// Вывод треугольника
void ShowTr( int p1,int p2,int p3 ){
int Triangle[6] =
{ XC(W[p1-1]), YC(W[p1-1]),
XC(W[p2-1]), YC(W[p2-1]),
XC(W[p3-1]), YC(W[p3-1]) };
fillpoly(sizeof(Triangle)/sizeof(pointtype),Triangle);
};
// Выводим числа
void ShowNamb(){
char st[2] = "1";
for (int i=0;i<DimNods;i++){
st[0]=Mask[i];
outtextxy( XC(W[i])-10,YC(W[i])-8,st);
};
};
// Выводим ребра
void ShowLoops( int Ind ){
int i,j;
for (i=0;i<DimLoops;i++)
for (j=0;j<2;j++)
switch (Ind) {
case 0: Loops[i][j]=LT3[i][j]; break;
case 1: Loops[i][j]=LC3[i][j]; break;
case 2: Loops[i][j]=LO3[i][j]; break;
case 3: Loops[i][j]=LT4[i][j]; break;
case 4: Loops[i][j]=LO4[i][j]; break;
case 5: Loops[i][j]=LL4[i][j]; break;
case 6: Loops[i][j]=LC4[i][j]; break;
case 7: Loops[i][j]=LC5[i][j]; break;
case 8: Loops[i][j]=LC6[i][j]; break;
case 9: Loops[i][j]=LI3[i][j]; break;
};
for (i=0;i<DimLoops;i++)
line( XC(W[Loops[i][0]-1]),YC(W[Loops[i][0]-1]),
XC(W[Loops[i][1]-1]),YC(W[Loops[i][1]-1]));
};
void pVGRID(float *xyz)
{
MULTIGRID *mg;
ELEMENT *e;
VERTEX *v;
int i;
mg = GetCurrentMultigrid();
ClearVertexMarkers(mg);
SURFACE_LOOP_BEGIN(mg, e)
for (i = 0; i < CORNERS_OF_ELEM(e); i++) {
v = MYVERTEX(CORNER(e, i));
if (USED(v)) continue;
SETUSED(v, 1);
*xyz++ = XC(v);
*xyz++ = YC(v);
*xyz++ = ZC(v);
}
SURFACE_LOOP_END
}
// Вывод четырехугольника
void ShowSq( int p1,int p2,int p3,int p4 ){
int Square[8] =
{ XC(W[p1-1]), YC(W[p1-1]), XC(W[p2-1]), YC(W[p2-1]),
XC(W[p3-1]), YC(W[p3-1]), XC(W[p4-1]), YC(W[p4-1]) };
fillpoly(sizeof(Square)/sizeof(pointtype),Square);
};
bool UnitTests::WeightedDataMatrixMothur()
{
std::vector< std::vector<double> > dissMatrix;
// weighted Bray-Curtis
DiversityCalculator BC("../unit-tests/DataMatrixMothur.env", "", "Bray-Curtis", 1000, true, false, false, false, false);
BC.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.8))
return false;
if(!Compare(dissMatrix[2][0], 0.6))
return false;
if(!Compare(dissMatrix[2][1], 0.8))
return false;
// weighted Canberra
DiversityCalculator Canberra("../unit-tests/DataMatrixMothur.env", "", "Canberra", 1000, true, false, false, false, false);
Canberra.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 6.35152))
return false;
if(!Compare(dissMatrix[2][0], 8.11111))
return false;
if(!Compare(dissMatrix[2][1], 5.92063))
return false;
// weighted Gower
DiversityCalculator Gower("../unit-tests/DataMatrixMothur.env", "", "Gower", 1000, true, false, false, false, false);
Gower.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 6.58333))
return false;
if(!Compare(dissMatrix[2][0], 7.88889))
return false;
if(!Compare(dissMatrix[2][1], 5.52778))
return false;
// weighted Hellinger
DiversityCalculator Hellinger("../unit-tests/DataMatrixMothur.env", "", "Hellinger", 1000, true, false, false, false, false);
Hellinger.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 1.13904))
return false;
if(!Compare(dissMatrix[2][0], 1.05146))
return false;
if(!Compare(dissMatrix[2][1], 1.17079))
return false;
// weighted Manhattan
DiversityCalculator Manhattan("../unit-tests/DataMatrixMothur.env", "", "Manhattan", 1000, true, false, false, false, false);
Manhattan.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 1.6))
