int mri_write_1D( char *fname , MRI_IMAGE *im ) /* 16 Nov 1999 */
{
MRI_IMAGE *fim ;
int jj ;
ENTRY("mri_write_1D") ;
if( im == NULL || im->nz > 1 ) RETURN( 0 ) ; /* stoopid user */
fim = mri_transpose( im ) ;
jj = mri_write_ascii( fname , fim ) ;
mri_free(fim) ;
RETURN( jj );
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *inset=NULL ;
byte *mask=NULL ; int mask_nx=0,mask_ny=0,mask_nz=0 , automask=0 , masknum=0 ;
int iarg=1 , verb=1 , ntype=0 , nev,kk,ii,nxyz,nt ;
float na,nb,nc , dx,dy,dz ;
MRI_IMARR *imar=NULL ; int *ivox ; MRI_IMAGE *pim ;
int do_vmean=0 , do_vnorm=0 , sval_itop=0 ;
int polort=-1 ; float *ev ;
MRI_IMARR *ortar ; MRI_IMAGE *ortim ; int nyort=0 ;
float bpass_L=0.0f , bpass_H=0.0f , dtime ; int do_bpass=0 ;
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: 3dmaskSVD [options] inputdataset\n"
"Author: Zhark the Gloriously Singular\n"
"\n"
"* Computes the principal singular vector of the time series\n"
" vectors extracted from the input dataset over the input mask.\n"
" ++ You can use the '-sval' option to change which singular\n"
" vectors are output.\n"
"* The sign of the output vector is chosen so that the average\n"
" of arctanh(correlation coefficient) over all input data\n"
" vectors (from the mask) is positive.\n"
"* The output vector is normalized: the sum of its components\n"
" squared is 1.\n"
"* You probably want to use 3dDetrend (or something similar) first,\n"
" to get rid of annoying artifacts, such as motion, breathing,\n"
" dark matter interactions with the brain, etc.\n"
" ++ If you are lazy scum like Zhark, you might be able to get\n"
" away with using the '-polort' option.\n"
" ++ In particular, if your data time series has a nonzero mean,\n"
" then you probably want at least '-polort 0' to remove the\n"
" mean, otherwise you'll pretty much just get a constant\n"
" time series as the principal singular vector!\n"
"* An alternative to this program would be 3dmaskdump followed\n"
" by 1dsvd, which could give you all the singular vectors you\n"
" could ever want, and much more -- enough to confuse you for days.\n"
" ++ In particular, although you COULD input a 1D file into\n"
" 3dmaskSVD, the 1dsvd program would make much more sense.\n"
"* This program will be pretty slow if there are over about 2000\n"
" voxels in the mask. It could be made more efficient for\n"
" such cases, but you'll have to give Zhark some 'incentive'.\n"
"* Result vector goes to stdout. Redirect per your pleasures and needs.\n"
"* Also see program 3dLocalSVD if you want to compute the principal\n"
" singular time series vector from a neighborhood of EACH voxel.\n"
" ++ (Which is a pretty slow operation!)\n"
"* http://en.wikipedia.org/wiki/Singular_value_decomposition\n"
"\n"
"-------\n"
"Options:\n"
"-------\n"
" -vnorm = L2 normalize all time series before SVD [recommended!]\n"
" -sval a = output singular vectors 0 .. a [default a=0 = first one only]\n"
" -mask mset = define the mask [default is entire dataset == slow!]\n"
" -automask = you'll have to guess what this option does\n"
" -polort p = if you are lazy and didn't run 3dDetrend (like Zhark)\n"
" -bpass L H = bandpass [mutually exclusive with -polort]\n"
" -ort xx.1D = time series to remove from the data before SVD-ization\n"
" ++ You can give more than 1 '-ort' option\n"
" ++ 'xx.1D' can contain more than 1 column\n"
" -input ddd = alternative way to give the input dataset name\n"
"\n"
"-------\n"
"Example:\n"
"-------\n"
" You have a mask dataset with discrete values 1, 2, ... 77 indicating\n"
