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 show_data_info(self, header=1):
"""checks that are specific to data
- class data existence and tree root
- assume $HOME if not found
- disk space under data root
- maybe check for mounted file system
- atlases (maybe just @Find TT_N27+tlrc?)
"""
if header: print(UTIL.section_divider('data checks', hchar='-'))
# locate various data trees, and possibly show recent history
rv = 0
rv += self.show_data_dir_info('AFNI_data6', 'history.txt')
rv += self.show_data_dir_info('AFNI_demos', 'history.txt')
rv += self.show_data_dir_info('suma_demo', 'README.archive_creation')
rv += self.show_data_dir_info('afni_handouts')
if rv: self.comments.append('insufficient data for AFNI bootcamp')
evar = 'AFNI_ATLAS_DIR'
tryenv = 0 # might suggest setting evar
haveenv = evar in os.environ
if haveenv: edir = os.environ[evar]
else: edir = ''
# look for atlases in multiple directories
atlas = 'TT_N27+tlrc'
if os.path.isfile('%s/%s.HEAD'%(edir,atlas)): glist = [edir]
else: glist = []
cmd = '@FindAfniDsetPath %s' % atlas
s, so, se = UTIL.limited_shell_exec(cmd, nlines=1)
if s: tryenv = 1 # failed
elif len(so) > 0: glist.append(so[0])
for ddir in ['/usr/share/afni/atlases', '/usr/local/afni/atlases']:
if os.path.isfile('%s/%s.HEAD'%(ddir,atlas)):
glist.append(ddir)
if tryenv:
self.comments.append('consider setting %s to %s' % (evar,ddir))
# fix to work with found after the fact
glist = UTIL.get_unique_sublist(glist)
if len(glist) == 0:
print('atlas : did not find %s' % atlas)
self.comments.append('possibly missing atlases')
else:
for ddir in glist:
print('atlas : found %-12s under %s' % (atlas, ddir))
if haveenv: print("\natlas var: %s = %s" % (evar, edir))
print('')
def find_data_dir(self, ddir, gdirs=[], depth=2):
"""search under a list of glob directories for the given ddir"""
if ddir == '' or len(gdirs) == 0: return None
dlist = []
for pdir in gdirs:
droot = pdir
for d in range(depth+1):
dlist.extend(glob.glob('%s/%s' % (droot, ddir)))
droot += '/*'
if self.verb > 3: print('-- found %s dirs %s' % (ddir, dlist))
dlist = UTIL.get_unique_sublist(dlist)
if self.verb > 2: print('-- found trimmed %s dirs %s' % (ddir, dlist))
if len(dlist) == 0: return None
dlen = len(ddir)+1
return dlist[0][0:-dlen]