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# interfaces.utility

## AssertEqual

Link to code

Inputs:

    [Mandatory]
    volume1: (an existing file name)
    volume2: (an existing file name)

    [Optional]
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run

Outputs:

    None

## CSVReader

Link to code

### Examples

    >>> reader = CSVReader()
    >>> reader.inputs.in_file = 'noHeader.csv'
    >>> out = reader.run()
    >>> out.outputs.column_0 == ['foo', 'bar', 'baz']
    True
    >>> out.outputs.column_1 == ['hello', 'world', 'goodbye']
    True
    >>> out.outputs.column_2 == ['300.1', '5', '0.3']
    True

    >>> reader = CSVReader()
    >>> reader.inputs.in_file = 'header.csv'
    >>> reader.inputs.header = True
    >>> out = reader.run()
    >>> out.outputs.files == ['foo', 'bar', 'baz']
    True
    >>> out.outputs.labels == ['hello', 'world', 'goodbye']
    True
    >>> out.outputs.erosion == ['300.1', '5', '0.3']
    True

Inputs:

    [Mandatory]
    in_file: (an existing file name)
            Input comma-seperated value (CSV) file

    [Optional]
    header: (a boolean, nipype default value: False)
            True if the first line is a column header

Outputs:

    None

## Function

Link to code

Runs arbitrary function as an interface

### Examples

    >>> func = 'def func(arg1, arg2=5): return arg1 + arg2'
    >>> fi = Function(input_names=['arg1', 'arg2'], output_names=['out'])
    >>> fi.inputs.function_str = func
    >>> res = fi.run(arg1=1)
    >>> res.outputs.out
    ~

Inputs:

    [Mandatory]
    function_str: (a string)
            code for function

    [Optional]
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run

Outputs:

    None

## IdentityInterface

Link to code

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.

Inputs:

    None

Outputs:

    None

## Merge

Link to code

Basic interface class to merge inputs into a single list

### 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]

Inputs:

    [Mandatory]

    [Optional]
    axis: ('vstack' or 'hstack', nipype default value: vstack)
            direction in which to merge, hstack requires same number of elements
            in each input
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    no_flatten: (a boolean, nipype default value: False)
            append to outlist instead of extending in vstack mode

Outputs:

    out: (a list of items which are any value)
            Merged output

## Rename

Link to code

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 = "zstat1.nii.gz"
    >>> rename1.inputs.format_string = "Faces-Scenes.nii.gz"
    >>> res = rename1.run()
    >>> print res.outputs.out_file
    'Faces-Scenes.nii.gz"

    >>> rename2 = Rename(format_string="%(subject_id)s_func_run%(run)02d")
    >>> rename2.inputs.in_file = "functional.nii"
    >>> rename2.inputs.keep_ext = True
    >>> rename2.inputs.subject_id = "subj_201"
    >>> rename2.inputs.run = 2
    >>> res = rename2.run()
    >>> print 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 = "func_epi_1_1.nii"
    >>> rename3.inputs.parse_string = "func_(?P<seq>\w*)_.*"
    >>> rename3.inputs.subject_id = "subj_201"
    >>> rename3.inputs.run = 2
    >>> res = rename3.run()
    >>> print res.outputs.out_file
    'subj_201_epi_run02.nii'

Inputs:

    [Mandatory]
    format_string: (a string)
            Python formatting string for output template
    in_file: (an existing file name)
            file to rename

    [Optional]
    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, nipype default value: False)
            Use full path as input to regex parser

Outputs:

    out_file: (a file name)
            softlink to original file with new name

## Select

Link to code

Basic interface class to select specific elements from a list

### Examples

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

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

Inputs:

    [Mandatory]
    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

    [Optional]
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run

Outputs:

    out: (a list of items which are any value)
            list of selected values

## Split

Link to code

Basic interface class to split lists into multiple outputs

### Examples

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

Inputs:

    [Mandatory]
    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]
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    squeeze: (a boolean, nipype default value: False)
            unfold one-element splits removing the list

Outputs:

    None