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satrasatra
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Merge pull request #2514 from kesshijordan/satra_fix_specs
FIX: DTITK Interface
2 parents dc09e00 + 62e3456 commit b5ccdab

39 files changed

+1908
-829
lines changed

‎nipype/interfaces/afni/preprocess.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2510,7 +2510,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
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rather than the value stored in the dataset header.""",
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argstr='-TR %g')
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mask = File(
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exist=True,
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exists=True,
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desc="""Only operate on voxels nonzero in the mset dataset.
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++ Voxels outside the mask will be filled with zeros.
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++ If no masking option is given, then all voxels

‎nipype/interfaces/afni/tests/test_auto_TProject.py

Lines changed: 1 addition & 4 deletions
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@@ -32,10 +32,7 @@ def test_TProject_inputs():
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mandatory=True,
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position=1,
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),
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mask=dict(
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argstr='-mask %s',
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exist=True,
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),
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mask=dict(argstr='-mask %s', ),
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noblock=dict(argstr='-noblock', ),
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norm=dict(argstr='-norm', ),
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num_threads=dict(

‎nipype/interfaces/dtitk/__init__.py

Lines changed: 5 additions & 7 deletions
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@@ -6,10 +6,8 @@
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"""
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# from .base import ()
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from .registration import (RigidTask, AffineTask, DiffeoTask,
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ComposeXfmTask, diffeoSymTensor3DVolTask,
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affSymTensor3DVolTask, affScalarVolTask,
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diffeoScalarVolTask)
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from .utils import (TVAdjustOriginTask, TVAdjustVoxSpTask,
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SVAdjustVoxSpTask, TVResampleTask, SVResampleTask,
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TVtoolTask, BinThreshTask)
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from .registration import (Rigid, Affine, Diffeo,
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ComposeXfm, DiffeoSymTensor3DVol, AffSymTensor3DVol,
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AffScalarVol, DiffeoScalarVol)
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from .utils import (TVAdjustVoxSp, SVAdjustVoxSp, TVResample, SVResample,
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TVtool, BinThresh)

‎nipype/interfaces/dtitk/base.py

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Original file line numberDiff line numberDiff line change
@@ -13,6 +13,12 @@
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* Rigid Tensor Registration
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* Affine Tensor Registration
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* Diffeomorphic Tensor Registration
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* Combine affiine and diffeomorphic transforms
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* Application of transform to tensor and scalar volumes
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* Threshold and Binarize
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* Adjusting the voxel space of tensor and scalar volumes
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* Resampling tensor and scalar volumes
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* Calculation of tensor metrics from tensor volume
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Examples
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--------
@@ -28,10 +34,26 @@
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from ...utils.filemanip import fname_presuffix
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from ..base import CommandLine
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from nipype.interfaces.fsl.base import Info
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import warnings
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LOGGER = logging.getLogger('interface')
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class DTITKRenameMixin(object):
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def __init__(self, *args, **kwargs):
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classes = [cls.__name__ for cls in self.__class__.mro()]
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dep_name = classes[0]
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rename_idx = classes.index('DTITKRenameMixin')
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new_name = classes[rename_idx + 1]
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warnings.warn('The {} interface has been renamed to {}\n'
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'Please see the documentation for DTI-TK '
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'interfaces, as some inputs have been '
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'added or renamed for clarity.'
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''.format(dep_name, new_name),
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DeprecationWarning)
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super(DTITKRenameMixin, self).__init__(*args, **kwargs)
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class CommandLineDtitk(CommandLine):
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def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,

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