Code cleanup after self code review, fix for Python 3 'filter' issue.

Author: Ben Cipollini

nibabel/analyze.py

@@ -829,7 +829,7 @@ def _chk_datatype(klass, hdr, fix=False):
             dtype = klass._data_type_codes.dtype[code]
         except KeyError:
             rep.problem_level = 40
-            rep.problem_msg = 'data code %d not recognized by %s' % (code, klass.__name__)
+            rep.problem_msg = 'data code %d not recognized' % code
         else:
             if dtype.itemsize == 0:
                 rep.problem_level = 40
@@ -899,10 +899,9 @@ class AnalyzeImage(SpatialImage):
     header_class = AnalyzeHeader
     files_types = (('image','.img'), ('header','.hdr'))
     _compressed_exts = ('.gz', '.bz2')
-    has_affine = False
+
     makeable = True
     rw = True
-    nickname = 'analyze'
 
     ImageArrayProxy = ArrayProxy
 

nibabel/filename_parser.py

@@ -133,8 +133,8 @@ def types_filenames(template_fname, types_exts,
         elif found_ext == found_ext.lower():
             proc_ext = lambda s : s.lower()
     for name, ext in types_exts:
-        if name in tfns:  # priority to those found first.
-            continue
+        if name in tfns:  # Allow multipe definitions of image, header, etc,
+            continue      # giving priority to those found first.
         if name == direct_set_name:
             tfns[name] = template_fname
             continue

nibabel/freesurfer/mghformat.py

@@ -461,8 +461,7 @@ class MGHImage(SpatialImage):
     files_types = (('image', '.mgh'),
                    ('image', '.mgz'))
     _compressed_exts = (('.gz',))
-    nickname = 'mgh'
-    has_affine = True
+
     makeable = True
     rw = True
 

nibabel/loadsave.py

@@ -72,22 +72,22 @@ def save(img, filename):
     lext = ext.lower()
 
     # Special-case Nifti singles and Pairs
-    from .nifti1 import Nifti1Image, Nifti1Pair  # Inline imports, as this file
+    from .nifti1 import Nifti1Image, Nifti1Pair  # Inline imports, as this module
     from .nifti2 import Nifti2Image, Nifti2Pair  # really shouldn't reference any image type
-    if type(img) == Nifti1Image and ext in ('.img', '.hdr'):
+    if type(img) == Nifti1Image and lext in ('.img', '.hdr'):
         klass = Nifti1Pair
-    elif type(img) == Nifti2Image and ext in ('.img', '.hdr'):
+    elif type(img) == Nifti2Image and lext in ('.img', '.hdr'):
         klass = Nifti2Pair
-    elif type(img) == Nifti1Pair and ext == '.nii':
+    elif type(img) == Nifti1Pair and lext == '.nii':
         klass = Nifti1Image
-    elif type(img) == Nifti2Pair and ext == '.nii':
+    elif type(img) == Nifti2Pair and lext == '.nii':
         klass = Nifti2Image
     else:  # arbitrary conversion
-        valid_klasses = filter(lambda klass: klass.is_valid_extension(lext),
+        valid_klasses = filter(lambda klass: klass.is_valid_extension(ext),
                                all_image_classes)
-        if len(valid_klasses) > 0:
-            klass = valid_klasses[0]
-        else:
+        try:
+            klass = next(iter(valid_klasses))
+        except StopIteration:  # if iterator is empty
             raise ImageFileError('Cannot work out file type of "%s"' %
                                  filename)
     converted = klass.from_image(img)

nibabel/minc1.py

@@ -301,10 +301,9 @@ class Minc1Image(SpatialImage):
     header_class = Minc1Header
     files_types = (('image', '.mnc'),)
     _compressed_exts = ('.gz', '.bz2')
-    has_affine = True
+
     makeable = True
     rw = False
-    nickname = 'minc'
 
     ImageArrayProxy = MincImageArrayProxy
 

nibabel/nifti1.py

@@ -1615,7 +1615,6 @@ class Nifti1Pair(analyze.AnalyzeImage):
     """ Class for NIfTI1 format image, header pair
     """
     header_class = Nifti1PairHeader
-    nickname = 'nifti_pair'
     rw = True
 
     def __init__(self, dataobj, affine, header=None,
@@ -1841,7 +1840,6 @@ class Nifti1Image(Nifti1Pair):
     """
     header_class = Nifti1Header
     files_types = (('image', '.nii'),)
-    nickname = 'nifti_single'
 
