Index: /issm/branches/trunk-larour-NatGeoScience2016/src/c/modules/Bamgx/Bamgx.cpp
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/src/c/modules/Bamgx/Bamgx.cpp	(revision 22085)
+++ /issm/branches/trunk-larour-NatGeoScience2016/src/c/modules/Bamgx/Bamgx.cpp	(revision 22086)
@@ -149,7 +149,4 @@
 		}
 
-		//Add geometry metric if provided
-		if(bamgopts->geometricalmetric) BTh.AddGeometryMetric(bamgopts);
-
 		//Smoothe metric
 		BTh.SmoothMetric(bamgopts->gradation);
Index: /issm/branches/trunk-larour-NatGeoScience2016/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp	(revision 22085)
+++ /issm/branches/trunk-larour-NatGeoScience2016/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp	(revision 22086)
@@ -24,10 +24,10 @@
 	R2     r;
 	I2     I;
-	int    i,j;
+	int    i,j,k;
 	int    it;
 	int    i0,i1,i2;
 	double areacoord[3];
 	double aa,bb;
-	Icoor2 dete[3];
+	long long dete[3];
 
 	/*Checks*/
@@ -66,4 +66,14 @@
 	}
 
+	/*Create Single vertex to element connectivity*/
+	int* connectivity = xNew<int>(nods_data);
+	for(i=0;i<nels_data;i++){
+		for(j=0;j<3;j++){
+			k = index_data[i*3+j]-1;
+			_assert_(k>=0 & k<nods_data);
+			connectivity[k]=i;
+		}
+	}
+
 	/*Loop over output nodes*/
 	for(i=0;i<N_interp;i++){
@@ -88,7 +98,7 @@
 
 			/*Area coordinates*/
-			areacoord[0]= (double) dete[0]/tb.det;
-			areacoord[1]= (double) dete[1]/tb.det;
-			areacoord[2]= (double) dete[2]/tb.det;
+			areacoord[0]= reCast<double>(dete[0])/reCast<double>(tb.det);
+			areacoord[1]= reCast<double>(dete[1])/reCast<double>(tb.det);
+			areacoord[2]= reCast<double>(dete[2])/reCast<double>(tb.det);
 			/*3 vertices of the triangle*/
 			i0=Th->GetId(tb[0]);
@@ -137,17 +147,16 @@
 			/*If we fall outside of the convex or outside of the mesh, return NaN*/
 			if(tb.det<0 || reft[it]<0){
-				for (j=0;j<N_data;j++){
-					data_interp[i*N_data+j]=NAN;
-				}
+				_assert_(i0>=0 & i0<nods_data);
+				it=connectivity[i0]; //or i1 or i2
+				_assert_(it>=0 && it<nels_data);
+				for(j=0;j<N_data;j++) data_interp[i*N_data+j]=data[N_data*it+j];
 			}
 			else{
+				/*Inside the mesh!*/
 				if(it<0 || it>=nels_data){
 					_error_("Triangle number " << it << " not in [0 " << nels_data
 								<< "], report bug to developers (interpolation point: " <<x_interp[i]<<" "<<y_interp[i]<<")");
 				}
-				for (j=0;j<N_data;j++){
-
-					data_interp[i*N_data+j]=data[N_data*it+j];
-				}
+				for (j=0;j<N_data;j++) data_interp[i*N_data+j]=data[N_data*it+j];
 			}
 		}
@@ -158,4 +167,5 @@
 	delete Th;
 	xDelete<long>(reft);
+	xDelete<int>(connectivity);
 	*pdata_interp=data_interp;
 	return 1;
Index: /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/ContourToMesh.m
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/ContourToMesh.m	(revision 22085)
+++ /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/ContourToMesh.m	(revision 22086)
@@ -6,5 +6,5 @@
 %	
 %   index,x,y: mesh triangulation
-%   contourname: name of .exp file containing the contours.
+%   contourname: name of .exp or .shp file containing the contours.
 %   interptype: string defining type of interpolation ('element', or 'node').
 %   edgevalue: integer (0, 1, or 2) defining the value associated to the nodes on the edges of the polygons.
@@ -25,4 +25,15 @@
 end
 
