def chk_error(obj, fix=True):
ret = Report(obj, KeyError)
if obj.has_key('thirdkey'):
return ret
ret.problem_msg = 'no "thirdkey"'
if fix:
obj['anotherkey'] = 'a string'
ret.fix_msg = 'added "anotherkey"'
else:
ret.problem_level = 40
return ret
def chk1(obj, fix=True):
ret = Report(obj, KeyError)
if obj.has_key('testkey'):
return ret
ret.problem_msg = 'no "testkey"'
if fix:
obj['testkey'] = 1
ret.fix_msg = 'added "testkey"'
else:
ret.problem_level = 20
return ret
def _chk_sizeof_hdr(hdr, fix=True):
ret = Report(hdr, HeaderDataError)
if hdr['sizeof_hdr'] == 348:
return ret
ret.problem_msg = 'sizeof_hdr should be 348'
if fix:
hdr['sizeof_hdr'] = 348
ret.fix_msg = 'set sizeof_hdr to 348'
else:
ret.problem_level = 30
return ret
def _chk_pixdims(hdr, fix=True):
ret = Report(hdr, HeaderDataError)
if not np.any(hdr['pixdim'][1:4] < 0):
return ret
ret.problem_msg = 'pixdim[1,2,3] should be positive'
if fix:
hdr['pixdim'][1:4] = np.abs(hdr['pixdim'][1:4])
ret.fix_msg = 'setting to abs of pixdim values'
else:
ret.problem_level = 40
return ret
def _chk_scale(klass, hdr, fix=True):
ret = Report(hdr, HeaderDataError)
scale, offset = hdr.get_slope_inter()
if not scale is None:
return ret
ret.problem_msg = "no valid scaling in scalefactor (=%s) " "or cal / gl fields; scalefactor assumed 1.0" % scale
if fix:
hdr["scl_slope"] = 1
ret.fix_msg = 'setting scalefactor "scl_slope" to 1'
else:
ret.problem_level = 30
return ret
def _chk_scale(hdr, fix=True):
ret = Report(hdr, HeaderDataError)
scale = hdr['scl_slope']
if scale and np.isfinite(scale):
return ret
ret.problem_msg = ('scale slope is %s; should !=0 and be finite'
% scale)
if fix:
hdr['scl_slope'] = 1
ret.fix_msg = 'setting scalefactor "scale" to 1'
else:
ret.problem_level = 30
return ret
def _chk_origin(hdr, fix=True):
ret = Report(hdr, HeaderDataError)
origin = hdr['origin'][0:3]
dims = hdr['dim'][1:4]
if (not np.any(origin) or
(np.all(origin > -dims) and np.all(origin < dims*2))):
return ret
ret.problem_msg = 'very large origin values relative to dims'
if fix:
ret.fix_msg = 'leaving as set, ignoring for affine'
else:
ret.problem_level = 20
return ret
def test_logging():
rep = Report('', ValueError, 20, 'msg', 'fix')
str_io = StringIO()
logger = logging.getLogger('test.logger')
logger.setLevel(30) # defaultish level
logger.addHandler(logging.StreamHandler(str_io))
rep.log_raise(logger)
yield assert_equal, str_io.getvalue(), ''
rep.problem_level = 30
rep.log_raise(logger)
yield assert_equal, str_io.getvalue(), 'msg; fix\n'
str_io.truncate(0)
def chk2(obj, fix=True):
# Can return different codes for different errors in same check
ret = Report(obj)
try:
ok = obj['testkey'] == 0
except KeyError:
ret.problem_msg = 'no "testkey"'
ret.error = KeyError
if fix:
obj['testkey'] = 1
ret.fix_msg = 'added "testkey"'
else:
ret.problem_level = 20
return ret
if ok:
return ret
ret.problem_msg = '"testkey" != 0'
ret.error = ValueError
if fix:
ret.fix_msg = 'set "testkey" to 0'
obj['testkey'] = 0
else:
ret.problem_level = 10
return ret
def _chk_bitpix(klass, hdr, fix=True):
ret = Report(hdr, HeaderDataError)
code = int(hdr['datatype'])
try:
dt = klass._data_type_codes.dtype[code]
except KeyError:
ret.problem_level = 10
ret.problem_msg = 'no valid datatype to fix bitpix'
if fix:
ret.fix_msg = 'no way to fix bitpix'
return ret
bitpix = dt.itemsize * 8
ret = Report(hdr)
if bitpix == hdr['bitpix']:
return ret
ret.problem_msg = 'bitpix does not match datatype'
if fix:
hdr['bitpix'] = bitpix # inplace modification
ret.fix_msg = 'setting bitpix to match datatype'
else:
ret.problem_level = 10
return ret
def _chk_datatype(klass, hdr, fix=True):
ret = Report(hdr, HeaderDataError)
code = int(hdr['datatype'])
try:
dtype = klass._data_type_codes.dtype[code]
except KeyError:
ret.problem_level = 40
ret.problem_msg = 'data code %d not recognized' % code
else:
if dtype.type is np.void:
ret.problem_level = 40
ret.problem_msg = 'data code %d not supported' % code
if fix:
ret.fix_problem_msg = 'not attempting fix'
return ret
def test_report_strings():
rep = Report()
yield assert_not_equal, rep.__str__(), ''
yield assert_equal, rep.message, ''
str_io = StringIO()
rep.write_raise(str_io)
yield assert_equal, str_io.getvalue(), ''
rep = Report('', ValueError, 20, 'msg', 'fix')
rep.write_raise(str_io)
yield assert_equal, str_io.getvalue(), ''
rep.problem_level = 30
rep.write_raise(str_io)
yield assert_equal, str_io.getvalue(), 'Level 30: msg; fix\n'
str_io.truncate(0)
# No fix string, no fix message
rep.fix_msg = ''
rep.write_raise(str_io)
yield assert_equal, str_io.getvalue(), 'Level 30: msg\n'
rep.fix_msg = 'fix'
str_io.truncate(0)
# If we drop the level, nothing goes to the log
rep.problem_level = 20
rep.write_raise(str_io)
yield assert_equal, str_io.getvalue(), ''
# Unless we set the default log level in the call
rep.write_raise(str_io, log_level=20)
yield assert_equal, str_io.getvalue(), 'Level 20: msg; fix\n'
str_io.truncate(0)
# If we set the error level down this low, we raise an error
yield assert_raises, ValueError, rep.write_raise, str_io, 20
# But the log level wasn't low enough to do a log entry
yield assert_equal, str_io.getvalue(), ''
# Error still raised with lower log threshold, but now we do get a
# log entry
yield assert_raises, ValueError, rep.write_raise, str_io, 20, 20
yield assert_equal, str_io.getvalue(), 'Level 20: msg; fix\n'
# If there's no error, we can't raise
str_io.truncate(0)
rep.error = None
rep.write_raise(str_io, 20)
yield assert_equal, str_io.getvalue(), ''
