int main( int argc , char * argv[] )
{
void (*smth)(int,float *) = linear3_func ; /* default filter */
char prefix[256] = "smooth" ;
int new_datum = ILLEGAL_TYPE , old_datum ;
int nopt ;
THD_3dim_dataset * old_dset , * new_dset ;
int ii,kk , nxyz , ntime , use_fac , ityp , nbytes ;
void * new_brick ;
byte ** bptr = NULL ; /* one of these will be the array of */
short ** sptr = NULL ; /* pointers to input dataset sub-bricks */
float ** fptr = NULL ; /* (depending on input datum type) */
byte ** new_bptr = NULL ; /* one of these will be the array of */
short ** new_sptr = NULL ; /* pointers to output dataset sub-bricks */
float ** new_fptr = NULL ; /* (depending on output datum type) */
float * fxar = NULL ; /* array loaded from input dataset */
float * fac = NULL ; /* array of brick scaling factors */
float * faci = NULL ;
#define BLACKMAN 1
#define HAMMING 2
#define CUSTOM 3
#define EXTEND 77
#define ZERO 78
#define TREND 79
int ntap=0 ; /* 01 Mar 2001 */
float *ftap=NULL ;
int nwin=0,nfil=EXTEND ; /* 03 Mar 2001 */
void (*lfil)(int,float *,int,float *) = linear_filter_extend ;
float * (*lwin)(int) = NULL ;
/* start of code */
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: 3dTsmooth [options] dataset\n"
"Smooths each voxel time series in a 3D+time dataset and produces\n"
"as output a new 3D+time dataset (e.g., lowpass filter in time).\n"
"\n"
"*** Also see program 3dBandpass ***\n"
"\n"
"General Options:\n"
" -prefix ppp = Sets the prefix of the output dataset to be 'ppp'.\n"
" [default = 'smooth']\n"
" -datum type = Coerce output dataset to be stored as the given type.\n"
" [default = input data type]\n"
"\n"
"Three Point Filtering Options [07 July 1999]\n"
"--------------------------------------------\n"
"The following options define the smoothing filter to be used.\n"
"All these filters use 3 input points to compute one output point:\n"
" Let a = input value before the current point\n"
" b = input value at the current point\n"
" c = input value after the current point\n"
" [at the left end, a=b; at the right end, c=b]\n"
"\n"
" -lin = 3 point linear filter: 0.15*a + 0.70*b + 0.15*c\n"
" [This is the default smoother]\n"
" -med = 3 point median filter: median(a,b,c)\n"
" -osf = 3 point order statistics filter:\n"
" 0.15*min(a,b,c) + 0.70*median(a,b,c) + 0.15*max(a,b,c)\n"
"\n"
" -3lin m = 3 point linear filter: 0.5*(1-m)*a + m*b + 0.5*(1-m)*c\n"
" Here, 'm' is a number strictly between 0 and 1.\n"
"\n"
"General Linear Filtering Options [03 Mar 2001]\n"
"----------------------------------------------\n"
" -hamming N = Use N point Hamming or Blackman windows.\n"
" -blackman N (N must be odd and bigger than 1.)\n"
" -custom coeff_filename.1D (odd # of coefficients must be in a \n"
" single column in ASCII file)\n"
" (-custom added Jan 2003)\n"
" WARNING: If you use long filters, you do NOT want to include the\n"
" large early images in the program. Do something like\n"
" 3dTsmooth -hamming 13 'fred+orig[4..$]'\n"
" to eliminate the first 4 images (say).\n"
" The following options determing how the general filters treat\n"
" time points before the beginning and after the end:\n"
" -EXTEND = BEFORE: use the first value; AFTER: use the last value\n"
" -ZERO = BEFORE and AFTER: use zero\n"
" -TREND = compute a linear trend, and extrapolate BEFORE and AFTER\n"
" The default is -EXTEND. These options do NOT affect the operation\n"
" of the 3 point filters described above, which always use -EXTEND.\n"
) ;
printf("\n" MASTER_SHORTHELP_STRING ) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
mainENTRY("3dTsmooth main"); machdep(); AFNI_logger("3dTsmooth",argc,argv);
PRINT_VERSION("3dTsmooth") ;
/* parse options */
nopt = 1 ;
while( nopt < argc && argv[nopt][0] == '-' ){
if( strcmp(argv[nopt],"-EXTEND") == 0 ){ /* 03 Mar 2001 */
nfil = EXTEND ; lfil = linear_filter_extend ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-ZERO") == 0 ){ /* 03 Mar 2001 */
nfil = ZERO ; lfil = linear_filter_zero ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-TREND") == 0 ){ /* 03 Mar 2001 */
nfil = TREND ; lfil = linear_filter_trend ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-hamming") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -hamming!\n");exit(1);}
ntap = (int) strtod(argv[nopt],NULL) ;
if( ntap < 3 || ntap%2 != 1 ){fprintf(stderr,"*** Illegal -hamming!\n");exit(1);}
nwin = HAMMING ; lwin = hamming_window ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-blackman") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -blackman!\n");exit(1);}
ntap = (int) strtod(argv[nopt],NULL) ;
if( ntap < 3 || ntap%2 != 1 ){fprintf(stderr,"*** Illegal -blackman!\n");exit(1);}
nwin = BLACKMAN ; lwin = blackman_window ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-custom") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -custom!\n");exit(1);}
strcpy(custom_file, argv[nopt]) ;
nwin = CUSTOM ; lwin = custom_filter ;
ntap = 1;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-prefix") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -prefix!\n");exit(1);}
strcpy(prefix,argv[nopt]) ;
if( !THD_filename_ok(prefix) ){fprintf(stderr,"*** Illegal -prefix!\n");exit(1);}
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-datum") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -datum!\n");exit(1);}
if( strcmp(argv[nopt],"short") == 0 ){
new_datum = MRI_short ;
} else if( strcmp(argv[nopt],"float") == 0 ){
new_datum = MRI_float ;
} else if( strcmp(argv[nopt],"byte") == 0 ){
new_datum = MRI_byte ;
} else {
fprintf(stderr,"*** Illegal -datum!\n");exit(1);
}
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-lin") == 0 ){
bf = 0.70 ; af = cf = 0.15 ;
smth = linear3_func ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-med") == 0 ){
smth = median3_func ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-osf") == 0 ){
smth = osfilt3_func ;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-3lin") == 0 ){
if( ++nopt >= argc ){fprintf(stderr,"*** Illegal -3lin!\n");exit(1);}
bf = strtod( argv[nopt] , NULL ) ;
if( bf <= 0.0 || bf >= 1.0 ){fprintf(stderr,"*** Illegal -3lin!\n");exit(1);}
af = cf = 0.5*(1.0-bf) ;
smth = linear3_func ;
nopt++ ; continue ;
}
fprintf(stderr,"*** Unknown option: %s\n",argv[nopt]) ; exit(1) ;
} /* end of loop over options */
if( nopt >= argc ){
fprintf(stderr,"*** No input dataset?!\n") ; exit(1) ;
}
/* open dataset */
old_dset = THD_open_dataset( argv[nopt] ) ;
if( old_dset == NULL ){
fprintf(stderr,"*** Can't open dataset %s\n",argv[nopt]) ; exit(1) ;
}
ntime = DSET_NVALS(old_dset) ;
nxyz = DSET_NVOX(old_dset) ;
if( ntime < 4 ){
fprintf(stderr,"*** Can't smooth dataset with less than 4 time points!\n") ;
exit(1) ;
}
DSET_load(old_dset) ; CHECK_LOAD_ERROR(old_dset) ;
old_datum = DSET_BRICK_TYPE(old_dset,0) ;
if( new_datum < 0 ) new_datum = old_datum ;
switch( old_datum ){ /* pointer type depends on input datum type */
/** create array of pointers into old dataset sub-bricks **/
/*--------- input is bytes ----------*/
/* voxel #i at time #k is bptr[k][i] */
/* for i=0..nxyz-1 and k=0..ntime-1. */
case MRI_byte:
bptr = (byte **) malloc( sizeof(byte *) * ntime ) ;
for( kk=0 ; kk < ntime ; kk++ )
bptr[kk] = (byte *) DSET_ARRAY(old_dset,kk) ;
break ;
/*--------- input is shorts ---------*/
/* voxel #i at time #k is sptr[k][i] */
/* for i=0..nxyz-1 and k=0..ntime-1. */
case MRI_short:
sptr = (short **) malloc( sizeof(short *) * ntime ) ;
for( kk=0 ; kk < ntime ; kk++ )
sptr[kk] = (short *) DSET_ARRAY(old_dset,kk) ;
break ;
/*--------- input is floats ---------*/
/* voxel #i at time #k is fptr[k][i] */
/* for i=0..nxyz-1 and k=0..ntime-1. */
case MRI_float:
fptr = (float **) malloc( sizeof(float *) * ntime ) ;
for( kk=0 ; kk < ntime ; kk++ )
fptr[kk] = (float *) DSET_ARRAY(old_dset,kk) ;
break ;
} /* end of switch on input type */
/*---- allocate space for 1 voxel timeseries ----*/
fxar = (float *) malloc( sizeof(float) * ntime ) ; /* voxel timeseries */
/*--- get scaling factors for sub-bricks ---*/
fac = (float *) malloc( sizeof(float) * ntime ) ; /* factors */
use_fac = 0 ;
for( kk=0 ; kk < ntime ; kk++ ){
fac[kk] = DSET_BRICK_FACTOR(old_dset,kk) ;
if( fac[kk] != 0.0 ) use_fac++ ;
else fac[kk] = 1.0 ;
}
if( !use_fac ){
free(fac) ; fac == NULL ;
} else {
faci = (float *) malloc( sizeof(float) * ntime ) ;
for( kk=0 ; kk < ntime ; kk++ ) faci[kk] = 1.0 / fac[kk] ;
}
/*---------------------- make a new dataset ----------------------*/
new_dset = EDIT_empty_copy( old_dset ) ;
tross_Copy_History( old_dset , new_dset ) ;
tross_Make_History( "3dTsmooth" , argc,argv , new_dset ) ;
/*-- edit some of its internal parameters --*/
EDIT_dset_items( new_dset ,
ADN_prefix , prefix ,
ADN_malloc_type , DATABLOCK_MEM_MALLOC ,
ADN_datum_all , new_datum ,
ADN_none ) ;
/*-- make brick(s) for this dataset --*/
switch( new_datum ){
case MRI_byte:
new_bptr = (byte **) malloc( sizeof(byte *) * ntime ) ;
break ;
case MRI_short:
new_sptr = (short **) malloc( sizeof(short *) * ntime ) ;
break ;
case MRI_float:
new_fptr = (float **) malloc( sizeof(float *) * ntime ) ;
break ;
}
for( kk=0 ; kk < ntime ; kk++ ){
ityp = DSET_BRICK_TYPE(new_dset,kk) ; /* type of data */
nbytes = DSET_BRICK_BYTES(new_dset,kk) ; /* how much data */
new_brick = malloc( nbytes ) ; /* make room */
if( new_brick == NULL ){
fprintf(stderr,"*** Can't get memory for output dataset!\n") ; exit(1) ;
}
EDIT_substitute_brick( new_dset , kk , ityp , new_brick ) ;
switch( new_datum ){
case MRI_byte: new_bptr[kk] = (byte * ) new_brick ; break ;
case MRI_short: new_sptr[kk] = (short *) new_brick ; break ;
case MRI_float: new_fptr[kk] = (float *) new_brick ; break ;
}
}
if( lwin != NULL && ntap > 0 ){ /* 03 Mar 2001 */
ftap = lwin(ntap) ;
if( lfil == NULL ) lfil = linear_filter_extend ;
if( nwin == CUSTOM ) ntap = custom_ntaps ;
}
/*----------------------------------------------------*/
/*----- Setup has ended. Now do some real work. -----*/
/***** loop over voxels *****/
for( ii=0 ; ii < nxyz ; ii++ ){ /* 1 time series at a time */
/*** load data from input dataset, depending on type ***/
switch( old_datum ){
case MRI_byte:
for( kk=0 ; kk < ntime ; kk++ ) fxar[kk] = bptr[kk][ii] ;
break ;
case MRI_short:
for( kk=0 ; kk < ntime ; kk++ ) fxar[kk] = sptr[kk][ii] ;
break ;
case MRI_float:
for( kk=0 ; kk < ntime ; kk++ ) fxar[kk] = fptr[kk][ii] ;
break ;
} /* end of switch over input type */
if( use_fac )
for( kk=0 ; kk < ntime ; kk++ ) fxar[kk] *= fac[kk] ;
/* do smoothing */
if( ftap != NULL )
lfil( ntap,ftap , ntime,fxar ) ; /* 01 Mar 2001 */
else
smth( ntime , fxar ) ; /* 3 point smoother */
/*** put data into output dataset ***/
switch( new_datum ){
case MRI_byte:
if( use_fac )
for( kk=0 ; kk < ntime ; kk++ ) new_bptr[kk][ii] = (byte)(fxar[kk] * faci[kk]) ;
else
for( kk=0 ; kk < ntime ; kk++ ) new_bptr[kk][ii] = (byte) fxar[kk] ;
break ;
case MRI_short:
if( use_fac )
for( kk=0 ; kk < ntime ; kk++ ) new_sptr[kk][ii] = (short)(fxar[kk] * faci[kk]) ;
else
for( kk=0 ; kk < ntime ; kk++ ) new_sptr[kk][ii] = (short) fxar[kk] ;
break ;
case MRI_float:
if( use_fac )
for( kk=0 ; kk < ntime ; kk++ ) new_fptr[kk][ii] = (float)(fxar[kk] * faci[kk]) ;
else
for( kk=0 ; kk < ntime ; kk++ ) new_fptr[kk][ii] = (float) fxar[kk] ;
break ;
}
} /* end of loop over voxels */
DSET_unload(old_dset) ; free(ftap) ;
if (DSET_write(new_dset) != False) {
fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(new_dset)) ;
exit(0) ;
} else {
fprintf(stderr,
"** 3dTsmooth: Failed to write output!\n" ) ;
exit(1) ;
}
}
int main(int argc, char *argv[])
{
int CHECK = 0;
int iarg;
char *Fname_input = NULL;
char *Fname_output = NULL;
char *Fname_outputBV = NULL;
char *Fname_bval = NULL;
int opt;
FILE *fin=NULL, *fout=NULL, *finbv=NULL, *foutBV=NULL;
int i,j,k;
int BZER=0,idx=0,idx2=0;
MRI_IMAGE *flim=NULL;
MRI_IMAGE *preREADIN=NULL;
MRI_IMAGE *preREADBVAL=NULL;
float *READIN=NULL;
float *READBVAL=NULL;
float OUT_MATR[MAXGRADS][7]; // b- or g-matrix
float OUT_GRAD[MAXGRADS][4]; // b- or g-matrix
int INV[3] = {1,1,1}; // if needing to switch
int FLAG[MAXGRADS];
float temp;
int YES_B = 0;
int EXTRA_ZEROS=0;
int HAVE_BVAL = 0;
int BVAL_OUT = 0;
int BVAL_OUT_SEP = 0;
float BMAX_REF = 1; // i.e., essentially zero
int IN_FORM = 0; // 0 for row, 1 for col
int OUT_FORM = 1; // 1 for col, 2 for bmatr
int HAVE_BMAX_REF=0 ; // referring to user input value
int count_in=0, count_out=0;
THD_3dim_dataset *dwset=NULL, *dwout=NULL;
int Nbrik = 0;
char *prefix=NULL ;
float **temp_arr=NULL, **temp_grad=NULL;
int Ndwi = 0, dwi=0, Ndwout = 0, Ndwi_final = 0, Ndwout_final = 0;
int Nvox = 0;
int DWI_COMP_FAC = 0;
int ct_dwi = 0;
float MaxDP = 0;
mainENTRY("1dDW_Grad_o_Mat"); machdep();
if (argc == 1) { usage_1dDW_Grad_o_Mat(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_1dDW_Grad_o_Mat(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-flip_x") == 0) {
INV[0] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-flip_y") == 0) {
INV[1] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-flip_z") == 0) {
INV[2] = -1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-keep_b0s") == 0) {
YES_B = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-put_zeros_top") == 0) {
EXTRA_ZEROS = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_grad_rows") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_grad_rows'\n") ;
Fname_input = argv[iarg];
count_in++;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_grad_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_grad_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_gmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matT_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 2;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_gmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matA_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 3;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matT_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 4;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_matA_cols'\n") ;
Fname_input = argv[iarg];
count_in++;
IN_FORM = 5;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_grad_rows") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_grad_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 0;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_grad_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_grad_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_gmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_gmatT_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 2;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_gmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_gmatA_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 3;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bmatT_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bmatT_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 4;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bmatA_cols") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bmatA_cols'\n") ;
Fname_output = argv[iarg];
count_out++;
OUT_FORM = 5;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_bvals") == 0 ){
if( ++iarg >= argc )
ERROR_exit("Need argument after '-in_bvals'\n") ;
Fname_bval = argv[iarg];
HAVE_BVAL = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-bmax_ref") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-bmax_ref'\n");
BMAX_REF = atof(argv[iarg]);
HAVE_BMAX_REF = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-out_bval_col") == 0) {
BVAL_OUT = 1;
iarg++ ; continue ;
}
// May,2015
if( strcmp(argv[iarg],"-out_bval_row_sep") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need argument after '-out_bval_row_sep'\n") ;
Fname_outputBV = argv[iarg];
BVAL_OUT_SEP = 1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-proc_dset") == 0 ){ // in DWIs
if( ++iarg >= argc )
ERROR_exit("Need argument after '-proc_dset'") ;
dwset = THD_open_dataset( argv[iarg] ) ;
if( dwset == NULL )
ERROR_exit("Can't open DWI dataset '%s'", argv[iarg]) ;
DSET_load(dwset) ; CHECK_LOAD_ERROR(dwset) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-pref_dset") == 0 ){ // will be output
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-pref_dset'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-pref_dset'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-dwi_comp_fac") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-dwi_comp_fac'\n");
DWI_COMP_FAC = atoi(argv[iarg]);
if (DWI_COMP_FAC <=1)
ERROR_exit("The compression factor after '-dwi_comp_fac'"
"must be >1!");
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * *
if( (Fname_input == NULL) ) {
fprintf(stderr,
"\n\tBad Command-lining! Option '-in_*' requires argument.\n");
exit(1);
}
if( (Fname_output == NULL) ) {
fprintf(stderr,
"\n\tBad Command-lining! Option '-out_*' requires arg.\n");
exit(2);
}
if( count_in > 1 ) {
fprintf(stderr,
"\n\tBad Command-lining! Can't have >1 vec file input.\n");
exit(3);
}
if( count_out > 1 ) {
fprintf(stderr,
"\n\tBad Command-lining! Can't have >1 output file opt.\n");
exit(4);
}
if(YES_B && dwset) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have '-keep_b0s' and '-proc_dset' together.\n");
exit(5);
}
if( !prefix && dwset) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Need an output '-pref_dset' when using '-proc_dset'.\n");
exit(6);
}
if(YES_B && DWI_COMP_FAC) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have '-keep_b0s' and '-dwi_comp_fac' together.\n");
exit(7);
}
if(!HAVE_BVAL && (BVAL_OUT || BVAL_OUT_SEP)) {
fprintf(stderr,
"\n** Bad Command-lining! "
"Can't have ask for outputting bvals with no '-in_bvals FILE'.\n");
exit(8);
}
// ********************************************************************
// ************************* start reading ****************************
// ********************************************************************
flim = mri_read_1D (Fname_input);
if (flim == NULL) {
ERROR_exit("Error reading gradient vector file");
}
if( IN_FORM )
preREADIN = mri_transpose(flim); // effectively *undoes* autotranspose
else
preREADIN = mri_copy(flim);
mri_free(flim);
idx = preREADIN->ny;
if( HAVE_BVAL ) {
flim = mri_read_1D (Fname_bval);
if (flim == NULL) {
ERROR_exit("Error reading b-value file");
