Index: /issm/trunk-jpl/src/mex/TriMesh/TriMesh.cpp
===================================================================
--- /issm/trunk-jpl/src/mex/TriMesh/TriMesh.cpp	(revision 11931)
+++ /issm/trunk-jpl/src/mex/TriMesh/TriMesh.cpp	(revision 11932)
@@ -1,305 +1,59 @@
 /*
- * TriMesh: out of a domain outline file ( Argus format ), 
- * use the Triangle package to create a triangular mesh 
- *
+ * TriMesh: mesh a domain using an .exp file
  */
 
 #include "./TriMesh.h"
 
-
-void mexFunction(	int nlhs, mxArray* plhs[],
-					int nrhs, const mxArray* prhs[] )
-{
-
-
-	/*Matlab arrays: */
-	mxArray* pmxa_array=NULL;
-	int i,j;
-	int counter,counter2,backcounter;
-	int prhs_counter;
+WRAPPER(TriMesh, char* DOMAINOUTLINE, double AREA, bool ORDER){ 
 	
-	/* returned quantities: */
-
-	double* index=NULL;
-	double* x=NULL;
-	double* y=NULL;
-	double* segments=NULL;
-	double*    segmentmarkerlist=NULL;
-
 	/* input: */
 	char*  domainname=NULL;
-	char*  riftname=NULL;
 	double area;
-	char*  order=NULL;
+	bool   order;
+
+	/*intermediary: */
+	DataSet* domain=NULL;
+
+	/* output: */
+	Matrix* index=NULL;
+	Vector* x=NULL;
+	Vector* y=NULL;
+	Matrix* segments=NULL;
+	Vector* segmentmarkerlist=NULL;
+
+	/*Boot module: */
+	MODULEBOOT();
+
+	/*checks on arguments on the matlab side: */
+	CHECKARGUMENTS(NLHS,NRHS,&TriMeshUsage);
 	
-	/*Domain outline variables: */
-	int      nprof;
-	int*     profnvertices=NULL;
-	double** pprofx=NULL;
-	double** pprofy=NULL;
-	double*  xprof=NULL;
-	double*  yprof=NULL;
-	int      numberofpoints;
+	/*Fetch data needed for meshing: */
+	FetchData(&domainname,DOMAINOUTLINE);
+	FetchData(&area,AREA);
+	FetchData(&order,ORDER);
 
-	/*Rift outline variables: */
-	int      numrifts;
-	int*     riftsnumvertices=NULL;
-	double** riftsverticesx=NULL;
-	double** riftsverticesy=NULL;
+	/*Read domain outline: */
+	domain=DomainOutlineRead(domainname,false);
 
-	/* Triangle structures: */
-	struct triangulateio in,out;
-	char   options[256];
+	/*call x core: */
+	TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,area,order);
 
-	/* verify correct usage: */
-	if (nlhs==0 && nrhs==0) {
-		/* special case: */
-		TriMeshUsage();
-		return;
-	}
+	/*write outputs: */
+	WriteData(INDEX,index);
+	WriteData(X,x);
+	WriteData(Y,y);
+	WriteData(SEGMENTS,segments);
+	WriteData(SEGMENTMARKERLIST,segmentmarkerlist);
 
-	if (!(  (nlhs==5) ||(nrhs==2) || (nrhs==3)  || (nrhs==4) )){
-		mexPrintf("   %s format error.\n", __FUNCT__);
-		TriMeshUsage();
-		printf("   ");
-		mexErrMsgTxt(" ");
-	}
+	/*free ressources: */
+	delete domain;
+	xdelete(&index);
+	xdelete(&x);
+	xdelete(&y);
+	xdelete(&segments);
+	xdelete(&segmentmarkerlist);
 
