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Editing the tests and docstring
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‎nipype/interfaces/niftyreg/reg.py

Lines changed: 21 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -15,8 +15,8 @@
1515
>>> os.chdir(datadir)
1616
"""
1717

18-
from __future__ import print_function, division, \
19-
unicode_literals, absolute_import
18+
from __future__ import (print_function, division, unicode_literals,
19+
absolute_import)
2020
from builtins import staticmethod
2121
import os
2222
import warnings
@@ -149,15 +149,15 @@ class RegAladin(NiftyRegCommand):
149149
150150
Examples
151151
--------
152-
>>> from nipype.interfaces.niftyreg import RegAladin
153-
>>> node = RegAladin() # doctest: +SKIP
154-
>>> node.inputs.ref_file = 'ref.nii.gz' # doctest: +SKIP
155-
>>> node.inputs.flo_file = 'flo.nii.gz' # doctest: +SKIP
156-
>>> node.inputs.rmask_file = 'rmask.nii.gz' # doctest: +SKIP
157-
>>> node.inputs.omp_core_val = 4 # doctest: +SKIP
158-
>>> node.cmdline # doctest: +SKIP
159-
'reg_aladin -aff flo_aff.txt -flo flo.nii.gz -omp 4 -ref ref.nii.gz \
160-
-rmask rmask.nii.gz -res flo_res.nii.gz'
152+
>>> from nipype.interfaces import niftyreg
153+
>>> node = niftyreg.RegAladin()
154+
>>> node.inputs.ref_file = 'ref.nii.gz'
155+
>>> node.inputs.flo_file = 'flo.nii.gz'
156+
>>> node.inputs.rmask_file = 'rmask.nii.gz'
157+
>>> node.inputs.omp_core_val = 4
158+
>>> node.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
159+
'reg_aladin -aff .../flo_aff.txt -flo flo.nii.gz -omp 4 -ref ref.nii.gz \
160+
-rmask rmask.nii.gz -res .../flo_res.nii.gz'
161161
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"""
163163
_cmd = get_custom_path('reg_aladin')
@@ -379,15 +379,16 @@ class RegF3D(NiftyRegCommand):
379379
380380
Examples
381381
--------
382-
>>> from nipype.interfaces.niftyreg import RegF3D
383-
>>> node = RegF3D() # doctest: +SKIP
384-
>>> node.inputs.ref_file = 'ref.nii.gz' # doctest: +SKIP
385-
>>> node.inputs.flo_file = 'flo.nii.gz' # doctest: +SKIP
386-
>>> node.inputs.rmask_file = 'rmask.nii.gz' # doctest: +SKIP
387-
>>> node.inputs.omp_core_val = 4 # doctest: +SKIP
388-
>>> node.cmdline # doctest: +SKIP
389-
'reg_f3d -be 0.100000 -cpp flo_cpp.nii.gz -flo flo.nii.gz -le 0.100000 \
390-
-omp 4 -ref ref.nii.gz -res flo_res.nii.gz -rmask rmask.nii.gz -vel'
382+
>>> from nipype.interfaces import niftyreg
383+
>>> node = niftyreg.RegF3D()
384+
>>> node.inputs.ref_file = 'ref.nii.gz'
385+
>>> node.inputs.flo_file = 'flo.nii.gz'
386+
>>> node.inputs.rmask_file = 'rmask.nii.gz'
387+
>>> node.inputs.omp_core_val = 4
388+
>>> node.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
389+
'reg_f3d -be 0.100000 -cpp .../flo_cpp.nii.gz -flo flo.nii.gz -le \
390+
0.100000 -omp 4 -ref ref.nii.gz -res .../flo_res.nii.gz -rmask rmask.nii.gz \
391+
-vel'
391392
392393
"""
393394
_cmd = get_custom_path('reg_f3d')

‎nipype/interfaces/niftyreg/regutils.py

Lines changed: 43 additions & 44 deletions
Original file line numberDiff line numberDiff line change
@@ -14,8 +14,8 @@
1414
>>> os.chdir(datadir)
1515
"""
1616

