def test_unique_join_node():
"""Test join with the ``unique`` flag set to True."""
global _sum_operands
_sum_operands = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [3, 1, 2, 1, 3])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# the set join node
join = pe.JoinNode(SumInterface(), joinsource='inputspec',
joinfield='input1', unique=True, name='join')
wf.connect(pre_join1, 'output1', join, 'input1')
wf.run()
assert_equal(_sum_operands[0], [4, 2, 3],
"The unique join output value is incorrect: %s." % _sum_operands[0])
os.chdir(cwd)
rmtree(wd)
def test_mlab_init():
yield assert_equal(mlab.MatlabCommand._cmd, 'matlab')
yield assert_equal(mlab.MatlabCommand.input_spec, mlab.MatlabInputSpec)
yield assert_equal(mlab.MatlabCommand().cmd, matlab_cmd)
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
yield assert_equal(mc.cmd, 'foo_m')
def test_set_join_node():
"""Test collecting join inputs to a set."""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2, 1, 3, 2])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# the set join node
join = pe.JoinNode(SetInterface(), joinsource='inputspec',
joinfield='input1', name='join')
wf.connect(pre_join1, 'output1', join, 'input1')
wf.run()
# the join length is the number of unique inputs
assert_equal(_set_len, 3,
"The join Set output value is incorrect: %s." % _set_len)
os.chdir(cwd)
rmtree(wd)
def test_set_join_node():
"""Test collecting join inputs to a set."""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2, 1, 3, 2])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# the set join node
join = pe.JoinNode(SetInterface(), joinsource='inputspec',
joinfield='input1', name='join')
wf.connect(pre_join1, 'output1', join, 'input1')
wf.run()
# the join length is the number of unique inputs
assert_equal(_set_len, 3,
"The join Set output value is incorrect: %s." % _set_len)
os.chdir(cwd)
rmtree(wd)
def test_unique_join_node():
"""Test join with the ``unique`` flag set to True."""
global _sum_operands
_sum_operands = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [3, 1, 2, 1, 3])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# the set join node
join = pe.JoinNode(SumInterface(), joinsource='inputspec',
joinfield='input1', unique=True, name='join')
wf.connect(pre_join1, 'output1', join, 'input1')
wf.run()
assert_equal(_sum_operands[0], [4, 2, 3],
"The unique join output value is incorrect: %s." % _sum_operands[0])
os.chdir(cwd)
rmtree(wd)
def test1():
pipe = pe.Workflow(name='pipe')
mod1 = pe.Node(interface=TestInterface(),name='mod1')
pipe.add_nodes([mod1])
pipe._create_flat_graph()
pipe._execgraph = pe._generate_expanded_graph(deepcopy(pipe._flatgraph))
yield assert_equal(len(pipe._execgraph.nodes()), 1)
yield assert_equal(len(pipe._execgraph.edges()), 0)
def _run_interface(self, runtime):
data1 = nb.load(self.inputs.volume1).get_data()
data2 = nb.load(self.inputs.volume2).get_data()
assert_equal(data1, data2)
return runtime
def _run_interface(self, runtime):
data1 = nb.load(self.inputs.volume1).get_data()
data2 = nb.load(self.inputs.volume2).get_data()
assert_equal(data1, data2)
return runtime
def test_itersource_join_source_node():
"""Test join on an input node which has an ``itersource``."""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2])]
# an intermediate node in the first iteration path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# an iterable pre-join node with an itersource
pre_join2 = pe.Node(ProductInterface(), name='pre_join2')
pre_join2.itersource = ('inputspec', 'n')
pre_join2.iterables = ('input1', {1: [3, 4], 2: [5, 6]})
wf.connect(pre_join1, 'output1', pre_join2, 'input2')
# an intermediate node in the second iteration path
pre_join3 = pe.Node(IncrementInterface(), name='pre_join3')
wf.connect(pre_join2, 'output1', pre_join3, 'input1')
# the join node
join = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='pre_join2',
joinfield='vector',
name='join')
wf.connect(pre_join3, 'output1', join, 'vector')
# a join successor node
post_join1 = pe.Node(SumInterface(), name='post_join1')
wf.connect(join, 'vector', post_join1, 'input1')
result = wf.run()
# the expanded graph contains
# 1 pre_join1 replicate for each inputspec iteration,
# 2 pre_join2 replicates for each inputspec iteration,
# 1 pre_join3 for each pre_join2 iteration,
# 1 join replicate for each inputspec iteration and
# 1 post_join1 replicate for each join replicate =
# 2 + (2 * 2) + 4 + 2 + 2 = 14 expansion graph nodes.
# Nipype factors away the iterable input
# IdentityInterface but keeps the join IdentityInterface.
assert_equal(len(result.nodes()), 14,
"The number of expanded nodes is incorrect.")