}
if( flim->ny == 1)
preREADBVAL = mri_transpose(flim); // effectively *undoes* autotransp
else
preREADBVAL = mri_copy(flim);
mri_free(flim);
idx2 = preREADBVAL->ny;
}
if(idx>= MAXGRADS ) {
printf("Error, too many input grads.\n");
mri_free (preREADIN);
if( HAVE_BVAL ) mri_free (preREADBVAL);
exit(4);
}
if( ( (preREADIN->nx != 3 ) && (preREADIN->ny != 3 )) &&
(preREADIN->nx != 6 ) )
printf("Probably an error, "
"because there aren't 3 or 6 numbers in columns!\n");
if( HAVE_BVAL && ( idx != idx2 ) ) {
printf("Error, because the number of bvecs (%d)\n"
"and bvals (%d) don't appear to match!\n", idx, idx2);
mri_free (preREADIN);
mri_free (preREADBVAL);
exit(3);
}
if(dwset) {
Nbrik = DSET_NVALS(dwset);
if( idx != Nbrik ) {
fprintf(stderr,
"\n** ERROR: the number of bvecs (%d) does not match the "
"number of briks in '-proc_dset' (%d).\n", idx, Nbrik);
exit(4);
}
}
READIN = MRI_FLOAT_PTR( preREADIN );
if( HAVE_BVAL )
READBVAL = MRI_FLOAT_PTR( preREADBVAL );
// 0 is grad row;
// 1 is grad col;
// 2 is gmatrRow col T;
// 3 is gmatrDiag col A;
// 4 is bmatrRow col T;
// 5 is bmatrDiag col A;
//if( IN_FORM == 0 ) // grad rows, no binfo
// for( i=0; i<idx ; i++ )
// for ( j=0; j<3 ; j++ )
// OUT_GRAD[i][j+1] = *(READIN +j*idx +i) ;
//else
if ( IN_FORM <= 1 ) // grad cols, no binfo
for( i=0; i<idx ; i++ )
for ( j=0; j<3 ; j++ )
OUT_GRAD[i][j+1] = *(READIN + 3*i+j);
// A/row/3dDWItoDT: Bxx, Byy, Bzz, Bxy, Bxz, Byz
// T/diag/TORTOISE: b_xx 2b_xy 2b_xz b_yy 2b_yz b_zz
else if ( (IN_FORM == 3) || (IN_FORM ==5 ) ) { // diag matr
for( i=0; i<idx ; i++ ) {
for( j=0; j<3 ; j++ ) {
OUT_MATR[i][j+1] = *(READIN+6*i+j);
OUT_MATR[i][3+j+1] = *(READIN+6*i+3+j);
}
for( j=0; j<3 ; j++ )
if(OUT_MATR[i][j] < 0 )
CHECK++;
}
if(CHECK > 0)
INFO_message("Warning: you *said* you input a mat'T',"
" but the matr diagonals don't appear to be uniformly"
" positive. If input cols 0, 3 and 5 are positive,"
" then you might have meant mat'A'?");
}
else if ( (IN_FORM ==2 ) || (IN_FORM ==4 ) ) { // row matr
CHECK = 0;
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][1] = *(READIN +6*i);
OUT_MATR[i][2] = *(READIN +6*i+3);
OUT_MATR[i][3] = *(READIN +6*i+5);
OUT_MATR[i][4] = *(READIN +6*i+1)/2.;
OUT_MATR[i][5] = *(READIN +6*i+2)/2.;
OUT_MATR[i][6] = *(READIN +6*i+4)/2.;
}
for( i=0; i<idx ; i++ )
for( j=0; j<3 ; j++ )
if(OUT_MATR[i][j] < 0 )
CHECK++;
if(CHECK > 0)
INFO_message("Warning: you *said* you input a mat'A',"
" but the matr diagonals don't appear to be uniformly"
" positive. If input cols 0, 1 and 2 are positive,"
" then you might have meant mat'T'?");
}
else{
fprintf(stderr, "Coding error with format number (%d), not allowed.\n",
IN_FORM);
exit(2);
}
// get bval info
if( ( (IN_FORM ==4 ) || (IN_FORM ==5 ) ) ) { //bval
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][0] = OUT_GRAD[i][0] =
OUT_MATR[i][1] + OUT_MATR[i][2] + OUT_MATR[i][3];
if( OUT_MATR[i][0] > 0.000001)
for( j=1 ; j<7 ; j++ )
OUT_MATR[i][j]/= OUT_MATR[i][0];
}
}
else if ( HAVE_BVAL )
for( i=0; i<idx ; i++ ) {
OUT_MATR[i][0] = OUT_GRAD[i][0] = *(READBVAL + i);
}
else if ( OUT_FORM > 3 || BVAL_OUT || BVAL_OUT_SEP || HAVE_BMAX_REF ) {
fprintf(stderr, "ERROR: you asked for b-value dependent output, "
"but gave me no bvals to work with.\n");
exit(2);
}
// * * * ** * * * * * * * * ** ** * * ** * * ** * ** * ** * * *
// at this point, all IN_FORM >1 cases which need bval have led to:
// + grad[0] has bval
// + matr[0] has bval
// + matr file normalized and in diagonal form
// * * * ** * * * * * * * * ** ** * * ** * * ** * ** * ** * * *
for( i=0; i<idx ; i++ )
if( IN_FORM > 1)
j = GradConv_Gsign_from_BmatA( OUT_GRAD[i]+1, OUT_MATR[i]+1);
else
j = GradConv_BmatA_from_Gsign( OUT_MATR[i]+1, OUT_GRAD[i]+1);
// flip if necessary
for( i=0 ; i<idx ; i++) {
for( j=0 ; j<3 ; j++)
OUT_GRAD[i][j+1]*= INV[j];
OUT_MATR[i][4]*= INV[0]*INV[1];
OUT_MATR[i][5]*= INV[0]*INV[2];
OUT_MATR[i][6]*= INV[1]*INV[2];
}
BZER=0;
for( i=0 ; i<idx ; i++) {
if( HAVE_BVAL || (IN_FORM ==4) || (IN_FORM ==5) )
if( OUT_GRAD[i][0] >= BMAX_REF )
FLAG[i] = 1;
else{
if( YES_B )
FLAG[i] = 1;
BZER++;
}
else {
temp = 0.;
for( j=1 ; j<4 ; j++)
temp+= pow(OUT_GRAD[i][j],2);
if( temp > 0.1 )
FLAG[i] = 1;
else{
if( YES_B )
FLAG[i] = 1;
BZER++;
}
}
}
if(YES_B) {
printf("\tChose to *keep* %d b0s,\tas well as \t%d grads\n",
BZER,idx-BZER);
BZER=0;
}
else {
printf("\tGetting rid of %d b0s,\tleaving the %d grads\n",
BZER,idx-BZER);
Ndwi = idx-BZER;
}
Ndwi_final = idx-BZER; // default: all DWIs
if( DWI_COMP_FAC ) {
if( Ndwi % DWI_COMP_FAC != 0 ) {
fprintf(stderr, "\n** ERROR can't compress: "
"Ndwi=%d, and %d/%d has a nonzero remainder (=%d).\n",
Ndwi,Ndwi,DWI_COMP_FAC, Ndwi % DWI_COMP_FAC );
exit(1);
}
else {
Ndwi_final = Ndwi/DWI_COMP_FAC;
INFO_message("You have chosen a compression factor of %d, "
"with %d DWIs,\n"
"\tso that afterward there will be %d DWIs.",
DWI_COMP_FAC, Ndwi, Ndwi_final);
}
}
if(BVAL_OUT_SEP)
if( (foutBV = fopen(Fname_outputBV, "w")) == NULL) {
fprintf(stderr, "\n\nError opening file %s.\n",Fname_outputBV);
exit(1);
}
if( (fout = fopen(Fname_output, "w")) == NULL) {
fprintf(stderr, "\n\nError opening file %s.\n",Fname_output);
exit(1);
}
// 0 is grad row;
// 1 is grad col;
// 2 is gmatrRow col T;
// 3 is gmatrDiag col A;
// 4 is bmatrRow col T;
// 5 is bmatrDiag col A;
if( OUT_FORM>0) {
if( EXTRA_ZEROS ) {
if( BVAL_OUT )
fprintf(fout,"%8d ", 0);
if( BVAL_OUT_SEP )
fprintf(foutBV,"%8d ", 0);
if( OUT_FORM == 1 )
for( k=1 ; k<4 ; k++ )
fprintf(fout,"%11.5f ", 0.0);
else if ( OUT_FORM > 1 ) // bit superfluous at this point
for( k=1 ; k<7 ; k++ )
fprintf(fout,"%11.5f ", 0.0);
fprintf(fout,"\n");
}
ct_dwi = 0;
for(i=0 ; i<idx ; i++){
if(FLAG[i]) {
if( BVAL_OUT )
fprintf(fout,"%8d ", (int) OUT_GRAD[i][0]);
if( BVAL_OUT_SEP )
fprintf(foutBV,"%8d ", (int) OUT_GRAD[i][0]);
if( (OUT_FORM == 4) || (OUT_FORM ==5) )
for( k=1 ; k<7 ; k++ )
OUT_MATR[i][k]*= OUT_MATR[i][0];
if( OUT_FORM == 1 ) // grad col
for( k=1 ; k<4 ; k++ )
fprintf(fout,"%11.5f ", OUT_GRAD[i][k]);
else if( (OUT_FORM == 3) || (OUT_FORM == 5) ) { // gmat
for( k=1 ; k<6 ; k++ )
fprintf(fout,"%11.5f ", OUT_MATR[i][k]);
fprintf(fout,"%11.5f", OUT_MATR[i][k]);
}
else if ( (OUT_FORM == 2 ) || (OUT_FORM ==4)) { // bmat
fprintf(fout,"%11.5f ", OUT_MATR[i][1]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][4]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][5]);
fprintf(fout,"%11.5f ", OUT_MATR[i][2]);
fprintf(fout,"%11.5f ", 2*OUT_MATR[i][6]);
fprintf(fout,"%11.5f", OUT_MATR[i][3]);
}
fprintf(fout,"\n");
ct_dwi++;
}
if( (ct_dwi == Ndwi_final) && DWI_COMP_FAC ) {
INFO_message("Reached compression level: DWI number %d",
Ndwi_final);
break;
}
}
}
else if(OUT_FORM ==0) {
if(BVAL_OUT)
WARNING_message("Ignoring '-out_bval_col' option, since "
" you are outputting in rows.");
for( k=1 ; k<4 ; k++ ) {
if(EXTRA_ZEROS){
fprintf(fout,"% -11.5f ", 0.0);
if( (k==1) && BVAL_OUT_SEP ) // only output 1 zeroin bval file
fprintf(foutBV,"%8d ", 0);
}
ct_dwi = 0;
for(i=0 ; i<idx ; i++) {
if(FLAG[i]) {
fprintf(fout,"% -11.5f ", OUT_GRAD[i][k]);
if( (k==1) && BVAL_OUT_SEP )// only output 1 zeroin bval file
fprintf(foutBV,"%8d ", (int) OUT_GRAD[i][0]);
ct_dwi++;
}
if( (ct_dwi == Ndwi_final) && DWI_COMP_FAC ) {
INFO_message("Reached compression level: DWI number %d",
Ndwi_final);
break;
}
}
fprintf(fout,"\n");
}
}
fclose(fout);
if( BVAL_OUT_SEP ) {
fprintf(foutBV,"\n");
fclose(foutBV);
}
if(dwset) {
INFO_message("Processing the B0+DWI file now.");
if(!BZER) {
fprintf(stderr, "\n** Error in processing data set: "
"no b=0 values from bvecs/bval info!\n");
exit(5);
}
// FLAG marks where DWIs are if not using '-keep_b0s'!
Nvox = DSET_NVOX(dwset);
Ndwout = Ndwi+1;
temp_arr = calloc( Ndwout,sizeof(temp_arr));
for( i=0 ; i<Ndwout ; i++)
temp_arr[i] = calloc( Nvox,sizeof(float));
temp_grad = calloc( Ndwi,sizeof(temp_grad));
for( i=0 ; i<Ndwi ; i++)
temp_grad[i] = calloc( 3,sizeof(float));
if( (temp_arr == NULL) || (temp_grad == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
dwi = 0; // keep track of DWI contraction
for( i=0 ; i<Nbrik ; i++)
if( !FLAG[i] ) // b=0
for( j=0 ; j<Nvox ; j++)
temp_arr[0][j]+= THD_get_voxel(dwset,j,i);
else {
for( j=0 ; j<3 ; j++)
temp_grad[dwi][j]= OUT_GRAD[i][j+1];
dwi++;
for( j=0 ; j<Nvox ; j++)
temp_arr[dwi][j]+= THD_get_voxel(dwset,j,i);
}
if( dwi != Ndwi ) {
fprintf(stderr, "\n** Mismatch in internal DWI counting!\n");
exit(6);
}
// average the values
for( j=0 ; j<Nvox ; j++)
temp_arr[0][j]/= BZER; // can't be zero here.
if( DWI_COMP_FAC ) {
INFO_message("Compressing DWI file");
for( k=1 ; k<DWI_COMP_FAC ; k++)
for( i=0 ; i<Ndwi_final ; i++)
for( j=0 ; j<Nvox ; j++)
temp_arr[1+i][j]+= temp_arr[1+k*Ndwi_final+i][j];
for( i=0 ; i<Ndwi_final ; i++)
for( j=0 ; j<Nvox ; j++)
temp_arr[1+i][j]/= DWI_COMP_FAC;
INFO_message("Checking closeness of compressed gradient values");
MaxDP = GradCloseness(temp_grad, Ndwi, DWI_COMP_FAC);
INFO_message("The max angular difference between matched/compressed\n"
"\tgradients is: %f", MaxDP);
if( MaxDP > 2)
WARNING_message("The max angular difference seem kinda big-- you\n"
" sure about the compression factor?");
}
Ndwout_final = Ndwi_final + 1;
INFO_message("Writing the processed data set.");
dwout = EDIT_empty_copy( dwset );
EDIT_dset_items(dwout,
ADN_nvals, Ndwout_final,
ADN_ntt, 0,
ADN_datum_all, MRI_float ,
ADN_prefix, prefix,
ADN_none );
for( i=0; i<Ndwout_final ; i++) {
EDIT_substitute_brick(dwout, i, MRI_float, temp_arr[i]);
temp_arr[i]=NULL;
}
// if necessary
for( i=Ndwout_final ; i<Ndwout ; i++)
temp_arr[i]=NULL;
THD_load_statistics( dwout );
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(dwout)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(dwout));
tross_Make_History("1dDW_Grad_o_Mat", argc, argv, dwout);
THD_write_3dim_dataset(NULL, NULL, dwout, True);
DSET_delete(dwout);
free(dwout);
DSET_delete(dwset);
free(dwset);
for( i=0 ; i<Ndwout_final ; i++)
free(temp_arr[i]);
free(temp_arr);
}
mri_free(preREADIN);
if( HAVE_BVAL )
mri_free(preREADBVAL);
if(prefix)
free(prefix);
printf("\n\tDone. Check output file '%s' for results",Fname_output);
if(dwset) {
printf("\n\t-> as well as the data_set '%s'",DSET_FILECODE(dwout));
}
if(BVAL_OUT_SEP)
printf("\n\t-> and even the b-value rows '%s'",Fname_outputBV);
printf("\n\n");
exit(0);
}
int main( int argc , char * argv[] )
{
int iarg , nvox=0 , iv,ii,cnum , verb=1 ;
int automask=1 ; /* allow masks as input 14 Jul 2010 [rickr] */
THD_3dim_dataset *aset , *bset ;
byte *amm , *bmm ; int naa , nbb , nabu,nabi , naout , nbout ;
float paout , pbout , xrat,yrat,zrat ;
float_triple axyz , bxyz ;
/*-- read command line arguments --*/
if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ){
printf(
"Usage: 3dABoverlap [options] A B\n"
"Output (to screen) is a count of various things about how\n"
"the automasks of datasets A and B overlap or don't overlap.\n"
"\n"
"* Dataset B will be resampled to match dataset A, if necessary,\n"
" which will be slow if A is high resolution. In such a case,\n"
" you should only use one sub-brick from dataset B.\n"
" ++ The resampling of B is done before the automask is generated.\n"
"* The values output are labeled thusly:\n"
" #A = number of voxels in the A mask\n"
" #B = number of voxels in the B mask\n"
" #(A uni B) = number of voxels in the either or both masks (set union)\n"
" #(A int B) = number of voxels present in BOTH masks (set intesection)\n"
" #(A \\ B) = number of voxels in A mask that aren't in B mask\n"
" #(B \\ A) = number of voxels in B mask that arent' in A mask\n"
" %%(A \\ B) = percentage of voxels from A mask that aren't in B mask\n"
" %%(B \\ A) = percentage of voxels from B mask that aren't in A mask\n"
" Rx(B/A) = radius of gyration of B mask / A mask, in x direction\n"
" Ry(B/A) = radius of gyration of B mask / A mask, in y direction\n"
" Rz(B/A) = radius of gyration of B mask / A mask, in z direction\n"
"* If B is an EPI dataset sub-brick, and A is a skull stripped anatomical\n"
" dataset, then %%(B \\ A) might be useful for assessing if the EPI\n"
" brick B is grossly misaligned with respect to the anatomical brick A.\n"
"* The radius of gyration ratios might be useful for determining if one\n"
" dataset is grossly larger or smaller than the other.\n"
"\n"
"OPTIONS\n"
"-------\n"
" -no_automask = consider input datasets as masks\n"
" (automask does not work on mask datasets)\n"
" -quiet = be as quiet as possible (without being entirely mute)\n"
" -verb = print out some progress reports (to stderr)\n"
"\n"
"NOTES\n"
"-----\n"
" * If an input dataset is comprised of bytes and contains only one\n"
" sub-brick, then this program assumes it is already an automask-\n"
" generated dataset and the automask operation will be skipped.\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
iarg = 1 ;
/*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/
/* check options */
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-verb") == 0 ){
verb++ ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-quiet") == 0 ){
verb = 0 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-no_automask") == 0 ){
automask = 0 ; iarg++ ; continue ;
}
ERROR_exit("Illegal option: %s",argv[iarg]) ;
}
mainENTRY("3dOverlap main") ; machdep() ;
if( verb ) PRINT_VERSION("3dOverlap") ;
AFNI_logger("3dOverlap",argc,argv) ;
/* input datasets */
if( iarg+1 >= argc ) ERROR_exit("Need 2 input datasets on command line") ;
aset = THD_open_dataset(argv[iarg]) ; CHECK_OPEN_ERROR(aset,argv[iarg]) ; iarg++ ;
bset = THD_open_dataset(argv[iarg]) ; CHECK_OPEN_ERROR(bset,argv[iarg]) ; iarg++ ;
nvox = DSET_NVOX(aset) ;
if( !EQUIV_GRIDS(aset,bset) ){ /** must resample **/
THD_3dim_dataset *cset ;
if( verb ) INFO_message("resampling dataset B to match dataset A") ;
cset = r_new_resam_dset( bset, aset, 0.0,0.0,0.0,NULL,
MRI_BILINEAR, NULL, 1, 0 ) ;
DSET_delete(bset) ; bset = cset ;
}
if( iarg < argc ) WARNING_message("Extra arguments?") ;
DSET_load(aset); CHECK_LOAD_ERROR(aset);
DSET_load(bset); CHECK_LOAD_ERROR(bset);
/* 10 Aug 2009: keep input datasets without automask, if appropriate */
if( DSET_NVALS(aset) > 1 || DSET_BRICK_TYPE(aset,0) != MRI_byte ){
/* allow masks as input (via -no_automask) 14 Jul 2010 [rickr] */
if( automask ) amm = THD_automask(aset);
else amm = THD_makemask(aset, 0, 1, 0); /* use any non-zero */
DSET_unload(aset);
} else {
amm = DSET_BRICK_ARRAY(aset,0) ;
}
if( DSET_NVALS(bset) > 1 || DSET_BRICK_TYPE(bset,0) != MRI_byte ){
/* allow masks as input (via -no_automask) 14 Jul 2010 [rickr] */
if( automask ) bmm = THD_automask(bset);
else bmm = THD_makemask(bset, 0, 1, 0); /* use any non-zero */
DSET_unload(bset);
} else {
bmm = DSET_BRICK_ARRAY(bset,0) ;
}
naa = mask_count ( nvox , amm ) ;
nbb = mask_count ( nvox , bmm ) ;
nabi = mask_intersect_count( nvox , amm , bmm ) ;
nabu = mask_union_count ( nvox , amm , bmm ) ;
naout = naa - nabi ;
nbout = nbb - nabi ;
paout = (naa > 0) ? naout/(float)naa : 0.0f ;
pbout = (nbb > 0) ? nbout/(float)nbb : 0.0f ;
axyz = mask_rgyrate( DSET_NX(aset),DSET_NY(aset),DSET_NZ(aset) , amm ) ;
bxyz = mask_rgyrate( DSET_NX(bset),DSET_NY(bset),DSET_NZ(bset) , bmm ) ;
xrat = (axyz.a > 0.0f && bxyz.a > 0.0f) ? bxyz.a / axyz.a : 0.0f ;
yrat = (axyz.b > 0.0f && bxyz.b > 0.0f) ? bxyz.b / axyz.b : 0.0f ;
zrat = (axyz.c > 0.0f && bxyz.c > 0.0f) ? bxyz.c / axyz.c : 0.0f ;
if( verb )
printf("#A=%s B=%s\n",DSET_BRIKNAME(aset),DSET_BRIKNAME(bset)) ;
if( verb )
printf("#A #B #(A uni B) #(A int B) "
"#(A \\ B) #(B \\ A) %%(A \\ B) %%(B \\ A) "
"Rx(B/A) Ry(B/A) Rz(B/A)\n") ;
printf("%-12d %-12d %-12d %-12d %-12d %-12d %7.4f %7.4f %7.4f %7.4f %7.4f\n",
naa , nbb , nabu, nabi, naout,nbout,100.0f*paout,100.0f*pbout,
xrat,yrat,zrat ) ;
exit(0) ;
}
int
main (int argc, char *argv[])
{
THD_3dim_dataset *old_dset, *new_dset, *I0_dset; /* input and output datasets */
int nopt, nbriks, nvox;
int i;
MRI_IMAGE *grad1Dptr = NULL;
MRI_IMAGE *anat_im = NULL;
MRI_IMAGE *data_im = NULL;
double fac;
short *sar = NULL, *tempsptr = NULL, tempval;
byte *maskptr = NULL, *tempbptr = NULL;
char tempstr[25];
/*----- Read command line -----*/
if (argc < 2 || strcmp (argv[1], "-help") == 0)
{
printf ("Usage: 3dDTtoDWI [options] gradient-file I0-dataset DT-dataset\n"
"Computes multiple gradient images from 6 principle direction tensors and\n"
" corresponding gradient vector coordinates applied to the I0-dataset.\n"
" The program takes three parameters as input : \n"
" a 1D file of the gradient vectors with lines of ASCII floats Gxi,Gyi,Gzi.\n"
" Only the non-zero gradient vectors are included in this file (no G0 line).\n"
" The I0 dataset is a volume without any gradient applied.\n"
" The DT dataset is the 6-sub-brick dataset containing the diffusion tensor data,\n"
" Dxx, Dxy, Dyy, Dxz, Dyz, Dzz (lower triangular row-wise order)\n"
" Options:\n"
" -prefix pname = Use 'pname' for the output dataset prefix name.\n"
" [default='DWI']\n"
" -automask = mask dataset so that the gradient images are computed only for\n"
" high-intensity (presumably brain) voxels. The intensity level is\n"
" determined the same way that 3dClipLevel works.\n\n"
" -datum type = output dataset type [float/short/byte] (default is float).\n"
" -help = show this help screen.\n"
" Example:\n"
" 3dDTtoDWI -prefix DWI -automask tensor25.1D 'DT+orig[26]' DT+orig.\n\n"
" The output is a n sub-brick bucket dataset containing computed DWI images.\n"
" where n is the number of vectors in the gradient file + 1\n"
"\n");
printf ("\n" MASTER_SHORTHELP_STRING);
exit (0);
}
mainENTRY ("3dDTtoDWI main");
machdep ();
AFNI_logger ("3dDTtoDWI", argc, argv);
PRINT_VERSION("3dDTtoDWI") ;
nopt = 1;
datum = MRI_float;
while (nopt < argc && argv[nopt][0] == '-')
{
/*-- prefix --*/
if (strcmp (argv[nopt], "-prefix") == 0)
{
if (++nopt >= argc)
{
fprintf (stderr, "*** Error - prefix needs an argument!\n");
exit (1);
}
MCW_strncpy (prefix, argv[nopt], THD_MAX_PREFIX); /* change name from default prefix */
/* check file name to be sure not to overwrite - mod drg 12/9/2004 */
if (!THD_filename_ok (prefix))
{
fprintf (stderr, "*** Error - %s is not a valid prefix!\n", prefix);
exit (1);
}
nopt++;
continue;
}
/*-- datum --*/
if (strcmp (argv[nopt], "-datum") == 0)
{
if (++nopt >= argc)
{
fprintf (stderr, "*** Error - datum needs an argument!\n");