17-
from __future__ import print_function, division, \
18-
unicode_literals, absolute_import
17+
from __future__ import (print_function, division, unicode_literals,
18+
absolute_import)
1919
from builtins import len, open, property, super
2020
import warnings
2121
import os
@@ -102,16 +102,16 @@ class RegResample(NiftyRegCommand):
102102
103103
Examples
104104
--------
105-
>>> from nipype.interfaces.niftyreg import RegResample
106-
>>> node = RegResample() # doctest: +SKIP
107-
>>> node.inputs.ref_file = 'ref.nii.gz' # doctest: +SKIP
108-
>>> node.inputs.flo_file = 'flo.nii.gz' # doctest: +SKIP
109-
>>> node.inputs.trans_file = 'warpfield.nii.gz' # doctest: +SKIP
110-
>>> node.inputs.inter_val = 'LIN' # doctest: +SKIP
111-
>>> node.inputs.omp_core_val = 4 # doctest: +SKIP
112-
>>> node.cmdline # doctest: +SKIP
105+
>>> from nipype.interfaces import niftyreg
106+
>>> node = niftyreg.RegResample()
107+
>>> node.inputs.ref_file = 'ref.nii.gz'
108+
>>> node.inputs.flo_file = 'flo.nii.gz'
109+
>>> node.inputs.trans_file = 'warpfield.nii.gz'
110+
>>> node.inputs.inter_val = 'LIN'
111+
>>> node.inputs.omp_core_val = 4
112+
>>> node.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
113113
'reg_resample -flo flo.nii.gz -inter 1 -omp 4 -ref ref.nii.gz -trans \
114-
warpfield.nii.gz -res flo_res.nii.gz'
114+
warpfield.nii.gz -res .../flo_res.nii.gz'
115115
116116
"""
117117
_cmd = get_custom_path('reg_resample')
@@ -175,14 +175,14 @@ class RegJacobian(NiftyRegCommand):
175175
176176
Examples
177177
--------
178-
>>> from nipype.interfaces.niftyreg import RegJacobian
179-
>>> node = RegJacobian() # doctest: +SKIP
180-
>>> node.inputs.ref_file = 'ref.nii.gz' # doctest: +SKIP
181-
>>> node.inputs.trans_file = 'warpfield.nii.gz' # doctest: +SKIP
182-
>>> node.inputs.omp_core_val = 4 # doctest: +SKIP
183-
>>> node.cmdline # doctest: +SKIP
178+
>>> from nipype.interfaces import niftyreg
179+
>>> node = niftyreg.RegJacobian()
180+
>>> node.inputs.ref_file = 'ref.nii.gz'
181+
>>> node.inputs.trans_file = 'warpfield.nii.gz'
182+
>>> node.inputs.omp_core_val = 4
183+
>>> node.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
184184
'reg_jacobian -omp 4 -ref ref.nii.gz -trans warpfield.nii.gz -jac \
185-
warpfield_jac.nii.gz'
185+
.../warpfield_jac.nii.gz'
186186
187187
"""
188188
_cmd = get_custom_path('reg_jacobian')
@@ -296,13 +296,13 @@ class RegTools(NiftyRegCommand):
296296
297297
Examples
298298
--------
299-
>>> from nipype.interfaces.niftyreg import RegTools
300-
>>> node = RegTools() # doctest: +SKIP
301-
>>> node.inputs.in_file = 'im1.nii.gz' # doctest: +SKIP
302-
>>> node.inputs.mul_val = 4 # doctest: +SKIP
303-
>>> node.inputs.omp_core_val = 4 # doctest: +SKIP
304-
>>> node.cmdline # doctest: +SKIP
305-
'reg_tools -in im1.nii.gz -mul 4.0 -omp 4 -out im1_tools.nii.gz'
299+
>>> from nipype.interfaces import niftyreg
300+
>>> node = niftyreg.RegTools()
301+
>>> node.inputs.in_file = 'im1.nii.gz'
302+
>>> node.inputs.mul_val = 4
303+
>>> node.inputs.omp_core_val = 4
304+
>>> node.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
305+
'reg_tools -in im1.nii.gz -mul 4.0 -omp 4 -out .../im1_tools.nii.gz'
