static char * EXTRACT_main( PLUGIN_interface * plint )
{
extract_data uda,*ud;
MRI_IMAGE * tsim;
MCW_idcode * idc ; /* input dataset idcode */
THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */
char *tmpstr , * str , *nprfxstr;
int ntime, nvec ,nprfx, Err=0 , itmp;
float * vec , fs , T ;
char * tag; /* plugin option tag */
/* Allocate as much character space as Bob specifies in afni.h + a bit more */
tmpstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
nprfxstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
if (tmpstr == NULL || nprfxstr == NULL)
return "********************\n"
"Could not Allocate\n"
"a teeni weeni bit of\n"
"Memory ! Go complain\n"
"to yer Mamma ! \n"
"********************\n";
ud = &uda; /* ud now points to an allocated space */
ud->errcode = 0; /*reset error flag */
/*--------------------------------------------------------------------*/
/*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
/*--------- go to first input line ---------*/
tag = PLUTO_get_optiontag(plint) ;
if (tag == NULL)
{
return "************************\n"
"Bad 1st line option \n"
"************************" ;
}
idc = PLUTO_get_idcode(plint) ; /* get dataset item */
old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */
if( old_dset == NULL )
return "*************************\n"
"Cannot find Input Dataset\n"
"*************************" ;
ud->dsetname = DSET_FILECODE (old_dset);
ud->ignore = PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ;
ud->dtrnd = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings );
/*--------- loop over ramining options ---------*/
ud->iloc = -1;
ud->xloc = -1;
ud->yloc = -1;
ud->zloc = -1;
do
{
tag = PLUTO_get_optiontag(plint) ;
if (tag == NULL) break;
if (strcmp (tag, "Mask") == 0)
{
ud->strin = PLUTO_get_string(plint) ;
ud->ncols = PLUTO_get_number(plint) ;
ud->pass = PLUTO_get_number(plint) ;
ud->fail = 0; /* Set voxels that don't make it to 0 */
continue;
}
if (strcmp (tag, "Index") == 0)
{
ud->iloc = PLUTO_get_number(plint) ; /* get number item */
continue;
}
if (strcmp (tag, "XYZ") == 0)
{
ud->xloc = PLUTO_get_number(plint) ; /* get number item */
ud->yloc = PLUTO_get_number(plint) ; /* get number item */
ud->zloc = PLUTO_get_number(plint) ; /* get number item */
continue;
}
if (strcmp (tag, "Output") == 0)
{
ud->new_prefix = PLUTO_get_string(plint) ; /* get string item (the output prefix) */
/* check to see if the field is empty */
if (ud->new_prefix == NULL)
nprfx = 0;
else
nprfx = 1;
/* check if the size is larger than 0. I did not want to check for this unless it's allocated */
if (nprfx == 1 && (int)strlen (ud->new_prefix) == 0)
nprfx = 0;
if (nprfx == 0) /* now create the new name and make new_prefix point to it */
{
sprintf (nprfxstr,"%s.XTRCT",DSET_PREFIX (old_dset));
ud->new_prefix = nprfxstr;
/*printf ("New prefix is set to be : %s\n\a",ud->new_prefix);*/
}
if( ! PLUTO_prefix_ok(ud->new_prefix) ) /* check if it is OK */
return "************************\n"
"Output Prefix is illegal\n"
"************************" ;
ud->strout = PLUTO_get_string(plint) ;
str = PLUTO_get_string(plint) ;
ud->format = (int)PLUTO_string_index( str , NUM_FORMAT_STRINGS , format_strings );
continue;
}
} while (1);
/* ------------------ Check for some errorsor inconsistencies ------------- */
if (ud->iloc == -1 && ud->xloc == -1)
{
return "**************************\n"
"At least iloc or x/y/zloc\n"
"must be specified\n"
"**************************\n"
;
}
if (ud->iloc != -1 && ud->xloc != -1)
{
return "***************************\n"
"iloc AND x/y/zloc can not\n"
"be simultaneously specified\n"
"***************************\n"
;
}
/* ------------------Done with user parameters ---------------------------- */
/* Now loadup that index list or the xyz list */
if (ud->iloc != -1)
{
itmp = 0; /* might want to give option of setting it to number of rows if*/
/* the users know it, otherwise, it is automatically determined*/
