class TestBrainRegions(unittest.TestCase):
@classmethod
def setUpClass(self):
self.brs = BrainRegions()
def test_get(self):
ctx = self.brs.get(688)
self.assertTrue(len(ctx.acronym) == 1 and ctx.acronym == 'CTX')
def test_ancestors_descendants(self):
# here we use the same brain region as in the alyx test
self.assertTrue(self.brs.descendants(ids=688).id.size == 567)
self.assertTrue(self.brs.ancestors(ids=688).id.size == 4)
# the leaves have no descendants but themselves
leaves = self.brs.leaves()
d = self.brs.descendants(ids=leaves['id'])
self.assertTrue(np.all(np.sort(leaves['id']) == np.sort(d['id'])))
def test_mappings_lateralized(self):
# the mapping assigns all non found regions to root (1:997), except for the void (0:0)
# here we're looking at the retina (1327:304325711), so we expect 1327 at index 1327
inds = self.brs._mapping_from_regions_list(np.array([304325711]),
lateralize=True)
inds_ = np.zeros_like(self.brs.id) + 1
inds_[int((inds.size - 1) / 2)] = 1327
inds_[-1] = 1327 * 2
inds_[0] = 0
assert np.all(inds == inds_)
def test_mappings_not_lateralized(self):
# if it's not lateralize, retina for both eyes should be in the
inds = self.brs._mapping_from_regions_list(np.array([304325711]),
lateralize=False)
inds_ = np.zeros_like(self.brs.id) + 1
inds_[int((inds.size - 1) / 2)] = 1327
inds_[-1] = 1327
inds_[0] = 0
assert np.all(inds == inds_)
class TestBrainRegions(unittest.TestCase):
@classmethod
def setUpClass(self):
self.brs = BrainRegions()
def test_rgba(self):
assert self.brs.rgba.shape == (self.brs.rgb.shape[0], 4)
def test_get(self):
ctx = self.brs.get(688)
self.assertTrue(len(ctx.acronym) == 1 and ctx.acronym == 'CTX')
def test_ancestors_descendants(self):
# here we use the same brain region as in the alyx test
self.assertTrue(self.brs.descendants(ids=688).id.size == 567)
self.assertTrue(self.brs.ancestors(ids=688).id.size == 4)
# the leaves have no descendants but themselves
leaves = self.brs.leaves()
d = self.brs.descendants(ids=leaves['id'])
self.assertTrue(np.all(np.sort(leaves['id']) == np.sort(d['id'])))
def test_ancestors_descendants_indices(self):
br = self.brs
tpath = np.array([997, 8, 567, 688, 695, 315, 453, 12993])
# /997/8/567/688/695/315/453/12993/
# check ancestors
ancs = br.ancestors(12993)
assert np.all(ancs.id == tpath)
# check ancestors with indices
ancs, inds = br.ancestors(12993, return_indices=True)
assert np.all(ancs.id == tpath)
# check descendants with indices
desdc, inds = br.descendants(12993, return_indices=True)
assert (inds == np.where(br.id == 12993))
# check full subtree
chemin = br.subtree(453)
assert np.all(
np.sort(chemin.id) == np.unique(np.r_[br.descendants(453).id,
br.ancestors(453).id]))
def test_mappings_lateralized(self):
# the mapping assigns all non found regions to root (1:997), except for the void (0:0)
# here we're looking at the retina (1327:304325711), so we expect 1327 at index 1327
inds = self.brs._mapping_from_regions_list(np.array([304325711]),
lateralize=True)
inds_ = np.zeros_like(self.brs.id) + 1
inds_[int((inds.size - 1) / 2)] = 1327
inds_[-1] = 1327 * 2
inds_[0] = 0
assert np.all(inds == inds_)
def test_mappings_not_lateralized(self):
