def script_set_vars(self):
"""use variables for dataset directories, only
"""
# init with a section comment
hdr = SUBJ.comment_section_string('set process variables') + '\n'
cmd = ''
# init to nothing
self.LV.dirA = ''
self.LV.dirB = ''
if self.uvars.mask:
cmd += 'set mask_dset = %s\n\n' \
% self.strip_suffix(self.uvars.mask, '.HEAD')
# set dirA and possibly dirB
dirs_set = 0
if not UTIL.is_trivial_dir(self.LV.parent_dirs[0]):
cmd += 'set dirA = %s\n' % self.LV.parent_dirs[0]
self.LV.dirA = '$dirA'
dirs_set = 1
if len(self.uvars.dsets_B) > 0:
if not UTIL.is_trivial_dir(self.LV.parent_dirs[1]):
if self.LV.parent_dirs[0] != self.LV.parent_dirs[1]:
cmd += 'set dirB = %s\n' % self.LV.parent_dirs[1]
self.LV.dirB = '$dirB'
dirs_set = 1
else:
self.LV.dirB = '$dirA'
if dirs_set: cmd += '\n'
if cmd: return hdr + cmd
else: return ''
def make_ttpp_set_list(self, bsub, indent=0):
"""return a multi-line string of the form:
SID1 "dset1[bsub]"
SID2 "dset2[bsub]"
...
indent is the initial indentation
"""
# note the max subject ID length
ml = 0
for subj in self.subjects:
if len(subj.sid) > ml: ml = len(subj.sid)
if not UTIL.is_trivial_dir(self.common_dir) and self.common_dname:
sdir = self.common_dname
else:
sdir = ''
sstr = ''
for subj in self.subjects:
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(self.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir): cstr = ''
else: cstr = '%s/' % cdir
dset = '$%s/%s%s' % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
sstr += '%*s%s "%s[%s]" \\\n' % (indent, '', subj.sid, dset, bsub)
return sstr
def make_generic_set_list(self, bsub, indent=0):
"""return a multi-line string of the form:
"dset1[bsub]"
"dset2[bsub]"
...
indent is per-line indentation
"""
if not UTIL.is_trivial_dir(self.common_dir) and self.common_dname:
sdir = self.common_dname
else:
sdir = ''
sstr = ''
for subj in self.subjects:
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(self.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir): cstr = ''
else: cstr = '%s/' % cdir
dset = '$%s/%s%s' % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
if bsub == None:
sstr += '%*s%s \\\n' % (indent, '', dset)
else: # use bsub
sstr += '%*s"%s[%s]" \\\n' % (indent, '', dset, bsub)
return sstr
def goto_proc_dir(dname):
""" go to processing directory, returning return_dir
- if proc_dir does not exist, create it
- cd
- return ret_dir
"""
if UTIL.is_trivial_dir(dname): return '' # nowhere to go
retdir = os.getcwd() # so need return directory
# if the directory does not yet exist, create it
if not os.path.isdir(dname):
try:
os.makedirs(dname)
except:
print('** failed makedirs(%s)' % dname)
return ''
# now try to go there
try:
os.chdir(dname)
except:
print('** failed to go to process dir, %s' % dname)
return ''
return retdir # only returned on success
def make_anova2_set_list(self, bsub, indent=0):
"""return a multi-line string of the form:
-alevels #bsub
-blevels #subj
-dset ALEVEL BLEVEL "dset#A[bsub#B]"
...
indent is the initial indentation
"""
sdir = self.common_dname
sstr = '%*s-alevels %d \\\n' \
'%*s-blevels %d \\\n' \
% (indent,'', len(bsub), indent, '', len(self.subjects))
for isubj, subj in enumerate(self.subjects):
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(self.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir): cstr = ''
else: cstr = '%s/' % cdir
dset = '$%s/%s%s' % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
for ibeta, beta in enumerate(bsub):
sstr += '%*s-dset %2d %2d "%s[%s]" \\\n' \
% (indent, '', ibeta+1, isubj+1, dset, beta)
return sstr
def set_common_data_dir(self, cname='data_dir'):
"""return the directory common to all subject ddir names"""
cdir = UTIL.common_dir([s.dset for s in self.subjects])
if UTIL.is_trivial_dir(cdir):
self.common_dir = ''
self.common_dname = ''
else:
self.common_dir = cdir
self.common_dname = cname
if self.verb > 1:
print('++ setting common dir, %s = %s' % (cname, cdir))
def make_anova3_t4_set_list(self, bsub, subjlists, factors, indent=0):
"""return a multi-line string of the form:
-alevels #alevels
-blevels #blevels
-clevels #subj
-dset ALEVEL BLEVEL SUBJ "dset#A[bsub#B]"
...
