enh: remove aggregate_outputs duplications, fix InputMultiPath

Author: oesteban

nipype/interfaces/ants/base.py

@@ -7,6 +7,7 @@
 # Local imports
 from ... import logging, LooseVersion
 from ..base import CommandLine, CommandLineInputSpec, traits, isdefined, PackageInfo
+from ...utils.imagemanip import copy_header as _copy_header
 
 iflogger = logging.getLogger("nipype.interface")
 
@@ -121,3 +122,17 @@ def set_default_num_threads(cls, num_threads):
     @property
     def version(self):
         return Info.version()
+
+
+class FixHeaderANTSCommand(ANTSCommand):
+    """Fix header if the copy_header input is on."""
+
+    def aggregate_outputs(self, runtime=None, needed_outputs=None):
+        """Overload the aggregation with header replacement, if required."""
+        outputs = super(FixHeaderANTSCommand, self).aggregate_outputs(
+            runtime, needed_outputs)
+        if self.inputs.copy_header:  # Fix headers
+            _copy_header(
+                self.inputs.op1, outputs["output_image"], keep_dtype=True
+            )
+        return outputs

nipype/interfaces/ants/tests/test_auto_FixHeaderANTSCommand.py

@@ -0,0 +1,15 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..base import FixHeaderANTSCommand
+
+
+def test_FixHeaderANTSCommand_inputs():
+    input_map = dict(
+        args=dict(argstr="%s",),
+        environ=dict(nohash=True, usedefault=True,),
+        num_threads=dict(nohash=True, usedefault=True,),
+    )
+    inputs = FixHeaderANTSCommand.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value

nipype/interfaces/ants/utils.py

@@ -1,8 +1,7 @@
 """ANTs' utilities."""
 import os
-from ...utils.imagemanip import copy_header as _copy_header
 from ..base import traits, isdefined, TraitedSpec, File, Str, InputMultiObject
-from .base import ANTSCommandInputSpec, ANTSCommand
+from .base import ANTSCommandInputSpec, ANTSCommand, FixHeaderANTSCommand
 
 
 class _ImageMathInputSpec(ANTSCommandInputSpec):
@@ -68,7 +67,7 @@ class _ImageMathOuputSpec(TraitedSpec):
     output_image = File(exists=True, desc="output image file")
 
 
-class ImageMath(ANTSCommand):
+class ImageMath(FixHeaderANTSCommand):
     """
     Operations over images.
 
@@ -98,16 +97,6 @@ class ImageMath(ANTSCommand):
     input_spec = _ImageMathInputSpec
     output_spec = _ImageMathOuputSpec
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
-        """Overload the aggregation with header replacement, if required."""
-        outputs = super(ImageMath, self).aggregate_outputs(
-            runtime, needed_outputs)
-        if self.inputs.copy_header:  # Fix headers
-            _copy_header(
-                self.inputs.op1, outputs["output_image"], keep_dtype=True
-            )
-        return outputs
-
 
 class _ResampleImageBySpacingInputSpec(ANTSCommandInputSpec):
     dimension = traits.Int(
@@ -157,7 +146,7 @@ class _ResampleImageBySpacingOutputSpec(TraitedSpec):
     output_image = File(exists=True, desc="resampled file")
 
 
-class ResampleImageBySpacing(ANTSCommand):
+class ResampleImageBySpacing(FixHeaderANTSCommand):
     """
     Resample an image with a given spacing.
 
@@ -203,16 +192,6 @@ def _format_arg(self, name, trait_spec, value):
 
         return super(ResampleImageBySpacing, self)._format_arg(name, trait_spec, value)
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
-        """Overload the aggregation with header replacement, if required."""
-        outputs = super(ResampleImageBySpacing, self).aggregate_outputs(
-            runtime, needed_outputs)
-        if self.inputs.copy_header:  # Fix headers
-            _copy_header(
-                self.inputs.input_image, outputs["output_image"], keep_dtype=True
-            )
-        return outputs
-
 
 class _ThresholdImageInputSpec(ANTSCommandInputSpec):
     dimension = traits.Int(
@@ -269,7 +248,7 @@ class _ThresholdImageOutputSpec(TraitedSpec):
     output_image = File(exists=True, desc="resampled file")
 
 
-class ThresholdImage(ANTSCommand):
+class ThresholdImage(FixHeaderANTSCommand):
     """
     Apply thresholds on images.
 
@@ -299,16 +278,6 @@ class ThresholdImage(ANTSCommand):
     input_spec = _ThresholdImageInputSpec
     output_spec = _ThresholdImageOutputSpec
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
-        """Overload the aggregation with header replacement, if required."""
-        outputs = super(ThresholdImage, self).aggregate_outputs(
-            runtime, needed_outputs)
-        if self.inputs.copy_header:  # Fix headers
-            _copy_header(
-                self.inputs.input_image, outputs["output_image"], keep_dtype=True
-            )
-        return outputs
-
 
 class _AIInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(
@@ -465,7 +434,7 @@ class AverageAffineTransformInputSpec(ANTSCommandInputSpec):
         position=1,
         desc="Outputfname.txt: the name of the resulting transform.",
     )
-    transforms = InputMultiPath(
+    transforms = InputMultiObject(
         File(exists=True),
         argstr="%s",
         mandatory=True,
@@ -526,7 +495,7 @@ class AverageImagesInputSpec(ANTSCommandInputSpec):
         desc="Normalize: if true, the 2nd image is divided by its mean. "
         "This will select the largest image to average into.",
     )
-    images = InputMultiPath(
+    images = InputMultiObject(
         File(exists=True),
         argstr="%s",
         mandatory=True,
@@ -767,7 +736,7 @@ class ComposeMultiTransformInputSpec(ANTSCommandInputSpec):
         position=2,
         desc="Reference image (only necessary when output is warpfield)",
     )
-    transforms = InputMultiPath(
+    transforms = InputMultiObject(
         File(exists=True),
         argstr="%s",
         mandatory=True,