# The first join inputs are:
# 1 + (3 * 2) and 1 + (4 * 2)
# The second join inputs are:
# 1 + (5 * 3) and 1 + (6 * 3)
# the post-join nodes execution order is indeterminate;
# therefore, compare the lists item-wise.
assert_true([16, 19] in _sum_operands,
"The join Sum input is incorrect: %s." % _sum_operands)
assert_true([7, 9] in _sum_operands,
"The join Sum input is incorrect: %s." % _sum_operands)
os.chdir(cwd)
rmtree(wd)
def test_multiple_join_nodes():
"""Test two join nodes, one downstream of the other."""
global _products
_products = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2, 3])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# the first join node
join1 = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='inputspec',
joinfield='vector',
name='join1')
wf.connect(pre_join1, 'output1', join1, 'vector')
# an uniterated post-join node
post_join1 = pe.Node(SumInterface(), name='post_join1')
wf.connect(join1, 'vector', post_join1, 'input1')
# the downstream join node connected to both an upstream join
# path output and a separate input in the iterated path
join2 = pe.JoinNode(IdentityInterface(fields=['vector', 'scalar']),
joinsource='inputspec',
joinfield='vector',
name='join2')
wf.connect(pre_join1, 'output1', join2, 'vector')
wf.connect(post_join1, 'output1', join2, 'scalar')
# a second post-join node
post_join2 = pe.Node(SumInterface(), name='post_join2')
wf.connect(join2, 'vector', post_join2, 'input1')
# a third post-join node
post_join3 = pe.Node(ProductInterface(), name='post_join3')
wf.connect(post_join2, 'output1', post_join3, 'input1')
wf.connect(join2, 'scalar', post_join3, 'input2')
result = wf.run()
# The expanded graph contains one pre_join1 replicate per inputspec
# replicate and one of each remaining node = 3 + 5 = 8 nodes.
# The replicated inputspec nodes are factored out of the expansion.
assert_equal(len(result.nodes()), 8,
"The number of expanded nodes is incorrect.")
# The outputs are:
# pre_join1: [2, 3, 4]
# post_join1: 9
# join2: [2, 3, 4] and 9
# post_join2: 9
# post_join3: 9 * 9 = 81
assert_equal(_products, [81], "The post-join product is incorrect")
os.chdir(cwd)
rmtree(wd)
def test2():
pipe = pe.Workflow(name='pipe')
mod1 = pe.Node(interface=TestInterface(),name='mod1')
mod1.iterables = dict(input1=lambda:[1,2],input2=lambda:[1,2])
pipe.add_nodes([mod1])
pipe._create_flat_graph()
pipe._execgraph = pe._generate_expanded_graph(deepcopy(pipe._flatgraph))
yield assert_equal(len(pipe._execgraph.nodes()), 4)
yield assert_equal(len(pipe._execgraph.edges()), 0)
def test_multiple_join_nodes():
"""Test two join nodes, one downstream of the other."""
global _products
_products = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2, 3])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# the first join node
join1 = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='inputspec', joinfield='vector',
name='join1')
wf.connect(pre_join1, 'output1', join1, 'vector')
# an uniterated post-join node
post_join1 = pe.Node(SumInterface(), name='post_join1')
wf.connect(join1, 'vector', post_join1, 'input1')
# the downstream join node connected to both an upstream join
# path output and a separate input in the iterated path
join2 = pe.JoinNode(IdentityInterface(fields=['vector', 'scalar']),
joinsource='inputspec', joinfield='vector',
name='join2')
wf.connect(pre_join1, 'output1', join2, 'vector')
wf.connect(post_join1, 'output1', join2, 'scalar')
# a second post-join node
post_join2 = pe.Node(SumInterface(), name='post_join2')
wf.connect(join2, 'vector', post_join2, 'input1')
# a third post-join node
post_join3 = pe.Node(ProductInterface(), name='post_join3')
wf.connect(post_join2, 'output1', post_join3, 'input1')
wf.connect(join2, 'scalar', post_join3, 'input2')
result = wf.run()
# The expanded graph contains one pre_join1 replicate per inputspec
# replicate and one of each remaining node = 3 + 5 = 8 nodes.
# The replicated inputspec nodes are factored out of the expansion.
assert_equal(len(result.nodes()), 8,
"The number of expanded nodes is incorrect.")
# The outputs are:
# pre_join1: [2, 3, 4]
# post_join1: 9
# join2: [2, 3, 4] and 9
# post_join2: 9
# post_join3: 9 * 9 = 81
assert_equal(_products, [81], "The post-join product is incorrect")
os.chdir(cwd)
rmtree(wd)
def test_itersource_join_source_node():
"""Test join on an input node which has an ``itersource``."""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2])]
# an intermediate node in the first iteration path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# an iterable pre-join node with an itersource
pre_join2 = pe.Node(ProductInterface(), name='pre_join2')
pre_join2.itersource = ('inputspec', 'n')
pre_join2.iterables = ('input1', {1: [3, 4], 2: [5, 6]})
wf.connect(pre_join1, 'output1', pre_join2, 'input2')
# an intermediate node in the second iteration path
pre_join3 = pe.Node(IncrementInterface(), name='pre_join3')
wf.connect(pre_join2, 'output1', pre_join3, 'input1')
# the join node
join = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='pre_join2', joinfield='vector', name='join')
wf.connect(pre_join3, 'output1', join, 'vector')
# a join successor node
post_join1 = pe.Node(SumInterface(), name='post_join1')
wf.connect(join, 'vector', post_join1, 'input1')
result = wf.run()
# the expanded graph contains
# 1 pre_join1 replicate for each inputspec iteration,
# 2 pre_join2 replicates for each inputspec iteration,
# 1 pre_join3 for each pre_join2 iteration,
# 1 join replicate for each inputspec iteration and
# 1 post_join1 replicate for each join replicate =
# 2 + (2 * 2) + 4 + 2 + 2 = 14 expansion graph nodes.
# Nipype factors away the iterable input
# IdentityInterface but keeps the join IdentityInterface.
assert_equal(len(result.nodes()), 14,
"The number of expanded nodes is incorrect.")
