def test_node_hash(tmpdir):
from nipype.interfaces.utility import Function
tmpdir.chdir()
config.set_default_config()
config.set('execution', 'stop_on_first_crash', True)
config.set('execution', 'crashdump_dir', os.getcwd())
def func1():
return 1
def func2(a):
return a + 1
n1 = pe.Node(Function(input_names=[], output_names=['a'], function=func1),
name='n1')
n2 = pe.Node(Function(input_names=['a'],
output_names=['b'],
function=func2),
name='n2')
w1 = pe.Workflow(name='test')
def modify(x):
return x + 1
n1.inputs.a = 1
w1.connect(n1, ('a', modify), n2, 'a')
w1.base_dir = os.getcwd()
# create dummy distributed plugin class
from nipype.pipeline.plugins.base import DistributedPluginBase
# create a custom exception
class EngineTestException(Exception):
pass
class RaiseError(DistributedPluginBase):
def _submit_job(self, node, updatehash=False):
raise EngineTestException('Submit called - cached=%s, updated=%s' %
node.is_cached())
# check if a proper exception is raised
with pytest.raises(EngineTestException) as excinfo:
w1.run(plugin=RaiseError())
assert str(excinfo.value).startswith('Submit called')
# generate outputs
w1.run(plugin='Linear')
# ensure plugin is being called
config.set('execution', 'local_hash_check', False)
# rerun to ensure we have outputs
w1.run(plugin='Linear')
# set local check
config.set('execution', 'local_hash_check', True)
w1 = pe.Workflow(name='test')
w1.connect(n1, ('a', modify), n2, 'a')
w1.base_dir = os.getcwd()
w1.run(plugin=RaiseError())
def test_mapnode_nested():
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
from nipype import MapNode, Function
def func1(in1):
return in1 + 1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
nested=True,
name='n1')
n1.inputs.in1 = [[1, [2]], 3, [4, 5]]
n1.run()
print(n1.get_output('out'))
yield assert_equal, n1.get_output('out'), [[2, [3]], 4, [5, 6]]
n2 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
nested=False,
name='n1')
n2.inputs.in1 = [[1, [2]], 3, [4, 5]]
error_raised = False
try:
n2.run()
except Exception as e:
pe.logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_true, error_raised
def test_old_config(tmpdir):
wd = str(tmpdir)
os.chdir(wd)
from nipype.interfaces.utility import Function
def func1():
return 1
def func2(a):
return a + 1
n1 = pe.Node(Function(input_names=[], output_names=['a'], function=func1),
name='n1')
n2 = pe.Node(Function(input_names=['a'],
output_names=['b'],
function=func2),
name='n2')
w1 = pe.Workflow(name='test')
modify = lambda x: x + 1
n1.inputs.a = 1
w1.connect(n1, ('a', modify), n2, 'a')
w1.base_dir = wd
w1.config['execution']['crashdump_dir'] = wd
# generate outputs
error_raised = False
try:
w1.run(plugin='Linear')
except Exception as e:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
assert not error_raised
def test_old_config():
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
from nipype.interfaces.utility import Function
def func1():
return 1
def func2(a):
return a + 1
n1 = pe.Node(Function(input_names=[], output_names=['a'], function=func1),
name='n1')
n2 = pe.Node(Function(input_names=['a'],
output_names=['b'],
function=func2),
name='n2')
w1 = pe.Workflow(name='test')
modify = lambda x: x + 1
n1.inputs.a = 1
w1.connect(n1, ('a', modify), n2, 'a')
w1.base_dir = wd
w1.config['execution']['crashdump_dir'] = wd
# generate outputs
error_raised = False
try:
w1.run(plugin='Linear')
except Exception as e:
pe.logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_false, error_raised
os.chdir(cwd)
rmtree(wd)
def test_old_config(tmpdir):
tmpdir.chdir()
wd = os.getcwd()
from nipype.interfaces.utility import Function
def func1():
return 1
def func2(a):
return a + 1
n1 = pe.Node(Function(input_names=[],
output_names=['a'],
function=func1),
name='n1')
n2 = pe.Node(Function(input_names=['a'],
output_names=['b'],
function=func2),
name='n2')
w1 = pe.Workflow(name='test')
modify = lambda x: x + 1
n1.inputs.a = 1
w1.connect(n1, ('a', modify), n2, 'a')
w1.base_dir = wd
w1.config['execution']['crashdump_dir'] = wd
# generate outputs
w1.run(plugin='Linear')
def test_mapnode_nested(tmpdir):
tmpdir.chdir()
from nipype import MapNode, Function
def func1(in1):
return in1 + 1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
nested=True,
name='n1')
n1.inputs.in1 = [[1, [2]], 3, [4, 5]]
n1.run()
print(n1.get_output('out'))
assert n1.get_output('out') == [[2, [3]], 4, [5, 6]]
n2 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
nested=False,
name='n1')
n2.inputs.in1 = [[1, [2]], 3, [4, 5]]
with pytest.raises(Exception) as excinfo:
n2.run()
assert "can only concatenate list" in str(excinfo.value)
def create_graphics(bids_dir, subject_label, session=None, t2w=None):
"""
Setup and run the graphics workflow which creates the static
plot(s) of defaced images with a brainmask overlaid and a
gif looping through slices of the defaced images.
