char * SUMA_BrainVoyager_Read_vmr(char *fnameorig, THD_3dim_dataset *dset, int LoadData,
byte Qxforce, byte bsforce, int viewforce, char *outname)
{
static char FuncName[]={"SUMA_BrainVoyager_Read_vmr"};
int i = 0, nf, iop, dchunk, End, bs, doff, ex,
data_type=SUMA_notypeset, view, endian, dblock;
THD_ivec3 iv3;
unsigned long len;
short qxver;
short nvox[3]; /* values are unsigned, so check for sign for bs... */
THD_mat33 m33;
THD_ivec3 orixyz , nxyz ;
THD_fvec3 dxyz , orgxyz ;
float ep[3], sp[3];
char sview[10], *fname = NULL, *scom=NULL, form[10], swp[10], orstr[10], xfov[100], yfov[100], zfov[100], *prefix = NULL, *dsetheadname = NULL;
FILE *fid = NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_ENTRY;
if (!dset || !fnameorig) {
SUMA_SL_Err("NULL fname || NULL dset!");
SUMA_RETURN(NOPE);
}
if (!SUMA_isExtension(fnameorig, ".vmr")) {
SUMA_SL_Err("vmr dset is expected to have .vmr for an extension");
SUMA_RETURN(NOPE);
}
if (!SUMA_filexists(fnameorig)) {
SUMA_SL_Err("file does not exist");
SUMA_RETURN(NOPE);
}
/* make fname be the new name without the extension*/
if (!outname) {
fname = SUMA_Extension(fnameorig,".vmr", YUP);
} else {
fname = SUMA_Extension(outname, ".vmr", YUP);
}
prefix = SUMA_AfniPrefix(fname, NULL, NULL, NULL);
if( !THD_filename_ok(prefix) ) {
SUMA_SL_Err("Bad prefix");
goto CLEAN_EXIT;
}
/* someday, guess format on your own...*/
qxver = 0;
if (Qxforce) {
SUMA_LH("Forcing qxver");
qxver = 1; /* set to 1 if qx format */
}
/* view ? */
SUMA_LHv("Viewforce = %d; [%d %d]\n", viewforce, VIEW_ORIGINAL_TYPE, VIEW_TALAIRACH_TYPE);
if (viewforce >= VIEW_ORIGINAL_TYPE && viewforce <= VIEW_TALAIRACH_TYPE) {
view = viewforce;
} else {
view = VIEW_ORIGINAL_TYPE;
if (SUMA_iswordin_ci(fnameorig, "_tal") == 1) { view = VIEW_TALAIRACH_TYPE; }
else if (SUMA_iswordin_ci(fnameorig, "_acpc") == 1) { view = VIEW_ACPCALIGNED_TYPE; }
else { view = VIEW_ORIGINAL_TYPE; }
}
switch (view) {
case VIEW_ORIGINAL_TYPE:
sprintf(sview,"+orig"); break;
case VIEW_ACPCALIGNED_TYPE:
sprintf(sview,"+acpc"); break;
case VIEW_TALAIRACH_TYPE:
sprintf(sview,"+tlrc"); break;
default:
SUMA_SL_Err("Bad view");
goto CLEAN_EXIT;
}
if (LocalHead) fprintf(SUMA_STDERR,"%s: View %s, %d\n", FuncName, sview, view);
dsetheadname = SUMA_append_replace_string(prefix,".HEAD", sview, 0);
if (SUMA_filexists(dsetheadname)) {
SUMA_S_Errv("Bad prefix, output dset %s exists\n", dsetheadname);
goto CLEAN_EXIT;
}
SUMA_free(dsetheadname); dsetheadname = NULL;
fid = fopen(fnameorig,"r");
if (!fid) {
SUMA_SL_Err("Could not open file for reading");
goto CLEAN_EXIT;
}
if (qxver) {
SUMA_LH("Reading dimensions, 2+ 1st 6 bytes and deciding on swap");
doff = 4*sizeof(short);/* data offset 2 + 6 bytes */
} else {
