int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"ScaleToMap"};
char *IntName = NULL, *Prfx, h[9],
*CmapFileName = NULL, *dbfile = NULL, *MapName=NULL;
MRI_IMAGE *im = NULL;
float *far=NULL;
int N_V, N_Int, kar, k, ii, i, icol=-1, vcol=-1, Sgn, interpmode, k3;
int Vminloc, Vmaxloc, *iV = NULL;
float Vmin, Vmax, brfact;
float *V = NULL, *Vsort = NULL;
float IntRange[2], MaskColor[3], MaskRange[2]={0.0, 0.0}, arange;
SUMA_Boolean ApplyClip, ApplyMask, setMaskCol, ApplyPercClip, Vopt;
SUMA_Boolean iVopt, inopt, NoMaskCol, MapSpecified, alaAFNI, MaskZero;
SUMA_Boolean brk, frf, ShowMap, ShowMapdb;
SUMA_COLOR_MAP *CM;
SUMA_SCALE_TO_MAP_OPT * OptScl;
int MapType, freecm = 1;
SUMA_COLOR_SCALED_VECT * SV;
SUMA_AFNI_COLORS *SAC=NULL;
SUMA_Boolean FromAFNI = NOPE;
int imap, isPmap, isNmap;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMAg_CF->isGraphical = YUP;
SUMA_mainENTRY;
/* this is placed down here to */
/*
if (argc < 3) {
SUMA_ScaleToMap_usage();
exit (1);
}
*/
kar = 1;
brfact = 1; /* the brightness factor */
MaskColor[0] = MaskColor[1] = MaskColor[2] = 0.3;
ApplyClip = NOPE;
ApplyPercClip = NOPE;
ApplyMask = NOPE;
NoMaskCol = NOPE;
MaskZero = NOPE;
setMaskCol = NOPE;
Vopt = NOPE;
iVopt = NOPE;
inopt = NOPE;
MapType = SUMA_CMAP_RGYBR20;
brk = NOPE;
MapSpecified = NOPE;
CmapFileName = NULL;
interpmode = SUMA_UNDEFINED_MODE;
ShowMap = NOPE;
alaAFNI = NOPE; /* applying the alaAFNI mapping */
frf = NOPE;
arange = -1.0; /* afni range specified */
Sgn = 0;
ShowMapdb = 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) {
SUMA_ScaleToMap_usage();
exit (1);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && strcmp(argv[kar], "-verb") == 0) {
LocalHead = NOPE;
brk = YUP;
}
if (!brk && strcmp(argv[kar], "-ionot") == 0) {
SUMA_SL_Err("-ionot is obsolete. \n"
"Use -trace option.");
exit (1);
SUMA_INOUT_NOTIFY_ON;
brk = YUP;
}
if (!brk && strcmp(argv[kar], "-msk_zero") == 0) {
MaskZero = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-input") == 0)) {
kar ++;
if (kar+2 >= argc) {
fprintf (SUMA_STDERR, "need 3 arguments after -input \n");
exit (1);
}
IntName = argv[kar]; kar ++;
icol = atoi(argv[kar]); kar ++;
vcol = atoi(argv[kar]);
inopt = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-apr") == 0)) {
if (arange >= 0) {
fprintf (SUMA_STDERR, "range has already been specified.\n");
exit (1);
}
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -apr \n");
exit (1);
}
arange = atof(argv[kar]);
if (arange < 0) {
fprintf (SUMA_STDERR, "range must be positive.\n");
exit (1);
}
Sgn = 1;
alaAFNI = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-anr") == 0)) {
if (arange >= 0) {
fprintf (SUMA_STDERR, "range has already been specified.\n");
exit (1);
}
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -anr \n");
exit (1);
}
arange = atof(argv[kar]);
if (arange < 0) {
fprintf (SUMA_STDERR, "range must be positive.\n");
exit (1);
}
Sgn = -1;
alaAFNI = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-v") == 0)) {
fprintf (SUMA_STDERR, "\n -v option is now obsolete.\nUse -input option instead.\n");
exit (1);
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -v \n");
exit (1);
}
IntName = argv[kar];
Vopt = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-iv") == 0)) {
fprintf (SUMA_STDERR, "\n -iv option is now obsolete.\nUse -input option instead.\n");
exit (1);
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -iv \n");
exit (1);
}
IntName = argv[kar];
iVopt = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-br") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -br \n");
exit (1);
}
brfact = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-frf") == 0)) {
frf = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-showmap") == 0)) {
ShowMap = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-showdb") == 0)) {
ShowMapdb = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-nointerp") == 0)) {
if (interpmode != SUMA_UNDEFINED_MODE) {
fprintf (SUMA_STDERR, "Color interpolation mode already set.\n");
}
interpmode = SUMA_NO_INTERP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-direct") == 0)) {
if (interpmode != SUMA_UNDEFINED_MODE) {
fprintf (SUMA_STDERR, "Color interpolation mode already set.\n");
}
interpmode = SUMA_DIRECT;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-interp") == 0)) {
if (interpmode != SUMA_UNDEFINED_MODE) {
fprintf (SUMA_STDERR, "Color interpolation mode already set.\n(-nointerp, -direct and -interp are mutually exclusive.\n");
}
interpmode = SUMA_INTERP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-clp") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 arguments after -clp \n");
exit (1);
}
ApplyClip = YUP;
IntRange[0] = atof(argv[kar]); kar ++;
IntRange[1] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-perc_clp") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 arguments after -perc_clp ");
exit (1);
}
ApplyPercClip = YUP;
IntRange[0] = atof(argv[kar]); kar ++;
IntRange[1] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-msk") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 arguments after -msk ");
exit (1);
}
ApplyMask = YUP;
MaskRange[0] = atof(argv[kar]); kar ++;
MaskRange[1] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-nomsk_col") == 0)) {
NoMaskCol = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-msk_col") == 0)) {
kar ++;
if (kar+2 >= argc) {
fprintf (SUMA_STDERR, "need 3 arguments after -msk_col ");
exit (1);
}
setMaskCol = YUP;
MaskColor[0] = atof(argv[kar]); kar ++;
MaskColor[1] = atof(argv[kar]); kar ++;
MaskColor[2] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-cmapfile") ==0)) {
if (MapSpecified) {
fprintf (SUMA_STDERR, "Color map already specified.\n-cmap and -cmapfile are mutually exclusive\n");
exit (1);
}
MapSpecified = YUP;
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 arguments after -cmapfile ");
exit (1);
}
CmapFileName = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-cmapdb") ==0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 arguments after -cmapdb ");
exit (1);
}
dbfile = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-cmap") ==0)) {
if (MapSpecified) {
fprintf (SUMA_STDERR, "Color map already specified.\n-cmap and -cmapfile are mutually exclusive\n");
exit (1);
}
MapSpecified = YUP;
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 arguments after -cmap ");
exit (1);
}
MapName = argv[kar];
brk = YUP;
}
if (!brk) {
fprintf (SUMA_STDERR,"Error %s: Option %s not understood. Try -help for usage\n", FuncName, argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}/* loop accross command ine options */
/* Get your colors straightened out */
if (!SUMAg_CF->scm) {
SUMAg_CF->scm = SUMA_Build_Color_maps();
if (!SUMAg_CF->scm) {
SUMA_SL_Err("Failed to build color maps.\n");
exit(1);
}
}
SAC = SUMAg_CF->scm;
/* are there database files to read */
if (dbfile) {
SUMA_LH("Now trying to read db file");
if (SUMA_AFNI_Extract_Colors ( dbfile, SAC ) < 0) {
SUMA_S_Errv("Failed to read %s colormap file.\n", dbfile);
exit(1);
}
}
FromAFNI = NOPE; /* assume colormap is not coming from SAC
(the colormap database structure) */
if (CmapFileName) {
/* load the color map */
CM = SUMA_Read_Color_Map_1D (CmapFileName);
if (CM == NULL) {
SUMA_S_Err("Could not load colormap.\n");
exit (1);
}
if (frf) {
SUMA_LH("Flipping colormap");
SUMA_Flip_Color_Map (CM);
}
if (!CM->Sgn) CM->Sgn = Sgn;
}else{
/* dunno what kind of map yet. Try default first */
if (MapName) {
CM = SUMA_FindNamedColMap (MapName);
freecm = 0;
if (CM) {
/* good, sign it and out you go */
CM->Sgn = Sgn;
} else {
SUMA_S_Err("Could not get standard colormap.\n");
exit (1);
}
} else {
SUMA_LH("An AFNI color map ");
/* a color from AFNI's maps */
FromAFNI = YUP;
imap = SUMA_Find_ColorMap ( MapName, SAC->CMv, SAC->N_maps, -2);
if (imap < 0) {
SUMA_S_Errv("Could not find colormap %s.\n", MapName);
exit (1);
}
CM = SAC->CMv[imap];
}
}
/* show the colromap on STDERR */
if (ShowMap) {
fprintf (SUMA_STDERR, "%s: Colormap used:\n", FuncName);
SUMA_Show_ColorMapVec (&CM, 1, NULL, 2);
{
SUMA_SurfaceObject *SO = NULL;
float orig[3] = { SUMA_CMAP_ORIGIN };
float topright[3] = { SUMA_CMAP_TOPLEFT };
SO = SUMA_Cmap_To_SO (CM, orig, topright, 2);
if (SO) SUMA_Free_Surface_Object(SO);
}
exit(0);
}
/* show all the colors and colormaps in SAC on STDERR */
if (ShowMapdb) {
fprintf (SUMA_STDERR, "%s: AFNI colormaps found in db:\n", FuncName);
SUMA_Show_ColorVec (SAC->Cv, SAC->N_cols, NULL);
SUMA_Show_ColorMapVec (SAC->CMv, SAC->N_maps, NULL, 2);
exit(0);
}
if (!IntName) {
fprintf (SUMA_STDERR,"Error %s: No input file specified.\n", FuncName);
exit(1);
}
/* default interpolation mode */
if (interpmode == SUMA_UNDEFINED_MODE) interpmode = SUMA_INTERP;
/* check input */
if (!SUMA_filexists (IntName)) {
fprintf (SUMA_STDERR,"Error %s: File %s could not be found.\n", FuncName, IntName);
exit(1);
}
if (frf && !CmapFileName) {
fprintf (SUMA_STDERR,"Error %s: -frf option is only valid with -cmapfile.\n", FuncName);
exit(1);
}
if (ApplyPercClip && ApplyClip) {
fprintf (SUMA_STDERR,"Error %s: Simultaneous use of -clp and -perc_clp. You should be punished.\n", FuncName);
