Doxygen Source Code Documentation
to3d.c File Reference
#include "to3d.h"Go to the source code of this file.
Defines | |
| #define | LABEL_ARG(str) XtVaTypedArg , XmNlabelString , XmRString , (str) , strlen(str)+1 |
| #define | NZBOT 1 |
| #define | FatalError(str) ( fprintf(stderr,"\n*** %s\n\n try 'to3d -help'\n",(str)) , exit(1) ) |
| #define | CURSOR_normalize |
| #define | CURSOR_watchize |
| #define | EMPTY_STRING(str) ((str)[0] = '\0') |
| #define | WarningError(str) { fprintf(stderr,"\n***Warning: %s\n",(str)) ; nopt++ ; continue ; } |
| #define | OUTERR "*** ILLEGAL INPUTS (cannot save) ***\n\n" |
| #define | DEBLANK(str) |
| #define | INERR "*** DATASET READ ERROR ***\n\n" |
| #define | NAME2INT(nnn, iii, bot, top) |
| #define | NAME2FLOAT(nnn, fff, bot, top) |
| #define | NAME2STRING(nnn, sss) |
| #define | BAD -999 |
Functions | |
| void | AFNI_handler (char *msg) |
| void | AFNI_startup_timeout_CB (XtPointer client_data, XtIntervalId *id) |
| int | main (int argc, char *argv[]) |
| void | T3D_create_widgets (void) |
| void | T3D_initialize_user_data (void) |
| void | Syntax () |
| void | T3D_centered_CB (Widget w, XtPointer client_data, XtPointer call_data) |
| void | T3D_set_dependent_geometries (void) |
| void | T3D_voxshape_CB (Widget w, XtPointer client_data, XtPointer call_data) |
| char * | T3D_text_display (MCW_arrowval *av, XtPointer cd) |
| void | T3D_quit_timeout_CB (XtPointer client_data, XtIntervalId *id) |
| void | T3D_quit_CB (Widget wcall, XtPointer client_data, XtPointer call_data) |
| void | T3D_swap_CB (Widget w, XtPointer cd, XtPointer call_data) |
| void | T3D_fov_av_CB (MCW_arrowval *av, XtPointer cd) |
| void | T3D_orient_av_CB (MCW_arrowval *av, XtPointer cd) |
| void | T3D_origin_av_CB (MCW_arrowval *av, XtPointer cd) |
| void | T3D_size_av_CB (MCW_arrowval *av, XtPointer cd) |
| void | T3D_type_av_CB (MCW_arrowval *av, XtPointer cd) |
| void | T3D_fix_dataset_dimen (void) |
| void | T3D_read_images (void) |
| void | T3D_open_view_CB (Widget w, XtPointer client_data, XtPointer call_data) |
| XtPointer | T3D_getim (int n, int type, FD_brick *br) |
| void | T3D_imseq_CB (MCW_imseq *seq, FD_brick *br, ISQ_cbs *cbs) |
| void | T3D_save_file_CB (Widget w, XtPointer client_data, XtPointer call_data) |
| void | T3D_widgets_to_data (void) |
| void | T3D_data_to_widgets (void) |
| Boolean | T3D_check_data (Boolean perr) |
| void | T3D_poperr (char *prefix_msg, char *msg) |
| void | T3D_pointer_leave_EV (Widget w, XtPointer client_data, XEvent *ev, Boolean *continue_to_dispatch) |
| void | T3D_geometry_parent_CB (Widget w, XtPointer client_data, XtPointer call_data) |
| void | T3D_anatomy_parent_CB (Widget w, XtPointer client_data, XtPointer call_data) |
| void | AFNI_load_defaults (Widget w) |
| void | T3D_stat_aux_CB (Widget w, XtPointer client_data, XtPointer call_data) |
| void | T3D_setup_stat_aux (void) |
| int | decode_location (char *str, float *val, int *dcode) |
| void | T3D_check_outliers (int opcode) |
Variables | |
| to3d_widget_set | wset |
| to3d_data | user_inputs |
| THD_3dim_dataset * | dset = NULL |
| THD_datablock * | dblk = NULL |
| THD_dataxes * | daxes = NULL |
| THD_diskptr * | dkptr = NULL |
| THD_marker_set * | markers = NULL |
| THD_string_array * | imnames = NULL |
| int | outliers_checked = 0 |
| char * | outliers_fname = NULL |
| int | Argc |
| int | First_Image_Arg = 1 |
| char ** | Argv |
| char * | dbrick = NULL |
| int | geomparent_loaded = 0 |
| int | geometry_loaded = 0 |
| int | negative_shorts = 0 |
| int | nvox_total = 0 |
| int | nfloat_err = 0 |
| float | imdx = 0.0 |
| float | imdy = 0.0 |
| float | imdz = 0.0 |
| float | zpad = 0 |
| int | zpad_mm = 0 |
| float | zoff |
| int | use_zoff = 0 |
| int | af_type_set = 0 |
| struct { | |
| int ncolor | |
| float gamma | |
| Boolean xtwarns | |
| float gsfac | |
| int datum_all | |
| int delay_input | |
| int editing | |
| int swap_two | |
| int swap_four | |
| int nofloatscan | |
| int swap_eight | |
| } | argopt |
| char * | FALLback [] |
| char * | commandline = NULL |
| to3d_data | default_user_inputs |
Define Documentation
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Value: do{ NORMAL_cursorize(wset.topshell) ; \ XSync( XtDisplay(wset.topshell), False ) ; \ XmUpdateDisplay( wset.topshell ) ; } while(0) Definition at line 100 of file to3d.c. Referenced by AFNI_startup_timeout_CB(), and T3D_check_outliers(). |
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Value: do{ WATCH_cursorize(wset.topshell) ; \ XSync( XtDisplay(wset.topshell), False ) ; \ XmUpdateDisplay( wset.topshell ) ; } while(0) Definition at line 105 of file to3d.c. Referenced by T3D_check_outliers(). |
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Value: { int iq ; \
for( iq=strlen(str)-1; iq >= 0 && str[iq]==' '; iq-- )str[iq]='\0'; \
}Definition at line 5336 of file to3d.c. Referenced by T3D_anatomy_parent_CB(), and T3D_geometry_parent_CB(). |
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Definition at line 5341 of file to3d.c. Referenced by T3D_anatomy_parent_CB(), and T3D_geometry_parent_CB(). |
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Definition at line 9 of file to3d.c. Referenced by T3D_create_widgets(). |
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Value: { xdef = RWC_getname(display,nnn) ; \
if( xdef != NULL ){ \
fval = strtod( xdef , &cpt ) ; \
if( *cpt == '\0' && fval >= (bot) && fval <= (top) ) (fff) = fval ; } } |
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Value: { xdef = RWC_getname(display,nnn) ; \
if( xdef != NULL ){ \
ival = strtol( xdef , &cpt , 10 ) ; \
if( *cpt == '\0' && ival >= (bot) && ival <= (top) ) (iii) = ival ; } } |
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Value: { xdef = RWC_getname(display,nnn) ; \
if( xdef != NULL ) sss = XtNewString(xdef) ; } |
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Definition at line 12 of file to3d.c. Referenced by Syntax(), T3D_initialize_user_data(), and T3D_read_images(). |
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Definition at line 5150 of file to3d.c. Referenced by T3D_check_data(). |
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Definition at line 1939 of file to3d.c. Referenced by T3D_initialize_user_data(). |
Function Documentation
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16 July 1997: orientation code change * Definition at line 98 of file to3d.c. Referenced by main().
00098 {}
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Definition at line 110 of file to3d.c. References AFNI_yesenv(), to3d_widget_set::anatomy_parent_label, client_data, CURSOR_normalize, to3d_widget_set::geometry_parent_label, MCW_help_CB(), MCW_popup_message(), MCW_TIMER_KILL, MCW_USER_KILL, myXtFree, myXtNew, negative_shorts, nfloat_err, THD_timeaxis::ntt, to3d_data::ntt, nvox_total, outliers_checked, T3D_check_outliers(), and THD_3dim_dataset::taxis. Referenced by main().
00111 {
00112 char msg[512] ;
00113
00114 MCW_help_CB(NULL,NULL,NULL) ;
00115 CURSOR_normalize ;
00116
00117 if( negative_shorts && !AFNI_yesenv("AFNI_NO_NEGATIVES_WARNING") ){ /* 19 Jan 2000 */
00118 float perc = (100.0*negative_shorts)/nvox_total ;
00119 sprintf(msg , " \n"
00120 " to3d WARNING: %d negative voxels (%g%%)\n"
00121 " were read in images of shorts.\n"
00122 " It is possible the input\n"
00123 " images need byte-swapping.\n \n"
00124 " ** I recommend that you View Images. **\n" ,
00125 negative_shorts , perc ) ;
00126
00127 (void) MCW_popup_message( wset.anatomy_parent_label , msg ,
00128 MCW_USER_KILL | MCW_TIMER_KILL ) ;
00129 }
00130
00131 if( nfloat_err ){ /* 20 Jan 2000 */
00132 sprintf(msg , " \n"
00133 " to3d WARNING: %d errors in floating point images\n"
00134 " were detected. It is possible that\n"
00135 " the inputs need to be 4swap-ed, or\n"
00136 " otherwise repaired.\n \n"
00137 " ** Erroneous values have been replaced by **\n"
00138 " ** zeros. I recommend that you View Images. **\n" ,
00139 nfloat_err ) ;
00140
00141 (void) MCW_popup_message( wset.geometry_parent_label , msg ,
00142 MCW_USER_KILL | MCW_TIMER_KILL ) ;
00143 }
00144
00145 if( user_inputs.ntt > 5 ){ /* 15 Aug 2001 */
00146 dset->taxis = myXtNew( THD_timeaxis ) ;
00147 dset->taxis->ntt = user_inputs.ntt ;
00148 T3D_check_outliers(0) ; outliers_checked = 1 ;
00149 myXtFree(dset->taxis) ;
00150 }
00151 }
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Definition at line 5743 of file to3d.c. References ORCODE, and strtod(). Referenced by T3D_initialize_user_data().
05744 {
05745 char acod , * ptr , * sstr = str ;
05746
05747 *val = WAY_BIG ;
05748 *dcode = ILLEGAL_TYPE ;
05749 if( sstr == NULL || sstr[0] == '\0' ) return 0 ;
05750
05751 /** see if we get a legal direction code here **/
05752
05753 acod = toupper(sstr[0]) ; *dcode = ORCODE(acod) ;
05754 if( *dcode >= 0 ) sstr++ ;
05755
05756 if( sstr[0] == '\0' ) return ((*dcode < 0) ? 0 : 1) ;
05757
05758 /** get number here **/
05759
05760 *val = strtod( sstr , &ptr ) ;
05761 if( *val == 0.0 && ptr == sstr ) return ((*dcode < 0) ? 0 : 1) ;
05762 sstr = ptr ;
05763
05764 if( *dcode >= 0 || sstr[0] == '\0' ) return (sstr-str) ;
05765
05766 acod = toupper(sstr[0]) ; *dcode = ORCODE(acod) ;
05767 if( *dcode >= 0 ) sstr++ ;
05768
05769 return (sstr-str) ;
05770 }
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Definition at line 157 of file to3d.c. References addto_args(), AFNI_handler(), AFNI_load_defaults(), AFNI_noenv(), AFNI_startup_timeout_CB(), to3d_data::anatomy_parent_filename, Argc, argc, argopt, Argv, enable_mcw_malloc(), FALLback, to3d_data::fov, GAMMA, geometry_loaded, to3d_data::geometry_parent_filename, geomparent_loaded, to3d_widget_set::good, imdx, imdy, imdz, machdep(), mainENTRY, MCW_help_CB(), MCW_hint_toggle(), MCW_isitmwm, negative_shorts, NGRAY, to3d_data::nosave, to3d_data::ntt, nvox_total, to3d_data::nx, to3d_data::ny, to3d_data::nz, to3d_data::nzz, ORCODE, STATUS, T3D_anatomy_parent_CB(), T3D_check_data(), T3D_create_widgets(), T3D_geometry_parent_CB(), T3D_initialize_user_data(), T3D_read_images(), T3D_save_file_CB(), to3d_widget_set::topshell, to3d_data::tpattern, to3d_data::TR, to3d_data::tunits, UNITS_SEC_TYPE, UNITS_TYPE_LABEL, to3d_data::voxshape, VOXSHAPE_CUBICAL, VOXSHAPE_IRREGULAR, VOXSHAPE_SQUARE, XCENTERED, to3d_data::xincode, to3d_data::xorient, to3d_data::xorigin, to3d_data::xsize, to3d_data::xyz_centered, YCENTERED, to3d_data::yincode, to3d_data::yorient, to3d_data::yorigin, to3d_data::ysize, ZCENTERED, to3d_data::zincode, zoff, to3d_data::zorient, to3d_data::zorigin, and to3d_data::zsize.
00158 {
00159 XtAppContext app ;
00160 XtErrorHandler old_handler ;
00161 Boolean all_good ;
00162
00163 mainENTRY("to3d:main") ;
00164 machdep() ; /* RWCox: 20 Apr 2001 */
00165
00166 if( DBG_trace ){ /* 10 Sep 2002 */
00167 fprintf(stderr,"Enabling mcw_malloc()\n") ;
00168 enable_mcw_malloc() ;
00169 }
00170
00171 /* read the user data from the command line, if any */
00172
00173 wset.topshell = NULL ; /* flag that X has yet to start */
00174 wset.good = 0 ;
00175
00176 /* initialize defaults for command line arguments
00177 that aren't related to dataset construction */
00178
00179 INIT_ngray = NGRAY ;
00180 INIT_gamma = GAMMA ;
00181 INIT_fov = 240.0 ;
00182 argopt.ncolor = -1 ;
00183 argopt.gamma = -1.0 ;
00184 argopt.xtwarns = False ; /* don't show Xt warnings */
00185 argopt.gsfac = 0.0 ; /* no global scaling factor */
00186 argopt.datum_all = ILLEGAL_TYPE ; /* use first image type */
00187 #ifdef USE_MRI_DELAY
00188 argopt.delay_input = FALSE ;
00189 #endif
00190 argopt.editing = FALSE ;
00191
00192 argopt.swap_two = argopt.swap_four = 0 ; /* 14 Sep 1998 */
00193 argopt.swap_eight = 0 ; /* 06 Feb 2003 */
00194
00195 argopt.nofloatscan = 0 ; /* 14 Sep 1999 */
00196
00197 /* read the inputs */
00198
00199 printf("to3d: 2D slices into 3D datasets for AFNI, by RW Cox\n") ;
00200
00201 /*-- 20 Apr 2001: addto the arglist, if user wants to --*/
00202
00203 { int new_argc ; char ** new_argv ;
00204 addto_args( argc , argv , &new_argc , &new_argv ) ;
00205 if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; }
00206 }
00207
00208 Argc = argc ; Argv = argv ;
00209
00210 T3D_initialize_user_data() ;
00211
00212 if( user_inputs.nosave ){
00213 printf("Opening X11 now") ; fflush(stdout) ;
00214 wset.topshell = XtVaAppInitialize( &app , "AFNI" , NULL , 0 ,
00215 &argc , argv , FALLback , NULL ) ;
00216 printf("..opened\n") ;
00217 }
00218
00219 T3D_read_images() ;
00220
00221 if( negative_shorts ){
00222 float perc = (100.0*negative_shorts)/nvox_total ;
00223 fprintf(stderr,
00224 "to3d WARNING: %d negative voxels (%g%%) were read in images of shorts.\n"
00225 " It is possible the input images need byte-swapping.\n",
00226 negative_shorts , perc ) ;
00227 }
00228
00229 if( strlen(user_inputs.geometry_parent_filename) > 0 )
00230 T3D_geometry_parent_CB( NULL , NULL , NULL ) ;
00231
00232 if( strlen(user_inputs.anatomy_parent_filename) > 0 )
00233 T3D_anatomy_parent_CB( NULL , NULL , NULL ) ;
00234
00235 /* 05 Feb 2001: [10 May 2001: moved up above auto-save]
00236 if geometry not loaded at all, maybe use globals imdx, etc. */
00237
00238 if( ! (geomparent_loaded || geometry_loaded) ){
00239 if( imdx <= 0.0 || imdy <= 0.0 ){
00240
00241 STATUS("setting default FOV") ;
00242
00243 user_inputs.fov = INIT_fov ; /* the old code */
00244
00245 } else { /* the new code */
00246 float size ;
00247
00248 STATUS("setting voxel size from imdx, etc.") ;
00249
00250 user_inputs.xsize = imdx ;
00251 user_inputs.ysize = imdy ;
00252 if( imdz > 0.0 ) user_inputs.zsize = imdz ;
00253
00254 /* 10 May 2001: make sure axes are centered */
00255
00256 size = 0.5 * (user_inputs.nx-1) * user_inputs.xsize ;
00257 user_inputs.xorigin = size ;
00258
00259 size = 0.5 * (user_inputs.ny-1) * user_inputs.ysize ;
00260 user_inputs.yorigin = size ;
00261
00262 size = 0.5 * (user_inputs.nz-1) * user_inputs.zsize ;
00263 user_inputs.zorigin = size ;
00264
00265 user_inputs.xyz_centered = (XCENTERED|YCENTERED|ZCENTERED) ;
00266
00267 /* adjust voxel shape flag (for widget initialization) */
00268
00269 if( user_inputs.xsize != user_inputs.ysize ){
00270 user_inputs.voxshape = VOXSHAPE_IRREGULAR ;
00271 } else {
00272 if( user_inputs.xsize != user_inputs.zsize ){
00273 user_inputs.voxshape = VOXSHAPE_SQUARE ;
00274 } else {
00275 user_inputs.voxshape = VOXSHAPE_CUBICAL ;
00276 }
00277 }
00278 user_inputs.fov = user_inputs.xsize * user_inputs.nx ;
00279 }
00280
00281 /* 12 Mar 2001: MRILIB_ global variables may contain useful info */
00282
00283 if( MRILIB_orients[0] != '\0' &&
00284 user_inputs.xorient == user_inputs.yorient &&
00285 user_inputs.xorient == user_inputs.zorient ){
00286
00287 char acod ; int icod ;
00288
00289 STATUS("setting orientation from MRILIB_orients") ;
00290
00291 acod=toupper(MRILIB_orients[0]); icod=ORCODE(acod); if(icod >= 0) user_inputs.xorient=icod;
00292 acod=toupper(MRILIB_orients[2]); icod=ORCODE(acod); if(icod >= 0) user_inputs.yorient=icod;
00293 acod=toupper(MRILIB_orients[4]); icod=ORCODE(acod); if(icod >= 0) user_inputs.zorient=icod;
00294
00295 if( use_MRILIB_zoff ){ /* use offset to voxel center from mri_read() */
00296 if( fabs(user_inputs.zorigin-MRILIB_zoff) > 0.01 ){
00297 user_inputs.zorigin = MRILIB_zoff ;
00298 user_inputs.xyz_centered &= ~ZCENTERED ;
00299 }
00300 }
00301
00302 if( use_MRILIB_xoff ){ /* 20 Dec 2001 */
00303 if( fabs(user_inputs.xorigin-MRILIB_xoff) > 0.01 ){
00304 user_inputs.xorigin = MRILIB_xoff ;
00305 user_inputs.xyz_centered &= ~XCENTERED ;
00306 }
00307 }
00308
00309 if( use_MRILIB_yoff ){ /* 20 Dec 2001 */
00310 if( fabs(user_inputs.yorigin-MRILIB_yoff) > 0.01 ){
00311 user_inputs.yorigin = MRILIB_yoff ;
00312 user_inputs.xyz_centered &= ~YCENTERED ;
00313 }
00314 }
00315 }
00316
00317 /* 10 May 2001: use global zoff, if given [will override MRILIB_zoff] */
00318
00319 if( use_zoff ){
00320 user_inputs.zorigin = zoff ;
00321 user_inputs.xyz_centered &= ~ZCENTERED ;
00322 }
00323 }
00324
00325 all_good = T3D_check_data( False ) ;
00326
00327 /** Mar 1997: if any FOV or SLAB command line inputs are used,
00328 then require that they all be given. **/
00329
00330 if( all_good ){
00331 int iii = (user_inputs.xincode > 0)
00332 + (user_inputs.yincode > 0) + (user_inputs.zincode > 0) ;
00333
00334 if( iii > 0 && iii < 3 ) all_good = False ;
00335 }
00336
00337 /* 03 Dec 2001: MRILIB_tr may have TR */
00338
00339 if( user_inputs.ntt > 1 && MRILIB_tr > 0.0 ){
00340 if( user_inputs.TR <= 0.0 ){
00341 int ii ;
00342 user_inputs.TR = MRILIB_tr ;
00343 user_inputs.tunits = UNITS_SEC_TYPE ;
00344 if( user_inputs.tpattern != NULL ){
00345 for( ii=0 ; ii < user_inputs.nzz ; ii++ ){
00346 user_inputs.tpattern[ii] *= MRILIB_tr ;
00347 }
00348 }
00349 printf("Setting TR=%gs from image header\n",MRILIB_tr) ;
00350
00351 } else {
00352 printf("Command line TR=%g%s ; Images TR=%gs\n",
00353 user_inputs.TR,UNITS_TYPE_LABEL(user_inputs.tunits),MRILIB_tr) ;
00354 }
00355 }
00356 if( user_inputs.ntt > 1 && user_inputs.TR <= 0.0 ){
00357 printf("Setting TR=1s by default\n") ;
00358 user_inputs.TR = 1.0 ; user_inputs.tunits = UNITS_SEC_TYPE ;
00359 }
00360
00361 if( all_good && !user_inputs.nosave ){ /* done! */
00362 T3D_save_file_CB( NULL , NULL , NULL ) ;
00363 printf("3D dataset written to disk\n") ;
00364 exit(0) ;
00365 }
00366
00367 /* Otherwise, initialize X11 and Xt */
00368
00369 printf("Making widgets") ; fflush(stdout) ;
00370
00371 if( wset.topshell == NULL )
00372 wset.topshell = XtVaAppInitialize( &app , "AFNI" , NULL , 0 ,
00373 &argc , argv , FALLback , NULL ) ;
00374
00375 AFNI_load_defaults( wset.topshell ) ;
00376 if( argopt.ncolor <= 2 ) argopt.ncolor = INIT_ngray ;
00377 if( argopt.gamma <= 0.0 ) argopt.gamma = INIT_gamma ;
00378
00379 if( argopt.xtwarns == False )
00380 old_handler = XtAppSetWarningHandler(app,AFNI_handler) ; /* turn off */
00381
00382 if( MCW_isitmwm(wset.topshell) ){
00383 XtVaSetValues( wset.topshell ,
00384 XmNmwmDecorations ,
00385 MWM_DECOR_ALL | MWM_DECOR_RESIZEH | MWM_DECOR_MAXIMIZE ,
00386 NULL ) ;
00387
00388 /* turn off Drag-n-Drop (courtesy the Motif FAQ) */
00389
00390 XtVaSetValues( XmGetXmDisplay(XtDisplay(wset.topshell)) ,
00391 XmNdragInitiatorProtocolStyle , XmDRAG_NONE ,
00392 XmNdragReceiverProtocolStyle , XmDRAG_NONE ,
00393 NULL ) ;
00394 }
00395
00396 /* make the rest of the widgets */
00397
00398 T3D_create_widgets() ;
00399 MCW_help_CB(wset.topshell,NULL,NULL) ; /* initialize help widget */
00400
00401 printf("\n") ; fflush(stdout) ;
00402
00403 if( AFNI_noenv("AFNI_HINTS") ) MCW_hint_toggle() ;
00404
00405 /* let the user do the rest */
00406
00407 (void) XtAppAddTimeOut( app , 999 , AFNI_startup_timeout_CB , NULL ) ;
00408 XtAppMainLoop(app) ;
00409 exit(0) ;
00410 }
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31 July 1996: be more specific about errors * Definition at line 2927 of file to3d.c. References FIRST_ANAT_TYPE, FIRST_FUNC_TYPE, LAST_ANAT_TYPE, LAST_FUNC_TYPE, NO_NAMES, NZBOT, VIEW_ACPCALIGNED_CODE, VIEW_ORIGINAL_CODE, and VIEW_TALAIRACH_CODE.
