def read_header(path):
from mrcfile.mrcinterpreter import MrcInterpreter
mi = MrcInterpreter(iostream=open(path, 'rb'))
mi._read_header()
mi._iostream.close()
return mi.header
def test_stream_writing_and_reading(self):
stream = io.BytesIO()
data = np.arange(30, dtype=np.int16).reshape(5, 6)
with MrcInterpreter() as mrc:
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_data(data)
stream.seek(0)
with MrcInterpreter(iostream=stream) as mrc:
np.testing.assert_array_equal(data, mrc.data)
assert mrc.header.mode == 1
mrc.set_data(data * 2)
assert mrc.header.mode == 1
def test_incorrect_map_id(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'map ')
stream.seek(0)
with self.assertRaisesRegex(ValueError, "Map ID string not found"):
MrcInterpreter(iostream=stream)
def test_permissive_read_mode_with_file_too_small(self):
stream = io.BytesIO()
mrc = MrcInterpreter()
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_data(np.arange(12, dtype=np.int16).reshape(1, 3, 4))
mrc.close()
stream.seek(-1, io.SEEK_CUR)
stream.truncate()
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
MrcInterpreter(iostream=stream, permissive=True)
assert len(w) == 1
assert ("Expected 24 bytes in data block but could only read 23"
in str(w[0].message))
def test_incorrect_machine_stamp(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'MAP ')
stream.seek(0)
with self.assertRaisesRegex(
ValueError, "Unrecognised machine stamp: "
"0x00 0x00 0x00 0x00"):
MrcInterpreter(iostream=stream)
def test_short_but_valid_map_id(self):
"""This tests the case of files where the map ID is almost correct.
For example, MotionCor2 writes files with ID 'MAP\0', which is not
valid according to the MRC2014 spec on the CCP-EM website, but could
be considered valid according to the MRC2014 paper (which just
specifies 'MAP', i.e. without the final byte). We should read such
files without errors or warnings (but they should fail a strict
validation check, tested elsewhere)."""
stream = io.BytesIO()
data = np.arange(30, dtype=np.int16).reshape(5, 6)
with MrcInterpreter() as mrc:
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_data(data)
mrc.header.map = b'MAP\0'
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
with MrcInterpreter(iostream=stream) as mrc:
np.testing.assert_array_equal(data, mrc.data)
# Ensure no warnings were raised
assert len(w) == 0
def test_permissive_read_mode_with_wrong_map_id_and_machine_stamp(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'map ')
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
MrcInterpreter(iostream=stream, permissive=True)
assert len(w) == 2
assert "Map ID string not found" in str(w[0].message)
assert "Unrecognised machine stamp" in str(w[1].message)
def test_stream_too_short(self):
stream = io.BytesIO()
stream.write(bytearray(1023))
with self.assertRaisesRegex(
ValueError, "Couldn't read enough bytes for MRC header"):
MrcInterpreter(iostream=stream)
def setUp(self):
super(MrcInterpreterTest, self).setUp()
# Set up parameters so MrcObject tests run on the MrcInterpreter class
self.mrcobject = MrcInterpreter()
self.mrcobject._create_default_attributes()
class MrcInterpreterTest(MrcObjectTest):
"""Unit tests for MrcInterpreter class.
Note that this test class inherits MrcObjectTest to ensure all of the tests
for MrcObject work correctly for the MrcInterpreter subclass.
"""
def setUp(self):
super(MrcInterpreterTest, self).setUp()
# Set up parameters so MrcObject tests run on the MrcInterpreter class
self.mrcobject = MrcInterpreter()
self.mrcobject._create_default_attributes()
def test_incorrect_map_id(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'map ')
stream.seek(0)
with self.assertRaisesRegex(ValueError, "Map ID string not found"):
MrcInterpreter(iostream=stream)
def test_incorrect_machine_stamp(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'MAP ')
stream.seek(0)
with self.assertRaisesRegex(
ValueError, "Unrecognised machine stamp: "
"0x00 0x00 0x00 0x00"):
MrcInterpreter(iostream=stream)
def test_stream_too_short(self):
stream = io.BytesIO()
stream.write(bytearray(1023))
with self.assertRaisesRegex(
ValueError, "Couldn't read enough bytes for MRC header"):
MrcInterpreter(iostream=stream)
def test_stream_writing_and_reading(self):
stream = io.BytesIO()
data = np.arange(30, dtype=np.int16).reshape(5, 6)
with MrcInterpreter() as mrc:
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_data(data)
stream.seek(0)
with MrcInterpreter(iostream=stream) as mrc:
np.testing.assert_array_equal(data, mrc.data)
assert mrc.header.mode == 1
mrc.set_data(data * 2)
assert mrc.header.mode == 1
def test_permissive_read_mode_with_wrong_map_id_and_machine_stamp(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'map ')
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
MrcInterpreter(iostream=stream, permissive=True)
assert len(w) == 2
assert "Map ID string not found" in str(w[0].message)
assert "Unrecognised machine stamp" in str(w[1].message)
def test_permissive_read_mode_with_file_too_small(self):
stream = io.BytesIO()
mrc = MrcInterpreter()
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_data(np.arange(12, dtype=np.int16).reshape(1, 3, 4))
mrc.close()
stream.seek(-1, io.SEEK_CUR)
stream.truncate()
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
MrcInterpreter(iostream=stream, permissive=True)
assert len(w) == 1
assert ("Expected 24 bytes in data block but could only read 23"
in str(w[0].message))
class MrcInterpreterTest(MrcObjectTest):
"""Unit tests for MrcInterpreter class.