" some ROIs; you want to get the SVD from each ROI's time series separately,\n"
" and then put these into 1 big 77 column .1D file. You can do this using\n"
" a csh shell script like the one below:\n"
"\n"
" # Compute the individual SVD vectors\n"
" foreach mm ( `count 1 77` )\n"
" 3dmaskSVD -vnorm -mask mymask+orig\"<${mm}..${mm}>\" epi+orig > qvec${mm}.1D\n"
" end\n"
" # Glue them together into 1 big file, then delete the individual files\n"
" 1dcat qvec*.1D > allvec.1D\n"
" /bin/rm -f qvec*.1D\n"
" # Plot the results to a JPEG file, then compute their correlation matrix\n"
" 1dplot -one -nopush -jpg allvec.jpg allvec.1D\n"
" 1ddot -terse allvec.1D > allvec_COR.1D\n"
"\n"
" [[ If you use the bash shell, you'll have to figure out the syntax ]]\n"
" [[ yourself. Zhark has no sympathy for you bash shell infidels, and ]]\n"
" [[ considers you only slightly better than those lowly Emacs users. ]]\n"
" [[ And do NOT ever even mention 'nedit' in Zhark's august presence! ]]\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
/*---- official startup ---*/
PRINT_VERSION("3dmaskSVD"); mainENTRY("3dmaskSVD main"); machdep();
AFNI_logger("3dmaskSVD",argc,argv); AUTHOR("Zhark the Singular");
/*---- loop over options ----*/
INIT_IMARR(ortar) ;
mpv_sign_meth = AFNI_yesenv("AFNI_3dmaskSVD_meansign") ;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcasecmp(argv[iarg],"-bpass") == 0 ){
if( iarg+2 >= argc ) ERROR_exit("need 2 args after -bpass") ;
bpass_L = (float)strtod(argv[++iarg],NULL) ;
bpass_H = (float)strtod(argv[++iarg],NULL) ;
if( bpass_L < 0.0f || bpass_H <= bpass_L )
ERROR_exit("Illegal values after -bpass: %g %g",bpass_L,bpass_H) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ort") == 0 ){ /* 01 Oct 2009 */
int nx,ny ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-ort'") ;
ortim = mri_read_1D( argv[iarg] ) ;
if( ortim == NULL ) ERROR_exit("-ort '%s': Can't read 1D file",argv[iarg]) ;
nx = ortim->nx ; ny = ortim->ny ;
if( nx == 1 && ny > 1 ){
MRI_IMAGE *tim=mri_transpose(ortim); mri_free(ortim); ortim = tim; ny = 1;
}
mri_add_name(argv[iarg],ortim) ; ADDTO_IMARR(ortar,ortim) ; nyort += ny ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-polort") == 0 ){
char *qpt ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-polort'") ;
polort = (int)strtod(argv[iarg],&qpt) ;
if( *qpt != '\0' ) WARNING_message("Illegal non-numeric value after -polort") ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-vnorm") == 0 ){
do_vnorm = 1 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 0 ){
if( inset != NULL ) ERROR_exit("Can't have two -input options") ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-input'") ;
inset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(inset,argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-sval") == 0 ){
if( ++iarg >= argc ) ERROR_exit("Need argument after '-sval'") ;
sval_itop = (int)strtod(argv[iarg],NULL) ;
if( sval_itop < 0 ){ sval_itop = 0 ; WARNING_message("'-sval' reset to 0") ; }
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask") == 0 ){
THD_3dim_dataset *mset ; int mmm ;
if( ++iarg >= argc ) ERROR_exit("Need argument after '-mask'") ;
if( mask != NULL || automask ) ERROR_exit("Can't have two mask inputs") ;
mset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(mset,argv[iarg]) ;
DSET_load(mset) ; CHECK_LOAD_ERROR(mset) ;
mask_nx = DSET_NX(mset); mask_ny = DSET_NY(mset); mask_nz = DSET_NZ(mset);
mask = THD_makemask( mset , 0 , 0.5f, 0.0f ) ; DSET_delete(mset) ;
if( mask == NULL ) ERROR_exit("Can't make mask from dataset '%s'",argv[iarg]) ;