SUMA_LH("Reading dimensions, 1st 6 bytes and deciding on swap");
doff = 3*sizeof(short);/* data offset */
}
SUMA_WHAT_ENDIAN(endian);
bs = 0;
swp[0] = '\0';
data_type = SUMA_byte; /* voxel data is bytes */
dchunk = sizeof(byte); /* voxel data is bytes */
sprintf(form,"3Db");
if (qxver) { SUMA_READ_NUM(&(qxver), fid, ex, sizeof(short)); if (LocalHead) fprintf(SUMA_STDERR,"%s: QXver = %d\n", FuncName, qxver);}/* is this a QX format?*/
SUMA_READ_NUM(&(nvox[2]), fid, ex, sizeof(short)); /* Z first */
SUMA_READ_NUM(&(nvox[1]), fid, ex, sizeof(short));
SUMA_READ_NUM(&(nvox[0]), fid, ex, sizeof(short));
if ((nvox[0] < 0 || nvox[1] < 0 || nvox[2] < 0 )) {
SUMA_LH("Byte swapping needed");
bs = 1;
}
if (bsforce) {
SUMA_LH("Byte swapping forced");
bs = 1;
}
if (bs) {
if (qxver) SUMA_swap_2(&(qxver));
SUMA_swap_2(&(nvox[0]));
SUMA_swap_2(&(nvox[1]));
SUMA_swap_2(&(nvox[2]));
sprintf(swp,"-2swap");
SUMA_OTHER_ENDIAN(endian);
}
/* 1 1 1???? */
if (nvox[0] == nvox[1] && nvox[1] == nvox[2] && nvox[2] == 1) {
if (LocalHead) { fprintf(SUMA_STDERR,"Warning %s: Voxel nums all 1. Trying from file size\n", FuncName); }
len = THD_filesize( fnameorig ) ;
len -= doff;
len /= dchunk;
nvox[0] = (int)pow((double)len, 1.0/3.0);
if (nvox[0] * nvox[0] * nvox[0] != len) {
fprintf(SUMA_STDERR,"Error %s: Bad voxel numbers and could not infer number from filesize.\n"
"Size of file: %lld, data offset: %d, datum size: %d, data number: %ld\n"
"Inferred nvox:%d\n",
FuncName,
THD_filesize( fnameorig ), doff, dchunk, len,
nvox[0]);
goto CLEAN_EXIT;
}
nvox[2] = nvox[1] = nvox[0];
if (LocalHead) { fprintf(SUMA_STDERR,"Warning %s: Using filesize inferred number of voxels: %d %d %d\n",
FuncName, nvox[0], nvox[1], nvox[2]); }
}
if (LocalHead) fprintf(SUMA_STDERR,"Number of voxels: %d %d %d. qxver %d\n", nvox[0], nvox[1], nvox[2], qxver);
/* check against filesize */
len = THD_filesize( fnameorig ) ;
dblock = nvox[0]*nvox[1]*nvox[2]*dchunk;
if (len != (dblock + doff)) {
if (!qxver) {
fprintf(SUMA_STDERR, "Mismatch between file size %ld\n"
"and expected size %d = (%d*%d*%d*%d+%d) \n",
len, (dblock + doff), nvox[0], nvox[1], nvox[2], dchunk, doff);
goto CLEAN_EXIT;
}else if (len < dblock + doff) {
fprintf(SUMA_STDERR, "Mismatch between file size %ld\n"
"and minimum expected size %d = (%d*%d*%d*%d+%d) \n",
len, (dblock + doff), nvox[0], nvox[1], nvox[2], dchunk, doff);
goto CLEAN_EXIT;
}else {
SUMA_LH("Proceeding");
}
}
if (LocalHead) fprintf(SUMA_STDERR,"File size passes test\n");
/* orientation */
orixyz.ijk[0] = ORI_A2P_TYPE;
orixyz.ijk[1] = ORI_S2I_TYPE;
orixyz.ijk[2] = ORI_R2L_TYPE;
/* load number of voxels */
LOAD_IVEC3( nxyz , nvox[0] , nvox[1] , nvox[2] ) ;
/* form the command */
SUMA_LH("Forming command");
{
float delta[3]={1.0, 1.0, 1.0};
