Commit 4193746d authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Fixing important pylint issues

parent ea38d1aa
......@@ -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
......
......@@ -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))
......
......@@ -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']
......@@ -310,7 +312,7 @@ class Nifti(notifier.Notifier):
val = self.header[key]
try: val = bytes(val).partition(b'\0')[0]
except: val = bytes(val)
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:
......
......@@ -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
......
......@@ -49,7 +49,7 @@ def isMelodicImage(path):
try:
path = fslimage.addExt(path, mustExist=True)
except:
except fslimage.PathError:
return False
dirname = op.dirname( path)
......
......@@ -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
......@@ -88,7 +88,7 @@ import threading
import collections
try: import queue
except: import Queue as 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:
......
......@@ -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))
return platform
return plat
@property
......
......@@ -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)
......@@ -153,4 +153,4 @@ class WeakFunctionRef(object):
# 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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