     @staticmethod
     def _get_fileholders(file_map):

nibabel/parrec.py

@@ -1009,8 +1009,7 @@ class PARRECImage(SpatialImage):
     """PAR/REC image"""
     header_class = PARRECHeader
     files_types = (('image', '.rec'), ('header', '.par'))
-    nickname = 'par'
-    has_affine = True
+
     makeable = False
     rw = False
 

nibabel/spatialimages.py

@@ -326,15 +326,8 @@ class SpatialImage(object):
     files_types = (('image', None),)
     _compressed_exts = ()
 
-    @classmethod
-    def is_valid_extension(klass, lext):
-        return np.any([ft[1] == lext for ft in klass.files_types])
-
-    @classmethod
-    def is_valid_filename(klass, filename):
-        froot, ext, trailing = splitext_addext(filename, klass._compressed_exts)
-        lext = ext.lower()
-        return klass.is_valid_extension(lext)
+    makeable = True  # Used in test code
+    rw = True  # Used in test code
 
     def __init__(self, dataobj, affine, header=None,
                  extra=None, file_map=None):
@@ -879,15 +872,23 @@ def from_image(klass, img):
                      klass.header_class.from_header(img.header),
                      extra=img.extra.copy())
 
+    @classmethod
+    def is_valid_extension(klass, ext):
+        return np.any([ft[1] == ext.lower() for ft in klass.files_types])
+
+    @classmethod
+    def is_valid_filename(klass, filename):
+        froot, ext, trailing = splitext_addext(filename, klass._compressed_exts)
+        return klass.is_valid_extension(ext)
+
     @classmethod
     def is_image(klass, filename, sniff=None):
         froot, ext, trailing = splitext_addext(filename, klass._compressed_exts)
-        lext = ext.lower()
 
-        if not klass.is_valid_extension(lext):
+        if not klass.is_valid_extension(ext):
             return False, sniff
-        elif (not hasattr(klass.header_class, 'sniff_size') or
-              not hasattr(klass.header_class, 'is_header')):
+        elif (getattr(klass.header_class, 'sniff_size', None) is None or
+              getattr(klass.header_class, 'is_header', None) is None):
             return True, sniff
 
         # Determine the metadata location, then sniff it

nibabel/spm2analyze.py

@@ -133,7 +133,6 @@ class Spm2AnalyzeImage(spm99.Spm99AnalyzeImage):
     """ Class for SPM2 variant of basic Analyze image
     """
     header_class = Spm2AnalyzeHeader
-    nickname = 'spm2analyze'
 
 load = Spm2AnalyzeImage.load
 save = Spm2AnalyzeImage.instance_to_filename

nibabel/spm99analyze.py

@@ -239,10 +239,9 @@ class Spm99AnalyzeImage(analyze.AnalyzeImage):
     files_types = (('image', '.img'),
                    ('header', '.hdr'),
                    ('mat','.mat'))
-    has_affine = True
+
     makeable = True
     rw = have_scipy
-    nickname = 'spm99analyze'
 
     @classmethod
     @kw_only_meth(1)

nibabel/tests/test_analyze.py

@@ -32,7 +32,7 @@
 from ..arraywriters import WriterError
 
 from nose.tools import (assert_equal, assert_not_equal, assert_true,
-                        assert_false, assert_raises, assert_in)
+                        assert_false, assert_raises)
 
 from numpy.testing import (assert_array_equal, assert_array_almost_equal)
 
@@ -157,8 +157,8 @@ def test_log_checks(self):
         hdr['datatype'] = -1 # severity 40
         with suppress_warnings():
             fhdr, message, raiser = self.log_chk(hdr, 40)
-        assert_in('data code -1 not recognized', message)
-        assert_in('not attempting fix', message)
+        assert_equal(message, 'data code -1 not recognized; '
+                           'not attempting fix')
 
         assert_raises(*raiser)
         # datatype not supported

nibabel/tests/test_filehandles.py

@@ -34,7 +34,7 @@ def test_multiload():
     if N > 5000:
         warn('It would take too long to test file handles, aborting')
         return
-    arr = np.arange(24).reshape((2, 3, 4))
+    arr = np.arange(24).reshape((2,3,4))
     img = Nifti1Image(arr, np.eye(4))
     imgs = []
     try:
@@ -43,10 +43,6 @@ def test_multiload():
         save(img, fname)
         for i in range(N):
             imgs.append(load(fname))
-    except Exception as e:
-        if 'i' in locals():
-            e.message += ' (i == %d)' % i
-        raise Exception(e.message)
     finally:
         del img, imgs
         shutil.rmtree(tmpdir)