return false;
if(!Compare(dissMatrix[2][0], 1.2))
return false;
if(!Compare(dissMatrix[2][1], 1.6))
return false;
// weighted Morisita-Horn
DiversityCalculator MH("../unit-tests/DataMatrixMothur.env", "", "Morisita-Horn", 1000, true, false, false, false, false);
MH.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.873239))
return false;
if(!Compare(dissMatrix[2][0], 0.333333))
return false;
if(!Compare(dissMatrix[2][1], 0.859155))
return false;
// weighted Soergel
DiversityCalculator Soergel("../unit-tests/DataMatrixMothur.env", "", "Soergel", 1000, true, false, false, false, false);
Soergel.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.88888901))
return false;
if(!Compare(dissMatrix[2][0], 0.75))
return false;
if(!Compare(dissMatrix[2][1], 0.88888901))
return false;
// weighted species profile
/*
DiversityCalculator SP("../unit-tests/DataMatrixMothur.env", "", "Species profile", 1000, true, false, false, false, false);
SP.Dissimilarity("../unit-tests/temp.diss");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.78740102))
return false;
if(!Compare(dissMatrix[2][0], 0.44721401))
return false;
if(!Compare(dissMatrix[2][1], 0.78102499))
return false;
*/
// weighted Chi-squared
// Note: EBD uses a slightly different form of the Chi-squared measure as suggested in Numerical Ecology by Legendre adn Legendre
// Nonetheless, it is easy to verify this using mothur. Simply divide by sqrt(N), N is the total number of sequences.
DiversityCalculator ChiSquared("../unit-tests/DataMatrixMothur.env", "", "Chi-squared", 1000, true, false, false, false, false);
ChiSquared.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 1.0973200))
return false;
if(!Compare(dissMatrix[2][0], 0.96513098))
return false;
if(!Compare(dissMatrix[2][1], 1.1147900))
return false;
// weighted Euclidean
DiversityCalculator Euclidean("../unit-tests/DataMatrixMothur.env", "", "Euclidean", 1000, true, false, false, false, false);
Euclidean.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.78740102))
return false;
if(!Compare(dissMatrix[2][0], 0.44721401))
return false;
if(!Compare(dissMatrix[2][1], 0.78102499))
return false;
// weighted Kulczynski
DiversityCalculator Kulczynski("../unit-tests/DataMatrixMothur.env", "", "Kulczynski", 1000, true, false, false, false, false);
Kulczynski.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.8))
return false;
if(!Compare(dissMatrix[2][0], 0.6))
return false;
if(!Compare(dissMatrix[2][1], 0.8))
return false;
// weighted Pearson
DiversityCalculator uPearson("../unit-tests/DataMatrixMothur.env", "", "Pearson", 1000, true, false, false, false, false);
uPearson.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 1.22089))
return false;
if(!Compare(dissMatrix[2][0], 0.5))
return false;
if(!Compare(dissMatrix[2][1], 1.2008))
return false;
// weighted Yue-Clayton
DiversityCalculator YC("../unit-tests/DataMatrixMothur.env", "", "YueClayton", 1000, true, false, false, false, false);
YC.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.93233103))
return false;
if(!Compare(dissMatrix[2][0], 0.5))
return false;
if(!Compare(dissMatrix[2][1], 0.92424202))
return false;
return true;
}
