diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 371404bc22438c8526386453de3d99183daaf155..482b9abfc76ebdbb9d69c384ad2b276ecbf4f92a 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -10,6 +10,8 @@ Added
^^^^^
+* New wrapper functions for the FSL :func:`.prelude` and :func:`applyxfm4D`
+ commands.
* New ``firstDot`` option to the :func:`.path.getExt`,
:func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering
rudimentary support for double-barrelled filenames.
@@ -21,9 +23,38 @@ Changed
* The :func:`.gifti.relatedFiles` function now supports files with
BIDS-style naming conventions.
+* The :func:`.run.run` and :func:`.run.runfsl` functions now pass through
+ any additional keyword arguments to ``subprocess.Popen``.
+* The :func:`.run.runfsl` function now raises an error on attempts to
+ run a command which is not present in ``$FSLDIR/bin/`` (e.g. ``ls``).
* The :mod:`.bids` module has been updated to support files with any
extension, not just those in the core BIDS specification (``.nii``,
``.nii.gz``, ``.json``, ``.tsv``).
+* The return value of a function decorated with :func:`.fileOrImage`,
+ :func:`.fileOrArray`, or :func:`.fileOrText` is now accessed via an attribute
+ called ``stdout``, instead of ``output``.
+* Output files of functions decorated with :func:`.fileOrImage`,
+ :func:`.fileOrArray`, or :func:`.fileOrText`, which have been loaded via the
+ :attr:`.LOAD` symbol, can now be accessed as attributes of the returned
+ results object, in addition to being accessed as dict items.
+* Wrapper functions decorated with the :func:`.fileOrImage`,
+ :func:`.fileOrArray`, or :func:`.fileOrText` decorators will now pass all
+ arguments and return values through unchanged if an argument called ``submit``
+ is passed in, and is set to ``True`` (or any non-``False``
+ value). Furthermore, in such a scenario a :exc:`ValueError` will be raised if
+ any in-memory objects or ``LOAD`` symbols are passed.
+* The :func:`.fileOrText` decorator has been updated to work with input
+ values - file paths must be passed in as ``pathlib.Path`` objects, so they
+ can be differentiated from input values.
+
+
+Fixed
+^^^^^
+
+
+* Updated the :func:`.prepareArgs` function to use ``shlex.split`` when
+ preparing shell command arguments, instead of performing a naive whitespace
+ split.
2.8.4 (Monday 2nd March 2020)
@@ -213,8 +244,8 @@ Changed
* The :class:`.Cache` class has a new ``lru`` option, allowing it to be used
as a least-recently-used cache.
-* The :mod:`.filetree` module has been refactored to make it easier for the
- :mod:`.query` module to work with file tree hierarchies.
+* The :mod:`fsl.utils.filetree` module has been refactored to make it easier
+ for the :mod:`.query` module to work with file tree hierarchies.
* The :meth:`.LabelAtlas.get` method has a new ``binary`` flag, allowing
either a binary mask, or a mask with the original label value, to be
returned.
diff --git a/doc/conf.py b/doc/conf.py
index 792b358e7bfa05bf7b5dcd050d4360dd61accec2..804db7ee21fadb60cb323c44f4cf71faee4253f5 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -56,7 +56,7 @@ master_doc = 'index'
# General information about the project.
project = u'fslpy'
-copyright = u'{}, Paul McCarthy, University of Oxford, Oxford, UK'.format(
+copyright = u'{}, FMRIB Centre, University of Oxford, Oxford, UK'.format(
date.year)
# Links to other things
diff --git a/fsl/utils/image/__init__.py b/fsl/utils/image/__init__.py
index 54dde4b2a7c40e1c97f8b7fcfaa4f86d1b5781b5..a0d9ace49d800c95f6a8e62921c1a97e9632d096 100644
--- a/fsl/utils/image/__init__.py
+++ b/fsl/utils/image/__init__.py
@@ -10,8 +10,7 @@ manipulating and working with :class:`.Image` objects.
The following modules are available:
.. autosummary::
- :nosignature
- .image.resample
- .image.roi
+ fsl.utils.image.resample
+ fsl.utils.image.roi
"""
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index 12cc036067d7c502afbca6cd90153c38ced00859..7211965d773f03d6c3abd583e3a4776bebaf7c2c 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -3,6 +3,7 @@
# run.py - Functions for running shell commands
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
#
"""This module provides some functions for running shell commands.
@@ -20,6 +21,7 @@
import sys
+import shlex
import logging
import threading
import contextlib
@@ -81,7 +83,7 @@ def prepareArgs(args):
# Argument was a command string
if isinstance(args[0], six.string_types):
- args = args[0].split()
+ args = shlex.split(args[0])
# Argument was an unpacked sequence
else:
@@ -164,17 +166,21 @@ def run(*args, **kwargs):
- cmd: Optional file-like object to which the command
itself is logged.
