diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 4c53811dc4f0cc282b779341f55cad9281e25a1a..a17ca031b429e21ef17a74c515db6ba128e5ff8d 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -100,7 +100,7 @@ log = logging.getLogger(__name__)
def listAtlases(refresh=False):
- """Returns a dictionary containing :class:`AtlasDescription` objects for
+ """Returns a list containing :class:`AtlasDescription` objects for
all available atlases.
:arg refresh: If ``True``, or if the atlas desriptions have not
@@ -119,7 +119,7 @@ def listAtlases(refresh=False):
refresh = True
if not refresh:
- return ATLAS_DESCRIPTIONS.values()
+ return list(ATLAS_DESCRIPTIONS.values())
atlasFiles = glob.glob(op.join(ATLAS_DIR, '*.xml'))
atlasDescs = map(AtlasDescription, atlasFiles)
@@ -131,7 +131,7 @@ def listAtlases(refresh=False):
desc.index = i
ATLAS_DESCRIPTIONS[desc.atlasID] = desc
- return atlasDescs
+ return list(atlasDescs)
def getAtlasDescription(atlasID):
diff --git a/fsl/data/featimage.py b/fsl/data/featimage.py
index 59cc9ce8929c1171d019dee99498d32fe8531138..7befd0d0636c19ba60f82b559e750845eef2e434 100644
--- a/fsl/data/featimage.py
+++ b/fsl/data/featimage.py
@@ -9,12 +9,12 @@
"""
-import os.path as op
+import os.path as op
-import numpy as np
+import numpy as np
-import image as fslimage
-import featresults
+from . import image as fslimage
+from . import featresults
class FEATImage(fslimage.Image):
diff --git a/fsl/data/featresults.py b/fsl/data/featresults.py
index 4772f05b09c228f669a06c3d6dc8e62e6de2dcb9..df2acbe5039799920f76829d1570359bcb665c8e 100644
--- a/fsl/data/featresults.py
+++ b/fsl/data/featresults.py
@@ -414,7 +414,7 @@ def loadClusterResults(featdir, settings, contrast):
# empty lines
lines = f.readlines()
lines = [l.strip() for l in lines]
- lines = filter(lambda l: l != '', lines)
+ lines = [l for l in lines if l != '']
# the first line should contain column
# names, and each other line should
@@ -554,19 +554,15 @@ def getEVNames(settings):
:arg settings: A FEAT settings dictionary (see :func:`loadSettings`).
"""
- numEVs = int(settings['evs_real'])
+ numEVs = int(settings['evs_real'])
+ titleKeys = [s for s in settings.keys() if s.startswith('evtitle')]
+ derivKeys = [s for s in settings.keys() if s.startswith('deriv_yn')]
- titleKeys = filter(lambda s: s.startswith('evtitle'), settings.keys())
- derivKeys = filter(lambda s: s.startswith('deriv_yn'), settings.keys())
-
- def _cmp(key1, key2):
- key1 = ''.join([c for c in key1 if c.isdigit()])
- key2 = ''.join([c for c in key2 if c.isdigit()])
-
- return cmp(int(key1), int(key2))
-
- titleKeys = sorted(titleKeys, cmp=_cmp)
- derivKeys = sorted(derivKeys, cmp=_cmp)
+ def key(k):
+ return int(''.join([c for c in k if c.isdigit()]))
+
+ titleKeys = sorted(titleKeys, key=key)
+ derivKeys = sorted(derivKeys, key=key)
evnames = []
for titleKey, derivKey in zip(titleKeys, derivKeys):
diff --git a/fsl/data/image.py b/fsl/data/image.py
index cc8ab09f87384fc9f8987859de3ad62491fc7a44..a9975f5a7c360ec33fcc780d81dcee6137e98792 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -38,6 +38,7 @@ import os
import os.path as op
import subprocess as sp
+import six
import numpy as np
import nibabel as nib
@@ -117,7 +118,7 @@ class Nifti1(object):
header = header.copy()
# The image parameter may be the name of an image file
- if isinstance(image, basestring):
+ if isinstance(image, six.string_types):
nibImage, filename = loadImage(addExt(image))
self.nibImage = nibImage
@@ -380,7 +381,7 @@ class Image(Nifti1, props.HasProperties):
# Or, if this image was loaded
# from disk, use the file name
- elif isinstance(image, basestring):
+ elif isinstance(image, six.string_types):
self.name = removeExt(op.basename(self.dataSource))
self.saved = True
@@ -594,7 +595,7 @@ def looksLikeImage(filename, allowedExts=None):