Parameters
----------
bids_dir : str
Path to BIDS root directory.
subject_label : str
Label of subject to be plotted (without 'sub-').
session : str, optional
If multiple sessions exist, include them in worklow.
session : bool, optional
If T2w image exists, include them in worklow.
"""
import nipype.pipeline.engine as pe
from nipype import Function
from nipype.interfaces import utility as niu
report_wf = pe.Workflow('report_wf')
inputnode = pe.Node(niu.IdentityInterface(
fields=['bids_dir', 'subject_label', 'session', 't2w']),
name='inputnode')
plt_defaced = pe.Node(Function(
input_names=['bids_dir', 'subject_label', 'session', 't2w'],
function=plot_defaced),
name='plt_defaced')
gf_defaced = pe.Node(Function(
input_names=['bids_dir', 'subject_label', 'session', 't2w'],
function=gif_defaced),
name='gf_defaced')
report_wf.connect([
(inputnode, plt_defaced, [('bids_dir', 'bids_dir'),
('subject_label', 'subject_label')]),
(inputnode, gf_defaced, [('bids_dir', 'bids_dir'),
('subject_label', 'subject_label')]),
])
if session:
inputnode.inputs.session = session
report_wf.connect([
(inputnode, plt_defaced, [('session', 'session')]),
(inputnode, gf_defaced, [('session', 'session')]),
])
if t2w:
inputnode.inputs.t2w = t2w
report_wf.connect([
(inputnode, plt_defaced, [('t2w', 't2w')]),
(inputnode, gf_defaced, [('t2w', 't2w')]),
])
inputnode.inputs.bids_dir = bids_dir
inputnode.inputs.subject_label = subject_label
report_wf.run()
def test_mapnode_nested(tmpdir):
os.chdir(str(tmpdir))
from nipype import MapNode, Function
def func1(in1):
return in1 + 1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
nested=True,
name='n1')
n1.inputs.in1 = [[1, [2]], 3, [4, 5]]
n1.run()
print(n1.get_output('out'))
assert n1.get_output('out') == [[2, [3]], 4, [5, 6]]
n2 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
nested=False,
name='n1')
n2.inputs.in1 = [[1, [2]], 3, [4, 5]]
error_raised = False
try:
n2.run()
except Exception as e:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
assert error_raised
def test_node_hash():
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
from nipype.interfaces.utility import Function
def func1():
return 1
def func2(a):
return a + 1
n1 = pe.Node(Function(input_names=[],
output_names=['a'],
function=func1),
name='n1')
n2 = pe.Node(Function(input_names=['a'],
output_names=['b'],
function=func2),
name='n2')
w1 = pe.Workflow(name='test')
modify = lambda x: x + 1
n1.inputs.a = 1
w1.connect(n1, ('a', modify), n2, 'a')
w1.base_dir = wd
# generate outputs
w1.run(plugin='Linear')
# ensure plugin is being called
w1.config['execution'] = {'stop_on_first_crash': 'true',
'local_hash_check': 'false',
'crashdump_dir': wd}
error_raised = False
# create dummy distributed plugin class
from nipype.pipeline.plugins.base import DistributedPluginBase
class RaiseError(DistributedPluginBase):
def _submit_job(self, node, updatehash=False):
raise Exception('Submit called')
try:
w1.run(plugin=RaiseError())
except Exception as e:
pe.logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_true, error_raised