ud->indvect = extract_index (ud->strin, ud->iloc, ud->ncols, &itmp, &Err);
}
else /* assuming the only other case is that x y z are specified */
{
itmp = 0;
ud->xyzvect = extract_xyz (ud->strin , ud->xloc , ud->yloc , ud->zloc , ud->ncols, &itmp, &Err);
}
ud->nrows = itmp;
switch (Err)
{
case (0):
break;
case (1):
return "****************************************\n"
"index location should be > 0 and < ncols\n"
"****************************************\n";
case (2):
return "********************************************\n"
"file size and number of columns do not match\n"
"********************************************\n";
case (3):
return "**********************\n"
"Can't find matrix file\n"
"**********************\n";
case (4):
return "*****************\n"
"ncols must be > 0\n"
"*****************\n";
case (5):
return "****************************************\n"
"x/y/z column numbers can NOT be the same\n"
"****************************************\n";
default:
return "****************************************\n"
"Should not have gotten here .....\n"
"****************************************\n";
}
if (strcmp (ud->strout,"") == 0) /* no output file is specified */
{
sprintf ( tmpstr , "%s" , ud->new_prefix);
ud->strout = tmpstr;
}
if (filexists(ud->strout) == 1)
{
return "*******************************\n"
"Outfile exists, won't overwrite\n"
"*******************************\n";
}
ud->outwritets = fopen (ud->strout ,"w");
sprintf ( tmpstr , "%s.log" , ud->strout);
if (filexists(tmpstr) == 1)
{
return "*******************************\n"
"Outfile.log exists, won't overwrite\n"
"*******************************\n";
}
ud->outlogfile = fopen (tmpstr ,"w");
if ((ud->outwritets == NULL) || (ud->outlogfile == NULL) )
{
ud->errcode = ERROR_FILEWRITE;
return "***********************\n"
"Could Not Write Outfile\n"
"***********************\n";
}
ud->nxx = (int)old_dset->daxes->nxx; /* get data set dimensions */
ud->nyy = (int)old_dset->daxes->nyy;
ud->nzz = (int)old_dset->daxes->nzz;
/* ready to dump the log file */
write_ud (ud);
/*------------- ready to compute new dataset -----------*/
new_dset = PLUTO_4D_to_typed_fim( old_dset , /* input dataset */
ud->new_prefix , /* output prefix */
-1, /* negative value indicating data type is like original brick */
ud->ignore , /* ignore count */
ud->dtrnd , /* detrend */
EXTRACT_tsfunc , /* timeseries processor */
(void *)ud /* data for tsfunc */
) ;
PLUTO_add_dset( plint , new_dset , DSET_ACTION_MAKE_CURRENT ) ;
fclose (ud->outlogfile);
fclose (ud->outwritets);
free (tmpstr);
free (nprfxstr);
return NULL ; /* null string returned means all was OK */
}
static char * DELAY_main( PLUGIN_interface * plint )
{
hilbert_data_V2 uda,*ud;
MRI_IMAGE * tsim;
MCW_idcode * idc ; /* input dataset idcode */
THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */
char *tmpstr , * str , *nprfxstr; /* strings from user */
int ntime, nvec ,nprfx, i;
float * vec , fs , T ;
/* Allocate as much character space as Bob specifies in afni.h + a bit more */
tmpstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
nprfxstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
if (tmpstr == NULL || nprfxstr == NULL)
return "********************\n"
"Could not Allocate\n"
"a teeni weeni bit of\n"
"Memory ! \n"
"********************\n";
ud = &uda; /* ud now points to an allocated space */
ud->errcode = 0; /*reset error flag */
/*--------------------------------------------------------------------*/
/*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
/*--------- go to first input line ---------*/
PLUTO_next_option(plint) ;
idc = PLUTO_get_idcode(plint) ; /* get dataset item */
old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */
if( old_dset == NULL )
return "*************************\n"
"Cannot find Input Dataset\n"
"*************************" ;
ud->dsetname = DSET_FILECODE (old_dset);
ud->nsamp = DSET_NUM_TIMES (old_dset);
ud->Navg = 1 ; /* Navg does not play a role for the p value, averaging increases sensitivity */