float origin[3]={0.0, 0.0, 0.0};
/* set origin of 0th voxel*/
origin[0] = (float)((nvox[0]*delta[0]))/2.0; /* ZSS: Changed from 0 0 0 Nov 1 07 */
origin[1] = (float)((nvox[1]*delta[1]))/2.0;
origin[2] = (float)((nvox[2]*delta[2]))/2.0;
/* dimensions, same for vmr*/
LOAD_FVEC3( dxyz , delta[0], delta[1], delta[2] ) ;
SUMA_sizeto3d_2_deltaHEAD(orixyz, &dxyz);
/* origin */
LOAD_FVEC3( orgxyz , origin[0], origin[1], origin[2] ) ;
SUMA_originto3d_2_originHEAD(orixyz, &orgxyz);
}
/* start point (edge of origin voxel) and end point (opposite to start ) */
sp[0] = orgxyz.xyz[0] + SUMA_ABS(dxyz.xyz[0]) / 2.0;
sp[1] = orgxyz.xyz[1] + SUMA_ABS(dxyz.xyz[1]) / 2.0;
sp[2] = orgxyz.xyz[2] + SUMA_ABS(dxyz.xyz[2]) / 2.0;
ep[0] = orgxyz.xyz[0] + (nxyz.ijk[0] - 0.5) * SUMA_ABS(dxyz.xyz[0]);
ep[1] = orgxyz.xyz[1] + (nxyz.ijk[1] - 0.5) * SUMA_ABS(dxyz.xyz[1]);
ep[2] = orgxyz.xyz[2] + (nxyz.ijk[2] - 0.5) * SUMA_ABS(dxyz.xyz[2]);
SUMA_orcode_to_orstring (orixyz.ijk[0], orixyz.ijk[1], orixyz.ijk[2], orstr);
sprintf(xfov," -xFOV %.2f%c-%.2f%c", sp[0], orstr[0], ep[0], orstr[3]);
sprintf(yfov," -yFOV %.2f%c-%.2f%c", sp[1], orstr[1], ep[1], orstr[4]);
sprintf(zfov," -zFOV %.2f%c-%.2f%c", sp[2], orstr[2], ep[2], orstr[5]);
scom = (char *)SUMA_calloc((strlen(fnameorig)+500), sizeof(char));
sprintf(scom,"to3d %s %s %s %s -prefix %s %s:%d:0:%d:%d:%d:%s ",
swp, xfov, yfov, zfov, prefix, form, doff,
nvox[0], nvox[1], nvox[0], fnameorig);
SUMA_LH("HERE");
if (dset) { /* form the dset header */
int nvals_read = 0;
SUMA_LH("Filling header");
EDIT_dset_items( dset ,
ADN_prefix , prefix ,
ADN_datum_all , data_type ,
ADN_nxyz , nxyz ,
ADN_xyzdel , dxyz ,
ADN_xyzorg , orgxyz ,
ADN_xyzorient , orixyz ,
ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
ADN_view_type , view ,
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type , ANAT_BUCK_TYPE ,
ADN_none ) ;
if (LoadData) {
void *vec=NULL;
SUMA_LH("Loading data");
if (!(vec = SUMA_BinarySuck(fnameorig, data_type, endian, 3*sizeof(short), -1, &nvals_read))) {
SUMA_SL_Err("Failed to read data file"); goto CLEAN_EXIT;
}
if (qxver) {
if (nvals_read < nvox[0]*nvox[1]*nvox[2]) {
SUMA_SL_Warn("Failed to read expected number of voxels\n proceeding...");
}
} else {
if (nvals_read != nvox[0]*nvox[1]*nvox[2]) {
SUMA_SL_Warn("Failed to read the appropriate number of voxels\n proceeding...");
}
}
EDIT_substitute_brick( dset , 0 , data_type , vec) ;
if (LocalHead) fprintf(SUMA_STDERR,"%s: Read %d values from file.\n", FuncName, nvals_read);
/* DSET_write(dset) ; */
}
}
CLEAN_EXIT:
if (prefix) SUMA_free(prefix); prefix = NULL;
if (fname) SUMA_free(fname); fname = NULL;
if (fid) fclose(fid); fid = NULL;
SUMA_RETURN(scom);
}
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);
}
/*!