masknum = mmm = THD_countmask( mask_nx*mask_ny*mask_nz , mask ) ;
INFO_message("Number of voxels in mask = %d",mmm) ;
if( mmm < 2 ) ERROR_exit("Mask is too small to process") ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-automask") == 0 ){
if( mask != NULL ) ERROR_exit("Can't have two mask inputs!") ;
automask = 1 ; iarg++ ; continue ;
}
ERROR_exit("Unknown option '%s'",argv[iarg]) ;
} /*--- end of loop over options ---*/
/*---- deal with input dataset ----*/
if( inset == NULL ){
if( iarg >= argc ) ERROR_exit("No input dataset on command line?") ;
inset = THD_open_dataset( argv[iarg] ) ;
CHECK_OPEN_ERROR(inset,argv[iarg]) ;
}
nt = DSET_NVALS(inset) ; /* vector lengths */
if( nt < 9 )
ERROR_exit("Must have at least 9 values per voxel") ;
if( polort+1 >= nt )
ERROR_exit("'-polort %d' too big for time series length = %d",polort,nt) ;
DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ;
nxyz = DSET_NVOX(inset) ;
DSET_UNMSEC(inset) ;
dtime = DSET_TR(inset) ;
if( dtime <= 0.0f ) dtime = 1.0f ;
do_bpass = (bpass_L < bpass_H) ;
if( do_bpass ){
kk = THD_bandpass_OK( nt , dtime , bpass_L , bpass_H , 1 ) ;
if( kk <= 0 ) ERROR_exit("Can't continue since -bpass setup is illegal") ;
polort = -1 ;
}
/*--- deal with the masking ---*/
if( mask != NULL ){
if( mask_nx != DSET_NX(inset) ||
mask_ny != DSET_NY(inset) ||
mask_nz != DSET_NZ(inset) )
ERROR_exit("-mask dataset grid doesn't match input dataset") ;
} else if( automask ){
int mmm ;
mask = THD_automask( inset ) ;
if( mask == NULL )
ERROR_message("Can't create -automask from input dataset?") ;
masknum = mmm = THD_countmask( DSET_NVOX(inset) , mask ) ;
INFO_message("Number of voxels in automask = %d",mmm) ;
if( mmm < 9 ) ERROR_exit("Automask is too small to process") ;
} else {
mask = (byte *)malloc(sizeof(byte)*nxyz) ; masknum = nxyz ;
memset( mask , 1 , sizeof(byte)*nxyz ) ;
INFO_message("Using all %d voxels in dataset",nxyz) ;
}
nev = MIN(nt,masknum) ; /* max possible number of eigenvalues */
if( sval_itop >= nev ){
sval_itop = nev-1 ;
WARNING_message("'-sval' reset to '%d'",sval_itop) ;
}
mri_principal_vector_params( 0 , do_vnorm , sval_itop ) ;
mri_principal_setev(nev) ;
/*-- get data vectors --*/
ivox = (int *)malloc(sizeof(int)*masknum) ;
for( kk=ii=0 ; ii < nxyz ; ii++ ) if( mask[ii] ) ivox[kk++] = ii ;
INFO_message("Extracting data vectors") ;
imar = THD_extract_many_series( masknum, ivox, inset ) ; DSET_unload(inset) ;
if( imar == NULL ) ERROR_exit("Can't get data vector?!") ;
/*-- detrending --*/
if( polort >= 0 || nyort > 0 || do_bpass ){
float **polref=NULL ; float *tsar ;
int nort=IMARR_COUNT(ortar) , nref=0 ;
if( polort >= 0 ){ /* polynomials */
nref = polort+1 ; polref = THD_build_polyref(nref,nt) ;
}
if( nort > 0 ){ /* other orts */
float *oar , *par ; int nx,ny , qq,tt ;
for( kk=0 ; kk < nort ; kk++ ){ /* loop over input -ort files */
ortim = IMARR_SUBIM(ortar,kk) ;
nx = ortim->nx ; ny = ortim->ny ;
if( nx < nt )
ERROR_exit("-ort '%s' length %d shorter than dataset length %d" ,
ortim->name , nx , nt ) ;
polref = (float **)realloc(polref,(nref+ny)*sizeof(float *)) ;
oar = MRI_FLOAT_PTR(ortim) ;
for( qq=0 ; qq < ny ; qq++,oar+=nx ){
par = polref[nref+qq] = (float *)malloc(sizeof(float)*nt) ;
for( tt=0 ; tt < nt ; tt++ ) par[tt] = oar[tt] ;
if( polort == 0 ) THD_const_detrend (nt,par,NULL) ;
else if( polort > 0 ) THD_linear_detrend(nt,par,NULL,NULL) ;
}
nref += ny ;
}
DESTROY_IMARR(ortar) ;
}
if( !do_bpass ){ /* old style ort-ification */
MRI_IMAGE *imq , *imp ; float *qar ;
INFO_message("Detrending data vectors") ;