exit(1);
}
if ((ApplyPercClip || ApplyClip) && arange >= 0.0) {
fprintf (SUMA_STDERR,"Error %s: Simultaneous use of -clp/-perc_clp and -apr/anr.\n Read the help.\n", FuncName);
exit(1);
}
if (iVopt || Vopt) {
fprintf (SUMA_STDERR,"Error %s: -v and -iv are obsolete.\n Use -input option instead.\n", FuncName);
exit(1);
}
if (!inopt) {
fprintf (SUMA_STDERR,"Error %s: -input option must be specified.\n", FuncName);
exit(1);
}
im = mri_read_1D (IntName);
if (!im) {
SUMA_S_Err("Failed to read file");
exit (1);
}
if (vcol < 0) {
fprintf (SUMA_STDERR,"Error %s: vcol must be > 0\n", FuncName);
exit(1);
}
far = MRI_FLOAT_PTR(im);
if (icol < 0 && icol != -1) {
fprintf (SUMA_STDERR,"Error %s: icol(%d) can only have -1 for a negative value\n", FuncName, icol);
exit(1);
}
if (icol >= im->ny || vcol >= im->ny) {
fprintf (SUMA_STDERR,"Error %s: icol(%d) and vcol(%d) must be < %d\nwhich is the number of columns in %s\n",
FuncName, icol, vcol, im->ny, IntName);
exit(1);
}
if (brfact <=0 || brfact > 1) {
fprintf (SUMA_STDERR,"Error %s: BrightFact must be > 0 and <= 1.\n", FuncName);
exit (1);
}
if (MaskColor[0] < 0 || MaskColor[0] > 1 || MaskColor[1] < 0 || MaskColor[1] > 1 || MaskColor[2] < 0 || MaskColor[2] > 1) {
fprintf (SUMA_STDERR,"Error %s: MaskColor values must be >=0 <=1.\n", FuncName);
exit(1);
}
N_V = im->nx;
V = (float *) SUMA_calloc (N_V, sizeof(float));
iV = (int *) SUMA_calloc (N_V, sizeof(int));
if (!V || !iV) {
fprintf (SUMA_STDERR,"Error %s: Could not allocate for V or iV.\n", FuncName);
exit(1);
}
if (icol < 0) {
for (ii=0; ii < N_V; ++ii) {
iV[ii] = ii;
V[ii] = far[vcol*N_V+ii];
}
} else {
for (ii=0; ii < N_V; ++ii) {
iV[ii] = (int)far[icol*N_V+ii];
V[ii] = far[vcol*N_V+ii];
}
}
mri_free(im); im = NULL;
/* read values per node */
/* SUMA_disp_vect (V, 3); */
/* find the min/max of V */
SUMA_MIN_MAX_VEC(V, N_V, Vmin, Vmax, Vminloc, Vmaxloc)
/* fprintf (SUMA_STDERR,"%s: Vmin=%f, Vmax = %f\n", FuncName, Vmin, Vmax);*/
if (arange == 0.0) {
if (fabs((double)Vmin) > fabs((double)Vmax)) arange = (float)fabs((double)Vmin);
else arange = (float)fabs((double)Vmax);
}
/* figure out the range if PercRange is used */
if (ApplyPercClip) {
fprintf (SUMA_STDERR,"%s: Percentile range [%f..%f] is equivalent to ", FuncName, IntRange[0], IntRange[1]);
Vsort = SUMA_PercRange (V, NULL, N_V, IntRange, IntRange, NULL);
fprintf (SUMA_STDERR,"[%f..%f]\n", IntRange[0], IntRange[1]);
ApplyClip = YUP;
if (Vsort) SUMA_free(Vsort);
else {
fprintf (SUMA_STDERR,"Error %s: Error in SUMA_PercRange.\n", FuncName);
exit(1);
}
}
/* get the options for creating the scaled color mapping */
OptScl = SUMA_ScaleToMapOptInit();
if (!OptScl) {
fprintf (SUMA_STDERR,
"Error %s: Could not get scaling option structure.\n", FuncName);
exit (1);
}
/* work the options a bit */
if (ApplyMask) {
OptScl->ApplyMask = ApplyMask;
OptScl->MaskRange[0] = MaskRange[0];
OptScl->MaskRange[1] = MaskRange[1];
OptScl->MaskColor[0] = MaskColor[0];
OptScl->MaskColor[1] = MaskColor[1];
OptScl->MaskColor[2] = MaskColor[2];
}
if (ApplyClip) {
OptScl->ApplyClip = YUP;
OptScl->IntRange[0] = IntRange[0]; OptScl->IntRange[1] = IntRange[1];
}
OptScl->interpmode = interpmode;
OptScl->BrightFact = brfact;
if (MaskZero) OptScl->MaskZero = YUP;
/* map the values in V to the colormap */
/* allocate space for the result */
SV = SUMA_Create_ColorScaledVect(N_V, 0);
if (!SV) {
fprintf (SUMA_STDERR,
"Error %s: Could not allocate for SV.\n", FuncName);
exit(1);
}
/* finally ! */
if (alaAFNI) {
if (LocalHead) {
fprintf (SUMA_STDERR,
"%s: Calling SUMA_ScaleToMap_alaAFNI\n", FuncName);
fprintf (SUMA_STDERR,"%s: arange = %f\n", FuncName, arange);
}
if (CM->frac) {
if (CM->frac[0] > 0 && CM->Sgn == -1) {
SUMA_S_Err ("Color map fractions positive with -anr option");
exit(1);
}
if (CM->frac[0] < 0 && CM->Sgn == 1) {
SUMA_S_Err ("Color map fractions negative with -apr option");
exit(1);
}
}
if (Sgn) {
if (Sgn != CM->Sgn) {
SUMA_S_Warn ("Mixing positive maps (all fractions > 0) "
"with -anr option\n"
"or vice versa. That is allowed but know what"
" you're doing.\n");
}
}
if (!SUMA_ScaleToMap_alaAFNI (V, N_V, arange, CM, OptScl, SV)) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_ScaleToMap_alaAFNI.\n", FuncName);
exit(1);
}
} else {
if (LocalHead)
fprintf (SUMA_STDERR,"%s: Calling SUMA_ScaleToMap\n", FuncName);
if (!SUMA_ScaleToMap (V, N_V, Vmin, Vmax, CM, OptScl, SV)) {
fprintf (SUMA_STDERR,
"Error %s: Failed in SUMA_ScaleToMap.\n", FuncName);
exit(1);
}
}
/* Now write the colored vector back to disk */
if (NoMaskCol) {
for (k=0; k < N_V; ++k) {
k3 = 3*k;
if (!SV->isMasked[k])
fprintf (SUMA_STDOUT, "%d %f %f %f\n",
iV[k], SV->cV[k3 ], SV->cV[k3+1], SV->cV[k3+2]);
}
} else {
for (k=0; k < N_V; ++k) {
k3 = 3*k;
fprintf (SUMA_STDOUT, "%d %f %f %f\n",
iV[k], SV->cV[k3 ], SV->cV[k3+1], SV->cV[k3+2]);
}
}
/* freeing time */
if (V) SUMA_free(V);
if (iV) SUMA_free(iV);
if (!FromAFNI && freecm) if (CM) SUMA_Free_ColorMap (CM); /* only free CM if
it was a pointer copy from a map in SAC */
if (OptScl) SUMA_free(OptScl);
if (SV) SUMA_Free_ColorScaledVect (SV);
#if 0
if (SAC) SAC = SUMA_DestroyAfniColors(SAC); /* destroy SAC */
#else
SAC = NULL; /* freeing is done in SUMAg_CF */
#endif
SUMA_Free_CommonFields(SUMAg_CF);
SUMA_RETURN (0);
}
SUMA_GENERIC_PROG_OPTIONS_STRUCT *
SUMA_SpharmReco_ParseInput(char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SpharmReco_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar;
SUMA_Boolean brk;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
Opt->iopt = 86;
Opt->out_prefix = NULL;
Opt->bases_prefix = NULL;
Opt->unit_sphere_name = NULL;
Opt->n_in_namev = 0;
Opt->v0 = 0.0001;
kar = 1;
brk = 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_SpharmReco(ps);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-coef") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need an prefix after -coef \n");
exit (1);
}
Opt->in_namev[Opt->n_in_namev++] = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-l") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need an integer after -l \n");
exit (1);
}
Opt->iopt = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -prefix\n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-bases_prefix") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -bases_prefix\n");
exit (1);
}
Opt->bases_prefix = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-bases") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -bases\n");
exit (1);
}
Opt->bases_prefix = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-unit_sph") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -unit_sph\n");
exit (1);
}
Opt->unit_sphere_name = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sigma") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -sigma \n");
exit (1);
}
Opt->v0 = atof(argv[++kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s:\n"
"Option %s not understood. Try -help for usage\n",
FuncName, argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
SUMA_RETURN(Opt);
}
/*!\**
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 */
SUMA_GENERIC_PROG_OPTIONS_STRUCT *
SUMA_SurfMatch_ParseInput( char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SurfMatch_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar;
SUMA_Boolean brk;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
Opt->s=NULL;
Opt->flt1 = 1.0;
Opt->b1 = 0;
Opt->efrac = 0.0;
kar = 1;
brk = 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_SurfMatch(ps, strlen(argv[kar])>3?1:0);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-warp") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a string after -warp \n");
exit (1);
}
++kar;
if (!strcmp(argv[kar],"shift_only") ||
!strcmp(argv[kar],"sho")) {
Opt->s = SUMA_copy_string("shft");
} else if (!strcmp(argv[kar],"shift_rotate") ||
!strcmp(argv[kar],"sro")) {
Opt->s = SUMA_copy_string("shft+rot");
} else if (!strcmp(argv[kar],"shift_rotate_scale") ||
!strcmp(argv[kar],"srs")) {
Opt->s = SUMA_copy_string("shft+rot+scl");
} else if (!strcmp(argv[kar],"affine_general") ||
!strcmp(argv[kar],"aff")) {
Opt->s = SUMA_copy_string("shft+rot+scl+shr");
} else {
SUMA_S_Errv("Bad -warp parameter of %s\n"
"Choose from sho, sro, srs, or aff\n",
argv[kar]);
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-city") == 0))
{
Opt->b1 = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-depthlimit") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -depthlimit \n");
exit (1);
}
Opt->flt1 = atof(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-reduce_ref") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -reduce_ref \n");
exit (1);
}
Opt->efrac = atof(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error SurfMatch: Option %s not understood\n", argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
if (!Opt->out_prefix) {
Opt->out_prefix = SUMA_copy_string("SurfMatch.gii");
THD_force_ok_overwrite(1) ;
}
if (!Opt->s) {
Opt->s = SUMA_copy_string("shft");
}
SUMA_RETURN(Opt);
}
/*!
\brief parse the arguments for SurfSmooth program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_SURFCLUST_OPTIONS *) options structure.
