/*USE This sample to start writing standalone programs.
Change NikoMap to the program name of your choosing.
*/
#include "SUMA_suma.h"
SUMA_SurfaceViewer *SUMAg_cSV = NULL; /*!< Global pointer to current Surface Viewer structure*/
SUMA_SurfaceViewer *SUMAg_SVv = NULL; /*!< Global pointer to the vector containing the various Surface Viewer Structures
SUMAg_SVv contains SUMA_MAX_SURF_VIEWERS structures */
int SUMAg_N_SVv = 0; /*!< Number of SVs realized by X */
SUMA_DO *SUMAg_DOv = NULL; /*!< Global pointer to Displayable Object structure vector*/
int SUMAg_N_DOv = 0; /*!< Number of DOs stored in DOv */
SUMA_CommonFields *SUMAg_CF = NULL; /*!< Global pointer to structure containing info common to all viewers */
void usage_NikoMap (SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"usage_NikoMap"};
char * s = NULL, *sio=NULL, *st = NULL, *sts = NULL;
int i;
s = SUMA_help_basics();
sio = SUMA_help_IO_Args(ps);
printf ( "\n"
"Usage: NikoMap <-i_TYPE SURFACE> <-prefix PREFIX>\n"
" <-grid_parent GRID_VOL> [-sv SURF_VOL] \n"
" \n"
" Mandatory Parameters:\n"
" -i_TYPE SURFACE: Specify input surface.\n"
" You can also use -t* and -spec and -surf\n"
" methods to input surfaces. See below\n"
" for more details.\n"
" -prefix PREFIX: Prefix of output datasets.\n"
" -grid_parent GRID_VOL: Specifies the grid for the\n"
" FMRI data volume."
" Patch options:\n"
" -patch_grow: Create surface patch growing data.\n"
" -grow_dist D: Grow patch up to Dmm away from each node.\n"
" Distance is the shortest along the edges of \n"
" the surface.\n"
" *** With these options you will get a file called:\n"
" PREFIX_pg.1D.dset with each row containing:\n"
" <node index (n)> <number of neighbors of n (Kn)> followed by\n"
" Kn sets of: \n"
" <neighbor node index (m)> <distance of m to n> \n"
" <X Y Z of estimated propagation location of m>\n"
" The last three parameters represent the estimated\n"
" location of m in the next contour (layer) of neighbors\n"
" of n\n"
"\n"
" Volume-->Surface options:\n"
" -closest_node: Create a file that outputs the closest\n"
" node for each voxel in GRID_VOL.\n"
" *** With this option you'll get a file called:\n"
" PREFIX_cn.1D.dset with each row containing:\n"
" <Voxel 1D index (v)> <I J K of v> <closest node n> <distance of n to v>\n"
"\n"
" Optional Options:\n"
" -debug BUG: Debug level\n"
" -node_debug NODE_DBG: Output lots of info for a particular node.\n"
" This option also produces a file called\n"
" PREFIX_pd_dbg_node_NODE_DBG.1D.dset\n"
"\n"
" Sample command:\n"
" NikoMap -i_ply rs_acpc_tal_LH_GM_half.ply \\\n"
" -sv rs_acpc_tal+tlrc. -prefix output \\\n"
" -grid_parent coarse+tlrc. \\\n"
" -closest_node \\\n"
" -patch_grow -grow_dist 7.5 \\\n"
" -debug 3 -node_debug 4 \\\n"
" \n"
"%s"
"%s"
"\n", sio, s);
SUMA_free(s); s = NULL; SUMA_free(st); st = NULL; SUMA_free(sio); sio = NULL;
s = SUMA_New_Additions(0, 1); printf("%s\n", s);SUMA_free(s); s = NULL;
printf(" Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov \n");
exit(0);
}
#define CLOSEST_NODE (1<<0)
#define PATCH_GROW (1<<1)
SUMA_GENERIC_PROG_OPTIONS_STRUCT *SUMA_NikoMap_ParseInput(char *argv[], int argc, SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_NikoMap_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 = 0;
Opt->r = 10.0;
Opt->NodeDbg = -1;
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_NikoMap(ps);
exit (0);
}
SUMA_SKIP_COMMON_OPTIONS(brk, kar);
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a number after -prefix \n");
exit (1);
}
