diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 956b527caed80d3f6bc1bba6d84ed188fe6bf232..a443c7b579be2a7906cbe37c215145d2ebac220f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -11,6 +11,7 @@ Added
* Added more functions to the :class:`.fslmaths` wrapper (!431).
+* New :func:`.smoothest` wrapper function (!432).
3.15.4 (Monday 27th November 2023)
diff --git a/doc/conf.py b/doc/conf.py
index 1e5e868f22fdc3ac48ad0fa58649f6225b32927b..073f4d5d29eb2d502bf516d2e81ed0764e24a7df 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -12,12 +12,70 @@
# All configuration values have a default; values that are commented out
# serve to show the default.
+import glob
+import itertools as it
import os
+import os.path as op
import sys
import datetime
date = datetime.date.today()
+
+def check_for_missing_stubs():
+
+ docdir = op.dirname(__file__)
+ basedir = op.join(docdir, '..')
+ modules = []
+
+ def tomodname(f):
+ if f.endswith('.py'):
+ f = f[:-3]
+ return op.relpath(op.join(dirpath, f), basedir).replace(op.sep, '.')
+
+ for dirpath, dirnames, filenames in os.walk(op.join(basedir, 'fsl')):
+ for d in dirnames:
+ if d == '__pycache__':
+ continue
+ if len(glob.glob(op.join(dirpath, d, '**', '*.py'), recursive=True)) == 0:
+ continue
+ modules.append(tomodname(d))
+
+ for f in filenames:
+ if not f.endswith('.py'):
+ continue
+ if f in ('__init__.py', '__main__.py'):
+ continue
+ modules.append(tomodname(f))
+
+ modules = [m for m in modules if not m.startswith('fsl.tests')]
+
+ # import fsl
+ # modules = recurse(fsl)
+ # modules = [m.name for m in modules]
+
+ # print()
+ # print()
+ # print()
+
+ for mod in modules:
+
+ docfile = op.join(docdir, f'{mod}.rst')
+
+ if not op.exists(docfile):
+ print(f'No doc file found for module: {mod}')
+
+ for docfile in glob.glob(op.join(docdir, '*.rst')):
+ docfile = op.relpath(docfile, basedir)
+ mod = op.splitext(op.basename(docfile))[0]
+ if mod not in modules:
+ print(f'No module found for doc file: {docfile}')
+
+
+if __name__ == '__main__':
+ check_for_missing_stubs()
+
+
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
diff --git a/doc/fsl.wrappers.cluster_commands.rst b/doc/fsl.wrappers.cluster_commands.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6749dc5be4c4ac104e436eaf39df919ac100f658
--- /dev/null
+++ b/doc/fsl.wrappers.cluster_commands.rst
@@ -0,0 +1,7 @@
+``fsl.wrappers.cluster_commands``
+=================================
+
+.. automodule:: fsl.wrappers.cluster_commands
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.wrappers.oxford_asl.rst b/doc/fsl.wrappers.oxford_asl.rst
new file mode 100644
index 0000000000000000000000000000000000000000..cfdbdccb7b2792c27b5c5029ac3ce481c0a2a5eb
--- /dev/null
+++ b/doc/fsl.wrappers.oxford_asl.rst
@@ -0,0 +1,7 @@
+``fsl.wrappers.oxford_asl``
+===========================
+
+.. automodule:: fsl.wrappers.oxford_asl
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.wrappers.rst b/doc/fsl.wrappers.rst
index 6277046d469cf4e0ce0cc6bd070ac286ab28b47e..792a188f11e2dab51ea062dc3ceff9a30a8c3dd7 100644
--- a/doc/fsl.wrappers.rst
+++ b/doc/fsl.wrappers.rst
@@ -8,6 +8,7 @@
fsl.wrappers.bedpostx
fsl.wrappers.bet
fsl.wrappers.bianca
+ fsl.wrappers.cluster_commands
fsl.wrappers.dtifit
fsl.wrappers.eddy
fsl.wrappers.epi_reg
@@ -23,6 +24,7 @@
fsl.wrappers.fugue
fsl.wrappers.melodic
fsl.wrappers.misc
+ fsl.wrappers.oxford_asl
fsl.wrappers.randomise
fsl.wrappers.tbss
fsl.wrappers.wrapperutils