+ All other keyword arguments are passed through to the ``subprocess.Popen``
+ object (via :func:`_realrun`), unless ``submit=True``, in which case they
+ are ignored.
+
:returns: If ``submit`` is provided, the return value of
:func:`.fslsub` is returned. Otherwise returns a single
value or a tuple, based on the based on the ``stdout``,
``stderr``, and ``exitcode`` arguments.
"""
- returnStdout = kwargs.get('stdout', True)
- returnStderr = kwargs.get('stderr', False)
- returnExitcode = kwargs.get('exitcode', False)
- submit = kwargs.get('submit', {})
- log = kwargs.get('log', {})
+ returnStdout = kwargs.pop('stdout', True)
+ returnStderr = kwargs.pop('stderr', False)
+ returnExitcode = kwargs.pop('exitcode', False)
+ submit = kwargs.pop('submit', {})
+ log = kwargs.pop('log', {})
tee = log .get('tee', False)
logStdout = log .get('stdout', None)
logStderr = log .get('stderr', None)
@@ -206,7 +212,7 @@ def run(*args, **kwargs):
# Run directly - delegate to _realrun
stdout, stderr, exitcode = _realrun(
- tee, logStdout, logStderr, logCmd, *args)
+ tee, logStdout, logStderr, logCmd, *args, **kwargs)
if not returnExitcode and (exitcode != 0):
raise RuntimeError('{} returned non-zero exit code: {}'.format(
@@ -221,7 +227,6 @@ def run(*args, **kwargs):
else: return tuple(results)
-
def _dryrun(submit, returnStdout, returnStderr, returnExitcode, *args):
"""Used by the :func:`run` function when the :attr:`DRY_RUN` flag is
active.
@@ -242,7 +247,7 @@ def _dryrun(submit, returnStdout, returnStderr, returnExitcode, *args):
else: return tuple(results)
-def _realrun(tee, logStdout, logStderr, logCmd, *args):
+def _realrun(tee, logStdout, logStderr, logCmd, *args, **kwargs):
"""Used by :func:`run`. Runs the given command and manages its standard
output and error streams.
@@ -261,12 +266,14 @@ def _realrun(tee, logStdout, logStderr, logCmd, *args):
:arg args: Command to run
+ :arg kwargs: Passed through to the ``subprocess.Popen`` object.
+
:returns: A tuple containing:
- the command's standard output as a string.
- the command's standard error as a string.
- the command's exit code.
"""
- proc = sp.Popen(args, stdout=sp.PIPE, stderr=sp.PIPE)
+ proc = sp.Popen(args, stdout=sp.PIPE, stderr=sp.PIPE, **kwargs)
with tempdir.tempdir(changeto=False) as td:
# We always direct the command's stdout/
@@ -352,6 +359,12 @@ def runfsl(*args, **kwargs):
args[0] = cmdpath
break
+ # error if the command cannot
+ # be found in a FSL directory
+ else:
+ raise FileNotFoundError('FSL tool {} not found (checked {})'.format(
+ args[0], ', '.join(prefixes)))
+
return run(*args, **kwargs)
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index 453313f2ca14e592732cf8866cabd78065413d29..5e1f61e89dda468017033e20b526712d70dda4c4 100644
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -87,6 +87,7 @@ from .fsl_anat import (fsl_anat,) # noqa
from .flirt import (flirt, # noqa
invxfm,
applyxfm,
+ applyxfm4D,
concatxfm,
mcflirt)
from .fnirt import (fnirt, # noqa
@@ -95,6 +96,7 @@ from .fnirt import (fnirt, # noqa
convertwarp)
from .fslmaths import (fslmaths,) # noqa
from .fugue import (fugue, # noqa
+ prelude,
sigloss)
from .melodic import (melodic, # noqa
fsl_regfilt)
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index 8b5d1d526dc6a893441204d788d58b7302d59260..df7eb2722b19954303ef36132f7d7f36365ac673 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -14,6 +14,7 @@ tools.
