fsl.wrappers.wrapperutils

This module contains functions and decorators used by the FSL wrapper functions.

The cmdwrapper() and fslwrapper() functions are convenience decorators which allow you to write your wrapper function such that it simply generates the command-line needed to respectively run a standard shell command or a FSL command. For example:

@fslwrapper
def fslreorient2std(input, output):
    return ['fslreorient2std', input, output]

When this fslreorient2std function is called, the fslwrapper decorator will take care of invoking the command in a standardised way.

The applyArgStyle() function can be used to automatically convert keyword arguments into command-line arguments, based on a set of standard patterns. For example:

@fslwrapper
def flirt(src, ref, **kwargs):
    cmd  = ['flirt', '-in', src, '-ref', ref]
    return cmd + applyArgStyle('-=', **kwargs)

The fileOrImage() and fileOrArray() functions can be used to decorate a wrapper function such that in-memory nibabel images or Numpy arrays can be passed in as arguments - they will be automatically saved out to files, and then the file names passed into the wrapper function. For example:

@fileOrImage('src', 'ref')
@fslwrapper
def flirt(src, ref, **kwargs):
    cmd  = ['flirt', '-in', src, '-ref', ref]
    return cmd + applyArgStyle('-=', **kwargs)

Now this flirt function can be called either with file names, or nibabel images.

Note

Because the fileOrImage() and fileOrArray() decorators manipulate the return value of the decorated function, they should be applied after any other decorators. Furthermore, if you need to apply both a fileOrImage and fileOrArray decorator to a function, they should be grouped together, e.g.:

@fileOrImage('a', 'b')
@fileOrArray('c', 'd')
@fslwrapper
def func(**kwargs):
    ...

Command outputs can also be loaded back into memory by using the special LOAD value when calling a wrapper function. For example:

@fileOrImage('src', 'ref', 'out')
@fslwrapper
def flirt(src, ref, **kwargs):
    cmd  = ['flirt', '-in', src, '-ref', ref]
    return cmd + applyArgStyle('-=', **kwargs)

If we set the out argument to LOAD, the output image will be loaded and returned:

src     = nib.load('src.nii')
ref     = nib.load('ref.nii')
aligned = flirt(src, ref, out=LOAD)['out']
fsl.wrappers.wrapperutils.cmdwrapper(func)

This decorator can be used on functions which generate a command line. It will pass the return value of the function to the fsl.utils.run.run() function in a standardised manner.

fsl.wrappers.wrapperutils.fslwrapper(func)

This decorator can be used on functions which generate a FSL command line. It will pass the return value of the function to the fsl.utils.run.runfsl() function in a standardised manner.

fsl.wrappers.wrapperutils.SHOW_IF_TRUE = <object object>

Constant to be used in the valmap passed to the applyArgStyle() function.

When a SHOW_IF_TRUE argument is True, it is added to the generated command line arguments.

fsl.wrappers.wrapperutils.HIDE_IF_TRUE = <object object>

Constant to be used in the valmap passed to the applyArgStyle() function.

When a HIDE_IF_TRUE argument is True, it is suppressed from the generated command line arguments.

fsl.wrappers.wrapperutils.applyArgStyle(style, valsep=None, argmap=None, valmap=None, singlechar_args=False, **kwargs)

Turns the given kwargs into command line options. This function is intended to be used to automatically generate command line options from arguments passed into a Python function.

The style and valsep arguments control how key-value pairs are converted into command-line options:

style

valsep

Result

'-'

' '

-name val1 val2 val3

'-'

'"'

-name "val1 val2 val3"

'-'

','

-name val1,val2,val3

'--'

' '

--name val1 val2 val3

'--'

'"'

--name "val1 val2 val3"

'--'

','

--name val1,val2,val3

'-='

' '

Not supported

'-='

'"'

-name="val1 val2 val3"

'-='

','

-name=val1,val2,val3

'--='

' '

Not supported

'--='

'"'

--name="val1 val2 val3"

'--='

','

--name=val1,val2,val3

Parameters
  • style – Controls how the kwargs are converted into command-line options - must be one of '-', '--', '-=', or '--='.

  • valsep – Controls how the values passed to command-line options which expect multiple arguments are delimited - must be one of ' ', ',' or '"'. Defaults to ' ' if '=' not in style, ',' otherwise.

  • argmap – Dictionary of {kwarg-name : cli-name} mappings. This can be used if you want to use different argument names in your Python function for the command-line options.

  • valmap

    Dictionary of {cli-name : value} mappings. This can be used to define specific semantics for some command-line options. Acceptable values for value are as follows

    • SHOW_IF_TRUE - if the argument is present, and True in kwargs, the command line option will be added (without any arguments).

    • HIDE_IF_TRUE - if the argument is present, and False in kwargs, the command line option will be added (without any arguments).

    • Any other constant value. If the argument is present in kwargs, its command-line option will be added, with the constant value as its argument.

    The argument for any options not specified in the valmap will be converted into strings.

  • singlechar_args – If True, single character arguments always take a single hyphen prefix (e.g. -h) regardless of the style.

  • kwargs – Arguments to be converted into command-line options.

Returns

A list containing the generated command-line options.

fsl.wrappers.wrapperutils.namedPositionals(func, args)

Given a function, and a sequence of positional arguments destined for that function, identifies the name for each positional argument. Variable positional arguments are given an automatic name.

Parameters
  • func – Function which will accept args as positionals.

  • args – Tuple of positional arguments to be passed to func.

fsl.wrappers.wrapperutils.LOAD = <object object>

Constant used by the _FileOrThing class to indicate that an output file should be loaded into memory and returned as a Python object.

fsl.wrappers.wrapperutils.fileOrImage(*args, **kwargs)

Decorator which can be used to ensure that any NIfTI images are saved to file, and output images can be loaded and returned as nibabel image objects or Image objects.

fsl.wrappers.wrapperutils.fileOrArray(*args, **kwargs)

Decorator which can be used to ensure that any Numpy arrays are saved to text files, and output files can be loaded and returned as Numpy arrays.

fsl.wrappers.wrapperutils.fileOrText(*args, **kwargs)

Decorator which can be used to ensure that any text output (e.g. log file) are saved to text files, and output files can be loaded and returned as strings.