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FIX: ANTs' tools maintenance overhaul #3180

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merged 19 commits into from
Mar 9, 2020
Merged

FIX: ANTs' tools maintenance overhaul #3180

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909301e
fix #3178: improve the parsing of ``Atropos``
oesteban Feb 27, 2020
8165242
enh: add a few new utilities to ANTs
oesteban Feb 27, 2020
167f6c9
enh: update ants' interfaces API
oesteban Feb 27, 2020
417b889
sty: black
oesteban Feb 27, 2020
1c5045d
enh,sty: update antsJointFusion + black et al.
oesteban Feb 27, 2020
9e7c997
fix: ``make specs``
oesteban Feb 28, 2020
dfe8501
tst: reduce some complexity and increase coverage
oesteban Feb 28, 2020
dffcb78
fix: copy header for ResampleImageBySpacing
oesteban Feb 28, 2020
cf48cbd
Apply suggestions from code review
oesteban Mar 3, 2020
051c1e5
fix(compat): ensure nibabel < 3 compatiblity of tests
oesteban Mar 4, 2020
774f41d
fix: use ``aggregate_outputs`` instead of ``_list_outputs``
oesteban Mar 4, 2020
0544124
enh: remove ``aggregate_outputs`` duplications, fix InputMultiPath
oesteban Mar 4, 2020
f88add4
fix: roll back under-i/o specs
oesteban Mar 4, 2020
6979cbd
RF: Move header copying to a mixin
effigies Mar 4, 2020
d50c185
STY: black
effigies Mar 4, 2020
545a5fe
MNT: make specs
effigies Mar 4, 2020
292e2e8
Merge pull request #10 from effigies/enh/ants-utils-overhaul
oesteban Mar 4, 2020
135d900
sty: fix unused import
oesteban Mar 5, 2020
4e1d601
fix: consider that some outputs might not be defined
oesteban Mar 8, 2020
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59 changes: 48 additions & 11 deletions nipype/interfaces/ants/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,13 @@
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Top-level namespace for ants."""

# Registraiton programs
# Registration programs
from .registration import (
ANTS,
Registration,
RegistrationSynQuick,
CompositeTransformUtil,
MeasureImageSimilarity,
Registration,
RegistrationSynQuick,
)

# Resampling Programs
Expand All @@ -22,26 +22,63 @@

# Segmentation Programs
from .segmentation import (
AntsJointFusion,
Atropos,
LaplacianThickness,
N4BiasFieldCorrection,
JointFusion,
CorticalThickness,
BrainExtraction,
CorticalThickness,
DenoiseImage,
AntsJointFusion,
JointFusion,
LaplacianThickness,
N4BiasFieldCorrection,
)

# Visualization Programs
from .visualization import ConvertScalarImageToRGB, CreateTiledMosaic

# Utility Programs
from .utils import (
AffineInitializer,
AI,
AverageAffineTransform,
AverageImages,
MultiplyImages,
CreateJacobianDeterminantImage,
AffineInitializer,
ComposeMultiTransform,
CreateJacobianDeterminantImage,
ImageMath,
LabelGeometry,
MultiplyImages,
ResampleImageBySpacing,
ThresholdImage,
)

__all__ = [
"AffineInitializer",
"AI",
"ANTS",
"AntsJointFusion",
"ApplyTransforms",
"ApplyTransformsToPoints",
"Atropos",
"AverageAffineTransform",
"AverageImages",
"BrainExtraction",
"ComposeMultiTransform",
"CompositeTransformUtil",
"ConvertScalarImageToRGB",
"CorticalThickness",
"CreateJacobianDeterminantImage",
"CreateTiledMosaic",
"DenoiseImage",
"ImageMath",
"JointFusion",
"LabelGeometry",
"LaplacianThickness",
"MeasureImageSimilarity",
"MultiplyImages",
"N4BiasFieldCorrection",
"Registration",
"RegistrationSynQuick",
"ResampleImageBySpacing",
"ThresholdImage",
"WarpImageMultiTransform",
"WarpTimeSeriesImageMultiTransform",
]
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