`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._update_wrapper(wrapper, wrapped, *args, **kwargs)[source]¶

Replacement for the built-in functools.update_wrapper. This implementation ensures that the wrapper function has an attribute called __wrapped__, which refers to the wrapped function.

This custom function is only needed in Python versions < 3.4.

fsl.wrappers.wrapperutils._unwrap(func)[source]¶: Replacement for the built-in inspect.unwrap function, which is not present in Python versions prior to 3.4.

fsl.wrappers.wrapperutils.cmdwrapper(func)[source]¶: 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)[source]¶: 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)[source]¶

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)[source]¶

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.

class fsl.wrappers.wrapperutils._FileOrThing(func, prepIn, prepOut, load, removeExt, *args, **kwargs)[source]¶

Bases: object

Decorator which ensures that certain arguments which are passed into the decorated function are always passed as file names. Both positional and keyword arguments can be specified.

The _FileOrThing class is not intended to be used directly - see the fileOrImage() and fileOrArray() decorator functions for more details.

These decorators are intended for functions which wrap a command-line tool, i.e. where some inputs/outputs need to be specified as file names.

Inputs

Any arguments which are not of type Thing are passed through to the decorated function unmodified. Arguments which are of type Thing are saved to a temporary file, and the name of that file is passed to the function.

Outputs

If an argument is given the special LOAD value, it is assumed to be an output argument. In this case, it is replaced with a temporary file name then, after the function has completed, that file is loaded into memory, and the value returned (along with the function’s output, and any other arguments with a value of LOAD).

Return value

Functions decorated with a _FileOrThing decorator will always return a dict-like object, where the function’s actual return value is accessible via an attribute called output. All output arguments with a value of LOAD will be present as dictionary entries, with the keyword argument names used as keys. Any LOAD output arguments which were not generated by the function will not be present in the dictionary.

Example

As an example of using the fileOrArray decorator on a function which concatenates two files containing affine transformations, and saves the output to a file:

# if atob, btoc, or output are passed
# in as arrays, they are converted to
# file names.
@fileOrArray('atob', 'btoc', 'output')
def concat(atob, btoc, output=None):

    # inputs are guaranteed to be files
    atob = np.loadtxt(atob)
    btoc = np.loadtxt(atoc)

    atoc = np.dot(btoc, atob)

    if output is not None:
        np.savetxt(output, atoc)

    return 'Done'

Because we have decorated the concat function with fileToArray(), it can be called with either file names, or Numpy arrays:

# All arguments are passed through
# unmodified - the output will be
# saved to a file called atoc.mat.
concat('atob.txt', 'btoc.txt', 'atoc.mat')

# The function's return value
# is accessed via an attribute called
# "output" on the dict
assert concat('atob.txt', 'btoc.txt', 'atoc.mat').output == 'Done'

# Outputs to be loaded into memory
# are returned in a dictionary,
# with argument names as keys.
atoc = concat('atob.txt', 'btoc.txt', LOAD)['atoc']

# In-memory inputs are saved to
# temporary files, and those file
# names are passed to the concat
# function.
atoc = concat(np.diag([2, 2, 2, 0]),
              np.diag([3, 3, 3, 3]), LOAD)['atoc']

Using with other decorators

_FileOrThing decorators can be chained with other _FileOrThing decorators, and other decorators. When multiple _FileOrThing decorators are used on a single function, the outputs from each decorator are merged together into a single dict-like object.

_FileOrThing decorators can be used with any other decorators as long as they do not manipulate the return value, and as long as the _FileOrThing decorators are adjacent to each other.

class _Results(output)[source]¶

Bases: dict

A custom dict type used to return outputs from a function decorated with _FileOrThing. All outputs are stored as dictionary items, with the argument name as key, and the output object (the “thing”) as value.

The decorated function’s actual return value is accessible via the output() property.

__init__(output)[source]¶: Initialize self. See help(type(self)) for accurate signature.

output¶: Access the return value of the decorated function.