exit (1);
}
if (strcmp (argv[nopt], "short") == 0)
{
datum = MRI_short;
}
else if (strcmp (argv[nopt], "float") == 0)
{
datum = MRI_float;
}
else if (strcmp (argv[nopt], "byte") == 0)
{
datum = MRI_byte;
}
else
{
fprintf (stderr, "-datum of type '%s' is not supported!\n",
argv[nopt]);
exit (1);
}
nopt++;
continue;
}
if (strcmp (argv[nopt], "-automask") == 0)
{
automask = 1;
nopt++;
continue;
}
fprintf(stderr, "*** Error - unknown option %s\n", argv[nopt]);
exit(1);
}
/*----- read input datasets -----*/
if (nopt >= argc)
{
fprintf (stderr, "*** Error - No input dataset!?\n");
exit (1);
}
/* first input dataset - should be gradient vector file of ascii floats Gx,Gy,Gz */
/* read gradient vector 1D file */
grad1Dptr = mri_read_1D (argv[nopt]);
if (grad1Dptr == NULL)
{
fprintf (stderr, "*** Error reading gradient vector file\n");
exit (1);
}
if (grad1Dptr->ny != 3)
{
fprintf (stderr, "*** Error - Only 3 columns of gradient vectors allowed\n");
fprintf (stderr, "%d columns found\n", grad1Dptr->nx);
mri_free (grad1Dptr);
exit (1);
}
if (grad1Dptr->nx < 6)
{
fprintf (stderr, "*** Error - Must have at least 6 gradient vectors\n");
fprintf (stderr, "%d columns found\n", grad1Dptr->nx);
mri_free (grad1Dptr);
exit (1);
}
nbriks = grad1Dptr->nx + 1; /* number of gradients specified here from file */
nopt++;
/* open I0 dataset - idealized no gradient image */
I0_dset = THD_open_dataset (argv[nopt]);
CHECK_OPEN_ERROR(I0_dset,argv[nopt]) ;
DSET_mallocize (I0_dset);
DSET_load (I0_dset); /* load dataset */
data_im = DSET_BRICK (I0_dset, 0); /* set pointer to the 0th sub-brik of the dataset */
fac = DSET_BRICK_FACTOR(I0_dset, 0); /* get scale factor for each sub-brik*/
if(fac==0.0) fac=1.0;
if((data_im->kind != MRI_float)) {
fprintf (stderr, "*** Error - Can only open float datasets. Use 3dcalc to convert.\n");
mri_free (grad1Dptr);
mri_free (data_im);
exit (1);
}
I0_ptr = mri_data_pointer(data_im) ; /* pointer to I0 data */
nopt++;
/* Now read in all the MRI volumes for each gradient vector */
/* assumes first one is no gradient */
old_dset = THD_open_dataset (argv[nopt]);
CHECK_OPEN_ERROR(old_dset,argv[nopt]) ;
/* expect at least 6 values per voxel - 6 sub-briks as input dataset */
if (DSET_NVALS (old_dset) <6)
{
fprintf (stderr,
"*** Error - Dataset must have at least 6 sub-briks to describe the diffusion tensor\n");
mri_free (grad1Dptr);
mri_free (data_im);
exit (1);
}
InitGlobals (grad1Dptr->nx + 1); /* initialize all the matrices and vectors */
Computebmatrix (grad1Dptr, BMAT_NZ); /* compute bij=GiGj */
INFO_message("The maximum magnitude of the bmatrix appears to be: %.2f", MAX_BVAL);
if (automask)
{
DSET_mallocize (old_dset);
DSET_load (old_dset); /* get B0 (anatomical image) from dataset */
/*anat_im = THD_extract_float_brick( 0, old_dset ); */
anat_im = DSET_BRICK (old_dset, 0); /* set pointer to the 0th sub-brik of the dataset */
maskptr = mri_automask_image (anat_im); /* maskptr is a byte pointer for volume */
/* convert byte mask to same format type as dataset */
nvox = DSET_NVOX (old_dset);
sar = (short *) calloc (nvox, sizeof (short));
/* copy maskptr values to far ptr */
tempsptr = sar;
tempbptr = maskptr;
for (i = 0; i < nvox; i++)
{
*tempsptr++ = (short) *tempbptr++;
tempval = *(tempsptr - 1);
}
free (maskptr);
/*old_dset->dblk->malloc_type = DATABLOCK_MEM_MALLOC; *//* had to set this? */
EDIT_add_brick (old_dset, MRI_short, 0.0, sar); /* add sub-brik to end */
}
/* temporarily set artificial timing to 1 second interval */
EDIT_dset_items (old_dset,
ADN_ntt, DSET_NVALS (old_dset),
ADN_ttorg, 0.0,
ADN_ttdel, 1.0, ADN_tunits, UNITS_SEC_TYPE, NULL);
/*------------- ready to compute new dataset -----------*/
new_dset = MAKER_4D_to_typed_fbuc (old_dset, /* input dataset */
prefix, /* output prefix */
datum, /* output datum */
0, /* ignore count */
0, /* can't detrend in maker function KRH 12/02 */
nbriks, /* number of briks */
DTtoDWI_tsfunc, /* timeseries processor */
NULL, /* data for tsfunc */
NULL, /* mask */
0 /* Allow auto scaling of output */
);
FreeGlobals ();
mri_free (grad1Dptr);
if (automask)
{
mri_free (anat_im);
DSET_unload_one (old_dset, 0);
sar = NULL;
}
if (new_dset != NULL)
{
tross_Copy_History (old_dset, new_dset);
for(i=0;i<nbriks;i++) {
sprintf(tempstr,"grad%3.3d", i);
EDIT_dset_items (new_dset, ADN_brick_label_one + i, tempstr, ADN_none);
}
tross_Make_History ("3dDTtoDWI", argc, argv, new_dset);
DSET_write (new_dset);
fprintf(stderr,"--- Output dataset %s\n", DSET_BRIKNAME(new_dset));
}
else
{
fprintf (stderr, "*** Error - Unable to compute output dataset!\n");
exit (1);
}
exit (0);
}
void UC_read_opts( int argc , char * argv[] )
{
int nopt = 1 ;
float val ;
int kk, nxyz, mm,nn ;
float * vv , * bb ;
while( nopt < argc && argv[nopt][0] == '-' ){
/**** -verbose ****/
if( strncmp(argv[nopt],"-verbose",5) == 0 ){
UC_be_quiet = 0 ;
nopt++ ; continue ;
}
/**** -prefix prefix ****/
if( strncmp(argv[nopt],"-prefix",6) == 0 ){
nopt++ ;
if( nopt >= argc ) UC_syntax("-prefix needs an argument!") ;
MCW_strncpy( UC_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
continue ;
}
/**** -mask mset ****/
if( strncmp(argv[nopt],"-mask",5) == 0 ){
THD_3dim_dataset * mset ; int ii,nn ;
nopt++ ;
if( nopt >= argc ) UC_syntax("need arguments after -mask!") ;
mset = THD_open_dataset( argv[nopt] ) ;
if( mset == NULL ) UC_syntax("can't open -mask dataset!") ;
UC_mask = THD_makemask( mset , 0 , 1.0,0.0 ) ;
UC_mask_nvox = DSET_NVOX(mset) ;
DSET_delete(mset) ;
if( UC_mask == NULL ) UC_syntax("can't use -mask dataset!") ;
UC_mask_hits = THD_countmask( UC_mask_nvox , UC_mask ) ;
if( UC_mask_hits == 0 ) UC_syntax("mask is all zeros!") ;
if( !UC_be_quiet ) printf("--- %d voxels in mask\n",UC_mask_hits) ;
UC_iv = (int *) malloc( sizeof(int) * UC_mask_hits ) ;
for( nn=ii=0 ; ii < UC_mask_nvox ; ii++ )
if( UC_mask[ii] ) UC_iv[nn++] = ii ;
nopt++ ; continue ;
}
/**** -ptail p ****/
if( strcmp(argv[nopt],"-ptail") == 0 ){
if( ++nopt >= argc ) UC_syntax("-ptail needs an argument!") ;
UC_ptail = strtod( argv[nopt] , NULL ) ;
if( UC_ptail <= 0.0 || UC_ptail >= 0.499 )
UC_syntax("value after -ptail is illegal!") ;
nopt++ ; continue ;
}
/**** unknown switch ****/
fprintf(stderr,"\n*** unrecognized option %s\n",argv[nopt]) ;
exit(1) ;
} /* end of loop over options */
/*--- a simple consistency check ---*/
/*--- last input is dataset name ---*/
if( nopt >= argc ) UC_syntax("no input dataset name?") ;
UC_dset = THD_open_dataset( argv[nopt] ) ;
if( !ISVALID_3DIM_DATASET(UC_dset) ){
fprintf(stderr,"\n*** can't open dataset file %s\n",argv[nopt]) ;
exit(1) ;
}
nxyz = DSET_NVOX(UC_dset) ;
if( UC_mask != NULL && nxyz != UC_mask_nvox )
UC_syntax("mask and input dataset size mismatch!") ;
/*--- load vectors ---*/
UC_nvec = (UC_mask_hits > 0) ? UC_mask_hits : nxyz ;
UC_vdim = DSET_NVALS(UC_dset) ;
if( UC_vdim < 4 )
UC_syntax("input dataset needs at least 4 sub-bricks!") ;
vv = (float *) malloc( sizeof(float) * UC_nvec * UC_vdim ) ;
UC_vec = (float **) malloc( sizeof(float *) * UC_nvec ) ;
for( kk=0 ; kk < UC_nvec ; kk++ ) UC_vec[kk] = vv + (kk*UC_vdim) ;
if( !UC_be_quiet ) printf("--- reading input dataset\n") ;
DSET_load(UC_dset) ; CHECK_LOAD_ERROR(UC_dset) ;
/* copy brick data into float storage */
if( !UC_be_quiet ) printf("--- loading vectors\n") ;
bb = (float *) malloc( sizeof(float) * nxyz ) ;
for( mm=0 ; mm < UC_vdim ; mm++ ){
EDIT_coerce_type( nxyz ,
DSET_BRICK_TYPE(UC_dset,mm) , DSET_ARRAY(UC_dset,mm) ,
MRI_float , bb ) ;
DSET_unload_one( UC_dset , mm ) ;
if( UC_mask == NULL ){
for( kk=0 ; kk < nxyz ; kk++ ) UC_vec[kk][mm] = bb[kk] ;
} else {
for( nn=kk=0 ; kk < nxyz ; kk++ )
if( UC_mask[kk] ) UC_vec[nn++][mm] = bb[kk] ;
}
}
free(bb) ; DSET_unload( UC_dset ) ;
/* detrend and normalize vectors */
if( !UC_be_quiet ) printf("--- normalizing vectors\n") ;
for( kk=0 ; kk < UC_nvec ; kk++ )
normalize( UC_vdim , UC_vec[kk] ) ;
return ;
}
void DT_read_opts( int argc , char * argv[] )
{
int nopt = 1 , nvals , ii , nvcheck , nerr=0 ;
MRI_IMARR *slice_imar ;
INIT_IMARR(DT_imar) ;
INIT_IMARR(slice_imar) ;
while( nopt < argc && argv[nopt][0] == '-' ){
/**** -polort p ****/
if( strncmp(argv[nopt],"-polort",6) == 0 ){
char *cpt ;
nopt++ ;
if( nopt >= argc ) ERROR_exit("Need argument after -polort") ;
DT_polort = (int)strtod(argv[nopt],&cpt) ;
if( *cpt != '\0' ) WARNING_message("Illegal non-numeric value after -polort") ;
if( DT_polort < 0 )
WARNING_message("Ignoring negative value after -polort") ;
nopt++ ; continue ;
}
/**** -prefix prefix ****/
if( strncmp(argv[nopt],"-prefix",6) == 0 ){
nopt++ ;
if( nopt >= argc ) ERROR_exit("Need argument after -prefix") ;
MCW_strncpy( DT_output_prefix , argv[nopt] , THD_MAX_PREFIX ) ;
if( !THD_filename_ok(DT_output_prefix) )
ERROR_exit("bad name '%s' after -prefix",argv[nopt]) ;
nopt++ ; continue ;
}
/**** -session directory ****/
if( strncmp(argv[nopt],"-session",6) == 0 ){
nopt++ ;
if( nopt >= argc ) ERROR_exit("Need argument after -session") ;
MCW_strncpy( DT_session , argv[nopt] , THD_MAX_NAME ) ;
if( !THD_filename_ok(DT_session) )
ERROR_exit("bad name '%s' after -session",argv[nopt]) ;
nopt++ ; continue ;
}
/**** -verb ****/
if( strncmp(argv[nopt],"-verb",5) == 0 ){
DT_verb++ ; nopt++ ; continue ;
}
/**** -replace ****/
if( strncmp(argv[nopt],"-replace",5) == 0 ){
DT_replace++ ; nopt++ ; continue ;
}
/**** -byslice [08 Dec 1999] ****/
if( strncmp(argv[nopt],"-byslice",5) == 0 ){
#ifdef ALLOW_BYSLICE
if( IMARR_COUNT(slice_imar) > 0 )
ERROR_exit("can't mix -byslice and -slicevector") ;
DT_byslice++ ; nopt++ ; continue ;
#else
ERROR_exit("-byslice is no longer suppported") ;
#endif
}
/**** -normalize [23 Nov 1999] ****/
if( strncmp(argv[nopt],"-normalize",5) == 0 ){
DT_norm++ ; nopt++ ; continue ;
}
/**** -vector ****/
if( strncmp(argv[nopt],"-vector",4) == 0 ){
MRI_IMAGE * flim ;
nopt++ ;
if( nopt >= argc ) ERROR_exit("need argument after -vector") ;
flim = mri_read_1D( argv[nopt++] ) ;
if( flim == NULL ) ERROR_exit("can't read -vector '%s'",argv[nopt-1]) ;
ADDTO_IMARR(DT_imar,flim) ;
if( DT_verb ) INFO_message("Read file %s: rows=%d cols=%d",
argv[nopt-1],flim->ny,flim->nx ) ;
continue ;
}
/**** -slicevector ****/
if( strncmp(argv[nopt],"-slicevector",6) == 0 ){
MRI_IMAGE *flim ;
nopt++ ;
if( nopt >= argc ) ERROR_exit("need argument after -slicevector") ;
#ifdef ALLOW_BYSLICE
if( DT_byslice ) ERROR_exit("can't mix -slicevector and -byslice") ;
#endif
flim = mri_read_1D( argv[nopt++] ) ;
if( flim == NULL ) ERROR_exit("can't read -slicevector '%s'",argv[nopt-1]) ;
ADDTO_IMARR(slice_imar,flim) ;
if( DT_verb ) INFO_message("Read file %s: rows=%d cols=%d",
argv[nopt-1],flim->ny,flim->nx ) ;
continue ;
}
/**** -del ****/
if( strncmp(argv[nopt],"-del",4) == 0 ){
nopt++ ;
if( nopt >= argc ) ERROR_exit("need argument after -del") ;
DT_current_del = strtod( argv[nopt++] , NULL ) ;
if( DT_verb )
INFO_message("Set expression stepsize = %g\n",DT_current_del) ;
continue ;
}
/**** -expr ****/
if( strncmp(argv[nopt],"-expr",4) == 0 ){
int nexp , qvar , kvar ;
char sym[4] ;
nopt++ ;
if( nopt >= argc ) ERROR_exit("need argument after -expr") ;
nexp = DT_exnum + 1 ;
if( DT_exnum == 0 ){ /* initialize storage */
DT_expr = (char **) malloc( sizeof(char *) ) ;
DT_excode = (PARSER_code **) malloc( sizeof(PARSER_code *) ) ;
DT_exdel = (float *) malloc( sizeof(float) ) ;
DT_exvar = (int *) malloc( sizeof(int) ) ;
} else {
DT_expr = (char **) realloc( DT_expr ,
sizeof(char *)*nexp ) ;
DT_excode = (PARSER_code **) realloc( DT_excode ,
sizeof(PARSER_code *)*nexp ) ;
DT_exdel = (float *) realloc( DT_exdel ,
sizeof(float)*nexp) ;
DT_exvar = (int *) realloc( DT_exvar ,
sizeof(int)*nexp) ;
}
DT_expr[DT_exnum] = argv[nopt] ; /* string */
DT_exdel[DT_exnum] = DT_current_del ; /* delta */
DT_excode[DT_exnum] = PARSER_generate_code( argv[nopt] ) ; /* compile */
if( DT_excode[DT_exnum] == NULL )
ERROR_exit("Illegal expression: '%s'",argv[nopt]) ;
qvar = 0 ; kvar = -1 ; /* find symbol */
for( ii=0 ; ii < 26 ; ii++ ){
sym[0] = 'A' + ii ; sym[1] = '\0' ;
if( PARSER_has_symbol(sym,DT_excode[DT_exnum]) ){
qvar++ ; if( kvar < 0 ) kvar = ii ;
if( DT_verb )
INFO_message("Found expression symbol %s\n",sym) ;
}
}
if( qvar > 1 )
ERROR_exit("-expr '%s' has too many symbols",DT_expr[DT_exnum]) ;
else if( qvar == 0 )
WARNING_message("-expr '%s' is constant",DT_expr[DT_exnum]) ;
DT_exvar[DT_exnum] = kvar ;
DT_exnum = nexp ; nopt++ ; continue ;
}
/**** ERROR ****/
ERROR_exit("Unknown option: %s\n",argv[nopt]) ;
} /* end of scan over options */
/*-- check for errors --*/
if( nopt >= argc ) ERROR_exit("No input dataset?!") ;
#ifdef ALLOW_BYSLICE
if( IMARR_COUNT(slice_imar) > 0 && DT_byslice )
ERROR_exit("Illegal mixing of -slicevector and -byslice") ;
#endif
DT_nvector = IMARR_COUNT(DT_imar) ;
if( DT_nvector + DT_exnum == 0 && DT_polort < 0 )
ERROR_exit("No detrending options ordered!") ;
#ifdef ALLOW_BYSLICE
if( DT_nvector == 0 && DT_byslice )
ERROR_exit("No -vector option supplied with -byslice!") ;
#endif
/*--- read input dataset ---*/
DT_dset = THD_open_dataset( argv[nopt] ) ;
CHECK_OPEN_ERROR(DT_dset,argv[nopt]) ;
if( DT_dset == NULL )
ERROR_exit("Can't open dataset %s\n",argv[nopt]) ;
DT_current_del = DSET_TR(DT_dset) ;
if( DT_current_del <= 0.0 ){
DT_current_del = 1.0 ;
if( DT_verb )
WARNING_message("Input has no TR value; setting TR=1.0\n") ;
} else if( DT_verb ){
INFO_message("Input has TR=%g\n",DT_current_del) ;
}
/*-- check vectors for good size --*/
nvcheck = nvals = DSET_NVALS(DT_dset) ;
#ifdef ALLOW_BYSLICE
if( DT_byslice ) nvcheck *= DSET_NZ(DT_dset) ;
#endif
for( ii=0 ; ii < DT_nvector ; ii++ ){
if( IMARR_SUBIMAGE(DT_imar,ii)->nx < nvcheck ){
ERROR_message("%d-th -vector is shorter (%d) than dataset (%d)",
ii+1,IMARR_SUBIMAGE(DT_imar,ii)->nx,nvcheck) ;
nerr++ ;
}
}
if( nerr > 0 ) ERROR_exit("Cannot continue") ;
/*--- create time series from expressions */
if( DT_exnum > 0 ){
double atoz[26] , del ;
int kvar , jj ;
MRI_IMAGE *flim ;
float *flar ;
for( jj=0 ; jj < DT_exnum ; jj++ ){
if( DT_verb ) INFO_message("Evaluating %d-th -expr\n",jj+1) ;
kvar = DT_exvar[jj] ;
del = DT_exdel[jj] ;
if( del <= 0.0 ) del = DT_current_del ;
flim = mri_new( nvals , 1 , MRI_float ) ;
flar = MRI_FLOAT_PTR(flim) ;
for( ii=0 ; ii < 26 ; ii++ ) atoz[ii] = 0.0 ;
for( ii=0 ; ii < nvals ; ii++ ){
if( kvar >= 0 ) atoz[kvar] = ii * del ;
flar[ii] = PARSER_evaluate_one( DT_excode[jj] , atoz ) ;
}
ADDTO_IMARR( DT_imar , flim ) ;
}
}
/*--- from polort [10 Apr 2006] ---*/
if( DT_polort >= 0 ){
int kk ;
MRI_IMAGE *flim ;
float *flar ; double fac=2.0/(nvals-1.0) ;
for( kk=0 ; kk <= DT_polort ; kk++ ){
flim = mri_new( nvals , 1 , MRI_float ) ;
flar = MRI_FLOAT_PTR(flim) ;
for( ii=0 ; ii < nvals ; ii++ ) flar[ii] = Plegendre(fac*ii-1.0,kk) ;
ADDTO_IMARR( DT_imar , flim ) ;
}
}
return ;
}
int main( int argc , char * argv[] )
{
int iarg ;
THD_3dim_dataset *inset , *outset ;
int add_I=0 , add_S=0 , add_A=0 , add_P=0 , add_L=0 , add_R=0 ;
int RLsiz=0, APsiz=0, ISsiz=0 ; /* 23 Mar 2004 */
char * prefix="zeropad" ;
int add_z=0 ; /* 07 Feb 2001 */
int mm_flag=0 ; /* 13 Feb 2001 */
int flag ;
THD_3dim_dataset *mset=NULL ; /* 14 May 2002 */
/*-- help? --*/
mainENTRY("3dZeropad main"); machdep(); AFNI_logger("3dZeropad",argc,argv);
PRINT_VERSION("3dZeropad") ;
/*-- read command line options --*/
if( argc == 1){ usage_3dZeropad(1); exit(0); } /* Bob's help shortcut */
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){
usage_3dZeropad(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
/*- -I, -S, etc. -*/
if( strlen(argv[iarg]) == 2 ){
switch( argv[iarg][1] ){
case 'I': add_I = (int) strtod(argv[++iarg],NULL) ; break ;
case 'S': add_S = (int) strtod(argv[++iarg],NULL) ; break ;
case 'A': add_A = (int) strtod(argv[++iarg],NULL) ; break ;
case 'P': add_P = (int) strtod(argv[++iarg],NULL) ; break ;
case 'L': add_L = (int) strtod(argv[++iarg],NULL) ; break ;
case 'R': add_R = (int) strtod(argv[++iarg],NULL) ; break ;
/* 07 Feb 2001: slice-direction is special */
case 'z':
case 'Z': add_z = (int) strtod(argv[++iarg],NULL) ; break ;
default:
fprintf(stderr,"** 3dZeropad: Illegal option: %s\n",argv[iarg]) ; exit(1) ;
}
if( mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use %s with -master!\n",argv[iarg-1]) ;
exit(1) ;
}
iarg++ ; continue ; /* skip to next argument */
}
/*- -RL, -AP, -IS [23 Mar 2004] -*/
if( strcmp(argv[iarg],"-RL") == 0 || strcmp(argv[iarg],"-LR") == 0 ){
if( add_R || add_L || mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use -RL with -R, -L, or -master!\n");
exit(1) ;
}
RLsiz = (int) strtod(argv[++iarg],NULL) ;
if( RLsiz < 1 ){
fprintf(stderr,"** 3dZeropad: value after -RL is illegal!\n") ;
exit(1) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-AP") == 0 || strcmp(argv[iarg],"-PA") == 0 ){
if( add_A || add_P || mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use -AP with -A, -P, or -master!\n");
exit(1) ;
}
APsiz = (int) strtod(argv[++iarg],NULL) ;
if( APsiz < 1 ){
fprintf(stderr,"** 3dZeropad: value after -AP is illegal!\n") ;
exit(1) ;
}
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-IS") == 0 || strcmp(argv[iarg],"-SI") == 0 ){
if( add_S || add_I || mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use -IS with -I, -S, or -master!\n");
exit(1) ;
}
ISsiz = (int) strtod(argv[++iarg],NULL) ;
if( ISsiz < 1 ){
fprintf(stderr,"** 3dZeropad: value after -IS is illegal!\n") ;
exit(1) ;
}
iarg++ ; continue ;
}
/*- -mm -*/
if( strcmp(argv[iarg],"-mm") == 0 ){
if( mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use %s with -master!\n",argv[iarg]) ;
exit(1) ;
}
mm_flag = 1 ;
iarg++ ; continue ;
}
/*- -prefix -*/
if( strcmp(argv[iarg],"-prefix") == 0 ){
prefix = argv[++iarg] ;
if( !THD_filename_ok(prefix) ){
fprintf(stderr,"** 3dZeropad: Illegal string after -prefix!\n"); exit(1) ;
}
iarg++ ; continue ;
}
/*-- -master [14 May 2002] --*/
if( strcmp(argv[iarg],"-master") == 0 ){
if( add_I || add_S || add_A || mm_flag ||
add_P || add_R || add_L || add_z ||
RLsiz || APsiz || ISsiz ){
fprintf(stderr,"** 3dZeropad: Can't use -master with -I,-S,-A,-P,-R,-L, or -mm!\n");
exit(1) ;
}
if( mset != NULL ){
fprintf(stderr,"** 3dZeropad: Can't use -master twice!\n"); exit(1);
}
mset = THD_open_dataset( argv[++iarg] ) ;
if( !ISVALID_DSET(mset) ){