306306
307307
"""
308308
_cmd = get_custom_path('reg_tools')
@@ -403,14 +403,13 @@ class RegAverage(NiftyRegCommand):
403403
404404
Examples
405405
--------
406-
>>> from nipype.interfaces.niftyreg import RegAverage
407-
>>> node = RegAverage() # doctest: +SKIP
406+
>>> from nipype.interfaces import niftyreg
407+
>>> node = niftyreg.RegAverage()
408408
>>> one_file = 'im1.nii'
409409
>>> two_file = 'im2.nii'
410410
>>> three_file = 'im3.nii'
411-
>>> node.inputs.avg_files = [one_file, two_file, three_file] \
412-
# doctest: +SKIP
413-
>>> node.cmdline # doctest: +SKIP
411+
>>> node.inputs.avg_files = [one_file, two_file, three_file]
412+
>>> node.cmdline
414413
'reg_average --cmd_file reg_average_cmd'
415414
416415
"""
@@ -605,12 +604,12 @@ class RegTransform(NiftyRegCommand):
605604
606605
Examples
607606
--------
608-
>>> from nipype.interfaces.niftyreg import RegResample
609-
>>> node = RegTransform() # doctest: +SKIP
610-
>>> node.inputs.def_input = 'warpfield.nii' # doctest: +SKIP
611-
>>> node.inputs.omp_core_val = 4 # doctest: +SKIP
612-
>>> node.cmdline # doctest: +SKIP
613-
'reg_transform -omp 4 -def warpfield.nii warpfield_trans.nii.gz'
607+
>>> from nipype.interfaces import niftyreg
608+
>>> node = niftyreg.RegTransform()
609+
>>> node.inputs.def_input = 'warpfield.nii'
610+
>>> node.inputs.omp_core_val = 4
611+
>>> node.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
612+
'reg_transform -omp 4 -def warpfield.nii .../warpfield_trans.nii.gz'
614613
615614
"""
616615
_cmd = get_custom_path('reg_transform')
@@ -717,14 +716,14 @@ class RegMeasure(NiftyRegCommand):
717716
718717
Examples
719718
--------
720-
>>> from nipype.interfaces.niftyreg import RegMeasure
721-
>>> node = RegMeasure() # doctest: +SKIP
722-
>>> node.inputs.ref_file = 'im1.nii' # doctest: +SKIP
723-
>>> node.inputs.flo_file = 'im2.nii' # doctest: +SKIP
724-
>>> node.inputs.measure_type = 'lncc' # doctest: +SKIP
725-
>>> node.inputs.omp_core_val = 4 # doctest: +SKIP
726-
>>> node.cmdline # doctest: +SKIP
727-
'reg_measure -flo {flo} -lncc -omp 4 -out {out} -ref {ref}'
719+
>>> from nipype.interfaces import niftyreg
720+
>>> node = niftyreg.RegMeasure()
721+
>>> node.inputs.ref_file = 'im1.nii'
722+
>>> node.inputs.flo_file = 'im2.nii'
723+
>>> node.inputs.measure_type = 'lncc'
724+
>>> node.inputs.omp_core_val = 4
725+
>>> node.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
726+
'reg_measure -flo im2.nii -lncc -omp 4 -out .../im2_lncc.txt -ref im1.nii'
728727
729728
"""
730729
_cmd = get_custom_path('reg_measure')

‎nipype/interfaces/niftyreg/tests/test_regutils.py

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -185,10 +185,6 @@ def test_reg_average():
185185
# Check if the command is properly defined
186186
assert nr_average.cmd == get_custom_path('reg_average')
187187

188-
# test raising error with mandatory args absent
189-
with pytest.raises(ValueError):
190-
nr_average.run()
191-
192188
# Average niis
193189
one_file = example_data('im1.nii')
194190
two_file = example_data('im2.nii')

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