def augmentconfig(c):
'''add more configuration values that are *derived* from the current configuration,
and also checks whether some options are set properly'''
# ensure surfdir is set properly.
# normally it should end in 'surf'
# try to be smart and deduce subject id from surfdir (if not set explicitly)
surfdir = c['surfdir']
if surfdir:
surfdir = os.path.abspath(surfdir)
parent, nm = os.path.split(surfdir)
if nm != 'surf':
jn = pathjoin(surfdir, 'surf')
if os.path.exists(jn):
surfdir = jn
elif nm == 'SUMA':
surfdir = parent
if not (os.path.exists(surfdir) or os.path.split(surfdir)[1] == 'surf'):
print('Warning: surface directory %s not does exist or does not end in "surf"' % surfdir)
surfdir = None
c['surfdir'] = surfdir
# set SUMADIR as well
c['sumadir'] = '%(surfdir)s/SUMA/' % c
# derive subject id from surfdir
sid = os.path.split(os.path.split(surfdir)[0])[1] if surfdir else None
if c.get('sid') is None:
c['sid'] = sid
if c['sid'] is None:
print"Warning: no subject id specified"
c['prefix_sv2anat'] = 'SurfVol2anat'
# update steps
if c.get('steps', 'all') == 'all':
c['steps'] = 'toafni+mapico+moresurfs+skullstrip+align+makespec+makespecboth+makesurfmasks'
hasanatvol = 'anatvol' in c and c['anatvol']
hasepivol = 'epivol' in c and c['epivol']
hasexpvol = 'expvol' in c and c['expvol']
hasisepi = 'isepi' in c
if hasexpvol:
if hasanatvol or hasepivol:
raise Exception("expvol specified, but also anatvol or epivol - illegal!")
if not hasisepi:
raise Exception("not specified whether expvol is EPI (yes) or anat (no)")
else:
if hasanatvol:
if 'epivol' in c and c['epivol']:
raise Exception("Cannot have both anatvol and epivol")
else:
c['expvol'] = c['anatvol']
c['isepi'] = False
del(c['anatvol'])
else:
if hasepivol:
c['expvol'] = c['epivol']
c['isepi'] = True
del(c['epivol'])
else:
print("Warning: no anatomical or functional experimental voume defined")
def yesno2bool(d, k): # dict, key
'''Assuming d[k] contains the word 'yes' or 'no', makes d[k] a boolean
(True=='yes',False=='no'); otherwise an exception is thrown. The dict is updated'''
val = d[k]
if val is None:
b = False
elif type(val) == bool:
b = val
else:
v = val.lower()
if v == 'yes':
b = True
elif v == 'no':
b = False
else:
raise Exception("Not yes or no: %s" % val)
d[k] = b
yesno2bool(c, 'AddEdge')
if c['identity']:
c['expvol_ss'] = c['anatval_ss'] = False
else:
yesno2bool(c, 'expvol_ss')
yesno2bool(c, 'isepi')
# see if we can get the fs_sid
# (only if surfdir is set properly)
# XXX not sure if this still makes sense
c['fs_sid'] = None
surfdir = c.get('surfdir', None)
if not surfdir is None and os.path.exists(surfdir):
fs_log_fn = pathjoin(surfdir, '..', 'scripts', 'recon-all.done')
print "Looking in %s" % fs_log_fn
if os.path.exists(fs_log_fn):
with open(fs_log_fn) as f:
lines = f.read().split('\n')
for line in lines:
