int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SampBias"};
int N_Spec = -1;
int i;
SUMA_SurfaceObject *SO = NULL;
SUMA_SurfSpecFile *Spec;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
void *SO_name = NULL;
SUMA_DSET *dset=NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_KUBATEST_OPTIONS Opt;
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, "-i;-spec;-sv;-s;-o;");
SUMA_SampBias_ParseInput (argv, argc, &Opt, ps);
if (argc < 4)
{
SUMA_S_Err("Too few arguments");
exit (0);
}
/* read surface */
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
SUMA_LH("Loading surface...");
SO = SUMA_Load_Spec_Surf_with_Metrics(Spec, 0, ps->sv[0], Opt.debug);
if (!SO) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (!(dset = calcWithOffsets(SO, &Opt))) {
SUMA_S_Err("Failed to calc ratios");
exit(1);
}
if (!SUMA_AddNgrHist(dset->ngr, "SampBias", argc, argv)) {
SUMA_S_Err("Failed to add history");
}
if (Opt.prefix) {
char *cc = SUMA_WriteDset_s(Opt.prefix, dset,
SUMA_NO_DSET_FORMAT, 1,1);
if (cc) SUMA_free(cc);
}
SUMA_LH("clean up");
if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv)) {
SUMA_SL_Err("DO Cleanup Failed!");
}
if (Opt.outfile) SUMA_free(Opt.outfile);
if (Opt.histnote) SUMA_free(Opt.histnote);
if (Opt.prefix) SUMA_free(Opt.prefix);
if (Opt.segdo) SUMA_free(Opt.segdo);
if (!SUMA_FreeSpecFields(Spec)) {
SUMA_S_Err("Failed to free SpecFields");
} SUMA_free(Spec); Spec = NULL;
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (!SUMA_Free_CommonFields(SUMAg_CF)) {
SUMA_SL_Err("SUMAg_CF Cleanup Failed!");}
SUMA_RETURN(0);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SurfMatch"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_SurfSpecFile *Spec = NULL;
int N_Spec=0, N_inmask;
byte *cmask=NULL;
SUMA_SurfaceObject *SO = NULL, *SOr=NULL;
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, "-i;-t;-spec;-s;-sv;");
if (argc < 2) {
usage_SurfMatch(ps, 0);
exit (1);
}
Opt = SUMA_SurfMatch_ParseInput (argv, argc, ps);
if (Opt->debug > 2) LocalHead = YUP;
/* check on inputs */
if (ps->s_N_surfnames + ps->i_N_surfnames + ps->t_N_surfnames != 2) {
SUMA_S_Err("Must have two surfaces");
exit(1);
}
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec != 1) {
SUMA_S_Err("Multiple spec at input.");
exit(1);
}
SOr = SUMA_Load_Spec_Surf_with_Metrics(Spec, 0, ps->sv[0], 1);
if (!SOr) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (Opt->efrac>0.0) {
SUMA_SurfaceObject *SOrr=NULL;
if (!(SOrr = SUMA_Mesh_Resample_nodes(SOr, Opt->efrac))) {
SUMA_S_Errv("Failed to resample initial mesh at %f\n",Opt->efrac);
exit(1);
}
SUMA_Free_Surface_Object(SOr); SOr=SOrr; SOrr=NULL;
SUMA_SurfaceMetrics_eng(SOr, "EdgeList|MemberFace", NULL, 0,
SUMAg_CF->DsetList);
if (!SOr->Label && !(SUMA_SurfaceFileName(SOr, NOPE))) {
SOr->Label = SUMA_copy_string("Le_Remaille");
}
}
SO = SUMA_Load_Spec_Surf_with_Metrics(Spec, 1, ps->sv[0], 1);
if (Opt->flt1 != 1.0) {
SUMA_LHv("Masking out nodes deeper than %f mm", Opt->flt1);
N_inmask = SUMA_NodeDepth(SO->NodeList, SO->N_Node, prjdir, NULL,
Opt->flt1, &cmask, NULL);
} else {
N_inmask = SO->N_Node;
}
SUMA_S_Notev("Have Reference %s %d nodes, input %s, %d nodes (%d in mask)\n",
SOr->Label, SOr->N_Node, SO->Label, SO->N_Node, N_inmask);
if (Opt->b1) {
Opt->s = SUMA_append_replace_string(Opt->s,"City", " ; ", 1);
}
SUMA_AlignCoords(SO->NodeList, SO->N_Node, cmask, 1, SOr, Opt->s);
/* write surface */
if (!SUMA_Save_Surface_Object_Wrap (Opt->out_prefix, NULL, SO,
SUMA_FT_NOT_SPECIFIED, SUMA_FF_NOT_SPECIFIED,
NULL)) {
SUMA_S_Err("Failed to write surface of whole head");
exit (1);
}
if (SOr) SUMA_Free_Surface_Object(SOr); SOr = NULL;
if (SO) SUMA_Free_Surface_Object(SO); SO = NULL;
if (cmask) SUMA_free(cmask); cmask=NULL;
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (N_Spec) {
int k=0;
for (k=0; k<N_Spec; ++k) {
if (!SUMA_FreeSpecFields(&(Spec[k]))) {
SUMA_S_Err("Failed to free spec fields");
}
}
SUMA_free(Spec); Spec = NULL; N_Spec = 0;
}
if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
if (!SUMA_Free_CommonFields(SUMAg_CF))
SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
exit(0);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SpharmReco"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_SurfSpecFile *Spec = NULL;
int *isin=NULL;
int i = -1, ii, jj, kk, il, N_Spec=0, i3, OK,
l, lc, ncol=0, nrow=0, dims[20], N_dims=0, N_surfs=0, j, j_l;
SUMA_Boolean exists=NOPE;
float *far=NULL, *xbuf=NULL, *ybuf=NULL, *zbuf=NULL;
double *dv=NULL, fac = 0.0;
complex *cv=NULL;
SUMA_FORM_AFNI_DSET_STRUCT *OptDs = NULL;
SUMA_SurfaceObject *SO = NULL, *SOt=NULL;
SUMA_VOLPAR *vp = NULL;
SUMA_MX_VEC *y_l=NULL, *y_l_t=NULL;
SUMA_MX_VEC *betal=NULL;
SUMA_MX_VEC *xe=NULL, *sm=NULL, *yc=NULL;
SUMA_MX_VEC **axe=NULL, **abeta=NULL;
char *oname=NULL, stmp[100], *pref=NULL;
SUMA_SO_File_Format form=SUMA_FF_NOT_SPECIFIED;
SUMA_SO_File_Type tp=SUMA_FT_NOT_SPECIFIED;
SUMA_OPT_SPHERICAL_BASES optb;
void *SO_name=NULL;
struct timeval tt;
int oform= SUMA_NO_DSET_FORMAT;
char *ooo=NULL;
float *fbuf=NULL;
SUMA_DSET *out_dset = NULL;
SUMA_Boolean do_surf_xyz = NOPE;
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, "-i;-spec;-talk;-o;");
if (argc < 2) {
usage_SpharmReco(ps);
exit (1);
}
Opt = SUMA_SpharmReco_ParseInput (argv, argc, ps);
if (Opt->debug) LocalHead = YUP;
if (Opt->n_in_namev < 1) {
SUMA_S_Err("No Coef!");
exit (1);
}
if (ps->o_N_surfnames) do_surf_xyz = YUP;
if (!ps->o_N_surfnames && !Opt->out_prefix) {
SUMA_S_Notev("Using default prefix of %s\n", "spharm_sm");
Opt->out_prefix = SUMA_copy_string("spharm_sm");
}
if ((Opt->n_in_namev % 3) && do_surf_xyz) {
SUMA_S_Errv("Number of coefficient options (%d) must be\n"
"a multiple of three if output is \n"
"to be treated as x, y, z coordinates\n", Opt->n_in_namev);
exit(1);
}
/* decide on output form */
if (Opt->out_prefix) {
oform = SUMA_GuessFormatFromExtension(Opt->out_prefix,"something.1D.dset");
}
if (Opt->debug > 2) LocalHead = YUP;
/* check on inputs */
optb.SOu=NULL;
optb.BasesFileRoot=Opt->bases_prefix;
optb.SaveBases=Opt->bases_prefix;
optb.debug = Opt->debug;
N_surfs = ps->s_N_surfnames + ps->i_N_surfnames + ps->t_N_surfnames;
if (( N_surfs != 1)) {
SUMA_S_Errv("You must provide only one surface.\n"
"Have %d on command line.\n", N_surfs);
exit(1);
}
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec != 1) {
SUMA_S_Err("Multiple spec at input.");
exit(1);
}
for (i=0; i<N_surfs; ++i) {
SO = SUMA_Load_Spec_Surf(Spec, i, ps->sv[i], 0);
if (!SO) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (Opt->debug > 2) SUMA_Print_Surface_Object(SO, SUMA_STDERR);
if (!SO->normdir) SO->normdir = 1; /* set it to something */
SOt = SUMA_CreateChildSO( SO, NULL, -1, NULL, -1, 0);
if (!SOt->State) {SOt->State = SUMA_copy_string("spharm_domain"); }
if (!SOt->Group) {SOt->Group = SUMA_copy_string("spharm_domain"); }
}
/* see if SUMA talk is turned on */
if (ps->cs->talk_suma) {
ps->cs->istream = SUMA_GEOMCOMP_LINE;
if (!SUMA_SendToSuma (SO, ps->cs, NULL, SUMA_NO_DSET_TYPE, 0)) {
SUMA_SL_Err("Failed to initialize SUMA_SendToSuma");
ps->cs->Send = NOPE;
ps->cs->talk_suma = NOPE;
}
SUMA_SendSumaNewSurface(SO, ps->cs);
}
/* Number of coefficients */
axe = (SUMA_MX_VEC **)SUMA_calloc(Opt->n_in_namev, sizeof(SUMA_MX_VEC*));
abeta = (SUMA_MX_VEC **)SUMA_calloc(Opt->n_in_namev, sizeof(SUMA_MX_VEC*));
/* initialize output variables */
for (i=0; i<Opt->n_in_namev; ++i) {
dims[0] = SO->N_Node; dims[1] = 1; N_dims = 2;
axe[i] = SUMA_NewMxVec(SUMA_double, 2, dims, 1);
if (Opt->debug > 1) SUMA_ShowMxVec(axe[i], 1, NULL, "\naxe[i]\n");
N_dims = -1; /* take whatever is in file, otherwise,
should setup dims[0] and dims[1] */
abeta[i] = SUMA_Read1DMxVec(SUMA_double, Opt->in_namev[i], dims, &N_dims);
if (Opt->debug > 1) SUMA_ShowMxVec(abeta[i], 1, NULL, "\nabeta[i]\n");
}
SUMA_Spherical_Bases(&l, NULL); /* init SUMA_Spherical_Bases */
/* start timer*/
SUMA_etime2(FuncName, NULL, NULL);
/* A record of matrices and processes to follow for spharm reconstruction
Here y_l, for each l, and beta are loaded from files created by SpharmDeco
N_Node : Number of points in parametrization of sphere
sigma : the smoothing kernel 0 == No smoothing, 0.01
(quite a bit of smoothing).
the higher the sigma the more the attenuation of higher
degree harmonics.
