Merge pull request #1 from chrisfilo/jacobian_determinant

Jacobian determinant

Author: idea-labs-admin

nipype/interfaces/ants/utils.py

@@ -16,14 +16,18 @@
 from ...utils.filemanip import split_filename
 from nipype.interfaces.base import InputMultiPath
 
+
 class AverageAffineTransformInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(3, 2, argstr='%d', usedefault=False, mandatory=True, position=0, desc='image dimension (2 or 3)')
     output_affine_transform = File(argstr='%s', mandatory=True, position=1, desc='Outputfname.txt: the name of the resulting transform.')
-    transforms = InputMultiPath(File(exists=True), argstr='%s', mandatory=True, position=3, desc=('transforms to average') )
+    transforms = InputMultiPath(File(exists=True), argstr='%s', mandatory=True,
+                                position=3, desc=('transforms to average'))
+
 
 class AverageAffineTransformOutputSpec(TraitedSpec):
     affine_transform = File(exists=True, desc='average transform file')
 
+
 class AverageAffineTransform(ANTSCommand):
     """
     Examples
@@ -45,20 +49,24 @@ def _format_arg(self, opt, spec, val):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['affine_transform'] = os.path.abspath(self.inputs.output_affine_transform)
+        outputs['affine_transform'] = os.path.abspath(
+            self.inputs.output_affine_transform)
         return outputs
 
 
 class AverageImagesInputSpec(ANTSCommandInputSpec):
-    dimension = traits.Enum(3, 2, argstr='%d', mandatory=True, position=0, desc='image dimension (2 or 3)')
+    dimension = traits.Enum(3, 2, argstr='%d', mandatory=True,
+                            position=0, desc='image dimension (2 or 3)')
     output_average_image = File("average.nii", argstr='%s', position=1, desc='the name of the resulting image.', usedefault=True, hash_files=False)
     normalize = traits.Bool(argstr="%d", mandatory=True, position=2, desc='Normalize: if true, the 2nd image' +
                             'is divided by its mean. This will select the largest image to average into.')
-    images = InputMultiPath(File(exists=True), argstr='%s', mandatory=True, position=3, desc=('image to apply transformation to (generally a coregistered functional)') )
+    images = InputMultiPath(File(exists=True), argstr='%s', mandatory=True, position=3, desc=('image to apply transformation to (generally a coregistered functional)'))
+
 
 class AverageImagesOutputSpec(TraitedSpec):
     output_average_image = File(exists=True, desc='average image file')
 
+
 class AverageImages(ANTSCommand):
     """
     Examples
@@ -81,18 +89,23 @@ def _format_arg(self, opt, spec, val):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['output_average_image'] = os.path.realpath(self.inputs.output_average_image)
+        outputs['output_average_image'] = os.path.realpath(
+            self.inputs.output_average_image)
         return outputs
 
+
 class MultiplyImagesInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(3, 2, argstr='%d', usedefault=False, mandatory=True, position=0, desc='image dimension (2 or 3)')
-    first_input = File(argstr='%s', exists=True, mandatory=True, position=1, desc='image 1')
+    first_input = File(
+        argstr='%s', exists=True, mandatory=True, position=1, desc='image 1')
     second_input = traits.Either(File(exists=True), traits.Float, argstr='%s', mandatory=True, position=2, desc='image 2 or multiplication weight')
     output_product_image = File(argstr='%s', mandatory=True, position=3, desc='Outputfname.nii.gz: the name of the resulting image.')
 
+
 class MultiplyImagesOutputSpec(TraitedSpec):
     output_product_image = File(exists=True, desc='average image file')
 
+
 class MultiplyImages(ANTSCommand):
     """
     Examples
@@ -115,34 +128,40 @@ def _format_arg(self, opt, spec, val):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['output_product_image'] = os.path.abspath(self.inputs.output_product_image)
+        outputs['output_product_image'] = os.path.abspath(
+            self.inputs.output_product_image)
         return outputs
 
 
 class JacobianDeterminantInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(3, 2, argstr='%d', usedefault=False, mandatory=True, position=0, desc='image dimension (2 or 3)')
-    warp_file = File(argstr='%s', exists=True, mandatory=True, position=1, desc='input warp file')
+    warp_file = File(argstr='%s', exists=True, mandatory=True,
+                     position=1, desc='input warp file')
     output_prefix = File(argstr='%s', genfile=True, hash_files=False, position=2, desc='prefix of the output image filename: PREFIX(log)jacobian.nii.gz')
-    use_log = traits.Enum(0, 1, argstr='%d', mandatory=False, position=3, desc='log transform the jacobian determinant')
-    template_mask = File(argstr='%s', exists=True, mandatory=False, position=4, desc='template mask to adjust for head size')
+    use_log = traits.Enum(0, 1, argstr='%d', mandatory=False, position=3,
+                          desc='log transform the jacobian determinant')
+    template_mask = File(argstr='%s', exists=True, mandatory=False, position=4,
+                         desc='template mask to adjust for head size')
     norm_by_total = traits.Enum(0, 1, argstr='%d', mandatory=False, position=5, desc='normalize jacobian by total in mask to adjust for head size')
     projection_vector = traits.List(traits.Float(), argstr='%s', sep='x', mandatory=False, position=6, desc='vector to project warp against')
 
+
 class JacobianDeterminantOutputSpec(TraitedSpec):
     jacobian_image = File(exists=True, desc='(log transformed) jacobian image')
 
+
 class JacobianDeterminant(ANTSCommand):
     """
     Examples
     --------
     >>> from nipype.interfaces.ants import JacobianDeterminant
     >>> jacobian = JacobianDeterminant()
     >>> jacobian.inputs.dimension = 3
-    >>> jacobian.inputs.warp_file = 'Sub001_2Warp.nii'
+    >>> jacobian.inputs.warp_file = 'ants_Warp.nii.gz'
     >>> jacobian.inputs.output_prefix = 'Sub001_'
     >>> jacobian.inputs.use_log = 1
     >>> jacobian.cmdline
-    'ANTSJacobian 3 Sub001_2Warp.nii.gz Sub001_ 1'
+    'ANTSJacobian 3 ants_Warp.nii.gz Sub001_ 1'
     """
 
     _cmd = 'ANTSJacobian'
@@ -161,7 +180,9 @@ def _gen_filename(self, name):
     def _list_outputs(self):
         outputs = self._outputs().get()
         if self.inputs.use_log == 1:
-            outputs['jacobian_image'] = os.path.abspath(self._gen_filename('output_prefix') + 'logjacobian.nii.gz')
+            outputs['jacobian_image'] = os.path.abspath(
+                self._gen_filename('output_prefix') + 'logjacobian.nii.gz')
         else:
-            outputs['jacobian_image'] = os.path.abspath(self._gen_filename('output_prefix') + 'jacobian.nii.gz')
+            outputs['jacobian_image'] = os.path.abspath(
+                self._gen_filename('output_prefix') + 'jacobian.nii.gz')
         return outputs