static INT TecplotCommand (INT argc, char **argv)
{
INT i,j,k,v; /* counters etc. */
INT counter; /* for formatting output */
char item[1024],it[256]; /* item buffers */
INT ic=0; /* item length */
VECTOR *vc; /* a vector pointer */
ELEMENT *el; /* an element pointer */
MULTIGRID *mg; /* our multigrid */
char filename[NAMESIZE]; /* file name for output file */
PFILE *pf; /* the output file pointer */
INT nv; /* number of variables (eval functions) */
EVALUES *ev[MAXVARIABLES]; /* pointers to eval function descriptors */
char ev_name[MAXVARIABLES][NAMESIZE]; /* names for eval functions */
char s[NAMESIZE]; /* name of eval proc */
char zonename[NAMESIZE+7] = ""; /* name for zone (initialized to
empty string) */
INT numNodes; /* number of data points */
INT numElements; /* number of elements */
INT gnumNodes; /* number of data points globally */
INT gnumElements; /* number of elements globallay */
PreprocessingProcPtr pre; /* pointer to prepare function */
ElementEvalProcPtr eval; /* pointer to evaluation function */
DOUBLE *CornersCoord[MAX_CORNERS_OF_ELEM]; /* pointers to coordinates */
DOUBLE LocalCoord[DIM]; /* is one of the corners local coordinates */
DOUBLE local[DIM]; /* local coordinate in DOUBLE */
DOUBLE value; /* returned by user eval proc */
INT oe,on;
INT saveGeometry; /* save geometry flag */
/* get current multigrid */
mg = GetCurrentMultigrid();
if (mg==NULL)
{
PrintErrorMessage('W',"tecplot","no multigrid open\n");
return (OKCODE);
}
/* scan options */
nv = 0; saveGeometry = 0;
for(i=1; i<argc; i++)
{
switch(argv[i][0])
{
case 'e' : /* read eval proc */
if (nv>=MAXVARIABLES)
{
PrintErrorMessage('E',"tecplot","too many variables specified\n");
break;
}
sscanf(argv[i],"e %s", s);
ev[nv] = GetElementValueEvalProc(s);
if (ev[nv]==NULL)
{
PrintErrorMessageF('E',"tecplot","could not find eval proc %s\n",s);
break;
}
if (sscanf(argv[i+1],"s %s", s) == 1)
{
strcpy(ev_name[nv],s);
i++;
}
else
strcpy(ev_name[nv],ev[nv]->v.name);
nv++;
break;
case 'z' :
sscanf(argv[i],"z %s", zonename+3);
memcpy(zonename, "T=\"", 3);
memcpy(zonename+strlen(zonename), "\", \0", 4);
break;
case 'g' :
sscanf(argv[i],"g %d", &saveGeometry);
if (saveGeometry<0) saveGeometry=0;
if (saveGeometry>1) saveGeometry=1;
break;
}
}
if (nv==0) UserWrite("tecplot: no variables given, printing mesh data only\n");
/* get file name and open output file */
if (sscanf(argv[0],expandfmt(CONCAT3(" tecplot %",NAMELENSTR,"[ -~]")),filename)!=1)
{
PrintErrorMessage('E',"tecplot","could not read name of logfile");
return(PARAMERRORCODE);
}
pf = pfile_open(filename);
if (pf==NULL) return(PARAMERRORCODE);
/********************************/
/* TITLE */
/********************************/
ic = 0;
sprintf(it,"TITLE = \"UG TECPLOT OUTPUT\"\n");
strcpy(item+ic,it); ic+=strlen(it);
sprintf(it,"VARIABLES = \"X\", \"Y\"");
strcpy(item+ic,it); ic+=strlen(it);
if (DIM==3) {
sprintf(it,", \"Z\"");
strcpy(item+ic,it); ic+=strlen(it);
}
for (i=0; i<nv; i++) {
sprintf(it,", \"%s\"",ev[i]->v.name);
strcpy(item+ic,it); ic+=strlen(it);
}
sprintf(it,"\n");
strcpy(item+ic,it); ic+=strlen(it);
pfile_master_puts(pf,item); ic=0;
/********************************/
/* compute sizes */