To free it, use
SUMA_free(Opt->out_name);
SUMA_free(Opt);
*/
SUMA_SURFCLUST_OPTIONS *SUMA_SurfClust_ParseInput (char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SurfClust_ParseInput"};
SUMA_SURFCLUST_OPTIONS *Opt=NULL;
int kar, i, ind;
char *outname;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_create_SurfClust_Opt("SurfClust");
kar = 1;
outname = NULL;
BuildMethod = SUMA_OFFSETS2_NO_REC;
brk = 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_SurfClust(strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-no_cent") == 0)) {
Opt->DoCentrality = 0;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-cent") == 0)) {
Opt->DoCentrality = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-O2") == 0)) {
BuildMethod = SUMA_OFFSETS2;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-O2_NR") == 0)) {
BuildMethod = SUMA_OFFSETS2_NO_REC;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-Oll") == 0)) {
BuildMethod = SUMA_OFFSETS_LL;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-update") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -update \n");
exit (1);
}
Opt->update = atof(argv[kar]);
if (Opt->update < 1 || Opt->update > 100) {
fprintf (SUMA_STDERR,
"-update needs a parameter between "
"1 and 50 (I have %.1f)\n", Opt->update);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -prefix \n");
exit (1);
}
Opt->oform = SUMA_GuessFormatFromExtension(argv[kar], NULL);
if (Opt->oform == SUMA_NO_DSET_FORMAT) Opt->oform = SUMA_ASCII_NIML;
Opt->out_prefix = SUMA_RemoveDsetExtension_s(argv[kar], Opt->oform);
Opt->WriteFile = YUP;
brk = YUP;
}
#if 0
if (!brk && (strcmp(argv[kar], "-spec") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -spec \n");
exit (1);
}
Opt->spec_file = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sv") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -sv \n");
exit (1);
}
Opt->sv_name = argv[kar];
brk = YUP;
}
if (!brk && (strncmp(argv[kar], "-surf_", 6) == 0)) {
if (kar + 1>= argc) {
fprintf (SUMA_STDERR, "need argument after -surf_X SURF_NAME \n");
exit (1);
}
ind = argv[kar][6] - 'A';
if (ind < 0 || ind >= SURFCLUST_MAX_SURF) {
fprintf (SUMA_STDERR,
"-surf_X SURF_NAME option is out of range.\n"
"Only %d surfaces are allowed. \n"
"Must start with surf_A for first surface.\n",
SURFCLUST_MAX_SURF);
exit (1);
}
kar ++;
Opt->surf_names[ind] = argv[kar];
Opt->N_surf = ind+1;
brk = YUP;
}
#endif
if (!brk && (strcmp(argv[kar], "-input") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 arguments after -input \n");
exit (1);
}
Opt->in_name = argv[kar]; kar ++;
/* no need for that one Opt->nodecol = atoi(argv[kar]); kar ++; */
Opt->labelcol = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-rmm") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -rmm \n");
exit (1);
}
Opt->DistLim = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-in_range") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need two arguments after -in_range \n");
exit (1);
}
Opt->DoThreshold = SUMA_THRESH_INSIDE_RANGE;
Opt->ThreshR[0] = atof(argv[kar]); ++kar;
Opt->ThreshR[1] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-ex_range") == 0)) {
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need two arguments after -ex_range \n");
exit (1);
}
Opt->DoThreshold = SUMA_THRESH_OUTSIDE_RANGE;
Opt->ThreshR[0] = atof(argv[kar]); ++kar;
Opt->ThreshR[1] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-thresh") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -thresh \n");
exit (1);
}
Opt->DoThreshold = SUMA_LESS_THAN;
Opt->ThreshR[0] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-athresh") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -athresh \n");
exit (1);
}
Opt->DoThreshold = SUMA_ABS_LESS_THAN;
Opt->ThreshR[0] = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-thresh_col") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -thresh_col \n");
exit (1);
}
Opt->tind = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-amm2") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -amm2 \n");
exit (1);
}
Opt->AreaLim = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-n") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -n \n");
exit (1);
}
Opt->NodeLim = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out_roidset") == 0)) {
Opt->OutROI = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prepend_node_index") == 0)) {
Opt->prepend_node_index = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out_clusterdset") == 0)) {
Opt->OutClustDset = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out_fulllist") == 0)) {
Opt->FullROIList = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sort_none") == 0)) {
Opt->SortMode = SUMA_SORT_CLUST_NO_SORT;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sort_n_nodes") == 0)) {
Opt->SortMode = SUMA_SORT_CLUST_BY_NUMBER_NODES;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sort_area") == 0)) {
Opt->SortMode = SUMA_SORT_CLUST_BY_AREA;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
SUMA_S_Errv("Option %s not understood.\n"
"Try -help for usage\n", argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
/* sanitorium */
if (Opt->DistLim == -1.5f) {
fprintf (SUMA_STDERR, "must use option -rmm \n");
exit(1);
}
if (!Opt->out_prefix) {
Opt->out_prefix =
SUMA_RemoveDsetExtension_s(Opt->in_name, SUMA_NO_DSET_FORMAT);
}
if (Opt->SortMode == SUMA_SORT_CLUST_NOT_SET) {
Opt->SortMode = SUMA_SORT_CLUST_BY_AREA; }
if (BuildMethod == SUMA_OFFSETS2) { SUMA_S_Note("Using Offsets2"); }
else if (BuildMethod == SUMA_OFFSETS_LL) { SUMA_S_Note("Using Offsets_ll"); }
else if (BuildMethod == SUMA_OFFSETS2_NO_REC) {
if (LocalHead) SUMA_S_Note("Using no recursion"); }
else {
SUMA_SL_Err("Bad BuildMethod");
exit(1);
}
SUMA_SurfClust_Set_Method(BuildMethod);
if (Opt->FullROIList && !(Opt->OutROI || Opt->OutClustDset)) {
SUMA_SL_Err("-out_fulllist must be used in conjunction "
"with -out_ROIdset or -out_clusterdset");
exit(1);
}
SUMA_RETURN(Opt);
}
SUMA_GENERIC_PROG_OPTIONS_STRUCT *SUMA_SurfToSurf_ParseInput(
char *argv[], int argc, SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_BrainWrap_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar;
SUMA_Boolean brk, accepting_out;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
kar = 1;
brk = NOPE;
Opt->in_1D = NULL;
Opt->NodeDbg = -1;
Opt->debug = 0;
Opt->NearestNode = 0;
Opt->NearestTriangle = 0;
Opt->DistanceToMesh = 0;
Opt->ProjectionOnMesh = 0;
Opt->NearestNodeCoords = 0;
Opt->Data = 0;
Opt->in_name = NULL;
Opt->out_prefix = NULL;
Opt->fix_winding = 0;
Opt->iopt = 0;
Opt->oform = SUMA_NO_DSET_FORMAT;
accepting_out = NOPE;
while (kar < argc) { /* loop accross command ine options */
/*fprintf(stdout, "%s verbose: Parsing command line...\n", FuncName);*/
if (!brk && accepting_out) {
/* make sure you have not begun with new options */
if (*(argv[kar]) == '-') accepting_out = NOPE;
}
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
usage_SurfToSurf(ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-node_debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -node_debug \n");
exit (1);
}
Opt->NodeDbg = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-node_indices") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a parameter after -node_indices \n");
exit (1);
}
Opt->in_nodeindices = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-closest_possible") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -closest_possible \n");
exit (1);
}
Opt->iopt = atoi(argv[++kar]);
if (Opt->iopt != 0 && Opt->iopt != 1 && Opt->iopt != 2 &&
Opt->iopt != 3) {
SUMA_S_Errv("Must choose from 0, 1, 2, or 3 for -closest_possible."
" Have %d\n",
Opt->iopt);
exit (1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-output_params") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR,
"need at least one parameter after output_params \n");
exit (1);
}
accepting_out = YUP;
brk = YUP;
}
if (!brk && accepting_out && (strcmp(argv[kar], "NearestNode") == 0)) {
if (Opt->NearestNode < 1) Opt->NearestNode = 1;
brk = YUP;
}
if (!brk && accepting_out &&
(strcmp(argv[kar], "NearestTriangleNodes") == 0)) {
if (Opt->NearestNode < 3) Opt->NearestNode = 3;
brk = YUP;
}
if (!brk && accepting_out && (strcmp(argv[kar], "NearestTriangle") == 0)) {
if (Opt->NearestTriangle < 1) Opt->NearestTriangle = 1;
brk = YUP;
}
if (!brk && accepting_out && (strcmp(argv[kar], "DistanceToSurf") == 0)) {
Opt->DistanceToMesh = 1;
brk = YUP;
}
if (!brk && accepting_out &&
(strcmp(argv[kar], "ProjectionOnSurf") == 0)) {
Opt->ProjectionOnMesh = 1;
brk = YUP;
}
if (!brk && accepting_out &&
(strcmp(argv[kar], "NearestNodeCoords") == 0)) {
Opt->NearestNodeCoords = 1;
brk = YUP;
}
if (!brk && accepting_out &&
(strcmp(argv[kar], "Data") == 0)) {
if (Opt->Data < 0) {
fprintf (SUMA_STDERR,
"Cannot mix parameter Data with -dset option \n");
exit (1);
}
Opt->Data = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-data") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -data \n");
exit (1);
}
++kar;
if (strcmp(argv[kar],"_XYZ_") == 0) {
/* default Opt->in_name = NULL*/
if (Opt->in_name) {
SUMA_SL_Err("Input already specified."
"Do not mix -data and -dset");
exit (1);
}
} else {
Opt->in_name = SUMA_copy_string(argv[kar]);
}
Opt->Data = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-dset") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -dset \n");
exit (1);
}
++kar;
if (strcmp(argv[kar],"_XYZ_") == 0 || Opt->Data > 0) {
/* default Opt->in_name = NULL*/
if (Opt->in_name || Opt->Data > 0) {
SUMA_SL_Err("Input already specified."
"Do not mix -data and -dset."
