[ENH] Add interface to antsAffineInitializer

Adds a very simple interface to `antsAffineInitializer`, which is used
in the `antsBrainExtraction.sh` script to initialize the registration to
template.

Author: oesteban

nipype/interfaces/ants/__init__.py

@@ -19,4 +19,5 @@
 from .visualization import ConvertScalarImageToRGB, CreateTiledMosaic
 
 # Utility Programs
-from .utils import AverageAffineTransform, AverageImages, MultiplyImages, CreateJacobianDeterminantImage
+from .utils import (AverageAffineTransform, AverageImages, MultiplyImages,
+                    CreateJacobianDeterminantImage, AffineInitializer)

nipype/interfaces/ants/tests/test_auto_AffineInitializer.py

@@ -0,0 +1,64 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import AffineInitializer
+
+
+def test_AffineInitializer_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    dimension=dict(argstr='%s',
+    position=0,
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    fixed_image=dict(argstr='%s',
+    mandatory=True,
+    position=1,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    local_search=dict(argstr='%d',
+    position=7,
+    usedefault=True,
+    ),
+    moving_image=dict(argstr='%s',
+    mandatory=True,
+    position=2,
+    ),
+    out_file=dict(argstr='%s',
+    position=3,
+    usedefault=True,
+    ),
+    principal_axes=dict(argstr='%d',
+    position=6,
+    usedefault=True,
+    ),
+    radian_fraction=dict(argstr='%f',
+    position=5,
+    usedefault=True,
+    ),
+    search_factor=dict(argstr='%f',
+    position=4,
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = AffineInitializer.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_AffineInitializer_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = AffineInitializer.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/ants/utils.py

@@ -12,7 +12,8 @@
 import os
 
 from ...utils.filemanip import split_filename
-from ..base import TraitedSpec, File, traits, isdefined, InputMultiPath
+from ..base import (TraitedSpec, File, traits, isdefined, InputMultiPath,
+                    CommandLine, CommandLineInputSpec)
 from .base import ANTSCommand, ANTSCommandInputSpec
 
 
@@ -178,3 +179,49 @@ def _list_outputs(self):
         outputs['jacobian_image'] = os.path.abspath(
             self.inputs.outputImage)
         return outputs
+
+
+class AffineInitializerInputSpec(CommandLineInputSpec):
+    dimension = traits.Enum(3, 2, usedefault=True, position=0, argstr='%s',
+                            desc='dimension')
+    fixed_image = File(exists=True, mandatory=True, position=1, argstr='%s',
+                       desc='reference image')
+    moving_image = File(exists=True, mandatory=True, position=2, argstr='%s',
+                        desc='moving image')
+    out_file = File('transform.mat', usedefault=True, position=3, argstr='%s',
+                    desc='output transform file')
+    # Defaults in antsBrainExtraction.sh -> 15 0.1 0 10
+    search_factor = traits.Float(15.0, usedefault=True, position=4, argstr='%f',
+                                 desc='increments (degrees) for affine search')
+    radian_fraction = traits.Range(0.0, 1.0, value=0.1, usedefault=True, position=5,
+                                   argstr='%f', desc='search this arc +/- principal axes')
+    principal_axes = traits.Bool(
+        False, usedefault=True, position=6, argstr='%d',
+        desc='whether the rotation is searched around an initial principal axis alignment.')
+    local_search = traits.Int(
+        10, usedefault=True, position=7, argstr='%d',
+        desc=' determines if a local optimization is run at each search point for the set '
+             'number of iterations')
+
+class AffineInitializerOutputSpec(TraitedSpec):
+    out_file = File(desc='output transform file')
+
+
+class AffineInitializer(CommandLine):
+    """
+    Initialize an affine transform (as in antsBrainExtraction.sh)
+
+    >>> from nipype.interfaces.ants import AffineInitializer
+    >>> init = AffineInitializer()
+    >>> init.inputs.fixed_image = 'fixed1.nii'
+    >>> init.inputs.moving_image = 'moving1.nii'
+    >>> init.cmdline # doctest: +ALLOW_UNICODE
+    'antsAffineInitializer 3 fixed1.nii moving1.nii transform.mat 15.000000 0.100000 0 10'
+
+    """
+    _cmd = 'antsAffineInitializer'
+    input_spec = AffineInitializerInputSpec
+    output_spec = AffineInitializerOutputSpec
+
+    def _list_outputs(self):
+        return {'out_file': os.path.abspath(self.inputs.out_file)}