for l = 0;
y_l : l th degree harmonic complex l+1 x N_Node
turned to real since
imaginary is all 0
y_l_t : y_l' double N_Node x l+1
XX vt : y_l * y_l_t double l+1 x l+1
XX vt2 : inv(vt) double l+1 x l+1
XX Ycommon : vt2 * y_l double l+1 x N_Node
XX betal : Ycommon * x double l+1 x 1
betal : filled from beta(l,0:2l) double l+1 x 1
(beta(0,0), really)
xe : y_l_t * betal double N_Node x 1
for l > 0;
y_l : l th degree harmonic complex l+1 x N_Node
turned to real of dimensions: double 2*l+1 x N_Node
where the imaginary part of y_l
is appended below the real part
y_l_t : y_l' double N_Node x 2*l+1
XX vt : y_l * y_l_t double 2*l+1 x 2*l+1
XX vt2 : inv(vt) double 2*l+1 x 2*l+1
XX Ycommon : vt2 * y_l double 2*l+1 x N_Node
XX dif_vec_x: x - xe double N_Node x 1
betal : filled from beta(l,0:2l) double 2*l+1 x 1
sm : y_l_t * betal double N_Node x 1
fac : exp((-l*(l+1))*sigma) double 1 x 1
xe : xe + fac * sm double N_Node x 1
xe is the estimate of x up to order l harmonics
beta : lower triangular matrix where betal double l+1 x 2l+1
are stored for all l degrees
*/
l=0;
do {
lc = l;
y_l = SUMA_Spherical_Bases(&lc, &optb);
/* y_l is equal to Y' in Moo's SPHARsmooth.m function */
if (lc < l) {
/* The function will read in the bases from disk */
Opt->iopt = lc; /* y_l is a (l+1 x N_Node) complex matrix. */
SUMA_S_Notev("Cannot go for order higher than %d\n.", lc);
goto NEXT_L;
}
do {
if (SO) {
if ((LocalHead && l == 0) || Opt->debug > 1)
SUMA_S_Notev("Using the mesh from %s for \n"
"a reconstruction of degree %d.\n", SO->Label, l);
if (Opt->debug > 2) SUMA_Print_Surface_Object (SO, SUMA_STDERR);
} else {
SUMA_S_Err("NULL SO!!!");
exit(1);
}
if (LocalHead || Opt->debug > 1) {
fprintf(SUMA_STDERR,"%s: Doing l = %d\n", FuncName, l);
SUMA_etime2(FuncName, "Entering loop", FuncName);
}
if (l==0) {
yc = SUMA_CoerceMxVec(y_l, SUMA_double, 0, NULL);
/* for l == 0, all imaginary comp. are 0 */
y_l = SUMA_FreeMxVec(y_l); y_l = yc; yc = NULL;
y_l_t = SUMA_MxVecTranspose(y_l, NULL);
/* y_l is equal to Y' in Moo's SPHARsmooth.m function*/
if (Opt->debug > 1)
SUMA_ShowMxVec(y_l_t, 1, NULL, "\ny_l_t matrix\n");
dims[0] = 2*l+1; dims[1] = 1;
betal = SUMA_NewMxVec(SUMA_double, 2, dims, 1);
for (jj=0; jj<Opt->n_in_namev; ++jj) {
for (i=0;i<=2*l;++i) { mxvd2(betal,i,0) = mxvd2(abeta[jj],l, i); }
if (Opt->debug > 1)
SUMA_ShowMxVec(betal, 1, NULL, "\nbetal matrix\n");
xe = SUMA_MxVecMult(y_l_t, betal, NULL, 0);
if (Opt->debug > 1) {
SUMA_ShowMxVec(xe, 1, NULL, "\nxe vector\n");
if (Opt->debug > 2)
SUMA_WriteMxVec(xe, "xe_l0.1D", "#xe vector");
}
axe[jj] = xe; xe = NULL;
}
} else { /* higher order, need to deal with real and imaginary parts*/
/* Catenate the columns of y_l with the real columns first
(negative harmonics), followed by imaginary ones (positive harms.)*/
sprintf(stmp, "Starting with order l=%d", l);
if (Opt->debug) SUMA_etime2(FuncName, stmp, FuncName);
y_l = SUMA_YLcomp_to_YLdoub(&y_l, Opt->debug); /* Now y_l is real */
if (Opt->debug ) SUMA_etime2(FuncName, "Created y_l", FuncName);
if (Opt->debug > 2) {
SUMA_WriteMxVec(y_l, "y_l.1D.dset", "#y_l real matrix\n");
}
y_l_t = SUMA_MxVecTranspose(y_l, NULL);
/* y_l is equal to Y' in Moo's SPHARsmooth.m function*/
if (Opt->debug > 1)
SUMA_ShowMxVec(y_l_t, 1, NULL, "\ny_l_t matrix\n");
if (Opt->debug ) SUMA_etime2(FuncName, "Trasnposed y_l", FuncName);
fac = exp((double)(-l*(l+1))*Opt->v0);
dims[0] = 2*l+1; dims[1] = 1;
betal = SUMA_NewMxVec(SUMA_double, 2, dims, 1);
for (jj=0; jj<Opt->n_in_namev; ++jj) {
xe = axe[jj];
for (i=0;i<=2*l;++i) { mxvd2(betal,i,0) = mxvd2(abeta[jj],l, i); }
if (Opt->debug > 1)
SUMA_ShowMxVec(betal, 1, NULL, "\nbetal matrix\n");
sm = SUMA_MxVecMult(y_l_t, betal, sm, 0);
if (Opt->debug > 1) {
sprintf(stmp,"\nsm_%d vector\n", jj);
SUMA_ShowMxVec(sm , 1, NULL, stmp);
}
for (i=0;i<xe->N_vals;++i) {
mxvd1(xe,i) += fac * mxvd1(sm,i);
}
if (Opt->debug > 1) {
sprintf(stmp,"\n%d_estimate vector\n", jj);
SUMA_ShowMxVec(xe, 1, NULL, stmp);
sprintf(stmp,"%d_estimate_l%d.1D.dset", jj, l);
if (Opt->debug > 2)
SUMA_WriteMxVec(xe, stmp, "#estimate at last l\n");
}
}
if (Opt->debug) SUMA_etime2(FuncName, "Refit residual", FuncName);
}
/* store new coordinates, in a temp surface, fun to update as we're
progressing in case want to feed suma at some point*/
if (do_surf_xyz) {
if (l==0 && ps->cs->Send && Opt->debug) {
SUMA_S_Warn("Assuming coefficients are XYZ of surfaces !\n"
"Only the 1st three data columns will be used\n"
"in talk_suma mode.\n"
"Warnings muted for l > 0\n");
}
for (i=0; i<SO->N_Node; ++i) {
i3 = 3*i;
SOt->NodeList[i3 ] = mxvd1(axe[0], i);
SOt->NodeList[i3+1] = mxvd1(axe[1], i);
SOt->NodeList[i3+2] = mxvd1(axe[2], i);
}
}
if (ps->cs->Send) { /* send the smoothed coords */
if (do_surf_xyz) { /* surface coordinates */
if (l > 0) {
if (Opt->debug) {
SUMA_S_Notev("[%f %f %f]\n",
SOt->NodeList[0],
SOt->NodeList[1], SOt->NodeList[2]);
}
if (!SUMA_SendToSuma ( SO, ps->cs, (void *)SOt->NodeList,
SUMA_NODE_XYZ, 1)) {
SUMA_SL_Warn( "Failed in SUMA_SendToSuma\n"
"Communication halted.");
}
}
} else {
if (l > 0) {
if (!fbuf) fbuf = (float *)SUMA_malloc(SO->N_Node*
sizeof(float));
for (i=0; i<SO->N_Node; ++i) fbuf[i] = mxvd1(axe[0], i);
if (!SUMA_SendToSuma ( SO, ps->cs,
(void *)fbuf,
SUMA_NODE_RGBAb, 1)) {
SUMA_SL_Warn( "Failed in SUMA_SendToSuma\n"
"Communication halted.");
}
}
}
}
/* Done with order l */
if (y_l) y_l = SUMA_FreeMxVec(y_l);
if (y_l_t) y_l_t = SUMA_FreeMxVec(y_l_t);
if (betal) betal = SUMA_FreeMxVec(betal);
if (Opt->debug ) {
SUMA_S_Note("MemCheck:");
MCHECK;
}
} while (0);
NEXT_L:
++l;
} while (l <= Opt->iopt);
--l; /* back to where you stopped, kid */
/* Now create an output data set for the reconstructed data */
out_dset = SUMA_CreateDsetPointer(
Opt->out_prefix ? Opt->out_prefix:"spharm_reco",
SUMA_NODE_BUCKET, /* mix and match */
NULL, /* no idcode, let the function create one from the filename*/
NULL, /* no domain str specified */
SO->N_Node /* Number of nodes allocated for */
);
/* add results */
for (jj=0; jj<Opt->n_in_namev; ++jj) {
if (!fbuf) fbuf = (float *)SUMA_malloc(SO->N_Node*sizeof(float));
for (i=0; i<SO->N_Node; ++i) fbuf[i] = mxvd1(axe[jj], i);
if (!SUMA_AddDsetNelCol( out_dset, "sp_reco", SUMA_NODE_FLOAT,
fbuf, NULL, 1)) {
SUMA_S_Err("Failed to update output.");
exit(1);
}
axe[jj] = SUMA_FreeMxVec(axe[jj]);
}
if (Opt->out_prefix) {
/* write out the data */
ooo = SUMA_WriteDset_s( Opt->out_prefix, out_dset,
oform, THD_ok_overwrite(), 0);
if (Opt->debug) SUMA_S_Notev("Wrote %s\n", ooo);
SUMA_free(ooo); ooo=NULL;
}
/* do we need to write out surfaces? */
if (do_surf_xyz && ps->o_N_surfnames) {
for (i=0; i<Opt->n_in_namev/3; ++i) {
if (ps->o_N_surfnames == Opt->n_in_namev/3) {
pref = SUMA_copy_string(ps->o_surfnames[i]);
tp = ps->o_FT[i];
form = ps->o_FF[i];
} else {
sprintf(stmp, "s%02d", i);
pref = SUMA_append_string(ps->o_surfnames[0], stmp);
tp = ps->o_FT[0];
form = ps->o_FF[0];
}
if (Opt->debug) {
SUMA_S_Notev("Prepping to write surface %s\n"
"with X Y Z from cols. %d %d %d\n"
, pref, i*3, 1+i*3, 2+i*3);
}
xbuf = (float*)out_dset->dnel->vec[0+i*3];
ybuf = (float*)out_dset->dnel->vec[1+i*3];
zbuf = (float*)out_dset->dnel->vec[2+i*3];
for (ii=0; ii<SO->N_Node; ++ii) {
i3 = 3*ii;
SO->NodeList[i3 ] = xbuf[ii];
SO->NodeList[i3+1] = ybuf[ii];
SO->NodeList[i3+2] = zbuf[ii];
}
/* write the surface */
SO_name = SUMA_Prefix2SurfaceName(pref, NULL, NULL, tp, &exists);
if (!THD_ok_overwrite() && exists) {
fprintf(SUMA_STDERR,"Warning %s:\nOutput surface %s* on disk.\n"
"Will not overwrite.\n", FuncName, pref);
exit(1);
}
if (Opt->debug) {
SUMA_S_Notev("Saving surface under prefix %s\n", pref);
}
if (!SUMA_Save_Surface_Object (SO_name, SO, tp, form, NULL)) {
SUMA_S_Err("Failed to write reconstructed surface!");
exit(1);
}
}
}
/* clean and quit */
if (fbuf) SUMA_free(fbuf);
for (i=0; i<Opt->n_in_namev; ++i) {
SUMA_FreeMxVec(abeta[i]);
}
SUMA_free(axe); axe = NULL;
SUMA_free(abeta); abeta = NULL;
if (sm) sm = SUMA_FreeMxVec(sm);
SUMA_Spherical_Bases(&l, NULL); /* clean SUMA_Spherical_Bases */
/* you don't want to exit rapidly because the
SUMA might not be done processing the last elements*/
if (ps->cs->Send && !ps->cs->GoneBad) {
/* cleanup and close connections */
if (!SUMA_SendToSuma (SO, ps->cs, NULL, SUMA_NODE_XYZ, 2)) {
SUMA_SL_Warn("Failed in SUMA_SendToSuma\nCleanup failed");
}
}
if (N_Spec) {
int k=0;
for (k=0; k<N_Spec; ++k) {
if (!SUMA_FreeSpecFields(&(Spec[k]))) {
SUMA_S_Err("Failed to free spec fields"); }
}
SUMA_free(Spec); Spec = NULL; N_Spec = 0;
}
if (out_dset) SUMA_FreeDset(out_dset); out_dset = NULL;
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
if (!SUMA_Free_CommonFields(SUMAg_CF))
SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
exit(0);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SurfToSurf"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_SurfaceObject *SO1=NULL, *SO2 = NULL;
SUMA_SurfSpecFile *Spec = NULL;
SUMA_M2M_STRUCT *M2M = NULL;
int N_Spec=0, *nodeind = NULL, N_nodeind, icol, i, j;
MRI_IMAGE *im = NULL, *im_data=NULL;
int nvec=0, ncol=0, nvec_data=0, ncol_data=0, Nchar=0;
float *far = NULL, *far_data=NULL, *dt = NULL, *projdir=NULL;
char *outname = NULL, *s=NULL, sbuf[100];
void *SO_name = NULL;
FILE *outptr=NULL;
SUMA_Boolean exists = NOPE;
SUMA_INDEXING_ORDER d_order = SUMA_NO_ORDER;
SUMA_STRING *SS=NULL;
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, "-i;-t;-spec;-s;-sv;-o;");
Opt = SUMA_SurfToSurf_ParseInput (argv, argc, ps);
if (argc < 2) {
SUMA_S_Err("Too few options");
usage_SurfToSurf(ps, 0);
exit (1);
}
/* if output surface requested, check on pre-existing file */
if (ps->o_N_surfnames) {
SO_name = SUMA_Prefix2SurfaceName(ps->o_surfnames[0],
NULL, NULL, ps->o_FT[0], &exists);
if (exists) {
fprintf(SUMA_STDERR,
"Error %s:\nOutput file(s) %s* on disk.\n"
"Will not overwrite.\n", FuncName, ps->o_surfnames[0]);
exit(1);
}
}
if (Opt->debug > 2) LocalHead = YUP;
outname = SUMA_append_extension(Opt->out_prefix,".1D");
if (SUMA_filexists(outname) && !THD_ok_overwrite()) {
fprintf(SUMA_STDERR,"Output file %s exists.\n", outname);
exit(1);
}
/* Load the surfaces from command line*/
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec != 1) {
SUMA_S_Err( "Multiple spec at input.\n"
"Do not mix surface input types together\n");
exit(1);
}
if (Spec->N_Surfs != 2) {
SUMA_S_Err("2 surfaces expected.");
exit(1);
}
SO1 = SUMA_Load_Spec_Surf(Spec, 0, ps->sv[0], 0);
if (!SO1) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (!SUMA_SurfaceMetrics(SO1, "EdgeList|MemberFace", NULL)) {
SUMA_SL_Err("Failed to create edge list for SO1");
exit(1);
}
if (Opt->fix_winding) {
int orient, trouble;
if (LocalHead)
fprintf(SUMA_STDERR,
"%s: Making sure S1 is consistently orientated\n", FuncName);
if (!SUMA_MakeConsistent (SO1->FaceSetList, SO1->N_FaceSet,
SO1->EL, Opt->debug, &trouble)) {
SUMA_SL_Err("Failed in SUMA_MakeConsistent");
}
if (trouble && LocalHead) {
fprintf(SUMA_STDERR,
"%s: trouble value of %d from SUMA_MakeConsistent.\n"
"Inconsistencies were found and corrected unless \n"
"stderr output messages from SUMA_MakeConsistent\n"
"indicate otherwise.\n", FuncName, trouble);
}
if (LocalHead)
fprintf(SUMA_STDERR,"%s: Checking orientation.\n", FuncName);
orient = SUMA_OrientTriangles (SO1->NodeList, SO1->N_Node,
SO1->FaceSetList, SO1->N_FaceSet,
