def initialize(self):
'''
This method provides some "post-constructor" initialization. It is
typically called after the constructor and after other class flags
have been set (or reset).
'''
# Set the stages
self._pipeline.stages_canRun(False)
lst_stages = list(self._stageslist)
for index in lst_stages:
stage = self._pipeline.stage_get(int(index))
stage.canRun(True)
# Check for FS env variable
self._log('Checking on FREESURFER_HOME', debug=9, lw=self._lw)
if not os.environ.get('FREESURFER_HOME'):
error.fatal(self, 'noFreeSurferEnv')
self._log('[ ok ]\n', debug=9, rw=self._rw, syslog=False)
for str_subj in self._l_subject:
self._log('Checking on subjectDir <%s>' % str_subj,
debug=9, lw=self._lw)
if os.path.isdir(str_subj):
self._log('[ ok ]\n', debug=9, rw=self._rw, syslog=False)
else:
self._log('[ not found ]\n', debug=9, rw=self._rw,
syslog=False)
error.fatal(self, 'subjectDirnotExist')
def initialize(self):
'''
This method provides some "post-constructor" initialization. It is
typically called after the constructor and after other class flags
have been set (or reset).
'''
# Set the stages
self._pipeline.stages_canRun(False)
lst_stages = list(self._stageslist)
for index in lst_stages:
stage = self._pipeline.stage_get(int(index))
stage.canRun(True)
def initialize(self):
'''
This method provides some "post-constructor" initialization. It is
typically called after the constructor and after other class flags
have been set (or reset).
'''
# Set the stages
self._pipeline.stages_canRun(False)
lst_stages = list(self._stageslist)
for index in lst_stages:
stage = self._pipeline.stage_get(int(index))
stage.canRun(True)
# Set absolute dir specs for topDir and outDir
log = self.log()
log('Setting dir specs...\n')
os.chdir(self.topDir())
self.topDir(os.path.abspath(self.topDir()))
if os.path.isdir(self.outDir()):
log('Existing output directory found. Deleting and recreating...\n')
shutil.rmtree(self.outDir())
misc.mkdir(self.outDir())
os.chdir(self.outDir())
self.outDir(os.getcwd())
os.chdir(self.topDir())
# check dirs for each subsample dir
# print(os.getcwd())
# print(self._l_subsample)
for directory in self._l_subsample:
if os.path.isdir(os.path.join(self.topDir(), directory)):
os.chdir(directory)
self._l_subsampleDir.append(os.path.abspath(os.getcwd()))
os.chdir(self.topDir())
else:
error.fatal(self, 'subsampleDirNotFound')
self._d_subsampleDir = dict(zip(self._l_subsample, self._l_subsampleDir))
# print(self._d_subsampleDir)
self.dtree_build()
self._dtree.tree_metaData_print(False)
def initialize(self):
'''
This method provides some "post-constructor" initialization. It is
typically called after the constructor and after other class flags
have been set (or reset).
'''
# Set the stages
self._pipeline.stages_canRun(False)
for index in self._l_stages:
stage = self._pipeline.stage_get(int(index))
stage.canRun(True)
stage.exitCode(False)
# Set absolute dir specs for topDir and outDir
log = self.log()
log('Setting dir specs...\n')
os.chdir(self.topDir())
self.topDir(os.path.abspath(self.topDir()))
def initialize(self):
'''
This method provides some "post-constructor" initialization. It is
typically called after the constructor and after other class flags
have been set (or reset).
'''
# First, this script should only be run on cluster nodes.
lst_clusterNodes = [
'rc-drno', 'rc-russia', 'rc-thunderball', 'rc-goldfinger',
'rc-twice'
]
str_hostname = socket.gethostname()
# Set the stages
self._pipeline.stages_canRun(False)
lst_stages = list(self._stageslist)
for index in lst_stages:
stage = self._pipeline.stage_get(int(index))
stage.canRun(True)
# Check for FS env variable
self._log('Checking on FREESURFER_HOME', debug=9, lw=self._lw)
if not os.environ.get('FREESURFER_HOME'):
error.fatal(self, 'noFreeSurferEnv')
self._log('[ ok ]\n', debug=9, rw=self._rw, syslog=False)
for str_subj in self._l_subject:
self._log('Checking on subjectDir <%s>' % str_subj,
debug=9,
lw=self._lw)
if os.path.isdir(str_subj):
self._log('[ ok ]\n', debug=9, rw=self._rw, syslog=False)
else:
self._log('[ not found ]\n',
debug=9,
rw=self._rw,
syslog=False)
error.fatal(self, 'subjectDirnotExist')
def initialize(self):
'''
This method provides some "post-constructor" initialization. It is
typically called after the constructor and after other class flags
have been set (or reset).
'''
# First, this script should only be run on cluster nodes.
lst_clusterNodes = ['rc-drno', 'rc-russia', 'rc-thunderball',
'rc-goldfinger', 'rc-twice']
str_hostname = socket.gethostname()
#if str_hostname not in lst_clusterNodes:
#error.fatal(self, 'notClusterNode', 'Current hostname = %s' % str_hostname)
# Set the stages
self._pipeline.stages_canRun(False)
lst_stages = list(self._stageslist)
for index in lst_stages:
stage = self._pipeline.stage_get(int(index))
stage.canRun(True)
# Check for FS env variable
self._log('Checking on FREESURFER_HOME', debug=9, lw=self._lw)
if not os.environ.get('FREESURFER_HOME'):
error.fatal(self, 'noFreeSurferEnv')
self._log('[ ok ]\n', debug=9, rw=self._rw, syslog=False)
for str_operand in self._l_operands:
self._log('Checking on operand <%s>' % str_operand,
debug=9, lw=self._lw)
if os.path.isfile(str_operand):
self._log('[ ok ]\n', debug=9, rw=self._rw, syslog=False)
else:
self._log('[ not found ]\n', debug=9, rw=self._rw,
syslog=False)
error.fatal(self, 'operandFilenotExist')
def initialize(self):
'''
This method provides some "post-constructor" initialization. It is
typically called after the constructor and after other class flags
have been set (or reset).
'''
# Set the stages
self._pipeline.stages_canRun(False)
lst_stages = list(self._stageslist)
for index in lst_stages:
stage = self._pipeline.stage_get(int(index))
stage.canRun(True)
# Set absolute dir specs for topDir and outDir
os.chdir(self.topDir())
self.topDir(os.path.abspath(self.topDir()))
if os.path.isdir(self.outDir()):
os.chdir(self.outDir())
self.outDir(os.path.abspath(self.outDir()))
else:
error.warn(self, 'outDirNotFound')
misc.mkdir(self.outDir())