/*****************************************************************************
Major portions of this software are copyrighted by the Medical College
of Wisconsin, 1994-2000, and are released under the Gnu General Public
License, Version 2. See the file README.Copyright for details.
******************************************************************************/
#include "mrilib.h"
void Syntax(char *str)
{
int ii ;
if( str != NULL ) ERROR_exit(str) ; /* does not return */
printf( "Changes some of the information inside a 3D dataset's header.\n"
"Note that this program does NOT change the .BRIK file at all;\n"
"the main purpose of 3drefit is to fix up errors made when\n"
"using to3d.\n"
"To see the current values stored in a .HEAD file, use the command\n"
"'3dinfo dataset'. Using 3dinfo both before and after 3drefit is\n"
"a good idea to make sure the changes have been made correctly!\n"
"\n"
"20 Jun 2006: 3drefit will now work on NIfTI datasets (but it will\n"
" write out the entire dataset)\n\n"
) ;
printf(
"Usage: 3drefit [options] dataset ...\n"
"where the options are\n"
" -orient code Sets the orientation of the 3D volume(s) in the .BRIK.\n"
" The code must be 3 letters, one each from the\n"
" pairs {R,L} {A,P} {I,S}. The first letter gives\n"
" the orientation of the x-axis, the second the\n"
" orientation of the y-axis, the third the z-axis:\n"
" R = right-to-left L = left-to-right\n"
" A = anterior-to-posterior P = posterior-to-anterior\n"
" I = inferior-to-superior S = superior-to-inferior\n"
" ** WARNING: when changing the orientation, you must be sure\n"
" to check the origins as well, to make sure that the volume\n"
" is positioned correctly in space.\n"
"\n"
" -xorigin distx Puts the center of the edge voxel off at the given\n"
" -yorigin disty distance, for the given axis (x,y,z); distances in mm.\n"
" -zorigin distz (x=first axis, y=second axis, z=third axis).\n"
" Usually, only -zorigin makes sense. Note that this\n"
" distance is in the direction given by the corresponding\n"
" letter in the -orient code. For example, '-orient RAI'\n"
" would mean that '-zorigin 30' sets the center of the\n"
" first slice at 30 mm Inferior. See the to3d manual\n"
" for more explanations of axes origins.\n"
" ** SPECIAL CASE: you can use the string 'cen' in place of\n"
" a distance to force that axis to be re-centered.\n"
"\n"
" -xorigin_raw xx Puts the center of the edge voxel at the given COORDINATE\n"
" -yorigin_raw yy rather than the given DISTANCE. That is, these values\n"
" -zorigin_raw zz directly replace the offsets in the dataset header,\n"
" without any possible sign changes.\n"
"\n"
" -duporigin cset Copies the xorigin, yorigin, and zorigin values from\n"
" the header of dataset 'cset'.\n"
"\n"
" -dxorigin dx Adds distance 'dx' (or 'dy', or 'dz') to the center\n"
" -dyorigin dy coordinate of the edge voxel. Can be used with the\n"
" -dzorigin dz values input to the 'Nudge xyz' plugin.\n"
" ** WARNING: you can't use these options at the same\n"
" time you use -orient.\n"
" ** WARNING: consider -shift_tags if dataset has tags\n"
"\n"
" -xdel dimx Makes the size of the voxel the given dimension,\n"
" -ydel dimy for the given axis (x,y,z); dimensions in mm.\n"
" -zdel dimz ** WARNING: if you change a voxel dimension, you will\n"
" probably have to change the origin as well.\n"
" -keepcen When changing a voxel dimension with -xdel (etc.),\n"
" also change the corresponding origin to keep the\n"
" center of the dataset at the same coordinate location.\n"
" -xyzscale fac Scale the size of the dataset voxels by the factor 'fac'.\n"
" This is equivalent to using -xdel, -ydel, -zdel together.\n"
" -keepcen is used on the first input dataset, and then\n"
" any others will be shifted the same amount, to maintain\n"
" their alignment with the first one.\n"
" ** WARNING: -xyzscale can't be used with any of the other\n"
" options that change the dataset grid coordinates!\n"
" ** N.B.: 'fac' must be positive, and using fac=1.0 is stupid.\n"
"\n"
" -TR time Changes the TR time to a new value (see 'to3d -help').\n"
" -notoff Removes the slice-dependent time-offsets.\n"
" -Torg ttt Set the time origin of the dataset to value 'ttt'.\n"
" (Time origins are set to 0 in to3d.)\n"
" ** WARNING: These 3 options apply only to 3D+time datasets.\n"
" **N.B.: Using '-TR' on a dataset without a time axis\n"
" will add a time axis to the dataset.\n"
"\n"
" -newid Changes the ID code of this dataset as well.\n"
"\n"
" -nowarp Removes all warping information from dataset.\n"
"\n"
" -apar aset Set the dataset's anatomy parent dataset to 'aset'\n"
" ** N.B.: The anatomy parent is the dataset from which the\n"
" transformation from +orig to +acpc and +tlrc coordinates\n"
" is taken. It is appropriate to use -apar when there is\n"
" more than 1 anatomical dataset in a directory that has\n"
" been transformed. In this way, you can be sure that\n"
" AFNI will choose the correct transformation. You would\n"
" use this option on all the +orig dataset that are\n"
" aligned with 'aset' (i.e., that were acquired in the\n"
" same scanning session).\n"
" ** N.B.: Special cases of 'aset'\n"
" aset = NULL --> remove the anat parent info from the dataset\n"
" aset = SELF --> set the anat parent to be the dataset itself\n"
"\n"
" -wpar wset Set the warp parent (the +orig version of a +tlrc dset).\n"
" This option is used by @auto_tlrc. Do not use it unless\n"
" you know what you're doing. \n"
"\n"
" -clear_bstat Clears the statistics (min and max) stored for each sub-brick\n"
" in the dataset. This is useful if you have done something to\n"
" modify the contents of the .BRIK file associated with this\n"
" dataset.\n"
" -redo_bstat Re-computes the statistics for each sub-brick. Requires\n"
" reading the .BRIK file, of course. Also does -clear_bstat\n"
" before recomputing statistics, so that if the .BRIK read\n"
" fails for some reason, then you'll be left without stats.\n"
"\n"
" -statpar v ... Changes the statistical parameters stored in this\n"
" dataset. See 'to3d -help' for more details.\n"
"\n"
" -markers Adds an empty set of AC-PC markers to the dataset,\n"