1, 0, NULL, NULL);
if (orient < 0) {
/* flipping was done, dump the edge list since it is not
automatically updated (should do that in function,
just like in SUMA_MakeConsistent, shame on you)
If you revisit this section, use the newer:
SUMA_OrientSOTriangles
*/
if (SO1->EL) SUMA_free_Edge_List(SO1->EL); SO1->EL = NULL;
if (!SUMA_SurfaceMetrics(SO1, "EdgeList", NULL)) {
SUMA_SL_Err("Failed to create edge list for SO1"); exit(1);
}
/* free normals, new ones needed (Normals should be flipped inside of
SUMA_OrientTriangles! (just like in SUMA_MakeConsistent) ) */
if (SO1->NodeNormList) SUMA_free(SO1->NodeNormList);
SO1->NodeNormList = NULL;
if (SO1->FaceNormList) SUMA_free(SO1->FaceNormList);
SO1->FaceNormList = NULL;
}
if (!orient) {
fprintf(SUMA_STDERR,
"Error %s:\nFailed in SUMA_OrientTriangles\n", FuncName);
}
if (LocalHead) {
if (orient < 0) { SUMA_SL_Note("S1 was reoriented"); }
else { SUMA_SL_Note("S1 was properly oriented"); }
}
}
if (!SO1->NodeNormList || !SO1->FaceNormList) {
SUMA_LH("Node Normals"); SUMA_RECOMPUTE_NORMALS(SO1);
}
if (Opt->NodeDbg >= SO1->N_Node) {
SUMA_SL_Warn( "node_debug index is larger than number "
"of nodes in surface, ignoring -node_debug.");
Opt->NodeDbg = -1;
}
SO2 = SUMA_Load_Spec_Surf(Spec, 1, ps->sv[1], 0);
if (!SO2) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (!SUMA_SurfaceMetrics(SO2, "EdgeList|MemberFace", NULL)) {
SUMA_SL_Err("Failed to create edge list for SO2"); exit(1);
}
if (!SO2->NodeNormList || !SO2->FaceNormList) {
SUMA_LH("Node Normals"); SUMA_RECOMPUTE_NORMALS(SO2);
}
if (LocalHead) {
SUMA_LH("Surf1");
SUMA_Print_Surface_Object(SO1, NULL);
SUMA_LH("Surf2");
SUMA_Print_Surface_Object(SO2, NULL);
}
/* a select list of nodes? */
nodeind = NULL; N_nodeind = 0;
if (Opt->in_nodeindices) {
im = mri_read_1D(Opt->in_nodeindices);
if (!im) { SUMA_SL_Err("Failed to read 1D file of node indices"); exit(1);}
far = MRI_FLOAT_PTR(im);
N_nodeind = nvec = im->nx;
ncol = im->ny;
if (ncol != 1) {
SUMA_SL_Err("More than one column in node index input file."); exit(1);
}
nodeind = (int *)SUMA_calloc(nvec, sizeof(int));
if (!nodeind) { SUMA_SL_Crit("Failed to allocate"); exit(1); }
for (i=0;i<nvec;++i) {
nodeind[i] = (int)far[i];
if (nodeind[i] < 0 || nodeind[i] >= SO1->N_Node) {
fprintf(SUMA_STDERR,
"Error %s:\n"
"A node index of %d was found in input file %s, entry %d.\n"
"Acceptable indices are positive and less than %d\n",
FuncName, nodeind[i], Opt->in_nodeindices, i, SO1->N_Node);
exit(1);
}
}
mri_free(im); im = NULL; /* done with that baby */
}
/* a preset directions vector ?*/
projdir = NULL;
if (Opt->in_1D) {
im = mri_read_1D(Opt->in_1D);
if (!im) {
SUMA_SL_Err("Failed to read 1D file of projection directions"); exit(1);
}
far = MRI_FLOAT_PTR(im);
if (im->ny != 3) {
SUMA_SL_Err("Need three columns in projection directions file.");
exit(1);
}
if (im->nx != SO1->N_Node) {
fprintf(SUMA_STDERR,
"Error %s: You must have a direction for each node in SO1.\n"
"%d directions found but SO1 has %d nodes.\n",
FuncName, im->nx, SO1->N_Node);
exit(1);
}
/* change to row major major and make it match nodeind */
projdir = (float *)SUMA_calloc(SO1->N_Node*3, sizeof(float));
if (!projdir) { SUMA_SL_Crit("Failed to allocate"); exit(1); }
for (i=0; i<SO1->N_Node; ++i) {
projdir[3*i ] = far[i ];
projdir[3*i+1] = far[i+ SO1->N_Node];
projdir[3*i+2] = far[i+2*SO1->N_Node];
}
mri_free(im); im = NULL; /* done with that baby */
}
if (SO_name) {
/* user is interpolating surface coords, check on other input insanity */
if (nodeind) {
fprintf( SUMA_STDERR,
"Error %s: You cannot combine "
"option -o_TYPE with -node_indices", FuncName);
exit(1);
}
if (Opt->in_name) {
fprintf(SUMA_STDERR,
"Error %s: You cannot combine option -o_TYPE with -data",
FuncName);
exit(1);
}
}
/* a 1D file containing data, or Data parameter (for XYZ)? */
if (Opt->Data > 0) {
if (Opt->in_name) {
/* When you are ready to work with dsets, you should
checkout the function morphDsetToStd. It uses M2M */
im_data = mri_read_1D(Opt->in_name);
if (!im_data) {
SUMA_SL_Err("Failed to read 1D file of data"); exit(1);}
far_data = MRI_FLOAT_PTR(im_data);
nvec_data = im_data->nx;
ncol_data = im_data->ny;
if (nvec_data != SO2->N_Node) {
SUMA_SL_Err("Your data file must have one row "
"for each node in surface 2.\n"); exit(1);
}
d_order = SUMA_COLUMN_MAJOR;
} else {
im_data = NULL;
far_data = SO2->NodeList;
nvec_data = SO2->N_Node;
ncol_data = 3;
d_order = SUMA_ROW_MAJOR;
}
} else {
/* just -dset */
}
if (!Opt->s) {
SUMA_LH("Going for the mapping of SO1 --> SO2");
M2M = SUMA_GetM2M_NN( SO1, SO2, nodeind, N_nodeind,
projdir, 0, Opt->NodeDbg, Opt->iopt);
SUMA_S_Notev("Saving M2M into %s\n\n",
Opt->out_prefix);
if (!(SUMA_Save_M2M(Opt->out_prefix, M2M))) {
SUMA_S_Err("Failed to save M2M");
exit(1);
}
} else {
SUMA_S_Notev("Reusing mapping of SO1 --> SO2 from %s\n\n",
Opt->s);
if (!(M2M = SUMA_Load_M2M(Opt->s))) {
SUMA_S_Errv("Failed to load %s\n", Opt->s);
exit(1);
}
}
/* Now show the mapping results for a debug node ? */
if (Opt->NodeDbg >= 0) {
char *s = NULL;
s = SUMA_M2M_node_Info(M2M, Opt->NodeDbg);
fprintf(SUMA_STDERR,"%s: Debug for node %d ([%f, %f, %f])of SO1:\n%s\n\n",
FuncName, Opt->NodeDbg,
SO1->NodeList[3*Opt->NodeDbg],
SO1->NodeList[3*Opt->NodeDbg+1],
SO1->NodeList[3*Opt->NodeDbg+2],
s);
SUMA_free(s); s = NULL;
}
/* Now please do the interpolation */
if (Opt->Data > 0) {
if (Opt->NearestNode > 1)
dt = SUMA_M2M_interpolate( M2M, far_data, ncol_data,
nvec_data, d_order, 0 );
else if (Opt->NearestNode == 1)
dt = SUMA_M2M_interpolate( M2M, far_data, ncol_data,
nvec_data, d_order, 1 );
if (!dt) {
SUMA_SL_Err("Failed to interpolate");
exit(1);
}
} else if (Opt->Data < 0) {
SUMA_DSET *dset=NULL, *dseto=NULL;
char *oname=NULL, *uname=NULL, *s1=NULL, *s2=NULL;
int iform=SUMA_NO_DSET_FORMAT;
if (Opt->NodeDbg>= 0) {
SUMA_S_Notev("Processing dset %s\n", Opt->in_name);
}
iform = SUMA_NO_DSET_FORMAT;
if (!(dset = SUMA_LoadDset_s (Opt->in_name, &iform, 0))) {
SUMA_S_Errv("Failed to load %s\n", Opt->in_name);
exit(1);
}
if (!(dseto = SUMA_morphDsetToStd ( dset, M2M,
Opt->NearestNode == 1 ? 1:0))) {
SUMA_S_Errv("Failed to map %s\n", Opt->in_name);
exit(1);
}
s1 = SUMA_append_string(
SUMA_FnameGet(Opt->in_name,"pa", SUMAg_CF->cwd),
Opt->out_prefix);
s2 = SUMA_RemoveDsetExtension_s(
SUMA_FnameGet(Opt->in_name,"l",SUMAg_CF->cwd),
SUMA_NO_DSET_FORMAT);
uname = SUMA_append_extension(s1,s2);
SUMA_free(s1); SUMA_free(s2);
oname = SUMA_WriteDset_s (uname, dseto, Opt->oform, 1, 1);
if (Opt->NodeDbg>= 0) SUMA_S_Notev("Wrote %s\n", oname);
if (oname) SUMA_free(oname); oname=NULL;
if (uname) SUMA_free(uname); oname=NULL;
if (dseto) SUMA_FreeDset(dseto); dseto = NULL;
if (dset) SUMA_FreeDset(dset); dset = NULL;
}
SUMA_LH("Forming the remaining output");
outptr = fopen(outname,"w");
if (!outptr) {
SUMA_SL_Err("Failed to open file for output.\n");
exit(1);
}
/* first create the header of the output */
SS = SUMA_StringAppend(NULL, NULL);
SS = SUMA_StringAppend_va(SS,
"#Mapping from nodes on surf 1 (S1) to nodes on surf 2 (S2)\n"
"# Surf 1 is labeled %s, idcode:%s\n"
"# Surf 2 is labeled %s, idcode:%s\n",
SO1->Label, SO1->idcode_str, SO2->Label, SO2->idcode_str);
icol = 0;
SS = SUMA_StringAppend_va(SS, "#Col. %d:\n"
"# S1n (or nj): Index of node on S1\n"
, icol);
++icol;
if (Opt->NearestNode > 1) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# S2ne_S1n: Indices of %d nodes on S2 \n"
"# that are closest neighbors of nj.\n"
"# The first index is that of the node on S2 that is closest \n"
"# to nj. If -1 then these values should be ignored because\n"
"# in such cases, nj's projection failed.\n"
, icol, icol+Opt->NearestNode-1, Opt->NearestNode);
icol += Opt->NearestNode;
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# S2we_S1n: Weights assigned to nodes on surf 2 (S2) \n"
"# that are closest neighbors of nj.\n"
, icol, icol+Opt->NearestNode-1, Opt->NearestNode);
icol += Opt->NearestNode;
} else if (Opt->NearestNode == 1) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d:\n"
"# S2ne_S1n: Index of the node on S2 (label:%s idcode:%s)\n"
"# that is the closest neighbor of nj.\n"
"# If -1 then this value should be ignored because\n"
"# nj's projection failed.\n"
, icol, SO2->Label, SO2->idcode_str);
++icol;
}
if (Opt->NearestTriangle) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d:\n"
"# S2t_S1n: Index of the S2 triangle that hosts node nj on S1.\n"
"# In other words, nj's closest projection onto S2 falls on \n"
"# triangle S2t_S1n\n"
"# If -1 then this value should be ignored because \n"
"# nj's projection failed.\n"
, icol);
++icol;
}
if (Opt->ProjectionOnMesh) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# S2p_S1n: Coordinates of projection of nj onto S2\n"
, icol, icol+2);
icol += 3;
}
if (Opt->DistanceToMesh) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d:\n"
"# Closest distance from nj to S2\n"
, icol);
++icol;
}
if (Opt->NearestNodeCoords) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d .. %d:\n"
"# X Y Z coords of nearest node\n"
, icol, icol+2);
icol += 3;
}
if (Opt->Data > 0) {
if (!Opt->in_name) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# Interpolation using XYZ coordinates of S2 nodes that neighbor nj\n"
"# (same as coordinates of node's projection onto triangle in S2, \n"
"# if using barycentric interpolation)\n"
, icol, icol+2);
icol += 3;
} else {
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# Interpolation of data at nodes on S2 that neighbor nj\n"
"# Data obtained from %s\n"
, icol, icol+ncol_data-1, Opt->in_name); icol += ncol_data;
}
}
s = SUMA_HistString("SurfToSurf", argc, argv, NULL);
SS = SUMA_StringAppend_va(SS,
"#History:\n"
"#%s\n", s); SUMA_free(s); s = NULL;
SUMA_SS2S(SS,s);
fprintf(outptr,"%s\n",s); SUMA_free(s); s = NULL;
/* put headers atop columns */
Nchar = 6; /* if you change this number you'll need to fix formats below */
for (i=0; i<icol; ++i) {
sprintf(sbuf,"#%s", MV_format_fval2(i, Nchar -1));
fprintf(outptr,"%6s ", sbuf);
}
fprintf(outptr,"\n");
/* Now put in the values, make sure you parallel columns above! */
for (i=0; i<M2M->M1Nn; ++i) {
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M1n[i], Nchar));
if (Opt->NearestNode > 0) {
for (j=0; j<Opt->NearestNode; ++j) {
if (j < M2M->M2Nne_M1n[i])
fprintf(outptr,"%6s ",
MV_format_fval2(M2M->M2ne_M1n[i][j], Nchar));
else fprintf(outptr,"%6s ", "-1");
} /* Neighboring nodes */
}
if (Opt->NearestNode > 1) { /* add the weights */
for (j=0; j<Opt->NearestNode; ++j) {
if (j < M2M->M2Nne_M1n[i])
fprintf(outptr,"%6s ",
MV_format_fval2(M2M->M2we_M1n[i][j], Nchar));
else fprintf(outptr,"%6s ", "0.0");
}
}
if (Opt->NearestTriangle) {
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M2t_M1n[i], Nchar));
}
if (Opt->ProjectionOnMesh) {
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M2p_M1n[3*i], Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M2p_M1n[3*i+1], Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M2p_M1n[3*i+2], Nchar));
}
if (Opt->DistanceToMesh) {
fprintf(outptr,"%6s ", MV_format_fval2(M2M->PD[i], Nchar));
}
if (Opt->NearestNodeCoords) {
float x=0.0,y=0.0,z=0.0;
int n = M2M->M2ne_M1n[i][0];
if (n>0) {
n = n * SO2->NodeDim;
x = SO2->NodeList[n];
y = SO2->NodeList[n+1];
z = SO2->NodeList[n+2];
}
