/*
* for each input dataset name
* open (check dims, etc.)
* dilate (zeropad, make binary, dilate, unpad, apply)
* fill list of bytemask datasets
*
* also, count total volumes
*/
int process_input_dsets(param_t * params)
{
THD_3dim_dataset * dset, * dfirst=NULL;
int iset, nxyz;
ENTRY("process_input_dsets");
if( !params ) ERROR_exit("NULL inputs to PID");
if( params->ndsets <= 0 ) {
ERROR_message("process_input_dsets: no input datasets");
RETURN(1);
}
/* allocate space for dsets array */
params->dsets = (THD_3dim_dataset **)malloc(params->ndsets*
sizeof(THD_3dim_dataset*));
if( !params->dsets ) ERROR_exit("failed to allocate dset pointers");
if( params->verb ) INFO_message("processing %d input datasets...",
params->ndsets);
/* warn user of dilations */
if(params->verb && params->ndsets) {
int pad = needed_padding(¶ms->IND);
INFO_message("padding all datasets by %d (for dilations)", pad);
}
/* process the datasets */
nxyz = 0;
for( iset=0; iset < params->ndsets; iset++ ) {
/* open and verify dataset */
dset = THD_open_dataset(params->inputs[iset]);
if( !dset ) ERROR_exit("failed to open mask dataset '%s'",
params->inputs[iset]);
DSET_load(dset); CHECK_LOAD_ERROR(dset);
if( params->verb>1 ) INFO_message("loaded dset %s, with %d volumes",
DSET_PREFIX(dset), DSET_NVALS(dset));
if( nxyz == 0 ) { /* make an empty copy of the first dataset */
nxyz = DSET_NVOX(dset);
dfirst = EDIT_empty_copy(dset);
}
/* check for consistency in voxels and grid */
if( DSET_NVOX(dset) != nxyz ) ERROR_exit("nvoxel mis-match");
if( ! EQUIV_GRIDS(dset, dfirst) )
WARNING_message("grid from dset %s does not match that of dset %s",
DSET_PREFIX(dset), DSET_PREFIX(dfirst));
/* apply dilations to all volumes, returning bytemask datasets */
params->dsets[iset] = apply_dilations(dset, ¶ms->IND,1,params->verb);
if( ! params->dsets[iset] ) RETURN(1);
}
DSET_delete(dfirst); /* and nuke */
RETURN(0);
}
/*
A debugging function to show the state of the various file naming fields
*/
void THD_show_dataset_names( THD_3dim_dataset *dset, char *head, FILE *out)
{
if (!dset) {
fprintf(stderr,"NULL dset");
return;
}
if (!out) out = stderr;
if (head && !strcmp(head,"FOR_3DINFO")) {
fprintf(out, " filecode: %s"
" header_name: %s"
" brick_name: %s"
" prefix: %s"
" storage_mode: %d",
dset->dblk->diskptr->filecode,
dset->dblk->diskptr->header_name,
dset->dblk->diskptr->brick_name,
DSET_PREFIX(dset),
dset->dblk->diskptr->storage_mode);
} else {
fprintf(out, "*** FileLove: %s\n"
" filecode: %s\n"
" header_name: %s\n"
" brick_name: %s\n"
" prefix: %s\n"
" storage_mode: %d\n",
head ? head:"",
dset->dblk->diskptr->filecode,
dset->dblk->diskptr->header_name,
dset->dblk->diskptr->brick_name,
DSET_PREFIX(dset),
dset->dblk->diskptr->storage_mode);
}
return;
}
THD_3dim_dataset *Seg_load_dset_eng( char *set_name, char *view )
{
static char FuncName[]={"Seg_load_dset_eng"};
THD_3dim_dataset *dset=NULL, *sdset=NULL;
int i=0;
byte make_cp=0;
int verb=0;
char sprefix[THD_MAX_PREFIX+10], *stmp=NULL;
SUMA_ENTRY;
dset = THD_open_dataset( set_name );
if( !ISVALID_DSET(dset) ){
fprintf(stderr,"**ERROR: can't open dataset %s\n",set_name) ;
SUMA_RETURN(NULL);
}
DSET_mallocize(dset) ; DSET_load(dset);
for (i=0; i<DSET_NVALS(dset); ++i) {
if (DSET_BRICK_TYPE(dset,i) != MRI_short) {
if (verb) INFO_message("Sub-brick %d in %s not of type short.\n"
"Creating new short copy of dset ",
i, DSET_PREFIX(dset));
make_cp=1; break;
}
}
if (make_cp) {
if (!SUMA_ShortizeDset(&dset, -1.0)) {
SUMA_S_Err("**ERROR: Failed to shortize");
SUMA_RETURN(NULL);
}
}
if (DSET_IS_MASTERED(dset)) {
if (verb) INFO_message("Dset is mastered, making copy...");
stmp = SUMA_ModifyName(set_name, "append", ".cp", NULL);
sdset = dset;
dset = EDIT_full_copy(sdset, stmp);
free(stmp); DSET_delete(sdset); sdset = NULL;
}
if (view) {
if (view) {
if (!strstr(view,"orig"))
EDIT_dset_items(dset,ADN_view_type, VIEW_ORIGINAL_TYPE, ADN_none);
else if (!strstr(view,"acpc"))
EDIT_dset_items(dset,ADN_view_type, VIEW_ACPCALIGNED_TYPE, ADN_none);
else if (!strstr(view,"tlrc"))
EDIT_dset_items(dset ,ADN_view_type, VIEW_TALAIRACH_TYPE, ADN_none);
else SUMA_S_Errv("View of %s is rubbish", view);
}
}
SUMA_RETURN(dset);
}
/* convert by hand, since no scaling will be done
* (byte seems inappropriate and float does not need it) */
int write_result(param_t * params, THD_3dim_dataset * oset,
int argc, char * argv[])
{
short * sptr;
int nvox = DSET_NVOX(oset), ind;
ENTRY("write_results");
EDIT_dset_items(oset, ADN_prefix, params->prefix, ADN_none);
if( params->verb )
INFO_message("writing result %s...\n", DSET_PREFIX(oset));
switch( params->datum ) {
default: ERROR_exit("invalid datum for result: %d", params->datum);
case MRI_short: break; /* nothing to do */
case MRI_float: {
float * data = (float *)malloc(nvox*sizeof(float));
sptr = DBLK_ARRAY(oset->dblk, 0);
if( ! data ) ERROR_exit("failed to alloc %d output floats\n", nvox);
for( ind = 0; ind < nvox; ind++ ) data[ind] = (float)sptr[ind];
EDIT_substitute_brick(oset, 0, params->datum, data);
}
break;
case MRI_byte: {
byte * data = (byte *)malloc(nvox*sizeof(byte));
int errs = 0;
sptr = DBLK_ARRAY(oset->dblk, 0);
if( ! data ) ERROR_exit("failed to alloc %d output bytes\n", nvox);
for( ind = 0; ind < nvox; ind++ ) {
if( sptr[ind] > 255 ) { /* watch for overflow */
data[ind] = (byte)255;
errs++;
} else data[ind] = (byte)sptr[ind];
}
EDIT_substitute_brick(oset, 0, params->datum, data);
if(errs) WARNING_message("convert to byte: %d truncated voxels",errs);
}
break;
}
tross_Make_History( "3dmask_tool", argc, argv, oset );
DSET_write(oset);
WROTE_DSET(oset);
RETURN(0);
}
/* Return the prefix of a dataset without file extensions
Returned string must be freed */
char *DSET_prefix_noext(THD_3dim_dataset *dset)
{
char *ppp, *eee, *ccc=NULL;
int ii;
if (!dset) return(NULL);
ppp = DSET_PREFIX(dset);
if (!ppp) ppp = "NO_PREFIX";
ccc = (char *)malloc(sizeof(char)*(1+strlen(ppp)));
ccc[0]='\0';
eee = find_filename_extension( ppp );
if (!eee) {
strcpy(ccc, ppp);
} else {
ii = 0;
while (ppp < eee) {
ccc[ii] = *ppp; ppp++; ++ii;
}
ccc[ii]='\0';
}
return(ccc);
}
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[] )
{
THD_3dim_dataset *mask_dset=NULL, *iset=NULL,
*sset=NULL, *xset=NULL, *vset=NULL;
char *prefix="toy";
int iarg=1 , mcount, udatum = MRI_float;
byte *maskvox=NULL;
mainENTRY("3dToyProg main"); machdep(); AFNI_logger("3dToyProg",argc,argv);
#ifdef USING_MCW_MALLOC
enable_mcw_malloc() ;
#endif
/*-- options --*/
set_obliquity_report(0); /* silence obliquity */
while( iarg < argc && argv[iarg][0] == '-' ){
CHECK_HELP(argv[iarg], help_3dToyProg);
if( strncmp(argv[iarg],"-mask",5) == 0 ){
if (iarg >= argc) ERROR_exit("Need dset after -mask");
mask_dset = THD_open_dataset( argv[++iarg] ) ;
if( mask_dset == NULL )
ERROR_exit("Cannot open mask dataset!\n") ;
if( DSET_BRICK_TYPE(mask_dset,0) == MRI_complex )
ERROR_exit("Cannot deal with complex-valued mask dataset!\n");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-input") == 0) {
if (iarg >= argc) ERROR_exit("Need dset after -mask");
if (!(iset = THD_open_dataset( argv[++iarg]))) {
ERROR_exit("Cannot open input dataset %s!\n", argv[iarg]) ;
}
DSET_mallocize(iset); DSET_load(iset); /* load data part of dataset */
iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-prefix",6) == 0) {
if (iarg >= argc) ERROR_exit("Need name after -prefix");
prefix = argv[++iarg];
iarg++ ; continue ;
continue ;
}
if( strcmp(argv[iarg],"-datum") == 0) {
if (iarg >= argc) ERROR_exit("Need datum type after -datum");
++iarg;
if (!strcmp(argv[iarg],"float")) udatum = MRI_float;
else if (!strcmp(argv[iarg],"short")) udatum = MRI_short;
else {
ERROR_exit(
"For the purpose of this demo, only float and short are allowed");
}
iarg++ ; continue ;
continue ;
}
ERROR_message("ILLEGAL option: %s\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
if( argc < 2 ){
help_3dToyProg(TXT, 0);
PRINT_COMPILE_DATE ; exit(0) ;
}
if( !iset )
ERROR_exit("No dataset on command line!?") ;
if (mask_dset) {
if (THD_dataset_mismatch(mask_dset, iset))
ERROR_exit("grid mismatch between input dset and mask dset");
maskvox = THD_makemask( mask_dset , 0 , 1.0, -1.0 ) ;
mcount = THD_countmask( DSET_NVOX(mask_dset) , maskvox ) ;
if( mcount <= 0 ) ERROR_exit("No voxels in the mask!\n") ;
INFO_message("%d voxels in the mask dset %s\n",
mcount, DSET_PREFIX(mask_dset)) ;
DSET_delete(mask_dset) ; mask_dset=NULL; /* Done with the mask dset */
}
/* An illustration of how volume navigation works */
Dataset_Navigation(iset);
/* Let us create a dataset from scratch */
sset = New_Dataset_From_Scratch(prefix);
/* Now for the output, add history, check for overwrite and write away */
tross_Copy_History( iset , sset );/* Copy the old history (not mandatory). */
tross_Make_History("3dToyProg", argc, argv ,sset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(sset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(sset));
} else DSET_write(sset);
/* Now we'll do some voxelwise computations */
xset = Voxelwise_Operations(sset, maskvox, prefix);
tross_Copy_History( iset , xset ) ; /* Copy the old */
tross_Make_History("3dToyProg", argc, argv ,xset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(xset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(xset));
} else DSET_write(xset);
/* Or some volumewise operations */
vset = Volumewise_Operations(sset, prefix, udatum);
tross_Copy_History( iset , vset ) ; /* Copy the old */
tross_Make_History("3dToyProg", argc, argv ,vset) ; /* add the new */
if( !THD_ok_overwrite() && THD_is_ondisk(DSET_HEADNAME(vset)) ) {
ERROR_message(
"Output %s already exists, use -overwrite to do you know what",
DSET_HEADNAME(vset));
} else DSET_write(vset);
/* cleanup */
DSET_delete(xset); xset = NULL;
DSET_delete(vset); vset = NULL;
DSET_delete(sset); sset = NULL;
exit(0) ;
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *dset=NULL;
int iarg , verbose = -1 ;
char *outbuf, *stmp=NULL;
char *labelName = NULL;
char *sbdelim = {"|"};
char *NAflag = {"NA"};
char *atrdelim = {"\t"}, *form=NULL;
INFO_FIELDS sing[512];
int iis=0, N_sing = 0, isb=0, withhead = 0, itmp=0;
int ip=0, needpair = 0, namelen=0, monog_pairs = 0;
THD_3dim_dataset *tttdset=NULL, *dsetp=NULL;
char *tempstr = NULL;
int extinit = 0;
float RL_AP_IS[6];
mainENTRY("3dinfo main") ; machdep() ;
if( argc < 2) { Syntax(TXT,1) ; RETURN(0); }
iarg = 1 ;
while (iarg < argc && argv[iarg][0] == '-') {
CHECK_HELP(argv[iarg],Syntax);
if( strncmp(argv[iarg],"-verb" ,5) == 0 ){
verbose = 0; iarg++; continue; }
else if( strncmp(argv[iarg],"-VERB" ,5) == 0 ){
verbose = 1; iarg++; continue; }
else if( strncmp(argv[iarg],"-short",5) == 0 ){
verbose = -1; iarg++; continue; }
else if( strcasecmp(argv[iarg],"-header_line") == 0 ||
strcasecmp(argv[iarg],"-hdr") == 0 ){
withhead = 1; iarg++; continue; }
else if( strcasecmp(argv[iarg],"-monog_pairs") == 0 ){
monog_pairs = 1; iarg++; continue; }
else if ( strncmp(argv[iarg],"-label2",7) == 0 )
{
iarg++;
if (iarg >= argc)
ERROR_exit( "3dinfo needs an argument after -label2number\n");
labelName = malloc(sizeof(char) * 2048);
strcpy(labelName, argv[iarg]);
iarg++; continue;
}
else if( strcasecmp(argv[iarg],"-sb_delim") == 0) {
iarg++;
if (iarg >= argc)
ERROR_exit( "3dinfo needs a string after -sb_delim\n");
sbdelim = argv[iarg];
iarg++; continue;
}
else if( strcasecmp(argv[iarg],"-NA_flag") == 0) {
iarg++;
if (iarg >= argc)
ERROR_exit( "3dinfo needs a string after -NA_flag\n");
NAflag = argv[iarg];
iarg++; continue;
}
else if( strcasecmp(argv[iarg],"-atr_delim") == 0) {
iarg++;
if (iarg >= argc)
ERROR_exit( "3dinfo needs a string after -atr_delim\n");
atrdelim = argv[iarg];
iarg++; continue;
}
else if( strcasecmp(argv[iarg],"-space") == 0) {
sing[N_sing++] = DSET_SPACE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-av_space") == 0) {
sing[N_sing++] = AV_DSET_SPACE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-gen_space") == 0) {
sing[N_sing++] = DSET_GEN_SPACE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-is_nifti") == 0) {
sing[N_sing++] = IS_NIFTI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-is_atlas") == 0) {
sing[N_sing++] = IS_ATLAS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-exists") == 0) {
sing[N_sing++] = DSET_EXISTS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-is_oblique") == 0) {
sing[N_sing++] = IS_OBLIQUE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-obliquity") == 0) {
sing[N_sing++] = OBLIQUITY; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-handedness") == 0) {
sing[N_sing++] = HANDEDNESS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-prefix") == 0) {
sing[N_sing++] = PREFIX; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-prefix_noext") == 0) {