"Or use parameter DATA with -dset");
exit (1);
}
} else {
Opt->in_name = SUMA_copy_string(argv[kar]);
}
Opt->Data = -1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_RemoveDsetExtension_eng(argv[++kar],
&(Opt->oform));
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-mapfile") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -mapfile \n");
exit (1);
}
Opt->s = SUMA_Extension(argv[++kar],".niml.M2M", NOPE);
if (!SUMA_filexists(Opt->s)) {
SUMA_S_Errv("File %s not found\n"
, Opt->s);
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-proj_dir") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a name after -proj_dir \n");
exit (1);
}
Opt->in_1D = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-make_consistent") == 0))
{
Opt->fix_winding = 1;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s:\n"
"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 ++;
}
}
/* set default for NearestNode if nothing has been set */
if (Opt->NearestNode < 1) Opt->NearestNode = 3;
if (!Opt->out_prefix) Opt->out_prefix = SUMA_copy_string("SurfToSurf");
if (Opt->in_1D && Opt->s) {
SUMA_S_Err("Cannot use -proj_dir along with -mapfile");
exit(1);
}
SUMA_RETURN(Opt);
}
SEG_OPTS *GenFeatureDist_ParseInput (SEG_OPTS *Opt, char *argv[], int argc)
{
static char FuncName[]={"GenFeatureDist_ParseInput"};
int kar, i, ind, exists;
char *outname, cview[10], *sbuf=NULL;
int brk = 0;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_ENTRY;
brk = 0;
kar = 1;
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) {
Opt->helpfunc(0);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
#ifdef USE_TRACING
if( strncmp(argv[kar],"-trace",5) == 0 ){
DBG_trace = 1 ;
brk = 1 ;
}
if( strncmp(argv[kar],"-TRACE",5) == 0 ){
DBG_trace = 2 ;
brk = 1 ;
}
#endif
if (!brk && (strcmp(argv[kar], "-debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-talk_afni") == 0)) {
Opt->ps->cs->talk_suma = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-openmp") == 0)) {
Opt->openmp = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_openmp") == 0)) {
Opt->openmp = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need 1D vox index after -vox_debug \n");
exit (1);
}
if (kar+2<argc) { /* see if we have ijk */
int iii, jjj, kkk;
if (argv[kar][0]!='-' && argv[kar][1]!='-' && argv[kar][2]!='-' &&
(iii = atoi(argv[kar ])) >= 0 &&
(jjj = atoi(argv[kar+1])) >= 0 &&
(kkk = atoi(argv[kar+2])) >= 0 ) {
Opt->VoxDbg3[0]=iii;
Opt->VoxDbg3[1]=jjj;
Opt->VoxDbg3[2]=kkk;
++kar; ++kar;
}
}
if (Opt->VoxDbg3[0] < 0) {
Opt->VoxDbg = atoi(argv[kar]);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug_file") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need filename after -vox_debug_file \n");
exit (1);
}
if (!strcmp(argv[kar],"-")) {
Opt->VoxDbgOut = stdout;
} else if (!strcmp(argv[kar],"+")) {
Opt->VoxDbgOut = stderr;
} else {
Opt->VoxDbgOut = fopen(argv[kar],"w");
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cmask") == 0)) {
kar ++;
if (kar >= argc) {
ERROR_exit("-cmask option requires a following argument!\n");
}
Opt->cmask = EDT_calcmask( argv[kar] , &(Opt->dimcmask), 0 ) ;
if( Opt->cmask == NULL ) ERROR_exit("Can't compute -cmask!\n");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mask") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -mask \n");
exit (1);
}
Opt->mset_name = argv[kar];
brk = 1;
}
if( !brk && (strncmp(argv[kar],"-mrange",5) == 0) ){
if( kar+2 >= argc )
ERROR_exit("-mrange option requires 2 following arguments!\n");
Opt->mask_bot = strtod( argv[++kar] , NULL ) ;
Opt->mask_top = strtod( argv[++kar] , NULL ) ;
if( Opt->mask_top < Opt->mask_bot )
ERROR_exit("-mrange inputs are illegal!\n") ;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-anat") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -anat \n");
exit (1);
}
Opt->aset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-sig") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -sig \n");
exit (1);
}
while (kar < argc && argv[kar][0] != '-') {
sbuf =
SUMA_append_replace_string(sbuf, argv[kar], " ", 1);
++kar;
}
if (kar < argc && argv[kar][0] == '-') --kar; /* unwind */
Opt->sig_names = SUMA_NI_str_array(Opt->sig_names, sbuf, "add");
SUMA_free(sbuf); sbuf = NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-samp") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -samp \n");
exit (1);
}
while (kar < argc && argv[kar][0] != '-') {
sbuf =
SUMA_append_replace_string(sbuf, argv[kar], " ", 1);
++kar;
}
if (kar < argc && argv[kar][0] == '-') --kar; /* unwind */
Opt->samp_names = SUMA_NI_str_array(Opt->samp_names, sbuf, "add");
SUMA_free(sbuf); sbuf = NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-hspec") == 0)) {
kar ++;
if (kar+3 >= argc) {
fprintf (stderr, "need 4 arguments after -hspec \n");
exit (1);
}
Opt->hspec = (SUMA_HIST **)
SUMA_realloc(Opt->hspec, (Opt->N_hspec+1)*sizeof(SUMA_HIST *));
Opt->hspec[Opt->N_hspec] = (SUMA_HIST*)SUMA_calloc(1,sizeof(SUMA_HIST));
Opt->hspec[Opt->N_hspec]->label = SUMA_copy_string(argv[kar++]);
Opt->hspec[Opt->N_hspec]->min = (float)strtod(argv[kar++],NULL);
Opt->hspec[Opt->N_hspec]->max = (float)strtod(argv[kar++],NULL);
Opt->hspec[Opt->N_hspec]->K = (float)strtod(argv[kar],NULL);
++Opt->N_hspec;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -prefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->proot = argv[kar];
Opt->prefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->crefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->pgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->cgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->frefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->xrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->prefix,"%s.p", argv[kar]);
sprintf(Opt->pgrefix,"%s.pg", argv[kar]);
sprintf(Opt->crefix,"%s.c", argv[kar]);
sprintf(Opt->cgrefix,"%s.cg", argv[kar]);
sprintf(Opt->frefix,"%s.f", argv[kar]);
sprintf(Opt->xrefix,"%s.x", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -classes \n");
exit (1);
}
Opt->clss = NI_strict_decode_string_list(argv[kar] ,";, ");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-features") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -features \n");
exit (1);
}
Opt->feats = NI_strict_decode_string_list(argv[kar] ,";, ");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-keys") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -keys \n");
exit (1);
}
if (!(nstr = NI_strict_decode_string_list(argv[kar] ,";, "))){
ERROR_exit("Bad option %s after -keys", argv[kar]);
}
Opt->keys = (int *)calloc(nstr->num, sizeof(int));
for (ii=0;ii<nstr->num; ++ii)
Opt->keys[ii] = strtol(nstr->str[ii],NULL,10);
NI_delete_str_array(nstr);nstr=NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-labeltable") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -labeltable \n");
exit (1);
}
Opt->labeltable_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-uid") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -uid \n");
exit (1);
}
snprintf(Opt->uid,128,"%s",argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-ShowTheseHists") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -ShowTheseHists \n");
exit (1);
}
{
NI_str_array *hisnames=NULL;
SUMA_HIST *hh=NULL;
int ii=0;
hisnames = NI_strict_decode_string_list(argv[kar],";, ");
for (ii=0; ii<hisnames->num; ++ii) {
if ((hh = SUMA_read_hist(hisnames->str[ii]))) {
SUMA_Show_hist(hh, 1, NULL);
hh = SUMA_Free_hist(hh);
} else {
SUMA_S_Errv("Hist %s not found.\n", hisnames->str[ii]);
exit(1);
}
}
hisnames = SUMA_free_NI_str_array(hisnames);
}
exit(0);
brk = 1;
}
if (!brk) {
fprintf (stderr,"Option #%d %s not understood. \n"
"Try -help for usage\n", kar, argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = 0;
kar ++;
}
}
if (!Opt->prefix) Opt->prefix = strdup("./GenFeatureDistOut.p");
if (!Opt->frefix) Opt->frefix = strdup("./GenFeatureDistOut.f");
if (!Opt->xrefix) Opt->xrefix = strdup("./GenFeatureDistOut.x");
if (!Opt->crefix) Opt->crefix = strdup("./GenFeatureDistOut.c");
if (Opt->uid[0]=='\0') UNIQ_idcode_fill(Opt->uid);
if (Opt->VoxDbg > -1 && !Opt->VoxDbgOut) {
char stmp[256];
sprintf(stmp,"%d.GFD.dbg", Opt->VoxDbg);
Opt->VoxDbgOut = fopen(stmp,"w");
}
SUMA_RETURN(Opt);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"MakeColorMap"};
char *fscolutname = NULL, *FidName = NULL,
*Prfx = NULL, h[9], *StdType=NULL, *dbfile=NULL, *MapName=NULL;
int Ncols = 0, N_Fid = 0, kar, i, ifact, *Nind = NULL,
imap = -1, MapSpecified = 0;
int fsbl0, fsbl1, showfscolut, exists=0;
float **Fid=NULL, **M=NULL;
MRI_IMAGE *im = NULL;
float *far=NULL;
int AfniHex=0, freesm;
int suc, idISi=0;
char stmp[256], *s=NULL, *ooo=NULL, *sdset_prefix;
SUMA_PARSED_NAME *sname=NULL;
NI_group *ngr=NULL;
SUMA_Boolean brk, SkipLast, PosMap,
Usage1, Usage2, Usage3, Usage4, flipud, fscolut,
LocalHead = NOPE;
SUMA_COLOR_MAP *SM=NULL;
SUMA_DSET_FORMAT iform;
SUMA_DSET *sdset=NULL;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
if (argc < 2) {
SUMA_MakeColorMap_usage();
exit (0);
}
kar = 1;
freesm = 1;
fscolutname = NULL;
fsbl0 = -1;
fsbl1 = -1;
brk = NOPE;
SkipLast = NOPE;
AfniHex = 0;
PosMap = NOPE;
Usage1 = NOPE;
Usage2 = NOPE;
Usage3 = NOPE;
Usage4 = NOPE;
flipud = NOPE;
fscolut = NOPE;
showfscolut = 0;
MapSpecified = NOPE;
idISi=0;
iform = SUMA_NO_DSET_FORMAT;
sdset_prefix=NULL;
while (kar < argc) { /* loop accross command ine options */
if (strcmp(argv[kar], "-h") == 0 || strcmp(argv[kar], "-help") == 0) {
SUMA_MakeColorMap_usage();
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-v") == 0))
{
LocalHead = NOPE;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-flipud") == 0))
{
flipud = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-f") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -f ");
exit (1);
}
FidName = argv[kar];
Usage1 = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-fscolutfile") == 0))
{
Usage4=YUP;
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -fscolutfile ");
exit (1);
}
fscolutname = argv[kar];
if (fsbl0 < 0) {
fsbl0 = 0;
fsbl1 = 255;
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-usercolutfile") == 0))
{
Usage4=YUP;
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 argument after -fscolutfile ");
exit (1);
}
fscolutname = argv[kar];
if (fsbl0 < 0) {
fsbl0 = 0;
fsbl1 = -1;
}
idISi=1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-fscolut") == 0))
