Fix various python 2/3 incompatibilities. Also simplified

featdesign.loadDesignMat function

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]

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))
 

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()
 
 

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)
 
 

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]

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()