Merge branch 'master' into volgeom3d

Conflicts:
	src/CudaBackProjectionAlgorithm3D.cpp

11 files changed, 53 insertions, 66 deletions

diff --git a/matlab/mex/astra_mex_algorithm_c.cpp b/matlab/mex/astra_mex_algorithm_c.cpp
index e4afa63..ec7aa72 100644
--- a/matlab/mex/astra_mex_algorithm_c.cpp
+++ b/matlab/mex/astra_mex_algorithm_c.cpp
@@ -81,7 +81,7 @@ void astra_mex_algorithm_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr
 	// turn MATLAB struct to an XML-based Config object
 	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 cfg;
 		mexErrMsgTxt("Unknown algorithm. \n");
diff --git a/matlab/mex/astra_mex_c.cpp b/matlab/mex/astra_mex_c.cpp
index 4a331f5..a9b9654 100644
--- a/matlab/mex/astra_mex_c.cpp
+++ b/matlab/mex/astra_mex_c.cpp
@@ -36,9 +36,9 @@ $Id$
 #include "mexInitFunctions.h"
 
 #include "astra/Globals.h"
-
+#ifdef ASTRA_CUDA
 #include "../cuda/2d/darthelper.h"
-
+#endif
 using namespace std;
 using namespace astra;
 
diff --git a/matlab/mex/astra_mex_data2d_c.cpp b/matlab/mex/astra_mex_data2d_c.cpp
index 9576896..909d229 100644
--- a/matlab/mex/astra_mex_data2d_c.cpp
+++ b/matlab/mex/astra_mex_data2d_c.cpp
@@ -149,7 +149,7 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra
 		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();
@@ -438,7 +438,7 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const
 		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();
diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp
index 6096adc..fe4ce37 100644
--- a/matlab/mex/astra_mex_data3d_c.cpp
+++ b/matlab/mex/astra_mex_data3d_c.cpp
@@ -346,7 +346,7 @@ void astra_mex_data3d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const
 		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();
diff --git a/matlab/mex/astra_mex_log_c.cpp b/matlab/mex/astra_mex_log_c.cpp
index ea4621e..905612c 100644
--- a/matlab/mex/astra_mex_log_c.cpp
+++ b/matlab/mex/astra_mex_log_c.cpp
@@ -55,7 +55,7 @@ void astra_mex_log_debug(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh
 	string filename = mexToString(prhs[1]);
 	int linenumber = (int)mxGetScalar(prhs[2]);
 	string message = mexToString(prhs[3]);
-	astra::CLogger::debug(filename.c_str(),linenumber,message.c_str());
+	astra::CLogger::debug(filename.c_str(),linenumber,"%s",message.c_str());
 }
 
 //-----------------------------------------------------------------------------------------
@@ -75,7 +75,7 @@ void astra_mex_log_info(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs
 	string filename = mexToString(prhs[1]);
 	int linenumber = (int)mxGetScalar(prhs[2]);
 	string message = mexToString(prhs[3]);
-	astra::CLogger::info(filename.c_str(),linenumber,message.c_str());
+	astra::CLogger::info(filename.c_str(),linenumber,"%s",message.c_str());
 }
 
 //-----------------------------------------------------------------------------------------
@@ -95,7 +95,7 @@ void astra_mex_log_warn(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs
 	string filename = mexToString(prhs[1]);
 	int linenumber = (int)mxGetScalar(prhs[2]);
 	string message = mexToString(prhs[3]);
-	astra::CLogger::warn(filename.c_str(),linenumber,message.c_str());
+	astra::CLogger::warn(filename.c_str(),linenumber,"%s",message.c_str());
 }
 
 //-----------------------------------------------------------------------------------------
@@ -115,7 +115,7 @@ void astra_mex_log_error(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh
 	string filename = mexToString(prhs[1]);
 	int linenumber = (int)mxGetScalar(prhs[2]);
 	string message = mexToString(prhs[3]);
-	astra::CLogger::error(filename.c_str(),linenumber,message.c_str());
+	astra::CLogger::error(filename.c_str(),linenumber,"%s",message.c_str());
 }
 
