static void rigid_orthogonalize_R(float R[][3])
{
HMatrix M, Q, S;
copy_m4_m3(M, R);
polar_decomp(M, Q, S);
copy_m3_m4(R, Q);
}
bool CVertexRingElement::_updateRotationMatrixSolidOrShell(const int isshell, const Vector3d* vertexpos)
{
const double ERRTOL = 1e-4;
double3x3 A;
int rank, dim=3;
m_quat0 = m_quat; //save last quat, also use it as the initial guess
m_R0 = m_R;
//asemble the matrix
const int strideP = sizeof(CVertexRingNode);
const int strideQ = sizeof(Vector3d);
const int strideW = sizeof(CVertexRingNode);
const double *P = &m_pVertexRingNode[0].m_lpos0.x;
const double *Q = &vertexpos[0].x;
const double *Weight = &m_pVertexRingNode[0].m_weight;
_computeLeastSquareMatrix(m_nv, P, strideP, Q, strideQ, Weight, strideW, A);
//test the sign of delta
const double delta = A.Det();
if (delta>=0){
//polar_decomp(dim, ERRTOL, A.x, m_R.x, rank);
//return true;
double Sxx=A.x[0], Sxy=A.x[1], Sxz=A.x[2];
double Syx=A.x[3], Syy=A.x[4], Syz=A.x[5];
double Szx=A.x[6], Szy=A.x[7], Szz=A.x[8];
Matrix2d m;
m.x[0][0]=Sxx + Syy + Szz, m.x[0][1]=Syz - Szy, m.x[0][2]=Szx - Sxz, m.x[0][3]=Sxy - Syx;
m.x[1][0]=m.x[0][1], m.x[1][1]=Sxx - Syy - Szz, m.x[1][2]=Sxy + Syx, m.x[1][3]=Szx + Sxz;
m.x[2][0]=m.x[0][2], m.x[2][1]=m.x[1][2]; m.x[2][2]= - Sxx + Syy - Szz, m.x[2][3]= Syz + Szy;
m.x[3][0]=m.x[0][3], m.x[3][1]=m.x[1][3], m.x[3][2]=m.x[2][3], m.x[3][3]= - Sxx - Syy + Szz;
const double ERRTOL = 1e-8;
double eigenvalue;
Vector4d quat, guess(m_quat.w, m_quat.x, m_quat.y, m_quat.z);
const bool r = RayleighQuotientIteration(m, guess, ERRTOL, quat, eigenvalue);
m_quat.x=quat[1], m_quat.y=quat[2], m_quat.z=quat[3], m_quat.w=quat[0];
Quaternion *pquat = (Quaternion*)&m_quat.x;
typedef double M33[3][3];
pquat->getRotationMatrix(*((M33*)&m_R.x));
return r;
}
//if solid, use lazzy approach to do nothing, since we don't know the axis to flip
if (!isshell){
return false;
}
//compute relfection of the shell vertices using vertex normal
bool r = true;
const double MATRIXDIST = 1.0;
Vector3d norm = m_normal;
_computeReflectedLeastSquareMatrix(m_nv, P, strideP, Q, strideQ, Weight, strideW, norm, A);
polar_decomp(dim, ERRTOL, A.x, m_R.x, rank);
const double l2dist = l2_norm(m_R, m_R0);
if (l2dist>=MATRIXDIST) r=false;
return r;
}
inline void CVertexRingElement::_computeRotationMatrix(
const Vector3d *vertexpos, double3x3& A, double3x3& rot, int& rank) const
{
const int strideP = sizeof(CVertexRingNode);
const int strideQ = sizeof(Vector3d);
const int strideW = sizeof(CVertexRingNode);
const double *P = &m_pVertexRingNode[0].m_lpos0.x;
const double *Q = &vertexpos[0].x;
const double *Weight = &m_pVertexRingNode[0].m_weight;
ASSERT0(m_nv>=2);
if (m_nv==2){
//BUG here, need to modify
computePlanarRotationMatrix(Q, strideQ, Weight, strideW, rot);
rank = 2;
}
else{
_computeLeastSquareMatrix(m_nv, P, strideP, Q, strideQ, Weight, strideW, A);
const double ERRTOL = 1e-4;
polar_decomp(3, ERRTOL, A.x, rot.x, rank);
}
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"ConvertSurface"};
int kar, volexists, i, j, Doinv, randseed, Domergesurfs=0, pciref;
float DoR2S, fv[3], *pcxyzref;
double xcen[3], sc[3];
double xform[4][4];
char *if_name = NULL, *of_name = NULL, *if_name2 = NULL,
*of_name2 = NULL, *sv_name = NULL, *vp_name = NULL,
*OF_name = NULL, *OF_name2 = NULL, *tlrc_name = NULL,
