Python CommandLine.set_default_terminal_output方法代码示例

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import set_default_terminal_output [as 别名]
def run_examples(example, pipelines, data_path, plugin=None, rm_base_dir=True):
    from nipype import config
    from nipype.interfaces.base import CommandLine

    if plugin is None:
        plugin = 'MultiProc'

    print('running example: %s with plugin: %s' % (example, plugin))
    config.enable_debug_mode()
    config.enable_provenance()
    CommandLine.set_default_terminal_output("stream")

    plugin_args = {}
    if plugin == 'MultiProc':
        plugin_args['n_procs'] = int(
            os.getenv('NIPYPE_NUMBER_OF_CPUS', cpu_count()))

    __import__(example)
    for pipeline in pipelines:
        wf = getattr(sys.modules[example], pipeline)
        wf.base_dir = os.path.join(os.getcwd(), 'output', example, plugin)

        results_dir = os.path.join(wf.base_dir, wf.name)
        if rm_base_dir and os.path.exists(results_dir):
            rmtree(results_dir)

        # Handle a logging directory
        log_dir = os.path.join(os.getcwd(), 'logs', example)
        if not os.path.exists(log_dir):
            os.makedirs(log_dir)
        wf.config = {
            'execution': {
                'hash_method': 'timestamp',
                'stop_on_first_rerun': 'true',
                'write_provenance': 'true',
                'poll_sleep_duration': 2
            },
            'logging': {
                'log_directory': log_dir,
                'log_to_file': True
            }
        }
        try:
            wf.inputs.inputnode.in_data = os.path.abspath(data_path)
        except AttributeError:
            pass  # the workflow does not have inputnode.in_data

        wf.run(plugin=plugin, plugin_args=plugin_args)
        # run twice to check if nothing is rerunning
        wf.run(plugin=plugin)

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import set_default_terminal_output [as 别名]
def run_examples(example, pipelines, plugin):
    print('running example: %s with plugin: %s' % (example, plugin))
    from nipype import config
    config.enable_debug_mode()
    from nipype.interfaces.base import CommandLine
    CommandLine.set_default_terminal_output("stream")

    __import__(example)
    for pipeline in pipelines:
        wf = getattr(sys.modules[example], pipeline)
        wf.base_dir = os.path.join(os.getcwd(), 'output', example, plugin)
        if os.path.exists(wf.base_dir):
            rmtree(wf.base_dir)
        wf.config = {'execution': {'hash_method': 'timestamp', 'stop_on_first_rerun': 'true'}}
        wf.run(plugin=plugin, plugin_args={'n_procs': 4})
        # run twice to check if nothing is rerunning
        wf.run(plugin=plugin)

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import set_default_terminal_output [as 别名]
http://mindboggle.info/data.html

specifically the 2mm versions of:

- `Joint Fusion Atlas <http://mindboggle.info/data/atlases/jointfusion/OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_2mm_v2.nii.gz>`_
- `MNI template <http://mindboggle.info/data/templates/ants/OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz>`_

"""

from __future__ import division, unicode_literals
from builtins import open, range, str

import os

from nipype.interfaces.base import CommandLine
CommandLine.set_default_terminal_output('allatonce')

# https://github.com/moloney/dcmstack
from dcmstack.extract import default_extractor
# pip install pydicom
from dicom import read_file

from nipype.interfaces import (fsl, Function, ants, freesurfer, nipy)
from nipype.interfaces.c3 import C3dAffineTool

fsl.FSLCommand.set_default_output_type('NIFTI_GZ')

from nipype import Workflow, Node, MapNode

from nipype.algorithms.rapidart import ArtifactDetect
from nipype.algorithms.misc import TSNR

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import set_default_terminal_output [as 别名]
The 2mm version was generated with::

   >>> from nipype import freesurfer as fs
   >>> rs = fs.Resample()
   >>> rs.inputs.in_file = 'OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152.nii.gz'
   >>> rs.inputs.resampled_file = 'OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_2mm.nii.gz'
   >>> rs.inputs.voxel_size = (2., 2., 2.)
   >>> rs.inputs.args = '-rt nearest -ns 1'
   >>> res = rs.run()

"""

import os

from nipype.interfaces.base import CommandLine
CommandLine.set_default_terminal_output('file')

from nipype import config
config.enable_provenance()

from nipype import (ants, afni, fsl, freesurfer, nipy, Function, DataSink)
from nipype import Workflow, Node, MapNode

from nipype.algorithms.rapidart import ArtifactDetect
from nipype.algorithms.misc import TSNR
from nipype.interfaces.fsl import EPIDeWarp
from nipype.interfaces.io import FreeSurferSource
from nipype.interfaces.c3 import C3dAffineTool
from nipype.interfaces.utility import Merge, IdentityInterface
from nipype.utils.filemanip import filename_to_list

