PLUGIN_interface * TEST_init( void )
{
PLUGIN_interface * plint ; /* will be the output of this routine */
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "Testing" ,
"Testing, Testing, 1-2-3 ..." ,
NULL ,
PLUGIN_CALL_VIA_MENU , TEST_main ) ;
PLUTO_add_hint( plint , "1-2-3, 1-2-3, ..." ) ;
PLUTO_add_option( plint ,
"Input" , /* label at left of input line */
"Input" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_dataset_list( plint ,
"Datasets" , /* label next to button */
ANAT_ALL_MASK , /* take any anat datasets */
FUNC_FIM_MASK , /* only allow fim funcs */
DIMEN_4D_MASK | /* need 3D+time datasets */
BRICK_ALLREAL_MASK /* need real-valued datasets */
) ;
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ;
if( ncall > 0 ) return NULL ; /* only one interface */
/*-- set titles and call point --*/
plint = PLUTO_new_interface( "Dataset Rename" , "Dataset Renaming" , helpstring ,
PLUGIN_CALL_VIA_MENU , RENAME_main ) ;
PLUTO_add_hint( plint , "Rename a Dataset" ) ;
PLUTO_set_sequence( plint , "A:afnicontrol:dset" ) ;
PLUTO_set_runlabels( plint , "Rename+Keep" , "Rename+Close" ) ; /* 04 Nov 2003 */
/*-- first line of input: Dataset --*/
PLUTO_add_option( plint , "Input" , "Input" , TRUE ) ;
PLUTO_add_dataset(plint , "Dataset" ,
ANAT_ALL_MASK , FUNC_ALL_MASK ,
WARP_ON_DEMAND_MASK | DIMEN_ALL_MASK |
SESSION_ALL_MASK | BRICK_ALLTYPE_MASK ) ;
/*-- second line of input: Prefix for output dataset --*/
PLUTO_add_option( plint , "Output" , "Output" , TRUE ) ;
PLUTO_add_string( plint , "Prefix" , 0,NULL , 19 ) ;
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ;
static char *yn[2] = {"No", "Yes"};
if( ncall > 0 ) return NULL ; /* only one interface */
/*-- set titles and call point --*/
/* Initialize variables so we can be a 1D transformer*/
low_fc=0; high_fc = 0; ignore=1; autocorr=FALSE; retrend=FALSE; output_prefix=NULL; idc=NULL;
PLUTO_register_1D_function( "Fourier", fourier_1D );
plint = PLUTO_new_interface( "Fourier Stuff" , "Filtering, autocorrelation and other stuff done with FFTs" , helpstring ,
PLUGIN_CALL_VIA_MENU , Fourier_Main ) ;
PLUTO_add_hint( plint , "Filtering, autocorrelation and other stuff done with FFTs" ) ;
PLUTO_set_sequence( plint , "z:Ross" ) ;
/*-- first line of input: Dataset --*/
PLUTO_add_option( plint , "Input" , "Input" , FALSE ) ;
PLUTO_add_dataset(plint , "Dataset" ,
ANAT_ALL_MASK , FUNC_ALL_MASK ,
DIMEN_4D_MASK | BRICK_ALLREAL_MASK ) ;
/*-- second line of input: Prefix for output dataset --*/
PLUTO_add_option( plint , "Output" , "Output" , FALSE ) ;
PLUTO_add_string( plint , "Prefix" , 0, NULL , 19 ) ;
/*-- third line of input: Preprocessing --*/
PLUTO_add_option( plint , "Preprocess" , "Preprocess" , TRUE ) ;
PLUTO_add_number( plint , "Ignore" , 0, 10, 0, 1 , FALSE) ;
PLUTO_add_string( plint, "Re-trend", 2, yn, 0);
/*-- fourth line of input: Lowpass option --*/
PLUTO_add_option( plint , "Lowpass" , "Lowpass" , FALSE ) ;
PLUTO_add_number( plint , "Fc" , 0, 5000, 3, 0 , TRUE) ;
/*-- fifth line of input: Highass option --*/
PLUTO_add_option( plint , "Highpass" , "Highpass" , FALSE ) ;
PLUTO_add_number( plint , "Fc" , 0, 5000, 3, 0 , TRUE) ;
/*-- sixt line of input: Autocorrelation option --*/
/*
PLUTO_add_option( plint , "Autocorrelate" , "Autocorrelate" , FALSE ) ;
*/
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
int ii ;
PLUGIN_interface * plint ; /* will be the output of this routine */
if( ncall > 0 ) return NULL ;
CHECK_IF_ALLOWED("L1FIT","L1_Fit & Dtr") ; /* 30 Sep 2016 */
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "L1_Fit & Dtr" ,
"Control L1_Fit and L1_Dtr Functions" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , L1F_main ) ;
global_plint = plint ; /* make global copy */
PLUTO_set_sequence( plint , "A:funcs:fitting" ) ;
PLUTO_add_hint( plint , "Control L1_Fit and L1_Dtr Functions" ) ;
PLUTO_set_runlabels( plint , "Set+Keep" , "Set+Close" ) ; /* 04 Nov 2003 */
/*----- Parameters -----*/
PLUTO_add_option( plint , "Parameters" , "Parameters" , TRUE ) ;
PLUTO_add_string( plint , "Baseline" , NBASE , baseline_strings , 1 ) ;
PLUTO_add_number( plint , "Ignore" , 0,20,0,3 , FALSE ) ;
/*----- Sinusoid -----*/
for( ii=0 ; ii < NRMAX_SIN ; ii++ ){
PLUTO_add_option( plint , "Sinusoid" , "Sinusoid" , FALSE ) ;
PLUTO_add_number( plint , "Period" , 0,99999,0,20, TRUE ) ;
PLUTO_add_number( plint , "Harmonics" , 1,HARM_MAX,0,1 , FALSE ) ;
}
/*----- Timeseries -----*/
for( ii=0 ; ii < NRMAX_TS ; ii++ ){
PLUTO_add_option( plint , "Timeseries" , "Timeseries" , FALSE ) ;
PLUTO_add_timeseries( plint , "File" ) ;
}
/*--------- done with interface setup ---------*/
PLUTO_register_1D_funcstr( "L1_Fit" , L1F_fitter ) ;
PLUTO_register_1D_funcstr( "L1_Dtr" , L1F_detrend ) ;
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ;
if( ncall > 0 ) return NULL ; /* only one interface */
CHECK_IF_ALLOWED("ROIAVERAGE","ROI Average") ; /* 30 Sep 2016 */
/*-- set titles and call point --*/
plint = PLUTO_new_interface( "ROI Average" , "Average Dataset over ROI" , helpstring ,
PLUGIN_CALL_VIA_MENU , MASKAVE_main ) ;
PLUTO_add_hint( plint , "Average Dataset over ROI" ) ;
PLUTO_set_sequence( plint , "A:afniinfo:dset" ) ;
/*-- first line of input --*/
PLUTO_add_option( plint , "Source" , "Source" , TRUE ) ;
PLUTO_add_dataset(plint , "Dataset" ,
ANAT_ALL_MASK , FUNC_ALL_MASK ,
DIMEN_ALL_MASK | BRICK_ALLREAL_MASK ) ;
PLUTO_add_number( plint , "Sub-brick" , -1,9999,0 , 0,1 ) ;
/*-- second line of input --*/
PLUTO_add_option( plint , "Mask" , "Mask" , TRUE ) ;
PLUTO_add_dataset( plint , "Dataset" ,
ANAT_ALL_MASK , FUNC_ALL_MASK ,
DIMEN_ALL_MASK | BRICK_ALLREAL_MASK ) ;
