Editing docstring to follow nipype template and add some tests.

Author: byvernault

nipype/interfaces/niftyseg/em.py

@@ -10,6 +10,12 @@
 Examples
 --------
 See the docstrings of the individual classes for examples.
+
+Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
 """
 
 import os
@@ -116,9 +122,9 @@ class EM(NiftySegCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import EM
-    >>> node = EM()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.EM()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.no_prior = 4
     >>> node.cmdline  # doctest: +SKIP
     'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii -out im1_em.nii \

nipype/interfaces/niftyseg/label_fusion.py

@@ -4,6 +4,12 @@
 """
 The fusion module provides higher-level interfaces to some of the operations
 that can be performed with the seg_LabFusion command-line program.
+
+Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
 """
 
 from builtins import str
@@ -114,12 +120,12 @@ class LabelFusion(NiftySegCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import LabelFusion
-    >>> node = LabelFusion()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.LabelFusion()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.kernel_size = 2.0
-    >>> node.inputs.file_to_seg = 'im2.nii'  # doctest: +SKIP
-    >>> node.inputs.template_file = 'im3.nii'  # doctest: +SKIP
+    >>> node.inputs.file_to_seg = 'im2.nii'
+    >>> node.inputs.template_file = 'im3.nii'
     >>> node.inputs.template_num = 2
     >>> node.inputs.classifier_type = 'STEPS'
     >>> node.cmdline  # doctest: +SKIP
@@ -277,11 +283,11 @@ class CalcTopNCC(NiftySegCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import CalcTopNCC
-    >>> node = CalcTopNCC()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.CalcTopNCC()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.num_templates = 2
-    >>> node.inputs.in_templates = ['im2.nii', 'im3.nii']  # doctest: +SKIP
+    >>> node.inputs.in_templates = ['im2.nii', 'im3.nii']
     >>> node.inputs.top_templates = 1
     >>> node.cmdline  # doctest: +SKIP
     'seg_CalcTopNCC -target im1.nii -templates 2 im2.nii im3.nii -n 1'

nipype/interfaces/niftyseg/lesions.py

@@ -10,6 +10,12 @@
 Examples
 --------
 See the docstrings of the individual classes for examples.
+
+Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
 """
 
 import os
@@ -98,10 +104,10 @@ class FillLesions(NiftySegCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import FillLesions
-    >>> node = FillLesions()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
-    >>> node.inputs.lesion_mask = 'im2.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.FillLesions()
+    >>> node.inputs.in_file = 'im1.nii'
+    >>> node.inputs.lesion_mask = 'im2.nii'
     >>> node.cmdline  # doctest: +SKIP
     'seg_FillLesions -i im1.nii -l im2.nii -o im1_lesions_filled.nii'
 

nipype/interfaces/niftyseg/maths.py

@@ -10,6 +10,12 @@
 Examples
 --------
 See the docstrings of the individual classes for examples.
+
+Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
 """
 import os
 
@@ -125,9 +131,9 @@ class UnaryMaths(MathsCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import UnaryMaths
-    >>> node = UnaryMaths()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.UnaryMaths()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.operation = 'sqrt'
     >>> node.inputs.output_datatype = 'float'
     >>> node.cmdline  # doctest: +SKIP
@@ -212,11 +218,11 @@ class BinaryMaths(MathsCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import BinaryMaths
-    >>> node = BinaryMaths()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.BinaryMaths()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.operation = 'sub'
-    >>> node.inputs.operand_file = 'im2.nii' # doctest: +SKIP
+    >>> node.inputs.operand_file = 'im2.nii'
     >>> node.inputs.output_datatype = 'float'
     >>> node.cmdline  # doctest: +SKIP
     'seg_maths im1.nii -odt float -sub im2.nii im1_sub.nii.gz'
@@ -289,7 +295,7 @@ class BinaryMathsInteger(MathsCommand):
     --------
     >>> from nipype.interfaces.niftyseg import BinaryMathsInteger
     >>> node = BinaryMathsInteger()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.operation = 'dil'
     >>> node.inputs.operand_value = 2
     >>> node.inputs.output_datatype = 'float'
@@ -357,11 +363,11 @@ class TupleMaths(MathsCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import TupleMaths
-    >>> node = TupleMaths()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.TupleMaths()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.operation = 'lncc'
-    >>> node.inputs.operand_file1 = 'im2.nii'  # doctest: +SKIP
+    >>> node.inputs.operand_file1 = 'im2.nii'
     >>> node.inputs.operand_value2 = 2.0
     >>> node.inputs.output_datatype = 'float'
     >>> node.cmdline  # doctest: +SKIP
@@ -398,11 +404,11 @@ class Merge(MathsCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import Merge
-    >>> node = Merge()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.Merge()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> files = ['im2.nii', 'im3.nii']
-    >>> node.inputs.merge_files = files  # doctest: +SKIP
+    >>> node.inputs.merge_files = files
     >>> node.inputs.dimension = 2
     >>> node.inputs.output_datatype = 'float'
     >>> node.cmdline  # doctest: +SKIP

nipype/interfaces/niftyseg/patchmatch.py

@@ -1,8 +1,15 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+
 """
 The fusion module provides higher-level interfaces to some of the operations
 that can be performed with the seg_DetectLesions command-line program.
+
+Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
 """
 import os
 import warnings
@@ -93,11 +100,11 @@ class PatchMatch(NiftySegCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import PatchMatch
-    >>> node = PatchMatch()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
-    >>> node.inputs.mask_file = 'im2.nii'  # doctest: +SKIP
-    >>> node.inputs.database_file = 'db.xml'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.PatchMatch()
+    >>> node.inputs.in_file = 'im1.nii'
+    >>> node.inputs.mask_file = 'im2.nii'
+    >>> node.inputs.database_file = 'db.xml'
     >>> node.cmdline  # doctest: +SKIP
     'seg_PatchMatch -i im1.nii -m im2.nii -db db.xml -o im1_pm.nii'
 

nipype/interfaces/niftyseg/stats.py

@@ -1,8 +1,15 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+
 """
 The stats module provides higher-level interfaces to some of the operations
-that can be performed with the niftysegstats (seg_stats) command-line program.
+that can be performed with the niftyseg stats (seg_stats) command-line program.
+
+Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
 """
 from __future__ import print_function
 import numpy as np
@@ -121,9 +128,9 @@ class UnaryStats(StatsCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import UnaryStats
-    >>> node = UnaryStats()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.UnaryStats()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.operation = 'v'
     >>> node.cmdline  # doctest: +SKIP
     'seg_stats im1.nii -v'
@@ -184,9 +191,9 @@ class BinaryStats(StatsCommand):
 
     Examples
     --------
-    >>> from nipype.interfaces.niftyseg import BinaryStats
-    >>> node = BinaryStats()
-    >>> node.inputs.in_file = 'im1.nii'  # doctest: +SKIP
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.BinaryStats()
+    >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.operation = 'sa'
     >>> node.inputs.operand_value = 2.0
     >>> node.cmdline  # doctest: +SKIP