# if it's not lateralize, retina for both eyes should be in the
inds = self.brs._mapping_from_regions_list(np.array([304325711]),
lateralize=False)
inds_ = np.zeros_like(self.brs.id) + 1
inds_[int((inds.size - 1) / 2)] = 1327
inds_[-1] = 1327
inds_[0] = 0
assert np.all(inds == inds_)
def test_remap(self):
# Test mapping atlas ids from one map to another
atlas_id = np.array([463, 685]) # CA3 and PO
cosmos_id = self.brs.remap(atlas_id,
source_map='Allen',
target_map='Cosmos')
expected_cosmos_id = [1089, 549] # HPF and TH
assert np.all(cosmos_id == expected_cosmos_id)
def test_id2id(self):
# Test remapping of atlas id to atlas id
atlas_id = np.array([463, 685])
# Allen mapping, positive ids -> positive ids
allen_id = self.brs.id2id(atlas_id, mapping='Allen')
assert np.all(allen_id == atlas_id)
# Allen mapping, negative ids -> positive ids
allen_id = self.brs.id2id(-1 * atlas_id, mapping='Allen')
assert np.all(allen_id == atlas_id)
# Allen-lr mapping, positive ids -> positive ids
allen_id = self.brs.id2id(atlas_id, mapping='Allen-lr')
assert np.all(allen_id == atlas_id)
# Allen-lr mapping, negative ids -> negative ids
allen_id = self.brs.id2id(-1 * atlas_id, mapping='Allen-lr')
assert np.all(allen_id == -1 * atlas_id)
expected_cosmos_id = np.array([1089, 549]) # HPF and TH
# Cosmos mapping, negative ids -> positive ids
cosmos_id = self.brs.id2id(-1 * atlas_id, mapping='Cosmos')
assert np.all(cosmos_id == expected_cosmos_id)
# Cosmos-lr mapping, negative ids -> negative ids
cosmos_id = self.brs.id2id(-1 * atlas_id, mapping='Cosmos-lr')
assert np.all(cosmos_id == -1 * expected_cosmos_id)
def test_id2acro(self):
atlas_id = np.array([463, 685]) # CA3 and VM
expected_allen_acronym = np.array(['CA3', 'VM'])
# Allen mapping, positive ids,
allen_acronym = self.brs.id2acronym(atlas_id, mapping='Allen')
assert np.all(allen_acronym == expected_allen_acronym)
# Allen-lr mapping, negative ids
allen_acronym = self.brs.id2acronym(-1 * atlas_id, mapping='Allen-lr')
assert np.all(allen_acronym == expected_allen_acronym)
expected_cosmos_acronym = np.array(['HPF', 'TH'])
cosmos_acronym = self.brs.id2acronym(atlas_id, mapping='Cosmos')
assert np.all(cosmos_acronym == expected_cosmos_acronym)
def test_id2index(self):
atlas_id = np.array([463, 685])
# Allen mapping, positive ids -> returns index on both side
allen_id, index_both = self.brs.id2index(atlas_id, mapping='Allen')
assert np.all(allen_id == atlas_id)
for exp, ind in zip(atlas_id, index_both):
assert np.all(ind == np.where(
self.brs.id[self.brs.mappings['Allen']] == exp)[0])
# Allen mapping, negative ids -> returns index on both side
allen_id, index_both = self.brs.id2index(-1 * atlas_id,
mapping='Allen')
assert np.all(allen_id == atlas_id)
for exp, ind in zip(atlas_id, index_both):
assert np.all(ind == np.where(
self.brs.id[self.brs.mappings['Allen']] == exp)[0])
# Allen-lr mapping, positive ids -> returns index on right side
allen_id, index = self.brs.id2index(atlas_id, mapping='Allen-lr')
assert np.all(allen_id == atlas_id)
for i, (exp, ind) in enumerate(zip(atlas_id, index)):
assert np.all(ind == index_both[i][index_both[i] <= self.brs.n_lr])
# Allen-lr mapping, negative ids -> returns index on left side
allen_id, index = self.brs.id2index(-1 * atlas_id, mapping='Allen-lr')