-	/*Fetch data needed by Triangle: */
-
-	prhs_counter=0;
-	/*First recover the domain outline file name: */
-	if (!mxIsChar(prhs[prhs_counter])){
-		mexPrintf("%s%s\n",__FUNCT__," error message; first argument should be the domain outline file name!");
-		mexErrMsgTxt(" ");
-	}
-	domainname = (char *) mxMalloc((mxGetN(prhs[prhs_counter])+1)*sizeof(char));
-	mxGetString(prhs[prhs_counter],domainname,mxGetN(prhs[prhs_counter])+1);
-
-	/*Look for optional rifts file name: */
-	prhs_counter++;
-	if (mxIsChar(prhs[prhs_counter])){
-		riftname = (char *) mxMalloc((mxGetN(prhs[prhs_counter])+1)*sizeof(char));
-		mxGetString(prhs[prhs_counter],riftname,mxGetN(prhs[prhs_counter])+1);
-		prhs_counter++;
-	}
-
-	/*Recover the mesh density desired:*/
-	area=mxGetScalar(prhs[prhs_counter]);
-
-	/*Optionaly, recover desired order: */
-	prhs_counter++;
-	if (mxIsChar(prhs[prhs_counter])){
-		order = (char *) mxMalloc((mxGetN(prhs[prhs_counter])+1)*sizeof(char));
-		mxGetString(prhs[prhs_counter],order,mxGetN(prhs[prhs_counter])+1);
-	}
-	
-	/*Start reading the domain outline file: */
-	if(!DomainOutlineRead(&nprof,&profnvertices,&pprofx,&pprofy,NULL,domainname,false)){
-		printf("%s%s%s\n",__FUNCT__," error message reading domain outline ",domainname);
-		mexErrMsgTxt(" ");
-	}
-
-	/*Read rifts file if present: */
-	if(riftname){
-		if(!DomainOutlineRead(&numrifts,&riftsnumvertices,&riftsverticesx,&riftsverticesy,NULL,riftname,false)){
-			printf("%s%s%s\n",__FUNCT__," error message reading rifts outline ",riftname);
-			mexErrMsgTxt(" ");
-		}
-	}
-
-	/*Create initial triangulation to call triangulate():*/
-	numberofpoints=0;
-	for (i=0;i<nprof;i++){
-		numberofpoints+=profnvertices[i];
-	}
-	if (riftname){
-		for (i=0;i<numrifts;i++){
-			numberofpoints+=riftsnumvertices[i];
-		}
-	}
-	in.numberofpoints=numberofpoints;
-
-	in.numberofpointattributes=1;
-	in.pointlist = (REAL *) mxMalloc(in.numberofpoints * 2 * sizeof(REAL));
-
-	counter=0;
-	for (i=0;i<nprof;i++){
-		xprof=pprofx[i];
-		yprof=pprofy[i];
-		for (j=0;j<profnvertices[i];j++){
-			in.pointlist[2*counter+0]=xprof[j];
-			in.pointlist[2*counter+1]=yprof[j];
-			counter++;
-		}
-	}
-	if(riftname){
-		for (i=0;i<numrifts;i++){
-			xprof=riftsverticesx[i];
-			yprof=riftsverticesy[i];
-			for (j=0;j<riftsnumvertices[i];j++){
-				in.pointlist[2*counter+0]=xprof[j];
-				in.pointlist[2*counter+1]=yprof[j];
-				counter++;
-			}
-		}
-	}
-	
-	in.pointattributelist = (REAL *) mxMalloc(in.numberofpoints *
-										  in.numberofpointattributes *
-										  sizeof(REAL));
-	for (i=0;i<in.numberofpoints;i++){
-		in.pointattributelist[i] = 0.0;
-	}
-	in.pointmarkerlist = (int *) mxMalloc(in.numberofpoints * sizeof(int));
-	for(i=0;i<in.numberofpoints;i++){
-		in.pointmarkerlist[i] = 0;
-	}
-
-	/*Build segments: */
-	/*Figure out number of segments: holes and closed outlines have as many segments as vertices, 
-	 *for rifts, we have one less segment as we have vertices*/
-	in.numberofsegments=0;
-	for (i=0;i<nprof;i++){
-		in.numberofsegments+=profnvertices[i];
-	}
-	if (riftname){
-		for (i=0;i<numrifts;i++){
-			in.numberofsegments+=riftsnumvertices[i]-1;
-		}
-	}
-	
-	in.segmentlist = (int *) mxMalloc(in.numberofsegments * 2 * sizeof(int));
-	in.segmentmarkerlist = (int *) mxCalloc(in.numberofsegments,sizeof(int));
-	counter=0;
-	backcounter=0;
-	for (i=0;i<nprof;i++){
-		for (j=0;j<(profnvertices[i]-1);j++){
-			in.segmentlist[2*counter+0]=counter;
-			in.segmentlist[2*counter+1]=counter+1;
-			in.segmentmarkerlist[counter]=0;
-			counter++;
-		}
-		/*Close this profile: */
-		 in.segmentlist[2*counter+0]=counter;
-		 in.segmentlist[2*counter+1]=backcounter;
-		 in.segmentmarkerlist[counter]=0;
-		 counter++;
-		 backcounter=counter;
-	}
-	counter2=counter;
-	if(riftname){
-		for (i=0;i<numrifts;i++){
-			for (j=0;j<(riftsnumvertices[i]-1);j++){
-				in.segmentlist[2*counter2+0]=counter;