# yield assert_true, 'Submit called' in e
# rerun to ensure we have outputs
w1.run(plugin='Linear')
# set local check
w1.config['execution'] = {'stop_on_first_crash': 'true',
'local_hash_check': 'true',
'crashdump_dir': wd}
error_raised = False
try:
w1.run(plugin=RaiseError())
except Exception as e:
pe.logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_false, error_raised
os.chdir(cwd)
rmtree(wd)
def test_node_hash(tmpdir):
wd = str(tmpdir)
os.chdir(wd)
from nipype.interfaces.utility import Function
def func1():
return 1
def func2(a):
return a + 1
n1 = pe.Node(Function(input_names=[], output_names=['a'], function=func1),
name='n1')
n2 = pe.Node(Function(input_names=['a'],
output_names=['b'],
function=func2),
name='n2')
w1 = pe.Workflow(name='test')
modify = lambda x: x + 1
n1.inputs.a = 1
w1.connect(n1, ('a', modify), n2, 'a')
w1.base_dir = wd
# generate outputs
w1.run(plugin='Linear')
# ensure plugin is being called
w1.config['execution'] = {
'stop_on_first_crash': 'true',
'local_hash_check': 'false',
'crashdump_dir': wd
}
# create dummy distributed plugin class
from nipype.pipeline.plugins.base import DistributedPluginBase
# create a custom exception
class EngineTestException(Exception):
pass
class RaiseError(DistributedPluginBase):
def _submit_job(self, node, updatehash=False):
raise EngineTestException('Submit called')
# check if a proper exception is raised
with pytest.raises(EngineTestException) as excinfo:
w1.run(plugin=RaiseError())
assert 'Submit called' == str(excinfo.value)
# rerun to ensure we have outputs
w1.run(plugin='Linear')
# set local check
w1.config['execution'] = {
'stop_on_first_crash': 'true',
'local_hash_check': 'true',
'crashdump_dir': wd
}
w1.run(plugin=RaiseError())
def test_execute(self, lyman_dir, execdir):
info = frontend.info(lyman_dir=lyman_dir)
def f(x):
return x**2
assert f(2) == 4
n1 = Node(Function("x", "y", f), "n1")
n2 = Node(Function("x", "y", f), "n2")
wf = Workflow("test", base_dir=info.cache_dir)
wf.connect(n1, "y", n2, "x")
wf.inputs.n1.x = 2
cache_dir = execdir.join("cache").join("test")
class args(object):
graph = False
n_procs = 1
debug = False
clear_cache = True
execute = True
frontend.execute(wf, args, info)
assert not cache_dir.exists()
args.debug = True
frontend.execute(wf, args, info)
assert cache_dir.exists()
args.debug = False
info.remove_cache = False
frontend.execute(wf, args, info)
assert cache_dir.exists()
args.execute = False
res = frontend.execute(wf, args, info)
assert res is None
args.execute = True
fname = str(execdir.join("graph").join("workflow.dot"))
args.graph = fname
res = frontend.execute(wf, args, info)
assert res == fname[:-4] + ".svg"
args.graph = True
args.stage = "preproc"
res = frontend.execute(wf, args, info)
assert res == cache_dir.join("preproc.svg")
def neck_removal_wf(usemodel):
"""Create a workflow to to remove the neck. This workflow requires a
model image (e.g. an MNI standard) and points on that image. The model
is registered to the T1 image, and the points transformed into T1 space.
The inferior most transformed point is used to determine the cutting
plane, which is aligned with the voxel coordinates.