*acpc_name=NULL, *xmat_name = NULL, *ifpar_name = NULL,
*ifpar_name2 = NULL;
SUMA_SO_File_Type iType = SUMA_FT_NOT_SPECIFIED,
iparType = SUMA_FT_NOT_SPECIFIED,
oType = SUMA_FT_NOT_SPECIFIED;
SUMA_SO_File_Format iForm = SUMA_FF_NOT_SPECIFIED,
iparForm = SUMA_FF_NOT_SPECIFIED,
oFormat = SUMA_FF_NOT_SPECIFIED;
SUMA_SurfaceObject *SO = NULL, *SOpar = NULL, *SOsurf = NULL;
SUMA_PARSED_NAME *of_name_strip = NULL, *of_name2_strip = NULL;
SUMA_SFname *SF_name = NULL;
void *SO_name = NULL;
char orsurf[6], orcode[6], *PCprojpref=NULL, *NodeDepthpref=NULL;
THD_warp *warp=NULL ;
THD_3dim_dataset *aset=NULL;
SUMA_Boolean brk, Do_tlrc, Do_mni_RAI, Do_mni_LPI, Do_acpc, Docen, Do_flip;
SUMA_Boolean Doxmat, Do_wind, Do_p2s, onemore, Do_native, Do_PolDec;
int Do_PCproj, Do_PCrot, Do_NodeDepth;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_Boolean exists;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
ps = SUMA_Parse_IO_Args(argc, argv, "-o;-i;-sv;-ipar;");
kar = 1;
xmat_name = NULL;
xcen[0] = 0.0; xcen[1] = 0.0; xcen[2] = 0.0;
brk = NOPE;
orcode[0] = '\0';
randseed = 1234;
sprintf(orsurf,"RAI");
Docen = NOPE;
Doxmat = NOPE;
Do_tlrc = NOPE;
Do_mni_RAI = NOPE;
Do_mni_LPI = NOPE;
Do_acpc = NOPE;
Do_wind = NOPE;
Do_flip = NOPE;
Do_p2s = NOPE;
Do_native = NOPE;
DoR2S = 0.0;
Do_PolDec = NOPE;
Do_PCproj = NO_PRJ;
Do_PCrot = NO_ROT;
pciref = -1;
pcxyzref = NULL;
PCprojpref = NULL;
NodeDepthpref = NULL;
Do_NodeDepth = 0;
Doinv = 0;
Domergesurfs = 0;
onemore = NOPE;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
usage_SUMA_ConvertSurface(ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
SUMA_TO_LOWER(argv[kar]);
if (!brk && (strcmp(argv[kar], "-seed") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 integer after -seed\n");
exit (1);
}
randseed = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xyzscale") == 0)) {
kar ++;
if (kar+2 >= argc) {
fprintf (SUMA_STDERR, "need 3 values after -XYZscale\n");
exit (1);
}
sc[0] = strtod(argv[kar], NULL); kar ++;
sc[1] = strtod(argv[kar], NULL); kar ++;
sc[2] = strtod(argv[kar], NULL);
xmat_name = "Scale";
Doxmat = YUP;
Doinv = 0;
brk = YUP;
}
if (!brk && ( (strcmp(argv[kar], "-xmat_1d") == 0) ||
(strcmp(argv[kar], "-xmat_1D") == 0) ) ) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -xmat_1D\n");
exit (1);
}
xmat_name = argv[kar];
Doxmat = YUP;
Doinv = 0;
brk = YUP;
}
if (!brk && ( (strcmp(argv[kar], "-ixmat_1d") == 0) ||
(strcmp(argv[kar], "-ixmat_1D") == 0) ) ) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -ixmat_1D\n");
exit (1);
}
xmat_name = argv[kar];
Doxmat = YUP;
Doinv = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-polar_decomp") == 0)) {
Do_PolDec = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-merge_surfs") == 0)) {
Domergesurfs = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-pc_proj") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 argument after -pc_proj\n");
exit (1);
}
if (!strcmp(argv[kar],"PC0_plane")) Do_PCproj = E1_PLN_PRJ;
else if (!strcmp(argv[kar],"PC1_plane")) Do_PCproj = E2_PLN_PRJ;
else if (!strcmp(argv[kar],"PC2_plane")) Do_PCproj = E3_PLN_PRJ;
else if (!strcmp(argv[kar],"PCZ_plane")) Do_PCproj = EZ_PLN_PRJ;
else if (!strcmp(argv[kar],"PCY_plane")) Do_PCproj = EY_PLN_PRJ;
else if (!strcmp(argv[kar],"PCX_plane")) Do_PCproj = EX_PLN_PRJ;