{
fscolut = YUP;
Usage4=YUP;
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 arguments after -fscolut ");
exit (1);
}
fsbl0 = atoi(argv[kar]); ++kar;
fsbl1 = atoi(argv[kar]);
if (fsbl0 > fsbl1 || fsbl0 < -1 || fsbl1 > 10000) {
SUMA_S_Errv("-fscolut values of %d and %d either\n"
"do not make sense or exceed range 0 to 10000\n",
fsbl0, fsbl1);
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-show_fscolut") == 0))
{
showfscolut = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-fn") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -fn ");
exit (1);
}
FidName = argv[kar];
Usage2 = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-nc") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -nc ");
exit (1);
}
Ncols = atoi(argv[kar]);
Usage1 = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-ah") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -ah ");
exit (1);
}
Prfx = argv[kar];
AfniHex = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-ahc") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -ahc ");
exit (1);
}
Prfx = argv[kar];
AfniHex = 2;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-suma_cmap") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -suma_cmap");
exit (1);
}
Prfx = argv[kar];
AfniHex = 3;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-std") == 0))
{
kar ++;
if (MapSpecified) {
SUMA_S_Err( "Color map already specified.\n"
"-cmap and -std are mutually exclusive\n");
exit (1);
}
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -std ");
exit (1);
}
MapSpecified = YUP;
StdType = argv[kar];
Usage3 = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-cmapdb") == 0))
{
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -cmapdb ");
exit (1);
}
SUMAg_CF->isGraphical = YUP;
/* WILL NEED X DISPLAY TO RESOLVE COLOR NAMES */
dbfile = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-cmap") ==0)) {
if (MapSpecified) {
SUMA_S_Err( "Color map already specified.\n"
"-cmap and -std are mutually exclusive\n");
exit (1);
}
MapSpecified = YUP;
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need 1 arguments after -cmap ");
exit (1);
}
Usage3 = YUP;
MapName = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sl") == 0))
{
SkipLast = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-pos") == 0))
{
/* obsolete */
PosMap = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sdset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need surface dataset after -sdset \n");
exit (1);
}
iform = SUMA_NO_DSET_FORMAT;
if (!(sdset = SUMA_LoadDset_s (argv[kar], &iform, 0))) {
SUMA_S_Err("Failed to load surface dset");
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sdset_prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need prefix dataset after -sdset_prefix \n");
exit (1);
}
sdset_prefix = argv[kar];
brk = YUP;
}
if (!brk) {
SUMA_S_Errv("Option %s not understood. Try -help for usage\n",
argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}/* loop accross command ine options */
/* check input */
if ( (Usage1 && (Usage2 || Usage3 || Usage4)) ||
(Usage2 && (Usage1 || Usage3 || Usage4)) ||
(Usage3 && (Usage1 || Usage2 || Usage4)) ||
(Usage4 && (Usage1 || Usage2 || Usage3)) ) {
SUMA_S_Err("Mixing options from multiple usage modes.\n");
exit(1);
}
if (!Usage1 && !Usage2 && !Usage3 && !Usage4) {
SUMA_S_Err("One of these options must be used:\n"
"-f, -fn, -std, or -fscolut.\n");
exit(1);
}
/* are there database files to read */
if (dbfile) {
SUMA_LH("Now trying to read db file");
if (!SUMAg_CF->scm) {
SUMAg_CF->scm = SUMA_Build_Color_maps();
if (!SUMAg_CF->scm) {
SUMA_SL_Err("Failed to build color maps.\n");
exit(1);
}
}
if (SUMA_AFNI_Extract_Colors ( dbfile, SUMAg_CF->scm ) < 0) {
SUMA_S_Errv("Failed to read %s colormap file.\n", dbfile);
exit(1);
}
}
if (Usage1 || Usage2) {
if (!SUMA_filexists (FidName)) {
SUMA_S_Errv("File %s could not be found.\n", FidName);
exit(1);
}
/* read the fiducials file */
im = mri_read_1D (FidName);
if (!im) {
SUMA_S_Err("Failed to read file");
exit(1);
}
far = MRI_FLOAT_PTR(im);
N_Fid = im->nx * im->ny;
}
if (PosMap) {
fprintf (SUMA_STDERR,"\nWarning %s: -pos option is obsolete.\n", FuncName);
}
/* allocate for fiducials */
if (Usage1) {
if (N_Fid % 3) {
fprintf (SUMA_STDERR,
"Error %s: Not all rows in %s appear to have RGB triplets.\n",
FuncName, FidName);
exit (1);
}
Fid = (float **) SUMA_allocate2D (N_Fid / 3, 3, sizeof(float));
if (Fid == NULL) {
fprintf (SUMA_STDERR,
"Error %s: Could not allocate for Fid.\n", FuncName);
exit(1);
}
for (i=0; i < im->nx; ++i) {
Fid[i][0] = far[i];
Fid[i][1] = far[i+im->nx];
Fid[i][2] = far[i+2*im->nx];
}
mri_free(im); im = NULL;
/* now create the color map */
SM = SUMA_MakeColorMap (Fid, N_Fid/3, 0, Ncols, SkipLast, FuncName);
if (SM == NULL) {
fprintf (SUMA_STDERR,
"Error %s: Error in SUMA_MakeColorMap.\n", FuncName);
exit(1);
}
}
if (Usage2) { /* second usage */
if (N_Fid % 4) {
fprintf (SUMA_STDERR,
"Error %s: Not all rows in %s appear to have "
"RGB N quadruplets.\n", FuncName, FidName);
exit (1);
}
Fid = (float **) SUMA_allocate2D (N_Fid / 4, 3, sizeof(float));
Nind = (int *) SUMA_calloc (N_Fid/4, sizeof(int));
if (Fid == NULL || !Nind) {
fprintf (SUMA_STDERR,
"Error %s: Could not allocate for Fid or Nind.\n", FuncName);
exit(1);
}
for (i=0; i < im->nx; ++i) {
Fid[i][0] = far[i];
Fid[i][1] = far[i+im->nx];
Fid[i][2] = far[i+2*im->nx];
Nind[i] = (int)far[i+3*im->nx];
}
mri_free(im); im = NULL;
/* now create the color map */
SM = SUMA_MakeColorMap_v2 (Fid, N_Fid/4, 0, Nind, SkipLast, FuncName);
if (SM == NULL) {
fprintf (SUMA_STDERR,
"Error %s: Error in SUMA_MakeColorMap.\n", FuncName);
exit(1);
}
Ncols = SM->N_M[0];
}
if (Usage3) { /* third usage */
if (!MapName) {
SM = SUMA_FindNamedColMap (StdType);
freesm = 0;
if (SM == NULL) {
fprintf (SUMA_STDERR,
"Error %s: Error in SUMA_MakeColorMap.\n", FuncName);
exit(1);
}
Ncols = SM->N_M[0];
} else {
imap = SUMA_Find_ColorMap ( MapName, SUMAg_CF->scm->CMv,
SUMAg_CF->scm->N_maps, -2);
if (imap < 0) {
fprintf (SUMA_STDERR,
"Error %s: Could not find colormap %s.\n",
FuncName, MapName);
exit (1);
}
SM = SUMAg_CF->scm->CMv[imap];
Ncols = SM->N_M[0];
}
}
if (Usage4) { /* 4th usage */
if (!(SM = SUMA_FScolutToColorMap(fscolutname, fsbl0,
fsbl1, showfscolut, idISi))) {
SUMA_S_Err("Failed to get FreeSurfer colormap.");
exit(1);
}
Ncols = SM->N_M[0];
}
if (flipud) {
SUMA_Flip_Color_Map (SM);
}
M = SM->M;
if (AfniHex && Ncols > 20) {
if (!Usage4) {
SUMA_S_Note("Writing colormap in colorscale format.\n");
}
}
if (!AfniHex) {
SUMA_disp_mat (M, Ncols, 3, 1);
/*SUMA_Show_ColorMapVec (&SM, 1, NULL, 2);*/
} else {
if (Usage4 || Ncols > 20) {
if (AfniHex == 1) {
fprintf (stdout, "%s \n", Prfx);
for (i=0; i < Ncols; ++i) {
/* Now create the hex form */
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][0]*255)), 1, 0);
fprintf (stdout, "#%s", h);
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][1]*255)), 1, 0);
fprintf (stdout, "%s", h);
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][2]*255)), 1, 0);
fprintf (stdout, "%s \n", h);
}
fprintf (stdout, "\n") ;
} else if (AfniHex == 2){ /* to go in the C code
(see pbardef.h and pbar.c)*/
char *p2 = SUMA_copy_string(Prfx);
SUMA_TO_UPPER(p2);
fprintf (stdout, "static char %s[] = {\n \"%s \"\n \"",
p2, Prfx); SUMA_free(p2); p2 = NULL;
for (i=0; i < Ncols; ++i) {
if (i) {
if (!(i % 4)) { fprintf (stdout, " \"\n \""); }
else { fprintf (stdout, " "); }
}
/* Now create the hex form */
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][0]*255)), 1, 0);
fprintf (stdout, "#%s", h);
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][1]*255)), 1, 0);
fprintf (stdout, "%s", h);
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][2]*255)), 1, 0);
fprintf (stdout, "%s", h);
}
fprintf (stdout, " \"\n};\n") ;
} else if (AfniHex == 3){
SUMA_LHv("Now turn %s to niml\n", SM->Name);
sname = SUMA_ParseFname(Prfx, NULL);
snprintf(stmp, 128*sizeof(char),
"file:%s.niml.cmap", sname->FileName_NoExt);
if (SM->Name) SUMA_free(SM->Name);
SM->Name = SUMA_copy_string(sname->FileName_NoExt);
ngr = SUMA_CmapToNICmap(SM);
NEL_WRITE_TX(ngr, stmp, suc);
if (!suc) {
SUMA_S_Errv("Failed to write %s\n", stmp);
}
SUMA_Free_Parsed_Name(sname); sname = NULL;
} else {
SUMA_S_Err("AfniHex should be 0, 1, or 2\n");
exit(1);
}
} else {
fprintf (stdout, "\n***COLORS\n");
for (i=0; i < Ncols; ++i) {
/* Now create the hex form */
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][0]*255)), 1, 0);
if (i<10) fprintf (stdout, "%s_0%d = #%s", Prfx, i, h);
else fprintf (stdout, "%s_%d = #%s", Prfx, i, h);
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][1]*255)), 1, 0);
fprintf (stdout, "%s", h);
r_sprintf_long_to_hex (h,
(unsigned long)rint((M[i][2]*255)), 1, 0);
fprintf (stdout, "%s\n", h);
}
/* color map */
fprintf (stdout, "\n***PALETTES %s [%d]\n//1 to -1 range\n",
Prfx, Ncols);
ifact = 2;
for (i=0; i < Ncols; ++i) {
fprintf (stdout, "%f -> ", 1.0 - (float)(ifact*i)/Ncols);
if (i<10) fprintf (stdout, "%s_0%d\n", Prfx, i);
else fprintf (stdout, "%s_%d\n", Prfx, i);
}
fprintf (stdout,
"\n***PALETTES %s [%d+]\n//1 to 0 range\n", Prfx, Ncols);
ifact = 1;
for (i=0; i < Ncols; ++i) {
fprintf (stdout, "%f -> ", 1.0 - (float)(ifact*i)/Ncols);
if (i<10) fprintf (stdout, "%s_0%d\n", Prfx, i);
else fprintf (stdout, "%s_%d\n", Prfx, i);
}
}
}
/* free allocated space */
if (Usage1) {
if (Fid) SUMA_free2D((char **)Fid, N_Fid / 3);
} else {
if (Fid) SUMA_free2D((char **)Fid, N_Fid / 4);
if (Nind) SUMA_free(Nind);
}
/* add colormap to a surface dset ? */
if (sdset) {
SUMA_DSET *idset;
if (!SUMA_is_AllConsistentCastType_dset(sdset, SUMA_int)) {
idset = SUMA_CoercedCopyofDset(sdset, SUMA_int, NULL);
} else {
idset = sdset;
}
if (!(SUMA_dset_to_Label_dset_cmap(idset, SM))) {
SUMA_S_Err("Failed to make change");
exit(1);
}
s = SUMA_OutputDsetFileStatus(
sdset_prefix?sdset_prefix:SDSET_FILENAME(sdset),
NULL, &iform,
NULL, ".lbl", &exists);
SUMA_AddNgrHist(sdset->ngr, FuncName, argc, argv);
ooo = SUMA_WriteDset_s(s, idset, iform,
THD_ok_overwrite(), 0);
SUMA_free(ooo); ooo=NULL; SUMA_free(s); s = NULL;
if (idset != sdset) SUMA_FreeDset(idset);
SUMA_FreeDset(sdset); sdset=NULL;
}
if (SM && !MapName && freesm) SUMA_Free_ColorMap(SM);
if (!SUMA_Free_CommonFields(SUMAg_CF)) {
SUMA_SL_Err("Failed to free commonfields.");
}
SUMA_RETURN (0);
}
/*!