-				in.segmentlist[2*counter2+1]=counter+1;
-				in.segmentmarkerlist[counter2]=2+i;
-				counter2++;
-				counter++;
-			}
-			counter++;
-		}
-	}
-
-	
-	/*Build regions: */
-	in.numberofregions = 0;
-
-	/*Build holes: */
-	in.numberofholes = nprof-1; /*everything is a hole, but for the first profile.*/
-	in.holelist = (REAL *) mxMalloc(in.numberofholes * 2 * sizeof(REAL));
-	for (i=0;i<nprof-1;i++){
-		/*We are looking for a vertex that lies inside the hole: */
-		GridInsideHole(&in.holelist[2*i+0],&in.holelist[2*i+1],profnvertices[i+1],pprofx[i+1],pprofy[i+1]);
-	}
-
-	/* Make necessary initializations so that Triangle can return a */
-	/*   triangulation in `out': */
-
-	out.pointlist = (REAL *) NULL;            
-	out.pointattributelist = (REAL *) NULL;
-	out.pointmarkerlist = (int *) NULL; 
-	out.trianglelist = (int *) NULL;          
-	out.triangleattributelist = (REAL *) NULL;
-	out.neighborlist = (int *) NULL;         
-	out.segmentlist = (int *) NULL;
-	out.segmentmarkerlist = (int *) NULL;
-	out.edgelist = (int *) NULL;             
-	out.edgemarkerlist = (int *) NULL;   
-
-	/* Triangulate the points:.  Switches are chosen to read and write a  */
-	/*   PSLG (p), preserve the convex hull (c), number everything from  */
-	/*   zero (z), assign a regional attribute to each element (A), and  */
-	/*   produce an edge list (e), a Voronoi diagram (v), and a triangle */
-	/*   neighbor list (n).                                              */
-
-	sprintf(options,"%s%lf","pQzDq30ia",area); /*replace V by Q to quiet down the logging*/
-  
-	triangulate(options, &in, &out, NULL);
-	/*report(&out, 0, 1, 1, 1, 1, 0);*/
-
-	/*Allocate index, x and y: */
-	index=(double*)mxMalloc(3*out.numberoftriangles*sizeof(double));
-	x=(double*)mxMalloc(out.numberofpoints*sizeof(double));
-	y=(double*)mxMalloc(out.numberofpoints*sizeof(double));
-	segments=(double*)mxMalloc(3*out.numberofsegments*sizeof(double));
-	segmentmarkerlist=(double*)mxMalloc(out.numberofsegments*sizeof(double));
-
-	for (i = 0; i < out.numberoftriangles; i++) {
-		for (j = 0; j < out.numberofcorners; j++) {
-			*(index+3*i+j)=(double)out.trianglelist[i * out.numberofcorners + j]+1;
-		}
-	}
-	for (i = 0; i < out.numberofpoints; i++) {
-		x[i]=out.pointlist[i * 2 + 0];
-		y[i]=out.pointlist[i * 2 + 1];
-	}
-	
-	for (i = 0; i < out.numberofsegments; i++) {
-		segments[3*i+0]=(double)out.segmentlist[i*2+0]+1;
-		segments[3*i+1]=(double)out.segmentlist[i*2+1]+1;
-		segmentmarkerlist[i]=(double)out.segmentmarkerlist[i];
-	}
-
-	/*Associate elements with segments: */
-	AssociateSegmentToElement(&segments,out.numberofsegments,index,out.numberoftriangles);
-
-	/*Order segments so that their normals point outside the domain: */
-	if(!strcmp(order,"yes")){
-		OrderSegments(&segments,out.numberofsegments, index,out.numberoftriangles);
-	}
-
-	/*Output : */
-	pmxa_array= mxCreateDoubleMatrix(0,0,mxREAL);
-	mxSetM(pmxa_array,3);
-	mxSetN(pmxa_array,out.numberoftriangles);
-	mxSetPr(pmxa_array,index);
-	mexCallMATLAB( 1, &plhs[0], 1, &pmxa_array, "transpose");
-
-	pmxa_array= mxCreateDoubleMatrix(0,0,mxREAL);
-	mxSetM(pmxa_array,1);
-	mxSetN(pmxa_array,out.numberofpoints);
-	mxSetPr(pmxa_array,x);
-	mexCallMATLAB( 1, &plhs[1], 1, &pmxa_array, "transpose");
-
-	pmxa_array= mxCreateDoubleMatrix(0,0,mxREAL);
-	mxSetM(pmxa_array,1);
-	mxSetN(pmxa_array,out.numberofpoints);
-	mxSetPr(pmxa_array,y);
-	mexCallMATLAB( 1, &plhs[2], 1, &pmxa_array, "transpose");
-
-	pmxa_array= mxCreateDoubleMatrix(0,0,mxREAL);
-	mxSetM(pmxa_array,3);
-	mxSetN(pmxa_array,out.numberofsegments);
-	mxSetPr(pmxa_array,segments);
-	mexCallMATLAB( 1, &plhs[3], 1, &pmxa_array, "transpose");
-
-	pmxa_array= mxCreateDoubleMatrix(0,0,mxREAL);
-	mxSetM(pmxa_array,1);
-	mxSetN(pmxa_array,out.numberofsegments);
-	mxSetPr(pmxa_array,segmentmarkerlist);
-	mexCallMATLAB( 1, &plhs[4], 1, &pmxa_array, "transpose");
-	
-	return;
+	/*end module: */
+	MODULEEND();
 }
 
