/*USE This sample to start writing standalone programs.
Change SurfFWHM 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_SurfFWHM (SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"usage_SurfFWHM"};
char * s = NULL, *sio=NULL, *st = NULL, *sts = NULL;
int i;
s = SUMA_help_basics();
sio = SUMA_help_IO_Args(ps);
printf ( "\n"
"Usage: A program for calculating local and global FWHM.\n"
" -hood R = Using this option indicates that you want local\n"
" -nbhd_rad R = as well as global measures of FWHM. Local measurements\n"
" at node n are obtained using a neighborhood that \n"
" consists of nodes within R distance from n \n"
" as measured by the shortest \n"
" distance along the mesh.\n"
" -prefix PREFIX = Prefix of output data set. Only need when doing \n"
" local FWHM calculations.\n"
" -vox_size D\n"
" -ok_warn\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);
}
static int ncode=-1 , code[MAX_NCODE];
SUMA_GENERIC_PROG_OPTIONS_STRUCT *SUMA_SurfFWHM_ParseInput(char *argv[], int argc, SUMA_GENERIC_ARGV_PARSE *ps)
{
static char FuncName[]={"SUMA_SurfFWHM_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; /* for convenience */
Opt->NodeDbg = -1;
Opt->out_prefix = NULL;
Opt->r = -1.0;
Opt->d1 = -1.0;
Opt->b1 = 0;
ncode = 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_SurfFWHM(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], "-node_debug") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a node index after -node_debug \n");
exit (1);
}
Opt->NodeDbg = atoi(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-prefix") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a dset prefix after -prefix \n");
exit (1);
}
Opt->out_prefix = SUMA_copy_string(argv[++kar]);
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-hood") == 0 || strcmp(argv[kar], "-nbhd_rad") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a value after -nbhd_rad \n");
exit (1);
}
Opt->r = atof(argv[++kar]);
if (Opt->r <= 0.0) {
fprintf (SUMA_STDERR,"Error %s:\nneighborhood radius is not valid (have %f from %s).\n", FuncName, Opt->r, argv[kar]);
exit (1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-vox_size") == 0))
{
if (kar+1 >= argc)
{
fprintf (SUMA_STDERR, "need a value after -vox_size \n");
exit (1);
}
Opt->d1 = atof(argv[++kar]);
if (Opt->d1 <= 0.0) {
fprintf (SUMA_STDERR,"Error %s:\nvoxel dimension is not valid (have %f from %s).\n", FuncName, Opt->d1, argv[kar]);
exit (1);
}
brk = YUP;
}
if (!brk && (strcmp(argv[kar], "-ok_warn") == 0))
{
Opt->b1 = 1;
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 ++;
}
}
if (!Opt->out_prefix) {
Opt->out_prefix = SUMA_copy_string("SurfLocalstat");
}
if (Opt->r > 0.0 && Opt->d1 > 0.0) {
if (Opt->r / Opt->d1 < 2.99) { /* no magic reason for 3 other than it results in approx. pi*(3*d)2 mm2 area, which would be approx. pi*3*3 voxels. */
SUMA_S_Warnv( "\n"
"**********************************************\n"
" "The neighborhood radius of %.3fmm is likely too\n"
" small, relative to the voxel size of %.3fmm, \n"
" to yield an appropriate estimate for FWHM. \n"
" A radius of at least %.3f would be more \n"
" appropriate. Use -ok_warn to proceed despite\n"
" warning.\n"
" ZSS. DC CC and its vanilla suburbs.\n"
"***********************************************\n"
"\n",
Opt->r, Opt->d1, Opt->d1*3.0 );
if (!Opt->b1) exit(1);
}
}
SUMA_RETURN(Opt);
}
int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SurfFWHM"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_SurfaceObject *SO=NULL;
int *icols=NULL, N_icols = -1;
SUMA_DSET_FORMAT iform = SUMA_NO_DSET_FORMAT;
SUMA_DSET *din=NULL, *dout=NULL;
SUMA_SurfSpecFile *Spec = NULL;
int i, N_Spec, N_inmask = -1;
float *fwhmv=NULL;
double MinArea = -1.0;
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;-m;-dset;-talk;");
if (argc < 2) {
usage_SurfFWHM(ps);
exit (1);
}
Opt = SUMA_SurfFWHM_ParseInput (argv, argc, ps);
if (Opt->debug > 2) LocalHead = YUP;
if (Opt->ps->N_dsetname != 1) {
SUMA_S_Errv("Need one and only one dset please. Have %d on command line.\n", Opt->ps->N_dsetname);
exit(1);
}
if (!(din = SUMA_LoadDset_s (Opt->ps->dsetname[0], &iform, 0))) {
SUMA_S_Errv("Failed to load dset named %s\n", Opt->ps->dsetname[0]);
exit(1);
}
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec == 0) {
SUMA_S_Err("No surfaces found.");
exit(1);
}
if (N_Spec != 1) {
SUMA_S_Err("Multiple spec at input.");
exit(1);
}
SUMA_LH("Loading surface...");
SO = SUMA_Load_Spec_Surf(Spec, 0, ps->sv[0], Opt->debug);
if (!SO) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (!(Opt->nmask = SUMA_load_all_command_masks(Opt->ps->bmaskname, Opt->ps->nmaskname, Opt->ps->cmask, SO->N_Node, &N_inmask)) && N_inmask < 0) {
SUMA_S_Err("Failed loading mask");
exit(1);
}
if (Opt->r > 0.0) { /* wants to do localized FWHM */
SUMA_S_Note("Doing local FWHM...");
code[0] = NSTAT_FWHMx;
ncode = 1;
if (Opt->d1 > 0.0) {
/* have a way of suggesting minimum number of nodes to enter in FWHM calculations */
MinArea = SUMA_PI * SUMA_POW2((3.0 * Opt->d1)); /* need at least area covering a radius of 3 voxels */
SUMA_SetFWHM_MinArea(MinArea);
}
if (!(dout = SUMA_CalculateLocalStats(SO, din,
Opt->nmask, 1,
Opt->r, NULL,
ncode, code,
NULL, Opt->NodeDbg))) {
SUMA_S_Err("Failed in SUMA_CalculateLocalStats");
exit(1);
}
/* write it out */
SUMA_WriteDset_s(Opt->out_prefix, dout, iform, 0, 0);
if (dout) SUMA_FreeDset(dout); dout = NULL;
}
SUMA_S_Note("Doing Global FWHM...");
/* what columns can we process ?*/
icols = SUMA_FindNumericDataDsetCols(din, &N_icols);
if (N_icols <= 0) {
SUMA_SL_Err("No approriate data columns in dset");
exit(1);
}
if (!(fwhmv = SUMA_estimate_dset_FWHM_1dif( SO, din,
icols, N_icols, Opt->nmask,
1, NULL))) {
SUMA_S_Err("Rien ne va plus");
exit(1);
}
fprintf(stdout,"Global FWHM estimates for each column:\n");
for (i=0; i<N_icols; ++i) {
fprintf(stdout,"FWHM[%4d]=%.4f\n", icols[i], fwhmv[i]);
}
if (din) SUMA_FreeDset(din); din = NULL;
if (dout) SUMA_FreeDset(dout); dout = NULL;
if (fwhmv) SUMA_free(fwhmv); fwhmv=NULL;
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
if (!SUMA_Free_CommonFields(SUMAg_CF)) SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
exit(0);
}
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