(enh) additional arguments to ANTs N4BiasFieldCorrection

Author: rciric

nipype/interfaces/ants/segmentation.py

@@ -317,6 +317,18 @@ class N4BiasFieldCorrectionInputSpec(ANTSCommandInputSpec):
 The result is that the range can "drift" from the original at each iteration.
 This option rescales to the [min,max] range of the original image intensities
 within the user-specified mask.""")
+    histogram_fwhm = traits.Float(
+        0.15, usedefault=True,
+        argstr='--histogram-sharpening %s',
+        desc='Histogram sharpening parameter: FWHM')
+    histogram_wiener_noise = traits.Float(
+        0.01, usedefault=True,
+        requires=['histogram_fwhm'],
+        desc='Histogram sharpening parameter: Wiener noise')
+    histogram_bins = traits.Int(
+        200, usedefault=True,
+        requires=['histogram_fwhm', 'histogram_wiener_noise'],
+        desc='Histogram sharpening parameter: number of bins')
 
 
 class N4BiasFieldCorrectionOutputSpec(TraitedSpec):
@@ -414,6 +426,16 @@ def _format_arg(self, name, trait_spec, value):
                     [str(elt) for elt in value])
             return trait_spec.argstr % newval
 
+        if name == 'histogram_fwhm':
+            newval = '[ %f' % value
+            if isdefined(self.inputs.histogram_wiener_noise):
+                newval = '%s, %f' % (
+                    newval, self.inputs.histogram_wiener_noise)
+            if isdefined(self.inputs.histogram_bins):
+                newval = '%s, %d' % (newval, self.inputs.histogram_bins)
+            newval = '%s ]' % newval
+            return trait_spec.argstr % newval
+
         return super(N4BiasFieldCorrection, self)._format_arg(
             name, trait_spec, value)
 

nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py

@@ -25,6 +25,18 @@ def test_N4BiasFieldCorrection_inputs():
             nohash=True,
             usedefault=True,
         ),
+        histogram_bins=dict(
+            requires=['histogram_fwhm', 'histogram_wiener_noise'],
+            usedefault=True,
+        ),
+        histogram_fwhm=dict(
+            argstr='--histogram-sharpening %s',
+            usedefault=True,
+        ),
+        histogram_wiener_noise=dict(
+            requires=['histogram_fwhm'],
+            usedefault=True,
+        ),
         input_image=dict(
             argstr='--input-image %s',
             extensions=None,
@@ -51,6 +63,7 @@ def test_N4BiasFieldCorrection_inputs():
             min_ver='2.1.0',
             usedefault=True,
         ),
+        rescale_intensities=dict(argstr='--rescale-intensities %d', ),
         save_bias=dict(
             mandatory=True,
             usedefault=True,