@@ -307,17 +61,19 @@
 {
 	printf("\n");
-	printf("   usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,riftsoutlinename,area,ordered) \n");
+	printf("   usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,area,ordered) \n");
 	printf("      where: index,x,y defines a triangulation, segments is an array made \n");
-	printf("      of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment \n");
-	printf("      (if rifts are present, markers >=2 flag them ), outlinefilename an Argus domain outline file.\n");
-	printf("      riftsoutlinename is an Argus domain file, defining rifts (ie: open profiles), \n");
-	printf("      area is the maximum area desired for any element of the resulting mesh. \n");
-	printf("      and ordered is a string ('yes' or 'no') that determines whether segments are output in the \n");
+	printf("      of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment, \n");
+	printf("      outlinefilename an Argus domain outline file, \n");
+	printf("      area is the maximum area desired for any element of the resulting mesh, \n");
+	printf("      and ordered is a bool that determines whether segments are output in the \n");
 	printf("      order they are made by Triangle (ie none), or ordered counter clockwise around the domain outline.\n");
-	printf("      riftsoutlinename and ordered are optional arguments.\n");
 	printf("\n");
 }
 
 
-
-
+#ifdef _HAVE_PYTHON_
+BOOST_PYTHON_MODULE(TriMesh){
+	boost::python::numeric::array::set_module_and_type( "numpy", "ndarray");
+	def("TriMesh",TriMesh);
+}
+#endif
Index: sm/trunk-jpl/src/mex/TriMesh/TriMesh.cpp.bak
===================================================================
--- /issm/trunk-jpl/src/mex/TriMesh/TriMesh.cpp.bak	(revision 11931)
+++ 	(revision )
@@ -1,78 +1,0 @@
-/*
- * TriMesh: mesh a domain using an .exp file
- */
-
-#include "./TriMesh.h"
-
-void mexFunction(	int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[] ){
-
-	/* input: */
-	char*  domainname=NULL;
-	double area;
-	bool   order;
-
-	/*intermediary: */
-	DataSet* domain=NULL;
-
-	/* output: */
-	Matrix* index=NULL;
-	Vector* x=NULL;
-	Vector* y=NULL;
-	Matrix* segments=NULL;
-	Vector* segmentmarkerlist=NULL;
-
-	/*Boot module: */
-	MODULEBOOT();
-printf("ok1\n");
-
-	/*checks on arguments on the matlab side: */
-	CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&TriMeshUsage);
-printf("ok2\n");
-
-	/*Fetch data needed for meshing: */
-
-	FetchMatlabData(&domainname,DOMAINOUTLINE);
-	FetchMatlabData(&area,AREA);
-	FetchMatlabData(&order,ORDER);
-printf("ok3 %g %s\n",area,domainname);
-
-	/*Read domain outline: */
-	domain=DomainOutlineRead(domainname,false);
-printf("ok4\n");
-
-	/*call x core: */
-	TriMeshx(&index,&x,&y,&segments,&segmentmarkerlist,domain,area,order);
-printf("ok5\n");
-
-	/*write outputs: */
-	/*WriteMatlabData(INDEX,index);
-	WriteMatlabData(X,x);
-	WriteMatlabData(Y,y);
-	WriteMatlabData(SEGMENTS,segments);
-	WriteMatlabData(SEGMENTMARKERLIST,segmentmarkerlist);*/
-
-	/*free ressources: */
-	delete domain;
-	/*
-	xdelete(&index);
-	xdelete(&x);
-	xdelete(&y);
-	xdelete(&segments);
-	xdelete(&segmentmarkerlist);*/
-
-	/*end module: */
-	MODULEEND();
-}
-
-void TriMeshUsage(void)
-{
-	printf("\n");
-	printf("   usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,area,ordered) \n");
-	printf("      where: index,x,y defines a triangulation, segments is an array made \n");
-	printf("      of exterior segments to the mesh domain outline, segmentmarkers is an array flagging each segment, \n");
-	printf("      outlinefilename an Argus domain outline file, \n");
-	printf("      area is the maximum area desired for any element of the resulting mesh, \n");
-	printf("      and ordered is a bool that determines whether segments are output in the \n");
-	printf("      order they are made by Triangle (ie none), or ordered counter clockwise around the domain outline.\n");
-	printf("\n");
-}
Index: /issm/trunk-jpl/src/mex/TriMesh/TriMesh.h
===================================================================
--- /issm/trunk-jpl/src/mex/TriMesh/TriMesh.h	(revision 11931)
+++ /issm/trunk-jpl/src/mex/TriMesh/TriMesh.h	(revision 11932)
@@ -1,21 +1,50 @@
-/*!\file:  TriMesh.h
- * \brief header prototype
- */ 
+/*
+	TriMesh.h
+*/
 