flirt
applyxfm
+ applyxfm4D
invxfm
concatxfm
mcflirt
@@ -70,6 +71,25 @@ def applyxfm(src, ref, mat, out, interp='spline', **kwargs):
**kwargs)
+@wutils.fileOrArray('mat')
+@wutils.fileOrImage('src', 'ref', 'out')
+@wutils.fslwrapper
+def applyxfm4D(src, ref, out, mat, **kwargs):
+ """Wrapper for the ``applyxfm4D`` command. """
+
+ asrt.assertIsNifti(src, ref)
+
+ valmap = {
+ 'singlematrix' : wutils.SHOW_IF_TRUE,
+ 'fourdigit' : wutils.SHOW_IF_TRUE,
+ }
+
+ cmd = ['applyxfm4D', src, ref, out, mat]
+ cmd += wutils.applyArgStyle('-', valmap=valmap, **kwargs)
+
+ return cmd
+
+
@wutils.fileOrArray()
@wutils.fslwrapper
def invxfm(inmat, omat):
diff --git a/fsl/wrappers/fugue.py b/fsl/wrappers/fugue.py
index ced52f2267bc3140794d2baddd7de778b6bd2daa..8b61f030c5e048888692569f1be9bfc2ec1dcc9e 100644
--- a/fsl/wrappers/fugue.py
+++ b/fsl/wrappers/fugue.py
@@ -62,3 +62,24 @@ def sigloss(input, sigloss, **kwargs):
cmd += wutils.applyArgStyle('--', valmap=valmap, **kwargs)
return cmd
+
+
+@wutils.fileOrImage('complex', 'abs', 'phase', 'mask',
+ 'out', 'unwrap', 'savemask', 'rawphase', 'labels')
+@wutils.fslwrapper
+def prelude(**kwargs):
+ """Wrapper for the ``sigloss`` command."""
+
+ valmap = {
+ 'labelslices' : wutils.SHOW_IF_TRUE,
+ 'slices' : wutils.SHOW_IF_TRUE,
+ 'force3D' : wutils.SHOW_IF_TRUE,
+ 'removeramps' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ }
+
+ cmd = ['prelude'] + wutils.applyArgStyle('--=',
+ valmap=valmap,
+ **kwargs)
+
+ return cmd
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 81fb86826849b6a4eb55c9012f71c0c61cf40cc6..f325bca18d5f5c38990b0db57c8066746acf392a 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -95,6 +95,7 @@ import sys
import glob
import random
import string
+import pathlib
import fnmatch
import inspect
import logging
@@ -154,12 +155,12 @@ def cmdwrapper(func):
:func:`fsl.utils.run.run` function in a standardised manner.
"""
def wrapper(*args, **kwargs):
- stdout = kwargs.pop('stdout', True)
- stderr = kwargs.pop('stderr', True)
+ stdout = kwargs.pop('stdout', True)
+ stderr = kwargs.pop('stderr', True)
exitcode = kwargs.pop('exitcode', False)
- submit = kwargs.pop('submit', None)
- log = kwargs.pop('log', {'tee' : True})
- cmd = func(*args, **kwargs)
+ submit = kwargs.pop('submit', None)
+ log = kwargs.pop('log', {'tee' : True})
+ cmd = func(*args, **kwargs)
return run.run(cmd,
stderr=stderr,
log=log,
@@ -175,12 +176,12 @@ def fslwrapper(func):
:func:`fsl.utils.run.runfsl` function in a standardised manner.
"""
def wrapper(*args, **kwargs):
- stdout = kwargs.pop('stdout', True)
- stderr = kwargs.pop('stderr', True)
+ stdout = kwargs.pop('stdout', True)
+ stderr = kwargs.pop('stderr', True)
exitcode = kwargs.pop('exitcode', False)
- submit = kwargs.pop('submit', None)
- log = kwargs.pop('log', {'tee' : True})
- cmd = func(*args, **kwargs)
+ submit = kwargs.pop('submit', None)
+ log = kwargs.pop('log', {'tee' : True})
+ cmd = func(*args, **kwargs)
return run.runfsl(cmd,
stderr=stderr,
log=log,
@@ -446,10 +447,33 @@ class _FileOrThing(object):
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
+ accessible via an attribute called ``stdout``. 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.
+ argument names used as keys; these values will also be accessible as
+ attributes of the results dict, when possible. Any ``LOAD`` 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 to
+ ``True``. In this case, the ``_FileOrThing`` 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
+ :func:`fileOrImage` or :func:`fileOrArray` decorators will invoke a call
+ to :func:`.run.run` or :func:`.runfsl`, where a value of ``submit=True``
+ will cause the command to be executed asynchronously on a cluster
+ platform.
+
+
+ A :exc:`ValueError` will be raised if the decorated function is called
+ with ``submit=True``, and with any in-memory objects or ``LOAD`` symbols.
**Example**
@@ -488,20 +512,23 @@ class _FileOrThing(object):
# 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'
+ # "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.
+ # 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']
+ np.diag([3, 3, 3, 3]), LOAD).atoc
**Using with other decorators**
@@ -525,16 +552,37 @@ class _FileOrThing(object):
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
- :meth:`output` property.
+ :meth:`stdout` property.
