diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index dc65d3cecb5e23f9346a90c2c32b1b844ab796ef..ddc2b8fc731700efdefd1d7410490b19ad672f68 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,17 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+3.5.3 (Tuesday 9th February 2021)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Fixed a bug in :func:`.featanalysis.loadClusterResults` (!281).
+
+
3.5.2 (Friday 29th January 2021)
---------------------------------
@@ -12,8 +23,8 @@ Fixed
* Adjusted the :func:`.dicom.scanDir` function so that it will set a
default value for ``SeriesDescription`` if it is not present in the
- ``dcm2niix`` ``json`` output.
-* Fixed some issues with API documentation generation.
+ ``dcm2niix`` ``json`` output (!279).
+* Fixed some issues with API documentation generation (!279).
3.5.1 (Thursday 21st January 2021)
diff --git a/fsl/data/featanalysis.py b/fsl/data/featanalysis.py
index 473e5662334ee8e329ff8986ccbe3240b8e374ff..42450399cdcd448c82adff1d9d104646bfc59c63 100644
--- a/fsl/data/featanalysis.py
+++ b/fsl/data/featanalysis.py
@@ -373,7 +373,7 @@ def loadClusterResults(featdir, settings, contrast):
if not op.exists(clusterFile):
return None
- # In higher levle analysis run in some standard
+ # In higher level analysis run in some standard
# space, the cluster coordinates are in standard
# space. We transform them to voxel coordinates.
# later on.
@@ -480,13 +480,13 @@ def loadClusterResults(featdir, settings, contrast):
zcog = [c.zcogx, c.zcogy, c.zcogz]
copemax = [c.copemaxx, c.copemaxy, c.copemaxz]
- zmax = affine.transform([zmax], coordXform)[0].round()
- zcog = affine.transform([zcog], coordXform)[0].round()
- copemax = affine.transform([copemax], coordXform)[0].round()
+ zmax = affine.transform([zmax], coordXform)[0]
+ zcog = affine.transform([zcog], coordXform)[0]
+ copemax = affine.transform([copemax], coordXform)[0]
- c.zmaxx, c.zmaxy, c.zmaxz = zmax
- c.zcogx, c.zcogy, c.zcogz = zcog
- c.copemax, c.copemaxy, c.copemaxz = copemax
+ c.zmaxx, c.zmaxy, c.zmaxz = zmax
+ c.zcogx, c.zcogy, c.zcogz = zcog
+ c.copemaxx, c.copemaxy, c.copemaxz = copemax
return clusters
diff --git a/tests/test_featanalysis.py b/tests/test_featanalysis.py
index ffb5d8b3c6ed4330d285a04d68cfe2e8da2cbd15..da3789847c21cf2094826f52eb2fed7f09622ea0 100644
--- a/tests/test_featanalysis.py
+++ b/tests/test_featanalysis.py
@@ -59,7 +59,7 @@ def test_isFEATDir():
# it's not a feat directory
assert not featanalysis.isFEATDir('nonexistent.feat')
- # If any of the above files are not
+ # If any of the above files are not
# present, it is not a FEAT directory
perms = it.chain(it.combinations(paths, 1),
it.combinations(paths, 2),
@@ -69,7 +69,7 @@ def test_isFEATDir():
assert not featanalysis.isFEATDir(
op.join(testdir, 'analysis.feat'))
-
+
def test_hasStats():
with tests.testdir(['analysis.feat/stats/zstat1.nii.gz']) as testdir:
@@ -78,7 +78,7 @@ def test_hasStats():
with tests.testdir(['analysis.feat/stats/zstat1.txt']) as testdir:
featdir = op.join(testdir, 'analysis.feat')
- assert not featanalysis.hasStats(featdir)
+ assert not featanalysis.hasStats(featdir)
def test_hasMelodicDir():
@@ -94,7 +94,7 @@ def test_getAnalysisDir():
'analysis.feat/design.fsf',
'analysis.feat/design.mat',
'analysis.feat/design.con']
-
+
testpaths = ['analysis.feat/filtered_func_data.nii.gz',
'analysis.feat/stats/zstat1.nii.gz',
'analysis.feat/logs/feat4_post',
@@ -106,7 +106,7 @@ def test_getAnalysisDir():
t = op.join(testdir, t)
assert featanalysis.getAnalysisDir(t) == expected
-
+
def test_getTopLevelAnalysisDir():
testcases = [
('analysis.feat/filtered_func_data.ica/melodic_IC.nii.gz', 'analysis.feat'),
@@ -127,7 +127,7 @@ def test_getReportFile():
for paths, expected in testcases:
with tests.testdir(paths) as testdir:
-
+
featdir = op.join(testdir, 'analysis.feat')
if expected:
@@ -145,7 +145,7 @@ def test_loadContrasts():
/ContrastName1 c1
/ContrastName2 c2
/ContrastName3 c3
- /NumContrasts 3
+ /NumContrasts 3
/Matrix
1 0 0
0 1 0
@@ -188,9 +188,9 @@ def test_loadContrasts():
0 1 1
""",
]
-
+
with pytest.raises(Exception):
- featanalysis.loadContrasts('no file')
+ featanalysis.loadContrasts('no file')
with tests.testdir() as testdir:
featdir = op.join(testdir, 'analysis.feat')
@@ -275,7 +275,7 @@ def test_isFirstLevelAnalysis():
'2ndlevel_1.gfeat', '2ndlevel_2.gfeat']
for featdir in featdirs:
-
+
expected = featdir.startswith('1')
featdir = op.join(datadir, featdir)
settings = featanalysis.loadSettings(featdir)
@@ -301,14 +301,15 @@ def test_loadClusterResults():
with tests.testdir() as testdir:
- # For higher level analyses, the
- # loadClusterResults function peeks
- # at the FEAT input data file
- # header, so we have to generate it.