__dict__ = mappingproxy({'__module__': 'fsl.wrappers.wrapperutils', '__doc__': 'A custom ``dict`` type used to return outputs from a function\n decorated with ``_FileOrThing``. All outputs are stored as dictionary\n items, with the argument name as key, and the output object (the\n "thing") as value.\n\n The decorated function\'s actual return value is accessible via the\n :meth:`output` property.\n ', '__init__': <function _FileOrThing._Results.__init__>, 'output': <property object>, '__dict__': <attribute '__dict__' of '_Results' objects>, '__weakref__': <attribute '__weakref__' of '_Results' objects>})¶

__module__ = 'fsl.wrappers.wrapperutils'¶

__weakref__¶: list of weak references to the object (if defined)

__init__(func, prepIn, prepOut, load, removeExt, *args, **kwargs)[source]¶

Initialise a _FileOrThing decorator.

Parameters:

func – The function to be decorated.
prepIn – Function which returns a file name to be used in place of an input argument.
prepOut – Function which generates a file name to use for arguments that were set to LOAD.
load – Function which is called to load items for arguments that were set to LOAD. Must accept a file path as its sole argument.
removeExt – Function which can remove a file extension from a file path.
outprefix – Must be passed as a keyword argument. The name of a positional or keyword argument to the function, which specifies an output file name prefix. All other arguments with names that begin with this prefix may be interpreted as things to LOAD.

All other positional arguments are interpreted as the names of the arguments to the function which will be handled by this _FileOrThing decorator. If not provided, all arguments passed to the function will be handled.

The prepIn and prepOut functions must accept the following positional arguments:

A directory in which all temporary input/output files should be stored

The name of the keyword argument to be processed

The argument value that was passed in

__call__(*args, **kwargs)[source]¶

Function which calls func, ensuring that any arguments of type Thing are saved to temporary files, and any arguments with the value LOAD are loaded and returned.

All other arguments are passed through to func.

_FileOrThing__generateResult(workdir, result, outprefix, outfiles, prefixes)¶

Loads function outputs and returns a _Results object.

Called by __call__() after the decorated function has been called. Figures out what files should be loaded, and loads them into a _Results object.

Parameters:

workdir – Directory which contains the function outputs.
result – Function return value.
outprefix – Original output prefix that was passed into the function (or None if one wasn’t passed)
outfiles – Dictionary containing output files to be loaded (see __prepareArgs()).
prefixes – Dictionary containing output-prefix patterns to be loaded (see __prepareArgs()).

Returns:

A _Results object containing all loaded outputs.

_FileOrThing__prepareArgs(parent, workdir, argnames, args, kwargs)¶

Prepares all input and output arguments to be passed to the decorated function. Any arguments with a value of LOAD are passed to the prepOut function specified at __init__(). All other arguments are passed through the prepIn function.

Parameters:

parent – True if this _FileOrThing is the first in a chain of _FileOrThing decorators.
workdir – Directory in which all temporary files should be stored.
args – Positional arguments to be passed to the decorated function.
kwargs – Keyword arguments to be passed to the decorated function.

Returns:

A tuple containing:

An updated copy of args.
An updated copy of kwargs.
The output file prefix that was actually passed in (it is subsequently modified so that prefixed outputs are redirected to a temporary location). All prefixed outputs that are not LOAD``ed should be moved into this directory. ``None if there is no output prefix.
A dictionary of { name : filename } mappings, for all arguments with a value of LOAD.
A dictionary { filepat : replstr } paths, for all output-prefix arguments with a value of LOAD.

