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)
def make_align_opts_str(self):
"""any align options, one per line"""
# keep comment separate to get indent length
cmnt = '# all other align_epi_anat.py options\n' \
cstr = 'set align_opts = ( '
clen = len(cstr)
istr = ' ' * clen
# put one option on first line
cstr += '%s \\\n' % '-tshift off'
# ---------- here is the main option application ---------
# then add each option offset by initial indentation
cstr += '%s%s \\\n' % (istr, '-volreg off')
if self.uvars.giant_move == 'yes':
cstr += '%s%s \\\n' % (istr, '-giant_move')
if self.uvars.add_edge == 'yes':
if len(self.uvars.cost_list) > 1:
self.errors.append(
'** -AddEdge does not currently work with -multi_cost')
else:
cstr += '%s%s \\\n' % (istr, '-AddEdge')
if len(self.uvars.aea_opts) > 0:
cstr += '%s%s \\\n' % (istr, ' '.join(self.uvars.aea_opts))
# does the anatomy have a skull?
if self.uvars.anat_has_skull != 'yes':
cstr += '%s%s \\\n' % (istr, '-anat_has_skull no')
# -epi_strip method
if self.uvars.epi_strip_meth != '3dSkullStrip':
cstr += '%s%s \\\n' % (istr,
'-epi_strip %s' % self.uvars.epi_strip_meth)
# want -save_all, -prep_off?
# last indent is left by 2 to align ()
cstr += '%*s)\n\n' % (clen - 2, '')
# finally, align the line wrappers
cstr = UTIL.add_line_wrappers(cstr)
return cmnt + cstr
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 make_uber_command(self):
"""generate a script that would invoke the uber_ttest.py interface
with control and user vars set (and so fields filled)
Put any key elements in quotes:
basis functions
gltsym
"""
if show_func_seq: print('=== xO ===')
# first apply subject variables
self.update_uvars_from_gui()
cmd = 'uber_ttest.py'
# apply each uvar with -uvar option
prefix = ' \\\n -uvar ' # append before next command
for atr in self.uvars.attributes():
if atr == 'name': continue # skip
if self.uvars.vals_are_equal(atr, LTT.g_udef_strs): continue
# show this one
val = self.uvars.val(atr)
# special cases first: stim_basis, gltsym
#if atr == 'gltsym': # special case
# val = ["'%s'" % v for v in val]
#elif atr == 'stim_basis': # special case
# val = ["'%s'" % v for v in val]
# cmd += (prefix + '%s %s' % (atr, ' '.join(val)))
# some options might need quotes
if self.uvars.has_simple_type(atr):
val = UTIL.quotize_list([val], quote_chars='#%<>')[0]
cmd += (prefix + '%s %s' % (atr, val))
elif type(val) == list:
val = UTIL.quotize_list(val, quote_chars='#%<>')
cmd += (prefix + '%s %s' % (atr, ' '.join(val)))
else:
print('** make_uber_command: bad attr %s' % atr)
return UTIL.add_line_wrappers(cmd + '\n')
def make_script(self):
"""create the review EPI (plugout_drive) script"""
c2 = "#!/bin/tcsh\n\n"
c2 += "# ------------------------------------------------------\n" \
"# review EPI data via 'afni' and 'plugout_drive'\n\n" \
"# note that when running this script, prompts to change\n" \
"# datasets will appear in the terminal window\n\n"
c2 += "# ------------------------------------------------------\n" \
"# set the list of datasets\n" \
"set dsets = ( %s )\n\n" % \
' '.join([dset.prefix for dset in self.adsets])
c2 += '# ------------------------------------------------------\n' \
'# verify that the input data exists\n' \
'if ( ! -f $dsets[1]+orig.HEAD ) then\n' \
' echo "** missing data to review (e.g. $dsets[1])"\n' \
' exit\n' \
'endif\n\n'
c2 += '# ------------------------------------------------------\n' \
'# start afni is listening mode, and take a brief nap\n\n' \
'afni -yesplugouts &\n\n' \
'sleep 5\n\n'
cmd = UTIL.add_line_wrappers(c2)
c2 = '# ------------------------------------------------------\n' \
'# tell afni to load the first dataset and open windows\n\n' \
'plugout_drive \\\n' \
' -com "SWITCH_UNDERLAY %s" \\\n' \
% self.adsets[0].prefix
# open windows in the list
if self.verb > 1:
print '++ opening windows: %s' % ', '.join(self.windows)
for ind in range(len(self.windows)):
c2 += ' -com "OPEN_WINDOW %simage \\\n' \
' geom=%dx%d+%d+%d" \\\n' % \
(self.windows[ind], self.im_size[0], self.im_size[1],
self.im_xoff+ind*self.im_size[0], self.im_yoff)
c2 += ' -com "OPEN_WINDOW sagittalgraph \\\n' \
' geom=%dx%d+%d+%d" \\\n' % \
(self.gr_size[0], self.gr_size[1], self.gr_xoff, self.gr_yoff)
# terminate the initial plugout_drive command
c2 += ' -quit\n\n'
c2 = UTIL.add_line_wrappers(c2) # do it early, for verb
if self.verb > 2: print 'initial drive command:\n%s' % c2
cmd += c2
cmd += 'sleep 2 # give afni time to open the windows\n\n\n'
c2 = '# ------------------------------------------------------\n' \
'# process each dataset using video mode\n\n' \
'foreach dset ( $dsets )\n' \
' plugout_drive \\\n' \
' -com "SWITCH_UNDERLAY $dset" \\\n' \
' -com "OPEN_WINDOW sagittalgraph \\\n' \
' keypress=a\\\n' \
' keypress=v"\\\n' \
' -quit\n\n' \
' sleep 2 # wait for plugout_drive output\n\n' \
' echo ""\n' \
' echo "++ now viewing $dset, hit enter to continue"\n' \
' set ret = $< # wait for user to hit enter\n' \
'end\n\n\n'
cmd += UTIL.add_line_wrappers(c2)
c2 = '# ------------------------------------------------------\n' \
'# stop video mode when the user is done\n\n' \
'plugout_drive -com "OPEN_WINDOW sagittalgraph keypress=s"' \
' -quit\n\n\n' \
'sleep 2 # wait for plugout_drive output\n\n' \
'echo ""\n' \
'echo "data review complete"\n\n\n'
cmd += UTIL.add_line_wrappers(c2)
c2 = '# ----------------------------------------------------------'\
"------\n# auto-generated by gen_epi_review.py, %s\n" % g_version
c2 += "#\n# %s %s\n" % (os.path.basename(sys.argv[0]), ' '.join(
UTIL.quotize_list(sys.argv[1:], '')))
cmd += UTIL.add_line_wrappers(c2)
fp = open(self.script, "w")
if not fp:
print '** failed to open %s for writing decon script' % self.script
return 1
fp.write(cmd)
fp.close()
try:
os.chmod(self.script, 0755)
except OSError, e:
print e