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Merge pull request #1405 from alexsavio/master
fix:test & fix bug using aux functions in connect
2 parents c96b3b1 + f3117e0 commit f504736

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‎nipype/interfaces/petpvc.py

Lines changed: 71 additions & 74 deletions
Original file line numberDiff line numberDiff line change
@@ -6,81 +6,8 @@
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>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
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>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
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>>> os.chdir(datadir)
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Nipype interface for PETPVC.
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PETPVC is a software from the Nuclear Medicine Department
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of the UCL University Hospital, London, UK.
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Its source code is here: https://github.com/UCL/PETPVC
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The methods that it implement are explained here:
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K. Erlandsson, I. Buvat, P. H. Pretorius, B. A. Thomas, and B. F. Hutton,
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"A review of partial volume correction techniques for emission tomography
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and their applications in neurology, cardiology and oncology," Phys. Med.
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Biol., vol. 57, no. 21, p. R119, 2012.
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There is a publication waiting to be accepted for this software tool.
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Its command line help shows this:
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-i --input < filename >
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= PET image file
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-o --output < filename >
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= Output file
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[ -m --mask < filename > ]
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= Mask image file
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-p --pvc < keyword >
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= Desired PVC method
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-x < X >
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= The full-width at half maximum in mm along x-axis
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-y < Y >
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= The full-width at half maximum in mm along y-axis
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-z < Z >
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= The full-width at half maximum in mm along z-axis
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[ -d --debug ]
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= Prints debug information
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[ -n --iter [ Val ] ]
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= Number of iterations
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With: Val (Default = 10)
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[ -k [ Val ] ]
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= Number of deconvolution iterations
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With: Val (Default = 10)
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[ -a --alpha [ aval ] ]
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= Alpha value
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With: aval (Default = 1.5)
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[ -s --stop [ stopval ] ]
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= Stopping criterion
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With: stopval (Default = 0.01)
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----------------------------------------------
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Technique - keyword
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Geometric transfer matrix - "GTM"
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Labbe approach - "LABBE"
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Richardson-Lucy - "RL"
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Van-Cittert - "VC"
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Region-based voxel-wise correction - "RBV"
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RBV with Labbe - "LABBE+RBV"
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RBV with Van-Cittert - "RBV+VC"
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RBV with Richardson-Lucy - "RBV+RL"
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RBV with Labbe and Van-Cittert - "LABBE+RBV+VC"
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RBV with Labbe and Richardson-Lucy- "LABBE+RBV+RL"
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Multi-target correction - "MTC"
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MTC with Labbe - "LABBE+MTC"
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MTC with Van-Cittert - "MTC+VC"
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MTC with Richardson-Lucy - "MTC+RL"
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MTC with Labbe and Van-Cittert - "LABBE+MTC+VC"
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MTC with Labbe and Richardson-Lucy- "LABBE+MTC+RL"
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Iterative Yang - "IY"
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Iterative Yang with Van-Cittert - "IY+VC"
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Iterative Yang with Richardson-Lucy - "IY+RL"
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Muller Gartner - "MG"
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Muller Gartner with Van-Cittert - "MG+VC"
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Muller Gartner with Richardson-Lucy - "MG+RL"
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"""
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from __future__ import print_function
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from __future__ import division
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@@ -144,6 +71,76 @@ class PETPVCOutputSpec(TraitedSpec):
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class PETPVC(CommandLine):
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""" Use PETPVC for partial volume correction of PET images.
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PETPVC is a software from the Nuclear Medicine Department
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of the UCL University Hospital, London, UK.
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Its source code is here: https://github.com/UCL/PETPVC
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The methods that it implement are explained here:
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K. Erlandsson, I. Buvat, P. H. Pretorius, B. A. Thomas, and B. F. Hutton,
81+
"A review of partial volume correction techniques for emission tomography
82+
and their applications in neurology, cardiology and oncology," Phys. Med.
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Biol., vol. 57, no. 21, p. R119, 2012.
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There is a publication waiting to be accepted for this software tool.
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Its command line help shows this:
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-i --input < filename >
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= PET image file
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-o --output < filename >
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= Output file
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[ -m --mask < filename > ]
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= Mask image file
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-p --pvc < keyword >
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= Desired PVC method
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-x < X >
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= The full-width at half maximum in mm along x-axis
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-y < Y >
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= The full-width at half maximum in mm along y-axis
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-z < Z >
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= The full-width at half maximum in mm along z-axis
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[ -d --debug ]
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= Prints debug information
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[ -n --iter [ Val ] ]
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= Number of iterations
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With: Val (Default = 10)
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[ -k [ Val ] ]
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= Number of deconvolution iterations
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With: Val (Default = 10)
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[ -a --alpha [ aval ] ]
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= Alpha value
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With: aval (Default = 1.5)
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[ -s --stop [ stopval ] ]
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= Stopping criterion
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With: stopval (Default = 0.01)
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----------------------------------------------
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Technique - keyword
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Geometric transfer matrix - "GTM"
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Labbe approach - "LABBE"
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Richardson-Lucy - "RL"
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Van-Cittert - "VC"
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Region-based voxel-wise correction - "RBV"
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RBV with Labbe - "LABBE+RBV"
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RBV with Van-Cittert - "RBV+VC"
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RBV with Richardson-Lucy - "RBV+RL"
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RBV with Labbe and Van-Cittert - "LABBE+RBV+VC"
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RBV with Labbe and Richardson-Lucy- "LABBE+RBV+RL"
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Multi-target correction - "MTC"
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MTC with Labbe - "LABBE+MTC"
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MTC with Van-Cittert - "MTC+VC"
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MTC with Richardson-Lucy - "MTC+RL"
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MTC with Labbe and Van-Cittert - "LABBE+MTC+VC"
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MTC with Labbe and Richardson-Lucy- "LABBE+MTC+RL"
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Iterative Yang - "IY"
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Iterative Yang with Van-Cittert - "IY+VC"
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Iterative Yang with Richardson-Lucy - "IY+RL"
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Muller Gartner - "MG"
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Muller Gartner with Van-Cittert - "MG+VC"
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Muller Gartner with Richardson-Lucy - "MG+RL"
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Examples
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--------
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>>> from ..testing import example_data

