def setUp(self):
# Set up as if for MrcFileTest
super(MrcMemmapTest, self).setUp()
# Set the newmrc method to the MrcMemmap constructor
self.newmrc = MrcMemmap
# Set up parameters so MrcObject tests run on the MrcMemmap class
obj_mrc_name = os.path.join(self.test_output, 'test_mrcobject.mrc')
self.mrcobject = MrcMemmap(obj_mrc_name, 'w+', overwrite=True)
class MrcMemmapTest(MrcFileTest):
"""Unit tests for MRC file I/O with memory-mapped files.
Note that this test class inherits MrcFileTest to ensure all of the tests
for MrcObject and MrcFile work correctly for the MrcMemmap subclass.
"""
def setUp(self):
# Set up as if for MrcFileTest
super(MrcMemmapTest, self).setUp()
# Set the newmrc method to the MrcMemmap constructor
self.newmrc = MrcMemmap
# Set up parameters so MrcObject tests run on the MrcMemmap class
obj_mrc_name = os.path.join(self.test_output, 'test_mrcobject.mrc')
self.mrcobject = MrcMemmap(obj_mrc_name, 'w+', overwrite=True)
def test_repr(self):
"""Override test to change expected repr string."""
with MrcMemmap(self.example_mrc_name) as mrc:
assert repr(mrc) == "MrcMemmap('{0}', mode='r')".format(
self.example_mrc_name)
def test_exception_raised_if_file_is_too_small(self):
"""Override test to change expected error message."""
with self.newmrc(self.temp_mrc_name, mode='w+') as mrc:
mrc.set_data(np.arange(24, dtype=np.int16).reshape(2, 3, 4))
assert mrc.header.mz == 2
mrc.header.mz = mrc.header.nz = 3
# The exception type and message are different on Linux and Windows
expected_error_msg = ("mmap length is greater than file size"
"|Not enough storage is available")
with self.assertRaisesRegex(Exception, expected_error_msg):
self.newmrc(self.temp_mrc_name)
def test_data_is_not_copied_unnecessarily(self):
"""Override test because data has to be copied for mmap."""
data = np.arange(6, dtype=np.int16).reshape(1, 2, 3)
self.mrcobject.set_data(data)
assert self.mrcobject.data is not data
def test_data_array_cannot_be_changed_after_closing_file(self):
mrc = self.newmrc(self.temp_mrc_name, mode='w+')
mrc.set_data(np.arange(12, dtype=np.int16).reshape(3, 4))
data_ref = mrc.data
# Check that writing to the data array does not raise an exception
data_ref[0, 0] = 1
mrc.close()
assert not data_ref.flags.writeable
with self.assertRaises(ValueError):
data_ref[0, 0] = 2
def access_mrc(path: Pathlike, mode: str, **kwargs):
# todo: add warning when kwargs are passed to this function
return MrcMemmap(path, mode=mode)
def test_repr(self):
"""Override test to change expected repr string."""
with MrcMemmap(self.example_mrc_name) as mrc:
assert repr(mrc) == "MrcMemmap('{0}', mode='r')".format(
self.example_mrc_name)
def access_mrc(path: Pathlike, mode: str, **kwargs):
return MrcMemmap(path, mode=mode, **kwargs)