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 = "$%s/%s%s" % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
sstr += '%*s%s "%s[%s]" \\\n' % (indent, "", subj.sid, dset, bsub)
return sstr
def make_anova3_t4_set_list(self, bsub, subjlists, factors, indent=0):
"""return a multi-line string of the form:
-alevels #alevels
-blevels #blevels
-clevels #subj
-dset ALEVEL BLEVEL SUBJ "dset#A[bsub#B]"
...
- factors should be of length 2
- indent is the initial indentation
- as in type 5, have A change slower than B, but subj be slowest
(so factor order per subject matches command line)
"""
errs = 0
if len(subjlists) != 1:
print "** MAt4SL: bad subject list count = %d" % len(subjlists)
return None
nA = factors[0]
nB = factors[1]
slist = subjlists[0]
if nA * nB != len(bsub):
print "** MAt4SL: bad factor count: %d, %d, %d" % (nA, nB, len(bsub))
return None
sstr = ""
sstr += "%*s-alevels %d \\\n" % (indent, "", nA)
sstr += "%*s-blevels %d \\\n" % (indent, "", nB)
sstr += "%*s-clevels %d \\\n" % (indent, "", len(slist.subjects))
sdir = slist.common_dname
for isubj, subj in enumerate(slist.subjects):
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(slist.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir):
cstr = ""
else:
cstr = "%s/" % cdir
dset = "$%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 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 = '$%s/%s%s' % (sdir, cstr, subj.dfile)
else: dset = subj.dset
if bsub == None:
sstr += '%*s%s \\\n' % (indent, '', dset)
else: # use bsub
sstr += '%*s"%s[%s]" \\\n' % (indent, '', dset, bsub)
return sstr
def make_anova2_set_list(self, bsub, indent=0):
"""return a multi-line string of the form:
-alevels #bsub
-blevels #subj
-dset ALEVEL BLEVEL "dset#A[bsub#B]"
...
indent is the initial indentation
"""
sdir = self.common_dname
sstr = "%*s-alevels %d \\\n" "%*s-blevels %d \\\n" % (indent, "", len(bsub), indent, "", len(self.subjects))
for isubj, subj in enumerate(self.subjects):
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(self.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir):
cstr = ""
else:
cstr = "%s/" % cdir
dset = "$%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 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 = '$%s/%s%s' % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
for ibeta, beta in enumerate(bsub):
sstr += '%*s-dset %2d %2d "%s[%s]" \\\n' \
% (indent, '', ibeta+1, isubj+1, dset, beta)
return sstr
def make_ttpp_set_list(self, bsub, indent=0):
"""return a multi-line string of the form:
SID1 "dset1[bsub]"
SID2 "dset2[bsub]"
...
indent is the initial indentation
"""
# note the max subject ID length
ml = 0
for subj in self.subjects:
if len(subj.sid) > ml: ml = len(subj.sid)
if not UTIL.is_trivial_dir(self.common_dir) and self.common_dname:
sdir = self.common_dname
else:
sdir = ''
sstr = ''
for subj in self.subjects:
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(self.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir): cstr = ''
else: cstr = '%s/' % cdir
dset = '$%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 = '$%s/%s%s' % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
if bsub == None:
sstr += '%*s%s \\\n' % (indent, '', dset)
else: # use bsub
sstr += '%*s"%s[%s]" \\\n' % (indent, '', dset, bsub)
return sstr
def script_set_vars(self):
"""use variables for inputs (anat, epi, epi_base) and for
options (cost_main, cost_list, align_opts)
"""
# init with a section comment
cmd = SUBJ.comment_section_string('set processing variables') + '\n'
# maybe init with top_dir
if not self.LV.is_trivial_dir('top_dir'):
cmd += '# top data directory\n' \
'set top_dir = %s\n\n' % self.LV.top_dir
# anat and epi might use top_dir
if self.LV.is_trivial_dir('top_dir'):
astr = self.uvars.anat
estr = self.uvars.epi
else:
astr = '$top_dir/%s' % self.LV.short_names[0][0]
estr = '$top_dir/%s' % self.LV.short_names[0][1]
# if we are aligning centers, set center_base variable (maybe w/top_dir)
if self.uvars.align_centers == 'yes':
if self.LV.is_trivial_dir('top_dir'): cstr = self.uvars.center_base
else:
cdir = UTIL.child_dir_name(self.LV.top_dir,
self.uvars.center_base)
if cdir == self.uvars.center_base: cstr = cdir
else: cstr = '$top_dir/%s' % cdir
ccmd = 'set center_base = %s\n' % cstr
else:
ccmd = ''
# now set variables for inputs, possibly including center_base
cmd += '# input dataset options (ebase is EPI index)\n' \
'set in_anat = %s\n' \
'set in_epi = %s\n' \
'set in_ebase = %d\n' \
'%s' \
'\n' \
% (astr, estr, self.uvars.epi_base, ccmd)
# note whether to use multi_cost
cmd += '# main options\n' \
'set cost_main = %s\n' % self.uvars.cost_list[0]
if len(self.uvars.cost_list) > 1:
cmd += 'set cost_list = ( %s )\n' % ' '.join(
self.uvars.cost_list[1:])
cmd += '\n'
# possibly add align_opts list variable
cmd += self.make_align_opts_str()
return 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 = "$%s/%s%s" % (sdir, cstr, subj.dfile)
else:
dset = subj.dset
for ibeta, beta in enumerate(bsub):
sstr += '%*s-dset %2d %2d %2d "%s[%s]" \\\n' % (
indent,
"",
ilist + 1,
ibeta + 1,
isubj + 1,
dset,
beta,
)
if errs:
return None
return sstr
def make_anova3_t4_set_list(self, bsub, subjlists, factors, indent=0):
"""return a multi-line string of the form:
-alevels #alevels
-blevels #blevels
-clevels #subj
-dset ALEVEL BLEVEL SUBJ "dset#A[bsub#B]"
...