‎nipype/interfaces/tests/test_utility.py

Lines changed: 54 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -63,7 +63,6 @@ def increment_array(in_array):
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f2 = pe.MapNode(utility.Function(input_names=['in_array'], output_names=['out_array'], function=increment_array), name='increment_array', iterfield=['in_array'])
6464

6565
wf.connect(f1, 'random_array', f2, 'in_array')
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6766
wf.run()
6867

6968
# Clean up
@@ -167,3 +166,57 @@ def test_csvReader():
167166
yield assert_equal, out.outputs.column_1, ['hello', 'world', 'goodbye']
168167
yield assert_equal, out.outputs.column_2, ['300.1', '5', '0.3']
169168
os.unlink(name)
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def test_aux_connect_function():
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""" This tests excution nodes with multiple inputs and auxiliary
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function inside the Workflow connect function.
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"""
175+
tempdir = os.path.realpath(mkdtemp())
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origdir = os.getcwd()
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os.chdir(tempdir)
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179+
wf = pe.Workflow(name="test_workflow")
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def _gen_tuple(size):
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return [1, ] * size
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def _sum_and_sub_mul(a, b, c):
185+
return (a+b)*c, (a-b)*c
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def _inc(x):
188+
return x + 1
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params = pe.Node(utility.IdentityInterface(fields=['size', 'num']), name='params')
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params.inputs.num = 42
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params.inputs.size = 1
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gen_tuple = pe.Node(utility.Function(input_names=['size'],
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output_names=['tuple'],
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function=_gen_tuple),
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name='gen_tuple')
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ssm = pe.Node(utility.Function(input_names=['a', 'b', 'c'],
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output_names=['sum', 'sub'],
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function=_sum_and_sub_mul),
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name='sum_and_sub_mul')
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split = pe.Node(utility.Split(splits=[1, 1],
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squeeze=True),
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name='split')
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wf.connect([
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(params, gen_tuple, [(("size", _inc), "size")]),
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(params, ssm, [(("num", _inc), "c")]),
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(gen_tuple, split, [("tuple", "inlist")]),
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(split, ssm, [(("out1", _inc), "a"),
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("out2", "b"),
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]),
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])
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wf.run()
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# Clean up
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os.chdir(origdir)
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shutil.rmtree(tempdir)

‎nipype/pipeline/engine/workflows.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -690,7 +690,7 @@ def _configure_exec_nodes(self, graph):
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node.input_source = {}
691691
for edge in graph.in_edges_iter(node):
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data = graph.get_edge_data(*edge)
693-
for sourceinfo, field in sorted(data['connect']):
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for sourceinfo, field in data['connect']:
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node.input_source[field] = \
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(op.join(edge[0].output_dir(),
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'result_%s.pklz' % edge[0].name),

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