Merge branch 'rel/3.5.1' into 'v3.5'

Rel/3.5.1

See merge request fsl/fslpy!278

CHANGELOG.rst

@@ -2,6 +2,26 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+3.5.1 (Thursday 21st January 2021)
+----------------------------------
+
+
+Added
+^^^^^
+
+
+* New :func:`.featanalysis.loadFsf` function, for loading arbitrary ``.fsf``
+  files (!276).
+
+
+Fixed
+^^^^^
+
+
+* Adjustments to :mod:`.dicom` tests to work with different versions of
+  ``dcm2niix`` (!277).
+
+
 3.5.0 (Wednesday 20th January 2021)
 -----------------------------------
 

fsl/data/featanalysis.py

@@ -22,6 +22,7 @@ following functions are provided:
    isFirstLevelAnalysis
    loadDesign
    loadContrasts
+   loadFsf
    loadSettings
    getThresholds
    loadClusterResults
@@ -216,17 +217,16 @@ def loadContrasts(featdir):
     return names, contrasts
 
 
-def loadSettings(featdir):
-    """Loads the analysis settings from a FEAT directory.
+def loadFsf(designfsf):
+    """Loads the analysis settings from a text file (.fsf) used to configure
+    FEAT.
 
-    Returns a dict containing the settings specified in the ``design.fsf``
-    file within the directory
+    Returns a dict containing the settings specified in the file
 
-    :arg featdir: A FEAT directory.
+    :arg designfsf: A .fsf file.
     """
 
     settings  = collections.OrderedDict()
-    designfsf = op.join(featdir, 'design.fsf')
 
     log.debug('Loading FEAT settings from {}'.format(designfsf))
 
@@ -251,6 +251,20 @@ def loadSettings(featdir):
     return settings
 
 
+def loadSettings(featdir):
+    """Loads the analysis settings from a FEAT directory.
+
+    Returns a dict containing the settings specified in the ``design.fsf``
+    file within the directory
+
+    :arg featdir: A FEAT directory.
+    """
+
+    designfsf = op.join(featdir, 'design.fsf')
+
+    return loadFsf(designfsf)
+
+
 def loadDesign(featdir, settings):
     """Loads the design matrix from a FEAT directory.
 

fsl/version.py

@@ -47,7 +47,7 @@ import            re
 import            string
 
 
-__version__ = '3.5.0'
+__version__ = '3.5.1'
 """Current version number, as a string. """
 
 

tests/test_dicom.py

@@ -130,7 +130,8 @@ def test_scanDir():
         for s in series:
             assert s['PatientName'] in ('MCCARTHY_PAUL',
                                         'MCCARTHY^PAUL',
-                                        'MCCARTHY_PAUL_2')
+                                        'MCCARTHY_PAUL_2',
+                                        'MCCARTHY^PAUL^2')
 
 
 def test_sersiesCRC():
@@ -183,11 +184,13 @@ def test_loadSeries():
                     assert img[:].shape               == expShape
                     assert img.getMeta('PatientName') in ('MCCARTHY_PAUL',
                                                           'MCCARTHY^PAUL',
-                                                          'MCCARTHY_PAUL_2')
+                                                          'MCCARTHY_PAUL_2',
+                                                          'MCCARTHY^PAUL^2')
                     assert 'PatientName'                      in img.metaKeys()
                     assert 'MCCARTHY_PAUL'                    in img.metaValues() or \
                            'MCCARTHY^PAUL'                    in img.metaValues() or \
                            'MCCARTHY_PAUL_2'                  in img.metaValues()
                     assert ('PatientName', 'MCCARTHY_PAUL')   in img.metaItems() or \
                            ('PatientName', 'MCCARTHY^PAUL')   in img.metaItems() or \
-                           ('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems()
+                           ('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems() or \
+                           ('PatientName', 'MCCARTHY^PAUL^2') in img.metaItems()

tests/test_featanalysis.py

@@ -240,9 +240,10 @@ def test_loadSettings():
 
     with tests.testdir() as testdir:
         featdir = op.join(testdir, 'analysis.feat')
-        tests.make_dummy_file(op.join(featdir, 'design.fsf'), contents)
-        result = featanalysis.loadSettings(featdir)
-        assert result == expected
+        designfsf = op.join(featdir, 'design.fsf')
+        tests.make_dummy_file(designfsf, contents)
+        assert featanalysis.loadSettings(featdir) == expected
+        assert featanalysis.loadFsf(designfsf) == expected
 
 
 def test_loadDesign():