-// turn an std vector<float32> object to an mxArray
-mxArray* vectorToMxArray(std::vector<astra::float32> mInput)
-{
-	mxArray* res = mxCreateDoubleMatrix(1, mInput.size(), mxREAL);
-	double* pdData = mxGetPr(res);
-	for (unsigned int i = 0; i < mInput.size(); i++) {
-		pdData[i] = mInput[i];
+			XMLNode* listbase = node->addChildNode("Option");
+			listbase->addAttribute("key", sFieldName);
+			listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField));
+			double* pdValues = mxGetPr(pField);
+			int index = 0;
+			for (unsigned int row = 0; row < mxGetM(pField); row++) {
+				for (unsigned int col = 0; col < mxGetN(pField); col++) {
+					XMLNode* item = listbase->addChildNode("ListItem");
+					item->addAttribute("index", index);
+					item->addAttribute("value", pdValues[col*mxGetM(pField)+row]);
+					index++;
+					delete item;
+				}
+			}
+			delete listbase;
+		} else {
+			mexErrMsgTxt("Unsupported option type");
+			return false;
+		}
 	}
-	return res;
+	return true;
 }
-
 //-----------------------------------------------------------------------------------------
-// turn a vector<vector<float32>> object to an mxArray
-mxArray* vector2DToMxArray(std::vector<std::vector<astra::float32> > mInput)
+// turn a matlab struct into a c++ map
+std::map<std::string, mxArray*> parseStruct(const mxArray* pInput) 
 {
-	unsigned int sizex = mInput.size();
-	if (sizex == 0) return mxCreateString("empty");
-	unsigned int sizey = mInput[0].size();
+	std::map<std::string, mxArray*> res;
 
-	mxArray* res = mxCreateDoubleMatrix(sizex, sizey, mxREAL);
-	double* pdData = mxGetPr(res);
-	for (unsigned int i = 0; i < sizex; i++) {
-		for (unsigned int j = 0; j < sizey && j < mInput[i].size(); j++) {
-			pdData[j*sizex+i] = mInput[i][j];
-		}
+	// check type
+	if (!mxIsStruct(pInput)) {
+      mexErrMsgTxt("Input must be a struct.");
+	  return res;
 	}
-	return res;
-}
 
-//-----------------------------------------------------------------------------------------
-// turn a boost::any object to an mxArray
-mxArray* anyToMxArray(boost::any _any) 
-{
-	if (_any.type() == typeid(std::string)) {
-		std::string str = boost::any_cast<std::string>(_any);
-		return mxCreateString(str.c_str());     
-	}
-	if (_any.type() == typeid(int)) {
-		return mxCreateDoubleScalar(boost::any_cast<int>(_any));
-	}
-	if (_any.type() == typeid(float32)) {
-		return mxCreateDoubleScalar(boost::any_cast<float32>(_any));
-	}
-	if (_any.type() == typeid(std::vector<astra::float32>)) {
-		return vectorToMxArray(boost::any_cast<std::vector<float32> >(_any));
-	}
-	if (_any.type() == typeid(std::vector<std::vector<astra::float32> >)) {
-		return vector2DToMxArray(boost::any_cast<std::vector<std::vector<float32> > >(_any));
+	// get field names
+	int nfields = mxGetNumberOfFields(pInput);
+	for (int i = 0; i < nfields; i++) {
+		std::string sFieldName = std::string(mxGetFieldNameByNumber(pInput, i));
+		res[sFieldName] = mxGetFieldByNumber(pInput,0,i);
 	}
-	return NULL;
-}
-//-----------------------------------------------------------------------------------------
-// return true ig the argument is a scalar
-bool mex_is_scalar(const mxArray* pInput)
-{
-	return (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1);
+	return res;
 }
 
 
@@ -509,18 +336,41 @@ bool mex_is_scalar(const mxArray* pInput)
 
 
 //-----------------------------------------------------------------------------------------
+// turn a Config object into a MATLAB struct
 mxArray* configToStruct(astra::Config* cfg)
 {
-	return XMLNode2struct(cfg->self);
+	return XMLNodeToStruct(cfg->self);
 }
 
 //-----------------------------------------------------------------------------------------
-mxArray* XML2struct(astra::XMLDocument* xml)
+mxArray* XMLNodeToStruct(astra::XMLNode* node)
 {
-	XMLNode* node = xml->getRootNode();
-	mxArray* str = XMLNode2struct(xml->getRootNode());
-	delete node;
-	return str;
+	std::map<std::string, mxArray*> mList;
+	std::map<std::string, mxArray*> mOptions;
+
+	// type_attribute
+	if (node->hasAttribute("type")) {
+		mList["type"] = mxCreateString(node->getAttribute("type").c_str());
+	}
+
+	list<XMLNode*> nodes = node->getNodes();
+	for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) {
+		XMLNode* subnode = (*it);
+
+		// option
+		if (subnode->getName() == "Option") {
+			mOptions[subnode->getAttribute("key")] = stringToMxArray(subnode->getAttribute("value"));
+		}
+
+		// regular content
+		else {
+			mList[subnode->getName()] = stringToMxArray(subnode->getContent());
+		}
+		delete subnode;
+	}
+
+	if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions);
+	return buildStruct(mList);
 }
 
