diff --git a/fsl/data/featanalysis.py b/fsl/data/featanalysis.py
index a35d81b54eabf8db23fabde9aeed175fa56ccf56..39e40c9122c163d68adbfe0d308bd9146ef37306 100644
--- a/fsl/data/featanalysis.py
+++ b/fsl/data/featanalysis.py
@@ -64,7 +64,7 @@ def isFEATImage(path):
try:
path = fslimage.addExt(path, mustExist=True)
- except:
+ except fslimage.PathError:
return False
dirname = op.dirname( path)
@@ -115,7 +115,7 @@ def hasStats(featdir):
try:
getZStatFile(featdir, 0)
return True
- except:
+ except fslimage.PathError:
return False
diff --git a/fsl/data/featdesign.py b/fsl/data/featdesign.py
index ed8d905994e98a1c6a240230cab56307f6a6b5b8..26c10595b9a207d91bfe341c1f70f4d8eb8aa65e 100644
--- a/fsl/data/featdesign.py
+++ b/fsl/data/featdesign.py
@@ -326,7 +326,8 @@ class VoxelwiseEV(NormalEV):
if op.exists(filename):
self.filename = filename
else:
- log.warning('Voxelwise EV file does not exist: '.format(filename))
+ log.warning('Voxelwise EV file does not '
+ 'exist: {}'.format(filename))
self.filename = None
@@ -406,8 +407,8 @@ class VoxelwiseConfoundEV(EV):
if op.exists(filename):
self.filename = filename
else:
- log.warning('Voxelwise confound EV file '
- 'does not exist: '.format(filename))
+ log.warning('Voxelwise confound EV file does '
+ 'not exist: {}'.format(filename))
self.filename = None
@@ -547,7 +548,7 @@ def getFirstLevelEVs(featDir, settings, designMat):
# Create the voxelwise confound EVs.
# We make a name for the EV from the
# file name.
- for i, (f, l) in enumerate(zip(voxConfFiles, voxConfLocs)):
+ for i, f in enumerate(voxConfFiles):
title = op.basename(fslimage.removeExt(f))
evs.append(VoxelwiseConfoundEV(len(evs), i, title, f))
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 0ec4fb1033e67d8a8f4185dbc081299676412e9d..b1c93c0873ab37fd2e620e0d391b65f276d86df3 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -222,6 +222,8 @@ class Nifti(notifier.Notifier):
# qform = header.get('qform_code', -1)
# sform = header.get('sform_code', -1)
#
+ # TODO Change this in fslpy 2.0.0
+ #
if isinstance(header, nib.nifti1.Nifti1Header):
intent = header['intent_code']
qform = header['qform_code']
@@ -309,8 +311,8 @@ class Nifti(notifier.Notifier):
val = self.header[key]
- try: val = bytes(val).partition(b'\0')[0]
- except: val = bytes(val)
+ try: val = bytes(val).partition(b'\0')[0]
+ except Exception: val = bytes(val)
val = val.decode('ascii')
@@ -611,12 +613,12 @@ class Nifti(notifier.Notifier):
:class:`Nifti` instance) has the same dimensions and is in the
same space as this image.
"""
- return np.all(np.isclose(self .__shape[:3],
- other.__shape[:3])) and \
- np.all(np.isclose(self .__pixdim[:3],
- other.__pixdim[:3])) and \
- np.all(np.isclose(self .__voxToWorldMat,
- other.__voxToWorldMat))
+ return np.all(np.isclose(self .shape[:3],
+ other.shape[:3])) and \
+ np.all(np.isclose(self .pixdim[:3],
+ other.pixdim[:3])) and \
+ np.all(np.isclose(self .voxToWorldMat,
+ other.voxToWorldMat))
def getOrientation(self, axis, xform):
@@ -1426,7 +1428,7 @@ def read_segments(fileobj, segments, n_bytes):
# actual file is available via the fobj attribute
lock = getattr(fileobj.fobj, '_arrayproxy_lock')
- except:
+ except AttributeError:
return fileslice.orig_read_segments(fileobj, segments, n_bytes)
if len(segments) == 0:
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index ab8362985b2ac73705e82d73da415c999ba8ccf0..22883780cc896248346e76afac34ab983b88382a 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -231,7 +231,7 @@ class ImageWrapper(notifier.Notifier):
self.__image = None
if self.__taskThread is not None:
self.__taskThread.stop()
- self.__taskThraed = None
+ self.__taskThread = None
def getTaskThread(self):
@@ -459,7 +459,7 @@ class ImageWrapper(notifier.Notifier):
# the min/max per volume/expansion, and
# iteratively update the stored per-volume
# coverage and data range.
- for i, exp in enumerate(expansions):
+ for exp in expansions:
data = self.__getData(exp, isTuple=True)
data = data.squeeze(squeezeDims)
@@ -750,7 +750,7 @@ def naninfrange(data):
# finite values in the array
try:
return data[finite].min(), data[finite].max()
- except:
+ except Exception:
return np.nan, np.nan
@@ -1097,7 +1097,7 @@ def calcExpansion(slices, coverage):