fprintf(stderr,"** 3dZeropad: Can't open -master %s\n",argv[iarg]); exit(1);
}
THD_make_cardinal(mset); /* deoblique 21 Oct, 2011 [rickr] */
iarg++ ; continue ;
}
/*- what the hell? -*/
fprintf(stderr,"** 3dZeropad: Illegal option: %s\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1) ;
}
if (iarg < 2) {
ERROR_message("Too few options, try %s -help for details\n",argv[0]);
exit(1);
}
/*- check to see if the user asked for something, anything -*/
if( mset == NULL ){
if( add_I==0 && add_S==0 && add_P==0 &&
add_A==0 && add_L==0 && add_R==0 && add_z==0 &&
RLsiz==0 && APsiz==0 && ISsiz==0 ){
fprintf(stderr,"++ 3dZeropad: All inputs are zero? Making a copy!\n") ;
}
}
/* check for conflicts [23 Mar 2004] */
if( RLsiz > 0 && (add_R || add_L || add_z) ){
fprintf(stderr,"** 3dZeropad: Can't use -R or -L or -z with -RL!\n"); exit(1);
}
if( APsiz > 0 && (add_A || add_P || add_z) ){
fprintf(stderr,"** 3dZeropad: Can't use -A or -P or -z with -AP!\n"); exit(1);
}
if( ISsiz > 0 && (add_I || add_S || add_z) ){
fprintf(stderr,"** 3dZeropad: Can't use -I or -S or -z with -IS!\n"); exit(1);
}
/*-- read the input dataset --*/
if( iarg >= argc ){
fprintf(stderr,"** 3dZeropad: No input dataset on command line!\n"); exit(1);
}
#if 0
if( strncmp(argv[iarg],"3dcalc(",7) == 0 ){
fprintf(stderr,"** 3dZeropad: Can't use '3dcalc()' input datasets here!\n"); exit(1);
}
#endif
inset = THD_open_dataset( argv[iarg] ) ;
if( inset == NULL ){
fprintf(stderr,"** 3dZeropad: Can't open dataset %s\n",argv[iarg]); exit(1);
}
THD_make_cardinal(inset); /* deoblique 21 Oct, 2011 [rickr] */
#if 0
if( DSET_IS_MASTERED(inset) ){
fprintf(stderr,"** 3dZeropad: Can't use partial datasets!\n"); exit(1);
}
#endif
/*-- 14 May 2002: use master dataset now? --*/
if( mset != NULL ){
THD_dataxes *max=mset->daxes, *iax=inset->daxes ;
int nerr=0 ;
float mxbot,mybot,mzbot , mxtop,mytop,mztop , mdx,mdy,mdz ;
float ixbot,iybot,izbot , ixtop,iytop,iztop , idx,idy,idz ;
int mnx,mny,mnz , inx,iny,inz ;
int add_xb,add_xt , add_yb,add_yt , add_zb,add_zt ;
/* check if datasets are oriented the same */
if( max->xxorient != iax->xxorient ||
max->yyorient != iax->yyorient ||
max->zzorient != iax->zzorient ){
fprintf(stderr,
"** 3dZeropad: Master (%s) and Input (%s) dataset not oriented the same!\n",
DSET_PREFIX(mset), DSET_PREFIX(inset));
nerr++ ;
}
/* check if datasets have same voxel dimensions */
mdx = max->xxdel ; mdy = max->yydel ; mdz = max->zzdel ;
idx = iax->xxdel ; idy = iax->yydel ; idz = iax->zzdel ;
mnx = max->nxx ; mny = max->nyy ; mnz = max->nzz ;
inx = iax->nxx ; iny = iax->nyy ; inz = iax->nzz ;
if( fabs(mdx-idx) > 0.01*fabs(mdx) ||
fabs(mdy-idy) > 0.01*fabs(mdy) ||
fabs(mdz-idz) > 0.01*fabs(mdz) ){
fprintf(stderr,"** 3dZeropad: Master and Input datasets don't have same voxel size!\n");
nerr++ ;
}
if( nerr ) exit(1) ;
/* calculate coords at top and bottom of each dataset */
mxbot = max->xxorg ; mxtop = mxbot + mnx*mdx ;
mybot = max->yyorg ; mytop = mybot + mny*mdy ;
mzbot = max->zzorg ; mztop = mzbot + mnz*mdz ;
ixbot = iax->xxorg ; ixtop = ixbot + inx*idx ;
iybot = iax->yyorg ; iytop = iybot + iny*idy ;
izbot = iax->zzorg ; iztop = izbot + inz*idz ;
/* calculate amount to add/trim at each face */
add_xb = (int) rint((ixbot-mxbot)/idx) ;
add_xt = (int) rint((mxtop-ixtop)/idx) ;
add_yb = (int) rint((iybot-mybot)/idy) ;
add_yt = (int) rint((mytop-iytop)/idy) ;
add_zb = (int) rint((izbot-mzbot)/idz) ;
add_zt = (int) rint((mztop-iztop)/idz) ;
/* map trims from x,y,z to RL,AP,IS coords */
switch( iax->xxorient ){
case ORI_R2L_TYPE: add_R = add_xb ; add_L = add_xt ; break ;
case ORI_L2R_TYPE: add_L = add_xb ; add_R = add_xt ; break ;
case ORI_I2S_TYPE: add_I = add_xb ; add_S = add_xt ; break ;
case ORI_S2I_TYPE: add_S = add_xb ; add_I = add_xt ; break ;
case ORI_A2P_TYPE: add_A = add_xb ; add_P = add_xt ; break ;
case ORI_P2A_TYPE: add_P = add_xb ; add_A = add_xt ; break ;
}
switch( iax->yyorient ){
case ORI_R2L_TYPE: add_R = add_yb ; add_L = add_yt ; break ;
case ORI_L2R_TYPE: add_L = add_yb ; add_R = add_yt ; break ;
case ORI_I2S_TYPE: add_I = add_yb ; add_S = add_yt ; break ;
case ORI_S2I_TYPE: add_S = add_yb ; add_I = add_yt ; break ;
case ORI_A2P_TYPE: add_A = add_yb ; add_P = add_yt ; break ;
case ORI_P2A_TYPE: add_P = add_yb ; add_A = add_yt ; break ;
}
switch( iax->zzorient ){
case ORI_R2L_TYPE: add_R = add_zb ; add_L = add_zt ; break ;
case ORI_L2R_TYPE: add_L = add_zb ; add_R = add_zt ; break ;
case ORI_I2S_TYPE: add_I = add_zb ; add_S = add_zt ; break ;
case ORI_S2I_TYPE: add_S = add_zb ; add_I = add_zt ; break ;
case ORI_A2P_TYPE: add_A = add_zb ; add_P = add_zt ; break ;
case ORI_P2A_TYPE: add_P = add_zb ; add_A = add_zt ; break ;
}
fprintf(stderr,"++ 3dZeropad -master => -I %d -S %d -A %d -P %d -R %d -L %d\n",
add_I,add_S,add_A,add_P,add_R,add_L ) ;
DSET_delete(mset) ;
}
/*-- 07 Feb 2001: if -z was used, fix that now --*/
if( add_z != 0 ){
switch( inset->daxes->zzorient ){
case ORI_R2L_TYPE:
case ORI_L2R_TYPE:
if( add_R != 0 && add_R != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -R\n");
if( add_L != 0 && add_L != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -L\n");
add_R = add_L = add_z ;
break ;
case ORI_P2A_TYPE:
case ORI_A2P_TYPE:
if( add_P != 0 && add_P != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -P\n");
if( add_A != 0 && add_A != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -A\n");
add_P = add_A = add_z ;
break ;
case ORI_I2S_TYPE:
case ORI_S2I_TYPE:
if( add_I != 0 && add_I != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -I\n");
if( add_I != 0 && add_S != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -S\n");
add_I = add_S = add_z ;
break ;
}
}
/*-- 23 Mar 2004: expand/contract if ordered --*/
if( RLsiz > 0 ){
int nold=0 ;
if( inset->daxes->xxorient == ORI_R2L_TYPE || inset->daxes->xxorient == ORI_L2R_TYPE )
nold = inset->daxes->nxx ;
else if( inset->daxes->yyorient == ORI_R2L_TYPE || inset->daxes->yyorient == ORI_L2R_TYPE )
nold = inset->daxes->nyy ;
else if( inset->daxes->zzorient == ORI_R2L_TYPE || inset->daxes->zzorient == ORI_L2R_TYPE )
nold = inset->daxes->nzz ;
if( nold > 0 ){
add_R = (RLsiz-nold) / 2 ;
add_L = RLsiz-(nold+add_R) ;
}
}
if( APsiz > 0 ){
int nold=0 ;
if( inset->daxes->xxorient == ORI_A2P_TYPE || inset->daxes->xxorient == ORI_P2A_TYPE )
nold = inset->daxes->nxx ;
else if( inset->daxes->yyorient == ORI_A2P_TYPE || inset->daxes->yyorient == ORI_P2A_TYPE )
nold = inset->daxes->nyy ;
else if( inset->daxes->zzorient == ORI_A2P_TYPE || inset->daxes->zzorient == ORI_P2A_TYPE )
nold = inset->daxes->nzz ;
if( nold > 0 ){
add_A = (APsiz-nold) / 2 ;
add_P = APsiz-(nold+add_A) ;
}
}
if( ISsiz > 0 ){
int nold=0 ;
if( inset->daxes->xxorient == ORI_I2S_TYPE || inset->daxes->xxorient == ORI_S2I_TYPE )
nold = inset->daxes->nxx ;
else if( inset->daxes->yyorient == ORI_I2S_TYPE || inset->daxes->yyorient == ORI_S2I_TYPE )
nold = inset->daxes->nyy ;
else if( inset->daxes->zzorient == ORI_I2S_TYPE || inset->daxes->zzorient == ORI_S2I_TYPE )
nold = inset->daxes->nzz ;
if( nold > 0 ){
add_I = (ISsiz-nold) / 2 ;
add_S = ISsiz-(nold+add_I) ;
}
}
/*-- 04 Oct 2000: all the real work is now in thd_zeropad.c --*/
flag = ZPAD_PURGE ;
if( mm_flag ) flag |= ZPAD_MM ;
outset = THD_zeropad( inset ,
add_I, add_S, add_A, add_P, add_L, add_R,
prefix , flag ) ;
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(outset)) ){
fprintf(stderr,
"** 3dZeropad: output file %s already exists - FATAL ERROR!\n",
DSET_HEADNAME(outset) ) ;
exit(1) ;
}
if( outset == NULL ){
fprintf(stderr,"** 3dZeropad: Some error occurred in processing!\n") ;
exit(1) ;
}
tross_Copy_History( inset , outset ) ; /* 31 Jan 2001 - RWCox */
tross_Make_History( "3dZeropad" , argc,argv , outset ) ;
if (DSET_write(outset) != False) {
fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(outset)) ;
exit(0) ;
} else {
fprintf(stderr,
"** 3dZeropad: Failed to write output!\n" ) ;
exit(1) ;
}
}
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);
}
int main( int argc , char * argv[] )
{
THD_3dim_dataset *inset=NULL , *outset=NULL , *mask_dset=NULL ;
MRI_IMAGE *fim=NULL ; float *far=NULL ;
int iarg , ndset , nvox , ii , mcount=0 ;
char *prefix = "rankizer" ;
byte *mmm=NULL ;
float brank=1.0f ;
/*-- read command line arguments --*/
if( argc < 3 || strncmp(argv[1],"-help",5) == 0 ){
printf("Usage: 3dRankizer [options] dataset\n"
"Output = Rank of each voxel as sorted into increasing value.\n"
" - Ties get the average rank.\n"
" - Not the same as 3dRank!\n"
" - Only sub-brick #0 is processed at this time!\n"
" - Ranks start at 1 and increase:\n"
" Input = 0 3 4 4 7 9\n"
" Output = 1 2 3.5 3.5 5 6\n"
"Options:\n"
" -brank bbb Set the 'base' rank to 'bbb' instead of 1.\n"
" (You could also do this with 3dcalc.)\n"
" -mask mset Means to use the dataset 'mset' as a mask:\n"
" Only voxels with nonzero values in 'mset'\n"
" will be used from 'dataset'. Voxels outside\n"
" the mask will get rank 0.\n"
" -prefix ppp Write results into float-format dataset 'ppp'\n"
" Output is in float format to allow for\n"
" non-integer ranks resulting from ties.\n"
"\n"
"Author: RW Cox [[a quick hack for his own purposes]]\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
/*---- official startup ---*/
PRINT_VERSION("3dRankizer"); mainENTRY("3dRankizer main"); machdep();
AFNI_logger("3dRankizer",argc,argv); AUTHOR("Zhark of the Ineffable Rank");
/*-- command line scan --*/
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strncmp(argv[iarg],"-brank",5) == 0 ){
if( iarg+1 >= argc )
ERROR_exit("-brank option requires a following argument!") ;
brank = (float)strtod(argv[++iarg],NULL) ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-mask",5) == 0 ){
if( mask_dset != NULL )
ERROR_exit("Cannot have two -mask options!") ;
if( iarg+1 >= argc )
ERROR_exit("-mask option requires a following argument!") ;
mask_dset = THD_open_dataset( argv[++iarg] ) ;
if( mask_dset == NULL )
ERROR_exit("Cannot open mask dataset!") ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ) ERROR_exit("Need argument after '-prefix'") ;
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) ) ERROR_exit("Illegal value after '-prefix'") ;
iarg++ ; continue ;
}
ERROR_exit("Unknown option: %s",argv[iarg]) ;
}
/* should have 1 more arg */
ndset = argc - iarg ;
if( ndset < 1 ) ERROR_exit("No input dataset!?") ;
else if( ndset > 1 ) WARNING_message("Too many input datasets!") ;
inset = THD_open_dataset( argv[iarg] ) ; CHECK_OPEN_ERROR(inset,argv[iarg]) ;
DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;
fim = THD_extract_float_brick(0,inset) ; DSET_unload(inset) ;
far = MRI_FLOAT_PTR(fim) ;
nvox= DSET_NVOX(inset) ;
/* make a byte mask from mask dataset */
if( mask_dset != NULL ){
if( DSET_NVOX(mask_dset) != nvox )
ERROR_exit("Input and mask datasets are not same dimensions!");
mmm = THD_makemask( mask_dset , 0 , 1.0f,-1.0f ) ;
mcount = THD_countmask( nvox , mmm ) ;
INFO_message("%d voxels in the mask",mcount) ;
if( mcount <= 5 ) ERROR_exit("Mask is too small!") ;
DSET_delete(mask_dset) ;
}
if( mmm == NULL ){
rank_order_float( nvox , far ) ;
for( ii=0 ; ii < nvox ; ii++ ) far[ii] += brank ;
} else {
float fmin=far[0] ;
for( ii=1 ; ii < nvox ; ii++ ) if( far[ii] < fmin ) fmin = far[ii] ;
if( fmin > 0.0f ) fmin = 0.0f ;
else if( fmin == 0.0f ) fmin = -1.0f ;
else fmin = -2.0f*fmin-1.0f ;
for( ii=0 ; ii < nvox ; ii++ ) if( !mmm[ii] ) far[ii] = fmin ;
rank_order_float( nvox , far ) ;
fmin = (nvox-mcount) - brank ;
for( ii=0 ; ii < nvox ; ii++ ){
if( mmm[ii] ) far[ii] = far[ii] - fmin ;
else far[ii] = 0.0f ;
}
}
outset = EDIT_empty_copy( inset ) ;
EDIT_dset_items( outset ,
ADN_prefix , prefix ,
ADN_brick_fac , NULL ,
ADN_nvals , 1 ,
ADN_ntt , 0 ,
ADN_none ) ;
EDIT_substitute_brick( outset , 0 , MRI_float , far ) ;
DSET_write(outset) ; WROTE_DSET(outset) ;
exit(0) ;
}
int main( int argc , char *argv[] )
{
char *drive_afni[128] ;
int ndrive=0 , iarg=1 ;
char host[1024]="localhost", nsname[2048], *geomstr, *cpt, temp[32] ;
int dt=1000 , ctold,ctnew , ctzero ;
int verbose=0 , kk,nn , nvox,nval , do_accum=0 ;
THD_3dim_dataset *dset ;
NI_element *nel ;
MRI_IMAGE *fim ; float *far ;
char *targname="niml_feedme" ;
/*-- help the ignorant user --*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: niml_feedme [options] dataset\n"
"\n"
"* Sends volumes from the dataset to AFNI via the NIML socket interface.\n"
"* You must run AFNI with the command 'afni -niml' so that the program\n"
" will be listening for the socket connection.\n"
"* Inside AFNI, the transmitted dataset will be named 'niml_feedme'.\n"
"* For another way to send image data to AFNI, see progam rtfeedme.\n"
"* At present, there is no way to attach statistical parameters to\n"
" a transmitted volume.\n"
"* This program sends all volumes in float format, simply because\n"
" that's easy for me. But you can also send byte, short, and\n"
" complex valued volumes.\n"
"* This program is really just a demo; it has little practical use.\n"
"\n"
"OPTIONS:\n"
" -host sname = Send data, via TCP/IP, to AFNI running on the\n"
" computer system 'sname'. By default, uses the\n"
" current system (localhost), if you don't use this\n"
" option.\n"
"\n"
" -dt ms = Tries to maintain an inter-transmit interval of 'ms'\n"
" milliseconds. The default is 1000 msec per volume.\n"
"\n"
" -verb = Be (very) talkative about actions.\n"
"\n"
" -accum = Send sub-bricks so that they accumulate in AFNI.\n"
" The default is to create only a 1 volume dataset\n"
" inside AFNI, and each sub-brick just replaces\n"
" that one volume when it is received.\n"
"\n"
" -target nam = Change the dataset name transmitted to AFNI from\n"
" 'niml_feedme' to 'nam'.\n"
"\n"
" -drive cmd = Send 'cmd' as a DRIVE_AFNI command.\n"
" * If cmd contains blanks, it must be in 'quotes'.\n"
" * Multiple -drive options may be used.\n"
" * These commands will be sent to AFNI just after\n"
" the first volume is transmitted.\n"
" * See file README.driver for a list of commands.\n"
"\n"
"EXAMPLE: Send volumes from a 3D+time dataset to AFNI:\n"
"\n"
" niml_feedme -dt 1000 -verb -accum -target Elvis \\\n"
" -drive 'OPEN_WINDOW axialimage' \\\n"
" -drive 'OPEN_WINDOW axialgraph' \\\n"
" -drive 'SWITCH_UNDERLAY Elvis' \\\n"
" timeseries+orig\n"
"\n"
"Author: RW Cox -- July 2009\n"
) ;
PRINT_COMPILE_DATE ;
exit(0) ;
}
mainENTRY("niml_feedme") ;
/*-- scan arguments --*/
while( iarg < argc && argv[iarg][0] == '-' ){
if( strncmp(argv[iarg],"-target",5) == 0 ){
targname = strdup(argv[++iarg]) ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-drive") == 0 ){
drive_afni[ndrive++] = argv[++iarg] ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-host") == 0 ){
strcpy( host , argv[++iarg] ) ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-dt") == 0 ){
dt = (int)strtod(argv[++iarg],NULL) ; if( dt < 9 ) dt = 9 ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-verbose",4) == 0 ){
verbose = 1 ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-accum",4) == 0 ){
do_accum = 1 ; iarg++ ; continue ;
}
ERROR_exit("Unrecognized option: %s",argv[iarg]) ;
}
if( iarg >= argc ) ERROR_exit("No dataset on command line?!") ;
/*-- read in the dataset --*/
dset = THD_open_dataset( argv[iarg] ) ;
if( dset == NULL ) ERROR_exit("Can't open dataset '%s'",argv[iarg]) ;
DSET_load(dset) ;
if( !DSET_LOADED(dset) ) ERROR_exit("Can't load dataset '%s'",argv[iarg]) ;
cpt = EDIT_get_geometry_string(dset) ;
geomstr = strdup(cpt) ; /* describes geometry of dataset grid */
if( verbose ) INFO_message("geometry string = '%s'",geomstr) ;
nvox = DSET_NVOX(dset); /* number of voxels in dataset */
nval = DSET_NVALS(dset); /* number of sub-bricks in dataset */
/*-- this stuff is one-time-only setup of the I/O to AFNI --*/
atexit(NF_exit) ; /* call this when program ends */
signal(SIGINT ,NF_sigfunc) ; /* setup signal handler */
signal(SIGBUS ,NF_sigfunc) ; /* for fatal errors */
signal(SIGSEGV,NF_sigfunc) ;
signal(SIGTERM,NF_sigfunc) ;
/* name of NIML stream (socket) to open */
sprintf( nsname , "tcp:%s:%d" , host , get_port_named("AFNI_DEFAULT_LISTEN_NIML"));
/* open the socket (i.e., dial the telephone call) */
fprintf(stderr,"opening NIML stream '%s' ",nsname) ;
NF_stream = NI_stream_open( nsname , "w" ) ;
/* loop until AFNI connects (answers the call),
printing a '.' every 1/2 second to keep the user happy */
while(1){
kk = NI_stream_writecheck( NF_stream , 500 ) ;
if( kk == 1 ){ fprintf(stderr," connected!\n") ; break ; }
if( kk < 0 ){ fprintf(stderr," ** connection fails **\n") ; exit(1) ; }
fprintf(stderr,".") ;
}
/*-- Create VOLUME_DATA NIML element to hold the brick data --*/
nel = NI_new_data_element( "VOLUME_DATA" , nvox ) ;
/* add attributes to the element to help AFNI construct the dataset */
/* define the grid of the dataset */
NI_set_attribute( nel , "geometry_string" , geomstr ) ;
/* define the name of the dataset */
NI_set_attribute( nel , "target_name" , targname ) ;
/* all sub-bricks in the input dataset will be sent to be
sub-brick #0 in the dataset inside AFNI
-- if you don't want this behavior, and want the dataset
inside AFNI to keep growing, then don't set this attribute! */
if( !do_accum ) NI_set_attribute( nel , "index" , "0" ) ;
/* +tlrc view? [default in AFNI is +orig view] */
if( dset->view_type == VIEW_TALAIRACH_TYPE )
NI_set_attribute( nel , "view" , "tlrc" ) ;
/**-- loop over sub-bricks and send them to AFNI --*/
ctzero = NI_clock_time() ; /* for later reference */
if( verbose ) INFO_message("Starting sub-brick loop") ;
for( kk=0 ; kk < nval ; kk++ ){
ctold = NI_clock_time() ; /* clock time at start of work (ms) */
/* get a float copy of the kk-th sub-brick */
fim = THD_extract_float_brick( kk , dset ) ;
DSET_unload_one(dset,kk) ; /* unload this sub-brick now */
if( fim == NULL ){ /* should never happen */
ERROR_message("Can't get sub-brick #%d?? -- skipping",kk) ;
NI_sleep(dt) ; continue ;
}
/* copy the float data into the NIML element for transmission */
far = MRI_FLOAT_PTR(fim) ;
if( kk == 0 ) /* first time: create data column in element */
NI_add_column( nel , NI_FLOAT , far ) ;
else /* later times: overwrite nel data column */
memcpy( nel->vec[0] , far , sizeof(float)*nvox ) ;
mri_free(fim) ; /* done with this now [data all copied to nel] */