diff --git a/fsl/tests/test_wrappers/test_cluster.py b/fsl/tests/test_wrappers/test_cluster.py
index f6b92c58e16bafe17a3ce0a5e2d3849a8c9d41cc..6e0cfb8763b73922634ef4d1a0963f31435a6f14 100644
--- a/fsl/tests/test_wrappers/test_cluster.py
+++ b/fsl/tests/test_wrappers/test_cluster.py
@@ -9,10 +9,17 @@ import contextlib
import os
import os.path as op
import sys
+import textwrap as tw
+
+from unittest import mock
import numpy as np
-from fsl.wrappers.cluster import cluster, _cluster
+from fsl.wrappers import wrapperutils as wutils
+from fsl.wrappers.cluster_commands import (cluster,
+ _cluster,
+ smoothest,
+ _smoothest)
from . import testenv
from .. import mockFSLDIR
@@ -67,3 +74,56 @@ def test_cluster():
assert np.all(np.isclose(data, expected))
assert ''.join(titles) == mock_titles
assert result1.stdout == result2.stdout
+
+
+def test_smoothest_wrapper():
+ with testenv('smoothest') as smoothest_exe:
+ result = _smoothest(res='res', zstat='zstat', d=5, V=True)
+ expected = f'{smoothest_exe} --res=res --zstat=zstat -d 5 -V'
+ assert result.stdout[0] == expected
+
+ # auto detect residuals vs zstat
+ result = _smoothest('res4d.nii.gz', d=5, V=True)
+ expected = f'{smoothest_exe} -d 5 -V --res=res4d.nii.gz'
+ assert result.stdout[0] == expected
+
+ result = _smoothest('zstat1.nii.gz', d=5, V=True)
+ expected = f'{smoothest_exe} -d 5 -V --zstat=zstat1.nii.gz'
+ assert result.stdout[0] == expected
+
+
+def test_smoothest():
+
+ result = tw.dedent("""
+ FWHMx = 4.763 mm, FWHMy = 5.06668 mm, FWHMz = 4.71527 mm
+ DLH 0.324569 voxels^-3
+ VOLUME 244531 voxels
+ RESELS 14.224 voxels per resel
+ DLH 0.324569
+ VOLUME 244531
+ RESELS 14.224
+ FWHMvoxel 2.3815 2.53334 2.35763
+ FWHMmm 4.763 5.06668 4.71527
+ """)
+
+ result = wutils.FileOrThing.Results((result, ''))
+
+ expect = {
+ 'DLH' : 0.324569,
+ 'VOLUME' : 244531,
+ 'RESELS' : 14.224,
+ 'FWHMvoxel' : [2.3815, 2.53334, 2.35763],
+ 'FWHMmm' : [4.763, 5.06668, 4.71527]
+ }
+
+ with mock.patch('fsl.wrappers.cluster_commands._smoothest',
+ return_value=result):
+
+ result = smoothest('inimage')
+
+ assert result.keys() == expect.keys()
+ assert np.isclose(result['DLH'], expect['DLH'])
+ assert np.isclose(result['VOLUME'], expect['VOLUME'])
+ assert np.isclose(result['RESELS'], expect['RESELS'])
+ assert np.all(np.isclose(result['FWHMvoxel'], expect['FWHMvoxel']))
+ assert np.all(np.isclose(result['FWHMmm'], expect['FWHMmm']))
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index aa90bb4566e7f7c8487d4344f8294bf05a9bc2ef..124c2115037eda8bcb23628f24ebe1261b45808c 100755
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -101,7 +101,8 @@ from fsl.wrappers.wrapperutils import (LOAD,
fslwrapper,
funcwrapper)
from fsl.wrappers import (tbss,)
-from fsl.wrappers.cluster import (cluster,)
+from fsl.wrappers.cluster_commands import (cluster,
+ smoothest)
from fsl.wrappers.bet import (bet,
robustfov)
from fsl.wrappers.eddy import (eddy,
diff --git a/fsl/wrappers/cluster.py b/fsl/wrappers/cluster_commands.py
similarity index 55%
rename from fsl/wrappers/cluster.py
rename to fsl/wrappers/cluster_commands.py
index 046a28ef597feeca52ec386a1956615acb5eb635..c3b28e96f1f91cd0b5c519afb6ac02505bcce7c0 100644
--- a/fsl/wrappers/cluster.py
+++ b/fsl/wrappers/cluster_commands.py
@@ -66,3 +66,59 @@ def _cluster(infile, thresh, **kwargs):
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
+
+
+def smoothest(inimg=None, **kwargs):
+ """Wrapper for the ``smoothest`` command.
