Merge pull request #2586 from satra/enh/labelgeom

enh: add interface for LabelGeometryMeasures

Author: effigies

nipype/interfaces/ants/__init__.py

@@ -23,4 +23,4 @@
 # Utility Programs
 from .utils import (AverageAffineTransform, AverageImages, MultiplyImages,
                     CreateJacobianDeterminantImage, AffineInitializer,
-                    ComposeMultiTransform)
+                    ComposeMultiTransform, LabelGeometry)

nipype/interfaces/ants/tests/test_auto_LabelGeometry.py

@@ -0,0 +1,60 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import LabelGeometry
+
+
+def test_LabelGeometry_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        dimension=dict(
+            argstr='%d',
+            position=0,
+            usedefault=True,
+        ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        ignore_exception=dict(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        intensity_image=dict(
+            argstr='%s',
+            mandatory=True,
+            position=2,
+            usedefault=True,
+        ),
+        label_image=dict(
+            argstr='%s',
+            mandatory=True,
+            position=1,
+        ),
+        num_threads=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        output_file=dict(
+            argstr='%s',
+            name_source=['label_image'],
+            name_template='%s.csv',
+            position=3,
+        ),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            nohash=True,
+        ),
+    )
+    inputs = LabelGeometry.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_LabelGeometry_outputs():
+    output_map = dict(output_file=dict(), )
+    outputs = LabelGeometry.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

@@ -357,3 +357,60 @@ class ComposeMultiTransform(ANTSCommand):
     _cmd = 'ComposeMultiTransform'
     input_spec = ComposeMultiTransformInputSpec
     output_spec = ComposeMultiTransformOutputSpec
+
+
+class LabelGeometryInputSpec(ANTSCommandInputSpec):
+    dimension = traits.Enum(
+        3,
+        2,
+        argstr='%d',
+        usedefault=True,
+        position=0,
+        desc='image dimension (2 or 3)')
+    label_image = File(
+        argstr='%s',
+        position=1,
+        mandatory=True,
+        desc='label image to use for extracting geometry measures')
+    intensity_image = File(
+        value='[]',
+        exists=True,
+        argstr='%s',
+        mandatory=True,
+        usedefault=True,
+        position=2,
+        desc='Intensity image to extract values from. '
+             'This is an optional input')
+    output_file = traits.Str(
+        name_source=['label_image'],
+        name_template='%s.csv',
+        argstr='%s',
+        position=3,
+        desc='name of output file')
+
+
+class LabelGeometryOutputSpec(TraitedSpec):
+    output_file = File(exists=True, desc='CSV file of geometry measures')
+
+
+class LabelGeometry(ANTSCommand):
+    """
+    Extracts geometry measures using a label file and an optional image file
+
+    Examples
+    --------
+    >>> from nipype.interfaces.ants import LabelGeometry
+    >>> label_extract = LabelGeometry()
+    >>> label_extract.inputs.dimension = 3
+    >>> label_extract.inputs.label_image = 'atlas.nii.gz'
+    >>> label_extract.cmdline
+    'LabelGeometryMeasures 3 atlas.nii.gz [] atlas.csv'
+
+    >>> label_extract.inputs.intensity_image = 'ants_Warp.nii.gz'
+    >>> label_extract.cmdline
+    'LabelGeometryMeasures 3 atlas.nii.gz ants_Warp.nii.gz atlas.csv'
+
+    """
+    _cmd = 'LabelGeometryMeasures'
+    input_spec = LabelGeometryInputSpec
+    output_spec = LabelGeometryOutputSpec