"""
- def __init__(self, output):
- self.__output = output
+
+
+ def __init__(self, stdout):
+ """Create a ``_Results`` dict.
+
+ :arg stdout: Return value of the decorated function (typically a
+ tuple containing the standard output and error of the
+ underlying command).
+ """
+ super().__init__()
+ self.__stdout = stdout
+
+
+ def __setitem__(self, key, val):
+ """Add an item to the dict. The item is also added as an attribute.
+ """
+ super().__setitem__(key, val)
+ setattr(self, key, val)
+
@property
- def output(self):
+ def stdout(self):
"""Access the return value of the decorated function. """
- return self.__output
+ return self.__stdout
def __init__(self,
@@ -604,6 +652,27 @@ class _FileOrThing(object):
func = self.__func
argnames = namedPositionals(func, args)
+ # Special case - if fsl.utils.run[fsl] is
+ # being decorated (e.g. via cmdwrapper/
+ # fslwrapper), and submit=True, this call
+ # will ultimately submit the job to the
+ # cluster, and will return immediately.
+ #
+ # We error if we are given any in-memory
+ # things, or LOAD symbols.
+ #
+ # n.b. testing values to be strings could
+ # interfere with the fileOrText decorator.
+ # Possible solution is to use pathlib?
+ if kwargs.get('submit', False):
+ allargs = {**dict(zip(argnames, args)), **kwargs}
+ for name, val in allargs.items():
+ if (name in self.__things) and \
+ (not isinstance(val, six.string_types)):
+ raise ValueError('Cannot use in-memory objects '
+ 'or LOAD with submit=True!')
+ return func(*args, **kwargs)
+
# If this _FileOrThing is being called
# by another _FileOrThing don't create
# another working directory. We do this
@@ -1032,14 +1101,39 @@ def 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.
+
+ 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 as ``pathlib.Path`` objects. For example, given a function
+ like this::
+
+ @fileOrText()
+ def myfunc(infile, outfile):
+ ...
+
+ if we want to pass file paths for both ``infile`` and ``outfile``, 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 :attr:`LOAD` symbol, e.g.::
+
+ myfunc(Path('input.txt'), LOAD)
"""
def prepIn(workdir, name, val):
infile = None
- if isinstance(val, six.string_types):
- with tempfile.NamedTemporaryFile(mode='w', suffix='.txt') as f:
+ if not isinstance(val, pathlib.Path):
+ with tempfile.NamedTemporaryFile(mode='w',
+ suffix='.txt',
+ delete=False) as f:
f.write(val)
infile = f.name
return infile
diff --git a/setup.py b/setup.py
index ea4b43f21f2978da1b4216d3bc4bffe3c8faa790..e1b4c967a72360f80883760c60f7dd25e9836097 100644
--- a/setup.py
+++ b/setup.py
@@ -105,6 +105,7 @@ setup(
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
+ 'Programming Language :: Python :: 3.8',
'Topic :: Software Development :: Libraries :: Python Modules'],
packages=packages,
diff --git a/tests/test_fslsub.py b/tests/test_fslsub.py
index 878e9b32c14d5dbb838290133b3b5ebdf87fcaa6..e2fb9ebcc934e93a2b03a160cfbe36f156754013 100644
--- a/tests/test_fslsub.py
+++ b/tests/test_fslsub.py
@@ -3,9 +3,70 @@
# test_fslsub.py - Tests functions in the fsl.utils.fslsub module.
#
# Author: Michiel Cottaar <Michiel.Cottaar@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-from fsl.utils import fslsub
+
+import os
+import os.path as op
+import sys
+import textwrap as tw
+import contextlib
+
+from fsl.utils import fslsub
+from fsl.utils.tempdir import tempdir
+
+from . import mockFSLDIR
+
+
+mock_fsl_sub = """
+#!{}
+
+import random
+import os
+import os.path as op
+import sys
+import subprocess as sp
+import fsl
+
+args = sys.argv[1:]
+
+for i in range(len(args)):
+ a = args[i]
+ if a[0] == '-':
+ if a[1] == 's':
+ i += 2
+ elif a[1] not in ('F', 'v'):
+ i += 1
+ continue
+ else:
+ break
+
+args = args[i:]
+
+env = dict(os.environ)
+env['PYTHONPATH'] = op.join(op.dirname(fsl.__file__), '..')