\brief parse the arguments for SurfSmooth program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_GETPATCH_OPTIONS *) options structure.
To free it, use
SUMA_free(Opt->out_prefix);
SUMA_free(Opt);
*/
SUMA_GETPATCH_OPTIONS *SUMA_GetPatch_ParseInput (char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_GetPatch_ParseInput"};
SUMA_GETPATCH_OPTIONS *Opt=NULL;
int kar, i, ind;
char *outprefix;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = (SUMA_GETPATCH_OPTIONS *)SUMA_malloc(sizeof(SUMA_GETPATCH_OPTIONS));
kar = 1;
Opt->iType = SUMA_FT_NOT_SPECIFIED;
Opt->out_prefix = NULL;
Opt->out_volprefix = NULL;
Opt->in_name = NULL;
Opt->minhits = 2;
Opt->labelcol = -1;
Opt->nodecol = -1;
Opt->thislabel = -1;
Opt->DoVol = 0;
Opt->VolOnly = 0;
Opt->coordgain = 0.0;
Opt->Do_p2s = NOPE;
Opt->FixBowTie = -1;
Opt->adjust_contour = -1;
Opt->oType = SUMA_FT_NOT_SPECIFIED;
Opt->verb = 1;
Opt->flip = 0;
brk = 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_getPatch(ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-hits") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -hits \n");
exit (1);
}
Opt->minhits = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-coord_gain") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -coord_gain \n");
exit (1);
}
Opt->coordgain = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-masklabel") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -masklabel \n");
exit (1);
}
Opt->thislabel = atoi(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-patch2surf") == 0)) {
Opt->Do_p2s = YUP;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-vol") == 0)) {
Opt->DoVol = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-flip_orientation") == 0)) {
Opt->flip = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-vol_only") == 0)) {
Opt->DoVol = 1;
Opt->VolOnly = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-adjust_contour") == 0)) {
Opt->adjust_contour = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-do-not-adjust_contour") == 0)) {
Opt->adjust_contour = 0;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-check_bowtie") == 0)) {
Opt->FixBowTie = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-fix_bowtie") == 0)) {
Opt->FixBowTie = 2;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-ok_bowtie") == 0)) {
Opt->FixBowTie = 0;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-verb") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -verb \n");
exit (1);
}
Opt->verb = atoi(argv[kar]);
if (Opt->verb < 0 || Opt->verb > 10) {
SUMA_S_Errv("Something fishy with -verb value of %s\n"
"Need integer from 0 to 2\n", argv[kar]);
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-stiched_surface") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -stiched_surface \n");
exit (1);
}
Opt->out_volprefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out_type") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -out_type \n");
exit (1);
}
Opt->oType = SUMA_guess_surftype_argv(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-input") == 0)) {
kar ++;
if (kar+2 >= argc) {
fprintf (SUMA_STDERR, "need 3 arguments after -input \n");
exit (1);
}
Opt->in_name = argv[kar]; kar ++;
Opt->nodecol = atoi(argv[kar]); kar ++;
Opt->labelcol = atoi(argv[kar]);
brk = YUP;
}
#if 0
if (!brk && (strcmp(argv[kar], "-spec") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -spec \n");
exit (1);
}
Opt->spec_file = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sv") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -sv \n");
exit (1);
}
Opt->sv_name = argv[kar];
brk = YUP;
}
if (!brk && (strncmp(argv[kar], "-surf_", 6) == 0)) {
if (kar + 1>= argc) {
fprintf (SUMA_STDERR, "need argument after -surf_X SURF_NAME \n");
exit (1);
}
ind = argv[kar][6] - 'A';
if (ind < 0 || ind >= SURFPATCH_MAX_SURF) {
fprintf (SUMA_STDERR, "-surf_X SURF_NAME option is out of range.\n");
exit (1);
}
kar ++;
Opt->surf_names[ind] = argv[kar];
Opt->N_surf = ind+1;
brk = YUP;
}
#endif
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s:\nOption %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 ++;
}
}
/* sanity checks */
if (Opt->FixBowTie < 0) {
if (Opt->DoVol) Opt->FixBowTie = 1; /* important to check in this case */
else Opt->FixBowTie = 0;
}
if (Opt->adjust_contour < 0) {
if (Opt->DoVol) Opt->adjust_contour = 0;
else Opt->adjust_contour = 0;
}
if (!Opt->out_prefix) Opt->out_prefix = SUMA_copy_string("SurfPatch");
if (Opt->thislabel >= 0 && Opt->labelcol < 0) {
SUMA_SL_Err("Cannot use -masklabel without specifying "
"ilabel in -input option");
exit(1);
}
if (Opt->minhits < 1 || Opt->minhits > 3) {
SUMA_SL_Err("minhits must be > 0 and < 3");
exit(1);
}
if (!Opt->in_name) {
SUMA_SL_Err("No input specified.");
exit(1);
}
SUMA_RETURN (Opt);
}
/*!
\brief parse the arguments for SurfQual program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_SURFQUAL_OPTIONS *) options structure.
To free it, use
SUMA_free(Opt->out_prefix);
SUMA_free(Opt);
*/
SUMA_SURFQUAL_OPTIONS *SUMA_SurfQual_ParseInput (char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]= {"SUMA_SurfQual_ParseInput"};
SUMA_SURFQUAL_OPTIONS *Opt=NULL;
int kar, i, ind;
char *outprefix;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = (SUMA_SURFQUAL_OPTIONS *)SUMA_malloc(sizeof(SUMA_SURFQUAL_OPTIONS));
kar = 1;
Opt->out_prefix = NULL;
Opt->surftype = NULL;
Opt->self_intersect = 0;
Opt->DoSum = 0;
brk = 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_SurfQual(ps, strlen(argv[kar]) > 3 ? 2:1);
exit (0);
}
/* skip the options parsed in SUMA_ParseInput_basics_s */
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-sphere") == 0)) {
if (Opt->surftype) {
SUMA_S_Err( "Surface type already specified.\n"
"Only one type allowed.");
exit(1);
}
Opt->surftype = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-self_intersect") == 0)) {
Opt->self_intersect = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-summary") == 0)) {
Opt->DoSum = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s:\nOption %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 0
if (Spec->N_Surfs < 1) {
SUMA_SL_Err("No surface specified.");
exit(1);
}
#endif
SUMA_RETURN (Opt);
}
/*!
\brief parse the arguments for SurfSmooth program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_GENERIC_PROG_OPTIONS_STRUCT *) options structure.
To free it, use
SUMA_free(Opt->out_name);
SUMA_free(Opt);
*/
SUMA_GENERIC_PROG_OPTIONS_STRUCT *SUMA_ConvexHull_ParseInput (char *argv[], int argc, SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_ConvexHull_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar, i, ind;
char *outname;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = (SUMA_GENERIC_PROG_OPTIONS_STRUCT *)SUMA_malloc(sizeof(SUMA_GENERIC_PROG_OPTIONS_STRUCT));
kar = 1;
Opt->spec_file = NULL;
Opt->out_prefix = NULL;
Opt->sv_name = NULL;
Opt->N_surf = -1;
Opt->in_name = NULL;
Opt->cmask = NULL;
Opt->MaskMode = SUMA_ISO_UNDEFINED;
for (i=0; i<SUMA_GENERIC_PROG_MAX_SURF; ++i) { Opt->surf_names[i] = NULL; }
outname = NULL;
Opt->in_vol = NULL;
Opt->nvox = -1;
Opt->ninmask = -1;
Opt->mcdatav = NULL;
Opt->debug = 0;
Opt->v0 = 0.0;
Opt->v1 = -1.0;
Opt->fvec = NULL;
Opt->SurfFileType = SUMA_PLY;
Opt->SurfFileFormat = SUMA_ASCII;
Opt->xform = SUMA_ISO_XFORM_MASK;
Opt->obj_type = -1;
Opt->obj_type_res = -1;
Opt->XYZ = NULL;
Opt->in_1D = NULL;
Opt->N_XYZ = 0;
Opt->s = SUMA_copy_string("convex_hull");
Opt->geom = 1;
Opt->corder = 0;
Opt->unif = 0;
Opt->UseThisBrain = NULL;
brk = 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_ConvexHull(ps);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-xform") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -xform \n");
exit (1);
}
if (!strcmp(argv[kar], "mask")) {
Opt->xform = SUMA_ISO_XFORM_MASK;
} else if (!strcmp(argv[kar], "none")) {
Opt->xform = SUMA_ISO_XFORM_NONE;
} else if (!strcmp(argv[kar], "shift")) {
Opt->xform = SUMA_ISO_XFORM_SHIFT;
}else {
fprintf (SUMA_STDERR,
"%s is a bad parameter for -xform option. \n", argv[kar]);
exit (1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-input_1D") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -input_1D \n");
exit (1);
}
Opt->in_1D = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-these_coords") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -these_coords \n");
exit (1);
}
Opt->UseThisBrain = argv[kar];
Opt->unif = 2;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-q_opt") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need option after -q_opt \n");
exit (1);
}
if (!strcmp(argv[kar],"triangulate_xy")) {
Opt->geom = 2;
} else if (!strcmp(argv[kar],"convex_hull")) {
Opt->geom = 1;
} else {
SUMA_S_Errv("Bad value of %s for -q_opt", argv[kar]);
exit(1);
}
Opt->s = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-proj_xy") == 0)) {
Opt->corder = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-orig_coord") == 0)) {
Opt->unif = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[kar]);
if (Opt->debug > 2) { LocalHead = YUP; }
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-isocmask") == 0)) {
if (Opt->MaskMode != SUMA_ISO_UNDEFINED) {
fprintf (SUMA_STDERR, "only one masking mode (-iso*) allowed.\n");
}
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -isocmask \n");
exit (1);
}
Opt->cmask = argv[kar];
Opt->MaskMode = SUMA_ISO_CMASK;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-isoval") == 0)) {
if (Opt->MaskMode != SUMA_ISO_UNDEFINED) {
fprintf (SUMA_STDERR, "only one masking mode (-iso*) allowed.\n");
}
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -isoval \n");
exit (1);
}
Opt->v0 = atof(argv[kar]);
Opt->MaskMode = SUMA_ISO_VAL;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-isorange") == 0)) {
if (Opt->MaskMode != SUMA_ISO_UNDEFINED) {
fprintf (SUMA_STDERR, "only one masking mode (-iso*) allowed.\n");
}
kar ++;
if (kar+1 >= argc) {
fprintf (SUMA_STDERR, "need 2 arguments after -isorange \n");
exit (1);
}
Opt->v0 = atof(argv[kar]);kar ++;
Opt->v1 = atof(argv[kar]);
Opt->MaskMode = SUMA_ISO_RANGE;
if (Opt->v1 < Opt->v0) {
fprintf (SUMA_STDERR,
"range values wrong. Must have %f <= %f \n",
Opt->v0, Opt->v1);
exit (1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-input") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -input \n");
exit (1);
}
Opt->in_name = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,
"Error %s:\n"
"Option %s not understood. Try -help for usage\n",
FuncName, argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
/* transfer some options to Opt from ps.