#if 1
imq = mri_new( nt , nref , MRI_float) ; qar = MRI_FLOAT_PTR(imq) ;
for( kk=0 ; kk < nref ; kk++ )
memcpy( qar+kk*nt , polref[kk] , sizeof(float)*nt ) ;
imp = mri_matrix_psinv( imq , NULL , 1.e-8 ) ;
for( kk=0 ; kk < IMARR_COUNT(imar) ; kk++ ){
mri_matrix_detrend( IMARR_SUBIM(imar,kk) , imq , imp ) ;
}
mri_free(imp) ; mri_free(imq) ;
#else
for( kk=0 ; kk < IMARR_COUNT(imar) ; kk++ ){
tsar = MRI_FLOAT_PTR(IMARR_SUBIM(imar,kk)) ;
THD_generic_detrend_LSQ( nt , tsar , -1 , nref , polref , NULL ) ;
}
#endif
} else { /* bandpass plus (maybe) orts */
float **vec = (float **)malloc(sizeof(float *)*IMARR_COUNT(imar)) ;
INFO_message("Bandpassing data vectors") ;
for( kk=0 ; kk < IMARR_COUNT(imar) ; kk++ )
vec[kk] = MRI_FLOAT_PTR(IMARR_SUBIM(imar,kk)) ;
(void)THD_bandpass_vectors( nt , IMARR_COUNT(imar) , vec ,
dtime , bpass_L , bpass_H ,
2 , nref , polref ) ;
free(vec) ;
}
for( kk=0 ; kk < nref; kk++ ) free(polref[kk]) ;
free(polref) ;
} /* end of detrendization */
/*--- the actual work ---*/
INFO_message("Computing SVD") ;
pim = mri_principal_vector( imar ) ; DESTROY_IMARR(imar) ;
if( pim == NULL ) ERROR_exit("SVD failure!?!") ;
ev = mri_principal_getev() ;
switch(sval_itop+1){
case 1:
INFO_message("First singular value: %g",ev[0]) ; break ;
case 2:
INFO_message("First 2 singular values: %g %g",ev[0],ev[1]) ; break ;
case 3:
INFO_message("First 3 singular values: %g %g %g",ev[0],ev[1],ev[2]) ; break ;
case 4:
INFO_message("First 4 singular values: %g %g %g %g",ev[0],ev[1],ev[2],ev[3]) ; break ;
default:
case 5:
INFO_message("First 5 singular values: %g %g %g %g %g",ev[0],ev[1],ev[2],ev[3],ev[4]) ; break ;
}
mri_write_1D(NULL,pim) ;
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 ;
}
/**** -ref file.1D ****/
if( strncmp(argv[nopt],"-ref",4) == 0 ){
MRI_IMAGE * im ;
nopt++ ;
if( nopt >= argc ) UC_syntax("-ref needs an argument!") ;
im = mri_read( argv[nopt] ) ;
if( im == NULL ) UC_syntax("Can't read -ref file!") ;
if( im->kind == MRI_float ){
UC_ref = im ;
} else {
UC_ref = mri_to_float(im) ; mri_free(im) ;
}
im = mri_transpose(UC_ref) ; mri_free(UC_ref) ; UC_ref = im ;
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 ;
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) ;
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!") ;
if( UC_ref == NULL || UC_ref->nx < UC_vdim )
UC_syntax("input ref not long enough for input dataset!") ;
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 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] ) ;
for( kk=0 ; kk < UC_ref->ny ; kk++ )
normalize( UC_vdim , MRI_FLOAT_PTR(UC_ref) + kk*UC_ref->nx ) ;
return ;
}
int main(int argc, char *argv[]) {
int i, k, ii;
int iarg;
char *prefix=NULL;
char *maskname=NULL;
char *gradsname=NULL;
char *dtsname=NULL;
THD_3dim_dataset *MASK=NULL;
THD_3dim_dataset *DTS=NULL;
MRI_IMAGE *GRADS=NULL, *GRADS_IN=NULL;
int Ngrads=0, Nfull=0;
int Nvox=-1; // tot number vox
int Dim[3]={0,0,0}; // dim in each dir
float NOISESCALE_DWI = -1.;
float NOISESCALE_B0 = -1;
float S0 = 1000.;
float bval = 1.;
int NOISE_IN_S0 = 0;
byte *mskd2=NULL; // not great, but another format of mask
float **dwi=NULL;
THD_3dim_dataset *DWI_OUT=NULL;
const gsl_rng_type * T;
gsl_rng *r;
long seed;
srand(time(0));
seed = time(NULL) ;
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc (T);
gsl_rng_set (r, seed);
// ###################################################################
// ######################### load ##################################
// ###################################################################