# The first join inputs are:
# 1 + (3 * 2) and 1 + (4 * 2)
# The second join inputs are:
# 1 + (5 * 3) and 1 + (6 * 3)
# the post-join nodes execution order is indeterminate;
# therefore, compare the lists item-wise.
assert_true([16, 19] in _sum_operands,
"The join Sum input is incorrect: %s." % _sum_operands)
assert_true([7, 9] in _sum_operands,
"The join Sum input is incorrect: %s." % _sum_operands)
os.chdir(cwd)
rmtree(wd)
def test5():
pipe = pe.Workflow(name='pipe')
mod1 = pe.Node(interface=TestInterface(),name='mod1')
mod2 = pe.Node(interface=TestInterface(),name='mod2')
mod1.iterables = dict(input1=lambda:[1,2])
mod2.iterables = dict(input1=lambda:[1,2])
pipe.connect([(mod1,mod2,[('output1','input2')])])
pipe._create_flat_graph()
pipe._execgraph = pe._generate_expanded_graph(deepcopy(pipe._flatgraph))
yield assert_equal(len(pipe._execgraph.nodes()), 6)
yield assert_equal(len(pipe._execgraph.edges()), 4)
def test_callback_multiproc_normal():
so = Status()
wf = pe.Workflow(name='test', base_dir='/tmp')
f_node = pe.Node(niu.Function(function=func, input_names=[], output_names=[]), name='f_node')
wf.add_nodes([f_node])
wf.run(plugin='MultiProc', plugin_args={'status_callback': so.callback})
assert_equal(len(so.statuses), 2)
for (n, s) in so.statuses:
yield assert_equal, n.name, 'f_node'
yield assert_equal, so.statuses[0][1], 'start'
yield assert_equal, so.statuses[1][1], 'end'
def test_split_filename():
res = split_filename('foo.nii')
yield assert_equal(res, ('', 'foo', '.nii'))
res = split_filename('foo.nii.gz')
yield assert_equal(res, ('', 'foo', '.nii.gz'))
res = split_filename('/usr/local/foo.nii.gz')
yield assert_equal(res, ('/usr/local', 'foo', '.nii.gz'))
res = split_filename('../usr/local/foo.nii')
yield assert_equal(res, ('../usr/local', 'foo', '.nii'))
res = split_filename('/usr/local/foo.a.b.c.d')
yield assert_equal(res, ('/usr/local', 'foo', '.a.b.c.d'))
def test_cmdline():
basedir = mkdtemp()
mi = mlab.MatlabCommand(script='whos',
script_file='testscript')
yield assert_equal(mi.cmdline, \
matlab_cmd + ' -nodesktop -nosplash -singleCompThread -r "fprintf(1,\'Executing code at %s:\\n\',datestr(now));ver,try,whos,catch ME,ME,ME.stack,fprintf(\'%s\\n\',ME.message);fprintf(2,\'<MatlabScriptException>\');fprintf(2,\'%s\\n\',ME.message);fprintf(2,\'File:%s\\nName:%s\\nLine:%d\\n\',ME.stack.file,ME.stack.name,ME.stack.line);fprintf(2,\'</MatlabScriptException>\');end;;exit"')
yield assert_equal(mi.inputs.script, 'whos')
yield assert_equal(mi.inputs.script_file, 'testscript')
path_exists = os.path.exists(os.path.join(basedir,'testscript.m'))
yield assert_false(path_exists)
rmtree(basedir)
def test_generate_dependency_list():
pipe = pe.Workflow(name='pipe')
mod1 = pe.Node(interface=TestInterface(),name='mod1')
mod2 = pe.Node(interface=TestInterface(),name='mod2')
pipe.connect([(mod1,mod2,[('output1','input1')])])
pipe._create_flat_graph()
pipe._execgraph = pe._generate_expanded_graph(deepcopy(pipe._flatgraph))
pipe._generate_dependency_list()
yield assert_false(pipe._execgraph == None)
yield assert_equal(len(pipe.procs), 2)
yield assert_false(pipe.proc_done[1])
yield assert_false(pipe.proc_pending[1])
yield assert_equal(pipe.depidx[0,1], 1)
def test_run_interface():
mc = mlab.MatlabCommand(matlab_cmd='foo_m')
yield assert_raises(ValueError, mc.run) # script is mandatory
mc.inputs.script = 'a=1;'
yield assert_raises(IOError, mc.run) # foo_m is not an executable
cwd = os.getcwd()
basedir = mkdtemp()
os.chdir(basedir)
res = mlab.MatlabCommand(script='foo', paths=[basedir], mfile=True).run() # bypasses ubuntu dash issue
yield assert_equal(res.runtime.returncode, 1)
res = mlab.MatlabCommand(script='a=1;', paths=[basedir], mfile=True).run() # bypasses ubuntu dash issue
yield assert_equal(res.runtime.returncode, 0)
os.chdir(cwd)
rmtree(basedir)
def test_callback_exception():
so = Status()
wf = pe.Workflow(name='test', base_dir='/tmp')
f_node = pe.Node(niu.Function(function=bad_func, input_names=[], output_names=[]), name='f_node')
