nipype.interfaces.utility.base module¶
# changing to temporary directories >>> tmp = getfixture(‘tmpdir’) >>> old = tmp.chdir()
AssertEqual¶
Bases: BaseInterface
- Mandatory Inputs
volume1 (a pathlike object or string representing an existing file)
volume2 (a pathlike object or string representing an existing file)
IdentityInterface¶
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.
- IdentityInterface.input_spec¶
- IdentityInterface.output_spec¶
Merge¶
Bases: IOBase
Basic interface class to merge inputs into a single list
Merge(1)
will merge a list of listsExamples
>>> 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_flatten (a boolean) – Append to outlist instead of extending in vstack mode. (Nipype default value:
False
)ravel_inputs (a boolean) – Ravel inputs when no_flatten is False. (Nipype default value:
False
)- Outputs
out (a list of items which are any value) – Merged output.
Rename¶
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_string (a string) – Python formatting string for output template.
in_file (a pathlike object or string representing an existing file) – File to rename.
- Optional Inputs
keep_ext (a boolean) – Keep in_file extension, replace non-extension component of name.
parse_string (a string) – Python regexp parse string to define replacement inputs.
use_fullpath (a boolean) – Use full path as input to regex parser. (Nipype default value:
False
)- Outputs
out_file (a pathlike object or string representing an existing file) – Softlink to original file with new name.
- Rename.input_spec¶
- class nipype.interfaces.utility.base.RenameInputSpec(**kwargs)¶
Select¶
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
index (a list of items which are an integer) – 0-based indices of values to choose.
inlist (a list of items which are any value) – List of values to choose from.
- Outputs
out (a list of items which are any value) – List of selected values.
Split¶
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
inlist (a list of items which are any value) – List of values to split.
splits (a list of items which are an integer) – Number of outputs in each split - should add to number of inputs.
- Optional Inputs
squeeze (a boolean) – Unfold one-element splits removing the list. (Nipype default value:
False
)
- Split.output_spec¶