From 4193746de28270134cf6dc10380549913192cb2c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 23 Oct 2017 18:01:37 +0100
Subject: [PATCH] Fixing important pylint issues
---
fsl/data/featanalysis.py | 4 ++--
fsl/data/featdesign.py | 9 +++++----
fsl/data/image.py | 20 +++++++++++---------
fsl/data/imagewrapper.py | 8 ++++----
fsl/data/melodicanalysis.py | 2 +-
fsl/data/mesh.py | 4 ++--
fsl/utils/async.py | 8 ++++----
fsl/utils/platform.py | 19 +++++++++----------
fsl/utils/settings.py | 6 +++---
fsl/utils/weakfuncref.py | 4 ++--
10 files changed, 43 insertions(+), 41 deletions(-)
diff --git a/fsl/data/featanalysis.py b/fsl/data/featanalysis.py
index a35d81b54..39e40c912 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 ed8d90599..26c10595b 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 0ec4fb103..b1c93c087 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 ab8362985..22883780c 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 d0074f27f..e13dd1e99 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 c3c701232..d052ccb39 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 373e49e64..4ff8dec15 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 972790abd..32e9d296a 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 491198adb..675ad29c4 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 71350145e..937481c01 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()
--
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