# TODO A much more robust approach would be
# to try loading the file using nibabel.
- return any(map(lambda ext: filename.endswith(ext), allowedExts))
+ return any([filename.endswith(ext) for ext in allowedExts])
def removeExt(filename):
diff --git a/fsl/data/melodicimage.py b/fsl/data/melodicimage.py
index 21bc8005e89a8c801b0972752ef234f8f9066cff..fc0cb0670970653cecc47f78f22d23c1407f3a21 100644
--- a/fsl/data/melodicimage.py
+++ b/fsl/data/melodicimage.py
@@ -14,8 +14,8 @@ import os.path as op
import props
-import image as fslimage
-import melodicresults as melresults
+from . import image as fslimage
+from . import melodicresults as melresults
class MelodicImage(fslimage.Image):
diff --git a/fsl/data/model.py b/fsl/data/model.py
index 3def2dff3b481f4763492fe4bb791f2c1de4bfa8..ededc41a58814eb78d5c9e9144affba05c600d3c 100644
--- a/fsl/data/model.py
+++ b/fsl/data/model.py
@@ -21,6 +21,8 @@ import logging
import os.path as op
import numpy as np
+import six
+
log = logging.getLogger(__name__)
@@ -43,7 +45,7 @@ class Model(object):
:arg indices: A list of indices into the vertex data.
"""
- if isinstance(data, basestring):
+ if isinstance(data, six.string_types):
infile = data
data, lengths, indices = loadVTKPolydataFile(infile)
@@ -131,6 +133,7 @@ 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
for i in range(nPolygons):
@@ -141,6 +144,7 @@ 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/data/tensorimage.py b/fsl/data/tensorimage.py
index 4d194b480c9a56985d1e877cff948e444753d943..86ae221cb496c91a0fb8ec36c14f97a76578e321 100644
--- a/fsl/data/tensorimage.py
+++ b/fsl/data/tensorimage.py
@@ -9,12 +9,14 @@ the diffusion tensor data generated by the FSL ``dtifit`` tool.
"""
-import logging
-import re
-import glob
-import os.path as op
+import logging
+import re
+import glob
+import os.path as op
-import fsl.data.image as fslimage
+import six
+
+from . import image as fslimage
log = logging.getLogger(__name__)
@@ -101,7 +103,7 @@ class TensorImage(fslimage.Nifti1):
eigenvalues.
"""
- dtifitDir = isinstance(path, basestring)
+ dtifitDir = isinstance(path, six.string_types)
if dtifitDir:
diff --git a/fsl/utils/async.py b/fsl/utils/async.py
index 801d0debbc0516623ca095390c0ea5431182b7a3..672102102525664b0380c85a4fce09bc6a99bbe3 100644
--- a/fsl/utils/async.py
+++ b/fsl/utils/async.py
@@ -33,11 +33,12 @@ the task (via :func:`idle`).
import time
-import Queue
import logging
import threading
import collections
+try: import queue
+except: import Queue as queue
log = logging.getLogger(__name__)
@@ -114,7 +115,7 @@ in the :func:`idle` function.
"""
-_idleQueue = Queue.Queue()
+_idleQueue = queue.Queue()
"""A ``Queue`` of functions which are to be run on the ``wx.EVT_IDLE``
loop.
"""
@@ -129,7 +130,7 @@ def _wxIdleLoop(ev):
try:
task, schedtime, timeout, args, kwargs = _idleQueue.get_nowait()
- except Queue.Empty:
+ except queue.Empty:
return
name = getattr(task, '__name__', '<unknown>')
diff --git a/fsl/utils/dialog.py b/fsl/utils/dialog.py
index a6e277f63e087deee87f575eb934b83eb4923f26..0a482defca6192def7dd7bba208d9823940e8ca5 100644
--- a/fsl/utils/dialog.py
+++ b/fsl/utils/dialog.py
@@ -22,7 +22,7 @@ import threading
import wx
-from fsl.utils.platform import platform as fslplatform
+from .platform import platform as fslplatform
class SimpleMessageDialog(wx.Dialog):
@@ -455,7 +455,12 @@ class TextEditDialog(wx.Dialog):
if icon is not None:
icon = wx.ArtProvider.GetMessageBoxIcon(icon)