" if it can handle them (is anatomical, is in the +orig\n"
" view, and isn't 3D+time).\n"
" ** WARNING: this will erase any markers that already exist!\n"
"\n"
" -shift_tags Apply -dxorigin (and y and z) changes to tags.\n"
"\n"
" -dxtag dx Add dx to the coordinates of all tags.\n"
" -dytag dy Add dy to the coordinates of all tags.\n"
" -dztag dz Add dz to the coordinates of all tags.\n"
"\n"
" -view code Changes the 'view' to be 'code', where the string 'code'\n"
" is one of 'orig', 'acpc', or 'tlrc'.\n"
" ** WARNING: The program will also change the .HEAD and .BRIK\n"
" filenames to match. If the dataset filenames already\n"
" exist in the '+code' view, then this option will fail.\n"
" You will have to rename the dataset files before trying\n"
" to use '-view'. If you COPY the files and then use\n"
" '-view', don't forget to use '-newid' as well!\n"
"\n"
" -label2 llll Set the 'label2' field in a dataset .HEAD file to the\n"
" string 'llll'. (Can be used as in AFNI window titlebars.)\n"
"\n"
" -denote Means to remove all possibly-identifying notes from\n"
" the header. This includes the History Note, other text\n"
" Notes, keywords, and labels.\n"
"\n"
" -byteorder bbb Sets the byte order string in the header.\n"
" Allowable values for 'bbb' are:\n"
" LSB_FIRST MSB_FIRST NATIVE_ORDER\n"
" Note that this does not change the .BRIK file!\n"
" This is done by programs 2swap and 4swap.\n"
"\n"
" -appkey ll Appends the string 'll' to the keyword list for the\n"
" whole dataset.\n"
" -repkey ll Replaces the keyword list for the dataset with the\n"
" string 'll'.\n"
" -empkey Destroys the keyword list for the dataset.\n"
) ;
printf(
"\n"
" -atrcopy dd nn Copy AFNI header attribute named 'nn' from dataset 'dd'\n"
" into the header of the dataset(s) being modified.\n"
" For more information on AFNI header attributes, see\n"
" documentation file README.attributes. More than one\n"
" '-atrcopy' option can be used.\n"
" **N.B.: This option is for those who know what they are doing!\n"
" Without the -saveatr option, this option is\n"
" meant to be used to alter attributes that are NOT\n"
" directly mapped into dataset internal structures, since\n"
" those structures are mapped back into attribute values\n"
" as the dataset is being written to disk. If you want\n"
" to change such an attribute, you have to use the\n"
" corresponding 3drefit option directly or use the \n"
" -saveatr option.\n"
"\n"
" If you are confused, try to understand this: \n"
" Option -atrcopy was never intended to modify AFNI-\n"
" specific attributes. Rather, it was meant to copy\n"
" user-specific attributes that had been added to some\n"
" dataset using -atrstring option. A cursed day came when\n"
" it was convenient to use -atrcopy to copy an AFNI-specific\n"
" attribute (BRICK_LABS to be exact) and for that to\n"
" take effect in the output, the option -saveatr was added.\n"
" Contact Daniel Glen and/or Rick Reynolds for further \n"
" clarification and any other needs you may have.\n"
"\n"
" Do NOT use -atrcopy or -atrstring with other modification\n"
" options.\n"
"\n"
" -atrstring n 'x' Copy the string 'x' into the dataset(s) being\n"
" modified, giving it the attribute name 'n'.\n"
" To be safe, the 'x' string should be in quotes.\n"
" **N.B.: You can store attributes with almost any name in\n"
" the .HEAD file. AFNI will ignore those it doesn't\n"
" know anything about. This technique can be a way of\n"
" communicating information between programs. However,\n"
" when most AFNI programs write a new dataset, they will\n"
" not preserve any such non-standard attributes.\n"
" -saveatr (default) Copy the attributes that are known to AFNI into \n"
" the dset->dblk structure thereby forcing changes to known\n"
" attributes to be present in the output.\n"
" This option only makes sense with -atrcopy\n"
" **N.B.: Don't do something like copy labels of a dataset with \n"
" 30 sub-bricks to one that has only 10, or vice versa.\n"
" This option is for those who would deservedly earn a\n"
" hunting license.\n"
" -nosaveatr Opposite of -saveatr\n"
" Example: \n"
" 3drefit -saveatr -atrcopy WithLabels+tlrc BRICK_LABS NeedsLabels+tlrc\n"
) ;
printf(
"\n"
" -'type' Changes the type of data that is declared for this\n"
" dataset, where 'type' is chosen from the following:\n"
) ;
printf(" ANATOMICAL TYPES\n") ;
for( ii=FIRST_ANAT_TYPE ; ii <= LAST_ANAT_TYPE ; ii++ ){
printf(" %8s == %-16.16s",ANAT_prefixstr[ii],ANAT_typestr[ii] ) ;
if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ;
}
if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ;
printf(" FUNCTIONAL TYPES\n") ;
for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){
printf(" %8s == %-16.16s",FUNC_prefixstr[ii],FUNC_typestr[ii] ) ;
if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ;
}
if( (ii-FIRST_ANAT_TYPE)%2 == 1 ) printf("\n") ;
printf( /* 08 Jun 2004 */
"-copyaux auxset Copies the 'auxiliary' data from dataset 'auxset'\n"
" over the auxiliary data for the dataset being\n"
" modified. Auxiliary data comprises sub-brick labels,\n"
" keywords, and statistics codes.\n"
" '-copyaux' occurs BEFORE the '-sub' operations below,\n"
" so you can use those to alter the auxiliary data\n"
" that is copied from auxset.\n"
"\n" ) ;
printf(
"The options below allow you to attach auxiliary data to sub-bricks\n"
"in the dataset. Each option may be used more than once so that\n"
"multiple sub-bricks can be modified in a single run of 3drefit.\n"
"\n"
" -sublabel n ll Attach to sub-brick #n the label string 'll'.\n"
" -subappkey n ll Add to sub-brick #n the keyword string 'll'.\n"
" -subrepkey n ll Replace sub-brick #n's keyword string with 'll'.\n"
" -subempkey n Empty out sub-brick #n' keyword string\n"
"\n"
" -substatpar n type v ...\n"
" Attach to sub-brick #n the statistical type and\n"
" the auxiliary parameters given by values 'v ...',\n"
" where 'type' is one of the following:\n"
) ;
printf(" type Description PARAMETERS\n"
" ---- ----------- ----------------------------------------\n" ) ;
for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){
if( FUNC_IS_STAT(ii) )
printf(" %4s %-11.11s %s\n",
FUNC_prefixstr[ii] , FUNC_typestr[ii]+6 , FUNC_label_stat_aux[ii] ) ;