:return: A :py:mod:`nipype` workflow
Workflow inputs/outputs
:param inputspec.T1: The T1 image to remove the neck from
:param inputspec.model: The reference image to register to the T1 image
:param inputspec.limits: Points in model roughly indicating the ideal cutting plane
:return: A :py:mod:`nipype` node
"""
name = 'neck_removal'
wf = pe.Workflow(name)
inputspec = pe.Node(IdentityInterface(['T1', 'model', 'limits']), name='inputspec')
wpoints = pe.Node(Function(input_names=['limits'], output_names=['points'], function=writepoints), name='write_points')
cut = pe.Node(CutImage(neckonly=True), name='cut')
outputspec = pe.Node(IdentityInterface(['cropped']), name='outputspec')
if usemodel:
trpoints = _tr_points_wf()
wf.connect([(inputspec, trpoints, [('T1', 'inputspec.T1'),
('model', 'inputspec.model')]),
(wpoints, trpoints, [('points', 'inputspec.points')]),
(trpoints, cut, [('outputspec.out_points', 'points_file')])])
else:
wf.connect([(wpoints, cut, [('points', 'points_file')])])
wf.connect([(inputspec, wpoints, [('limits', 'limits')]),
(inputspec, cut, [('T1', 'in_file')]),
(cut, outputspec, [('out_file', 'cropped')])])
return wf
def embed_metadata_from_dicoms(bids_options, item_dicoms, outname,
outname_bids, prov_file, scaninfo, tempdirs,
with_prov):
"""
Enhance sidecar information file with more information from DICOMs
Parameters
----------
bids_options
item_dicoms
outname
outname_bids
prov_file
scaninfo
tempdirs
with_prov
Returns
-------
"""
from nipype import Node, Function
tmpdir = tempdirs(prefix='embedmeta')
# We need to assure that paths are absolute if they are relative
item_dicoms = list(map(op.abspath, item_dicoms))
embedfunc = Node(Function(input_names=[
'dcmfiles',
'niftifile',
'infofile',
'bids_info',
],
function=embed_dicom_and_nifti_metadata),
name='embedder')
embedfunc.inputs.dcmfiles = item_dicoms
embedfunc.inputs.niftifile = op.abspath(outname)
embedfunc.inputs.infofile = op.abspath(scaninfo)
embedfunc.inputs.bids_info = load_json(
op.abspath(outname_bids)) if (bids_options is not None) else None
embedfunc.base_dir = tmpdir
cwd = os.getcwd()
lgr.debug("Embedding into %s based on dicoms[0]=%s for nifti %s", scaninfo,
item_dicoms[0], outname)
try:
if op.lexists(scaninfo):
# TODO: handle annexed file case
if not op.islink(scaninfo):
set_readonly(scaninfo, False)
res = embedfunc.run()
set_readonly(scaninfo)
if with_prov:
g = res.provenance.rdf()
g.parse(prov_file, format='turtle')
g.serialize(prov_file, format='turtle')
set_readonly(prov_file)
except Exception as exc:
lgr.error("Embedding failed: %s", str(exc))
os.chdir(cwd)
def NodeJoinFeatures():
node = Node(Function(
function=joinFeatures,
input_names=["data", "prefix", "output_dir", "confName", "kindConn"],
output_names=["graphFeatures"]),
name="JoinFeatures")
return node
def run_brain_extraction_nb(image, subject_label, bids_dir):
"""
Setup and run nobrainer brainextraction workflow.
Parameters
----------
image : str
Path to image that should be defaced.
outfile : str
Name of the defaced file.
bids_dir : str
Path to BIDS root directory.
"""
brainextraction_wf = pe.Workflow('brainextraction_wf')
inputnode = pe.Node(niu.IdentityInterface(['in_file']), name='inputnode')
brainextraction = pe.Node(Function(
input_names=['image', 'subject_label', 'bids_dir'],
output_names=['outfile'],
function=brain_extraction_nb),
name='brainextraction')
brainextraction_wf.connect([(inputnode, brainextraction, [('in_file',
'image')])])
inputnode.inputs.in_file = image
brainextraction.inputs.subject_label = subject_label
brainextraction.inputs.bids_dir = bids_dir
brainextraction_wf.run()
def run_t2w_deface(image, t1w_deface_mask, outfile):
"""
Setup and run t2w defacing workflow.
Parameters
----------
image : str
Path to image that should be defaced.
t1w_deface_mask : str
Path to the defaced T1w image that will be used
as defacing mask.
outfile : str
Name of the defaced file.