else if (!strcmp(argv[kar],"PC0_dir")) Do_PCproj = E1_DIR_PRJ;
else if (!strcmp(argv[kar],"PC1_dir")) Do_PCproj = E2_DIR_PRJ;
else if (!strcmp(argv[kar],"PC2_dir")) Do_PCproj = E3_DIR_PRJ;
else if (!strcmp(argv[kar],"PCZ_dir")) Do_PCproj = EZ_DIR_PRJ;
else if (!strcmp(argv[kar],"PCY_dir")) Do_PCproj = EY_DIR_PRJ;
else if (!strcmp(argv[kar],"PCX_dir")) Do_PCproj = EX_DIR_PRJ;
else {
SUMA_S_Err("Bad value of %s for -pca_proj", argv[kar]);
exit(1);
}
++kar;
if (argv[kar][0] == '-') {
SUMA_S_Err("Prefix for -pc_proj should not start with '-'.\n"
"Could it be that %s is another option and \n"
"the prefix was forgtotten?", argv[kar]);
exit(1);
}
PCprojpref = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-node_depth") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need a prefix argument after -node_depth\n");
exit (1);
}
Do_NodeDepth = 1;
if (argv[kar][0] == '-') {
SUMA_S_Err("Prefix for -node_depth should not start with '-'.\n"
"Could it be that %s is another option and \n"
"the prefix was forgtotten?", argv[kar]);
exit(1);
}
NodeDepthpref = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-make_consistent") == 0)) {
Do_wind = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-flip_orient") == 0)) {
Do_flip = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xcenter") == 0)) {
kar ++;
if (kar+2>= argc) {
fprintf (SUMA_STDERR, "need 3 arguments after -xcenter\n");
exit (1);
}
xcen[0] = atof(argv[kar]); ++kar;
xcen[1] = atof(argv[kar]); ++kar;
xcen[2] = atof(argv[kar]);
Docen = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-native") == 0)) {
Do_native = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-orient_out") == 0)) {
kar ++;
if (kar>= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -orient_out\n");
exit (1);
}
snprintf(orcode, 4*sizeof(char), "%s", argv[kar]);
if (!SUMA_ok_orstring(orcode)) {
fprintf (SUMA_STDERR, "%s is a bad orientation string\n", orcode);
exit (1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-radial_to_sphere") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -radial_to_sphere\n");
exit (1);
}
DoR2S = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-patch2surf") == 0)) {
Do_p2s = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xml_ascii") == 0)) {
oFormat = SUMA_XML_ASCII_SURF;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xml_b64") == 0)) {
oFormat = SUMA_XML_B64_SURF;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-xml_b64gz") == 0)) {
oFormat = SUMA_XML_B64GZ_SURF;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-tlrc") == 0)) {
Do_tlrc = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-acpc") == 0)) {
Do_acpc = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-mni_rai") == 0)) {
Do_mni_RAI = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-mni_lpi") == 0)) {
Do_mni_LPI = YUP;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s: Option %s not understood. Try -help for usage\n",
FuncName, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
if (argc < 3) {
SUMA_S_Err("Too few options");
usage_SUMA_ConvertSurface (ps, 0);
exit (1);
}
/* transfer info from ps structure (backward compat) */
if (ps->o_N_surfnames) {
of_name = ps->o_surfnames[0];
of_name2 = ps->o_surftopo[0];
oType = ps->o_FT[0];
if (oFormat == SUMA_FF_NOT_SPECIFIED) {