PLUTO_add_number( plint , "Sub-brick" , 0,9999,0 , 0,1 ) ; /* 06 Aug 1998 */
/*-- third line of input --*/
PLUTO_add_option( plint , "Range" , "Range" , FALSE ) ;
PLUTO_add_number( plint , "Bottom" , -99999,99999, 1, 0,1 ) ;
PLUTO_add_number( plint , "Top" , -99999,99999,-1, 0,1 ) ;
/*-- 4th line of input (06 Aug 1998) --*/
PLUTO_add_option( plint , "1D Save" , "1D Save" , FALSE ) ;
PLUTO_add_string( plint , "Name" , 0,NULL , 12 ) ;
PLUTO_add_string( plint , "To Disk?" , NUM_yesno_list , yesno_list , 1 ) ;
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ; /* will be the output of this routine */
int meth ;
if( ncall > 0 ) return NULL ; /* only one interface */
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "Coord Order" ,
"Coordinate Order Display" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , CORD_main ) ;
PLUTO_add_hint( plint , "Coordinate Order Display" ) ;
PLUTO_set_sequence( plint , "A:afnicontrol:display" ) ;
PLUTO_set_runlabels( plint , "Set+Keep" , "Set+Close" ) ; /* 04 Nov 2003 */
/*---------- 2nd line: other inputs ----------*/
PLUTO_add_option( plint ,
"Input" , /* label at left of input line */
"Input" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
meth = PLUTO_string_index( GLOBAL_library.cord.orcode ,
NUM_CORD_STRINGS ,
cord_strings ) ;
if( meth < 0 || meth >= NUM_CORD_STRINGS ) meth = 0 ;
PLUTO_add_string( plint ,
"Order" , /* label next to chooser button */
NUM_CORD_STRINGS , /* number of strings to choose among */
cord_strings , /* list of strings to choose among */
meth /* index of default string */
) ;
/*--------- done with interface setup ---------*/
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ; /* will be the output of this routine */
if( ncall > 0 ) return NULL ; /* only one interface */
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "PlaceHolder" , "PlaceHolder" , NULL ,
PLUGIN_CALL_IMMEDIATELY , JUNK_main ) ;
PLUTO_set_sequence( plint , "A:funcs:junk" ) ;
AFNI_register_2D_function( "Lacy9" , lacy9_box_func ) ;
AFNI_register_2D_function( "Outer9" , outer9_box_func ) ;
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ;
if( ncall > 0 ) return NULL ; /* only one interface */
CHECK_IF_ALLOWED("HEMISUBTRACT","Hemi-subtract") ; /* 30 Sep 2016 */
/* create the new interface */
plint = PLUTO_new_interface( "Hemi-subtract", "hemisphere subtraction",
helpstring, PLUGIN_CALL_VIA_MENU , HEMISUB_main );
PLUTO_add_hint( plint,
"from each voxel's value, subtract that of the reflected voxel" );
PLUTO_set_sequence( plint , "z:Reynolds" ) ;
/*-- first line of input: input dataset --*/
PLUTO_add_option( plint, "Input" , "Input" , TRUE );
PLUTO_add_hint( plint, "choose dataset for input" );
PLUTO_add_dataset(plint, "Dataset" , ANAT_ALL_MASK , FUNC_ALL_MASK,
DIMEN_3D_MASK | BRICK_SHORT_MASK );
/*-- second line of input: prefix for output dataset --*/
PLUTO_add_option( plint, "Output" , "prefix" , TRUE );
PLUTO_add_hint( plint, "option: choose dataset prefix for output" );
PLUTO_add_string( plint, "Prefix", 0, NULL, 19 );
/*-- third line of input: threshold type option --*/
PLUTO_add_option( plint, "Thresh Type", "Thresh Type", FALSE );
PLUTO_add_string( plint, "Type", NUM_T_OPTS, thresh_opts, 0 );
return plint;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ; /* will be the output of this routine */
if( ncall > 0 ) return NULL ; /* only one interface */
CHECK_IF_ALLOWED("2DREGISTRATION","2D Registration") ; /* 30 Sep 2016 */
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "2D Registration" ,
"2D Registration of a 3D+time Dataset" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , IMREG_main ) ;
PLUTO_add_hint( plint , "2D Registration of a 3D+time Dataset" ) ;
global_plint = plint ; /* make global copy */
PLUTO_set_sequence( plint , "A:newdset:reg" ) ;
/*--------- 1st line ---------*/
PLUTO_add_option( plint ,
"Datasets" , /* label at left of input line */
"DAtasets" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_dataset( plint ,
"Input" , /* label next to button */
ANAT_ALL_MASK , /* take any anat datasets */
FUNC_FIM_MASK , /* only allow fim funcs */
DIMEN_4D_MASK | /* need 3D+time datasets */
BRICK_ALLREAL_MASK /* need real-valued datasets */
) ;
PLUTO_add_string( plint ,
"Output" , /* label next to textfield */
0,NULL , /* no fixed strings to choose among */
19 /* 19 spaces for typing in value */
) ;
/*---------- 2nd line --------*/
PLUTO_add_option( plint ,
"Parameters" , /* label at left of input line */
"Parameters" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_number( plint ,
"Base" , /* label next to chooser */
0 , /* smallest possible value */
98 , /* largest possible value */
0 , /* decimal shift (none in this case) */
3 , /* default value */
FALSE /* allow user to edit value? */
) ;
/*---------- 3rd line --------*/
PLUTO_add_option( plint ,
"Fine Fit" ,
"Fine Fit" ,
FALSE
) ;
PLUTO_add_number( plint , "Blur" , 0 , 40 , 1 , 10 , FALSE ) ;
PLUTO_add_number( plint , "Dxy" , 1 , 20 , 2 , 7 , FALSE ) ;
PLUTO_add_number( plint , "Dphi" , 1 , 50 , 2 , 21 , FALSE ) ;
/*--------- done with interface setup ---------*/
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ; /* will be the output of this routine */
if( ncall > 0 ) return NULL ; /* one interfaces */
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "SingleTrial Avg" ,
"Averaging of epochs in Single Trial data" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , STAVG_main ) ;
PLUTO_add_hint( plint , "Averaging of epochs in Single Trial data" ) ;
global_plint = plint ; /* make global copy */
PLUTO_set_sequence( plint , "z:Birn" ) ;
/*--------- 1st line ---------*/
PLUTO_add_option( plint ,
