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Commit ecd5871

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Merge pull request #3447 from jdkent/enh/add_Text2Vest
[ENH] Add Text2Vest and Vest2Text interfaces
2 parents f8f7fb5 + 62d8c46 commit ecd5871

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6 files changed

+190
-0
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6 files changed

+190
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‎nipype/interfaces/fsl/__init__.py‎

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@@ -69,6 +69,8 @@
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RobustFOV,
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CopyGeom,
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MotionOutliers,
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Text2Vest,
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Vest2Text,
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)
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from .epi import (
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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..utils import Text2Vest
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def test_Text2Vest_inputs():
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input_map = dict(
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args=dict(
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argstr="%s",
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),
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environ=dict(
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nohash=True,
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usedefault=True,
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),
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in_file=dict(
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argstr="%s",
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extensions=None,
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mandatory=True,
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position=0,
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),
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out_file=dict(
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argstr="%s",
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extensions=None,
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mandatory=True,
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position=1,
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),
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output_type=dict(),
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)
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inputs = Text2Vest.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_Text2Vest_outputs():
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output_map = dict(
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out_file=dict(
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extensions=None,
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),
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)
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outputs = Text2Vest.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value
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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..utils import Vest2Text
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def test_Vest2Text_inputs():
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input_map = dict(
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args=dict(
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argstr="%s",
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),
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environ=dict(
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nohash=True,
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usedefault=True,
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),
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in_file=dict(
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argstr="%s",
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extensions=None,
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mandatory=True,
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position=0,
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),
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out_file=dict(
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argstr="%s",
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extensions=None,
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position=1,
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usedefault=True,
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),
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output_type=dict(),
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)
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inputs = Vest2Text.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_Vest2Text_outputs():
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output_map = dict(
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out_file=dict(
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extensions=None,
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),
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)
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outputs = Vest2Text.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

‎nipype/interfaces/fsl/utils.py‎

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@@ -2834,3 +2834,92 @@ class MotionOutliers(FSLCommand):
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input_spec = MotionOutliersInputSpec
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output_spec = MotionOutliersOutputSpec
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_cmd = "fsl_motion_outliers"
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class Text2VestInputSpec(FSLCommandInputSpec):
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in_file = File(
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exists=True,
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mandatory=True,
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desc="plain text file representing your design, contrast, or f-test matrix",
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argstr="%s",
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position=0,
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)
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out_file = File(
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mandatory=True,
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desc=(
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"file name to store matrix data in the format used by FSL tools"
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" (e.g., design.mat, design.con design.fts)"
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),
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argstr="%s",
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position=1,
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)
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class Text2VestOutputSpec(TraitedSpec):
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out_file = File(desc="matrix data in the format used by FSL tools")
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class Text2Vest(FSLCommand):
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"""
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Use FSL Text2Vest`https://web.mit.edu/fsl_v5.0.10/fsl/doc/wiki/GLM(2f)CreatingDesignMatricesByHand.html`_
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to convert your plain text design matrix data into the format used by the FSL tools.
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Examples
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--------
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>>> from nipype.interfaces.fsl import Text2Vest
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>>> t2v = Text2Vest()
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>>> t2v.inputs.in_file = "design.txt"
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>>> t2v.inputs.out_file = "design.mat"
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>>> t2v.cmdline
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'Text2Vest design.txt design.mat'
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>>> res = t2v.run() # doctest: +SKIP
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"""
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input_spec = Text2VestInputSpec
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output_spec = Text2VestOutputSpec
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_cmd = "Text2Vest"
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class Vest2TextInputSpec(FSLCommandInputSpec):
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in_file = File(
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exists=True,
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mandatory=True,
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desc="matrix data stored in the format used by FSL tools",
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argstr="%s",
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position=0,
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)
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out_file = File(
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"design.txt",
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usedefault=True,
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desc="file name to store text output from matrix",
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argstr="%s",
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position=1,
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)
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class Vest2TextOutputSpec(TraitedSpec):
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out_file = File(desc="plain text representation of FSL matrix")
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class Vest2Text(FSLCommand):
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"""
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Use FSL Vest2Text`https://web.mit.edu/fsl_v5.0.10/fsl/doc/wiki/GLM(2f)CreatingDesignMatricesByHand.html`_
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to convert your design.mat design.con and design.fts files into plain text.
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Examples
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--------
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>>> from nipype.interfaces.fsl import Vest2Text
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>>> v2t = Vest2Text()
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>>> v2t.inputs.in_file = "design.mat"
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>>> v2t.cmdline
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'Vest2Text design.mat design.txt'
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>>> res = v2t.run() # doctest: +SKIP
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"""
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input_spec = Vest2TextInputSpec
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output_spec = Vest2TextOutputSpec
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_cmd = "Vest2Text"

‎nipype/testing/data/design.mat‎

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/NumWaves 3
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/NumPoints 3
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/Matrix
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0 0 0
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0 0 0
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0 0 0

‎nipype/testing/data/design.txt‎

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0 0 0
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0 0 0
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0 0 0

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