assert np.all(allen_id == -1 * atlas_id)
for i, (exp, ind) in enumerate(zip(atlas_id, index)):
assert np.all(ind == index_both[i][index_both[i] > self.brs.n_lr])
# Cosmos mapping, positive ids -> returns index on both sides
expected_cosmos_id = [1089, 549] # HPF and TH
cosmos_id, index_both = self.brs.id2index(atlas_id, mapping='Cosmos')
assert np.all(cosmos_id == expected_cosmos_id)
for exp, ind in zip(expected_cosmos_id, index_both):
assert np.all(ind == np.where(
self.brs.id[self.brs.mappings['Cosmos']] == exp)[0])
def test_acro2acro(self):
acronym = np.array(['CA3', 'VM'])
# Allen mapping
allen_acronym = self.brs.acronym2acronym(acronym, mapping='Allen')
assert np.all(acronym == allen_acronym)
expected_cosmos_acronym = np.array(['HPF', 'TH'])
# Cosmos mapping
cosmos_acronym = self.brs.acronym2acronym(acronym, mapping='Cosmos-lr')
assert np.all(cosmos_acronym == expected_cosmos_acronym)
def test_acro2id(self):
acronym = np.array(['CA3', 'VM'])
expected_allen_id = np.array([463, 685])
# Allen mapping, both hemisphere -> positive ids
allen_id = self.brs.acronym2id(acronym,
mapping='Allen',
hemisphere=None)
assert np.all(allen_id == expected_allen_id)
# Allen mapping, left hemisphere -> positive ids
allen_id = self.brs.acronym2id(acronym,
mapping='Allen',
hemisphere='left')
assert np.all(allen_id == expected_allen_id)
# Allen mapping, right hemisphere -> positive ids
allen_id = self.brs.acronym2id(acronym,
mapping='Allen',
hemisphere='right')
assert np.all(allen_id == expected_allen_id)
# Allen-lr mapping, both hemisphere -> negative and positive ids
allen_id = self.brs.acronym2id(acronym,
mapping='Allen-lr',
hemisphere=None)
assert np.all(allen_id.ravel() == np.c_[-1 * expected_allen_id,
expected_allen_id].ravel())
# Allen-lr mapping, left hemisphere -> negative ids
allen_id = self.brs.acronym2id(acronym,
mapping='Allen-lr',
hemisphere='left')
assert np.all(allen_id == -1 * expected_allen_id)
# Allen-lr mapping, right hemisphere -> positive ids
allen_id = self.brs.acronym2id(acronym,
mapping='Allen-lr',
hemisphere='right')
assert np.all(allen_id == expected_allen_id)
expected_cosmos_id = np.array([1089, 549])
# Cosmos-lr mapping, left hemisphere -> negative ids
cosmos_id = self.brs.acronym2id(acronym,
mapping='Cosmos-lr',
hemisphere='left')
assert np.all(cosmos_id == -1 * expected_cosmos_id)
# Cosmos mapping, left hemisphere -> positive ids
cosmos_id = self.brs.acronym2id(acronym,
mapping='Cosmos',
hemisphere='left')
assert np.all(cosmos_id == expected_cosmos_id)
def test_acro2index(self):
acronym = np.array(['CA3', 'VM'])
# Expect it to be same regardless of lateralised or non lateralised mapping
for map, expected_acronym in zip(
['Allen', 'Allen-lr', 'Cosmos', 'Cosmos-lr'], [
np.array(['CA3', 'VM']),
np.array(['CA3', 'VM']),
np.array(['HPF', 'TH']),
np.array(['HPF', 'TH'])
]):
# Mapping, both hemisphere, returns index on both sides
map_acronym, index_both = self.brs.acronym2index(acronym,
mapping=map,
hemisphere=None)
assert np.all(map_acronym == expected_acronym)
for exp, ind in zip(expected_acronym, index_both):
assert np.all(ind == np.where(
self.brs.acronym[self.brs.mappings[map]] == exp)[0])
# Mapping, left hemisphere, returns index that are > 1327
map_acronym, index = self.brs.acronym2index(acronym,