wf.add_nodes([f_node])
try:
wf.run(plugin_args={'status_callback': so.callback})
except:
pass
assert_equal(len(so.statuses), 2)
for (n, s) in so.statuses:
yield assert_equal, n.name, 'f_node'
yield assert_equal, so.statuses[0][1], 'start'
yield assert_equal, so.statuses[1][1], 'exception'
def test_callback_normal():
so = Status()
wf = pe.Workflow(name='test', base_dir=mkdtemp())
f_node = pe.Node(niu.Function(function=func, input_names=[],
output_names=[]),
name='f_node')
wf.add_nodes([f_node])
wf.config['execution'] = {'crashdump_dir': wf.base_dir}
wf.run(plugin="Linear", plugin_args={'status_callback': so.callback})
assert_equal(len(so.statuses), 2)
for (n, s) in so.statuses:
yield assert_equal, n.name, 'f_node'
yield assert_equal, so.statuses[0][1], 'start'
yield assert_equal, so.statuses[1][1], 'end'
rmtree(wf.base_dir)
def test_callback_multiproc_normal():
so = Status()
wf = pe.Workflow(name='test', base_dir=mkdtemp())
f_node = pe.Node(niu.Function(function=func, input_names=[],
output_names=[]),
name='f_node')
wf.add_nodes([f_node])
wf.config['execution'] = {'crashdump_dir': wf.base_dir}
wf.run(plugin='MultiProc', plugin_args={'status_callback': so.callback})
assert_equal(len(so.statuses), 2)
for (n, s) in so.statuses:
yield assert_equal, n.name, 'f_node'
yield assert_equal, so.statuses[0][1], 'start'
yield assert_equal, so.statuses[1][1], 'end'
rmtree(wf.base_dir)
def test_itersource_two_join_nodes():
"""Test join with a midstream ``itersource`` and an upstream
iterable."""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2])]
# an intermediate node in the first iteration path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# an iterable pre-join node with an itersource
pre_join2 = pe.Node(ProductInterface(), name='pre_join2')
pre_join2.itersource = ('inputspec', 'n')
pre_join2.iterables = ('input1', {1: [3, 4], 2: [5, 6]})
wf.connect(pre_join1, 'output1', pre_join2, 'input2')
# an intermediate node in the second iteration path
pre_join3 = pe.Node(IncrementInterface(), name='pre_join3')
wf.connect(pre_join2, 'output1', pre_join3, 'input1')
# the first join node
join1 = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='pre_join2',
joinfield='vector',
name='join1')
wf.connect(pre_join3, 'output1', join1, 'vector')
# a join successor node
post_join1 = pe.Node(SumInterface(), name='post_join1')
wf.connect(join1, 'vector', post_join1, 'input1')
# a summary join node
join2 = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='inputspec',
joinfield='vector',
name='join2')
wf.connect(post_join1, 'output1', join2, 'vector')
result = wf.run()
# the expanded graph contains the 14 test_itersource_join_source_node
# nodes plus the summary join node.
assert_equal(len(result.nodes()), 15,
"The number of expanded nodes is incorrect.")
os.chdir(cwd)
rmtree(wd)
def test_synchronize_join_node():
"""Test join on an input node which has the ``synchronize`` flag set to True."""
global _products
_products = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['m', 'n']), name='inputspec')
inputspec.iterables = [('m', [1, 2]), ('n', [3, 4])]
inputspec.synchronize = True
# two pre-join nodes in a parallel iterated path
inc1 = pe.Node(IncrementInterface(), name='inc1')
wf.connect(inputspec, 'm', inc1, 'input1')
inc2 = pe.Node(IncrementInterface(), name='inc2')
wf.connect(inputspec, 'n', inc2, 'input1')
# the join node
join = pe.JoinNode(IdentityInterface(fields=['vector1', 'vector2']),
joinsource='inputspec',
name='join')
wf.connect(inc1, 'output1', join, 'vector1')
wf.connect(inc2, 'output1', join, 'vector2')
# a post-join node
prod = pe.MapNode(ProductInterface(),
name='prod',
iterfield=['input1', 'input2'])
wf.connect(join, 'vector1', prod, 'input1')
wf.connect(join, 'vector2', prod, 'input2')
result = wf.run()
# there are 3 iterables expansions.
# thus, the expanded graph contains 2 * 2 iteration pre-join nodes, 1 join
# node and 1 post-join node.
assert_equal(len(result.nodes()), 6,
"The number of expanded nodes is incorrect.")