\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);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SurfPatch"};
SUMA_GETPATCH_OPTIONS *Opt;
char *ppref=NULL, ext[5];
float *far=NULL;
MRI_IMAGE *im = NULL;
int SO_read = -1;
int *NodePatch=NULL, N_NodePatch=-1, *FaceSetList=NULL ,
N_FaceSet = -1, N_Node = -1, N_Spec=0;
int i, inodeoff=-1, ilabeloff=-1, nvec, ncol, cnt;
SUMA_SurfaceObject *SO = NULL;
SUMA_PATCH *ptch = NULL;
SUMA_SurfSpecFile *Spec;
SUMA_INDEXING_ORDER d_order;
void *SO_name = NULL;
SUMA_Boolean exists = NOPE;
SUMA_SO_File_Type typetmp;
SUMA_SurfaceObject *SOnew = NULL;
float *NodeList = NULL;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-spec;-s;-sv;");
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
Opt = SUMA_GetPatch_ParseInput (argv, argc, ps);
if (argc < 2)
{
SUMA_S_Err("Too few options");
usage_SUMA_getPatch(ps, 0);
exit (1);
}
/* read all surfaces */
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec > 1 ) {
SUMA_S_Err( "Mike, you cannot mix -spec with -i or -t options "
"for specifying surfaces.");
exit(1);
}
if (Spec->N_Surfs < 1) {
SUMA_S_Err("No surfaces");
exit(1);
}
if (Opt->DoVol && Spec->N_Surfs != 2) {
SUMA_S_Errv("Must specify 2 and only 2 surfaces with -vol options\n"
"Have %d from the command line\n",Spec->N_Surfs);
exit(1);
}
if (Opt->oType != SUMA_FT_NOT_SPECIFIED && !Opt->VolOnly) {
for (i=0; i < Spec->N_Surfs; ++i) {
if (Spec->N_Surfs > 1) {
sprintf(ext, "_%c", 65+i);
ppref = SUMA_append_string(Opt->out_prefix, ext);
} else {
ppref = SUMA_copy_string(Opt->out_prefix);
}
SO_name = SUMA_Prefix2SurfaceName(ppref, NULL, NULL,
Opt->oType, &exists);
if (exists && !THD_ok_overwrite()) {
fprintf(SUMA_STDERR, "Error %s:\nOutput file(s) %s* on disk.\n"
"Will not overwrite.\n", FuncName, ppref);
exit(1);
}
if (ppref) SUMA_free(ppref); ppref = NULL;
if (SO_name) SUMA_free(SO_name); SO_name = NULL;
}
}
/* read in the file containing the node information */
im = mri_read_1D (Opt->in_name);
if (!im) {
SUMA_S_Errv("Failed to read 1D file '%s'\n", Opt->in_name);
exit(1);
}
far = MRI_FLOAT_PTR(im);
nvec = im->nx;
ncol = im->ny;
if (Opt->nodecol >= ncol || Opt->labelcol >= ncol) {
fprintf(SUMA_STDERR, "\n"
"Error %s: Input file has a total of %d columns.\n"
"One or both user-specified node (%d) and \n"
"label (%d) columns are too high. Maximum usable\n"
"column index is %d.\n"
, FuncName, ncol, Opt->nodecol,
Opt->labelcol, ncol -1 );
exit(1);
}
d_order = SUMA_COLUMN_MAJOR;
if (!nvec) {
SUMA_SL_Err("Empty file");
exit(1);
}
/* form the node vector */
NodePatch = (int *)SUMA_malloc(sizeof(int)*nvec);
if (!NodePatch) {
SUMA_SL_Crit("Failed to allocate.");
exit(1);
}
inodeoff = Opt->nodecol*nvec;
if (Opt->labelcol < 0) { /* all listed nodes */
for (i=0; i<nvec; ++i) {