02928 {
02929 int ii ;
02930
02931 printf(
02932 "Usage: to3d [options] image_files ...\n"
02933 " Creates 3D datasets for use with AFNI from 2D image files\n"
02934 "\n"
02935 "The available options are\n"
02936 " -help show this message\n"
02937 " -'type' declare images to contain data of a given type\n"
02938 " where 'type' is chosen from the following options:\n" ) ;
02939
02940 printf(" ANATOMICAL TYPES\n") ;
02941 for( ii=FIRST_ANAT_TYPE ; ii <= LAST_ANAT_TYPE ; ii++ )
02942 printf(" %8s == %s\n",ANAT_prefixstr[ii],ANAT_typestr[ii] ) ;
02943
02944 printf(" FUNCTIONAL TYPES\n") ;
02945 for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ )
02946 printf(" %8s == %s\n",FUNC_prefixstr[ii],FUNC_typestr[ii] ) ;
02947
02948 printf(
02949 " [for paired (+) types above, images are fim first,]\n"
02950 " [then followed by the threshold (etc.) image files]\n" ) ;
02951
02952 printf(
02953 "\n"
02954 " -statpar value value ... value [* NEW IN 1996 *]\n"
02955 " This option is used to supply the auxiliary statistical parameters\n"
02956 " needed for certain dataset types (e.g., 'fico' and 'fitt'). For\n"
02957 " example, a correlation coefficient computed using program 'fim2'\n"
02958 " from 64 images, with 1 ideal, and with 2 orts could be specified with\n"
02959 " -statpar 64 1 2\n"
02960 ) ;
02961
02962 printf(
02963 "\n"
02964 #ifndef NO_NAMES
02965 " -dname name will make 3D dataset's name = 'name'\n"
02966 " -dlabel name will make 3D dataset's short label = 'name'\n"
02967 #endif
02968 " -prefix name will write 3D dataset using prefix 'name'\n"
02969 " -session name will write 3D dataset into session directory 'name'\n"
02970 " -geomparent fname will read geometry data from dataset file 'fname'\n"
02971 " N.B.: geometry data does NOT include time-dependence\n"
02972 " -anatparent fname will take anatomy parent from dataset file 'fname'\n"
02973 "\n"
02974 " -nosave will suppress autosave of 3D dataset, which normally occurs\n"
02975 " when the command line options supply all needed data correctly\n"
02976 "\n"
02977 " -view type [* NEW IN 1996 *]\n"
02978 " Will set the dataset's viewing coordinates to 'type', which\n"
02979 " must be one of these strings: "
02980 VIEW_ORIGINAL_CODE " "
02981 VIEW_ACPCALIGNED_CODE " "
02982 VIEW_TALAIRACH_CODE "\n"
02983 ) ;
02984
02985 printf(
02986 "\n"
02987 "TIME DEPENDENT DATASETS [* NEW IN 1996 *]\n"
02988 " -time:zt nz nt TR tpattern OR -time:tz nt nz TR tpattern\n"
02989 "\n"
02990 " These options are used to specify a time dependent dataset.\n"
02991 " '-time:zt' is used when the slices are input in the order\n"
02992 " z-axis first, then t-axis.\n"
02993 " '-time:tz' is used when the slices are input in the order\n"
02994 " t-axis first, then z-axis.\n"
02995 "\n"
02996 " nz = number of points in the z-direction (minimum %d)\n"
02997 " nt = number of points in the t-direction\n"
02998 " (thus exactly nt * nz slices must be read in)\n"
02999 " TR = repetition interval between acquisitions of the\n"
03000 " same slice, in milliseconds (or other units, as given below)\n"
03001 "\n"
03002 " tpattern = Code word that identifies how the slices (z-direction)\n"
03003 " were gathered in time. The values that can be used:\n"
03004 "\n"
03005 " alt+z = altplus = alternating in the plus direction\n"
03006 " alt+z2 = alternating, starting at slice #1\n"
03007 " alt-z = altminus = alternating in the minus direction\n"
03008 " alt-z2 = alternating, starting at slice #nz-2\n"
03009 " seq+z = seqplus = sequential in the plus direction\n"
03010 " seq-z = seqminus = sequential in the minus direction\n"
03011 " zero = simult = simultaneous acquisition\n"
03012 " @filename = read temporal offsets from 'filename'\n"\
03013 "\n"
03014 " For example if nz = 5 and TR = 1000, then the inter-slice\n"
03015 " time is taken to be dt = TR/nz = 200. In this case, the\n"
03016 " slices are offset in time by the following amounts:\n"
03017 "\n"
03018 " S L I C E N U M B E R\n"
03019 " tpattern 0 1 2 3 4 Comment\n"
03020 " ---------- ---- ---- ---- ---- ---- -------------------------------\n"
03021 " altplus 0 600 200 800 400 Alternating in the +z direction\n"
03022 " alt+z2 400 0 600 200 800 Alternating, but starting at #1\n"
03023 " altminus 400 800 200 600 0 Alternating in the -z direction\n"
03024 " alt-z2 800 200 600 0 400 Alternating, starting at #nz-2 \n"
03025 " seqplus 0 200 400 600 800 Sequential in the +z direction\n"
03026 " seqminus 800 600 400 200 0 Sequential in the -z direction\n"
03027 " simult 0 0 0 0 0 All slices acquired at once\n"
03028 "\n"
03029 " If @filename is used for tpattern, then nz ASCII-formatted numbers are\n"
03030 " read from the file. These are used to indicate the time offsets (in ms)\n"
03031 " for each slice. For example, if 'filename' contains\n"
03032 " 0 600 200 800 400\n"
03033 " then this is equivalent to 'altplus' in the above example.\n"
03034 "\n"
03035 " Notes:\n"
03036 " * Time-dependent functional datasets are not yet supported by\n"
03037 " to3d or any other AFNI package software. For many users,\n"
03038 " the proper dataset type for these datasets is '-epan'.\n"
03039 " * Time-dependent datasets with more than one value per time point\n"
03040 " (e.g., 'fith', 'fico', 'fitt') are also not allowed by to3d.\n"
03041 " * If you use 'abut' to fill in gaps in the data and/or to\n"
03042 " subdivide the data slices, you will have to use the @filename\n"
03043 " form for tpattern, unless 'simult' or 'zero' is acceptable.\n"
03044 " * At this time, the value of 'tpattern' is not actually used in\n"
03045 " any AFNI program. The values are stored in the dataset\n"
03046 " .HEAD files, and will be used in the future.\n"
03047 " * The values set on the command line can't be altered interactively.\n"
03048 " * The units of TR can be specified by the command line options below:\n"
03049 " -t=ms or -t=msec --> milliseconds (the default)\n"
03050 " -t=s or -t=sec --> seconds\n"
03051 " -t=Hz or -t=Hertz --> Hertz (for chemical shift images?)\n"
03052 " Alternatively, the units symbol ('ms', 'msec', 's', 'sec',\n"
03053 " 'Hz', or 'Hertz') may be attached to TR in the '-time:' option,\n"
03054 " as in '-time:zt 16 64 4.0sec alt+z'\n"
03055
03056 "\n"
03057 " -Torg ttt = set time origin of dataset to 'ttt' [default=0.0]\n"
03058
03059 , NZBOT
03060 ) ;
03061
03062 printf(
03063 "\n"
03064 "COMMAND LINE GEOMETRY SPECIFICATION [* NEW IN 1996 *]\n"
03065 " -xFOV <dimen1><direc1>-<dimen2><direc2>\n"
03066 " or or\n"
03067 " -xSLAB <dimen1><direc1>-<direc2>\n"
03068 "\n"
03069 " (Similar -yFOV, -ySLAB, -zFOV and -zSLAB option are also present.)\n"
03070 "\n"
03071 " These options specify the size and orientation of the x-axis extent\n"
03072 " of the dataset. <dimen#> means a dimension (in mm); <direc> is\n"
03073 " an anatomical direction code, chosen from\n"
03074 " A (Anterior) P (Posterior) L (Left)\n"
03075 " I (Inferior) S (Superior) R (Right)\n"
03076 " Thus, 20A-30P means that the x-axis of the input images runs from\n"
03077 " 20 mm Anterior to 30 mm Posterior. For convenience, 20A-20P can be\n"
03078 " abbreviated as 20A-P.\n"
03079 "\n"
03080 " -xFOV is used to mean that the distances are from edge-to-edge of\n"
03081 " the outermost voxels in the x-direction.\n"
03082 " -xSLAB is used to mean that the distances are from center-to-center\n"
03083 " of the outermost voxels in the x-direction.\n"
03084 "\n"
03085 " Under most circumstance, -xFOV , -yFOV , and -zSLAB would be the\n"
03086 " correct combination of geometry specifiers to use. For example,\n"
03087 " a common type of run at MCW would be entered as\n"
03088 " -xFOV 120L-R -yFOV 120A-P -zSLAB 60S-50I\n"
03089 ) ;
03090
03091 printf(
03092 "\n"
03093 "Z-AXIS SLICE OFFSET ONLY\n"
03094 " -zorigin distz Puts the center of the 1st slice off at the\n"
03095 " given distance ('distz' in mm). This distance\n"
03096 " is in the direction given by the corresponding\n"
03097 " letter in the -orient code. For example,\n"
03098 " -orient RAI -zorigin 30\n"
03099 " would set the center of the first slice at\n"
03100 " 30 mm Inferior.\n"
03101 " N.B.: This option has no effect if the FOV or SLAB options\n"
03102 " described above are used.\n"
03103 ) ;
03104
03105 printf(
03106 "\n"
03107 "INPUT IMAGE FORMATS [* SIGNIFICANTLY CHANGED IN 1996 *]\n"
03108 " Image files may be single images of unsigned bytes or signed shorts\n"
03109 " (64x64, 128x128, 256x256, 512x512, or 1024x1024) or may be grouped\n"
03110 " images (that is, 3- or 4-dimensional blocks of data).\n"
03111 " In the grouped case, the string for the command line file spec is like\n"
03112 "\n"
03113 " 3D:hglobal:himage:nx:ny:nz:fname [16 bit input]\n"
03114 " 3Ds:hglobal:himage:nx:ny:nz:fname [16 bit input, swapped bytes]\n"
03115 " 3Db:hglobal:himage:nx:ny:nz:fname [ 8 bit input]\n"
03116 " 3Di:hglobal:himage:nx:ny:nz:fname [32 bit input]\n"
03117 " 3Df:hglobal:himage:nx:ny:nz:fname [floating point input]\n"
03118 " 3Dc:hglobal:himage:nx:ny:nz:fname [complex input]\n"
03119 " 3Dd:hglobal:himage:nx:ny:nz:fname [double input]\n"
03120 "\n"
03121 " where '3D:' or '3Ds': signals this is a 3D input file of signed shorts\n"
03122 " '3Db:' signals this is a 3D input file of unsigned bytes\n"
03123 " '3Di:' signals this is a 3D input file of signed ints\n"
03124 " '3Df:' signals this is a 3D input file of floats\n"
03125 " '3Dc:' signals this is a 3D input file of complex numbers\n"
03126 " (real and imaginary pairs of floats)\n"
03127 " '3Dd:' signals this is a 3D input file of double numbers\n"
03128 " (will be converted to floats)\n"
03129 " hglobal = number of bytes to skip at start of whole file\n"
03130 " himage = number of bytes to skip at start of each 2D image\n"
03131 " nx = x dimension of each 2D image in the file\n"
03132 " ny = y dimension of each 2D image in the file\n"
03133 " nz = number of 2D images in the file\n"
03134 " fname = actual filename on disk to read\n"
03135 "\n"
03136 " * The ':' separators are required. The k-th image starts at\n"
03137 " BYTE offset hglobal+(k+1)*himage+vs*k*nx*ny in file 'fname'\n"
03138 " for k=0,1,...,nz-1.\n"
03139 " * Here, vs=voxel length=1 for bytes, 2 for shorts, 4 for ints and floats,\n"
03140 " and 8 for complex numbers.\n"
03141 " * As a special case, hglobal = -1 means read data starting at\n"
03142 " offset len-nz*(vs*nx*ny+himage), where len=file size in bytes.\n"
03143 " (That is, to read the needed data from the END of the file.)\n"
03144 " * Note that there is no provision for skips between data rows inside\n"
03145 " a 2D slice, only for skips between 2D slice images.\n"
03146 " * The int, float, and complex formats presume that the data in\n"
03147 " the image file are in the 'native' format for this CPU; that is,\n"
03148 " there is no provision for data conversion (unlike the 3Ds: format).\n"
03149 " * Double input will be converted to floats (or whatever -datum is)\n"
03150 " since AFNI doesn't support double precision datasets.\n"
03151 " * Whether the 2D image data is interpreted as a 3D block or a 3D+time\n"
03152 " block depends on the rest of the command line parameters. The\n"
03153 " various 3D: input formats are just ways of inputting multiple 2D\n"
03154 " slices from a single file.\n"
03155 " * SPECIAL CASE: If fname is ALLZERO, then this means not to read\n"
03156 " data from disk, but instead to create nz nx*ny images filled\n"
03157 " with zeros. One application of this is to make it easy to create\n"
03158 " a dataset of a specified geometry for use with other programs.\n"
03159 "\n"
03160 "The 'raw pgm' image format is also supported; it reads data into 'byte' images.\n"
03161 "\n"
03162 "* ANALYZE (TM) .hdr/.img files can now be read - give the .hdr filename on\n"
03163 " the command line. The program will detect if byte-swapping is needed on\n"
03164 " these images, and can also set the voxel grid sizes from the first .hdr file.\n"
03165 " If the 'funused1' field in the .hdr is positive, it will be used to scale the\n"
03166 " input values. If the environment variable AFNI_ANALYZE_FLOATIZE is YES, then\n"
03167 " .img files will be converted to floats on input.\n"
03168 "\n"
03169 "* Siemens .ima image files can now be read. The program will detect if\n"
03170 " byte-swapping is needed on these images, and can also set voxel grid\n"
03171 " sizes and orientations (correctly, I hope).\n"
03172 "* Some Siemens .ima files seems to have their EPI slices stored in\n"
03173 " spatial order, and some in acquisition (interleaved) order. This\n"
03174 " program doesn't try to figure this out. You can use the command\n"
03175 " line option '-sinter' to tell the program to assume that the images\n"
03176 " in a single .ima file are interleaved; for example, if there are\n"
03177 " 7 images in a file, then without -sinter, the program will assume\n"
03178 " their order is '0 1 2 3 4 5 6'; with -sinter, the program will\n"
03179 " assume their order is '0 2 4 6 1 3 5' (here, the number refers\n"
03180 " to the slice location in space).\n"
03181 "\n"
03182 "* GEMS I.* (IMGF) 16-bit files can now be read. The program will detect\n"
03183 " if byte-swapping is needed on these images, and can also set voxel\n"
03184 " grid sizes and orientations. It can also detect the TR in the\n"
03185 " image header. If you wish to rely on this TR, you can set TR=0\n"
03186 " in the -time:zt or -time:tz option.\n"
03187 "* If you use the image header's TR and also use @filename for the\n"
03188 " tpattern, then the values in the tpattern file should be fractions\n"
03189 " of the true TR; they will be multiplied by the true TR once it is\n"
03190 " read from the image header.\n"
03191 "\n"
03192 " NOTES:\n"
03193 " * Not all AFNI programs support all datum types. Shorts and\n"
03194 " floats are safest. (See the '-datum' option below.)\n"
03195 " * If '-datum short' is used or implied, then int, float, and complex\n"
03196 " data will be scaled to fit into a 16 bit integer. If the '-gsfac'\n"
03197 " option below is NOT used, then each slice will be SEPARATELY\n"
03198 " scaled according to the following choice:\n"
03199 " (a) If the slice values all fall in the range -32767 .. 32767,\n"
03200 " then no scaling is performed.\n"
03201 " (b) Otherwise, the image values are scaled to lie in the range\n"
03202 " 0 .. 10000 (original slice min -> 0, original max -> 10000).\n"
03203 " This latter option is almost surely not what you want! Therefore,\n"
03204 " if you use the 3Di:, 3Df:, or 3Dc: input methods and store the\n"
03205 " data as shorts, I suggest you supply a global scaling factor.\n"
03206 " Similar remarks apply to '-datum byte' scaling, with even more force.\n"
03207 " * To3d now incoporates POSIX filename 'globbing', which means that\n"
03208 " you can input filenames using 'escaped wildcards', and then to3d\n"
03209 " will internally do the expansion to the list of files. This is\n"
03210 " only desirable because some systems limit the number of command-line\n"
03211 " arguments to a program. It is possible that you would wish to input\n"
03212 " more slice files than your computer supports. For example,\n"
03213 " to3d exp.?.*\n"
03214 " might overflow the system command line limitations. The way to do\n"
03215 " this using internal globbing would be\n"
03216 " to3d exp.\\?.\\*\n"
03217 " where the \\ characters indicate to pass the wildcards ? and *\n"
03218 " through to the program, rather than expand them in the shell.\n"
03219 " (a) Note that if you choose to use this feature, ALL wildcards in\n"
03220 " a filename must be escaped with \\ or NONE must be escaped.\n"
03221 " (b) Using the C shell, it is possible to turn off shell globbing\n"
03222 " by using the command 'set noglob' -- if you do this, then you\n"
03223 " do not need to use the \\ character to escape the wildcards.\n"
03224 " (c) Internal globbing of 3D: file specifiers is supported in to3d.\n"
03225 " For example, '3D:0:0:64:64:100:sl.\\*' could be used to input\n"
03226 " a series of 64x64x100 files with names 'sl.01', 'sl.02' ....\n"
03227 " This type of expansion is specific to to3d; the shell will not\n"
03228 " properly expand such 3D: file specifications.\n"
03229 " (d) In the C shell (csh or tcsh), you can use forward single 'quotes'\n"
03230 " to prevent shell expansion of the wildcards, as in the command\n"
03231 " to3d '3D:0:0:64:64:100:sl.*'\n"
03232 " The globbing code is adapted from software developed by the\n"
03233 " University of California, Berkeley, and is copyrighted by the\n"
03234 " Regents of the University of California (see file mcw_glob.c).\n"
03235 "\n"
03236 "RGB datasets [Apr 2002]\n"
03237 "-----------------------\n"
03238 "You can now create RGB-valued datasets. Each voxel contains 3 byte values\n"
03239 "ranging from 0..255. RGB values may be input to to3d in one of two ways:\n"
03240 " * Using raw PPM formatted 2D image files.\n"
03241 " * Using JPEG formatted 2D files.\n"
03242 " * Using TIFF, BMP, GIF, PNG formatted 2D files [if netpbm is installed].\n"
03243 " * Using the 3Dr: input format, analogous to 3Df:, etc., described above.\n"
03244 "RGB datasets can be created as functional FIM datasets, or as anatomical\n"
03245 "datasets:\n"
03246 " * RGB fim overlays are transparent in AFNI only where all three\n"
03247 " bytes are zero - that is, you can't overlay solid black.\n"
03248 " * At present, there is limited support for RGB datasets.\n"
03249 " About the only thing you can do is display them in 2D slice\n"
03250 " viewers in AFNI.\n"
03251 "You can also create RGB-valued datasets using program 3dThreetoRGB.\n"
03252 "\n"
03253 "Other Data Options\n"
03254 "------------------\n"
03255 " -2swap\n"
03256 " This option will force all input 2 byte images to be byte-swapped\n"
03257 " after they are read in.\n"
03258 " -4swap\n"
03259 " This option will force all input 4 byte images to be byte-swapped\n"
03260 " after they are read in.\n"
03261 " -8swap\n"
03262 " This option will force all input 8 byte images to be byte-swapped\n"
03263 " after they are read in.\n"
03264 " BUT PLEASE NOTE:\n"
03265 " Input images that are auto-detected to need byte-swapping\n"
03266 " (GEMS I.*, Siemens *.ima, ANALYZE *.img, and 3Ds: files)\n"
03267 " will NOT be swapped again by one of the above options.\n"
03268 " If you want to swap them again for some bizarre reason,\n"
03269 " you'll have to use the 'Byte Swap' button on the GUI.\n"
03270 " That is, -2swap/-4swap will swap bytes on input files only\n"
03271 " if they haven't already been swapped by the image input\n"
03272 " function.\n"
03273 "\n"
03274 " -zpad N OR\n"
03275 " -zpad Nmm \n"
03276 " This option tells to3d to write 'N' slices of all zeros on each side\n"
03277 " in the z-direction. This will make the dataset 'fatter', but make it\n"
03278 " simpler to align with datasets from other scanning sessions. This same\n"
03279 " function can be accomplished later using program 3dZeropad.\n"
03280 " N.B.: The zero slices will NOT be visible in the image viewer in to3d, but\n"
03281 " will be visible when you use AFNI to look at the dataset.\n"
03282 " N.B.: If 'mm' follows the integer N, then the padding is measured in mm.\n"
03283 " The actual number of slices of padding will be rounded up. So if\n"
03284 " the slice thickness is 5 mm, then '-zpad 16mm' would be the equivalent\n"
03285 " of '-zpad 4' -- that is, 4 slices on each z-face of the volume.\n"
03286 " N.B.: If the geometry parent dataset was created with -zpad, the spatial\n"
03287 " location (origin) of the slices is set using the geometry dataset's\n"
03288 " origin BEFORE the padding slices were added. This is correct, since\n"
03289 " you need to set the origin on the current dataset as if the padding\n"
03290 " slices were not present.\n"
03291 " N.B.: Unlike the '-zpad' option to 3drotate and 3dvolreg, this adds slices\n"
03292 " only in the z-direction.\n"
03293 " N.B.: You can set the environment variable 'AFNI_TO3D_ZPAD' to provide a\n"
03294 " default for this option.\n"
03295 "\n"
03296 " -gsfac value\n"
03297 " will scale each input slice by 'value'. For example,\n"
03298 " '-gsfac 0.31830989' will scale by 1/Pi (approximately).\n"
03299 " This option only has meaning if one of '-datum short' or\n"
03300 " '-datum byte' is used or implied. Otherwise, it is ignored.\n"
03301 "\n"
03302 " -datum type\n"
03303 " will set the voxel data to be stored as 'type', which is currently\n"
03304 " allowed to be short, float, byte, or complex.\n"
03305 " If -datum is not used, then the datum type of the first input image\n"
03306 " will determine what is used. In that case, the first input image will\n"
03307 " determine the type as follows:\n"
03308 " byte --> byte\n"
03309 " short --> short\n"
03310 " int, float --> float\n"
03311 " complex --> complex\n"
03312 " If -datum IS specified, then all input images will be converted\n"
03313 " to the desired type. Note that the list of allowed types may\n"
03314 " grow in the future, so you should not rely on the automatic\n"
03315 " conversion scheme. Also note that floating point datasets may\n"
03316 " not be portable between CPU architectures.\n"
03317 "\n"
03318 " -nofloatscan\n"
03319 " tells to3d NOT to scan input float and complex data files for\n"
03320 " illegal values - the default is to scan and replace illegal\n"
03321 " floating point values with zeros (cf. program float_scan).\n"
03322 #ifdef USE_MRI_DELAY
03323 "\n"
03324 " -in:1\n"
03325 " Input of huge 3D: files (with all the data from a 3D+time run, say)\n"
03326 " can cause to3d to fail from lack of memory. The reason is that\n"
03327 " the images are from a file are all read into RAM at once, and then\n"
03328 " are scaled, converted, etc., as needed, then put into the final\n"
03329 " dataset brick. This switch will cause the images from a 3D: file\n"
03330 " to be read and processed one slice at a time, which will lower the\n"
03331 " amount of memory needed. The penalty is somewhat more I/O overhead.\n"
03332 #endif
03333 ) ;
03334
03335 printf(
03336 "\n"
03337 "NEW IN 1997:\n"
03338 " -orient code\n"
03339 " Tells the orientation of the 3D volumes. The code must be 3 letters,\n"
03340 " one each from the pairs {R,L} {A,P} {I,S}. The first letter gives\n"
03341 " the orientation of the x-axis, the second the orientation of the\n"
03342 " y-axis, the third the z-axis:\n"
03343 " R = right-to-left L = left-to-right\n"
03344 " A = anterior-to-posterior P = posterior-to-anterior\n"
03345 " I = inferior-to-superior S = superior-to-inferior\n"
03346 " Note that the -xFOV, -zSLAB constructions can convey this information.\n"
03347 ) ;
03348
03349 printf(
03350 "\n"
03351 "NEW IN 2001:\n"
03352 " -skip_outliers\n"
03353 " If present, this tells the program to skip the outlier check that is\n"
03354 " automatically performed for 3D+time datasets. You can also turn this\n"
03355 " feature off by setting the environment variable AFNI_TO3D_OUTLIERS\n"
03356 " to \"No\".\n"
03357 " -text_outliers\n"
03358 " If present, tells the program to only print out the outlier check\n"
03359 " results in text form, not graph them. You can make this the default\n"
03360 " by setting the environment variable AFNI_TO3D_OUTLIERS to \"Text\".\n"
03361 " N.B.: If to3d is run in batch mode, then no graph can be produced.\n"
03362 " Thus, this option only has meaning when to3d is run with the\n"
03363 " interactive graphical user interface.\n"
03364 " -save_outliers fname\n"
03365 " Tells the program to save the outliers count into a 1D file with\n"
03366 " name 'fname'. You could graph this file later with the command\n"
03367 " 1dplot -one fname\n"
03368 " If this option is used, the outlier count will be saved even if\n"
03369 " nothing appears 'suspicious' (whatever that means).\n"
03370 " NOTES on outliers:\n"
03371 " * See '3dToutcount -help' for a description of how outliers are\n"
03372 " defined.\n"
03373 " * The outlier count is not done if the input images are shorts\n"
03374 " and there is a significant (> 1%%) number of negative inputs.\n"
03375 " * There must be at least 6 time points for the outlier count to\n"
03376 " be carried out.\n"
03377 ) ;
03378
03379 printf(
03380 "\n"
03381 "OPTIONS THAT AFFECT THE X11 IMAGE DISPLAY\n"
03382 " -gamma gg the gamma correction factor for the\n"
03383 " monitor is 'gg' (default gg is 1.0; greater than\n"
03384 " 1.0 makes the image contrast larger -- this may\n"
03385 " also be adjusted interactively)\n"
03386 " -ncolors nn use 'nn' gray levels for the image\n"
03387 " displays (default is %d)\n"
03388 " -xtwarns turn on display of Xt warning messages\n" ,
03389 INIT_ngray
03390 ) ;
03391
03392 exit(0) ;
03393 }
|
|
||||||||||||||||
|
Definition at line 5543 of file to3d.c. References to3d_data::anatomy_dataname, to3d_data::anatomy_parent_filename, to3d_data::anatomy_parent_idcode, client_data, DEBLANK, ENTRY, FILENAME_TO_PREFIX, THD_3dim_dataset::idcode, INERR, ISFUNC, MCW_strncpy, myXtFree, PATH_CONCAT, THD_3dim_dataset::self_name, to3d_widget_set::session_file_textfield, to3d_data::session_filename, T3D_poperr(), THD_delete_3dim_dataset(), THD_MAX_NAME, and THD_open_one_dataset(). Referenced by main(), and T3D_create_widgets().