"""
from bidsonym.utils import deface_t2w
deface_wf = pe.Workflow('deface_wf')
inputnode = pe.Node(niu.IdentityInterface(['in_file']),
name='inputnode')
flirtnode = pe.Node(FLIRT(cost_func='mutualinfo',
output_type="NIFTI_GZ"),
name='flirtnode')
deface_t2w = pe.Node(Function(input_names=['image', 'warped_mask', 'outfile'],
output_names=['outfile'],
function=deface_t2w),
name='deface_t2w')
deface_wf.connect([(inputnode, flirtnode, [('in_file', 'reference')]),
(inputnode, deface_t2w, [('in_file', 'image')]),
(flirtnode, deface_t2w, [('out_file', 'warped_mask')])])
inputnode.inputs.in_file = image
flirtnode.inputs.in_file = t1w_deface_mask
deface_t2w.inputs.outfile = outfile
deface_wf.run()
def NodePandasAdj2Nx():
node = Node(Function(function=pandasAdj2Nx,
input_names=["df"],
output_names=["graph"]),
name="Pandas2Graph")
return node
def run_deepdefacer(image, subject_label, bids_dir):
"""
Setup and run mridefacer workflow.
Parameters
----------
image : str
Path to image that should be defaced.
subject_label : str
Label of subject to operate on (without 'sub-').
bids_dir : str
Path to BIDS root directory.
"""
deface_wf = pe.Workflow('deface_wf')
inputnode = pe.Node(niu.IdentityInterface(['in_file']),
name='inputnode')
deepdefacer = pe.Node(Function(input_names=['image', 'subject_label', 'bids_dir'],
output_names=['outfile'],
function=deepdefacer_cmd),
name='deepdefacer')
deface_wf.connect([(inputnode, deepdefacer, [('in_file', 'image')])])
inputnode.inputs.in_file = image
deepdefacer.inputs.subject_label = subject_label
deepdefacer.inputs.bids_dir = bids_dir
deface_wf.run()
def test_io_subclass():
"""Ensure any io subclass allows dynamic traits"""
from nipype.interfaces.io import IOBase
from nipype.interfaces.base import DynamicTraitedSpec
class TestKV(IOBase):
_always_run = True
output_spec = DynamicTraitedSpec
def _list_outputs(self):
outputs = {}
outputs['test'] = 1
outputs['foo'] = 'bar'
return outputs
wf = pe.Workflow('testkv')
def testx2(test):
return test * 2
kvnode = pe.Node(TestKV(), name='testkv')
from nipype.interfaces.utility import Function
func = pe.Node(
Function(input_names=['test'], output_names=['test2'], function=testx2),
name='func')
exception_not_raised = True
try:
wf.connect(kvnode, 'test', func, 'test')
except Exception as e:
if 'Module testkv has no output called test' in e:
exception_not_raised = False
assert exception_not_raised
def test_serial_input(tmpdir):
tmpdir.chdir()
wd = os.getcwd()
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
name='n1')
n1.inputs.in1 = [1, 2, 3]
w1 = Workflow(name='test')
w1.base_dir = wd
w1.add_nodes([n1])
# set local check
w1.config['execution'] = {'stop_on_first_crash': 'true',
'local_hash_check': 'true',
'crashdump_dir': wd,
'poll_sleep_duration': 2}
# test output of num_subnodes method when serial is default (False)
assert n1.num_subnodes() == len(n1.inputs.in1)
# test running the workflow on default conditions
w1.run(plugin='MultiProc')
# test output of num_subnodes method when serial is True
n1._serial = True
assert n1.num_subnodes() == 1
# test running the workflow on serial conditions
w1.run(plugin='MultiProc')
def bids(self):
from bids_conversion import create_bids
if not getattr(self,'_bids',None):
self._bids = pe.Node(name="bids", interface=Function(
input_names=["dicom_info","bids_info","bids_output","subj","ses"],
output_names=["out"],
function=create_bids))
self._bids.inputs.ses = 'bl'
return self._bids
def embed_metadata_from_dicoms(bids, item_dicoms, outname, outname_bids,
prov_file, scaninfo, tempdirs, with_prov,
min_meta):
"""
Enhance sidecar information file with more information from DICOMs
Parameters
----------
bids
item_dicoms
outname
outname_bids
prov_file
scaninfo
tempdirs
with_prov
min_meta
Returns
-------
"""
from nipype import Node, Function