# the product inputs are [2, 3] and [4, 5]
assert_equal(_products, [8, 15],
"The post-join products is incorrect: %s." % _products)
os.chdir(cwd)
rmtree(wd)
def test_callback_exception():
so = Status()
wf = pe.Workflow(name='test', base_dir=mkdtemp())
f_node = pe.Node(niu.Function(function=bad_func, input_names=[],
output_names=[]),
name='f_node')
wf.add_nodes([f_node])
wf.config['execution'] = {'crashdump_dir': wf.base_dir}
try:
wf.run(plugin="Linear", plugin_args={'status_callback': so.callback})
except:
pass
assert_equal(len(so.statuses), 2)
for (n, s) in so.statuses:
yield assert_equal, n.name, 'f_node'
yield assert_equal, so.statuses[0][1], 'start'
yield assert_equal, so.statuses[1][1], 'exception'
rmtree(wf.base_dir)
def test8():
pipe = pe.Workflow(name='pipe')
mod1 = pe.Node(interface=TestInterface(),name='mod1')
mod2 = pe.Node(interface=TestInterface(),name='mod2')
mod3 = pe.Node(interface=TestInterface(),name='mod3')
mod1.iterables = dict(input1=lambda:[1,2])
mod2.iterables = dict(input1=lambda:[1,2])
mod3.iterables = {}
pipe.connect([(mod1,mod3,[('output1','input2')]),
(mod2,mod3,[('output1','input2')])])
pipe._create_flat_graph()
pipe._execgraph = pe._generate_expanded_graph(deepcopy(pipe._flatgraph))
yield assert_equal(len(pipe._execgraph.nodes()), 8)
yield assert_equal(len(pipe._execgraph.edges()), 8)
edgenum = sorted([(len(pipe._execgraph.in_edges(node)) + \
len(pipe._execgraph.out_edges(node))) \
for node in pipe._execgraph.nodes()])
yield assert_true(edgenum[0]>0)
def test_connect():
pipe = pe.Workflow(name='pipe')
mod1 = pe.Node(interface=TestInterface(),name='mod1')
mod2 = pe.Node(interface=TestInterface(),name='mod2')
pipe.connect([(mod1,mod2,[('output1','input1')])])
yield assert_true(mod1 in pipe._graph.nodes())
yield assert_true(mod2 in pipe._graph.nodes())
yield assert_equal(pipe._graph.get_edge_data(mod1,mod2), {'connect':[('output1','input1')]})
def test_mlab_inputspec():
spec = mlab.MatlabInputSpec()
for k in ['paths', 'script', 'nosplash', 'mfile', 'logfile', 'script_file',
'nodesktop']:
yield assert_true(k in spec.copyable_trait_names())
yield assert_true(spec.nodesktop)
yield assert_true(spec.nosplash)
yield assert_false(spec.mfile)
yield assert_equal(spec.script_file, 'pyscript.m')
def test_itersource_two_join_nodes():
"""Test join with a midstream ``itersource`` and an upstream
iterable."""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2])]
# an intermediate node in the first iteration path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# an iterable pre-join node with an itersource
pre_join2 = pe.Node(ProductInterface(), name='pre_join2')
pre_join2.itersource = ('inputspec', 'n')
pre_join2.iterables = ('input1', {1: [3, 4], 2: [5, 6]})
wf.connect(pre_join1, 'output1', pre_join2, 'input2')
# an intermediate node in the second iteration path
pre_join3 = pe.Node(IncrementInterface(), name='pre_join3')
wf.connect(pre_join2, 'output1', pre_join3, 'input1')
# the first join node
join1 = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='pre_join2', joinfield='vector', name='join1')
wf.connect(pre_join3, 'output1', join1, 'vector')
# a join successor node
post_join1 = pe.Node(SumInterface(), name='post_join1')
wf.connect(join1, 'vector', post_join1, 'input1')
# a summary join node
join2 = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='inputspec', joinfield='vector', name='join2')
wf.connect(post_join1, 'output1', join2, 'vector')
result = wf.run()
# the expanded graph contains the 14 test_itersource_join_source_node
# nodes plus the summary join node.
assert_equal(len(result.nodes()), 15,
"The number of expanded nodes is incorrect.")
os.chdir(cwd)
rmtree(wd)
def test_multifield_join_node():
"""Test join on several fields."""
global _products
_products = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['m', 'n']), name='inputspec')
inputspec.iterables = [('m', [1, 2]), ('n', [3, 4])]
# two pre-join nodes in a parallel iterated path
inc1 = pe.Node(IncrementInterface(), name='inc1')
wf.connect(inputspec, 'm', inc1, 'input1')
inc2 = pe.Node(IncrementInterface(), name='inc2')
wf.connect(inputspec, 'n', inc2, 'input1')
# the join node
join = pe.JoinNode(IdentityInterface(fields=['vector1', 'vector2']),
joinsource='inputspec',
name='join')
wf.connect(inc1, 'output1', join, 'vector1')
wf.connect(inc2, 'output1', join, 'vector2')
# a post-join node
prod = pe.MapNode(ProductInterface(),
name='prod',
iterfield=['input1', 'input2'])
wf.connect(join, 'vector1', prod, 'input1')
wf.connect(join, 'vector2', prod, 'input2')
result = wf.run()
# the iterables are expanded as the cartesian product of the iterables values.
# thus, the expanded graph contains 2 * (2 * 2) iteration pre-join nodes, 1 join
# node and 1 post-join node.
assert_equal(len(result.nodes()), 10,
"The number of expanded nodes is incorrect.")