if line.startswith('SUBJECT'):
fs_sid = line[8:]
c['fs_sid'] = fs_sid
print "Found Freesurfer sid %s" % fs_sid
break
if c['fs_sid'] is None:
c['fs_sid'] = sid
print "Unable to find proper Freesurfer sid"
pathvars = ['anatvol', 'expvol', 'epivol', 'refdir', 'surfdir']
for pathvar in pathvars:
if pathvar in c and c[pathvar]:
c[pathvar] = os.path.abspath(c[pathvar])
print "Set absolute path for %s: %s" % (pathvar, c[pathvar])
if c['template'] and c['notemplate']:
error('Cannot have both template and notemplate')
if 'expvol' in c:
p, n, o, e = utils.afni_fileparts(c['expvol'])
if c.get('outvol_space', None) is None:
cmd = '3dAttribute TEMPLATE_SPACE %s' % c['expvol']
outvol_space = utils.cmd_capture_output(cmd)
outvol_space = outvol_space.split('~')[0].strip()
if len(outvol_space) and not c['notemplate'] and outvol_space.lower() != 'orig':
print "Detected TEMPLATE_SPACE=%s" % outvol_space
c['outvol_space'] = outvol_space
if o == '+orig':
o = '+tlrc'
print "Template space '%s' detected: output has extension %s" % (outvol_space, o)
c['template'] = True
else:
c['outvol_space'] = '+orig'
if len(o): #'+orig' or '+tlrc'
c['outvol_ext'] = o
c['outvol_fullext'] = o + e
c['outvol_view'] = o[1:]
else:
# For NIFTI - output in orig or tlrc
c['outvol_view'] = 'tlrc' if c['template'] else 'orig'
c['outvol_ext'] = '+' + c['outvol_view']
c['outvol_fullext'] = c['outvol_ext'] + '.HEAD'
return c
def augmentconfig(c):
'''add more configuration values that are *derived* from the current configuration,
and also checks whether some options are set properly'''
# ensure surfdir is set properly.
# normally it should end in 'surf'
# try to be smart and deduce subject id from surfdir (if not set explicitly)
surfdir = c['surfdir']
if surfdir:
surfdir = os.path.abspath(surfdir)
parent, nm = os.path.split(surfdir)
if nm != 'surf':
jn = os.path.join(surfdir, 'surf')
if os.path.exists(jn):
surfdir = jn
elif nm == 'SUMA':
surfdir = parent
if not (os.path.exists(surfdir)
or os.path.split(surfdir)[1] == 'surf'):
print(
'Warning: surface directory %s not does exist or does not end in "surf"'
% surfdir)
surfdir = None
c['surfdir'] = surfdir
# set SUMADIR as well
c['sumadir'] = '%(surfdir)s/SUMA/' % c
# derive subject id from surfdir
sid = os.path.split(os.path.split(surfdir)[0])[1] if surfdir else None
if c.get('sid') is None:
c['sid'] = sid
if c['sid'] is None:
print "Warning: no subject id specified"
c['prefix_sv2anat'] = 'SurfVol2anat'
# update steps
if c.get('steps', 'all') == 'all':
c['steps'] = 'toafni+mapico+moresurfs+skullstrip+align+makespec+makespecboth+makesurfmasks'
hasanatvol = 'anatvol' in c and c['anatvol']
hasepivol = 'epivol' in c and c['epivol']
hasexpvol = 'expvol' in c and c['expvol']
hasisepi = 'isepi' in c
if hasexpvol:
if hasanatvol or hasepivol:
raise Exception(
"expvol specified, but also anatvol or epivol - illegal!")
