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 get_joined_strings(self, opt_name=None, opt=None, prefix=''):
"""like get_string_list(), but join any list together and only
return a string
only apply 'prefix' if something is found"""
olist, rv = self.get_string_list(opt_name=opt_name, opt=opt)
if rv or olist == None: return ''
if len(olist) < 1: return ''
# we have something
return prefix + ' '.join(UTIL.quotize_list(olist))
def get_joined_strings(self, opt_name=None, opt=None, prefix=''):
"""like get_string_list(), but join any list together and only
return a string
only apply 'prefix' if something is found"""
olist, rv = self.get_string_list(opt_name=opt_name, opt=opt)
if rv or olist == None: return ''
if len(olist) < 1: return ''
# we have something
return prefix + ' '.join(UTIL.quotize_list(olist))
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, 0o755)
except OSError as e:
print(e)
return
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()
os.chmod(self.script, 0755)
return