mainENTRY("3dDTtoNoisyDWI"); machdep();
if (argc == 1) { usage_DTtoNoisyDWI(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_DTtoNoisyDWI(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-dt_in") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-eig_vecs'");
dtsname = strdup(argv[iarg]) ;
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],"-mask") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
maskname = strdup(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-grads") == 0) {
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
gradsname = strdup(argv[iarg]) ;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-noise_DWI") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-noise_DWI'");
NOISESCALE_DWI = atof(argv[iarg]);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-noise_B0") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-noise_B0'");
NOISESCALE_B0 = atof(argv[iarg]);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-S0") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-S0'");
S0 = atof(argv[iarg]);
if(S0 <= 0 )
ERROR_exit("The '-S0' value must be >0.");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-bval") == 0) {
if( ++iarg >= argc )
ERROR_exit("Need numerical argument after '-bval'");
bval = atof(argv[iarg]);
if(bval <= 0 )
ERROR_exit("The '-bval' value must be >0.");
iarg++ ; continue ;
}
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
// ###################################################################
// #################### some checks ###############################
// ###################################################################
if(!prefix)
ERROR_exit("Need to give a '-prefix'.");
if(!dtsname)
ERROR_exit("Need to input diffusion tensor file after '-dt_in'.");
if(!gradsname)
ERROR_exit("Need to input gradient file after '-grads'.");
if( NOISESCALE_DWI<0 )
ERROR_exit("Fractional noise value after '-snr0' needs to be >0. "
"It sets the noise scale of ref signal S0.");
if(NOISESCALE_DWI > 0)
INFO_message("You have chosen an SNR0 of approximately %.2f for DWIs",
1./NOISESCALE_DWI);
else
INFO_message("You have noiseless (i.e., infinite SNR) set of DWIs");
if( NOISESCALE_B0 < 0 )
NOISESCALE_B0 = NOISESCALE_DWI;
if(NOISESCALE_B0 > 0)
INFO_message("You have chosen an SNR0 of approximately %.2f for the B0",
1./NOISESCALE_B0);
else
INFO_message("You have noiseless (i.e., infinite SNR) reference B0.");
// ###################################################################
if(dtsname) {
DTS = THD_open_dataset(dtsname);
DSET_load(DTS); CHECK_LOAD_ERROR(DTS);
if( 6 != DSET_NVALS(DTS) )
ERROR_exit("DT file '%s' must have 6 bricks-- "
"it has %d bricks!",
dtsname, DSET_NVALS(DTS));
}
Nvox = DSET_NVOX(DTS);
Dim[0] = DSET_NX(DTS);
Dim[1] = DSET_NY(DTS);
Dim[2] = DSET_NZ(DTS);
if(Nvox<0)
ERROR_exit("Error reading Nvox from eigenvalue file.");
mskd2 = (byte *)calloc(Nvox,sizeof(byte));
if( (mskd2 == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure (masks).\n\n");
exit(122);
}
if(maskname) {
MASK = THD_open_dataset(maskname);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
if( 1 != DSET_NVALS(MASK) )
ERROR_exit("Mask file '%s' is not scalar-- "
"it has %d bricks!",
maskname, DSET_NVALS(MASK));
for( k=0 ; k<Nvox ; k++ )
if (THD_get_voxel(MASK, k, 0) > 0 )
mskd2[k] = 1;
DSET_delete(MASK);
free(MASK);
free(maskname);
}
else {
for( k=0 ; k<Nvox ; k++ )
if( fabs(THD_get_voxel(DTS,k,0) > EPS_V) )
mskd2[k] = 1;
}
GRADS_IN = mri_read_1D (gradsname);
GRADS = mri_transpose(GRADS_IN); // get rid of autotranspose...