# the product inputs are [2, 4], [2, 5], [3, 4], [3, 5]
assert_equal(set(_products), set([8, 10, 12, 15]),
"The post-join products is incorrect: %s." % _products)
os.chdir(cwd)
rmtree(wd)
def test_multifield_join_node():
"""Test join on several fields."""
global _products
_products = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['m', 'n']),
name='inputspec')
inputspec.iterables = [('m', [1, 2]), ('n', [3, 4])]
# two pre-join nodes in a parallel iterated path
inc1 = pe.Node(IncrementInterface(), name='inc1')
wf.connect(inputspec, 'm', inc1, 'input1')
inc2 = pe.Node(IncrementInterface(), name='inc2')
wf.connect(inputspec, 'n', inc2, 'input1')
# the join node
join = pe.JoinNode(IdentityInterface(fields=['vector1', 'vector2']),
joinsource='inputspec', name='join')
wf.connect(inc1, 'output1', join, 'vector1')
wf.connect(inc2, 'output1', join, 'vector2')
# a post-join node
prod = pe.MapNode(ProductInterface(), name='prod',
iterfield=['input1', 'input2'])
wf.connect(join, 'vector1', prod, 'input1')
wf.connect(join, 'vector2', prod, 'input2')
result = wf.run()
# the iterables are expanded as the cartesian product of the iterables values.
# thus, the expanded graph contains 2 * (2 * 2) iteration pre-join nodes, 1 join
# node and 1 post-join node.
assert_equal(len(result.nodes()), 10,
"The number of expanded nodes is incorrect.")
# the product inputs are [2, 4], [2, 5], [3, 4], [3, 5]
assert_equal(set(_products), set([8, 10, 12, 15]),
"The post-join products is incorrect: %s." % _products)
os.chdir(cwd)
rmtree(wd)
def test_synchronize_join_node():
"""Test join on an input node which has the ``synchronize`` flag set to True."""
global _products
_products = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['m', 'n']), name='inputspec')
inputspec.iterables = [('m', [1, 2]), ('n', [3, 4])]
inputspec.synchronize = True
# two pre-join nodes in a parallel iterated path
inc1 = pe.Node(IncrementInterface(), name='inc1')
wf.connect(inputspec, 'm', inc1, 'input1')
inc2 = pe.Node(IncrementInterface(), name='inc2')
wf.connect(inputspec, 'n', inc2, 'input1')
# the join node
join = pe.JoinNode(IdentityInterface(fields=['vector1', 'vector2']),
joinsource='inputspec', name='join')
wf.connect(inc1, 'output1', join, 'vector1')
wf.connect(inc2, 'output1', join, 'vector2')
# a post-join node
prod = pe.MapNode(ProductInterface(), name='prod', iterfield=['input1', 'input2'])
wf.connect(join, 'vector1', prod, 'input1')
wf.connect(join, 'vector2', prod, 'input2')
result = wf.run()
# there are 3 iterables expansions.
# thus, the expanded graph contains 2 * 2 iteration pre-join nodes, 1 join
# node and 1 post-join node.
assert_equal(len(result.nodes()), 6,
"The number of expanded nodes is incorrect.")
# the product inputs are [2, 3] and [4, 5]
assert_equal(_products, [8, 15],
"The post-join products is incorrect: %s." % _products)
os.chdir(cwd)
rmtree(wd)
def test_callback_multiproc_exception():
so = Status()
wf = pe.Workflow(name='test', base_dir=mkdtemp())
f_node = pe.Node(niu.Function(function=bad_func,
input_names=[],
output_names=[]),
name='f_node')
wf.add_nodes([f_node])
wf.config['execution']['crashdump_dir'] = wf.base_dir
try:
wf.run(plugin='MultiProc',
plugin_args={'status_callback': so.callback})
except:
pass
assert_equal(len(so.statuses), 2)
for (n, s) in so.statuses:
yield assert_equal, n.name, 'f_node'
yield assert_equal, so.statuses[0][1], 'start'
yield assert_equal, so.statuses[1][1], 'exception'
rmtree(wf.base_dir)
def test_node_joinsource():
"""Test setting the joinsource to a Node."""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2])]
# the join node
join = pe.JoinNode(SetInterface(), joinsource=inputspec,
joinfield='input1', name='join')
# the joinsource is the inputspec name
assert_equal(join.joinsource, inputspec.name,
"The joinsource is not set to the node name.")
os.chdir(cwd)
rmtree(wd)
def test_node_joinsource():
"""Test setting the joinsource to a Node."""
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2])]
# the join node
join = pe.JoinNode(SetInterface(), joinsource=inputspec,
joinfield='input1', name='join')
# the joinsource is the inputspec name
assert_equal(join.joinsource, inputspec.name,
"The joinsource is not set to the node name.")
os.chdir(cwd)
rmtree(wd)
def test_gen_fname():
# Test _gen_fname method of FSLCommand
cmd = fsl.FSLCommand(command = 'junk',output_type = 'NIFTI_GZ')
pth = os.getcwd()
# just the filename
fname = cmd._gen_fname('foo.nii.gz',suffix='_fsl')
desired = os.path.join(pth, 'foo_fsl.nii.gz')
yield assert_equal(fname, desired)
# filename with suffix
fname = cmd._gen_fname('foo.nii.gz', suffix = '_brain')
desired = os.path.join(pth, 'foo_brain.nii.gz')
yield assert_equal(fname, desired)
# filename with suffix and working directory
fname = cmd._gen_fname('foo.nii.gz', suffix = '_brain', cwd = '/data')
desired = os.path.join('/data', 'foo_brain.nii.gz')
yield assert_equal(fname, desired)
# filename with suffix and no file extension change
fname = cmd._gen_fname('foo.nii.gz', suffix = '_brain.mat',
change_ext = False)
desired = os.path.join(pth, 'foo_brain.mat')
yield assert_equal(fname, desired)
def test_identity_join_node():
"""Test an IdentityInterface join."""