Opt->out_vol_prefix = SUMA_AfniPrefix(argv[++kar], Opt->out_vol_view, NULL, &(Opt->out_vol_exists));
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-grid_parent") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a dataset after -grid_parent \n");
exit (1);
}
Opt->out_grid_prefix = SUMA_AfniPrefix(argv[++kar], Opt->out_grid_view, NULL, &(Opt->out_grid_exists));
if (!SUMA_AfniExistsView(Opt->out_grid_exists, Opt->out_grid_view)) {
fprintf(SUMA_STDERR, "Error 3dSurfMask:\nGrid parent %s%s does not exist.\n", Opt->out_grid_prefix, Opt->out_grid_view);
exit(1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-closest_node") == 0))
{
Opt->iopt = Opt->iopt | CLOSEST_NODE;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-patch_grow") == 0))
{
Opt->iopt = Opt->iopt | PATCH_GROW;
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-grow_dist") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a value after -grow_dist \n");
exit (1);
}
Opt->r = atof(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-node_debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a value after -node_debug \n");
exit (1);
}
Opt->NodeDbg = atoi(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 NikoMap:\nOption %s not understood. Try -help for usage\n", argv[kar]);
exit (1);
} else {
brk = NOPE;
kar ++;
}
}
SUMA_RETURN(Opt);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"NikoMap"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_SurfSpecFile *Spec = NULL;
int *isin=NULL;
int i = -1, ii, jj, kk, il, N_Spec=0;
SUMA_FORM_AFNI_DSET_STRUCT *OptDs = NULL;
SUMA_SurfaceObject *SO = NULL;
SUMA_VOLPAR *vp = NULL;
THD_3dim_dataset *dset = NULL;
char *vpname=NULL;
int *closest_node = NULL;
float *closest_dist = NULL;
SUMA_OFFSET_STRUCT *OffS_out=NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-spec;-sv;-o;");
if (argc < 2) {
usage_NikoMap(ps);
exit (1);
}
Opt = SUMA_NikoMap_ParseInput (argv, argc, ps);
if (Opt->debug > 2) LocalHead = YUP;
/* check on inputs */
if (ps->s_N_surfnames + ps->i_N_surfnames + ps->t_N_surfnames != 1) {
SUMA_S_Err("Multiple surface specifications used. Only one surface allowed.");
exit(1);
}
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec != 1) {
SUMA_S_Err("Multiple spec at input.");
exit(1);
}
/* read in one surface for now */
SO = SUMA_Load_Spec_Surf(Spec, 0, ps->sv[0], 0);
if (!SO) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (Opt->out_grid_prefix) {
vpname = SUMA_append_string(Opt->out_grid_prefix, Opt->out_grid_view);
vp = SUMA_VolPar_Attr(vpname);
} else {
vp = SO->VolPar;
if (!vp) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Need a grid parent.\n",
FuncName );
exit(1);
}
vpname = SUMA_copy_string(ps->sv[0]);
if (!SUMA_AfniView(ps->sv[0], Opt->out_grid_view)) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to get view!!!\n",
FuncName );
exit(1);
}
}
if (LocalHead) {
fprintf(SUMA_STDERR,"%s: Using %s for grid\n", FuncName, vpname);
}
/* some checks ...*/
if (!Opt->out_vol_prefix) {
Opt->out_vol_prefix = SUMA_AfniPrefix("3dSurfMask", NULL, NULL, &(Opt->out_vol_exists));
sprintf(Opt->out_vol_view, Opt->out_grid_view);
}
if (SUMA_AfniExistsView(Opt->out_vol_exists, Opt->out_vol_view)) {
fprintf(SUMA_STDERR, "Error 3dSurfMask:\nOutput volume %s%s exists.\n", Opt->out_vol_prefix, Opt->out_vol_view);
exit(1);
}
if (Opt->out_grid_prefix) {
if (!SUMA_AfniExistsView(Opt->out_grid_exists, Opt->out_grid_view)) {
fprintf(SUMA_STDERR, "Error 3dSurfMask:\nGrid parent %s%s does not exist.\n", Opt->out_grid_prefix, Opt->out_grid_view);
