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)[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 theapplyArgStyle()
function.When a
SHOW_IF_TRUE
argument isTrue
, 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 theapplyArgStyle()
function.When a
HIDE_IF_TRUE
argument isTrue
, 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
andvalsep
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 forvalue
are as followsSHOW_IF_TRUE
- if the argument is present, andTrue
inkwargs
, the command line option will be added (without any arguments).HIDE_IF_TRUE
- if the argument is present, andFalse
inkwargs
, 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 thefileOrImage()
andfileOrArray()
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 typeThing
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 ofLOAD
).Return value
Functions decorated with a
FileOrThing
decorator will always return adict
-like object, where the function’s actual return value is accessible via an attribute calledstdout
. All output arguments with a value ofLOAD
will be present as dictionary entries, with the keyword argument names used as keys; these values will also be accessible as attributes of the results dict, when possible. AnyLOAD
output arguments which were not generated by the function will not be present in the dictionary.Cluster submission
The above description holds in all situations, except when an argument called
submit
is passed, and is set to a value which evaluates toTrue
. In this case, theFileOrThing
decorator will pass all arguments straight through to the decorated function, and will return its return value unchanged.This is because most functions that are decorated with the
fileOrImage()
orfileOrArray()
decorators will invoke a call torun.run()
orrunfsl()
, where a value ofsubmit=True
will cause the command to be executed asynchronously on a cluster platform.A
ValueError
will be raised if the decorated function is called withsubmit=True
, and with any in-memory objects orLOAD
symbols.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 withfileToArray()
, 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 # "stdout" on the dict assert concat('atob.txt', 'btoc.txt', 'atoc.mat').stdout == 'Done' # Outputs to be loaded into memory # are returned in a dictionary, # with argument names as keys. Values # can be accessed as dict items, or # as attributes. atoc = concat('atob.txt', 'btoc.txt', LOAD)['atoc'] 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 otherFileOrThing
decorators, and other decorators. When multipleFileOrThing
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 theFileOrThing
decorators are adjacent to each other.-
class
Results
(stdout)[source]¶ Bases:
dict
A custom
dict
type used to return outputs from a function decorated withFileOrThing
. All outputs are stored as dictionary items, with the argument name as key, and the output object (the “thing”) as value.Where possible (i.e. for outputs named with a valid Python identifier), the outputs are also made accessible as attributes of the
Results
object.The decorated function’s actual return value is accessible via the
stdout()
property.-
property
stdout
¶ Access the return value of the decorated function.
-
property
-
class
-
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 orImage
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.
To be able to distinguish between input values and input file paths, the
fileOrText
decorator requires that input and output file paths are passed in aspathlib.Path
objects. For example, given a function like this:@fileOrText() def myfunc(infile, outfile): ...
if we want to pass file paths for both
infile
andoutfile
, we would do this:from pathlib import Path myfunc(Path('input.txt'), Path('output.txt'))
Input values may be passed in as normal strings, e.g.:
myfunc('input data', Path('output.txt'))
Output values can be loaded as normal via the
LOAD
symbol, e.g.:myfunc(Path('input.txt'), LOAD)