- factors should be of length 2
- indent is the initial indentation
- as in type 5, have A change slower than B, but subj be slowest
(so factor order per subject matches command line)
"""
errs = 0
if len(subjlists) != 1:
print('** MAt4SL: bad subject list count = %d' % len(subjlists))
return None
nA = factors[0]
nB = factors[1]
slist = subjlists[0]
if nA * nB != len(bsub):
print('** MAt4SL: bad factor count: %d, %d, %d' %
(nA, nB, len(bsub)))
return None
sstr = ''
sstr += '%*s-alevels %d \\\n' % (indent, '', nA)
sstr += '%*s-blevels %d \\\n' % (indent, '', nB)
sstr += '%*s-clevels %d \\\n' % (indent, '', len(slist.subjects))
sdir = slist.common_dname
for isubj, subj in enumerate(slist.subjects):
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(slist.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir): cstr = ''
else: cstr = '%s/' % cdir
dset = '$%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 script_set_vars(self):
"""use variables for inputs (anat, epi, epi_base) and for
options (cost_main, cost_list, align_opts)
"""
# init with a section comment
cmd = SUBJ.comment_section_string('set processing variables') + '\n'
# maybe init with top_dir
if not self.LV.is_trivial_dir('top_dir'):
cmd += '# top data directory\n' \
'set top_dir = %s\n\n' % self.LV.top_dir
# anat and epi might use top_dir
if self.LV.is_trivial_dir('top_dir'):
astr = self.uvars.anat
estr = self.uvars.epi
else:
astr = '$top_dir/%s' % self.LV.short_names[0][0]
estr = '$top_dir/%s' % self.LV.short_names[0][1]
# if we are aligning centers, set center_base variable (maybe w/top_dir)
if self.uvars.align_centers == 'yes':
if self.LV.is_trivial_dir('top_dir'): cstr = self.uvars.center_base
else:
cdir = UTIL.child_dir_name(self.LV.top_dir, self.uvars.center_base)
if cdir == self.uvars.center_base: cstr = cdir
else: cstr = '$top_dir/%s' % cdir
ccmd = 'set center_base = %s\n' % cstr
else: ccmd = ''
# now set variables for inputs, possibly including center_base
cmd += '# input dataset options (ebase is EPI index)\n' \
'set in_anat = %s\n' \
'set in_epi = %s\n' \
'set in_ebase = %d\n' \
'%s' \
'\n' \
% (astr, estr, self.uvars.epi_base, ccmd)
# note whether to use multi_cost
cmd += '# main options\n' \
'set cost_main = %s\n' % self.uvars.cost_list[0]
if len(self.uvars.cost_list) > 1:
cmd += 'set cost_list = ( %s )\n' % ' '.join(self.uvars.cost_list[1:])
cmd += '\n'
# possibly add align_opts list variable
cmd += self.make_align_opts_str()
return cmd
def make_anova3_t5_set_list(self, bsub, subjlists, factors=0, indent=0):
"""return a multi-line string of the form:
-alevels #subjlists
-blevels #bsub
-clevels #subj
-dset GROUP BLEVEL SUBJ "dset#A[bsub#B]"
...
factors is ignored, and exists only to match type4 function
indent is the initial indentation
"""
sstr = ''
sstr += '%*s-alevels %d \\\n' % (indent, '', len(subjlists))
sstr += '%*s-blevels %d \\\n' % (indent, '', len(bsub))
sstr += '%*s-clevels %d \\\n' % (indent, '', len(
subjlists[0].subjects))
slen0 = len(subjlists[0].subjects)
errs = 0
for ilist, slist in enumerate(subjlists):
if len(slist.subjects) != slen0:
print('** subject list %d length differs from SL 1 (%d != %d)\n'\
% (ilist+1, len(slist.subjects), slen0))
errs += 1
sdir = slist.common_dname
for isubj, subj in enumerate(slist.subjects):
if sdir:
# see if the dataset is in a directory underneath
cdir = UTIL.child_dir_name(slist.common_dir, subj.ddir)
if UTIL.is_trivial_dir(cdir): cstr = ''
else: cstr = '%s/' % cdir
dset = '$%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