oFormat = ps->o_FF[0];
}
}
if (ps->i_N_surfnames) {
if_name = ps->i_surfnames[0];
if_name2 = ps->i_surftopo[0];
iType = ps->i_FT[0];
iForm = ps->i_FF[0];
}
if (ps->ipar_N_surfnames) {
ifpar_name = ps->ipar_surfnames[0];
ifpar_name2 = ps->ipar_surftopo[0];
iparType = ps->ipar_FT[0];
iparForm = ps->ipar_FF[0];
}
if (ps->N_sv) sv_name = ps->sv[0];
if (ps->N_vp) vp_name = ps->vp[0];
/* sanity checks */
if (Do_native && orcode[0] != '\0') {
SUMA_S_Err("Options -native and -orient_out are mutually exclusive");
exit(1);
}
if (Do_mni_LPI && Do_mni_RAI) {
SUMA_S_Err("\nCombining -MNI_lpi and -MNI_rai options.\nNot good.");
exit(1);
}
if (!if_name) {
SUMA_S_Err("input surface not specified.\n");
exit(1);
}
if (!of_name && (Do_PCproj < 0 && !Do_NodeDepth) ) {
SUMA_S_Err("output surface or projection PREFIX not specified.\n");
exit(1);
}
if (iType == SUMA_FT_NOT_SPECIFIED) {
SUMA_S_Err("input type not recognized.\n");
exit(1);
}
if (oType == SUMA_FT_NOT_SPECIFIED && (Do_PCproj < 0 && !Do_NodeDepth) ) {
SUMA_S_Err("output type not recognized.\n");
exit(1);
}
if ( oType != SUMA_GIFTI &&
oFormat >= SUMA_XML_SURF &&
oFormat <= SUMA_XML_B64GZ_SURF &&
(Do_PCproj < 0 && !Do_NodeDepth) ){
SUMA_S_Err("XML output options only valid with -o_gii\n");
exit(1);
}
if (iType == SUMA_SUREFIT) {
if (!if_name2) {
SUMA_S_Err("input SureFit surface incorrectly specified.\n");
exit(1);
}
if (sv_name && !vp_name) {
SUMA_S_Err("VolParent needs the -sv option for SureFit surfaces.");
exit(1);
}
}
if (iType == SUMA_VEC) {
if (!if_name2) {
SUMA_S_Err("Input vec surface incorrectly specified.\n");
exit(1);
}
}
if (( Do_mni_RAI || Do_mni_LPI) && !Do_tlrc) {
SUMA_SL_Warn ( "I hope you know what you're doing.\n"
"The MNI transform should only be applied to a\n"
"Surface in the AFNI tlrc coordinate space.\n");
}
if (Do_acpc && Do_tlrc) {
SUMA_S_Err("You can't do -tlrc and -acpc simultaneously.");
exit(1);
}
if ((Doxmat || Docen) && (Do_acpc || Do_tlrc)) {
SUMA_S_Err("You can't do -tlrc or -acpc with -xmat_1D and -xcenter.\n");
exit(1);
}
if ((!Doxmat && Docen)) {
SUMA_S_Err("You can't use -xcenter without -xmat_1D.\n");
exit(1);
}
if (oType == SUMA_SUREFIT) {
if (!of_name2) {
SUMA_S_Err("output SureFit surface incorrectly specified. \n");
exit(1);
}
}
if (oType == SUMA_VEC) {
if (!of_name2) {
SUMA_S_Err("output vec surface incorrectly specified. \n");
exit(1);
}
}
if ( ps->i_N_surfnames > 1 && !Domergesurfs) {
SUMA_S_Err("Multiple surfaces specified without -merge_surfs option\n"
"Nothing to do for such an input\n");
exit(1);
}
/* test for existence of input files */
if (!SUMA_is_predefined_SO_name(if_name, NULL, NULL, NULL, NULL) &&
!SUMA_filexists(if_name)) {
SUMA_S_Errv("if_name %s not found.\n", if_name);
exit(1);
}
if (if_name2) {
if (!SUMA_filexists(if_name2)) {
SUMA_S_Errv("if_name2 %s not found.\n", if_name2);
exit(1);
}
}
if (ifpar_name2) {
if (!SUMA_filexists(ifpar_name2)) {
SUMA_S_Errv("ifpar_name2 %s not found.\n", ifpar_name2);
exit(1);
}
}
if (ifpar_name) {
if (!SUMA_filexists(ifpar_name)) {
SUMA_S_Errv("ifpar_name %s not found.\n", ifpar_name);
exit(1);
}
}
if (xmat_name) {
if (!strstr(special_xmats,xmat_name) && !SUMA_filexists(xmat_name)) {
SUMA_S_Errv("xmat file %s not found.\n", xmat_name);
exit(1);
}
} else {
if (Do_PolDec) {