"Datasets" , /* label at left of input line */
"Datasets" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_dataset( plint ,
"Input" , /* label next to button */
ANAT_ALL_MASK , /* take any anat datasets */
FUNC_FIM_MASK , /* only allow fim funcs */
DIMEN_4D_MASK | /* need 3D+time datasets */
BRICK_ALLREAL_MASK /* need real-valued datasets */
) ;
PLUTO_add_hint( plint , "Input 3d+t dataset" ) ;
PLUTO_add_string( plint ,
"Output" , /* label next to textfield */
0,NULL , /* no fixed strings to choose among */
19 /* 19 spaces for typing in value */
) ;
PLUTO_add_hint( plint , "Name of output dataset" ) ;
/*---------- 2nd line --------*/
PLUTO_add_option( plint ,
"Timing" ,
"Timing" ,
TRUE
) ;
PLUTO_add_timeseries(plint, "Stim. Timing");
PLUTO_add_hint( plint , "Stimulus Timing (0 = no task, 1 = task)" ) ;
PLUTO_add_number( plint ,
"delta" ,
-1000 ,
1000 ,
0 ,
0 ,
TRUE
) ;
PLUTO_add_hint( plint , "Shift data timecourse by delta before splitting and averaging" ) ;
/*---------- 3rd line: computation ----------*/
PLUTO_add_option( plint ,
"Compute" , /* label at left of input line */
"Compute" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_string( plint ,
"Method" , /* label next to chooser button */
_STAVG_NUM_METHODS, /* number of strings in list */
method_strings , /* list of strings to choose among */
_STAVG_METH_MEAN /* index of default string */
) ;
PLUTO_add_hint( plint , "Choose statistic to compute" ) ;
/*---------- 4th line --------*/
PLUTO_add_option( plint ,
"Parameters" , /* label at left of input line */
"Parameters" , /* tag to return to plugin */
FALSE /* is this mandatory? */
) ;
PLUTO_add_number( plint ,
"maxlength" , /* label next to chooser */
0 , /* smallest possible value */
1000 , /* largest possible value */
0 , /* decimal shift (none in this case) */
15 , /* default value */
TRUE /* allow user to edit value? */
) ;
PLUTO_add_hint( plint , "maximum # of timepoints of output dataset" ) ;
PLUTO_add_string( plint ,
"no1?" , /* label next to chooser button */
2 , /* number of strings to choose among */
yes_no_strings , /* list of strings to choose among */
1 /* index of default string */
) ;
PLUTO_add_hint( plint , "ignore timepoints where only one image is in average" ) ;
/*--------- done with interface setup ---------*/
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ; /* will be the output of this routine */
if( ncall > 0 ) return NULL ; /* only one interface */
CHECK_IF_ALLOWED("3DEXTRACT","3D+t Extract") ; /* 30 Sep 2016 */
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "3D+t Extract" ,
"Extract voxel time courses given their index or XYZ coordinates" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , EXTRACT_main ) ;
global_plint = plint ; /* make global copy */
/*--------- 1st line: Input dataset and mask files ---------*/
PLUTO_add_option( plint ,
"Data" , /* label at left of input line */
"Data" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_dataset( plint ,
"3D+time" , /* label next to button */
ANAT_ALL_MASK , /* take only EPI datasets */
FUNC_ALL_MASK , /* No fim funcs */
DIMEN_4D_MASK | /* need 3D+time datasets */
BRICK_ALLREAL_MASK /* need real-valued datasets */
) ;
PLUTO_add_number( plint ,
"Ignore" , /* label next to chooser */
0 , /* smallest possible value */
50 , /* largest possible value (inactivated for now)*/
0 , /* decimal shift (none in this case) */
0 , /* default value */
FALSE /* allow user to edit value? */
) ;
PLUTO_add_string( plint ,
"Dtrnd" , /* label next to textfield */
2,yn_strings, /* strings to choose among */
1 /* Default option */
) ;
/*---------- 2nd line: Mask file info ----------*/
PLUTO_add_option( plint ,
"Mask file" , /* label at left of input line */
"Mask" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_string( plint , "Mask File" , 0 , NULL , 19 ) ;
PLUTO_add_number( plint ,
"N Columns" , /* label next to chooser */
1 , /* smallest possible value */
1000 , /* largest possible value (inactivated for now)*/
0 , /* decimal shift (none in this case) */
3 , /* default value */
TRUE /* allow user to edit value? */
) ;
PLUTO_add_number( plint ,
"Pass Value" , /* label next to chooser */
-10000 , /* smallest possible value */
10000 , /* largest possible value (inactivated for now)*/
0 , /* decimal shift (none in this case) */
1 , /* default value */
TRUE /* allow user to edit value? */
) ;
/*---------- 3rd line: index mask location ----------*/
PLUTO_add_option( plint ,
"Index Mask ?" , /* label at left of input line */
"Index" , /* tag to return to plugin */
FALSE /* is this mandatory? */
) ;
PLUTO_add_number( plint ,
"i col." , /* label next to chooser */
1 , /* smallest possible value */
1000 , /* largest possible value (inactivated for now)*/
0 , /* decimal shift (none in this case) */
1 , /* default value */
TRUE /* allow user to edit value? */
) ;
/*---------- 4th line: xyz mask location ----------*/
PLUTO_add_option( plint ,
"XYZ Mask ?" , /* label at left of input line */
"XYZ" , /* tag to return to plugin */
FALSE /* is this mandatory? */
) ;
PLUTO_add_number( plint ,
"x col." , /* label next to chooser */
1 , /* smallest possible value */
1000 , /* largest possible value */
0 , /* decimal shift (none in this case) */
2 , /* default value */
TRUE /* allow user to edit value? */
) ;
PLUTO_add_number( plint ,
"y col." , /* label next to chooser */
1 , /* smallest possible value */
1000 , /* largest possible value */
0 , /* decimal shift (none in this case) */
3 , /* default value */
TRUE /* allow user to edit value? */
) ;
PLUTO_add_number( plint ,
"z col." , /* label next to chooser */
1 , /* smallest possible value */
