def script_set_vars(self):
"""use variables for dataset directories, only
"""
# init with a section comment
hdr = SUBJ.comment_section_string('set process variables') + '\n'
cmd = ''
# init to nothing
self.LV.dirA = ''
self.LV.dirB = ''
if self.uvars.mask:
cmd += 'set mask_dset = %s\n\n' \
% self.strip_suffix(self.uvars.mask, '.HEAD')
# set dirA and possibly dirB
dirs_set = 0
if not UTIL.is_trivial_dir(self.LV.parent_dirs[0]):
cmd += 'set dirA = %s\n' % self.LV.parent_dirs[0]
self.LV.dirA = '$dirA'
dirs_set = 1
if len(self.uvars.dsets_B) > 0:
if not UTIL.is_trivial_dir(self.LV.parent_dirs[1]):
if self.LV.parent_dirs[0] != self.LV.parent_dirs[1]:
cmd += 'set dirB = %s\n' % self.LV.parent_dirs[1]
self.LV.dirB = '$dirB'
dirs_set = 1
else:
self.LV.dirB = '$dirA'
if dirs_set: cmd += '\n'
if cmd: return hdr + cmd
else: return ''
def script_tabulate_areas(self):
"""for each zthr, for each clust file, extract max area"""
cmd = SUBJ.comment_section_string('extract cluster counts') + '\n'
cmd += '# tabulate all results for each uncorrected p-threshold\n' \
'set maxa_list = () # track all max areas\n' \
'set failures = () # track cluster failures\n' \
'foreach pthr ( $pthr_list )\n' \
' # make note of current file\n' \
' set zfile = z.max.area.$pthr\n' \
'\n' \
' # create empty file for this p-value\n' \
' echo -n "" > $zfile\n' \
'\n' \
' set file_list = ( clust.out.*.$pthr )\n' \
' echo "-- processing $#file_list files for p = $pthr"\n' \
'\n' \
' # process each file, counting through them\n' \
' foreach findex ( `count -digits 1 1 $#file_list` )\n' \
' set file = $file_list[$findex]\n' \
'\n' \
' # print pacifier every 100 files\n' \
' if ( ! ($findex % 100) ) echo -n .\n' \
' if ( ! ($findex % 5000) ) echo ""\n' \
'\n' \
' # grab the area field from first (largest) cluster\n' \
" set maxa = `awk '$1 == 1 {print $3}' $file`\n" \
'\n' \
' # and append it to the max file (if results exist)\n' \
' if ( $maxa != "" ) echo $maxa >> $zfile\n' \
'\n' \
' end # file index\n' \
'\n' \
' # grab the max area for this p-value, and add to list\n' \
' # (if the max.area file is not empty for some reason)\n' \
' set nlines = `cat $zfile | wc -l`\n' \
' if ( $nlines != 0 ) then\n' \
' set maxa = `sort -rn $zfile | head -n 1`\n' \
' else\n' \
' set failures = ( $failures $pthr )\n' \
' set maxa = 0\n' \
' endif\n' \
'\n' \
' set maxa_list = ( $maxa_list $maxa )\n' \
'\n' \
'end # pthr\n' \
'\n' \
'echo ""\n' \
'echo "p-value thresholds : $pthr_list"\n' \
'echo "z-score thresholds : $zthr_list"\n' \
'echo "maximum cluster areas: $maxa_list"\n' \
'\n' \
'if ( $#failures ) then\n' \
' echo ""\n' \
' echo "** no clusters for p = $failures"\n' \
'endif\n' \
'\n'
return cmd
def script_set_vars(self):
"""use variables for inputs (anat, epi, epi_base) and for
options (cost_main, cost_list, align_opts)
"""
# init with a section comment
cmd = SUBJ.comment_section_string('set processing variables') + '\n'
# maybe init with top_dir
if not self.LV.is_trivial_dir('top_dir'):
cmd += '# top data directory\n' \
'set top_dir = %s\n\n' % self.LV.top_dir
# anat and epi might use top_dir
if self.LV.is_trivial_dir('top_dir'):
astr = self.uvars.anat
estr = self.uvars.epi
else:
astr = '$top_dir/%s' % self.LV.short_names[0][0]
estr = '$top_dir/%s' % self.LV.short_names[0][1]
# if we are aligning centers, set center_base variable (maybe w/top_dir)
if self.uvars.align_centers == 'yes':
if self.LV.is_trivial_dir('top_dir'): cstr = self.uvars.center_base
else:
cdir = UTIL.child_dir_name(self.LV.top_dir,
self.uvars.center_base)
if cdir == self.uvars.center_base: cstr = cdir