mapping=map,
hemisphere='left')
assert np.all(map_acronym == expected_acronym)
for i, (exp, ind) in enumerate(zip(expected_acronym, index)):
assert np.all(
ind == index_both[i][index_both[i] > self.brs.n_lr])
# Mapping, right hemisphere, returns index that are < 1327
map_acronym, index = self.brs.acronym2index(acronym,
mapping=map,
hemisphere='right')
assert np.all(map_acronym == expected_acronym)
for i, (exp, ind) in enumerate(zip(expected_acronym, index)):
assert np.all(
ind == index_both[i][index_both[i] <= self.brs.n_lr])
def test_index2id(self):
index = np.array([468, 646, 1973])
# Allen mapping
allen_id = np.array([463, 685, 685])
assert np.all(self.brs.index2id(index, mapping='Allen') == allen_id)
# Allen-lr mapping
allen_id = np.array([463, 685, -685])
assert np.all(self.brs.index2id(index, mapping='Allen-lr') == allen_id)
# Cosmos-lr mapping
cosmos_id = np.array([1089, 549, -549])
assert np.all(
self.brs.index2id(index, mapping='Cosmos-lr') == cosmos_id)
def test_index2acronym(self):
index = np.array([468, 646, 1973])
# Allen mapping
allen_acronym = np.array(['CA3', 'VM', 'VM'])
assert np.all(
self.brs.index2acronym(index, mapping='Allen') == allen_acronym)
# Allen-lr mapping
allen_acronym = np.array(['CA3', 'VM', 'VM'])
assert np.all(
self.brs.index2acronym(index, mapping='Allen-lr') == allen_acronym)
# Cosmos-lr mapping
cosmos_acronym = np.array(['HPF', 'TH', 'TH'])
assert np.all(
self.brs.index2acronym(index, mapping='Cosmos-lr') ==
cosmos_acronym)
def test_prepare_lr_data(self):
acronyms_lh = np.array(['VPM', 'VPL', 'PO'])
values_lh = np.array([0, 1, 2])
acronyms_rh = np.array(['VPL', 'PO', 'CA1'])
values_rh = np.array([3, 4, 5])
acronyms, values = prepare_lr_data(acronyms_lh, values_lh, acronyms_rh,
values_rh)
assert np.array_equal(np.unique(np.r_[acronyms_lh, acronyms_rh]),
acronyms)
assert np.array_equal(values[acronyms == 'VPL'][0], np.array([1, 3]))
np.testing.assert_equal(values[acronyms == 'VPM'][0],
np.array([0, np.nan]))
np.testing.assert_equal(values[acronyms == 'CA1'][0],
np.array([np.nan, 5]))
def test_reorder_data(self):
acronyms = np.array(['AUDp1', 'AUDpo1', 'AUDv1', 'SSp-m1', 'SSp-n1'])
values = np.array([0, 1, 2, 3, 4])
_, idx = ismember(acronyms, self.brs.acronym)
expected_acronyms = acronyms[np.argsort(self.brs.order[idx])]
expected_values = values[np.argsort(self.brs.order[idx])]
values = np.array([0, 1, 2, 3, 4])
acronnyms_ordered, values_ordered = reorder_data(acronyms, values)
assert np.array_equal(acronnyms_ordered, expected_acronyms)
assert np.array_equal(values_ordered, expected_values)
def test_argument_parser(self):
acronyms = ['AUDp1', 'AUDpo1', 'AUDv1', 'SSp-m1', 'SSp-n1']
ids = self.brs.acronym2id(acronyms)
assert np.all(self.brs.parse_acronyms_argument(acronyms) == ids)
assert np.all(
self.brs.parse_acronyms_argument(np.array(acronyms)) == ids)
assert np.all(self.brs.parse_acronyms_argument(ids) == ids)
assert np.all(self.brs.parse_acronyms_argument(list(ids)) == ids)
# makes sure it handles exception
with self.assertRaises(AssertionError):
self.brs.parse_acronyms_argument(acronyms + ['toto'])
assert np.all(
self.brs.parse_acronyms_argument(acronyms +
['toto'], mode='clip') == ids)