fprintf(outptr,"%6s ", MV_format_fval2(x, Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(y, Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(z, Nchar));
}
if (dt && Opt->Data > 0) {
if (!Opt->in_name) {
fprintf(outptr,"%6s ", MV_format_fval2(dt[3*i], Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(dt[3*i+1], Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(dt[3*i+2], Nchar));
} else { /* Column major business */
for (j=0; j<ncol_data; ++j) {
fprintf(outptr,"%6s ",
MV_format_fval2(dt[i+j*M2M->M1Nn], Nchar)); }
}
}
fprintf(outptr,"\n");
}
/* do they want an output surface ? */
if (SO_name) {
float *tmpfv = NULL;
SUMA_LH("Writing surface");
tmpfv = SO1->NodeList;
SO1->NodeList = dt;
if (!SUMA_Save_Surface_Object (SO_name, SO1,
ps->o_FT[0], ps->o_FF[0], NULL)) {
SUMA_S_Err("Failed to write surface object.\n");
exit (1);
}
SO1->NodeList = tmpfv; tmpfv = NULL;
}
if (N_Spec) {
int k=0;
for (k=0; k<N_Spec; ++k) {
if (!SUMA_FreeSpecFields(&(Spec[k]))) {
SUMA_S_Err("Failed to free spec fields");
}
}
SUMA_free(Spec); Spec = NULL; N_Spec = 0;
}
if (projdir) SUMA_free(projdir); projdir = NULL;
if (SO_name) SUMA_free(SO_name); SO_name = NULL;
if (outptr) fclose(outptr); outptr = NULL;
if (dt) SUMA_free(dt); dt = NULL;
if (s) SUMA_free(s); s = NULL;
if (im_data) mri_free(im_data); im_data = NULL; /* done with the data */
if (nodeind) SUMA_free(nodeind); nodeind = NULL;
if (M2M) M2M = SUMA_FreeM2M(M2M);
if (SO1) SUMA_Free_Surface_Object(SO1); SO1 = NULL;
if (SO2) SUMA_Free_Surface_Object(SO2); SO2 = NULL;
if (Spec) SUMA_free(Spec); Spec = NULL;
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
if (!SUMA_Free_CommonFields(SUMAg_CF)) SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
exit(0);
}
/*!\**
File : SUMA.c
\author : Ziad Saad
Date : Thu Dec 27 16:21:01 EST 2001
Purpose :
Input paramters :
\param
\param
Usage :
SUMA ( )
Returns :
\return
\return
Support :
\sa OpenGL prog. Guide 3rd edition
\sa varray.c from book's sample code
Side effects :
***/
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"suma"};
int kar, i;
SUMA_SFname *SF_name;
SUMA_Boolean brk, SurfIn;
char *NameParam, *AfniHostName = NULL, *s = NULL, *pdspec=NULL, *pdsv=NULL;
char *specfilename[SUMA_MAX_N_GROUPS], *VolParName[SUMA_MAX_N_GROUPS];
byte InMem[SUMA_MAX_N_GROUPS];
SUMA_SurfSpecFile *Specp[SUMA_MAX_N_GROUPS];
SUMA_Axis *EyeAxis;
SUMA_EngineData *ED= NULL;
DList *list = NULL;
DListElmt *Element= NULL;
int iv15[15], N_iv15, ispec, nspec;
struct stat stbuf;
float fff=0.0;
int Start_niml = 0;
SUMA_Boolean Domemtrace = YUP;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
SUMAg_CF->isGraphical = YUP;
ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-dset;-do;");
/* initialize Volume Parent and AfniHostName to nothing */
for (ispec=0; ispec < SUMA_MAX_N_GROUPS; ++ispec) {
specfilename[ispec] = NULL;
VolParName[ispec] = NULL;
Specp[ispec] = NULL;
InMem[ispec] = 0;
}
AfniHostName = NULL;
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
/* call the function to parse the other surface mode inputs */
ispec = 0;
if (LocalHead) SUMA_Show_IO_args(ps);
if (ps->i_N_surfnames || ps->t_N_surfnames || ps->N_DO) {
SUMA_LH("-i and/or -t surfaces on command line!");
Specp[ispec] = SUMA_IO_args_2_spec (ps, &nspec);
if (Specp[ispec]) {
++ispec;
if (nspec != 1) {
SUMA_S_Errv("-spec is being parsed separately here, "
"expecting one spec only from SUMA_IO_args_2_spec, \n"
"got %d\n", nspec);
exit (1);
}
} else {
SUMA_S_Err("Failed to load -i/-t surfaces");
exit(1);
}
}
/* Work the options */
kar = 1;
brk = NOPE;
SurfIn = NOPE;
Domemtrace = YUP;
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) {
SUMA_usage (ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0); /* return a good status on -help 12 Jul 2013 [rickr] */
}
/* -list_ports list and quit */
if( strncmp(argv[kar],"-list_ports", 8) == 0) {
show_ports_list(); exit(0);
}
/* -port_number and quit */
if( strncmp(argv[kar],"-port_number", 8) == 0) {
int pp = 0;
if( ++kar >= argc )
ERROR_exit("need an argument after -port_number!");
pp = get_port_named(argv[kar]);
if (strcmp(argv[kar-1], "-port_number_quiet")) {
fprintf(stdout, "\nPort %s: %d\n", argv[kar], pp);
} else {
fprintf(stdout, "%d\n", pp);
}
if (pp < 1) exit(1);
else exit(0);
}
if (strcmp(argv[kar], "-visuals") == 0) {
SUMA_ShowAllVisuals ();
exit (0);
}
if (strcmp(argv[kar], "-brethren_windows") == 0) {
Display *dd=NULL; Window ww;
if (!(dd = XOpenDisplay(NULL))) {
SUMA_S_Err("No display "); exit(1);
}
ww = XDefaultRootWindow(dd);
SUMA_WindowsOnRootDisplay(dd, ww , 0);
exit (0);
}
if (strcmp(argv[kar], "-version") == 0) {
s = SUMA_New_Additions (0.0, 1);
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-sources") == 0) {
s = SUMA_sources_Info();
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-help_nido") == 0) {
s = SUMA_NIDO_Info();
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-all_latest_news") == 0) {
s = SUMA_New_Additions (-1.0, 0);
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-help_sphinx_interactive") == 0) {
FILE *fout = NULL;
if( ++kar >= argc )
ERROR_exit("need a file name after -help_sphinx_interactive!");
fout = fopen(argv[kar],"w");
if (!fout) {
SUMA_S_Err("Failed to open %s for writing", argv[kar]);
exit(1);
}
SUMA_help_message(fout,SPX);
fclose(fout); fout = NULL;
exit (0);
}
if (strcmp(argv[kar], "-help_interactive") == 0) {
FILE *fout = fopen("Mouse_Keyboard_Controls.txt","w");
if (!fout) {
SUMA_S_Err("Failed to open Mouse_Keyboard_Controls.txt for writing");
exit(1);
}
SUMA_help_message(fout,TXT);
fclose(fout); fout = NULL;
exit (0);
}
if (strcmp(argv[kar], "-test_help_string_edit") == 0) {
SUMA_Sphinx_String_Edit_Help(SUMA_STDOUT, 0);
exit(0);
}
if (strcmp(argv[kar], "-test_help_string_edit_web") == 0) {
SUMA_Sphinx_String_Edit_Help(SUMA_STDOUT, 1);
exit(0);
}
if (strcmp(argv[kar], "-environment") == 0) {
s = SUMA_env_list_help (0, TXT);
fprintf (SUMA_STDOUT,
"#SUMA ENVIRONMENT \n"
"# If you do not have a ~/.sumarc file, cannot find a SUMA\n"
"# environment variable that's been mentioned in documentation,\n"
"# or fervently desire to update your current ~/.sumarc with \n"
"# all the latest variables that SUMA uses, you should run: \n"
"# \n"
"# suma -update_env\n"
"# \n"
"# Unless you have setup SUMA environment variables outside of\n"
"# your ~/.sumarc file, updating your ~/.sumarc file with \n"
"# 'suma -update_env' WILL NOT ALTER changes you have already\n"
"# made to the variables in your current ~/.sumarc. \n"
"# For this reason consider running the update command after each \n"
"# upgrade of your AFNI/SUMA binaries.\n"
"***ENVIRONMENT\n"
"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-default_env") == 0) {
s = SUMA_env_list_help (1, NO_FORMAT);
fprintf (SUMA_STDOUT,
"#SUMA DEFAULT ENVIRONMENT (user settings ignored)\n"
"# see also suma -udate_env or suma -environment\n"
"# \n"
"***ENVIRONMENT\n"
"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-update_env") == 0) {
if (system("suma -environment > ___sumarc")) {
SUMA_S_Err("Failed to create env file.");
exit(1);
}
if (SUMA_filexists("~/.sumarc")) {
if (system("\\cp -f ~/.sumarc ~/.sumarc-bak")) {
SUMA_S_Err("Failed to backup ~/.sumarc to ~/.sumarc-bak.");
exit(1);
}
}
if (system("\\mv ___sumarc ~/.sumarc")) {
SUMA_S_Err("Failed to copy newrc (___sumarc) to ~/.sumarc");
exit(1);
}
SUMA_S_Note("Environment update done.");
exit(0);
}
if (strcmp(argv[kar], "-latest_news") == 0) {
s = SUMA_New_Additions (0.0, 0);
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-progs") == 0) {
s = SUMA_All_Programs();
fprintf (SUMA_STDOUT,"%s\n", s);
SUMA_free(s); s = NULL;
exit (0);
}
if (strcmp(argv[kar], "-motif_ver") == 0) { /* 9 Mar 2009 [rickr] */
show_motif_version_string();
exit (0);
}
if (!brk && (strcmp(argv[kar], "-iodbg") == 0)) {
fprintf(SUMA_STDERR,"Error %s: Obsolete, use -trace\n", FuncName);
exit (0);
/*
fprintf(SUMA_STDOUT,
"Warning %s: SUMA running in in/out debug mode.\n", FuncName);
SUMA_INOUT_NOTIFY_ON;
brk = YUP;
*/
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
#if SUMA_MEMTRACE_FLAG
if (!brk && (strcmp(argv[kar], "-memdbg") == 0)) {
fprintf(SUMA_STDOUT,"Error %s: -memdbg is obsolete, use -trace\n",
FuncName);
exit (0);
fprintf( SUMA_STDOUT,
"Warning %s: SUMA running in memory trace mode.\n",
FuncName);
SUMAg_CF->MemTrace = YUP;
#ifdef USING_MCW_MALLOC
#endif
brk = YUP;
}
#endif
if (!brk && (strcmp(argv[kar], "-dev") == 0)) {
fprintf(SUMA_STDOUT,
"Warning %s: SUMA running in developer mode, "
"some options may malfunction.\n", FuncName);
SUMAg_CF->Dev = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-fake_cmap") == 0)) {
SUMA_S_Warn("-fake_cmap is for automatic selfies of the widgets.\n"
"You should not use this option for any other reason\n");
SUMAg_CF->Fake_Cmap = YUP;
brk = YUP;
}
if (!brk && SUMAg_CF->Dev && (strcmp(argv[kar], "-truth_table") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need expression after -truth_table \n");
exit (1);
}
SUMA_bool_eval_truth_table(argv[kar], 0); exit(0);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-niml") == 0)) {
Start_niml = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-noniml") == 0)) {
Start_niml = -1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-vp") == 0 ||
strcmp(argv[kar], "-sa") == 0 ||
strcmp(argv[kar], "-sv") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -vp|-sa|-sv \n");
exit (1);
}
if (ispec < 1) {
fprintf (SUMA_STDERR,
"a -spec option must precede the first -sv option\n");
exit (1);
}
if (!specfilename[ispec-1] && !Specp[ispec-1]) {
fprintf (SUMA_STDERR,
"a -spec option must precede each -sv option\n");
exit (1);
}
VolParName[ispec-1] = argv[kar];
if (LocalHead) {
fprintf(SUMA_STDOUT, "Found: %s\n", VolParName[ispec]);
}
brk = YUP;
}
if (!brk && strcmp(argv[kar], "-drive_com") == 0)
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -drive_com\n");
exit (1);
}
SUMAg_CF->dcom = (char **)SUMA_realloc(SUMAg_CF->dcom,
(SUMAg_CF->N_dcom+1)*sizeof(char *));
SUMAg_CF->dcom[SUMAg_CF->N_dcom] = SUMA_copy_string(argv[kar]);
++SUMAg_CF->N_dcom;
brk = YUP;
}
if (!brk && strcmp(argv[kar], "-ah") == 0)
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -ah\n");
exit (1);
}
if (strcmp(argv[kar],"localhost") != 0) {
AfniHostName = argv[kar];
}else {
fprintf (SUMA_STDERR,
"localhost is the default for -ah\n"
"No need to specify it.\n");
}
/*fprintf(SUMA_STDOUT, "Found: %s\n", AfniHostName);*/
brk = YUP;
}
if (!brk && strcmp(argv[kar], "-spec") == 0)
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -spec \n");
exit (1);
}
if (ispec >= SUMA_MAX_N_GROUPS) {
fprintf (SUMA_STDERR,
"Cannot accept more than %d spec files.\n",
SUMA_MAX_N_GROUPS);
exit(1);
}
if (SUMA_is_predefined_SO_name(argv[kar], NULL,
&pdspec, &pdsv, NULL) == 3) {
specfilename[ispec] = pdspec; pdspec = NULL; /* Memory leak! */
VolParName[ispec] = pdsv; pdsv = NULL; /* Memory leak! */
} else {
specfilename[ispec] = argv[kar];
}
if (LocalHead) {
fprintf(SUMA_STDOUT, "Found: %s\n", specfilename[ispec]);
}
++ispec;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
if ( !strcmp(argv[kar], "-i") ||
!strncmp(argv[kar], "-i_",3) ) {
fprintf (SUMA_STDERR,
"Error %s: Option %s not understood. \n"
" Make sure parameter after -i or -i_ is the full name of a surface.\n"
"%s",
FuncName, argv[kar],
strlen(argv[kar])==2 ?