else: cstr = '$top_dir/%s' % cdir
ccmd = 'set center_base = %s\n' % cstr
else:
ccmd = ''
# now set variables for inputs, possibly including center_base
cmd += '# input dataset options (ebase is EPI index)\n' \
'set in_anat = %s\n' \
'set in_epi = %s\n' \
'set in_ebase = %d\n' \
'%s' \
'\n' \
% (astr, estr, self.uvars.epi_base, ccmd)
# note whether to use multi_cost
cmd += '# main options\n' \
'set cost_main = %s\n' % self.uvars.cost_list[0]
if len(self.uvars.cost_list) > 1:
cmd += 'set cost_list = ( %s )\n' % ' '.join(
self.uvars.cost_list[1:])
cmd += '\n'
# possibly add align_opts list variable
cmd += self.make_align_opts_str()
return cmd
def script_main(self):
"""write command with prefix, datasets and extra options
"""
cmd = SUBJ.comment_section_string('process the data') + '\n'
if self.uvars.program == '3dttest++':
cmd += self.script_ttest()
elif self.uvars.program == '3dMEMA':
cmd += self.script_MEMA()
else:
self.errors.append('** bad program name: %s' % self.uvars.program)
return ''
return UTIL.add_line_wrappers(cmd)
def script_copy_data(self):
"""these commands only vary based on results_dir"""
cmd = SUBJ.comment_section_string('copy data') + '\n'
if self.uvars.is_trivial_dir('results_dir'): rdir = '.'
else: rdir = '$results_dir'
cmd += '# copy dataset to processing directory\n' \
'3dbucket -prefix %s/anat $in_anat\n' \
'3dbucket -prefix %s/epi $in_epi"[$in_ebase]"\n' \
'\n' % (rdir, rdir)
if rdir != '.':
cmd += '# enter the processing directory\n' \
'cd %s\n\n' % rdir
return cmd
def script_align_datasets(self):
"""actually run align_epi_anat.py
only current option is -mult_cost, everything else is via variables
"""
if len(self.uvars.cost_list) > 1: mstr = ' -multi_cost $cost_list'
else: mstr = ''
cmd = SUBJ.comment_section_string('align data') + '\n'
cmd += \
'# test alignment, using variables set above\n' \
'align_epi_anat.py -anat anat+orig -epi epi+orig ' \
'-epi_base $in_ebase \\\n' \
' -cost $cost_main%s $align_opts\n' \
'\n' % mstr
return cmd
def script_align_centers(self):
"""if align_centers should be run, deoblique both and align with
center_base (probably TT_N27+tlrc)
note: these commands should be fixed, since the dataset names are
"""
if self.uvars.align_centers != 'yes': return ''
cmd = SUBJ.comment_section_string('align centers') + '\n'
cmd += '# since altering grid, remove any oblique transformation\n' \
'3drefit -deoblique anat+orig epi+orig\n' \
'\n' \
'# align volume centers (we do not trust spatial locations)\n' \
'@Align_Centers -no_cp -base $center_base -dset anat+orig\n' \
'@Align_Centers -no_cp -base $center_base -dset epi+orig\n\n' \
return cmd
def script_results_dir(self):
# if no results dir, just put everything here
if self.uvars.is_trivial_dir('results_dir'): return ''
cmd = SUBJ.comment_section_string('test and create results dir') + '\n'
cmd += '# note directory for results\n' \
'set results_dir = %s\n\n' % self.uvars.results_dir
cmd += '# make sure it does not yet exist\n' \
'if ( -e $results_dir ) then\n' \
' echo "** results dir \'$results_dir\' already exists"\n' \
' exit\n' \
'endif\n\n'
cmd += '# create results directory, where the work will be done\n' \
'mkdir $results_dir\n\n'
return cmd
def script_analysis_prep(self):
"""return a set of commands to:
convert pthr_list to zthr_list
create a dummy time series of lenth itersize (if > 1)
divide (ceil) niter by itersize (if > 1)
"""
cmd = SUBJ.comment_section_string('prep: make z-scores, etc.') + '\n'
cmd += '# make zthr_list (convert p-values to z-scores)\n' \
'# (2-tailed computation mirrors athresh() in SurfClust)\n'\
'set zthr_list = ()\n' \