sing[N_sing++] = PREFIX_NOEXT; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-ni") == 0) {
sing[N_sing++] = NI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nj") == 0) {
sing[N_sing++] = NJ; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nk") == 0) {
sing[N_sing++] = NK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-n4") == 0) {
sing[N_sing++] = NI;
sing[N_sing++] = NJ;
sing[N_sing++] = NK;
sing[N_sing++] = NV; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Rextent") == 0) {
sing[N_sing++] = EXTENT_R; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Lextent") == 0) {
sing[N_sing++] = EXTENT_L; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Aextent") == 0) {
sing[N_sing++] = EXTENT_A; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Pextent") == 0) {
sing[N_sing++] = EXTENT_P; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Iextent") == 0) {
sing[N_sing++] = EXTENT_I; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-Sextent") == 0) {
sing[N_sing++] = EXTENT_S; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-extent") == 0) {
sing[N_sing++] = EXTENT_R;
sing[N_sing++] = EXTENT_L;
sing[N_sing++] = EXTENT_A;
sing[N_sing++] = EXTENT_P;
sing[N_sing++] = EXTENT_I;
sing[N_sing++] = EXTENT_S;
iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-di") == 0) {
sing[N_sing++] = DI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dj") == 0) {
sing[N_sing++] = DJ; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dk") == 0) {
sing[N_sing++] = DK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-d3") == 0) {
sing[N_sing++] = DI;
sing[N_sing++] = DJ;
sing[N_sing++] = DK; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-adi") == 0) {
sing[N_sing++] = ADI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-adj") == 0) {
sing[N_sing++] = ADJ; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-adk") == 0) {
sing[N_sing++] = ADK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-ad3") == 0) {
sing[N_sing++] = ADI;
sing[N_sing++] = ADJ;
sing[N_sing++] = ADK; iarg++;
continue;
} else if( strcasecmp(argv[iarg],"-voxvol") == 0) {
sing[N_sing++] = VOXVOL; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-iname") == 0) {
sing[N_sing++] = INAME; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-oi") == 0) {
sing[N_sing++] = OI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-oj") == 0) {
sing[N_sing++] = OJ; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-ok") == 0) {
sing[N_sing++] = OK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-o3") == 0) {
sing[N_sing++] = OI;
sing[N_sing++] = OJ;
sing[N_sing++] = OK; iarg++;
continue;
}else if( strcasecmp(argv[iarg],"-nt") == 0) {
sing[N_sing++] = NT; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nti") == 0) {
sing[N_sing++] = NTI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nv") == 0) {
sing[N_sing++] = NV; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nvi") == 0) {
sing[N_sing++] = NVI; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-ntimes") == 0) {
sing[N_sing++] = NTIMES; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-max_node") == 0) {
sing[N_sing++] = MAX_NODE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-nijk") == 0) {
sing[N_sing++] = NIJK; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-labeltable") == 0) {
sing[N_sing++] = LTABLE; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-labeltable_as_atlas_points") == 0) {
sing[N_sing++] = LTABLE_AS_ATLAS_POINT_LIST; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-atlas_points") == 0) {
sing[N_sing++] = ATLAS_POINTS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-fac") == 0) {
sing[N_sing++] = FAC; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-datum") == 0) {
sing[N_sing++] = DATUM; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-label") == 0) {
sing[N_sing++] = LABEL; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-min") == 0) {
sing[N_sing++] = MIN; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-max") == 0) {
sing[N_sing++] = MAX; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-minus") == 0) {
sing[N_sing++] = MINUS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-maxus") == 0) {
sing[N_sing++] = MAXUS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dmin") == 0) {
sing[N_sing++] = DMIN; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dmax") == 0) {
sing[N_sing++] = DMAX; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dminus") == 0) {
sing[N_sing++] = DMINUS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-dmaxus") == 0) {
sing[N_sing++] = DMAXUS; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-TR") == 0) {
sing[N_sing++] = TR; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-header_name") == 0) {
sing[N_sing++] = HEADER_NAME; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-brick_name") == 0) {
sing[N_sing++] = BRICK_NAME; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-history") == 0) {
sing[N_sing++] = HISTORY; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-all_names") == 0) {
sing[N_sing++] = ALL_NAMES; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-orient") == 0) {
sing[N_sing++] = ORIENT; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_grid") == 0) {
sing[N_sing++] = SAME_GRID; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_dim") == 0) {
sing[N_sing++] = SAME_DIM; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_delta") == 0) {
sing[N_sing++] = SAME_DELTA; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_orient") == 0) {
sing[N_sing++] = SAME_ORIENT; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_center") == 0) {
sing[N_sing++] = SAME_CENTER; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_obl") == 0) {
sing[N_sing++] = SAME_OBL; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-slice_timing") == 0) {
sing[N_sing++] = SLICE_TIMING; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-sval_diff") == 0) {
sing[N_sing++] = SVAL_DIFF; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-val_diff") == 0) {
sing[N_sing++] = VAL_DIFF; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-same_all_grid") == 0) {
sing[N_sing++] = SAME_DIM;
sing[N_sing++] = SAME_DELTA;
sing[N_sing++] = SAME_ORIENT;
sing[N_sing++] = SAME_CENTER;
sing[N_sing++] = SAME_OBL; needpair = 1; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-id") == 0) {
sing[N_sing++] = ID; iarg++; continue;
} else if( strcasecmp(argv[iarg],"-smode") == 0) {
sing[N_sing++] = SMODE; iarg++; continue;
} else {
ERROR_message("Option %s unknown", argv[iarg]);
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
}
if (N_sing == 0) {
sing[N_sing++] = CLASSIC;
}
if (sing[iis] == CLASSIC) PRINT_VERSION("3dinfo") ;
THD_allow_empty_dataset(1) ; /* 21 Mar 2007 */
if (iarg == argc) {
ERROR_message("No dsets on command line? I have nothing to do.\n");
exit(1);
}
if (needpair && monog_pairs) needpair = 2; /* pair each couple separately */
if (needpair==2 && (argc-iarg) % 2) {
ERROR_message("Using options requiring dset pairs but have odd number\n"
"of dsets (%d) on command line.\n", (argc-iarg));
exit (1);
} else if (needpair==1 && (argc-iarg) < 2) {
ERROR_message("Using options requiring dset pairs but have less than\n"
"two dsets (%d) on command line.\n", (argc-iarg));
exit (1);
}
ip = 0;
for( ; iarg < argc ; iarg++ ){
if (ip == 0) {
int kkk, nml; char *etr;
namelen = 0;
for (kkk=iarg; kkk<argc; ++kkk) {
if ((etr = THD_trailname(argv[kkk],0))) {
nml=strlen(etr);
if (nml < 48 && nml > namelen) namelen = nml;
}
}
if (namelen < 6) namelen = 6;
if (withhead) {
int havenew=0;
for (iis = 0; iis < N_sing; ++iis) {
if (sing[iis] != CLASSIC) {
++havenew;
form = PrintForm(sing[iis], namelen, 1);
/*fprintf(stderr,"ZSS: %d %s >%s<\n",
sing[iis], Field_Names[sing[iis]], form);*/
fprintf(stdout, form, Field_Names[sing[iis]]);
}
if (havenew) {
if (N_sing > 1 && iis < N_sing-1)
fprintf(stdout,"%s",atrdelim);
else fprintf(stdout,"\n");
}
}
}
}
if( argv[iarg][0] == '\0' ) continue ; /* bad filename */
set_obliquity_report(0); /* silence obliquity */
if (!needpair) {
if (!(dset = load_3dinfo_dataset(argv[iarg]))) {
/* exit(1); */
}
} else {
if (needpair == 2) { /* Crazy idea of comparing each pair separately */
if (ip % 2 == 0) {
if (!(dset = load_3dinfo_dataset(argv[iarg] ))) {
/* exit(1); */
}
if (iarg+1==argc || argv[iarg+1][0] == '\0') {
ERROR_message("Bad dset pair for %s\n", argv[iarg]);
exit(1);
}
if (!(dsetp = load_3dinfo_dataset(argv[iarg+1] ))) {
/* exit(1); */
}
} else { /* swap the pair - this allows non pair requiring functions
to work as before.*/
tttdset = dsetp;
dsetp = dset;
dset = tttdset; tttdset=NULL;
}
} else { /* always compare to very first dset */
if (ip==0) {
if (!(dset = load_3dinfo_dataset(argv[iarg] ))) {
/*exit(1);*/
}
if (!(dsetp = load_3dinfo_dataset(argv[iarg+1] ))) {
/*exit(1);*/
}
} else if (ip==1) { /* switch order of first two */
tttdset = dsetp;
dsetp = dset; /* now dsetp is the very first dset */
dset = tttdset; tttdset=NULL;
} else { /* pair with very first, which is dsetp */
if (!(dset = load_3dinfo_dataset(argv[iarg] ))) {
/*exit(1);*/
}
}
}
}
++ip;
if (0 && !dset) { /* allow for DSET_EXISTS option */
ERROR_exit("Should not get here");
}
/* we should re-capture this per dataset 5 Feb 2019 [rickr] */
extinit = 0;
for (iis = 0; iis < N_sing; ++iis) {
if (!dset) {
if (sing[iis] == CLASSIC) {
if( dset == NULL ){ /* still not open? */
ERROR_exit("Can't open dataset %s\n", argv[iarg]) ;
}
} else if (sing[iis] != DSET_EXISTS && sing[iis] != INAME) {
fprintf(stdout, "NO-DSET");
SPIT_DELIM(iis, N_sing, atrdelim);
continue;
}
}
switch (sing[iis]) {
case CLASSIC:
if (labelName == NULL ) /*** get and output info ***/
{
outbuf = THD_dataset_info( dset , verbose ) ;
if( outbuf != NULL ){
printf("\n") ;
puts(outbuf) ;
free(outbuf) ; outbuf = NULL ;
} else {
ERROR_exit("Can't get info for dataset %s",argv[iarg]) ;
}
}
else /*** get and output label ***/
{
int nval_per = dset->dblk->nvals;
int foundLabel = 0;
int ival=0;
for (ival=0 ; ival < nval_per && !foundLabel; ival++ )
{
if (strcmp(DSET_BRICK_LAB(dset,ival), labelName) == 0)
{
printf("%d\n", ival); foundLabel = 1;
}
} /* end of for (ival=0 ; ival < nval_per ; ival++ ) */
if (!foundLabel) printf("\n");
}
THD_delete_3dim_dataset( dset , False ) ;
free(labelName);
break;
case DSET_EXISTS:
fprintf(stdout, "%d", dset ? 1:0);
break;
case DSET_SPACE:
tempstr = THD_get_space(dset);
if(tempstr==NULL)
fprintf(stdout, "-----");
else
fprintf(stdout, "%s", tempstr);
break;
case DSET_GEN_SPACE:
tempstr = THD_get_generic_space(dset);
if(tempstr==NULL)
fprintf(stdout, "-----");
else
fprintf(stdout, "%s", tempstr);
break;
case AV_DSET_SPACE:
/* don't allow anything but the three AFNI views */
tempstr = THD_get_view_space(dset);
if(tempstr==NULL)
fprintf(stdout, "+orig");
else if (!strncasecmp(tempstr,"ORIG",4))
fprintf(stdout, "+orig");
else if (!strncasecmp(tempstr,"ACPC",4))
fprintf(stdout, "+acpc");
else if (!strncasecmp(tempstr,"TLRC",4))
fprintf(stdout, "+tlrc");
else /* shouldn't get here */
fprintf(stdout, "+orig");
break;
case IS_NIFTI:
if ( dset->dblk->diskptr &&
dset->dblk->diskptr->storage_mode == STORAGE_BY_NIFTI ) {
fprintf(stdout,"1");
} else {
fprintf(stdout,"0");
}
break;
case IS_ATLAS:
if ( is_Dset_Atlasy(dset, NULL) ) {
fprintf(stdout,"1");
} else {
fprintf(stdout,"0");
}
break;
case IS_OBLIQUE:
if (dset_obliquity(dset,NULL) > 0) {
fprintf(stdout,"1");
} else {
fprintf(stdout,"0");
}
break;
case HANDEDNESS:
if (THD_handedness(dset) > 0) {
fprintf(stdout,"R");
} else {
fprintf(stdout,"L");
}
break;
case OBLIQUITY:
fprintf(stdout,"%.3f",
THD_compute_oblique_angle(dset->daxes->ijk_to_dicom_real, 0));
break;
case PREFIX:
form = PrintForm(sing[iis], namelen, 1);
fprintf(stdout,form, DSET_PREFIX(dset));
break;
case PREFIX_NOEXT:
{
form = PrintForm(sing[iis], namelen, 1);
stmp=DSET_prefix_noext(dset);
fprintf(stdout,form, stmp);
free(stmp); stmp=NULL;
}
break;
case HEADER_NAME:
fprintf(stdout,"%s", dset->dblk->diskptr->header_name);
break;
case BRICK_NAME:
fprintf(stdout,"%s", dset->dblk->diskptr->brick_name);
break;
case ALL_NAMES:
THD_show_dataset_names(dset, "FOR_3DINFO", stdout);
break;
case HISTORY:
stmp = tross_Get_History(dset);
fprintf(stdout,"%s", stmp ? stmp:NAflag);
if (stmp) free(stmp); stmp=NULL;
break;
case NI:
fprintf(stdout,"%d", DSET_NX(dset));
break;
case NJ:
fprintf(stdout,"%d", DSET_NY(dset));
break;
case NK:
fprintf(stdout,"%d", DSET_NZ(dset));
break;
case NIJK:
fprintf(stdout,"%d", DSET_NVOX(dset));
break;
case NTIMES:
fprintf(stdout,"%d", DSET_NUM_TIMES(dset));
break;
case MAX_NODE:
DSET_MAX_NODE(dset,itmp);
