Index: /issm/trunk-jpl/src/mex/TriMesh/TriMesh.cpp
===================================================================
--- /issm/trunk-jpl/src/mex/TriMesh/TriMesh.cpp	(revision 11881)
+++ /issm/trunk-jpl/src/mex/TriMesh/TriMesh.cpp	(revision 11882)
@@ -1,66 +1,305 @@
 /*
- * TriMesh: mesh a domain using an .exp file
+ * TriMesh: out of a domain outline file ( Argus format ), 
+ * use the Triangle package to create a triangular mesh 
+ *
  */
 
 #include "./TriMesh.h"
 
-void mexFunction(	int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[] ){
+
+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;
+	
+	/* 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;
-	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();
+	char*  order=NULL;
+	
+	/*Domain outline variables: */
+	int      nprof;
+	int*     profnvertices=NULL;
+	double** pprofx=NULL;
+	double** pprofy=NULL;
+	double*  xprof=NULL;
+	double*  yprof=NULL;
+	int      numberofpoints;
+
+	/*Rift outline variables: */
+	int      numrifts;
+	int*     riftsnumvertices=NULL;
+	double** riftsverticesx=NULL;
+	double** riftsverticesy=NULL;
+
+	/* Triangle structures: */
+	struct triangulateio in,out;
+	char   options[256];
+
+	/* verify correct usage: */
+	if (nlhs==0 && nrhs==0) {
+		/* special case: */
+		TriMeshUsage();
+		return;
+	}
+
+	if (!(  (nlhs==5) ||(nrhs==2) || (nrhs==3)  || (nrhs==4) )){
+		mexPrintf("   %s format error.\n", __FUNCT__);
+		TriMeshUsage();
+		printf("   ");
+		mexErrMsgTxt(" ");
+	}
+
+	/*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;
 }
 
@@ -68,11 +307,17 @@
 {
 	printf("\n");
-	printf("   usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,area,ordered) \n");
+	printf("   usage: [index,x,y,segments,segmentmarkers]=TriMesh(domainoutlinefilename,riftsoutlinename,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("      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("      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");
 }
+
+
+
+