Example #1
0
    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
Example #2
0
File: core.py Project: Solvi/pyhrf
    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
Example #3
0
File: core.py Project: Solvi/pyhrf
    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
Example #4
0
File: jde.py Project: Solvi/pyhrf
    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