Merge remote branch 'nipy/master'

Author: mih

nibabel/analyze.py

@@ -680,10 +680,12 @@ def items(self):
         ''' Return items from header data'''
         return zip(self.keys(), self.values())
 
-    def check_fix(self,
-              logger=imageglobals.logger,
-              error_level=imageglobals.error_level):
+    def check_fix(self, logger=None, error_level=None):
         ''' Check header data with checks '''
+        if logger is None:
+            logger = imageglobals.logger
+        if error_level is None:
+            error_level = imageglobals.error_level
         battrun = BatteryRunner(self.__class__._get_checks())
         self, reports = battrun.check_fix(self)
         for report in reports:

nibabel/imageglobals.py

@@ -6,11 +6,21 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-''' Defaults for images and headers '''
+""" Defaults for images and headers
+
+error_level is the problem level (see BatteryRunners) at which an error will be
+raised, by the batteryrunners ``log_raise`` method.  Thus a level of 0 will
+result in an error for any problem at all, and a level of 50 will mean no errors
+will be raised (unless someone's put some strange problem_level > 50 code in).
+
+``logger`` is the default logger (python log instance)
+
+To set the log level (log message appears for problem of level >= log level),
+use e.g. ``logger.level = 40``
+"""
 
 import logging
 
 error_level = 40
-log_level = 30
-logger = logging.getLogger('nifti.global')
+logger = logging.getLogger('nibabel.global')
 logger.addHandler(logging.StreamHandler())

nibabel/tests/test_analyze.py

@@ -55,6 +55,7 @@
     ImageDataError
 from ..analyze import AnalyzeHeader, AnalyzeImage
 from ..loadsave import read_img_data
+from .. import imageglobals
 
 from ..testing import parametric, data_path, ParametricTestCase
 
@@ -64,6 +65,7 @@
 
 header_file = os.path.join(data_path, 'analyze.hdr')
 
+PIXDIM0_MSG = 'pixdim[1,2,3] should be non-zero; setting 0 dims to 1'
 
 def _log_chk(hdr, level):
     # utility function to check header checking / logging
@@ -189,8 +191,7 @@ def test_log_checks(self):
         hdr['pixdim'][1] = 0 # severity 30
         fhdr, message, raiser = _log_chk(hdr, 30)
         yield assert_equal(fhdr['pixdim'][1], 1)
-        yield assert_equal(message, 'pixdim[1,2,3] should be '
-                           'non-zero; setting 0 dims to 1')
+        yield assert_equal(message, PIXDIM0_MSG)
         yield assert_raises(*raiser)
         # both
         hdr = HC()
@@ -205,6 +206,30 @@ def test_log_checks(self):
                            'and setting to abs of pixdim values')
         yield assert_raises(*raiser)
 
+    def test_logger_error(self):
+        # Check that we can reset the logger and error level
+        HC = self.header_class
+        hdr = HC()
+        # Make a new logger
+        str_io = StringIO()
+        logger = logging.getLogger('test.logger')
+        logger.setLevel(30) # defaultish level
+        logger.addHandler(logging.StreamHandler(str_io))
+        # Prepare an error
+        hdr['pixdim'][1] = 0 # severity 30
+        log_cache = imageglobals.logger, imageglobals.error_level
+        try:
+            # Check log message appears in new logger
+            imageglobals.logger = logger
+            hdr.copy().check_fix()
+            assert_equal(str_io.getvalue(), PIXDIM0_MSG + '\n')
+            # Check that error_level in fact causes error to be raised
+            imageglobals.error_level = 30
+            assert_raises(HeaderDataError, hdr.copy().check_fix)
+        finally:
+            imageglobals.logger, imageglobals.error_level = log_cache
+
+
     def test_datatype(self):
         ehdr = self.header_class()
         codes = self.header_class._data_type_codes