Merge pull request #3236 from nipy/oesteban-patch-1

FIX: ANTs' utilities revision - bug fixes and add more operations to ``ants.ImageMath``

Author: oesteban

nipype/interfaces/ants/tests/test_auto_ResampleImageBySpacing.py

@@ -7,7 +7,6 @@ def test_ResampleImageBySpacing_inputs():
         addvox=dict(argstr="%d", position=6, requires=["apply_smoothing"],),
         apply_smoothing=dict(argstr="%d", position=5,),
         args=dict(argstr="%s",),
-        copy_header=dict(mandatory=True, usedefault=True,),
         dimension=dict(argstr="%d", position=1, usedefault=True,),
         environ=dict(nohash=True, usedefault=True,),
         input_image=dict(argstr="%s", extensions=None, mandatory=True, position=2,),

nipype/interfaces/ants/utils.py

@@ -1,5 +1,6 @@
 """ANTs' utilities."""
 import os
+from warnings import warn
 from ..base import traits, isdefined, TraitedSpec, File, Str, InputMultiObject
 from ..mixins import CopyHeaderInterface
 from .base import ANTSCommandInputSpec, ANTSCommand
@@ -47,6 +48,10 @@ class ImageMathInputSpec(ANTSCommandInputSpec):
         "GO",
         "GC",
         "TruncateImageIntensity",
+        "Laplacian",
+        "GetLargestComponent",
+        "FillHoles",
+        "PadImage",
         mandatory=True,
         position=3,
         argstr="%s",
@@ -73,8 +78,8 @@ class ImageMath(ANTSCommand, CopyHeaderInterface):
     """
     Operations over images.
 
-    Example
-    -------
+    Examples
+    --------
     >>> ImageMath(
     ...     op1='structural.nii',
     ...     operation='+',
@@ -99,13 +104,55 @@ class ImageMath(ANTSCommand, CopyHeaderInterface):
     ...     op2='0.005 0.999 256').cmdline
     'ImageMath 3 structural_maths.nii TruncateImageIntensity structural.nii 0.005 0.999 256'
 
+    By default, Nipype copies headers from the first input image (``op1``)
+    to the output image.
+    For the ``PadImage`` operation, the header cannot be copied from inputs to
+    outputs, and so ``copy_header`` option is automatically set to ``False``.
+
+    >>> pad = ImageMath(
+    ...     op1='structural.nii',
+    ...     operation='PadImage')
+    >>> pad.inputs.copy_header
+    False
+
+    While the operation is set to ``PadImage``,
+    setting ``copy_header = True`` will have no effect.
+
+    >>> pad.inputs.copy_header = True
+    >>> pad.inputs.copy_header
+    False
+
+    For any other operation, ``copy_header`` can be enabled/disabled normally:
+
+    >>> pad.inputs.operation = "ME"
+    >>> pad.inputs.copy_header = True
+    >>> pad.inputs.copy_header
+    True
+
     """
 
     _cmd = "ImageMath"
     input_spec = ImageMathInputSpec
     output_spec = ImageMathOuputSpec
     _copy_header_map = {"output_image": "op1"}
 
+    def __init__(self, **inputs):
+        super(ImageMath, self).__init__(**inputs)
+        if self.inputs.operation in ("PadImage", ):
+            self.inputs.copy_header = False
+
+        self.inputs.on_trait_change(self._operation_update, "operation")
+        self.inputs.on_trait_change(self._copyheader_update, "copy_header")
+
+    def _operation_update(self):
+        if self.inputs.operation in ("PadImage", ):
+            self.inputs.copy_header = False
+
+    def _copyheader_update(self):
+        if self.inputs.copy_header and self.inputs.operation in ("PadImage", ):
+            warn("copy_header cannot be updated to True with PadImage as operation.")
+            self.inputs.copy_header = False
+
 
 class ResampleImageBySpacingInputSpec(ANTSCommandInputSpec):
     dimension = traits.Int(
@@ -143,19 +190,13 @@ class ResampleImageBySpacingInputSpec(ANTSCommandInputSpec):
     nn_interp = traits.Bool(
         argstr="%d", desc="nn interpolation", position=-1, requires=["addvox"]
     )
-    copy_header = traits.Bool(
-        True,
-        mandatory=True,
-        usedefault=True,
-        desc="copy headers of the original image into the output (corrected) file",
-    )
 
 
 class ResampleImageBySpacingOutputSpec(TraitedSpec):
     output_image = File(exists=True, desc="resampled file")
 
 
-class ResampleImageBySpacing(ANTSCommand, CopyHeaderInterface):
+class ResampleImageBySpacing(ANTSCommand):
     """
     Resample an image with a given spacing.
 
@@ -191,7 +232,6 @@ class ResampleImageBySpacing(ANTSCommand, CopyHeaderInterface):
     _cmd = "ResampleImageBySpacing"
     input_spec = ResampleImageBySpacingInputSpec
     output_spec = ResampleImageBySpacingOutputSpec
-    _copy_header_map = {"output_image": "input_image"}
 
     def _format_arg(self, name, trait_spec, value):
         if name == "out_spacing":