+
+cmd = op.basename(args[0])
+jobid = random.randint(1, 9999)
+
+with open('{{}}.o{{}}'.format(cmd, jobid), 'w') as stdout, \
+ open('{{}}.e{{}}'.format(cmd, jobid), 'w') as stderr:
+ result = sp.run(args, stdout=stdout, stderr=stderr, env=env)
+
+print(str(jobid))
+sys.exit(0)
+""".format(sys.executable).strip()
+
+
+@contextlib.contextmanager
+def fslsub_mockFSLDIR():
+ with mockFSLDIR() as fsldir:
+ fslsubbin = op.join(fsldir, 'bin', 'fsl_sub')
+ with open(fslsubbin, 'wt') as f:
+ f.write(mock_fsl_sub)
+ os.chmod(fslsubbin, 0o755)
+ yield fsldir
def test_flatten_jobids():
@@ -18,3 +79,42 @@ def test_flatten_jobids():
assert fslsub._flatten_job_ids([job_ids[:2], job_ids[2:]]) == res
assert fslsub._flatten_job_ids([set(job_ids[:2]), job_ids[2:]]) == res
assert fslsub._flatten_job_ids(((job_ids, ), job_ids + job_ids)) == res
+
+
+def test_submit():
+ script = tw.dedent("""#!/usr/bin/env bash
+ echo "standard output"
+ echo "standard error" >&2
+ exit 0
+ """).strip()
+
+ with fslsub_mockFSLDIR(), tempdir():
+ cmd = op.join('.', 'myscript')
+ with open(cmd, 'wt') as f:
+ f.write(script)
+ os.chmod(cmd, 0o755)
+
+ jid = fslsub.submit(cmd)
+ fslsub.wait(jid)
+ stdout, stderr = fslsub.output(jid)
+
+ assert stdout.strip() == 'standard output'
+ assert stderr.strip() == 'standard error'
+
+
+def myfunc():
+ print('standard output')
+ print('standard error', file=sys.stderr)
+
+
+def test_func_to_cmd():
+ with fslsub_mockFSLDIR(), tempdir():
+ cmd = fslsub.func_to_cmd(myfunc, (), {})
+ jid = fslsub.submit(cmd)
+
+ fslsub.wait(jid)
+
+ stdout, stderr = fslsub.output(jid)
+
+ assert stdout.strip() == 'standard output'
+ assert stderr.strip() == 'standard error'
diff --git a/tests/test_run.py b/tests/test_run.py
index 8e7a7a8b1327508cb9b39ba6f2a84f8867be38fc..be9e443ca5d6b6da98b3bbf6187eff339d5c11b8 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -36,6 +36,17 @@ def mkexec(path, contents):
os.chmod(path, 0o755)
+def test_prepareArgs():
+ tests = [
+ ('a b c', ['a', 'b', 'c']),
+ (['a', 'b', 'c'], ['a', 'b', 'c']),
+ ('abc "woop woop"', ['abc', 'woop woop']),
+ (['abc', 'woop woop'], ['abc', 'woop woop']),
+ ]
+
+ for args, expected in tests:
+ assert run.prepareArgs((args, )) == expected
+
def test_run():
test_script = textwrap.dedent("""
@@ -149,6 +160,25 @@ def test_run_tee():
assert capture.stdout == expstdout
+def test_run_passthrough():
+
+ test_script = textwrap.dedent("""
+ #!/bin/bash
+
+ echo "env: $RUN_TEST_ENV_VAR"
+ """).strip()
+
+ with tempdir.tempdir():
+
+ # return code == 0
+ mkexec('script.sh', test_script.format(0))
+
+ env = {'RUN_TEST_ENV_VAR' : 'howdy ho'}
+ expstdout = "env: howdy ho\n"
+
+ assert run.run('./script.sh', env=env) == expstdout
+
+
def test_dryrun():
test_script = textwrap.dedent("""
@@ -203,6 +233,10 @@ def test_runfsl():
fslplatform.fsldir = fsldir
assert run.runfsl('fslhd').strip() == 'fsldir'
+ # non-FSL command - should error
+ with pytest.raises(FileNotFoundError):
+ run.runfsl('ls')
+
# FSLDEVDIR should take precedence
fsldevdir = './fsldev'
fslhd = op.join(fsldevdir, 'bin', 'fslhd')
diff --git a/tests/test_wrappers.py b/tests/test_wrappers.py
index 9f4819af0580ac61061e6e12dfa7306be9bf779e..1759672a94c96c77cbe7946d86431d63b4cd0e83 100644
--- a/tests/test_wrappers.py
+++ b/tests/test_wrappers.py
@@ -48,7 +48,7 @@ def test_bet():
bet = op.join(fsldir, 'bin', 'bet')
result = fw.bet('input', 'output', mask=True, c=(10, 20, 30))
expected = (bet + ' input output', ('-m', '-c 10 20 30'))
- assert checkResult(result.output[0], *expected, stripdir=[2])
+ assert checkResult(result.stdout[0], *expected, stripdir=[2])
def test_robustfov():
@@ -56,7 +56,7 @@ def test_robustfov():
rfov = op.join(fsldir, 'bin', 'robustfov')
result = fw.robustfov('input', 'output', b=180)
expected = (rfov + ' -i input', ('-r output', '-b 180'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_eddy_cuda():
@@ -73,7 +73,7 @@ def test_eddy_cuda():