}
printf(
"\n"
"The following options allow you to modify VOLREG fields:\n"
" -vr_mat val1 ... val12 Use these twelve values for VOLREG_MATVEC_index.\n"
" -vr_mat_ind index Index of VOLREG_MATVEC_index field to be modified.\n"
" Optional, default index is 0.\n"
" NB: You can only modify one VOLREG_MATVEC_index at a time\n"
" -vr_center_old x y z Use these 3 values for VOLREG_CENTER_OLD.\n"
" -vr_center_base x y z Use these 3 values for VOLREG_CENTER_BASE.\n"
"\n"
);
printf("++ Last program update: 08 Jul 2005\n");
exit(0) ;
}
#define ASET_NULL 1
#define ASET_SELF 2
int main( int argc , char * argv[] )
{
THD_3dim_dataset * dset , * aset = NULL , *waset = NULL;
int aset_code = 0 ; /* 14 Dec 1999 */
int waset_code = 0;
THD_dataxes * daxes ;
int new_stuff = 0 ;
int new_orient = 0 ; char orient_code[4] ; int xxor,yyor,zzor ;
int new_xorg = 0 ; float xorg ; int cxorg=0, dxorg=0 , duporg=0 ;
int new_yorg = 0 ; float yorg ; int cyorg=0, dyorg=0 ;
int new_zorg = 0 ; float zorg ; int czorg=0, dzorg=0 ;
int new_tags = 0 ; int shift_tags = 0 ; /* 08 May 2006 [rickr] */
float dxtag=0.0, dytag=0.0, dztag=0.0 ;
int new_xdel = 0 ; float xdel ;
int new_ydel = 0 ; float ydel ;
int new_zdel = 0 ; float zdel ;
int new_TR = 0 ; float TR ;
int new_Torg = 0 ; float Torg ; /* 29 Jan 2003 */
int new_tunits = 0 ; int tunits ;
int new_idcode = 0 ;
int new_nowarp = 0 ;
int new_stataux= 0 ; float stataux[MAX_STAT_AUX] ;
int new_type = 0 ; int dtype , ftype , nvals ;
int new_markers= 0 ;
int new_view = 0 ; int vtype ;
int new_key = 0 ; char * key ;
int new_byte_order = 0 ; /* 25 Apr 1998 */
int new_toff_sl = 0 ; /* 12 Feb 2001 */
int clear_bstat = 0 ; /* 28 May 2002 */
int redo_bstat = 0 ; /* 01 Feb 2005 */
int copyaux = 0 ; /* 08 Jun 2004 */
THD_3dim_dataset *auxset=NULL ; /* 08 Jun 2004 */
char *new_label2 = NULL ; /* 21 Dec 2004 */
int denote = 0 ; /* 08 Jul 2005 */
Boolean write_output ; /* 20 Jun 2006 [rickr] */
int keepcen = 0 ; /* 17 Jul 2006 [RWCox] */
float xyzscale = 0.0f ; /* 17 Jul 2006 */
int ndone=0 ; /* 18 Jul 2006 */
int verb =0 ;
#define VINFO(x) if(verb)ININFO_message(x)
char str[256] ;
int iarg , ii ;
typedef struct { int iv ; char lab[32] ; } SUBlabel ;
typedef struct { int iv ; float par[MAX_STAT_AUX+2] ; } SUBstatpar ;
typedef struct { int iv , code ; char * keyword ; } SUBkeyword ;
int nsublab = 0 ; SUBlabel * sublab = NULL ;
int nsubstatpar = 0 ; SUBstatpar * substatpar = NULL ;
int nsubkeyword = 0 ; SUBkeyword * subkeyword = NULL ;
char *cpt ;
int iv ;
float volreg_mat[12];
float center_old[3];
float center_base[3];
int Do_volreg_mat = 0, Do_center_old = 0, Do_center_base = 0,
volreg_matind = 0, icnt = 0;
char *lcpt=NULL;
int num_atrcopy = 0 ; /* 03 Aug 2005 */
ATR_any **atrcopy = NULL ;
int saveatr = 1;
int atrmod = 0; /* if no ATR is modified, don't overwrite normal changes */
/* 28 Jul 2006 [rickr] */
/*-------------------------- help me if you can? --------------------------*/
if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) Syntax(NULL) ;
iarg = 1 ;
/*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/
mainENTRY("3drefit main"); machdep() ; PRINT_VERSION("3drefit") ; AUTHOR("RW Cox") ;
{ 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("3drefit",argc,argv) ;
while( iarg < argc && argv[iarg][0] == '-' ){
/*----- -atrcopy dd nn [03 Aug 2005] -----*/
if( strcmp(argv[iarg],"-atrcopy") == 0 ){
THD_3dim_dataset *qset ; ATR_any *atr ;
if( iarg+2 >= argc ) Syntax("need 2 arguments after -atrcopy!") ;
qset = THD_open_dataset( argv[++iarg] ) ;
if( qset == NULL ){
WARNING_message("Can't open -atrcopy dataset %s",argv[iarg]) ;
iarg++ ; goto atrcopy_done ;
}
atr = THD_find_atr( qset->dblk , argv[++iarg] ) ;
if( atr == NULL ){
WARNING_message("Can't find attribute %s in -atrcopy dataset %s",
argv[iarg],argv[iarg-1]) ;
DSET_delete(qset) ; goto atrcopy_done ;
}
atrcopy = (ATR_any **)realloc( (void *)atrcopy ,
sizeof(ATR_any *)*(num_atrcopy+1) ) ;
atrcopy[num_atrcopy++] = THD_copy_atr( atr ) ;
/* atr_print( atr, NULL , NULL, '\0', 1) ; */
DSET_delete(qset) ; atrmod = 1; /* replaced new_stuff 28 Jul 2006 rcr */
atrcopy_done:
iarg++ ; continue ;
}
/*----- -atrstring nn xx [03 Aug 2005] -----*/
if( strcmp(argv[iarg],"-atrstring") == 0 ){
ATR_string *atr ; char *aname , *xx ;
if( iarg+2 >= argc ) Syntax("need 2 arguments after -atrstring!") ;
aname = argv[++iarg] ;
if( !THD_filename_pure(aname) ){
WARNING_message("Illegal -atrstring name %s",aname) ;
iarg++ ; goto atrstring_done ;
}
xx = argv[++iarg] ;
atr = (ATR_string *)XtMalloc(sizeof(ATR_string)) ;
atr->type = ATR_STRING_TYPE ;
atr->name = XtNewString( aname ) ;
atr->nch = strlen(xx)+1 ; ;
atr->ch = (char *)XtMalloc( sizeof(char) * atr->nch ) ;
memcpy( atr->ch , xx , sizeof(char) * atr->nch ) ;
atrcopy = (ATR_any **)realloc( (void *)atrcopy ,
sizeof(ATR_any *)*(num_atrcopy+1) ) ;
atrcopy[num_atrcopy++] = (ATR_any *)atr ;
atrmod = 1; /* replaced new_stuff++ 28 Jul 2006 [rickr] */
atrstring_done:
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-saveatr") == 0 ){
saveatr = 1 ; iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-nosaveatr") == 0 ){
saveatr = 0 ; iarg++ ; continue ;
}
/*----- -denote [08 Jul 2005] -----*/
if( strcmp(argv[iarg],"-denote") == 0 ){
denote = 1 ; new_stuff++ ; iarg++ ; continue ;
}
/*----- -copyaux auxset [08 Jun 2004] -----*/
if( strcmp(argv[iarg],"-copyaux") == 0 ){
if( iarg+1 >= argc ) Syntax("need 1 argument after -copyaux!") ;
if( auxset != NULL ) Syntax("Can't have more than one -copyaux option!") ;
iarg++ ; copyaux = 1 ;
if( strcmp(argv[iarg],"NULL") == 0 ){ /* special case */
auxset = NULL ;
} else {
auxset = THD_open_one_dataset( argv[iarg] ) ;
if( auxset == NULL ) Syntax("Can't open -copyaux dataset!") ;
}
new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/*----- -apar aset [14 Oct 1999] -----*/
if( strcmp(argv[iarg],"-apar") == 0 ||
strcmp(argv[iarg],"-anatparent") == 0 ||
strcmp(argv[iarg],"-aset") == 0 ){
if( iarg+1 >= argc )
Syntax("need 1 argument after -apar!") ;
if( aset != NULL || aset_code != 0 ) /* 13-14 Dec 1999 */
Syntax("Can't have more than one -apar option!");
iarg++ ;