SUMA_S_Err("-polar_decomp is useless without -xmat_1D");
exit(1);
}
}
if (sv_name) {
char *head = NULL, view[10];
head = SUMA_AfniPrefix(sv_name, view, NULL, &volexists);
if (!SUMA_AfniExistsView(volexists, view) && !SUMA_filexists(sv_name)) {
fprintf (SUMA_STDERR,
"Error %s: volume %s not found.\n", FuncName, head);
exit(1);
}
if (head) SUMA_free(head); head = NULL;
}
if ((Do_tlrc || Do_acpc) && (!sv_name)) {
fprintf (SUMA_STDERR,
"Error %s: -tlrc must be used with -sv option.\n", FuncName);
exit(1);
}
if (vp_name) {
if (!SUMA_filexists(vp_name)) {
fprintf (SUMA_STDERR,
"Error %s: %s not found.\n", FuncName, vp_name);
exit(1);
}
}
/* check for existence of output files */
if ((Do_PCproj < 0 && !Do_NodeDepth) ) {
if (of_name2) {
SUMA_SFname *SFname;
SO_name = SUMA_2Prefix2SurfaceName (of_name, of_name2, NULL,
vp_name, oType, &exists);
SFname = (SUMA_SFname *)SO_name;
OF_name2 = SUMA_copy_string(SFname->name_topo);
OF_name = SUMA_copy_string(SFname->name_coord);
} else {
SO_name = SUMA_Prefix2SurfaceName (of_name, NULL, vp_name,
oType, &exists);
OF_name = SUMA_copy_string((char *) SO_name);
}
if (exists && !THD_ok_overwrite()) {
if (OF_name2)
fprintf (SUMA_STDERR,
"Error %s: output file(s) %s and/or %s exist already.\n",
FuncName, OF_name, OF_name2);
else fprintf ( SUMA_STDERR,
"Error %s: output file %s exists already.\n",
FuncName, OF_name);
exit(1);
}
}
/* now for the real work */
if (Doxmat) {
MRI_IMAGE *im = NULL;
double *far=NULL;
int nrow, ncol;
if (!strcmp(xmat_name,"RandRigid")) {
SUMA_FillRandXform(xform, randseed, 2);
} else if (!strcmp(xmat_name,"RandAffine")) {
SUMA_FillRandXform(xform, randseed, 3);
} else if (!strcmp(xmat_name,"RandShift")) {
SUMA_FillRandXform(xform, randseed, 1);
} else if (!strcmp(xmat_name,"Scale")) {
SUMA_FillScaleXform(xform, sc);
} else if (!strcmp(xmat_name,"NegXY")) {
SUMA_FillXYnegXform(xform);
} else {
im = mri_read_double_1D (xmat_name);
if (!im) {
SUMA_SLP_Err("Failed to read 1D file");
exit(1);
}
far = MRI_DOUBLE_PTR(im);
nrow = im->nx;
ncol = im->ny;
if (nrow == 1) {
if (ncol != 12) {
SUMA_SL_Err("Mat file must have\n"
"one row of 12 columns.");
mri_free(im); im = NULL; /* done with that baby */
exit(1);
}
i = 0;
while (i < 12) {
xform[i/4][0] = far[i]; ++i;
xform[i/4][1] = far[i]; ++i;
xform[i/4][2] = far[i]; ++i;
xform[i/4][3] = far[i]; ++i;
}
xform[3][0] = 0.0;
xform[3][1] = 0.0;
xform[3][2] = 0.0;
xform[3][3] = 1.0;
} else {
if (ncol < 4 ) {
SUMA_SL_Err("Mat file must have\n"
"at least 4 columns.");
mri_free(im); im = NULL; /* done with that baby */
exit(1);
}
if (nrow < 3 ) {
SUMA_SL_Err("Mat file must have\n"
"at least 3 rows.");
mri_free(im); im = NULL; /* done with that baby */
exit(1);
}
if (ncol > 4) {
SUMA_SL_Warn( "Ignoring entries beyond 4th \n"
"column in transform file.");
}
if (nrow > 3) {
SUMA_SL_Warn( "Ignoring entries beyond 3rd\n"
"row in transform file.\n");
}
for (i=0; i < 3; ++i) {
xform[i][0] = far[i];
xform[i][1] = far[i+nrow];
xform[i][2] = far[i+2*nrow];
xform[i][3] = far[i+3*nrow];
}
xform[3][0] = 0.0;
xform[3][1] = 0.0;
xform[3][2] = 0.0;
xform[3][3] = 1.0;
}
}
if (LocalHead) {
fprintf(SUMA_STDERR,"\n++ ConvertSurface xform:\n");
for (i=0; i < 4; ++i) {
fprintf(SUMA_STDERR," %+.5f\t%+.5f\t%+.5f\t%+.5f\n",
xform[i][0], xform[i][1],
xform[i][2], xform[i][3]);
}
fprintf(SUMA_STDERR,"\n");
}
