correcting docstrings of the utils file

Author: oesteban

nipype/interfaces/fsl/utils.py

@@ -159,6 +159,7 @@ class Merge(FSLCommand):
 
     Examples
     --------
+
     >>> from nipype.interfaces.fsl import Merge
     >>> merger = Merge()
     >>> merger.inputs.in_files = ['functional2.nii', 'functional3.nii']
@@ -169,6 +170,8 @@ class Merge(FSLCommand):
     >>> merger.inputs.tr = 2.25
     >>> merger.cmdline
     'fslmerge -tr functional2_merged.nii.gz functional2.nii functional3.nii 2.25'
+
+
     """
 
     _cmd = 'fslmerge'
@@ -223,6 +226,7 @@ class ExtractROI(FSLCommand):
     extract voxels 10 to 12 inclusive you would specify 10 and 3 (not
     10 and 12).
 
+
     Examples
     --------
 
@@ -232,6 +236,8 @@ class ExtractROI(FSLCommand):
     ...                     t_size=1)
     >>> fslroi.cmdline == 'fslroi %s bar.nii 0 1' % anatfile
     True
+
+
     """
 
     _cmd = 'fslroi'
@@ -249,8 +255,10 @@ def _list_outputs(self):
         by running the interface.  Some files are always generated, others
         depending on which ``inputs`` options are set.
 
+
         Returns
         -------
+
         outputs : Bunch object
             Bunch object containing all possible files generated by
             interface object.
@@ -301,6 +309,7 @@ def _list_outputs(self):
 
         Returns
         -------
+
         outputs : Bunch object
             Bunch object containing all possible files generated by
             interface object.
@@ -338,9 +347,9 @@ class ImageMathsOutputSpec(TraitedSpec):
 
 class ImageMaths(FSLCommand):
     """Use FSL fslmaths command to allow mathematical manipulation of images
-
     `FSL info <http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/intro/index.htm#fslutils>`_
 
+
     Examples
     --------
 
@@ -350,6 +359,8 @@ class ImageMaths(FSLCommand):
     ...                        out_file='foo_maths.nii')
     >>> maths.cmdline == 'fslmaths %s -add 5 foo_maths.nii' % anatfile
     True
+
+
     """
     input_spec = ImageMathsInputSpec
     output_spec = ImageMathsOutputSpec
@@ -465,8 +476,9 @@ class ImageStatsOutputSpec(TraitedSpec):
 
 class ImageStats(FSLCommand):
     """Use FSL fslstats command to calculate stats from images
+    `FSL info
+    <http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/intro/index.htm#fslutils>`_
 
-    `FSL info <http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/intro/index.htm#fslutils>`_
 
     Examples
     --------
@@ -477,6 +489,7 @@ class ImageStats(FSLCommand):
     >>> stats.cmdline == 'fslstats %s -M'%funcfile
     True
 
+
     """
     input_spec = ImageStatsInputSpec
     output_spec = ImageStatsOutputSpec
@@ -543,9 +556,11 @@ class AvScale(FSLCommand):
 
     Examples
     --------
-    avscale = AvScale()
-    avscale.inputs.mat_file = 'flirt.mat'
-    res = avscale.run()  # doctest: +SKIP
+
+    >>> avscale = AvScale()
+    >>> avscale.inputs.mat_file = 'flirt.mat'
+    >>> res = avscale.run()  # doctest: +SKIP
+
 
     """
     input_spec = AvScaleInputSpec
@@ -634,8 +649,10 @@ class Overlay(FSLCommand):
     """ Use FSL's overlay command to combine background and statistical images
         into one volume
 
+
     Examples
     --------
+
     >>> from nipype.interfaces import fsl
     >>> combine = fsl.Overlay()
     >>> combine.inputs.background_image = 'mean_func.nii.gz'
@@ -645,6 +662,7 @@ class Overlay(FSLCommand):
     >>> combine.inputs.show_negative_stats = True
     >>> res = combine.run() #doctest: +SKIP
 
+
     """
     _cmd = 'overlay'
     input_spec = OverlayInputSpec
@@ -745,8 +763,10 @@ class SlicerOutputSpec(TraitedSpec):
 class Slicer(FSLCommand):
     """Use FSL's slicer command to output a png image from a volume.
 
