MRG: refactor for common Python 2/3 code

nibabel/analyze.py

@@ -512,8 +512,8 @@ def data_to_fileobj(self, data, fileobj):
         >>> hdr = AnalyzeHeader()
         >>> hdr.set_data_shape((1, 2, 3))
         >>> hdr.set_data_dtype(np.float64)
-        >>> from StringIO import StringIO #23dt : BytesIO
-        >>> str_io = StringIO() #23dt : BytesIO
+        >>> from io import BytesIO
+        >>> str_io = BytesIO()
         >>> data = np.arange(6).reshape(1,2,3)
         >>> hdr.data_to_fileobj(data, str_io)
         >>> data.astype(np.float64).tostring('F') == str_io.getvalue()

nibabel/benchmarks/bench_load_save.py

@@ -9,11 +9,13 @@
 environment variable), and you have a numpy version <= 1.6.1, this will also run
 the doctests, let's hope they pass.
 """
+from __future__ import division, print_function
+
 import sys
 
 import numpy as np
 
-from ..py3k import BytesIO
+from ..externals.six import BytesIO
 from .. import Nifti1Image
 
 from numpy.testing import measure
@@ -28,18 +30,18 @@ def bench_load_save():
     img.file_map['image'].fileobj = sio
     hdr = img.get_header()
     sys.stdout.flush()
-    print "\nImage load save"
-    print "----------------"
+    print("\nImage load save")
+    print("----------------")
     hdr.set_data_dtype(np.float32)
     mtime = measure('img.to_file_map()', repeat)
-    print '%30s %6.2f' % ('Save float64 to float32', mtime)
+    print('%30s %6.2f' % ('Save float64 to float32', mtime))
     mtime = measure('img.from_file_map(img.file_map)', repeat)
-    print '%30s %6.2f' % ('Load from float32', mtime)
+    print('%30s %6.2f' % ('Load from float32', mtime))
     hdr.set_data_dtype(np.int16)
     mtime = measure('img.to_file_map()', repeat)
-    print '%30s %6.2f' % ('Save float64 to int16', mtime)
+    print('%30s %6.2f' % ('Save float64 to int16', mtime))
     mtime = measure('img.from_file_map(img.file_map)', repeat)
-    print '%30s %6.2f' % ('Load from int16', mtime)
+    print('%30s %6.2f' % ('Load from int16', mtime))
     arr = np.random.random_integers(low=-1000,high=-1000, size=img_shape)
     arr = arr.astype(np.int16)
     img = Nifti1Image(arr, np.eye(4))
@@ -48,5 +50,5 @@ def bench_load_save():
     hdr = img.get_header()
     hdr.set_data_dtype(np.float32)
     mtime = measure('img.to_file_map()', repeat)
-    print '%30s %6.2f' % ('Save Int16 to float32', mtime)
+    print('%30s %6.2f' % ('Save Int16 to float32', mtime))
     sys.stdout.flush()

nibabel/casting.py

@@ -428,6 +428,7 @@ def int_to_float(val, flt_type):
     """
     if not flt_type is np.longdouble:
         return flt_type(val)
+    val = int(val)
     faval = np.longdouble(0)
     while val != 0:
         f64 = np.float64(val)

nibabel/checkwarns.py

@@ -8,6 +8,8 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 ''' Contexts for *with* statement allowing checks for warnings
 '''
+from __future__ import division, print_function
+
 import warnings
 
 
@@ -21,7 +23,7 @@ class ErrorWarnings(warnings.catch_warnings):
     ...     try:
     ...         warnings.warn('Message', UserWarning)
     ...     except UserWarning:
-    ...         print 'I consider myself warned'
+    ...         print('I consider myself warned')
     I consider myself warned
     """
     filter = 'error'

nibabel/data.py

@@ -8,7 +8,7 @@
 from os.path import join as pjoin
 import glob
 import sys
-import ConfigParser
+from .externals.six.moves import configparser
 from distutils.version import LooseVersion
 
 from .environment import get_nipy_user_dir, get_nipy_system_dir
@@ -122,14 +122,14 @@ def __init__(self, base_path, config_filename=None):
         Datasource.__init__(self, base_path)
         if config_filename is None:
             config_filename = 'config.ini'
-        self.config = ConfigParser.SafeConfigParser()
+        self.config = configparser.SafeConfigParser()
         cfg_file = self.get_filename(config_filename)
         readfiles = self.config.read(cfg_file)
         if not readfiles:
             raise DataError('Could not read config file %s' % cfg_file)
         try:
             self.version = self.config.get('DEFAULT', 'version')
-        except ConfigParser.Error:
+        except configparser.Error:
             raise DataError('Could not get version from %s' % cfg_file)
         version_parts = self.version.split('.')
         self.major_version = int(version_parts[0])
@@ -140,13 +140,13 @@ def __init__(self, base_path, config_filename=None):
 
 def _cfg_value(fname, section='DATA', value='path'):
     """ Utility function to fetch value from config file """
-    configp =  ConfigParser.ConfigParser()
+    configp =  configparser.ConfigParser()
     readfiles = configp.read(fname)
     if not readfiles:
         return ''
     try:
         return configp.get(section, value)
-    except ConfigParser.Error:
+    except configparser.Error:
         return ''
 