/* set sub-brick index in AFNI if doing accumulation */
if( do_accum ){
sprintf(temp,"%d",kk) ; NI_set_attribute( nel , "index" , temp ) ;
}
/*** send the data element to AFNI ***/
nn = NI_write_element( NF_stream , nel , NI_BINARY_MODE ) ;
/* if something bad happened in the transmission, report it */
if( nn <= 0 ){
ERROR_message("Can't write sub-brick #%d to AFNI!",kk) ; break ;
}
/*** first time through ==>
do the '-drive' commands now by sending processing instructions ***/
if( kk == 0 && ndrive > 0 ){
int ii ; NI_procins *npi ;
if( verbose )
ININFO_message("Sending %d 'drive_afni' elements now",ndrive) ;
npi = NI_new_processing_instruction( "DRIVE_AFNI" ) ;
NI_sleep(1) ; /* give AFNI a msec to digest the data */
for( ii=0 ; ii < ndrive ; ii++ ){
NI_set_attribute( npi , "cmd" , drive_afni[ii] ) ;
(void)NI_write_element( NF_stream , npi , NI_TEXT_MODE ) ;
}
NI_free_element(npi) ; /* delete this struct from the world! */
}
ctnew = NI_clock_time() ; /* clock time now */
if( verbose ) ININFO_message("Sent %d bytes for sub-brick #%d in %d ms",
nn , kk , ctnew-ctold ) ;
NI_sleep( dt - (ctnew-ctold) ) ; /* sleep so that time delay is right */
} /* end of loop over sub-bricks */
/** summarize, do some cleanup, and exit stage left **/
if( verbose && kk > 0 ){
float dtav = (NI_clock_time()-ctzero) / (float)kk ;
INFO_message("Transmission finished: %.1f ms = average time per volume",dtav) ;
}
NI_free_element(nel) ; /* destroy the data element */
DSET_delete(dset) ; /* destroy the dataset */
exit(0) ;
}
int main( int argc , char * argv[] )
{
THD_3dim_dataset * dset ;
THD_dataxes * daxes ;
FD_brick ** brarr , * baxi , * bsag , * bcor ;
int iarg , ii ;
Boolean ok ;
MRI_IMAGE * pim , * flim , * slim ;
float * flar ;
dset_range dr ;
float val , fimfac ;
int ival,ityp , kk ;
float xbot=BIGG,xtop=BIGG , ybot=BIGG,ytop=BIGG , zbot=BIGG,ztop=BIGG ;
int xgood=0 , ygood=0 , zgood=0 ,
proj_code=PROJ_SUM , mirror_code=MIRR_NO , nsize=0 ;
char root[THD_MAX_NAME] = "proj." ;
char fname[THD_MAX_NAME] ;
int ixbot=0,ixtop=0 , jybot=0,jytop=0 , kzbot=0,kztop=0 ;
THD_fvec3 fv ;
THD_ivec3 iv ;
/*--- read command line arguments ---*/
WARNING_message("This program (3dproject) is old, not maintained, and probably useless!") ;
if( argc < 2 || strncmp(argv[1],"-help",6) == 0 ) Syntax() ;
INIT_EDOPT( &PRED_edopt ) ;
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
DB("new arg:",argv[iarg]) ;
/**** check for editing option ****/
ii = EDIT_check_argv( argc , argv , iarg , &PRED_edopt ) ;
if( ii > 0 ){
iarg += ii ;
continue ;
}
/**** -sum or -max ****/
if( strncmp(argv[iarg],"-sum",6) == 0 ){
proj_code = PROJ_SUM ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-max",6) == 0 ){
proj_code = PROJ_MMAX ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-amax",6) == 0 ){
proj_code = PROJ_AMAX ;
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-smax",6) == 0 ){
proj_code = PROJ_SMAX ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-first") == 0 ){ /* 02 Nov 2000 */
proj_code = PROJ_FIRST ;
first_thresh = strtod( argv[++iarg] , NULL ) ;
iarg++ ; continue ;
}
/**** -mirror ****/
if( strncmp(argv[iarg],"-mirror",6) == 0 ){
mirror_code = MIRR_YES ;
iarg++ ; continue ;
}
/**** -nsize ****/
if( strncmp(argv[iarg],"-nsize",6) == 0 ){
nsize = 1 ;
iarg++ ; continue ;
}
/**** -output root ****/
if( strncmp(argv[iarg],"-output",6) == 0 ||
strncmp(argv[iarg],"-root",6) == 0 ){
if( iarg+1 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
MCW_strncpy( root , argv[++iarg] , THD_MAX_NAME-1 ) ;
ii = strlen(root) ;
if( ii == 0 ){
fprintf(stderr,"\n*** illegal rootname!\n") ; exit(-1) ;
}
if( root[ii-1] != '.' ){ root[ii] = '.' ; root[ii+1] = '\0' ; }
iarg++ ; continue ;
}
/**** -ALL ****/
if( strncmp(argv[iarg],"-ALL",6) == 0 ||
strncmp(argv[iarg],"-all",6) == 0 ){
xgood = ygood = zgood = 1 ;
xbot = ybot = zbot = -BIGG ;
xtop = ytop = ztop = BIGG ;
iarg++ ; continue ;
}
/**** -RL {all | x1 x2} ****/
if( strncmp(argv[iarg],"-RL",6) == 0 ||
strncmp(argv[iarg],"-LR",6) == 0 ||
strncmp(argv[iarg],"-rl",6) == 0 ||
strncmp(argv[iarg],"-lr",6) == 0 ||
strncmp(argv[iarg],"-sag",6)== 0 ){
char * cerr ; float tf ;
xgood = 1 ; /* mark for x projection */
if( iarg+1 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
if( strncmp(argv[iarg+1],"all",6) == 0 ||
strncmp(argv[iarg+1],"ALL",6) == 0 ){
xbot = -BIGG;
xtop = BIGG ;
iarg += 2 ; continue ;
}
if( iarg+2 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
xbot = strtod( argv[iarg+1] , &cerr ) ;
if( cerr == argv[iarg+1] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+1] ) ; exit(-1) ;
}
if( *cerr == 'R' && xbot > 0.0 ) xbot = -xbot ;
xtop = strtod( argv[iarg+2] , &cerr ) ;
if( cerr == argv[iarg+2] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+2] ) ; exit(-1) ;
}
if( *cerr == 'R' && xtop > 0.0 ) xtop = -xtop ;
if( xbot > xtop ){ tf = xbot ; xbot = xtop ; xtop = tf ; }
iarg +=3 ; continue ;
}
/**** -AP {all | y1 y2} ****/
if( strncmp(argv[iarg],"-AP",6) == 0 ||
strncmp(argv[iarg],"-PA",6) == 0 ||
strncmp(argv[iarg],"-ap",6) == 0 ||
strncmp(argv[iarg],"-pa",6) == 0 ||
strncmp(argv[iarg],"-cor",6)== 0 ){
char * cerr ; float tf ;
ygood = 1 ; /* mark for y projection */
if( iarg+1 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
if( strncmp(argv[iarg+1],"all",6) == 0 ||
strncmp(argv[iarg+1],"ALL",6) == 0 ){
ybot = -BIGG ;
ytop = BIGG ;
iarg += 2 ; continue ;
}
if( iarg+2 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
ybot = strtod( argv[iarg+1] , &cerr ) ;
if( cerr == argv[iarg+1] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+1] ) ; exit(-1) ;
}
if( *cerr == 'A' && ybot > 0.0 ) ybot = -ybot ;
ytop = strtod( argv[iarg+2] , &cerr ) ;
if( cerr == argv[iarg+2] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+2] ) ; exit(-1) ;
}
if( *cerr == 'A' && ytop > 0.0 ) ytop = -ytop ;
if( ybot > ytop ){ tf = ybot ; ybot = ytop ; ytop = tf ; }
iarg +=3 ; continue ;
}
/**** -IS {all | z1 z2} ****/
if( strncmp(argv[iarg],"-IS",6) == 0 ||
strncmp(argv[iarg],"-SI",6) == 0 ||
strncmp(argv[iarg],"-is",6) == 0 ||
strncmp(argv[iarg],"-si",6) == 0 ||
strncmp(argv[iarg],"-axi",6)== 0 ){
char * cerr ; float tf ;
zgood = 1 ; /* mark for y projection */
if( iarg+1 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
if( strncmp(argv[iarg+1],"all",6) == 0 ||
strncmp(argv[iarg+1],"ALL",6) == 0 ){
zbot = -BIGG ;
ztop = BIGG ;
iarg += 2 ; continue ;
}
if( iarg+2 >= argc ){
fprintf(stderr,"\n*** no argument after option %s\n",argv[iarg]) ;
exit(-1) ;
}
zbot = strtod( argv[iarg+1] , &cerr ) ;
if( cerr == argv[iarg+1] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+1] ) ; exit(-1) ;
}
if( *cerr == 'I' && zbot > 0.0 ) zbot = -zbot ;
ztop = strtod( argv[iarg+2] , &cerr ) ;
if( cerr == argv[iarg+2] ){
fprintf(stderr,"\n*** illegal argument after %s: %s\n",
argv[iarg],argv[iarg+2] ) ; exit(-1) ;
}
if( *cerr == 'I' && ztop > 0.0 ) ztop = -ztop ;
if( zbot > ztop ){ tf = zbot ; zbot = ztop ; ztop = tf ; }
iarg +=3 ; continue ;
}
/**** unknown option ****/
fprintf(stderr,"\n*** Unknown option: %s\n",argv[iarg]) ;
exit(-1) ;
} /* end of loop over input options */
if( ! xgood && ! ygood && ! zgood ){
fprintf(stderr,"\n*** No projections ordered!?\n") ; exit(-1) ;
}
/*--- open dataset and set up to extract data slices ---*/
dset = THD_open_dataset( argv[iarg] ) ;
if( dset == NULL ){
fprintf(stderr,"\n*** Can't open dataset file %s\n",argv[iarg]) ;
exit(-1) ;
}
if( DSET_NUM_TIMES(dset) > 1 ){
fprintf(stderr,"\n*** Can't project time-dependent dataset!\n") ;
exit(1) ;
}
EDIT_one_dataset( dset, &PRED_edopt ) ;
daxes = dset->daxes ;
brarr = THD_setup_bricks( dset ) ;
baxi = brarr[0] ; bsag = brarr[1] ; bcor = brarr[2] ;
/*--- determine index range for each direction ---*/
dr = PR_get_range( dset ) ;
if( xgood ){
if( xbot < dr.xbot ) xbot = dr.xbot ;
if( xtop > dr.xtop ) xtop = dr.xtop ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(xbot,0,0) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( bsag , iv ) ; ixbot = iv.ijk[2] ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(xtop,0,0) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( bsag , iv ) ; ixtop = iv.ijk[2] ;
if( ixbot > ixtop ) { ii = ixbot ; ixbot = ixtop ; ixtop = ii ; }
if( ixbot < 0 ) ixbot = 0 ;
if( ixtop >= bsag->n3 ) ixtop = bsag->n3 - 1 ;
}
if( ygood ){
if( ybot < dr.ybot ) ybot = dr.ybot ;
if( ytop > dr.ytop ) ytop = dr.ytop ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(0,ybot,0) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( bcor , iv ) ; jybot = iv.ijk[2] ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(0,ytop,0) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( bcor , iv ) ; jytop = iv.ijk[2] ;
if( jybot > jytop ) { ii = jybot ; jybot = jytop ; jytop = ii ; }
if( jybot < 0 ) jybot = 0 ;
if( jytop >= bcor->n3 ) jytop = bcor->n3 - 1 ;
}
if( zgood ){
if( zbot < dr.zbot ) zbot = dr.zbot ;
if( ztop > dr.ztop ) ztop = dr.ztop ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(0,0,zbot) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( baxi , iv ) ; kzbot = iv.ijk[2] ;
fv = THD_dicomm_to_3dmm( dset , TEMP_FVEC3(0,0,ztop) ) ;
iv = THD_3dmm_to_3dind ( dset , fv ) ;
iv = THD_3dind_to_fdind( baxi , iv ) ; kztop = iv.ijk[2] ;
if( kzbot > kztop ) { ii = kzbot ; kzbot = kztop ; kztop = ii ; }
if( kzbot < 0 ) kzbot = 0 ;
if( kztop >= baxi->n3 ) kztop = baxi->n3 - 1 ;
}
ival = DSET_PRINCIPAL_VALUE(dset) ; /* index to project */
ityp = DSET_BRICK_TYPE(dset,ival) ; /* type of this data */
fimfac = DSET_BRICK_FACTOR(dset,ival) ; /* scale factor of this data */
/*--- project the x direction, if desired ---*/
if( xgood ){
int n1 = bsag->n1 , n2 = bsag->n2 ;
int ss , npix ;
float fmax , fmin , scl ;
/*-- set up --*/
npix = n1*n2 ;
flim = mri_new( n1 , n2 , MRI_float ) ;
flar = mri_data_pointer( flim ) ;
for( ii=0 ; ii < npix ; ii++ ) flar[ii] = 0.0 ;
/*-- actually project --*/
for( ss=ixbot ; ss <= ixtop ; ss++ ){
slim = FD_brick_to_mri( ss , ival , bsag ) ;
if( slim->kind != MRI_float ){
pim = mri_to_float( slim ) ;
mri_free( slim ) ; slim = pim ;
}
PR_one_slice( proj_code , slim , flim ) ;
mri_free( slim ) ;
}
/*-- form output --*/
if( fimfac != 0.0 && fimfac != 1.0 ){
slim = mri_scale_to_float( 1.0/fimfac , flim ) ;
mri_free(flim) ; flim = slim ;
}
scl = PR_type_scale( ityp , flim ) ;
pim = mri_to_mri_scl( ityp , scl , flim ) ; mri_free( flim ) ;
if( nsize ){
slim = mri_nsize( pim ) ;
if( slim != NULL && slim != pim ) { mri_free(pim) ; pim = slim ; }
}
if( scl != 1.0 )
printf("Sagittal projection pixels scaled by %g to avoid overflow!\n",
scl ) ;
fmax = mri_max(pim) ; fmin = mri_min(pim) ;
printf("Sagittal projection min = %g max = %g\n",fmin,fmax) ;
strcpy(fname,root) ; strcat(fname,"sag") ;
mri_write( fname, pim ) ;
mri_free(pim) ;
}
/*--- project the y direction, if desired ---*/
if( ygood ){
int n1 = bcor->n1 , n2 = bcor->n2 ;
int ss , npix ;
float fmax , fmin , scl ;
/*-- set up --*/
npix = n1*n2 ;
flim = mri_new( n1 , n2 , MRI_float ) ;
flar = mri_data_pointer( flim ) ;
for( ii=0 ; ii < npix ; ii++ ) flar[ii] = 0.0 ;
/*-- actually project --*/
for( ss=jybot ; ss <= jytop ; ss++ ){
slim = FD_brick_to_mri( ss , ival , bcor ) ;
if( slim->kind != MRI_float ){
pim = mri_to_float( slim ) ;
mri_free( slim ) ; slim = pim ;
}
PR_one_slice( proj_code , slim , flim ) ;
mri_free( slim ) ;
}
/*-- form output --*/
if( fimfac != 0.0 && fimfac != 1.0 ){
slim = mri_scale_to_float( 1.0/fimfac , flim ) ;
mri_free(flim) ; flim = slim ;
}
scl = PR_type_scale( ityp , flim ) ;
pim = mri_to_mri_scl( ityp , scl , flim ) ; mri_free( flim ) ;
if( nsize ){
slim = mri_nsize( pim ) ;
if( slim != NULL && slim != pim ) { mri_free(pim) ; pim = slim ; }
}
if( scl != 1.0 )
printf("Coronal projection pixels scaled by %g to avoid overflow!\n",
scl ) ;
fmax = mri_max(pim) ; fmin = mri_min(pim) ;
printf("Coronal projection min = %g max = %g\n",fmin,fmax) ;
if( mirror_code == MIRR_YES ){
slim = mri_flippo( MRI_ROT_0 , TRUE , pim ) ;
mri_free(pim) ; pim = slim ;
}
strcpy(fname,root) ; strcat(fname,"cor") ;
mri_write( fname, pim ) ;
mri_free(pim) ;
}
/*--- project the z direction, if desired ---*/
if( zgood ){
int n1 = baxi->n1 , n2 = baxi->n2 ;
int ss , npix ;
float fmax , fmin , scl ;
/*-- set up --*/
npix = n1*n2 ;
flim = mri_new( n1 , n2 , MRI_float ) ;
flar = mri_data_pointer( flim ) ;
for( ii=0 ; ii < npix ; ii++ ) flar[ii] = 0.0 ;
/*-- actually project --*/
for( ss=kzbot ; ss <= kztop ; ss++ ){
slim = FD_brick_to_mri( ss , ival , baxi ) ;
if( slim->kind != MRI_float ){
pim = mri_to_float( slim ) ;
mri_free( slim ) ; slim = pim ;
}
PR_one_slice( proj_code , slim , flim ) ;
mri_free( slim ) ;
}
/*-- form output --*/
if( fimfac != 0.0 && fimfac != 1.0 ){
slim = mri_scale_to_float( 1.0/fimfac , flim ) ;
mri_free(flim) ; flim = slim ;
}
scl = PR_type_scale( ityp , flim ) ;
pim = mri_to_mri_scl( ityp , scl , flim ) ; mri_free( flim ) ;
if( nsize ){
slim = mri_nsize( pim ) ;
if( slim != NULL && slim != pim ) { mri_free(pim) ; pim = slim ; }
}
if( scl != 1.0 )
printf("Axial projection pixels scaled by %g to avoid overflow!\n",
scl ) ;
fmax = mri_max(pim) ; fmin = mri_min(pim) ;
printf("Axial projection min = %g max = %g\n",fmin,fmax) ;
if( mirror_code == MIRR_YES ){
slim = mri_flippo( MRI_ROT_0 , TRUE , pim ) ;
mri_free(pim) ; pim = slim ;
}
strcpy(fname,root) ; strcat(fname,"axi") ;
mri_write( fname, pim ) ;
mri_free(pim) ;
}
exit(0) ;
}
int main( int argc , char *argv[] )
{
int force=0 ; /* KRH loudly deprecating usage 04/13/05/ */
int iarg=1 ;
THD_3dim_dataset *dset ; /* output dataset */
int nvals , ii , jj , kk ;
MRI_IMARR *anar ; /* stuff from ANALYZE headers */
MRI_IMAGE *anim ;
int nxan=0,nyan=0,nzan=0 , an_datum=0 , an_swapped=0 ;
float dxan=-1.0,dyan=0.0,dzan=0.0 ;
char anor[8] = "\0" ;
THD_ivec3 nxyz , orixyz ;
THD_fvec3 dxyz , orgxyz ;
float TR=1.0 ; int tunits=UNITS_SEC_TYPE ;
int is_fbuc=0 , is_abuc=0 , is_3dtime=0 ;
int view_type=VIEW_ORIGINAL_TYPE ;
char *prefix="a2a" ;
int xorient=-1, yorient=-1, zorient=-1 ;
int use_zoff=0,use_xoff=0,use_yoff=0 ; float zoff=0.0,xoff=0.0,yoff=0.0 ;
THD_3dim_dataset *gset=NULL ; /* geometry parent */
float *fac ;
char **flab , *fatr ;
/*-- help the poor user? --*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ A2A_help(); exit(0); }
mainENTRY("3dANALYZEtoAFNI main"); machdep(); PRINT_VERSION("3dANALYZEtoAFNI");
/*-- parse options --*/
while( iarg < argc && argv[iarg][0] == '-' ){
/* -prefix */
if( strcmp(argv[iarg],"-prefix") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"** -prefix needs an argument!\n"); exit(1);
}
prefix = argv[iarg] ;
if( !THD_filename_ok(prefix) ){
fprintf(stderr,"** Illegal prefix!\n"); exit(1);
}
if( strstr(prefix,"/") != NULL ){
fprintf(stderr,"** Can't use directory names in the prefix!\n"); exit(1);
}
iarg++ ; continue ;
}
/* -view */
if( strcmp(argv[iarg],"-view") == 0 ){
char *str ;
if( ++iarg >= argc ){
fprintf(stderr,"** -view needs an argument!\n"); exit(1);
}
str = argv[iarg] ; if( str[0] == '+' ) str++ ;
for( ii=FIRST_VIEW_TYPE ; ii <= LAST_VIEW_TYPE ; ii++ )
if( strcmp(str,VIEW_codestr[ii]) == 0 ) break ;
if( ii <= LAST_VIEW_TYPE ){
view_type = ii ;
} else {
fprintf(stderr,"** Illegal -view code!\n"); exit(1);
}
iarg++ ; continue ;
}
/* -zorigin */
if( strcmp(argv[iarg],"-zorigin") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"** -zorigin needs an argument!\n"); exit(1);
}
zoff = strtod( argv[iarg] , NULL ) ;
use_zoff = 1 ;
iarg++ ; continue ;
}
/* -orient */
#define ORCODE(aa) \
( (aa)=='R' ? ORI_R2L_TYPE : (aa)=='L' ? ORI_L2R_TYPE : \
(aa)=='P' ? ORI_P2A_TYPE : (aa)=='A' ? ORI_A2P_TYPE : \
(aa)=='I' ? ORI_I2S_TYPE : (aa)=='S' ? ORI_S2I_TYPE : ILLEGAL_TYPE )
#define OR3OK(x,y,z) ( ((x)&6) + ((y)&6) + ((z)&6) == 6 )
if( strcmp(argv[iarg],"-orient") == 0 ){
char acod ;
if( ++iarg >= argc ){
fprintf(stderr,"** -orient needs an argument!\n"); exit(1);
}
if( strlen(argv[iarg]) != 3 ){
fprintf(stderr,"** Illegal -orient code!\n"); exit(1);
}
acod = toupper(argv[iarg][0]) ; xorient = ORCODE(acod) ;
acod = toupper(argv[iarg][1]) ; yorient = ORCODE(acod) ;
acod = toupper(argv[iarg][2]) ; zorient = ORCODE(acod) ;
if( xorient<0 || yorient<0 || zorient<0 ||
! OR3OK(xorient,yorient,zorient) ){
fprintf(stderr,"** Unusable -orient code!\n"); exit(1);
}
iarg++ ; continue ;
}
/* -geomparent */
if( strcmp(argv[iarg],"-geomparent") == 0 ){
if( ++iarg >= argc ){
fprintf(stderr,"** -geomparent needs an argument!\n"); exit(1);
}
gset = THD_open_dataset( argv[iarg] ); CHECK_OPEN_ERROR(gset,argv[iarg]);
iarg++ ; continue ;
}
/* -TR */
if( strcmp(argv[iarg],"-TR") == 0 ){
char *eptr ;
if( ++iarg >= argc ){
fprintf(stderr,"** -geomparent needs an argument!\n"); exit(1);
}
TR = strtod( argv[iarg] , &eptr ) ;
if( TR <= 0.0 ){
fprintf(stderr,"** -TR needs a positive value after it!\n"); exit(1);
}
if( strcmp(eptr,"ms")==0 || strcmp(eptr,"msec")==0 ){
tunits = UNITS_MSEC_TYPE ;
WARNING_message("TR in millisecond units is deprecated.") ;
} else if( strcmp(eptr,"s")==0 || strcmp(eptr,"sec")==0 ){
tunits = UNITS_SEC_TYPE ;
} else if( strcmp(eptr,"Hz")==0 || strcmp(eptr,"Hertz")==0 ){
tunits = UNITS_HZ_TYPE ;
}
is_3dtime = 1 ; is_abuc = is_fbuc = 0 ;
iarg++ ; continue ;
}
/* -fbuc */
if( strcmp(argv[iarg],"-fbuc") == 0 ){
is_fbuc = 1 ; is_abuc = is_3dtime = 0 ;
iarg++ ; continue ;
}
/* -abuc */
if( strcmp(argv[iarg],"-abuc") == 0 ){
is_abuc = 1 ; is_fbuc = is_3dtime = 0 ;
iarg++ ; continue ;
}
/* -OK */
if( strcmp(argv[iarg],"-OK") == 0 ){
force = 1 ;
iarg++ ; continue ;
}
/** don't know this one **/
fprintf(stderr,"** Illegal option %s\n",argv[iarg]); exit(1);
}
if (!force) { A2A_help(); exit(0);
}
/*-- check number of remaining args --*/
nvals = argc - iarg ;
if( nvals <= 0 ){
fprintf(stderr,"** No ANALYZE files on command line!?\n"); exit(1);
}
/*-- try to read each ANALYZE file and glean info from it --*/
CLEAR_MRILIB_globals ; /* setup */
fac = (float *) malloc(sizeof(float)*nvals) ;
for( ii=iarg ; ii < argc ; ii++ ){
if( strstr(argv[ii],"/") != NULL ){
fprintf(stderr,"** ANALYZE files must all be in current directory!\n") ;
exit(1) ;
}
anar = mri_read_analyze75( argv[ii] ) ; /* read it */
if( anar == NULL || IMARR_COUNT(anar) == 0 ){
fprintf(stderr,"** Can't read %s as ANALYZE-75 format .hdr file!\n",argv[ii]);