-#ifndef _TRIMESH_H_
-#define _TRIMESH_H_
+#ifndef _TRIMESH_H
+#define _TRIMESH_H
 
-#include "mex.h"
-#include "triangle.h"
-#include "string.h"
 
+#ifdef HAVE_CONFIG_H
+	#include <config.h>
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+#include "../../c/include/globals.h"
+#include "../../c/include/include.h"
 #include "../../c/modules/modules.h"
 #include "../../c/Container/Container.h"
 #include "../../c/shared/shared.h"
+#include "../../c/io/io.h"
+#include "../../c/EnumDefinitions/EnumDefinitions.h"
 
+#ifdef _HAVE_MATLAB_
+/* serial input macros: */
+#define DOMAINOUTLINE     (mxArray *)prhs[0]
+#define AREA        (mxArray *)prhs[1]
+#define ORDER     (mxArray *)prhs[2]
+
+/* serial output macros: */
+#define INDEX  (mxArray**)&plhs[0]
+#define X  (mxArray**)&plhs[1]
+#define Y   (mxArray**)&plhs[2]
+#define SEGMENTS   (mxArray**)&plhs[3]
+#define SEGMENTMARKERLIST (mxArray**)&plhs[4]
+
+#endif
+
+/* local prototypes: */
 void TriMeshUsage(void);
 
 #undef __FUNCT__ 
-#define __FUNCT__ "TriMesh"
+#define __FUNCT__  "TriMesh"
 
-#endif
+/* serial arg counts: */
+#undef NLHS
+#define NLHS  5
+#undef NRHS
+#define NRHS  3
+
+#endif  /* _TRIMESH_H */
Index: sm/trunk-jpl/src/mex/TriMesh/TriMesh.h.bak
===================================================================
--- /issm/trunk-jpl/src/mex/TriMesh/TriMesh.h.bak	(revision 11931)
+++ 	(revision )
@@ -1,38 +1,0 @@
-/*
-	TriMesh.h
-*/
-
-#ifndef _TRIMESH_H
-#define _TRIMESH_H
-
-/* local prototypes: */
-void TriMeshUsage(void);
-
-#include "../../c/modules/modules.h"
-#include "../../c/Container/Container.h"
-#include "../../c/shared/shared.h"
-#include "../../c/EnumDefinitions/EnumDefinitions.h"
-
-
-#undef __FUNCT__ 
-#define __FUNCT__  "TriMesh"
-
-/* serial input macros: */
-#define DOMAINOUTLINE     (mxArray *)prhs[0]
-#define AREA        (mxArray *)prhs[1]
-#define ORDER     (mxArray *)prhs[2]
-
-/* serial output macros: */
-#define INDEX  (mxArray**)&plhs[0]
-#define X  (mxArray**)&plhs[1]
-#define Y   (mxArray**)&plhs[2]
-#define SEGMENTS   (mxArray**)&plhs[3]
-#define SEGMENTMARKERLIST (mxArray**)&plhs[4]
-
-/* serial arg counts: */
-#undef NLHS
-#define NLHS  5
-#undef NRHS
-#define NRHS  3
-
-#endif  /* _TRIMESH_H */