if( strcmp(argv[iarg],"NULL") == 0 ){ /* 14 Dec 1999: special cases */
aset_code = ASET_NULL ;
} else if( strcmp(argv[iarg],"SELF") == 0 ){
aset_code = ASET_SELF ;
} else {
aset = THD_open_one_dataset( argv[iarg] ) ;
if( aset == NULL )
Syntax("Can't open -apar dataset!") ;
}
new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/*----- -wpar wset [ZSS June 06] -----*/
if( strcmp(argv[iarg],"-wpar") == 0 ||
strcmp(argv[iarg],"-warpparent") == 0 ||
strcmp(argv[iarg],"-wset") == 0 ){
if( iarg+1 >= argc )
Syntax("need 1 argument after -wpar!") ;
if( waset != NULL || waset_code != 0 )
Syntax("Can't have more than one -wpar option!");
iarg++ ;
if( strcmp(argv[iarg],"NULL") == 0 ){
waset_code = ASET_NULL ;
} else if( strcmp(argv[iarg],"SELF") == 0 ){
waset_code = ASET_SELF ;
} else {
waset = THD_open_one_dataset( argv[iarg] ) ;
if( waset == NULL )
Syntax("Can't open -wpar dataset!") ;
}
new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/*----- -clear_bstat option [28 May 2002] -----*/
if( strcmp(argv[iarg],"-clear_bstat") == 0 ){
clear_bstat = 1 ;
new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-redo_bstat") == 0 ){ /* 01 Feb 2005 */
clear_bstat = 1 ; redo_bstat = 1 ;
new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/*----- -byteorder option [25 April 1998] -----*/
if( strncmp(argv[iarg],"-byteorder",7) == 0 ){
if( iarg+1 >= argc )
Syntax("need 1 argument after -byteorder!") ;
iarg++ ;
if( strcmp(argv[iarg],LSB_FIRST_STRING) == 0 )
new_byte_order = LSB_FIRST ;
else if( strcmp(argv[iarg],MSB_FIRST_STRING) == 0 )
new_byte_order = MSB_FIRST ;
else if( strcmp(argv[iarg],NATIVE_STRING) == 0 )
new_byte_order = mri_short_order() ;
else
Syntax("illegal argument after -byteorder!") ;
new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/*----- -sublabel option -----*/
if( strncmp(argv[iarg],"-sublabel",7) == 0 ){
if( iarg+2 >= argc )
Syntax("need 2 arguments after -sublabel!") ;
iv = strtol( argv[++iarg] , &cpt , 10 ) ;
if( iv < 0 || iv == 0 && cpt == argv[iarg] )
Syntax("illegal sub-brick index after -sublabel!") ;
sublab = (SUBlabel *) XtRealloc( (char *)sublab ,
sizeof(SUBlabel) * (nsublab+1) ) ;
sublab[nsublab].iv = iv ;
MCW_strncpy( sublab[nsublab].lab , argv[++iarg] , 32 ) ;
nsublab++ ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/*----- -subkeyword options -----*/
if( strncmp(argv[iarg],"-subappkey",7) == 0 ||
strncmp(argv[iarg],"-subrepkey",7) == 0 ||
strncmp(argv[iarg],"-subempkey",7) == 0 ){
int code , npl ;
if( strncmp(argv[iarg],"-subappkey",7) == 0 ) code = 1 ;
else if( strncmp(argv[iarg],"-subrepkey",7) == 0 ) code = 2 ;
else code = 3 ;
npl = (code == 3) ? 1 : 2 ;
if( iarg+npl >= argc )
Syntax("need arguments after -sub...key!") ;
iv = strtol( argv[++iarg] , &cpt , 10 ) ;
if( iv < 0 || iv == 0 && cpt == argv[iarg] )
Syntax("illegal sub-brick index after -sub...key!") ;
subkeyword = (SUBkeyword *) XtRealloc( (char *)subkeyword ,
sizeof(SUBkeyword)*(nsubkeyword+1) ) ;
subkeyword[nsubkeyword].iv = iv ;
subkeyword[nsubkeyword].code = code ;
if( code != 3 ) subkeyword[nsubkeyword].keyword = argv[++iarg] ;
nsubkeyword++ ; new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/*----- -keywords options -----*/
if( strncmp(argv[iarg],"-appkey",4) == 0 ||
strncmp(argv[iarg],"-repkey",4) == 0 ||
strncmp(argv[iarg],"-empkey",4) == 0 ){
int code , npl ;
if( strncmp(argv[iarg],"-appkey",4) == 0 ) code = 1 ;
else if( strncmp(argv[iarg],"-repkey",4) == 0 ) code = 2 ;
else code = 3 ;
npl = (code == 3) ? 0 : 1 ;
if( iarg+code >= argc )
Syntax("need arguments after -...key!") ;
new_key = code ;
if( code != 3 ) key = argv[++iarg] ;
new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/*----- -substatpar option -----*/
if( strncmp(argv[iarg],"-substatpar",7) == 0 ){
int fc ; float val ;
if( iarg+2 >= argc )
Syntax("need at least 2 arguments after -substatpar!") ;
iv = strtol( argv[++iarg] , &cpt , 10 ) ;
if( iv < 0 || iv == 0 && cpt == argv[iarg] )
Syntax("illegal sub-brick index after -substatpar!") ;
iarg++ ;
if( strlen(argv[iarg]) < 3 )
Syntax("illegal type code after -substatpar!") ;
fc = (argv[iarg][0] == '-') ? 1 : 0 ;
for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ ){
if( ! FUNC_IS_STAT(ii) ) continue ;
if( strncmp( &(argv[iarg][fc]) ,
FUNC_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ;
}
if( ii > LAST_FUNC_TYPE )
Syntax("unknown type code after -substatpar!") ;
substatpar = (SUBstatpar *) XtRealloc( (char *)substatpar ,
sizeof(SUBstatpar) * (nsubstatpar+1) ) ;
substatpar[nsubstatpar].iv = iv ;
substatpar[nsubstatpar].par[0] = ii ;
substatpar[nsubstatpar].par[1] = MAX_STAT_AUX ;
for( ii=0 ; ii < MAX_STAT_AUX ; ii++ )
substatpar[nsubstatpar].par[ii+2] = 0.0 ;
ii = 2 ; iarg++ ;
do{
val = strtod( argv[iarg] , &cpt ) ;
if( *cpt != '\0' ) break ;
substatpar[nsubstatpar].par[ii++] = val ;
iarg++ ;
} while( iarg < argc ) ;
nsubstatpar++ ; new_stuff++ ; continue ; /* go to next arg */
}
/*----- -orient code option -----*/
#define ORCODE(aa) \
( (aa)=='R' ? ORI_R2L_TYPE : (aa)=='L' ? ORI_L2R_TYPE : \
(aa)=='P' ? ORI_P2A_TYPE : (aa)=='A' ? ORI_A2P_TYPE : \
(aa)=='I' ? ORI_I2S_TYPE : (aa)=='S' ? ORI_S2I_TYPE : ILLEGAL_TYPE )
#define OR3OK(x,y,z) ( ((x)&6) + ((y)&6) + ((z)&6) == 6 )
if( strncmp(argv[iarg],"-orient",4) == 0 ){
char acod ;
if( iarg+1 >= argc ) Syntax("need an argument after -orient!");
MCW_strncpy(orient_code,argv[++iarg],4) ;
if( strlen(orient_code) != 3 ) Syntax("Illegal -orient code") ;
acod = toupper(orient_code[0]) ; xxor = ORCODE(acod) ;
acod = toupper(orient_code[1]) ; yyor = ORCODE(acod) ;
acod = toupper(orient_code[2]) ; zzor = ORCODE(acod) ;
if( xxor<0 || yyor<0 || zzor<0 || ! OR3OK(xxor,yyor,zzor) )
Syntax("Unusable -orient code!") ;
new_orient = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** -?origin dist **/
if( strcmp(argv[iarg],"-xorigin") == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -xorigin!");
if( strncmp(argv[iarg],"cen",3) == 0 ) cxorg = 1 ;
else xorg = strtod(argv[iarg],NULL) ;
dxorg = 0 ; new_xorg = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-yorigin") == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -yorigin!");
if( strncmp(argv[iarg],"cen",3) == 0 ) cyorg = 1 ;