__dict__ = mappingproxy({'__module__': 'fsl.wrappers.wrapperutils', '__doc__': 'Decorator which ensures that certain arguments which are passed into the\n decorated function are always passed as file names. Both positional and\n keyword arguments can be specified.\n\n\n The ``_FileOrThing`` class is not intended to be used directly - see the\n :func:`fileOrImage` and :func:`fileOrArray` decorator functions for more\n details.\n\n\n These decorators are intended for functions which wrap a command-line tool,\n i.e. where some inputs/outputs need to be specified as file names.\n\n\n **Inputs**\n\n\n Any arguments which are not of type ``Thing`` are passed through to the\n decorated function unmodified. Arguments which are of type ``Thing`` are\n saved to a temporary file, and the name of that file is passed to the\n function.\n\n\n **Outputs**\n\n\n If an argument is given the special :data:`LOAD` value, it is assumed\n to be an output argument. In this case, it is replaced with a temporary\n file name then, after the function has completed, that file is loaded\n into memory, and the value returned (along with the function\'s output,\n and any other arguments with a value of ``LOAD``).\n\n\n **Return value**\n\n\n Functions decorated with a ``_FileOrThing`` decorator will always return a\n ``dict``-like object, where the function\'s actual return value is\n accessible via an attribute called ``output``. All output arguments with a\n value of ``LOAD`` will be present as dictionary entries, with the keyword\n argument names used as keys. Any ``LOAD`` output arguments which were not\n generated by the function will not be present in the dictionary.\n\n\n **Example**\n\n\n As an example of using the ``fileOrArray`` decorator on a function\n which concatenates two files containing affine transformations, and\n saves the output to a file::\n\n # if atob, btoc, or output are passed\n # in as arrays, they are converted to\n # file names.\n @fileOrArray(\'atob\', \'btoc\', \'output\')\n def concat(atob, btoc, output=None):\n\n # inputs are guaranteed to be files\n atob = np.loadtxt(atob)\n btoc = np.loadtxt(atoc)\n\n atoc = np.dot(btoc, atob)\n\n if output is not None:\n np.savetxt(output, atoc)\n\n return \'Done\'\n\n\n Because we have decorated the ``concat`` function with :func:`fileToArray`,\n it can be called with either file names, or Numpy arrays::\n\n\n # All arguments are passed through\n # unmodified - the output will be\n # saved to a file called atoc.mat.\n concat(\'atob.txt\', \'btoc.txt\', \'atoc.mat\')\n\n # The function\'s return value\n # is accessed via an attribute called\n # "output" on the dict\n assert concat(\'atob.txt\', \'btoc.txt\', \'atoc.mat\').output == \'Done\'\n\n # Outputs to be loaded into memory\n # are returned in a dictionary,\n # with argument names as keys.\n atoc = concat(\'atob.txt\', \'btoc.txt\', LOAD)[\'atoc\']\n\n # In-memory inputs are saved to\n # temporary files, and those file\n # names are passed to the concat\n # function.\n atoc = concat(np.diag([2, 2, 2, 0]),\n np.diag([3, 3, 3, 3]), LOAD)[\'atoc\']\n\n\n **Using with other decorators**\n\n\n ``_FileOrThing`` decorators can be chained with other ``_FileOrThing``\n decorators, and other decorators. When multiple ``_FileOrThing``\n decorators are used on a single function, the outputs from each decorator\n are merged together into a single dict-like object.\n\n\n ``_FileOrThing`` decorators can be used with any other decorators\n **as long as** they do not manipulate the return value, and as long as\n the ``_FileOrThing`` decorators are adjacent to each other.\n ', '_Results': <class 'fsl.wrappers.wrapperutils._FileOrThing._Results'>, '__init__': <function _FileOrThing.__init__>, '__call__': <function _FileOrThing.__call__>, '_FileOrThing__prepareArgs': <function _FileOrThing.__prepareArgs>, '_FileOrThing__generateResult': <function _FileOrThing.__generateResult>, '__dict__': <attribute '__dict__' of '_FileOrThing' objects>, '__weakref__': <attribute '__weakref__' of '_FileOrThing' objects>})¶

__module__ = 'fsl.wrappers.wrapperutils'¶

__weakref__¶: list of weak references to the object (if defined)

fsl.wrappers.wrapperutils.fileOrImage(*args, **kwargs)[source]¶: 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)[source]¶: 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)[source]¶: 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.

fsl.wrappers.wrapperutils¶

`fsl.wrappers.wrapperutils`¶