nipype.interfaces.utility.base module

# changing to temporary directories >>> tmp = getfixture(‘tmpdir’) >>> old = tmp.chdir()

class nipype.interfaces.utility.base.AssertEqual(from_file=None, resource_monitor=None, ignore_exception=False, **inputs)

Bases: BaseInterface

Mandatory Inputs

volume1 : a pathlike object or string representing an existing file volume2 : a pathlike object or string representing an existing file

class nipype.interfaces.utility.base.IdentityInterface(fields=None, mandatory_inputs=True, **inputs)

Bases: IOBase

Basic interface class generates identity mappings

Examples

>>> from nipype.interfaces.utility import IdentityInterface
>>> ii = IdentityInterface(fields=['a', 'b'], mandatory_inputs=False)
>>> ii.inputs.a
<undefined>

>>> ii.inputs.a = 'foo'
>>> out = ii._outputs()
>>> out.a
<undefined>

>>> out = ii.run()
>>> out.outputs.a
'foo'

>>> ii2 = IdentityInterface(fields=['a', 'b'], mandatory_inputs=True)
>>> ii2.inputs.a = 'foo'
>>> out = ii2.run()
ValueError: IdentityInterface requires a value for input 'b' because it was listed in 'fields' Interface IdentityInterface failed to run.

input_spec

alias of DynamicTraitedSpec

output_spec

alias of DynamicTraitedSpec

class nipype.interfaces.utility.base.Merge(numinputs=0, **inputs)

Bases: IOBase

Basic interface class to merge inputs into a single list

Merge(1) will merge a list of lists

Examples

>>> from nipype.interfaces.utility import Merge
>>> mi = Merge(3)
>>> mi.inputs.in1 = 1
>>> mi.inputs.in2 = [2, 5]
>>> mi.inputs.in3 = 3
>>> out = mi.run()
>>> out.outputs.out
[1, 2, 5, 3]

>>> merge = Merge(1)
>>> merge.inputs.in1 = [1, [2, 5], 3]
>>> out = merge.run()
>>> out.outputs.out
[1, [2, 5], 3]

>>> merge = Merge(1)
>>> merge.inputs.in1 = [1, [2, 5], 3]
>>> merge.inputs.ravel_inputs = True
>>> out = merge.run()
>>> out.outputs.out
[1, 2, 5, 3]

>>> merge = Merge(1)
>>> merge.inputs.in1 = [1, [2, 5], 3]
>>> merge.inputs.no_flatten = True
>>> out = merge.run()
>>> out.outputs.out
[[1, [2, 5], 3]]

Optional Inputs

axis‘vstack’ or ‘hstack’

Direction in which to merge, hstack requires same number of elements in each input. (Nipype default value: vstack)

no_flattena boolean

Append to outlist instead of extending in vstack mode. (Nipype default value: False)

ravel_inputsa boolean

Ravel inputs when no_flatten is False. (Nipype default value: False)

Outputs

outa list of items which are any value

Merged output.

class nipype.interfaces.utility.base.Rename(format_string=None, **inputs)

Bases: SimpleInterface, IOBase

Change the name of a file based on a mapped format string.

To use additional inputs that will be defined at run-time, the class constructor must be called with the format template, and the fields identified will become inputs to the interface.

Additionally, you may set the parse_string input, which will be run over the input filename with a regular expressions search, and will fill in additional input fields from matched groups. Fields set with inputs have precedence over fields filled in with the regexp match.

Examples

>>> from nipype.interfaces.utility import Rename
>>> rename1 = Rename()
>>> rename1.inputs.in_file = os.path.join(datadir, "zstat1.nii.gz") # datadir is a directory with exemplary files, defined in conftest.py
>>> rename1.inputs.format_string = "Faces-Scenes.nii.gz"
>>> res = rename1.run()
>>> res.outputs.out_file
'Faces-Scenes.nii.gz"

>>> rename2 = Rename(format_string="%(subject_id)s_func_run%(run)02d")
>>> rename2.inputs.in_file = os.path.join(datadir, "functional.nii")
>>> rename2.inputs.keep_ext = True
>>> rename2.inputs.subject_id = "subj_201"
>>> rename2.inputs.run = 2
>>> res = rename2.run()
>>> res.outputs.out_file
'subj_201_func_run02.nii'

>>> rename3 = Rename(format_string="%(subject_id)s_%(seq)s_run%(run)02d.nii")
>>> rename3.inputs.in_file = os.path.join(datadir, "func_epi_1_1.nii")
>>> rename3.inputs.parse_string = r"func_(?P<seq>\w*)_.*"
>>> rename3.inputs.subject_id = "subj_201"
>>> rename3.inputs.run = 2
>>> res = rename3.run()
>>> res.outputs.out_file
'subj_201_epi_run02.nii'

Mandatory Inputs

format_stringa string

Python formatting string for output template.

in_filea pathlike object or string representing an existing file

File to rename.

Optional Inputs

keep_exta boolean

Keep in_file extension, replace non-extension component of name.

parse_stringa string

Python regexp parse string to define replacement inputs.

use_fullpatha boolean

Use full path as input to regex parser. (Nipype default value: False)

Outputs

out_filea pathlike object or string representing an existing file

Softlink to original file with new name.

input_spec

alias of RenameInputSpec

class nipype.interfaces.utility.base.RenameInputSpec(**kwargs)

Bases: DynamicTraitedSpec

class nipype.interfaces.utility.base.Select(from_file=None, resource_monitor=None, ignore_exception=False, **inputs)

Bases: IOBase

Basic interface class to select specific elements from a list

Examples

>>> from nipype.interfaces.utility import Select
>>> sl = Select()
>>> _ = sl.inputs.trait_set(inlist=[1, 2, 3, 4, 5], index=[3])
>>> out = sl.run()
>>> out.outputs.out
4

>>> _ = sl.inputs.trait_set(inlist=[1, 2, 3, 4, 5], index=[3, 4])
>>> out = sl.run()
>>> out.outputs.out
[4, 5]

Mandatory Inputs

indexa list of items which are an integer

0-based indices of values to choose.

inlista list of items which are any value

List of values to choose from.

Outputs

outa list of items which are any value

List of selected values.

class nipype.interfaces.utility.base.Split(from_file=None, resource_monitor=None, ignore_exception=False, **inputs)

Bases: IOBase

Basic interface class to split lists into multiple outputs

Examples

>>> from nipype.interfaces.utility import Split
>>> sp = Split()
>>> _ = sp.inputs.trait_set(inlist=[1, 2, 3], splits=[2, 1])
>>> out = sp.run()
>>> out.outputs.out1
[1, 2]

Mandatory Inputs

inlista list of items which are any value

List of values to split.

splitsa list of items which are an integer

Number of outputs in each split - should add to number of inputs.

Optional Inputs

squeezea boolean

Unfold one-element splits removing the list. (Nipype default value: False)

output_spec

alias of DynamicTraitedSpec