 

nibabel/dft.py

@@ -8,7 +8,7 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # Copyright (C) 2011 Christian Haselgrove
 
-from __future__ import with_statement
+from __future__ import division, print_function, absolute_import
 
 import os
 from os.path import join as pjoin
@@ -20,7 +20,7 @@
 
 import numpy
 
-from .py3k import BytesIO
+from .externals.six import BytesIO
 
 from .nifti1 import Nifti1Header
 
@@ -119,13 +119,13 @@ def __getattribute__(self, name):
     def as_png(self, index=None, scale_to_slice=True):
         import PIL.Image
         if index is None:
-            index = len(self.storage_instances) / 2
+            index = len(self.storage_instances) // 2
         d = self.storage_instances[index].dicom()
         data = d.pixel_array.copy()
         if self.bits_allocated != 16:
-            raise VolumeError, 'unsupported bits allocated'
+            raise VolumeError('unsupported bits allocated')
         if self.bits_stored != 12:
-            raise VolumeError, 'unsupported bits stored'
+            raise VolumeError('unsupported bits stored')
         data = data / 16
         if scale_to_slice:
             min = data.min()
@@ -142,12 +142,12 @@ def png_size(self, index=None, scale_to_slice=True):
 
     def as_nifti(self):
         if len(self.storage_instances) < 2:
-            raise VolumeError, 'too few slices'
+            raise VolumeError('too few slices')
         d = self.storage_instances[0].dicom()
         if self.bits_allocated != 16:
-            raise VolumeError, 'unsupported bits allocated'
+            raise VolumeError('unsupported bits allocated')
         if self.bits_stored != 12:
-            raise VolumeError, 'unsupported bits stored'
+            raise VolumeError('unsupported bits stored')
         data = numpy.ndarray((len(self.storage_instances), 
                               self.rows, 
                               self.columns), 
@@ -266,7 +266,7 @@ def _get_subdirs(base_dir, files_dict=None, followlinks=False):
     for (dirpath, dirnames, filenames) in os.walk(base_dir, **kwargs):
         abs_dir = os.path.realpath(dirpath)
         if abs_dir in dirs:
-            raise CachingError, 'link cycle detected under %s' % base_dir
+            raise CachingError('link cycle detected under %s' % base_dir)
         dirs.append(abs_dir)
         if files_dict is not None:
             files_dict[abs_dir] = filenames
@@ -391,10 +391,10 @@ def _update_file(c, path, fname, studies, series, storage_instances):
                       do.StudyDate, 
                       do.StudyTime, 
                       study_comments, 
-                      do.PatientsName, 
+                      str(do.PatientName),
                       do.PatientID, 
-                      do.PatientsBirthDate, 
-                      do.PatientsSex)
+                      do.PatientBirthDate,
+                      do.PatientSex)
             c.execute(query, params)
             studies.append(str(do.StudyInstanceUID))
         if str(do.SeriesInstanceUID) not in series:
@@ -423,7 +423,7 @@ def _update_file(c, path, fname, studies, series, storage_instances):
             params = (str(do.SOPInstanceUID), do.InstanceNumber, str(do.SeriesInstanceUID))
             c.execute(query, params)
             storage_instances.append(str(do.SOPInstanceUID))
-    except AttributeError, data:
+    except AttributeError as data:
         logger.debug('        %s' % str(data))
         return None
     return str(do.SOPInstanceUID)

nibabel/ecat.py

@@ -343,8 +343,8 @@ def __getitem__(self, item):
         Examples
         --------
         >>> hdr = EcatHeader()
-        >>> hdr['magic_number'] #23dt next : bytes
-        'MATRIX72'
+        >>> hdr['magic_number'] == b'MATRIX72'
+        True
         '''
         return self._header_data[item].item()
 
@@ -365,7 +365,7 @@ def get_patient_orient(self):
         in header, not always reliable"""
         orient_code = dict(self._patient_orient_defs)
         code = self._header_data['patient_orientation'].item()
-        if not orient_code.has_key(code):
+        if not code in orient_code:
             raise KeyError('Ecat Orientation CODE %d not recognized'%code)
         return orient_code[code]
 
@@ -374,7 +374,7 @@ def get_filetype(self):
         code stored in header"""
         ft_codes = dict(self._ft_defs)
         code = self._header_data['file_type'].item()
-        if not ft_codes.has_key(code):
+        if not code in ft_codes:
             raise KeyError('Ecat Filetype CODE %d not recognized'%code)
         return ft_codes[code]
 
@@ -972,7 +972,7 @@ def to_file_map(self, file_map=None):
         hdr.write_to(hdrf)
 
         #Write every frames
-        for index in xrange(0, self.get_header()['num_frames']):
+        for index in range(0, self.get_header()['num_frames']):
             #Move to subheader offset
             frame_offset = subheaders._get_frame_offset(index) - 512
             imgf.seek(frame_offset)

nibabel/eulerangles.py

@@ -85,6 +85,8 @@
 
 import math
 
+from .externals.six.moves import reduce
+
 import numpy as np