+%Some conversion of files: 
+[path,name,ext]=fileparts(contourname); 
+if strcmpi(ext,'.shp'),
+	%read contour from shapefile:
+	contour=shpread(contourname); 
+
+	%write it to a temporary filename: 
+	contourname=tempname; 
+	expwrite(contour,contourname);
+end
+
 %Call mex module
 [in_nod,in_elem] = ContourToMesh_matlab(index,x,y,contourname,interptype,edgevalue);
Index: /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/ContourToNodes.m
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/ContourToNodes.m	(revision 22085)
+++ /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/ContourToNodes.m	(revision 22086)
@@ -6,5 +6,5 @@
 %
 %   x,y: list of nodes
-%   contourname: name of .exp file containing the contours, or resulting structure from call to expread
+%   contourname: name of Argus or Shape file containing the contours, or resulting structure from call to expread
 %   edgevalue: integer (0, 1 or 2) defining the value associated to the nodes on the edges of the polygons
 %   flags: vector of flags (0 or 1), of size nodes
@@ -16,13 +16,15 @@
 end
 
-%Some conversion of files: 
-[path,name,ext]=fileparts(contourname); 
-if strcmpi(ext,'.shp'),
-	%read contour from shapefile:
-	contour=shpread(contourname); 
+%Some conversion of files:  
+if ischar(contourname),
+	[path,name,ext]=fileparts(contourname); 
+	if strcmpi(ext,'.shp'),
+		%read contour from shapefile:
+		contour=shpread(contourname); 
 
-	%write it to a temporary filename: 
-	contourname=tempname; 
-	expwrite(contour,contourname);
+		%write it to a temporary filename: 
+		contourname=tempname; 
+		expwrite(contour,contourname);
+	end
 end
 
Index: /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/MeshProfileIntersection.m
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/MeshProfileIntersection.m	(revision 22085)
+++ /issm/branches/trunk-larour-NatGeoScience2016/src/m/modules/MeshProfileIntersection.m	(revision 22086)
@@ -7,5 +7,5 @@
 %	   input:
 %	        index,x,y is a triangulation
-%	        filename: name of Argus style .exp file containing the segments (can be groups of disconnected segments)
+%	        filename: name of Argus or Shape file containing the segments (can be groups of disconnected segments)
 %	   output:
 %	        segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremities for a segment 
@@ -19,4 +19,13 @@
 end
 
+[path,name,ext]=fileparts(filename); 
+if strcmpi(ext,'.shp'),
+	
+	%convert to expfile and store in a temporary directory: 
+	oldfilename=filename;
+	filename=[tempname '.exp'];
+	shp2exp(oldfilename,filename);
+end
+
 % Call mex module
 [segments] = MeshProfileIntersection_matlab(index,x,y,filename);
Index: /issm/branches/trunk-larour-NatGeoScience2016/src/wrappers/matlab/io/FetchMatlabData.cpp
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/src/wrappers/matlab/io/FetchMatlabData.cpp	(revision 22085)
+++ /issm/branches/trunk-larour-NatGeoScience2016/src/wrappers/matlab/io/FetchMatlabData.cpp	(revision 22086)
@@ -537,5 +537,4 @@
 	FetchData(&bamgopts->gradation,mxGetField(dataref,0,"gradation"));
 	FetchData(&bamgopts->Hessiantype,mxGetField(dataref,0,"Hessiantype"));
-	FetchData(&bamgopts->MaxCornerAngle,mxGetField(dataref,0,"MaxCornerAngle"));
 	FetchData(&bamgopts->maxnbv,mxGetField(dataref,0,"maxnbv"));
 	FetchData(&bamgopts->maxsubdiv,mxGetField(dataref,0,"maxsubdiv"));
@@ -545,9 +544,7 @@
 	FetchData(&bamgopts->omega,mxGetField(dataref,0,"omega"));
 	FetchData(&bamgopts->power,mxGetField(dataref,0,"power"));
-	FetchData(&bamgopts->random,mxGetField(dataref,0,"random"));
 	FetchData(&bamgopts->verbose,mxGetField(dataref,0,"verbose"));
 