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import set_default_terminal_output [as 别名]
available from:

http://mindboggle.info/data.html

specifically the 2mm versions of:

- `Joint Fusion Atlas <http://mindboggle.info/data/atlases/jointfusion/OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_2mm_v2.nii.gz>`_
- `MNI template <http://mindboggle.info/data/templates/ants/OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz>`_

"""

import os

from nipype.interfaces.base import CommandLine

CommandLine.set_default_terminal_output("allatonce")

from dcmstack.extract import default_extractor
from dicom import read_file

from nipype.interfaces import fsl, Function, ants, freesurfer, nipy
from nipype.interfaces.c3 import C3dAffineTool

fsl.FSLCommand.set_default_output_type("NIFTI_GZ")

from nipype import Workflow, Node, MapNode

from nipype.algorithms.rapidart import ArtifactDetect
from nipype.algorithms.misc import TSNR
from nipype.interfaces.utility import Rename, Merge, IdentityInterface
from nipype.utils.filemanip import filename_to_list

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import set_default_terminal_output [as 别名]
def run_examples(example, pipelines, data_path, plugin=None):
    '''
    Run example workflows
    '''

    # Import packages
    from nipype import config
    from nipype.interfaces.base import CommandLine
    from nipype.utils import draw_gantt_chart
    from nipype.pipeline.plugins import log_nodes_cb

    if plugin is None:
        plugin = 'MultiProc'

    print('running example: %s with plugin: %s' % (example, plugin))
    config.enable_debug_mode()
    config.enable_provenance()
    CommandLine.set_default_terminal_output("stream")

    plugin_args = {}
    if plugin == 'MultiProc':
        plugin_args['n_procs'] = cpu_count()

    __import__(example)

    for pipeline in pipelines:
        # Init and run workflow
        wf = getattr(sys.modules[example], pipeline)
        wf.base_dir = os.path.join(os.getcwd(), 'output', example, plugin)
        if os.path.exists(wf.base_dir):
            rmtree(wf.base_dir)

        # Handle a logging directory
        log_dir = os.path.join(os.getcwd(), 'logs', example)
        if os.path.exists(log_dir):
            rmtree(log_dir)
        os.makedirs(log_dir)
        wf.config = {'execution': {'hash_method': 'timestamp',
                                   'stop_on_first_rerun': 'true',
                                   'write_provenance': 'true'}}

        # Callback log setup
        if example == 'fmri_spm_nested' and plugin == 'MultiProc' and \
           pipeline == 'l2pipeline':
            # Init callback log
            import logging
            cb_log_path = os.path.join(os.path.expanduser('~'), 'callback.log')
            cb_logger = logging.getLogger('callback')
            cb_logger.setLevel(logging.DEBUG)
            handler = logging.FileHandler(cb_log_path)
            cb_logger.addHandler(handler)
            plugin_args = {'n_procs' : 4, 'status_callback' : log_nodes_cb}
        else:
            plugin_args = {'n_procs' : 4}
        try:
            wf.inputs.inputnode.in_data = os.path.abspath(data_path)
        except AttributeError:
            pass # the workflow does not have inputnode.in_data

        wf.run(plugin=plugin, plugin_args=plugin_args)

        # Draw gantt chart only if pandas is installed
        try:
            import pandas
            pandas_flg = True
        except ImportError as exc:
            pandas_flg = False

        if plugin_args.has_key('status_callback') and pandas_flg:
            draw_gantt_chart.generate_gantt_chart(cb_log_path, 4)
            dst_log_html = os.path.join(os.path.expanduser('~'), 'callback.log.html')
            copyfile(cb_log_path+'.html', dst_log_html)

# 需要导入模块: from nipype.interfaces.base import CommandLine [as 别名]
# 或者: from nipype.interfaces.base.CommandLine import set_default_terminal_output [as 别名]
   >>> from nipype import freesurfer as fs
   >>> rs = fs.Resample()
   >>> rs.inputs.in_file = 'OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152.nii.gz'
   >>> rs.inputs.resampled_file = 'OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_2mm.nii.gz'
   >>> rs.inputs.voxel_size = (2., 2., 2.)
   >>> rs.inputs.args = '-rt nearest -ns 1'
   >>> res = rs.run()

"""

import os

from nipype.interfaces.base import CommandLine

CommandLine.set_default_terminal_output("file")

from nipype import config

config.enable_provenance()

from nipype import ants, afni, fsl, freesurfer, nipy, Function, DataSink
from nipype import Workflow, Node, MapNode

from nipype.algorithms.rapidart import ArtifactDetect
from nipype.algorithms.misc import TSNR
from nipype.interfaces.fsl import EPIDeWarp
from nipype.interfaces.io import FreeSurferSource
from nipype.interfaces.c3 import C3dAffineTool
from nipype.interfaces.utility import Merge, IdentityInterface
from nipype.utils.filemanip import filename_to_list