05545 {
05546 static char * old_name = NULL ;
05547 char * new_name ;
05548 char new_path[THD_MAX_NAME] , new_pref[THD_MAX_NAME] ;
05549 Boolean isfunc ;
05550 THD_3dim_dataset * anat_dset ;
05551
05552 ENTRY("T3D_anatomy_parent_CB") ;
05553
05554 if( old_name == NULL ) old_name = XtNewString("Elvis Lives!!!") ;
05555
05556 /* see if the new text is any different from the old one */
05557
05558 if( w != NULL ){
05559 new_name = XmTextFieldGetString( w ) ; /* get the new text */
05560 } else {
05561 new_name = XtNewString( user_inputs.anatomy_parent_filename ) ;
05562 }
05563 DEBLANK(new_name) ;
05564
05565 if( strlen(new_name) == 0 ) { old_name = new_name ; EXRETURN ; }
05566 if( strcmp(new_name,old_name) == 0 ){ myXtFree(new_name) ; EXRETURN ; }
05567
05568 /* have a new filename --> try to read dataset from it */
05569
05570 myXtFree(old_name) ; old_name = new_name ;
05571
05572 /* make a pathname to the anatomy dataset */
05573
05574 if( strstr(new_name,"/") == NULL ){
05575 char * sess ;
05576 if( w != NULL ) sess = XmTextFieldGetString(wset.session_file_textfield);
05577 else sess = XtNewString( user_inputs.session_filename ) ;
05578 DEBLANK(sess) ;
05579 if( strlen(sess) > 0 ){
05580 PATH_CONCAT( new_path , sess , new_name ) ;
05581 } else {
05582 strcpy( new_path , new_name ) ;
05583 }
05584 myXtFree(sess) ;
05585 } else {
05586 strcpy( new_path , new_name ) ;
05587 }
05588
05589 FILENAME_TO_PREFIX(new_path,new_pref) ;
05590 if( strlen(new_pref) == 0 ) strcat(new_path,"+orig") ;
05591
05592 anat_dset = THD_open_one_dataset( new_path ) ;
05593 if( anat_dset == NULL ){
05594 T3D_poperr( INERR ,
05595 "Cannot read 3D dataset\nin anatomy parent file" ) ;
05596 EXRETURN ;
05597 }
05598
05599 isfunc = ISFUNC(anat_dset) ;
05600 if( isfunc ){
05601 T3D_poperr( INERR ,
05602 "Anatomy parent dataset\nis actually Function data!" ) ;
05603 THD_delete_3dim_dataset( anat_dset , False ) ;
05604 EXRETURN ;
05605 }
05606
05607 /* at this point, the anat dataset seems OK, so use it */
05608
05609 MCW_strncpy( user_inputs.anatomy_dataname ,
05610 anat_dset->self_name , THD_MAX_NAME ) ;
05611 user_inputs.anatomy_parent_idcode = anat_dset->idcode ;
05612
05613 #ifndef NO_NAMES
05614 if( w != NULL ) XmTextFieldSetString( wset.anatomy_dataname_textfield ,
05615 user_inputs.anatomy_dataname ) ;
05616 #endif
05617
05618 MCW_strncpy( user_inputs.anatomy_parent_filename ,
05619 new_name , THD_MAX_NAME ) ;
05620
05621 THD_delete_3dim_dataset( anat_dset , False ) ;
05622
05623 EXRETURN ;
05624 }
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|
||||||||||||||||
|
|
Definition at line 5152 of file to3d.c. References AFNI_GOOD_DTYPE, AFNI_GOOD_FUNC_DTYPE, to3d_data::anatomy_dataname, argopt, DATASET_HEADER_SUFFIX, to3d_data::dataset_name, to3d_data::dataset_type, ENTRY, to3d_data::function_type, ISFUNCTYPE, to3d_data::need_stat_aux, OUTERR, to3d_data::output_filename, PATH_CONCAT, RETURN, to3d_data::session_filename, to3d_data::stat_aux, STATUS, T3D_poperr(), T3D_setup_stat_aux(), THD_is_directory(), THD_is_file(), THD_MAX_NAME, to3d_data::xorient, to3d_data::yorient, and to3d_data::zorient. Referenced by main(), and T3D_save_file_CB().
05153 {
05154 char xlab,ylab,zlab ;
05155 int ii , ll , ll_out , ll_sess ;
05156 Boolean good = True , isfunc ;
05157 char new_name[THD_MAX_NAME] ;
05158
05159 ENTRY("T3D_check_data") ;
05160
05161 /*-- check that orientations are legal --*/
05162
05163 xlab = ORIENT_xyz[user_inputs.xorient] ;
05164 ylab = ORIENT_xyz[user_inputs.yorient] ;
05165 zlab = ORIENT_xyz[user_inputs.zorient] ;
05166
05167 if( xlab == ylab || xlab == zlab || ylab == zlab ){
05168 if(perr)T3D_poperr( OUTERR , "Axes orientations are not consistent!" ) ;
05169 good = False ;
05170 }
05171
05172 /*-- check that the output filename is acceptable --*/
05173
05174 STATUS("check output filename") ;
05175
05176 ll_out = ll = strlen( user_inputs.output_filename ) ;
05177 if( ll == 0 ){
05178 if(perr)T3D_poperr( OUTERR , "No output filename provided!" ) ;
05179 good = False ;
05180 } else {
05181 for( ii=0 ; ii < ll ; ii++ )
05182 if( iscntrl(user_inputs.output_filename[ii]) ||
05183 isspace(user_inputs.output_filename[ii]) ||
05184 user_inputs.output_filename[ii] == '/' ) break ;
05185
05186 if( ii < ll ){
05187 if(perr)T3D_poperr( OUTERR ,
05188 "Output filename contains illegal character!" ) ;
05189 good = False ;
05190 }
05191 }
05192
05193 /*-- check that the session filename is acceptable --*/
05194
05195 STATUS("check session name") ;
05196
05197 ll_sess = ll = strlen( user_inputs.session_filename ) ;
05198 if( ll == 0 ){
05199 if(perr)T3D_poperr( OUTERR , "No session directory name provided!" ) ;
05200 good = False ;
05201 } else {
05202 for( ii=0 ; ii < ll ; ii++ )
05203 if( iscntrl(user_inputs.session_filename[ii]) ||
05204 isspace(user_inputs.session_filename[ii]) ) break ;
05205
05206 if( ii < ll ){
05207 if(perr)T3D_poperr( OUTERR ,
05208 "Session filename contains illegal character!" ) ;
05209 good = False ;
05210 }
05211 }
05212
05213 /* Check if the file already exists */
05214
05215 STATUS("check if file exists") ;
05216
05217 if( ll_sess > 0 && ll_out > 0 ){
05218 PATH_CONCAT( new_name , user_inputs.session_filename ,
05219 user_inputs.output_filename ) ;
05220 strcat(new_name , "+orig." DATASET_HEADER_SUFFIX ) ;
05221 ll = THD_is_file( new_name ) || THD_is_directory( new_name ) ;
05222 if( ll ){
05223 if(perr) T3D_poperr( OUTERR , "Output file already exists!" ) ;
05224 good = False ;
05225 }
05226 }
05227
05228 /*-- if the image type is functional, check
05229 that the anatomy parent dataset name has been set --*/
05230
05231 isfunc = ISFUNCTYPE(user_inputs.dataset_type) ;
05232
05233 #ifdef REQUIRE_ANAT_PARENT
05234 if( isfunc && strlen(user_inputs.anatomy_dataname) == 0 ){
05235 if(perr)T3D_poperr( OUTERR , "Anatomy parent not properly set!" ) ;
05236 good = False ;
05237 }
05238 #endif
05239
05240 /*-- check for good data types in the bricks --*/
05241
05242 STATUS("check data types") ;
05243
05244 if( isfunc ){
05245 if( ! AFNI_GOOD_FUNC_DTYPE(argopt.datum_all) ){
05246 if(perr)T3D_poperr(OUTERR , "Illegal functional datum type!" ) ;
05247 good = False ;
05248 }
05249 } else {
05250 if( ! AFNI_GOOD_DTYPE(argopt.datum_all) ){
05251 if(perr)T3D_poperr(OUTERR , "Illegal anatomical datum type!" ) ;
05252 good = False ;
05253 }
05254 }
05255
05256 /*-- check if a dataset name has been defined --*/
05257
05258 #ifndef NO_NAMES
05259 if( strlen(user_inputs.dataset_name) == 0 ){
05260 if(perr)T3D_poperr( OUTERR,"You **MUST** supply a name for the dataset!" ) ;
05261 good = False ;
05262 }
05263 #endif
05264
05265 /*-- check if the stat_aux parameters are good --*/
05266
05267 STATUS("check stat aux") ;
05268
05269 T3D_setup_stat_aux() ;
05270 if( user_inputs.need_stat_aux ){
05271
05272 for( ii=0 ; ii < FUNC_need_stat_aux[user_inputs.function_type] ; ii++ )
05273 if( user_inputs.stat_aux[ii] <= 0.0 ) break ;
05274
05275 if( ii < FUNC_need_stat_aux[user_inputs.function_type] ){
05276 if(perr)T3D_poperr(OUTERR , "Invalid statistical parameters!" ) ;
05277 good = False ;
05278 }
05279 }
05280
05281 /*-- return the status we found --*/
05282
05283 RETURN( good );
05284 }
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get number here * Definition at line 5775 of file to3d.c. References AFMALL, CURSOR_normalize, CURSOR_watchize, to3d_data::dataset_type, ENTRY, free, to3d_widget_set::good, ISANATTYPE, MCW_CALLER_KILL, MCW_popup_message(), MCW_TIMER_KILL, MCW_USER_KILL, my_getenv(), negative_shorts, THD_timeaxis::ntt, nvox_total, outliers_fname, to3d_data::output_filename, plot_ts_lab(), to3d_widget_set::save_file_pb, skip, THD_3dim_dataset::taxis, THD_outlier_count(), to3d_widget_set::topshell, MCW_arrowval::wrowcol, and to3d_widget_set::xsize_av. Referenced by AFNI_startup_timeout_CB(), T3D_save_file_CB(), and T3D_swap_CB().
05776 {
05777 char *eee = my_getenv("AFNI_TO3D_OUTLIERS") ;
05778 int skip = (eee != NULL && (*eee == 'N' || *eee == 'n')) ;
05779 int text = (eee != NULL && (*eee == 'T' || *eee == 't')) ;
05780
05781 ENTRY("T3D_check_outliers") ;
05782
05783 if( dset->taxis != NULL &&
05784 dset->taxis->ntt > 5 &&
05785 !skip &&
05786 ISANATTYPE(user_inputs.dataset_type) &&
05787 negative_shorts < 0.01*nvox_total ){
05788
05789 int *out_count, out_ctop , cc=0 ;
05790 Widget wmsg ;
05791
05792 if( wset.topshell != NULL && wset.good ){
05793 wmsg = MCW_popup_message( wset.save_file_pb ,
05794 "****************\n"
05795 "* Checking for *\n"
05796 "* time series *\n"
05797 "* outliers *\n"
05798 "****************" ,
05799 MCW_CALLER_KILL ) ;
05800 CURSOR_watchize ;
05801 } else {
05802 fprintf(stderr,"Checking for time series outliers\n") ;
05803 }
05804
05805 THD_outlier_count( dset , 0.01 , &out_count , &out_ctop ) ;
05806
05807 if( out_count != NULL && out_ctop > 0 ){ /* compute the output message */
05808 int iv,nvals=dset->taxis->ntt ; char *msg = AFMALL(char,2048+8*nvals) ;
05809
05810 strcpy(msg," \nto3d WARNING:\nSignificant outliers detected in these sub-bricks:\n") ;
05811
05812 for( iv=0 ; iv < nvals ; iv++ ){
05813 if( out_count[iv] > out_ctop ){
05814 sprintf(msg+strlen(msg)," %3d",iv) ; cc++ ;
05815 if( cc%12 == 0 ) strcat(msg,"\n") ;
05816 }
05817 }
05818
05819 if( outliers_fname != NULL ){ /* 26 Aug 2001 */
05820 FILE *fp = fopen( outliers_fname , "w" ) ;
05821 if( fp == NULL ){
05822 fprintf(stderr,"** Can't open -save_outliers %s\n",outliers_fname);
05823 } else {
05824 for( iv=0 ; iv < nvals ; iv++ )
05825 fprintf(fp,"%3d %3d\n",out_count[iv],out_ctop) ;
05826 fclose(fp) ;
05827 }
05828 }
05829
05830 if( cc > 0 ){ /* any sub-bricks fail? */
05831 if( cc%12 > 0 ) strcat(msg,"\n") ;
05832 strcat(msg,"You should inspect the dataset for possible corruption.\n");
05833 strcat(msg," [Outliers are defined as in program 3dToutcount. ]\n");
05834 strcat(msg," [Outliers early in an EPI time series may be due to ]\n");
05835 strcat(msg," [the longitudinal magnetization equilibration effect.]\n");
05836 strcat(msg," [Other causes are subject movement, scanner problems,]\n");
05837 strcat(msg," [or anything that makes a time series look irregular.]\n");
05838 strcat(msg," [ 3dToutcount -save outnam dataset | 1dplot -stdin ]\n");
05839 strcat(msg," [can be used to make a dataset 'outnam' that marks ]\n");
05840 strcat(msg," [outlier voxels; see 3dToutcount -help for details. ]\n");
05841
05842 fprintf(stderr,"%s\n",msg) ; /* print message */
05843 if( wset.topshell != NULL && !text && wset.good ){ /* graph outlier count */
05844 float *y[2] ;
05845 y[0] = AFMALL(float, sizeof(float)*nvals) ;
05846 y[1] = AFMALL(float, sizeof(float)*nvals) ;
05847 for( iv=0 ; iv < nvals ; iv++ ){
05848 y[0][iv] = out_count[iv] ; y[1][iv] = out_ctop ;
05849 }
05850 plot_ts_lab( XtDisplay(wset.topshell) , /* graph */
05851 nvals , NULL , 2 , y ,
05852 "Sub-brick Index" ,
05853 "Outlier Count (and Threshold)" ,
05854 user_inputs.output_filename , NULL , NULL ) ;
05855 free(y[0]); free(y[1]) ;
05856 (void) MCW_popup_message( wset.xsize_av->wrowcol , /* message */
05857 msg , MCW_USER_KILL ) ;
05858 }
05859 }
05860 free(msg) ;
05861 }
05862
05863 if( out_count != NULL ) free(out_count) ;
05864
05865 if( wset.topshell != NULL && wset.good ){
05866 XtDestroyWidget(wmsg); CURSOR_normalize;
05867 if( cc == 0 )
05868 (void) MCW_popup_message( wset.save_file_pb ,
05869 " \n"
05870 "** No unusual outlier **\n"
05871 "** concentration found **\n" ,
05872 MCW_USER_KILL | MCW_TIMER_KILL ) ;
05873 } else {
05874 if( cc == 0 )
05875 fprintf(stderr,"No unusual outlier concentration found\n") ;
05876 }
05877 }
05878
05879 EXRETURN ;
05880 }
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Mar 1997: if any FOV or SLAB command line inputs are used, then require that they all be given. * Definition at line 414 of file to3d.c. References to3d_widget_set::action_frame, to3d_widget_set::action_rowcol, MCW_arrowval::allow_wrap, to3d_data::anatomy_parent_filename, to3d_widget_set::anatomy_parent_label, to3d_widget_set::anatomy_parent_textfield, to3d_data::anatomy_type, to3d_widget_set::anatomy_type_av, argopt, AV_SENSITIZE, to3d_widget_set::button_help_pb, to3d_widget_set::centered_bbox, DATASET_BRICK_SUFFIX, DATASET_HEADER_SUFFIX, to3d_data::dataset_name, to3d_data::dataset_type, to3d_widget_set::dataset_type_av, to3d_widget_set::datum_label, to3d_widget_set::dc, ENTRY, FIRST_3DIM_TYPE, FIRST_ANAT_TYPE, FIRST_FUNC_TYPE, FIRST_ORIENT_TYPE, FIRST_VIEW_TYPE, to3d_data::fov, to3d_widget_set::fov_av, to3d_data::function_type, to3d_widget_set::function_type_av, to3d_data::geometry_parent_filename, to3d_widget_set::geometry_parent_label, to3d_widget_set::geometry_parent_textfield, to3d_widget_set::good, LABEL_ARG, LAST_3DIM_TYPE, LAST_ANAT_TYPE, LAST_FUNC_TYPE, LAST_ORIENT_TYPE, LAST_VIEW_TYPE, LONGEST_3DIM_TYPESTR, LONGEST_ANAT_TYPESTR, LONGEST_FUNC_TYPESTR, LONGEST_ORIENT_TYPESTR, LONGEST_VIEW_TYPESTR, MCW_AV_downup, MCW_AV_editext, MCW_AV_readtext, MCW_BB_check, MCW_BB_frame, MCW_BB_radio_one, MCW_new_DC(), MCW_reghelp_children(), MCW_reghint_children(), MCW_register_help(), MCW_register_hint(), MCW_set_widget_bg(), mri_datum_size(), NCOLOVR, new_MCW_arrowval(), new_MCW_bbox(), NO_NAMES, to3d_data::ntt, to3d_data::nx, to3d_data::ny, to3d_data::nzz, to3d_widget_set::open_view_pb, to3d_widget_set::output_file_label, to3d_widget_set::output_file_textfield, to3d_data::output_filename, to3d_widget_set::quit_pb, to3d_widget_set::region_separator, to3d_widget_set::save_file_pb, to3d_widget_set::seq, to3d_widget_set::session_file_label, to3d_widget_set::session_file_textfield, to3d_data::session_filename, to3d_data::short_label1, to3d_widget_set::stat_aux_label, to3d_widget_set::stat_aux_textfield, to3d_widget_set::swap_pb, T3D_anatomy_parent_CB(), T3D_centered_CB(), T3D_data_to_widgets(), T3D_FORM_SPACING, T3D_fov_av_CB(), T3D_geometry_parent_CB(), T3D_NAME_WIDTH, T3D_open_view_CB(), T3D_orient_av_CB(), T3D_origin_av_CB(), T3D_pointer_leave_EV(), T3D_quit_CB(), T3D_save_file_CB(), T3D_set_dependent_geometries(), T3D_size_av_CB(), T3D_stat_aux_CB(), T3D_swap_CB(), T3D_text_display(), T3D_type_av_CB(), T3D_voxcontig_CB(), T3D_voxshape_CB(), THD_MAX_LABEL, THD_MAX_NAME, THD_MAX_PREFIX, to3d_widget_set::topform, to3d_widget_set::topshell, to3d_data::Torg, to3d_data::TR, to3d_widget_set::TR_label, tt, to3d_data::tunits, UNITS_TYPE_LABEL, VIEW_ORIGINAL_STR, to3d_data::view_type, to3d_widget_set::view_type_av, to3d_widget_set::voxcontig_bbox, to3d_data::voxshape, to3d_widget_set::voxshape_bbox, VOXSHAPE_CUBICAL, VOXSHAPE_IRREGULAR, VOXSHAPE_SQUARE, WAIT_for_window, MCW_bbox::wbut, MCW_arrowval::wrowcol, MCW_bbox::wrowcol, MCW_arrowval::wtext, MCW_bbox::wtop, to3d_data::xorient, to3d_widget_set::xorient_av, to3d_data::xorigin, to3d_widget_set::xorigin_av, to3d_widget_set::xorigin_label, to3d_data::xsize, to3d_widget_set::xsize_av, to3d_data::yorient, to3d_widget_set::yorient_av, to3d_data::yorigin, to3d_widget_set::yorigin_av, to3d_widget_set::yorigin_label, to3d_data::ysize, to3d_widget_set::ysize_av, to3d_data::zorient, to3d_widget_set::zorient_av, to3d_data::zorigin, to3d_widget_set::zorigin_av, to3d_widget_set::zorigin_label, to3d_data::zsize, to3d_widget_set::zsize_av, to3d_data::zspacing, and to3d_widget_set::zspacing_av. Referenced by main().
00415 {
00416 ENTRY("T3D_create_widgets") ;
00417 wset.dc = MCW_new_DC( wset.topshell, argopt.ncolor,
00418 NCOLOVR,FD_colovr,FD_colovr, argopt.gamma , 0 );
00419 wset.seq = NULL ; /* no viewing open now */
00420
00421 /*---- form to hold all widgets ----*/
00422
00423 wset.topform = XtVaCreateWidget(
00424 "dialog" , xmFormWidgetClass , wset.topshell ,
00425 XmNborderWidth , 0 ,
00426 #if 1
00427 XmNtraversalOn , False ,
00428 #endif
00429 NULL ) ;
00430
00431 MCW_register_help( wset.topform ,
00432 "I weep for Adonais--he is dead!\n"
00433 "Oh, weep for Adonais! though our tears\n"
00434 "Thaw not the frost which binds so dear a head!\n"
00435 "And thou, sad Hour, selected from all years\n"
00436 "To mourn our loss, rouse thy obscure compeers,\n"
00437 "And teach them thine own sorrow, say: 'With me\n"
00438 "Died Adonais; till the Future dares\n"
00439 "Forget the Past, his fate and fame shall be\n"
00440 "An echo and a light unto eternity!'"