else yorg = strtod(argv[iarg],NULL) ;
dyorg = 0 ; new_yorg = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-zorigin") == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -zorigin!");
if( strncmp(argv[iarg],"cen",3) == 0 ) czorg = 1 ;
else zorg = strtod(argv[iarg],NULL) ;
dzorg = 0 ; new_zorg = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/* 13 Sep 2000: -duporigin */
if( strcmp(argv[iarg],"-duporigin") == 0 ){
THD_3dim_dataset * cset ;
if( ++iarg >= argc ) Syntax("need an argument after -duporigin!");
cset = THD_open_dataset( argv[iarg] ) ;
if( cset == NULL ) Syntax("couldn't open -duporigin dataset!");
daxes = cset->daxes ;
xorg = daxes->xxorg ; yorg = daxes->yyorg ; zorg = daxes->zzorg ;
cxorg = cyorg = czorg = dxorg = dyorg = dzorg = 0 ;
new_xorg = new_yorg = new_zorg = duporg = 1 ; new_stuff++ ;
DSET_delete(cset) ;
iarg++ ; continue ; /* go to next arg */
}
/* 02 Mar 2000: -d?origin stuff, to go with plug_nudge.c */
if( strncmp(argv[iarg],"-dxorigin",4) == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -dxorigin!");
xorg = strtod(argv[iarg],NULL) ; dxorg = 1 ; cxorg = 0 ;
new_xorg = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strncmp(argv[iarg],"-dyorigin",4) == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -dyorigin!");
yorg = strtod(argv[iarg],NULL) ; dyorg = 1 ; cyorg = 0 ;
new_yorg = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strncmp(argv[iarg],"-dzorigin",4) == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -dzorigin!");
zorg = strtod(argv[iarg],NULL) ; dzorg = 1 ; czorg = 0 ;
new_zorg = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** 04 Oct 2002: _raw origins **/
if( strcmp(argv[iarg],"-xorigin_raw") == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -xorigin_raw!");
xorg = strtod(argv[iarg],NULL) ; cxorg = dxorg = 0 ;
new_xorg = 2 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-yorigin_raw") == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -yorigin_raw!");
yorg = strtod(argv[iarg],NULL) ; cyorg = dyorg = 0 ;
new_yorg = 2 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-zorigin_raw") == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -zorigin_raw!");
zorg = strtod(argv[iarg],NULL) ; czorg = dzorg = 0 ;
new_zorg = 2 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** 04 Oct 2002: zadd VOLREG fields **/
if( strcmp(argv[iarg],"-vr_mat") == 0 ){
if( iarg+12 >= argc ) Syntax("need 12 arguments after -vr_mat!");
icnt = 0;
while (icnt < 12) {
++iarg;
volreg_mat[icnt] = strtod(argv[iarg], &lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
++icnt;
}
Do_volreg_mat = 1; new_stuff++ ;
++iarg;
continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-vr_mat_ind") == 0) {
if (++iarg >= argc) Syntax("need 1 argument after -vr_mat_ind!");
volreg_matind = (int)strtol(argv[iarg], &lcpt, 10); if (*lcpt != '\0') Syntax("Bad syntax in number argument!");
++iarg;
continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-vr_cen_old") == 0) {
if (iarg+3 >= argc) Syntax("need 3 arguments after -vr_cen_old");
++iarg;
center_old[0] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
center_old[1] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
center_old[2] = strtod(argv[iarg],&lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
Do_center_old = 1; new_stuff++ ;
++iarg;
continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-vr_cen_base") == 0) {
if (iarg+3 >= argc) Syntax("need 3 arguments after -vr_cen_base");
++iarg;
center_base[0] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
center_base[1] = strtod(argv[iarg],&lcpt) ; ++iarg; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
center_base[2] = strtod(argv[iarg],&lcpt) ; if (*lcpt != '\0') Syntax("Bad syntax in list of numbers!");
Do_center_base = 1; new_stuff++ ;
++iarg;
continue ; /* go to next arg */
}
/** -?del dim **/
if( strncmp(argv[iarg],"-xdel",4) == 0 ){
if( iarg+1 >= argc ) Syntax("need an argument after -xdel!");
xdel = strtod( argv[++iarg] , NULL ) ;
if( xdel <= 0.0 ) Syntax("argument after -xdel must be positive!") ;
new_xdel = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strncmp(argv[iarg],"-ydel",4) == 0 ){
if( iarg+1 >= argc ) Syntax("need an argument after -ydel!");
ydel = strtod( argv[++iarg] , NULL ) ;
if( ydel <= 0.0 ) Syntax("argument after -ydel must be positive!") ;
new_ydel = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strncmp(argv[iarg],"-zdel",4) == 0 ){
if( iarg+1 >= argc ) Syntax("need an argument after -zdel!");
zdel = strtod( argv[++iarg] , NULL ) ;
if( zdel <= 0.0 ) Syntax("argument after -zdel must be positive!") ;
new_zdel = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strncmp(argv[iarg],"-keepcen",7) == 0 ){ /* 17 Jul 2006 */
keepcen = 1 ;
iarg++ ; continue ; /* go to next arg */
}
if( strcmp(argv[iarg],"-verb") == 0 ){
verb++ ; iarg++ ; continue ;
}
if( strncmp(argv[iarg],"-xyzscale",8) == 0 ){ /* 17 Jul 2006 */
if( iarg+1 >= argc ) Syntax("need an argument after -xyzscale!");
xyzscale = strtod( argv[++iarg] , NULL ) ;
if( xyzscale <= 0.0f ) Syntax("argument after -xyzscale must be positive!");
if( xyzscale == 1.0f )
WARNING_message(
"-xyzscale 1.0 really makes no sense, but if that's what you want" ) ;
new_stuff++ ; iarg++ ; continue ; /* go to next arg */
}
/** -TR **/
if( strncmp(argv[iarg],"-TR",3) == 0 ){
char * eptr ;
if( iarg+1 >= argc ) Syntax("need an argument after -TR!");
TR = strtod( argv[++iarg] , &eptr ) ;
if( TR <= 0.0 ) Syntax("argument after -TR must be positive!") ;
if( strcmp(eptr,"ms")==0 || strcmp(eptr,"msec")==0 ){
new_tunits = 1 ; tunits = UNITS_MSEC_TYPE ;
WARNING_message("TR expressed in milliseconds is deprecated.") ;
} else if( strcmp(eptr,"s")==0 || strcmp(eptr,"sec")==0 ){
new_tunits = 1 ; tunits = UNITS_SEC_TYPE ;
} else if( strcmp(eptr,"Hz")==0 || strcmp(eptr,"Hertz")==0 ){
new_tunits = 1 ; tunits = UNITS_HZ_TYPE ;
}
new_TR = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** -notoff (12 Feb 2001) **/
if( strncmp(argv[iarg],"-notoff",7) == 0 ){
new_toff_sl = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** -Torg (29 Jan 2003) **/
if( strncmp(argv[iarg],"-Torg",5) == 0 ){
char *eptr ;