+
+ The residual or zstatistic image may be passed as the first positional
+ argument (``inimg``) - its type is inferred from the image file name if
+ possible. If this is not possible (e.g. non-standard file names or
+ in-memory images), you must specify residual images via ``res``, or
+ zstatistic images via ``zstat``.
+
+ Returns a dictionary containing the parameters estimated by ``smoothest``,
+ e.g.::
+
+ {
+ 'DLH' : 1.25903,
+ 'VOLUME' : 239991,
+ 'RESELS' : 3.69574,
+ 'FWHMvoxel' : [1.57816, 1.64219, 1.42603],
+ 'FWHMmm' : [3.15631, 3.28437, 2.85206]
+ }
+ """
+ result = _smoothest(**kwargs)
+ result = result.stdout[0]
+ result = result.strip().split('\n')[-5:]
+ values = {}
+
+ for line in result:
+ key, vals = line.split(maxsplit=1)
+ vals = [float(v) for v in vals.split()]
+
+ if len(vals) == 1:
+ vals = vals[0]
+
+ values[key] = vals
+
+ return values
+
+
+@wutils.fileOrImage('inimg', 'r', 'res', 'z', 'zstat', 'm', 'mask')
+@wutils.fslwrapper
+def _smoothest(inimg=None, **kwargs):
+ """Actual wrapper for the ``smoothest`` command."""
+
+ if inimg is not None:
+ if 'res4d' in inimg: kwargs['res'] = inimg
+ elif 'zstat' in inimg: kwargs['zstat'] = inimg
+ else: raise RuntimeError('Cannot infer type of input '
+ f'image {inimg.name}')
+
+ valmap = {
+ 'V' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ }
+
+ return ['smoothest'] + wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
diff --git a/fsl/wrappers/fnirt.py b/fsl/wrappers/fnirt.py
index f4ca120fceebed4cdd97310087a1f816e544a979..d5c5bd21a02603522e74b810152ed0c9ea665e50 100644
--- a/fsl/wrappers/fnirt.py
+++ b/fsl/wrappers/fnirt.py
@@ -32,8 +32,13 @@ def fnirt(src, **kwargs):
asrt.assertIsNifti(src)
+ valmap = {
+ 'v' : wutils.SHOW_IF_TRUE,
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ }
+
cmd = ['fnirt', '--in={}'.format(src)]
- cmd += wutils.applyArgStyle('--=', **kwargs)
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
diff --git a/fsl/wrappers/fslstats.py b/fsl/wrappers/fslstats.py
index 67942fba59f1b79f34d5a18a93bcd34778a2fc35..c25dc238d55169962b2f0776f4ab472ee14ac788 100644
--- a/fsl/wrappers/fslstats.py
+++ b/fsl/wrappers/fslstats.py
@@ -31,20 +31,28 @@ class fslstats:
present in older versions.
+ This ``fslstats`` command::
+
+ fslstats image -r -p 95 -R
+
+
+ is equivalent to this function call::
+
+ fslstats('image').r.p(95).R.run()
+
+
Any ``fslstats`` command-line option which does not require any arguments
(e.g. ``-r``) can be set by accessing an attribute on a ``fslstats``
object, e.g.::
- stats = fslstats('image.nii.gz')
- stats.r
+ fslstats('image.nii.gz').r.run()
``fslstats`` command-line options which do require additional arguments
(e.g. ``-k``) can be set by calling a method on an ``fslstats`` object,
e.g.::
- stats = fslstats('image.nii.gz')
- stats.k('mask.nii.gz')
+ stats = fslstats('image.nii.gz').k('mask.nii.gz').run()
The ``fslstats`` command can be executed via the :meth:`run` method.