'--out=out',
'--dont_mask_output'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_topup():
@@ -81,7 +81,7 @@ def test_topup():
topup = op.join(fsldir, 'bin', 'topup')
result = fw.topup('imain', 'datain', minmet=1)
expected = topup + ' --imain=imain --datain=datain --minmet=1'
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
def test_flirt():
@@ -90,7 +90,7 @@ def test_flirt():
result = fw.flirt('src', 'ref', usesqform=True, anglerep='euler')
expected = (flirt + ' -in src -ref ref',
('-usesqform', '-anglerep euler'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_applyxfm():
@@ -102,7 +102,18 @@ def test_applyxfm():
'-out out',
'-init mat',
'-interp trilinear'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
+
+
+def test_applyxfm4D():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('applyxfm4D',)) as fsldir:
+ applyxfm = op.join(fsldir, 'bin', 'applyxfm4D')
+ result = fw.applyxfm4D(
+ 'src', 'ref', 'out', 'mat', fourdigit=True, userprefix='boo')
+ expected = (applyxfm + ' src ref out mat',
+ ('-fourdigit',
+ '-userprefix boo'))
+ assert checkResult(result.stdout[0], *expected)
def test_invxfm():
@@ -110,7 +121,7 @@ def test_invxfm():
cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
result = fw.invxfm('mat', 'output')
expected = cnvxfm + ' -omat output -inverse mat'
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
def test_concatxfm():
@@ -118,7 +129,7 @@ def test_concatxfm():
cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
result = fw.concatxfm('mat1', 'mat2', 'output')
expected = cnvxfm + ' -omat output -concat mat2 mat1'
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
def test_mcflirt():
@@ -129,7 +140,7 @@ def test_mcflirt():
('-out output',
'-cost normcorr',
'-dof 12'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_fnirt():
@@ -142,7 +153,7 @@ def test_fnirt():
'--iout=iout',
'--fout=fout',
'--subsamp=8,6,4,2'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_applywarp():
@@ -151,7 +162,7 @@ def test_applywarp():
result = fw.applywarp('src', 'ref', 'out', warp='warp', abs=True, super=True)
expected = (applywarp + ' --in=src --ref=ref --out=out',
('--warp=warp', '--abs', '--super'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_invwarp():
@@ -161,7 +172,7 @@ def test_invwarp():
rel=True, noconstraint=True)
expected = (invwarp + ' --warp=warp --ref=ref --out=out',
('--rel', '--noconstraint'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_convertwarp():
@@ -170,7 +181,7 @@ def test_convertwarp():
result = fw.convertwarp('out', 'ref', absout=True, jacobian='jacobian')
expected = (cnvwarp + ' --ref=ref --out=out',
('--absout', '--jacobian=jacobian'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_fugue():
@@ -182,7 +193,7 @@ def test_fugue():
'--warp=warp',
'--median',
'--dwell=10'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
@@ -192,7 +203,21 @@ def test_sigloss():
result = fw.sigloss('input', 'sigloss', mask='mask', te=0.5)
expected = (sigloss + ' --in input --sigloss sigloss',
('--mask mask', '--te 0.5'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
+
+
+def test_prelude():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('prelude',)) as fsldir:
+ prelude = op.join(fsldir, 'bin', 'prelude')
+ result = fw.prelude(complex='complex',
+ out='out',
+ labelslices=True,
+ start=5)
+ expected = (prelude, ('--complex=complex',
+ '--out=out',
+ '--labelslices',
+ '--start=5'))
+ assert checkResult(result.stdout[0], *expected)
def test_melodic():
@@ -201,7 +226,7 @@ def test_melodic():
result = fw.melodic('input', dim=50, mask='mask', Oall=True)
expected = (melodic + ' --in=input',
('--dim=50', '--mask=mask', '--Oall'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_fsl_regfilt():
@@ -211,7 +236,7 @@ def test_fsl_regfilt():
filter=(1, 2, 3, 4), vn=True)
expected = (regfilt + ' --in=input --out=output --design=design',