if( iarg+1 >= argc ) Syntax("need an argument after -Torg!");
Torg = strtod( argv[++iarg] , &eptr ) ;
if( *eptr != '\0' )
WARNING_message("-Torg %s ends in unexpected character\n",argv[iarg]) ;
new_Torg = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** -newid **/
if( strncmp(argv[iarg],"-newid",4) == 0 ){
new_idcode = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** -nowarp **/
if( strncmp(argv[iarg],"-nowarp",6) == 0 ){
new_nowarp = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** -statpar x x x **/
if( strncmp(argv[iarg],"-statpar",4) == 0 ){
float val ; char * ptr ;
if( ++iarg >= argc ) Syntax("need an argument after -statpar!") ;
for( ii=0 ; ii < MAX_STAT_AUX ; ii++ ) stataux[ii] = 0.0 ;
ii = 0 ;
do{
val = strtod( argv[iarg] , &ptr ) ;
if( *ptr != '\0' ) break ;
stataux[ii++] = val ;
iarg++ ;
} while( iarg < argc ) ;
if( ii == 0 ) Syntax("No numbers given after -statpar?") ;
new_stataux = 1 ; new_stuff++ ;
continue ;
}
/** -markers **/
if( strncmp(argv[iarg],"-markers",4) == 0 ){
new_markers = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** -label2 [21 Dec 2004] **/
if( strcmp(argv[iarg],"-label2") == 0 ){
new_label2 = argv[++iarg] ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** -view code **/
if( strncmp(argv[iarg],"-view",4) == 0 ){
char * code ;
if( iarg+1 >= argc ) Syntax("need an argument after -view!") ;
code = argv[++iarg] ; if( code[0] == '+' ) code++ ;
for( vtype=0 ; vtype <= LAST_VIEW_TYPE ; vtype++ )
if( strcmp(code,VIEW_codestr[vtype]) == 0 ) break ;
if( vtype > LAST_VIEW_TYPE ) Syntax("argument after -view is illegal!") ;
new_view = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/* tag options 08 May 2006 [rickr] */
/* -shift_tags, apply -d?origin to tags */
if( strncmp(argv[iarg],"-shift_tags",11) == 0 ){
shift_tags = 1 ;
iarg++ ; continue ; /* go to next arg */
}
if( strncmp(argv[iarg],"-dxtag",6) == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -dxtag!");
dxtag = strtod(argv[iarg],NULL) ;
new_tags = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strncmp(argv[iarg],"-dytag",6) == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -dytag!");
dytag = strtod(argv[iarg],NULL) ;
new_tags = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
if( strncmp(argv[iarg],"-dztag",6) == 0 ){
if( ++iarg >= argc ) Syntax("need an argument after -dztag!");
dztag = strtod(argv[iarg],NULL) ;
new_tags = 1 ; new_stuff++ ;
iarg++ ; continue ; /* go to next arg */
}
/** anything else must be a -type **/
/* try the anatomy prefixes */
for( ii=FIRST_ANAT_TYPE ; ii <= LAST_ANAT_TYPE ; ii++ )
if( strncmp( &(argv[iarg][1]) ,
ANAT_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ;
if( ii <= LAST_ANAT_TYPE ){
ftype = ii ;
dtype = HEAD_ANAT_TYPE ;
nvals = ANAT_nvals[ftype] ;
new_type = 1 ; new_stuff++ ;
iarg++ ; continue ;
}
/* try the function prefixes */
for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ )
if( strncmp( &(argv[iarg][1]) ,
FUNC_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ;
if( ii <= LAST_FUNC_TYPE ){
ftype = ii ;
dtype = HEAD_FUNC_TYPE ;
nvals = FUNC_nvals[ftype] ;
new_type = 1 ; new_stuff++ ;
iarg++ ; continue ;
}
/** error **/
{ char str[256] ;
sprintf(str,"Unknown option %s",argv[iarg]) ;
Syntax(str) ;
}
} /* end of loop over switches */
/*-- some checks for erroneous inputs --*/
if( new_stuff == 0 && atrmod == 0 ) Syntax("No options given!?") ;
if( new_stuff == 1 && atrmod == 1 ){ /* 28 Jul 2006 [rickr] */
fprintf(stderr,"** Cannot use -atrcopy or -atrstring with other "
"modification options.\n");
Syntax("Illegal attribute syntax.");
}
if( iarg >= argc ) Syntax("No datasets given!?") ;
if( xyzscale != 0.0f &&
(new_orient || new_xorg || new_yorg || new_zorg ||
keepcen || new_xdel || new_ydel || new_zdel ) ){ /* 18 Jul 2006 */
Syntax(
"-xyzscale is incompatible with other options for changing voxel grid");
}
if( new_orient && (dxorg || dyorg || dzorg) ) /* 02 Mar 2000 */
Syntax("Can't use -orient with -d?origin!?") ;
if( new_tags || shift_tags ){ /* 08 May 2006 [rickr] */
if( new_tags && shift_tags )
Syntax("Cant' use -shift_tags with -d{xyz}tag") ;
if( new_orient )
Syntax("Can't use -orient with -shift_tags or -d{xyz}tags") ;
if( shift_tags && !dxorg && !dyorg && !dzorg )
Syntax("-shift_tags option requires a -d{xyz}origin option") ;
if( shift_tags ){ /* then copy shifts to tag vars */
if( dxorg ) dxtag = xorg ;
if( dyorg ) dytag = yorg ;
if( dzorg ) dztag = zorg ;
}
}
/*--- process datasets ---*/
for( ; iarg < argc ; iarg++ ){
write_output = False ; /* some datasets will be overwritten */
dset = THD_open_one_dataset( argv[iarg] ) ;
if( dset == NULL ){
ERROR_message("Can't open dataset %s\n",argv[iarg]) ;
continue ;
}
if( DSET_IS_MINC(dset) ){
ERROR_message("Can't process MINC dataset %s\n",argv[iarg]);
continue ;
}
if( DSET_IS_ANALYZE(dset) ){
ERROR_message("Can't process ANALYZE dataset %s\n",argv[iarg]);
continue ;
}
if( DSET_IS_1D(dset) ){
ERROR_message("Can't process 1D dataset %s\n",argv[iarg]);
continue ;
}
if( DSET_IS_CTFMRI(dset) || DSET_IS_CTFSAM(dset) ){
ERROR_message("Can't process CTF dataset %s\n",argv[iarg]);
continue ;
}
if( DSET_IS_MPEG(dset) ){
ERROR_message("Can't process MPEG dataset %s\n",argv[iarg]);
continue ;
}
/* any surviving non-AFNI dataset needs the data written out */
if( IS_VALID_NON_AFNI_DSET(dset) ){
write_output = True ; /* 13 Jul 2006 [rickr] */
}
INFO_message("Processing AFNI dataset %s\n",argv[iarg]) ;
tross_Make_History( "3drefit" , argc,argv, dset ) ;
/* 21 Dec 2004: -label2 option */
if( new_label2 != NULL ){
EDIT_dset_items( dset , ADN_label2 , new_label2 , ADN_none ) ;
VINFO("setting label2") ;
}
/* 14 Oct 1999: change anat parent */
/* 14 Dec 1999: allow special cases: SELF and NULL */
if( aset != NULL ){
EDIT_dset_items( dset , ADN_anat_parent , aset , ADN_none ) ;
VINFO("setting Anat parent") ;
} else if( aset_code == ASET_SELF ){
EDIT_dset_items( dset , ADN_anat_parent , dset , ADN_none ) ;
VINFO("setting Anat parent") ;
} else if( aset_code == ASET_NULL ){
EDIT_ZERO_ANATOMY_PARENT_ID( dset ) ;
dset->anat_parent_name[0] = '\0' ;
VINFO("clearing Anat parent") ;
}
/* ZSS June 06, add a warp parent field please */
if( waset != NULL ){