Clunky because this is retrofitting */
if (ps->o_N_surfnames) {
Opt->out_prefix = SUMA_copy_string(ps->o_surfnames[0]);
Opt->SurfFileType = ps->o_FT[0];
Opt->SurfFileFormat = ps->o_FF[0];
}
if (ps->i_N_surfnames) {
if (Opt->in_name || Opt->in_1D) {
SUMA_S_Err( "Options -i_TYPE, -input and -input_1D"
" are mutually exclusive.");
exit(1);
}
}
if (Opt->in_name) {
if (ps->i_N_surfnames !=0 || Opt->in_1D) {
fprintf (SUMA_STDERR,"Error %s:\nOptions -i_TYPE, -input and -input_1D are mutually exclusive.\n", FuncName);
exit(1);
}
}
if (Opt->in_1D) {
if (ps->i_N_surfnames !=0 || Opt->in_name) {
fprintf (SUMA_STDERR,"Error %s:\nOptions -i_TYPE, -input and -input_1D are mutually exclusive.\n", FuncName);
exit(1);
}
}
if (Opt->in_name && Opt->obj_type >= 0) {
fprintf (SUMA_STDERR,"Error %s:\nOptions -input and -shape are mutually exclusive.\n", FuncName);
exit(1);
}
if ((!Opt->in_name && Opt->obj_type < 0) && (!Opt->in_1D && !ps->i_N_surfnames)) {
fprintf (SUMA_STDERR,"Error %s:\nEither -input or -input_1D or -i_TYPE options must be used.\n", FuncName);
exit(1);
}
if (Opt->in_1D || ps->i_N_surfnames) {
if (Opt->MaskMode != SUMA_ISO_UNDEFINED) {
fprintf (SUMA_STDERR,"Error %s:\nCannot use -iso* options with either -input_1D or -i_TYPE options.\n", FuncName);
exit(1);
}
if (Opt->xform != SUMA_ISO_XFORM_MASK) {
fprintf (SUMA_STDERR,"Error %s:\nCannot use -xform option with either -input_1D or -i_TYPE options.\n", FuncName);
exit(1);
}
}
if (!Opt->out_prefix) Opt->out_prefix = SUMA_copy_string("convexhull_out");
if (Opt->xform == SUMA_ISO_XFORM_NONE) {
if (Opt->v0 != 0) {
fprintf (SUMA_STDERR,"Error %s: Bad %f isovalue\nWith -xform none you can only extract the 0 isosurface.\n(i.e. -isoval 0)\n", FuncName, Opt->v0);
exit(1);
}
if (Opt->MaskMode != SUMA_ISO_VAL) {
fprintf (SUMA_STDERR,"Error %s: \nWith -xform none you can only use -isoval 0\n", FuncName);
exit(1);
}
}
if (Opt->xform == SUMA_ISO_XFORM_SHIFT) {
if (Opt->MaskMode != SUMA_ISO_VAL) {
fprintf (SUMA_STDERR,"Error %s: \nWith -xform shift you can only use -isoval val\n", FuncName);
exit(1);
}
}
SUMA_RETURN(Opt);
}
SUMA_GENERIC_PROG_OPTIONS_STRUCT *SUMA_SurfInfo_ParseInput(char *argv[], int argc, SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SurfInfo_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar;
SUMA_Boolean brk;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
Opt->b2=0;
Opt->in_1D=" ; ";
kar = 1;
brk = 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_SurfInfo(ps);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-detail") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -detail \n");
exit (1);
}
Opt->b1 = (byte)atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-sep") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a string after -sep \n");
exit (1);
}
Opt->in_1D = argv[++kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-input") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need surface dset after -input \n");
exit (1);
}
if (Opt->n_in_namev < SUMA_GENERIC_PROG_MAX_IN_NAME) {
Opt->in_namev[Opt->n_in_namev] = argv[++kar];
++Opt->n_in_namev;
} else {
SUMA_S_Err("Too many input dsets on command line");
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-N_Node") == 0))
{
Opt->s = SUMA_append_replace_string(Opt->s,"N_Node","|",1);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-COM") == 0))
{
Opt->s = SUMA_append_replace_string(Opt->s,"COM","|",1);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-N_FaceSet") == 0
|| strcmp(argv[kar], "-N_Tri") == 0))
{
Opt->s = SUMA_append_replace_string(Opt->s,(argv[kar]+1),"|",1);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-quiet") == 0))
{
Opt->b2 = 1;
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
/* Assume the rest is input data */
while (kar < argc) {
if (Opt->n_in_namev < SUMA_GENERIC_PROG_MAX_IN_NAME) {
Opt->in_namev[Opt->n_in_namev] = argv[kar];
++Opt->n_in_namev; ++kar;
} else {
SUMA_S_Err("Too many input surfaces on command line");
}
}
} else {
brk = NOPE;
kar ++;
}
}
SUMA_RETURN(Opt);
}
SEG_OPTS *Seg_ParseInput (SEG_OPTS *Opt, char *argv[], int argc)
{
static char FuncName[]={"Seg_ParseInput"};
int kar, i, ind, exists;
char *outname, cview[10];
int brk = 0;
ENTRY("Seg_ParseInput");
brk = 0;
kar = 1;
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) {
Opt->helpfunc(0);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
#ifdef USE_TRACING
if( strncmp(argv[kar],"-trace",5) == 0 ){
DBG_trace = 1 ;
brk = 1 ;
}
if( strncmp(argv[kar],"-TRACE",5) == 0 ){
DBG_trace = 2 ;
brk = 1 ;
}
#endif
if (!brk && (strcmp(argv[kar], "-debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-talk_afni") == 0)) {
Opt->ps->cs->talk_suma = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-do") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -do \n");
exit (1);
}
if (strchr(argv[kar], 'c')) Opt->DO_c = 1;
if (strchr(argv[kar], 'f')) Opt->DO_f = 1;
if (strchr(argv[kar], 'x')) Opt->DO_x = 1;
if (strchr(argv[kar], 'p')) Opt->DO_p = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-L2") == 0)) {
Opt->fitmeth = SEG_LSQFIT;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-L1") == 0)) {
Opt->fitmeth = SEG_L1FIT;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-openmp") == 0)) {
Opt->openmp = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_openmp") == 0)) {
Opt->openmp = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pweight") == 0)) {
Opt->pweight = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_pweight") == 0)) {
Opt->pweight = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_edge") == 0)) {
Opt->edge = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-edge") == 0)) {
Opt->edge = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-edge1") == 0)) {
Opt->edge = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-edge2") == 0)) {
Opt->edge = 2;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need 1D vox index after -vox_debug \n");
exit (1);
}
if (kar+2<argc) { /* see if we have ijk */
int iii, jjj, kkk;
if ( argv[kar ][0]!='-' &&
argv[kar+1][0]!='-' &&
argv[kar+2][0]!='-' &&
(iii = atoi(argv[kar ])) >= 0 &&
(jjj = atoi(argv[kar+1])) >= 0 &&
(kkk = atoi(argv[kar+2])) >= 0 ) {
Opt->VoxDbg3[0]=iii;
Opt->VoxDbg3[1]=jjj;
Opt->VoxDbg3[2]=kkk;
++kar; ++kar;
}
}
if (Opt->VoxDbg3[0] < 0) {
Opt->VoxDbg = atoi(argv[kar]);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug_file") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need filename after -vox_debug_file \n");
exit (1);
}
if (!strcmp(argv[kar],"-")) {
Opt->VoxDbgOut = stdout;
} else if (!strcmp(argv[kar],"+")) {
Opt->VoxDbgOut = stderr;
} else {
Opt->VoxDbgOut = fopen(argv[kar],"w");
}
brk = 1;
}
if (strcmp(argv[kar],"-logp") == 0 ) {
Opt->logp = 1;
brk = 1;
}
if (strcmp(argv[kar],"-p") == 0 ) {
Opt->logp = 0;
brk = 1;
}
if( strcmp(argv[kar],"-use_tmp") == 0 ){
Opt->UseTmp = 1 ;
brk = 1;
}
if( strcmp(argv[kar],"-no_tmp") == 0 ){
Opt->UseTmp = 0 ;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-vox_debug") == 0)) {
kar ++;
if (kar+2 >= argc) {
fprintf (stderr, "need 3 arguments after -vox_debug \n");
exit (1);
}
Opt->idbg = atoi(argv[kar]); ++kar;
Opt->jdbg = atoi(argv[kar]); ++kar;
Opt->kdbg = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cmask") == 0)) {
kar ++;
if (kar >= argc) {
ERROR_exit("-cmask option requires a following argument!\n");
}
Opt->cmask = EDT_calcmask( argv[kar] , &(Opt->dimcmask), 0 ) ;
if( Opt->cmask == NULL ) ERROR_exit("Can't compute -cmask!\n");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mask") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -mask \n");
exit (1);
}
Opt->mset_name = argv[kar];
brk = 1;
}
if( !brk && (strncmp(argv[kar],"-mrange",5) == 0) ){
if( kar+2 >= argc )
ERROR_exit("-mrange option requires 2 following arguments!\n");
Opt->mask_bot = strtod( argv[++kar] , NULL ) ;
Opt->mask_top = strtod( argv[++kar] , NULL ) ;
if( Opt->mask_top < Opt->mask_bot )
ERROR_exit("-mrange inputs are illegal!\n") ;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-anat") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -anat \n");
exit (1);
}
Opt->aset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-sig") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -sig \n");
exit (1);
}
Opt->sig_name = SUMA_copy_string(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -pset \n");
exit (1);
}
Opt->this_pset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-gold") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -gold \n");
exit (1);
}
Opt->gold_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-gold_bias") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -gold_bias \n");
exit (1);
}
Opt->gold_bias_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pstCgALL") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -pstCgALL \n");
exit (1);
}
Opt->pstCgALLname = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-priCgL") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -priCgL \n");
exit (1);
}
Opt->priCgLname = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-priCgALL") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -priCgALL \n");
exit (1);
}
Opt->priCgALLname = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-wL") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -wL \n");
exit (1);
}
Opt->wL = atof(argv[kar]);
if (Opt->wL < 0.0 || Opt->wL > 1.0) {
SUMA_S_Errv("-wL must be between 0 and 1.0, have %s", argv[kar]);
exit(1);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-priCgA") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -priCgA \n");
exit (1);
}
Opt->priCgAname = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-wA") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -wA \n");
exit (1);
}
Opt->wA = atof(argv[kar]);
if (Opt->wA < 0.0 || Opt->wA > 1.0) {
SUMA_S_Errv("-wA must be between 0 and 1.0, have %s", argv[kar]);
exit(1);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -cset \n");
exit (1);
}
Opt->this_cset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-fset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -fset \n");
exit (1);
}
Opt->this_fset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-xset") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -xset \n");
exit (1);
}
Opt->this_xset_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-tdist") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -tdist \n");
exit (1);
}
Opt->ndist_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-labeltable") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -labeltable \n");
exit (1);
}
Opt->labeltable_name = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-sphere_hood") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -sphere_hood \n");
exit (1);
}
Opt->na = atof(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-blur_meth") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -blur_meth \n");
exit (1);
}
if (!strcmp(argv[kar],"BIM")) Opt->blur_meth = SEG_BIM;
else if (!strncmp(argv[kar],"LS",2)) Opt->blur_meth = SEG_LSB;
else if (!strcmp(argv[kar],"BNN")) Opt->blur_meth = SEG_BNN;
else if (!strcmp(argv[kar],"BFT")) Opt->blur_meth = SEG_BFT;
else {
SUMA_S_Errv("-blur_meth %s not valid\n", argv[kar]);
exit(1);
}
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -prefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->proot = argv[kar];