fprintf(stdout,"%d", itmp);
break;
case NT:
case NV:
fprintf(stdout,"%d", DSET_NVALS(dset));
break;
case NTI:
case NVI:
fprintf(stdout,"%d", DSET_NVALS(dset)-1);
break;
case DI:
fprintf(stdout,"%f", DSET_DX(dset));
break;
case DJ:
fprintf(stdout,"%f", DSET_DY(dset));
break;
case DK:
fprintf(stdout,"%f", DSET_DZ(dset));
break;
case OI:
fprintf(stdout,"%f", DSET_XORG(dset));
break;
case OJ:
fprintf(stdout,"%f", DSET_YORG(dset));
break;
case OK:
fprintf(stdout,"%f", DSET_ZORG(dset));
break;
case ADI:
fprintf(stdout,"%f", fabs(DSET_DX(dset)));
break;
case EXTENT_R:
case EXTENT_L:
case EXTENT_A:
case EXTENT_P:
case EXTENT_I:
case EXTENT_S:
{
if (!extinit) {
THD_dset_extent(dset, '-', RL_AP_IS);
extinit = 1;
}
fprintf(stdout,"%f", RL_AP_IS[sing[iis]-EXTENT_R]);
}
break;
case ADJ:
fprintf(stdout,"%f", fabs(DSET_DY(dset)));
break;
case ADK:
fprintf(stdout,"%f", fabs(DSET_DZ(dset)));
break;
case VOXVOL:
fprintf(stdout,"%f", fabs(DSET_DX(dset))*
fabs(DSET_DY(dset))*fabs(DSET_DZ(dset)));
break;
case INAME:
fprintf(stdout,"%s", argv[iarg]);
break;
case LTABLE:
{
char *str;
if ((str = Dtable_to_nimlstring(DSET_Label_Dtable(dset), "VALUE_LABEL_DTABLE"))) {
fprintf(stdout,"%s", str);
free(str);
} else {
fprintf(stdout,"NO_LABEL_TABLE");
}
}
break;
case LTABLE_AS_ATLAS_POINT_LIST:
{
ATLAS_POINT_LIST *apl=NULL;
if ((apl =
label_table_to_atlas_point_list(DSET_Label_Dtable(dset)))) {
atlas_list_to_niml(apl,NULL);
free_atlas_point_list(apl);
} else {
fprintf(stdout,"NO_LABEL_TABLE");
}
}
break;
case ATLAS_POINTS:
{
ATR_string *atr =
THD_find_string_atr( dset->dblk, "ATLAS_LABEL_TABLE");
if (atr) {
fprintf(stdout,"%s", atr->ch);
} else {
fprintf(stdout,"NO_APL");
}
}
break;
case FAC:
{
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
fprintf(stdout,"%f%s",
DSET_BRICK_FACTOR(dset,isb),
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
break;
}
case DATUM:
{
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
fprintf(stdout,"%s%s",
MRI_TYPE_name[DSET_BRICK_TYPE(dset,isb)],
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
break;
}
case LABEL:
{
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
fprintf(stdout,"%s%s",
DSET_BRICK_LABEL(dset,isb) ? DSET_BRICK_LABEL(dset,isb):NAflag,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
break;
}
case MIN:
case MINUS:
case MAX:
case MAXUS:
{
float vv=0.0, min, max;
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
if (!THD_subbrick_minmax(dset, isb,
(sing[iis] == MINUS || sing[iis] == MAXUS) ? 0:1,
&min, &max)) {
fprintf(stdout,"%s%s",
NAflag,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
} else {
if (sing[iis] == MINUS)
vv = min;
else if (sing[iis] == MAXUS)
vv = max;
else if (sing[iis] == MIN)
vv = min;
else if (sing[iis] == MAX)
vv = max;
fprintf(stdout,"%g%s",
vv,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
}
break;
}
case DMIN:
case DMINUS:
case DMAX:
case DMAXUS:
{
float vv=0.0, min, max;
if (!THD_dset_minmax(dset,
(sing[iis] == DMINUS || sing[iis] == DMAXUS) ? 0:1,
&min, &max)) {
fprintf(stdout,"%s%s",
NAflag,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
} else {
if (sing[iis] == DMINUS)
vv = min;
else if (sing[iis] == DMAXUS)
vv = max;
else if (sing[iis] == DMIN)
vv = min;
else if (sing[iis] == DMAX)
vv = max;
fprintf(stdout,"%g%s",
vv,
(isb == (DSET_NVALS(dset)-1)) ? "" : sbdelim);
}
break;
}
case TR:
#if 0
fprintf(stdout,"%f", DSET_TR_SEC(dset));
#else
fprintf(stdout,"%f", DSET_TR(dset));
#endif
break;
case ORIENT:
{
/* fprintf(stdout,"%c%c%c",
* ORIENT_typestr[dset->daxes->xxorient][0], ... ); */
char ostr[4]; /* just to show 23 Jan 2013 [rickr] */
THD_fill_orient_str_3(dset->daxes, ostr);
fprintf(stdout,"%3s", ostr);
}
break;
case SAME_GRID:
fprintf(stdout,"%d",
!THD_dataset_mismatch( dset , dsetp ));
break;
case SAME_DIM:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_DIMEN));
break;
case SAME_DELTA:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_DELTA));
break;
case SAME_ORIENT:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_ORIENT));
break;
case SAME_CENTER:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_CENTER));
break;
case SAME_OBL:
fprintf(stdout,"%d",
!(THD_dataset_mismatch( dset , dsetp ) & MISMATCH_OBLIQ));
break;
case SLICE_TIMING: /* 6 May 2013 [rickr] */
{
if( DSET_HAS_SLICE_TIMING(dset) ) {
DSET_UNMSEC(dset); /* make sure times are in seconds */
for (isb=0; isb<dset->taxis->nsl; ++isb) {
fprintf(stdout,"%s%f",
(isb > 0) ? sbdelim : "",
dset->taxis->toff_sl[isb]);
}
} else { /* all slices times are at t=0.0 */
for (isb=0; isb<DSET_NZ(dset); ++isb) {
fprintf(stdout,"%s%f", (isb > 0) ? sbdelim : "", 0.0);
}
}
}
break;
case SVAL_DIFF:
fprintf(stdout,"%f",THD_diff_vol_vals(dset, dsetp, 1));
break;
case VAL_DIFF:
fprintf(stdout,"%f",THD_diff_vol_vals(dset, dsetp, 0));
break;
case ID:
fprintf(stdout,"%s", DSET_IDCODE_STR(dset));
break;
case SMODE:
fprintf(stdout,"%s", DSET_STORAGE_MODE_STR(dset));
break;
default:
ERROR_message("Info field not set properly (%d)\n", sing[iis]);
exit(1);
}
if (sing[iis] != CLASSIC) {
SPIT_DELIM(iis, N_sing, atrdelim);
}
}
}
exit(0) ;
}
char * POWER_main( PLUGIN_interface * plint )
{
MCW_idcode * idc ; /* input dataset idcode */
THD_3dim_dataset * old_dset , * new_dsetD3 , * new_dsetA3, * new_dsetavgD3 ; /* input and output datasets */
char * new_prefix , * str , * namestr, * filename; /* strings from user */
int new_datum , ignore , nfft , ninp , /* control parameters */
old_datum , nuse , ntaper , ktbot,
image_type, scale,OutputFlag ,numT,flip;
float avFac;
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) */
float * this = NULL ; /* array loaded from input dataset */
float ** foutD3 = NULL ; /* will be array of output floats */
float ** foutA3 = NULL ; /* will be array of output floats */
float ** foutavgD3 = NULL ; /* will be array of output floats */
float * tarD3 = NULL ; /* will be array of taper coefficients */
float * tarA3 = NULL ; /* will be array of taper coefficients */
float * taravgD3 = NULL ; /* will be array of taper coefficients */
/*float * flip;*/
float * numAv;
float dfreq , pfact , phi , xr,xi , yr,yi ;
float x0,x1 , y0,y1 , d0fac,d1fac ;
int nfreq , nvox , perc , new_units ;
int istr , ii,iip , ibot,itop , kk , icx ; /* temp variables */
new_prefix = (char *)calloc(100, sizeof(char));
filename = (char *)calloc(100, sizeof(char));
str = (char *)calloc(100, sizeof(char));
namestr = (char *)calloc(100, sizeof(char));
OutputFlag=0;
/*--------------------------------------------------------------------*/
/*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
/*--------- go to first input line ---------*/
PLUTO_next_option(plint) ;
idc = PLUTO_get_idcode(plint) ; /* get dataset item */
old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */
namestr = DSET_PREFIX(old_dset) ;
if( old_dset == NULL )
return "*************************\n"
"Cannot find Input Dataset\n"
"*************************" ;
/*--------- go to second input line ---------*/
PLUTO_next_option(plint) ;
filename = PLUTO_get_string(plint) ; /* get string item (the output prefix) */
sprintf(new_prefix,"%s%s",filename,"_D3");
if (strcmp(new_prefix,"_D3")==0){
OutputFlag=1;
sprintf(new_prefix,"%s%s",namestr,"_D3");
}
if (! PLUTO_prefix_ok(new_prefix) ){
PLUTO_popup_transient(plint,new_prefix);
return "*************************\n"
"Output filename already exists\n"
"*************************" ;
}
PLUTO_popup_transient(plint,"Output file tags set automatically");
str = PLUTO_get_string(plint) ; /* get string item (the datum type) */
istr = PLUTO_string_index( str , /* find it in the list it came from */
NUM_TYPE_STRINGS ,
type_strings ) ;
switch( istr ){
default:
case 0:
new_datum = MRI_float ; break ;
break ;
case 1: new_datum = MRI_byte ; break ; /* assign type of user's choice */
case 2: new_datum = MRI_short ; break ;
case 3: new_datum = DSET_BRICK_TYPE( old_dset , 0 ) ; /* use old dataset type */
}
/*--------- go to next input lines ---------*/
PLUTO_next_option(plint) ; /* skip to next line */
ignore = PLUTO_get_number(plint) ; /* get number item (ignore) */
ninp = DSET_NUM_TIMES(old_dset) ; /* number of values in input */
nuse = ninp; /* number of values to actually use */
nfreq=nuse;
nfft=nuse;
str = PLUTO_get_string(plint) ; /* get string item (the datum type) */
istr = PLUTO_string_index( str , /* find it in the list it came from */
NUM_TYPE_STRINGSX ,
type_stringsx ) ;
switch( istr ){
default:
case 0: image_type = 0; break;
}
PLUTO_next_option(plint) ; /* skip to next line */
scale = PLUTO_get_number(plint) ; /* get number item (scale) */
/*------------------------------------------------------*/
/*---------- At this point, the inputs are OK ----------*/
PLUTO_popup_meter( plint ) ; /* popup a progress meter */
/*--------- set up pointers to each sub-brick in the input dataset ---------*/
DSET_load( old_dset ) ; /* must be in memory before we get pointers to it */
old_datum = DSET_BRICK_TYPE( old_dset , 0 ) ; /* get old dataset datum type */
switch( old_datum ){ /* pointer type depends on input datum type */
default:
return "******************************\n"
"Illegal datum in Input Dataset\n"
"******************************" ;
/** create array of pointers into old dataset sub-bricks **/
/** Note that we skip the first 'ignore' sub-bricks here **/
/*--------- input is bytes ----------*/
/* voxel #i at time #k is bptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_byte:
bptr = (byte **) malloc( sizeof(byte *) * nuse ) ;
if( bptr == NULL ) return "Malloc\nFailure!\n [bptr]" ;
for( kk=0 ; kk < nuse ; 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..nvox-1 and k=0..nuse-1. */
case MRI_short:
sptr = (short **) malloc( sizeof(short *) * nuse ) ;
if( sptr == NULL ) return "Malloc\nFailure!\n [sptr]" ;
for( kk=0 ; kk < nuse ; 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..nvox-1 and k=0..nuse-1. */
case MRI_float:
fptr = (float **) malloc( sizeof(float *) * nuse ) ;
if( fptr == NULL ) return "Malloc\nFailure!\n [fptr]" ;
for( kk=0 ; kk < nuse ; kk++ )
fptr[kk] = (float *) DSET_ARRAY(old_dset,kk) ;
break ;
} /* end of switch on input type */
/*---- allocate space for 2 voxel timeseries and 1 FFT ----*/
this = (float *) malloc( sizeof(float) * nuse ) ; /* input */
tarD3 = (float *) malloc( sizeof(float) * MAX(nuse,nfreq) ) ;
tarA3 = (float *) malloc( sizeof(float) * MAX(nuse,nfreq) ) ;
taravgD3 = (float *) malloc( sizeof(float) * MAX(nuse,nfreq) ) ;
/*flip = (float *)malloc( sizeof(float) * 1);*/
numAv = (float *)malloc( sizeof(float) * 1);
numT=nuse-ignore;
if (OutputFlag==1)
sprintf(new_prefix,"%s%s",namestr,"_D3");
else
sprintf(new_prefix,"%s%s",filename,"_D3");
new_dsetD3 = EDIT_empty_copy( old_dset );
{ char * his = PLUTO_commandstring(plint) ;
tross_Copy_History( old_dset , new_dsetD3 ) ;
tross_Append_History( new_dsetD3 , his ) ; free(his) ;
}
/*-- edit some of its internal parameters --*/
ii = EDIT_dset_items(
new_dsetD3 ,
ADN_prefix , new_prefix , /* filename prefix */
ADN_malloc_type , DATABLOCK_MEM_MALLOC , /* store in memory */
ADN_datum_all , new_datum , /* atomic datum */
ADN_nvals , numT ,
ADN_ntt ,numT,
ADN_none ) ;
if (OutputFlag==1)
sprintf(new_prefix,"%s%s",namestr,"_A3");
else
sprintf(new_prefix,"%s%s",filename,"_A3");
numT=nuse-ignore;
new_dsetA3 = EDIT_empty_copy( old_dset );
{ char * his = PLUTO_commandstring(plint) ;
tross_Copy_History( old_dset , new_dsetA3 ) ;
tross_Append_History( new_dsetA3 , his ) ; free(his) ;
}
/*-- edit some of its internal parameters --*/
ii = EDIT_dset_items(
new_dsetA3 ,
ADN_prefix , new_prefix , /* filename prefix */
ADN_malloc_type , DATABLOCK_MEM_MALLOC , /* store in memory */
ADN_datum_all , new_datum , /* atomic datum */
ADN_nvals , numT,
ADN_ntt ,numT,
ADN_none ) ;
if (OutputFlag==1)
sprintf(new_prefix,"%s%s",namestr,"_avgD3");
else
sprintf(new_prefix,"%s%s",filename,"_avgD3");
new_dsetavgD3 = EDIT_empty_copy( old_dset );
{ char * his = PLUTO_commandstring(plint) ;
tross_Copy_History( old_dset , new_dsetavgD3 ) ;
tross_Append_History( new_dsetavgD3 , his ) ; free(his) ;
}
/*-- edit some of its internal parameters --*/
ii = EDIT_dset_items(
new_dsetavgD3 ,
ADN_prefix , new_prefix , /* filename prefix */
ADN_malloc_type , DATABLOCK_MEM_MALLOC , /* store in memory */
ADN_datum_all , new_datum , /* atomic datum */
ADN_nvals , 1,
ADN_ntt ,1,
ADN_none ) ;
/*---------------------- make a new dataset ----------------------*/
/*-------------------making a new dataset------------------------------------*/
/*------ make floating point output sub-bricks
(only at the end will scale to byte or shorts)
Output #ii at freq #kk will go into fout[kk][ii],
for kk=0..nfreq-1, and for ii=0..nvox-1. ------*/