"For -i to work, SUMA needs to guess at the surface type from\n"
" the filename extensions. If SUMA fails try the full -i_* option"
" instead.\n" : ""
);
} else {
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 ++;
}
}/* loop accross command ine options */
/* -ah option now checked for in ps */
if (ps->cs->afni_host_name && !AfniHostName) {
AfniHostName = SUMA_copy_string(ps->cs->afni_host_name);
}
#if 0
SUMA_S_Note("KILL ME");
{
int i,j, nl;
SUMA_TextBoxSize("Hello", &i,&j,&nl,NULL);
SUMA_TextBoxSize("",
&i,&j,&nl,GLUT_BITMAP_8_BY_13);
SUMA_TextBoxSize("O",
&i,&j,&nl,GLUT_BITMAP_8_BY_13);
SUMA_TextBoxSize(NULL,
&i,&j,&nl,GLUT_BITMAP_8_BY_13);
}
SUMA_ReadNIDO("/Users/ziad/SUMA_test_dirs/DO/TextDO/sample.niml.do", NULL);
exit(1);
#endif
/* Make surface loading pacifying */
SetLoadPacify(1);
#if 0
if (ps->N_DO) { /* Have DOs on command line */
if (Specp[0]) { /* Add to Specp[0] */
if (ps->N_DO + Specp[0]->N_DO > SUMA_MAX_DO_SPEC) {
SUMA_S_Warn("Too many DOs, increase static limit..");
/* ignore extras for now */
ps->N_DO = SUMA_MAX_DO_SPEC - Specp[0]->N_DO;
}
for (i=0; i<ps->N_DO; ++i) {
strcpy(Specp[0]->DO_name[Specp[0]->N_DO], ps->DO_name[i]);
Specp[0]->DO_type[Specp[0]->N_DO] = ps->DO_type[i];
++Specp[0]->N_DO;
}
} else {
Specp[0]
}
}
#endif
/* any Specp to be found ?*/
if (specfilename[0] == NULL && Specp[0] == NULL) {
SUMA_SurfaceObject **SOv=NULL;
int N_SOv = 0;
fprintf (SUMA_STDERR,
"\n"
"%s: \n"
" No input specified, loading some toy surfaces...\n"
" Use '.' and ',' to cycle between them.\n"
" See suma -help for assistance.\n"
"\n", FuncName);
/* create your own surface and put it in a spec file */
SOv = SUMA_GimmeSomeSOs(&N_SOv);
Specp[ispec] = SUMA_SOGroup_2_Spec (SOv, N_SOv);
SUMA_free(SOv); SOv = NULL;
InMem[ispec] = 1;
++ispec;
}
if(!SUMA_Assign_HostName (SUMAg_CF, AfniHostName, -1)) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_Assign_HostName\n", FuncName);
exit (1);
}
#ifdef SUMA_DISASTER
/* a function to test Memtracing */
{
int *jnk;
jnk = SUMA_disaster();
SUMA_free(jnk); /* without the -trace, you'll get a
warning here if jnk is corrupted */
}
#endif
/* create an Eye Axis DO */
EyeAxis = SUMA_Alloc_Axis ("Eye Axis", AO_type);
if (EyeAxis == NULL) {
SUMA_error_message (FuncName,"Error Creating Eye Axis",1);
exit(1);
}
/* Store it into SUMAg_DOv */
if (!SUMA_AddDO( SUMAg_DOv, &SUMAg_N_DOv,
(void *)EyeAxis, AO_type, SUMA_SCREEN)) {
SUMA_error_message (FuncName,"Error Adding DO", 1);
exit(1);
}
/*fprintf (SUMA_STDERR, "SUMAg_N_DOv = %d created\n", SUMAg_N_DOv);
SUMA_Show_DOv(SUMAg_DOv, SUMAg_N_DOv, NULL);*/
/* Allocate space (and initialize) Surface Viewer Structure */
SUMAg_SVv = SUMA_Alloc_SurfaceViewer_Struct (SUMA_MAX_SURF_VIEWERS);
/* SUMAg_N_SVv gets updated in SUMA_X_SurfaceViewer_Create
and reflects not the number of elements in SUMAg_SVv which is
SUMA_MAX_SURF_VIEWERS, but the number of viewers that were realized
by X */
/* Check on initialization */
/*SUMA_Show_SurfaceViewer_Struct (SUMAg_cSV, stdout);*/
/* Create the Surface Viewer Window */
if (!SUMA_X_SurfaceViewer_Create ()) {
fprintf(stderr,"Error in SUMA_X_SurfaceViewer_Create. Exiting\n");
return 1;
}
for (i=0; i<ispec; ++i) {
if (!list) list = SUMA_CreateList();
ED = SUMA_InitializeEngineListData (SE_Load_Group);
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_cp, (void *)specfilename[i],
SES_Suma, NULL, NOPE,
SEI_Head, NULL ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_ip, (void *)Specp[i],
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
fff = (float) InMem[i];
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_f, (void *)&fff,
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_vp, (void *)VolParName[i],
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
N_iv15 = SUMA_MAX_SURF_VIEWERS;
if (N_iv15 > 15) {
fprintf( SUMA_STDERR,
"Error %s: trying to register more than 15 viewers!\n",
FuncName);
exit(1);
}
for (kar=0; kar<N_iv15; ++kar) iv15[kar] = kar;
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_iv15, (void *)iv15,
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
if (!( Element = SUMA_RegisterEngineListCommand ( list, ED,
SEF_i, (void *)&N_iv15,
SES_Suma, NULL, NOPE,
SEI_In, Element ))) {
fprintf(SUMA_STDERR,"Error %s: Failed to register command\n", FuncName);
exit (1);
}
}
if (ispec > 0 && !SUMA_Engine (&list)) {
fprintf(SUMA_STDERR,"Error %s: Failed in SUMA_Engine\n", FuncName);
exit (1);
}
/* For some reason, I had to add the glLightfv line below
to force the lightflipping done in SUMA_SetupSVforDOs to take place
in the A viewer when first opened. I don't know why that is, especially
since other controllers would show up lit correctly without this
glLightfv line below.
To make matters worse, the A controller's light0_position is correctly
flipped.
It is just that the shading is done as if the position was never flipped.
Actually, without the line below, the first time you hit the F key (to
manually flip the light), nothing changes, that's because the light's position is unflipped, which is supposed to show the incorrect lighting.
You'll have to hit F again to have the lighting correctly flipped
and the shading reflecting it.... ZSS, Aug. 05 04 */
glLightfv(GL_LIGHT0, GL_POSITION, SUMAg_SVv[0].light0_position);
if (Start_niml != -1 && (Start_niml == 1|| AFNI_yesenv("SUMA_START_NIML"))) {
if (!list) list = SUMA_CreateList();
SUMA_REGISTER_HEAD_COMMAND_NO_DATA( list, SE_StartListening,
SES_Suma, NULL);
if (!SUMA_Engine (&list)) {
fprintf(SUMA_STDERR, "Error %s: SUMA_Engine call failed.\n", FuncName);
exit (1);
}
}
/* load the datasets onto the first SO, if any, else hope that dset
is some form of DO */
if (ps->N_dsetname>0) {
SUMA_SurfaceObject *SO = SUMA_findanySOp_inDOv(SUMAg_DOv,
SUMAg_N_DOv, NULL);
if (!SO) {
SUMA_LH("Could not find any SO, here is hoping dset is a DO");
}
for (i=0; i<ps->N_dsetname; ++i) {
if (!(SUMA_LoadDsetOntoSO_eng(ps->dsetname[i], SO, 1, 1, 1, NULL))) {
SUMA_S_Errv("Failed to load %s onto %s\n",
ps->dsetname[i], SO?SO->Label:"NULL");
}
}
}
SUMA_FreeGenericArgParse(ps); ps = NULL;
/* A Warning about no sumarc */
if (NoSumaRcFound()) {
SUMA_S_Warn(
"\n"
" No sumarc file found. You should create one by running the following:\n"
"\n"
" suma -update_env\n"
"\n"
" I also recommend you run 'suma -update_env' whenever you update AFNI.\n"
"\n"
" See details for -environment and -update_env options in suma -help's output.\n"
"\n");
}
/*Main loop */
XtAppMainLoop(SUMAg_CF->X->App);
/* Done, clean up time */
if (ispec) {
int k=0;
for (k=0; k<ispec; ++k) {
if (!SUMA_FreeSpecFields((Specp[k]))) {
SUMA_S_Err("Failed to free spec fields");
}
Specp[k] = NULL;
}
} ispec = 0;
if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv))
SUMA_error_message(FuncName,"DO Cleanup Failed!",1);
if (!SUMA_Free_SurfaceViewer_Struct_Vect (SUMAg_SVv, SUMA_MAX_SURF_VIEWERS))
SUMA_error_message(FuncName,"SUMAg_SVv Cleanup Failed!",1);
if (!SUMA_Free_CommonFields(SUMAg_CF))
SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
SUMA_RETURN(0); /* ANSI C requires main to return int. */
}/* Main */
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SurfClust"};
int kar, SO_read, *ni=NULL, N_ni, cnt, i, *nip=NULL, N_Spec = 0;
float *data_old = NULL, *far = NULL, *nv=NULL, *nt = NULL;
void *SO_name = NULL;
SUMA_SurfaceObject *SO = NULL, *SOnew = NULL;
MRI_IMAGE *im = NULL;
SUMA_DSET_FORMAT iform;
SUMA_SURFCLUST_OPTIONS *Opt;
SUMA_SurfSpecFile *Spec=NULL;
DList *list = NULL;
SUMA_DSET *dset = NULL;
float *NodeArea = NULL;
FILE *clustout=NULL;
char *ClustOutName = NULL, *params=NULL, stmp[200];
char sapa[32]={""}, sapd[32]={""}, sapn[32]={""}, sap[100]={""};
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
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, "-spec;-i;-t;-sv;-s;");
Opt = SUMA_SurfClust_ParseInput (argv, argc, ps);
if (argc < 6)
{
SUMA_S_Err("Too few options");
usage_SUMA_SurfClust(0);
exit (1);
}
if (Opt->DistLim >= 0.0) {
sprintf(sapd, "_r%.1f", Opt->DistLim);
} else {
sprintf(sapd, "_e%d", -(int)Opt->DistLim);
}
if (Opt->AreaLim < 0) {
sapa[0]='\0';
} else {
sprintf(sapa, "_a%.1f", Opt->AreaLim);
}
if (Opt->NodeLim < 0) {
sapn[0]='\0';
} else {
sprintf(sapn, "_n%d", Opt->NodeLim);
}
sprintf(sap, "%s%s%s", sapd, sapa, sapn);
if (Opt->WriteFile) {
sprintf(stmp,"_ClstTable%s.1D", sap);
ClustOutName = SUMA_append_string(Opt->out_prefix, stmp);
if (SUMA_filexists(ClustOutName) && !THD_ok_overwrite()) {
fprintf (SUMA_STDERR,
"Error %s:\n"
"Output file %s exists, will not overwrite.\n",
FuncName, ClustOutName);
exit(1);
}
}
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec != 1) {
SUMA_S_Err("Multiple spec at input.");
exit(1);
}
if (Spec->N_Surfs != 1) {
SUMA_S_Err("1 and only 1 surface expected at input");
exit(1);
}
SUMA_LH("Loading surface...");
SO = SUMA_Load_Spec_Surf(Spec, 0, ps->sv[0], 0);
if (!SO) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (!SUMA_SurfaceMetrics(SO, "EdgeList", NULL)) {
SUMA_S_Err("Failed to compute edgelist");
exit(1);
}
NodeArea = SUMA_CalculateNodeAreas(SO, NULL);
if (!NodeArea) {
SUMA_S_Err("Failed to calculate Node Areas.\n");
exit(1);
}
/* load the data */
iform = SUMA_NO_DSET_FORMAT;
dset = SUMA_LoadDset_s (Opt->in_name, &iform, 0);
if (LocalHead) SUMA_ShowDset(dset, 0, NULL);
if (!dset) { SUMA_S_Err( "Failed to load dataset.\n"
"Make sure file exists\n"
"and is of the specified\n"
"format.");
exit(1); }
if (!SUMA_OKassign(dset, SO)) {
SUMA_SL_Err("Failed to assign data set to surface.");
exit(1);
}
/* get the node index column */
