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FIX Ants N4BiasFieldCorrection rescale_intensities bug #3139

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FIX Ants N4BiasFieldCorrection rescale_intensities bug #3139

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12d5186
remove use_default for rescale_intensities trait
salma1601 Jan 4, 2020
5851a63
remove use_default from rescale_intensities
salma1601 Jan 4, 2020
f3a33f4
Merge branch 'master' into ants_rescale_intensities
effigies Mar 16, 2024
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1 change: 0 additions & 1 deletion nipype/interfaces/ants/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -335,7 +335,6 @@ class N4BiasFieldCorrectionInputSpec(ANTSCommandInputSpec):
)
rescale_intensities = traits.Bool(
False,
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There was a move a while back to either remove defaults if unused, or set usedefault=True if the default was specified. In this case, if we're removing usedefault, we should also remove the default.

Suggested change
False,

usedefault=True,
argstr="-r",
min_ver="2.1.0",
desc="""\
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36 changes: 18 additions & 18 deletions nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py
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Expand Up @@ -4,30 +4,30 @@

def test_N4BiasFieldCorrection_inputs():
input_map = dict(
args=dict(argstr="%s",),
bias_image=dict(extensions=None, hash_files=False,),
bspline_fitting_distance=dict(argstr="--bspline-fitting %s",),
bspline_order=dict(requires=["bspline_fitting_distance"],),
convergence_threshold=dict(requires=["n_iterations"],),
copy_header=dict(mandatory=True, usedefault=True,),
dimension=dict(argstr="-d %d", usedefault=True,),
environ=dict(nohash=True, usedefault=True,),
histogram_sharpening=dict(argstr="--histogram-sharpening [%g,%g,%d]",),
input_image=dict(argstr="--input-image %s", extensions=None, mandatory=True,),
mask_image=dict(argstr="--mask-image %s", extensions=None,),
n_iterations=dict(argstr="--convergence %s",),
num_threads=dict(nohash=True, usedefault=True,),
args=dict(argstr="%s"),
bias_image=dict(extensions=None, hash_files=False),
bspline_fitting_distance=dict(argstr="--bspline-fitting %s"),
bspline_order=dict(requires=["bspline_fitting_distance"]),
convergence_threshold=dict(requires=["n_iterations"]),
copy_header=dict(mandatory=True, usedefault=True),
dimension=dict(argstr="-d %d", usedefault=True),
environ=dict(nohash=True, usedefault=True),
histogram_sharpening=dict(argstr="--histogram-sharpening [%g,%g,%d]"),
input_image=dict(argstr="--input-image %s", extensions=None, mandatory=True),
mask_image=dict(argstr="--mask-image %s", extensions=None),
n_iterations=dict(argstr="--convergence %s"),
num_threads=dict(nohash=True, usedefault=True),
output_image=dict(
argstr="--output %s",
hash_files=False,
keep_extension=True,
name_source=["input_image"],
name_template="%s_corrected",
),
rescale_intensities=dict(argstr="-r", min_ver="2.1.0", usedefault=True,),
save_bias=dict(mandatory=True, usedefault=True, xor=["bias_image"],),
shrink_factor=dict(argstr="--shrink-factor %d",),
weight_image=dict(argstr="--weight-image %s", extensions=None,),
rescale_intensities=dict(argstr="-r", min_ver="2.1.0"),
save_bias=dict(mandatory=True, usedefault=True, xor=["bias_image"]),
shrink_factor=dict(argstr="--shrink-factor %d"),
weight_image=dict(argstr="--weight-image %s", extensions=None),
)
inputs = N4BiasFieldCorrection.input_spec()

Expand All @@ -38,7 +38,7 @@ def test_N4BiasFieldCorrection_inputs():

def test_N4BiasFieldCorrection_outputs():
output_map = dict(
bias_image=dict(extensions=None,), output_image=dict(extensions=None,),
bias_image=dict(extensions=None), output_image=dict(extensions=None)
)
outputs = N4BiasFieldCorrection.output_spec()

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