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:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
yield assert_true, error_raised
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:
from nipype.pipeline.engine.base import logger
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(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_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}
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:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
assert error_raised
# 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:
from nipype.pipeline.engine.base import logger
logger.info('Exception: %s' % str(e))
error_raised = True
assert not error_raised
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 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)