nip = SUMA_GetNodeDef(dset);
N_ni = SDSET_VECLEN(dset);
if (!nip) {
SUMA_S_Err("Failed to find node index column");
exit(1);
}
/* copy nip's contents because you will be modifying in the
thresholding below */
ni = (int *)SUMA_malloc(N_ni*sizeof(int));
memcpy (ni, nip, N_ni*sizeof(int));
nv = SUMA_DsetCol2Float(dset, Opt->labelcol, 0);
if (!nv) {
SUMA_S_Err("Failed to find node value column");
exit(1);
}
/* any thresholding ? */
if (Opt->DoThreshold > SUMA_NO_THRESH) {
nt = SUMA_DsetCol2Float(dset, Opt->tind, 0);
if (!nt) {
SUMA_S_Err("Failed to find threshold column");
exit(1);
}
cnt = 0;
if (Opt->DoThreshold == SUMA_LESS_THAN) {
if (Opt->update)
fprintf( SUMA_STDERR,
"%s: Thresholding at %f...\n", FuncName, Opt->ThreshR[0]);
for (i=0;i<N_ni; ++i) {
if (nt[i] >= Opt->ThreshR[0]) {
ni[cnt] = ni[i];
nv[cnt] = nv[i];
++cnt;
}
}
} else if (Opt->DoThreshold == SUMA_ABS_LESS_THAN) {
SUMA_LH("ABS Thresholding at %f...", Opt->ThreshR[0]);
for (i=0;i<N_ni; ++i) {
if (fabs(nt[i]) >= Opt->ThreshR[0]) {
ni[cnt] = ni[i];
nv[cnt] = nv[i];
++cnt;
}
}
} else if (Opt->DoThreshold == SUMA_THRESH_INSIDE_RANGE) {
SUMA_LH("Range Thresholding at %f %f...",
Opt->ThreshR[0], Opt->ThreshR[1]);
for (i=0;i<N_ni; ++i) {
if (nt[i] >= Opt->ThreshR[0] && nt[i] <= Opt->ThreshR[1]) {
ni[cnt] = ni[i];
nv[cnt] = nv[i];
++cnt;
}
}
} else if (Opt->DoThreshold == SUMA_THRESH_OUTSIDE_RANGE) {
SUMA_LH("Ex Range Thresholding at %f %f...",
Opt->ThreshR[0], Opt->ThreshR[1]);
for (i=0;i<N_ni; ++i) {
if (nt[i] < Opt->ThreshR[0] || nt[i] > Opt->ThreshR[1]) {
ni[cnt] = ni[i];
nv[cnt] = nv[i];
++cnt;
}
}
} else {
SUMA_S_Err("Not ready for threshold mode of %d", Opt->DoThreshold);
}
N_ni = cnt;
}
if (Opt->update) {
Opt->update = -(N_ni * Opt->update / 100); /* make it negative
before you begin a
clustering operation */
if (LocalHead) {
fprintf( SUMA_STDERR,
"Update parameter, once every %d nodes\n"
"%d nodes to work with.\n",
-(int)Opt->update, N_ni);
}
}
/* make the call */
list = SUMA_FindClusters (SO, ni, nv, N_ni, -1, Opt, NodeArea);
if (!list) {
SUMA_S_Err("Failed in SUMA_FindClusters");
exit(1);
}
if (list->size) {
/* sort the list */
if (!SUMA_Sort_ClustersList (list, Opt->SortMode)) {
SUMA_S_Err("Failed to sort cluster list");
exit(1);
}
}
/* Show the results */
params = SUMA_HistString(FuncName, argc, argv, NULL);
if (Opt->WriteFile) {
if (0) {
/* You can also write a NIML formatted cluster table with */
NI_element *nel=NULL;
int suc; char sbuf[512]={""};
nel = SUMA_SurfClust_list_2_nel(list, 0, params, NULL);
snprintf(sbuf, 510, "file:%s%s.niml.clstbl", Opt->out_prefix, sap);
NEL_WRITE_TXH(nel, sbuf, suc);
NI_free_element(nel); nel=NULL;
}
clustout = fopen(ClustOutName, "w");
if (!clustout) {
fprintf (SUMA_STDERR,
"Error %s:\n"
"Failed to open %s for writing.\n"
"Check permissions.\n",
FuncName, ClustOutName);
exit(1);
}
SUMA_Show_SurfClust_list(list, clustout, 0, params, NULL);
fclose(clustout);clustout = NULL;
} else SUMA_Show_SurfClust_list(list, NULL, 0, params, NULL);
if (!list->size) {
/* nothing left to do, quit */
exit(0);
}
if (Opt->OutROI) {
SUMA_DSET *dset_roi = NULL;
char *ROIprefix = NULL;
char *NameOut = NULL;
sprintf(stmp,"_ClstMsk%s", sap);
ROIprefix = SUMA_append_string(Opt->out_prefix, stmp);
/* Call this function, write out the resultant dset to disk
then cleanup */
dset_roi =
SUMA_SurfClust_list_2_DsetMask(SO, list, Opt->FullROIList, ROIprefix);
if (!dset_roi) {
SUMA_S_Err("NULL dset_roi");
exit(1);
}
if (Opt->prepend_node_index) {/* prepend node index? */
if (!SUMA_InsertDsetNelCol (
dset_roi, "Node Index Copy", SUMA_NODE_INT,
(void *)(dset_roi->inel->vec[0]), NULL ,1, 0)) {
SUMA_S_Err("Failed to insert column");
}
if (LocalHead) SUMA_ShowDset(dset_roi,0, NULL);
}
NameOut = SUMA_WriteDset_s ( ROIprefix, dset_roi, Opt->oform,
THD_ok_overwrite(), 0);
if (!NameOut) { SUMA_SL_Err("Failed to write dataset."); exit(1); }
SUMA_FreeDset((void *)dset_roi); dset_roi = NULL;
if (NameOut) SUMA_free(NameOut); NameOut = NULL;
if (ROIprefix) SUMA_free(ROIprefix); ROIprefix = NULL;
}
if (Opt->OutClustDset) {
SUMA_DSET *dset_clust = NULL;
char *Clustprefix = NULL;
char *NameOut = NULL;
sprintf(stmp,"_Clustered%s", sap);
Clustprefix = SUMA_append_string(Opt->out_prefix, stmp);
/* Call this function, write out the resultant dset to disk
then cleanup */
dset_clust =
SUMA_MaskDsetByClustList( dset, SO, list,
Opt->FullROIList, Clustprefix);
if (!dset_clust) {
SUMA_S_Err("NULL dset_clust");
exit(1);
}
NameOut = SUMA_WriteDset_s ( Clustprefix, dset_clust, Opt->oform,
THD_ok_overwrite(), 0);
if (!NameOut) { SUMA_SL_Err("Failed to write dataset."); exit(1); }
SUMA_FreeDset((void *)dset_clust); dset_clust = NULL;
if (NameOut) SUMA_free(NameOut); NameOut = NULL;
if (Clustprefix) SUMA_free(Clustprefix); Clustprefix = NULL;
}
if (ClustOutName) SUMA_free(ClustOutName); ClustOutName = NULL;
if (list) dlist_destroy(list); SUMA_free(list); list = NULL;
if (ni) SUMA_free(ni); ni = NULL;
if (nv) SUMA_free(nv); nv = NULL;
if (nt) SUMA_free(nt); nt = NULL;
if (Opt->out_prefix) SUMA_free(Opt->out_prefix); Opt->out_prefix = NULL;
if (Opt) SUMA_free_SurfClust_Opt(Opt);
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (dset) SUMA_FreeDset((void *)dset); dset = NULL;
if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv)) {
SUMA_SL_Err("DO Cleanup Failed!");
}
exit(0);
}
int main (int argc,char *argv[])
{ /* Main */
static char FuncName[]= {"SurfQual"};
char *OutName = NULL, ext[5], *prefix = NULL, *shist=NULL;
SUMA_SURFQUAL_OPTIONS *Opt;
int SO_read = -1;
int i, cnt, trouble, consistent = -1, eu = -1, nsi = -1, N_Spec=0;
SUMA_SurfaceObject *SO = NULL;
SUMA_SurfSpecFile *Spec=NULL;
void *SO_name = NULL;
SUMA_Boolean DoConv = NOPE, DoSphQ = NOPE, DoSelfInt = NOPE;
int N_bad_nodes, N_bad_facesets;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-spec;-s;-sv;");
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
Opt = SUMA_SurfQual_ParseInput (argv, argc, ps);
if (argc < 2)
{
SUMA_S_Err("Too few options");
usage_SUMA_SurfQual(ps, 0);
exit (1);
}
/* read all surfaces */
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec > 1 ) {
SUMA_S_Err( "Mike, you cannot mix -spec with -i or -t options "
"for specifying surfaces.");
exit(1);
}
if (Spec->N_Surfs < 1) {
SUMA_S_Err("No surfaces");
exit(1);
}
if (Opt->self_intersect) DoSelfInt = YUP;
DoConv = NOPE;
DoSphQ = NOPE;
if (Opt->surftype) {
if (!strcmp(Opt->surftype, "-sphere")) {
DoSphQ = YUP;
} else {
/* Don't complain anymore, maybe winding checking is all users need */
}
}
for (i=0; i < Spec->N_Surfs; ++i) {/* loop to read in surfaces */
/* now identify surface needed */
if (!(SO = SUMA_Load_Spec_Surf_with_Metrics(Spec, i, ps->sv[0], 0))) {
SUMA_S_Err("Failed to load surface .\n");
exit(1);
}
fprintf(SUMA_STDERR,"\nReport for Surface %s\n", SO->Label);
/* do the quality thing based on the Opt->surftype */
if (!Opt->out_prefix) prefix = SUMA_copy_string(SO->Label);
else prefix = SUMA_copy_string (Opt->out_prefix);
/* check the winding */
if (!SUMA_MakeConsistent (SO->FaceSetList, SO->N_FaceSet,
SO->EL, 0, &trouble)) {
SUMA_S_Warn(
"Failed to make sure surface's mesh is consistently wound.\n"
"You should fix the mesh.\n");
consistent = 0;
}
{
int iii=0, isbad=0, ht0;
int *badedge=(int*)SUMA_calloc(SO->N_Node, sizeof(int));
/* check on troubled edges */
while (iii < SO->EL->N_EL) {
ht0 = SO->EL->ELps[iii][1];
/* make sure edge is not part of three triangles, if it is,skip it*/
if (SO->EL->ELps[iii][2] > 2) {
++iii;
fprintf( SUMA_STDERR,
"%s: Bad edge (#%d: %d--%d), \n"
" part of more than 2 triangles, skip it\n",
FuncName, i, SO->EL->EL[iii][0], SO->EL->EL[iii][1]);
++badedge[SO->EL->EL[iii][0]];
++badedge[SO->EL->EL[iii][1]];
isbad = 1;
continue;
}
++iii;
}
if (isbad) {
if (Spec->N_Surfs > 1) {
sprintf(ext,"_%c", 65+i);
OutName = SUMA_append_replace_string (
prefix,
"_BadEdgeNodes.1D.dset",
ext, 0);
} else {
OutName = SUMA_append_string (prefix, "_BadEdgeNodes.1D.dset");
}
SUMA_WRITE_ARRAY_1D(badedge,SO->N_Node,1,OutName);
if (OutName) SUMA_free(OutName);
OutName = NULL;
}
SUMA_free(badedge);
badedge = NULL;
}
if (DoConv) {
float *Cx = NULL;
if (Spec->N_Surfs > 1) {
sprintf(ext,"_%c", 65+i);
OutName = SUMA_append_replace_string
(prefix, "_Conv_detail.1D.dset", ext, 0);
} else {
OutName = SUMA_append_string (prefix, "_Conv_detail.1D.dset");
}
Cx = SUMA_Convexity_Engine ( SO->NodeList, SO->N_Node,
SO->NodeNormList, SO->FN, OutName, NULL);
if (Cx) SUMA_free(Cx);
Cx = NULL;
if (OutName) SUMA_free(OutName);
OutName = NULL;
}
if (DoSphQ) {
if (Spec->N_Surfs > 1) {
sprintf(ext,"_%c", 65+i);
OutName = SUMA_append_string (prefix, ext);
} else {
OutName = SUMA_copy_string (prefix);
}
shist = SUMA_HistString (NULL, argc, argv, NULL);
SUMA_SphereQuality (SO, OutName, shist, &N_bad_nodes, &N_bad_facesets);
if (shist) SUMA_free(shist);
shist = NULL;
if (OutName) SUMA_free(OutName);
OutName = NULL;
}
if (trouble) { /* put winding problem here to make it visible */
fprintf (SUMA_STDERR,"\n");
SUMA_S_Warn(
"Mesh is not consistent, use ConvertSurface's -make_consistent \n"
"option to fix the problem before proceeding further.\n"
"Other results reported by this and other programs\n"
"may be incorrect if mesh is not consistently wound.\n" );
consistent = 0;
} else {
consistent = 1;
fprintf (SUMA_STDERR,"\n");
fprintf (SUMA_STDERR,"Surface is consistently wound\n");
}
{
SUMA_EULER_SO(SO, eu);
fprintf (SUMA_STDERR,"\n");
fprintf(SUMA_STDERR,"Surface Euler Characteristic is: %d\n", eu);
}
if ((SO->EL->min_N_Hosts == 1 || SO->EL->max_N_Hosts == 1)) {