- factors should be of length 2
- indent is the initial indentation
- as in type 5, have A change slower than B, but subj be slowest
(so factor order per subject matches command line)
"""
errs = 0
if len(subjlists) != 1:
print('** MAt4SL: bad subject list count = %d' % len(subjlists))
return None
nA = factors[0]
nB = factors[1]
slist = subjlists[0]
if nA * nB != len(bsub):
print('** MAt4SL: bad factor count: %d, %d, %d' %
(nA, nB, len(bsub)))
return None
sstr = ''
sstr += '%*s-alevels %d \\\n' % (indent, '', nA)
sstr += '%*s-blevels %d \\\n' % (indent, '', nB)
sstr += '%*s-clevels %d \\\n' % (indent, '', len(slist.subjects))
sdir = slist.common_dname
for isubj, subj in enumerate(slist.subjects):
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(slist.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir): cstr = ''
else: cstr = '%s/' % cdir
dset = '$%s/%s%s' % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
for iA in range(nA):
for iB in range(nB):
sstr += '%*s-dset %2d %2d %2d "%s[%s]" \\\n' \
% (indent, '', iA+1, iB+1, isubj+1, dset,
bsub[iA*nB+iB])
if errs: return None
return sstr
def set_data_dirs(self, subjlist2=None):
"""Given 1 or 2 file lists, set directories and return initial
script to apply them with variables.
return status and script text
if there are 0 or 1 common dirs use them
if there are 2 and they are different, adjust var names
"""
s2 = subjlist2 # so much typing...
self.set_common_data_dir()
uses2dir = 0
diffdirs = 0
if s2 != None:
s2.set_common_data_dir()
uses2dir = not UTIL.is_trivial_dir(s2.common_dir)
if not UTIL.is_trivial_dir(s2.common_dir) and \
not UTIL.is_trivial_dir(self.common_dir) and \
self.common_dir != s2.common_dir:
# differentiate the directory variable names
self.common_dname = 'data1'
s2.common_dname = 'data2'
diffdirs = 1
cmd = ''
if not UTIL.is_trivial_dir(self.common_dir) or uses2dir:
cmd += '# apply any data directories with variables\n'
if not UTIL.is_trivial_dir(self.common_dir):
cmd += 'set %s = %s\n' % (self.common_dname, self.common_dir)
if diffdirs:
cmd += 'set %s = %s\n' % (s2.common_dname, s2.common_dir)
if cmd: cmd += '\n'
return 0, cmd
def make_anova3_t5_set_list(self, bsub, subjlists, factors=0, indent=0):
"""return a multi-line string of the form:
-alevels #subjlists
-blevels #bsub
-clevels #subj
-dset GROUP BLEVEL SUBJ "dset#A[bsub#B]"
...
factors is ignored, and exists only to match type4 function
indent is the initial indentation
"""
sstr = ''
sstr += '%*s-alevels %d \\\n' % (indent, '', len(subjlists))
sstr += '%*s-blevels %d \\\n' % (indent, '', len(bsub))
sstr += '%*s-clevels %d \\\n' % (indent, '', len(
subjlists[0].subjects))
slen0 = len(subjlists[0].subjects)
errs = 0
for ilist, slist in enumerate(subjlists):
if len(slist.subjects) != slen0:
print('** subject list %d length differs from SL 1 (%d != %d)\n'\
% (ilist+1, len(slist.subjects), slen0))
errs += 1
sdir = slist.common_dname
for isubj, subj in enumerate(slist.subjects):
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(slist.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir): cstr = ''
else: cstr = '%s/' % cdir
dset = '$%s/%s%s' % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
for ibeta, beta in enumerate(bsub):
sstr += '%*s-dset %2d %2d %2d "%s[%s]" \\\n' \
% (indent, '', ilist+1, ibeta+1, isubj+1, dset, beta)
if errs: return None
return sstr
def make_mema_command(self,
set_labs=None,
bsubs=None,
tsubs=None,
subjlist2=None,
prefix=None,
ttype=None,
options=None,
verb=1):
"""create a basic 3dMEMA command
** labs, bsubs, tsubs should be lists of strings, even if they are
integral sub-bricks
if set_labs=None, use defaults depending on # of subject lists
else, set_labs must have 1 or 2 elements, for 1 or 2 sets of subjects
bsubs and tsubs can be of length 1 even with 2 set_labs, in that case:
- length 1: must have subjlist2 set, and apply to it
- length 2: no subjlist2, use with subjlist 1
attach options after subject lists
set_labs - set labels (None, 1 or 2 labels)
bsubs - beta sub-bricks (length 1 or 2, matching labels)
tsubs - t-stat sub-bricks (as with bsubs)
subjlist2 - second subject list for 2-sample test (want if the
datasets differ across sets)
prefix - prefix for 3dMEMA output
ttype - used for a 2-sample test, to distinguish between
paired and unpaired (results is using either
-conditions (paired) or -group (un-))
** ttype == paired is no longer valid
options - other options added to the 3dMEMA command
verb - verbose level
return None on failure, command on success
"""
if prefix == '' or prefix == None: prefix = 'mema_result'
if verb > 1: print('++ make_mema_cmd: have prefix %s' % prefix)
s2 = subjlist2 # sooooo much typing...