- bmp = wx.EmptyBitmap(icon.GetWidth(), icon.GetHeight())
+
+ if fslplatform.wxFlavour == fslplatform.WX_PHOENIX:
+ bmp = wx.Bitmap()
+ else:
+ bmp = wx.EmptyBitmap(icon.GetWidth(), icon.GetHeight())
+
bmp.CopyFromIcon(icon)
self.__icon = wx.StaticBitmap(self)
self.__icon.SetBitmap(bmp)
@@ -634,7 +639,12 @@ class FSLDirDialog(wx.Dialog):
self.__skip = wx.Button( self, id=wx.ID_CANCEL)
icon = wx.ArtProvider.GetMessageBoxIcon(wx.ICON_EXCLAMATION)
- bmp = wx.EmptyBitmap(icon.GetWidth(), icon.GetHeight())
+
+ if fslplatform.wxFlavour == fslplatform.WX_PYTHON:
+ bmp = wx.EmptyBitmap(icon.GetWidth(), icon.GetHeight())
+ else:
+ bmp = wx.Bitmap()
+
bmp.CopyFromIcon(icon)
self.__icon.SetBitmap(bmp)
@@ -756,7 +766,12 @@ class CheckBoxMessageDialog(wx.Dialog):
if icon is not None:
icon = wx.ArtProvider.GetMessageBoxIcon(icon)
self.__icon = wx.StaticBitmap(self)
- bmp = wx.EmptyBitmap(icon.GetWidth(), icon.GetHeight())
+
+ if fslplatform.wxFlavour == fslplatform.WX_PYTHON:
+ bmp = wx.EmptyBitmap(icon.GetWidth(), icon.GetHeight())
+ else:
+ bmp = wx.Bitmap()
+
bmp.CopyFromIcon(icon)
self.__icon.SetBitmap(bmp)
else:
diff --git a/fsl/utils/imagepanel.py b/fsl/utils/imagepanel.py
index cf74b453fcc3fcc5265c8312f7dc791f988103fe..5352bd100b2cb98718a74ae1858040aeab3343f5 100644
--- a/fsl/utils/imagepanel.py
+++ b/fsl/utils/imagepanel.py
@@ -12,12 +12,18 @@ import logging
import wx
+from fsl.utils.platform import platform as fslplatform
+
log = logging.getLogger(__name__)
-class ImagePanel(wx.PyPanel):
- """A :class:`wx.PyPanel` which may be used to display a resizeable
+if fslplatform.wxFlavour == fslplatform.WX_PHOENIX: ImagePanelBase = wx.Panel
+else: ImagePanelBase = wx.PyPanel
+
+
+class ImagePanel(ImagePanelBase):
+ """A :class:`wx.Panel` which may be used to display a resizeable
:class:`wx.Image`. The image is scaled to the size of the panel.
"""
@@ -32,7 +38,7 @@ class ImagePanel(wx.PyPanel):
:arg image: The :class:`wx.Image` object to display.
"""
- wx.PyPanel.__init__(self, parent)
+ ImagePanelBase.__init__(self, parent)
self.Bind(wx.EVT_PAINT, self.Draw)
self.Bind(wx.EVT_SIZE, self.__onSize)
@@ -46,6 +52,11 @@ class ImagePanel(wx.PyPanel):
:arg image: The :class:`wx.Image` object to display.
"""
self.__image = image
+
+
+ if image is not None: self.SetMinSize(image.GetSize())
+ else: self.SetMinSize((0, 0))
+
self.Refresh()
@@ -86,6 +97,6 @@ class ImagePanel(wx.PyPanel):
if width == 0 or height == 0:
return
- bitmap = wx.BitmapFromImage(self.__image.Scale(width, height))
+ bitmap = self.__image.Scale(width, height).ConvertToBitmap()
dc.DrawBitmap(bitmap, 0, 0, False)
diff --git a/fsl/utils/memoize.py b/fsl/utils/memoize.py
index 07f6f1242643c7c25288e789639e4bf0de8d712b..9de2ef726963f0b19f278cf2f0ef2d1531d5b658 100644
--- a/fsl/utils/memoize.py
+++ b/fsl/utils/memoize.py
@@ -18,6 +18,7 @@ a function:
import hashlib
import functools
+import six
def memoizeMD5(func):
@@ -35,7 +36,8 @@ def memoizeMD5(func):
hashobj = hashlib.md5()
for arg in args:
- hashobj.update(str(arg))
+ arg = six.u(arg).encode('utf-8')
+ hashobj.update(arg)
digest = hashobj.hexdigest()
cached = cache.get(digest)
diff --git a/fsl/utils/notifier.py b/fsl/utils/notifier.py
index 154f67521e17560ceebb44d53ee11adbd51798a5..faa3fb7e6c0e232b76719654ce5ceaf42cfabce6 100644
--- a/fsl/utils/notifier.py
+++ b/fsl/utils/notifier.py
@@ -34,7 +34,7 @@ class Notifier(object):
"""Initialises a dictionary of listeners on a new ``Notifier``
instance.