1000 , /* largest possible value */
0 , /* decimal shift (none in this case) */
4 , /* default value */
TRUE /* allow user to edit value? */
) ;
/*---------- 5th line: output stuff ----------*/
PLUTO_add_option( plint ,
"Output" , /* label at left of input line */
"Output" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_string( plint ,
"AFNI Prfx" , /* label next to textfield */
0,NULL , /* no fixed strings to choose among */
19 /* 19 spaces for typing in value */
) ;
PLUTO_add_string( plint , "Filename" , 0 , NULL , 19 ) ;
PLUTO_add_string( plint ,
"Format" , /* label next to textfield */
2,format_strings, /* strings to choose among */
0 /* Default option */
) ;
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ; /* will be the output of this routine */
if( ncall > 0 ) return NULL ; /* only one interface */
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "Hilbert Delay98" ,
"Time delay between FMRI and reference time series" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , DELAY_main ) ;
global_plint = plint ; /* make global copy */
/*--------- 1st line: Input dataset ---------*/
PLUTO_add_option( plint ,
"Data" , /* label at left of input line */
"Data" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_dataset( plint ,
"3D+time" , /* label next to button */
ANAT_ALL_MASK , /* take only EPI datasets */
FUNC_ALL_MASK , /* No fim funcs */
DIMEN_4D_MASK | /* need 3D+time datasets */
BRICK_ALLREAL_MASK /* need real-valued datasets */
) ;
PLUTO_add_number( plint ,
"Nort" , /* label next to chooser */
1 , /* smallest possible value */
100 , /* largest possible value (inactivated for now)*/
0 , /* decimal shift (none in this case) */
2 , /* default value */
FALSE /* allow user to edit value? */
) ;
/*---------- 2nd line: Input time series ----------*/
PLUTO_add_option( plint ,
"Ref." , /* label at left of input line */
"Ref." , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_timeseries(plint,"Ref. Vect.");
PLUTO_add_number( plint ,
"Ignore" , /* label next to chooser */
0 , /* smallest possible value */
50 , /* largest possible value (inactivated for now)*/
0 , /* decimal shift (none in this case) */
0 , /* default value */
FALSE /* allow user to edit value? */
) ;
PLUTO_add_string( plint ,
"Dsamp" , /*label next to textfield */
2,yn_strings, /* strings to choose among */
1 /* Default option */
) ;
/*---------- 3rd line: sampling frequency ----------*/
PLUTO_add_option( plint ,
"Sig." , /* label at left of input line */
"Sig." , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_number( plint ,
"fs in Hz" , /* label next to chooser */
0 , /* smallest possible value */
2000 , /* largest possible value */
1 , /* decimal shift (none in this case) */
5 , /* default value */
TRUE /* allow user to edit value? */
) ;
PLUTO_add_number( plint ,
"Tstim sec" , /* label next to chooser */
0.0 , /* smallest possible value */
500 , /* largest possible value */
0 , /* decimal shift (none in this case) */
40 , /* default value */
TRUE /* allow user to edit value? */
) ;
PLUTO_add_number( plint ,
"C-Off" , /* label next to chooser */
-10 , /* smallest possible value */
10 , /* largest possible value */
1 , /* decimal shift */
5 , /* default value */
TRUE /* allow user to edit value? */
) ;
PLUTO_add_string( plint ,
"No-bias" , /*label next to textfield */
2,yn_strings, /* strings to choose among */
1 /* Default option */
) ;
/*---------- 4th line: Delay Units ----------*/
PLUTO_add_option( plint ,
"Alg." , /* label at left of input line */
"Alg." , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_number( plint ,
"N seg." , /* label next to chooser */
1 , /* smallest possible value */
1 , /* largest possible value (turned Off for the moment, supporting code is present)*/
0 , /* decimal shift (none in this case) */
1 , /* default value */
FALSE /* allow user to edit value? */
) ;
PLUTO_add_number( plint ,
"% ovrlp" , /* label next to chooser */
0 , /* smallest possible value */
0 , /* largest possible value (not implemented)*/
0 , /* decimal shift (none in this case) */
0 , /* default value */
FALSE /* allow user to edit value? */
) ;
PLUTO_add_string( plint ,
"Units" , /* label next to textfield */
3,method_strings, /* strings to choose among */
0 /* Default option */
) ;
PLUTO_add_string( plint ,
"Phz Wrp" , /* label next to textfield */
2,yn_strings, /* strings to choose among */
0 /* Default option */
) ;
/*---------- 5th line: Output dataset ----------*/
PLUTO_add_option( plint ,
"Output" , /* label at left of input line */
"Output" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_string( plint ,
"AFNI Prfx" , /* label next to textfield */
0,NULL , /* no fixed strings to choose among */
19 /* 19 spaces for typing in value */
) ;
PLUTO_add_string( plint ,
"Write" , /* label next to textfield */
2,yn_strings ,
1
) ;
PLUTO_add_string( plint , "Filename" , 0 , NULL , 19 ) ;
PLUTO_add_string( plint ,
"Write ts" , /* label next to textfield */
2,yn_strings ,
1
) ;
/*--------- done with interface setup ---------*/
return plint ;
}
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ; /* will be the output of this routine */
if( ncall > 1 ) return NULL ; /* two interfaces */
CHECK_IF_ALLOWED("ASL","ASL a3/d3") ; /* 30 Sep 2016 */
#ifdef ALLOW_TESTING
if( ncall == 1 ) return TEST_init() ;
#else
if( ncall == 1 ) return NULL ;
#endif
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "ASL a3/d3" ,
"ASL a3/d3 of a 3D+time Dataset" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , POWER_main ) ;
PLUTO_add_hint( plint , "ASL a3/d3 of a 3D+time Dataset" ) ;
PLUTO_set_sequence( plint , "A:newdset:statistics" ) ;