fprintf (SUMA_STDERR,"\n");
fprintf(SUMA_STDERR,
"Warning %s:\n"
" Min/Max number of edge hosting triangles: [%d/%d] \n",
FuncName, SO->EL->min_N_Hosts, SO->EL->max_N_Hosts);
fprintf( SUMA_STDERR,
" You have edges that form a border in the surface.\n");
}
if (SO->EL->min_N_Hosts == 2 && SO->EL->max_N_Hosts == 2) {
fprintf (SUMA_STDERR,"\n");
fprintf(SUMA_STDERR,"Surface is closed and is a 2-manifold.");
}
if (SO->EL->min_N_Hosts > 2 || SO->EL->max_N_Hosts > 2) {
fprintf (SUMA_STDERR,"\n");
fprintf( SUMA_STDERR,
"Warning %s:\n"
"Min/Max number of edge hosting triangles: [%d/%d] \n",
FuncName, SO->EL->min_N_Hosts, SO->EL->max_N_Hosts);
fprintf(SUMA_STDERR,
"Warning %s:\n"
" You have edges that belong to more than two triangles.\n"
" Bad for analysis assuming surface is a 2-manifold.\n",
FuncName);
if (1) {
int iii=0;
fprintf( SUMA_STDERR,
" These edges are formed by the following nodes:\n");
for (iii = 0; iii < SO->EL->N_EL; ++iii) {
if (SO->EL->ELps[iii][2] > 2)
fprintf (SUMA_STDERR,
" %d: Edge [%d %d] shared by %d triangles.\n",
iii+1, SO->EL->EL[iii][0], SO->EL->EL[iii][1] ,
SO->EL->ELps[iii][2] );
}
}
}
if (DoSelfInt) {
int iii;
FILE *fout=NULL;
byte *report = (byte *)SUMA_calloc(SO->N_Node, sizeof(byte));
if (!report) {
SUMA_SL_Crit("Failed to allocate for report");
report = NULL;
}
fprintf( SUMA_STDERR, "\n\nChecking for intersections...:\n");
nsi = SUMA_isSelfIntersect(SO, 500, report);
if (nsi) {
fprintf( SUMA_STDERR,
" Surface is self intersecting.\n"
"%d segments were found to intersect the surface.\n", nsi);
if (nsi >= 500) {
fprintf( SUMA_STDERR,
" It is possible that you have additional segments"
" intersecting the surface.\n");
}
if (report) {
if (Spec->N_Surfs > 1) {
sprintf(ext,"_%c", 65+i);
OutName = SUMA_append_replace_string ( prefix,
"_IntersNodes.1D.dset",
ext, 0);
} else {
OutName = SUMA_append_string (prefix, "_IntersNodes.1D.dset");
}
fout = fopen(OutName, "w");
if (fout) {
fprintf(fout,
"#List of nodes that are part of segments which intersect "
"the surface\n"
"#%s\n"
"#A total of %d segments (search limit is 500) were found to "
"intersect the surface.\n"
"#Col.1 : Node index\n"
"#Col.2 : Dummy flag, always 1\n",
SUMA_CHECK_NULL_STR(SO->Label), nsi );
for (iii=0; iii<SO->N_Node; ++iii)
if (report[iii]) fprintf(fout, "%d\t1\n", iii);
fclose(fout);
fout = NULL;
} else {
SUMA_SL_Err("Failed to open file for output.");
}
if (OutName) SUMA_free(OutName);
}
} else {
fprintf(SUMA_STDERR, " Surface is not self intersecting.\n");
}
if (report) SUMA_free(report);
report = NULL;
}
fprintf (SUMA_STDERR,"\n");
if (Opt->DoSum) { /* do not change syntax, scripts depend on this */
fprintf(stdout,"Summary for %s:\n", SO->Label);
fprintf(stdout,"Euler_Charac. %d\n", eu);
fprintf(stdout,"Consistent_Winding %d\n", consistent);
if (DoSphQ) {
fprintf(stdout,"Folding_Triangles %d\n", N_bad_facesets);
fprintf(stdout,"Sketchy_nodes %d\n", N_bad_nodes);
}
if (DoSelfInt)
fprintf(stdout,"Self_Intersections %d\n", nsi);
fprintf(stdout,"\n");
}
}
SUMA_LH("clean up");
if (!SUMA_FreeSpecFields(Spec)) {
SUMA_S_Err("Failed to free spec fields");
}
SUMA_free(Spec);
Spec = NULL;
if (prefix) SUMA_free(prefix);
prefix = NULL;
if (Opt->out_prefix) SUMA_free(Opt->out_prefix);
Opt->out_prefix = NULL;
if (Opt) SUMA_free(Opt);
if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv)) {
SUMA_SL_Err("DO Cleanup Failed!");
}
if (!SUMA_Free_CommonFields(SUMAg_CF))
SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
SUMA_RETURN(0);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SurfPatch"};
SUMA_GETPATCH_OPTIONS *Opt;
char *ppref=NULL, ext[5];
float *far=NULL;
MRI_IMAGE *im = NULL;
int SO_read = -1;
int *NodePatch=NULL, N_NodePatch=-1, *FaceSetList=NULL ,
N_FaceSet = -1, N_Node = -1, N_Spec=0;
int i, inodeoff=-1, ilabeloff=-1, nvec, ncol, cnt;
SUMA_SurfaceObject *SO = NULL;
SUMA_PATCH *ptch = NULL;
SUMA_SurfSpecFile *Spec;
SUMA_INDEXING_ORDER d_order;
void *SO_name = NULL;
SUMA_Boolean exists = NOPE;
SUMA_SO_File_Type typetmp;
SUMA_SurfaceObject *SOnew = NULL;
float *NodeList = NULL;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-spec;-s;-sv;");
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
Opt = SUMA_GetPatch_ParseInput (argv, argc, ps);
if (argc < 2)
{
SUMA_S_Err("Too few options");
usage_SUMA_getPatch(ps, 0);
exit (1);
}
/* read all surfaces */
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec > 1 ) {
SUMA_S_Err( "Mike, you cannot mix -spec with -i or -t options "
"for specifying surfaces.");
exit(1);
}
if (Spec->N_Surfs < 1) {
SUMA_S_Err("No surfaces");
exit(1);
}
if (Opt->DoVol && Spec->N_Surfs != 2) {
SUMA_S_Errv("Must specify 2 and only 2 surfaces with -vol options\n"
"Have %d from the command line\n",Spec->N_Surfs);
exit(1);
}
if (Opt->oType != SUMA_FT_NOT_SPECIFIED && !Opt->VolOnly) {
for (i=0; i < Spec->N_Surfs; ++i) {
if (Spec->N_Surfs > 1) {
sprintf(ext, "_%c", 65+i);
ppref = SUMA_append_string(Opt->out_prefix, ext);
} else {
ppref = SUMA_copy_string(Opt->out_prefix);
}
SO_name = SUMA_Prefix2SurfaceName(ppref, NULL, NULL,
Opt->oType, &exists);
if (exists && !THD_ok_overwrite()) {
fprintf(SUMA_STDERR, "Error %s:\nOutput file(s) %s* on disk.\n"
"Will not overwrite.\n", FuncName, ppref);
exit(1);
}
if (ppref) SUMA_free(ppref); ppref = NULL;
if (SO_name) SUMA_free(SO_name); SO_name = NULL;
}
}
/* read in the file containing the node information */
im = mri_read_1D (Opt->in_name);
if (!im) {
SUMA_S_Errv("Failed to read 1D file '%s'\n", Opt->in_name);
exit(1);
}
far = MRI_FLOAT_PTR(im);
nvec = im->nx;
ncol = im->ny;
if (Opt->nodecol >= ncol || Opt->labelcol >= ncol) {
fprintf(SUMA_STDERR, "\n"
"Error %s: Input file has a total of %d columns.\n"
"One or both user-specified node (%d) and \n"
"label (%d) columns are too high. Maximum usable\n"
"column index is %d.\n"
, FuncName, ncol, Opt->nodecol,
Opt->labelcol, ncol -1 );
exit(1);
}
d_order = SUMA_COLUMN_MAJOR;
if (!nvec) {
SUMA_SL_Err("Empty file");
exit(1);
}
/* form the node vector */
NodePatch = (int *)SUMA_malloc(sizeof(int)*nvec);
if (!NodePatch) {
SUMA_SL_Crit("Failed to allocate.");
exit(1);
}
inodeoff = Opt->nodecol*nvec;
if (Opt->labelcol < 0) { /* all listed nodes */
for (i=0; i<nvec; ++i) {
NodePatch[i] = far[i+inodeoff];
}
N_NodePatch = nvec;
} else {
ilabeloff = Opt->labelcol*nvec;
if (Opt->thislabel < 0) { /* all nodes with non zero labels */
cnt = 0;
for (i=0; i<nvec; ++i) {
if (far[i+ilabeloff]) {
NodePatch[cnt] = far[i+inodeoff];
++cnt;
}
}
N_NodePatch = cnt;
} else { /* select labels */
cnt = 0;
for (i=0; i<nvec; ++i) {
if (far[i+ilabeloff] == Opt->thislabel) {
NodePatch[cnt] = far[i+inodeoff];
++cnt;
}
}
N_NodePatch = cnt;
}
NodePatch = (int *) SUMA_realloc(NodePatch , sizeof(int)*N_NodePatch);
}
/* done with im, free it */
mri_free(im); im = NULL;
if (Opt->DoVol) {
SUMA_SurfaceObject *SO1 =
SUMA_Load_Spec_Surf_with_Metrics(Spec, 0, ps->sv[0], 0);
SUMA_SurfaceObject *SO2 =
SUMA_Load_Spec_Surf_with_Metrics(Spec, 1, ps->sv[0], 0);
double Vol = 0.0;
SUMA_SurfaceObject *SOp = SUMA_Alloc_SurfObject_Struct(1);
byte *adj_N=NULL;
if (Opt->adjust_contour)
adj_N = SUMA_calloc(SO1->N_Node, sizeof(byte));
if (!SO1 || !SO2) {
SUMA_SL_Err("Failed to load surfaces.");
exit(1);
}
/* a chunk used to test SUMA_Pattie_Volume */
Vol = SUMA_Pattie_Volume(SO1, SO2, NodePatch, N_NodePatch,
SOp, Opt->minhits,
Opt->FixBowTie, Opt->adjust_contour,
adj_N, Opt->verb);
fprintf (SUMA_STDOUT,"Volume = %f\n", fabs(Vol));
if (Opt->out_volprefix) {
if (Opt->oType != SUMA_FT_NOT_SPECIFIED) SOp->FileType = Opt->oType;
if (Opt->flip) {
if (Opt->verb > 1)
SUMA_S_Note("Flipping stitched surf's triangles\n");
SUMA_FlipSOTriangles (SOp);
}
if (!(SUMA_Save_Surface_Object_Wrap ( Opt->out_volprefix, NULL,
SOp, SUMA_PLY, SUMA_ASCII,
NULL))) {
fprintf (SUMA_STDERR,
"Error %s: Failed to write surface object.\n", FuncName);
}
if (Opt->adjust_contour && adj_N) {
Opt->out_volprefix =
SUMA_append_replace_string(Opt->out_volprefix,
".adjneighb","",1);
ppref = SUMA_Extension(Opt->out_volprefix, ".1D.dset", NOPE);
SUMA_WRITE_IND_ARRAY_1D(adj_N, NULL, SO1->N_Node, 1, ppref);
SUMA_free(ppref); ppref=NULL;
}
}
if (SOp) SUMA_Free_Surface_Object(SOp); SOp = NULL;
}
if (!Opt->VolOnly) {
FaceSetList = NULL;
N_FaceSet = -1;
for (i=0; i < Spec->N_Surfs; ++i) {/* loop to read in surfaces */
/* now identify surface needed */
if (!(SO = SUMA_Load_Spec_Surf_with_Metrics(Spec, i, ps->sv[0], 0))) {
SUMA_S_Err("Failed to load surface .\n");
exit(1);
}
if (SO->aSO) {
/* otherwise, when you reset the number of FaceSets for example,
and you still write in GIFTI, the old contents of aSO will
prevail */
SO->aSO = SUMA_FreeAfniSurfaceObject(SO->aSO);
}
/* extract the patch */
ptch = SUMA_getPatch (NodePatch, N_NodePatch, SO->N_Node,
SO->FaceSetList, SO->N_FaceSet,
SO->MF, Opt->minhits,
Opt->FixBowTie, (!i && !Opt->DoVol));
/* verbose only for first patch, and
if no volume computation was required
This is to keep the warnings to a minimum*/
if (!ptch) {
SUMA_SL_Err("Failed to form patch.");
exit(1);
}
if (LocalHead) SUMA_ShowPatch(ptch, NULL);
/* Now create a surface with that patch */
if (Spec->N_Surfs > 1) {
sprintf(ext, "_%c", 65+i);
ppref = SUMA_append_string(Opt->out_prefix, ext);
} else {
ppref = SUMA_copy_string(Opt->out_prefix);
}
/* save the original type */
typetmp = SO->FileType;
if (Opt->oType != SUMA_FT_NOT_SPECIFIED) SO->FileType = Opt->oType;
SO_name = SUMA_Prefix2SurfaceName(ppref, NULL, NULL,
SO->FileType, &exists);
if (ppref) SUMA_free(ppref); ppref = NULL;