('--filter=1,2,3,4', '--vn'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
@@ -220,7 +245,7 @@ def test_fslreorient2std():
r2std = op.join(fsldir, 'bin', 'fslreorient2std')
result = fw.fslreorient2std('input', 'output')
expected = r2std + ' input output'
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
def test_fslroi():
@@ -229,15 +254,15 @@ def test_fslroi():
result = fw.fslroi('input', 'output', 1, 10)
expected = fslroi + ' input output 1 10'
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
result = fw.fslroi('input', 'output', 1, 10, 2, 20, 3, 30)
expected = fslroi + ' input output 1 10 2 20 3 30'
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
result = fw.fslroi('input', 'output', 1, 10, 2, 20, 3, 30, 4, 40)
expected = fslroi + ' input output 1 10 2 20 3 30 4 40'
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
def test_slicer():
@@ -245,7 +270,7 @@ def test_slicer():
slicer = op.join(fsldir, 'bin', 'slicer')
result = fw.slicer('input1', 'input2', i=(20, 100), x=(20, 'x.png'))
expected = slicer + ' input1 input2 -i 20 100 -x 20 x.png'
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
def test_cluster():
@@ -255,7 +280,7 @@ def test_cluster():
fractional=True, osize='osize')
expected = (cluster + ' --in=input --thresh=thresh',
('--fractional', '--osize=osize'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.stdout[0], *expected)
def test_fslmaths():
@@ -275,7 +300,7 @@ def test_fslmaths():
'-inm inmim', '-bptf 1 10', 'output']
expected = ' '.join(expected)
- assert result.output[0] == expected
+ assert result.stdout[0] == expected
# test LOAD output
with tempdir() as td, mockFSLDIR(bin=('fslmaths',)) as fsldir:
@@ -303,12 +328,12 @@ def test_fast():
result = fw.fast('input', 'myseg', n_classes=3)
expected = [cmd, '-v', '--out=myseg', '--class=3', 'input']
- assert result.output[0] == ' '.join(expected)
+ assert result.stdout[0] == ' '.join(expected)
result = fw.fast(('in1', 'in2', 'in3'), 'myseg', n_classes=3)
expected = [cmd, '-v', '--out=myseg', '--class=3', 'in1', 'in2', 'in3']
- assert result.output[0] == ' '.join(expected)
+ assert result.stdout[0] == ' '.join(expected)
@@ -323,4 +348,4 @@ def test_fsl_anat():
expected = [cmd, '-i', 't1', '-o', 'fsl_anat', '-t', 'T1',
'-s', '25']
- assert result.output[0] == ' '.join(expected)
+ assert result.stdout[0] == ' '.join(expected)
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index 9e1d5d6a82c56801a60918801c28bfeb81f4e825..c943ae5cf4d02f174793d2e25d8ddce779569d0c 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -8,6 +8,7 @@
import os.path as op
import os
import shlex
+import pathlib
import textwrap
try: from unittest import mock
@@ -353,6 +354,30 @@ def test_fileOrThing_sequence():
assert np.all(func(infiles[0], wutils.LOAD)['out'] == inputs[0])
+def test_fileOrText():
+
+ @wutils.fileOrText('input', 'output')
+ def func(input, output):
+ data = open(input).read()
+ data = ''.join(['{}{}'.format(c, c) for c in data])
+ open(output, 'wt').write(data)
+
+ with tempdir.tempdir():
+
+ data = 'abcdefg'
+ exp = 'aabbccddeeffgg'
+
+ open('input.txt', 'wt').write(data)
+
+ func(pathlib.Path('input.txt'), pathlib.Path('output.txt'))
+ assert open('output.txt').read() == exp
+
+ func('abcdefg', pathlib.Path('output.txt'))
+ assert open('output.txt').read() == exp
+
+ assert func('12345', wutils.LOAD).output == '1122334455'
+
+
def test_fileOrThing_outprefix():
@wutils.fileOrImage('img', outprefix='output_base')
@@ -496,6 +521,111 @@ def test_fileOrThing_outprefix_directory():
assert np.all(np.asanyarray(res[op.join('foo', 'myout_imgs', 'img4')].dataobj) == exp4)
+
+def test_fileOrThing_results():
+ @wutils.fileOrArray('input', 'regular_output', outprefix='outpref')
+ def func(input, regular_output, outpref):
+
+ input = np.loadtxt(input)
+
+ regout = input * 2
+ prefouts = []
+ for i in range(3, 6):
+ prefouts.append(input * i)
+
+ np.savetxt(regular_output, regout)