/*--------- 1st line: Input dataset ---------*/
PLUTO_add_option( plint ,
"Input" , /* label at left of input line */
"Input" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_dataset( plint ,
"---->>" , /* label next to button */
ANAT_ALL_MASK , /* take any anat datasets */
FUNC_FIM_MASK , /* only allow fim funcs */
DIMEN_4D_MASK | /* need 3D+time datasets */
BRICK_ALLREAL_MASK /* need real-valued datasets */
) ;
/*---------- 2nd line: Output dataset ----------*/
PLUTO_add_option( plint ,
"Output" , /* label at left of input line */
"Output" , /* tag to return to plugin */
TRUE /* is this mandatory? */
) ;
PLUTO_add_string( plint ,
"Prefix" , /* label next to textfield */
0,NULL , /* no fixed strings to choose among */
19 /* 19 spaces for typing in value */
) ;
PLUTO_add_string( plint ,
"Datum" , /* label next to chooser button */
NUM_TYPE_STRINGS , /* number of strings to choose among */
type_strings , /* list of strings to choose among */
0 /* index of default string */
) ;
/*--------- Other lines: Parameters ---------*/
PLUTO_add_option( plint , "Ignore" , "Ignore" , TRUE ) ;
PLUTO_add_number( plint ,
"Count" , /* label next to chooser */
0 , /* smallest possible value */
999 , /* largest possible value */
0 , /* decimal shift (none in this case) */
4 , /* default value */
TRUE /* allow user to edit value? */
) ;
PLUTO_add_string( plint ,
"Image Output" , /* label next to chooser button */
NUM_TYPE_STRINGSX , /* number of strings to choose among */
type_stringsx , /* list of strings to choose among */
0 /* index of default string */
) ;
PLUTO_add_option( plint , "Scale" , "Scale" , TRUE ) ;
PLUTO_add_number( plint ,
"Scale Factor" , /* label next to chooser */
0 , /* smallest possible value */
999 , /* largest possible value */
0 , /* decimal shift (none in this case) */
1 , /* default value */
TRUE /* allow user to edit value? */
) ;
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
int ii ;
PLUGIN_interface * plint ; /* will be the output of this routine */
int ok;
NLFIT_MODEL_array * model_array = NULL; /* array of SO models */
int im; /* model index */
int ip; /* parameter index */
char message[MAX_NAME_LENGTH]; /* error message */
if( ncall > 0 ) return NULL ; /* generate interfaces for ncall 0 */
jump_on_NLfit_error = 1 ; /* 01 May 2003: */
if( setjmp(NLfit_error_jmpbuf) != 0 ) { /* NLfit_error() was invoked */
jump_on_NLfit_error = 0 ; /* somewhere below here */
fprintf(stderr,"\n*** Can't load NLfit plugin! ***\n");
return NULL ;
}
/***** otherwise, do interface # 0 *****/
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "NLfit & NLerr" ,
"Control NLfit and NLerr Functions" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , NL_main ) ;
{ char *eee = getenv("AFNI_NLFIM_METHOD") , str[94] ;
if( eee == NULL || strcasecmp(eee,"simplex") == 0 )
N_newuoa = 0 ;
else if( strcasecmp(eee,"powell") == 0 )
N_newuoa = 1 ;
else if( strcasecmp(eee,"both") == 0 )
N_newuoa = 2 ;
else
N_newuoa = 0 ;
sprintf(str,"Optimizer (AFNI_NLFIM_METHOD) is %s" ,
(N_newuoa==0) ? "SIMPLEX"
:(N_newuoa==1) ? "POWELL" : "BOTH (SIMPLEX+POWELL)" ) ;
PLUTO_report(plint,str) ;
}
PLUTO_add_hint( plint , "Control NLfit and NLerr Functions" ) ;
global_plint = plint ; /* make global copy */
PLUTO_set_sequence( plint , "A:funcs:fitting" ) ;
PLUTO_set_runlabels( plint , "Set+Keep" , "Set+Close" ) ; /* 04 Nov 2003 */
/*----- initialize the model array -----*/
model_array = NLFIT_get_many_MODELs ();
if ((model_array == NULL) || (model_array->num == 0))
#if 1
{ PLUTO_report( plint , "Found no models!") ;
jump_on_NLfit_error = 0 ;
return NULL ;
}
#else
NLfit_error ("Unable to locate any models");
#endif
#if 1
else
{ char str[64] ;
PLUGIN_interface * ENV_init(void)
{
PLUGIN_interface *plint ; /* will be the output of this routine */
char *helpstring=NULL , *ept , *eval ;
int ii ;
/*------- some environment variables for AFNI ------*/
{ static char buf[VAL_NMAX] = "AFNI_CWD=" ; /* 22 Feb 2001 */
ept = getcwd( buf+9 , VAL_NMAX-9 ) ;
if( ept != NULL ){
putenv(buf) ;
ENV_add_string( "AFNI_CWD" ,
"Current working directory (gets output files)" ,
0,NULL , ENV_cwd ) ;
}
}
ENV_add_string( "AFNI_ENFORCE_ASPECT" ,
"To make AFNI enforce image window aspect ratio?" ,
NUM_yesno_list , yesno_list , NULL ) ;
ENV_add_numeric( "AFNI_FIM_PERCENT_LIMIT" ,
"Upper limit on % Change in FIM" ,
10,1000,0,100 , NULL ) ;
ENV_add_numeric( "AFNI_IMAGE_MINFRAC" ,
"Minimum size of image window" ,
0,10,2,2 , NULL ) ;
ENV_add_string( "AFNI_LEFT_IS_LEFT" ,
"To show subject's left on image left?" ,
NUM_yesno_list , yesno_list , ENV_leftisleft ) ;
ENV_add_string( "AFNI_NO_SIDES_LABELS" ,
"Skip showing image window left-side label?" ,
NUM_yesno_list , yesno_list , NULL ) ;
ENV_add_string( "AFNI_VIEW_ANAT_BRICK" ,
"Show OverLay brick whenever possible" ,
NUM_yesno_list , yesno_list , NULL ) ;
ENV_add_string( "AFNI_VIEW_FUNC_BRICK" ,
"Show UnderLay brick whenever possible" ,
NUM_yesno_list , yesno_list , NULL ) ;
ENV_add_string( "AFNI_ORIENT" ,
"Coordinate display orientation" ,
NUM_cord_strings,cord_strings , ENV_coorder ) ;
ENV_add_string( "AFNI_MARKERS_NOQUAL" ,
"Skip markers quality checking?" ,
NUM_yesno_list , yesno_list , ENV_marksquality ) ;
ENV_add_string( "AFNI_COMPRESSOR" ,
"Output BRIK compression method" ,
NUM_COMPRESS_elist,COMPRESS_elist , ENV_compressor ) ;
ENV_add_string( "AFNI_AUTOGZIP" ,
"Use gzip on output if BRIK seems highly compressible" ,
NUM_yesno_list , yesno_list , NULL ) ;
#if 0
ENV_add_string( "AFNI_BYTEORDER" ,
"Byte ordering for output BRIKs" ,
NUM_byteorder_list , byteorder_list , ENV_byteorder ) ;
#endif
#if 0
