// Read Symmetry file ======================================================
// crystal symmetry matices from http://cci.lbl.gov/asu_gallery/
int SymList::read_sym_file(FileName fn_sym)
{
int i, j;
FILE *fpoii;
char line[80];
char *auxstr;
DOUBLE ang_incr, rot_ang;
int fold;
Matrix2D<DOUBLE> L(4, 4), R(4, 4);
Matrix1D<DOUBLE> axis(3);
int pgGroup = 0, pgOrder = 0;
std::vector<std::string> fileContent;
//check if reserved word
// Open file ---------------------------------------------------------
if ((fpoii = fopen(fn_sym.c_str(), "r")) == NULL)
{
//check if reserved word and return group and order
if (isSymmetryGroup(fn_sym, pgGroup, pgOrder))
{
fill_symmetry_class(fn_sym, pgGroup, pgOrder, fileContent);
}
else
REPORT_ERROR((std::string)"SymList::read_sym_file:Can't open file: "
+ " or do not recognize symmetry group" + fn_sym);
}
else
{
while (fgets(line, 79, fpoii) != NULL)
{
if (line[0] == ';' || line[0] == '#' || line[0] == '\0')
continue;
fileContent.push_back(line);
}
fclose(fpoii);
}
// Count the number of symmetries ------------------------------------
true_symNo = 0;
// count number of axis and mirror planes. It will help to identify
// the crystallographic symmetry
int no_axis, no_mirror_planes, no_inversion_points;
no_axis = no_mirror_planes = no_inversion_points = 0;
for (int n=0; n<fileContent.size(); n++)
{
strcpy(line,fileContent[n].c_str());
auxstr = firstToken(line);
if (auxstr == NULL)
{
std::cout << line;
std::cout << "Wrong line in symmetry file, the line is skipped\n";
continue;
}
if (strcmp(auxstr, "rot_axis") == 0)
{
auxstr = nextToken();
fold = textToInteger(auxstr);
true_symNo += (fold - 1);
no_axis++;
}
else if (strcmp(auxstr, "mirror_plane") == 0)
{
true_symNo++;
no_mirror_planes++;
}
else if (strcmp(auxstr, "inversion") == 0)
{
true_symNo += 1;
no_inversion_points = 1;
}
}
// Ask for memory
__L.resize(4*true_symNo, 4);
__R.resize(4*true_symNo, 4);
__chain_length.resize(true_symNo);
__chain_length.initConstant(1);
// Read symmetry parameters
i = 0;
for (int n=0; n<fileContent.size(); n++)
{
strcpy(line,fileContent[n].c_str());
auxstr = firstToken(line);
// Rotational axis ---------------------------------------------------
if (strcmp(auxstr, "rot_axis") == 0)
{
auxstr = nextToken();
fold = textToInteger(auxstr);
auxstr = nextToken();
XX(axis) = textToDOUBLE(auxstr);
auxstr = nextToken();
YY(axis) = textToDOUBLE(auxstr);
auxstr = nextToken();
ZZ(axis) = textToDOUBLE(auxstr);
ang_incr = 360. / fold;
L.initIdentity();
for (j = 1, rot_ang = ang_incr; j < fold; j++, rot_ang += ang_incr)
{
rotation3DMatrix(rot_ang, axis, R);
R.setSmallValuesToZero();
set_matrices(i++, L, R.transpose());
}
__sym_elements++;
// inversion ------------------------------------------------------
}
else if (strcmp(auxstr, "inversion") == 0)
{
L.initIdentity();
L(2, 2) = -1;
R.initIdentity();
R(0, 0) = -1.;
R(1, 1) = -1.;
R(2, 2) = -1.;
set_matrices(i++, L, R);
__sym_elements++;
// mirror plane -------------------------------------------------------------
}
else if (strcmp(auxstr, "mirror_plane") == 0)
{
auxstr = nextToken();
XX(axis) = textToFloat(auxstr);
auxstr = nextToken();
YY(axis) = textToFloat(auxstr);
auxstr = nextToken();
ZZ(axis) = textToFloat(auxstr);
L.initIdentity();
L(2, 2) = -1;
Matrix2D<DOUBLE> A;
alignWithZ(axis,A);
A = A.transpose();
R = A * L * A.inv();
L.initIdentity();
set_matrices(i++, L, R);
__sym_elements++;
}
}
compute_subgroup();
return pgGroup;
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[])
{
double angs[3];
const double *p_angs=mxGetPr(prhs[1]);
angs[0]=(double)p_angs[0];
angs[1]=(double)p_angs[1];
angs[2]=(double)p_angs[2];
Matrix1D<double> axis;
getMatrix1D(prhs[2],axis);
Matrix2D<double> A3D, A2D;
bool wrap = (bool)mxGetScalar(prhs[5]);
mwSize ndims = mxGetNumberOfDimensions(prhs[0]);
/*mode: 1 euler, 2 align_with_Z, 3 axis, 4 tform*/
switch ((int)mxGetScalar(prhs[3])) {
case 1:
Euler_angles2matrix(angs[0], angs[1], angs[2], A3D, true);
break;
case 2:
alignWithZ(axis,A3D);
break;
case 3:
rotation3DMatrix(angs[0], axis, A3D);
A2D.resize(3,3);
A2D(0,0)=A3D(0,0); A2D(0,1)=A3D(0,1); A2D(0,2)=A3D(0,2);
A2D(1,0)=A3D(1,0); A2D(1,1)=A3D(1,1); A2D(1,2)=A3D(1,2);
A2D(2,0)=A3D(2,0); A2D(2,1)=A3D(2,1); A2D(2,2)=A3D(2,2);
break;
case 4:
getMatrix2D(prhs[6],A2D);
A3D = A2D;
break;
}
if (ndims == 2)
{
Image<double> img, img_out;
getMatrix2D(prhs[0],img());
if (MAT_XSIZE(A2D) != 0)
{
applyGeometry(BSPLINE3,img_out(), img(), A2D, IS_NOT_INV, wrap);
setMatrix2D(img_out(),plhs[0]);
}
else
{
setMatrix2D(img(),plhs[0]);
}
}
else
{
Image<double> vol, vol_out;
getMatrix3D(prhs[0],vol());
applyGeometry(BSPLINE3, vol_out(), vol(), A3D, IS_NOT_INV, wrap);
setMatrix3D(vol_out(),plhs[0]);
}
}