ud->Nort = PLUTO_get_number(plint) ; /* Should be two by default, for mean and linear trend */
ud->Nfit = 2 ; /* Always 2 for phase and amplitude for this plugin */
/*--------- go to 2nd input line, input time series ---------*/
PLUTO_next_option(plint) ;
tsim = PLUTO_get_timeseries(plint);
if (tsim == NULL) return "No Timeseries Input";
ud->ln = (int)tsim -> nx; /* number of points in each vector */
nvec = tsim -> ny; /* number of vectors */
ud->rvec = (float *) MRI_FLOAT_PTR(tsim); /* vec[i+j*nx] = ith point of jth vector */
/* for i=0 .. ntime-1 and j=0 .. nvec-1 */
if (is_vect_null (ud->rvec,ud->ln) == 1) /* check if ref vect is all zeroes */
{
return "Reference vector is all zeros";
}
ud->refname = tsim->name;
ud->ignore = PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ;
ud->Dsamp = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings ) ;
/*--------- go to 3rd input line, sampling frequency, and stimulus period ---------*/
PLUTO_next_option(plint) ;
ud->fs = PLUTO_get_number(plint) ; /* get number item */
ud->T = PLUTO_get_number(plint) ; /* get number item */
ud->co = PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ;
ud->biasrem = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings ) ;
/*--------- go to 4th input line, delay units and wrp option---------*/
PLUTO_next_option(plint) ;
ud->Nseg = (int)PLUTO_get_number(plint) ; /* get number item */
ud->Pover = (int)PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ; /* get string item (the method) */
ud->unt = (int)PLUTO_string_index( str , /* find it in list it is from */
NUM_METHOD_STRINGS ,
method_strings ) ;
str = PLUTO_get_string(plint) ;
ud->wrp = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings ) ;
/*--------- go to 5th input line Output prefix ---------*/
PLUTO_next_option(plint) ;
ud->new_prefix = PLUTO_get_string(plint) ; /* get string item (the output prefix) */
/* check to see if the field is empty */
if (ud->new_prefix == NULL)
nprfx = 0;
else
nprfx = 1;
/* check if the size is larger than 0. I did not want to check for this unless it's allocated */
if (nprfx == 1 && (int)strlen (ud->new_prefix) == 0)
nprfx = 0;
if (nprfx == 0) /* now create the new name and make new_prefix point to it */
{
sprintf (nprfxstr,"%s.DEL",DSET_PREFIX (old_dset));
ud->new_prefix = nprfxstr;
/*printf ("New prefix is set to be : %s\n\a",ud->new_prefix);*/
}
if( ! PLUTO_prefix_ok(ud->new_prefix) ) /* check if it is OK */
return "************************\n"
"Output Prefix is illegal\n"
"************************" ;
str = PLUTO_get_string(plint) ; /* write delays to file ? */
ud->out = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings );
ud->strout = PLUTO_get_string(plint) ; /* strout is for the outiflename, which will be used after the debugging section */
if (ud->strout == NULL) /* if no output name is given, use the new_prefix */
{ud->strout = ud->new_prefix;}
else
{
if((int)strlen (ud->strout) == 0) ud->strout = ud->new_prefix;
}
str = PLUTO_get_string(plint) ;
ud->outts = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings );
/* ------------------Done with user parameters ---------------------------- */
ud->nxx = (int)old_dset->daxes->nxx; /* get data set dimensions */
ud->nyy = (int)old_dset->daxes->nyy;
ud->nzz = (int)old_dset->daxes->nzz;
/* No need for users to set these options ...*/
ud->dtrnd = 0;
if (ud->ln != (ud->nsamp - ud->ignore))
{
ud->errcode = ERROR_BADLENGTH;
return "***************************\n"
"Bad time series length \n"
"Check reference time series\n"
" or the ignore parameter \n"
"***************************\n";
}
if ((ud->unt < 0) || (ud->unt > 2)) /* unt error Check */
{
ud->errcode = ERROR_WRONGUNIT;
return "***********************\n"
" internal error: (ziad)\n"
"unt values out of bound\n"
"***********************\n"; /*unt must be between 0 and 2 */
}
if ((ud->wrp < 0) || (ud->wrp > 1)) /* wrp error Check */