mri_free(im); im = NULL;
if (Doinv) {
mat44 A, A0;
LOAD_MAT44( A0, \
xform[0][0], xform[0][1], xform[0][2], xform[0][3], \
xform[1][0], xform[1][1], xform[1][2], xform[1][3], \
xform[2][0], xform[2][1], xform[2][2], xform[2][3] );
A = nifti_mat44_inverse(A0);
UNLOAD_MAT44(A, \
xform[0][0], xform[0][1], xform[0][2], xform[0][3], \
xform[1][0], xform[1][1], xform[1][2], xform[1][3], \
xform[2][0], xform[2][1], xform[2][2], xform[2][3] );
}
if (Do_PolDec) {
#ifdef USE_DECOMPOSE_SHOEMAKE
/* a little something to do a polar decomposition on M into M = Q*S*/
{
float det, m[4][4], q[4][4], s[4][4];
char *stmp = SUMA_append_string("QS_",xmat_name);
FILE *fout = fopen(stmp,"w"); SUMA_free(stmp); stmp = NULL;
SUMA_S_Note("FixMe! #include above and if(1) here ...");
det = polar_decomp(M, q,s);
fprintf(fout,"#[M][D]: (D is the shift)\n");
for (i=0;i<3; ++i)
fprintf(fout, "#%.5f %.5f %.5f %.5f\n",
M[i][0], M[i][1], M[i][2], M[i][3]);
fprintf(fout,"#Q:\n");
for (i=0;i<3; ++i)
fprintf(fout, "#%.5f %.5f %.5f %.5f\n",
q[i][0], q[i][1], q[i][2], q[i][3]);
fprintf(fout,"#S:\n");
for (i=0;i<3; ++i)
fprintf(fout, "#%.5f %.5f %.5f %.5f\n",
s[i][0], s[i][1], s[i][2], s[i][3]);
fprintf(fout,"#det: %f\n", det);
fprintf(fout, "#[Q][D]: A close xform to [M][D], "
"without scaling.\n#M = Q*S\n");
for (i=0;i<3; ++i)
fprintf(fout, "%.5f %.5f %.5f %.5f\n",
q[i][0], q[i][1], q[i][2], M[i][3]);
fclose(fout); SUMA_free(stmp); stmp = NULL;
}
/* replace user's xform with orthogonal one: */
fprintf(SUMA_STDOUT,"Replacing matrix:\n");
for (i=0;i<3; ++i)
fprintf( SUMA_STDOUT,
" %.5f %.5f %.5f %.5f\n",
M[i][0], M[i][1], M[i][2], M[i][3]);
fprintf(SUMA_STDOUT," with matrix:\n");
for (i=0;i<3; ++i)
fprintf(SUMA_STDOUT,
" %.5f %.5f %.5f %.5f\n",
q[i][0], q[i][1], q[i][2], M[i][3]);
for (i=0;i<3; ++i) {
M[i][0] = q[i][0]; M[i][1] = q[i][1]; M[i][2] = q[i][2];
}
#else
{/* use the NIFTI polar decomposition function
(same results as above)*/
mat33 Q, A;
for (i=0;i<3;++i) {
A.m[i][0] = xform[i][0];
A.m[i][1] = xform[i][1];
A.m[i][2] = xform[i][2];
}
Q = nifti_mat33_polar( A );
/* replace user's xform with orthogonal one: */
fprintf(SUMA_STDOUT,"Replacing matrix:\n");
for (i=0;i<3; ++i)
fprintf( SUMA_STDOUT,
" %.5f %.5f %.5f %.5f\n",
xform[i][0], xform[i][1],
xform[i][2], xform[i][3]);
fprintf(SUMA_STDOUT," with matrix:\n");
for (i=0;i<3; ++i)
fprintf( SUMA_STDOUT,
" %.5f %.5f %.5f %.5f\n",
Q.m[i][0], Q.m[i][1], Q.m[i][2], xform[i][3]);
for (i=0;i<3; ++i) {
xform[i][0] = Q.m[i][0];
xform[i][1] = Q.m[i][1];
xform[i][2] = Q.m[i][2];
}
}
#endif
}
}
if ( ps->i_N_surfnames == 1) {
/* load that one surface */
SO = SUMA_Load_Surface_Object_Wrapper ( if_name, if_name2, vp_name,
iType, iForm, sv_name, 1);
if (!SO) {
SUMA_S_Err("Failed to read input surface.\n");
exit (1);
}
} else if ( ps->i_N_surfnames > 1 && Domergesurfs) {
SUMA_SurfaceObject **SOar=NULL;
int ii;
SUMA_S_Notev("Merging %d surfaces into 1\n", ps->i_N_surfnames);
SOar = (SUMA_SurfaceObject **)
SUMA_calloc(ps->i_N_surfnames, sizeof(SUMA_SurfaceObject *));
if (ps->N_sv > 1 || ps->N_vp > 1) {
SUMA_S_Errv("Cannot handle multiple (%d) -sv or multiple (%d) -vp\n",
ps->N_sv, ps->N_vp);
exit(1);
}
for (ii = 0; ii<ps->i_N_surfnames; ++ii) {
SOar[ii] = SUMA_Load_Surface_Object_Wrapper(ps->i_surfnames[ii],
ps->i_surftopo[ii],
vp_name,