 	FetchData(&bamgopts->Crack,mxGetField(dataref,0,"Crack"));
-	FetchData(&bamgopts->geometricalmetric,mxGetField(dataref,0,"geometricalmetric"));
 	FetchData(&bamgopts->KeepVertices,mxGetField(dataref,0,"KeepVertices"));
 	FetchData(&bamgopts->splitcorners,mxGetField(dataref,0,"splitcorners"));
@@ -999,27 +996,31 @@
 mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number,const char* field){
 
-	//output
-	mxArray* mxfield=NULL;
-
-	//input
-	mxArray    *inputs[2];
-	mxArray    *pindex      = NULL;
-	const char *fnames[2];
-	mwSize      ndim        = 2;
-	mwSize      onebyone[2] = {1,1};
-
-	//We want to call the subsasgn method, and get the returned array.This ensures that if we are running 
-	//large sized problems, the data is truly loaded from disk by the model subsasgn class method.
-	inputs[0]=(mxArray*)pmxa_array; //this is the model
-
-	//create index structure used in the assignment (index.type='.' and index.subs='x' for field x for ex)
-	fnames[0] = "type";
-	fnames[1] = "subs";
-	pindex=mxCreateStructArray( ndim,onebyone,2,fnames);
-	mxSetField( pindex, 0, "type",mxCreateString("."));
-	mxSetField( pindex, 0, "subs",mxCreateString(field));
-	inputs[1]=pindex;
-
-	mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref");
+	/*Output*/
+	mxArray *mxfield = NULL;
+
+	if(mxIsStruct(pmxa_array)){
+		mxfield = mxGetField(pmxa_array,number,field);
+	}
+	else{
+		/*This is an object, mxGetField returns NULL in old version of matlab (we do not have access to them)*/
+
+		/*Intermediaries*/
+		mxArray    *inputs[2];
+		mwSize      ndim        = 2;
+		mwSize      onebyone[2] = {1,1};
+
+		/*create index structure used in the assignment (index.type='.' and index.subs='x' for field x*/
+		const char *fnames[2];
+		fnames[0] = "type"; fnames[1] = "subs";
+		mxArray* pindex=mxCreateStructArray( ndim,onebyone,2,fnames);
+		mxSetField( pindex, 0, "type",mxCreateString("."));
+		mxSetField( pindex, 0, "subs",mxCreateString(field));
+		inputs[0]=(mxArray*)pmxa_array; //this is the model
+		inputs[1]=pindex;
+
+		mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref");
+	}
+
+	if(mxfield == NULL) _error_("Could not find field "<< field <<" in structure");
 