+ for i, o in enumerate(prefouts):
+ np.savetxt('{}_{}.txt'.format(outpref, i), o)
+
+ return ('return', 'value')
+
+ input = np.random.randint(1, 10, (3, 3))
+ infile = 'input.txt'
+ exp = [input * i for i in range(2, 6)]
+
+ with tempdir.tempdir():
+
+ np.savetxt(infile, input)
+
+ result = func('input.txt', 'regout.txt', 'outpref')
+ assert len(result) == 0
+ assert result.stdout == ('return', 'value')
+ assert (np.loadtxt('regout.txt') == exp[0]).all()
+ for i in range(3):
+ assert (np.loadtxt('outpref_{}.txt'.format(i)) == exp[i+1]).all()
+
+ result = func(input, 'regout.txt', 'outpref')
+ assert len(result) == 0
+ assert result.stdout == ('return', 'value')
+ assert (np.loadtxt('regout.txt') == exp[0]).all()
+ for i in range(3):
+ assert (np.loadtxt('outpref_{}.txt'.format(i)) == exp[i+1]).all()
+
+ result = func(input, wutils.LOAD, 'outpref')
+ assert len(result) == 1
+ assert result.stdout == ('return', 'value')
+ assert (result .regular_output == exp[0]).all()
+ assert (result['regular_output'] == exp[0]).all()
+ for i in range(3):
+ assert (np.loadtxt('outpref_{}.txt'.format(i)) == exp[i+1]).all()
+
+ # todo outpref
+ result = func(input, wutils.LOAD, wutils.LOAD)
+ assert len(result) == 4
+ assert result.stdout == ('return', 'value')
+ assert (result .regular_output == exp[0]).all()
+ assert (result['regular_output'] == exp[0]).all()
+
+ assert (result .outpref_0 == exp[1]).all()
+ assert (result['outpref_0'] == exp[1]).all()
+ assert (result .outpref_1 == exp[2]).all()
+ assert (result['outpref_1'] == exp[2]).all()
+ assert (result .outpref_2 == exp[3]).all()
+ assert (result['outpref_2'] == exp[3]).all()
+
+ for i in range(3):
+ assert (np.loadtxt('outpref_{}.txt'.format(i)) == exp[i+1]).all()
+
+ result = func(input, wutils.LOAD, wutils.LOAD)
+ assert len(result) == 4
+
+
+def test_FileOrThing_invalid_identifiers():
+ # unlikely to ever happen, but let's test arguments with
+ # names that are not valid python identifiers
+ @wutils.fileOrArray('in val', '2out')
+ def func(**kwargs):
+
+ infile = kwargs['in val']
+ outfile = kwargs['2out']
+
+ input = np.loadtxt(infile)
+ np.savetxt(outfile, input * 2)
+
+ return ('return', 'value')
+
+ input = np.random.randint(1, 10, (3, 3))
+ infile = 'input.txt'
+ exp = input * 2
+
+ with tempdir.tempdir():
+
+ np.savetxt(infile, input)
+
+ res = func(**{'in val' : infile, '2out' : 'output.txt'})
+ assert res.stdout == ('return', 'value')
+ assert (np.loadtxt('output.txt') == exp).all()
+
+ res = func(**{'in val' : input, '2out' : 'output.txt'})
+ assert res.stdout == ('return', 'value')
+ assert (np.loadtxt('output.txt') == exp).all()
+
+ res = func(**{'in val' : input, '2out' : wutils.LOAD})
+ assert res.stdout == ('return', 'value')
+ assert (res['2out'] == exp).all()
+
+
+
def test_chained_fileOrImageAndArray():
@wutils.fileOrImage('image', 'outimage')
@wutils.fileOrArray('array', 'outarray')
@@ -584,6 +714,37 @@ def test_fileOrThing_chained_outprefix():
assert np.all(res['out_array'] == exparr)
+def test_fileOrThing_submit():
+
+ @wutils.fileOrImage('input', 'output')
+ def func(input, output, submit=False):
+
+ if submit:
+ return 'submitted!'
+
+ img = nib.load(input)
+ img = nib.nifti1.Nifti1Image(np.asanyarray(img.dataobj) * 2, np.eye(4))
+
+ nib.save(img, output)
+
+ with tempdir.tempdir() as td:
+ img = nib.nifti1.Nifti1Image(np.array([[1, 2], [3, 4]]), np.eye(4))
+ exp = np.asanyarray(img.dataobj) * 2
+ nib.save(img, 'input.nii.gz')
+
+ result = func(img, wutils.LOAD)
+ assert np.all(np.asanyarray(result['output'].dataobj) == exp)
+
+ assert func('input.nii.gz', 'output.nii.gz', submit=True) == 'submitted!'
+
+ with pytest.raises(ValueError):
+ func(img, wutils.LOAD, submit=True)
+ with pytest.raises(ValueError):
+ func(img, 'output.nii.gz', submit=True)
+ with pytest.raises(ValueError):
+ func('input.nii.gz', wutils.LOAD, submit=True)
+
+
def test_cmdwrapper():
@wutils.cmdwrapper
def func(a, b):