Merge pull request #905 from oesteban/fix/ElastixDocumentation

Fix elastix documentation

Author: oesteban

nipype/interfaces/elastix/registration.py

@@ -6,7 +6,7 @@
 # @Author: oesteban - code@oscaresteban.es
 # @Date:   2014-06-02 12:06:50
 # @Last Modified by:   oesteban
-# @Last Modified time: 2014-06-17 10:19:23
+# @Last Modified time: 2014-09-01 21:03:57
 """
 Interfaces to perform image registrations and to apply the resulting
 displacement maps to images and points.
@@ -18,8 +18,6 @@
 
 from ..base import (CommandLine, CommandLineInputSpec, isdefined,
                     TraitedSpec, File, traits, InputMultiPath)
-
-
 from base import ElastixBaseInputSpec
 
 from ... import logging
@@ -31,10 +29,8 @@ class RegistrationInputSpec(ElastixBaseInputSpec):
            desc='fixed image')
     moving_image = File(exists=True, mandatory=True, argstr='-m %s',
            desc='moving image')
-
     parameters = InputMultiPath(File(exists=True), mandatory=True, argstr='-p %s...',
                                 desc='parameter file, elastix handles 1 or more -p')
-
     fixed_mask = File(exists=True, argstr='-fMask %s', desc='mask for fixed image')
     moving_mask = File(exists=True, argstr='-mMask %s', desc='mask for moving image')
     initial_transform = File(exists=True, argstr='-t0 %s',
@@ -51,7 +47,8 @@ class RegistrationOutputSpec(TraitedSpec):
 
 
 class Registration(CommandLine):
-    """Elastix nonlinear registration interface
+    """
+    Elastix nonlinear registration interface
 
     Example
     -------
@@ -63,6 +60,8 @@ class Registration(CommandLine):
     >>> reg.inputs.parameters = ['elastix.txt']
     >>> reg.cmdline
     'elastix -f fixed1.nii -m moving1.nii -out ./ -p elastix.txt'
+
+
     """
 
     _cmd = 'elastix'
@@ -140,17 +139,21 @@ class ApplyWarpOutputSpec(TraitedSpec):
     warped_file = File(desc='input moving image warped to fixed image')
 
 class ApplyWarp(CommandLine):
-    """Use `transformix` to apply a transform on an input image.
+    """
+    Use ``transformix`` to apply a transform on an input image.
     The transform is specified in the transform-parameter file.
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import ApplyWarp
     >>> reg = ApplyWarp()
     >>> reg.inputs.moving_image = 'moving1.nii'
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
     'transformix -in moving1.nii -out ./ -tp TransformParameters.0.txt'
+
+
     """
 
     _cmd = 'transformix'
@@ -170,22 +173,26 @@ class AnalyzeWarpInputSpec(ElastixBaseInputSpec):
 
 
 class AnalyzeWarpOutputSpec(TraitedSpec):
-    disp_field = File(exists=True, desc='displacements field')
-    jacdet_map = File(exists=True, desc='det(Jacobian) map')
-    jacmat_map = File(exists=True, desc='Jacobian matrix map')
+    disp_field = File(desc='displacements field')
+    jacdet_map = File(desc='det(Jacobian) map')
+    jacmat_map = File(desc='Jacobian matrix map')
 
 class AnalyzeWarp(CommandLine):
-    """Use `transformix` to get details from the input transform (generate
+    """
+    Use transformix to get details from the input transform (generate
     the corresponding deformation field, generate the determinant of the
     Jacobian map or the Jacobian map itself)
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import AnalyzeWarp
     >>> reg = AnalyzeWarp()
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
     'transformix -def all -jac all -jacmat all -out ./ -tp TransformParameters.0.txt'
+
+
     """
 
     _cmd = 'transformix -def all -jac all -jacmat all'
@@ -213,17 +220,20 @@ class PointsWarpOutputSpec(TraitedSpec):
     warped_file = File(desc='input points displaced in fixed image domain')
 
 class PointsWarp(CommandLine):
-    """Use `transformix` to apply a transform on an input point set.
+    """Use ``transformix`` to apply a transform on an input point set.
     The transform is specified in the transform-parameter file.
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import PointsWarp
     >>> reg = PointsWarp()
     >>> reg.inputs.points_file = 'surf1.vtk'
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
     'transformix -out ./ -def surf1.vtk -tp TransformParameters.0.txt'
+
+
     """
 
     _cmd = 'transformix'

nipype/interfaces/elastix/utils.py

@@ -6,7 +6,7 @@
 # @Author: oesteban - code@oscaresteban.es
 # @Date:   2014-06-17 10:17:07
 # @Last Modified by:   oesteban
-# @Last Modified time: 2014-06-27 10:25:36
+# @Last Modified time: 2014-09-01 21:05:33
 """
 Generic interfaces to manipulate registration parameters files, including
 transform files (to configure warpings)
@@ -51,14 +51,17 @@ class EditTransform(BaseInterface):
     """
     Manipulates an existing transform file generated with elastix
 
-    Example::
+    Example
+    -------
 
     >>> from nipype.interfaces.elastix import EditTransform
     >>> tfm = EditTransform()
     >>> tfm.inputs.transform_file = 'TransformParameters.0.txt'
     >>> tfm.inputs.reference_image = 'fixed1.nii'
     >>> tfm.inputs.output_type = 'unsigned char'
     >>> tfm.run() # doctest: +SKIP
+
+
     """
 
     input_spec = EditTransformInputSpec