if set_labs == None:
if s2 == None: set_labs = ['setA']
else: set_labs = ['setA', 'setB']
if verb > 2: print('++ mema_cmd: adding default set labels')
if bsubs == None: bsubs, tsubs = ['0'], ['1']
# maybe we will use directory variables
self.set_common_data_dir()
if not UTIL.is_trivial_dir(self.common_dir):
if s2 != None:
s2.set_common_data_dir()
if UTIL.is_trivial_dir(s2.common_dir):
# then do not use either
self.common_dir = ''
self.common_dname = ''
# else, use both (if same, default variable is okay)
elif self.common_dir != s2.common_dir:
# different, so update the names to be different
self.common_dname = 'data1'
s2.common_dname = 'data2'
cmd = ''
if not UTIL.is_trivial_dir(self.common_dir):
cmd += '# apply any data directories with variables\n' \
'set %s = %s\n' % (self.common_dname, self.common_dir)
if s2 != None:
if not UTIL.is_trivial_dir(s2.common_dir) \
and s2.common_dir != self.common_dir:
cmd += 'set %s = %s\n' % (s2.common_dname, s2.common_dir)
cmd += '\n'
# command and first set of subject files
cmd += '3dMEMA -prefix %s \\\n' \
' -set %s \\\n%s' % \
(prefix,set_labs[0],self.make_mema_set_list(bsubs[0],tsubs[0],10))
# maybe add second set of subject files
if len(set_labs) > 1:
if verb > 2:
print('-- mema_cmd: have labels for second subject set')
# note subject list and sub-brick labels
if s2 != None:
S = s2
if verb > 2: print('-- second subject list was passed')
else:
S = self
if verb > 2:
print('-- no second subject list, using same list')
if len(bsubs) > 1: b, t = bsubs[1], tsubs[1]
else:
if S != s2:
print('** make_mema_cmd: same subject list in comparison')
b, t = bsubs[0], tsubs[0]
cmd += '%7s-set %s \\\n%s' % \
(' ', set_labs[1], S.make_mema_set_list(b, t, 10))
# either 2-sample or paired
if ttype not in g_mema_tests:
print("** invalid 3dMEMA test %s, not in %s" %
(ttype, g_mema_tests))
return None
if ttype == 'paired':
print('** 3dMEMA -type paired: no longer valid\n' \
' (input contrast and t-stat from original regression)')
return None
else:
opt = '-groups'
cmd += '%7s%s %s %s \\\n' % ('', opt, set_labs[0], set_labs[1])
if len(options) > 0: cmd += '%7s%s' % ('', ' '.join(options))
# strip trailing backslash (must dupe memory)
if cmd[-2:] == '\\\n': cmd = cmd[0:-2]
cmd += '\n\n'
return cmd
def make_ttestpp_command(self,
set_labs=None,
bsubs=None,
subjlist2=None,
prefix=None,
comp_dir=None,
options=None,
verb=1):
"""create a basic 3dttest++ command
Note: this is almost identical to make_mema_command, except for use
of tsubs.
** labs, bsubs should be lists of strings, even if they are integral
sub-bricks
if set_labs=None, use defaults depending on # of subject lists
else, set_labs must have 1 or 2 elements, for 1 or 2 sets of subjects
bsubs can be of length 1 even with 2 set_labs, in that case:
- length 1: must have subjlist2 set, and apply to it
- length 2: no subjlist2, use with subjlist 1
attach options after subject lists
set_labs - set labels (None, 1 or 2 labels)
bsubs - beta sub-bricks (length 1 or 2, matching labels)
subjlist2 - second subject list for 2-sample test (want if the
datasets differ across sets)
prefix - prefix for 3dtest++ output
comp_dir - comparison direction, either -AminusB or -BminusA
(if 2 sets)
options - other options added to the 3dtest++ command
verb - verbose level
return None on failure, command on success
"""
if prefix == '' or prefix == None: prefix = 'ttest++_result'
if verb > 1: print('-- make_ttest++_command: have prefix %s' % prefix)
s2 = subjlist2 # sooooo much typing...