global _sum_operands
_sum_operands = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']),
name='inputspec')
inputspec.iterables = [('n', [1, 2, 3])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# the IdentityInterface join node
join = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='inputspec', joinfield='vector',
name='join')
wf.connect(pre_join1, 'output1', join, 'vector')
# an uniterated post-join node
post_join1 = pe.Node(SumInterface(), name='post_join1')
wf.connect(join, 'vector', post_join1, 'input1')
result = wf.run()
# the expanded graph contains 1 * 3 iteration pre-join nodes, 1 join
# node and 1 post-join node. Nipype factors away the iterable input
# IdentityInterface but keeps the join IdentityInterface.
assert_equal(len(result.nodes()), 5,
"The number of expanded nodes is incorrect.")
assert_equal(_sum_operands[0], [2, 3, 4],
"The join Sum input is incorrect: %s." %_sum_operands[0])
os.chdir(cwd)
rmtree(wd)
def test_identity_join_node():
"""Test an IdentityInterface join."""
global _sum_operands
_sum_operands = []
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']),
name='inputspec')
inputspec.iterables = [('n', [1, 2, 3])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# the IdentityInterface join node
join = pe.JoinNode(IdentityInterface(fields=['vector']),
joinsource='inputspec', joinfield='vector',
name='join')
wf.connect(pre_join1, 'output1', join, 'vector')
# an uniterated post-join node
post_join1 = pe.Node(SumInterface(), name='post_join1')
wf.connect(join, 'vector', post_join1, 'input1')
result = wf.run()
# the expanded graph contains 1 * 3 iteration pre-join nodes, 1 join
# node and 1 post-join node. Nipype factors away the iterable input
# IdentityInterface but keeps the join IdentityInterface.
assert_equal(len(result.nodes()), 5,
"The number of expanded nodes is incorrect.")
assert_equal(_sum_operands[0], [2, 3, 4],
"The join Sum input is incorrect: %s." % _sum_operands[0])
os.chdir(cwd)
rmtree(wd)
def test_coreg():
moving = example_data(infile='functional.nii')
target = example_data(infile='T1.nii')
mat = example_data(infile='trans.mat')
coreg = spmu.CalcCoregAffine(matlab_cmd='mymatlab')
coreg.inputs.target = target
assert_equal(coreg.inputs.matlab_cmd, 'mymatlab')
coreg.inputs.moving = moving
assert_equal(isdefined(coreg.inputs.mat), False)
pth, mov, _ = split_filename(moving)
_, tgt, _ = split_filename(target)
mat = os.path.join(pth, '%s_to_%s.mat' % (mov, tgt))
invmat = fname_presuffix(mat, prefix='inverse_')
scrpt = coreg._make_matlab_command(None)
assert_equal(coreg.inputs.mat, mat)
assert_equal(coreg.inputs.invmat, invmat)
def test_coreg():
moving = example_data(infile="functional.nii")
target = example_data(infile="T1.nii")
mat = example_data(infile="trans.mat")
coreg = spmu.CalcCoregAffine(matlab_cmd="mymatlab")
coreg.inputs.target = target
assert_equal(coreg.inputs.matlab_cmd, "mymatlab")
coreg.inputs.moving = moving
assert_equal(isdefined(coreg.inputs.mat), False)
pth, mov, _ = split_filename(moving)
_, tgt, _ = split_filename(target)
mat = os.path.join(pth, "%s_to_%s.mat" % (mov, tgt))
invmat = fname_presuffix(mat, prefix="inverse_")
scrpt = coreg._make_matlab_command(None)
assert_equal(coreg.inputs.mat, mat)
assert_equal(coreg.inputs.invmat, invmat)
def test_apply_transform():
moving = example_data(infile = 'functional.nii')
mat = example_data(infile = 'trans.mat')
applymat = spmu.ApplyTransform(matlab_cmd = 'mymatlab')
assert_equal( applymat.inputs.matlab_cmd, 'mymatlab' )
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = 'img_space = spm_get_space(infile);'
assert_equal( expected in scrpt, True)
expected = 'spm_get_space(infile, transform.M * img_space);'
assert_equal(expected in scrpt, True)
def test_apply_transform():
moving = example_data(infile='functional.nii')
mat = example_data(infile='trans.mat')
applymat = spmu.ApplyTransform(matlab_cmd='mymatlab')
assert_equal(applymat.inputs.matlab_cmd, 'mymatlab')
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = '[p n e v] = spm_fileparts(V.fname);'
assert_equal(expected in scrpt, True)
expected = 'V.mat = transform.M * V.mat;'
assert_equal(expected in scrpt, True)
def test_apply_transform():
moving = example_data(infile="functional.nii")
mat = example_data(infile="trans.mat")
applymat = spmu.ApplyTransform(matlab_cmd="mymatlab")
assert_equal(applymat.inputs.matlab_cmd, "mymatlab")
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = "img_space = spm_get_space(infile);"
assert_equal(expected in scrpt, True)
expected = "spm_get_space(infile, M * img_space);"
assert_equal(expected in scrpt, True)
def test_apply_transform():
moving = example_data(infile='functional.nii')
mat = example_data(infile='trans.mat')
applymat = spmu.ApplyTransform(matlab_cmd='mymatlab')
assert_equal(applymat.inputs.matlab_cmd, 'mymatlab')
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = '[p n e v] = spm_fileparts(V.fname);'
assert_equal(expected in scrpt, True)
expected = 'V.mat = transform.M * V.mat;'
assert_equal(expected in scrpt, True)
def test_apply_transform():
moving = example_data(infile='functional.nii')
mat = example_data(infile='trans.mat')
applymat = spmu.ApplyTransform(matlab_cmd='mymatlab')
assert_equal(applymat.inputs.matlab_cmd, 'mymatlab')
applymat.inputs.in_file = moving
applymat.inputs.mat = mat
scrpt = applymat._make_matlab_command(None)
expected = 'img_space = spm_get_space(infile);'
assert_equal(expected in scrpt, True)
expected = 'spm_get_space(infile, transform.M * img_space);'
assert_equal(expected in scrpt, True)
def test_join_expansion():
cwd = os.getcwd()
wd = mkdtemp()
os.chdir(wd)