exit(1) ;
}
anim = IMARR_SUBIM(anar,0) ; /* first 2D image */
fac[ii-iarg] = anim->dv ; /* save scale factor, if any */
if( ii == iarg ){ /* first time in: store header values */
nxan = anim->nx ; nyan = anim->ny ; nzan = IMARR_COUNT(anar) ;
if( MRILIB_orients[0] != '\0' ) strcpy(anor,MRILIB_orients) ;
an_datum = anim->kind ;
if( anim->dw > 0.0 ){ dxan = anim->dx; dyan = anim->dy; dzan = anim->dz; }
an_swapped = anim->was_swapped ;
} else { /* check later sub-bricks */
if( nxan != anim->nx || nyan != anim->ny || nzan != IMARR_COUNT(anar) ){
fprintf(stderr,"** File %s has different dimensions than %s\n",
argv[ii] , argv[iarg] ) ;
exit(1) ;
}
if( an_datum != anim->kind ){
fprintf(stderr,"** File %s has different kind of data than %s\n",
argv[ii] , argv[iarg] ) ;
exit(1) ;
}
if( an_swapped != anim->was_swapped ){
fprintf(stderr,"** File %s %s byte-swapped, but %s %s\n",
argv[ii] , (anim->was_swapped) ? "is" : "isn't" ,
argv[iarg] , (an_swapped) ? "is" : "isn't" ) ;
exit(1) ;
}
if( anim->dw > 0.0 ){
if( dxan < 0.0 ){
dxan = anim->dx; dyan = anim->dy; dzan = anim->dz;
} else {
if( dxan != anim->dx || dyan != anim->dy || dzan != anim->dz ){
fprintf(stderr,"++ WARNING: File %s has variant voxel sizes!\n",
argv[ii]) ;
}
}
}
if( anor[0] == '\0' && MRILIB_orients[0] != '\0' )
strcpy(anor,MRILIB_orients) ;
} /* end of checking later volumes for compatibility */
/* destroy this data (we've sucked it dry) */
DESTROY_IMARR(anar) ;
} /* end of loop over ANALYZE files */
/*-- check geomparent, if present --*/
if( gset != NULL ){
if( DSET_NX(gset)!=nxan || DSET_NY(gset)!=nyan || DSET_NZ(gset)!=nzan ){
fprintf(stderr,"** geomparent and ANALYZE files have different dimensions!\n");
exit(1) ;
}
if( xorient >= 0 ){
fprintf(stderr,"++ WARNING: geomparent overrides -orient!\n") ;
}
xorient = gset->daxes->xxorient ;
yorient = gset->daxes->yyorient ;
zorient = gset->daxes->zzorient ;
if( use_zoff ){
fprintf(stderr,"++ WARNING: geomparent overrides -zorigin!\n") ;
}
use_xoff = use_yoff = use_zoff = 1 ;
xoff = gset->daxes->xxorg ;
yoff = gset->daxes->yyorg ;
zoff = gset->daxes->zzorg ;
dxan = gset->daxes->xxdel ;
dyan = gset->daxes->yydel ;
dzan = gset->daxes->zzdel ;
if( gset->taxis != NULL ){
TR = gset->taxis->ttdel ;
tunits = gset->taxis->units_type ;
}
DSET_delete(gset) ; /* delete to save memory */
} else { /* don't have geomparent, so check if other data is OK */
if( xorient < 0 ){
xorient = ORI_R2L_TYPE ;
yorient = ORI_A2P_TYPE ;
zorient = ORI_I2S_TYPE ;
fprintf(stderr,"++ WARNING: orientation defaults to RAI\n") ;
}
if( dxan <= 0.0 ){
dxan = dyan = dzan = 1.0 ;
fprintf(stderr,"++ WARNING: voxel size defaults to 1 mm\n") ;
}
if( ORIENT_sign[xorient] == '-' ) dxan = -dxan ;
if( ORIENT_sign[yorient] == '-' ) dyan = -dyan ;
if( ORIENT_sign[zorient] == '-' ) dzan = -dzan ;
} /* end of setup for new dataset parameters */
/*-- At last: create empty output dataset --*/
dset = EDIT_empty_copy(NULL) ;
nxyz.ijk[0] = nxan ; dxyz.xyz[0] = dxan ;
nxyz.ijk[1] = nyan ; dxyz.xyz[1] = dyan ;
nxyz.ijk[2] = nzan ; dxyz.xyz[2] = dzan ;
orixyz.ijk[0] = xorient ;
orixyz.ijk[1] = yorient ;
orixyz.ijk[2] = zorient ;
orgxyz.xyz[0] = (use_xoff) ? xoff : -0.5*(nxan-1)*dxan ;
orgxyz.xyz[1] = (use_yoff) ? yoff : -0.5*(nyan-1)*dyan ;
orgxyz.xyz[2] = (use_zoff) ? zoff : -0.5*(nzan-1)*dzan ;
EDIT_dset_items( dset ,
ADN_prefix , prefix ,
ADN_datum_all , an_datum ,
ADN_nxyz , nxyz ,
ADN_xyzdel , dxyz ,
ADN_xyzorg , orgxyz ,
ADN_xyzorient , orixyz ,
ADN_nvals , nvals ,
ADN_view_type , view_type ,
ADN_brick_fac , fac ,
ADN_none ) ;
/*-- select dataset type (3D+time or bucket) --*/
if( nvals == 1 && is_3dtime ){
is_3dtime = 0; is_abuc = 1;
fprintf(stderr,"++ WARNING: can't make a 3D+time dataset from 1 volume!\n") ;
}
if( !is_3dtime && !is_abuc && !is_fbuc ){
if( nvals > 1 ) is_3dtime = 1 ;
else is_abuc = 1 ;
}
if( is_3dtime ){
EDIT_dset_items( dset ,
ADN_ntt , nvals ,
ADN_ttorg , 0.0 ,
ADN_ttdel , TR ,
ADN_ttdur , 0.0 ,
ADN_tunits , tunits ,
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type, ANAT_EPI_TYPE ,
ADN_none ) ;
} else if( is_abuc ){
EDIT_dset_items( dset ,
ADN_type , HEAD_ANAT_TYPE ,
ADN_func_type, ANAT_BUCK_TYPE ,
ADN_none ) ;
} else if( is_fbuc ){
EDIT_dset_items( dset ,
ADN_type , HEAD_FUNC_TYPE ,
ADN_func_type, FUNC_BUCK_TYPE ,
ADN_none ) ;
}
/*-- make filename array and store it in dataset header --*/
flab = (char **) malloc(sizeof(char *)*nvals) ;
kk = 0 ;
for( ii=0 ; ii < nvals ; ii++ ){
jj = strlen( argv[iarg+ii] ) ; /* convert .hdr */
flab[ii] = strdup( argv[iarg+ii] ) ; /* filename to */
strcpy( flab[ii]+jj-3 , "img" ) ; /* .img name */
kk += (jj+2) ;
THD_store_datablock_label( dset->dblk , ii , flab[ii] ) ;
}
fatr = malloc(kk) ; fatr[0] = '\0' ; /* all filenames */
for( ii=0 ; ii < nvals ; ii++ ){ /* into one big */
strcat(fatr,flab[ii] ); strcat(fatr," "); /* string */
free(flab[ii]) ;
}
/*-- setting this attribute marks the dataset as being
stored by volumes, rather than all data in one .BRIK file --*/
THD_set_string_atr( dset->dblk , "VOLUME_FILENAMES" , fatr ) ;
free(fatr) ; free(flab) ;
/*-- set byte ordering flag --*/
jj = mri_short_order() ; /* order of this CPU */
if( an_swapped )
dset->dblk->diskptr->byte_order = REVERSE_ORDER(jj) ;
else
dset->dblk->diskptr->byte_order = jj ;
/*-- set history attribute --*/
tross_Make_History( "3dANALYZEtoAFNI" , argc,argv , dset ) ;
/*-- write dataset header --*/
THD_write_3dim_dataset( NULL,NULL , dset , False ) ;
fprintf(stderr,"++ Wrote dataset header %s\n",DSET_HEADNAME(dset)) ;
exit(0) ;
}
int main( int argc , char * argv[] )
{
int narg=1, do_automask=0 , iv , nxyz , do_set=0 ,
*rois=NULL, N_rois=0, all_rois = 0;
THD_3dim_dataset *xset ;
byte *mmm=NULL ; int nmask=0 , nvox_mask=0 ;
THD_fvec3 cmv , setv ;
/*-- read command line arguments --*/
if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ){
printf("Usage: 3dCM [options] dset\n"
"Output = center of mass of dataset, to stdout.\n"
" -mask mset Means to use the dataset 'mset' as a mask:\n"
" Only voxels with nonzero values in 'mset'\n"
" will be averaged from 'dataset'. Note\n"
" that the mask dataset and the input dataset\n"
" must have the same number of voxels.\n"
" -automask Generate the mask automatically.\n"
" -set x y z After computing the CM of the dataset, set the\n"
" origin fields in the header so that the CM\n"
" will be at (x,y,z) in DICOM coords.\n"
" -roi_vals v0 v1 v2 ... : Compute center of mass for each blob\n"
" with voxel value of v0, v1, v2, etc.\n"
" This option is handy for getting ROI \n"
" centers of mass.\n"
" -all_rois Don't bother listing the values of ROIs you want\n"
" the program will find all of them and produce a \n"
" full list.\n"
" NOTE: Masking options are ignored with -roi_vals and -all_rois\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
LOAD_FVEC3(setv,0,0,0) ; /* ZSS: To quiet init. warnings */
narg = 1 ;
while( narg < argc && argv[narg][0] == '-' ){
if( strcmp(argv[narg],"-set") == 0 ){
float xset,yset,zset ;
if( narg+3 >= argc ){
fprintf(stderr,"*** -set need 3 args following!\n") ; exit(1) ;
}
xset = strtod( argv[++narg] , NULL ) ;
yset = strtod( argv[++narg] , NULL ) ;
zset = strtod( argv[++narg] , NULL ) ;
LOAD_FVEC3(setv,xset,yset,zset) ; do_set = 1 ;
THD_set_write_compression(COMPRESS_NONE); /* do not alter compression*/
narg++ ; continue ;
}
if( strncmp(argv[narg],"-mask",5) == 0 ){
THD_3dim_dataset *mask_dset ;
if( mmm != NULL ){
fprintf(stderr,"*** Cannot have two -mask options!\n") ; exit(1) ;
}
if( do_automask ){
fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ;
}
if( narg+1 >= argc ){
fprintf(stderr,"*** -mask option requires a following argument!\n");
exit(1) ;
}
mask_dset = THD_open_dataset( argv[++narg] ) ;
CHECK_OPEN_ERROR(mask_dset,argv[narg]) ;
if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex ){
fprintf(stderr,"*** Cannot deal with complex-valued mask dataset!\n");
exit(1) ;
}
mmm = THD_makemask( mask_dset , 0 , 1.0,0.0 ) ;
nvox_mask = DSET_NVOX(mask_dset) ;
nmask = THD_countmask( nvox_mask , mmm ) ;
if( mmm == NULL || nmask <= 0 ){
fprintf(stderr,"*** Can't make mask from dataset %s\n",argv[narg-1]);
exit(1) ;
}
DSET_delete( mask_dset ) ;
narg++ ; continue ;
}
if( strncmp(argv[narg],"-roi_vals",5) == 0 ){
if( narg+1 >= argc ){
fprintf(stderr,"*** -mask option requires a following argument(s)!\n");
exit(1) ;
}
rois = (int *)calloc(argc, sizeof(int));
N_rois = 0;
++narg;
while (narg < argc-1 && argv[narg][0] != '-') {
rois[N_rois++] = atoi(argv[narg]);
++narg;
}
continue ;
}
if( strncmp(argv[narg],"-all_rois",5) == 0 ){
all_rois = 1;
narg++ ; continue ;
}
if( strcmp(argv[narg],"-automask") == 0 ){
if( mmm != NULL ){
fprintf(stderr,"*** Can't have -mask and -automask!\n") ; exit(1) ;
}
do_automask = 1 ; narg++ ; continue ;
}
fprintf(stderr,"*** Unknown option: %s\n",argv[narg]) ; exit(1) ;
}
/* should have at least 1 more argument */
if( argc <= narg ){
fprintf(stderr,"*** No input dataset!?\n") ; exit(1) ;
}
for( ; narg < argc ; narg++ ){
xset = THD_open_dataset( argv[narg] ) ;
if( xset == NULL ){
fprintf(stderr,"+++ Can't open dataset %s -- skipping\n",argv[narg]);
continue ;
}
DSET_load(xset) ;
if( !DSET_LOADED(xset) ){
fprintf(stderr,"+++ Can't load dataset %s -- skipping\n",argv[narg]);
DSET_delete(xset) ; continue ;
}
if( do_automask ){
if( mmm != NULL ){ free(mmm); mmm = NULL; }
mmm = THD_automask(xset) ;
nvox_mask = DSET_NVOX(xset) ;
nmask = THD_countmask( nvox_mask , mmm ) ;
if( mmm == NULL || nmask <= 0 ){
fprintf( stderr,
"+++ Can't make automask from dataset %s "
"-- skipping\n",argv[narg]) ;
DSET_delete(xset) ; continue ;
}
}
nxyz = DSET_NVOX(xset) ;
if( mmm != NULL && nxyz != nvox_mask ){
fprintf(stderr,"+++ Mask/Dataset grid size mismatch at %s\n -- skipping\n",argv[narg]) ;
DSET_delete(xset) ; continue ;
}
if (all_rois) {
if (!(rois = THD_unique_vals(xset, 0, &N_rois, NULL)) || N_rois == 0) {
ERROR_message("No rois or error in THD_unique_vals"); continue;
}
fprintf(stderr,"#%d distinct ROIs", N_rois);
}
if (!N_rois) {
cmv = THD_cmass( xset , 0 , mmm ) ;
printf("%g %g %g\n",cmv.xyz[0],cmv.xyz[1],cmv.xyz[2]) ;
DSET_unload(xset) ;
if( do_set ){
THD_fvec3 dv , ov ;
if( DSET_IS_MASTERED(xset) ){
fprintf(stderr,"+++ Can't modify CM of dataset %s\n",argv[narg]) ;
} else {
/* lose obliquity */
/* recompute Tc(Cardinal transformation matrix for new grid output */
THD_make_cardinal(xset);
LOAD_FVEC3(ov,DSET_XORG(xset),DSET_YORG(xset),DSET_ZORG(xset)) ;
ov = THD_3dmm_to_dicomm( xset , ov ) ;
dv = SUB_FVEC3(setv,cmv) ;
ov = ADD_FVEC3(dv,ov) ;
ov = THD_dicomm_to_3dmm( xset , ov ) ;
xset->daxes->xxorg = ov.xyz[0] ;
xset->daxes->yyorg = ov.xyz[1] ;
xset->daxes->zzorg = ov.xyz[2] ;
/* allow overwriting header for all types of output data */
putenv("AFNI_DECONFLICT=OVERWRITE") ;
tross_Make_History( "3dCM" , argc,argv , xset );/* ZSS Dec. 09 08 */
if(DSET_IS_BRIK(xset)) {
INFO_message("Rewriting header %s",DSET_HEADNAME(xset)) ;
DSET_overwrite_header( xset ) ;
}
else { /* for other dataset types like NIFTI, rewrite whole dset */
DSET_load( xset ) ;
DSET_overwrite(xset) ;
INFO_message("Wrote new dataset: %s",DSET_BRIKNAME(xset)) ;
}
}
}
} else {
float *xyz;
if ((xyz = THD_roi_cmass(xset , 0 , rois, N_rois))) {
printf("#Dset %s\n",DSET_BRIKNAME(xset));
for (iv=0; iv<N_rois; ++iv) {
printf("#ROI %d\n", rois[iv]);
printf("%g %g %g\n",xyz[3*iv],xyz[3*iv+1],xyz[3*iv+2]) ;
}
free(xyz); free(rois);
} else {
ERROR_message("Failed in THD_roi_cmass"); continue;
}
}
DSET_delete(xset) ;
}
exit(0);
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *dset_in=NULL , *dset_out ;
int Lxx=-1 , Lyy=-1 , Lzz=-1 , Mode=FFT_ABS , Sign=-1 , do_alt=0 ;
char *prefix = "FFTout" ;
int iarg ;
MRI_IMAGE *inim , *outim ; float fac ; int nx,ny,nz ;
THD_ivec3 iv ;
if( argc < 2 || strcasecmp(argv[1],"-help") == 0 ){
printf(
"Usage: 3dFFT [options] dataset\n"
"\n"
"* Does the FFT of the input dataset in 3 directions (x,y,z) and\n"
" produces the output dataset.\n"
"\n"
"* Why you'd want to do this is an interesting question.\n"
"\n"
"* Program 3dcalc can operate on complex-valued datasets, but\n"
" only on one component at a time (cf. the '-cx2r' option).\n"
"\n"
"* Most other AFNI programs can only operate on real-valued\n"
" datasets.\n"
"\n"
"* You could use 3dcalc (twice) to split a complex-valued dataset\n"
" into two real-valued datasets, do your will on those with other\n"
" AFNI programs, then merge the results back into a complex-valued\n"
" dataset with 3dTwotoComplex.\n"
"\n"
"Options\n"
"=======\n"
" -abs = Outputs the magnitude of the FFT [default]\n"
" -phase = Outputs the phase of the FFT (-PI..PI == no unwrapping!)\n"
" -complex = Outputs the complex-valued FFT\n"
" -inverse = Does the inverse FFT instead of the forward FFT\n"
"\n"
" -Lx xx = Use FFT of length 'xx' in the x-direction\n"
" -Ly yy = Use FFT of length 'yy' in the y-direction\n"
" -Lz zz = Use FFT of length 'zz' in the z-direction\n"
" * Set a length to 0 to skip the FFT in that direction\n"
"\n"
" -altIN = Alternate signs of input data before FFT, to bring\n"
" zero frequency from edge of FFT-space to center of grid\n"
" for cosmetic purposes.\n"
" -altOUT = Alternate signs of output data after FFT. If you\n"
" use '-altI' on the forward transform, then you should\n"
" use '-altO' an the inverse transform, to get the\n"
" signs of the recovered image correct.\n"
" **N.B.: You cannot use '-altIN' and '-altOUT' in the same run!\n"
"\n"
" -input dd = Read the input dataset from 'dd', instead of\n"
" from the last argument on the command line.\n"
"\n"
" -prefix pp = Use 'pp' for the output dataset prefix.\n"
"\n"
"Notes\n"
"=====\n"
" * In the present avatar, only 1 sub-brick will be processed.\n"
"\n"
#if 0
" * The program can only do FFT lengths that are factorable\n"
" into a product of powers of 2, 3, and 5, and are even.\n"
" + The largest power of 3 that is allowed is 3^3 = 27.\n"
" + The largest power of 5 that is allowed is 5^3 = 125.\n"
" + e.g., FFT of length 3*5*8=120 is possible.\n"
" + e.g., FFT of length 4*31 =124 is not possible.\n"
#else
" * The program can only do FFT lengths that are positive\n"
" even integers.\n"
#endif
"\n"
" * The 'x', 'y', and 'z' axes here refer to the order the\n"
" data is stored, not DICOM coordinates; cf. 3dinfo.\n"
"\n"
" * If you force (via '-Lx' etc.) an FFT length that is not\n"
" allowed, the program will stop with an error message.\n"
"\n"
" * If you force an FFT length that is shorter than an dataset\n"
" axis dimension, the program will stop with an error message.\n"
"\n"
" * If you don't force an FFT length along a particular axis,\n"
" the program will pick the smallest legal value that is\n"
" greater than or equal to the corresponding dataset dimension.\n"
#if 0
" + e.g., 124 would be increased to 128.\n"
#else
" + e.g., 123 would be increased to 124.\n"
#endif
"\n"
" * If an FFT length is longer than an axis length, then the\n"
" input data in that direction is zero-padded at the end.\n"
"\n"
" * For -abs and -phase, the output dataset is in float format.\n"
"\n"
" * If you do the forward and inverse FFT, then you should get back\n"
" the original dataset, except for roundoff error and except that\n"
" the new dataset axis dimensions may be longer than the original.\n"
"\n"
" * Forward FFT = sum_{k=0..N-1} [ exp(-2*PI*i*k/N) * data(k) ]\n"
"\n"
" * Inverse FFT = sum_{k=0..N-1} [ exp(+2*PI*i*k/N) * data(k) ] / N\n"
"\n"
" * Started a long time ago, but only finished in Aug 2009 at the\n"
" request of John Butman, because he asked so nicely. (Now pay up!)\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
PRINT_VERSION("3dFFT") ;
mainENTRY("3dFFT main") ; machdep() ; AUTHOR("RW Cox") ;
AFNI_logger("3dFFT",argc,argv) ;
/*--- scan args ---*/
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strncasecmp(argv[iarg],"-altI",5) == 0 ){
do_alt = 1 ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-altOUT",5) == 0 ){
do_alt = -1 ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-inverse",4) == 0 ){
Sign = +1 ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-abs",4) == 0 ){
Mode = FFT_ABS ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-phase",4) == 0 ){
Mode = FFT_PHASE ; iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-complex",4) == 0 ){
Mode = FFT_COMPLEX ; iarg++ ; continue ;
}
if( strlen(argv[iarg]) == 3 && strncmp(argv[iarg],"-L",2) == 0 ){
int lll=-1 , mmm ; char *ept ;
iarg++ ;
if( iarg >= argc )
ERROR_exit("need an argument after option %s",argv[iarg-1]) ;
lll = strtol( argv[iarg] , &ept , 10 ) ;
if( *ept != '\0' )
ERROR_exit("bad argument after option %s",argv[iarg-1]) ;
if( lll > 0 && (mmm = csfft_nextup_even(lll)) != lll )
ERROR_exit(
"'%s %d' is not a legal FFT length here: next largest legal value = %d" ,
argv[iarg-1] , lll , mmm ) ;
switch( argv[iarg-1][2] ){
case 'x': case 'X': Lxx = lll ; break ;
case 'y': case 'Y': Lyy = lll ; break ;
case 'z': case 'Z': Lzz = lll ; break ;
default: ERROR_exit("unknown option '%s'",argv[iarg-1]) ;
}
iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-prefix",4) == 0 ){
iarg++ ;
if( iarg >= argc )
ERROR_exit("need an argument after %s\n",argv[iarg-1]) ;
prefix = strdup( argv[iarg] ) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("bad argument after %s\n",argv[iarg-1]) ;
iarg++ ; continue ;
}
if( strncasecmp(argv[iarg],"-input",4) == 0 ){
iarg++ ;
if( iarg >= argc )
ERROR_exit("need an argument after %s\n",argv[iarg-1]) ;
dset_in = THD_open_dataset(argv[iarg]); CHECK_OPEN_ERROR(dset_in,argv[iarg]);
iarg++ ; continue ;
}
ERROR_exit("unknown option '%s'\n",argv[iarg]) ;
}
/* check for simple errors */
if( Lxx == 0 && Lyy == 0 && Lzz == 0 )
ERROR_exit("-Lx, -Ly, -Lz all given as zero?!") ;
/* open input dataset */
if( dset_in == NULL ){
if( iarg >= argc ) ERROR_exit("no input dataset on command line?!\n") ;
dset_in = THD_open_dataset(argv[iarg]); CHECK_OPEN_ERROR(dset_in,argv[iarg]);
}
nx = DSET_NX(dset_in) ; ny = DSET_NY(dset_in) ; nz = DSET_NZ(dset_in) ;
if( DSET_NVALS(dset_in) > 1 )
WARNING_message("only 3dFFT-ing sub-brick #0 of input dataset") ;
/* establish actual FFT lengths now (0 ==> no FFT) */
if( nx == 1 ) Lxx = 0 ; /* can't FFT if dataset is shrimpy! */
if( ny == 1 ) Lyy = 0 ;
if( nz == 1 ) Lzz = 0 ;
