コード例 #1
0
ファイル: test_memory.py プロジェクト: IBIC/nipype
def test_caching():
    temp_dir = mkdtemp(prefix='test_memory_')
    old_rerun = config.get('execution', 'stop_on_first_rerun')
    try:
        # Prevent rerun to check that evaluation is computed only once
        config.set('execution', 'stop_on_first_rerun', 'true')
        mem = Memory(temp_dir)
        first_nb_run = nb_runs
        results = mem.cache(SideEffectInterface)(input1=2, input2=1)
        assert_equal(nb_runs, first_nb_run + 1)
        assert_equal(results.outputs.output1, [1, 2])
        results = mem.cache(SideEffectInterface)(input1=2, input2=1)
        # Check that the node hasn't been rerun
        assert_equal(nb_runs, first_nb_run + 1)
        assert_equal(results.outputs.output1, [1, 2])
        results = mem.cache(SideEffectInterface)(input1=1, input2=1)
        # Check that the node hasn been rerun
        assert_equal(nb_runs, first_nb_run + 2)
        assert_equal(results.outputs.output1, [1, 1])
    finally:
        rmtree(temp_dir)
        config.set('execution', 'stop_on_first_rerun', old_rerun)
コード例 #2
0
ファイル: baw_exp.py プロジェクト: lwen/BAW_Nipype
##   for details.
##
##      This software is distributed WITHOUT ANY WARRANTY; without even
##      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
##      PURPOSE.  See the above copyright notices for more information.
##
#################################################################################

import os
import csv
import sys
import string
import argparse
"""Import necessary modules from nipype."""
from nipype.utils.config import config
config.set('logging', 'log_to_file', 'false')
#--config.set('logging', 'workflow_level', 'DEBUG')
#--config.set('logging', 'interface_level', 'DEBUG')
config.set_log_dir(os.getcwd())

from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory, traits, isdefined, BaseInterface
from nipype.interfaces.utility import Merge, Split, Function, Rename, IdentityInterface

import nipype.interfaces.io as nio           # Data i/o
import nipype.pipeline.engine as pe          # pypeline engine

from nipype.interfaces.freesurfer import ReconAll

from nipype.utils.misc import package_check
package_check('numpy', '1.3', 'tutorial1')
package_check('scipy', '0.7', 'tutorial1')
コード例 #3
0
ファイル: baw_exp.py プロジェクト: lwen/BAW_Nipype
##
##      This software is distributed WITHOUT ANY WARRANTY; without even
##      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
##      PURPOSE.  See the above copyright notices for more information.
##
#################################################################################

import os
import csv
import sys
import string
import argparse
"""Import necessary modules from nipype."""
from nipype.utils.config import config

config.set('logging', 'log_to_file', 'false')
#--config.set('logging', 'workflow_level', 'DEBUG')
#--config.set('logging', 'interface_level', 'DEBUG')
config.set_log_dir(os.getcwd())

from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory, traits, isdefined, BaseInterface
from nipype.interfaces.utility import Merge, Split, Function, Rename, IdentityInterface

import nipype.interfaces.io as nio  # Data i/o
import nipype.pipeline.engine as pe  # pypeline engine

from nipype.interfaces.freesurfer import ReconAll

from nipype.utils.misc import package_check

package_check('numpy', '1.3', 'tutorial1')
コード例 #4
0
ファイル: fmri_fsl_reuse.py プロジェクト: B-Rich/nipype
    python fmri_fsl_reuse.py


First tell python where to find the appropriate functions.
"""

import os  # system functions

"""
.. note::
    config for logging should be set before anything else
"""

from nipype.utils.config import config

config.set("logging", "log_to_file", "false")
config.set_log_dir(os.getcwd())

import nipype.interfaces.io as nio  # Data i/o
import nipype.interfaces.fsl as fsl  # fsl
import nipype.interfaces.utility as util  # utility
import nipype.pipeline.engine as pe  # pypeline engine
import nipype.algorithms.modelgen as model  # model generation
import nipype.algorithms.rapidart as ra  # artifact detection

from nipype.workflows.fmri.fsl import create_featreg_preproc, create_modelfit_workflow, create_fixed_effects_flow


"""
Preliminaries
-------------