exit(1);
}
}
if (Opt->iopt & CLOSEST_NODE) {
SUMA_LH("Doing closest node");
/* closest node to each voxel in volume */
closest_node = (int *)SUMA_malloc(sizeof(int)*vp->nx*vp->ny*vp->nz);
closest_dist = (float *)SUMA_malloc(sizeof(float)*vp->nx*vp->ny*vp->nz);
if (!closest_node || !closest_dist) {
SUMA_SL_Err("Failed to allocate");
exit(1);
}
if (!SUMA_ClosestNodeToVoxels(SO, vp, closest_node, closest_dist, NULL, 1)) {
SUMA_SL_Err("Failed to find closest nodes to voxels");
exit(1);
}
/*----- output volume dset */
OptDs = SUMA_New_FormAfniDset_Opt();
if (Opt->out_vol_prefix) {
SUMA_FileName NewName = SUMA_StripPath(Opt->out_vol_prefix);
OptDs->prefix = SUMA_append_string(NewName.FileName,"_cn"); SUMA_free(NewName.FileName); NewName.FileName = NULL;
OptDs->prefix_path = NewName.Path; NewName.Path = NULL;
} else {
OptDs->prefix = SUMA_copy_string("NikoMap_cn");
OptDs->prefix_path = SUMA_copy_string("./");
}
/* write dset */
OptDs->master = SUMA_copy_string(vpname);
OptDs->datum = MRI_float;
OptDs->full_list = 1;
{
dset = SUMA_FormAfnidset (NULL, closest_dist, vp->nx*vp->ny*vp->nz, OptDs);
if (!dset) {
SUMA_SL_Err("Failed to create output dataset!");
} else {
tross_Make_History( FuncName , argc,argv , dset ) ;
DSET_write(dset) ;
}
if (dset) { DSET_delete(dset); dset = NULL; }
}
/*----- output files in table form*/
{
char *stmp = NULL, *nameout = NULL, *histnote=NULL;
FILE *fout=NULL;
nameout = SUMA_append_string(Opt->out_vol_prefix, "_cn.1D.dset");
fout = fopen(nameout,"w");
if (!fout) {
SUMA_S_Err("Failed to open file for output");
exit(1);
}
histnote = SUMA_HistString (NULL, argc, argv, NULL);
fprintf(fout, "#Col. 0 Voxel index (1D)\n"
"#Col. 1..4 Voxel i,j,k index\n"
"#Col. 5 Closest node\n"
"#Col. 6 Closest node's distance\n"
"#History:%s\n", histnote);
for (i=0; i<vp->nx*vp->ny*vp->nz; ++i) {
SUMA_1D_2_3D_index(i, ii, jj, kk, vp->nx, vp->nx*vp->ny);
fprintf(fout, "%8d %4d %4d %4d %8d %4.5f\n",
i, ii, jj, kk, closest_node[i], closest_dist[i]);
}
fclose(fout); fout = NULL;
if (stmp) SUMA_free(stmp); stmp = NULL;
if (nameout) SUMA_free(nameout); nameout = NULL;
if (histnote) SUMA_free(histnote); histnote = NULL;
}
}
if (Opt->iopt && PATCH_GROW) {
int cnt = 0;
char *stmp = NULL, *nameout = NULL, *histnote=NULL, sbuf[500], OptS[]={"DoProp"};
FILE *fout=NULL, *fout_dbg=NULL;
nameout = SUMA_append_string(Opt->out_vol_prefix, "_pg.1D.dset");
fout = fopen(nameout,"w");
if (!fout) {
SUMA_S_Err("Failed to open file for output");
exit(1);
}
histnote = SUMA_HistString (NULL, argc, argv, NULL);
if (SUMA_iswordin(OptS,"DoProp") == 1) {
fprintf(fout, "#Col. 0 Node n's index \n"
"#Col. 1 Number of neighbors listed for node n \n"
"#Col. 2+5*i ith neighbor of Node n (i=0..)\n"
"#Col. 3+5*i distance of ith neighbor from Node n\n"
"#Col. 4..6+5*i Propagation location of ith neighbor of Node n\n"
"#History:%s\n", histnote);
} else {
fprintf(fout, "#Col. 0 Node n's index \n"
"#Col. 1 Number of neighbors listed for node n \n"
"#Col. 2+2*i ith neighbor of Node n (i=0..)\n"
"#Col. 3+2*i distance of ith neighbor from Node n\n"
"#History:%s\n", histnote);
}
if (Opt->NodeDbg >= 0) {
sprintf(sbuf,"_pg_dbg_node_%d.1D.dset", Opt->NodeDbg);
stmp = SUMA_append_string(Opt->out_vol_prefix, sbuf);
fout_dbg = fopen(stmp,"w");
if (!fout_dbg) {
SUMA_S_Err("Failed to open file for output");
exit(1);
}
if (Opt->NodeDbg >= 0) {
fprintf(fout_dbg,
"#The first row is special, it is used to indicate\n"
"#the index of node n (%d) about which the patch is grown.\n"