ps->i_FT[0], ps->i_FF[0],
sv_name, 1);
}
if (!(SO = SUMA_MergeSurfs(SOar, ps->i_N_surfnames))) {
SUMA_S_Err("Failed to merge");
exit(1);
}
for (ii = 0; ii<ps->i_N_surfnames; ++ii) {
SUMA_Free_Surface_Object(SOar[ii]);
SOar[ii]=NULL;
} SUMA_free(SOar); SOar=NULL;
}
if (DoR2S > 0.0000001) {
if (!SUMA_ProjectSurfaceToSphere(SO, NULL , DoR2S , NULL)) {
SUMA_S_Err("Failed to project to surface");
exit(1);
}
}
if (ifpar_name) {
SOpar = SUMA_Load_Surface_Object_Wrapper ( ifpar_name, ifpar_name2,
vp_name, iparType, iparForm, sv_name, 1);
if (!SOpar) {
SUMA_S_Err("Failed to read input parent surface.\n");
exit (1);
}
/* need edge list */
if (!SUMA_SurfaceMetrics_eng (SOpar,"EdgeList", NULL, 0,
SUMAg_CF->DsetList)) {
SUMA_SL_Err("Failed to create edgelist for parent");
exit(1);
}
}
/* if Do_wind */
if (Do_wind) {
fprintf (SUMA_STDOUT,
"Checking and repairing mesh's winding consistency...\n");
/* check the winding, but that won't fix the normals,
you'll have to recalculate those things, if need be ... */
if (!SUMA_SurfaceMetrics_eng (SO, "CheckWind", NULL, 0,
SUMAg_CF->DsetList)) {
SUMA_S_Err("Failed in SUMA_SurfaceMetrics.\n");
exit(1);
}
}
if (Do_flip) {
fprintf (SUMA_STDOUT,
"Flipping triangle winding...\n");
SUMA_FlipSOTriangles(SO);
}
if (Do_tlrc) {
fprintf (SUMA_STDOUT,"Performing talairach transform...\n");
/* form the tlrc version of the surface volume */
tlrc_name = (char *) SUMA_calloc (strlen(SO->VolPar->dirname)+
strlen(SO->VolPar->prefix)+60,
sizeof(char));
sprintf (tlrc_name, "%s%s+tlrc.HEAD",
SO->VolPar->dirname, SO->VolPar->prefix);
if (!SUMA_filexists(tlrc_name)) {
fprintf (SUMA_STDERR,"Error %s: %s not found.\n", FuncName, tlrc_name);
exit(1);
}
/* read the tlrc header */
aset = THD_open_dataset(tlrc_name) ;
if( !ISVALID_DSET(aset) ){
SUMA_S_Err("%s is not a valid data set.\n", tlrc_name) ;
exit(1);
}
if( aset->warp == NULL ){
SUMA_S_Err("tlrc_name does not contain a talairach transform.\n");
exit(1);
}
warp = aset->warp ;
/* now warp the coordinates, one node at a time */
if (!SUMA_AFNI_forward_warp_xyz(warp, SO->NodeList, SO->N_Node)) {
SUMA_S_Err("Failed in SUMA_AFNI_forward_warp_xyz.\n");
exit(1);
}
}
if (Do_acpc) {
fprintf (SUMA_STDOUT,"Performing acpc transform...\n");
/* form the acpc version of the surface volume */
acpc_name = (char *) SUMA_calloc (strlen(SO->VolPar->dirname)+
strlen(SO->VolPar->prefix)+60,
sizeof(char));
sprintf (acpc_name,
"%s%s+acpc.HEAD", SO->VolPar->dirname, SO->VolPar->prefix);
if (!SUMA_filexists(acpc_name)) {
fprintf (SUMA_STDERR,"Error %s: %s not found.\n", FuncName, acpc_name);
exit(1);
}
/* read the acpc header */
aset = THD_open_dataset(acpc_name) ;
if( !ISVALID_DSET(aset) ){
fprintf (SUMA_STDERR,
"Error %s: %s is not a valid data set.\n",
FuncName, acpc_name) ;
exit(1);
}
if( aset->warp == NULL ){
fprintf (SUMA_STDERR,
"Error %s: acpc_name does not contain an acpc transform.\n",
FuncName);
exit(1);
}
warp = aset->warp ;
/* now warp the coordinates, one node at a time */
if (!SUMA_AFNI_forward_warp_xyz(warp, SO->NodeList, SO->N_Node)) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_AFNI_forward_warp_xyz.\n", FuncName);
exit(1);
}
}
if (Do_mni_RAI) {
fprintf (SUMA_STDOUT,"Performing MNI_RAI transform...\n");
/* apply the mni warp */