nvox = old_dset->daxes->nxx * old_dset->daxes->nyy * old_dset->daxes->nzz ;
foutD3 = (float **) malloc( sizeof(float *) * nuse ) ; /* ptrs to sub-bricks */
foutA3 = (float **) malloc( sizeof(float *) * nuse ) ; /* ptrs to sub-bricks */
foutavgD3 = (float **) malloc( sizeof(float *) * 1 ) ; /* ptrs to sub-bricks */
if( foutD3 == NULL | foutA3 == NULL | foutavgD3 == NULL){
THD_delete_3dim_dataset( new_dsetD3 , False ) ;
THD_delete_3dim_dataset( new_dsetA3 , False ) ;
THD_delete_3dim_dataset( new_dsetavgD3 , False ) ;
FREE_WORKSPACE ;
return "Malloc\nFailure!\n [fout]" ;
}
for( kk=0 ; kk < nfreq ; kk++ ){
foutD3[kk] = (float *) malloc( sizeof(float) * nvox ) ; /* sub-brick # kk */
foutA3[kk] = (float *) malloc( sizeof(float) * nvox ) ; /* sub-brick # kk */
foutavgD3[0] = (float *) malloc( sizeof(float) * nvox ) ; /* sub-brick # kk */
if( foutD3[kk] == NULL ) break ;
if( foutA3[kk] == NULL ) break ;
if( foutavgD3[0] == NULL ) break ;
}
if( kk < nfreq ){
for( ; kk >= 0 ; kk-- ){
FREEUP(foutD3[kk]) ;
FREEUP(foutA3[kk]) ;
FREEUP(foutavgD3[0]) ;
}/* free all we did get */
THD_delete_3dim_dataset( new_dsetD3 , False ) ;
THD_delete_3dim_dataset( new_dsetA3 , False ) ;
THD_delete_3dim_dataset( new_dsetavgD3 , False ) ;
FREE_WORKSPACE ;
return "Malloc\nFailure!\n [arrays]" ;
}
{ char buf[128] ;
ii = (nfreq * nvox * sizeof(float)) / (1024*1024) ;
sprintf( buf , " \n"
"*** 3D+time ASL a3/d3:\n"
"*** Using %d MBytes of workspace,\n "
"*** with # time points = %d\n" , ii,numT ) ;
PLUTO_popup_transient( plint , buf ) ;
}
/*----------------------------------------------------*/
/*----- Setup has ended. Now do some real work. -----*/
/***** loop over voxels *****/
/* *(flip)=scale; */
*(numAv)= nuse-ignore;
for( ii=0 ; ii < nvox ; ii ++ ){ /* time series */
switch( old_datum ){
case MRI_byte:
for( kk=0 ; kk < nuse ; kk++ ){
this[kk] = bptr[kk][ii] ;
}
break ;
case MRI_short:
for( kk=0 ; kk < nuse ; kk++ ){
this[kk] = sptr[kk][ii] ;
}
break ;
case MRI_float:
for( kk=0 ; kk < nuse ; kk++ ){
this[kk] = fptr[kk][ii] ;
}
break ;
}
flip=scale*pow(-1,ignore+1);
for( kk=0 ; kk < nuse-ignore ; kk++ ){
if (kk==nuse-1-ignore){
*(*(foutD3+kk)+ii)=
flip*( *(this+kk+ignore-1)-*(this+kk+ignore) );
*(*(foutA3+kk)+ii)=
2*(*(this+kk+ignore-1)+*(this+kk+ignore));
}
else if (kk==0){
/*D3 tag - control*/
*(*(foutD3+kk)+ii)=
flip*( *(this+kk+ignore)-*(this+kk+ignore+1) );
*(*(foutA3+kk)+ii)=
2*(*(this+kk+ignore)+*(this+kk+ignore+1));
}
else{
*(*(foutD3+kk)+ii)=
flip*( 1*(*(this+kk+ignore-1))+-2*(*(this+kk+ignore))+1*(*(this+kk+ignore+1)) );
*(*(foutA3+kk)+ii)=
((*(this+kk+ignore-1))+2*(*(this+kk+ignore))+(*(this+kk+ignore+1)));
flip=-1*flip;
}
}
for( kk=0 ; kk < nuse-ignore ; kk++ )
*(*(foutavgD3)+ii)= *(*(foutavgD3)+ii)+(*(*(foutD3+kk)+ii));
*(*(foutavgD3)+ii)=*(*(foutavgD3)+ii) / (*(numAv));
}
DSET_unload( old_dset ) ; /* don't need this no more */
switch( new_datum ){
/*** output is floats is the simplest:
we just have to attach the fout bricks to the dataset ***/
case MRI_float:
for( kk=0 ; kk < nuse-ignore ; kk++ )
EDIT_substitute_brick( new_dsetD3 , kk , MRI_float , foutD3[kk] ) ;
break ;
/*** output is shorts:
we have to create a scaled sub-brick from fout ***/
case MRI_short:{
short * boutD3 ;
float facD3 ;
for( kk=0 ; kk < nuse-ignore ; kk++ ){ /* loop over sub-bricks */
/*-- get output sub-brick --*/
boutD3 = (short *) malloc( sizeof(short) * nvox ) ;
if( boutD3 == NULL ){
fprintf(stderr,"\nFinal malloc error in plug_power!\n\a") ;
EXIT(1) ;
}
/*-- find scaling and then scale --*/
facD3 = MCW_vol_amax( nvox,1,1 , MRI_float , foutD3[kk] ) ;
if( facD3 > 0.0 ){
facD3 = 32767.0 / facD3 ;
EDIT_coerce_scale_type( nvox,facD3 ,
MRI_float,foutD3[kk] , MRI_short,boutD3 ) ;
facD3 = 1.0 / facD3 ;
}
free( foutD3[kk] ) ; /* don't need this anymore */
/*-- put output brick into dataset, and store scale factor --*/
EDIT_substitute_brick( new_dsetD3 , kk , MRI_short , boutD3 ) ;
tarD3 [kk] = facD3 ;
}
/*-- save scale factor array into dataset --*/
EDIT_dset_items( new_dsetD3 , ADN_brick_fac , tarD3 , ADN_none ) ;
}
break ;
/*** output is bytes (byte = unsigned char)
we have to create a scaled sub-brick from fout ***/
case MRI_byte:{
byte * boutD3 ;
float facD3 ;
for( kk=0 ; kk < nuse-ignore ; kk++ ){ /* loop over sub-bricks */
/*-- get output sub-brick --*/
boutD3 = (byte *) malloc( sizeof(byte) * nvox ) ;
if( boutD3 == NULL ){
fprintf(stderr,"\nFinal malloc error in plug_power!\n\a") ;
EXIT(1) ;
}
/*-- find scaling and then scale --*/
facD3 = MCW_vol_amax( nvox,1,1 , MRI_float , foutD3[kk] ) ;
if( facD3 > 0.0 ){
facD3 = 255.0 / facD3 ;
EDIT_coerce_scale_type( nvox,facD3 ,
MRI_float,foutD3[kk] , MRI_byte,boutD3 ) ;
facD3 = 1.0 / facD3 ;
}
free( foutD3[kk] ) ; /* don't need this anymore */
/*-- put output brick into dataset, and store scale factor --*/
EDIT_substitute_brick( new_dsetD3 , kk , MRI_byte , boutD3 ) ;
tarD3 [kk] = facD3 ;
}
/*-- save scale factor array into dataset --*/
EDIT_dset_items( new_dsetD3 , ADN_brick_fac , tarD3 , ADN_none ) ;
}
break ;
} /* end of switch on output data type */
switch( new_datum ){
/*** output is floats is the simplest:
we just have to attach the fout bricks to the dataset ***/
case MRI_float:
for( kk=0 ; kk < nuse-ignore ; kk++ )
EDIT_substitute_brick( new_dsetA3 , kk , MRI_float , foutA3[kk] ) ;
break ;
/*** output is shorts:
we have to create a scaled sub-brick from fout ***/
case MRI_short:{
short * boutA3 ;
float facA3 ;
for( kk=0 ; kk < nuse-ignore ; kk++ ){ /* loop over sub-bricks */
/*-- get output sub-brick --*/
boutA3 = (short *) malloc( sizeof(short) * nvox ) ;
if( boutA3 == NULL ){
fprintf(stderr,"\nFinal malloc error in plug_power!\n\a") ;
EXIT(1) ;
}
/*-- find scaling and then scale --*/
facA3 = MCW_vol_amax( nvox,1,1 , MRI_float , foutA3[kk] ) ;
if( facA3 > 0.0 ){
facA3 = 32767.0 / facA3 ;
EDIT_coerce_scale_type( nvox,facA3 ,
MRI_float,foutA3[kk] , MRI_short,boutA3 ) ;
facA3 = 1.0 / facA3 ;
}
free( foutA3[kk] ) ; /* don't need this anymore */
/*-- put output brick into dataset, and store scale factor --*/
EDIT_substitute_brick( new_dsetA3 , kk , MRI_short , boutA3 ) ;
tarA3[kk] = facA3 ;
}
/*-- save scale factor array into dataset --*/
EDIT_dset_items( new_dsetA3 , ADN_brick_fac , tarA3 , ADN_none ) ;
}
break ;
/*** output is bytes (byte = unsigned char)
we have to create a scaled sub-brick from fout ***/
case MRI_byte:{
byte * boutA3 ;
float facA3 ;
for( kk=0 ; kk < nuse-ignore ; kk++ ){ /* loop over sub-bricks */
/*-- get output sub-brick --*/
boutA3 = (byte *) malloc( sizeof(byte) * nvox ) ;
if( boutA3 == NULL ){
fprintf(stderr,"\nFinal malloc error in plug_power!\n\a") ;
EXIT(1) ;
}
/*-- find scaling and then scale --*/
facA3 = MCW_vol_amax( nvox,1,1 , MRI_float , foutA3[kk] ) ;
if( facA3 > 0.0 ){
facA3 = 255.0 / facA3 ;
EDIT_coerce_scale_type( nvox,facA3 ,
MRI_float,foutA3[kk] , MRI_byte,boutA3 ) ;
facA3 = 1.0 / facA3 ;
}
free( foutA3[kk] ) ; /* don't need this anymore */
/*-- put output brick into dataset, and store scale factor --*/
EDIT_substitute_brick( new_dsetA3 , kk , MRI_byte , boutA3 ) ;
tarA3[kk]= facA3 ;
}
/*-- save scale factor array into dataset --*/
EDIT_dset_items( new_dsetA3 , ADN_brick_fac , tarA3 , ADN_none ) ;
}
break ;
} /* end of switch on output data type */
switch( new_datum ){
case MRI_float:{
EDIT_substitute_brick( new_dsetavgD3 , 0 , MRI_float , foutavgD3[0] ) ;
}
break ;
case MRI_short:{
short * boutavgD3 ;
float facavgD3 ;
boutavgD3 = (short *) malloc( sizeof(short) * nvox ) ;
if( boutavgD3 == NULL ){
fprintf(stderr,"\nFinal malloc error in plug_power!\n\a") ;
EXIT(1) ;
}
facavgD3 = MCW_vol_amax( nvox,1,1 , MRI_float , foutavgD3[0] ) ;
if( facavgD3 > 0.0 ){
facavgD3 = 32767.0 / facavgD3 ;
EDIT_coerce_scale_type( nvox,facavgD3 ,
MRI_float,foutavgD3[0] , MRI_short,boutavgD3 ) ;
facavgD3 = 1.0 / facavgD3 ;
}
EDIT_substitute_brick( new_dsetavgD3 , 0 , MRI_short , boutavgD3 ) ;
taravgD3[0] = facavgD3 ;
EDIT_dset_items( new_dsetavgD3 , ADN_brick_fac , taravgD3 , ADN_none ) ;
}
break ;
case MRI_byte:{
byte * boutavgD3 ;
float facavgD3 ;
boutavgD3 = (byte *) malloc( sizeof(byte) * nvox ) ;
if( boutavgD3 == NULL ){
fprintf(stderr,"\nFinal malloc error in plug_power!\n\a") ;
EXIT(1) ;
}
facavgD3 = MCW_vol_amax( nvox,1,1 , MRI_float , foutavgD3[0] ) ;
if( facavgD3 > 0.0 ){
facavgD3 = 255.0 / facavgD3 ;
EDIT_coerce_scale_type( nvox,facavgD3 ,
MRI_float,foutavgD3[0] , MRI_byte,boutavgD3 ) ;
facavgD3 = 1.0 / facavgD3 ;
}
EDIT_substitute_brick( new_dsetavgD3 , 0 , MRI_byte , boutavgD3 ) ;
taravgD3[0]= facavgD3 ;
EDIT_dset_items( new_dsetavgD3 , ADN_brick_fac , taravgD3 , ADN_none ) ;
}
break ;
} /* endasda of switch on output data type */
/*-------------- Cleanup and go home ----------------*/
PLUTO_add_dset( plint , new_dsetD3 , DSET_ACTION_NONE ) ;
PLUTO_add_dset( plint , new_dsetA3 , DSET_ACTION_NONE ) ;
PLUTO_add_dset( plint , new_dsetavgD3 , DSET_ACTION_NONE ) ;
FREE_WORKSPACE ;
free(numAv);
return NULL ; /* null string returned means all was OK */
}
/*!
\brief out_set = thd_polyfit( in_set,
mask, polorder,
prefix, verb);
fits a polynomial model of order polorder to
the time series of voxels in in_set
\param in_set (THD_3dim_dataset* ) An AFNI dset pointer to input data
\param mask (byte *) if mask is not NULL then voxel i will be processed
if mask[i] != 0.
if mask is NULL then all voxels are processed.
\param polorder (int) polynomial order
\param prefix (char *) prefix of output dset
\param verb (int) verbosity flag
\return out_set (THD_3dim_dataset* ) Dset containing polynomial fits.
*/
THD_3dim_dataset *thd_polyfit(THD_3dim_dataset *in_set,
byte *mask, int polorder,
char *prefix, int verb)
{
int i=0, j=0, nl=0, k=0,
posi=0, posj=0, posk=0, nrow=0,
ncol = 0;
double xi=0.0, yi=0.0, yy=0.0, ei=0.0, sumsq=0.0, med=0.0;
gsl_matrix *X=NULL, *cov=NULL;
gsl_vector *y=NULL, *w=NULL, *c=NULL;
MRI_IMAGE *im = NULL;
THD_3dim_dataset *out_set=NULL;
double *dar = NULL;
float *cbuf=NULL;
float *dvec = NULL;
gsl_multifit_linear_workspace *work=NULL;
ENTRY("thd_polyfit");
/* prepare output */
out_set = EDIT_empty_copy(in_set) ;
EDIT_dset_items( out_set ,
ADN_nvals , polorder ,
ADN_ntt , polorder ,
ADN_datum_all , MRI_float ,
ADN_brick_fac , NULL ,
ADN_prefix , prefix ? prefix : "OMG!" ,
ADN_none ) ;
for( j=0 ; j < polorder ; j++ ) /* create empty bricks to be filled below */
EDIT_substitute_brick( out_set , j , MRI_float , NULL ) ;
/* do the fitting */
if (verb) fprintf (stderr,"Now fitting...\n");
ncol = DSET_NVALS(in_set);
nrow = DSET_NVOX(in_set);
X = gsl_matrix_alloc (ncol, polorder);
y = gsl_vector_alloc (ncol);
c = gsl_vector_alloc (polorder);
cov = gsl_matrix_alloc (polorder, polorder);
for (i = 0; i < ncol; i++) {
xi = i+1;
gsl_matrix_set (X, i, 0, 1.0);
gsl_matrix_set (X, i, 1, xi);
gsl_matrix_set (X, i, 2, xi*xi);
gsl_matrix_set (X, i, 3, xi*xi*xi);
gsl_matrix_set (X, i, 4, xi*xi*xi*xi);
// printf ("%lg ",xi);
}
/*make header
printf ("matrvola\n");
ZSS: By adding # to the text line,
I made the output file be a .1D format */
if (verb > 1)
fprintf(stdout, "#%s_0\t%s_1\t%s_2\t%s_3\t%s_4\n",
DSET_PREFIX(in_set),DSET_PREFIX(in_set),
DSET_PREFIX(in_set),DSET_PREFIX(in_set),
DSET_PREFIX(in_set));
// go by lines - signatures
/* pre-allocate, I think this should be just fine,
there should be no need to reinitialize work
all the time */
work = gsl_multifit_linear_alloc (ncol, polorder);
dvec = (float * )malloc(sizeof(float)*ncol) ; /* array to hold signature */
cbuf = (float *)malloc(sizeof(float)*polorder) ;
/* array to hold fit */
for (nl=0; nl<nrow; ++nl) {
if (!mask || mask[nl]) {
posi = -1;
posj = -1;
posk = -1;
THD_extract_array( nl , in_set , 0 , dvec ) ;
/*get signature from voxel */
for (k = 0; k < ncol; k++) {
gsl_vector_set (y, k, dvec[k]);
}
gsl_multifit_linear (X, y, c, cov,
&sumsq, work);
/* printf ( "\n # best fit: Y = %g + %g X + %g X^2 +%g X^3 + %g X^4\n",
C(0), C(1), C(2), C(3), C(4));
printf ("# sumsq = %g\n", sumsq); */
for (i=0;i<polorder;++i) cbuf[i] = (float)C(i);
THD_insert_series( nl , out_set , polorder , MRI_float , cbuf , 1 ) ;
/* stick result in output */
if (verb > 1)
fprintf (stdout, "%11g\t%11g\t%11g\t%11g\t%11g\n",
C(0), C(1), C(2), C(3), C(4));
/*
printf ("# covariance matrix:\n");
printf ("[ %+.5e, %+.5e, %+.5e \n",
COV(0,0), COV(0,1), COV(0,2));
printf (" %+.5e, %+.5e, %+.5e \n",
COV(1,0), COV(1,1), COV(1,2));
printf (" %+.5e, %+.5e, %+.5e ]\n",
COV(2,0), COV(2,1), COV(2,2));
printf ("# chisq = %g\n", chisq);
*/
}
}
gsl_multifit_linear_free (work); work = NULL;
free(dvec); dvec = NULL;
free(cbuf); cbuf = NULL;
gsl_vector_free (y);
gsl_vector_free (c);
gsl_matrix_free (cov);
gsl_matrix_free (X);
//gsl_vector_free (w);
free(dvec); dvec = NULL;
RETURN(out_set);
}
/*!