'foreach pthr ( $pthr_list )\n' \
' # convert from p to z (code for N(0,1) is 5)\n' \
' set zthr = `ccalc "cdf2stat(1-$pthr,5,0,0,0)"`\n' \
' set zthr_list = ( $zthr_list $zthr )\n' \
'end\n\n'
cmd += 'echo have p-values: $pthr_list\n' \
'echo have z-scores: $zthr_list\n\n'
cmd += '# make a dummy time file of length $itersize for 3dcalc\n' \
'1deval -num $itersize -expr t > dummy.TRs.$itersize.1D\n\n'
cmd += '# divide niter by itersize (take ceiling)\n' \
'@ niter = ( $niter + $itersize - 1 ) / $itersize\n\n'
# always create an empty surface, and then an all-1 surface
cmd += g_make_empty_surf_str
if self.LV.val('smask'):
cmd += '# make an all-1 masked surface for 3dmaskave\n' \
'3dcalc -a $empty_surf -b $surf_mask' \
' -expr "bool(b)" -prefix all_1.gii\n\n'
else:
cmd += '# make an all-1 surface for 3dmaskave\n' \
'3dcalc -a $empty_surf -expr 1 -prefix all_1.gii\n\n'
return cmd
def script_set_vars(self):
"""use variables for inputs (anat, epi, epi_base) and for
options (cost_main, cost_list, align_opts)
"""
U = self.uvars # for convenience
# init with a section comment
cmd = SUBJ.comment_section_string('set processing variables') + '\n'
# maybe init with top_dir
if not self.LV.is_trivial_dir('top_dir'):
cmd += '# top data directory\n' \
'set top_dir = %s\n\n' % self.LV.top_dir
# surf_vol and vol_mask might use top_dir
if self.LV.is_trivial_dir('top_dir'):
# if self.cvars.val('on_surface') != 'yes': self.LV.svol = U.surf_vol
#
# rcr - fix this, surf_vol should not be needed if only on surface
# (for getting the node count, avoid SurfMeasures or any other
# program that uses -sv)
self.LV.svol = U.surf_vol
self.LV.svset = BASE.afni_name(self.LV.svol)
self.LV.vmask = U.vol_mask
self.LV.vmset = BASE.afni_name(U.vol_mask)
self.LV.spec = U.spec_file
if self.uvars.surf_mask != '':
self.LV.smset = BASE.afni_name(self.uvars.surf_mask)
self.LV.smask = self.LV.smset.real_input()
else:
self.LV.svol = '$top_dir/%s' % self.LV.short_names[0][0]
self.LV.svset = BASE.afni_name(self.LV.svol)
self.LV.spec = '$top_dir/%s' % self.LV.short_names[0][1]
if self.cvars.val('on_surface') == 'yes':
if self.uvars.surf_mask != '':
self.LV.smask = '$top_dir/%s' % self.LV.short_names[0][2]
self.LV.smset = BASE.afni_name(self.LV.smask)
else:
self.LV.vmask = '$top_dir/%s' % self.LV.short_names[0][2]
self.LV.vmset = BASE.afni_name(self.LV.vmask)
cmd += '# input datasets and surface specification file\n' \
'# (absolute paths are used since inputs are not copied)\n' \
'set surf_vol = %s\n' \
'set spec_file = %s\n' % (self.LV.svol, self.LV.spec)
if self.cvars.val('on_surface') != 'yes':
cmd += 'set vol_mask = %s\n' % self.LV.vmask
if self.LV.val('smask'):
cmd += 'set surf_mask = %s\n' % self.LV.smask
# as a list, these might come is as strings or floats, be generic
plist = ['%s' % p for p in U.pthr_list]
cmd += '\n' \
'# iterations and blur/clust parameters\n' \
'set niter = %d\n' \
'set itersize = %d\n' \
'set pthr_list = ( %s )\n\n' \
'set blur = %g\n' \
'set rmm = %g\n\n' \
% (U.niter, U.itersize, ' '.join(plist), U.blur, U.rmm)
cmd += '# surface mapping parameters\n' \
'set surfA = %s\n' \
'set surfB = %s\n' \
'set map_func = %s\n' \
'set nsteps = %d\n\n' \
% (U.surfA, U.surfB, U.map_func, self.cvars.nsteps)
if self.cvars.keepblocks > 0:
cmd += '# note how many blocks to keep output datasets for\n' \
'set keepblocks = %d\n\n' % self.cvars.keepblocks
if self.cvars.time_process:
cmd += "# prepare to possibly time programs (/usr/bin/time or '')\n" \
"set time_str = /usr/bin/time \n\n"
self.LV.time_str = '$time_str \\\n'
else:
self.LV.time_str = ''
return cmd