if set_labs == None:
if s2 == None: set_labs = ['setA']
else: set_labs = ['setA', 'setB']
if verb > 2: print('-- tt++_cmd: adding default set labels')
if bsubs == None: bsubs, tsubs = ['0'], ['1']
indent = 10 # minimum indent: spaces to following -set option
# want any '-AminusB' option at top of command
if len(set_labs) > 1: copt = '%*s%s \\\n' % (indent, '', comp_dir)
else: copt = ''
# maybe we will use directory variables
self.set_common_data_dir()
if not UTIL.is_trivial_dir(self.common_dir):
if s2 != None:
s2.set_common_data_dir()
if UTIL.is_trivial_dir(s2.common_dir):
# then do not use either
self.common_dir = ''
self.common_dname = ''
# else, use both (if same, default variable is okay)
elif self.common_dir != s2.common_dir:
# different, so update the names to be different
self.common_dname = 'data1'
s2.common_dname = 'data2'
cmd = ''
if not UTIL.is_trivial_dir(self.common_dir):
cmd += '# apply any data directories with variables\n' \
'set %s = %s\n' % (self.common_dname, self.common_dir)
if s2 != None:
if not UTIL.is_trivial_dir(s2.common_dir) \
and s2.common_dir != self.common_dir:
cmd += 'set %s = %s\n' % (s2.common_dname, s2.common_dir)
cmd += '\n'
# command and first set of subject files
cmd += '3dttest++ -prefix %s \\\n' \
'%s' \
' -setA %s \\\n%s' % (prefix, copt, set_labs[0],
self.make_ttpp_set_list(bsubs[0], indent+3))
# maybe add second set of subject files
if len(set_labs) > 1:
if verb > 2:
print('-- tt++_cmd: have labels for second subject set')
# separate tests for bad test types
if comp_dir == None:
print('** make_tt++_cmd: missing test type, should be in %s' \
% g_ttpp_tests)
return # failure
if comp_dir not in g_ttpp_tests:
print('** make_tt++_cmd: comp_dir (%s) must be in the list %s' \
% (comp_dir, g_ttpp_tests))
return # failure
# note subject list and sub-brick labels
if s2 != None:
S = s2
if verb > 2: print('-- second subject list was passed')
else:
S = self
if verb > 2:
print('-- no second subject list, using same list')
if len(bsubs) > 1: b = bsubs[1]
else:
if S != s2:
print('** make_tt++_cmd: same subject list in comparison')
b = bsubs[0]
cmd += '%*s-setB %s \\\n%s' % \
(indent, ' ', set_labs[1], S.make_ttpp_set_list(b, indent+3))
if len(options) > 0: cmd += '%*s%s' % (indent, '', ' '.join(options))
# strip trailing backslash (must dupe memory)
if cmd[-2:] == '\\\n': cmd = cmd[0:-2]
cmd += '\n\n'
return cmd
def make_anova3_command(self,
bsubs=None,
prefix=None,
subjlists=None,
options=None,
factors=[],
verb=1):
"""create a basic 3dANOVA3 -type 5 command
** other types may be added later...
** bsubs should be lists of strings, even if integral sub-bricks
(they are applied as sub-brick selectors)
attach options after subject lists
bsubs - beta sub-bricks (1 list of sub-brick selectors)
prefix - prefix for command output
subjlists - len > 1 for type 5
options - other options added to the command
atype - 3dANOVA3 -type (should be 4 or 5)
factors - if type 4, #factors of each type (f0*f1 = len(b))
verb - verbose level
Note: for type 5: factor A is group, B is condition, C is subject
return None on failure, command on success
"""
if prefix == '' or prefix == None: prefix = 'anova3_result'
if verb > 1: print('-- make_anova2_command: have prefix %s' % prefix)
if bsubs == None:
print('** missing sub-brick selection list')
return None
if len(bsubs) < 2:
print('** anova3_command: need at least 2 sub-bricks (have %d)' \
% len(bsubs))
return None
ncond = len(factors)
ngroups = len(subjlists)
atype = 0
if ngroups > 1: atype = 5
elif ncond == 2: atype = 4
if atype == 4:
if ngroups != 1:
print('** anova3_cmd: -type 4 requires only 1 dset group')
return None
if ncond != 2:
print('** anova3_cmd: -type 4 requires 2 factor lengths')
print(' (product should be length -subs_betas)')
return None
if factors[0] * factors[1] != len(bsubs):
print('** anova3_cmd: -type 4 factor mismatch')
print(' (%d x %d design requires %d betas, have %d' \
% (factors[0], factors[1], factors[0]*factors[1], len(bsubs)))
return None
elif atype == 5:
if ngroups < 2:
print('** anova3_cmd: -type 5 requires >= 2 subject lists')
return None
if ncond > 1:
print('** anova3_cmd: -type 5 should not have sets of factors')
return None
else:
print(
'** anova3_cmd: cannot detect -type 4 or -type 5, seek -help!')
