diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index cdfbb2f92eee621164e0b7dbe392f7813e107d03..150331aa3f44643b9b7b622419e9a3a32e40aa92 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,19 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+3.0.1 (Wednesday 15th April 2020)
+---------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* The :func:`.isMelodicDir` function now accepts directories that do not end
+ with ``.ica``, as long as all required files are present.
+
+
+
3.0.0 (Sunday 29th March 2020)
------------------------------
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 1dc0aaf93bd1def53bb793d27c0033269eba82e2..eb9c468cc50a9831833b50bbe3cd758576297e18 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -622,8 +622,9 @@ class Nifti(notifier.Notifier, meta.Meta):
if from_ not in ('voxel', 'fsl', 'world') or \
to not in ('voxel', 'fsl', 'world'):
- raise ValueError('Invalid source/reference spaces: '
- '{} -> {}'.format(from_, to))
+ raise ValueError('Invalid source/reference spaces: "{}" -> "{}".'
+ 'Recognised spaces are "voxel", "fsl", and '
+ '"world"'.format(from_, to))
return np.copy(self.__affines[from_, to])
diff --git a/fsl/data/melodicanalysis.py b/fsl/data/melodicanalysis.py
index f3779d5ccecd139cc80730ea1ae66dc07ff9044a..ba0048234d8e72abe5210bb2fc708d2fd07eb16e 100644
--- a/fsl/data/melodicanalysis.py
+++ b/fsl/data/melodicanalysis.py
@@ -33,7 +33,6 @@ import logging
import os.path as op
import numpy as np
-import fsl.utils.path as fslpath
import fsl.data.image as fslimage
import fsl.data.featanalysis as featanalysis
@@ -63,10 +62,9 @@ def isMelodicImage(path):
def isMelodicDir(path):
- """Returns ``True`` if the given path looks like it is contained within
- a MELODIC directory, ``False`` otherwise. A melodic directory:
+ """Returns ``True`` if the given path looks like it is a MELODIC directory,
+ ``False`` otherwise. A MELODIC directory:
- - Must be named ``*.ica``.
- Must contain a file called ``melodic_IC.nii.gz`` or
``melodic_oIC.nii.gz``.
- Must contain a file called ``melodic_mix``.
@@ -75,12 +73,7 @@ def isMelodicDir(path):
path = op.abspath(path)
- if op.isdir(path): dirname = path
- else: dirname = op.dirname(path)
-
- sufs = ['.ica']
-
- if not any([dirname.endswith(suf) for suf in sufs]):
+ if not op.isdir(path):
return False
# Must contain an image file called
@@ -88,7 +81,7 @@ def isMelodicDir(path):
prefixes = ['melodic_IC', 'melodic_oIC']
for p in prefixes:
try:
- fslimage.addExt(op.join(dirname, p))
+ fslimage.addExt(op.join(path, p))
break
except fslimage.PathError:
pass
@@ -97,8 +90,8 @@ def isMelodicDir(path):
# Must contain files called
# melodic_mix and melodic_FTmix
- if not op.exists(op.join(dirname, 'melodic_mix')): return False
- if not op.exists(op.join(dirname, 'melodic_FTmix')): return False
+ if not op.exists(op.join(path, 'melodic_mix')): return False
+ if not op.exists(op.join(path, 'melodic_FTmix')): return False
return True
@@ -108,10 +101,13 @@ def getAnalysisDir(path):
to that MELODIC directory is returned. Otherwise, ``None`` is returned.
"""
- meldir = fslpath.deepest(path, ['.ica'])
+ if not op.isdir(path):
+ path = op.dirname(path)
- if meldir is not None and isMelodicDir(meldir):
- return meldir
+ while path not in (op.sep, ''):
+ if isMelodicDir(path):
+ return path
+ path = op.dirname(path)
return None
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index df7eb2722b19954303ef36132f7d7f36365ac673..eaee2d0ac10daa5e43743c071d23ca316f5c254f 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -98,19 +98,26 @@ def invxfm(inmat, omat):
return ['convert_xfm', '-omat', omat, '-inverse', inmat]
-@wutils.fileOrArray('inmat1', 'inmat2', 'outmat')
+@wutils.fileOrArray('atob', 'atoc', 'btoc')
@wutils.fslwrapper
-def concatxfm(inmat1, inmat2, outmat):
- """Use ``convert_xfm`` to concatenate two affines."""
+def concatxfm(atob, btoc, atoc):
+ """Use ``convert_xfm`` to concatenate two affines. Note that the
+ order of the input matrices is the opposite of the order expected
+ by ``convert_xfm``.
+
+ :arg atob: Input matrix, transforming from "A" to "B".
+ :arg btoc: Input matrix, transforming from "B" to "C".
+ :arg atoc: Output matrix, transforming from "A" to "C".