NodePatch[i] = far[i+inodeoff];
}
N_NodePatch = nvec;
} else {
ilabeloff = Opt->labelcol*nvec;
if (Opt->thislabel < 0) { /* all nodes with non zero labels */
cnt = 0;
for (i=0; i<nvec; ++i) {
if (far[i+ilabeloff]) {
NodePatch[cnt] = far[i+inodeoff];
++cnt;
}
}
N_NodePatch = cnt;
} else { /* select labels */
cnt = 0;
for (i=0; i<nvec; ++i) {
if (far[i+ilabeloff] == Opt->thislabel) {
NodePatch[cnt] = far[i+inodeoff];
++cnt;
}
}
N_NodePatch = cnt;
}
NodePatch = (int *) SUMA_realloc(NodePatch , sizeof(int)*N_NodePatch);
}
/* done with im, free it */
mri_free(im); im = NULL;
if (Opt->DoVol) {
SUMA_SurfaceObject *SO1 =
SUMA_Load_Spec_Surf_with_Metrics(Spec, 0, ps->sv[0], 0);
SUMA_SurfaceObject *SO2 =
SUMA_Load_Spec_Surf_with_Metrics(Spec, 1, ps->sv[0], 0);
double Vol = 0.0;
SUMA_SurfaceObject *SOp = SUMA_Alloc_SurfObject_Struct(1);
byte *adj_N=NULL;
if (Opt->adjust_contour)
adj_N = SUMA_calloc(SO1->N_Node, sizeof(byte));
if (!SO1 || !SO2) {
SUMA_SL_Err("Failed to load surfaces.");
exit(1);
}
/* a chunk used to test SUMA_Pattie_Volume */
Vol = SUMA_Pattie_Volume(SO1, SO2, NodePatch, N_NodePatch,
SOp, Opt->minhits,
Opt->FixBowTie, Opt->adjust_contour,
adj_N, Opt->verb);
fprintf (SUMA_STDOUT,"Volume = %f\n", fabs(Vol));
if (Opt->out_volprefix) {
if (Opt->oType != SUMA_FT_NOT_SPECIFIED) SOp->FileType = Opt->oType;
if (Opt->flip) {
if (Opt->verb > 1)
SUMA_S_Note("Flipping stitched surf's triangles\n");
SUMA_FlipSOTriangles (SOp);
}
if (!(SUMA_Save_Surface_Object_Wrap ( Opt->out_volprefix, NULL,
SOp, SUMA_PLY, SUMA_ASCII,
NULL))) {
fprintf (SUMA_STDERR,
"Error %s: Failed to write surface object.\n", FuncName);
}
if (Opt->adjust_contour && adj_N) {
Opt->out_volprefix =
SUMA_append_replace_string(Opt->out_volprefix,
".adjneighb","",1);
ppref = SUMA_Extension(Opt->out_volprefix, ".1D.dset", NOPE);
SUMA_WRITE_IND_ARRAY_1D(adj_N, NULL, SO1->N_Node, 1, ppref);
SUMA_free(ppref); ppref=NULL;
}
}
if (SOp) SUMA_Free_Surface_Object(SOp); SOp = NULL;
}
if (!Opt->VolOnly) {
FaceSetList = NULL;
N_FaceSet = -1;
for (i=0; i < Spec->N_Surfs; ++i) {/* loop to read in surfaces */
/* now identify surface needed */
if (!(SO = SUMA_Load_Spec_Surf_with_Metrics(Spec, i, ps->sv[0], 0))) {
SUMA_S_Err("Failed to load surface .\n");
exit(1);
}
if (SO->aSO) {
/* otherwise, when you reset the number of FaceSets for example,
and you still write in GIFTI, the old contents of aSO will
prevail */
SO->aSO = SUMA_FreeAfniSurfaceObject(SO->aSO);
}
/* extract the patch */
ptch = SUMA_getPatch (NodePatch, N_NodePatch, SO->N_Node,
SO->FaceSetList, SO->N_FaceSet,
SO->MF, Opt->minhits,
Opt->FixBowTie, (!i && !Opt->DoVol));
/* verbose only for first patch, and
if no volume computation was required
This is to keep the warnings to a minimum*/
if (!ptch) {