Put some help like for function thd_polyfit
*/
int thd_Acluster ( THD_3dim_dataset *in_set,
byte *mask, int nmask,
THD_3dim_dataset **clust_set,
THD_3dim_dataset **dist_set,
OPT_KMEANS oc )
{
int ii, nl, nc;
double **D=NULL, **distmatrix=NULL; /* this double business is a waste of
memory, at least for D..*/
int ncol = -1;
float *dvec=NULL;
int* clusterid = NULL;
short *sc = NULL;
ENTRY("thd_Acluster");
if (!clust_set || *clust_set) {
fprintf(stderr,
"ERROR: output volume pointer pointers must point to NULL\n");
RETURN(0);
}
if (!mask) nmask = DSET_NVOX(in_set);
ncol = DSET_NVALS(in_set);
if (ncol < DSET_NUM_TIMES(in_set)) ncol = DSET_NUM_TIMES(in_set);
if (oc.verb) {
ININFO_message("Have %d/%d voxels to process "
"with %d dimensions per voxel.\n",
nmask, DSET_NVOX(in_set), ncol);
}
/* Create data matrix */
D = (double **)calloc(sizeof(double*), nmask);
for (ii=0;ii<(nmask);++ii) {
if (!(D[ii] = (double *)calloc(sizeof(double), ncol))) {
fprintf(stderr,"ERROR: Failed while allocating %dx%d double matrix\n",
nmask, ncol);
RETURN(0);
}
}
dvec = (float * )malloc(sizeof(float)*ncol) ; /* array to hold series */
if (oc.verb) {
ININFO_message("Filling D(%dx%d) (mask=%p).\n", nmask, ncol, mask);
}
ii = 0;
for (nl=0; nl<DSET_NVOX(in_set); ++nl) {
if (!mask || mask[nl]) {
THD_extract_array( nl , in_set , 0 , dvec ) ;
for (nc=0; nc<ncol; ++nc) D[ii][nc] = dvec[nc];
++ii;
}
}
/* allocate for answer arrays */
if (!(clusterid = (int *)calloc(sizeof(int), nmask))) {
fprintf(stderr,"ERROR: Failed to allocate for clusterid\n");
RETURN(0);
}
/* now do the clustering
(ANDREJ: I do not know why the counting skipped 1st row and 1st col....) */
if (oc.k > 0) {
if (oc.verb) {
ININFO_message("Going to cluster: k=%d, r=%d\n"
"distmetric %c, jobname %s\n",
oc.k, oc.r, oc.distmetric, oc.jobname);
}
example_kmeans( nmask, ncol, D,
oc.k, oc.r, oc.distmetric,
oc.jobname, clusterid);
} else if (oc.kh > 0) {
if (oc.verb) {
ININFO_message("Going to h cluster: kh=%d\n"
"jobname %s\n",
oc.kh, oc.jobname);
}
if ((distmatrix = example_distance_gene(nmask, ncol, D))) {
example_hierarchical( nmask, ncol, D,
oc.jobname, oc.kh,
distmatrix,
clusterid);
/* YOU SHOULD FREE distmatrix here ...*/
} else {
ERROR_message("Failed to create distmatrix");
RETURN(0);
}
} else {
ERROR_message("Bad option selection");
RETURN(0);
}
/* create output datasets, if required*/
*clust_set = EDIT_empty_copy(in_set) ;
EDIT_dset_items( *clust_set ,
ADN_nvals , 1 ,
ADN_ntt , 1 ,
ADN_datum_all , MRI_short ,
ADN_brick_fac , NULL ,
ADN_prefix , "OML!" ,
ADN_none ) ;
/* MRI_float */
if (oc.verb) {
ININFO_message("loading results into %s\n",
DSET_PREFIX(*clust_set));
}
/* transfer ints in clusterid to shorts array */
sc = (short *)calloc(sizeof(short),DSET_NVOX(in_set));
ii = 0;
for (nl=0; nl<DSET_NVOX(in_set); ++nl) {
if (!mask || mask[nl]) {
sc[nl] = (short)clusterid[ii]+1;
++ii;
}
}
free(clusterid); clusterid = NULL;
EDIT_substitute_brick( *clust_set , 0 , MRI_short , sc ) ;
sc = NULL; /* array now in brick */
if (oc.verb) {
ININFO_message("Freedom");
}
if (dvec) free(dvec); dvec=NULL;
// To free D
for (ii=0;ii<nmask;++ii) {
if (D[ii]) free(D[ii]);
}
free(D); D = NULL;
RETURN(1);
}
int *THD_unique_vals( THD_3dim_dataset *mask_dset ,
int miv,
int *n_unique ,
byte *cmask)
{
int nvox , ii, *unq = NULL, *vals=NULL;
*n_unique = 0;
unq = NULL ;
if( !ISVALID_DSET(mask_dset) ||
miv < 0 ||
miv >= DSET_NVALS(mask_dset) ) {
fprintf(stderr,"** Bad mask_dset or sub-brick index.\n");
return (unq) ;
}
nvox = DSET_NVOX(mask_dset) ;
DSET_load(mask_dset) ; if( !DSET_LOADED(mask_dset) ) return (unq) ;
if (!is_integral_sub_brick (mask_dset, miv, 0)) {
fprintf(stderr,"** Sub-brick %d of %s is not of an integral data type.\n",
miv, DSET_PREFIX(mask_dset) ? DSET_PREFIX(mask_dset):"NULL");
return (unq) ;
}
vals = (int *)malloc(sizeof(int)*nvox);
if (!vals) {
fprintf(stderr,"** Failed to allocate.\n");
return (unq) ;
}
switch( DSET_BRICK_TYPE(mask_dset,miv) ){
default:
fprintf(stderr,"** Bad dset type for unique operation.\n"
"Only integral valued dsets are allowed.\n");
DSET_unload(mask_dset) ; if (vals) free(vals); return (unq) ;
case MRI_short:{
short *mar = (short *) DSET_ARRAY(mask_dset,miv) ;
if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if (cmask[ii]) vals[ii] = (int)(mar[ii]); else vals[ii] = 0;
} else {
for( ii=0 ; ii < nvox ; ii++ )
vals[ii] = (int)(mar[ii]);
}
}
break ;
case MRI_byte:{
byte *mar = (byte *) DSET_ARRAY(mask_dset,miv) ;
if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if (cmask[ii]) vals[ii] = (int)(mar[ii]); else vals[ii] = 0;
} else {
for( ii=0 ; ii < nvox ; ii++ )
vals[ii] = (int)(mar[ii]);
}
}
break ;
case MRI_float:{
float *mar = (float *) DSET_ARRAY(mask_dset,miv) ;
if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if (cmask[ii]) vals[ii] = (int)(mar[ii]); else vals[ii] = 0;
} else {
for( ii=0 ; ii < nvox ; ii++ )
vals[ii] = (int)(mar[ii]);
}
}
break ;
}
/* unique */
unq = UniqueInt (vals, nvox, n_unique, 0 );
free(vals); vals = NULL;
return (unq) ;
}
static char * DELAY_main( PLUGIN_interface * plint )
{
hilbert_data_V2 uda,*ud;
MRI_IMAGE * tsim;
MCW_idcode * idc ; /* input dataset idcode */
THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */
char *tmpstr , * str , *nprfxstr; /* strings from user */
int ntime, nvec ,nprfx, i;
float * vec , fs , T ;
/* Allocate as much character space as Bob specifies in afni.h + a bit more */
tmpstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
nprfxstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
if (tmpstr == NULL || nprfxstr == NULL)
return "********************\n"
"Could not Allocate\n"
"a teeni weeni bit of\n"
"Memory ! \n"
"********************\n";
ud = &uda; /* ud now points to an allocated space */
ud->errcode = 0; /*reset error flag */
/*--------------------------------------------------------------------*/
/*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
/*--------- go to first input line ---------*/
PLUTO_next_option(plint) ;
idc = PLUTO_get_idcode(plint) ; /* get dataset item */
old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */
if( old_dset == NULL )
return "*************************\n"
"Cannot find Input Dataset\n"
"*************************" ;
ud->dsetname = DSET_FILECODE (old_dset);
ud->nsamp = DSET_NUM_TIMES (old_dset);
ud->Navg = 1 ; /* Navg does not play a role for the p value, averaging increases sensitivity */
ud->Nort = PLUTO_get_number(plint) ; /* Should be two by default, for mean and linear trend */
ud->Nfit = 2 ; /* Always 2 for phase and amplitude for this plugin */
/*--------- go to 2nd input line, input time series ---------*/
PLUTO_next_option(plint) ;
tsim = PLUTO_get_timeseries(plint);
if (tsim == NULL) return "No Timeseries Input";
ud->ln = (int)tsim -> nx; /* number of points in each vector */
nvec = tsim -> ny; /* number of vectors */
ud->rvec = (float *) MRI_FLOAT_PTR(tsim); /* vec[i+j*nx] = ith point of jth vector */
/* for i=0 .. ntime-1 and j=0 .. nvec-1 */
if (is_vect_null (ud->rvec,ud->ln) == 1) /* check if ref vect is all zeroes */
{
return "Reference vector is all zeros";
}
ud->refname = tsim->name;
ud->ignore = PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ;
ud->Dsamp = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings ) ;
/*--------- go to 3rd input line, sampling frequency, and stimulus period ---------*/
PLUTO_next_option(plint) ;
ud->fs = PLUTO_get_number(plint) ; /* get number item */
ud->T = PLUTO_get_number(plint) ; /* get number item */
ud->co = PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ;
ud->biasrem = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings ) ;
/*--------- go to 4th input line, delay units and wrp option---------*/
PLUTO_next_option(plint) ;
ud->Nseg = (int)PLUTO_get_number(plint) ; /* get number item */
ud->Pover = (int)PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ; /* get string item (the method) */
ud->unt = (int)PLUTO_string_index( str , /* find it in list it is from */
NUM_METHOD_STRINGS ,
method_strings ) ;
str = PLUTO_get_string(plint) ;
ud->wrp = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings ) ;
/*--------- go to 5th input line Output prefix ---------*/
PLUTO_next_option(plint) ;
ud->new_prefix = PLUTO_get_string(plint) ; /* get string item (the output prefix) */
/* check to see if the field is empty */
if (ud->new_prefix == NULL)
nprfx = 0;
else
nprfx = 1;
/* check if the size is larger than 0. I did not want to check for this unless it's allocated */
if (nprfx == 1 && (int)strlen (ud->new_prefix) == 0)
nprfx = 0;
if (nprfx == 0) /* now create the new name and make new_prefix point to it */
{
sprintf (nprfxstr,"%s.DEL",DSET_PREFIX (old_dset));
ud->new_prefix = nprfxstr;
/*printf ("New prefix is set to be : %s\n\a",ud->new_prefix);*/
}
if( ! PLUTO_prefix_ok(ud->new_prefix) ) /* check if it is OK */
return "************************\n"
"Output Prefix is illegal\n"
"************************" ;
str = PLUTO_get_string(plint) ; /* write delays to file ? */
ud->out = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings );
ud->strout = PLUTO_get_string(plint) ; /* strout is for the outiflename, which will be used after the debugging section */
if (ud->strout == NULL) /* if no output name is given, use the new_prefix */
{ud->strout = ud->new_prefix;}
else
{
if((int)strlen (ud->strout) == 0) ud->strout = ud->new_prefix;
}
str = PLUTO_get_string(plint) ;
ud->outts = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings );
/* ------------------Done with user parameters ---------------------------- */
ud->nxx = (int)old_dset->daxes->nxx; /* get data set dimensions */
ud->nyy = (int)old_dset->daxes->nyy;
ud->nzz = (int)old_dset->daxes->nzz;
/* No need for users to set these options ...*/
ud->dtrnd = 0;
if (ud->ln != (ud->nsamp - ud->ignore))
{
ud->errcode = ERROR_BADLENGTH;
return "***************************\n"
"Bad time series length \n"
"Check reference time series\n"
" or the ignore parameter \n"
"***************************\n";
}
if ((ud->unt < 0) || (ud->unt > 2)) /* unt error Check */
{
ud->errcode = ERROR_WRONGUNIT;
return "***********************\n"
" internal error: (ziad)\n"
"unt values out of bound\n"
"***********************\n"; /*unt must be between 0 and 2 */
}
if ((ud->wrp < 0) || (ud->wrp > 1)) /* wrp error Check */
{
ud->errcode = ERROR_WARPVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"wrp values out of bound\n"
"***********************\n"; /* wrp must be between 0 and 1*/
}
if (ud->fs < 0.0) { /* fs error Check */
ud->errcode = ERROR_FSVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"fs value is negative !\n"
"***********************\n"; /* fs must be >= 0*/
}
if (ud->T < 0.0) { /* T error Check */
ud->errcode = ERROR_TVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"T value is negative !\n"
"***********************\n"; /*T must be >= 0 */
}
if ((ud->T == 0.0) && (ud->unt > 0)) /* unt error Check */
{
ud->errcode = ERROR_TaUNITVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"T and unt val. mismatch\n"
"***********************\n"; /*T must be specified, and > 0 in order to use polar units*/
}
if ((ud->wrp == 1) && (ud->T == 0.0)) /* wrp error Check */
{
ud->errcode = ERROR_TaWRAPVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"wrp and T val. mismatch\n"
"***********************\n"; /*T must be specified, and > 0 in order to use polar warp*/
}
if ((ud->out == NOPE) && (ud->outts == YUP))
{
ud->errcode = ERROR_OUTCONFLICT;
return"***********************\n"
"error: \n"
"Write flag must be on\n"
"to use Write ts\n"
"***********************\n";
}
/* Open the logfile, regardless of the ascii output files */
sprintf ( tmpstr , "%s.log" , ud->strout);
ud->outlogfile = fopen (tmpstr,"w");
if (ud->out == YUP) /* open outfile */
{
ud->outwrite = fopen (ud->strout,"w");
if (ud->outts == YUP)
{
sprintf ( tmpstr , "%s.ts" , ud->strout);
ud->outwritets = fopen (tmpstr,"w");
}
if ((ud->outwrite == NULL) || (ud->outlogfile == NULL) ||\
(ud->outwritets == NULL && ud->outts == YUP) )
{
ud->errcode = ERROR_FILEOPEN;
return "***********************\n"
"Could Not Write Outfile\n"
"***********************\n";
}
}
/* Write out user variables to Logfile */
write_ud (ud); /* writes user data to a file */
/*show_ud (ud,0); */ /* For some debugging */
/*------------- ready to compute new dataset -----------*/
new_dset = MAKER_4D_to_typed_fbuc ( old_dset , /* input dataset */
ud->new_prefix , /* output prefix */
-1, /* negative value indicating data type is like original brick */
ud->ignore , /* ignore count */
1 , /* detrend = ON Let BOB do it*/
NBUCKETS, /*Number of values at each voxel*/
DELAY_tsfuncV2 , /* timeseries processor (bucket version)*/
(void *)ud, /* data for tsfunc */
NULL, 0 ) ;
/* Setup the label, keywords and types of subbricks */
i = 0;
while (i < NBUCKETS)
{
switch (i)
{
case DELINDX: /* delay value in results vector */
EDIT_BRICK_LABEL (new_dset,i,"Delay");
EDIT_BRICK_ADDKEY (new_dset,i,"D");
++i;
break;
case COVINDX: /* covariance value in results vector */
EDIT_BRICK_LABEL (new_dset,i,"Covariance");
EDIT_BRICK_ADDKEY (new_dset,i,"I");
++i;
break;
case COFINDX: /* cross correlation coefficient value in results vector */
EDIT_BRICK_LABEL (new_dset,i,"Corr. Coef.");
EDIT_BRICK_ADDKEY (new_dset,i,"r");
/* Here you must modify either ud->Nfit or ud->Nort or most likely ud->nsamp based on ud->Navg */
EDIT_BRICK_TO_FICO (new_dset,i,ud->nsamp - ud->ignore,ud->Nfit,ud->Nort);
++i;
break;
case VARINDX: /* FMRI time course variance value in results vector */