if not hasisepi:
raise Exception(
"not specified whether expvol is EPI (yes) or anat (no)")
else:
if hasanatvol:
if 'epivol' in c and c['epivol']:
raise Exception("Cannot have both anatvol and epivol")
else:
c['expvol'] = c['anatvol']
c['isepi'] = False
del (c['anatvol'])
else:
if hasepivol:
c['expvol'] = c['epivol']
c['isepi'] = True
del (c['epivol'])
else:
print(
"Warning: no anatomical or functional experimental voume defined"
)
def yesno2bool(d, k): # dict, key
'''Assuming d[k] contains the word 'yes' or 'no', makes d[k] a boolean
(True=='yes',False=='no'); otherwise an exception is thrown. The dict is updated'''
val = d[k]
if val is None:
b = False
elif type(val) == bool:
b = val
else:
v = val.lower()
if v == 'yes':
b = True
elif v == 'no':
b = False
else:
raise Exception("Not yes or no: %s" % val)
d[k] = b
yesno2bool(c, 'AddEdge')
if c['identity']:
c['expvol_ss'] = c['anatval_ss'] = False
else:
yesno2bool(c, 'expvol_ss')
yesno2bool(c, 'isepi')
# see if we can get the fs_sid
# (only if surfdir is set properly)
# XXX not sure if this still makes sense
c['fs_sid'] = None
surfdir = c.get('surfdir', None)
if not surfdir is None and os.path.exists(surfdir):
fs_log_fn = os.path.join(surfdir, '..', 'scripts', 'recon-all.done')
print "Looking in %s" % fs_log_fn
if os.path.exists(fs_log_fn):
with open(fs_log_fn) as f:
lines = f.read().split('\n')
for line in lines:
if line.startswith('SUBJECT'):
fs_sid = line[8:]
c['fs_sid'] = fs_sid
print "Found Freesurfer sid %s" % fs_sid
break
if c['fs_sid'] is None:
c['fs_sid'] = sid
print "Unable to find proper Freesurfer sid"
pathvars = ['anatvol', 'expvol', 'epivol', 'refdir', 'surfdir']
for pathvar in pathvars:
if pathvar in c and c[pathvar]:
c[pathvar] = os.path.abspath(c[pathvar])
print "Set absolute path for %s: %s" % (pathvar, c[pathvar])
if c['template'] and c['notemplate']:
error('Cannot have both template and notemplate')
if 'expvol' in c:
p, n, o, e = utils.afni_fileparts(c['expvol'])
if c.get('outvol_space', None) is None:
cmd = '3dAttribute TEMPLATE_SPACE %s' % c['expvol']
outvol_space = utils.cmd_capture_output(cmd)
outvol_space = outvol_space.split('~')[0].strip()
if len(outvol_space) and not c[
'notemplate'] and outvol_space.lower() != 'orig':
print "Detected TEMPLATE_SPACE=%s" % outvol_space
c['outvol_space'] = outvol_space
if o == '+orig':
o = '+tlrc'
print "Template space '%s' detected: output has extension %s" % (
outvol_space, o)
c['template'] = True
else:
c['outvol_space'] = '+orig'
if len(o): #'+orig' or '+tlrc'
c['outvol_ext'] = o
c['outvol_fullext'] = o + e
c['outvol_view'] = o[1:]
else:
# For NIFTI - output in orig or tlrc
c['outvol_view'] = 'tlrc' if c['template'] else 'orig'
c['outvol_ext'] = '+' + c['outvol_view']
c['outvol_fullext'] = c['outvol_ext'] + '.HEAD'
return c
def augmentconfig(c):
"""add more configuration values that are *derived* from the current configuration,
and also checks whether some options are set properly"""
# ensure surfdir is set properly.
# normally it should end in 'surf'
# try to be smart and deduce subject id from surfdir (if not set explicitly)
surfdir = c["surfdir"]
if surfdir:
surfdir = os.path.abspath(surfdir)
parent, nm = os.path.split(surfdir)
if nm != "surf":
jn = pathjoin(surfdir, "surf")
if os.path.exists(jn):
surfdir = jn
elif nm == "SUMA":
surfdir = parent
if not (os.path.exists(surfdir) or os.path.split(surfdir)[1] == "surf"):
print ('Warning: surface directory %s not does exist or does not end in "surf"' % surfdir)
surfdir = None
c["surfdir"] = surfdir
# set SUMADIR as well
c["sumadir"] = "%(surfdir)s/SUMA/" % c
# derive subject id from surfdir
sid = os.path.split(os.path.split(surfdir)[0])[1] if surfdir else None
if c.get("sid") is None:
c["sid"] = sid
if c["sid"] is None:
print "Warning: no subject id specified"
c["prefix_sv2anat"] = "SurfVol2anat"
# update steps
if c.get("steps", "all") == "all":
c["steps"] = "toafni+mapico+moresurfs+skullstrip+align+makespec+makespecboth+makesurfmasks"
hasanatvol = "anatvol" in c and c["anatvol"]
hasepivol = "epivol" in c and c["epivol"]
hasexpvol = "expvol" in c and c["expvol"]
hasisepi = "isepi" in c
if hasexpvol:
if hasanatvol or hasepivol:
raise Exception("expvol specified, but also anatvol or epivol - illegal!")