SUMA_SL_Err("Failed to form patch.");
exit(1);
}
if (LocalHead) SUMA_ShowPatch(ptch, NULL);
/* Now create a surface with that patch */
if (Spec->N_Surfs > 1) {
sprintf(ext, "_%c", 65+i);
ppref = SUMA_append_string(Opt->out_prefix, ext);
} else {
ppref = SUMA_copy_string(Opt->out_prefix);
}
/* save the original type */
typetmp = SO->FileType;
if (Opt->oType != SUMA_FT_NOT_SPECIFIED) SO->FileType = Opt->oType;
SO_name = SUMA_Prefix2SurfaceName(ppref, NULL, NULL,
SO->FileType, &exists);
if (ppref) SUMA_free(ppref); ppref = NULL;
/* save the original pointers to the facesets and their number */
FaceSetList = SO->FaceSetList;
N_FaceSet = SO->N_FaceSet;
NodeList = SO->NodeList;
N_Node = SO->N_Node;
/* replace with Patch */
SO->FaceSetList = ptch->FaceSetList;
SO->N_FaceSet = ptch->N_FaceSet;
if (Opt->Do_p2s) {
if (LocalHead)
fprintf (SUMA_STDERR,
"%s: Changing patch to surface...\n", FuncName);
SOnew = SUMA_Patch2Surf(SO->NodeList, SO->N_Node,
SO->FaceSetList, SO->N_FaceSet, 3);
if (!SOnew) {
SUMA_S_Err("Failed to change patch to surface.");
exit(1);
}
SO->FaceSetList = SOnew->FaceSetList;
SO->N_FaceSet = SOnew->N_FaceSet;
SO->N_Node = SOnew->N_Node;
SO->NodeList = SOnew->NodeList;
}
if (SO->N_FaceSet <= 0) {
SUMA_S_Warn("The patch is empty.\n"
" Non existing surface not written to disk.\n");
} else {
/* Is the gain wanted? */
if (Opt->coordgain) {
SUMA_SL_Note("Applying coord gain to surface nodes!");
for (cnt=0; cnt < SO->NodeDim*SO->N_Node; ++cnt)
SO->NodeList[cnt] *= Opt->coordgain;
}
if (Opt->flip) {
if (Opt->verb > 1) SUMA_S_Note("Flipping triangles\n");
SUMA_FlipTriangles (SO->FaceSetList, SO->N_FaceSet);
SUMA_RECOMPUTE_NORMALS(SO);
}
if (!SUMA_Save_Surface_Object (SO_name, SO, SO->FileType,
SUMA_ASCII, NULL)) {
fprintf (SUMA_STDERR,
"Error %s: Failed to write surface object.\n",
FuncName);
exit (1);
}
}
/* bring SO back to shape */
SO->FileType = typetmp;
SO->FaceSetList = FaceSetList; FaceSetList = NULL;
SO->N_FaceSet = N_FaceSet; N_FaceSet = -1;
SO->NodeList = NodeList; NodeList = NULL;
SO->N_Node = N_Node; N_Node = -1;
if (SO_name) SUMA_free(SO_name); SO_name = NULL;
if (ptch) SUMA_freePatch(ptch); ptch = NULL;
if (SOnew) SUMA_Free_Surface_Object(SOnew); SOnew = NULL;
/* get rid of old surface object */
}
}
SUMA_LH("clean up");
if (!SUMA_FreeSpecFields(Spec)) { SUMA_S_Err("Failed to free spec fields"); }
SUMA_free(Spec); Spec = NULL;
if (Opt->out_prefix) SUMA_free(Opt->out_prefix); Opt->out_prefix = NULL;
if (Opt->out_volprefix) SUMA_free(Opt->out_volprefix);
Opt->out_volprefix = NULL;
if (Opt) SUMA_free(Opt);
if (!SUMA_Free_Displayable_Object_Vect (SUMAg_DOv, SUMAg_N_DOv)) {
SUMA_SL_Err("DO Cleanup Failed!");
}
if (!SUMA_Free_CommonFields(SUMAg_CF)) {
SUMA_SL_Err("SUMAg_CF Cleanup Failed!");
}
SUMA_RETURN(0);
}
