Added ComposeMultiTransform to ants.utils

Author: Gilles86

nipype/interfaces/ants/__init__.py

@@ -20,4 +20,5 @@
 
 # Utility Programs
 from .utils import (AverageAffineTransform, AverageImages, MultiplyImages,
-                    CreateJacobianDeterminantImage, AffineInitializer)
+                    CreateJacobianDeterminantImage, AffineInitializer,
+                    ComposeMultiTransform)

nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py

@@ -0,0 +1,52 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import ComposeMultiTransform
+
+
+def test_ComposeMultiTransform_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    dimension=dict(argstr='%d',
+    mandatory=True,
+    position=0,
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    output_transform=dict(argstr='%s',
+    mandatory=True,
+    position=1,
+    ),
+    reference_image=dict(argstr='%s',
+    mandatory=False,
+    position=2,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    transforms=dict(argstr='%s',
+    mandatory=True,
+    position=3,
+    ),
+    )
+    inputs = ComposeMultiTransform.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_ComposeMultiTransform_outputs():
+    output_map = dict(output_transform=dict(),
+    )
+    outputs = ComposeMultiTransform.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

@@ -225,3 +225,46 @@ class AffineInitializer(ANTSCommand):
 
     def _list_outputs(self):
         return {'out_file': os.path.abspath(self.inputs.out_file)}
+   
+
+class ComposeMultiTransformInputSpec(ANTSCommandInputSpec):
+    dimension = traits.Enum(3, 2, argstr='%d', usedefault=True, mandatory=True,
+                            position=0, desc='image dimension (2 or 3)')
+    output_transform = File(argstr='%s', mandatory=True, position=1,
+                                   desc='Outputfname.txt: the name of the resulting transform.')
+    reference_image = File(argstr='%s', mandatory=False, position=2,
+                                   desc='Reference image (only necessary when output is warpfield)')
+    transforms = InputMultiPath(File(exists=True), argstr='%s', mandatory=True,
+                                position=3, desc='transforms to average')
+
+
+class ComposeMultiTransformOutputSpec(TraitedSpec):
+    output_transform = File(exists=True, desc='Composed transform file')
+
+
+class ComposeMultiTransform(ANTSCommand):
+    """
+    Examples
+    --------
+    >>> from nipype.interfaces.ants import ComposeMultiTransform
+    >>> compose = ComposeMultiTransform()
+    >>> compose_transform.inputs.dimension = 3
+    >>> compose_transform.inputs.transforms = ['struct_to_template.mat', 'func_to_struct.mat']
+    >>> compose_transform.inputs.output_transform = 'func_to_template.mat'
+    >>> compose_transform.cmdline # doctest: +ALLOW_UNICODE
+    'TODO TODO TODO'
+    """
+    _cmd = 'ComposeMultiTransform'
+    input_spec = ComposeMultiTransformInputSpec
+    output_spec = ComposeMultiTransformOutputSpec
+
+    def _format_arg(self, opt, spec, val):
+        return super(ComposeMultiTransform, self)._format_arg(opt, spec, val)
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['output_transform'] = os.path.abspath(
+            self.inputs.output_transform)
+        return outputs
+
+