Opt->prefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->crefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->pgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->cgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->frefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
Opt->xrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->prefix,"%s.p", argv[kar]);
sprintf(Opt->pgrefix,"%s.pg", argv[kar]);
sprintf(Opt->crefix,"%s.c", argv[kar]);
sprintf(Opt->cgrefix,"%s.cg", argv[kar]);
sprintf(Opt->frefix,"%s.f", argv[kar]);
sprintf(Opt->xrefix,"%s.x", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -pprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->prefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->prefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-fprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -fprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->frefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->frefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -cprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->crefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->crefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-cgprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -cgprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->cgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->cgrefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-pgprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -pgprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->pgrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->pgrefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-xprefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -xprefix \n");
exit (1);
}
Opt->smode = storage_mode_from_filename(argv[kar]);
Opt->xrefix = (char*)calloc(strlen(argv[kar])+20, sizeof(char));
sprintf(Opt->xrefix,"%s", argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-bias_classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -bias_classes \n");
exit (1);
}
Opt->bias_classes = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-group_classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -group_classes \n");
exit (1);
}
Opt->group_classes = NI_strict_decode_string_list(argv[kar] ,";");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-group_keys") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -group_keys \n");
exit (1);
}
if (!(nstr = NI_strict_decode_string_list(argv[kar] ,";, "))){
ERROR_exit("Bad option %s after -group_keys", argv[kar]);
}
Opt->group_keys = (int *)calloc(nstr->num, sizeof(int));
for (ii=0;ii<nstr->num; ++ii)
Opt->group_keys[ii] = strtol(nstr->str[ii],NULL,10);
NI_delete_str_array(nstr);nstr=NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-classes") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -classes \n");
exit (1);
}
Opt->clss = NI_strict_decode_string_list(argv[kar] ,";, ");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-split_classes") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -split_classes \n");
exit (1);
}
nstr = NI_strict_decode_string_list(argv[kar] ,";, ");
Opt->Split = (int *)calloc(nstr->num+1, sizeof(int));
for (ii=0;ii<nstr->num; ++ii) {
Opt->Split[ii] = strtol(nstr->str[ii],NULL,10);
if (Opt->Split[ii]<1 || Opt->Split[ii]>9) {
SUMA_S_Errv("Bad split value of %d in %s\n",
Opt->Split[ii], argv[kar]);
exit(1);
}
}
Opt->Split[nstr->num]=-1; /* plug */
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-other") == 0)) {
Opt->Other = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_other") == 0)) {
Opt->Other = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-keys") == 0)) {
NI_str_array *nstr=NULL; int ii;
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -keys \n");
exit (1);
}
if (!(nstr = NI_strict_decode_string_list(argv[kar] ,";, "))){
ERROR_exit("Bad option %s after -keys", argv[kar]);
}
Opt->keys = (int *)calloc(nstr->num, sizeof(int));
for (ii=0;ii<nstr->num; ++ii)
Opt->keys[ii] = strtol(nstr->str[ii],NULL,10);
NI_delete_str_array(nstr);nstr=NULL;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-bias_order") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need integer after -bias_order \n");
exit (1);
}
Opt->bias_param = atof(argv[kar]);
Opt->bias_meth = "Poly";
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-bias_fwhm") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need integer after -bias_fwhm \n");
exit (1);
}
Opt->bias_param = atof(argv[kar]);
Opt->bias_meth = "Wells";
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-enhance_cset_init") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need integer after -enhance_cset_init \n");
exit (1);
}
Opt->N_enhance_cset_init = atoi(argv[kar]);
SUMA_S_Err("Option not in use at the moment");
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-main_N") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need integer after -main_N \n");
exit (1);
}
Opt->N_main = atoi(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mixfloor") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need value between 0 and 1/(number of classes)"
" after -mixfloor \n");
exit (1);
}
Opt->mix_frac_floor = atof(argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-clust_cset_init") == 0)) {
Opt->clust_cset_init = 1;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-no_clust_cset_init") == 0)) {
Opt->clust_cset_init = 0;
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-uid") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -uid \n");
exit (1);
}
snprintf(Opt->uid,128,"%s",argv[kar]);
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-mixfrac") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need argument after -mixfrac \n");
exit (1);
}
Opt->mixopt = argv[kar];
brk = 1;
}
if (!brk && (strcmp(argv[kar], "-Bmrf") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (stderr, "need value after -Bmrf \n");
exit (1);
}
Opt->B = atof(argv[kar]);
brk = 1;
}
if (!brk) {
fprintf (stderr,"Option %s not understood. \n"
"Try -help for usage\n", argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else {
brk = 0;
kar ++;
}
}
if (!Opt->prefix) Opt->prefix = strdup("./GenPriorsOut.p");
if (!Opt->frefix) Opt->frefix = strdup("./GenPriorsOut.f");
if (!Opt->xrefix) Opt->xrefix = strdup("./GenPriorsOut.x");
if (!Opt->crefix) Opt->crefix = strdup("./GenPriorsOut.c");
if (Opt->uid[0]=='\0') UNIQ_idcode_fill(Opt->uid);
if (Opt->VoxDbg > -1 && !Opt->VoxDbgOut) {
char stmp[256];
sprintf(stmp,"%d.dbg", Opt->VoxDbg);
Opt->VoxDbgOut = fopen(stmp,"w");
}
RETURN(Opt);
}
/*!
\brief parse the arguments for SurfSmooth program
\param argv (char *)
\param argc (int)
\return Opt (SUMA_GETPATCH_OPTIONS *) options structure.
To free it, use
SUMA_free(Opt->outfile);
SUMA_free(Opt->histnote);
SUMA_free(Opt);
*/
SUMA_KUBATEST_OPTIONS *SUMA_SampBias_ParseInput(
char *argv[], int argc, SUMA_KUBATEST_OPTIONS* Opt,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SampBias_ParseInput"};
int kar, i, ind;
char *outprefix;
SUMA_Boolean brk = NOPE;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
kar = 1;
brk = NOPE;
Opt->debug = 0;
Opt->plimit = 50;
Opt->dlimit = 1000;
Opt->outfile = NULL;
Opt->prefix = NULL;
Opt->segdo = NULL;
Opt->ps=ps;
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)
{
ps->hverb = strlen(argv[kar])>3?2:1;
usage_SUMA_SampBias(ps);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-plimit") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -plimit \n");
exit (1);
}
Opt->plimit = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-dlimit") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -dlimit \n");
exit (1);
}
Opt->dlimit = atof(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-out") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -out \n");
exit (1);
}
Opt->outfile = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-segdo") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -segdo \n");
exit (1);
}
Opt->segdo = SUMA_Extension(argv[kar], ".1D.do", NOPE);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
kar++;
if (kar >= argc)
{
fprintf (SUMA_STDERR, "need argument after -prefix \n");
exit (1);
}
Opt->prefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar])
{
SUMA_S_Errv("Option %s not understood. Try -help for usage\n",
argv[kar]);
suggest_best_prog_option(argv[0], argv[kar]);
exit (1);
} else
{
brk = NOPE;
kar ++;
}
}
/* sanity checks */
if (Opt->outfile == NULL && Opt->prefix == NULL)
{
SUMA_SL_Err("No outfile, or prefix specified.");
exit(1);
}
if (Opt->outfile) {
if (!THD_ok_overwrite() && SUMA_filexists(Opt->outfile)) {
SUMA_S_Errv("Outfile %s already exists\n", Opt->outfile);
exit(1);
}
}
if (Opt->prefix) {
SUMA_DSET_NAME_CHECK(Opt->prefix);
}
Opt->histnote = SUMA_HistString (NULL, argc, argv, NULL);
SUMA_RETURN (Opt);
}
SUMA_GENERIC_PROG_OPTIONS_STRUCT *SUMA_prompt_user_ParseInput(
char *argv[], int argc, SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_prompt_user_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar;
SUMA_Boolean brk;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
Opt->ps = ps; /* just hold it there for convenience */
Opt->ps = ps; /* for convenience */
kar = 1;
brk = 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) {
ps->hverb = 1;
usage_prompt_user(ps);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -debug \n");
exit (1);
}
Opt->debug = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-pause") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a string after -pause \n");
exit (1);
}
Opt->b1 = 1;
Opt->in_name = argv[++kar];
brk = YUP;
if (!strcmp(Opt->in_name, "-")) Opt->in_name = read_file_text(stdin);
}
if (!brk && !ps->arg_checked[kar]) {
SUMA_S_Errv("Option %s not understood.\n"
"Try -help for usage\n",
argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
SUMA_RETURN(Opt);
}
SUMA_GENERIC_PROG_OPTIONS_STRUCT *
SUMA_3dBRAIN_VOYAGERtoAFNI_ParseInput(char *argv[], int argc,
SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_3dBRAIN_VOYAGERtoAFNI_ParseInput"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt=NULL;
int kar;
SUMA_Boolean brk;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
Opt = SUMA_Alloc_Generic_Prog_Options_Struct();
Opt->b1 = 0;
Opt->b2 = 0;
Opt->Icold = -1;
Opt->out_prefix = NULL;
kar = 1;
brk = 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_3dBRAIN_VOYAGERtoAFNI(ps);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-input") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -input\n");
exit (1);
}
Opt->in_name = argv[kar];
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need argument after -prefix\n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-tlrc") == 0)) {
Opt->Icold = VIEW_TALAIRACH_TYPE;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-acpc") == 0)) {
Opt->Icold = VIEW_ACPCALIGNED_TYPE;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-orig") == 0)) {
Opt->Icold = VIEW_ORIGINAL_TYPE;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-bs") == 0)) {
Opt->b1 = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-qx") == 0)) {
Opt->b2 = 1;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-debug") == 0)) {
kar ++;
if (kar >= argc) {
fprintf (SUMA_STDERR, "need integer argument after -debug\n");
exit (1);
}
Opt->debug = atoi(argv[kar]);
brk = YUP;
}
if (!brk && !ps->arg_checked[kar]) {
fprintf (SUMA_STDERR,"Error %s:\nOption %s not understood. Try -help for usage\n", FuncName, argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
SUMA_RETURN(Opt);
}
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);
}
