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Merge remote-tracking branch 'nipy/master' into fix/mrtrix3-tckgen-option
2 parents 8e2fad2 + ebbd062 commit beb062c

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4 files changed

+34
-15
lines changed

4 files changed

+34
-15
lines changed

.travis.yml

+3
Original file line numberDiff line numberDiff line change
@@ -60,6 +60,9 @@ matrix:
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NIPYPE_EXTRAS="doc,tests,nipy,profiler"
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EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS"
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CI_SKIP_TEST=1
63+
allow_failures:
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- python: 2.7
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env: INSTALL_DEB_DEPENDECIES=true NIPYPE_EXTRAS="doc,tests,nipy,profiler" EXTRA_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --find-links $PRE_WHEELS" CI_SKIP_TEST=1
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addons:
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apt:

nipype/info.py

+3-1
Original file line numberDiff line numberDiff line change
@@ -105,6 +105,7 @@ def get_nipype_gitversion():
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# Numpy bug in python 3.7:
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# https://www.opensourceanswers.com/blog/you-shouldnt-use-python-37-for-data-science-right-now.html
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NUMPY_MIN_VERSION_37 = '1.15.3'
108+
NUMPY_BAD_VERSION_27 = '1.16.0'
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SCIPY_MIN_VERSION = '0.14'
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TRAITS_MIN_VERSION = '4.6'
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DATEUTIL_MIN_VERSION = '2.2'
@@ -136,7 +137,8 @@ def get_nipype_gitversion():
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REQUIRES = [
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'nibabel>=%s' % NIBABEL_MIN_VERSION,
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'networkx>=%s' % NETWORKX_MIN_VERSION,
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'numpy>=%s ; python_version < "3.7"' % NUMPY_MIN_VERSION,
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'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27),
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'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION,
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'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37,
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'python-dateutil>=%s' % DATEUTIL_MIN_VERSION,
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'scipy>=%s' % SCIPY_MIN_VERSION,

nipype/interfaces/ants/segmentation.py

+20-6
Original file line numberDiff line numberDiff line change
@@ -207,13 +207,27 @@ class LaplacianThicknessInputSpec(ANTSCommandInputSpec):
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name_template='%s_thickness',
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keep_extension=True,
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hash_files=False)
210-
smooth_param = traits.Float(argstr='smoothparam=%d', desc='', position=4)
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smooth_param = traits.Float(
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argstr='%f',
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desc='Sigma of the Laplacian Recursive Image Filter (defaults to 1)',
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position=4)
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prior_thickness = traits.Float(
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argstr='priorthickval=%d', desc='', position=5)
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dT = traits.Float(argstr='dT=%d', desc='', position=6)
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sulcus_prior = traits.Bool(argstr='use-sulcus-prior', desc='', position=7)
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opt_tolerance = traits.Float(
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argstr='optional-laplacian-tolerance=%d', desc='', position=8)
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argstr='%f',
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desc='Prior thickness (defaults to 500)',
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position=5)
218+
dT = traits.Float(
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argstr='%f',
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desc='Time delta used during integration (defaults to 0.01)',
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position=6)
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sulcus_prior = traits.Float(
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argstr='%f',
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desc='Positive floating point number for sulcus prior. '
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'Authors said that 0.15 might be a reasonable value',
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position=7)
227+
tolerance = traits.Float(
228+
argstr='%f',
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desc='Tolerance to reach during optimization (defaults to 0.001)',
230+
position=8)
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class LaplacianThicknessOutputSpec(TraitedSpec):

nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py

+8-8
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ def test_LaplacianThickness_inputs():
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input_map = dict(
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args=dict(argstr='%s', ),
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dT=dict(
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argstr='dT=%d',
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argstr='%f',
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position=6,
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),
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environ=dict(
@@ -30,10 +30,6 @@ def test_LaplacianThickness_inputs():
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nohash=True,
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usedefault=True,
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),
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opt_tolerance=dict(
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argstr='optional-laplacian-tolerance=%d',
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position=8,
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),
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output_image=dict(
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argstr='%s',
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hash_files=False,
@@ -43,17 +39,21 @@ def test_LaplacianThickness_inputs():
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position=3,
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),
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prior_thickness=dict(
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argstr='priorthickval=%d',
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argstr='%f',
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position=5,
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),
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smooth_param=dict(
50-
argstr='smoothparam=%d',
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argstr='%f',
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position=4,
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),
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sulcus_prior=dict(
54-
argstr='use-sulcus-prior',
50+
argstr='%f',
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position=7,
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),
53+
tolerance=dict(
54+
argstr='%f',
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position=8,
56+
),
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)
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inputs = LaplacianThickness.input_spec()
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