 	return mxfield;
@@ -1091,96 +1092,4 @@
 
 	return(ochar);
-}/*}}}*/
-GenericOption<Options**>* OptionStructParse( char* name, const mxArray* prhs[]){ /*{{{*/
-
-	int            i;
-	char           namei[161];
-	Option*                   option      = NULL;
-	GenericOption<Options**>  *ostruct    = NULL;
-	const mwSize  *ipt        = NULL;
-	const mxArray *structi;
-	mwIndex        sindex;
-
-	/*check and parse the name  */
-	ostruct=new GenericOption<Options**>();
-	ostruct->name =xNew<char>(strlen(name)+1);
-	memcpy(ostruct->name,name,(strlen(name)+1)*sizeof(char));
-
-	/*check and parse the value  */
-	if (!mxIsClass(prhs[0],"struct")){
-		_error_("Value of option \"" << ostruct->name  << "\" must be class \"struct\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
-	}
-	ostruct->numel=mxGetNumberOfElements(prhs[0]);
-	ostruct->ndims=mxGetNumberOfDimensions(prhs[0]);
-	ipt           =mxGetDimensions(prhs[0]);
-	ostruct->size =xNew<int>(ostruct->ndims);
-	for (i=0; i<ostruct->ndims; i++) ostruct->size[i]=(int)ipt[i];
-	if (ostruct->numel) ostruct->value=xNew<Options*>(ostruct->numel);
-
-	/*loop through and process each element of the struct array  */
-	for (sindex=0; sindex<ostruct->numel; sindex++) {
-		ostruct->value[sindex]=new Options;
-
-		/*loop through and process each field for the element  */
-		for (i=0; i<mxGetNumberOfFields(prhs[0]); i++) {
-			sprintf(namei,"%s.%s",name,mxGetFieldNameByNumber(prhs[0],i));
-			structi=mxGetFieldByNumber(prhs[0],sindex,i);
-
-			option=(Option*)OptionParse(namei,&structi);
-			ostruct->value[sindex]->AddObject((Object*)option);
-			option=NULL;
-		}
-	}
-
-	return(ostruct);
-}/*}}}*/
-GenericOption<Options*>* OptionCellParse( char* name, const mxArray* prhs[]){ /*{{{*/
-
-	int            i;
-	int           *dims;
-	char           namei[161];
-	char           cstr[81];
-	GenericOption<Options*> *ocell      = NULL;
-	Option        *option     = NULL;
-	const mwSize  *ipt        = NULL;
-	const mxArray *celli;
-	mwIndex        cindex;
-
-	/*check and parse the name  */
-	ocell=new GenericOption<Options*>();
-	ocell->name =xNew<char>(strlen(name)+1);
-	memcpy(ocell->name,name,(strlen(name)+1)*sizeof(char));
-
-	/*check and parse the value  */
-	if (!mxIsClass(prhs[0],"cell")){
-		_error_("Value of option \"" << ocell->name  << "\" must be class \"cell\", not class \"" << mxGetClassName(prhs[0]) <<"\".");
-	}
-
-	ocell->numel=mxGetNumberOfElements(prhs[0]);
-	ocell->ndims=mxGetNumberOfDimensions(prhs[0]);
-	ipt         =mxGetDimensions(prhs[0]);
-	ocell->size =xNew<int>(ocell->ndims);
-	for (i=0; i<ocell->ndims; i++) ocell->size[i]=(int)ipt[i];
-	ocell->value=new Options;
-
-	/*loop through and process each element of the cell array  */
-	dims=xNew<int>(ocell->ndims);
-	for (cindex=0; cindex<ocell->numel; cindex++) {
-		ColumnWiseDimsFromIndex(dims,(int)cindex,ocell->size,ocell->ndims);
-		StringFromDims(cstr,dims,ocell->ndims);
-		#ifdef _INTEL_WIN_
-			_snprintf(namei,161,"%s%s",name,cstr);
-		#else
-			snprintf(namei,161,"%s%s",name,cstr);
-		#endif
-		celli=mxGetCell(prhs[0],cindex);
-
-		option=(Option*)OptionParse(namei,&celli);
-		ocell->value->AddObject((Object*)option);
-		option=NULL;
-	}
-	xDelete<int>(dims);
-
-	return(ocell);
 }/*}}}*/
 Option* OptionParse(char* name, const mxArray* prhs[]){ /*{{{*/
@@ -1198,15 +1107,6 @@
 	else if(mxIsClass(prhs[0],"char"))
 	 option=(Option*)OptionCharParse(name,prhs);
-	else if(mxIsClass(prhs[0],"struct"))
-	 option=(Option*)OptionStructParse(name,prhs);
-	else if(mxIsClass(prhs[0],"cell"))
-	 option=(Option*)OptionCellParse(name,prhs);
 	else {
-		_printf0_("  Converting value of option \"" << name << "\" from unrecognized class \"" << mxGetClassName(prhs[0]) << "\" to class \"" << "struct" << "\".\n");
-		if (!mexCallMATLAB(1,lhs,1,(mxArray**)prhs,"struct")) {
-			option=(Option*)OptionStructParse(name,(const mxArray**)lhs);
-			mxDestroyArray(lhs[0]);
-		}
-		else _error_("Second argument value of option \""<< name <<"\" is of unrecognized class \""<< mxGetClassName(prhs[0]) <<"\".");
+		_error_("Second argument value of option \""<< name <<"\" is of unrecognized class \""<< mxGetClassName(prhs[0]) <<"\".");
 	}