EDIT_dset_items( dset , ADN_warp_parent , waset , ADN_none ) ;
VINFO("setting Warp parent") ;
} else if( waset_code == ASET_SELF ){
EDIT_dset_items( dset , ADN_warp_parent , dset , ADN_none ) ;
VINFO("setting Warp parent") ;
} else if( waset_code == ASET_NULL ){
EDIT_ZERO_ANATOMY_PARENT_ID( dset ) ;
dset->warp_parent_name[0] = '\0' ;
VINFO("clearing Warp parent") ;
}
/* Oct 04/02: zmodify volreg fields */
if (Do_volreg_mat) {
sprintf(str,"VOLREG_MATVEC_%06d", volreg_matind) ;
if( verb ) ININFO_message("Modifying %s ...\n", str);
THD_set_float_atr( dset->dblk , str , 12 , volreg_mat ) ;
}
if (Do_center_old) {
VINFO("Modifying VOLREG_CENTER_OLD ...\n");
THD_set_float_atr( dset->dblk , "VOLREG_CENTER_OLD" , 3 , center_old ) ;
}
if (Do_center_base) {
VINFO("Modifying VOLREG_CENTER_BASE ...\n");
THD_set_float_atr( dset->dblk , "VOLREG_CENTER_BASE" , 3 , center_base ) ;
}
/* 28 May 2002: clear brick stats */
if( clear_bstat ){
if( !ISVALID_STATISTIC(dset->stats) ){
WARNING_message("-clear_bstat: dataset has no brick statistics\n") ;
} else {
KILL_STATISTIC(dset->stats) ;
REMOVEFROM_KILL( dset->kl , dset->stats ) ;
REMOVEFROM_KILL( dset->kl , dset->stats->bstat ) ;
dset->stats = NULL ;
VINFO("clearing brick statistics") ;
}
}
if( redo_bstat ){
VINFO("reloading brick statistics") ;
THD_load_statistics( dset ) ; /* 01 Feb 2005 */
}
if( new_byte_order > 0 ){
VINFO("changing byte order") ;
dset->dblk->diskptr->byte_order = new_byte_order ; /* 25 April 1998 */
}
/*-- change space axes (lots of possibilities here) --*/
daxes = dset->daxes ;
if( new_orient ){
VINFO("changing orientation codes") ;
daxes->xxorient = xxor ;
daxes->yyorient = yyor ;
daxes->zzorient = zzor ;
}
if( xyzscale > 0.0f ){ /* 18 Jul 2006 */
float dxp = daxes->xxdel * xyzscale ; /* new grid */
float dyp = daxes->yydel * xyzscale ; /* spacings */
float dzp = daxes->zzdel * xyzscale ;
int rl = abs(THD_get_axis_direction(daxes,ORI_R2L_TYPE)) ;
int ap = abs(THD_get_axis_direction(daxes,ORI_A2P_TYPE)) ;
int is = abs(THD_get_axis_direction(daxes,ORI_I2S_TYPE)) ;
float xop , yop , zop ;
static float shift[3] ;
VINFO("applying -xyzscale") ;
if( rl == 0 || ap == 0 || is == 0 )
ERROR_exit("-xyzscale: Indeterminate axis directions!") ;
if( ndone == 0 ){ /* for the first dataset */
float op[3] , oo[3] ;
op[0] = xop = daxes->xxorg + (daxes->xxdel-dxp)*0.5f*(daxes->nxx-1) ;
op[1] = yop = daxes->yyorg + (daxes->yydel-dyp)*0.5f*(daxes->nyy-1) ;
op[2] = zop = daxes->zzorg + (daxes->zzdel-dzp)*0.5f*(daxes->nzz-1) ;
oo[0] = daxes->xxorg ;
oo[1] = daxes->yyorg ;
oo[2] = daxes->zzorg ;
shift[0] = op[rl-1] - xyzscale * oo[rl-1] ; /* RL shift */
shift[1] = op[ap-1] - xyzscale * oo[ap-1] ; /* AP shift */
shift[2] = op[is-1] - xyzscale * oo[is-1] ; /* IS shift */
} else { /* for later datasets */
xop = xyzscale * daxes->xxorg + shift[daxes->xxorient/2] ;
yop = xyzscale * daxes->yyorg + shift[daxes->yyorient/2] ;
zop = xyzscale * daxes->zzorg + shift[daxes->zzorient/2] ;
}
daxes->xxdel = dxp ; daxes->yydel = dyp ; daxes->zzdel = dzp ;
daxes->xxorg = xop ; daxes->yyorg = yop ; daxes->zzorg = zop ;
}
if( !new_xorg ) xorg = fabs(daxes->xxorg) ;
if( !new_yorg ) yorg = fabs(daxes->yyorg) ;
if( !new_zorg ) zorg = fabs(daxes->zzorg) ;
if( !new_xdel ) xdel = fabs(daxes->xxdel) ;
if( !new_ydel ) ydel = fabs(daxes->yydel) ;
if( !new_zdel ) zdel = fabs(daxes->zzdel) ;
/* 17 Jul 2006 - deal with the '-keepcen' option */
if( keepcen && !new_xdel && !new_ydel && !new_zdel ){
WARNING_message("-keepcen needs at least one of -xdel, -ydel, -zdel") ;
keepcen = 0 ;
}
if( keepcen && (new_xorg || new_yorg || new_zorg || new_orient) ){
WARNING_message(
"-keepcen incompatible with explicit origin or orientation changes") ;
keepcen = 0 ;
}
if( keepcen ){
VINFO("applying -keepcen") ;
if( new_xdel ){
dxorg = 1 ; xorg = 0.5f*(daxes->nxx-1)*(fabs(daxes->xxdel)-xdel) ;
if( ORIENT_sign[daxes->xxorient] == '-' ) xorg = -xorg ;
}
if( new_ydel ){
dyorg = 1 ; yorg = 0.5f*(daxes->nyy-1)*(fabs(daxes->yydel)-ydel) ;
if( ORIENT_sign[daxes->yyorient] == '-' ) yorg = -yorg ;
}
if( new_zdel ){
dzorg = 1 ; zorg = 0.5f*(daxes->nzz-1)*(fabs(daxes->zzdel)-zdel) ;
if( ORIENT_sign[daxes->zzorient] == '-' ) zorg = -zorg ;
}
}
if( cxorg ) xorg = 0.5 * (daxes->nxx - 1) * xdel ;
if( cyorg ) yorg = 0.5 * (daxes->nyy - 1) * ydel ;
if( czorg ) zorg = 0.5 * (daxes->nzz - 1) * zdel ;
if( dxorg )
daxes->xxorg += xorg ;
else if( duporg || new_xorg==2 )
daxes->xxorg = xorg ;
else if( new_xorg==1 || new_orient )
daxes->xxorg = (ORIENT_sign[daxes->xxorient] == '+') ? (-xorg) : (xorg) ;
if( dyorg )
daxes->yyorg += yorg ;
else if( duporg || new_yorg==2 )
daxes->yyorg = yorg ;
else if( new_yorg==1 || new_orient )
daxes->yyorg = (ORIENT_sign[daxes->yyorient] == '+') ? (-yorg) : (yorg) ;
if( dzorg )
daxes->zzorg += zorg ;
else if( duporg || new_zorg==2 )
daxes->zzorg = zorg ;
else if( new_zorg==1 || new_orient )
daxes->zzorg = (ORIENT_sign[daxes->zzorient] == '+') ? (-zorg) : (zorg) ;
if( new_xdel || new_orient )
daxes->xxdel = (ORIENT_sign[daxes->xxorient] == '+') ? (xdel) : (-xdel) ;
if( new_ydel || new_orient )
daxes->yydel = (ORIENT_sign[daxes->yyorient] == '+') ? (ydel) : (-ydel) ;
if( new_zdel || new_orient )
daxes->zzdel = (ORIENT_sign[daxes->zzorient] == '+') ? (zdel) : (-zdel) ;
/*-- change time axis --*/
if( new_TR ){
if( dset->taxis == NULL ){
if( DSET_NVALS(dset) < 2 ){
WARNING_message("Can't process -TR for this dataset!") ;
} else {
WARNING_message("Adding time axis to this dataset") ;
EDIT_dset_items( dset ,
ADN_ntt , DSET_NVALS(dset) ,
ADN_ttdel , TR ,
ADN_tunits, UNITS_SEC_TYPE ,
ADN_nsl , 0 ,
ADN_none ) ;
}
} else {
float frac = TR / dset->taxis->ttdel ;
int ii ;
VINFO("changing TR") ;
dset->taxis->ttdel = TR ;
if( new_tunits ) dset->taxis->units_type = tunits ;
if( dset->taxis->nsl > 0 ){
for( ii=0 ; ii < dset->taxis->nsl ; ii++ )
dset->taxis->toff_sl[ii] *= frac ;
}
}
}
if( new_Torg ){ /* 29 Jan 2003 */
if( dset->taxis == NULL ){
WARNING_message("Can't process -Torg for this dataset!\n") ;
} else {
VINFO("changing Torg") ;
dset->taxis->ttorg = Torg ;
}
}
if( new_toff_sl ){ /* 12 Feb 2001 */
if( dset->taxis == NULL ){