/********************************/
/* clear VCFLAG on all levels */
for (k=0; k<=TOPLEVEL(mg); k++)
for (vc=FIRSTVECTOR(GRID_ON_LEVEL(mg,k)); vc!=NULL; vc=SUCCVC(vc))
SETVCFLAG(vc,0);
/* run thru all levels of elements and set index */
numNodes = numElements = 0;
for (k=0; k<=TOPLEVEL(mg); k++)
for (el=FIRSTELEMENT(GRID_ON_LEVEL(mg,k)); el!=NULL; el=SUCCE(el))
{
if (!EstimateHere(el)) continue; /* process finest level elements only */
numElements++; /* increase element counter */
for (i=0; i<CORNERS_OF_ELEM(el); i++)
{
vc = NVECTOR(CORNER(el,i));
if (VCFLAG(vc)) continue; /* we have this one already */
VINDEX(vc) = ++numNodes; /* number of data points, begins with 1 ! */
SETVCFLAG(vc,1); /* tag vector as visited */
}
}
#ifdef ModelP
gnumNodes = TPL_GlobalSumINT(numNodes);
gnumElements = TPL_GlobalSumINT(numElements);
on=get_offset(numNodes);
oe=get_offset(numElements);
/* clear VCFLAG on all levels */
for (k=0; k<=TOPLEVEL(mg); k++)
for (vc=FIRSTVECTOR(GRID_ON_LEVEL(mg,k)); vc!=NULL; vc=SUCCVC(vc))
SETVCFLAG(vc,0);
/* number in unique way */
for (k=0; k<=TOPLEVEL(mg); k++)
for (el=FIRSTELEMENT(GRID_ON_LEVEL(mg,k)); el!=NULL; el=SUCCE(el))
{
if (!EstimateHere(el)) continue; /* process finest level elements only */
for (i=0; i<CORNERS_OF_ELEM(el); i++)
{
vc = NVECTOR(CORNER(el,i));
if (VCFLAG(vc)) continue; /* we have this one already */
VINDEX(vc) += on; /* add offset */
SETVCFLAG(vc,1); /* tag vector as visited */
}
}
#else
gnumNodes = numNodes;
gnumElements = numElements;
oe=on=0;
#endif
/********************************/
/* write ZONE data */
/* uses FEPOINT for data */
/* uses QUADRILATERAL in 2D */
/* and BRICK in 3D */
/********************************/
/* write zone record header */
if (DIM==2) sprintf(it,"ZONE %sN=%d, E=%d, F=FEPOINT, ET=QUADRILATERAL\n", zonename, gnumNodes,gnumElements);
if (DIM==3) sprintf(it,"ZONE %sN=%d, E=%d, F=FEPOINT, ET=BRICK\n", zonename, gnumNodes,gnumElements);
strcpy(item+ic,it); ic+=strlen(it);
pfile_master_puts(pf,item); ic=0;
/* write data in FEPOINT format, i.e. all variables of a node per line*/
for (k=0; k<=TOPLEVEL(mg); k++)
for (vc=FIRSTVECTOR(GRID_ON_LEVEL(mg,k)); vc!=NULL; vc=SUCCVC(vc))
SETVCFLAG(vc,0); /* clear all flags */
counter=0;
for (k=0; k<=TOPLEVEL(mg); k++)
for (el=FIRSTELEMENT(GRID_ON_LEVEL(mg,k)); el!=NULL; el=SUCCE(el))
{
if (!EstimateHere(el)) continue; /* process finest level elements only */
for (i=0; i<CORNERS_OF_ELEM(el); i++)
CornersCoord[i] = CVECT(MYVERTEX(CORNER(el,i))); /* x,y,z of corners */
for (i=0; i<CORNERS_OF_ELEM(el); i++)
{
vc = NVECTOR(CORNER(el,i));
if (VCFLAG(vc)) continue; /* we have this one alre ady */
SETVCFLAG(vc,1); /* tag vector as visited */
sprintf(it,"%g",(double)XC(MYVERTEX(CORNER(el,i))));
strcpy(item+ic,it); ic+=strlen(it);
sprintf(it," %g",(double)YC(MYVERTEX(CORNER(el,i))));
strcpy(item+ic,it); ic+=strlen(it);
if (DIM == 3)
{
sprintf(it," %g",(double)ZC(MYVERTEX(CORNER(el,i))));
strcpy(item+ic,it); ic+=strlen(it);
}
/* now all the user variables */
/* get local coordinate of corner */
LocalCornerCoordinates(DIM,TAG(el),i,local);
for (j=0; j<DIM; j++) LocalCoord[j] = local[j];
for (v=0; v<nv; v++)
{
pre = ev[v]->PreprocessProc;