tmpdir = tempdirs(prefix='embedmeta')
embedfunc = Node(Function(input_names=[
'dcmfiles', 'niftifile', 'infofile', 'bids_info', 'force', 'min_meta'
],
output_names=['outfile', 'meta'],
function=embed_nifti),
name='embedder')
embedfunc.inputs.dcmfiles = item_dicoms
embedfunc.inputs.niftifile = op.abspath(outname)
embedfunc.inputs.infofile = op.abspath(scaninfo)
embedfunc.inputs.min_meta = min_meta
if bids:
embedfunc.inputs.bids_info = load_json(op.abspath(outname_bids))
else:
embedfunc.inputs.bids_info = None
embedfunc.inputs.force = True
embedfunc.base_dir = tmpdir
cwd = os.getcwd()
try:
if op.lexists(scaninfo):
# TODO: handle annexed file case
if not op.islink(scaninfo):
set_readonly(scaninfo, False)
res = embedfunc.run()
set_readonly(scaninfo)
if with_prov:
g = res.provenance.rdf()
g.parse(prov_file, format='turtle')
g.serialize(prov_file, format='turtle')
set_readonly(prov_file)
except Exception as exc:
lgr.error("Embedding failed: %s", str(exc))
os.chdir(cwd)
def test_serial_input():
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
from nipype import MapNode, Function, Workflow
def func1(in1):
return in1
n1 = MapNode(Function(input_names=['in1'],
output_names=['out'],
function=func1),
iterfield=['in1'],
name='n1')
n1.inputs.in1 = [1, 2, 3]
w1 = Workflow(name='test')
w1.base_dir = wd
w1.add_nodes([n1])
# set local check
w1.config['execution'] = {
'stop_on_first_crash': 'true',
'local_hash_check': 'true',
'crashdump_dir': wd,
'poll_sleep_duration': 2
}
# test output of num_subnodes method when serial is default (False)
yield assert_equal, n1.num_subnodes(), len(n1.inputs.in1)
# test running the workflow on default conditions
error_raised = False
try:
w1.run(plugin='MultiProc')
except Exception as e:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_false, error_raised
# test output of num_subnodes method when serial is True
n1._serial = True
yield assert_equal, n1.num_subnodes(), 1
# test running the workflow on serial conditions
error_raised = False
try:
w1.run(plugin='MultiProc')
except Exception as e:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_false, error_raised
os.chdir(cwd)
rmtree(wd)
def get_time_series_extractor_node():
return Node(Function(function=extract_time_series,
input_names=[
"lh_surf", "rh_surf", "lh_annot", "rh_annot",
"output_dir", "prefix", "confoundsName"
],
output_names=["time_series", "roiLabels",
"confName"]),
name="SurfaceTimeSeriesExtractor")
def computed_avg_node(node_name,
nnodes,
work_dir,
chunk=None,
delay=0,
benchmark_dir=None,
benchmark=False,
cli=False,
avg=None):
files = get_partitions(chunk, nnodes)
if delay is None:
delay = 0
ca_name = 'ca1_{0}'.format(node_name)
ca2_name = 'ca2_{0}'.format(node_name)
ca_1 = MapNode(Function(input_names=[
'chunk', 'delay', 'benchmark', 'benchmark_dir', 'cli', 'wf_name',
'avg', 'work_dir'
],
output_names=['inc_chunk'],
function=increment_wf),
name=ca_name,
iterfield='chunk')
ca_1.inputs.chunk = files
ca_1.inputs.delay = delay
ca_1.inputs.benchmark = benchmark
ca_1.inputs.benchmark_dir = benchmark_dir
ca_1.inputs.cli = cli
ca_1.inputs.wf_name = 'incwf_{}'.format(ca_name)
ca_1.inputs.avg = avg
ca_1.inputs.work_dir = work_dir
ca_2 = Node(Function(input_names=['chunks', 'benchmark', 'benchmark_dir'],
output_names=['avg_chunk'],
function=compute_avg),
name=ca2_name)
ca_2.inputs.benchmark = benchmark
ca_2.inputs.benchmark_dir = benchmark_dir
return ca_1, ca_2
def test_mapnode_iterfield_type(x_inp, f_exp):
from nipype import MapNode, Function
def double_func(x):
return 2 * x
double = Function(["x"], ["f_x"], double_func)
double_node = MapNode(double, name="double", iterfield=["x"])
double_node.inputs.x = x_inp
res = double_node.run()
assert res.outputs.f_x == f_exp
def sum2args():
""" Return a nipype function that sums up two args: `arg1` and `arg2` and
leaves the result in `out`.