00441 ) ;
00442
00443 /*---- 3 arrowvals for orientation ----*/
00444
00445 wset.xorient_av = new_MCW_arrowval(
00446 wset.topform , /* parent */
00447 "x orientation\n(across screen)" , /* label */
00448 MCW_AV_downup , /* arrows */
00449 FIRST_ORIENT_TYPE , /* min */
00450 LAST_ORIENT_TYPE , /* max */
00451 user_inputs.xorient , /* init */
00452 MCW_AV_readtext , /* text */
00453 0 , /* decimals */
00454 T3D_orient_av_CB , NULL , /* callback */
00455 T3D_text_display , /* text maker */
00456 ORIENT_typestr /* and data */
00457 ) ;
00458
00459 XtVaSetValues( wset.xorient_av->wrowcol ,
00460 XmNleftAttachment , XmATTACH_FORM ,
00461 XmNleftOffset , T3D_FORM_SPACING ,
00462 XmNtopAttachment , XmATTACH_FORM ,
00463 XmNtopOffset , T3D_FORM_SPACING ,
00464 NULL ) ;
00465
00466 wset.yorient_av = new_MCW_arrowval(
00467 wset.topform , /* parent */
00468 "y orientation\n (down screen) " , /* label */
00469 MCW_AV_downup , /* arrows */
00470 FIRST_ORIENT_TYPE , /* min */
00471 LAST_ORIENT_TYPE , /* max */
00472 user_inputs.yorient , /* init */
00473 MCW_AV_readtext , /* text */
00474 0 , /* decimals */
00475 T3D_orient_av_CB , NULL , /* callback */
00476 T3D_text_display , /* text maker */
00477 ORIENT_typestr /* and data */
00478 ) ;
00479
00480 XtVaSetValues( wset.yorient_av->wrowcol ,
00481 XmNtopAttachment , XmATTACH_WIDGET ,
00482 XmNtopWidget , wset.xorient_av->wrowcol ,
00483 XmNtopOffset , T3D_FORM_SPACING ,
00484 XmNleftAttachment , XmATTACH_FORM ,
00485 XmNleftOffset , T3D_FORM_SPACING ,
00486 NULL ) ;
00487
00488 wset.zorient_av = new_MCW_arrowval(
00489 wset.topform , /* parent */
00490 "z orientation\n(slices 0,1,..)" , /* label */
00491 MCW_AV_downup , /* arrows */
00492 FIRST_ORIENT_TYPE , /* min */
00493 LAST_ORIENT_TYPE , /* max */
00494 user_inputs.zorient , /* init */
00495 MCW_AV_readtext , /* text */
00496 0 , /* decimals */
00497 T3D_orient_av_CB , NULL , /* callback */
00498 T3D_text_display , /* text maker */
00499 ORIENT_typestr /* and data */
00500 ) ;
00501
00502 XtVaSetValues( wset.zorient_av->wrowcol ,
00503 XmNtopAttachment , XmATTACH_WIDGET ,
00504 XmNtopWidget , wset.yorient_av->wrowcol ,
00505 XmNtopOffset , T3D_FORM_SPACING ,
00506 XmNleftAttachment , XmATTACH_FORM ,
00507 XmNleftOffset , T3D_FORM_SPACING ,
00508 NULL ) ;
00509
00510 XtVaSetValues( wset.xorient_av->wtext ,
00511 XmNcolumns , LONGEST_ORIENT_TYPESTR ,
00512 XmNmaxLength , LONGEST_ORIENT_TYPESTR ,
00513 NULL ) ;
00514
00515 XtVaSetValues( wset.yorient_av->wtext ,
00516 XmNcolumns , LONGEST_ORIENT_TYPESTR ,
00517 XmNmaxLength , LONGEST_ORIENT_TYPESTR ,
00518 NULL ) ;
00519
00520 XtVaSetValues( wset.zorient_av->wtext ,
00521 XmNcolumns , LONGEST_ORIENT_TYPESTR ,
00522 XmNmaxLength , LONGEST_ORIENT_TYPESTR ,
00523 NULL ) ;
00524
00525 wset.xorient_av->allow_wrap = 1 ;
00526 wset.yorient_av->allow_wrap = 1 ;
00527 wset.zorient_av->allow_wrap = 1 ;
00528
00529 MCW_reghelp_children( wset.xorient_av->wrowcol ,
00530 "Choose the anatomical orientation\n"
00531 "which fits the images when displayed\n"
00532 "in their ORIGINAL orientation:\n"
00533 "left->right, across the screen" ) ;
00534 MCW_reghint_children( wset.xorient_av->wrowcol ,
00535 "Anatomical orientation across screen" ) ;
00536
00537 MCW_reghelp_children( wset.yorient_av->wrowcol ,
00538 "Choose the anatomical orientation\n"
00539 "which fits the images when displayed\n"
00540 "in their ORIGINAL orientation:\n"
00541 "top->bottom, down the screen" ) ;
00542 MCW_reghint_children( wset.yorient_av->wrowcol ,
00543 "Anatomical orientation down screen" ) ;
00544
00545 MCW_reghelp_children( wset.zorient_av->wrowcol ,
00546 "Choose the anatomical orientation\n"
00547 "which fits the images when displayed\n"
00548 "in their ORIGINAL orientation:\n"
00549 "slice order, `thru' the screen" ) ;
00550 MCW_reghint_children( wset.zorient_av->wrowcol ,
00551 "Anatomical orientation in slice direction" ) ;
00552
00553 printf(".");fflush(stdout);
00554
00555 /*---- bbox and arrowvals for voxel sizes ----*/
00556
00557 wset.xsize_av = new_MCW_arrowval(
00558 wset.topform , /* parent */
00559 "x voxel\nsize (mm)" , /* label */
00560 MCW_AV_downup , /* arrows */
00561 1 , /* min */
00562 9999 , /* max */
00563 (int)(100*user_inputs.xsize), /* init */
00564 MCW_AV_editext , /* text */
00565 2 , /* decimals */
00566 T3D_size_av_CB , NULL , /* callback */
00567 NULL , NULL /* text maker */
00568 ) ;
00569
00570 XtVaSetValues( wset.xsize_av->wrowcol ,
00571 XmNtopAttachment , XmATTACH_FORM ,
00572 XmNtopOffset , T3D_FORM_SPACING ,
00573 XmNleftAttachment , XmATTACH_WIDGET ,
00574 XmNleftWidget , wset.xorient_av->wrowcol ,
00575 XmNleftOffset , T3D_FORM_SPACING ,
00576 NULL ) ;
00577
00578 /*
00579 AV_assign_fval( wset.xsize_av , user_inputs.xsize ) ;
00580 */
00581
00582 wset.ysize_av = new_MCW_arrowval(
00583 wset.topform , /* parent */
00584 "y voxel\nsize (mm)" , /* label */
00585 MCW_AV_downup , /* arrows */
00586 1 , /* min */
00587 9999 , /* max */
00588 (int)(100*user_inputs.ysize), /* init */
00589 MCW_AV_editext , /* text */
00590 2 , /* decimals */
00591 T3D_size_av_CB , NULL , /* callback */
00592 NULL , NULL /* text maker */
00593 ) ;
00594
00595 XtVaSetValues( wset.ysize_av->wrowcol ,
00596 XmNtopAttachment , XmATTACH_WIDGET ,
00597 XmNtopWidget , wset.xsize_av->wrowcol ,
00598 XmNtopOffset , T3D_FORM_SPACING ,
00599 XmNleftAttachment , XmATTACH_WIDGET ,
00600 XmNleftWidget , wset.xorient_av->wrowcol ,
00601 XmNleftOffset , T3D_FORM_SPACING ,
00602 NULL ) ;
00603
00604 wset.zsize_av = new_MCW_arrowval(
00605 wset.topform , /* parent */
00606 "z voxel\nsize (mm)" , /* label */
00607 MCW_AV_downup , /* arrows */
00608 1 , /* min */
00609 9999 , /* max */
00610 (int)(100*user_inputs.zsize), /* init */
00611 MCW_AV_editext , /* text */
00612 2 , /* decimals */
00613 T3D_size_av_CB , NULL , /* callback */
00614 NULL , NULL /* text maker */
00615 ) ;
00616
00617 XtVaSetValues( wset.zsize_av->wrowcol ,
00618 XmNtopAttachment , XmATTACH_WIDGET ,
00619 XmNtopWidget , wset.ysize_av->wrowcol ,
00620 XmNtopOffset , T3D_FORM_SPACING ,
00621 XmNleftAttachment , XmATTACH_WIDGET ,
00622 XmNleftWidget , wset.xorient_av->wrowcol ,
00623 XmNleftOffset , T3D_FORM_SPACING ,
00624 NULL ) ;
00625
00626 #ifdef ALLOW_NONCONTIG
00627 wset.zspacing_av = new_MCW_arrowval(
00628 wset.topform , /* parent */
00629 "z voxel\nspacing " , /* label */
00630 MCW_AV_downup , /* arrows */
00631 1 , /* min */
00632 9999 , /* max */
00633 (int)(100*user_inputs.zspacing), /* init */
00634 MCW_AV_editext , /* text */
00635 2 , /* decimals */
00636 T3D_size_av_CB , NULL , /* callback */
00637 NULL , NULL /* text maker */
00638 ) ;
00639
00640 XtVaSetValues( wset.zspacing_av->wrowcol ,
00641 XmNtopAttachment , XmATTACH_WIDGET ,
00642 XmNtopWidget , wset.zsize_av->wrowcol ,
00643 XmNtopOffset , T3D_FORM_SPACING ,
00644 XmNleftAttachment , XmATTACH_WIDGET ,
00645 XmNleftWidget , wset.xorient_av->wrowcol ,
00646 XmNleftOffset , T3D_FORM_SPACING ,
00647 NULL ) ;
00648 #endif /* ALLOW_NONCONTIG */
00649
00650 wset.fov_av = new_MCW_arrowval(
00651 wset.topform , /* parent */
00652 "Field of\nview (mm)" , /* label */
00653 MCW_AV_downup , /* arrows */
00654 1 , /* min */
00655 99999 , /* max */
00656 (int)(10*user_inputs.fov), /* init */
00657 MCW_AV_editext , /* text */
00658 1 , /* decimals */
00659 T3D_fov_av_CB , NULL , /* callback */
00660 NULL , NULL /* text maker */
00661 ) ;
00662
00663 XtVaSetValues( wset.fov_av->wrowcol ,
00664 XmNtopAttachment , XmATTACH_WIDGET ,
00665 #ifdef ALLOW_NONCONTIG
00666 XmNtopWidget , wset.zspacing_av->wrowcol ,
00667 #else
00668 XmNtopWidget , wset.zsize_av->wrowcol ,
00669 #endif
00670 XmNtopOffset , T3D_FORM_SPACING ,
00671 XmNleftAttachment , XmATTACH_WIDGET ,
00672 XmNleftWidget , wset.xorient_av->wrowcol ,
00673 XmNleftOffset , T3D_FORM_SPACING ,
00674 NULL ) ;
00675
00676 wset.voxshape_bbox = new_MCW_bbox(
00677 wset.topform , /* parent */
00678 3 , /* num buttons */
00679 T3D_voxshape_label , /* labels */
00680 MCW_BB_radio_one , /* bbox type */
00681 MCW_BB_frame , /* use a frame */
00682 T3D_voxshape_CB , /* callback */
00683 NULL /* callback data */
00684 ) ;
00685
00686 XtVaSetValues( wset.voxshape_bbox->wtop ,
00687 XmNrightAttachment , XmATTACH_WIDGET ,
00688 XmNrightWidget , wset.fov_av->wrowcol ,
00689 XmNrightOffset , T3D_FORM_SPACING ,
00690 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
00691 XmNtopWidget , wset.fov_av->wrowcol ,
00692 XmNtopOffset , 0 ,
00693 NULL ) ;
00694
00695 #ifdef ALLOW_NONCONTIG
00696 wset.voxcontig_bbox = new_MCW_bbox(
00697 wset.topform , /* parent */
00698 3 , /* num buttons */
00699 T3D_voxcontig_label , /* labels */
00700 MCW_BB_radio_one , /* bbox type */
00701 MCW_BB_frame , /* use a frame */
00702 T3D_voxcontig_CB , /* callback */
00703 NULL /* callback data */
00704 ) ;
00705
00706 XtSetSensitive( wset.voxcontig_bbox->wbut[1] , False ) ;
00707 XtSetSensitive( wset.voxcontig_bbox->wbut[2] , False ) ;
00708
00709 XtVaSetValues( wset.voxcontig_bbox->wtop ,
00710 XmNrightAttachment , XmATTACH_WIDGET ,
00711 XmNrightWidget , wset.voxshape_bbox->wtop ,
00712 XmNrightOffset , T3D_FORM_SPACING ,
00713 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
00714 XmNtopWidget , wset.voxshape_bbox->wtop ,
00715 XmNtopOffset , 0 ,
00716 NULL ) ;
00717 #endif /* ALLOW_NONCONTIG */
00718
00719 MCW_reghelp_children( wset.xsize_av->wrowcol ,
00720 "If in-slice voxel dimensions are\n"
00721 "not square, use this to set the\n"
00722 "x axis (across screen) dimension" ) ;
00723 MCW_reghint_children( wset.xsize_av->wrowcol ,
00724 "Across screen voxel size" ) ;
00725
00726 MCW_reghelp_children( wset.ysize_av->wrowcol ,
00727 "If in-slice voxel dimensions are\n"
00728 "not square, use this to set the\n"
00729 "y axis (down screen) dimension" ) ;
00730 MCW_reghint_children( wset.ysize_av->wrowcol ,
00731 "Down screen voxel size" ) ;
00732
00733 MCW_reghelp_children( wset.zsize_av->wrowcol ,
00734 "If voxels are not cubical,\n"
00735 "use this to set the z axis\n"
00736 "(slice direction) thickness" ) ;
00737 MCW_reghint_children( wset.ysize_av->wrowcol ,
00738 "Slice direction voxel size" ) ;
00739
00740 #ifdef ALLOW_NONCONTIG
00741 MCW_reghelp_children( wset.zspacing_av->wrowcol ,
00742 "If the slices are not\n"
00743 "contiguous, use this to\n"
00744 "set the center-to-center\n"
00745 "slice spacing" ) ;
00746 #endif /* ALLOW_NONCONTIG */
00747
00748 MCW_reghelp_children( wset.fov_av->wrowcol ,
00749 "If the voxels are cubical,\n"
00750 "or at least square, use this\n"
00751 "to specify the sizes by giving\n"
00752 "the Field-Of-View dimension\n"
00753 "(the width across screen of images)" ) ;
00754 MCW_reghint_children( wset.fov_av->wrowcol ,
00755 "In-slice width of entire image" ) ;
00756
00757 MCW_reghelp_children( wset.voxshape_bbox->wrowcol ,
00758 "Choose one button to\n"
00759 "specify the voxel 'shape':\n"
00760 " cubical = all dimensions equal\n"
00761 " square = x & y dimensions\n"
00762 " equal, z different\n"
00763 " irregular= all dimensions unequal" ) ;
00764 MCW_reghint_children( wset.voxshape_bbox->wrowcol ,
00765 "Specify voxel shape" ) ;
00766
00767 #ifdef ALLOW_NONCONTIG
00768 MCW_reghelp_children( wset.voxcontig_bbox->wrowcol ,
00769 "Pressed IN: slices are contiguous\n"
00770 "Pressed OUT: slices are not contiguous\n"
00771 "(i.e., z size and z spacing differ)" ) ;
00772 #endif /* ALLOW_NONCONTIG */
00773
00774 /*-- set the vox*_bbox values depending on initial sizes --*/
00775
00776 if( user_inputs.xsize != user_inputs.ysize ){
00777 user_inputs.voxshape = VOXSHAPE_IRREGULAR ;
00778 } else {
00779 if( user_inputs.xsize != user_inputs.zsize ){
00780 user_inputs.voxshape = VOXSHAPE_SQUARE ;
00781 } else {
00782 user_inputs.voxshape = VOXSHAPE_CUBICAL ;
00783 }
00784 }
00785
00786 printf(".");fflush(stdout);
00787
00788 /*---- Label to show the TR (for 3D+time datasets) ----*/
00789
00790 { char buf[96] ;
00791 XmString xstr ;
00792
00793 sprintf( buf,"TR=%.3f%s Torg=%.3f\nNR=%d Nz=%d",
00794 user_inputs.TR , UNITS_TYPE_LABEL(user_inputs.tunits) ,
00795 user_inputs.Torg,
00796 user_inputs.ntt , user_inputs.nzz ) ;
00797 xstr = XmStringCreateLtoR( buf , XmFONTLIST_DEFAULT_TAG ) ;
00798
00799 wset.TR_label =
00800 XtVaCreateManagedWidget(
00801 "dialog" , xmLabelWidgetClass , wset.topform ,
00802 XmNlabelString , xstr ,
00803 XmNrecomputeSize , False ,
00804 XmNalignment , XmALIGNMENT_BEGINNING ,
00805 XmNtopAttachment , XmATTACH_WIDGET ,
00806 XmNtopWidget , wset.fov_av->wrowcol ,
00807 XmNtopOffset , T3D_FORM_SPACING ,
00808 XmNleftAttachment , XmATTACH_WIDGET ,
00809 XmNleftWidget , wset.voxshape_bbox->wtop ,
00810 XmNleftOffset , T3D_FORM_SPACING ,
00811 NULL ) ;
00812
00813 XmStringFree( xstr ) ;
00814
00815 MCW_register_help( wset.TR_label ,
00816 "Shows the TR (inter-brick time), number\n"
00817 "of bricks NR, and number of slizes Nz,\n"
00818 "for time-dependent datasets.\n"
00819 "These CANNOT be changed interactively.\n"
00820 "They can only be set on the command line." ) ;
00821
00822 MCW_register_hint( wset.TR_label , "3D+time parameters" ) ;
00823
00824 if( user_inputs.ntt < 2 )
00825 XtUnmanageChild( wset.TR_label ) ;
00826 }
00827
00828 /*---- arrowvals for origin ----*/
00829
00830 wset.xorigin_av = new_MCW_arrowval(
00831 wset.topform , /* parent */
00832 "x origin (mm)\n[left edge]" , /* label */
00833 MCW_AV_downup , /* arrows */
00834 -99999 , /* min */
00835 99999 , /* max */
00836 (int)(100*user_inputs.xorigin), /* init */
00837 MCW_AV_editext , /* text */
00838 2 , /* decimals */
00839 T3D_origin_av_CB , NULL , /* callback */
00840 NULL , NULL /* text maker */
00841 ) ;
00842
00843 XtVaSetValues( wset.xorigin_av->wrowcol ,
00844 XmNleftAttachment , XmATTACH_WIDGET ,
00845 XmNleftWidget , wset.xsize_av->wrowcol ,
00846 XmNleftOffset , T3D_FORM_SPACING ,
00847 XmNtopAttachment , XmATTACH_FORM ,
00848 XmNtopOffset , T3D_FORM_SPACING ,
00849 NULL ) ;
00850
00851 wset.xorigin_label =
00852 XtVaCreateManagedWidget(
00853 "dialog" , xmLabelWidgetClass , wset.topform ,
00854 LABEL_ARG("X") ,
00855 XmNrecomputeSize , False ,
00856 XmNleftAttachment , XmATTACH_WIDGET ,
00857 XmNleftWidget , wset.xorigin_av->wrowcol ,
00858 XmNleftOffset , 1 ,
00859 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
00860 XmNtopWidget , wset.xorigin_av->wrowcol ,
00861 XmNtopOffset , 2 ,
00862 NULL ) ;
00863
00864 wset.yorigin_av = new_MCW_arrowval(
00865 wset.topform , /* parent */
00866 "y origin (mm)\n[top edge]" , /* label */
00867 MCW_AV_downup , /* arrows */
00868 -99999 , /* min */
00869 99999 , /* max */
00870 (int)(100*user_inputs.yorigin), /* init */
00871 MCW_AV_editext , /* text */
00872 2 , /* decimals */
00873 T3D_origin_av_CB , NULL , /* callback */
00874 NULL , NULL /* text maker */
00875 ) ;
00876
00877 XtVaSetValues( wset.yorigin_av->wrowcol ,
00878 XmNtopAttachment , XmATTACH_WIDGET ,
00879 XmNtopWidget , wset.xorigin_av->wrowcol ,
00880 XmNtopOffset , T3D_FORM_SPACING ,
00881 XmNleftAttachment , XmATTACH_WIDGET ,
00882 XmNleftWidget , wset.xsize_av->wrowcol ,
00883 XmNleftOffset , T3D_FORM_SPACING ,
00884 NULL ) ;
00885
00886 wset.yorigin_label =
00887 XtVaCreateManagedWidget(
00888 "dialog" , xmLabelWidgetClass , wset.topform ,
00889 LABEL_ARG("X") ,
00890 XmNrecomputeSize , False ,
00891 XmNleftAttachment , XmATTACH_WIDGET ,
00892 XmNleftWidget , wset.yorigin_av->wrowcol ,
00893 XmNleftOffset , 1 ,
00894 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
00895 XmNtopWidget , wset.yorigin_av->wrowcol ,
00896 XmNtopOffset , 2 ,
00897 NULL ) ;
00898
00899 wset.zorigin_av = new_MCW_arrowval(
00900 wset.topform , /* parent */
00901 "z origin (mm)\n[slice 0]" , /* label */
00902 MCW_AV_downup , /* arrows */
00903 -99999 , /* min */
00904 99999 , /* max */
00905 (int)(100*user_inputs.zorigin), /* init */
00906 MCW_AV_editext , /* text */
00907 2 , /* decimals */
00908 T3D_origin_av_CB , NULL , /* callback */
00909 NULL , NULL /* text maker */
00910 ) ;
00911
00912 XtVaSetValues( wset.zorigin_av->wrowcol ,
00913 XmNtopAttachment , XmATTACH_WIDGET ,
00914 XmNtopWidget , wset.yorigin_av->wrowcol ,
00915 XmNtopOffset , T3D_FORM_SPACING ,
00916 XmNleftAttachment , XmATTACH_WIDGET ,
00917 XmNleftWidget , wset.xsize_av->wrowcol ,
00918 XmNleftOffset , T3D_FORM_SPACING ,
00919 NULL ) ;
00920
00921 wset.zorigin_label =
00922 XtVaCreateManagedWidget(
00923 "dialog" , xmLabelWidgetClass , wset.topform ,
00924 LABEL_ARG("X") ,
00925 XmNrecomputeSize , False ,
00926 XmNleftAttachment , XmATTACH_WIDGET ,
00927 XmNleftWidget , wset.zorigin_av->wrowcol ,
00928 XmNleftOffset , 1 ,
00929 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
00930 XmNtopWidget , wset.zorigin_av->wrowcol ,
00931 XmNtopOffset , 2 ,
00932 NULL ) ;
00933
00934 wset.centered_bbox = new_MCW_bbox(
00935 wset.topform , /* parent */
00936 3 , /* num buttons */
00937 T3D_centered_label , /* labels */
00938 MCW_BB_check , /* bbox type */
00939 MCW_BB_frame , /* use a frame */
00940 T3D_centered_CB , /* callback */
00941 NULL /* callback data */
00942 ) ;
00943
00944 XtVaSetValues( wset.centered_bbox->wtop ,
00945 #if 0
00946 XmNleftAttachment , XmATTACH_WIDGET ,
00947 XmNleftWidget , wset.fov_av->wrowcol ,
00948 XmNleftOffset , T3D_FORM_SPACING ,
00949 #else
00950 XmNrightAttachment , XmATTACH_OPPOSITE_WIDGET ,
00951 XmNrightWidget , wset.zorigin_av->wrowcol ,
00952 XmNrightOffset , 0 ,
00953 #endif
00954 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
00955 XmNtopWidget , wset.fov_av->wrowcol ,
00956 XmNtopOffset , 0 ,
00957 NULL ) ;
00958
00959 MCW_reghelp_children( wset.centered_bbox->wrowcol ,
00960 "Choose any combination of\n"
00961 "buttons to indicate whether\n"
00962 "each axis is centered\n"
00963 "in the gradient coil fields:\n"
00964 "Pressed IN means centered\n"
00965 "Pressed OUT means not centered" ) ;
00966 MCW_reghint_children( wset.centered_bbox->wrowcol ,
00967 "Is data domain centered around 0?" ) ;
00968
00969 MCW_reghelp_children( wset.xorigin_av->wrowcol ,
00970 "Use the arrows (or type) to enter\n"
00971 "the x-axis distance from the center of\n"
00972 "the first voxel to the\n"
00973 "gradient coil (0,0,0) point" ) ;
00974 MCW_reghint_children( wset.xorigin_av->wrowcol ,
00975 "X-axis distance to 1st voxel center" ) ;
00976
00977 MCW_reghelp_children( wset.yorigin_av->wrowcol ,
00978 "Use the arrows (or type) to enter\n"
00979 "the y-axis distance from the center of\n"
00980 "the first voxel to the\n"
00981 "gradient coil (0,0,0) point" ) ;
00982 MCW_reghint_children( wset.yorigin_av->wrowcol ,
00983 "Y-axis distance to 1st voxel center" ) ;
00984
00985 MCW_reghelp_children( wset.zorigin_av->wrowcol ,
00986 "Use the arrows (or type) to enter\n"
00987 "the z-axis distance from the center of\n"
00988 "the first voxel to the\n"
00989 "gradient coil (0,0,0) point" ) ;
00990 MCW_reghint_children( wset.zorigin_av->wrowcol ,
00991 "Z-axis distance to 1st voxel center" ) ;
00992
00993 MCW_register_help( wset.xorigin_label ,
00994 "Shows the direction that the\n"
00995 "x origin distance applies" ) ;
00996 MCW_register_hint( wset.xorigin_label ,
00997 "Direction of x origin distance" ) ;
00998
00999 MCW_register_help( wset.yorigin_label ,
01000 "Shows the direction that the\n"
01001 "y origin distance applies" ) ;
01002 MCW_register_hint( wset.yorigin_label ,
01003 "Direction of y origin distance" ) ;
01004
01005 MCW_register_help( wset.zorigin_label ,
01006 "Shows the direction that the\n"
01007 "z origin distance applies" ) ;
01008 MCW_register_hint( wset.zorigin_label ,
01009 "Direction of z origin distance" ) ;
01010
01011 printf(".");fflush(stdout);
01012
01013 /*----- a separator to keep the geometry stuff separate -----*/
01014
01015 wset.region_separator =
01016 XtVaCreateManagedWidget(
01017 "dialog" , xmSeparatorGadgetClass , wset.topform ,
01018 XmNseparatorType , XmDOUBLE_LINE ,
01019 XmNmargin , 3 ,
01020 XmNleftAttachment , XmATTACH_FORM ,
01021 XmNrightAttachment , XmATTACH_FORM ,
01022 XmNtopAttachment , XmATTACH_WIDGET ,
01023 XmNtopOffset , T3D_FORM_SPACING ,
01024 XmNtopWidget , wset.voxshape_bbox->wtop ,
01025 NULL ) ;
01026
01027 MCW_register_help( wset.region_separator ,
01028 "Thou art indeed just, Lord, if I contend\n"
01029 "With thee; but, sir, so what I plead is just.\n"
01030 "Why do sinners' ways prosper? and why must\n"
01031 "Disappointment all I endeavour end?\n"
01032 "Wert thou my enemy, O thou my friend,\n"
01033 "How wouldst thou worse, I wonder, than thou dost\n"
01034 "Defeat, thwart me? Oh, the sots and thralls of lust\n"
01035 "Do in spare hours more thrive than I that spend,\n"
01036 "Sir, life upon thy cause. See, banks and brakes\n"
01037 "Now, leav`ed how thick! lac`ed they are again\n"
01038 "With fretty chervil, look, and fresh wind shakes\n"
01039 "Them; birds build -- but not I build; no, but strain,\n"
01040 "Time's eunuch, and not breed one work that wakes.\n"
01041 "Mine, O thou lord of life, send my roots rain."
