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DOCTEST: De-indent or remove testsetup blocks
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+52
-103
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5 files changed

+52
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‎nipype/interfaces/base/core.py

-13
Original file line numberDiff line numberDiff line change
@@ -692,14 +692,6 @@ class SimpleInterface(BaseInterface):
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Examples
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--------
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.. testsetup::
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>>> from .specs import TraitedSpec
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>>> tmp = getfixture('tmpdir')
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>>> old = tmp.chdir() # changing to a temporary directory
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.. doctest::
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>>> def double(x):
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... return 2 * x
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...
@@ -721,11 +713,6 @@ class SimpleInterface(BaseInterface):
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>>> dbl.inputs.x = 2
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>>> dbl.run().outputs.doubled
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4.0
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.. testsetup::
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>>> os.chdir(old.strpath)
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"""
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def __init__(self, from_file=None, resource_monitor=None, **inputs):

‎nipype/interfaces/dcm2nii.py

+4-16
Original file line numberDiff line numberDiff line change
@@ -106,26 +106,14 @@ class Dcm2nii(CommandLine):
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Examples
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========
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.. testsetup::
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>>> tmp = getfixture('tmpdir')
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>>> old = tmp.chdir() # changing to a temporary directory
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.. doctest::
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>>> from nipype.interfaces.dcm2nii import Dcm2nii
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>>> converter = Dcm2nii()
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>>> converter.inputs.source_names = [os.path.join(datadir, 'functional_1.dcm'), os.path.join(datadir, 'functional_2.dcm')]
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>>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
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>>> converter.inputs.gzip_output = True
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>>> converter.inputs.output_dir = '.'
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>>> converter.cmdline #doctest: +ELLIPSIS
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'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n ...functional_1.dcm'
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.. testsetup::
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>>> os.chdir(old.strpath)
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"""
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>>> converter.cmdline # doctest: +ELLIPSIS
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'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
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"""
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input_spec = Dcm2niiInputSpec
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output_spec = Dcm2niiOutputSpec