Returns
-------
fi: nipype.interfaces.utility.Function
"""
func = 'def func(arg1, arg2): return arg1 + arg2'
fi = Function(input_names=['arg1', 'arg2'], output_names=['out'])
fi.inputs.function_str = func
return fi
def run_mri_deface(image, outfile):
deface_wf = pe.Workflow('deface_wf')
inputnode = pe.Node(niu.IdentityInterface(['in_file']), name='inputnode')
mri_deface = pe.Node(Function(input_names=['image', 'outfile'],
output_names=['outfile'],
function=mri_deface_cmd),
name='mri_deface')
deface_wf.connect([(inputnode, mri_deface, [('in_file', 'image')])])
inputnode.inputs.in_file = image
mri_deface.inputs.outfile = outfile
deface_wf.run()
def run_tbss_non_FA(tbss_info_dict,
maps,
subjects_list,
output_dir,
output_name='non_fa',
recalculate=True):
"""Run TBSS non FA on the given subjects.
Args:
tbss_info_dict (dict): the information dict from 'run_tbss()'.
maps (dict): mapping subjects to filenames containing the map to register to the FA skeleton.
subjects_list (list of str): the list of subjects names. We provide these to make sure the images are
all analyzed in the correct order.
output_dir (str): the output directory
output_name (str): the name of the output file (without extension)
Returns:
The full path the output file containing the tracts.
"""
work_dir = os.path.join(output_dir, '_nipype_work_dir',
output_name.replace('.', '_'))
output_file = os.path.join(output_dir, output_name + '.nii.gz')
if not recalculate and os.path.isfile(output_file):
return output_file
maps_list = [maps[subject] for subject in subjects_list]
field_list = [
tbss_info_dict['field_list'][subject] for subject in subjects_list
]
tbss_non_fa = create_tbss_non_FA(output_file=output_file)
tbss_non_fa.base_dir = work_dir
tbss_non_fa.inputs.inputnode.file_list = maps_list
tbss_non_fa.inputs.inputnode.field_list = field_list
tbss_non_fa.inputs.inputnode.skeleton_thresh = 0.2
tbss_non_fa.inputs.inputnode.groupmask = tbss_info_dict['group_mask']
tbss_non_fa.inputs.inputnode.meanfa_file = tbss_info_dict['mean_fa']
tbss_non_fa.inputs.inputnode.distance_map = tbss_info_dict['distance_map']
tbss_non_fa.inputs.inputnode.all_FA_file = tbss_info_dict['merge_fa']
data_sink = pe.Node(Function(['input'], [], function=void), 'DataSink')
wf = Workflow(name='tbss_non_fa_wf', base_dir=work_dir)
wf.connect([(tbss_non_fa, data_sink, [('outputnode.projected_nonFA_file',
'input')])])
wf.run(plugin='MultiProc')
shutil.rmtree(work_dir)
return output_file
def run_mridefacer(image, subject_label):
deface_wf = pe.Workflow('deface_wf')
inputnode = pe.Node(niu.IdentityInterface(['in_file']), name='inputnode')
mridefacer = pe.Node(Function(input_names=['image', 'subject_label'],
output_names=['outfile'],
function=mri_deface_cmd),
name='pydeface')
mridefacer.connect([
(inputnode, mridefacer, [('in_file', 'image')]),
])
inputnode.inputs.in_file = image
mridefacer.inputs.subject_label = subject_label
res = deface_wf.run()