01042 ) ;
01043
01044 /*---- April 1996: arrowval for view_type ----*/
01045
01046 wset.view_type_av = new_MCW_arrowval(
01047 wset.topform , /* parent */
01048 "View: " , /* label */
01049 MCW_AV_downup , /* arrows */
01050 FIRST_VIEW_TYPE , /* min */
01051 LAST_VIEW_TYPE , /* max */
01052 user_inputs.view_type , /* init */
01053 MCW_AV_readtext , /* text */
01054 0 , /* decimals */
01055 T3D_orient_av_CB , NULL , /* callback */
01056 T3D_text_display , /* text maker */
01057 VIEW_typestr /* and data */
01058 ) ;
01059
01060 XtVaSetValues( wset.view_type_av->wrowcol ,
01061 XmNbottomAttachment , XmATTACH_WIDGET ,
01062 XmNbottomWidget , wset.region_separator ,
01063 XmNbottomOffset , T3D_FORM_SPACING ,
01064 XmNleftAttachment , XmATTACH_FORM ,
01065 XmNleftOffset , T3D_FORM_SPACING ,
01066 NULL ) ;
01067
01068 XtVaSetValues( wset.view_type_av->wtext ,
01069 XmNcolumns , LONGEST_VIEW_TYPESTR ,
01070 XmNmaxLength , LONGEST_VIEW_TYPESTR ,
01071 NULL ) ;
01072
01073 MCW_reghelp_children( wset.view_type_av->wrowcol ,
01074 "Sets the view type for the\n"
01075 "dataset being created. Except\n"
01076 "under unusual circumstances,\n"
01077 "this should be " VIEW_ORIGINAL_STR ) ;
01078
01079 /*---- Label to show what kind of data is stored ----*/
01080
01081 { char buf[32] ;
01082 sprintf( buf , "Datum: %s [%dx%d]\n" ,
01083 MRI_TYPE_name[argopt.datum_all], user_inputs.nx,user_inputs.ny ) ;
01084 wset.datum_label =
01085 XtVaCreateManagedWidget(
01086 "dialog" , xmLabelWidgetClass , wset.topform ,
01087 LABEL_ARG(buf) ,
01088 XmNbottomAttachment , XmATTACH_WIDGET ,
01089 XmNbottomWidget , wset.view_type_av->wrowcol ,
01090 XmNbottomOffset , 1 ,
01091 XmNleftAttachment , XmATTACH_FORM ,
01092 XmNleftOffset , T3D_FORM_SPACING ,
01093 XmNmarginHeight , 0 ,
01094 XmNmarginWidth , 0 ,
01095 NULL ) ;
01096
01097 }
01098 MCW_register_help( wset.datum_label ,
01099 "This shows the type of data stored\n"
01100 "in the images as read into to3d.\n"
01101 "You can only alter this by exiting\n"
01102 "the program and using the -datum\n"
01103 "option when you run to3d again." ) ;
01104 MCW_register_hint( wset.datum_label , "Type of data stored in images" ) ;
01105
01106 /*----- textfield widgets below the bar -----*/
01107
01108 /** name widgets not being used no more **/
01109
01110 #ifndef NO_NAMES
01111 wset.dataset_name_label =
01112 XtVaCreateManagedWidget(
01113 "dialog" , xmLabelWidgetClass , wset.topform ,
01114 LABEL_ARG("Dataset name: ") ,
01115 XmNtopAttachment , XmATTACH_WIDGET ,
01116 XmNtopWidget , wset.region_separator ,
01117 XmNtopOffset , T3D_FORM_SPACING ,
01118 XmNleftAttachment , XmATTACH_FORM ,
01119 XmNleftOffset , T3D_FORM_SPACING ,
01120 NULL ) ;
01121
01122 wset.dataset_name_textfield =
01123 XtVaCreateManagedWidget(
01124 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01125 XmNcolumns , 80 ,
01126 XmNeditable , True ,
01127 XmNmaxLength , THD_MAX_NAME-1 ,
01128 XmNresizeWidth , False ,
01129 XmNcursorPositionVisible , True ,
01130 XmNblinkRate , 0 ,
01131 /*
01132 XmNmarginHeight , 1 ,
01133 XmNmarginWidth , 1 ,
01134 */
01135 XmNvalue , user_inputs.dataset_name ,
01136
01137 XmNleftAttachment , XmATTACH_WIDGET ,
01138 XmNleftWidget , wset.dataset_name_label ,
01139 XmNleftOffset , T3D_FORM_SPACING ,
01140 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
01141 XmNtopWidget , wset.dataset_name_label ,
01142 XmNtopOffset , 0 ,
01143 NULL ) ;
01144
01145 MCW_register_help( wset.dataset_name_label ,
01146 "Every 3D dataset needs a name;\n"
01147 "Type in what you need to remind\n"
01148 "you of the subject/experiment" ) ;
01149
01150 MCW_register_help( wset.dataset_name_textfield ,
01151 "Every 3D dataset needs a label;\n"
01152 "Type in what you need to remind\n"
01153 "you of the subject/experiment" ) ;
01154
01155 wset.short_label1_label =
01156 XtVaCreateManagedWidget(
01157 "dialog" , xmLabelWidgetClass , wset.topform ,
01158 LABEL_ARG("Short label: ") ,
01159 XmNleftAttachment , XmATTACH_FORM ,
01160 XmNleftOffset , T3D_FORM_SPACING ,
01161 XmNtopAttachment , XmATTACH_WIDGET ,
01162 XmNtopWidget , wset.dataset_name_textfield ,
01163 XmNtopOffset , T3D_FORM_SPACING ,
01164 NULL ) ;
01165
01166 wset.short_label1_textfield =
01167 XtVaCreateManagedWidget(
01168 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01169 XmNcolumns , T3D_NAME_WIDTH ,
01170 XmNeditable , True ,
01171 XmNmaxLength , THD_MAX_LABEL-1 ,
01172 XmNresizeWidth , False ,
01173 XmNcursorPositionVisible , True ,
01174 XmNblinkRate , 0 ,
01175 /*
01176 XmNmarginHeight , 1 ,
01177 XmNmarginWidth , 1 ,
01178 */
01179 XmNvalue , user_inputs.short_label1 ,
01180
01181 XmNleftAttachment , XmATTACH_WIDGET ,
01182 XmNleftWidget , wset.short_label1_label ,
01183 XmNleftOffset , T3D_FORM_SPACING ,
01184 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
01185 XmNtopWidget , wset.short_label1_label ,
01186 XmNtopOffset , 0 ,
01187 NULL ) ;
01188
01189 MCW_register_help( wset.short_label1_label ,
01190 "The short label is used\n"
01191 "for a compact reminder of\n"
01192 "the dataset contents;\n"
01193 "type your choice in" ) ;
01194
01195 MCW_register_help( wset.short_label1_textfield ,
01196 "The short label is used\n"
01197 "for a compact reminder of\n"
01198 "the dataset contents;\n"
01199 "type your choice in" ) ;
01200 #endif /* NO_NAMES */
01201
01202 wset.geometry_parent_label =
01203 XtVaCreateManagedWidget(
01204 "dialog" , xmLabelWidgetClass , wset.topform ,
01205 LABEL_ARG("Copy geometry \nof this dataset") ,
01206 XmNleftAttachment , XmATTACH_FORM ,
01207 XmNleftOffset , T3D_FORM_SPACING ,
01208 XmNtopAttachment , XmATTACH_WIDGET ,
01209 #ifdef NO_NAMES
01210 XmNtopWidget , wset.region_separator ,
01211 #else
01212 XmNtopWidget , wset.short_label1_textfield ,
01213 #endif
01214 XmNtopOffset , T3D_FORM_SPACING ,
01215 NULL ) ;
01216
01217 wset.geometry_parent_textfield =
01218 XtVaCreateManagedWidget(
01219 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01220 XmNcolumns , T3D_NAME_WIDTH ,
01221 XmNeditable , True ,
01222 XmNmaxLength , THD_MAX_NAME-1 ,
01223 XmNresizeWidth , False ,
01224 XmNcursorPositionVisible , True ,
01225 XmNblinkRate , 0 ,
01226 /*
01227 XmNmarginHeight , 1 ,
01228 XmNmarginWidth , 1 ,
01229 */
01230 XmNvalue , user_inputs.geometry_parent_filename ,
01231
01232 XmNleftAttachment , XmATTACH_WIDGET ,
01233 XmNleftWidget , wset.geometry_parent_label ,
01234 XmNleftOffset , T3D_FORM_SPACING ,
01235 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
01236 XmNtopWidget , wset.geometry_parent_label ,
01237 XmNtopOffset , 0 ,
01238 NULL ) ;
01239
01240 XtAddCallback( wset.geometry_parent_textfield ,
01241 XmNactivateCallback ,
01242 T3D_geometry_parent_CB , NULL ) ; /* return key */
01243
01244 XtAddCallback( wset.geometry_parent_textfield ,
01245 XmNlosingFocusCallback ,
01246 T3D_geometry_parent_CB , NULL ) ; /* Tab key */
01247
01248 XtInsertEventHandler( wset.geometry_parent_textfield ,
01249 LeaveWindowMask , /* pointer leaves */
01250 FALSE ,
01251 T3D_pointer_leave_EV , NULL ,
01252 XtListTail ) ; /* last in queue */
01253
01254 MCW_register_help( wset.geometry_parent_label ,
01255 "If a previously created 3D dataset\n"
01256 "has the same geometry (voxel sizes,\n"
01257 "etc.), enter its header filename\n"
01258 "and press the Enter key" ) ;
01259 MCW_register_hint( wset.geometry_parent_label ,
01260 "Use the geometry of another dataset" ) ;
01261
01262 MCW_register_help( wset.geometry_parent_textfield ,
01263 "If a previously created 3D dataset\n"
01264 "has the same geometry (voxel sizes,\n"
01265 "etc.), enter its header filename name\n"
01266 "here and press the Enter key" ) ;
01267 MCW_register_hint( wset.geometry_parent_textfield ,
01268 "Use the geometry of another dataset" ) ;
01269
01270 wset.anatomy_parent_label =
01271 XtVaCreateManagedWidget(
01272 "dialog" , xmLabelWidgetClass , wset.topform ,
01273 LABEL_ARG("Anatomy parent \nis this dataset") ,
01274 XmNleftAttachment , XmATTACH_WIDGET ,
01275 XmNleftWidget , wset.geometry_parent_textfield ,
01276 XmNleftOffset , T3D_FORM_SPACING ,
01277 XmNtopAttachment , XmATTACH_WIDGET ,
01278 #ifdef NO_NAMES
01279 XmNtopWidget , wset.region_separator ,
01280 #else
01281 XmNtopWidget , wset.short_label1_textfield ,
01282 #endif
01283 XmNtopOffset , T3D_FORM_SPACING ,
01284 NULL ) ;
01285
01286 wset.anatomy_parent_textfield =
01287 XtVaCreateManagedWidget(
01288 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01289 XmNcolumns , T3D_NAME_WIDTH ,
01290 XmNeditable , True ,
01291 XmNmaxLength , THD_MAX_NAME-1 ,
01292 XmNresizeWidth , False ,
01293 XmNcursorPositionVisible , True ,
01294 XmNblinkRate , 0 ,
01295 /*
01296 XmNmarginHeight , 1 ,
01297 XmNmarginWidth , 1 ,
01298 */
01299 XmNvalue , user_inputs.anatomy_parent_filename ,
01300
01301 XmNleftAttachment , XmATTACH_WIDGET ,
01302 XmNleftOffset , T3D_FORM_SPACING ,
01303 XmNleftWidget , wset.anatomy_parent_label ,
01304 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
01305 XmNtopWidget , wset.anatomy_parent_label ,
01306 XmNtopOffset , 0 ,
01307 NULL ) ;
01308
01309 XtAddCallback( wset.anatomy_parent_textfield ,
01310 XmNactivateCallback ,
01311 T3D_anatomy_parent_CB , NULL ) ; /* return key */
01312
01313 XtAddCallback( wset.anatomy_parent_textfield ,
01314 XmNlosingFocusCallback ,
01315 T3D_anatomy_parent_CB , NULL ) ; /* Tab key */
01316
01317 XtInsertEventHandler( wset.anatomy_parent_textfield ,
01318 LeaveWindowMask , /* pointer leaves */
01319 FALSE ,
01320 T3D_pointer_leave_EV , NULL ,
01321 XtListTail ) ; /* last in queue */
01322
01323 MCW_register_help( wset.anatomy_parent_label ,
01324 "A dataset may optionally be attached\n"
01325 "to an 'anatomy parent' -- that is, an\n"
01326 "anatomical dataset which is aligned\n"
01327 "with the current dataset; usually, the\n"
01328 "anatomy parent should have been acquired\n"
01329 "during the same imaging session as the\n"
01330 "current dataset, so that this requisite\n"
01331 "alignment is assured. If no anatomy parent\n"
01332 "is given, then at the time one is needed,\n"
01333 "an appropriate dataset will be chosen from\n"
01334 "the same session directory.\n"
01335 "\n"
01336 #ifdef REQUIRE_ANAT_PARENT
01337 "N.B.: Functional datasets require anatomy parents;\n"
01338 " for anatomical datasets, anatomy parents are\n"
01339 " optional."
01340 #else
01341 "N.B.: You only need specify an anatomy parent\n"
01342 " here if a specific dataset is required."
01343 #endif
01344 ) ;
01345
01346 MCW_register_help( wset.anatomy_parent_textfield ,
01347 "A dataset may optionally be attached\n"
01348 "to an 'anatomy parent' -- that is, an\n"
01349 "anatomical dataset which is aligned\n"
01350 "with the current dataset; usually, the\n"
01351 "anatomy parent should have been acquired\n"
01352 "during the same imaging session as the\n"
01353 "current dataset, so that this requisite\n"
01354 "alignment is assured. If no anatomy parent\n"
01355 "is given, then at the time one is needed,\n"
01356 "an appropriate dataset will be chosen from\n"
01357 "the same session directory.\n"
01358 "\n"
01359 #ifdef REQUIRE_ANAT_PARENT
01360 "N.B.: functional datasets require anatomy parents;\n"
01361 " for anatomical datasets, anatomy parents are\n"
01362 " optional."
01363 #else
01364 "N.B.: You only need specify an anatomy parent\n"
01365 " here if a specific dataset is required."
01366 #endif
01367 ) ;
01368
01369 #ifndef NO_NAMES
01370 wset.geometry_dataname_label =
01371 XtVaCreateManagedWidget(
01372 "dialog" , xmLabelWidgetClass , wset.topform ,
01373 LABEL_ARG("Geometry parent\nDataset name ") ,
01374 XmNleftAttachment , XmATTACH_FORM ,
01375 XmNleftOffset , T3D_FORM_SPACING ,
01376 XmNtopAttachment , XmATTACH_WIDGET ,
01377 XmNtopWidget , wset.geometry_parent_textfield ,
01378 XmNtopOffset , T3D_FORM_SPACING ,
01379 XmNsensitive , False ,
01380 NULL ) ;
01381
01382 wset.geometry_dataname_textfield =
01383 XtVaCreateManagedWidget(
01384 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01385 XmNcolumns , T3D_NAME_WIDTH ,
01386 XmNeditable , False ,
01387 XmNmaxLength , THD_MAX_NAME-1 ,
01388 XmNresizeWidth , False ,
01389
01390 XmNcursorPositionVisible , False ,
01391 XmNsensitive , False ,
01392 /*
01393 XmNmarginHeight , 1 ,
01394 XmNmarginWidth , 1 ,
01395 */
01396 XmNvalue , " " ,
01397
01398 XmNleftAttachment , XmATTACH_WIDGET ,
01399 XmNleftWidget , wset.geometry_dataname_label ,
01400 XmNleftOffset , T3D_FORM_SPACING ,
01401 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
01402 XmNtopWidget , wset.geometry_dataname_label ,
01403 XmNtopOffset , 0 ,
01404 NULL ) ;
01405
01406 MCW_register_help( wset.geometry_dataname_label ,
01407 "This item just shows the\n"
01408 "dataset name of the 'geometry\n"
01409 "parent' you selected (e.g., to\n"
01410 "let you decide if you've got\n"
01411 "the right one)." ) ;
01412
01413 MCW_register_help( wset.geometry_dataname_textfield ,
01414 "This item just shows the\n"
01415 "dataset name of the 'geometry\n"
01416 "parent' you selected (e.g., to\n"
01417 "let you decide if you've got\n"
01418 "the right one)." ) ;
01419
01420 wset.anatomy_dataname_label =
01421 XtVaCreateManagedWidget(
01422 "dialog" , xmLabelWidgetClass , wset.topform ,
01423 LABEL_ARG("Anatomy parent \nDataset name ") ,
01424 XmNleftAttachment , XmATTACH_WIDGET ,
01425 XmNleftWidget , wset.geometry_dataname_textfield ,
01426 XmNleftOffset , T3D_FORM_SPACING ,
01427 XmNtopAttachment , XmATTACH_WIDGET ,
01428 XmNtopWidget , wset.geometry_parent_textfield ,
01429 XmNtopOffset , T3D_FORM_SPACING ,
01430 XmNsensitive , False ,
01431 NULL ) ;
01432
01433 wset.anatomy_dataname_textfield =
01434 XtVaCreateManagedWidget(
01435 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01436 XmNcolumns , T3D_NAME_WIDTH ,
01437 XmNeditable , False ,
01438 XmNmaxLength , THD_MAX_NAME-1 ,
01439 XmNresizeWidth , False ,
01440
01441 XmNcursorPositionVisible , False ,
01442 XmNsensitive , False ,
01443 /*
01444 XmNmarginHeight , 1 ,
01445 XmNmarginWidth , 1 ,
01446 */
01447 XmNvalue , " " ,
01448
01449 XmNleftAttachment , XmATTACH_WIDGET ,
01450 XmNleftWidget , wset.anatomy_dataname_label ,
01451 XmNleftOffset , T3D_FORM_SPACING ,
01452 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
01453 XmNtopWidget , wset.anatomy_dataname_label ,
01454 XmNtopOffset , 0 ,
01455 NULL ) ;
01456
01457 MCW_register_help( wset.anatomy_dataname_label ,
01458 "This item just shows the\n"
01459 "dataset name of the 'anatomy\n"
01460 "parent' you selected" ) ;
01461
01462 MCW_register_help( wset.anatomy_dataname_textfield ,
01463 "This item just shows the\n"
01464 "dataset name of the 'anatomy\n"
01465 "parent' you selected" ) ;
01466
01467 printf(".");fflush(stdout);
01468 #endif /* NO_NAMES */
01469
01470 /*----- arrowvals for dataset and function types -----*/
01471
01472 wset.dataset_type_av =
01473 new_MCW_arrowval(
01474 wset.topform , /* parent */
01475 "Type of data\nin the images ", /* label */
01476 MCW_AV_downup , /* arrows */
01477 FIRST_3DIM_TYPE , /* min */
01478 LAST_3DIM_TYPE , /* max */
01479 user_inputs.dataset_type , /* init */
01480 MCW_AV_readtext , /* text type */
01481 0 , /* decimals */
01482 T3D_type_av_CB , NULL , /* callback */
01483 T3D_text_display , /* text maker */
01484 DATASET_typestr /* and data */
01485 ) ;
01486
01487 wset.dataset_type_av->allow_wrap = 1 ;
01488
01489 XtVaSetValues( wset.dataset_type_av->wtext ,
01490 XmNcolumns , LONGEST_3DIM_TYPESTR ,
01491 XmNmaxLength , LONGEST_3DIM_TYPESTR ,
01492 NULL ) ;
01493
01494 XtVaSetValues( wset.dataset_type_av->wrowcol ,
01495 XmNleftAttachment , XmATTACH_FORM ,
01496 XmNleftOffset , T3D_FORM_SPACING ,
01497 XmNtopAttachment , XmATTACH_WIDGET ,
01498 #ifndef NO_NAMES
01499 XmNtopWidget , wset.geometry_dataname_label ,
01500 #else
01501 XmNtopWidget , wset.geometry_parent_label ,
01502 #endif
01503 XmNtopOffset , T3D_FORM_SPACING ,
01504 NULL ) ;
01505
01506 MCW_reghelp_children( wset.dataset_type_av->wrowcol ,
01507 "Use the arrows to specify\n"
01508 "the type of data stored\n"
01509 "in the image files.\n"
01510 "N.B.: 3D+time datasets\n"
01511 " must be anatomical." ) ;
01512 MCW_reghint_children( wset.dataset_type_av->wrowcol ,
01513 "Type of data you acquired" ) ;
01514
01515 if( user_inputs.ntt > 0 )
01516 AV_SENSITIZE( wset.dataset_type_av , False ) ;
01517
01518 wset.function_type_av =
01519 new_MCW_arrowval(
01520 wset.topform , /* parent */
01521 "Type of function \nin the images", /* label */
01522 MCW_AV_downup , /* arrows */
01523 FIRST_FUNC_TYPE , /* min */
01524 LAST_FUNC_TYPE , /* max */
01525 user_inputs.function_type , /* init */
01526 MCW_AV_readtext , /* text type */
01527 0 , /* decimals */
01528 T3D_type_av_CB , NULL , /* callback */
01529 T3D_text_display , /* text maker */
01530 FUNC_typestr /* and data */
01531 ) ;
01532
01533 wset.function_type_av->allow_wrap = 1 ;
01534
01535 XtVaSetValues( wset.function_type_av->wtext ,
01536 XmNcolumns , LONGEST_FUNC_TYPESTR ,
01537 XmNmaxLength , LONGEST_FUNC_TYPESTR ,
01538 NULL ) ;
01539
01540 XtVaSetValues( wset.function_type_av->wrowcol ,
01541 XmNleftAttachment , XmATTACH_WIDGET ,
01542 XmNleftOffset , T3D_FORM_SPACING ,
01543 XmNtopAttachment , XmATTACH_WIDGET ,
01544 XmNtopOffset , T3D_FORM_SPACING ,
01545 XmNleftWidget , wset.geometry_parent_textfield ,
01546 #ifndef NO_NAMES
01547 XmNtopWidget , wset.geometry_dataname_textfield ,
01548 #else
01549 XmNtopWidget , wset.geometry_parent_textfield ,
01550 #endif
01551 XtNmappedWhenManaged , False ,
01552 NULL ) ;
01553
01554 MCW_reghelp_children( wset.function_type_av->wrowcol ,
01555 "Use the arrows to specify\n"
01556 "the type of functional data\n"
01557 "stored in the image files" ) ;
01558 MCW_reghint_children( wset.function_type_av->wrowcol ,
01559 "Type of functional data" ) ;
01560
01561 wset.anatomy_type_av =
01562 new_MCW_arrowval(
01563 wset.topform , /* parent */
01564 "Type of anatomy \nin the images", /* label */
01565 MCW_AV_downup , /* arrows */
01566 FIRST_ANAT_TYPE , /* min */
01567 LAST_ANAT_TYPE , /* max */
01568 user_inputs.anatomy_type , /* init */
01569 MCW_AV_readtext , /* text type */
01570 0 , /* decimals */
01571 T3D_type_av_CB , NULL , /* callback */
01572 T3D_text_display , /* text maker */
01573 ANAT_typestr /* and data */
01574 ) ;
01575
01576 wset.anatomy_type_av->allow_wrap = 1 ;
01577
01578 XtVaSetValues( wset.anatomy_type_av->wtext ,
01579 XmNcolumns , LONGEST_ANAT_TYPESTR ,
01580 XmNmaxLength , LONGEST_ANAT_TYPESTR ,
01581 NULL ) ;
01582
01583 XtVaSetValues( wset.anatomy_type_av->wrowcol ,
01584 XmNleftAttachment , XmATTACH_WIDGET ,
01585 XmNleftWidget , wset.geometry_parent_textfield ,
01586 #ifndef NO_NAMES
01587 XmNtopWidget , wset.geometry_dataname_textfield ,
01588 #else
01589 XmNtopWidget , wset.geometry_parent_textfield ,
01590 #endif
01591 XmNleftOffset , T3D_FORM_SPACING ,
01592 XmNtopAttachment , XmATTACH_WIDGET ,
01593 XmNtopOffset , T3D_FORM_SPACING ,
01594 XtNmappedWhenManaged , False ,
01595 NULL ) ;
01596
01597 MCW_reghelp_children( wset.anatomy_type_av->wrowcol ,
01598 "Use the arrows to specify\n"
01599 "the type of anatomical data\n"
01600 "stored in the image files" ) ;
01601 MCW_reghint_children( wset.anatomy_type_av->wrowcol ,
01602 "Type of anatomical data" ) ;
01603
01604 /*----- stat_aux data fields -----*/
01605
01606 wset.stat_aux_label =
01607 XtVaCreateManagedWidget(
01608 "dialog" , xmLabelWidgetClass , wset.topform ,
01609 XmNleftAttachment , XmATTACH_FORM ,
01610 XmNleftOffset , T3D_FORM_SPACING ,
01611 XmNtopAttachment , XmATTACH_WIDGET ,
01612 XmNtopWidget , wset.dataset_type_av->wrowcol ,
01613 XmNtopOffset , T3D_FORM_SPACING ,
01614 NULL ) ;
01615
01616 wset.stat_aux_textfield =
01617 XtVaCreateManagedWidget(
01618 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01619 XmNcolumns , 80 ,
01620 XmNeditable , True ,
01621 XmNmaxLength , THD_MAX_NAME-1 ,
01622 XmNresizeWidth , False ,
01623 XmNcursorPositionVisible , True ,
01624 XmNblinkRate , 0 ,
01625 XmNleftAttachment , XmATTACH_FORM ,
01626 XmNleftOffset , T3D_FORM_SPACING ,
01627 XmNtopAttachment , XmATTACH_WIDGET ,
01628 XmNtopWidget , wset.stat_aux_label ,
01629 XmNtopOffset , 1 ,
01630 NULL ) ;
01631
01632 MCW_register_help( wset.stat_aux_label ,
01633 "Some types of functional data require input\n"
01634 "of extra statistical parameters. These\n"
01635 "values should be entered in the text field\n"
01636 "below, separated by spaces and/or commas.\n"
01637 "\n"
01638 " Inten+Cor requires the number of\n"
01639 " samples (images) used, the number of\n"
01640 " fitting parameters, and the number of\n"
01641 " orthogonalization parameters.\n"
01642 "\n"
01643 " Inten+Ttest requires the number of\n"
01644 " degrees-of-freedom in the t-test."