Note that this test class inherits MrcObjectTest to ensure all of the tests
for MrcObject work correctly for the MrcInterpreter subclass.
"""
def setUp(self):
super(MrcInterpreterTest, self).setUp()
# Set up parameters so MrcObject tests run on the MrcInterpreter class
self.mrcobject = MrcInterpreter()
self.mrcobject._create_default_attributes()
def test_incorrect_map_id(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'map ')
stream.seek(0)
with self.assertRaisesRegex(ValueError, "Map ID string not found"):
MrcInterpreter(iostream=stream)
def test_incorrect_machine_stamp(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'MAP ')
stream.seek(0)
with self.assertRaisesRegex(
ValueError, "Unrecognised machine stamp: "
"0x00 0x00 0x00 0x00"):
MrcInterpreter(iostream=stream)
def test_stream_too_short(self):
stream = io.BytesIO()
stream.write(bytearray(1023))
with self.assertRaisesRegex(
ValueError, "Couldn't read enough bytes for MRC header"):
MrcInterpreter(iostream=stream)
def test_stream_writing_and_reading(self):
stream = io.BytesIO()
data = np.arange(30, dtype=np.int16).reshape(5, 6)
with MrcInterpreter() as mrc:
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_data(data)
stream.seek(0)
with MrcInterpreter(iostream=stream) as mrc:
np.testing.assert_array_equal(data, mrc.data)
assert mrc.header.mode == 1
mrc.set_data(data * 2)
assert mrc.header.mode == 1
def test_short_but_valid_map_id(self):
"""This tests the case of files where the map ID is almost correct.
For example, MotionCor2 writes files with ID 'MAP\0', which is not
valid according to the MRC2014 spec on the CCP-EM website, but could
be considered valid according to the MRC2014 paper (which just
specifies 'MAP', i.e. without the final byte). We should read such
files without errors or warnings (but they should fail a strict
validation check, tested elsewhere)."""
stream = io.BytesIO()
data = np.arange(30, dtype=np.int16).reshape(5, 6)
with MrcInterpreter() as mrc:
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_data(data)
mrc.header.map = b'MAP\0'
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
with MrcInterpreter(iostream=stream) as mrc:
np.testing.assert_array_equal(data, mrc.data)
# Ensure no warnings were raised
assert len(w) == 0
def test_permissive_read_mode_with_wrong_map_id_and_machine_stamp(self):
stream = io.BytesIO()
stream.write(bytearray(1024))
stream.seek(MAP_ID_OFFSET_BYTES)
stream.write(b'map ')
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
MrcInterpreter(iostream=stream, permissive=True)
assert len(w) == 2
assert "Map ID string not found" in str(w[0].message)
assert "Unrecognised machine stamp" in str(w[1].message)
def test_permissive_read_mode_with_file_too_small_for_extended_header(
self):
stream = io.BytesIO()
mrc = MrcInterpreter()
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_extended_header(np.arange(12, dtype=np.int16).reshape(1, 3, 4))
mrc.close()
stream.seek(-1, io.SEEK_CUR)
stream.truncate()
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
MrcInterpreter(iostream=stream, permissive=True)
assert len(w) == 1
assert (
"Expected 24 bytes in extended header but could only read 23"
in str(w[0].message))
def test_permissive_read_mode_with_file_too_small_for_data(self):
stream = io.BytesIO()
mrc = MrcInterpreter()
mrc._iostream = stream
mrc._create_default_attributes()
mrc.set_data(np.arange(12, dtype=np.int16).reshape(1, 3, 4))
mrc.close()
stream.seek(-1, io.SEEK_CUR)
stream.truncate()
stream.seek(0)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
MrcInterpreter(iostream=stream, permissive=True)
assert len(w) == 1
assert ("Expected 24 bytes in data block but could only read 23"
in str(w[0].message))