ENV_add_string( "AFNI_NOMMAP" ,
"Whether to read BRIKs using mmap()" ,
NUM_yesno_list , yesno_list , NULL ) ;
#endif
ENV_add_string( "AFNI_FLOATSCAN" ,
"Scan floating BRIKs for errors on input?" ,
NUM_yesno_list , yesno_list , NULL ) ;
#ifdef USE_SESSTRAIL
ENV_add_numeric( "AFNI_SESSTRAIL" ,
"# directory levels seen in Switch Session, etc." ,
0,9,0,SESSTRAIL , ENV_sesstrail ) ;
#endif
ENV_add_string( "AFNI_PBAR_IMXY" ,
"Sizes of 'Save to PPM' for color pbars" ,
0,NULL , NULL ) ;
ENV_add_string( "AFNI_PSPRINT" ,
"Command to send stdin to PostScript printer" ,
0,NULL , NULL ) ;
ENV_add_string( "AFNI_TRUSTHOST" ,
"Name of host to trust for plugouts and realtime data" ,
0,NULL , ENV_trusthost ) ;
ENV_add_string( "AFNI_IMAGE_LABEL_COLOR" ,
"Name of color for image overlay labels" , /* 21 Sep 2001 */
0,NULL , NULL ) ;
ENV_add_numeric( "AFNI_IMAGE_LABEL_SETBACK" ,
"Size of setback for image overlay labels" ,
0 , 40 , 3 , 3 , NULL ) ;
if( SUMA_ENABLED ){
ENV_add_string( "AFNI_SUMA_BOXCOLOR" , /* 21 Sep 2001 */
"Color name for surface node overlays [or none]" ,
0,NULL , NULL ) ;
ENV_add_numeric( "AFNI_SUMA_BOXSIZE" , /* 10 Mar 2002 */
"Box size for surface node overlays" ,
1 , 10 , 1 , 2 , NULL ) ;
ENV_add_string( "AFNI_SUMA_LINECOLOR" , /* 10 Mar 2002 */
"Color name for surface line overlays [or none]" ,
0,NULL , NULL ) ;
ENV_add_numeric( "AFNI_SUMA_LINESIZE" , /* 15 Jan 2003 */
"Line thickness for surface intersection overlay" ,
0 , 30 , 3 , 0 , NULL ) ;
}
#ifndef NO_FRIVOLITIES
ENV_add_string( "AFNI_IMAGE_PGMFILE" ,
"Image file for AFNI splash window" ,
0,NULL , NULL ) ;
#endif
/* 08 Aug 2001 */
ENV_add_yesno( "AFNI_DONT_MOVE_MENUS" ,
"Move popup menus to enhance visibility?" ) ;
/* 07 Mar 2002 */
ENV_add_numeric( "AFNI_GRAPH_TEXTLIMIT" ,
"Max rows in Graph Button-3 popup" ,
1 , 99 , 0 , 40 , NULL ) ;
/* 16 Mar 2002 */
ENV_add_string( "AFNI_KEEP_PANNING" ,
"Keep 'pan' turned on in image viewers?" ,
NUM_yesno_list , yesno_list , NULL ) ;
/* 18 Mar 2002 */
ENV_add_string( "AFNI_VALUE_LABEL" ,
"Turn on the Define Overlay dataset value label?" ,
NUM_yesno_list , yesno_list , NULL ) ;
/* 22 Mar 2002 */
ENV_add_string( "AFNI_CROSSHAIR_LINES" ,
"Draw crosshairs with lines, not overlay voxels?" ,
NUM_yesno_list , yesno_list , NULL ) ;
/* 25 Mar 2002 */
ENV_add_string( "AFNI_CROP_ZOOMSAVE" ,
"Crop zoomed images when saving to disk?" ,
NUM_yesno_list , yesno_list , NULL ) ;
/* 23 Aug 2003 */
ENV_add_numeric( "AFNI_MAX_OPTMENU" ,
"Max buttons in an Option Menu" ,
100 , 100000 , 0 , 255 , NULL ) ;
/* 23 Oct 2003 */
ENV_add_numeric( "AFNI_STROKE_THRESHOLD" ,
"Coarseness of grayscale stroking" ,
8 , 99 , 0 , 32 , NULL ) ;
ENV_add_string( "AFNI_STROKE_AUTOPLOT" ,
"To automatically draw grayscale-data value plot?" ,
NUM_yesno_list , yesno_list , NULL ) ;
/* 04 Nov 2003 */
ENV_add_string( "AFNI_IMAGE_MINTOMAX" ,
"Set new image viewers to do min-to-max grayscaling?" ,
NUM_yesno_list , yesno_list , ENV_redisplay ) ;
ENV_add_string( "AFNI_IMAGE_GLOBALRANGE" ,
"Set image viewers to use 3D global data range by slice, volume or dataset min-max?",
NUM_globalrange_strings , globalrange_strings , ENV_globalrange_view ) ;
/* 19 Nov 2003 */
ENV_add_numeric( "AFNI_DRAW_UNDOSIZE" ,
"Megabytes allowed for Drawing Undo" ,
1 , 999 , 0 , 6 , NULL ) ;
#if !defined(NO_FRIVOLITIES) && defined(DARWIN)
ENV_add_yesno( "AFNI_SPEECH" , "Allow speech synthesis?" ) ; /* 03 Dec 2003 */
#endif
ENV_add_numeric( "AFNI_VIDEO_DELAY" , /* 04 Dec 2003 */
"Image redraw interval for 'V' or 'v' (ms)." ,
1,9000,0,1 , NULL ) ;
ENV_add_numeric( "AFNI_IMAGE_ENTROPY" ,
"Entropy threshold: below this, 2%-98% is off." ,
0,10,1,0 , NULL ) ;
ENV_add_string( "AFNI_THRESH_LOCK" , /* 06 Feb 2004 */
"Lock Threshold slider values together?" ,
NUM_threshlock_list , threshlock_list , ENV_thresh_lock ) ;
ENV_add_string( "AFNI_GRAPH_CX2R" , /* 18 Apr 2011 */
"Graph display of complex time series" ,
NUM_cx2r_list , cx2r_list , NULL ) ;
ENV_add_string( "AFNI_GRAPH_BOXLAB" , /* 18 Apr 2011 */
"Box graph display of brick labels" ,
NUM_boxlab_list , boxlab_list , NULL ) ;
ENV_add_yesno( "AFNI_PBAR_LOCK" , "Lock Color Pbars together?" ) ; /* 07 Feb 2004 */
ENV_add_yesno( "AFNI_RANGE_LOCK", "Lock OLay Ranges together?" ) ; /* 23 Feb 2004 */
ENV_add_yesno( "AFNI_DISP_SCROLLBARS" , "Image Disp menu get scrollbars?" ) ;
/* 23 Feb 2004 [rickr] */
ENV_add_yesno( "AFNI_IMAGE_ZOOM_NN" ,
"Use Nearest Neighbor interpolation for image Zoom?" ) ;
/* 22 Mar 2004 [RWCox] */
ENV_add_yesno( "AFNI_SLAVE_FUNCTIME" , "Time Index affects functional overlay?" ) ;
#if 0
ENV_add_yesno( "AFNI_SLAVE_THRTIME" , "Time Index affects threshold overlay?" ) ;
#endif
ENV_add_string( "AFNI_REALTIME_MP_HOST_PORT" , /* 31 Mar 2004 [rickr] */
"Supply host:port string for realtime motion parameters." ,
0,NULL , NULL ) ;
/* 07 Apr 2004 [RWCox] */
ENV_add_yesno( "AFNI_X11_REDECORATE" , "Try to set X11 window 'decorations'?" ) ;
/* 21 Dec 2004 [RWCox] */
ENV_add_string( "AFNI_TITLE_LABEL2" ,
"Use 'label2' field for window titles?" ,
NUM_yesno_list , yesno_list , ENV_redraw_titles ) ;
/* 21 Mar 2005 [RWCox] */
ENV_add_string( "AFNI_EDGIZE_OVERLAY" ,
"Display color overlay as edges?" ,
NUM_yesno_list , yesno_list , ENV_redisplay ) ;
/* 11 Dec 2014 [RWCox] */
ENV_add_string( "AFNI_EDGIZE_COLOR" ,
"Name of color for EDGIZE+Alpha overlays." , /* 21 Sep 2001 */
0,NULL , NULL ) ;
/* 08 Apr 2005 [rickr] */
ENV_add_numeric( "AFNI_NIFTI_DEBUG" ,
"Set nifti_io debug level (should then do Rescan:This)" ,
0,5,0,0 , NULL ) ;
/* 20 Apr 2005 [RWCox] */
ENV_add_string( "AFNI_OVERLAY_ZERO" ,
"Do 0 values get color in an Overlay?" ,
NUM_yesno_list , yesno_list , ENV_redisplay ) ;
