Merge branch 'rel/3.5.3' into 'v3.5'

Rel/3.5.3

See merge request fsl/fslpy!282

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)

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.copemaxx, c.copemaxy, c.copemaxz = copemax
 
     return clusters
 

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '3.5.2'
+__version__ = '3.5.3'
 """Current version number, as a string. """
 
 

tests/test_featanalysis.py

@@ -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',