 //-----------------------------------------------------------------------------------------
diff --git a/matlab/mex/astra_mex_projector3d_c.cpp b/matlab/mex/astra_mex_projector3d_c.cpp
index c3b547f..e25802c 100644
--- a/matlab/mex/astra_mex_projector3d_c.cpp
+++ b/matlab/mex/astra_mex_projector3d_c.cpp
@@ -137,7 +137,9 @@ void astra_mex_projector3d_get_projection_geometry(int nlhs, mxArray* plhs[], in
 
 	// step3: get projection_geometry and turn it into a MATLAB struct
 	if (1 <= nlhs) {
-		plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration());
+		Config *cfg = pProjector->getProjectionGeometry()->getConfiguration();
+		plhs[0] = configToStruct(cfg);
+		delete cfg;
 	}
 }
 
@@ -163,7 +165,9 @@ void astra_mex_projector3d_get_volume_geometry(int nlhs, mxArray* plhs[], int nr
 
 	// step3: get projection_geometry and turn it into a MATLAB struct
 	if (1 <= nlhs) {
-		plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration());
+		Config *cfg = pProjector->getVolumeGeometry()->getConfiguration();
+		plhs[0] = configToStruct(cfg);
+		delete cfg;
 	}
 }
 
diff --git a/matlab/mex/astra_mex_projector_c.cpp b/matlab/mex/astra_mex_projector_c.cpp
index 204ba8e..bf701af 100644
--- a/matlab/mex/astra_mex_projector_c.cpp
+++ b/matlab/mex/astra_mex_projector_c.cpp
@@ -160,7 +160,9 @@ void astra_mex_projector_projection_geometry(int nlhs, mxArray* plhs[], int nrhs
 
 	// step3: get projection_geometry and turn it into a MATLAB struct
 	if (1 <= nlhs) {
-		plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration());
+		Config *cfg =  pProjector->getProjectionGeometry()->getConfiguration();
+		plhs[0] = configToStruct(cfg);
+		delete cfg;
 	}
 }
 
@@ -189,8 +191,9 @@ void astra_mex_projector_volume_geometry(int nlhs, mxArray* plhs[], int nrhs, co
 
 	// step3: get projection_geometry and turn it into a MATLAB struct
 	if (1 <= nlhs) {
-		plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration());
-
+		Config *cfg = pProjector->getVolumeGeometry()->getConfiguration();
+		plhs[0] = configToStruct(cfg);
+		delete cfg;
 	}
 }
 
diff --git a/matlab/mex/mexDataManagerHelpFunctions.cpp b/matlab/mex/mexDataManagerHelpFunctions.cpp
index d482428..1794abb 100644
--- a/matlab/mex/mexDataManagerHelpFunctions.cpp
+++ b/matlab/mex/mexDataManagerHelpFunctions.cpp
@@ -285,7 +285,7 @@ allocateDataObject(const std::string & sDataType,
 		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();
diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp
index c0ac711..58e84d2 100644
--- a/matlab/mex/mexHelpFunctions.cpp
+++ b/matlab/mex/mexHelpFunctions.cpp
@@ -185,7 +185,7 @@ Config* structToConfig(string rootname, const mxArray* pStruct)
 }
 
 //-----------------------------------------------------------------------------------------
-bool structToXMLNode(XMLNode* node, const mxArray* pStruct) 
+bool structToXMLNode(XMLNode node, const mxArray* pStruct) 
 {
 	// loop all fields
 	int nfields = mxGetNumberOfFields(pStruct);
@@ -199,16 +199,16 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct)
 		if (mxIsChar(pField)) {
 			string sValue = mexToString(pField);
 			if (sFieldName == "type") {
-				node->addAttribute("type", sValue);
+				node.addAttribute("type", sValue);
 			} else {
-				delete node->addChildNode(sFieldName, sValue);
+				node.addChildNode(sFieldName, sValue);
 			}
 		}
 
 		// scalar
 		else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) {
 			string sValue = mexToString(pField);
-			delete node->addChildNode(sFieldName, sValue);
+			node.addChildNode(sFieldName, sValue);
 		}
 