if( Lxx < 0 ) Lxx = csfft_nextup_even(nx) ; /* get FFT length from */
if( Lyy < 0 ) Lyy = csfft_nextup_even(ny) ; /* dataset dimensions */
if( Lzz < 0 ) Lzz = csfft_nextup_even(nz) ;
INFO_message("x-axis length=%d ; FFT length=%d %s",nx,Lxx,(Lxx==0)?"==> none":"\0") ;
INFO_message("y-axis length=%d ; FFT length=%d %s",ny,Lyy,(Lyy==0)?"==> none":"\0") ;
INFO_message("z-axis length=%d ; FFT length=%d %s",nz,Lzz,(Lzz==0)?"==> none":"\0") ;
if( Lxx > 0 && Lxx < nx ) ERROR_exit("x-axis FFT length too short for data!") ;
if( Lyy > 0 && Lyy < ny ) ERROR_exit("y-axis FFT length too short for data!") ;
if( Lzz > 0 && Lzz < nz ) ERROR_exit("z-axis FFT length too short for data!") ;
/* extract sub-brick #0 */
DSET_load(dset_in) ; CHECK_LOAD_ERROR(dset_in) ;
inim = mri_to_complex( DSET_BRICK(dset_in,0) ) ; /* convert input to complex */
fac = DSET_BRICK_FACTOR(dset_in,0) ;
if( fac > 0.0f && fac != 1.0f ){ /* scale it if needed */
int ii , nvox = nx*ny*nz ; complex *car = MRI_COMPLEX_PTR(inim) ;
for( ii=0 ; ii < nvox ; ii++ ){ car[ii].r *= fac ; car[ii].i *= fac ; }
}
DSET_unload(dset_in) ; /* input data is all copied now */
/* FFT to get output image */
csfft_scale_inverse(1) ; /* scale by 1/N for inverse FFTs */
outim = mri_fft_3D( Sign , inim , Lxx,Lyy,Lzz , do_alt ) ;
mri_free(inim) ;
/* post-process output? */
switch( Mode ){
case FFT_ABS:{
MRI_IMAGE *qim = mri_complex_abs(outim) ;
mri_free(outim) ; outim = qim ;
}
break ;
case FFT_PHASE:{
MRI_IMAGE *qim = mri_complex_phase(outim) ;
mri_free(outim) ; outim = qim ;
}
break ;
}
/* create and write output dataset */
dset_out = EDIT_empty_copy( dset_in ) ;
tross_Copy_History( dset_in , dset_out ) ;
tross_Make_History( "3dFFT" , argc,argv , dset_out ) ;
LOAD_IVEC3( iv , outim->nx , outim->ny , outim->nz ) ;
EDIT_dset_items( dset_out ,
ADN_prefix , prefix ,
ADN_nvals , 1 ,
ADN_ntt , 0 ,
ADN_nxyz , iv , /* change dimensions, possibly */
ADN_none ) ;
EDIT_BRICK_FACTOR( dset_out , 0 , 0.0 ) ;
EDIT_substitute_brick( dset_out , 0 , outim->kind , mri_data_pointer(outim) ) ;
DSET_write(dset_out) ; WROTE_DSET(dset_out) ; DSET_unload(dset_out) ;
exit(0) ;
}
void BUCK_read_opts( int argc , char * argv[] )
{
int nopt = 1 , ii ;
char dname[THD_MAX_NAME] ;
char subv[THD_MAX_NAME] ;
char *cpt ;
THD_3dim_dataset *dset , *fset=NULL ;
int *svar ;
char *str;
int ok, ilen, nlen;
INIT_3DARR(BUCK_dsar) ;
INIT_XTARR(BUCK_subv) ;
while( nopt < argc ){
if( strcmp(argv[nopt],"-help") == 0 ||
strcmp(argv[nopt],"-h") == 0) {
BUCK_Syntax(strlen(argv[nopt])>3?2:1) ;
exit(0);
}
/**** -prefix prefix ****/
if( strncmp(argv[nopt],"-prefix",6) == 0 ||
strncmp(argv[nopt],"-output",6) == 0 ){
if (BUCK_glue){
fprintf(stderr,"-prefix and -glueto options are not compatible\n");
exit(1) ;
}
nopt++ ;
if( nopt >= argc ){
fprintf(stderr,"need argument after -prefix!\n") ; exit(1) ;
}
MCW_strncpy( BUCK_output_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
continue ;
}
/**** -session directory ****/
if( strncmp(argv[nopt],"-session",6) == 0 ){
if (BUCK_glue){
fprintf(stderr,
"-session and -glueto options are not compatible\n");
exit(1) ;
}
nopt++ ;
if( nopt >= argc ){
fprintf(stderr,"need argument after -session!\n") ; exit(1) ;
}
MCW_strncpy( BUCK_session , argv[nopt++] , THD_MAX_NAME ) ;
continue ;
}
if( strncmp(argv[nopt],"-dry",3) == 0 ){
BUCK_dry = BUCK_verb = 1 ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-fbuc",4) == 0 ){
BUCK_type = HEAD_FUNC_TYPE ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-abuc",4) == 0 ){
BUCK_type = HEAD_ANAT_TYPE ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-verb",5) == 0 ){
BUCK_verb = 1 ;
nopt++ ; continue ;
}
if( strncmp(argv[nopt],"-glueto",5) == 0 ||
strncmp(argv[nopt],"-aglueto",5) == 0){ /* ZSS April 16 2010 */
if( strncmp(BUCK_output_prefix, "buck", 5) != 0 ){
fprintf(stderr,
"-prefix, -glueto, and -aglueto options are not compatible\n");
exit(1) ;
}
if( strncmp(BUCK_session, "./", 5) != 0 ){
fprintf(stderr,
"-session, -glueto, and -aglueto options are not compatible\n");
exit(1) ;
}
nopt++ ;
if( nopt >= argc ){
fprintf(stderr,"need argument after -glueto or -aglueto!\n") ;
exit(1) ;
}
if (strncmp(argv[nopt-1],"-aglueto",5) == 0) { /* ZSS April 16 2010 */
THD_3dim_dataset *ddd = THD_open_dataset( argv[nopt] );
if( !ISVALID_DSET(ddd) ){
/* treat as -prefix */
MCW_strncpy( BUCK_output_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
continue ;
} else {
/* go on as standard -glueto option */
}
}
BUCK_glue = 1 ;
/*----- Verify that file name ends in View Type -----*/
ok = 1;
nlen = strlen(argv[nopt]);
if (nlen <= 5) ok = 0;
if (ok)
{
#if 0 /* old code - scan from end, instead */
for (ilen = 0; ilen < nlen; ilen++)
{
str = argv[nopt] + ilen;
if (str[0] == '+') break;
}
if (ilen == nlen) ok = 0;
#endif
/* scan from end for view type extension, require one char */
/* 30 Oct 2003 [rickr] */
for (ilen = nlen - 1; ilen > 0; ilen--)
{
str = argv[nopt] + ilen;
if (str[0] == '+') break;
}
if (ilen == 0) ok = 0;
}
if (ok)
{
str = argv[nopt] + ilen + 1;
for (ii=FIRST_VIEW_TYPE ; ii <= LAST_VIEW_TYPE ; ii++)
if (! strncmp(str,VIEW_codestr[ii],4)) break ;
if( ii > LAST_VIEW_TYPE ) ok = 0;
}
if (! ok)
{
fprintf(stderr,
"File name must end in +orig, +acpc, or +tlrc after -glueto\n"
"(consider: 3dbucket -prefix dsetA -overwrite dsetA dsetB ...)\n");
exit(1);
}
/*----- Remove View Type from string to make output prefix -----*/
MCW_strncpy( BUCK_output_prefix , argv[nopt] , ilen+1) ;
/*----- Note: no "continue" statement here. File name will now
be processed as an input dataset -----*/
}
if( strncmp(argv[nopt],"-aglueto",5) == 0 ){
if( strncmp(BUCK_output_prefix, "buck", 5) != 0 ){
fprintf(stderr,"-prefix and -aglueto options are not compatible.\n"
"Make sure you do not have two -agluto options on command.\n");
exit(1) ;
}
if( strncmp(BUCK_session, "./", 5) != 0 ){
fprintf(stderr,
"-session and -aglueto options are not compatible\n");
exit(1) ;
}
BUCK_glue = 1 ;
nopt++ ;
if( nopt >= argc ){
fprintf(stderr,"need argument after -glueto!\n") ; exit(1) ;
}
/*----- Verify that file name ends in View Type -----*/
ok = 1;
nlen = strlen(argv[nopt]);
if (nlen <= 5) ok = 0;
if (ok)
{
#if 0 /* old code - scan from end, instead */
for (ilen = 0; ilen < nlen; ilen++)
{
str = argv[nopt] + ilen;
if (str[0] == '+') break;
}
if (ilen == nlen) ok = 0;
#endif
/* scan from end for view type extension, require one char */
/* 30 Oct 2003 [rickr] */
for (ilen = nlen - 1; ilen > 0; ilen--)
{
str = argv[nopt] + ilen;
if (str[0] == '+') break;
}
if (ilen == 0) ok = 0;
}
if (ok)
{
str = argv[nopt] + ilen + 1;
for (ii=FIRST_VIEW_TYPE ; ii <= LAST_VIEW_TYPE ; ii++)
if (! strncmp(str,VIEW_codestr[ii],4)) break ;
if( ii > LAST_VIEW_TYPE ) ok = 0;
}
if (! ok)
{
fprintf(stderr,
"File name must end in +orig, +acpc, or +tlrc after -glueto\n"
"(consider: 3dbucket -prefix dsetA -overwrite dsetA dsetB ...)\n");
exit(1);
}
/*----- Remove View Type from string to make output prefix -----*/
MCW_strncpy( BUCK_output_prefix , argv[nopt] , ilen+1) ;
/*----- Note: no "continue" statement here. File name will now
be processed as an input dataset -----*/
}
if( argv[nopt][0] == '-' ){
fprintf(stderr,"Unknown option: %s\n",argv[nopt]) ;
suggest_best_prog_option(argv[0], argv[nopt]);
exit(1) ;
}
/**** read dataset ****/
cpt = strstr(argv[nopt],"[") ;
if( cpt == NULL ){
if (strlen(argv[nopt]) > THD_MAX_NAME-1) {
ERROR_exit( "Too long a filename for '%s'\n"
"Maximum limit is %d\n", argv[nopt], THD_MAX_NAME-1);
}
strcpy(dname,argv[nopt]) ;
subv[0] = '\0' ; /* make sure subv is reset ZSS Nov. 2010*/
} else if( cpt == argv[nopt] ){
fprintf(stderr,"illegal dataset specifier: %s\n",argv[nopt]) ;
exit(1) ;
} else {
ii = cpt - argv[nopt] ;
if (ii > THD_MAX_NAME-1) {
ERROR_exit( "Too long a filename for '%s'\n"
"Maximum character limit is %d, have %d\\n",
argv[nopt], THD_MAX_NAME-1, ii);
}
if (strlen(argv[nopt])-ii > THD_MAX_NAME-1) {
ERROR_exit( "Too long a sub-brick selection for '%s'\n"
"Maximum limit is %d, have %d\n"
"Consider using '[1dcat FF.1D]' or '[count ...]' methods\n"
"for sub-brick selection. See 3dTcat -help for details.\n",
argv[nopt], THD_MAX_NAME-1, strlen(argv[nopt])-ii);
}
memcpy(dname,argv[nopt],ii) ; dname[ii] = '\0' ;
strcpy(subv,cpt) ;
}
nopt++ ;
dset = THD_open_one_dataset( dname ) ;
if( dset == NULL ){
fprintf(stderr,"can't open dataset %s\n",dname) ; exit(1) ;
}
THD_force_malloc_type( dset->dblk , DATABLOCK_MEM_MALLOC ) ;
if( BUCK_type < 0 ) BUCK_type = dset->type ;
BUCK_ccode = COMPRESS_filecode(dset->dblk->diskptr->brick_name) ;
/* 16 Mar 2010 */
ii = dset->daxes->nxx * dset->daxes->nyy * dset->daxes->nzz ;
if( BUCK_nvox < 0 ){
BUCK_nvox = ii ; fset = dset ;
} else if( ii != BUCK_nvox ){
ERROR_exit("Dataset %s differs in size from first one",dname);
} else if( !EQUIV_GRIDS(dset,fset) ){
WARNING_message("Dataset %s grid differs from first one",dname) ;
}
ADDTO_3DARR(BUCK_dsar,dset) ;
if (subv == NULL || subv[0] == '\0') { /* lazy way for 3dbucket special */
svar = BUCK_get_subv( DSET_NVALS(dset) , subv ) ; /* ZSS Dec 09 */
} else {
svar = MCW_get_thd_intlist (dset, subv); /* ZSS Dec 09 */
}
if( svar == NULL || svar[0] <= 0 ){
fprintf(stderr,"can't decipher index codes from %s%s\n",dname,subv) ;
exit(1) ;
}
ADDTO_XTARR(BUCK_subv,svar) ;
} /* end of loop over command line arguments */
if( argc < 2) {
ERROR_message("Too few options");
BUCK_Syntax(0) ;
exit(1);
}
return ;
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *dset , *oset=NULL , *tset=NULL ;
int nvals , iv , nxyz , ii,jj,kk , iarg , kz,kzold ;
float cut1=2.5,cut2=4.0 , sq2p,sfac , fq ;
MRI_IMAGE *flim ;
char *prefix="despike" , *tprefix=NULL ;
int corder=-1 , nref , ignore=0 , polort=2 , nuse , nomask=0 ;
int nspike, nbig, nproc ;
float **ref ;
float c21,ic21 , pspike,pbig ;
short *sar , *qar ;
byte *tar , *mask=NULL ;
float *zar , *yar ;
int datum ;
int localedit=0 ; /* 04 Apr 2007 */
int verb=1 ;
int do_NEW = 0 ; /* 29 Nov 2013 */
MRI_IMAGE *NEW_psinv=NULL ;
int dilate = 4 ; /* 04 Dec 2013 */
int ctim = 0 ;
/*----- Read command line -----*/
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: 3dDespike [options] dataset\n"
"Removes 'spikes' from the 3D+time input dataset and writes\n"
"a new dataset with the spike values replaced by something\n"
"more pleasing to the eye.\n"
"\n"
"Method:\n"
" * L1 fit a smooth-ish curve to each voxel time series\n"
" [see -corder option for description of the curve]\n"
" [see -NEW option for a different & faster fitting method]\n"
" * Compute the MAD of the difference between the curve and\n"
" the data time series (the residuals).\n"
" * Estimate the standard deviation 'sigma' of the residuals\n"
" as sqrt(PI/2)*MAD.\n"
" * For each voxel value, define s = (value-curve)/sigma.\n"
" * Values with s > c1 are replaced with a value that yields\n"
" a modified s' = c1+(c2-c1)*tanh((s-c1)/(c2-c1)).\n"
" * c1 is the threshold value of s for a 'spike' [default c1=2.5].\n"
" * c2 is the upper range of the allowed deviation from the curve:\n"
" s=[c1..infinity) is mapped to s'=[c1..c2) [default c2=4].\n"
"\n"
"Options:\n"
" -ignore I = Ignore the first I points in the time series:\n"
" these values will just be copied to the\n"
" output dataset [default I=0].\n"
" -corder L = Set the curve fit order to L:\n"
" the curve that is fit to voxel data v(t) is\n"
"\n"
" k=L [ (2*PI*k*t) (2*PI*k*t) ]\n"
" f(t) = a+b*t+c*t*t + SUM [ d * sin(--------) + e * cos(--------) ]\n"
" k=1 [ k ( T ) k ( T ) ]\n"
"\n"
" where T = duration of time series;\n"
" the a,b,c,d,e parameters are chosen to minimize\n"
" the sum over t of |v(t)-f(t)| (L1 regression);\n"
" this type of fitting is is insensitive to large\n"
" spikes in the data. The default value of L is\n"
" NT/30, where NT = number of time points.\n"
"\n"
" -cut c1 c2 = Alter default values for the spike cut values\n"
" [default c1=2.5, c2=4.0].\n"
" -prefix pp = Save de-spiked dataset with prefix 'pp'\n"
" [default pp='despike']\n"
" -ssave ttt = Save 'spikiness' measure s for each voxel into a\n"
" 3D+time dataset with prefix 'ttt' [default=no save]\n"
" -nomask = Process all voxels\n"
" [default=use a mask of high-intensity voxels, ]\n"
" [as created via '3dAutomask -dilate 4 dataset'].\n"
" -dilate nd = Dilate 'nd' times (as in 3dAutomask). The default\n"
" value of 'nd' is 4.\n"
" -q[uiet] = Don't print '++' informational messages.\n"
"\n"
" -localedit = Change the editing process to the following:\n"
" If a voxel |s| value is >= c2, then replace\n"
" the voxel value with the average of the two\n"
" nearest non-spike (|s| < c2) values; the first\n"
" one previous and the first one after.\n"
" Note that the c1 cut value is not used here.\n"
"\n"
" -NEW = Use the 'new' method for computing the fit, which\n"
" should be faster than the L1 method for long time\n"
" series (200+ time points); however, the results\n"
" are similar but NOT identical. [29 Nov 2013]\n"
" * You can also make the program use the 'new'\n"
" method by setting the environment variable\n"
" AFNI_3dDespike_NEW\n"
" to the value YES; as in\n"
" setenv AFNI_3dDespike_NEW YES (csh)\n"
" export AFNI_3dDespike_NEW=YES (bash)\n"
" * If this variable is set to YES, you can turn off\n"
" the '-NEW' processing by using the '-OLD' option.\n"
" -->>* For time series more than 500 points long, the\n"
" '-OLD' algorithm is tremendously slow. You should\n"
" use the '-NEW' algorith in such cases.\n"
" ** At some indeterminate point in the future, the '-NEW'\n"
" method will become the default!\n"
" -->>* As of 29 Sep 2016, '-NEW' is the default if there\n"
" is more than 500 points in the time series dataset.\n"
"\n"
" -NEW25 = A slightly more aggressive despiking approach than\n"
" the '-NEW' method.\n"
"\n"
"Caveats:\n"
"* Despiking may interfere with image registration, since head\n"
" movement may produce 'spikes' at the edge of the brain, and\n"
" this information would be used in the registration process.\n"
" This possibility has not been explored or calibrated.\n"
"* [LATER] Actually, it seems like the registration problem\n"
" does NOT happen, and in fact, despiking seems to help!\n"
"* Check your data visually before and after despiking and\n"
" registration!\n"
" [Hint: open 2 AFNI controllers, and turn Time Lock on.]\n"
) ;
PRINT_AFNI_OMP_USAGE("3dDespike",NULL) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
/** AFNI package setup and logging **/
mainENTRY("3dDespike main"); machdep(); AFNI_logger("3dDespike",argc,argv);
PRINT_VERSION("3dDespike") ; AUTHOR("RW Cox") ;
/** parse options **/
if( AFNI_yesenv("AFNI_3dDespike_NEW") ) do_NEW = 1 ; /* 29 Nov 2013 */
iarg = 1 ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strncmp(argv[iarg],"-q",2) == 0 ){ /* 04 Apr 2007 */
verb = 0 ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-v",2) == 0 ){
verb++ ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-NEW") == 0 ){ /* 29 Nov 2013 */
do_NEW = 1 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-NEW25") == 0 ){ /* 29 Sep 2016 */
do_NEW = 1 ; use_des25 = 1 ; cut1 = 2.5f ; cut2 = 3.2f ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-OLD") == 0 ){
do_NEW = 0 ; iarg++ ; continue ;
}
/** -localedit **/
if( strcmp(argv[iarg],"-localedit") == 0 ){ /* 04 Apr 2007 */
localedit = 1 ; iarg++ ; continue ;
}
/** don't use masking **/
if( strcmp(argv[iarg],"-nomask") == 0 ){
nomask = 1 ; iarg++ ; continue ;
}
/** dilation count [04 Dec 2013] **/
if( strcmp(argv[iarg],"-dilate") == 0 ){
dilate = (int)strtod(argv[++iarg],NULL) ;
if( dilate <= 0 ) dilate = 1 ;
else if( dilate > 99 ) dilate = 99 ;
iarg++ ; continue ;
}
/** output dataset prefix **/
if( strcmp(argv[iarg],"-prefix") == 0 ){
prefix = argv[++iarg] ;
if( !THD_filename_ok(prefix) ) ERROR_exit("-prefix is not good");
iarg++ ; continue ;
}
/** ratio dataset prefix **/
if( strcmp(argv[iarg],"-ssave") == 0 ){
tprefix = argv[++iarg] ;
if( !THD_filename_ok(tprefix) ) ERROR_exit("-ssave prefix is not good");
iarg++ ; continue ;
}
/** trigonometric polynomial order **/
if( strcmp(argv[iarg],"-corder") == 0 ){
corder = strtol( argv[++iarg] , NULL , 10 ) ;
if( corder < 0 ) ERROR_exit("Illegal value of -corder");
iarg++ ; continue ;
}
/** how much to ignore at start **/
if( strcmp(argv[iarg],"-ignore") == 0 ){
ignore = strtol( argv[++iarg] , NULL , 10 ) ;
if( ignore < 0 ) ERROR_exit("Illegal value of -ignore");
iarg++ ; continue ;
}
/** thresholds for s ratio **/
if( strcmp(argv[iarg],"-cut") == 0 ){
cut1 = strtod( argv[++iarg] , NULL ) ;
cut2 = strtod( argv[++iarg] , NULL ) ;
if( cut1 < 1.0 || cut2 < cut1+0.5 )
ERROR_exit("Illegal values after -cut");
iarg++ ; continue ;
}
ERROR_exit("Unknown option: %s",argv[iarg]) ;
}
c21 = cut2-cut1 ; ic21 = 1.0/c21 ;
/*----- read input dataset -----*/
if( iarg >= argc ) ERROR_exit("No input dataset!!??");
dset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(dset,argv[iarg]) ;
datum = DSET_BRICK_TYPE(dset,0) ;
if( (datum != MRI_short && datum != MRI_float) || !DSET_datum_constant(dset) )
ERROR_exit("Can't process non-short, non-float dataset!") ;
if( verb ) INFO_message("Input data type = %s\n",MRI_TYPE_name[datum]) ;
nvals = DSET_NUM_TIMES(dset) ; nuse = nvals - ignore ;
if( nuse < 15 )
ERROR_exit("Can't use dataset with < 15 time points per voxel!") ;
if( nuse > 500 && !do_NEW ){
INFO_message("Switching to '-NEW' method since number of time points = %d > 500",nuse) ;
do_NEW = 1 ;
}
if( use_des25 && nuse < 99 ) use_des25 = 0 ;
if( verb ) INFO_message("ignoring first %d time points, using last %d",ignore,nuse);
if( corder > 0 && 4*corder+2 > nuse ){
ERROR_exit("-corder %d is too big for NT=%d",corder,nvals) ;
} else if( corder < 0 ){
corder = rint(nuse/30.0) ; if( corder > 50 && !do_NEW ) corder = 50 ;
if( verb ) INFO_message("using %d time points => -corder %d",nuse,corder) ;
} else {
if( verb ) INFO_message("-corder %d set from command line",corder) ;
}
nxyz = DSET_NVOX(dset) ;
if( verb ) INFO_message("Loading dataset %s",argv[iarg]) ;
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
/*-- create automask --*/
if( !nomask ){
mask = THD_automask( dset ) ;
if( verb ){
ii = THD_countmask( DSET_NVOX(dset) , mask ) ;
INFO_message("%d voxels in the automask [out of %d in dataset]",ii,DSET_NVOX(dset)) ;
}
for( ii=0 ; ii < dilate ; ii++ )