EDIT_BRICK_LABEL (new_dset,i,"Variance");
EDIT_BRICK_ADDKEY (new_dset,i,"S2");
++i;
break;
default :
return "*********************\n"
"Internal Error (ziad)\n"
" Bad i value \n"
"*********************\n";
break;
}
}
if (!AFNI_noenv("AFNI_AUTOMATIC_FDR")) {
THD_create_all_fdrcurves( new_dset );
}
PLUTO_add_dset( plint , new_dset , DSET_ACTION_MAKE_CURRENT ) ;
if (ud->out == YUP) /* close outfile and outlogfile*/
{
fclose (ud->outlogfile);
fclose (ud->outwrite);
if (ud->outts == YUP) fclose (ud->outwritets);
}
else
{
if (ud->outlogfile != NULL) fclose (ud->outlogfile); /* close outlogfile */
}
free (tmpstr);
free (nprfxstr);
return NULL ; /* null string returned means all was OK */
}
static char * EXTRACT_main( PLUGIN_interface * plint )
{
extract_data uda,*ud;
MRI_IMAGE * tsim;
MCW_idcode * idc ; /* input dataset idcode */
THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */
char *tmpstr , * str , *nprfxstr;
int ntime, nvec ,nprfx, Err=0 , itmp;
float * vec , fs , T ;
char * tag; /* plugin option tag */
/* Allocate as much character space as Bob specifies in afni.h + a bit more */
tmpstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
nprfxstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
if (tmpstr == NULL || nprfxstr == NULL)
return "********************\n"
"Could not Allocate\n"
"a teeni weeni bit of\n"
"Memory ! Go complain\n"
"to yer Mamma ! \n"
"********************\n";
ud = &uda; /* ud now points to an allocated space */
ud->errcode = 0; /*reset error flag */
/*--------------------------------------------------------------------*/
/*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
/*--------- go to first input line ---------*/
tag = PLUTO_get_optiontag(plint) ;
if (tag == NULL)
{
return "************************\n"
"Bad 1st line option \n"
"************************" ;
}
idc = PLUTO_get_idcode(plint) ; /* get dataset item */
old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */
if( old_dset == NULL )
return "*************************\n"
"Cannot find Input Dataset\n"
"*************************" ;
ud->dsetname = DSET_FILECODE (old_dset);
ud->ignore = PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ;
ud->dtrnd = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings );
/*--------- loop over ramining options ---------*/
ud->iloc = -1;
ud->xloc = -1;
ud->yloc = -1;
ud->zloc = -1;
do
{
tag = PLUTO_get_optiontag(plint) ;
if (tag == NULL) break;
if (strcmp (tag, "Mask") == 0)
{
ud->strin = PLUTO_get_string(plint) ;
ud->ncols = PLUTO_get_number(plint) ;
ud->pass = PLUTO_get_number(plint) ;
ud->fail = 0; /* Set voxels that don't make it to 0 */
continue;
}
if (strcmp (tag, "Index") == 0)
{
ud->iloc = PLUTO_get_number(plint) ; /* get number item */
continue;
}
if (strcmp (tag, "XYZ") == 0)
{
ud->xloc = PLUTO_get_number(plint) ; /* get number item */
ud->yloc = PLUTO_get_number(plint) ; /* get number item */
ud->zloc = PLUTO_get_number(plint) ; /* get number item */
continue;
}
if (strcmp (tag, "Output") == 0)
{
ud->new_prefix = PLUTO_get_string(plint) ; /* get string item (the output prefix) */
/* check to see if the field is empty */
if (ud->new_prefix == NULL)
nprfx = 0;
else
nprfx = 1;
/* check if the size is larger than 0. I did not want to check for this unless it's allocated */
if (nprfx == 1 && (int)strlen (ud->new_prefix) == 0)
nprfx = 0;
if (nprfx == 0) /* now create the new name and make new_prefix point to it */
{
sprintf (nprfxstr,"%s.XTRCT",DSET_PREFIX (old_dset));
ud->new_prefix = nprfxstr;
/*printf ("New prefix is set to be : %s\n\a",ud->new_prefix);*/
}
if( ! PLUTO_prefix_ok(ud->new_prefix) ) /* check if it is OK */
return "************************\n"
"Output Prefix is illegal\n"
"************************" ;
ud->strout = PLUTO_get_string(plint) ;
str = PLUTO_get_string(plint) ;
ud->format = (int)PLUTO_string_index( str , NUM_FORMAT_STRINGS , format_strings );
continue;
}
} while (1);
/* ------------------ Check for some errorsor inconsistencies ------------- */
if (ud->iloc == -1 && ud->xloc == -1)
{
return "**************************\n"
"At least iloc or x/y/zloc\n"
"must be specified\n"
"**************************\n"
;
}
if (ud->iloc != -1 && ud->xloc != -1)
{
return "***************************\n"
"iloc AND x/y/zloc can not\n"
"be simultaneously specified\n"
"***************************\n"
;
}
/* ------------------Done with user parameters ---------------------------- */
/* Now loadup that index list or the xyz list */
if (ud->iloc != -1)
{
itmp = 0; /* might want to give option of setting it to number of rows if*/
/* the users know it, otherwise, it is automatically determined*/
ud->indvect = extract_index (ud->strin, ud->iloc, ud->ncols, &itmp, &Err);
}
else /* assuming the only other case is that x y z are specified */
{
itmp = 0;
ud->xyzvect = extract_xyz (ud->strin , ud->xloc , ud->yloc , ud->zloc , ud->ncols, &itmp, &Err);
}
ud->nrows = itmp;
switch (Err)
{
case (0):
break;
case (1):
return "****************************************\n"
"index location should be > 0 and < ncols\n"
"****************************************\n";
case (2):
return "********************************************\n"
"file size and number of columns do not match\n"
"********************************************\n";
case (3):
return "**********************\n"
"Can't find matrix file\n"
"**********************\n";
case (4):
return "*****************\n"
"ncols must be > 0\n"
"*****************\n";
case (5):
return "****************************************\n"
"x/y/z column numbers can NOT be the same\n"
"****************************************\n";
default:
return "****************************************\n"
"Should not have gotten here .....\n"
"****************************************\n";
}
if (strcmp (ud->strout,"") == 0) /* no output file is specified */
{
sprintf ( tmpstr , "%s" , ud->new_prefix);
ud->strout = tmpstr;
}
if (filexists(ud->strout) == 1)
{
return "*******************************\n"
"Outfile exists, won't overwrite\n"
"*******************************\n";
}
ud->outwritets = fopen (ud->strout ,"w");
sprintf ( tmpstr , "%s.log" , ud->strout);
if (filexists(tmpstr) == 1)
{
return "*******************************\n"
"Outfile.log exists, won't overwrite\n"
"*******************************\n";
}
ud->outlogfile = fopen (tmpstr ,"w");
if ((ud->outwritets == NULL) || (ud->outlogfile == NULL) )
{
ud->errcode = ERROR_FILEWRITE;
return "***********************\n"
"Could Not Write Outfile\n"
"***********************\n";
}
ud->nxx = (int)old_dset->daxes->nxx; /* get data set dimensions */
ud->nyy = (int)old_dset->daxes->nyy;
ud->nzz = (int)old_dset->daxes->nzz;
/* ready to dump the log file */
write_ud (ud);
/*------------- ready to compute new dataset -----------*/
new_dset = PLUTO_4D_to_typed_fim( old_dset , /* input dataset */
ud->new_prefix , /* output prefix */
-1, /* negative value indicating data type is like original brick */
ud->ignore , /* ignore count */
ud->dtrnd , /* detrend */
EXTRACT_tsfunc , /* timeseries processor */
(void *)ud /* data for tsfunc */
) ;
PLUTO_add_dset( plint , new_dset , DSET_ACTION_MAKE_CURRENT ) ;
fclose (ud->outlogfile);
fclose (ud->outwritets);
free (tmpstr);
free (nprfxstr);
return NULL ; /* null string returned means all was OK */
}
THD_3dim_dataset * Volumewise_Operations(THD_3dim_dataset *dset, char *prefix,
int datum)
{
int iv6[] = { 17, 0, 13, 4, 6, 8 };
float fv = 3.14159;
THD_3dim_dataset *oset = NULL;
int nvox, isb, ivx;
float *sb=NULL, *vout=NULL, *yout=NULL;
char *stmp;
ENTRY("Volumewise_Operations");
DSET_load(dset);
nvox = DSET_NVOX(dset);
vout = (float *)calloc(nvox, sizeof(float)); /* Allocate for one whole volume,
one sub-brick that is */
yout = (float *)calloc(nvox, sizeof(float)); /* and another */
for (isb=0; isb<DSET_NVALS(dset); ++isb) {
if (!(sb = THD_extract_to_float(isb, dset))) {
ERROR_message("Failed to extract sub-brick %d from %s\n",
isb, DSET_PREFIX(dset));
RETURN(NULL);
}
for (ivx=0; ivx<nvox; ++ivx) {
vout[ivx] += sb[ivx];
yout[ivx] += 1./(sqrt(fabs(sb[ivx])+0.1));
}
free(sb); sb = NULL;
}
/* Put the results in a new dataset */
oset = EDIT_empty_copy( dset ) ;
if (datum == MRI_float) { /* store results as float */
stmp = modify_afni_prefix(prefix,NULL,".volops.float");
EDIT_dset_items( oset ,
ADN_prefix , stmp,
ADN_datum_all, MRI_float ,
ADN_nvals , 2 ,
ADN_ntt, 0,
ADN_none ) ;
EDIT_substitute_brick( oset , 0 , MRI_float , vout ) ;
vout = NULL; /* do not free vout, oset uses the same pointer
because column types is oset are float */
EDIT_substitute_brick( oset , 1 , MRI_float , yout ) ; yout = NULL;
} else { /* store results as short */
stmp = modify_afni_prefix(prefix,NULL,".volops.short");
EDIT_dset_items( oset ,
ADN_prefix , stmp,
ADN_datum_all, MRI_short ,
ADN_nvals , 2 ,
ADN_none ) ;
/* Store the results using short precision and auto scale */
EDIT_substscale_brick(oset, 0, MRI_float, vout, MRI_short, -1.0);
free(vout); vout = NULL; /* vout got copied by value, so free it */
/* Store the results using short precision and set your own scale
(here out of laziness I used the same scale as for sub-brick 0) */
EDIT_substscale_brick(oset, 1, MRI_float, yout,
MRI_short, DSET_BRICK_FACTOR(oset,0));
free(yout); yout = NULL; /* vout got copied by value, so free it */
}
/* Label the sub-bricks */
EDIT_BRICK_LABEL(oset , 0, "sum");
EDIT_BRICK_LABEL(oset , 1, "sisqrt");
/* Add your own special attribute -- Note that private attributes
are not preserved when making copies of datasets */
THD_set_string_atr( oset->dblk , "Pinot_Noir" , "sideways" ) ;
THD_set_int_atr ( oset->dblk , "Lottery_Numbers", 6, iv6 );
THD_set_float_atr( oset->dblk , "PI", 1, &fv );
RETURN(oset);
}
int main( int argc , char *argv[] )
{
THD_3dim_dataset *dset ;
char *prefix=NULL , *fname ;
int narg=1 , flags=0 , ii , swap = 0;
#ifndef DONT_ALLOW_MINC
WARNING_message("This program (3dAFNItoMINC) is old, not maintained, and probably useless!") ;
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
printf("Usage: 3dAFNItoMINC [options] dataset\n"
"Reads in an AFNI dataset, and writes it out as a MINC file.\n"
"\n"
"OPTIONS:\n"
" -prefix ppp = Write result into file ppp.mnc;\n"
" default prefix is same as AFNI dataset's.\n"
" -floatize = Write MINC file in float format.\n"
" -swap = Swap bytes when passing data to rawtominc\n"
"\n"
"NOTES:\n"
"* Multi-brick datasets are written as 4D (x,y,z,t) MINC\n"
" files.\n"
"* If the dataset has complex-valued sub-bricks, then this\n"
" program won't write the MINC file.\n"
"* If any of the sub-bricks have floating point scale\n"
" factors attached, then the output will be in float\n"
" format (regardless of the presence of -floatize).\n"
"* This program uses the MNI program 'rawtominc' to create\n"
" the MINC file; rawtominc must be in your path. If you\n"
" don't have rawtominc, you must install the MINC tools\n"
" software package from MNI. (But if you don't have the\n"
" MINC tools already, why do you want to convert to MINC\n"
" format anyway?)\n"
"* At this time, you can find the MINC tools at\n"
" ftp://ftp.bic.mni.mcgill.ca/pub/minc/\n"
" You need the latest version of minc-*.tar.gz and also\n"
" of netcdf-*.tar.gz.\n"
"\n"
"-- RWCox - April 2002\n"
) ;
PRINT_COMPILE_DATE; exit(0) ;
}
mainENTRY("3dAFNItoMINC main"); machdep(); PRINT_VERSION("3dAFNItoMINC");
while( narg < argc && argv[narg][0] == '-' ){
if( strcmp(argv[narg],"-prefix") == 0 ){
prefix = argv[++narg] ;
if( !THD_filename_ok(prefix) || prefix[0] == '-' ){
fprintf(stderr,"** Prefix string is illegal: %s\n",prefix) ;
exit(1) ;
}
narg++ ; continue ;
}
if( strcmp(argv[narg],"-floatize") == 0 ){
flags |= MINC_FLOATIZE_MASK ;
narg++ ; continue ;
}
if( strcmp(argv[narg],"-swap") == 0 ){
flags |= MINC_SWAPIZE_MASK ;
narg++ ; continue ;
}
fprintf(stderr,"** ERROR: unknown option: %s\n",argv[narg]); exit(1);
}
if( narg >= argc ){
fprintf(stderr,"** ERROR: no dataset on command line?\n"); exit(1);
}
dset = THD_open_dataset(argv[narg]); CHECK_OPEN_ERROR(dset,argv[narg]) ;
if( prefix == NULL ) prefix = DSET_PREFIX(dset) ;
fname = malloc( strlen(prefix)+16 ) ;
strcpy(fname,prefix) ;
if( strstr(fname,".mnc") == NULL ) strcat(fname,".mnc") ;
ii = THD_write_minc( fname , dset , flags ) ;
exit(0) ;
#else
ERROR_exit("program 3dAFNItoMINC is no longer compiled") ;
#endif
}
int THD_conformist( int ndset, THD_3dim_dataset **dset, int flags , int *ijkpad )
{
int iset , xpad_m,xpad_p , ypad_m,ypad_p , zpad_m,zpad_p , nwrit ;
THD_dataxes *cx , *dx ;
THD_3dim_dataset *qset ;
int_pair pm ;
int do_norefit = (flags & CONFORM_NOREFIT) ;
int do_rewrite = (flags & CONFORM_REWRITE) && !do_norefit ;
int do_ijkpad = (ijkpad != NULL) ;
ENTRY("THD_conformist") ;
/* check for good inputs */
if( ndset <= 0 || dset == NULL ) RETURN(-1) ;
for( iset=0 ; iset < ndset ; iset++ )
if( !ISVALID_DSET(dset[iset]) ) RETURN(-2) ;
/* check if all inputs are on the same grid (i.e., no work to do) */
for( iset=1 ; iset < ndset ; iset++ ){
if( ! EQUIV_DATAXES(dset[0]->daxes,dset[iset]->daxes) ) break ;
}
if( iset == ndset ){
if( do_ijkpad ){
for( iset=0 ; iset < 6*ndset ; iset++ ) ijkpad[iset] = 0 ;
}
RETURN(0) ;
}
/* construct the dataxes that encloses all the input datasets */
cx = THD_superset_dataxes( dset[0]->daxes , dset[1]->daxes ) ;
if( cx == NULL ){
ERROR_message("3dConformist: '%s' and '%s' aren't compatible",
DSET_HEADNAME(dset[0]) , DSET_HEADNAME(dset[1]) ) ;
RETURN(-3) ;
}
for( iset=2 ; iset < ndset ; iset++ ){
dx = THD_superset_dataxes( cx , dset[iset]->daxes ) ;
if( dx == NULL ){
ERROR_message("3dConformist: '%s' is not compatible with others",