 		// numerical array
@@ -217,20 +217,9 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct)
 				mexErrMsgTxt("Numeric input must be double.");
 				return false;
 			}
-			XMLNode* listbase = node->addChildNode(sFieldName);
-			listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField));
+			XMLNode listbase = node.addChildNode(sFieldName);
 			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;
+			listbase.setContent(pdValues, mxGetN(pField), mxGetM(pField), true);
 		}
 
 		// not castable to a single string
@@ -240,9 +229,8 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct)
 				if (!ret)
 					return false;
 			} else {
-				XMLNode* newNode = node->addChildNode(sFieldName);
+				XMLNode newNode = node.addChildNode(sFieldName);
 				bool ret = structToXMLNode(newNode, pField);
-				delete newNode;
 				if (!ret)
 					return false;
 			}
@@ -254,7 +242,7 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct)
 }
 //-----------------------------------------------------------------------------------------
 // Options struct to xml node
-bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct)
+bool optionsToXMLNode(XMLNode node, const mxArray* pOptionStruct)
 {
 	// loop all fields
 	int nfields = mxGetNumberOfFields(pOptionStruct);
@@ -262,7 +250,7 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct)
 		std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i));
 		const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i);
 
-		if (node->hasOption(sFieldName)) {
+		if (node.hasOption(sFieldName)) {
 			mexErrMsgTxt("Duplicate option");
 			return false;
 		}
@@ -270,7 +258,7 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct)
 		// string or scalar
 		if (mxIsChar(pField) || mexIsScalar(pField)) {
 			string sValue = mexToString(pField);
-			node->addOption(sFieldName, sValue);
+			node.addOption(sFieldName, sValue);
 		}
 		// numerical array
 		else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) {
@@ -279,21 +267,10 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct)
 				return false;
 			}
 
-			XMLNode* listbase = node->addChildNode("Option");
-			listbase->addAttribute("key", sFieldName);
-			listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField));
+			XMLNode listbase = node.addChildNode("Option");
+			listbase.addAttribute("key", sFieldName);
 			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;
+			listbase.setContent(pdValues, mxGetN(pField), mxGetM(pField), true);
 		} else {
 			mexErrMsgTxt("Unsupported option type");
 			return false;
@@ -343,30 +320,33 @@ mxArray* configToStruct(astra::Config* cfg)
 }
 
 //-----------------------------------------------------------------------------------------
-mxArray* XMLNodeToStruct(astra::XMLNode* node)
+mxArray* XMLNodeToStruct(astra::XMLNode node)
 {
 	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());
+	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);
+	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"));
+		if (subnode.getName() == "Option") {
+			if(subnode.hasAttribute("value")){
+				mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getAttribute("value"));
+			}else{
+				mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getContent());
+			}
 		}
 
 		// regular content
 		else {
-			mList[subnode->getName()] = stringToMxArray(subnode->getContent());
+			mList[subnode.getName()] = stringToMxArray(subnode.getContent());
 		}
-		delete subnode;
 	}
 
 	if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions);
diff --git a/matlab/mex/mexHelpFunctions.h b/matlab/mex/mexHelpFunctions.h
index f9ffcf2..3ac5bd8 100644
--- a/matlab/mex/mexHelpFunctions.h
+++ b/matlab/mex/mexHelpFunctions.h
@@ -58,13 +58,13 @@ mxArray* anyToMxArray(boost::any _any);
 
 // 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);
+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* XMLNodeToStruct(astra::XMLNode* xml);
+mxArray* XMLNodeToStruct(astra::XMLNode xml);
 mxArray* stringToMxArray(std::string input);
 mxArray* buildStruct(std::map<std::string, mxArray*> mInput);
 
diff --git a/matlab/mex/mexInitFunctions.cpp b/matlab/mex/mexInitFunctions.cpp
index d8a50d7..89a31a1 100644
--- a/matlab/mex/mexInitFunctions.cpp
+++ b/matlab/mex/mexInitFunctions.cpp
@@ -8,7 +8,7 @@ bool mexIsInitialized=false;
  *
  */
 void logCallBack(const char *msg, size_t len){
-    mexPrintf(msg);
+    mexPrintf("%s",msg);
 }
 
 /**