 //-----------------------------------------------------------------------------------------
@@ -583,36 +433,18 @@ mxArray* stringToMxArray(std::string input)
 	// string
 	return mxCreateString(input.c_str());
 }
-
 //-----------------------------------------------------------------------------------------
-mxArray* XMLNode2struct(astra::XMLNode* node)
+// turn a c++ map into a matlab struct
+mxArray* buildStruct(std::map<std::string, mxArray*> mInput) 
 {
-	std::map<std::string, mxArray*> mList;
-	std::map<std::string, mxArray*> mOptions;
-
-	// type_attribute
-	if (node->hasAttribute("type")) {
-		mList["type"] = mxCreateString(node->getAttribute("type").c_str());
-	}
-
-	list<XMLNode*> nodes = node->getNodes();
-	for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) {
-		XMLNode* subnode = (*it);
-
-		// option
-		if (subnode->getName() == "Option") {
-			mOptions[subnode->getAttribute("key")] = stringToMxArray(subnode->getAttribute("value"));
-		}
-
-		// regular content
-		else {
-			mList[subnode->getName()] = stringToMxArray(subnode->getContent());
-		}
-		delete subnode;
+	mwSize dims[2] = {1, 1};
+	mxArray* res = mxCreateStructArray(2,dims,0,0);
+	
+	for (std::map<std::string, mxArray*>::iterator it = mInput.begin(); it != mInput.end(); it++) {
+		mxAddField(res, (*it).first.c_str());
+		mxSetField(res, 0, (*it).first.c_str(), (*it).second);
 	}
-
-	if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions);
-	return buildStruct(mList);
+	return res;
 }
 
 
@@ -624,26 +456,3 @@ mxArray* XMLNode2struct(astra::XMLNode* node)
 
 
 
-//-----------------------------------------------------------------------------------------
-void get3DMatrixDims(const mxArray* x, mwSize *dims)
-{
-	const mwSize* mdims = mxGetDimensions(x);
-	mwSize dimCount = mxGetNumberOfDimensions(x);
-	if (dimCount == 1) {
-		dims[0] = mdims[0];
-		dims[1] = 1;
-		dims[2] = 1;
-	} else if (dimCount == 2) {
-		dims[0] = mdims[0];
-		dims[1] = mdims[1];
-		dims[2] = 1;
-	} else if (dimCount == 3) {
-		dims[0] = mdims[0];
-		dims[1] = mdims[1];
-		dims[2] = mdims[2];
-	} else {
-		dims[0] = 0;
-		dims[1] = 0;
-		dims[2] = 0;
-	}
-} 
diff --git a/matlab/mex/mexHelpFunctions.h b/matlab/mex/mexHelpFunctions.h
index 6c80f8c..f9ffcf2 100644
--- a/matlab/mex/mexHelpFunctions.h
+++ b/matlab/mex/mexHelpFunctions.h
@@ -43,42 +43,31 @@ $Id$
 #include "astra/Globals.h"
 #include "astra/Utilities.h"
 
-#include "astra/ParallelProjectionGeometry2D.h"
-#include "astra/FanFlatProjectionGeometry2D.h"
-#include "astra/ParallelProjectionGeometry3D.h"
-#include "astra/ParallelVecProjectionGeometry3D.h"
-#include "astra/ConeProjectionGeometry3D.h"
-#include "astra/ConeVecProjectionGeometry3D.h"
-
-#include "astra/VolumeGeometry2D.h"
-#include "astra/VolumeGeometry3D.h"
-
-
+#include "astra/Config.h"
 #include "astra/XMLDocument.h"
 #include "astra/XMLNode.h"
 
-std::string mex_util_get_string(const mxArray* pInput);
-bool isOption(std::list<std::string> lOptions, std::string sOption);
-
-bool mex_is_scalar(const mxArray* pInput);
+// utility functions
+string mexToString(const mxArray* pInput);
+bool mexIsScalar(const mxArray* pInput);
+void get3DMatrixDims(const mxArray* x, mwSize *dims);
 
-std::map<std::string, mxArray*> parseStruct(const mxArray* pInput);
-mxArray* buildStruct(std::map<std::string, mxArray*> mInput);
+// convert boost::any into a MALTAB object
 mxArray* vectorToMxArray(std::vector<astra::float32> mInput);
-
 mxArray* anyToMxArray(boost::any _any);
 
-astra::CProjectionGeometry2D* parseProjectionGeometryStruct(const mxArray*);
-astra::CVolumeGeometry2D* parseVolumeGeometryStruct(const mxArray*);
-
-astra::XMLDocument* struct2XML(string rootname, const mxArray* pStruct);
+// turn a MATLAB struct into a Config object
+astra::Config* structToConfig(string rootname, const mxArray* pStruct);
+bool structToXMLNode(astra::XMLNode* node, const mxArray* pStruct);
+bool optionsToXMLNode(astra::XMLNode* node, const mxArray* pOptionStruct);
+std::map<std::string, mxArray*> parseStruct(const mxArray* pInput);
 
+// turn a Config object into a MATLAB struct
 mxArray* configToStruct(astra::Config* cfg);
-mxArray* XML2struct(astra::XMLDocument* xml);
-mxArray* XMLNode2struct(astra::XMLNode* xml);
+mxArray* XMLNodeToStruct(astra::XMLNode* xml);
 mxArray* stringToMxArray(std::string input);
+mxArray* buildStruct(std::map<std::string, mxArray*> mInput);
 
 
-void get3DMatrixDims(const mxArray* x, mwSize *dims);
 
 #endif