if (GRADS == NULL)
ERROR_exit("Error reading gradient vector file");
mri_free(GRADS_IN);
Ngrads = GRADS->ny;
if(Ngrads < 6)
ERROR_exit("Too few grads (there appear to be only %d).",Ngrads);
if(GRADS->nx !=3 )
ERROR_exit("Wrong number of columns in the grad file: "
" am reading %d instead of 3.",GRADS->nx);
Nfull = Ngrads+1;
INFO_message("Have surmised there are %d total grads; "
"output file will have %d bricks", Ngrads,Nfull);
dwi = calloc(Nfull,sizeof(dwi));
for(i=0 ; i<Nfull ; i++)
dwi[i] = calloc( Nvox,sizeof(float));
INFO_message("Calculating the DWIs.");
i = RicianNoiseDWIs( dwi, Nvox, Ngrads, DTS,
NOISESCALE_DWI, NOISESCALE_B0,
GRADS, mskd2,
S0, bval, r);
INFO_message("Writing the DWIs.");
DWI_OUT = EDIT_empty_copy( DTS );
EDIT_dset_items(DWI_OUT,
ADN_nvals, Nfull,
ADN_datum_all, MRI_float ,
ADN_prefix, prefix,
ADN_none );
for( i=0; i<Nfull ; i++) {
EDIT_substitute_brick(DWI_OUT, i, MRI_float, dwi[i]);
dwi[i]=NULL;
}
THD_load_statistics( DWI_OUT );
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(DWI_OUT)) )
ERROR_exit("Can't overwrite existing dataset '%s'",
DSET_HEADNAME(DWI_OUT));
tross_Make_History("3dDTtoNoisyDWI", argc, argv, DWI_OUT);
THD_write_3dim_dataset(NULL, NULL, DWI_OUT, True);
DSET_delete(DWI_OUT);
free(DWI_OUT);
// #################################################################
// ########################## free ###############################
// #################################################################
DSET_delete(DTS);
free(DTS);
for( i=0 ; i<Nfull ; i++)
free(dwi[i]);
free(dwi);
free(prefix);
free(gradsname);
free(dtsname);
mri_free(GRADS);
return 0;
}
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 nim , ii , jj , kk , nx, narg, oform ;
MRI_IMAGE **inim ;
float *far;
char *formatstr=NULL, *sel=NULL, *fname=NULL;
int nonconst=0 , ncol,ncold , cc , nonfixed=0 , stack=0;
intvec *ncv=NULL ;
char *hline=NULL ;
mainENTRY("1dcat:main");
/*-- help? --*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf(
"Usage: 1dcat [options] a.1D b.1D ...\n"
" where each file a.1D, b.1D, etc. is a 1D file.\n"
" In the simplest form, a 1D file is an ASCII file of numbers\n"
" arranged in rows and columns.\n"
"\n"
"1dcat takes as input one or more 1D files, and writes out a 1D file\n"
"containing the side-by-side concatenation of all or a subset of the\n"
"columns from the input files.\n"
"\n"
"* Output goes to stdout (the screen); redirect (e.g., '>') to save elsewhere.\n"
"* All files MUST have the same number of rows!\n"
"* Any header lines (i.e., lines that start with '#') will be lost.\n"
"* For generic 1D file usage help and information, see '1dplot -help'\n"
"\n"
"OPTIONS:\n"
"--------\n"
" -nonconst: Columns that are identically constant should be omitted\n"
" from the output.\n"
"\n"
" -nonfixed: Keep only columns that are marked as 'free' in the \n"
" 3dAllineate header from '-1Dparam_save'.\n"
" If there is no such header, all columns are kept.\n"
"\n"
" -form FORM: Format of the numbers to be output.\n"
" You can also substitute -form FORM with shortcuts such \n"
" as -i, -f, or -c.\n"
" For help on -form's usage, and its shortcut versions\n"
" see ccalc's help for the option of the same name. \n"
"\n"
" -stack: Stack the columns of the resultant matrix in the output.\n"
"\n"
" -sel SEL: Apply the same column/row selection string to all filenames\n"
" on the command line.\n"
" For example:\n"
" 1dcat -sel '[0,2]' f1.1D f2.1D\n"
" is the same as: 1dcat f1.1D'[1,2]' f2.1D'[1,2]'\n"
" The advantage of the option is that it allows wildcard use\n"
" in file specification so that you can run something like:\n"