if (!SUMA_AFNItlrc_toMNI(SO->NodeList, SO->N_Node, "RAI")) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_AFNItlrc_toMNI.\n", FuncName);
exit(1);
}
sprintf(orsurf,"RAI");
}
if (Do_mni_LPI) {
fprintf (SUMA_STDOUT,"Performing MNI_LPI transform...\n");
/* apply the mni warp */
if (!SUMA_AFNItlrc_toMNI(SO->NodeList, SO->N_Node, "LPI")) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_AFNItlrc_toMNI.\n", FuncName);
exit(1);
}
sprintf(orsurf,"LPI");
}
if (Doxmat) {
fprintf (SUMA_STDOUT,"Performing affine transform...\n");
if (LocalHead) {
for (i=0; i<3 ; ++i) {
fprintf (SUMA_STDERR,
"M[%d][:] = %f %f %f %f\n",
i, xform[i][0], xform[i][1], xform[i][2], xform[i][3]);
}
fprintf (SUMA_STDERR,"Cen[:] %f %f %f\n", xcen[0], xcen[1], xcen[2]);
}
if (Docen) {
if (!SUMA_Apply_Coord_xform( SO->NodeList, SO->N_Node, SO->NodeDim,
xform, 0, xcen)) {
SUMA_SL_Err("Failed to xform coordinates"); exit(1);
}
} else {
if (!SUMA_Apply_Coord_xform( SO->NodeList, SO->N_Node, SO->NodeDim,
xform, 0, NULL)) {
SUMA_SL_Err("Failed to xform coordinates"); exit(1);
}
}
SUMA_Blank_AfniSO_Coord_System(SO->aSO);
}
if (orcode[0] != '\0') {
SUMA_LHv("Changing coordinates from %s to %s\n", orsurf, orcode);
if (!SUMA_CoordChange(orsurf, orcode, SO->NodeList, SO->N_Node)) {
SUMA_S_Err("Failed to change coords.");
exit(1);
}
SUMA_Blank_AfniSO_Coord_System(SO->aSO);
}
if (Do_p2s) {
SUMA_SurfaceObject *SOold = SO;
SUMA_LH("Changing patch to surface...");
SO = SUMA_Patch2Surf(SOold->NodeList, SOold->N_Node,
SO->FaceSetList, SO->N_FaceSet, 3);
if (!SO) {
SUMA_S_Err("Failed to change patch to surface.");
exit(1);
}
/* get rid of old surface object */
SUMA_Free_Surface_Object(SOold);
}
if (Do_native) {
if (!SUMA_Delign_to_VolPar (SO, NULL)) {
SUMA_S_Err("Failed to transform coordinates to native space");
exit(1);
}
}
if (Do_NodeDepth) {
float *dpth=NULL, mx=0.0;
SUMA_PC_XYZ_PROJ *pcp=NULL;
if (SUMA_NodeDepth(SO->NodeList, SO->N_Node, E1_DIR_PRJ, &dpth,
0.0, NULL, &mx, &pcp) < 0) {
SUMA_S_Err("Failed to compute node depth");
exit(1);
} else {
if (!SUMA_WriteNodeDepth(NodeDepthpref,pcp,dpth, mx)) {
SUMA_S_Err("Failed to write node depth");
exit(1);
}
}
SUMA_ifree(dpth);
pcp = SUMA_Free_PC_XYZ_Proj(pcp);
}
if (Do_PCproj > NO_PRJ) {
SUMA_PC_XYZ_PROJ *pcp=NULL;
pciref = 0; pcxyzref = NULL;
if (!(pcp = SUMA_Project_Coords_PCA(SO->NodeList, SO->N_Node,
pciref, pcxyzref, Do_PCproj, Do_PCrot, 1))) {
SUMA_S_Err("Failed to project");
exit(1);
} else {
if (!SUMA_Write_PC_XYZ_Proj(pcp, PCprojpref)) {
SUMA_S_Err("Failed to write out projections");
exit(1);
} else {
pcp = SUMA_Free_PC_XYZ_Proj(pcp);
}
exit(0);
}
}
/* write the surface object */
if (SO_name) {
if (LocalHead) SUMA_Print_Surface_Object (SO, stderr);
fprintf (SUMA_STDOUT,"Writing surface...\n");
if (!(SUMA_Save_Surface_Object ( SO_name,
SO, oType, oFormat, SOpar))) {
fprintf (SUMA_STDERR,
"Error %s: Failed to write surface object.\n",
FuncName);
exit (1);
}
}
if (of_name_strip) of_name_strip = SUMA_Free_Parsed_Name (of_name_strip);
if (of_name2_strip) of_name2_strip = SUMA_Free_Parsed_Name (of_name2_strip);
if (OF_name) SUMA_free(OF_name);
if (OF_name2) SUMA_free(OF_name2);
if (SF_name) SUMA_free(SF_name);
if (SO_name) SUMA_free(SO_name);
if (SO) SUMA_Free_Surface_Object(SO);
if (SOpar) SUMA_Free_Surface_Object(SOpar);
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
return (0);
}