return None
indent = 4 # indent after main command
# maybe we will use directory variables
cmd = '#!/bin/tcsh\n\n'
found = 0
slen0 = len(subjlists[0].subjects)
subjlists[0].set_common_data_dir()
cd0 = subjlists[0].common_dir
for ilist, slist in enumerate(subjlists):
slist.set_common_data_dir()
if not UTIL.is_trivial_dir(slist.common_dir):
if not found: # first time found
cmd += '# apply any data directories with variables\n'
found = 1
if ilist > 0 and slist.common_dir == cd0:
slist.common_dname = 'data1'
else:
slist.common_dname = 'data%d' % (ilist + 1)
cmd += 'set %s = %s\n' % (slist.common_dname,
slist.common_dir)
if found: cmd += '\n'
if atype == 4:
cmd += '# note: factor A is cond 1, B is cond 2, C is subject\n\n'
sfunc = self.make_anova3_t4_set_list
else:
cmd += '# note: factor A is group, B is condition, C is subject\n\n'
sfunc = self.make_anova3_t5_set_list
# command and first set of subject files
cstr = sfunc(bsubs, subjlists, factors, indent)
if cstr == None: return None
cmd += '3dANOVA3 -type %d \\\n' '%s' % (atype, cstr)
if len(options) > 0:
cmd += '%*s%s \\\n' % (indent, '', ' '.join(options))
else: # add some basic options
opt = '-amean 1 amean1 -bmean 1 bmean1'
cmd += '%*s-amean 1 amean1 \\\n' \
'%*s-bmean 1 bmean1 \\\n' % (indent, '', indent, '')
print('++ no contrast options given, adding simple: %s' % opt)
if prefix.find('/') >= 0: pp = prefix
else: pp = './%s' % prefix
cmd += '%*s-bucket %s\n' % (indent, '', pp)
cmd += '\n'
return cmd
def make_anova2_command(self,
bsubs=None,
prefix=None,
options=None,
verb=1):
"""create a basic 3dANOVA2 -type 3 command
** bsubs should be lists of strings, even if integral sub-bricks
(they are applied as sub-brick selectors)
attach options after subject lists
bsubs - beta sub-bricks (1 list of sub-brick selectors)
prefix - prefix for command output
options - other options added to the command
verb - verbose level
return None on failure, command on success
"""
if prefix == '' or prefix == None: prefix = 'anova2_result'
if verb > 1: print('-- make_anova2_command: have prefix %s' % prefix)
if bsubs == None:
print('** missing sub-brick selection list')
return None
if len(bsubs) < 2:
print('** anova2_command: need at least 2 sub-bricks (have %d)' \
% len(bsubs))
return None
indent = 9 # minimum indent: spaces to following -set option
cmd = '#!/bin/tcsh\n\n'
# maybe we will use directory variables
self.set_common_data_dir()
if not UTIL.is_trivial_dir(self.common_dir):
self.common_dname = 'data'
cmd += '# apply any data directories with variables\n' \
'set %s = %s\n' % (self.common_dname, self.common_dir)
cmd += '\n'
cmd += '# note: factor A is condition, B is subject\n\n'
# command and first set of subject files
cmd += '3dANOVA2 -type 3 \\\n' \
'%s' % self.make_anova2_set_list(bsubs, indent)
if len(options) > 0:
cmd += '%*s%s \\\n' % (indent, '', ' '.join(options))
else: # add some basic option
opt = '-amean 1 amean1'
cmd += '%*s%s \\\n' % (indent, '', opt)
print('++ no contrast options given, adding simple: %s' % opt)
if prefix.find('/') >= 0: pp = prefix
else: pp = './%s' % prefix
cmd += '%*s-bucket %s\n' % (indent, '', pp)
cmd += '\n'
return cmd
def proc_dir_file_exists(dname, fname):
if UTIL.is_trivial_dir(dname): pathname = fname
else: pathname = '%s/%s' % (dname, fname)
return os.path.isfile(pathname)