nipype.interfaces.utility.base module¶
# changing to temporary directories >>> tmp = getfixture(‘tmpdir’) >>> old = tmp.chdir()
AssertEqual¶
Bases: BaseInterface
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¶
alias of
DynamicTraitedSpec
- IdentityInterface.output_spec¶
alias of
DynamicTraitedSpec
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]]
- 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
)
- outa 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'
- format_stringa string
Python formatting string for output template.
- in_filea pathlike object or string representing an existing file
File to rename.
- 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
)
- out_filea pathlike object or string representing an existing file
Softlink to original file with new name.
- Rename.input_spec¶
alias of
RenameInputSpec
- 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]
- 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.
- outa 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]
- 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.
- squeezea boolean
Unfold one-element splits removing the list. (Nipype default value:
False
)
- Split.output_spec¶
alias of
DynamicTraitedSpec