From 42f1c4130a9213fca86a58ec268e93a1d508ca9d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 2 May 2017 18:37:18 +0100
Subject: [PATCH] Fix various python 2/3 incompatibilities. Also simplified
featdesign.loadDesignMat function
---
fsl/data/atlases.py | 12 ++++++++----
fsl/data/featdesign.py | 21 +++------------------
fsl/data/image.py | 6 +++---
fsl/data/imagewrapper.py | 2 +-
fsl/data/mesh.py | 2 --
fsl/utils/async.py | 7 +++++--
6 files changed, 20 insertions(+), 30 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index db1925fa4..9f6b9fe8d 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -40,6 +40,8 @@ load an atlas image, which will be one of the following atlas-specific
"""
+from __future__ import division
+
import xml.etree.ElementTree as et
import os.path as op
import glob
@@ -521,11 +523,11 @@ class AtlasDescription(object):
return self.atlasID != other.atlasID
- def __cmp__(self, other):
+ def __lt__(self, other):
"""Compares this ``AtlasDescription`` with another by their ``name``
attribute.
"""
- return cmp(self.name.lower(), other.name.lower())
+ return self.name.lower() < other.name.lower()
class Atlas(fslimage.Image):
@@ -559,8 +561,10 @@ class Atlas(fslimage.Image):
res = resolution
reses = np.concatenate(atlasDesc.pixdims)
- if resolution is None: imageIdx = np.argmin(reses) / 3
- else: imageIdx = np.argmin(np.abs(reses - res)) / 3
+ if resolution is None: imageIdx = np.argmin(reses)
+ else: imageIdx = np.argmin(np.abs(reses - res))
+
+ imageIdx = imageIdx // 3
if isLabel: imageFile = atlasDesc.summaryImages[imageIdx]
else: imageFile = atlasDesc.images[ imageIdx]
diff --git a/fsl/data/featdesign.py b/fsl/data/featdesign.py
index ee5843064..ed8d90599 100644
--- a/fsl/data/featdesign.py
+++ b/fsl/data/featdesign.py
@@ -540,7 +540,7 @@ def getFirstLevelEVs(featDir, settings, designMat):
# above, about the voxelwise
# confound EV locations, holds
startIdx = len(evs) + 1
- if voxConfLocs != range(startIdx, startIdx + len(voxConfFiles)):
+ if voxConfLocs != list(range(startIdx, startIdx + len(voxConfFiles))):
raise FSFError('Unsupported voxelwise confound ordering '
'({} -> {})'.format(startIdx, voxConfLocs))
@@ -640,26 +640,11 @@ def loadDesignMat(designmat):
:arg designmat: Path to the ``design.mat`` file.
"""
- matrix = None
-
log.debug('Loading FEAT design matrix from {}'.format(designmat))
- with open(designmat, 'rt') as f:
-
- while True:
- line = f.readline()
-
- # readline returns an empty string at EOF
- if line == '':
- break
-
- # Matrix data starts after "/Matrix"
- if line.strip() == '/Matrix':
- break
-
- matrix = np.loadtxt(f, ndmin=2)
+ matrix = np.loadtxt(designmat, comments='/', ndmin=2)
- if matrix is None or matrix.size == 0:
+ if matrix is None or matrix.size == 0 or len(matrix.shape) != 2:
raise FSFError('{} does not appear to be a '
'valid design.mat file'.format(designmat))
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 1b93982be..f44c3bec5 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -470,8 +470,8 @@ class Nifti(notifier.Notifier):
elif qform_code != constants.NIFTI_XFORM_UNKNOWN: code = qform_code
# Invalid values
- if code > 4: code = constants.NIFTI_XFORM_UNKNOWN
- elif code < 0: code = constants.NIFTI_XFORM_UNKNOWN
+ if code not in range(5):
+ code = constants.NIFTI_XFORM_UNKNOWN
return int(code)
@@ -836,7 +836,7 @@ class Image(Nifti):
self.__nibImage = None
self.__imageWrapper = None
- if self.__fileobj is not None:
+ if getattr(self, '__fileobj', None) is not None:
self.__fileobj.close()
diff --git a/fsl/data/imagewrapper.py b/fsl/data/imagewrapper.py
index 810624daa..81658f594 100644
--- a/fsl/data/imagewrapper.py
+++ b/fsl/data/imagewrapper.py
@@ -415,7 +415,7 @@ class ImageWrapper(notifier.Notifier):
"""
shape = self.__image.shape
- slices = zip([0] * len(shape), shape)
+ slices = [[0, s] for s in shape]
return sliceCovered(slices, self.__coverage)
diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py
index e34ebf2a7..2a9c47df7 100644
--- a/fsl/data/mesh.py
+++ b/fsl/data/mesh.py
@@ -221,7 +221,6 @@ def loadVTKPolydataFile(infile):
for i in range(nVertices):
vertLine = lines[i + 5]
- vertices[i, :] = map(float, vertLine.split())
vertices[i, :] = [float(w) for w in vertLine.split()]
indexOffset = 0
@@ -232,7 +231,6 @@ def loadVTKPolydataFile(infile):
start = indexOffset
end = indexOffset + polygonLengths[i]
- indices[start:end] = map(int, polyLine[1:])
indices[start:end] = [int(w) for w in polyLine[1:]]
indexOffset += polygonLengths[i]
diff --git a/fsl/utils/async.py b/fsl/utils/async.py
index 938a83c38..a8e8efa0e 100644
--- a/fsl/utils/async.py
+++ b/fsl/utils/async.py
@@ -290,8 +290,11 @@ def _wxIdleLoop(ev):
except queue.Empty:
# Make sure that we get called periodically,
- # if EVT_IDLE decides to stop firing.
- _idleTimer.Start(_idleCallRate, wx.TIMER_ONE_SHOT)
+ # if EVT_IDLE decides to stop firing. If
+ # _idleTimer is None, then idleReset has
+ # probably been called.
+ if _idleTimer is not None:
+ _idleTimer.Start(_idleCallRate, wx.TIMER_ONE_SHOT)
return
now = time.time()
--
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