/* save the original pointers to the facesets and their number */
FaceSetList = SO->FaceSetList;
N_FaceSet = SO->N_FaceSet;
NodeList = SO->NodeList;
N_Node = SO->N_Node;
/* replace with Patch */
SO->FaceSetList = ptch->FaceSetList;
SO->N_FaceSet = ptch->N_FaceSet;
if (Opt->Do_p2s) {
if (LocalHead)
fprintf (SUMA_STDERR,
"%s: Changing patch to surface...\n", FuncName);
SOnew = SUMA_Patch2Surf(SO->NodeList, SO->N_Node,
SO->FaceSetList, SO->N_FaceSet, 3);
if (!SOnew) {
SUMA_S_Err("Failed to change patch to surface.");
exit(1);
}
SO->FaceSetList = SOnew->FaceSetList;
SO->N_FaceSet = SOnew->N_FaceSet;
SO->N_Node = SOnew->N_Node;
SO->NodeList = SOnew->NodeList;
}
if (SO->N_FaceSet <= 0) {
SUMA_S_Warn("The patch is empty.\n"
" Non existing surface not written to disk.\n");
} else {
/* Is the gain wanted? */
if (Opt->coordgain) {
SUMA_SL_Note("Applying coord gain to surface nodes!");
for (cnt=0; cnt < SO->NodeDim*SO->N_Node; ++cnt)
SO->NodeList[cnt] *= Opt->coordgain;
}
if (Opt->flip) {
if (Opt->verb > 1) SUMA_S_Note("Flipping triangles\n");
SUMA_FlipTriangles (SO->FaceSetList, SO->N_FaceSet);
SUMA_RECOMPUTE_NORMALS(SO);
}
if (!SUMA_Save_Surface_Object (SO_name, SO, SO->FileType,
SUMA_ASCII, NULL)) {
fprintf (SUMA_STDERR,
"Error %s: Failed to write surface object.\n",
FuncName);
exit (1);
}
}
/* bring SO back to shape */
SO->FileType = typetmp;
SO->FaceSetList = FaceSetList; FaceSetList = NULL;
SO->N_FaceSet = N_FaceSet; N_FaceSet = -1;
SO->NodeList = NodeList; NodeList = NULL;
SO->N_Node = N_Node; N_Node = -1;
if (SO_name) SUMA_free(SO_name); SO_name = NULL;
if (ptch) SUMA_freePatch(ptch); ptch = NULL;
if (SOnew) SUMA_Free_Surface_Object(SOnew); SOnew = NULL;
/* get rid of old surface object */
}
}
SUMA_LH("clean up");
if (!SUMA_FreeSpecFields(Spec)) { SUMA_S_Err("Failed to free spec fields"); }
SUMA_free(Spec); Spec = NULL;
if (Opt->out_prefix) SUMA_free(Opt->out_prefix); Opt->out_prefix = NULL;
if (Opt->out_volprefix) SUMA_free(Opt->out_volprefix);
Opt->out_volprefix = NULL;
if (Opt) SUMA_free(Opt);
if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv)) {
SUMA_SL_Err("DO Cleanup Failed!");
}
if (!SUMA_Free_CommonFields(SUMAg_CF)) {
SUMA_SL_Err("SUMAg_CF Cleanup Failed!");
}
SUMA_RETURN(0);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"ConvexHull"};
int i, i3, nspec = 0;
void *SO_name=NULL;
SUMA_SurfaceObject *SO = NULL;
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
char stmp[200];
SUMA_Boolean exists = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
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;");
if (argc < 2) {
usage_SUMA_ConvexHull(ps);
exit (1);
}
Opt = SUMA_ConvexHull_ParseInput (argv, argc, ps);
SO_name = SUMA_Prefix2SurfaceName(Opt->out_prefix, NULL, NULL,
Opt->SurfFileType, &exists);
if (exists && !THD_ok_overwrite()) {
SUMA_S_Err("Output file(s) %s* on disk.\nWill not overwrite.\n",
Opt->out_prefix);
exit(1);
}
if (Opt->obj_type < 0) {
if (Opt->in_name) {
if (Opt->debug) {
SUMA_S_Note("Creating mask...");
}
if (!SUMA_Get_isosurface_datasets (Opt)) {
SUMA_SL_Err("Failed to get data.");
exit(1);
}
if (Opt->debug > 1) {
if (Opt->debug == 2) {
FILE *fout=fopen("inmaskvec.1D","w");
SUMA_S_Note("Writing masked values...\n");
if (!fout) {
SUMA_SL_Err("Failed to write maskvec");
exit(1);
}
fprintf(fout, "#Col. 0 Voxel Index\n"
"#Col. 1 Is a mask (all values here should be 1)\n" );
for (i=0; i<Opt->nvox; ++i) {
if (Opt->mcdatav[i]) {
fprintf(fout,"%d %.2f\n", i, Opt->mcdatav[i]);
}
}
fclose(fout); fout = NULL;
} else {
FILE *fout=fopen("maskvec.1D","w");
SUMA_S_Note("Writing all mask values...\n");
if (!fout) {
SUMA_S_Err("Failed to write maskvec");
exit(1);
}
fprintf(fout, "#Col. 0 Voxel Index\n"
"#Col. 1 Is in mask ?\n" );
for (i=0; i<Opt->nvox; ++i) {
fprintf(fout,"%d %.2f\n", i, Opt->mcdatav[i]);
}
fclose(fout); fout = NULL;
}
}
} else if (Opt->in_1D) {
MRI_IMAGE *im = NULL;
float *far=NULL;
int nx2;
/* load the 1D file */
im = mri_read_1D (Opt->in_1D);
if (!im) {
SUMA_S_Err("Failed to read file");
exit(1);
}
far = MRI_FLOAT_PTR(im);
if (im->nx == 0) {
fprintf(SUMA_STDERR,"Error %s:\n Empty file %s.\n", FuncName, Opt->in_1D);
exit(1);
}
if (im->ny != 3) {
fprintf(SUMA_STDERR,"Error %s:\n Found %d columns in %s. Expecting 3\n", FuncName, im->ny, Opt->in_1D);
exit(1);
}
/* copy the columns */
Opt->N_XYZ = im->nx;
Opt->XYZ = (float *)SUMA_malloc(im->nx*im->ny*sizeof(float));
if (!Opt->XYZ) {
SUMA_S_Crit("Failed to allocate.");
exit(1);
}
nx2 = 2*im->nx;
for (i=0;i<Opt->N_XYZ; ++i) {
i3 = 3*i;
Opt->XYZ[i3 ] = far[i];
Opt->XYZ[i3+1] = far[i+im->nx];
Opt->XYZ[i3+2] = far[i+nx2];
}
/* done, clean up and out you go */
if (im) mri_free(im); im = NULL;
} else if (ps->i_N_surfnames) {
SUMA_SurfSpecFile *Spec=NULL;
SUMA_SurfaceObject *SO=NULL;
if (ps->i_N_surfnames > 1) {
SUMA_S_Err("Only 1 input surface allowed!");
exit(1);
}
Spec = SUMA_IO_args_2_spec(ps, &nspec);
if (!Spec) {
SUMA_S_Err("Failed to create spec!");
exit(1);
}
if (nspec != 1) {
SUMA_S_Warn("Expected one spec and nothing else");
}
/* load the surface object */
SO = SUMA_Load_Spec_Surf(Spec, 0, ps->sv[0], 0);
if (!SO) {
SUMA_S_Err("Failed to read surface.");
exit(1);
}
/* transfer coords */
if(SO->NodeDim != 3) {
SUMA_S_Err("bad node coords.");
exit(1);
}
Opt->N_XYZ = SO->N_Node;
Opt->XYZ = (float *)SUMA_malloc(SO->N_Node * SO->NodeDim * sizeof(float));
if (!Opt->XYZ) {
SUMA_S_Crit("Failed to allocate.");
exit(1);
}
for (i=0;i<SO->NodeDim*SO->N_Node; ++i) Opt->XYZ[i] = SO->NodeList[i];
if (nspec) {
int k=0;
for (k=0; k<nspec; ++k) {
if (!SUMA_FreeSpecFields(&(Spec[k]))) { SUMA_S_Err("Failed to free spec fields"); }
}
SUMA_free(Spec); Spec = NULL; nspec = 0;
}
if (SO) SUMA_Free_Surface_Object(SO); SO = NULL;
} else {
SUMA_S_Err("No input!");
exit(1);
}
} else {
SUMA_S_Err("Bad input!");
exit(1);
}
/* Now call Marching Cube functions */
if (!(SO = SUMA_ConvexHullSurface(Opt))) {
SUMA_S_Err("Failed to create surface.\n");
exit(1);
}
/* write the surface to disk */
if (!SUMA_Save_Surface_Object (SO_name, SO,
Opt->SurfFileType, Opt->SurfFileFormat, NULL)) {
fprintf (SUMA_STDERR,
"Error %s: Failed to write surface object.\n", FuncName);
exit (1);
}
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (Opt->fvec) SUMA_free(Opt->fvec); Opt->fvec = NULL;
if (Opt->mcdatav) {SUMA_free(Opt->mcdatav); Opt->mcdatav = NULL;}
if (Opt->in_vol) { DSET_delete( Opt->in_vol); Opt->in_vol = NULL;}
if (Opt->out_prefix) SUMA_free(Opt->out_prefix); Opt->out_prefix = NULL;
if (Opt->XYZ) SUMA_free(Opt->XYZ); Opt->XYZ = NULL;
if (Opt) SUMA_free(Opt);
if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv)) {
SUMA_SL_Err("DO Cleanup Failed!");
}
if (SO_name) SUMA_free(SO_name); SO_name = NULL;
if (!SUMA_Free_CommonFields(SUMAg_CF)) SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
exit(0);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SurfInfo"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_SurfSpecFile *Spec = NULL;
int i, N_Spec;
char *s = NULL;
SUMA_SurfaceObject *SO=NULL;
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, "-i;-t;-spec;-s;-sv;");
if (argc < 2) {
usage_SurfInfo(ps);
exit (1);
}
Opt = SUMA_SurfInfo_ParseInput (argv, argc, ps);
if (Opt->debug > 2) LocalHead = YUP;
if (ps->s_N_surfnames + ps->i_N_surfnames + ps->t_N_surfnames != 1) {
SUMA_S_Err("Multiple surface specifications used. "
"Only one surface allowed.");
exit(1);
}
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec != 1) {
SUMA_S_Err("Multiple spec at input.");
exit(1);
}
SUMA_LH("Loading surface...");
SO = SUMA_Load_Spec_Surf(Spec, 0, ps->sv[0], Opt->debug);
if (!SO) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (Opt->b1) {
SUMA_LH("Calculating all metrics, be patient...");
/* calc trimmings */
if (!SUMA_SurfaceMetrics_eng(SO, "Convexity|EdgeList|PolyArea|Curvature|"
"EdgeList|MemberFace|CheckWind",
NULL, Opt->debug, SUMAg_CF->DsetList)) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_SurfaceMetrics.\n", FuncName);
}
}
if (!Opt->s) { /* the whole thing */
SUMA_Print_Surface_Object(SO, stdout);
} else { /* just the specifics */
char *s=NULL;
i = 0;
while ( (s=SUMA_NI_get_ith_string(Opt->s,"|",i) ) ) {
if (!strcmp(s,"N_Node")) {
if (Opt->b2) {
if (i) fprintf(SUMA_STDOUT, "%s%d", Opt->in_1D, SO->N_Node);
else fprintf(SUMA_STDOUT, "%d", SO->N_Node);
} else {
if (i) fprintf(SUMA_STDOUT, "%s%s=%d", Opt->in_1D, s, SO->N_Node);
else fprintf(SUMA_STDOUT, "%s=%d", s, SO->N_Node);
}
} else if (!strcmp(s,"N_Tri") || !strcmp(s,"N_FaceSet")) {
if (Opt->b2) {
if (i) fprintf(SUMA_STDOUT, "%s%d", Opt->in_1D, SO->N_FaceSet);
else fprintf(SUMA_STDOUT, "%d", SO->N_FaceSet);
} else {
if (i) fprintf(SUMA_STDOUT, "%s%s=%d",
Opt->in_1D, s, SO->N_FaceSet);
else fprintf(SUMA_STDOUT, "%s=%d", s, SO->N_FaceSet);
}
} else if (!strcmp(s,"COM")) {
if (Opt->b2) {
if (i) fprintf(SUMA_STDOUT, "%s%f %f %f",
Opt->in_1D,
SO->Center[0], SO->Center[1],SO->Center[2]);
else fprintf(SUMA_STDOUT, "%f %f %f",
SO->Center[0], SO->Center[1],SO->Center[2]);
} else {
if (i) fprintf(SUMA_STDOUT, "%s%s=%f %f %f",
Opt->in_1D, s,
SO->Center[0], SO->Center[1],SO->Center[2]);
else fprintf(SUMA_STDOUT, "%s=%f %f %f", s,
SO->Center[0], SO->Center[1],SO->Center[2]);
}
} else {
SUMA_S_Errv("Don't know about parameter >>%s<<\n", s);
exit(1);
}
SUMA_free(s);
++i;
}
fprintf(SUMA_STDOUT,"\n");
}
if (SO) SUMA_Free_Surface_Object(SO); SO = NULL;
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
if (!SUMA_Free_CommonFields(SUMAg_CF))
SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
exit(0);
}