" 1dcat -sel '[0,2]' f?.1D\n"
"\n"
"EXAMPLE:\n"
"--------\n"
" Input file 1:\n 1\n 2\n 3\n 4\n"
" Input file 2:\n 5\n 6\n 7\n 8\n"
"\n"
" 1dcat data1.1D data2.1D > catout.1D\n"
" Output file: \n 1 5\n 2 6\n 3 7\n 4 8\n"
"\n"
) ;
PRINT_COMPILE_DATE ; exit(0) ;
}
machdep() ;
/* do we have any options? */
oform = CCALC_NOT_SET;
sel = NULL;
stack = 0;
narg = 1;
while (narg < argc && argv[narg][0] == '-') {
if( strncmp(argv[narg],"-nonconst",7) == 0 ){ /* 04 Dec 2010 */
nonconst++ ; narg++ ; continue ;
}
if( strncmp(argv[narg],"-nonfixed",7) == 0 ){ /* 06 Dec 2010 */
nonfixed++ ; narg++ ; continue ;
}
if( strncmp(argv[narg],"-stack",6) == 0 ){ /* 05 Sep 2013 */
stack = 1 ; narg++ ; continue ;
}
if (strcmp(argv[narg],"-form") == 0) {
++narg;
if (narg >= argc) {
fprintf (stderr, "need argument after -form ");
exit (1);
}
if (strcmp(argv[narg],"double") == 0 ) oform = CCALC_DOUBLE;
else if (strcmp(argv[narg],"nice") == 0 ) oform = CCALC_NICE;
else if (strcmp(argv[narg],"int") == 0 ) oform = CCALC_INT;
else if (strcmp(argv[narg],"rint") == 0 ) oform = CCALC_INT;
else if (strcmp(argv[narg],"fint") == 0 ) oform = CCALC_FINT;
else if (strcmp(argv[narg],"cint") == 0 ) oform = CCALC_CINT;
else if (strlen(argv[narg])<=256) {
oform = CCALC_CUSTOM;
formatstr = argv[narg];
}
else {
fprintf (stderr, "Format type '%s' not supported.\n"
"See -help for details.\n", argv[narg]);
exit (1);
}
++narg;
} else if (strcmp(argv[narg],"-sel") == 0) {
++narg;
if (narg >= argc) {
fprintf (stderr, "need argument after -sel ");
exit (1);
}
sel = argv[narg]; ++narg;
} else if (strncmp(argv[narg],"-d",2) == 0) {
oform = CCALC_DOUBLE; ++narg;
} else if (strncmp(argv[narg],"-n",2) == 0) {
oform = CCALC_NICE; ++narg;
} else if (strncmp(argv[narg],"-i",2) == 0) {
oform = CCALC_INT; ++narg;
} else if (strncmp(argv[narg],"-r",2) == 0) {
oform = CCALC_INT; ++narg;
} else if (strncmp(argv[narg],"-f",2) == 0) {
oform = CCALC_FINT; ++narg;
} else if (strncmp(argv[narg],"-c",2) == 0) {
oform = CCALC_CINT; ++narg;
} else { /* break if option is not recognized */
++narg;
break;
}
}
/* read input files */
nim = argc-narg ;
inim = (MRI_IMAGE **) malloc( sizeof(MRI_IMAGE *) * nim ) ;
ncol = 0 ;
if( nonconst || nonfixed ) MAKE_intvec(ncv,1) ;
for( jj=0 ; jj < nim ; jj++ ){
#if 0 /** for testing only **/
if( AFNI_yesenv("ragged") ){
MRI_IMAGE *qim ;
qim = mri_read_ascii_ragged( argv[jj+narg] , 3.e+33 ) ;
fprintf(stderr,"qim: nx=%d ny=%d\n",qim->nx,qim->ny) ;
inim[jj] = mri_transpose(qim) ; mri_free(qim) ;
} else
#endif
if (sel) {
fname = (char *)
calloc((strlen(argv[jj+narg])+strlen(sel)+1), sizeof(char));
strcat(fname, argv[jj+narg]); strcat(fname, sel);
} else {
fname = argv[jj+narg];
}
inim[jj] = mri_read_1D( fname ) ;
if( inim[jj] == NULL )
ERROR_exit("Can't read input file '%s'",fname) ;
if( jj > 0 && inim[jj]->nx != inim[0]->nx )
ERROR_exit("Input file %s doesn't match first file %s in length!",
fname,argv[1]) ;
ncold = ncol ; ncol += inim[jj]->ny ;
if( ncv != NULL ){ /* check for constant columns [04 Dec 2010] */
RESIZE_intvec(ncv,ncol) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++ ) ncv->ar[ncold+kk] = 1 ;
far = MRI_FLOAT_PTR(inim[jj]) ; nx = inim[jj]->nx ;
if( nonconst ){
for( kk=0 ; kk < inim[jj]->ny ; kk++ ){ /* loop over columns */
for( ii=1 ; ii < nx ; ii++ ){ /* loop down column */
if( far[ii+kk*nx] != far[kk*nx] ) break ;
}
if( ii == nx ) ncv->ar[ncold+kk] = 0 ; /* constant */
}
}
if( nonfixed ){
char *hl = mri_read_1D_headerlines( fname ) ;
if( hl != NULL && *hl == '#' ){
char *spt = strchr(hl,'\n') ;
if( spt != NULL ) spt = strchr(spt,'#') ; /* start of line 2 */
if( spt != NULL ){
