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)
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()))
module = import_module('.' + example, 'niflow.nipype1.examples')
for pipeline in pipelines:
wf = getattr(module, 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)
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)
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)
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)
def run_examples(example, pipelines, data_path, plugin=None):
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'] = 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)
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'},
'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)
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
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)
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')
from dicom import read_file
from nipype.interfaces import (spm, fsl, Function, ants, freesurfer)
from nipype.interfaces.c3 import C3dAffineTool
fsl.FSLCommand.set_default_output_type('NIFTI')
from nipype import Workflow, Node, MapNode
from nipype.interfaces import matlab as mlab
mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodisplay")
# If SPM is not in your MATLAB path you should add it here
# mlab.MatlabCommand.set_default_paths('/software/matlab/spm12')
# The script is largely based on nipype's dmri_mrtrix_dti.py, copied from http://nipy.sourceforge.net/nipype/users/examples/dmri_mrtrix_dti.html
import nipype.interfaces.io as nio # Data i/o
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import nipype.interfaces.mrtrix as mrtrix #<---- The important new part!
import nipype.interfaces.fsl as fsl
import nipype.algorithms.misc as misc
import os
from dipy.tracking.utils import move_streamlines
global move_streamlines
from nipype.interfaces.base import CommandLine
CommandLine.set_default_terminal_output('none')
fsl.FSLCommand.set_default_output_type('NIFTI')
project_dir = os.path.abspath('/om/user/ksitek/exvivo/')
data_dir = os.path.join(project_dir,'data/')
out_dir = os.path.join(project_dir,'mrtrix')
subject_list = ['Reg_S64550']
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
from builtins import open, range, str
import os
from nipype.interfaces import (spm, fsl, Function, ants, freesurfer)
from nipype.interfaces.c3 import C3dAffineTool
fsl.FSLCommand.set_default_output_type('NIFTI')
from nipype import Workflow, Node, MapNode
from nipype.interfaces import matlab as mlab
mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodisplay")
from nipype.interfaces.base import CommandLine
CommandLine.set_default_terminal_output("allatonce")
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
from nipype.interfaces.io import DataSink, FreeSurferSource
import numpy as np
import scipy as sp
import nibabel as nb
imports = [
'import os', 'import nibabel as nb', 'import numpy as np',
'import scipy as sp',
'from nipype.utils.filemanip import filename_to_list, list_to_filename, split_filename',
'from scipy.special import legendre'
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
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)
>>> 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