+
     Examples
     --------
+
     >>> from nipype.interfaces import fsl
     >>> from nipype.testing import example_data
     >>> slice = fsl.Slicer()
@@ -755,6 +775,7 @@ class Slicer(FSLCommand):
     >>> slice.inputs.image_width = 750
     >>> res = slice.run() #doctest: +SKIP
 
+
     """
     _cmd = 'slicer'
     input_spec = SlicerInputSpec
@@ -835,13 +856,15 @@ class PlotTimeSeries(FSLCommand):
 
     Examples
     --------
+
     >>> import nipype.interfaces.fsl as fsl
     >>> plotter = fsl.PlotTimeSeries()
     >>> plotter.inputs.in_file = 'functional.par'
     >>> plotter.inputs.title = 'Functional timeseries'
     >>> plotter.inputs.labels = ['run1', 'run2']
     >>> plotter.run() #doctest: +SKIP
 
+
     """
     _cmd = "fsl_tsplot"
     input_spec = PlotTimeSeriesInputSpec
@@ -915,23 +938,28 @@ class PlotMotionParams(FSLCommand):
     """Use fsl_tsplot to plot the estimated motion parameters from a realignment
     program.
 
+
     Examples
     --------
+
     >>> import nipype.interfaces.fsl as fsl
     >>> plotter = fsl.PlotMotionParams()
     >>> plotter.inputs.in_file = 'functional.par'
     >>> plotter.inputs.in_source = 'fsl'
     >>> plotter.inputs.plot_type = 'rotations'
     >>> res = plotter.run() #doctest: +SKIP
 
+
     Notes
     -----
+
     The 'in_source' attribute determines the order of columns that are expected
     in the source file.  FSL prints motion parameters in the order rotations,
     translations, while SPM prints them in the opposite order.  This interface
     should be able to plot timecourses of motion parameters generated from other
     sources as long as they fall under one of these two patterns.  For more
     flexibilty, see the :class:`fsl.PlotTimeSeries` interface.
+
     """
     _cmd = 'fsl_tsplot'
     input_spec = PlotMotionParamsInputSpec
@@ -1024,13 +1052,16 @@ class ConvertXFM(FSLCommand):
 
     Examples
     --------
+
     >>> import nipype.interfaces.fsl as fsl
     >>> invt = fsl.ConvertXFM()
     >>> invt.inputs.in_file = "flirt.mat"
     >>> invt.inputs.invert_xfm = True
     >>> invt.inputs.out_file = 'flirt_inv.mat'
     >>> invt.cmdline
     'convert_xfm -omat flirt_inv.mat -inverse flirt.mat'
+
+
     """
 
     _cmd = "convert_xfm"
@@ -1134,11 +1165,13 @@ class PowerSpectrum(FSLCommand):
 
     Examples
     --------
+
     >>> from nipype.interfaces import fsl
     >>> pspec = fsl.PowerSpectrum()
     >>> pspec.inputs.in_file = 'functional.nii'
     >>> res = pspec.run() # doctest: +SKIP
 
+
     """
 
     _cmd = 'fslpspec'
@@ -1189,10 +1222,13 @@ class SigLoss(FSLCommand):
 
     Examples
     --------
+
     >>> sigloss = SigLoss()
     >>> sigloss.inputs.in_file = "phase.nii"
     >>> sigloss.inputs.echo_time = 0.03
     >>> res = sigloss.run() # doctest: +SKIP
+
+
     """
     input_spec = SigLossInputSpec
     output_spec = SigLossOuputSpec
@@ -1226,8 +1262,10 @@ class Reorient2Std(FSLCommand):
     """fslreorient2std is a tool for reorienting the image to match the
     approximate orientation of the standard template images (MNI152).
 
