def make_labels(self, ilines):
"""parse a list of the form
LABEL : VALUES ...
and return a LABEL list (with no trailing separator (':'))
initialize maxcounts, subjcounts here
"""
llist = []
for lind, lstr in enumerate(ilines):
# get label and value list
rv, label, vals = self.get_label_vals(lstr)
if rv < 1: continue
nvals = len(vals)
# label = self.find_parent_label(label)
if self.verb > 2: print('++ label: %s, %d val(s)' % (label, nvals))
llist.append(label)
self.maxcounts[label] = nvals
self.subjcounts[label] = 0
if not UTIL.vals_are_unique(llist):
print(
'** warning: labels are not unique, will use only last values')
llist = UTIL.get_unique_sublist(llist)
return 0, llist
def set_ids_from_dsets(self, prefix='', suffix='', hpad=0, tpad=0, dpre=0):
"""use the varying part of the dataset names for subject IDs
If hpad > 0 or tpad > 0, expand into the head or tail of the dsets.
If prefix or suffix is passed, apply them.
return 0 on success, 1 on error
"""
if hpad < 0 or tpad < 0:
print('** set_ids_from_dsets: will not apply negative padding')
return 1
# try filenames without paths, first
dlist = [s.dset.split('/')[-1] for s in self.subjects]
if UTIL.vals_are_constant(dlist):
print('** constant dataset names (%s)' % dlist[0])
print(' trying directories...')
dlist = [s.dset for s in self.subjects]
slist = UTIL.list_minus_glob_form(dlist,
hpad,
tpad,
keep_dent_pre=dpre)
# in the case of diretories, check for success
# (maybe we can try to skip past them, that might be okay)
for index in range(len(slist)):
if '/' in slist[index]:
posn = slist[index].rfind('/')
slist[index] = slist[index][posn + 1:]
if len(slist[index]) < 1:
print(
'** failed to extract subject IDs from directory list')
print(' (directories do not vary at single level)')
return 1
if len(slist) != len(self.subjects):
print('** failed to set SIDs from dset names\n' \
' dsets = %s\n' \
' slist = %s' % (dlist, slist))
return 1
if not UTIL.vals_are_unique(slist):
print('** cannot set IDs from dsets, labels not unique: %s' %
slist)
print('-- labels come from dsets: %s' % dlist)
return 1
for ind, subj in enumerate(self.subjects):
subj.sid = '%s%s%s' % (prefix, slist[ind], suffix)
return 0
def check_inputs(self):
"""check for required inputs: anat, epi (check existence?)"""
if self.uvars.is_empty('anat'):
self.errors.append('** unspecified anatomical dataset')
if self.uvars.is_empty('epi'):
self.errors.append('** unspecified EPI dataset')
if len(self.uvars.cost_list) < 1:
self.errors.append('** unspecified cost function(s)')
if not UTIL.vals_are_unique(self.uvars.cost_list):
self.errors.append('** cost functions are not unique')
return len(self.errors)
def check_inputs(self):
"""check for required inputs: anat, epi (check existence?)"""
if self.uvars.is_empty('anat'):
self.errors.append('** unspecified anatomical dataset')
if self.uvars.is_empty('epi'):
self.errors.append('** unspecified EPI dataset')
if len(self.uvars.cost_list) < 1:
self.errors.append('** unspecified cost function(s)')
if not UTIL.vals_are_unique(self.uvars.cost_list):
self.errors.append('** cost functions are not unique')
if self.uvars.align_centers == 'yes' and self.uvars.giant_move == 'no':
self.warnings.append( \
"** 'align centers' without 'giant move' is dangerous,\n" \
" consider adding 'giant move'")
return len(self.errors)
def parse_infile_names(self):
"""try to get subject and possibly group names from infiles
fill self.snames and self.gnames, if possible
1. get SID
- if files look like out.ss_review.SID.txt, that is a good start
- else, look for varying part of filename
2. get GID
- replace SID in infile names and for varying group name
"""
rv, slist = UTIL.list_minus_pref_suf(self.infiles, 'out.ss_review.',
'.txt')
if rv < 0: return
if rv > 0:
if self.verb > 1: print('++ trying to get SID from glob form')
slist = UTIL.list_minus_glob_form(self.infiles, strip='dir')
else:
if self.verb > 1: print("++ have SIDs from 'out.ss_reiview' form")
if len(slist) == 0:
if self.verb > 1: print("-- empty SID list")
return
# make sure names are unique and not empty
if not UTIL.vals_are_unique(slist):
if self.verb > 1: print('-- SIDs not detected: not unique')
return
minlen = min([len(ss) for ss in slist])
if minlen < 1:
if self.verb > 1:
print('-- SIDs not detected: some would be empty')
return
# we have a subject list
self.snames = slist
# now go for GID, start by replacing SIDs in infiles
newfiles = [
fname.replace(slist[ind], 'SUBJ')
for ind, fname in enumerate(self.infiles)
]
if UTIL.vals_are_constant(newfiles):
print('-- no groups detected from filenames')
return
# okay, try to make a group list
glist = UTIL.list_minus_glob_form(newfiles)
# cannot have dirs in result
for gid in glist:
if gid.find('/') >= 0:
if self.verb > 1:
print('-- no GIDs, dirs vary in multiple places')
return
minlen = min([len(ss) for ss in glist])
if minlen < 1:
if self.verb > 1:
print('-- GIDs not detected: some would be empty')
return
if self.verb > 1: print("++ have GIDs from infiles")
self.gnames = glist