if not hasisepi:
raise Exception("not specified whether expvol is EPI (yes) or anat (no)")
else:
if hasanatvol:
if "epivol" in c and c["epivol"]:
raise Exception("Cannot have both anatvol and epivol")
else:
c["expvol"] = c["anatvol"]
c["isepi"] = False
del (c["anatvol"])
else:
if hasepivol:
c["expvol"] = c["epivol"]
c["isepi"] = True
del (c["epivol"])
else:
print ("Warning: no anatomical or functional experimental voume defined")
def yesno2bool(d, k): # dict, key
"""Assuming d[k] contains the word 'yes' or 'no', makes d[k] a boolean
(True=='yes',False=='no'); otherwise an exception is thrown. The dict is updated"""
val = d[k]
if val is None:
b = False
elif type(val) == bool:
b = val
else:
v = val.lower()
if v == "yes":
b = True
elif v == "no":
b = False
else:
raise Exception("Not yes or no: %s" % val)
d[k] = b
yesno2bool(c, "AddEdge")
if c["identity"]:
c["expvol_ss"] = c["anatval_ss"] = False
else:
yesno2bool(c, "expvol_ss")
yesno2bool(c, "isepi")
# see if we can get the fs_sid
# (only if surfdir is set properly)
# XXX not sure if this still makes sense
c["fs_sid"] = None
surfdir = c.get("surfdir", None)
if surfdir is not None and os.path.exists(surfdir):
fs_log_fn = pathjoin(surfdir, "..", "scripts", "recon-all.done")
print "Looking in %s" % fs_log_fn
if os.path.exists(fs_log_fn):
with open(fs_log_fn) as f:
lines = f.read().split("\n")
for line in lines:
if line.startswith("SUBJECT"):
fs_sid = line[8:]
c["fs_sid"] = fs_sid
print "Found Freesurfer sid %s" % fs_sid
break
if c["fs_sid"] is None:
c["fs_sid"] = sid
print "Unable to find proper Freesurfer sid"
pathvars = ["anatvol", "expvol", "epivol", "refdir", "surfdir"]
for pathvar in pathvars:
if pathvar in c and c[pathvar]:
c[pathvar] = os.path.abspath(c[pathvar])
print "Set absolute path for %s: %s" % (pathvar, c[pathvar])
if c["template"] and c["notemplate"]:
error("Cannot have both template and notemplate")
if "expvol" in c:
p, n, o, e = utils.afni_fileparts(c["expvol"])
if c.get("outvol_space", None) is None:
cmd = "3dAttribute TEMPLATE_SPACE %s" % c["expvol"]
outvol_space = utils.cmd_capture_output(cmd)
outvol_space = outvol_space.split("~")[0].strip()
if len(outvol_space) and not c["notemplate"] and outvol_space.lower() != "orig":
print "Detected TEMPLATE_SPACE=%s" % outvol_space
c["outvol_space"] = outvol_space
if o == "+orig":
o = "+tlrc"
print "Template space '%s' detected: output has extension %s" % (outvol_space, o)
c["template"] = True
else:
c["outvol_space"] = "+orig"
if len(o): #'+orig' or '+tlrc'
c["outvol_ext"] = o
c["outvol_fullext"] = o + e
c["outvol_view"] = o[1:]
else:
# For NIFTI - output in orig or tlrc
c["outvol_view"] = "tlrc" if c["template"] else "orig"
c["outvol_ext"] = "+" + c["outvol_view"]
c["outvol_fullext"] = c["outvol_ext"] + ".HEAD"
return c
