def test_extract_value_should_fail_with_map_name_mismatch(self):
mapper = mapping.PeakMapper("test", n_peaks=10, atom_names=["N", "H"])
m = mapping.PeakMapping(map_name="fail", peak_id=0, atom_name="H")
state = mapper.get_initial_state()
with self.assertRaises(KeyError):
mapper.extract_value(m, state)
def test_extract_value_should_raise_with_illegal_peak_id(self):
mapper = mapping.PeakMapper("test", n_peaks=1, atom_names=["N", "H"])
mapper.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
mapper.add_atom_group(N=AtomIndex(2), H=AtomIndex(3))
mapper.add_atom_group(N=AtomIndex(4), H=AtomIndex(5))
state = mapper.get_initial_state()
with self.assertRaises(KeyError):
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="H"),
state)
def test_extract_value_should_return_not_mapped(self):
mapper = mapping.PeakMapper("test", n_peaks=3, atom_names=["N", "H"])
mapper.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
state = mapper.get_initial_state()
val1 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=0, atom_name="N"),
state)
val2 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=0, atom_name="H"),
state)
val3 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="N"),
state)
val4 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="H"),
state)
val5 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=2, atom_name="N"),
state)
val6 = mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=2, atom_name="H"),
state)
# We have 3 peaks, but only one atom group, so only one peak will
# map to something. With the default initialization, this will be
# the first peak.
self.assertEqual(val1, 0)
self.assertEqual(val2, 1)
self.assertIsInstance(val3, mapping.NotMapped)
self.assertIsInstance(val4, mapping.NotMapped)
self.assertIsInstance(val5, mapping.NotMapped)
self.assertIsInstance(val6, mapping.NotMapped)
def test_extract_value_should_return_correct_values(self):
manager = mapping.PeakMapManager()
# map1 has 2 pekas, 2 atom_groups
map1 = manager.add_map("map1", 2, atom_names=["N", "H"])
map1.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
map1.add_atom_group(N=AtomIndex(2), H=AtomIndex(3))
# map2 has 2 peaks, but only 1 atom_group -> 1 peak will be NotMapped
map2 = manager.add_map("map2", 2, atom_names=["N", "H"])
map2.add_atom_group(N=AtomIndex(4), H=AtomIndex(5))
state = manager.get_initial_state()
ind1 = manager.extract_value(mapping.PeakMapping("map1", 0, "N"),
state)
ind2 = manager.extract_value(mapping.PeakMapping("map1", 0, "H"),
state)
ind3 = manager.extract_value(mapping.PeakMapping("map1", 1, "N"),
state)
ind4 = manager.extract_value(mapping.PeakMapping("map1", 1, "H"),
state)
ind5 = manager.extract_value(mapping.PeakMapping("map2", 0, "N"),
state)
ind6 = manager.extract_value(mapping.PeakMapping("map2", 0, "H"),
state)
ind7 = manager.extract_value(mapping.PeakMapping("map2", 1, "N"),
state)
ind8 = manager.extract_value(mapping.PeakMapping("map2", 1, "H"),
state)
self.assertEqual(ind1, 0)
self.assertEqual(ind2, 1)
self.assertEqual(ind3, 2)
self.assertEqual(ind4, 3)
self.assertEqual(ind5, 4)
self.assertEqual(ind6, 5)
self.assertIsInstance(ind7, mapping.NotMapped)
self.assertIsInstance(ind8, mapping.NotMapped)
def test_extract_value_should_give_correct_indices_with_equal_length(self):
mapper = mapping.PeakMapper("test", n_peaks=3, atom_names=["N", "H"])
mapper.add_atom_group(N=AtomIndex(0), H=AtomIndex(1))
mapper.add_atom_group(N=AtomIndex(2), H=AtomIndex(3))
mapper.add_atom_group(N=AtomIndex(4), H=AtomIndex(5))
state = mapper.get_initial_state()
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=0, atom_name="N"),
state),
0,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=0, atom_name="H"),
state),
1,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="N"),
state),
2,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=1, atom_name="H"),
state),
3,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=2, atom_name="N"),
state),
4,
)
self.assertEqual(
mapper.extract_value(
mapping.PeakMapping(map_name="test", peak_id=2, atom_name="H"),
state),
5,
)