/* 20 Oct 2005 [RWCox] */
ENV_add_yesno("AFNI_TTATLAS_CAUTION","Add caution to 'Where Am I' output?");
/* 10 May 2006 [drg] */
ENV_add_numeric( "AFNI_JPEG_COMPRESS" ,
"JPEG compression quality %" ,
1,100,0,95 , ENV_setjpegquality ) ;
/* 21 Feb 2007 [RWCox] */
ENV_add_yesno( "AFNI_DATASET_BROWSE" , "Switch datasets upon selection?" ) ;
/* 05 Mar 2007 [RWCox] */
ENV_add_yesno( "AFNI_THRESH_AUTO" , "Reset threshold on Switch Overlay?" ) ;
/* 18 Sep 2007 [RWCox] */
ENV_add_string( "AFNI_IMAGE_CLIPPED" ,
"Set new image viewers to do clipped grayscaling?" ,
NUM_yesno_list , yesno_list , ENV_redisplay ) ;
ENV_add_numeric( "AFNI_IMAGE_CLIPBOT" ,
"Set clipped grayscale bottom = fraction of top default" ,
0,50,2,25 , ENV_redisplay ) ;
ENV_add_numeric( "AFNI_IMAGE_CLIPTOP" ,
"Set clipped grayscale top = fraction of default" ,
60,190,2,100 , ENV_redisplay ) ;
ENV_add_numeric( "AFNI_1DPLOT_THIK" ,
"Set 1dplot-style line thickness" ,
0,20,3,3 , NULL ) ;
#if 0
/* 20 Dec 2007 [RWCox] */
ENV_add_string( "AFNI_CLUSTER_PREFIX" ,
"Prefix for Clusterize 1D file Saves" , 0 , NULL , NULL ) ;
#endif
/* 10 Jan 2008 [RWCox] */
ENV_add_numeric( "AFNI_CLUSTER_REPMAX" ,
"Max number rows in Clusterize Rpt table" ,
10,99,0,15 , NULL ) ;
/* 04 Aug 2010 [RWCox] */
ENV_add_numeric( "AFNI_CLUSTER_WAMIMAX" ,
"Max clusters sent to 'whereami'" ,
1,99,0,20 , NULL ) ;
/* 28 Feb 2011 [RWCox] */
ENV_add_yesno( "AFNI_CLUSTER_EBAR" ,
"Error bars in Clusterize plots?" ) ;
/* 03 Jun 2008 [RWCox] */
ENV_add_yesno( "AFNI_IMAGE_TICK_DIV_IN_MM" ,
"Image tick divisions count is in mm?" ) ;
/* 09 Feb 2009 [RWCox] */
ENV_add_numeric( "AFNI_ANIM_DUP" ,
"Duplication factor for MPEG save" ,
1,99,0,1 , NULL ) ;
/* 29 Apr 2009 [RWCox] */
{ static char *fsize[3] = { "Normal" , "Big" , "Small" } ;
ENV_add_string( "AFNI_TTATLAS_FONTSIZE" ,
"Size of 'Where am I?' window font" ,
3 , fsize , NULL ) ;
}
/* 11 May 2009 [RWCox] */
ENV_add_yesno( "AFNI_INSTACORR_FDR" ,
"Compute FDR curve for InstaCorr correlations?" ) ;
/* 27 Aug 2009 [RWCox] */
ENV_add_numeric( "AFNI_IMAGE_CROPSTEP" ,
"Cropped image panning step size" ,
-9,9,0,1 , NULL ) ;
/* 06 Oct 2010 [RWCox] */
ENV_add_string( "AFNI_IDEAL_COLORS" ,
"Colors for the FIM Ideal in AFNI Graph viewer" ,
0,NULL , NULL ) ;
ENV_add_string( "AFNI_ORT_COLORS" ,
"Colors for the FIM Ort in AFNI Graph viewer" ,
0,NULL , NULL ) ;
/* 27 Jun 2011 [DRG] */
ENV_add_numeric( "AFNI_WHEREAMI_DEC_PLACES" ,
"Number of decimal places for whereami output" ,
0,4,0,0 , NULL ) ;
ENV_add_numeric( "AFNI_WHEREAMI_MAX_FIND" ,
"Maximum limit for structures from an atlas for whereami output" ,
1,50,0,9 , ENV_wami_maxfind ) ;
ENV_add_string( "AFNI_WHEREAMI_MAX_SEARCH_RAD" ,
"Maximum radius for structures from an atlas for whereami output" ,
0, NULL, ENV_wami_maxrad ) ;
/* 01 Jul 2011 [DRG] */
ENV_add_string( "AFNI_ATLAS_COLORS" ,
"Atlas to use in Atlas colors, Draw Dataset, Go to atlas location" ,
0, NULL, ENV_atlas_reset ) ;
/* 08 Nov 2011 [RWC] */
ENV_add_string( "AFNI_IMAGE_COLORANGLE" ,
"Image view color scale angle" ,
NUM_angle_strings,angle_strings , ENV_angle_string ) ;
/* 23 Dec 2011 [RWC] */
ENV_add_string( "AFNI_IMAGE_LABEL_STRING" ,
"Extra string for image view overlay labels" ,
0,NULL , NULL ) ;
/* 21 Feb 2013 [RWC] */
ENV_add_yesno( "AFNI_HISTOG_CUMULATIVE" ,
"Show cumulative histogram in plugins?" ) ;
/* 25 Jun 2013 [RWC] */
ENV_add_numeric( "AFNI_PBAR_TICK" ,
"Number of tick marks for colorscale" ,
0,63,0,9 , NULL ) ;
/* 23 Jul 2013 [RWC] */
ENV_add_yesno( "AFNI_RECENTER_VIEWING" ,
"Re-center xhairs when switching UnderLay?" ) ;
ENV_add_string( "AFNI_JUMPTO_SPACE" ,
"Space name to use in Jump to (spacename)" ,
0, NULL, ENV_jumpspace_reset ) ;
/*--------- Sort list of variables [21 Feb 2007] -----------*/
if( !AFNI_yesenv("AFNI_DONT_SORT_ENVIRONMENT") )
qsort( env_var , (size_t)NUM_env_var , sizeof(ENV_var) , ENV_compare ) ;
/*---------------- compute helpstring -----------------------*/
helpstring = THD_zzprintf( helpstring , "%s\n" , help_start ) ;
for( ii=0 ; ii < NUM_env_fixed ; ii++ ){
ept = getenv(env_fixed[ii]) ;
if( ept == NULL )
eval = "(Not set)" ;
else if( ept[0] == '\0' )
eval = "(Set to empty string)" ;
else
eval = ept ;
helpstring = THD_zzprintf( helpstring, " %-25.25s= %s\n",
env_fixed[ii],eval ) ;
}
helpstring = THD_zzprintf( helpstring , "%s\n" , help_mid ) ;
for( ii=0 ; ii < NUM_env_var ; ii++ ){
helpstring = THD_zzprintf( helpstring, " %-25.25s: %s\n" ,
env_var[ii].vname , env_var[ii].vhint ) ;
}
helpstring = THD_zzprintf( helpstring , "%s\n" , help_end ) ;
/*---------------- set titles and call point ----------------*/
plint = PLUTO_new_interface( "Environment" ,
"Environment variables control" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , ENV_main ) ;
free(helpstring) ;
PLUTO_add_hint( plint , "Environment variables control" ) ;
PLUTO_set_runlabels( plint , "Set+Keep" , "Set+Close" ) ; /* 04 Nov 2003 */
/*--------- make interface lines: 1 for each variable -----------*/
for( ii=0 ; ii < NUM_env_var ; ii++ ){
PLUTO_add_option( plint ,
"" , /* label at left of input line */
env_var[ii].vname , /* tag to return to plugin */
FALSE /* is this mandatory? */
) ;
ept = getenv( env_var[ii].vname ) ;
switch( env_var[ii].vtype ){
default: break ; /* should never happen */
case ENV_NUMBER_FIXED:
case ENV_NUMBER_EDITABLE:{
double dval=env_var[ii].vdef ; int ival ;
if( ept != NULL ){
dval = strtod(ept,NULL) ;
AV_SHIFT_VAL(-env_var[ii].vdecim,dval) ;
}
ival = rint(dval) ;
if( ival < env_var[ii].vbot ) ival = env_var[ii].vbot ;
else if( ival > env_var[ii].vtop ) ival = env_var[ii].vtop ;
PLUTO_add_number( plint ,
