def __init__(self, fmri_data=FmriData.from_vol_ui(),
analyser=JDEMCMCAnalyser(), output_dir='./',
make_outputs=True, result_dump_file=DEFAULT_DUMP_FILE):
XMLable2.__init__(self)
self.analyser = analyser
self.output_dir = output_dir
if result_dump_file is None:
if self.output_dir is not None and DEFAULT_DUMP_FILE is not None:
self.result_dump_file = op.join(self.output_dir,
DEFAULT_DUMP_FILE)
else:
self.result_dump_file = None
else:
self.result_dump_file = op.join(self.output_dir, result_dump_file)
self.data = fmri_data
#self.result_dump_file = op.join(self.output_dir, 'result.pck')
#print 'test:', op.join(self.output_dir, 'result.pck')
#print 'self.result_dump_file:', self.result_dump_file
self.make_outputs = make_outputs
def __init__(self, onsets=DEFAULT_ONSETS,
durations=DEFAULT_STIM_DURATIONS,
simulation_file=DEFAULT_SIMULATION_FILE):
XMLable2.__init__(self)
assert isinstance(onsets, dict)
assert durations is None or isinstance(durations, dict)
self.onsets = onsets
self.durations = durations
self.simulation_file = simulation_file
def __init__(self, onsets=DEFAULT_ONSETS,
durations=DEFAULT_STIM_DURATIONS,
bold_file=DEFAULT_BOLD_SURF_FILE):
XMLable2.__init__(self)
assert isinstance(onsets, dict)
assert durations is None or isinstance(durations, dict)
#assert bold_file.endswith('gii') or bold_file.endswith('gii.gz')
self.onsets = onsets
self.durations = durations
self.bold_file = bold_file
def __init__(self, sampler=BOLDGibbsSampler(), osfMax=4, dtMin=.4,
dt=.6, driftParam=4, driftType='polynomial',
outputFile=DEFAULT_OUTPUT_FILE,outputPrefix='jde_mcmc_',
randomSeed=None, pass_error=True):
JDEAnalyser.__init__(self, outputPrefix, pass_error=pass_error)
XMLable2.__init__(self)
self.sampler = copyModule.copy(sampler)
self.osfMax = osfMax
self.dtMin = dtMin
self.dt = dt
self.driftLfdParam = driftParam
self.driftLfdType = driftType