# Make the workflow.
wf = pe.Workflow(name='test')
# the iterated input node
inputspec = pe.Node(IdentityInterface(fields=['n']), name='inputspec')
inputspec.iterables = [('n', [1, 2])]
# a pre-join node in the iterated path
pre_join1 = pe.Node(IncrementInterface(), name='pre_join1')
wf.connect(inputspec, 'n', pre_join1, 'input1')
# another pre-join node in the iterated path
pre_join2 = pe.Node(IncrementInterface(), name='pre_join2')
wf.connect(pre_join1, 'output1', pre_join2, 'input1')
# the join node
join = pe.JoinNode(SumInterface(), joinsource='inputspec',
joinfield='input1', name='join')
wf.connect(pre_join2, 'output1', join, 'input1')
# an uniterated post-join node
post_join1 = pe.Node(IncrementInterface(), name='post_join1')
wf.connect(join, 'output1', post_join1, 'input1')
# a post-join node in the iterated path
post_join2 = pe.Node(ProductInterface(), name='post_join2')
wf.connect(join, 'output1', post_join2, 'input1')
wf.connect(pre_join1, 'output1', post_join2, 'input2')
result = wf.run()
# the two expanded pre-join predecessor nodes feed into one join node
joins = [node for node in result.nodes() if node.name == 'join']
assert_equal(len(joins), 1, "The number of join result nodes is incorrect.")
# the expanded graph contains 2 * 2 = 4 iteration pre-join nodes, 1 join
# node, 1 non-iterated post-join node and 2 * 1 iteration post-join nodes.
# Nipype factors away the IdentityInterface.
assert_equal(len(result.nodes()), 8, "The number of expanded nodes is incorrect.")
# the join Sum result is (1 + 1 + 1) + (2 + 1 + 1)
assert_equal(len(_sums), 1,
"The number of join outputs is incorrect")
assert_equal(_sums[0], 7, "The join Sum output value is incorrect: %s." % _sums[0])
# the join input preserves the iterables input order
assert_equal(_sum_operands[0], [3, 4],
"The join Sum input is incorrect: %s." % _sum_operands[0])
# there are two iterations of the post-join node in the iterable path
assert_equal(len(_products), 2,
"The number of iterated post-join outputs is incorrect")
os.chdir(cwd)
rmtree(wd)
def test_reslice():
moving = example_data(infile='functional.nii')
space_defining = example_data(infile='T1.nii')
reslice = spmu.Reslice(matlab_cmd='mymatlab_version')
assert_equal(reslice.inputs.matlab_cmd, 'mymatlab_version')
reslice.inputs.in_file = moving
reslice.inputs.space_defining = space_defining
assert_equal(reslice.inputs.interp, 0)
assert_raises(TraitError, reslice.inputs.trait_set, interp='nearest')
assert_raises(TraitError, reslice.inputs.trait_set, interp=10)
reslice.inputs.interp = 1
script = reslice._make_matlab_command(None)
outfile = fname_presuffix(moving, prefix='r')
assert_equal(reslice.inputs.out_file, outfile)
expected = '\nflags.mean=0;\nflags.which=1;\nflags.mask=0;'
assert_equal(expected in script.replace(' ', ''), True)
expected_interp = 'flags.interp = 1;\n'
assert_equal(expected_interp in script, True)
assert_equal('spm_reslice(invols, flags);' in script, True)
def test_dicom_import():
dicom = example_data(infile='dicomdir/123456-1-1.dcm')
di = spmu.DicomImport(matlab_cmd='mymatlab')
assert_equal(di.inputs.matlab_cmd, 'mymatlab')
assert_equal(di.inputs.output_dir_struct, 'flat')
assert_equal(di.inputs.output_dir, './converted_dicom')
assert_equal(di.inputs.format, 'nii')
assert_equal(di.inputs.icedims, False)
assert_raises(TraitError, di.inputs.trait_set, output_dir_struct='wrong')
assert_raises(TraitError, di.inputs.trait_set, format='FAT')
assert_raises(TraitError, di.inputs.trait_set, in_files=['does_sfd_not_32fn_exist.dcm'])
di.inputs.in_files = [dicom]
assert_equal(di.inputs.in_files, [dicom])