DSET_HEADNAME(dset[iset]) ) ;
myXtFree(cx) ; RETURN(-3) ;
}
myXtFree(cx) ; cx = dx ; dx = NULL ;
}
/* now, re-create and re-write all datasets */
if( do_rewrite )
fprintf(stderr," + thd_conformist re-write loop: ") ;
for( nwrit=iset=0 ; iset < ndset ; iset++ ){
if( EQUIV_DATAXES(cx,dset[iset]->daxes) ){ /* already OK */
if( do_rewrite ) fprintf(stderr,"-") ;
if( do_ijkpad )
ijkpad[6*iset+0] = ijkpad[6*iset+1] = ijkpad[6*iset+2]
= ijkpad[6*iset+3] = ijkpad[6*iset+4] = ijkpad[6*iset+5] = 0 ;
continue ;
}
pm = zpadax_pm( cx->nxx , cx->xxorg ,
dset[iset]->daxes->nxx , dset[iset]->daxes->xxorg ,
cx->xxdel ) ;
xpad_m = pm.i ; xpad_p = pm.j ;
pm = zpadax_pm( cx->nyy , cx->yyorg ,
dset[iset]->daxes->nyy , dset[iset]->daxes->yyorg ,
cx->yydel ) ;
ypad_m = pm.i ; ypad_p = pm.j ;
pm = zpadax_pm( cx->nzz , cx->zzorg ,
dset[iset]->daxes->nzz , dset[iset]->daxes->zzorg ,
cx->zzdel ) ;
zpad_m = pm.i ; zpad_p = pm.j ;
if( do_ijkpad ){
ijkpad[6*iset+0] = xpad_m; ijkpad[6*iset+1] = xpad_p;
ijkpad[6*iset+2] = ypad_m; ijkpad[6*iset+3] = ypad_p;
ijkpad[6*iset+4] = zpad_m; ijkpad[6*iset+5] = zpad_p;
}
if( do_norefit ) continue ; /* just wanted ijkpad, I guess */
qset = THD_zeropad( dset[iset] ,
xpad_m,xpad_p , ypad_m,ypad_p , zpad_m,zpad_p ,
"BertieWooster" , ZPAD_PURGE | ZPAD_IJK ) ;
if( qset == NULL ){ /* this should never happen */
if( do_rewrite ) fprintf(stderr,"\n") ;
ERROR_message("thd_conformist: skipping dataset %s",
DSET_HEADNAME(dset[iset])) ;
continue ;
}
qset->idcode = dset[iset]->idcode ;
EDIT_dset_items( qset , ADN_prefix , DSET_PREFIX(dset[iset]) , ADN_none ) ;
if( do_rewrite ){
THD_delete_3dim_dataset( dset[iset] , True ) ;
DSET_overwrite(qset) ; DSET_unload(qset) ;
fprintf(stderr,"+") ;
} else {
THD_delete_3dim_dataset( dset[iset] , False ) ;
}
dset[iset] = qset ; nwrit++ ;
}
if( do_rewrite ) fprintf(stderr,"\n") ;
RETURN(nwrit) ;
}
int *THD_unique_rank( THD_3dim_dataset *mask_dset ,
int miv,
byte *cmask,
char *mapname,
int **unqp, int *N_unq)
{
int nvox , ii, *unq = NULL, *vals=NULL, imax=0;
INT_HASH_DATUM *rmap=NULL, *hd=NULL;
int n_unique, r;
FILE *fout=NULL;
n_unique = 0;
unq = NULL ;
if (unqp && *unqp!=NULL) {
fprintf(stderr,"** unqp (%p) not initialized properly to NULL", *unqp);
return (vals) ;
}
if( !ISVALID_DSET(mask_dset) ||
miv < 0 ||
miv >= DSET_NVALS(mask_dset) ) {
fprintf(stderr,"** Bad mask_dset or sub-brick index.\n");
return (vals) ;
}
nvox = DSET_NVOX(mask_dset) ;
DSET_load(mask_dset) ; if( !DSET_LOADED(mask_dset) ) return (vals) ;
if (!is_integral_sub_brick (mask_dset, miv, 0)) {
fprintf(stderr,"** Sub-brick %d of %s is not integral valued.\n",
miv, DSET_PREFIX(mask_dset) ? DSET_PREFIX(mask_dset):"NULL");
return (vals) ;
}
vals = (int *)malloc(sizeof(int)*nvox);
if (!vals) {
fprintf(stderr,"** Failed to allocate.\n");
return (vals) ;
}
switch( DSET_BRICK_TYPE(mask_dset,miv) ){
default:
fprintf( stderr,
"** Bad dset type for unique operation.\n"
"Only Byte, Short and float dsets are allowed.\n");
DSET_unload(mask_dset) ;
if (vals) free(vals); vals = NULL; return (vals) ;
case MRI_short:{
short *mar = (short *) DSET_ARRAY(mask_dset,miv) ;
if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if (cmask[ii]) vals[ii] = (int)(mar[ii]); else vals[ii] = 0;
} else {
for( ii=0 ; ii < nvox ; ii++ )
vals[ii] = (int)(mar[ii]);
}
}
break ;
case MRI_byte:{
byte *mar = (byte *) DSET_ARRAY(mask_dset,miv) ;
if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if (cmask[ii]) vals[ii] = (int)(mar[ii]); else vals[ii] = 0;
} else {
for( ii=0 ; ii < nvox ; ii++ )
vals[ii] = (int)(mar[ii]);
}
}
break ;
case MRI_float:{ /* not an integral type but we store ints (from NIFTI)
as floats */
float *mar = (float *) DSET_ARRAY(mask_dset,miv) ;
if (cmask) {
for( ii=0 ; ii < nvox ; ii++ )
if (cmask[ii]) vals[ii] = (int)(mar[ii]); else vals[ii] = 0;
} else {
for( ii=0 ; ii < nvox ; ii++ )
vals[ii] = (int)(mar[ii]);
}
}
break ;
}
/* unique */
unq = UniqueInt (vals, nvox, &n_unique, 0 );
/* fprintf(stderr,"-- Have %d unique values\n", n_unique); */
if (!unq) {
fprintf(stderr,"** Failed to create unique list\n");
free(vals); return (NULL);
}
if (mapname && mapname[0]) {
/*fprintf(stderr,"-- Writing mapping to >>%s<<\n", mapname);*/
if ((fout = fopen(mapname,"w"))) {
fprintf(fout, "#Rank Map (%d unique values)\n", n_unique);
fprintf(fout, "#Col. 0: Rank\n");
fprintf(fout, "#Col. 1: Input Dset Value\n");
}
}
/* now replace by rank */
#if 0
for (r=0; r<n_unique; ++r) {
/* fprintf(stderr,"-- Doing %d ...\n", unq[r]); */
if (cmask) {
for (ii=0; ii<nvox; ii++) {
if (cmask[ii]) {
if (vals[ii] == unq[r]) vals[ii] = r;
} else vals[ii] = 0;
}
} else {
for( ii=0 ; ii < nvox ; ii++ ) if (vals[ii] == unq[r]) vals[ii] = r;
}
}
#else /* faster approach */
imax=0;
for (r=0; r<n_unique; ++r) {
if (imax < unq[r]) imax = unq[r];
if (fout) fprintf(fout, "%d %d\n", r, unq[r]);
hd = (INT_HASH_DATUM*)calloc(1,sizeof(INT_HASH_DATUM));
hd->id = unq[r];
hd->index = r;
HASH_ADD_INT(rmap, id, hd);
}
for (ii=0; ii<nvox; ii++)
if (!cmask || cmask[ii]) {
HASH_FIND_INT(rmap,&(vals[ii]),hd);
if (hd) vals[ii] = hd->index;
else {
fprintf(stderr,
"** Failed to find key %d inhash table\n",
vals[ii]);
free(vals);
while (rmap) { hd=rmap; HASH_DEL(rmap,hd); free(hd); }
return (NULL);
}
}
/* destroy hash */
while (rmap) {
hd=rmap;
HASH_DEL(rmap,hd);
if (hd) free(hd);
}
#endif
if (!unqp) free(unq); else *unqp = unq; unq = NULL;
if (N_unq) *N_unq = n_unique;
if (fout) fclose(fout); fout = NULL;
return (vals) ;
}
/*! Replace a voxel's value by the value's rank in the entire set of input datasets */
int main( int argc , char * argv[] )
{
THD_3dim_dataset ** dsets_in = NULL, *dset=NULL; /*input and output datasets*/
int nopt=0, nbriks=0, nsubbriks=0, ib=0, isb=0;
byte *cmask=NULL;
int *all_uniques=NULL, **uniques=NULL, *final_unq=NULL, *N_uniques=NULL;
int N_final_unq=0, iun=0, total_unq=0;
INT_HASH_DATUM *rmap=NULL, *hd=NULL;
int imax=0, iunq=0, ii=0, id = 0;
long int off=0;
char *prefix=NULL;
char stmp[THD_MAX_PREFIX+1]={""};
FILE *fout=NULL;
/*----- Read command line -----*/
if( argc < 2 || strcmp(argv[1],"-help") == 0 ){
Rank_help ();
exit(0) ;
}
mainENTRY("3dRank main"); machdep(); AFNI_logger("3dRank",argc,argv);
nopt = 1 ;
while( nopt < argc && argv[nopt][0] == '-' ){
if( strcmp(argv[nopt],"-ver") == 0 ){
PRINT_VERSION("3dRank"); AUTHOR("Ziad Saad");
nopt++; continue;
}
if( strcmp(argv[nopt],"-help") == 0 ){
Rank_help();
exit(0) ;
}
if( strcmp(argv[nopt],"-prefix") == 0 ){
++nopt;
if (nopt>=argc) {
fprintf(stderr,"**ERROR: Need string after -prefix\n");
exit(1);
}
prefix = argv[nopt] ;
++nopt; continue;
}
if( strcmp(argv[nopt],"-input") == 0 ){
dsets_in = (THD_3dim_dataset**)
calloc(argc-nopt+1, sizeof(THD_3dim_dataset*));
++nopt; nbriks=0;
while (nopt < argc ) {
dsets_in[nbriks] = THD_open_dataset( argv[nopt] );
if( !ISVALID_DSET(dsets_in[nbriks]) ){
fprintf(stderr,"**ERROR: can't open dataset %s\n",argv[nopt]) ;
exit(1);
}
++nopt; ++nbriks;
}
continue;
}
ERROR_exit( " Error - unknown option %s", argv[nopt]);
}
if (nopt < argc) {
ERROR_exit( " Error unexplained trailing option: %s\n", argv[nopt]);
}
if (!nbriks) {
ERROR_exit( " Error no volumes entered on command line?");
}
/* some checks and inits*/
nsubbriks = 0;
for (ib = 0; ib<nbriks; ++ib) {
if (!is_integral_dset(dsets_in[ib], 0)) {
ERROR_exit("Dset %s is not of an integral data type.",
DSET_PREFIX(dsets_in[ib]));
}
nsubbriks += DSET_NVALS(dsets_in[ib]);
}
/* Now get unique arrays */
uniques = (int **)calloc(nsubbriks, sizeof(int*));
N_uniques = (int *)calloc(nsubbriks, sizeof(int));
total_unq = 0;
iun = 0;
for (ib = 0; ib<nbriks; ++ib) {
DSET_mallocize(dsets_in[ib]); DSET_load(dsets_in[ib]);
for (isb=0; isb<DSET_NVALS(dsets_in[ib]); ++isb) {
uniques[iun] = THD_unique_vals(dsets_in[ib], isb,
&(N_uniques[iun]), cmask);
total_unq += N_uniques[iun];
++iun;
}
}
/* put all the arrays together and get the unique of the uniques */
all_uniques = (int *)calloc(total_unq, sizeof(int));
off=0;
for (iun=0; iun<nsubbriks; ++iun) {
memcpy(all_uniques+off, uniques[iun], N_uniques[iun]*sizeof(int));
off += N_uniques[iun];
}
/* free intermediate unique arrays */
for (iun=0; iun<nsubbriks; ++iun) {
free(uniques[iun]);
}
free(uniques); uniques=NULL;
free(N_uniques); N_uniques=NULL;
/* get unique of catenated array */
if (!(final_unq = UniqueInt (all_uniques, total_unq, &N_final_unq, 0 ))) {
ERROR_exit( " Failed to get unique list (%d, %d, %d) ",
total_unq, N_final_unq, nsubbriks);
}
free(all_uniques); all_uniques=NULL;
if (prefix) {
snprintf(stmp, sizeof(char)*THD_MAX_PREFIX,
"%s.rankmap.1D", prefix);
} else {
if (nbriks == 1) {
snprintf(stmp, sizeof(char)*THD_MAX_PREFIX,
"%s.rankmap.1D", DSET_PREFIX(dsets_in[0]));
} else {
snprintf(stmp, sizeof(char)*THD_MAX_PREFIX,
"%s+.rankmap.1D", DSET_PREFIX(dsets_in[0]));
}
}
if (stmp[0]) {
if ((fout = fopen(stmp,"w"))) {
fprintf(fout, "#Rank Map (%d unique values)\n", N_final_unq);
fprintf(fout, "#Col. 0: Rank\n");
fprintf(fout, "#Col. 1: Input Dset Value\n");
}
}
/* get the maximum integer in the unique array */
imax = 0;
for (iunq=0; iunq<N_final_unq; ++iunq) {
if (final_unq[iunq] > imax) imax = final_unq[iunq];
if (fout) fprintf(fout, "%d %d\n", iunq, final_unq[iunq]);
hd = (INT_HASH_DATUM*)calloc(1,sizeof(INT_HASH_DATUM));
hd->id = final_unq[iunq];
hd->index = iunq;
HASH_ADD_INT(rmap, id, hd);
}
fclose(fout); fout=NULL;
/* now cycle over all dsets and replace their voxel values with rank */
for (ib = 0; ib<nbriks; ++ib) {
for (isb=0; isb<DSET_NVALS(dsets_in[ib]); ++isb) {
EDIT_BRICK_LABEL( dsets_in[ib],isb, "rank" ) ;
EDIT_BRICK_TO_NOSTAT( dsets_in[ib],isb ) ;
EDIT_BRICK_FACTOR( dsets_in[ib],isb, 0.0);/* no factors for rank*/
switch (DSET_BRICK_TYPE(dsets_in[ib],isb) ){
default:
fprintf(stderr,
"** Bad dset type for unique operation.\n"
"Only Byte, Short, and float dsets are allowed.\n");
break ; /* this should not happen here,
so don't bother returning*/
case MRI_short:{
short *mar = (short *) DSET_ARRAY(dsets_in[ib],isb) ;
if (imax > MRI_TYPE_maxval[MRI_short]) {
WARNING_message("Maximum rank value of %d is\n"
"than maximum value for dset datatype of %d\n",
imax, MRI_TYPE_maxval[MRI_short]);
}
for( ii=0 ; ii < DSET_NVOX(dsets_in[ib]) ; ii++ )
if (!cmask || cmask[ii]) {
id = (int)mar[ii];
HASH_FIND_INT(rmap,&id ,hd);
if (hd) mar[ii] = (short)(hd->index);
else
ERROR_exit("** Failed to find key %d in hash table\n",id);
} else mar[ii] = 0;
}
break ;
case MRI_byte:{
byte *mar ;
if (imax > MRI_TYPE_maxval[MRI_short]) {
WARNING_message("Maximum rank value of %d is\n"
"than maximum value for dset datatype of %d\n",
imax, MRI_TYPE_maxval[MRI_byte]);
}
mar = (byte *) DSET_ARRAY(dsets_in[ib],isb) ;
for( ii=0 ; ii < DSET_NVOX(dsets_in[ib]) ; ii++ )
if (!cmask || cmask[ii]) {
id = (int)mar[ii];
HASH_FIND_INT(rmap,&id ,hd);
if (hd) mar[ii] = (byte)(hd->index);
else
ERROR_exit("** Failed to find key %d in hash table\n",id);
} else mar[ii] = 0;
}
break ;
case MRI_float:{
float *mar = (float *) DSET_ARRAY(dsets_in[ib],isb) ;
for( ii=0 ; ii < DSET_NVOX(dsets_in[ib]) ; ii++ )
if (!cmask || cmask[ii]) {
id = (int)mar[ii]; /* Assuming float is integral valued */
HASH_FIND_INT(rmap,&id ,hd);
if (hd) mar[ii] = (float)(hd->index);
else
ERROR_exit("** Failed to find key %d in hash table\n",id);
} else mar[ii] = 0;
}
break ;
}
}
/* update range, etc. */
THD_load_statistics(dsets_in[ib]);
/* Now write the bricks */
if (prefix) {
if (nbriks == 1) {
snprintf(stmp, sizeof(char)*THD_MAX_PREFIX,
"%s", prefix);
} else {
snprintf(stmp, sizeof(char)*THD_MAX_PREFIX,
"r%02d.%s", ib, prefix);
}
} else {
snprintf(stmp, sizeof(char)*THD_MAX_PREFIX,
"rank.%s", DSET_PREFIX(dsets_in[ib]));
}
EDIT_dset_items( dsets_in[ib] ,
ADN_prefix , stmp ,
ADN_none ) ;
/* change storage mode, this way prefix will determine
format of output dset */
dsets_in[ib]->dblk->diskptr->storage_mode = STORAGE_BY_BRICK;
tross_Make_History( "3dRank" , argc, argv , dsets_in[ib] ) ;
if (DSET_IS_MASTERED(dsets_in[ib])) {
/* THD_write_3dim_dataset won't write a mastered dude */
dset = EDIT_full_copy(dsets_in[ib],stmp);
} else {
dset = dsets_in[ib];
}
/* New ID */
ZERO_IDCODE(dset->idcode);
dset->idcode = MCW_new_idcode() ;
if (!THD_write_3dim_dataset( NULL, stmp, dset,True )) {
ERROR_message("Failed to write %s", stmp);
exit(1);
} else {
WROTE_DSET(dsets_in[ib]);
if (dset != dsets_in[ib]) DSET_deletepp(dset);
DSET_deletepp(dsets_in[ib]);
}
}
/* destroy hash */
while (rmap) {
hd = rmap;
HASH_DEL(rmap,hd);
free(hd);
}
free(final_unq); final_unq=NULL;
exit(0);
}
int main( int argc , char * argv[] )
{
int ninp , ids , nv , iv,jv,kv , ivout , new_nvals , have_fdr = 0, nfdr = 0 ;
THD_3dim_dataset * new_dset=NULL , * dset ;
char buf[256] ;
double angle;
/*----- identify program -----*/
#if 0
printf ("\n\nProgram %s \n", PROGRAM_NAME);
printf ("Last revision: %s \n\n", LAST_MOD_DATE);
#endif
/*** read input options ***/
mainENTRY("3dbucket main"); machdep(); PRINT_VERSION("3dbucket") ;
set_obliquity_report(0); /* silence obliquity */
/*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/
{ int new_argc ; char ** new_argv ;
addto_args( argc , argv , &new_argc , &new_argv ) ;
if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; }
}
AFNI_logger("3dbucket",argc,argv) ;
BUCK_read_opts( argc , argv ) ;
/*** create new dataset (empty) ***/
ninp = BUCK_dsar->num ;
if( ninp < 1 ){
fprintf(stderr,"*** No input datasets?\n") ; exit(1) ;
}
new_nvals = 0 ;
for( ids=0 ; ids < ninp ; ids++ ) new_nvals += NSUBV(ids) ;
if( BUCK_verb ) printf("-verb: output will have %d sub-bricks\n",new_nvals) ;