‎nipype/interfaces/image.py

+48-50
Original file line numberDiff line numberDiff line change
@@ -32,65 +32,63 @@ class ReorientOutputSpec(TraitedSpec):
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class Reorient(SimpleInterface):
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"""Conform an image to a given orientation
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Flips and reorder the image data array so that the axes match the
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directions indicated in ``orientation``.
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The default ``RAS`` orientation corresponds to the first axis being ordered
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from left to right, the second axis from posterior to anterior, and the
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third axis from inferior to superior.
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Flips and reorder the image data array so that the axes match the
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directions indicated in ``orientation``.
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The default ``RAS`` orientation corresponds to the first axis being ordered
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from left to right, the second axis from posterior to anterior, and the
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third axis from inferior to superior.
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For oblique images, the original orientation is considered to be the
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closest plumb orientation.
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For oblique images, the original orientation is considered to be the
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closest plumb orientation.
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No resampling is performed, and thus the output image is not de-obliqued
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or registered to any other image or template.
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No resampling is performed, and thus the output image is not de-obliqued
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or registered to any other image or template.
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The effective transform is calculated from the original affine matrix to
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the reoriented affine matrix.
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The effective transform is calculated from the original affine matrix to
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the reoriented affine matrix.
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Examples
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--------
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Examples
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--------
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.. testsetup::
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If an image is not reoriented, the original file is not modified
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.. testsetup::
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>>> def print_affine(matrix):
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... print(str(matrix).replace(']', ' ').replace('[', ' '))
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.. doctest::
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If an image is not reoriented, the original file is not modified
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>>> import numpy as np
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>>> from nipype.interfaces.image import Reorient
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>>> reorient = Reorient(orientation='LPS')
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>>> reorient.inputs.in_file = 'segmentation0.nii.gz'
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>>> res = reorient.run()
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>>> res.outputs.out_file
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'segmentation0.nii.gz'
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>>> print_affine(np.loadtxt(res.outputs.transform))
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1. 0. 0. 0.
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0. 1. 0. 0.
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0. 0. 1. 0.
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0. 0. 0. 1.
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>>> reorient.inputs.orientation = 'RAS'
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>>> res = reorient.run()
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>>> res.outputs.out_file # doctest: +ELLIPSIS
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'.../segmentation0_ras.nii.gz'
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>>> print_affine(np.loadtxt(res.outputs.transform))
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-1. 0. 0. 60.
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0. -1. 0. 72.
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0. 0. 1. 0.
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0. 0. 0. 1.
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.. testcleanup::
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>>> import os
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>>> os.unlink(res.outputs.out_file)
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>>> os.unlink(res.outputs.transform)
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"""
60+
>>> import numpy as np
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>>> from nipype.interfaces.image import Reorient
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>>> reorient = Reorient(orientation='LPS')
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>>> reorient.inputs.in_file = 'segmentation0.nii.gz'
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>>> res = reorient.run()
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>>> res.outputs.out_file
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'segmentation0.nii.gz'
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>>> print_affine(np.loadtxt(res.outputs.transform))
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1. 0. 0. 0.
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0. 1. 0. 0.
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0. 0. 1. 0.
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0. 0. 0. 1.
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>>> reorient.inputs.orientation = 'RAS'
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>>> res = reorient.run()
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>>> res.outputs.out_file # doctest: +ELLIPSIS
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'.../segmentation0_ras.nii.gz'
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>>> print_affine(np.loadtxt(res.outputs.transform))
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-1. 0. 0. 60.
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0. -1. 0. 72.
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0. 0. 1. 0.
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0. 0. 0. 1.
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.. testcleanup::
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>>> import os
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>>> os.unlink(res.outputs.out_file)
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>>> os.unlink(res.outputs.transform)
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"""
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input_spec = ReorientInputSpec
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output_spec = ReorientOutputSpec
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‎nipype/interfaces/io.py

-12
Original file line numberDiff line numberDiff line change
@@ -2585,13 +2585,6 @@ class JSONFileGrabber(IOBase):
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Example
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-------
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.. testsetup::
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>>> tmp = getfixture('tmpdir')
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>>> old = tmp.chdir() # changing to a temporary directory
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.. doctest::
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>>> import pprint
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>>> from nipype.interfaces.io import JSONFileGrabber
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>>> jsonSource = JSONFileGrabber()
@@ -2603,11 +2596,6 @@ class JSONFileGrabber(IOBase):
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>>> res = jsonSource.run()
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>>> pprint.pprint(res.outputs.get()) # doctest:, +ELLIPSIS
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{'param1': 'exampleStr', 'param2': 4, 'param3': 1.0}
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.. testsetup::
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>>> os.chdir(old.strpath)
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"""
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input_spec = JSONFileGrabberInputSpec
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output_spec = DynamicTraitedSpec

‎nipype/interfaces/niftyreg/regutils.py

-12
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@@ -450,13 +450,6 @@ class RegAverage(NiftyRegCommand):
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Examples
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--------
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.. testsetup::
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>>> tmp = getfixture('tmpdir')
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>>> old = tmp.chdir() # changing to temporary file
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.. doctest::
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>>> from nipype.interfaces import niftyreg
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>>> node = niftyreg.RegAverage()
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>>> one_file = 'im1.nii'
@@ -465,11 +458,6 @@ class RegAverage(NiftyRegCommand):
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>>> node.inputs.avg_files = [one_file, two_file, three_file]
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>>> node.cmdline # doctest: +ELLIPSIS
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'reg_average --cmd_file .../reg_average_cmd'
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.. testsetup::
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>>> os.chdir(old.strpath)
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473461
"""
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_cmd = get_custom_path('reg_average')
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input_spec = RegAverageInputSpec

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