NI_str_array *sar = NI_decode_string_list( spt+1 , "~" ) ;
if( sar != NULL && sar->num >= inim[jj]->ny ){
for( kk=0 ; kk < inim[jj]->ny ; kk++ ){
spt = strchr(sar->str[kk],'$') ;
if( spt != NULL && spt[1] == '\0' ) ncv->ar[ncold+kk] = 0 ;
else {
if( hline == NULL ) hline = strdup("#") ;
hline = THD_zzprintf( hline , " %s" , sar->str[kk] ) ;
}
}
}
NI_delete_str_array(sar) ;
}
}
}
} /* end of computing ncv = array marking non-constant vectors */
if (sel) {
free(fname); fname = NULL;
}
} /* end of input loop */
/* now do the output */
if( hline != NULL ) printf("%s\n",hline) ;
nx = inim[0]->nx ;
if (stack) {
if (oform == CCALC_NOT_SET) {
for( cc=jj=0 ; jj < nim ; jj++ ){
far = MRI_FLOAT_PTR(inim[jj]) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++,cc++ ){
for( ii=0 ; ii < nx ; ii++ ){
if( ncv == NULL || ncv->ar[cc] )
printf(" %g\n", far[ii+kk*nx] ) ;
}
}
}
} else {
for( cc=jj=0 ; jj < nim ; jj++ ){
far = MRI_FLOAT_PTR(inim[jj]) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++,cc++ ){
for( ii=0 ; ii < nx ; ii++ ){
if( ncv == NULL || ncv->ar[cc] )
printf(" %s\n",
format_value_4print(far[ii+kk*nx], oform, formatstr ));
}
}
}
}
} else {
if (oform == CCALC_NOT_SET) {
for( ii=0 ; ii < nx ; ii++ ){
for( cc=jj=0 ; jj < nim ; jj++ ){
far = MRI_FLOAT_PTR(inim[jj]) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++,cc++ ){
if( ncv == NULL || ncv->ar[cc] )
printf(" %g", far[ii+kk*nx] ) ;
/* printf(" %+.2f", far[ii+kk*nx] ) ;*/
}
}
printf("\n") ;
}
} else {
for( ii=0 ; ii < nx ; ii++ ){
for( cc=jj=0 ; jj < nim ; jj++ ){
far = MRI_FLOAT_PTR(inim[jj]) ;
for( kk=0 ; kk < inim[jj]->ny ; kk++,cc++ ){
if( ncv == NULL || ncv->ar[cc] )
printf(" %s",
format_value_4print(far[ii+kk*nx], oform, formatstr ));
}
}
printf("\n") ;
}
}
}
exit(0) ;
}
DEFINE_MODEL_PROTOTYPE
MODEL_interface * initialize_model ()
{
MODEL_interface * mi = NULL;
MRI_IMAGE * im;
char * envp;
int ii;
/*----- allocate memory space for model interface -----*/
mi = (MODEL_interface *) XtMalloc (sizeof(MODEL_interface));
/*----- define interface for the differential - exponential model -----*/
/*----- name of this model -----*/
strcpy (mi->label, "expMEMRI");
/*----- this is a signal model -----*/
mi->model_type = MODEL_SIGNAL_TYPE;
/*----- number of parameters in the model -----*/
mi->params = 3;
/*----- parameter labels -----*/
strcpy (mi->plabel[0], "a");
strcpy (mi->plabel[1], "b");
strcpy (mi->plabel[2], "c scalefactor");
/*----- minimum and maximum parameter constraints -----*/
mi->min_constr[0] = 0.0; mi->max_constr[0] = 100.0;
mi->min_constr[1] = -100.00; mi->max_constr[1] = 0.00;
mi->min_constr[2] = 0.0; mi->max_constr[2] = 100.0;
/*----- function which implements the model -----*/
mi->call_func = &signal_model;
#if 0
envp = my_getenv("AFNI_MODEL_EXPMEMRI_T_FILE");
if( !envp )
{
fprintf(stderr,"\n** NLfim: need env var AFNI_EXPMEMRI_T_FILE\n");
fprintf(stderr," (a 1D file of time values for each sub-brick)\n");
return(NULL);
}
im = mri_read_1D(envp);
if( !im )
{
fprintf(stderr,"** failed to open time file %s for model\n", envp);
return(NULL);
}
/* nx == 1 and ny > 1, take the transpose */
if( im->nx == 1 && im->ny > 1 )
{
MRI_IMAGE * flim = mri_transpose(im);
mri_free(im);
im = flim;
if( !im ) { fprintf(stderr,"** time transposing failure\n"); return(NULL); }
fprintf(stderr,"taking transpose of time file, new len = %d\n",im->nx);
}
rt = MRI_FLOAT_PTR(im); /* do not free this */
rt_len = im->nx;
fprintf(stderr,"Times at each sub-brick :\n");
for(ii=0;ii<im->nx;ii++)
fprintf(stderr, "%f ", rt[ii]);
fprintf(stderr, "\n");
#endif
/*----- return pointer to the model interface -----*/
return (mi);
}