{
ud->errcode = ERROR_WARPVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"wrp values out of bound\n"
"***********************\n"; /* wrp must be between 0 and 1*/
}
if (ud->fs < 0.0) { /* fs error Check */
ud->errcode = ERROR_FSVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"fs value is negative !\n"
"***********************\n"; /* fs must be >= 0*/
}
if (ud->T < 0.0) { /* T error Check */
ud->errcode = ERROR_TVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"T value is negative !\n"
"***********************\n"; /*T must be >= 0 */
}
if ((ud->T == 0.0) && (ud->unt > 0)) /* unt error Check */
{
ud->errcode = ERROR_TaUNITVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"T and unt val. mismatch\n"
"***********************\n"; /*T must be specified, and > 0 in order to use polar units*/
}
if ((ud->wrp == 1) && (ud->T == 0.0)) /* wrp error Check */
{
ud->errcode = ERROR_TaWRAPVALUES;
return "***********************\n"
" internal error: (ziad)\n"
"wrp and T val. mismatch\n"
"***********************\n"; /*T must be specified, and > 0 in order to use polar warp*/
}
if ((ud->out == NOPE) && (ud->outts == YUP))
{
ud->errcode = ERROR_OUTCONFLICT;
return"***********************\n"
"error: \n"
"Write flag must be on\n"
"to use Write ts\n"
"***********************\n";
}
/* Open the logfile, regardless of the ascii output files */
sprintf ( tmpstr , "%s.log" , ud->strout);
ud->outlogfile = fopen (tmpstr,"w");
if (ud->out == YUP) /* open outfile */
{
ud->outwrite = fopen (ud->strout,"w");
if (ud->outts == YUP)
{
sprintf ( tmpstr , "%s.ts" , ud->strout);
ud->outwritets = fopen (tmpstr,"w");
}
if ((ud->outwrite == NULL) || (ud->outlogfile == NULL) ||\
(ud->outwritets == NULL && ud->outts == YUP) )
{
ud->errcode = ERROR_FILEOPEN;
return "***********************\n"
"Could Not Write Outfile\n"
"***********************\n";
}
}
/* Write out user variables to Logfile */
write_ud (ud); /* writes user data to a file */
/*show_ud (ud,0); */ /* For some debugging */
/*------------- ready to compute new dataset -----------*/
new_dset = MAKER_4D_to_typed_fbuc ( old_dset , /* input dataset */
ud->new_prefix , /* output prefix */
-1, /* negative value indicating data type is like original brick */
ud->ignore , /* ignore count */
1 , /* detrend = ON Let BOB do it*/
NBUCKETS, /*Number of values at each voxel*/
DELAY_tsfuncV2 , /* timeseries processor (bucket version)*/
(void *)ud, /* data for tsfunc */
NULL, 0 ) ;
/* Setup the label, keywords and types of subbricks */
i = 0;
while (i < NBUCKETS)
{
switch (i)
{
case DELINDX: /* delay value in results vector */
EDIT_BRICK_LABEL (new_dset,i,"Delay");
EDIT_BRICK_ADDKEY (new_dset,i,"D");
++i;
break;
case COVINDX: /* covariance value in results vector */
EDIT_BRICK_LABEL (new_dset,i,"Covariance");
EDIT_BRICK_ADDKEY (new_dset,i,"I");
++i;
break;
case COFINDX: /* cross correlation coefficient value in results vector */
EDIT_BRICK_LABEL (new_dset,i,"Corr. Coef.");
EDIT_BRICK_ADDKEY (new_dset,i,"r");
/* Here you must modify either ud->Nfit or ud->Nort or most likely ud->nsamp based on ud->Navg */
EDIT_BRICK_TO_FICO (new_dset,i,ud->nsamp - ud->ignore,ud->Nfit,ud->Nort);
++i;
break;
case VARINDX: /* FMRI time course variance value in results vector */
EDIT_BRICK_LABEL (new_dset,i,"Variance");
EDIT_BRICK_ADDKEY (new_dset,i,"S2");
++i;
break;
default :
return "*********************\n"
"Internal Error (ziad)\n"
" Bad i value \n"
"*********************\n";
break;
}
}
if (!AFNI_noenv("AFNI_AUTOMATIC_FDR")) {
THD_create_all_fdrcurves( new_dset );
}
PLUTO_add_dset( plint , new_dset , DSET_ACTION_MAKE_CURRENT ) ;
if (ud->out == YUP) /* close outfile and outlogfile*/
{
fclose (ud->outlogfile);
fclose (ud->outwrite);
if (ud->outts == YUP) fclose (ud->outwritets);
}
else
{
if (ud->outlogfile != NULL) fclose (ud->outlogfile); /* close outlogfile */
}
free (tmpstr);
free (nprfxstr);
return NULL ; /* null string returned means all was OK */
}