env_var[ii].vname ,
env_var[ii].vbot ,
env_var[ii].vtop ,
env_var[ii].vdecim,
ival,(env_var[ii].vtype==ENV_NUMBER_EDITABLE) ) ;
PLUTO_add_hint( plint , env_var[ii].vhint ) ; /* 8 Apr 2005 rickr */
}
break ;
case ENV_STRING:{
if( env_var[ii].vcount <= 0 ){
PLUTO_add_string( plint ,
env_var[ii].vname ,
0 , &ept , NAME_NMAX ) ;
PLUTO_add_hint( plint , env_var[ii].vhint ) ;
} else {
int dval , jj ;
char ** sval ;
dval = 1 + PLUTO_string_index( ept , env_var[ii].vcount ,
env_var[ii].vlist ) ;
sval = (char **) malloc( sizeof(char *)*(1+env_var[ii].vcount) ) ;
sval[0] = "(Not set)" ;
for( jj=0 ; jj < env_var[ii].vcount ; jj++ )
sval[jj+1] = env_var[ii].vlist[jj] ;
PLUTO_add_string( plint ,
env_var[ii].vname ,
1+env_var[ii].vcount , sval , dval ) ;
PLUTO_add_hint( plint , env_var[ii].vhint ) ;
free(sval) ;
}
}
break ;
} /* end of switch over variable type */
} /* end of loop over variables */
/*--------- done with interface setup ---------*/
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init( int ncall )
{
PLUGIN_interface * plint ;
/*----- plugin option labels -----*/ /* 19 June 1998 */
char * boolean_types[2] = {"False", "True"};
char * cluster_types[7] = {"Keep", "Mean", "Max", "AMax", "SMax", "Size",
"Order"};
if( ncall > 0 ) return NULL ; /* only one interface */
/*-- set titles and call point --*/
plint = PLUTO_new_interface( "3D Cluster" , "Dataset Clustering" , helpstring ,
PLUGIN_CALL_VIA_MENU , CLUST_main ) ;
PLUTO_add_hint( plint , "Dataset Clustering" ) ;
PLUTO_set_sequence( plint , "A:afniinfo:dsetcluster" ) ;
/*-- first line of input: Dataset --*/
PLUTO_add_option( plint , "Dataset" , "Dataset" , TRUE ) ;
PLUTO_add_dataset(plint , "Function" ,
ANAT_ALL_MASK , FUNC_ALL_MASK ,
DIMEN_3D_MASK | BRICK_ALLREAL_MASK ) ;
PLUTO_add_hint( plint , "Choose input dataset" ) ;
/*-- second line of input: Cluster Parameters --*/
PLUTO_add_option( plint , "Params" , "Params" , TRUE ) ;
PLUTO_add_hint( plint , "Find and reject small clusters" ) ;
PLUTO_add_string (plint, "Type", 7, cluster_types, 0); /* 19 June 1998 */
PLUTO_add_hint( plint , "How to process data inside clusters" ) ;
PLUTO_add_number( plint , "Radius(mm)" , 0, 100,1 , 20,TRUE ) ;
PLUTO_add_hint( plint , "Max distance between 'neighbors'" ) ;
PLUTO_add_number( plint , "MinVol(ul)" , 0,1000,-1,100,TRUE ) ;
PLUTO_add_hint( plint , "Min size for cluster to survive" ) ;
/*---- 3rd line of input: Erosion/Dilation option ----*/ /* 19 June 1998 */
PLUTO_add_option (plint, "Erode/Dilate", "Erode/Dilate", FALSE);
PLUTO_add_hint (plint , "Sever narrow connecting paths between clusters");
PLUTO_add_number (plint, "% Voxels", 0, 100, 0, 50, TRUE);
PLUTO_add_hint (plint ,
"Min % of active 'neighbors' for a voxel to survive");
PLUTO_add_string (plint, "Dilate?", 2, boolean_types, 0);
PLUTO_add_hint (plint , "Restore voxels near main body of cluster");
/*-- fourth line of input: Threshold (optional) --*/
PLUTO_add_option( plint , "Threshold" , "Threshold" , FALSE ) ;
PLUTO_add_hint( plint , "Zero out if threshold brick too small" ) ;
PLUTO_add_number( plint , "Cutoff" , 0,1000,2 , 50,TRUE ) ;
PLUTO_add_hint( plint , "Threshold values < this => 0" ) ;
/*-- fifth line of input: Prefix for output dataset --*/
PLUTO_add_option( plint , "Output" , "Output" , FALSE ) ;
PLUTO_add_string( plint , "Prefix" , 0,NULL , 19 ) ;
PLUTO_add_hint( plint , "Name output dataset" ) ;
return plint ;
}
DEFINE_PLUGIN_PROTOTYPE
PLUGIN_interface * PLUGIN_init(int ncall)
{
PLUGIN_interface * plint ;
if( ncall > 0 ) return NULL ; /* only one interface */
/*-- set titles and call point --*/
plint = PLUTO_new_interface( "Histogram: BFit" ,
"Betafit Histogram" ,
helpstring ,
PLUGIN_CALL_VIA_MENU , BFIT_main ) ;
PLUTO_add_hint( plint , "Histogram: Betafit" ) ;
PLUTO_set_sequence( plint , "A:afniinfo:dsethistog" ) ;
/*-- first line of input --*/
PLUTO_add_option( plint , "Source" , "Source" , TRUE ) ;
PLUTO_add_dataset( plint ,
"Dataset" , /* label next to button */
ANAT_ALL_MASK , /* take any anat datasets */
FUNC_ALL_MASK , /* only allow fim funcs */
DIMEN_3D_MASK | /* need 3D+time datasets */
BRICK_ALLREAL_MASK /* need real-valued datasets */
) ;
PLUTO_add_number( plint , "Brick" , 0,9999,0, 0,1 ) ;
PLUTO_add_string( plint , "Square" , NYESNO , YESNO_strings , 1 ) ;
/*-- second line of input --*/
PLUTO_add_option( plint , "a Params" , "Params" , TRUE ) ;
PLUTO_add_number( plint , "a bot" , 2,50 ,1 , 5 , 1 ) ;
PLUTO_add_number( plint , "a top" , 2,500,1 , 20 , 1 ) ;
PLUTO_add_option( plint , "b Params" , "Params" , TRUE ) ;
PLUTO_add_number( plint , "b bot" , 10,400 ,0 , 10 , 1 ) ;
PLUTO_add_number( plint , "b top" , 10,9999,0 , 200 , 1 ) ;
PLUTO_add_number( plint , "H last", 0,1000,-1 , 0,1 ) ;
PLUTO_add_option( plint , "Misc" , "Params" , TRUE ) ;
PLUTO_add_number( plint , "N ran" , 10,1000,-2 , 100 , 1 ) ;
PLUTO_add_number( plint , "% cut" , 20,90,0 , 70,1 ) ;
PLUTO_add_string( plint , "HSqrt" , NYESNO , YESNO_strings , 0 ) ;
/*-- (optional) line of input --*/
PLUTO_add_option( plint , "Mask" , "Mask" , FALSE ) ;
PLUTO_add_dataset( plint , "Dataset" ,
ANAT_ALL_MASK , FUNC_ALL_MASK ,
DIMEN_ALL_MASK | BRICK_ALLREAL_MASK ) ;
PLUTO_add_number( plint , "Brick" , 0,9999,0 , 0,1 ) ;
/*-- (optional) line of input --*/
PLUTO_add_option( plint , "Range" , "Range" , FALSE ) ;
PLUTO_add_number( plint , "Bottom" , -99999,99999, 1, 0,1 ) ;
PLUTO_add_number( plint , "Top" , -99999,99999,-1, 0,1 ) ;
/*-- (optional) line of input --*/
PLUTO_add_option( plint , "Extra" , "Extra" , FALSE ) ;
PLUTO_add_number( plint , "a" , 2,50,1 , 5 , 1 ) ;
PLUTO_add_number( plint , "b" , 10,999,0 , 200 , 1 ) ;
return plint ;
}