+ # work from a copy of the test data directory
newfeatdir = op.join(testdir, 'analysis.feat')
shutil.copytree(op.join(datadir, featdir), newfeatdir)
featdir = newfeatdir
+ # For higher level analyses, the
+ # loadClusterResults function peeks
+ # at the FEAT input data file
+ # header, so we have to generate it.
if not firstlevel:
datafile = op.join(featdir, 'filtered_func_data.nii.gz')
data = np.random.randint(1, 10, (91, 109, 91))
@@ -333,6 +334,35 @@ def test_loadClusterResults():
assert featanalysis.loadClusterResults(
featdir, settings, 0) is None
+ # The above loop just checks that the number of
+ # clusters loaded for each analysis was correct.
+ # Below we check that the cluster data was loaded
+ # correctly, just for one analysis
+ featdir = op.join(datadir, '1stlevel_1.feat')
+ settings = featanalysis.loadSettings(featdir)
+ cluster = featanalysis.loadClusterResults(featdir, settings, 0)[0]
+ expected = {
+ 'index' : 1,
+ 'nvoxels' : 296,
+ 'p' : 1.79e-27,
+ 'logp' : 26.7,
+ 'zmax' : 6.03,
+ 'zmaxx' : 34,
+ 'zmaxy' : 10,
+ 'zmaxz' : 1,
+ 'zcogx' : 31.4,
+ 'zcogy' : 12.3,
+ 'zcogz' : 1.72,
+ 'copemax' : 612,
+ 'copemaxx' : 34,
+ 'copemaxy' : 10,
+ 'copemaxz' : 1,
+ 'copemean' : 143
+ }
+
+ for k, v in expected.items():
+ assert np.isclose(v, getattr(cluster, k))
+
def test_getDataFile():
paths = ['analysis.feat/filtered_func_data.nii.gz',
@@ -393,9 +423,9 @@ def test_getResidualFile():
assert featanalysis.getResidualFile(featdir) == expect
else:
with pytest.raises(fslpath.PathError):
- featanalysis.getResidualFile(featdir)
+ featanalysis.getResidualFile(featdir)
+
-
def test_getPEFile():
testcases = [
(['analysis.feat/stats/pe1.nii.gz',
@@ -417,7 +447,7 @@ def test_getPEFile():
assert featanalysis.getPEFile(featdir, pei) == expect
else:
with pytest.raises(fslpath.PathError):
- featanalysis.getPEFile(featdir, pei)
+ featanalysis.getPEFile(featdir, pei)
def test_getCOPEFile():
@@ -441,8 +471,8 @@ def test_getCOPEFile():
assert featanalysis.getCOPEFile(featdir, ci) == expect
else:
with pytest.raises(fslpath.PathError):
- featanalysis.getCOPEFile(featdir, ci)
-
+ featanalysis.getCOPEFile(featdir, ci)
+
def test_getZStatFile():
testcases = [
@@ -465,8 +495,8 @@ def test_getZStatFile():
assert featanalysis.getZStatFile(featdir, zi) == expect
else:
with pytest.raises(fslpath.PathError):
- featanalysis.getZStatFile(featdir, zi)
-
+ featanalysis.getZStatFile(featdir, zi)
+
def test_getClusterMaskFile():
testcases = [
@@ -489,4 +519,4 @@ def test_getClusterMaskFile():
assert featanalysis.getClusterMaskFile(featdir, ci) == expect
else:
with pytest.raises(fslpath.PathError):
- featanalysis.getClusterMaskFile(featdir, ci)
+ featanalysis.getClusterMaskFile(featdir, ci)