def write_uber_command(self):
if show_func_seq: print('=== R ===') # rcr - not called
pdir = self.ttobj.cvars.val('proc_dir')
if os.path.isdir(pdir):
sstr = self.make_uber_command()
UTIL.write_text_to_file('%s/.orig.cmd.utt' % pdir, sstr)
def write_script(self, fname=''):
"""write processing script to a file (in the proc_dir)
- if fname is set, use it, else generate
- set rvars.file_proc and output_proc
"""
if not self.script:
print('** no script to write out')
return 1
if fname: name = fname
else: name = 'script.ttest'
# store (intended) names for calling tool to execute with
self.rvars.file_proc = name # store which file we have written to
self.rvars.output_proc = 'output.%s' % name # file for command output
if self.cvars.verb > 0: print('++ writing script to %s' % name)
# if requested, make an original copy
self.LV.retdir = SUBJ.goto_proc_dir(self.cvars.proc_dir)
if self.cvars.copy_scripts == 'yes': # make an orig copy
UTIL.write_text_to_file('.orig.%s' % name, self.script, exe=1)
rv = UTIL.write_text_to_file(name, self.script, exe=1)
self.LV.retdir = SUBJ.ret_from_proc_dir(self.LV.retdir)
return rv
def execute(self):
if not self.ready_for_action(): return 1
if self.verb > 1:
print('-- make %s command with %d set(s) of dsets of length(s): %s' \
% (self.command, len(self.dsets),
', '.join([str(len(dlist)) for dlist in self.dsets]) ))
# might deal with subject IDs and attributes later
for ind, dlist in enumerate(self.dsets):
slist = SUBJ.SubjectList(dset_l=dlist, verb=self.verb)
if slist.status: return 1
if slist.set_ids_from_dsets(prefix=self.subj_prefix,
suffix=self.subj_suffix,
dpre=self.dent_pre):
print('** cannot set subject IDs from datasets')
return 1
self.slist.append(slist)
if self.verb > 2: slist.show("slist %d" % ind)
cmd = None
if self.command == '3dMEMA':
cmd = self.get_mema_command()
elif self.command == '3dttest++':
cmd = self.get_ttpp_command()
elif self.command == '3dANOVA2':
cmd = self.get_anova2_command()
elif self.command == '3dANOVA3':
cmd = self.get_anova3_command()
elif self.command:
cmd = self.get_generic_command()
else:
print('** command not implemented: %s' % self.command)
# bail on failure, else wrap command
if cmd == None:
print('** failed making %s command' % self.command)
return 1
cmd = UTIL.add_line_wrappers(cmd)
# either write to file or print
if self.write_script:
if UTIL.write_text_to_file(self.write_script, cmd):
print("** failed to write command to file '%s'" %
self.write_script)
return 1
if self.verb > 0:
print('++ command written to file %s' % self.write_script)
else:
print(cmd)
3dBrickStat -mask $mask -percentile $bot $step 100 -non-zero \\
$pre.abs+tlrc > $pre.abs.1D
# have percentile p-values, remove unwanted percentile rankings
1dcat $pre.abs.1D'[1..$(2)]' > $pre.at.1D
# transpose and convert t to p
1deval -a $pre.at.1D\\' -expr "fitt_t2p(a,$dof)" > $pre.p.1D
# convert p to q (** note: the minimum is not applied, we do not want it)
1deval -a $pre.p.1D -expr "a*$nv/($nv-t)" > $pre.q.1D
# put both together in output file
1dcat $pre.p.1D $pre.q.1D > $output
# ----------------------------------------
# nuke temporary files (comment out to keep)
rm -f $pre.*
"""
ss += static_script
# and write output
U.write_text_to_file(outfile, ss)
try:
os.chmod(outfile, 0755)
except OSError, e:
print e
def write_uber_command(self):
pdir = self.atest.cvars.val('proc_dir')
if os.path.isdir(pdir):
sstr = self.make_uber_command()
UTIL.write_text_to_file('%s/.orig.cmd.uat' % pdir, sstr)