eval = ev[v]->EvalProc;
/* execute prepare function */
/* This is not really equivalent to
the FEBLOCK-version sinc we call "pre" more
often than there. D.Werner */
if (pre!=NULL) pre(ev_name[v],mg);
/* call eval function */
value = eval(el,(const DOUBLE **)CornersCoord,LocalCoord);
sprintf(it," %g",value);
strcpy(item+ic,it); ic+=strlen(it);
}
sprintf(it,"\n");
strcpy(item+ic,it); ic+=strlen(it);
pfile_tagged_puts(pf,item,counter+on); ic=0;
counter++;
}
}
pfile_sync(pf); /* end of segment */
sprintf(it,"\n");
strcpy(item+ic,it); ic+=strlen(it);
pfile_master_puts(pf,item); ic=0;
/* finally write the connectivity list */
counter=0;
for (k=0; k<=TOPLEVEL(mg); k++)
for (el=FIRSTELEMENT(GRID_ON_LEVEL(mg,k)); el!=NULL; el=SUCCE(el))
{
if (!EstimateHere(el)) continue; /* process finest level elements only */
switch(DIM) {
case 2 :
switch(TAG(el)) {
case TRIANGLE :
sprintf(it,"%d %d %d %d\n",
VINDEX(NVECTOR(CORNER(el,0))),
VINDEX(NVECTOR(CORNER(el,1))),
VINDEX(NVECTOR(CORNER(el,2))),
VINDEX(NVECTOR(CORNER(el,2)))
);
break;
case QUADRILATERAL :
sprintf(it,"%d %d %d %d\n",
VINDEX(NVECTOR(CORNER(el,0))),
VINDEX(NVECTOR(CORNER(el,1))),
VINDEX(NVECTOR(CORNER(el,2))),
VINDEX(NVECTOR(CORNER(el,3)))
);
break;
default :
UserWriteF("tecplot: unknown 2D element type with tag(el) = %d detected. Aborting further processing of command tecplot\n", TAG(el));
return CMDERRORCODE;
break;
}
break;
case 3 :
switch(TAG(el)) {
case HEXAHEDRON :
sprintf(it,"%d %d %d %d "
"%d %d %d %d\n",
VINDEX(NVECTOR(CORNER(el,0))),
VINDEX(NVECTOR(CORNER(el,1))),
VINDEX(NVECTOR(CORNER(el,2))),
VINDEX(NVECTOR(CORNER(el,3))),
VINDEX(NVECTOR(CORNER(el,4))),
VINDEX(NVECTOR(CORNER(el,5))),
VINDEX(NVECTOR(CORNER(el,6))),
VINDEX(NVECTOR(CORNER(el,7)))
);
break;
case TETRAHEDRON :
sprintf(it,"%d %d %d %d "
"%d %d %d %d\n",
VINDEX(NVECTOR(CORNER(el,0))),
VINDEX(NVECTOR(CORNER(el,1))),
VINDEX(NVECTOR(CORNER(el,2))),
VINDEX(NVECTOR(CORNER(el,2))),
VINDEX(NVECTOR(CORNER(el,3))),
VINDEX(NVECTOR(CORNER(el,3))),
VINDEX(NVECTOR(CORNER(el,3))),
VINDEX(NVECTOR(CORNER(el,3)))
);
break;
case PYRAMID :
sprintf(it,"%d %d %d %d "
"%d %d %d %d\n",
VINDEX(NVECTOR(CORNER(el,0))),
VINDEX(NVECTOR(CORNER(el,1))),
VINDEX(NVECTOR(CORNER(el,2))),
VINDEX(NVECTOR(CORNER(el,3))),
VINDEX(NVECTOR(CORNER(el,4))),
VINDEX(NVECTOR(CORNER(el,4))),
VINDEX(NVECTOR(CORNER(el,4))),
VINDEX(NVECTOR(CORNER(el,4)))
);
break;
case PRISM :
sprintf(it,"%d %d %d %d "
"%d %d %d %d\n",
VINDEX(NVECTOR(CORNER(el,0))),
VINDEX(NVECTOR(CORNER(el,1))),
VINDEX(NVECTOR(CORNER(el,2))),
VINDEX(NVECTOR(CORNER(el,2))),
VINDEX(NVECTOR(CORNER(el,3))),
VINDEX(NVECTOR(CORNER(el,4))),
VINDEX(NVECTOR(CORNER(el,5))),
VINDEX(NVECTOR(CORNER(el,5)))
);
break;
default :
UserWriteF("tecplot: unknown 3D element type with tag(el) = %d detected. Aborting further processing of command tecplot\n", TAG(el));
return CMDERRORCODE;
break;
}
break;
}
strcpy(item+ic,it); ic+=strlen(it);
pfile_tagged_puts(pf,item,counter+oe); ic=0;
counter++;
}
pfile_sync(pf); /* end of segment */
/********************************/
/* GEOMETRY */
/* we will do this later, since */
/* domain interface will change */
/********************************/
pfile_close(pf);
return(OKCODE);
}