+
     Examples
     --------
+
     >>> reorient = Reorient2Std()
     >>> reorient.inputs.in_file = "functional.nii"
     >>> res = reorient.run() # doctest: +SKIP
@@ -1310,7 +1348,9 @@ class InvWarpOutputSpec(TraitedSpec):
 
 
 class InvWarp(FSLCommand):
-    """Use FSL Invwarp to inverse a FNIRT warp
+    """
+    Use FSL Invwarp to invert a FNIRT warp
+
 
     Examples
     --------
@@ -1322,6 +1362,8 @@ class InvWarp(FSLCommand):
     >>> invwarp.cmdline
     'invwarp --out=struct2mni_inverse.nii.gz --ref=anatomical.nii --warp=struct2mni.nii'
     >>> res = invwarp.run() # doctest: +SKIP
+
+
     """
 
     input_spec = InvWarpInputSpec
@@ -1390,13 +1432,16 @@ class ComplexOuputSpec(TraitedSpec):
 
 class Complex(FSLCommand):
     """fslcomplex is a tool for converting complex data
+
     Examples
     --------
+
     >>> cplx = Complex()
     >>> cplx.inputs.complex_in_file = "complex.nii"
     >>> cplx.real_polar = True
     >>> res = cplx.run() # doctest: +SKIP
 
+
     """
     _cmd = 'fslcomplex'
     input_spec = ComplexInputSpec
@@ -1524,7 +1569,8 @@ class WarpUtils(FSLCommand):
     to convert field->coefficients, coefficients->field, coefficients->other_coefficients etc
 
 
-    Examples::
+    Examples
+    --------
 
     >>> from nipype.interfaces.fsl import WarpUtils
     >>> warputils = WarpUtils()
@@ -1535,6 +1581,8 @@ class WarpUtils(FSLCommand):
     >>> warputils.cmdline # doctest: +ELLIPSIS
     'fnirtfileutils --in=warpfield.nii --outformat=spline --ref=T1.nii --warpres=10.0000,10.0000,10.0000 --out=warpfield_coeffs.nii.gz'
     >>> res = invwarp.run() # doctest: +SKIP
+
+
     """
 
     input_spec = WarpUtilsInputSpec
@@ -1649,7 +1697,8 @@ class ConvertWarp(FSLCommand):
     for combining multiple transforms into one.
 
 
-    Examples::
+    Examples
+    --------
 
     >>> from nipype.interfaces.fsl import ConvertWarp
     >>> warputils = ConvertWarp()
@@ -1659,6 +1708,8 @@ class ConvertWarp(FSLCommand):
     >>> warputils.cmdline # doctest: +ELLIPSIS
     'convertwarp --ref=T1.nii --rel --warp1=warpfield.nii --out=T1_concatwarp.nii.gz'
     >>> res = invwarp.run() # doctest: +SKIP
+
+
     """
 
     input_spec = ConvertWarpInputSpec
@@ -1701,7 +1752,8 @@ class WarpPoints(CommandLine):
     .. Note:: transformation of TrackVis trk files is not yet implemented
 
 
-    Examples::
+    Examples
+    --------
 
     >>> from nipype.interfaces.fsl import WarpPoints
     >>> warppoints = WarpPoints()
@@ -1713,6 +1765,8 @@ class WarpPoints(CommandLine):
     >>> warppoints.cmdline # doctest: +ELLIPSIS
     'img2imgcoord -mm -dest T1.nii -src epi.nii -warp warpfield.nii surf.txt'
     >>> res = invwarp.run() # doctest: +SKIP
+
+
     """
 
     input_spec = WarpPointsInputSpec
@@ -1858,7 +1912,9 @@ class WarpPointsToStd(WarpPoints):
 
     .. Note:: transformation of TrackVis trk files is not yet implemented
 
-    Examples::
+
+    Examples
+    --------
 
     >>> from nipype.interfaces.fsl import WarpPointsToStd
     >>> warppoints = WarpPointsToStd()
@@ -1870,6 +1926,8 @@ class WarpPointsToStd(WarpPoints):
     >>> warppoints.cmdline # doctest: +ELLIPSIS
     'img2stdcoord -mm -img T1.nii -std mni.nii -warp warpfield.nii surf.txt'
     >>> res = invwarp.run() # doctest: +SKIP
+
+
     """
 
     input_spec = WarpPointsToStdInputSpec