+ """
- asrt.assertFileExists(inmat1, inmat2)
+ asrt.assertFileExists(atob, btoc)
cmd = ['convert_xfm',
'-omat',
- outmat,
+ atoc,
'-concat',
- inmat2,
- inmat1]
+ btoc,
+ atob]
return cmd
diff --git a/tests/test_assertions.py b/tests/test_assertions.py
index 61b483f4bc2826b5dafefa5809dd04da1897b6d6..5d35f7507507503f353763619fc157f4132740f2 100644
--- a/tests/test_assertions.py
+++ b/tests/test_assertions.py
@@ -160,14 +160,14 @@ def test_assertIsMelodicDir():
('analysis.ica', [ 'melodic_mix', 'melodic_FTmix'], False),
('analysis.ica', ['melodic_IC.nii.gz', 'melodic_FTmix'], False),
('analysis.ica', ['melodic_IC.nii.gz', 'melodic_mix'], False),
- ('analysis', ['melodic_IC.nii.gz', 'melodic_mix', 'melodic_FTmix'], False),
- ('analysis', ['melodic_oIC.nii.gz', 'melodic_mix', 'melodic_FTmix'], False),
+ ('analysis', ['melodic_IC.nii.gz', 'melodic_mix', 'melodic_FTmix'], True),
+ ('analysis', [ 'melodic_mix', 'melodic_FTmix'], False),
]
for dirname, paths, expected in tests:
with testdir(paths, dirname):
if expected:
- assertions.assertIsMelodicDir(dirname)
+ assertions.assertIsMelodicDir('.')
else:
with pytest.raises(AssertionError):
assertions.assertIsMelodicDir(dirname)
diff --git a/tests/test_atlases.py b/tests/test_atlases.py
index 1c7abc0dfe6d2d8720c86edf605f0bd782af5c6d..ebfe1ba8579f0f550a9d6f1984c88bd349d87662 100644
--- a/tests/test_atlases.py
+++ b/tests/test_atlases.py
@@ -13,7 +13,8 @@ import os
import os.path as op
import numpy as np
-import mock
+
+from unittest import mock
import pytest
import tests
diff --git a/tests/test_fslsub.py b/tests/test_fslsub.py
index 40d7668285c813b332c8da91574cc34ffa671681..d7c6460cafe5428d36833a953befe27207a4c626 100644
--- a/tests/test_fslsub.py
+++ b/tests/test_fslsub.py
@@ -22,7 +22,7 @@ from . import mockFSLDIR
mock_fsl_sub = """
-#!{}
+#!/usr/bin/env python3
import random
import os
@@ -62,8 +62,7 @@ with open('{{}}.o{{}}'.format(cmd, jobid), 'w') as stdout, \
print(str(jobid))
sys.exit(0)
-""".format(sys.executable, op.dirname(fsl.__file__)).strip()
-
+""".format(op.dirname(fsl.__file__)).strip()
@contextlib.contextmanager
def fslsub_mockFSLDIR():
diff --git a/tests/test_melodicanalysis.py b/tests/test_melodicanalysis.py
index 907f3c3ba0c892d17206acb156aab830acefb283..9a8c251ac34dae1e8664614a5e9e5551db630c78 100644
--- a/tests/test_melodicanalysis.py
+++ b/tests/test_melodicanalysis.py
@@ -55,10 +55,10 @@ def test_isMelodicDir():
meldir = op.join(testdir, 'analysis.ica')
assert mela.isMelodicDir(meldir)
- # Directory must end in .ica
+ # non-.ica prefix is ok
with tests.testdir([p.replace('.ica', '.blob') for p in paths]) as testdir:
meldir = op.join(testdir, 'analysis.blob')
- assert not mela.isMelodicDir(meldir)
+ assert mela.isMelodicDir(meldir)
# Directory must exist!
assert not mela.isMelodicDir('non-existent.ica')
diff --git a/tests/test_wrappers/test_fslstats.py b/tests/test_wrappers/test_fslstats.py
index 8d20b4accaf7416a42d02c136d43129028f06fde..a38bf86d5b8eb42f746fec669315e57bba2488b6 100644
--- a/tests/test_wrappers/test_fslstats.py
+++ b/tests/test_wrappers/test_fslstats.py
@@ -18,9 +18,9 @@ from .. import mockFSLDIR as mockFSLDIR_base, make_random_image
mock_fslstats = """
-#!{}
+#!/usr/bin/env python3
-shape = {{outshape}}
+shape = {outshape}
import sys
import numpy as np
@@ -31,7 +31,7 @@ if len(shape) == 1:
data = data.reshape(1, -1)
np.savetxt(sys.stdout, data, fmt='%i')
-""".format(sys.executable).strip()
+""".strip()
@contextlib.contextmanager