01645 ) ;
01646
01647 MCW_register_help( wset.stat_aux_textfield ,
01648 "Some types of functional data require input\n"
01649 "of extra statistical parameters. These\n"
01650 "values should be entered in this text field,\n"
01651 "separated by spaces and/or commas.\n"
01652 "\n"
01653 " Inten+Cor requires the number of\n"
01654 " samples (images) used, the number of\n"
01655 " fitting parameters, and the number of\n"
01656 " orthogonalization parameters.\n"
01657 "\n"
01658 " Inten+Ttest requires the number of\n"
01659 " degrees-of-freedom in the t-test."
01660 ) ;
01661
01662 MCW_register_hint( wset.stat_aux_label , "Extra statistical parameters" ) ;
01663 MCW_register_hint( wset.stat_aux_textfield , "Extra statistical parameters" ) ;
01664
01665 /** The stuff below is commented out,
01666 since the textfield is scanned only at the write-out time **/
01667
01668 #if 0
01669 XtAddCallback( wset.stat_aux_textfield ,
01670 XmNactivateCallback ,
01671 T3D_stat_aux_CB , NULL ) ; /* return key */
01672
01673 XtAddCallback( wset.stat_aux_textfield ,
01674 XmNlosingFocusCallback ,
01675 T3D_stat_aux_CB , NULL ) ; /* Tab key */
01676
01677 XtInsertEventHandler( wset.stat_aux_textfield ,
01678 LeaveWindowMask , /* pointer leaves */
01679 FALSE ,
01680 T3D_pointer_leave_EV , NULL ,
01681 XtListTail ) ; /* last in queue */
01682 #endif
01683
01684 /*--- output locations ---*/
01685
01686 wset.output_file_label =
01687 XtVaCreateManagedWidget(
01688 "dialog" , xmLabelWidgetClass , wset.topform ,
01689 LABEL_ARG("Prefix for 3D \nDataset file ") ,
01690
01691 XmNleftAttachment , XmATTACH_WIDGET ,
01692 XmNleftWidget , wset.geometry_parent_textfield ,
01693 XmNleftOffset , T3D_FORM_SPACING ,
01694 XmNtopAttachment , XmATTACH_WIDGET ,
01695 XmNtopWidget , wset.stat_aux_textfield ,
01696 XmNtopOffset , T3D_FORM_SPACING ,
01697 XmNbottomAttachment , XmATTACH_FORM ,
01698 XmNbottomOffset , T3D_FORM_SPACING ,
01699 NULL ) ;
01700
01701 wset.output_file_textfield =
01702 XtVaCreateManagedWidget(
01703 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01704 XmNcolumns , T3D_NAME_WIDTH ,
01705 XmNeditable , True ,
01706 XmNmaxLength , THD_MAX_PREFIX-1 ,
01707 XmNresizeWidth , False ,
01708 XmNcursorPositionVisible , True ,
01709 XmNblinkRate , 0 ,
01710 /*
01711 XmNmarginHeight , 1 ,
01712 XmNmarginWidth , 1 ,
01713 */
01714 XmNvalue , user_inputs.output_filename ,
01715
01716 XmNleftAttachment , XmATTACH_WIDGET ,
01717 XmNleftOffset , T3D_FORM_SPACING ,
01718 XmNleftWidget , wset.output_file_label ,
01719 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
01720 XmNtopWidget , wset.output_file_label ,
01721 XmNtopOffset , 0 ,
01722
01723 NULL ) ;
01724
01725 MCW_register_help( wset.output_file_label ,
01726 "Type in the 'prefix' for the filenames\n"
01727 "that the 3D dataset will be saved in.\n"
01728 "[The actual filenames will be of the\n"
01729 " form prefix+orig.suff, where suff =\n"
01730 " " DATASET_HEADER_SUFFIX " and " DATASET_BRICK_SUFFIX "]" ) ;
01731
01732 MCW_register_help( wset.output_file_textfield ,
01733 "Type in the 'prefix' for the filenames\n"
01734 "that the 3D dataset will be saved in.\n"
01735 "[The actual filenames will be of the\n"
01736 " form prefix+orig.suff, where suff =\n"
01737 " " DATASET_HEADER_SUFFIX " and " DATASET_BRICK_SUFFIX "]" ) ;
01738
01739 MCW_register_hint( wset.output_file_label ,
01740 "New dataset's 'prefix' for filenames" ) ;
01741 MCW_register_hint( wset.output_file_textfield ,
01742 "New dataset's 'prefix' for filenames" ) ;
01743
01744 wset.session_file_label =
01745 XtVaCreateManagedWidget(
01746 "dialog" , xmLabelWidgetClass , wset.topform ,
01747 LABEL_ARG("Session direct.\nfor 3D Datasets") ,
01748
01749 XmNleftAttachment , XmATTACH_FORM ,
01750 XmNleftOffset , T3D_FORM_SPACING ,
01751 XmNtopAttachment , XmATTACH_WIDGET ,
01752 XmNtopWidget , wset.stat_aux_textfield ,
01753 XmNtopOffset , T3D_FORM_SPACING ,
01754 NULL ) ;
01755
01756 wset.session_file_textfield =
01757 XtVaCreateManagedWidget(
01758 "dialog" , xmTextFieldWidgetClass , wset.topform ,
01759 XmNcolumns , T3D_NAME_WIDTH ,
01760 XmNeditable , True ,
01761 XmNmaxLength , THD_MAX_NAME-1 ,
01762 XmNresizeWidth , False ,
01763 XmNcursorPositionVisible , True ,
01764 XmNblinkRate , 0 ,
01765 /*
01766 XmNmarginHeight , 1 ,
01767 XmNmarginWidth , 1 ,
01768 */
01769 XmNvalue , user_inputs.session_filename ,
01770
01771 XmNleftAttachment , XmATTACH_WIDGET ,
01772 XmNleftOffset , T3D_FORM_SPACING ,
01773 XmNleftWidget , wset.session_file_label ,
01774 XmNtopAttachment , XmATTACH_OPPOSITE_WIDGET ,
01775 XmNtopWidget , wset.session_file_label ,
01776 XmNtopOffset , 0 ,
01777
01778 NULL ) ;
01779
01780 MCW_register_help( wset.session_file_label ,
01781 "Type in the name of the session\n"
01782 "directory in which to save this\n"
01783 "3D dataset, and in which to look\n"
01784 "for the 'parent' datasets" ) ;
01785
01786 MCW_register_help( wset.session_file_textfield ,
01787 "Type in the name of the session\n"
01788 "directory in which to save this\n"
01789 "3D dataset, and in which to look\n"
01790 "for the 'parent' datasets" ) ;
01791
01792 MCW_register_hint( wset.session_file_label , "New dataset's directory" ) ;
01793 MCW_register_hint( wset.session_file_textfield , "New dataset's directory" ) ;
01794
01795 printf(".");fflush(stdout);
01796
01797 /*----- action controls at lower right corner -----*/
01798
01799 wset.action_frame =
01800 XtVaCreateManagedWidget(
01801 "dialog" , xmFrameWidgetClass , wset.topform ,
01802 XmNshadowType , XmSHADOW_ETCHED_IN ,
01803 XmNleftAttachment , XmATTACH_WIDGET ,
01804 XmNleftWidget , wset.anatomy_parent_textfield ,
01805 XmNleftOffset , T3D_FORM_SPACING ,
01806 XmNbottomAttachment , XmATTACH_FORM ,
01807 XmNbottomOffset , T3D_FORM_SPACING ,
01808 NULL ) ;
01809
01810 wset.action_rowcol =
01811 XtVaCreateWidget(
01812 "dialog" , xmRowColumnWidgetClass , wset.action_frame ,
01813 XmNorientation , XmVERTICAL ,
01814 XmNpacking , XmPACK_TIGHT ,
01815 NULL ) ;
01816
01817 /* 14 Sep 1998: add a button to swap bytes in the image data */
01818
01819 { int dd = mri_datum_size((MRI_TYPE)argopt.datum_all) ;
01820 char * tt = "Byte Swap[2]" ;
01821 char * ff = "Byte Swap[4]" ;
01822 if( dd == 2 || dd == 4 ){
01823 if( dd == 2 )
01824 wset.swap_pb =
01825 XtVaCreateManagedWidget(
01826 "dialog" , xmPushButtonWidgetClass , wset.action_rowcol ,
01827 LABEL_ARG(tt) , NULL ) ;
01828 else
01829 wset.swap_pb =
01830 XtVaCreateManagedWidget(
01831 "dialog" , xmPushButtonWidgetClass , wset.action_rowcol ,
01832 LABEL_ARG(ff) , NULL ) ;
01833
01834 XtAddCallback( wset.swap_pb , XmNactivateCallback ,
01835 T3D_swap_CB , NULL ) ;
01836 MCW_register_hint( wset.swap_pb , "Use if images need this" ) ;
01837 } else {
01838 wset.swap_pb = NULL ;
01839 }
01840 }
01841
01842 wset.button_help_pb =
01843 XtVaCreateManagedWidget(
01844 "dialog" , xmPushButtonWidgetClass , wset.action_rowcol ,
01845 LABEL_ARG("button help") ,
01846 NULL ) ;
01847 XtAddCallback( wset.button_help_pb , XmNactivateCallback ,
01848 MCW_click_help_CB , NULL ) ;
01849 MCW_register_help( wset.button_help_pb ,
01850 "Click the hand\non any button to get\na little help" ) ;
01851 MCW_register_hint( wset.button_help_pb , "Get more help" ) ;
01852
01853 wset.open_view_pb =
01854 XtVaCreateManagedWidget(
01855 "dialog" , xmPushButtonWidgetClass , wset.action_rowcol ,
01856 LABEL_ARG("View Images") ,
01857 NULL ) ;
01858 XtAddCallback( wset.open_view_pb , XmNactivateCallback ,
01859 T3D_open_view_CB , NULL ) ;
01860 MCW_register_help( wset.open_view_pb ,
01861 "Use this to open a window to see the images;\n"
01862 "N.B.: If you use the viewing controls to change the\n"
01863 " orientation of the images, then you must be\n"
01864 " aware that 'x' and 'y' in the geometry controls\n"
01865 " above refer to the images in their ORIGINAL\n"
01866 " orientation on the screen, NOT in the rotated\n"
01867 " and/or mirrored orientation you will be viewing." ) ;
01868 MCW_register_hint( wset.open_view_pb , "See the input images" ) ;
01869
01870 wset.save_file_pb =
01871 XtVaCreateManagedWidget(
01872 "dialog" , xmPushButtonWidgetClass , wset.action_rowcol ,
01873 LABEL_ARG("Save Dataset") ,
01874 NULL ) ;
01875 XtAddCallback( wset.save_file_pb , XmNactivateCallback ,
01876 T3D_save_file_CB , NULL ) ;
01877 MCW_register_help( wset.save_file_pb ,
01878 "Use this to save the volume data\n"
01879 "into 3D dataset files when you\n"
01880 "have set all the control data." ) ;
01881 MCW_register_hint( wset.save_file_pb , "Write new dataset to disk" ) ;
01882
01883 wset.quit_pb =
01884 XtVaCreateManagedWidget(
01885 "dialog" , xmPushButtonWidgetClass , wset.action_rowcol ,
01886 XmNrecomputeSize , False ,
01887 LABEL_ARG("quit") ,
01888 NULL ) ;
01889 XtAddCallback( wset.quit_pb , XmNactivateCallback ,
01890 T3D_quit_CB , NULL ) ;
01891 MCW_register_help( wset.quit_pb ,
01892 "Press this button TWICE\nto exit the program" ) ;
01893 MCW_register_hint( wset.quit_pb , "Press twice to exit program" ) ;
01894
01895 MCW_set_widget_bg( wset.quit_pb , MCW_hotcolor(wset.quit_pb) , 0 ) ;
01896
01897 XtManageChild( wset.action_rowcol ) ;
01898
01899 printf(".");fflush(stdout);
01900
01901 /*----- all done -----*/
01902
01903 XtManageChild( wset.topform ) ;
01904
01905 XtRealizeWidget( wset.topshell ) ;
01906
01907 WAIT_for_window( wset.topshell ) ; /* 10 Sep 2002 */
01908 wset.good = 1 ;
01909
01910 T3D_data_to_widgets() ;
01911 T3D_set_dependent_geometries() ;
01912
01913 EXRETURN ;
01914 }
|
|
|
|
||||||||||||
|
Definition at line 3674 of file to3d.c. References to3d_data::fov, to3d_widget_set::fov_av, MCW_arrowval::fval, RESET_QUIT, and T3D_set_dependent_geometries(). Referenced by T3D_create_widgets().
03675 {
03676 user_inputs.fov = wset.fov_av->fval ;
03677 T3D_set_dependent_geometries() ;
03678 RESET_QUIT ;
03679 }
|
|
||||||||||||||||
|
Definition at line 5343 of file to3d.c. References THD_3dim_dataset::anat_parent_idcode, THD_3dim_dataset::anat_parent_name, to3d_data::anatomy_dataname, to3d_data::anatomy_parent_idcode, client_data, THD_3dim_dataset::daxes, THD_3dim_dataset::dblk, DEBLANK, ENTRY, FILENAME_TO_PREFIX, to3d_data::fov, to3d_data::geometry_dataname, geometry_loaded, to3d_data::geometry_parent_filename, geomparent_loaded, ATR_int::in, INERR, MCW_strncpy, myXtFree, ATR_int::nin, to3d_data::nx, THD_dataxes::nxx, to3d_data::ny, THD_dataxes::nyy, to3d_data::nz, THD_dataxes::nzz, PATH_CONCAT, THD_3dim_dataset::self_name, to3d_widget_set::session_file_textfield, to3d_data::session_filename, T3D_data_to_widgets(), T3D_poperr(), T3D_widgets_to_data(), THD_delete_3dim_dataset(), THD_find_int_atr(), THD_MAX_NAME, THD_open_one_dataset(), to3d_data::voxcontig, VOXCONTIG_UNIF, VOXCONTIG_YES, to3d_data::voxshape, VOXSHAPE_CUBICAL, VOXSHAPE_IRREGULAR, VOXSHAPE_SQUARE, XCENTERED, to3d_data::xorient, to3d_data::xorigin, to3d_data::xsize, THD_dataxes::xxdel, THD_dataxes::xxorg, THD_dataxes::xxorient, to3d_data::xyz_centered, YCENTERED, to3d_data::yorient, to3d_data::yorigin, to3d_data::ysize, THD_dataxes::yydel, THD_dataxes::yyorg, THD_dataxes::yyorient, ZCENTERED, to3d_data::zorient, to3d_data::zorigin, zpad, to3d_data::zsize, to3d_data::zspacing, THD_dataxes::zzdel, THD_dataxes::zzorg, and THD_dataxes::zzorient. Referenced by main(), and T3D_create_widgets().
05345 {
05346 static char * old_name = NULL ;
05347 char * new_name ;
05348 float size ;
05349 char new_path[THD_MAX_NAME] , new_pref[THD_MAX_NAME] ;
05350 THD_3dim_dataset * geom_dset ;
05351 THD_dataxes * geom_daxes ;
05352
05353 int xpad=0,ypad=0,zpad=0 ; /* 05 Feb 2001 */
05354
05355 ENTRY("T3D_geometry_parent_CB") ;
05356
05357 if( old_name == NULL ) old_name = XtNewString("Elvis Lives!!!") ;
05358
05359 if( w != NULL ){
05360 new_name = XmTextFieldGetString( w ) ; /* get the new text */
05361 } else {
05362 new_name = XtNewString( user_inputs.geometry_parent_filename ) ;
05363 }
05364 DEBLANK(new_name) ;
05365
05366 if( strlen(new_name) == 0 ) { old_name = new_name ; geomparent_loaded = 0 ; EXRETURN ; }
05367 if( strcmp(new_name,old_name) == 0 ){ myXtFree(new_name) ; geomparent_loaded = 0 ; EXRETURN ; }
05368
05369 /* have a new filename --> try to read dataset from it */
05370
05371 myXtFree(old_name) ; old_name = new_name ;
05372
05373 /* make a pathname to the geometry dataset */
05374
05375 if( strstr(new_name,"/") == NULL ){
05376 char * sess ;
05377 if( w != NULL ) sess = XmTextFieldGetString(wset.session_file_textfield);
05378 else sess = XtNewString( user_inputs.session_filename ) ;
05379 DEBLANK(sess) ;
05380 if( strlen(sess) > 0 ){
05381 PATH_CONCAT( new_path , sess , new_name ) ;
05382 } else {
05383 strcpy( new_path , new_name ) ;
05384 }
05385 myXtFree(sess) ;
05386 } else {
05387 strcpy( new_path , new_name ) ;
05388 }
05389
05390 FILENAME_TO_PREFIX(new_path,new_pref) ;
05391 if( strlen(new_pref) == 0 ) strcat(new_path,"+orig") ;
05392
05393 /* read dataset from this path */
05394
05395 geom_dset = THD_open_one_dataset( new_path ) ;
05396 if( geom_dset == NULL ){
05397 T3D_poperr( INERR ,
05398 "Cannot read 3D dataset\nin geometry parent file" ) ;
05399 geomparent_loaded = 0 ; EXRETURN ;
05400 }
05401
05402 /* 05 Feb 2001: set if this was a 'padded' dataset from an earlier to3d */
05403
05404 { ATR_int * atr ;
05405 atr = THD_find_int_atr( geom_dset->dblk , "TO3D_ZPAD" ) ;
05406 if( atr != NULL && atr->nin >= 3 ){
05407 xpad = atr->in[0] ;
05408 ypad = atr->in[1] ;
05409 zpad = atr->in[2] ;
05410 }
05411 }
05412
05413 geom_daxes = geom_dset->daxes ;
05414
05415 if( geom_daxes->nxx - 2*xpad != user_inputs.nx ||
05416 geom_daxes->nyy - 2*ypad != user_inputs.ny ||
05417 geom_daxes->nzz - 2*zpad != user_inputs.nz ){
05418
05419 char msg[256] ;
05420
05421 sprintf(msg,
05422 "*** Shape mismatch!! ***\n"
05423 "file nx=%d ny=%d nz=%d (zpad=%d)\n"
05424 "images nx=%d ny=%d nz=%d",
05425 geom_daxes->nxx,geom_daxes->nyy,geom_daxes->nzz,zpad,
05426 user_inputs.nx ,user_inputs.ny ,user_inputs.nz ) ;
05427
05428 T3D_poperr( INERR , msg ) ;
05429 THD_delete_3dim_dataset( geom_dset , False ) ;
05430 geomparent_loaded = 0 ; EXRETURN ;
05431 }
05432
05433 #ifdef ALLOW_NONCONTIG
05434 if( geom_daxes->xxskip != 0.0 || geom_daxes->yyskip != 0.0 ){
05435 T3D_poperr( INERR , "Nonzero skip factors for x and y!" ) ;
05436 THD_delete_3dim_dataset( geom_dset , False ) ;
05437 geomparent_loaded = 0 ; EXRETURN ;
05438 }
05439 #endif
05440
05441 /* at this point, the geom dataset seems OK, so copy its axes data */
05442
05443 /* but first, load all data from the widgets into the user_inputs
05444 (this will mean that the T3D_data_to_widgets call later won't
05445 clobber any un-altered but currently un-saved data fields */
05446
05447 T3D_widgets_to_data() ;
05448
05449 #ifdef REQUIRE_ANAT_PARENT
05450 if( strlen(geom_dset->anat_parent_name) > 0 ){
05451 MCW_strncpy( user_inputs.anatomy_dataname ,
05452 geom_dset->anat_parent_name, THD_MAX_NAME ) ;
05453 user_inputs.anatomy_parent_idcode = geom_dset->anat_parent_idcode ;
05454 }
05455 #endif
05456
05457 MCW_strncpy( user_inputs.geometry_dataname ,
05458 geom_dset->self_name , THD_MAX_NAME ) ;
05459
05460 MCW_strncpy( user_inputs.geometry_parent_filename ,
05461 new_name , THD_MAX_NAME ) ;
05462
05463 user_inputs.xorient = geom_daxes->xxorient ;
05464 user_inputs.yorient = geom_daxes->yyorient ;
05465 user_inputs.zorient = geom_daxes->zzorient ;
05466
05467 #if 0 /* Bad stuff, replaced June 20, 1995 */
05468
05469 user_inputs.xorigin = fabs(geom_daxes->xxorg) ;
05470 user_inputs.yorigin = fabs(geom_daxes->yyorg) ;
05471 user_inputs.zorigin = fabs(geom_daxes->zzorg) ;
05472
05473 #else /* newer stuff [05 Feb 2001] - allow for padding in to3d before */
05474
05475 { float xorg = geom_daxes->xxorg + xpad * geom_daxes->xxdel ;
05476 float yorg = geom_daxes->yyorg + ypad * geom_daxes->yydel ;
05477 float zorg = geom_daxes->zzorg + zpad * geom_daxes->zzdel ;
05478
05479 user_inputs.xorigin = (ORIENT_sign[user_inputs.xorient] == '+')
05480 ? (-xorg) : (xorg) ;
05481 user_inputs.yorigin = (ORIENT_sign[user_inputs.yorient] == '+')
05482 ? (-yorg) : (yorg) ;
05483 user_inputs.zorigin = (ORIENT_sign[user_inputs.zorient] == '+')
05484 ? (-zorg) : (zorg) ;
05485 }
05486 #endif
05487
05488 user_inputs.xsize = fabs(geom_daxes->xxdel) ;
05489 user_inputs.ysize = fabs(geom_daxes->yydel) ;
05490 #ifdef ALLOW_NONCONTIG
05491 user_inputs.zspacing = fabs(geom_daxes->zzdel) ;
05492 user_inputs.zsize = user_inputs.zspacing - geom_daxes->zzskip ;
05493 #else
05494 user_inputs.zsize = fabs(geom_daxes->zzdel) ;
05495 #endif
05496
05497 /*-- set the vox*_bbox values depending on initial sizes --*/
05498
05499 if( user_inputs.xsize != user_inputs.ysize ){
05500 user_inputs.voxshape = VOXSHAPE_IRREGULAR ;
05501 } else {
05502 if( user_inputs.xsize != user_inputs.zsize ){
05503 user_inputs.voxshape = VOXSHAPE_SQUARE ;
05504 } else {
05505 user_inputs.voxshape = VOXSHAPE_CUBICAL ;
05506 }
05507 }
05508 user_inputs.fov = user_inputs.xsize * user_inputs.nx ;
05509
05510 #ifdef ALLOW_NONCONTIG
05511 if( geom_daxes->zzskip == 0 ) user_inputs.voxcontig = VOXCONTIG_YES ;
05512 else user_inputs.voxcontig = VOXCONTIG_UNIF ;
05513 #endif
05514
05515 user_inputs.xyz_centered = 0 ;
05516
05517 size = 0.5 * (user_inputs.nx-1) * user_inputs.xsize ;
05518 if( fabs(size - user_inputs.xorigin) < 0.01 )
05519 user_inputs.xyz_centered |= XCENTERED ;
05520
05521 size = 0.5 * (user_inputs.ny-1) * user_inputs.ysize ;
05522 if( fabs(size - user_inputs.yorigin) < 0.01 )
05523 user_inputs.xyz_centered |= YCENTERED ;
05524
05525 size = 0.5 * (user_inputs.nz-1) * user_inputs.zsize ;
05526 if( fabs(size - user_inputs.zorigin) < 0.01 )
05527 user_inputs.xyz_centered |= ZCENTERED ;
05528
05529 T3D_data_to_widgets() ;
05530
05531 THD_delete_3dim_dataset( geom_dset , False ) ;
05532
05533 geometry_loaded = 1 ;
05534 geomparent_loaded = 1 ; /* flag that load was OK */
05535
05536 EXRETURN ;
05537 }
|
|
||||||||||||||||
|
Definition at line 4601 of file to3d.c. References MCW_imseq_status::aux, FD_brick_to_mri(), isqCR_getimage, isqCR_getoverlay, isqCR_getqimage, isqCR_getstatus, myXtNew, FD_brick::n3, MCW_imseq_status::num_series, MCW_imseq_status::num_total, MCW_imseq_status::parent, MCW_imseq_status::send_CB, MCW_imseq_status::slice_proj, T3D_imseq_CB(), MCW_imseq_status::transforms0D, and MCW_imseq_status::transforms2D. Referenced by T3D_open_view_CB().
04602 {
04603 MCW_imseq_status * stat ;
04604
04605 if( n < 0 || n >= br->n3 || type == isqCR_getoverlay ) return NULL ;
04606
04607 if( type == isqCR_getstatus ){
04608 stat = myXtNew( MCW_imseq_status ) ;
04609
04610 stat->num_total = br->n3 ;
04611 stat->num_series = br->n3 ;
04612 stat->send_CB = T3D_imseq_CB ;
04613 stat->parent = (XtPointer) br ;
04614 stat->aux = NULL ;
04615
04616 stat->transforms0D = NULL ;
04617 stat->transforms2D = NULL ;
04618 stat->slice_proj = NULL ;
04619
04620 return (XtPointer) stat ;
04621 }
04622
04623 if( type == isqCR_getimage || type == isqCR_getqimage ){
04624 return (XtPointer) FD_brick_to_mri( n , 0 , br ) ;
04625 }
04626
04627 return NULL ; /* should never be reached */
04628 }
|
|
||||||||||||||||
|
Definition at line 4632 of file to3d.c. References THD_string_array::ar, drive_MCW_imseq(), MCW_imseq::im_nr, isqCR_destroy, isqCR_force_redisplay, isqCR_newimage, isqDR_display, isqDR_rebar, isqDR_title, MCW_invert_widget(), myXtFree, ISQ_cbs::nim, to3d_widget_set::open_view_pb, ISQ_cbs::reason, and to3d_widget_set::seq. Referenced by T3D_getim().
