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 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 partition(self, part_file, prefix):
"""partition timing based on part_file labels, write each part to
prefix_label.1D"""
if not self.ready:
print('** Timing element not ready for partitioning')
return 1
labels = read_value_file(part_file)
if labels == None:
print("** failed to read partition label file '%s'" % part_file)
return 1
nlabr = len(labels)
if self.verb > 3:
print('-- partition: %d labels: %s' % (nlabr, labels))
# first test nrows, then test lengths per row
if self.nrows != nlabr:
print('** Timing nrows differs from partition nrows (%d, %d)' % \
(self.nrows,nlabr))
return 1
for ind in range(self.nrows):
if len(self.data[ind]) != len(labels[ind]):
print("** timing and label row lengths differ at line %d" %
(ind + 1))
print(" (%d != %d)" %
(len(self.data[ind]), len(labels[ind])))
return 1
# make unique label list
ulabs = []
for line in labels:
ulabs.extend(line)
ulabs = UTIL.get_unique_sublist(ulabs)
if self.verb > 2: print('-- partition: unique label list: %s' % ulabs)
if ulabs.count('0'): ulabs.remove('0')
if self.verb > 1: print('++ Timing: partitioning with %s' % part_file)
# ------------------------------------------------------------
# do the work, starting with copy:
# for each label, extract those times and write out as timing file
dupe = self.copy() # keep results in new class instance
for lab in ulabs:
# extract timing for this label 'lab'
mdata = []
for r in range(nlabr):
drow = [] # make one row of times for this label
for c in range(len(labels[r])):
if labels[r][c] == lab: drow.append(self.mdata[r][c])
mdata.append(drow) # and append the new row
del (dupe.mdata) # out with the old,
dupe.mdata = mdata # and in with the new
dupe.write_times('%s_%s.1D' % (prefix, lab)) # and write, yay
del (dupe) # nuke the temporary instance
return 0
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 partition(self, part_file, prefix):
"""partition timing based on part_file labels, write each part to
prefix_label.1D"""
if not self.ready:
print '** Timing element not ready for partitioning'
return 1
labels = read_value_file(part_file)
if labels == None:
print "** failed to read partition label file '%s'" % part_file
return 1
nlabr = len(labels)
if self.verb > 3: print '-- partition: %d labels: %s' % (nlabr, labels)
# first test nrows, then test lengths per row
if self.nrows != nlabr:
print '** Timing nrows differs from partition nrows (%d, %d)' % \
(self.nrows,nlabr)
return 1
for ind in range(self.nrows):
if len(self.data[ind]) != len(labels[ind]):
print "** timing and label row lengths differ at line %d"%(ind+1)
return 1
# make unique label list
ulabs = []
for line in labels:
ulabs.extend(line)
ulabs = UTIL.get_unique_sublist(ulabs)
if self.verb > 2: print '-- partition: unique label list: %s' % ulabs
if ulabs.count('0'): ulabs.remove('0')
if self.verb > 1: print '++ Timing: partitioning with %s' % part_file
# ------------------------------------------------------------
# do the work, starting with copy:
# for each label, extract those times and write out as timing file
dupe = self.copy() # keep results in new class instance
for lab in ulabs:
# extract timing for this label 'lab'
mdata = []
for r in range(nlabr):
drow = [] # make one row of times for this label
for c in range(len(labels[r])):
if labels[r][c] == lab: drow.append(self.mdata[r][c])
mdata.append(drow) # and append the new row
del(dupe.mdata) # out with the old,
dupe.mdata = mdata # and in with the new
dupe.write_times('%s_%s.1D' % (prefix,lab)) # and write, yay
del(dupe) # nuke the temporary instance
return 0
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('suma_demo', 'README.archive_creation')
rv += self.show_data_dir_info('FATCAT_DEMO', 'README.timestamp')
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 = os.environ.has_key(evar)
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]
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]