"#Col. 0 Node m's index (m is the node neighboring n)\n"
"#Col. 1 Graph distance (along surface edges) from n to m \n"
"#Col. 2..4 Propagation location of node m\n"
"# this is the projected location of node m\n"
"# if the contour was stretched to the next \n"
"# neighborhood layer.\n"
"#History:%s\n", Opt->NodeDbg, histnote);
fprintf(fout_dbg,"%8d 0.0 -1.0 -1.0 -1.0\n", Opt->NodeDbg);
} else {
fprintf(fout_dbg,
"#The first row is special, it is used to indicate\n"
"#the index of node n (%d) about which the patch is grown.\n"
"#Col. 0 Node m's index (m is the node neighboring n)\n"
"#Col. 1 Graph distance (along surface edges) from n to m \n"
"#History:%s\n", Opt->NodeDbg, histnote);
fprintf(fout_dbg,"%8d 0.0\n", Opt->NodeDbg);
}
}
if (!SO->FN) {
if (!SUMA_SurfaceMetrics_eng(SO, "EdgeList", NULL, 0, SUMAg_CF->DsetList)) {
SUMA_S_Err("Failed to create EdgeList");
exit(1);
}
}
SUMA_LH( "Patch Grow, the memory expensive way\n"
"Calculating OffS_out ... Very SLOWWWW...");
if (Opt->NodeDbg >= 0) SUMA_Set_OffsetDebugNode(Opt->NodeDbg);
OffS_out = SUMA_FormNeighbOffset (SO, Opt->r, OptS, NULL, -1.0);
SUMA_LH("Writing OffS_out ... ");
for (i=0; i < SO->N_Node; ++i) {
fprintf(fout,"%d %d ", i, OffS_out[i].N_Neighb); /* node index */
if (OffS_out[i].Neighb_PropLoc) {
for (il=0; il<OffS_out[i].N_Neighb; ++il) {
if (OffS_out[i].Neighb_dist[il] <= Opt->r) {
fprintf(fout,"%d %.2f %.2f %.2f %.2f ",
OffS_out[i].Neighb_ind[il], OffS_out[i].Neighb_dist[il],
OffS_out[i].Neighb_PropLoc[3*il],
OffS_out[i].Neighb_PropLoc[3*il+1],
OffS_out[i].Neighb_PropLoc[3*il+2]);
}
}
} else {
for (il=0; il<OffS_out[i].N_Neighb; ++il) {
if (OffS_out[i].Neighb_dist[il] <= Opt->r) {
fprintf(fout,"%d %.2f",
OffS_out[i].Neighb_ind[il], OffS_out[i].Neighb_dist[il]);
}
}
}
fprintf(fout,"\n");
if (Opt->NodeDbg == i) {
if (OffS_out[i].Neighb_PropLoc) {
for (il=0; il<OffS_out[i].N_Neighb; ++il) {
fprintf(fout_dbg,"%8d %3.3f %4.2f %4.2f %4.2f \n",
OffS_out[i].Neighb_ind[il], OffS_out[i].Neighb_dist[il],
OffS_out[i].Neighb_PropLoc[3*il],
OffS_out[i].Neighb_PropLoc[3*il+1],
OffS_out[i].Neighb_PropLoc[3*il+2]);
}
} else {
for (il=0; il<OffS_out[i].N_Neighb; ++il) {
fprintf(fout_dbg,"%8d %3.3f \n",
OffS_out[i].Neighb_ind[il], OffS_out[i].Neighb_dist[il]);
}
}
}
if (Opt->debug) {
++cnt;
if (!(cnt % 1000)) {
fprintf(SUMA_STDERR,". @ %8d (%3.2f%%)\n",
i, (float)cnt/(float)(SO->N_Node)*100.0); fflush(SUMA_STDERR);
}
}
}
if (fout) fclose(fout); fout = NULL;
if (fout_dbg) fclose(fout_dbg); fout_dbg = NULL;
if (stmp) SUMA_free(stmp); stmp = NULL;
if (nameout) SUMA_free(nameout); nameout = NULL;
if (histnote) SUMA_free(histnote); histnote = NULL;
OffS_out = SUMA_free_NeighbOffset(SO, OffS_out);
}
/* Frenching */
if (closest_node) SUMA_free(closest_node); closest_node = NULL;
if (closest_dist) SUMA_free(closest_dist); closest_dist = NULL;
if (vpname) SUMA_free(vpname); vpname = NULL;
if (OptDs) { OptDs->mset = NULL; OptDs = SUMA_Free_FormAfniDset_Opt(OptDs); }
if (vp != SO->VolPar) SUMA_Free_VolPar(vp); vp = NULL;
if (SO) SUMA_Free_Surface_Object(SO); SO = NULL;
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (N_Spec) {
int k=0;
for (k=0; k<N_Spec; ++k) {
if (!SUMA_FreeSpecFields(&(Spec[k]))) { SUMA_S_Err("Failed to free spec fields"); }
}
SUMA_free(Spec); Spec = NULL; N_Spec = 0;
}
if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
if (!SUMA_Free_CommonFields(SUMAg_CF)) SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
exit(0);
}
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