# 'padding' dimensions of size 1.
def finishExpansion(exp, vol):
exp.append((vol, vol + 1))
- for i in range(padDims):
+ for _ in range(padDims):
exp.append((0, 1))
return exp
diff --git a/fsl/data/melodicanalysis.py b/fsl/data/melodicanalysis.py
index d0074f27f2637e9e882b8e3c2fbf33d14b9ee8cc..e13dd1e9906448fe90a72a249d82d690facc8031 100644
--- a/fsl/data/melodicanalysis.py
+++ b/fsl/data/melodicanalysis.py
@@ -49,7 +49,7 @@ def isMelodicImage(path):
try:
path = fslimage.addExt(path, mustExist=True)
- except:
+ except fslimage.PathError:
return False
dirname = op.dirname( path)
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index c3c701232406c37d3bdd0ddff8e54cd63d3fab28..d052ccb399df3afd1a7fad3c2ead762eac6e3663 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -380,7 +380,7 @@ def findReferenceImage(modelfile):
dirname = op.dirname(modelfile)
prefixes = [getFIRSTPrefix(modelfile)]
- except:
+ except ValueError:
return None
if prefixes[0].endswith('_first'):
@@ -389,7 +389,7 @@ def findReferenceImage(modelfile):
for p in prefixes:
try:
return fslimage.addExt(op.join(dirname, p), mustExist=True)
- except:
+ except fslimage.PathError:
continue
return None
diff --git a/fsl/utils/async.py b/fsl/utils/async.py
index 373e49e64ce5270ca2f8a5013cc898f18cd7720a..4ff8dec1568defff31edc67dda1c76f8e88dcf55 100644
--- a/fsl/utils/async.py
+++ b/fsl/utils/async.py
@@ -87,8 +87,8 @@ import functools
import threading
import collections
-try: import queue
-except: import Queue as queue
+try: import queue
+except ImportError: import Queue as queue
log = logging.getLogger(__name__)
@@ -142,7 +142,7 @@ def run(task, onFinish=None, onError=None, name=None):
except Exception as e:
- log.warn('Task "{}" crashed'.format(name), exc_info=True)
+ log.warning('Task "{}" crashed'.format(name), exc_info=True)
callback(onError, e)
# If WX, run on a thread
@@ -759,7 +759,7 @@ class TaskThread(threading.Thread):
# Any other error typically indicates
# that this is a daemon thread, and
# the TaskThread object has been GC'd
- except:
+ except Exception:
break
finally:
diff --git a/fsl/utils/platform.py b/fsl/utils/platform.py
index 972790abd7b1621bf2010f670bc56e6bb8bd2436..32e9d296a84219ef6d3700e721b8a83e87f57718 100644
--- a/fsl/utils/platform.py
+++ b/fsl/utils/platform.py
@@ -146,6 +146,7 @@ class Platform(notifier.Notifier):
self.__glRenderer = None
self.__glIsSoftware = None
self.__fslVersion = None
+ self.__fsldir = None
self.fsldir = os.environ.get('FSLDIR', None)
# Determine if a display is available. We do
@@ -239,18 +240,16 @@ class Platform(notifier.Notifier):
pi = [t.lower() for t in wx.PlatformInfo]
- for tag in pi:
-
- if any(['cocoa' in p for p in pi]): platform = WX_MAC_COCOA
- elif any(['carbon' in p for p in pi]): platform = WX_MAC_CARBON
- elif any(['gtk' in p for p in pi]): platform = WX_GTK
- else: platform = WX_UNKNOWN
+ if any(['cocoa' in p for p in pi]): plat = WX_MAC_COCOA
+ elif any(['carbon' in p for p in pi]): plat = WX_MAC_CARBON
+ elif any(['gtk' in p for p in pi]): plat = WX_GTK
+ else: plat = WX_UNKNOWN
- if platform is WX_UNKNOWN:
- log.warning('Could not determine wx platform from '
- 'information: {}'.format(pi))
+ if platform is WX_UNKNOWN:
+ log.warning('Could not determine wx platform from '
+ 'information: {}'.format(pi))
- return platform
+ return plat
@property
diff --git a/fsl/utils/settings.py b/fsl/utils/settings.py
index 491198adb5f86729e93e9b7d80859b6e8047f35a..675ad29c4880f466e7c113f9f7100ad4be4883d7 100644
--- a/fsl/utils/settings.py
+++ b/fsl/utils/settings.py
@@ -341,7 +341,7 @@ class Settings(object):
if not op.exists(cfgdir):
try:
os.makedirs(cfgdir)
- except:
+ except OSError:
log.warning(
'Unable to create {} configuration '
'directory: {}'.format(cid, cfgdir),
@@ -372,7 +372,7 @@ class Settings(object):
try:
with open(configFile, 'rb') as f:
return pickle.load(f)
- except:
+ except (IOError, pickle.UnpicklingError):
log.debug('Unable to load stored {} configuration file '
'{}'.format(self.__configID, configFile),
exc_info=True)
@@ -391,7 +391,7 @@ class Settings(object):
try:
with open(configFile, 'wb') as f:
pickle.dump(config, f)
- except:
+ except (IOError, pickle.PicklingError):
log.warning('Unable to save {} configuration file '
'{}'.format(self.__configID, configFile),
exc_info=True)
diff --git a/fsl/utils/weakfuncref.py b/fsl/utils/weakfuncref.py
index 71350145ec3e8a54d1e94a63e9d0e54be90c34c5..937481c014c00b71bda39e7c2985bf78ecbb084d 100644
--- a/fsl/utils/weakfuncref.py
+++ b/fsl/utils/weakfuncref.py
@@ -148,9 +148,9 @@ class WeakFunctionRef(object):
obj = self.obj()
# Return the bound method object
- try: return getattr(obj, self.funcName)
+ try: return getattr(obj, self.funcName)
# If the function is a bound private method,
# its name on the instance will have been
# mangled, so we need to search for it
- except: return self.__findPrivateMethod()
+ except AttributeError: return self.__findPrivateMethod()