04633 {
04634 switch( cbs->reason ){
04635
04636 case isqCR_destroy:
04637 myXtFree( seq ) ; wset.seq = NULL ;
04638 myXtFree( br ) ;
04639 MCW_invert_widget( wset.open_view_pb ) ;
04640 break ;
04641
04642 case isqCR_newimage:
04643 drive_MCW_imseq( seq, isqDR_title, (XtPointer) imnames->ar[cbs->nim] ) ;
04644 break ;
04645
04646 case isqCR_force_redisplay:{ /* 22 Aug 1998 */
04647 drive_MCW_imseq( seq , isqDR_display , (XtPointer) seq->im_nr ) ;
04648 drive_MCW_imseq( seq , isqDR_rebar , (XtPointer) seq->im_nr ) ;
04649 }
04650
04651 }
04652 return ;
04653 }
|
|
|
Definition at line 1942 of file to3d.c. References af_type_set, AFNI_log_string, ANAT_EPI_TYPE, to3d_data::anatomy_dataname, to3d_data::anatomy_parent_filename, to3d_data::anatomy_parent_idcode, to3d_data::anatomy_type, to3d_data::anatomy_type_string, Argc, argopt, Argv, commandline, to3d_data::dataset_name, to3d_data::dataset_type, to3d_data::dataset_type_string, decode_location(), EMPTY_STRING, ENTRY, FatalError, FIRST_ANAT_TYPE, FIRST_FUNC_TYPE, First_Image_Arg, FIRST_VIEW_TYPE, free, to3d_data::function_type, to3d_data::function_type_string, to3d_data::geometry_dataname, to3d_data::geometry_parent_filename, HEAD_ANAT_TYPE, HEAD_FUNC_TYPE, INCODE_FOV, INCODE_NONE, INCODE_SLAB, LAST_ANAT_TYPE, LAST_FUNC_TYPE, LAST_VIEW_TYPE, malloc, MAX_STAT_AUX, MCW_strncpy, my_getenv(), to3d_data::nosave, to3d_data::ntt, NZBOT, to3d_data::nzz, ORCODE, ORIENT_OPPOSITE, outliers_fname, to3d_data::output_filename, to3d_data::session_filename, to3d_data::short_label1, to3d_data::short_label2, to3d_data::stat_aux, strtod(), Syntax(), to3d_data::t_then_z, THD_filename_ok(), THD_MAX_LABEL, THD_MAX_NAME, THD_MAX_PREFIX, to3d_data::Torg, to3d_data::tpattern, to3d_data::TR, TR, tross_commandline(), to3d_data::tunits, UNITS_HZ_TYPE, UNITS_MSEC_TYPE, UNITS_SEC_TYPE, use_zoff, VIEW_ORIGINAL_TYPE, to3d_data::view_type, WarningError, to3d_data::xin_bot, to3d_data::xin_top, to3d_data::xincode, to3d_data::xorient, to3d_data::yin_bot, to3d_data::yin_top, to3d_data::yincode, to3d_data::yorient, ZERO_IDCODE, to3d_data::zin_bot, to3d_data::zin_top, to3d_data::zincode, zoff, to3d_data::zorient, zpad, and zpad_mm. Referenced by main().
01943 {
01944 int nopt , ii ;
01945
01946 ENTRY("T3D_initialize_user_data") ;
01947
01948 user_inputs = default_user_inputs ; /* copy defaults */
01949 user_inputs.nosave = 0 ;
01950
01951 /*-- initialize strings --*/
01952
01953 EMPTY_STRING( user_inputs.dataset_name ) ;
01954 EMPTY_STRING( user_inputs.short_label1 ) ;
01955 EMPTY_STRING( user_inputs.short_label2 ) ;
01956 EMPTY_STRING( user_inputs.geometry_parent_filename ) ;
01957 EMPTY_STRING( user_inputs.anatomy_parent_filename ) ;
01958 EMPTY_STRING( user_inputs.anatomy_dataname ) ;
01959 EMPTY_STRING( user_inputs.geometry_dataname ) ;
01960 EMPTY_STRING( user_inputs.output_filename ) ;
01961 ZERO_IDCODE( user_inputs.anatomy_parent_idcode ) ;
01962
01963 strcpy( user_inputs.session_filename , "./" ) ;
01964
01965 strcpy( user_inputs.dataset_type_string ,
01966 DATASET_typestr[user_inputs.dataset_type] ) ;
01967
01968 strcpy( user_inputs.function_type_string ,
01969 FUNC_typestr[user_inputs.function_type] ) ;
01970
01971 user_inputs.view_type = VIEW_ORIGINAL_TYPE ;
01972
01973 for( ii=0 ; ii < MAX_STAT_AUX ; ii++ )
01974 user_inputs.stat_aux[ii] = 0.0 ;
01975
01976 user_inputs.xincode = user_inputs.yincode = user_inputs.zincode = INCODE_NONE ;
01977
01978 user_inputs.ntt = 0 ;
01979 user_inputs.TR = 1.0 ;
01980 user_inputs.Torg = 0.0 ; /* 23 Feb 2005 */
01981 user_inputs.nzz = 0 ;
01982 user_inputs.t_then_z = 0 ;
01983 user_inputs.tpattern = NULL ;
01984 user_inputs.tunits = UNITS_MSEC_TYPE ;
01985
01986 /*-- 05 Feb 2000: zpad environment --*/
01987
01988 { char *eee=my_getenv("AFNI_TO3D_ZPAD") , *fff ;
01989 if( eee != NULL ){
01990 zpad = strtod( eee , &fff ) ;
01991 if( zpad < 0.0 ) FatalError("AFNI_TO3D_ZPAD is negative") ;
01992 zpad_mm = (*fff == 'm') ;
01993 }
01994 }
01995
01996 /*-- scan options --*/
01997
01998 nopt = 1 ;
01999 while( nopt < Argc && Argv[nopt][0] == '-' ){
02000
02001 if( strncmp(Argv[nopt],"-help",4) == 0 ){
02002 Syntax() ;
02003 }
02004
02005 /* -type from the anatomy prefixes */
02006
02007 for( ii=FIRST_ANAT_TYPE ; ii <= LAST_ANAT_TYPE ; ii++ )
02008 if( strncmp( &(Argv[nopt][1]) ,
02009 ANAT_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ;
02010
02011 if( ii <= LAST_ANAT_TYPE ){
02012 user_inputs.anatomy_type = ii ;
02013 user_inputs.dataset_type = HEAD_ANAT_TYPE ;
02014 strcpy( user_inputs.dataset_type_string ,
02015 DATASET_typestr[user_inputs.dataset_type] ) ;
02016 strcpy( user_inputs.anatomy_type_string ,
02017 ANAT_typestr[user_inputs.anatomy_type] ) ;
02018
02019 af_type_set = 1 ; nopt++ ; continue ;
02020 }
02021
02022 /* -type from the function prefixes */
02023
02024 for( ii=FIRST_FUNC_TYPE ; ii <= LAST_FUNC_TYPE ; ii++ )
02025 if( strncmp( &(Argv[nopt][1]) ,
02026 FUNC_prefixstr[ii] , THD_MAX_PREFIX ) == 0 ) break ;
02027
02028 if( ii <= LAST_FUNC_TYPE ){
02029 user_inputs.function_type = ii ;
02030 user_inputs.dataset_type = HEAD_FUNC_TYPE ;
02031 strcpy( user_inputs.dataset_type_string ,
02032 DATASET_typestr[user_inputs.dataset_type] ) ;
02033 strcpy( user_inputs.function_type_string ,
02034 FUNC_typestr[user_inputs.function_type] ) ;
02035
02036 af_type_set = 1 ; nopt++ ; continue ;
02037 }
02038
02039 #ifdef USE_MRI_DELAY
02040 /*--- -in:1 ---*/
02041
02042 if( strncmp(Argv[nopt],"-in:1",5) == 0 ){
02043 argopt.delay_input = TRUE ;
02044 nopt++ ; continue ;
02045 }
02046 #endif
02047
02048 /*--- -view type ---*/
02049
02050 if( strncmp(Argv[nopt],"-view",4) == 0 ){
02051 char * str ;
02052
02053 if( ++nopt >= Argc ) FatalError("-view needs a type") ;
02054
02055 str = Argv[nopt] ; if( str[0] == '+' ) str++ ;
02056
02057 for( ii=FIRST_VIEW_TYPE ; ii <= LAST_VIEW_TYPE ; ii++ )
02058 if( strcmp(str,VIEW_codestr[ii]) == 0 ) break ;
02059
02060 if( ii <= LAST_VIEW_TYPE ){
02061 user_inputs.view_type = ii ;
02062 } else {
02063 WarningError("Unknown view type after -view!") ;
02064 }
02065 nopt++ ; continue ;
02066 }
02067
02068 /* 05 Feb 2001: -zpad option */
02069
02070 if( strncmp(Argv[nopt],"-zpad",5) == 0 ){
02071 char * eee ;
02072 if( ++nopt >= Argc ) FatalError("-zpad needs a count") ;
02073 if( zpad > 0.0 ) fprintf(stderr,"+++ WARNING: second -zpad option found!\n") ;
02074 zpad = strtod( Argv[nopt] , &eee ) ;
02075 if( zpad < 0.0 ) FatalError("-zpad is negative") ;
02076 zpad_mm = (*eee == 'm') ;
02077 nopt++ ; continue ;
02078 }
02079
02080 /*--- -session name ---*/
02081
02082 if( strncmp(Argv[nopt],"-session",4) == 0 ){
02083 if( ++nopt >= Argc ) FatalError("-session needs a name") ;
02084 MCW_strncpy( user_inputs.session_filename, Argv[nopt], THD_MAX_NAME ) ;
02085 nopt++ ; continue ;
02086 }
02087
02088 /*--- -prefix name ---*/
02089
02090 if( strncmp(Argv[nopt],"-prefix",4) == 0 ){
02091 if( ++nopt >= Argc ) FatalError("-prefix needs a name") ;
02092 MCW_strncpy( user_inputs.output_filename , Argv[nopt] , THD_MAX_NAME ) ;
02093 nopt++ ; continue ;
02094 }
02095
02096 #ifndef NO_NAMES
02097 /*--- -dname name ---*/
02098
02099 if( strncmp(Argv[nopt],"-dname",4) == 0 ){
02100 if( ++nopt >= Argc ) FatalError("-dname needs a name") ;
02101 MCW_strncpy( user_inputs.dataset_name , Argv[nopt] , THD_MAX_NAME ) ;
02102 nopt++ ; continue ;
02103 }
02104
02105 /*--- -dlabel name ---*/
02106
02107 if( strncmp(Argv[nopt],"-dlabel",4) == 0 ){
02108 if( ++nopt >= Argc ) FatalError("-dlabel needs a name") ;
02109 MCW_strncpy( user_inputs.short_label1 , Argv[nopt] , THD_MAX_LABEL ) ;
02110 nopt++ ; continue ;
02111 }
02112 #endif
02113
02114 /*--- -geomparent headerfile ---*/
02115
02116 if( strncmp(Argv[nopt],"-geomparent",6) == 0 ){
02117 if( ++nopt >= Argc ) FatalError("-geomparent needs a headerfile" ) ;
02118 MCW_strncpy( user_inputs.geometry_parent_filename ,
02119 Argv[nopt] , THD_MAX_NAME ) ;
02120 nopt++ ; continue ;
02121 }
02122
02123 /*--- -anatparent headerfile ---*/
02124
02125 if( strncmp(Argv[nopt],"-anatparent",6) == 0 ){
02126 if( ++nopt >= Argc ) FatalError("-anatparent needs a headerfile" ) ;
02127 MCW_strncpy( user_inputs.anatomy_parent_filename ,
02128 Argv[nopt] , THD_MAX_NAME ) ;
02129 nopt++ ; continue ;
02130 }
02131
02132 /*--- -nosave ---*/
02133
02134 if( strncmp(Argv[nopt],"-nosave",4) == 0 ){
02135 user_inputs.nosave = 1 ;
02136 nopt++ ; continue ;
02137 }
02138
02139 /*--- 25 Sep 2001: -sinter option ---*/
02140
02141 if( strcmp(Argv[nopt],"-sinter") == 0 ){
02142 putenv("AFNI_SIEMENS_INTERLEAVE=Yes") ; nopt++ ; continue ;
02143 }
02144
02145 /*--- 15 Aug 2001: -skip_outliers ---*/
02146
02147 if( strcmp(Argv[nopt],"-skip_outliers") == 0 ){
02148 putenv("AFNI_TO3D_OUTLIERS=No") ; nopt++ ; continue ;
02149 }
02150
02151 if( strcmp(Argv[nopt],"-text_outliers") == 0 ){
02152 putenv("AFNI_TO3D_OUTLIERS=Text") ; nopt++ ; continue ;
02153 }
02154
02155 /*--- 26 Aug 2001: -save_outliers ---*/
02156
02157 if( strcmp(Argv[nopt],"-save_outliers") == 0 ){
02158 if(++nopt > Argc) FatalError("-save_outliers needs a filename") ;
02159 outliers_fname = Argv[nopt] ;
02160 if( !THD_filename_ok(outliers_fname) )
02161 FatalError("-save_outliers filename is illegal") ;
02162 nopt++ ; continue ;
02163 }
02164
02165 /*--- July 1997: -orient code ---*/
02166
02167 if( strncmp(Argv[nopt],"-orient",4) == 0 ){
02168 char acod ;
02169
02170 if( ++nopt >= Argc ) FatalError("-orient needs a code") ;
02171 if( strlen(Argv[nopt]) != 3 ) FatalError("Illegal -orient code") ;
02172 acod = toupper(Argv[nopt][0]) ; user_inputs.xorient = ORCODE(acod) ;
02173 acod = toupper(Argv[nopt][1]) ; user_inputs.yorient = ORCODE(acod) ;
02174 acod = toupper(Argv[nopt][2]) ; user_inputs.zorient = ORCODE(acod) ;
02175 nopt++ ; continue ;
02176 }
02177
02178 if( strncmp(Argv[nopt],"-zorigin",7) == 0 ){
02179 if( ++nopt >= Argc ) FatalError("-zorigin needs a value") ;
02180 zoff = strtod( Argv[nopt] , NULL ) ;
02181 use_zoff = 1 ;
02182 nopt++ ; continue ;
02183 }
02184
02185 /********** April 1996: new options for setting dimensions **********/
02186
02187 /** 21 Nov 1997: alter the way dimensions are decoded **/
02188 #undef USE_OLD_DCODE
02189
02190 /*--- -xFOV or -xSLAB ---*/
02191
02192 if( strncmp(Argv[nopt],"-xFOV",5)==0 || strncmp(Argv[nopt],"-xSLAB",5)==0 ||
02193 strncmp(Argv[nopt],"-xfov",5)==0 || strncmp(Argv[nopt],"-xslab",5)==0 ){
02194 float val , xin_bot , xin_top ;
02195 char * ptr , * ptr2 , acod ;
02196 int dcod1 , dcod2 , xincode ;
02197
02198 xincode = ( strncmp(Argv[nopt],"-xFOV",5)==0 ||
02199 strncmp(Argv[nopt],"-xfov",5)==0 ) ? INCODE_FOV : INCODE_SLAB ;
02200
02201 if( ++nopt >= Argc ) WarningError("need an argument after -xFOV/-xSLAB!") ;
02202
02203 /* should now have something of one of the forms
02204 <number> <dircode> : <number> <dircode>
02205 <number> <dircode> - <number> <dircode>
02206 <number> <dircode> : <dircode>
02207 <number> <dircode> - <dircode>
02208
02209 Step 1: get the first <number> */
02210
02211 #ifdef USE_OLD_DCODE
02212 val = strtod( Argv[nopt] , &ptr ) ;
02213 if( val < 0.0 || (val == 0.0 && ptr == Argv[nopt]) )
02214 WarningError("a nonegative number should follow -xFOV/-xSLAB!") ;
02215
02216 xin_bot = val ;
02217
02218 /* Step 2: get the first <dircode> */
02219
02220 acod = toupper( *ptr ) ; dcod1 = ORCODE(acod) ; ptr++ ;
02221 if( dcod1 < 0 )
02222 WarningError("orientation code should follow first dimension in -xFOV/-xSLAB!") ;
02223 #else
02224 { int nused ;
02225 nused = decode_location( Argv[nopt] , &xin_bot , &dcod1 ) ;
02226 if( xin_bot < 0.0 || xin_bot == WAY_BIG )
02227 WarningError("a nonegative number should follow -xFOV/-xSLAB!") ;
02228 if( dcod1 < 0 )
02229 WarningError("1st orientation code illegal after -xFOV/-xSLAB!") ;
02230 ptr = Argv[nopt] + nused ;
02231 }
02232 #endif
02233
02234
02235 /* Step 3: get the separator */
02236
02237 if( *ptr != ':' && *ptr != '-' )
02238 #ifdef USE_OLD_DCODE
02239 WarningError(": or - should follow orientation code in -xFOV/-xSLAB!") ;
02240 #else
02241 WarningError(": or - should follow 1st dimension in -xFOV/-xSLAB!") ;
02242 #endif
02243 ptr++ ;
02244 if( *ptr == '\0' )
02245 WarningError("orientation code or dimension should follow : or - in -xFOV/-xSLAB!") ;
02246
02247 /* Step 4: try to get the second <dircode>. If that fails, then get
02248 the second <number> first, then the second <dircode>.
02249 If the second <dircode> works, however, then the second
02250 <number> is defined to be equal to the first <number>. */
02251
02252 #ifdef USE_OLD_DCODE
02253 acod = toupper( *ptr ) ; dcod2 = ORCODE(acod) ;
02254 if( dcod2 < 0 ){
02255 val = strtod( ptr , &ptr2 ) ;
02256 if( val < 0.0 || (val == 0.0 && ptr2 == ptr) )
02257 WarningError("orientation code or dimension should follow : or - in -xFOV/-xSLAB!") ;
02258 xin_top = val ;
02259 ptr = ptr2 ;
02260 acod = toupper( *ptr ) ; dcod2 = ORCODE(acod) ;
02261 if( dcod2 < 0 )
02262 WarningError("orientation code should follow second dimension in -xFOV/-xSLAB!") ;
02263 } else {
02264 xin_top = xin_bot ;
02265 }
02266 #else
02267 { int nused ;
02268 nused = decode_location( ptr , &xin_top , &dcod2 ) ;
02269 if( dcod2 < 0 )
02270 WarningError("need 2nd orientation code in -xFOV/-xSLAB!") ;
02271 if( xin_top < 0.0 )
02272 WarningError("need nonegative 2nd dimension in -xFOV/-xSLAB!") ;
02273 if( xin_top == WAY_BIG ) xin_top = xin_bot ;
02274 }
02275 #endif
02276
02277 /* Now, check for consistency:
02278 Direction codes should be in the same or opposite directions;
02279 however, must be opposite if the two <number>s are identical.
02280 For example 120A-120A makes no sense,
02281 but 120A-120P is reasonable, and 10A-30A is also reasonable. */
02282
02283 if( xin_top == xin_bot && dcod1 != ORIENT_OPPOSITE(dcod2) )
02284 WarningError("zero thickness slab specified in -xFOV/-xSLAB!") ;
02285
02286 if( dcod1 != dcod2 && dcod1 != ORIENT_OPPOSITE(dcod2) )
02287 WarningError("inconsistent directions given in -xFOV/-xSLAB!") ;
02288
02289 /* If the direction codes are the same, then if the first <number>
02290 is smaller, reverse the first direction code and negate the
02291 first number. For example, 10A:30A becomes -10P:30A, which is
02292 equivalent. If the first number is larger, then reverse the
02293 second code and number. For example, 30A:10A becomes 30A:-10P.
02294 Why do this? Then the first direction code correctly expresses
02295 the sense of the input direction. The sum of numbers becomes
02296 the cross-slab thickness, needed to compute various stuff later. */
02297
02298 if( dcod1 == dcod2 ){
02299 if( xin_bot < xin_top ){
02300 dcod1 = ORIENT_OPPOSITE(dcod1) ;
02301 xin_bot = -xin_bot ;
02302 } else {
02303 dcod2 = ORIENT_OPPOSITE(dcod2) ;
02304 xin_top = -xin_top ;
02305 }
02306 }
02307
02308 /* All is OK, so store the results */
02309
02310 user_inputs.xincode = xincode + dcod1 ;
02311 user_inputs.xin_bot = xin_bot ;
02312 user_inputs.xin_top = xin_top ;
02313
02314 #if 0
02315 printf("decoded %s to give xincode=%d bot=%f top=%f\n",Argv[nopt],
02316 user_inputs.xincode, user_inputs.xin_bot, user_inputs.xin_top ) ;
02317 #endif
02318
02319 nopt++ ; continue ;
02320 }
02321
02322 /*--- -yFOV or -ySLAB ---*/
02323
02324 if( strncmp(Argv[nopt],"-yFOV",5)==0 || strncmp(Argv[nopt],"-ySLAB",5)==0 ||
02325 strncmp(Argv[nopt],"-yfov",5)==0 || strncmp(Argv[nopt],"-yslab",5)==0 ){
02326
02327 float val , yin_bot , yin_top ;
02328 char * ptr , * ptr2 , acod ;
02329 int dcod1 , dcod2 , yincode ;
02330
02331 yincode = ( strncmp(Argv[nopt],"-yFOV",5)==0 ||
02332 strncmp(Argv[nopt],"-yfov",5)==0 ) ? INCODE_FOV : INCODE_SLAB ;
02333
02334 if( ++nopt >= Argc ) WarningError("need an argument after -yFOV/-ySLAB!") ;
02335
02336 /* should now have something of one of the forms
02337 <number> <dircode> : <number> <dircode>
02338 <number> <dircode> - <number> <dircode>
02339 <number> <dircode> : <dircode>
02340 <number> <dircode> - <dircode>
02341
02342 Step 1: get the first <number> */
02343
02344 #ifdef USE_OLD_DCODE
02345 val = strtod( Argv[nopt] , &ptr ) ;
02346 if( val < 0.0 || (val == 0.0 && ptr == Argv[nopt]) )
02347 WarningError("a nonegative number should follow -yFOV/-ySLAB!") ;
02348
02349 yin_bot = val ;
02350
02351 /* Step 2: get the first <dircode> */
02352
02353 acod = toupper( *ptr ) ; dcod1 = ORCODE(acod) ; ptr++ ;
02354 if( dcod1 < 0 )
02355 WarningError("orientation code should follow first dimension in -yFOV/-ySLAB!") ;
02356 #else
02357 { int nused ;
02358 nused = decode_location( Argv[nopt] , &yin_bot , &dcod1 ) ;
02359 if( yin_bot < 0.0 || yin_bot == WAY_BIG )
02360 WarningError("a nonegative number should follow -yFOV/-ySLAB!") ;
02361 if( dcod1 < 0 )
02362 WarningError("1st orientation code illegal after -yFOV/-ySLAB!") ;
02363 ptr = Argv[nopt] + nused ;
02364 }
02365 #endif
02366
02367 /* Step 3: get the separator */
02368
02369 if( *ptr != ':' && *ptr != '-' )
02370 #ifdef USE_OLD_DCODE
02371 WarningError(": or - should follow orientation code in -yFOV/-ySLAB!") ;
02372 #else
02373 WarningError(": or - should follow 1st dimension in -yFOV/-ySLAB!") ;
02374 #endif
02375
02376 ptr++ ;
02377 if( *ptr == '\0' )
02378 WarningError("orientation code or dimension should follow : or - in -yFOV/-ySLAB!") ;
02379
02380 /* Step 4: try to get the second <dircode>. If that fails, then get
02381 the second <number> first, then the second <dircode>.
02382 If the second <dircode> works, however, then the second
02383 <number> is defined to be equal to the first <number>. */
02384
02385 #ifdef USE_OLD_DCODE
02386 acod = toupper( *ptr ) ; dcod2 = ORCODE(acod) ;
02387 if( dcod2 < 0 ){
02388 val = strtod( ptr , &ptr2 ) ;
02389 if( val < 0.0 || (val == 0.0 && ptr2 == ptr) )
02390 WarningError("orientation code or dimension should follow : or - in -yFOV/-ySLAB!") ;
02391 yin_top = val ;
02392 ptr = ptr2 ;
02393 acod = toupper( *ptr ) ; dcod2 = ORCODE(acod) ;
02394 if( dcod2 < 0 )
02395 WarningError("orientation code should follow second dimension in -yFOV/-ySLAB!") ;
02396 } else {
02397 yin_top = yin_bot ;
02398 }
02399 #else
02400 { int nused ;
02401 nused = decode_location( ptr , &yin_top , &dcod2 ) ;
02402 if( dcod2 < 0 )
02403 WarningError("need 2nd orientation code in -yFOV/-ySLAB!") ;
02404 if( yin_top < 0.0 )
02405 WarningError("need nonegative 2nd dimension in -yFOV/-ySLAB!") ;
02406 if( yin_top == WAY_BIG ) yin_top = yin_bot ;
02407 }
02408 #endif
02409
02410 /* Now, check for consistency:
02411 Direction codes should be in the same or opposite directions;
02412 however, must be opposite if the two <number>s are identical.