new_dset = EDIT_empty_copy( DSUB(0) ) ;
/* 23 May 2005: check for axis consistency */
/* 06 Feb 2008: and see if there are fdrcurves to perpetuate */
if( DSUB(0)->dblk->brick_fdrcurve ) have_fdr = 1 ;
for( iv=1 ; iv < ninp ; iv++ ){
if( !EQUIV_DATAXES(new_dset->daxes,DSUB(iv)->daxes) )
fprintf(stderr,"++ WARNING: %s grid mismatch with %s\n",
DSET_BRIKNAME(DSUB(0)) , DSET_BRIKNAME(DSUB(iv)) ) ;
if( DSUB(iv)->dblk->brick_fdrcurve ) have_fdr = 1 ;
angle = dset_obliquity_angle_diff(new_dset, DSUB(iv), -1.0);
if (angle > 0.0) {
WARNING_message(
"dataset %s has an obliquity difference of %f degress with %s\n",
new_dset ,
angle, DSUB(iv) );
}
}
/* if( ninp == 1 ) */ tross_Copy_History( DSUB(0) , new_dset ) ;
tross_Make_History( "3dbucket" , argc,argv , new_dset ) ;
EDIT_dset_items( new_dset ,
ADN_prefix , BUCK_output_prefix ,
ADN_directory_name, BUCK_session ,
ADN_type , BUCK_type ,
ADN_func_type , ISANATTYPE(BUCK_type) ? ANAT_BUCK_TYPE
: FUNC_BUCK_TYPE,
ADN_ntt , 0 ,
ADN_nvals , new_nvals ,
ADN_none ) ;
/* can't re-write existing dataset, unless glueing is used */
if (! BUCK_glue){
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(new_dset)) ){
fprintf(stderr,"*** Fatal error: file %s already exists!\n",
DSET_HEADNAME(new_dset) ) ;
exit(1) ;
}
} else { /* if glueing is used, make the 'new'
dataset have the same idcode as the old one */
new_dset->idcode = DSUB(0) -> idcode ; /* copy the struct */
}
THD_force_malloc_type( new_dset->dblk , DATABLOCK_MEM_MALLOC ) ;
/* if there are fdr curves, allocate space 06 Feb 2008 [rickr] */
if( have_fdr ){
new_dset->dblk->brick_fdrcurve = (floatvec **)calloc(sizeof(floatvec *),
new_nvals) ;
if( !new_dset->dblk->brick_fdrcurve ){
fprintf(stderr,"** failed to alloc %d fdrcurves\n",new_nvals);
exit(1);
}
if( BUCK_verb ) printf("-verb: adding fdrcurve list\n");
new_dset->dblk->brick_mdfcurve = (floatvec **)calloc(sizeof(floatvec *),
/* 22 Oct 2008 */ new_nvals) ;
}
/*** loop over input datasets ***/
if( ninp > 1 ) myXtFree( new_dset->keywords ) ;
ivout = 0 ;
for( ids=0 ; ids < ninp ; ids++ ){
dset = DSUB(ids) ;
nv = NSUBV(ids) ;
if( ! BUCK_dry ){
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
}
/** loop over sub-bricks to output **/
for( iv=0 ; iv < nv ; iv++ ){
jv = SUBV(ids,iv) ; /* which sub-brick to use */
if( ! BUCK_dry ){
EDIT_substitute_brick( new_dset , ivout ,
DSET_BRICK_TYPE(dset,jv) , DSET_ARRAY(dset,jv) ) ;
/*----- preserve label when one exists --- Modified March 2010 ZSS*/
if (DSET_HAS_LABEL(dset, jv) )
sprintf (buf, "%s", DSET_BRICK_LABEL(dset,jv));
else
sprintf(buf,"%.12s[%d]",DSET_PREFIX(dset),jv) ;
EDIT_dset_items( new_dset , ADN_brick_label_one+ivout, buf , ADN_none ) ;
#if 0
sprintf(buf,"%s[%d]",DSET_FILECODE(dset),jv) ;
EDIT_dset_items(
new_dset, ADN_brick_keywords_replace_one+ivout, buf, ADN_none ) ;
#endif
EDIT_dset_items(
new_dset ,
ADN_brick_fac_one +ivout, DSET_BRICK_FACTOR(dset,jv),
#if 0
ADN_brick_keywords_append_one+ivout, DSET_BRICK_KEYWORDS(dset,jv) ,
#endif
ADN_none ) ;
/** possibly write statistical parameters for this sub-brick **/
kv = DSET_BRICK_STATCODE(dset,jv) ;
if( FUNC_IS_STAT(kv) ){ /* input sub-brick has stat params */
int npar = FUNC_need_stat_aux[kv] , lv ;
float * par = (float *) malloc( sizeof(float) * (npar+2) ) ;
float * sax = DSET_BRICK_STATAUX(dset,jv) ;
par[0] = kv ;
par[1] = npar ;
for( lv=0 ; lv < npar ; lv++ )
par[lv+2] = (sax != NULL) ? sax[lv] : 0.0 ;
EDIT_dset_items(new_dset ,
ADN_brick_stataux_one+ivout , par ,
ADN_none ) ;
free(par) ;
/* 2: if the input dataset has statistical parameters */
} else if( ISFUNC(dset) && /* dset has stat */
FUNC_IS_STAT(dset->func_type) && /* params */
jv == FUNC_ival_thr[dset->func_type] ){ /* thr sub-brick */
int npar , lv ;
float * par , * sax ;
kv = dset->func_type ;
npar = FUNC_need_stat_aux[kv] ;
par = (float *) malloc( sizeof(float) * (npar+2) ) ;
sax = dset->stat_aux ;
par[0] = kv ;
par[1] = npar ;
for( lv=0 ; lv < npar ; lv++ )
par[lv+2] = (sax != NULL) ? sax[lv] : 0.0 ;
EDIT_dset_items(new_dset ,
ADN_brick_stataux_one+ivout , par ,
ADN_none ) ;
free(par) ;
}
/** append any fdrcurve **/
if( have_fdr ){
/* fixed iv->jv (ick!), noticed by dglen 16 Mar 2010 [rickr] */
if(dset->dblk->brick_fdrcurve && dset->dblk->brick_fdrcurve[jv]){
COPY_floatvec(new_dset->dblk->brick_fdrcurve[ivout],
dset->dblk->brick_fdrcurve[jv]) ;
nfdr++;
}
else new_dset->dblk->brick_fdrcurve[ivout] = NULL ;
if(dset->dblk->brick_mdfcurve && dset->dblk->brick_mdfcurve[jv]){
COPY_floatvec(new_dset->dblk->brick_mdfcurve[ivout],
dset->dblk->brick_mdfcurve[jv]) ;
}
else new_dset->dblk->brick_mdfcurve[ivout] = NULL ;
}
/** print a message? **/
if( BUCK_verb ) printf("-verb: copied %s[%d] into %s[%d]\n" ,
DSET_FILECODE(dset) , jv ,
DSET_FILECODE(new_dset) , ivout ) ;
} else {
printf("-dry: would copy %s[%d] into %s[%d]\n" ,
DSET_FILECODE(dset) , jv ,
DSET_FILECODE(new_dset) , ivout ) ;
}
ivout++ ;
}
/** loop over all bricks in input dataset and
unload them if they aren't going into the output
(not required, but is done to economize on memory) **/
if( ! BUCK_dry && nv < DSET_NVALS(dset) ){
for( kv=0 ; kv < DSET_NVALS(dset) ; kv++ ){ /* all input sub-bricks */
for( iv=0 ; iv < nv ; iv++ ){ /* all output sub-bricks */
jv = SUBV(ids,iv) ;
if( jv == kv ) break ; /* input matches output */
}
if( iv == nv ){
mri_free( DSET_BRICK(dset,kv) ) ;
#if 0
if( BUCK_verb ) printf("-verb: unloaded unused %s[%d]\n" ,
DSET_FILECODE(dset) , kv ) ;
#endif
}
}
}
} /* end of loop over input datasets */
if( ! BUCK_dry ){
if( BUCK_verb ){
if( have_fdr ) fprintf(stderr,"-verb: added %d of %d fdr curves\n",
nfdr, new_nvals);
fprintf(stderr,"-verb: loading statistics\n") ;
}
THD_load_statistics( new_dset ) ;
if( BUCK_glue ) putenv("AFNI_DECONFLICT=OVERWRITE") ;
if( BUCK_glue && BUCK_ccode >= 0 )
THD_set_write_compression(BUCK_ccode) ; /* 16 Mar 2010 */
THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ;
if( BUCK_verb ) fprintf(stderr,"-verb: wrote output: %s\n",DSET_BRIKNAME(new_dset)) ;
}
exit(0) ;
}
THD_slist_find THD_dset_in_session( int find_type , void *target ,
THD_session *sess )
{
int id , iv , im ;
THD_3dim_dataset *dset ;
THD_slist_find find ;
/*-- sanity check --*/
ZZME(find) ;
if( ! ISVALID_SESSION(sess) || target == NULL ){
BADFIND(find) ; return find ;
}
switch( find_type ){
/**** search for a name ****/
case FIND_NAME:{
char *target_name = (char *) target ;
if( strlen(target_name) == 0 ){
BADFIND(find) ; return find ;
}
for( id=0 ; id < sess->num_dsset ; id++ ){
for( iv=FIRST_VIEW_TYPE ; iv <= LAST_VIEW_TYPE ; iv++ ){
dset = GET_SESSION_DSET(sess, id, iv);
/* dset = sess->dsset_xform_table[id][iv] ;*/
if( dset != NULL && strcmp(dset->self_name,target_name) == 0 ){
find.dset = dset ; find.dset_index = id ; find.view_index = iv ;
return find ;
}
}
}
}
break ;
/**** search for a prefix ****/
case FIND_PREFIX:{
char *target_prefix , *pp ;
target_prefix = strdup((char *)target) ;
pp = strstr(target_prefix,"+orig") ; /* 03 Jan 2012: */
if( pp == NULL ) pp = strstr(target_prefix,"+acpc") ; /* truncate +view */
if( pp == NULL ) pp = strstr(target_prefix,"+tlrc") ; /* if present */
if( pp == NULL ) pp = strstr(target_prefix,"[") ;
if( pp != NULL ) *pp = '\0' ;
if( *target_prefix == '\0' ){ free(target_prefix); BADFIND(find); return find; }
for( id=0 ; id < sess->num_dsset ; id++ ){
for( iv=FIRST_VIEW_TYPE ; iv <= LAST_VIEW_TYPE ; iv++ ){
dset = GET_SESSION_DSET(sess, id, iv);
/* dset = sess->dsset_xform_table[id][iv] ;*/
if( dset != NULL && strcmp(DSET_PREFIX(dset),target_prefix) == 0 ){
find.dset = dset ; find.dset_index = id ; find.view_index = iv ;
free(target_prefix) ; return find ;
}
}
}
free(target_prefix) ; /* failed */
}
break ;
/**** search for an idcode ****/
case FIND_IDCODE:{
MCW_idcode target_id = *((MCW_idcode *) target) ;
if( ISZERO_IDCODE(target_id) ){
BADFIND(find) ; return find ;
}
for( id=0 ; id < sess->num_dsset ; id++ ){
for( iv=FIRST_VIEW_TYPE ; iv <= LAST_VIEW_TYPE ; iv++ ){
dset = GET_SESSION_DSET(sess, id, iv);
/* dset = sess->dsset_xform_table[id][iv] ;*/
if( dset != NULL && EQUIV_IDCODES(target_id,dset->idcode) ){
find.dset = dset ; find.dset_index = id ; find.view_index = iv ;
return find ;
}
}
}
}
break ;
} /* end of switch on find_type */
/*-- fall thru --> not found --*/
BADFIND(find) ; return find ;
}
int main( int argc , char * argv[] )
{
int ninp , ids , nv , iv,jv,kv , ivout , new_nvals ;
THD_3dim_dataset * new_dset=NULL , * dset ;
char buf[256] ;
/*----- Identify software -----*/
#if 0
printf ("\n\n");
printf ("Program: %s \n", PROGRAM_NAME);
printf ("Author: %s \n", PROGRAM_AUTHOR);
printf ("Initial Release: %s \n", PROGRAM_INITIAL);
printf ("Latest Revision: %s \n", PROGRAM_LATEST);
printf ("\n");
#endif
/*** read input options ***/
if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) B2F_Syntax() ;
mainENTRY("3dbuc2fim main"); machdep(); AFNI_logger(PROGRAM_NAME,argc,argv);
PRINT_VERSION("3dbuc2fim") ; AUTHOR(PROGRAM_AUTHOR);
B2F_read_opts( argc , argv ) ;
/*** create new dataset (empty) ***/
ninp = B2F_dsar->num ;
if( ninp < 1 ){
fprintf(stderr,"*** No input datasets?\n") ; exit(1) ;
}
new_nvals = 0 ;
for( ids=0 ; ids < ninp ; ids++ ) new_nvals += NSUBV(ids) ;
/*----- Check for acceptable number of sub-bricks -----*/
if (new_nvals < 1)
{ fprintf(stderr,"*** Less than 1 sub-brick specified\n") ; exit(1) ; }
if (new_nvals > 2)
{ fprintf(stderr,"*** More than 2 sub-bricks specified\n") ; exit(1) ; }
if( B2F_verb ) printf("-verb: output will have %d sub-bricks\n",new_nvals) ;
new_dset = EDIT_empty_copy( DSUB(0) ) ;
if( ninp == 1 ) tross_Copy_History( DSUB(0) , new_dset ) ;
tross_Make_History( "3dbuc2fim" , argc,argv , new_dset ) ;
/*----- Set default value for function type. This will be changed later,
if the second sub-brick has a statistic type. -----*/
if (new_nvals == 1)
B2F_func_type = FUNC_FIM_TYPE;
else
B2F_func_type = FUNC_THR_TYPE;
EDIT_dset_items (new_dset ,
ADN_prefix , B2F_output_prefix ,
ADN_directory_name, B2F_session ,
ADN_type , HEAD_FUNC_TYPE,
ADN_func_type , B2F_func_type,
ADN_ntt , 0 ,
ADN_nvals , new_nvals ,
ADN_none ) ;
if( THD_deathcon() && THD_is_file(DSET_HEADNAME(new_dset)) ){
fprintf(stderr,"*** Fatal error: file %s already exists!\n",
DSET_HEADNAME(new_dset) ) ;
exit(1) ;
}
THD_force_malloc_type( new_dset->dblk , DATABLOCK_MEM_MALLOC ) ;
/*** loop over input datasets ***/
if( ninp > 1 ) myXtFree( new_dset->keywords ) ;
ivout = 0 ;
for( ids=0 ; ids < ninp ; ids++ ){
dset = DSUB(ids) ;
nv = NSUBV(ids) ;
DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ;
/** loop over sub-bricks to output **/
for( iv=0 ; iv < nv ; iv++ ){
jv = SUBV(ids,iv) ; /* which sub-brick to use */
EDIT_substitute_brick( new_dset , ivout ,
DSET_BRICK_TYPE(dset,jv) , DSET_ARRAY(dset,jv) ) ;
/*----- If this sub-brick is from a bucket dataset,
preserve the label for this sub-brick -----*/
if (dset->func_type == FUNC_BUCK_TYPE)
sprintf (buf, "%s", DSET_BRICK_LABEL(dset,jv));
else
sprintf(buf,"%.12s[%d]",DSET_PREFIX(dset),jv) ;
EDIT_dset_items( new_dset , ADN_brick_label_one+ivout, buf , ADN_none ) ;
#if 0
sprintf(buf,"%s[%d]",DSET_FILECODE(dset),jv) ;
EDIT_dset_items(
new_dset, ADN_brick_keywords_replace_one+ivout, buf, ADN_none ) ;
#endif
EDIT_dset_items(
new_dset ,
ADN_brick_fac_one +ivout, DSET_BRICK_FACTOR(dset,jv),
#if 0
ADN_brick_keywords_append_one+ivout, DSET_BRICK_KEYWORDS(dset,jv) ,
#endif
ADN_none ) ;
/** possibly write statistical parameters for this sub-brick **/
kv = DSET_BRICK_STATCODE(dset,jv) ;
if( FUNC_IS_STAT(kv) ){ /* input sub-brick has stat params */
int npar = MAX_STAT_AUX , lv ;
float * par = (float *) malloc( sizeof(float) * (npar) ) ;
float * sax = DSET_BRICK_STATAUX(dset,jv) ;
for( lv=0 ; lv < npar ; lv++ )
par[lv] = (sax != NULL && lv < FUNC_need_stat_aux[kv]) ? sax[lv] : 0.0;
if (ivout == 1)
{
EDIT_dset_items(new_dset ,
ADN_func_type , kv,
ADN_stat_aux, par ,
ADN_none ) ;
}
free(par) ;
/* 2: if the input dataset has statistical parameters */
} else if( ISFUNC(dset) && /* dset has stat */
FUNC_IS_STAT(dset->func_type) && /* params */
jv == FUNC_ival_thr[dset->func_type] ){ /* thr sub-brick */
int npar , lv ;
float * par , * sax ;
kv = dset->func_type ;
npar = MAX_STAT_AUX ;
par = (float *) malloc( sizeof(float) * (npar+2) ) ;
sax = dset->stat_aux ;
for( lv=0 ; lv < npar ; lv++ )
par[lv] = (sax != NULL) ? sax[lv] : 0.0 ;
if (ivout == 1)
{
for( lv=0 ; lv < npar+2 ; lv++ )
printf ("par[%d] = %f \n", lv, par[lv]);
EDIT_dset_items(new_dset ,
ADN_func_type , kv,
ADN_stat_aux, par ,
ADN_none ) ;
}
free(par) ;
}
/** print a message? **/
if( B2F_verb ) printf("-verb: copied %s[%d] into %s[%d]\n" ,
DSET_FILECODE(dset) , jv ,
DSET_FILECODE(new_dset) , ivout ) ;
ivout++ ;
}
/** loop over all bricks in input dataset and
unload them if they aren't going into the output
(not required, but is done to economize on memory) **/
if( nv < DSET_NVALS(dset) ){
for( kv=0 ; kv < DSET_NVALS(dset) ; kv++ ){ /* all input sub-bricks */
for( iv=0 ; iv < nv ; iv++ ){ /* all output sub-bricks */
jv = SUBV(ids,iv) ;
if( jv == kv ) break ; /* input matches output */
}
if( iv == nv ){
mri_free( DSET_BRICK(dset,kv) ) ;
#if 0
if( B2F_verb ) printf("-verb: unloaded unused %s[%d]\n" ,
DSET_FILECODE(dset) , kv ) ;
#endif
}
}
}
} /* end of loop over input datasets */
if( B2F_verb ) fprintf(stderr,"-verb: loading statistics\n") ;
THD_load_statistics( new_dset ) ;
THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ;
if( B2F_verb ) fprintf(stderr,"-verb: wrote output: %s\n",DSET_BRIKNAME(new_dset)) ;
exit(0) ;
}