WARNING_message("-notoff: dataset has no time axis to clear!\n") ;
} else if( dset->taxis->nsl <= 0 ){
WARNING_message("-notoff: dataset has no time-offsets to clear!\n") ;
} else {
VINFO("clearing time-offsets") ;
EDIT_dset_items( dset , ADN_nsl,0 , ADN_none ) ;
}
}
if( (new_orient || new_zorg) && dset->taxis != NULL && dset->taxis->nsl > 0 ){
VINFO("changing time axis slice offset z-origin") ;
dset->taxis->zorg_sl = daxes->zzorg ;
}
if( (new_orient || new_zdel) && dset->taxis != NULL && dset->taxis->nsl > 0 ){
VINFO("changing time axis slice offset z-spacing") ;
dset->taxis->dz_sl = daxes->zzdel ;
}
if( new_idcode ){
VINFO("changing ID code") ;
dset->idcode = MCW_new_idcode() ;
}
if( new_nowarp ){
VINFO("clearing warp") ;
ZERO_IDCODE( dset->warp_parent_idcode ) ;
dset->warp_parent_name[0] = '\0' ;
dset->warp = NULL ;
}
if( new_type ){
if( nvals > 1 && dset->taxis != NULL ){
ERROR_message("Can't change 3D+time dataset to new type:\n"
" * new type has more than one value per voxel!\n") ;
} else if( dset->taxis == NULL && nvals != dset->dblk->nvals &&
((dtype==HEAD_FUNC_TYPE && ftype!=FUNC_BUCK_TYPE)||
(dtype==HEAD_ANAT_TYPE && ftype!=ANAT_BUCK_TYPE) ) ){
ERROR_message("Can't change dataset to new type:\n"
" * mismatch in number of sub-bricks!\n") ;
} else {
VINFO("changing dataset 'type' marker") ;
dset->type = dtype ;
dset->func_type = ftype ;
if( ISBUCKET(dset) && dset->taxis != NULL ){ /* 29 April 1998 */
WARNING_message("changing 3D+time dataset to bucket\n") ;
EDIT_dset_items( dset , ADN_ntt , 0 , ADN_none ) ;
}
}
}
if( new_stataux ){
for( ii=0 ; ii < MAX_STAT_AUX ; ii++ ){
dset->stat_aux[ii] = stataux[ii] ;
}
}
if( new_view && dset->view_type != vtype ){
int old_vtype = dset->view_type ;
char old_head[THD_MAX_NAME] , old_brik[THD_MAX_NAME] ;
char new_head[THD_MAX_NAME] , new_brik[THD_MAX_NAME] ;
int brick_ccode = COMPRESS_filecode( DSET_BRIKNAME(dset) ) ;
VINFO("changing dataset view code") ;
strcpy(old_head,DSET_HEADNAME(dset)) ;
strcpy(old_brik,DSET_BRIKNAME(dset)) ;
dset->view_type = vtype ;
THD_init_diskptr_names( dset->dblk->diskptr ,
NULL , NULL , NULL , vtype , True ) ;
strcpy(new_head,DSET_DIRNAME(dset)) ; strcat(new_head,DSET_HEADNAME(dset)) ;
strcpy(new_brik,DSET_DIRNAME(dset)) ; strcat(new_brik,DSET_BRIKNAME(dset)) ;
if( THD_is_file(new_head) ){
dset->view_type = old_vtype ;
THD_init_diskptr_names( dset->dblk->diskptr ,
NULL , NULL , NULL , old_vtype , True ) ;
ERROR_message("Can't change view: would overwrite existing files!\n") ;
} else {
rename( old_head , new_head ) ;
{ char * fff = COMPRESS_filename(old_brik) ;
if( fff != NULL ){
char * ggg = malloc( sizeof(char) * (strlen(fff)+32) ) ;
strcpy(ggg,new_brik) ;
if( brick_ccode >= 0 ) strcat(ggg,COMPRESS_suffix[brick_ccode]) ;
rename( fff , ggg ) ;
free(fff) ; free(ggg) ;
}
}
ININFO_message("Changed dataset view type and filenames.\n") ;
}
}
/* check for tag shifts 08 May 2006 [rickr] */
if( new_tags || shift_tags ){
THD_usertag * tag;
if( !dset->tagset ) WARNING_message("No tags to shift\n") ;
else {
ININFO_message("modifying tags") ;
for( ii = 0; ii < dset->tagset->num; ii++ ){
tag = dset->tagset->tag + ii ;
tag->x += dxtag; tag->y += dytag; tag->z += dztag;
}
}
} else if ( dset->tagset && ( new_xorg || new_yorg || new_zorg ||
new_xdel || new_ydel || new_zdel ) )
WARNING_message("modifying coordinates of dataset with tags") ;
/* code moved to edt_emptycopy.c 13 Sep 2005 [rickr] */
if( new_markers && okay_to_add_markers(dset) ){
dset->markers = create_empty_marker_set() ;
} else if( new_markers ){
WARNING_message("Can't add markers to this dataset\n") ;
} /* end of markers */
/*-- 08 Jun 2004: copyaux? --*/
if( copyaux ){
if( auxset != NULL ){
THD_copy_datablock_auxdata( auxset->dblk , dset->dblk );
INIT_STAT_AUX( dset , MAX_STAT_AUX , auxset->stat_aux ) ;
} else {
THD_copy_datablock_auxdata( NULL , dset->dblk );
}
}
/*-- new aux data? --*/
if( nsublab > 0 ){
for( ii=0 ; ii < nsublab ; ii++ ){
iv = sublab[ii].iv ;
if( iv < 0 || iv >= DSET_NVALS(dset) ){
WARNING_message("Can't put label on sub-brick %d\n",iv) ;
} else {
EDIT_dset_items( dset ,
ADN_brick_label_one + iv , sublab[ii].lab ,
ADN_none ) ;
}
}
}
if( nsubkeyword > 0 ){
int code ;
for( ii=0 ; ii < nsubkeyword ; ii++ ){
iv = subkeyword[ii].iv ; code = subkeyword[ii].code ;
if( iv < 0 || iv >= DSET_NVALS(dset) ){
WARNING_message("Can't put keyword on sub-brick %d\n",iv) ;
} else if( code == 1 ){
EDIT_dset_items( dset ,
ADN_brick_keywords_append_one + iv ,
subkeyword[ii].keyword ,
ADN_none ) ;
} else if( code == 2 ){
EDIT_dset_items( dset ,
ADN_brick_keywords_replace_one + iv ,
subkeyword[ii].keyword ,
ADN_none ) ;
} else if( code == 3 && dset->dblk->brick_keywords != NULL ){
EDIT_dset_items( dset ,
ADN_brick_keywords_replace_one + iv ,
NULL ,
ADN_none ) ;
}
}
}
switch( new_key ){
case 1: EDIT_dset_items(dset, ADN_keywords_append , key , ADN_none); break;
case 2: EDIT_dset_items(dset, ADN_keywords_replace, key , ADN_none); break;
case 3: EDIT_dset_items(dset, ADN_keywords_replace, NULL, ADN_none); break;
}
if( nsubstatpar > 0 ){
for( ii=0 ; ii < nsubstatpar ; ii++ ){
iv = substatpar[ii].iv ;
if( iv < 0 || iv >= DSET_NVALS(dset) ){
WARNING_message("Can't put statpar on sub-brick %d",iv) ;
} else {
EDIT_dset_items( dset ,
ADN_brick_stataux_one + iv , substatpar[ii].par ,
ADN_none ) ;
}
}
}
/* 03 Aug 2005: implement atrcopy */
for( ii=0 ; ii < num_atrcopy ; ii++ ) {
THD_insert_atr( dset->dblk , atrcopy[ii] ) ;
}
/* Do we want to force new attributes into output ? ZSS Jun 06*/
/* (only if -atrcopy or -atrstring) 28 Jul 2006 [rickr] */
if ( saveatr && atrmod )
THD_datablock_from_atr(dset->dblk , DSET_DIRNAME(dset) ,
dset->dblk->diskptr->header_name);
if( denote ) THD_anonymize_write(1) ; /* 08 Jul 2005 */
if( write_output ) DSET_load(dset) ; /* 20 Jun 2006 */
putenv("AFNI_DONT_DECONFLICT=YES") ; /* 07 Jun 2007 */
THD_write_3dim_dataset( NULL,NULL , dset , write_output ) ;
THD_delete_3dim_dataset( dset , False ) ;
ndone++ ; /* 18 Jul 2006: number of datasets done */
} /* end of loop over datasets to be refitted */
/*--- DONE ---*/
INFO_message("3drefit processed %d datasets",ndone) ;
exit(0) ;
}
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