"""
- new = object.__new__(cls, *args, **kwargs)
+ new = object.__new__(cls)
new.__listeners = collections.OrderedDict()
return new
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index cacc25b0f9756e4055bad480efc21c0166c2ec04..408b77c23ba7eed3579c7d4876caa5052dce546a 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -91,8 +91,8 @@ def addExt(prefix, allowedExts, mustExist=True, defaultExt=None):
if not mustExist:
# the provided file name already
- # ends with a supported extension
- if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
+ # ends with a supported extension
+ if any([prefix.endswith(ext) for ext in allowedExts]):
return prefix
if defaultExt is not None: return prefix + defaultExt
@@ -100,16 +100,16 @@ def addExt(prefix, allowedExts, mustExist=True, defaultExt=None):
# If the provided prefix already ends with a
# supported extension , check to see that it exists
- if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
+ if any([prefix.endswith(ext) for ext in allowedExts]):
extended = [prefix]
# Otherwise, make a bunch of file names, one per
# supported extension, and test to see if exactly
# one of them exists.
else:
- extended = map(lambda ext: prefix + ext, allowedExts)
+ extended = [prefix + ext for ext in allowedExts]
- exists = map(op.isfile, extended)
+ exists = [op.isfile(e) for e in extended]
# Could not find any supported file
# with the specified prefix
@@ -119,7 +119,7 @@ def addExt(prefix, allowedExts, mustExist=True, defaultExt=None):
# Ambiguity! More than one supported
# file with the specified prefix
- if len(filter(bool, exists)) > 1:
+ if sum(exists) > 1:
raise ValueError('More than one file with prefix {}'.format(prefix))
# Return the full file name of the
@@ -139,7 +139,7 @@ def removeExt(filename, allowedExts):
"""
# figure out the extension of the given file
- extMatches = map(lambda ext: filename.endswith(ext), allowedExts)
+ extMatches = [filename.endswith(ext) for ext in allowedExts]
# the file does not have a supported extension
if not any(extMatches):
diff --git a/fsl/utils/platform.py b/fsl/utils/platform.py
index 2510f8830d34e9914b1e957a60d46990d37212b6..9b95faf966326ce116c058bbb54517ce2185541f 100644
--- a/fsl/utils/platform.py
+++ b/fsl/utils/platform.py
@@ -8,17 +8,14 @@
of information about the current platform we are running on. A single
``Platform`` instance is created when this module is first imported, and
is available as a module attribute called :attr:`platform`.
-
-.. note:: The ``Platform`` class only contains information which is not
- already accessible from the built-in ``platform`` module
- (e.g. operating system information), or the ``six`` module (e.g.
- python 2 vs 3).
"""
import logging
import os
+import sys
+import platform as builtin_platform
import fsl.utils.notifier as notifier
@@ -67,6 +64,8 @@ class Platform(notifier.Notifier):
.. autosummary::
+ os
+ frozen
fsldir
haveGui
wxPlatform
@@ -125,6 +124,22 @@ class Platform(notifier.Notifier):
log.warning('Could not determine wx platform from '
'information: {}'.format(pi))
+
+ @property
+ def os(self):
+ """The operating system name. Whatever is returned by the built-in
+ ``platform.system`` function.
+ """
+ return builtin_platform.system()
+
+
+ @property
+ def frozen(self):
+ """``True`` if we are running in a compiled/frozen application,
+ ``False`` otherwise.
+ """
+ return getattr(sys, 'frozen', False)
+
@property
def haveGui(self):
diff --git a/fsl/utils/runwindow.py b/fsl/utils/runwindow.py
index f344c1483eaeb1e087366844ded4c86ca3556112..a26969e9f3d06b753c9d8975f8730b30a8a7a12a 100644
--- a/fsl/utils/runwindow.py
+++ b/fsl/utils/runwindow.py
@@ -26,7 +26,9 @@ import logging
import subprocess as subp
import threading as thread
-import Queue as queue
+
+try: import queue
+except: import Queue as queue
import wx
diff --git a/fsl/utils/typedict.py b/fsl/utils/typedict.py
index 0a498ca74880e18041a2753c8a3fdbb220e8511d..0ac4cdcde3c3f2853fcf645e866e6641ae0b7c1a 100644
--- a/fsl/utils/typedict.py
+++ b/fsl/utils/typedict.py
@@ -8,6 +8,8 @@
"""
+import six
+
import collections
@@ -164,7 +166,7 @@ class TypeDict(object):
string, or a combination of strings and types, into a tuple.
"""
- if isinstance(key, basestring):
+ if isinstance(key, six.string_types):
if '.' in key: return tuple(key.split('.'))
else: return key
@@ -174,7 +176,7 @@ class TypeDict(object):
key = []
for tk in tKeys:
- if isinstance(tk, basestring): key.append(tk)
+ if isinstance(tk, six.string_types): key.append(tk)
elif isinstance(tk, collections.Sequence): key += list(tk)
else: key.append(tk)