THD_mask_dilate( DSET_NX(dset), DSET_NY(dset), DSET_NZ(dset), mask, 3 ) ;
if( verb ){
ii = THD_countmask( DSET_NVOX(dset) , mask ) ;
INFO_message("%d voxels in the dilated automask [out of %d in dataset]",ii,DSET_NVOX(dset)) ;
}
} else {
if( verb ) INFO_message("processing all %d voxels in dataset",DSET_NVOX(dset)) ;
}
/*-- create empty despiked dataset --*/
oset = EDIT_empty_copy( dset ) ;
EDIT_dset_items( oset ,
ADN_prefix , prefix ,
ADN_brick_fac , NULL ,
ADN_datum_all , datum ,
ADN_none ) ;
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(oset)) )
ERROR_exit("output dataset already exists: %s",DSET_HEADNAME(oset));
tross_Copy_History( oset , dset ) ;
tross_Make_History( "3dDespike" , argc , argv , oset ) ;
/* create bricks (will be filled with zeros) */
for( iv=0 ; iv < nvals ; iv++ )
EDIT_substitute_brick( oset , iv , datum , NULL ) ;
/* copy the ignored bricks */
switch( datum ){
case MRI_short:
for( iv=0 ; iv < ignore ; iv++ ){
sar = DSET_ARRAY(oset,iv) ;
qar = DSET_ARRAY(dset,iv) ;
memcpy( sar , qar , DSET_BRICK_BYTES(dset,iv) ) ;
DSET_unload_one(dset,iv) ;
}
break ;
case MRI_float:
for( iv=0 ; iv < ignore ; iv++ ){
zar = DSET_ARRAY(oset,iv) ;
yar = DSET_ARRAY(dset,iv) ;
memcpy( zar , yar , DSET_BRICK_BYTES(dset,iv) ) ;
DSET_unload_one(dset,iv) ;
}
break ;
}
/*-- setup to save a threshold statistic dataset, if desired --*/
if( tprefix != NULL ){
float *fac ;
tset = EDIT_empty_copy( dset ) ;
fac = (float *) malloc( sizeof(float) * nvals ) ;
for( ii=0 ; ii < nvals ; ii++ ) fac[ii] = TFAC ;
EDIT_dset_items( tset ,
ADN_prefix , tprefix ,
ADN_brick_fac , fac ,
ADN_datum_all , MRI_byte ,
ADN_func_type , FUNC_FIM_TYPE ,
ADN_none ) ;
free(fac) ;
tross_Copy_History( tset , dset ) ;
tross_Make_History( "3dDespike" , argc , argv , tset ) ;
#if 0
if( THD_is_file(DSET_HEADNAME(tset)) )
ERROR_exit("-ssave dataset already exists");
#endif
tross_Copy_History( tset , dset ) ;
tross_Make_History( "3dDespike" , argc , argv , tset ) ;
for( iv=0 ; iv < nvals ; iv++ )
EDIT_substitute_brick( tset , iv , MRI_byte , NULL ) ;
}
/*-- setup to find spikes --*/
sq2p = sqrt(0.5*PI) ;
sfac = sq2p / 1.4826f ;
/* make ref functions */
nref = 2*corder+3 ;
ref = (float **) malloc( sizeof(float *) * nref ) ;
for( jj=0 ; jj < nref ; jj++ )
ref[jj] = (float *) malloc( sizeof(float) * nuse ) ;
/* r(t) = 1 */
for( iv=0 ; iv < nuse ; iv++ ) ref[0][iv] = 1.0 ;
jj = 1 ;
/* r(t) = t - tmid */
{ float tm = 0.5 * (nuse-1.0) ; float fac = 2.0 / nuse ;
for( iv=0 ; iv < nuse ; iv++ ) ref[1][iv] = (iv-tm)*fac ;
jj = 2 ;
/* r(t) = (t-tmid)**jj */
for( ; jj <= polort ; jj++ )
for( iv=0 ; iv < nuse ; iv++ )
ref[jj][iv] = pow( (iv-tm)*fac , (double)jj ) ;
}
for( kk=1 ; kk <= corder ; kk++ ){
fq = (2.0*PI*kk)/nuse ;
/* r(t) = sin(2*PI*k*t/N) */
for( iv=0 ; iv < nuse ; iv++ )
ref[jj][iv] = sin(fq*iv) ;
jj++ ;
/* r(t) = cos(2*PI*k*t/N) */
for( iv=0 ; iv < nuse ; iv++ )
ref[jj][iv] = cos(fq*iv) ;
jj++ ;
}
/****** setup for the NEW solution method [29 Nov 2013] ******/
if( do_NEW ){
NEW_psinv = DES_get_psinv(nuse,nref,ref) ;
INFO_message("Procesing time series with NEW model fit algorithm") ;
} else {
INFO_message("Procesing time series with OLD model fit algorithm") ;
}
/*--- loop over voxels and do work ---*/
#define Laplace_t2p(val) ( 1.0 - nifti_stat2cdf( (val), 15, 0.0, 1.4427 , 0.0 ) )
if( verb ){
if( !localedit ){
INFO_message("smash edit thresholds: %.1f .. %.1f MADs",cut1*sq2p,cut2*sq2p) ;
ININFO_message(" [ %.3f%% .. %.3f%% of normal distribution]",
200.0*qg(cut1*sfac) , 200.0*qg(cut2*sfac) ) ;
ININFO_message(" [ %.3f%% .. %.3f%% of Laplace distribution]" ,
100.0*Laplace_t2p(cut1) , 100.0*Laplace_t2p(cut2) ) ;
} else {
INFO_message("local edit threshold: %.1f MADS",cut2*sq2p) ;
ININFO_message(" [ %.3f%% of normal distribution]",
200.0*qg(cut2*sfac) ) ;
ININFO_message(" [ %.3f%% of Laplace distribution]",
100.0*Laplace_t2p(cut1) ) ;
}
INFO_message("%d slices to process",DSET_NZ(dset)) ;
}
kzold = -1 ;
nspike = 0 ; nbig = 0 ; nproc = 0 ; ctim = NI_clock_time() ;
AFNI_OMP_START ;
#pragma omp parallel if( nxyz > 6666 )
{ int ii , iv , iu , id , jj ;
float *far , *dar , *var , *fitar , *ssp , *fit , *zar ;
short *sar , *qar ; byte *tar ;
float fsig , fq , cls , snew , val ;
float *NEW_wks=NULL ;
#pragma omp critical (DESPIKE_malloc)
{ far = (float *) malloc( sizeof(float) * nvals ) ;
dar = (float *) malloc( sizeof(float) * nvals ) ;
var = (float *) malloc( sizeof(float) * nvals ) ;
fitar = (float *) malloc( sizeof(float) * nvals ) ;
ssp = (float *) malloc( sizeof(float) * nvals ) ;
fit = (float *) malloc( sizeof(float) * nref ) ;
if( do_NEW ) NEW_wks = (float *)malloc(sizeof(float)*DES_workspace_size(nuse,nref)) ;
}
#ifdef USE_OMP
INFO_message("start OpenMP thread #%d",omp_get_thread_num()) ;
#endif
#pragma omp for
for( ii=0 ; ii < nxyz ; ii++ ){ /* ii = voxel index */
if( mask != NULL && mask[ii] == 0 ) continue ; /* skip this voxel */
#ifndef USE_OMP
kz = DSET_index_to_kz(dset,ii) ; /* starting a new slice */
if( kz != kzold ){
if( verb ){
fprintf(stderr, "++ start slice %2d",kz ) ;
if( nproc > 0 ){
pspike = (100.0*nspike)/nproc ;
pbig = (100.0*nbig )/nproc ;
fprintf(stderr,
"; so far %d data points, %d edits [%.3f%%], %d big edits [%.3f%%]",
nproc,nspike,pspike,nbig,pbig ) ;
}
fprintf(stderr,"\n") ;
}
kzold = kz ;
}
#else
if( verb && ii % 2345 == 1234 ) fprintf(stderr,".") ;
#endif
/*** extract ii-th time series into far[] ***/
switch( datum ){
case MRI_short:
for( iv=0 ; iv < nuse ; iv++ ){
qar = DSET_ARRAY(dset,iv+ignore) ; /* skip ignored data */
far[iv] = (float)qar[ii] ;
}
break ;
case MRI_float:
for( iv=0 ; iv < nuse ; iv++ ){
zar = DSET_ARRAY(dset,iv+ignore) ;
far[iv] = zar[ii] ;
}
break ;
}
AAmemcpy(dar,far,sizeof(float)*nuse) ; /* copy time series into dar[] */
/*** solve for L1 fit ***/
if( do_NEW )
cls = DES_solve( NEW_psinv , far , fit , NEW_wks ) ; /* 29 Nov 2013 */
else
cls = cl1_solve( nuse , nref , far , ref , fit,0 ) ; /* the slow part */
if( cls < 0.0f ){ /* fit failed! */
#if 0
fprintf(stderr,"curve fit fails at voxel %d %d %d\n",
DSET_index_to_ix(dset,ii) ,
DSET_index_to_jy(dset,ii) ,
DSET_index_to_kz(dset,ii) ) ;
#endif
continue ; /* skip this voxel */
}
for( iv=0 ; iv < nuse ; iv++ ){ /* detrend */
val = fit[0]
+ fit[1]*ref[1][iv] /* quadratic part of curve fit */
+ fit[2]*ref[2][iv] ;
for( jj=3 ; jj < nref ; jj++ ) /* rest of curve fit */
val += fit[jj] * ref[jj][iv] ;
fitar[iv] = val ; /* save curve fit value */
var[iv] = dar[iv]-val ; /* remove fitted value = resid */
far[iv] = fabsf(var[iv]) ; /* abs value of resid */
}
/*** compute estimate standard deviation of detrended data ***/
fsig = sq2p * qmed_float(nuse,far) ; /* also mangles far array */
/*** process time series for spikes, editing data in dar[] ***/
if( fsig > 0.0f ){ /* data wasn't fit perfectly */
/* find spikiness for each point in time */
fq = 1.0f / fsig ;
for( iv=0 ; iv < nuse ; iv++ ){
ssp[iv] = fq * var[iv] ; /* spikiness s = how many sigma out */
}
/* save spikiness in -ssave datset */
if( tset != NULL ){
for( iv=0 ; iv < nuse ; iv++ ){
tar = DSET_ARRAY(tset,iv+ignore) ;
snew = ITFAC*fabsf(ssp[iv]) ; /* scale for byte storage */
tar[ii] = BYTEIZE(snew) ; /* cf. mrilib.h */
}
}
/* process values of |s| > cut1, editing dar[] */
for( iv=0 ; iv < nuse ; iv++ ){ /* loop over time points */
if( !localedit ){ /** classic 'smash' edit **/
if( ssp[iv] > cut1 ){
snew = cut1 + c21*mytanh((ssp[iv]-cut1)*ic21) ; /* edit s down */
dar[iv] = fitar[iv] + snew*fsig ;
#pragma omp critical (DESPIKE_counter)
{ nspike++ ; if( ssp[iv] > cut2 ) nbig++ ; }
} else if( ssp[iv] < -cut1 ){
snew = -cut1 + c21*mytanh((ssp[iv]+cut1)*ic21) ; /* edit s up */
dar[iv] = fitar[iv] + snew*fsig ;
#pragma omp critical (DESPIKE_counter)
{ nspike++ ; if( ssp[iv] < -cut2 ) nbig++ ; }
}
} else { /** local edit: 04 Apr 2007 **/
if( ssp[iv] >= cut2 || ssp[iv] <= -cut2 ){
for( iu=iv+1 ; iu < nuse ; iu++ ) /* find non-spike above */
if( ssp[iu] < cut2 && ssp[iu] > -cut2 ) break ;
for( id=iv-1 ; id >= 0 ; id-- ) /* find non-spike below */
if( ssp[id] < cut2 && ssp[id] > -cut2 ) break ;
switch( (id>=0) + 2*(iu<nuse) ){ /* compute replacement val */
case 3: val = 0.5*(dar[iu]+dar[id]); break; /* iu and id OK */
case 2: val = dar[iu] ; break; /* only iu OK */
case 1: val = dar[id] ; break; /* only id OK */
default: val = fitar[iv] ; break; /* shouldn't be */
}
dar[iv] = val ;
#pragma omp critical (DESPIKE_counter)
{ nspike++ ; nbig++ ; }
}
}
} /* end of loop over time points */
#pragma omp atomic
nproc += nuse ; /* number data points processed */
} /* end of processing time series when fsig is positive */
/* put dar[] time series (possibly edited above) into output bricks */
switch( datum ){
case MRI_short:
for( iv=0 ; iv < nuse ; iv++ ){
sar = DSET_ARRAY(oset,iv+ignore) ; /* output brick */
sar[ii] = (short)dar[iv] ; /* original or mutated data */
}
break ;
case MRI_float:
for( iv=0 ; iv < nuse ; iv++ ){
zar = DSET_ARRAY(oset,iv+ignore) ; /* output brick */
zar[ii] = dar[iv] ; /* original or mutated data */
}
break ;
}
} /* end of loop over voxels #ii */
#pragma omp critical (DESPIKE_malloc)
{ free(fit); free(ssp); free(fitar); free(var); free(dar); free(far);
if( do_NEW ) free(NEW_wks) ; }
} /* end OpenMP */
AFNI_OMP_END ;
#ifdef USE_OMP
if( verb ) fprintf(stderr,"\n") ;
#endif
ctim = NI_clock_time() - ctim ;
INFO_message( "Elapsed despike time = %s" , nice_time_string(ctim) ) ;
if( ctim > 345678 && !do_NEW )
ININFO_message("That was SLOW -- try the '-NEW' option for a speedup") ;
#ifdef USE_OMP
if( verb ) fprintf(stderr,"\n") ;
#endif
/*--- finish up ---*/
if( do_NEW ) mri_free(NEW_psinv) ;
DSET_delete(dset) ; /* delete input dataset */
if( verb ){
if( nproc > 0 ){
pspike = (100.0*nspike)/nproc ;
pbig = (100.0*nbig )/nproc ;
INFO_message("FINAL: %d data points, %d edits [%.3f%%], %d big edits [%.3f%%]",
nproc,nspike,pspike,nbig,pbig ) ;
} else {
INFO_message("FINAL: no good voxels found to process!!??") ;
}
}
/* write results */
DSET_write(oset) ;
if( verb ) WROTE_DSET(oset) ;
DSET_delete(oset) ;
if( tset != NULL ){
DSET_write(tset) ;
if( verb ) WROTE_DSET(tset) ;
DSET_delete(tset) ;
}
exit( THD_get_write_error_count() ) ;
}
int main(int argc, char *argv[]) {
int i,j,k,l,m,n,mm,ii;
int idx;
int iarg;
THD_3dim_dataset *insetTIME = NULL;
// THD_3dim_dataset *inset0 = NULL;
THD_3dim_dataset *MASK=NULL;
char *prefix="REHO" ;
char in_name[300];
char in_mask[300];
THD_3dim_dataset *outset=NULL;
char outname[300];
int NIFTI_OUT=0;
int DTYPE=0;
int HAVE_MASK = 0;
int ***mskd; // define mask of where time series are nonzero
double temp_sum;
// FILE *fout0, *fout1;
int Nvox=-1; // tot number vox
int Dim[4]={0,0,0,0};
float fbot = -1., ftop = -1;
float delF = -1;
float *allF=NULL;
float **allPar=NULL;
int Npar=NRSFC; // currently... see list below
char *namePar[NRSFC]={"ALFF", "MALFF", "FALFF",
"RSFA", "MRSFA", "FRSFA"};
int MIN_full=0, MAX_full=-1; // indices of full spect
int MIN_bp=0, MAX_bp = -1; // indices of lff/bp region
mainENTRY("3dAmpToRSFC"); machdep();
// ****************************************************************
// ****************************************************************
// load AFNI stuff
// ****************************************************************
// ****************************************************************
// INFO_message("version: NU");
/** scan args **/
if (argc == 1) { usage_AmpToRSFC(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_AmpToRSFC(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strncmp(argv[iarg],"-band",5) == 0 ){
if( ++iarg >= argc-1 ) ERROR_exit("need 2 arguments after -band!") ;
fbot = strtod(argv[iarg++],NULL) ;
ftop = strtod(argv[iarg++],NULL) ;
continue ;
}
if( strcmp(argv[iarg],"-mask") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
HAVE_MASK=1;
sprintf(in_mask,"%s", argv[iarg]);
MASK = THD_open_dataset(in_mask) ;
if( (MASK == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_mask);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-prefix'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-prefix'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_amp") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-in_amp'");
sprintf(in_name,"%s", argv[iarg]);
DTYPE = 1; // for amps
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_pow") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-in_pow'");
sprintf(in_name,"%s", argv[iarg]);
DTYPE = 2; // for pow
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
HAVE_MASK=1;
sprintf(in_mask,"%s", argv[iarg]);
MASK = THD_open_dataset(in_mask) ;
if( (MASK == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_mask);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-nifti") == 0) {
NIFTI_OUT=1;
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
// ---------------------------------------------------------------
// TEST BASIC INPUT PROPERTIES
if (iarg < 3) {
ERROR_message("Too few options. Try -help for details.\n");
exit(1);
}
if( !DTYPE ) {
ERROR_message("Think somebody forgot to specify an input file"
" using '-in_amp ...' or '-in_pow ...'.");
exit(12);
}
else{
insetTIME = THD_open_dataset(in_name) ;
if( (insetTIME == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_name);
DSET_load(insetTIME); CHECK_LOAD_ERROR(insetTIME);
Nvox = DSET_NVOX(insetTIME) ;
Dim[0] = DSET_NX(insetTIME); Dim[1] = DSET_NY(insetTIME);
Dim[2] = DSET_NZ(insetTIME); Dim[3]= DSET_NVALS(insetTIME);
delF = DSET_TR(insetTIME);
}
if( (fbot<0) || (ftop<0) ) {
ERROR_message("Think somebody forgot to specify upper and lower"
" frequency bounds using '-band ... ...'.");
exit(11);
}
if( fbot > ftop )
ERROR_exit("Can't have ftop < fbot! Try entering frequency"
"band limits again");
if( MASK )
if ( Dim[0] != DSET_NX(MASK) || Dim[1] != DSET_NY(MASK) ||
Dim[2] != DSET_NZ(MASK) ) {
ERROR_message("Mask and inset don't appear to have the same "
"dimensions.\n");
exit(1);
}
// ****************************************************************
// ****************************************************************
// pre-stuff, make storage
// ****************************************************************
// ****************************************************************
// array of freqs-- starts at delta F, not zero, as the current
// input data sets must!
allF = (float *)calloc(Dim[3], sizeof(float));
// will be the output
allPar = calloc(Npar,sizeof(allPar));
for(i=0 ; i<Npar ; i++)
allPar[i] = calloc(Nvox,sizeof(float));
// MASK
mskd = (int ***) calloc( Dim[0], sizeof(int **) );
for ( i = 0 ; i < Dim[0] ; i++ )
mskd[i] = (int **) calloc( Dim[1], sizeof(int *) );
for ( i = 0 ; i < Dim[0] ; i++ )
for ( j = 0 ; j < Dim[1] ; j++ )
mskd[i][j] = (int *) calloc( Dim[2], sizeof(int) );
if( (mskd == NULL) || (allF == NULL) || (allPar == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure (mask).\n\n");
exit(33);
}
// *************************************************************
// *************************************************************
// Beginning of main loops
// *************************************************************
// *************************************************************
// Populate freq bands. For now, delF is constant. Later.... who
// knows, so make flexible
allF[0] = DSET_TIMEORIGIN(insetTIME);
if( allF[0] < EPS_V )
ERROR_exit("The t-axis (here, frequency) origin is 0!"
"\n\t-> but you shouldn't have a baseline 0-frequency!");
for( i=1 ; i<Dim[3] ; i++ )
allF[i] = allF[i-1] + delF;
// fill in rest of freq ranges; MIN_full=0 already
MAX_full = Dim[3]-1;
// these should be in order, so we can pass through like this.
for( i=0 ; i<Dim[3] ; i++ ) {
ii = Dim[3] - 1 - i;
if( allF[ii] >= fbot )
MIN_bp = ii;
if( allF[i] <= ftop )
MAX_bp = i;
}
if(MAX_bp < MIN_bp) // shouldn't happen...
ERROR_exit("Something went horribly wrong with reading in the "
"bandpass limits! bot:%f, top:%f",MIN_bp, MAX_bp);
INFO_message("Actual BP range: indices [%d, %d] -> "
"freqs [%.4f, %.4f]", MIN_bp, MAX_bp,
allF[MIN_bp], allF[MAX_bp]);
INFO_message("Full freq range: indices [%d, %d] -> "
"freqs [%.4f, %.4f]", MIN_full, MAX_full,
allF[MIN_full], allF[MAX_full]);
// go through once: define data vox
idx = 0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( HAVE_MASK ) {
if( THD_get_voxel(MASK,idx,0)>0 )
mskd[i][j][k] = 1;
}
else {
temp_sum = 0.;
for ( l=0 ; l<Dim[3] ; l++ )
temp_sum+= abs(THD_get_voxel(insetTIME,idx,l));
if ( temp_sum > EPS_V )
mskd[i][j][k] = 1;
}
idx++;
}
INFO_message("Done masking.");
Spect_to_RSFC( insetTIME,
DTYPE,
Dim,
mskd,
MIN_bp, MAX_bp,
MIN_full, MAX_full,
allPar,
Npar
);
INFO_message("Done calculating parameters.");
// **************************************************************
// **************************************************************
// Store and output
// **************************************************************
// **************************************************************
for( m=0; m<Npar ; m++) {
outset = EDIT_empty_copy(insetTIME) ;
if(NIFTI_OUT)
sprintf(outname,"%s_%s.nii.gz",prefix, namePar[m]);
else
sprintf(outname,"%s_%s",prefix, namePar[m]);
INFO_message(" writing: %s %s", prefix, outname);
EDIT_dset_items( outset,
ADN_nvals , 1 ,
ADN_datum_all , MRI_float ,
ADN_prefix , outname ,
ADN_none ) ;
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(outset)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(outset));
EDIT_substitute_brick(outset, 0, MRI_float, allPar[m]);
allPar[m]=NULL;
THD_load_statistics(outset);
tross_Make_History("3dAmpToRSFC", argc, argv, outset);
THD_write_3dim_dataset(NULL, NULL, outset, True);
if(outset) {
DSET_delete(outset);
free(outset);
}
}
// ************************************************************
// ************************************************************
// Freeing
// ************************************************************
// ************************************************************
if(allF)
free(allF);
if(MASK) {
DSET_delete(MASK);
free(MASK);
}
if(insetTIME) {
DSET_delete(insetTIME);
free(insetTIME);
}
if(mskd) {
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++)
free(mskd[i][j]);
for( i=0 ; i<Dim[0] ; i++)
free(mskd[i]);
free(mskd);
}
if(allPar) { // have freed other parts of this above
free(allPar);
}
return 0;
}