02413 For example 120A-120A makes no sense,
02414 but 120A-120P is reasonable, and 10A-30A is also reasonable. */
02415
02416 if( yin_top == yin_bot && dcod1 != ORIENT_OPPOSITE(dcod2) )
02417 WarningError("zero thickness slab specified in -yFOV/-ySLAB!") ;
02418
02419 if( dcod1 != dcod2 && dcod1 != ORIENT_OPPOSITE(dcod2) )
02420 WarningError("inconsistent directions given in -yFOV/-ySLAB!") ;
02421
02422 /* If the direction codes are the same, then if the first <number>
02423 is smaller, reverse the first direction code and negate the
02424 first number. For example, 10A:30A becomes -10P:30A, which is
02425 equivalent. If the first number is larger, then reverse the
02426 second code and number. For example, 30A:10A becomes 30A:-10P.
02427 Why do this? Then the first direction code correctly expresses
02428 the sense of the input direction. The sum of numbers becomes
02429 the cross-slab thickness, needed to compute various stuff later. */
02430
02431 if( dcod1 == dcod2 ){
02432 if( yin_bot < yin_top ){
02433 dcod1 = ORIENT_OPPOSITE(dcod1) ;
02434 yin_bot = -yin_bot ;
02435 } else {
02436 dcod2 = ORIENT_OPPOSITE(dcod2) ;
02437 yin_top = -yin_top ;
02438 }
02439 }
02440
02441 /* All is OK, so store the results */
02442
02443 user_inputs.yincode = yincode + dcod1 ;
02444 user_inputs.yin_bot = yin_bot ;
02445 user_inputs.yin_top = yin_top ;
02446
02447 #if 0
02448 printf("decoded %s to give yincode=%d bot=%f top=%f\n",Argv[nopt],
02449 user_inputs.yincode, user_inputs.yin_bot, user_inputs.yin_top ) ;
02450 #endif
02451
02452 nopt++ ; continue ;
02453 }
02454
02455 /*--- -zFOV or -zSLAB ---*/
02456
02457 if( strncmp(Argv[nopt],"-zFOV",5)==0 || strncmp(Argv[nopt],"-zSLAB",5)==0 ||
02458 strncmp(Argv[nopt],"-zfov",5)==0 || strncmp(Argv[nopt],"-zslab",5)==0 ){
02459
02460 float val , zin_bot , zin_top ;
02461 char * ptr , * ptr2 , acod ;
02462 int dcod1 , dcod2 , zincode ;
02463
02464 zincode = ( strncmp(Argv[nopt],"-zFOV",5)==0 ||
02465 strncmp(Argv[nopt],"-zfov",5)==0 ) ? INCODE_FOV : INCODE_SLAB ;
02466
02467 if( ++nopt >= Argc ) WarningError("need an argument after -zFOV/-zSLAB!") ;
02468
02469 /* should now have something of one of the forms
02470 <number> <dircode> : <number> <dircode>
02471 <number> <dircode> - <number> <dircode>
02472 <number> <dircode> : <dircode>
02473 <number> <dircode> - <dircode>
02474
02475 Step 1: get the first <number> */
02476
02477 #ifdef USE_OLD_DCODE
02478 val = strtod( Argv[nopt] , &ptr ) ;
02479 if( val < 0.0 || (val == 0.0 && ptr == Argv[nopt]) )
02480 WarningError("a nonegative number should follow -zFOV/-zSLAB!") ;
02481
02482 zin_bot = val ;
02483
02484 /* Step 2: get the first <dircode> */
02485
02486 acod = toupper( *ptr ) ; dcod1 = ORCODE(acod) ; ptr++ ;
02487 if( dcod1 < 0 )
02488 WarningError("orientation code should follow first dimension in -zFOV/-zSLAB!") ;
02489 #else
02490 { int nused ;
02491 nused = decode_location( Argv[nopt] , &zin_bot , &dcod1 ) ;
02492 if( zin_bot < 0.0 || zin_bot == WAY_BIG )
02493 WarningError("a nonegative number should follow -yFOV/-ySLAB!") ;
02494 if( dcod1 < 0 )
02495 WarningError("1st orientation code illegal after -yFOV/-ySLAB!") ;
02496 ptr = Argv[nopt] + nused ;
02497 }
02498 #endif
02499
02500 /* Step 3: get the separator */
02501
02502 if( *ptr != ':' && *ptr != '-' )
02503 #ifdef USE_OLD_DCODE
02504 WarningError(": or - should follow orientation code in -zFOV/-zSLAB!") ;
02505 #else
02506 WarningError(": or - should follow 1st dimension in -zFOV/-zSLAB!") ;
02507 #endif
02508
02509 ptr++ ;
02510 if( *ptr == '\0' )
02511 WarningError("orientation code or dimension should follow : or - in -zFOV/-zSLAB!") ;
02512
02513 /* Step 4: try to get the second <dircode>. If that fails, then get
02514 the second <number> first, then the second <dircode>.
02515 If the second <dircode> works, however, then the second
02516 <number> is defined to be equal to the first <number>. */
02517
02518 #ifdef USE_OLD_DCODE
02519 acod = toupper( *ptr ) ; dcod2 = ORCODE(acod) ;
02520 if( dcod2 < 0 ){
02521 val = strtod( ptr , &ptr2 ) ;
02522 if( val < 0.0 || (val == 0.0 && ptr2 == ptr) )
02523 WarningError("orientation code or dimension should follow : or - in -zFOV/-zSLAB!") ;
02524 zin_top = val ;
02525 ptr = ptr2 ;
02526 acod = toupper( *ptr ) ; dcod2 = ORCODE(acod) ;
02527 if( dcod2 < 0 )
02528 WarningError("orientation code should follow second dimension in -zFOV/-zSLAB!") ;
02529 } else {
02530 zin_top = zin_bot ;
02531 }
02532 #else
02533 { int nused ;
02534 nused = decode_location( ptr , &zin_top , &dcod2 ) ;
02535 if( dcod2 < 0 )
02536 WarningError("need 2nd orientation code in -zFOV/-zSLAB!") ;
02537 if( zin_top < 0.0 )
02538 WarningError("need nonegative 2nd dimension in -zFOV/-zSLAB!") ;
02539 if( zin_top == WAY_BIG ) zin_top = zin_bot ;
02540 }
02541 #endif
02542
02543 /* Now, check for consistency:
02544 Direction codes should be in the same or opposite directions;
02545 however, must be opposite if the two <number>s are identical.
02546 For example 120A-120A makes no sense,
02547 but 120A-120P is reasonable, and 10A-30A is also reasonable. */
02548
02549 if( zin_top == zin_bot && dcod1 != ORIENT_OPPOSITE(dcod2) )
02550 WarningError("zero thickness slab specified in -zFOV/-zSLAB!") ;
02551
02552 if( dcod1 != dcod2 && dcod1 != ORIENT_OPPOSITE(dcod2) )
02553 WarningError("inconsistent directions given in -zFOV/-zSLAB!") ;
02554
02555 /* If the direction codes are the same, then if the first <number>
02556 is smaller, reverse the first direction code and negate the
02557 first number. For example, 10A:30A becomes -10P:30A, which is
02558 equivalent. If the first number is larger, then reverse the
02559 second code and number. For example, 30A:10A becomes 30A:-10P.
02560 Why do this? Then the first direction code correctly expresses
02561 the sense of the input direction. The sum of numbers becomes
02562 the cross-slab thickness, needed to compute various stuff later. */
02563
02564 if( dcod1 == dcod2 ){
02565 if( zin_bot < zin_top ){
02566 dcod1 = ORIENT_OPPOSITE(dcod1) ;
02567 zin_bot = -zin_bot ;
02568 } else {
02569 dcod2 = ORIENT_OPPOSITE(dcod2) ;
02570 zin_top = -zin_top ;
02571 }
02572 }
02573
02574 /* All is OK, so store the results */
02575
02576 user_inputs.zincode = zincode + dcod1 ;
02577 user_inputs.zin_bot = zin_bot ;
02578 user_inputs.zin_top = zin_top ;
02579
02580 #if 0
02581 printf("decoded %s to give zincode=%d bot=%f top=%f\n",Argv[nopt],
02582 user_inputs.zincode, user_inputs.zin_bot, user_inputs.zin_top ) ;
02583 #endif
02584
02585 nopt++ ; continue ;
02586 }
02587
02588 /*---- -statpar x x x ----*/
02589
02590 if( strncmp(Argv[nopt],"-statpar",5) == 0 ){
02591 float val ;
02592 char * ptr ;
02593
02594 if( ++nopt >= Argc ) FatalError("need an argument after -statpar!") ;
02595
02596 ii = 0 ;
02597 do{
02598 val = strtod( Argv[nopt] , &ptr ) ;
02599 if( *ptr != '\0' ) break ;
02600 user_inputs.stat_aux[ii++] = val ;
02601 nopt++ ;
02602 } while( nopt < Argc ) ;
02603
02604 if( ii == 0 )
02605 WarningError("No numbers given after -statpar?") ;
02606 continue ;
02607 }
02608
02609 /***** 21 Oct 1996: options for time units *****/
02610
02611 if( strcmp(Argv[nopt],"-t=ms")==0 || strcmp(Argv[nopt],"-t=msec")==0 ){
02612 user_inputs.tunits = UNITS_MSEC_TYPE ;
02613 nopt++ ; continue ;
02614 }
02615
02616 if( strcmp(Argv[nopt],"-t=s")==0 || strcmp(Argv[nopt],"-t=sec")==0 ){
02617 user_inputs.tunits = UNITS_SEC_TYPE ;
02618 nopt++ ; continue ;
02619 }
02620
02621 if( strcmp(Argv[nopt],"-t=Hz")==0 || strcmp(Argv[nopt],"-t=Hertz")==0 ){
02622 user_inputs.tunits = UNITS_HZ_TYPE ;
02623 nopt++ ; continue ;
02624 }
02625
02626 /**** 23 Feb 2005: -Torg option ****/
02627
02628 if( strncmp(Argv[nopt],"-Torg",5) == 0 ){
02629 if( nopt+1 >= Argc ) FatalError("need 1 argument after -Torg") ;
02630 user_inputs.Torg = strtod( Argv[++nopt] , NULL ) ;
02631 nopt++ ; continue ;
02632 }
02633
02634 /************* Aprille 1996: New options for specifying time ***********/
02635
02636 if( strncmp(Argv[nopt],"-time:zt",8)==0 || strncmp(Argv[nopt],"-time:tz",8)==0 ){
02637 int t_then_z , ntt , nzz , nerr ;
02638 float TR , tframe , tsl ;
02639 char *tpattern , *eptr ;
02640
02641 if( nopt+4 >= Argc ) FatalError("need 4 arguments after -time: options") ;
02642
02643 t_then_z = ( strncmp(Argv[nopt],"-time:tz",8)==0 ) ;
02644
02645 ntt = strtol( Argv[++nopt] , NULL , 10 ) ;
02646 nzz = strtol( Argv[++nopt] , NULL , 10 ) ;
02647 if( ! t_then_z ){ ii = ntt ; ntt = nzz ; nzz = ii ; }
02648
02649 TR = strtod( Argv[++nopt] , &eptr ) ;
02650 tpattern = Argv[++nopt] ;
02651
02652 /** 03 Nov 1996: allow units to be written after TR **/
02653
02654 if( strcmp(eptr,"ms")==0 || strcmp(eptr,"msec")==0 ){
02655 user_inputs.tunits = UNITS_MSEC_TYPE ;
02656 } else if( strcmp(eptr,"s")==0 || strcmp(eptr,"sec")==0 ){
02657 user_inputs.tunits = UNITS_SEC_TYPE ;
02658 } else if( strcmp(eptr,"Hz")==0 || strcmp(eptr,"Hertz")==0 ){
02659 user_inputs.tunits = UNITS_HZ_TYPE ;
02660 }
02661
02662 /** 31 July 1996: be more specific about errors **/
02663
02664 nerr = 0 ;
02665 if( ntt < 2 ){
02666 fprintf(stderr,"Illegal value of nt after -time: option\n") ; nerr++ ;
02667 }
02668 if( nzz < NZBOT ){
02669 fprintf(stderr,"Illegal value of nz after -time: option\n") ; nerr++ ;
02670 }
02671 if( TR < 0.0 ){
02672 fprintf(stderr,"Illegal value of TR after -time: option\n") ; nerr++ ;
02673 }
02674 if( nerr > 0 ){
02675 nopt++ ; continue ; /* skip on to next option, this one is bad! */
02676 }
02677
02678 user_inputs.tpattern = (float *) malloc( sizeof(float) * nzz ) ;
02679 for( ii=0 ; ii < nzz ; ii++ ) user_inputs.tpattern[ii] = 0.0 ;
02680
02681 user_inputs.ntt = ntt ;
02682 user_inputs.nzz = nzz ;
02683 user_inputs.t_then_z = t_then_z ;
02684 user_inputs.TR = TR ;
02685
02686 if( TR == 0.0 ){ TR = 1.0; user_inputs.tunits = UNITS_SEC_TYPE; }
02687
02688 tframe = TR / nzz ; /* time per slice */
02689
02690 if( nzz > 1 && tpattern[0] == '@' ){
02691 FILE * fp ;
02692
02693 /*--- read pattern file (ignore EOFs!) ---*/
02694
02695 fp = fopen( tpattern+1 , "r" ) ;
02696 if( fp == NULL ){
02697 fprintf(stderr,"Cannot open tpattern file %s\n",tpattern+1) ;
02698 } else {
02699 for( ii=0 ; ii < nzz ; ii++ )
02700 fscanf( fp , "%f" , user_inputs.tpattern + ii ) ;
02701 fclose( fp ) ;
02702 }
02703 } else if( nzz > 1 &&
02704 (strcmp(tpattern,"alt+z")==0 || strcmp(tpattern,"altplus")==0) ){
02705
02706 /*--- set up alternating in the +z direction ---*/
02707
02708 tsl = 0.0 ;
02709 for( ii=0 ; ii < nzz ; ii+=2 ){
02710 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02711 }
02712 for( ii=1 ; ii < nzz ; ii+=2 ){
02713 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02714 }
02715 } else if( nzz > 1 && strcmp(tpattern,"alt+z2")==0 ){ /* 22 Feb 2005 */
02716
02717 /*--- set up alternating in the +z direction ---*/
02718
02719 tsl = 0.0 ;
02720 for( ii=1 ; ii < nzz ; ii+=2 ){
02721 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02722 }
02723 for( ii=0 ; ii < nzz ; ii+=2 ){
02724 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02725 }
02726 } else if( nzz > 1 &&
02727 (strcmp(tpattern,"alt-z")==0 || strcmp(tpattern,"altminus")==0) ){
02728
02729 /*--- set up alternating in the -z direction ---*/
02730
02731 tsl = 0.0 ;
02732 for( ii=nzz-1 ; ii >=0 ; ii-=2 ){
02733 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02734 }
02735 for( ii=nzz-2 ; ii >=0 ; ii-=2 ){
02736 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02737 }
02738 } else if( nzz > 1 && strcmp(tpattern,"alt-z2")==0 ){ /* 22 Feb 2005 */
02739
02740 /*--- set up alternating in the -z direction ---*/
02741
02742 tsl = 0.0 ;
02743 for( ii=nzz-2 ; ii >=0 ; ii-=2 ){
02744 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02745 }
02746 for( ii=nzz-1 ; ii >=0 ; ii-=2 ){
02747 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02748 }
02749 } else if( nzz > 1 &&
02750 (strcmp(tpattern,"seq+z")==0 || strcmp(tpattern,"seqplus")==0) ){
02751
02752 /*--- set up sequential in the +z direction ---*/
02753
02754 tsl = 0.0 ;
02755 for( ii=0 ; ii < nzz ; ii++ ){
02756 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02757 }
02758 } else if( nzz > 1 &&
02759 (strcmp(tpattern,"seq-z")==0 || strcmp(tpattern,"seqminus")==0) ){
02760
02761 /*--- set up sequential in the -z direction ---*/
02762
02763 tsl = 0.0 ;
02764 for( ii=nzz-1 ; ii >=0 ; ii-- ){
02765 user_inputs.tpattern[ii] = tsl ; tsl += tframe ;
02766 }
02767 } else if( nzz == 1 ||
02768 (strcmp(tpattern,"zero")==0 || strcmp(tpattern,"simult")==0) ){
02769
02770 /*--- delete the tpattern ---*/
02771
02772 free(user_inputs.tpattern) ;
02773 user_inputs.tpattern = NULL ;
02774
02775 } else {
02776 fprintf(stderr,"Unknown tpattern = %s\n",tpattern) ;
02777 }
02778
02779 nopt++ ; continue ;
02780 }
02781
02782 /********** non-dataset arguments ************/
02783
02784 /*----- -gamma # option -----*/
02785
02786 if( strncmp(Argv[nopt],"-gamma",4) == 0 ){
02787 float val ;
02788 if( nopt+1 >= Argc ) FatalError("need an argument after -gamma!");
02789
02790 val = strtod( Argv[++nopt] , NULL ) ;
02791 if( val > 0 ) argopt.gamma = val ;
02792 else fprintf(stderr,
02793 "\n*** warning: -gamma value %s illegal\n", Argv[nopt]);
02794
02795 nopt++ ; continue ; /* go to next arg */
02796 }
02797
02798 /*----- -gsfac value option -----*/
02799
02800 if( strncmp(Argv[nopt],"-gsfac",4) == 0 ){
02801 float val ;
02802 if( nopt+1 >= Argc ) FatalError("need an argument after -gsfac!");
02803
02804 val = strtod( Argv[++nopt] , NULL ) ;
02805 if( val != 0.0 ) argopt.gsfac = val ;
02806 else fprintf(stderr,
02807 "\n*** warning: -gsfac value %s illegal\n", Argv[nopt]);
02808
02809 nopt++ ; continue ; /* go to next arg */
02810 }
02811
02812 /*----- -datum type option -----*/
02813
02814 if( strncmp(Argv[nopt],"-datum",6) == 0 ){
02815 if( ++nopt >= Argc ) FatalError("need an argument after -datum!") ;
02816
02817 if( strcmp(Argv[nopt],"short") == 0 ){
02818 argopt.datum_all = MRI_short ;
02819 } else if( strcmp(Argv[nopt],"float") == 0 ){
02820 argopt.datum_all = MRI_float ;
02821 } else if( strcmp(Argv[nopt],"complex") == 0 ){
02822 argopt.datum_all = MRI_complex ;
02823 } else if( strcmp(Argv[nopt],"byte") == 0 ){
02824 argopt.datum_all = MRI_byte ;
02825 } else if( strcmp(Argv[nopt],"rgb") == 0 ){
02826 argopt.datum_all = MRI_rgb ;
02827 } else {
02828 char buf[256] ;
02829 sprintf(buf,"-datum of type '%s' is not supported in AFNI!",
02830 Argv[nopt] ) ;
02831 FatalError(buf) ;
02832 }
02833
02834 nopt++ ; continue ; /* go to next arg */
02835 }
02836
02837 /*----- -ncolor # option -----*/
02838
02839 if( strncmp(Argv[nopt],"-ncolor",4) == 0 ){
02840 float val ;
02841 if( nopt+1 >= Argc ) FatalError("need an argument after -ncolor!");
02842
02843 val = strtod( Argv[++nopt] , NULL ) ;
02844 if( val > 4 ) argopt.ncolor = val ;
02845 else fprintf(stderr,
02846 "\n*** warning: -ncolor value %s illegal\n", Argv[nopt]);
02847
02848 nopt++ ; continue ; /* go to next arg */
02849 }
02850
02851 /*----- -xtwarns option -----*/
02852
02853 if( strncmp(Argv[nopt],"-xtwarns",6) == 0 ){
02854 argopt.xtwarns = True ;
02855 nopt++ ; continue ; /* go to next arg */
02856 }
02857
02858 /*----- -2swap and -4swap options -----*/
02859
02860 if( strncmp(Argv[nopt],"-2swap",4) == 0 ){
02861 argopt.swap_two = 1 ;
02862 nopt++ ; continue ; /* go to next arg */
02863 }
02864
02865 if( strncmp(Argv[nopt],"-4swap",4) == 0 ){
02866 argopt.swap_four = 1 ;
02867 nopt++ ; continue ; /* go to next arg */
02868 }
02869
02870 if( strncmp(Argv[nopt],"-8swap",4) == 0 ){ /* 06 Feb 2003 */
02871 argopt.swap_eight = 1 ;
02872 nopt++ ; continue ; /* go to next arg */
02873 }
02874
02875 /*----- -nofloatscan -----*/
02876
02877 if( strncmp(Argv[nopt],"-nofloatscan",6) == 0 ){
02878 argopt.nofloatscan = 1 ;
02879 nopt++ ; continue ; /* go to next arg */
02880 }
02881
02882 /*--- illegal option ---*/
02883
02884 printf("*** ILLEGAL OPTION: %s\n\n",Argv[nopt]) ;
02885 FatalError("cannot continue") ;
02886
02887 }
02888
02889 if( user_inputs.ntt > 1 && !af_type_set ){
02890 user_inputs.anatomy_type = ANAT_EPI_TYPE ; /* 20 Dec 2001 */
02891 }
02892
02893 First_Image_Arg = nopt ;
02894
02895 /* 14 Sep 1999: manufacture a command line for History,
02896 but with (possibly) fewer image inputs */
02897
02898 { int nim=Argc-First_Image_Arg , ii ;
02899 char ** qargv ;
02900
02901 if( nim < 9 ){ /* 8 or fewer images ==> copy them all */
02902
02903 qargv = Argv ;
02904
02905 } else { /* im0 im1 im2 ... im<last-1> im<last> */
02906
02907 qargv = (char **) malloc( sizeof(char *) * Argc ) ; /* copy all */
02908 for( ii=0 ; ii < Argc ; ii++ ) qargv[ii] = Argv[ii] ; /* argv's */
02909
02910 qargv[First_Image_Arg+3] = "..." ; /* notice of omission */
02911
02912 for( ii=First_Image_Arg+4 ; ii < Argc-2 ; ii++ ) /* these will */
02913 qargv[ii] = NULL ; /* be omitted */
02914 }
02915
02916 commandline = tross_commandline( "to3d" , Argc , qargv ) ;
02917 AFNI_log_string(commandline) ; /* 14 Aug 2001 */
02918
02919 if( qargv != Argv ) free(qargv) ;
02920 }
02921
02922 EXRETURN ;
02923 }
|
|
||||||||||||||||
|
--- fix dimensions if user input axes stuff ---* Definition at line 4543 of file to3d.c. References THD_string_array::ar, client_data, to3d_widget_set::dc, drive_MCW_imseq(), ISQ_REALZ, isqDR_display, isqDR_getimnr, isqDR_opacitybut, isqDR_penbbox, isqDR_realize, isqDR_record_disable, isqDR_title, isqDR_winfosides, isqDR_zoombut, MCW_invert_widget(), NORMAL_cursorize, open_MCW_imseq(), to3d_widget_set::open_view_pb, RESET_QUIT, to3d_widget_set::seq, T3D_getim(), THD_3dim_dataset_to_brick(), to3d_widget_set::topshell, MCW_imseq::wimage, MCW_imseq::wtop, to3d_data::xsize, THD_dataxes::xxdel, to3d_data::ysize, THD_dataxes::yydel, to3d_data::zsize, to3d_data::zspacing, and THD_dataxes::zzdel. Referenced by T3D_create_widgets().
04545 {
04546 FD_brick * br ;
04547 char * title = "to3d" ;
04548 int nim ;
04549
04550 if( wset.seq != NULL ){
04551 if( ISQ_REALZ(wset.seq) )
04552 XMapRaised( XtDisplay(wset.topshell) , XtWindow(wset.seq->wtop) ) ;
04553 else
04554 XBell( XtDisplay(wset.topshell) , 100 ) ; /* should never happen */
04555 return ;
04556 }
04557
04558 daxes->xxdel = user_inputs.xsize ; /* these are here to make */
04559 daxes->yydel = user_inputs.ysize ; /* the aspect ratio work */
04560 #ifdef ALLOW_NONCONTIG
04561 daxes->zzdel = user_inputs.zspacing ;
04562 #else
04563 daxes->zzdel = user_inputs.zsize ;
04564 #endif
04565
04566 br = THD_3dim_dataset_to_brick( dset , 1,2,3 ) ;
04567
04568 if( br == NULL ){
04569 XBell( XtDisplay(wset.topshell) , 100 ) ;
04570 fprintf(stderr,"\n*** bad data in THD_3dim_dataset_to_brick!\n");
04571 return ;
04572 }
04573
04574 wset.seq = open_MCW_imseq( wset.dc , T3D_getim , br ) ;
04575 drive_MCW_imseq( wset.seq,isqDR_realize , NULL ) ;
04576 NORMAL_cursorize( wset.seq->wimage ) ; /* 07 Dec 2001 */
04577
04578 drive_MCW_imseq(wset.seq,isqDR_getimnr, (XtPointer) &nim ) ;
04579 drive_MCW_imseq(wset.seq,isqDR_title , (XtP |